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