def test_read_rect_jp2_levels(_sample_jp2):
"""Test jp2 read rect with resolution in levels.
Location coordinate is in baseline (level 0) reference frame.
"""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
location = (0, 0)
size = JP2_TEST_TISSUE_SIZE
width, height = size
for level in range(wsi.info.level_count):
level_width, level_height = wsi.info.level_dimensions[level]
im_region = wsi.read_rect(location,
size,
resolution=level,
units="level")
assert isinstance(im_region, np.ndarray)
assert im_region.dtype == "uint8"
assert approx(
im_region.shape,
(
min(height, level_height),
min(width, level_width),
3,
),
abs=1,
)
def test__relative_level_scales_jp2_mpp(_sample_jp2):
"""Test jp2 calculation of relative level scales for mpp."""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
level_scales = wsi._relative_level_scales(0.5, "mpp")
level_scales = np.array(level_scales)
assert strictly_increasing(level_scales[:, 0])
assert strictly_increasing(level_scales[:, 1])
assert all(level_scales[0] == wsi.info.mpp / 0.5)
def test_read_rect_jp2_mpp(_sample_jp2):
"""Test jp2 read rect with resolution in microns per pixel.
Location coordinate is in baseline (level 0) reference frame.
"""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
location = JP2_TEST_TISSUE_LOCATION
size = JP2_TEST_TISSUE_SIZE
read_rect_mpp(wsi, location, size)
def test_find_optimal_level_and_downsample_jp2_interpolation_warning(
_sample_jp2):
"""Test finding optimal level for mpp read with scale > 1.
This tests the case where the scale is found to be > 1 and interpolation
will be applied to the output. A UserWarning should be raised in this case.
"""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
with pytest.warns(UserWarning):
_, _ = wsi._find_optimal_level_and_downsample(0.1, "mpp")
def test_read_bounds_jp2_baseline(_sample_jp2):
"""Test jp2 read bounds at baseline.
Coordinates in baseline (level 0) reference frame.
"""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
bounds = JP2_TEST_TISSUE_BOUNDS
size = JP2_TEST_TISSUE_SIZE
im_region = wsi.read_bounds(bounds, resolution=0, units="level")
assert isinstance(im_region, np.ndarray)
assert im_region.dtype == "uint8"
assert im_region.shape == (*size[::-1], 3)
def test_read_rect_jp2_baseline(_sample_jp2):
"""Test jp2 read rect at baseline.
Location coordinate is in baseline (level 0) reference frame.
"""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
location = JP2_TEST_TISSUE_LOCATION
size = JP2_TEST_TISSUE_SIZE
im_region = wsi.read_rect(location, size, resolution=0, units="level")
assert isinstance(im_region, np.ndarray)
assert im_region.dtype == "uint8"
assert im_region.shape == (*size[::-1], 3)
def test_wsireader_jp2_save_tiles(_sample_jp2, tmp_path):
"""Test for save_tiles in wsireader as a python function."""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
wsi.save_tiles(
output_dir=str(
pathlib.Path(tmp_path).joinpath("test_wsireader_jp2_save_tiles")),
tile_objective_value=5,
tile_read_size=(5000, 5000),
verbose=True,
)
assert (pathlib.Path(tmp_path).joinpath("test_wsireader_jp2_save_tiles").
joinpath("test1.jp2").joinpath("Output.csv").exists())
assert (pathlib.Path(tmp_path).joinpath("test_wsireader_jp2_save_tiles").
joinpath("test1.jp2").joinpath("slide_thumbnail.jpg").exists())
assert (pathlib.Path(tmp_path).joinpath("test_wsireader_jp2_save_tiles").
joinpath("test1.jp2").joinpath("Tile_5_0_0.jpg").exists())
def test_read_bounds_level_consistency_jp2(_sample_jp2):
"""Test read_bounds produces the same visual field across resolution levels."""
bounds = JP2_TEST_TISSUE_BOUNDS
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
imgs = [
wsi.read_bounds(bounds, power, "power") for power in [60, 40, 20, 10]
]
smallest_size = imgs[-1].shape[:2][::-1]
resized = [
cv2.GaussianBlur(cv2.resize(img, smallest_size), (5, 5),
cv2.BORDER_REFLECT) for img in imgs
]
# Pair-wise check resolutions for mean squared error
for a in resized:
for b in resized:
assert np.sum((a - b)**2) / np.prod(a.shape) < 16
def test_read_bounds_jp2_levels(_sample_jp2):
"""Test jp2 read bounds with resolution in levels.
Coordinates in baseline (level 0) reference frame.
"""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
bounds = JP2_TEST_TISSUE_BOUNDS
width, height = JP2_TEST_TISSUE_SIZE
for level, downsample in enumerate(wsi.info.level_downsamples):
im_region = wsi.read_bounds(bounds, resolution=level, units="level")
assert isinstance(im_region, np.ndarray)
assert im_region.dtype == "uint8"
expected_output_shape = tuple(
np.round([height / downsample, width / downsample]))
assert im_region.shape[:2] == approx(expected_output_shape, abs=1)
assert im_region.shape[2] == 3
def test_read_rect_jp2_objective_power(_sample_jp2):
"""Test jp2 read rect with resolution in objective power.
Location coordinate is in baseline (level 0) reference frame.
"""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
location = JP2_TEST_TISSUE_LOCATION
size = JP2_TEST_TISSUE_SIZE
for objective_power in [20, 10, 5, 2.5, 1.25]:
im_region = wsi.read_rect(location,
size,
resolution=objective_power,
units="mpp")
assert isinstance(im_region, np.ndarray)
assert im_region.dtype == "uint8"
assert im_region.shape == (*size[::-1], 3)
def test_read_bounds_jp2_mpp(_sample_jp2):
"""Test jp2 read bounds with resolution in microns per pixel.
Coordinates in baseline (level 0) reference frame.
"""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
bounds = JP2_TEST_TISSUE_BOUNDS
size = JP2_TEST_TISSUE_SIZE
slide_mpp = wsi.info.mpp
for factor in range(1, 10):
mpp = slide_mpp * factor
downsample = mpp / slide_mpp
im_region = wsi.read_bounds(bounds, resolution=mpp, units="mpp")
assert isinstance(im_region, np.ndarray)
assert im_region.dtype == "uint8"
expected_output_shape = tuple(
np.round((np.array(size[::-1]) / downsample)).astype(int))
assert im_region.shape[:2] == approx(expected_output_shape, abs=1)
assert im_region.shape[2] == 3
def test_read_bounds_jp2_objective_power(_sample_jp2):
"""Test jp2 read bounds with resolution in objective power.
Coordinates in baseline (level 0) reference frame.
"""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
bounds = JP2_TEST_TISSUE_BOUNDS
size = JP2_TEST_TISSUE_SIZE
slide_power = wsi.info.objective_power
for objective_power in [20, 10, 5, 2.5, 1.25]:
downsample = slide_power / objective_power
im_region = wsi.read_bounds(
bounds,
resolution=objective_power,
units="power",
)
assert isinstance(im_region, np.ndarray)
assert im_region.dtype == "uint8"
expected_output_shape = tuple(
np.round((np.array(size[::-1]) / downsample)).astype(int))
assert im_region.shape[:2] == approx(expected_output_shape[:2], abs=1)
assert im_region.shape[2] == 3
def test_wsireader_get_thumbnail_jp2(_sample_jp2):
"""Test for get_thumbnail as a python function."""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
slide_thumbnail = wsi.slide_thumbnail()
assert isinstance(slide_thumbnail, np.ndarray)
assert slide_thumbnail.dtype == "uint8"
def test__relative_level_scales_jp2_level_float(_sample_jp2):
"""Test jp2 calculation of relative level scales for fractional level."""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
relative_level_scales_float(wsi)
def test__relative_level_scales_jp2_power(_sample_jp2):
"""Test jp2 calculation of relative level scales for objective power."""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
relative_level_scales_power(wsi)
def test__relative_level_scales_jp2_baseline(_sample_jp2):
"""Test jp2 relative level scales for pixels per baseline pixel."""
wsi = wsireader.OmnyxJP2WSIReader(_sample_jp2)
relative_level_scales_baseline(wsi)