mirror of
https://github.com/wassname/scikit-image.git
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Kyle Mandli
122 lines
4.5 KiB
Plaintext
122 lines
4.5 KiB
Plaintext
How to contribute to ``scikits.image``
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======================================
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Developing Open Source is great fun! Join us on the `scikits-image 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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.. 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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Infrastructure
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--------------
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- 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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* Connected components
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* `Grey-level co-occurrence matrices <http://mentat.za.net/hg>`_
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* Marching squares
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* Nadav's bilateral filtering (first compare against CellProfile's code)
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* 2D iso-contour finding (sub-pixel precision) [ask Zach Pincus]
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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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* Canny filter (Canny, J., *A Computational Approach To Edge Detection*,
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IEEE Trans. Pattern Analysis and Machine Intelligence, 8:679-714, 1986)
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* Prewitt filter - convolution with ``[[1,1,1], [0,0,0], [-1,-1,-1]]`` to
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detect edges
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* Sobel filter - convolution with ``[[1,2,1], [0,0,0], [-1,-2,-1]]`` to
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detect edges
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* Roberts filter - convolution with diagonal and anti-diagonal
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kernels to detect edges
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* Bilateral filter
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(http://groups.csail.mit.edu/graphics/bilagrid/bilagrid_web.pdf)
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- edge detection using both spatial and intensity information
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* Convex hulls of objects in a labels matrix
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* Minimum enclosing circles of objects in a labels matrix
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* Map-coloring of a labels matrix - assign each label a color so that
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all adjacent labels have different colors
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* Skeletonize, spur removal, thinning, thickening, and other morphological
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operations on binary images, framework for creating arbitrary morphological
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operations using a 3x3 grid.
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* Skeletonize objects in a labels matrix
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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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* 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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* Due to the above, the tests run unnecessarily slowly
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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 medical / biological and GIS image format plugins.
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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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* Write topics for the `user guide
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<http://stefanv.github.com/scikits.image/user_guide.html>`_:
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- Introduction to I/O and image processing with examples
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* Build docs outside source directory
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* Integrate BiBTeX plugin into Sphinx build
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* Create a kick-ass website
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Implement Algorithms
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````````````````````
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- Histograms of oriented gradients
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- Fast radon transform
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- Graph cut segmentation
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- Probabilistic Hough transform
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