def it_knows_its_n_tiles(self):
n_tiles = 4
score_tiler = ScoreTiler(RandomScorer(), (512, 512), n_tiles, 0)
n_tiles_ = score_tiler.n_tiles
assert type(n_tiles_) == int
assert n_tiles_ == n_tiles
def it_knows_its_scorer(self):
random_scorer = RandomScorer()
score_tiler = ScoreTiler(random_scorer, (512, 512), 4, 0)
scorer_ = score_tiler.scorer
assert callable(scorer_)
assert isinstance(scorer_, RandomScorer)
def it_knows_if_it_has_valid_tile_size(self, tmpdir, tile_size,
expected_result):
slide, _ = base_test_slide(tmpdir,
PILIMG.RGBA_COLOR_500X500_155_249_240)
score_tiler = ScoreTiler(RandomScorer(), tile_size, 2, 0)
result = score_tiler._has_valid_tile_size(slide)
assert type(result) == bool
assert result == expected_result
def it_constructs_from_args(self, request):
_init = initializer_mock(request, ScoreTiler)
rs = RandomScorer()
grid_tiler = ScoreTiler(rs, (512, 512), 4, 2, True, 0, "", ".png")
_init.assert_called_once_with(ANY, rs, (512, 512), 4, 2, True, 0, "", ".png")
assert isinstance(grid_tiler, ScoreTiler)
assert isinstance(grid_tiler, GridTiler)
assert isinstance(grid_tiler, Tiler)
def it_can_extract_score_tiles_and_save_report(self, request, tmpdir):
_extract_tile = method_mock(request, Slide, "extract_tile")
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"))
coords = CP(0, 10, 0, 10)
_tiles_generator = method_mock(
request,
ScoreTiler,
"_tiles_generator",
)
tile = Tile(image, coords)
_extract_tile.return_value = tile
_tiles_generator.return_value = (
[(0.8, coords), (0.7, coords)],
[(0.8, coords), (0.7, coords)],
)
_tile_filename = method_mock(request, GridTiler, "_tile_filename")
_tile_filename.side_effect = [
f"tile_{i}_level2_0-10-0-10.png" for i in range(2)
]
_save_report = method_mock(request,
ScoreTiler,
"_save_report",
autospec=False)
random_scorer = RandomScorer()
score_tiler = ScoreTiler(random_scorer, (10, 10), 2, 0)
binary_mask = BiggestTissueBoxMask()
score_tiler.extract(slide, binary_mask, "report.csv")
assert _extract_tile.call_args_list == [
call(slide, coords, 0, (10, 10)),
call(slide, coords, 0, (10, 10)),
]
_tiles_generator.assert_called_with(score_tiler, slide, binary_mask)
assert _tile_filename.call_args_list == [
call(score_tiler, coords, 0),
call(score_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"))
_save_report.assert_called_once_with(
"report.csv",
[(0.8, coords), (0.7, coords)],
[(0.8, coords), (0.7, coords)],
[f"tile_{i}_level2_0-10-0-10.png" for i in range(2)],
)
def it_can_extract_score_tiles(self, request, tmpdir):
_extract_tile = method_mock(request, Slide, "extract_tile")
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"))
_highest_score_tiles = method_mock(request, ScoreTiler, "_highest_score_tiles")
coords = CP(0, 10, 0, 10)
tile = Tile(image, coords)
_extract_tile.return_value = tile
_highest_score_tiles.return_value = (
[(0.8, coords), (0.7, coords)],
[(0.8, coords), (0.7, coords)],
)
_tile_filename = method_mock(request, GridTiler, "_tile_filename")
_tile_filename.side_effect = [
f"tile_{i}_level2_0-10-0-10.png" for i in range(2)
]
_save_report = method_mock(request, ScoreTiler, "_save_report")
random_scorer = RandomScorer()
score_tiler = ScoreTiler(random_scorer, (10, 10), 2, 2)
score_tiler.extract(slide)
assert _extract_tile.call_args_list == [
call(slide, coords, 2),
call(slide, coords, 2),
]
_highest_score_tiles.assert_called_once_with(score_tiler, slide)
assert _tile_filename.call_args_list == [
call(score_tiler, coords, 0),
call(score_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")
)
_save_report.assert_not_called()
