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| <div class="floatcenter">[[File:ITK_Examples_Baseline_Registration_TestWatchRegistration.png]]</div>
| | {{warning|1=The media wiki content on this page is no longer maintained. The examples presented on the https://itk.org/Wiki/* pages likely require ITK version 4.13 or earlier releases. In many cases, the examples on this page no longer conform to the best practices for modern ITK versions.}} |
| This example uses a command observer to visualize the iterations of the registration process.
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| '''Usage:''' WatchRegistration ''fixedImage movingImage''
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| Try with these two images: [https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKWikiExamples/master/Testing/Data/BrainProtonDensitySliceBorder20.png BrainProtonDensitySliceBorder20.png] and [https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKWikiExamples/master/Testing/Data/BrainProtonDensitySliceRotated10.png BrainProtonDensitySliceRotated10.png] as follows
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| ''WatchRegistration BrainProtonDensitySliceBorder20.png BrainProtonDensitySliceRotated10.png''
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| ==WatchRegistration.cxx==
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| <source lang="cpp">
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| #include "itkImageRegistrationMethod.h"
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| #include "itkAffineTransform.h"
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| #include "itkMattesMutualInformationImageToImageMetric.h"
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| #include "itkRegularStepGradientDescentOptimizer.h"
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| #include "itkNormalizeImageFilter.h"
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| #include "itkDiscreteGaussianImageFilter.h"
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| #include "itkResampleImageFilter.h"
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| #include "itkCheckerBoardImageFilter.h"
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| #include "itkFlipImageFilter.h"
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| #include "itkImageFileReader.h"
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| #include "itkImageToVTKImageFilter.h"
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| #include "itkCenteredTransformInitializer.h"
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| #include "vtkVersion.h"
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| #include "vtkSmartPointer.h"
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| #include "vtkRenderWindow.h"
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| #include "vtkRenderer.h"
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| #include "vtkInteractorStyleImage.h"
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| #include "vtkRenderWindowInteractor.h"
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| #include "vtkImageActor.h"
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| #include "vtkImageMapper3D.h"
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| | |
| const unsigned int Dimension = 2;
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| typedef unsigned char PixelType;
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| | |
| typedef itk::Image< PixelType, Dimension > InputImageType;
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| typedef itk::Image< unsigned char, Dimension > OutputImageType;
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| | |
| // Command observer to visualize the evolution of the registration process.
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| //
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| #include "itkCommand.h"
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| template< typename TImage >
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| class IterationUpdate : public itk::Command
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| { | |
| public:
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| typedef IterationUpdate Self;
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| typedef itk::Command Superclass;
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| typedef itk::SmartPointer<Self> Pointer;
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| itkNewMacro( Self );
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| | |
| protected:
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| IterationUpdate() {};
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| | |
| public:
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| typedef itk::Image< float, 2> InternalImageType;
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| typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
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| typedef const OptimizerType * OptimizerPointer;
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| typedef itk::ResampleImageFilter<
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| TImage,
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| TImage > ResampleFilterType;
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| typedef itk::AffineTransform< double, 2 > TransformType;
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| typedef itk::ImageToVTKImageFilter<TImage > ConnectorType;
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| typedef itk::FlipImageFilter<TImage> FilterType;
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| void Execute(itk::Object *caller, const itk::EventObject & event) ITK_OVERRIDE
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| {
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| Execute( (const itk::Object *) caller, event);
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| }
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| | |
| void Execute(const itk::Object * object, const itk::EventObject & event) ITK_OVERRIDE
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| {
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| OptimizerPointer optimizer = static_cast< OptimizerPointer >( object );
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| if( !(itk::IterationEvent().CheckEvent( &event )) )
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| {
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| return;
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| }
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| | |
| m_Transform->SetParameters(optimizer->GetCurrentPosition());
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| m_Filter->Update();
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| m_Connector->SetInput(m_Filter->GetOutput());
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| m_Connector->Update();
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| | |
| #if VTK_MAJOR_VERSION <= 5
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| m_ImageActor->SetInput(m_Connector->GetOutput());
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| #else
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| m_Connector->Update();
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| m_ImageActor->GetMapper()->SetInputData(m_Connector->GetOutput());
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| #endif
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| m_RenderWindow->Render();
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| }
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| void SetTransform(TransformType::Pointer &transform)
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| {
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| m_Transform = transform;
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| }
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| void SetFilter(typename FilterType::Pointer &filter)
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| {
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| m_Filter = filter;
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| }
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| void SetConnector(typename ConnectorType::Pointer &connector)
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| {
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| m_Connector = connector;
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| }
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| void SetImageActor(vtkImageActor *actor)
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| {
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| m_ImageActor = actor;
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| }
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| void SetRenderWindow(vtkRenderWindow *renderWindow)
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| {
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| m_RenderWindow = renderWindow;
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| }
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| TransformType::Pointer m_Transform;
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| typename FilterType::Pointer m_Filter;
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| typename ConnectorType::Pointer m_Connector;
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| vtkImageActor * m_ImageActor;
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| vtkRenderWindow * m_RenderWindow;
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| };
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| | |
| int main( int argc, char *argv[] )
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| {
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| InputImageType::Pointer fixedImage = InputImageType::New();
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| InputImageType::Pointer movingImage = InputImageType::New();
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| if (argc > 2)
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| {
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| typedef itk::ImageFileReader<InputImageType> ReaderType;
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| ReaderType::Pointer fixedReader = ReaderType::New();
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| fixedReader->SetFileName( argv[1] );
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| fixedReader->Update();
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| fixedImage = fixedReader->GetOutput();
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| ReaderType::Pointer movingReader = ReaderType::New();
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| movingReader->SetFileName( argv[2] );
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| movingReader->Update();
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| movingImage = movingReader->GetOutput();
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| }
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| else
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| {
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| std::cout << "Usage: " << argv[0] << " fixedImage movingImage" << std::endl;
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| return EXIT_FAILURE;
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| }
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| | |
| // Use floats internally
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| typedef float InternalPixelType;
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| typedef itk::Image< float, Dimension> InternalImageType;
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| | |
| // Normalize the images
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| typedef itk::NormalizeImageFilter<InputImageType, InternalImageType> NormalizeFilterType;
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| NormalizeFilterType::Pointer fixedNormalizer =
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| NormalizeFilterType::New();
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| NormalizeFilterType::Pointer movingNormalizer =
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| NormalizeFilterType::New();
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| fixedNormalizer->SetInput( fixedImage);
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| movingNormalizer->SetInput( movingImage);
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| // Smooth the normalized images
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| typedef itk::DiscreteGaussianImageFilter<InternalImageType,InternalImageType> GaussianFilterType;
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| GaussianFilterType::Pointer fixedSmoother =
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| GaussianFilterType::New();
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| GaussianFilterType::Pointer movingSmoother =
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| GaussianFilterType::New();
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| fixedSmoother->SetVariance( 3.0 );
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| fixedSmoother->SetInput( fixedNormalizer->GetOutput() );
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| movingSmoother->SetVariance( 3.0 );
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| movingSmoother->SetInput( movingNormalizer->GetOutput() );
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| | |
| // Set up registration
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| typedef itk::AffineTransform< double, Dimension > TransformType;
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| typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
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| typedef itk::LinearInterpolateImageFunction<
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| InternalImageType,
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| double > InterpolatorType;
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| typedef itk::MattesMutualInformationImageToImageMetric<
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| InternalImageType,
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| InternalImageType > MetricType;
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| typedef itk::ImageRegistrationMethod<
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| InternalImageType,
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| InternalImageType > RegistrationType;
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| typedef itk::CenteredTransformInitializer<
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| TransformType,
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| InputImageType,
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| InputImageType >
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| InitializerType;
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| InitializerType::Pointer initializer = InitializerType::New();
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| TransformType::Pointer transform = TransformType::New();
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| OptimizerType::Pointer optimizer = OptimizerType::New();
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| InterpolatorType::Pointer interpolator = InterpolatorType::New();
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| RegistrationType::Pointer registration = RegistrationType::New();
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| | |
| // Set up the registration framework
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| initializer->SetFixedImage( fixedImage );
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| initializer->SetMovingImage( movingImage );
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| initializer->SetTransform( transform );
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| transform->SetIdentity();
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| initializer->GeometryOn();
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| initializer->InitializeTransform();
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| registration->SetOptimizer( optimizer );
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| registration->SetTransform( transform );
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| registration->SetInterpolator( interpolator );
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| MetricType::Pointer metric = MetricType::New();
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| registration->SetMetric( metric );
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| registration->SetFixedImage( fixedSmoother->GetOutput() );
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| registration->SetMovingImage(movingSmoother->GetOutput() );
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| // Update to get the size of the region
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| fixedNormalizer->Update();
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| InputImageType::RegionType fixedImageRegion =
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| fixedNormalizer->GetOutput()->GetBufferedRegion();
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| registration->SetFixedImageRegion( fixedImageRegion );
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| | |
| typedef RegistrationType::ParametersType ParametersType;
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| ParametersType initialParameters( transform->GetNumberOfParameters() );
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| | |
| // rotation matrix (identity)
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| initialParameters[0] = 1.0; // R(0,0)
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| initialParameters[1] = 0.0; // R(0,1)
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| initialParameters[2] = 0.0; // R(1,0)
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| initialParameters[3] = 1.0; // R(1,1)
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| | |
| // translation vector
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| initialParameters[4] = 0.0;
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| initialParameters[5] = 0.0;
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| registration->SetInitialTransformParameters( initialParameters );
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| | |
| const unsigned int numberOfPixels = fixedImageRegion.GetNumberOfPixels();
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| const unsigned int numberOfSamples =
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| static_cast< unsigned int >( numberOfPixels * 0.05 );
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| | |
| metric->SetNumberOfHistogramBins( 26 );
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| metric->SetNumberOfSpatialSamples( numberOfSamples );
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| optimizer->MinimizeOn();
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| optimizer->SetMaximumStepLength( 0.500 );
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| optimizer->SetMinimumStepLength( 0.001 );
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| optimizer->SetNumberOfIterations( 1000 );
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| | |
| const unsigned int numberOfParameters = transform->GetNumberOfParameters();
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| typedef OptimizerType::ScalesType OptimizerScalesType;
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| OptimizerScalesType optimizerScales( numberOfParameters );
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| double translationScale = 1.0 / 1000.0;
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| optimizerScales[0] = 1.0;
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| optimizerScales[1] = 1.0;
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| optimizerScales[2] = 1.0;
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| optimizerScales[3] = 1.0;
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| optimizerScales[4] = translationScale;
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| optimizerScales[5] = translationScale;
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| optimizer->SetScales( optimizerScales );
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| | |
| TransformType::Pointer finalTransform =
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| TransformType::New();
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| finalTransform->SetParameters( initialParameters ); | |
| finalTransform->SetFixedParameters( transform->GetFixedParameters() );
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| | |
| typedef itk::ResampleImageFilter< InputImageType, InputImageType >
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| ResampleFilterType;
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| ResampleFilterType::Pointer resample =
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| ResampleFilterType::New();
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| resample->SetTransform( finalTransform );
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| resample->SetInput( movingImage);
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| resample->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
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| resample->SetOutputOrigin( fixedImage->GetOrigin() );
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| resample->SetOutputSpacing( fixedImage->GetSpacing() );
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| resample->SetOutputDirection( fixedImage->GetDirection() );
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| resample->SetDefaultPixelValue( 100 );
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| resample->Update();
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| | |
| // Set up the visualization pipeline
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| typedef itk::CheckerBoardImageFilter< InputImageType > CheckerBoardFilterType;
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| CheckerBoardFilterType::Pointer checkerboard =
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| CheckerBoardFilterType::New();
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| CheckerBoardFilterType::PatternArrayType pattern;
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| pattern[0] = 4;
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| pattern[1] = 4;
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| | |
| checkerboard->SetCheckerPattern( pattern );
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| checkerboard->SetInput1( fixedImage);
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| checkerboard->SetInput2( resample->GetOutput());
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| | |
| typedef itk::FlipImageFilter< InputImageType> FlipFilterType;
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| FlipFilterType::Pointer flip =
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| FlipFilterType::New();
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| bool flipAxes[3] = { false, true, false };
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| flip->SetFlipAxes(flipAxes);
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| flip->SetInput(checkerboard->GetOutput());
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| flip->Update();
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| | |
| // VTK visualization pipeline
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| typedef itk::ImageToVTKImageFilter<InputImageType > ConnectorType;
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| ConnectorType::Pointer connector =
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| ConnectorType::New();
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| connector->SetInput(flip->GetOutput());
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| | |
| vtkSmartPointer<vtkImageActor> actor =
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| vtkSmartPointer<vtkImageActor>::New();
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| #if VTK_MAJOR_VERSION <= 5
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| actor->SetInput(connector->GetOutput());
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| #else
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| connector->Update();
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| actor->GetMapper()->SetInputData(connector->GetOutput());
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| #endif
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| vtkSmartPointer<vtkRenderWindow> renderWindow =
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| vtkSmartPointer<vtkRenderWindow>::New();
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| vtkSmartPointer<vtkRenderer> renderer =
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| vtkSmartPointer<vtkRenderer>::New();
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| renderer->SetBackground(.4, .5, .6);
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| renderer->AddActor(actor);
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| renderWindow->SetSize(640, 480);;
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| renderWindow->AddRenderer(renderer);
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| renderWindow->Render();
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| | |
| // Set up the iteration event observer
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| IterationUpdate<InputImageType>::Pointer observer =
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| IterationUpdate<InputImageType>::New();
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| optimizer->AddObserver( itk::IterationEvent(), observer );
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| | |
| observer->SetTransform(finalTransform);
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| observer->SetFilter(flip);
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| observer->SetConnector(connector);
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| observer->SetImageActor(actor);
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| observer->SetRenderWindow(renderWindow);
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| try
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| {
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| registration->Update();
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| std::cout << "Optimizer stop condition: "
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| << registration->GetOptimizer()->GetStopConditionDescription()
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| << std::endl;
| |
| }
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| catch( itk::ExceptionObject & err )
| |
| {
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| std::cout << "ExceptionObject caught !" << std::endl;
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| std::cout << err << std::endl;
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| return EXIT_FAILURE;
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| }
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| std::cout << "Final Transform: " << finalTransform << std::endl;
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| | |
| ParametersType finalParameters = registration->GetLastTransformParameters();
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| std::cout << "Final Parameters: " << finalParameters << std::endl;
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| | |
| unsigned int numberOfIterations = optimizer->GetCurrentIteration();
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| double bestValue = optimizer->GetValue();
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| | |
| // Print out results
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| std::cout << std::endl;
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| std::cout << "Result = " << std::endl;
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| std::cout << " Iterations = " << numberOfIterations << std::endl;
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| std::cout << " Metric value = " << bestValue << std::endl;
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| std::cout << " Numb. Samples = " << numberOfSamples << std::endl;
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| | |
| // Interact with the image
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| vtkSmartPointer<vtkRenderWindowInteractor> interactor =
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| vtkSmartPointer<vtkRenderWindowInteractor>::New();
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| vtkSmartPointer<vtkInteractorStyleImage> style =
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| vtkSmartPointer<vtkInteractorStyleImage>::New();
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| interactor->SetInteractorStyle(style);
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| interactor->SetRenderWindow(renderWindow);
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| interactor->Start();
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| return EXIT_SUCCESS;
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| }
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| </source>
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| {{ITKVTKCMakeLists|{{SUBPAGENAME}}}}
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