GetSubSequenceData.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 "gdcmImage.h"
#include "gdcmImageWriter.h"
#include "gdcmDataElement.h"
#include "gdcmPrivateTag.h"
#include "gdcmUIDGenerator.h"
 
#include <iostream>
#include <string>
 
#include <map>
 
/*
 * This example will extract the Movie from the private group of
 * GEMS_Ultrasound_MovieGroup_001 See Attribute
 * (7fe1,60,GEMS_Ultrasound_MovieGroup_001)
 *
 * The output file will be stored in `outvid.dcm` as
 * MultiframeGrayscaleByteSecondaryCaptureImageStorage
 */
int main(int argc, char *argv[])
{
  if( argc < 2 ) return 1;
  using namespace gdcm;
  const char *filename = argv[1];
  gdcm::Reader reader;
  reader.SetFileName( filename );
  reader.Read();
 
  gdcm::File &file = reader.GetFile();
  gdcm::DataSet &ds = file.GetDataSet();
  const PrivateTag tseq(0x7fe1,0x1,"GEMS_Ultrasound_MovieGroup_001");
 
  if( !ds.FindDataElement( tseq ) ) return 1;
  const DataElement& seq = ds.GetDataElement( tseq );
 
  SmartPointer<SequenceOfItems> sqi = seq.GetValueAsSQ();
  assert( sqi->GetNumberOfItems() == 1 );
  Item &item = sqi->GetItem(1);
  DataSet &subds = item.GetNestedDataSet();
 
  const PrivateTag tseq1(0x7fe1,0x10,"GEMS_Ultrasound_MovieGroup_001");
 
  if( !subds.FindDataElement( tseq1 ) ) return 1;
  const DataElement& seq1 = subds.GetDataElement( tseq1 );
 
  SmartPointer<SequenceOfItems> sqi2 = seq1.GetValueAsSQ();
  //int n = sqi2->GetNumberOfItems();
  int index = 1;
  Item &item2 = sqi2->GetItem(index);
  DataSet &subds2 = item2.GetNestedDataSet();
 
  const PrivateTag tseq2(0x7fe1,0x20,"GEMS_Ultrasound_MovieGroup_001");
 
  if( !subds2.FindDataElement( tseq2 ) ) return 1;
  const DataElement& seq2 = subds2.GetDataElement( tseq2 );
 
//    std::cout << seq2 << std::endl;
 
  SmartPointer<SequenceOfItems> sqi3 = seq2.GetValueAsSQ();
  size_t ni3 = sqi3->GetNumberOfItems(); (void)ni3;
  assert( sqi3->GetNumberOfItems() >= 1 );
  Item &item3 = sqi3->GetItem(1);
  DataSet &subds3 = item3.GetNestedDataSet();
 
  const PrivateTag tseq6(0x7fe1,0x26,"GEMS_Ultrasound_MovieGroup_001");
  if( !subds3.FindDataElement( tseq6 ) ) return true;
  const DataElement& seq6 = subds3.GetDataElement( tseq6 );
  SmartPointer<SequenceOfItems> sqi6 = seq6.GetValueAsSQ();
  size_t ni6= sqi6->GetNumberOfItems();
  assert( sqi6->GetNumberOfItems() >= 1 );
  const PrivateTag tseq7(0x7fe1,0x86,"GEMS_Ultrasound_MovieGroup_001");
  int dimx = 0, dimy = 0;
  for( size_t i6 = 1; i6 <= ni6; ++i6 )
    {
    Item &item6 = sqi6->GetItem(i6);
    DataSet &subds6 = item6.GetNestedDataSet();
 
    if( subds6.FindDataElement( tseq7 ) )
      {
      Element<VR::SL, VM::VM4> el;
      el.SetFromDataElement( subds6.GetDataElement( tseq7 ) );
      std::cout << "El= " << el.GetValue() << std::endl;
      dimx = el.GetValue(0);
      dimy = el.GetValue(1);
      }
    }
 
  const PrivateTag tseq3(0x7fe1,0x36,"GEMS_Ultrasound_MovieGroup_001");
  if( !subds3.FindDataElement( tseq3 ) ) return true;
  const DataElement& seq3 = subds3.GetDataElement( tseq3 );
 
//    std::cout << seq3 << std::endl;
 
  SmartPointer<SequenceOfItems> sqi4 = seq3.GetValueAsSQ();
  size_t ni4= sqi4->GetNumberOfItems();
  assert( sqi4->GetNumberOfItems() >= 1 );
  const PrivateTag tseq8(0x7fe1,0x37,"GEMS_Ultrasound_MovieGroup_001");
  const PrivateTag tseq4(0x7fe1,0x43,"GEMS_Ultrasound_MovieGroup_001");
  const PrivateTag tseq5(0x7fe1,0x60,"GEMS_Ultrasound_MovieGroup_001");
 
  std::vector<char> imbuffer;
  int dimz = 0;
  for( size_t i4 = 1; i4 <= ni4; ++i4 )
    {
    Item &item4 = sqi4->GetItem(i4);
    DataSet &subds4 = item4.GetNestedDataSet();
 
    if( !subds4.FindDataElement( tseq8 ) ) return true;
    const DataElement& de8 = subds4.GetDataElement( tseq8 );
    Element<VR::UL,VM::VM1> ldimz;
    ldimz.SetFromDataElement( de8 );
    dimz += ldimz.GetValue();
    if( !subds4.FindDataElement( tseq4 ) ) return true;
    const DataElement& seq4 = subds4.GetDataElement( tseq4 );
    if( !subds4.FindDataElement( tseq5 ) ) return true;
    const DataElement& seq5 = subds4.GetDataElement( tseq5 );
 
    //    std::cout << seq4 << std::endl;
    //    std::cout << seq5 << std::endl;
 
    const ByteValue *bv4 = seq4.GetByteValue();
    (void)bv4;
#if 0
      {
      std::ofstream out( "/tmp/mo4", std::ios::binary );
      out.write( bv4->GetPointer(), bv4->GetLength());
      out.close();
      }
#endif
  const ByteValue *bv5 = seq5.GetByteValue();
#if 0
    {
    std::ofstream out( "/tmp/mo5", std::ios::binary );
    out.write( bv5->GetPointer(), bv5->GetLength());
    out.close();
    }
#endif
 
    std::cout << bv5->GetLength() << std::endl;
    imbuffer.insert( imbuffer.begin(), bv5->GetPointer(), bv5->GetPointer() + bv5->GetLength() );
    }
  DataElement fakedata;
  fakedata.SetByteValue( imbuffer.data(), (uint32_t)imbuffer.size() );
 
 
  gdcm::SmartPointer<gdcm::Image> im = new gdcm::Image;
  im->SetNumberOfDimensions( 3 );
 
  im->SetDimension(0, dimx );
  im->SetDimension(1, dimy );
  im->SetDimension(2, dimz );
  size_t l1 = imbuffer.size();
  (void)l1;
  size_t l2 = im->GetBufferLength();
  (void)l2;
  assert( im->GetBufferLength() == imbuffer.size() );
  im->SetPhotometricInterpretation( gdcm::PhotometricInterpretation::MONOCHROME2 );
 
  im->SetDataElement( fakedata );
 
  gdcm::ImageWriter w;
  w.SetImage( *im );
  DataSet &dataset = w.GetFile().GetDataSet();
 
  gdcm::UIDGenerator uid;
  gdcm::DataElement de( Tag(0x8,0x18) ); // SOP Instance UID
  de.SetVR( VR::UI );
  const char *u = uid.Generate();
  de.SetByteValue( u, (uint32_t)strlen(u) );
  //ds.Insert( de );
  dataset.Replace( de );
 
  de.SetTag( Tag(0x8,0x16) ); // SOP Class UID
  de.SetVR( VR::UI );
  gdcm::MediaStorage ms(
    gdcm::MediaStorage::MultiframeGrayscaleByteSecondaryCaptureImageStorage );
  de.SetByteValue( ms.GetString(), (uint32_t)strlen(ms.GetString()));
  dataset.Replace( de ); // replace !
 
  w.SetFileName( "outvid.dcm" );
  if( !w.Write() )
    {
    return 1;
    }
 
  return 0;
}