/// <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>
/// Get filename of the inner structures mask of an image.
/// </summary>
/// <param name="filename">filename of the image</param>
/// <returns>filename of the masked image</returns>
private string GetInnerStructureSegmentationFilename(string filename)
{
string outputFilename = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\mask_" + Path.GetFileName(filename);
InnerTissueSegmentation seg = GetInnerStructureSegmentation(filename);
seg.GetOutput()[1].Save(filename);
seg.Dispose();
return(filename);
}
/// <summary>
/// Get image of the inner structures mask of an image.
/// </summary>
/// <param name="filename">filename of the image</param>
/// <returns>masked image</returns>
private sitk.Image GetInnerStructureMask(string filename)
{
string outputFilename = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\mask_" + Path.GetFileName(filename);
InnerTissueSegmentation seg = GetInnerStructureSegmentation(filename);
seg.GetOutput()[1].Save(outputFilename);
seg.Dispose();
sitk.Image mask = ReadWriteUtils.ReadITKImageFromFile(outputFilename);
return(mask);
}
private string GetWholeParticleMaskFilename(string filename)
{
string outputFilename = ReadWriteUtils.GetOutputDirectory(_parameters, _parameters.Iteration) + "\\mask_" + Path.GetFileName(filename);
Image <Bgr, byte> image = ReadWriteUtils.ReadOpenCVImageFromFile <Bgr, byte>(filename);
WholeTissueSegmentation segImage = new WholeTissueSegmentation(image, _parameters.WholeTissueSegParams);
segImage.Execute();
segImage.GetOutput().Save(outputFilename);
segImage.Dispose();
return(outputFilename);
}
/// <summary>
/// Execute transformation of rgb image.
/// </summary>
public void Execute()
{
string outputDir = ReadWriteUtils.GetOutputDirectory(registrationParameters, registrationParameters.Iteration);
if (Directory.Exists(outputDir))
{
Directory.CreateDirectory(outputDir);
}
// split rgb channels
sitk.VectorIndexSelectionCastImageFilter rgbVector = new sitk.VectorIndexSelectionCastImageFilter();
sitk.Image redChannel = rgbVector.Execute(movingImage, 0, sitk.PixelIDValueEnum.sitkFloat32);
sitk.Image greenChannel = rgbVector.Execute(movingImage, 1, sitk.PixelIDValueEnum.sitkFloat32);
sitk.Image blueChannel = rgbVector.Execute(movingImage, 2, sitk.PixelIDValueEnum.sitkFloat32);
foreach (var parameter in parameterMaps[0])
{
parameter["DefaultPixelValue"][0] = "255.0";
parameter["ResultImagePixelType"][0] = "short";
if (parameter.ContainsKey("UseBinaryFormatForTransformationParameters"))
{
parameter.Remove("UseBinaryFormatForTransformationParameters");
}
if (interpolationOrder != -1)
{
parameter["FinalBSplineInterpolationOrder"][0] = interpolationOrder.ToString();
}
else
{
parameter["FinalBSplineInterpolationOrder"][0] = "3";
}
if (parameter["Transform"][0] == "SimilarityTransform" ||
registrationParameters.RegistrationDefaultParams == RegistrationDefaultParameters.similarity)
{
sitk.VectorString vec = new sitk.VectorString();
vec.Add((registrationParameters.LargestImageWidth / 2).ToString()); // fixed image width / 2
vec.Add((registrationParameters.LargestImageHeight / 2).ToString()); // fixed image height / 2
parameter.Add("CenterOfRotationPoint", vec);
}
}
// initialize transformix
transformix.SetOutputDirectory(outputDir);
transformix.SetTransformParameterMap(parameterMaps.First()[0]);
// add further transform parameters
if (parameterMaps[0].Count > 1)
{
for (int i = 1; i < parameterMaps[0].Count; i++)
{
var vectorParameterMap = parameterMaps[0][i];
transformix.AddTransformParameterMap(vectorParameterMap);
}
}
transformix.ComputeDeformationFieldOn();
transformix.LogToFileOn();
if (registrationParameters.ComputeJaccobian)
{
transformix.ComputeSpatialJacobianOn();
transformix.ComputeDeterminantOfSpatialJacobianOn();
}
transformix.PrintParameterMap();
// red
transformix.SetMovingImage(redChannel);
sitk.Image resultRedChannel = transformix.Execute();
resultRedChannel = TransformationUtils.InterpolateImage(resultRedChannel, sitk.InterpolatorEnum.sitkBSplineResamplerOrder3, sitk.PixelIDValueEnum.sitkUInt8);
//ReadWriteUtils.WriteSitkImageWithPreCast(resultRedChannel, registrationParameters.OutputDirectory + "\\red_channel.png");
// green
transformix.SetMovingImage(greenChannel);
sitk.Image resultGreenChannel = transformix.Execute();
resultGreenChannel = TransformationUtils.InterpolateImage(resultGreenChannel, sitk.InterpolatorEnum.sitkBSplineResamplerOrder3, sitk.PixelIDValueEnum.sitkUInt8);
//ReadWriteUtils.WriteSitkImageWithPreCast(resultGreenChannel, registrationParameters.OutputDirectory + "\\green_channel.png");
// blue
transformix.SetMovingImage(blueChannel);
sitk.Image resultBlueChannel = transformix.Execute();
resultBlueChannel = TransformationUtils.InterpolateImage(resultBlueChannel, sitk.InterpolatorEnum.sitkBSplineResamplerOrder3, sitk.PixelIDValueEnum.sitkUInt8);
//ReadWriteUtils.WriteSitkImageWithPreCast(resultBlueChannel, registrationParameters.OutputDirectory + "\\blue_channel.png");
// compose image channels
sitk.VectorOfImage vectorImages = new sitk.VectorOfImage();
vectorImages.Add(resultRedChannel);
vectorImages.Add(resultGreenChannel);
vectorImages.Add(resultBlueChannel);
sitk.ComposeImageFilter composeImageFilter = new sitk.ComposeImageFilter();
sitk.Image composedImage = composeImageFilter.Execute(vectorImages);
if (registrationParameters.Type == RegistrationType.NonRigid)
{
transformedImage = TransformationUtils.InterpolateImage(composedImage, sitk.InterpolatorEnum.sitkBSplineResamplerOrder5, composedImage.GetPixelID());
}
else
{
transformedImage = composedImage;
}
transformedImage = composedImage;
// interpolation of output image (needs to be improved -> currently theres a little loss in quality)
// possible solution: interpolate grayscale images and compose afterwards
/*sitk.ExpandImageFilter expandImageFilter = new sitk.ExpandImageFilter();
* expandImageFilter.SetInterpolator(sitk.InterpolatorEnum.sitkLinear);
* transformedImage = expandImageFilter.Execute(composedImage);*/
//transformedImage = composedImage;
}
