doc/source/release_notes/release_0.19.rst
We're happy to announce the release of scikit-image v0.19.3!
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.
For more information, examples, and documentation, please visit our website:
skimage.restoration.cycle_spin (now defaults to single channel again)tifffile release.skimage.future.manual_polygon_segmentation to work with Matplotlib 3.5.skimage.io.imread to avoid warnings when using imageio>=2.16.2.test_tifffile_kwarg_passthrough) (#6357)We're happy to announce the release of scikit-image v0.19.2! This is primarily a bug fix release, although there is one new gallery example related to detection of fluorescence at the nuclear envelope of mammalian cells.
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.
For more information, examples, and documentation, please visit our website:
enforce_connectivity=True and start_label > 0) (gh-6246)We're happy to announce the release of scikit-image v0.19.1!
This is a small bug fix release that resolves a couple of backwards compatibility issues and a couple of issues with the wheels on PyPI. Specifically, MacOs wheels for Apple M1 (arm64) on PyPI were broken in 0.19.0, but should now be repaired. The arm64 wheels are for MacOs >= 12 only. Wheel sizes are also greatly reduced relative to 0.19.0 by stripping debug symbols from the binaries and making sure that Cython-generated source files are not bundled in the wheels.
channel_axis parameter in transform functions) (gh-6100)We're happy to announce the release of scikit-image v0.19.0!
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.
For more information, examples, and documentation, please visit our website:
A highlight of this release is the addition of the popular scale-invariant feature transform (SIFT) feature detector and descriptor. This release also introduces a perceptual blur metric, new pixel graph algorithms, and most functions now operate in single-precision when single-precision inputs are provided. Many other bug fixes, enhancements and performance improvements are detailed below.
A significant change in this release is in the treatment of multichannel
images. The existing multichannel argument to functions has been deprecated
in favor of a new channel_axis argument. channel_axis can be used to
specify which axis of an array contains channel information (with
channel_axis=None indicating a grayscale image).
scikit-image now uses "lazy loading", which enables users to access the
functions from all skimage submodules without the overhead of eagerly
importing all submodules. As a concrete example, after calling "import skimage"
a user can directly call a function such as skimage.transform.warp whereas
previously it would have been required to first "import skimage.transform".
An exciting change on the development side is the introduction of support for Pythran as an alternative to Cython for generating compiled code. We plan to keep Cython support as well going forward, so developers are free to use either one as appropriate. For those curious about Pythran, a good overview was given in the SciPy 2021 presentation, "Building SciPy Kernels with Pythran" (https://www.youtube.com/watch?v=6a9D9WL6ZjQ).
This release now supports Python 3.7-3.10. Apple M1 architecture (arm64) support is new to this release. MacOS 12 wheels are provided for Python 3.8-3.10.
channel_axis
argument under the API section of the release notes.skimage.measure.blur_effect).skimage.restoration.denoise_nl_means) now supports
3D multichannel, 4D and 4D multichannel data when fast_mode=True.skimage.filters.butterworth) was added.channel_axis keyword argument
that allows specification of which axis of an array corresponds to channels.
For backwards compatibility, this parameter defaults to channel_axis=-1,
indicating that channels are along the last axis.random_state to
morphology.medial_axis and restoration.unsupervised_wiener.numpy.random.Generator.saturation parameter to skimage.color.label2rgbskimage.metrics.normalized_mutual_informationskimage.util.label_points function for assigning labels to points.skimage.metrics.hausdorff_pair to find points separated by the
Hausdorff distance.illuminants and observers parameter options
were added to skimage.color.lab2rgb, skimage.color.rgb2lab,
skimage.color.xyz2lab, skimage.color.lab2xyz,
skimage.color.xyz2luv and skimage.color.luv2xyz.skimage.filters.threshold_multiotsu has a new hist keyword argument
to allow use with a user-supplied histogram. (gh-5543)skimage.restoration.denoise_bilateral added support for images containing
negative values. (gh-5527)skimage.feature functions blob_dog, blob_doh and blob_log
now support a threshold_rel keyword argument that can be used to specify
a relative threshold (in range [0, 1]) rather than an absolute one. (gh-5517)skimage.graph:
pixel_graph generates a graph (network) of pixels
according to their adjacency, and central_pixel finds
the geodesic center of the pixels. (gh-5602)latest.plot_thresholding.py example.plot_local_equalize.py.label variable in plot_regionprops.py to circumvent link issue
in docs.gaussian docs.adjust_sigmoid function.shape_index docstring modification to specify 2D array.channel_axis rather than
multichannel. (gh-5554)skimage.restoration.inpaint_biharmonic) was
refactored and is orders of magnitude faster than before.skimage.util.random_noise is now
faster.skimage.segmentation.slice) was improved for the case where a mask
is supplied by the user (gh-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 thanks to
a LUT (gh-4966).measure.label has been accelerated for boolean input images, by using
scipy.ndimage's implementation for this case (gh-4945).util.apply_parallel now works with multichannel data (gh-4927).skimage.feature.peak_local_max supports now any Minkowski distance.skimage.filters.correlate_sparse.skimage.filters.try_all_threshold.skimage.filters.find_local_max when given a finite num_peaks.skimage.filters.rank module now release the GIL,
enabling multithreaded use.skimage.restoration.denoise_tv_bregman and
skimage.restoration.denoise_bilateral now release the GIL, enabling
multithreaded use.skimage.color.label2rgb performance regression was addressed.CircleModel.estimate. (gh-5190)skimage.restoration.denoise_tv_bregman, skimage.measure.block_reduce,
and skimage.filters.threshold_local. (gh-5454)multichannel boolean argument has been deprecated. All functions with
multichannel support now use an integer channel_axis to specify which
axis corresponds to channels. Setting channel_axis to None is used to
indicate that the image is grayscale. Specifically, existing code with
multichannel=True should be updated to use channel_axis=-1 and code
with multichannel=False should now specify channel_axis=None.measure.find_contours, corresponding to
the half distance between the min and max values of the image
(gh-4862).data.cat has been introduced as an alias of data.chelsea for a more
descriptive name.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.skimage.transforms.integral_image now promotes floating point inputs to
double precision by default (for accuracy). A new dtype keyword argument
can be used to override this behavior when desired.channel_axis keyword argument
(see New Features section).compactness
parameter has an effect that is independent of the input image's scaling.skimage.register.phase_cross_correlation may result in a different result
as compared to prior releases. The prior behavior of "unnormalized" cross
correlation is still available by explicitly setting normalization=None.
There is no change to the masked cross-correlation case, which uses a
different algorithm.labels argument renumbering in skimage.feature.peak_local_max
is avoided (gh-5047).find_bounaries with mode='subpixel' (gh-5447)._label2rgb_avg function.skimage.color.separate_stains does not return negative values.EllipseModel.skimage.transform.hough_line.skimage.filters.gaussian.skimage.segmentation.random_walker.skimage.measure.regionprops_table) dtype bugfix.skimage.transform.rescale when using a small scale factor.skimage.measure.label segfault.skimage.segmentation.watershed): consider connectivity when
calculating markers.skimage.transform.warp output dtype when order=0.intensity_image extra_properties in regionprops.skimage.metric.structural_similarity when image is
too small.skimage.segmentation.find_boundaries.skimage.exposure.is_low_contrast for boolean inputs.skimage.metric.structural_similarity .skimage.filters.threshold_otsu.skimage.feature.blob_dog docstring example and normalization.skimage.exposure.adjust_gamma.offsets attribute of skimage.graph.MCP is now public. (gh-5547)skimage.exposure.histogram and
skimage.measure.regionprops_table. (gh-5522)skimage.register.phase_cross_correlation.
(gh-5461)convex_hull) (gh-6008)Completed deprecations from prior releases
- In ``measure.label``, the deprecated ``neighbors`` parameter has been
removed (use ``connectivity`` instead).
- The deprecated ``skimage.color.rgb2grey`` and ``skimage.color.grey2rgb``
functions have been removed (use ``skimage.color.rgb2gray`` and
``skimage.color.gray2rgb`` instead).
- ``skimage.color.rgb2gray`` no longer allows grayscale or RGBA inputs.
- The deprecated ``alpha`` parameter of ``skimage.color.gray2rgb`` has now been
removed. Use ``skimage.color.gray2rgba`` for conversion to RGBA.
- Attempting to warp a boolean image with ``order > 0`` now raises a
ValueError.
- When warping or rescaling boolean images, setting ``anti-aliasing=True`` will
raise a ValueError.
- The ``bg_label`` parameter of ``skimage.color.label2rgb`` is now 0.
- The deprecated ``filter`` parameter of ``skimage.transform.iradon`` has now
been removed (use ``filter_name`` instead).
- The deprecated ``skimage.draw.circle`` function has been removed (use
``skimage.draw.disk`` instead).
- The deprecated ``skimage.feature.register_translation`` function has
been removed (use ``skimage.registration.phase_cross_correlation`` instead).
- The deprecated ``skimage.feature.masked_register_translation`` function has
been removed (use ``skimage.registration.phase_cross_correlation`` instead).
- The deprecated ``skimage.measure.marching_cubes_classic`` function has
been removed (use ``skimage.measure.marching_cubes`` instead).
- The deprecated ``skimage.measure.marching_cubes_lewiner`` function has
been removed (use ``skimage.measure.marching_cubes`` instead).
- The deprecated ``skimage.segmentation.circle_level_set`` function has been
removed (use ``skimage.segmentation.disk_level_set`` instead).
- The deprecated ``inplace`` parameter of ``skimage.morphology.flood_fill``
- The deprecated ``skimage.util.pad`` function has been removed (use
``numpy.pad`` instead).
been removed (use ``in_place`` instead).
- The default ``mode`` in ``skimage.filters.hessian`` is now
``'reflect'``.
- The default boundary ``mode`` in ``skimage.filters.sato`` is now
``'reflect'``.
- The default boundary ``mode`` in ``skimage.measure.profile_line`` is now
``'reflect'``.
- The default value of ``preserve_range`` in
``skimage.restoration.denoise_nl_means`` is now False.
- The default value of ``start_label`` in ``skimage.segmentation.slic`` is now
1.
Newly introduced deprecations:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- The ``multichannel`` argument is now deprecated throughout the library and
will be removed in 1.0. The new ``channel_axis`` argument should be used
instead. Existing code with ``multichannel=True`` should be updated to use
``channel_axis=-1`` and code with ``multichannel=False`` should now specify
``channel_axis=None``.
- ``skimage.feature.greycomatrix`` and ``skimage.feature.greycoprops`` are
deprecated in favor of ``skimage.feature.graycomatrix`` and
``skimage.feature.graycoprops``.
- The ``skimage.morphology.grey`` module has been renamed
``skimage.morphology.gray``. The old name is deprecated.
- The ``skimage.morphology.greyreconstruct`` module has been renamed
``skimage.morphology.grayreconstruct``. The old name is deprecated.
- see **API Changes** section regarding functions with deprecated argument
names related to the number of iterations. ``num_iterations`` and
``max_num_iter`` are now used throughout the library.
- see **API Changes** section on deprecation of the ``selem`` argument in favor
of ``footprint`` throughout the library
- Deprecate ``in_place`` in favor of the use of an explicit ``out`` argument
in ``skimage.morphology.remove_small_objects``,
``skimage.morphology.remove_small_holes`` and
``skimage.segmentation.clear_border``
- The ``input`` argument of ``skimage.measure.label`` has been renamed
``label_image``. The old name is deprecated.
- standardize on ``num_iter`` for parameters describing the number of iterations
and ``max_num_iter`` for parameters specifying an iteration limit. Functions
where the old argument names have now been deprecated are::
skimage.filters.threshold_minimum
skimage.morphology.thin
skimage.restoration.denoise_tv_bregman
skimage.restoration.richardson_lucy
skimage.segmentation.active_contour
skimage.segmentation.chan_vese
skimage.segmentation.morphological_chan_vese
skimage.segmentation.morphological_geodesic_active_contour
skimage.segmentation.slic
- The names of several parameters in ``skimage.measure.regionprops`` have been
updated so that properties are better grouped by the first word(s) of the
name. The old names will continue to work for backwards compatibility.
The specific names that were updated are::
============================ ============================
Old Name New Name
============================ ============================
max_intensity intensity_max
mean_intensity intensity_mean
min_intensity intensity_min
bbox_area area_bbox
convex_area area_convex
filled_area area_filled
convex_image image_convex
filled_image image_filled
intensity_image image_intensity
local_centroid centroid_local
weighted_centroid centroid_weighted
weighted_local_centroid centroid_weighted_local
major_axis_length axis_major_length
minor_axis_length axis_minor_length
weighted_moments moments_weighted
weighted_moments_central moments_weighted_central
weighted_moments_hu moments_weighted_hu
weighted_moments_normalized moments_weighted_normalized
equivalent_diameter equivalent_diameter_area
============================ ============================
- The ``selem`` argument has been renamed to ``footprint`` throughout the
library. The ``selem`` argument is now deprecated.
Development process
-------------------
- Test setup and teardown functions added to allow raising an error on any
uncaught warnings via ``SKIMAGE_TEST_STRICT_WARNINGS_GLOBAL`` environment
variable.
- Increase automation in release process.
- Release wheels before source
- update minimum supported Matplotlib, NumPy, SciPy and Pillow
- Pin pillow to !=8.3.0
- Rename `master` to `main` throughout
- Ensure that README.txt has write permissions for subsequent imports.
- Run face classification gallery example with a single thread
- Enable pip and skimage.data caching on Azure
- Fix CircleCI and Azure CI caching.
- Address Cython warnings.
- Disable calls to plotly.io.show when running on Azure.
- Remove legacy Travis-CI scripts and update contributor documentation
accordingly.
- Increase cibuildwheel verbosity.
- Update pip during dev environment installation.
- Add benchmark checks to CI.
- Resolve stochastic rank filter test failures on CI.
- Ensure that README.txt has write permissions for subsequent imports.
- Decorators for helping with the transition between the keyword argument
multichannel and channel_axis.
- Add missing import in lch2lab docstring example (gh-5998)
- Prefer importing build_py and sdist from setuptools (gh-6007)
- Reintroduce skimage.test utility (gh-5909)
Other Updates
-------------
- Refactor np.random.x to use np.random.Generator.
- Avoid warnings about use of deprecated ``scipy.linalg.pinv2``.
- Simplify resize implementation using new SciPy 1.6 zoom option.
- Fix duplicate test function names in ``test_unsharp_mask.py``.
- Benchmarks: ``fix ResizeLocalMeanSuite.time_resize_local_mean`` signature.
- Prefer use of new-style NumPy random API in tests (gh-5450)
- Add fixture enforcing SimpleITK I/O in test_simpleitk.py (gh-5526)
- MNT: Remove unused stat import from skimage data (gh-5566)
- MAINT: Remove unused imports (gh-5595)
- MAINT: Refactor duplicated tests, remove unnecessary assignments and
variables (gh-5596)
- Remove obsolete lazy import (gh-5992)
- Lazily load data_dir into the top-level namespace (gh-5996)
- Update scipy requirement to 1.4.1 and use scipy.fft instead of scipy.fftpack
(gh-5999)
- Remove lines generating Requires metadata (gh-6017)
- Update wheel builds to include Python 3.10 (gh-6021)
- Update pyproject.toml to handle Python 3.10 and Apple arm64 (gh-6022)
- Add python 3.10 test runs on GitHub Actions and Appveyor (gh-6027)
- Pin sphinx to <4.3 until new sphinx-gallery release is available (gh-6029)
- Relax a couple of equality tests causing i686 test failures on cibuildwheel
(gh-6031)
- Avoid matplotlib import overhead during 'import skimage' (gh-6032)
- Update sphinx gallery pin (gh-6034)
Contributors to this release
----------------------------
80 authors added to this release [alphabetical by first name or login]
----------------------------------------------------------------------
- Abhinavmishra8960 (Abhinavmishra8960)
- abouysso
- Alessia Marcolini
- Alex Brooks
- Alexandre de Siqueira
- Andres Fernandez
- Andrew Hurlbatt
- andrewnags (andrewnags)
- Antoine Bierret
- BMaster123 (BMaster123)
- Boaz Mohar
- Bozhidar Karaargirov
- Carlos Andrés Álvarez Restrepo
- Christoph Gohlke
- Christoph Sommer
- Clement Ng
- cmarasinou
- Cris Luengo
- David Manthey
- Devanshu Shah
- Dhiraj Kumar Sah
- divyank agarwal
- Egor Panfilov
- Emmanuelle Gouillart
- Erik Reed
- erykoff (erykoff)
- Fabian Schneider
- Felipe Gutierrez-Barragan
- François Boulogne
- Fred Bunt
- Fukai Yohsuke
- Gregory R. Lee
- Hari Prasad
- Harish Venkataraman
- Harshit Dixit
- Ian Hunt-Isaak
- Jaime Rodríguez-Guerra
- Jan-Hendrik Müller
- Janakarajan Natarajan
- Jenny Vo
- john lee
- Jonathan Striebel
- Joseph Fox-Rabinovitz
- Juan Antonio Barragan Noguera
- Juan Nunez-Iglesias
- Julien Jerphanion
- Jurneo
- klaussfreire (klaussfreire)
- Larkinnjm1 (Larkinnjm1)
- Lars Grüter
- Mads Dyrmann
- Marianne Corvellec
- Marios Achilias
- Mark Boer
- Mark Harfouche
- Matthias Bussonnier
- Mauro Silberberg
- Max Frei
- michalkrawczyk (michalkrawczyk)
- Niels Cautaerts
- Pamphile ROY
- Pradyumna Rahul
- R
- Raphael
- Riadh Fezzani
- Robert Haase
- Sebastian Gonzalez Tirado
- Sebastián Vanrell
- serge-sans-paille (serge-sans-paille)
- Stefan van der Walt
- t.ae
- that1solodev (Xyno18)
- Thomas Walter
- Tim Gates
- Tom Flux
- Vinicius D. Cerutti
- Volker Hilsenstein
- WeiChungChang
- yacth
- Yash-10 (Yash-10)
63 reviewers added to this release [alphabetical by first name or login]
------------------------------------------------------------------------
- Abhinavmishra8960
- Alessia Marcolini
- Alex Brooks
- Alexandre de Siqueira
- Andres Fernandez
- Andrew Hurlbatt
- andrewnags
- BMaster123
- Boaz Mohar
- Carlos Andrés Álvarez Restrepo
- Clement Ng
- Cris Luengo
- Dan Schult
- David Manthey
- Egor Panfilov
- Emmanuelle Gouillart
- erykoff
- Fabian Schneider
- Felipe Gutierrez-Barragan
- François Boulogne
- Fukai Yohsuke
- Genevieve Buckley
- Gregory R. Lee
- Jan Eglinger
- Jan-Hendrik Müller
- Janakarajan Natarajan
- Jarrod Millman
- Jirka Borovec
- Joan Massich
- Johannes Schönberger
- john lee
- Jon Crall
- Joseph Fox-Rabinovitz
- Josh Warner
- Juan Nunez-Iglesias
- Julien Jerphanion
- Kenneth Hoste
- klaussfreire
- Larkinnjm1
- Lars Grüter
- Marianne Corvellec
- Mark Boer
- Mark Harfouche
- Matthias Bussonnier
- Max Frei
- michalkrawczyk
- Niels Cautaerts
- Pamphile ROY
- Pomax
- R
- Raphael
- Riadh Fezzani
- Robert Kern
- Ross Barnowski
- Sebastian Berg
- Sebastian Gonzalez Tirado
- Sebastian Wallkötter
- serge-sans-paille
- Stefan van der Walt
- t.ae
- Vinicius D. Cerutti
- Volker Hilsenstein
- Yash-10