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"""
Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine
License: GNU GPL 2.0
"""
import reprlib
from collections import OrderedDict
import numpy as np
import pathml.core.h5managers
class Masks:
"""
Object wrapping a dict of masks.
Args:
h5manager(pathml.core.h5pathManager)
masks(dict): dictionary of np.ndarray objects representing ex. labels, segmentations.
"""
def __init__(self, h5manager, masks=None):
assert isinstance(
h5manager, pathml.core.h5managers.h5pathManager
), f"expecting type pathml.core.h5pathManager but passed type {type(h5manager)}"
self.h5manager = h5manager
# if masks are supplied, add them to the h5manager
if masks:
if not isinstance(masks, dict):
raise ValueError(
"masks must be passed as dicts of the form {key1:mask1, key2:mask2, ...}"
)
for val in masks.values():
if not isinstance(val, np.ndarray):
raise ValueError(
f"can not add {type(val)}, mask must be of type np.ndarray"
)
for key in masks.keys():
if not isinstance(key, str):
raise ValueError(
f"can not add {type(key)}, key must be of type str"
)
self._masks = OrderedDict(masks)
else:
self._masks = OrderedDict()
for mask in self._masks:
self.h5manager.add_mask(mask, self._masks[mask])
del self._masks
def __repr__(self):
rep = f"{len(self.h5manager.h5['masks'])} masks: {reprlib.repr(list(self.h5manager.h5['masks'].keys()))}"
return rep
def __len__(self):
return len(self.h5manager.h5["masks"].keys())
def __getitem__(self, item):
return self.h5manager.get_mask(item)
def __setitem__(self, key, mask):
self.h5manager.update_mask(key, mask)
@property
def keys(self):
return list(self.h5manager.h5["masks"].keys())
def add(self, key, mask):
"""
Add mask indexed by key to self.h5manager.
Args:
key (str): key
mask (np.ndarray): array of mask. Must contain elements of type int8
"""
self.h5manager.add_mask(key, mask)
def slice(self, slicer):
"""
Slice all masks in self.h5manager extending of numpy array slicing.
Args:
slices: list where each element is an object of type slice indicating
how the dimension should be sliced
"""
if not (
isinstance(slicer, list) and all([isinstance(a, slice) for a in slicer])
):
raise KeyError(
f"slices must of of type list[slice] but is {type(slicer)} with elements {type(slicer[0])}"
)
sliced = {key: mask for key, mask in self.h5manager.slice_masks(slicer)}
return sliced
def remove(self, key):
"""
Remove mask.
Args:
key(str): key indicating mask to be removed
"""
self.h5manager.remove_mask(key)
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