[Insight-users] deformable registration in binary image

[Marc Ruiz]

Skipped content of type multipart/alternative-------------- next part --------------
/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: MaskDeformableRegistration.cxx,v $
  Language:  C++
 =========================================================================*/


#include "itkImageRegistrationMethod.h"
#include "itkMatchCardinalityImageToImageMetric.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkImage.h"

#include "itkTimeProbesCollectorBase.h"

#include "itkBSplineDeformableTransform.h"
#include "itkLBFGSBOptimizer.h"

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

#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.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::LBFGSBOptimizer     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->GetInfinityNormOfProjectedGradient() << 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 outputImagefile  ";
    return 1;
    }
  
  const    unsigned int    ImageDimension = 3;
  typedef  signed short    PixelType;

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


  const unsigned int SpaceDimension = ImageDimension;
  const unsigned int SplineOrder = 3;
  typedef double CoordinateRepType;

  typedef itk::BSplineDeformableTransform<
                            CoordinateRepType,
                            SpaceDimension,
                            SplineOrder >     TransformType;


  typedef itk::LBFGSBOptimizer       OptimizerType;

  typedef itk::MatchCardinalityImageToImageMetric< 
                                    FixedImageType, 
                                    MovingImageType >    MetricType;

  typedef itk:: NearestNeighborInterpolateImageFunction< 
                                    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();
  MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();

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

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

  registration->SetFixedImage(  fixedImage   );
  registration->SetMovingImage(   movingImageReader->GetOutput()   );

  fixedImageReader->Update();

  FixedImageType::RegionType fixedRegion = fixedImage->GetBufferedRegion();
  
  registration->SetFixedImageRegion( fixedRegion );

  
  typedef TransformType::RegionType RegionType;
  RegionType bsplineRegion;
  RegionType::SizeType   gridSizeOnImage;
  RegionType::SizeType   gridBorderSize;
  RegionType::SizeType   totalGridSize;

  gridSizeOnImage.Fill( 12 );
  gridSizeOnImage[2] = 3;
  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();;

  FixedImageType::SizeType fixedImageSize = fixedRegion.GetSize();

  for(unsigned int r=0; r<ImageDimension; r++)
    {
    spacing[r] *= floor( static_cast<double>(fixedImageSize[r] - 1)  / 
                  static_cast<double>(gridSizeOnImage[r] - 1) );
    origin[r]  -=  spacing[r]; 
    }

  transform->SetGridSpacing( spacing );
  transform->SetGridOrigin( origin );
  transform->SetGridRegion( bsplineRegion );
  

  typedef TransformType::ParametersType     ParametersType;

  const unsigned int numberOfParameters =
               transform->GetNumberOfParameters();
  
  ParametersType parameters( numberOfParameters );

  parameters.Fill( 0.0 );

  transform->SetParameters( parameters );
  

  registration->SetInitialTransformParameters( transform->GetParameters() );
  
  metric->MeasureMatchesOff();
  
  OptimizerType::BoundSelectionType boundSelect( transform->GetNumberOfParameters() );
  OptimizerType::BoundValueType upperBound( transform->GetNumberOfParameters() );
  OptimizerType::BoundValueType lowerBound( transform->GetNumberOfParameters() );

  boundSelect.Fill( 0 );
  upperBound.Fill( 0.0 );
  lowerBound.Fill( 0.0 );

  optimizer->SetBoundSelection( boundSelect );
  optimizer->SetUpperBound( upperBound );
  optimizer->SetLowerBound( lowerBound );

  optimizer->SetCostFunctionConvergenceFactor( 1e1 );
  optimizer->SetProjectedGradientTolerance( 3.5e-7);
  optimizer->SetMaximumNumberOfIterations( 500 );
  optimizer->SetMaximumNumberOfEvaluations( 500 );
  optimizer->SetMaximumNumberOfCorrections( 12 );
  

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

  
  // Add a time probe
  itk::TimeProbesCollectorBase collector;

  std::cout << std::endl << "Starting Registration" << std::endl;

  try 
    { 
    collector.Start( "Registration" );
    registration->StartRegistration(); 
    collector.Stop( "Registration" );
    } 
  catch( itk::ExceptionObject & err ) 
    { 
    std::cerr << "ExceptionObject caught !" << std::endl; 
    std::cerr << err << std::endl; 
    return -1;
    } 
  
  OptimizerType::ParametersType finalParameters = 
                    registration->GetLastTransformParameters();

//  std::cout << "Last Transform Parameters" << std::endl;
//  std::cout << finalParameters << std::endl;


  // Report the time taken by the registration
  collector.Report();

  
  transform->SetParameters( finalParameters );
 

  std::cout << optimizer->GetCurrentIteration() << "   ";
  std::cout << optimizer->GetValue() << "   ";
  std::cout << optimizer->GetInfinityNormOfProjectedGradient() << std::endl;


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

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

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

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

  typedef itk::Image< OutputPixelType, ImageDimension > 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()   );


  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & err ) 
    { 
    std::cerr << "ExceptionObject caught !" << std::endl; 
    std::cerr << err << std::endl; 
    return -1;
    } 
 

  return 0;
}