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Fix channel_dim bug in TiffFileWSIReader and CuCIMWSIReader #6514

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Merged
merged 3 commits into from
May 12, 2023
Merged

Fix channel_dim bug in TiffFileWSIReader and CuCIMWSIReader #6514

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e022915
fix #6511
KumoLiu May 12, 2023
5dbd100
update unittests
KumoLiu May 12, 2023
8c0b6be
fix flake8
KumoLiu May 12, 2023
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4 changes: 2 additions & 2 deletions monai/data/wsi_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -824,7 +824,7 @@ def _get_patch(
f"The image is expected to have three or four color channels in '{mode}' mode but has "
f"{patch.shape[self.channel_dim]}. "
)
patch = patch[:3]
patch = np.take(patch, [0, 1, 2], self.channel_dim)

return patch

Expand Down Expand Up @@ -1183,6 +1183,6 @@ def _get_patch(
f"The image is expected to have three or four color channels in '{mode}' mode but has "
f"{patch.shape[self.channel_dim]}. "
)
patch = patch[:3]
patch = np.take(patch, [0, 1, 2], self.channel_dim)

return patch
20 changes: 16 additions & 4 deletions tests/test_wsireader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,15 +81,27 @@
TEST_CASE_3 = [
WSI_GENERIC_TIFF_PATH,
{"channel_dim": -1},
{"location": (WSI_GENERIC_TIFF_HEIGHT // 2, WSI_GENERIC_TIFF_WIDTH // 2), "size": (2, 1), "level": 0},
np.moveaxis(np.array([[[246], [246]], [[246], [246]], [[246], [246]]], dtype=np.uint8), 0, -1),
{"location": (WSI_GENERIC_TIFF_HEIGHT // 2, WSI_GENERIC_TIFF_WIDTH // 2), "size": (4, 1), "level": 0},
np.moveaxis(
np.array(
[[[246], [246], [246], [246]], [[246], [246], [246], [246]], [[246], [246], [246], [246]]], dtype=np.uint8
),
0,
-1,
),
]

TEST_CASE_4 = [
WSI_GENERIC_TIFF_PATH,
{"channel_dim": 2},
{"location": (0, 0), "size": (2, 1), "level": 8},
np.moveaxis(np.array([[[242], [242]], [[242], [242]], [[242], [242]]], dtype=np.uint8), 0, -1),
{"location": (0, 0), "size": (4, 1), "level": 8},
np.moveaxis(
np.array(
[[[242], [242], [242], [242]], [[242], [242], [242], [242]], [[242], [242], [242], [242]]], dtype=np.uint8
),
0,
-1,
),
]

TEST_CASE_5 = [
Expand Down