Difference between revisions of "Summer2009:Extension of the Command Line XML Syntax/Interface"

Revision as of 15:38, 25 June 2009

Home < Summer2009:Extension of the Command Line XML Syntax < Interface

JIST Pipeline
Multi-Core and Grid Processing
MIPAV Plugins
Example: Fully automatic surface, DTI, and sub-cortical analysis
Project Week Main Page

Key Investigators

Johns Hopkins/Vanderbilt: Bennett Landman
GE Research: Jim Miller
Johns Hopkins: Heba Mustufa (not attending in person)

Objective

We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

Approach, Plan

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.

Progress

Surveyed existing CLI interface and identified areas for extension
Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
Communicated with XIP team about generating a common/compatible interface layer

See detailed results below.

Results

Areas for Investigation with CLI and Existing Limitations

Multiple “programs” per executable.
De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
Report to both stdout (via xml markup) [optional]
Generalize the calling syntax --- especially the ability to control argument structure.
Allow authors to provide more meta-information about the algorithm (which may be ignored).
Enable the concept of an “ignorable” parameter which need not be understood to use the program.
Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
Provide preferred and supported format syntax for resource (file) based communication.
Ability to model dependencies between flags
Workflow level perspective – “sample a bunch of points” = harness level things
Ability to have variable number of output arguments and determine the number / names at RUNTIME

JIST/MIPAV->CLI Bridge

Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
- Adding Noise edu.jhu.bme.smile.demo.AddingNoise <il>Chebyshev Fitting edu.jhu.bme.smile.demo.ChebyShevFitting <il>Demo3: Image Algebra edu.jhu.bme.smile.demo.ImageAlgebra <il>Image Arithmetic edu.jhu.bme.smile.demo.ImageArithmetic <il>Demo2: Generate Random Volumes edu.jhu.bme.smile.demo.RandomVol <il>Demo4: Scale input image edu.jhu.bme.smile.demo.ScaleImageDemo <il>staple edu.jhu.bme.smile.demo.SmileAlgorithmDemo <il>...

Automated self-documenting executables

usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
       [-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
       <arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
       [-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
       [-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
       [-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
       [-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
       [-outExecution] [-outRegistered] [-outTransformation]
       [-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
       <arg>]

Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
Linear Registration algorithm based on FLIRT.
 -h,--help               Print this message.
 -inApply <arg>          Apply rotation [option:All|X|Y|Z] (required,
                         default=All)
 -inCoarse <arg>         Coarse angle increment [double] (required,
                         default=15.0)
 -inCost <arg>           Cost function [option:Correlation ratio|Least
                         squares|Normalized cross correlation|Normalized
                         mutual information] (required,
                         default=Correlation ratio)
 -inDegrees <arg>        Degrees of freedom [option:Rigid - 6|Global
                         rescale - 7|Specific rescale - 9|Affine - 12]
                         (required, default=Affine - 12)
 -inFine <arg>           Fine angle increment [double] (required,
                         default=6.0)
 -inInput <arg>          Input Weighted volume [file] (optional)
 -inMaximum <arg>        Maximum angle [double] (required, default=30.0)
 -inMinimum <arg>        Minimum angle [double] (required, default=-30.0)
 -inMultiple <arg>       Multiple of tolerance to bracket the minimum
                         [integer] (required, default=10)
 -inNumber <arg>         Number of iterations [integer] (required,
                         default=2)
 -inNumber2 <arg>        Number of minima from Level 8 to test at Level 4
                         [integer] (required, default=3)
 -inOutput <arg>         Output interpolation [option:Trilinear|Bspline
                         3rd order|Bspline 4th order|Cubic
                         Lagrangian|Quintic Lagrangian|Heptic
                         Lagrangian|Windowed sinc|Nearest Neighbor]
                         (required, default=Trilinear)
 -inReference <arg>      Reference Weighted volume [file] (optional)
 -inRegistration <arg>   Registration interpolation
                         [option:Trilinear|Bspline 3rd order|Bspline 4th
                         order|Cubic Lagrangian|Quintic Lagrangian|Heptic
                         Lagrangian|Windowed sinc] (required,
                         default=Trilinear)
 -inSkip <arg>           Skip multilevel search (Assume images are close
                         to alignment) [boolean] (required, default=false)
 -inSource <arg>         Source Volumes [file collection: semi-colon
                         delimited list] (required, default=)
 -inSubsample <arg>      Subsample image for speed [boolean] (required,
                         default=true)
 -inTarget <arg>         Target volume [file] (required)
 -inUse <arg>            Use the max of the min resolutions of the two
                         datasets when resampling [boolean] (required,
                         default=true)
 -outExecution           Execution Time [string] (required)
 -outRegistered          Registered Volumes [file collection: semi-colon
                         delimited list] (required, default=)
 -outTransformation      Transformation Matrix [matrix semi-colon
                         delimited rows in text] (optional)
 -outTransformation2     Transformation Matrices [file] (optional)
 -outTransformations     Transformations [file collection: semi-colon
                         delimited list] (required, default=)
 -xDir <arg>             Request Output: Processing Directory (default
                         current) [directory] (optional)
 -xFile <arg>            Request Output: Results File (default output.txt)
                         [file] (optional)

Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
http://www.nitrc.org/projects/jist/

References

MIPAV: http://mipav.cit.nih.gov/
JIST: http://www.nitrc.org/projects/jist/
SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation

Difference between revisions of "Summer2009:Extension of the Command Line XML Syntax/Interface"

Revision as of 15:38, 25 June 2009

Key Investigators

Objective

Approach, Plan

Progress

Results

References

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@@ 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
+<li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
+<li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
+<li>Communicated with XIP team about generating a common/compatible interface layer
+</ul>
+''See detailed results below.''
 </div>
@@ Line 40: / Line 45: @@
 <div style="width: 970%; float: left;">
+==Results==
+Areas for Investigation with CLI and Existing Limitations
+<ul>
+<li>Multiple “programs” per executable.
+<li>De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
+<li>Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
+<li>Report to both stdout (via xml markup) [optional]
+<li>Generalize the calling syntax --- especially the ability to control argument structure.
+<li>Allow authors to provide more meta-information about the algorithm (which may be ignored).
+<li>Enable the concept of an “ignorable” parameter which need not be understood to use the program.
+<li>Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
+<li>Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
+<li>Provide preferred and supported format syntax for resource (file) based communication.
+<li>Ability to model dependencies between flags
+<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>
+JIST/MIPAV->CLI Bridge
+<ul>
+<li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
+<ul>
+<li>Adding Noise                            	edu.jhu.bme.smile.demo.AddingNoise
+<il>Chebyshev Fitting                       	edu.jhu.bme.smile.demo.ChebyShevFitting
+<il>Demo3: Image Algebra                    	edu.jhu.bme.smile.demo.ImageAlgebra
+<il>Image Arithmetic                        	edu.jhu.bme.smile.demo.ImageArithmetic
+<il>Demo2: Generate Random Volumes          	edu.jhu.bme.smile.demo.RandomVol
+<il>Demo4: Scale input image                	edu.jhu.bme.smile.demo.ScaleImageDemo
+<il>staple                                  	edu.jhu.bme.smile.demo.SmileAlgorithmDemo
+<il>...
+</ul>
+<li> Automated self-documenting executables
+<ul>
+<li><pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
+       [-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
+       <arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
+       [-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
+       [-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
+       [-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
+       [-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
+       [-outExecution] [-outRegistered] [-outTransformation]
+       [-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
+       <arg>]
+Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
+Linear Registration algorithm based on FLIRT.
+ -h,--help               Print this message.
+ -inApply <arg>          Apply rotation [option:All|X|Y|Z] (required,
+                         default=All)
+ -inCoarse <arg>         Coarse angle increment [double] (required,
+                         default=15.0)
+ -inCost <arg>           Cost function [option:Correlation ratio|Least
+                         squares|Normalized cross correlation|Normalized
+                         mutual information] (required,
+                         default=Correlation ratio)
+ -inDegrees <arg>        Degrees of freedom [option:Rigid - 6|Global
+                         rescale - 7|Specific rescale - 9|Affine - 12]
+                         (required, default=Affine - 12)
+ -inFine <arg>           Fine angle increment [double] (required,
+                         default=6.0)
+ -inInput <arg>          Input Weighted volume [file] (optional)
+ -inMaximum <arg>        Maximum angle [double] (required, default=30.0)
+ -inMinimum <arg>        Minimum angle [double] (required, default=-30.0)
+ -inMultiple <arg>       Multiple of tolerance to bracket the minimum
+                         [integer] (required, default=10)
+ -inNumber <arg>         Number of iterations [integer] (required,
+                         default=2)
+ -inNumber2 <arg>        Number of minima from Level 8 to test at Level 4
+                         [integer] (required, default=3)
+ -inOutput <arg>         Output interpolation [option:Trilinear|Bspline
+rd order|Bspline 4th order|Cubic
+                         Lagrangian|Quintic Lagrangian|Heptic
+                         Lagrangian|Windowed sinc|Nearest Neighbor]
+                         (required, default=Trilinear)
+ -inReference <arg>      Reference Weighted volume [file] (optional)
+ -inRegistration <arg>   Registration interpolation
+                         [option:Trilinear|Bspline 3rd order|Bspline 4th
+                         order|Cubic Lagrangian|Quintic Lagrangian|Heptic
+                         Lagrangian|Windowed sinc] (required,
+                         default=Trilinear)
+ -inSkip <arg>           Skip multilevel search (Assume images are close
+                         to alignment) [boolean] (required, default=false)
+ -inSource <arg>         Source Volumes [file collection: semi-colon
+                         delimited list] (required, default=)
+ -inSubsample <arg>      Subsample image for speed [boolean] (required,
+                         default=true)
+ -inTarget <arg>         Target volume [file] (required)
+ -inUse <arg>            Use the max of the min resolutions of the two
+                         datasets when resampling [boolean] (required,
+                         default=true)
+ -outExecution           Execution Time [string] (required)
+ -outRegistered          Registered Volumes [file collection: semi-colon
+                         delimited list] (required, default=)
+ -outTransformation      Transformation Matrix [matrix semi-colon
+                         delimited rows in text] (optional)
+ -outTransformation2     Transformation Matrices [file] (optional)
+ -outTransformations     Transformations [file collection: semi-colon
+                         delimited list] (required, default=)
+ -xDir <arg>             Request Output: Processing Directory (default
+                         current) [directory] (optional)
+ -xFile <arg>            Request Output: Results File (default output.txt)
+                         [file] (optional)
+Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
+http://www.nitrc.org/projects/jist/
+</pre>
+</ul>
 ==References==