VeSPA
VeSPA is an open source software funded with public money. They are investing time, money and expertise into it. Something good is going to happen. Here is what the software manual says:
The Vespa package enhances and extends three previously developed magnetic resonance spectroscopy (MRS) software tools by migrating them into an integrated, open source, open development platform. Vespa stands for Versatile Simulation, Pulses and Analysis. The original tools that have been migrated into this package include:
- GAVA/Gamma - software for spectral simulation
- MatPulse – software for RF pulse design
- IDL_Vespa – a package for spectral data processing and analysis
The new Vespa project addresses current software limitations, including:
non-standard data access, closed source multiple language software that complicates algorithm extension and comparison, lack of integration between programs for sharing prior information, and incomplete or missing documentation and educational content.
I am interested into the spectral simulation module only, because pulse design is not my field (yet) and because there are already too many programs for processing.
Installing VeSPA is not an easy task. VeSPA depends on a lot of other software, which in turn depends on other software, etc.. You need a guide, which is this page:
http://scion.duhs.duke.edu/vespa/pro...i/Installation
Install the 8 packages in the listed order. For some of these packages you will be prompted to install an outdated version. Resist to the temptation of installing the latest version, because this will break the inter-dependencies of the other packages. Installing the first packages of the list is a merely mechanical process: click to download, click to accept the license agreement, etc.. The last packages, instead, are written in Python and are a little more complicated to install. In my case, it was necessary to use the unix commands cd, su, sudo and exit repeatedly. Renounce if you don't know these commands. Such a complicated installation is quite discouraging. I see no reason, for example, why anybody should try to install the processing part of VeSPA, while other software is available that can be installed with a single click. I can see the other side of the coin, however, and it brights.
Instead that reinventing the wheel once again, they put together many bricks, old and new ones, that were already available. Do you remember
this old article of mine?
There has been the terrible tradition, in our field, that every newcomer reinvents the wheel. We have seen a lot of simulation programs and nothing is available or working and supported. Now I welcome the VeSPA team because they have apparently embraced the opposite philosophy.
The big problem I see, after the installation, is that, at this writing moment, VeSPA is not a complete substitute for Gamma. The new program is devoted to in-vivo metabolomics. In theory there is space to grow and include what is left outside, yet this will not be easy in practice. Who is going to do it? Who is going to pay for it? I bet nobody will do.
The VeSPA web site is:
http://scion.duhs.duke.edu/vespa/
My current situation is: I have VeSPA installed but it's not what I wanted. I wanted Gamma. I have also installed Gamma in the process, but it does not work. If I try running gamma, I get the error message:
Apparently You Do Not Have A Proper Path Set To GAMMA......
Please Set The Variable GAMMA_PATH To Reflect The Base GAMMA
Directory, The One Off Of Which The Subdirectory share Exists.
This Change Can Be Done In The gamma Script You Are Running
Or You Can Set GAMMA_PATH As An Environment Variable.
Currently GAMMA_PATH is Set To /E/gamma/gamma-4.2.1
which means absolutely nothing to me, because there is no "share" subdirectory. I have tried to set the variable:
GAMMA_PATH='~/gamma'
and the error persists unchanged. The last chance was to use pygamma. Not exactly what I want, but they say it's equivalent to gamma and I remember having installed it in the process of installing VeSPA. My first attempt was:
pygamma
The answer: command not found.
Then I have tried something more... detailed:
python "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pygamma/pygamma.py"
The answer was:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pygamma/pygamma.py", line 7, in
import _pygamma
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pygamma/_pygamma.so, 2): no suitable image found. Did find:
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pygamma/_pygamma.so: mach-o, but wrong architecture
What kind of joke is this? They really have no idea of what a user is.
I have my theory why everybody writes his own simulation software: it's because nobody is able to install somebody else's software.
Source:
NMR Software blog
VeSPA
Linear Mode
