|
|
| (10 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| − | = Chain CLMs =
| + | <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").
| |
| − | | |
| − | == Jim's notes ==
| |
| − | | |
| − | = Key Investigators =
| |
| − | | |
| − | * UCSD BIRN-CC: Jeffrey Grethe, Marco Ruiz
| |
| − | * Isomics: Steve Pieper
| |
| − | * GE: Jim Miller
| |
| − | * Kitware: Will Schroeder
| |
| − | | |
| − | = Links =
| |
