//----------------------------------------------------------------------------- // Testing LightImplicitDigitalSurface //----------------------------------------------------------------------------- bool testLightImplicitDigitalSurface() { using namespace Z3i; typedef ImplicitDigitalEllipse3<Point> ImplicitDigitalEllipse; typedef LightImplicitDigitalSurface<KSpace,ImplicitDigitalEllipse> Boundary; typedef Boundary::SurfelConstIterator ConstIterator; typedef Boundary::Tracker Tracker; typedef Boundary::Surfel Surfel; unsigned int nbok = 0; unsigned int nb = 0; trace.beginBlock ( "Testing block ... LightImplicitDigitalSurface" ); Point p1( -10, -10, -10 ); Point p2( 10, 10, 10 ); KSpace K; nbok += K.init( p1, p2, true ) ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << "K.init() is ok" << std::endl; ImplicitDigitalEllipse ellipse( 6.0, 4.5, 3.4 ); Surfel bel = Surfaces<KSpace>::findABel( K, ellipse, 10000 ); Boundary boundary( K, ellipse, SurfelAdjacency<KSpace::dimension>( true ), bel ); unsigned int nbsurfels = 0; for ( ConstIterator it = boundary.begin(), it_end = boundary.end(); it != it_end; ++it ) { ++nbsurfels; } trace.info() << nbsurfels << " surfels found." << std::endl; trace.beginBlock ( "Checks if adjacent surfels are part of the surface." ); for ( ConstIterator it = boundary.begin(), it_end = boundary.end(); it != it_end; ++it ) { Tracker* ptrTracker = boundary.newTracker( *it ); Surfel s = ptrTracker->current(); Dimension trackDir = * K.sDirs( s ); Surfel s1, s2; // unsigned int m1 = ptrTracker->adjacent( s1, trackDir, true ); // unsigned int m2 = ptrTracker->adjacent( s2, trackDir, false ); // trace.info() << "s = " << s << std::endl; // trace.info() << "s1 = " << s1 << " m1 = " << m1 << std::endl; // trace.info() << "s2 = " << s2 << " m2 = " << m2 << std::endl; nb++, nbok += boundary.isInside( s1 ) ? 1 : 0; // trace.info() << "(" << nbok << "/" << nb << ") " // << "boundary.isInside( s1 )" << std::endl; nb++, nbok += boundary.isInside( s2 ) ? 1 : 0; // trace.info() << "(" << nbok << "/" << nb << ") " // << "boundary.isInside( s2 )" << std::endl; delete ptrTracker; } trace.info() << "(" << nbok << "/" << nb << ") isInside tests." << std::endl; trace.endBlock(); trace.endBlock(); return nbok == nb; }
/** * Example of a test. To be completed. * */ bool testDigitalSetBoundary() { unsigned int nbok = 0; unsigned int nb = 0; trace.beginBlock ( "Testing block ... DigitalSetBoundary" ); using namespace Z2i; typedef DigitalSetBoundary<KSpace,DigitalSet> Boundary; typedef Boundary::SurfelConstIterator ConstIterator; typedef Boundary::Tracker Tracker; typedef Boundary::Surfel Surfel; Point p1( -10, -10 ); Point p2( 10, 10 ); Domain domain( p1, p2 ); DigitalSet dig_set( domain ); Shapes<Domain>::addNorm2Ball( dig_set, Point( 0, 0 ), 5 ); Shapes<Domain>::removeNorm2Ball( dig_set, Point( 0, 0 ), 1 ); KSpace K; nbok += K.init( domain.lowerBound(), domain.upperBound(), true ) ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << "K.init() is ok" << std::endl; Boundary boundary( K, dig_set ); unsigned int nbsurfels = 0; for ( ConstIterator it = boundary.begin(), it_end = boundary.end(); it != it_end; ++it ) { ++nbsurfels; } trace.info() << nbsurfels << " surfels found." << std::endl; nb++, nbok += nbsurfels == ( 12 + 44 ) ? 1 : 0; trace.info() << "(" << nbok << "/" << nb << ") " << "nbsurfels == (12 + 44 )" << std::endl; for ( ConstIterator it = boundary.begin(), it_end = boundary.end(); it != it_end; ++it ) { Tracker* ptrTracker = boundary.newTracker( *it ); Surfel s = ptrTracker->current(); Dimension trackDir = * K.sDirs( s ); Surfel s1, s2; unsigned int m1 = ptrTracker->adjacent( s1, trackDir, true ); unsigned int m2 = ptrTracker->adjacent( s2, trackDir, false ); trace.info() << "s = " << s << std::endl; trace.info() << "s1 = " << s1 << " m1 = " << m1 << std::endl; trace.info() << "s2 = " << s2 << " m2 = " << m2 << std::endl; nb++, nbok += boundary.isInside( s1 ) ? 1 : 0; trace.info() << "(" << nbok << "/" << nb << ") " << "boundary.isInside( s1 )" << std::endl; nb++, nbok += boundary.isInside( s2 ) ? 1 : 0; trace.info() << "(" << nbok << "/" << nb << ") " << "boundary.isInside( s2 )" << std::endl; delete ptrTracker; } trace.endBlock(); return nbok == nb; }
bool testCellularGridSpaceND() { 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, -2, -2, -1 }; int xhigh[ 4 ] = { 5, 3, 2, 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; int spel[ 4 ] = { 1, 1, 1, 1 }; // pixel Point kp( spel ); Cell center = K.uCell( kp ); Cell c1 = K.uCell( kp ); Cell clow = K.uCell( low, kp ); Cell chigh = K.uCell( high, kp ); trace.info() << c1 << clow << chigh << " topo(c1)=" << K.uTopology( c1 ) << " dirs="; for ( DirIterator q = K.uDirs( clow ); q != 0; ++q ) trace.info() << " " << *q; trace.info() << endl; Cell f = K.uFirst( c1 ); Cell l = K.uLast( c1 ); trace.info() << "Loop in " << clow << chigh << endl; c1 = f; unsigned int nbelems = 0; do { ++nbelems; // trace.info() << c1; } while ( K.uNext( c1, f, l ) ); trace.info() << " -> " << nbelems << " elements." << endl; unsigned int exp_nbelems = 1; for ( Dimension i = 0; i < K.dimension; ++i ) exp_nbelems *= K.size( i ); nbok += nbelems == exp_nbelems ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << nbelems << " scanned elements == " << exp_nbelems << " space size." << std::endl; trace.endBlock(); trace.beginBlock ( "Testing neighborhoods in KSpace..." ); Cells N = K.uNeighborhood( center ); nbok += N.size() == ( K.dimension*2 + 1 ) ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << N.size() << "(neighborhood size) == " << ( K.dimension*2 + 1 ) << "(2*dim()+1)" << endl; Cells Np = K.uProperNeighborhood( center ); nbok += Np.size() == ( K.dimension*2 ) ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << Np.size() << "(proper neighborhood size) == " << ( K.dimension*2 ) << "(2*dim())" << endl; trace.endBlock(); trace.beginBlock ( "Testing faces in KSpace..." ); Cells Nf = K.uFaces( center ); nbok += Nf.size() == ceil( std::pow( 3.0 ,(int) K.dimension ) - 1 ) ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << Nf.size() << "(faces size) == " << floor( std::pow( 3.0, (int)K.dimension ) - 1 ) << "(3^dim()-1)" << endl; trace.endBlock(); trace.beginBlock ( "Testing block Incidence in KSpace..." ); SCell sspel = K.sCell( kp, K.POS ); for ( DirIterator q1 = K.sDirs( sspel ); q1 != 0; ++q1 ) for ( DirIterator q2 = K.sDirs( sspel ); q2 != 0; ++q2 ) { if ( *q1 != *q2 ) { SCell s0 = K.sIncident( sspel, *q1, true ); SCell s1 = K.sIncident( sspel, *q2, true ); SCell l10 = K.sIncident( s0, *q2, true ); SCell l01 = K.sIncident( s1, *q1, true ); trace.info() << "D+_" << *q2 << "(D+_" << *q1 << "(V))=" << l10 << " D+_" << *q1 << "(D+_" << *q2 << "(V))=" << l01 << endl; nbok += l10 == K.sOpp( l01 ) ? 1 : 0; nb++; } } trace.info() << "(" << nbok << "/" << nb << ") " << "anti-commutativity of incidence operators." << std::endl; trace.endBlock(); trace.beginBlock ( "Testing direct Incidence in KSpace..." ); for ( DirIterator q1 = K.sDirs( sspel ); q1 != 0; ++q1 ) for ( DirIterator q2 = K.sDirs( sspel ); q2 != 0; ++q2 ) { if ( *q1 != *q2 ) { SCell s0 = K.sDirectIncident( sspel, *q1 ); SCell l10 = K.sDirectIncident( s0, *q2 ); SCell s1 = K.sDirectIncident( sspel, *q2 ); SCell l01 = K.sDirectIncident( s1, *q1 ); trace.info() << "Dd_" << *q2 << "(Dd_" << *q1 << "(V))=" << l10 << " Dd_" << *q1 << "(Dd_" << *q2 << "(V))=" << l01 << endl; nbok += l10 != l01 ? 1 : 0; nbok += K.sSign( s0 ) == K.POS ? 1 : 0; nbok += K.sSign( s1 ) == K.POS ? 1 : 0; nbok += K.sSign( l10 ) == K.POS ? 1 : 0; nbok += K.sSign( l01 ) == K.POS ? 1 : 0; nbok += s0 == K.sIncident( sspel, *q1, K.sDirect( sspel, *q1 ) ) ? 1 : 0; nbok += s1 == K.sIncident( sspel, *q2, K.sDirect( sspel, *q2 ) ) ? 1 : 0; nbok += l10 == K.sIncident( s0, *q2, K.sDirect( s0, *q2 ) ) ? 1 : 0; nbok += l01 == K.sIncident( s1, *q1, K.sDirect( s1, *q1 ) ) ? 1 : 0; nb += 9; } } trace.info() << "(" << nbok << "/" << nb << ") " << "correctness of direct and indirect orientations." << std::endl; trace.endBlock(); return nbok == nb; }
int main( int argc, char** argv ) { // for 3D display with Viewer3D QApplication application(argc,argv); //! [digitalSurfaceSlice-readVol] trace.beginBlock( "Reading vol file into an image." ); typedef ImageSelector < Domain, int>::Type Image; std::string inputFilename = examplesPath + "samples/Al.100.vol"; Image image = VolReader<Image>::importVol(inputFilename); DigitalSet set3d (image.domain()); SetPredicate<DigitalSet> set3dPredicate( set3d ); SetFromImage<DigitalSet>::append<Image>(set3d, image, 0, 1 ); Viewer3D viewer; viewer.show(); trace.endBlock(); //! [digitalSurfaceSlice-readVol] //! [digitalSurfaceSlice-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."<<std::endl; return 2; } trace.endBlock(); //! [digitalSurfaceSlice-KSpace] //! [digitalSurfaceSlice-SurfelAdjacency] typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency; MySurfelAdjacency surfAdj( true ); // interior in all directions. //! [digitalSurfaceSlice-SurfelAdjacency] //! [digitalSurfaceSlice-ExtractingSurface] trace.beginBlock( "Extracting boundary by scanning the space. " ); typedef KSpace::Surfel Surfel; typedef KSpace::SurfelSet SurfelSet; typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels; typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface; MySetOfSurfels theSetOfSurfels( ks, surfAdj ); Surfaces<KSpace>::sMakeBoundary( theSetOfSurfels.surfelSet(), ks, set3dPredicate, image.domain().lowerBound(), image.domain().upperBound() ); MyDigitalSurface digSurf( theSetOfSurfels ); trace.info() << "Digital surface has " << digSurf.size() << " surfels." << std::endl; trace.endBlock(); //! [digitalSurfaceSlice-ExtractingSurface] //! [digitalSurfaceSlice-ExtractingSlice] trace.beginBlock( "Extract slices." ); typedef MyDigitalSurface::DigitalSurfaceTracker MyTracker; typedef DigitalSurface2DSlice< MyTracker > My2DSlice; //Extract an initial boundary cell Surfel surf = *digSurf.begin(); MyTracker* tracker1 = digSurf.container().newTracker( surf ); MyTracker* tracker2 = digSurf.container().newTracker( surf ); // Extract the bondary contour associated to the initial surfel in // its first direction My2DSlice slice1( tracker1, *(ks.sDirs( surf )) ); // Extract the bondary contour associated to the initial surfel in // its second direction My2DSlice slice2( tracker2, *++(ks.sDirs( surf )) ); delete tracker1; delete tracker2; trace.endBlock(); //! [digitalSurfaceSlice-ExtractingSlice] ASSERT( slice1.start() == slice1.begin() ); ASSERT( slice1.cstart() == slice1.c() ); ASSERT( *slice1.begin() == surf ); ASSERT( *slice1.c() == surf ); ASSERT( *slice1.start() == surf ); ASSERT( *slice1.cstart() == surf ); ASSERT( *slice1.rcstart() == surf ); ASSERT( slice1.rcstart() == slice1.rc() ); ASSERT( *slice1.rc() == surf ); ASSERT( *(slice1.c()+1) == *(slice1.begin()+1) ); ASSERT( *(slice1.rc()+1) == *(slice1.rbegin()) ); //! [digitalSurfaceSlice-displayingAll] trace.beginBlock( "Display all with QGLViewer." ); // Displaying all the surfels in transparent mode viewer << SetMode3D( surf.className(), "Transparent"); for( MyDigitalSurface::ConstIterator it = theSetOfSurfels.begin(), it_end = theSetOfSurfels.end(); it != it_end; ++it ) viewer<< *it; // Displaying First surfels cut with gradient colors.; GradientColorMap<int> cmap_grad( 0, slice1.size() ); cmap_grad.addColor( Color( 50, 50, 255 ) ); cmap_grad.addColor( Color( 255, 0, 0 ) ); cmap_grad.addColor( Color( 255, 255, 10 ) ); // Need to avoid surfel superposition (the surfel size in increased) viewer << Viewer3D::shiftSurfelVisu; viewer << SetMode3D( surf.className(), ""); viewer.setFillColor(Color(180, 200, 25, 255)); int d=0; for ( My2DSlice::ConstIterator it = slice1.begin(), it_end = slice1.end(); it != it_end; ++it ) { Color col= cmap_grad(d); viewer.setFillColor(Color(col.red(),col.green() ,col.blue(), 255)); viewer<< *it; d++; } GradientColorMap<int> cmap_grad2( 0, slice2.size() ); cmap_grad2.addColor( Color( 50, 50, 255 ) ); cmap_grad2.addColor( Color( 255, 0, 0 ) ); cmap_grad2.addColor( Color( 255, 255, 10 ) ); d=0; for ( My2DSlice::ConstIterator it = slice2.begin(), it_end = slice2.end(); it != it_end; ++it ) { Color col= cmap_grad2(d); viewer.setFillColor(Color(col.red(),col.green() ,col.blue(), 255)); viewer<< *it; d++; } // One need once again to avoid superposition. viewer << Viewer3D::shiftSurfelVisu; viewer.setFillColor(Color(18, 200, 25, 255)); viewer << surf ; viewer << Viewer3D::updateDisplay; trace.endBlock(); return application.exec(); //! [digitalSurfaceSlice-displayingAll] }
int main( int argc, char** argv ) { trace.info() << "exampleGridCurve3d: the type can be changed in example source code with <gridcurve>, <inner>, <outer>, <incident> " << std::endl; string type = "gridcurve"; //vol reading and digital set construction trace.beginBlock( "Reading vol file into an image." ); typedef ImageSelector < Domain, int>::Type Image; std::string inputFilename = examplesPath + "samples/cat10.vol"; Image image = VolReader<Image>::importVol(inputFilename); DigitalSet set3d (image.domain()); setFromImage( image, DigitalSetInserter<DigitalSet>(set3d), 1); trace.info() << set3d.size() << " voxels." << std::endl; trace.endBlock(); //Khalimsky space construction 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."<<std::endl; return 2; }*/ trace.endBlock(); //digital surface construction typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency; MySurfelAdjacency surfAdj( true ); // interior in all directions. trace.beginBlock( "Extracting boundary by scanning the space. " ); typedef KSpace::Surfel Surfel; typedef KSpace::SurfelSet SurfelSet; typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels; typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface; MySetOfSurfels theSetOfSurfels( ks, surfAdj ); Surfaces<KSpace>::sMakeBoundary( theSetOfSurfels.surfelSet(), ks, set3d, image.domain().lowerBound(), image.domain().upperBound() ); MyDigitalSurface digSurf( theSetOfSurfels ); trace.info() << digSurf.size() << " surfels." << std::endl; trace.endBlock(); //slice retrieving trace.beginBlock( "Extracting slice and constructing a grid curve. " ); typedef MyDigitalSurface::DigitalSurfaceTracker MyTracker; typedef DigitalSurface2DSlice< MyTracker > My2DSlice; //Extract an initial boundary cell Surfel surf = *digSurf.begin(); MyTracker* tracker = digSurf.container().newTracker( surf ); // Extract the bondary contour associated to the initial surfel in // its first direction My2DSlice slice( tracker, *(ks.sDirs( surf )) ); delete tracker; //! [exampleGridCurve3d-Construction] GridCurve<KSpace> gc(ks); gc.initFromSCellsRange( slice.begin(), slice.end() ); //! [exampleGridCurve3d-Construction] trace.endBlock(); // for 3D display with Viewer3D QApplication application(argc,argv); trace.beginBlock( "Display all with QGLViewer." ); Viewer3D<> viewer; viewer.show(); // Displaying all the surfels in transparent mode viewer << SetMode3D( surf.className(), "Transparent"); for( MyDigitalSurface::ConstIterator it = theSetOfSurfels.begin(), it_end = theSetOfSurfels.end(); it != it_end; ++it ) viewer<< *it; // Displaying slice viewer << Viewer3D<>::shiftSurfelVisu; viewer << SetMode3D( surf.className(), ""); viewer.setFillColor( Color( 50, 50, 255 ) ); if (type == "gridcurve") { viewer << gc; } else if (type == "inner") { viewer << gc.getInnerPointsRange(); } else if (type == "outer") { viewer << gc.getOuterPointsRange(); } else if (type == "incident") { viewer << gc.getIncidentPointsRange(); } else { trace.info() << "Display type not known. Use option -h" << std::endl; } viewer << Viewer3D<>::updateDisplay; trace.endBlock(); return application.exec(); }
bool testUmbrellaComputer() { using namespace Z3i; typedef Space::RealPoint RealPoint; typedef ImplicitBall<Space> EuclideanShape; typedef GaussDigitizer<Space,EuclideanShape> DigitalShape; typedef GaussDigitizer<Space,EuclideanShape>::Domain Domain; typedef LightImplicitDigitalSurface<KSpace,DigitalShape> Boundary; typedef Boundary::SurfelConstIterator ConstIterator; //typedef Boundary::Tracker Tracker; typedef Boundary::Surfel Surfel; typedef Boundary::DigitalSurfaceTracker DigitalSurfaceTracker; typedef DigitalSurface<Boundary> MyDigitalSurface; typedef UmbrellaComputer<DigitalSurfaceTracker> MyUmbrellaComputer; unsigned int nbok = 0; unsigned int nb = 0; trace.beginBlock ( "Testing block ... UmbrellaComputer" ); // Creating shape Point c( 0, 0, 0 ); EuclideanShape ball( c, 2 ); // ball r=4 DigitalShape shape; shape.attach( ball ); shape.init( RealPoint( -10.0, -10.0, -10.0 ), RealPoint( 10.0, 10.0, 10.0 ), 1.0 ); // Creating cellular grid space around. Domain domain = shape.getDomain(); KSpace K; nbok += K.init( domain.lowerBound(), domain.upperBound(), true ) ? 1 : 0; nb++; trace.info() << "(" << nbok << "/" << nb << ") " << "K.init() is ok" << std::endl; // Find start surfel on surface. Surfel bel = Surfaces<KSpace>::findABel( K, shape, 10000 ); // Define surface container then surface itself. Boundary boundary( K, // cellular space shape, // point predicate SurfelAdjacency<KSpace::dimension>( true ), // adjacency bel // starting surfel ); MyDigitalSurface digSurf( boundary ); // boundary is cloned // Get tracker on surface. DigitalSurfaceTracker* ptrTracker = boundary.newTracker( bel ); MyUmbrellaComputer umbrella; KSpace::DirIterator dirIt = K.sDirs( bel ); Dimension k = *dirIt; Dimension j = *(++dirIt); trace.beginBlock ( "Testing block ... forward umbrella" ); umbrella.init( *ptrTracker, k, true, j ); unsigned int nb_forward = 0; Surfel init_bel = bel; do { Point x = K.sKCoords( bel ); trace.info() << x << std::endl; umbrella.next(); ++nb_forward; bel = umbrella.surfel(); } while ( bel != init_bel ); trace.endBlock(); trace.beginBlock ( "Testing block ... backward umbrella" ); unsigned int nb_backward = 0; do { Point x = K.sKCoords( bel ); trace.info() << x << std::endl; umbrella.previous(); ++nb_backward; bel = umbrella.surfel(); } while ( bel != init_bel ); nb++, nbok += nb_forward == nb_backward ? 1 : 0; trace.info() << "(" << nbok << "/" << nb << ") " << " nb_forward(" << nb_forward << ") == nb_backward(" << nb_backward << ")" << std::endl; trace.endBlock(); unsigned int nbsurfels = 0; for ( ConstIterator it = boundary.begin(), it_end = boundary.end(); it != it_end; ++it ) { ++nbsurfels; } trace.info() << nbsurfels << " surfels found." << std::endl; trace.endBlock(); delete ptrTracker; return nbok == nb; }
int main( int argc, char** argv ) { // 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") ("trivial-radius,t", po::value<double>()->default_value( 3 ), "the parameter t defining the radius for the Trivial estimator, which is used for reorienting II or VCM normal estimations." ) ("r-radius,r", po::value< double >(), "Kernel radius r for IntegralInvariant estimator" ) ("noise,k", po::value< double >()->default_value(0.5), "Level of Kanungo noise ]0;1[" ) ("min,l", po::value< int >()->default_value(0), "set the minimal image threshold to define the image object (object defined by the voxel with intensity belonging to ]min, max ] )." ) ("max,u", po::value< int >()->default_value(255), "set the minimal image threshold to define the image object (object defined by the voxel with intensity belonging to ]min, max] )." ) ("lambda,L", po::value<double>()->default_value( 0.05 ), "the parameter lambda of AT functional." ) ("alpha,a", po::value<double>()->default_value( 0.1 ), "the parameter alpha of AT functional." ) ("epsilon,e", po::value<double>()->default_value( 4.0 ), "the initial parameter epsilon of AT functional." ); 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.error() << " Error checking program options: " << ex.what() << std::endl; } bool neededArgsGiven=true; if (parseOK && !(vm.count("input"))){ missingParam("--input"); neededArgsGiven=false; } if (parseOK && !(vm.count("r-radius"))){ missingParam("--r-radius"); neededArgsGiven=false; } double noiseLevel = vm["noise"].as< double >(); if( noiseLevel < 0.0 || noiseLevel > 1.0 ) { parseOK = false; trace.error() << "The noise level should be in the interval: [0, 1]"<< std::endl; } if(!neededArgsGiven || !parseOK || vm.count("help") || argc <= 1 ) { trace.info()<< "Vol file viewer, with normals regularized by Ambrosio-Tortorelli functionnal" <<std::endl << general_opt << "\n" << "Basic usage: "<<std::endl << "\t at-3d-normals -i file.vol -r 5 --noise 0.1"<<std::endl << std::endl; return 0; } QApplication application(argc,argv); int min = vm["min"].as< int >(); int max = vm["max"].as< int >(); const double h = 1.0; // not pertinent for now. //----------------------------------------------------------------------------- // Types. typedef Z3i::Space Space; typedef Z3i::KSpace KSpace; typedef Space::RealVector RealVector; typedef KSpace::SCell SCell; typedef KSpace::Cell Cell; typedef KSpace::Surfel Surfel; typedef Z3i::Domain Domain; typedef ImageSelector<Domain, unsigned char>::Type Image; typedef IntervalForegroundPredicate< Image > Object; typedef KanungoNoise< Object, Domain > KanungoPredicate; typedef BinaryPointPredicate<DomainPredicate<Domain>, KanungoPredicate, AndBoolFct2 > NoisyObject; typedef KSpace::SurfelSet SurfelSet; typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels; typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface; typedef MyDigitalSurface::ConstIterator ConstIterator; //----------------------------------------------------------------------------- // Loading vol file. trace.beginBlock( "Loading vol file." ); std::string inputFile = vm[ "input" ].as< std::string >(); std::string extension = inputFile.substr(inputFile.find_last_of(".") + 1); if(extension!="vol" && extension != "p3d" && extension != "pgm3D" && extension != "pgm3d" && extension != "sdp" && extension != "pgm" ) { trace.info() << "File extension not recognized: "<< extension << std::endl; return 0; } Image image = GenericReader<Image>::import (inputFile ); trace.endBlock(); //----------------------------------------------------------------------------- // Extracting object with possible noise. trace.beginBlock( "Extracting object with possible noise." ); Object object( image, min, max ); KanungoPredicate kanungo_pred( object, image.domain(), noiseLevel ); DomainPredicate<Domain> domain_pred( image.domain() ); AndBoolFct2 andF; NoisyObject noisy_object(domain_pred, kanungo_pred, andF ); Domain domain = image.domain(); KSpace K; bool space_ok = K.init( domain.lowerBound()-Z3i::Domain::Point::diagonal(), domain.upperBound()+Z3i::Domain::Point::diagonal(), true ); if (!space_ok) { trace.error() << "Error in the Khalimsky space construction."<<std::endl; return 2; } CanonicSCellEmbedder< KSpace > embedder( K ); SurfelAdjacency< KSpace::dimension > surfAdj( true ); trace.endBlock(); //----------------------------------------------------------------------------- //! [3dVolBoundaryViewer-ExtractingSurface] trace.beginBlock( "Extracting boundary by scanning the space. " ); MySetOfSurfels theSetOfSurfels( K, surfAdj ); Surfaces<KSpace>::sMakeBoundary( theSetOfSurfels.surfelSet(), K, image, domain.lowerBound(), domain.upperBound() ); MyDigitalSurface digSurf( theSetOfSurfels ); trace.info() << "Digital surface has " << digSurf.size() << " surfels." << std::endl; trace.endBlock(); //! [3dVolBoundaryViewer-ExtractingSurface] // Map surfel -> estimated normals. std::map<SCell,RealVector> n_estimations; //----------------------------------------------------------------------------- // Estimating orientation of normals trace.beginBlock( "Estimating orientation of normals by simple convolutions of trivial surfel normals." ); double t = vm["trivial-radius"].as<double>(); typedef RealVector::Component Scalar; typedef functors::HatFunction<Scalar> Functor; typedef functors::ElementaryConvolutionNormalVectorEstimator< Surfel, CanonicSCellEmbedder<KSpace> > SurfelFunctor; typedef ExactPredicateLpSeparableMetric<Space,2> Metric; typedef LocalEstimatorFromSurfelFunctorAdapter< MySetOfSurfels, Metric, SurfelFunctor, Functor> NormalEstimator; Functor fct( 1.0, t ); CanonicSCellEmbedder<KSpace> canonic_embedder( K ); SurfelFunctor surfelFct( canonic_embedder, 1.0 ); NormalEstimator nt_estimator; Metric aMetric; std::vector<RealVector> nt_estimations; nt_estimator.attach( digSurf ); nt_estimator.setParams( aMetric, surfelFct, fct, t ); nt_estimator.init( h, digSurf.begin(), digSurf.end()); nt_estimator.eval( digSurf.begin(), digSurf.end(), std::back_inserter( nt_estimations ) ); trace.endBlock(); //----------------------------------------------------------------------------- // Estimating normals trace.beginBlock( "Estimating normals with II." ); typedef typename Domain::ConstIterator DomainConstIterator; typedef functors::IINormalDirectionFunctor<Space> IINormalFunctor; typedef IntegralInvariantCovarianceEstimator<KSpace, NoisyObject, IINormalFunctor> IINormalEstimator; std::vector<RealVector> nii_estimations; const double r = vm["r-radius"].as<double>(); IINormalEstimator nii_estimator( K, noisy_object ); trace.info() << " r=" << r << std::endl; nii_estimator.setParams( r ); nii_estimator.init( h, digSurf.begin(), digSurf.end() ); nii_estimator.eval( digSurf.begin(), digSurf.end(), std::back_inserter( nii_estimations ) ); // Fix orientations of ii. for ( unsigned int i = 0; i < nii_estimations.size(); ++i ) { if ( nii_estimations[ i ].dot( nt_estimations[ i ] ) < 0.0 ) nii_estimations[ i ] *= -1.0; } trace.info() << "- nb estimations = " << nii_estimations.size() << std::endl; trace.endBlock(); // The chosen estimator is II. { unsigned int i = 0; for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it, ++i ) { RealVector nii = nii_estimations[ i ]; nii /= nii.norm(); n_estimations[ *it ] = nii; } } //----------------------------------------------------------------------------- //! [3dVolBoundaryViewer-ViewingSurface] trace.beginBlock( "Displaying everything. " ); Viewer3D<Space,KSpace> viewer( K ); viewer.setWindowTitle("Simple boundary of volume Viewer"); viewer.show(); viewer << SetMode3D(K.unsigns( *(digSurf.begin()) ).className(), "Basic"); unsigned int i = 0; for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it, ++i ) { viewer.setFillColor( Color( 200, 200, 250 ) ); Display3DFactory<Space,KSpace>::drawOrientedSurfelWithNormal( viewer, *it, n_estimations[ *it ], false ); } viewer << Viewer3D<>::updateDisplay; trace.endBlock(); //----------------------------------------------------------------------------- // Defining Discrete Calculus. typedef CubicalComplex< KSpace > CComplex; typedef DiscreteExteriorCalculus<2,3, EigenLinearAlgebraBackend> Calculus; typedef Calculus::Index Index; typedef Calculus::PrimalForm0 PrimalForm0; typedef Calculus::PrimalForm1 PrimalForm1; typedef Calculus::PrimalForm2 PrimalForm2; typedef Calculus::PrimalIdentity0 PrimalIdentity0; typedef Calculus::PrimalIdentity1 PrimalIdentity1; typedef Calculus::PrimalIdentity2 PrimalIdentity2; trace.beginBlock( "Creating Discrete Exterior Calculus. " ); Calculus calculus; calculus.initKSpace<Domain>( domain ); const KSpace& Kc = calculus.myKSpace; // should not be used. // Use a cubical complex to find all lower incident cells easily. CComplex complex( K ); for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it ) complex.insertCell( 2, K.unsigns( *it ) ); complex.close(); for ( CComplex::CellMapIterator it = complex.begin( 0 ), itE = complex.end( 0 ); it != itE; ++it ) calculus.insertSCell( K.signs( it->first, K.POS ) ); for ( CComplex::CellMapIterator it = complex.begin( 1 ), itE = complex.end( 1 ); it != itE; ++it ) { SCell linel = K.signs( it->first, K.POS ); Dimension k = * K.sDirs( linel ); bool pos = K.sDirect( linel, k ); calculus.insertSCell( pos ? linel : K.sOpp( linel ) ); // calculus.insertSCell( K.signs( it->first, K.POS ) ); } // for ( CComplex::CellMapIterator it = complex.begin( 2 ), itE = complex.end( 2 ); it != itE; ++it ) // calculus.insertSCell( K.signs( it->first, K.POS ) ); for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it ) { calculus.insertSCell( *it ); // SCell surfel = *it; // Dimension k = K.sOrthDir( surfel ); // bool pos = K.sDirect( surfel, k ); // calculus.insertSCell( pos ? *it : K.sOpp( *it ) ); } calculus.updateIndexes(); trace.info() << calculus << endl; std::vector<PrimalForm2> g; g.reserve( 3 ); g.push_back( PrimalForm2( calculus ) ); g.push_back( PrimalForm2( calculus ) ); g.push_back( PrimalForm2( calculus ) ); Index nb2 = g[ 0 ].myContainer.rows(); for ( Index index = 0; index < nb2; index++) { const Calculus::SCell& cell = g[ 0 ].getSCell( index ); if ( theSetOfSurfels.isInside( cell ) ) { const RealVector& n = n_estimations[ cell ]; g[ 0 ].myContainer( index ) = n[ 0 ]; g[ 1 ].myContainer( index ) = n[ 1 ]; g[ 2 ].myContainer( index ) = n[ 2 ]; } else { const RealVector& n = n_estimations[ K.sOpp( cell ) ]; g[ 0 ].myContainer( index ) = n[ 0 ]; g[ 1 ].myContainer( index ) = n[ 1 ]; g[ 2 ].myContainer( index ) = n[ 2 ]; } } cout << endl; trace.info() << "primal_D0" << endl; const Calculus::PrimalDerivative0 primal_D0 = calculus.derivative<0,PRIMAL>(); trace.info() << "primal_D1" << endl; const Calculus::PrimalDerivative1 primal_D1 = calculus.derivative<1,PRIMAL>(); trace.info() << "dual_D0" << endl; const Calculus::DualDerivative0 dual_D0 = calculus.derivative<0,DUAL>(); trace.info() << "dual_D1" << endl; const Calculus::DualDerivative1 dual_D1 = calculus.derivative<1,DUAL>(); trace.info() << "primal_h0" << endl; const Calculus::PrimalHodge0 primal_h0 = calculus.hodge<0,PRIMAL>(); trace.info() << "primal_h1" << endl; const Calculus::PrimalHodge1 primal_h1 = calculus.hodge<1,PRIMAL>(); trace.info() << "primal_h2" << endl; const Calculus::PrimalHodge2 primal_h2 = calculus.hodge<2,PRIMAL>(); trace.info() << "dual_h1" << endl; const Calculus::DualHodge1 dual_h1 = calculus.hodge<1,DUAL>(); trace.info() << "dual_h2" << endl; const Calculus::DualHodge2 dual_h2 = calculus.hodge<2,DUAL>(); trace.endBlock(); //----------------------------------------------------------------------------- // Building AT functional. trace.beginBlock( "Building AT functional. " ); double a = vm[ "alpha" ].as<double>(); double e = vm[ "epsilon" ].as<double>(); double l = vm[ "lambda" ].as<double>(); // u = g at the beginning trace.info() << "u[0,1,2]" << endl; std::vector<PrimalForm2> u; u.push_back( g[ 0 ] ); u.push_back( g[ 1 ] ); u.push_back( g[ 2 ] ); // v = 1 at the beginning trace.info() << "v" << endl; PrimalForm1 v( calculus ); Index nb1 = v.myContainer.rows(); for ( Index index = 0; index < nb1; index++) v.myContainer( index ) = 1.0; const PrimalIdentity0 Id0 = calculus.identity<0, PRIMAL>(); const PrimalIdentity1 Id1 = calculus.identity<1, PRIMAL>(); const PrimalIdentity2 Id2 = calculus.identity<2, PRIMAL>(); // Building alpha_ trace.info() << "alpha_g" << endl; const PrimalIdentity2 alpha_Id2 = a * Id2; // a * invG0; vector<PrimalForm2> alpha_g; alpha_g.push_back( alpha_Id2 * g[ 0 ] ); alpha_g.push_back( alpha_Id2 * g[ 1 ] ); alpha_g.push_back( alpha_Id2 * g[ 2 ] ); trace.info() << "lap_operator_v" << endl; const PrimalIdentity1 lap_operator_v = -1.0 * ( primal_D0 * dual_h2 * dual_D1 * primal_h1 + dual_h1 * dual_D0 * primal_h2 * primal_D1 ); // SparseLU is so much faster than SparseQR // SimplicialLLT is much faster than SparseLU // typedef EigenLinearAlgebraBackend::SolverSparseQR LinearAlgebraSolver; // typedef EigenLinearAlgebraBackend::SolverSparseLU LinearAlgebraSolver; typedef EigenLinearAlgebraBackend::SolverSimplicialLLT LinearAlgebraSolver; typedef DiscreteExteriorCalculusSolver<Calculus, LinearAlgebraSolver, 2, PRIMAL, 2, PRIMAL> SolverU; SolverU solver_u; typedef DiscreteExteriorCalculusSolver<Calculus, LinearAlgebraSolver, 1, PRIMAL, 1, PRIMAL> SolverV; SolverV solver_v; trace.info() << "lB'B'" << endl; const PrimalIdentity1 lBB = l * lap_operator_v; PrimalForm1 l_sur_4( calculus ); for ( Index index = 0; index < nb1; index++) l_sur_4.myContainer( index ) = l / 4.0; double coef_eps = 2.0; double eps = 2.0 * e; const int n = 10; trace.endBlock(); //----------------------------------------------------------------------------- // Solving AT functional. trace.beginBlock( "Solving AT functional. " ); while ( eps / coef_eps >= h ) { eps /= coef_eps; trace.info() << "************** epsilon = " << eps << "***************************************" << endl; const PrimalIdentity1 BB = eps * lBB + ( l/(4.0*eps) ) * Id1; // tS_S; for ( int i = 0; i < n; ++i ) { trace.info() << "---------- Iteration " << i << "/" << n << " ------------------------------" << endl; trace.info() << "-------------------------------------------------------------------------------" << endl; trace.beginBlock("Solving for u"); trace.info() << "Building matrix Av2A" << endl; PrimalIdentity1 diag_v = diag( calculus, v ); PrimalIdentity2 U_Id2 = -1.0 * primal_D1 * diag_v * diag_v * dual_h1 * dual_D0 * primal_h2 + alpha_Id2; trace.info() << "Prefactoring matrix Av2A + alpha_iG0" << endl; solver_u.compute( U_Id2 ); for ( unsigned int d = 0; d < 3; ++d ) { trace.info() << "Solving (Av2A + alpha_iG0) u[" << d << "] = ag[" << d << "]" << endl; u[ d ] = solver_u.solve( alpha_g[ d ] ); trace.info() << " => " << ( solver_u.isValid() ? "OK" : "ERROR" ) << " " << solver_u.myLinearAlgebraSolver.info() << endl; } trace.info() << "-------------------------------------------------------------------------------" << endl; trace.endBlock(); trace.beginBlock("Solving for v"); const PrimalForm1 former_v = v; trace.info() << "Building matrix tu_tA_A_u + BB + Mw2" << endl; PrimalIdentity1 V_Id1 = BB; for ( unsigned int d = 0; d < 3; ++d ) { const PrimalIdentity1 A_u = diag( calculus, dual_h1 * dual_D0 * primal_h2 * u[ d ] ); V_Id1.myContainer += square( calculus, A_u ).myContainer; } trace.info() << "Prefactoring matrix tu_tA_A_u + BB + Mw2" << endl; solver_v.compute( V_Id1 ); trace.info() << "Solving (tu_tA_A_u + BB + Mw2) v = 1/(4eps) * l" << endl; v = solver_v.solve( (1.0/eps) * l_sur_4 ); trace.info() << " => " << ( solver_v.isValid() ? "OK" : "ERROR" ) << " " << solver_v.myLinearAlgebraSolver.info() << endl; trace.info() << "-------------------------------------------------------------------------------" << endl; trace.endBlock(); for ( Index index = 0; index < nb2; index++) { double n2 = 0.0; for ( unsigned int d = 0; d < 3; ++d ) n2 += u[ d ].myContainer( index ) * u[ d ].myContainer( index ); double norm = sqrt( n2 ); for ( unsigned int d = 0; d < 3; ++d ) u[ d ].myContainer( index ) /= norm; } trace.beginBlock("Checking v, computing norms"); double m1 = 1.0; double m2 = 0.0; double ma = 0.0; for ( Index index = 0; index < nb1; index++) { double val = v.myContainer( index ); m1 = std::min( m1, val ); m2 = std::max( m2, val ); ma += val; } trace.info() << "1-form v: min=" << m1 << " avg=" << ( ma / nb1 ) << " max=" << m2 << std::endl; for ( Index index = 0; index < nb1; index++) v.myContainer( index ) = std::min( std::max(v.myContainer( index ), 0.0) , 1.0 ); double n_infty = 0.0; double n_2 = 0.0; double n_1 = 0.0; for ( Index index = 0; index < nb1; index++) { n_infty = std::max( n_infty, fabs( v.myContainer( index ) - former_v.myContainer( index ) ) ); n_2 += ( v.myContainer( index ) - former_v.myContainer( index ) ) * ( v.myContainer( index ) - former_v.myContainer( index ) ); n_1 += fabs( v.myContainer( index ) - former_v.myContainer( index ) ); } n_1 /= v.myContainer.rows(); n_2 = sqrt( n_2 / v.myContainer.rows() ); trace.info() << "Variation |v^k+1 - v^k|_oo = " << n_infty << endl; trace.info() << "Variation |v^k+1 - v^k|_2 = " << n_2 << endl; trace.info() << "Variation |v^k+1 - v^k|_1 = " << n_1 << endl; trace.endBlock(); if ( n_infty < 1e-4 ) break; } // for ( int i = 0; i < n; ++i ) } trace.endBlock(); //----------------------------------------------------------------------------- // Displaying regularized normals trace.beginBlock( "Displaying regularized normals. " ); Viewer3D<Space,KSpace> viewerR( K ); viewerR.setWindowTitle("Regularized normals"); viewerR.show(); viewerR << SetMode3D(K.unsigns( *(digSurf.begin()) ).className(), "Basic"); viewerR.setFillColor( Color( 200, 200, 250 ) ); for ( Index index = 0; index < nb2; index++) { const SCell& cell = u[ 0 ].getSCell( index ); // const RealVector& n = n_estimations[ cell ]; RealVector nr = RealVector( u[ 0 ].myContainer( index ), u[ 1 ].myContainer( index ), u[ 2 ].myContainer( index ) ); nr /= nr.norm(); if ( theSetOfSurfels.isInside( cell ) ) Display3DFactory<Space,KSpace>::drawOrientedSurfelWithNormal( viewerR, cell, nr, false ); else Display3DFactory<Space,KSpace>::drawOrientedSurfelWithNormal( viewerR, K.sOpp( cell ), nr, false ); } viewerR.setLineColor( Color( 255, 0, 0 ) ); for ( Index index = 0; index < nb1; index++) { const SCell& cell = v.getSCell( index ); Dimension k = * K.sDirs( cell ); const SCell p0 = K.sIncident( cell, k, true ); const SCell p1 = K.sIncident( cell, k, false ); if ( v.myContainer( index ) >= 0.5 ) continue; viewerR.addLine( embedder.embed( p0 ), embedder.embed( p1 ), (0.5 - v.myContainer( index ))/ 5.0 ); } viewerR << Viewer3D<>::updateDisplay; trace.endBlock(); return application.exec(); }