# csa2img.cxx

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

      Program: GDCM (Grassroots DICOM). A DICOM library
      Module:  $URL$

      Copyright (c) 2006-2010 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;
    }