private sitk.VectorOfParameterMap InvertTransformParameters(string parameterFilename)
{
sitk.Image fixedImage = ReadWriteUtils.ReadITKImageFromFile(registrationParameters.FixedImageFilename, sitk.PixelIDValueEnum.sitkFloat32);
sitk.ElastixImageFilter elastix = null;
try
{
// elastix manual 6.1.6: DisplacementMagnitudePenalty
elastix = new sitk.ElastixImageFilter();
elastix.SetInitialTransformParameterFileName(parameterFilename);
elastix.SetParameterMap(sitk.SimpleITK.GetDefaultParameterMap("rigid"));
elastix.SetFixedImage(fixedImage);
elastix.SetMovingImage(fixedImage);
elastix.SetParameter("HowToCombineTransforms", "Compose");
elastix.SetParameter("Metric", "DisplacementMagnitudePenalty");
elastix.SetParameter("NumberOfResolutions", "1");
elastix.Execute();
return(elastix.GetTransformParameterMap());
/*sitk.TransformixImageFilter transformix = new sitk.TransformixImageFilter();
* transformix.SetTransformParameterMap(elastix.GetTransformParameterMap());
* transformix.SetTransformParameter("InitialTransformParametersFileName", "NoInitialTransform");
* transformix.Execute();*/
}
catch (Exception ex)
{
Console.WriteLine(ex);
return(null);
} finally
{
elastix.Dispose();
fixedImage.Dispose();
}
}
/// <summary>
/// Write transformed image and deformation field to disk
/// </summary>
/// <param name="filename"></param>
/// <param name="transformparams"></param>
private void WriteTransform(string filename, List <sitk.VectorOfParameterMap> transformparams)
{
string resultFilename = ReadWriteUtils.GetOutputDirectory(_parameters) + "\\" + Path.GetFileNameWithoutExtension(filename) + ".png";
// add transform parameter map to registration parameters
if (_parameters.TransformationParameterMap.ContainsKey(resultFilename))
{
_parameters.TransformationParameterMap.Remove(resultFilename);
}
_parameters.TransformationParameterMap.Add(resultFilename, transformparams);
// read moving image from file
sitk.Image movingImageToTransform = ReadWriteUtils.ReadITKImageFromFile(filename, sitk.PixelIDValueEnum.sitkVectorUInt8);
// initialize transform instance
TransformRGB trans = new TransformRGB(movingImageToTransform, transformparams, _parameters);
if (_parameters.IsBinaryTransform)
{
// for binary reg set interpolation order to zero
trans.SetInterpolationOrder(0);
}
trans.Execute();
trans.WriteTransformedImage(resultFilename);
// write deformation field
sitk.Image deformationField = trans.GetDeformationField();
string filenameDeformationField = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\deformationField.mhd";
ReadWriteUtils.WriteSitkImage(deformationField, filenameDeformationField);
trans.Dispose();
movingImageToTransform.Dispose();
}
/// <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);
}
/// <summary>
/// Create a checkerboard image of two corresponding images.
/// </summary>
/// <param name="fImg01">image 1</param>
/// <param name="fImg02">image 2</param>
/// <param name="size">grid size of the checker boar</param>
/// <returns>checker board image</returns>
public static sitk.Image GetCheckerBoardV2(string fImg01, string fImg02, uint size = 0)
{
sitk.Image img01 = ReadWriteUtils.ReadITKImageFromFile(fImg01);
sitk.Image img02 = ReadWriteUtils.ReadITKImageFromFile(fImg02);
uint width = img01.GetWidth() > img02.GetWidth() ? img01.GetWidth() : img02.GetWidth();
uint height = img01.GetHeight() > img02.GetHeight() ? img01.GetHeight() : img02.GetHeight();
sitk.Image reference = ImageUtils.ResizeImage(img01, width, height);
sitk.Image transformed = ImageUtils.ResizeImage(img02, width, height);
sitk.CheckerBoardImageFilter checkerBoard = new sitk.CheckerBoardImageFilter();
uint lx = size;
uint ly = width / (height / size);
if (size != 0)
{
sitk.VectorUInt32 vec = new sitk.VectorUInt32();
vec.Add(ly);
vec.Add(lx);
checkerBoard.SetCheckerPattern(vec);
}
sitk.Image result = checkerBoard.Execute(reference, transformed);
img01.Dispose();
img02.Dispose();
reference.Dispose();
transformed.Dispose();
return(result);
}
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>
/// Transform a pointset for given transform parameters.
/// </summary>
/// <param name="transformParameters">transform params</param>
/// <param name="parameters">registration params</param>
/// <returns>filename of transformed point set</returns>
public static string TransfromPointSet(List <sitk.VectorOfParameterMap> transformParameters, RegistrationParameters parameters, string movingImageName = null)
{
sitk.TransformixImageFilter transformix = null;
try
{
transformix = new sitk.TransformixImageFilter();
transformix.SetTransformParameterMap(transformParameters.First());
transformix.LogToConsoleOn();
transformix.LogToFileOn();
transformix.SetLogFileName("transformix.log");
//transformix.SetLogToFile(true);
if (transformParameters.Count > 1)
{
for (int i = 1; i < transformParameters.Count; i++)
{
var vectorParameterMap = transformParameters[i];
foreach (var paramMap in vectorParameterMap.AsEnumerable())
{
transformix.AddTransformParameterMap(paramMap);
}
}
}
if (parameters.Type == RegistrationType.Rigid)
{
transformix.SetFixedPointSetFileName(parameters.FixedImagePointSetFilename);
}
else
{
transformix.SetFixedPointSetFileName(parameters.MovingImagePointSetFilename);
}
transformix.SetOutputDirectory(ReadWriteUtils.GetOutputDirectory(parameters));
//transformix.SetTransformParameter(0, "UseBinaryFormatForTransformationParameters", "true" );
var par = transformix.GetTransformParameter(0, "TransformParameters");
if (movingImageName != null)
{
sitk.Image movImg = ReadWriteUtils.ReadITKImageFromFile(movingImageName, sitk.PixelIDValueEnum.sitkFloat32);
transformix.SetMovingImage(movImg);
}
sitk.Image image = transformix.Execute();
string output = ReadWriteUtils.GetOutputDirectory(parameters) + "\\outputpoints.txt";
image.Dispose();
return(output);
}
catch (Exception ex)
{
Console.WriteLine(ex);
return(null);
} finally
{
transformix.Dispose();
}
}
private static sitk.LabelOverlapMeasuresImageFilter GetOverlapImageFilter(string mask01iFn, string mask02iFn)
{
sitk.LabelOverlapMeasuresImageFilter overlapFilter;
sitk.Image sImg01 = ReadWriteUtils.ReadITKImageFromFile(mask01iFn);
sitk.Image sImg02 = ReadWriteUtils.ReadITKImageFromFile(mask02iFn);
overlapFilter = VisualizationEvaluationUtils.GetOverlapImageFilter(sImg01, sImg02);
sImg01.Dispose();
sImg02.Dispose();
return(overlapFilter);
}
/// <summary>
/// Create a label map image for a given image.
/// </summary>
/// <param name="img">image</param>
/// <returns>label map</returns>
public static sitk.Image CreateLabelMapImage(sitk.Image img)
{
sitk.BinaryImageToLabelMapFilter binaryImageToLabel = new sitk.BinaryImageToLabelMapFilter();
sitk.Image temp = binaryImageToLabel.Execute(img);
sitk.LabelMapToLabelImageFilter labelMapToLabel = new sitk.LabelMapToLabelImageFilter();
sitk.Image result = labelMapToLabel.Execute(temp);
temp.Dispose();
return(result);
}
/// <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);
}
/// <summary>
/// Resize image by width and height and set output pixel type.
/// </summary>
/// <param name="img">input image</param>
/// <param name="width">width</param>
/// <param name="height">height</param>
/// <param name="pixelType">output pixel type</param>
/// <returns>resampled image</returns>
public static sitk.Image ResizeImage(sitk.Image img, uint width, uint height, sitk.PixelIDValueEnum pixelType)
{
sitk.VectorUInt32 vec = new sitk.VectorUInt32();
vec.Add(width);
vec.Add(height);
sitk.ResampleImageFilter resampleFilter = new sitk.ResampleImageFilter();
resampleFilter.SetSize(vec);
resampleFilter.SetOutputOrigin(img.GetOrigin());
resampleFilter.SetOutputDirection(img.GetDirection());
resampleFilter.SetOutputSpacing(img.GetSpacing());
resampleFilter.SetOutputPixelType(pixelType);
resampleFilter.SetDefaultPixelValue(255.0);
sitk.Image resultImage = resampleFilter.Execute(img);
img.Dispose();
return(resultImage);
}
/// <summary>
/// Dispose used instances.
/// </summary>
public void Dispose()
{
transformix.Dispose();
movingImage.Dispose();
transformedImage.Dispose();
}