def it_can_extract_grid_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, GridTiler, "_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, GridTiler, "_tile_filename")
_tile_filename.side_effect = [
os.path.join(tmp_path_, "processed", "tiles",
f"tile_{i}_level2_0-10-0-10.png") for i in range(2)
]
_has_valid_tile_size = method_mock(request, GridTiler,
"_has_valid_tile_size")
_has_valid_tile_size.return_value = True
grid_tiler = GridTiler((10, 10), level=0)
grid_tiler.extract(slide)
assert _tile_filename.call_args_list == [
call(grid_tiler, coords, 0),
call(grid_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(grid_tiler, slide)
def or_it_has_not_available_level_value(self, tmpdir):
slide, _ = base_test_slide(tmpdir, PILIMG.RGB_RANDOM_COLOR_500X500)
binary_mask = BiggestTissueBoxMask()
grid_tiler = GridTiler((128, 128), 3)
with pytest.raises(LevelError) as err:
grid_tiler.extract(slide, binary_mask)
assert isinstance(err.value, LevelError)
assert str(err.value
) == "Level 3 not available. Number of available levels: 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")
grid_tiler = GridTiler((128, 128), 3)
with pytest.raises(LevelError) as err:
grid_tiler.extract(slide)
assert isinstance(err.value, LevelError)
assert str(err.value) == "Level 3 not available. Number of available levels: 1"
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, GridTiler,
"_has_valid_tile_size")
_has_valid_tile_size.return_value = False
grid_tiler = GridTiler((50, 52), level=0)
with pytest.raises(TileSizeError) as err:
grid_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(grid_tiler, slide)
check_tissue=
check_tissue, # Whether to check if the tile has enough tissue to be saved. Default is True.
pixel_overlap=
0, # Number of overlapping pixels (for both height and width) between two adjacent tiles.
prefix=
'', # Prefix to be added to the tile filename. Default is an empty string.
suffix=".png" # default
)
# Find the smallest slide
idx = meta_df['openslide.level[0].height'].isin(
[meta_df['openslide.level[0].height'].min()])
img_name = meta_df.loc[idx, 'aperio.ImageID'].values[0]
fname = imgpath / f'{img_name}.svs'
# Slide instance
# path: path to WSI file
# processed_path: path to save thumbnails and scaled images
img_inpath = str(fname)
sfx = 'tissue' if check_tissue else 'all'
img_outpath = os.path.join(str(datapath), 'tiles', sfx, f'{tile_sz}px',
fname.with_suffix('').name)
# os.makedirs(grid_tiles_path, exist_ok=True)
pdx_slide = Slide(path=img_inpath, processed_path=img_outpath)
print(pdx_slide.dimensions)
# Extract
import ipdb
ipdb.set_trace(context=11)
grid_tiler.extract(pdx_slide)