//Scaling a 3D object

#include <stdio.h>
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRegionOfInterestImageFilter.h"

#include "itkResampleImageFilter.h"
#include "itkAffineTransform.h"
#include "itkIdentityTransform.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkLinearInterpolateImageFunction.h"

using namespace std;

int main(void)
{
  typedef unsigned char  InputPixelType;
  typedef unsigned char  OutputPixelType;
  const   unsigned int   Dimension = 3;

  typedef itk::Image< InputPixelType,  Dimension >    InputImageType;
  typedef itk::Image< OutputPixelType, Dimension >    OutputImageType; 
  typedef itk::ImageFileReader< InputImageType  >  ReaderType;
  typedef itk::ImageFileWriter< OutputImageType >  WriterType;
  typedef itk::NearestNeighborInterpolateImageFunction< InputImageType, double >  InterpolatorType; 
  typedef itk::AffineTransform< double, Dimension >  TransformType;  
  //   typedef itk::IdentityTransform< double, Dimension >  TransformType;
  typedef itk::ResampleImageFilter<InputImageType,OutputImageType> FilterTypeResample;  

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();
  InterpolatorType::Pointer interpolator = InterpolatorType::New();
  TransformType::Pointer transform = TransformType::New();
  FilterTypeResample::Pointer filterResample = FilterTypeResample::New();

  // working
  //reader->SetFileName("C:/Images/brainweb165a10f17.mha");
  //writer->SetFileName("C:/Images/AffineTransform_brainweb165a10f17.hdr");

  //not working
  reader->SetFileName("C:/Images/ConfiConnect_brainweb165a10f17_whiteMatter.mha");
  writer->SetFileName("C:/Images/AffineTransform_ConfiConnect_brainweb165a10f17_whiteMatter.hdr");

  reader->Update();

  InputImageType::RegionType   region = reader->GetOutput()->GetLargestPossibleRegion();  
  InputImageType::SizeType     size  = region.GetSize();
  InputImageType::IndexType    start = region.GetIndex();

  //----- set the spacing of the filter
  double spacing[ Dimension ];
  const InputImageType::SpacingType& sp = reader->GetOutput()->GetSpacing();
  //spacing[0] = sp[0]; // pixel spacing in millimeters along X
  //spacing[1] = sp[1]; // pixel spacing in millimeters along Y
  //spacing[2] = sp[2]; // pixel spacing in millimeters along Y
  spacing[0] = 2.82; // pixel spacing in millimeters along X
  spacing[1] = 3.39; // pixel spacing in millimeters along Y
  spacing[2] = 2.81; // pixel spacing in millimeters along Y
  filterResample->SetOutputSpacing( spacing );
  cout << "Spacing = "; cout << sp[0] << ", " << sp[1] << ", " << sp[2] << std::endl;
  
  //----- set the origin of the filter
  double origin[ Dimension ];
  const InputImageType::PointType& orgn = reader->GetOutput()->GetOrigin(); // instead of filter
  origin[0] = orgn[0];  // X space coordinate of origin
  origin[1] = orgn[1];  // Y space coordinate of origin
  origin[2] = orgn[2];  // Y space coordinate of origin
  filterResample->SetOutputOrigin( origin );
  cout << "Origin = "; cout << orgn[0] << ", " << orgn[1] << ", " << orgn[2] << std::endl;

  //----- set the size of the filter
  InputImageType::SizeType size2, imageSize =reader->GetOutput()->GetLargestPossibleRegion().GetSize();  
  //size2[0] =imageSize[0];  // number of pixels along X
  //size2[1] =imageSize[1];  // number of pixels along Y
  //size2[2] =imageSize[2];  // number of pixels along Y
  size2[0] =64;  // number of pixels along X
  size2[1] =64;  // number of pixels along Y
  size2[2] =64;  // number of pixels along Y
  filterResample->SetSize( size2 ); 
  cout << "ImageSize= "; cout << imageSize[0] << ", " << imageSize[1] << ", " << imageSize[2]<< std::endl;



  // Image Scaling
  TransformType::OutputVectorType scale;
  scale[0] = 1;  // X translation in millimeters
  scale[1] = 1;  // Y translation in millimeters
  scale[2] = 1;  // Y translation in millimeters
  //transform->Scale( scale );
  transform->SetIdentity();


  //filterResample->SetDefaultPixelValue( 100 );
  filterResample->SetOutputStartIndex( start );
  filterResample->SetTransform( transform );
  filterResample->SetInterpolator( interpolator );
  filterResample->SetInput( reader->GetOutput() );
  writer->SetInput( filterResample->GetOutput() );
  writer->Update();
  
  transform->Print( std::cout );


  cout << "Code end !" << std::endl;
  cin.get();
  return EXIT_SUCCESS;
}