<?xml version="1.0" encoding="UTF-8"?>
<executable>
  <category>Legacy.Segmentation</category>
  <title>Simple Region Growing Segmentation</title>
  <description><![CDATA[A simple region growing segmentation algorithm based on intensity statistics. To create a list of fiducials (Seeds) for this algorithm, click on the tool bar icon of an arrow pointing to a sphere fiducial to enter the 'place a new object mode' and then use the Markups module. This module uses the Slicer Command Line Interface (CLI) and the ITK filters CurvatureFlowImageFilter and ConfidenceConnectedImageFilter.]]></description>
  <version>0.1.0.$Revision$(alpha)</version>
  <documentation-url>https://slicer.readthedocs.io/en/latest/user_guide/modules/simpleregiongrowingsegmentation.html</documentation-url>
  <license/>
  <contributor>Jim Miller (GE)</contributor>
  <acknowledgements><![CDATA[This command module was derived from Insight/Examples (copyright) Insight Software Consortium]]></acknowledgements>
  <parameters advanced="true">
    <label>Smoothing Parameters</label>
    <description><![CDATA[Parameters to denoise the image prior to segmenting]]></description>
    <integer>
      <name>smoothingIterations</name>
      <label>Smoothing iterations</label>
      <longflag>--smoothingIterations</longflag>
      <description><![CDATA[Number of smoothing iterations]]></description>
      <default>5</default>
    </integer>
    <double>
      <name>timestep</name>
      <label>Timestep</label>
      <longflag>--timestep</longflag>
      <description><![CDATA[Timestep for curvature flow]]></description>
      <default>0.0625</default>
      <constraints>
        <minimum>0.001</minimum>
        <maximum>1</maximum>
        <step>0.0001</step>
      </constraints>
    </double>
  </parameters>
  <parameters>
    <label>Segmentation Parameters</label>
    <description><![CDATA[Parameters to prescribe the region growing]]></description>
    <integer>
      <name>iterations</name>
      <longflag>--iterations</longflag>
      <description><![CDATA[Number of iterations of region growing]]></description>
      <label>Number of iterations</label>
      <default>5</default>
      <constraints>
        <minimum>0</minimum>
        <maximum>100</maximum>
      </constraints>
    </integer>
    <double>
      <name>multiplier</name>
      <longflag>--multiplier</longflag>
      <description><![CDATA[Number of standard deviations to include in intensity model]]></description>
      <label>Multiplier</label>
      <default>2.5</default>
      <constraints>
        <minimum>0</minimum>
        <maximum>10</maximum>
        <step>0.01</step>
      </constraints>
    </double>
    <integer>
      <name>neighborhood</name>
      <longflag>--neighborhood</longflag>
      <description><![CDATA[The radius of the neighborhood over which to calculate intensity model]]></description>
      <label>Neighborhood Radius</label>
      <default>1</default>
    </integer>
    <integer>
      <name>labelvalue</name>
      <longflag>--labelvalue</longflag>
      <description><![CDATA[The integer value (0-255) to use for the segmentation results. This will determine the color of the segmentation that will be generated by the Region growing algorithm]]></description>
      <label>Output Label Value</label>
      <default>2</default>
      <constraints>
        <minimum>1</minimum>
        <maximum>255</maximum>
      </constraints>
    </integer>
    <point multiple="true" coordinateSystem="ras">
      <name>seed</name>
      <label>Seeds</label>
      <longflag>--seed</longflag>
      <description><![CDATA[Seed point(s) for region growing]]></description>
      <default>0,0,0</default>
    </point>
  </parameters>
  <parameters>
    <label>IO</label>
    <description><![CDATA[Input/output parameters]]></description>
    <image>
      <name>inputVolume</name>
      <label>Input Volume</label>
      <channel>input</channel>
      <index>0</index>
      <description><![CDATA[Input volume to be filtered]]></description>
    </image>
    <image type="label" reference="inputVolume">
      <name>outputVolume</name>
      <label>Output Volume</label>
      <channel>output</channel>
      <index>1</index>
      <description><![CDATA[Output filtered]]></description>
    </image>
  </parameters>
</executable>
