Tutorial "Image -> Region -> Volume -> 3dVolViewer : a simple 3D volume viewer in less than 50 lines"

Author:

Bertrand Kerautret

 This part of the manual describes a simple tool written in less 
 than 50 lines which allows to perform a simple 3D volume
 viewer.

 The viewer is based on Viewer3D and the input file is simply a ".vol" and all voxels contained
 in an interval can be displayed in 3D. The source program 3dVolViewer.cpp can be found in the directory  
 \c tools/volumetric . We give here a rapid description of the main parts of the simple viewer.

 First we set the program option using boost 

   namespace po = boost::program_options;   
    general_opt.add_options()
    ("help,h", "display this message")
    ("input-file,i", po::value<std::string>(), "volume file" " (default: standard input)")
    ("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" )
    ("transparency,t",  po::value<uint>()->default_value(255), "transparency") ; 

Then argument are parsed and stored:

   po::variables_map vm;
   po::store(po::parse_command_line(argc, argv, general_opt), vm);  
   po::notify(vm);     
   
   string inputFilename = vm["input-file"].as<std::string>();
   int thresholdMin = vm["thresholdMin"].as<int>();
   int thresholdMax = vm["thresholdMax"].as<int>();
   unsigned char transp = vm["transparency"].as<uint>();

The image can be loaded simply as follows:

    typedef ImageSelector<Domain, unsigned char>::Type Image;
    Image image = VolReader<Image>::importVol( inputFilename );

and its associated domain is obtain with:

   Domain domain(image.lowerBound(), image.upperBound());

We use the GradientColorMap to obtain a pretty rendering a grey level volume information.

   GradientColorMap<long> gradient( thresholdMin, thresholdMax);
   gradient.addColor(LibBoard::Color::Blue);
   gradient.addColor(LibBoard::Color::Green);
   gradient.addColor(LibBoard::Color::Yellow);
   gradient.addColor(LibBoard::Color::Red);

Finally we only have to display the voxels with Viewer3D:

   for(Domain::ConstIterator it = domain.begin(), itend=domain.end(); it!=itend; ++it){
      unsigned char  val= image( (*it) );     
      LibBoard::Color c= gradient(val);
      if(val<=thresholdMax && val >=thresholdMin){
          viewer <<  CustomColors3D(QColor((float)(c.red()), (float)(c.green()),(float)(c.blue()), transp),
                                    QColor((float)(c.red()), (float)(c.green()),(float)(c.blue()), transp));     
          viewer << *it;     
     }     
   }
   viewer << Viewer3D::updateDisplay;

By executing the following command line from the build directory:

   /tools/volumetric/3dVolViewer -i ../examples/samples/lobster.vol  -m 30 -M 255 -t 10

You will get the following visualisation:

Example of visualisation obtained with 3dVolViewer

You can also add a clipping plane:

   viewer << ClippingPlane(0,0,-1, 20);

You will get the following visualisation:

Example of visualisation obtained with 3dVolViewer