public RigidRegistration(sitk.Image fixedImage, sitk.Image movingImage, RegistrationParameters parameters) : base(parameters)
{
this.fixedImage = ImageUtils.CastImageToFloat32(fixedImage);
this.movingImage = ImageUtils.CastImageToFloat32(movingImage);
this.registrationParameters = parameters;
elastix = new sitk.ElastixImageFilter();
if (parameterMap == null)
{
parameterMap = RegistrationUtils.GetDefaultParameterMap(parameters.RegistrationDefaultParams);
}
// set output dir
outputDirectory = Path.Combine(registrationParameters.OutputDirectory, registrationParameters.Iteration.ToString());
if (!Directory.Exists(outputDirectory))
{
Directory.CreateDirectory(outputDirectory);
}
elastix.SetOutputDirectory(outputDirectory);
//elastix.SetLogFileName(Path.Combine(outputDirectory, registrationParameters.ElastixLogFileName));
elastix.LogToFileOn();
//base.SetGeneralParameters();
}
public MultipleParameterFileRegistration(sitk.Image fixedImage, sitk.Image movingImage, RegistrationParameters parameters) : base(parameters)
{
this.fixedImage = ImageUtils.CastImageToFloat32(fixedImage);
this.movingImage = ImageUtils.CastImageToFloat32(movingImage);
elastix = new sitk.ElastixImageFilter();
for (int i = 0; i < parameters.ParameterFiles.Count; i++)
{
if (i == 0)
{
elastix.SetParameterMap(elastix.ReadParameterFile(parameters.ParameterFiles[i]));
}
else
{
elastix.AddParameterMap(elastix.ReadParameterFile(parameters.ParameterFiles[i]));
}
}
// set output dir
outputDirectory = Path.Combine(registrationParameters.OutputDirectory, "multiple_" + DateTime.Now.ToShortDateString());
if (!Directory.Exists(outputDirectory))
{
Directory.CreateDirectory(outputDirectory);
}
elastix.SetOutputDirectory(outputDirectory);
//elastix.SetLogFileName(Path.Combine(outputDirectory, registrationParameters.ElastixLogFileName));
elastix.LogToFileOn();
}
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();
}