void buildKdTree(KdNode *nodes, float *tmp, Item *items, int n, int depth, int thisNode, int &freeNode) {
KdNode *node = nodes + thisNode;
int keyIndex = depth%2;
if (n==0) {
node->child_node = -1;
return;
}
if (n<2) {
node->child_node = 0;
node->leftBounds[0] = items->bbox[keyIndex][0];
node->leftBounds[1] = items->bbox[keyIndex][1];
*((void**)(node->rightBounds)) = items->data;
if (this->maxDepth<depth)
this->maxDepth = depth;
return;
}
int medianIndex = n/2-1;
for (size_t i=0; i<n; i++)
tmp[i] = items[i].bbox[keyIndex][0];
std::sort(tmp, tmp+n);
float median = tmp[n/2-1];
int l = 0;
int r = n-1;
while (l<r) {
while (l<n && items[l].bbox[keyIndex][0]<=median) l++;
while (r>=0 && items[r].bbox[keyIndex][0]>median) r--;
if (l<r)
std::swap(items[l], items[r]);
}
medianIndex = r;
if (medianIndex==n-1)
medianIndex = n-2;
node->leftBounds[0] = node->rightBounds[0] = FLT_MAX;
node->leftBounds[1] = node->rightBounds[1] = -FLT_MAX;
for (unsigned i=0; i<=medianIndex; i++) {
if (items[i].bbox[keyIndex][0]<node->leftBounds[0])
node->leftBounds[0] = items[i].bbox[keyIndex][0];
if (items[i].bbox[keyIndex][1]>node->leftBounds[1])
node->leftBounds[1] = items[i].bbox[keyIndex][1];
}
for (unsigned i=medianIndex+1; i<n; i++) {
if (items[i].bbox[keyIndex][0]<node->rightBounds[0])
node->rightBounds[0] = items[i].bbox[keyIndex][0];
if (items[i].bbox[keyIndex][1]>node->rightBounds[1])
node->rightBounds[1] = items[i].bbox[keyIndex][1];
}
node->child_node = freeNode;
freeNode += 2;
buildKdTree(nodes, tmp, items, medianIndex+1, depth+1, node->child_node, freeNode);
if (medianIndex<n-1)
buildKdTree(nodes, tmp, items + medianIndex+1, n-medianIndex-1, depth+1,
node->child_node+1, freeNode);
else
nodes[node->child_node+1].child_node = -1;
}
void createKdTree(Item *items, int n) {
this->maxDepth = 0;
this->nodes.resize(std::max(n*4,1));
float *tmp = (float*)malloc(sizeof(float)*n);
int freeNode = 1;
buildKdTree(this->nodes.data(), tmp, items, n, 0, 0, freeNode);
fprintf(stderr, "Created a Kd tree for bounding boxes with %d nodes and depth %d.\n", freeNode, this->maxDepth);
free(tmp);
}
void Centerline::run()
{
double t1 = Cpu();
if (update_needed){
std::ifstream input;
//std::string pattern = FixRelativePath(fileName, "./");
//Msg::StatusBar(true, "Reading TEST '%s'...", pattern.c_str());
//input.open(pattern.c_str());
input.open(fileName.c_str());
if(StatFile(fileName))
Msg::Fatal("Centerline file '%s' does not exist ", fileName.c_str());
importFile(fileName);
buildKdTree();
update_needed = false;
}
if (is_cut) cutMesh();
else{
GFace *gf = current->getFaceByTag(1);
gf->addPhysicalEntity(1);
current->setPhysicalName("wall", 2, 1);//tag 1
current->createTopologyFromMesh();
NV = current->getMaxElementaryNumber(0);
NE = current->getMaxElementaryNumber(1);
NF = current->getMaxElementaryNumber(2);
NR = current->getMaxElementaryNumber(3);
}
//identify the boundary edges by looping over all discreteFaces
std::vector<GEdge*> boundEdges;
double dist_inlet = 1.e6;
GEdge *gin = NULL;
for (int i= 0; i< NF; i++){
GFace *gf = current->getFaceByTag(i+1);
std::list<GEdge*> l_edges = gf->edges();
for(std::list<GEdge*>::iterator it = l_edges.begin(); it != l_edges.end(); it++){
std::vector<GEdge*>::iterator ite = std::find(boundEdges.begin(),
boundEdges.end(), *it);
if (ite != boundEdges.end()) boundEdges.erase(ite);
else boundEdges.push_back(*it);
GVertex *gv = (*it)->getBeginVertex();
SPoint3 pt(gv->x(), gv->y(), gv->z());
double dist = pt.distance(ptin);
if(dist < dist_inlet){
dist_inlet = dist;
gin = *it;
}
}
}
if (is_closed) createClosedVolume(gin, boundEdges);
if (is_extruded) extrudeBoundaryLayerWall(gin, boundEdges);
double t2 = Cpu();
Msg::Info("Centerline operators computed in %g (s) ",t2-t1);
}
double Centerline::operator() (double x, double y, double z, GEntity *ge)
{
if (update_needed){
std::ifstream input;
input.open(fileName.c_str());
if(StatFile(fileName))
Msg::Fatal("Centerline file '%s' does not exist", fileName.c_str());
importFile(fileName);
buildKdTree();
update_needed = false;
}
double xyz[3] = {x,y,z};
//take xyz = closest point on boundary in case we are on the planar in/out faces
//or in the volume
bool isCompound = false;
if(ge){
if (ge->dim() == 2 && ge->geomType() == GEntity::CompoundSurface) isCompound = true;
std::list<GFace*> cFaces;
if (isCompound) cFaces = ((GFaceCompound*)ge)->getCompounds();
if ( ge->dim() == 3 || (ge->dim() == 2 && ge->geomType() == GEntity::Plane) ||
(isCompound && (*cFaces.begin())->geomType() == GEntity::Plane) ){
const int num_neighbours = 1;
ANNidx index[num_neighbours];
ANNdist dist[num_neighbours];
kdtreeR->annkSearch(xyz, num_neighbours, index, dist);
ANNpointArray nodesR = kdtreeR->thePoints();
xyz[0] = nodesR[index[0]][0];
xyz[1] = nodesR[index[0]][1];
xyz[2] = nodesR[index[0]][2];
}
}
const int num_neighbours = 1;
ANNidx index[num_neighbours];
ANNdist dist[num_neighbours];
kdtree->annkSearch(xyz, num_neighbours, index, dist);
double rad = sqrt(dist[0]);
//double cmax, cmin;
//SVector3 dirMax,dirMin;
//cmax = ge->curvatures(SPoint2(u, v),&dirMax, &dirMin, &cmax,&cmin);
//cmax = ge->curvatureMax(SPoint2(u,v));
//double radC = 1./cmax;
double lc = 2*M_PI*rad/nbPoints;
if(!ge) { return rad;}
else return lc;
}
Centerline::Centerline(std::string fileName): kdtree(0), kdtreeR(0)
{
recombine = (CTX::instance()->mesh.recombineAll) || (CTX::instance()->mesh.recombine3DAll);
nbPoints = 25;
hLayer = 0.3;
hSecondLayer = 0.3;
nbElemLayer = 3;
nbElemSecondLayer = 0;
is_cut = 0;
is_closed = 0;
is_extruded = 0;
importFile(fileName);
buildKdTree();
update_needed = false;
}
void MultiObjectSeg::addGraphEdge(PCloudGraph& pcGraph, Sample& smp)
{
IndexType nSize = smp.num_vertices();
unordered_map<IndexType,bool> recordEdges;
buildKdTree(smp);
IndexType gIndex = 0;
const IndexType k = 6;
IndexType neighbours[k];
ScalarType dist[k];
IndexType edNum = 0;
for (; gIndex < nSize; ++ gIndex)
{
downSample->neighbours(gIndex,k,neighbours,dist);
for (IndexType i = 1; i < k; ++i)
{
bool temp = recordEdges[frame_index_to_key(gIndex,neighbours[i]) ];
if (!temp)
{
PCEdgeProperty ep;
ep.index = edNum;
ep.start_ = gIndex;
ep.end_ = neighbours[i];
ep.dist = dist[i];
boost::add_edge(gIndex,neighbours[i],ep,pcGraph);
recordEdges[frame_index_to_key(neighbours[i],gIndex)] = true;
++ edNum;
}
}
}
}
void Centerline::operator() (double x, double y, double z, SMetric3 &metr, GEntity *ge)
{
if (update_needed){
std::ifstream input;
input.open(fileName.c_str());
if(StatFile(fileName))
Msg::Fatal("Centerline file '%s' does not exist", fileName.c_str());
importFile(fileName);
buildKdTree();
update_needed = false;
}
//take xyz = closest point on boundary in case we are on
//the planar IN/OUT FACES or in VOLUME
double xyz[3] = {x,y,z};
bool onTubularSurface = true;
double ds = 0.0;
bool isCompound = (ge->dim() == 2 && ge->geomType() == GEntity::CompoundSurface) ?
true : false;
bool onInOutlets = (ge->geomType() == GEntity::Plane) ? true: false;
std::list<GFace*> cFaces;
if (isCompound) cFaces = ((GFaceCompound*)ge)->getCompounds();
if ( ge->dim() == 3 || (ge->dim() == 2 && ge->geomType() == GEntity::Plane) ||
(isCompound && (*cFaces.begin())->geomType() == GEntity::Plane) ){
onTubularSurface = false;
}
ANNidx index[1];
ANNdist dist[1];
kdtreeR->annkSearch(xyz, 1, index, dist);
if (! onTubularSurface){
ANNpointArray nodesR = kdtreeR->thePoints();
ds = sqrt(dist[0]);
xyz[0] = nodesR[index[0]][0];
xyz[1] = nodesR[index[0]][1];
xyz[2] = nodesR[index[0]][2];
}
ANNidx index2[2];
ANNdist dist2[2];
kdtree->annkSearch(xyz, 2, index2, dist2);
double radMax = sqrt(dist2[0]);
ANNpointArray nodes = kdtree->thePoints();
SVector3 p0(nodes[index2[0]][0], nodes[index2[0]][1], nodes[index2[0]][2]);
SVector3 p1(nodes[index2[1]][0], nodes[index2[1]][1], nodes[index2[1]][2]);
//dir_a = direction along the centerline
//dir_n = normal direction of the disk
//dir_t = tangential direction of the disk
SVector3 dir_a = p1-p0; dir_a.normalize();
SVector3 dir_n(xyz[0]-p0.x(), xyz[1]-p0.y(), xyz[2]-p0.z()); dir_n.normalize();
SVector3 dir_cross = crossprod(dir_a,dir_n); dir_cross.normalize();
// if (ge->dim()==3){
// printf("coucou dim ==3 !!!!!!!!!!!!!!! \n");
// SVector3 d1,d2,d3;
// computeCrossField(x,y,z,d1,d2,d3);
// exit(1);
// }
//find discrete curvature at closest vertex
Curvature& curvature = Curvature::getInstance();
if( !Curvature::valueAlreadyComputed() ) {
Msg::Info("Need to compute discrete curvature");
Curvature::typeOfCurvature type = Curvature::RUSIN;
curvature.computeCurvature(current, type);
}
double curv, cMin, cMax;
SVector3 dMin, dMax;
int isAbs = 1.0;
curvature.vertexNodalValuesAndDirections(vertices[index[0]],&dMax, &dMin, &cMax, &cMin, isAbs);
curvature.vertexNodalValues(vertices[index[0]], curv, 1);
if (cMin == 0) cMin =1.e-12;
if (cMax == 0) cMax =1.e-12;
double rhoMin = 1./cMin;
double rhoMax = 1./cMax;
//double signMin = (rhoMin > 0.0) ? -1.0: 1.0;
//double signMax = (rhoMax > 0.0) ? -1.0: 1.0;
//user-defined parameters
//define h_n, h_t1, and h_t2
double thickness = radMax/3.;
double h_far = radMax/5.;
double beta = (ds <= thickness) ? 1.2 : 2.1; //CTX::instance()->mesh.smoothRatio;
double ddist = (ds <= thickness) ? ds: thickness;
double h_n_0 = thickness/20.;
double h_n = std::min( (h_n_0+ds*log(beta)), h_far);
double betaMin = 10.0;
double betaMax = 3.1;
double oneOverD2_min = 1./(2.*rhoMin*rhoMin*(betaMin*betaMin-1)) *
(sqrt(1+ (4.*rhoMin*rhoMin*(betaMin*betaMin-1))/(h_n*h_n))-1.);
double oneOverD2_max = 1./(2.*rhoMax*rhoMax*(betaMax*betaMax-1)) *
(sqrt(1+ (4.*rhoMax*rhoMax*(betaMax*betaMax-1))/(h_n*h_n))-1.);
double h_t1_0 = sqrt(1./oneOverD2_min);
double h_t2_0 = sqrt(1./oneOverD2_max);
//double h_t1 = h_t1_0*(rhoMin+signMin*ddist)/rhoMin ;
//double h_t2 = h_t2_0*(rhoMax+signMax*ddist)/rhoMax ;
double h_t1 = std::min( (h_t1_0+(ddist*log(beta))), radMax);
double h_t2 = std::min( (h_t2_0+(ddist*log(beta))), h_far);
double dCenter = radMax-ds;
double h_a_0 = 0.5*radMax;
double h_a = h_a_0 - (h_a_0-h_t1_0)/(radMax)*dCenter;
//length between min and max
double lcMin = ((2 * M_PI *radMax) /( 50*nbPoints )); //CTX::instance()->mesh.lcMin;
double lcMax = lcMin*2000.; //CTX::instance()->mesh.lcMax;
h_n = std::max(h_n, lcMin); h_n = std::min(h_n, lcMax);
h_t1 = std::max(h_t1, lcMin); h_t1 = std::min(h_t1, lcMax);
h_t2 = std::max(h_t2, lcMin); h_t2 = std::min(h_t2, lcMax);
//curvature metric
SMetric3 curvMetric, curvMetric1, curvMetric2;
SMetric3 centMetric1, centMetric2, centMetric;
if (onInOutlets){
metr = buildMetricTangentToCurve(dir_n,h_n,h_t2);
}
else {
//on surface and in volume boundary layer
if ( ds < thickness ){
metr = metricBasedOnSurfaceCurvature(dMin, dMax, cMin, cMax, h_n, h_t1, h_t2);
}
//in volume
else {
//curvMetric = metricBasedOnSurfaceCurvature(dMin, dMax, cMin, cMax, h_n, h_t1, h_t2);
metr = SMetric3( 1./(h_a*h_a), 1./(h_n*h_n), 1./(h_n*h_n), dir_a, dir_n, dir_cross);
//metr = intersection_conserveM1_bis(metr, curvMetric);
//metr = intersection_conserveM1(metr,curvMetric);
//metr = intersection_conserve_mostaniso(metr, curvMetric);
//metr = intersection(metr,curvMetric);
}
}
return;
}
