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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: LandmarkWarping2.cxx,v $
  Language:  C++
  Date:      $Date: 2005/08/31 14:14:16 $
  Version:   $Revision: 1.12 $

  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 deform an image using a KernelBase spline
//  and two sets of landmarks.
// 
//  \index{WarpImageFilter}
//  \index{DeformationFieldSource}
//
//  Software Guide : EndLatex 



// Software Guide : BeginCodeSnippet
#include "itkVector.h"
#include "itkImage.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkDeformationFieldSource.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkWarpImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"
// Software Guide : EndCodeSnippet

#include <fstream>


int main( int argc, char * argv[] )
{

  if( argc < 3 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " landmarksFile fixedImage ";
    std::cerr << "movingImage deformedMovingImage" << std::endl;
    return 1;
    }

  const     unsigned int   Dimension = 2;
  typedef   float          VectorComponentType;

  typedef   itk::Vector< VectorComponentType, Dimension >    VectorType;

  typedef   itk::Image< VectorType,  Dimension >   DeformationFieldType;


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

  typedef   itk::ImageFileReader< FixedImageType  >  FixedReaderType;
  typedef   itk::ImageFileReader< MovingImageType >  MovingReaderType;

  typedef   itk::ImageFileWriter< MovingImageType >  MovingWriterType;


  FixedReaderType::Pointer fixedReader = FixedReaderType::New();
  fixedReader->SetFileName( argv[2] );

  try
    {
    fixedReader->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown " << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }


  MovingReaderType::Pointer movingReader = MovingReaderType::New();
  MovingWriterType::Pointer movingWriter = MovingWriterType::New();

  movingReader->SetFileName( argv[3] );
  movingWriter->SetFileName( argv[4] );


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


  typedef itk::DeformationFieldSource<
                                DeformationFieldType 
                                             >  DeformationSourceType;

  DeformationSourceType::Pointer deformer = DeformationSourceType::New();



  deformer->SetOutputSpacing( fixedImage->GetSpacing() );
  deformer->SetOutputOrigin(  fixedImage->GetOrigin() );
  deformer->SetOutputRegion(  fixedImage->GetLargestPossibleRegion() );



  //  Create source and target landmarks.
  //  
  typedef DeformationSourceType::LandmarkContainerPointer   LandmarkContainerPointer;
  typedef DeformationSourceType::LandmarkContainer          LandmarkContainerType;
  typedef DeformationSourceType::LandmarkPointType          LandmarkPointType;

  LandmarkContainerType::Pointer sourceLandmarks = LandmarkContainerType::New();
  LandmarkContainerType::Pointer targetLandmarks = LandmarkContainerType::New();

  LandmarkPointType sourcePoint;
  LandmarkPointType targetPoint;

  std::ifstream pointsFile;
  pointsFile.open( argv[1] );

  unsigned int pointId = 0;

  pointsFile >> sourcePoint;
  pointsFile >> targetPoint;

  while( !pointsFile.fail() )
    {
    sourceLandmarks->InsertElement( pointId, sourcePoint );
    targetLandmarks->InsertElement( pointId, targetPoint );
    pointId++;

    pointsFile >> sourcePoint;
    pointsFile >> targetPoint;

    }

  pointsFile.close();

  
  deformer->SetSourceLandmarks( sourceLandmarks.GetPointer() );
  deformer->SetTargetLandmarks( targetLandmarks.GetPointer() );

  try
    {
    deformer->UpdateLargestPossibleRegion();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown " << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }

  DeformationFieldType::ConstPointer deformationField = deformer->GetOutput();

  typedef itk::WarpImageFilter< MovingImageType, 
                                MovingImageType, 
                                DeformationFieldType  >  FilterType;

  FilterType::Pointer warper = FilterType::New();

  typedef itk::LinearInterpolateImageFunction< 
                       MovingImageType, double >  InterpolatorType;

  InterpolatorType::Pointer interpolator = InterpolatorType::New();

  warper->SetInterpolator( interpolator );


  warper->SetOutputSpacing( deformationField->GetSpacing() );
  warper->SetOutputOrigin(  deformationField->GetOrigin() );

  warper->SetDeformationField( deformationField );

  warper->SetInput( movingReader->GetOutput() );
  
  movingWriter->SetInput( warper->GetOutput() );


  
  try
    {
    movingWriter->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown " << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }


  return EXIT_SUCCESS;

}

