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/*=========================================================================
Program: Advanced Normalization Tools
Module: $RCSfile: ConvertToJpg.cxx,v $
Language: C++
Date: $Date: 2008/11/15 23:46:06 $
Version: $Revision: 1.19 $
Copyright (c) ConsortiumOfANTS. All rights reserved.
See accompanying COPYING.txt or
http://sourceforge.net/projects/advants/files/ANTS/ANTSCopyright.txt 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.
=========================================================================*/
#include <iostream>
#include <fstream>
#include <stdio.h>
#include <limits.h>
#include "itkImage.h"
#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "itkCastImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
template <unsigned int ImageDimension,class TPIXELTYPE>
int ConvertType(int argc, char *argv[] , double MINVAL, double MAXVAL)
{
typedef TPIXELTYPE outPixelType;
typedef float floatPixelType;
typedef float inPixelType;
typedef itk::Image<inPixelType,ImageDimension> ImageType;
typedef itk::Image<floatPixelType,ImageDimension> IntermediateType;
typedef itk::Image<outPixelType,ImageDimension> OutImageType;
typedef itk::ImageFileReader<ImageType> readertype;
typedef itk::ImageFileWriter<OutImageType> writertype;
typename readertype::Pointer reader = readertype::New();
reader->SetFileName(argv[1]);
reader->Update();
std::cout << " Updated reader " << std::endl;
typedef itk::CastImageFilter<ImageType,IntermediateType> castertype;
typename castertype::Pointer caster=castertype::New();
caster->SetInput(reader->GetOutput());
caster->Update();
// Rescale the image intensities so that they fall between 0 and 255
typedef itk::RescaleIntensityImageFilter<IntermediateType,IntermediateType> FilterType;
typename FilterType::Pointer fixedrescalefilter = FilterType::New();
fixedrescalefilter->SetInput(caster->GetOutput());
const double desiredMinimum = MINVAL;
double desiredMaximum = MAXVAL;
fixedrescalefilter->SetOutputMinimum( desiredMinimum );
fixedrescalefilter->SetOutputMaximum( desiredMaximum );
fixedrescalefilter->UpdateLargestPossibleRegion();
typedef itk::CastImageFilter<IntermediateType,OutImageType> castertype2;
typename castertype2::Pointer caster2=castertype2::New();
caster2->SetInput(fixedrescalefilter->GetOutput());
caster2->Update();
typename OutImageType::Pointer outim = caster2->GetOutput();
typename OutImageType::SpacingType spc = outim->GetSpacing();
outim->SetSpacing(spc);
std::cout << " Dire in " << reader->GetOutput()->GetDirection() << std::endl;
std::cout << " Dire out " << outim->GetDirection() << std::endl;
typename writertype::Pointer writer = writertype::New();
writer->SetFileName(argv[2]);
writer->SetInput(outim);
writer->Update();
writer->Write();
return 0;
}
int main(int argc, char *argv[])
{
if ( argc < 3 )
{ std::cout << "Usage: " << argv[0] << " infile.nii out.ext TYPE-OPTION " << std::endl;
std::cout <<" ext is the extension you want, e.g. tif. " << std::endl;
std::cout << " TYPE-OPTION : TYPE " << std::endl;
std::cout << " 0 : char " << std::endl;
std::cout << " 1 : unsigned char " << std::endl;
std::cout << " 2 : short " << std::endl;
std::cout << " 3 : unsigned short " << std::endl;
std::cout << " 4 : int " << std::endl;
std::cout << " 5 : unsigned int " << std::endl;
std::cout << " Note that some pixel types are not supported by some image formats. e.g. int is not supported by jpg. " << std::endl;
std::cout << " You can easily extend this for other pixel types with a few lines of code and adding usage info. " << std::endl;
std::cout <<" The image intensity will be scaled to the dynamic range of the pixel type. E.g. uchar => 0 (min), 255 (max). " << std::endl;
return 1;
}
unsigned int typeoption=0;
if ( argc > 3 ) { typeoption=atoi(argv[3]); }
// Get the image dimension
std::string fn = std::string(argv[1]);
itk::ImageIOBase::Pointer imageIO =
itk::ImageIOFactory::CreateImageIO(
fn.c_str(), itk::ImageIOFactory::ReadMode);
imageIO->SetFileName(fn.c_str());
imageIO->ReadImageInformation();
if ( typeoption == 0 ) {
switch ( imageIO->GetNumberOfDimensions() )
{
case 2:
ConvertType<2,char>(argc,argv, SCHAR_MIN, SCHAR_MAX );
break;
case 3:
ConvertType<3,char>(argc,argv, SCHAR_MIN, SCHAR_MAX );
break;
default:
std::cerr << "Unsupported dimension" << std::endl;
exit( EXIT_FAILURE );
}
}
else if ( typeoption == 1 ) {
switch ( imageIO->GetNumberOfDimensions() )
{
case 2:
ConvertType<2,unsigned char>(argc,argv, 0, UCHAR_MAX );
break;
case 3:
ConvertType<3,unsigned char>(argc,argv, 0, UCHAR_MAX );
break;
default:
std::cerr << "Unsupported dimension" << std::endl;
exit( EXIT_FAILURE );
}
}
else if ( typeoption == 2 ) {
switch ( imageIO->GetNumberOfDimensions() )
{
case 2:
ConvertType<2, short>(argc,argv, SHRT_MIN, SHRT_MAX);
break;
case 3:
ConvertType<3, short>(argc,argv, SHRT_MIN, SHRT_MAX);
break;
default:
std::cerr << "Unsupported dimension" << std::endl;
exit( EXIT_FAILURE );
}
}
else if ( typeoption == 3 ) {
switch ( imageIO->GetNumberOfDimensions() )
{
case 2:
ConvertType<2,unsigned short>(argc,argv, 0, USHRT_MAX );
break;
case 3:
ConvertType<3,unsigned short>(argc,argv, 0, USHRT_MAX );
break;
default:
std::cerr << "Unsupported dimension" << std::endl;
exit( EXIT_FAILURE );
}
}
else if ( typeoption == 4 ) {
switch ( imageIO->GetNumberOfDimensions() )
{
case 2:
ConvertType<2,int>(argc,argv, INT_MIN, INT_MAX);
break;
case 3:
ConvertType<3,int>(argc,argv, INT_MIN, INT_MAX);
break;
default:
std::cerr << "Unsupported dimension" << std::endl;
exit( EXIT_FAILURE );
}
}
else if ( typeoption == 5 ) {
switch ( imageIO->GetNumberOfDimensions() )
{
case 2:
ConvertType<2,unsigned int>(argc,argv, 0, UINT_MAX );
break;
case 3:
ConvertType<3,unsigned int>(argc,argv, 0, UINT_MAX );
break;
default:
std::cerr << "Unsupported dimension" << std::endl;
exit( EXIT_FAILURE );
}
}
return 0;
}
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