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Disable pylint error and fix CI tests of new tifffile #4162

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Merged
merged 8 commits into from
Apr 23, 2022
Merged

Disable pylint error and fix CI tests of new tifffile #4162

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42a45e0
Merge pull request #19 from Project-MONAI/master
Nic-Ma Feb 1, 2021
cd16a13
Merge pull request #32 from Project-MONAI/master
Nic-Ma Feb 24, 2021
6f87afd
Merge pull request #180 from Project-MONAI/dev
Nic-Ma Jul 22, 2021
f398298
Merge pull request #214 from Project-MONAI/dev
Nic-Ma Sep 8, 2021
ec463d6
Merge pull request #397 from Project-MONAI/dev
Nic-Ma Apr 4, 2022
da85db8
Merge pull request #406 from Project-MONAI/dev
Nic-Ma Apr 23, 2022
0a00c61
workaround
Nic-Ma Apr 23, 2022
7e0d6af
[DLMED] fix tifffile issue
Nic-Ma Apr 23, 2022
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2 changes: 1 addition & 1 deletion monai/bundle/scripts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -429,7 +429,7 @@ def verify_metadata(
try:
# the rest key-values in the _args are for `validate` API
validate(instance=metadata, schema=schema, **_args)
except ValidationError as e:
except ValidationError as e: # pylint: disable=E0712
# as the error message is very long, only extract the key information
logger.info(re.compile(r".*Failed validating", re.S).findall(str(e))[0] + f" against schema `{url}`.")
return
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2 changes: 1 addition & 1 deletion tests/test_lesion_froc.py
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Expand Up @@ -31,7 +31,7 @@ def save_as_tif(filename, array):
if not filename.endswith(".tif"):
filename += ".tif"
file_path = os.path.join("tests", "testing_data", filename)
imwrite(file_path, array, compress="jpeg", tile=(16, 16))
imwrite(file_path, array, compression="jpeg", tile=(16, 16))


def around(val, interval=3):
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4 changes: 2 additions & 2 deletions tests/test_wsireader.py
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Expand Up @@ -84,7 +84,7 @@

TEST_CASE_RGB_1 = [np.ones((3, 100, 100), dtype=np.uint8)] # CHW

TEST_CASE_ERROR_GRAY = [np.ones((16, 16), dtype=np.uint8)] # no color channel
TEST_CASE_ERROR_GRAY = [np.ones((16, 16, 2), dtype=np.uint8)] # wrong color channel
TEST_CASE_ERROR_3D = [np.ones((16, 16, 16, 3), dtype=np.uint8)] # 3D + color


Expand Down Expand Up @@ -115,7 +115,7 @@ def save_gray_tiff(array: np.ndarray, filename: str):
filename: the filename to be used for the tiff file.
"""
img_gray = array
imwrite(filename, img_gray, shape=img_gray.shape, photometric="rgb")
imwrite(filename, img_gray, shape=img_gray.shape, photometric="minisblack")

return filename

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4 changes: 2 additions & 2 deletions tests/test_wsireader_new.py
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Expand Up @@ -72,7 +72,7 @@

TEST_CASE_RGB_1 = [np.ones((3, 100, 100), dtype=np.uint8)] # CHW

TEST_CASE_ERROR_GRAY = [np.ones((16, 16), dtype=np.uint8)] # no color channel
TEST_CASE_ERROR_GRAY = [np.ones((16, 16, 2), dtype=np.uint8)] # wrong color channel
TEST_CASE_ERROR_3D = [np.ones((16, 16, 16, 3), dtype=np.uint8)] # 3D + color


Expand Down Expand Up @@ -103,7 +103,7 @@ def save_gray_tiff(array: np.ndarray, filename: str):
filename: the filename to be used for the tiff file.
"""
img_gray = array
imwrite(filename, img_gray, shape=img_gray.shape, photometric="rgb")
imwrite(filename, img_gray, shape=img_gray.shape, photometric="minisblack")

return filename

Expand Down