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;
}