/// <summary>
/// Get the coefficient map of inner structures of tissue for the transform rigidity penalty term.
/// </summary>
/// <param name="filename">image filename</param>
/// <returns>return coefficient map filename</returns>
private string GetInnerStructureSegmentationsAsCoefficientMap(string filename)
{
InnerTissueSegmentation innerSegImage = GetInnerStructureSegmentation(filename);
string filenameCoefficientMap = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + Constants.cCoefficientFilename;
ReadWriteUtils.WriteUMatToFile(filenameCoefficientMap, innerSegImage.GetOutput().FirstOrDefault());
innerSegImage.Dispose();
// rescale image
sitk.Image img = ReadWriteUtils.ReadITKImageFromFile(filenameCoefficientMap);
sitk.CastImageFilter castFilter = new sitk.CastImageFilter();
castFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkFloat32);
img = castFilter.Execute(img);
sitk.RescaleIntensityImageFilter filter = new sitk.RescaleIntensityImageFilter();
filter.SetOutputMinimum(0.0);
filter.SetOutputMaximum(1.0);
sitk.Image coefficientMap = filter.Execute(img);
// save as mhd
filenameCoefficientMap = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + Constants.cCoefficientFilename;
ReadWriteUtils.WriteSitkImage(coefficientMap, filenameCoefficientMap);
coefficientMap.Dispose();
return(filenameCoefficientMap);
}
public static sitk.Image BinaryThinning(sitk.Image inputImage)
{
sitk.VectorIndexSelectionCastImageFilter vectorIndexSelectionCastImageFilter = new sitk.VectorIndexSelectionCastImageFilter();
sitk.CastImageFilter castImageFilter = new sitk.CastImageFilter();
sitk.Image image = vectorIndexSelectionCastImageFilter.Execute(inputImage, 0, castImageFilter.GetOutputPixelType());
sitk.BinaryThresholdImageFilter binaryThresholdImageFilter = new sitk.BinaryThresholdImageFilter();
binaryThresholdImageFilter.SetInsideValue(0);
binaryThresholdImageFilter.SetOutsideValue(255);
binaryThresholdImageFilter.SetLowerThreshold(0);
binaryThresholdImageFilter.SetUpperThreshold(100);
sitk.Image binaryThresholdImage = binaryThresholdImageFilter.Execute(image);
sitk.BinaryThinningImageFilter binaryThinningImageFilter = new sitk.BinaryThinningImageFilter();
sitk.Image binaryThinningImage = binaryThinningImageFilter.Execute(binaryThresholdImage);
sitk.RescaleIntensityImageFilter rescaleIntensityImageFilter = new sitk.RescaleIntensityImageFilter();
rescaleIntensityImageFilter.SetOutputMinimum(0);
rescaleIntensityImageFilter.SetOutputMaximum(255);
sitk.Image rescaleIntensityImage = rescaleIntensityImageFilter.Execute(binaryThinningImage);
return(rescaleIntensityImage);
}
