void PrintMatchKeys(string key, const VertexSet& s)
{
vector<string> tokens;
split((char*)key.c_str(), "_", tokens);
if (tokens.size() == 0) {
return;
}
cout << "MATCH,";
vector<int> pivots;
for (int i = 0; i < tokens.size(); i++) {
if (tokens[i].size() > 0) {
int u = atoi(tokens[i].c_str());
cout << GetLabel(gSearch__, u) << ", ";
pivots.push_back(u);
}
}
for (unordered_set<uint64_t>::const_iterator s_it = s.begin();
s_it != s.end(); s_it++) {
cout << GetLabel(gSearch__, *s_it) << ", ";
}
cout << endl;
/*
for (unordered_set<uint64_t>::const_iterator s_it = s.begin();
s_it != s.end(); s_it++) {
for (int j = 0; j < pivots.size(); j++) {
GephiStreamingClient::GetInstance().PostEdge(*s_it, pivots[j]);
}
}
*/
}
void Geometry::Face2Polygon(const TopoDS_Face &f, pcl::PlanarPolygon<PointT>& poly) {
VertexSet vertices;
GetVertices(f,vertices);
PointCloud cloud;
for (VertexSet::iterator it=vertices.begin();it!=vertices.end();++it ){
PointT p;
Vertex2Point(*it,p);
cloud.push_back(p);
}
poly.setContour(cloud);
}
bool Decompress(
const std::vector<unsigned int>& indices,
const std::vector<unsigned int>& normalIndices,
const std::vector<unsigned int>& textureIndices,
const std::vector<Vector3f>& vertices,
const std::vector<Vector3f>& normals,
const std::vector<Vector3f>& textureCoords,
const std::vector<Vector4f>& tangents,
std::vector<Vertex>& outVertices,
std::vector<TriangleFace>& outFaces
) {
VertexSet vertexSet;
unsigned int triangleCount = static_cast<unsigned int>(indices.size()) / TRIANGLE_EDGE_COUNT;
unsigned int index = 0;
unsigned int freeIndex = 0;
Vector3f v1, v2, v3;
Vector3f n1, n2, n3;
Vector3f t1, t2, t3;
TriangleFace face;
Vertex v;
for ( unsigned int i = 0; i < triangleCount; i++ ) {
unsigned int vIndex, nIndex, tIndex;
for ( unsigned int j = 0; j < TRIANGLE_EDGE_COUNT; j++ ) {
vIndex = indices[index + j];
nIndex = normalIndices[index + j];
tIndex = textureIndices[index + j];
v.position = vertices[vIndex];
v.normal = normals[nIndex];
v.textureCoord = textureCoords[tIndex];
VertexSet::const_iterator it = vertexSet.find(v);
if ( it != vertexSet.end() ) {
face.indices[j] = vertexSet.find(v)->second;
}
else {
vertexSet.insert(std::make_pair(v, freeIndex));
face.indices[j] = freeIndex;
outVertices.push_back(v);
freeIndex++;
}
}
outFaces.push_back(face);
index += TRIANGLE_EDGE_COUNT;
}
return true;
}
void ShGraph<G>::vertexHeight(const VertexSet &roots, HeightMap &heights) {
heights.clear();
VertexPairMap<int> dist;
NegativeWeigher<G> weigher;
typename VertexSet::const_iterator U, V;
floydWarshall(weigher, dist);
for(U = verts.begin(); U != verts.end(); ++U) {
for(V = roots.begin(); V != roots.end(); ++V) {
heights[*U] = std::max(heights[*U], -dist(*V, *U));
}
}
}
void Delaunay::Triangulate(const VertexSet& vertices, TriangleSet& output)
{
if (vertices.size() < 3)
{
return;
}
cVertexIterator iterVertex = vertices.begin();
double xMin = iterVertex->GetX();
double yMin = iterVertex->GetY();
double xMax = xMin;
double yMax = yMin;
++iterVertex;
for (; iterVertex != vertices.end(); ++iterVertex)
{
xMax = iterVertex->GetX();
double y = iterVertex->GetY();
if (y < yMin)
{
yMin = y;
}
if (y > yMax)
{
yMax = y;
}
}
double dx = xMax - xMin;
double dy = yMax - yMin;
double ddx = dx * 0.01;
double ddy = dy * 0.01;
xMin -= ddx;
xMax += ddx;
dx += 2 * ddx;
yMin -= ddy;
yMax += ddy;
dy += 2 * ddy;
Vertex vSuper[3];
vSuper[0] = Vertex(xMin - dy * sqrt3 / 3.0, yMin);
vSuper[1] = Vertex(xMax + dy * sqrt3 / 3.0, yMin);
vSuper[2] = Vertex((xMin + xMax) * 0.5, yMax + dx * sqrt3 * 0.5);
TriangleSet workset;
workset.insert(Triangle(vSuper));
for (iterVertex = vertices.begin(); iterVertex != vertices.end(); ++iterVertex)
{
TriangleIsCompleted pred1(iterVertex, output, vSuper);
TriangleSet::iterator iter = workset.begin();
while (iter != workset.end())
{
if (pred1(*iter))
{
iter = workset.erase(iter);
}
else
{
++iter;
}
}
EdgeSet edges;
VertexIsInCircumstanceCircle pred2(iterVertex, edges);
iter = workset.begin();
while (iter != workset.end())
{
if (pred2(*iter))
{
iter = workset.erase(iter);
}
else
{
++iter;
}
}
for (EdgeIterator edgeIter = edges.begin(); edgeIter != edges.end(); ++edgeIter)
{
workset.insert(Triangle(edgeIter->m_pv0, edgeIter->m_pv1, &(*iterVertex)));
}
}
TriangleIterator where = output.begin();
TriangleHasVertex pred(vSuper);
for (auto t : workset)
{
if (!pred(t))
{
output.insert(output.begin(), t);
}
}
}
/**
* Main function.
*
* Usage: VtkToFld session.xml input.vtk output.fld [options]
*/
int main(int argc, char* argv[])
{
// Set up available options
po::options_description desc("Available options");
desc.add_options()
("help,h", "Produce this help message.")
("name,n", po::value<string>()->default_value("Intensity"),
"Name of field in VTK file to use for intensity.")
("outname,m", po::value<string>()->default_value("intensity"),
"Name of field in output FLD file.")
("precision,p", po::value<double>()->default_value(1),
"Precision of vertex matching.");
po::options_description hidden("Hidden options");
hidden.add_options()
("file", po::value<vector<string> >(), "Input filename");
po::options_description cmdline_options;
cmdline_options.add(desc).add(hidden);
po::positional_options_description p;
p.add("file", -1);
po::variables_map vm;
// Parse command-line options
try
{
po::store(po::command_line_parser(argc, argv).
options(cmdline_options).positional(p).run(), vm);
po::notify(vm);
}
catch (const std::exception& e)
{
cerr << e.what() << endl;
cerr << desc;
return 1;
}
if ( vm.count("help") || vm.count("file") == 0 ||
vm["file"].as<vector<string> >().size() != 3) {
cerr << "Usage: VtkToFld session.xml intensity.vtk output.fld [options]"
<< endl;
cerr << desc;
return 1;
}
// Extract command-line argument values
std::vector<std::string> vFiles = vm["file"].as<vector<string> >();
const string infile = vFiles[1];
const string outfile = vFiles[2];
const double factor = vm["precision"].as<double>();
const string name = vm["name"].as<string>();
const string outname = vm["outname"].as<string>();
std::vector<std::string> vFilenames;
LibUtilities::SessionReaderSharedPtr vSession;
SpatialDomains::MeshGraphSharedPtr graph2D;
MultiRegions::ExpList2DSharedPtr Exp;
vFilenames.push_back(vFiles[0]);
vSession = LibUtilities::SessionReader::CreateInstance(2, argv, vFilenames);
try
{
//----------------------------------------------
// Read in mesh from input file
graph2D = MemoryManager<SpatialDomains::MeshGraph2D>::
AllocateSharedPtr(vSession);
//----------------------------------------------
//----------------------------------------------
// Define Expansion
Exp = MemoryManager<MultiRegions::ExpList2D>::
AllocateSharedPtr(vSession,graph2D);
//----------------------------------------------
//----------------------------------------------
// Set up coordinates of mesh
int coordim = Exp->GetCoordim(0);
int nq = Exp->GetNpoints();
Array<OneD, NekDouble> xc0(nq,0.0);
Array<OneD, NekDouble> xc1(nq,0.0);
Array<OneD, NekDouble> xc2(nq,0.0);
switch(coordim)
{
case 2:
Exp->GetCoords(xc0,xc1);
break;
case 3:
Exp->GetCoords(xc0,xc1,xc2);
break;
default:
ASSERTL0(false,"Coordim not valid");
break;
}
//----------------------------------------------
vtkPolyDataReader *vtkMeshReader = vtkPolyDataReader::New();
vtkMeshReader->SetFileName(infile.c_str());
vtkMeshReader->Update();
vtkPolyData *vtkMesh = vtkMeshReader->GetOutput();
vtkCellDataToPointData* c2p = vtkCellDataToPointData::New();
#if VTK_MAJOR_VERSION <= 5
c2p->SetInput(vtkMesh);
#else
c2p->SetInputData(vtkMesh);
#endif
c2p->PassCellDataOn();
c2p->Update();
vtkPolyData *vtkDataAtPoints = c2p->GetPolyDataOutput();
vtkPoints *vtkPoints = vtkMesh->GetPoints();
ASSERTL0(vtkPoints, "ERROR: cannot get points from mesh.");
vtkCellArray *vtkPolys = vtkMesh->GetPolys();
ASSERTL0(vtkPolys, "ERROR: cannot get polygons from mesh.");
vtkPointData *vtkPData = vtkDataAtPoints->GetPointData();
ASSERTL0(vtkPolys, "ERROR: cannot get point data from file.");
VertexSet points;
VertexSet::iterator vIter;
double p[3];
double val;
double x, y, z;
int coeff_idx;
int i,j,n;
if (!vtkDataAtPoints->GetPointData()->HasArray(name.c_str())) {
n = vtkDataAtPoints->GetPointData()->GetNumberOfArrays();
cerr << "Input file '" << infile
<< "' does not have a field named '"
<< name << "'" << endl;
cerr << "There are " << n << " arrays in this file." << endl;
for (int i = 0; i < n; ++i)
{
cerr << " "
<< vtkDataAtPoints->GetPointData()->GetArray(i)->GetName()
<< endl;
}
return 1;
}
// Build up an unordered set of vertices from the VTK file. For each
// vertex a hashed value of the coordinates is generated to within a
// given tolerance.
n = vtkPoints->GetNumberOfPoints();
for (i = 0; i < n; ++i)
{
vtkPoints->GetPoint(i,p);
val = vtkPData->GetScalars(name.c_str())->GetTuple1(i);
boost::shared_ptr<Vertex> v(new Vertex(p[0],p[1],p[2],val,factor));
points.insert(v);
}
// Now process each vertex of each element in the mesh
SpatialDomains::PointGeomSharedPtr vert;
for (i = 0; i < Exp->GetNumElmts(); ++i)
{
StdRegions::StdExpansionSharedPtr e = Exp->GetExp(i);
for (j = 0; j < e->GetNverts(); ++j)
{
// Get the index of the coefficient corresponding to this vertex
coeff_idx = Exp->GetCoeff_Offset(i) + e->GetVertexMap(j);
// Get the coordinates of the vertex
vert = e->as<LocalRegions::Expansion2D>()->GetGeom2D()
->GetVertex(j);
vert->GetCoords(x,y,z);
// Look up the vertex in the VertexSet
boost::shared_ptr<Vertex> v(new Vertex(x,y,z,0.0,factor));
vIter = points.find(v);
// If not found, maybe the tolerance should be reduced?
// If found, record the scalar value from the VTK file in the
// corresponding coefficient.
if (vIter == points.end())
{
cerr << "Vertex " << i << " not found. Looking for ("
<< x << ", " << y << ", " << z << ")" << endl;
}
else
{
Exp->UpdateCoeffs()[coeff_idx] = (*vIter)->scalar;
}
}
}
Exp->SetPhysState(false);
//-----------------------------------------------
// Write solution to file
std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef
= Exp->GetFieldDefinitions();
std::vector<std::vector<NekDouble> > FieldData(FieldDef.size());
for(i = 0; i < FieldDef.size(); ++i)
{
FieldDef[i]->m_fields.push_back(outname);
Exp->AppendFieldData(FieldDef[i], FieldData[i]);
}
LibUtilities::FieldIO vFld(vSession->GetComm());
vFld.Write(outfile, FieldDef, FieldData);
//-----------------------------------------------
}
catch (...) {
cout << "An error occurred." << endl;
}
}
