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[FEA] port new features and bug fixes from scikit-image 0.20 #419

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grlee77 opened this issue Oct 18, 2022 · 2 comments
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[FEA] port new features and bug fixes from scikit-image 0.20 #419

grlee77 opened this issue Oct 18, 2022 · 2 comments
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feature request New feature or request
Milestone
v22.12.00

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@grlee77
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grlee77 commented Oct 18, 2022 •
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Is your feature request related to a problem? Please describe.
A scikit-image 0.20 release is planned in the near future. That release will add several new features and has a number of bug fixes. It also will add wheels for Python 3.11.

Current draft of the release notes

Describe the solution you'd like
We should port the relevant features here, ideally for inclusion in 22.12.00. Fortunately, one of the larger ones (footprint decompositions for morphology) was already previously merged here.

Describe alternatives you've considered
N/A

Additional context
N/A
@grlee77 grlee77 added the feature request New feature or request label Oct 18, 2022
@grlee77 grlee77 added this to the v22.12.00 milestone Oct 18, 2022
This was referenced Nov 1, 2022
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grlee77 commented Nov 1, 2022

All remaining features for 0.20 should be covered across #421, #422, #423, #424

@caryr35 caryr35 added this to cucim Nov 15, 2022
rapids-bot bot pushed a commit that referenced this issue Nov 16, 2022
@grlee77
improved implementation of ridge filters (bug fixes and reduced memor…
cebd032 
…y footprint) (#423)

related to #419

A large overhaul of the ridge filters, addressing inaccuracies and errors has been implemented for scikit-image 0.20. This PR ports the same changes to these functions to cuCIM.

upstream PRs: 
 - scikit-image/scikit-image#6149
 - scikit-image/scikit-image#6440 
 - scikit-image/scikit-image#6446
 - scikit-image/scikit-image#6509

These fix various bugs, simplify the implementation and reduce the memory footprint

Authors:
  - Gregory Lee (https://github.com/grlee77)

Approvers:
  - Gigon Bae (https://github.com/gigony)

URL: #423
rapids-bot bot pushed a commit that referenced this issue Nov 16, 2022
@grlee77
analytical moments computations, support pixel spacings in moments an…
f54b560 
…d regionprops (#422)

related to #419

This PR ports features related to image moments and `regionprops` from scikit-image 0.20 to cuCIM

- Improve performance of ``cucim.skimage.measure.moments_central`` by ~2x by avoiding redundant computations (adaptation of scikit-image/scikit-image#6188 to the GPU)
- Support anisotropic images with different voxel spacings.  Spacings can be defined with the new parameter ``spacing`` of the following functions in ``skimage.measure``: ``regionprops``, ``regionprops_table``, ``moments``, ``moments_central``, ``moments_normalized``, ``centroid``, ``inertia_tensor``, and ``inertia_tensor_eigvals`` (scikit-image/scikit-image#6296)
- Voxel spacing is taken into account for the following existing properties in ``skimage.measure.regionprops``: ``area``, ``area_bbox``, ``centroid``, ``area_convex``, ``extent``, ``feret_diameter_max``, ``area_filled``, ``inertia_tensor``, ``moments``, ``moments_central``, ``moments_hu``, ``moments_normalized``, ``perimeter``, ``perimeter_crofton``, ``solidity``, ``moments_weighted_central``, and ``moments_weighted_hu``. (scikit-image/scikit-image#6296)
- Raise a specific error message when accessing region properties from skimage.measure.regionprops when the required intensity_image is unavailable (scikit-image/scikit-image#6584).

Authors:
  - Gregory Lee (https://github.com/grlee77)

Approvers:
  - Gigon Bae (https://github.com/gigony)

URL: #422
rapids-bot bot pushed a commit that referenced this issue Nov 17, 2022
@grlee77
Misc updates for consistency with scikit-image 0.20 (#424)
706b6c0 
related to #419

The larger feature updates related to skimage 0.20 were opened in separate PRs. This one contains any other minor bug fixes and documentation tweaks.

Authors:
  - Gregory Lee (https://github.com/grlee77)

Approvers:
  - Gigon Bae (https://github.com/gigony)

URL: #424
@grlee77 grlee77 mentioned this issue Nov 18, 2022
Merged
rapids-bot bot pushed a commit that referenced this issue Nov 29, 2022
@grlee77
add isotropic binary morphology functions (#421)
f5408d0 
related to #419

These are based on the distance transform and are a faster way of computing binary morphological operations for large diameter disk or ball footprints. Unlike the sequence footprint decomposition methods, the footprint is exactly circular (spherical).

One test case `test_isotropic_erosion_spacing` will require #407 to be merged first. 

#406 will also improve the performance of this implementation

Authors:
  - Gregory Lee (https://github.com/grlee77)

Approvers:
  - Gigon Bae (https://github.com/gigony)

URL: #421
rapids-bot bot pushed a commit that referenced this issue Nov 30, 2022
@grlee77
Implement additional deprecations carried out for scikit-image 0.20 (#…
a7490ca 
…451)

related to #419

This PR removes most of the deprecated parameters that are being removed in scikit-image 0.20.

There are a few exceptions (e.g. `selem`) where they will be removed in scikit-image 0.20, but we had previously advertised a specific removal date like `2022.03.02`. For those, I will delay the removal until the previously advertised release.

It will be nice to be rid of all the deprecated `multichannel` code! The first, large commit here is just the multichannel deprecation. The rest of the commits are much smaller.

Authors:
  - Gregory Lee (https://github.com/grlee77)

Approvers:
  - Gigon Bae (https://github.com/gigony)

URL: #451
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grlee77 commented Nov 30, 2022

closed by the 4 PRs mentioned above as well as #451, #455

There are a handful of deprecations mentioned in #451 that are delayed to a future release, but I will go ahead and close this as largely resolved.

@grlee77 grlee77 closed this as completed Nov 30, 2022
@grlee77 grlee77 moved this to Done in cucim Nov 30, 2022
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