volBoundary2obj.cpp

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

#include "DGtal/base/Common.h"
#include "DGtal/base/BasicFunctors.h"
#include "DGtal/kernel/SpaceND.h"
#include "DGtal/kernel/domains/HyperRectDomain.h"
#include "DGtal/images/ImageSelector.h"
#include "DGtal/images/IntervalForegroundPredicate.h"
#include "DGtal/topology/KhalimskySpaceND.h"
#include "DGtal/topology/DigitalSurface.h"
#include "DGtal/topology/SetOfSurfels.h"
#include "DGtal/io/boards/Board3D.h"
#include "DGtal/io/readers/PointListReader.h"
#include "DGtal/io/readers/GenericReader.h"
#ifdef WITH_ITK
#include "DGtal/io/readers/DicomReader.h"
#endif
#include "DGtal/io/Color.h"
#include "DGtal/io/colormaps/GradientColorMap.h"


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

namespace po = boost::program_options;

int main( int argc, char** argv )
{
  typedef SpaceND<3,int> Space;
  typedef KhalimskySpaceND<3,int> KSpace;
  typedef HyperRectDomain<Space> Domain;
  typedef ImageSelector<Domain, unsigned char>::Type Image;
  typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency;

  // 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) , pgm3d (.p3d or .pgm3d, pgm (with 3 dims)) file or sdp (sequence of discrete points)" )
    ("output,o", po::value<std::string>(), "output obj file (.obj)" )
    ("thresholdMin,m",  po::value<int>()->default_value(0), "threshold min (excluded) to define binary shape" )
    ("thresholdMax,M",  po::value<int>()->default_value(255), "threshold max (included) to define binary shape" )
#ifdef WITH_ITK
    ("dicomMin", po::value<int>()->default_value(-1000), "set minimum density threshold on Hounsfield scale")
    ("dicomMax", po::value<int>()->default_value(3000), "set maximum density threshold on Hounsfield scale")
#endif
    ("mode",  po::value<std::string>()->default_value("BDRY"), "set mode for display: INNER: inner voxels, OUTER: outer voxels, BDRY: surfels (default), CLOSURE: surfels with linels and pointels.")
   ("normalization,n", "Normalization so that the geometry fits in [-1/2,1/2]^3") ;

  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] << " -i [input] -o [output]\n"
                << "Export the boundary of a volume file to OBJ format. The mode specifies if you wish to see surface elements (BDRY), the inner voxels (INNER) or the outer voxels (OUTER) that touch the boundary."<< endl
                << general_opt << "\n";
      return 0;
    }

  if(! vm.count("input"))
    {
      trace.error() << " The file name 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>();
  int thresholdMin = vm["thresholdMin"].as<int>();
  int thresholdMax = vm["thresholdMax"].as<int>();
  string mode = vm["mode"].as<string>();
  bool normalization = false;
  if  (vm.count("normalization"))
    normalization = true;
  
  string extension = inputFilename.substr(inputFilename.find_last_of(".") + 1);
  if(extension!="vol" && extension != "p3d" && extension != "pgm3D" && extension != "pgm3d" && extension != "sdp" && extension != "pgm"
#ifdef WITH_ITK
     && extension !="dcm"
#endif
     ){
    trace.info() << "File extension not recognized: "<< extension << std::endl;
    return 0;
  }

  if(extension=="vol" || extension=="pgm3d" || extension=="pgm3D"
#ifdef WITH_ITK
     || extension =="dcm"
#endif
     ){
    trace.beginBlock( "Loading image into memory." );
#ifdef WITH_ITK
    int dicomMin = vm["dicomMin"].as<int>();
    int dicomMax = vm["dicomMax"].as<int>();
    typedef DGtal::functors::Rescaling<int ,unsigned char > RescalFCT;
    Image image = extension == "dcm" ? DicomReader< Image,  RescalFCT  >::importDicom( inputFilename,
                                                                                       RescalFCT(dicomMin,
                                                                                                 dicomMax,
                                                                                                 0, 255) ) :
      GenericReader<Image>::import( inputFilename );
#else
    Image image = GenericReader<Image>::import (inputFilename );
#endif
    trace.info() << "Image loaded: "<<image<< std::endl;
    trace.endBlock();

    trace.beginBlock( "Construct the Khalimsky space from the image domain." );
    Domain domain = image.domain();
    KSpace ks;
    bool space_ok = ks.init( domain.lowerBound(), domain.upperBound(), true );
    if (!space_ok)
      {
        trace.error() << "Error in the Khamisky space construction."<<std::endl;
        return 2;
      }
    trace.endBlock();

    trace.beginBlock( "Wrapping a digital set around image. " );
    typedef functors::IntervalForegroundPredicate<Image> ThresholdedImage;
    ThresholdedImage thresholdedImage( image, thresholdMin, thresholdMax );
    trace.endBlock();

    trace.beginBlock( "Extracting boundary by scanning the space. " );
    typedef KSpace::SurfelSet SurfelSet;
    typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels;
    typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface;
    MySurfelAdjacency surfAdj( true ); // interior in all directions.
    MySetOfSurfels theSetOfSurfels( ks, surfAdj );
    Surfaces<KSpace>::sMakeBoundary( theSetOfSurfels.surfelSet(),
                                     ks, thresholdedImage,
                                     domain.lowerBound(),
                                     domain.upperBound() );
    MyDigitalSurface digSurf( theSetOfSurfels );
    trace.info() << "Digital surface has " << digSurf.size() << " surfels."
                 << std::endl;
    trace.endBlock();

    trace.beginBlock( "Exporting everything." );
    Board3D<Space,KSpace> board(ks);

    board << SetMode3D(  ks.unsigns( *digSurf.begin() ).className(), "Basic" );

    typedef MyDigitalSurface::ConstIterator ConstIterator;
    if ( mode == "BDRY" )
      for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
        board << ks.unsigns( *it );
    else if ( mode == "INNER" )
      for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
        board << ks.sCoords( ks.sDirectIncident( *it, ks.sOrthDir( *it ) ) );
    else if ( mode == "OUTER" )
      for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
        board << ks.sCoords( ks.sIndirectIncident( *it, ks.sOrthDir( *it ) ) );
    else  if (mode == "CLOSURE")
    {
        std::set<KSpace::Cell> container;
        for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
        {
          container.insert( ks.unsigns( *it ) );
          KSpace::SCells oneNeig = ks.sLowerIncident(*it);
          //Processing linels
          for(KSpace::SCells::ConstIterator itt = oneNeig.begin(), ittend = oneNeig.end(); itt != ittend; ++itt)
          {
            container.insert( ks.unsigns( *itt) );
            KSpace::SCells oneNeig2 = ks.sLowerIncident(*itt);
            //Processing pointels
            for(KSpace::SCells::ConstIterator ittt = oneNeig2.begin(), itttend = oneNeig2.end(); ittt != itttend; ++ittt)
              container.insert( ks.unsigns(*ittt) );
          }
        }
      trace.info()<< "Exporting "<< container.size() << " cells"<<std::endl;
      for(auto cell: container)
        board << cell;
    }
    
    string outputFilename = vm["output"].as<std::string>();

    board.saveOBJ(outputFilename, normalization);
    trace.endBlock();
  }
  return 0;
}