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| :orphan: | ||
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| scikit-image 0.X.0 (not released) | ||
| ================================= | ||
|
|
||
| scikit-image is an image processing library for the scientific Python | ||
| ecosystem that includes algorithms for segmentation, geometric | ||
| transformations, feature detection, registration, color space | ||
| manipulation, analysis, filtering, morphology, and more. | ||
| New Features | ||
| ------------ | ||
|
|
||
| For more information, examples, and documentation, please visit our website: | ||
| - 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 functions ``mirror_footprint`` and ``pad_footprint`` to ``skimage.morphology`` (`#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>`_). | ||
| - Add new parameter ``spacing`` to ``segmentation.expand_labels`` to support anisotropic images (`#7080 <https://github.com/scikit-image/scikit-image/pull/7080>`_). | ||
|
|
||
| https://scikit-image.org | ||
| 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>`_). | ||
|
|
||
| New Features | ||
| ------------ | ||
| Performance | ||
| ----------- | ||
|
|
||
| - Add parameters ``mode`` and ``cval`` to ``erosion``, ``dilation``, ``opening``, ``closing``, ``white_tophat``, and ``black_tophat`` in ``skimage.morphology``; | ||
| add parameter ``mode`` to ``binary_erosion``, ``binary_dilation``, ``binary_opening`` and ``binary_closing`` in ``skimage.morphology``; | ||
| add functions ``mirror_footprint`` and ``pad_footprint`` to ``skimage.morphology``; | ||
| (`#6695 <https://github.com/scikit-image/scikit-image/pull/6695>`_). | ||
| - 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>`_). | ||
|
|
||
| Improvements | ||
| ------------ | ||
| 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>`_). | ||
| - Function docstring was changed to follow the conventions adopted in the original paper. τ was replaced with θ (`#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>`_). | ||
|
|
||
| Bugfixes | ||
| -------- | ||
| Infrastructure | ||
| -------------- | ||
|
|
||
| - ``skimage.morphology.closing`` and ``skimage.morphology.opening`` were not extensive and anti-extensive, respectively, if the footprint was not mirror symmetric | ||
| (`#6695 <https://github.com/scikit-image/scikit-image/pull/6695>`_). | ||
| - 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>`_). | ||
|
|
||
| Deprecations | ||
| 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 (`#7367 <https://github.com/scikit-image/scikit-image/pull/7367>`_). | ||
|
|
||
| Contributors | ||
| ------------ | ||
|
|
||
| - Parameters ``shift_x`` and ``shift_y`` in ``skimage.morphology.erosion`` and ``skimage.morphology.dilation`` are deprecated and a warning is emitted if they are given. | ||
| (`#6695 <https://github.com/scikit-image/scikit-image/pull/6695>`_). | ||
| 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._ | ||
|
|
||
| Contributors to this release | ||
| ---------------------------- |
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