3dImageViewer.cpp

#include <iostream>

#include "DGtal/base/Common.h"
#include "DGtal/base/BasicFunctors.h"
#include "DGtal/helpers/StdDefs.h"
#include "DGtal/io/readers/VolReader.h"
#include "DGtal/io/viewers/Viewer3D.h"
#include "DGtal/io/DrawWithDisplay3DModifier.h"
#include "DGtal/io/readers/PointListReader.h"
#include "DGtal/io/readers/MeshReader.h"
#include "DGtal/topology/helpers/Surfaces.h"
#include "DGtal/topology/SurfelAdjacency.h"

#include "DGtal/io/Color.h"
#include "DGtal/io/colormaps/GradientColorMap.h"
#include "DGtal/io/readers/GenericReader.h"
#ifdef WITH_ITK
#include "DGtal/io/readers/DicomReader.h"
#endif

#include "DGtal/images/ImageSelector.h"



#include "specificClasses/Viewer3DImage.cpp"

#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 )
{

  typedef DGtal::ImageContainerBySTLVector<DGtal::Z3i::Domain,  unsigned char > Image3D;
  typedef DGtal::ImageContainerBySTLVector<DGtal::Z2i::Domain,  unsigned char > Image2D;


  // 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) file or sdp (sequence of discrete points)" )
    ("grid", "draw slice images using grid mode. " )
    ("intergrid", "draw slice images using inter grid mode. " )
    ("emptyMode", "remove the default boundingbox display " )
    ("thresholdImage", "threshold the image to define binary shape" )
    ("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" )
    ("displaySDP,s", po::value<std::string>(), "display a set of discrete points (.sdp)" )
    ("SDPindex", po::value<std::vector <unsigned int> >()->multitoken(), "specify the sdp index (by default 0,1,2).")
    ("SDPball", po::value<double>()->default_value(0.5), "use balls to display a set of discrete points (used with displaySDP option)")
    ("displayMesh", po::value<std::string>(), "display a Mesh given in OFF or OFS format. " )
    ("displayDigitalSurface", "display the digital surface instead of display all the set of voxels (used with thresholdImage or displaySDP options)" )
    ("colorizeCC", "colorize each Connected Components of the surface displayed by displayDigitalSurface option." )
    ("colorSDP,c", po::value<std::vector <int> >()->multitoken(), "set the color  discrete points: r g b a " )
    ("colorMesh", po::value<std::vector <int> >()->multitoken(), "set the color of Mesh (given from displayMesh option) : r g b a " )
    ("scaleX,x",  po::value<float>()->default_value(1.0), "set the scale value in the X direction (default 1.0)" )
    ("scaleY,y",  po::value<float>()->default_value(1.0), "set the scale value in the Y direction (default 1.0)" )
    ("scaleZ,z",  po::value<float>()->default_value(1.0), "set the scale value in the Z direction (default 1.0)")
#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
    ("transparency,t",  po::value<uint>()->default_value(255), "transparency") ;

  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]\n"
    << "Displays volume file as a voxel set by using QGLviewer"
    << general_opt << "\n";
      return 0;
    }

  if(! vm.count("input"))
    {
      trace.error() << " The file name was defined" << endl;
      return 0;
    }
  string inputFilename = vm["input"].as<std::string>();
  int thresholdMin = vm["thresholdMin"].as<int>();
  int thresholdMax = vm["thresholdMax"].as<int>();
  unsigned char transp = vm["transparency"].as<uint>();

  QApplication application(argc,argv);
  
  float sx = vm["scaleX"].as<float>();
  float sy = vm["scaleY"].as<float>();
  float sz = vm["scaleZ"].as<float>();

  double ballRadius = vm["SDPball"].as<double>();
  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;
  }
  Viewer3DImage<>::ModeVisu mode;
  if(vm.count("emptyMode"))
    mode=Viewer3DImage<>::Empty;
  else if(vm.count("grid"))
    mode=Viewer3DImage<>::Grid;
  else if(vm.count("intergrid"))
    mode=Viewer3DImage<>::InterGrid;
  else
    mode=Viewer3DImage<>::BoundingBox;

  Viewer3DImage<> viewer(mode);
  viewer.setWindowTitle("simple Volume Viewer");
  viewer.show();
  viewer.setGLScale(sx, sy, sz);

#ifdef WITH_ITK
  int dicomMin = vm["dicomMin"].as<int>();
  int dicomMax = vm["dicomMax"].as<int>();
  typedef DGtal::functors::Rescaling<int ,unsigned char > RescalFCT;

  Image3D image = extension == "dcm" ? DicomReader< Image3D,  RescalFCT  >::importDicom( inputFilename,
                                                                                         RescalFCT(dicomMin,
                                                                                                   dicomMax,
                                                                                                   0, 255) ) :
    GenericReader<Image3D>::import( inputFilename );
#else
  Image3D image = GenericReader<Image3D>::import( inputFilename );
#endif
  Domain domain = image.domain();

  trace.info() << "Image loaded: "<<image<< std::endl;
  viewer.setVolImage(&image);
  viewer << Z3i::Point(512, 512, 0);
  // Used to display 3D surface
  Z3i::DigitalSet set3d(domain);



  viewer << Viewer3D<>::updateDisplay;
  if(vm.count("thresholdImage")){
    GradientColorMap<long> gradient( thresholdMin, thresholdMax);
    gradient.addColor(Color::Blue);
    gradient.addColor(Color::Green);
    gradient.addColor(Color::Yellow);
    gradient.addColor(Color::Red);
    for(Domain::ConstIterator it = domain.begin(), itend=domain.end(); it!=itend; ++it){
      unsigned char  val= image( (*it) );
      Color c= gradient(val);
      if(val<=thresholdMax && val >=thresholdMin){
  if(!vm.count("displayDigitalSurface")){
          viewer <<  CustomColors3D(Color((float)(c.red()), (float)(c.green()),(float)(c.blue()), transp),
                                    Color((float)(c.red()), (float)(c.green()),(float)(c.blue()), transp));
          viewer << *it;
  }
      }else{
  set3d.insert(*it);
      }
    }
  }

  if(vm.count("displaySDP")){
    if(vm.count("colorSDP")){
      std::vector<int> vcol= vm["colorSDP"].as<std::vector<int > >();
      if(vcol.size()<4){
        trace.error() << "Not enough parameter: color specification should contains four elements: red, green, blue and alpha values."  << std::endl;
        return 0;
      }
      Color c(vcol[0], vcol[1], vcol[2], vcol[3]);
      viewer << CustomColors3D(c, c);
    }

    vector<Z3i::Point> vectVoxels;
    if(vm.count("SDPindex")) {
      std::vector<unsigned int > vectIndex = vm["SDPindex"].as<std::vector<unsigned int > >();
      if(vectIndex.size()!=3){
        trace.error() << "you need to specify the three indexes of vertex." << std::endl;
        return 0;
      }
      vectVoxels = PointListReader<Z3i::Point>::getPointsFromFile(vm["displaySDP"].as<std::string>(), vectIndex);
    }else{
      vectVoxels = PointListReader<Z3i::Point>::getPointsFromFile(vm["displaySDP"].as<std::string>());
    }
    for(unsigned int i=0;i< vectVoxels.size(); i++){
      if(!vm.count("displayDigitalSurface")){
        if(vm.count("SDPball")){
          viewer.addBall (vectVoxels.at(i), ballRadius);
        }else{
          viewer << vectVoxels.at(i);
        }
      }else{
        set3d.insert(vectVoxels.at(i));
      }
    }
  }

  if(vm.count("displayMesh")){
    if(vm.count("colorMesh")){
      std::vector<int> vcol= vm["colorMesh"].as<std::vector<int > >();
      if(vcol.size()<4){
        trace.error() << "Not enough parameter: color specification should contains four elements: red, green, blue and alpha values." << std::endl;
        return 0;
      }
      Color c(vcol[0], vcol[1], vcol[2], vcol[3]);
      viewer.setFillColor(c);
    }

    DGtal::Mesh<Z3i::RealPoint> aMesh(!vm.count("colorMesh"));
    MeshReader<Z3i::RealPoint>::importOFFFile(vm["displayMesh"].as<std::string>(), aMesh);
    viewer << aMesh;
  }

  if(vm.count("displayDigitalSurface")){
    KSpace K;
    Point low = domain.lowerBound(); low[0]=low[0]-1; low[1]=low[1]-1; low[2]=low[2]-1;
    Point upp = domain.upperBound(); upp[0]=upp[0]+1; upp[1]=upp[1]+1; upp[2]=upp[2]+1;
    K.init(low, upp , true);
    SurfelAdjacency<3> SAdj( true );
    vector<vector<SCell> > vectConnectedSCell;
    trace.info() << "Extracting surface  set ... " ;
    Surfaces<KSpace>::extractAllConnectedSCell(vectConnectedSCell,K, SAdj, set3d, true);
    trace.info()<< " [done] " <<std::endl;
    GradientColorMap<long> gradient( 0, vectConnectedSCell.size());
    gradient.addColor(DGtal::Color::Red);
    gradient.addColor(DGtal::Color::Yellow);
    gradient.addColor(DGtal::Color::Green);
    gradient.addColor(DGtal::Color::Cyan);
    gradient.addColor(DGtal::Color::Blue);
    gradient.addColor(DGtal::Color::Magenta);
    gradient.addColor(DGtal::Color::Red);

    viewer << DGtal::SetMode3D(vectConnectedSCell.at(0).at(0).className(), "Basic");
    for(unsigned int i= 0; i <vectConnectedSCell.size(); i++){
      for(unsigned int j= 0; j <vectConnectedSCell.at(i).size(); j++){
  if(vm.count("colorizeCC")){
    DGtal::Color c= gradient(i);
    viewer << CustomColors3D(Color(250, 0,0, transp), Color(c.red(),
                  c.green(),
                  c.blue(), transp));
  }else  if(vm.count("colorSDP")){
    std::vector<int> vcol= vm["colorSDP"].as<std::vector<int > >();
    Color c(vcol[0], vcol[1], vcol[2], vcol[3]);
    viewer << CustomColors3D(c, c);
  }

  viewer << vectConnectedSCell.at(i).at(j);
      }
    }
  }
  
  viewer << Viewer3D<>::updateDisplay;
  return application.exec();
}