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oceanprotocol/squid-py
|
squid_py/keeper/conditions/condition_base.py
|
ConditionBase.generate_id
|
def generate_id(self, agreement_id, types, values):
"""
Generate id for the condition.
:param agreement_id: id of the agreement, hex str
:param types: list of types
:param values: list of values
:return: id, str
"""
values_hash = utils.generate_multi_value_hash(types, values)
return utils.generate_multi_value_hash(
['bytes32', 'address', 'bytes32'],
[agreement_id, self.address, values_hash]
)
|
python
|
def generate_id(self, agreement_id, types, values):
values_hash = utils.generate_multi_value_hash(types, values)
return utils.generate_multi_value_hash(
['bytes32', 'address', 'bytes32'],
[agreement_id, self.address, values_hash]
)
|
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Generate id for the condition.
:param agreement_id: id of the agreement, hex str
:param types: list of types
:param values: list of values
:return: id, str
|
[
"Generate",
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"condition",
"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/conditions/condition_base.py#L16-L29
|
oceanprotocol/squid-py
|
squid_py/keeper/conditions/condition_base.py
|
ConditionBase._fulfill
|
def _fulfill(self, *args, **kwargs):
"""
Fulfill the condition.
:param args:
:param kwargs:
:return: true if the condition was successfully fulfilled, bool
"""
tx_hash = self.send_transaction('fulfill', args, **kwargs)
receipt = self.get_tx_receipt(tx_hash)
return receipt.status == 1
|
python
|
def _fulfill(self, *args, **kwargs):
tx_hash = self.send_transaction('fulfill', args, **kwargs)
receipt = self.get_tx_receipt(tx_hash)
return receipt.status == 1
|
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|
[
"Fulfill",
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train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/conditions/condition_base.py#L31-L41
|
oceanprotocol/squid-py
|
squid_py/keeper/conditions/condition_base.py
|
ConditionBase.subscribe_condition_fulfilled
|
def subscribe_condition_fulfilled(self, agreement_id, timeout, callback, args,
timeout_callback=None, wait=False):
"""
Subscribe to the condition fullfilled event.
:param agreement_id: id of the agreement, hex str
:param timeout:
:param callback:
:param args:
:param timeout_callback:
:param wait: if true block the listener until get the event, bool
:return:
"""
logger.info(
f'Subscribing {self.FULFILLED_EVENT} event with agreement id {agreement_id}.')
return self.subscribe_to_event(
self.FULFILLED_EVENT,
timeout,
{'_agreementId': Web3Provider.get_web3().toBytes(hexstr=agreement_id)},
callback=callback,
timeout_callback=timeout_callback,
args=args,
wait=wait
)
|
python
|
def subscribe_condition_fulfilled(self, agreement_id, timeout, callback, args,
timeout_callback=None, wait=False):
logger.info(
f'Subscribing {self.FULFILLED_EVENT} event with agreement id {agreement_id}.')
return self.subscribe_to_event(
self.FULFILLED_EVENT,
timeout,
{'_agreementId': Web3Provider.get_web3().toBytes(hexstr=agreement_id)},
callback=callback,
timeout_callback=timeout_callback,
args=args,
wait=wait
)
|
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Subscribe to the condition fullfilled event.
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:param args:
:param timeout_callback:
:param wait: if true block the listener until get the event, bool
:return:
|
[
"Subscribe",
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] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/conditions/condition_base.py#L62-L85
|
oceanprotocol/squid-py
|
squid_py/keeper/web3/contract.py
|
transact_with_contract_function
|
def transact_with_contract_function(
address,
web3,
function_name=None,
transaction=None,
contract_abi=None,
fn_abi=None,
*args,
**kwargs):
"""
Helper function for interacting with a contract function by sending a
transaction. This is copied from web3 `transact_with_contract_function`
so we can use `personal_sendTransaction` when possible.
"""
transact_transaction = prepare_transaction(
address,
web3,
fn_identifier=function_name,
contract_abi=contract_abi,
transaction=transaction,
fn_abi=fn_abi,
fn_args=args,
fn_kwargs=kwargs,
)
passphrase = None
if transaction and 'passphrase' in transaction:
passphrase = transaction['passphrase']
transact_transaction.pop('passphrase')
if passphrase:
txn_hash = web3.personal.sendTransaction(transact_transaction, passphrase)
else:
txn_hash = web3.eth.sendTransaction(transact_transaction)
return txn_hash
|
python
|
def transact_with_contract_function(
address,
web3,
function_name=None,
transaction=None,
contract_abi=None,
fn_abi=None,
*args,
**kwargs):
transact_transaction = prepare_transaction(
address,
web3,
fn_identifier=function_name,
contract_abi=contract_abi,
transaction=transaction,
fn_abi=fn_abi,
fn_args=args,
fn_kwargs=kwargs,
)
passphrase = None
if transaction and 'passphrase' in transaction:
passphrase = transaction['passphrase']
transact_transaction.pop('passphrase')
if passphrase:
txn_hash = web3.personal.sendTransaction(transact_transaction, passphrase)
else:
txn_hash = web3.eth.sendTransaction(transact_transaction)
return txn_hash
|
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] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/web3/contract.py#L67-L102
|
oceanprotocol/squid-py
|
squid_py/keeper/web3/contract.py
|
SquidContractFunction.transact
|
def transact(self, transaction=None):
"""
Customize calling smart contract transaction functions to use `personal_sendTransaction`
instead of `eth_sendTransaction` and to estimate gas limit. This function
is largely copied from web3 ContractFunction with important addition.
Note: will fallback to `eth_sendTransaction` if `passphrase` is not provided in the
`transaction` dict.
:param transaction: dict which has the required transaction arguments per
`personal_sendTransaction` requirements.
:return: hex str transaction hash
"""
if transaction is None:
transact_transaction = {}
else:
transact_transaction = dict(**transaction)
if 'data' in transact_transaction:
raise ValueError("Cannot set data in transact transaction")
cf = self._contract_function
if cf.address is not None:
transact_transaction.setdefault('to', cf.address)
if cf.web3.eth.defaultAccount is not empty:
transact_transaction.setdefault('from', cf.web3.eth.defaultAccount)
if 'to' not in transact_transaction:
if isinstance(self, type):
raise ValueError(
"When using `Contract.transact` from a contract factory you "
"must provide a `to` address with the transaction"
)
else:
raise ValueError(
"Please ensure that this contract instance has an address."
)
if 'gas' not in transact_transaction:
tx = transaction.copy()
if 'passphrase' in tx:
tx.pop('passphrase')
gas = cf.estimateGas(tx)
transact_transaction['gas'] = gas
return transact_with_contract_function(
cf.address,
cf.web3,
cf.function_identifier,
transact_transaction,
cf.contract_abi,
cf.abi,
*cf.args,
**cf.kwargs
)
|
python
|
def transact(self, transaction=None):
if transaction is None:
transact_transaction = {}
else:
transact_transaction = dict(**transaction)
if 'data' in transact_transaction:
raise ValueError("Cannot set data in transact transaction")
cf = self._contract_function
if cf.address is not None:
transact_transaction.setdefault('to', cf.address)
if cf.web3.eth.defaultAccount is not empty:
transact_transaction.setdefault('from', cf.web3.eth.defaultAccount)
if 'to' not in transact_transaction:
if isinstance(self, type):
raise ValueError(
"When using `Contract.transact` from a contract factory you "
"must provide a `to` address with the transaction"
)
else:
raise ValueError(
"Please ensure that this contract instance has an address."
)
if 'gas' not in transact_transaction:
tx = transaction.copy()
if 'passphrase' in tx:
tx.pop('passphrase')
gas = cf.estimateGas(tx)
transact_transaction['gas'] = gas
return transact_with_contract_function(
cf.address,
cf.web3,
cf.function_identifier,
transact_transaction,
cf.contract_abi,
cf.abi,
*cf.args,
**cf.kwargs
)
|
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Note: will fallback to `eth_sendTransaction` if `passphrase` is not provided in the
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:param transaction: dict which has the required transaction arguments per
`personal_sendTransaction` requirements.
:return: hex str transaction hash
|
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"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/web3/contract.py#L10-L64
|
oceanprotocol/squid-py
|
squid_py/keeper/conditions/escrow_reward.py
|
EscrowRewardCondition.fulfill
|
def fulfill(self,
agreement_id,
amount,
receiver_address,
sender_address,
lock_condition_id,
release_condition_id,
account):
"""
Fulfill the escrow reward condition.
:param agreement_id: id of the agreement, hex str
:param amount: Amount of tokens, int
:param receiver_address: ethereum address of the receiver, hex str
:param sender_address: ethereum address of the sender, hex str
:param lock_condition_id: id of the condition, str
:param release_condition_id: id of the condition, str
:param account: Account instance
:return:
"""
return self._fulfill(
agreement_id,
amount,
receiver_address,
sender_address,
lock_condition_id,
release_condition_id,
transact={'from': account.address,
'passphrase': account.password}
)
|
python
|
def fulfill(self,
agreement_id,
amount,
receiver_address,
sender_address,
lock_condition_id,
release_condition_id,
account):
return self._fulfill(
agreement_id,
amount,
receiver_address,
sender_address,
lock_condition_id,
release_condition_id,
transact={'from': account.address,
'passphrase': account.password}
)
|
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Fulfill the escrow reward condition.
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:param amount: Amount of tokens, int
:param receiver_address: ethereum address of the receiver, hex str
:param sender_address: ethereum address of the sender, hex str
:param lock_condition_id: id of the condition, str
:param release_condition_id: id of the condition, str
:param account: Account instance
:return:
|
[
"Fulfill",
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"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/conditions/escrow_reward.py#L11-L40
|
oceanprotocol/squid-py
|
squid_py/keeper/conditions/escrow_reward.py
|
EscrowRewardCondition.hash_values
|
def hash_values(self, amount, receiver_address, sender_address, lock_condition_id,
release_condition_id):
"""
Hash the values of the escrow reward condition.
:param amount: Amount of tokens, int
:param receiver_address: ethereum address of the receiver, hex str
:param sender_address: ethereum address of the sender, hex str
:param lock_condition_id: id of the condition, str
:param release_condition_id: id of the condition, str
:return: hex str
"""
return self._hash_values(
amount,
receiver_address,
sender_address,
lock_condition_id,
release_condition_id
)
|
python
|
def hash_values(self, amount, receiver_address, sender_address, lock_condition_id,
release_condition_id):
return self._hash_values(
amount,
receiver_address,
sender_address,
lock_condition_id,
release_condition_id
)
|
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",",
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Hash the values of the escrow reward condition.
:param amount: Amount of tokens, int
:param receiver_address: ethereum address of the receiver, hex str
:param sender_address: ethereum address of the sender, hex str
:param lock_condition_id: id of the condition, str
:param release_condition_id: id of the condition, str
:return: hex str
|
[
"Hash",
"the",
"values",
"of",
"the",
"escrow",
"reward",
"condition",
"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/conditions/escrow_reward.py#L42-L60
|
oceanprotocol/squid-py
|
squid_py/agreements/service_agreement_condition.py
|
Parameter.as_dictionary
|
def as_dictionary(self):
"""
Return the parameter as a dictionary.
:return: dict
"""
return {
"name": self.name,
"type": self.type,
"value": remove_0x_prefix(self.value) if self.type == 'bytes32' else self.value
}
|
python
|
def as_dictionary(self):
return {
"name": self.name,
"type": self.type,
"value": remove_0x_prefix(self.value) if self.type == 'bytes32' else self.value
}
|
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Return the parameter as a dictionary.
:return: dict
|
[
"Return",
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] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/agreements/service_agreement_condition.py#L21-L31
|
oceanprotocol/squid-py
|
squid_py/agreements/service_agreement_condition.py
|
ServiceAgreementCondition.init_from_condition_json
|
def init_from_condition_json(self, condition_json):
"""
Init the condition values from a condition json.
:param condition_json: dict
"""
self.name = condition_json['name']
self.timelock = condition_json['timelock']
self.timeout = condition_json['timeout']
self.contract_name = condition_json['contractName']
self.function_name = condition_json['functionName']
self.parameters = [Parameter(p) for p in condition_json['parameters']]
self.events = [Event(e) for e in condition_json['events']]
|
python
|
def init_from_condition_json(self, condition_json):
self.name = condition_json['name']
self.timelock = condition_json['timelock']
self.timeout = condition_json['timeout']
self.contract_name = condition_json['contractName']
self.function_name = condition_json['functionName']
self.parameters = [Parameter(p) for p in condition_json['parameters']]
self.events = [Event(e) for e in condition_json['events']]
|
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Init the condition values from a condition json.
:param condition_json: dict
|
[
"Init",
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"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/agreements/service_agreement_condition.py#L93-L105
|
oceanprotocol/squid-py
|
squid_py/agreements/service_agreement_condition.py
|
ServiceAgreementCondition.as_dictionary
|
def as_dictionary(self):
"""
Return the condition as a dictionary.
:return: dict
"""
condition_dict = {
"name": self.name,
"timelock": self.timelock,
"timeout": self.timeout,
"contractName": self.contract_name,
"functionName": self.function_name,
"events": [e.as_dictionary() for e in self.events],
"parameters": [p.as_dictionary() for p in self.parameters],
}
return condition_dict
|
python
|
def as_dictionary(self):
condition_dict = {
"name": self.name,
"timelock": self.timelock,
"timeout": self.timeout,
"contractName": self.contract_name,
"functionName": self.function_name,
"events": [e.as_dictionary() for e in self.events],
"parameters": [p.as_dictionary() for p in self.parameters],
}
return condition_dict
|
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Return the condition as a dictionary.
:return: dict
|
[
"Return",
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] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/agreements/service_agreement_condition.py#L107-L123
|
oceanprotocol/squid-py
|
squid_py/ddo/service.py
|
Service.update_value
|
def update_value(self, name, value):
"""
Update value in the array of values.
:param name: Key of the value, str
:param value: New value, str
:return: None
"""
if name not in {'id', self.SERVICE_ENDPOINT, self.CONSUME_ENDPOINT, 'type'}:
self._values[name] = value
|
python
|
def update_value(self, name, value):
if name not in {'id', self.SERVICE_ENDPOINT, self.CONSUME_ENDPOINT, 'type'}:
self._values[name] = value
|
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"def",
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"}",
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Update value in the array of values.
:param name: Key of the value, str
:param value: New value, str
:return: None
|
[
"Update",
"value",
"in",
"the",
"array",
"of",
"values",
"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/ddo/service.py#L92-L101
|
oceanprotocol/squid-py
|
squid_py/ddo/service.py
|
Service.as_text
|
def as_text(self, is_pretty=False):
"""Return the service as a JSON string."""
values = {
'type': self._type,
self.SERVICE_ENDPOINT: self._service_endpoint,
}
if self._consume_endpoint is not None:
values[self.CONSUME_ENDPOINT] = self._consume_endpoint
if self._values:
# add extra service values to the dictionary
for name, value in self._values.items():
values[name] = value
if is_pretty:
return json.dumps(values, indent=4, separators=(',', ': '))
return json.dumps(values)
|
python
|
def as_text(self, is_pretty=False):
values = {
'type': self._type,
self.SERVICE_ENDPOINT: self._service_endpoint,
}
if self._consume_endpoint is not None:
values[self.CONSUME_ENDPOINT] = self._consume_endpoint
if self._values:
for name, value in self._values.items():
values[name] = value
if is_pretty:
return json.dumps(values, indent=4, separators=(',', ': '))
return json.dumps(values)
|
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Return the service as a JSON string.
|
[
"Return",
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"string",
"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/ddo/service.py#L116-L132
|
oceanprotocol/squid-py
|
squid_py/ddo/service.py
|
Service.as_dictionary
|
def as_dictionary(self):
"""Return the service as a python dictionary."""
values = {
'type': self._type,
self.SERVICE_ENDPOINT: self._service_endpoint,
}
if self._consume_endpoint is not None:
values[self.CONSUME_ENDPOINT] = self._consume_endpoint
if self._values:
# add extra service values to the dictionary
for name, value in self._values.items():
if isinstance(value, object) and hasattr(value, 'as_dictionary'):
value = value.as_dictionary()
elif isinstance(value, list):
value = [v.as_dictionary() if hasattr(v, 'as_dictionary') else v for v in value]
values[name] = value
return values
|
python
|
def as_dictionary(self):
values = {
'type': self._type,
self.SERVICE_ENDPOINT: self._service_endpoint,
}
if self._consume_endpoint is not None:
values[self.CONSUME_ENDPOINT] = self._consume_endpoint
if self._values:
for name, value in self._values.items():
if isinstance(value, object) and hasattr(value, 'as_dictionary'):
value = value.as_dictionary()
elif isinstance(value, list):
value = [v.as_dictionary() if hasattr(v, 'as_dictionary') else v for v in value]
values[name] = value
return values
|
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Return the service as a python dictionary.
|
[
"Return",
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] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/ddo/service.py#L134-L151
|
oceanprotocol/squid-py
|
squid_py/ddo/service.py
|
Service.from_json
|
def from_json(cls, service_dict):
"""Create a service object from a JSON string."""
sd = service_dict.copy()
service_endpoint = sd.get(cls.SERVICE_ENDPOINT)
if not service_endpoint:
logger.error(
'Service definition in DDO document is missing the "serviceEndpoint" key/value.')
raise IndexError
_type = sd.get('type')
if not _type:
logger.error('Service definition in DDO document is missing the "type" key/value.')
raise IndexError
sd.pop(cls.SERVICE_ENDPOINT)
sd.pop('type')
return cls(
service_endpoint,
_type,
sd
)
|
python
|
def from_json(cls, service_dict):
sd = service_dict.copy()
service_endpoint = sd.get(cls.SERVICE_ENDPOINT)
if not service_endpoint:
logger.error(
'Service definition in DDO document is missing the "serviceEndpoint" key/value.')
raise IndexError
_type = sd.get('type')
if not _type:
logger.error('Service definition in DDO document is missing the "type" key/value.')
raise IndexError
sd.pop(cls.SERVICE_ENDPOINT)
sd.pop('type')
return cls(
service_endpoint,
_type,
sd
)
|
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Create a service object from a JSON string.
|
[
"Create",
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] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/ddo/service.py#L154-L174
|
oceanprotocol/squid-py
|
squid_py/keeper/conditions/access.py
|
AccessSecretStoreCondition.fulfill
|
def fulfill(self, agreement_id, document_id, grantee_address, account):
"""
Fulfill the access secret store condition.
:param agreement_id: id of the agreement, hex str
:param document_id: refers to the DID in which secret store will issue the decryption
keys, DID
:param grantee_address: is the address of the granted user, str
:param account: Account instance
:return: true if the condition was successfully fulfilled, bool
"""
return self._fulfill(
agreement_id,
document_id,
grantee_address,
transact={'from': account.address,
'passphrase': account.password}
)
|
python
|
def fulfill(self, agreement_id, document_id, grantee_address, account):
return self._fulfill(
agreement_id,
document_id,
grantee_address,
transact={'from': account.address,
'passphrase': account.password}
)
|
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Fulfill the access secret store condition.
:param agreement_id: id of the agreement, hex str
:param document_id: refers to the DID in which secret store will issue the decryption
keys, DID
:param grantee_address: is the address of the granted user, str
:param account: Account instance
:return: true if the condition was successfully fulfilled, bool
|
[
"Fulfill",
"the",
"access",
"secret",
"store",
"condition",
"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/conditions/access.py#L13-L30
|
oceanprotocol/squid-py
|
squid_py/keeper/conditions/access.py
|
AccessSecretStoreCondition.get_purchased_assets_by_address
|
def get_purchased_assets_by_address(self, address, from_block=0, to_block='latest'):
"""
Get the list of the assets dids consumed for an address.
:param address: is the address of the granted user, hex-str
:param from_block: block to start to listen
:param to_block: block to stop to listen
:return: list of dids
"""
block_filter = EventFilter(
ConditionBase.FULFILLED_EVENT,
getattr(self.events, ConditionBase.FULFILLED_EVENT),
from_block=from_block,
to_block=to_block,
argument_filters={'_grantee': address}
)
log_items = block_filter.get_all_entries(max_tries=5)
did_list = []
for log_i in log_items:
did_list.append(id_to_did(log_i.args['_documentId']))
return did_list
|
python
|
def get_purchased_assets_by_address(self, address, from_block=0, to_block='latest'):
block_filter = EventFilter(
ConditionBase.FULFILLED_EVENT,
getattr(self.events, ConditionBase.FULFILLED_EVENT),
from_block=from_block,
to_block=to_block,
argument_filters={'_grantee': address}
)
log_items = block_filter.get_all_entries(max_tries=5)
did_list = []
for log_i in log_items:
did_list.append(id_to_did(log_i.args['_documentId']))
return did_list
|
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Get the list of the assets dids consumed for an address.
:param address: is the address of the granted user, hex-str
:param from_block: block to start to listen
:param to_block: block to stop to listen
:return: list of dids
|
[
"Get",
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"the",
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"dids",
"consumed",
"for",
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"address",
"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/conditions/access.py#L55-L76
|
oceanprotocol/squid-py
|
squid_py/keeper/web3_provider.py
|
Web3Provider.get_web3
|
def get_web3():
"""Return the web3 instance to interact with the ethereum client."""
if Web3Provider._web3 is None:
config = ConfigProvider.get_config()
provider = (
config.web3_provider
if config.web3_provider
else CustomHTTPProvider(
config.keeper_url
)
)
Web3Provider._web3 = Web3(provider)
# Reset attributes to avoid lint issue about no attribute
Web3Provider._web3.eth = getattr(Web3Provider._web3, 'eth')
Web3Provider._web3.net = getattr(Web3Provider._web3, 'net')
Web3Provider._web3.personal = getattr(Web3Provider._web3, 'personal')
Web3Provider._web3.version = getattr(Web3Provider._web3, 'version')
Web3Provider._web3.txpool = getattr(Web3Provider._web3, 'txpool')
Web3Provider._web3.miner = getattr(Web3Provider._web3, 'miner')
Web3Provider._web3.admin = getattr(Web3Provider._web3, 'admin')
Web3Provider._web3.parity = getattr(Web3Provider._web3, 'parity')
Web3Provider._web3.testing = getattr(Web3Provider._web3, 'testing')
return Web3Provider._web3
|
python
|
def get_web3():
if Web3Provider._web3 is None:
config = ConfigProvider.get_config()
provider = (
config.web3_provider
if config.web3_provider
else CustomHTTPProvider(
config.keeper_url
)
)
Web3Provider._web3 = Web3(provider)
Web3Provider._web3.eth = getattr(Web3Provider._web3, 'eth')
Web3Provider._web3.net = getattr(Web3Provider._web3, 'net')
Web3Provider._web3.personal = getattr(Web3Provider._web3, 'personal')
Web3Provider._web3.version = getattr(Web3Provider._web3, 'version')
Web3Provider._web3.txpool = getattr(Web3Provider._web3, 'txpool')
Web3Provider._web3.miner = getattr(Web3Provider._web3, 'miner')
Web3Provider._web3.admin = getattr(Web3Provider._web3, 'admin')
Web3Provider._web3.parity = getattr(Web3Provider._web3, 'parity')
Web3Provider._web3.testing = getattr(Web3Provider._web3, 'testing')
return Web3Provider._web3
|
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Return the web3 instance to interact with the ethereum client.
|
[
"Return",
"the",
"web3",
"instance",
"to",
"interact",
"with",
"the",
"ethereum",
"client",
"."
] |
train
|
https://github.com/oceanprotocol/squid-py/blob/43a5b7431627e4c9ab7382ed9eb8153e96ed4483/squid_py/keeper/web3_provider.py#L15-L38
|
BlueBrain/NeuroM
|
neurom/core/_soma.py
|
_get_type
|
def _get_type(points, soma_class):
'''get the type of the soma
Args:
points: Soma points
soma_class(str): one of 'contour' or 'cylinder' to specify the type
'''
assert soma_class in (SOMA_CONTOUR, SOMA_CYLINDER)
npoints = len(points)
if soma_class == SOMA_CONTOUR:
return {0: None,
1: SomaSinglePoint,
2: None}.get(npoints, SomaSimpleContour)
if(npoints == 3 and
points[0][COLS.P] == -1 and
points[1][COLS.P] == 1 and
points[2][COLS.P] == 1):
L.warning('Using neuromorpho 3-Point soma')
# NeuroMorpho is the main provider of morphologies, but they
# with SWC as their default file format: they convert all
# uploads to SWC. In the process of conversion, they turn all
# somas into their custom 'Three-point soma representation':
# http://neuromorpho.org/SomaFormat.html
return SomaNeuromorphoThreePointCylinders
return {0: None,
1: SomaSinglePoint}.get(npoints, SomaCylinders)
|
python
|
def _get_type(points, soma_class):
assert soma_class in (SOMA_CONTOUR, SOMA_CYLINDER)
npoints = len(points)
if soma_class == SOMA_CONTOUR:
return {0: None,
1: SomaSinglePoint,
2: None}.get(npoints, SomaSimpleContour)
if(npoints == 3 and
points[0][COLS.P] == -1 and
points[1][COLS.P] == 1 and
points[2][COLS.P] == 1):
L.warning('Using neuromorpho 3-Point soma')
return SomaNeuromorphoThreePointCylinders
return {0: None,
1: SomaSinglePoint}.get(npoints, SomaCylinders)
|
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".",
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",",
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")"
] |
get the type of the soma
Args:
points: Soma points
soma_class(str): one of 'contour' or 'cylinder' to specify the type
|
[
"get",
"the",
"type",
"of",
"the",
"soma"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/core/_soma.py#L203-L232
|
BlueBrain/NeuroM
|
neurom/core/_soma.py
|
make_soma
|
def make_soma(points, soma_check=None, soma_class=SOMA_CONTOUR):
'''Make a soma object from a set of points
Infers the soma type (SomaSinglePoint, SomaSimpleContour)
from the points and the 'soma_class'
Parameters:
points: collection of points forming a soma.
soma_check: optional validation function applied to points. Should
raise a SomaError if points not valid.
soma_class(str): one of 'contour' or 'cylinder' to specify the type
Raises:
SomaError if no soma points found, points incompatible with soma, or
if soma_check(points) fails.
'''
if soma_check:
soma_check(points)
stype = _get_type(points, soma_class)
if stype is None:
raise SomaError('Invalid soma points')
return stype(points)
|
python
|
def make_soma(points, soma_check=None, soma_class=SOMA_CONTOUR):
if soma_check:
soma_check(points)
stype = _get_type(points, soma_class)
if stype is None:
raise SomaError('Invalid soma points')
return stype(points)
|
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"SomaError",
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"'Invalid soma points'",
")",
"return",
"stype",
"(",
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")"
] |
Make a soma object from a set of points
Infers the soma type (SomaSinglePoint, SomaSimpleContour)
from the points and the 'soma_class'
Parameters:
points: collection of points forming a soma.
soma_check: optional validation function applied to points. Should
raise a SomaError if points not valid.
soma_class(str): one of 'contour' or 'cylinder' to specify the type
Raises:
SomaError if no soma points found, points incompatible with soma, or
if soma_check(points) fails.
|
[
"Make",
"a",
"soma",
"object",
"from",
"a",
"set",
"of",
"points"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/core/_soma.py#L235-L260
|
BlueBrain/NeuroM
|
neurom/core/_soma.py
|
SomaSimpleContour.center
|
def center(self):
'''Obtain the center from the average of all points'''
points = np.array(self._points)
return np.mean(points[:, COLS.XYZ], axis=0)
|
python
|
def center(self):
points = np.array(self._points)
return np.mean(points[:, COLS.XYZ], axis=0)
|
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"center",
"(",
"self",
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"[",
":",
",",
"COLS",
".",
"XYZ",
"]",
",",
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"=",
"0",
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Obtain the center from the average of all points
|
[
"Obtain",
"the",
"center",
"from",
"the",
"average",
"of",
"all",
"points"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/core/_soma.py#L188-L191
|
BlueBrain/NeuroM
|
neurom/fst/sectionfunc.py
|
section_tortuosity
|
def section_tortuosity(section):
'''Tortuosity of a section
The tortuosity is defined as the ratio of the path length of a section
and the euclidian distnce between its end points.
The path length is the sum of distances between consecutive points.
If the section contains less than 2 points, the value 1 is returned.
'''
pts = section.points
return 1 if len(pts) < 2 else mm.section_length(pts) / mm.point_dist(pts[-1], pts[0])
|
python
|
def section_tortuosity(section):
pts = section.points
return 1 if len(pts) < 2 else mm.section_length(pts) / mm.point_dist(pts[-1], pts[0])
|
[
"def",
"section_tortuosity",
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".",
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"(",
"pts",
"[",
"-",
"1",
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",",
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"[",
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")"
] |
Tortuosity of a section
The tortuosity is defined as the ratio of the path length of a section
and the euclidian distnce between its end points.
The path length is the sum of distances between consecutive points.
If the section contains less than 2 points, the value 1 is returned.
|
[
"Tortuosity",
"of",
"a",
"section"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/sectionfunc.py#L50-L61
|
BlueBrain/NeuroM
|
neurom/fst/sectionfunc.py
|
section_end_distance
|
def section_end_distance(section):
'''End to end distance of a section
The end to end distance of a section is defined as
the euclidian distnce between its end points.
If the section contains less than 2 points, the value 0 is returned.
'''
pts = section.points
return 0 if len(pts) < 2 else mm.point_dist(pts[-1], pts[0])
|
python
|
def section_end_distance(section):
pts = section.points
return 0 if len(pts) < 2 else mm.point_dist(pts[-1], pts[0])
|
[
"def",
"section_end_distance",
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"[",
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"1",
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"[",
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] |
End to end distance of a section
The end to end distance of a section is defined as
the euclidian distnce between its end points.
If the section contains less than 2 points, the value 0 is returned.
|
[
"End",
"to",
"end",
"distance",
"of",
"a",
"section"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/sectionfunc.py#L64-L73
|
BlueBrain/NeuroM
|
neurom/fst/sectionfunc.py
|
section_meander_angles
|
def section_meander_angles(section):
'''Inter-segment opening angles in a section'''
p = section.points
return [mm.angle_3points(p[i - 1], p[i - 2], p[i])
for i in range(2, len(p))]
|
python
|
def section_meander_angles(section):
p = section.points
return [mm.angle_3points(p[i - 1], p[i - 2], p[i])
for i in range(2, len(p))]
|
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Inter-segment opening angles in a section
|
[
"Inter",
"-",
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"a",
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/sectionfunc.py#L101-L105
|
BlueBrain/NeuroM
|
neurom/fst/sectionfunc.py
|
strahler_order
|
def strahler_order(section):
'''Branching order of a tree section
The strahler order is the inverse of the branch order,
since this is computed from the tips of the tree
towards the root.
This implementation is a translation of the three steps described in
Wikipedia (https://en.wikipedia.org/wiki/Strahler_number):
- If the node is a leaf (has no children), its Strahler number is one.
- If the node has one child with Strahler number i, and all other children
have Strahler numbers less than i, then the Strahler number of the node
is i again.
- If the node has two or more children with Strahler number i, and no
children with greater number, then the Strahler number of the node is
i + 1.
No efforts have been invested in making it computationnaly efficient, but
it computes acceptably fast on tested morphologies (i.e., no waiting time).
'''
if section.children:
child_orders = [strahler_order(child) for child in section.children]
max_so_children = max(child_orders)
it = iter(co == max_so_children for co in child_orders)
# check if there are *two* or more children w/ the max_so_children
any(it)
if any(it):
return max_so_children + 1
return max_so_children
return 1
|
python
|
def strahler_order(section):
if section.children:
child_orders = [strahler_order(child) for child in section.children]
max_so_children = max(child_orders)
it = iter(co == max_so_children for co in child_orders)
any(it)
if any(it):
return max_so_children + 1
return max_so_children
return 1
|
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Branching order of a tree section
The strahler order is the inverse of the branch order,
since this is computed from the tips of the tree
towards the root.
This implementation is a translation of the three steps described in
Wikipedia (https://en.wikipedia.org/wiki/Strahler_number):
- If the node is a leaf (has no children), its Strahler number is one.
- If the node has one child with Strahler number i, and all other children
have Strahler numbers less than i, then the Strahler number of the node
is i again.
- If the node has two or more children with Strahler number i, and no
children with greater number, then the Strahler number of the node is
i + 1.
No efforts have been invested in making it computationnaly efficient, but
it computes acceptably fast on tested morphologies (i.e., no waiting time).
|
[
"Branching",
"order",
"of",
"a",
"tree",
"section"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/sectionfunc.py#L108-L138
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
figure_naming
|
def figure_naming(pretitle='', posttitle='', prefile='', postfile=''):
"""
Helper function to define the strings that handle pre-post conventions
for viewing - plotting title and saving options.
Args:
pretitle(str): String to include before the general title of the figure.
posttitle(str): String to include after the general title of the figure.
prefile(str): String to include before the general filename of the figure.
postfile(str): String to include after the general filename of the figure.
Returns:
str: String to include in the figure name and title, in a suitable form.
"""
if pretitle:
pretitle = "%s -- " % pretitle
if posttitle:
posttitle = " -- %s" % posttitle
if prefile:
prefile = "%s_" % prefile
if postfile:
postfile = "_%s" % postfile
return pretitle, posttitle, prefile, postfile
|
python
|
def figure_naming(pretitle='', posttitle='', prefile='', postfile=''):
if pretitle:
pretitle = "%s -- " % pretitle
if posttitle:
posttitle = " -- %s" % posttitle
if prefile:
prefile = "%s_" % prefile
if postfile:
postfile = "_%s" % postfile
return pretitle, posttitle, prefile, postfile
|
[
"def",
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"return",
"pretitle",
",",
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",",
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Helper function to define the strings that handle pre-post conventions
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Args:
pretitle(str): String to include before the general title of the figure.
posttitle(str): String to include after the general title of the figure.
prefile(str): String to include before the general filename of the figure.
postfile(str): String to include after the general filename of the figure.
Returns:
str: String to include in the figure name and title, in a suitable form.
|
[
"Helper",
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"strings",
"that",
"handle",
"pre",
"-",
"post",
"conventions",
"for",
"viewing",
"-",
"plotting",
"title",
"and",
"saving",
"options",
"."
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L56-L82
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
get_figure
|
def get_figure(new_fig=True, subplot='111', params=None):
"""
Function to be used for viewing - plotting,
to initialize the matplotlib figure - axes.
Args:
new_fig(bool): Defines if a new figure will be created, if false current figure is used
subplot (tuple or matplolib subplot specifier string): Create axes with these parameters
params (dict): extra options passed to add_subplot()
Returns:
Matplotlib Figure and Axes
"""
_get_plt()
if new_fig:
fig = plt.figure()
else:
fig = plt.gcf()
params = dict_if_none(params)
if isinstance(subplot, (tuple, list)):
ax = fig.add_subplot(*subplot, **params)
else:
ax = fig.add_subplot(subplot, **params)
return fig, ax
|
python
|
def get_figure(new_fig=True, subplot='111', params=None):
_get_plt()
if new_fig:
fig = plt.figure()
else:
fig = plt.gcf()
params = dict_if_none(params)
if isinstance(subplot, (tuple, list)):
ax = fig.add_subplot(*subplot, **params)
else:
ax = fig.add_subplot(subplot, **params)
return fig, ax
|
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Function to be used for viewing - plotting,
to initialize the matplotlib figure - axes.
Args:
new_fig(bool): Defines if a new figure will be created, if false current figure is used
subplot (tuple or matplolib subplot specifier string): Create axes with these parameters
params (dict): extra options passed to add_subplot()
Returns:
Matplotlib Figure and Axes
|
[
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"-",
"plotting",
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"initialize",
"the",
"matplotlib",
"figure",
"-",
"axes",
"."
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L85-L112
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
save_plot
|
def save_plot(fig, prefile='', postfile='', output_path='./', output_name='Figure',
output_format='png', dpi=300, transparent=False, **_):
"""Generates a figure file in the selected directory.
Args:
fig: matplotlib figure
prefile(str): Include before the general filename of the figure
postfile(str): Included after the general filename of the figure
output_path(str): Define the path to the output directory
output_name(str): String to define the name of the output figure
output_format(str): String to define the format of the output figure
dpi(int): Define the DPI (Dots per Inch) of the figure
transparent(bool): If True the saved figure will have a transparent background
"""
if not os.path.exists(output_path):
os.makedirs(output_path) # Make output directory if non-exsiting
output = os.path.join(output_path,
prefile + output_name + postfile + "." + output_format)
fig.savefig(output, dpi=dpi, transparent=transparent)
|
python
|
def save_plot(fig, prefile='', postfile='', output_path='./', output_name='Figure',
output_format='png', dpi=300, transparent=False, **_):
if not os.path.exists(output_path):
os.makedirs(output_path)
output = os.path.join(output_path,
prefile + output_name + postfile + "." + output_format)
fig.savefig(output, dpi=dpi, transparent=transparent)
|
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Generates a figure file in the selected directory.
Args:
fig: matplotlib figure
prefile(str): Include before the general filename of the figure
postfile(str): Included after the general filename of the figure
output_path(str): Define the path to the output directory
output_name(str): String to define the name of the output figure
output_format(str): String to define the format of the output figure
dpi(int): Define the DPI (Dots per Inch) of the figure
transparent(bool): If True the saved figure will have a transparent background
|
[
"Generates",
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"."
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L115-L135
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
plot_style
|
def plot_style(fig, ax, # pylint: disable=too-many-arguments, too-many-locals
# plot_title
pretitle='',
title='Figure',
posttitle='',
title_fontsize=14,
title_arg=None,
# plot_labels
label_fontsize=14,
xlabel=None,
xlabel_arg=None,
ylabel=None,
ylabel_arg=None,
zlabel=None,
zlabel_arg=None,
# plot_ticks
tick_fontsize=12,
xticks=None,
xticks_args=None,
yticks=None,
yticks_args=None,
zticks=None,
zticks_args=None,
# update_plot_limits
white_space=30,
# plot_legend
no_legend=True,
legend_arg=None,
# internal
no_axes=False,
aspect_ratio='equal',
tight=False,
**_):
"""Set the basic options of a matplotlib figure, to be used by viewing - plotting functions
Args:
fig(matplotlib figure): figure
ax(matplotlib axes, belonging to `fig`): axes
pretitle(str): String to include before the general title of the figure
posttitle (str): String to include after the general title of the figure
title (str): Set the title for the figure
title_fontsize (int): Defines the size of the title's font
title_arg (dict): Addition arguments for matplotlib.title() call
label_fontsize(int): Size of the labels' font
xlabel(str): The xlabel for the figure
xlabel_arg(dict): Passsed into matplotlib as xlabel arguments
ylabel(str): The ylabel for the figure
ylabel_arg(dict): Passsed into matplotlib as ylabel arguments
zlabel(str): The zlabel for the figure
zlabel_arg(dict): Passsed into matplotlib as zlabel arguments
tick_fontsize (int): Defines the size of the ticks' font
xticks([list of ticks]): Defines the values of x ticks in the figure
xticks_args(dict): Passsed into matplotlib as xticks arguments
yticks([list of ticks]): Defines the values of y ticks in the figure
yticks_args(dict): Passsed into matplotlib as yticks arguments
zticks([list of ticks]): Defines the values of z ticks in the figure
zticks_args(dict): Passsed into matplotlib as zticks arguments
white_space(float): whitespace added to surround the tight limit of the data
no_legend (bool): Defines the presence of a legend in the figure
legend_arg (dict): Addition arguments for matplotlib.legend() call
no_axes(bool): If True the labels and the frame will be set off
aspect_ratio(str): Sets aspect ratio of the figure, according to matplotlib aspect_ratio
tight(bool): If True the tight layout of matplotlib will be activated
Returns:
Matplotlib figure, matplotlib axes
"""
plot_title(ax, pretitle, title, posttitle, title_fontsize, title_arg)
plot_labels(ax, label_fontsize, xlabel, xlabel_arg, ylabel, ylabel_arg, zlabel, zlabel_arg)
plot_ticks(ax, tick_fontsize, xticks, xticks_args, yticks, yticks_args, zticks, zticks_args)
update_plot_limits(ax, white_space)
plot_legend(ax, no_legend, legend_arg)
if no_axes:
ax.set_frame_on(False)
ax.xaxis.set_visible(False)
ax.yaxis.set_visible(False)
ax.set_aspect(aspect_ratio)
if tight:
fig.set_tight_layout(True)
|
python
|
def plot_style(fig, ax,
pretitle='',
title='Figure',
posttitle='',
title_fontsize=14,
title_arg=None,
label_fontsize=14,
xlabel=None,
xlabel_arg=None,
ylabel=None,
ylabel_arg=None,
zlabel=None,
zlabel_arg=None,
tick_fontsize=12,
xticks=None,
xticks_args=None,
yticks=None,
yticks_args=None,
zticks=None,
zticks_args=None,
white_space=30,
no_legend=True,
legend_arg=None,
no_axes=False,
aspect_ratio='equal',
tight=False,
**_):
plot_title(ax, pretitle, title, posttitle, title_fontsize, title_arg)
plot_labels(ax, label_fontsize, xlabel, xlabel_arg, ylabel, ylabel_arg, zlabel, zlabel_arg)
plot_ticks(ax, tick_fontsize, xticks, xticks_args, yticks, yticks_args, zticks, zticks_args)
update_plot_limits(ax, white_space)
plot_legend(ax, no_legend, legend_arg)
if no_axes:
ax.set_frame_on(False)
ax.xaxis.set_visible(False)
ax.yaxis.set_visible(False)
ax.set_aspect(aspect_ratio)
if tight:
fig.set_tight_layout(True)
|
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Set the basic options of a matplotlib figure, to be used by viewing - plotting functions
Args:
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ax(matplotlib axes, belonging to `fig`): axes
pretitle(str): String to include before the general title of the figure
posttitle (str): String to include after the general title of the figure
title (str): Set the title for the figure
title_fontsize (int): Defines the size of the title's font
title_arg (dict): Addition arguments for matplotlib.title() call
label_fontsize(int): Size of the labels' font
xlabel(str): The xlabel for the figure
xlabel_arg(dict): Passsed into matplotlib as xlabel arguments
ylabel(str): The ylabel for the figure
ylabel_arg(dict): Passsed into matplotlib as ylabel arguments
zlabel(str): The zlabel for the figure
zlabel_arg(dict): Passsed into matplotlib as zlabel arguments
tick_fontsize (int): Defines the size of the ticks' font
xticks([list of ticks]): Defines the values of x ticks in the figure
xticks_args(dict): Passsed into matplotlib as xticks arguments
yticks([list of ticks]): Defines the values of y ticks in the figure
yticks_args(dict): Passsed into matplotlib as yticks arguments
zticks([list of ticks]): Defines the values of z ticks in the figure
zticks_args(dict): Passsed into matplotlib as zticks arguments
white_space(float): whitespace added to surround the tight limit of the data
no_legend (bool): Defines the presence of a legend in the figure
legend_arg (dict): Addition arguments for matplotlib.legend() call
no_axes(bool): If True the labels and the frame will be set off
aspect_ratio(str): Sets aspect ratio of the figure, according to matplotlib aspect_ratio
tight(bool): If True the tight layout of matplotlib will be activated
Returns:
Matplotlib figure, matplotlib axes
|
[
"Set",
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"a",
"matplotlib",
"figure",
"to",
"be",
"used",
"by",
"viewing",
"-",
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"functions"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L138-L225
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
plot_title
|
def plot_title(ax, pretitle='', title='Figure', posttitle='', title_fontsize=14, title_arg=None):
"""Set title options of a matplotlib plot
Args:
ax: matplotlib axes
pretitle(str): String to include before the general title of the figure
posttitle (str): String to include after the general title of the figure
title (str): Set the title for the figure
title_fontsize (int): Defines the size of the title's font
title_arg (dict): Addition arguments for matplotlib.title() call
"""
current_title = ax.get_title()
if not current_title:
current_title = pretitle + title + posttitle
title_arg = dict_if_none(title_arg)
ax.set_title(current_title, fontsize=title_fontsize, **title_arg)
|
python
|
def plot_title(ax, pretitle='', title='Figure', posttitle='', title_fontsize=14, title_arg=None):
current_title = ax.get_title()
if not current_title:
current_title = pretitle + title + posttitle
title_arg = dict_if_none(title_arg)
ax.set_title(current_title, fontsize=title_fontsize, **title_arg)
|
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Set title options of a matplotlib plot
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ax: matplotlib axes
pretitle(str): String to include before the general title of the figure
posttitle (str): String to include after the general title of the figure
title (str): Set the title for the figure
title_fontsize (int): Defines the size of the title's font
title_arg (dict): Addition arguments for matplotlib.title() call
|
[
"Set",
"title",
"options",
"of",
"a",
"matplotlib",
"plot"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L228-L246
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
plot_labels
|
def plot_labels(ax, label_fontsize=14,
xlabel=None, xlabel_arg=None,
ylabel=None, ylabel_arg=None,
zlabel=None, zlabel_arg=None):
"""Sets the labels options of a matplotlib plot
Args:
ax: matplotlib axes
label_fontsize(int): Size of the labels' font
xlabel(str): The xlabel for the figure
xlabel_arg(dict): Passsed into matplotlib as xlabel arguments
ylabel(str): The ylabel for the figure
ylabel_arg(dict): Passsed into matplotlib as ylabel arguments
zlabel(str): The zlabel for the figure
zlabel_arg(dict): Passsed into matplotlib as zlabel arguments
"""
xlabel = xlabel if xlabel is not None else ax.get_xlabel() or 'X'
ylabel = ylabel if ylabel is not None else ax.get_ylabel() or 'Y'
xlabel_arg = dict_if_none(xlabel_arg)
ylabel_arg = dict_if_none(ylabel_arg)
ax.set_xlabel(xlabel, fontsize=label_fontsize, **xlabel_arg)
ax.set_ylabel(ylabel, fontsize=label_fontsize, **ylabel_arg)
if hasattr(ax, 'zaxis'):
zlabel = zlabel if zlabel is not None else ax.get_zlabel() or 'Z'
zlabel_arg = dict_if_none(zlabel_arg)
ax.set_zlabel(zlabel, fontsize=label_fontsize, **zlabel_arg)
|
python
|
def plot_labels(ax, label_fontsize=14,
xlabel=None, xlabel_arg=None,
ylabel=None, ylabel_arg=None,
zlabel=None, zlabel_arg=None):
xlabel = xlabel if xlabel is not None else ax.get_xlabel() or 'X'
ylabel = ylabel if ylabel is not None else ax.get_ylabel() or 'Y'
xlabel_arg = dict_if_none(xlabel_arg)
ylabel_arg = dict_if_none(ylabel_arg)
ax.set_xlabel(xlabel, fontsize=label_fontsize, **xlabel_arg)
ax.set_ylabel(ylabel, fontsize=label_fontsize, **ylabel_arg)
if hasattr(ax, 'zaxis'):
zlabel = zlabel if zlabel is not None else ax.get_zlabel() or 'Z'
zlabel_arg = dict_if_none(zlabel_arg)
ax.set_zlabel(zlabel, fontsize=label_fontsize, **zlabel_arg)
|
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Sets the labels options of a matplotlib plot
Args:
ax: matplotlib axes
label_fontsize(int): Size of the labels' font
xlabel(str): The xlabel for the figure
xlabel_arg(dict): Passsed into matplotlib as xlabel arguments
ylabel(str): The ylabel for the figure
ylabel_arg(dict): Passsed into matplotlib as ylabel arguments
zlabel(str): The zlabel for the figure
zlabel_arg(dict): Passsed into matplotlib as zlabel arguments
|
[
"Sets",
"the",
"labels",
"options",
"of",
"a",
"matplotlib",
"plot"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L249-L277
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
plot_ticks
|
def plot_ticks(ax, tick_fontsize=12,
xticks=None, xticks_args=None,
yticks=None, yticks_args=None,
zticks=None, zticks_args=None):
"""Function that defines the labels options of a matplotlib plot.
Args:
ax: matplotlib axes
tick_fontsize (int): Defines the size of the ticks' font
xticks([list of ticks]): Defines the values of x ticks in the figure
xticks_arg(dict): Passsed into matplotlib as xticks arguments
yticks([list of ticks]): Defines the values of y ticks in the figure
yticks_arg(dict): Passsed into matplotlib as yticks arguments
zticks([list of ticks]): Defines the values of z ticks in the figure
zticks_arg(dict): Passsed into matplotlib as zticks arguments
"""
if xticks is not None:
ax.set_xticks(xticks)
xticks_args = dict_if_none(xticks_args)
ax.xaxis.set_tick_params(labelsize=tick_fontsize, **xticks_args)
if yticks is not None:
ax.set_yticks(yticks)
yticks_args = dict_if_none(yticks_args)
ax.yaxis.set_tick_params(labelsize=tick_fontsize, **yticks_args)
if zticks is not None:
ax.set_zticks(zticks)
zticks_args = dict_if_none(zticks_args)
ax.zaxis.set_tick_params(labelsize=tick_fontsize, **zticks_args)
|
python
|
def plot_ticks(ax, tick_fontsize=12,
xticks=None, xticks_args=None,
yticks=None, yticks_args=None,
zticks=None, zticks_args=None):
if xticks is not None:
ax.set_xticks(xticks)
xticks_args = dict_if_none(xticks_args)
ax.xaxis.set_tick_params(labelsize=tick_fontsize, **xticks_args)
if yticks is not None:
ax.set_yticks(yticks)
yticks_args = dict_if_none(yticks_args)
ax.yaxis.set_tick_params(labelsize=tick_fontsize, **yticks_args)
if zticks is not None:
ax.set_zticks(zticks)
zticks_args = dict_if_none(zticks_args)
ax.zaxis.set_tick_params(labelsize=tick_fontsize, **zticks_args)
|
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Function that defines the labels options of a matplotlib plot.
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tick_fontsize (int): Defines the size of the ticks' font
xticks([list of ticks]): Defines the values of x ticks in the figure
xticks_arg(dict): Passsed into matplotlib as xticks arguments
yticks([list of ticks]): Defines the values of y ticks in the figure
yticks_arg(dict): Passsed into matplotlib as yticks arguments
zticks([list of ticks]): Defines the values of z ticks in the figure
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L280-L309
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
update_plot_limits
|
def update_plot_limits(ax, white_space):
"""Sets the limit options of a matplotlib plot.
Args:
ax: matplotlib axes
white_space(float): whitespace added to surround the tight limit of the data
Note: This relies on ax.dataLim (in 2d) and ax.[xy, zz]_dataLim being set in 3d
"""
if hasattr(ax, 'zz_dataLim'):
bounds = ax.xy_dataLim.bounds
ax.set_xlim(bounds[0] - white_space, bounds[0] + bounds[2] + white_space)
ax.set_ylim(bounds[1] - white_space, bounds[1] + bounds[3] + white_space)
bounds = ax.zz_dataLim.bounds
ax.set_zlim(bounds[0] - white_space, bounds[0] + bounds[2] + white_space)
else:
bounds = ax.dataLim.bounds
assert not any(map(np.isinf, bounds)), 'Cannot set bounds if dataLim has infinite elements'
ax.set_xlim(bounds[0] - white_space, bounds[0] + bounds[2] + white_space)
ax.set_ylim(bounds[1] - white_space, bounds[1] + bounds[3] + white_space)
|
python
|
def update_plot_limits(ax, white_space):
if hasattr(ax, 'zz_dataLim'):
bounds = ax.xy_dataLim.bounds
ax.set_xlim(bounds[0] - white_space, bounds[0] + bounds[2] + white_space)
ax.set_ylim(bounds[1] - white_space, bounds[1] + bounds[3] + white_space)
bounds = ax.zz_dataLim.bounds
ax.set_zlim(bounds[0] - white_space, bounds[0] + bounds[2] + white_space)
else:
bounds = ax.dataLim.bounds
assert not any(map(np.isinf, bounds)), 'Cannot set bounds if dataLim has infinite elements'
ax.set_xlim(bounds[0] - white_space, bounds[0] + bounds[2] + white_space)
ax.set_ylim(bounds[1] - white_space, bounds[1] + bounds[3] + white_space)
|
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Sets the limit options of a matplotlib plot.
Args:
ax: matplotlib axes
white_space(float): whitespace added to surround the tight limit of the data
Note: This relies on ax.dataLim (in 2d) and ax.[xy, zz]_dataLim being set in 3d
|
[
"Sets",
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"a",
"matplotlib",
"plot",
"."
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L312-L333
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
plot_legend
|
def plot_legend(ax, no_legend=True, legend_arg=None):
"""
Function that defines the legend options
of a matplotlib plot.
Args:
ax: matplotlib axes
no_legend (bool): Defines the presence of a legend in the figure
legend_arg (dict): Addition arguments for matplotlib.legend() call
"""
legend_arg = dict_if_none(legend_arg)
if not no_legend:
ax.legend(**legend_arg)
|
python
|
def plot_legend(ax, no_legend=True, legend_arg=None):
legend_arg = dict_if_none(legend_arg)
if not no_legend:
ax.legend(**legend_arg)
|
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":",
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"(",
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"*",
"legend_arg",
")"
] |
Function that defines the legend options
of a matplotlib plot.
Args:
ax: matplotlib axes
no_legend (bool): Defines the presence of a legend in the figure
legend_arg (dict): Addition arguments for matplotlib.legend() call
|
[
"Function",
"that",
"defines",
"the",
"legend",
"options",
"of",
"a",
"matplotlib",
"plot",
"."
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L336-L349
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
_get_normals
|
def _get_normals(v):
'''get two vectors that form a basis w/ v
Note: returned vectors are unit
'''
not_v = np.array([1, 0, 0])
if np.all(np.abs(v) == not_v):
not_v = np.array([0, 1, 0])
n1 = np.cross(v, not_v)
n1 /= norm(n1)
n2 = np.cross(v, n1)
return n1, n2
|
python
|
def _get_normals(v):
not_v = np.array([1, 0, 0])
if np.all(np.abs(v) == not_v):
not_v = np.array([0, 1, 0])
n1 = np.cross(v, not_v)
n1 /= norm(n1)
n2 = np.cross(v, n1)
return n1, n2
|
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get two vectors that form a basis w/ v
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[
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"/",
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L355-L366
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
generate_cylindrical_points
|
def generate_cylindrical_points(start, end, start_radius, end_radius,
linspace_count=_LINSPACE_COUNT):
'''Generate a 3d mesh of a cylinder with start and end points, and varying radius
Based on: http://stackoverflow.com/a/32383775
'''
v = end - start
length = norm(v)
v = v / length
n1, n2 = _get_normals(v)
# pylint: disable=unbalanced-tuple-unpacking
l, theta = np.meshgrid(np.linspace(0, length, linspace_count),
np.linspace(0, 2 * np.pi, linspace_count))
radii = np.linspace(start_radius, end_radius, linspace_count)
rsin = np.multiply(radii, np.sin(theta))
rcos = np.multiply(radii, np.cos(theta))
return np.array([start[i] +
v[i] * l +
n1[i] * rsin + n2[i] * rcos
for i in range(3)])
|
python
|
def generate_cylindrical_points(start, end, start_radius, end_radius,
linspace_count=_LINSPACE_COUNT):
v = end - start
length = norm(v)
v = v / length
n1, n2 = _get_normals(v)
l, theta = np.meshgrid(np.linspace(0, length, linspace_count),
np.linspace(0, 2 * np.pi, linspace_count))
radii = np.linspace(start_radius, end_radius, linspace_count)
rsin = np.multiply(radii, np.sin(theta))
rcos = np.multiply(radii, np.cos(theta))
return np.array([start[i] +
v[i] * l +
n1[i] * rsin + n2[i] * rcos
for i in range(3)])
|
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Generate a 3d mesh of a cylinder with start and end points, and varying radius
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|
[
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L369-L391
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
project_cylinder_onto_2d
|
def project_cylinder_onto_2d(ax, plane,
start, end, start_radius, end_radius,
color='black', alpha=1.):
'''take cylinder defined by start/end, and project it onto the plane
Args:
ax: matplotlib axes
plane(tuple of int): where x, y, z = 0, 1, 2, so (0, 1) is the xy axis
start(np.array): start coordinates
end(np.array): end coordinates
start_radius(float): start radius
end_radius(float): end radius
color: matplotlib color
alpha(float): alpha value
Note: There are probably more efficient ways of doing this: here the
3d outline is calculated, the non-used plane coordinates are dropped, a
tight convex hull is found, and that is used for a filled polygon
'''
points = generate_cylindrical_points(start, end, start_radius, end_radius, 10)
points = np.vstack([points[plane[0]].ravel(),
points[plane[1]].ravel()])
points = points.T
hull = ConvexHull(points)
ax.add_patch(Polygon(points[hull.vertices], fill=True, color=color, alpha=alpha))
|
python
|
def project_cylinder_onto_2d(ax, plane,
start, end, start_radius, end_radius,
color='black', alpha=1.):
points = generate_cylindrical_points(start, end, start_radius, end_radius, 10)
points = np.vstack([points[plane[0]].ravel(),
points[plane[1]].ravel()])
points = points.T
hull = ConvexHull(points)
ax.add_patch(Polygon(points[hull.vertices], fill=True, color=color, alpha=alpha))
|
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Args:
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start(np.array): start coordinates
end(np.array): end coordinates
start_radius(float): start radius
end_radius(float): end radius
color: matplotlib color
alpha(float): alpha value
Note: There are probably more efficient ways of doing this: here the
3d outline is calculated, the non-used plane coordinates are dropped, a
tight convex hull is found, and that is used for a filled polygon
|
[
"take",
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"defined",
"by",
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"/",
"end",
"and",
"project",
"it",
"onto",
"the",
"plane"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L394-L418
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
plot_cylinder
|
def plot_cylinder(ax, start, end, start_radius, end_radius,
color='black', alpha=1., linspace_count=_LINSPACE_COUNT):
'''plot a 3d cylinder'''
assert not np.all(start == end), 'Cylinder must have length'
x, y, z = generate_cylindrical_points(start, end, start_radius, end_radius,
linspace_count=linspace_count)
ax.plot_surface(x, y, z, color=color, alpha=alpha)
|
python
|
def plot_cylinder(ax, start, end, start_radius, end_radius,
color='black', alpha=1., linspace_count=_LINSPACE_COUNT):
assert not np.all(start == end), 'Cylinder must have length'
x, y, z = generate_cylindrical_points(start, end, start_radius, end_radius,
linspace_count=linspace_count)
ax.plot_surface(x, y, z, color=color, alpha=alpha)
|
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plot a 3d cylinder
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[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L421-L427
|
BlueBrain/NeuroM
|
neurom/view/common.py
|
plot_sphere
|
def plot_sphere(ax, center, radius, color='black', alpha=1., linspace_count=_LINSPACE_COUNT):
""" Plots a 3d sphere, given the center and the radius. """
u = np.linspace(0, 2 * np.pi, linspace_count)
v = np.linspace(0, np.pi, linspace_count)
sin_v = np.sin(v)
x = center[0] + radius * np.outer(np.cos(u), sin_v)
y = center[1] + radius * np.outer(np.sin(u), sin_v)
z = center[2] + radius * np.outer(np.ones_like(u), np.cos(v))
ax.plot_surface(x, y, z, linewidth=0.0, color=color, alpha=alpha)
|
python
|
def plot_sphere(ax, center, radius, color='black', alpha=1., linspace_count=_LINSPACE_COUNT):
u = np.linspace(0, 2 * np.pi, linspace_count)
v = np.linspace(0, np.pi, linspace_count)
sin_v = np.sin(v)
x = center[0] + radius * np.outer(np.cos(u), sin_v)
y = center[1] + radius * np.outer(np.sin(u), sin_v)
z = center[2] + radius * np.outer(np.ones_like(u), np.cos(v))
ax.plot_surface(x, y, z, linewidth=0.0, color=color, alpha=alpha)
|
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|
[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/common.py#L430-L440
|
BlueBrain/NeuroM
|
neurom/check/structural_checks.py
|
has_sequential_ids
|
def has_sequential_ids(data_wrapper):
'''Check that IDs are increasing and consecutive
returns tuple (bool, list of IDs that are not consecutive
with their predecessor)
'''
db = data_wrapper.data_block
ids = db[:, COLS.ID]
steps = ids[np.where(np.diff(ids) != 1)[0] + 1].astype(int)
return CheckResult(len(steps) == 0, steps)
|
python
|
def has_sequential_ids(data_wrapper):
db = data_wrapper.data_block
ids = db[:, COLS.ID]
steps = ids[np.where(np.diff(ids) != 1)[0] + 1].astype(int)
return CheckResult(len(steps) == 0, steps)
|
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Check that IDs are increasing and consecutive
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|
[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/structural_checks.py#L39-L48
|
BlueBrain/NeuroM
|
neurom/check/structural_checks.py
|
no_missing_parents
|
def no_missing_parents(data_wrapper):
'''Check that all points have existing parents
Point's parent ID must exist and parent must be declared
before child.
Returns:
CheckResult with result and list of IDs that have no parent
'''
db = data_wrapper.data_block
ids = np.setdiff1d(db[:, COLS.P], db[:, COLS.ID])[1:]
return CheckResult(len(ids) == 0, ids.astype(np.int) + 1)
|
python
|
def no_missing_parents(data_wrapper):
db = data_wrapper.data_block
ids = np.setdiff1d(db[:, COLS.P], db[:, COLS.ID])[1:]
return CheckResult(len(ids) == 0, ids.astype(np.int) + 1)
|
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Check that all points have existing parents
Point's parent ID must exist and parent must be declared
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Returns:
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"child",
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/structural_checks.py#L51-L61
|
BlueBrain/NeuroM
|
neurom/check/structural_checks.py
|
is_single_tree
|
def is_single_tree(data_wrapper):
'''Check that data forms a single tree
Only the first point has ID of -1.
Returns:
CheckResult with result and list of IDs
Note:
This assumes no_missing_parents passed.
'''
db = data_wrapper.data_block
bad_ids = db[db[:, COLS.P] == -1][1:, COLS.ID]
return CheckResult(len(bad_ids) == 0, bad_ids.tolist())
|
python
|
def is_single_tree(data_wrapper):
db = data_wrapper.data_block
bad_ids = db[db[:, COLS.P] == -1][1:, COLS.ID]
return CheckResult(len(bad_ids) == 0, bad_ids.tolist())
|
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Check that data forms a single tree
Only the first point has ID of -1.
Returns:
CheckResult with result and list of IDs
Note:
This assumes no_missing_parents passed.
|
[
"Check",
"that",
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"forms",
"a",
"single",
"tree"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/structural_checks.py#L64-L77
|
BlueBrain/NeuroM
|
neurom/check/structural_checks.py
|
has_soma_points
|
def has_soma_points(data_wrapper):
'''Checks if the TYPE column of raw data block has an element of type soma
Returns:
CheckResult with result
'''
db = data_wrapper.data_block
return CheckResult(POINT_TYPE.SOMA in db[:, COLS.TYPE], None)
|
python
|
def has_soma_points(data_wrapper):
db = data_wrapper.data_block
return CheckResult(POINT_TYPE.SOMA in db[:, COLS.TYPE], None)
|
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Checks if the TYPE column of raw data block has an element of type soma
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|
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/structural_checks.py#L93-L100
|
BlueBrain/NeuroM
|
neurom/check/structural_checks.py
|
has_all_finite_radius_neurites
|
def has_all_finite_radius_neurites(data_wrapper, threshold=0.0):
'''Check that all points with neurite type have a finite radius
Returns:
CheckResult with result and list of IDs of neurite points with zero radius
'''
db = data_wrapper.data_block
neurite_ids = np.in1d(db[:, COLS.TYPE], POINT_TYPE.NEURITES)
zero_radius_ids = db[:, COLS.R] <= threshold
bad_pts = np.array(db[neurite_ids & zero_radius_ids][:, COLS.ID],
dtype=int).tolist()
return CheckResult(len(bad_pts) == 0, bad_pts)
|
python
|
def has_all_finite_radius_neurites(data_wrapper, threshold=0.0):
db = data_wrapper.data_block
neurite_ids = np.in1d(db[:, COLS.TYPE], POINT_TYPE.NEURITES)
zero_radius_ids = db[:, COLS.R] <= threshold
bad_pts = np.array(db[neurite_ids & zero_radius_ids][:, COLS.ID],
dtype=int).tolist()
return CheckResult(len(bad_pts) == 0, bad_pts)
|
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Check that all points with neurite type have a finite radius
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|
[
"Check",
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"neurite",
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/structural_checks.py#L103-L114
|
BlueBrain/NeuroM
|
neurom/check/structural_checks.py
|
has_valid_soma
|
def has_valid_soma(data_wrapper):
'''Check if a data block has a valid soma
Returns:
CheckResult with result
'''
try:
make_soma(data_wrapper.soma_points())
return CheckResult(True)
except SomaError:
return CheckResult(False)
|
python
|
def has_valid_soma(data_wrapper):
try:
make_soma(data_wrapper.soma_points())
return CheckResult(True)
except SomaError:
return CheckResult(False)
|
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Check if a data block has a valid soma
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|
[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/structural_checks.py#L117-L127
|
BlueBrain/NeuroM
|
doc/source/conf.py
|
_pelita_member_filter
|
def _pelita_member_filter(parent_name, item_names):
"""
Filter a list of autodoc items for which to generate documentation.
Include only imports that come from the documented module or its
submodules.
"""
filtered_names = []
if parent_name not in sys.modules:
return item_names
module = sys.modules[parent_name]
for item_name in item_names:
item = getattr(module, item_name, None)
location = getattr(item, '__module__', None)
if location is None or (location + ".").startswith(parent_name + "."):
filtered_names.append(item_name)
return filtered_names
|
python
|
def _pelita_member_filter(parent_name, item_names):
filtered_names = []
if parent_name not in sys.modules:
return item_names
module = sys.modules[parent_name]
for item_name in item_names:
item = getattr(module, item_name, None)
location = getattr(item, '__module__', None)
if location is None or (location + ".").startswith(parent_name + "."):
filtered_names.append(item_name)
return filtered_names
|
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Filter a list of autodoc items for which to generate documentation.
Include only imports that come from the documented module or its
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[
"Filter",
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"to",
"generate",
"documentation",
"."
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/doc/source/conf.py#L158-L179
|
BlueBrain/NeuroM
|
examples/boxplot.py
|
boxplot
|
def boxplot(neurons, feature, new_fig=True, subplot=False):
'''
Plot a histogram of the selected feature for the population of neurons.
Plots x-axis versus y-axis on a scatter|histogram|binned values plot.
More information about the plot and how it works.
Parameters
----------
neurons : list
List of Neurons. Single neurons must be encapsulated in a list.
feature : str
The feature of interest.
Options
-------
subplot : bool
Default is False, which returns a matplotlib figure object. If True,
returns a matplotlib axis object, for use as a subplot.
'''
feature_values = [getattr(neu, 'get_' + feature)() for neu in neurons]
_, ax = common.get_figure(new_fig=new_fig, subplot=subplot)
ax.boxplot(feature_values)
x_labels = ['neuron_id' for _ in neurons]
ax.set_xticklabels(x_labels)
|
python
|
def boxplot(neurons, feature, new_fig=True, subplot=False):
feature_values = [getattr(neu, 'get_' + feature)() for neu in neurons]
_, ax = common.get_figure(new_fig=new_fig, subplot=subplot)
ax.boxplot(feature_values)
x_labels = ['neuron_id' for _ in neurons]
ax.set_xticklabels(x_labels)
|
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Plot a histogram of the selected feature for the population of neurons.
Plots x-axis versus y-axis on a scatter|histogram|binned values plot.
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Parameters
----------
neurons : list
List of Neurons. Single neurons must be encapsulated in a list.
feature : str
The feature of interest.
Options
-------
subplot : bool
Default is False, which returns a matplotlib figure object. If True,
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[
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"plot",
"."
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/examples/boxplot.py#L36-L67
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_axon
|
def has_axon(neuron, treefun=_read_neurite_type):
'''Check if a neuron has an axon
Arguments:
neuron(Neuron): The neuron object to test
treefun: Optional function to calculate the tree type of
neuron's neurites
Returns:
CheckResult with result
'''
return CheckResult(NeuriteType.axon in (treefun(n) for n in neuron.neurites))
|
python
|
def has_axon(neuron, treefun=_read_neurite_type):
return CheckResult(NeuriteType.axon in (treefun(n) for n in neuron.neurites))
|
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"(",
"n",
")",
"for",
"n",
"in",
"neuron",
".",
"neurites",
")",
")"
] |
Check if a neuron has an axon
Arguments:
neuron(Neuron): The neuron object to test
treefun: Optional function to calculate the tree type of
neuron's neurites
Returns:
CheckResult with result
|
[
"Check",
"if",
"a",
"neuron",
"has",
"an",
"axon"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L54-L65
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_apical_dendrite
|
def has_apical_dendrite(neuron, min_number=1, treefun=_read_neurite_type):
'''Check if a neuron has apical dendrites
Arguments:
neuron(Neuron): The neuron object to test
min_number: minimum number of apical dendrites required
treefun: Optional function to calculate the tree type of neuron's
neurites
Returns:
CheckResult with result
'''
types = [treefun(n) for n in neuron.neurites]
return CheckResult(types.count(NeuriteType.apical_dendrite) >= min_number)
|
python
|
def has_apical_dendrite(neuron, min_number=1, treefun=_read_neurite_type):
types = [treefun(n) for n in neuron.neurites]
return CheckResult(types.count(NeuriteType.apical_dendrite) >= min_number)
|
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Check if a neuron has apical dendrites
Arguments:
neuron(Neuron): The neuron object to test
min_number: minimum number of apical dendrites required
treefun: Optional function to calculate the tree type of neuron's
neurites
Returns:
CheckResult with result
|
[
"Check",
"if",
"a",
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L68-L81
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_basal_dendrite
|
def has_basal_dendrite(neuron, min_number=1, treefun=_read_neurite_type):
'''Check if a neuron has basal dendrites
Arguments:
neuron(Neuron): The neuron object to test
min_number: minimum number of basal dendrites required
treefun: Optional function to calculate the tree type of neuron's
neurites
Returns:
CheckResult with result
'''
types = [treefun(n) for n in neuron.neurites]
return CheckResult(types.count(NeuriteType.basal_dendrite) >= min_number)
|
python
|
def has_basal_dendrite(neuron, min_number=1, treefun=_read_neurite_type):
types = [treefun(n) for n in neuron.neurites]
return CheckResult(types.count(NeuriteType.basal_dendrite) >= min_number)
|
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"(",
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] |
Check if a neuron has basal dendrites
Arguments:
neuron(Neuron): The neuron object to test
min_number: minimum number of basal dendrites required
treefun: Optional function to calculate the tree type of neuron's
neurites
Returns:
CheckResult with result
|
[
"Check",
"if",
"a",
"neuron",
"has",
"basal",
"dendrites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L84-L97
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_no_flat_neurites
|
def has_no_flat_neurites(neuron, tol=0.1, method='ratio'):
'''Check that a neuron has no flat neurites
Arguments:
neuron(Neuron): The neuron object to test
tol(float): tolerance
method(string): way of determining flatness, 'tolerance', 'ratio' \
as described in :meth:`neurom.check.morphtree.get_flat_neurites`
Returns:
CheckResult with result
'''
return CheckResult(len(get_flat_neurites(neuron, tol, method)) == 0)
|
python
|
def has_no_flat_neurites(neuron, tol=0.1, method='ratio'):
return CheckResult(len(get_flat_neurites(neuron, tol, method)) == 0)
|
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"(",
"neuron",
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"==",
"0",
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] |
Check that a neuron has no flat neurites
Arguments:
neuron(Neuron): The neuron object to test
tol(float): tolerance
method(string): way of determining flatness, 'tolerance', 'ratio' \
as described in :meth:`neurom.check.morphtree.get_flat_neurites`
Returns:
CheckResult with result
|
[
"Check",
"that",
"a",
"neuron",
"has",
"no",
"flat",
"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L100-L112
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_all_nonzero_segment_lengths
|
def has_all_nonzero_segment_lengths(neuron, threshold=0.0):
'''Check presence of neuron segments with length not above threshold
Arguments:
neuron(Neuron): The neuron object to test
threshold(float): value above which a segment length is considered to
be non-zero
Returns:
CheckResult with result including list of (section_id, segment_id)
of zero length segments
'''
bad_ids = []
for sec in _nf.iter_sections(neuron):
p = sec.points
for i, s in enumerate(zip(p[:-1], p[1:])):
if segment_length(s) <= threshold:
bad_ids.append((sec.id, i))
return CheckResult(len(bad_ids) == 0, bad_ids)
|
python
|
def has_all_nonzero_segment_lengths(neuron, threshold=0.0):
bad_ids = []
for sec in _nf.iter_sections(neuron):
p = sec.points
for i, s in enumerate(zip(p[:-1], p[1:])):
if segment_length(s) <= threshold:
bad_ids.append((sec.id, i))
return CheckResult(len(bad_ids) == 0, bad_ids)
|
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Check presence of neuron segments with length not above threshold
Arguments:
neuron(Neuron): The neuron object to test
threshold(float): value above which a segment length is considered to
be non-zero
Returns:
CheckResult with result including list of (section_id, segment_id)
of zero length segments
|
[
"Check",
"presence",
"of",
"neuron",
"segments",
"with",
"length",
"not",
"above",
"threshold"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L128-L147
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_all_nonzero_section_lengths
|
def has_all_nonzero_section_lengths(neuron, threshold=0.0):
'''Check presence of neuron sections with length not above threshold
Arguments:
neuron(Neuron): The neuron object to test
threshold(float): value above which a section length is considered
to be non-zero
Returns:
CheckResult with result including list of ids of bad sections
'''
bad_ids = [s.id for s in _nf.iter_sections(neuron.neurites)
if section_length(s.points) <= threshold]
return CheckResult(len(bad_ids) == 0, bad_ids)
|
python
|
def has_all_nonzero_section_lengths(neuron, threshold=0.0):
bad_ids = [s.id for s in _nf.iter_sections(neuron.neurites)
if section_length(s.points) <= threshold]
return CheckResult(len(bad_ids) == 0, bad_ids)
|
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Check presence of neuron sections with length not above threshold
Arguments:
neuron(Neuron): The neuron object to test
threshold(float): value above which a section length is considered
to be non-zero
Returns:
CheckResult with result including list of ids of bad sections
|
[
"Check",
"presence",
"of",
"neuron",
"sections",
"with",
"length",
"not",
"above",
"threshold"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L150-L164
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_all_nonzero_neurite_radii
|
def has_all_nonzero_neurite_radii(neuron, threshold=0.0):
'''Check presence of neurite points with radius not above threshold
Arguments:
neuron(Neuron): The neuron object to test
threshold: value above which a radius is considered to be non-zero
Returns:
CheckResult with result including list of (section ID, point ID) pairs
of zero-radius points
'''
bad_ids = []
seen_ids = set()
for s in _nf.iter_sections(neuron):
for i, p in enumerate(s.points):
info = (s.id, i)
if p[COLS.R] <= threshold and info not in seen_ids:
seen_ids.add(info)
bad_ids.append(info)
return CheckResult(len(bad_ids) == 0, bad_ids)
|
python
|
def has_all_nonzero_neurite_radii(neuron, threshold=0.0):
bad_ids = []
seen_ids = set()
for s in _nf.iter_sections(neuron):
for i, p in enumerate(s.points):
info = (s.id, i)
if p[COLS.R] <= threshold and info not in seen_ids:
seen_ids.add(info)
bad_ids.append(info)
return CheckResult(len(bad_ids) == 0, bad_ids)
|
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Check presence of neurite points with radius not above threshold
Arguments:
neuron(Neuron): The neuron object to test
threshold: value above which a radius is considered to be non-zero
Returns:
CheckResult with result including list of (section ID, point ID) pairs
of zero-radius points
|
[
"Check",
"presence",
"of",
"neurite",
"points",
"with",
"radius",
"not",
"above",
"threshold"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L167-L187
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_no_jumps
|
def has_no_jumps(neuron, max_distance=30.0, axis='z'):
'''Check if there are jumps (large movements in the `axis`)
Arguments:
neuron(Neuron): The neuron object to test
max_distance(float): value above which consecutive z-values are
considered a jump
axis(str): one of x/y/z, which axis to check for jumps
Returns:
CheckResult with result list of ids of bad sections
'''
bad_ids = []
axis = {'x': COLS.X, 'y': COLS.Y, 'z': COLS.Z, }[axis.lower()]
for neurite in iter_neurites(neuron):
section_segment = ((sec, seg) for sec in iter_sections(neurite)
for seg in iter_segments(sec))
for sec, (p0, p1) in islice(section_segment, 1, None): # Skip neurite root segment
if max_distance < abs(p0[axis] - p1[axis]):
bad_ids.append((sec.id, [p0, p1]))
return CheckResult(len(bad_ids) == 0, bad_ids)
|
python
|
def has_no_jumps(neuron, max_distance=30.0, axis='z'):
bad_ids = []
axis = {'x': COLS.X, 'y': COLS.Y, 'z': COLS.Z, }[axis.lower()]
for neurite in iter_neurites(neuron):
section_segment = ((sec, seg) for sec in iter_sections(neurite)
for seg in iter_segments(sec))
for sec, (p0, p1) in islice(section_segment, 1, None):
if max_distance < abs(p0[axis] - p1[axis]):
bad_ids.append((sec.id, [p0, p1]))
return CheckResult(len(bad_ids) == 0, bad_ids)
|
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Check if there are jumps (large movements in the `axis`)
Arguments:
neuron(Neuron): The neuron object to test
max_distance(float): value above which consecutive z-values are
considered a jump
axis(str): one of x/y/z, which axis to check for jumps
Returns:
CheckResult with result list of ids of bad sections
|
[
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"large",
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"in",
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L203-L223
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_no_fat_ends
|
def has_no_fat_ends(neuron, multiple_of_mean=2.0, final_point_count=5):
'''Check if leaf points are too large
Arguments:
neuron(Neuron): The neuron object to test
multiple_of_mean(float): how many times larger the final radius
has to be compared to the mean of the final points
final_point_count(int): how many points to include in the mean
Returns:
CheckResult with result list of ids of bad sections
Note:
A fat end is defined as a leaf segment whose last point is larger
by a factor of `multiple_of_mean` than the mean of the points in
`final_point_count`
'''
bad_ids = []
for leaf in _nf.iter_sections(neuron.neurites, iterator_type=Tree.ileaf):
mean_radius = np.mean(leaf.points[1:][-final_point_count:, COLS.R])
if mean_radius * multiple_of_mean <= leaf.points[-1, COLS.R]:
bad_ids.append((leaf.id, leaf.points[-1:]))
return CheckResult(len(bad_ids) == 0, bad_ids)
|
python
|
def has_no_fat_ends(neuron, multiple_of_mean=2.0, final_point_count=5):
bad_ids = []
for leaf in _nf.iter_sections(neuron.neurites, iterator_type=Tree.ileaf):
mean_radius = np.mean(leaf.points[1:][-final_point_count:, COLS.R])
if mean_radius * multiple_of_mean <= leaf.points[-1, COLS.R]:
bad_ids.append((leaf.id, leaf.points[-1:]))
return CheckResult(len(bad_ids) == 0, bad_ids)
|
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Check if leaf points are too large
Arguments:
neuron(Neuron): The neuron object to test
multiple_of_mean(float): how many times larger the final radius
has to be compared to the mean of the final points
final_point_count(int): how many points to include in the mean
Returns:
CheckResult with result list of ids of bad sections
Note:
A fat end is defined as a leaf segment whose last point is larger
by a factor of `multiple_of_mean` than the mean of the points in
`final_point_count`
|
[
"Check",
"if",
"leaf",
"points",
"are",
"too",
"large"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L226-L250
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_no_narrow_start
|
def has_no_narrow_start(neuron, frac=0.9):
'''Check if neurites have a narrow start
Arguments:
neuron(Neuron): The neuron object to test
frac(float): Ratio that the second point must be smaller than the first
Returns:
CheckResult with a list of all first segments of neurites with a narrow start
'''
bad_ids = [(neurite.root_node.id, [neurite.root_node.points[1]])
for neurite in neuron.neurites
if neurite.root_node.points[1][COLS.R] < frac * neurite.root_node.points[2][COLS.R]]
return CheckResult(len(bad_ids) == 0, bad_ids)
|
python
|
def has_no_narrow_start(neuron, frac=0.9):
bad_ids = [(neurite.root_node.id, [neurite.root_node.points[1]])
for neurite in neuron.neurites
if neurite.root_node.points[1][COLS.R] < frac * neurite.root_node.points[2][COLS.R]]
return CheckResult(len(bad_ids) == 0, bad_ids)
|
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Check if neurites have a narrow start
Arguments:
neuron(Neuron): The neuron object to test
frac(float): Ratio that the second point must be smaller than the first
Returns:
CheckResult with a list of all first segments of neurites with a narrow start
|
[
"Check",
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"narrow",
"start"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L253-L266
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_no_dangling_branch
|
def has_no_dangling_branch(neuron):
'''Check if the neuron has dangling neurites'''
soma_center = neuron.soma.points[:, COLS.XYZ].mean(axis=0)
recentered_soma = neuron.soma.points[:, COLS.XYZ] - soma_center
radius = np.linalg.norm(recentered_soma, axis=1)
soma_max_radius = radius.max()
def is_dangling(neurite):
'''Is the neurite dangling ?'''
starting_point = neurite.points[1][COLS.XYZ]
if np.linalg.norm(starting_point - soma_center) - soma_max_radius <= 12.:
return False
if neurite.type != NeuriteType.axon:
return True
all_points = list(chain.from_iterable(n.points[1:]
for n in iter_neurites(neurite)
if n.type != NeuriteType.axon))
res = [np.linalg.norm(starting_point - p[COLS.XYZ]) >= 2 * p[COLS.R] + 2
for p in all_points]
return all(res)
bad_ids = [(n.root_node.id, [n.root_node.points[1]])
for n in iter_neurites(neuron) if is_dangling(n)]
return CheckResult(len(bad_ids) == 0, bad_ids)
|
python
|
def has_no_dangling_branch(neuron):
soma_center = neuron.soma.points[:, COLS.XYZ].mean(axis=0)
recentered_soma = neuron.soma.points[:, COLS.XYZ] - soma_center
radius = np.linalg.norm(recentered_soma, axis=1)
soma_max_radius = radius.max()
def is_dangling(neurite):
starting_point = neurite.points[1][COLS.XYZ]
if np.linalg.norm(starting_point - soma_center) - soma_max_radius <= 12.:
return False
if neurite.type != NeuriteType.axon:
return True
all_points = list(chain.from_iterable(n.points[1:]
for n in iter_neurites(neurite)
if n.type != NeuriteType.axon))
res = [np.linalg.norm(starting_point - p[COLS.XYZ]) >= 2 * p[COLS.R] + 2
for p in all_points]
return all(res)
bad_ids = [(n.root_node.id, [n.root_node.points[1]])
for n in iter_neurites(neuron) if is_dangling(n)]
return CheckResult(len(bad_ids) == 0, bad_ids)
|
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Check if the neuron has dangling neurites
|
[
"Check",
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"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L269-L295
|
BlueBrain/NeuroM
|
neurom/check/neuron_checks.py
|
has_no_narrow_neurite_section
|
def has_no_narrow_neurite_section(neuron,
neurite_filter,
radius_threshold=0.05,
considered_section_min_length=50):
'''Check if the neuron has dendrites with narrow sections
Arguments:
neuron(Neuron): The neuron object to test
neurite_filter(callable): filter the neurites by this callable
radius_threshold(float): radii below this are considered narro
considered_section_min_length(float): sections with length below
this are not taken into account
Returns:
CheckResult with result. result.info contains the narrow section ids and their
first point
'''
considered_sections = (sec for sec in iter_sections(neuron, neurite_filter=neurite_filter)
if sec.length > considered_section_min_length)
def narrow_section(section):
'''Select narrow sections'''
return section.points[:, COLS.R].mean() < radius_threshold
bad_ids = [(section.id, section.points[1])
for section in considered_sections if narrow_section(section)]
return CheckResult(len(bad_ids) == 0, bad_ids)
|
python
|
def has_no_narrow_neurite_section(neuron,
neurite_filter,
radius_threshold=0.05,
considered_section_min_length=50):
considered_sections = (sec for sec in iter_sections(neuron, neurite_filter=neurite_filter)
if sec.length > considered_section_min_length)
def narrow_section(section):
return section.points[:, COLS.R].mean() < radius_threshold
bad_ids = [(section.id, section.points[1])
for section in considered_sections if narrow_section(section)]
return CheckResult(len(bad_ids) == 0, bad_ids)
|
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Check if the neuron has dendrites with narrow sections
Arguments:
neuron(Neuron): The neuron object to test
neurite_filter(callable): filter the neurites by this callable
radius_threshold(float): radii below this are considered narro
considered_section_min_length(float): sections with length below
this are not taken into account
Returns:
CheckResult with result. result.info contains the narrow section ids and their
first point
|
[
"Check",
"if",
"the",
"neuron",
"has",
"dendrites",
"with",
"narrow",
"sections"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/check/neuron_checks.py#L298-L325
|
BlueBrain/NeuroM
|
examples/synthesis_json.py
|
extract_data
|
def extract_data(neurons, feature, params=None):
'''Extracts feature from a list of neurons
and transforms the fitted distribution in the correct format.
Returns the optimal distribution and corresponding parameters.
Normal distribution params (mean, std)
Exponential distribution params (loc, scale)
Uniform distribution params (min, range)
'''
if params is None:
params = {}
feature_data = [get(FEATURE_MAP[feature], n, **params) for n in neurons]
feature_data = list(chain(*feature_data))
return stats.optimal_distribution(feature_data)
|
python
|
def extract_data(neurons, feature, params=None):
if params is None:
params = {}
feature_data = [get(FEATURE_MAP[feature], n, **params) for n in neurons]
feature_data = list(chain(*feature_data))
return stats.optimal_distribution(feature_data)
|
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Extracts feature from a list of neurons
and transforms the fitted distribution in the correct format.
Returns the optimal distribution and corresponding parameters.
Normal distribution params (mean, std)
Exponential distribution params (loc, scale)
Uniform distribution params (min, range)
|
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"(",
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")"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/examples/synthesis_json.py#L76-L89
|
BlueBrain/NeuroM
|
examples/synthesis_json.py
|
transform_header
|
def transform_header(mtype_name):
'''Add header to json output to wrap around distribution data.
'''
head_dict = OrderedDict()
head_dict["m-type"] = mtype_name
head_dict["components"] = defaultdict(OrderedDict)
return head_dict
|
python
|
def transform_header(mtype_name):
head_dict = OrderedDict()
head_dict["m-type"] = mtype_name
head_dict["components"] = defaultdict(OrderedDict)
return head_dict
|
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Add header to json output to wrap around distribution data.
|
[
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/examples/synthesis_json.py#L92-L100
|
BlueBrain/NeuroM
|
examples/synthesis_json.py
|
transform_package
|
def transform_package(mtype, files, components):
'''Put together header and list of data into one json output.
feature_list contains all the information about the data to be extracted:
features, feature_names, feature_components, feature_min, feature_max
'''
data_dict = transform_header(mtype)
neurons = load_neurons(files)
for comp in components:
params = PARAM_MAP[comp.name]
for feature in comp.features:
result = stats.fit_results_to_dict(
extract_data(neurons, feature.name, params),
feature.limits.min, feature.limits.max
)
# When the distribution is normal with sigma = 0
# it will be replaced with constant
if result['type'] == 'normal' and result['sigma'] == 0.0:
replace_result = OrderedDict((('type', 'constant'),
('val', result['mu'])))
result = replace_result
data_dict["components"][comp.name].update({feature.name: result})
return data_dict
|
python
|
def transform_package(mtype, files, components):
data_dict = transform_header(mtype)
neurons = load_neurons(files)
for comp in components:
params = PARAM_MAP[comp.name]
for feature in comp.features:
result = stats.fit_results_to_dict(
extract_data(neurons, feature.name, params),
feature.limits.min, feature.limits.max
)
if result['type'] == 'normal' and result['sigma'] == 0.0:
replace_result = OrderedDict((('type', 'constant'),
('val', result['mu'])))
result = replace_result
data_dict["components"][comp.name].update({feature.name: result})
return data_dict
|
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|
[
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/examples/synthesis_json.py#L103-L128
|
BlueBrain/NeuroM
|
examples/synthesis_json.py
|
parse_args
|
def parse_args():
'''Parse command line arguments'''
parser = argparse.ArgumentParser(
description='Morphology fit distribution extractor',
epilog='Note: Outputs json of the optimal distribution \
and corresponding parameters.')
parser.add_argument('datapaths',
nargs='+',
help='Morphology data directory paths')
parser.add_argument('--mtype', choices=MTYPE_GETTERS.keys(),
help='Get mtype from filename or parent directory')
return parser.parse_args()
|
python
|
def parse_args():
parser = argparse.ArgumentParser(
description='Morphology fit distribution extractor',
epilog='Note: Outputs json of the optimal distribution \
and corresponding parameters.')
parser.add_argument('datapaths',
nargs='+',
help='Morphology data directory paths')
parser.add_argument('--mtype', choices=MTYPE_GETTERS.keys(),
help='Get mtype from filename or parent directory')
return parser.parse_args()
|
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Parse command line arguments
|
[
"Parse",
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"line",
"arguments"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/examples/synthesis_json.py#L153-L167
|
BlueBrain/NeuroM
|
neurom/view/plotly.py
|
draw
|
def draw(obj, plane='3d', inline=False, **kwargs):
'''Draw the morphology using in the given plane
plane (str): a string representing the 2D plane (example: 'xy')
or '3d', '3D' for a 3D view
inline (bool): must be set to True for interactive ipython notebook plotting
'''
if plane.lower() == '3d':
return _plot_neuron3d(obj, inline, **kwargs)
return _plot_neuron(obj, plane, inline, **kwargs)
|
python
|
def draw(obj, plane='3d', inline=False, **kwargs):
if plane.lower() == '3d':
return _plot_neuron3d(obj, inline, **kwargs)
return _plot_neuron(obj, plane, inline, **kwargs)
|
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Draw the morphology using in the given plane
plane (str): a string representing the 2D plane (example: 'xy')
or '3d', '3D' for a 3D view
inline (bool): must be set to True for interactive ipython notebook plotting
|
[
"Draw",
"the",
"morphology",
"using",
"in",
"the",
"given",
"plane"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/plotly.py#L21-L31
|
BlueBrain/NeuroM
|
neurom/view/plotly.py
|
_plot_neuron3d
|
def _plot_neuron3d(neuron, inline, **kwargs):
'''
Generates a figure of the neuron,
that contains a soma and a list of trees.
'''
return _plotly(neuron, plane='3d', title='neuron-3D', inline=inline, **kwargs)
|
python
|
def _plot_neuron3d(neuron, inline, **kwargs):
return _plotly(neuron, plane='3d', title='neuron-3D', inline=inline, **kwargs)
|
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Generates a figure of the neuron,
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/plotly.py#L38-L43
|
BlueBrain/NeuroM
|
neurom/view/plotly.py
|
_make_trace
|
def _make_trace(neuron, plane):
'''Create the trace to be plotted'''
for neurite in iter_neurites(neuron):
segments = list(iter_segments(neurite))
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ]) for s in segments]
coords = dict(x=list(chain.from_iterable((p1[0], p2[0], None) for p1, p2 in segs)),
y=list(chain.from_iterable((p1[1], p2[1], None) for p1, p2 in segs)),
z=list(chain.from_iterable((p1[2], p2[2], None) for p1, p2 in segs)))
color = TREE_COLOR.get(neurite.root_node.type, 'black')
if plane.lower() == '3d':
plot_fun = go.Scatter3d
else:
plot_fun = go.Scatter
coords = dict(x=coords[plane[0]], y=coords[plane[1]])
yield plot_fun(
line=dict(color=color, width=2),
mode='lines',
**coords
)
|
python
|
def _make_trace(neuron, plane):
for neurite in iter_neurites(neuron):
segments = list(iter_segments(neurite))
segs = [(s[0][COLS.XYZ], s[1][COLS.XYZ]) for s in segments]
coords = dict(x=list(chain.from_iterable((p1[0], p2[0], None) for p1, p2 in segs)),
y=list(chain.from_iterable((p1[1], p2[1], None) for p1, p2 in segs)),
z=list(chain.from_iterable((p1[2], p2[2], None) for p1, p2 in segs)))
color = TREE_COLOR.get(neurite.root_node.type, 'black')
if plane.lower() == '3d':
plot_fun = go.Scatter3d
else:
plot_fun = go.Scatter
coords = dict(x=coords[plane[0]], y=coords[plane[1]])
yield plot_fun(
line=dict(color=color, width=2),
mode='lines',
**coords
)
|
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Create the trace to be plotted
|
[
"Create",
"the",
"trace",
"to",
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/plotly.py#L46-L67
|
BlueBrain/NeuroM
|
neurom/view/plotly.py
|
get_figure
|
def get_figure(neuron, plane, title):
'''Returns the plotly figure containing the neuron'''
data = list(_make_trace(neuron, plane))
axis = dict(
gridcolor='rgb(255, 255, 255)',
zerolinecolor='rgb(255, 255, 255)',
showbackground=True,
backgroundcolor='rgb(230, 230,230)'
)
if plane != '3d':
soma_2d = [
# filled circle
{
'type': 'circle',
'xref': 'x',
'yref': 'y',
'fillcolor': 'rgba(50, 171, 96, 0.7)',
'x0': neuron.soma.center[0] - neuron.soma.radius,
'y0': neuron.soma.center[1] - neuron.soma.radius,
'x1': neuron.soma.center[0] + neuron.soma.radius,
'y1': neuron.soma.center[1] + neuron.soma.radius,
'line': {
'color': 'rgba(50, 171, 96, 1)',
},
},
]
else:
soma_2d = []
theta = np.linspace(0, 2 * np.pi, 100)
phi = np.linspace(0, np.pi, 100)
z = np.outer(np.ones(100), np.cos(phi)) + neuron.soma.center[2]
r = neuron.soma.radius
data.append(
go.Surface(
x=(np.outer(np.cos(theta), np.sin(phi)) + neuron.soma.center[0]) * r,
y=(np.outer(np.sin(theta), np.sin(phi)) + neuron.soma.center[1]) * r,
z=z * r,
cauto=False,
surfacecolor=['black'] * len(z),
showscale=False,
)
)
layout = dict(
autosize=True,
title=title,
scene=dict( # This is used for 3D plots
xaxis=axis, yaxis=axis, zaxis=axis,
camera=dict(up=dict(x=0, y=0, z=1), eye=dict(x=-1.7428, y=1.0707, z=0.7100,)),
aspectmode='data'
),
yaxis=dict(scaleanchor="x"), # This is used for 2D plots
shapes=soma_2d,
)
res = dict(data=data, layout=layout)
return res
|
python
|
def get_figure(neuron, plane, title):
data = list(_make_trace(neuron, plane))
axis = dict(
gridcolor='rgb(255, 255, 255)',
zerolinecolor='rgb(255, 255, 255)',
showbackground=True,
backgroundcolor='rgb(230, 230,230)'
)
if plane != '3d':
soma_2d = [
{
'type': 'circle',
'xref': 'x',
'yref': 'y',
'fillcolor': 'rgba(50, 171, 96, 0.7)',
'x0': neuron.soma.center[0] - neuron.soma.radius,
'y0': neuron.soma.center[1] - neuron.soma.radius,
'x1': neuron.soma.center[0] + neuron.soma.radius,
'y1': neuron.soma.center[1] + neuron.soma.radius,
'line': {
'color': 'rgba(50, 171, 96, 1)',
},
},
]
else:
soma_2d = []
theta = np.linspace(0, 2 * np.pi, 100)
phi = np.linspace(0, np.pi, 100)
z = np.outer(np.ones(100), np.cos(phi)) + neuron.soma.center[2]
r = neuron.soma.radius
data.append(
go.Surface(
x=(np.outer(np.cos(theta), np.sin(phi)) + neuron.soma.center[0]) * r,
y=(np.outer(np.sin(theta), np.sin(phi)) + neuron.soma.center[1]) * r,
z=z * r,
cauto=False,
surfacecolor=['black'] * len(z),
showscale=False,
)
)
layout = dict(
autosize=True,
title=title,
scene=dict(
xaxis=axis, yaxis=axis, zaxis=axis,
camera=dict(up=dict(x=0, y=0, z=1), eye=dict(x=-1.7428, y=1.0707, z=0.7100,)),
aspectmode='data'
),
yaxis=dict(scaleanchor="x"),
shapes=soma_2d,
)
res = dict(data=data, layout=layout)
return res
|
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Returns the plotly figure containing the neuron
|
[
"Returns",
"the",
"plotly",
"figure",
"containing",
"the",
"neuron"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/view/plotly.py#L70-L129
|
BlueBrain/NeuroM
|
neurom/geom/transform.py
|
rotate
|
def rotate(obj, axis, angle, origin=None):
'''
Rotation around unit vector following the right hand rule
Parameters:
obj : obj to be rotated (e.g. neurite, neuron).
Must implement a transform method.
axis : unit vector for the axis of rotation
angle : rotation angle in rads
Returns:
A copy of the object with the applied translation.
'''
R = _rodrigues_to_dcm(axis, angle)
try:
return obj.transform(PivotRotation(R, origin))
except AttributeError:
raise NotImplementedError
|
python
|
def rotate(obj, axis, angle, origin=None):
R = _rodrigues_to_dcm(axis, angle)
try:
return obj.transform(PivotRotation(R, origin))
except AttributeError:
raise NotImplementedError
|
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Rotation around unit vector following the right hand rule
Parameters:
obj : obj to be rotated (e.g. neurite, neuron).
Must implement a transform method.
axis : unit vector for the axis of rotation
angle : rotation angle in rads
Returns:
A copy of the object with the applied translation.
|
[
"Rotation",
"around",
"unit",
"vector",
"following",
"the",
"right",
"hand",
"rule"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/geom/transform.py#L128-L146
|
BlueBrain/NeuroM
|
neurom/geom/transform.py
|
_sin
|
def _sin(x):
'''sine with case for pi multiples'''
return 0. if np.isclose(np.mod(x, np.pi), 0.) else np.sin(x)
|
python
|
def _sin(x):
return 0. if np.isclose(np.mod(x, np.pi), 0.) else np.sin(x)
|
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sine with case for pi multiples
|
[
"sine",
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"for",
"pi",
"multiples"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/geom/transform.py#L149-L151
|
BlueBrain/NeuroM
|
neurom/geom/transform.py
|
_rodrigues_to_dcm
|
def _rodrigues_to_dcm(axis, angle):
'''
Generates transformation matrix from unit vector
and rotation angle. The rotation is applied in the direction
of the axis which is a unit vector following the right hand rule.
Inputs :
axis : unit vector of the direction of the rotation
angle : angle of rotation in rads
Returns : 3x3 Rotation matrix
'''
ux, uy, uz = axis / np.linalg.norm(axis)
uxx = ux * ux
uyy = uy * uy
uzz = uz * uz
uxy = ux * uy
uxz = ux * uz
uyz = uy * uz
sn = _sin(angle)
cs = _sin(np.pi / 2. - angle)
cs1 = 1. - cs
R = np.zeros([3, 3])
R[0, 0] = cs + uxx * cs1
R[0, 1] = uxy * cs1 - uz * sn
R[0, 2] = uxz * cs1 + uy * sn
R[1, 0] = uxy * cs1 + uz * sn
R[1, 1] = cs + uyy * cs1
R[1, 2] = uyz * cs1 - ux * sn
R[2, 0] = uxz * cs1 - uy * sn
R[2, 1] = uyz * cs1 + ux * sn
R[2, 2] = cs + uzz * cs1
return R
|
python
|
def _rodrigues_to_dcm(axis, angle):
ux, uy, uz = axis / np.linalg.norm(axis)
uxx = ux * ux
uyy = uy * uy
uzz = uz * uz
uxy = ux * uy
uxz = ux * uz
uyz = uy * uz
sn = _sin(angle)
cs = _sin(np.pi / 2. - angle)
cs1 = 1. - cs
R = np.zeros([3, 3])
R[0, 0] = cs + uxx * cs1
R[0, 1] = uxy * cs1 - uz * sn
R[0, 2] = uxz * cs1 + uy * sn
R[1, 0] = uxy * cs1 + uz * sn
R[1, 1] = cs + uyy * cs1
R[1, 2] = uyz * cs1 - ux * sn
R[2, 0] = uxz * cs1 - uy * sn
R[2, 1] = uyz * cs1 + ux * sn
R[2, 2] = cs + uzz * cs1
return R
|
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Generates transformation matrix from unit vector
and rotation angle. The rotation is applied in the direction
of the axis which is a unit vector following the right hand rule.
Inputs :
axis : unit vector of the direction of the rotation
angle : angle of rotation in rads
Returns : 3x3 Rotation matrix
|
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/geom/transform.py#L154-L194
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
total_length
|
def total_length(nrn_pop, neurite_type=NeuriteType.all):
'''Get the total length of all sections in the group of neurons or neurites'''
nrns = _neuronfunc.neuron_population(nrn_pop)
return list(sum(section_lengths(n, neurite_type=neurite_type)) for n in nrns)
|
python
|
def total_length(nrn_pop, neurite_type=NeuriteType.all):
nrns = _neuronfunc.neuron_population(nrn_pop)
return list(sum(section_lengths(n, neurite_type=neurite_type)) for n in nrns)
|
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L45-L48
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
n_segments
|
def n_segments(neurites, neurite_type=NeuriteType.all):
'''Number of segments in a collection of neurites'''
return sum(len(s.points) - 1
for s in iter_sections(neurites, neurite_filter=is_type(neurite_type)))
|
python
|
def n_segments(neurites, neurite_type=NeuriteType.all):
return sum(len(s.points) - 1
for s in iter_sections(neurites, neurite_filter=is_type(neurite_type)))
|
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[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L51-L54
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
n_neurites
|
def n_neurites(neurites, neurite_type=NeuriteType.all):
'''Number of neurites in a collection of neurites'''
return sum(1 for _ in iter_neurites(neurites, filt=is_type(neurite_type)))
|
python
|
def n_neurites(neurites, neurite_type=NeuriteType.all):
return sum(1 for _ in iter_neurites(neurites, filt=is_type(neurite_type)))
|
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[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L57-L59
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
n_sections
|
def n_sections(neurites, neurite_type=NeuriteType.all, iterator_type=Tree.ipreorder):
'''Number of sections in a collection of neurites'''
return sum(1 for _ in iter_sections(neurites,
iterator_type=iterator_type,
neurite_filter=is_type(neurite_type)))
|
python
|
def n_sections(neurites, neurite_type=NeuriteType.all, iterator_type=Tree.ipreorder):
return sum(1 for _ in iter_sections(neurites,
iterator_type=iterator_type,
neurite_filter=is_type(neurite_type)))
|
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[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L62-L66
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
n_bifurcation_points
|
def n_bifurcation_points(neurites, neurite_type=NeuriteType.all):
'''number of bifurcation points in a collection of neurites'''
return n_sections(neurites, neurite_type=neurite_type, iterator_type=Tree.ibifurcation_point)
|
python
|
def n_bifurcation_points(neurites, neurite_type=NeuriteType.all):
return n_sections(neurites, neurite_type=neurite_type, iterator_type=Tree.ibifurcation_point)
|
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number of bifurcation points in a collection of neurites
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L69-L71
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
n_forking_points
|
def n_forking_points(neurites, neurite_type=NeuriteType.all):
'''number of forking points in a collection of neurites'''
return n_sections(neurites, neurite_type=neurite_type, iterator_type=Tree.iforking_point)
|
python
|
def n_forking_points(neurites, neurite_type=NeuriteType.all):
return n_sections(neurites, neurite_type=neurite_type, iterator_type=Tree.iforking_point)
|
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number of forking points in a collection of neurites
|
[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L74-L76
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
n_leaves
|
def n_leaves(neurites, neurite_type=NeuriteType.all):
'''number of leaves points in a collection of neurites'''
return n_sections(neurites, neurite_type=neurite_type, iterator_type=Tree.ileaf)
|
python
|
def n_leaves(neurites, neurite_type=NeuriteType.all):
return n_sections(neurites, neurite_type=neurite_type, iterator_type=Tree.ileaf)
|
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number of leaves points in a collection of neurites
|
[
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"neurites"
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L79-L81
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
total_area_per_neurite
|
def total_area_per_neurite(neurites, neurite_type=NeuriteType.all):
'''Surface area in a collection of neurites.
The area is defined as the sum of the area of the sections.
'''
return [neurite.area for neurite in iter_neurites(neurites, filt=is_type(neurite_type))]
|
python
|
def total_area_per_neurite(neurites, neurite_type=NeuriteType.all):
return [neurite.area for neurite in iter_neurites(neurites, filt=is_type(neurite_type))]
|
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Surface area in a collection of neurites.
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|
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L84-L89
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
map_sections
|
def map_sections(fun, neurites, neurite_type=NeuriteType.all, iterator_type=Tree.ipreorder):
'''Map `fun` to all the sections in a collection of neurites'''
return map(fun, iter_sections(neurites,
iterator_type=iterator_type,
neurite_filter=is_type(neurite_type)))
|
python
|
def map_sections(fun, neurites, neurite_type=NeuriteType.all, iterator_type=Tree.ipreorder):
return map(fun, iter_sections(neurites,
iterator_type=iterator_type,
neurite_filter=is_type(neurite_type)))
|
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[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L92-L96
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
section_lengths
|
def section_lengths(neurites, neurite_type=NeuriteType.all):
'''section lengths in a collection of neurites'''
return map_sections(_section_length, neurites, neurite_type=neurite_type)
|
python
|
def section_lengths(neurites, neurite_type=NeuriteType.all):
return map_sections(_section_length, neurites, neurite_type=neurite_type)
|
[
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section lengths in a collection of neurites
|
[
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L104-L106
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
section_term_lengths
|
def section_term_lengths(neurites, neurite_type=NeuriteType.all):
'''Termination section lengths in a collection of neurites'''
return map_sections(_section_length, neurites, neurite_type=neurite_type,
iterator_type=Tree.ileaf)
|
python
|
def section_term_lengths(neurites, neurite_type=NeuriteType.all):
return map_sections(_section_length, neurites, neurite_type=neurite_type,
iterator_type=Tree.ileaf)
|
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Termination section lengths in a collection of neurites
|
[
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"a",
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"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L109-L112
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
section_bif_lengths
|
def section_bif_lengths(neurites, neurite_type=NeuriteType.all):
'''Bifurcation section lengths in a collection of neurites'''
return map_sections(_section_length, neurites, neurite_type=neurite_type,
iterator_type=Tree.ibifurcation_point)
|
python
|
def section_bif_lengths(neurites, neurite_type=NeuriteType.all):
return map_sections(_section_length, neurites, neurite_type=neurite_type,
iterator_type=Tree.ibifurcation_point)
|
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Bifurcation section lengths in a collection of neurites
|
[
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"of",
"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L115-L118
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
section_branch_orders
|
def section_branch_orders(neurites, neurite_type=NeuriteType.all):
'''section branch orders in a collection of neurites'''
return map_sections(sectionfunc.branch_order, neurites, neurite_type=neurite_type)
|
python
|
def section_branch_orders(neurites, neurite_type=NeuriteType.all):
return map_sections(sectionfunc.branch_order, neurites, neurite_type=neurite_type)
|
[
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section branch orders in a collection of neurites
|
[
"section",
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"orders",
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"a",
"collection",
"of",
"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L121-L123
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
section_bif_branch_orders
|
def section_bif_branch_orders(neurites, neurite_type=NeuriteType.all):
'''Bifurcation section branch orders in a collection of neurites'''
return map_sections(sectionfunc.branch_order, neurites, neurite_type=neurite_type,
iterator_type=Tree.ibifurcation_point)
|
python
|
def section_bif_branch_orders(neurites, neurite_type=NeuriteType.all):
return map_sections(sectionfunc.branch_order, neurites, neurite_type=neurite_type,
iterator_type=Tree.ibifurcation_point)
|
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Bifurcation section branch orders in a collection of neurites
|
[
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"orders",
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"collection",
"of",
"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L126-L129
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
section_term_branch_orders
|
def section_term_branch_orders(neurites, neurite_type=NeuriteType.all):
'''Termination section branch orders in a collection of neurites'''
return map_sections(sectionfunc.branch_order, neurites, neurite_type=neurite_type,
iterator_type=Tree.ileaf)
|
python
|
def section_term_branch_orders(neurites, neurite_type=NeuriteType.all):
return map_sections(sectionfunc.branch_order, neurites, neurite_type=neurite_type,
iterator_type=Tree.ileaf)
|
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[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L132-L135
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
section_path_lengths
|
def section_path_lengths(neurites, neurite_type=NeuriteType.all):
'''Path lengths of a collection of neurites '''
# Calculates and stores the section lengths in one pass,
# then queries the lengths in the path length iterations.
# This avoids repeatedly calculating the lengths of the
# same sections.
dist = {}
neurite_filter = is_type(neurite_type)
for s in iter_sections(neurites, neurite_filter=neurite_filter):
dist[s] = s.length
def pl2(node):
'''Calculate the path length using cached section lengths'''
return sum(dist[n] for n in node.iupstream())
return map_sections(pl2, neurites, neurite_type=neurite_type)
|
python
|
def section_path_lengths(neurites, neurite_type=NeuriteType.all):
dist = {}
neurite_filter = is_type(neurite_type)
for s in iter_sections(neurites, neurite_filter=neurite_filter):
dist[s] = s.length
def pl2(node):
return sum(dist[n] for n in node.iupstream())
return map_sections(pl2, neurites, neurite_type=neurite_type)
|
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Path lengths of a collection of neurites
|
[
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L138-L154
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
map_neurons
|
def map_neurons(fun, neurites, neurite_type):
'''Map `fun` to all the neurites in a single or collection of neurons'''
nrns = _neuronfunc.neuron_population(neurites)
return [fun(n, neurite_type=neurite_type) for n in nrns]
|
python
|
def map_neurons(fun, neurites, neurite_type):
nrns = _neuronfunc.neuron_population(neurites)
return [fun(n, neurite_type=neurite_type) for n in nrns]
|
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L157-L160
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
map_segments
|
def map_segments(func, neurites, neurite_type):
''' Map `func` to all the segments in a collection of neurites
`func` accepts a section and returns list of values corresponding to each segment.
'''
neurite_filter = is_type(neurite_type)
return [
s for ss in iter_sections(neurites, neurite_filter=neurite_filter) for s in func(ss)
]
|
python
|
def map_segments(func, neurites, neurite_type):
neurite_filter = is_type(neurite_type)
return [
s for ss in iter_sections(neurites, neurite_filter=neurite_filter) for s in func(ss)
]
|
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Map `func` to all the segments in a collection of neurites
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L193-L201
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
segment_lengths
|
def segment_lengths(neurites, neurite_type=NeuriteType.all):
'''Lengths of the segments in a collection of neurites'''
def _seg_len(sec):
'''list of segment lengths of a section'''
return np.linalg.norm(np.diff(sec.points[:, COLS.XYZ], axis=0), axis=1)
return map_segments(_seg_len, neurites, neurite_type)
|
python
|
def segment_lengths(neurites, neurite_type=NeuriteType.all):
def _seg_len(sec):
return np.linalg.norm(np.diff(sec.points[:, COLS.XYZ], axis=0), axis=1)
return map_segments(_seg_len, neurites, neurite_type)
|
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Lengths of the segments in a collection of neurites
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[
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L204-L210
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
segment_volumes
|
def segment_volumes(neurites, neurite_type=NeuriteType.all):
'''Volumes of the segments in a collection of neurites'''
def _func(sec):
'''list of segment volumes of a section'''
return [morphmath.segment_volume(seg) for seg in zip(sec.points[:-1], sec.points[1:])]
return map_segments(_func, neurites, neurite_type)
|
python
|
def segment_volumes(neurites, neurite_type=NeuriteType.all):
def _func(sec):
return [morphmath.segment_volume(seg) for seg in zip(sec.points[:-1], sec.points[1:])]
return map_segments(_func, neurites, neurite_type)
|
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[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L213-L219
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
segment_radii
|
def segment_radii(neurites, neurite_type=NeuriteType.all):
'''arithmetic mean of the radii of the points in segments in a collection of neurites'''
def _seg_radii(sec):
'''vectorized mean radii'''
pts = sec.points[:, COLS.R]
return np.divide(np.add(pts[:-1], pts[1:]), 2.0)
return map_segments(_seg_radii, neurites, neurite_type)
|
python
|
def segment_radii(neurites, neurite_type=NeuriteType.all):
def _seg_radii(sec):
pts = sec.points[:, COLS.R]
return np.divide(np.add(pts[:-1], pts[1:]), 2.0)
return map_segments(_seg_radii, neurites, neurite_type)
|
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L222-L229
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
segment_taper_rates
|
def segment_taper_rates(neurites, neurite_type=NeuriteType.all):
'''taper rates of the segments in a collection of neurites
The taper rate is defined as the absolute radii differences divided by length of the section
'''
def _seg_taper_rates(sec):
'''vectorized taper rates'''
pts = sec.points[:, COLS.XYZR]
diff = np.diff(pts, axis=0)
distance = np.linalg.norm(diff[:, COLS.XYZ], axis=1)
return np.divide(2 * np.abs(diff[:, COLS.R]), distance)
return map_segments(_seg_taper_rates, neurites, neurite_type)
|
python
|
def segment_taper_rates(neurites, neurite_type=NeuriteType.all):
def _seg_taper_rates(sec):
pts = sec.points[:, COLS.XYZR]
diff = np.diff(pts, axis=0)
distance = np.linalg.norm(diff[:, COLS.XYZ], axis=1)
return np.divide(2 * np.abs(diff[:, COLS.R]), distance)
return map_segments(_seg_taper_rates, neurites, neurite_type)
|
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[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L232-L244
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
segment_meander_angles
|
def segment_meander_angles(neurites, neurite_type=NeuriteType.all):
'''Inter-segment opening angles in a section'''
return list(chain.from_iterable(map_sections(
sectionfunc.section_meander_angles, neurites, neurite_type)))
|
python
|
def segment_meander_angles(neurites, neurite_type=NeuriteType.all):
return list(chain.from_iterable(map_sections(
sectionfunc.section_meander_angles, neurites, neurite_type)))
|
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Inter-segment opening angles in a section
|
[
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L247-L250
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
segment_midpoints
|
def segment_midpoints(neurites, neurite_type=NeuriteType.all):
'''Return a list of segment mid-points in a collection of neurites'''
def _seg_midpoint(sec):
'''Return the mid-points of segments in a section'''
pts = sec.points[:, COLS.XYZ]
return np.divide(np.add(pts[:-1], pts[1:]), 2.0)
return map_segments(_seg_midpoint, neurites, neurite_type)
|
python
|
def segment_midpoints(neurites, neurite_type=NeuriteType.all):
def _seg_midpoint(sec):
pts = sec.points[:, COLS.XYZ]
return np.divide(np.add(pts[:-1], pts[1:]), 2.0)
return map_segments(_seg_midpoint, neurites, neurite_type)
|
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train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L253-L260
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
segment_radial_distances
|
def segment_radial_distances(neurites, neurite_type=NeuriteType.all, origin=None):
'''Lengths of the segments in a collection of neurites'''
def _seg_rd(sec, pos):
'''list of radial distances of all segments of a section'''
# TODO: remove this disable when pylint is fixed
# pylint: disable=assignment-from-no-return
mid_pts = np.divide(np.add(sec.points[:-1], sec.points[1:])[:, :3], 2.0)
return np.sqrt([morphmath.point_dist2(p, pos) for p in mid_pts])
dist = []
for n in iter_neurites(neurites, filt=is_type(neurite_type)):
pos = n.root_node.points[0] if origin is None else origin
dist.extend([s for ss in n.iter_sections() for s in _seg_rd(ss, pos)])
return dist
|
python
|
def segment_radial_distances(neurites, neurite_type=NeuriteType.all, origin=None):
def _seg_rd(sec, pos):
mid_pts = np.divide(np.add(sec.points[:-1], sec.points[1:])[:, :3], 2.0)
return np.sqrt([morphmath.point_dist2(p, pos) for p in mid_pts])
dist = []
for n in iter_neurites(neurites, filt=is_type(neurite_type)):
pos = n.root_node.points[0] if origin is None else origin
dist.extend([s for ss in n.iter_sections() for s in _seg_rd(ss, pos)])
return dist
|
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"(",
"ss",
",",
"pos",
")",
"]",
")",
"return",
"dist"
] |
Lengths of the segments in a collection of neurites
|
[
"Lengths",
"of",
"the",
"segments",
"in",
"a",
"collection",
"of",
"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L263-L277
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
local_bifurcation_angles
|
def local_bifurcation_angles(neurites, neurite_type=NeuriteType.all):
'''Get a list of local bifurcation angles in a collection of neurites'''
return map_sections(_bifurcationfunc.local_bifurcation_angle,
neurites,
neurite_type=neurite_type,
iterator_type=Tree.ibifurcation_point)
|
python
|
def local_bifurcation_angles(neurites, neurite_type=NeuriteType.all):
return map_sections(_bifurcationfunc.local_bifurcation_angle,
neurites,
neurite_type=neurite_type,
iterator_type=Tree.ibifurcation_point)
|
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Get a list of local bifurcation angles in a collection of neurites
|
[
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"of",
"local",
"bifurcation",
"angles",
"in",
"a",
"collection",
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] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L280-L285
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
remote_bifurcation_angles
|
def remote_bifurcation_angles(neurites, neurite_type=NeuriteType.all):
'''Get a list of remote bifurcation angles in a collection of neurites'''
return map_sections(_bifurcationfunc.remote_bifurcation_angle,
neurites,
neurite_type=neurite_type,
iterator_type=Tree.ibifurcation_point)
|
python
|
def remote_bifurcation_angles(neurites, neurite_type=NeuriteType.all):
return map_sections(_bifurcationfunc.remote_bifurcation_angle,
neurites,
neurite_type=neurite_type,
iterator_type=Tree.ibifurcation_point)
|
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"=",
"neurite_type",
",",
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Get a list of remote bifurcation angles in a collection of neurites
|
[
"Get",
"a",
"list",
"of",
"remote",
"bifurcation",
"angles",
"in",
"a",
"collection",
"of",
"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L288-L293
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
bifurcation_partitions
|
def bifurcation_partitions(neurites, neurite_type=NeuriteType.all):
'''Partition at bifurcation points of a collection of neurites'''
return map(_bifurcationfunc.bifurcation_partition,
iter_sections(neurites,
iterator_type=Tree.ibifurcation_point,
neurite_filter=is_type(neurite_type)))
|
python
|
def bifurcation_partitions(neurites, neurite_type=NeuriteType.all):
return map(_bifurcationfunc.bifurcation_partition,
iter_sections(neurites,
iterator_type=Tree.ibifurcation_point,
neurite_filter=is_type(neurite_type)))
|
[
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",",
"neurite_filter",
"=",
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"(",
"neurite_type",
")",
")",
")"
] |
Partition at bifurcation points of a collection of neurites
|
[
"Partition",
"at",
"bifurcation",
"points",
"of",
"a",
"collection",
"of",
"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L296-L301
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
partition_asymmetries
|
def partition_asymmetries(neurites, neurite_type=NeuriteType.all):
'''Partition asymmetry at bifurcation points of a collection of neurites'''
return map(_bifurcationfunc.partition_asymmetry,
iter_sections(neurites,
iterator_type=Tree.ibifurcation_point,
neurite_filter=is_type(neurite_type)))
|
python
|
def partition_asymmetries(neurites, neurite_type=NeuriteType.all):
return map(_bifurcationfunc.partition_asymmetry,
iter_sections(neurites,
iterator_type=Tree.ibifurcation_point,
neurite_filter=is_type(neurite_type)))
|
[
"def",
"partition_asymmetries",
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"=",
"NeuriteType",
".",
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"partition_asymmetry",
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".",
"ibifurcation_point",
",",
"neurite_filter",
"=",
"is_type",
"(",
"neurite_type",
")",
")",
")"
] |
Partition asymmetry at bifurcation points of a collection of neurites
|
[
"Partition",
"asymmetry",
"at",
"bifurcation",
"points",
"of",
"a",
"collection",
"of",
"neurites"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L304-L309
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
partition_pairs
|
def partition_pairs(neurites, neurite_type=NeuriteType.all):
'''Partition pairs at bifurcation points of a collection of neurites.
Partition pait is defined as the number of bifurcations at the two
daughters of the bifurcating section'''
return map(_bifurcationfunc.partition_pair,
iter_sections(neurites,
iterator_type=Tree.ibifurcation_point,
neurite_filter=is_type(neurite_type)))
|
python
|
def partition_pairs(neurites, neurite_type=NeuriteType.all):
return map(_bifurcationfunc.partition_pair,
iter_sections(neurites,
iterator_type=Tree.ibifurcation_point,
neurite_filter=is_type(neurite_type)))
|
[
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"partition_pairs",
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".",
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"=",
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")",
")",
")"
] |
Partition pairs at bifurcation points of a collection of neurites.
Partition pait is defined as the number of bifurcations at the two
daughters of the bifurcating section
|
[
"Partition",
"pairs",
"at",
"bifurcation",
"points",
"of",
"a",
"collection",
"of",
"neurites",
".",
"Partition",
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"is",
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"of",
"bifurcations",
"at",
"the",
"two",
"daughters",
"of",
"the",
"bifurcating",
"section"
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L312-L319
|
BlueBrain/NeuroM
|
neurom/fst/_neuritefunc.py
|
section_radial_distances
|
def section_radial_distances(neurites, neurite_type=NeuriteType.all, origin=None,
iterator_type=Tree.ipreorder):
'''Section radial distances in a collection of neurites.
The iterator_type can be used to select only terminal sections (ileaf)
or only bifurcations (ibifurcation_point).'''
dist = []
for n in iter_neurites(neurites, filt=is_type(neurite_type)):
pos = n.root_node.points[0] if origin is None else origin
dist.extend(sectionfunc.section_radial_distance(s, pos)
for s in iter_sections(n,
iterator_type=iterator_type))
return dist
|
python
|
def section_radial_distances(neurites, neurite_type=NeuriteType.all, origin=None,
iterator_type=Tree.ipreorder):
dist = []
for n in iter_neurites(neurites, filt=is_type(neurite_type)):
pos = n.root_node.points[0] if origin is None else origin
dist.extend(sectionfunc.section_radial_distance(s, pos)
for s in iter_sections(n,
iterator_type=iterator_type))
return dist
|
[
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] |
Section radial distances in a collection of neurites.
The iterator_type can be used to select only terminal sections (ileaf)
or only bifurcations (ibifurcation_point).
|
[
"Section",
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"distances",
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"or",
"only",
"bifurcations",
"(",
"ibifurcation_point",
")",
"."
] |
train
|
https://github.com/BlueBrain/NeuroM/blob/254bb73535b20053d175bc4725bade662177d12b/neurom/fst/_neuritefunc.py#L322-L333
|
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