|
|
| (One intermediate revision by one other user not shown) |
| Line 1: |
Line 1: |
| <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| | {{warning|1=The media wiki content on this page is no longer maintained.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.
| |
| | |
| '''Usage:''' WatchRegistration ''fixedImage movingImage''
| |
| | |
| 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
| |
| | |
| ''WatchRegistration BrainProtonDensitySliceBorder20.png BrainProtonDensitySliceRotated10.png''
| |
| | |
| ==WatchRegistration.cxx==
| |
| <source lang="cpp">
| |
| #include "itkImageRegistrationMethod.h"
| |
| #include "itkAffineTransform.h"
| |
| #include "itkMattesMutualInformationImageToImageMetric.h"
| |
| #include "itkRegularStepGradientDescentOptimizer.h"
| |
| #include "itkNormalizeImageFilter.h"
| |
| #include "itkDiscreteGaussianImageFilter.h"
| |
| #include "itkResampleImageFilter.h"
| |
| #include "itkCheckerBoardImageFilter.h"
| |
| #include "itkFlipImageFilter.h"
| |
| #include "itkImageFileReader.h"
| |
| #include "itkImageToVTKImageFilter.h"
| |
| #include "itkCenteredTransformInitializer.h"
| |
| | |
| #include "vtkVersion.h"
| |
| | |
| #include "vtkSmartPointer.h"
| |
| #include "vtkRenderWindow.h"
| |
| #include "vtkRenderer.h"
| |
| #include "vtkInteractorStyleImage.h"
| |
| #include "vtkRenderWindowInteractor.h"
| |
| #include "vtkImageActor.h"
| |
| #include "vtkImageMapper3D.h"
| |
| | |
| const unsigned int Dimension = 2;
| |
| typedef unsigned char PixelType;
| |
| | |
| typedef itk::Image< PixelType, Dimension > InputImageType;
| |
| typedef itk::Image< unsigned char, Dimension > OutputImageType;
| |
| | |
| // Command observer to visualize the evolution of the registration process.
| |
| //
| |
| #include "itkCommand.h"
| |
| template< typename TImage >
| |
| class IterationUpdate : public itk::Command
| |
| { | |
| public:
| |
| typedef IterationUpdate Self;
| |
| typedef itk::Command Superclass;
| |
| typedef itk::SmartPointer<Self> Pointer;
| |
| itkNewMacro( Self );
| |
| | |
| protected:
| |
| IterationUpdate() {};
| |
| | |
| public:
| |
| typedef itk::Image< float, 2> InternalImageType;
| |
| typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
| |
| typedef const OptimizerType * OptimizerPointer;
| |
| typedef itk::ResampleImageFilter<
| |
| TImage,
| |
| TImage > ResampleFilterType;
| |
| typedef itk::AffineTransform< double, 2 > TransformType;
| |
| typedef itk::ImageToVTKImageFilter<TImage > ConnectorType;
| |
| typedef itk::FlipImageFilter<TImage> FilterType;
| |
| void Execute(itk::Object *caller, const itk::EventObject & event) ITK_OVERRIDE
| |
| {
| |
| Execute( (const itk::Object *) caller, event);
| |
| }
| |
| | |
| void Execute(const itk::Object * object, const itk::EventObject & event) ITK_OVERRIDE
| |
| {
| |
| OptimizerPointer optimizer = static_cast< OptimizerPointer >( object );
| |
| if( !(itk::IterationEvent().CheckEvent( &event )) )
| |
| {
| |
| return;
| |
| }
| |
| | |
| m_Transform->SetParameters(optimizer->GetCurrentPosition());
| |
| m_Filter->Update();
| |
| m_Connector->SetInput(m_Filter->GetOutput());
| |
| m_Connector->Update();
| |
| | |
| #if VTK_MAJOR_VERSION <= 5
| |
| m_ImageActor->SetInput(m_Connector->GetOutput());
| |
| #else
| |
| m_Connector->Update();
| |
| m_ImageActor->GetMapper()->SetInputData(m_Connector->GetOutput());
| |
| #endif
| |
| m_RenderWindow->Render();
| |
| }
| |
| void SetTransform(TransformType::Pointer &transform)
| |
| {
| |
| m_Transform = transform;
| |
| }
| |
| void SetFilter(typename FilterType::Pointer &filter)
| |
| {
| |
| m_Filter = filter;
| |
| }
| |
| void SetConnector(typename ConnectorType::Pointer &connector)
| |
| {
| |
| m_Connector = connector;
| |
| }
| |
| void SetImageActor(vtkImageActor *actor)
| |
| {
| |
| m_ImageActor = actor;
| |
| }
| |
| void SetRenderWindow(vtkRenderWindow *renderWindow)
| |
| {
| |
| m_RenderWindow = renderWindow;
| |
| }
| |
| TransformType::Pointer m_Transform;
| |
| typename FilterType::Pointer m_Filter;
| |
| typename ConnectorType::Pointer m_Connector;
| |
| vtkImageActor * m_ImageActor;
| |
| vtkRenderWindow * m_RenderWindow;
| |
| };
| |
| | |
| int main( int argc, char *argv[] )
| |
| {
| |
| InputImageType::Pointer fixedImage = InputImageType::New();
| |
| InputImageType::Pointer movingImage = InputImageType::New();
| |
| | |
| if (argc > 2)
| |
| {
| |
| typedef itk::ImageFileReader<InputImageType> ReaderType;
| |
| ReaderType::Pointer fixedReader = ReaderType::New();
| |
| fixedReader->SetFileName( argv[1] );
| |
| fixedReader->Update();
| |
| fixedImage = fixedReader->GetOutput();
| |
| | |
| ReaderType::Pointer movingReader = ReaderType::New();
| |
| movingReader->SetFileName( argv[2] );
| |
| movingReader->Update();
| |
| movingImage = movingReader->GetOutput();
| |
| }
| |
| else
| |
| {
| |
| std::cout << "Usage: " << argv[0] << " fixedImage movingImage" << std::endl;
| |
| return EXIT_FAILURE;
| |
| }
| |
| | |
| // Use floats internally
| |
| typedef float InternalPixelType;
| |
| typedef itk::Image< float, Dimension> InternalImageType;
| |
| | |
| // Normalize the images
| |
| typedef itk::NormalizeImageFilter<InputImageType, InternalImageType> NormalizeFilterType;
| |
| NormalizeFilterType::Pointer fixedNormalizer =
| |
| NormalizeFilterType::New();
| |
| NormalizeFilterType::Pointer movingNormalizer =
| |
| NormalizeFilterType::New();
| |
| | |
| fixedNormalizer->SetInput( fixedImage);
| |
| movingNormalizer->SetInput( movingImage);
| |
| | |
| // Smooth the normalized images
| |
| typedef itk::DiscreteGaussianImageFilter<InternalImageType,InternalImageType> GaussianFilterType;
| |
| GaussianFilterType::Pointer fixedSmoother =
| |
| GaussianFilterType::New();
| |
| GaussianFilterType::Pointer movingSmoother =
| |
| GaussianFilterType::New();
| |
| | |
| fixedSmoother->SetVariance( 3.0 );
| |
| fixedSmoother->SetInput( fixedNormalizer->GetOutput() );
| |
| movingSmoother->SetVariance( 3.0 );
| |
| movingSmoother->SetInput( movingNormalizer->GetOutput() );
| |
| | |
| // Set up registration
| |
| typedef itk::AffineTransform< double, Dimension > TransformType;
| |
| typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
| |
| typedef itk::LinearInterpolateImageFunction<
| |
| InternalImageType,
| |
| double > InterpolatorType;
| |
| typedef itk::MattesMutualInformationImageToImageMetric<
| |
| InternalImageType,
| |
| InternalImageType > MetricType;
| |
| typedef itk::ImageRegistrationMethod<
| |
| InternalImageType,
| |
| InternalImageType > RegistrationType;
| |
| typedef itk::CenteredTransformInitializer<
| |
| TransformType,
| |
| InputImageType,
| |
| InputImageType >
| |
| InitializerType;
| |
| | |
| InitializerType::Pointer initializer = InitializerType::New();
| |
| TransformType::Pointer transform = TransformType::New();
| |
| OptimizerType::Pointer optimizer = OptimizerType::New();
| |
| InterpolatorType::Pointer interpolator = InterpolatorType::New();
| |
| RegistrationType::Pointer registration = RegistrationType::New();
| |
| | |
| // Set up the registration framework
| |
| initializer->SetFixedImage( fixedImage );
| |
| initializer->SetMovingImage( movingImage );
| |
| initializer->SetTransform( transform );
| |
| | |
| transform->SetIdentity();
| |
| initializer->GeometryOn();
| |
| initializer->InitializeTransform();
| |
| | |
| registration->SetOptimizer( optimizer );
| |
| registration->SetTransform( transform );
| |
| registration->SetInterpolator( interpolator );
| |
| | |
| MetricType::Pointer metric = MetricType::New();
| |
| | |
| registration->SetMetric( metric );
| |
| registration->SetFixedImage( fixedSmoother->GetOutput() );
| |
| registration->SetMovingImage(movingSmoother->GetOutput() );
| |
| | |
| // Update to get the size of the region
| |
| fixedNormalizer->Update();
| |
| InputImageType::RegionType fixedImageRegion =
| |
| fixedNormalizer->GetOutput()->GetBufferedRegion();
| |
| registration->SetFixedImageRegion( fixedImageRegion );
| |
| | |
| typedef RegistrationType::ParametersType ParametersType;
| |
| ParametersType initialParameters( transform->GetNumberOfParameters() );
| |
| | |
| // rotation matrix (identity)
| |
| initialParameters[0] = 1.0; // R(0,0)
| |
| initialParameters[1] = 0.0; // R(0,1)
| |
| initialParameters[2] = 0.0; // R(1,0)
| |
| initialParameters[3] = 1.0; // R(1,1)
| |
| | |
| // translation vector
| |
| initialParameters[4] = 0.0;
| |
| initialParameters[5] = 0.0;
| |
| | |
| registration->SetInitialTransformParameters( initialParameters );
| |
| | |
| const unsigned int numberOfPixels = fixedImageRegion.GetNumberOfPixels();
| |
| const unsigned int numberOfSamples =
| |
| static_cast< unsigned int >( numberOfPixels * 0.05 );
| |
| | |
| metric->SetNumberOfHistogramBins( 26 );
| |
| metric->SetNumberOfSpatialSamples( numberOfSamples );
| |
| | |
| optimizer->MinimizeOn();
| |
| optimizer->SetMaximumStepLength( 2.00 );
| |
| optimizer->SetMinimumStepLength( 0.001 );
| |
| optimizer->SetNumberOfIterations( 1000 );
| |
| | |
| const unsigned int numberOfParameters = transform->GetNumberOfParameters();
| |
| typedef OptimizerType::ScalesType OptimizerScalesType;
| |
| OptimizerScalesType optimizerScales( numberOfParameters );
| |
| double translationScale = 1.0 / 1000.0;
| |
| optimizerScales[0] = 1.0;
| |
| optimizerScales[1] = 1.0;
| |
| optimizerScales[2] = 1.0;
| |
| optimizerScales[3] = 1.0;
| |
| optimizerScales[4] = translationScale;
| |
| optimizerScales[5] = translationScale;
| |
| | |
| optimizer->SetScales( optimizerScales );
| |
| | |
| TransformType::Pointer finalTransform =
| |
| TransformType::New();
| |
| finalTransform->SetParameters( initialParameters ); | |
| finalTransform->SetFixedParameters( transform->GetFixedParameters() );
| |
| | |
| typedef itk::ResampleImageFilter< InputImageType, InputImageType >
| |
| ResampleFilterType;
| |
| ResampleFilterType::Pointer resample =
| |
| ResampleFilterType::New();
| |
| resample->SetTransform( finalTransform );
| |
| resample->SetInput( movingImage);
| |
| resample->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
| |
| resample->SetOutputOrigin( fixedImage->GetOrigin() );
| |
| resample->SetOutputSpacing( fixedImage->GetSpacing() );
| |
| resample->SetOutputDirection( fixedImage->GetDirection() );
| |
| resample->SetDefaultPixelValue( 100 );
| |
| resample->Update();
| |
| | |
| // Set up the visualization pipeline
| |
| typedef itk::CheckerBoardImageFilter< InputImageType > CheckerBoardFilterType;
| |
| CheckerBoardFilterType::Pointer checkerboard =
| |
| CheckerBoardFilterType::New();
| |
| CheckerBoardFilterType::PatternArrayType pattern;
| |
| pattern[0] = 4;
| |
| pattern[1] = 4;
| |
| | |
| checkerboard->SetCheckerPattern( pattern );
| |
| checkerboard->SetInput1( fixedImage);
| |
| checkerboard->SetInput2( resample->GetOutput());
| |
| | |
| typedef itk::FlipImageFilter< InputImageType> FlipFilterType;
| |
| FlipFilterType::Pointer flip =
| |
| FlipFilterType::New();
| |
| bool flipAxes[3] = { false, true, false };
| |
| flip->SetFlipAxes(flipAxes);
| |
| flip->SetInput(checkerboard->GetOutput());
| |
| flip->Update();
| |
| | |
| // VTK visualization pipeline
| |
| typedef itk::ImageToVTKImageFilter<InputImageType > ConnectorType;
| |
| ConnectorType::Pointer connector =
| |
| ConnectorType::New();
| |
| connector->SetInput(flip->GetOutput());
| |
| | |
| vtkSmartPointer<vtkImageActor> actor =
| |
| vtkSmartPointer<vtkImageActor>::New();
| |
| #if VTK_MAJOR_VERSION <= 5
| |
| actor->SetInput(connector->GetOutput());
| |
| #else
| |
| connector->Update();
| |
| actor->GetMapper()->SetInputData(connector->GetOutput());
| |
| #endif
| |
| vtkSmartPointer<vtkRenderWindow> renderWindow =
| |
| vtkSmartPointer<vtkRenderWindow>::New();
| |
| vtkSmartPointer<vtkRenderer> renderer =
| |
| vtkSmartPointer<vtkRenderer>::New();
| |
| renderer->SetBackground(.4, .5, .6);
| |
| renderer->AddActor(actor);
| |
| renderWindow->SetSize(640, 480);;
| |
| renderWindow->AddRenderer(renderer);
| |
| renderWindow->Render();
| |
| | |
| // Set up the iteration event observer
| |
| IterationUpdate<InputImageType>::Pointer observer =
| |
| IterationUpdate<InputImageType>::New();
| |
| optimizer->AddObserver( itk::IterationEvent(), observer );
| |
| | |
| observer->SetTransform(finalTransform);
| |
| observer->SetFilter(flip);
| |
| observer->SetConnector(connector);
| |
| observer->SetImageActor(actor);
| |
| observer->SetRenderWindow(renderWindow);
| |
| try
| |
| {
| |
| registration->Update();
| |
| std::cout << "Optimizer stop condition: "
| |
| << registration->GetOptimizer()->GetStopConditionDescription()
| |
| << std::endl;
| |
| }
| |
| catch( itk::ExceptionObject & err )
| |
| {
| |
| std::cout << "ExceptionObject caught !" << std::endl;
| |
| std::cout << err << std::endl;
| |
| return EXIT_FAILURE;
| |
| }
| |
| std::cout << "Final Transform: " << finalTransform << std::endl;
| |
| | |
| ParametersType finalParameters = registration->GetLastTransformParameters();
| |
| std::cout << "Final Parameters: " << finalParameters << std::endl;
| |
| | |
| unsigned int numberOfIterations = optimizer->GetCurrentIteration();
| |
| double bestValue = optimizer->GetValue();
| |
| | |
| // Print out results
| |
| std::cout << std::endl;
| |
| std::cout << "Result = " << std::endl;
| |
| std::cout << " Iterations = " << numberOfIterations << std::endl;
| |
| std::cout << " Metric value = " << bestValue << std::endl;
| |
| std::cout << " Numb. Samples = " << numberOfSamples << std::endl;
| |
| | |
| // Interact with the image
| |
| vtkSmartPointer<vtkRenderWindowInteractor> interactor =
| |
| vtkSmartPointer<vtkRenderWindowInteractor>::New();
| |
| vtkSmartPointer<vtkInteractorStyleImage> style =
| |
| vtkSmartPointer<vtkInteractorStyleImage>::New();
| |
| interactor->SetInteractorStyle(style);
| |
| interactor->SetRenderWindow(renderWindow);
| |
| interactor->Start();
| |
| | |
| return EXIT_SUCCESS;
| |
| }
| |
| </source>
| |
| {{ITKVTKCMakeLists|{{SUBPAGENAME}}}}
| |
