wiki:WikiStart

Version 33 (modified by flip, 10 years ago) (diff)

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Welcome to the GAMMA Library

This site is a collaboration of Karl Young at UCSF and Brian Soher at Duke.

Recent work on GAMMA and this website is supported by a grant from the NIH.

GAMMA Overview : Software for simulating magnetic resonance phenomena.

GAMMA is written in C++ and some of GAMMA's API's have been exported to Python, using SWIG.

The original version of GAMMA was written by Scott A. Smith and Tilo Levante under the guidance of B.H. Meier and R.R. Ernst at the ETH in Zürich.

Some additional information about GAMMA can be retrieved from the following site:

Example of real-world applications of GAMMA, see:

Obtaining and Building GAMMA (and PyGamma)

Obtaining and Building the GAMMA Library - Learn how to get a copy of the source code and what to do with it once you get it.

If you're interested in pyGamma, we provide prebuilt binaries for most platforms. We also have instructions on how to build pyGamma.

Extending PyGamma

Extending Pygamma can be a relatively simple process and is described here.

Issues With PyGamma and SWIG

Issues with simply Swigging the C++ code can cause the semantics of pointers and reference counting in python to be different than expected. In some circumstances this will cause a Segfault or other serious and unpredictable errors in your code execution, sometimes with few error messages. We plan to address this in a future release of pyGamma. For now, we list some details of the issue and some work-arounds?.

You should also be aware that PyGAMMA can't accept Python's Unicode strings.

GAMMA - Updates and Changes

Code Changes - To get GAMMA to compile on gcc 4.3.3 (on Ubuntu 9.04), windows XP, visual studio 2008 express, and Mac OSX (gcc 4.0.1).

Swig Issues (and working code) - Found while getting environment setup and testing the basic functionality of SWIG. While using gcc 4.3.3/Ubuntu 9.04/Swig 1.3.9/python2.5 and 2.6

Swig Implementation notes - Including organization of code, some (potentially remaining) issues, and Makefile and visual-studio modifications.

GAMMA Testing Situation - Tools and Environment setup for testing the GAMMA library.

Merging C++ code with that from Zurich (Matthais Ernst) - Changes, Issues, etc.

Code Cleanup Notes - Directories that have been deleted but can still be recovered.

Performance Issues

GAMMA vs. PyGamma

Relative performance of pyGamma, the swigged versions of GAMMA.

GAMMA Timing vs. Spin Count

GAMMA Performance as a function of the number of spins, in the metabolite being studied.

Speeding up GAMMA and PyGamma

Speeding up GAMMA with Lapack/Atlas, etc.

To Do List

List of to-do-items that are necessary, or just good, to implement for the GAMMA code base and project.

Proper Citation in Papers and Presentations

Proper reference should be given, using the citation below, when GAMMA simulations are utilized in papers and/or presentations.

"Computer Simulations in Magnetic Resonance. An Object Oriented Programming Approach", S.A. Smith, T.O. Levante, B.H. Meier, and R.R. Ernst, J. Magn. Reson., 106a.

For more information about NMR on the web

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