FixJAIBugJPEGLS.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.
 
=========================================================================*/
#include "gdcmReader.h"
#include "gdcmWriter.h"
#include "gdcmImageReader.h"
 
#include <fstream>
 
#include "gdcm_charls.h"
 
/*
 * This small example should show how one can handle the famous JAI-JPEGLS bug
 * It will take in as invalid DICOM/JAI-JPEG-LS and write out as Explicit Little
 * Endian. One can use `gdcmconv --jpegls` to recompress properly
 *
 * References:
 * http://charls.codeplex.com/discussions/230307?ProjectName=charls
 * http://charls.codeplex.com/workitem/7297
 * http://www.dcm4che.org/jira/browse/DCM-442
 * http://www.dcm4che.org/jira/browse/DCMEE-1144
 * http://java.net/jira/browse/JAI_IMAGEIO_CORE-183
 *
 * Explanation of the issue:
 *
 * Seems, the error is in the calculation of the default values for thresholds T1,
 * T2, T3, in particular min(MAXVAL, 4095) is not applied in
 *
 * FACTOR = (min(MAXVAL, 4095) + 128)/256
 *
 * as specified in http://www.itu.int/rec/T-REC-T.87-199806-I/en .
 *
 */
int main(int argc, char *argv[])
{
  if( argc < 3 )
    {
    std::cerr << argv[0] << " input.dcm output.dcm" << std::endl;
    return 1;
    }
  const char *filename = argv[1];
  const char *outfilename = argv[2];
  gdcm::FileMetaInformation::SetSourceApplicationEntityTitle( "FixJAIBugJPEGLS" );
 
  gdcm::ImageReader reader;
  reader.SetFileName( filename );
  if( !reader.Read() )
    {
    return 1;
    }
 
  gdcm::Image &image = reader.GetImage();
  //unsigned long len = image.GetBufferLength();
  const gdcm::DataElement & in =
    reader.GetFile().GetDataSet().GetDataElement( gdcm::Tag(0x7fe0,0x0010) );
  const gdcm::SequenceOfFragments *sf = in.GetSequenceOfFragments();
  if( !sf )
    {
    std::cerr << "No pixel data (or not encapsulated)" << std::endl;
    return 1;
    }
  const unsigned int *dims = image.GetDimensions();
  if ( sf->GetNumberOfFragments() != dims[2] )
    {
    std::cerr << "Unsupported" << std::endl;
    return 1;
    }
 
//  unsigned long totalLen = sf->ComputeByteLength();
  std::vector<unsigned char> rgbyteOutall;
  for(unsigned int i = 0; i < sf->GetNumberOfFragments(); ++i)
    {
    const gdcm::Fragment &frag = sf->GetFragment(i);
    if( frag.IsEmpty() ) return 1;
    const gdcm::ByteValue *bv = frag.GetByteValue();
    if( !bv ) return 1;
    unsigned long totalLen = bv->GetLength();
 
    std::vector<char> vbuffer;
    vbuffer.resize( totalLen );
    char *buffer = vbuffer.data();
    bv->GetBuffer(buffer, totalLen);
    const unsigned char* pbyteCompressed0 = (const unsigned char*)buffer;
    while( totalLen > 0 && pbyteCompressed0[totalLen-1] != 0xd9 )
      {
      totalLen--;
      }
 
    JlsParameters metadata;
    char errorMsg[256+1]={'\0'};
    if (JpegLsReadHeader(buffer, totalLen, &metadata, errorMsg) != charls::ApiResult::OK)
      {
      std::cerr << "Can't parse jpegls: " << errorMsg << std::endl;
      return 1;
      }
 
    std::cout << metadata.width << std::endl;
    std::cout << metadata.height << std::endl;
    std::cout << metadata.bitsPerSample << std::endl;
 
    gdcm::PixelFormat const & pf = image.GetPixelFormat();
    std::cout << pf << std::endl;
 
    // http://charls.codeplex.com/discussions/230307?ProjectName=charls
    unsigned char marker_lse_13[] = {
      0xFF, 0xF8, 0x00, 0x0D,
      0x01,
      0x1F, 0xFF,
      0x00, 0x22,  // T1 = 34
      0x00, 0x83,  // T2 = 131
      0x02, 0x24,  // T3 = 548
      0x00, 0x40
    };
 
    unsigned char marker_lse_14[] = {
      0xFF, 0xF8, 0x00, 0x0D,
      0x01,
      0x3F, 0xFF,
      0x00, 0x42, // T1 = 66
      0x01, 0x03, // T2 = 259
      0x04, 0x44, // T3 = 1092
      0x00, 0x40
    };
 
    unsigned char marker_lse_15[] = {
      0xFF, 0xF8, 0x00, 0x0D,
      0x01,
      0x7F, 0xFF,
      0x00, 0x82, // T1 = 130
      0x02, 0x03, // T2 = 515
      0x08, 0x84, // T3 = 2180
      0x00, 0x40
    };
 
    unsigned char marker_lse_16[] = {
      0xFF, 0xF8, 0x00, 0x0D,
      0x01,
      0xFF, 0xFF,
      0x01, 0x02, // T1 = 258
      0x04, 0x03, // T2 = 1027
      0x11, 0x04, // T3 = 4356
      0x00, 0x40
    };
 
    const unsigned char *marker_lse = nullptr;
    switch( metadata.bitsPerSample )
      {
    case 13:
      marker_lse = marker_lse_13;
      break;
    case 14:
      marker_lse = marker_lse_14;
      break;
    case 15:
      marker_lse = marker_lse_15;
      break;
    case 16:
      marker_lse = marker_lse_16;
      break;
      }
    if( !marker_lse )
      {
      std::cerr << "Can't handle: " << metadata.bitsPerSample << std::endl;
      return 1;
      }
 
    // FIXME: One should recompute the value for 0x0F
    vbuffer.insert (vbuffer.begin() + 0x0F, marker_lse, marker_lse+15);
 
#if 0
    std::ofstream of( "/tmp/d.jls", std::ios::binary );
    of.write( &vbuffer[0], vbuffer.size() );
    of.close();
#endif
 
    const char *pbyteCompressed = vbuffer.data();
    size_t cbyteCompressed = vbuffer.size(); // updated length
 
    JlsParameters params;
    JpegLsReadHeader(pbyteCompressed, cbyteCompressed, &params, nullptr);
 
    std::vector<unsigned char> rgbyteOut;
    //rgbyteOut.resize( image.GetBufferLength() );
    rgbyteOut.resize(params.height *params.width * ((params.bitsPerSample + 7)
        / 8) * params.components);
 
    CharlsApiResultType result =
      JpegLsDecode(rgbyteOut.data(), rgbyteOut.size(), pbyteCompressed, cbyteCompressed, &params, errorMsg );
    if (result != charls::ApiResult::OK)
      {
      std::cerr << "Could not patch JAI-JPEGLS: " << errorMsg << std::endl;
      return 1;
      }
    rgbyteOutall.insert( rgbyteOutall.end(), rgbyteOut.begin(), rgbyteOut.end() );
    }
 
  gdcm::DataElement pixeldata( gdcm::Tag(0x7fe0,0x0010) );
  pixeldata.SetVR( gdcm::VR::OW );
  pixeldata.SetByteValue( (char*)rgbyteOutall.data(), (uint32_t)rgbyteOutall.size() );
 
 
  // Add the pixel data element
  reader.GetFile().GetDataSet().Replace( pixeldata );
  reader.GetFile().GetHeader().SetDataSetTransferSyntax(
    gdcm::TransferSyntax::ExplicitVRLittleEndian);
 
  gdcm::Writer writer;
  writer.SetFileName( outfilename );
  writer.SetFile( reader.GetFile() );
  writer.Write();
 
  std::cout << "Success !" << std::endl;
 
  return 0;
}