def test_wsimeta_setter(_sample_svs):
"""Test setter for metadata."""
wsi = wsireader.OpenSlideWSIReader(_sample_svs)
meta = wsi.info
assert not np.array_equal(meta.mpp, np.array([1, 1]))
meta.mpp = np.array([1, 1])
wsi.info = meta
assert meta.validate()
assert np.array_equal(wsi.info.mpp, np.array([1, 1]))
def test_wsimeta_openslidewsireader_svs(_sample_svs, tmp_path):
"""Test OpenSlide reader metadata for svs."""
wsi_obj = wsireader.OpenSlideWSIReader(_sample_svs)
meta = wsi_obj.info
assert meta.validate()
meta.mpp = None
m = meta.as_dict()
assert isinstance(m["mpp"], tuple)
def test_morphological_masker(_sample_svs):
"""Test simple morphological thresholding."""
wsi = wsireader.OpenSlideWSIReader(_sample_svs)
thumb = wsi.slide_thumbnail()
masker = tissuemask.MorphologicalMasker()
mask_a = masker.fit_transform([thumb])[0]
masker.fit([thumb])
mask_b = masker.transform([thumb])[0]
assert np.array_equal(mask_a, mask_b)
assert masker.threshold is not None
assert len(np.unique(mask_a)) == 2
assert mask_a.shape == thumb.shape[:2]
def test_otsu_masker(_sample_svs):
"""Test Otsu's thresholding method."""
wsi = wsireader.OpenSlideWSIReader(_sample_svs)
mpp = 32
thumb = wsi.slide_thumbnail(mpp, "mpp")
masker = tissuemask.OtsuTissueMasker()
mask_a = masker.fit_transform([thumb])[0]
masker.fit([thumb])
mask_b = masker.transform([thumb])[0]
assert np.array_equal(mask_a, mask_b)
assert masker.threshold is not None
assert len(np.unique(mask_a)) == 2
assert mask_a.shape == thumb.shape[:2]
def test_morphological_greyscale_masker(_sample_svs):
"""Test morphological masker with greyscale inputs."""
wsi = wsireader.OpenSlideWSIReader(_sample_svs)
mpp = 32
thumb = wsi.slide_thumbnail(mpp, "mpp")
thumb = cv2.cvtColor(thumb, cv2.COLOR_RGB2GRAY)
inputs = thumb[np.newaxis, ..., np.newaxis]
masker = tissuemask.MorphologicalMasker()
mask_a = masker.fit_transform(inputs)[0]
masker.fit(inputs)
mask_b = masker.transform(inputs)[0]
assert np.array_equal(mask_a, mask_b)
assert masker.threshold is not None
assert len(np.unique(mask_a)) == 2
assert mask_a.shape == thumb.shape[:2]
def test_morphological_masker_mpp(_sample_svs):
"""Test simple morphological thresholding with mpp."""
wsi = wsireader.OpenSlideWSIReader(_sample_svs)
mpp = 32
thumb = wsi.slide_thumbnail(mpp, "mpp")
kwarg_sets = [
dict(mpp=mpp),
dict(mpp=[mpp, mpp]),
]
for kwargs in kwarg_sets:
masker = tissuemask.MorphologicalMasker(**kwargs)
mask_a = masker.fit_transform([thumb])[0]
masker.fit([thumb])
mask_b = masker.transform([thumb])[0]
assert np.array_equal(mask_a, mask_b)
assert masker.threshold is not None
assert len(np.unique(mask_a)) == 2
assert mask_a.shape == thumb.shape[:2]
def test_wsimeta_openslidewsireader_ndpi(_sample_ndpi, tmp_path):
"""Test OpenSlide reader metadata for ndpi."""
wsi_obj = wsireader.OpenSlideWSIReader(_sample_ndpi)
meta = wsi_obj.info
assert meta.validate()