[skimage] branch master updated (8ac72e0 -> d10e0b7)
Andreas Tille
tille at debian.org
Thu Aug 17 20:50:01 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository skimage.
from 8ac72e0 Changelog for 0.12.3-9
new 47aea76 Apply patch by Michael Hudson-Doyle
adds fa8a914 New upstream version 0.13.0
new d10e0b7 Updated version 0.13.0 from 'upstream/0.13.0'
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
CONTRIBUTING.txt => .github/CONTRIBUTING.txt | 84 +-
.github/ISSUE_TEMPLATE.md | 15 +
.github/PULL_REQUEST_TEMPLATE.md | 18 +
.gitignore | 7 +-
.mailmap | 1 +
.travis.yml | 43 +-
CONTRIBUTORS.txt | 27 +-
DEPENDS.txt | 28 +-
MANIFEST.in | 8 +-
Makefile | 2 +-
README.md | 4 +-
RELEASE.txt | 4 +-
TASKS.txt | 4 +-
TODO.txt | 42 +-
appveyor.yml | 28 +-
bento.info | 13 +-
debian/changelog | 15 +
debian/control | 27 +-
...t_6807f4ee8f5501703e447f95701190c836deaae1.diff | 14 -
debian/patches/dask-optional-dep.patch | 77 -
debian/patches/doc-privacy.patch | 2 +-
debian/patches/fix-doc-links.patch | 6 +-
debian/patches/fix_shape_type.patch | 15 -
debian/patches/search-html.patch | 21 -
debian/patches/series | 7 +-
.../patches/skip-failing-test-on-big-endian.patch | 22 +
debian/patches/skip-failing-test-on-i386.patch | 47 +
.../skip_tests_failing_on_some_architectures.patch | 91 -
debian/rules | 2 +-
doc/Makefile | 16 +-
doc/examples/README.txt | 5 +-
doc/examples/color_exposure/plot_adapt_rgb.py | 82 +-
doc/examples/color_exposure/plot_equalize.py | 12 +-
.../color_exposure/plot_ihc_color_separation.py | 50 +-
.../color_exposure/plot_regional_maxima.py | 113 +-
.../plot_tinting_grayscale_images.py | 105 +-
doc/examples/edges/plot_active_contours.py | 22 +-
.../plot_circular_elliptical_hough_transform.py | 95 +-
doc/examples/edges/plot_contours.py | 6 +-
doc/examples/edges/plot_convex_hull.py | 51 +-
doc/examples/edges/plot_edge_filter.py | 90 +-
doc/examples/edges/plot_line_hough_transform.py | 107 +-
doc/examples/edges/plot_marching_cubes.py | 9 +-
doc/examples/edges/plot_medial_transform.py | 66 -
doc/examples/edges/plot_skeleton.py | 207 +-
doc/examples/features_detection/plot_blob.py | 21 +-
doc/examples/features_detection/plot_brief.py | 18 +-
doc/examples/features_detection/plot_censure.py | 10 +-
.../plot_gabors_from_astronaut.py | 24 +-
doc/examples/features_detection/plot_glcm.py | 9 +-
doc/examples/features_detection/plot_hog.py | 10 +-
.../features_detection/plot_holes_and_peaks.py | 91 +-
.../plot_local_binary_pattern.py | 52 +-
.../plot_multiblock_local_binary_pattern.py | 22 +-
doc/examples/features_detection/plot_orb.py | 5 +-
.../features_detection/plot_shape_index.py | 166 +
doc/examples/features_detection/plot_template.py | 8 +-
.../features_detection/plot_windowed_histogram.py | 13 +-
doc/examples/filters/plot_deconvolution.py | 55 +
doc/examples/filters/plot_denoise.py | 72 +-
doc/examples/filters/plot_entropy.py | 14 +-
doc/examples/filters/plot_frangi.py | 31 +
doc/examples/filters/plot_inpaint.py | 27 +-
doc/examples/filters/plot_nonlocal_means.py | 2 +-
doc/examples/filters/plot_phase_unwrap.py | 52 +-
doc/examples/filters/plot_rank_mean.py | 9 +-
.../numpy_operations/plot_view_as_blocks.py | 49 +-
doc/examples/segmentation/plot_boundary_merge.py | 90 +
.../segmentation/plot_compact_watershed.py | 43 +
doc/examples/segmentation/plot_extrema.py | 84 +
.../segmentation/plot_join_segmentations.py | 54 +-
doc/examples/segmentation/plot_label.py | 32 +-
doc/examples/segmentation/plot_local_otsu.py | 60 -
doc/examples/segmentation/plot_marked_watershed.py | 32 +-
doc/examples/segmentation/plot_ncut.py | 17 +-
doc/examples/segmentation/plot_niblack_sauvola.py | 66 +
doc/examples/segmentation/plot_otsu.py | 49 -
doc/examples/segmentation/plot_peak_local_max.py | 32 +-
doc/examples/segmentation/plot_rag.py | 15 +-
doc/examples/segmentation/plot_rag_boundary.py | 18 +-
doc/examples/segmentation/plot_rag_draw.py | 41 +-
doc/examples/segmentation/plot_rag_mean_color.py | 16 +-
doc/examples/segmentation/plot_rag_merge.py | 9 +-
doc/examples/segmentation/plot_segmentations.py | 67 +-
.../segmentation/plot_threshold_adaptive.py | 48 -
doc/examples/segmentation/plot_thresholding.py | 72 +
doc/examples/segmentation/plot_watershed.py | 20 +-
doc/examples/transform/plot_edge_modes.py | 29 +-
doc/examples/transform/plot_fundamental_matrix.py | 83 +
doc/examples/transform/plot_pyramid.py | 4 +-
doc/examples/transform/plot_radon_transform.py | 162 +-
.../transform/plot_register_translation.py | 33 +-
doc/examples/transform/plot_seam_carving.py | 47 +-
doc/examples/transform/plot_ssim.py | 40 +-
doc/examples/transform/plot_swirl.py | 4 +-
.../xx_applications/plot_coins_segmentation.py | 185 +-
doc/examples/xx_applications/plot_geometric.py | 153 +-
doc/examples/xx_applications/plot_morphology.py | 306 +-
doc/examples/xx_applications/plot_rank_filters.py | 747 ++---
doc/examples/xx_applications/plot_thresholding.py | 234 ++
doc/ext/docscrape.py | 543 ----
doc/ext/docscrape_sphinx.py | 274 --
doc/ext/numpydoc.py | 192 --
doc/ext/plot_directive.py | 642 ----
doc/ext/sphinx_gallery/LICENSE | 27 +
doc/ext/sphinx_gallery/README.txt | 6 +
doc/ext/sphinx_gallery/__init__.py | 13 +
doc/ext/sphinx_gallery/_static/broken_example.png | Bin 0 -> 21404 bytes
doc/ext/sphinx_gallery/_static/broken_stamp.svg | 90 +
doc/ext/sphinx_gallery/_static/gallery.css | 192 ++
doc/ext/sphinx_gallery/_static/no_image.png | Bin 0 -> 4315 bytes
doc/ext/sphinx_gallery/backreferences.py | 193 ++
doc/ext/sphinx_gallery/docs_resolv.py | 462 +++
doc/ext/sphinx_gallery/downloads.py | 117 +
doc/ext/sphinx_gallery/gen_gallery.py | 252 ++
doc/ext/sphinx_gallery/gen_rst.py | 643 ++++
doc/ext/sphinx_gallery/notebook.py | 194 ++
doc/ext/sphinx_gallery/py_source_parser.py | 99 +
doc/release/contribs.py | 60 +-
doc/release/{release_0.10.txt => release_0.10.rst} | 0
doc/release/{release_0.11.txt => release_0.11.rst} | 0
doc/release/{release_0.12.txt => release_0.12.rst} | 0
doc/release/release_0.13.rst | 447 +++
doc/release/{release_0.3.txt => release_0.3.rst} | 0
doc/release/{release_0.4.txt => release_0.4.rst} | 0
doc/release/{release_0.5.txt => release_0.5.rst} | 0
doc/release/{release_0.6.txt => release_0.6.rst} | 0
doc/release/{release_0.7.txt => release_0.7.rst} | 0
doc/release/{release_0.8.txt => release_0.8.rst} | 0
doc/release/{release_0.9.txt => release_0.9.rst} | 0
doc/release/{release_dev.txt => release_dev.rst} | 0
.../{release_template.txt => release_template.rst} | 2 +
doc/source/_static/docversions.js | 2 +-
doc/source/_static/favicon.ico | Bin 2324 -> 15086 bytes
doc/source/_templates/navbar.html | 2 +
doc/source/_templates/searchbox.html | 7 +
doc/source/{api_changes.txt => api_changes.rst} | 22 +
doc/source/auto_examples/images/blank_image.png | Bin 1508 -> 0 bytes
.../{cell_profiler.txt => cell_profiler.rst} | 0
doc/source/conf.py | 38 +-
doc/source/contribute.rst | 2 +
doc/source/contribute.txt | 2 -
.../{configure_git.txt => configure_git.rst} | 0
...pment_workflow.txt => development_workflow.rst} | 0
.../{following_latest.txt => following_latest.rst} | 0
.../gitwash/{forking_hell.txt => forking_hell.rst} | 0
.../{git_development.txt => git_development.rst} | 0
.../gitwash/{git_install.txt => git_install.rst} | 0
.../gitwash/{git_intro.txt => git_intro.rst} | 0
doc/source/gitwash/git_links.inc | 2 +-
.../{git_resources.txt => git_resources.rst} | 0
doc/source/gitwash/{index.txt => index.rst} | 0
...tainer_workflow.txt => maintainer_workflow.rst} | 0
doc/source/gitwash/{patching.txt => patching.rst} | 0
.../gitwash/{set_up_fork.txt => set_up_fork.rst} | 0
doc/source/gitwash/this_project.inc | 2 +-
doc/source/{gsoc2011.txt => gsoc2011.rst} | 0
doc/source/{index.txt => index.rst} | 0
doc/source/install.rst | 160 +
doc/source/install.txt | 122 -
doc/source/{license.txt => license.rst} | 0
doc/source/{overview.txt => overview.rst} | 2 +-
doc/source/plots/hough_tf.py | 21 +-
...tion.txt => release_notes_and_installation.rst} | 4 +-
doc/source/themes/scikit-image/layout.html | 5 -
doc/source/themes/scikit-image/search.html | 10 +-
.../themes/scikit-image/static/img/favicon.ico | Bin 2324 -> 15086 bytes
.../themes/scikit-image/static/js/bootstrap.min.js | 6 -
doc/source/{user_guide.txt => user_guide.rst} | 1 +
.../user_guide/{data_types.txt => data_types.rst} | 53 +-
.../{getting_help.txt => getting_help.rst} | 6 +-
.../{getting_started.txt => getting_started.rst} | 0
.../{numpy_images.txt => numpy_images.rst} | 17 +-
doc/source/user_guide/{plugins.txt => plugins.rst} | 0
..._image_data.txt => transforming_image_data.rst} | 46 +-
...lelization.txt => tutorial_parallelization.rst} | 0
..._segmentation.txt => tutorial_segmentation.rst} | 18 +-
.../user_guide/{tutorials.txt => tutorials.rst} | 0
doc/source/user_guide/video.rst | 178 ++
doc/source/user_guide/{viewer.txt => viewer.rst} | 0
doc/tools/apigen.py | 2 +-
doc/tools/plot_pr.py | 2 +-
optional_requirements.txt | 3 +-
requirements.txt | 6 +-
setup.py | 11 +-
skimage/__init__.py | 9 +-
skimage/_build.py | 22 +-
skimage/_shared/_geometry.py | 2 +-
skimage/_shared/_warnings.py | 9 +-
skimage/_shared/interpolation.pyx | 48 -
skimage/_shared/setup.py | 2 +-
skimage/_shared/testing.py | 9 +-
skimage/_shared/tests/test_testing.py | 58 +-
skimage/_shared/tests/test_utils.py | 10 +-
skimage/_shared/tests/test_version_requirements.py | 7 +-
skimage/_shared/transform.pxd | 3 -
skimage/_shared/transform.pyx | 1 -
skimage/_shared/utils.py | 86 +-
skimage/color/__init__.py | 19 +
skimage/color/colorconv.py | 414 ++-
skimage/color/colorlabel.py | 38 +-
skimage/color/tests/test_colorconv.py | 51 +
skimage/color/tests/test_colorlabel.py | 13 +-
skimage/data/__init__.py | 184 +-
skimage/data/_binary_blobs.py | 1 +
skimage/data/astronaut_GRAY_hog.npy | Bin 2490992 -> 0 bytes
skimage/data/astronaut_GRAY_hog_L1.npy | Bin 0 -> 2490992 bytes
skimage/data/astronaut_GRAY_hog_L2-Hys.npy | Bin 0 -> 2490992 bytes
skimage/data/logo.png | Bin 0 -> 179723 bytes
skimage/data/motorcycle_disp.npz | Bin 0 -> 1146173 bytes
skimage/data/motorcycle_left.png | Bin 0 -> 644701 bytes
skimage/data/motorcycle_right.png | Bin 0 -> 640373 bytes
skimage/data/tests/test_data.py | 65 +-
skimage/draw/__init__.py | 10 +-
skimage/draw/_draw.pyx | 861 +++---
skimage/draw/draw.py | 511 ++-
skimage/draw/setup.py | 3 +-
skimage/draw/tests/test_draw.py | 117 +-
skimage/exposure/_adapthist.py | 62 +-
skimage/exposure/exposure.py | 12 +-
skimage/exposure/setup.py | 7 +-
skimage/exposure/tests/test_exposure.py | 90 +-
skimage/external/setup.py | 2 +-
skimage/external/test_tifffile.py | 22 +-
skimage/external/tifffile/tifffile.c | 675 ++--
skimage/external/tifffile/tifffile.py | 3252 +++++++++++++++-----
skimage/feature/__init__.py | 6 +-
skimage/feature/_canny.py | 18 +-
skimage/feature/_hog.py | 136 +-
skimage/feature/_hoghistogram.pyx | 25 +-
skimage/feature/_texture.pyx | 23 +-
skimage/feature/blob.py | 119 +-
skimage/feature/corner.py | 293 +-
skimage/feature/corner_cy.pyx | 10 +-
skimage/feature/orb.py | 5 +
skimage/feature/peak.py | 153 +-
skimage/feature/register_translation.py | 6 +-
skimage/feature/setup.py | 2 +-
skimage/feature/template.py | 49 +-
skimage/feature/tests/test_blob.py | 12 +
skimage/feature/tests/test_brief.py | 2 -
skimage/feature/tests/test_canny.py | 7 +-
skimage/feature/tests/test_corner.py | 99 +-
skimage/feature/tests/test_hog.py | 37 +-
skimage/feature/tests/test_orb.py | 9 +-
skimage/feature/tests/test_peak.py | 782 ++---
skimage/feature/tests/test_template.py | 11 +
skimage/feature/tests/test_texture.py | 31 +-
skimage/feature/tests/test_util.py | 4 +-
skimage/feature/texture.py | 60 +-
skimage/filter/__init__.py | 84 -
skimage/filter/rank/__init__.py | 42 -
skimage/filters/__init__.py | 49 +-
skimage/filters/_frangi.py | 185 ++
skimage/filters/_gaussian.py | 35 +-
skimage/filters/edges.py | 266 +-
skimage/filters/rank/README.rst | 32 -
skimage/filters/rank/__init__.py | 4 +-
skimage/filters/rank/_percentile.py | 1 -
skimage/filters/rank/bilateral.py | 3 +-
skimage/filters/rank/generic.py | 77 +-
skimage/filters/rank/tests/test_rank.py | 1302 ++++----
skimage/filters/setup.py | 2 +-
skimage/filters/tests/test_deprecated_imports.py | 19 -
skimage/filters/tests/test_edges.py | 48 +-
skimage/filters/tests/test_frangi.py | 38 +
skimage/filters/tests/test_gaussian.py | 10 +
skimage/filters/tests/test_thresholding.py | 178 +-
skimage/filters/thresholding.py | 569 +++-
skimage/future/graph/__init__.py | 4 +-
skimage/future/graph/graph_cut.py | 3 +-
skimage/future/graph/rag.py | 191 +-
skimage/future/graph/setup.py | 2 +-
skimage/future/graph/tests/test_rag.py | 8 +-
skimage/graph/setup.py | 2 +-
skimage/io/_io.py | 2 +-
skimage/io/_plugins/freeimage_plugin.py | 742 +----
skimage/io/_plugins/matplotlib_plugin.py | 14 +-
skimage/io/_plugins/pil_plugin.py | 2 +-
skimage/io/_plugins/qt_plugin.py | 5 +-
skimage/io/collection.py | 16 +-
skimage/io/setup.py | 2 +-
skimage/io/sift.py | 15 +-
skimage/io/tests/test_collection.py | 8 +
skimage/io/tests/test_freeimage.py | 129 -
skimage/io/tests/test_imageio.py | 4 +-
skimage/io/tests/test_mpl_imshow.py | 20 +-
skimage/io/tests/test_multi_image.py | 2 +-
skimage/io/tests/test_pil.py | 8 +-
skimage/io/tests/test_sift.py | 15 +-
skimage/measure/__init__.py | 12 +-
skimage/measure/_ccomp.pyx | 166 +-
skimage/measure/_label.py | 92 +-
...arching_cubes.py => _marching_cubes_classic.py} | 66 +-
...cubes_cy.pyx => _marching_cubes_classic_cy.pyx} | 0
skimage/measure/_marching_cubes_lewiner.py | 289 ++
skimage/measure/_marching_cubes_lewiner_cy.pyx | 1434 +++++++++
skimage/measure/_marching_cubes_lewiner_luts.py | 528 ++++
skimage/measure/_pnpoly.pyx | 4 +-
skimage/measure/_regionprops.py | 32 +-
skimage/measure/_structural_similarity.py | 60 +-
skimage/measure/block.py | 6 +-
skimage/measure/entropy.py | 37 +
skimage/measure/fit.py | 201 +-
skimage/measure/mc_meta/LookUpTable.h | 2322 ++++++++++++++
skimage/measure/mc_meta/MarchingCubes.cpp | 1302 ++++++++
skimage/measure/mc_meta/README.md | 8 +
skimage/measure/mc_meta/createluts.py | 172 ++
skimage/measure/mc_meta/visual_test.py | 72 +
skimage/measure/pnpoly.py | 53 +
skimage/measure/profile.py | 4 +-
skimage/measure/setup.py | 12 +-
skimage/measure/simple_metrics.py | 27 +-
skimage/measure/tests/test_entropy.py | 15 +
skimage/measure/tests/test_fit.py | 104 +-
skimage/measure/tests/test_marching_cubes.py | 138 +-
skimage/measure/tests/test_regionprops.py | 11 +-
skimage/measure/tests/test_simple_metrics.py | 14 +-
.../measure/tests/test_structural_similarity.py | 29 +-
skimage/morphology/__init__.py | 14 +-
skimage/morphology/_skeletonize.py | 194 +-
skimage/morphology/_watershed.pyx | 153 +-
skimage/morphology/convex_hull.py | 2 +-
skimage/morphology/extrema.py | 352 +++
skimage/morphology/grey.py | 14 +-
skimage/morphology/greyreconstruct.py | 4 +-
skimage/morphology/heap_watershed.pxi | 5 +-
skimage/morphology/setup.py | 2 +-
skimage/morphology/tests/test_ccomp.py | 38 +-
skimage/morphology/tests/test_extrema.py | 298 ++
skimage/morphology/tests/test_skeletonize.py | 53 +-
skimage/morphology/tests/test_watershed.py | 65 +-
skimage/morphology/watershed.py | 377 +--
skimage/restoration/__init__.py | 3 +-
skimage/restoration/_denoise.py | 356 ++-
skimage/restoration/_denoise_cy.pyx | 23 +-
skimage/restoration/_nl_means_denoising.pyx | 9 +-
skimage/restoration/inpaint.py | 22 +-
skimage/restoration/non_local_means.py | 7 +-
skimage/restoration/setup.py | 2 +-
skimage/restoration/tests/test_denoise.py | 357 ++-
skimage/restoration/tests/test_unwrap.py | 39 +-
skimage/segmentation/__init__.py | 4 +-
skimage/segmentation/_clear_border.py | 26 +-
skimage/segmentation/_felzenszwalb.py | 57 +-
skimage/segmentation/_felzenszwalb_cy.pyx | 54 +-
skimage/segmentation/_quickshift.py | 74 +
skimage/segmentation/_quickshift.pyx | 167 -
skimage/segmentation/_quickshift_cy.pyx | 136 +
skimage/segmentation/active_contour_model.py | 18 +-
skimage/segmentation/boundaries.py | 6 +-
skimage/segmentation/random_walker_segmentation.py | 3 +
skimage/segmentation/setup.py | 6 +-
skimage/segmentation/slic_superpixels.py | 1 -
.../tests/test_active_contour_model.py | 32 +-
skimage/segmentation/tests/test_clear_border.py | 102 +
skimage/segmentation/tests/test_felzenszwalb.py | 35 +-
skimage/segmentation/tests/test_quickshift.py | 2 +-
skimage/segmentation/tests/test_random_walker.py | 38 +-
skimage/transform/__init__.py | 20 +-
skimage/transform/_geometric.py | 1017 +++---
skimage/transform/_hough_transform.pyx | 23 +-
skimage/transform/_warps.py | 451 ++-
skimage/transform/hough_transform.py | 402 +--
skimage/transform/pyramids.py | 2 +-
skimage/transform/radon_transform.py | 66 +-
skimage/transform/setup.py | 2 +-
skimage/transform/tests/test_geometric.py | 190 +-
skimage/transform/tests/test_hough_transform.py | 40 +
skimage/transform/tests/test_radon_transform.py | 25 +-
skimage/transform/tests/test_warps.py | 58 +-
skimage/util/__init__.py | 12 +-
skimage/util/_invert.py | 33 +
skimage/util/_regular_grid.py | 33 +
skimage/util/apply_parallel.py | 11 +-
skimage/util/arraycrop.py | 178 ++
skimage/util/arraypad.py | 1538 ---------
skimage/util/colormap.py | 271 +-
skimage/util/dtype.py | 263 +-
skimage/util/noise.py | 32 +-
skimage/util/tests/test_apply_parallel.py | 13 +-
skimage/util/tests/test_arraycrop.py | 54 +
skimage/util/tests/test_arraypad.py | 50 +-
skimage/util/tests/test_invert.py | 52 +
skimage/util/tests/test_random_noise.py | 15 +-
skimage/viewer/canvastools/painttool.py | 18 +
skimage/viewer/plugins/canny.py | 2 +-
tools/appveyor/install.ps1 | 27 +-
tools/appveyor/requirements.txt | 17 -
check_bento_build.py => tools/check_bento_build.py | 1 +
tools/check_sdist.py | 60 +
tools/deploy_docs.sh | 11 +-
tools/travis_before_install.sh | 51 +-
tools/travis_osx_install.sh | 16 +
tools/travis_script.sh | 46 +-
395 files changed, 25888 insertions(+), 12846 deletions(-)
rename CONTRIBUTING.txt => .github/CONTRIBUTING.txt (77%)
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delete mode 100644 debian/patches/changeset_6807f4ee8f5501703e447f95701190c836deaae1.diff
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create mode 100644 doc/examples/features_detection/plot_shape_index.py
create mode 100644 doc/examples/filters/plot_deconvolution.py
create mode 100644 doc/examples/filters/plot_frangi.py
create mode 100644 doc/examples/segmentation/plot_boundary_merge.py
create mode 100644 doc/examples/segmentation/plot_compact_watershed.py
create mode 100644 doc/examples/segmentation/plot_extrema.py
delete mode 100644 doc/examples/segmentation/plot_local_otsu.py
create mode 100644 doc/examples/segmentation/plot_niblack_sauvola.py
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delete mode 100644 doc/examples/segmentation/plot_threshold_adaptive.py
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create mode 100644 doc/examples/transform/plot_fundamental_matrix.py
create mode 100644 doc/examples/xx_applications/plot_thresholding.py
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rename doc/release/{release_0.10.txt => release_0.10.rst} (100%)
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