Skip to content

@grlee77 grlee77 released this Aug 24, 2021

scikit-image 0.18.3

This is a small bugfix release for compatibility with Pooch 1.5 and SciPy 1.7.

Bug fixes

  • Only import from Pooch's public API. This resolves an import failure with
    Pooch 1.5.0. (#5531, backport of #5529)
  • Do not use deprecated scipy.linalg.pinv2 in random_walker when
    using the multigrid solver. (#5531, backport of #5437)
Assets 2

@sciunto sciunto released this Jan 19, 2021

scikit-image 0.18.1

This is a bug fix release and contains the following two bug fixes:

  • Fix indexing error for labelling in large (>2GB) arrays (#5143, #5151)
  • Only use retry_if_failed with recent pooch (#5148)

See below for the new features and API changes in 0.18.0.

Announcement: scikit-image 0.18.0

We're happy to announce the release of scikit-image v0.18.0!

scikit-image is an image processing toolbox for SciPy that includes algorithms
for segmentation, geometric transformations, color space manipulation,
analysis, filtering, morphology, feature detection, and more.

This release of scikit-image drops support for Python 3.6 in accordance with
the NEP-29 Python and Numpy version support community standard <https://numpy.org/neps/nep-0029-deprecation_policy.html>_: Python 3.7 or
newer is required to run this version.

For more information, examples, and documentation, please visit our website:

https://scikit-image.org

New Features

  • Add the iterative Lucas-Kanade (iLK) optical flow method (#4161)
  • Add Feret diameter in region properties (#4379, #4820)
  • Add functions to compute Euler number and Crofton perimeter estimation (#4380)
  • Add a function to compute the Hausdorff distance (#4382)
  • Added 3D support for many filters in skimage.filters.rank.
  • An experimental implementation of trainable pixel segmentation, aiming for
    compatibility with the scikit-learn API, has been added to
    skimage.future. Try it out! (#4739)
  • Add a new function segmentation.expand_labels to dilate labels while
    preventing overlap (#4795)
  • It is now possible to pass extra measurement functions to
    measure.regionprops and regionprops_table (#4810)
  • Add rolling ball algorithm for background subtraction (#4851)
  • New sample images have been added in the data subpackage: data.eagle
    (#4922), data.human_mitosis (#4939), data.cells3d (#4951), and
    data.vortex (#5041). Also note that the image for data.camera has
    been changed due to copyright issues (#4913).
  • skimage.feature.structure_tensor now supports 3D (and nD) images as input
    (#5002)
  • Many thresholding methods can now receive a precomputed histogram as input,
    resulting in significant speedups if multiple methods are tried on the same
    image, or if a fast histogram method is used. (#5006)
  • measure.regionprops now supports multichannel intensity images (#5037)

Documentation

  • Add an example to the flood fill tutorial (#4619)
  • Docstring enhancements for marching cubes and find_contours (#4641)
  • A new tutorial presenting a cell biology example has been added to the
    gallery (#4648). Special thanks to Pierre Poulain and Fred Bernard
    (Université de Paris and Institut Jacques Monod) for scientific review of
    this example!
  • Improve register rotation example with notes and references (#4723)
  • Add versionadded for new scalar type support for "scale" param in
    transform.AffineTransform (#4733)
  • New tutorial on visualizing 3D data <https://scikit-image.org/docs/dev/auto_examples/applications/plot_3d_image_processing.html>_ (#4850)
  • Add example for 3D adaptive histogram equalization (AHE) (#4658)
  • Automatic formatting of docstrings for improved consistency (#4849)
  • Improved docstring for rgb2lab (#4839) and marching_cubes (#4846)
  • Improved docstring for measure.marching_cubes, mentioning how to decimate a
    mesh using mayavi (#4846)
  • Document how to contribute a gallery example. (#4857)
  • Fix and improve entropy example (#4904)
  • expand the benchmarking section of the developer docs (#4905)
  • Improved docstring for util.random_noise (#5001)
  • Improved docstrings for morphology.h_maxima and morphology.h_minima
    (#4929).
  • Improved docstring for util.img_as_int (#4888).
  • A new example demonstrates interactive exploration of regionprops results
    using the PyData stack (pandas, seaborn) at
    https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_regionprops.html`_
    (#5010).
  • Documentation has been added to explain
    how to download example datasets <https://scikit-image.org/docs/dev/install.html#downloading-all-demo-datasets>_
    which are not installed with scikit-image (#4984). Similarly, the contributor
    guide has been updated to mention how to host new datasets in a gitlab
    repository (#4892).
  • The benchmarking section of the developer documentation <https://scikit-image.org/docs/dev/contribute.html#benchmarks>_
    has been expanded (#4905).
  • Added links to the image.sc forum in example pages (#5094, #5096)
  • Added missing datasets to gallery examples (#5116, #5118)
  • Add farid filters in all, to populate the documentation (#5128, #5129)
  • Proofread gallery example for rank filters. (#5126, #5136)

Improvements

  • float32 support for SLIC (#4683), ORB (#4684, #4697), BRIEF (#4685),
    pyramid_gaussian (#4696), Richardson-Lucy deconvolution (#4880)
  • In skimage.restoration.richardson_lucy, computations are now done in
    single-precision when the input image is single-precision. This can give a
    substantial performance improvement when working with single precision data.
  • Richardson-Lucy deconvolution now has a filter_epsilon keyword argument
    to avoid division by very small numbers (#4823)
  • Add default level parameter (max-min) / 2 in measure.find_contours (#4862)
  • The performance of the SLIC superpixels algorithm
    (skimage.segmentation.slice) was improved for the case where a mask
    is supplied by the user (#4903). The specific superpixels produced by
    masked SLIC will not be identical to those produced by prior releases.
  • exposure.adjust_gamma has been accelerated for uint8 images by using
    a look-up table (LUT) (#4966).
  • measure.label has been accelerated for boolean input images, by using
    scipy.ndimage's implementation for this case (#4945).
  • util.apply_parallel now works with multichannel data (#4927).
  • skimage.feature.peak_local_max supports now any Minkowski distance.
  • We now use sparse cross-correlation to accelerate local thresholding
    functions (#4912)
  • morphology.convex_hull_image now uses much less memory by checking hull
    inequalities in sequence (#5020)
  • Polygon rasterization is more precise and will no longer potentially exclude
    input vertices. (#5029)
  • Add data optional requirements to allow pip install scikit-image[data]
    (#5105, #5111)
  • OpenMP support in MSVC (#4924, #5111)
  • Restandardize handling of Multi-Image files (#2815, #5132)
  • Consistent zoom boundary behavior across SciPy versions (#5131, #5133)

API Changes

  • skimage.restoration.richardson_lucy returns a single-precision output
    when the input is single-precision. Prior to this release, double-precision
    was always used. (#4880)
  • The default value of threshold_rel in skimage.feature.corner has
    changed from 0.1 to None, which corresponds to letting
    skimage.feature.peak_local_max decide on the default. This is currently
    equivalent to threshold_rel=0.
  • In measure.label, the deprecated neighbors parameter has been
    removed. (#4942)
  • The image returned by data.camera has changed because of copyright
    issues (#4913).

Bug fixes

  • A bug in label2rgb has been fixed when the input image had np.uint8
    dtype (#4661)
  • Fixed incorrect implementation of skimage.color.separate_stains (#4725)
  • Many bug fixes have been made in peak_local_max (#2592, #4756, #4760,
    #5047)
  • Fix bug in random_walker when input labels have negative values (#4771)
  • PSF flipping is now correct for Richardson-Lucy deconvolution work in >2D (#4823)
  • Fix equalize_adapthist (CLAHE) for clip value 1.0 (#4828)
  • For the RANSAC algorithm, improved the case where all data points are
    outliers, which was previously raising an error
    (#4844)
  • An error-causing bug has been corrected for the bg_color parameter in
    label2rgb when its value is a string (#4840)
  • A normalization bug was fixed in metrics.variation_of_information
    (#4875)
  • Euler characteristic property of skimage.measure.regionprops was erroneous
    for 3D objects, since it did not take tunnels into account. A new implementation
    based on integral geometry fixes this bug (#4380).
  • In skimage.morphology.selem.rectangle the height argument
    controlled the width and the width argument controlled the height.
    They have been replaced with nrow and ncol. (#4906)
  • skimage.segmentation.flood_fill and skimage.segmentation.flood
    now consistently handle negative values for seed_point.
  • Segmentation faults in segmentation.flood have been fixed (#4948, #4972)
  • A segfault in draw.polygon for the case of 0-d input has been fixed
    (#4943).
  • In registration.phase_cross_correlation, a ValueError is raised when
    NaNs are found in the computation (as a result of NaNs in input images).
    Before this fix, an incorrect value could be returned where the input images
    had NaNs (#4886).
  • Fix edge filters not respecting padding mode (#4907)
  • Use v{} for version tags with pooch (#5104, #5110)
  • Fix compilation error in XCode 12 (#5107, #5111)

Deprecations

  • The indices argument in skimage.feature.peak_local_max has been
    deprecated. Indices will always be returned. (#4752)
  • In skimage.feature.structure_tensor, an order argument has been
    introduced which will default to 'rc' starting in version 0.20. (#4841)
  • skimage.feature.structure_tensor_eigvals has been deprecated and will be
    removed in version 0.20. Use skimage.feature.structure_tensor_eigenvalues
    instead.
  • The skimage.viewer subpackage and the skivi script have been
    deprecated and will be removed in version 0.20. For interactive visualization
    we recommend using dedicated tools such as napari <https://napari.org>_ or
    plotly <https://plotly.com>_. In a similar vein, the qt and skivi
    plugins of skimage.io have been deprecated
    and will be removed in version 0.20. (#4941, #4954)
  • In skimage.morphology.selem.rectangle the arguments width and
    height have been deprecated. Use nrow and ncol instead.
  • The explicit setting threshold_rel=0` was removed from the Examples of the following docstrings: skimage.feature.BRIEF, skimage.feature.corner_harris, skimage.feature.corner_shi_tomasi, skimage.feature.corner_foerstner, skimage.feature.corner_fast, skimage.feature.corner_subpix, skimage.feature.corner_peaks, skimage.feature.corner_orientations, and skimage.feature._detect_octave``.
  • In skimage.restoration._denoise, the warning regarding
    rescale_sigma=None was removed.
  • In skimage.restoration._cycle_spin, the # doctest: +SKIP was removed.

Development process

  • Fix #3327: Add functionality for benchmark coverage (#3329)
  • Release process notes have been improved. (#4228)
  • pyproject.toml has been added to the sdist.
  • Build and deploy dev/master documentation using GitHub Actions (#4852)
  • Website now deploys itself (#4870)
  • build doc on circle ci and link artifact (#4881)
  • Benchmarks can now run on older scikit-image commits (#4891)
  • Website analytics are tracked using plausible.io and can be visualized on
    https://plausible.io/scikit-image.org (#4893)
  • Artifacts for the documentation build are now found in each pull request
    (#4881).
  • Documentation source files can now be written in Markdown in addition to
    ReST, thanks to myst (#4863).
  • update trove classifiers and tests for Python 3.9 + fix pytest config (#5052)
  • fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8 (#5054)
  • Moved our testing from Travis to GitHub Actions (#5074)
  • We now build our wheels on GitHub Actions on the main repo using
    cibuildwheel. Many thanks to the matplotlib and scikit-learn developers for
    paving the way for us! (#5080)
  • Disable Travis-CI builds (#5099, #5111)
  • Improvements to CircleCI build: no parallelization and caching) (#5097, #5119)

Other Pull Requests

  • Manage iradon input and output data type (#4298)
  • random walker: Display a warning when the probability is outsite [0,1] for a given tol (#4631)
  • MAINT: remove unused cython file (#4633)
  • Forget legacy data dir (#4662)
  • Setup longdesc markdown and switch to 0.18dev (#4663)
  • Optional pooch dependency (#4666)
  • Adding new default values to functions on doc/examples/segmentation/plot_ncut (#4676)
  • Reintroduced convert with a strong deprecation warning (#4681)
  • In release notes, better describe skimage's relationship to ecosystem (#4689)
  • Perform some todo tasks for 0.18 (#4690)
  • Perform todo tasks for 0.17! (#4691)
  • suppressing warnings from gallery examples (#4692)
  • release notes for 0.17.2 (#4702)
  • Fix gallery example mentioning deprecated argument (#4706)
  • Specify the encoding of files opened in the setup phase (#4713)
  • Remove duplicate fused type definition (#4724)
  • Blacklist cython version 0.29.18 (#4730)
  • Fix CI failures related to conversion of np.floating to dtype (#4731)
  • Fix Ci failures related to array ragged input numpy deprecation (#4735)
  • Unwrap decorators before resolving link to source (sphinx.ext.linkcode) (#4740)
  • Fix plotting error in j-invariant denoising tutorial (#4744)
  • Highlight all source lines with HTML doc "source" links (sphinx.ext.linkcode) (#4746)
  • Turn checklist boxes into bullet points inside the pull request template (#4747)
  • Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max (#4753)
  • forbid dask 2.17.0 to fix CI (#4758)
  • try to fix ci which is broken because of pyqt5 last version (#4788)
  • Remove unused variable in j invariant docs (#4792)
  • include all md files in manifest.in (#4793)
  • Remove additional "::" to make plot directive work. (#4798)
  • Use optipng to compress images/thumbnails in our gallery (#4800)
  • Fix runtime warning in blob.py (#4803)
  • Add TODO task for sphinx-gallery>=0.9.0 to remove enforced thumbnail_size (#4804)
  • Change SSIM code example to use real MSE (#4807)
  • Let biomed example load image data with Pooch. (#4809)
  • Tweak threshold_otsu error checking - closes #4811 (#4812)
  • Ensure assert messages from Cython rank filters are informative (#4815)
  • Simplify equivalent_diameter function (#4819)
  • DOC: update subpackage descriptions (#4825)
  • style: be explicit when stacking arrays (#4826)
  • MAINT: import Iterable from collections.abc (Python 3.9 compatibility) (#4834)
  • Silence several warnings in the test suite (#4837)
  • Silence a few RuntimeWarnings in the test suite (#4838)
  • handle color string mapping correctly (#4840)
  • DOC: Autoformat docstrings in io.*.py (#4845)
  • Update min req for pillow due to CVE-2020-10379 and co. (#4861)
  • DOC: First pass at format conversion, rst -> myst (#4863)
  • Fixed typo in comment (#4867)
  • Alternative wording for install guide PR #4750 (#4871)
  • DOC: Clarify condition on unique vertices returned by marching cubes (#4872)
  • Remove unmaintained wiki page link in contributor guidelines (#4873)
  • new matomo config (#4879)
  • Fix Incorrect documentation for skimage.util.img_as_int Issue (#4888)
  • Minor edit for proper doc rendering (#4897)
  • Changelog back-log (#4898)
  • minor refactoring in phase_cross_correlation (#4901)
  • Fix draw.circle/disk deprecation message, fixes #4884 (#4908)
  • Add versionchanged tag for new opt param in measure.find_contours() (#4909)
  • Declare build dependencies (#4920)
  • Replace words with racial connotations (#4921)
  • Fixes to apply_parallel for functions working with multichannel data (#4927)
  • Improve description of h_maxima and h_minima functions (#4928) (#4929)
  • CI: Skip doc build for PYTHONOPTIMIZE=2 (#4930)
  • MAINT: Remove custom fused type in skimage/morphology/_max_tree.pyx (#4931)
  • MAINT: remove numpydoc option, issue fixed in numpydoc 1.0 (#4932)
  • modify development version string to allow use with NumpyVersion (#4947)
  • CI: Add verbose option to avoid travis timeout for OSX install script (#4956)
  • Fix CI: ban sphinx-gallery 0.8.0 (#4960)
  • Alias for data.chelsea: data.cat() (#4962)
  • Fix typo. (#4963)
  • CI: Use Travis wait improved to avoid timeout for OSX builds (#4965)
  • Small enhancement in "Contour finding" example: Removed unused variable n (#4967)
  • MAINT: remove unused imports (#4968)
  • MAINT: Remove conditional import on networkx (#4970)
  • forbid latest version of pyqt (#4973)
  • Remove warnings/explicit settings on feature, restoration (#4974)
  • Docstring improvements for label and regionprops_label (#4983)
  • try to fix timeout problem with circleci (#4986)
  • improve Euler number example (#4989)
  • [website] Standardize Documentation index page. (#4990)
  • Proofread INSTALL file. (#4991)
  • Catch leftover typos in INSTALL file. (#4992)
  • Let tifffile.imread handle additional keyword arguments (#4997)
  • Update docstring for random_noise function (#5001)
  • Update sphinx mapping for sklearn and numpy (#5003)
  • Update docstring slic superpixels (#5014)
  • Bump numpy versions to match scipy (kinda) (#5016)
  • Fix usage of numpy.pad for old versions of numpy (#5017)
  • [MRG] Update documentation to new data.camera() (#5018)
  • bumped plotly requirement for docs (#5021)
  • Fix IndexError when calling hough_line_peaks with too few angles (#5024)
  • Code simplification after latest numpy bump (#5027)
  • Fixes broken link to CODE_OF_CONDUCT.md (#5030)
  • Specify whether core dev should merge right after second approving review. (#5040)
  • Update pytest configuration to include test_ functions (#5044)
  • MAINT Build fix for pyodide (#5059)
  • reduce OSX build time so that Travis is happy (#5067)
  • DOC: document the normalized kernel in prewitt_h, prewitt_v (#5076)
  • Some minor tweaks to CI (#5079)
  • removed usage of numpy's private functions from util.arraycrop (#5081)
  • peak_local_max: remove deprecated indices argument from examples (#5082)
  • Replace np.bool, np.float, and np.int with bool, float, and int (#5103, #5108)
  • change plausible script to track outbound links (#5115, #5123)
  • Remove Python 3.6 support (#5117, #5125)
  • Optimize ensure_spacing (#5062, #5135)

52 authors added to this release [alphabetical by first name or login]

A warm thank you to all contributors who added to this release. A fraction of contributors were first-time contributors to open source and a much larger fraction first-time contributors to scikit-image. It's a great feeling for maintainers to welcome new contributors, and the diversity of scikit-image contributors is surely a big strength of the package.

  • Abhishek Arya
  • Abhishek Patil
  • Alexandre de Siqueira
  • Ben Nathanson
  • Cameron Blocker
  • Chris Roat
  • Christoph Gohlke
  • Clement Ng
  • Corey Harris
  • David McMahon
  • David Mellert
  • Devi Sandeep
  • Egor Panfilov
  • Emmanuelle Gouillart
  • François Boulogne
  • Genevieve Buckley
  • Gregory R. Lee
  • Harry Kwon
  • iofall (cedarfall)
  • Jan Funke
  • Juan Nunez-Iglesias
  • Julian Gilbey
  • Julien Jerphanion
  • kalpana
  • kolibril13 (kolibril13)
  • Kushaan Gupta
  • Lars Grüter
  • Marianne Corvellec
  • Mark Harfouche
  • Marvin Albert
  • Matthias Bussonnier
  • Max Frei
  • Nathan
  • neeraj3029 (neeraj3029)
  • Nick
  • notmatthancock (matt)
  • OGordon100 (OGordon100)
  • Owen Solberg
  • Riadh Fezzani
  • Robert Haase
  • Roman Yurchak
  • Ronak Sharma
  • Ross Barnowski
  • Ruby Werman
  • ryanlu41 (ryanlu41)
  • Sebastian Wallkötter
  • Shyam Saladi
  • Stefan van der Walt
  • Terence Honles
  • Volker Hilsenstein
  • Wendy Mak
  • Yogendra Sharma

41 reviewers added to this release [alphabetical by first name or login]

  • Abhishek Arya
  • Abhishek Patil
  • Alexandre de Siqueira
  • Ben Nathanson
  • Chris Roat
  • Clement Ng
  • Corey Harris
  • Cris Luengo
  • David Mellert
  • Egor Panfilov
  • Emmanuelle Gouillart
  • François Boulogne
  • Gregory R. Lee
  • Harry Kwon
  • Jan Funke
  • Juan Nunez-Iglesias
  • Julien Jerphanion
  • kalpana
  • Kushaan Gupta
  • Lars Grüter
  • Marianne Corvellec
  • Mark Harfouche
  • Marvin Albert
  • neeraj3029
  • Nick
  • OGordon100
  • Riadh Fezzani
  • Robert Haase
  • Ross Barnowski
  • Ruby Werman
  • ryanlu41
  • Scott Trinkle
  • Sebastian Wallkötter
  • Stanley_Wang
  • Stefan van der Walt
  • Steven Brown
  • Stuart Mumford
  • Terence Honles
  • Volker Hilsenstein
  • Wendy Mak
Assets 2

@sciunto sciunto released this Jan 19, 2021

Announcement: scikit-image 0.18.0

We're happy to announce the release of scikit-image v0.18.0!

scikit-image is an image processing toolbox for SciPy that includes algorithms
for segmentation, geometric transformations, color space manipulation,
analysis, filtering, morphology, feature detection, and more.

This release of scikit-image drops support for Python 3.6 in accordance with
the NEP-29 Python and Numpy version support community standard <https://numpy.org/neps/nep-0029-deprecation_policy.html>_: Python 3.7 or
newer is required to run this version.

For more information, examples, and documentation, please visit our website:

https://scikit-image.org

New Features

  • Add the iterative Lucas-Kanade (iLK) optical flow method (#4161)
  • Add Feret diameter in region properties (#4379, #4820)
  • Add functions to compute Euler number and Crofton perimeter estimation (#4380)
  • Add a function to compute the Hausdorff distance (#4382)
  • Added 3D support for many filters in skimage.filters.rank.
  • An experimental implementation of trainable pixel segmentation, aiming for
    compatibility with the scikit-learn API, has been added to
    skimage.future. Try it out! (#4739)
  • Add a new function segmentation.expand_labels to dilate labels while
    preventing overlap (#4795)
  • It is now possible to pass extra measurement functions to
    measure.regionprops and regionprops_table (#4810)
  • Add rolling ball algorithm for background subtraction (#4851)
  • New sample images have been added in the data subpackage: data.eagle
    (#4922), data.human_mitosis (#4939), data.cells3d (#4951), and
    data.vortex (#5041). Also note that the image for data.camera has
    been changed due to copyright issues (#4913).
  • skimage.feature.structure_tensor now supports 3D (and nD) images as input
    (#5002)
  • Many thresholding methods can now receive a precomputed histogram as input,
    resulting in significant speedups if multiple methods are tried on the same
    image, or if a fast histogram method is used. (#5006)
  • measure.regionprops now supports multichannel intensity images (#5037)

Documentation

  • Add an example to the flood fill tutorial (#4619)
  • Docstring enhancements for marching cubes and find_contours (#4641)
  • A new tutorial presenting a cell biology example has been added to the
    gallery (#4648). Special thanks to Pierre Poulain and Fred Bernard
    (Université de Paris and Institut Jacques Monod) for scientific review of
    this example!
  • Improve register rotation example with notes and references (#4723)
  • Add versionadded for new scalar type support for "scale" param in
    transform.AffineTransform (#4733)
  • New tutorial on visualizing 3D data <https://scikit-image.org/docs/dev/auto_examples/applications/plot_3d_image_processing.html>_ (#4850)
  • Add example for 3D adaptive histogram equalization (AHE) (#4658)
  • Automatic formatting of docstrings for improved consistency (#4849)
  • Improved docstring for rgb2lab (#4839) and marching_cubes (#4846)
  • Improved docstring for measure.marching_cubes, mentioning how to decimate a
    mesh using mayavi (#4846)
  • Document how to contribute a gallery example. (#4857)
  • Fix and improve entropy example (#4904)
  • expand the benchmarking section of the developer docs (#4905)
  • Improved docstring for util.random_noise (#5001)
  • Improved docstrings for morphology.h_maxima and morphology.h_minima
    (#4929).
  • Improved docstring for util.img_as_int (#4888).
  • A new example demonstrates interactive exploration of regionprops results
    using the PyData stack (pandas, seaborn) at
    https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_regionprops.html`_
    (#5010).
  • Documentation has been added to explain
    how to download example datasets <https://scikit-image.org/docs/dev/install.html#downloading-all-demo-datasets>_
    which are not installed with scikit-image (#4984). Similarly, the contributor
    guide has been updated to mention how to host new datasets in a gitlab
    repository (#4892).
  • The benchmarking section of the developer documentation <https://scikit-image.org/docs/dev/contribute.html#benchmarks>_
    has been expanded (#4905).
  • Added links to the image.sc forum in example pages (#5094, #5096)
  • Added missing datasets to gallery examples (#5116, #5118)
  • Add farid filters in all, to populate the documentation (#5128, #5129)
  • Proofread gallery example for rank filters. (#5126, #5136)

Improvements

  • float32 support for SLIC (#4683), ORB (#4684, #4697), BRIEF (#4685),
    pyramid_gaussian (#4696), Richardson-Lucy deconvolution (#4880)
  • In skimage.restoration.richardson_lucy, computations are now done in
    single-precision when the input image is single-precision. This can give a
    substantial performance improvement when working with single precision data.
  • Richardson-Lucy deconvolution now has a filter_epsilon keyword argument
    to avoid division by very small numbers (#4823)
  • Add default level parameter (max-min) / 2 in measure.find_contours (#4862)
  • The performance of the SLIC superpixels algorithm
    (skimage.segmentation.slice) was improved for the case where a mask
    is supplied by the user (#4903). The specific superpixels produced by
    masked SLIC will not be identical to those produced by prior releases.
  • exposure.adjust_gamma has been accelerated for uint8 images by using
    a look-up table (LUT) (#4966).
  • measure.label has been accelerated for boolean input images, by using
    scipy.ndimage's implementation for this case (#4945).
  • util.apply_parallel now works with multichannel data (#4927).
  • skimage.feature.peak_local_max supports now any Minkowski distance.
  • We now use sparse cross-correlation to accelerate local thresholding
    functions (#4912)
  • morphology.convex_hull_image now uses much less memory by checking hull
    inequalities in sequence (#5020)
  • Polygon rasterization is more precise and will no longer potentially exclude
    input vertices. (#5029)
  • Add data optional requirements to allow pip install scikit-image[data]
    (#5105, #5111)
  • OpenMP support in MSVC (#4924, #5111)
  • Restandardize handling of Multi-Image files (#2815, #5132)
  • Consistent zoom boundary behavior across SciPy versions (#5131, #5133)

API Changes

  • skimage.restoration.richardson_lucy returns a single-precision output
    when the input is single-precision. Prior to this release, double-precision
    was always used. (#4880)
  • The default value of threshold_rel in skimage.feature.corner has
    changed from 0.1 to None, which corresponds to letting
    skimage.feature.peak_local_max decide on the default. This is currently
    equivalent to threshold_rel=0.
  • In measure.label, the deprecated neighbors parameter has been
    removed. (#4942)
  • The image returned by data.camera has changed because of copyright
    issues (#4913).

Bug fixes

  • A bug in label2rgb has been fixed when the input image had np.uint8
    dtype (#4661)
  • Fixed incorrect implementation of skimage.color.separate_stains (#4725)
  • Many bug fixes have been made in peak_local_max (#2592, #4756, #4760,
    #5047)
  • Fix bug in random_walker when input labels have negative values (#4771)
  • PSF flipping is now correct for Richardson-Lucy deconvolution work in >2D (#4823)
  • Fix equalize_adapthist (CLAHE) for clip value 1.0 (#4828)
  • For the RANSAC algorithm, improved the case where all data points are
    outliers, which was previously raising an error
    (#4844)
  • An error-causing bug has been corrected for the bg_color parameter in
    label2rgb when its value is a string (#4840)
  • A normalization bug was fixed in metrics.variation_of_information
    (#4875)
  • Euler characteristic property of skimage.measure.regionprops was erroneous
    for 3D objects, since it did not take tunnels into account. A new implementation
    based on integral geometry fixes this bug (#4380).
  • In skimage.morphology.selem.rectangle the height argument
    controlled the width and the width argument controlled the height.
    They have been replaced with nrow and ncol. (#4906)
  • skimage.segmentation.flood_fill and skimage.segmentation.flood
    now consistently handle negative values for seed_point.
  • Segmentation faults in segmentation.flood have been fixed (#4948, #4972)
  • A segfault in draw.polygon for the case of 0-d input has been fixed
    (#4943).
  • In registration.phase_cross_correlation, a ValueError is raised when
    NaNs are found in the computation (as a result of NaNs in input images).
    Before this fix, an incorrect value could be returned where the input images
    had NaNs (#4886).
  • Fix edge filters not respecting padding mode (#4907)
  • Use v{} for version tags with pooch (#5104, #5110)
  • Fix compilation error in XCode 12 (#5107, #5111)

Deprecations

  • The indices argument in skimage.feature.peak_local_max has been
    deprecated. Indices will always be returned. (#4752)
  • In skimage.feature.structure_tensor, an order argument has been
    introduced which will default to 'rc' starting in version 0.20. (#4841)
  • skimage.feature.structure_tensor_eigvals has been deprecated and will be
    removed in version 0.20. Use skimage.feature.structure_tensor_eigenvalues
    instead.
  • The skimage.viewer subpackage and the skivi script have been
    deprecated and will be removed in version 0.20. For interactive visualization
    we recommend using dedicated tools such as napari <https://napari.org>_ or
    plotly <https://plotly.com>_. In a similar vein, the qt and skivi
    plugins of skimage.io have been deprecated
    and will be removed in version 0.20. (#4941, #4954)
  • In skimage.morphology.selem.rectangle the arguments width and
    height have been deprecated. Use nrow and ncol instead.
  • The explicit setting threshold_rel=0` was removed from the Examples of the following docstrings: skimage.feature.BRIEF, skimage.feature.corner_harris, skimage.feature.corner_shi_tomasi, skimage.feature.corner_foerstner, skimage.feature.corner_fast, skimage.feature.corner_subpix, skimage.feature.corner_peaks, skimage.feature.corner_orientations, and skimage.feature._detect_octave``.
  • In skimage.restoration._denoise, the warning regarding
    rescale_sigma=None was removed.
  • In skimage.restoration._cycle_spin, the # doctest: +SKIP was removed.

Development process

  • Fix #3327: Add functionality for benchmark coverage (#3329)
  • Release process notes have been improved. (#4228)
  • pyproject.toml has been added to the sdist.
  • Build and deploy dev/master documentation using GitHub Actions (#4852)
  • Website now deploys itself (#4870)
  • build doc on circle ci and link artifact (#4881)
  • Benchmarks can now run on older scikit-image commits (#4891)
  • Website analytics are tracked using plausible.io and can be visualized on
    https://plausible.io/scikit-image.org (#4893)
  • Artifacts for the documentation build are now found in each pull request
    (#4881).
  • Documentation source files can now be written in Markdown in addition to
    ReST, thanks to myst (#4863).
  • update trove classifiers and tests for Python 3.9 + fix pytest config (#5052)
  • fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8 (#5054)
  • Moved our testing from Travis to GitHub Actions (#5074)
  • We now build our wheels on GitHub Actions on the main repo using
    cibuildwheel. Many thanks to the matplotlib and scikit-learn developers for
    paving the way for us! (#5080)
  • Disable Travis-CI builds (#5099, #5111)
  • Improvements to CircleCI build: no parallelization and caching) (#5097, #5119)

Other Pull Requests

  • Manage iradon input and output data type (#4298)
  • random walker: Display a warning when the probability is outsite [0,1] for a given tol (#4631)
  • MAINT: remove unused cython file (#4633)
  • Forget legacy data dir (#4662)
  • Setup longdesc markdown and switch to 0.18dev (#4663)
  • Optional pooch dependency (#4666)
  • Adding new default values to functions on doc/examples/segmentation/plot_ncut (#4676)
  • Reintroduced convert with a strong deprecation warning (#4681)
  • In release notes, better describe skimage's relationship to ecosystem (#4689)
  • Perform some todo tasks for 0.18 (#4690)
  • Perform todo tasks for 0.17! (#4691)
  • suppressing warnings from gallery examples (#4692)
  • release notes for 0.17.2 (#4702)
  • Fix gallery example mentioning deprecated argument (#4706)
  • Specify the encoding of files opened in the setup phase (#4713)
  • Remove duplicate fused type definition (#4724)
  • Blacklist cython version 0.29.18 (#4730)
  • Fix CI failures related to conversion of np.floating to dtype (#4731)
  • Fix Ci failures related to array ragged input numpy deprecation (#4735)
  • Unwrap decorators before resolving link to source (sphinx.ext.linkcode) (#4740)
  • Fix plotting error in j-invariant denoising tutorial (#4744)
  • Highlight all source lines with HTML doc "source" links (sphinx.ext.linkcode) (#4746)
  • Turn checklist boxes into bullet points inside the pull request template (#4747)
  • Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max (#4753)
  • forbid dask 2.17.0 to fix CI (#4758)
  • try to fix ci which is broken because of pyqt5 last version (#4788)
  • Remove unused variable in j invariant docs (#4792)
  • include all md files in manifest.in (#4793)
  • Remove additional "::" to make plot directive work. (#4798)
  • Use optipng to compress images/thumbnails in our gallery (#4800)
  • Fix runtime warning in blob.py (#4803)
  • Add TODO task for sphinx-gallery>=0.9.0 to remove enforced thumbnail_size (#4804)
  • Change SSIM code example to use real MSE (#4807)
  • Let biomed example load image data with Pooch. (#4809)
  • Tweak threshold_otsu error checking - closes #4811 (#4812)
  • Ensure assert messages from Cython rank filters are informative (#4815)
  • Simplify equivalent_diameter function (#4819)
  • DOC: update subpackage descriptions (#4825)
  • style: be explicit when stacking arrays (#4826)
  • MAINT: import Iterable from collections.abc (Python 3.9 compatibility) (#4834)
  • Silence several warnings in the test suite (#4837)
  • Silence a few RuntimeWarnings in the test suite (#4838)
  • handle color string mapping correctly (#4840)
  • DOC: Autoformat docstrings in io.*.py (#4845)
  • Update min req for pillow due to CVE-2020-10379 and co. (#4861)
  • DOC: First pass at format conversion, rst -> myst (#4863)
  • Fixed typo in comment (#4867)
  • Alternative wording for install guide PR #4750 (#4871)
  • DOC: Clarify condition on unique vertices returned by marching cubes (#4872)
  • Remove unmaintained wiki page link in contributor guidelines (#4873)
  • new matomo config (#4879)
  • Fix Incorrect documentation for skimage.util.img_as_int Issue (#4888)
  • Minor edit for proper doc rendering (#4897)
  • Changelog back-log (#4898)
  • minor refactoring in phase_cross_correlation (#4901)
  • Fix draw.circle/disk deprecation message, fixes #4884 (#4908)
  • Add versionchanged tag for new opt param in measure.find_contours() (#4909)
  • Declare build dependencies (#4920)
  • Replace words with racial connotations (#4921)
  • Fixes to apply_parallel for functions working with multichannel data (#4927)
  • Improve description of h_maxima and h_minima functions (#4928) (#4929)
  • CI: Skip doc build for PYTHONOPTIMIZE=2 (#4930)
  • MAINT: Remove custom fused type in skimage/morphology/_max_tree.pyx (#4931)
  • MAINT: remove numpydoc option, issue fixed in numpydoc 1.0 (#4932)
  • modify development version string to allow use with NumpyVersion (#4947)
  • CI: Add verbose option to avoid travis timeout for OSX install script (#4956)
  • Fix CI: ban sphinx-gallery 0.8.0 (#4960)
  • Alias for data.chelsea: data.cat() (#4962)
  • Fix typo. (#4963)
  • CI: Use Travis wait improved to avoid timeout for OSX builds (#4965)
  • Small enhancement in "Contour finding" example: Removed unused variable n (#4967)
  • MAINT: remove unused imports (#4968)
  • MAINT: Remove conditional import on networkx (#4970)
  • forbid latest version of pyqt (#4973)
  • Remove warnings/explicit settings on feature, restoration (#4974)
  • Docstring improvements for label and regionprops_label (#4983)
  • try to fix timeout problem with circleci (#4986)
  • improve Euler number example (#4989)
  • [website] Standardize Documentation index page. (#4990)
  • Proofread INSTALL file. (#4991)
  • Catch leftover typos in INSTALL file. (#4992)
  • Let tifffile.imread handle additional keyword arguments (#4997)
  • Update docstring for random_noise function (#5001)
  • Update sphinx mapping for sklearn and numpy (#5003)
  • Update docstring slic superpixels (#5014)
  • Bump numpy versions to match scipy (kinda) (#5016)
  • Fix usage of numpy.pad for old versions of numpy (#5017)
  • [MRG] Update documentation to new data.camera() (#5018)
  • bumped plotly requirement for docs (#5021)
  • Fix IndexError when calling hough_line_peaks with too few angles (#5024)
  • Code simplification after latest numpy bump (#5027)
  • Fixes broken link to CODE_OF_CONDUCT.md (#5030)
  • Specify whether core dev should merge right after second approving review. (#5040)
  • Update pytest configuration to include test_ functions (#5044)
  • MAINT Build fix for pyodide (#5059)
  • reduce OSX build time so that Travis is happy (#5067)
  • DOC: document the normalized kernel in prewitt_h, prewitt_v (#5076)
  • Some minor tweaks to CI (#5079)
  • removed usage of numpy's private functions from util.arraycrop (#5081)
  • peak_local_max: remove deprecated indices argument from examples (#5082)
  • Replace np.bool, np.float, and np.int with bool, float, and int (#5103, #5108)
  • change plausible script to track outbound links (#5115, #5123)
  • Remove Python 3.6 support (#5117, #5125)
  • Optimize ensure_spacing (#5062, #5135)

52 authors added to this release [alphabetical by first name or login]

A warm thank you to all contributors who added to this release. A fraction of contributors were first-time contributors to open source and a much larger fraction first-time contributors to scikit-image. It's a great feeling for maintainers to welcome new contributors, and the diversity of scikit-image contributors is surely a big strength of the package.

  • Abhishek Arya
  • Abhishek Patil
  • Alexandre de Siqueira
  • Ben Nathanson
  • Cameron Blocker
  • Chris Roat
  • Christoph Gohlke
  • Clement Ng
  • Corey Harris
  • David McMahon
  • David Mellert
  • Devi Sandeep
  • Egor Panfilov
  • Emmanuelle Gouillart
  • François Boulogne
  • Genevieve Buckley
  • Gregory R. Lee
  • Harry Kwon
  • iofall (cedarfall)
  • Jan Funke
  • Juan Nunez-Iglesias
  • Julian Gilbey
  • Julien Jerphanion
  • kalpana
  • kolibril13 (kolibril13)
  • Kushaan Gupta
  • Lars Grüter
  • Marianne Corvellec
  • Mark Harfouche
  • Marvin Albert
  • Matthias Bussonnier
  • Max Frei
  • Nathan
  • neeraj3029 (neeraj3029)
  • Nick
  • notmatthancock (matt)
  • OGordon100 (OGordon100)
  • Owen Solberg
  • Riadh Fezzani
  • Robert Haase
  • Roman Yurchak
  • Ronak Sharma
  • Ross Barnowski
  • Ruby Werman
  • ryanlu41 (ryanlu41)
  • Sebastian Wallkötter
  • Shyam Saladi
  • Stefan van der Walt
  • Terence Honles
  • Volker Hilsenstein
  • Wendy Mak
  • Yogendra Sharma

41 reviewers added to this release [alphabetical by first name or login]

  • Abhishek Arya
  • Abhishek Patil
  • Alexandre de Siqueira
  • Ben Nathanson
  • Chris Roat
  • Clement Ng
  • Corey Harris
  • Cris Luengo
  • David Mellert
  • Egor Panfilov
  • Emmanuelle Gouillart
  • François Boulogne
  • Gregory R. Lee
  • Harry Kwon
  • Jan Funke
  • Juan Nunez-Iglesias
  • Julien Jerphanion
  • kalpana
  • Kushaan Gupta
  • Lars Grüter
  • Marianne Corvellec
  • Mark Harfouche
  • Marvin Albert
  • neeraj3029
  • Nick
  • OGordon100
  • Riadh Fezzani
  • Robert Haase
  • Ross Barnowski
  • Ruby Werman
  • ryanlu41
  • Scott Trinkle
  • Sebastian Wallkötter
  • Stanley_Wang
  • Stefan van der Walt
  • Steven Brown
  • Stuart Mumford
  • Terence Honles
  • Volker Hilsenstein
  • Wendy Mak
Assets 2
Dec 13, 2020
Dec 8, 2020
v0.18.0rc1