ReadResampleWriteNifti.cxx

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

Program:   Insight Segmentation & Registration Toolkit
Module:    ReadResampleWriteNifti.cxx
Language:  C++
Date:      Date: 2010/12/13
Version:   1.0
Author:    Jian Wu (eewujian@hotmail.com)
           Univerisity of Florida
		   Virginia Commonwealth University

This Program read a 3D image volume, downsample it, and save it in NIFTI
image format.

This program was modified from the ITK example--ResampleImageFilter2.cxx

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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkNiftiImageIO.h"
#include "itkResampleImageFilter.h"
#include "itkAffineTransform.h"
#include "itkLinearInterpolateImageFunction.h"



int main( int argc, char * argv[] )
{
  if( argc < 3 )
    {
    std::cerr << "Usage: " << std::endl;
	std::cerr << argv[0] << "  inputImageFile  outputImageFile" << std::endl; 
    return EXIT_FAILURE;
    }

  if( argc > 3 )
    {
		std::cerr << "Too many arguments" << std::endl; 
  }

  const     unsigned int   Dimension = 3;

  double outputSpacing[ Dimension ];
  outputSpacing[0] = 2.0; // pixel spacing in millimeters along X
  outputSpacing[1] = 2.0; // pixel spacing in millimeters along Y
  outputSpacing[2] = 2.0; // pixel spacing in millimeters along Z

  typedef   short  InputPixelType;
  typedef   short  OutputPixelType;

  typedef itk::Image< InputPixelType,  Dimension >   InputImageType;
  typedef itk::Image< OutputPixelType, Dimension >   OutputImageType;


  typedef itk::ImageFileReader< InputImageType  >  ReaderType;
  typedef itk::ImageFileWriter< OutputImageType >  WriterType;

  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName( argv[1] );
  reader->Update();

  typedef itk::ResampleImageFilter<
                  InputImageType, OutputImageType >  FilterType;

  FilterType::Pointer filter = FilterType::New();
  typedef itk::AffineTransform< double, Dimension >  TransformType;
  TransformType::Pointer transform = TransformType::New();

  typedef itk::LinearInterpolateImageFunction< 
                       InputImageType, double >  InterpolatorType;
  InterpolatorType::Pointer interpolator = InterpolatorType::New();
  filter->SetInterpolator( interpolator );

  filter->SetDefaultPixelValue( 0 );

  InputImageType::SpacingType inputSpacing = reader->GetOutput()->GetSpacing();
  InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion();
  InputImageType::SizeType inputSize = inputRegion.GetSize();

  double resampleRatio[ Dimension ];
  resampleRatio[0] = outputSpacing[0] / inputSpacing[0]; // resample ratio along X
  resampleRatio[1] = outputSpacing[1] / inputSpacing[1]; // resample ratio along Y
  resampleRatio[2] = outputSpacing[2] / inputSpacing[2]; // resample ratio along Z


  filter->SetOutputSpacing( outputSpacing );
 
  filter->SetOutputOrigin( reader->GetOutput()->GetOrigin() );


  InputImageType::SizeType   outputSize;

  outputSize[0] = floor(inputSize[0] / resampleRatio[0] + 0.5);  // number of pixels along X
  outputSize[1] = floor(inputSize[1] / resampleRatio[1] + 0.5);  // number of pixels along Y
  outputSize[2] = floor(inputSize[2] / resampleRatio[2] + 0.5);  // number of pixels along Z

  filter->SetSize( outputSize );

  filter->SetInput( reader->GetOutput() );

  transform->SetIdentity();
  filter->SetTransform( transform );

  WriterType::Pointer writer = WriterType::New();

  typedef itk::NiftiImageIO                   ImageIOType;    
  ImageIOType::Pointer niftiIO = ImageIOType::New();

  //  The NiftiImageIO object is then connected to the
  //  ImageFileWriter.  This will short-circuit the action of the
  //  ImageIOFactory mechanism. The ImageFileWriter will
  //  not attempt to look for other ImageIO objects capable of
  //  performing the writing tasks. It will simply invoke the one provided by
  //  the user.
  writer->SetImageIO( niftiIO );
  writer->SetFileName( argv[2] );
  writer->SetInput( filter->GetOutput() );
  writer->Update();

  return EXIT_SUCCESS;
}