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.
   *
   *=========================================================================*/
  
  //
  // This example is the 3D version of the 2D example in MultiResImageRegistration1.cxx
  //
  
  #include "itkMultiResolutionImageRegistrationMethod.h"
  #include "itkTranslationTransform.h"
  #include "itkMattesMutualInformationImageToImageMetric.h"
  #include "itkRegularStepGradientDescentOptimizer.h"
  #include "itkImage.h"
  #include "itkImageFileReader.h"
  #include "itkImageFileWriter.h"
  #include "itkResampleImageFilter.h"
  #include "itkCastImageFilter.h"
  #include "itkCheckerBoardImageFilter.h"
  
  
  #include "itkCommand.h"
  
  
  template <typename TRegistration>
  class RegistrationInterfaceCommand : public itk::Command
  {
  public:
    typedef  RegistrationInterfaceCommand   Self;
    typedef  itk::Command                   Superclass;
    typedef  itk::SmartPointer<Self>        Pointer;
    itkNewMacro( Self );
  
  protected:
    RegistrationInterfaceCommand() {};
  
  public:
    typedef   TRegistration                              RegistrationType;
    typedef   RegistrationType *                         RegistrationPointer;
    typedef   itk::RegularStepGradientDescentOptimizer   OptimizerType;
    typedef   OptimizerType *                            OptimizerPointer;
  
    void Execute(itk::Object * object, const itk::EventObject & event)
      {
      if( !(itk::IterationEvent().CheckEvent( &event )) )
        {
        return;
        }
      RegistrationPointer registration = static_cast<RegistrationPointer>( object );
      if(registration == ITK_NULLPTR)
        {
        return;
        }
      OptimizerPointer optimizer = static_cast< OptimizerPointer >(registration->GetModifiableOptimizer() );
  
      std::cout << "-------------------------------------" << std::endl;
      std::cout << "MultiResolution Level : "
                << registration->GetCurrentLevel()  << std::endl;
      std::cout << std::endl;
  
      if ( registration->GetCurrentLevel() == 0 )
        {
        optimizer->SetMaximumStepLength( 16.00 );
        optimizer->SetMinimumStepLength( 0.01 );
        }
      else
        {
        optimizer->SetMaximumStepLength( optimizer->GetMaximumStepLength() / 4.0 );
        optimizer->SetMinimumStepLength( optimizer->GetMinimumStepLength() / 10.0 );
        }
      }
  
    void Execute(const itk::Object * , const itk::EventObject & )
      { return; }
  };
  
  
  //  The following section of code implements an observer
  //  that will monitor the evolution of the registration process.
  //
  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 = static_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 < 4 )
      {
      std::cerr << "Missing Parameters " << std::endl;
      std::cerr << "Usage: " << argv[0];
      std::cerr << " fixedImageFile  movingImageFile ";
      std::cerr << " outputImagefile [backgroundGrayLevel]";
      std::cerr << " [checkerBoardBefore] [checkerBoardAfter]";
      std::cerr << " [useExplicitPDFderivatives ] " << std::endl;
      std::cerr << " [numberOfBins] [numberOfSamples ] " << std::endl;
      return EXIT_FAILURE;
      }
  
    const    unsigned int    Dimension = 3;
    typedef  unsigned short  PixelType;
  
    typedef itk::Image< PixelType, Dimension >  FixedImageType;
    typedef itk::Image< PixelType, Dimension >  MovingImageType;
  
    typedef   float                                    InternalPixelType;
    typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
  
    typedef itk::TranslationTransform< double, Dimension > TransformType;
    typedef itk::RegularStepGradientDescentOptimizer       OptimizerType;
    typedef itk::LinearInterpolateImageFunction<
                                      InternalImageType,
                                      double             > InterpolatorType;
    typedef itk::MattesMutualInformationImageToImageMetric<
                                      InternalImageType,
                                      InternalImageType >   MetricType;
    typedef itk::MultiResolutionImageRegistrationMethod<
                                      InternalImageType,
                                      InternalImageType >   RegistrationType;
  
    typedef itk::MultiResolutionPyramidImageFilter<
                                      InternalImageType,
                                      InternalImageType >   FixedImagePyramidType;
    typedef itk::MultiResolutionPyramidImageFilter<
                                      InternalImageType,
                                      InternalImageType >   MovingImagePyramidType;
  
  
    //  All the components are instantiated using their \code{New()} method
    //  and connected to the registration object as in previous example.
    //
    TransformType::Pointer      transform     = TransformType::New();
    OptimizerType::Pointer      optimizer     = OptimizerType::New();
    InterpolatorType::Pointer   interpolator  = InterpolatorType::New();
    RegistrationType::Pointer   registration  = RegistrationType::New();
    MetricType::Pointer         metric        = MetricType::New();
  
    FixedImagePyramidType::Pointer fixedImagePyramid =
        FixedImagePyramidType::New();
    MovingImagePyramidType::Pointer movingImagePyramid =
        MovingImagePyramidType::New();
  
    registration->SetOptimizer(     optimizer     );
    registration->SetTransform(     transform     );
    registration->SetInterpolator(  interpolator  );
    registration->SetMetric( metric  );
    registration->SetFixedImagePyramid( fixedImagePyramid );
    registration->SetMovingImagePyramid( movingImagePyramid );
  
  
    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::CastImageFilter<
                          FixedImageType, InternalImageType > FixedCastFilterType;
    typedef itk::CastImageFilter<
                          MovingImageType, InternalImageType > MovingCastFilterType;
  
    FixedCastFilterType::Pointer fixedCaster   = FixedCastFilterType::New();
    MovingCastFilterType::Pointer movingCaster = MovingCastFilterType::New();
  
    fixedCaster->SetInput(  fixedImageReader->GetOutput() );
    movingCaster->SetInput( movingImageReader->GetOutput() );
  
    registration->SetFixedImage(    fixedCaster->GetOutput()    );
    registration->SetMovingImage(   movingCaster->GetOutput()   );
  
  
    fixedCaster->Update();
  
    registration->SetFixedImageRegion(
         fixedCaster->GetOutput()->GetBufferedRegion() );
  
  
    typedef RegistrationType::ParametersType ParametersType;
    ParametersType initialParameters( transform->GetNumberOfParameters() );
  
    initialParameters[0] = 0.0;  // Initial offset in mm along X
    initialParameters[1] = 0.0;  // Initial offset in mm along Y
    initialParameters[2] = 0.0;  // Initial offset in mm along Z
  
    registration->SetInitialTransformParameters( initialParameters );
  
    metric->SetNumberOfHistogramBins( 128 );
    metric->SetNumberOfSpatialSamples( 50000 );
  
    if( argc > 8 )
      {
      // optionally, override the values with numbers taken from the command line arguments.
      metric->SetNumberOfHistogramBins( atoi( argv[8] ) );
      }
  
    if( argc > 9 )
      {
      // optionally, override the values with numbers taken from the command line arguments.
      metric->SetNumberOfSpatialSamples( atoi( argv[9] ) );
      }
  
    metric->ReinitializeSeed( 76926294 );
  
  
    if( argc > 7 )
      {
      // Define whether to calculate the metric derivative by explicitly
      // computing the derivatives of the joint PDF with respect to the Transform
      // parameters, or doing it by progressively accumulating contributions from
      // each bin in the joint PDF.
      metric->SetUseExplicitPDFDerivatives( atoi( argv[7] ) );
      }
  
  
    optimizer->SetNumberOfIterations( 200 );
    optimizer->SetRelaxationFactor( 0.9 );
  
  
    // Create the Command observer and register it with the optimizer.
    //
    CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
    optimizer->AddObserver( itk::IterationEvent(), observer );
  
    typedef RegistrationInterfaceCommand<RegistrationType> CommandType;
    CommandType::Pointer command = CommandType::New();
    registration->AddObserver( itk::IterationEvent(), command );
  
  
    registration->SetNumberOfLevels( 3 );
  
    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();
  
    double TranslationAlongX = finalParameters[0];
    double TranslationAlongY = finalParameters[1];
    double TranslationAlongZ = finalParameters[2];
  
    unsigned int numberOfIterations = optimizer->GetCurrentIteration();
  
    double bestValue = optimizer->GetValue();
  
  
    // Print out results
    //
    std::cout << "Result = " << std::endl;
    std::cout << " Translation X = " << TranslationAlongX  << std::endl;
    std::cout << " Translation Y = " << TranslationAlongY  << std::endl;
    std::cout << " Translation Z = " << TranslationAlongZ  << 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() );
  
    FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
  
    PixelType backgroundGrayLevel = 100;
    if( argc > 4 )
      {
      backgroundGrayLevel = atoi( argv[4] );
      }
  
    resample->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
    resample->SetOutputOrigin(  fixedImage->GetOrigin() );
    resample->SetOutputSpacing( fixedImage->GetSpacing() );
    resample->SetOutputDirection( fixedImage->GetDirection() );
    resample->SetDefaultPixelValue( backgroundGrayLevel );
  
  
    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();
  
    //
    // Generate checkerboards before and after registration
    //
    typedef itk::CheckerBoardImageFilter< FixedImageType > CheckerBoardFilterType;
  
    CheckerBoardFilterType::Pointer checker = CheckerBoardFilterType::New();
  
    checker->SetInput1( fixedImage );
    checker->SetInput2( resample->GetOutput() );
  
    caster->SetInput( checker->GetOutput() );
    writer->SetInput( caster->GetOutput()   );
  
    resample->SetDefaultPixelValue( 0 );
  
    // Before registration
    TransformType::Pointer identityTransform = TransformType::New();
    identityTransform->SetIdentity();
    resample->SetTransform( identityTransform );
  
    if( argc > 5 )
      {
      writer->SetFileName( argv[5] );
      writer->Update();
      }
  
  
    // After registration
    resample->SetTransform( finalTransform );
    if( argc > 6 )
      {
      writer->SetFileName( argv[6] );
      writer->Update();
      }
  
    return EXIT_SUCCESS;
  }
  