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| <div class="floatcenter">[[File:ITK_Examples_Baseline_Registration_TestImageRegistrationMethodBSpline.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| | {{warning|1=The media wiki content on this page is no longer maintained.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.}} |
| ==ImageRegistrationMethodBSpline.cxx==
| |
| <source lang="cpp">
| |
| #include "itkImageRegistrationMethod.h"
| |
| #include "itkMeanSquaresImageToImageMetric.h"
| |
| #include "itkTimeProbesCollectorBase.h"
| |
| #include "itkSpatialObjectToImageFilter.h"
| |
| #include "itkEllipseSpatialObject.h"
| |
| | |
| #include "itkBSplineDeformableTransform.h"
| |
| #include "itkLBFGSOptimizer.h"
| |
| #include "itkImageFileWriter.h"
| |
| #include "itkResampleImageFilter.h"
| |
| #include "itkCastImageFilter.h"
| |
| #include "itkSquaredDifferenceImageFilter.h"
| |
| | |
| #include "QuickView.h"
| |
| | |
| const unsigned int ImageDimension = 2;
| |
| typedef float PixelType;
| |
| | |
| typedef itk::Image< PixelType, ImageDimension > ImageType;
| |
| | |
| static void CreateEllipseImage(ImageType::Pointer image);
| |
| static void CreateCircleImage(ImageType::Pointer image);
| |
| | |
| int main( int argc, char *argv[] )
| |
| {
| |
| | |
| const unsigned int SpaceDimension = ImageDimension;
| |
| const unsigned int SplineOrder = 3;
| |
| typedef double CoordinateRepType;
| |
| | |
| typedef itk::BSplineDeformableTransform<
| |
| CoordinateRepType,
| |
| SpaceDimension,
| |
| SplineOrder > TransformType;
| |
| | |
| typedef itk::LBFGSOptimizer OptimizerType;
| |
| | |
| | |
| typedef itk::MeanSquaresImageToImageMetric<
| |
| ImageType,
| |
| ImageType > MetricType;
| |
| | |
| typedef itk:: LinearInterpolateImageFunction<
| |
| ImageType,
| |
| double > InterpolatorType;
| |
| | |
| typedef itk::ImageRegistrationMethod<
| |
| ImageType,
| |
| ImageType > RegistrationType;
| |
| | |
| MetricType::Pointer metric = MetricType::New();
| |
| OptimizerType::Pointer optimizer = OptimizerType::New();
| |
| InterpolatorType::Pointer interpolator = InterpolatorType::New();
| |
| RegistrationType::Pointer registration = RegistrationType::New();
| |
| | |
| | |
| registration->SetMetric( metric );
| |
| registration->SetOptimizer( optimizer );
| |
| registration->SetInterpolator( interpolator );
| |
| | |
| TransformType::Pointer transform = TransformType::New();
| |
| registration->SetTransform( transform );
| |
| | |
| // Create the synthetic images
| |
| ImageType::Pointer fixedImage = ImageType::New();
| |
| CreateCircleImage(fixedImage);
| |
| | |
| ImageType::Pointer movingImage = ImageType::New();
| |
| CreateEllipseImage(movingImage);
| |
| | |
| // Write the images
| |
| typedef itk::ImageFileWriter< ImageType > WriterType;
| |
| /*
| |
| WriterType::Pointer fixedWriter = WriterType::New();
| |
| fixedWriter->SetFileName("fixed.png");
| |
| fixedWriter->SetInput( fixedImage);
| |
| fixedWriter->Update();
| |
| | |
| WriterType::Pointer movingWriter = WriterType::New();
| |
| movingWriter->SetFileName("moving.png");
| |
| movingWriter->SetInput( movingImage);
| |
| movingWriter->Update();
| |
| */
| |
| | |
| // Setup the registration
| |
| registration->SetFixedImage( fixedImage );
| |
| registration->SetMovingImage( movingImage);
| |
| | |
| ImageType::RegionType fixedRegion = fixedImage->GetBufferedRegion();
| |
| registration->SetFixedImageRegion( fixedRegion );
| |
| | |
| // Here we define the parameters of the BSplineDeformableTransform grid. We
| |
| // arbitrarily decide to use a grid with $5 \times 5$ nodes within the image.
| |
| // The reader should note that the BSpline computation requires a | |
| // finite support region ( 1 grid node at the lower borders and 2
| |
| // grid nodes at upper borders). Therefore in this example, we set
| |
| // the grid size to be $8 \times 8$ and place the grid origin such that
| |
| // grid node (1,1) coincides with the first pixel in the fixed image.
| |
| | |
| #if ITK_VERSION_MAJOR < 4
| |
| typedef TransformType::RegionType RegionType;
| |
| RegionType bsplineRegion;
| |
| RegionType::SizeType gridSizeOnImage;
| |
| RegionType::SizeType gridBorderSize;
| |
| RegionType::SizeType totalGridSize;
| |
| | |
| gridSizeOnImage.Fill( 5 );
| |
| gridBorderSize.Fill( 3 ); // Border for spline order = 3 ( 1 lower, 2 upper )
| |
| totalGridSize = gridSizeOnImage + gridBorderSize;
| |
| | |
| bsplineRegion.SetSize( totalGridSize );
| |
| | |
| typedef TransformType::SpacingType SpacingType;
| |
| SpacingType spacing = fixedImage->GetSpacing();
| |
| | |
| typedef TransformType::OriginType OriginType;
| |
| OriginType origin = fixedImage->GetOrigin();
| |
| | |
| ImageType::SizeType fixedImageSize = fixedRegion.GetSize();
| |
| | |
| for(unsigned int r=0; r<ImageDimension; r++)
| |
| {
| |
| spacing[r] *= static_cast<double>(fixedImageSize[r] - 1) /
| |
| static_cast<double>(gridSizeOnImage[r] - 1);
| |
| }
| |
| | |
| ImageType::DirectionType gridDirection = fixedImage->GetDirection();
| |
| SpacingType gridOriginOffset = gridDirection * spacing;
| |
| | |
| OriginType gridOrigin = origin - gridOriginOffset;
| |
| | |
| transform->SetGridSpacing( spacing );
| |
| transform->SetGridOrigin( gridOrigin );
| |
| transform->SetGridRegion( bsplineRegion );
| |
| transform->SetGridDirection( gridDirection );
| |
| #else
| |
| TransformType::PhysicalDimensionsType fixedPhysicalDimensions;
| |
| TransformType::MeshSizeType meshSize;
| |
| for( unsigned int i=0; i < ImageDimension; i++ )
| |
| {
| |
| fixedPhysicalDimensions[i] = fixedImage->GetSpacing()[i] *
| |
| static_cast<double>(
| |
| fixedImage->GetLargestPossibleRegion().GetSize()[i] - 1 );
| |
| }
| |
| unsigned int numberOfGridNodesInOneDimension = 5;
| |
| meshSize.Fill( numberOfGridNodesInOneDimension - SplineOrder );
| |
| transform->SetTransformDomainOrigin( fixedImage->GetOrigin() );
| |
| transform->SetTransformDomainPhysicalDimensions( fixedPhysicalDimensions );
| |
| transform->SetTransformDomainMeshSize( meshSize );
| |
| transform->SetTransformDomainDirection( fixedImage->GetDirection() );
| |
| #endif
| |
| | |
| typedef TransformType::ParametersType ParametersType;
| |
| | |
| const unsigned int numberOfParameters =
| |
| transform->GetNumberOfParameters();
| |
| | |
| ParametersType parameters( 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;
| |
| | |
| // Next we set the parameters of the LBFGS Optimizer.
| |
| | |
| optimizer->SetGradientConvergenceTolerance( 0.05 );
| |
| optimizer->SetLineSearchAccuracy( 0.9 );
| |
| optimizer->SetDefaultStepLength( .5 );
| |
| optimizer->TraceOn();
| |
| optimizer->SetMaximumNumberOfFunctionEvaluations( 1000 );
| |
| | |
| std::cout << std::endl << "Starting Registration" << std::endl;
| |
| | |
| try
| |
| {
| |
| registration->StartRegistration();
| |
| 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();
| |
| | |
| std::cout << "Last Transform Parameters" << std::endl;
| |
| std::cout << finalParameters << std::endl;
| |
| | |
| transform->SetParameters( finalParameters );
| |
| | |
| typedef itk::ResampleImageFilter<
| |
| ImageType,
| |
| ImageType > ResampleFilterType;
| |
| | |
| ResampleFilterType::Pointer resample = ResampleFilterType::New();
| |
| | |
| resample->SetTransform( transform );
| |
| resample->SetInput( movingImage );
| |
| | |
| resample->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
| |
| resample->SetOutputOrigin( fixedImage->GetOrigin() );
| |
| resample->SetOutputSpacing( fixedImage->GetSpacing() );
| |
| resample->SetOutputDirection( fixedImage->GetDirection() );
| |
| resample->SetDefaultPixelValue( 100 );
| |
| | |
| typedef unsigned char OutputPixelType;
| |
| | |
| typedef itk::Image< OutputPixelType, ImageDimension > OutputImageType;
| |
| | |
| typedef itk::CastImageFilter<
| |
| ImageType,
| |
| OutputImageType > CastFilterType;
| |
| | |
| typedef itk::ImageFileWriter< OutputImageType > OutputWriterType;
| |
|
| |
| OutputWriterType::Pointer writer = OutputWriterType::New();
| |
| CastFilterType::Pointer caster = CastFilterType::New();
| |
| | |
| | |
| writer->SetFileName("output.png");
| |
| | |
| caster->SetInput( resample->GetOutput() );
| |
| writer->SetInput( caster->GetOutput() );
| |
| | |
| try
| |
| {
| |
| writer->Update();
| |
| }
| |
| catch( itk::ExceptionObject & err )
| |
| {
| |
| std::cerr << "ExceptionObject caught !" << std::endl;
| |
| std::cerr << err << std::endl;
| |
| return EXIT_FAILURE;
| |
| }
| |
| | |
| QuickView viewer;
| |
| viewer.AddImage(
| |
| fixedImage.GetPointer(),true,
| |
| "Fixed Image");
| |
| viewer.AddImage(
| |
| movingImage.GetPointer(),true,
| |
| "Moving Image");
| |
| viewer.AddImage(
| |
| resample->GetOutput(),true,
| |
| "Resampled Moving Image");
| |
| | |
| viewer.Visualize();
| |
| | |
| return EXIT_SUCCESS;
| |
| }
| |
| | |
| void CreateEllipseImage(ImageType::Pointer image)
| |
| {
| |
| typedef itk::EllipseSpatialObject< ImageDimension > EllipseType;
| |
| | |
| typedef itk::SpatialObjectToImageFilter<
| |
| EllipseType, ImageType > SpatialObjectToImageFilterType;
| |
| | |
| SpatialObjectToImageFilterType::Pointer imageFilter =
| |
| SpatialObjectToImageFilterType::New();
| |
| | |
| ImageType::SizeType size;
| |
| size[ 0 ] = 100;
| |
| size[ 1 ] = 100;
| |
| | |
| imageFilter->SetSize( size );
| |
| | |
| ImageType::SpacingType spacing;
| |
| spacing.Fill(1);
| |
| imageFilter->SetSpacing(spacing);
| |
| | |
| EllipseType::Pointer ellipse = EllipseType::New();
| |
| EllipseType::ArrayType radiusArray;
| |
| radiusArray[0] = 10;
| |
| radiusArray[1] = 20;
| |
| ellipse->SetRadius(radiusArray);
| |
| | |
| typedef EllipseType::TransformType TransformType;
| |
| TransformType::Pointer transform = TransformType::New();
| |
| transform->SetIdentity();
| |
| | |
| TransformType::OutputVectorType translation;
| |
| TransformType::CenterType center;
| |
| | |
| translation[ 0 ] = 65;
| |
| translation[ 1 ] = 45;
| |
| transform->Translate( translation, false );
| |
| | |
| ellipse->SetObjectToParentTransform( transform );
| |
| | |
| imageFilter->SetInput(ellipse);
| |
| | |
| ellipse->SetDefaultInsideValue(255);
| |
| ellipse->SetDefaultOutsideValue(0);
| |
| imageFilter->SetUseObjectValue( true );
| |
| imageFilter->SetOutsideValue( 0 );
| |
| | |
| imageFilter->Update();
| |
| | |
| image->Graft(imageFilter->GetOutput());
| |
| | |
| }
| |
| | |
| void CreateCircleImage(ImageType::Pointer image)
| |
| {
| |
| typedef itk::EllipseSpatialObject< ImageDimension > EllipseType;
| |
| | |
| typedef itk::SpatialObjectToImageFilter<
| |
| EllipseType, ImageType > SpatialObjectToImageFilterType;
| |
| | |
| SpatialObjectToImageFilterType::Pointer imageFilter =
| |
| SpatialObjectToImageFilterType::New();
| |
| | |
| ImageType::SizeType size;
| |
| size[ 0 ] = 100;
| |
| size[ 1 ] = 100;
| |
| | |
| imageFilter->SetSize( size );
| |
| | |
| ImageType::SpacingType spacing;
| |
| spacing.Fill(1);
| |
| imageFilter->SetSpacing(spacing);
| |
| | |
| EllipseType::Pointer ellipse = EllipseType::New();
| |
| EllipseType::ArrayType radiusArray;
| |
| radiusArray[0] = 10;
| |
| radiusArray[1] = 10;
| |
| ellipse->SetRadius(radiusArray);
| |
| | |
| typedef EllipseType::TransformType TransformType;
| |
| TransformType::Pointer transform = TransformType::New();
| |
| transform->SetIdentity();
| |
| | |
| TransformType::OutputVectorType translation;
| |
| TransformType::CenterType center;
| |
| | |
| translation[ 0 ] = 50;
| |
| translation[ 1 ] = 50;
| |
| transform->Translate( translation, false );
| |
| | |
| ellipse->SetObjectToParentTransform( transform );
| |
| | |
| imageFilter->SetInput(ellipse);
| |
| | |
| ellipse->SetDefaultInsideValue(255);
| |
| ellipse->SetDefaultOutsideValue(0);
| |
| imageFilter->SetUseObjectValue( true );
| |
| imageFilter->SetOutsideValue( 0 );
| |
| | |
| imageFilter->Update();
| |
| | |
| image->Graft(imageFilter->GetOutput());
| |
| }
| |
| </source>
| |
| | |
| ==CMakeLists.txt==
| |
| <source lang="cmake">
| |
| cmake_minimum_required(VERSION 2.6)
| |
| | |
| PROJECT(BSpline)
| |
| | |
| FIND_PACKAGE(ITK REQUIRED)
| |
| INCLUDE(${ITK_USE_FILE})
| |
| | |
| ADD_EXECUTABLE(BSpline BSpline.cxx)
| |
| TARGET_LINK_LIBRARIES(BSpline ITKIO ITKNumerics)
| |
| | |
| | |
| </source>
| |
