mirror of
https://github.com/wassname/scikit-image.git
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Stefan van der Walt
126 lines
4.5 KiB
Plaintext
126 lines
4.5 KiB
Plaintext
.. role:: strike
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.. _howto_contribute:
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How to contribute to ``skimage``
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======================================
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.. toctree::
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:hidden:
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gitwash/index
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gsoc2011
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coverage_table
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cell_profiler
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Developing Open Source is great fun! Join us on the `skimage mailing
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list <http://groups.google.com/group/scikits-image>`_ and tell us which of the
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following challenges you'd like to solve.
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* Mentoring is available for those new to scientific programming in Python.
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* The technical detail of the `development process`_ is given below.
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* :doc:`How to use GitHub <gitwash/index>` when developing skimage
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.. contents::
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:local:
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Tasks
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-----
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.. :doc:`gsoc2011`
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.. :doc:`coverage_table`
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Implement Algorithms
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````````````````````
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- Graph cut segmentation
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- `Image colorization <http://www.cs.huji.ac.il/~yweiss/Colorization/>`__
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- Fast 2D convex hull (consider using CellProfiler version)
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`Algorithm overview <http://www.tcs.fudan.edu.cn/rudolf/Courses/Algorithms/Alg_cs_07w/Webprojects/Zhaobo_hull/index.html#section26>`__.
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`One free implementation
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<http://cm.bell-labs.com/cm/cs/who/clarkson/2dch.c>`_.
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[Compare against current implementation]
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- Convex hulls of objects in a labels matrix (simply adapt current convex hull
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image code--this one's low hanging fruit). Generalise this solution to also
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skeletonize objects in a labels matrix.
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Drawing (directly on an ndarray)
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````````````````````````````````
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- Wu's algorithm for circles
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- Text rendering
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Infrastructure
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--------------
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- :strike:`Implement a new backend system so that we may start including
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PyOpenCL-based algorithms`
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Adapt existing code for use
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```````````````````````````
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These snippets and packages have already been written. Some need to be
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modified to work as part of the scikit, others may be lacking in documentation
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or tests.
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* :strike:`Connected components`
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* Nadav's bilateral filtering (first compare against CellProfiler's
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code, based on http://groups.csail.mit.edu/graphics/bilagrid/bilagrid_web.pdf)
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Also see https://github.com/stefanv/scikits-image/tree/bilateral
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* 2D image warping via thin-plate splines [ask Zach Pincus]
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Merge code provided by `CellProfiler <http://www.cellprofiler.org>`_ team
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`````````````````````````````````````````````````````````````````````````
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* Roberts filter - convolution with diagonal and anti-diagonal
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kernels to detect edges
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* Minimum enclosing circles of objects in a labels matrix
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* spur removal, thinning, thickening, and other morphological operations on
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binary images, framework for creating arbitrary morphological operations
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using a 3x3 grid.
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Their SVN repository is read-accessible at
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- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler
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The files for the above algorithms are
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- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/cpmorphology.py
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- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/filter.py
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There are test suites for the files at
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- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/tests/test_cpmorphology.py
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- https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/cellprofiler/cpmath/tests/test_filter.py
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Quoting a message from Lee Kamentsky to Stefan van der Walt sent on
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5 August 2009::
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We're part of the Broad Institute which is non-profit. We would be happy
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to include our algorithm code in SciPy under the BSD license since that is
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more appropriate for a library that might be integrated into a
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commercial product whereas CellProfiler needs the more stringent
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protection of GPL as an application.
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In 2010, Vebjorn Ljosa officially released parts of the code under a
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BSD license (:doc:`cell_profiler` | `original message
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<http://groups.google.com/group/scikits-image/browse_thread/thread/c4f8fc584bfd839d>`_).
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Thanks to Lee Kamentsky, Thouis Jones and Anne Carpenter and their colleagues
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who contributed.
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Rework linear filters
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`````````````````````
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* Fast, SSE2 convolution (high priority) (see prototype in pull requests)
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* Should take kernel or function for parameter (currently only takes function)
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* Kernel shape should be specifiable (currently defaults to image shape)
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io
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``
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* Update ``qt_plugin.py`` and other plugins to view collections.
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* Rewrite GTK backend using GObject Introspection for Py3K compatibility.
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* Add DICOM plugin for `GDCM <http://sourceforge.net/apps/mediawiki/gdcm>`__.
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docs
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````
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* Add examples to the gallery
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* Write topics for the `user guide
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<http://scikits-image.org/docs/dev/user_guide.html>`_
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* Integrate BiBTeX plugin into Sphinx build
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