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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 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)
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