diff --git a/CONTRIBUTORS.txt b/CONTRIBUTORS.txt index 5f18e821..c73b14e2 100644 --- a/CONTRIBUTORS.txt +++ b/CONTRIBUTORS.txt @@ -107,7 +107,7 @@ - Johannes Schönberger Drawing functions, adaptive thresholding, regionprops, geometric - transformations, LBPs, polygon approximations, and more. + transformations, LBPs, polygon approximations, web layout, and more. - Pavel Campr Fixes and tests for Histograms of Oriented Gradients. diff --git a/DEVELOPMENT.txt b/DEVELOPMENT.txt index 0dd0a102..509cf322 100644 --- a/DEVELOPMENT.txt +++ b/DEVELOPMENT.txt @@ -4,8 +4,8 @@ Development process :doc:`Read this overview ` of how to use Git with ``skimage``. Here's the long and short of it: - * Go to `https://github.com/scikits-image/scikits-image - `_ and follow the + * Go to `https://github.com/scikit-image/scikit-image + `_ and follow the instructions on making your own fork. * Create a new branch for the feature you want to work on. Since the branch name will appear in the merge message, use a sensible name @@ -42,7 +42,7 @@ Guidelines * Follow the `Python PEPs `_ where possible. * No major changes should be committed without review. Ask on the - `mailing list `_ if + `mailing list `_ if you get no response to your pull request. * Examples in the gallery should have a maximum figure width of 8 inches. @@ -99,4 +99,4 @@ detailing the test coverage:: Bugs ```` -Please `report bugs on Github `_. +Please `report bugs on Github `_. diff --git a/LICENSE.txt b/LICENSE.txt index b75d150d..6586c853 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,7 +1,7 @@ Unless otherwise specified by LICENSE.txt files in individual directories, all code is -Copyright (C) 2011, the scikits-image team +Copyright (C) 2011, the scikit-image team All rights reserved. Redistribution and use in source and binary forms, with or without diff --git a/README.rst b/README.rst index a419b83a..508db396 100644 --- a/README.rst +++ b/README.rst @@ -3,11 +3,11 @@ Image Processing SciKit Source ------ -https://github.com/scikits-image/scikits-image +https://github.com/scikit-image/scikit-image Mailing List ------------ -http://groups.google.com/group/scikits-image +http://groups.google.com/group/scikit-image Installation from source ------------------------ diff --git a/RELEASE.txt b/RELEASE.txt index 4821d68d..ce05e24e 100644 --- a/RELEASE.txt +++ b/RELEASE.txt @@ -2,34 +2,52 @@ How to make a new release of ``skimage`` ======================================== - Update release notes. -- Update the version number in setup.py and bento.info and commit + + - To show a list contributors, run ``doc/release/contributors.sh ``, + where ```` is the first commit since the previous release. + +- Update the version number in ``setup.py`` and ``bento.info`` and commit + - Update the docs: + - Edit ``doc/source/themes/agogo/static/docversions.js`` and commit - - Build a clean version of the docs. Run "make" in the root dir, then - ``rm build -rf; make html`` in the docs. Make sure the random.js + - Build a clean version of the docs. Run ``make`` in the root dir, then + ``rm build -rf; make html`` in the docs. - Run ``make html`` again to copy the newly generated ``random.js`` into place. Double check ``random.js``, otherwise the skimage.org front page gets broken! - - Push upstream using "make gh-pages" + - Build using ``make gh-pages``. + - Push upstream: ``git push`` in ``doc/gh-pages``. + - Add the version number as a tag in git:: - git tag v0.6 + git tag v0.X.0 - Push the new meta-data to github:: - git push --tags origin master + git push --tags origin master -- Publish on PyPi: +- Publish on PyPi:: - python setup.py register - python setup.py sdist upload + python setup.py register + python setup.py sdist upload -- Increase the version number in the setup.py file to ``0.Xdev``. +- Increase the version number + + - In ``setup.py``, set to ``0.Xdev``. + - In ``bento.info``, set to ``0.X.dev0``. - Update the web frontpage: - The webpage is kept in a separate repo: scikits-image-web - - ``_templates/sidebar_versions.html`` - - ``index.rst`` + The webpage is kept in a separate repo: scikit-image-web + + - Sync your branch with the remote repo: ``git pull``. + If you try to ``make gh-pages`` when your branch is out of sync, it + creates headaches. + - Update stable and development version numbers in + ``_templates/sidebar_versions.html``. + - Add release date to ``index.rst`` under "Announcements". + - Build using ``make gh-pages``. + - Push upstream: ``git push`` in ``gh-pages``. - Post release notes on mailing lists, blog, G+, etc. diff --git a/TASKS.txt b/TASKS.txt index da715573..a2fcffe2 100644 --- a/TASKS.txt +++ b/TASKS.txt @@ -16,122 +16,14 @@ How to contribute to ``skimage`` Developing Open Source is great fun! Join us on the `skimage mailing -list `_ and tell us which of the +list `_ and tell us which of the following challenges you'd like to solve. * Mentoring is available for those new to scientific programming in Python. * The technical detail of the `development process`_ is given below. * :doc:`How to use GitHub ` when developing skimage +* If you're looking something to implement, you can find a list of `requested features on github `__. In addition, you can browse the `open issues on github `__. .. contents:: :local: -Tasks ------ - -.. :doc:`gsoc2011` -.. :doc:`coverage_table` - -Implement Algorithms -```````````````````` -- Graph cut segmentation -- `Image colorization `__ -- Fast 2D convex hull (consider using CellProfiler version) - `Algorithm overview `__. - `One free implementation - `_. - [Compare against current implementation] -- Convex hulls of objects in a labels matrix (simply adapt current convex hull - image code--this one's low hanging fruit). Generalise this solution to also - skeletonize objects in a labels matrix. -- Add binary features (BRIEF, BRISK, FREAK) -- Add `STAR features `__ -- `Blurring kernel estimation `__ - -Drawing (directly on an ndarray) -```````````````````````````````` -- Wu's algorithm for circles -- Text rendering -- Add anti-aliasing - -Infrastructure --------------- -- Add @greyimage decorator to check if input is a greyscale image -- :strike:`Implement a new backend system so that we may start including - PyOpenCL-based algorithms` - -Adapt existing code for use -``````````````````````````` -These snippets and packages have already been written. Some need to be -modified to work as part of the scikit, others may be lacking in documentation -or tests. - - * :strike:`Connected components` - * Nadav's bilateral filtering (first compare against CellProfiler's - code, based on http://groups.csail.mit.edu/graphics/bilagrid/bilagrid_web.pdf) - Also see https://github.com/stefanv/scikits-image/tree/bilateral - * 2D image warping via thin-plate splines [ask Zach Pincus] - -Merge code provided by `CellProfiler `_ team -````````````````````````````````````````````````````````````````````````` -* Roberts filter - convolution with diagonal and anti-diagonal - kernels to detect edges -* Minimum enclosing circles of objects in a labels matrix -* spur removal, thinning, thickening, and other morphological operations on - binary images, framework for creating arbitrary morphological operations - using a 3x3 grid. - -Their SVN repository is read-accessible at - -- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler - -The files for the above algorithms are - -- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/cpmorphology.py -- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/filter.py - -There are test suites for the files at - -- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/tests/test_cpmorphology.py -- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/tests/test_filter.py - -Quoting a message from Lee Kamentsky to Stefan van der Walt sent on -5 August 2009:: - - We're part of the Broad Institute which is non-profit. We would be happy - to include our algorithm code in SciPy under the BSD license since that is - more appropriate for a library that might be integrated into a - commercial product whereas CellProfiler needs the more stringent - protection of GPL as an application. - -In 2010, Vebjorn Ljosa officially released parts of the code under a -BSD license (:doc:`cell_profiler` | `original message -`_). - -Thanks to Lee Kamentsky, Thouis Jones and Anne Carpenter and their colleagues -who contributed. - -Rework linear filters -````````````````````` -* Fast, SSE2 convolution (high priority) (see prototype in pull requests) -* Should take kernel or function for parameter (currently only takes function) -* Kernel shape should be specifiable (currently defaults to image shape) - -io -`` -* Update ``qt_plugin.py`` and other plugins to view collections. -* Rewrite GTK backend using GObject Introspection for Py3K compatibility. -* Add DICOM plugin for `GDCM `__. -* Add ``imread_collection`` to all ``imread`` backends -* Better video loading (move to plugin framework, add backends) - -viewer -`````` -* Using the visualization tools, add an FFT-domain image editor - -docs -```` -* Add examples to the gallery -* Write topics for the `user guide - `_ -* Integrate BiBTeX plugin into Sphinx build diff --git a/bento.info b/bento.info index 149407a3..a6424eb1 100644 --- a/bento.info +++ b/bento.info @@ -1,15 +1,15 @@ -Name: scikits-image -Version: 0.7.1 +Name: scikit-image +Version: 0.7.2 Summary: Image processing routines for SciPy -Url: http://scikits-image.org -DownloadUrl: http://github.com/scikits-image/scikits-image +Url: http://scikit-image.org +DownloadUrl: http://github.com/scikit-image/scikit-image Description: Image Processing SciKit Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Please refer to the online documentation at - http://scikits-image.org/ + http://scikit-image.org/ Maintainer: Stefan van der Walt MaintainerEmail: stefan@sun.ac.za License: Modified BSD diff --git a/check_bento_build.py b/check_bento_build.py index d085b3ba..108b0aad 100644 --- a/check_bento_build.py +++ b/check_bento_build.py @@ -69,7 +69,8 @@ def print_results(cy_bento, cy_setup): print(text) print('-' * len(text)) - print # blank line; just for aesthetics + print "Bento errors:" + print "-------------" if cy_bento: info("The following extensions in 'bento.info' were not found:") diff --git a/doc/Makefile b/doc/Makefile index f7866969..7552be6b 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -77,17 +77,17 @@ qthelp: @echo @echo "Build finished; now you can run "qcollectiongenerator" with the" \ ".qhcp project file in build/qthelp, like this:" - @echo "# qcollectiongenerator build/qthelp/scikitsimage.qhcp" + @echo "# qcollectiongenerator build/qthelp/scikitimage.qhcp" @echo "To view the help file:" - @echo "# assistant -collectionFile build/qthelp/scikitsimage.qhc" + @echo "# assistant -collectionFile build/qthelp/scikitimage.qhc" devhelp: $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(DEST)/devhelp @echo @echo "Build finished." @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/scikitsimage" - @echo "# ln -s build/devhelp $$HOME/.local/share/devhelp/scikitsimage" + @echo "# mkdir -p $$HOME/.local/share/devhelp/scikitimage" + @echo "# ln -s build/devhelp $$HOME/.local/share/devhelp/scikitimage" @echo "# devhelp" latex: @@ -123,9 +123,9 @@ gh-pages: python gh-pages.py gitwash: - python tools/gitwash/gitwash_dumper.py source scikits-image \ - --project-url=http://scikits-image.org \ - --project-ml-url=http://groups.google.com/group/scikits-image \ - --repo-name=scikits-image \ - --github-user=scikits-image \ + python tools/gitwash/gitwash_dumper.py source scikit-image \ + --project-url=http://scikit-image.org \ + --project-ml-url=http://groups.google.com/group/scikit-image \ + --repo-name=scikit-image \ + --github-user=scikit-image \ --source-suffix=.txt diff --git a/doc/ext/plot2rst.py b/doc/ext/plot2rst.py index 67355289..65c77521 100644 --- a/doc/ext/plot2rst.py +++ b/doc/ext/plot2rst.py @@ -9,7 +9,7 @@ To generate your own examples, add this extension to the list of example directory(ies) in `plot2rst_paths` (see below) points to a directory with examples named `plot_*.py` and include an `index.rst` file. -This code was adapted from scikits-image, which took it from scikits-learn. +This code was adapted from scikit-image, which took it from scikit-learn. Options ------- @@ -27,9 +27,10 @@ plot2rst_rcparams : dict plot2rst_default_thumb : str Path (relative to doc root) of default thumbnail image. -plot2rst_thumb_scale : float - Scale factor for thumbnail (e.g., 0.2 to scale plot to 1/5th the - original size). +plot2rst_thumb_shape : float + Shape of thumbnail in pixels. The image is resized to fit within this shape + and the excess is filled with white pixels. This fixed size ensures that + that gallery images are displayed in a grid. plot2rst_plot_tag : str When this tag is found in the example file, the current plot is saved and @@ -73,7 +74,10 @@ import numpy as np import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt -from matplotlib import image + +from skimage import io +from skimage import transform +from skimage.util.dtype import dtype_range LITERALINCLUDE = """ @@ -160,7 +164,7 @@ def setup(app): ('../examples', 'auto_examples'), True) app.add_config_value('plot2rst_rcparams', {}, True) app.add_config_value('plot2rst_default_thumb', None, True) - app.add_config_value('plot2rst_thumb_scale', 0.25, True) + app.add_config_value('plot2rst_thumb_shape', (250, 300), True) app.add_config_value('plot2rst_plot_tag', 'PLOT2RST.current_figure', True) app.add_config_value('plot2rst_index_name', 'index', True) @@ -335,7 +339,8 @@ def write_example(src_name, src_dir, rst_dir, cfg): thumb_path = thumb_dir.pjoin(src_name[:-3] + '.png') first_image_file = image_dir.pjoin(figure_list[0].lstrip('/')) if first_image_file.exists: - image.thumbnail(first_image_file, thumb_path, cfg.plot2rst_thumb_scale) + first_image = io.imread(first_image_file) + save_thumbnail(first_image, thumb_path, cfg.plot2rst_thumb_shape) if not thumb_path.exists: if cfg.plot2rst_default_thumb is None: @@ -345,6 +350,28 @@ def write_example(src_name, src_dir, rst_dir, cfg): shutil.copy(cfg.plot2rst_default_thumb, thumb_path) +def save_thumbnail(image, thumb_path, shape): + """Save image as a thumbnail with the specified shape. + + The image is first resized to fit within the specified shape and then + centered in an array of the specified shape before saving. + """ + rescale = min(float(w_1) / w_2 for w_1, w_2 in zip(shape, image.shape)) + small_shape = (rescale * np.asarray(image.shape[:2])).astype(int) + small_image = transform.resize(image, small_shape) + + if len(image.shape) == 3: + shape = shape + (image.shape[2],) + background_value = dtype_range[small_image.dtype.type][1] + thumb = background_value * np.ones(shape, dtype=small_image.dtype) + + i = (shape[0] - small_shape[0]) // 2 + j = (shape[1] - small_shape[1]) // 2 + thumb[i:i+small_shape[0], j:j+small_shape[1]] = small_image + + io.imsave(thumb_path, thumb) + + def _plots_are_current(src_path, image_path): first_image_file = Path(image_path.format(1)) needs_replot = (not first_image_file.exists or diff --git a/doc/gh-pages.py b/doc/gh-pages.py index 849b7053..ab29959e 100644 --- a/doc/gh-pages.py +++ b/doc/gh-pages.py @@ -30,7 +30,7 @@ from subprocess import Popen, PIPE, CalledProcessError, check_call pages_dir = 'gh-pages' html_dir = 'build/html' pdf_dir = 'build/latex' -pages_repo = 'git@github.com:scikits-image/docs.git' +pages_repo = 'git@github.com:scikit-image/docs.git' #----------------------------------------------------------------------------- # Functions @@ -108,7 +108,7 @@ if __name__ == '__main__': shutil.copytree(html_dir, dest) # copy pdf file into tree #shutil.copy(pjoin(pdf_dir, 'scikits.image.pdf'), pjoin(dest, 'scikits.image.pdf')) - + try: cd(pages_dir) status = sh2('git status | head -1') @@ -117,7 +117,7 @@ if __name__ == '__main__': e = 'On %r, git branch is %r, MUST be "gh-pages"' % (pages_dir, branch) raise RuntimeError(e) - sh("touch .nojekyll") + sh("touch .nojekyll") sh('git add .nojekyll') sh('git add index.html') sh('git add %s' % tag) @@ -131,4 +131,4 @@ if __name__ == '__main__': print print 'Now verify the build in: %r' % dest - print "If everything looks good, 'git push'" + print "If everything looks good, run 'git push' inside doc/gh-pages." diff --git a/doc/logo/Makefile b/doc/logo/Makefile index 46c36fda..1cf861bd 100644 --- a/doc/logo/Makefile +++ b/doc/logo/Makefile @@ -1,11 +1,11 @@ .PHONY: logo logo: green_orange_snake.png snake_logo.svg - inkscape --export-png=scikits_image_logo.png --export-dpi=100 \ + inkscape --export-png=scikit_image_logo.png --export-dpi=100 \ --export-area-drawing --export-background-opacity=1 \ snake_logo.svg python shrink_logo.py green_orange_snake.png: - python scikits_image_logo.py --no-plot + python scikit_image_logo.py --no-plot diff --git a/doc/logo/scikits_image_logo.py b/doc/logo/scikit_image_logo.py similarity index 100% rename from doc/logo/scikits_image_logo.py rename to doc/logo/scikit_image_logo.py diff --git a/doc/logo/shrink_logo.py b/doc/logo/shrink_logo.py index 3b7d91ba..205e1bf4 100644 --- a/doc/logo/shrink_logo.py +++ b/doc/logo/shrink_logo.py @@ -2,7 +2,7 @@ from skimage import io, transform s = 0.7 -img = io.imread('scikits_image_logo.png') +img = io.imread('scikit_image_logo.png') h, w, c = img.shape print "\nScaling down logo by %.1fx..." % s @@ -13,4 +13,4 @@ img = transform.homography(img, [[s, 0, 0], output_shape=(int(h*s), int(w*s), 4), order=3) -io.imsave('scikits_image_logo_small.png', img) +io.imsave('scikit_image_logo_small.png', img) diff --git a/doc/logo/snake_logo.svg b/doc/logo/snake_logo.svg index caa47694..5f9f634f 100644 --- a/doc/logo/snake_logo.svg +++ b/doc/logo/snake_logo.svg @@ -74,7 +74,7 @@ y="278.58533" x="261.22247" id="tspan3152" - sodipodi:role="line">scikits-image + sodipodi:role="line">scikit-image qcollectiongenerator build\qthelp\scikitsimage.qhcp + echo.^> qcollectiongenerator build\qthelp\scikitimage.qhcp echo.To view the help file: - echo.^> assistant -collectionFile build\qthelp\scikitsimage.ghc + echo.^> assistant -collectionFile build\qthelp\scikitimage.ghc goto end ) diff --git a/doc/source/_static/default.css_t b/doc/source/_static/default.css_t deleted file mode 100644 index 4497c5e6..00000000 --- a/doc/source/_static/default.css_t +++ /dev/null @@ -1,144 +0,0 @@ -/* This CSS stylesheet is no longer used. Edit agogo.css instead. */ - -/** - * Sphinx stylesheet -- default theme - * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - */ - -@import url("basic.css"); - -/* -- page layout ----------------------------------------------------------- */ - -body { - font-family: {{ theme_bodyfont }}; - font-size: 100%; - background-color: {{ theme_footerbgcolor }}; - color: #000; - margin: 0; - padding: 0; -} - -div.document { - background-color: {{ theme_sidebarbgcolor }}; -} - -div.documentwrapper { - float: left; - width: 100%; -} - -div.bodywrapper { - margin: 0 0 0 230px; -} - -div.body { - background-color: {{ theme_bgcolor }}; - color: {{ theme_textcolor }}; - padding: 0 20px 30px 20px; - overflow: auto; -} - -{%- if theme_rightsidebar|tobool %} -div.bodywrapper { - margin: 0 230px 0 0; -} -{%- endif %} - -div.footer { - color: {{ theme_footertextcolor }}; - width: 100%; - padding: 9px 0 9px 0; - text-align: center; - font-size: 75%; -} - -div.footer a { - color: {{ theme_footertextcolor }}; - text-decoration: underline; -} - -div.related { - background-color: {{ theme_relbarbgcolor }}; - line-height: 30px; - color: {{ theme_relbartextcolor }}; -} - -div.related a { - color: {{ theme_relbarlinkcolor }}; -} - -div.sphinxsidebar { - {%- if theme_stickysidebar|tobool %} - top: 30px; - margin: 0; - position: fixed; - overflow: auto; - height: 100%; - {%- endif %} - {%- if theme_rightsidebar|tobool %} - float: right; - {%- if theme_stickysidebar|tobool %} - right: 0; - {%- endif %} - {%- endif %} -} - -{%- if theme_stickysidebar|tobool %} -/* this is nice, but it it leads to hidden headings when jumping - to an anchor */ -/* -div.related { - position: fixed; -} - -div.documentwrapper { - margin-top: 30px; -} -*/ -{%- endif %} - -div.sphinxsidebar h3 { - font-family: {{ theme_headfont }}; - color: {{ theme_sidebartextcolor }}; - font-size: 1.4em; - font-weight: normal; - margin: 0; - padding: 0; -} - -div.sphinxsidebar h3 a { - color: {{ theme_sidebartextcolor }}; -} - -div.sphinxsidebar h4 { - font-family: {{ theme_headfont }}; - color: {{ theme_sidebartextcolor }}; - font-size: 1.3em; - font-weight: normal; - margin: 5px 0 0 0; - padding: 0; -} - -div.sphinxsidebar p { - color: {{ theme_sidebartextcolor }}; -} - -div.sphinxsidebar p.topless { - margin: 5px 10px 10px 10px; -} - -div.sphinxsidebar ul { - margin: 10px; - padding: 0; - color: {{ theme_sidebartextcolor }}; -} - -div.sphinxsidebar a { - color: {{ theme_sidebarlinkcolor }}; -} - -div.sphinxsidebar input { - border: 1px solid {{ theme_sidebarlinkcolor }}; - font-family: sans-serif; - font-size: 1em; -} diff --git a/doc/source/themes/agogo/static/docversions.js b/doc/source/_static/docversions.js similarity index 78% rename from doc/source/themes/agogo/static/docversions.js rename to doc/source/_static/docversions.js index 30f17f40..0b414325 100644 --- a/doc/source/themes/agogo/static/docversions.js +++ b/doc/source/_static/docversions.js @@ -1,8 +1,6 @@ function insert_version_links() { var labels = ['dev', '0.7.0', '0.6', '0.5', '0.4', '0.3']; - document.write('
    \n'); - for (i = 0; i < labels.length; i++){ open_list = '
  • ' if (typeof(DOCUMENTATION_OPTIONS) !== 'undefined') { @@ -14,7 +12,6 @@ function insert_version_links() { document.write(open_list); document.write('skimage VERSION
    • \n' .replace('VERSION', labels[i]) - .replace('URL', 'http://scikits-image.org/docs/' + labels[i])); + .replace('URL', 'http://scikit-image.org/docs/' + labels[i])); } - document.write('
\n'); } diff --git a/doc/source/_static/scikits_image_logo_small.png b/doc/source/_static/scikits_image_logo_small.png deleted file mode 100644 index efd71678..00000000 Binary files a/doc/source/_static/scikits_image_logo_small.png and /dev/null differ diff --git a/doc/source/_templates/layout.html b/doc/source/_templates/layout.html deleted file mode 100644 index 1ddc127c..00000000 --- a/doc/source/_templates/layout.html +++ /dev/null @@ -1,6 +0,0 @@ -{% extends "!layout.html" %} -{% block rootrellink %} -
  • scikits-image home »
    • - {{ super() }} -{% endblock %} - diff --git a/doc/source/_templates/localtoc.html b/doc/source/_templates/localtoc.html index 3a26d6fa..6866649c 100644 --- a/doc/source/_templates/localtoc.html +++ b/doc/source/_templates/localtoc.html @@ -1,8 +1,10 @@ {% if pagename != 'index' %} - {%- if display_toc %} -

    Contents

    - {{ toc }} - {%- endif %} + {%- if display_toc %} +

    Contents

    +
    + {{ toc|replace('
      ', '
        ') }} +
    + {%- endif %} {% endif %} diff --git a/doc/source/_templates/navbar.html b/doc/source/_templates/navbar.html new file mode 100644 index 00000000..267af8e7 --- /dev/null +++ b/doc/source/_templates/navbar.html @@ -0,0 +1,5 @@ +
  • Home
    • +
  • Download
    • +
  • Gallery
    • +
  • Documentation
    • +
  • Source
    • diff --git a/doc/source/_templates/navigation.html b/doc/source/_templates/navigation.html index 587d95a1..66244695 100644 --- a/doc/source/_templates/navigation.html +++ b/doc/source/_templates/navigation.html @@ -1,12 +1,22 @@ -{%- block navigation %} - - {% if pagename != 'index' %} -

    Navigation

    -

    - Documentation Home -

    -

     

    - {% endif %} - - -{%- endblock %} +

    {{ _('Navigation') }}

    +
    + +
    +{%- if prev %} +

    {{ _('Previous topic') }}

    +
    + +
    +{%- endif %} +{%- if next %} +

    {{ _('Next topic') }}

    +
    + +
    +{%- endif %} diff --git a/doc/source/_templates/versions.html b/doc/source/_templates/versions.html index a0da9d70..6dbb1962 100644 --- a/doc/source/_templates/versions.html +++ b/doc/source/_templates/versions.html @@ -1,9 +1,9 @@ -{%- block versions %} - -

    Version

    - - - -{%- endblock %} +

    {{ _('Versions') }}

    +
    +
      + + +
    +
    diff --git a/doc/source/cell_profiler.txt b/doc/source/cell_profiler.txt index cf24f53c..13918596 100644 --- a/doc/source/cell_profiler.txt +++ b/doc/source/cell_profiler.txt @@ -4,7 +4,7 @@ CellProfiler BSD license announcement :: From: Vebjorn Ljosa - To: scikits-image@googlegroups.com + To: scikit-image@googlegroups.com Date: June 3, 2010 We have changed the license of some parts of CellProfiler from GNU GPL diff --git a/doc/source/conf.py b/doc/source/conf.py index cb22e6f0..5071fab1 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -43,7 +43,7 @@ master_doc = 'index' # General information about the project. project = u'skimage' -copyright = u'2011, the scikits-image team' +copyright = u'2011, the scikit-image team' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -103,8 +103,7 @@ pygments_style = 'sphinx' # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. -html_theme = 'agogo' -html_style = 'agogo.css' +html_theme = 'scikit-image' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the @@ -121,10 +120,6 @@ html_title = 'skimage v%s docs' % version # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -html_logo = "scikits_image_logo_small.png" - # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. @@ -147,9 +142,7 @@ html_static_path = ['_static'] html_sidebars = { '**': ['navigation.html', 'localtoc.html', - 'relations.html', - 'versions.html', - 'searchbox.html'], + 'versions.html'], } # Additional templates that should be rendered to pages, maps page names to @@ -183,7 +176,7 @@ html_sidebars = { #html_file_suffix = '' # Output file base name for HTML help builder. -htmlhelp_basename = 'scikitsimagedoc' +htmlhelp_basename = 'scikitimagedoc' # -- Options for LaTeX output -------------------------------------------------- @@ -197,7 +190,7 @@ htmlhelp_basename = 'scikitsimagedoc' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('contents', 'scikitsimage.tex', u'The Image Scikit Documentation', + ('contents', 'scikitimage.tex', u'The Image Scikit Documentation', u'SciPy Developers', 'manual'), ] diff --git a/doc/source/gitwash/development_workflow.txt b/doc/source/gitwash/development_workflow.txt index b5344da8..47bdead0 100644 --- a/doc/source/gitwash/development_workflow.txt +++ b/doc/source/gitwash/development_workflow.txt @@ -4,14 +4,14 @@ Development workflow #################### -You already have your own forked copy of the scikits-image_ repository, by +You already have your own forked copy of the scikit-image_ repository, by following :ref:`forking`. You have :ref:`set-up-fork`. You have configured git by following :ref:`configure-git`. Now you are ready for some real work. Workflow summary ================ -In what follows we'll refer to the upstream scikits-image ``master`` branch, as +In what follows we'll refer to the upstream scikit-image ``master`` branch, as "trunk". * Don't use your ``master`` branch for anything. Consider deleting it. @@ -22,9 +22,9 @@ In what follows we'll refer to the upstream scikits-image ``master`` branch, as * Name your branch for the purpose of the changes - e.g. ``bugfix-for-issue-14`` or ``refactor-database-code``. * If you can possibly avoid it, avoid merging trunk or any other branches into - your feature branch while you are working. + your feature branch while you are working. * If you do find yourself merging from trunk, consider :ref:`rebase-on-trunk` -* Ask on the `scikits-image mailing list`_ if you get stuck. +* Ask on the `scikit-image mailing list`_ if you get stuck. * Ask for code review! This way of working helps to keep work well organized, with readable history. @@ -81,7 +81,7 @@ what the changes in the branch are for. For example ``add-ability-to-fly``, or git checkout my-new-feature Generally, you will want to keep your feature branches on your public github_ -fork of scikits-image_. To do this, you `git push`_ this new branch up to your +fork of scikit-image_. To do this, you `git push`_ this new branch up to your github repo. Generally (if you followed the instructions in these pages, and by default), git will have a link to your github repo, called ``origin``. You push up to your own repo on github with:: @@ -150,7 +150,7 @@ Ask for your changes to be reviewed or merged When you are ready to ask for someone to review your code and consider a merge: #. Go to the URL of your forked repo, say - ``http://github.com/your-user-name/scikits-image``. + ``http://github.com/your-user-name/scikit-image``. #. Use the 'Switch Branches' dropdown menu near the top left of the page to select the branch with your changes: @@ -192,10 +192,10 @@ If you want to work on some stuff with other people, where you are all committing into the same repository, or even the same branch, then just share it via github. -First fork scikits-image into your account, as from :ref:`forking`. +First fork scikit-image into your account, as from :ref:`forking`. Then, go to your forked repository github page, say -``http://github.com/your-user-name/scikits-image`` +``http://github.com/your-user-name/scikit-image`` Click on the 'Admin' button, and add anyone else to the repo as a collaborator: @@ -204,7 +204,7 @@ collaborator: Now all those people can do:: - git clone git@githhub.com:your-user-name/scikits-image.git + git clone git@githhub.com:your-user-name/scikit-image.git Remember that links starting with ``git@`` use the ssh protocol and are read-write; links starting with ``git://`` are read-only. diff --git a/doc/source/gitwash/following_latest.txt b/doc/source/gitwash/following_latest.txt index 69e5ee13..df0842a0 100644 --- a/doc/source/gitwash/following_latest.txt +++ b/doc/source/gitwash/following_latest.txt @@ -5,12 +5,12 @@ ============================= These are the instructions if you just want to follow the latest -*scikits-image* source, but you don't need to do any development for now. +*scikit-image* source, but you don't need to do any development for now. The steps are: * :ref:`install-git` -* get local copy of the `scikits-image github`_ git repository +* get local copy of the `scikit-image github`_ git repository * update local copy from time to time Get the local copy of the code @@ -18,19 +18,19 @@ Get the local copy of the code From the command line:: - git clone git://github.com/scikits-image/scikits-image.git + git clone git://github.com/scikit-image/scikit-image.git -You now have a copy of the code tree in the new ``scikits-image`` directory. +You now have a copy of the code tree in the new ``scikit-image`` directory. Updating the code ================= From time to time you may want to pull down the latest code. Do this with:: - cd scikits-image + cd scikit-image git pull -The tree in ``scikits-image`` will now have the latest changes from the initial +The tree in ``scikit-image`` will now have the latest changes from the initial repository. .. include:: links.inc diff --git a/doc/source/gitwash/forking_hell.txt b/doc/source/gitwash/forking_hell.txt index 58e12fee..02c14b25 100644 --- a/doc/source/gitwash/forking_hell.txt +++ b/doc/source/gitwash/forking_hell.txt @@ -1,13 +1,13 @@ .. _forking: ============================================ -Making your own copy (fork) of scikits-image +Making your own copy (fork) of scikit-image ============================================ You need to do this only once. The instructions here are very similar to the instructions at http://help.github.com/forking/ |emdash| please see that page for more detail. We're repeating some of it here just to give the -specifics for the scikits-image_ project, and to suggest some default names. +specifics for the scikit-image_ project, and to suggest some default names. Set up and configure a github account ====================================== @@ -17,17 +17,17 @@ If you don't have a github account, go to the github page, and make one. You then need to configure your account to allow write access |emdash| see the ``Generating SSH keys`` help on `github help`_. -Create your own forked copy of scikits-image_ +Create your own forked copy of scikit-image_ ============================================= #. Log into your github account. -#. Go to the scikits-image_ github home at `scikits-image github`_. +#. Go to the scikit-image_ github home at `scikit-image github`_. #. Click on the *fork* button: .. image:: forking_button.png Now, after a short pause and some 'Hardcore forking action', you - should find yourself at the home page for your own forked copy of scikits-image_. + should find yourself at the home page for your own forked copy of scikit-image_. .. include:: links.inc diff --git a/doc/source/gitwash/git_intro.txt b/doc/source/gitwash/git_intro.txt index cb8e16cc..8b4d42bc 100644 --- a/doc/source/gitwash/git_intro.txt +++ b/doc/source/gitwash/git_intro.txt @@ -2,11 +2,11 @@ Introduction ============== -These pages describe a git_ and github_ workflow for the scikits-image_ +These pages describe a git_ and github_ workflow for the scikit-image_ project. There are several different workflows here, for different ways of -working with *scikits-image*. +working with *scikit-image*. This is not a comprehensive git reference, it's just a workflow for our own project. It's tailored to the github hosting service. You may well diff --git a/doc/source/gitwash/index.txt b/doc/source/gitwash/index.txt index d0eac669..7d26110e 100644 --- a/doc/source/gitwash/index.txt +++ b/doc/source/gitwash/index.txt @@ -1,6 +1,6 @@ .. _using-git: -Working with *scikits-image* source code +Working with *scikit-image* source code ======================================== Contents: diff --git a/doc/source/gitwash/maintainer_workflow.txt b/doc/source/gitwash/maintainer_workflow.txt index 7e2b21ab..e661784c 100644 --- a/doc/source/gitwash/maintainer_workflow.txt +++ b/doc/source/gitwash/maintainer_workflow.txt @@ -16,7 +16,7 @@ access to the upstream repo. Being a maintainer, you've got read-write access. It's good to have your upstream remote have a scary name, to remind you that it's a read-write remote:: - git remote add upstream-rw git@github.com:scikits-image/scikits-image.git + git remote add upstream-rw git@github.com:scikit-image/scikit-image.git git fetch upstream-rw ******************* @@ -29,7 +29,7 @@ Let's say you have some changes that need to go into trunk The changes are in some branch that you are currently on. For example, you are looking at someone's changes like this:: - git remote add someone git://github.com/someone/scikits-image.git + git remote add someone git://github.com/someone/scikit-image.git git fetch someone git branch cool-feature --track someone/cool-feature git checkout cool-feature diff --git a/doc/source/gitwash/patching.txt b/doc/source/gitwash/patching.txt index acec9fa6..b40118af 100644 --- a/doc/source/gitwash/patching.txt +++ b/doc/source/gitwash/patching.txt @@ -3,7 +3,7 @@ ================ You've discovered a bug or something else you want to change -in scikits-image_ .. |emdash| excellent! +in scikit-image_ .. |emdash| excellent! You've worked out a way to fix it |emdash| even better! @@ -29,9 +29,9 @@ Overview git config --global user.email you@yourdomain.example.com git config --global user.name "Your Name Comes Here" # get the repository if you don't have it - git clone git://github.com/scikits-image/scikits-image.git + git clone git://github.com/scikit-image/scikit-image.git # make a branch for your patching - cd scikits-image + cd scikit-image git branch the-fix-im-thinking-of git checkout the-fix-im-thinking-of # hack, hack, hack @@ -44,7 +44,7 @@ Overview # make the patch files git format-patch -M -C master -Then, send the generated patch files to the `scikits-image +Then, send the generated patch files to the `scikit-image mailing list`_ |emdash| where we will thank you warmly. In detail @@ -57,10 +57,10 @@ In detail git config --global user.name "Your Name Comes Here" #. If you don't already have one, clone a copy of the - scikits-image_ repository:: + scikit-image_ repository:: - git clone git://github.com/scikits-image/scikits-image.git - cd scikits-image + git clone git://github.com/scikit-image/scikit-image.git + cd scikit-image #. Make a 'feature branch'. This will be where you work on your bug fix. It's nice and safe and leaves you with @@ -100,7 +100,7 @@ In detail 0001-BF-added-tests-for-Funny-bug.patch 0002-BF-added-fix-for-Funny-bug.patch - Send these files to the `scikits-image mailing list`_. + Send these files to the `scikit-image mailing list`_. When you are done, to switch back to the main copy of the code, just return to the ``master`` branch:: @@ -115,7 +115,7 @@ more feature branches, you will probably want to switch to development mode. You can do this with the repository you have. -Fork the scikits-image_ repository on github |emdash| :ref:`forking`. +Fork the scikit-image_ repository on github |emdash| :ref:`forking`. Then:: # checkout and refresh master branch from main repo @@ -124,7 +124,7 @@ Then:: # rename pointer to main repository to 'upstream' git remote rename origin upstream # point your repo to default read / write to your fork on github - git remote add origin git@github.com:your-user-name/scikits-image.git + git remote add origin git@github.com:your-user-name/scikit-image.git # push up any branches you've made and want to keep git push origin the-fix-im-thinking-of diff --git a/doc/source/gitwash/set_up_fork.txt b/doc/source/gitwash/set_up_fork.txt index f59aa57a..36153e7d 100644 --- a/doc/source/gitwash/set_up_fork.txt +++ b/doc/source/gitwash/set_up_fork.txt @@ -11,9 +11,9 @@ Overview :: - git clone git@github.com:your-user-name/scikits-image.git - cd scikits-image - git remote add upstream git://github.com/scikits-image/scikits-image.git + git clone git@github.com:your-user-name/scikit-image.git + cd scikit-image + git remote add upstream git://github.com/scikit-image/scikit-image.git In detail ========= @@ -22,8 +22,8 @@ Clone your fork --------------- #. Clone your fork to the local computer with ``git clone - git@github.com:your-user-name/scikits-image.git`` -#. Investigate. Change directory to your new repo: ``cd scikits-image``. Then + git@github.com:your-user-name/scikit-image.git`` +#. Investigate. Change directory to your new repo: ``cd scikit-image``. Then ``git branch -a`` to show you all branches. You'll get something like:: @@ -35,7 +35,7 @@ Clone your fork What remote repository is ``remote/origin``? Try ``git remote -v`` to see the URLs for the remote. They will point to your github fork. - Now you want to connect to the upstream `scikits-image github`_ repository, so + Now you want to connect to the upstream `scikit-image github`_ repository, so you can merge in changes from trunk. .. _linking-to-upstream: @@ -45,11 +45,11 @@ Linking your repository to the upstream repo :: - cd scikits-image - git remote add upstream git://github.com/scikits-image/scikits-image.git + cd scikit-image + git remote add upstream git://github.com/scikit-image/scikit-image.git ``upstream`` here is just the arbitrary name we're using to refer to the -main scikits-image_ repository at `scikits-image github`_. +main scikit-image_ repository at `scikit-image github`_. Note that we've used ``git://`` for the URL rather than ``git@``. The ``git://`` URL is read only. This means we that we can't accidentally @@ -59,10 +59,10 @@ use it to merge into our own code. Just for your own satisfaction, show yourself that you now have a new 'remote', with ``git remote -v show``, giving you something like:: - upstream git://github.com/scikits-image/scikits-image.git (fetch) - upstream git://github.com/scikits-image/scikits-image.git (push) - origin git@github.com:your-user-name/scikits-image.git (fetch) - origin git@github.com:your-user-name/scikits-image.git (push) + upstream git://github.com/scikit-image/scikit-image.git (fetch) + upstream git://github.com/scikit-image/scikit-image.git (push) + origin git@github.com:your-user-name/scikit-image.git (fetch) + origin git@github.com:your-user-name/scikit-image.git (push) .. include:: links.inc diff --git a/doc/source/gitwash/this_project.inc b/doc/source/gitwash/this_project.inc index 0bfd7306..349b92ba 100644 --- a/doc/source/gitwash/this_project.inc +++ b/doc/source/gitwash/this_project.inc @@ -1,5 +1,5 @@ -.. scikits-image -.. _scikits-image: http://scikits-image.org -.. _`scikits-image github`: http://github.com/scikits-image/scikits-image +.. scikit-image +.. _scikit-image: http://scikit-image.org +.. _`scikit-image github`: http://github.com/scikit-image/scikit-image -.. _`scikits-image mailing list`: http://groups.google.com/group/scikits-image +.. _`scikit-image mailing list`: http://groups.google.com/group/scikit-image diff --git a/doc/source/install.txt b/doc/source/install.txt index 5aa3f43f..7c886549 100644 --- a/doc/source/install.txt +++ b/doc/source/install.txt @@ -1,8 +1,6 @@ Pre-built installation ---------------------- -.. !! Also update scikits-image-web !! - `Windows binaries `__ are kindly provided by Christoph Gohlke. @@ -12,37 +10,37 @@ Distribution (EPD) `__ and `Python(x,y) `__. On systems that support setuptools, the package can be installed from the -`Python packaging index `__ using +`Python packaging index `__ using :: - easy_install -U scikits-image + easy_install -U scikit-image or :: - pip -U scikits-image + pip install -U scikit-image Installation from source ------------------------ Obtain the source from the git-repository at -`http://github.com/scikits-image/scikits-image -`_. +`http://github.com/scikit-image/scikit-image +`_. by running :: - git clone http://github.com/scikits-image/scikits-image.git + git clone http://github.com/scikit-image/scikit-image.git in a terminal (You will need to have git installed on your machine). If you do not have git installed, you can also download a zipball from -`https://github.com/scikits-image/scikits-image/zipball/master -`_. +`https://github.com/scikit-image/scikit-image/zipball/master +`_. The SciKit can be installed globally using diff --git a/doc/source/overview.txt b/doc/source/overview.txt index 0bd9d658..5a4e6123 100644 --- a/doc/source/overview.txt +++ b/doc/source/overview.txt @@ -1,7 +1,7 @@ Image Processing SciKit ======================= -The `scikits-image `__ SciKit (toolkit for +The `scikit-image `__ SciKit (toolkit for `SciPy `__) extends ``scipy.ndimage`` to provide a versatile set of image processing routines. It is written in the `Python `_ language. @@ -12,15 +12,15 @@ mailing list (address provided below). Homepage -------- -http://scikits-image.org +http://scikit-image.org Source, bugs and patches ------------------------ -http://github.com/scikits-image/scikits-image +http://github.com/scikit-image/scikit-image Mailing List ------------ -http://groups.google.com/group/scikits-image +http://groups.google.com/group/scikit-image Contact ------- diff --git a/doc/source/random_gallery.py b/doc/source/random_gallery.py index 6c5a40a2..47ce89a2 100644 --- a/doc/source/random_gallery.py +++ b/doc/source/random_gallery.py @@ -32,8 +32,8 @@ gallery_div = '''\ examples = glob.glob(os.path.join(example_dir, 'plot_*.py')) images, links = [], [] -image_url = 'http://scikits-image.org/docs/dev/_images/%s.png' -link_url = 'http://scikits-image.org/docs/dev/auto_examples/%s.html' +image_url = 'http://scikit-image.org/docs/dev/_images/%s.png' +link_url = 'http://scikit-image.org/docs/dev/auto_examples/%s.html' for e in examples: e = os.path.basename(e) diff --git a/doc/source/themes/agogo/layout.html b/doc/source/themes/agogo/layout.html deleted file mode 100644 index 260f06bf..00000000 --- a/doc/source/themes/agogo/layout.html +++ /dev/null @@ -1,58 +0,0 @@ -{# - agogo/layout.html - ~~~~~~~~~~~~~~~~~ - - Sphinx layout template for the agogo theme, originally written - by Andi Albrecht. - - :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS. - :license: BSD, see LICENSE for details. -#} -{% extends "basic/layout.html" %} -{% set script_files = script_files + ['_static/docversions.js'] %} - -{% block header %} -
    -
    - {%- block headertitle %} - - {%- if logo %} - - {%- endif %} - {#

    {{ shorttitle|e }}

    #} - {%- endblock %} -
    -
    -{% endblock %} - - - -{% block content %} -
    -
    - {%- block sidebar2 %} - {# We don't want the logo here #} - {%- block sidebarlogo %} {% endblock %} - {{ sidebar() }} - {% endblock %} -
    - {%- block document %} - {{ super() }} - {%- endblock %} -
    -
    -
    -
    -{% endblock %} - -{% block footer %} -
    - {{ super() }} -
    -{% endblock %} - -{% block relbar1 %}{% endblock %} - -{% block relbar2 %}{% endblock %} diff --git a/doc/source/themes/agogo/static/agogo.css_t b/doc/source/themes/agogo/static/agogo.css_t deleted file mode 100644 index f47167c0..00000000 --- a/doc/source/themes/agogo/static/agogo.css_t +++ /dev/null @@ -1,754 +0,0 @@ -/* - * agogo.css_t - * ~~~~~~~~~~~ - * - * Sphinx stylesheet -- agogo theme. - * - * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -* { - margin: 0px; - padding: 0px; -} - - -div.header-wrapper { - border-top: 0px solid #babdb6; - padding: 1em 1em 0; - min-height: 0px; -} - -body { - font-family: {{ theme_bodyfont }}; - font-size: 10pt; - line-height: 1.4em; - color: black; - background-color: {{ theme_bgcolor }}; -} - - -/* Page layout */ - -div.header, div.content, div.footer { - max-width: {{ theme_pagewidth }}; - margin-left: auto; - margin-right: auto; -} - -div.header-wrapper { - border-bottom: 0px solid #2e3436; -} - - -/* Default body styles */ -a { - color: {{ theme_linkcolor }}; -} - -div.bodywrapper a, div.footer a { - text-decoration: underline; -} - -.clearer { - clear: both; -} - -.left { - float: left; -} - -.right { - float: right; -} - -.line-block { - display: block; - margin-top: 1em; - margin-bottom: 1em; -} - -.line-block .line-block { - margin-top: 0; - margin-bottom: 0; - margin-left: 1.5em; -} - -h1, h2, h3, h4 { - font-weight: normal; - color: {{ theme_headercolor2 }}; - margin-bottom: .8em; - clear: left; -} - -h1 { - color: {{ theme_headercolor1 }}; - line-height: 1.1em; - text-align: left; -} - -h2 { - padding-bottom: .5em; - color: {{ theme_headercolor1 }}; - border-bottom: 1px solid {{ theme_headercolor1 }}; -} - -a.headerlink { - visibility: hidden; - color: #dddddd; - padding-left: .3em; -} - -h1:hover > a.headerlink, -h2:hover > a.headerlink, -h3:hover > a.headerlink, -h4:hover > a.headerlink, -h5:hover > a.headerlink, -h6:hover > a.headerlink, -dt:hover > a.headerlink { - visibility: visible; -} - -img { - border: 0; -} - -div.admonition { - margin-top: 10px; - margin-bottom: 10px; - padding: 2px 7px 1px 7px; - border-left: 0.2em solid black; -} - -p.admonition-title { - margin: 0px 10px 5px 0px; - font-weight: bold; -} - -dt:target, .highlighted { - background-color: #fbe54e; -} - -/* Header */ - -div.header {} - -div.header h1 { - font-family: "Trebuchet MS", Helvetica, sans-serif; - font-weight: normal; - font-size: 250%; - letter-spacing: .08em; - line-height: 70px; - margin-bottom: 0; -} - -div.header h1 a { - color: white; -} - -div.header h1 a:hover { - text-decoration: none; -} - -div.header div.rel { - margin-top: 1em; - border-top: 1px solid #AAA; - border-bottom: 1px solid #AAA; - border-radius: 5px; - padding: 3px 1em; -} - -div.header div.rel a { - color: {{ theme_linkcolor }}; - letter-spacing: .05em; - font-weight: bold; -} - -div.logo {} - -img.logo { - border: 0; -} - - -/* Content */ -div.content-wrapper { - background-color: white; - padding: 1em; -} - -div.document { - max-width: {{ theme_documentwidth }}; -} - -div.body { - padding-right: 2em; - min-width: 20em; - overflow: hidden; - font-size: 90%; - text-align: {{ theme_textalign }}; -} - -div.document ul { - margin: 1.5em; - list-style-type: square; -} - -div.document dd { - margin-left: 1.2em; - margin-top: .4em; - margin-bottom: 1em; -} - -div.document .section { - margin-top: 1.7em; -} -div.document .section:first-child { - margin-top: 0px; -} - -div.document div.highlight { - padding: 3px; - background-color: #eeeeec; - border-top: 2px solid #dddddd; - border-bottom: 2px solid #dddddd; - margin-top: .8em; - margin-bottom: .8em; -} - -div.document h2 { - margin-top: .7em; -} - -div.document p { - margin-bottom: 1.5em; -} - -div.document li.toctree-l1 { - margin-bottom: 1em; -} - -div.document .descname { - font-weight: bold; -} - -div.document .docutils.literal { - background-color: #eeeeec; - padding: 1px; -} - -div.document .docutils.xref.literal { - background-color: transparent; - padding: 0px; -} - -div.document blockquote { - margin: 1em; -} - -div.document ol { - margin: 1.5em; -} - - -/* Sidebar */ - -div.sphinxsidebar { - width: {{ theme_sidebarwidth }}; - padding: 0 1em; - float: right; - font-size: .93em; - background-color: white; -} - -div.sphinxsidebar a, div.header a { - text-decoration: none; -} - -div.sphinxsidebar a:hover, div.header a:hover { - text-decoration: underline; -} - -div.sphinxsidebar h3 { - color: #2e3436; - text-transform: uppercase; - font-size: 130%; - letter-spacing: .1em; - margin-bottom: .4em; -} - -div.sphinxsidebar h4 { - margin-bottom: 0; - font-weight: bold; -} - -div.sphinxsidebar .tile { - border: 1px solid #D1DDE2; - border-radius: 10px; - background-color: #E1E8EC; - padding-left: 0.5em; - margin: 1em 0; -} - -div.sphinxsidebar ul { - margin-bottom: 1.5em; - list-style-type: none; -} - -div.sphinxsidebar li.toctree-l1 a { - display: block; - padding: 1px; - border: 1px solid #dddddd; - background-color: #eeeeec; - margin-bottom: .4em; - padding-left: 3px; - color: #2e3436; -} - -div.sphinxsidebar li.toctree-l2 a { - background-color: transparent; - border: none; - margin-left: 1em; - border-bottom: 1px solid #dddddd; -} - -div.sphinxsidebar li.toctree-l3 a { - background-color: transparent; - border: none; - margin-left: 2em; - border-bottom: 1px solid #dddddd; -} - -div.sphinxsidebar li.toctree-l2:last-child a { - border-bottom: none; -} - -div.sphinxsidebar li.toctree-l1.current a { - border-right: 5px solid {{ theme_headerlinkcolor }}; -} - -div.sphinxsidebar li.toctree-l1.current li.toctree-l2 a { - border-right: none; -} - -div.sidebarblock { - padding-bottom: .4em; - border-bottom: 1px solid #AAA; - margin-bottom: .8em; -} - -ul.versions li { - color: gray; - list-style: circle inside; -} - -ul.versions li#current { - list-style: disc inside; -} - -/* Footer */ - -div.footer-wrapper { - padding-top: 10px; - padding-bottom: 10px; -} - -div.footer { - border-top: 2px solid #aaa; - text-align: right; -} - -div.footer, div.footer a { - color: #888a85; -} - -.figure { - float: left; - margin: 1em; -} - -.figure img { - display: block; - margin-left: auto; - margin-right: auto; - max-height: 150px; -} - -.figure .caption { - width: 200px; - text-align: center !important; -} - - -/* Styles copied from basic theme */ - -img.align-left, .figure.align-left, object.align-left { - clear: left; - float: left; - margin-right: 1em; -} - -img.align-right, .figure.align-right, object.align-right { - clear: right; - float: right; - margin-left: 1em; -} - -img.align-center, .figure.align-center, object.align-center { - display: block; - margin-left: auto; - margin-right: auto; -} - -.align-left { - text-align: left; -} - -.align-center { - clear: both; - text-align: center; -} - -.align-right { - text-align: right; -} - -/* -- search page ----------------------------------------------------------- */ - -ul.search { - margin: 10px 0 0 20px; - padding: 0; -} - -ul.search li { - padding: 5px 0 5px 20px; - background-image: url(file.png); - background-repeat: no-repeat; - background-position: 0 7px; -} - -ul.search li a { - font-weight: bold; -} - -ul.search li div.context { - color: #888; - margin: 2px 0 0 30px; - text-align: left; -} - -ul.keywordmatches li.goodmatch a { - font-weight: bold; -} - -/* -- index page ------------------------------------------------------------ */ - -table.contentstable p.biglink { - line-height: 150%; -} - -table.contentstable, table.contentstable td, table.contentstable th { - border-style: none; -} - -div.body table.contentstable p { - margin: 0.5em; - text-align: left; -} - -table.contentstable a { - text-decoration: none; - font-size: 120%; -} - -a.biglink { - font-size: 1.3em; -} - -span.linkdescr { - font-style: italic; - padding-top: 5px; - font-size: 90%; -} - -/* -- general index --------------------------------------------------------- */ - -table.indextable td { - text-align: left; - vertical-align: top; -} - -table.indextable dl, table.indextable dd { - margin-top: 0; - margin-bottom: 0; -} - -table.indextable tr.pcap { - height: 10px; -} - -table.indextable tr.cap { - margin-top: 10px; - background-color: #f2f2f2; -} - -img.toggler { - margin-right: 3px; - margin-top: 3px; - cursor: pointer; -} - -/* -- viewcode extension ---------------------------------------------------- */ - -.viewcode-link { - float: right; -} - -.viewcode-back { - float: right; - font-family:: {{ theme_bodyfont }}; -} - -div.viewcode-block:target { - margin: -1px -3px; - padding: 0 3px; - background-color: #f4debf; - border-top: 1px solid #ac9; - border-bottom: 1px solid #ac9; -} - -span.strike { text-decoration: line-through; } - -/* -- body styles ----------------------------------------------------------- */ - -a { - color: {{ theme_linkcolor }}; - text-decoration: none; -} - -a:visited { - color: {{ theme_visitedlinkcolor }}; - text-decoration: none; -} - -a:hover { - text-decoration: underline; -} - -div.body h1, -div.body h2, -div.body h3, -div.body h4, -div.body h5, -div.body h6 { - font-family: {{ theme_headfont }}; - background-color: {{ theme_headbgcolor }}; - font-weight: normal; - color: {{ theme_headtextcolor }}; - border-bottom: 1px solid #ccc; - margin: 20px 20px 10px 0px; - padding: 3px 0 3px 0px; -} - -div.body h1 { margin-top: 0; font-size: 180%; } -div.body h2 { font-size: 150%; } -div.body h3 { font-size: 130%; } -div.body h4 { font-size: 120%; } -div.body h5 { font-size: 110%; } -div.body h6 { font-size: 100%; } - -a.headerlink { - color: {{ theme_headlinkcolor }}; - font-size: 0.8em; - padding: 0 4px 0 4px; - text-decoration: none; -} - -a.headerlink:hover { - background-color: {{ theme_headlinkcolor }}; - color: white; -} - -div.body p, div.body dd, div.body li { - text-align: justify; - line-height: 130%; -} - -div.admonition p.admonition-title + p { - display: inline; -} - -div.note { - background-color: #eee; - border: 1px solid #ccc; -} - -div.seealso { - background-color: #ffc; - border: 1px solid #ff6; -} - -div.topic { - background-color: #eee; -} - -div.warning { - background-color: #ffe4e4; - border: 1px solid #f66; -} - -p.admonition-title { - display: inline; -} - -p.admonition-title:after { - content: ":"; -} - -pre { - padding: 1em; - margin-bottom: 0.5em; - background-color: {{ theme_codebgcolor }}; - color: {{ theme_codetextcolor }}; - line-height: 120%; - border: 0px solid #ac9; - border-left: none; - border-right: none; -} - -sup { - font-size: x-small; - line-height: 0; -} - -tt { - background-color: #ecf0f3; - padding: 0 1px 0 1px; - font-size: 1em; -} - -table { - border-collapse: collapse; - margin-bottom: 1em; - margin-top: 1em; -} - -table, th, td { - border: 1px solid #ccc; -} - -th, td { - padding: 5px; -} - -th { - color: #333; - background-color: #eee; -} - -#api-reference ul:first-child { - float: left; - width: 35em; - margin-top: 0; - padding-top: 0; - list-style: none; - overflow: auto; -} - -#api-reference li { - float: left; - position: relative; - margin-right: 1em; - width: 17em; - padding: 0; -} - -.field-list { - font-size: 80%; -} - -/* ----------------- Example Gallery ----------------- */ - -.gallery { - height: 200px; -} - -.gallery p.caption a{ - text-decoration: none; -} - -/* ----------------- Coverage States ----------------- */ -span.missing{ - color: #000; - background-color: #ff5840; - border-color: #A77272; - font-weight: bold; -} -span.partial{ - color: #806600; - background-color: #ffc343; - font-weight: bold; -} -span.done{ - color: #106600; - background-color: #60f030; - border-color: #4F8530; - font-weight: bold; -} -span.na{ - color: #A8A8A8; - border-color: #4F8530; -} - -table.coverage { - border: solid 1px; -} - -td.missing-bar{ - color: #ff5840; - background-color: #ff5840; - border-color: #A77272; - font-weight: normal; - font-style: normal; -} -td.partial-bar{ - color: #ffc343; - background-color: #ffc343; - font-weight: normal; - font-style: normal; -} -td.done-bar{ - color: #60f030; - background-color: #60f030; - border-color: #4F8530; - font-weight: normal; - font-style: normal; -} -td.na-bar{ - color: #FFF; - background-color: #FFF; - border-color: #4F8530; - font-weight: normal; - font-style: normal; -} - -/* Adjust doc headers such as Notes, References, etc. */ -p.rubric { - font-weight: bold; - font-size: 120%; -} - -/* Math */ -img.math { - vertical-align: middle; -} - -div.body div.math p { - text-align: center; -} - -span.eqno { - float: right; -} diff --git a/doc/source/themes/agogo/theme.conf b/doc/source/themes/agogo/theme.conf deleted file mode 100644 index a991e5c0..00000000 --- a/doc/source/themes/agogo/theme.conf +++ /dev/null @@ -1,19 +0,0 @@ -[theme] -inherit = basic -stylesheet = agogo.css -pygments_style = tango - -[options] -bodyfont = "Verdana", Arial, sans-serif -pagewidth = 70em -documentwidth = 55em -sidebarwidth = 14em -bgcolor = white -headerbg = url(bgtop.png) top left repeat-x -footerbg = url(bgfooter.png) top left repeat-x -linkcolor = #FC852B -headercolor1 = #555 -headercolor2 = #555 -headerlinkcolor = #fcaf3e -codebgcolor = #EEE -textalign = justify diff --git a/doc/source/themes/scikit-image/layout.html b/doc/source/themes/scikit-image/layout.html new file mode 100644 index 00000000..58424f2f --- /dev/null +++ b/doc/source/themes/scikit-image/layout.html @@ -0,0 +1,113 @@ +{# + scikit-image/layout.html + ~~~~~~~~~~~~~~~~~ + + Sphinx layout template for the scikit-image theme, written by + Johannes Schönberger. + +#} + +{%- set url_root = pathto('', 1) %} +{# XXX necessary? #} +{%- if url_root == '#' %}{% set url_root = '' %}{% endif %} +{%- if not embedded and docstitle %} + {%- set titlesuffix = " — "|safe + docstitle|e %} +{%- else %} + {%- set titlesuffix = "" %} +{%- endif %} + +{%- macro script() %} + + + + {%- for scriptfile in script_files %} + + {%- endfor %} +{%- endmacro %} + +{%- macro css() %} + + + + + {%- for cssfile in css_files %} + + {%- endfor %} +{%- endmacro %} + + + + + {%- block htmltitle %} + {{ title|striptags|e }}{{ titlesuffix }} + {%- endblock %} + {{ metatags }} + {{ css() }} + {{ script() }} + {%- if hasdoc('about') %} + + {%- endif %} + {%- if hasdoc('genindex') %} + + {%- endif %} + {%- if hasdoc('search') %} + + {%- endif %} + {%- if hasdoc('copyright') %} + + {%- endif %} + + {%- if parents %} + + {%- endif %} + {%- if next %} + + {%- endif %} + {%- if prev %} + + {%- endif %} + + + {%- block extrahead %}{% endblock %} + + + +
    +
    +
    +
      + {% include 'navbar.html' %} +
    +
    + + + +
    +
    +
    +
    +
    + {% block body %}{% endblock %} +
    +
    + {%- for sidebartemplate in sidebars %} + {%- include sidebartemplate %} + {%- endfor %} +
    +
    +
    + + © Copyright the scikit-image development team. + Created using Bootstrap and Sphinx. + +
    + + diff --git a/doc/source/themes/scikit-image/search.html b/doc/source/themes/scikit-image/search.html new file mode 100644 index 00000000..61520e6b --- /dev/null +++ b/doc/source/themes/scikit-image/search.html @@ -0,0 +1,46 @@ +{# + basic/search.html + ~~~~~~~~~~~~~~~~~ + + Template for the search page. + + :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. + :license: BSD, see LICENSE for details. +#} +{% extends "layout.html" %} +{% set title = _('Search') %} +{% set script_files = script_files + ['_static/searchtools.js'] %} +{% set script_files = script_files + ['searchindex.js'] %} +{% block body %} +

    {{ _('Search') }}

    +
    + +

    + {% trans %}Please activate JavaScript to enable the search + functionality.{% endtrans %} +

    +
    +

    + {% trans %}From here you can search these documents. Enter your search + words into the box in the navigation bar and press "Enter". Note that the + search function will automatically search for all of the words. Pages + containing fewer words won't appear in the result list.{% endtrans %} +

    + {% if search_performed %} + {% if not search_results %} +

    {{ _('Your search did not match any results.') }}

    + {% endif %} + {% endif %} +
    + {% if search_results %} +
      + {% for href, caption, context in search_results %} +
    • {{ caption }}
      • + {% endfor %} +
    + {% endif %} +
    +{% endblock %} diff --git a/doc/source/themes/scikit-image/static/css/bootstrap-responsive.min.css b/doc/source/themes/scikit-image/static/css/bootstrap-responsive.min.css new file mode 100644 index 00000000..7b0158da --- /dev/null +++ b/doc/source/themes/scikit-image/static/css/bootstrap-responsive.min.css @@ -0,0 +1,9 @@ +/*! + * Bootstrap Responsive v2.1.1 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + */.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;line-height:0;content:""}.clearfix:after{clear:both}.hide-text{font:0/0 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Mailing-list ------------ -The scikits-image mailing-list is scikits-image@googlegroups.com (users +The scikit-image mailing-list is scikit-image@googlegroups.com (users should join the `Google Group -`_ before posting). This +`_ before posting). This mailing-list is shared by users and developers, and it is the right place to ask any question about ``skimage``, or in general, image processing using Python. Posting snippets of code with minimal examples -ensures to get more relevant and focused answers. +ensures to get more relevant and focused answers. We would love to hear from how you use ``skimage`` for your work on the -mailing-list! +mailing-list! diff --git a/doc/source/user_guide/viewer.txt b/doc/source/user_guide/viewer.txt index 17387240..82bb5949 100644 --- a/doc/source/user_guide/viewer.txt +++ b/doc/source/user_guide/viewer.txt @@ -65,7 +65,7 @@ slider: denoise_plugin += SaveButtons() Here, we connect a slider widget to the filter's 'weight' argument. We also -added some buttons for saving the image to file or to the ``scikits-image`` +added some buttons for saving the image to file or to the ``scikit-image`` image stack (see ``skimage.io.push`` and ``skimage.io.pop``). All that's left is to create an image viewer and add the plugin to that viewer. diff --git a/doc/tools/plot_pr.py b/doc/tools/plot_pr.py index 63c0ad44..09a9f91e 100644 --- a/doc/tools/plot_pr.py +++ b/doc/tools/plot_pr.py @@ -33,7 +33,7 @@ month_duration = 24 for r in releases: releases[r] = dateutil.parser.parse(releases[r]) -def fetch_PRs(user='scikits-image', repo='scikits-image', state='open'): +def fetch_PRs(user='scikit-image', repo='scikit-image', state='open'): params = {'state': state, 'per_page': 100, 'page': 1} diff --git a/setup.py b/setup.py index bf8f6fbc..e4a7fc07 100644 --- a/setup.py +++ b/setup.py @@ -6,18 +6,18 @@ Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. Please refer to the online documentation at -http://scikits-image.org/ +http://scikit-image.org/ """ -DISTNAME = 'scikits-image' +DISTNAME = 'scikit-image' DESCRIPTION = 'Image processing routines for SciPy' LONG_DESCRIPTION = descr MAINTAINER = 'Stefan van der Walt' MAINTAINER_EMAIL = 'stefan@sun.ac.za' -URL = 'http://scikits-image.org' +URL = 'http://scikit-image.org' LICENSE = 'Modified BSD' -DOWNLOAD_URL = 'http://github.com/scikits-image/scikits-image' -VERSION = '0.7.1' +DOWNLOAD_URL = 'http://github.com/scikit-image/scikit-image' +VERSION = '0.7.2' PYTHON_VERSION = (2, 5) DEPENDENCIES = { 'numpy': (1, 6), diff --git a/skimage/__init__.py b/skimage/__init__.py index c8935cb6..1ac121b3 100644 --- a/skimage/__init__.py +++ b/skimage/__init__.py @@ -1,6 +1,6 @@ """Image Processing SciKit (Toolbox for SciPy) -``scikits-image`` (a.k.a. ``skimage``) is a collection of algorithms for image +``scikit-image`` (a.k.a. ``skimage``) is a collection of algorithms for image processing and computer vision. The main package of ``skimage`` only provides a few utilities for converting @@ -65,7 +65,7 @@ except ImportError: def _setup_test(verbose=False): import functools - args = ['', '--exe', '-w', pkg_dir] + args = ['', pkg_dir, '--exe'] if verbose: args.extend(['-v', '-s']) diff --git a/skimage/_shared/setup.py b/skimage/_shared/setup.py index 81113656..765c30de 100644 --- a/skimage/_shared/setup.py +++ b/skimage/_shared/setup.py @@ -28,11 +28,11 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='Scikits-image Developers', - author='Scikits-image Developers', - maintainer_email='scikits-image@googlegroups.com', + setup(maintainer='scikit-image Developers', + author='scikit-image Developers', + maintainer_email='scikit-image@googlegroups.com', description='Transforms', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='SciPy License (BSD Style)', **(configuration(top_path='').todict()) ) diff --git a/skimage/data/tests/test_data.py b/skimage/data/tests/test_data.py index 1d85802b..b5f6bcaa 100644 --- a/skimage/data/tests/test_data.py +++ b/skimage/data/tests/test_data.py @@ -15,9 +15,25 @@ def test_camera(): def test_checkerboard(): - """ Test that checkerboard image can be loaded. """ + """ Test that "checkerboard" image can be loaded. """ data.checkerboard() + +def test_text(): + """ Test that "text" image can be loaded. """ + data.text() + + +def test_moon(): + """ Test that "moon" image can be loaded. """ + data.moon() + + +def test_page(): + """ Test that "page" image can be loaded. """ + data.page() + + if __name__ == "__main__": from numpy.testing import run_module_suite run_module_suite() diff --git a/skimage/draw/setup.py b/skimage/draw/setup.py index 59067f9a..5b8e237d 100644 --- a/skimage/draw/setup.py +++ b/skimage/draw/setup.py @@ -21,11 +21,11 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='scikits-image developers', - author='scikits-image developers', - maintainer_email='scikits-image@googlegroups.com', + setup(maintainer='scikit-image developers', + author='scikit-image developers', + maintainer_email='scikit-image@googlegroups.com', description='Drawing', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='SciPy License (BSD Style)', **(configuration(top_path='').todict()) ) diff --git a/skimage/feature/setup.py b/skimage/feature/setup.py index 9c9074be..6f820163 100644 --- a/skimage/feature/setup.py +++ b/skimage/feature/setup.py @@ -24,11 +24,11 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='scikits-image Developers', - author='scikits-image Developers', - maintainer_email='scikits-image@googlegroups.com', + setup(maintainer='scikit-image Developers', + author='scikit-image Developers', + maintainer_email='scikit-image@googlegroups.com', description='Features', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='SciPy License (BSD Style)', **(configuration(top_path='').todict()) ) diff --git a/skimage/filter/lpi_filter.py b/skimage/filter/lpi_filter.py index 3826f5e7..2af74d7a 100644 --- a/skimage/filter/lpi_filter.py +++ b/skimage/filter/lpi_filter.py @@ -75,7 +75,7 @@ class LPIFilter2D(object): >>> filter = LPIFilter2D(filt_func) """ - if impulse_response is None: + if not callable(impulse_response): raise ValueError("Impulse response must be a callable.") self.impulse_response = impulse_response diff --git a/skimage/filter/setup.py b/skimage/filter/setup.py index 03ea7def..3e573aec 100644 --- a/skimage/filter/setup.py +++ b/skimage/filter/setup.py @@ -21,11 +21,11 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='scikits-image Developers', - author='scikits-image Developers', - maintainer_email='scikits-image@googlegroups.com', + setup(maintainer='scikit-image Developers', + author='scikit-image Developers', + maintainer_email='scikit-image@googlegroups.com', description='Filters', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='SciPy License (BSD Style)', **(configuration(top_path='').todict()) ) diff --git a/skimage/filter/tests/test_canny.py b/skimage/filter/tests/test_canny.py index 1e406008..2c758edf 100644 --- a/skimage/filter/tests/test_canny.py +++ b/skimage/filter/tests/test_canny.py @@ -61,3 +61,8 @@ class TestCanny(unittest.TestCase): def test_image_shape(self): self.assertRaises(TypeError, F.canny, np.zeros((20, 20, 20)), 4, 0, 0) + + def test_mask_none(self): + result1 = F.canny(np.zeros((20, 20)), 4, 0, 0, np.ones((20, 20), bool)) + result2 = F.canny(np.zeros((20, 20)), 4, 0, 0) + self.assertTrue(np.all(result1 == result2)) diff --git a/skimage/filter/tests/test_ctmf.py b/skimage/filter/tests/test_ctmf.py index fd820469..c4f6d10e 100644 --- a/skimage/filter/tests/test_ctmf.py +++ b/skimage/filter/tests/test_ctmf.py @@ -117,5 +117,11 @@ def test_insufficient_size(): median_filter(img, radius=1) +@raises(TypeError) +def test_wrong_shape(): + img = np.empty((10, 10, 3)) + median_filter(img) + + if __name__ == "__main__": np.testing.run_module_suite() diff --git a/skimage/filter/tests/test_lpi_filter.py b/skimage/filter/tests/test_lpi_filter.py index 08e46a58..f6176691 100644 --- a/skimage/filter/tests/test_lpi_filter.py +++ b/skimage/filter/tests/test_lpi_filter.py @@ -8,7 +8,8 @@ from skimage.io import * from skimage.filter import * -class TestLPIFilter2D(): +class TestLPIFilter2D(object): + img = imread(os.path.join(data_dir, 'camera.png'), flatten=True)[:50, :50] @@ -55,5 +56,9 @@ class TestLPIFilter2D(): g1 = wiener(F[::-1, ::-1], self.filt_func) assert ((g - g1[::-1, ::-1]).sum() < 1) + def test_non_callable(self): + assert_raises(ValueError, LPIFilter2D, None) + + if __name__ == "__main__": run_module_suite() diff --git a/skimage/graph/setup.py b/skimage/graph/setup.py index 2c432011..463d2739 100644 --- a/skimage/graph/setup.py +++ b/skimage/graph/setup.py @@ -29,10 +29,10 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='scikits-image Developers', - maintainer_email='scikits-image@googlegroups.com', + setup(maintainer='scikit-image Developers', + maintainer_email='scikit-image@googlegroups.com', description='Graph-based Image-processing Algorithms', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='Modified BSD', **(configuration(top_path='').todict()) ) diff --git a/skimage/io/_plugins/skivi.py b/skimage/io/_plugins/skivi.py index fb652638..fcfe8bc6 100644 --- a/skimage/io/_plugins/skivi.py +++ b/skimage/io/_plugins/skivi.py @@ -3,9 +3,9 @@ Skivi is written/maintained/developed by: S. Chris Colbert - sccolbert@gmail.com -Skivi is free software and is part of the scikits-image project. +Skivi is free software and is part of the scikit-image project. -Skivi is governed by the licenses of the scikits-image project. +Skivi is governed by the licenses of the scikit-image project. Please report any bugs to the author. diff --git a/skimage/io/collection.py b/skimage/io/collection.py index d420b58d..5a5dfff6 100644 --- a/skimage/io/collection.py +++ b/skimage/io/collection.py @@ -11,6 +11,7 @@ from copy import copy import numpy as np from ._io import imread + def concatenate_images(ic): """Concatenate all images in the image collection into an array. @@ -66,6 +67,7 @@ def alphanumeric_key(s): k = [int(c) if c.isdigit() else c for c in re.split('([0-9]+)', s)] return k + class MultiImage(object): """A class containing a single multi-frame image. @@ -217,6 +219,7 @@ class MultiImage(object): """ return concatenate_images(self) + class ImageCollection(object): """Load and manage a collection of image files. @@ -428,4 +431,3 @@ class ImageCollection(object): If images in the `ImageCollection` don't have identical shapes. """ return concatenate_images(self) - diff --git a/skimage/io/setup.py b/skimage/io/setup.py index 55526461..4e3c09c3 100644 --- a/skimage/io/setup.py +++ b/skimage/io/setup.py @@ -31,10 +31,10 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='scikits-image Developers', - maintainer_email='scikits-image@googlegroups.com', + setup(maintainer='scikit-image Developers', + maintainer_email='scikit-image@googlegroups.com', description='Image I/O Routines', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='Modified BSD', **(configuration(top_path='').todict()) ) diff --git a/skimage/measure/_polygon.py b/skimage/measure/_polygon.py index add4b5fb..7b9b920b 100644 --- a/skimage/measure/_polygon.py +++ b/skimage/measure/_polygon.py @@ -28,7 +28,7 @@ def approximate_polygon(coords, tolerance): ---------- .. [1] http://en.wikipedia.org/wiki/Ramer-Douglas-Peucker_algorithm """ - if tolerance == 0: + if tolerance <= 0: return coords chain = np.zeros(coords.shape[0], 'bool') diff --git a/skimage/measure/find_contours.py b/skimage/measure/find_contours.py index 68e1d53c..3a546ccf 100755 --- a/skimage/measure/find_contours.py +++ b/skimage/measure/find_contours.py @@ -98,7 +98,7 @@ def find_contours(array, level, """ array = np.asarray(array, dtype=np.double) if array.ndim != 2: - raise RuntimeError('Only 2D arrays are supported.') + raise ValueError('Only 2D arrays are supported.') level = float(level) if (fully_connected not in _param_options or positive_orientation not in _param_options): diff --git a/skimage/measure/setup.py b/skimage/measure/setup.py index 7e4ecf0f..21d9964e 100644 --- a/skimage/measure/setup.py +++ b/skimage/measure/setup.py @@ -24,10 +24,10 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='scikits-image Developers', - maintainer_email='scikits-image@googlegroups.com', + setup(maintainer='scikit-image Developers', + maintainer_email='scikit-image@googlegroups.com', description='Graph-based Image-processing Algorithms', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='Modified BSD', **(configuration(top_path='').todict()) ) diff --git a/skimage/measure/tests/test_find_contours.py b/skimage/measure/tests/test_find_contours.py index 62b39b3f..11b9b443 100644 --- a/skimage/measure/tests/test_find_contours.py +++ b/skimage/measure/tests/test_find_contours.py @@ -21,34 +21,37 @@ r = np.sqrt(x**2 + y**2) def test_binary(): - contours = find_contours(a, 0.5) + ref = [[6. , 1.5], + [5. , 1.5], + [4. , 1.5], + [3. , 1.5], + [2. , 1.5], + [1.5, 2. ], + [1.5, 3. ], + [1.5, 4. ], + [1.5, 5. ], + [1.5, 6. ], + [1. , 6.5], + [0.5, 6. ], + [0.5, 5. ], + [0.5, 4. ], + [0.5, 3. ], + [0.5, 2. ], + [0.5, 1. ], + [1. , 0.5], + [2. , 0.5], + [3. , 0.5], + [4. , 0.5], + [5. , 0.5], + [6. , 0.5], + [6.5, 1. ], + [6. , 1.5]] + + contours = find_contours(a, 0.5, positive_orientation='high') assert len(contours) == 1 - assert_array_equal(contours[0], - [[6. , 1.5], - [5. , 1.5], - [4. , 1.5], - [3. , 1.5], - [2. , 1.5], - [1.5, 2. ], - [1.5, 3. ], - [1.5, 4. ], - [1.5, 5. ], - [1.5, 6. ], - [1. , 6.5], - [0.5, 6. ], - [0.5, 5. ], - [0.5, 4. ], - [0.5, 3. ], - [0.5, 2. ], - [0.5, 1. ], - [1. , 0.5], - [2. , 0.5], - [3. , 0.5], - [4. , 0.5], - [5. , 0.5], - [6. , 0.5], - [6.5, 1. ], - [6. , 1.5]]) + assert_array_equal(contours[0][::-1], ref) + + def test_float(): @@ -70,6 +73,11 @@ def test_memory_order(): assert len(contours) == 1 +def test_invalid_input(): + assert_raises(ValueError, find_contours, r, 0.5, 'foo', 'bar') + assert_raises(ValueError, find_contours, r[..., None], 0.5) + + if __name__ == '__main__': from numpy.testing import run_module_suite run_module_suite() diff --git a/skimage/measure/tests/test_polygon.py b/skimage/measure/tests/test_polygon.py index 1907d7cb..c96aed88 100644 --- a/skimage/measure/tests/test_polygon.py +++ b/skimage/measure/tests/test_polygon.py @@ -22,6 +22,8 @@ def test_approximate_polygon(): out = approximate_polygon(square, -1) np.testing.assert_array_equal(out, square) + out = approximate_polygon(square, 0) + np.testing.assert_array_equal(out, square) def test_subdivide_polygon(): @@ -51,6 +53,10 @@ def test_subdivide_polygon(): np.testing.assert_equal(new_square3.shape[0], 2 * (square3.shape[0] - mask_len + 2)) + # not supported B-Spline degree + np.testing.assert_raises(ValueError, subdivide_polygon, square, 0) + np.testing.assert_raises(ValueError, subdivide_polygon, square, 8) + if __name__ == "__main__": np.testing.run_module_suite() diff --git a/skimage/measure/tests/test_regionprops.py b/skimage/measure/tests/test_regionprops.py index 271c1ec4..bd23d8b3 100644 --- a/skimage/measure/tests/test_regionprops.py +++ b/skimage/measure/tests/test_regionprops.py @@ -1,9 +1,9 @@ from numpy.testing import assert_array_equal, assert_almost_equal, \ - assert_array_almost_equal + assert_array_almost_equal, assert_raises import numpy as np import math -from skimage.measure import regionprops +from skimage.measure._regionprops import regionprops, PROPS, perimeter SAMPLE = np.array( @@ -22,6 +22,16 @@ INTENSITY_SAMPLE = SAMPLE.copy() INTENSITY_SAMPLE[1, 9:11] = 2 +def test_unsupported_dtype(): + assert_raises(TypeError, regionprops, np.zeros((10, 10), dtype=np.double)) + + +def test_all_props(): + props = regionprops(SAMPLE, 'all', INTENSITY_SAMPLE)[0] + for prop in PROPS: + assert prop in props + + def test_area(): area = regionprops(SAMPLE, ['Area'])[0]['Area'] assert area == np.sum(SAMPLE) @@ -36,6 +46,7 @@ def test_bbox(): bbox = regionprops(SAMPLE_mod, ['BoundingBox'])[0]['BoundingBox'] assert_array_almost_equal(bbox, (0, 0, SAMPLE.shape[0], SAMPLE.shape[1]-1)) + def test_central_moments(): mu = regionprops(SAMPLE, ['CentralMoments'])[0]['CentralMoments'] #: determined with OpenCV @@ -48,6 +59,7 @@ def test_central_moments(): assert_almost_equal(mu[2,1], 2000.296296296291) assert_almost_equal(mu[3,0], -760.0246913580195) + def test_centroid(): centroid = regionprops(SAMPLE, ['Centroid'])[0]['Centroid'] # determined with MATLAB @@ -90,6 +102,11 @@ def test_eccentricity(): eps = regionprops(SAMPLE, ['Eccentricity'])[0]['Eccentricity'] assert_almost_equal(eps, 0.814629313427) + img = np.zeros((5, 5), dtype=np.int) + img[2, 2] = 1 + eps = regionprops(img, ['Eccentricity'])[0]['Eccentricity'] + assert_almost_equal(eps, 0) + def test_equiv_diameter(): diameter = regionprops(SAMPLE, ['EquivDiameter'])[0]['EquivDiameter'] @@ -142,6 +159,11 @@ def test_filled_area(): assert area == np.sum(SAMPLE) +def test_filled_image(): + img = regionprops(SAMPLE, ['FilledImage'])[0]['FilledImage'] + assert_array_equal(img, SAMPLE) + + def test_major_axis_length(): length = regionprops(SAMPLE, ['MajorAxisLength'])[0]['MajorAxisLength'] # MATLAB has different interpretation of ellipse than found in literature, @@ -188,6 +210,7 @@ def test_moments(): assert_almost_equal(m[2,1], 43882.0) assert_almost_equal(m[3,0], 95588.0) + def test_normalized_moments(): nu = regionprops(SAMPLE, ['NormalizedMoments'])[0]['NormalizedMoments'] #: determined with OpenCV @@ -198,6 +221,7 @@ def test_normalized_moments(): assert_almost_equal(nu[2,1], 0.045473992910668816) assert_almost_equal(nu[3,0], -0.017278118992041805) + def test_orientation(): orientation = regionprops(SAMPLE, ['Orientation'])[0]['Orientation'] # determined with MATLAB @@ -219,15 +243,21 @@ def test_orientation(): )[0]['Orientation'] assert_almost_equal(orientation_diag, -math.pi / 4) + def test_perimeter(): - perimeter = regionprops(SAMPLE, ['Perimeter'])[0]['Perimeter'] - assert_almost_equal(perimeter, 59.2132034355964) + per = regionprops(SAMPLE, ['Perimeter'])[0]['Perimeter'] + assert_almost_equal(per, 59.2132034355964) + + per = perimeter(SAMPLE.astype('double'), neighbourhood=8) + assert_almost_equal(per, 43.1213203436) + def test_solidity(): solidity = regionprops(SAMPLE, ['Solidity'])[0]['Solidity'] # determined with MATLAB assert_almost_equal(solidity, 0.580645161290323) + def test_weighted_central_moments(): wmu = regionprops(SAMPLE, ['WeightedCentralMoments'], INTENSITY_SAMPLE )[0]['WeightedCentralMoments'] @@ -281,6 +311,7 @@ def test_weighted_moments(): ) assert_array_almost_equal(wm, ref) + def test_weighted_normalized_moments(): wnu = regionprops(SAMPLE, ['WeightedNormalizedMoments'], INTENSITY_SAMPLE )[0]['WeightedNormalizedMoments'] @@ -292,6 +323,7 @@ def test_weighted_normalized_moments(): ) assert_array_almost_equal(wnu, ref) + if __name__ == "__main__": from numpy.testing import run_module_suite run_module_suite() diff --git a/skimage/measure/tests/test_structural_similarity.py b/skimage/measure/tests/test_structural_similarity.py index 3eb2a7e9..84bd7cc6 100644 --- a/skimage/measure/tests/test_structural_similarity.py +++ b/skimage/measure/tests/test_structural_similarity.py @@ -1,5 +1,5 @@ import numpy as np -from numpy.testing import assert_equal +from numpy.testing import assert_equal, assert_raises from skimage.measure import structural_similarity as ssim @@ -24,20 +24,19 @@ def test_ssim_image(): S1 = ssim(X, Y, win_size=3) assert(S1 < 0.3) -## Come up with a better way of testing the gradient -## + +## # NOTE: This test is known to randomly fail on some systems (Mac OS X 10.6) ## def test_ssim_grad(): ## N = 30 ## X = np.random.random((N, N)) * 255 ## Y = np.random.random((N, N)) * 255 -## def func(Y): -## return ssim(X, Y, dynamic_range=255) +## f = ssim(X, Y, dynamic_range=255) +## g = ssim(X, Y, dynamic_range=255, gradient=True) -## def grad(Y): -## return ssim(X, Y, dynamic_range=255, gradient=True)[1] - -## assert(np.all(opt.check_grad(func, grad, Y) < 0.05)) +## assert f < 0.05 +## assert g[0] < 0.05 +## assert np.all(g[1] < 0.05) def test_ssim_dtype(): @@ -56,5 +55,15 @@ def test_ssim_dtype(): assert S2 < 0.1 +def test_invalid_input(): + X = np.zeros((3, 3), dtype=np.double) + Y = np.zeros((3, 3), dtype=np.int) + assert_raises(ValueError, ssim, X, Y) + + Y = np.zeros((4, 4), dtype=np.double) + assert_raises(ValueError, ssim, X, Y) + + assert_raises(ValueError, ssim, X, X, win_size=8) + if __name__ == "__main__": np.testing.run_module_suite() diff --git a/skimage/morphology/grey.py b/skimage/morphology/grey.py index e7e52de4..2cca69b6 100644 --- a/skimage/morphology/grey.py +++ b/skimage/morphology/grey.py @@ -1,10 +1,3 @@ -""" -:author: Damian Eads, 2009 -:license: modified BSD -""" - -__docformat__ = 'restructuredtext en' - import warnings from skimage import img_as_ubyte @@ -45,6 +38,7 @@ def erosion(image, selem, out=None, shift_x=False, shift_y=False): Examples -------- >>> # Erosion shrinks bright regions + >>> import numpy as np >>> from skimage.morphology import square >>> bright_square = np.array([[0, 0, 0, 0, 0], ... [0, 1, 1, 1, 0], @@ -97,6 +91,7 @@ def dilation(image, selem, out=None, shift_x=False, shift_y=False): Examples -------- >>> # Dilation enlarges bright regions + >>> import numpy as np >>> from skimage.morphology import square >>> bright_pixel = np.array([[0, 0, 0, 0, 0], ... [0, 0, 0, 0, 0], @@ -146,6 +141,7 @@ def opening(image, selem, out=None): Examples -------- >>> # Open up gap between two bright regions (but also shrink regions) + >>> import numpy as np >>> from skimage.morphology import square >>> bad_connection = np.array([[1, 0, 0, 0, 1], ... [1, 1, 0, 1, 1], @@ -196,6 +192,7 @@ def closing(image, selem, out=None): Examples -------- >>> # Close a gap between two bright lines + >>> import numpy as np >>> from skimage.morphology import square >>> broken_line = np.array([[0, 0, 0, 0, 0], ... [0, 0, 0, 0, 0], @@ -245,6 +242,7 @@ def white_tophat(image, selem, out=None): Examples -------- >>> # Subtract grey background from bright peak + >>> import numpy as np >>> from skimage.morphology import square >>> bright_on_grey = np.array([[2, 3, 3, 3, 2], ... [3, 4, 5, 4, 3], @@ -261,7 +259,6 @@ def white_tophat(image, selem, out=None): """ if image is out: raise NotImplementedError("Cannot perform white top hat in place.") - image = img_as_ubyte(image) out = opening(image, selem, out=out) out = image - out @@ -294,6 +291,7 @@ def black_tophat(image, selem, out=None): Examples -------- >>> # Change dark peak to bright peak and subtract background + >>> import numpy as np >>> from skimage.morphology import square >>> dark_on_grey = np.array([[7, 6, 6, 6, 7], ... [6, 5, 4, 5, 6], @@ -311,7 +309,6 @@ def black_tophat(image, selem, out=None): if image is out: raise NotImplementedError("Cannot perform white top hat in place.") - image = img_as_ubyte(image) out = closing(image, selem, out=out) out = out - image diff --git a/skimage/morphology/setup.py b/skimage/morphology/setup.py index 02c39ae7..b8564ce4 100644 --- a/skimage/morphology/setup.py +++ b/skimage/morphology/setup.py @@ -39,11 +39,11 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='scikits-image Developers', + setup(maintainer='scikit-image Developers', author='Damian Eads', - maintainer_email='scikits-image@googlegroups.com', + maintainer_email='scikit-image@googlegroups.com', description='Morphology Wrapper', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='SciPy License (BSD Style)', **(configuration(top_path='').todict()) ) diff --git a/skimage/segmentation/setup.py b/skimage/segmentation/setup.py index b9e19078..ec4ac4ff 100644 --- a/skimage/segmentation/setup.py +++ b/skimage/segmentation/setup.py @@ -25,10 +25,10 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='scikits-image Developers', - maintainer_email='scikits-image@googlegroups.com', + setup(maintainer='scikit-image Developers', + maintainer_email='scikit-image@googlegroups.com', description='Segmentation Algorithms', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='SciPy License (BSD Style)', **(configuration(top_path='').todict()) ) diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py index 6e04a271..1179811d 100644 --- a/skimage/transform/_geometric.py +++ b/skimage/transform/_geometric.py @@ -1015,7 +1015,8 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1, if mode == 'constant' and not (0 <= cval <= 1): clipped[out == cval] = cval - if clipped.shape[0] == 1 or clipped.shape[1] == 1: + if clipped.ndim == 3 and orig_ndim == 2: + # remove singleton dim introduced by atleast_3d + return clipped[..., 0] + else: return clipped - else: # remove singleton dim introduced by atleast_3d - return clipped.squeeze() diff --git a/skimage/transform/pyramids.py b/skimage/transform/pyramids.py index dd274834..19001de8 100644 --- a/skimage/transform/pyramids.py +++ b/skimage/transform/pyramids.py @@ -57,7 +57,7 @@ def pyramid_reduce(image, downscale=2, sigma=None, order=1, References ---------- - ..[1] http://web.mit.edu/persci/people/adelson/pub_pdfs/pyramid83.pdf + .. [1] http://web.mit.edu/persci/people/adelson/pub_pdfs/pyramid83.pdf """ @@ -111,7 +111,7 @@ def pyramid_expand(image, upscale=2, sigma=None, order=1, References ---------- - ..[1] http://web.mit.edu/persci/people/adelson/pub_pdfs/pyramid83.pdf + .. [1] http://web.mit.edu/persci/people/adelson/pub_pdfs/pyramid83.pdf """ @@ -143,9 +143,9 @@ def pyramid_gaussian(image, max_layer=-1, downscale=2, sigma=None, order=1, the downscaled images. Note that the first image of the pyramid will be the original, unscaled - image. The total number of images is `max_layer + 1`. In case all layers are - computed, the last image is either a one-pixel image or the image where the - reduction does not change its shape. + image. The total number of images is `max_layer + 1`. In case all layers + are computed, the last image is either a one-pixel image or the image where + the reduction does not change its shape. Parameters ---------- @@ -176,7 +176,7 @@ def pyramid_gaussian(image, max_layer=-1, downscale=2, sigma=None, order=1, References ---------- - ..[1] http://web.mit.edu/persci/people/adelson/pub_pdfs/pyramid83.pdf + .. [1] http://web.mit.edu/persci/people/adelson/pub_pdfs/pyramid83.pdf """ @@ -225,8 +225,8 @@ def pyramid_laplacian(image, max_layer=-1, downscale=2, sigma=None, order=1, Note that the first image of the pyramid will be the difference between the original, unscaled image and its smoothed version. The total number of images is `max_layer + 1`. In case all layers are computed, the last image - is either a one-pixel image or the image where the reduction does not change - its shape. + is either a one-pixel image or the image where the reduction does not + change its shape. Parameters ---------- @@ -257,8 +257,8 @@ def pyramid_laplacian(image, max_layer=-1, downscale=2, sigma=None, order=1, References ---------- - ..[1] http://web.mit.edu/persci/people/adelson/pub_pdfs/pyramid83.pdf - ..[2] http://sepwww.stanford.edu/~morgan/texturematch/paper_html/node3.html + .. [1] http://web.mit.edu/persci/people/adelson/pub_pdfs/pyramid83.pdf + .. [2] http://sepwww.stanford.edu/~morgan/texturematch/paper_html/node3.html """ diff --git a/skimage/transform/setup.py b/skimage/transform/setup.py index 0e415bad..b0093d87 100644 --- a/skimage/transform/setup.py +++ b/skimage/transform/setup.py @@ -26,11 +26,11 @@ def configuration(parent_package='', top_path=None): if __name__ == '__main__': from numpy.distutils.core import setup - setup(maintainer='Scikits-image Developers', - author='Scikits-image Developers', - maintainer_email='scikits-image@googlegroups.com', + setup(maintainer='scikit-image Developers', + author='scikit-image Developers', + maintainer_email='scikit-image@googlegroups.com', description='Transforms', - url='https://github.com/scikits-image/scikits-image', + url='https://github.com/scikit-image/scikit-image', license='SciPy License (BSD Style)', **(configuration(top_path='').todict()) ) diff --git a/skimage/transform/tests/test_pyramids.py b/skimage/transform/tests/test_pyramids.py index 611ecdec..6d0609e0 100644 --- a/skimage/transform/tests/test_pyramids.py +++ b/skimage/transform/tests/test_pyramids.py @@ -1,41 +1,72 @@ -from numpy.testing import assert_array_equal, run_module_suite +from numpy.testing import assert_array_equal, assert_raises, run_module_suite from skimage import data -from skimage.transform import (pyramid_reduce, pyramid_expand, - pyramid_gaussian, pyramid_laplacian) +from skimage.transform import pyramids image = data.lena() +image_gray = image[..., 0] -def test_pyramid_reduce(): +def test_pyramid_reduce_rgb(): rows, cols, dim = image.shape - out = pyramid_reduce(image, downscale=2) + out = pyramids.pyramid_reduce(image, downscale=2) assert_array_equal(out.shape, (rows / 2, cols / 2, dim)) -def test_pyramid_expand(): +def test_pyramid_reduce_gray(): + rows, cols = image_gray.shape + out = pyramids.pyramid_reduce(image_gray, downscale=2) + assert_array_equal(out.shape, (rows / 2, cols / 2)) + + +def test_pyramid_expand_rgb(): rows, cols, dim = image.shape - out = pyramid_expand(image, upscale=2) + out = pyramids.pyramid_expand(image, upscale=2) assert_array_equal(out.shape, (rows * 2, cols * 2, dim)) -def test_build_gaussian_pyramid(): - rows, cols, dim = image.shape - pyramid = pyramid_gaussian(image, downscale=2) +def test_pyramid_expand_gray(): + rows, cols = image_gray.shape + out = pyramids.pyramid_expand(image_gray, upscale=2) + assert_array_equal(out.shape, (rows * 2, cols * 2)) + +def test_build_gaussian_pyramid_rgb(): + rows, cols, dim = image.shape + pyramid = pyramids.pyramid_gaussian(image, downscale=2) for layer, out in enumerate(pyramid): layer_shape = (rows / 2 ** layer, cols / 2 ** layer, dim) assert_array_equal(out.shape, layer_shape) -def test_build_laplacian_pyramid(): - rows, cols, dim = image.shape - pyramid = pyramid_laplacian(image, downscale=2) +def test_build_gaussian_pyramid_gray(): + rows, cols = image_gray.shape + pyramid = pyramids.pyramid_gaussian(image_gray, downscale=2) + for layer, out in enumerate(pyramid): + layer_shape = (rows / 2 ** layer, cols / 2 ** layer) + assert_array_equal(out.shape, layer_shape) + +def test_build_laplacian_pyramid_rgb(): + rows, cols, dim = image.shape + pyramid = pyramids.pyramid_laplacian(image, downscale=2) for layer, out in enumerate(pyramid): layer_shape = (rows / 2 ** layer, cols / 2 ** layer, dim) assert_array_equal(out.shape, layer_shape) +def test_build_laplacian_pyramid_gray(): + rows, cols = image_gray.shape + pyramid = pyramids.pyramid_laplacian(image_gray, downscale=2) + for layer, out in enumerate(pyramid): + layer_shape = (rows / 2 ** layer, cols / 2 ** layer) + assert_array_equal(out.shape, layer_shape) + + +def test_check_factor(): + assert_raises(ValueError, pyramids._check_factor, 0.99) + assert_raises(ValueError, pyramids._check_factor, - 2) + + if __name__ == "__main__": run_module_suite() diff --git a/skimage/util/montage.py b/skimage/util/montage.py index 1a8cda23..587c0939 100644 --- a/skimage/util/montage.py +++ b/skimage/util/montage.py @@ -71,6 +71,8 @@ def montage2d(arr_in, fill='mean', rescale_intensity=False): assert arr_in.ndim == 3 n_images, height, width = arr_in.shape + + arr_in = arr_in.copy() # -- rescale intensity if necessary if rescale_intensity: