text: /*=========================================================================
   *
   *  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
   *
   *  Unless required by applicable law or agreed to in writing, software
   *  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 Translation Transform,
  //  the Normalized Mutual Information metric and the One+One evolutionary optimizer.
  //
  // Software Guide : EndLatex
  
  
  // Software Guide : BeginCodeSnippet
  #include "itkImageRegistrationMethod.h"
  
  #include "itkTranslationTransform.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] [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::TranslationTransform< double, Dimension > 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() );
  
    transform->SetIdentity();
    typedef RegistrationType::ParametersType ParametersType;
    ParametersType initialParameters =  transform->GetParameters();
    initialParameters[0] = 0.0;
    initialParameters[1] = 0.0;
  
    if( argc > 8 )
      {
      initialParameters[0] = atof( argv[7] );
      initialParameters[1] = atof( argv[8] );
      }
    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 * size[0] * spacing[0] );
    optimizerScales[1] = 1.0 / ( 0.1 * size[1] * spacing[1] );
    optimizer->SetScales( optimizerScales );
  
    typedef itk::Statistics::NormalVariateGenerator  GeneratorType;
    GeneratorType::Pointer generator = GeneratorType::New();
    generator->Initialize(12345);
  
    optimizer->MaximizeOn();
    optimizer->SetNormalVariateGenerator( generator );
    double initialRadius = 0.01;
    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;
      }
  
    ParametersType finalParameters = registration->GetLastTransformParameters();
    const double finalTranslationX    = finalParameters[0];
    const double finalTranslationY    = finalParameters[1];
    unsigned int numberOfIterations = optimizer->GetCurrentIteration();
    const double bestValue = optimizer->GetValue();
  
    // Print out results
    std::cout << "Result = " << 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;
  }
  