Scikit-image: Calendar of community management

Created on 3 Mar 2020 · 35Comments · Source: scikit-image/scikit-image

As an experiment, we are trying to set up a rotating duty to take a first look at all contributions (PRs and issues) from the community, label them and ping relevant reviewers.

Scripts for generating the reports are available in this repository.

mar/2020

2020/03/02 - 2020/03/08: @emmanuelle
2020/03/09 - 2020/03/15: @jni
2020/03/16 - 2020/03/22 @alexdesiqueira
2020/03/23 - 2020/03/29 @sciunto

apr/2020

2020/03/30 - 2020/04/05: @rfezzani
2020/04/06 - 2020/04/12: @emmanuelle
2020/04/13 - 2020/04/19: @jni
2020/04/20 - 2020/04/26: @sciunto

may/2020

2020/04/27 - 2020/05/03: @alexdesiqueira (covered by @emmanuelle)
2020/05/04 - 2020/05/10: @emmanuelle
2020/05/11 - 2020/05/17: @alexdesiqueira
2020/05/18 - 2020/05/24: @lagru
2020/05/25 - 2020/05/31: @rfezzani

jun/2020

2020/06/01 - 2020/06/07: @alexdesiqueira
2020/06/08 - 2020/06/14: @alexdesiqueira
2020/06/15 - 2020/06/21: @rfezzani
2020/06/22 - 2020/06/28: @emmanuelle

jul/2020

2020/06/29 - 2020/07/05: @jni
2020/07/06 - 2020/07/12: @alexdesiqueira
2020/07/13 - 2020/07/19: @emmanuelle
2020/07/20 - 2020/07/26: @alexdesiqueira

ago/2020

2020/07/27 - 2020/08/02: @alexdesiqueira
2020/08/03 - 2020/08/09: @sciunto
2020/08/10 - 2020/08/16: @emmanuelle
2020/08/17 - 2020/08/23: @alexdesiqueira
2020/08/24 - 2020/08/30: @rfezzani

sep/2020

2020/08/31 - 2020/09/06: @sciunto
2020/09/07 - 2020/09/13: @jni
2020/09/14 - 2020/09/20: @alexdesiqueira
2020/09/21 - 2020/09/27: @emmanuelle

oct/2020

2020/09/28 - 2020/10/04: @mkcor
2020/10/05 - 2020/10/11: @alexdesiqueira
2020/10/12 - 2020/10/18: @rfezzani
2020/10/19 - 2020/10/25: @jni

nov/2020

2020/10/26 - 2020/11/01:
2020/11/02 - 2020/11/08: @alexdesiqueira
2020/11/09 - 2020/11/15:
2020/11/16 - 2020/11/22: @mkcor
2020/11/23 - 2020/11/29: @rfezzani

dec/2020

2020/11/30 - 2020/12/06: @grlee77
2020/12/07 - 2020/12/13: @alexdesiqueira
2020/12/14 - 2020/12/20:
2020/12/21 - 2020/12/27:
2020/12/28 - 2020/12/31: :tada:

planning maintenance

Source

emmanuelle

Most helpful comment

2020/4/20 - 2020/4/27

A good activity this week. An issue #4603 raised again the question how to decide the min version of requirements. @soupault opened a great issue (https://github.com/scikit-image/scikit-image/issues/4608) summarizing our current decisions and proposing policies for the different cases. This PR requires attention of @scikit-image/core in particular.

Kudos again to @soupault who fixed a ton of broken links in our code: https://github.com/scikit-image/scikit-image/pull/4600

@emmanuelle put the script to generate this report in a repository, so we can easily submit PRs.

I tried to fix an issue in skeletonize3D based on a patch that have been submitted to the matlab implementation of this algorithm. I might not have fully understood the matlab code, but the modifications seem to be too drastic and lead to another incorrect behavior. Fiji still have the bug. I have not done the work to read carefully the paper to check the current implementation regarding the original algorithm.

I also investigated the loading page performances of our gallery. It turns out that the page is slow due to thumbnails. We merged a PR to reduce the resolution of thumbnails, which decreases by a factor 2 the image sizes, while keeping a correct rendering. I opened an issue on the sphinx-gallery tracker to raise this problem. Matplotlib and scikit-learn are also interested in better performances. One sphinx-gallery dev proposed a PR to use optipng (after @GaelVaroquaux's recommendations). This has to be tested.

I hope I did not missed any other important point.

2020/4/20 - 2020/4/27

New pull requests open last week

4620 Add .mypy_cache to the gitignore

4619 added one example to flood fill tutorial

4617 Change math formatting in the docstrings

4615 Fixed wrong behaviour of `exposure.rescale_intensity` for constant input.

4614 Change label2rgb default background value from -1 to 0

4613 Improve loading speed of our gallery by reducing the thumbnail size

4612 Allow very large values in relabel_sequential

4610 Add notes on deprecation warnings in marching_cube_* and gray2rgb

4609 Fix register_translation warning message

4607 Clarify error message when montaging multichannel nD images and multichannel=False

4604 Update min required sphinx version for sphinx-copybutton

4602 Fix typo in cython import_array

4600 Fix broken and permanently moved links

4599 Add example of natsort usage in documentation

4598 Extended existing `equalize_adapthist` implementation (CLAHE) to N dimensions

Closed pull requests (not merged)

4417 Fix rgb2gray docstring to show that 2-D arrays are allowed as inputs

Merged pull requests

4620 Add .mypy_cache to the gitignore

4617 Change math formatting in the docstrings

4615 Fixed wrong behaviour of `exposure.rescale_intensity` for constant input.

4613 Improve loading speed of our gallery by reducing the thumbnail size

4610 Add notes on deprecation warnings in marching_cube_* and gray2rgb

4609 Fix register_translation warning message

4607 Clarify error message when montaging multichannel nD images and multichannel=False

4604 Update min required sphinx version for sphinx-copybutton

4602 Fix typo in cython import_array

4600 Fix broken and permanently moved links

4599 Add example of natsort usage in documentation

4590 Rename convert to _convert, as it is a private function

4585 Update rescale_intensity to prevent under/overflow and produce proper output dtype

4528 Add example code for generating structuring elements.

4502 Move register_translation from skimage.feature to skimage.registration

4496 Fix h_maxima/minima strange behaviors on floating point image input

4467 Complete deprecation of circle in morphsnakes

Older pull requests with new comments or commits

4531 Fixed automatic color generation in label2rgb function

4517 WIP: stub sphinx example to illustrate data type relevance

4515 example: register rotation and scaling with no shared center

4503 Move masked_register_translation from feature to registration

4435 3D Rank Filters WIP

new issues

4621 Does Difference of Gaussian need normalization?

4618 flood_fill and flood are both in segmentation and morphology

4616 Search links broken in dev documentation

4611 Can't load most images from data package

4608 RFC: Support cycle for the upstream and the downstream dependencies

4606 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage

4605 Check in CI whether we can bump the versions of the requirements

4603 Documentation build failure with sphinx 2.4

4601 Discuss gallery structure to bring out bioimaging examples.

4597 `equalize_adapthist` border artifacts still present

4596 `exposure.equalize_adapthist` can fail for constant inputs due to incorrect behavior in `rescale_intensity`

Older issues updated last week

4594 Broken link in `separate_stains` docstring

4544 Simplify the release process

4507 Automatic color generation in the label2rgb function

4486 Calendar of community management

3015 WIP: Turn off relabelling in label2rgb

2761 Generalised existing CLAHE implementation to support n dimensions

Closed issues

4611 Can't load most images from data package

4603 Documentation build failure with sphinx 2.4

4596 `exposure.equalize_adapthist` can fail for constant inputs due to incorrect behavior in `rescale_intensity`

4595 Broken links in docs

4583 funky behavior of `rescale_intensity`

4513 Add example of natsort usage in documentation

4431 Add examples to docstring for structuring elements to visualize the shape

4194 h_maxima/minima strange behaviors on floating point image input

3014 Magic dimensionality guessing in gray2rgb

sciunto on 27 Apr 2020

👍5

All 35 comments

2020/04/06 - 2020/04/12

The script to generate the report below is on https://gist.github.com/emmanuelle/6937f6ad426754d40f5e9bcfdebd013d For now it's only a gist, you need to put your own Github token in the script. There is room for improvement in the script, in particular I use aggressive thresholds to cap the number of queried pull requests and issues (because it takes a lot of time) but we might miss some updates about very old PRs and issues.

Some other comments

The CI was broken at some point on OSX (some Tex issue) but started working again without us having to do anything, but now one of our tests is failing on all python 3.7 (Travis, Azure, Appveyor).
All PRs opened this week have been merged (or closed for a debugging PR) :tada:
It is possible to give your opinion in the RFC issue #4563 about out vs inplace
I added the lists of PRs and issues with traffic (new comments or commits) last week since it can be good candidates for reviews if you find the time
I added a new label "solution: identified" for bug issues where a possible solution is explained. This could be useful for potential contributors. (Even if you don't have the time to work on an issue, explaining how it could be solved is useful).

Many thanks to all reviewers!!

new pull requests open last week

4576 Remove importing skimage.transform as tf

4575 section on registration in gallery

4571 Remove binary specification from match_descriptors docstring

4569 Strip backslash in sphinx 3.0.0

4568 Bump Pywavelets min requirement to 1.1.1

4565 Disable key check for texlive in travis-mac as a temporary workaround

4562 Fix inconsistency in docstring (filters.median)

4561 Remove "backport to 0.14" in github template

4560 Do not enforce pil plugin in skimage.data

closed pull requests (not merged)

4554 Debug plot directive

merged pull requests

4576 Remove importing skimage.transform as tf

4575 section on registration in gallery

4571 Remove binary specification from match_descriptors docstring

4569 Strip backslash in sphinx 3.0.0

4568 Bump Pywavelets min requirement to 1.1.1

4565 Disable key check for texlive in travis-mac as a temporary workaround

4562 Fix inconsistency in docstring (filters.median)

4561 Remove "backport to 0.14" in github template

4560 Do not enforce pil plugin in skimage.data

4512 Fix bool array save with imageio plugin

4470 Fix bool array warping

4438 Deprecate gray scale image support for rgb2gray

4424 Add gray2rgba and deprecate RGBA support in gray2rgb

4416 Fix profile_line interpolation errors

4385 Document geometrical transformations in user guide

4209 Refactor/move neighborhood utility functions in morphology

Older pull requests with new comments or commits

4541 Broken plot in userguide fixed

4531 Fixed automatic color generation in label2rgb function

4528 Add example code for generating structuring elements.

4508 API: Add cross_correlation regularization to register_translation

4503 Move masked_register_translation from feature to registration

4502 Move register_translation from skimage.feature to skimage.registration

4496 Fix h_maxima/minima strange behaviors on floating point image input

4435 3D Rank Filters WIP

4418 Add nD support to colorconv module

4380 Euler number and Crofton perimeter

4307 Manage moments_hu output dtype

4298 Manage iradon input and output data type

4218 Add Minkowski distance metric support to corner_peak

4165 Add function to remove near objects in nd-image

4087 WIP: Allow regionprops to reuse objects

4051 [WIP] Add distance transform function

3850 Add mask support for slic

3772 Compute histograms for multichannel images

3614 removed tophat and bottomhat from filters.rank

new issues

4577 CI fails on Azure for Default-Python-x64-Pre build

4574 Built-images in `data` module don't work [Windows]

4573 Broken CI on OSX

4572 Avoid importing skimage.transform as tf

4570 match_descriptors docstring describes descriptors too narrowly

4567 Relax dimension requirements for structuring elements in morphology?

4566 Signatures in dev API have backslashes before *

4564 Broken travis CI for mac

4563 SKIP: in_place vs out kwarg

4559 Memory leak in CollectionViewer with repeated use

4558 segmentation.find_boundaries: different results for different platforms

closed issues

4574 Built-images in `data` module don't work [Windows]

4573 Broken CI on OSX

4572 Avoid importing skimage.transform as tf

4570 match_descriptors docstring describes descriptors too narrowly

4566 Signatures in dev API have backslashes before *

4564 Broken travis CI for mac

4553 Examples in `doc/examples/registration` are not displayed in the gallery

4511 ValueError raised when bool array saving with imageio plugin

4292 Rescaling boolean arrays yields plausible result or array of zeros depending on the scale factor

4279 Interpolation error in measure.profile_line

3699 Issues with regionprops

3200 Should rgb2gray accept gray images?

older issues updated last week

4557 Add origin argument for morpholgy function using structuring elements

4538 Put our example data on a GitHub pages site

4514 Specify that rgb2lab function is relative only to sRGB colorspace

4454 Make travis fail on warnings

4358 Status of regionprops PRs

4294 Proposal: deprecate `multichannel=` in favour of `channel_axis=`

4261 sdist review (Oct 2019)

4105 Medial axis in 3D / Scale axis transform

3850 Add mask support for slic

3772 Compute histograms for multichannel images

3614 removed tophat and bottomhat from filters.rank

3049 Migrate to travis-ci.com

2761 Generalised existing CLAHE implementation to support n dimensions

2616 WIP: document our guidelines/coding conventions

2613 SKIP: Consistency of `multichannel` parameter handling

2604 SKIP: gray vs grey

2592 peak_local_max fails to enforce min_distance

emmanuelle on 12 Apr 2020

Hi all!

Thanks to @emmanuelle this issue is going to get really long. =P See the output of her script below. I didn't reach her very high standard of merging every PR, but I reckon that's because people are being nitpicky about my brilliant #4585. =P Thanks @emmanuelle in particular for getting our CI green again, that's just excellent.

Could @scikit-image/core comment on the behaviour change picked up by @lagru in: https://github.com/scikit-image/scikit-image/pull/4585/files#r411019161

Thanks!

new pull requests open last week

4593 Recommend cnp.import_array in contribution guide

4592 [CI fix] add import_array in cython files where numpy is cimport-ed

4591 Do not overwrite data module in plot_skeleton.py

4590 Add convert to the API

4589 [MRG] Fix Negative eigenvalue in inertia_tensor_eigvals due to floating point precision

4587 DO NOT MERGE Fix empty image after skeletonize_3D

4586 Revert "Skip extra deps on OSX (#3898)"

4585 Update rescale_intensity to prevent under/overflow and produce proper output dtype

4582 Sort naturally peaks coordinates of same amplitude in peak_local_max

4579 update task in TODO.txt

4578 Add note to remove option in doc config when numpydoc will be patched

closed pull requests (not merged)

4586 Revert "Skip extra deps on OSX (#3898)"

merged pull requests

4593 Recommend cnp.import_array in contribution guide

4592 [CI fix] add import_array in cython files where numpy is cimport-ed

4591 Do not overwrite data module in plot_skeleton.py

4589 [MRG] Fix Negative eigenvalue in inertia_tensor_eigvals due to floating point precision

4582 Sort naturally peaks coordinates of same amplitude in peak_local_max

4579 update task in TODO.txt

4578 Add note to remove option in doc config when numpydoc will be patched

Older pull requests with new comments or commits

4528 Add example code for generating structuring elements.

4502 Move register_translation from skimage.feature to skimage.registration

4496 Fix h_maxima/minima strange behaviors on floating point image input

4467 Complete deprecation of circle in morphsnakes

4435 3D Rank Filters WIP

4418 Add nD support to colorconv module

4228 MAINT+DOC update RELEASE.txt

4218 Add Minkowski distance metric support to corner_peak

4165 Add function to remove near objects in nd-image

3850 Add mask support for slic

new issues

4595 Broken links in docs

4594 Broken link in `separate_stains` docstring

4588 Negative eigenvalue in inertia_tensor_eigvals due to floating point precision

4584 imread published wheels, consider to revert a workaround in travis?

4583 funky behavior of `rescale_intensity`

4581 Merge connectivity resolving helper functions in morphology._util

4580 corner_harris returns peaks in a non "natural" order when the peaks have the same amplitude

older issues updated last week

4559 Memory leak in CollectionViewer with repeated use

4557 Add origin argument for morpholgy function using structuring elements

4540 Broken plot in userguide

4486 Calendar of community management

4154 Define standard common argument's names

4105 Medial axis in 3D

3850 Add mask support for slic

3757 skeletonize_3d produces a zero array in certain conditions

2616 WIP: document our guidelines/coding conventions

closed issues

4588 Negative eigenvalue in inertia_tensor_eigvals due to floating point precision

4584 imread published wheels, consider to revert a workaround in travis?

4580 corner_harris returns peaks in a non "natural" order when the peaks have the same amplitude

4577 CI fails on Azure for Default-Python-x64-Pre build

4436 chroma subsampling not supported

jni on 20 Apr 2020

2020/4/20 - 2020/4/27

Kudos again to @soupault who fixed a ton of broken links in our code: https://github.com/scikit-image/scikit-image/pull/4600

@emmanuelle put the script to generate this report in a repository, so we can easily submit PRs.

I hope I did not missed any other important point.

2020/4/20 - 2020/4/27

New pull requests open last week

4620 Add .mypy_cache to the gitignore

4619 added one example to flood fill tutorial

4617 Change math formatting in the docstrings

4615 Fixed wrong behaviour of `exposure.rescale_intensity` for constant input.

4614 Change label2rgb default background value from -1 to 0

4613 Improve loading speed of our gallery by reducing the thumbnail size

4612 Allow very large values in relabel_sequential

4610 Add notes on deprecation warnings in marching_cube_* and gray2rgb

4609 Fix register_translation warning message

4607 Clarify error message when montaging multichannel nD images and multichannel=False

4604 Update min required sphinx version for sphinx-copybutton

4602 Fix typo in cython import_array

4600 Fix broken and permanently moved links

4599 Add example of natsort usage in documentation

4598 Extended existing `equalize_adapthist` implementation (CLAHE) to N dimensions

Closed pull requests (not merged)

4417 Fix rgb2gray docstring to show that 2-D arrays are allowed as inputs

Merged pull requests

4620 Add .mypy_cache to the gitignore

4617 Change math formatting in the docstrings

4615 Fixed wrong behaviour of `exposure.rescale_intensity` for constant input.

4613 Improve loading speed of our gallery by reducing the thumbnail size

4610 Add notes on deprecation warnings in marching_cube_* and gray2rgb

4609 Fix register_translation warning message

4607 Clarify error message when montaging multichannel nD images and multichannel=False

4604 Update min required sphinx version for sphinx-copybutton

4602 Fix typo in cython import_array

4600 Fix broken and permanently moved links

4599 Add example of natsort usage in documentation

4590 Rename convert to _convert, as it is a private function

4585 Update rescale_intensity to prevent under/overflow and produce proper output dtype

4528 Add example code for generating structuring elements.

4502 Move register_translation from skimage.feature to skimage.registration

4496 Fix h_maxima/minima strange behaviors on floating point image input

4467 Complete deprecation of circle in morphsnakes

Older pull requests with new comments or commits

4531 Fixed automatic color generation in label2rgb function

4517 WIP: stub sphinx example to illustrate data type relevance

4515 example: register rotation and scaling with no shared center

4503 Move masked_register_translation from feature to registration

4435 3D Rank Filters WIP

new issues

4621 Does Difference of Gaussian need normalization?

4618 flood_fill and flood are both in segmentation and morphology

4616 Search links broken in dev documentation

4611 Can't load most images from data package

4608 RFC: Support cycle for the upstream and the downstream dependencies

4606 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage

4605 Check in CI whether we can bump the versions of the requirements

4603 Documentation build failure with sphinx 2.4

4601 Discuss gallery structure to bring out bioimaging examples.

4597 `equalize_adapthist` border artifacts still present

4596 `exposure.equalize_adapthist` can fail for constant inputs due to incorrect behavior in `rescale_intensity`

Older issues updated last week

4594 Broken link in `separate_stains` docstring

4544 Simplify the release process

4507 Automatic color generation in the label2rgb function

4486 Calendar of community management

3015 WIP: Turn off relabelling in label2rgb

2761 Generalised existing CLAHE implementation to support n dimensions

Closed issues

4611 Can't load most images from data package

4603 Documentation build failure with sphinx 2.4

4596 `exposure.equalize_adapthist` can fail for constant inputs due to incorrect behavior in `rescale_intensity`

4595 Broken links in docs

4583 funky behavior of `rescale_intensity`

4513 Add example of natsort usage in documentation

4431 Add examples to docstring for structuring elements to visualize the shape

4194 h_maxima/minima strange behaviors on floating point image input

3014 Magic dimensionality guessing in gray2rgb

sciunto on 27 Apr 2020

👍5

2020/4/27 - 2020/5/4

Thank you @alexdesiqueira who did most of the work. Our CI is still failing because of Cython pre-release, I hope that they have a new pre-release coming soon because it's not nice to have a red CI. I hope that we can release 0.17 this week, I will take care of it with the help of @jni.

4612 is I think ready and waiting for a second approval, it would be great if it could make it for the release.

2020/4/27 - 2020/5/4

New pull requests open last week

4635 Update pooch registry with new file location

4633 MAINT: remove unused cython file

4632 add docstring examples for moments_hu and centroid

4631 random walker: Display a warning when the probability is outsite [0,1] for a given tol

4630 Random walker: minor corrections (typos, comments, added TODO task)

4628 Fix deprecation warnings due to invalid escape sequences.

4627 Userguide: add a visualization chapter

Closed pull requests (not merged)

4587 DO NOT MERGE Fix empty image after skeletonize_3D

Merged pull requests

4635 Update pooch registry with new file location

4630 Random walker: minor corrections (typos, comments, added TODO task)

4628 Fix deprecation warnings due to invalid escape sequences.

4627 Userguide: add a visualization chapter

4614 Change label2rgb default background value from -1 to 0

4598 Extended existing `equalize_adapthist` implementation (CLAHE) to N dimensions

4503 Move masked_register_translation from feature to registration

Older pull requests with new comments or commits

4619 added one example to flood fill tutorial

4612 Allow very large values in relabel_sequential

4468 Added implementation of SSIM max/min algorithm from paper

4435 3D Rank Filters WIP

4418 Add nD support to colorconv module

4390 Lddmm registration

4342 Refactor canny edge detector

4228 MAINT+DOC update RELEASE.txt

4218 Add Minkowski distance metric support to corner_peak

3883 move the location of fast_exp to help compilation with strange flags

3651 Update image's luminance extraction to current recommendation.

3316 Add benchmark suite for weiner and inverse functions

3255 Add benchmarks for morphology.local_maxima

new issues

4637 unsupervised_wiener for RGB images

4636 win_size exceeds image extent. If the input is a multichannel (color) image, set multichannel=True.

4634 Test for availability of the Pooch resources in CI

4629 separate_stains output issue

4626 Image Viewer produces two windows in Jupyter notebook

4625 Optimize gallery images with optipng

4624 [CI] Build broken with cython 3.0a3

Older issues updated last week

4618 flood_fill and flood are both in segmentation and morphology

3883 move the location of fast_exp to help compilation with strange flags

3858 separate_stains output

3651 Update image's luminance extraction to current recommendation.

3316 Add benchmark suite for weiner and inverse functions

3255 Add benchmarks for morphology.local_maxima

3153 Python 3.7 Typing

3009 Fixes for data types and other common sources of errors

2698 RANSAC: Check for updates

2360 Numerical inaccuracies with the random_walker

Closed issues

4636 win_size exceeds image extent. If the input is a multichannel (color) image, set multichannel=True.

4626 Image Viewer produces two windows in Jupyter notebook

4597 `equalize_adapthist` border artifacts still present

3324 Move restoration and color data to the combined data directory

2761 Generalised existing CLAHE implementation to support n dimensions

emmanuelle on 4 May 2020

2020/5/4 - 2020/5/11

As you know last week was a release week and we're still in release-land with 0.17.2 coming up this week (meaning some backports of bug fixes for bugs introduced in 0.17). Apart from release stuff it'd be great to take a look at #3226 (pythran demo)

New pull requests open last week

4678 Backport PR #4651 on branch v0.17.x (Fix doxstring and micro-optimization in SLIC)

4676 Adding new default values to functions on doc/examples/segmentation/plot_ncut

4670 [WIP] Make Pooch lazily create directories for python 3.7+

4668 Add blind Richardson-Lucy deconvolution (supersedes #3524)

4666 Optional pooch dependency

4663 Setup longdesc markdown and switch to 0.18dev

4662 Forget legacy data dir

4661 Fix label2rgb

4658 Add example for 3D adaptive histogram equalization (AHE)

4655 `equalize_adapthist`: More efficient processing scheme with symmetrical padding

4653 DOC: fix broken DOI links

4652 Update version for release

4651 Fix doxstring and micro-optimization in SLIC

4650 Updates to plot_j_invariant.py

4649 release notes for 0.17

4648 Add first biology example: segmentation of human cells with mitosis.

4646 Expose recently introduced map_array function in skimage.util

4645 Fix ArrayMap test

4644 Fix sphinx

4643 Fix CI - cython 3.0a4

4642 AffineTransform: Allow a single value for 'scale' to apply to both sx & sy

4641 DOC: docstring enhancements for Marching cube and find_contours

4640 Refactor ArrayMap.setitem to prevent memory allocation

4639 Fix broken link

4638 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage

Closed pull requests (not merged)

4652 Update version for release

4640 Refactor ArrayMap.setitem to prevent memory allocation

4306 [WIP] Major cleanup to install instructions

Merged pull requests

4676 Adding new default values to functions on doc/examples/segmentation/plot_ncut

4666 Optional pooch dependency

4663 Setup longdesc markdown and switch to 0.18dev

4662 Forget legacy data dir

4661 Fix label2rgb

4653 DOC: fix broken DOI links

4651 Fix doxstring and micro-optimization in SLIC

4650 Updates to plot_j_invariant.py

4649 release notes for 0.17

4646 Expose recently introduced map_array function in skimage.util

4645 Fix ArrayMap test

4644 Fix sphinx

4643 Fix CI - cython 3.0a4

4642 AffineTransform: Allow a single value for 'scale' to apply to both sx & sy

4641 DOC: docstring enhancements for Marching cube and find_contours

4639 Fix broken link

4638 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage

Older pull requests with new comments or commits

4633 MAINT: remove unused cython file

4444 WIP: Move RAGs from future to segmentation

4390 Lddmm registration

4382 Hausdorff Distance (updated)

4342 Refactor canny edge detector

4298 Manage iradon input and output data type

4126 morphology.rectangle() dimensions swapped, Fixes Issue #4125

3524 Blind Richardson–Lucy deconvolution

3329 Fix #3327: Add functionality for benchmark coverage

3226 Tentative pythran support - demo

new issues

4680 Reintroduce `dtype.convert`

4679 Allow for calculation of single property in regionprops

4677 BRIEF fails for float32 data type

4675 ORB detection doesn't work on 32 bit float input

4674 users are forced to upgrade their pip for 0.17

4673 pip3 install failing on Ubuntu 18.04 + Python 3.6

4672 INSTALL.rst confounds enduser installation with development instructions

4671 Skipping tests that depend on pooch is confusing

4669 test_hdx_rgb_roundtrip fails when running multithreaded?

4667 ERROR - sudo pip3 install -U scikit-image

4665 pooch is a hard requirement

4664 PermissionError when creating data_dir when user doesn't have permissions

4660 When running in multi-process Pooch tries to create a directory that already exist

4659 data_dir always falling back to legacy_data_dir

4657 Bugs in label2rgb

4656 Master broken after commit bcd03b4ba147ce00cb646b4fc8c750434213f637

4654 Broken doc examples using label2rgb

4647 Update blacklisted versions for sphinx in requirement.txt

Older issues updated last week

4629 separate_stains output issue

4534 BUG: name of bg_color is not supported in skimage.color.label2rgb

4486 Calendar of community management

4259 Bump numpy to >= 1.16

3620 Adding new ConicSectionModel?

3577 rank filter maximum incorrect doc of output dtype

3539 Port CI from AppVeyor to Azure

3524 Blind Richardson–Lucy deconvolution

3329 Fix #3327: Add functionality for benchmark coverage

3226 Tentative pythran support - demo

3124 Recursive Montage / ND Montage?

3092 Failure in test_spacing_1 on 32-bit Linux builds

3031 Use `plane, row, col` notation in all docstrings

2993 Non-blocking ImageViewer

2815 Restandardize handling of Multi-Image files

2801 Choose 8 as opposed to default of 4-connectivity in measure.regionprops perimeter

2740 Fit output in warp function

2698 RANSAC: Check for updates

2276 Use `plane, row, col` dimensions ordering as specified in the `skimage` conventions page

Closed issues

4673 pip3 install failing on Ubuntu 18.04 + Python 3.6

4665 pooch is a hard requirement

4659 data_dir always falling back to legacy_data_dir

4657 Bugs in label2rgb

4656 Master broken after commit bcd03b4ba147ce00cb646b4fc8c750434213f637

4654 Broken doc examples using label2rgb

4616 Search links broken in dev documentation

4606 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage

4594 Broken link in `separate_stains` docstring

3850 Add mask support for slic

3824 J-invariant denoising

3722 Consider returning segments starting from 1 from SLIC

3684 test_adapthist_grayscale fails on linux 64 and conda

1569 Consider adding mask support for SLIC

emmanuelle on 12 May 2020

2020/5/11 - 2020/5/17

Lots of new documentation and small fixes proposed, some backports and a discussion on our install docs — it would be interesting to have some thoughts from all @scikit-image/core to find a consensus and work on that quickly.

new pull requests open last week

4725 [WIP] Fixing color/colorconv/separate_stains

4724 Remove duplicate fused type definition

4723 Improving register rotation example with notes and references

4718 Backport PR #4713 on branch v0.17.x (Specify the encoding of files opened in the setup phase)

4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)

4714 Anki xyz blind deconvolution

4713 Specify the encoding of files opened in the setup phase

4710 Backport PR #4702 on branch v0.17.x (release notes for 0.17.2)

4709 Backport PR #4706 on branch v0.17.x (Fix gallery example mentioning deprecated argument)

4708 Add pyramid_gaussian support for float32

4706 Fix gallery example mentioning deprecated argument

4704 [WIP] MNT: Use an image fetcher class instead of global variables.

4703 Add exception for PermissionError at data_dir creation

4702 release notes for 0.17.2

4701 Backport PR #4696 on branch v0.17.x (Add pyramid_gaussian support for float32)

4700 Backport PR #4697 on branch v0.17.x (Add ORB full float32 support)

4699 Backport PR #4692 on branch v0.17.x (suppressing warnings from gallery examples)

4698 Backport PR #4691 on branch v0.17.x (Perform todo tasks for 0.17!)

4697 Add ORB full float32 support

4696 Add pyramid_gaussian support for float32

4694 Backport PR #4676 on branch v0.17.x (Adding new default values to functions on doc/examples/segmentation/plot_ncut)

4693 Backport PR #4681 on branch v0.17.x (Reintroduced convert with a strong deprecation warning)

4692 suppressing warnings from gallery examples

4691 Perform todo tasks for 0.17!

4690 Perform some todo tasks for 0.18

4689 In release notes, better describe skimage's relationship to ecosystem

4688 Backport PR #4684 on branch v0.17.x (Add ORB float32 support)

4687 Backport PR #4685 on branch v0.17.x (Add BRIEF float32 support)

4686 Backport PR #4683 on branch v0.17.x (Fix slic float32 support regression)

4685 Add BRIEF float32 support

4684 Add ORB float32 support

4683 Fix slic float32 support regression

4681 Reintroduced convert with a strong deprecation warning

4678 Backport PR #4651 on branch v0.17.x (Fix doxstring and micro-optimization in SLIC)

4676 Adding new default values to functions on doc/examples/segmentation/plot_ncut

closed pull requests (not merged)

4714 Anki xyz blind deconvolution

4701 Backport PR #4696 on branch v0.17.x (Add pyramid_gaussian support for float32)

4668 Add blind Richardson-Lucy deconvolution (supersedes #3524)

merged pull requests

4724 Remove duplicate fused type definition

4718 Backport PR #4713 on branch v0.17.x (Specify the encoding of files opened in the setup phase)

4713 Specify the encoding of files opened in the setup phase

4710 Backport PR #4702 on branch v0.17.x (release notes for 0.17.2)

4709 Backport PR #4706 on branch v0.17.x (Fix gallery example mentioning deprecated argument)

4708 Add pyramid_gaussian support for float32

4706 Fix gallery example mentioning deprecated argument

4702 release notes for 0.17.2

4700 Backport PR #4697 on branch v0.17.x (Add ORB full float32 support)

4699 Backport PR #4692 on branch v0.17.x (suppressing warnings from gallery examples)

4698 Backport PR #4691 on branch v0.17.x (Perform todo tasks for 0.17!)

4697 Add ORB full float32 support

4696 Add pyramid_gaussian support for float32

4694 Backport PR #4676 on branch v0.17.x (Adding new default values to functions on doc/examples/segmentation/plot_ncut)

4693 Backport PR #4681 on branch v0.17.x (Reintroduced convert with a strong deprecation warning)

4692 suppressing warnings from gallery examples

4691 Perform todo tasks for 0.17!

4689 In release notes, better describe skimage's relationship to ecosystem

4688 Backport PR #4684 on branch v0.17.x (Add ORB float32 support)

4687 Backport PR #4685 on branch v0.17.x (Add BRIEF float32 support)

4686 Backport PR #4683 on branch v0.17.x (Fix slic float32 support regression)

4685 Add BRIEF float32 support

4684 Add ORB float32 support

4683 Fix slic float32 support regression

4681 Reintroduced convert with a strong deprecation warning

4678 Backport PR #4651 on branch v0.17.x (Fix doxstring and micro-optimization in SLIC)

4676 Adding new default values to functions on doc/examples/segmentation/plot_ncut

4666 Optional pooch dependency

Older pull requests with new comments or commits

4670 [WIP] Make Pooch lazily create directories for python 3.7+

4658 Add example for 3D adaptive histogram equalization (AHE)

4648 Add first biology example: segmentation of human cells with mitosis.

4631 random walker: Display a warning when the probability is outsite [0,1] for a given tol

3524 Blind Richardson–Lucy deconvolution

new issues

4722 cannot import name 'regionprops_table' from 'skimage.measure'

4721 Install fails on rpi due to missing imagecodecs from tifffile

4720 Error installing scikit-image

4719 Pooch, usability, and the future of examples

4716 Using rag_mean_color and merge_hierarchical with a custom weight_func uses default 'distance' or 'similarity' on first iteration?

4715 Crash on specific computer

4712 Measure region properties (scikit-image) on external images

4711 single scale AffineTransform not supported

4707 contradiction between example and docstring for active contour.

4705 Unable to build on Jetson Nano (arm64): UnicodeDecodeError: 'ascii' codec ...

4695 pyramid_gaussian doesn't support float32

4682 slic float32 support regression

4680 Reintroduce `dtype.convert`

4679 Allow for calculation of single property in regionprops

4677 BRIEF fails for float32 data type

4675 ORB detection doesn't work on 32 bit float input

older issues updated last week

4672 INSTALL.rst confounds enduser installation with development instructions

4671 Skipping tests that depend on pooch is confusing

4664 PermissionError when creating data_dir when user doesn't have permissions

4647 Update blacklisted versions for sphinx in requirement.txt

4629 separate_stains output issue

4486 Calendar of community management

3524 Blind Richardson–Lucy deconvolution

closed issues

4722 cannot import name 'regionprops_table' from 'skimage.measure'

4721 Install fails on rpi due to missing imagecodecs from tifffile

4720 Error installing scikit-image

4715 Crash on specific computer

4705 Unable to build on Jetson Nano (arm64): UnicodeDecodeError: 'ascii' codec ...

4695 pyramid_gaussian doesn't support float32

4682 slic float32 support regression

4680 Reintroduce `dtype.convert`

4679 Allow for calculation of single property in regionprops

4677 BRIEF fails for float32 data type

4675 ORB detection doesn't work on 32 bit float input

4674 users are forced to upgrade their pip for 0.17

4667 ERROR - sudo pip3 install -U scikit-image

4665 pooch is a hard requirement

4660 When running in multi-process Pooch tries to create a directory that already exist

alexdesiqueira on 18 May 2020

2020/05/18 - 2020/05/24

This seemed like a productive week to me. Some highlights:

The CI seems to be working again (see #4735, #4731) and we had another issue with a Cython release (see #3622, addressed in #4730).
A lot of work went into fixing our stain separation (#4725) and how it deals with log artifacts (special thanks to @alexdesiqueira for investigating and to @crisluengo for his insights).
3 new beautiful gallery examples are shaping up: 3D adaptive histogram equalization (#4658), segmentation of human cells (our first biology example, #4648) and an example on trainable segmentation (#4739). The latter two introduce new data files, so https://gitlab.com/scikit-image/data is starting to get some exercise!

The gallery examples mentioned above and #4717 as well as #4734 might be good places to review if you find the time. And we still need someone to take over the community management this week (2020/05/25 - 2020/05/31)!

new pull requests open last week

4747 Turn checklist boxes into bullet points inside the pull request template

4746 Highlight all source lines with HTML doc "source" links (sphinx.ext.linkcode)

4745 Backport NumPy deprecation fixes to v0.17.x

4744 Fix plotting error in j-invariant denoising tutorial

4742 Backport PR #4740 on branch v0.17.x (Unwrap decorators before resolving link to source (sphinx.ext.linkcode))

4740 Unwrap decorators before resolving link to source (sphinx.ext.linkcode)

4739 gallery example on trainable segmentation

4738 Add pooch in requirements/test.txt

4737 Backport PR #4733 on branch v0.17.x (Add versionadded for new scalar type support for "scale" param in transform.AffineTransform)

4735 Fix Ci failures related to array ragged input numpy deprecation

4734 Add Phansalkar local threshold algorithm

4733 Add versionadded for new scalar type support for "scale" param in transform.AffineTransform

4731 Fix CI failures related to conversion of np.floating to dtype

4730 Blacklist cython version 0.29.18

closed pull requests (not merged)

none

merged pull requests

4746 Highlight all source lines with HTML doc "source" links (sphinx.ext.linkcode)

4745 Backport NumPy deprecation fixes to v0.17.x

4744 Fix plotting error in j-invariant denoising tutorial

4742 Backport PR #4740 on branch v0.17.x (Unwrap decorators before resolving link to source (sphinx.ext.linkcode))

4740 Unwrap decorators before resolving link to source (sphinx.ext.linkcode)

4737 Backport PR #4733 on branch v0.17.x (Add versionadded for new scalar type support for "scale" param in transform.AffineTransform)

4735 Fix Ci failures related to array ragged input numpy deprecation

4733 Add versionadded for new scalar type support for "scale" param in transform.AffineTransform

4731 Fix CI failures related to conversion of np.floating to dtype

4730 Blacklist cython version 0.29.18

4725 Fixing color/colorconv/separate_stains

4690 Perform some todo tasks for 0.18

4631 random walker: Display a warning when the probability is outsite [0,1] for a given tol

Older pull requests with new comments or commits

4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)

4658 Add example for 3D adaptive histogram equalization (AHE)

4648 Add first biology example: segmentation of human cells with mitosis.

4435 3D Rank Filters WIP

4390 Lddmm registration

4382 Hausdorff Distance (updated)

new issues

4748 Sphinx gallery issues

4743 Wrong MSE computation in the SSIM code example

4741 Turn checkmarks in pull request templates into bullet points

4736 Blob finding runtime warning

4732 warp on rotated image provides wrong results

4729 RuntimeWarning in blob.py (division by zero)

4728 does scikit-image have C or C++ version code?

4727 Broken CI on py3.8 and Windows following Cython 0.29.18 release

4726 Add `..versionchanged::` tags to all API changes from 0.17

older issues updated last week

4707 contradiction between example and docstring for active contour.

4672 INSTALL.rst confounds enduser installation with development instructions

4621 Does Difference of Gaussian need normalization?

4486 Calendar of community management

3990 Trivial image check for peak_local_max

3892 some edge points not included in points_in_poly result

3547 Allow animations in the documentation

2546 skimage.color.rgb2hed scale not between (-1,1)

closed issues

4732 warp on rotated image provides wrong results

4728 does scikit-image have C or C++ version code?

4727 Broken CI on py3.8 and Windows following Cython 0.29.18 release

4712 Measure region properties (scikit-image) on external images

4711 single scale AffineTransform not supported

4629 separate_stains output issue

3858 separate_stains output

2360 Numerical inaccuracies with the random_walker

2221 docs link to decorator rather than function itself

lagru on 25 May 2020

2020/05/25 - 2020/05/31

Last week looks like a quite week compared to the previous weeks, but as the following highlights shows, things are going very well:

dask related CI failures fixed #4758 (thx @emmanuelle ),
the gallery examples #4648, #4658 are almost ready to enrich the documentation examples,
#4739 now proposes the trainable_segmentation method which is a good candidate for integration in skimage.segmentation,
#4760 may fix all the reported issues concerning peak_local_max but waits for some review,
#4761 needs some more @scikit-image/core members feedback ;)

There is no one in charge for the community management this week, we are still looking for a last minute volunteer ;)

new pull requests open last week

4762 [WIP] wip on viz libraries

4761 Deprecate min_size in remove_small_objects

4760 Refactor and fix peack_local_max

4758 forbid dask 2.17.0 to fix CI

4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max

4752 Deprecate indices in peak_local_max

4751 Optimize peak_local_max trivial image test

4750 Rewrite INSTALL instructions for python novices

closed pull requests (not merged)

4751 Optimize peak_local_max trivial image test

4738 Add pooch in requirements/test.txt

merged pull requests

4758 forbid dask 2.17.0 to fix CI

Older pull requests with new comments or commits

4747 Turn checklist boxes into bullet points inside the pull request template

4739 [WIP] trainable segmentation (algorithm + gallery example)

4734 Add Phansalkar local threshold algorithm

4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)

4658 Add example for 3D adaptive histogram equalization (AHE)

4648 Add first biology example: segmentation of human cells with mitosis.

4435 3D Rank Filters WIP

4390 Lddmm registration

4201 Add rescale_local_mean

4161 Add the iterative Lucas-Kanade (iLK) optical flow method

new issues

4759 Arctan2 being passed arguments in wrong order in Approximate_polygon

4757 CI broken following dask 2.17.0 release

4756 Peaks may not be detected in peak_local_max when label is provided

4755 ImportError in skimage.exposure

4754 Compiling from sources (?)

4749 Deprecate edge cases in peak_local_max

older issues updated last week

4748 Sphinx gallery issues

4741 Turn checkmarks in pull request templates into bullet points

4672 INSTALL.rst confounds enduser installation with development instructions

3990 Trivial image check for peak_local_max

2592 peak_local_max fails to enforce min_distance

closed issues

4757 CI broken following dask 2.17.0 release

4755 ImportError in skimage.exposure

4754 Compiling from sources (?)

2758 `peak_local_max` takes a very long time to complete

rfezzani on 1 Jun 2020

2020/06/01 - 2020/06/08

Not too much activity this week, but several issues related to Mac/Win were described.

new pull requests open last week

4771 Fix random_walker regression

4767 Handle NaNs in phase_cross_correlation

closed pull requests (not merged)

none

merged pull requests

none

Older pull requests with new comments or commits

4739 [WIP] trainable segmentation (algorithm + gallery example)

4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)

4648 Add first biology example: segmentation of human cells with mitosis.

4390 Lddmm registration

4382 Hausdorff Distance (updated)

new issues

4783 [feature request] skimage.feature.greycomatrix should add support for different distances

4782 test_free_reference fails on ppc64le with python 3.6

4781 test_ellipse_rotated fails on python3.8

4780 Getting "ImportError: DLL load failed: The specified module could not be found."

4779 sigma_range not used in denoiser calibration examples

4778 test_hed_rgb_float_roundtrip fails on ppc64le python 3.8

4777 test_uint16 fails on win

4776 test_hed_rgb_roundtrip fails on osx with python3.8 and ppc64le with python 3.6

4775 test_hdx_rgb_roundtrip fail son osx with python 3.8

4774 test_end_points fails on ppc64le with python 3.6, 3.7, 3.8

4773 test_RGB fails on ppc64le with python 3.7

4772 test_periodic_reference fails on ppc64le python 3.7 (conda feedstock)

4770 segmentation.random_walker error, masking problem

4769 _masked_phase_cross_correlation: is it truly a phase cross-correlation?

4768 Broken tests on ppc64le

4766 Missing attribute 'offsets' in skimage.graph.MCP_Geometric

4765 Is cross_correlate_masked() now superseded by phase_cross_correlation() with kwargs?

4764 API inconsistency: phase_cross_correlation does not return error & phasediff

4763 phase_cross_correlation with NaN pixels returns an invalid result

older issues updated last week

4486 Calendar of community management

3306 What's the use of tform.inverse() in transform.PiecewiseAffineTransform?

1131 Tracing the boundary curve of an image region

closed issues

4765 Is cross_correlate_masked() now superseded by phase_cross_correlation() with kwargs?

alexdesiqueira on 9 Jun 2020

👍1

2020/06/09 - 2020/06/15

This week we merged an awesome biology example and fixed random_walker.

new pull requests open last week

4792 Remove unused variable in j invariant docs

4788 try to fix ci which is broken because of pyqt5 last version

closed pull requests (not merged)

none

merged pull requests

4792 Remove unused variable in j invariant docs

4788 try to fix ci which is broken because of pyqt5 last version

4771 Fix random_walker regression

4747 Turn checklist boxes into bullet points inside the pull request template

4648 Add first biology example: segmentation of human cells with mitosis.

Older pull requests with new comments or commits

4767 Handle NaNs in phase_cross_correlation

4761 Deprecate min_size in remove_small_objects

4390 Lddmm registration

4121 Crofton perimeter and Euler number

new issues

4791 Another missing attribute '__reduce_cython__'

4790 how to mark object centroid in the video

4789 how to read properties in regionprops

4787 label2rgb only color the contour not the area

4786 Backport bugfix #4771

4785 test_fixed_reference fails on ppc64le with python 3.7

4784 segmentation.random_walker bug with float32 image, masking and 'bf' optimization

older issues updated last week

4783 [feature request] skimage.feature.greycomatrix should add support for different distances

4780 Getting "ImportError: DLL load failed: The specified module could not be found."

4768 Broken tests on ppc64le

4622 Feature: Weighted phase unwrapping

4499 SIFT patent expired

4486 Calendar of community management

closed issues

4791 Another missing attribute '__reduce_cython__'

4790 how to mark object centroid in the video

4789 how to read properties in regionprops

4787 label2rgb only color the contour not the area

4785 test_fixed_reference fails on ppc64le with python 3.7

4782 test_free_reference fails on ppc64le with python 3.6

4781 test_ellipse_rotated fails on python3.8

4779 sigma_range not used in denoiser calibration examples

4778 test_hed_rgb_float_roundtrip fails on ppc64le python 3.8

4777 test_uint16 fails on win

4776 test_hed_rgb_roundtrip fails on osx with python3.8 and ppc64le with python 3.6

4774 test_end_points fails on ppc64le with python 3.6, 3.7, 3.8

4770 segmentation.random_walker error, masking problem

4741 Turn checkmarks in pull request templates into bullet points

alexdesiqueira on 15 Jun 2020

2020/06/15 - 2020/06/22

Last week highlights:

:tada: @emmanuelle started the huge task of type annotation in #4794.
feedback is needed for #4767, #4739
#4752 and #4379 are almost ready for merge
review still needed for #4760

new pull requests open last week

4795 [WIP] added expand_labels

4794 [wip] add type annotations in some modules in skimage.segmentation

4793 include all md files in manifest.in

4792 Remove unused variable in j invariant docs

closed pull requests (not merged)

none

merged pull requests

4792 Remove unused variable in j invariant docs

Older pull requests with new comments or commits

4767 Handle NaNs in phase_cross_correlation

4761 Deprecate min_size in remove_small_objects

4752 Deprecate indices in peak_local_max

4739 [WIP] trainable segmentation (algorithm + gallery example)

4723 Improving register rotation example with notes and references

4658 Add example for 3D adaptive histogram equalization (AHE)

4619 added one example to flood fill tutorial

4390 Lddmm registration

4382 Hausdorff Distance (updated)

4379 Feret diameter

new issues

4797 API: replace array by image in measure.find_contours()

4796 Cannot upload by imread() files containing char "–"

older issues updated last week

4780 Getting "ImportError: DLL load failed: The specified module could not be found."

4622 Feature: Weighted phase unwrapping

4486 Calendar of community management

3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation

3153 Python 3.7 Typing

3070 Allow passing callable for high and low threshold of Canny

3009 Fixes for data types and other common sources of errors

1131 Tracing the boundary curve of an image region

closed issues

4796 Cannot upload by imread() files containing char "–"

4779 sigma_range not used in denoiser calibration examples

rfezzani on 22 Jun 2020

An average level of activity last week I'd say. The CI is currently broken because of matplotlib pre-release which is annoying, I opened #4805 to discuss our general CI process related to pre-releases. Several open PRs have a good momentum but need some input, for example #4767, #4794, #4739, #4444.

New pull requests open last week

4809 Let biomed example load image data with Pooch.

4807 Change SSIM code example to use real MSE

4806 API change: Replace array by image in measure.find_contour

4804 Add TODO task for sphinx-gallery>=0.9.0 to remove enforced thumbnail_size

4803 Fix runtime warning in blob.py

4800 Use optipng to compress images/thumbnails in our gallery

4798 Remove additional "::" to make plot directive work.

Merged pull requests

4803 Fix runtime warning in blob.py

4798 Remove additional "::" to make plot directive work.

4795 Add expand_labels function to dilate segments while avoiding overlaps

4793 include all md files in manifest.in

Older pull requests with new comments or commits

4794 [wip] add type annotations in some modules in skimage.segmentation

4767 Handle NaNs in phase_cross_correlation

4750 Rewrite INSTALL instructions for python novices

4739 [WIP] trainable segmentation (algorithm + gallery example)

4444 WIP: Move RAGs from future to segmentation

4435 3D Rank Filters WIP

4390 Lddmm registration

4382 Hausdorff Distance (updated)

4121 Crofton perimeter and Euler number

new issues

4808 skimage/feature/censure_cy.c:16073:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? *type = tstate->exc_type;

4805 dev doc is not deployed when pre build is failing on Travis

4802 AttributeError: 'tuple' object has no attribute 'rgb2hsv'

4801 Monitor the decision taken by sphinx-gallery dev on the thumbnail size in future release

4799 Prerelease builds broken by matplotlib 3.3.0rc1

Older issues updated last week

4797 API: replace array by image in measure.find_contours()

4748 Sphinx gallery issues

4486 Calendar of community management

4121 Crofton perimeter and Euler number

Closed issues

4802 AttributeError: 'tuple' object has no attribute 'rgb2hsv'

4729 RuntimeWarning in blob.py (division by zero)

4540 Broken plot in userguide

1780 maximum Feret diameter in regionprops

emmanuelle on 29 Jun 2020

👍1

Hello all! And hello @alexdesiqueira, thanks for picking SciPy week to be on call, a brave move! :sweat_smile:

Here's the summary for last week from @emmanuelle's script. Note that I've modified it to do Monday to Monday at midnight UTC, rather than at whatever time the current maintainer decides to run it. (I'll submit a PR for this tomorrow.) This will make sure that issues etc are always caught by a run of the script.

I'm also going to curate the output to display PRs and issues opened and closed in the same week as ~~crossed out~~, which should give a better sense of how we are doing on response time. And I'll comment on PRs/issues inline below.

Long term, I want to modify the script to produce some data analysis about how we are doing. Response time, sentiment, etc. Ambitious perhaps but I think it would be both motivating and informative!

Ok enough planning:

2020/6/29 - 2020/7/6

New pull requests open last week

4823 Richardson-Lucy deconv: add optional filtering, work in > 2d (:point_left: this one just got in during the weekend and I haven't had a chance to comment, can someone take a look?)

4820 Change feret_diameter to feret_diameter_max (:point_left: needs discussion!)

4819 Simplify equivalent_diameter function (:point_left: mrg+1)

4815 Ensure assert messages from Cython rank filters are informative (:point_left: super simple, should be quick review+merge!)

4812 Tweak threshold_otsu error checking - closes #4811 (:point_left: very close and waiting for second review.)

4810 allow passing extra measurement functions to regionprops and regionprops_table (:point_left: this is very exciting imho and almost ready, just needs some CI to get fixed! Help appreciated tracking it down!)

4809 Let biomed example load image data with Pooch.

Closed pull requests (not merged)

none

Merged pull requests

4809 Let biomed example load image data with Pooch.

4807 Change SSIM code example to use real MSE

4806 API change: Replace array by image in measure.find_contour

4804 Add TODO task for sphinx-gallery>=0.9.0 to remove enforced thumbnail_size

4795 Add expand_labels function to dilate segments while avoiding overlaps (:point_left: some nice new functionality!)

4752 Deprecate indices in peak_local_max

Older pull requests with new comments or commits

4794 add type annotations in some modules in skimage.segmentation (:point_left: this needs comments from the team. What do people think? Do we like type annotations enough to add them everywhere? Or do we want to go with the harder-to-maintain-but-cleaner-to-read annotation stub files?)

4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max

4750 Rewrite INSTALL instructions for python novices (:point_left: sphinx issues, otherwise 100% ready, so if anyone has an inclination to flex their sphinx muscles, this is a great candidate to push over the line!)

4739 [WIP] trainable segmentation (algorithm + gallery example)

4723 Improving register rotation example with notes and references (:point_left: just merged!)

4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)

4619 added one example to flood fill tutorial (:point_left: just merged this now while making these notes! :joy:)

4444 WIP: Move RAGs from future to segmentation (:point_left: I still need to work on debugging this one...!)

4435 3D Rank Filters WIP

new issues

4824 Distance-based discrete interpolation in affine transformation

4822 DeprecationWarning using segmentation.slic

4821 regionprops: rename `equivalent_diameter` -> `equivalent_diameter_area` (:point_left: needs discussion)

4818 Does skimage.feature.haar_like_feature computes all the features?

4817 rename `feret_diameter` -> `max_feret_diameter` ? (:point_left: needs discussion)

4816 skimage.image's ransac function does not handle well when best_inliers are all False

4814 IndexError when calling hough_line_peaks (:point_left: significant bug)

4813 Make level parameter optional in measure.find_contours

4811 threshold_otsu check for single-colour is slow on large arrays

4808 skimage/feature/censure_cy.c:16073:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? *type = tstate->exc_type;

Older issues updated last week

4805 dev doc is not deployed when pre build is failing on Travis

4622 Feature: Weighted phase unwrapping

4199 Work on Transonic for scikit-image kernels: need small help

3412 Is it possible to plot half-ellipses?

Closed issues

4808 skimage/feature/censure_cy.c:16073:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? *type = tstate->exc_type;

4801 Monitor the decision taken by sphinx-gallery dev on the thumbnail size in future release

4797 API: replace array by image in measure.find_contours()

1780 maximum Feret diameter in regionprops

PS

Going through these notes manually, rather than just posting the output, led me to merge two PRs that might have just sat there for months. So it's a really good exercise to go through these slowly at the end of a shift!

Also, thanks to those two merges, we merged 8 PRs this week but 7 were opened, so we are net negative for PRs! :tada: For issues we are +5 so there is some work to be done! :grimacing:

Again, good luck @alexdesiqueira this week! :blush:

jni on 6 Jul 2020

❤1

2020/07/06 - 2020/07/14

Lots of work this week due to our SciPy 2020 sprint. Again, we'd like to thank everyone for your time, discussions and contributions!

new pull requests open last week

4847 [WIP] Adding @eldad-a's ridge directed ring detector

4846 DOC: Add a link to Mayavi example for mesh decimation

4845 DOC: Autoformat docstrings in io.*.py

4844 fix the issue where ransac fails if all the inliers are false and add tests

4843 Github action to build docs

4841 Change structure_tensor to use row/col-notation instead of x/y.

4840 handle color string mapping correctly

4839 Update docstring for rgb2lab

4838 Silence a few RuntimeWarnings in the test suite

4837 Silence several warnings in the test suite

4834 MAINT: import Iterable from collections.abc (Python 3.9 compatibility)

4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings

4826 style: be explicit when stacking arrays

4825 DOC: update subpackage descriptions

4823 Richardson-Lucy deconv: add optional filtering, work in > 2d

closed pull requests (not merged)

4508 API: Add cross_correlation regularization to register_translation

merged pull requests

4846 DOC: Add a link to Mayavi example for mesh decimation

4845 DOC: Autoformat docstrings in io.*.py

4841 Change structure_tensor to use row/col-notation instead of x/y.

4839 Update docstring for rgb2lab

4838 Silence a few RuntimeWarnings in the test suite

4837 Silence several warnings in the test suite

4834 MAINT: import Iterable from collections.abc (Python 3.9 compatibility)

4826 style: be explicit when stacking arrays

4825 DOC: update subpackage descriptions

4820 Change feret_diameter to feret_diameter_max

4819 Simplify equivalent_diameter function

4815 Ensure assert messages from Cython rank filters are informative

4812 Tweak threshold_otsu error checking - closes #4811

4810 allow passing extra measurement functions to regionprops and regionprops_table

4723 Improving register rotation example with notes and references

4619 added one example to flood fill tutorial

Older pull requests with new comments or commits

4800 Use optipng to compress images/thumbnails in our gallery

4794 add type annotations in some modules in skimage.segmentation

4739 [WIP] trainable segmentation (algorithm + gallery example)

4658 Add example for 3D adaptive histogram equalization (AHE)

4655 `equalize_adapthist`: More efficient processing scheme with symmetrical padding

4435 3D Rank Filters WIP

4390 Lddmm registration

3772 Compute histograms for multichannel images

3590 WIP NEW histogram backprojection

3544 Affine Image Registration

new issues

4848 Numpy deprecation warning in convert_to_float()

4842 [doc] width and height order

4836 pyiodide compatibility

4835 KeyError: 'ellipse'

4833 measure.label speed

4832 Future of graph cuts

4831 Work on structure_tensor: gallery example, row/col notation, port to 3D

4830 Key error when using `skimage.measure.find_contours`

4829 equalize_adapthist rescales intensities based on global min/max

4827 `equalize_adapthist` returns input image for clip value of 1.0

4824 Distance-based discrete interpolation in affine transformation

older issues updated last week

4822 DeprecationWarning using segmentation.slic

4818 Does skimage.feature.haar_like_feature computes all the features?

4814 IndexError when calling hough_line_peaks

4813 Make level parameter optional in measure.find_contours

4805 dev doc is not deployed when pre build is failing on Travis

4759 Arctan2 being passed arguments in wrong order in Approximate_polygon

4736 Blob finding runtime warning

4622 Feature: Weighted phase unwrapping

4558 segmentation.find_boundaries: different results for different platforms

4537 Feature request: mesh decimation algorithm

4534 BUG: name of bg_color is not supported in skimage.color.label2rgb

4488 Add a link to forum at the bottom of gallery examples

4486 Calendar of community management

4455 Add definitions to glossary for disk and perimeter

4454 Make travis fail on warnings

4294 Proposal: deprecate `multichannel=` in favour of `channel_axis=`

4284 regionprops_table behaves differently than regionprops list on no-regions found

3772 Compute histograms for multichannel images

3590 WIP NEW histogram backprojection

3547 Allow animations in the documentation

3544 Affine Image Registration

3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation

3412 Is it possible to plot half-ellipses?

3384 Missing scientific (domain-specific) images and corresponding examples and tutorials

2987 WIP: Adds 3D structure tensor capability

2720 Attempting to build documentation on circle-ci

2613 SKIP: Consistency of `multichannel` parameter handling

2563 Warning in local binary pattern if image dtype is not integer

1131 Tracing the boundary curve of an image region

closed issues

4848 Numpy deprecation warning in convert_to_float()

4835 KeyError: 'ellipse'

4817 rename `feret_diameter` -> `max_feret_diameter` ?

4811 threshold_otsu check for single-colour is slow on large arrays

4624 [CI] Build broken with cython 3.0a3

4514 Specify that rgb2lab function is relative only to sRGB colorspace

4466 Feature suggestion: passing user-defined measurement functions to regionprops

1706 added ridge-directed-ring-detector + demo notebook

PS.

@jni:

Going through these notes manually, rather than just posting the output, led me to merge two PRs that might have just sat there for months. So it's a really good exercise to go through these slowly at the end of a shift!

This is a great idea! I tried that in the past, but I couldn't do it effectively yet. I'll try to add it to my process as well.

alexdesiqueira on 14 Jul 2020

2020/7/13 - 2020/7/20

It was the week just after the scipy sprint, so quite a lot of activity. #4844, #4847, #4850, #4852 and #4853 are open PRs resulting from the sprint, so let's keep an eye on them (I think #4844 and #4852 can be merged quite soon). #4850 needs a review (3D tutorial).

Our CI is currently broken due to a matplotlib bug with PYTHONOPTIMIZE=2 (see #4854).

There have been interesting discussions in #4794 about type annotations, I'm thinking of organizing a dev meeting which would discuss specifically this topic.

Please also take a look at the list of "Older pull requests with new comments or commits", some of them would need a round of review.

New pull requests open last week

4853 WIP: Add a boundary tracing algorithm

4852 Dev/GitHub action doc build

4851 added rolling ball algorithm example

4850 Port 3D image processing tutorial into gallery.

4849 DOC: autoformat docstrings of segmentation/*.py

Closed pull requests (not merged)

4843 Github action to build docs

Merged pull requests

4849 DOC: autoformat docstrings of segmentation/*.py

4845 DOC: Autoformat docstrings in io.*.py

4840 handle color string mapping correctly

4823 Richardson-Lucy deconv: add optional filtering, work in > 2d

4820 Change feret_diameter to feret_diameter_max

Older pull requests with new comments or commits

4847 [WIP] Adding @eldad-a's ridge directed ring detector

4844 fix the issue where ransac fails if all the inliers are false and add tests

4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings

4800 Use optipng to compress images/thumbnails in our gallery

4794 add type annotations in some modules in skimage.segmentation

4761 Deprecate min_size in remove_small_objects

4760 Refactor and fix peack_local_max

4739 trainable segmentation (algorithm + gallery example)

4717 Add blind Richardson-Lucy deconvolution (supersedes #3524)

4390 Lddmm registration

4165 Add function to remove near objects in nd-image

3544 Affine Image Registration

new issues

4854 CI fails with PYTHONOPTIMIZE >= 1 due to matplotlib code using docstring

4848 Numpy deprecation warning in convert_to_float()

Older issues updated last week

4836 pyiodide compatibility

4486 Calendar of community management

4165 Add function to remove near objects in nd-image

3544 Affine Image Registration

3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation

3384 Missing scientific (domain-specific) images and corresponding examples and tutorials

Closed issues

4848 Numpy deprecation warning in convert_to_float()

4817 rename `feret_diameter` -> `max_feret_diameter` ?

4534 BUG: name of bg_color is not supported in skimage.color.label2rgb

emmanuelle on 20 Jul 2020

2020/7/20 - 2020/7/27

This week we merged the great 3D AHE example and some documentation on how to contribute with a gallery example. Thanks @m-albert @mkcor!

new pull requests open last week

4861 Update min req for pillow due to CVE-2020-10379 and co.

4859 WIP Restandardize handling of Multi-Image files (rebased #2815)

4857 Document how to contribute a gallery example.

closed pull requests (not merged)

none

merged pull requests

4857 Document how to contribute a gallery example.

4658 Add example for 3D adaptive histogram equalization (AHE)

Older pull requests with new comments or commits

4853 WIP: Add a boundary tracing algorithm

4852 Dev/GitHub action doc build

4851 New: add rolling ball algorithm for background substraction

4850 Port 3D image processing tutorial into gallery.

4847 [WIP] Adding @eldad-a's ridge directed ring detector

4844 fix the issue where ransac fails if all the inliers are false and add tests

4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings

4800 Use optipng to compress images/thumbnails in our gallery

4794 add type annotations in some modules in skimage.segmentation

4760 Refactor and fix peack_local_max

4750 Rewrite INSTALL instructions for python novices

4655 `equalize_adapthist`: More efficient processing scheme with symmetrical padding

4435 3D Rank Filters WIP

4390 Lddmm registration

new issues

4860 Pillow security alert

4858 Proposal: new feature for morphology.skeletonize

4856 Problem in variation of infromation, should we ignore 0 in pred?

4855 Proposal: speed up regionprops region finding

older issues updated last week

4486 Calendar of community management

3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation

3120 Trying to accelerate slic

closed issues

none

alexdesiqueira on 28 Jul 2020

🎉1

2020/8/3 - 2020/8/10

Nice features of the week. We now have doc builds for PRs by @emmanuelle . A 3D dataset has been contributed this week by @GenevieveBuckley which is extremely valuable. I noted also the nice ongoing contribution #4851 by @FirefoxMetzger on background substraction, which received a lot of comments already and for which we must converge anytime soon.

We also have several PRs/issues for documentation and performance issues.

New pull requests open last week

4905 expand the benchmarking section of the developer docs

4904 Fix and improve entropy example

4903 WIP: accelerate the masked slic superpixels algorithm

4901 minor refactoring in phase_cross_correlation

4898 Changelog back-log

4897 Minor edit for proper doc rendering

4896 [WIP] Sphinx gallery thumbnailsoptim

4893 added script for plausible analytics

4892 Contributor guide: add info about gitlab repository for data

4891 Fix benchmarks so they can be run on older scikit-image commits

4888 Fix Incorrect documentation for skimage.util.img_as_int Issue

4886 Raise ValueError if NaN found in phase_cross_correlation result

Closed pull requests (not merged)

4896 [WIP] Sphinx gallery thumbnailsoptim

4882 [WIP] Circleci doc

4767 Handle NaNs in phase_cross_correlation

Merged pull requests

4897 Minor edit for proper doc rendering

4888 Fix Incorrect documentation for skimage.util.img_as_int Issue

4886 Raise ValueError if NaN found in phase_cross_correlation result

4881 build doc on circle ci and link artifact

4875 Fix variation_of_information

4872 DOC: Clarify condition on unique vertices returned by marching cubes

4862 Add default level parameter in measure.find_contours

4852 Build and deploy dev/master documentation using GitHub Actions

4850 Port 3D image processing tutorial into gallery.

4633 MAINT: remove unused cython file

Older pull requests with new comments or commits

4880 Richardson-Lucy deconvolution: allow single-precision computation

4878 Add pre-commit configuration and instructions

4877 Use matplotlib's infinite axline to demonstrate hough transform

4873 Remove unmaintained wiki page link in contributor guidelines

4871 Alternative wording for install guide PR #4750

4863 DOC: First pass at format conversion, rst -> myst

4861 Update min req for pillow due to CVE-2020-10379 and co.

4853 WIP: Add a boundary tracing algorithm

4851 New: add rolling ball algorithm for background substraction

4800 Use optipng to compress images/thumbnails in our gallery

4750 Rewrite INSTALL instructions for python novices

4739 trainable segmentation (algorithm + gallery example)

4435 3D Rank Filters WIP

4390 Lddmm registration

4380 Euler number and Crofton perimeter

new issues

4902 slic is much slower when using a mask

4900 IndexError with util.apply_parallel

4899 Update contributing / core dev notes with more information about CI

4895 Reversed values in entropy example

4894 Algorithm to remove padding / find largest valid sub-image given a mask

4890 Sporadic pooch failures in CI

4889 Add a note in our documentation/on website saying that we have a gitlab repo

4887 Incorrect documentation for skimage.util.img_as_int

4885 Differences between random_noise and numpy.random.poisson

4884 Incorrect deprecation message for `draw.circle`

4883 skimage.segmentation.slic crashes when passed NaNs

Older issues updated last week

4831 Work on structure_tensor: gallery example, row/col notation, port to 3D

4822 DeprecationWarning using segmentation.slic

4537 Feature request: mesh decimation algorithm

4083 Explore performance of parallel Richardson-Lucy deconvolution

3384 Missing scientific (domain-specific) images and corresponding examples and tutorials

3120 Trying to accelerate slic

Closed issues

4887 Incorrect documentation for skimage.util.img_as_int

4856 Problem in variation of infromation, should we ignore 0 in pred?

4842 [doc] width and height order

4813 Make level parameter optional in measure.find_contours

4805 dev doc is not deployed when pre build is failing on Travis

4763 phase_cross_correlation with NaN pixels returns an invalid result

4736 Blob finding runtime warning

2720 Attempting to build documentation on circle-ci

sciunto on 10 Aug 2020

2020/8/10 - 2020/8/17

Quite a busy week for mid-August standard. Alex is introducing a new eagle image and replacing the camera man image by a new one due to license issues. This change might cause some tests to fail, so please pay attention to #4913.

4851 (rolling ball for background substraction) is ready for a round of review. #4390 (lddmm registration) also saw new activity and the API needs to be discussed for this new feature. #4739 (trainable segmentation) is also awaiting a review.

For the coming week we don't have anybody yet registered to be in charge, and same for the following weeks. For this week I can follow up but only until Thursday and then I'm on vacation for 10 days, so we'd need someone else to take over starting from Friday (or for the whole week depending on their availability).

New pull requests open last week

4924 OpenMP support in MSVC

4922 Adding data/eagle.png

4921 Replace words with racial connotations

4920 Declare build dependencies

4913 Replacing data/camera.png due to copyright

4912 Use sparse cross-correlation to accelerate local thresholding functions

4910 Block sphinx versions for which links from search engine are broken

4909 Add versionchanged tag for new opt param in measure.find_contours()

4908 Fix draw.circle/disk deprecation message, fixes #4884

4907 Fix edge filters do not respect padding mode

4906 Fix deprecation message in draw.circle()

Closed pull requests (not merged)

4906 Fix deprecation message in draw.circle()

Merged pull requests

4921 Replace words with racial connotations

4909 Add versionchanged tag for new opt param in measure.find_contours()

4908 Fix draw.circle/disk deprecation message, fixes #4884

4907 Fix edge filters do not respect padding mode

4905 expand the benchmarking section of the developer docs

4904 Fix and improve entropy example

4901 minor refactoring in phase_cross_correlation

4893 added script for plausible analytics

4892 Contributor guide: add info about gitlab repository for data

4891 Fix benchmarks so they can be run on older scikit-image commits

4873 Remove unmaintained wiki page link in contributor guidelines

4863 DOC: First pass at format conversion, rst -> myst

Older pull requests with new comments or commits

4903 WIP: accelerate the masked slic superpixels algorithm

4898 Changelog back-log

4880 Richardson-Lucy deconvolution: allow single-precision computation

4861 Update min req for pillow due to CVE-2020-10379 and co.

4851 New: add rolling ball algorithm for background substraction

4800 Use optipng to compress images/thumbnails in our gallery

4390 Lddmm registration

new issues

4923 CI fails with PYTHONOPTIMIZE=2 due to ipywidgets

4919 scikit-image is not installable from source

4918 Memory corruption in flood_fill

4917 `hough_line_peaks` does not respect `min_distance` argument

4916 A short book has been created from your examples

4915 rgb2gray should work on gray image

4914 Proposing a substitute for cameraman

4911 OpenMP build not supported for MSVC

Older issues updated last week

4900 IndexError with util.apply_parallel (RGB images)

4883 skimage.segmentation.slic crashes when passed NaNs

4876 Terminology: n_jobs vs num_workers vs ncpu etc.

4647 Update blacklisted versions for sphinx in requirement.txt

4486 Calendar of community management

4270 Windows Build of 0.16.2 on python 3.6 seems to be incompatible with numpy 1.15.4

3927 camera(man) image must be removed for license issues

3384 Missing scientific (domain-specific) images and corresponding examples and tutorials

2429 2D image warping via thin-plate splines

Closed issues

4916 A short book has been created from your examples

4914 Proposing a substitute for cameraman

4889 Add a note in our documentation/on website saying that we have a gitlab repo

4884 Incorrect deprecation message for `draw.circle`

4854 CI fails with PYTHONOPTIMIZE >= 1 due to matplotlib code using docstring

emmanuelle on 17 Aug 2020

Lots of infrastructure work this week. Also, data/eagle.png is now available :tada:

new pull requests open last week

4939 Add fluorescence microscopy images to data registry.

4937 Backport PR #4930 on branch v0.17.x (CI: Skip doc build for PYTHONOPTIMIZE=2)

4936 Backport PR #4879 on branch v0.17.x (new matomo config)

4935 Backport PR #4861 on branch v0.17.x (Update min req for pillow due to CVE-2020-10379 and co.)

4932 MAINT: remove numpydoc option, issue fixed in numpydoc 1.0

4931 MAINT: Remove custom fused type in skimage/morphology/_max_tree.pyx

4930 CI: Skip doc build for PYTHONOPTIMIZE=2

4929 Improve description of h_maxima and h_minima functions (#4928)

4927 Fixes to apply_parallel for functions working with multichannel data

4926 swap rectangle variable names

4924 OpenMP support in MSVC

closed pull requests (not merged)

none

merged pull requests

4936 Backport PR #4879 on branch v0.17.x (new matomo config)

4935 Backport PR #4861 on branch v0.17.x (Update min req for pillow due to CVE-2020-10379 and co.)

4932 MAINT: remove numpydoc option, issue fixed in numpydoc 1.0

4931 MAINT: Remove custom fused type in skimage/morphology/_max_tree.pyx

4930 CI: Skip doc build for PYTHONOPTIMIZE=2

4922 Add new high resolution grayscale image data/eagle.png

4880 Richardson-Lucy deconvolution: allow single-precision computation

4861 Update min req for pillow due to CVE-2020-10379 and co.

4844 fix the issue where ransac fails if all the inliers are false and add tests

4800 Use optipng to compress images/thumbnails in our gallery

Older pull requests with new comments or commits

4920 Declare build dependencies

4913 [WIP] Replacing data/camera.png due to copyright

4912 Use sparse cross-correlation to accelerate local thresholding functions

4910 Block sphinx versions for which links from search engine are broken

4903 accelerate the masked slic superpixels algorithm

4898 Changelog back-log

4878 Add pre-commit configuration and instructions

4871 Alternative wording for install guide PR #4750

4859 WIP Restandardize handling of Multi-Image files (rebased #2815)

4853 WIP: Add a boundary tracing algorithm

4851 New: add rolling ball algorithm for background substraction

4847 [WIP] Adding @eldad-a's ridge directed ring detector

4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings

4762 [WIP] wip on viz libraries

4435 3D Rank Filters WIP

4390 Lddmm registration

4126 morphology.rectangle() dimensions swapped, Fixes Issue #4125

new issues

4938 skimage.draw.polygon segmentation fault with np.nan

4934 ipywidgets somehow making Travis fail on py3.6

4933 Deprecate skivi

4928 morphology.extrema.h_maxima and h_minima: slightly confusing function descriptions

4925 `width` and `height` swapped in `morphology.rectangle`

older issues updated last week

4919 scikit-image is not installable from source

4915 rgb2gray should work on gray image

4900 IndexError with util.apply_parallel (RGB images)

4869 `image` description in docstring: towards uniformity?

4786 Backport bugfix #4771

4748 Sphinx gallery issues

4647 Update blocked versions for sphinx in requirement.txt

4537 Feature request: mesh decimation algorithm

4486 Calendar of community management

4407 array or ndarray as argument type documentation?

4259 Bump numpy to >= 1.16

4126 morphology.rectangle() dimensions swapped, Fixes Issue #4125

4081 Consider deprecating `viewer` and `skivi`

3846 Identifying scikit-image incompatibilities with dask input arrays

closed issues

4934 ipywidgets somehow making Travis fail on py3.6

4933 Deprecate skivi

4925 `width` and `height` swapped in `morphology.rectangle`

4923 CI fails with PYTHONOPTIMIZE=2 due to ipywidgets

4895 Reversed values in entropy example

4860 Pillow security alert

4816 skimage.image's ransac function does not handle well when best_inliers are all False

4799 Prerelease builds broken by matplotlib 3.3.0rc1

4625 Optimize gallery images with optipng

3853 References formatting is broken in plot_segmentations

alexdesiqueira on 24 Aug 2020

Last week was quite productive with two bug fixes merged! Thanks to @sciunto we also now deprecate skivi :tada: I would be very happy if we keep moving on this way and soon deprecate skimage.io and skimage.viewer :wink:.

I just finally want to bring your attention to a decision to be taken concerning edge cases of peak_local_max

new pull requests open last week

4953 Add (interactive) slice explorer in plotly.

4952 Provide a public method for iradon_filters

4951 Add missing datasets to public API

4950 DRAFT: Iradon filter tests 2020

4948 Fix corrupt floodfill

4947 modify development version string to allow use with NumpyVersion

4946 Start example using 3D multichannel image.

4945 PERF: improve label speed for bool input by using the scipy.ndimage implementation

4943 Fix draw.polygon segfault caused by 0d input

4942 MAINT: remove deprecated parameter neighbors in measure.label()

4941 Deprecate qt and skivi plugins in skimage.io

4939 Add fluorescence microscopy images to data registry.

closed pull requests (not merged)

4950 DRAFT: Iradon filter tests 2020

4670 [WIP] Make Pooch lazily create directories for python 3.7+

merged pull requests

4947 modify development version string to allow use with NumpyVersion

4945 PERF: improve label speed for bool input by using the scipy.ndimage implementation

4943 Fix draw.polygon segfault caused by 0d input

4942 MAINT: remove deprecated parameter neighbors in measure.label()

4941 Deprecate qt and skivi plugins in skimage.io

4926 swap rectangle variable names

Older pull requests with new comments or commits

4937 Backport PR #4930 on branch v0.17.x (CI: Skip doc build for PYTHONOPTIMIZE=2)

4920 Declare build dependencies

4912 Use sparse cross-correlation to accelerate local thresholding functions

4910 Block sphinx versions for which links from search engine are broken

4853 WIP: Add a boundary tracing algorithm

4851 New: add rolling ball algorithm for background substraction

4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings

4760 Refactor and fix peak_local_max

4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max

4435 3D Rank Filters WIP

4390 Lddmm registration

4215 WIP Accelerate fundamental functions with OpenCL using gputools

new issues

4949 Unable to install on Nvidia Xavier. Stuck at 100%.

4944 Is `filled_area` in measure.regionprop wrong? -> regionprop fails to fill a shape

4940 Add a way to drop rows / columns of un-dividable 2D arrays using 'block_reduce'

4938 skimage.draw.polygon segmentation fault with np.nan

older issues updated last week

4918 Memory corruption in flood_fill

4917 `hough_line_peaks` does not respect `min_distance` argument

4915 rgb2gray should work on gray image

4830 Key error when using `skimage.measure.find_contours`

4749 Deprecate edge cases in peak_local_max

4486 Calendar of community management

4407 array or ndarray as argument type documentation?

4215 WIP Accelerate fundamental functions with OpenCL using gputools

4081 Consider deprecating `viewer` and `skivi`

3099 iradon filter function

2616 WIP: document our guidelines/coding conventions

1131 Tracing the boundary curve of an image region

closed issues

4938 skimage.draw.polygon segmentation fault with np.nan

4833 measure.label speed

4126 morphology.rectangle() dimensions swapped, Fixes Issue #4125

4125 BUG: morphology.rectangle() dimensions swapped

rfezzani on 31 Aug 2020

2020/8/31 - 2020/9/7

During this first week of september, the activity was lower than usual. We had a broken CI for two reasons. With @hmaarrfk we worked on fixing it. There is still issues with OSX jobs on travis caused by a timeout. We added a verbose flag to the command, which helps from time to time, but is not always sufficient. We were unsuccessful applying correctly travis_wait, we must try again. See #4955

I noted activities around PRs on 3D data sets by @mkcor and @hmaarrfk

I also made triage on old issues.

New pull requests open last week

4963 Fix typo.

4962 Alias for data.chelsea: data.cat()

4960 Fix CI: ban sphinx-gallery 0.8.0

4959 TEST - DO NOT MERGE remove lily

4957 PERF: faster Hog computation

4956 CI: Add verbose option to avoid travis timeout for OSX install script

4954 Deprecate viewer and skivi script, will be removed in 0.20

4953 Add (interactive) slice explorer in plotly.

Closed pull requests (not merged)

4959 TEST - DO NOT MERGE remove lily

4750 Rewrite INSTALL instructions for python novices

Merged pull requests

4963 Fix typo.

4960 Fix CI: ban sphinx-gallery 0.8.0

4956 CI: Add verbose option to avoid travis timeout for OSX install script

4954 Deprecate viewer and skivi script, will be removed in 0.20

4945 PERF: improve label speed for bool input by using the scipy.ndimage implementation

4939 Add fluorescence microscopy images to data registry.

4937 Backport PR #4930 on branch v0.17.x (CI: Skip doc build for PYTHONOPTIMIZE=2)

4929 Improve description of h_maxima and h_minima functions (#4928)

4927 Fixes to apply_parallel for functions working with multichannel data

4912 Use sparse cross-correlation to accelerate local thresholding functions

4871 Alternative wording for install guide PR #4750

Older pull requests with new comments or commits

4951 Add missing datasets to public API

4948 Fix corrupt floodfill

4913 [WIP] Replacing data/camera.png due to copyright

4903 accelerate the masked slic superpixels algorithm

4853 WIP: Add a boundary tracing algorithm

4851 New: add rolling ball algorithm for background substraction

4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max

4399 Boost Haar feature calculation for meeting training and real-time inference request

4390 Lddmm registration

4214 Usage of util.apply_parallel in tutorial_parallelization.rst.

3524 Blind Richardson–Lucy deconvolution

3386 Example batch processing

new issues

4961 Raster-to-vector conversion of color images using scikit-image.

4958 CI failure, path issue for windows in gallery

4955 Random frequent CI failures due to tex and travis timeout

Older issues updated last week

4944 measure.regionprop fails to fill a circle, `filled_area` is wrong

4917 `hough_line_peaks` does not respect `min_distance` argument

4537 Feature request: mesh decimation algorithm

4486 Calendar of community management

4214 Usage of util.apply_parallel in tutorial_parallelization.rst.

3927 camera(man) image must be removed for license issues

3524 Blind Richardson–Lucy deconvolution

3386 Example batch processing

2239 Moments documentation is confusing to users

1131 Tracing the boundary curve of an image region

Closed issues

4961 Raster-to-vector conversion of color images using scikit-image.

4958 CI failure, path issue for windows in gallery

4955 Random frequent CI failures due to tex and travis timeout

4949 Unable to install on Nvidia Xavier. Stuck at 100%.

4928 morphology.extrema.h_maxima and h_minima: slightly confusing function descriptions

4900 IndexError with util.apply_parallel (RGB images)

4833 measure.label speed

4822 DeprecationWarning using segmentation.slic

4780 Getting "ImportError: DLL load failed: The specified module could not be found."

4081 Consider deprecating `viewer` and `skivi`

3328 Coverage low hanging fruits

sciunto on 7 Sep 2020

Hi @alexdesiqueira! Here's the report for this week. =) We're -2 on PRs (:tada:) but +1 on issues (:disappointed:). Pretty good week though. :blush:

Note: I manually edited the report below to mark the PRs that were opened and closed this week.

2020/9/7 - 2020/9/14

New pull requests open last week

4973 forbid latest version of pyqt MERGED

4972 Fix floodfill segmentation fault MERGED

4970 MAINT: Remove conditional import on networkx MERGED

4968 MAINT: remove unused imports MERGED

4967 Small enhancement in "Contour finding" example: Removed unused variable n MERGED

4966 Accelerate gamma_adjust for uint8 images MERGED

4965 CI: Use Travis wait improved to avoid timeout for OSX builds MERGED

4964 Delegate standard images load to imageio

Closed pull requests (not merged)

none

Merged older pull requests

4962 Alias for data.chelsea: data.cat()

4948 Fix corrupt floodfill

4903 accelerate the masked slic superpixels algorithm

Older pull requests with new comments or commits

4957 PERF: faster Hog computation

4953 Add (interactive) slice explorer in plotly.

4952 Provide a public method for iradon_filters

4951 Add missing datasets to public API

4913 [WIP] Replacing data/camera.png due to copyright

4851 New: add rolling ball algorithm for background substraction

4761 Deprecate min_size in remove_small_objects

4760 Refactor and fix peak_local_max

4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max

4739 trainable segmentation (algorithm + gallery example)

4435 3D Rank Filters WIP

4390 Lddmm registration

4380 Euler number and Crofton perimeter

4291 New threshold_tpoint function

4161 Add the iterative Lucas-Kanade (iLK) optical flow method

3772 Compute histograms for multichannel images

new issues

4971 Write a piece of documentation on data.download_all() in the install procedure

4969 Tackle remaining todo tasks for 0.18

Older issues updated last week

4902 slic is much slower when using a mask

4890 Sporadic pooch failures in CI

4486 Calendar of community management

4291 New threshold_tpoint function

4161 Add the iterative Lucas-Kanade (iLK) optical flow method

3772 Compute histograms for multichannel images

2704 Gabor filters are not 3-D compatible

2698 RANSAC: Check for updates

2239 Moments documentation is confusing to users

Closed issues

4918 Memory corruption in flood_fill

jni on 14 Sep 2020

🎉1

2020/9/14 – 2020/9/21

I'd consider not too much movement this week (although I was taking care of #4913, so didn't see too much outside that :slightly_smiling_face: ). We had our Atlantic meeting today — with @emmanuelle @jni @grlee77 @lagru @sciunto and myself — preparing for 0.18. Great to see you all!

new pull requests open last week

4974 Remove warnings/explicit settings on feature, restoration

4973 forbid latest version of pyqt

closed pull requests (not merged)

none

merged pull requests

4973 forbid latest version of pyqt

4966 Accelerate gamma_adjust for uint8 images

Older pull requests with new comments or commits

4953 Add (interactive) slice explorer in plotly.

4952 Provide a public method for iradon_filters

4951 Add missing datasets to public API

4913 Replacing data/camera.png due to copyright

4760 Refactor and fix peak_local_max

4753 Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max

4739 trainable segmentation (algorithm + gallery example)

4444 WIP: Move RAGs from future to segmentation

4435 3D Rank Filters WIP

4390 Lddmm registration

4380 Euler number and Crofton perimeter

4161 Add the iterative Lucas-Kanade (iLK) optical flow method

new issues

4979 TypeError: unexpected keyword argument: img_num

4978 skimage.feature.peak_local_max problem

4977 Error using scikit-image

4976 graph module goal_reached method not implemented?

4975 Faster SLIC implementation

older issues updated last week

4971 Write a piece of documentation on data.download_all() in the install procedure

4969 Tackle remaining todo tasks for 0.18

4855 Proposal: speed up regionprops region finding

4486 Calendar of community management

4161 Add the iterative Lucas-Kanade (iLK) optical flow method

3538 Rolling Ball/Sliding Paraboloid Algorithm for background estimation

closed issues

4978 skimage.feature.peak_local_max problem

4977 Error using scikit-image

4976 graph module goal_reached method not implemented?

4902 slic is much slower when using a mask

alexdesiqueira on 22 Sep 2020

2020/9/21 - 2020/9/28

Not a lot of new PRs this week, but I think this is because the core team is busy trying to merge existing ones (the "Older pull requests with new comments or commits") for the 0.18 milestone https://github.com/scikit-image/scikit-image/pulls?q=is%3Aopen+is%3Apr+milestone%3A0.18

We need someone for next week!

New pull requests open last week

4986 try to fix timeout problem with circleci MERGED

4984 Add instructions to download the entire dataset

4983 Docstring improvements for label and regionprops_label CLOSED

4981 3D rank filters (ctd', follow up of 4435) CLOSED

Closed pull requests (not merged)

4981 3D rank filters (ctd', follow up of 4435)

Merged pull requests

4986 try to fix timeout problem with circleci

4983 Docstring improvements for label and regionprops_label

4974 Remove warnings/explicit settings on feature, restoration

4920 Declare build dependencies

Older pull requests with new comments or commits

4924 OpenMP support in MSVC

4913 Replacing data/camera.png due to copyright

4851 New: add rolling ball algorithm for background substraction

4739 trainable segmentation (algorithm + gallery example)

4444 WIP: Move RAGs from future to segmentation

4390 Lddmm registration

4380 Euler number and Crofton perimeter

4161 Add the iterative Lucas-Kanade (iLK) optical flow method

4087 WIP: Allow regionprops to reuse objects

3883 move the location of fast_exp to help compilation with strange flags

new issues

4987 Pyinstaller cannot implement scikit-image

4985 Issue in Structural_Similarity and SSIM MATLAB implementation

4982 ImportError: cannot import name 'phase_cross_correlation' from 'skimage.registration'

4980 phase_cross_correlation does not work with 3D arrays and masks

Older issues updated last week

4883 skimage.segmentation.slic crashes when passed NaNs

4764 API inconsistency: phase_cross_correlation does not return error & phasediff

4486 Calendar of community management

4161 Add the iterative Lucas-Kanade (iLK) optical flow method

4087 WIP: Allow regionprops to reuse objects

3883 move the location of fast_exp to help compilation with strange flags

Closed issues

4985 Issue in Structural_Similarity and SSIM MATLAB implementation

4982 ImportError: cannot import name 'phase_cross_correlation' from 'skimage.registration'

4969 Tackle remaining todo tasks for 0.18

4919 scikit-image is not installable from source

emmanuelle on 29 Sep 2020

2020/9/28 - 2020/10/4

This has been my first week as the person in charge, yay! I'm not sure I've followed everything as closely as I should have; the beginning of the week was pretty quiet.

PS: Just so you know, the utility script for this weekly update spit out "2020/9/28 - 2020/10/5" as the title for this post, and I shamelessly edited to "2020/9/28 - 2020/10/4" (meant to fix the inconsistency, but then I ran out of GitHub API pokes, even though I generated a token, but didn't export it, and anyway... next time). :wink:

New pull requests open last week

5006 Refactoring: threshold methods with histogram parameters

5003 Update sphinx mapping for sklearn and numpy

5002 [WIP] Make structure_tensor support 3d

5001 Update docstring for random_noise function

4999 Update Hough ellipse

4997 Let tifffile.imread handle additional keyword arguments

4992 Catch leftover typos in INSTALL file.

4991 Proofread INSTALL file.

4990 [website] Standardize Documentation index page.

4989 improve Euler number example

Closed pull requests (not merged)

none

Merged pull requests

5003 Update sphinx mapping for sklearn and numpy

5001 Update docstring for random_noise function

4997 Let tifffile.imread handle additional keyword arguments

4992 Catch leftover typos in INSTALL file.

4991 Proofread INSTALL file.

4989 improve Euler number example

4984 Add instructions to download the entire dataset

4913 Replacing data/camera.png due to copyright

Older pull requests with new comments or commits

4953 Add (interactive) slice explorer in plotly.

4946 Start example using 3D multichannel image.

4924 OpenMP support in MSVC

4851 New: add rolling ball algorithm for background substraction

4760 Refactor and fix peak_local_max

4444 WIP: Move RAGs from future to segmentation

new issues

5007 Is the structural similarity index calculated correctly within skimage?

5005 (Windows 10) import skimage.io is not work for me

5004 Expression for speckle noise addition might need correction

5000 Docstring of the function random_noise requires correction

4998 Resizing a binary image as a bool array failed to produced the result as expected.

4996 CI broken on master following tifffile release

4995 Active Contour does not work properly

4994 Not able to install scikit-image

4993 Update documentation to new data.camera()

4988 Add link to API in website homepage

Older issues updated last week

4987 Pyinstaller cannot implement scikit-image

4883 skimage.segmentation.slic crashes when passed NaNs

4868 More default values for parameters

4865 Why is morphology.convex_hull_object 2D only?

4831 Work on structure_tensor: gallery example, row/col notation, port to 3D

4748 Sphinx gallery issues

4486 Calendar of community management

3812 Regionprops for 3D surfaces and perimeters

Closed issues

5000 Docstring of the function random_noise requires correction

4998 Resizing a binary image as a bool array failed to produced the result as expected.

4996 CI broken on master following tifffile release

4995 Active Contour does not work properly

4994 Not able to install scikit-image

4971 Write a piece of documentation on data.download_all() in the install procedure

4161 Add the iterative Lucas-Kanade (iLK) optical flow method

3927 camera(man) image must be removed for license issues

716 Adding a mask parameter to SLIC segmentation

mkcor on 5 Oct 2020

❤2

2020/10/5 - 2020/10/12

Some movement this week. I'll point to #4898, which will help a lot when we release 0.18. #4739 needs some reviews; please check it out if you can.

new pull requests open last week

5018 [WIP] Update documentation to new data.camera()

5017 Fix usage of numpy.pad for old versions of numpy

5016 Bump numpy versions to match scipy (kinda)

5015 Updates to setup.py

5014 Update docstring slic superpixels

5013 Added README to binary (wheel) distribution

5012 Add gallery example for structure_tensor... in 3D!

5010 example with interactive exploration of properties obtained with regionprops

closed pull requests (not merged)

5013 Added README to binary (wheel) distribution

merged pull requests

5017 Fix usage of numpy.pad for old versions of numpy

5010 example with interactive exploration of properties obtained with regionprops

5002 Make structure_tensor support 3d

4990 [website] Standardize Documentation index page.

Older pull requests with new comments or commits

5006 Refactoring: threshold methods with histogram parameters

4999 Update Hough ellipse

4898 Changelog back-log

4760 Refactor and fix peak_local_max

4739 trainable segmentation (algorithm + gallery example)

4390 Lddmm registration

new issues

5019 MemoryError in computing Convex Hull of a large 3D image

5011 No DLL module _fblas when importing skimage.io

5009 AttributeError: module 'skimage' has no attribute 'filters' (On Ubuntu 20.04, conda-forge channel installation)

5008 TypeError: _open() got an unexpected keyword argument 'as_grey'

5007 Is the structural similarity index calculated correctly within skimage?

older issues updated last week

4993 Update documentation to new data.camera()

4883 skimage.segmentation.slic crashes when passed NaNs

4831 Work on structure_tensor: gallery example, row/col notation, port to 3D

4486 Calendar of community management

2591 Divide by Zero Error in exposure.py:465

closed issues

5011 No DLL module _fblas when importing skimage.io

5009 AttributeError: module 'skimage' has no attribute 'filters' (On Ubuntu 20.04, conda-forge channel installation)

5008 TypeError: _open() got an unexpected keyword argument 'as_grey'

5007 Is the structural similarity index calculated correctly within skimage?

5005 (Windows 10) import skimage.io is not work for me

3019 Small bug in skimage.feature.peak_local_max()

1912 MCP_Geometric generates negative cumulative costs

1035 Interpolation: fast code path may yield different results

alexdesiqueira on 13 Oct 2020

Last week was in positive balance with 6 new PR VS 6 merged PR and 4 closed issues VS 3 new ones :tada:. I just want to draw your attention to #5020, #5006, #4760 and #4739 for some review, thank you all :wink:.

new pull requests open last week

5024 Fix IndexError when calling hough_line_peaks with too few angles

5021 bumped plotly requirement for docs

5020 ENH: Reduce memory use for convex_hull_image by checking hull inequalities in sequence

5018 [MRG] Update documentation to new data.camera()

5017 Fix usage of numpy.pad for old versions of numpy

5016 Bump numpy versions to match scipy (kinda)

merged pull requests

5021 bumped plotly requirement for docs

5018 [MRG] Update documentation to new data.camera()

5017 Fix usage of numpy.pad for old versions of numpy

5016 Bump numpy versions to match scipy (kinda)

5014 Update docstring slic superpixels

4898 Changelog back-log

Older pull requests with new comments or commits

5015 Updates to setup.py

5012 Add gallery example for structure_tensor... in 3D!

5006 Refactoring: threshold methods with histogram parameters

4951 Add missing datasets to public API

4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings

4760 Refactor and fix peak_local_max

4739 trainable segmentation (algorithm + gallery example)

new issues

5025 Possible data type issue and unchecked parameter limit with local_binary_pattern

5022 Store pivchallenge data on gitlab

5019 MemoryError in computing Convex Hull of a large 3D image

older issues updated last week

4865 Why is morphology.convex_hull_object 2D only?

closed issues

4993 Update documentation to new data.camera()

3019 Small bug in skimage.feature.peak_local_max()

2591 Divide by Zero Error in exposure.py:465

1912 MCP_Geometric generates negative cumulative costs

rfezzani on 19 Oct 2020

❤1

Thank you @rfezzani! Gotta love paying down that debt! :tada:

I notice another gap in the calendar. I'll take this week. Been wanting to make another push on 0.18! :crossed_fingers:

jni on 19 Oct 2020

2020/10/19 - 2020/10/26

Hi everyone,

Last week was pretty quiet but we still managed to accrue a negative balance. :disappointed: I made a push on #4444 (thank you @emmanuelle for the help there) as well as some issues related to 0.18.

As always, I'd like to point everyone to the list of PRs with one approved review, to see if we can merge some of these soon!

New pull requests open last week

5030 Fixes broken link to CODE_OF_CONDUCT.md

5029 Fix point_in_polygon

5027 Code simplification after latest numpy bump

5026 Deconvolution with Gauss Prior

Closed pull requests (not merged)

none

Merged pull requests

5030 Fixes broken link to CODE_OF_CONDUCT.md

5027 Code simplification after latest numpy bump

Older pull requests with new comments or commits

5020 ENH: Reduce memory use for convex_hull_image by checking hull inequalities in sequence

5006 Refactoring: threshold methods with histogram parameters

4999 Update Hough ellipse

4951 Add missing datasets to public API

4828 Fix equalize_adapthist (CLAHE) for clip value 1.0, fix docstrings

4760 Refactor and fix peak_local_max

4739 trainable segmentation (algorithm + gallery example)

4444 WIP: Move RAGs from future to segmentation

4342 Refactor canny edge detector

3883 move the location of fast_exp to help compilation with strange flags

3329 Fix #3327: Add functionality for benchmark coverage

new issues

5036 Discussion: deprecating (most of) skimage.io in favour of imageio

5035 Idea: additive regionprops

5034 random_walker segmentation can create incorrect laplacian matrix

5033 threshold_li could be sped up by using histogram

5032 Error appeared everytime i ran sckit image

5031 mark_boundaries documentation needs improvement

5028 Remove usage of numpy's private functions

5025 Possible data type issue and unchecked parameter limit with local_binary_pattern

Older issues updated last week

4883 skimage.segmentation.slic crashes when passed NaNs

4486 Calendar of community management

4342 Refactor canny edge detector

3929 skimage.draw.ellipse_perimeter falls into an endless loop

3892 some edge points not included in points_in_poly result

3883 move the location of fast_exp to help compilation with strange flags

3828 "Dilation" of drawing function outputs

3329 Fix #3327: Add functionality for benchmark coverage

Closed issues

jni on 27 Oct 2020

2020/11/02 – 2020/11/09

Please keep an eye on #5053 y'all; we're dropping support to py3.6 and improving machinery for py3.8.

new pull requests open last week

5057 [WIP] Use nep29 to help with the Python 3.6 -> 3.9 transition

5056 Clarify disk documentation inconsistency regarding 'shape'

5055 debug travis build

5054 fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8

5052 update trove classifiers and tests for Python 3.9 + fix pytest config

5050 [ENH] Changing threshold_li using histogram for integer images

5046 [WIP] Drop python 3.6 from the build matrix

5045 [WIP] Automate release process

closed pull requests (not merged)

5055 debug travis build

5046 [WIP] Drop python 3.6 from the build matrix

merged pull requests

5054 fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8

5006 Refactoring: threshold methods with histogram parameters

4760 Refactor and fix peak_local_max

Older pull requests with new comments or commits

4342 Refactor canny edge detector

new issues

5053 dropping 3.6 and a few other things

5051 pip install error: implicit declaration of function 'unwrap2D' is invalid in C99

5049 Missing documentation for ordering of labels in skimage.measure.label

5048 when missing intensity_image, regionprop_table fails with less explicit error message than regionprop

5047 feature.peak_local_max changes labels

older issues updated last week

5038 disk Inconsistency between `shape=None` and `shape=actual_shape`

5036 Discussion: deprecating (most of) skimage.io in favour of imageio

5033 threshold_li could be sped up by using histogram

5028 Remove usage of numpy's private functions

4766 Missing attribute 'offsets' in skimage.graph.MCP_Geometric

4342 Refactor canny edge detector

closed issues

5047 feature.peak_local_max changes labels

4756 Peaks may not be detected in peak_local_max when label is provided

4743 Wrong MSE computation in the SSIM code example

3990 Trivial image check for peak_local_max

2592 peak_local_max fails to enforce min_distance

alexdesiqueira on 10 Nov 2020

2020/11/9 - 2020/11/16

Hello! Since they don't appear below, maybe I should draw our attention to PRs #2815 and #3070 ? Both are in for 0.18 and have one approval at the moment.

New pull requests open last week

5067 reduce OSX build time so that Travis is happy

5062 Optimize ensure_spacing

5059 MAINT Build fix for pyodide

Closed pull requests (not merged)

none

Merged pull requests

5067 reduce OSX build time so that Travis is happy

5006 Refactoring: threshold methods with histogram parameters

Older pull requests with new comments or commits

5057 [WIP] Use nep29 to help with the Python 3.6 -> 3.9 transition

5056 Clarify disk documentation inconsistency regarding 'shape'

5052 update trove classifiers and tests for Python 3.9 + fix pytest config

5050 [ENH] Changing threshold_li using histogram for integer images

4342 Refactor canny edge detector

new issues

5066 OSX build in Travis is taking too long

5065 poetry add scikit-image fails with WinError 123

5064 enable scipy grid-constant boundary handling

5063 pip install scikit-image fails for python3.9 freshly installed with brew

5061 ensure_spacing function may be slow

5060 pip install fails under Python 3.9 if numpy isn't already installed

5058 Frangi/Hessian for Anisotropic Voxel

Older issues updated last week

5053 dropping 3.6 and a few other things

5051 pip install error: implicit declaration of function 'unwrap2D' is invalid in C99

4486 Calendar of community management

4342 Refactor canny edge detector

Closed issues

5063 pip install scikit-image fails for python3.9 freshly installed with brew

1585 Inconsistent 2D vs 3D interpolation behavior for mode 'reflect'

mkcor on 16 Nov 2020

Oups! I am so sorry, I just realized that it was my turn last week :disappointed:

rfezzani on 2 Dec 2020

Oups! I am so sorry, I just realized that it was my turn last week 😞

you will change that emoji to something glad if you realize that your effort will happy a kid in paint by python app and or continue to rescue a father from cancer die by scikit scientific image recognition :)

NinjaAtWork on 2 Dec 2020

😕1

2020/11/30 - 2020/12/7

The last week has mostly been work related to preparing the 0.18 release. In the last few weeks, CI and wheel building jobs were moved off of Travis-CI now that free credits are much more limited. We may keep ARM wheel builds on Travis, but all x86 jobs have been moved elsewhere.

A new proposed feature is installing scikit-image[data] instead of just scikit-image to get an install with the optional pooch dependency included. The lazy importing proposed in #5101 looks like a nice convenience.

Also, there is a request for comments on imagio API imageio/imageio#569 (related to IO offloading issue #5036)

New pull requests open last week

5111 Recent backports from skimage master

5110 Backport PR #5104 on branch v0.18.x (Use v{} for version tags with pooch)

5109 revert bool back to np.bool_ for np.issubdtype calls

5108 Backport PR #5103 on branch v0.18.x (Replace np.bool, np.int, np.float with bool, int, float)

5107 Fix compilation error in XCode 12

5106 Add 0.18 release notes (#5085)

5105 Add data optional reqs to allow pip install scikit-image[data]

5104 Use v{} for version tags with pooch

5103 Replace np.bool, np.int, np.float with bool, int, float

5101 Implement lazy submodule importing

5099 disable Travis-CI builds

5098 Add builds for aarch64

5097 Improvements to CircleCI build: no parallelization and caching

5096 Backport PR #5094 on branch v0.18.x (added link to imagesc forum in example pages)

5094 added link to imagesc forum in example pages

5090 BUG: random_walker: fix import path for umfpack

Closed pull requests (not merged)

none

Merged pull requests

5109 revert bool back to np.bool_ for np.issubdtype calls

5108 Backport PR #5103 on branch v0.18.x (Replace np.bool, np.int, np.float with bool, int, float)

5107 Fix compilation error in XCode 12

5105 Add data optional reqs to allow pip install scikit-image[data]

5104 Use v{} for version tags with pooch

5103 Replace np.bool, np.int, np.float with bool, int, float

5099 disable Travis-CI builds

5097 Improvements to CircleCI build: no parallelization and caching

5096 Backport PR #5094 on branch v0.18.x (added link to imagesc forum in example pages)

5094 added link to imagesc forum in example pages

5090 BUG: random_walker: fix import path for umfpack

4924 OpenMP support in MSVC

Older pull requests with new comments or commits

4762 [WIP] wip on viz libraries

new issues

5112 Feature request: add voxel spacing to skimage.measure.regionprops

5102 feret_diameter_max not available

5100 skimage.measure.label is not working correctly for non binary 3d array

5095 Image License correction

5093 SLIC does not work for grayscale images, or RGB with convert2lab = False

5092 issue: centroid property of skimage.measure.regionprops is outside of regions

5091 Building from source on master fails on Windows 10.0.19041

Older issues updated last week

5087 Feature request: points to labels

5036 Discussion: deprecating (most of) skimage.io in favour of imageio

4537 Feature request: mesh decimation algorithm

4507 Automatic color generation in the label2rgb function

4486 Calendar of community management

Closed issues

5100 skimage.measure.label is not working correctly for non binary 3d array

5093 SLIC does not work for grayscale images, or RGB with convert2lab = False

5066 OSX build in Travis is taking too long

5051 pip install error: implicit declaration of function 'unwrap2D' is invalid in C99

4890 Sporadic pooch failures in CI

4488 Add a link to forum at the bottom of gallery examples

grlee77 on 7 Dec 2020

2020/12/07 - 2020/12/15

Lots of movement this week as we (as in @jni :slightly_smiling_face:) prepare our 0.18 release! Thank you all for your hard work!

new pull requests open last week

5137 Update release notes with latest backports

5136 Backport PR #5126 on branch v0.18.x (Proofread gallery example for rank filters.)

5135 Backport PR #5062 on branch v0.18.x (Optimize ensure_spacing)

5134 Improve error message when installing from source and cython isn't installed.

5133 Backport PR #5131 on branch v0.18.x (consistent zoom boundary behavior across SciPy versions)

5132 Backport PR #2815 on branch v0.18.x (Restandardize handling of Multi-Image files)

5131 consistent zoom boundary behavior across SciPy versions

5129 Backport PR #5128 on branch v0.18.x (Add farid filters in all, to populate the documentation)

5128 Add farid filters in all, to populate the documentation

5126 Proofread gallery example for rank filters.

5125 Backport PR #5117 on branch v0.18.x (Remove Python 3.6 support)

5123 Backport PR #5115 on branch v0.18.x (change plausible script to track outbound links)

5120 example to show the 3d dataset

5119 Backport PR #5097 on branch v0.18.x (Improvements to CircleCI build: no parallelization and caching)

5118 Backport PR #5116 on branch v0.18.x (added missing datasets to gallery examples)

5117 Remove Python 3.6 support

5116 added missing datasets to gallery examples

5115 change plausible script to track outbound links

5114 Deprecate high_threshold and low_threshold in canny

5113 Update release notes with latest backported changes from master

5111 Recent backports from skimage master

5110 Backport PR #5104 on branch v0.18.x (Use v{} for version tags with pooch)

closed pull requests (not merged)

5114 Deprecate high_threshold and low_threshold in canny

merged pull requests

5137 Update release notes with latest backports

5136 Backport PR #5126 on branch v0.18.x (Proofread gallery example for rank filters.)

5135 Backport PR #5062 on branch v0.18.x (Optimize ensure_spacing)

5134 Improve error message when installing from source and cython isn't installed.

5133 Backport PR #5131 on branch v0.18.x (consistent zoom boundary behavior across SciPy versions)

5132 Backport PR #2815 on branch v0.18.x (Restandardize handling of Multi-Image files)

5131 consistent zoom boundary behavior across SciPy versions

5129 Backport PR #5128 on branch v0.18.x (Add farid filters in all, to populate the documentation)

5128 Add farid filters in all, to populate the documentation

5126 Proofread gallery example for rank filters.

5125 Backport PR #5117 on branch v0.18.x (Remove Python 3.6 support)

5123 Backport PR #5115 on branch v0.18.x (change plausible script to track outbound links)

5119 Backport PR #5097 on branch v0.18.x (Improvements to CircleCI build: no parallelization and caching)

5118 Backport PR #5116 on branch v0.18.x (added missing datasets to gallery examples)

5117 Remove Python 3.6 support

5116 added missing datasets to gallery examples

5115 change plausible script to track outbound links

5113 Update release notes with latest backported changes from master

5111 Recent backports from skimage master

5110 Backport PR #5104 on branch v0.18.x (Use v{} for version tags with pooch)

5108 Backport PR #5103 on branch v0.18.x (Replace np.bool, np.int, np.float with bool, int, float)

5107 Fix compilation error in XCode 12

5106 Add 0.18 release notes (#5085)

5105 Add data optional reqs to allow pip install scikit-image[data]

5104 Use v{} for version tags with pooch

5062 Optimize ensure_spacing

Older pull requests with new comments or commits

4953 Add (interactive) slice explorer in plotly.

4201 Add rescale_local_mean

new issues

5140 upgrade from 0.16.2 to 0.17.2 destroys skimage.external

5139 Potential optimisation need in new 3D warps code

5138 phase_cross_correlation returns only 1 argument in the masked case

5130 pre builds broken by scipy 1.6.0rc1

5127 Confusing error message when Cython is not installed

5124 Possible bug in label connected regions in large volume crushes all kernel

5122 Feature request: Draw line with specific width

5121 Pip3 install of scikit-image fails for Python 3.9 on macOS 10.15 (Catalina)

5112 Feature request: add voxel spacing to skimage.measure.regionprops

older issues updated last week

5095 Image License correction

5065 poetry add scikit-image fails with WinError 123

4544 Simplify the release process

4507 Automatic color generation in the label2rgb function

4486 Calendar of community management

4201 Add rescale_local_mean

3070 Allow passing callable for high and low threshold of Canny

closed issues

5130 pre builds broken by scipy 1.6.0rc1

5127 Confusing error message when Cython is not installed

5121 Pip3 install of scikit-image fails for Python 3.9 on macOS 10.15 (Catalina)

5102 feret_diameter_max not available

5100 skimage.measure.label is not working correctly for non binary 3d array

5088 filters.farid missing from skimage.filters documentation

5061 ensure_spacing function may be slow

5053 dropping 3.6 and a few other things

5051 pip install error: implicit declaration of function 'unwrap2D' is invalid in C99

4890 Sporadic pooch failures in CI

2815 Restandardize handling of Multi-Image files

alexdesiqueira on 15 Dec 2020

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Scikit-image: Calendar of community management

Most helpful comment

2020/4/20 - 2020/4/27

2020/4/20 - 2020/4/27

New pull requests open last week

4620 Add .mypy_cache to the gitignore

4619 added one example to flood fill tutorial

4617 Change math formatting in the docstrings

4615 Fixed wrong behaviour of exposure.rescale_intensity for constant input.

4614 Change label2rgb default background value from -1 to 0

4613 Improve loading speed of our gallery by reducing the thumbnail size

4612 Allow very large values in relabel_sequential

4610 Add notes on deprecation warnings in marching_cube_* and gray2rgb

4609 Fix register_translation warning message

4607 Clarify error message when montaging multichannel nD images and multichannel=False

4604 Update min required sphinx version for sphinx-copybutton

4602 Fix typo in cython import_array

4600 Fix broken and permanently moved links

4599 Add example of natsort usage in documentation

4598 Extended existing equalize_adapthist implementation (CLAHE) to N dimensions

Closed pull requests (not merged)

4417 Fix rgb2gray docstring to show that 2-D arrays are allowed as inputs

Merged pull requests

4620 Add .mypy_cache to the gitignore

4617 Change math formatting in the docstrings

4615 Fixed wrong behaviour of exposure.rescale_intensity for constant input.

4613 Improve loading speed of our gallery by reducing the thumbnail size

4610 Add notes on deprecation warnings in marching_cube_* and gray2rgb

4609 Fix register_translation warning message

4607 Clarify error message when montaging multichannel nD images and multichannel=False

4604 Update min required sphinx version for sphinx-copybutton

4602 Fix typo in cython import_array

4600 Fix broken and permanently moved links

4599 Add example of natsort usage in documentation

4590 Rename convert to _convert, as it is a private function

4585 Update rescale_intensity to prevent under/overflow and produce proper output dtype

4528 Add example code for generating structuring elements.

4502 Move register_translation from skimage.feature to skimage.registration

4496 Fix h_maxima/minima strange behaviors on floating point image input

4467 Complete deprecation of circle in morphsnakes

Older pull requests with new comments or commits

4531 Fixed automatic color generation in label2rgb function

4517 WIP: stub sphinx example to illustrate data type relevance

4515 example: register rotation and scaling with no shared center

4503 Move masked_register_translation from feature to registration

4435 3D Rank Filters WIP

new issues

4621 Does Difference of Gaussian need normalization?

4618 flood_fill and flood are both in segmentation and morphology

4616 Search links broken in dev documentation

4611 Can't load most images from data package

4608 RFC: Support cycle for the upstream and the downstream dependencies

4606 Misleading "ValueError: Input array has to be either 3- or 4-dimensional" in montage

4605 Check in CI whether we can bump the versions of the requirements

4603 Documentation build failure with sphinx 2.4

4601 Discuss gallery structure to bring out bioimaging examples.

4597 equalize_adapthist border artifacts still present

4596 exposure.equalize_adapthist can fail for constant inputs due to incorrect behavior in rescale_intensity

Older issues updated last week

4594 Broken link in separate_stains docstring

4544 Simplify the release process

4507 Automatic color generation in the label2rgb function

4486 Calendar of community management

3015 WIP: Turn off relabelling in label2rgb

2761 Generalised existing CLAHE implementation to support n dimensions

Closed issues

4611 Can't load most images from data package

4603 Documentation build failure with sphinx 2.4

4596 exposure.equalize_adapthist can fail for constant inputs due to incorrect behavior in rescale_intensity

4595 Broken links in docs

4583 funky behavior of rescale_intensity

4513 Add example of natsort usage in documentation

4431 Add examples to docstring for structuring elements to visualize the shape

4194 h_maxima/minima strange behaviors on floating point image input

3014 Magic dimensionality guessing in gray2rgb

All 35 comments

2020/04/06 - 2020/04/12

new pull requests open last week

4576 Remove importing skimage.transform as tf

4575 section on registration in gallery

4615 Fixed wrong behaviour of `exposure.rescale_intensity` for constant input.

4598 Extended existing `equalize_adapthist` implementation (CLAHE) to N dimensions

4615 Fixed wrong behaviour of `exposure.rescale_intensity` for constant input.

4597 `equalize_adapthist` border artifacts still present

4596 `exposure.equalize_adapthist` can fail for constant inputs due to incorrect behavior in `rescale_intensity`

4594 Broken link in `separate_stains` docstring

4596 `exposure.equalize_adapthist` can fail for constant inputs due to incorrect behavior in `rescale_intensity`

4583 funky behavior of `rescale_intensity`

4574 Built-images in `data` module don't work [Windows]

4574 Built-images in `data` module don't work [Windows]

4553 Examples in `doc/examples/registration` are not displayed in the gallery