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multichannel to channel_axis (6 of 6): segmentation #5289

Merged
merged 19 commits into from
May 12, 2021
Merged

multichannel to channel_axis (6 of 6): segmentation #5289

merged 19 commits into from
May 12, 2021

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grlee77
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@grlee77 grlee77 commented Mar 23, 2021 •
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follows #5288. Implements channel_axis for the segmentation module

This PR also removes use of the deprecated multichannel argument in all gallery examples.

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For reviewers

  • Check that the PR title is short, concise, and will make sense 1 year
    later.
  • Check that new functions are imported in corresponding __init__.py.
  • Check that new features, API changes, and deprecations are mentioned in
    doc/release/release_dev.rst.

@grlee77 grlee77 added the 📜 type: API Involves API change(s) label Mar 23, 2021
@grlee77 grlee77 added this to In progress in skimage2 API Mar 23, 2021
@grlee77 grlee77 force-pushed the channel_axis_segmentation branch 2 times, most recently from 45ede68 to 337c44c Compare March 29, 2021 00:37
@alexdesiqueira alexdesiqueira mentioned this pull request Mar 31, 2021
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@grlee77
filters: multichannel->channel_axis
4d15980
@grlee77
check positional multichannel warning for gaussian
f16bc46
@grlee77
consistent use of backticks for variable names in warning messages
e4ec5b9
@grlee77
add slice_at_axis utility
7057018 
slice_at_axis is a vendored copy of numpy.lib.arraypad._slice_at_axis
@grlee77
add channel_axis support to metrics.structural_similarity
5abe82f
@grlee77
DOC: add channel axis note to regionprops docstrings
144a2e5 
If needed can revisit adding custom channel_axis support to the underlying RegionProps class
@grlee77
consistent use of backticks for variable names in warning messages
7f9b4f3
@grlee77
add channel_axis support to denoise_wavelet, estimate_sigma, cycle_spin
e72d85f
@grlee77
finish adding channel_axis support to denoising functions
0c80b96
@grlee77
support channel_axis kwarg in j_invariant denoiser
7dec264
@grlee77
add channel_axis support to inpaint biharmonic
26bb23a
@grlee77
fix expected warnings list for case when dask is not available
412cb6f
@grlee77
catch possible additional warning in inpaint multichannel test
8a68303
@grlee77
catch possible additional warning in inpaint multichannel test
98d9c6c
@grlee77
consistent use of backticks for variable names in warning messages
b2d49ee
@grlee77
segmentation: multichannel->channel_axis
f990bfa
@grlee77
DOC: update multichannel -> channel_axis in gallery examples
1b5d5ef
@grlee77
consistent use of backticks for variable names in warning messages
dd69d59
@grlee77 grlee77 added this to the 0.19 milestone Apr 21, 2021
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grlee77 commented May 11, 2021

This one has accumulated quite a few conflicts now, so I will rebase it

@grlee77 grlee77 force-pushed the channel_axis_segmentation branch from 337c44c to dd69d59 Compare May 11, 2021 13:19
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grlee77 commented May 11, 2021

I would wait until #5287 and #5288 are merged before reviewing this so the diff will be smaller.

@alexdesiqueira
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LGTM, thanks Greg! @jni if you could check this after #5288 — and merge it, before I break anything 😉

@jni jni merged commit 4397765 into scikit-image:main May 12, 2021
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jni commented May 12, 2021

Boom. Transformation complete. 🤖 Thanks @grlee77!!! 🎉

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grlee77 commented May 12, 2021

Thanks for reviewing!

@grlee77 grlee77 moved this from In progress to Done in skimage2 API Jun 21, 2021
@grlee77 grlee77 deleted the channel_axis_segmentation branch July 8, 2021 20:44
@grlee77 grlee77 mentioned this pull request Sep 7, 2021
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@grlee77 grlee77 mentioned this pull request Dec 24, 2021
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@jni jni jni approved these changes

@alexdesiqueira alexdesiqueira alexdesiqueira approved these changes

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📜 type: API Involves API change(s)
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skimage2 API
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