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scikit-image v0.16.2 Release Notes

Release Date: 2019-10-22 // over 4 years ago

  • Announcement: scikit-image 0.16.2

    🚀 We're happy to announce the release of scikit-image v0.16.2!

    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 is a bug fix release that addresses several critical issues from 0.16.1.

    🐛 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)

    🚀 4 authors added to this release [alphabetical by first name or login]

    • François Boulogne
    • Jarrod Millman
    • Mark Harfouche
    • Ondrej Pesek

    🚀 6 reviewers added to this release [alphabetical by first name or login]

    • Alexandre de Siqueira
    • Egor Panfilov
    • François Boulogne
    • Juan Nunez-Iglesias
    • Mark Harfouche
    • Nelle Varoquaux

    Announcement: scikit-image 0.16.1

    🚀 We're happy to announce the release of scikit-image v0.16.1!

    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

    🚀 Starting from this release, scikit-image will follow the recently
    introduced NumPy deprecation policy, NEP 29 <https://github.com/numpy/numpy/blob/master/doc/neps/nep-0029-deprecation_policy.rst>__.
    👍 Accordingly, scikit-image 0.16 drops support for Python 3.5.
    🚀 This release of scikit-image officially supports Python 3.6 and 3.7.

    Special thanks to Matthias Bussonnier for Frappuccino <https://github.com/Carreau/frappuccino>__, which helped us catch all API
    🔄 changes and nail down the APIs for new features.

    🆕 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 --
      skimage.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
      skimage.color.label2rgb (#4055)
    • 👍 All functions from skimage.drawing now supports multi-channel 2D images (#4134)

    API Changes

    • 📦 Deprecated subpackage skimage.novice has been removed.
    • 0️⃣ Default value of multichannel parameters has been set to False in
      skimage.transform.rescale, skimage.transform.pyramid_reduce,
      skimage.transform.pyramid_laplacian,
      skimage.transform.pyramid_gaussian, and
      skimage.transform.pyramid_expand. Guessing is no longer performed for 3D
      arrays.
    • 🚚 Deprecated argument visualise has been removed from
      skimage.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
      row-column coordinates. Old x-y interface is not longer available.
    • 0️⃣ 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.
    • 0️⃣ 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
    0️⃣ of integer type to float by default in 0.18. To preserve current behaviour,
    set the new argument preserve_range to True. (#4131)

    📚 Documentation improvements

    • DOC: Improve the documentation of transform.resize with respect to the anti_aliasing_sigma parameter (#3911)
    • 🛠 Fix URL for stain deconvolution reference (#3862)
    • 🛠 Fix doc for denoise guassian (#3869)
    • DOC: various enhancements (cross links, gallery, ref...), mainly for corner detection (#3996)
    • 📚 [DOC] clarify that the inertia_tensor may be nD in documentation (#4013)
    • ✅ [DOC] How to test and write benchmarks (#4016)
    • Spellcheck @CONTRIBUTING.txt (#4008)
    • Spellcheck @doc/examples/segmentation/plot_watershed.py (#4009)
    • Spellcheck @doc/examples/segmentation/plot_thresholding.py (#4010)
    • Spellcheck @skimage/morphology/binary.py (#4011)
    • Spellcheck @skimage/morphology/extrema.py (#4012)
    • docs update for downscale_local_mean and N-dimensional images (#4079)
    • ✂ Remove fancy language from 0.15 release notes (#3827)
    • 📚 Documentation formatting / compilation fixes (#3838)
    • ✂ Remove duplicated section in INSTALL.txt. (#3876)
    • ENH: doc of ridge functions (#3933)
    • 🛠 Fix docstring for Threshold Niblack (#3917)
    • adding docs to circle_perimeter_aa (#4155)
    • ⚡️ Update link to NumPy docstring standard in Contribution Guide (replaces #4191) (#4192)
    • DOC: Improve downscale_local_mean() docstring (#4180)
    • ✨ DOC: enhance the result display in ransac gallery example (#4109)
    • 👍 Gallery: use fstrings for better readability (#4110)
    • MNT: Document stacklevel parameter in contribution guide (#4066)
    • 🛠 Fix minor typo (#3988)
    • 📄 MIN: docstring improvements in canny functions (#3920)
    • 🛠 Minor docstring fixes for #4150 (#4184)
    • 🛠 Fix full parameter description in compare_ssim (#3860)
    • 📄 State Bradley threshold equivalence in Niblack docstring (#3891)
    • ➕ Add plt.show() to example-code for consistency. (#3908)
    • CC0 is not equivalent to public domain. Fix the note of the horse image (#3931)
    • ⚡️ Update the joblib link in tutorial_parallelization.rst (#3943)
    • Fix plot_edge_filter.py references (#3946)
    • ➕ Add missing argument to docstring of PaintTool (#3970)
    • 📚 Improving documentation and tests for directional filters (#3956)
    • ➕ Added new thorough examples on the inner working of
      skimage.filters.threshold_li (#3966)
    • 🚚 matplotlib: remove interpolation=nearest, none in our examples (#4002)
    • 🛠 fix URL encoding for wikipedia references in filters.rank.entropy and filters.rank.shannon_entropy docstring (#4007)
    • 🛠 Fixup integer division in examples (#4032)
    • ⚡️ Update the links the installation guide (#4118)
    • Gallery hough line transform (#4124)
    • 📚 Cross-linking between function documentation should now be much improved! (#4188)
    • Better documentation of the num_peaks of skimage.feature.corner_peaks (#4195)

    Other Pull Requests

    • ➕ Add benchmark suite for exposure module (#3312)
    • Remove precision and sign loss warnings from skimage.util.img_as_ (#3575)
    • Propose SKIPs and add mission/vision/values, governance (#3585)
    • 👉 Use user-installed tifffile if available (#3650)
    • 📌 Simplify benchmarks pinnings (#3711)
    • ➕ Add project_urls to setup for PyPI and other services (#3834)
    • ➕ Address deprecations for 0.16 release (#3841)
    • 🗄 Followup deprecations for 0.16 (#3851)
    • 🏗 Build and test the docs in Azure (#3873)
    • 📌 Pin numpydoc to pre-0.8 to fix dev docs formatting (#3893)
    • 🔄 Change all HTTP links to HTTPS (#3896)
    • Skip extra deps on OSX (#3898)
    • ➕ Add location for Sphinx 2.0.1 search results; clean up templates (#3899)
    • 🛠 Fix CSS styling of Sphinx 2.0.1 + numpydoc 0.9 rendered docs (#3900)
    • Travis CI: The sudo: tag is deprcated in Travis (#4164)
    • 🚀 MNT Preparing the 0.16 release (#4204)
    • 🚀 FIX generate_release_note when contributor_set contains None (#4205)
    • Specify that travis should use Ubuntu xenial (14.04) not trusty (16.04) (#4082)
    • MNT: set stack level accordingly in lab2xyz (#4067)
    • MNT: fixup stack level for filters ridges (#4068)
    • 🚚 MNT: remove unused import deprecated from filters.thresholding (#4069)
    • 🔌 MNT: Set stacklevel correctly in io matplotlib plugin (#4070)
    • MNT: set stacklevel accordingly in felzenszwalb_cython (#4071)
    • MNT: Set stacklevel accordingly in img_as_* (convert) (#4072)
    • MNT: set stacklevel accordingly in util.shape (#4073)
    • 🚚 MNT: remove extreneous matplotlib warning (#4074)
    • ✅ Suppress warnings in tests for viewer (#4017)
    • ✅ Suppress warnings in test suite regarding measure.label (#4018)
    • ✅ Suppress warnings in test_rank due to type conversion (#4019)
    • ➕ Add todo item for imread plugin testing (#3907)
    • ✂ Remove matplotlib agg warning when using the sphinx gallery. (#3897)
    • 🚀 Forward-port release notes for 0.14.4 (#4137)
    • ➕ Add tests for pathological arrays in threshold_li (#4143)
    • setup.py: Fail gracefully when NumPy is not installed (#4181)
    • ⬇️ Drop Python 3.5 support (#4102)
    • 👮 Force imageio reader to return NumPy arrays (#3837)
    • 🛠 Fixing connecting to GitHub with SSH info. (#3875)
    • Small fix to an error message of skimage.measure.regionprops (#3884)
    • Unify skeletonize and skeletonize 3D APIs (#3904)
    • ➕ Add location for Sphinx 2.0.1 search results; clean up templates (#3910)
    • 📌 Pin numpy version forward (#3925)
    • Replacing pyfits with Astropy to read FITS (#3930)
    • ➕ Add warning for future dtype kwarg removal (#3932)
    • ⚡️ MAINT: cleanup regionprop add PYTHONOPTIMIZE=2 to travis array (#3934)
    • ➕ Adding complexity and new tests for filters.threshold_multiotsu (#3935)
    • 🛠 Fixup dtype kwarg warning in certain image plugins (#3948)
    • 🔊 don't cast integer to float before using it as integer in numpy logspace (#3949)
    • ✅ avoid low contrast image save in a doctest. (#3953)
    • MAINT: Remove unused _convert_input from filters._gaussian (#4001)
    • 🐧 Set minimum version for imread so that it compiles from source on linux in test builds (#3960)
    • ✅ Cleanup plugin utilization in data.load and testsuite (#3961)
    • Select minimum imageio such that it is compatible with pathlib (#3969)
    • ✂ Remove pytest-faulthandler from test dependencies (#3987)
    • Fix tifffile and array_function failures in our CI (#3992)
    • 👻 MAINT: Do not use assert in code, raise an exception instead. (#4006)
    • 📦 Enable packagers to disable failures on warnings. (#4021)
    • 🛠 Fix numpy 117 rc and dask in thresholding filters (#4022)
    • ⚠ silence r,c warnings when property does not depend on r,c (#4027)
    • ✂ remove warning filter, fix doc wrt r,c (#4028)
    • Import Iterable from collections.abc (#4033)
    • Import Iterable from collections.abc in vendored tifffile code (#4034)
    • ✏️ Correction of typos after #4025 (#4036)
    • Rename internal function called assert_* -> check_* (#4037)
    • 👌 Improve import time (#4039)
    • ✂ Remove .meeseeksdev.yml (#4045)
    • 🛠 Fix mpl deprecation on grid() (#4049)
    • 🛠 Fix gallery after deprecation from #4025 (#4050)
    • 🛠 fix mpl future deprecation normed -> density (#4053)
    • ➕ Add shape= to circle perimeter in hough_circle example (#4047)
    • 🚑 Critical: address internal warnings in test suite related to metrics 4025 (#4063)
    • 👉 Use functools instead of a real function for the internal warn function (#4062)
    • ✅ Test rank capture warnings in threadsafe manner (#4064)
    • 👉 Make use of FFTs more consistent across the library (#4084)
    • 🛠 Fixup region props test (#4099)
    • Turn single backquotes to double backquotes in filters (#4127)
    • 🔨 Refactor radon transform module (#4136)
    • 🛠 Fix broken import of rgb2gray in benchmark suite (#4176)
    • 🛠 Fix doc building issues with SKIPs (#4182)
    • Remove several future imports (#4198)
    • ⏪ Restore deprecated coordinates arg to regionprops (#4144)
    • 🔨 Refactor/optimize threshold_multiotsu (#4167)
    • ✂ Remove Python2-specific code (#4170)
    • view_as_windows incorrectly assumes that a contiguous array is needed (#4171)
    • 🖐 Handle case in which NamedTemporaryFile fails (#4172)
    • 🛠 Fix incorrect resolution date on SKIP1 (#4183)
    • ⚡️ API updates before 0.16 (#4187)
    • 🛠 Fix conversion to float32 dtype (#4193)

    🚀 Contributors to this release

    • Abhishek Arya
    • Alexandre de Siqueira
    • Alexis Mignon
    • Anthony Carapetis
    • Bastian Eichenberger
    • Bharat Raghunathan
    • Christian Clauss
    • Clement Ng
    • David Breuer
    • David Haberthür
    • Dominik Kutra
    • Dominik Straub
    • Egor Panfilov
    • Emmanuelle Gouillart
    • Etienne Landuré
    • François Boulogne
    • Genevieve Buckley
    • Gregory R. Lee
    • Hadrien Mary
    • Hamdi Sahloul
    • Holly Gibbs
    • Huang-Wei Chang
    • i3v (i3v)
    • Jarrod Millman
    • Jirka Borovec
    • Johan Jeppsson
    • Johannes Schönberger
    • Jon Crall
    • Josh Warner
    • Juan Nunez-Iglesias
    • Kaligule (Kaligule)
    • kczimm (kczimm)
    • Lars Grueter
    • Shachar Ben Harim
    • Luis F. de Figueiredo
    • Mark Harfouche
    • Mars Huang
    • Dave Mellert
    • Nelle Varoquaux
    • Ollin Boer Bohan
    • Patrick J Zager
    • Riadh Fezzani
    • Ryan Avery
    • Srinath Kailasa
    • Stefan van der Walt
    • Stuart Berg
    • Uwe Schmidt

    🚀 Reviewers for this release

    • Alexandre de Siqueira
    • Anthony Carapetis
    • Bastian Eichenberger
    • Clement Ng
    • David Breuer
    • Egor Panfilov
    • Emmanuelle Gouillart
    • Etienne Landuré
    • François Boulogne
    • Genevieve Buckley
    • Gregory R. Lee
    • Hadrien Mary
    • Hamdi Sahloul
    • Holly Gibbs
    • Jarrod Millman
    • Jirka Borovec
    • Johan Jeppsson
    • Johannes Schönberger
    • Jon Crall
    • Josh Warner
    • jrmarsha
    • Juan Nunez-Iglesias
    • kczimm
    • Lars Grueter
    • leGIT-bot
    • Mark Harfouche
    • Mars Huang
    • Dave Mellert
    • Paul Müller
    • Phil Starkey
    • Ralf Gommers
    • Riadh Fezzani
    • Ryan Avery
    • Sebastian Berg
    • Stefan van der Walt
    • Uwe Schmidt