""" 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)