Difference between revisions of "2009 Winter Project Week GWE Catalogs"

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<h1>Objective</h1>
 
<h1>Objective</h1>
  
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To integrate Grid Wizard Enterprise (GWE) with XML based catalogs containing a description of parameter exploration experiments to process (in terms of target/moving images and algorithmic parameters for example). GWE is being enhanced with a XPath parser which allows it to introspect any XML file. This will allow GWE to read structured data from standard catalogs by creating the appropriate XPath expressions to query for this data. The specific goal is to identify these catalogs, their schema and the data to extract from them, generate the XPath expressions necessary to read the desired data and create a GWE function/macro to run an experiment (in the grid) described in a particular catalog file.
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To integrate Grid Wizard Enterprise (GWE) with XML based catalogs containing a description "experiments". An "experiment" is a set of inter-independent process runs of a particular algorithm over a collection of parameters which can include algorithmic parameter exploration set and/or image set.
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<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</h1>
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GWE is being enhanced with a XPath parser which allows it to introspect any XML file. This will allow GWE to read structured data from standard catalogs by creating the appropriate XPath expressions to query for this data. In that sense, for this project, we will need to:
 +
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* Identify standard (industry/community) XML types of catalogs that can describe an "experiment".
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* Gather their XML schema and the knowledge on how to interpret its data to map to an "experiment".
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* Generate the XPath expressions necessary to query the desired data from XML files conforming to those schemas.
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* Create GWE function(s)/macro(s) to translate these catalogs into "experiment" descriptors (P2EL) for GWE to run.
  
 
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<h1>Progress</h1>
 
<h1>Progress</h1>
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Right now we are testing a rudimentary study case to run Slicer's bspline deformable registration of a hardcoded fixed image against images from the OASIS database which identifiers are read from this file:
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http://www.gridwizardenterprise.org/test/oasis-id.xcat
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With a P2EL command that looks like this (using features not yet released as of 12/18/08; but will be released before 01/05/09):
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<pre>
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${ITER}=$const(5,10,20) ${HIST}=$range(20,100,010) ${SAM}=$range(500,5000,200)
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${FIX}=$oasis(0101,1)
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${MOV}=$oasis_xcat(http://www.gridwizardenterprise.org/test/oasis-id.xcat)
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${BSPLINE}=$bspline(${SLICER_HOME},${ITER},${HIST},${SAM})
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${OUT}=$uploadHDR(${SYSTEM.USER_HOME}/res-${FIX_ID}/${BSPLINE_EXPLORATION_ID}/out-${MOV_OASIS_ID})
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${BSPLINE_CMD} ${OUT_HDR} ${FIX_HDR} ${MOV_OASIS_HDR}
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</pre>
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A new topic has been created with the XNAT discussion group to gather any standards they may have to offer:
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http://groups.google.com/group/xnat_discussion/browse_thread/thread/93d6e2643a46a0b6#
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Revision as of 20:09, 18 December 2008

Home < 2009 Winter Project Week GWE Catalogs
Return to Project Week Main Page



Key Investigators

  • UCSD: Marco Ruiz


Objective

To integrate Grid Wizard Enterprise (GWE) with XML based catalogs containing a description "experiments". An "experiment" is a set of inter-independent process runs of a particular algorithm over a collection of parameters which can include algorithmic parameter exploration set and/or image set.

Approach, Plan

GWE is being enhanced with a XPath parser which allows it to introspect any XML file. This will allow GWE to read structured data from standard catalogs by creating the appropriate XPath expressions to query for this data. In that sense, for this project, we will need to:

  • Identify standard (industry/community) XML types of catalogs that can describe an "experiment".
  • Gather their XML schema and the knowledge on how to interpret its data to map to an "experiment".
  • Generate the XPath expressions necessary to query the desired data from XML files conforming to those schemas.
  • Create GWE function(s)/macro(s) to translate these catalogs into "experiment" descriptors (P2EL) for GWE to run.

Progress

Right now we are testing a rudimentary study case to run Slicer's bspline deformable registration of a hardcoded fixed image against images from the OASIS database which identifiers are read from this file:

http://www.gridwizardenterprise.org/test/oasis-id.xcat

With a P2EL command that looks like this (using features not yet released as of 12/18/08; but will be released before 01/05/09): 

${ITER}=$const(5,10,20) ${HIST}=$range(20,100,010) ${SAM}=$range(500,5000,200)
${FIX}=$oasis(0101,1)
${MOV}=$oasis_xcat(http://www.gridwizardenterprise.org/test/oasis-id.xcat)
${BSPLINE}=$bspline(${SLICER_HOME},${ITER},${HIST},${SAM})
${OUT}=$uploadHDR(${SYSTEM.USER_HOME}/res-${FIX_ID}/${BSPLINE_EXPLORATION_ID}/out-${MOV_OASIS_ID})
${BSPLINE_CMD} ${OUT_HDR} ${FIX_HDR} ${MOV_OASIS_HDR}

A new topic has been created with the XNAT discussion group to gather any standards they may have to offer:

http://groups.google.com/group/xnat_discussion/browse_thread/thread/93d6e2643a46a0b6#



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