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[BUG] some thresholding functions require scikit-image>=0.19 #363

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grlee77 opened this issue Aug 1, 2022 · 3 comments
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[BUG] some thresholding functions require scikit-image>=0.19 #363

grlee77 opened this issue Aug 1, 2022 · 3 comments
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@grlee77
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grlee77 commented Aug 1, 2022

Describe the bug

Changes made in #276 break use of some thresholding functions if the user does not have scikit-image >= 0.19. We should either bump our minimum requirement to 0.19 or provide a fallback.

Steps/Code to reproduce bug
many test failures are seen for cucim/skimage/filters/tests/test_thresholding.py

Expected behavior
all tests should pass

Environment details (please complete the following information):
cuCIM branch 22.08

@grlee77 grlee77 added the bug Something isn't working label Aug 1, 2022
@jakirkham
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jakirkham commented Aug 15, 2022

It looks like we didn't bump this dependency. Should we be doing this? Also is this only test related or would users see this in workflows?

- scikit-image >=0.18.1,<0.20.0a0

@grlee77
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grlee77 commented Aug 15, 2022

The functions failing with 0.18 are;

  • threshold_multiotsu (hist kwarg isn't present in 0.18.x)
  • threshold_minimum (max_iter was deprecated in 0.19 and we use the new max_num_iter which wasn't present in 0.18)
  • try_all_threshold (fails due to the same threshold_minimum failure)

All will work if the user upgrades to >=0.19.

@grlee77
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grlee77 commented Aug 15, 2022

This commit where we deferred some computations to scikit-image and removed duplicate code is what lead to the issue.

grlee77 added a commit to grlee77/cucim that referenced this issue Aug 16, 2022
this will avoid the scikit-image 0.18.x issues with 3 thresholding functions observed
in rapidsaigh-363: rapidsai#363
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