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FixBrokenJ2K.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.

=========================================================================*/
#include "gdcmReader.h"
#include "gdcmWriter.h"
#include "gdcmImageReader.h"
#include "gdcmSequenceOfFragments.h"
#include "gdcmFile.h"

// http://www.lost.in.ua/dicom/c.dcm
//
// -> BuggyJ2Kvvvua-fixed2-j2k.dcm

/*
 * This program attemps to fix a broken J2K/DICOM:
 * It contains 2 bugs:
 * 1. The first 8 bytes seems to be random bytes: remove them
 * 2. YCC is set to 1, while image is grayscale need to set it back to 0
 *
 * Ref:
 * It's a software from http://rentgenprom.ru/ , shipped with universal digital radiographic units 
 * "ProScan-2000". The Ukrainian manufacturer developed own digital radiographic unit and it is 
 * compatible with software from "ProScan-2000". 
 */
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::Reader reader;
  reader.SetFileName( filename );
  if( !reader.Read() )
    {
    return 1;
    }

  gdcm::File &file = reader.GetFile();
  const gdcm::DataElement &pixeldata = file.GetDataSet().GetDataElement( gdcm::Tag(0x7fe0,0x0010) );
  const gdcm::SequenceOfFragments *sqf = pixeldata.GetSequenceOfFragments();
  if( !sqf )
    {
    return 1;
    }
  const gdcm::Fragment &frag = sqf->GetFragment(0);

  const gdcm::ByteValue *bv = frag.GetByteValue();
  const char *ptr = bv->GetPointer();
  size_t len = bv->GetLength();

  const char sig[] = "\x00\x00\x00\x00\x6A\x70\x32\x63";
  if( memcmp(ptr, sig, sizeof(sig) != 0 ) )
    {
    std::cerr << "magic random signature not found" << std::endl;
    return 1;
    }

  // Apparently the flag to enable a color transform on 3 color components is set in
  // the COD marker. (YCC is byte[6] in the COD marker)
  // we need to disable this flag;
  const char *cod_marker = ptr + 0x35; /* 0x2d + 0x8 */ // FIXME
  if( cod_marker[0] == (char)0xff && cod_marker[1] == 0x52 )
    {
    // found start of COD
    if( cod_marker[6+2] == 1 )
      {
      // Change in place:
      *((char*)cod_marker + 6+2) = 0;
      // Prepare a new DataElement:
      gdcm::DataElement pixeldata( gdcm::Tag(0x7fe0,0x0010) );
      pixeldata.SetVR( gdcm::VR::OB );
      gdcm::SmartPointer<gdcm::SequenceOfFragments> sq = new gdcm::SequenceOfFragments;

      gdcm::Fragment frag;
      // remove 8 first bytes:
      frag.SetByteValue( ptr + 8, len - 8 );
      sq->AddFragment( frag );
      pixeldata.SetValue( *sq );
      file.GetDataSet().Replace( pixeldata );
      }
    else
      {
      return 1;
      }
    }
  else
    {
    std::cerr << "COD not found" << (int)cod_marker[0] << std::endl;
    return 1;
    }

  gdcm::Writer writer;
  writer.SetFile( reader.GetFile() );
  writer.SetFileName( outfilename );
  writer.CheckFileMetaInformationOff();
  if( !writer.Write() )
    {
    std::cerr << "Could not write" << std::endl;
    }

  // paranoid check:
  gdcm::ImageReader ireader;
  ireader.SetFileName( outfilename );
  if( !ireader.Read() )
    {
    std::cerr << "file written is still not valid, please report" << std::endl;
    return 1;
    }


  return 0;
}


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