""" Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine License: GNU GPL 2.0 """ import reprlib from collections import OrderedDict import pathml.core.h5managers import pathml.core.masks import pathml.core.tile class Tiles: """ Object wrapping a dict of tiles. Args: tiles (Union[dict[tuple[int], `~pathml.core.tiles.Tile`], list[`~pathml.core.tiles.Tile`]]): tile objects """ def __init__(self, h5manager, tiles=None): assert isinstance(h5manager, pathml.core.h5managers.h5pathManager) self.h5manager = h5manager # if tiles are supplied, add them to the h5manager if tiles: assert isinstance(tiles, list) and all( [isinstance(tile, pathml.core.Tile) for tile in tiles] ), f"tiles are of type {reprlib.repr([type(t) for t in tiles])} but must all be pathml.core.Tile" tiledictionary = {} for tile in tiles: if not isinstance(tile, pathml.core.Tile): raise ValueError( f"Tiles expects a list of type Tile but was given {type(tile)}" ) if tile.coords is None: raise ValueError("tiles must contain valid coords") coords = tile.coords tiledictionary[coords] = tile self._tiles = OrderedDict(tiledictionary) # add tiles in _tiles to h5manager for key, val in self._tiles.items(): self.h5manager.add_tile(val) del self._tiles @property def tile_shape(self): return self.h5manager.h5["tiles"].attrs["tile_shape"] @property def keys(self): return list(self.h5manager.h5["tiles"].keys()) def __repr__(self): rep = f"{len(self.h5manager.h5['tiles'])} tiles: {reprlib.repr(list(self.h5manager.h5['tiles'].keys()))}" return rep def __len__(self): return len(self.h5manager.h5["tiles"].keys()) def __getitem__(self, item): return self.h5manager.get_tile(item) def add(self, tile): """ Add tile indexed by tile.coords to tiles. Args: tile(Tile): tile object """ if not isinstance(tile, pathml.core.tile.Tile): raise ValueError( f"can not add {type(tile)}, tile must be of type pathml.core.tiles.Tile" ) self.h5manager.add_tile(tile) def update(self, tile): """ Update a tile. Args: tile(pathml.core.tile.Tiles): key of tile to be updated """ self.h5manager.add_tile(tile) def remove(self, key): """ Remove tile from tiles. Args: key(str): key (coords) indicating tile to be removed """ self.h5manager.remove_tile(key)