def it_can_generate_random_tiles_with_no_check_tissue(
self,
request,
tmpdir,
tile1,
tile2,
has_enough_tissue,
max_iter,
expected_value,
_random_tile_coordinates,
):
slide, _ = base_test_slide(tmpdir,
PILIMG.RGBA_COLOR_500X500_155_249_240)
_extract_tile = method_mock(request, Slide, "extract_tile")
_has_enough_tissue = method_mock(request, Tile, "has_enough_tissue")
_has_enough_tissue.side_effect = has_enough_tissue * (max_iter // 2)
tiles = [tile1, tile2]
_extract_tile.side_effect = tiles * (max_iter // 2)
random_tiler = RandomTiler(
(10, 10),
2,
level=0,
max_iter=max_iter,
check_tissue=False,
)
generated_tiles = list(random_tiler._tiles_generator(slide))
_random_tile_coordinates.assert_called_with(random_tiler, slide)
_has_enough_tissue.assert_not_called()
assert _random_tile_coordinates.call_count <= random_tiler.max_iter
assert len(generated_tiles) == expected_value
for i, tile in enumerate(generated_tiles):
assert tile[0] == tiles[i]
def it_can_generate_random_tiles(
self,
request,
tmpdir,
tile1,
tile2,
check_tissue,
has_enough_tissue,
max_iter,
expected_value,
_random_tile_coordinates,
):
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, "processed")
_extract_tile = method_mock(request, Slide, "extract_tile")
_has_enough_tissue = method_mock(request, Tile, "has_enough_tissue")
_has_enough_tissue.side_effect = has_enough_tissue * (max_iter // 2)
tiles = [tile1, tile2]
_extract_tile.side_effect = tiles * (max_iter // 2)
random_tiler = RandomTiler(
(10, 10), 2, level=0, max_iter=max_iter, check_tissue=check_tissue
)
generated_tiles = list(random_tiler._tiles_generator(slide))
_random_tile_coordinates.assert_called_with(random_tiler, slide)
assert _random_tile_coordinates.call_count <= random_tiler.max_iter
assert len(generated_tiles) == expected_value
for i, tile in enumerate(generated_tiles):
assert tile[0] == tiles[i]
def it_can_generate_random_tiles_even_when_coords_are_not_valid(
self, tmpdir, _random_tile_coordinates
):
random_tiler = RandomTiler((10, 10), 1, level=0, max_iter=1, check_tissue=False)
_random_tile_coordinates.side_effect = [CP(-1, -1, -1, -1), CP(0, 10, 0, 10)]
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, "processed")
generated_tiles = list(random_tiler._tiles_generator(slide))
assert generated_tiles[0][1] == CP(0, 10, 0, 10)
assert isinstance(generated_tiles[0][0], Tile)
def it_can_generate_random_tiles_even_when_coords_are_not_valid(
self, tmpdir, _random_tile_coordinates):
random_tiler = RandomTiler((10, 10),
1,
level=0,
max_iter=1,
check_tissue=False)
_random_tile_coordinates.side_effect = [
CP(-1, -1, -1, -1), CP(0, 10, 0, 10)
]
slide, _ = base_test_slide(tmpdir,
PILIMG.RGBA_COLOR_500X500_155_249_240)
generated_tiles = list(random_tiler._tiles_generator(slide))
assert generated_tiles[0][1] == CP(0, 10, 0, 10)
assert isinstance(generated_tiles[0][0], Tile)
def it_can_generate_random_tiles_with_check_tissue(
self,
request,
tmpdir,
tile1,
tile2,
has_enough_tissue,
max_iter,
expected_value,
_random_tile_coordinates,
):
slide, _ = base_test_slide(tmpdir,
PILIMG.RGBA_COLOR_500X500_155_249_240)
_extract_tile = method_mock(request, Slide, "extract_tile")
_has_enough_tissue = method_mock(request, Tile, "has_enough_tissue")
_has_enough_tissue.side_effect = has_enough_tissue * (max_iter // 2)
binary_mask = BiggestTissueBoxMask()
tiles = [tile1, tile2]
_extract_tile.side_effect = tiles * (max_iter // 2)
random_tiler = RandomTiler(
(10, 10),
2,
level=0,
max_iter=max_iter,
check_tissue=True,
tissue_percent=60,
)
generated_tiles = list(
random_tiler._tiles_generator(slide, binary_mask))
_random_tile_coordinates.assert_called_with(random_tiler, slide,
binary_mask)
assert _has_enough_tissue.call_args_list == [
call(tile1, 60), call(tile2, 60)
]
assert _random_tile_coordinates.call_count <= random_tiler.max_iter
assert len(generated_tiles) == expected_value
for i, tile in enumerate(generated_tiles):
assert tile[0] == tiles[i]
def it_can_generate_random_tiles_with_check_tissue_but_tiles_without_tissue(
self,
request,
tmpdir,
_random_tile_coordinates,
):
slide, _ = base_test_slide(tmpdir,
PILIMG.RGBA_COLOR_500X500_155_249_240)
_extract_tile = method_mock(request, Slide, "extract_tile")
_has_enough_tissue = method_mock(request, Tile, "has_enough_tissue")
_has_enough_tissue.side_effect = [False, False] * 5
binary_mask = BiggestTissueBoxMask()
tiles = [
Tile(PILIMG.RGBA_COLOR_500X500_155_249_240, CP(0, 10, 0, 10)),
Tile(PILIMG.RGBA_COLOR_500X500_155_249_240, CP(0, 10, 0, 10)),
]
_extract_tile.side_effect = tiles * 5
random_tiler = RandomTiler(
(10, 10),
2,
level=0,
max_iter=10,
check_tissue=True,
tissue_percent=60,
)
generated_tiles = list(
random_tiler._tiles_generator(slide, binary_mask))
_random_tile_coordinates.assert_called_with(random_tiler, slide,
binary_mask)
assert (_has_enough_tissue.call_args_list == [
call(tiles[0], 60),
call(tiles[1], 60),
] * 5)
assert _random_tile_coordinates.call_count <= random_tiler.max_iter
assert len(generated_tiles) == 0
for i, tile in enumerate(generated_tiles):
assert tile[0] == tiles[i]
