/// <summary>
/// Add a parameter to the parameter map.
/// </summary>
/// <param name="parameterName">parameter key</param>
/// <param name="value">parameter value</param>
protected void AddParameter(string parameterName, sitk.VectorString value)
{
if (parameterMap.ContainsKey(parameterName))
{
parameterMap.Remove(parameterName);
}
parameterMap.Add(parameterName, value);
}
/// <summary>
/// Change or add a parameter (if param does not exist) to parameter map.
/// </summary>
/// <param name="paramMap">reference to parameter map</param>
/// <param name="key">parameter key</param>
/// <param name="value">values as a vector of strings</param>
public static void ChangeOrAddParamIfNotExist(ref sitk.ParameterMap paramMap, string key, sitk.VectorString value)
{
if (paramMap.ContainsKey(key))
{
paramMap[key] = value;
}
else
{
paramMap.Add(key, value);
}
}
/// <summary>
/// Get a default parameter map for a specific registration type.
/// </summary>
/// <param name="type">registration type</param>
/// <returns>sitk parameter map</returns>
public static sitk.ParameterMap GetDefaultParameterMap(RegistrationDefaultParameters type)
{
if ((int)type < 4)
{
// rigid registration types
if (type == RegistrationDefaultParameters.similarity)
{
sitk.ParameterMap parameterMap = GetDefaultRigidParameterMap(RegistrationDefaultParameters.translation);
parameterMap["Transform"][0] = "SimilarityTransform";
return(parameterMap);
}
else
{
return(GetDefaultRigidParameterMap(type));
}
}
else
{
// non rigid registration types
if (type == RegistrationDefaultParameters.spline ||
type == RegistrationDefaultParameters.bspline ||
type == RegistrationDefaultParameters.nonrigid)
{
return(GetDefaultNonRigidParameterMap());
}
else
{
sitk.ParameterMap parameterMap = GetDefaultNonRigidParameterMap();
if (type == RegistrationDefaultParameters.diffusion)
{
parameterMap["Transform"][0] = "BSplineTransformWithDiffusion";
// default parameters for bspline diffusion registration
parameterMap.Add("FinalGridSpacing", GetVectorString("8.0", "8.0", "8.0"));
parameterMap.Add("UpsampleGridOption", GetVectorString("true"));
parameterMap.Add("FilterPattern", GetVectorString("1"));
parameterMap.Add("DiffusionEachNIterations", GetVectorString("1"));
parameterMap.Add("AfterIterations", GetVectorString("50", "100"));
parameterMap.Add("HowManyIterations", GetVectorString("1", "5", "10"));
parameterMap.Add("NumberOfDiffusionIterations", GetVectorString("1"));
parameterMap.Add("Radius", GetVectorString("1"));
parameterMap.Add("ThresholdBool", GetVectorString("true"));
parameterMap.Add("ThresholdHU", GetVectorString("150"));
parameterMap.Add("GrayValueImageAlsoBasedOnFixedImage", GetVectorString("true"));
//parameterMap.Add("UseFixedSegmentation", GetVectorString("false"));
//parameterMap.Add("FixedSegmentationFileName", GetVectorString("filename"));
parameterMap.Add("UseMovingSegmentation", GetVectorString("false"));
parameterMap.Add("MovingSegmentationFileName", GetVectorString("filename"));
return(parameterMap);
}
else if (type == RegistrationDefaultParameters.recursive)
{
parameterMap["Transform"][0] = "RecursiveBSplineTransform";
parameterMap.Add("PassiveEdgeWidth", GetVectorString("0"));
return(parameterMap);
}
else
{
return(parameterMap);
}
}
}
}
/// <summary>
/// Create default non rigid parameter map.
/// </summary>
/// <returns>default paramerets</returns>
private static sitk.ParameterMap GetDefaultNonRigidParameterMap()
{
sitk.ParameterMap paramMap = new sitk.ParameterMap();
paramMap.Add("FixedInternalImagePixelType", GetVectorString("float"));
paramMap.Add("MovingInternalImagePixelType", GetVectorString("float"));
paramMap.Add("FixedImageDimension", GetVectorString("2"));
paramMap.Add("MovingImageDimension", GetVectorString("2"));
paramMap.Add("UseDirectionCosines", GetVectorString("true"));
paramMap.Add("Registration", GetVectorString("MultiResolutionRegistration"));
paramMap.Add("Interpolator", GetVectorString("BSplineInterpolator"));
paramMap.Add("ResampleInterpolator", GetVectorString("FinalBSplineInterpolator"));
paramMap.Add("Resampler", GetVectorString("DefaultResampler"));
paramMap.Add("FixedImagePyramid", GetVectorString("FixedRecursiveImagePyramid"));
paramMap.Add("MovingImagePyramid", GetVectorString("MovingRecursiveImagePyramid"));
paramMap.Add("Optimizer", GetVectorString("AdaptiveStochasticGradientDescent"));
paramMap.Add("Transform", GetVectorString("BSplineTransform"));
paramMap.Add("Metric", GetVectorString("AdvancedMeanSquares"));
paramMap.Add("FinalGridSpacingInPhysicalUnits", GetVectorString("16"));
paramMap.Add("GridSpacingSchedule", GetVectorString("5.0", "5.0", "4.0", "4.0", "3.0", "3.0", "2.0", "2.0", "1.0", "1.0"));
paramMap.Add("HowToCombineTransforms", GetVectorString("Compose"));
paramMap.Add("ErodeMask", GetVectorString("false"));
paramMap.Add("NumberOfResolutions", GetVectorString("5"));
paramMap.Add("MaximumNumberOfIterations", GetVectorString("1024"));
paramMap.Add("NumberOfSpatialSamples", GetVectorString("4096"));
paramMap.Add("NumberOfSamplesForExactGradient", GetVectorString("4096"));
paramMap.Add("NewSamplesEveryIteration", GetVectorString("true"));
paramMap.Add("ImageSampler", GetVectorString("Random"));
paramMap.Add("BSplineInterpolationOrder", GetVectorString("1"));
paramMap.Add("FinalBSplineInterpolationOrder", GetVectorString("3"));
paramMap.Add("DefaultPixelValue", GetVectorString("255.0"));
paramMap.Add("WriteResultImage", GetVectorString("true"));
paramMap.Add("ResultImagePixelType", GetVectorString("short"));
paramMap.Add("ResultImageFormat", GetVectorString("mhd"));
return(paramMap);
}
