def it_can_extract_random_tiles(self, request, tmpdir):
tmp_path_ = tmpdir.mkdir("myslide")
image = PILIMG.RGBA_COLOR_500X500_155_249_240
image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
slide_path = os.path.join(tmp_path_, "mywsi.png")
slide = Slide(slide_path, os.path.join(tmp_path_, "processed"))
_tiles_generator = method_mock(request, RandomTiler,
"_tiles_generator")
coords = CP(0, 10, 0, 10)
tile = Tile(image, coords)
_tiles_generator.return_value = [(tile, coords), (tile, coords)]
_tile_filename = method_mock(request, RandomTiler, "_tile_filename")
_tile_filename.side_effect = [
f"tile_{i}_level2_0-10-0-10.png" for i in range(2)
]
_has_valid_tile_size = method_mock(request, RandomTiler,
"_has_valid_tile_size")
_has_valid_tile_size.return_value = True
random_tiler = RandomTiler((10, 10), n_tiles=2, level=0)
random_tiler.extract(slide)
assert _tile_filename.call_args_list == [
call(random_tiler, coords, 0),
call(random_tiler, coords, 1),
]
assert os.path.exists(
os.path.join(tmp_path_, "processed", "tiles",
"tile_0_level2_0-10-0-10.png"))
assert os.path.exists(
os.path.join(tmp_path_, "processed", "tiles",
"tile_1_level2_0-10-0-10.png"))
_has_valid_tile_size.assert_called_once_with(random_tiler, slide)
def or_it_has_wrong_seed(self, tmpdir):
slide, _ = base_test_slide(tmpdir, PILIMG.RGB_RANDOM_COLOR_500X500)
random_tiler = RandomTiler((128, 128), 10, 0, seed=-1)
with pytest.raises(ValueError) as err:
random_tiler.extract(slide)
assert isinstance(err.value, ValueError)
assert str(err.value) == "Seed must be between 0 and 2**32 - 1"
def or_it_has_not_available_level_value(self, tmpdir):
slide, _ = base_test_slide(tmpdir, PILIMG.RGB_RANDOM_COLOR_500X500)
random_tiler = RandomTiler((128, 128), 10, 3)
with pytest.raises(LevelError) as err:
random_tiler.extract(slide)
assert isinstance(err.value, LevelError)
assert str(err.value
) == "Level 3 not available. Number of available levels: 1"
def or_it_has_wrong_seed(self, request, tmpdir):
tmp_path_ = tmpdir.mkdir("myslide")
image = PILImageMock.DIMS_50X50_RGB_RANDOM_COLOR
image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
slide_path = os.path.join(tmp_path_, "mywsi.png")
slide = Slide(slide_path, "processed")
random_tiler = RandomTiler((512, 512), 10, 0, seed=-1)
with pytest.raises(ValueError) as err:
random_tiler.extract(slide)
assert isinstance(err.value, ValueError)
assert str(err.value) == "Seed must be between 0 and 2**32 - 1"
def or_it_has_not_available_level_value(self, tmpdir):
tmp_path_ = tmpdir.mkdir("myslide")
image = PILIMG.RGB_RANDOM_COLOR_500X500
image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
slide_path = os.path.join(tmp_path_, "mywsi.png")
slide = Slide(slide_path, "processed")
random_tiler = RandomTiler((128, 128), 10, 3)
with pytest.raises(LevelError) as err:
random_tiler.extract(slide)
assert isinstance(err.value, LevelError)
assert str(err.value) == "Level 3 not available. Number of available levels: 1"
def test_extract_tiles_respecting_the_given_tile_size(
self, tmpdir, tile_size, level, seed, n_tiles):
processed_path = os.path.join(tmpdir, "processed")
slide = Slide(SVS.TCGA_CR_7395_01A_01_TS1, processed_path)
random_tiles_extractor = RandomTiler(
tile_size=tile_size,
n_tiles=n_tiles,
level=level,
seed=seed,
check_tissue=True,
)
binary_mask = BiggestTissueBoxMask()
random_tiles_extractor.extract(slide, binary_mask)
for tile in os.listdir(processed_path):
assert Image.open(os.path.join(processed_path,
tile)).size == tile_size
def but_it_raises_tilesizeerror_if_tilesize_larger_than_slidesize(
self, request, tmpdir, image, size):
tmp_path_ = tmpdir.mkdir("myslide")
image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
slide_path = os.path.join(tmp_path_, "mywsi.png")
slide = Slide(slide_path, os.path.join(tmp_path_, "processed"))
_has_valid_tile_size = method_mock(request, RandomTiler,
"_has_valid_tile_size")
_has_valid_tile_size.return_value = False
random_tiler = RandomTiler((50, 52), n_tiles=10, level=0)
with pytest.raises(TileSizeError) as err:
random_tiler.extract(slide)
assert isinstance(err.value, TileSizeError)
assert (str(
err.value
) == f"Tile size (50, 52) is larger than slide size {size} at level 0")
_has_valid_tile_size.assert_called_once_with(random_tiler, slide)
def extract_random_tiles(
dataset_dir: str,
processed_path: str,
tile_size: Tuple[int, int],
n_tiles: int,
level: int,
seed: int,
check_tissue: bool,
) -> None:
"""Save random tiles extracted from WSIs in `dataset_dir` into
`processed_path`/tiles/
Parameters
----------
dataset_dir : str
Path were the WSIs are saved
processed_path : str
Path where to store the tiles (will be concatenated with /tiles)
tile_size : Tuple[int, int]
width and height of the cropped tiles
n_tiles : int
Maximum number of tiles to extract
level : int
Magnification level from which extract the tiles
seed : int
Seed for RandomState
check_tissue : bool
Whether to check if the tile has enough tissue to be saved
"""
slideset = SlideSet(dataset_dir, processed_path, valid_extensions=[".svs"])
for slide in tqdm(slideset.slides):
prefix = f"{slide.name}_"
random_tiles_extractor = RandomTiler(
tile_size=tile_size,
n_tiles=n_tiles,
level=level,
seed=seed,
check_tissue=check_tissue,
prefix=prefix,
)
random_tiles_extractor.extract(slide)
def it_can_extract_random_tiles(self, request, tmpdir, caplog):
tmp_path_ = tmpdir.mkdir("myslide")
image = PILIMG.RGBA_COLOR_500X500_155_249_240
image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
slide_path = os.path.join(tmp_path_, "mywsi.png")
slide = Slide(slide_path, os.path.join(tmp_path_, "processed"))
_tiles_generator = method_mock(request, RandomTiler,
"_tiles_generator")
coords = CP(0, 10, 0, 10)
tile = Tile(image, coords)
_tiles_generator.return_value = [(tile, coords), (tile, coords)]
_tile_filename = method_mock(request, RandomTiler, "_tile_filename")
_tile_filename.side_effect = [
f"tile_{i}_level2_0-10-0-10.png" for i in range(2)
]
_has_valid_tile_size = method_mock(request, RandomTiler,
"_has_valid_tile_size")
_has_valid_tile_size.return_value = True
random_tiler = RandomTiler((10, 10), n_tiles=2, level=0)
binary_mask = BiggestTissueBoxMask()
with caplog.at_level(logging.INFO):
random_tiler.extract(slide, binary_mask)
assert re.sub(r":+\d{3}", "", caplog.text).splitlines() == [
"INFO tiler:tiler.py \t Tile 0 saved: tile_0_level2_0-10-0-10.png",
"INFO tiler:tiler.py \t Tile 1 saved: tile_1_level2_0-10-0-10.png",
"INFO tiler:tiler.py 2 Random Tiles have been saved.",
]
assert _tile_filename.call_args_list == [
call(random_tiler, coords, 0),
call(random_tiler, coords, 1),
]
assert os.path.exists(
os.path.join(tmp_path_, "processed",
"tile_0_level2_0-10-0-10.png"))
assert os.path.exists(
os.path.join(tmp_path_, "processed",
"tile_1_level2_0-10-0-10.png"))
_has_valid_tile_size.assert_called_once_with(random_tiler, slide)