pmsct_rgb1.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_RGB1 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:
 * Jean-Pierre Roux for providing the sample datasets
 */
#include "gdcmReader.h"
#include "gdcmPrivateTag.h"
#include "gdcmAttribute.h"
#include "gdcmImageWriter.h"
 
void delta_decode(const unsigned char *data_in, size_t data_size,
  std::vector<unsigned char> &new_stream, unsigned short pc, size_t w, size_t h)
{
  const size_t plane_size = h * w;
  const size_t outputlen = 3 * plane_size;
  new_stream.resize( outputlen );
 
  assert( data_size != outputlen );
  if( data_size == outputlen )
    {
    return;
    }
  typedef unsigned char byte;
  enum {
    COLORMODE  = 0x81,
    ESCMODE    = 0x82,
    REPEATMODE = 0x83
  };
 
  const byte* src = (const byte*)data_in;
  byte* dest = (byte*)new_stream.data();
  union { byte gray; byte rgb[3]; } pixel;
  pixel.rgb[0] = pixel.rgb[1] = pixel.rgb[2] = 0;
  // always start in grayscale mode
  bool graymode = true;
  size_t dx = 1;
  size_t dy = 3;
  // algorithm works with both planar configuration
  // It does produce surprising greenish background color for planar
  // configuration is 0, while the nested Icon SQ display a nice black
  // background
  if (pc)
    {
    dx = plane_size;
    dy = 1;
    }
  size_t ps = plane_size;
 
  // The following is highly unoptimized as we have nested if statement in a while loop
  // we need to switch from one algorithm to the other (RGB <-> GRAY)
  while (ps)
    {
    // next byte:
    byte b = *src++;
    assert( src < data_in + data_size );
    // mode selection:
    switch ( b )
      {
    case ESCMODE:
      // Used to treat a byte 81/82/83 as a normal byte
      if (graymode)
        {
        pixel.gray += *src++;
        dest[0*dx] = pixel.gray;
        dest[1*dx] = pixel.gray;
        dest[2*dx] = pixel.gray;
        }
      else
        {
        pixel.rgb[0] += *src++;
        pixel.rgb[1] += *src++;
        pixel.rgb[2] += *src++;
        dest[0*dx] = pixel.rgb[0];
        dest[1*dx] = pixel.rgb[1];
        dest[2*dx] = pixel.rgb[2];
        }
      dest += dy;
      ps--;
      break;
    case REPEATMODE:
      // repeat mode (RLE)
      b = *src++;
      ps -= b;
      if (graymode)
        {
        while (b-- > 0)
          {
          dest[0*dx] = pixel.gray;
          dest[1*dx] = pixel.gray;
          dest[2*dx] = pixel.gray;
          dest += dy;
          }
        }
      else
        {
        while (b-- > 0)
          {
          dest[0*dx] = pixel.rgb[0];
          dest[1*dx] = pixel.rgb[1];
          dest[2*dx] = pixel.rgb[2];
          dest += dy;
          }
        }
      break;
    case COLORMODE:
      // We are switching from one mode to the other. The stream contains an intermixed
      // compression of RGB codec and GRAY codec. Each one not knowing of the other
      // reset old value to 0.
      if (graymode)
        {
        graymode = false;
        pixel.rgb[0] = pixel.rgb[1] = pixel.rgb[2] = 0;
        }
      else
        {
        graymode = true;
        pixel.gray = 0;
        }
      break;
    default:
      // This is identical to ESCMODE, it would be nicer to use fall-through
      if (graymode)
        {
        pixel.gray += b;
        dest[0*dx] = pixel.gray;
        dest[1*dx] = pixel.gray;
        dest[2*dx] = pixel.gray;
        }
      else
        {
        pixel.rgb[0] += b;
        pixel.rgb[1] += *src++;
        pixel.rgb[2] += *src++;
        dest[0*dx] = pixel.rgb[0];
        dest[1*dx] = pixel.rgb[1];
        dest[2*dx] = pixel.rgb[2];
        }
      dest += dy;
      ps--;
      break;
      } // end switch
    } // end while
}
 
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_RGB1]                                       # 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;
    return 1;
    }
  if( strncmp( bv->GetPointer(), comprgb.c_str(), comprgb.size() ) == 0 )
    {
    isrgb = true;
    }
  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();
 
  gdcm::Attribute<0x0028,0x0006> at0;
  at0.SetFromDataSet( ds );
  gdcm::Attribute<0x0028,0x0010> at1;
  at1.SetFromDataSet( ds );
  gdcm::Attribute<0x0028,0x0011> at2;
  at2.SetFromDataSet( ds );
 
  std::vector<unsigned char> buffer;
  delta_decode((const unsigned char*)bv2->GetPointer(), bv2->GetLength(), buffer,
    at0.GetValue(), at1.GetValue(), at2.GetValue() );
 
  gdcm::DataElement pixeldata( gdcm::Tag(0x7fe0,0x0010) );
  pixeldata.SetVR( gdcm::VR::OW );
  pixeldata.SetByteValue( (char*)buffer.data(), (uint32_t)buffer.size() );
  // 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 = "outrgb.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;
}