vol2obj.cpp

#include <iostream>
#include "DGtal/base/Common.h"
#include "DGtal/helpers/StdDefs.h"
#include "DGtal/io/readers/GenericReader.h"
#include "DGtal/io/boards/Board3D.h"
#include "DGtal/io/DrawWithDisplay3DModifier.h"
#include "DGtal/io/readers/PointListReader.h"

#include "DGtal/images/ImageSelector.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;

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>(), "vol file (.vol, .longvol .p3d, .pgm3d and if WITH_ITK is selected: dicom, dcm, mha, mhd) or sdp (sequence of discrete points)." )
  ("output,o", po::value<std::string>(),
  "Output OBJ filename (each grid point with value between [ @a thresholdMin, @a thresholdMax ] is exported as a unit cube ) " )
  ( "thresholdMin,m", po::value<int>()->default_value( 0 ),"threshold min to define binary shape" )
  ("thresholdMax,M", po::value<int>()->default_value( 255 ),"threshold max to define binary shape" )
  ("rescaleInputMin", po::value<DGtal::int64_t>()->default_value( 0 ), "min value used to rescale the input intensity (to avoid basic cast into 8 bits image)." )
  ( "rescaleInputMax",po::value<DGtal::int64_t>()->default_value( 255 ),
                    "max value used to rescale the input intensity (to avoid "
                    "basic cast into 8 bits image)." );

  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)
    {
      std::cout << "Usage: " << argv[0] << " [input-file]\n"
                << "Convert a  volume file into OBJ format\n"
                << general_opt << "\n";
      return 0;
    }

  if(! vm.count("input"))
    {
      trace.error() << " The input filename was defined" << endl;
      return 0;
    }
  if(! vm.count("output"))
    {
      trace.error() << " The output filename was defined" << endl;
      return 0;
    }

  string inputFilename = vm["input"].as<std::string>();
  string outputFilename = vm["output"].as<std::string>();
  int thresholdMin = vm["thresholdMin"].as<int>();
  int thresholdMax = vm["thresholdMax"].as<int>();

  Board3D<> board;

  typedef ImageSelector<Domain, unsigned char>::Type Image;
  string extension = inputFilename.substr(inputFilename.find_last_of(".") + 1);

  if(extension!="sdp")
    {
      DGtal::int64_t rescaleInputMin = vm["rescaleInputMin"].as<DGtal::int64_t>();
      DGtal::int64_t rescaleInputMax = vm["rescaleInputMax"].as<DGtal::int64_t>();

      typedef DGtal::functors::Rescaling<DGtal::int64_t ,unsigned char > RescalFCT;
      Image image =  GenericReader< Image >::importWithValueFunctor( inputFilename,RescalFCT(rescaleInputMin,
                                                                                             rescaleInputMax,
                                                                                             0, 255) );
      trace.info() << "Image loaded: "<<image<< std::endl;
      Domain domain = image.domain();
      for(Domain::ConstIterator it = domain.begin(), itend=domain.end(); it!=itend; ++it){
        unsigned char  val= image( (*it) );
        if(val<=thresholdMax && val >=thresholdMin){
          board << *it;
        }
      }
    }
  else
    if(extension=="sdp")
      {
        vector<Z3i::Point> vectVoxels = PointListReader<Z3i::Point>::getPointsFromFile(inputFilename);
        for(unsigned int i=0;i< vectVoxels.size(); i++){
          board << vectVoxels.at(i);
        }
      }


  board.saveOBJ(outputFilename);
  return 0;
}