Z3i::DigitalSet linkTwoPointsWithTangents(const Z3i::Point& start,
const Z3i::Point& end,
const Z3i::RealPoint& tStart,
const Z3i::RealPoint& tEnd,
const Domain& domain) {
Z3i::DigitalSet aSet(domain);
Z3i::RealPoint vector = tStart;
Z3i::RealPoint current = start;
double initialDistance = Z3i::l2Metric(start, end)/2;
while (Z3i::l2Metric(current, end) > sqrt(3) && Z3i::l2Metric(current, end) <= Z3i::l2Metric(start, end)) {
current += vector;
aSet.insert(current);
double distanceToStart = std::abs(start.norm()- current.norm()) - initialDistance;
if (distanceToStart < 0)
distanceToStart = 1;
double distanceToEnd = -std::abs(end.norm()- current.norm()) + initialDistance;
double weightStart = 1/distanceToStart;
double weightEnd;
if (distanceToEnd < 0)
weightEnd = 0;
else
weightEnd = 1/distanceToEnd;
vector = ((weightStart * tStart + weightEnd * tEnd) / (weightStart + weightEnd)).getNormalized();
}
return aSet;
}
void
computerBasicNormalsFromHeightField(const TImage &anHeightMap, TImageVector &vectorField)
{
for(typename TImage::Domain::ConstIterator it = anHeightMap.domain().begin();
it != anHeightMap.domain().end(); it++){
if(anHeightMap.domain().isInside(*it+Z2i::Point::diagonal(1))&&
anHeightMap.domain().isInside(*it-Z2i::Point::diagonal(1))){
double dx = (anHeightMap(*it-Z2i::Point(1,0))-anHeightMap(*it+Z2i::Point(1,0)))/2.0;
double dy = (anHeightMap(*it-Z2i::Point(0,1))-anHeightMap(*it+Z2i::Point(0,1)))/2.0;
Z3i::RealPoint n (dx, dy, 1);
n /= n.norm();
vectorField.setValue(*it,n);
}
}
}
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 argc, char** argv )
{
srand(time(NULL));
QApplication application(argc,argv);
Viewer3D<> viewer;
viewer.show();
typedef Z3i::Space Space;
typedef Z3i::Point Point;
typedef Z3i::RealPoint RealPoint;
typedef Z3i::RealVector RealVector;
typedef HyperRectDomain<Space> Domain;
typedef ExactPredicateLpSeparableMetric<Space, 2> Metric; // L2-metric
typedef EigenDecomposition<3,double> LinearAlgebraTool;
typedef LinearAlgebraTool::Matrix Matrix;
typedef ImageSelector<Domain, unsigned char>::Type Image;
typedef VoronoiCovarianceMeasure<Space,Metric> VCM;
typedef functors::HatPointFunction<Point,double> KernelFunction;
typedef MSTTangent<Point> Tangent;
typedef Pencil<Point, Tangent, RealPoint> Pencil;
typedef DGtal::ConstImageAdapter<Image,Z2i::Domain,DGtal::functors::Point2DEmbedderIn3D<DGtal::Z3i::Domain>, Image::Value, DGtal::functors::Identity> ImageAdapterExtractor;
typedef WeightedPoint<Z3i::Point> WeightedPoint;
typedef WeightedPointCount<Z3i::Point> WeightedPointCount;
typedef Z3i::KSpace KSpace;
typedef functors::NotPointPredicate<Z3i::DigitalSet> NotPointPredicate;
typedef functors::IntervalForegroundPredicate<Image> ThresholdedImage;
typedef DGtal::functors::NotPointPredicate<ThresholdedImage> BackgroundPredicate;
typedef ImplicitDigitalSurface< KSpace, BackgroundPredicate > DigitalSurfaceContainer;
typedef DGtal::DistanceTransformation<Space, ThresholdedImage, Z3i::L2Metric> DTL2;
typedef VoronoiCovarianceMeasureOnDigitalSurface< DigitalSurfaceContainer, Metric, KernelFunction, DTL2 > VCMOnSurface;
typedef KSpace::Surfel Surfel;
typedef Eigen::MatrixXd MatrixXd;
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 (corresponding volume)")
("volume,v", po::value<std::string>(), "vol file (corresponding volume)")
("delta,d", po::value<int>()->default_value(1), "delta")
("radius,R", po::value<int>()->default_value(5), "big radius")
("output,o", po::value<std::string>(), "output skeleton filename")
("thresholdMin,m", po::value<int>()->default_value(0), "minimum threshold for binarization")
("thresholdMax,M", po::value<int>()->default_value(255), "maximum threshold for binarization")
("thresholdFeature,T",po::value<double>()->default_value(0.1), "threshold feature")
;
bool parseOK=true;
po::variables_map vm;
try{
po::store(po::parse_command_line(argc, argv, general_opt), vm);
} catch(const std::exception& ex){
parseOK=false;
trace.info()<< "Error checking program options: "<< ex.what()<< endl;
}
po::notify(vm);
if( !parseOK || vm.count("help")||argc<=1)
{
std::cout << "Usage: " << argv[0] << " [input]\n"
<< "Display volume file as a voxel set by using QGLviewer"<< endl
<< general_opt << "\n";
return 0;
}
if(!vm.count("input"))
{
trace.error() << " The file name was not defined" << endl;
return 0;
}
string outFilename = vm["output"].as<std::string>();
string inputFilename = vm["input"].as<std::string>();
int thresholdMin = vm["thresholdMin"].as<int>();
int thresholdMax = vm["thresholdMax"].as<int>();
int R = vm["radius"].as<int>();
int delta = vm["delta"].as<int>();
string volumeFilename = vm["volume"].as<std::string>();
double thresholdFeature = vm["thresholdFeature"].as<double>();
Image skeleton = VolReader<Image>::importVol(inputFilename);
Image volume = VolReader<Image>::importVol(volumeFilename);
Z3i::DigitalSet setVolume(volume.domain());
Z3i::Domain domainVolume = setVolume.domain();
SetFromImage<Z3i::DigitalSet>::append<Image> (setVolume, volume,
thresholdMin-1, thresholdMax);
Z3i::Object26_6 object(Z3i::dt26_6, setVolume);
Z3i::DigitalSet setSurface = SurfaceUtils::extractSurfaceVoxels(volume, thresholdMin, thresholdMax);
set<WeightedPointCount*, WeightedPointCountComparator<WeightedPointCount> > setVolumeWeighted;
Image volumeBinary(volume.domain());
for (auto it = volume.domain().begin(), ite = volume.domain().end(); it != ite; ++it) {
if (volume(*it) >= thresholdMin && volume(*it) <= thresholdMax)
volumeBinary.setValue(*it, 255);
else
volumeBinary.setValue(*it, 0);
}
Z3i::DigitalSet skeletonPoints(domainVolume);
SetFromImage<Z3i::DigitalSet>::append<Image>(skeletonPoints, skeleton,
thresholdMin-1, thresholdMax);
ThresholdedImage binarizer(volume, thresholdMin-1, thresholdMax);
DTL2 dt(&volume.domain(), &binarizer, &Z3i::l2Metric);
BackgroundPredicate backgroundPredicate(binarizer);
Metric l2;
VCM vcm( R, 1, l2, true );
vcm.init( setVolume.begin(), setVolume.end() );
Domain domain = vcm.domain();
KernelFunction chi( 1.0, 1 );
DTL2::Domain domainDT = dt.domain();
for (auto it = domainDT.begin(), ite = domainDT.end(); it != ite; ++it) {
double value = dt(*it);
if (value > 0) {
setVolumeWeighted.insert(new WeightedPointCount(*it, value));
}
}
double distanceMax = (*setVolumeWeighted.begin())->myWeight;
Z3i::DigitalSet cleanSkeletonPoints = ensureConnexity(skeletonPoints);
vector<Z3i::Point> v = findEndPoints(cleanSkeletonPoints);
// set<Z3i::Point> setV(v.begin(), v.end());
// Z3i::RealPoint normal;
// Z3i::Object26_6 objSkeleton(Z3i::dt26_6, cleanSkeletonPoints);
// map<Z3i::Point, Z3i::RealPoint> mapPointToNormal;
// for (auto it = setV.begin(), ite = setV.end(); it != ite; ++it) {
// Z3i::Point current = *it;
// double radius = dt(current);
// Z3i::DigitalSet set = VCMUtil::computeDiscretePlane(vcm, chi, domainVolume, setVolumeWeighted, current, normal, 0, radius, 100, true);
// vector<Z3i::Point> neighborsCurrent;
// back_insert_iterator<vector<Z3i::Point>> inserter(neighborsCurrent);
// objSkeleton.writeNeighbors(inserter, current);
// if (neighborsCurrent.size() > 0) {
// Z3i::RealPoint dirVector = (current - neighborsCurrent[0]).getNormalized();
// if (dirVector.dot(normal) < 0)
// normal = -normal;
// }
// mapPointToNormal[current] = normal;
// }
// Z3i::DigitalSet junctions(setVolume.domain());
// map<Z3i::Point, Z3i::Point> pairToLink;
// for (auto it = mapPointToNormal.begin(), ite = mapPointToNormal.end(); it != ite; ++it) {
// Z3i::Point point = it->first;
// Z3i::RealPoint normal = it->second;
// Z3i::DigitalSet initialSet(setVolume.domain());
// for (auto itS = setVolume.begin(), itSe = setVolume.end(); itS != itSe; ++itS) {
// if (VCMUtil::abovePlane(*itS, normal, point))
// initialSet.insert(*itS);
// }
// Z3i::DigitalSet currentSet = initialSet;
// for (auto itO = mapPointToNormal.begin(), itOe = mapPointToNormal.end(); itO != itOe; ++itO) {
// Z3i::Point otherPoint = itO->first;
// if (otherPoint == point) continue;
// Z3i::RealPoint otherNormal = itO->second;
// if (VCMUtil::abovePlane(point, otherNormal, otherPoint)) {
// Z3i::DigitalSet newSet(initialSet.domain());
// for (auto itS = currentSet.begin(), itSe = currentSet.end(); itS != itSe; ++itS) {
// if (VCMUtil::abovePlane(*itS, otherNormal, otherPoint))
// newSet.insert(*itS);
// }
// if (newSet.size() < currentSet.size()) {
// currentSet = newSet;
// pairToLink[point] = otherPoint;
// }
// }
// }
// junctions.insert(currentSet.begin(), currentSet.end());
// // viewer << CustomColors3D(Color::Green, Color::Green) << currentSet;
// }
// // for (const auto& pair : pairToLink) {
// // Z3i::Point initial = pair.first;
// // Z3i::Point toLink = pair.second;
// // Z3i::DigitalSet candidates(setVolume.domain());
// // do {
// // candidates.insert(toLink);
// // toLink = pairToLink[toLink];
// // } while (candidates.find(toLink) == candidates.end());
// // for (const auto& sEP : candidates) {
// // for (const auto& sOEP : candidates) {
// // vector<Z3i::Point> link = PointUtil::linkTwoPoints(sEP, sOEP);
// // for (const auto& l : link)
// // viewer << l;
// // }
// // }
// // }
// Z3i::Object26_6 objJunctions(Z3i::dt26_6, junctions);
// vector<Z3i::Object26_6> objectsJunctions;
// back_insert_iterator< std::vector<Z3i::Object26_6> > inserterJ( objectsJunctions );
// objJunctions.writeComponents(inserterJ);
// for (const auto& objJunction : objectsJunctions) {
// Z3i::DigitalSet setJunction = objJunction.pointSet();
// int r = rand() % 256, g = rand() % 256, b = rand() % 256;
// Color c(r,g,b);
// set<Z3i::Point> sameEndPoint;
// for (const auto & p : setV) {
// if (setJunction.find(p) != setJunction.end()){
// viewer << CustomColors3D(c,c) << p;
// sameEndPoint.insert(p);
// }
// }
// if (sameEndPoint.size() == 1) {
// vector<Z3i::DigitalSet> v;
// for (const auto& objOther : objectsJunctions) {
// v.push_back(objOther.pointSet());
// }
// Z3i::DigitalSet closest = closestSet(setJunction, v);
// for (const auto & p : setV) {
// if (closest.find(p) != closest.end()){
// sameEndPoint.insert(p);
// }
// }
// }
// for (const auto& sEP : sameEndPoint) {
// for (const auto& sOEP : sameEndPoint) {
// vector<Z3i::Point> link = PointUtil::linkTwoPoints(sEP, sOEP);
// for (const auto& l : link)
// viewer << l;
// }
// }
// }
// for (auto it = cleanSkeletonPoints.begin(), ite = cleanSkeletonPoints.end(); it != ite; ++it) {
// viewer << CustomColors3D(Color::Red, Color::Red) << *it;
// }
// viewer << Viewer3D<>::updateDisplay;
// application.exec();
// return 0;
KSpace ks;
ks.init( volume.domain().lowerBound(),
volume.domain().upperBound(), true );
SurfelAdjacency<KSpace::dimension> surfAdj( true ); // interior in all directions.
Surfel bel = Surfaces<KSpace>::findABel( ks, backgroundPredicate, 1000000 );
DigitalSurfaceContainer* container =
new DigitalSurfaceContainer( ks, backgroundPredicate, surfAdj, bel, false );
DigitalSurface< DigitalSurfaceContainer > surface( container ); //acquired
//! [DVCM3D-instantiation]
Surfel2PointEmbedding embType = Pointels; // Could be Pointels|InnerSpel|OuterSpel;
KernelFunction chiSurface( 1.0, R ); // hat function with support of radius r
VCMOnSurface* vcm_surface = new VCMOnSurface( surface, embType, R, 1, chiSurface, dt, delta, l2, true);
Z3i::DigitalSet branchingPoints = computeBranchingPartsWithVCMFeature(*vcm_surface, domainVolume, thresholdFeature);
Z3i::Object26_6 obj(Z3i::dt26_6, branchingPoints);
vector<Z3i::Object26_6> objectsBranching;
back_insert_iterator< std::vector<Z3i::Object26_6> > inserterBranching( objectsBranching );
obj.writeComponents(inserterBranching);
Z3i::DigitalSet maxCurvaturePoints(domainVolume);
for (auto it = objectsBranching.begin(), ite = objectsBranching.end(); it != ite; ++it) {
double ratioMax = 0;
Point maximizingCurvaturePoint;
for (auto itPoint = it->pointSet().begin(), itPointE = it->pointSet().end(); itPoint != itPointE; ++itPoint) {
auto lambda = (vcm_surface->mapPoint2ChiVCM()).at(*itPoint).values;
double ratio = lambda[0] / (lambda[0] + lambda[1] + lambda[2]);
if (ratio > ratioMax) {
ratioMax = ratio;
maximizingCurvaturePoint = *itPoint;
}
}
maxCurvaturePoints.insert(maximizingCurvaturePoint);
}
typedef Z3i::Object26_6 ObjectType;
set<Z3i::Point> pointsToProcess;
ObjectType objectImage(Z3i::dt26_6, skeletonPoints);
vector<ObjectType> objects;
back_insert_iterator< std::vector<ObjectType> > inserter( objects );
unsigned int nbConnectedComponents = objectImage.writeComponents(inserter);
trace.info() << nbConnectedComponents << endl;
sort(objects.begin(), objects.end(), [&](ObjectType a, ObjectType b)->bool {
double maxa = 0, maxb = 0;
for (auto it = a.begin(), ite = a.end(); it != ite; ++it) {
if (dt(*it) > maxa)
maxa = dt(*it);
}
for (auto it = b.begin(), ite = b.end(); it != ite; ++it) {
if (dt(*it) > maxb)
maxb = dt(*it);
}
return maxa > maxb;
});
ObjectType reference = *(objects.begin());
objects.erase(objects.begin());
Point closestBranchingCurrent;
trace.beginBlock("Connecting disconnected components");
while (objects.size() > 0) {
trace.progressBar(nbConnectedComponents-objects.size(), nbConnectedComponents);
vector<ObjectType>::iterator minimizingObjectToReference = objects.end();
double distanceMin = numeric_limits<double>::max();
vector<Z3i::Point> points;
Z3i::Point belongingToCurrentObject, belongingToReference;
// for (auto it = objects.begin(), ite = objects.end(); it != ite; ++it) {
ObjectType currentObject = *(objects.begin());
for (auto itCurrentObject = currentObject.pointSet().begin(),
itCurrentObjectE = currentObject.pointSet().end(); itCurrentObject != itCurrentObjectE; ++itCurrentObject) {
for (auto itReference = reference.pointSet().begin(), itReferenceE = reference.pointSet().end(); itReference != itReferenceE; ++itReference) {
Point closestBranchingPoint = *min_element(maxCurvaturePoints.begin(), maxCurvaturePoints.end(), [&](const Point& one, const Point& two) {
return Z3i::l2Metric(one, *itCurrentObject) < Z3i::l2Metric(two, *itCurrentObject);
});
vector<Point> points = PointUtil::linkTwoPoints(*itReference, *itCurrentObject);
bool add = true;
double distanceDT = min(dt(*itCurrentObject), dt(*itReference));
for (auto itP = points.begin(), itPe = points.end(); itP != itPe; ++itP) {
if (Z3i::l2Metric(*itP, closestBranchingPoint)+1 < distanceDT ||
dt(*itP) == 0) {
add = false;
break;
}
}
double distance = Z3i::l2Metric(*itCurrentObject, *itReference);
if (distance < distanceMin && add) {
minimizingObjectToReference = objects.begin();
distanceMin = distance;
belongingToCurrentObject = *itCurrentObject;
belongingToReference = *itReference;
closestBranchingCurrent = closestBranchingPoint;
}
}
}
//}
if (minimizingObjectToReference == objects.end()) {
minimizingObjectToReference = objects.begin();
objects.erase(minimizingObjectToReference);
}
else {
// vector<Point> newPoints = PointUtil::linkTwoPoints(belongingToCurrentObject, belongingToReference);
// Z3i::RealPoint normal = (belongingToReference - belongingToCurrentObject).getNormalized();
// Point current = belongingToCurrentObject;
// Z3i::DigitalSet curve(domain);
// do {
// vector<Point> neighbors;
// back_insert_iterator<vector<Point>> inserter(neighbors);
// MetricAdjacency<Space, 3>::writeNeighbors(inserter, current);
// Z3i::DigitalSet setNeighbors(domain);
// for (auto it = neighbors.begin(), ite = neighbors.end(); it != ite; ++it) {
// if (VCMUtil::abovePlane(*it, normal, current) && curve.find(*it) == curve.end())
// setNeighbors.insert(*it);
// }
// Z3i::Point p = findMaxDTInSet(setNeighbors, dt, current);
// viewer << CustomColors3D(Color::Blue, Color::Blue) << p;
// current = p;
// curve.insert(current);
// } while (VCMUtil::abovePlane(belongingToReference, normal, current));
// viewer << Viewer3D<>::updateDisplay;
// qApp->processEvents();
for (auto it = minimizingObjectToReference->pointSet().begin(), ite = minimizingObjectToReference->pointSet().end();
it != ite; ++it) {
reference.pointSet().insert(*it);
}
double radiusCurrentObject = dt(belongingToCurrentObject) ;
chi = KernelFunction( 1.0, radiusCurrentObject );
vcm.setMySmallR(radiusCurrentObject);
Z3i::RealPoint normalCurrentObject;
VCMUtil::computeDiscretePlane(vcm, chi, domainVolume, setVolumeWeighted,
belongingToCurrentObject, normalCurrentObject,
0, radiusCurrentObject, distanceMax, true);
double radiusReference = dt(belongingToReference);
chi = KernelFunction( 1.0, radiusReference );
vcm.setMySmallR(radiusReference);
Z3i::RealPoint normalReference;
VCMUtil::computeDiscretePlane(vcm, chi, domainVolume, setVolumeWeighted,
belongingToReference, normalReference,
0, radiusReference, distanceMax, true);
Z3i::RealPoint dirVectorCurrent = (belongingToReference - belongingToCurrentObject).getNormalized();
if (normalCurrentObject.dot(dirVectorCurrent) < 0)
normalCurrentObject = -normalCurrentObject;
Z3i::RealPoint dirVectorReference = (belongingToCurrentObject - belongingToReference).getNormalized();
if (normalReference.dot(dirVectorReference) < 0)
normalReference = -normalReference;
vector<Point> newPoints;
// if (Z3i::l2Metric(belongingToReference, belongingToCurrentObject) <= 2 * sqrt(3))
newPoints = PointUtil::linkTwoPoints(belongingToCurrentObject, belongingToReference);
// else
// newPoints = PointUtil::bezierCurve(belongingToCurrentObject, belongingToReference, controlCurrent, controlReference);
vector<Point> computationPoints = newPoints;
extendSubVolume(newPoints, reference.pointSet(), belongingToReference, -normalReference, dt(belongingToReference));
extendSubVolume(newPoints, reference.pointSet(), belongingToCurrentObject, -normalCurrentObject, dt(belongingToCurrentObject));
Z3i::DigitalSet newPointsSet(setVolume.domain());
newPointsSet.insert(newPoints.begin(), newPoints.end());
Z3i::DigitalSet computationVolume = computeBallAroundVector(newPoints, setVolume, dt);
Z3i::DigitalSet restrictedComputationVolume = computeBallAroundVector(computationPoints, setVolume, dt);
int r = rand() % 256, g = rand() % 256, b = rand() % 256;
Color c(r,g,b);
// viewer << CustomColors3D(c,c) << computationVolume;
set<WeightedPointCount*, WeightedPointCountComparator<WeightedPointCount> > subVolumeWeighted;
for (auto it = computationVolume.begin(), ite = computationVolume.end(); it != ite; ++it) {
auto itW = find_if(setVolumeWeighted.begin(), setVolumeWeighted.end(), [&](WeightedPointCount* wpc) {
return (wpc->myPoint == *it);
});
if (itW != setVolumeWeighted.end()) {
subVolumeWeighted.insert(new WeightedPointCount(*(*itW)));
}
}
set<WeightedPointCount*, WeightedPointCountComparator<WeightedPointCount> > subVolumeWeightedComputation;
for (auto it = restrictedComputationVolume.begin(), ite = restrictedComputationVolume.end(); it != ite; ++it) {
auto itW = find_if(setVolumeWeighted.begin(), setVolumeWeighted.end(), [&](WeightedPointCount* wpc) {
return (wpc->myPoint == *it);
});
if (itW != setVolumeWeighted.end()) {
subVolumeWeightedComputation.insert(new WeightedPointCount(*(*itW)));
}
}
Z3i::DigitalSet connectedComponent3D(setVolume.domain());
Z3i::RealPoint realCenter, normalSub;
WeightedPointCount* currentWPC;
double distance = std::numeric_limits<double>::max();
for (auto it = subVolumeWeightedComputation.begin(), ite = subVolumeWeightedComputation.end(); it != ite; ++it) {
double currentDistance = Z3i::l2Metric((*it)->myPoint, belongingToCurrentObject);
if (currentDistance < distance) {
distance = currentDistance;
currentWPC = *it;
}
}
int numberLeft = subVolumeWeightedComputation.size();
while (numberLeft > 0 && (VCMUtil::abovePlane(belongingToReference, normalSub, realCenter))) {
// for (auto it = newPointsSet.begin(), ite = newPointsSet.end(); it != ite; ++it) {
// auto currentPoint = find_if(subVolumeWeighted.begin(), subVolumeWeighted.end(), [&](WeightedPointCount* wpc) {
// return wpc->myPoint == *it;
// });
// if (currentPoint == subVolumeWeighted.end()) continue;
// currentWPC = *currentPoint;
currentWPC->myProcessed = true;
double radius = dt(currentWPC->myPoint);
connectedComponent3D = VCMUtil::computeDiscretePlane(vcm, chi, domainVolume, subVolumeWeighted, currentWPC->myPoint, normalSub, 0, radius, 100, true);
realCenter = Statistics::extractCenterOfMass3D(connectedComponent3D);
Z3i::Point centerOfMass = extractNearestNeighborInSetFromPoint(connectedComponent3D, realCenter);
viewer << CustomColors3D(Color::Blue, Color::Blue) << centerOfMass;
viewer << Viewer3D<>::updateDisplay;
qApp->processEvents();
bool processed = false;
for (auto it = connectedComponent3D.begin(), ite = connectedComponent3D.end(); it != ite; ++it) {
for (auto itS = skeletonPoints.begin(), itSe = skeletonPoints.end(); itS != itSe; ++itS) {
if (*itS == *it)
processed = true;
}
}
if (!processed && Z3i::l2Metric(currentWPC->myPoint, centerOfMass) <= sqrt(3))
skeletonPoints.insert(centerOfMass);
if (normalSub.dot(dirVectorCurrent) < 0)
normalSub = -normalSub;
VCMUtil::markConnectedComponent3D(subVolumeWeightedComputation, connectedComponent3D, 0);
VCMUtil::trackNextPoint(currentWPC, subVolumeWeightedComputation, connectedComponent3D, centerOfMass, normalSub);
numberLeft = count_if(subVolumeWeightedComputation.begin(), subVolumeWeightedComputation.end(),
[&](WeightedPointCount* wpc) {
return (!wpc->myProcessed);
});
if (currentWPC == (*subVolumeWeightedComputation.end()))
break;
}
objects.erase(minimizingObjectToReference);
}
}
trace.endBlock();
delete vcm_surface;
for (auto it = skeletonPoints.begin(), ite = skeletonPoints.end(); it != ite; ++it) {
viewer << CustomColors3D(Color::Red, Color::Red) << *it;
}
for (auto it = setVolume.begin(), ite = setVolume.end(); it != ite; ++it) {
viewer << CustomColors3D(Color(0,0,255,30), Color(0,0,255,30)) << *it;
}
Image outImage(volume.domain());
DGtal::imageFromRangeAndValue(skeletonPoints.begin(), skeletonPoints.end(), outImage, 10);
VolWriter<Image>::exportVol(outFilename, outImage);
viewer << Viewer3D<>::updateDisplay;
application.exec();
return 0;
}