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scikit-image 0.23.2 (2024-04-20)

doc/source/release_notes/release_0.23.rst

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scikit-image 0.23.2 (2024-04-20)

We're happy to announce the release of scikit-image 0.23.2!

Bug Fixes

  • Make sure skimage.util.img_as_ubyte supports the edge case where dtype('uint64').type of the provided image is np.ulonglong instead of np.uint64 (#7392 <https://github.com/scikit-image/scikit-image/pull/7392>_).

Documentation

  • Add date to 0.23.1 release notes (#7384 <https://github.com/scikit-image/scikit-image/pull/7384>_).
  • Fix docstring of connectivity parameter in skimage.segmentation.watershed (#7360 <https://github.com/scikit-image/scikit-image/pull/7360>_).

Infrastructure

  • Ignore Sphinx warning about unpickable cache (#7400 <https://github.com/scikit-image/scikit-image/pull/7400>_).
  • Simplify instructions on changelist in PR template (#7401 <https://github.com/scikit-image/scikit-image/pull/7401>_).

Maintenance

  • Use numpy.inf instead of deprecated numpy.infty (#7386 <https://github.com/scikit-image/scikit-image/pull/7386>_).
  • Update Ruff config (#7387 <https://github.com/scikit-image/scikit-image/pull/7387>_).
  • Update matrix and names of Azure pipelines configuration (#7390 <https://github.com/scikit-image/scikit-image/pull/7390>_).
  • Use upload- and download-artifact v4 (#7389 <https://github.com/scikit-image/scikit-image/pull/7389>_).
  • Ignore arch specific cast warnings originating from astype in tests (#7393 <https://github.com/scikit-image/scikit-image/pull/7393>_).
  • Update link to numpydoc example.py (#7395 <https://github.com/scikit-image/scikit-image/pull/7395>_).

Contributors

4 authors added to this release (alphabetically):

  • @pitkajuh <https://github.com/pitkajuh>_
  • Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
  • Lars Grüter (@lagru <https://github.com/lagru>_)
  • Marianne Corvellec (@mkcor <https://github.com/mkcor>_)

4 reviewers added to this release (alphabetically):

  • Egor Panfilov (@soupault <https://github.com/soupault>_)
  • Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
  • Lars Grüter (@lagru <https://github.com/lagru>_)
  • Marianne Corvellec (@mkcor <https://github.com/mkcor>_)

These lists are automatically generated, and may not be complete or may contain duplicates.

scikit-image 0.23.1 (2024-04-10)

We're happy to announce the release of scikit-image 0.23.1!

.. note::

Due to an issue with the CI system scikit-image 0.23.0 was never released. This release is identical to what 0.23.0 would have been other than the CI fix and the version number.

Highlights

  • Ensure skimage.morphology.closing and skimage.morphology.opening are extensive and anti-extensive, respectively, if the footprint is not mirror symmetric (#6695 <https://github.com/scikit-image/scikit-image/pull/6695>_).
  • Add parameters mode and cval to erosion, dilation, opening, closing, white_tophat, and black_tophat in skimage.morphology. These new parameters determine how array borders are handled (#6695 <https://github.com/scikit-image/scikit-image/pull/6695>_).
  • Add parameter mode to binary_erosion, binary_dilation, binary_opening and binary_closing in skimage.morphology. These new parameters determine how array borders are handled (#6695 <https://github.com/scikit-image/scikit-image/pull/6695>_).
  • Speedup skimage.util.map_array by parallelization with Cython's prange (#7266 <https://github.com/scikit-image/scikit-image/pull/7266>_).

New Features

  • Add new intensity_std property to skimage.measure.regionprops which computes the standard deviation of the intensity in a region (#6712 <https://github.com/scikit-image/scikit-image/pull/6712>_).
  • Add parameters mode and cval to erosion, dilation, opening, closing, white_tophat, and black_tophat in skimage.morphology. These new parameters determine how array borders are handled (#6695 <https://github.com/scikit-image/scikit-image/pull/6695>_).
  • Add parameter mode to binary_erosion, binary_dilation, binary_opening and binary_closing in skimage.morphology. These new parameters determine how array borders are handled (#6695 <https://github.com/scikit-image/scikit-image/pull/6695>_).
  • Add functions mirror_footprint and pad_footprint to skimage.morphology (#6695 <https://github.com/scikit-image/scikit-image/pull/6695>_).
  • Add new parameter spacing to segmentation.expand_labels to support anisotropic images (#7080 <https://github.com/scikit-image/scikit-image/pull/7080>_).

API Changes

  • Drop support for Python 3.9 (#7217 <https://github.com/scikit-image/scikit-image/pull/7217>_).
  • Parameters shift_x and shift_y in skimage.morphology.erosion and skimage.morphology.dilation are deprecated. Use pad_footprint or modify the footprint manually instead (#6695 <https://github.com/scikit-image/scikit-image/pull/6695>_).
  • Remove unexpected value scaling in skimage.morphology.skeletonize_3d for non-binary input images. skeletonize_3d now always returns a binary array like similar functions (#7095 <https://github.com/scikit-image/scikit-image/pull/7095>_).
  • Deprecate function skimage.feature.plot_matches in favor of skimage.feature.plot_matched_features (#7255 <https://github.com/scikit-image/scikit-image/pull/7255>_).
  • Deprecate skimage.morphology.skeletonize_3d in favor of just skimage.morphology.skeletonize (#7094 <https://github.com/scikit-image/scikit-image/pull/7094>_).
  • Deprecate parameter output in skimage.filters.gaussian; use out instead (#7225 <https://github.com/scikit-image/scikit-image/pull/7225>_).
  • Change the default value of the parameters shift_x, shift_y and shift_z from False to 0 in the skimage.filters.rank functions. This has not impact on the results. Warn in case boolean shifts are provided from now on (#7320 <https://github.com/scikit-image/scikit-image/pull/7320>_).

Performance

  • Add lazy loading to skimage.metrics module (#7211 <https://github.com/scikit-image/scikit-image/pull/7211>_).
  • Speedup skimage.util.map_array by parallelization with Cython's prange (#7266 <https://github.com/scikit-image/scikit-image/pull/7266>_).

Bug Fixes

  • Add exception to avoid surprising result when image is too small for the given parameters in skimage.feature.hog (#7153 <https://github.com/scikit-image/scikit-image/pull/7153>_).
  • Ensure skimage.morphology.closing and skimage.morphology.opening are extensive and anti-extensive, respectively, if the footprint is not mirror symmetric (#6695 <https://github.com/scikit-image/scikit-image/pull/6695>_).
  • Avoid a TypeError in skimage.registration.phase_cross_correlation when the real-time shift cannot be determined (disambiguate=True). Display a warning instead (#7259 <https://github.com/scikit-image/scikit-image/pull/7259>_).
  • Fix logic in skimage.graph.pixel_graph which raised a TypeError when the parameter edge_function was provided without a mask (#7310 <https://github.com/scikit-image/scikit-image/pull/7310>_).
  • Ensure cache stays empty when cache=False is passed to skimage.measure.regionprops (#7333 <https://github.com/scikit-image/scikit-image/pull/7333>_).

Documentation

  • Update instructions for updating dev environment (#7160 <https://github.com/scikit-image/scikit-image/pull/7160>_).
  • Make titles in RAG gallery examples more explicit (#7202 <https://github.com/scikit-image/scikit-image/pull/7202>_).
  • Add docstring to skimage.graph module (#7192 <https://github.com/scikit-image/scikit-image/pull/7192>_).
  • Use consistent notation for array dimensions in the docstrings (#3031 <https://github.com/scikit-image/scikit-image/pull/3031>_).
  • Specify default markers in watershed docstring (#7154 <https://github.com/scikit-image/scikit-image/pull/7154>_).
  • Stop HTML documentation from intercepting left and right-arrow keys to improve keyboard accessibility (#7226 <https://github.com/scikit-image/scikit-image/pull/7226>_).
  • Fix reference formatting for nitpicky sphinx (#7228 <https://github.com/scikit-image/scikit-image/pull/7228>_).
  • Document how to deal with other array-likes such as xarray.DataArray and pandas.DataFrame in the crash course on NumPy for images (#7159 <https://github.com/scikit-image/scikit-image/pull/7159>_).
  • Fix broken function calls and syntax issues in user guide (#7234 <https://github.com/scikit-image/scikit-image/pull/7234>_).
  • Use correct default mode in docstring of skimage.transform.swirl (#7241 <https://github.com/scikit-image/scikit-image/pull/7241>_).
  • Add missing documentation about spacing parameter in moments_normalized (#7248 <https://github.com/scikit-image/scikit-image/pull/7248>_).
  • Update docstring & example in the hough_ellipse transform (#6893 <https://github.com/scikit-image/scikit-image/pull/6893>_).
  • Point binder tag/branch to commit corresponding to docs/release (#7252 <https://github.com/scikit-image/scikit-image/pull/7252>_).
  • Add example to FundamentalMatrixTransform class (#6863 <https://github.com/scikit-image/scikit-image/pull/6863>_).
  • Adds explanation of what the optional dependency on Matplotlib offers to the install instructions (#7286 <https://github.com/scikit-image/scikit-image/pull/7286>_).
  • Use correct symbol θ for tightness in the docstring of skimage.registration.optical_flow_tvl1 (#7314 <https://github.com/scikit-image/scikit-image/pull/7314>_).
  • The description of the parameter cval is modified in "int or float". cval is a numerical value not a string (#7319 <https://github.com/scikit-image/scikit-image/pull/7319>_).
  • Remove obsolete instruction about documenting changes (#7321 <https://github.com/scikit-image/scikit-image/pull/7321>_).
  • Added comment to clarify that dt corresponds to tau, i.e. the time step. Changed gray scale in grayscale in the entire registration module (#7324 <https://github.com/scikit-image/scikit-image/pull/7324>_).
  • Create SECURITY.md (#7230 <https://github.com/scikit-image/scikit-image/pull/7230>_).
  • Remove deprecated parameter coordinates from docstring example of skimage.segmentation.active_contour (#7329 <https://github.com/scikit-image/scikit-image/pull/7329>_).
  • Include dates in release note headings (#7269 <https://github.com/scikit-image/scikit-image/pull/7269>_).
  • Update description of how to document pull requests for inclusion in the release notes (#7267 <https://github.com/scikit-image/scikit-image/pull/7267>_).
  • Clarify description of data_range parameter in skimage.metrics.structural_similarity (#7345 <https://github.com/scikit-image/scikit-image/pull/7345>_).
  • Use object-oriented Matplotlib style in longer gallery examples and demonstrations (doc/examples/applications) (#7346 <https://github.com/scikit-image/scikit-image/pull/7346>_).
  • In the gallery example on segmenting human cells (in mitosis), include the border when generating basin markers for watershed (#7362 <https://github.com/scikit-image/scikit-image/pull/7362>_).
  • Add missing minus sign in docstring of skimage.transform.EuclideanTransform (#7097 <https://github.com/scikit-image/scikit-image/pull/7097>_).

Infrastructure

  • Update wording on the stale bot to assume the core team dropped the ball (#7196 <https://github.com/scikit-image/scikit-image/pull/7196>_).
  • Update Azure job name following the drop of Python 3.9 (#7218 <https://github.com/scikit-image/scikit-image/pull/7218>_).
  • Schedule nightly wheel builds at uncommon time (#7254 <https://github.com/scikit-image/scikit-image/pull/7254>_).
  • Build nightly wheels with nightly NumPy 2.0 (#7251 <https://github.com/scikit-image/scikit-image/pull/7251>_).
  • Use pytest-doctestplus instead of classic pytest-doctest (#7289 <https://github.com/scikit-image/scikit-image/pull/7289>_).
  • Update the scientific-python/upload-nightly-action to v0.5.0 for dependency stability and to take advantage of Anaconda Cloud upload bug fixes (#7325 <https://github.com/scikit-image/scikit-image/pull/7325>_).
  • Add assert_stacklevel helper to check stacklevel of captured warnings (#7294 <https://github.com/scikit-image/scikit-image/pull/7294>_).
  • Exclude pre-commit[bot] from changelist's contributor list (#7358 <https://github.com/scikit-image/scikit-image/pull/7358>_).

Maintenance

  • Remove outdated & duplicate "preferred" field in version_switcher.json (#7184 <https://github.com/scikit-image/scikit-image/pull/7184>_).
  • Upgrade to spin 0.7 (#7168 <https://github.com/scikit-image/scikit-image/pull/7168>_).
  • Do not compare types, use isinstance (#7186 <https://github.com/scikit-image/scikit-image/pull/7186>_).
  • [pre-commit.ci] pre-commit autoupdate (#7181 <https://github.com/scikit-image/scikit-image/pull/7181>_).
  • Increase tolerance for moments test for 32 bit floats (#7188 <https://github.com/scikit-image/scikit-image/pull/7188>_).
  • Temporarily pin Cython to <3.0.3 until CI is fixed (#7189 <https://github.com/scikit-image/scikit-image/pull/7189>_).
  • Remove obsolete meson instructions (#7193 <https://github.com/scikit-image/scikit-image/pull/7193>_).
  • Temporarily pin Cython to <3.0.3 until CI is fixed, take 2 (#7201 <https://github.com/scikit-image/scikit-image/pull/7201>_).
  • Fix chocolatey (#7200 <https://github.com/scikit-image/scikit-image/pull/7200>_).
  • Pin Pillow to <10.1.0 until incompatibility with imageio is fixed (#7208 <https://github.com/scikit-image/scikit-image/pull/7208>_).
  • Use Black (#7197 <https://github.com/scikit-image/scikit-image/pull/7197>_).
  • Apply black to _hog.py after previous merge lacking black (#7215 <https://github.com/scikit-image/scikit-image/pull/7215>_).
  • Unpin Cython after release of Cython 3.0.4 (#7214 <https://github.com/scikit-image/scikit-image/pull/7214>_).
  • [pre-commit.ci] pre-commit autoupdate (#7236 <https://github.com/scikit-image/scikit-image/pull/7236>_).
  • Cleanup for Python 3.12 (#7173 <https://github.com/scikit-image/scikit-image/pull/7173>_).
  • Make Python 3.12 default CI Python (#7244 <https://github.com/scikit-image/scikit-image/pull/7244>_).
  • Add explicit noexcept to address Cython 3.0 warnings (#7250 <https://github.com/scikit-image/scikit-image/pull/7250>_).
  • Update imageio to fix Pillow incompatibility (#7245 <https://github.com/scikit-image/scikit-image/pull/7245>_).
  • Upgrade docker/setup-qemu-action to v3 (#7134 <https://github.com/scikit-image/scikit-image/pull/7134>_).
  • Fix warningfilter for deprecation in SciPy 1.12.0rc1 (#7275 <https://github.com/scikit-image/scikit-image/pull/7275>_).
  • Update to numpy>=1.23 and matplotlib>=3.6 according to SPEC 0 (#7284 <https://github.com/scikit-image/scikit-image/pull/7284>_).
  • Add new deprecate_parameter helper (#7256 <https://github.com/scikit-image/scikit-image/pull/7256>_).
  • Update meson and Cython (#7283 <https://github.com/scikit-image/scikit-image/pull/7283>_).
  • Handle floating point warning for empty images in skimage.registration.phase_cross_correlation (#7287 <https://github.com/scikit-image/scikit-image/pull/7287>_).
  • Update spin (0.8) (#7285 <https://github.com/scikit-image/scikit-image/pull/7285>_).
  • Complete deprecations that were scheduled for our 0.23 release. Remove now unused deprecate_kwarg and remove_arg; they are entirely succeeded by deprecate_parameter (#7290 <https://github.com/scikit-image/scikit-image/pull/7290>_).
  • For security best practices, use the scientific-python/upload-nightly-action GitHub Action from known commit shas that correspond to tagged releases. These can be updated automatically via Dependabot (#7306 <https://github.com/scikit-image/scikit-image/pull/7306>_).
  • Update pre-commits repos (#7303 <https://github.com/scikit-image/scikit-image/pull/7303>_).
  • The test suite can now be run without numpydoc installed (#7307 <https://github.com/scikit-image/scikit-image/pull/7307>_).
  • Deal with parallel write warning from Pydata theme (#7311 <https://github.com/scikit-image/scikit-image/pull/7311>_).
  • Test nightly wheel build with NumPy 2.0 (#7288 <https://github.com/scikit-image/scikit-image/pull/7288>_).
  • Make it clear that funcs in _optical_flow_utils are private (#7328 <https://github.com/scikit-image/scikit-image/pull/7328>_).
  • Update dependencies (spec 0) (#7335 <https://github.com/scikit-image/scikit-image/pull/7335>_).
  • Follow-up cleaning & fixes for compatibility with NumPy 1 & 2 (#7326 <https://github.com/scikit-image/scikit-image/pull/7326>_).
  • Replace ignored teardown with autouse fixture in test_fits.py (#7340 <https://github.com/scikit-image/scikit-image/pull/7340>_).
  • Address new copy semantics & broadcasting in np.solve in NumPy 2 (#7341 <https://github.com/scikit-image/scikit-image/pull/7341>_).
  • Ignore table of execution times by Sphinx gallery (#7327 <https://github.com/scikit-image/scikit-image/pull/7327>_).
  • Allow a very small floating point tolerance for pearson test (#7356 <https://github.com/scikit-image/scikit-image/pull/7356>_).
  • Update numpydoc to version 1.7 (#7355 <https://github.com/scikit-image/scikit-image/pull/7355>_).
  • [pre-commit.ci] pre-commit autoupdate (#7365 <https://github.com/scikit-image/scikit-image/pull/7365>_).
  • Simplify warning filters in test suite (#7349 <https://github.com/scikit-image/scikit-image/pull/7349>_).
  • Build against NumPy >=2.0.0rc1 (#7367 <https://github.com/scikit-image/scikit-image/pull/7367>_).
  • Remove ensure_python_version function (#7370 <https://github.com/scikit-image/scikit-image/pull/7370>_).
  • Update GitHub actions to setup-python@v5, cache@v4, upload-artifact@v4, and download-artifact@v4 (#7368 <https://github.com/scikit-image/scikit-image/pull/7368>_).
  • Update lazyloader to v0.4 (#7373 <https://github.com/scikit-image/scikit-image/pull/7373>_).

Contributors

29 authors added to this release (alphabetically):

  • @GParolini <https://github.com/GParolini>_
  • @tokiAi <https://github.com/tokiAi>_
  • Adrien Foucart (@adfoucart <https://github.com/adfoucart>_)
  • Anam Fatima (@anamfatima1304 <https://github.com/anamfatima1304>_)
  • Ananya Srivastava (@ana42742 <https://github.com/ana42742>_)
  • Ben Harvie (@benharvie <https://github.com/benharvie>_)
  • Christian Clauss (@cclauss <https://github.com/cclauss>_)
  • Cris Luengo (@crisluengo <https://github.com/crisluengo>_)
  • Egor Panfilov (@soupault <https://github.com/soupault>_)
  • Grzegorz Bokota (@Czaki <https://github.com/Czaki>_)
  • Jan Lebert (@sitic <https://github.com/sitic>_)
  • Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
  • Jeremy Farrell (@farrjere <https://github.com/farrjere>_)
  • Juan Nunez-Iglesias (@jni <https://github.com/jni>_)
  • Lars Grüter (@lagru <https://github.com/lagru>_)
  • Mao Nishino (@mao1756 <https://github.com/mao1756>_)
  • Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
  • Mark Harfouche (@hmaarrfk <https://github.com/hmaarrfk>_)
  • Matthew Feickert (@matthewfeickert <https://github.com/matthewfeickert>_)
  • Matthew Vine (@MattTheCuber <https://github.com/MattTheCuber>_)
  • Maxime Corbé (@Maxime-corbe <https://github.com/Maxime-corbe>_)
  • Michał Górny (@mgorny <https://github.com/mgorny>_)
  • Neil Shephard (@ns-rse <https://github.com/ns-rse>_)
  • Ole Streicher (@olebole <https://github.com/olebole>_)
  • Peter Suter (@petsuter <https://github.com/petsuter>_)
  • Robert Haase (@haesleinhuepf <https://github.com/haesleinhuepf>_)
  • Sean McKinney (@jouyun <https://github.com/jouyun>_)
  • Stefan van der Walt (@stefanv <https://github.com/stefanv>_)
  • vfdev (@vfdev-5 <https://github.com/vfdev-5>_)

21 reviewers added to this release (alphabetically):

  • @GParolini <https://github.com/GParolini>_
  • Adrien Foucart (@adfoucart <https://github.com/adfoucart>_)
  • Anam Fatima (@anamfatima1304 <https://github.com/anamfatima1304>_)
  • Ben Harvie (@benharvie <https://github.com/benharvie>_)
  • Christian Clauss (@cclauss <https://github.com/cclauss>_)
  • Cris Luengo (@crisluengo <https://github.com/crisluengo>_)
  • Egor Panfilov (@soupault <https://github.com/soupault>_)
  • Grzegorz Bokota (@Czaki <https://github.com/Czaki>_)
  • Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
  • Jeremy Farrell (@farrjere <https://github.com/farrjere>_)
  • Juan Nunez-Iglesias (@jni <https://github.com/jni>_)
  • Lars Grüter (@lagru <https://github.com/lagru>_)
  • M Bussonnier (@Carreau <https://github.com/Carreau>_)
  • Mao Nishino (@mao1756 <https://github.com/mao1756>_)
  • Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
  • Mark Harfouche (@hmaarrfk <https://github.com/hmaarrfk>_)
  • Maxime Corbé (@Maxime-corbe <https://github.com/Maxime-corbe>_)
  • P. L. Lim (@pllim <https://github.com/pllim>_)
  • Peter Suter (@petsuter <https://github.com/petsuter>_)
  • Sebastian Berg (@seberg <https://github.com/seberg>_)
  • Stefan van der Walt (@stefanv <https://github.com/stefanv>_)

These lists are automatically generated, and may not be complete or may contain duplicates.