<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category> Filtering </category>
  <title>ChangeTracker Command-line </title>
  <description>
ChangeTracker command-line module description and help. This is the new version of the command line module to reflect the changes that took place in the workflow in Slicer 3.5
  </description>
  <contributor>Andriy Fedorov, Kilian Pohl</contributor>
  <acknowledgements>Brain Science Foundation</acknowledgements>
   <parameters>
    <label>Inputs and Outputs</label>
    <description>Altorithm input and output. </description>
    <image> 
      <name>tgScan1</name>
      <label>Scan 1</label>
      <channel>input</channel>
      <longflag>scan1</longflag>
      <description>First Scan</description> 
      <default>None</default>
    </image>
    <image> 
      <name>tgScan2</name>
      <label>Scan 2</label>
      <channel>input</channel>
      <longflag>scan2</longflag>
      <description>Second Scan</description> 
      <default>None</default>
    </image>

    <transform>
      <name>scan1tfm</name>
      <label>Transform for Scan1</label>
      <channel>input</channel>
      <longflag>scan1tfm</longflag>
      <description>Optional transform to be applied to scan1 before processing</description>
    </transform>

    <transform>
      <name>scan2tfm</name>
      <label>Transform aligning Scan2 with Scan1</label>
      <channel>input</channel>
      <longflag>scan2tfm</longflag>
      <description>Transform that brings Scan2 in alignment with Scan1</description>
    </transform>

    <image type="label">
      <name>tgScan1segmented</name>
      <label>Scan 1 segmentation</label>
      <channel>input</channel>
      <longflag>scan1segmentation</longflag>
      <description>Segmentation of the structure of interest in the First Scan</description> 
      <default>None</default>
    </image>

    <image>
      <name>tgOutput</name>
      <longflag>output</longflag>
      <channel>output</channel>
      <label>Output image</label>
      <description>Result of the processing. The output depends on the selection of the termination step. If the complete workflow is run, the output will be the final analysis image. If both intensity- and deformation-based analyses are requested, only intensity-based results are saved.</description>
    </image>
    
    <directory>
      <name>tmpDirName</name>
      <longflag>--tmpdirname</longflag>
      <description>Location of the directory on disk where temporary files will be stored</description>
      <label>Temporary directory</label>
    </directory>

  </parameters> 
  <parameters> 
    <label>Parameters</label>
    <description>Algorithm Parameters</description>
    <boolean>
     <name>tgIntensityAnalysisFlag</name>
     <longflag>intensity_analysis</longflag>
     <label>Analyze Intensity Pattern</label>
     <description>Growth Metric is based on changes in the the local intensity patterns</description> 
     <default>true</default>
    </boolean>  
    <boolean>
     <name>tgDeformableAnalysisFlag</name>
     <longflag>deformable_analysis</longflag>
     <label>Analyze Deformation Map</label>
     <description>Growth Metric is based on deformation map between scan1 and scan2</description> 
     <default>true</default>
    </boolean>  
    <boolean>
      <name>saveResultsLog</name>
      <longflag>save_results_log</longflag>
      <label>Save results log</label>
      <description>If set, the results of the analysis will be saved in the working directory in the file AnalysisOutcome.log</description>
      <default>false</default>
    </boolean>
    <double-vector>
     <name>tgROIXYZ</name>
     <longflag>roi_xyz</longflag>
     <description>Center of rectangular ROI in physical space</description> 
     <label>ROI XYZ</label>
     <default>0,0,0</default>
    </double-vector> 
    <double-vector>
     <name>tgROIRadius</name>
     <longflag>roi_radius</longflag>
     <description>Radius of the rectangular ROI in physical space units</description> 
     <label>ROI Radius</label>
     <default>10,10,10</default>
   </double-vector> 
   <integer-vector> 
     <name>tgThreshold</name>
     <longflag>threshold</longflag>
     <description>Intensity threshold defining tumor in scan 1</description> 
     <label>Threshold</label>
     <default>0,0</default>
   </integer-vector> 
   <double>
     <name>tgSensitivity</name>
     <longflag>sensitivity</longflag>
     <description>Sensitivity Parameter (between 0 and 1) - only relevant for 'Analyze Intensity Pattern'</description>
     <label>Threshold</label>
     <default>0.96</default>
   </double> 
    <boolean>
     <name>tgSaveFlag</name>
     <longflag>save_data</longflag>
     <label>Save</label>
     <description>Save all intermediate results</description> 
     <default>true</default>
   </boolean>
    <boolean>
     <name>tgDebugFlag</name>
     <longflag>debug</longflag>
     <label>Debug</label>
     <description>Run in debug mode</description> 
     <default>false</default>
   </boolean>
   <integer>
     <name>TerminationStep</name>
     <longflag>terminationstep</longflag>
     <label>TerminationStep</label>
     <description>Specifies the stage of the implementation after which the code saves the output and terminates (mostly for testing purposes). 0 value instructs to run the complete analysis workflow.</description>
     <default>0</default>
   </integer>
   <integer>
     <name>ResampleChoice</name>
     <longflag>resamplechoice</longflag>
     <label>ResampleChoice</label>
     <description>The strategy for defining the voxel size to be used in the ROI resampling.</description>
     <default>2</default>
   </integer>

  </parameters>
</executable>

