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];
      unsigned short value = (unsigned short)(v2 * 256 + v1);
      output.push_back( value );
      delta = value;
      i+=2;
      }
    else
      {
      unsigned short value = (unsigned short)(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 )
    {
    std::cerr << argv[0] << "input.dcm [output.dcm]" << std::endl;
    std::cerr << "will default to 'outrle.dcm' unless output.dcm is specified."
      << std::endl;
    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;
    std::cerr << "See: pmsct_rgb1.cxx instead" << std::endl;
    return 1;
    }
  if( !isrgb && !isrle ) return 1;
 
  // check if compressed pixel data reside in private or standard tag
  const gdcm::PrivateTag tprivatepixeldata(0x07a1,0x100a,"ELSCINT1");
  const gdcm::Tag tstandardpixeldata(0x7fe0, 0x0010);
  gdcm::Tag tpixeldata;
  if(ds.FindDataElement(tprivatepixeldata)) tpixeldata = tprivatepixeldata;
  else if(ds.FindDataElement(tstandardpixeldata)) tpixeldata = tstandardpixeldata;
  if(!ds.FindDataElement(tpixeldata)) return 1;
 
  const gdcm::DataElement& compressionpixeldata = ds.GetDataElement( tpixeldata);
  if ( compressionpixeldata.IsEmpty() ) return 1;
  const gdcm::ByteValue * bv2 = compressionpixeldata.GetByteValue();
 
  gdcm::Attribute<0x0028,0x0010> at1;
  at1.SetFromDataSet( ds );
  gdcm::Attribute<0x0028,0x0011> at2;
  at2.SetFromDataSet( ds );
 
  gdcm::DataElement pixeldata;
  // if standard voxel data element does not exist, create it
  if( !reader.GetFile().GetDataSet().FindDataElement( tpixeldata ) )
  {
    pixeldata = gdcm::DataElement( tpixeldata, 0, gdcm::VR::OW );
  }
  else{
    pixeldata = reader.GetFile().GetDataSet().GetDataElement( tpixeldata );
  }
 
  pixeldata.SetVR( gdcm::VR::OW );
  gdcm::VL bv2l = bv2->GetLength();
  gdcm::VL at1l = at1.GetValue() * at2.GetValue() * 2; /* sizeof(unsigned short) == 2 */
  // Handle special case that is not compressed:
  if( bv2l == at1l )
    {
    pixeldata.SetByteValue( bv2->GetPointer(), bv2->GetLength() );
    }
  else
    {
    std::vector<unsigned short> buffer;
    delta_decode(bv2->GetPointer(), bv2->GetLength(), buffer);
    pixeldata.SetByteValue( (char*)buffer.data(), (uint32_t)(buffer.size() * sizeof( unsigned short )) );
    }
  // TODO we should check that decompress byte buffer match the expected size (row*col*...)
 
  // Add the pixel data element
  if( reader.GetFile().GetDataSet().FindDataElement( tpixeldata ) )
  {
    reader.GetFile().GetDataSet().Replace( pixeldata );
  }
  else
  {
    reader.GetFile().GetDataSet().ReplaceEmpty( pixeldata );
  }
 
 
  reader.GetFile().GetHeader().SetDataSetTransferSyntax(
    gdcm::TransferSyntax::ExplicitVRLittleEndian);
  gdcm::Writer writer;
  writer.SetFile( reader.GetFile() );
 
  // Cleanup stuff:
  // This makes the code equivalent to Philips workstation IntelliSpace Portal
  if( writer.GetFile().GetDataSet().FindDataElement( tcompressiontype ) )
  {
    writer.GetFile().GetDataSet().Remove( gdcm::Tag(0x07a1,0x1011) );
  }
  if( writer.GetFile().GetDataSet().FindDataElement( tprivatepixeldata ) )
  {
    writer.GetFile().GetDataSet().Remove( gdcm::Tag(0x07a1,0x100a) );
  }
 
  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;
}