Update dependency scikit-image to v0.25.0 #205
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This PR contains the following updates:
==0.17.2
->==0.25.0
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Release Notes
scikit-image/scikit-image (scikit-image)
v0.25.0
Compare Source
scikit-image 0.25.0
We're happy to announce the release of scikit-image 0.25.0!
New Features
skimage.feature.texture.graycoprops
(#7375).skimage.morphology.footprint_rectangle
supporting generation of rectangular or hyper-rectangular footprints in one function (#7566).API Changes
skimage.feature.plot_matches
. Useskimage.feature.plot_matched_features
going forward (#7487).skimage.io.imshow
,skimage.io.imshow_collection
andskimage.io.show
. Please usematplotlib
,napari
, etc. to visualize images (#7508).skimage.morphology.skeletonize_3d
; useskimage.morphology.skeletonize
instead (#7572).skimage.io
plugin infrastructure (#7353).scipy.sparse
array interface. For more details, see the note about the newscipy.sparse
array interface here (#7576).skimage.morphology.rectangle
in favor of the new functionskimage.morphology.footprint_rectangle
(#7566).skimage.morphology.square
in favor of the new functionskimage.morphology.footprint_rectangle
(#7566).skimage.morphology.cube
in favor of the new functionskimage.morphology.footprint_rectangle
(#7566).Enhancements
skimage.morphology.local_minima
for extremely small floats (#7534).skimage.feature.plot_matched_features
uses the same random colors, ifmatches_color
isn't provided explicitly (#7541).matches_color
inskimage.feature.plot_matched_features
(#7541).Performance
skimage.feature.peak_local_max
will now skip unnecessary distance computations in the case ofmin_distance=1
. This results in performance improvements to functions likeskimage.feature.blob_dog
,skimage.feature.blob_log
,skimage.feature.blob_doh
andskimage.feature.corner_peaks
that callpeak_local_max
internally (#7548).skimage.featurepeak_local_max
, skip unnecessary check for cases wheremin_distance > 1
is passed (#7548).Bug Fixes
skimage.morphology.remove_objects_by_distance
doesn't fail if the given integer dtype cannot be safely cast to the architecture specific size ofintp
, e.g. on i386 architectures (#7453).skimage.draw.ellipsoid_stats
when all semi-axes have the same length (#7473).skimage.morphology.thin
from accidentally modifying the input image in case it is of dtype uint8 (#7469).skimage.measure.ransac
. In some cases,ransac
was stopping at the first iteration (#7065).skimage.measure.ransac
; very small probabilities lead to -0 number of max trials (#7496).RegionProperties
objects returned byskimage.measure.regionprops
can be deserialized with pickle (#7569).watershed_lines=True
inskimage.segmentation.watershed
resulted in an incorrect solution (#7071).skimage.segmentation.watershed
when the markers don't align with local minima by making sure every marker is evaluated before successive pixels (#7071).skimage.segmentation.join_segmentations
ifnumpy.uint
is used with NumPy<2 (#7292).Documentation
skimage.morphology.skeletonize
, clarify the expected image dtypes and how objects of different intensities are handled (#7456).skimage.feature.graycomatrix
(#7297).CITATION.cff
instead ofCITATION.bib
(#7505).spin test --coverage
in contribution guide (#7515).image
parameter inskimage.restoration.richardson_lucy
(#7477).radius
inskimage.morphology.ball
fromint
tofloat
(#7627).Infrastructure
currentmodule
directive again (#7492).type:
label is present in PRs (#7512).s_cmp
unresolved symbol error, update Emscripten CI testing (#7525).Maintenance
spin sdist
(#7438).Rotation.from_euler
to compute 3D rotation matrix (#7503).lazy_loader
as private symbol in top-level namespaces (#7540).io.show
andio.imshow
(#7556).assert_stacklevel
(#7558).changelist
to v0.5 (#7601).intersphinx_registry
package inconf.py
to keep intersphinx urls up to date. This means that building docs now requires theintersphinx-registry
package (#7611).square
,cube
&rectangle
(#7624).skimage
top module (#6892).Contributors
30 authors added to this release (alphabetically):
25 reviewers added to this release (alphabetically):
These lists are automatically generated, and may not be complete or may contain duplicates.
v0.24.0
Compare Source
scikit-image 0.24.0
We're happy to announce the release of scikit-image 0.24.0!
Highlights
skimage.transform.ThinPlateSplineTransform
, which can estimate and model non-linear transforms with thin-plate splines and allows image warping withskimage.transform.warp
(#7040).New Features
skimage.transform.ThinPlateSplineTransform
, which can estimate and model non-linear transforms with thin-plate splines and allows image warping withskimage.transform.warp
(#7040).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
skimage.feature.corner_fast
, test four directions earlier, which should more than half the computation time for most cases (#7394).Documentation
data_range
parameter inskimage.metrics.structural_similarity
(#7345).skimage.measure.regionprops
(#7405).skimage.measure.find_contours
(#7411).skimage.restoration.rolling_ball
docstring (#7424).Infrastructure
scikit-image
(#7350).Maintenance
skimage.util.compare_images
, deprecate the parameterimage2
. Instead useimage0
,image1
to pass the compared images. Furthermore, all other parameters will be turned into keyword-only parameters once the deprecation is complete (#7322).Contributors
13 authors added to this release (alphabetically):
15 reviewers added to this release (alphabetically):
These lists are automatically generated, and may not be complete or may contain duplicates.
v0.23.2
Compare Source
scikit-image 0.23.2
We're happy to announce the release of scikit-image 0.23.2!
Bug Fixes
skimage.util.img_as_ubyte
supports the edge case wheredtype('uint64').type
of the provided image isnp.ulonglong
instead ofnp.uint64
(#7392).Documentation
connectivity
parameter inskimage.segmentation.watershed
(#7360).Infrastructure
Maintenance
numpy.inf
instead of deprecatednumpy.infty
(#7386).astype
in tests (#7393).Contributors
4 authors added to this release (alphabetically):
4 reviewers added to this release (alphabetically):
These lists are automatically generated, and may not be complete or may contain duplicates.
v0.23.1
Compare Source
scikit-image 0.23.1
We're happy to announce the release of scikit-image 0.23.1!
Highlights
skimage.morphology.closing
andskimage.morphology.opening
are extensive and anti-extensive, respectively, if the footprint is not mirror symmetric (#6695).mode
tobinary_erosion
,binary_dilation
,binary_opening
andbinary_closing
inskimage.morphology
. These new parameters determine how array borders are handled (#6695).mode
andcval
toerosion
,dilation
,opening
,closing
,white_tophat
, andblack_tophat
inskimage.morphology
. These new parameters determine how array borders are handled (#6695).skimage.util.map_array
by parallelization with Cython'sprange
(#7266).New Features
intensity_std
property toskimage.measure.regionprops
which computes the standard deviation of the intensity in a region (#6712).mode
tobinary_erosion
,binary_dilation
,binary_opening
andbinary_closing
inskimage.morphology
. These new parameters determine how array borders are handled (#6695).mirror_footprint
andpad_footprint
toskimage.morphology
(#6695).mode
andcval
toerosion
,dilation
,opening
,closing
,white_tophat
, andblack_tophat
inskimage.morphology
. These new parameters determine how array borders are handled (#6695).spacing
tosegmentation.expand_labels
to support anisotropic images (#7080).API Changes
shift_x
andshift_y
inskimage.morphology.erosion
andskimage.morphology.dilation
are deprecated. Usepad_footprint
or modify the footprint manually instead (#6695).skimage.morphology.skeletonize_3d
for non-binary input images.skeletonize_3d
now always returns a binary array like similar functions (#7095).skimage.feature.plot_matches
in favor ofskimage.feature.plot_matched_features
(#7255).skimage.morphology.skeletonize_3d
in favor of justskimage.morphology.skeletonize
(#7094).output
inskimage.filters.gaussian
; useout
instead (#7225).shift_x
,shift_y
andshift_z
fromFalse
to0
in theskimage.filters.rank
functions. This has not impact on the results. Warn in case boolean shifts are provided from now on (#7320).Performance
skimage.metrics
module (#7211).skimage.util.map_array
by parallelization with Cython'sprange
(#7266).Bug Fixes
skimage.feature.hog
(#7153).skimage.morphology.closing
andskimage.morphology.opening
are extensive and anti-extensive, respectively, if the footprint is not mirror symmetric (#6695).skimage.registration.phase_cross_correlation
when the real-time shift cannot be determined (disambiguate=True
). Display a warning instead (#7259).skimage.graph.pixel_graph
which raised aTypeError
when the parameteredge_function
was provided without amask
(#7310).cache=False
is passed toskimage.measure.regionprops
(#7333).Documentation
skimage.graph
module (#7192).xarray.DataArray
andpandas.DataFrame
in the crash course on NumPy for images (#7159).skimage.transform.swirl
(#7241).moments_normalized
(#7248).skimage.registration.optical_flow_tvl1
(#7314).coordinates
from docstring example ofskimage.segmentation.active_contour
(#7329).data_range
parameter inskimage.metrics.structural_similarity
(#7345).skimage.transform.EuclideanTransform
(#7097).Infrastructure
assert_stacklevel
helper to check stacklevel of captured warnings (#7294).pre-commit[bot]
from changelist's contributor list (#7358).Maintenance
version_switcher.json
(#7184)._hog.py
after previous merge lacking black (#7215).noexcept
to address Cython 3.0 warnings (#7250).deprecate_parameter
helper (#7256).skimage.registration.phase_cross_correlation
(#7287).deprecate_kwarg
andremove_arg
; they are entirely succeeded bydeprecate_parameter
(#7290).numpydoc
installed (#7307)._optical_flow_utils
are private (#7328).test_fits.py
(#7340).np.solve
in NumPy 2 (#7341).ensure_python_version
function (#7370).setup-python@v5
,cache@v4
,upload-artifact@v4
, anddownload-artifact@v4
(#7368).Contributors
29 authors added to this release (alphabetically):
21 reviewers added to this release (alphabetically):
These lists are automatically generated, and may not be complete or may contain duplicates.
v0.23.0
Compare Source
v0.22.0
Compare Source
v0.21.0
Compare Source
We're happy to announce the release of scikit-image 0.21.0! 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: https://scikit-image.org
Highlights
New Features
API Changes
In this release, we unify the way seeds are specified for algorithms that make use of pseudo-random numbers. Before, various keyword arguments (
sample_seed
,seed
,random_seed
, andrandom_state
) served the same purpose in different places. These have all been replaced with a singlerng
argument, that handles both integer seeds and NumPy Generators. Please see the related SciPy discussion, as well as Scientific Python SPEC 7 that attempts to summarize the argument._invariant_denoise
to denoise_invariant (#6660).color.get_xyz_coords
in public API (#6696).join_segmentations
return array maps from output to input labels (#6786).Enhancements
spacing
parameter is tuple inregionprops
(#6907).rescale_intensity
with dask array (#6910).Performance
Bug Fixes
deprecated
decorator todeprecate_func
(#6594)._invariant_denoise
todenoise_invariant
(#6660).color.get_xyz_coords
in public API (#6696).AffineTransform
(#6717).footprints.diamond
test case (#6756).segmentation.watershed
(#6839).transform.resize
(#6852).Configuration
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