GDCM 2.2.0

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rle2img.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.

    =========================================================================*/
    /*
     * This example shows how to rewrite a ELSCINT1/PMSCT_RLE1 compressed
     * image so that it is readable by most 3rd party software (DICOM does
     * not specify this particular encoding).
     * This is required for the sake of interoperability with any standard
     * conforming DICOM system.
     *
     * 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.
     *
     * Everything you do with this code is at your own risk, since decompression
     * algorithm was not written from specification documents.
     *
     * Special thanks to:
     * Mauro Maiorca for bringing to our attention on this new ELSCINT1
     * compression algorithm : PMSCT_RLE1 (different from the 'LOSSLESS RICE')
     * See post at:
     * http://groups.google.com/group/comp.protocols.dicom/msg/f2b99bf706a7f8ca
     *
     * Thanks to Jesus Spinola, for more datasets,
     * http://www.itk.org/pipermail/insight-users/2008-April/025571.html
     *
     * And last but not least, a very big thank to Ivo van Poorten, without
     * whom we would still be looking at this compressed byte stream as if
     * it was RLE compressed.
     */
    #include "gdcmReader.h"
    #include "gdcmPrivateTag.h"
    #include "gdcmAttribute.h"
    #include "gdcmImageWriter.h"

    /* FIXME: Why is PhilipsLosslessRice.dcm a 512x512 image ... */
    void delta_decode(const char *inbuffer, size_t length, std::vector<unsigned short> &output)
    {
      // RLE pass
      std::vector<char> temp;
      for(size_t i = 0; i < length; ++i)
        {
        if( inbuffer[i] == (char)0xa5 )
          {
          //unsigned char repeat = (unsigned char)inbuffer[i+1] + 1;
          //assert( (unsigned char)inbuffer[i+1] != 255 );
          int repeat = (unsigned char)inbuffer[i+1] + 1;
          char value = inbuffer[i+2];
          while(repeat)
            {
            temp.push_back( value );
            --repeat;
            }
          i+=2;
          }
        else
          {
          temp.push_back( inbuffer[i] );
          }
        }

      // Delta encoding pass
      unsigned short delta = 0;
      for(size_t i = 0; i < temp.size(); ++i)
        {
        if( temp[i] == 0x5a )
          {
          unsigned char v1 = (unsigned char)temp[i+1];
          unsigned char v2 = (unsigned char)temp[i+2];
          int value = v2 * 256 + v1;
          output.push_back( value );
          delta = value;
          i+=2;
          }
        else
          {
          int value = temp[i] + delta;
          output.push_back( value );
          delta = value;
          }
        //assert( output[output.size()-1] == ref[output.size()-1] );
        }

      if ( output.size() % 2 )
        {
        output.resize( output.size() - 1 );
        }
      std::cout << length << " -> " << output.size() * 2 << std::endl;
    }

    int main(int argc, char *argv [])
    {
      if( argc < 2 ) return 1;
      const char *filename = argv[1];
      gdcm::Reader reader;
      reader.SetFileName( filename );
      if( !reader.Read() )
        {
        std::cerr << "Failed to read: " << filename << std::endl;
        return 1;
        }
      const gdcm::DataSet& ds = reader.GetFile().GetDataSet();

      // (07a1,1011) CS [PMSCT_RLE1]                                       # 10,1 Tamar Compression Type
      const gdcm::PrivateTag tcompressiontype(0x07a1,0x0011,"ELSCINT1");
      if( !ds.FindDataElement( tcompressiontype ) ) return 1;
      const gdcm::DataElement& compressiontype = ds.GetDataElement( tcompressiontype );
      if ( compressiontype.IsEmpty() ) return 1;
      const gdcm::ByteValue * bv = compressiontype.GetByteValue();
      std::string comprle = "PMSCT_RLE1";
      std::string comprgb = "PMSCT_RGB1";
      bool isrle = false;
      bool isrgb = false;
      if( strncmp( bv->GetPointer(), comprle.c_str(), comprle.size() ) == 0 )
        {
        isrle = true;
        }
      if( strncmp( bv->GetPointer(), comprgb.c_str(), comprgb.size() ) == 0 )
        {
        isrgb = true;
        return 1;
        }
      if( !isrgb && !isrle ) return 1;

      const gdcm::PrivateTag tcompressedpixeldata(0x07a1,0x000a,"ELSCINT1");
      if( !ds.FindDataElement( tcompressedpixeldata) ) return 1;
      const gdcm::DataElement& compressionpixeldata = ds.GetDataElement( tcompressedpixeldata);
      if ( compressionpixeldata.IsEmpty() ) return 1;
      const gdcm::ByteValue * bv2 = compressionpixeldata.GetByteValue();

      std::vector<unsigned short> buffer;
      delta_decode(bv2->GetPointer(), bv2->GetLength(), buffer);

      gdcm::DataElement pixeldata( gdcm::Tag(0x7fe0,0x0010) );
      pixeldata.SetVR( gdcm::VR::OW );
      pixeldata.SetByteValue( (char*)&buffer[0], buffer.size() * sizeof( unsigned short ) );
      // TODO we should check that decompress byte buffer match the expected size (row*col*...)

      // Add the pixel data element
      reader.GetFile().GetDataSet().Replace( pixeldata );

      reader.GetFile().GetHeader().SetDataSetTransferSyntax(
        gdcm::TransferSyntax::ExplicitVRLittleEndian);
      gdcm::Writer writer;
      writer.SetFile( reader.GetFile() );

      // Cleanup stuff:
      // remove the compressed pixel data:
      // FIXME: should I remove more private tags ? all of them ?
      // oh well this is just an example
      // use gdcm::Anonymizer::RemovePrivateTags if needed...
      writer.GetFile().GetDataSet().Remove( compressionpixeldata.GetTag() );
      std::string outfilename;
      if (argc > 2)
         outfilename = argv[2];
      else
         outfilename = "outrle.dcm";
      writer.SetFileName( outfilename.c_str() );
      if( !writer.Write() )
        {
        std::cerr << "Failed to write" << std::endl;
        return 1;
        }

      std::cout << "success !" << std::endl;

      return 0;
    }