// Return the number of connected components from the graph containing all edges and give, for each vertex, which component it belongs to (use BOOST GRAPH LIBRAIRY)
int EdgeSetTopologyContainer::getNumberConnectedComponents(sofa::helper::vector<unsigned int>& components)
{
using namespace boost;
typedef adjacency_list <vecS, vecS, undirectedS> Graph;
Graph G;
helper::ReadAccessor< Data< sofa::helper::vector<Edge> > > m_edge = d_edge;
for (size_t k=0; k<m_edge.size(); ++k)
{
add_edge(m_edge[k][0], m_edge[k][1], G);
}
components.resize(num_vertices(G));
int num = (int) connected_components(G, &components[0]);
return num;
}
void Rendering::Mesh::init(FEMMesh* inputMesh)
{
if (inputMesh)
{
LOGI("Creating mapping between simulation mesh \"%s\" and surface mesh" ,inputMesh->filename.c_str());
static std::string input_filename;
static sofa::helper::vector<Mat3x3d> bases;
static sofa::helper::vector<Vec3d> centers;
static Octree<Vec3d> octree;
const TVecTetra& tetras = inputMesh->tetrahedra;
const TVecCoord& in = inputMesh->positions;
const TVecCoord& out = m_vertices;
d_map_i.resize(out.size());
d_map_f.resize(out.size());
if (input_filename != inputMesh->filename || bases.size() != tetras.size()) // we have to recompute the octree and bases
{
input_filename = inputMesh->filename;
sofa::helper::vector< BBox<Vec3d> > bbox;
bases.resize(tetras.size());
centers.resize(tetras.size());
bbox.resize(tetras.size());
LOGI(" Preparing tetrahedra");
for (unsigned int t=0; t<tetras.size(); ++t)
{
Mat3x3d m, mt;
m[0] = in[tetras[t][1]]-in[tetras[t][0]];
m[1] = in[tetras[t][2]]-in[tetras[t][0]];
m[2] = in[tetras[t][3]]-in[tetras[t][0]];
mt.transpose(m);
bases[t].invert(mt);
centers[t] = (in[tetras[t][0]]+in[tetras[t][1]]+in[tetras[t][2]]+in[tetras[t][3]])*0.25;
bbox[t].add(tetras[t].begin(), tetras[t].end(), in);
}
LOGI(" Building octree");
octree.init(bbox,8,8);
}
LOGI( " Processing vertices" );
int outside = 0;
sofa::helper::vector<Octree<Vec3d>*> cells;
for (unsigned int i=0;i<out.size();i++)
{
Vec3d pos = out[i];
Vec3d coefs;
int index = -1;
double distance = 1e10;
Octree<Vec3d>* cell = octree.findNear(pos);
if (cell)
{
const sofa::helper::vector<int>& elems = cell->elems();
for (unsigned int e = 0; e < elems.size(); e++)
{
unsigned int t = elems[e];
Vec3d v = bases[t] * (pos - in[tetras[t][0]]);
double d = std::max(std::max(-v[0],-v[1]),std::max(-v[2],v[0]+v[1]+v[2]-1));
if (d>0) d = (pos-centers[t]).norm2();
if (d<distance) { coefs = v; distance = d; index = t; }
}
}
if (distance > 0)
{ // pos is outside of the fem mesh, find the nearest tetra
// first let's find at least one tetra that is close, if not already found
if (index >= 0) // we already have a close tetra, we need to look only for closer ones
{
cells.clear();
octree.findAllAround(cells, pos, sqrt(distance)*1.5);
for (unsigned int ci = 0; ci < cells.size(); ++ci)
{
if (cells[ci] == cell) continue; // already processed this cell
const sofa::helper::vector<int>& elems = cells[ci]->elems();
for (unsigned int e = 0; e < elems.size(); e++)
{
unsigned int t = elems[e];
double d = (pos-centers[t]).norm2();
if (d<distance)
{
coefs = bases[t] * (pos - in[tetras[t][0]]);
distance = d; index = t;
}
}
}
}
else
{
// failsafe case (should not happen...), to be sure we do a brute-force search
for (unsigned int t = 0; t < tetras.size(); t++)
{
double d = (pos-centers[t]).norm2();
if (d<distance)
{
coefs = bases[t] * (pos - in[tetras[t][0]]);
distance = d; index = t;
}
}
}
if (index >= 0)
{
//if (verbose >= 1) std::cout << "Surface vertex " << i << " mapped outside of tetra " << index << " with coefs " << coefs << std::endl;
++outside;
}
}
if (index >= 0)
{
//std::cout << "Surface vertex " << i << " mapped from tetra " << index << " with coefs " << coefs << std::endl;
d_map_i[i][0] = tetras[index][0]; d_map_f[i][0] = (float)(1-coefs[0]-coefs[1]-coefs[2]);
d_map_i[i][1] = tetras[index][1]; d_map_f[i][1] = (float)(coefs[0]);
d_map_i[i][2] = tetras[index][2]; d_map_f[i][2] = (float)(coefs[1]);
d_map_i[i][3] = tetras[index][3]; d_map_f[i][3] = (float)(coefs[2]);
}
}
LOGI( "Mapping done: %d - vertices outside of simulation mesh: %d", outside , out.size() );
}
}
void SurfaceMesh::init(FEMMesh* inputMesh)
{
// elements <-> particles table
#ifdef PARALLEL_GATHER
{
const int nbp = positions.size();
const int nbe = triangles.size();
const int nbBp = (nbp + BSIZE-1)/BSIZE;
const int nbBe = (nbe + BSIZE-1)/BSIZE;
// first find number of elements per particle
std::vector<int> p_nbe;
p_nbe.resize(nbp);
for (int eindex = 0; eindex < nbe; ++eindex)
for (int j = 0; j < 3; ++j)
++p_nbe[triangles[eindex][j]];
// then compute max value
nbElemPerVertex = 0;
for (int i=0;i<nbp;++i)
if (p_nbe[i] > nbElemPerVertex) nbElemPerVertex = p_nbe[i];
// finally fill velems array
velems.resize(nbBp*nbElemPerVertex*BSIZE);
p_nbe.clear();
p_nbe.resize(nbp);
for (int eindex = 0; eindex < nbe; ++eindex)
for (int j = 0; j < 3; ++j)
{
int p = triangles[eindex][j];
int num = p_nbe[p]++;
const int block = p / BSIZE;
const int thread = p % BSIZE;
velems[ block * (nbElemPerVertex * BSIZE) +
num * BSIZE + thread ] = 1 + eindex;
}
}
#endif
// FEMMesh -> SurfaceMesh mapping
if (inputMesh)
{
std::cout << "Creating mapping between simulation mesh \"" << inputMesh->filename << "\" and surface mesh \"" << filename << "\"..." << std::endl;
static std::string input_filename;
static sofa::helper::vector<Mat3x3d> bases;
static sofa::helper::vector<Vec3d> centers;
static Octree<Vec3d> octree;
const TVecTetra& tetras = inputMesh->tetrahedra;
const TVecCoord& in = inputMesh->positions;
const TVecCoord& out = positions;
map_i.resize(out.size());
map_f.resize(out.size());
if (input_filename != inputMesh->filename || bases.size() != tetras.size()) // we have to recompute the octree and bases
{
input_filename = inputMesh->filename;
sofa::helper::vector< BBox<Vec3d> > bbox;
bases.resize(tetras.size());
centers.resize(tetras.size());
bbox.resize(tetras.size());
std::cout << " Preparing tetrahedra" << std::endl;
for (unsigned int t=0; t<tetras.size(); ++t)
{
Mat3x3d m, mt;
m[0] = in[tetras[t][1]]-in[tetras[t][0]];
m[1] = in[tetras[t][2]]-in[tetras[t][0]];
m[2] = in[tetras[t][3]]-in[tetras[t][0]];
mt.transpose(m);
bases[t].invert(mt);
centers[t] = (in[tetras[t][0]]+in[tetras[t][1]]+in[tetras[t][2]]+in[tetras[t][3]])*0.25;
bbox[t].add(tetras[t].begin(), tetras[t].end(), in);
}
std::cout << " Building octree" << std::endl;
octree.init(bbox,8,8);
}
std::cout << " Processing vertices" << std::endl;
int outside = 0;
sofa::helper::vector<Octree<Vec3d>*> cells;
for (unsigned int i=0;i<out.size();i++)
{
Vec3d pos = out[i];
Vec3d coefs;
int index = -1;
double distance = 1e10;
Octree<Vec3d>* cell = octree.findNear(pos);
if (cell)
{
const sofa::helper::vector<int>& elems = cell->elems();
for (unsigned int e = 0; e < elems.size(); e++)
{
unsigned int t = elems[e];
Vec3d v = bases[t] * (pos - in[tetras[t][0]]);
double d = std::max(std::max(-v[0],-v[1]),std::max(-v[2],v[0]+v[1]+v[2]-1));
if (d>0) d = (pos-centers[t]).norm2();
if (d<distance) { coefs = v; distance = d; index = t; }
}
}
if (distance > 0)
{ // pos is outside of the fem mesh, find the nearest tetra
// first let's find at least one tetra that is close, if not already found
if (index >= 0) // we already have a close tetra, we need to look only for closer ones
{
cells.clear();
octree.findAllAround(cells, pos, sqrt(distance)*1.5);
for (unsigned int ci = 0; ci < cells.size(); ++ci)
{
if (cells[ci] == cell) continue; // already processed this cell
const sofa::helper::vector<int>& elems = cells[ci]->elems();
for (unsigned int e = 0; e < elems.size(); e++)
{
unsigned int t = elems[e];
double d = (pos-centers[t]).norm2();
if (d<distance)
{
coefs = bases[t] * (pos - in[tetras[t][0]]);
distance = d; index = t;
}
}
}
}
else
{
// failsafe case (should not happen...), to be sure we do a brute-force search
for (unsigned int t = 0; t < tetras.size(); t++)
{
double d = (pos-centers[t]).norm2();
if (d<distance)
{
coefs = bases[t] * (pos - in[tetras[t][0]]);
distance = d; index = t;
}
}
}
if (index >= 0)
{
if (verbose >= 1) std::cout << "Surface vertex " << i << " mapped outside of tetra " << index << " with coefs " << coefs << std::endl;
++outside;
}
}
if (index >= 0)
{
//std::cout << "Surface vertex " << i << " mapped from tetra " << index << " with coefs " << coefs << std::endl;
map_i[i][0] = tetras[index][0]; map_f[i][0] = (float)(1-coefs[0]-coefs[1]-coefs[2]);
map_i[i][1] = tetras[index][1]; map_f[i][1] = (float)(coefs[0]);
map_i[i][2] = tetras[index][2]; map_f[i][2] = (float)(coefs[1]);
map_i[i][3] = tetras[index][3]; map_f[i][3] = (float)(coefs[2]);
}
}
std::cout << "Mapping done: " << outside << " / " << out.size() << " vertices outside of simulation mesh" << std::endl;
}
}