Changes between Version 3 and Version 4 of ShortVersion


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Timestamp:
Oct 28, 2010, 7:09:36 PM (9 years ago)
Author:
kyoung
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  • ShortVersion

    v3 v4  
    1 = Vespa Overview - the Short Version =
     1= Vespa Overview - the Novel =
    22
    3 The Vespa package extends the maintenance and development of three previously
    4 developed magnetic resonance spectroscopy (MRS) software tools by migrating
    5 them into an integrated, open source, open development platform. Vespa stands
    6 for Versatile Simulation Pulses and Analysis.
     3VeSPA is a project, the goal of which is to utilize current software engineering "best practices" to refactor 3 existing and widely used MRS software packages, written by the authors and colleagues, to create an integrated open source package for performing and analyzing MRS experiments. VeSPA, the resulting integrated package, provides a greatly enhanced, more complete, easier to use, easier to extend set of tools for MRS simulation and analysis.
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    8 Vespa consists of three combined applications called RFPulse, Simulation and
    9 Analysis that were migrated from three previous standalone applications:
     5The original applications were written in closed source languages ([http://cds.ismrm.org/ismrm-2003/0852.pdf GAVA/Gamma] and IDL_Vespa in [http://www.ittvis.com/ProductServices/IDL.aspx IDL], and [http://www.rrmind.research.va.gov/software/matpulse.asp MatPulse] in [http://www.mathworks.com/ Matlab]) that have licensing issues (primarily restricted use and substantial fees) that make their use for scientific collaboration problematic, as well as make them relatively difficult to extend and virtually impossible to integrate. Rewriting the applications in the open source language, [http://www.python.org/ Python], and utilizing the powerful [http://numpy.scipy.org/ NumPy], [http://www.scipy.org SciPy], and [http://matplotlib.sourceforge.net/ Matplotlib] libraries allows for a clean, robust, full featured and open source (i.e. FREE) integration of the packages. Itprovides a much more natural work flow for researchers as well as making the integrated package much more easily extended by those who need added functionality. As an example it has been straightforward for the authors to add functionality corresponding to recent developments in MRS, providing substantial added value to the integrated VeSPA package for a modest coding effort.
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    11  * RFPulse    <-> MatPulse - software for RF pulse design written in Matlab
    12  * Simulation <-> GAVA/Gamma - software for spectral simulation written in IDL
    13  * Analysis   <-> IDL_Vespa - a package for spectral data processing and analysis written in IDL
     7One of the goals of the earlier individual packages as well as the integrated package is to provide sophisticated tools to non experts who would otherwise have great difficulty in taking advantage of capabilities that have become available to researchers in MRS.
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    15 The new Vespa project addresses previous software limitations, including:
    16 non-standard data access, closed source multiple language software that
    17 complicatee algorithm extension and comparison, lack of integration between
    18 programs for sharing prior information, and incomplete or missing d
    19 ocumentation and educational content.
     9The original MatPulse package written by Professor Gerald Matson encapsulated a large body of knowledge regarding RF pulse design allowed users with relatively little experience to explore and utilize that knowledge in a straightforward manner that resulted in rapid development of useful RF pulses.
    2010
    21 These applications can be run separately but can communicate among
    22 themselves via a shared database of objects/results. One example of inter-
    23 application sharing might be that Simulation would make use of an RF pulse
    24 designed in RFPulse application to create a more realistic MR simulation.
    2511
    26 '''NIH grant number 1R01EB008387-01A1''' funded the maintenance and extension of these
    27 separate applications into a combined environment based entirely on the Python
    28 language.
     12Similarly the gamma NMR simulation library written by Dr. Scott Smith allowed users with with limited knowledge of the underlying quantum mechanical details to write C++ programs that explored the effects of various pulse and pulse sequence designs using full quantum mechanical density matrix calculations. The GAVA/Gamma package was an attempt to further simplify NMR simulations by providing a graphical interface to a subset of the gamma library thus freeing users with no knowledge or interest in C++ programming to explore pulse and pulse sequence designs. The Simulation component of VeSPA goes even further by using the SWIG package to provide a python interface to gamma, referred to as pygamma. Simulation itself provides a graphical interface with powerful plotting and analysis functionality that is built on top of pygamma. But pygamma can be be used independently to produce powerful NMR simulations in python with the majority of the calculations performed in underlying fast C++ code.
     13
     14The Analysis component of VeSPA provides an updated, greatly extended, python version of the IDL_Vespa spectral fitting package originally written by the authors and colleagues. The updating and integration of these 3 packages provides greatly enhanced possibilities for exploring, developing, and analyzing MRS experiments; in the following we briefly describe some possible scenarios.