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 DGtalTools project. 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 of DGtalTools:

./visualisation/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