csa2img.cxx

/*=========================================================================
 
  Program: GDCM (Grassroots DICOM). A DICOM library
 
  Copyright (c) 2006-2011 Mathieu Malaterre
  All rights reserved.
  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html 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 notice for more information.
 
=========================================================================*/
/*
 * I do not know what the format is, just guessing from info found on the net:
 *
 * http://atonal.ucdavis.edu/matlab/fmri/spm5/spm_dicom_convert.m
 *
 * This example is an attempt at understanding the format used by SIEMENS
 * their "SIEMENS CSA NON-IMAGE" DICOM file (1.3.12.2.1107.5.9.1)
 *
 * Everything done in this code is for the sole purpose of writing interoperable
 * software under Sect. 1201 (f) Reverse Engineering exception of the DMCA.
 * If you believe anything in this code violates any law or any of your rights,
 * please contact us (gdcm-developers@lists.sourceforge.net) so that we can
 * find a solution.
 *
 */
#include "gdcmReader.h"
#include "gdcmImageReader.h"
#include "gdcmImageWriter.h"
#include "gdcmCSAHeader.h"
#include "gdcmAttribute.h"
#include "gdcmPrivateTag.h"
 
#include <math.h>
 
int main(int argc, char *argv [])
{
  if( argc < 2 ) return 1;
  // gdcmDataExtra/gdcmNonImageData/exCSA_Non-Image_Storage.dcm
  // PHANTOM.MR.CARDIO_COEUR_S_QUENCE_DE_REP_RAGE.9.257.2008.03.20.14.53.25.578125.43151705.IMA
  const char *filename = argv[1];
 
  gdcm::Reader reader; // Do not use ImageReader
  reader.SetFileName( filename );
  if( !reader.Read() )
    {
    std::cerr << "Failed to read: " << filename << std::endl;
    return 1;
    }
 
  gdcm::CSAHeader csa;
  const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
 
  const gdcm::PrivateTag &t1 = csa.GetCSAImageHeaderInfoTag();
  //std::cout << t1 << std::endl;
  //const gdcm::PrivateTag &t2 = csa.GetCSASeriesHeaderInfoTag();
 
  if( ds.FindDataElement( t1 ) )
    {
    csa.LoadFromDataElement( ds.GetDataElement( t1 ) );
    csa.Print( std::cout );
    }
  int dims[2] = {};
  if( csa.FindCSAElementByName( "Columns" ) )
    {
    const gdcm::CSAElement &csael = csa.GetCSAElementByName( "Columns" );
    std::cout << csael << std::endl;
    //const gdcm::ByteValue *bv = csael.GetByteValue();
    gdcm::Element<gdcm::VR::IS, gdcm::VM::VM1> el;
    el.Set( csael.GetValue() );
    dims[0] = el.GetValue();
    std::cout << "Columns:" << el.GetValue() << std::endl;
    }
 
  if( csa.FindCSAElementByName( "Rows" ) )
    {
    const gdcm::CSAElement &csael2 = csa.GetCSAElementByName( "Rows" );
    std::cout << csael2 << std::endl;
    gdcm::Element<gdcm::VR::IS, gdcm::VM::VM1> el2;
    el2.Set( csael2.GetValue() );
    dims[1] = el2.GetValue();
    std::cout << "Rows:" << el2.GetValue() << std::endl;
    }
 
  double spacing[2] = { 1. , 1. };
  bool spacingfound = false;
  if( csa.FindCSAElementByName( "PixelSpacing" ) )
    {
    const gdcm::CSAElement &csael3 = csa.GetCSAElementByName( "PixelSpacing" );
    if( !csael3.IsEmpty() )
      {
      std::cout << csael3 << std::endl;
      gdcm::Element<gdcm::VR::DS, gdcm::VM::VM2> el3;
      el3.Set( csael3.GetValue() );
      spacing[0] = el3.GetValue(0);
      spacing[1] = el3.GetValue(1);
      std::cout << "PixelSpacing:" << el3.GetValue() << "," << el3.GetValue(1) << std::endl;
      spacingfound = true;
      }
    }
 
  if( !spacingfound )
    {
    std::cerr << "Problem with PixelSpacing" << std::endl;
    //return 1;
    }
  if( !dims[0] || !dims[1] )
    {
    std::cerr << "Problem with dims" << std::endl;
    return 1;
    }
 
  gdcm::ImageWriter writer;
 
  gdcm::Image &image = writer.GetImage();
  image.SetNumberOfDimensions( 2 ); // good default
  image.SetDimension(0, dims[0] );
  image.SetDimension(1, dims[1] );
  image.SetSpacing(0, spacing[0] );
  image.SetSpacing(1, spacing[1] );
  gdcm::PixelFormat pixeltype = gdcm::PixelFormat::INT16; // bytepix = spm_type('int16','bits')/8;
 
  //unsigned long l = image.GetBufferLength();
  //const int p =  l / (dims[0] * dims[1]);
 
  //image.SetNumberOfDimensions( 3 );
  //image.SetDimension(2, p / pixeltype.GetPixelSize() );
 
  gdcm::PhotometricInterpretation pi;
  pi = gdcm::PhotometricInterpretation::MONOCHROME2;
  //pixeltype.SetSamplesPerPixel(  );
  image.SetPhotometricInterpretation( pi );
  image.SetPixelFormat( pixeltype );
  //image.SetIntercept( inputimage.GetIntercept() );
  //image.SetSlope( inputimage.GetSlope() );
 
  //gdcm::DataElement pixeldata( gdcm::Tag(0x7fe1,0x1010) );
  //pixeldata.SetByteValue( &outbuf[0], outbuf.size() );
  gdcm::PrivateTag csanonimaget(0x7fe1,0x10,"SIEMENS CSA NON-IMAGE");
  const gdcm::DataElement &pixeldata = ds.GetDataElement( csanonimaget );
  image.SetDataElement( pixeldata );
 
  std::string outfilename = "outcsa.dcm";
  //writer.SetFile( reader.GetFile() );
  writer.SetFileName( outfilename.c_str() );
  if( !writer.Write() )
    {
    std::cerr << "could not write: " << outfilename << std::endl;
    return 1;
    }
 
 
  return 0;
}