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= Chain CLMs =
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<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Chain_CLMs here]</font></big>
 
 
''Goals''
 
 
 
* Create an infrastructure for Slicer3 that allows the user to create custom CLMs capable of executing a subset of predefined CLMs in a predefined sequential order.
 
* These custom CLMs must be capable to apply a user-defined argument replacement policy, before invoking a CLM. In essence the values of predefined outputs of some aggregated CLMs will be passed as inputs to other predefined aggregated CLMs (with a higher sequential execution order).
 
 
 
= Description =
 
 
 
The following is a design of an infrastructure to provide basic CLM chaining capabilities in Slicer3.
 
 
 
== Generic Chain CLM Application ==
 
 
 
* The generic chain CLM application is the engine of the infrastructure.
 
* This application takes all information regarding how to chain a list of CLM modules and carries on such tasks when required.
 
* Chaining a list of CLM modules is done by proxying to them in order to create an appropriate composite CLM descriptor and to execute the aggregated CLMs in the custom pre-configured way.
 
* A particular "Chain CLM" will be a script which internally:
 
** Invokes this generic application.
 
** Configures it with a specific fixed "Chain Descriptor".
 
* A particular "Chain CLM" script (X-ChainCLM.sh) will look like:
 
 
 
#!/bin/sh
 
java -cp slicerCLMPs.jar ChainCLMApp X-Modules.xml
 
 
 
where "X-Modules.xml" is the "Chain Descriptor" that shall be used to determine how to sequentially execute and chain the results and arguments of an ordered list of CLMs.
 
 
 
== Chain Descriptor ==
 
 
 
* This is an XML file which contains all the information necessary to deterministically proxy into CLMs and "chain them".
 
* 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" example 1:
 
 
 
<?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>
 
 
* "Chain Descriptor" example 2:
 
 
 
<?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="RicianFilterDWI"/>
 
  <module id="TensorEstimatorDTI">
 
      <argument name="inputDWI" value-ref="RicianFilterDWI.outputDWI" />
 
  </module>
 
  <module id="DiffusionScalar">
 
      <argument name="inputDTI" value-ref="TensorEstimatorDTI.outputDiffusionTensorDTI" />
 
  </module>
 
</modules>
 
 
== Internal Functionality ==
 
 
 
* Configuring the generic "ChainCLMApp" application with a specific "Chain Descriptor" allows:
 
** The generation of the appropriate CLM descriptor by tweaking the CLM descriptors of its aggregated CLMs.
 
** The sequential invocation of the aggregated CLMs with a deterministic argument replacement policy (described by the "argument" elements of the "Chain Descriptor").
 
 
 
= Key Investigators =
 
 
 
* UCSD BIRN-CC: Jeffrey Grethe, Marco Ruiz
 
* Isomics: Steve Pieper
 
* GE: Jim Miller
 
 
 
= Links =
 

Latest revision as of 17:40, 10 July 2017

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