ITK/Examples/Registration/ImageRegistrationMethodBSpline

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ITK Examples Baseline Registration TestImageRegistrationMethodBSpline.png

ImageRegistrationMethodBSpline.cxx

#include "itkImageRegistrationMethod.h"
#include "itkMeanSquaresImageToImageMetric.h"
#include "itkTimeProbesCollectorBase.h"
#include "itkSpatialObjectToImageFilter.h"
#include "itkEllipseSpatialObject.h"
 
#if ITK_VERSION_MAJOR < 4
#include "itkBSplineDeformableTransform.h"
#else
#include "itkBSplineTransform.h"
#endif
#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;
 
#if ITK_VERSION_MAJOR < 4
  typedef itk::BSplineDeformableTransform<
                            CoordinateRepType,
                            SpaceDimension,
                            SplineOrder >     TransformType;
#else
  typedef itk::BSplineTransform<
                            CoordinateRepType,
                            SpaceDimension,
                            SplineOrder >     TransformType;
#endif
  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();
 
 
 
  // The old registration framework has problems with multi-threading
  // For now, we set the number of threads to 1
  registration->SetNumberOfThreads(1);
 
  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);
 
  // 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->Update();
    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());
}

CMakeLists.txt

cmake_minimum_required(VERSION 2.8)
 
project(ImageRegistrationMethodBSpline)
 
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})
if (ITKVtkGlue_LOADED)
  find_package(VTK REQUIRED)
  include(${VTK_USE_FILE})
else()
  find_package(ItkVtkGlue REQUIRED)
  include(${ItkVtkGlue_USE_FILE})
  set(Glue ItkVtkGlue)
endif()
 
add_executable(ImageRegistrationMethodBSpline MACOSX_BUNDLE ImageRegistrationMethodBSpline.cxx)
target_link_libraries(ImageRegistrationMethodBSpline
  ${Glue}  ${VTK_LIBRARIES} ${ITK_LIBRARIES})

Download and Build ImageRegistrationMethodBSpline

Click here to download ImageRegistrationMethodBSpline. and its CMakeLists.txt file. Once the tarball ImageRegistrationMethodBSpline.tar has been downloaded and extracted,

cd ImageRegistrationMethodBSpline/build 
  • If ITK is installed:
cmake ..
  • If ITK is not installed but compiled on your system, you will need to specify the path to your ITK build:
cmake -DITK_DIR:PATH=/home/me/itk_build ..

Build the project,

make

and run it:

./ImageRegistrationMethodBSpline

WINDOWS USERS PLEASE NOTE: Be sure to add the VTK and ITK bin directories to your path. This will resolve the VTK and ITK dll's at run time.

Building All of the Examples

Many of the examples in the ITK Wiki Examples Collection require VTK. You can build all of the the examples by following these instructions. If you are a new VTK user, you may want to try the Superbuild which will build a proper ITK and VTK.

ItkVtkGlue

ITK >= 4

For examples that use QuickView (which depends on VTK), you must have built ITK with Module_ITKVtkGlue=ON.

ITK < 4

Some of the ITK Examples require VTK to display the images. If you download the entire ITK Wiki Examples Collection, the ItkVtkGlue directory will be included and configured. If you wish to just build a few examples, then you will need to download ItkVtkGlue and build it. When you run cmake it will ask you to specify the location of the ItkVtkGlue binary directory.