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 runKernelTransform(MatlabImportFilter::Pointer matlabImport, MatlabExportFilter::Pointer matlabExport) { // check number of input arguments (the kernel transform syntax // accepts up to 4 arguments only. Thus, we cannot use InputIndexType_MAX) matlabImport->CheckNumberOfArguments(4, 4); // retrieve pointers to the inputs that we are going to need here typedef MatlabImportFilter::MatlabInputPointer MatlabInputPointer; MatlabInputPointer inX = matlabImport->GetRegisteredInput("X"); MatlabInputPointer inY = matlabImport->GetRegisteredInput("Y"); MatlabInputPointer inXI = matlabImport->GetRegisteredInput("XI"); // register the outputs for this function at the export filter typedef MatlabExportFilter::MatlabOutputPointer MatlabOutputPointer; MatlabOutputPointer outYI = matlabExport->RegisterOutput(OUT_YI, "YI"); // get size of input arguments mwSize Mx = mxGetM(inX->pm); // number of source points mwSize Mxi = mxGetM(inXI->pm); // number of points to be warped mwSize ndimxi; // number of dimension of points to be warped const mwSize *dimsxi; // dimensions vector of array of points to be warped // create pointers to input matrices TScalarType *x = (TScalarType *)mxGetData(inX->pm); // source points TScalarType *y = (TScalarType *)mxGetData(inY->pm); // target points TScalarType *xi = (TScalarType *)mxGetData(inXI->pm); // points to be warped if (x == NULL) { mexErrMsgTxt("Cannot get a pointer to input X"); } if (y == NULL) { mexErrMsgTxt("Cannot get a pointer to input Y"); } if (xi == NULL) { mexErrMsgTxt("Cannot get a pointer to input XI"); } // type definitions and variables to store points for the kernel transform typedef typename TransformType::PointSetType PointSetType; typename PointSetType::Pointer fixedPointSet = PointSetType::New(); typename PointSetType::Pointer movingPointSet = PointSetType::New(); typename PointSetType::Pointer toWarpPointSet = PointSetType::New(); typedef typename PointSetType::PointsContainer PointsContainer; typename PointsContainer::Pointer fixedPointContainer = PointsContainer::New(); typename PointsContainer::Pointer movingPointContainer = PointsContainer::New(); typedef typename PointSetType::PointType PointType; PointType fixedPoint; PointType movingPoint; PointType toWarpPoint; PointType warpedPoint; // duplicate the input x and y matrices to PointSet format so that // we can pass it to the ITK function mwSize pointId=0; for (mwSize row=0; row < Mx; ++row) { for (mwSize col=0; col < (mwSize)Dimension; ++col) { fixedPoint[CAST2MWSIZE(col)] = y[Mx * col + row]; movingPoint[CAST2MWSIZE(col)] = x[Mx * col + row]; } fixedPointContainer->InsertElement(pointId, fixedPoint); movingPointContainer->InsertElement(pointId, movingPoint); ++pointId; } fixedPointSet->SetPoints(fixedPointContainer); movingPointSet->SetPoints(movingPointContainer); // compute the transform typename TransformType::Pointer transform; transform = TransformType::New(); transform->SetSourceLandmarks(movingPointSet); transform->SetTargetLandmarks(fixedPointSet); transform->ComputeWMatrix(); // create output vector and pointer to populate it ndimxi = mxGetNumberOfDimensions(inXI->pm); dimsxi = mxGetDimensions(inXI->pm); std::vector<mwSize> size; for (mwIndex i = 0; i < ndimxi; ++i) { size.push_back(dimsxi[i]); } TScalarType *yi = matlabExport->AllocateNDArrayInMatlab<TScalarType>(outYI, size); // transform points for (mwSize row=0; row < Mxi; ++row) { for (mwSize col=0; col < (mwSize)Dimension; ++col) { toWarpPoint[CAST2MWSIZE(col)] = xi[Mxi * col + row]; } warpedPoint = transform->TransformPoint(toWarpPoint); for (mwSize col=0; col < (mwSize)Dimension; ++col) { yi[Mxi * col + row] = warpedPoint[CAST2MWSIZE(col)]; } } // exit function return; }