def it_can_generate_grid_tiles_with_no_check_tissue(
self,
request,
tmpdir,
tile1,
tile2,
has_enough_tissue,
expected_n_tiles,
):
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
_grid_coordinates_generator = method_mock(
request, GridTiler, "_grid_coordinates_generator")
_grid_coordinates_generator.return_value = [
CP(0, 10, 0, 10), CP(0, 10, 0, 10)
]
_extract_tile.side_effect = [tile1, tile2]
grid_tiler = GridTiler((10, 10), level=0, check_tissue=False)
tiles = [tile1, tile2]
generated_tiles = list(grid_tiler._tiles_generator(slide))
_grid_coordinates_generator.assert_called_once_with(grid_tiler, slide)
assert _extract_tile.call_args_list == ([
call(slide, CP(0, 10, 0, 10), 0),
call(slide, CP(0, 10, 0, 10), 0)
])
_has_enough_tissue.assert_not_called()
assert len(generated_tiles) == expected_n_tiles
for i, tile in enumerate(generated_tiles):
assert tile[0] == tiles[i]
def it_can_generate_grid_tiles(
self,
request,
tmpdir,
tile1,
tile2,
check_tissue,
has_enough_tissue,
expected_n_tiles,
):
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
_grid_coordinates_generator = method_mock(
request, GridTiler, "_grid_coordinates_generator"
)
_grid_coordinates_generator.return_value = [CP(0, 10, 0, 10), CP(0, 10, 0, 10)]
_extract_tile.side_effect = [tile1, tile2]
grid_tiler = GridTiler((10, 10), level=0, check_tissue=check_tissue)
tiles = [tile1, tile2]
generated_tiles = list(grid_tiler._tiles_generator(slide))
_grid_coordinates_generator.assert_called_once_with(grid_tiler, slide)
assert _extract_tile.call_args_list == (
[call(slide, CP(0, 10, 0, 10), 0), call(slide, CP(0, 10, 0, 10), 0)]
)
assert len(generated_tiles) == expected_n_tiles
for i, tile in enumerate(generated_tiles):
assert tile[0] == tiles[i]
def and_doesnt_raise_error_with_wrong_coordinates(self, request, tmpdir):
slide, _ = base_test_slide(tmpdir,
PILIMG.RGBA_COLOR_500X500_155_249_240)
coords = CP(5800, 6000, 5800, 6000)
_grid_coordinates_generator = method_mock(
request, GridTiler, "_grid_coordinates_generator")
_grid_coordinates_generator.return_value = [coords]
grid_tiler = GridTiler((10, 10))
generated_tiles = list(grid_tiler._tiles_generator(slide))
assert len(generated_tiles) == 0
_grid_coordinates_generator.assert_called_once_with(grid_tiler, slide)
def and_doesnt_raise_error_with_wrong_coordinates(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, "processed")
coords = CP(5800, 6000, 5800, 6000)
_grid_coordinates_generator = method_mock(
request, GridTiler, "_grid_coordinates_generator"
)
_grid_coordinates_generator.return_value = [coords]
grid_tiler = GridTiler((10, 10))
generated_tiles = list(grid_tiler._tiles_generator(slide))
assert len(generated_tiles) == 0
_grid_coordinates_generator.assert_called_once_with(grid_tiler, slide)
def but_with_wrong_coordinates(self, request, tmpdir):
slide, _ = base_test_slide(tmpdir,
PILIMG.RGBA_COLOR_500X500_155_249_240)
_has_enough_tissue = method_mock(request, Tile, "has_enough_tissue")
_has_enough_tissue.return_value = False
_grid_coordinates_generator = method_mock(
request, GridTiler, "_grid_coordinates_generator")
coords1 = CP(600, 610, 600, 610)
coords2 = CP(0, 10, 0, 10)
_grid_coordinates_generator.return_value = [coords1, coords2]
grid_tiler = GridTiler((10, 10), level=0, check_tissue=False)
generated_tiles = list(grid_tiler._tiles_generator(slide))
_grid_coordinates_generator.assert_called_once_with(grid_tiler, slide)
assert len(generated_tiles) == 1
# generated_tiles[0][0] is a Tile object but we don't know what object it is
# because Slide.extract_tile is not mocked (for the exception to happen inside)
assert isinstance(generated_tiles[0][0], Tile)
assert generated_tiles[0][1] == coords2
def but_with_wrong_coordinates(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, "processed")
_has_enough_tissue = method_mock(request, Tile, "has_enough_tissue")
_has_enough_tissue.return_value = False
_grid_coordinates_generator = method_mock(
request, GridTiler, "_grid_coordinates_generator"
)
coords1 = CP(600, 610, 600, 610)
coords2 = CP(0, 10, 0, 10)
_grid_coordinates_generator.return_value = [coords1, coords2]
grid_tiler = GridTiler((10, 10), level=0, check_tissue=False)
generated_tiles = list(grid_tiler._tiles_generator(slide))
_grid_coordinates_generator.assert_called_once_with(grid_tiler, slide)
assert len(generated_tiles) == 1
# generated_tiles[0][0] is a Tile object but we don't know what object it is
# because Slide.extract_tile is not mocked (for the exception to happen inside)
assert isinstance(generated_tiles[0][0], Tile)
assert generated_tiles[0][1] == coords2