Summer2009:Extension of the Command Line XML Syntax/Interface - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:07:36Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2009-06-25T16:40:00Z

2009-06-25T16:09:14Z

2009-06-25T15:59:29Z

2009-06-25T15:59:07Z

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@@ Line 178: / Line 178: @@
 <li>MIPAV: http://mipav.cit.nih.gov/
 <li>JIST: http://www.nitrc.org/projects/jist/
-<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
+<li>SLICER CLI: https://www.slicer.org/wiki/Slicer3:Execution_Model_Documentation
 </ul>
 </div>

@@ Line 8: / Line 8: @@
 Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
 </gallery>
 ==Key Investigators==
@@ Line 35: / Line 33: @@
 <ul>
 <li>Surveyed existing CLI interface and identified areas for extension
 <li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
 <li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
@@ Line 62: / Line 61: @@
 <li>Workflow level perspective – “sample a bunch of points” = harness level things
 <li>Ability to have variable number of output arguments and determine the number / names at RUNTIME
 </ul>

@@ Line 67: / Line 67: @@
 <ul>
 <li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
-<li><pre>
+<li>
 Adding Noise                            	edu.jhu.bme.smile.demo.AddingNoise
 Chebyshev Fitting                       	edu.jhu.bme.smile.demo.ChebyShevFitting
@@ Line 76: / Line 78: @@
 staple                                  	edu.jhu.bme.smile.demo.SmileAlgorithmDemo
 ...
-</pre>
+</pre></div>
 <li> Automated self-documenting executables
-<li><pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
+<li>
         [-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
         <arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
@@ Line 151: / Line 155: @@
 Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
 http://www.nitrc.org/projects/jist/
-</pre>
+</pre></div>
 <li> These features will be released in the next version of JIST.
 </ul>

@@ Line 67: / Line 67: @@
 <ul>
 <li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
-<li><pre width=100>
+<li><pre>
 Adding Noise                            	edu.jhu.bme.smile.demo.AddingNoise
 Chebyshev Fitting                       	edu.jhu.bme.smile.demo.ChebyShevFitting

@@ Line 67: / Line 67: @@
 <ul>
 <li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
-<li><pre>
+<li><pre width=100>
 Adding Noise                            	edu.jhu.bme.smile.demo.AddingNoise
 Chebyshev Fitting                       	edu.jhu.bme.smile.demo.ChebyShevFitting

@@ Line 161: / Line 161: @@
 <li>If we are going to address the problem of inter-communication, perhaps it would be best to develop a SIMPLE architecture agnostic XML syntax for functionality query, programmatic direction, and result response.
 <li>Started a NITRC project (FOPA - Framework for Open Programmatic Access) to develop multi-platform reference implementations. http://www.nitrc.org/projects/fopa/
-<ul>
+</ul>
 ==References==
 <ul>

@@ Line 47: / Line 47: @@
 ==Results==
-Areas for Investigation with CLI and Existing Limitations
+'''Areas for Investigation with CLI and Existing Limitations'''
 <ul>
 <li>Multiple “programs” per executable.
@@ Line 64: / Line 64: @@
 </ul>
-JIST/MIPAV->CLI Bridge
+'''JIST/MIPAV->CLI Bridge'''
 <ul>
 <li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
@@ Line 72: / Line 72: @@
 Demo3: Image Algebra                    	edu.jhu.bme.smile.demo.ImageAlgebra
 Image Arithmetic                        	edu.jhu.bme.smile.demo.ImageArithmetic
-Demo2: Generate Random Volumes          	edu.jhu.bme.smile.demo.RandomVolDemo4: Scale input image                	edu.jhu.bme.smile.demo.ScaleImageDemo
+Demo2: Generate Random Volumes          	edu.jhu.bme.smile.demo.RandomVol
 staple                                  	edu.jhu.bme.smile.demo.SmileAlgorithmDemo
 ...
@@ Line 150: / Line 151: @@
 Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
 http://www.nitrc.org/projects/jist/
 </pre>
 </ul>
 ==References==
 <ul>

@@ Line 27: / Line 27: @@
 <h3>Approach, Plan</h3>
-The XML syntax and parser implementation for the SLICER CLI interface will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
+The XML syntax and parser implementation for the SLICER command line interface (CLI) will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
 </div>
@@ Line 33: / Line 33: @@
 <h3>Progress</h3>
-To be filled in later.
+<ul>
+<li>Surveyed existing CLI interface and identified areas for extension
 </div>
@@ Line 40: / Line 45: @@
 <div style="width: 970%; float: left;">
 ==References==

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
 Image:JSIT-fig2.png|JIST Pipeline
 Image:JIST-fig3.png|Multi-Core and Grid Processing
 Image:JIST-fig1.png|MIPAV Plugins
 Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
 </gallery>