177 lines
8.3 KiB
ReStructuredText
177 lines
8.3 KiB
ReStructuredText
Announcement: scikit-image 0.X.0
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================================
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We're happy to announce the release of scikit-image v0.X.0!
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scikit-image is an image processing toolbox for SciPy that includes algorithms
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for segmentation, geometric transformations, color space manipulation,
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analysis, filtering, morphology, feature detection, and more.
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For more information, examples, and documentation, please visit our website:
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https://scikit-image.org
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New Features
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------------
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- A new function ``segmentation.expand_labels`` has been added in order to dilate
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labels while preventing overlap (#4795)
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- It is now possible to pass extra measurement functions to
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``measure.regionprops`` and ``regionprops_table`` (#4810)
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- Added a new perimeter function - ``measure.perimeter_crofton``.
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- Added 3D support for many filters in skimage.filters.rank.
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- New images have been added in the ``data`` subpackage: ``data.eagle``
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(#4922), TODO for other images
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Also note that the image for ``data.camera`` has been changed due to
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copyright issues (#4913).
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Documentation
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-------------
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- A new doc tutorial presenting a cell biology example has been added to the
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gallery (#4648). The scientific content benefited from a much appreciated
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review by Pierre Poulain and Fred Bernard, both assistant professors at
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Université de Paris and Institut Jacques Monod.
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- New tutorial on `visualizing 3D data <https://scikit-image.org/docs/dev/auto_examples/applications/plot_3d_image_processing.html>`_ (#4850)
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- Documentation has been added to the contributing notes about how to submit a
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gallery example
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- Automatic formatting of docstrings for improved consistency (#4849)
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- Improved docstring for ``rgb2lab`` (#4839) and ``marching_cubes`` (#4846)
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- Improved docstring for ``measure.marching_cubes``, mentioning how to decimate a
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mesh using mayavi (#4846)
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- Improved docstring for ``util.random_noise`` (#5001)
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- Improved docstrings for ``morphology.h_maxima`` and ``morphology.h_minima``
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(#4929).
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- Improved docstring for ``util.img_as_int`` (#4888).
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- An example showing how to explore interactively the properties of labelled
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regions `has been added <https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_regionprops.html>`_
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(#5010).
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- Documentation has been added to explain
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`how to download example datasets <https://scikit-image.org/docs/dev/install.html#downloading-all-demo-datasets>`_
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which are not installed with scikit-image (#4984). Similarly, the contributor
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guide has been updated to mention how to host new datasets in a gitlab
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repository (#4892).
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- The `benchmarking section of the developer documentation <https://scikit-image.org/docs/dev/contribute.html#benchmarks>`_
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has been expanded (#4905).
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Improvements
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------------
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- In ``skimage.restoration.richardson_lucy``, computations are now be done in
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single-precision when the input image is single-precision. This can give a
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substantial performance improvement when working with single precision data.
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- ``pyproject.toml`` has been added to the sdist.
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- The performance of the SLIC superpixels algorithm
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(``skimage.segmentation.slice``) was improved for the case where a mask
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is supplied by the user (#4903). The specific superpixels produced by
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masked SLIC will not be identical to those produced by prior releases.
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- ``exposure.adjust_gamma`` has been accelerated for ``uint8`` images thanks to a
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LUT (#4966).
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- ``measure.label`` has been accelerated for boolean input images, by using
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``scipy.ndimage``'s implementation for this case (#4945).
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- ``util.apply_parallel`` now works with multichannel data (#4927).
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- ``skimage.feature.peak_local_max`` supports now any Minkowski distance.
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API Changes
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-----------
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- A default value has been added to ``measure.find_contours``, corresponding to
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the half distance between the min and max values of the image
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#4862
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- ``skimage.restoration.richardson_lucy`` returns a single-precision output
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when the input is single-precision. Prior to this release, double-precision
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was always used.
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- The default value of ``threshold_rel`` in ``skimage.feature.corner`` has
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changed from 0.1 to None, which corresponds to letting
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``skimage.feature.peak_local_max`` decide on the default. This is currently
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equivalent to ``threshold_rel=0``.
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- ``data.cat`` has been introduced as an alias of ``data.chelsea`` for a more
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descriptive name.
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- The ``level`` parameter of ``measure.find_contours`` is now a keyword
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argument, with a default value set to (max(image) - min(image)) / 2.
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- ``p_norm`` argument was added to ``skimage.feature.peak_local_max``
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to add support for Minkowski distances.
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Bugfixes
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--------
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- For the RANSAC algorithm, improved the case where all data points are
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outliers, which was previously raising an error
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(#4844)
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- An error-causing bug has been corrected for the ``bg_color`` parameter in
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``label2rgb`` when its value is a string (#4840)
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- A normalization bug was fixed in ``metrics.variation_of_information``
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(#4875)
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- Fixed the behaviour of Richardson-Lucy deconvolution for images with 3
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dimensions or more (#4823)
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- Euler characteristic property of ``skimage.measure.regionprops`` was erroneous
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for 3D objects, since it did not take tunnels into account. A new implementation
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based on integral geometry fixes this bug.
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- In ``skimage.morphology.selem.rectangle`` the ``height`` argument
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controlled the width and the ``width`` argument controlled the height.
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They have been replaced with ``nrow`` and ``ncol``.
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- ``skimage.segmentation.flood_fill`` and ``skimage.segmentation.flood``
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now consistently handle negative values for ``seed_point``.
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- Segmentation faults in ``segmentation.flood`` have been fixed in #4948 and #4972
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- A segfault in ``draw.polygon`` for the case of 0-d input has been fixed
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(#4943).
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- In ``registration.phase_cross_correlation``, a ``ValueError`` is raised when
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NaNs are found in the computation (as a result of NaNs in input images).
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Before this fix, an incorrect value could be returned where the input images
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had NaNs (#4886).
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- ``min_distance`` is now enforced for ``skimage.feature.peak_local_max``
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(#2592).
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- Peak detection in labels is fixed in ``skimage.feature.peak_local_max``
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(#4756).
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- Input ``labels`` argument renumbering in ``skimage.feature.peak_local_max``
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is avoided (#5047).
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Deprecations
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------------
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- In ``skimage.feature.structure_tensor``, an ``order`` argument has been
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introduced which will default to 'rc' starting in version 0.20.
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- ``skimage.feature.structure_tensor_eigvals`` has been deprecated and will be
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removed in version 0.20. Use ``skimage.feature.structure_tensor_eigenvalues``
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instead.
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- The ``skimage.viewer`` subpackage and the ``skivi`` script have been
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deprecated and will be removed in version 0.20. For interactive visualization
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we recommend using dedicated tools such as napari or plotly. In a similar
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vein, the ``qt`` and ``skivi`` plugins of ``skimage.io`` have been deprecated
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and will be removed in version 0.20.
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- In ``skimage.morphology.selem.rectangle`` the arguments ``width`` and
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``height`` have been deprecated. Use ``nrow`` and ``ncol`` instead.
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- The explicit setting ``threshold_rel=0` was removed from the Examples of the
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following docstrings: ``skimage.feature.BRIEF``,
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``skimage.feature.corner_harris``, ``skimage.feature.corner_shi_tomasi``,
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``skimage.feature.corner_foerstner``, ``skimage.feature.corner_fast``,
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``skimage.feature.corner_subpix``, ``skimage.feature.corner_peaks``,
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``skimage.feature.corner_orientations``, and
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``skimage.feature._detect_octave``.
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- In ``skimage.restoration._denoise``, the warning regarding
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``rescale_sigma=None`` was removed.
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- In ``skimage.restoration._cycle_spin``, the ``# doctest: +SKIP`` was removed.
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- In ``measure.label``, the deprecated ``neighbors`` parameter has been
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removed.
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Development process
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-------------------
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- Benchmarks can now run on older scikit-image commits (#4891)
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- Website analytics are tracked using plausible.io and can be visualized on
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https://plausible.io/scikit-image.org (#4893)
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- Artifacts for the documentation build are now found in each pull request
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(#4881).
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- Documentation source files can now be written in Markdown in addition to
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ResT, thanks to ``myst`` (#4863).
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Contributors to this release
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----------------------------
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