Dear skimagers, I’ve just pushed scikit-image 0.18.0 release candidate 2 to PyPI. I think this is the real one! If I don’t hear objections by tomorrow morning (~24h from the timestamp on this email), I’ll tag and (finally!) release 0.18.0. 🎉 Please try this release candidate out by using `pip install -U --pre scikit-image`. Since we have started adding further dependencies to our documentation examples, in order to run some of the examples you will need to `pip install -U --pre scikit-image[docs]`. Or, if you only want access to our new example datasets, you can use `pip install -U --pre scikit-image[data]`. Finally, if you want to systematically test this release on your machine, you can use `pip install -U --pre scikit-image[test]`, then run `pytest --pyargs skimage`. You can find the release notes below. Happy image analysis! Juan. 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. - 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``. - ``data.cat`` has been introduced as an alias of ``data.chelsea`` for a more descriptive name. - The ``level`` parameter of ``measure.find_contours`` is now a keyword argument, with a default value set to (max(image) - min(image)) / 2. - ``p_norm`` argument was added to ``skimage.feature.peak_local_max`` to add support for Minkowski distances. - In ``measure.label``, the deprecated ``neighbors`` parameter has been removed. (#4942) 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