scikit-image 0.18.1
===================

This is a bug fix release and contains the following two bug fixes:

- Fix indexing error for labelling in large (>2GB) arrays (#5143, #5151)
- Only use retry_if_failed with recent pooch (#5148)

See below for the new features and API changes in 0.18.0.

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. (#4880)
- 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``.
- In ``measure.label``, the deprecated ``neighbors`` parameter has been
  removed. (#4942)
- The image returned by ``data.camera`` has changed because of copyright
  issues (#4913).

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
