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[pkgsrc/trunk]: pkgsrc/math/py-scikit-image py-scikit-image: update to 0.14.1
details: https://anonhg.NetBSD.org/pkgsrc/rev/b2c904f1d4fb
branches: trunk
changeset: 387249:b2c904f1d4fb
user: markd <markd%pkgsrc.org@localhost>
date: Tue Nov 13 09:57:10 2018 +0000
description:
py-scikit-image: update to 0.14.1
This release contains the following changes from 0.14.0:
Enhancements
* "Reflect" mode in transforms now works fine when an image dimension has
size 1
* img_as_float now allows single-precision (32-bit) float arrays to pass
through unmodified, rather than being up-converted to 64-bit
* Speed up rgb2gray computation
* The scikit-image viewer now works with different PyQt versions
* The cycle_spin function for enhanced denoising works single-threaded when
dask is not installed now
* scikit-image's io module will no longer inadvertently set the matplotlib
backend when imported
* Fix deprecated get keyword from dask in favor of scheduler
* Add missing cval parameter to threshold_local
API changes
* Remove deprecated dynamic_range in measure.compare_psnr
0.14.0
New Features
* Lookfor function to search across the library: skimage.lookfor.
* nD support for skimage.transform.rescale, skimage.transform.resize,
and skimage.transform.pyramid_* transforms.
* Chan-Vese segmentation algorithm.
* Manual segmentation with matplotlib for fast data annotation:
skimage.future.manual_polygon_segmentation,
skimage.future.manual_lasso_segmentation.
* Hysteresis thresholding: skimage.filters.apply_hysteresis_threshold.
* Segmentation with morphological snakes:
skimage.segmentation.morphological_chan_vese (2D),
skimage.segmentation.morphological_geodesic_active_contour (2D and 3D).
* 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.
* Image moments from coordinate input: skimage.measure.moments_coords,
skimage.measure.moments_coords_central.
* Added 3D support to blob_dog and blob_log.
* Inertia tensor and its eigenvalues can now be computed outside of
regionprops; available in skimage.measure.inertia_tensor.
* Cycle-spinning function for approximating shift-invariance by averaging
results from a series of spatial shifts: skimage.restoration.cycle_spin.
* Haar-like feature: skimage.feature.haar_like_feature,
skimage.feature.haar_like_feature_coord,
skimage.feature.draw_haar_like_feature.
* Data generation with random_shapes function: skimage.draw.random_shapes.
* Subset of LFW (Labeled Faces in the Wild) database:
skimage.data.cbcl_face_database.
* Fully reworked montage function (now with a better padding behavior):
skimage.util.montage.
* YDbDr colorspace conversion routines: skimage.color.rgb2ydbdr,
skimage.color.ydbdr2rgb.
Improvements
* VisuShrink method for skimage.restoration.denoise_wavelet.
* New max_ratio parameter for skimage.feature.match_descriptors.
* skimage.transform.resize and skimage.transform.rescale have a new
anti_aliasing option to avoid aliasing artifacts when down-sampling images.
* Support for multichannel images for skimage.feature.hog.
* 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.
* New alignment parameter in skimage.feature.plot_matches.
* New seed parameter in skimage.transform.probabilistic_hough_line.
* Various performance improvements.
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.
* skimage.morphology.remove_small_holes min_size argument is deprecated
and will be removed in 0.16. Use area_threshold instead.
diffstat:
math/py-scikit-image/Makefile | 6 ++-
math/py-scikit-image/PLIST | 58 ++++++++++++++++++++++++++++++------------
math/py-scikit-image/distinfo | 10 +++---
3 files changed, 50 insertions(+), 24 deletions(-)
diffs (234 lines):
diff -r c90d0d427221 -r b2c904f1d4fb math/py-scikit-image/Makefile
--- a/math/py-scikit-image/Makefile Tue Nov 13 09:34:47 2018 +0000
+++ b/math/py-scikit-image/Makefile Tue Nov 13 09:57:10 2018 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.2 2018/01/30 10:20:11 adam Exp $
+# $NetBSD: Makefile,v 1.3 2018/11/13 09:57:10 markd Exp $
-DISTNAME= scikit-image-0.13.1
+DISTNAME= scikit-image-0.14.1
PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
CATEGORIES= graphics python
MASTER_SITES= ${MASTER_SITE_PYPI:=s/scikit-image/}
@@ -10,6 +10,8 @@
COMMENT= Image processing routines for SciPy
LICENSE= modified-bsd
+USE_LANGUAGES= c c++
+
DEPENDS+= ${PYPKGPREFIX}-Pillow>=2.9.0:../../graphics/py-Pillow
DEPENDS+= ${PYPKGPREFIX}-PyWavelets>=0.5.2:../../math/py-pywavelets
DEPENDS+= ${PYPKGPREFIX}-matplotlib-[0-9]*:../../graphics/py-matplotlib
diff -r c90d0d427221 -r b2c904f1d4fb math/py-scikit-image/PLIST
--- a/math/py-scikit-image/PLIST Tue Nov 13 09:34:47 2018 +0000
+++ b/math/py-scikit-image/PLIST Tue Nov 13 09:57:10 2018 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2017/11/22 11:14:52 markd Exp $
+@comment $NetBSD: PLIST,v 1.2 2018/11/13 09:57:10 markd Exp $
bin/skivi${PYVERSSUFFIX}
${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
@@ -149,9 +149,11 @@
${PYSITELIB}/skimage/data/foo3x5x4indexed.png
${PYSITELIB}/skimage/data/grass.png
${PYSITELIB}/skimage/data/gray_morph_output.npz
+${PYSITELIB}/skimage/data/green_palette.png
${PYSITELIB}/skimage/data/horse.png
${PYSITELIB}/skimage/data/hubble_deep_field.jpg
${PYSITELIB}/skimage/data/ihc.png
+${PYSITELIB}/skimage/data/lfw_subset.npy
${PYSITELIB}/skimage/data/logo.png
${PYSITELIB}/skimage/data/moon.png
${PYSITELIB}/skimage/data/motorcycle_disp.npz
@@ -183,6 +185,9 @@
${PYSITELIB}/skimage/draw/__init__.pyc
${PYSITELIB}/skimage/draw/__init__.pyo
${PYSITELIB}/skimage/draw/_draw.so
+${PYSITELIB}/skimage/draw/_random_shapes.py
+${PYSITELIB}/skimage/draw/_random_shapes.pyc
+${PYSITELIB}/skimage/draw/_random_shapes.pyo
${PYSITELIB}/skimage/draw/draw.py
${PYSITELIB}/skimage/draw/draw.pyc
${PYSITELIB}/skimage/draw/draw.pyo
@@ -201,6 +206,9 @@
${PYSITELIB}/skimage/draw/tests/test_draw3d.py
${PYSITELIB}/skimage/draw/tests/test_draw3d.pyc
${PYSITELIB}/skimage/draw/tests/test_draw3d.pyo
+${PYSITELIB}/skimage/draw/tests/test_random_shapes.py
+${PYSITELIB}/skimage/draw/tests/test_random_shapes.pyc
+${PYSITELIB}/skimage/draw/tests/test_random_shapes.pyo
${PYSITELIB}/skimage/exposure/__init__.py
${PYSITELIB}/skimage/exposure/__init__.pyc
${PYSITELIB}/skimage/exposure/__init__.pyo
@@ -244,6 +252,7 @@
${PYSITELIB}/skimage/feature/_daisy.py
${PYSITELIB}/skimage/feature/_daisy.pyc
${PYSITELIB}/skimage/feature/_daisy.pyo
+${PYSITELIB}/skimage/feature/_haar.so
${PYSITELIB}/skimage/feature/_hessian_det_appx.so
${PYSITELIB}/skimage/feature/_hog.py
${PYSITELIB}/skimage/feature/_hog.pyc
@@ -265,6 +274,9 @@
${PYSITELIB}/skimage/feature/corner.pyc
${PYSITELIB}/skimage/feature/corner.pyo
${PYSITELIB}/skimage/feature/corner_cy.so
+${PYSITELIB}/skimage/feature/haar.py
+${PYSITELIB}/skimage/feature/haar.pyc
+${PYSITELIB}/skimage/feature/haar.pyo
${PYSITELIB}/skimage/feature/match.py
${PYSITELIB}/skimage/feature/match.pyc
${PYSITELIB}/skimage/feature/match.pyo
@@ -305,6 +317,9 @@
${PYSITELIB}/skimage/feature/tests/test_daisy.py
${PYSITELIB}/skimage/feature/tests/test_daisy.pyc
${PYSITELIB}/skimage/feature/tests/test_daisy.pyo
+${PYSITELIB}/skimage/feature/tests/test_haar.py
+${PYSITELIB}/skimage/feature/tests/test_haar.pyc
+${PYSITELIB}/skimage/feature/tests/test_haar.pyo
${PYSITELIB}/skimage/feature/tests/test_hog.py
${PYSITELIB}/skimage/feature/tests/test_hog.pyc
${PYSITELIB}/skimage/feature/tests/test_hog.pyo
@@ -382,6 +397,7 @@
${PYSITELIB}/skimage/filters/setup.py
${PYSITELIB}/skimage/filters/setup.pyc
${PYSITELIB}/skimage/filters/setup.pyo
+${PYSITELIB}/skimage/filters/tests/.coverage
${PYSITELIB}/skimage/filters/tests/__init__.py
${PYSITELIB}/skimage/filters/tests/__init__.pyc
${PYSITELIB}/skimage/filters/tests/__init__.pyo
@@ -432,6 +448,9 @@
${PYSITELIB}/skimage/future/graph/setup.pyc
${PYSITELIB}/skimage/future/graph/setup.pyo
${PYSITELIB}/skimage/future/graph/tests/test_rag.py
+${PYSITELIB}/skimage/future/manual_segmentation.py
+${PYSITELIB}/skimage/future/manual_segmentation.pyc
+${PYSITELIB}/skimage/future/manual_segmentation.pyo
${PYSITELIB}/skimage/future/setup.py
${PYSITELIB}/skimage/future/setup.pyc
${PYSITELIB}/skimage/future/setup.pyo
@@ -489,10 +508,6 @@
${PYSITELIB}/skimage/io/_plugins/fits_plugin.py
${PYSITELIB}/skimage/io/_plugins/fits_plugin.pyc
${PYSITELIB}/skimage/io/_plugins/fits_plugin.pyo
-${PYSITELIB}/skimage/io/_plugins/freeimage_plugin.ini
-${PYSITELIB}/skimage/io/_plugins/freeimage_plugin.py
-${PYSITELIB}/skimage/io/_plugins/freeimage_plugin.pyc
-${PYSITELIB}/skimage/io/_plugins/freeimage_plugin.pyo
${PYSITELIB}/skimage/io/_plugins/gdal_plugin.ini
${PYSITELIB}/skimage/io/_plugins/gdal_plugin.py
${PYSITELIB}/skimage/io/_plugins/gdal_plugin.pyc
@@ -534,10 +549,6 @@
${PYSITELIB}/skimage/io/_plugins/skivi.py
${PYSITELIB}/skimage/io/_plugins/skivi.pyc
${PYSITELIB}/skimage/io/_plugins/skivi.pyo
-${PYSITELIB}/skimage/io/_plugins/test_plugin.ini
-${PYSITELIB}/skimage/io/_plugins/test_plugin.py
-${PYSITELIB}/skimage/io/_plugins/test_plugin.pyc
-${PYSITELIB}/skimage/io/_plugins/test_plugin.pyo
${PYSITELIB}/skimage/io/_plugins/tifffile_plugin.ini
${PYSITELIB}/skimage/io/_plugins/tifffile_plugin.py
${PYSITELIB}/skimage/io/_plugins/tifffile_plugin.pyc
@@ -796,6 +807,9 @@
${PYSITELIB}/skimage/restoration/__init__.py
${PYSITELIB}/skimage/restoration/__init__.pyc
${PYSITELIB}/skimage/restoration/__init__.pyo
+${PYSITELIB}/skimage/restoration/_cycle_spin.py
+${PYSITELIB}/skimage/restoration/_cycle_spin.pyc
+${PYSITELIB}/skimage/restoration/_cycle_spin.pyo
${PYSITELIB}/skimage/restoration/_denoise.py
${PYSITELIB}/skimage/restoration/_denoise.pyc
${PYSITELIB}/skimage/restoration/_denoise.pyo
@@ -841,9 +855,6 @@
${PYSITELIB}/skimage/restoration/unwrap.py
${PYSITELIB}/skimage/restoration/unwrap.pyc
${PYSITELIB}/skimage/restoration/unwrap.pyo
-${PYSITELIB}/skimage/run-hessian.py
-${PYSITELIB}/skimage/run-hessian.pyc
-${PYSITELIB}/skimage/run-hessian.pyo
${PYSITELIB}/skimage/scripts/__init__.py
${PYSITELIB}/skimage/scripts/__init__.pyc
${PYSITELIB}/skimage/scripts/__init__.pyo
@@ -853,6 +864,9 @@
${PYSITELIB}/skimage/segmentation/__init__.py
${PYSITELIB}/skimage/segmentation/__init__.pyc
${PYSITELIB}/skimage/segmentation/__init__.pyo
+${PYSITELIB}/skimage/segmentation/_chan_vese.py
+${PYSITELIB}/skimage/segmentation/_chan_vese.pyc
+${PYSITELIB}/skimage/segmentation/_chan_vese.pyo
${PYSITELIB}/skimage/segmentation/_clear_border.py
${PYSITELIB}/skimage/segmentation/_clear_border.pyc
${PYSITELIB}/skimage/segmentation/_clear_border.pyo
@@ -874,6 +888,9 @@
${PYSITELIB}/skimage/segmentation/boundaries.py
${PYSITELIB}/skimage/segmentation/boundaries.pyc
${PYSITELIB}/skimage/segmentation/boundaries.pyo
+${PYSITELIB}/skimage/segmentation/morphsnakes.py
+${PYSITELIB}/skimage/segmentation/morphsnakes.pyc
+${PYSITELIB}/skimage/segmentation/morphsnakes.pyo
${PYSITELIB}/skimage/segmentation/random_walker_segmentation.py
${PYSITELIB}/skimage/segmentation/random_walker_segmentation.pyc
${PYSITELIB}/skimage/segmentation/random_walker_segmentation.pyo
@@ -892,6 +909,9 @@
${PYSITELIB}/skimage/segmentation/tests/test_boundaries.py
${PYSITELIB}/skimage/segmentation/tests/test_boundaries.pyc
${PYSITELIB}/skimage/segmentation/tests/test_boundaries.pyo
+${PYSITELIB}/skimage/segmentation/tests/test_chan_vese.py
+${PYSITELIB}/skimage/segmentation/tests/test_chan_vese.pyc
+${PYSITELIB}/skimage/segmentation/tests/test_chan_vese.pyo
${PYSITELIB}/skimage/segmentation/tests/test_clear_border.py
${PYSITELIB}/skimage/segmentation/tests/test_clear_border.pyc
${PYSITELIB}/skimage/segmentation/tests/test_clear_border.pyo
@@ -901,6 +921,9 @@
${PYSITELIB}/skimage/segmentation/tests/test_join.py
${PYSITELIB}/skimage/segmentation/tests/test_join.pyc
${PYSITELIB}/skimage/segmentation/tests/test_join.pyo
+${PYSITELIB}/skimage/segmentation/tests/test_morphsnakes.py
+${PYSITELIB}/skimage/segmentation/tests/test_morphsnakes.pyc
+${PYSITELIB}/skimage/segmentation/tests/test_morphsnakes.pyo
${PYSITELIB}/skimage/segmentation/tests/test_quickshift.py
${PYSITELIB}/skimage/segmentation/tests/test_quickshift.pyc
${PYSITELIB}/skimage/segmentation/tests/test_quickshift.pyo
@@ -980,6 +1003,9 @@
${PYSITELIB}/skimage/util/_invert.py
${PYSITELIB}/skimage/util/_invert.pyc
${PYSITELIB}/skimage/util/_invert.pyo
+${PYSITELIB}/skimage/util/_montage.py
+${PYSITELIB}/skimage/util/_montage.pyc
+${PYSITELIB}/skimage/util/_montage.pyo
${PYSITELIB}/skimage/util/_regular_grid.py
${PYSITELIB}/skimage/util/_regular_grid.pyc
${PYSITELIB}/skimage/util/_regular_grid.pyo
@@ -995,9 +1021,9 @@
${PYSITELIB}/skimage/util/dtype.py
${PYSITELIB}/skimage/util/dtype.pyc
${PYSITELIB}/skimage/util/dtype.pyo
-${PYSITELIB}/skimage/util/montage.py
-${PYSITELIB}/skimage/util/montage.pyc
-${PYSITELIB}/skimage/util/montage.pyo
+${PYSITELIB}/skimage/util/lookfor.py
+${PYSITELIB}/skimage/util/lookfor.pyc
+${PYSITELIB}/skimage/util/lookfor.pyo
${PYSITELIB}/skimage/util/noise.py
${PYSITELIB}/skimage/util/noise.pyc
${PYSITELIB}/skimage/util/noise.pyo
@@ -1136,5 +1162,3 @@
${PYSITELIB}/skimage/viewer/widgets/history.py
${PYSITELIB}/skimage/viewer/widgets/history.pyc
${PYSITELIB}/skimage/viewer/widgets/history.pyo
-@pkgdir lib/python${PYVERSSUFFIX}/site-packages/skimage/data/tests/__pycache__
-@pkgdir lib/python${PYVERSSUFFIX}/site-packages/skimage/data/__pycache__
diff -r c90d0d427221 -r b2c904f1d4fb math/py-scikit-image/distinfo
--- a/math/py-scikit-image/distinfo Tue Nov 13 09:34:47 2018 +0000
+++ b/math/py-scikit-image/distinfo Tue Nov 13 09:57:10 2018 +0000
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.1 2017/11/22 11:14:52 markd Exp $
+$NetBSD: distinfo,v 1.2 2018/11/13 09:57:10 markd Exp $
-SHA1 (scikit-image-0.13.1.tar.gz) = 5b56f200d13fc71a98fcb431265b18b3b06d80d2
-RMD160 (scikit-image-0.13.1.tar.gz) = ddd8855e696d62b0c2c0aaa1f2981c5dffea1357
-SHA512 (scikit-image-0.13.1.tar.gz) = fba2700743486e1c556c697ec307ed972b8a70d7829a6fab3360f91542322a250d2f0fd32c5ec442409f5ebbec01b0550bfce037d8bb0667ff2286731b7a6263
-Size (scikit-image-0.13.1.tar.gz) = 26142438 bytes
+SHA1 (scikit-image-0.14.1.tar.gz) = c5c17be69bdd0938423a4baf660750c94d6f6708
+RMD160 (scikit-image-0.14.1.tar.gz) = 47acd78a5cf9749dd6287e41adb885d2f0070178
+SHA512 (scikit-image-0.14.1.tar.gz) = 30c2b7c985568f9b03b82be4839c16882adfdec664f69293aaccf1deee12305e88d42ff9a6f193a46e4ecd1337b032d319a1b7ea1a0fdbb01f96451cf7ed73cf
+Size (scikit-image-0.14.1.tar.gz) = 27521651 bytes
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