void SimMesh::ReadTetgenMesh(string mesh_name){
//Read vertices
string line;
stringstream temp_ss;
ifstream node_file((mesh_name+".node").c_str());
if (node_file.is_open())
{
while ( getline (node_file,line) )
{
if(line[line.find_first_not_of(" ")] == '#' )
continue;
else{
temp_ss.str(line);
temp_ss >> num_vertices;
break;
}
}
while ( getline (node_file,line) ){
if(line[line.find_first_not_of(" ")] == '#' )
continue;
else{
temp_ss.str(line);
int counter;
glm::vec4 vertex;
temp_ss >> counter >> vertex.x >> vertex.y >> vertex.z;
vertex.w = 1;
vertices.push_back(vertex);
}
}
}
else{
int main(int argc, char** argv)
{
std::cout<<"exec volmesh.vtk|vtu surfmesh.vtk out_labels.txt arrayname volmesh_out.vtk scale correct_orientation(0|1)"<<std::endl;
std::cout<<"Scale - rescale mesh by this factor, !!! for now works only for ALYA, for everything else put 1"<<std::endl;
std::cout<<"correct_orientation - 1 or 0 whether to correct cell orientation or not"<<std::endl;
std::cout<<"Labels must be celldata"<<std::endl;
std::cout<<"Add extension .bsc to volmesh_out to get mesh in Alya format"<<std::endl;
std::cout<<"Skip extension in volmesh_out to get mesh in Elmer format"<<std::endl;
std::cout<<"out_labels.txt -- faces with labels, format: label point1 point2 point3 tetra_id"<<std::endl;
if(argc<4) return -1;
const char* volmesh_file = argv[1];
const char* surfmesh_file = argv[2];
const char* outfile = argv[3];
const char* array_name = argv[4];
const char* volmeshout = argv[5];
float scale = atof(argv[6]);
bool correct_orientation = atoi(argv[7])==1;
std::cout<<"Volumetric mesh: "<<volmesh_file<<std::endl;
std::cout<<"Surface mesh: "<<surfmesh_file<<std::endl;
std::cout<<"Labels: "<<outfile<<std::endl;
std::cout<<"Label array: "<<array_name<<std::endl;
std::cout<<"Output mesh: "<<volmeshout<<std::endl;
std::cout<<"Scale: "<<scale<<std::endl;
if(correct_orientation)
std::cout<<"Correcting orientation: ON"<<std::endl;
else
std::cout<<"Correcting orientation: OFF"<<std::endl;
bool vtkoutput_mesh = false;
bool alyaoutput_mesh = false;
if(volmeshout!=NULL)
{
const char *ext = volmeshout+strlen(volmeshout)-4;
if(strcmp(ext,".vtk")==0) //if we are requesting .node .element volumetric mesh
vtkoutput_mesh = true;
else if(strcmp(ext,".bsc")==0)
alyaoutput_mesh = true;
}
vtkSmartPointer<vtkUnstructuredGrid> volmesh = vtkSmartPointer<vtkUnstructuredGrid>::New();
if (volmesh_file[ strlen(volmesh_file)-1 ] == 'k') //vtk
{
vtkSmartPointer<vtkDataSetReader> vol_rdr = vtkSmartPointer<vtkDataSetReader>::New();
CommonTools::AssociateProgressFunction(vol_rdr);
vol_rdr->SetFileName(volmesh_file);
vol_rdr->Update();
volmesh->DeepCopy( (vtkUnstructuredGrid*)vol_rdr->GetOutput() );
}
else
{
vtkSmartPointer<vtkXMLUnstructuredGridReader> vol_rdr = vtkSmartPointer<vtkXMLUnstructuredGridReader>::New();
CommonTools::AssociateProgressFunction(vol_rdr);
vol_rdr->SetFileName(volmesh_file);
vol_rdr->Update();
volmesh->DeepCopy( (vtkUnstructuredGrid*)vol_rdr->GetOutput() );
}
if(volmesh->GetCell(0)->GetNumberOfPoints()<4)
{
std::cout<<"Supplied volumetric mesh has cells with : "<<volmesh->GetCell(0)->GetNumberOfPoints()<<" vertices"<<std::endl;
std::cout<<"Make sure your mesh is actually volumetric"<<std::endl;
exit(-1);
}
vtkSmartPointer<vtkPolyDataReader> poly_rdr = vtkSmartPointer<vtkPolyDataReader>::New();
CommonTools::AssociateProgressFunction(poly_rdr);
poly_rdr->SetFileName(surfmesh_file);
poly_rdr->Update();
vtkPolyData* surfmesh = poly_rdr->GetOutput();
//read cell scalars from the surface mesh (labels)
auto scalars = surfmesh->GetCellData()->GetArray(array_name);
vtkSmartPointer<vtkPointLocator> ptloc = vtkSmartPointer<vtkPointLocator>::New();
ptloc->SetDataSet(volmesh);
ptloc->BuildLocator();
vtkSmartPointer<vtkCellLocator> cellloc = vtkSmartPointer<vtkCellLocator>::New();
cellloc->SetDataSet(volmesh);
cellloc->BuildLocator();
if(volmeshout!=NULL)
{
//create PointData array in the volumetric mesh with labels
//pass the cell array with labels to point array
vtkSmartPointer<vtkCellDataToPointData> c2pdata = vtkSmartPointer<vtkCellDataToPointData>::New();
c2pdata->SetInputData(surfmesh);
c2pdata->PassCellDataOn();
c2pdata->Update();
auto pscalars = c2pdata->GetOutput()->GetPointData()->GetArray(array_name);
//to store ids with the tetra mesh points
vtkSmartPointer<vtkShortArray> volmesh_regions = vtkSmartPointer<vtkShortArray>::New();
volmesh_regions->SetName(array_name);
volmesh_regions->SetNumberOfComponents(1);
volmesh_regions->SetNumberOfValues(volmesh->GetNumberOfPoints());
//fill the array of scalars to store with volumetric mesh
for(vtkIdType i=0; i<volmesh->GetNumberOfPoints();i++)
{
volmesh_regions->SetTuple1(i,0);
}
//for every cell of the surface mesh
for(vtkIdType i=0; i<surfmesh->GetNumberOfPoints(); i++)
{
vtkIdType ptid = ptloc->FindClosestPoint(surfmesh->GetPoint(i));
volmesh_regions->SetTuple1(ptid, pscalars->GetTuple1(i));
}
volmesh->GetPointData()->AddArray(volmesh_regions);
//:~ create PointData array in the volumetric mesh with labels
}
std::vector<BscEntry> labeldata;
//create std::vector with information about the cell and point ids for every label
//for every cell of the surface mesh
std::cout<<"Looking for boundaries"<<std::endl;
for(vtkIdType i=0; i<surfmesh->GetNumberOfCells(); i++)
{
if( i%10000 == 0 )
std::cout<<"Cell "<<i<<"/"<<surfmesh->GetNumberOfCells()<<"\r"<<std::flush;
vtkCell* cell = surfmesh->GetCell(i);
BscEntry entry;
//if( cell->GetNumberOfPoints()!=3 )
//{
// std::cout<<"Face does not have 3 vertices. Id= "<<i<<std::endl;
// continue;
//}
entry.id = scalars->GetTuple1(i);
entry.pt1 = ptloc->FindClosestPoint(cell->GetPoints()->GetPoint(0));
entry.pt2 = ptloc->FindClosestPoint(cell->GetPoints()->GetPoint(1));
entry.pt3 = ptloc->FindClosestPoint(cell->GetPoints()->GetPoint(2));
if( cell->GetNumberOfPoints()==4 )
{
entry.pt4 = ptloc->FindClosestPoint(cell->GetPoints()->GetPoint(3));
entry.nvertices=4;
}
else if(cell->GetNumberOfPoints()==3)
{
entry.nvertices=3;
}
else
{
cout<<"cell "<<i<<" has "<<cell->GetNumberOfPoints()<<" vertices, it is unsupported"<<endl;
exit(-1);
}
double pt1[3];
double pt2[3];
double pt3[3];
double pt4[3];
volmesh->GetPoint(entry.pt1, pt1);
volmesh->GetPoint(entry.pt2, pt2);
volmesh->GetPoint(entry.pt3, pt3);
if( entry.nvertices==4 )
{
volmesh->GetPoint(entry.pt4, pt4);
}
else
{
pt4[0]=0;
pt4[1]=0;
pt4[2]=0;
}
double c[3];
c[0] = (pt1[0]+pt2[0]+pt3[0]+pt4[0])/entry.nvertices;
c[1] = (pt1[1]+pt2[1]+pt3[1]+pt4[1])/entry.nvertices;
c[2] = (pt1[2]+pt2[2]+pt3[2]+pt4[2])/entry.nvertices;
vtkIdType cellid = cellloc->FindCell(c);
if(cellid==-1)
{
std::cout<<"Cell not found. Look for an error. Closest point:"<<c[0]<<" "<<c[1]<<" "<<c[2]<<" "<<std::endl;
}
entry.tet_id = cellid;
labeldata.push_back(entry);
}
std::cout<<std::endl;
//to store labels for cells
vtkSmartPointer<vtkShortArray> volmesh_regions_cells = vtkSmartPointer<vtkShortArray>::New();
volmesh_regions_cells->SetName(array_name);
volmesh_regions_cells->SetNumberOfComponents(1);
volmesh_regions_cells->SetNumberOfValues(volmesh->GetNumberOfCells());
for(vtkIdType i1=0; i1<volmesh->GetNumberOfCells(); i1++)
{
volmesh_regions_cells->SetTuple1(i1,0); //reset
}
//store the labels
std::ofstream file(outfile);
for(vtkIdType i=0; i<labeldata.size(); i++)
{
BscEntry entry = labeldata[i];
file<<entry.id<<" "<<
entry.pt1+1<<" "<<
entry.pt2+1<<" "<<
entry.pt3+1<<" ";
if( entry.nvertices==4 )
file<<entry.pt4+1<<" ";
file<<entry.tet_id+1<<LINEBREAK;
if(volmeshout!=NULL)
{
volmesh_regions_cells->SetTuple1(entry.tet_id, entry.id);
}
}
//store the labels 1
std::ofstream file1((std::string(outfile)+".1").c_str());
for(vtkIdType i=0; i<labeldata.size(); i++)
{
BscEntry entry = labeldata[i];
file1<<i+1<<" "<<entry.id<<endl;
}
if(volmeshout!=NULL)
{
volmesh->GetCellData()->AddArray(volmesh_regions_cells);
if(vtkoutput_mesh)
{
vtkSmartPointer<vtkDataSetWriter> wrwr = vtkSmartPointer<vtkDataSetWriter>::New();
CommonTools::AssociateProgressFunction(wrwr);
wrwr->SetFileTypeToBinary();
wrwr->SetFileName(volmeshout);
wrwr->SetInputData(volmesh);
wrwr->Update();
}
else if(alyaoutput_mesh)
{
std::cout<<"Writing alya format"<<std::endl;
CommonTools::SaveVolMeshBSC(volmesh, volmeshout, scale, correct_orientation);
//add the boundary
char boundary_file[256];
char boundary_elemtype_file[256];
sprintf(boundary_file, "%s.bound", volmeshout);
sprintf(boundary_elemtype_file, "%s.bound_type", volmeshout);
std::ofstream file(boundary_file);
std::ofstream file_elemtype(boundary_elemtype_file);
for(vtkIdType i=0; i<labeldata.size(); i++)
{
BscEntry entry = labeldata[i];
file<<i+1<<" "<<
entry.pt1+1<<" "<<
entry.pt2+1<<" "<<
entry.pt3+1<<" ";
if( entry.nvertices==4 )
file<<entry.pt4+1;
file<<LINEBREAK;
file_elemtype<<i+1<<" "<<entry.nvertices<<LINEBREAK;
}
}
else //Write elmer mesh
{
std::cout<<"Writing elmer file"<<std::endl;
std::string header_filename = "mesh.header";
std::ofstream header_file(header_filename.c_str());
header_file<<volmesh->GetNumberOfPoints()<<" "<<volmesh->GetNumberOfCells()<<" "<<labeldata.size()<<std::endl;
header_file<<"2"<<std::endl;
header_file<<"303 "<<labeldata.size()<<std::endl;
header_file<<"504 "<<volmesh->GetNumberOfCells()<<std::endl;
std::string node_filename = "mesh.nodes";
std::ofstream node_file(node_filename.c_str());
for(vtkIdType i=0; i<volmesh->GetNumberOfPoints(); i++)
{
double* pt = volmesh->GetPoint(i);
node_file<<i+1<<" -1 "<<pt[0]<<" "<<pt[1]<<" "<<pt[2]<<std::endl;
}
std::string ele_filename = "mesh.elements";
std::ofstream ele_file(ele_filename.c_str());
for(vtkIdType i=0; i<volmesh->GetNumberOfCells(); i++)
{
vtkCell* cell = volmesh->GetCell(i);
ele_file<<i+1<<" 1 504";
for(int k=0; k<cell->GetNumberOfPoints(); k++)
ele_file<<" "<<cell->GetPointId(k)+1;
ele_file<<std::endl;
}
std::string bound_filename = "mesh.boundary";
std::ofstream bound_file(bound_filename.c_str());
for(vtkIdType i=0; i<labeldata.size(); i++)
{
BscEntry entry = labeldata[i];
bound_file<<i+1<<" "<<
entry.id<<" "<<
entry.tet_id+1<<" 0 303 "<<
entry.pt1+1<<" "<<
entry.pt2+1<<" "<<
entry.pt3+1;
if( entry.nvertices==4 )
bound_file<<" "<<entry.pt4+1;
bound_file<<std::endl;
}
}
}
return 0;
}
