<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>
  Segmentation
  </category>
  <title>
  EMSegment Simple
  </title>
  <description>
  This module is under construction.\n\nThe EMSegment Simple module provides a simplified interface to the EMSegment algorithm.  It should be used to segment new images once a parameter set has been established.  You must specify (1) the MRML scene that contains the EMSegment parameters, (2) a file that the output labelmap will be stored in, and (3) a set of target input images.\n\nThe MRML scene that contains the parameters should be generated using the EMSegment module.  A library of example parameter files is available at the wiki page.  If you have one that might be useful to others, please consider contributing it.\n\nThe result labelmap can be any file name that you want to create (e.g., SegmentationResult.mhd).\n\nYou should specify as many target images as are present in the EMSegment parameter set (e.g., 2 if the set uses an MR T1 and MR T2 image).  
  </description>
  <version>0.1.0.$Revision: 2085 $(alpha)</version>
  <documentation-url>http://wiki.na-mic.org/Wiki/index.php/Slicer3:EM</documentation-url>
  <license></license>
  <contributor>Many people and organizations have contributed to the funding, design, and development of the EMSegment algorithm and its various implementations.</contributor>

  <parameters>
    <label>Inputs and Outputs</label>
    <description>Altorithm input and output.</description>

    <file>
      <name>mrmlSceneFileName</name>
      <longflag>mrmlSceneFileName</longflag>

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

      <label>MRML Scene</label>
    </file>    

    <image type="label">
      <name>resultVolumeFileName</name>
      <longflag>resultVolumeFileName</longflag>

      <description>The file name that the segmentation result volume will be written to.</description>
      <label>Result Labelmap</label>
      <channel>output</channel>
    </image>    

    <image>
      <name>targetVolumeFileName1</name>
      <longflag>targetVolumeFileName1</longflag>

      <description>File names of target volumes (to be segmented).  The number of target images must be equal to the number of target images specified in the parameter set, and these images must be spatially aligned.</description>

      <label>Target Volume 1</label>      
      <channel>input</channel>
    </image>

    <image>
      <name>targetVolumeFileName2</name>
      <longflag>targetVolumeFileName2</longflag>

      <description>File names of target volumes (to be segmented).  The number of target images must be equal to the number of target images specified in the parameter set, and these images must be spatially aligned.</description>

      <label>Target Volume 2</label>      
      <channel>input</channel>
    </image>

    <image>
      <name>targetVolumeFileName3</name>
      <longflag>targetVolumeFileName3</longflag>

      <description>File names of target volumes (to be segmented).  The number of target images must be equal to the number of target images specified in the parameter set, and these images must be spatially aligned.</description>

      <label>Target Volume 3</label>      
      <channel>input</channel>
    </image>

    <image>
      <name>targetVolumeFileName4</name>
      <longflag>targetVolumeFileName4</longflag>

      <description>File names of target volumes (to be segmented).  The number of target images must be equal to the number of target images specified in the parameter set, and these images must be spatially aligned.</description>

      <label>Target Volume 4</label>      
      <channel>input</channel>
    </image>

    <image>
      <name>targetVolumeFileName5</name>
      <longflag>targetVolumeFileName5</longflag>

      <description>File names of target volumes (to be segmented).  The number of target images must be equal to the number of target images specified in the parameter set, and these images must be spatially aligned.</description>

      <label>Target Volume 5</label>      
      <channel>input</channel>
    </image>

  </parameters>

  <parameters advanced="true">
    <label>Parameters</label>
    <description>Algorithm Parameters</description>

    <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>

    <directory multiple="false">
      <name>intermediateResultsDirectory</name>
      <longflag>intermediateResultsDirectory</longflag>

      <description>Directory where EMSegmenter will write intermediate data (e.g., aligned atlas data).</description>
      <label>Intermediate Results Directory</label>      
      <channel>input</channel>
    </directory>

  </parameters>

</executable>

