bool testRaySurface()
{
typedef ImplicitBall<Z3i::Space> ImplicitShape;
typedef GaussDigitizer<Z3i::Space, ImplicitShape> DigitalShape;
typedef LightImplicitDigitalSurface<Z3i::KSpace,DigitalShape> Boundary;
typedef DigitalSurface< Boundary > MyDigitalSurface;
trace.beginBlock(" Ray shooting in digital surface");
trace.beginBlock( "Shape initialisation ..." );
ImplicitShape ishape( Z3i::RealPoint( 0, 0 ,0), 12 );
DigitalShape dshape;
dshape.attach( ishape );
dshape.init( Z3i::RealPoint( -20.0, -20.0 ,-20.0 ), Z3i::RealPoint( 20.0, 20.0, 20.0 ), 1.0 );
Z3i::KSpace K;
if ( !K.init( dshape.getLowerBound(), dshape.getUpperBound(), true ) )
{
trace.error() << "Problem with Khalimsky space init" << std::endl;
return false;
}
Z3i::KSpace::Surfel bel = Surfaces<Z3i::KSpace>::findABel( K, dshape, 10000 );
Boundary boundary( K, dshape, SurfelAdjacency<Z3i::KSpace::dimension>( true ), bel );
MyDigitalSurface surf ( boundary );
trace.endBlock();
trace.beginBlock(" Ray shooting the shape");
RayIntersectionPredicate<Z3i::KSpace::Cell::Point> ray(Z3i::KSpace::Cell::Point(0,0,0),
Z3i::KSpace::Cell::Point(2,2,2));
RayIntersectionPredicate<Z3i::KSpace::Cell::Point> ray2(Z3i::KSpace::Cell::Point(0,0,0),
Z3i::KSpace::Cell::Point(1,0,0));
MyDigitalSurface::ConstIterator it = std::find_if(surf.begin(), surf.end(), ray);
trace.info() << "Ray shooting returns : "<< *it<<std::endl;
MyDigitalSurface::ConstIterator it2 = std::find_if(surf.begin(), surf.end(), ray2);
trace.info() << "Ray shooting returns : "<< *it2<<std::endl;
trace.endBlock();
trace.endBlock();
return true;
}
int main()
{
const double h = 1;
const double radiusBall = 12.0;
trace.beginBlock( "Make parametric shape..." );
typedef Ball3D< Z3i::Space > Shape;
RealPoint center( 0.0, 0.0, 0.0 );
Shape ball( center, radiusBall );
RealPoint centerBis(18.0,0.0,0.0);
Shape ballBis( centerBis, radiusBall);
trace.endBlock();
trace.beginBlock( "Make digital shape..." );
typedef GaussDigitizer< Z3i::Space, Shape > DigitalShape;
typedef DigitalShape::Domain Domain;
DigitalShape digitalBall;
digitalBall.attach( ball );
digitalBall.init( ball.getLowerBound() - Z3i::RealPoint( 1.0, 1.0, 1.0 ),
ball.getUpperBound() + Z3i::RealPoint( 1.0, 1.0, 1.0 ),
h );
DigitalShape digitalBallBis;
digitalBallBis.attach( ballBis );
digitalBallBis.init( ballBis.getLowerBound() - Z3i::RealPoint( 1.0, 1.0, 1.0 ),
ballBis.getUpperBound() + Z3i::RealPoint( 1.0, 1.0, 1.0 ),
h );
Domain domain( digitalBall.getDomain().lowerBound().inf( digitalBallBis.getDomain().lowerBound() ),
digitalBall.getDomain().upperBound().sup( digitalBallBis.getDomain().upperBound() ));
Z3i::KSpace kspace;
kspace.init( domain.lowerBound(), domain.upperBound(), true );
trace.info()<< domain <<std::endl;
trace.endBlock();
trace.beginBlock( "Make first digital surface..." );
typedef LightImplicitDigitalSurface< Z3i::KSpace, DigitalShape > LightDigitalSurface;
typedef DigitalSurface< LightDigitalSurface > DigitalSurface;
typedef Z3i::KSpace::Surfel Surfel;
Surfel bel = Surfaces< Z3i::KSpace >::findABel( kspace, digitalBall, 500 );
SurfelAdjacency< Z3i::KSpace::dimension > surfelAdjacency( true );
LightDigitalSurface lightDigitalSurface( kspace, digitalBall, surfelAdjacency, bel );
DigitalSurface digitalSurface( lightDigitalSurface );
bel = Surfaces< Z3i::KSpace >::findABel( kspace, digitalBallBis, 500 );
LightDigitalSurface lightDigitalSurfaceBis( kspace, digitalBallBis, surfelAdjacency, bel );
DigitalSurface digitalSurfaceBis( lightDigitalSurfaceBis );
trace.endBlock();
std::set<Surfel> storage;
trace.beginBlock("Exporting the first ball");
std::ofstream handle("output.csv");
for(auto cell : digitalSurface)
{
const Point p = kspace.sKCoords(cell);
if (p[0] < -7.5) continue;
const KSpace::Sign sign = kspace.sSign(cell);
for (int dim=0; dim<3; dim++)
handle << p[dim] << " ";
handle << ( sign == KSpace::POS ) << " ";
for (int dim=0; dim<3; ++dim)
handle << (p-center)[dim]<<" ";
handle << std::endl;
//std::cout << "exporting "<< cell<<std::endl;
storage.insert( cell );
}
trace.endBlock();
trace.beginBlock("Exporting the second ball");
for(auto cell : digitalSurfaceBis)
{
if (storage.find(cell) != storage.end())
continue;
const Point p = kspace.sKCoords(cell);
const KSpace::Sign sign = kspace.sSign(cell);
// "2.0*" to map centerbis to Kspace
const RealPoint normal = (p-2.0*centerBis).getNormalized();
for (int dim=0; dim<3; dim++)
handle << p[dim] << " ";
handle << ( sign == KSpace::POS ) << " ";
for (int dim=0; dim<3; ++dim)
handle << normal[dim] <<" ";
handle << std::endl;
//std::cout << "exporting "<< cell<<std::endl;
}
trace.endBlock();
handle.close();
return 0;
}
int main( int argc, char** argv )
{
trace.beginBlock ( "Example ctopo-2-3d" );
// for 3D display with Viewer3D
QApplication application(argc,argv);
typedef ImageSelector < Z3i::Domain, int>::Type Image;
std::string inputFilename = examplesPath + "samples/cat10.vol";
Image image = VolReader<Image>::importVol(inputFilename);
Z3i::DigitalSet set3d (image.domain());
SetPredicate<Z3i::DigitalSet> set3dPredicate( set3d );
SetFromImage<Z3i::DigitalSet>::append<Image>(set3d, image, 0,255);
Viewer3D viewer;
viewer.show();
// Construct the Khalimsky space from the image domain
Z3i::KSpace ks;
bool space_ok = ks.init( image.domain().lowerBound(), image.domain().upperBound(), true );
ASSERT(space_ok);
std::vector<Z3i::SCell> vectBdrySCell;
std::vector<Z3i::SCell> vectBdrySCell2;
std::set<Z3i::SCell> vectBdrySCellALL;
SurfelAdjacency<3> SAdj( true );
//Extract an initial boundary cell
Z3i::SCell aCell = Surfaces<Z3i::KSpace>::findABel(ks, set3dPredicate);
// Extracting all boundary surfels which are connected to the initial boundary Cell.
Surfaces<Z3i::KSpace>::trackBoundary( vectBdrySCellALL,
ks,SAdj, set3dPredicate, aCell );
// Extract the bondary contour associated to the initial surfel in its first direction
Surfaces<Z3i::KSpace>::track2DBoundary( vectBdrySCell,
ks, *(ks.sDirs( aCell )), SAdj,
set3dPredicate, aCell );
// Extract the bondary contour associated to the initial surfel in its second direction
Surfaces<Z3i::KSpace>::track2DBoundary( vectBdrySCell2,
ks, *(++(ks.sDirs( aCell ))), SAdj,
set3dPredicate, aCell );
// Displaying all the surfels in transparent mode
viewer << SetMode3D((*(vectBdrySCellALL.begin())).styleName(), "Transparent");
for( std::set<Z3i::SCell>::iterator it=vectBdrySCellALL.begin();
it!= vectBdrySCellALL.end(); it++){
viewer<< *it;
}
// Displaying First surfels cut with gradient colors.;
GradientColorMap<int> cmap_grad( 0, vectBdrySCell2.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((*(vectBdrySCell2.begin())).styleName(), "");
viewer.setFillColor(Color(180, 200, 25, 255));
int d=0;
for( std::vector<Z3i::SCell>::iterator it=vectBdrySCell2.begin();
it!= vectBdrySCell2.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, vectBdrySCell.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( std::vector<Z3i::SCell>::iterator it=vectBdrySCell.begin();
it!= vectBdrySCell.end(); it++){
Color col= cmap_grad2(d);
viewer.setFillColor(Color(col.red(),col.green() ,col.blue(), 255));
viewer<< *it;
d++;
}
// On need once again to avoid superposition.
viewer << Viewer3D::shiftSurfelVisu;
viewer.setFillColor(Color(18, 200, 25, 255));
viewer << aCell ;
viewer << Viewer3D::updateDisplay;
return application.exec();
}
/**
* Example of a test. To be completed.
*
*/
bool testEstimatorCache(double h)
{
unsigned int nbok = 0;
unsigned int nb = 0;
typedef ImplicitBall<Z3i::Space> ImplicitShape;
typedef GaussDigitizer<Z3i::Space, ImplicitShape> DigitalShape;
typedef LightImplicitDigitalSurface<Z3i::KSpace,DigitalShape> Boundary;
typedef DigitalSurface< Boundary > MyDigitalSurface;
typedef DepthFirstVisitor< MyDigitalSurface > Visitor;
typedef GraphVisitorRange< Visitor > VisitorRange;
typedef VisitorRange::ConstIterator VisitorConstIterator;
typedef functors::IIGaussianCurvature3DFunctor<Z3i::Space> MyIICurvatureFunctor;
typedef IntegralInvariantCovarianceEstimator< Z3i::KSpace, DigitalShape, MyIICurvatureFunctor > MyIICurvatureEstimator;
// typedef MyIICurvatureFunctor::Value Value;
double re = 5.0;
double radius = 5.0;
trace.beginBlock( "Shape initialisation ..." );
ImplicitShape ishape( Z3i::RealPoint( 0, 0, 0 ), radius );
DigitalShape dshape;
dshape.attach( ishape );
dshape.init( Z3i::RealPoint( -10.0, -10.0, -10.0 ), Z3i::RealPoint( 10.0, 10.0, 10.0 ), h );
Z3i::KSpace K;
if ( !K.init( dshape.getLowerBound(), dshape.getUpperBound(), true ) )
{
trace.error() << "Problem with Khalimsky space" << std::endl;
return false;
}
Z3i::KSpace::Surfel bel = Surfaces<Z3i::KSpace>::findABel( K, dshape, 10000 );
Boundary boundary( K, dshape, SurfelAdjacency<Z3i::KSpace::dimension>( true ), bel );
MyDigitalSurface surf ( boundary );
trace.endBlock();
trace.beginBlock( "Curvature estimator computation ...");
VisitorRange range( new Visitor( surf, *surf.begin() ));
VisitorConstIterator ibegin = range.begin();
VisitorConstIterator iend = range.end();
MyIICurvatureFunctor curvatureFunctor;
curvatureFunctor.init( h, re );
MyIICurvatureEstimator curvatureEstimator( curvatureFunctor );
curvatureEstimator.attach( K, dshape );
curvatureEstimator.setParams( re/h );
curvatureEstimator.init( h, ibegin, iend );
std::vector<MyIICurvatureEstimator::Quantity> results;
std::back_insert_iterator< std::vector<MyIICurvatureEstimator::Quantity> > itback(results);
curvatureEstimator.eval(ibegin,iend,itback);
trace.info() << "Number of values = "<< results.size()<<std::endl;
trace.endBlock();
trace.beginBlock( "Caching values ...");
VisitorRange range2( new Visitor( surf, *surf.begin() ));
VisitorConstIterator ibegin2 = range2.begin();
VisitorConstIterator iend2 = range2.end();
typedef EstimatorCache<MyIICurvatureEstimator> GaussianCache;
BOOST_CONCEPT_ASSERT(( concepts::CSurfelLocalEstimator<GaussianCache> ));
GaussianCache cache( curvatureEstimator );
cache.init( h, ibegin2, iend2 );
trace.info() << "Number of cached values = "<< cache.size()<<std::endl;
trace.info() << "Value at begin="<< cache.eval(surf.begin())<<" expected = "<< curvatureEstimator.eval(surf.begin())<<std::endl;
trace.endBlock();
trace.beginBlock( "Complete test ...");
bool ok=true;
for(MyDigitalSurface::ConstIterator it = surf.begin(), itend=surf.end(); it != itend; ++it)
{
if ( cache.eval(it) != curvatureEstimator.eval(it) )
{
ok=false;
trace.error() << "Incorrect values at "<<*it<<" read " <<cache.eval(it)<< " and expecting "<<curvatureEstimator.eval(it)<<std::endl;
}
}
trace.endBlock();
trace.beginBlock( "Timing cache access ...");
for(MyDigitalSurface::ConstIterator it = surf.begin(), itend=surf.end(); it != itend; ++it)
{
if ( cache.eval(it) == 12345678 ) //making sure to visit
//all surfels
{
ok=false;
trace.error() << "Incorrect values at "<<*it<<std::endl;
}
}
trace.endBlock();
trace.beginBlock( "Copy construction and timing cache access ...");
GaussianCache cache2(cache);
trace.info() << "Number of cached values = "<< cache.size()<<std::endl;
trace.info() << "Value at begin="<< cache2.eval(surf.begin())<<" expected = "<< curvatureEstimator.eval(surf.begin())<<std::endl;
for(MyDigitalSurface::ConstIterator it = surf.begin(), itend=surf.end(); it != itend; ++it)
{
if ( cache.eval(it) == 12345678 ) //making sure to visit
//all surfels
{
ok=false;
trace.error() << "Incorrect values at "<<*it<<std::endl;
}
}
trace.endBlock();
nbok += ok ? 1 : 0;
nb++;
trace.info() << "(" << nbok << "/" << nb << ") "
<< "cache == eval" << std::endl;
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")
("radius,r", po::value< double >(), "Kernel radius for IntegralInvariant" )
("threshold,t", po::value< unsigned int >()->default_value(8), "Min size of SCell boundary of an object" )
("minImageThreshold,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 ]minImageThreshold, maxImageThreshold ] )." )
("maxImageThreshold,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 ]minImageThreshold, maxImageThreshold] )." )
("mode,m", po::value< std::string >()->default_value("mean"), "type of output : mean, gaussian, k1, k2, prindir1, prindir2 or normal (default mean)")
("exportOBJ,o", po::value< std::string >(), "Export the scene to specified OBJ/MTL filename (extensions added)." )
("exportDAT,d", po::value<std::string>(), "Export resulting curvature (for mean, gaussian, k1 or k2 mode) in a simple data file each line representing a surfel. ")
("exportOnly", "Used to only export the result without the 3d Visualisation (usefull for scripts)." )
("imageScale,s", po::value<std::vector<double> >()->multitoken(), "scaleX, scaleY, scaleZ: re sample the source image according with a grid of size 1.0/scale (usefull to compute curvature on image defined on anisotropic grid). Set by default to 1.0 for the three axis. ")
("normalization,n", "When exporting to OBJ, performs a 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.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("radius"))){
missingParam("--radius");
neededArgsGiven=false;
}
bool normalization = false;
if (parseOK && vm.count("normalization"))
normalization = true;
std::string mode;
if( parseOK )
mode = vm["mode"].as< std::string >();
if ( parseOK && ( mode.compare("gaussian") != 0 ) && ( mode.compare("mean") != 0 ) &&
( mode.compare("k1") != 0 ) && ( mode.compare("k2") != 0 ) &&
( mode.compare("prindir1") != 0 ) && ( mode.compare("prindir2") != 0 ) && ( mode.compare("normal") != 0 ))
{
parseOK = false;
trace.error() << " The selected mode ("<<mode << ") is not defined."<<std::endl;
}
#ifndef WITH_VISU3D_QGLVIEWER
bool enable_visu = false;
#else
bool enable_visu = !vm.count("exportOnly"); ///<! Default QGLViewer viewer. Disabled if exportOnly is set.
#endif
bool enable_obj = vm.count("exportOBJ"); ///<! Export to a .obj file.
bool enable_dat = vm.count("exportDAT"); ///<! Export to a .dat file.
if( !enable_visu && !enable_obj && !enable_dat )
{
#ifndef WITH_VISU3D_QGLVIEWER
trace.error() << "You should specify what you want to export with --export and/or --exportDat." << std::endl;
#else
trace.error() << "You should specify what you want to export with --export and/or --exportDat, or remove --exportOnly." << std::endl;
#endif
neededArgsGiven = false;
}
if(!neededArgsGiven || !parseOK || vm.count("help") || argc <= 1 )
{
trace.info()<< "Visualisation of 3d curvature from .vol file using curvature from Integral Invariant" <<std::endl
<< general_opt << "\n"
<< "Basic usage: "<<std::endl
<< "\t3dCurvatureViewer -i file.vol --radius 5 --mode mean"<<std::endl
<< std::endl
<< "Below are the different available modes: " << std::endl
<< "\t - \"mean\" for the mean curvature" << std::endl
<< "\t - \"gaussian\" for the Gaussian curvature" << std::endl
<< "\t - \"k1\" for the first principal curvature" << std::endl
<< "\t - \"k2\" for the second principal curvature" << std::endl
<< "\t - \"prindir1\" for the first principal curvature direction" << std::endl
<< "\t - \"prindir2\" for the second principal curvature direction" << std::endl
<< "\t - \"normal\" for the normal vector" << std::endl
<< std::endl;
return 0;
}
unsigned int threshold = vm["threshold"].as< unsigned int >();
int minImageThreshold = vm["minImageThreshold"].as< int >();
int maxImageThreshold = vm["maxImageThreshold"].as< int >();
double h = 1.0;
std::string export_obj_filename;
std::string export_dat_filename;
if( enable_obj )
{
export_obj_filename = vm["exportOBJ"].as< std::string >();
if( export_obj_filename.find(".obj") == std::string::npos )
{
std::ostringstream oss;
oss << export_obj_filename << ".obj" << std::endl;
export_obj_filename = oss.str();
}
}
if( enable_dat )
{
export_dat_filename = vm["exportDAT"].as<std::string>();
}
double re_convolution_kernel = vm["radius"].as< double >();
std::vector< double > aGridSizeReSample;
if( vm.count( "imageScale" ))
{
std::vector< double> vectScale = vm["imageScale"].as<std::vector<double > >();
if( vectScale.size() != 3 )
{
trace.error() << "The grid size should contains 3 elements" << std::endl;
return 0;
}
else
{
aGridSizeReSample.push_back(1.0/vectScale.at(0));
aGridSizeReSample.push_back(1.0/vectScale.at(1));
aGridSizeReSample.push_back(1.0/vectScale.at(2));
}
}
else
{
aGridSizeReSample.push_back(1.0);
aGridSizeReSample.push_back(1.0);
aGridSizeReSample.push_back(1.0);
}
// Construction of the shape from vol file
typedef Z3i::Space::RealPoint RealPoint;
typedef Z3i::Point Point;
typedef ImageSelector< Z3i::Domain, int>::Type Image;
typedef DGtal::functors::BasicDomainSubSampler< HyperRectDomain<SpaceND<3, int> >,
DGtal::int32_t, double > ReSampler;
typedef DGtal::ConstImageAdapter<Image, Image::Domain, ReSampler,
Image::Value, DGtal::functors::Identity > SamplerImageAdapter;
typedef IntervalForegroundPredicate< SamplerImageAdapter > ImagePredicate;
typedef BinaryPointPredicate<DomainPredicate<Image::Domain>, ImagePredicate, AndBoolFct2 > Predicate;
typedef Z3i::KSpace KSpace;
typedef KSpace::SCell SCell;
typedef KSpace::Cell Cell;
trace.beginBlock("Loading the file");
std::string filename = vm["input"].as< std::string >();
Image image = GenericReader<Image>::import( filename );
PointVector<3,int> shiftVector3D( 0 ,0, 0 );
DGtal::functors::BasicDomainSubSampler< HyperRectDomain< SpaceND< 3, int > >,
DGtal::int32_t, double > reSampler(image.domain(),
aGridSizeReSample, shiftVector3D);
const functors::Identity identityFunctor{};
SamplerImageAdapter sampledImage ( image, reSampler.getSubSampledDomain(), reSampler, identityFunctor );
ImagePredicate predicateIMG = ImagePredicate( sampledImage, minImageThreshold, maxImageThreshold );
DomainPredicate<Z3i::Domain> domainPredicate( sampledImage.domain() );
AndBoolFct2 andF;
Predicate predicate(domainPredicate, predicateIMG, andF );
Z3i::Domain domain = sampledImage.domain();
Z3i::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< Z3i::KSpace::dimension > Sadj( true );
trace.endBlock();
// Viewer settings
// Extraction of components
typedef KSpace::SurfelSet SurfelSet;
typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels;
typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface;
trace.beginBlock("Extracting surfaces");
std::vector< std::vector<SCell > > vectConnectedSCell;
Surfaces<KSpace>::extractAllConnectedSCell(vectConnectedSCell,K, Sadj, predicate, false);
std::ofstream outDat;
if( enable_dat )
{
trace.info() << "Exporting curvature as dat file: "<< export_dat_filename <<std::endl;
outDat.open( export_dat_filename.c_str() );
outDat << "# data exported from 3dCurvatureViewer implementing the II curvature estimator (Coeurjolly, D.; Lachaud, J.O; Levallois, J., (2013). Integral based Curvature"
<< " Estimators in Digital Geometry. DGCI 2013.) " << std::endl;
outDat << "# format: surfel coordinates (in Khalimsky space) curvature: "<< mode << std::endl;
}
trace.info()<<"Number of components= "<<vectConnectedSCell.size()<<std::endl;
trace.endBlock();
if( vectConnectedSCell.size() == 0 )
{
trace.error()<< "No surface component exists. Please check the vol file threshold parameter.";
trace.info()<<std::endl;
exit(2);
}
#ifdef WITH_VISU3D_QGLVIEWER
QApplication application( argc, argv );
typedef Viewer3D<Z3i::Space, Z3i::KSpace> Viewer;
#endif
typedef Board3D<Z3i::Space, Z3i::KSpace> Board;
#ifdef WITH_VISU3D_QGLVIEWER
Viewer viewer( K );
#endif
Board board( K );
#ifdef WITH_VISU3D_QGLVIEWER
if( enable_visu )
{
viewer.show();
}
#endif
for( unsigned int i = 0; i<vectConnectedSCell.size(); ++i )
{
if( vectConnectedSCell[i].size() <= threshold )
{
continue;
}
MySetOfSurfels aSet(K, Sadj);
for( std::vector<SCell>::const_iterator it = vectConnectedSCell.at(i).begin();
it != vectConnectedSCell.at(i).end();
++it )
{
aSet.surfelSet().insert( *it);
}
MyDigitalSurface digSurf( aSet );
typedef DepthFirstVisitor<MyDigitalSurface> Visitor;
typedef GraphVisitorRange< Visitor > VisitorRange;
typedef VisitorRange::ConstIterator SurfelConstIterator;
VisitorRange range( new Visitor( digSurf, *digSurf.begin() ) );
SurfelConstIterator abegin = range.begin();
SurfelConstIterator aend = range.end();
VisitorRange range2( new Visitor( digSurf, *digSurf.begin() ) );
SurfelConstIterator abegin2 = range2.begin();
trace.beginBlock("Curvature computation on a component");
if( ( mode.compare("gaussian") == 0 ) || ( mode.compare("mean") == 0 )
|| ( mode.compare("k1") == 0 ) || ( mode.compare("k2") == 0 ))
{
typedef double Quantity;
std::vector< Quantity > results;
std::back_insert_iterator< std::vector< Quantity > > resultsIterator( results );
if ( mode.compare("mean") == 0 )
{
typedef functors::IIMeanCurvature3DFunctor<Z3i::Space> MyIICurvatureFunctor;
typedef IntegralInvariantVolumeEstimator<Z3i::KSpace, Predicate, MyIICurvatureFunctor> MyIIEstimator;
MyIICurvatureFunctor functor;
functor.init( h, re_convolution_kernel );
MyIIEstimator estimator( functor );
estimator.attach( K, predicate );
estimator.setParams( re_convolution_kernel/h );
estimator.init( h, abegin, aend );
estimator.eval( abegin, aend, resultsIterator );
}
else if ( mode.compare("gaussian") == 0 )
{
typedef functors::IIGaussianCurvature3DFunctor<Z3i::Space> MyIICurvatureFunctor;
typedef IntegralInvariantCovarianceEstimator<Z3i::KSpace, Predicate, MyIICurvatureFunctor> MyIIEstimator;
MyIICurvatureFunctor functor;
functor.init( h, re_convolution_kernel );
MyIIEstimator estimator( functor ); estimator.attach( K,
predicate ); estimator.setParams( re_convolution_kernel/h );
estimator.init( h, abegin, aend );
estimator.eval( abegin, aend, resultsIterator );
}
else if ( mode.compare("k1") == 0 )
{
typedef functors::IIFirstPrincipalCurvature3DFunctor<Z3i::Space> MyIICurvatureFunctor;
typedef IntegralInvariantCovarianceEstimator<Z3i::KSpace, Predicate, MyIICurvatureFunctor> MyIIEstimator;
MyIICurvatureFunctor functor;
functor.init( h, re_convolution_kernel );
MyIIEstimator estimator( functor );
estimator.attach( K, predicate );
estimator.setParams( re_convolution_kernel/h );
estimator.init( h, abegin, aend );
estimator.eval( abegin, aend, resultsIterator );
}
else if ( mode.compare("k2") == 0 )
{
typedef functors::IISecondPrincipalCurvature3DFunctor<Z3i::Space> MyIICurvatureFunctor;
typedef IntegralInvariantCovarianceEstimator<Z3i::KSpace, Predicate, MyIICurvatureFunctor> MyIIEstimator;
MyIICurvatureFunctor functor;
functor.init( h, re_convolution_kernel );
MyIIEstimator estimator( functor );
estimator.attach( K, predicate );
estimator.setParams( re_convolution_kernel/h );
estimator.init( h, abegin, aend );
estimator.eval( abegin, aend, resultsIterator );
}
trace.endBlock();
// Drawing results
trace.beginBlock("Visualisation");
Quantity min = results[ 0 ];
Quantity max = results[ 0 ];
for ( unsigned int i = 1; i < results.size(); ++i )
{
if ( results[ i ] < min )
{
min = results[ i ];
}
else if ( results[ i ] > max )
{
max = results[ i ];
}
}
trace.info() << "Max value= "<<max<<" min value= "<<min<<std::endl;
ASSERT( min <= max );
typedef GradientColorMap< Quantity > Gradient;
Gradient cmap_grad( min, (max==min)? max+1: max );
cmap_grad.addColor( Color( 50, 50, 255 ) );
cmap_grad.addColor( Color( 255, 0, 0 ) );
cmap_grad.addColor( Color( 255, 255, 10 ) );
#ifdef WITH_VISU3D_QGLVIEWER
if( enable_visu )
{
viewer << SetMode3D((*abegin2).className(), "Basic" );
}
#endif
if( enable_obj )
{
board << SetMode3D((K.unsigns(*abegin2)).className(), "Basic" );
}
for ( unsigned int i = 0; i < results.size(); ++i )
{
#ifdef WITH_VISU3D_QGLVIEWER
if( enable_visu )
{
viewer << CustomColors3D( Color::Black, cmap_grad( results[ i ] ));
viewer << *abegin2;
}
#endif
if( enable_obj )
{
board << CustomColors3D( Color::Black, cmap_grad( results[ i ] ));
board << K.unsigns(*abegin2);
}
if( enable_dat )
{
Point kCoords = K.uKCoords(K.unsigns(*abegin2));
outDat << kCoords[0] << " " << kCoords[1] << " " << kCoords[2] << " " << results[i] << std::endl;
}
++abegin2;
}
}
else
{
typedef Z3i::Space::RealVector Quantity;
std::vector< Quantity > results;
std::back_insert_iterator< std::vector< Quantity > > resultsIterator( results );
if( mode.compare("prindir1") == 0 )
{
typedef functors::IIFirstPrincipalDirectionFunctor<Z3i::Space> MyIICurvatureFunctor;
typedef IntegralInvariantCovarianceEstimator<Z3i::KSpace, Predicate, MyIICurvatureFunctor> MyIIEstimator;
MyIICurvatureFunctor functor;
functor.init( h, re_convolution_kernel );
MyIIEstimator estimator( functor );
estimator.attach( K, predicate );
estimator.setParams( re_convolution_kernel/h );
estimator.init( h, abegin, aend );
estimator.eval( abegin, aend, resultsIterator );
}
else if( mode.compare("prindir2") == 0 )
{
typedef functors::IISecondPrincipalDirectionFunctor<Z3i::Space> MyIICurvatureFunctor;
typedef IntegralInvariantCovarianceEstimator<Z3i::KSpace, Predicate, MyIICurvatureFunctor> MyIIEstimator;
MyIICurvatureFunctor functor;
functor.init( h, re_convolution_kernel );
MyIIEstimator estimator( functor );
estimator.attach( K, predicate );
estimator.setParams( re_convolution_kernel/h );
estimator.init( h, abegin, aend );
estimator.eval( abegin, aend, resultsIterator );
}
else
if( mode.compare("normal") == 0 )
{
typedef functors::IINormalDirectionFunctor<Z3i::Space> MyIICurvatureFunctor;
typedef IntegralInvariantCovarianceEstimator<Z3i::KSpace, Predicate, MyIICurvatureFunctor> MyIIEstimator;
MyIICurvatureFunctor functor;
functor.init( h, re_convolution_kernel );
MyIIEstimator estimator( functor );
estimator.attach( K, predicate );
estimator.setParams( re_convolution_kernel/h );
estimator.init( h, abegin, aend );
estimator.eval( abegin, aend, resultsIterator );
}
///Visualizaton / export
#ifdef WITH_VISU3D_QGLVIEWER
if( enable_visu )
{
viewer << SetMode3D(K.uCell( K.sKCoords(*abegin2) ).className(), "Basic" );
}
#endif
if( enable_obj )
{
board << SetMode3D(K.uCell( K.sKCoords(*abegin2) ).className(), "Basic" );
}
for ( unsigned int i = 0; i < results.size(); ++i )
{
DGtal::Dimension kDim = K.sOrthDir( *abegin2 );
SCell outer = K.sIndirectIncident( *abegin2, kDim);
if ( predicate(embedder(outer)) )
{
outer = K.sDirectIncident( *abegin2, kDim);
}
Cell unsignedSurfel = K.uCell( K.sKCoords(*abegin2) );
#ifdef WITH_VISU3D_QGLVIEWER
if( enable_visu )
{
viewer << CustomColors3D( DGtal::Color(255,255,255,255),
DGtal::Color(255,255,255,255))
<< unsignedSurfel;
}
#endif
if( enable_obj )
{
board << CustomColors3D( DGtal::Color(255,255,255,255),
DGtal::Color(255,255,255,255))
<< unsignedSurfel;
}
if( enable_dat )
{
Point kCoords = K.uKCoords(K.unsigns(*abegin2));
outDat << kCoords[0] << " " << kCoords[1] << " " << kCoords[2] << " "
<< results[i][0] << " " << results[i][1] << " " << results[i][2]
<< std::endl;
}
RealPoint center = embedder( outer );
#ifdef WITH_VISU3D_QGLVIEWER
if( enable_visu )
{
if( mode.compare("prindir1") == 0 )
{
viewer.setLineColor( AXIS_COLOR_BLUE );
}
else if( mode.compare("prindir2") == 0 )
{
viewer.setLineColor( AXIS_COLOR_RED );
}
else if( mode.compare("normal") == 0 )
{
viewer.setLineColor( AXIS_COLOR_GREEN );
}
viewer.addLine (
RealPoint(
center[0] - 0.5 * results[i][0],
center[1] - 0.5 * results[i][1],
center[2] - 0.5 * results[i][2]
),
RealPoint(
center[0] + 0.5 * results[i][0],
center[1] + 0.5 * results[i][1],
center[2] + 0.5 * results[i][2]
),
AXIS_LINESIZE );
}
#endif
if( enable_obj )
{
if( mode.compare("prindir1") == 0 )
{
board.setFillColor( AXIS_COLOR_BLUE );
}
else if( mode.compare("prindir2") == 0 )
{
board.setFillColor( AXIS_COLOR_RED );
}
else if( mode.compare("normal") == 0 )
{
board.setFillColor( AXIS_COLOR_GREEN );
}
board.addCylinder (
RealPoint(
center[0] - 0.5 * results[i][0],
center[1] - 0.5 * results[i][1],
center[2] - 0.5 * results[i][2]),
RealPoint(
center[0] + 0.5 * results[i][0],
center[1] + 0.5 * results[i][1],
center[2] + 0.5 * results[i][2]),
0.2 );
}
++abegin2;
}
}
trace.endBlock();
}
#ifdef WITH_VISU3D_QGLVIEWER
if( enable_visu )
{
viewer << Viewer3D<>::updateDisplay;
}
#endif
if( enable_obj )
{
trace.info()<< "Exporting object: " << export_obj_filename << " ...";
board.saveOBJ(export_obj_filename,normalization);
trace.info() << "[done]" << std::endl;
}
if( enable_dat )
{
outDat.close();
}
#ifdef WITH_VISU3D_QGLVIEWER
if( enable_visu )
{
return application.exec();
}
#endif
return 0;
}
int main( int argc, char** argv )
{
const double h = 1;
const double radiusBall = 12.0;
const double radiusII = 6;
const double trueAreaSurface = 4.0*M_PI*radiusBall*radiusBall;
trace.beginBlock( "Make parametric shape..." );
typedef Ball3D< Z3i::Space > Shape;
Z3i::RealPoint center( 0.0, 0.0, 0.0 );
Shape ball( center, radiusBall );
trace.endBlock();
trace.beginBlock( "Make digital shape..." );
typedef GaussDigitizer< Z3i::Space, Shape > DigitalShape;
typedef DigitalShape::Domain Domain;
DigitalShape digitalBall;
digitalBall.attach( ball );
digitalBall.init( ball.getLowerBound() - Z3i::RealPoint( 1.0, 1.0, 1.0 ),
ball.getUpperBound() + Z3i::RealPoint( 1.0, 1.0, 1.0 ),
h );
Domain domain = digitalBall.getDomain();
Z3i::KSpace kspace;
kspace.init( domain.lowerBound(), domain.upperBound(), true );
trace.endBlock();
trace.beginBlock( "Make digital surface..." );
typedef LightImplicitDigitalSurface< Z3i::KSpace, DigitalShape > LightDigitalSurface;
typedef DigitalSurface< LightDigitalSurface > DigitalSurface;
typedef DepthFirstVisitor< DigitalSurface > DepthFirstVisitor;
typedef GraphVisitorRange< DepthFirstVisitor > GraphVisitorRange;
typedef GraphVisitorRange::ConstIterator SurfelConstIterator;
typedef Z3i::KSpace::Surfel Surfel;
Surfel bel = Surfaces< Z3i::KSpace >::findABel( kspace, digitalBall, 500 );
SurfelAdjacency< Z3i::KSpace::dimension > surfelAdjacency( true );
LightDigitalSurface lightDigitalSurface( kspace, digitalBall, surfelAdjacency, bel );
DigitalSurface digitalSurface( lightDigitalSurface );
GraphVisitorRange graphVisitorRange( new DepthFirstVisitor( digitalSurface, *digitalSurface.begin() ) );
SurfelConstIterator sbegin = graphVisitorRange.begin();
SurfelConstIterator send = graphVisitorRange.end();
std::vector< Surfel > v_border;
while( sbegin != send )
{
v_border.push_back( *sbegin );
++sbegin;
}
trace.endBlock();
trace.beginBlock( "Computation with normal estimation ..." );
typedef IIGeometricFunctors::IINormalDirectionFunctor< Z3i::Space > NormalFunctor;
typedef IntegralInvariantCovarianceEstimator< Z3i::KSpace, DigitalShape, NormalFunctor > IINormalEstimator;
NormalFunctor normalFunctor;
IINormalEstimator normalEstimator( normalFunctor );
normalEstimator.attach( kspace, digitalBall );
normalEstimator.setParams( radiusII / h );
normalEstimator.init( h, v_border.begin(), v_border.end() );
double areaSurfaceEstimated = 0.0;
for( unsigned int i_position = 0; i_position < v_border.size(); ++i_position )
{
Z3i::RealPoint normalEstimated = normalEstimator.eval( &(v_border[i_position]) );
Z3i::RealPoint normalSurfel = kspace.sKCoords( kspace.sDirectIncident( v_border[i_position], kspace.sOrthDir( v_border[i_position] ))) - kspace.sKCoords( v_border[i_position] );
normalEstimated = normalEstimated.getNormalized();
areaSurfaceEstimated += std::abs( normalEstimated.dot( normalSurfel )) * h * h;
}
trace.endBlock();
trace.info() << "Area Surface estimated : " << areaSurfaceEstimated << std::endl;
trace.info() << "True areaSurface : " << trueAreaSurface << std::endl;
trace.info() << "Ratio : " << areaSurfaceEstimated / trueAreaSurface << std::endl;
return 0;
}
int main( int narg, char **argv )
{
trace.beginBlock("Identifying the domain.");
Z3i::Domain domain = scene_dimensions( argv[1] ) ;
if ( domain.lowerBound() == domain.upperBound() ) {
trace.error()<<"Invalid domain ("<<__FILE__<<")"<<std::endl;
return -1 ;
}
trace.endBlock() ;
trace.beginBlock("Reading slices.");
Z3i::DigitalSet set3d( domain ) ;
SetPredicate<Z3i::DigitalSet> set3dPredicate( set3d ) ;
for ( uint depth = 0 ; depth < domain.upperBound().at(2) ; depth++ )
process_slice( argv[1], depth, set3d ) ;
trace.endBlock() ;
if ( 0) {
try {
Gray3DImage aImage( domain );
for ( Z3i::Domain::ConstIterator pt = domain.begin() ; pt != domain.end() ; pt++ )
aImage.setValue( (*pt), 255 ) ;
boost::filesystem::path pathvolname = argv[1] ;
pathvolname /= "obj.vol" ;
if ( ! DGtal::VolWriter< Gray3DImage, GrayColorMap >::exportVol ( pathvolname.string(), aImage, 0, 255 ) )
{
trace.error() <<"Can not export data (generated 3D object)"<<std::endl;
return -4 ;
} else {
trace.info()<<"export data to "<<pathvolname.string()<<std::endl;
}
pathvolname = argv[1] ;
pathvolname /= "obj.pgm3d" ;
if ( ! PNMWriter<Gray3DImage, GrayColorMap >::exportPGM3D( pathvolname.string(), aImage, 0, 255 ) )
{
trace.error() <<"Can not export data (generated 3D object)"<<std::endl;
return -4 ;
} else {
trace.info()<<"export data to "<<pathvolname.string()<<std::endl;
}
} catch ( std::exception &e ) {
trace.error() <<"Can not export data (generated 3D object) "<<e.what()<<std::endl;
return -8 ;
}
}
trace.beginBlock( "Decompose the object into connected components." );
{
DGtal::Z3i::Object6_18 scene( DGtal::Z3i::dt6_18, set3d ) ;
std::vector< Z3i::Object6_18 > v_obj ;
back_insert_iterator< std::vector< Z3i::Object6_18 > > it( v_obj ) ;
scene.writeComponents( it ) ;
boost::filesystem::path scenefilename = argv[1] ;
scenefilename /= "scene.pgm3d" ;
IOPgm3d::write( v_obj, scenefilename.string().c_str() ) ;
}
trace.endBlock( );
return -64;
trace.beginBlock( "Construct the Khalimsky space from the image domain." );
Z3i::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();
typedef SurfelAdjacency<Z3i::KSpace::dimension> MySurfelAdjacency;
MySurfelAdjacency surfAdj( true ); // interior in all directions.
trace.beginBlock( "Extracting boundary by tracking from an initial bel." );
Z3i::KSpace::SCellSet boundary;
Z3i::SCell bel = Surfaces<Z3i::KSpace>::findABel( ks, set3dPredicate, 100000 );
Surfaces<Z3i::KSpace>::trackBoundary( boundary, ks, surfAdj, set3dPredicate, bel );
trace.endBlock();
trace.beginBlock( "Displaying surface in Viewer3D." );
QApplication application(narg,argv);
Viewer3D viewer;
viewer.show();
viewer << SetMode3D( boundary.begin()->className(), "") ; //CustomColors3D(Color(250, 0, 0 ), Color( 128, 128, 128 ) );
unsigned long nbSurfels = 0;
for ( Z3i::KSpace::SCellSet::const_iterator it = boundary.begin(), it_end = boundary.end(); it != it_end; ++it, ++nbSurfels )
viewer << ks.uCell( Z3i::Point( (*it).myCoordinates.at(0), (*it).myCoordinates.at(1), (*it).myCoordinates.at(2) ) ) ;
/**
for ( Z3i::KSpace::SCellSet::const_iterator it = boundary.begin(), it_end = boundary.end(); it != it_end; ++it, ++nbSurfels )
viewer << (*it) ;
*/
trace.info() << *boundary.begin()<<std::endl;
viewer << Viewer3D::updateDisplay;
trace.info() << "nb surfels = " << nbSurfels << std::endl;
trace.endBlock();
return application.exec();
}
int main( int argc, char** argv )
{
if ( argc != 4 )
{
trace.error() << "Usage: " << argv[0]
<< " <fileName.vol> <threshold> <re_convolution_kernel>" << std::endl;
trace.error() << "Example : "<< argv[0] << " Al.150.vol 0 7.39247665" << std::endl;
return 0;
}
trace.beginBlock ( "Example IntegralInvariantCurvature3D" );
trace.info() << "Args:";
for ( int i = 0; i < argc; ++i )
trace.info() << " " << argv[ i ];
trace.info() << endl;
double h = 1.0;
unsigned int threshold = atoi( argv[ 2 ] );
/// Construction of the shape from vol file
typedef ImageSelector< Z3i::Domain, unsigned int >::Type Image;
typedef SimpleThresholdForegroundPredicate< Image > ImagePredicate;
typedef Z3i::KSpace::Surfel Surfel;
typedef LightImplicitDigitalSurface< Z3i::KSpace, ImagePredicate > MyLightImplicitDigitalSurface;
typedef DigitalSurface< MyLightImplicitDigitalSurface > MyDigitalSurface;
std::string filename = argv[1];
Image image = VolReader<Image>::importVol( filename );
ImagePredicate predicate = ImagePredicate( image, threshold );
Z3i::Domain domain = image.domain();
Z3i::KSpace KSpaceShape;
bool space_ok = KSpaceShape.init( domain.lowerBound(), domain.upperBound(), true );
if (!space_ok)
{
trace.error() << "Error in the Khalimsky space construction."<<std::endl;
return 2;
}
SurfelAdjacency< Z3i::KSpace::dimension > SAdj( true );
Surfel bel = Surfaces< Z3i::KSpace >::findABel( KSpaceShape, predicate, 100000 );
MyLightImplicitDigitalSurface LightImplDigSurf( KSpaceShape, predicate, SAdj, bel );
MyDigitalSurface digSurf( LightImplDigSurf );
typedef DepthFirstVisitor< MyDigitalSurface > Visitor;
typedef GraphVisitorRange< Visitor > VisitorRange;
typedef VisitorRange::ConstIterator SurfelConstIterator;
VisitorRange range( new Visitor( digSurf, *digSurf.begin() ) );
SurfelConstIterator abegin = range.begin();
SurfelConstIterator aend = range.end();
typedef ImageToConstantFunctor< Image, ImagePredicate > MyPointFunctor;
MyPointFunctor pointFunctor( &image, &predicate, 1 );
/// Integral Invariant stuff
//! [IntegralInvariantUsage]
double re_convolution_kernel = atof(argv[3]);
typedef FunctorOnCells< MyPointFunctor, Z3i::KSpace > MyCellFunctor;
typedef IntegralInvariantGaussianCurvatureEstimator< Z3i::KSpace, MyCellFunctor > MyCurvatureEstimator; // Gaussian curvature estimator
MyCellFunctor functor ( pointFunctor, KSpaceShape ); // Creation of a functor on Cells, returning true if the cell is inside the shape
MyCurvatureEstimator estimator ( KSpaceShape, functor );
estimator.init( h, re_convolution_kernel ); // Initialisation for a given Euclidean radius of convolution kernel
std::vector< double > results;
back_insert_iterator< std::vector< double > > resultsIterator( results ); // output iterator for results of Integral Invariante curvature computation
estimator.eval ( abegin, aend, resultsIterator ); // Computation
//! [IntegralInvariantUsage]
/// Drawing results
typedef MyCurvatureEstimator::Quantity Quantity;
Quantity min = numeric_limits < Quantity >::max();
Quantity max = numeric_limits < Quantity >::min();
for ( unsigned int i = 0; i < results.size(); ++i )
{
if ( results[ i ] < min )
{
min = results[ i ];
}
else if ( results[ i ] > max )
{
max = results[ i ];
}
}
QApplication application( argc, argv );
Viewer3D<> viewer;
viewer.show();
typedef GradientColorMap< Quantity > Gradient;
Gradient cmap_grad( min, max );
cmap_grad.addColor( Color( 50, 50, 255 ) );
cmap_grad.addColor( Color( 255, 0, 0 ) );
cmap_grad.addColor( Color( 255, 255, 10 ) );
VisitorRange range2( new Visitor( digSurf, *digSurf.begin() ) );
abegin = range2.begin();
for ( unsigned int i = 0; i < results.size(); ++i )
{
viewer << CustomColors3D( Color::Black, cmap_grad( results[ i ] ))
<< *abegin;
++abegin;
}
viewer << Viewer3D<>::updateDisplay;
trace.endBlock();
return application.exec();
}
int main( int argc, char** argv )
{
typedef PointVector<4, double> Point4D;
typedef PointVector<1, int> Point1D;
// 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>(), "input file: sdp (sequence of discrete points with attribute)" )
("noWindows,n", "Don't display Viewer windows." )
("doSnapShotAndExit,d", po::value<std::string>(), "save display snapshot into file." )
("fixMaxColorValue", po::value<double>(), "fix the maximal color value for the scale error display (else the scale is set from the maximal value)" )
("fixMinColorValue", po::value<double>(), "fix the minimal color value for the scale error display (else the scale is set from the minimal value)" )
("labelIndex", po::value<unsigned int>(), "set the index of the label (by default set to 3) " )
("SDPindex", po::value<std::vector <unsigned int> >()->multitoken(), "specify the sdp index (by default 0,1,2).");
bool parseOK=true;
bool cannotStart= false;
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()<< endl;
}
po::notify(vm);
if(parseOK && ! vm.count("input"))
{
trace.error() << " The input file name was not defined" << endl;
cannotStart = true;
}
if( !parseOK || cannotStart || vm.count("help")||argc<=1)
{
trace.info() << "Usage: " << argv[0] << " [input]\n"
<< "Display surfel data from SDP file with color attributes given as scalar interpreted as color."
<< general_opt << "\n";
return 0;
}
Z3i::KSpace K;
string inputFilename = vm["input"].as<std::string>();
std::vector<Point4D> surfelAndScalarInput;
if(vm.count("SDPindex")) {
std::vector<unsigned int > vectIndex = vm["SDPindex"].as<std::vector<unsigned int > >();
if(vectIndex.size()!=4){
trace.error() << "you need to specify the three indexes of vertex." << std::endl;
return 0;
}
surfelAndScalarInput = PointListReader<Point4D>::getPointsFromFile(inputFilename, vectIndex);
}else{
surfelAndScalarInput = PointListReader<Point4D>::getPointsFromFile(inputFilename);
}
Point4D ptLower = surfelAndScalarInput.at(0);
Point4D ptUpper = surfelAndScalarInput.at(0);
getBoundingUpperAndLowerPoint(surfelAndScalarInput, ptLower, ptUpper);
K.init(Z3i::Point(2*ptLower[0]+1, 2*ptLower[1]+1, 2*ptLower[2]+1),
Z3i::Point(2*ptUpper[0]+1, 2*ptUpper[1]+1, 2*ptUpper[2]+1), true);
std::vector<Cell> vectSurfelsInput;
// Construction of the set of surfels
for(unsigned int i =0; i<surfelAndScalarInput.size(); i++){
Point4D pt4d = surfelAndScalarInput.at(i);
Cell c = K.uCell(Z3i::Point(pt4d[0], pt4d[1], pt4d[2]));
vectSurfelsInput.push_back(c);
}
CanonicCellEmbedder<KSpace> embeder(K);
std::vector<unsigned int> vectIndexMinToReference;
//-------------------------
// Displaying input with color given from scalar values
QApplication application(argc,argv);
typedef ViewerSnap<> Viewer;
Viewer viewer(K, vm.count("doSnapShotAndExit"));
if(vm.count("doSnapShotAndExit")){
viewer.setSnapshotFileName(QString(vm["doSnapShotAndExit"].as<std::string>().c_str()));
}
viewer.setWindowTitle("3dCompSurfel Viewer");
viewer.show();
viewer.restoreStateFromFile();
double minScalarVal=surfelAndScalarInput.at(0)[3];
double maxScalarVal=surfelAndScalarInput.at(0)[3];
for(unsigned int i=1; i <surfelAndScalarInput.size(); i++){
double scalVal = surfelAndScalarInput.at(i)[3];
if(scalVal < minScalarVal){
minScalarVal = scalVal;
}
if(scalVal > maxScalarVal){
maxScalarVal = scalVal;
}
}
if(vm.count("fixMaxColorValue")){
maxScalarVal = vm["fixMaxColorValue"].as<double>();
}
if(vm.count("fixMinColorValue")){
minScalarVal = vm["fixMinColorValue"].as<double>();
}
GradientColorMap<double> gradientColorMap( minScalarVal, maxScalarVal );
gradientColorMap.addColor( Color(255,0,0,100 ) );
gradientColorMap.addColor( Color(0,255,0,100 ) );
gradientColorMap.addColor( Color(0,0,255,100 ) );
bool useGrad = minScalarVal!=maxScalarVal;
viewer << SetMode3D(vectSurfelsInput.at(0).className(), "Basic");
for(unsigned int i=0; i <surfelAndScalarInput.size(); i++){
double valInput = surfelAndScalarInput.at(i)[3];
if(useGrad){
viewer.setFillColor(gradientColorMap(valInput));
}else{
viewer.setFillColor(Color::White);
}
viewer << vectSurfelsInput.at(i);
}
viewer << Viewer::updateDisplay;
if(vm.count("doSnapShotAndExit")){
// Appy cleaning just save the last snap
std::string name = vm["doSnapShotAndExit"].as<std::string>();
std::string extension = name.substr(name.find_last_of(".") + 1);
std::string basename = name.substr(0, name.find_last_of("."));
for(int i=0; i< viewer.snapshotCounter()-1; i++){
std::stringstream s;
s << basename << "-"<< setfill('0') << setw(4)<< i << "." << extension;
trace.info() << "erase temp file: " << s.str() << std::endl;
remove(s.str().c_str());
}
std::stringstream s;
s << basename << "-"<< setfill('0') << setw(4)<< viewer.snapshotCounter()-1 << "." << extension;
rename(s.str().c_str(), name.c_str());
return 0;
}
if(vm.count("noWindows")){
return 0;
}else{
return application.exec();
}
}
int main(int argc, char** argv)
{
QApplication application(argc,argv);
Point ptL(-1, -1, -1);
Point ptU(3, 3, 1);
Domain d (ptL, ptU);
Point pt0(0,0, 0);
Point pt1(1,0,0 );
Point pt2(0,1,0 );
Point pt3(2,1,0);
Point pt4(1,2,0);
Point pt5(2,2,0);
DigitalSet aSet( d );
aSet.insert(pt0);
aSet.insert(pt1);
aSet.insert(pt2);
aSet.insert(pt3);
aSet.insert(pt4);
std::set<SCell> bdry;
Z3i::KSpace ks;
ks.init( ptL, ptU, true );
SCell v0 = ks.sSpel(pt0, KSpace::POS);
SCell v1 = ks.sSpel(pt1, KSpace::POS);
SCell v2 = ks.sSpel(pt2, KSpace::POS);
SCell v3 = ks.sSpel(pt3, KSpace::POS);
SCell v4 = ks.sSpel(pt4, KSpace::POS);
Viewer3D viewerAdjSRC;
viewerAdjSRC.show();
viewerAdjSRC << d;
viewerAdjSRC << SetMode3D( v0.className(), "Illustration" );
viewerAdjSRC << pt0 << pt1 << pt2 << pt3 << pt4;
Viewer3D viewerAdj;
viewerAdj.show();
viewerAdj << SetMode3D( v0.className(), "Illustration" );
viewerAdj << v0 << v1 << v2 << v3 << v4;
Viewer3D viewerAdj2;
viewerAdj2.show();
// Extracting the surface boundary of the shape
Surfaces<Z3i::KSpace>::sMakeBoundary( bdry, ks, aSet, ks.lowerBound(), ks.upperBound() );
SurfelAdjacency<Z3i::KSpace::dimension> sAdjInt( true );
SurfelAdjacency<Z3i::KSpace::dimension> sAdjExt( false );
viewerAdj << SetMode3D( v0.className(), "Illustration" );
viewerAdj << v0 << v1 << v2 << v3 << v4;
//Displaying the boundary bels
std::set<SCell>::iterator itBoundary;
int i=0;
for(itBoundary= bdry.begin(); itBoundary!= bdry.end(); itBoundary++){
viewerAdj << *itBoundary;
}
viewerAdj2 << SetMode3D( v0.className(), "Illustration" );
viewerAdj2 << v0 << v1 << v2 << v3 << v4;
itBoundary = bdry.begin();
for (int i =0; i<17; i++) itBoundary++;
SCell surfel = *itBoundary;
// Defining surfel Neighborhood given an surfel Adjacency
SurfelNeighborhood<KSpace> sNeighInt;
sNeighInt.init( &ks, &sAdjInt, surfel );
SurfelNeighborhood<KSpace> sNeighExt;
sNeighExt.init( &ks, &sAdjExt, surfel );
SCell surfelFollowerInt;
SCell surfelFollowerExt;
sNeighInt.getAdjacentOnDigitalSet ( surfelFollowerInt, aSet, *(ks.sDirs(surfel)), true);
sNeighExt.getAdjacentOnDigitalSet ( surfelFollowerExt, aSet, *(ks.sDirs(surfel)), true);
viewerAdj2 << CustomColors3D(Color(220, 220,255),Color(220, 220,255));
viewerAdj2 << surfel;
viewerAdj2 << CustomColors3D(Color(250, 0,0),Color(250, 0,0));
viewerAdj2 << surfelFollowerInt;
viewerAdj2 << CustomColors3D(Color(0, 250,0),Color(0, 250,0));
viewerAdj2 << surfelFollowerExt;
// Extraction of contour
std::set<SCell> aContour1;
Surfaces<Z3i::KSpace>::trackBoundary( aContour1, ks,
sAdjExt,
aSet, surfel );
Viewer3D viewerContour1;
viewerContour1.show();
viewerContour1 << SetMode3D( v0.className(), "Illustration" );
viewerContour1 << v0 << v1 << v2 << v3 << v4;
std::set<SCell>::iterator iterOnContour;
for( iterOnContour= aContour1.begin(); iterOnContour != aContour1.end(); iterOnContour++){
if(*iterOnContour != surfel){
viewerContour1 << CustomColors3D(Color(0, 250,0),Color(0, 250,0));
viewerContour1<< *iterOnContour;
}else{
viewerContour1 << CustomColors3D(Color(220, 220,255),Color(220, 220,255));
viewerContour1<< *iterOnContour;
}
}
// Extraction of contour
std::set<SCell> aContour2;
Surfaces<Z3i::KSpace>::trackBoundary( aContour2, ks,
sAdjInt,
aSet, surfel );
Viewer3D viewerContour2;
viewerContour2.show();
viewerContour2 << SetMode3D( v0.className(), "Illustration" );
viewerContour2 << v0 << v1 << v2 << v3 << v4;
std::set<SCell>::iterator iterOnContour2;
for( iterOnContour2= aContour2.begin(); iterOnContour2 != aContour2.end(); iterOnContour2++){
if(*iterOnContour2 != surfel){
viewerContour2 << CustomColors3D(Color(250, 0,0),Color(250, 0,0));
viewerContour2<< *iterOnContour2;
}else{
viewerContour2 << CustomColors3D(Color(220, 220,255),Color(220, 220,255));
viewerContour2<< *iterOnContour2;
}
}
viewerAdjSRC << Viewer3D:: updateDisplay;
viewerAdj<< Viewer3D::updateDisplay;
viewerAdj2<< Viewer3D::updateDisplay;
viewerContour1 << Viewer3D::updateDisplay;
viewerContour2 << Viewer3D::updateDisplay;
return application.exec();
return 0;
}