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).

Documentation#

  • Add date to 0.23.1 release notes (#7384).

  • Fix docstring of connectivity parameter in skimage.segmentation.watershed (#7360).

Infrastructure#

  • Ignore Sphinx warning about unpickable cache (#7400).

  • Simplify instructions on changelist in PR template (#7401).

Maintenance#

  • Use numpy.inf instead of deprecated numpy.infty (#7386).

  • Update Ruff config (#7387).

  • Update matrix and names of Azure pipelines configuration (#7390).

  • Use upload- and download-artifact v4 (#7389).

  • Ignore arch specific cast warnings originating from astype in tests (#7393).

  • Update link to numpydoc example.py (#7395).

Contributors#

4 authors added to this release (alphabetically):

4 reviewers added to this release (alphabetically):

_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).

  • 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).

  • 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).

  • Speedup skimage.util.map_array by parallelization with Cython’s prange (#7266).

New Features#

  • Add new intensity_std property to skimage.measure.regionprops which computes the standard deviation of the intensity in a region (#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).

  • 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).

  • Add functions mirror_footprint and pad_footprint to skimage.morphology (#6695).

  • Add new parameter spacing to segmentation.expand_labels to support anisotropic images (#7080).

API Changes#

  • Drop support for Python 3.9 (#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).

  • 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).

  • Deprecate function skimage.feature.plot_matches in favor of skimage.feature.plot_matched_features (#7255).

  • Deprecate skimage.morphology.skeletonize_3d in favor of just skimage.morphology.skeletonize (#7094).

  • Deprecate parameter output in skimage.filters.gaussian; use out instead (#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).

Performance#

  • Add lazy loading to skimage.metrics module (#7211).

  • Speedup skimage.util.map_array by parallelization with Cython’s prange (#7266).

Bug Fixes#

  • Add exception to avoid surprising result when image is too small for the given parameters in skimage.feature.hog (#7153).

  • Ensure skimage.morphology.closing and skimage.morphology.opening are extensive and anti-extensive, respectively, if the footprint is not mirror symmetric (#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).

  • Fix logic in skimage.graph.pixel_graph which raised a TypeError when the parameter edge_function was provided without a mask (#7310).

  • Ensure cache stays empty when cache=False is passed to skimage.measure.regionprops (#7333).

Documentation#

  • Update instructions for updating dev environment (#7160).

  • Make titles in RAG gallery examples more explicit (#7202).

  • Add docstring to skimage.graph module (#7192).

  • Use consistent notation for array dimensions in the docstrings (#3031).

  • Specify default markers in watershed docstring (#7154).

  • Stop HTML documentation from intercepting left and right-arrow keys to improve keyboard accessibility (#7226).

  • Fix reference formatting for nitpicky sphinx (#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).

  • Fix broken function calls and syntax issues in user guide (#7234).

  • Use correct default mode in docstring of skimage.transform.swirl (#7241).

  • Add missing documentation about spacing parameter in moments_normalized (#7248).

  • Update docstring & example in the hough_ellipse transform (#6893).

  • Point binder tag/branch to commit corresponding to docs/release (#7252).

  • Add example to FundamentalMatrixTransform class (#6863).

  • Adds explanation of what the optional dependency on Matplotlib offers to the install instructions (#7286).

  • Use correct symbol θ for tightness in the docstring of skimage.registration.optical_flow_tvl1 (#7314).

  • The description of the parameter cval is modified in “int or float”. cval is a numerical value not a string (#7319).

  • Remove obsolete instruction about documenting changes (#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).

  • Create SECURITY.md (#7230).

  • Remove deprecated parameter coordinates from docstring example of skimage.segmentation.active_contour (#7329).

  • Include dates in release note headings (#7269).

  • Update description of how to document pull requests for inclusion in the release notes (#7267).

  • Clarify description of data_range parameter in skimage.metrics.structural_similarity (#7345).

  • Use object-oriented Matplotlib style in longer gallery examples and demonstrations (doc/examples/applications) (#7346).

  • In the gallery example on segmenting human cells (in mitosis), include the border when generating basin markers for watershed (#7362).

  • Add missing minus sign in docstring of skimage.transform.EuclideanTransform (#7097).

Infrastructure#

  • Update wording on the stale bot to assume the core team dropped the ball (#7196).

  • Update Azure job name following the drop of Python 3.9 (#7218).

  • Schedule nightly wheel builds at uncommon time (#7254).

  • Build nightly wheels with nightly NumPy 2.0 (#7251).

  • Use pytest-doctestplus instead of classic pytest-doctest (#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).

  • Add assert_stacklevel helper to check stacklevel of captured warnings (#7294).

  • Exclude pre-commit[bot] from changelist’s contributor list (#7358).

Maintenance#

  • Remove outdated & duplicate “preferred” field in version_switcher.json (#7184).

  • Upgrade to spin 0.7 (#7168).

  • Do not compare types, use isinstance (#7186).

  • [pre-commit.ci] pre-commit autoupdate (#7181).

  • Increase tolerance for moments test for 32 bit floats (#7188).

  • Temporarily pin Cython to <3.0.3 until CI is fixed (#7189).

  • Remove obsolete meson instructions (#7193).

  • Temporarily pin Cython to <3.0.3 until CI is fixed, take 2 (#7201).

  • Fix chocolatey (#7200).

  • Pin Pillow to <10.1.0 until incompatibility with imageio is fixed (#7208).

  • Use Black (#7197).

  • Apply black to _hog.py after previous merge lacking black (#7215).

  • Unpin Cython after release of Cython 3.0.4 (#7214).

  • [pre-commit.ci] pre-commit autoupdate (#7236).

  • Cleanup for Python 3.12 (#7173).

  • Make Python 3.12 default CI Python (#7244).

  • Add explicit noexcept to address Cython 3.0 warnings (#7250).

  • Update imageio to fix Pillow incompatibility (#7245).

  • Upgrade docker/setup-qemu-action to v3 (#7134).

  • Fix warningfilter for deprecation in SciPy 1.12.0rc1 (#7275).

  • Update to numpy>=1.23 and matplotlib>=3.6 according to SPEC 0 (#7284).

  • Add new deprecate_parameter helper (#7256).

  • Update meson and Cython (#7283).

  • Handle floating point warning for empty images in skimage.registration.phase_cross_correlation (#7287).

  • Update spin (0.8) (#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).

  • 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).

  • Update pre-commits repos (#7303).

  • The test suite can now be run without numpydoc installed (#7307).

  • Deal with parallel write warning from Pydata theme (#7311).

  • Test nightly wheel build with NumPy 2.0 (#7288).

  • Make it clear that funcs in _optical_flow_utils are private (#7328).

  • Update dependencies (spec 0) (#7335).

  • Follow-up cleaning & fixes for compatibility with NumPy 1 & 2 (#7326).

  • Replace ignored teardown with autouse fixture in test_fits.py (#7340).

  • Address new copy semantics & broadcasting in np.solve in NumPy 2 (#7341).

  • Ignore table of execution times by Sphinx gallery (#7327).

  • Allow a very small floating point tolerance for pearson test (#7356).

  • Update numpydoc to version 1.7 (#7355).

  • [pre-commit.ci] pre-commit autoupdate (#7365).

  • Simplify warning filters in test suite (#7349).

  • Build against NumPy >=2.0.0rc1 (#7367).

  • Remove ensure_python_version function (#7370).

  • Update GitHub actions to setup-python@v5, cache@v4, upload-artifact@v4, and download-artifact@v4 (#7368).

  • Update lazyloader to v0.4 (#7373).

Contributors#

29 authors added to this release (alphabetically):

21 reviewers added to this release (alphabetically):

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