void computeEstimation ( const po::variables_map& vm, //< command-line parameters const KSpace& K, //< cellular grid space const ImplicitShape& shape, //< implicit shape "ground truth" const Surface& surface, //< digital surface approximating shape Estimator& estimator ) //< an initialized estimator { typedef typename Surface::ConstIterator ConstIterator; typedef typename Surface::Surfel Surfel; typedef typename Estimator::Quantity Quantity; typedef double Scalar; typedef DepthFirstVisitor< Surface > Visitor; typedef GraphVisitorRange< Visitor > VisitorRange; typedef typename VisitorRange::ConstIterator VisitorConstIterator; std::string fname = vm[ "output" ].as<std::string>(); string nameEstimator = vm[ "estimator" ].as<string>(); trace.beginBlock( "Computing " + nameEstimator + " estimations." ); CountedPtr<VisitorRange> range( new VisitorRange( new Visitor( surface, *(surface.begin()) )) ); std::vector<Quantity> n_estimations; estimator.eval( range->begin(), range->end(), std::back_inserter( n_estimations ) ); trace.info() << "- nb estimations = " << n_estimations.size() << std::endl; trace.endBlock(); trace.beginBlock( "Computing areas." ); range = CountedPtr<VisitorRange>( new VisitorRange( new Visitor( surface, *(surface.begin()) )) ); double area_est = 0.0; // normal integration with absolute value. unsigned int i = 0; for ( typename VisitorRange::ConstIterator it = range->begin(), itE = range->end(); it != itE; ++it, ++i ) { Surfel s = *it; Dimension k = K.sOrthDir( s ); area_est += abs( n_estimations[ i ][ k ] ); } double h = vm["gridstep"].as<double>(); trace.info() << setprecision(10) << "- Area_est " << ( area_est * h * h ) << std::endl; std::ostringstream area_sstr; area_sstr << fname << "-" << nameEstimator << "-area-" << h << ".txt"; std::ofstream area_output( area_sstr.str().c_str() ); area_output << "# Area estimation by digital surface integration." << std::endl; area_output << "# X: " << nameEstimator << std::endl; area_output << "# h Area[X] nb_surf" << std::endl; area_output << setprecision(10) << h << " " << ( area_est * h * h ) << " " << i << std::endl; area_output.close(); trace.endBlock(); }
int main( int argc, char** argv ) { //! [greedy-plane-segmentation-ex3-parseCommandLine] trace.info() << "Segments the surface at given threshold within given volume into digital planes of rational width num/den." << std::endl; // Setting default options: ---------------------------------------------- // input file used: string inputFilename = examplesPath + "samples/Al.100.vol" ; trace.info() << "input file used " << inputFilename << std::endl; // parameter threshold unsigned int threshold = 0; trace.info() << "the value that defines the isosurface in the image (an integer between 0 and 255)= " << threshold<< std::endl; // parameter widthNum unsigned int widthNum = 1; trace.info() << "the numerator of the rational width (a non-null integer) =" << widthNum<< std::endl; // parameter widthDen unsigned int widthDen = 1; trace.info() << "the denominator of the rational width (a non-null integer)= " << widthDen<< std::endl; //! [greedy-plane-segmentation-ex3-parseCommandLine] //! [greedy-plane-segmentation-ex3-loadVolume] QApplication application(argc,argv); typedef ImageSelector < Domain, int>::Type Image; Image image = VolReader<Image>::importVol(inputFilename); DigitalSet set3d (image.domain()); SetFromImage<DigitalSet>::append<Image>(set3d, image, threshold,255); //! [greedy-plane-segmentation-ex3-loadVolume] //! [greedy-plane-segmentation-ex3-makeSurface] trace.beginBlock( "Set up digital surface." ); // We initializes the cellular grid space used for defining the // digital surface. KSpace ks; bool ok = ks.init( set3d.domain().lowerBound(), set3d.domain().upperBound(), true ); if ( ! ok ) std::cerr << "[KSpace.init] Failed." << std::endl; SurfelAdjacency<KSpace::dimension> surfAdj( true ); // interior in all directions. MyDigitalSurfaceContainer* ptrSurfContainer = new MyDigitalSurfaceContainer( ks, set3d, surfAdj ); MyDigitalSurface digSurf( ptrSurfContainer ); // acquired trace.endBlock(); //! [greedy-plane-segmentation-ex3-makeSurface] //! [greedy-plane-segmentation-ex3-segment] Point p; Dimension axis; unsigned int j = 0; unsigned int nb = digSurf.size(); // First pass to find biggest planes. trace.beginBlock( "1) Segmentation first pass. Computes all planes so as to sort vertices by the plane size." ); std::map<Vertex,unsigned int> v2size; NaivePlaneComputer planeComputer; std::priority_queue<VertexSize> Q; std::vector<Point> layer; for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it ) { if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb ); Vertex v = *it; axis = ks.sOrthDir( v ); planeComputer.init( axis, 500, widthNum, widthDen ); // The visitor takes care of all the breadth-first traversal. Visitor visitor( digSurf, v ); layer.clear(); Visitor::Size currentSize = visitor.current().second; while ( ! visitor.finished() ) { Visitor::Node node = visitor.current(); v = node.first; axis = ks.sOrthDir( v ); p = ks.sCoords( ks.sDirectIncident( v, axis ) ); if ( node.second != currentSize ) { // std::cerr << "Layer " << currentSize << ", size=" << layer.size() << std::endl; bool isExtended = planeComputer.extend( layer.begin(), layer.end() ); if ( ! isExtended ) break; layer.clear(); currentSize = node.second; } layer.push_back( p ); visitor.expand(); } // std::cerr << v << " -> " << planeComputer.size() << std::endl; Q.push( VertexSize( v, planeComputer.size() ) ); } trace.endBlock(); trace.beginBlock( "2) Segmentation second pass. Visits vertices from the one with biggest plane to the one with smallest plane." ); std::set<Vertex> processedVertices; std::map<Vertex,SegmentedPlane*> v2plane; std::vector<SegmentedPlane*> segmentedPlanes; j = 0; while ( ! Q.empty() ) { if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb ); Vertex v = Q.top().v; Q.pop(); if ( processedVertices.find( v ) != processedVertices.end() ) // already in set continue; // process to next vertex SegmentedPlane* ptrSegment = new SegmentedPlane; segmentedPlanes.push_back( ptrSegment ); // to delete them afterwards. axis = ks.sOrthDir( v ); ptrSegment->plane.init( axis, 500, widthNum, widthDen ); // The visitor takes care of all the breadth-first traversal. Visitor visitor( digSurf, v ); while ( ! visitor.finished() ) { Visitor::Node node = visitor.current(); v = node.first; if ( processedVertices.find( v ) == processedVertices.end() ) { // Vertex is not in processedVertices axis = ks.sOrthDir( v ); p = ks.sCoords( ks.sDirectIncident( v, axis ) ); bool isExtended = ptrSegment->plane.extend( p ); if ( isExtended ) { // surfel is in plane. processedVertices.insert( v ); v2plane[ v ] = ptrSegment; visitor.expand(); } else // surfel is not in plane and should not be used in the visit. visitor.ignore(); } else // surfel is already in some plane. visitor.ignore(); } // Assign random color for each plane. ptrSegment->color = Color( rand() % 256, rand() % 256, rand() % 256, 255 ); } trace.endBlock(); //! [greedy-plane-segmentation-ex3-segment] //! [greedy-plane-segmentation-ex3-visualization] Viewer3D<> viewer( ks ); viewer.show(); Color col( 255, 255, 120 ); for ( std::map<Vertex,SegmentedPlane*>::const_iterator it = v2plane.begin(), itE = v2plane.end(); it != itE; ++it ) { viewer << CustomColors3D( it->second->color, it->second->color ); viewer << ks.unsigns( it->first ); } viewer << Viewer3D<>::updateDisplay; //! [greedy-plane-segmentation-ex3-visualization] //! [greedy-plane-segmentation-ex3-freeMemory] for ( std::vector<SegmentedPlane*>::iterator it = segmentedPlanes.begin(), itE = segmentedPlanes.end(); it != itE; ++it ) delete *it; segmentedPlanes.clear(); v2plane.clear(); //! [greedy-plane-segmentation-ex3-freeMemory] return application.exec(); }
int main( int argc, char** argv ) { //! [greedy-plane-segmentation-parseCommandLine] // parse command line ---------------------------------------------- po::options_description general_opt("Allowed options are: "); general_opt.add_options() ("help,h", "display this message") ("input-file,i", po::value<std::string>()->default_value( examplesPath + "samples/Al.100.vol" ), "the volume file (.vol)" ) ("threshold,t", po::value<unsigned int>()->default_value(1), "the value that defines the isosurface in the image (an integer between 0 and 255)." ) ("width-num,w", po::value<unsigned int>()->default_value(1), "the numerator of the rational width (a non-null integer)." ) ("width-den,d", po::value<unsigned int>()->default_value(1), "the denominator of the rational width (a non-null integer)." ); 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 <fileName.vol>] [-t <threshold>] [-w <num>] [-d <den>]" << std::endl << "Segments the surface at given threshold within given volume into digital planes of rational width num/den." << std::endl << general_opt << std::endl; return 0; } string inputFilename = vm["input-file"].as<std::string>(); unsigned int threshold = vm["threshold"].as<unsigned int>(); unsigned int widthNum = vm["width-num"].as<unsigned int>(); unsigned int widthDen = vm["width-den"].as<unsigned int>(); //! [greedy-plane-segmentation-parseCommandLine] //! [greedy-plane-segmentation-loadVolume] QApplication application(argc,argv); typedef ImageSelector < Domain, int>::Type Image; Image image = VolReader<Image>::importVol(inputFilename); DigitalSet set3d (image.domain()); SetFromImage<DigitalSet>::append<Image>(set3d, image, threshold,255); //! [greedy-plane-segmentation-loadVolume] //! [greedy-plane-segmentation-makeSurface] trace.beginBlock( "Set up digital surface." ); // We initializes the cellular grid space used for defining the // digital surface. KSpace ks; bool ok = ks.init( set3d.domain().lowerBound(), set3d.domain().upperBound(), true ); if ( ! ok ) std::cerr << "[KSpace.init] Failed." << std::endl; SurfelAdjacency<KSpace::dimension> surfAdj( true ); // interior in all directions. MyDigitalSurfaceContainer* ptrSurfContainer = new MyDigitalSurfaceContainer( ks, set3d, surfAdj ); MyDigitalSurface digSurf( ptrSurfContainer ); // acquired trace.endBlock(); //! [greedy-plane-segmentation-makeSurface] //! [greedy-plane-segmentation-segment] trace.beginBlock( "Segment into planes." ); std::set<Vertex> processedVertices; std::vector<SegmentedPlane*> segmentedPlanes; std::map<Vertex,SegmentedPlane*> v2plane; Point p; Dimension axis; unsigned int j = 0; unsigned int nb = digSurf.size(); for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it ) { if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb ); Vertex v = *it; if ( processedVertices.find( v ) != processedVertices.end() ) // already in set continue; // process to next vertex SegmentedPlane* ptrSegment = new SegmentedPlane; segmentedPlanes.push_back( ptrSegment ); // to delete them afterwards. axis = ks.sOrthDir( v ); ptrSegment->plane.init( axis, 500, widthNum, widthDen ); // The visitor takes care of all the breadth-first traversal. Visitor visitor( digSurf, v ); while ( ! visitor.finished() ) { Visitor::Node node = visitor.current(); v = node.first; if ( processedVertices.find( v ) == processedVertices.end() ) { // Vertex is not in processedVertices axis = ks.sOrthDir( v ); p = ks.sCoords( ks.sDirectIncident( v, axis ) ); bool isExtended = ptrSegment->plane.extend( p ); if ( isExtended ) { // surfel is in plane. processedVertices.insert( v ); v2plane[ v ] = ptrSegment; visitor.expand(); } else // surfel is not in plane and should not be used in the visit. visitor.ignore(); } else // surfel is already in some plane. visitor.ignore(); } // Assign random color for each plane. ptrSegment->color = Color( random() % 256, random() % 256, random() % 256, 255 ); } trace.endBlock(); //! [greedy-plane-segmentation-segment] //! [greedy-plane-segmentation-visualization] Viewer3D viewer; viewer.show(); for ( std::map<Vertex,SegmentedPlane*>::const_iterator it = v2plane.begin(), itE = v2plane.end(); it != itE; ++it ) { viewer << CustomColors3D( it->second->color, it->second->color ); viewer << ks.unsigns( it->first ); } viewer << Display3D::updateDisplay; //! [greedy-plane-segmentation-visualization] //! [greedy-plane-segmentation-freeMemory] for ( std::vector<SegmentedPlane*>::iterator it = segmentedPlanes.begin(), itE = segmentedPlanes.end(); it != itE; ++it ) delete *it; segmentedPlanes.clear(); v2plane.clear(); //! [greedy-plane-segmentation-freeMemory] return application.exec(); }
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; }
bool testSurfelAdjacency() { typedef typename KSpace::Integer Integer; typedef typename KSpace::Cell Cell; typedef typename KSpace::SCell SCell; typedef typename KSpace::Point Point; typedef typename KSpace::DirIterator DirIterator; typedef typename KSpace::Cells Cells; typedef typename KSpace::SCells SCells; unsigned int nbok = 0; unsigned int nb = 0; trace.beginBlock ( "Testing block KSpace instantiation and scan ..." ); KSpace K; int xlow[ 4 ] = { -3, -3, -3, -3 }; int xhigh[ 4 ] = { 5, 3, 3, 3 }; Point low( xlow ); Point high( xhigh ); bool space_ok = K.init( low, high, true ); nbok += space_ok ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << "K.init( low, high )" << std::endl; trace.info() << "K.dim()=" << K.dimension << endl; trace.endBlock(); trace.beginBlock ( "Testing surfel adjacency ..." ); SurfelAdjacency<KSpace::dimension> SAdj( true ); for ( Dimension i = 0; i < K.dimension; ++i ) for ( Dimension j = 0; j < K.dimension; ++j ) if ( i != j ) trace.info() << "(" << i << "," << j << ")=" << ( SAdj.getAdjacency( i, j ) ? "i2e" : "e2i" ); trace.info() << endl; trace.endBlock(); int spel[ 4 ] = { 1, 1, 1, 1 }; // pixel Point kp( spel ); SCell sspel = K.sCell( kp, K.POS ); trace.beginBlock ( "Testing surfel directness ..." ); for ( Dimension k = 0; k < K.dimension; ++k ) { SCell surfel = K.sIncident( sspel, k, true ); SCell innerspel = K.sDirectIncident( surfel, K.sOrthDir( surfel ) ); trace.info() << "spel=" << sspel << " surfel=" << surfel << " innerspel=" << innerspel << endl; nbok += sspel == innerspel ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << "spel == innerspel" << std::endl; surfel = K.sIncident( sspel, k, false ); innerspel = K.sDirectIncident( surfel, K.sOrthDir( surfel ) ); trace.info() << "spel=" << sspel << " surfel=" << surfel << " innerspel=" << innerspel << endl; nbok += sspel == innerspel ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << "spel == innerspel" << std::endl; } trace.endBlock(); SurfelNeighborhood<KSpace> SN; trace.beginBlock ( "Testing surfel neighborhood ..." ); SCell surfel = K.sIncident( sspel, 0, false ); SN.init( &K, &SAdj, surfel ); trace.info() << "surfel =" << surfel << endl; trace.info() << "follower1(+)=" << SN.follower1( 1, true ) << endl; trace.info() << "follower2(+)=" << SN.follower2( 1, true ) << endl; trace.info() << "follower3(+)=" << SN.follower3( 1, true ) << endl; trace.info() << "follower1(-)=" << SN.follower1( 1, false ) << endl; trace.info() << "follower2(-)=" << SN.follower2( 1, false ) << endl; trace.info() << "follower3(-)=" << SN.follower3( 1, false ) << endl; trace.endBlock(); trace.beginBlock ( "Testing surface tracking ..." ); typedef SpaceND< KSpace::dimension, Integer > Space; typedef HyperRectDomain<Space> Domain; typedef typename DigitalSetSelector< Domain, BIG_DS+HIGH_BEL_DS >::Type DigitalSet; Domain domain( low, high ); DigitalSet shape_set( domain ); SetPredicate<DigitalSet> shape_set_predicate( shape_set ); int center[ 4 ] = { 1, 0, 0, 0 }; // pixel Point pcenter( center ); Shapes<Domain>::addNorm1Ball( shape_set, pcenter, 1 ); trace.info() << "surfel = " << surfel << endl; SCell other1, other2; SN.getAdjacentOnDigitalSet( other1, shape_set, 1, K.sDirect( surfel, 1 ) ); SN.getAdjacentOnDigitalSet( other2, shape_set, 1, !K.sDirect( surfel, 1 ) ); trace.info() << "directNext = " << other1 << endl; trace.info() << "indirectNext= " << other2 << endl; std::set<SCell> bdry; // surfel = Surfaces<KSpace>::findABel( K, shape_set ); Surfaces<KSpace>::trackBoundary( bdry, K, SAdj, shape_set_predicate, surfel ); trace.info() << "tracking finished, size=" << bdry.size() << ", should be " << 2*K.dimension*(2*K.dimension-1) << endl; nbok += bdry.size() == ( 2*K.dimension*(2*K.dimension-1) ) ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << "bdry.size() == ( 2*K.dimension*(2*K.dimension-1) )" << std::endl; std::set<SCell> bdry_direct; Surfaces<KSpace>::trackClosedBoundary( bdry_direct, K, SAdj, shape_set_predicate, surfel ); trace.info() << "fast direct tracking finished, size=" << bdry_direct.size() << ", should be " << 2*K.dimension*(2*K.dimension-1) << endl; nbok += bdry_direct.size() == ( 2*K.dimension*(2*K.dimension-1) ) ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << "bdry_direct.size() == ( 2*K.dimension*(2*K.dimension-1) )" << std::endl; trace.endBlock(); if ( K.dimension == 2 ) { Board2D board; board.setUnit( LibBoard::Board::UCentimeter ); board << SetMode( domain.className(), "Paving" ) << domain; for ( typename std::set<SCell>::const_iterator it = bdry_direct.begin(), it_end = bdry_direct.end(); it != it_end; ++it ) board << *it; board.saveEPS( "cells-2.eps" ); board.saveSVG( "cells-2.svg" ); } return nbok == nb; }
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; }
int main( int argc, char** argv ) { QApplication application(argc,argv); string inputFilename = argc > 1 ? argv[ 1 ] : examplesPath+"/samples/Al.100.vol"; int threshold = argc > 2 ? atoi( argv[ 2 ] ) : 0; int widthNum = argc > 3 ? atoi( argv[ 3 ] ) : 2; int widthDen = argc > 4 ? atoi( argv[ 4 ] ) : 1; //! [polyhedralizer-readVol] trace.beginBlock( "Reading vol file into an image." ); typedef ImageContainerBySTLVector< Domain, int> Image; Image image = VolReader<Image>::importVol(inputFilename); typedef functors::SimpleThresholdForegroundPredicate<Image> DigitalObject; DigitalObject digitalObject( image, threshold ); trace.endBlock(); //! [polyhedralizer-readVol] //! [polyhedralizer-KSpace] trace.beginBlock( "Construct the Khalimsky space from the image domain." ); KSpace ks; bool space_ok = ks.init( image.domain().lowerBound(), image.domain().upperBound(), true ); if (!space_ok) { trace.error() << "Error in the Khamisky space construction."<<endl; return 2; } trace.endBlock(); //! [polyhedralizer-KSpace] //! [polyhedralizer-SurfelAdjacency] typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency; MySurfelAdjacency surfAdj( false ); // exterior in all directions. //! [polyhedralizer-SurfelAdjacency] //! [polyhedralizer-ExtractingSurface] trace.beginBlock( "Extracting boundary by tracking the surface. " ); typedef KSpace::Surfel Surfel; Surfel start_surfel = Surfaces<KSpace>::findABel( ks, digitalObject, 100000 ); typedef ImplicitDigitalSurface< KSpace, DigitalObject > MyContainer; typedef DigitalSurface< MyContainer > MyDigitalSurface; typedef MyDigitalSurface::ConstIterator ConstIterator; MyContainer container( ks, digitalObject, surfAdj, start_surfel ); MyDigitalSurface digSurf( container ); trace.info() << "Digital surface has " << digSurf.size() << " surfels." << endl; trace.endBlock(); //! [polyhedralizer-ExtractingSurface] //! [polyhedralizer-ComputingPlaneSize] // First pass to find biggest planes. trace.beginBlock( "Decomposition first pass. Computes all planes so as to sort vertices by the plane size." ); typedef BreadthFirstVisitor<MyDigitalSurface> Visitor; typedef ChordGenericNaivePlaneComputer<Z3,Z3::Point, DGtal::int64_t> NaivePlaneComputer; map<Surfel,unsigned int> v2size; for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it ) v2size[ *it ] = 0; int j = 0; int nb = digSurf.size(); NaivePlaneComputer planeComputer; vector<Point> layer; vector<Surfel> layer_surfel; for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it ) { if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb ); Surfel v = *it; planeComputer.init( widthNum, widthDen ); // The visitor takes care of all the breadth-first traversal. Visitor visitor( digSurf, v ); layer.clear(); layer_surfel.clear(); Visitor::Size currentSize = visitor.current().second; while ( ! visitor.finished() ) { Visitor::Node node = visitor.current(); v = node.first; int axis = ks.sOrthDir( v ); Point p = ks.sCoords( ks.sDirectIncident( v, axis ) ); if ( node.second != currentSize ) { bool isExtended = planeComputer.extend( layer.begin(), layer.end() ); if ( isExtended ) { for ( vector<Surfel>::const_iterator it_layer = layer_surfel.begin(), it_layer_end = layer_surfel.end(); it_layer != it_layer_end; ++it_layer ) { ++v2size[ *it_layer ]; } layer_surfel.clear(); layer.clear(); currentSize = node.second; } else break; } layer_surfel.push_back( v ); layer.push_back( p ); visitor.expand(); } } // Prepare queue typedef PairSorted2nd<Surfel,int> SurfelWeight; priority_queue<SurfelWeight> Q; for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it ) Q.push( SurfelWeight( *it, v2size[ *it ] ) ); trace.endBlock(); //! [polyhedralizer-ComputingPlaneSize] //! [polyhedralizer-segment] // Segmentation into planes trace.beginBlock( "Decomposition second pass. Visits vertices from the one with biggest plane to the one with smallest plane." ); typedef Triple<NaivePlaneComputer, Color, pair<RealVector,double> > RoundPlane; set<Surfel> processedVertices; vector<RoundPlane*> roundPlanes; map<Surfel,RoundPlane*> v2plane; j = 0; while ( ! Q.empty() ) { if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb ); Surfel v = Q.top().first; Q.pop(); if ( processedVertices.find( v ) != processedVertices.end() ) // already in set continue; // process to next vertex RoundPlane* ptrRoundPlane = new RoundPlane; roundPlanes.push_back( ptrRoundPlane ); // to delete them afterwards. v2plane[ v ] = ptrRoundPlane; ptrRoundPlane->first.init( widthNum, widthDen ); ptrRoundPlane->third = make_pair( RealVector::zero, 0.0 ); // The visitor takes care of all the breadth-first traversal. Visitor visitor( digSurf, v ); layer.clear(); layer_surfel.clear(); Visitor::Size currentSize = visitor.current().second; while ( ! visitor.finished() ) { Visitor::Node node = visitor.current(); v = node.first; Dimension axis = ks.sOrthDir( v ); Point p = ks.sCoords( ks.sDirectIncident( v, axis ) ); if ( node.second != currentSize ) { bool isExtended = ptrRoundPlane->first.extend( layer.begin(), layer.end() ); if ( isExtended ) { for ( vector<Surfel>::const_iterator it_layer = layer_surfel.begin(), it_layer_end = layer_surfel.end(); it_layer != it_layer_end; ++it_layer ) { Surfel s = *it_layer; processedVertices.insert( s ); if ( v2plane.find( s ) == v2plane.end() ) v2plane[ s ] = ptrRoundPlane; } layer.clear(); layer_surfel.clear(); currentSize = node.second; } else break; } layer_surfel.push_back( v ); layer.push_back( p ); if ( processedVertices.find( v ) != processedVertices.end() ) // surfel is already in some plane. visitor.ignore(); else visitor.expand(); } if ( visitor.finished() ) { for ( vector<Surfel>::const_iterator it_layer = layer_surfel.begin(), it_layer_end = layer_surfel.end(); it_layer != it_layer_end; ++it_layer ) { Surfel s = *it_layer; processedVertices.insert( s ); if ( v2plane.find( s ) == v2plane.end() ) v2plane[ s ] = ptrRoundPlane; } } // Assign random color for each plane. ptrRoundPlane->second = Color( rand() % 192 + 64, rand() % 192 + 64, rand() % 192 + 64, 255 ); } trace.endBlock(); //! [polyhedralizer-segment] //! [polyhedralizer-lsf] for ( vector<RoundPlane*>::iterator it = roundPlanes.begin(), itE = roundPlanes.end(); it != itE; ++it ) { NaivePlaneComputer& computer = (*it)->first; RealVector normal; double mu = LSF( normal, computer.begin(), computer.end() ); (*it)->third = make_pair( normal, mu ); } //! [polyhedralizer-lsf] //! [polyhedralizer-projection] map<Surfel, RealPoint> coordinates; for ( map<Surfel,RoundPlane*>::const_iterator it = v2plane.begin(), itE = v2plane.end(); it != itE; ++it ) { Surfel v = it->first; RoundPlane* rplane = it->second; Point p = ks.sKCoords( v ); RealPoint rp( (double)p[ 0 ]/2.0, (double)p[ 1 ]/2.0, (double)p[ 2 ]/2.0 ); double mu = rplane->third.second; RealVector normal = rplane->third.first; double lambda = mu - rp.dot( normal ); coordinates[ v ] = rp + lambda*normal; } typedef vector<Surfel> SurfelRange; map<Surfel, RealPoint> new_coordinates; for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it ) { Surfel s = *it; SurfelRange neighbors; back_insert_iterator<SurfelRange> writeIt = back_inserter( neighbors ); digSurf.writeNeighbors( writeIt, *it ); RealPoint x = RealPoint::zero; for ( SurfelRange::const_iterator its = neighbors.begin(), itsE = neighbors.end(); its != itsE; ++its ) x += coordinates[ *its ]; new_coordinates[ s ] = x / neighbors.size(); } //! [polyhedralizer-projection] //! [polyhedralizer-MakeMesh] typedef unsigned int Number; typedef Mesh<RealPoint> MyMesh; typedef MyMesh::MeshFace MeshFace; typedef MyDigitalSurface::FaceSet FaceSet; typedef MyDigitalSurface::VertexRange VertexRange; map<Surfel, Number> index; // Numbers all vertices. Number nbv = 0; MyMesh polyhedron( true ); // Insert all projected surfels as vertices of the polyhedral surface. for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it ) { polyhedron.addVertex( new_coordinates[ *it ] ); index[ *it ] = nbv++; } // Define faces of the mesh. Outputs closed faces. FaceSet faces = digSurf.allClosedFaces(); for ( typename FaceSet::const_iterator itf = faces.begin(), itf_end = faces.end(); itf != itf_end; ++itf ) { MeshFace mface( itf->nbVertices ); VertexRange vtcs = digSurf.verticesAroundFace( *itf ); int i = 0; for ( typename VertexRange::const_iterator itv = vtcs.begin(), itv_end = vtcs.end(); itv != itv_end; ++itv ) { mface[ i++ ] = index[ *itv ]; } polyhedron.addFace( mface, Color( 255, 243, 150, 255 ) ); } //! [polyhedralizer-MakeMesh] //! [polyhedralizer-visualization] typedef Viewer3D<Space,KSpace> MyViewer3D; MyViewer3D viewer( ks ); viewer.show(); bool isOK = polyhedron >> "test.off"; bool isOK2 = polyhedron >> "test.obj"; viewer << polyhedron; viewer << MyViewer3D::updateDisplay; application.exec(); //! [polyhedralizer-visualization] //! [polyhedralizer-freeMemory] for ( vector<RoundPlane*>::iterator it = roundPlanes.begin(), itE = roundPlanes.end(); it != itE; ++it ) delete *it; //! [polyhedralizer-freeMemory] if (isOK && isOK2) return 0; else return 1; }