[Insight-users] Reading Analyse 7.5 image

[chaitanya chitale]

Hi,

I am new to ITK and I am trying to read the Analyse 7.5 image.
Its an image created by imageJ and is a 16 bit grayscale image of the
dimension 512*512*24

I am getting a segmentation fault while doing reader1->update().
The code is a sample code which reads an image and writes it back. I am
using iterators because they will help manipulate the image for other
purposes.

Heres the code.

#include "itkImage.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionIterator.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRGBPixel.h"
#include "stdio.h"
using namespace std;

int main()
{
 const unsigned char Dimension = 3;

 typedef signed short PixelType;
 typedef itk::Image< PixelType, Dimension > ImageType;

 typedef itk::ImageRegionConstIterator< ImageType > ConstIteratorType;
 typedef itk::ImageRegionIterator< ImageType>       IteratorType;

 typedef itk::ImageFileReader< ImageType > ReaderType;
 typedef itk::ImageFileWriter< ImageType > WriterType;

 ImageType::RegionType inputRegion;

 ImageType::RegionType::IndexType inputStart;
 // Imput image size
 ImageType::RegionType::SizeType  size_ip;
 // Output image size
 ImageType::RegionType::SizeType  size_op;

 inputStart[0] = 0;
 inputStart[1] = 0;
 inputStart[2] = 0;

 size_ip[0]  = 512;
 size_ip[1]  = 512;
 size_ip[2]  = 24;

 inputRegion.SetSize( size_ip );
 inputRegion.SetIndex( inputStart );

 ImageType::RegionType outputRegion;

 ImageType::RegionType::IndexType outputStart;

 outputStart[0] = 0;
 outputStart[1] = 0;
 outputStart[2] = 0;

 outputRegion.SetSize( size_ip );
 outputRegion.SetIndex( outputStart );


 ReaderType::Pointer reader1 = ReaderType::New();
 reader1->SetFileName( "psf-green-bead-35nm.img" );
 try
   {
   reader1->Update();
   }
 catch ( itk::ExceptionObject &err)
   {
   std::cerr << "ExceptionObject caught !" << std::endl;
   std::cerr << err << std::endl;
   return -1;
   }


 ImageType::Pointer outputImage = ImageType::New();
 outputImage->SetRegions( outputRegion );
 const ImageType::SpacingType& spacing =
reader1->GetOutput()->GetSpacing();
 const ImageType::PointType& inputOrigin =
reader1->GetOutput()->GetOrigin();
 double   outputOrigin[ Dimension ];

 for(unsigned int i=0; i< Dimension; i++)
   {
   outputOrigin[i] = inputOrigin[i] + spacing[i] * inputStart[i];
   }

 outputImage->SetSpacing( spacing );
 outputImage->SetOrigin(  outputOrigin );
 outputImage->Allocate();

 ConstIteratorType inputIt1(   reader1->GetOutput(), inputRegion  );
 IteratorType outputIt( outputImage,outputRegion );

 inputIt1.GoToBegin();
 outputIt.GoToBegin();

 while( !inputIt1.IsAtEnd() )
 {
       outputIt.Set(inputIt1.Get());

   ++inputIt1;
       ++outputIt;
 }

 WriterType::Pointer writer = WriterType::New();
 writer->SetFileName("copy.img");
 writer->SetInput( outputImage );

 try
   {
   writer->Update();
   }
 catch ( itk::ExceptionObject &err)
   {
   std::cerr << "ExceptionObject caught !" << std::endl;
   std::cerr << err << std::endl;
   return -1;
   }


}


Can you please help?
Thank you in advance.
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