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;
}
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 DigitalSetSelector< Domain, BIG_DS+HIGH_BEL_DS >::Type DigitalSet;
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)" )
("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("INNER"), "set mode for display: INNER: inner voxels, OUTER: outer voxels, BDRY: surfels") ;
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]\n"
<< "Display the boundary of a volume file by using QGLviewer. 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;
}
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>();
QApplication application(argc,argv);
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();
//! [3dVolBoundaryViewer-KSpace]
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();
//! [3dVolBoundaryViewer-KSpace]
//! [3dVolBoundaryViewer-Set3D]
trace.beginBlock( "Wrapping a digital set around image. " );
typedef functors::IntervalForegroundPredicate<Image> ThresholdedImage;
ThresholdedImage thresholdedImage( image, thresholdMin, thresholdMax );
trace.endBlock();
//! [3dVolBoundaryViewer-Set3D]
//! [3dVolBoundaryViewer-ExtractingSurface]
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();
//! [3dVolBoundaryViewer-ExtractingSurface]
//! [3dVolBoundaryViewer-ViewingSurface]
trace.beginBlock( "Displaying everything. " );
Viewer3D<Space,KSpace> viewer(ks);
viewer.setWindowTitle("Simple boundary of volume Viewer");
viewer.show();
typedef MyDigitalSurface::ConstIterator ConstIterator;
if ( mode == "BDRY" ){
viewer << SetMode3D(ks.unsigns( *(digSurf.begin()) ).className(), "Basic");
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
viewer << ks.unsigns( *it );
}else if ( mode == "INNER" )
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
viewer << ks.sCoords( ks.sDirectIncident( *it, ks.sOrthDir( *it ) ) );
else if ( mode == "OUTER" )
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
viewer << ks.sCoords( ks.sIndirectIncident( *it, ks.sOrthDir( *it ) ) );
else{
trace.error() << "Warning display mode (" << mode << ") not implemented." << std::endl;
trace.error() << "The display will be empty." << std::endl;
}
viewer << Viewer3D<>::updateDisplay;
trace.endBlock();
return application.exec();
}
return 0;
}
