/// <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();
}
}
/// <summary>
/// Execute actual transformation.
/// </summary>
/// <param name="parameterMaps">parameter maps</param>
/// <param name="channel">image channel as grayscale image</param>
/// <returns></returns>
private sitk.Image ExecuteTransform(sitk.VectorOfParameterMap parameterMaps, sitk.Image channel)
{
using (sitk.TransformixImageFilter transformix = new sitk.TransformixImageFilter())
{
transformix.SetTransformParameterMap(parameterMaps);
transformix.SetMovingImage(channel);
transformix.SetLogToConsole(true);
transformix.SetOutputDirectory(ApplicationContext.OutputPath);
return(transformix.Execute());
}
}
/// <summary>
/// Transform a pointset for given transform parameters.
/// </summary>
/// <param name="transformParameters"></param>
/// <param name="pointSetFilename"></param>
/// <param name="outputDir"></param>
/// <param name="movingImageName"></param>
public static void TransfromPointSet(List <sitk.VectorOfParameterMap> transformParameters, string pointSetFilename, string outputDir, string movingImageName = null)
{
sitk.TransformixImageFilter transformix = null;
try
{
transformix = new sitk.TransformixImageFilter();
transformix.SetTransformParameterMap(transformParameters.First());
transformix.LogToConsoleOn();
transformix.LogToFileOn();
transformix.SetLogFileName("transformix.log");
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);
}
}
}
transformix.SetFixedPointSetFileName(pointSetFilename);
transformix.SetOutputDirectory(Path.GetDirectoryName(pointSetFilename));
if (movingImageName != null)
{
sitk.Image movImg = ReadWriteUtils.ReadITKImageFromFile(movingImageName, sitk.PixelIDValueEnum.sitkFloat32);
transformix.SetMovingImage(movImg);
}
sitk.Image image = transformix.Execute();
}
catch (Exception ex)
{
Console.WriteLine(ex);
}
finally
{
transformix.Dispose();
}
}
/// <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;
}