[Insight-users] registration example 2 and 9

Mr Gaffe lagaffe74130 at yahoo.fr
Wed Nov 10 05:36:13 EST 2004


Hi all,
I try to combine registration example: ImageRegistration2 and 9 to perform an CenteredAffine+MutualInfo registration.
The code bellow compile well, but when I try with: BrainT1SliceBorder20.png and BrainProtonDensitySliceR10X13Y17S12.png I have the following error:
 
---------------
Initial Transform Parameters
[1, 0, 0, 1, -1.00276e+008, -4.25387e+008, 4.90708e+007, 3.85172e+008]
ExceptionObject caught !
itk::ExceptionObject (00FCFD30)
Location: "Unknown"
File: D:\InsightToolkit-1.8.1\Code\Algorithms\itkMutualInformationImageToImageMetric.txx
Line: 155
Description: itk::ERROR: MutualInformationImageToImageMetric(012F4780): All the sampled point mapped to outside of the moving image
-----------------
 
->The Typedef is set to float since Images are unsigned chart is it the problem ? 
If I change the initialisation of the CenteredTransformInitializer as:
 initializer->SetFixedImage(  fixedImageReader->GetOutput() );
  initializer->SetMovingImage( movingImageReader->GetOutput() );
There is no error, but the after 9 iterations it stop with a wrong image results....
 
Is it just a problem of initial typeddef for my fixed and moved image ?
 
thanks,
 
lagaffe
 
---------------------------------------------------------------------------------------------------------------------
/*
* Code from ImageRegistration2 and ImageRegistration9 
*/
#include "itkImageRegistrationMethod.h"
//#include "itkMeanSquaresImageToImageMetric.h"
#include "itkMutualInformationImageToImageMetric.h"
#include "itkNormalizeImageFilter.h"
#include "itkDiscreteGaussianImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkRegularStepGradientDescentOptimizer.h"
#include "itkImage.h"

#include "itkCenteredTransformInitializer.h"
#include "itkCenteredAffineTransform.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkSquaredDifferenceImageFilter.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( typeid( event ) != typeid( itk::IterationEvent ) )
      {
      return;
      }
      std::cout << optimizer->GetCurrentIteration() << "   ";
      std::cout << optimizer->GetValue() << "   ";
      std::cout << optimizer->GetCurrentPosition() << std::endl;
  }
};

int main( int argc, char *argv[] )
{
  if( argc < 4 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << "   fixedImageFile  movingImageFile " << std::endl;
    std::cerr << "   outputImagefile  [differenceOutputfile] [differenceBeforeRegistration] " << std::endl;
    std::cerr << "   [stepLength] [maxNumberOfIterations] "<< std::endl;
    return 1;
    }
  const    unsigned int    Dimension = 2;
  typedef  float           PixelType;
  typedef   float     InternalPixelType;
  typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
  typedef itk::Image< PixelType, Dimension >  FixedImageType;
  typedef itk::Image< PixelType, Dimension >  MovingImageType;
  
  typedef itk::CenteredAffineTransform< 
                                  double, 
                                  Dimension  >     TransformType;
  typedef itk::RegularStepGradientDescentOptimizer       OptimizerType;
  /*
  typedef itk::MeanSquaresImageToImageMetric< 
                                    FixedImageType, 
                                    MovingImageType >    MetricType;
  */
 typedef itk::MutualInformationImageToImageMetric< 
                                          InternalImageType, 
                                          InternalImageType >    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();
  TransformType::Pointer  transform = TransformType::New();

  registration->SetMetric(        metric        );
  registration->SetOptimizer(     optimizer     );
  registration->SetInterpolator(  interpolator  );
  registration->SetTransform( transform );
  metric->SetFixedImageStandardDeviation(  0.4 );
  metric->SetMovingImageStandardDeviation( 0.4 );
  metric->SetNumberOfSpatialSamples( 50 );
  typedef itk::ImageFileReader< FixedImageType  > FixedImageReaderType;
  typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
  FixedImageReaderType::Pointer  fixedImageReader  = FixedImageReaderType::New();
  MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();
  fixedImageReader->SetFileName(  argv[1] );
  movingImageReader->SetFileName( argv[2] );
typedef itk::NormalizeImageFilter< 
                                FixedImageType, 
                                InternalImageType 
                                        > FixedNormalizeFilterType;
  typedef itk::NormalizeImageFilter< 
                                MovingImageType, 
                                InternalImageType 
                                              > MovingNormalizeFilterType;
  FixedNormalizeFilterType::Pointer fixedNormalizer = 
                                            FixedNormalizeFilterType::New();
  MovingNormalizeFilterType::Pointer movingNormalizer =
                                            MovingNormalizeFilterType::New();
 
  typedef itk::DiscreteGaussianImageFilter<
                                      InternalImageType, 
                                      InternalImageType
                                                    > GaussianFilterType;
  
  GaussianFilterType::Pointer fixedSmoother  = GaussianFilterType::New();
  GaussianFilterType::Pointer movingSmoother = GaussianFilterType::New();
  fixedSmoother->SetVariance( 2.0 );
  movingSmoother->SetVariance( 2.0 );
 
  fixedNormalizer->SetInput(  fixedImageReader->GetOutput() );
  movingNormalizer->SetInput( movingImageReader->GetOutput() );
  fixedSmoother->SetInput( fixedNormalizer->GetOutput() );
  movingSmoother->SetInput( movingNormalizer->GetOutput() );
  registration->SetFixedImage(    fixedSmoother->GetOutput()    );
  registration->SetMovingImage(   movingSmoother->GetOutput()   );
  
  fixedNormalizer->Update();
  registration->SetFixedImageRegion( 
       fixedNormalizer->GetOutput()->GetBufferedRegion() );

  typedef itk::CenteredTransformInitializer< 
                                    TransformType, 
                                    FixedImageType, 
                                    MovingImageType >  TransformInitializerType;
  TransformInitializerType::Pointer initializer = TransformInitializerType::New();
  initializer->SetTransform(   transform );
  /*
  initializer->SetFixedImage(  fixedImageReader->GetOutput() );
  initializer->SetMovingImage( movingImageReader->GetOutput() );
*/
 
  initializer->SetFixedImage(  fixedSmoother->GetOutput() );
  initializer->SetMovingImage( movingSmoother->GetOutput() );
  initializer->MomentsOn();
  initializer->InitializeTransform();
  std::cout << "Initial Transform Parameters " << std::endl;
  std::cout << transform->GetParameters() << std::endl;
  
// -----------------------
  registration->SetInitialTransformParameters( 
                                 transform->GetParameters() );

  double translationScale = 1.0 / 1000.0;
  if( argc > 8 )
    {
    translationScale = atof( argv[8] );
    }
 typedef OptimizerType::ScalesType       OptimizerScalesType;
  OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
  optimizerScales[0] =  1.0;
  optimizerScales[1] =  1.0;
  optimizerScales[2] =  1.0;
  optimizerScales[3] =  1.0;
  optimizerScales[4] =  translationScale;
  optimizerScales[5] =  translationScale;
  optimizerScales[6] =  translationScale;
  optimizerScales[7] =  translationScale;
  optimizer->SetScales( optimizerScales );
  double steplength = 0.1;
  if( argc > 6 )
    {
    steplength = atof( argv[6] );
    }

  unsigned int maxNumberOfIterations = 300;
  if( argc > 7 )
    {
    maxNumberOfIterations = atoi( argv[7] );
    }
  optimizer->SetMaximumStepLength( steplength ); 
  optimizer->SetMinimumStepLength( 0.001 );
  optimizer->SetNumberOfIterations( maxNumberOfIterations );
  optimizer->MinimizeOn();
  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 -1;
    } 
  OptimizerType::ParametersType finalParameters = 
                    registration->GetLastTransformParameters();
  const double finalRotationCenterX = finalParameters[4];
  const double finalRotationCenterY = finalParameters[5];
  const double finalTranslationX    = finalParameters[6];
  const double finalTranslationY    = finalParameters[7];
  const unsigned int numberOfIterations = optimizer->GetCurrentIteration();
  const double bestValue = optimizer->GetValue();
  // Software Guide : EndCodeSnippet

  // Print out results
  //
  std::cout << "Result = " << 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();
  resample->SetTransform( finalTransform );
  resample->SetInput( movingImageReader->GetOutput() );
  FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
  resample->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
  resample->SetOutputOrigin(  fixedImage->GetOrigin() );
  resample->SetOutputSpacing( fixedImage->GetSpacing() );
  resample->SetDefaultPixelValue( 100 );
  
  typedef  unsigned char  OutputPixelType;
  typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
  
  typedef itk::CastImageFilter< 
                        FixedImageType,
                        OutputImageType > CastFilterType;
                    
  typedef itk::ImageFileWriter< OutputImageType >  WriterType;

  WriterType::Pointer      writer =  WriterType::New();
  CastFilterType::Pointer  caster =  CastFilterType::New();

  writer->SetFileName( argv[3] );

  caster->SetInput( resample->GetOutput() );
  writer->SetInput( caster->GetOutput()   );
  writer->Update();

  typedef itk::SquaredDifferenceImageFilter< 
                                  FixedImageType, 
                                  FixedImageType, 
                                  OutputImageType > DifferenceFilterType;
  DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
  WriterType::Pointer writer2 = WriterType::New();
  writer2->SetInput( difference->GetOutput() );  
  
  if( argc > 4 )
    {
    difference->SetInput1( fixedImageReader->GetOutput() );
    difference->SetInput2( resample->GetOutput() );
    writer2->SetFileName( argv[4] );
    writer2->Update();
    }

  if( argc > 5 )
    {
    writer2->SetFileName( argv[5] );
    difference->SetInput1( fixedImageReader->GetOutput() );
    difference->SetInput2( movingImageReader->GetOutput() );
    writer2->Update();
    }

  return 0;
}
 

		
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