/// <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 GetCheckerBoard(sitk.Image img01, sitk.Image img02, uint size = 0)
{
uint width = img01.GetWidth() > img02.GetWidth() ? img01.GetWidth() : img02.GetWidth();
uint height = img01.GetHeight() > img02.GetHeight() ? img01.GetHeight() : img02.GetHeight();
//Console.WriteLine(string.Format("width: Img01 [{0}] - Img02 [{1}]", img01.GetWidth(), img02.GetWidth()));
//Console.WriteLine(string.Format("height: Img01 [{0}] - Img02 [{1}]", img01.GetHeight(), img02.GetHeight()));
//Console.WriteLine(string.Format("pixel type: Img01 [{0}] - Img02 [{1}]", img01.GetPixelIDTypeAsString(), img02.GetPixelIDTypeAsString()));
sitk.Image reference = ImageUtils.ResizeImage(img01, width, height, sitk.PixelIDValueEnum.sitkFloat32);
sitk.Image transformed = ImageUtils.ResizeImage(img02, width, height, sitk.PixelIDValueEnum.sitkFloat32);
sitk.CheckerBoardImageFilter checkerBoard = new sitk.CheckerBoardImageFilter();
if (size != 0)
{
sitk.VectorUInt32 vec = new sitk.VectorUInt32();
vec.Add(size);
vec.Add(size);
checkerBoard.SetCheckerPattern(vec);
}
sitk.Image temp = checkerBoard.Execute(reference, transformed);
sitk.CastImageFilter castImageFilter = new sitk.CastImageFilter();
castImageFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkUInt8);
sitk.Image result = castImageFilter.Execute(temp);
temp.Dispose();
return(result);
}
/// <summary>
/// Write transformed file to disk.
/// </summary>
/// <param name="imagename">filename</param>
public static void WriteTransformedImage(sitk.Image img, string fullFilename)
{
sitk.CastImageFilter castImageFilter = new sitk.CastImageFilter();
castImageFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkVectorUInt8);
sitk.Image temp = castImageFilter.Execute(img);
sitk.ImageFileWriter writer = new sitk.ImageFileWriter();
writer.SetFileName(fullFilename);
writer.Execute(temp);
}
/// <summary>
/// Write transformed image to disk.
/// </summary>
/// <param name="imagename">image filename</param>
public void WriteTransformedImage(string imagename)
{
sitk.CastImageFilter castImageFilter = new sitk.CastImageFilter();
castImageFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkVectorUInt8);
sitk.Image temp = castImageFilter.Execute(transformedImage);
sitk.ImageFileWriter writer = new sitk.ImageFileWriter();
writer.SetFileName(Path.Combine(registrationParameters.OutputDirectory, imagename));
writer.Execute(temp);
}
/// <summary>
/// Set moving mask for registration process.
/// </summary>
/// <param name="movingMask">moving mask</param>
public virtual void SetMovingMask(sitk.Image movingMask)
{
try
{
sitk.CastImageFilter castImageFilter = new sitk.CastImageFilter();
castImageFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkUInt8);
this.movingMask = castImageFilter.Execute(movingMask);
} catch (Exception)
{
// ignore when mask of pixeltype uint8
}
}
/// <summary>
/// Cast image to float 32.
/// </summary>
/// <param name="img">image</param>
/// <returns>casted image</returns>
public static sitk.Image CastImageToFloat32(sitk.Image img)
{
sitk.CastImageFilter castImageFilter = new sitk.CastImageFilter();
castImageFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkVectorFloat32);
sitk.Image vector = castImageFilter.Execute(img);
sitk.VectorIndexSelectionCastImageFilter vectorFilter = new sitk.VectorIndexSelectionCastImageFilter();
sitk.Image tempImage = vectorFilter.Execute(vector, 0, sitk.PixelIDValueEnum.sitkFloat32);
castImageFilter.Dispose();
vector.Dispose();
return(tempImage);
}
public NonRigidRegistration(sitk.Image fixedImage, sitk.Image movingImage, RegistrationParameters parameters) : base(parameters)
{
// cast images to from pixel type uint to vector of float
sitk.CastImageFilter castImageFilter = new sitk.CastImageFilter();
castImageFilter.SetOutputPixelType(sitk.PixelIDValueEnum.sitkVectorFloat32);
sitk.Image vector1 = castImageFilter.Execute(fixedImage);
sitk.Image vector2 = castImageFilter.Execute(movingImage);
sitk.Image tempImage1 = TransformationUtils.GetColorChannelAsImage(vector1, ColorChannel.R);
sitk.Image tempImage2 = TransformationUtils.GetColorChannelAsImage(vector2, ColorChannel.R);
this.fixedImage = tempImage1;
this.movingImage = tempImage2;
// initiate elastix and set default registration params
elastix = new sitk.ElastixImageFilter();
if (parameterMap == null)
{
parameterMap = RegistrationUtils.GetDefaultParameterMap(parameters.RegistrationDefaultParams);
}
// coefficient map is used for penalty term
if (parameters.CoefficientMapFilename != null && parameters.NonRigidOptions == MaskedNonRigidRegistrationOptions.BsplineWithPenaltyTermAndCoefficientMap)
{
RegistrationUtils.ChangeOrAddParamIfNotExist(ref parameterMap, "DilateRigidityImages", RegistrationUtils.GetVectorString("true"));
RegistrationUtils.ChangeOrAddParamIfNotExist(ref parameterMap, "FixedRigidityImageName", RegistrationUtils.GetVectorString(parameters.CoefficientMapFilename));
}
// coefficient map is used for diffuse registration
if (parameters.CoefficientMapFilename != null && parameters.NonRigidOptions == MaskedNonRigidRegistrationOptions.DiffuseRegistration)
{
RegistrationUtils.ChangeOrAddParamIfNotExist(ref parameterMap, "UseMovingSegmentation", RegistrationUtils.GetVectorString("true"));
RegistrationUtils.ChangeOrAddParamIfNotExist(ref parameterMap, "MovingSegmentationFileName", RegistrationUtils.GetVectorString(parameters.CoefficientMapFilename));
}
// set output dir and log file
outputDirectory = Path.Combine(registrationParameters.OutputDirectory, registrationParameters.Iteration.ToString());
if (!Directory.Exists(outputDirectory))
{
Directory.CreateDirectory(outputDirectory);
}
elastix.SetOutputDirectory(outputDirectory);
elastix.SetLogFileName(outputDirectory + registrationParameters.ElastixLogFileName);
elastix.LogToConsoleOn();
}
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);
}
