https://www.na-mic.org/w/index.php?action=history&feed=atom&title=Mbirn%3A_Data_Provenance%3ADocumentation%3AParsing 2026-04-19T12:46:42Z Revision history for this page on the wiki MediaWiki 1.33.0 https://www.na-mic.org/w/index.php?title=Mbirn:_Data_Provenance:Documentation:Parsing&diff=9732&oldid=prev 2007-04-25T22:08:35Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 22:08, 25 April 2007</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">''[http://132.239.132.249:8080/xwiki/bin/view/Morphometry-BIRN/mBIRN_Provenance_Main This is version 1.0, see BIRN xwiki for 2.0+]''</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Parsing of raw output'''</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Parsing of raw output'''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> </table>

Naucoin https://www.na-mic.org/w/index.php?title=Mbirn:_Data_Provenance:Documentation:Parsing&diff=4164&oldid=prev 2006-12-18T13:37:09Z

<p>Update from Wiki</p> <p><b>New page</b></p><div>'''Parsing of raw output'''<br /> <br /> The script file dataprov.tcl will parse the output from the processing script and construct a tree of information as follows:<br /> <br /> * Processing Tool1<br /> ** field: value pairs<br /> * Processing Tool2<br /> ** field: value pairs<br /> <br /> It is important that all processing tools start their data provenance output with the ProgramName flag. The rest of the flags can be in any order, but this one marks the beginning of a new tool's information.<br /> <br /> '''Processing Script'''<br /> <br /> The procesing script will call the processing steps with the --all-info flag, and the programs will print out their data provenance information to the standard output. The output of the processing script will be redirected to a file, and that file will be processed by dataprov.tcl. The following example uses a processing script that converts from a Freesurfer MGH volume to a Freesurfer COR voluem and displays it in Slicer.<br /> <br /> # convertandshow.sh<br /> mri_convert -all-info<br /> rm -rf /home/nicole/data/flash40cor<br /> mkdir /home/nicole/data/flash40cor<br /> mri_convert --out_type cor /home/nicole/data/flash40.mgh /home/nicole/data/flash40cor<br /> /extra/nicole/slicer2/slicer2-linux-x86 --no-tkcon --all-info --load-freesurfer-volume /home/nicole/data/flash40cor/COR-.info<br /> exit<br /> <br /> The script is called from another script that redirects and parses the output:<br /> <br /> # dataprov.sh<br /> convertandshow.sh &gt; /home/nicole/dataprov/convertandshow.txt<br /> dataprov.tcl /home/nicole/dataprov/convertandshow.txt<br /> <br /> Once you exit Slicer, the xml file appears on the standard output, and can be redirected to an xml file by calling the script like so:<br /> <br /> dataprov.sh &gt; dataprov.xml<br /> <br /> &lt;br /&gt;<br /> <br /> &lt;br /&gt;[[Data_Provenance:Documentation|Back]]</div>

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