itk::Object::Pointer QmitkAffineTransformView::GetTransform2(itk::Image<TPixelType, VImageDimension>* /*itkImage1*/)
{
typedef typename itk::Image< TPixelType, VImageDimension > FixedImageType;
typedef typename itk::Image< TPixelType, VImageDimension > MovingImageType;
typename FixedImageType::Pointer fixedImage;
mitk::CastToItkImage(m_FixedImage, fixedImage);
typename MovingImageType::Pointer movingImage;
mitk::CastToItkImage(m_MovingImage, movingImage);
typename itk::AffineTransform< double, VImageDimension>::Pointer transformPointer = itk::AffineTransform< double, VImageDimension>::New();
transformPointer->SetIdentity();
if (m_Controls.m_CenterForInitializerAffine->isChecked())
{
typedef typename itk::AffineTransform< double, VImageDimension > AffineTransformType;
typedef typename itk::CenteredTransformInitializer<AffineTransformType, FixedImageType, MovingImageType> TransformInitializerType;
typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New();
transformInitializer->SetFixedImage( fixedImage );
transformInitializer->SetMovingImage( movingImage );
transformInitializer->SetTransform( transformPointer );
if (m_Controls.m_MomentsAffine->isChecked())
{
transformInitializer->MomentsOn();
}
else
{
transformInitializer->GeometryOn();
}
transformInitializer->InitializeTransform();
}
m_CenterX = transformPointer->GetCenter()[0];
m_CenterY = transformPointer->GetCenter()[1];
m_CenterZ = transformPointer->GetCenter()[2];
m_TransformObject = transformPointer.GetPointer();
return transformPointer.GetPointer();
}
itk::Object::Pointer QmitkVersorRigid3DTransformView::GetTransform2(itk::Image<TPixelType, VImageDimension>* itkImage1)
{
if (VImageDimension == 3)
{
typedef typename itk::Image< TPixelType, 3 > FixedImage3DType;
typedef typename itk::Image< TPixelType, 3 > MovingImage3DType;
// the fixedImage is the input parameter (fix for Bug #14626)
typename FixedImage3DType::Pointer fixedImage = itkImage1;
// the movingImage type is known, use the ImageToItk filter (fix for Bug #14626)
typename mitk::ImageToItk<MovingImage3DType>::Pointer movingImageToItk = mitk::ImageToItk<MovingImage3DType>::New();
movingImageToItk->SetInput(m_MovingImage);
movingImageToItk->Update();
typename MovingImage3DType::Pointer movingImage = movingImageToItk->GetOutput();
typename itk::VersorRigid3DTransform< double >::Pointer transformPointer = itk::VersorRigid3DTransform< double >::New();
transformPointer->SetIdentity();
typedef typename itk::VersorRigid3DTransform< double > VersorRigid3DTransformType;
if (m_Controls.m_CenterForInitializerVersorRigid3D->isChecked())
{
typedef typename itk::CenteredTransformInitializer<VersorRigid3DTransformType, FixedImage3DType, MovingImage3DType> TransformInitializerType;
typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New();
transformInitializer->SetFixedImage( fixedImage );
transformInitializer->SetMovingImage( movingImage );
transformInitializer->SetTransform( transformPointer );
if (m_Controls.m_MomentsVersorRigid3D->isChecked())
{
transformInitializer->MomentsOn();
}
else
{
transformInitializer->GeometryOn();
}
transformInitializer->InitializeTransform();
}
typedef VersorRigid3DTransformType::VersorType VersorType;
typedef VersorType::VectorType VectorType;
VersorType rotation;
VectorType axis;
axis[0] = 0.0;
axis[1] = 0.0;
axis[2] = 1.0;
const double angle = 0;
rotation.Set( axis, angle );
transformPointer->SetRotation( rotation );
m_CenterX = transformPointer->GetCenter()[0];
m_CenterY = transformPointer->GetCenter()[1];
m_CenterZ = transformPointer->GetCenter()[2];
m_TransformObject = transformPointer.GetPointer();
return transformPointer.GetPointer();
}
return NULL;
}
itk::Object::Pointer QmitkVersorRigid3DTransformView::GetTransform2(itk::Image<TPixelType, VImageDimension>* /*itkImage1*/)
{
if (VImageDimension == 3)
{
typedef typename itk::Image< TPixelType, 3 > FixedImage3DType;
typedef typename itk::Image< TPixelType, 3 > MovingImage3DType;
typename FixedImage3DType::Pointer fixedImage3D;
mitk::CastToItkImage(m_FixedImage, fixedImage3D);
typename MovingImage3DType::Pointer movingImage3D;
mitk::CastToItkImage(m_MovingImage, movingImage3D);
typename itk::VersorRigid3DTransform< double >::Pointer transformPointer = itk::VersorRigid3DTransform< double >::New();
transformPointer->SetIdentity();
typedef typename itk::VersorRigid3DTransform< double > VersorRigid3DTransformType;
if (m_Controls.m_CenterForInitializerVersorRigid3D->isChecked())
{
typedef typename itk::CenteredTransformInitializer<VersorRigid3DTransformType, FixedImage3DType, MovingImage3DType> TransformInitializerType;
typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New();
transformInitializer->SetFixedImage( fixedImage3D );
transformInitializer->SetMovingImage( movingImage3D );
transformInitializer->SetTransform( transformPointer );
if (m_Controls.m_MomentsVersorRigid3D->isChecked())
{
transformInitializer->MomentsOn();
}
else
{
transformInitializer->GeometryOn();
}
transformInitializer->InitializeTransform();
}
typedef VersorRigid3DTransformType::VersorType VersorType;
typedef VersorType::VectorType VectorType;
VersorType rotation;
VectorType axis;
axis[0] = 0.0;
axis[1] = 0.0;
axis[2] = 1.0;
const double angle = 0;
rotation.Set( axis, angle );
transformPointer->SetRotation( rotation );
m_CenterX = transformPointer->GetCenter()[0];
m_CenterY = transformPointer->GetCenter()[1];
m_CenterZ = transformPointer->GetCenter()[2];
m_TransformObject = transformPointer.GetPointer();
return transformPointer.GetPointer();
}
return NULL;
}
itk::Object::Pointer QmitkCenteredRigid2DTransformView::GetTransform2(
itk::Image<TPixelType, VImageDimension> *itkImage1)
{
if (VImageDimension == 2)
{
typedef typename itk::Image<TPixelType, 2> FixedImage2DType;
typedef typename itk::Image<TPixelType, 2> MovingImage2DType;
// the fixedImage is the input parameter (fix for Bug #14626)
typename FixedImage2DType::Pointer fixedImage2D = itkImage1;
// the movingImage type is known, use the ImageToItk filter (fix for Bug #14626)
typename mitk::ImageToItk<MovingImage2DType>::Pointer movingImageToItk = mitk::ImageToItk<MovingImage2DType>::New();
movingImageToItk->SetInput(m_MovingImage);
movingImageToItk->Update();
typename MovingImage2DType::Pointer movingImage2D = movingImageToItk->GetOutput();
typename itk::CenteredRigid2DTransform<double>::Pointer transformPointer =
itk::CenteredRigid2DTransform<double>::New();
transformPointer->SetIdentity();
if (m_Controls.m_CenterForInitializerCenteredRigid2D->isChecked())
{
typedef typename itk::CenteredRigid2DTransform<double> CenteredRigid2DTransformType;
typedef
typename itk::CenteredTransformInitializer<CenteredRigid2DTransformType, FixedImage2DType, MovingImage2DType>
TransformInitializerType;
typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New();
transformInitializer->SetFixedImage(fixedImage2D);
transformInitializer->SetMovingImage(movingImage2D);
transformInitializer->SetTransform(transformPointer);
if (m_Controls.m_MomentsCenteredRigid2D->isChecked())
{
transformInitializer->MomentsOn();
}
else
{
transformInitializer->GeometryOn();
}
transformInitializer->InitializeTransform();
}
transformPointer->SetAngle(m_Controls.m_AngleCenteredRigid2D->text().toFloat());
m_CenterX = transformPointer->GetCenter()[0];
m_CenterY = transformPointer->GetCenter()[1];
m_TransformObject = transformPointer.GetPointer();
return transformPointer.GetPointer();
}
return nullptr;
}
itk::Object::Pointer QmitkAffineTransformView::GetTransform2(itk::Image<TPixelType, VImageDimension>* itkImage1)
{
typedef typename itk::Image< TPixelType, VImageDimension > FixedImageType;
typedef typename itk::Image< TPixelType, VImageDimension > MovingImageType;
// the fixedImage is the input parameter (fix for Bug #14626)
typename FixedImageType::Pointer fixedImage = itkImage1;
// the movingImage type is known, use the ImageToItk filter (fix for Bug #14626)
typename mitk::ImageToItk<MovingImageType>::Pointer movingImageToItk = mitk::ImageToItk<MovingImageType>::New();
movingImageToItk->SetInput(m_MovingImage);
movingImageToItk->Update();
typename MovingImageType::Pointer movingImage = movingImageToItk->GetOutput();
typename itk::AffineTransform< double, VImageDimension>::Pointer transformPointer = itk::AffineTransform< double, VImageDimension>::New();
transformPointer->SetIdentity();
if (m_Controls.m_CenterForInitializerAffine->isChecked())
{
typedef typename itk::AffineTransform< double, VImageDimension > AffineTransformType;
typedef typename itk::CenteredTransformInitializer<AffineTransformType, FixedImageType, MovingImageType> TransformInitializerType;
typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New();
transformInitializer->SetFixedImage( fixedImage );
transformInitializer->SetMovingImage( movingImage );
transformInitializer->SetTransform( transformPointer );
if (m_Controls.m_MomentsAffine->isChecked())
{
transformInitializer->MomentsOn();
}
else
{
transformInitializer->GeometryOn();
}
transformInitializer->InitializeTransform();
}
m_CenterX = transformPointer->GetCenter()[0];
m_CenterY = transformPointer->GetCenter()[1];
m_CenterZ = transformPointer->GetCenter()[2];
m_TransformObject = transformPointer.GetPointer();
return transformPointer.GetPointer();
}
itk::Object::Pointer QmitkCenteredSimilarity2DTransformView::GetTransform2(itk::Image<TPixelType, VImageDimension>* /* itkImage1 */)
{
if (VImageDimension == 2)
{
typedef typename itk::Image< TPixelType, 2 > FixedImage2DType;
typedef typename itk::Image< TPixelType, 2 > MovingImage2DType;
typename FixedImage2DType::Pointer fixedImage2D;
mitk::CastToItkImage(m_FixedImage, fixedImage2D);
typename MovingImage2DType::Pointer movingImage2D;
mitk::CastToItkImage(m_MovingImage, movingImage2D);
typename itk::CenteredSimilarity2DTransform< double >::Pointer transformPointer = itk::CenteredSimilarity2DTransform< double >::New();
transformPointer->SetIdentity();
if (m_Controls.m_CenterForInitializerCenteredSimilarity2D->isChecked())
{
typedef typename itk::CenteredSimilarity2DTransform< double > CenteredSimilarity2DTransformType;
typedef typename itk::CenteredTransformInitializer<CenteredSimilarity2DTransformType, FixedImage2DType, MovingImage2DType> TransformInitializerType;
typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New();
transformInitializer->SetFixedImage( fixedImage2D );
transformInitializer->SetMovingImage( movingImage2D );
transformInitializer->SetTransform( transformPointer );
if (m_Controls.m_MomentsCenteredSimilarity2D->isChecked())
{
transformInitializer->MomentsOn();
}
else
{
transformInitializer->GeometryOn();
}
transformInitializer->InitializeTransform();
}
transformPointer->SetScale( m_Controls.m_InitialScaleCenteredSimilarity2D->text().toFloat() );
transformPointer->SetAngle( m_Controls.m_AngleCenteredSimilarity2D->text().toFloat() );
m_CenterX = transformPointer->GetCenter()[0];
m_CenterY = transformPointer->GetCenter()[1];
m_TransformObject = transformPointer.GetPointer();
return transformPointer.GetPointer();
}
return NULL;
}
itk::Object::Pointer QmitkScaleSkewVersor3DTransformView::GetTransform2(itk::Image<TPixelType, VImageDimension>* /*itkImage1*/)
{
if (VImageDimension == 3)
{
typedef typename itk::Image< TPixelType, 3 > FixedImage3DType;
typedef typename itk::Image< TPixelType, 3 > MovingImage3DType;
typename FixedImage3DType::Pointer fixedImage3D;
mitk::CastToItkImage(m_FixedImage, fixedImage3D);
typename MovingImage3DType::Pointer movingImage3D;
mitk::CastToItkImage(m_MovingImage, movingImage3D);
typename itk::ScaleSkewVersor3DTransform< double >::Pointer transformPointer = itk::ScaleSkewVersor3DTransform< double >::New();
transformPointer->SetIdentity();
if (m_Controls.m_CenterForInitializerScaleSkewVersorRigid3D->isChecked())
{
typedef typename itk::ScaleSkewVersor3DTransform< double > ScaleSkewVersor3DTransformType;
typedef typename itk::CenteredTransformInitializer<ScaleSkewVersor3DTransformType, FixedImage3DType, MovingImage3DType> TransformInitializerType;
typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New();
transformInitializer->SetFixedImage( fixedImage3D );
transformInitializer->SetMovingImage( movingImage3D );
transformInitializer->SetTransform( transformPointer );
if (m_Controls.m_MomentsScaleSkewVersorRigid3D->isChecked())
{
transformInitializer->MomentsOn();
}
else
{
transformInitializer->GeometryOn();
}
transformInitializer->InitializeTransform();
}
m_CenterX = transformPointer->GetCenter()[0];
m_CenterY = transformPointer->GetCenter()[1];
m_CenterZ = transformPointer->GetCenter()[2];
m_TransformObject = transformPointer.GetPointer();
return transformPointer.GetPointer();
}
return NULL;
}
template<class FixedImageType,class MovingImageType,class TransformType> void RegisterPair(const typename FixedImageType::Pointer & fixedImage, const typename MovingImageType::Pointer & movingImage, typename TransformType::Pointer & transform ){
typedef itk::LogImageAdaptor<FixedImageType,float> LogFixedImageType;
typedef itk::CenteredTransformInitializer< TransformType,LogFixedImageType,MovingImageType> TransformInitializerType;
typename TransformInitializerType::Pointer initializer = TransformInitializerType::New();
typename LogFixedImageType::Pointer logAdaptor=LogFixedImageType::New();
logAdaptor->SetImage(fixedImage);
initializer->SetTransform( transform );
initializer->SetFixedImage( logAdaptor );
initializer->SetMovingImage( movingImage);
initializer->MomentsOn();
initializer->InitializeTransform();
// Optimizer Type
typedef itk::VersorRigid3DTransformOptimizer OptimizerType;
//typedef itk::ConjugateGradientOptimizer OptimizerType;
// Metric Type
typedef
//itk::NormalizedMutualInformationHistogramImageToImageMetric< FixedImageType, MovingImageType >
//itk::MutualInformationImageToImageMetric<FixedImageType,MovingImageType >
//itk::GradientDifferenceImageToImageMetric<FixedImageType,MovingImageType>
itk::NormalizedCorrelationImageToImageMetric< FixedImageType, MovingImageType >
// itk::KullbackLeiblerCompareHistogramImageToImageMetric< FixedImageType, MovingImageType >
//itk::MattesMutualInformationImageToImageMetric<FixedImageType,MovingImageType>
//itk::MutualInformationHistogramImageToImageMetric<FixedImageType,MovingImageType>
//itk::MeanSquaresImageToImageMetric< FixedImageType, MovingImageType >
MetricType;
// Interpolation technique
typedef itk:: LinearInterpolateImageFunction<
MovingImageType,
double > InterpolatorType;
// Registration Method
typedef itk::ImageRegistrationMethod<
FixedImageType,
MovingImageType > RegistrationType;
typename MetricType::Pointer metric = MetricType::New();
typename OptimizerType::Pointer optimizer = OptimizerType::New();
typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
typename RegistrationType::Pointer registration = RegistrationType::New();
/******************************************************************
* Set up the optimizer.
******************************************************************/
typedef typename TransformType::VersorType VersorType;
typedef typename VersorType::VectorType VectorType;
VersorType rotation;
VectorType axis;
axis[0] = 0.0;
axis[1] = 0.0;
axis[2] = 1.0;
const double angle = 0;
rotation.Set( axis, angle );
transform->SetRotation( rotation );
registration->SetInitialTransformParameters( transform->GetParameters() );
// Software Guide : EndCodeSnippet
typedef OptimizerType::ScalesType OptimizerScalesType;
OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
const double translationScale = 1.0 / 1000.0;
optimizerScales[0] = 1.0;
optimizerScales[1] = 1.0;
optimizerScales[2] = 1.0;
optimizerScales[3] = translationScale;
optimizerScales[4] = translationScale;
optimizerScales[5] = translationScale;
optimizer->SetScales( optimizerScales );
//optimizer->SetMaximumStepLength( 0.1 );
optimizer->SetMaximumStepLength( 1);
optimizer->SetMinimumStepLength( 0.000000001 );
optimizer->SetNumberOfIterations( 10 );
optimizer->SetMinimize(true);
/******************************************************************
* Set up the metric.
******************************************************************/
//metric->SetMovingImageStandardDeviation( 1.0 );
//metric->SetFixedImageStandardDeviation( 1.0 );
//metric->SetNumberOfSpatialSamples( 50000000 );
metric->SetUseAllPixels(true);
//metric->SetFixedImageRegion( fixedImage->GetBufferedRegion() );
/******************************************************************
* Set up the registrator.
******************************************************************/
// connect up the components
registration->SetMetric( metric );
registration->SetOptimizer( optimizer );
registration->SetTransform( transform );
registration->SetFixedImage( fixedImage );
registration->SetMovingImage( movingImage );
registration->SetInterpolator( interpolator );
// transform->SetIdentity();
// // set initial parameters to identity
// typename RegistrationType::ParametersType initialParameters(
// transform->GetNumberOfParameters() );
//
// initialParameters.Fill( 0.0 );
// //initialParameters[3] = 1.0;
CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
optimizer->AddObserver( itk::IterationEvent(), observer );
try
{
registration->Update();
std::cout << "Optimizer stop condition: "
<< registration->GetOptimizer()->GetStopConditionDescription()
<< std::endl;
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
//return EXIT_FAILURE;
}
OptimizerType::ParametersType finalParameters =
registration->GetLastTransformParameters();
const double versorX = finalParameters[0];
const double versorY = finalParameters[1];
const double versorZ = finalParameters[2];
const double finalTranslationX = finalParameters[3];
const double finalTranslationY = finalParameters[4];
const double finalTranslationZ = finalParameters[5];
const unsigned int numberOfIterations = optimizer->GetCurrentIteration();
const double bestValue = optimizer->GetValue();
// Print out results
//
std::cout << std::endl << std::endl;
std::cout << "Result = " << std::endl;
std::cout << " versor X = " << versorX << std::endl;
std::cout << " versor Y = " << versorY << std::endl;
std::cout << " versor Z = " << versorZ << std::endl;
std::cout << " Translation X = " << finalTranslationX << std::endl;
std::cout << " Translation Y = " << finalTranslationY << std::endl;
std::cout << " Translation Z = " << finalTranslationZ << std::endl;
std::cout << " Iterations = " << numberOfIterations << std::endl;
std::cout << " Metric value = " << bestValue << std::endl;
}