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TASKS.txt
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TASKS.txt
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.. role:: strike
.. _howto_contribute:
How to contribute to ``skimage``
======================================
.. toctree::
:hidden:
gitwash/index
gsoc2011
coverage_table
cell_profiler
Developing Open Source is great fun! Join us on the `skimage mailing
list <http://groups.google.com/group/scikits-image>`_ 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 <gitwash/index>` when developing skimage
.. contents::
:local:
Tasks
-----
.. :doc:`gsoc2011`
.. :doc:`coverage_table`
Implement Algorithms
````````````````````
- Graph cut segmentation
- `Image colorization <http://www.cs.huji.ac.il/~yweiss/Colorization/>`__
- Fast 2D convex hull (consider using CellProfiler version)
`Algorithm overview <http://www.tcs.fudan.edu.cn/rudolf/Courses/Algorithms/Alg_cs_07w/Webprojects/Zhaobo_hull/index.html#section26>`__.
`One free implementation
<http://cm.bell-labs.com/cm/cs/who/clarkson/2dch.c>`_.
[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.
Drawing (directly on an ndarray)
````````````````````````````````
- Wu's algorithm for circles
- Text rendering
Infrastructure
--------------
- :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 <http://www.cellprofiler.org>`_ 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
<http://groups.google.com/group/scikits-image/browse_thread/thread/c4f8fc584bfd839d>`_).
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 <http://sourceforge.net/apps/mediawiki/gdcm>`__.
docs
````
* Add examples to the gallery
* Write topics for the `user guide
<http://scikits-image.org/docs/dev/user_guide.html>`_
* Integrate BiBTeX plugin into Sphinx build