File python-scikit-image.changes of Package python-scikit-image
-------------------------------------------------------------------
Fri Jul 4 10:34:05 UTC 2025 - Lubos Kocman <lubos.kocman@suse.com>
- Do not build -test on Leap 16.0 as we lack many of its dependencies
This is part of hplip enablement on 16.0
-------------------------------------------------------------------
Mon Dec 16 07:09:20 UTC 2024 - Steve Kowalik <steven.kowalik@suse.com>
- Update to 0.25.0:
* New Features
+ Add the new Gray-Level Co-occurrence Matrix (GLCM) properties "mean",
"variance", "standard deviation" and "entropy" to
skimage.feature.texture.graycoprops (#7375).
+ Add the new skimage.morphology.footprint_rectangle supporting
generation of rectangular or hyper-rectangular footprints in one
function (#7566).
* API Changes
+ Complete the deprecation of and remove skimage.feature.plot_matches.
Use skimage.feature.plot_matched_features going forward (#7487).
+ Deprecate skimage.io.imshow, skimage.io.imshow_collection and
skimage.io.show. Please use matplotlib, napari, etc. to visualize
images (#7508).
+ Remove deprecated skimage.morphology.skeletonize_3d; use
skimage.morphology.skeletonize instead (#7572).
+ Deprecate skimage.io plugin infrastructure (#7353).
+ Switched to using the scipy.sparse array interface. For more details,
see the note about the new scipy.sparse array interface here (#7576).
+ Deprecate skimage.morphology.rectangle in favor of the new function
skimage.morphology.footprint_rectangle (#7566).
+ Deprecate skimage.morphology.square in favor of the new function
skimage.morphology.footprint_rectangle (#7566).
+ Deprecate skimage.morphology.cube in favor of the new function
skimage.morphology.footprint_rectangle (#7566).
* Enhancements
+ Improve numerical stability of skimage.morphology.local_minima for
extremely small floats (#7534).
+ Make sure that skimage.feature.plot_matched_features uses the same
random colors, if matches_color isn't provided explicitly (#7541).
+ Allow passing a sequence of colors to the parameter matches_color in
skimage.feature.plot_matched_features (#7541).
* Performance
+ skimage.feature.peak_local_max will now skip unnecessary distance
computations in the case of min_distance=1. This results in performance
improvements to functions like skimage.feature.blob_dog,
skimage.feature.blob_log, skimage.feature.blob_doh and
skimage.feature.corner_peaks that call peak_local_max
internally (#7548).
+ In skimage.featurepeak_local_max, skip unnecessary check for cases
where min_distance > 1 is passed (#7548).
* Bug Fixes
+ Ensure that skimage.morphology.remove_objects_by_distance doesn't fail
if the given integer dtype cannot be safely cast to the architecture
specific size of intp, e.g. on i386 architectures (#7453).
+ Fix degeneracy in skimage.draw.ellipsoid_stats when all semi-axes have
the same length (#7473).
+ Prevent skimage.morphology.thin from accidentally modifying the input
image in case it is of dtype uint8 (#7469).
+ Fix numerical precision error in skimage.measure.ransac. In some cases,
ransac was stopping at the first iteration (#7065).
+ Fix numerical precision error in skimage.measure.ransac; very small
probabilities lead to -0 number of max trials (#7496).
+ Ensure that RegionProperties objects returned by
skimage.measure.regionprops can be deserialized with pickle (#7569).
+ Fix edge case where setting watershed_lines=True in
skimage.segmentation.watershed resulted in an incorrect
solution (#7071).
+ Fix the behavior of skimage.segmentation.watershed when the markers
don't align with local minima by making sure every marker is
evaluated before successive pixels (#7071).
+ Fix dtype promotion in skimage.segmentation.join_segmentations if
numpy.uint is used with NumPy<2 (#7292).
* Maintenance
+ Set -DNPY_NO_DEPRECATED_API=NPY_1_23_API_VERSION on build (#7538).
+ Don't use deprecated io.show and io.imshow (#7556).
+ Drop Python 3.9 support (#7561).
+ Support Python 3.13 (#7565).
+ Remove deprecated gaussian output parameter (#7574).
-------------------------------------------------------------------
Mon Dec 2 21:16:40 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Not ready for python313 yet: gh#scikit-image/scikit-image#7585
-------------------------------------------------------------------
Fri Nov 15 17:20:23 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Fix tests
* Avoid random test collection order for np types
gh#pytest-dev/pytest-xdist#432
* Disable dask test gh#scikit-image/scikit-image#7491
-------------------------------------------------------------------
Wed Jul 17 07:05:51 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Revert. Numpy 2 is supported.
-------------------------------------------------------------------
Wed Jul 17 04:27:49 UTC 2024 - Steve Kowalik <steven.kowalik@suse.com>
- Restrict numpy to < 2 for now.
-------------------------------------------------------------------
Wed Jun 26 08:27:58 UTC 2024 - John Paul Adrian Glaubitz <adrian.glaubitz@suse.com>
- Update to 0.24.0
## Highlights
* Add new class ``skimage.transform.ThinPlateSplineTransform``, which can estimate
and model non-linear transforms with thin-plate splines and allows image warping
with ``skimage.transform.warp`` (#7040)
## New Features
* Add new class ``skimage.transform.ThinPlateSplineTransform``, which can estimate
and model non-linear transforms with thin-plate splines and allows image warping
with ``skimage.transform.warp`` (#7040)
* Add ``skimage.morphology.remove_objects_by_distance``, which removes labeled objects,
ordered by size (default), until the remaining objects are a given distance apart (#4165)
## Performance
* In ``skimage.feature.corner_fast``, test four directions earlier, which should more
than half the computation time for most cases (#7394)
## Documentation
* Remove obsolete instruction about documenting changes (#7321)
* Clarify description of ``data_range`` parameter in
``skimage.metrics.structural_similarity`` (#7345)
* Update release process notes (#7402)
* Fix typo in docstring of ``skimage.measure.regionprops`` (#7405)
* Fix typos in ``skimage.measure.find_contours`` (#7411)
* Add algorithmic complexity description + suggested alternatives to
``skimage.restoration.rolling_ball`` docstring (#7424)
* Remove ineffective PR contribution clause (#7429)
* Clarify objection period for lazy consensus in SKIP 1 (#7020)
* Add a new gallery example "Use thin-plate splines for image warping" (#7040)
* Add a new gallery example on "Removing objects" based on their size or distance (#4165)
## Infrastructure
* Escape user-controlled variables in GA workflow (#7415)
* Add generation of GitHub artifact attestations to built
sdist and wheels before upload to PyPI (#7427)
* For publishing actions use the full length commit SHA (#7433)
* Be mindful of resources by canceling in-progress workflows (#7436)
* Add out-of-tree Pyodide builds in CI for ``scikit-image`` (#7350)
## Maintenance
* Replace deprecated nose style setup/teardown with autouse fixtures (#7343)
* Temporarily pin macos-12 runner in CI (#7408)
* Fix NumPy2 dtype promotion issues in pywt dependent code (#7414)
* In ``skimage.util.compare_images``, deprecate the parameter ``image2``.
Instead use ``image0``, ``image1`` to pass the compared images. Furthermore,
all other parameters will be turned into keyword-only parameters once the
deprecation is complete (#7322)
* Add support back for Python 3.9 to enhance compatibility with Numpy 2 (#7412)
* Disable ruff/pyupgrade rule UP038 (#7430)
* Stop verifying wheel attestations temporarily (#7444)
- Drop patches for issues fixed upstream
* skimage-pr7414-np2.patch
-------------------------------------------------------------------
Thu Jun 6 17:13:16 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Add skimage-pr7414-np2.patch gh#scikit-image/scikit-image#7414
-------------------------------------------------------------------
Sun May 5 14:31:34 UTC 2024 - Ben Greiner <code@bnavigator.de>
- Update to 0.23.2
## Bug Fixes
* Make sure skimage.util.img_as_ubyte supports the edge case
where dtype('uint64').type of the provided image is
np.ulonglong instead of np.uint64 (#7392).
## Documentation
* Add date to 0.23.1 release notes (#7384).
* Fix docstring of connectivity parameter in
skimage.segmentation.watershed (#7360).
## Infrastructure
* Ignore Sphinx warning about unpickable cache (#7400).
* Simplify instructions on changelist in PR template (#7401).
## Maintenance
* Use numpy.inf instead of deprecated numpy.infty (#7386).
* Update Ruff config (#7387).
* Update matrix and names of Azure pipelines configuration
(#7390).
* Use upload- and download-artifact v4 (#7389).
* Ignore arch specific cast warnings originating from astype in
tests (#7393).
* Update link to numpydoc example.py (#7395).
- Release 0.23.1/0.23.0
## Highlights
* Ensure skimage.morphology.closing and
skimage.morphology.opening are extensive and anti-extensive,
respectively, if the footprint is not mirror symmetric (#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).
* 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).
* Speedup skimage.util.map_array by parallelization with Cython's
prange (#7266).
## New Features
* Add new intensity_std property to skimage.measure.regionprops
which computes the standard deviation of the intensity in a
region (#6712).
* 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).
* Add functions mirror_footprint and pad_footprint to
skimage.morphology (#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).
* Add new parameter spacing to segmentation.expand_labels to
support anisotropic images (#7080).
## API Changes
* Drop support for Python 3.9 (#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).
* 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).
* Deprecate function skimage.feature.plot_matches in favor of
skimage.feature.plot_matched_features (#7255).
* Deprecate skimage.morphology.skeletonize_3d in favor of just
skimage.morphology.skeletonize (#7094).
* Deprecate parameter output in skimage.filters.gaussian; use out
instead (#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).
* Performance
* Add lazy loading to skimage.metrics module (#7211).
* Speedup skimage.util.map_array by parallelization with Cython's
prange (#7266).
## Bug Fixes
* Add exception to avoid surprising result when image is too
small for the given parameters in skimage.feature.hog (#7153).
* Ensure skimage.morphology.closing and
skimage.morphology.opening are extensive and anti-extensive,
respectively, if the footprint is not mirror symmetric (#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).
* Fix logic in skimage.graph.pixel_graph which raised a TypeError
when the parameter edge_function was provided without a mask
(#7310).
* Ensure cache stays empty when cache=False is passed to
skimage.measure.regionprops (#7333).
-------------------------------------------------------------------
Sat Mar 16 20:10:32 UTC 2024 - Atri Bhattacharya <badshah400@gmail.com>
- Update to version 0.22.0:
* Long list of changes, see
https://scikit-image.org/docs/stable/release_notes/release_0.22.html
- Drop upstreamed patches
* np-warn.patch
* skimage-numpy125.patch
- Enable no longer failing tests.
-------------------------------------------------------------------
Tue Aug 22 19:18:49 UTC 2023 - Markéta Machová <mmachova@suse.com>
- Add upstream patches np-warn.patch and skimage-numpy125.patch
to fix build with NumPy 1.25
-------------------------------------------------------------------
Thu Jul 6 06:31:16 UTC 2023 - Atri Bhattacharya <badshah400@gmail.com>
- Update to version 0.21.0
* Too many changes to list, see
https://github.com/scikit-image/scikit-image/releases/tag/v0.21.0
- Update minimum versions of Requires/BuildRequires in keeping
with upstream.
- Use pyproject_* macros to build and install since there is no
setup.py any more.
- Drop skimage-fix-module-install.patch: fixed upstream.
- Fix some hashbangs before build.
- New Requires: python-lazy-loader.
- Set PYTEST_DEBUG_TEMPROOT to a tmp dir created within the
working dir as tests now require it to be writable.
- Some more tests disabled due to flaky floating point issues.
-------------------------------------------------------------------
Fri Jul 1 09:19:38 UTC 2022 - Ben Greiner <code@bnavigator.de>
- Update to 0.19.3
* Revert unintentional change to default multichannel behavior
introduced in v0.19.0 for skimage.restoration.cycle_spin (now
defaults to single channel again)
* Fix corner case with an optimal angle of 0 degrees in
hough_line_peaks
* Fixed the gallery example involving registration with log-polar
transformations
* Update test suite for compatibility with the most recent
tifffile release.
* warp/rotate: fixed a bug with clipping when cval is not in the
input range
* Fix computation of histogram bins for multichannel
integer-valued images
* Update skimage.future.manual_polygon_segmentation to work with
Matplotlib 3.5.
* Update skimage.io.imread to avoid warnings when using
imageio>=2.16.2.
* Now compatible with Pillow >= 9.1 (palette may contain <256
entries)
* Added support for NumPy 1.23
- Release 0.19.2
* 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.
- Release 0.19.1
* This is a small bug fix release that resolves a couple of
backwards compatibility issues.
- Release 0.19.0
* 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.
- Release 0.18.3
* This is a small bugfix release for compatibility with Pooch 1.5
and SciPy 1.7.
- Release 0.18.2
* This release fixes a couple of minor bugs.
- Add skimage-fix-module-install.patch
* gh#scikit-image/scikit-image#6428
-------------------------------------------------------------------
Fri Jan 22 19:18:32 UTC 2021 - Benjamin Greiner <code@bnavigator.de>
- Update to 0.18.1
* Fix indexing error for labelling in large (>2GB) arrays (#5143,
#5151)
* Only use retry_if_failed with recent pooch (#5148)
- 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.
-------------------------------------------------------------------
Thu Jan 7 17:04:54 UTC 2021 - Markéta Machová <mmachova@suse.com>
- Deleted patches:
* scikit-image-pr4735-ragged.patch
* scikit-image-pr4731-floatingwarnings.patch
-------------------------------------------------------------------
Wed Aug 12 10:22:23 UTC 2020 - Benjamin Greiner <code@bnavigator.de>
- Apply patches to fix errors due to numpy warnings
* scikit-image-pr4731-floatingwarnings.patch
gh#scikit-image/scikit-image#4731
* scikit-image-pr4735-ragged.patch
gh#scikit-image/scikit-image#4735
- Update requirements
- make multibuild
-------------------------------------------------------------------
Sat May 30 23:41:41 UTC 2020 - Arun Persaud <arun@gmx.de>
- update to version 0.17.2:
* Bug fixes
+ We made pooch an optional dependency, since it has been added as
required dependency by mistake (#4666), and we fixed a bug about
the path used for pooch to download data (#4662)
+ The support of float 32 images was corrected for slic
segmentation, ORB and BRIEF feature detectors (#4683, #4684,
#4685, #4696, #4697)
+ We removed deprecated arguments (#4691)
mask, shift_x, and shift_y from skimage.filters.median
beta1 and beta2 from skimage.filters.frangi
beta1 and beta2 from skimage.filters.hessian
dtype from skimage.io.imread
img from skimage.morphology.skeletonize_3d.
+ Gallery examples were updated to suppress warnings and take into
account new default values in some functions (#4692 and #4676)
-------------------------------------------------------------------
Tue May 12 10:19:23 UTC 2020 - Tomáš Chvátal <tchvatal@suse.com>
- We need at least pytest 4.x series
-------------------------------------------------------------------
Sat May 9 16:20:28 UTC 2020 - Arun Persaud <arun@gmx.de>
- update to version 0.17.1:
* fixed bug in label2rgb
- changes from version 0.17.0:
* New Features
+ Hyperparameter calibration of denoising algorithms with
restoration.calibrate_denoiser (#3824), with corresponding
gallery example and tutorial.
+ measure.profile_line has a new reduce_func parameter to accept a
reduction operation to be computed on pixel values along the
profile (#4206)
+ nD windows for reducing spectral leakage when computing the FFT
of n-dimensional images, with filters.window (#4252) (with new
gallery example)
+ Add Minkowski distance metric support to corner_peak (#4218)
+ util.map_array was introduced to map a set of pixel values to
another one (for example to map region labels to the size of
regions in an image of labels) #4612 and #4646
+ Masked marching cubes (#3829)
+ The SLIC superpixel algorithm now accepts a mask to exclude some
parts of the image and force the superpixel boundaries to follow
the boundary of the mask (#3850)
+ Pooch -- on the fly download of datasets from github: we
introduced the possibility to include larger datasets in the
data submodule, thanks to the pooch library. data.download_all
fetches all datasets. (#3945)
+ Starting with this version, our gallery examples now have links
to run the example notebook on a binder instance. (#4543)
+ New doc tutorials and gallery examples have been added to the
use of regionprops_table (#4348) geometrical transformations
(#4385), and the registration of rotation and scaling with no
shared center (#4515). A new section on registration has been
added to the gallery (#4575).
* Improvements
+ scikit-image aims at being fully compatible with 3D arrays, and
when possible with nD arrays. nD support has been added to color
conversion functions (#4418), to the CLAHE
exposure.equalize_adapthist algorithm (#4598) and to the Sobel,
Scharr, and Prewitt filters (#4347).
+ Multichannel support for denoise_tv_bregman (#4446)
+ The memory footprint of segmentation.relabel_sequential has been
reduced in the case of labels much larger than the number of
labels (#4612)
+ Random ellipses are now possible in draw.random_shapes (#4493)
+ Add border conditions to ridge filters (#4396)
+ segmentation.random_walker new Jacobi preconditioned conjugate
gradient mode (#4359) and minor corrections #4630
+ Warn when rescaling with NaN in exposure.intensity_range (#4265)
+ We have also improved the consistency of several functions
regarding the way they handle data types
+ Make dtype consistent in filters.rank functions (#4289)
+ Fix colorconv float32 to double cast (#4296)
+ Prevent radon from upcasting float32 arrays to double (#4297)
+ Manage iradon_sart input and output data type (#4300)
* API Changes
+ When used with floating point inputs, denoise_wavelet no longer
rescales the range of the data or clips the output to the range
[0, 1] or [-1, 1]. For non-float inputs, rescaling and clipping
still occurs as in prior releases (although with a bugfix
related to the scaling of sigma).
+ For 2D input, edge filters (Sobel, Scharr, Prewitt, Roberts, and
Farid) no longer set the boundary pixels to 0 when a mask is not
supplied. This was changed because the boundary mode for
scipy.ndimage.convolve is now 'reflect', which allows meaningful
values at the borders for these filters. To retain the old
behavior, pass mask=np.ones(image.shape, dtype=bool) (#4347)
+ When out_range is a range of numbers and not a dtype in
:func:`skimage.exposure.rescale_intensity`, the output data type
will always be float (#4585)
+ The values returned by
:func:`skimage.exposure.equalize_adapthist` will be slightly
different from previous versions due to different rounding
behavior (#4585)
+ Move masked_register_translation from feature to registration
(#4503)
+ Move register_translation from skimage.feature to
skimage.registration (#4502)
+ Move watershed from morphology to segmentation (#4443)
+ Rename draw.circle() to draw.disk() (#4428)
+ The forward and backward maps returned by
:func:`skimage.segmentation.relabel_sequential` are no longer
NumPy arrays, but more memory-efficient ArrayMap objects that
behave the same way for mapping. See the relabel_sequential
documentation for more details. To get NumPy arrays back, cast
it as a NumPy array: np.asarray(forward_map) (#4612)
* Bugfixes
+ denoise_wavelet: For user-supplied sigma, if the input image
gets rescaled via img_as_float, the same scaling will be applied
to sigma to preserve the relative scale of the noise
estimate. To restore the old, behaviour, the user can manually
specify rescale_sigma=False.
+ Fix Frangi artefacts around the image (#4343)
+ Fix Negative eigenvalue in inertia_tensor_eigvals due to
floating point precision (#4589)
+ Fix morphology.flood for F-ordered images (#4556)
+ Fix h_maxima/minima strange behaviors on floating point image
input (#4496)
+ Fix peak_local_max coordinates ordering (#4501)
+ Sort naturally peaks coordinates of same amplitude in
peak_local_max (#4582)
+ Fix denoise_nl_means data type management (#4322)
+ Update rescale_intensity to prevent under/overflow and produce
proper output dtype (#4585)
* Deprecations
+ The minimal supported Python version by this release is 3.6.
+ Parameter inplace in skimage.morphology.flood_fill has been
deprecated in favor of in_place and will be removed in version
scikit-image 0.19.0 (#4250).
+ skimage.segmentation.circle_level_set has been deprecated and
will be removed in 0.19. Use skimage.segmentation.disk_level_set
instead.
+ skimage.draw.circle has been deprecated and will be removed in
0.19. Use skimage.draw.disk instead.
+ Deprecate filter argument in iradon due to clash with python
keyword (#4158)
+ Deprecate marching_cubes_classic (#4287)
+ Change label2rgb default background value from -1 to 0 (#4614)
+ Deprecate rgb2grey and grey2rgb (#4420)
+ Complete deprecation of circle in morphsnakes (#4467)
+ Deprecate non RGB image conversion in rgb2gray (#4838, #4439),
and deprecate non gray scale image conversion in gray2rgb
(#4440)
-------------------------------------------------------------------
Fri Jan 17 12:52:19 UTC 2020 - Tomáš Chvátal <tchvatal@suse.com>
- Skip 2 failing tests on 32bit
- Do not buildrequire nose
-------------------------------------------------------------------
Wed Dec 4 09:11:03 UTC 2019 - Tomáš Chvátal <tchvatal@suse.com>
- Use xdist to speed up the testing that takes bit too much time
-------------------------------------------------------------------
Sat Nov 9 14:58:21 UTC 2019 - Arun Persaud <arun@gmx.de>
- specfile:
* remove two patched (included upstream):
- fix_numpy_1_17.patch
- fix_numpy_matrix_warning_test.patch
* add test requirement imageio
- update to version 0.16.2 (bsc#1157707):
* Bug fixes
+ Migrate to networkx 2.x (#4236, #4237)
+ Sync required numpy and dask to runtime versions (#4233, #4239)
+ Fix wrong argument parsing in structural_similarity (#4246,
#4247)
+ Fix active contour gallery example after change to rc
coordinates (#4257, #4262)
- changes from version 0.16.1:
* New Features
+ New `skimage.evaluate` module containing simple metrics (mse,
nrme, psd) and segmentation metrics (adapted rand error,
variation of information) (#4025)
+ n-dimensional TV-L1 optical flow algorithm for registration --
`skimage.registration.optical_flow_tvl1` (#3983)
+ Draw a line in an n-dimensional array -- `skimage.draw.line_nd`
(#2043)
+ 2D Farid & Simoncelli edge filters - `skimage.filters.farid`,
`skimage.filters.farid_h`, and `skimage.filters.farid_v` (#3775)
+ 2D majority voting filter assigning to each pixel the most
commonly occurring value within its neighborhood --
`skimage.filters.majority` (#3836, #3839)
+ Multi-level threshold "multi-Otsu" method, a thresholding
algorithm used to separate the pixels of an input image into
several classes by maximizing the variances between classes --
`skimage.filters.threshold_multiotsu` (#3872, #4174)
+ New example data -- `skimage.data.shepp_logan_phantom`,
`skimage.data.colorwheel`, `skimage.data.brick`,
`skimage.data.grass`, `skimage.data.roughwall`,
`skimage.data.cell` (#3958, #3966)
+ Compute and format image region properties as a table
--.measure.regionprops_table` (#3959)
+ Convert a polygon into a mask -- `skimage.draw.poly2mask`
(#3971, #3977)
+ Visual image comparison helper `skimage.util.compare_images`,
that returns an image showing the difference between two input
images (#4089)
+ `skimage.transform.warp_polar` to remap image into polar or
log-polar coordinates. (#4097)
* Improvements
+ RANSAC: new option to set initial samples selected for
initialization (#2992)
+ Better repr and str for `skimage.transform.ProjectiveTransform`
(#3525, #3967)
+ Better error messages and data type stability to
`skimage.segmentation.relabel_sequential` (#3740)
+ Improved compatibility with dask arrays in some image
thresholding methods (#3823)
+ `skimage.io.ImageCollection` can now receive lists of patterns
(#3928)
+ Speed up `skimage.feature.peak_local_max` (#3984)
+ Better error message when incorrect value for keyword argument
`kind` in.color.label2rgb` (#4055)
+ All functions from `skimage.drawing` now supports multi-channel
2D images (#4134)
* API Changes
+ Deprecated subpackage "skimage.novice" has been removed.
+ Default value of "multichannel" parameters has been set to False
in `skimage.transform.rescale`,
`skimage.transform.pyramid_reduce`,
`skimage.transform.pyramid_laplacian`,.transform.pyramid_gaussian`,
and `skimage.transform.pyramid_expand`. Guessing is no longer
performed for 3D.
+ Deprecated argument "visualise" has been removed
from.feature.hog`. Use "visualize" instead.¨
+ `skimage.transform.seam_carve` has been completely removed from
the library due to licensing restrictions.
+ Parameter "as_grey" has been removed from `skimage.data.load`
and `skimage.io.imread`. Use "as_gray" instead.
+ Parameter "min_size" has been removed from
`skimage.morphology.remove_small_holes`. Use "area_threshold"
instead.
+ Deprecated "correct_mesh_orientation" in `skimage.measure` has
been removed.
+ `skimage.measure._regionprops` has been completely switched to
using-column coordinates. Old x-y interface is not longer
available.
+ Default value of "behavior" parameter has been set to "ndimage"
in `skimage.filters.median`.
+ Parameter "flatten" in `skimage.io.imread` has been removed in
favor of "as_gray".
+ Parameters "Hxx, Hxy, Hyy" have been removed from
`skimage.feature.corner.hessian_matrix_eigvals` in favor of
"H_elems".
+ Default value of "order" parameter has been set to "rc" in
`skimage.feature.hessian_matrix`.
+ "skimage.util.img_as_*" functions no longer raise precision
and/or loss warnings.
* Bugfixes
+ Corrected error with scales attribute in ORB.detect_and_extract
(#2835) The scales attribute wasn't taking into account the
mask, and thus was using an incorrect array size.
+ Correct for bias in Inverse Randon Transform
(`skimage.transform.irandon`) (#3067) Fixed by using the Ramp
filter equation in the spatial domain as described in the
reference
+ Fix a rounding issue that caused a rotated image to have a
different size than the input (`skimage.transform.rotate`)
(#3173)
+ RANSAC uses random subsets of the original data and not
bootstraps. (#3901, #3915)
+ Canny now produces the same output regardless of dtype (#3919)
+ Geometry Transforms: avoid division by zero & some degenerate
cases (#3926)
+ Fixed float32 support in denoise_bilateral and
denoise_tv_bregman (#3936)
+ Fixed computation of Meijering filter and avoid
ZeroDivisionError (#3957)
+ Fixed `skimage.filters.threshold_li` to prevent being stuck on
stationnary points, and thus at local minima or maxima (#3966)
+ Edited `skimage.exposure.rescale_intensity` to return input
image instead of nans when all 0 (#4015)
+ Fixed `skimage.morphology.medial_axis`. A wrong indentation in
Cython caused the function to not behave as intended. (#4060)
+ Fixed `skimage.restoration.denoise_bilateral` by correcting the
padding in the gaussian filter(#4080)
+ Fixed `skimage.measure.find_contours` when input image contains
NaN. Contours interesting NaN will be left open (#4150)
+ Fixed `skimage.feature.blob_log` and `skimage.feature.blob_dog`
for 3D images and anisotropic data (#4162)
+ Fixed `skimage.exposure.adjust_gamma`,
`skimage.exposure.adjust_log`, and
`skimage.exposure.adjust_sigmoid` such that when provided with a
1 by 1 ndarray, it returns 1 by 1 ndarrays and not single number
floats (#4169)
* Deprecations
+ Parameter "neighbors" in `skimage.measure.convex_hull_object`
has been deprecated in favor of "connectivity" and will be
removed in version 0.18.0.
+ The following functions are deprecated in favor of the
`skimage.metrics` module (#4025):
- `skimage.measure.compare_mse`
- `skimage.measure.compare_nrmse`
- `skimage.measure.compare_psnr`
- `skimage.measure.compare_ssim`
+ The function `skimage.color.guess_spatial_dimensions` is
deprecated and will be removed in 0.18 (#4031)
+ The argument "bc" in `skimage.segmentation.active_contour` is
deprecated.
+ The function `skimage.data.load` is deprecated and will be
removed in 0.18 (#4061)
+ The function `skimage.transform.match_histogram` is deprecated
in favor of `skimage.exposure.match_histogram` (#4107)
+ The parameter "neighbors" of
`skimage.morphology.convex_hull_object` is deprecated.
+ The `skimage.transform.randon_tranform` function will convert
input image of integer type to float by default in 0.18. To
preserve current behaviour, set the new argument
"preserve_range" to True. (#4131)
* For further documentation improvements and misc pull request see
https://github.com/scikit-image/scikit-image/blob/v0.16.x/doc/release/release_0.16.rst
-------------------------------------------------------------------
Wed Jul 31 20:59:24 UTC 2019 - Todd R <toddrme2178@gmail.com>
- Add fix_numpy_1_17.patch
Fixes building with numpy 1.17
From gh#scikit-image/scikit-image#3992
-------------------------------------------------------------------
Sat Jul 27 18:12:14 UTC 2019 - Bernhard Wiedemann <bwiedemann@suse.com>
- do not write unreproducible test_random_walker.cpython-37-PYTEST.pyc
files (boo#1062303)
-------------------------------------------------------------------
Tue Jul 23 17:22:19 UTC 2019 - Todd R <toddrme2178@gmail.com>
+ New Features
* N-dimensional flood fill, with tolerance
* Attribute operators
* Extension of register_translation to enable subpixel precision in 3D and
optionally disable error calculation
* unsharp mask filtering
* New options ``connectivity``, ``indices`` and ``allow_borders`` for
``skimage.morphology.local_maxima`` and ``local_minima``.
* Image translation registration for masked data
(``skimage.feature.masked_register_translation``)
* Frangi (vesselness), Meijering (neuriteness), and Sato (tubeness) filters
* Allow float->float conversion of any range
* Let lower precision float arrays pass through ``img_as_float``
* Lazy apply_parallel (allows optimization of dask array operations)
* Add range option for histogram.
* Add histogram matching
+ Improvements
* Replace ``morphology.local_maxima`` with faster flood-fill based Cython
version
* ``skivi`` is now using ``qtpy`` for Qt4/Qt5/PySide/PySide2 compatibility (a
new optional dependency).
* Performance is now monitored by
`Airspeed Velocity <https://asv.readthedocs.io/en/stable/>`_. Benchmark
results will appear at https://pandas.pydata.org/speed/
* Speed up inner loop of GLCM
* Allow tuple to define kernel in threshold_niblack and threshold_sauvola
* Add support for anisotropic blob detection in blob_log and blob_dog
+ API Changes
* ``skimage.transform.seam_carve`` has been removed because the algorithm is
patented.
* Parameter ``dynamic_range`` in ``skimage.measure.compare_psnr`` has been
removed. Use parameter ``data_range`` instead.
* imageio is now the preferred plugin for reading and writing images.
* imageio is now a dependency of scikit-image.
* ``regular_grid`` now returns a tuple instead of a list for compatibility
with numpy 1.15
* ``colorconv.separate_stains`` and ``colorconv.combine_stains`` now uses
base10 instead of the natural logarithm as discussed in issue #2995.
* Default value of ``clip_negative`` parameter in ``skimage.util.dtype_limits``
has been set to ``False``.
* Default value of ``circle`` parameter in ``skimage.transform.radon``
has been set to ``True``.
* Default value of ``circle`` parameter in ``skimage.transform.iradon``
has been set to ``True``.
* Default value of ``mode`` parameter in ``skimage.transform.swirl``
has been set to ``reflect``.
* Deprecated ``skimage.filters.threshold_adaptive`` has been removed.
Use ``skimage.filters.threshold_local`` instead.
* Default value of ``multichannel`` parameter in
``skimage.restoration.denoise_bilateral`` has been set to ``False``.
* Default value of ``multichannel`` parameter in
``skimage.restoration.denoise_nl_means`` has been set to ``False``.
* Default value of ``mode`` parameter in ``skimage.transform.resize``
and ``skimage.transform.rescale`` has been set to ``reflect``.
* Default value of ``anti_aliasing`` parameter in ``skimage.transform.resize``
and ``skimage.transform.rescale`` has been set to ``True``.
* Removed the ``skimage.test`` function. This functionality can be achieved
by calling ``pytest`` directly.
* ``morphology.local_maxima`` now returns a boolean array
+ Bugfixes
* Correct bright ridge detection for Frangi filter
* ``skimage.morphology.local_maxima`` and ``skimage.morphology.local_minima``
no longer raise an error if any dimension of the image is smaller 3 and
the keyword ``allow_borders`` was false.
* ``skimage.morphology.local_maxima`` and ``skimage.morphology.local_minima``
will return a boolean array instead of an array of 0s and 1s if the
parameter ``indices`` was false.
* When ``compare_ssim`` is used with ``gaussian_weights`` set to True, the
boundary crop used when computing the mean structural similarity will now
exactly match the width of the Gaussian used. The Gaussian filter window is
also now truncated at 3.5 rather than 4.0 standard deviations to exactly match
the original publication on the SSIM. These changes should produce only a very
small change in the computed SSIM value. There is no change to the existing
behavior when ``gaussian_weights`` is False.
* erroneous use of cython wrap around
* Speed up block reduce by providing the appropriate parameters to numpy
* Add urllib.request again
* Repeat pixels in reflect mode when image has dimension 1
* Improve Li thresholding
+ Deprecations
* Python 2 support has been dropped. Users should have Python >= 3.5.
* ``skimage.util.montage2d`` has been removed. Use ``skimage.util.montage`` instead.
* ``skimage.novice`` is deprecated and will be removed in 0.16.
* ``skimage.transform.resize`` and ``skimage.transform.rescale`` option
``anti_aliasing`` has been enabled by default.
* ``regionprops`` will use row-column coordinates in 0.16. You can start
using them now with ``regionprops(..., coordinates='rc')``. You can silence
warning messages, and retain the old behavior, with
``regionprops(..., coordinates='xy')``. However, that option will go away
in 0.16 and result in an error. This change has a number of consequences.
Specifically, the "orientation" region property will measure the
anticlockwise angle from a *vertical* line, i.e. from the vector (1, 0) in
row-column coordinates.
* ``skimage.morphology.remove_small_holes`` ``min_size`` argument is deprecated
and will be removed in 0.16. Use ``area_threshold`` instead.
* ``skimage.filters.median`` will change behavior in the future to have an
identical behavior as ``scipy.ndimage.median_filter``. This behavior can be
set already using ``behavior='ndimage'``. In 0.16, it will be the default
behavior and removed in 0.17 as well as the parameter of the previous
behavior (i.e., ``mask``, ``shift_x``, ``shift_y``) will be removed.
+ Documentation improvements
* Correct rotate method's center parameter doc
* Add Sphinx copybutton
* Add glossary to the documentation
* Add image of retina to our data
* Add microaneurysms() to gallery
* Better document remove_small_objects behaviour: int vs bool
* Linking preserve_range parameter calls to docs
* Update the documentation regarding datalocality
* Specify conda-forge channel for scikit-image conda install
* Turn DOIs into web links in docstrings
* Update documentation for regionprops
* DOC: Improve the RANSAC gallery example
* DOC: "feature.peak_local_max" : explanation of multiple same-intensity peaks returned by the function; added details on ``exclude_border`` parameter
+ Improvements
* MNT: handle a deprecation warning for np.linspace and floats for the num parameter
* TST: numpy empty arrays are not inherently Falsy
* handle warning in scipy cdist for unused parameters
* MNT: don't use filter_warnings in test suite.
* Add doc notes on setting up the build environment
* Release the GIL in numerous cython functions
* Cython touchups to use float32 and float64
* rank_filters: Change how the bitdepth and max_bin are computed to ensure exact warnings.
* Rank: Optimize OTSU filter
* Rank - Fix rank entropy and OTSU tests
* delay importing pyplot in manual segmentation
* Get rid of the requirements-parser dependency
* filter warning from ``correct_mesh_orientation`` in tests
* cloudpickle is really a doc dependency, not a core one
* optional dependencies on pip
* Fewer test warnings in 3.7
* collections.abc nit
* Streamlined issue template
* Tighten the PR Template
* Use language level to 3 in cython for future compatibility
* Update ISSUE_TEMPLATE.md with info about numpy and skimage versions
* Use relative imports for many cython modules
* Pass tests that don't raise floating point exceptions on arm with soft-fp
+ Other improvements
* BUG: Fix greycoprops correlation always returning 1
* Add section on API discovery via ``skimage.lookfor``
* Speedup 2D warping for affine transformations
* Credit Reviewers in Release Notes
* Added small galleries in the API
* Use skimage gaussian filter to avoid integer rounding artifacts
* Remove Python 2 compatibility
* Add ``rectangle_perimeter`` feature to ``skimage.draw``
* Update installation instructions to reference existing requirements specification
* Updated release notes with pre 0.13.1 phase
* Release guidelines update
* Ensure we are installing with / running on Python 3
* Hide warnings in test_unsharp_mask
* Process 0.15 deprecations
* Documentation: always use dev branch javascript
* Add initial airspeed velocity (asv) framework
* Supress warnings for flatten during io testing
* Recover from exceptions in filters.try_all_threshold()
* Fix skimage.test() to run the unittests
* skivi: Use qtpy to handle different Qt versions
* Refactor python version checking.
* Move data_dir to within ``data/__init__.py``
* Move the definition of lookfor out of __init__.py
* Normalize the package number to PEP440
* Remove skimage.test as it was never used.
* Added a message about qtpy to the INSTALL.rst
* Regression fix: Travis should fail if tests fail
* Set minimum cython version to ``0.23.4``
* Add rgba2rgb to API docs
* Minor doc formatting fixes in video.rst
* Decrease the verbosity of the testing
* Speedup rgb2gray using matrix multiply
* Add instructions for meeseeksdev to PR template
* Remove installation instructions for video packages
* Big image labeling fix
* Handle dask deprecation in cycle_spin
* Fix Qt viewer painttool indexing
* build_versions.py is no longer hard coded.
* Remove dtype constructor call in exposure.rescale_intensity
* Various updates to the ASV benchmarks
* Add a link to stack overflow on github README
* MAINT: remove encoding information in file headers (python 3)
* Build tools: Dedicate a --pre build in appveyor and ensure other builds don't download --pre
* Fix the human readable error message on a bad build.
* Respect input array type in apply_parallel by default
* Travis cleanup pip commands
* Add benchmarks for morphology.watershed
* Correcte docstring formatting so that code block is displayed as code
* Defer skimage.io import of matplotlib.pyplot until needed
* Add benchmark for Sobel filters
* Remove cython md5 hashing since it breaks the build process
* Fix typo in documentation.
* Issue 3156: skimage/__init__.py Update docstring and fix import *
* Object detector module
* Do not import submodules while building
* Add benchmark suite for canny
* improve segmentation.felzenszwalb document #3264
* Update _canny.py
* Add benchmark suite for histogram equalization
* fix link to equalist_hist blog reference
* .gitignore: novice: Ignore save-demo.jpg
* Guide the user of denoise_wavelet to choose an orthogonal wavelet.
* Remove unused lib in skimage/__init__.py
* BUILD: Add pyproject.toml to ensure cython is present
* Handle intersphinx and mpl deprecation warnings in docs
* Minor PEP8 fixes
* cython: check for presence of cpp files during install from sdist
* appveyor: don't upload any artifacts
* Add benchmark suite for hough_line()
* Novice skip url test
* Remove benchmarks from wheel
* Add license file to the wheel (binary) distribution
* codecov: ignore build scripts in coverage and don't comment on PRs
* Matplotlib 2.2.3 + PyQt5.11
* Allow @hmaarrfk to mention MeeseeksDev to backport.
* Add Python 3.7 to the test matrix
* Fix deprecated keyword from dask
* Incompatible modes with anti-aliasing in skimage.transform.resize
* Missing cval parameter in threshold_local
* Avoid Sphinx 1.7.8
* Show our data in the gallery
* Minor updates to grammar in numpy images page
* assert_all_close doesn't exist, make it ``assert_array_equal``
* Better behavior of Gaussian filter for arrays with a large number of dimensions
* Allow import/execution with -OO
* Mark tests known to fail on 32bit architectures with xfail
* Hardcode the inputs to test_ssim_grad
* TST: make test_wavelet_denoising_levels compatible with PyWavelets 1.0
* Allow tifffile.py to handle I/O.
* Add explicit Trove classifier for Python 3
* Fix error in contribs.py
* MAINT: remove pyside restriction since we don't support Python 3.4 anymore
* Build tools: simplify how MPL_DIR is obtained.
* Build tools: Don't run tests twice in travis.
* Build tools: Add an OSX build with optional dependencies.
* MAINT: Reverted the changes in #3300 that broke the MINIMIUM_REQUIREMENTS tests
* MNT: Convert links using http to https
* MAINT: Use upstream colormaps now that matplotlib has been upgraded
* Build tools: Make pyamg an optional dependency and remove custom logic
* Build tools: Fix PyQt installed in minimum requirements build
* MNT: multiprocessing should always be available since we depend on python >=2.7
* MAINT Use np.full instead of cst*np.ones
* DOC: Fix LaTeX build via ``make latexpdf``
* Update instructions et al for releases after 0.14.1
* Remove code specific to python 2
* Fix default value of ``methods`` in ``_try_all`` to avoid exception
* Fix morphology.local_maxima for input with any dimension < 3
* Use raw strings to avoid unknown escape symbol warnings
* Speed up xyz2rgb by clipping output in place
* MNT; handle deprecation warnings in tifffile
* Build tools: TST: filter away novice deprecation warnings during testing
* Build tools: don't use the pytest.fixtures decorator anymore in class fixtures
* Preserving the fill_value of a masked array
* Fix VisibleDeprecationWarning from np.histogram, normed=True
* Build Tools: DOC: Document that now PYTHONOPTMIZE build is blocked by SciPy
* DOC: Replace broken links by webarchive equivalent links
* FIX: making the plot_marching_cubes example visible.
* Avoid Travis failure regarding ``skimage.lookfor``
* Fix Python executable for sphinx-build in docs Makefile
* Build Tools: Blacklist specific Cython versions
* Fix typos
* Add "optional" indications to docstrings
* Rename 'mnxc' (masked normalize cross-correlation) to something more descriptive
* Random walker bug fix: no error should be raised when there is nothing to do
* Various minor edits for active contour
* Fix range for uint32 dtype in user guide
* Raise meaningful exception in warping when image is empty
* DOC: Development installation instructions for Ubuntu are missing tkinter
* Better gallery examples and tests for masked translation registration
* DOC: make more docstrings compliant with our standards
* Build tools: Remove restriction on simpleitk for python 3.7
* Speedup and add benchmark for ``skeletonize_3d``
* Update requirements/README.md on justification of matplotlib 3.0.0 in favor of #3476
* Doc enhancements around denoising features.
* Use 'getconf _NPROCESSORS_ONLN' as fallback for nproc in Makefile of docs
* Fix matplotlib set_*lim API deprecations
* Switched from np.power to np.cbrt
* Filtered out DeprecationPendingWarning for matrix subclass
* Add RGB to grayscale example to gallery
* Build tools: Refactor check_sdist so that it takes a filename as a parameter
* Turn dask to an optional requirement
* _marching_cubes_lewiner_cy: mark char as signed
* Hyperlink DOIs to preferred resolver
* Missing parameter description in ``morphology.reconstruction`` docstring #3581
* Update chat location
* Remove orphan code (skimage/filters/_ctmf.pyx).
* More explicit example title, better list rendering in plot_cycle_spinning.py
* Add rgb to hsv example in the gallery
* Update documentation of ``perimeter`` and add input validation
* Additionnal mask option to clear_border
* Set up CI with Azure Pipelines
* [MRG] EHN: median filters will accept floating image
* Update Travis-CI to xcode 10.1
* Minor tweaks to _mean_std code
* Add explicit ordering of gallery sections
* Delete broken links
* Build tools: Fix test_mpl_imshow for matplotlib 2.2.3 and numpy 1.16
* First draft of core dev guide
* Add more details about the home page build process
* Ensure images resources with long querystrings can be read
* Delay matplotlib import in skimage/future/manual_segmentation.py
* make the low contrast check optional when saving images
* Correctly ignore release notes auto-generated for docs
* Remove MANIFEST file when making the 'clean' target
* Clarify return values in _overlap docstrings in feature/blob.py
* Contribution script: allow specification of GitHub development branch
* Update core dev guide: deprecation, contributor guide, required experience
* Add release notes for 0.14.2
* FIX gallery: Add multichannel=True to match_histogram
* MAINT Minor code style improvements
* Pass parameters through tifffile plugin
* DOC unusused im3d_t in example
* Remove wrong cast of Py_ssize_t to int
* Build tools: allow python 3.7 to fail, but travis to continue
* Build tools: remove pyproject.toml
* Fix ValueError: not enough values to unpack
* Several fixes for heap.pyx
* Enable the faulthandler module during testing
* Build tools: Fix Python 3.7 builds on travis
* Replace np.einsum with np.tensordot in _upsampled_dft
* Fix potential use of NULL pointers
* Fix potential memory leak
* Fix potential use of NULL pointers
* Fix and improve core_cy.pyx
* Build tools: Downgrade Xcode to 9.4 on master
* Improve visual_test.py
* Updated painttool to work with color images and properly scale labels.
* Add image.sc forum badge to README
* Blacklist PyQt 5.12.0 on Travis
* Build tools: Fix matplotlib + qt 5.12 the same way upstream does it
* gallery: remove xx or yy sorted directory names
* Allow for f-contiguous 2D arrays in convex_hull_image
* Build tools: Set astropy minimum requirement to 1.2 to help the CIs.
* Avoid NumPy warning while stacking arrays.
* Set CC0 for microaneurysms
* Unify LICENSE files for easier interpretation
* Readme: Remove expectation for future fix from matplotlib
* Improved documentation/test in ``flood()``
* Use ssize_t in denoise cython
* Removed non-existent parameter in docstring
* Remove redundant point in draw.polygon docstring example
* Ensure watershed auto-markers respect mask
- Add fix_numpy_matrix_warning_test.patch
to fixup the test for the warnings for scipy 1.3 and the
matrix subsclass. From gh#scikit-image/scikit-image#3869
-------------------------------------------------------------------
Sun Jan 20 04:53:23 UTC 2019 - Arun Persaud <arun@gmx.de>
- specfile:
* update copyright year
- update to version 0.14.2:
* API changes
+ "skimage.measure.regionprops" no longer removes singleton
dimensions from label images (#3284). To recover the old
behavior, replace "regionprops(label_image)" calls with
"regionprops(np.squeeze(label_image))"
* Bug fixes
+ Address deprecation of NumPy "_validate_lengths" (backport of
#3556)
+ Correctly handle the maximum number of lines in Hough transforms
(backport of #3514)
+ Correctly implement early stopping criterion for rank kernel
noise filter (backport of #3503)
+ Fix "skimage.measure.regionprops" for 1x1 inputs (backport of
#3284)
* Enhancements
+ Rewrite of "local_maxima" with flood-fill (backport of #3022,
#3447)
* Build Process & Testing
+ Dedicate a "--pre" build in appveyor (backport of #3222)
+ Avoid Travis-CI failure regarding "skimage.lookfor" (backport of
#3477)
+ Stop using the "pytest.fixtures" decorator (#3558)
+ Filter out DeprecationPendingWarning for matrix subclass (#3637)
+ Fix matplotlib test warnings and circular import (#3632)
-------------------------------------------------------------------
Mon Oct 8 14:59:23 UTC 2018 - Arun Persaud <arun@gmx.de>
- specfile:
* increase Cython requirement to 0.23.4
- update to version 0.14.1:
* Bug fixes
+ skimage.color.adapt_rgb was applying input functions to the
wrong axis (#3097)
+ CollectionViewer now indexes correctly (it had been broken by an
update to NumPy indexing) (#3288)
+ Handle deprecated indexing-by-list and NumPy matrix from NumPy
1.15 (#3238, #3242, #3292)
+ Fix incorrect inertia tensor calculation (#3303) (Special thanks
to JP Cornil for reporting this bug and for their patient help
with this fix)
+ Fix missing comma in __all__ listing of moments_coord_central,
so it and moments_normalized can now be correctly imported from
the measure namespace (#3374)
+ Fix background color in label2rgb(..., kind='avg') (#3280)
* Enhancements
+ "Reflect" mode in transforms now works fine when an image
dimension has size 1 (#3174)
+ img_as_float now allows single-precision (32-bit) float arrays
to pass through unmodified, rather than being up-converted to
64-bit (#3110, #3052, #3391)
+ Speed up rgb2gray computation (#3187)
+ The scikit-image viewer now works with different PyQt versions
(#3157)
+ The cycle_spin function for enhanced denoising works
single-threaded when dask is not installed now (#3218)
+ scikit-image's io module will no longer inadvertently set the
matplotlib backend when imported (#3243)
+ Fix deprecated get keyword from dask in favor of scheduler
(#3366)
+ Add missing cval parameter to threshold_local (#3370)
* API changes
+ Remove deprecated dynamic_range in measure.compare_psnr (#3313)
* Documentation
+ Improve the documentation on data locality (#3127)
+ Improve the documentation on dealing with video (#3176)
+ Update broken link for Canny filter documentation (#3276)
+ Fix incorrect documentation for the center parameter of
skimage.transform.rotate (#3341)
+ Fix incorrect formatting of docstring in measure.profile_line
(#3236)
* Build process / development
+ Ensure Cython is 0.23.4 or newer (#3171)
+ Suppress warnings during testing (#3143)
+ Fix skimage.test (#3152)
+ Don't upload artifacts to AppVeyor (there is no way to delete
them) (#3315)
+ Remove import * from the scikit-image package root (#3265)
+ Allow named non-core contributors to issue MeeseeksDev commands
(#3357, #3358)
+ Add testing in Python 3.7 (#3359)
+ Add license file to the binary distribution (#3322)
+ lookfor is no longer defined in __init__.py but rather imported
to it (#3162)
+ Add pyproject.toml to ensure Cython is present before building
(#3295)
+ Add explicit Python version Trove classifiers for PyPI (#3417)
+ Ignore known test failures in 32-bit releases, allowing 32-bit
wheel builds (#3434)
+ Ignore failure to raise floating point warnings on certain ARM
platforms (#3337)
+ Fix tests to be compatible with PyWavelets 1.0 (#3406)
-------------------------------------------------------------------
Sun Sep 2 16:58:45 UTC 2018 - arun@gmx.de
- specfile:
* update copyright year
* TASKS file not in tar-ball anymore, removed it, added CONTRIBUTING.txt file
- update to version 0.14.0:
* New Features
+ Lookfor function to search across the library:
skimage.lookfor. (#2713)
+ nD support for skimage.transform.rescale,
skimage.transform.resize, and skimage.transform.pyramid_*
transforms. (#1522)
+ Chan-Vese segmentation algorithm. (#1957)
+ Manual segmentation with matplotlib for fast data annotation:
skimage.future.manual_polygon_segmentation,
skimage.future.manual_lasso_segmentation. (#2584)
+ Hysteresis thresholding:
skimage.filters.apply_hysteresis_threshold. (#2665)
+ Segmentation with morphological snakes:
skimage.segmentation.morphological_chan_vese (2D),
skimage.segmentation.morphological_geodesic_active_contour (2D
and 3D). (#2791)
+ nD support for image moments: skimage.measure.moments_central,
skimage.measure.moments_central,
skimage.measure.moments_normalized,
skimage.measure.moments_hu. This change leads to 3D/nD
compatibility for many regionprops. (#2603)
+ Image moments from coordinate input:
skimage.measure.moments_coords,
skimage.measure.moments_coords_central. (#2859)
+ Added 3D support to blob_dog and blob_log. (#2854)
+ Inertia tensor and its eigenvalues can now be computed outside
of regionprops; available in
skimage.measure.inertia_tensor. (#2603)
+ Cycle-spinning function for approximating shift-invariance by
averaging results from a series of spatial shifts:
skimage.restoration.cycle_spin. (#2647)
+ Haar-like feature: skimage.feature.haar_like_feature,
skimage.feature.haar_like_feature_coord,
skimage.feature.draw_haar_like_feature. (#2848)
+ Data generation with random_shapes function:
skimage.draw.random_shapes. (#2773)
+ Subset of LFW (Labeled Faces in the Wild) database:
skimage.data.cbcl_face_database. (#2905)
+ Fully reworked montage function (now with a better padding
behavior): skimage.util.montage. (#2626)
+ YDbDr colorspace conversion routines: skimage.color.rgb2ydbdr,
skimage.color.ydbdr2rgb. (#3018)
* Improvements
+ VisuShrink method for
skimage.restoration.denoise_wavelet. (#2470)
+ New max_ratio parameter for
skimage.feature.match_descriptors. (#2472)
+ skimage.transform.resize and skimage.transform.rescale have a
new anti_aliasing option to avoid aliasing artifacts when
down-sampling images. (#2802)
+ Support for multichannel images for skimage.feature.hog. (#2870)
+ Non-local means denoising (skimage.restoration.denoise_nl_means)
has a new optional parameter, sigma, that can be used to specify
the noise standard deviation. This enables noise-robust patch
distance estimation. (#2890)
+ Mixed dtypes support for skimage.measure.compare_ssim,
skimage.measure.compare_psnr, etc. (#2893)
+ New alignment parameter in skimage.feature.plot_matches. (#2955)
+ New seed parameter in
skimage.transform.probabilistic_hough_line. (#2960)
+ Various performance improvements. (#2821, #2878, #2967, #3035,
#3056, #3100)
* Bugfixes
+ Fixed skimage.measure.regionprops.bbox_area returning incorrect
value. (#2837)
+ Changed gradient and L2-Hys norm computation in
skimage.feature.hog to closely follow the paper. (#2864)
+ Fixed skimage.color.convert_colorspace not working for YCbCr,
YPbPr. (#2780)
+ Fixed incorrect composition of projective tranformation with
inverse transformation. (#2826)
+ Fixed bug in random walker appearing when seed pixels are
isolated inside pruned zones. (#2946)
+ Fixed rescale not working properly with different rescale
factors in multichannel case. (#2959)
+ Fixed float and integer dtype support in
skimage.util.invert. (#3030)
+ Fixed skimage.measure.find_contours raising StopIteration on
Python 3.7. (#3038)
+ Fixed platform-specific issues appearing in Windows and/or
32-bit environments. (#2867, #3033)
* API Changes
+ skimage.util.montage. namespace has been removed, and
skimage.util.montage.montage2d function is now available as
skimage.util.montage2d.
+ skimage.morphology.binary_erosion now uses True as border value,
and is now consistent with skimage.morphology.erosion.
* Deprecations
+ freeimage plugin has been removed from skimage.io.
+ skimage.util.montage2d is deprecated and will be removed in
0.15. Use skimage.util.montage function instead.
+ skimage.novice is deprecated and will be removed in 0.16.
+ skimage.transform.resize and skimage.transform.rescale have a
new anti_aliasing option that avoids aliasing artifacts when
down-sampling images. This option will be enabled by default in
0.15.
+ regionprops will use row-column coordinates in 0.16. You can
start using them now with regionprops(...,
coordinates='rc'). You can silence warning messages, and retain
the old behavior, with regionprops(...,
coordinates='xy'). However, that option will go away in 0.16 and
result in an error. This change has a number of
consequences. Specifically, the "orientation" region property
will measure the anticlockwise angle from a vertical line,
i.e. from the vector (1, 0) in row-column coordinates.
+ skimage.morphology.remove_small_holes min_size argument is
deprecated and will be removed in 0.16. Use area_threshold
instead.
-------------------------------------------------------------------
Sat Sep 30 16:13:22 UTC 2017 - arun@gmx.de
- update to version 0.13.1:
* no upstream changelog available for 0.13.1
- 0.13.0 changelog available at: https://github.com/scikit-image/scikit-image/blob/master/doc/release/release_0.13.rst
-------------------------------------------------------------------
Mon Jun 12 14:56:44 UTC 2017 - toddrme2178@gmail.com
- Implement single-spec version
- Update source URL
- Update to version 0.13.0
* No upstream changelog
-------------------------------------------------------------------
Mon Jan 11 10:31:34 UTC 2016 - toddrme2178@gmail.com
- update to version 0.11.3:
(no changelog entry, taken from git log)
* Fix handling of non-gif and tiff files
* Fix setup to allow installing from PyPI
* Fix support for Sphinx 1.3
* Add a helper function to check for low contrast
* Fix RANSAC for invalid model estimation and confidence corner case
- Fix update-alternatives usage
-------------------------------------------------------------------
Sat Nov 23 17:59:48 UTC 2013 - p.drouand@gmail.com
- Missing 0.9.3 tarball in previous commit; upload it and remove old
tarball
-------------------------------------------------------------------
Mon Oct 21 13:31:08 UTC 2013 - toddrme2178@gmail.com
- Update to 0.9.3
* No upstream changelog
- Rename to python-scikit-image to match new naming policy
-------------------------------------------------------------------
Sat Oct 13 11:25:57 UTC 2012 - Angelos Tzotsos <tzotsos@opensuse.org>
- update version to 0.7.0
-------------------------------------------------------------------
Sun Mar 11 21:00:00 UTC 2012 - Angelos Tzotsos <tzotsos@opensuse.org>
- initial OBS Build (v0.5.0)
