[Insight-users] Multi-images registration

Wed Dec 26 09:42:01 EST 2007

Hi everybody,

I would like to perform multiple image registration, i tried to make a
loop unsuccessfully. I seems like there is a problem with
ImagetoImagemetric, but i don't understand why. Here is my code lines if
somebody can give me a help. Thanks a lot,

Josiane

#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#include "itkImageRegistrationMethod.h"
#include "itkMeanSquaresImageToImageMetric.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkRegularStepGradientDescentOptimizer.h"
#include "itkImage.h"

#include "itkCenteredRigid2DTransform.h"

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkResampleImageFilter.h"
#include "itkSubtractImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"

//
#include "itkCommand.h"
class CommandIterationUpdate : public itk::Command
{
public:
  typedef  CommandIterationUpdate   Self;
  typedef  itk::Command             Superclass;
  typedef itk::SmartPointer<Self>  Pointer;
  itkNewMacro( Self );
protected:
  CommandIterationUpdate() {};
public:
  typedef itk::RegularStepGradientDescentOptimizer     OptimizerType;
  typedef   const OptimizerType   *    OptimizerPointer;

  void Execute(itk::Object *caller, const itk::EventObject & event)
    {
      Execute( (const itk::Object *)caller, event);
    }

  void Execute(const itk::Object * object, const itk::EventObject & event)
    {
      OptimizerPointer optimizer =
        dynamic_cast< OptimizerPointer >( object );
      if( ! itk::IterationEvent().CheckEvent( &event ) )
        {
        return;
        }
      std::cout << optimizer->GetCurrentIteration() << "   ";
      std::cout << optimizer->GetValue() << "   ";
      std::cout << optimizer->GetCurrentPosition() << std::endl;
    }
};

int main( int argc, char *argv[] )
{
  if( argc < 8)
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " fixedImageFile  movingImageFile1 movingImageFile2
movingImageFile3 movingImageFile4";
    std::cerr << " outputImagefile  [differenceAfterRegistration] ";
    std::cerr << " [differenceBeforeRegistration] ";
    std::cerr << " [initialStepLength] "<< std::endl;
    return EXIT_FAILURE;
    }

  const    unsigned int    Dimension = 2;
  typedef  unsigned char   PixelType²²;

  typedef itk::Image< PixelType, Dimension >  FixedImageType;
  typedef itk::Image< PixelType, Dimension >  MovingImageType;

  typedef itk::CenteredRigid2DTransform< double > TransformType;

  typedef itk::RegularStepGradientDescentOptimizer       OptimizerType;
  typedef itk::MeanSquaresImageToImageMetric<
                                    FixedImageType,
                                    MovingImageType >    MetricType;
  typedef itk:: LinearInterpolateImageFunction<
                                    MovingImageType,
                                    double          >    InterpolatorType;
  typedef itk::ImageRegistrationMethod<
                                    FixedImageType,
                                    MovingImageType >    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 );

  typedef itk::ImageFileReader< FixedImageType  > FixedImageReaderType;
  typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;

  FixedImageReaderType::Pointer  fixedImageReader  =
FixedImageReaderType::New();
  //FixedImageReaderType::Pointer  fixedImageReader1  =
FixedImageReaderType::New();
  MovingImageReaderType::Pointer movingImageReader =
MovingImageReaderType::New();

  fixedImageReader->SetFileName(  argv[1] );
  //fixedImageReader1->SetFileName(  argv[1] );
  movingImageReader->SetFileName( argv[2] );

  registration->SetFixedImage(    fixedImageReader->GetOutput()    );
  registration->SetMovingImage(   movingImageReader->GetOutput()   );
  fixedImageReader->Update();

  registration->SetFixedImageRegion(
     fixedImageReader->GetOutput()->GetBufferedRegion() );

  fixedImageReader->Update();
  movingImageReader->Update();

  typedef FixedImageType::SpacingType    SpacingType;
  typedef FixedImageType::PointType      OriginType;
  typedef FixedImageType::RegionType     RegionType;
  typedef FixedImageType::SizeType       SizeType;

  FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();

  const SpacingType fixedSpacing = fixedImage->GetSpacing();
  const OriginType  fixedOrigin  = fixedImage->GetOrigin();
  const RegionType  fixedRegion  = fixedImage->GetLargestPossibleRegion();
  const SizeType    fixedSize    = fixedRegion.GetSize();

  TransformType::InputPointType centerFixed;

  centerFixed[0] = fixedOrigin[0] + fixedSpacing[0] * fixedSize[0] / 2.0;
  centerFixed[1] = fixedOrigin[1] + fixedSpacing[1] * fixedSize[1] / 2.0;

  MovingImageType::Pointer movingImage = movingImageReader->GetOutput();

  const SpacingType movingSpacing = movingImage->GetSpacing();
  const OriginType  movingOrigin  = movingImage->GetOrigin();
  const RegionType  movingRegion  = movingImage->GetLargestPossibleRegion();
  const SizeType    movingSize    = movingRegion.GetSize();

  TransformType::InputPointType centerMoving;

  centerMoving[0] = movingOrigin[0] + movingSpacing[0] * movingSize[0] / 2.0;
  centerMoving[1] = movingOrigin[1] + movingSpacing[1] * movingSize[1] / 2.0;

  transform->SetCenter( centerFixed );
  transform->SetTranslation( centerMoving - centerFixed );

  transform->SetAngle( 0.0 );

  registration->SetInitialTransformParameters( transform->GetParameters() );

  typedef OptimizerType::ScalesType       OptimizerScalesType;
  OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
  const double translationScale = 1.0 / 1000.0;

  optimizerScales[0] = 1.0;
  optimizerScales[1] = translationScale;
  optimizerScales[2] = translationScale;
  optimizerScales[3] = translationScale;
  optimizerScales[4] = translationScale;

  optimizer->SetScales( optimizerScales );

  double initialStepLength = 0.1;

  if( argc > 6 )// 3 translations and 3 rotations
    {
    initialStepLength = atof( argv[6] );
    }

  optimizer->SetRelaxationFactor( 0.6 );
  optimizer->SetMaximumStepLength( initialStepLength );
  optimizer->SetMinimumStepLength( 0.001 );
  optimizer->SetNumberOfIterations( 200 );

  CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
  optimizer->AddObserver( itk::IterationEvent(), observer );

  try
    {
    registration->StartRegistration();
    }
  catch( itk::ExceptionObject & err )
    {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_FAILURE;
    }

  OptimizerType::ParametersType finalParameters =
                    registration->GetLastTransformParameters();

  const double finalAngle           = finalParameters[0];
  const double finalRotationCenterX = finalParameters[1];
  const double finalRotationCenterY = finalParameters[2];
  const double finalTranslationX    = finalParameters[3];
  const double finalTranslationY    = finalParameters[4];

  const unsigned int numberOfIterations = optimizer->GetCurrentIteration();

  const double bestValue = optimizer->GetValue();

  // Print out results
  //
  const double finalAngleInDegrees = finalAngle * 45.0 / atan(1.0);

  std::cout << "Result = " << std::endl;
  std::cout << " Angle (radians)   = " << finalAngle  << std::endl;
  std::cout << " Angle (degrees)   = " << finalAngleInDegrees  << std::endl;
  std::cout << " Center X      = " << finalRotationCenterX  << std::endl;
  std::cout << " Center Y      = " << finalRotationCenterY  << std::endl;
  std::cout << " Translation X = " << finalTranslationX  << std::endl;
  std::cout << " Translation Y = " << finalTranslationY  << std::endl;
  std::cout << " Iterations    = " << numberOfIterations << std::endl;
  std::cout << " Metric value  = " << bestValue          << std::endl;

  //

  typedef itk::ResampleImageFilter<
                            MovingImageType,
                            FixedImageType >    ResampleFilterType;

  TransformType::Pointer finalTransform = TransformType::New();

  finalTransform->SetParameters( finalParameters );

  ResampleFilterType::Pointer resample = ResampleFilterType::New();
  //ResampleFilterType::Pointer resample1 = ResampleFilterType::New();

  resample->SetTransform( finalTransform );
  resample->SetInput( movingImageReader->GetOutput() );

  resample->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
  resample->SetOutputOrigin(  fixedImage->GetOrigin() );
  resample->SetOutputSpacing( fixedImage->GetSpacing() );
  resample->SetDefaultPixelValue( 100 );
  //resample1->SetInput(resample->GetOutput() );

  typedef itk::ImageFileWriter< FixedImageType >  WriterFixedType;

  int i;

  for (i=2; i<5; i++)
  {

  WriterFixedType::Pointer      writer =  WriterFixedType::New();
  writer->SetInput( resample->GetOutput()  );

  RegistrationType::Pointer   registration  = RegistrationType::New();
  TransformType::Pointer  transform = TransformType::New();
  MetricType::Pointer         metric        = MetricType::New();

  registration->SetMetric(        metric        );
  registration->SetOptimizer(     optimizer     );
  registration->SetInterpolator(  interpolator  );
  registration->SetTransform( transform );

  transform->SetAngle( 0.0 );
  registration->SetInitialTransformParameters( transform->GetParameters() );

  movingImageReader->SetFileName( argv[i+1] );
  registration->SetFixedImage(writer->GetOutput());
  registration->SetMovingImage(   movingImageReader->GetOutput()   );

  registration->SetFixedImageRegion(
     writer->GetOutput()->GetBufferedRegion() );

  writer->Update();
  movingImageReader->Update();

  FixedImageType::Pointer fixedImage = writer->GetOutput();

  const SpacingType fixedSpacing = fixedImage->GetSpacing();
  const OriginType  fixedOrigin  = fixedImage->GetOrigin();
  const RegionType  fixedRegion  = fixedImage->GetLargestPossibleRegion();
  const SizeType    fixedSize    = fixedRegion.GetSize();

  TransformType::InputPointType centerFixed;

  centerFixed[0] = fixedOrigin[0] + fixedSpacing[0] * fixedSize[0] / 2.0;
  centerFixed[1] = fixedOrigin[1] + fixedSpacing[1] * fixedSize[1] / 2.0;

  MovingImageType::Pointer movingImage = movingImageReader->GetOutput();

  const SpacingType movingSpacing = movingImage->GetSpacing();
  const OriginType  movingOrigin  = movingImage->GetOrigin();
  const RegionType  movingRegion  = movingImage->GetLargestPossibleRegion();
  const SizeType    movingSize    = movingRegion.GetSize();

  TransformType::InputPointType centerMoving;

  centerMoving[0] = movingOrigin[0] + movingSpacing[0] * movingSize[0] / 2.0;
  centerMoving[1] = movingOrigin[1] + movingSpacing[1] * movingSize[1] / 2.0;

  transform->SetCenter( centerFixed );
  transform->SetTranslation( centerMoving - centerFixed );

  transform->SetAngle( 0.0 );

  registration->SetInitialTransformParameters( transform->GetParameters() );

  typedef OptimizerType::ScalesType       OptimizerScalesType;
  OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
  const double translationScale = 1.0 / 1000.0;

  optimizerScales[0] = 1.0;
  optimizerScales[1] = translationScale;
  optimizerScales[2] = translationScale;
  optimizerScales[3] = translationScale;
  optimizerScales[4] = translationScale;

  optimizer->SetScales( optimizerScales );

  double initialStepLength = 0.1;

  if( argc > 6 )// 3 translations and 3 rotations
    {
    initialStepLength = atof( argv[6] );
    }

  optimizer->SetRelaxationFactor( 0.6 );
  optimizer->SetMaximumStepLength( initialStepLength );
  optimizer->SetMinimumStepLength( 0.001 );
  optimizer->SetNumberOfIterations( 200 );

  CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
  optimizer->AddObserver( itk::IterationEvent(), observer );

  try
    {
    registration->StartRegistration();
    }
  catch( itk::ExceptionObject & err )
    {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_FAILURE;
    }

  OptimizerType::ParametersType finalParameters =
                    registration->GetLastTransformParameters();

  const double finalAngle           = finalParameters[0];
  const double finalRotationCenterX = finalParameters[1];
  const double finalRotationCenterY = finalParameters[2];
  const double finalTranslationX    = finalParameters[3];
  const double finalTranslationY    = finalParameters[4];

  const unsigned int numberOfIterations = optimizer->GetCurrentIteration();

  const double bestValue = optimizer->GetValue();

  // Print out results
  //
  const double finalAngleInDegrees = finalAngle * 45.0 / atan(1.0);

  std::cout << "Result = " << std::endl;
  std::cout << " Angle (radians)   = " << finalAngle  << std::endl;
  std::cout << " Angle (degrees)   = " << finalAngleInDegrees  << std::endl;
  std::cout << " Center X      = " << finalRotationCenterX  << std::endl;
  std::cout << " Center Y      = " << finalRotationCenterY  << std::endl;
  std::cout << " Translation X = " << finalTranslationX  << std::endl;
  std::cout << " Translation Y = " << finalTranslationY  << std::endl;
  std::cout << " Iterations    = " << numberOfIterations << std::endl;
  std::cout << " Metric value  = " << bestValue          << std::endl;

  //

  //typedef itk::ResampleImageFilter<
                            //MovingImageType,
                           // FixedImageType >    ResampleFilterType;

  TransformType::Pointer finalTransform = TransformType::New();

  finalTransform->SetParameters( finalParameters );

  //ResampleFilterType::Pointer resample = ResampleFilterType::New();
  ResampleFilterType::Pointer resample = ResampleFilterType::New();

  resample->SetTransform( finalTransform );

  resample->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
  resample->SetOutputOrigin(  fixedImage->GetOrigin() );
  resample->SetOutputSpacing( fixedImage->GetSpacing() );
  resample->SetDefaultPixelValue( 100 );

  }

  WriterFixedType::Pointer      writer =  WriterFixedType::New();

  writer->SetFileName( argv[6] );

  writer->SetInput( resample1->GetOutput()  );

  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "ExceptionObject while writing the resampled image !" <<
std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }

return EXIT_SUCCESS;
}

Josiane NJIWA, PhD

CREATIS  CNRS UMR 5220, INSERM U630,
         INSA Bât. Blaise Pascal
         7 rue Jean Capelle
         F-69100 Villeurbanne
         tel :+33 (0)4 72 43 82 26
         fax: +33 (0)4 72 43 85 26