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

  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 "gdcmAttribute.h"
#include "gdcmFileExplicitFilter.h"
#include "gdcmSequenceOfItems.h"

/**
 * This example is used to generate the file:
 *
 *  gdcmConformanceTests/RTStruct_VRDSAsVRUN.dcm
 *
 * This is an advanced example. Its goal is to explain one dark corner of DICOM PS 3.10
 * file format. The idea is that when writting an Attribute in an Explicit Transfer
 * Syntax one, cannot always use V:DS for writing a VR:DS attribute since dong so
 * would imply using a VL:16bits.
 * This example shows that converting from Implicit to Explicit should preserver VR:UN
 * when the VL is larger than 16bits limit.
 *
 * Usage:
 * ./LargeVRDSExplicit gdcmDataExtra/gdcmNonImageData/RT/RTStruct.dcm out.dcm
 */

bool interpolate(const double * pts, unsigned int npts, std::vector<double> &out )
{
  out.clear();
  for(unsigned int i = 0; i < 2*npts; ++i )
    {
    const unsigned int j = i / 2;
    if( i % 2 )
      {
      if( j != npts - 1 )
        {
        assert( j >= 0 && 3*j+5 < 3*npts );
        const double midpointx = (pts[3*j+0] + pts[3*j+3]) / 2;
        const double midpointy = (pts[3*j+1] + pts[3*j+4]) / 2;
        const double midpointz = (pts[3*j+2] + pts[3*j+5]) / 2;
        out.push_back( midpointx );
        out.push_back( midpointy );
        out.push_back( midpointz );
        }
      }
    else
      {
      assert( j >= 0 && j < npts );
      out.push_back( pts[3*j+0] );
      out.push_back( pts[3*j+1] );
      out.push_back( pts[3*j+2] );
      }
    }
  assert( out.size() == 2 * npts * 3 - 3 );
  return true;
}

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();
  gdcm::DataSet &ds = file.GetDataSet();

  gdcm::FileExplicitFilter fef;
  //fef.SetChangePrivateTags( changeprivatetags );
  fef.SetFile( reader.GetFile() );
  if( !fef.Change() )
    {
    std::cerr << "Failed to change: " << filename << std::endl;
    return 1;
    }

  // (3006,0039) SQ (Sequence with undefined length #=4)     # u/l, 1 ROIContourSequence
  gdcm::Tag tag(0x3006,0x0039);

  const gdcm::DataElement &roicsq = ds.GetDataElement( tag );
  gdcm::SmartPointer<gdcm::SequenceOfItems> sqi = roicsq.GetValueAsSQ();
  //sqi->SetNumberOfItems( 1 );
  const gdcm::Item & item = sqi->GetItem(1); // Item start at #1
  const gdcm::DataSet& nestedds = item.GetNestedDataSet();

  gdcm::Tag tcsq(0x3006,0x0040);
  if( !nestedds.FindDataElement( tcsq ) )
    {
    return 0;
    }
  const gdcm::DataElement& csq = nestedds.GetDataElement( tcsq );
  gdcm::SmartPointer<gdcm::SequenceOfItems> sqi2 = csq.GetValueAsSQ();
  if( !sqi2 || !sqi2->GetNumberOfItems() )
    {
    return 0;
    }
  unsigned int nitems = sqi2->GetNumberOfItems();
  gdcm::Item & item2 = sqi2->GetItem(1); // Item start at #1

  gdcm::DataSet& nestedds2 = item2.GetNestedDataSet();
  //item2.SetVLToUndefined();
  //std::cout << nestedds2 << std::endl;
  // (3006,0050) DS [43.57636\65.52504\-10.0\46.043102\62.564945\-10.0\49.126537\60.714... # 398,48 ContourData
  gdcm::Tag tcontourdata(0x3006,0x0050);
  const gdcm::DataElement & contourdata = nestedds2.GetDataElement( tcontourdata );
  //std::cout << contourdata << std::endl;

  //const gdcm::ByteValue *bv = contourdata.GetByteValue();
  gdcm::Attribute<0x3006,0x0046> ncontourpoints;
  ncontourpoints.Set( nestedds2 );

  gdcm::Attribute<0x3006,0x0050> at;
  at.SetFromDataElement( contourdata );
  const double* pts = at.GetValues();
  unsigned int npts = at.GetNumberOfValues() / 3;

  std::vector<double> out( pts, pts + npts * 3 );
  std::vector<double> out2;

  //const unsigned int niter = 7;
  const unsigned int niter = 8;
  for( unsigned int i = 0; i < niter; ++i)
    {
    bool b = interpolate(&out[0], out.size() / 3, out2);
    //const double *pout = &out[0];
    out = out2;
    out2.clear();
    }
  assert( out.size() % 3 == 0 );

  gdcm::Attribute<0x3006,0x0050> at_interpolate;
  at_interpolate.SetNumberOfValues( out.size() / 3 );
  at_interpolate.SetValues( &out[0], out.size() );

  ncontourpoints.SetValue( at_interpolate.GetNumberOfValues() / 3 );
  nestedds2.Replace( at_interpolate.GetAsDataElement() );
  nestedds2.Replace( ncontourpoints.GetAsDataElement() );

  //assert(0);

  // Let's take item one and subdivide it

  gdcm::TransferSyntax ts = gdcm::TransferSyntax::ImplicitVRLittleEndian;
  ts = gdcm::TransferSyntax::ExplicitVRLittleEndian;

  gdcm::FileMetaInformation &fmi = file.GetHeader();
  const char *tsuid = gdcm::TransferSyntax::GetTSString( ts );
  // const char * is ok since padding is \0 anyway...
  gdcm::DataElement de( gdcm::Tag(0x0002,0x0010) );
  de.SetByteValue( tsuid, strlen(tsuid) );
  de.SetVR( gdcm::Attribute<0x0002, 0x0010>::GetVR() );
  fmi.Replace( de );
  fmi.Remove( gdcm::Tag(0x0002,0x0012) ); // will be regenerated
  fmi.Remove( gdcm::Tag(0x0002,0x0013) ); //  '   '    '
  fmi.SetDataSetTransferSyntax(ts);


  gdcm::Writer w;
  w.SetFile( file );
  w.SetFileName( outfilename );
  if (!w.Write() )
    {
    return 1;
    }

  return 0;
}