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