void BSplineRegistration::GenerateData2( itk::Image<TPixel, VImageDimension>* itkImage1)
{
std::cout << "start bspline registration" << std::endl;
// Typedefs
typedef typename itk::Image< TPixel, VImageDimension > InternalImageType;
typedef typename itk::Vector< float, VImageDimension > VectorPixelType;
typedef typename itk::Image< VectorPixelType, VImageDimension > DeformationFieldType;
typedef itk::BSplineDeformableTransform<
double,
VImageDimension,
3 > TransformType;
typedef typename TransformType::ParametersType ParametersType;
//typedef itk::LBFGSOptimizer OptimizerType;
typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
//typedef itk::SingleValuedCostFunction MetricType;
typedef itk::MattesMutualInformationImageToImageMetric<
InternalImageType,
InternalImageType > MetricType;
typedef itk::MeanSquaresImageToImageMetric<
InternalImageType,
InternalImageType > MetricTypeMS;
typedef itk::LinearInterpolateImageFunction<
InternalImageType,
double > InterpolatorType;
typedef itk::ImageRegistrationMethod<
InternalImageType,
InternalImageType > RegistrationType;
typedef typename itk::WarpImageFilter<
InternalImageType,
InternalImageType,
DeformationFieldType > WarperType;
typedef typename TransformType::SpacingType SpacingType;
typedef typename TransformType::OriginType OriginType;
typedef itk::ResampleImageFilter<
InternalImageType,
InternalImageType > ResampleFilterType;
typedef itk::Image< TPixel, VImageDimension > OutputImageType;
// Sample new image with the same image type as the fixed image
typedef itk::CastImageFilter<
InternalImageType,
InternalImageType > CastFilterType;
typedef itk::Vector< float, VImageDimension > VectorType;
typedef itk::Image< VectorType, VImageDimension > DeformationFieldType;
typedef itk::BSplineDeformableTransformInitializer <
TransformType,
InternalImageType > InitializerType;
typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
typename RegistrationType::Pointer registration = RegistrationType::New();
typename InitializerType::Pointer initializer = InitializerType::New();
typename TransformType::Pointer transform = TransformType::New();
if(m_Metric==0 || m_Metric==1)
{
typename MetricType::Pointer metric = MetricType::New();
metric->SetNumberOfHistogramBins( 32);
metric->SetNumberOfSpatialSamples(90000);
registration->SetMetric( metric );
}
else{
typename MetricTypeMS::Pointer metric = MetricTypeMS::New();
registration->SetMetric( metric );
}
typename OptimizerFactory::Pointer optFac = OptimizerFactory::New();
optFac->SetOptimizerParameters(m_OptimizerParameters);
optFac->SetNumberOfTransformParameters(transform->GetNumberOfParameters());
OptimizerType::Pointer optimizer = optFac->GetOptimizer();
optimizer->AddObserver(itk::AnyEvent(), m_Observer);
//typedef mitk::MetricFactory <TPixel, VImageDimension> MetricFactoryType;
//typename MetricFactoryType::Pointer metricFac = MetricFactoryType::New();
//metricFac->SetMetricParameters(m_MetricParameters);
////MetricType::Pointer metric = metricFac->GetMetric();
typename InternalImageType::Pointer fixedImage = InternalImageType::New();
mitk::CastToItkImage(m_ReferenceImage, fixedImage);
typename InternalImageType::Pointer movingImage = itkImage1;
typename InternalImageType::RegionType fixedRegion = fixedImage->GetBufferedRegion();
typename InternalImageType::RegionType movingRegion = movingImage->GetBufferedRegion();
if(m_MatchHistograms)
{
typedef itk::RescaleIntensityImageFilter<InternalImageType,InternalImageType> FilterType;
typedef itk::HistogramMatchingImageFilter<InternalImageType,InternalImageType> HEFilterType;
typename FilterType::Pointer inputRescaleFilter = FilterType::New();
typename FilterType::Pointer referenceRescaleFilter = FilterType::New();
referenceRescaleFilter->SetInput(fixedImage);
inputRescaleFilter->SetInput(movingImage);
TPixel desiredMinimum = 0;
TPixel desiredMaximum = 255;
referenceRescaleFilter->SetOutputMinimum( desiredMinimum );
referenceRescaleFilter->SetOutputMaximum( desiredMaximum );
referenceRescaleFilter->UpdateLargestPossibleRegion();
inputRescaleFilter->SetOutputMinimum( desiredMinimum );
inputRescaleFilter->SetOutputMaximum( desiredMaximum );
inputRescaleFilter->UpdateLargestPossibleRegion();
// Histogram match the images
typename HEFilterType::Pointer intensityEqualizeFilter = HEFilterType::New();
intensityEqualizeFilter->SetReferenceImage( inputRescaleFilter->GetOutput() );
intensityEqualizeFilter->SetInput( referenceRescaleFilter->GetOutput() );
intensityEqualizeFilter->SetNumberOfHistogramLevels( 64 );
intensityEqualizeFilter->SetNumberOfMatchPoints( 12 );
intensityEqualizeFilter->ThresholdAtMeanIntensityOn();
intensityEqualizeFilter->Update();
//fixedImage = referenceRescaleFilter->GetOutput();
//movingImage = IntensityEqualizeFilter->GetOutput();
fixedImage = intensityEqualizeFilter->GetOutput();
movingImage = inputRescaleFilter->GetOutput();
}
//
registration->SetOptimizer( optimizer );
registration->SetInterpolator( interpolator );
registration->SetFixedImage( fixedImage );
registration->SetMovingImage( movingImage );
registration->SetFixedImageRegion(fixedRegion );
initializer->SetTransform(transform);
initializer->SetImage(fixedImage);
initializer->SetNumberOfGridNodesInsideTheImage( m_NumberOfGridPoints );
initializer->InitializeTransform();
registration->SetTransform( transform );
const unsigned int numberOfParameters = transform->GetNumberOfParameters();
typename itk::BSplineDeformableTransform<
double,
VImageDimension,
3 >::ParametersType parameters;
parameters.set_size(numberOfParameters);
parameters.Fill( 0.0 );
transform->SetParameters( parameters );
// We now pass the parameters of the current transform as the initial
// parameters to be used when the registration process starts.
registration->SetInitialTransformParameters( transform->GetParameters() );
std::cout << "Intial Parameters = " << std::endl;
std::cout << transform->GetParameters() << std::endl;
std::cout << std::endl << "Starting Registration" << std::endl;
try
{
double tstart(clock());
registration->StartRegistration();
double time = clock() - tstart;
time = time / CLOCKS_PER_SEC;
MITK_INFO << "Registration time: " << time;
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
}
typename OptimizerType::ParametersType finalParameters =
registration->GetLastTransformParameters();
std::cout << "Last Transform Parameters" << std::endl;
std::cout << finalParameters << std::endl;
transform->SetParameters( finalParameters );
/*
ResampleFilterType::Pointer resampler = ResampleFilterType::New();
resampler->SetTransform( transform );
resampler->SetInput( movingImage );
resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
resampler->SetOutputOrigin( fixedImage->GetOrigin() );
resampler->SetOutputSpacing( fixedImage->GetSpacing() );
resampler->SetOutputDirection( fixedImage->GetDirection() );
resampler->SetDefaultPixelValue( 100 );
resampler->SetInterpolator( interpolator);
resampler->Update();*/
// Generate deformation field
typename DeformationFieldType::Pointer field = DeformationFieldType::New();
field->SetRegions( movingRegion );
field->SetOrigin( movingImage->GetOrigin() );
field->SetSpacing( movingImage->GetSpacing() );
field->SetDirection( movingImage->GetDirection() );
field->Allocate();
typedef itk::ImageRegionIterator< DeformationFieldType > FieldIterator;
FieldIterator fi( field, movingRegion );
fi.GoToBegin();
typename TransformType::InputPointType fixedPoint;
typename TransformType::OutputPointType movingPoint;
typename DeformationFieldType::IndexType index;
VectorType displacement;
while( ! fi.IsAtEnd() )
{
index = fi.GetIndex();
field->TransformIndexToPhysicalPoint( index, fixedPoint );
movingPoint = transform->TransformPoint( fixedPoint );
displacement = movingPoint - fixedPoint;
fi.Set( displacement );
++fi;
}
// Use the deformation field to warp the moving image
typename WarperType::Pointer warper = WarperType::New();
warper->SetInput( movingImage );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( movingImage->GetSpacing() );
warper->SetOutputOrigin( movingImage->GetOrigin() );
warper->SetOutputDirection( movingImage->GetDirection() );
warper->SetDeformationField( field );
warper->Update();
typename InternalImageType::Pointer result = warper->GetOutput();
if(m_UpdateInputImage)
{
Image::Pointer outputImage = this->GetOutput();
mitk::CastToMitkImage( result, outputImage );
}
// Save the deformationfield resulting from the registration
if(m_SaveDeformationField)
{
typedef itk::ImageFileWriter< DeformationFieldType > FieldWriterType;
typename FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
fieldWriter->SetInput( field );
fieldWriter->SetFileName( m_DeformationFileName );
try
{
fieldWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << std::endl;
std::cerr << excp << std::endl;
//return EXIT_FAILURE;
}
}
}
void DemonsRegistration::GenerateData2(const itk::Image<TPixel, VImageDimension>* itkImage1)
{
typedef typename itk::Image< TPixel, VImageDimension > FixedImageType;
typedef typename itk::Image< TPixel, VImageDimension > MovingImageType;
typedef float InternalPixelType;
typedef typename itk::Image< InternalPixelType, VImageDimension > InternalImageType;
typedef typename itk::CastImageFilter< FixedImageType,
InternalImageType > FixedImageCasterType;
typedef typename itk::CastImageFilter< MovingImageType,
InternalImageType > MovingImageCasterType;
typedef typename itk::Image< InternalPixelType, VImageDimension > InternalImageType;
typedef typename itk::Vector< float, VImageDimension > VectorPixelType;
typedef typename itk::Image< VectorPixelType, VImageDimension > DeformationFieldType;
typedef typename itk::DemonsRegistrationFilter<
InternalImageType,
InternalImageType,
DeformationFieldType> RegistrationFilterType;
typedef typename itk::WarpImageFilter<
MovingImageType,
MovingImageType,
DeformationFieldType > WarperType;
typedef typename itk::LinearInterpolateImageFunction<
MovingImageType,
double > InterpolatorType;
typedef TPixel OutputPixelType;
typedef typename itk::Image< OutputPixelType, VImageDimension > OutputImageType;
typedef typename itk::CastImageFilter<
MovingImageType,
OutputImageType > CastFilterType;
typedef typename itk::ImageFileWriter< OutputImageType > WriterType;
typedef typename itk::ImageFileWriter< DeformationFieldType > FieldWriterType;
typename FixedImageType::Pointer fixedImage = FixedImageType::New();
mitk::CastToItkImage(m_ReferenceImage, fixedImage);
typename MovingImageType::ConstPointer movingImage = itkImage1;
if (fixedImage.IsNotNull() && movingImage.IsNotNull())
{
typename RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
this->AddStepsToDo(4);
typename itk::ReceptorMemberCommand<DemonsRegistration>::Pointer command = itk::ReceptorMemberCommand<DemonsRegistration>::New();
command->SetCallbackFunction(this, &DemonsRegistration::SetProgress);
filter->AddObserver( itk::IterationEvent(), command );
typename FixedImageCasterType::Pointer fixedImageCaster = FixedImageCasterType::New();
fixedImageCaster->SetInput(fixedImage);
filter->SetFixedImage( fixedImageCaster->GetOutput() );
typename MovingImageCasterType::Pointer movingImageCaster = MovingImageCasterType::New();
movingImageCaster->SetInput(movingImage);
filter->SetMovingImage(movingImageCaster->GetOutput());
filter->SetNumberOfIterations( m_Iterations );
filter->SetStandardDeviations( m_StandardDeviation );
filter->Update();
typename WarperType::Pointer warper = WarperType::New();
typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
warper->SetInput( movingImage );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( fixedImage->GetSpacing() );
warper->SetOutputOrigin( fixedImage->GetOrigin() );
warper->SetOutputDirection( fixedImage->GetDirection());
warper->SetDisplacementField( filter->GetOutput() );
warper->Update();
Image::Pointer outputImage = this->GetOutput();
mitk::CastToMitkImage( warper->GetOutput(), outputImage );
typename WriterType::Pointer writer = WriterType::New();
typename CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName( m_ResultName );
caster->SetInput( warper->GetOutput() );
writer->SetInput( caster->GetOutput() );
if(m_SaveResult)
{
writer->Update();
}
if (VImageDimension == 2)
{
typedef DeformationFieldType VectorImage2DType;
typedef typename DeformationFieldType::PixelType Vector2DType;
typename VectorImage2DType::ConstPointer vectorImage2D = filter->GetOutput();
typename VectorImage2DType::RegionType region2D = vectorImage2D->GetBufferedRegion();
typename VectorImage2DType::IndexType index2D = region2D.GetIndex();
typename VectorImage2DType::SizeType size2D = region2D.GetSize();
typedef typename itk::Vector< float, 3 > Vector3DType;
typedef typename itk::Image< Vector3DType, 3 > VectorImage3DType;
typedef typename itk::ImageFileWriter< VectorImage3DType > WriterType;
typename WriterType::Pointer writer3D = WriterType::New();
typename VectorImage3DType::Pointer vectorImage3D = VectorImage3DType::New();
typename VectorImage3DType::RegionType region3D;
typename VectorImage3DType::IndexType index3D;
typename VectorImage3DType::SizeType size3D;
index3D[0] = index2D[0];
index3D[1] = index2D[1];
index3D[2] = 0;
size3D[0] = size2D[0];
size3D[1] = size2D[1];
size3D[2] = 1;
region3D.SetSize( size3D );
region3D.SetIndex( index3D );
typename VectorImage2DType::SpacingType spacing2D = vectorImage2D->GetSpacing();
typename VectorImage3DType::SpacingType spacing3D;
spacing3D[0] = spacing2D[0];
spacing3D[1] = spacing2D[1];
spacing3D[2] = 1.0;
vectorImage3D->SetSpacing( spacing3D );
vectorImage3D->SetRegions( region3D );
vectorImage3D->Allocate();
typedef typename itk::ImageRegionConstIterator< VectorImage2DType > Iterator2DType;
typedef typename itk::ImageRegionIterator< VectorImage3DType > Iterator3DType;
Iterator2DType it2( vectorImage2D, region2D );
Iterator3DType it3( vectorImage3D, region3D );
it2.GoToBegin();
it3.GoToBegin();
Vector2DType vector2D;
Vector3DType vector3D;
vector3D[2] = 0; // set Z component to zero.
while( !it2.IsAtEnd() )
{
vector2D = it2.Get();
vector3D[0] = vector2D[0];
vector3D[1] = vector2D[1];
it3.Set( vector3D );
++it2;
++it3;
}
writer3D->SetInput( vectorImage3D );
m_DeformationField = vectorImage3D;
writer3D->SetFileName( m_FieldName );
try
{
if(m_SaveField)
{
writer3D->Update();
}
}
catch( itk::ExceptionObject & excp )
{
MITK_ERROR << excp << std::endl;
}
}
else
{
typename FieldWriterType::Pointer fieldwriter = FieldWriterType::New();
fieldwriter->SetFileName(m_FieldName);
fieldwriter->SetInput( filter->GetOutput() );
m_DeformationField = (itk::Image<itk::Vector<float, 3>,3> *)(filter->GetOutput());
if(m_SaveField)
{
fieldwriter->Update();
}
}
this->SetRemainingProgress(4);
}
}
typename TImage::Pointer modelBasedImageToImageRegistration(std::string referenceFilename,
std::string targetFilename,
typename TStatisticalModelType::Pointer model,
std::string outputDfFilename,
unsigned numberOfIterations){
typedef itk::ImageFileReader<TImage> ImageReaderType;
typedef itk::InterpolatingStatisticalDeformationModelTransform<TRepresenter, double, VImageDimension> TransformType;
typedef itk::LBFGSOptimizer OptimizerType;
typedef itk::ImageRegistrationMethod<TImage, TImage> RegistrationFilterType;
typedef itk::WarpImageFilter< TImage, TImage, TVectorImage > WarperType;
typedef itk::LinearInterpolateImageFunction< TImage, double > InterpolatorType;
typename ImageReaderType::Pointer referenceReader = ImageReaderType::New();
referenceReader->SetFileName(referenceFilename.c_str());
referenceReader->Update();
typename TImage::Pointer referenceImage = referenceReader->GetOutput();
referenceImage->Update();
typename ImageReaderType::Pointer targetReader = ImageReaderType::New();
targetReader->SetFileName(targetFilename.c_str());
targetReader->Update();
typename TImage::Pointer targetImage = targetReader->GetOutput();
targetImage->Update();
// do the fitting
typename TransformType::Pointer transform = TransformType::New();
transform->SetStatisticalModel(model);
transform->SetIdentity();
// Setting up the fitting
OptimizerType::Pointer optimizer = OptimizerType::New();
optimizer->MinimizeOn();
optimizer->SetMaximumNumberOfFunctionEvaluations(numberOfIterations);
typedef IterationStatusObserver ObserverType;
ObserverType::Pointer observer = ObserverType::New();
optimizer->AddObserver( itk::IterationEvent(), observer );
typename TMetricType::Pointer metric = TMetricType::New();
typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
typename RegistrationFilterType::Pointer registration = RegistrationFilterType::New();
registration->SetInitialTransformParameters(transform->GetParameters());
registration->SetMetric(metric);
registration->SetOptimizer( optimizer );
registration->SetTransform( transform );
registration->SetInterpolator( interpolator );
registration->SetFixedImage( targetImage );
registration->SetFixedImageRegion(targetImage->GetBufferedRegion() );
registration->SetMovingImage( referenceImage );
try {
std::cout << "Performing registration... " << std::flush;
registration->Update();
std::cout << "[done]" << std::endl;
} catch ( itk::ExceptionObject& o ) {
std::cout << "caught exception " << o << std::endl;
}
typename TVectorImage::Pointer df = model->DrawSample(transform->GetCoefficients());
// write deformation field
if(outputDfFilename.size()>0){
typename itk::ImageFileWriter<TVectorImage>::Pointer df_writer = itk::ImageFileWriter<TVectorImage>::New();
df_writer->SetFileName(outputDfFilename);
df_writer->SetInput(df);
df_writer->Update();
}
// warp reference
std::cout << "Warping reference... " << std::flush;
typename WarperType::Pointer warper = WarperType::New();
warper->SetInput(referenceImage );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( targetImage->GetSpacing() );
warper->SetOutputOrigin( targetImage->GetOrigin() );
warper->SetOutputDirection( targetImage->GetDirection() );
warper->SetDisplacementField( df );
warper->Update();
std::cout << "[done]" << std::endl;
return warper->GetOutput();
}