Slicer3:JavaBasedChainCLMsEngine - Revision history

Jgrethe at 15:10, 5 January 2009

2009-01-05T15:10:04Z

Cvachet: /* Real Examples */

2008-06-27T14:06:59Z

Real Examples

Cvachet: /* Real Examples */

2008-06-27T14:02:52Z

Real Examples

Mruiz at 02:50, 26 June 2008

2008-06-26T02:50:27Z

Mruiz at 16:49, 25 June 2008

2008-06-25T16:49:23Z

Mruiz at 16:46, 25 June 2008

2008-06-25T16:46:28Z

Mruiz: New page: = Java Based Chain CLMs Engine = == Introduction == * Java application which behaves as a regular Slicer3 module. * Requires as its first parameter the location of a chain descriptor. * ...

2008-06-25T16:42:13Z

New page: = Java Based Chain CLMs Engine = == Introduction == * Java application which behaves as a regular Slicer3 module. * Requires as its first parameter the location of a chain descriptor. * ...

New page

= Java Based Chain CLMs Engine =

== Introduction ==

* Java application which behaves as a regular Slicer3 module.
* Requires as its first parameter the location of a chain descriptor.
* The rest of its parameters are the usual Slicer3 modules parameters.
* This java application is currently wrapped in a shell script; which would be the actual Slicer3 chain module.
* As such this script has to be deployed in the Slicer's Plugins folder.
* This script does pre and post processing before invoking the engine and hardcodes a chain descriptor.

== Installation ==

* Unbundle the [http://www.gridwizardenterprise.org/maven/org/gwe/client/0.6.3.alpha/gwe-0.6.3.alpha-client.zip chain module engine] right under your Slicer3 installation.
* Set the environmental variable SLICER_HOME to point to your Slicer3 installation. For example:

export SLICER_HOME=~/Slicer3.2-2008-06-02-darwin-x86

* For each chain module desired create:
** A "X-Chain.xml" chain descriptor file(see "Chain Descriptor" section for details).
** A chain script module for "X-Chain.xml"; which should look like:

#!/bin/sh
# Chain Slicer Module

export GWE_HOME=`ls -d -t $SLICER_HOME/gwe-*/ | head -1`
export GWE_FAT_JAR=`ls $GWE_HOME/lib/gwe-*-fatjar.jar`
rm -fdr $SLICER_HOME/chains
mkdir $SLICER_HOME/chains
java -Xmx512m -cp $GWE_HOME/conf:$GWE_FAT_JAR org.gwe.integration.slicer.chains.ChainCLMProxyApp $SLICER_HOME/lib/Slicer3/Plugins/X-Chain.xml $@
if [ "x$1" != "x--xml" ]
then
chmod a+x $SLICER_HOME/chains/chain.sh
$SLICER_HOME/chains/chain.sh > $SLICER_HOME/chains/result.log
fi

== Chain Descriptor ==

* This is an XML file which contains all the information necessary to deterministically proxy into CLMs and:
** Build the new XML descriptor corresponding to the composition of the modules (removing chain arguments, applying namespaces, autogenerating certain values, etc.)
** Invoke them when necessary in sequential order respecting the argument piping instructions and the corresponding arguments for each modules' (using its namespaces).
* It must conform to the following schema:

<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:clm="http://www.na-mic.org/clm" targetNamespace="http://www.na-mic.org/clm" elementFormDefault="qualified">
<xs:element name="modules">
<xs:complexType>
<xs:sequence>
<xs:element name="module" type="clm:module" minOccurs="2" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:complexType name="module">
<xs:sequence>
<xs:element name="argument" type="clm:argument" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="id" type="xs:string"/>
</xs:complexType>
<xs:complexType name="argument">
<xs:attribute name="name" type="xs:string"/>
<xs:attribute name="value-ref" type="xs:string"/>
</xs:complexType>
</xs:schema>

* "Chain Descriptor" template example:

<?xml version="1.0" encoding="UTF-8"?>
<modules xmlns="http://www.na-mic.org/clm" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.na-mic.org/schemas/chainCLM.xsd">
<module id="Module1"/>
<module id="Module2">
<argument name="param2A" value-ref="Module1.param1A" />
<argument name="param2B" value-ref="Module1.param1B" />
</module>
<module id="Module3">
<argument name="param3C" value-ref="Module1.param1C" />
<argument name="param3D" value-ref="Module2.param2D" />
</module>
</modules>

== Real Examples ==

[[Image:ChainSamples-Menu.png]]

* Chaining modules GaussianBlurImageFilter and OtsuThresholdSegmentation:

<?xml version="1.0" encoding="UTF-8"?>
<modules xmlns="http://www.na-mic.org/clm" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.na-mic.org/schemas/chainCLM.xsd">
<module id="GaussianBlurImageFilter"/>
<module id="OtsuThresholdSegmentation">
<argument name="inputVolume" value-ref="GaussianBlurImageFilter.outputVolume" />
</module>
</modules>

[[Image:Chain1GeneratedUI.png]]

* Chaining modules dwiNoiseFilter, CurvatureAnisotropicDiffusion and GradientAnisotropicDiffusion:

<?xml version="1.0" encoding="UTF-8"?>
<modules xmlns="http://www.na-mic.org/clm" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.na-mic.org/schemas/chainCLM.xsd">
<module id="dwiNoiseFilter"/>
<module id="CurvatureAnisotropicDiffusion">
<argument name="inputVolume" value-ref="dwiNoiseFilter.outputVolume" />
</module>
<module id="GradientAnisotropicDiffusion">
<argument name="inputVolume" value-ref="CurvatureAnisotropicDiffusion.outputVolume" />
</module>
</modules>

[[Image:Chain2GeneratedUI.png]]

= Key Investigators =

* UCSD BIRN-CC: Marco Ruiz
* Isomics: Steve Pieper
* GE: Jim Miller

@@ Line 130: / Line 130: @@
   </modules>
-[[Image:RegionalCorticalThicknessChain.png]]
+[[Image:RegionalCorticalThicknessChain.jpg]]
 = Key Investigators =

← Older revision		Revision as of 14:02, 27 June 2008
Line 108:		Line 108:

	[[Image:Chain2GeneratedUI.png]]		[[Image:Chain2GeneratedUI.png]]
		+
		+	* Chaining modules brainsegCLP, AffineRegistration, BSplineDeformableRegistration, ResampleVolume2, CortThickCLP
		+
		+	<?xml version="1.0" encoding="UTF-8"?>
		+	<modules xmlns="http://www.na-mic.org/clm" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.na-mic.org/schemas/chainCLM.xsd">
		+	<module id="brainsegCLP"/>
		+	<module id="AffineRegistration"/>
		+	<module id="BSplineDeformableRegistration">
		+	<argument name="inputVolume" value-ref="AffineRegistration.ResampledImageFileName" />
		+	<argument name="InitialTransform" value-ref="AffineRegistration.OutputTransform" />
		+	<argument name="FixedImageFileName" value-ref="AffineRegistration.FixedImageFileName" />
		+	<argument name="MovingImageFileName" value-ref="AffineRegistration.MovingImageFileName" />
		+	</module>
		+	<module id="ResampleVolume2">
		+	<argument name="InitialTransform" value-ref="BSplineRegistration.OutputTransform" />
		+	</module>
		+	<module id="CortThickCLP">
		+	<argument name="SegmentationInput" value-ref="brainseg.SegmentationFile" />
		+	<argument name="ParcellationOption" value-ref="ResampleVolume2.outputVolume" />
		+	</module>
		+	</modules>
		+
		+	[[Image:RegionalCorticalThicknessChain.png]]

	= Key Investigators =		= Key Investigators =

← Older revision		Revision as of 16:49, 25 June 2008
Line 1:		Line 1:
−	= ~~Java Based~~ Chain CLMs Engine =	+	= Chain CLMs Engine =

	== Introduction ==		== Introduction ==

@@ Line 134: / Line 134: @@
 = Key Investigators =
-* UCSD BIRN-CC: Marco Ruiz
+* UCSD: Marco Ruiz
 * Isomics: Steve Pieper
 * GE: Jim Miller

@@ Line 18: / Line 18: @@
 * For each chain module desired create:
-** A "X-Chain.xml" chain descriptor file(see "Chain Descriptor" section for details).
+** A "X-Chain.xml" chain descriptor file to be stored under the Slicer3 "Plugins" directory (see "Chain Descriptor" section for details).
 ** A chain script module for "X-Chain.xml"; which should look like:

@@ Line 3: / Line 3: @@
 == Introduction ==
-* Java application which behaves as a regular Slicer3 module.
+* Java application which behaves as a regular Slicer3 module (JVM 1.5 or higher required).
 * Requires as its first parameter the location of a chain descriptor.
 * The rest of its parameters are the usual Slicer3 modules parameters.