void fillImage3D( Image3D & img,
typename Image3D::Point low,
typename Image3D::Point up,
typename Image3D::Value value )
{
typedef typename Image3D::Point Point;
typedef typename Image3D::Integer Integer;
for ( Integer z = low[ 2 ]; z <= up[ 2 ]; ++z )
for ( Integer y = low[ 1 ]; y <= up[ 1 ]; ++y )
for ( Integer x = low[ 0 ]; x <= up[ 0 ]; ++x )
img.setValue( Point( x, y, z ), value );
}
int main( int argc, char** argv )
{
typedef ImageContainerBySTLVector < Z3i::Domain, unsigned char > Image3D;
typedef ImageContainerBySTLVector < 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")
("sliceOrientation,s", po::value<unsigned int>()->default_value(2), "specify the slice orientation for which the slice are considered (by default =2 (Z direction))" )
("input,i", po::value<std::vector <std::string> >()->multitoken(), "input 2D files (.pgm) " )
("output,o", po::value<std::string>(), "volumetric file (.vol, .longvol .pgm3d) " );
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"))
{
std::cout << "Usage: " << argv[0] << " [input-files] [output]\n"
<< "Convert set of 2D images into volumetric file (pgm3d, vol, longvol) "
<< general_opt << "\n";
std::cout << "Example:\n"
<< "slice2vol -i slice1.pgm slice2.pgm slice3.pgm -o vol.p3d \n"
<< "see vol2slice"<<endl;
return 0;
}
if(! vm.count("input-files")||! vm.count("output"))
{
trace.error() << " Input and output filename are needed to be defined" << endl;
return 0;
}
std::string outputFileName = vm["output"].as<std::string>();
std::vector<string> vectImage2DNames = vm["input"].as<std::vector<std::string> >();
unsigned int sliceOrientation = vm["sliceOrientation"].as<unsigned int>();
std::vector<Image2D> vectImages2D;
// Reading all images
for(unsigned int i=0; i< vectImage2DNames.size(); i++){
trace.info() << "Reading image " << i ;
Image2D image = GenericReader<Image2D>::import(vectImage2DNames.at(i));
vectImages2D.push_back(image);
trace.info() << " [done]" << std::endl;
}
Image2D::Domain domImage2D = vectImages2D.at(0).domain();
DGtal::functors::Projector<DGtal::Z3i::Space> projIn3Dlower(0);
DGtal::functors::Projector<DGtal::Z3i::Space> projIn3Dupper(vectImages2D.size()-1);
projIn3Dlower.initAddOneDim(sliceOrientation);
projIn3Dupper.initAddOneDim(sliceOrientation);
Image3D::Domain domImage3D (projIn3Dlower(vectImages2D.at(0).domain().lowerBound()),
projIn3Dupper(vectImages2D.at(0).domain().upperBound()));
Image3D imageResult (domImage3D);
for( unsigned int i=0; i<vectImages2D.size(); i++){
Image2D sliceImage = vectImages2D.at(i);
DGtal::functors::Projector<DGtal::Z3i::Space> projIn3D(i);
projIn3D.initAddOneDim(sliceOrientation);
for(Image2D::Domain::ConstIterator it = sliceImage.domain().begin();
it!= sliceImage.domain().end(); it++){
Z3i::Point pt =projIn3D(*it);
imageResult.setValue(pt, sliceImage(*it));
}
}
trace.info() << "Exporting 3d image ... " << std::endl ;
GenericWriter<Image3D>::exportFile(outputFileName, imageResult);
trace.info() << "[done]";
return 0;
}
