vol2vox.cpp

#include <iostream>
#include <DGtal/base/Common.h>
#include <DGtal/io/readers/VolReader.h>
#include <DGtal/helpers/StdDefs.h>
#include <DGtal/images/Image.h>
#include <DGtal/images/ImageContainerBySTLVector.h>

#include <boost/program_options/options_description.hpp>
#include <boost/program_options/parsers.hpp>
#include <boost/program_options/variables_map.hpp>

using namespace std;
using namespace DGtal;
using namespace Z3i;

namespace po = boost::program_options;


void missingParam ( const std::string &param )
{
  trace.error() <<" Parameter: "<<param<<" is required..";
  trace.info() <<std::endl;
  exit ( 1 );
}

template <typename Word>
static
std::ostream& write_word( std::ostream& outs, Word value )
{
  for (unsigned size = sizeof( Word ); size; --size, value >>= 8)
    outs.put( static_cast <char> (value & 0xFF) );
  return outs;
}


int main(int argc, char**argv)
{

  // parse command line ----------------------------------------------
  po::options_description general_opt ( "Allowed options are: " );
  general_opt.add_options()
  ( "help,h", "display this message." )
  ( "input,i", po::value<std::string>(), "Input vol file." )
  ( "output,o", po::value<string>(),"Output filename." );
  bool parseOK=true;
  po::variables_map vm;
  try{
    po::store(po::parse_command_line(argc, argv, general_opt), vm);
  }catch(const std::exception& ex){
    parseOK=false;
    trace.info()<< "Error checking program options: "<< ex.what()<< endl;
  }
  po::notify ( vm );
  if ( !parseOK || vm.count ( "help" ) ||argc<=1 )
  {
    trace.info() << "Convert a vol (up to [0,126]^3) to a vox. The current exporter does not support custom colormaps, only the voxel values are exported." <<std::endl
    << std::endl << "Basic usage: "<<std::endl
    << "\tvol2vox --input <volFileName> --o <volOutputFileName> "<<std::endl
    << general_opt << "\n";
    return 0;
  }

  //Parse options
  if ( ! ( vm.count ( "input" ) ) ) missingParam ( "--input" );
  std::string filename = vm["input"].as<std::string>();
  if ( ! ( vm.count ( "output" ) ) ) missingParam ( "--output" );
  std::string outputFileName = vm["output"].as<std::string>();

  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  MyImageC;

  trace.beginBlock("Loading..");
  MyImageC  imageL = VolReader< MyImageC >::importVol ( filename );
  trace.endBlock();
 
  if ( (imageL.domain().upperBound() - imageL.domain().lowerBound()).max() > 126 )
  {
    trace.error() << "Vol file too large (width > 126)."<<std::endl;
    trace.info() << std::endl;
    exit(2);
  }
 
  trace.beginBlock("Exporting...");
  ofstream myfile;
  myfile.open (outputFileName, ios::out | ios::binary);

  DGtal::uint32_t cpt=0;
  for(auto it = imageL.range().begin(), itend = imageL.range().end();
      it!=itend; ++it)
    if (*it != 0)
      cpt++;

  Point size = imageL.domain().upperBound() - imageL.domain().lowerBound();

  /*
   * VOX file format:
   *
   4b VOX' '
   4b version (150)

   4b MAIN (chunckid)
   4b size chucnk content (n)
   4b size chunck children (m)

   4b SIZE (chunckid)
   4b chunck content
   4b chunck children
   4bx3  x,y,z

   4b VOXEL (chunckid)
   4b chunck content
   4b chunck children
   4b number of voxels
   1b x 4 (x,y,z,idcol)  x numVoxels

   */

  trace.info()<<size<<std::endl;

  //HEADER
  myfile <<'V'<<'O'<<'X'<<' ';
  //  version 150
  write_word(myfile, (DGtal::uint32_t)150);

  //Chunck MAIN
  myfile <<'M'<<'A'<<'I'<<'N';
  write_word(myfile,DGtal::uint32_t(0)); //size content
  write_word(myfile,DGtal::uint32_t( (4+4+4 + 12 ) + ((4+ 4 + 4) + (4+ cpt*4)))); //size children

  //Chunck SIZE
  myfile <<'S'<<'I'<<'Z'<<'E';
  write_word(myfile,DGtal::uint32_t(12)); //3x4
  write_word(myfile,DGtal::uint32_t(0));  //0 children
  write_word(myfile,DGtal::uint32_t(size[0]+1));
  write_word(myfile,DGtal::uint32_t(size[1]+1));
  write_word(myfile,DGtal::uint32_t(size[2]+1));

  //Chunck VOXEL
  myfile << 'X'<<'Y'<<'Z'<<'I';
  write_word(myfile, (DGtal::uint32_t)(4+cpt*4));  // 4 + numvoxel * 4
  write_word(myfile,DGtal::uint32_t(0));  //0 children
  write_word(myfile, DGtal::uint32_t(cpt)); //numvoxels

  trace.info() << "Number of voxels= "<<cpt<<std::endl;

  //Data
  for(auto it = imageL.domain().begin(), itend = imageL.domain().end();
      it!=itend; ++it)
    if (imageL(*it) != 0)
    {
      Point p = (*it) - imageL.domain().lowerBound();
      myfile.put((DGtal::uint8_t)p[0]);
      myfile.put( (DGtal::uint8_t)p[1]);
      myfile.put( (DGtal::uint8_t)p[2]);
      myfile.put(imageL(*it));
    }

  myfile.close();
  trace.endBlock();

  return 0;
}