<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>
  Batch Processing
  </category>
  <title>
  EMSegment BatchMake
  </title>
  <description>
  Run EMSegment Module as a batch process.
  </description>
  <version>0.1.0.$Revision: 1.1 $(alpha)</version>
  <documentation-url>http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentBatch-Documentation-3.6</documentation-url>
  <license></license>
  <contributor>Julien Jomier, Stephen Aylward, and Brad Davis at Kitware Inc.</contributor>
  <acknowledgements>This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.\nhttp://www.batchmake.org </acknowledgements>
  <parameters advanced="true">
    <label>Parameters</label>
    <description>Algorithm Parameters</description>

    <string>
      <name>parametersMRMLNodeName</name>
      <longflag>parametersMRMLNodeName</longflag>

      <description>The name of the EMSegment parameters node within the active MRML scene.  Leave blank for default.</description>

      <label>EMSegment Parameters Node Name</label>
    </string>    

    <boolean>
      <name>disableMultithreading</name>
      <longflag>disableMultithreading</longflag>
      <description>Disable multithreading.</description>
      <label>Disable Multithreading</label>
      <default>false</default>
    </boolean>

    <boolean>
      <name>verbose</name>
      <longflag>verbose</longflag>
      <description>Enable verbose output.</description>
      <label>Verbose Output</label>
      <default>false</default>
    </boolean>
  </parameters>

  <parameters>
    <label>Input Datasets</label>
    <description>Input Datasets</description>

    <file fileExtensions=".mrml">
      <name>mrmlSceneFileName</name>
      <longflag>mrmlSceneFileName</longflag>

      <description>Active MRML scene that contains EMSegment algorithm parameters.</description>

      <label>MRML Scene</label>
    </file>    
     
    <directory>
      <name>dataDir</name>
      <label>Data directory</label>
      <channel>input</channel>
      <index>0</index>
      <description>Directory where to find input images</description>
    </directory>

     <string>
      <name>DataMask</name>
      <label>Directory Mask</label>
      <default>Patient*</default>
      <longflag>dirmask</longflag>
     </string>

    <string>
      <name>Target1Mask</name>
      <label>Target 1 Mask</label>
      <default>*T1*.mha</default>
      <longflag>t1m</longflag>
     </string>
   
     <string>
      <name>Target2Mask</name>
      <label>Target 2 Mask</label>
      <default>*T2*.mha</default>
      <longflag>t2m</longflag>
     </string>
  </parameters>

  <parameters>
    <label>Output Directory</label>
    <description>Output Directory</description>

    <directory>
      <name>outputDir</name>
      <label>Output directory</label>
      <channel>output</channel>
      <index>1</index>
      <description>Directory where to put the processed images</description>
    </directory>
  </parameters>

  <parameters advanced="true">
    <label>BatchMake</label>
    <description>BatchMake specific parameters</description>
    
    <boolean>
      <name>runUsingCondor</name>
      <description>Select to run on local grid using Condor (BatchMake must have been compiled using Condor)</description>
      <label>Run using Grid/Condor</label>
      <longflag>condor</longflag> 
      <default>false</default>
    </boolean>
  </parameters>

</executable>
