<commit_before><?xml version="1.0" encoding="utf-8"?>
<executable>

  <category>Registration</category>
  <title>Anisotropic Diffusive Deformable Registration (TubeTK)</title>
  <description>Performs registration between images depicting sliding organs, using an anisotropic diffusive regularization.</description>
  <version>0.1.0.$Revision: 2104 $(alpha)</version>
  <documentation-url>http://public.kitware.com/Wiki/TubeTK</documentation-url>
  <license>Apache 2.0</license>
  <contributor><NAME>, Kitware</contributor>
  <acknowledgements>This work is part of the TubeTK project at Kitware</acknowledgements>

  <parameters>
    <label>Registration Parameters</label>
    <description>Parameters used for registration</description>
    <integer>
      <name>numberOfIterations</name>
      <flag>i</flag>
      <longflag>iterations</longflag>
      <label>Iterations</label>
      <channel>input</channel>
      <description>Number of iterations.</description>
      <default>20</default>
    </integer>
    <double>
      <name>timeStep</name>
      <flag>s</flag>
      <longflag>timestep</longflag>
      <label>Time Step</label>
      <channel>input</channel>
      <description>Time step duration.</description>
      <default>0.125</default>
    </double>
  </parameters>

  <parameters>
    <label>Organ Boundaries and Weights</label>
    <description>Parameters specifying organ boundaries and weighting terms</description>
    <geometry type="model">
      <name>organBoundaryFileName</name>
      <channel>input</channel>
      <label>Input Organ Boundary</label>
      <flag>b</flag>
      <longflag>organBoundary</longflag>
      <description>Filename of the organ boundary surface model.  This should be in the space of the fixed image</description>
    </geometry>
    <image type="vector">
      <name>inputNormalVectorImageFileName</name>
      <label>Input Normal Vector Image</label>
      <flag>n</flag>
      <longflag>inputNormalVectorImage</longflag>
      <channel>input</channel>
      <description>Image specifying the normal vectors.  This should be in the space of the fixed image.  Optional: supply a normal vector image or an organ boundary surface.  If both are provided, the organ boundary surface is used.</description>
    </image>
    <image>
      <name>inputWeightImageFileName</name>
      <label>Input Weight Image</label>
      <flag>w</flag>
      <longflag>inputWeightImage</longflag>
      <channel>input</channel>
      <description>Image specifying the weights between the anisotropic diffusive regularization and the diffusive regularization, typically a function of distance to the organ boundary.  This should be in the space of the fixed image.  Optional: supply a weight image or an organ boundary surface (and a lambda).  If both are provided, the organ boundary surface is used.</description>
    </image>
  </parameters>

  <parameters>
    <label>IO</label>
    <description>Input/output parameters</description>
    <transform fileExtensions=".txt" type="linear">
      <name>initialTransform</name>
      <flag>t</flag>
      <longflag>initialTransform</longflag>
      <description>Initial transform for aligning the fixed and moving image. Maps positions in the fixed coordinate frame to positions in the moving coordinate frame. Optional.</description>
      <label>Initial Transform</label>
      <channel>input</channel>
    </transform>
    <image>
      <name>fixedImageFileName</name>
      <label>Input Fixed Image</label>
      <channel>input</channel>
      <index>0</index>
      <description>Fixed image to which to register</description>
    </image>
    <image><commit_msg>ENH: We can handle linear and b-spline transforms<commit_after><?xml version="1.0" encoding="utf-8"?>
<executable>

  <category>Registration</category>
  <title>Anisotropic Diffusive Deformable Registration (TubeTK)</title>
  <description>Performs registration between images depicting sliding organs, using an anisotropic diffusive regularization.</description>
  <version>0.1.0.$Revision: 2104 $(alpha)</version>
  <documentation-url>http://public.kitware.com/Wiki/TubeTK</documentation-url>
  <license>Apache 2.0</license>
  <contributor><NAME>, Kitware</contributor>
  <acknowledgements>This work is part of the TubeTK project at Kitware</acknowledgements>

  <parameters>
    <label>Registration Parameters</label>
    <description>Parameters used for registration</description>
    <integer>
      <name>numberOfIterations</name>
      <flag>i</flag>
      <longflag>iterations</longflag>
      <label>Iterations</label>
      <channel>input</channel>
      <description>Number of iterations.</description>
      <default>20</default>
    </integer>
    <double>
      <name>timeStep</name>
      <flag>s</flag>
      <longflag>timestep</longflag>
      <label>Time Step</label>
      <channel>input</channel>
      <description>Time step duration.</description>
      <default>0.125</default>
    </double>
  </parameters>

  <parameters>
    <label>Organ Boundaries and Weights</label>
    <description>Parameters specifying organ boundaries and weighting terms</description>
    <geometry type="model">
      <name>organBoundaryFileName</name>
      <channel>input</channel>
      <label>Input Organ Boundary</label>
      <flag>b</flag>
      <longflag>organBoundary</longflag>
      <description>Filename of the organ boundary surface model.  This should be in the space of the fixed image</description>
    </geometry>
    <image type="vector">
      <name>inputNormalVectorImageFileName</name>
      <label>Input Normal Vector Image</label>
      <flag>n</flag>
      <longflag>inputNormalVectorImage</longflag>
      <channel>input</channel>
      <description>Image specifying the normal vectors.  This should be in the space of the fixed image.  Optional: supply a normal vector image or an organ boundary surface.  If both are provided, the organ boundary surface is used.</description>
    </image>
    <image>
      <name>inputWeightImageFileName</name>
      <label>Input Weight Image</label>
      <flag>w</flag>
      <longflag>inputWeightImage</longflag>
      <channel>input</channel>
      <description>Image specifying the weights between the anisotropic diffusive regularization and the diffusive regularization, typically a function of distance to the organ boundary.  This should be in the space of the fixed image.  Optional: supply a weight image or an organ boundary surface (and a lambda).  If both are provided, the organ boundary surface is used.</description>
    </image>
  </parameters>

  <parameters>
    <label>IO</label>
    <description>Input/output parameters</description>
    <transform fileExtensions=".txt">
      <name>initialTransform</name>
      <flag>t</flag>
      <longflag>initialTransform</longflag>
      <description>Initial transform for aligning the fixed and moving image. Maps positions in the fixed coordinate frame to positions in the moving coordinate frame. Optional.</description>
      <label>Initial Transform</label>
      <channel>input</channel>
    </transform>
    <image>
      <name>fixedImageFileName</name>
      <label>Input Fixed Image</label>
      <channel>input</channel>
      <index>0</index>
      <description>Fixed image to which to register</description>
    </image>
    <image>
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