ITK/Examples/Registration/ImageRegistrationMethodBSpline

ImageRegistrationMethodBSpline.cxx

<source lang="cpp">

1. include "itkImageRegistrationMethod.h"
2. include "itkMeanSquaresImageToImageMetric.h"
3. include "itkTimeProbesCollectorBase.h"
4. include "itkSpatialObjectToImageFilter.h"
5. include "itkEllipseSpatialObject.h"

1. include "itkBSplineDeformableTransform.h"
2. include "itkLBFGSOptimizer.h"
3. include "itkImageFileWriter.h"
4. include "itkResampleImageFilter.h"
5. include "itkCastImageFilter.h"
6. include "itkSquaredDifferenceImageFilter.h"

1. 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.

1. 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 );

1. 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() );

1. 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>