Differences between revisions 11 and 12

1. NextGenCode

Contents

NextGenCode

a grab-bag of notes on what we'd like to see in the ideal freesurfer source code environment, and runtime

1.1. Newer respository

evaluate DVCS like git. if not something relatively modern like SVN which lets you do admin operations easily unlike CVS.
source only checkout which excludes all distribution data. For faster and thinner local builds.
Integrate an Issue tracking system. If FS is open source maybe Github or Google Code or even SourceForge are good ideas

1.2. CMake building

cmake replacing autotools as the build enviro

1.3. Third-Party Packages

one-stop-shopping build of all 3rd party packages --> like neurodebian
evaluate necessity of 3rd-party packages, eg PetSc

1.4. Source Code cleanups

continued source code cleanup:
- remove all #if 0 code and duplicated stuff
source code documentation
more low-level unit tests

1.5. GPU Transition

memory structures changed to allow easier cpu (and gpu) parallelization (see rge notes)

1.6. recon-all

complete replacement of recon-all with ????

1.7. Installation details

eliminate clutter in $FREESURFER_HOME ( for the installation ).
- for instance, the distribution data after installation should be in $FREESURFER_HOME/data. GEMS, the newest FS package, already uses this. It's data is in $FREESURFER_HOME/data/GEMS

1.8. Scripting language support

First phase is to wrap IO and utils so that it's possible for everyone to write scripts (Python, Numpy) in FreeSurfer instead of adding binaries to the source distribution. evaluate Cython as possible means.

When done properly, instead of adding a directory ( by mimicking the dummy/ project we have ) and toying with the Autotools, one can simply write a Python script like following:

import fs.utils as u
import fs.io as io

im = io.MRIread('test.mgz')
m = u.MRImean(im, 5)

1.9. Code Style Uniformization

Use some standard for C89 and C++0x - e.g. [http://google-styleguide.googlecode.com/svn/trunk/cppguide.xml] and [http://code.google.com/p/google-styleguide/]
Avoid mixing C and C++ styles (in C++ use templates, Boost libraries, etc)

-Deletions are marked like this.
+Additions are marked like this.
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-=== Newer respository ===
+== Newer respository ==
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+ * Integrate an Issue tracking system. If FS is open source maybe [[http://github.com | Github]] or Google Code or even [[http://sourceforge.net | SourceForge]] are good ideas
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-=== CMake building ===
+== CMake building ==
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-=== Third-Party Packages ===
+== Third-Party Packages ==
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-=== Source Code cleanups ===
+== Source Code cleanups ==
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-=== GPU Transition ===
+== GPU Transition ==
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-=== recon-all ===
+== recon-all ==
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-=== Installation details ===
+== Installation details ==
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-=== Scripting language support ===
+== Scripting language support ==
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-=== Code Style Uniformization ===
+== Code Style Uniformization ==