/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: ImageRegistration13.cxx,v $
  Language:  C++
  Date:      $Date: 2006/05/14 12:16:22 $
  Version:   $Revision: 1.20 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even 
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif





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


#include "itkImageRegistrationMethod.h"

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

// Software Guide : BeginCodeSnippet
#include "itkMattesMutualInformationImageToImageMetric.h"
// Software Guide : EndCodeSnippet

#include "itkLinearInterpolateImageFunction.h"
#include "itkRegularStepGradientDescentOptimizer.h"
#include "itkImage.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() {};
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( ! 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 < 3 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " fixedImageFile  movingImageFile ";
    std::cerr << "outputImagefile " << std::endl;
    return 1;
    }
  
  const    unsigned int    Dimension = 2;
  typedef  unsigned char   PixelType;
  
  typedef itk::Image< PixelType, Dimension >  FixedImageType;
  typedef itk::Image< PixelType, Dimension >  MovingImageType;

  // Software Guide : BeginLatex
  // The CenteredRigid2DTransform applies a rigid transform in 2D space.
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  typedef itk::CenteredRigid2DTransform< double > TransformType;
  typedef itk::RegularStepGradientDescentOptimizer       OptimizerType;
  // Software Guide : EndCodeSnippet
   
  typedef itk::LinearInterpolateImageFunction< 
                                    MovingImageType,
                                    double             > InterpolatorType;
  typedef itk::ImageRegistrationMethod< 
                                    FixedImageType, 
                                    MovingImageType    > RegistrationType;


  // Software Guide : BeginCodeSnippet
  typedef itk::MattesMutualInformationImageToImageMetric< 
                                          FixedImageType, 
                                          MovingImageType >    MetricType;
  // Software Guide : EndCodeSnippet




  // Software Guide : BeginCodeSnippet
  TransformType::Pointer      transform     = TransformType::New();
  OptimizerType::Pointer      optimizer     = OptimizerType::New();
  // Software Guide : EndCodeSnippet
  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  );



  metric->SetNumberOfHistogramBins( 20 );
  metric->SetNumberOfSpatialSamples( 10000 );

  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();

  registration->SetFixedImageRegion( 
       fixedImageReader->GetOutput()->GetBufferedRegion() );

  // Software Guide : BeginLatex
  // The \doxygen{CenteredRigid2DTransform} is initialized by 5 parameters, 
  // indicating the angle of rotation, the center coordinates and the 
  // translation to be applied after rotation. The initialization is done 
  // by the \doxygen{CenteredTransformInitializer}. 
  // The transform can operate in two modes, one assumes that the 
  // anatomical objects to be registered are centered in their respective 
  // images. Hence the best initial guess for the registration is the one
  // that superimposes those two centers.
  // This second approach assumes that the moments of the anatomical 
  // objects are similar for both images and hence the best initial guess 
  // for registration is to superimpose both mass centers. The center of
  // mass is computed from the moments obtained from the gray level values.
  // Here we adopt the first approach. The \code{GeometryOn()} method
  // toggles between the approaches.
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  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();
  // Software Guide : EndCodeSnippet

  transform->SetAngle( 0.0 );


  registration->SetInitialTransformParameters( transform->GetParameters() );

  // Software Guide : BeginLatex
  // The optimizer scales the metrics (the gradient in this case) by the 
  // scales during each iteration. Hence a large value of the center scale
  // will prevent movement along the center during optimization. Here we
  // assume that the fixed and moving images are likely to be related by 
  // a translation.
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  typedef OptimizerType::ScalesType       OptimizerScalesType;
  OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );

  const double translationScale = 1.0 / 128.0;
  const double centerScale      = 1000.0; // prevents it from moving 
                                          // during the optimization
  optimizerScales[0] = 1.0;
  optimizerScales[1] = centerScale;
  optimizerScales[2] = centerScale;
  optimizerScales[3] = translationScale;
  optimizerScales[4] = translationScale;

  optimizer->SetScales( optimizerScales );

  optimizer->SetMaximumStepLength( 0.5   ); 
  optimizer->SetMinimumStepLength( 0.0001 );
  optimizer->SetNumberOfIterations( 400 );
  // Software Guide : EndCodeSnippet

  // Create the Command observer and register it with the optimizer.
  //
  CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
  optimizer->AddObserver( itk::IterationEvent(), observer );


  try 
    { 
    registration->StartRegistration(); 
    } 
  catch( itk::ExceptionObject & err ) 
    { 
    std::cout << "ExceptionObject caught !" << std::endl; 
    std::cout << err << std::endl; 
    return -1;
    } 

  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];

  unsigned int numberOfIterations = optimizer->GetCurrentIteration();
  
  double bestValue = optimizer->GetValue();

  // Print out results
  //

  const double finalAngleInDegrees = finalAngle * 45.0 / atan(1.0);

  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 );

  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 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();

  return 0;
}

  //  Software Guide : BeginLatex
  //  
  //  Let's execute this example over some of the images provided in
  //  \code{Examples/Data}, for example:
  //  
  //  \begin{itemize}
  //  \item \code{BrainProtonDensitySlice.png} 
  //  \item \code{BrainProtonDensitySliceBorder20.png}
  //  \end{itemize}
  //
  //  The second image is the result of intentionally shifting the first
  //  image by $20mm$ in $X$ and $20mm$ in
  //  $Y$. Both images have unit-spacing and are shown in Figure
  //  \ref{fig:FixedMovingImageRegistration1}. The example 
  //  yielded the following results.
  //  
  //  \begin{verbatim}
  //  Translation X = 20
  //  Translation Y = 20
  //  \end{verbatim}
  //  These values match the true misalignment introduced in the moving image.
  //  Software Guide : EndLatex 

