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Refactor Stain Normalization

Open bhashemian opened this issue 4 years ago • 6 comments

Description

This PR refactor stain normalization to support channel first input (instead of channel last), and modifies the code to be more readable with more meaningful names.

Status

Ready

Types of changes

  • [x] Breaking change (fix or new feature that would cause existing functionality to change).
  • [x] New tests added to cover the changes.
  • [x] Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • [x] Quick tests passed locally by running ./runtests.sh --quick --unittests.
  • [x] In-line docstrings updated.
  • [x] Documentation updated, tested make html command in the docs/ folder.

bhashemian avatar Dec 18 '21 01:12 bhashemian

Hi @drbeh there's a discussion about rearranging the pathology modules into monai.transforms, monai.data etc, perhaps we can include those changes together within this one? (please see https://github.com/Project-MONAI/MONAI/milestone/36)

also do we want to keep the previous names as alias so that it's backward compatible?

wyli avatar Feb 24 '22 17:02 wyli

Hi @drbeh there's a discussion about rearranging the pathology modules into monai.transforms, monai.data etc, perhaps we can include those changes together within this one? (please see https://github.com/Project-MONAI/MONAI/milestone/36)

also do we want to keep the previous names as alias so that it's backward compatible?

Hi @wyli, that's right! but it would make it much harder for reviewing if we combine rearranging all components and refactoring this component together. This PR is ready for review so, while I'm working on the re-organizing pathology components, why don't we review and merge it?

bhashemian avatar Feb 24 '22 18:02 bhashemian

@wyli can we have this PR reviewed and merged?

bhashemian avatar Mar 23 '22 19:03 bhashemian

Hi, we haven't finished the discussions in overall design and naming convention https://github.com/Project-MONAI/MONAI/issues/3868, please could you work on that first?

wyli avatar Mar 23 '22 20:03 wyli

Hi, we haven't finished the discussions in overall design and naming convention #3868, please could you work on that first?

Hi @wyli, I'm not sure how it is related. Can you let me know what exactly you want for this stain normalizer specifically? I can revert the name of the components here if that's the problem.

bhashemian avatar Mar 23 '22 20:03 bhashemian

Hi, we haven't finished the discussions in overall design and naming convention #3868, please could you work on that first?

Hi @wyli, I'm not sure how it is related. Can you let me know what exactly you want for this stain normalizer specifically? I can revert the name of the components here if that's the problem.

Actually, never mind! We'll review it when we are adding it to monai core.

bhashemian avatar Mar 24 '22 18:03 bhashemian