522 lines
23 KiB
ReStructuredText
522 lines
23 KiB
ReStructuredText
Announcement: scikit-image 0.15.0
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=================================
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We're happy to announce the release of scikit-image v0.15.0!
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scikit-image is an image processing toolbox for SciPy that includes algorithms
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for segmentation, geometric transformations, color space manipulation,
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analysis, filtering, morphology, feature detection, and more.
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For more information, examples, and documentation, please visit our website:
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https://scikit-image.org
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0.15 is the first scikit-image release that is only compatible with Python 3.5
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and above. Python 2.7 users should strongly consider upgrading to Python 3.5+,
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or use the 0.14 long term support releases.
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New Features
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------------
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- N-dimensional flood fill, with tolerance (#3245)
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- Attribute operators (#2680)
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- Extension of register_translation to enable subpixel precision in 3D and
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optionally disable error calculation (#2880)
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- unsharp mask filtering (#2772)
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- New options ``connectivity``, ``indices`` and ``allow_borders`` for
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``skimage.morphology.local_maxima`` and ``local_minima``. (#3022)
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- Image translation registration for masked data
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(``skimage.feature.masked_register_translation``) (#3334)
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- Frangi (vesselness), Meijering (neuriteness), and Sato (tubeness) filters
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(#3515)
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- Allow float->float conversion of any range (#3052)
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- Let lower precision float arrays pass through ``img_as_float`` (#3110)
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- Lazy apply_parallel (allows optimization of dask array operations) (#3121)
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- Add range option for histogram. (#2479)
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- Add histogram matching (#3568)
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Improvements
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------------
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- Replace ``morphology.local_maxima`` with faster flood-fill based Cython
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version (#3022)
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- ``skivi`` is now using ``qtpy`` for Qt4/Qt5/PySide/PySide2 compatibility (a
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new optional dependency).
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- Performance is now monitored by
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`Airspeed Velocity <https://asv.readthedocs.io/en/stable/>`_. Benchmark
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results will appear at https://pandas.pydata.org/speed/ (#3137)
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- Speed up inner loop of GLCM (#3378)
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- Allow tuple to define kernel in threshold_niblack and threshold_sauvola (#3596)
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- Add support for anisotropic blob detection in blob_log and blob_dog (#3690)
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API Changes
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-----------
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- ``skimage.transform.seam_carve`` has been removed because the algorithm is
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patented. (#3751)
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- Parameter ``dynamic_range`` in ``skimage.measure.compare_psnr`` has been
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removed. Use parameter ``data_range`` instead. (#3313)
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- imageio is now the preferred plugin for reading and writing images. (#3126)
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- imageio is now a dependency of scikit-image. (#3126)
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- ``regular_grid`` now returns a tuple instead of a list for compatibility
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with numpy 1.15 (#3238)
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- ``colorconv.separate_stains`` and ``colorconv.combine_stains`` now uses
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base10 instead of the natural logarithm as discussed in issue #2995. (#3146)
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- Default value of ``clip_negative`` parameter in ``skimage.util.dtype_limits``
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has been set to ``False``.
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- Default value of ``circle`` parameter in ``skimage.transform.radon``
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has been set to ``True``.
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- Default value of ``circle`` parameter in ``skimage.transform.iradon``
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has been set to ``True``.
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- Default value of ``mode`` parameter in ``skimage.transform.swirl``
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has been set to ``reflect``.
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- Deprecated ``skimage.filters.threshold_adaptive`` has been removed.
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Use ``skimage.filters.threshold_local`` instead.
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- Default value of ``multichannel`` parameter in
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``skimage.restoration.denoise_bilateral`` has been set to ``False``.
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- Default value of ``multichannel`` parameter in
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``skimage.restoration.denoise_nl_means`` has been set to ``False``.
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- Default value of ``mode`` parameter in ``skimage.transform.resize``
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and ``skimage.transform.rescale`` has been set to ``reflect``.
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- Default value of ``anti_aliasing`` parameter in ``skimage.transform.resize``
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and ``skimage.transform.rescale`` has been set to ``True``.
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- Removed the ``skimage.test`` function. This functionality can be achieved
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by calling ``pytest`` directly.
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- ``morphology.local_maxima`` now returns a boolean array (#3749)
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Bugfixes
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--------
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- Correct bright ridge detection for Frangi filter (#2700)
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- ``skimage.morphology.local_maxima`` and ``skimage.morphology.local_minima``
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no longer raise an error if any dimension of the image is smaller 3 and
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the keyword ``allow_borders`` was false.
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- ``skimage.morphology.local_maxima`` and ``skimage.morphology.local_minima``
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will return a boolean array instead of an array of 0s and 1s if the
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parameter ``indices`` was false.
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- When ``compare_ssim`` is used with ``gaussian_weights`` set to True, the
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boundary crop used when computing the mean structural similarity will now
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exactly match the width of the Gaussian used. The Gaussian filter window is
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also now truncated at 3.5 rather than 4.0 standard deviations to exactly match
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the original publication on the SSIM. These changes should produce only a very
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small change in the computed SSIM value. There is no change to the existing
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behavior when ``gaussian_weights`` is False. (#3802)
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- erroneous use of cython wrap around (#3481)
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- Speed up block reduce by providing the appropriate parameters to numpy (#3522)
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- Add urllib.request again (#3766)
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- Repeat pixels in reflect mode when image has dimension 1 (#3174)
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- Improve Li thresholding (#3402, 3622)
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Deprecations
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------------
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- Python 2 support has been dropped. Users should have Python >= 3.5. (#3000)
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- ``skimage.util.montage2d`` has been removed. Use ``skimage.util.montage`` instead.
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- ``skimage.novice`` is deprecated and will be removed in 0.16.
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- ``skimage.transform.resize`` and ``skimage.transform.rescale`` option
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``anti_aliasing`` has been enabled by default.
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- ``regionprops`` will use row-column coordinates in 0.16. You can start
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using them now with ``regionprops(..., coordinates='rc')``. You can silence
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warning messages, and retain the old behavior, with
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``regionprops(..., coordinates='xy')``. However, that option will go away
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in 0.16 and result in an error. This change has a number of consequences.
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Specifically, the "orientation" region property will measure the
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anticlockwise angle from a *vertical* line, i.e. from the vector (1, 0) in
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row-column coordinates.
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- ``skimage.morphology.remove_small_holes`` ``min_size`` argument is deprecated
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and will be removed in 0.16. Use ``area_threshold`` instead.
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- ``skimage.filters.median`` will change behavior in the future to have an
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identical behavior as ``scipy.ndimage.median_filter``. This behavior can be
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set already using ``behavior='ndimage'``. In 0.16, it will be the default
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behavior and removed in 0.17 as well as the parameter of the previous
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behavior (i.e., ``mask``, ``shift_x``, ``shift_y``) will be removed.
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Documentation improvements
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--------------------------
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- Correct rotate method's center parameter doc (#3341)
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- Add Sphinx copybutton (#3530)
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- Add glossary to the documentation (#3626)
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- Add image of retina to our data (#3748)
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- Add microaneurysms() to gallery (#3765)
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- Better document remove_small_objects behaviour: int vs bool (#2830)
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- Linking preserve_range parameter calls to docs (#3109)
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- Update the documentation regarding datalocality (#3127)
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- Specify conda-forge channel for scikit-image conda install (#3189)
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- Turn DOIs into web links in docstrings (#3367)
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- Update documentation for regionprops (#3602)
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- DOC: Improve the RANSAC gallery example (#3554)
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- DOC: "feature.peak_local_max" : explanation of multiple same-intensity peaks returned by the function; added details on ``exclude_border`` parameter (#3600)
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Improvements
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------------
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- MNT: handle a deprecation warning for np.linspace and floats for the num parameter (#3453)
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- TST: numpy empty arrays are not inherently Falsy (#3455)
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- handle warning in scipy cdist for unused parameters (#3456)
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- MNT: don't use filter_warnings in test suite. (#3459)
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- Add doc notes on setting up the build environment (#3472)
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- Release the GIL in numerous cython functions (#3490)
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- Cython touchups to use float32 and float64 (#3493)
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- rank_filters: Change how the bitdepth and max_bin are computed to ensure exact warnings. (#3501)
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- Rank: Optimize OTSU filter (#3504)
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- Rank - Fix rank entropy and OTSU tests (#3506)
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- delay importing pyplot in manual segmentation (#3533)
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- Get rid of the requirements-parser dependency (#3534)
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- filter warning from ``correct_mesh_orientation`` in tests (#3549)
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- cloudpickle is really a doc dependency, not a core one (#3634)
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- optional dependencies on pip (#3645)
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- Fewer test warnings in 3.7 (#3687)
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- collections.abc nit (#3692)
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- Streamlined issue template (#3697)
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- Tighten the PR Template (#3701)
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- Use language level to 3 in cython for future compatibility (#3707)
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- Update ISSUE_TEMPLATE.md with info about numpy and skimage versions (#3730)
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- Use relative imports for many cython modules (#3759)
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- Pass tests that don't raise floating point exceptions on arm with soft-fp (#3337)
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Other improvements
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------------------
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- BUG: Fix greycoprops correlation always returning 1 (#2532)
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- Add section on API discovery via ``skimage.lookfor`` (#2539)
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- Speedup 2D warping for affine transformations (#2902)
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- Credit Reviewers in Release Notes (#2927)
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- Added small galleries in the API (#2940)
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- Use skimage gaussian filter to avoid integer rounding artifacts (#2983)
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- Remove Python 2 compatibility (#3000)
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- Add ``rectangle_perimeter`` feature to ``skimage.draw`` (#3069)
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- Update installation instructions to reference existing requirements specification (#3113)
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- Updated release notes with pre 0.13.1 phase (#3114)
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- Release guidelines update (#3115)
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- Ensure we are installing with / running on Python 3 (#3119)
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- Hide warnings in test_unsharp_mask (#3130)
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- Process 0.15 deprecations (#3132)
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- Documentation: always use dev branch javascript (#3136)
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- Add initial airspeed velocity (asv) framework (#3137)
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- Supress warnings for flatten during io testing (#3143)
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- Recover from exceptions in filters.try_all_threshold() (#3149)
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- Fix skimage.test() to run the unittests (#3152)
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- skivi: Use qtpy to handle different Qt versions (#3157)
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- Refactor python version checking. (#3160)
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- Move data_dir to within ``data/__init__.py`` (#3161)
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- Move the definition of lookfor out of __init__.py (#3162)
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- Normalize the package number to PEP440 (#3163)
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- Remove skimage.test as it was never used. (#3164)
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- Added a message about qtpy to the INSTALL.rst (#3168)
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- Regression fix: Travis should fail if tests fail (#3170)
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- Set minimum cython version to ``0.23.4`` (#3171)
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- Add rgba2rgb to API docs (#3175)
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- Minor doc formatting fixes in video.rst (#3176)
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- Decrease the verbosity of the testing (#3182)
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- Speedup rgb2gray using matrix multiply (#3187)
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- Add instructions for meeseeksdev to PR template (#3194)
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- Remove installation instructions for video packages (#3197)
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- Big image labeling fix (#3202)
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- Handle dask deprecation in cycle_spin (#3205)
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- Fix Qt viewer painttool indexing (#3210)
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- build_versions.py is no longer hard coded. (#3211)
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- Remove dtype constructor call in exposure.rescale_intensity (#3213)
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- Various updates to the ASV benchmarks (#3215)
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- Add a link to stack overflow on github README (#3217)
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- MAINT: remove encoding information in file headers (python 3) (#3219)
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- Build tools: Dedicate a --pre build in appveyor and ensure other builds don't download --pre (#3222)
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- Fix the human readable error message on a bad build. (#3223)
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- Respect input array type in apply_parallel by default (#3225)
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- Travis cleanup pip commands (#3227)
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- Add benchmarks for morphology.watershed (#3234)
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- Correcte docstring formatting so that code block is displayed as code (#3236)
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- Defer skimage.io import of matplotlib.pyplot until needed (#3243)
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- Add benchmark for Sobel filters (#3249)
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- Remove cython md5 hashing since it breaks the build process (#3254)
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- Fix typo in documentation. (#3262)
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- Issue 3156: skimage/__init__.py Update docstring and fix import * (#3265)
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- Object detector module (#3267)
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- Do not import submodules while building (#3270)
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- Add benchmark suite for canny (#3271)
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- improve segmentation.felzenszwalb document #3264 (#3272)
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- Update _canny.py (#3276)
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- Add benchmark suite for histogram equalization (#3285)
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- fix link to equalist_hist blog reference (#3287)
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- .gitignore: novice: Ignore save-demo.jpg (#3289)
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- Guide the user of denoise_wavelet to choose an orthogonal wavelet. (#3290)
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- Remove unused lib in skimage/__init__.py (#3291)
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- BUILD: Add pyproject.toml to ensure cython is present (#3295)
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- Handle intersphinx and mpl deprecation warnings in docs (#3300)
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- Minor PEP8 fixes (#3305)
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- cython: check for presence of cpp files during install from sdist (#3311)
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- appveyor: don't upload any artifacts (#3315)
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- Add benchmark suite for hough_line() (#3319)
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- Novice skip url test (#3320)
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- Remove benchmarks from wheel (#3321)
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- Add license file to the wheel (binary) distribution (#3322)
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- codecov: ignore build scripts in coverage and don't comment on PRs (#3326)
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- Matplotlib 2.2.3 + PyQt5.11 (#3345)
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- Allow @hmaarrfk to mention MeeseeksDev to backport. (#3357)
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- Add Python 3.7 to the test matrix (#3359)
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- Fix deprecated keyword from dask (#3366)
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- Incompatible modes with anti-aliasing in skimage.transform.resize (#3368)
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- Missing cval parameter in threshold_local (#3370)
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- Avoid Sphinx 1.7.8 (#3381)
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- Show our data in the gallery (#3388)
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- Minor updates to grammar in numpy images page (#3389)
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- assert_all_close doesn't exist, make it ``assert_array_equal`` (#3391)
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- Better behavior of Gaussian filter for arrays with a large number of dimensions (#3394)
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- Allow import/execution with -OO (#3398)
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- Mark tests known to fail on 32bit architectures with xfail (#3399)
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- Hardcode the inputs to test_ssim_grad (#3403)
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- TST: make test_wavelet_denoising_levels compatible with PyWavelets 1.0 (#3406)
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- Allow tifffile.py to handle I/O. (#3409)
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- Add explicit Trove classifier for Python 3 (#3415)
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- Fix error in contribs.py (#3418)
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- MAINT: remove pyside restriction since we don't support Python 3.4 anymore (#3421)
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- Build tools: simplify how MPL_DIR is obtained. (#3422)
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- Build tools: Don't run tests twice in travis. (#3423)
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- Build tools: Add an OSX build with optional dependencies. (#3424)
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- MAINT: Reverted the changes in #3300 that broke the MINIMIUM_REQUIREMENTS tests (#3427)
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- MNT: Convert links using http to https (#3428)
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- MAINT: Use upstream colormaps now that matplotlib has been upgraded (#3429)
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- Build tools: Make pyamg an optional dependency and remove custom logic (#3431)
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- Build tools: Fix PyQt installed in minimum requirements build (#3432)
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- MNT: multiprocessing should always be available since we depend on python >=2.7 (#3434)
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- MAINT Use np.full instead of cst*np.ones (#3440)
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- DOC: Fix LaTeX build via ``make latexpdf`` (#3441)
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- Update instructions et al for releases after 0.14.1 (#3442)
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- Remove code specific to python 2 (#3443)
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- Fix default value of ``methods`` in ``_try_all`` to avoid exception (#3444)
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- Fix morphology.local_maxima for input with any dimension < 3 (#3447)
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- Use raw strings to avoid unknown escape symbol warnings (#3450)
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- Speed up xyz2rgb by clipping output in place (#3451)
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- MNT; handle deprecation warnings in tifffile (#3452)
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- Build tools: TST: filter away novice deprecation warnings during testing (#3454)
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- Build tools: don't use the pytest.fixtures decorator anymore in class fixtures (#3458)
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- Preserving the fill_value of a masked array (#3461)
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- Fix VisibleDeprecationWarning from np.histogram, normed=True (#3463)
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- Build Tools: DOC: Document that now PYTHONOPTMIZE build is blocked by SciPy (#3470)
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- DOC: Replace broken links by webarchive equivalent links (#3471)
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- FIX: making the plot_marching_cubes example visible. (#3474)
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- Avoid Travis failure regarding ``skimage.lookfor`` (#3477)
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- Fix Python executable for sphinx-build in docs Makefile (#3478)
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- Build Tools: Block specific Cython versions (#3479)
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- Fix typos (#3480)
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- Add "optional" indications to docstrings (#3495)
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- Rename 'mnxc' (masked normalize cross-correlation) to something more descriptive (#3497)
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- Random walker bug fix: no error should be raised when there is nothing to do (#3500)
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- Various minor edits for active contour (#3508)
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- Fix range for uint32 dtype in user guide (#3512)
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- Raise meaningful exception in warping when image is empty (#3518)
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- DOC: Development installation instructions for Ubuntu are missing tkinter (#3520)
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- Better gallery examples and tests for masked translation registration (#3528)
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- DOC: make more docstrings compliant with our standards (#3529)
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- Build tools: Remove restriction on simpleitk for python 3.7 (#3535)
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- Speedup and add benchmark for ``skeletonize_3d`` (#3536)
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- Update requirements/README.md on justification of matplotlib 3.0.0 in favor of #3476 (#3542)
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- Doc enhancements around denoising features. (#3553)
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- Use 'getconf _NPROCESSORS_ONLN' as fallback for nproc in Makefile of docs (#3563)
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- Fix matplotlib set_*lim API deprecations (#3564)
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- Switched from np.power to np.cbrt (#3570)
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- Filtered out DeprecationPendingWarning for matrix subclass (#3572)
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- Add RGB to grayscale example to gallery (#3574)
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- Build tools: Refactor check_sdist so that it takes a filename as a parameter (#3579)
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- Turn dask to an optional requirement (#3582)
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- _marching_cubes_lewiner_cy: mark char as signed (#3587)
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- Hyperlink DOIs to preferred resolver (#3589)
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- Missing parameter description in ``morphology.reconstruction`` docstring #3581 (#3591)
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- Update chat location (#3598)
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- Remove orphan code (skimage/filters/_ctmf.pyx). (#3601)
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- More explicit example title, better list rendering in plot_cycle_spinning.py (#3606)
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- Add rgb to hsv example in the gallery (#3607)
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- Update documentation of ``perimeter`` and add input validation (#3608)
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- Additionnal mask option to clear_border (#3610)
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- Set up CI with Azure Pipelines (#3612)
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- [MRG] EHN: median filters will accept floating image (#3616)
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- Update Travis-CI to xcode 10.1 (#3617)
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- Minor tweaks to _mean_std code (#3619)
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- Add explicit ordering of gallery sections (#3627)
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- Delete broken links (#3628)
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- Build tools: Fix test_mpl_imshow for matplotlib 2.2.3 and numpy 1.16 (#3635)
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- First draft of core dev guide (#3636)
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- Add more details about the home page build process (#3639)
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- Ensure images resources with long querystrings can be read (#3642)
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- Delay matplotlib import in skimage/future/manual_segmentation.py (#3648)
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- make the low contrast check optional when saving images (#3653)
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- Correctly ignore release notes auto-generated for docs (#3656)
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- Remove MANIFEST file when making the 'clean' target (#3657)
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- Clarify return values in _overlap docstrings in feature/blob.py (#3660)
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- Contribution script: allow specification of GitHub development branch (#3661)
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- Update core dev guide: deprecation, contributor guide, required experience (#3662)
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- Add release notes for 0.14.2 (#3664)
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- FIX gallery: Add multichannel=True to match_histogram (#3672)
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- MAINT Minor code style improvements (#3673)
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- Pass parameters through tifffile plugin (#3675)
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- DOC unusused im3d_t in example (#3677)
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- Remove wrong cast of Py_ssize_t to int (#3682)
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- Build tools: allow python 3.7 to fail, but travis to continue (#3683)
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- Build tools: remove pyproject.toml (#3688)
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- Fix ValueError: not enough values to unpack (#3703)
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- Several fixes for heap.pyx (#3704)
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- Enable the faulthandler module during testing (#3708)
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- Build tools: Fix Python 3.7 builds on travis (#3709)
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- Replace np.einsum with np.tensordot in _upsampled_dft (#3710)
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- Fix potential use of NULL pointers (#3717)
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- Fix potential memory leak (#3718)
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- Fix potential use of NULL pointers (#3719)
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- Fix and improve core_cy.pyx (#3720)
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- Build tools: Downgrade Xcode to 9.4 on master (#3723)
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- Improve visual_test.py (#3732)
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- Updated painttool to work with color images and properly scale labels. (#3733)
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- Add image.sc forum badge to README (#3738)
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- Block PyQt 5.12.0 on Travis (#3743)
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- Build tools: Fix matplotlib + qt 5.12 the same way upstream does it (#3744)
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- gallery: remove xx or yy sorted directory names (#3761)
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- Allow for f-contiguous 2D arrays in convex_hull_image (#3762)
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- Build tools: Set astropy minimum requirement to 1.2 to help the CIs. (#3767)
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- Avoid NumPy warning while stacking arrays. (#3768)
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- Set CC0 for microaneurysms (#3778)
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- Unify LICENSE files for easier interpretation (#3791)
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- Readme: Remove expectation for future fix from matplotlib (#3794)
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- Improved documentation/test in ``flood()`` (#3796)
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- Use ssize_t in denoise cython (#3800)
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- Removed non-existent parameter in docstring (#3803)
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- Remove redundant point in draw.polygon docstring example (#3806)
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- Ensure watershed auto-markers respect mask (#3809)
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75 authors added to this release [alphabetical by first name or login]
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----------------------------------------------------------------------
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- Abhishek Arya
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- Adrian Roth
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- alexis-cvetkov (Alexis Cvetkov-Iliev)
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- Ambrose J Carr
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- Arthur Imbert
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- blochl (Leonid Bloch)
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- Brian Smith
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- Casper da Costa-Luis
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- Christian Rauch
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- Christoph Deil
|
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- Christoph Gohlke
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- Constantin Pape
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- David Breuer
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- Egor Panfilov
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- Emmanuelle Gouillart
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- fivemok
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- François Boulogne
|
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- François Cokelaer
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- François-Michel De Rainville
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- Genevieve Buckley
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- Gregory R. Lee
|
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- Gregory Starck
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- Guillaume Lemaitre
|
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- Hugo
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- jakirkham (John Kirkham)
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- Jan
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- Jan Eglinger
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- Jathrone
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- Jeremy Metz
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- Jesse Pangburn
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- Johannes Schönberger
|
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- Jonathan J. Helmus
|
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- Josh Warner
|
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- Jotham Apaloo
|
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- Juan Nunez-Iglesias
|
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- Justin
|
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- Katrin Leinweber
|
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- Kim Newell
|
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- Kira Evans
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- Kirill Klimov
|
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- Lars Grueter
|
|
- Laurent P. René de Cotret
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- Legodev
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- mamrehn
|
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- Marcel Beining
|
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- Mark Harfouche
|
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- Matt McCormick
|
|
- Matthias Bussonnier
|
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- mrastgoo
|
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- Nehal J Wani
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- Nelle Varoquaux
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- Onomatopeia
|
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- Oscar Javier Hernandez
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|
- Page-David
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- PeterJackNaylor
|
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- PinkFloyded
|
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- R S Nikhil Krishna
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- ratijas
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- Rob
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- robroooh
|
|
- Roman Yurchak
|
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- Sarkis Dallakian
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|
- Scott Staniewicz
|
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- Sean Budd
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- shcrela
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- Stefan van der Walt
|
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- Taylor D. Scott
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|
- Thein Oo
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- Thomas Walter
|
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- Tom Augspurger
|
|
- Tommy Löfstedt
|
|
- Tony Tung
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- Vilim Štih
|
|
- yangfl
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- Zhanwen "Phil" Chen
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46 reviewers added to this release [alphabetical by first name or login]
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------------------------------------------------------------------------
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- Abhishek Arya
|
|
- Adrian Roth
|
|
- Alexandre de Siqueira
|
|
- Ambrose J Carr
|
|
- Arthur Imbert
|
|
- Brian Smith
|
|
- Christian Rauch
|
|
- Christoph Gohlke
|
|
- David Breuer
|
|
- Egor Panfilov
|
|
- Emmanuelle Gouillart
|
|
- Evan Putra Limanto
|
|
- François Boulogne
|
|
- François Cokelaer
|
|
- Gregory R. Lee
|
|
- Grégory Starck
|
|
- Guillaume Lemaitre
|
|
- Ilya Flyamer
|
|
- jakirkham
|
|
- Jarrod Millman
|
|
- Johannes Schönberger
|
|
- Josh Warner
|
|
- Jotham Apaloo
|
|
- Juan Nunez-Iglesias
|
|
- Justin
|
|
- Lars Grueter
|
|
- Laurent P. René de Cotret
|
|
- Marcel Beining
|
|
- Mark Harfouche
|
|
- Matthew Brett
|
|
- Matthew Rocklin
|
|
- Matti Picus
|
|
- mrastgoo
|
|
- Onomatopeia
|
|
- PeterJackNaylor
|
|
- Rob
|
|
- Roman Yurchak
|
|
- Scott Staniewicz
|
|
- Stefan van der Walt
|
|
- Thein Oo
|
|
- Thomas A Caswell
|
|
- Thomas Walter
|
|
- Tom Augspurger
|
|
- Tomas Kazmar
|
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- Tommy Löfstedt
|
|
- Vilim Štih
|