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gdcmOverlay.cxx

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

  Program: GDCM (Grassroots DICOM). A DICOM library
  Module:  $URL$

  Copyright (c) 2006-2009 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 "gdcmOverlay.h"
#include "gdcmTag.h"
#include "gdcmDataElement.h"
#include "gdcmDataSet.h"
#include "gdcmAttribute.h"

#include <vector>

namespace gdcm
{

class OverlayInternal
{
public:
  OverlayInternal():
  InPixelData(false),
  Group(0), // invalid default
  Rows(0),
  Columns(0),
  NumberOfFrames(0),
  Description(),
  Type(),
  //Origin[2],
  FrameOrigin(0),
  BitsAllocated(0),
  BitPosition(0),
  Data() { Origin[0] = Origin[1] = 0; }
  /*
  (6000,0010) US 484                                      #   2, 1 OverlayRows
  (6000,0011) US 484                                      #   2, 1 OverlayColumns
  (6000,0015) IS [1]                                      #   2, 1 NumberOfFramesInOverlay
  (6000,0022) LO [Siemens MedCom Object Graphics]         #  30, 1 OverlayDescription
  (6000,0040) CS [G]                                      #   2, 1 OverlayType
  (6000,0050) SS 1\1                                      #   4, 2 OverlayOrigin
  (6000,0051) US 1                                        #   2, 1 ImageFrameOrigin
  (6000,0100) US 1                                        #   2, 1 OverlayBitsAllocated
  (6000,0102) US 0                                        #   2, 1 OverlayBitPosition
  (6000,3000) OW 0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000... # 29282, 1 OverlayData
  */

  bool InPixelData;
// Identifier need to be in the [6000,60FF] range (no odd number):
  unsigned short Group;
// Descriptor:
  unsigned short Rows;           // (6000,0010) US 484                                      #   2, 1 OverlayRows
  unsigned short Columns;        // (6000,0011) US 484                                      #   2, 1 OverlayColumns
  unsigned int   NumberOfFrames; // (6000,0015) IS [1]                                      #   2, 1 NumberOfFramesInOverlay
  std::string    Description;    // (6000,0022) LO [Siemens MedCom Object Graphics]         #  30, 1 OverlayDescription
  std::string    Type;           // (6000,0040) CS [G]                                      #   2, 1 OverlayType
  signed short   Origin[2];      // (6000,0050) SS 1\1                                      #   4, 2 OverlayOrigin
  unsigned short FrameOrigin;    // (6000,0051) US 1                                        #   2, 1 ImageFrameOrigin
  unsigned short BitsAllocated;  // (6000,0100) US 1                                        #   2, 1 OverlayBitsAllocated
  unsigned short BitPosition;    // (6000,0102) US 0                                        #   2, 1 OverlayBitPosition
  //std::vector<bool> Data;
  std::vector<char> Data;
  void Print(std::ostream &os) const {
    os << "Group           0x" <<  std::hex << Group << std::dec << std::endl;
    os << "Rows            " <<  Rows << std::endl;
    os << "Columns         " <<  Columns << std::endl;
    os << "NumberOfFrames  " <<  NumberOfFrames << std::endl;
    os << "Description     " <<  Description << std::endl;
    os << "Type            " <<  Type << std::endl;
    os << "Origin[2]       " <<  Origin[0] << "," << Origin[1] << std::endl;
    os << "FrameOrigin     " <<  FrameOrigin << std::endl;
    os << "BitsAllocated   " <<  BitsAllocated << std::endl;
    os << "BitPosition     " <<  BitPosition << std::endl;
    //std::vector<bool> Data;
  }
};

Overlay::Overlay()
{
  Internal = new OverlayInternal;
}

Overlay::~Overlay()
{
  delete Internal;
}

Overlay::Overlay(Overlay const &ov):Object(ov)
{
  //delete Internal;
  Internal = new OverlayInternal;
  // TODO: copy OverlayInternal into other...
  *Internal = *ov.Internal;
}

00103 unsigned int Overlay::GetNumberOfOverlays(DataSet const & ds)
{
  Tag overlay(0x6000,0x0000); // First possible overlay
  bool finished = false;
  unsigned int numoverlays = 0;
  while( !finished )
    {
    const DataElement &de = ds.FindNextDataElement( overlay );
    if( de.GetTag().GetGroup() > 0x60FF ) // last possible curve
      {
      finished = true;
      }
    else if( de.GetTag().IsPrivate() )
      {
      // Move on to the next public one:
      overlay.SetGroup( de.GetTag().GetGroup() + 1 );
      overlay.SetElement( 0 ); // reset just in case...
      }
    else
      {
      // Yeah this is a potential overlay element, let's check this is not a broken LEADTOOL image,
      // or prova0001.dcm:
      // (5000,0000) UL 0                                        #   4, 1 GenericGroupLength
      // (6000,0000) UL 0                                        #   4, 1 GenericGroupLength
      // (6001,0000) UL 28                                       #   4, 1 PrivateGroupLength
      // (6001,0010) LT [PAPYRUS 3.0]                            #  12, 1 PrivateCreator
      // (6001,1001) LT (no value available)                     #   0, 0 Unknown Tag & Data
/*
 * FIXME:
 * In order to support : gdcmData/SIEMENS_GBS_III-16-ACR_NEMA_1.acr
 *                       gdcmDataExtra/gdcmSampleData/images_of_interest/XA_GE_JPEG_02_with_Overlays.dcm  
 * I cannot simply check for overlay_group,3000 this would not work
 * I would need a strong euristick
 */
      if( ds.FindDataElement( Tag(overlay.GetGroup(),0x3000 ) ) )
      //if( ds.FindDataElement( Tag(overlay.GetGroup(),0x0010 ) ) )
        {
        // ok so far so good...
        const DataElement& overlaydata = ds.GetDataElement(Tag(overlay.GetGroup(),0x3000));
        //const DataElement& overlaydata = ds.GetDataElement(Tag(overlay.GetGroup(),0x0010));
        if( !overlaydata.IsEmpty() )
          {
          ++numoverlays;
          }
        }
        // Store found tag in overlay:
        overlay = de.GetTag();
        // Move on to the next possible one:
        overlay.SetGroup( overlay.GetGroup() + 2 );
        // reset to element 0x0 just in case...
        overlay.SetElement( 0 );
      }
    }

  // at most one out of two :
  assert( numoverlays < 0x00ff / 2 );
  return numoverlays;
}

00162 void Overlay::Update(const DataElement & de)
{
/*
  8.1.2 Overlay data encoding of related data elements
    Encoded Overlay Planes always have a bit depth of 1, and are encoded separately from the Pixel Data in Overlay Data (60xx,3000). The following two Data Elements shall define the Overlay Plane structure:
     Overlay Bits Allocated (60xx,0100)
     Overlay Bit Position (60xx,0102)
    Notes: 1. There is no Data Element analogous to Bits Stored (0028,0101) since Overlay Planes always have a bit depth of 1.
    2. Restrictions on the allowed values for these Data Elements are defined in PS 3.3. Formerly overlay data stored in unused bits of Pixel Data (7FE0,0010) was described, and these attributes had meaningful values but this usage has been retired. See PS 3.5 2004. For overlays encoded in Overlay Data Element (60xx,3000), Overlay Bits Allocated (60xx,0100) is always 1 and Overlay Bit Position (60xx,0102) is always 0.
*/

  assert( de.GetTag().IsPublic() );
  const ByteValue* bv = de.GetByteValue();
  if( !bv ) return; // Discard any empty element (will default to another value)
  assert( bv->GetPointer() && bv->GetLength() );
  std::string s( bv->GetPointer(), bv->GetLength() );
  // What if a \0 can be found before the end of string...
  //assert( strlen( s.c_str() ) == s.size() );

  // First thing check consistency:
  if( !GetGroup() )
    {
    SetGroup( de.GetTag().GetGroup() );
    }
  else // check consistency
    {
    assert( GetGroup() == de.GetTag().GetGroup() ); // programmer error
    }

  //std::cerr << "Tag: " << de.GetTag() << std::endl;
  if( de.GetTag().GetElement() == 0x0000 ) // OverlayGroupLength
    {
    // ??
    }
  else if( de.GetTag().GetElement() == 0x0010 ) // OverlayRows
    {
    Attribute<0x6000,0x0010> at;
    at.SetFromDataElement( de );
    SetRows( at.GetValue() );
    }
  else if( de.GetTag().GetElement() == 0x0011 ) // OverlayColumns
    {
    Attribute<0x6000,0x0011> at;
    at.SetFromDataElement( de );
    SetColumns( at.GetValue() );
    }
  else if( de.GetTag().GetElement() == 0x0015 ) // NumberOfFramesInOverlay
    {
    Attribute<0x6000,0x0015> at;
    at.SetFromDataElement( de );
    SetNumberOfFrames( at.GetValue() );
    }
  else if( de.GetTag().GetElement() == 0x0022 ) // OverlayDescription
    {
    SetDescription( s.c_str() );
    }
  else if( de.GetTag().GetElement() == 0x0040 ) // OverlayType
    {
    SetType( s.c_str() );
    }
  else if( de.GetTag().GetElement() == 0x0045 ) // OverlaySubtype
    {
    gdcmWarningMacro( "FIXME" );
    }
  else if( de.GetTag().GetElement() == 0x0050 ) // OverlayOrigin
    {
    Attribute<0x6000,0x0050> at;
    at.SetFromDataElement( de );
    SetOrigin( at.GetValues() );
    }
  else if( de.GetTag().GetElement() == 0x0051 ) // ImageFrameOrigin
    {
    Attribute<0x6000,0x0051> at;
    at.SetFromDataElement( de );
    SetFrameOrigin( at.GetValue() );
    }
  else if( de.GetTag().GetElement() == 0x0060 ) // OverlayCompressionCode (RET)
    {
    assert( s == "NONE" ); // FIXME ??
    }
  else if( de.GetTag().GetElement() == 0x0100 ) // OverlayBitsAllocated
    {
    Attribute<0x6000,0x0100> at;
    at.SetFromDataElement( de );
    if( at.GetValue() != 1 )
      {
      gdcmWarningMacro( "Unsuported OverlayBitsAllocated: " << at.GetValue() );
      }
    SetBitsAllocated( at.GetValue() );
    }
  else if( de.GetTag().GetElement() == 0x0102 ) // OverlayBitPosition
    {
    Attribute<0x6000,0x0102> at;
    at.SetFromDataElement( de );
    if( at.GetValue() != 0 ) // For old ACR when using unused bits...
      {
      gdcmWarningMacro( "Unsuported OverlayBitPosition: " << at.GetValue() );
      }
    SetBitPosition( at.GetValue() );
    }
  else if( de.GetTag().GetElement() == 0x0110 ) // OverlayFormat (RET)
    {
    assert( s == "RECT" );
    }
  else if( de.GetTag().GetElement() == 0x0200 ) // OverlayLocation (RET)
    {
    Attribute<0x6000,0x0200> at;
    at.SetFromDataElement( de );
    gdcmWarningMacro( "FIXME: " << at.GetValue() );
    }
  else if( de.GetTag().GetElement() == 0x1301 ) // ROIArea
    {
    gdcmWarningMacro( "FIXME" );
    }
  else if( de.GetTag().GetElement() == 0x1302 ) // ROIMean
    {
    gdcmWarningMacro( "FIXME" );
    }
  else if( de.GetTag().GetElement() == 0x1303 ) // ROIStandardDeviation
    {
    gdcmWarningMacro( "FIXME" );
    }
  else if( de.GetTag().GetElement() == 0x1500 ) // OverlayLabel
    {
    gdcmWarningMacro( "FIXME" );
    }
  else if( de.GetTag().GetElement() == 0x3000 ) // OverlayData
    {
    SetOverlay(bv->GetPointer(), bv->GetLength());
    }
  else
    {
    gdcmErrorMacro( "Tag is not supported: " << de.GetTag() << std::endl );
    assert(0);
    }
}

bool Overlay::GrabOverlayFromPixelData(DataSet const &ds)
{
  const unsigned int ovlength = Internal->Rows * Internal->Columns / 8;
  Internal->Data.resize( ovlength ); // set to 0
  if( Internal->BitsAllocated == 16 )
    {
    //assert( Internal->BitPosition >= 12 );
    assert( ds.FindDataElement( Tag(0x7fe0,0x0010) ) );
    const DataElement &pixeldata = ds.GetDataElement( Tag(0x7fe0,0x0010) );
    const ByteValue *bv = pixeldata.GetByteValue();
    assert( bv );
    const char *array = bv->GetPointer();
    // SIEMENS_GBS_III-16-ACR_NEMA_1.acr is pain to support,
    // I cannot simply use the bv->GetLength I have to use the image dim:
    const unsigned int length = ovlength * 8 * 2; //bv->GetLength();
    const uint16_t *p = (uint16_t*)array;
    const uint16_t *end = (uint16_t*)(array + length);
    //const unsigned int ovlength = length / (8*2);
    assert( 8 * ovlength == (unsigned int)Internal->Rows * Internal->Columns );
    unsigned char * overlay = (unsigned char*)&Internal->Data[0];
    int c = 0;
    uint16_t pmask = 1 << Internal->BitPosition;
    assert( length / 2 == ovlength * 8 );
    while( p != end )
      {
      const uint16_t val = *p & pmask;
      assert( val == 0x0 || val == pmask );
      // 128 -> 0x80
      if( val )
        {
        overlay[ c / 8 ] |= (0x1 << c%8);
        }
      else
        {
        // else overlay[ c / 8 ] is already 0
        }
      ++p;
      ++c;
      }
    assert( (unsigned)c / 8 == ovlength );
    }
  else
    {
    gdcmErrorMacro( "Could not grab Overlay from image. Please report." );
    return false;
    }
  return true;
}

00348 void Overlay::SetGroup(unsigned short group) { Internal->Group = group; }
00349 unsigned short Overlay::GetGroup() const { return Internal->Group; }

00351 void Overlay::SetRows(unsigned short rows) { Internal->Rows = rows; }
00352 unsigned short Overlay::GetRows() const { return Internal->Rows; }
00353 void Overlay::SetColumns(unsigned short columns) { Internal->Columns = columns; }
00354 unsigned short Overlay::GetColumns() const { return Internal->Columns; }
00355 void Overlay::SetNumberOfFrames(unsigned int numberofframes) { Internal->NumberOfFrames = numberofframes; }
00356 void Overlay::SetDescription(const char* description) { Internal->Description = description; }
00357 const char *Overlay::GetDescription() const { return Internal->Description.c_str(); }
00358 void Overlay::SetType(const char* type) { Internal->Type = type; }
00359 const char *Overlay::GetType() const { return Internal->Type.c_str(); }
00360 void Overlay::SetOrigin(const signed short *origin)
{
  Internal->Origin[0] = origin[0];
  Internal->Origin[1] = origin[1];
}
00365 const signed short * Overlay::GetOrigin() const
{
  return &Internal->Origin[0];
}
00369 void Overlay::SetFrameOrigin(unsigned short frameorigin) { Internal->FrameOrigin = frameorigin; }
00370 void Overlay::SetBitsAllocated(unsigned short bitsallocated) { Internal->BitsAllocated = bitsallocated; }
00371 unsigned short Overlay::GetBitsAllocated() const { return Internal->BitsAllocated; }
00372 void Overlay::SetBitPosition(unsigned short bitposition) { Internal->BitPosition = bitposition; }
00373 unsigned short Overlay::GetBitPosition() const { return Internal->BitPosition; }

bool Overlay::IsEmpty() const
{
  return Internal->Data.empty();
}
00379 bool Overlay::IsZero() const
{
  if( IsEmpty() ) return false;

  std::vector<char>::const_iterator it = Internal->Data.begin();
  for(; it != Internal->Data.end(); ++it )
    {
    if( *it ) return true;
    }
  return false;
}
bool Overlay::IsInPixelData() const { return Internal->InPixelData; }
void Overlay::IsInPixelData(bool b) { Internal->InPixelData = b; }

/*
 * row,col = 400,400   => 20000
 * row,col = 1665,1453 => 302406
 * row,col = 20,198    => 495 words + 1 dicom \0 padding
 */
inline unsigned int compute_bit_and_dicom_padding(unsigned short rows, unsigned short columns)
{
  unsigned int word_padding = ( rows * columns + 7 ) / 8; // need to send full word (8bits at a time)
  return word_padding + word_padding%2; // Cannot have odd length
}

00404 void Overlay::SetOverlay(const char *array, unsigned int length)
{
  if( !array || length == 0 ) return;
  //char * p = (char*)&Internal->Data[0];
  unsigned int computed_length = (Internal->Rows * Internal->Columns + 7) / 8;
  Internal->Data.resize( computed_length ); // filled with 0 if length < computed_length
  if( length < computed_length )
    {
    gdcmWarningMacro( "Not enough data found in Overlay. Proceed with caution" );
    std::copy(array, array+length, Internal->Data.begin());
    }
  else
    {
    if( length > computed_length )
      {
      gdcmWarningMacro( "Too much data found in Overlay. Discarding extra data: " << (length - computed_length) << " bytes." );
      }
    // do not try to copy more than allocated:
    std::copy(array, array+computed_length, Internal->Data.begin());
    }
  /* warning need to take into account padding to the next word (8bits) */
  //assert( length == compute_bit_and_dicom_padding(Internal->Rows, Internal->Columns) );
  assert( Internal->Data.size() == computed_length );
}

const ByteValue &Overlay::GetOverlayData() const
{
  static ByteValue bv;
  bv = ByteValue( Internal->Data );
  return bv;
}

void Overlay::Decode(std::istream &is, std::ostream &os)
{
  unsigned char packedbytes;
  unsigned char unpackedbytes[8];
  while( is.read((char*)&packedbytes,1) )
    {
    unsigned char mask = 1;
    for (unsigned int i = 0; i < 8; ++i)
      {
      if ( (packedbytes & mask) == 0)
        {
        unpackedbytes[i] = 0;
        }
      else
        {
        unpackedbytes[i] = 1;
        }
      mask <<= 1;
      }
    os.write(reinterpret_cast<char*>(unpackedbytes), 8);
    }
}

bool Overlay::GetBuffer(char *buffer) const
{
  unsigned long length = Internal->Data.size();
  std::copy(buffer, buffer+length, Internal->Data.begin());
  return true;
}

bool Overlay::GetUnpackBuffer(unsigned char *buffer) const
{
  unsigned char *unpackedbytes = buffer;
  for( std::vector<char>::const_iterator it = Internal->Data.begin(); it != Internal->Data.end(); ++it )
    {
    // const unsigned char &packedbytes = *it;
    // weird bug with gcc 3.3 (prerelease on SuSE) apparently:
    unsigned char packedbytes = static_cast<unsigned char>(*it);
    unsigned char mask = 1;
    for (unsigned int i = 0; i < 8; ++i)
      {
      if ( (packedbytes & mask) == 0)
        {
        *unpackedbytes = 0;
        }
      else
        {
        *unpackedbytes = 255;
        }
      ++unpackedbytes;
      mask <<= 1;
      }
    }
  return true;
}

void Overlay::Decompress(std::ostream &os) const
{
  unsigned char unpackedbytes[8];
  for( std::vector<char>::const_iterator it = Internal->Data.begin(); it != Internal->Data.end(); ++it )
    {
    unsigned char packedbytes = *it;
    unsigned char mask = 1;
    for (unsigned int i = 0; i < 8; ++i)
      {
      if ( (packedbytes & mask) == 0)
        {
        unpackedbytes[i] = 0;
        }
      else
        {
        unpackedbytes[i] = 255;
        }
      mask <<= 1;
      }
    os.write(reinterpret_cast<char*>(unpackedbytes), 8);
    }
}

00515 void Overlay::Print(std::ostream &os) const
{
  Internal->Print( os );
}

} // end namespace gdcm

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