gdcm_conv 0.2.0

/*=========================================================================

  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 "gdcmRLECodec.h"
#include "gdcmTransferSyntax.h"
#include "gdcmTrace.h"
#include "gdcmByteSwap.txx"
#include "gdcmDataElement.h"
#include "gdcmSequenceOfFragments.h"
#include "gdcmSmartPointer.h"
#include "gdcmSwapper.h"

#include <algorithm> // req C++11
#include <cstddef> // ptrdiff_t fix
#include <cstring>
#include <vector>
#include <array>

#include <gdcmrle/rle.h>

namespace gdcm
{

// TODO ideally this code should be in utilities for ease of reuse
class RLEHeader
{
private:
  uint32_t NumSegments = 0;
  uint32_t Offset[15] = {0};

public:
  uint32_t GetNumSegments() const { return NumSegments; }
  bool SetNumSegments(uint32_t num) 
    { 
      if (num > 15) 
        {
          gdcmErrorMacro("Number of segments cannot be bigger than 15");
          return false;
        }
      NumSegments = num;
      return true;
    };
  bool SetOffset(const std::array<uint32_t, 15> &offset) 
    {
      std::copy(offset.begin(), offset.end(), Offset);
      return true;
    };
  uint32_t GetOffset(size_t index) const 
    {
      if (index < 15) return Offset[index];
      return 0;
    };
  bool SetOffset(size_t index, uint32_t value) {
    if (index >= 15) return false;

    Offset[index] = value;
    return true;
  }

  bool Read(std::istream &is) 
    {
      // read Header (64 bytes)
      uint32_t buffer[16] = {0};
      is.read(reinterpret_cast<char *>(buffer), 64);
      if (static_cast<size_t>(is.gcount()) != 64) 
        {
          gdcmErrorMacro("RLE Header truncated: expected 64 bytes, got " << is.gcount());
          return false;
        }
      gdcm_assert(sizeof(uint32_t) * 16 == 64);
      SwapperNoOp::SwapArray(reinterpret_cast<uint32_t *>(buffer), 16);
      if (!SetNumSegments(buffer[0])) return false;
      memcpy(Offset, &buffer[1], sizeof(uint32_t) * 15);
      if (NumSegments >= 1) {
        if (Offset[0] != 64) return false;
      }
      // We just check that we are indeed at the proper position start+64
      return true;
    }
  void Print(std::ostream &os) 
    {
      os << "NumSegments:" << NumSegments << "\n";
      for (int i = 0; i < 15; ++i) {
        os << i << ":" << Offset[i] << "\n";
      }
    }

};
static_assert(sizeof(RLEHeader) == 64, "RLEHeader size must be 64 bits to comply with dicom standard");
class RLEFrame
{
public:
  bool Read(std::istream &is)
    {
    return Header.Read(is);
    }
  void Print(std::ostream &os)
    {
    Header.Print(os);
    }
//private:
  RLEHeader Header;
  std::vector<char> Bytes;
};

class RLEInternals
{
public:
  RLEFrame Frame;
  std::vector<uint32_t> SegmentLength;
};

RLECodec::RLECodec()
{
  Internals = new RLEInternals;
  Length = 0;
  BufferLength = 0;
}

RLECodec::~RLECodec()
{
  delete Internals;
}

bool RLECodec::CanDecode(TransferSyntax const &ts) const
{
  return ts == TransferSyntax::RLELossless;
}

bool RLECodec::CanCode(TransferSyntax const &ts) const
{
  return ts == TransferSyntax::RLELossless;
}

/*
G.3 THE RLE ALGORITHM
The RLE algorithm described in this section is used to compress Byte Segments into RLE Segments.
There is a one-to-one correspondence between Byte Segments and RLE Segments. Each RLE segment
must be an even number of bytes or padded at its end with zero to make it even.
G.3.1 The RLE encoder
A sequence of identical bytes (Replicate Run) is encoded as a two-byte code:
< -count + 1 > <byte value>, where
count = the number of bytes in the run, and
2 <= count <= 128
and a non-repetitive sequence of bytes (Literal Run) is encoded as:
< count - 1 > <Iiteral sequence of bytes>, where
count = number of bytes in the sequence, and
1 <= count <= 128.
The value of -128 may not be used to prefix a byte value.
Note: It is common to encode a 2-byte repeat run as a Replicate Run except when preceded and followed by
a Literal Run, in which case it's best to merge the three runs into a Literal Run.
Three-byte repeats shall be encoded as Replicate Runs. Each row of the image shall be encoded
separately and not cross a row boundary.
*/
inline int count_identical_bytes(const char *start, size_t len)
{
  gdcm_assert( len );
#if 0
  const char *p = start + 1;
  const unsigned int cmin = std::min(128u,len);
  const char *end = start + cmin;
  while( p < end && *p == *start )
    {
    ++p;
    }
  return p - start;
#else
  const char ref = start[0];
  unsigned int count = 1; // start at one; make unsigned for comparison
  const size_t cmin = std::min((size_t)128,len);
  while( count < cmin && start[count] == ref )
    {
  //std::cerr << "count/len:" << count << "," << len << std::endl;
    ++count;
    }
  gdcm_assert( /*2 <= count && */ count <= 128 ); // remove post condition as it will be our return error code
  gdcm_assert( count >= 1 );
  return count;
#endif
}

inline int count_nonrepetitive_bytes(const char *start, size_t len)
{
/*
 * TODO:
 * I need a special handling when there is only a one repetition that break the Literal run...
Note: It is common to encode a 2-byte repeat run as a Replicate Run except when preceded and followed by
a Literal Run, in which case it's best to merge the three runs into a Literal Run.
*/
  gdcm_assert( len );
#if 0
  const char *prev = start;
  const char *p = start + 1;
  const unsigned int cmin = std::min(128u,len);
  const char *end = start + cmin;
  while( p < end && *p != *prev )
    {
    ++prev;
    ++p;
    }
  return p - start;
#else
  unsigned int count = 1;
  const size_t cmin = std::min((size_t)128,len);
#if 0
  // TODO: this version that handles the note still does not work...
  while( count < cmin )
    {
    if ( start[count] != start[count-1] )
      {
      // Special case:
      if( count + 1 < cmin && start[count] != start[count+1] )
        {
        continue;
        }
      break;
      }
    ++count;
    }
#else
#if 1
  // This version properly encode: 0 1 1 0 as: 3 0 1 1 0 ...
  for( count = 1; count < cmin; ++count )
    {
    if( start[count] == start[count-1] )
      {
      if( count + 1 < cmin && start[count] != start[count+1] )
        {
        continue;
        }
      --count;//Note that count can go negative, or wrapped if unsigned!
      break;
      }
    }
#else
  // This version does not handle 0 1 1 0 as specified in the note in the DICOM standard
  while( count < cmin && start[count] != start[count-1] )
    {
    ++count;
    }
#endif
#endif
  gdcm_assert( 1 <= count && count <= 128 );
  return count;
#endif
}

/* return output length */
ptrdiff_t rle_encode(char *output, size_t outputlength, const char *input, size_t inputlength)
{
  char *pout = output;
  const char *pin = input;
  size_t length = inputlength;
  while( pin != input + inputlength )
    {
    gdcm_assert( length <= inputlength );
    gdcm_assert( pin <= input + inputlength );
    int count = count_identical_bytes(pin, length);
    if( count > 1 ) /* or 2 ? */
      {
      // repeat case:
      //
      // Test first we are allowed to write two bytes:
      if( pout + 1 + 1 > output + outputlength ) return -1;
      *pout = (char)(-count + 1);
      gdcm_assert( /**pout != -128 &&*/ 1 - *pout == count );
      gdcm_assert( *pout <= -1 && *pout >= -127 );
      ++pout;
      *pout = *pin;
      ++pout;
      }
    else
      {
      // non repeat case:
      // ok need to compute non-repeat:
      count = count_nonrepetitive_bytes(pin, length);
      // first test we are allowed to write 1 + count bytes in the output buffer:
      if( pout + count + 1 > output + outputlength ) return -1;
      *pout = (char)(count - 1);
      gdcm_assert( *pout != -128 && *pout+1 == count );
      gdcm_assert( *pout >= 0 );
      ++pout;
      memcpy(pout, pin, count);
      pout += count;
      }
    // count byte where read, move pin to new position:
    pin += count;
    // compute remaining length:
    gdcm_assert( count <= (int)length );
    length -= count;
    }
  return pout - output;
}

template <typename T>
bool DoInvertPlanarConfiguration(T *output, const T *input, uint32_t inputlength)
{
  const T *r = input+0;
  const T *g = input+1;
  const T *b = input+2;
  uint32_t length = (inputlength / 3) * 3; // remove the 0 padding
  gdcm_assert( length == inputlength || length == inputlength - 1 );
  gdcm_assert( length % 3 == 0 );
  uint32_t plane_length = length / 3;
  T *pout = output;
  // copy red plane:
  while( pout != output + plane_length * 1 )
    {
    *pout++ = *r;
    r += 3;
    }
  gdcm_assert( r == input + length );
  // copy green plane:
  gdcm_assert( pout == output + plane_length );
  while( pout != output + plane_length * 2 )
    {
    *pout++ = *g;
    g += 3;
    }
  gdcm_assert( g == input + length + 1);
  // copy blue plane:
  gdcm_assert( pout == output + 2*plane_length );
  while( pout != output + plane_length * 3 )
    {
    *pout++ = *b;
    b += 3;
    }
  gdcm_assert( b == input + length + 2);
  assert ( pout == output + length );
  return true;
}


bool RLECodec::Code(DataElement const &in, DataElement &out)
{
  const unsigned int *dims = this->GetDimensions();
  const unsigned int n = 256*256;
  char *outbuf;
  // At most we are encoding a single row at a time, so we would be very unlucky
  // if the row *after* compression would not fit in 256*256 bytes...
  char small_buffer[n];
  outbuf = small_buffer;

  // Create a Sequence Of Fragments:
  SmartPointer<SequenceOfFragments> sq = new SequenceOfFragments;
  const Tag itemStart(0xfffe, 0xe000);
  //sq->GetTable().SetTag( itemStart );
  // FIXME  ? Is this compulsory ?
  //const char dummy[4] = {};
  //sq->GetTable().SetByteValue( dummy, sizeof(dummy) );

  const ByteValue *bv = in.GetByteValue();
  gdcm_assert( bv );
  const char *input = bv->GetPointer();
  unsigned long bvl = bv->GetLength();
  unsigned long image_len = bvl / dims[2];

  // If 16bits, need to do the padded composite...
  char *buffer = nullptr;
  // if rgb (3 comp) need to the planar configuration
  char *bufferrgb = nullptr;
  if( GetPixelFormat().GetBitsAllocated() > 8 )
    {
    //RequestPaddedCompositePixelCode = true;
    buffer = new char [ image_len ];
    }

  if ( GetPhotometricInterpretation() == PhotometricInterpretation::RGB
    || GetPhotometricInterpretation() == PhotometricInterpretation::YBR_FULL
    || GetPhotometricInterpretation() == PhotometricInterpretation::YBR_RCT
    || GetPhotometricInterpretation() == PhotometricInterpretation::YBR_FULL_422 )
    {
    bufferrgb = new char [ image_len ];
    }

  unsigned int MaxNumSegments = 1;
  if( GetPixelFormat().GetBitsAllocated() == 8 )
    {
    MaxNumSegments *= 1;
    }
  else if( GetPixelFormat().GetBitsAllocated() == 16 )
    {
    MaxNumSegments *= 2;
    }
  else if( GetPixelFormat().GetBitsAllocated() == 32 )
    {
    MaxNumSegments *= 4;
    }
  else
    {
    delete[] buffer;
    delete[] bufferrgb;
    return false;
    }

  if( GetPhotometricInterpretation() == PhotometricInterpretation::RGB
    || GetPhotometricInterpretation() == PhotometricInterpretation::YBR_FULL
    || GetPhotometricInterpretation() == PhotometricInterpretation::YBR_RCT
    || GetPhotometricInterpretation() == PhotometricInterpretation::YBR_FULL_422 )
    {
    MaxNumSegments *= 3;
    }

  gdcm_assert( GetPixelFormat().GetBitsAllocated() == 8 || GetPixelFormat().GetBitsAllocated() == 16
    || GetPixelFormat().GetBitsAllocated() == 32 );
  if( GetPixelFormat().GetSamplesPerPixel() == 3 )
    {
    gdcm_assert( MaxNumSegments % 3 == 0 );
    }

  RLEHeader header;
  header.SetNumSegments(static_cast<uint32_t>(MaxNumSegments));
  header.SetOffset({64});
  // there cannot be any space in between the end of the RLE header and the start
  // of the first RLE segment
  //
  // Create a RLE Frame for each frame:
  for(unsigned int dim = 0; dim < dims[2]; ++dim)
    {
    // Within each frame, create the RLE Segments:
    // lets' try a simple scheme where each Segments is given an equal portion
    // of the input image.
    const char *ptr_img = input + dim * image_len;
    if( GetPlanarConfiguration() == 0 && GetPixelFormat().GetSamplesPerPixel() == 3 )
      {
      if( GetPixelFormat().GetBitsAllocated() == 8 )
        {
        DoInvertPlanarConfiguration<char>(bufferrgb, ptr_img, (uint32_t)(image_len / sizeof(char)));
        }
      else if ( GetPixelFormat().GetBitsAllocated() == 16 )
        {
        DoInvertPlanarConfiguration<short>((short*)(void*)bufferrgb, (const short*)(const void*)ptr_img, (uint32_t)(image_len / sizeof(short)));
        }
      else /* ( GetPixelFormat().GetBitsAllocated() == 32 ) */
        {
        gdcm_assert( GetPixelFormat().GetBitsAllocated() == 32 );
        DoInvertPlanarConfiguration<int32_t>(
          (int32_t*)(void*)bufferrgb,
          (const int32_t*)(const void*)ptr_img,
          (uint32_t)(image_len / sizeof(int32_t))
        );
        }
      ptr_img = bufferrgb;
      }
    if( GetPixelFormat().GetBitsAllocated() == 32 )
      {
      gdcm_assert( !(image_len % 4) );
      //gdcm_assert( image_len % 3 == 0 );
      unsigned int div = GetPixelFormat().GetSamplesPerPixel();
      for(unsigned int j = 0; j < div; ++j)
        {
        unsigned long iimage_len = image_len / div;
        char *ibuffer = buffer + j * iimage_len;
        const char *iptr_img = ptr_img + j * iimage_len;
        gdcm_assert( iimage_len % 4 == 0 );
        for(unsigned long i = 0; i < iimage_len/4; ++i)
          {
#ifdef GDCM_WORDS_BIGENDIAN
          ibuffer[i] = iptr_img[4*i+0];
#else
          ibuffer[i] = iptr_img[4*i+3];
#endif
          }
        for(unsigned long i = 0; i < iimage_len/4; ++i)
          {
#ifdef GDCM_WORDS_BIGENDIAN
          ibuffer[i+iimage_len/4] = iptr_img[4*i+1];
#else
          ibuffer[i+iimage_len/4] = iptr_img[4*i+2];
#endif
          }
        for(unsigned long i = 0; i < iimage_len/4; ++i)
          {
#ifdef GDCM_WORDS_BIGENDIAN
          ibuffer[i+2*iimage_len/4] = iptr_img[4*i+2];
#else
          ibuffer[i+2*iimage_len/4] = iptr_img[4*i+1];
#endif
          }
        for(unsigned long i = 0; i < iimage_len/4; ++i)
          {
#ifdef GDCM_WORDS_BIGENDIAN
          ibuffer[i+3*iimage_len/4] = iptr_img[4*i+3];
#else
          ibuffer[i+3*iimage_len/4] = iptr_img[4*i+0];
#endif
          }
        }
      ptr_img = buffer;
      }
    else if( GetPixelFormat().GetBitsAllocated() == 16 )
      {
      gdcm_assert( !(image_len % 2) );
      //gdcm_assert( image_len % 3 == 0 );
      unsigned int div = GetPixelFormat().GetSamplesPerPixel();
      for(unsigned int j = 0; j < div; ++j)
        {
        unsigned long iimage_len = image_len / div;
        char *ibuffer = buffer + j * iimage_len;
        const char *iptr_img = ptr_img + j * iimage_len;
        gdcm_assert( iimage_len % 2 == 0 );
        for(unsigned long i = 0; i < iimage_len/2; ++i)
          {
#ifdef GDCM_WORDS_BIGENDIAN
          ibuffer[i] = iptr_img[2*i];
#else
          ibuffer[i] = iptr_img[2*i+1];
#endif
          }
        for(unsigned long i = 0; i < iimage_len/2; ++i)
          {
#ifdef GDCM_WORDS_BIGENDIAN
          ibuffer[i+iimage_len/2] = iptr_img[2*i+1];
#else
          ibuffer[i+iimage_len/2] = iptr_img[2*i];
#endif
          }
        }
      ptr_img = buffer;
      }
    gdcm_assert( image_len % MaxNumSegments == 0 );
    const size_t input_seg_length = image_len / MaxNumSegments;
    std::string datastr;
    for(unsigned int seg = 0; seg < MaxNumSegments; ++seg )
      {
      size_t partition = input_seg_length;
      const char *ptr = ptr_img + seg * input_seg_length;
      gdcm_assert( ptr < ptr_img + image_len );
      if( seg == MaxNumSegments - 1 )
        {
        partition += image_len % MaxNumSegments;
        gdcm_assert( (MaxNumSegments-1) * input_seg_length + partition == (size_t)image_len );
        }
      gdcm_assert( partition == input_seg_length );

      std::stringstream data;
      gdcm_assert( partition % dims[1] == 0 );
      size_t length = 0;
      // Do not cross row boundary:
      for(unsigned int y = 0; y < dims[1]; ++y)
        {
        ptrdiff_t llength = rle_encode(outbuf, n, ptr + y*dims[0], partition / dims[1] /*image_len*/);
        if( llength < 0 )
          {
          gdcmErrorMacro( "RLE compressor error" );
          delete[] buffer;
          delete[] bufferrgb;
          return false;
          }
        gdcm_assert( llength );
        data.write((char*)outbuf, llength);
        length += llength;
        }
      // update header
      header.SetOffset(1 + seg, (uint32_t)(header.GetOffset(seg) + length));

      gdcm_assert( data.str().size() == length );
      datastr += data.str();
      }
    header.SetOffset(MaxNumSegments, 0);
    std::stringstream os;
    //header.Print( std::cout );
    os.write((char*)&header,sizeof(header));
    std::string str = os.str() + datastr;
    gdcm_assert( !str.empty() );
    Fragment frag;
    //frag.SetTag( itemStart );
    VL::Type strSize = (VL::Type)str.size();
    frag.SetByteValue( str.data(), strSize );
    sq->AddFragment( frag );
    }
  out.SetValue( *sq );

  delete[] buffer;
  delete[] bufferrgb;

  return true;
}

// G.3.2 The RLE decoder
// Pseudo code for the RLE decoder is shown below:
// Loop until the number of output bytes equals the uncompressed segment size
// Read the next source byte into n
// If n> =0 and n <= 127 then
// output the next n+1 bytes literally
// Elseif n <= - 1 and n >= -127 then
// output the next byte -n+1 times
// Elseif n = - 128 then
// output nothing
// Endif
// Endloop

size_t RLECodec::DecodeFragment(Fragment const & frag, char *buffer, size_t llen)
{

  std::stringstream is;
  const ByteValue &bv = dynamic_cast<const ByteValue&>(frag.GetValue());
  size_t bv_len = bv.GetLength();
  char *mybuffer = new char[bv_len];
  bv.GetBuffer(mybuffer, bv.GetLength());
  is.write(mybuffer, bv.GetLength());
  delete[] mybuffer;
  std::stringstream os;
  SetLength( (unsigned long)llen );
#if !defined(NDEBUG)
  const unsigned int * const dimensions = this->GetDimensions();
  const PixelFormat & pf = this->GetPixelFormat();
  gdcm_assert( llen == dimensions[0] * dimensions[1] * pf.GetPixelSize() );
#endif
  bool r = DecodeByStreams(is, os);
  if( !r ) return 0;
  (void)r; //warning removal
  std::streampos p = is.tellg();
  // http://groups.google.com/group/microsoft.public.vc.stl/browse_thread/thread/96740930d0e4e6b8
  if( !!is )
    {
    // Indeed the length of the RLE stream has been padded with a \0
    // which is discarded
    std::streamoff check = bv.GetLength() - p;
    // check == 2 for gdcmDataExtra/gdcmSampleData/US_DataSet/GE_US/2929J686-breaker
    //gdcm_assert( check == 0 || check == 1 || check == 2 );
    if( check ) { gdcmDebugMacro( "tiny offset detected in between RLE segments: " << check ); }
    }
  else
    {
    // ALOKA_SSD-8-MONO2-RLE-SQ.dcm
    gdcmWarningMacro( "Bad RLE stream" );
    }
  std::string::size_type check = os.str().size();
  // If the following assert fail expect big troubles:
  memcpy(buffer, os.str().c_str(), check);
//  pos += check;
  return check;
}

bool RLECodec::Decode(DataElement const &in, DataElement &out)
{
  if( NumberOfDimensions == 2 )
    {
    out = in;
    const SequenceOfFragments *sf = in.GetSequenceOfFragments();
    if( !sf ) return false;
    unsigned long len = GetBufferLength();
    std::stringstream is;
    sf->WriteBuffer( is );
    SetLength( len );
    std::stringstream os;
    bool r = DecodeByStreams(is, os);
    if( !r )
    {
      gdcmErrorMacro( "DecodeByStreams failure."  );
      return false;
    }
    std::string str = os.str();
    std::string::size_type check = str.size();
    gdcm_assert( check == len );
    VL::Type checkCast = (VL::Type)check;
    out.SetByteValue( str.data(), checkCast );
    return true;
    }
  else if ( NumberOfDimensions == 3 )
    {
    out = in;
    const SequenceOfFragments *sf = in.GetSequenceOfFragments();
    if( !sf ) return false;
    const unsigned long len = GetBufferLength();
    unsigned long pos = 0;
    // Each RLE Frame store a 2D frame. len is the 3d length
    const size_t nframes = sf->GetNumberOfFragments();
    const size_t zdim = Dimensions[2];
    if( nframes != zdim )
    {
      gdcmErrorMacro( "Invalid number of fragments: " << nframes << " should be: " << zdim  );
      return false;
    }
    char *buffer = new char[len];
    const std::size_t llen = len / nframes;
    // gdcm_assert( GetNumberOfDimensions() == 2
    //      || GetDimension(2) == sf->GetNumberOfFragments() );
    bool corruption = false;
    for(unsigned int i = 0; i < nframes; ++i)
      {
      const Fragment &frag = sf->GetFragment(i);
      const size_t check = DecodeFragment(frag, buffer + pos, llen); (void)check;
      if( check != llen )
      {
        gdcmDebugMacro( "RLE pb with frag: " << i );
        corruption = true;
      }
      pos += (unsigned long)llen;
      }
    if( !corruption )
      gdcm_assert( pos == len );
    out.SetByteValue( buffer, (uint32_t)len );
    delete[] buffer;
    return !corruption;
    }
  return false;
}

bool RLECodec::DecodeExtent(
  char *buffer,
  unsigned int xmin, unsigned int xmax,
  unsigned int ymin, unsigned int ymax,
  unsigned int zmin, unsigned int zmax,
  std::istream & is
)
{
  std::stringstream tmpos;
  BasicOffsetTable bot;
  bot.Read<SwapperNoOp>( is );
  //std::cout << bot << std::endl;

  const unsigned int * dimensions = this->GetDimensions();
  const PixelFormat & pf = this->GetPixelFormat();
  gdcm_assert( pf.GetBitsAllocated() % 8 == 0 );
  gdcm_assert( pf != PixelFormat::SINGLEBIT );
  gdcm_assert( pf != PixelFormat::UINT12 && pf != PixelFormat::INT12 );

  // skip
  std::stringstream os;
  Fragment frag;
  for( unsigned int z = 0; z < zmin; ++z )
    {
    frag.ReadPreValue<SwapperNoOp>(is);
    std::streamoff off = frag.GetVL();
    is.seekg( off, std::ios::cur );
    }
  for( unsigned int z = zmin; z <= zmax; ++z )
    {
    frag.ReadPreValue<SwapperNoOp>(is);
    std::streampos start = is.tellg();

    SetLength( dimensions[0] * dimensions[1] * pf.GetPixelSize() );
    const bool r = DecodeByStreams(is, os); (void)r;
    if( !r ) return false;
    gdcm_assert( r );

    // handle DICOM padding
    std::streampos end = is.tellg();
    size_t numberOfReadBytes = (size_t)(end - start);
    if( numberOfReadBytes > frag.GetVL() )
      {
      // Special handling for ALOKA_SSD-8-MONO2-RLE-SQ.dcm
      size_t diff = numberOfReadBytes - frag.GetVL();
      gdcm_assert( diff == 1 );
      os.seekp( 0 - (int)diff, std::ios::cur );
      os.put( 0 );
      end = (size_t)end - 1;
      }
    gdcm_assert( end - start == frag.GetVL() || (size_t)(end - start) + 1 == frag.GetVL() );
    // sync is (rle16loo.dcm)
    if( (end - start) % 2 == 1 )
      {
      is.get();
      }
    } // for each z

  os.seekg(0, std::ios::beg );
  gdcm_assert( os.good() );
  std::istream *theStream = &os;

  unsigned int rowsize = xmax - xmin + 1;
  unsigned int colsize = ymax - ymin + 1;
  unsigned int bytesPerPixel = pf.GetPixelSize();

  std::vector<char> buffer1;
  buffer1.resize( rowsize*bytesPerPixel );
  char *tmpBuffer1 = buffer1.data();
  unsigned int y, z;
  std::streamoff theOffset;
  for (z = zmin; z <= zmax; ++z)
    {
    for (y = ymin; y <= ymax; ++y)
      {
      theStream->seekg(std::ios::beg);
      theOffset = 0 + ((z-zmin)*dimensions[1]*dimensions[0] + y*dimensions[0] + xmin)*bytesPerPixel;
      theStream->seekg(theOffset);
      theStream->read(tmpBuffer1, rowsize*bytesPerPixel);
      memcpy(&(buffer[((z-zmin)*rowsize*colsize +
            (y-ymin)*rowsize)*bytesPerPixel]),
        tmpBuffer1, rowsize*bytesPerPixel);
      }
    }
  return true;
}

bool RLECodec::DecodeByStreamsCommon(std::istream &, std::ostream &)
{
  return false;
}

bool RLECodec::DecodeByStreams(std::istream &is, std::ostream &os)
{
  std::streampos start = is.tellg();
  // FIXME: Do some stupid work:
  char dummy_buffer[256];
  std::stringstream tmpos;

  RLEFrame &frame = Internals->Frame;
  if( !frame.Read(is) )
     return false;
  unsigned long numSegments = frame.Header.GetNumSegments();

  unsigned long length = Length;
  gdcm_assert( length );
  // Special case:
  gdcm_assert( GetPixelFormat().GetBitsAllocated() == 32 ||
          GetPixelFormat().GetBitsAllocated() == 16 ||
          GetPixelFormat().GetBitsAllocated() == 8 );
  if( GetPixelFormat().GetBitsAllocated() > 8 )
    {
    RequestPaddedCompositePixelCode = true;
    }

  gdcm_assert( GetPixelFormat().GetSamplesPerPixel() == 3 || GetPixelFormat().GetSamplesPerPixel() == 1 );
  // A footnote:
  // RLE *by definition* with more than one component will have applied the
  // Planar Configuration because it simply does not make sense to do it
  // otherwise. So implicitly RLE is indeed PlanarConfiguration == 1. However
  // when the image says: "hey I am PlanarConfiguration = 0 AND RLE", then
  // apply the PlanarConfiguration internally so that people don't get lost
  // Because GDCM internally set PlanarConfiguration == 0 by default, even if
  // the Attribute is not sent, it will still default to 0 and we will be
  // consistent with ourselves...
  if( GetPixelFormat().GetSamplesPerPixel() == 3 && GetPlanarConfiguration() == 0 )
    {
    RequestPlanarConfiguration = true;
    }
  length /= numSegments;
  for(unsigned long i = 0; i<numSegments; ++i)
    {
    unsigned long numberOfReadBytes = 0;
    std::streampos pos = is.tellg() - start;
    if (frame.Header.GetOffset(i) > BufferLength) 
      {
        gdcmErrorMacro("Offset is bigger then buffer Length");
        return false;
      }

    if ( frame.Header.GetOffset(i) - pos != 0 )
      {
      // ACUSON-24-YBR_FULL-RLE.dcm
      // D_CLUNIE_CT1_RLE.dcm
      // This should be at most the \0 padding
      //gdcmWarningMacro( "RLE Header says: " << frame.Header.Offset[i] <<
      //   " when it should says: " << pos << std::endl );
      std::streamoff check = frame.Header.GetOffset(i) - pos;//should it be a streampos or a uint32? mmr
      // check == 2 for gdcmDataExtra/gdcmSampleData/US_DataSet/GE_US/2929J686-breaker
      //gdcm_assert( check == 1 || check == 2);
      (void)check; //warning removal
      is.seekg(frame.Header.GetOffset(i) + start, std::ios::beg);
      }

    unsigned long numOutBytes = 0;
    signed char byte;

    // FIXME: ALOKA_SSD-8-MONO2-RLE-SQ.dcm I think the RLE decoder is off by
    // one, we are reading in 128001 byte, while only 128000 are present
    while( numOutBytes < length )
      {
      is.read((char*)&byte, 1);
      if( !is.good() )
      {
        gdcmErrorMacro( "Could not decode" );
        return false;
      }
      numberOfReadBytes++;
      if( byte >= 0 /*&& byte <= 127*/ ) /* 2nd is always true */
        {
        is.read( dummy_buffer, byte+1 );
        //gdcm_assert( is.good() ); // impossible because ALOKA_SSD-8-MONO2-RLE-SQ.dc
        numberOfReadBytes += byte+1;
        numOutBytes += byte+ 1;
        tmpos.write( dummy_buffer, byte+1 );
        }
      else if( byte <= -1 && byte >= -127 )
        {
        char nextByte;
        is.read( &nextByte, 1);
        numberOfReadBytes += 1;
        memset(dummy_buffer, nextByte, -byte + 1);
        numOutBytes += -byte + 1;
        tmpos.write( dummy_buffer, -byte+1 );
        }
      else /* byte == -128 */
        {
        gdcm_assert( byte == -128 );
        }
      //gdcm_assert( numberOfReadBytes + frame.Header.Offset[i] - is.tellg() + start == 0);
      }
    if( numOutBytes != length ) return false;
    }

  return ImageCodec::DecodeByStreams(tmpos,os);
}

bool RLECodec::GetHeaderInfo(std::istream &is, TransferSyntax &ts)
{
  RLEFrame frame;
  if( !frame.Read(is) )
     return false;
  // numsegments = num_comp * bpp / 8;
  // numsegments >0 && numsegments <= 12
  uint32_t bytespercomp = frame.Header.GetNumSegments();
  if (frame.Header.GetNumSegments() % 3 == 0)
  {
    PI = PhotometricInterpretation::RGB;
    PlanarConfiguration = 1;
    this->PF.SetSamplesPerPixel( 3 );
    bytespercomp /= 3;
  }
  else
  {
    PI = PhotometricInterpretation::MONOCHROME2;
    this->PF.SetSamplesPerPixel( 1 );
  }
  this->PF.SetBitsAllocated( bytespercomp * 8 );
  ts = TransferSyntax::RLELossless;
  return true;
}

ImageCodec * RLECodec::Clone() const
{
  return new RLECodec;
}

bool RLECodec::StartEncode( std::ostream & )
{
  return true;
}
bool RLECodec::IsRowEncoder()
{
  return false;
}

bool RLECodec::IsFrameEncoder()
{
  return true;
}

class memsrc : public ::rle::source
{
public:
  memsrc( const char * data, size_t datalen ):ptr(data),cur(data),len(datalen)
    {
    }
  int read( char * out, int l ) override
    {
    memcpy( out, cur, l );
    cur += l;
    gdcm_assert( cur <= ptr + len );
    return l;
    }
  streampos_t tell() override
    {
    gdcm_assert( cur <= ptr + len );
    return (streampos_t)(cur - ptr);
    }
  bool seek(streampos_t pos) override
    {
    cur = ptr + pos;
    gdcm_assert( cur <= ptr + len && cur >= ptr );
    return true;
    }
  bool eof() override
    {
    gdcm_assert( cur <= ptr + len );
    return cur == ptr + len;
    }
  memsrc * clone() override
    {
    memsrc * ret = new memsrc( ptr, len );
    return ret;
    }
private:
  const char * ptr;
  const char * cur;
  size_t len;
};

bool RLECodec::AppendRowEncode( std::ostream & os, const char * data, size_t datalen)
{
  (void)os; (void)data; (void)datalen;
  gdcm_assert(0);
  return false;
}

class streamdest : public rle::dest
{
public:
  streamdest( std::ostream & os ):stream(os)
  {
  start = os.tellp();
  }
  int write( const char * in, int len ) override
    {
    stream.write(in, len );
    return len;
    }
  bool seek( streampos_t abs_pos ) override
    {
    stream.seekp( abs_pos + start );
    return true;
    }
private:
  std::ostream & stream;
  std::streampos start;
};

bool RLECodec::AppendFrameEncode( std::ostream & out, const char * data, size_t datalen )
{
  try {
  const PixelFormat & pf = this->GetPixelFormat();
  unsigned int pc = this->GetPlanarConfiguration();
  bool isLittleEndian = !this->GetNeedByteSwap();
  rle::pixel_info pi((unsigned char)pf.GetSamplesPerPixel(), (unsigned char)(pf.GetBitsAllocated()));

  const unsigned int * dimensions = this->GetDimensions();
  rle::image_info ii(dimensions[0], dimensions[1], pi, pc ? true : false, isLittleEndian);
  const int h = dimensions[1];

  memsrc src( data, datalen );
  rle::rle_encoder re(src, ii);

  streamdest fd( out );

  if( !re.write_header( fd ) )
    {
    gdcmErrorMacro( "could not write header" );
    return false;
    }

  for( int y = 0; y < h; ++y )
    {
    const int ret = re.encode_row( fd );
    if( ret < 0 )
      {
      gdcmErrorMacro( "problem at row: " << y );
      return false;
      }
    }
  } catch( std::exception &  ) {
    gdcmErrorMacro( "invalid compression params (not supported for now)." );
    return false;
  }

  return true;
}

bool RLECodec::StopEncode( std::ostream & )
{
  return true;
}

} // end namespace gdcm