ImageRegistration14.cxx

/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
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 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

// Software Guide : BeginLatex
//
//  This example illustrates how to do registration with a 2D Rigid Transform
//  and with the Normalized Mutual Information metric.
//
// Software Guide : EndLatex


// Software Guide : BeginCodeSnippet
#include "itkImageRegistrationMethod.h"

#include "itkCenteredRigid2DTransform.h"
#include "itkCenteredTransformInitializer.h"

#include "itkNormalizedMutualInformationHistogramImageToImageMetric.h"
#include "itkOnePlusOneEvolutionaryOptimizer.h"
#include "itkNormalVariateGenerator.h"

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

#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.h"


//  The following section of code implements a Command observer
//  used to monitor the evolution of the registration process.
//
#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() {m_LastMetricValue = 0;}

public:
  typedef itk::OnePlusOneEvolutionaryOptimizer  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 = static_cast< OptimizerPointer >( object );
      if( ! itk::IterationEvent().CheckEvent( &event ) )
        {
        return;
        }
      double currentValue = optimizer->GetValue();
      // Only print out when the Metric value changes
      if( std::fabs( m_LastMetricValue - currentValue ) > 1e-7 )
        {
        std::cout << optimizer->GetCurrentIteration() << "   ";
        std::cout << currentValue << "   ";
        std::cout << optimizer->GetFrobeniusNorm() << "   ";
        std::cout << optimizer->GetCurrentPosition() << std::endl;
        m_LastMetricValue = currentValue;
        }
    }

private:
  double m_LastMetricValue;
};


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::cerr << "outputImagefile [numberOfHistogramBins] ";
    std::cerr << "[initialRadius] [epsilon]" << std::endl;
    std::cerr << "[initialAngle(radians)] [initialTx] [initialTy]"
              << std::endl;
    return EXIT_FAILURE;
    }

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

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

  typedef itk::CenteredRigid2DTransform< double > TransformType;

  typedef itk::OnePlusOneEvolutionaryOptimizer       OptimizerType;
  typedef itk::LinearInterpolateImageFunction<
                                    MovingImageType,
                                    double             > InterpolatorType;
  typedef itk::ImageRegistrationMethod<
                                    FixedImageType,
                                    MovingImageType    > RegistrationType;


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

  TransformType::Pointer      transform     = TransformType::New();
  OptimizerType::Pointer      optimizer     = OptimizerType::New();
  InterpolatorType::Pointer   interpolator  = InterpolatorType::New();
  RegistrationType::Pointer   registration  = RegistrationType::New();

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


  MetricType::Pointer metric = MetricType::New();
  registration->SetMetric( metric  );


  unsigned int numberOfHistogramBins = 32;
  if( argc > 4 )
    {
    numberOfHistogramBins = atoi( argv[4] );
    std::cout << "Using " << numberOfHistogramBins << " Histogram bins"
              << std::endl;
    }

  MetricType::HistogramType::SizeType histogramSize;

  histogramSize.SetSize(2);

  histogramSize[0] = numberOfHistogramBins;
  histogramSize[1] = numberOfHistogramBins;
  metric->SetHistogramSize( histogramSize );

  const unsigned int numberOfParameters = transform->GetNumberOfParameters();
  typedef MetricType::ScalesType ScalesType;
  ScalesType scales( numberOfParameters );

  scales.Fill( 1.0 );

  metric->SetDerivativeStepLengthScales(scales);

  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] );

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

  FixedImageType::ConstPointer fixedImage = fixedImageReader->GetOutput();
  registration->SetFixedImageRegion( fixedImage->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->GeometryOn();
  initializer->InitializeTransform();

  double initialAngle = 0.0;
  if( argc > 7 )
    {
    initialAngle = atof( argv[7] );
    }
  transform->SetAngle( initialAngle );
  TransformType::OutputVectorType initialTranslation
                                                 = transform->GetTranslation();
  if( argc > 9 )
    {
    initialTranslation[0] += atof( argv[8] );
    initialTranslation[1] += atof( argv[9] );
    }
  transform->SetTranslation( initialTranslation );

  typedef RegistrationType::ParametersType ParametersType;
  ParametersType initialParameters =  transform->GetParameters();
  registration->SetInitialTransformParameters( initialParameters );
  std::cout << "Initial transform parameters = ";
  std::cout << initialParameters << std::endl;

  typedef OptimizerType::ScalesType       OptimizerScalesType;
  OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );

  FixedImageType::RegionType region = fixedImage->GetLargestPossibleRegion();
  FixedImageType::SizeType size = region.GetSize();
  FixedImageType::SpacingType spacing = fixedImage->GetSpacing();

  optimizerScales[0] = 1.0 / 0.1;  // make angle move slowly
  optimizerScales[1] = 10000.0;    // prevent the center from moving
  optimizerScales[2] = 10000.0;    // prevent the center from moving
  optimizerScales[3] = 1.0 / ( 0.1 * size[0] * spacing[0] );
  optimizerScales[4] = 1.0 / ( 0.1 * size[1] * spacing[1] );
  std::cout << "optimizerScales = " << optimizerScales << std::endl;
  optimizer->SetScales( optimizerScales );

  typedef itk::Statistics::NormalVariateGenerator  GeneratorType;
  GeneratorType::Pointer generator = GeneratorType::New();
  generator->Initialize(12345);
  optimizer->MaximizeOn();
  optimizer->SetNormalVariateGenerator( generator );

  double initialRadius = 0.05;
  if( argc > 5 )
    {
    initialRadius = atof( argv[5] );
    std::cout << "Using initial radius = " << initialRadius << std::endl;
    }
  optimizer->Initialize( initialRadius );
  double epsilon = 0.001;
  if( argc > 6 )
    {
    epsilon = atof( argv[6] );
    std::cout << "Using epsilon = " << epsilon << std::endl;
    }
  optimizer->SetEpsilon( epsilon );
  optimizer->SetMaximumIteration( 2000 );

  // Create the Command observer and register it with the optimizer.
  //
  CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
  optimizer->AddObserver( itk::IterationEvent(), observer );
  try
    {
    registration->Update();
    std::cout << "Optimizer stop condition: "
              << registration->GetOptimizer()->GetStopConditionDescription()
              << std::endl;
    }
  catch( itk::ExceptionObject & err )
    {
    std::cout << "ExceptionObject caught !" << std::endl;
    std::cout << err << std::endl;
    return EXIT_FAILURE;
    }

  typedef RegistrationType::ParametersType ParametersType;
  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 * 180.0 / itk::Math::pi;
  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 );
  finalTransform->SetFixedParameters( transform->GetFixedParameters() );

  ResampleFilterType::Pointer resample = ResampleFilterType::New();
  resample->SetTransform( finalTransform );
  resample->SetInput( movingImageReader->GetOutput() );
  resample->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
  resample->SetOutputOrigin(  fixedImage->GetOrigin() );
  resample->SetOutputSpacing( fixedImage->GetSpacing() );
  resample->SetOutputDirection( fixedImage->GetDirection() );
  resample->SetDefaultPixelValue( 100 );

  typedef itk::Image< PixelType, Dimension >      OutputImageType;
  typedef itk::ImageFileWriter< OutputImageType > WriterType;

  WriterType::Pointer writer =  WriterType::New();
  writer->SetFileName( argv[3] );
  writer->SetInput( resample->GetOutput() );
  writer->Update();
  // Software Guide : EndCodeSnippet
  return EXIT_SUCCESS;
}