bool convertMeshToGeo(const MeshLib::Mesh &mesh, GeoLib::GEOObjects &geo_objects, double eps)
{
if (mesh.getDimension() != 2)
{
ERR ("Mesh to geometry conversion is only working for 2D meshes.");
return false;
}
// nodes to points conversion
std::string mesh_name(mesh.getName());
{
auto points = std::make_unique<std::vector<GeoLib::Point*>>();
points->reserve(mesh.getNumberOfNodes());
for (auto node_ptr : mesh.getNodes())
points->push_back(new GeoLib::Point(*node_ptr, node_ptr->getID()));
geo_objects.addPointVec(std::move(points), mesh_name, nullptr, eps);
}
const std::vector<std::size_t> id_map (geo_objects.getPointVecObj(mesh_name)->getIDMap());
// elements to surface triangles conversion
std::string const mat_name ("MaterialIDs");
auto bounds (MeshInformation::getValueBounds<int>(mesh, mat_name));
const unsigned nMatGroups(bounds.second-bounds.first+1);
auto sfcs = std::make_unique<std::vector<GeoLib::Surface*>>();
sfcs->reserve(nMatGroups);
auto const& points = *geo_objects.getPointVec(mesh_name);
for (unsigned i=0; i<nMatGroups; ++i)
sfcs->push_back(new GeoLib::Surface(points));
const std::vector<MeshLib::Element*> &elements = mesh.getElements();
const std::size_t nElems (mesh.getNumberOfElements());
MeshLib::PropertyVector<int> const*const materialIds =
mesh.getProperties().existsPropertyVector<int>("MaterialIDs")
? mesh.getProperties().getPropertyVector<int>("MaterialIDs")
: nullptr;
for (unsigned i=0; i<nElems; ++i)
{
auto surfaceId = !materialIds ? 0 : ((*materialIds)[i] - bounds.first);
MeshLib::Element* e (elements[i]);
if (e->getGeomType() == MeshElemType::TRIANGLE)
(*sfcs)[surfaceId]->addTriangle(id_map[e->getNodeIndex(0)], id_map[e->getNodeIndex(1)], id_map[e->getNodeIndex(2)]);
if (e->getGeomType() == MeshElemType::QUAD)
{
(*sfcs)[surfaceId]->addTriangle(id_map[e->getNodeIndex(0)], id_map[e->getNodeIndex(1)], id_map[e->getNodeIndex(2)]);
(*sfcs)[surfaceId]->addTriangle(id_map[e->getNodeIndex(0)], id_map[e->getNodeIndex(2)], id_map[e->getNodeIndex(3)]);
}
// all other element types are ignored (i.e. lines)
}
std::for_each(sfcs->begin(), sfcs->end(), [](GeoLib::Surface* sfc){ if (sfc->getNumberOfTriangles()==0) delete sfc; sfc = nullptr;});
auto sfcs_end = std::remove(sfcs->begin(), sfcs->end(), nullptr);
sfcs->erase(sfcs_end, sfcs->end());
geo_objects.addSurfaceVec(std::move(sfcs), mesh_name);
return true;
}
MeshLib::Mesh* MeshSurfaceExtraction::getMeshBoundary(const MeshLib::Mesh &mesh)
{
if (mesh.getDimension()==1)
return nullptr;
// For 3D meshes return the 2D surface
if (mesh.getDimension()==3)
{
MathLib::Vector3 dir(0,0,0);
return getMeshSurface(mesh, dir, 90);
}
// For 2D meshes return the boundary lines
std::vector<MeshLib::Node*> nodes = MeshLib::copyNodeVector(mesh.getNodes());
std::vector<MeshLib::Element*> boundary_elements;
std::vector<MeshLib::Element*> const& org_elems (mesh.getElements());
for (auto it=org_elems.begin(); it!=org_elems.end(); ++it)
{
MeshLib::Element* elem (*it);
std::size_t const n_edges (elem->getNEdges());
for (std::size_t i=0; i<n_edges; ++i)
if (elem->getNeighbor(i) == nullptr)
{
MeshLib::Element const*const edge (elem->getEdge(i));
boundary_elements.push_back(MeshLib::copyElement(edge, nodes));
delete edge;
}
}
MeshLib::Mesh* result = new MeshLib::Mesh("Boundary Mesh", nodes, boundary_elements);
MeshLib::NodeSearch ns(*result);
if (ns.searchUnused() == 0) {
return result;
} else {
auto removed = MeshLib::removeNodes(*result, ns.getSearchedNodeIDs(), result->getName());
delete result;
return removed;
}
}
std::unique_ptr<MeshLib::Mesh> appendLinesAlongPolylines(
const MeshLib::Mesh& mesh, const GeoLib::PolylineVec& ply_vec)
{
// copy existing nodes and elements
std::vector<MeshLib::Node*> vec_new_nodes = MeshLib::copyNodeVector(mesh.getNodes());
std::vector<MeshLib::Element*> vec_new_eles = MeshLib::copyElementVector(mesh.getElements(), vec_new_nodes);
auto const material_ids = materialIDs(mesh);
int const max_matID =
material_ids
? *(std::max_element(begin(*material_ids), end(*material_ids)))
: 0;
std::vector<int> new_mat_ids;
const std::size_t n_ply (ply_vec.size());
// for each polyline
for (std::size_t k(0); k < n_ply; k++)
{
const GeoLib::Polyline* ply = (*ply_vec.getVector())[k];
// search nodes on the polyline
MeshGeoToolsLib::MeshNodesAlongPolyline mshNodesAlongPoly(
mesh, *ply, mesh.getMinEdgeLength() * 0.5,
MeshGeoToolsLib::SearchAllNodes::Yes);
auto &vec_nodes_on_ply = mshNodesAlongPoly.getNodeIDs();
if (vec_nodes_on_ply.empty()) {
std::string ply_name;
ply_vec.getNameOfElementByID(k, ply_name);
INFO("No nodes found on polyline %s", ply_name.c_str());
continue;
}
// add line elements
for (std::size_t i=0; i<vec_nodes_on_ply.size()-1; i++) {
std::array<MeshLib::Node*, 2> element_nodes;
element_nodes[0] = vec_new_nodes[vec_nodes_on_ply[i]];
element_nodes[1] = vec_new_nodes[vec_nodes_on_ply[i+1]];
vec_new_eles.push_back(
new MeshLib::Line(element_nodes, vec_new_eles.size()));
new_mat_ids.push_back(max_matID+k+1);
}
}
// generate a mesh
const std::string name = mesh.getName() + "_with_lines";
auto new_mesh =
std::make_unique<MeshLib::Mesh>(name, vec_new_nodes, vec_new_eles);
auto new_material_ids =
new_mesh->getProperties().createNewPropertyVector<int>(
"MaterialIDs", MeshLib::MeshItemType::Cell);
if (!new_material_ids)
{
OGS_FATAL("Could not create MaterialIDs cell vector in new mesh.");
}
new_material_ids->reserve(new_mesh->getNumberOfElements());
if (material_ids != nullptr)
{
std::copy(begin(*material_ids), end(*material_ids),
std::back_inserter(*new_material_ids));
}
else
{
new_material_ids->resize(mesh.getNumberOfElements());
}
std::copy(begin(new_mat_ids), end(new_mat_ids),
std::back_inserter(*new_material_ids));
return new_mesh;
}
PostProcessTool::PostProcessTool(
MeshLib::Mesh const& org_mesh,
std::vector<MeshLib::Node*> const& vec_fracture_nodes,
std::vector<MeshLib::Element*> const& vec_fracutre_matrix_elements)
:_org_mesh(org_mesh)
{
if (!org_mesh.getProperties().hasPropertyVector("displacement")
|| !org_mesh.getProperties().hasPropertyVector("displacement_jump1")
|| !org_mesh.getProperties().hasPropertyVector("levelset1")
)
{
OGS_FATAL("The given mesh does not have relevant properties");
}
// clone nodes and elements
std::vector<MeshLib::Node*> new_nodes(MeshLib::copyNodeVector(org_mesh.getNodes()));
std::vector<MeshLib::Element*> new_eles(
MeshLib::copyElementVector(org_mesh.getElements(), new_nodes));
// duplicate fracture nodes
for (auto const* org_node : vec_fracture_nodes)
{
auto duplicated_node = new MeshLib::Node(org_node->getCoords(), new_nodes.size());
new_nodes.push_back(duplicated_node);
_map_dup_newNodeIDs[org_node->getID()] = duplicated_node->getID();
}
// split elements using the new duplicated nodes
auto prop_levelset = org_mesh.getProperties().getPropertyVector<double>("levelset1");
for (auto const* org_e : vec_fracutre_matrix_elements)
{
// only matrix elements
if (org_e->getDimension() != org_mesh.getDimension())
continue;
auto const eid = org_e->getID();
// keep original if the element has levelset=0
if ((*prop_levelset)[eid] == 0)
continue;
// replace fracture nodes with duplicated ones
MeshLib::Element* e = new_eles[eid];
for (unsigned i=0; i<e->getNumberOfNodes(); i++)
{
// only fracture nodes
auto itr = _map_dup_newNodeIDs.find(e->getNodeIndex(i));
if (itr == _map_dup_newNodeIDs.end())
continue;
// check if a node belongs to the particular fracture group
auto itr2 = std::find_if(vec_fracture_nodes.begin(), vec_fracture_nodes.end(),
[&](MeshLib::Node const*node) { return node->getID()==e->getNodeIndex(i);});
if (itr2 == vec_fracture_nodes.end())
continue;
e->setNode(i, new_nodes[itr->second]);
}
}
// new mesh
_output_mesh.reset(new MeshLib::Mesh(org_mesh.getName(), new_nodes, new_eles));
createProperties<int>();
createProperties<double>();
copyProperties<int>();
copyProperties<double>();
calculateTotalDisplacement();
}
void ElementTreeModel::setMesh(MeshLib::Mesh const& mesh)
{
this->clearView();
QList<QVariant> mesh_name;
mesh_name << "Name:" << QString::fromStdString(mesh.getName()) << "" << "" << "";
TreeItem* name_item = new TreeItem(mesh_name, _rootItem);
_rootItem->appendChild(name_item);
QList<QVariant> nodes_number;
nodes_number << "#Nodes: " << QString::number(mesh.getNumberOfNodes()) << "" << "";
TreeItem* nodes_item = new TreeItem(nodes_number, _rootItem);
_rootItem->appendChild(nodes_item);
QList<QVariant> elements_number;
elements_number << "#Elements: " << QString::number(mesh.getNumberOfElements()) << "" << "";
TreeItem* elements_item = new TreeItem(elements_number, _rootItem);
_rootItem->appendChild(elements_item);
const std::array<QString, 7> n_element_names = {{ "Lines:", "Triangles:", "Quads:", "Tetrahedra:", "Hexahedra:", "Pyramids:", "Prisms:" }};
const std::array<unsigned, 7>& n_element_types (MeshLib::MeshInformation::getNumberOfElementTypes(mesh));
for (std::size_t i=0; i<n_element_types.size(); ++i)
{
if (n_element_types[i])
{
QList<QVariant> elements_number;
elements_number << n_element_names[i] << QString::number(n_element_types[i]) << "" << "";
TreeItem* type_item = new TreeItem(elements_number, elements_item);
elements_item->appendChild(type_item);
}
}
QList<QVariant> bounding_box;
bounding_box << "Bounding Box" << "" << "" << "";
TreeItem* aabb_item = new TreeItem(bounding_box, _rootItem);
_rootItem->appendChild(aabb_item);
const GeoLib::AABB aabb (MeshLib::MeshInformation::getBoundingBox(mesh));
auto const& min = aabb.getMinPoint();
auto const& max = aabb.getMaxPoint();
QList<QVariant> min_aabb;
min_aabb << "Min:" << QString::number(min[0], 'f') << QString::number(min[1], 'f') << QString::number(min[2], 'f');
TreeItem* min_item = new TreeItem(min_aabb, aabb_item);
aabb_item->appendChild(min_item);
QList<QVariant> max_aabb;
max_aabb << "Max:" << QString::number(max[0], 'f') << QString::number(max[1], 'f') << QString::number(max[2], 'f');
TreeItem* max_item = new TreeItem(max_aabb, aabb_item);
aabb_item->appendChild(max_item);
QList<QVariant> edges;
edges << "Edge Length: " << "[" + QString::number(mesh.getMinEdgeLength(), 'f') + "," << QString::number(mesh.getMaxEdgeLength(), 'f') + "]" << "";
TreeItem* edge_item = new TreeItem(edges, _rootItem);
_rootItem->appendChild(edge_item);
std::vector<std::string> const& vec_names (mesh.getProperties().getPropertyVectorNames());
for (std::size_t i=0; i<vec_names.size(); ++i)
{
QList<QVariant> array_info;
array_info << QString::fromStdString(vec_names[i]) + ": ";
auto vec_bounds (MeshLib::MeshInformation::getValueBounds<int>(mesh, vec_names[i]));
if (vec_bounds.second != std::numeric_limits<int>::max())
array_info << "[" + QString::number(vec_bounds.first) + "," << QString::number(vec_bounds.second) + "]" << "";
else
{
auto vec_bounds (MeshLib::MeshInformation::getValueBounds<double>(mesh, vec_names[i]));
if (vec_bounds.second != std::numeric_limits<double>::max())
array_info << "[" + QString::number(vec_bounds.first) + "," << QString::number(vec_bounds.second) + "]" << "";
}
if (array_info.size() == 1)
array_info << "[ ?" << "? ]" << "";
TreeItem* vec_item = new TreeItem(array_info, _rootItem);
_rootItem->appendChild(vec_item);
}
reset();
}
std::unique_ptr<MeshLib::Mesh> appendLinesAlongPolylines(
const MeshLib::Mesh& mesh, const GeoLib::PolylineVec& ply_vec)
{
// copy existing nodes and elements
std::vector<MeshLib::Node*> vec_new_nodes = MeshLib::copyNodeVector(mesh.getNodes());
std::vector<MeshLib::Element*> vec_new_eles = MeshLib::copyElementVector(mesh.getElements(), vec_new_nodes);
std::vector<int> new_mat_ids;
{
if (mesh.getProperties().existsPropertyVector<int>("MaterialIDs")) {
auto ids =
mesh.getProperties().getPropertyVector<int>("MaterialIDs");
new_mat_ids.reserve(ids->size());
std::copy(ids->cbegin(), ids->cend(),
std::back_inserter(new_mat_ids));
}
}
int max_matID(0);
if (!new_mat_ids.empty())
max_matID = *(std::max_element(new_mat_ids.cbegin(), new_mat_ids.cend()));
const std::size_t n_ply (ply_vec.size());
// for each polyline
for (std::size_t k(0); k < n_ply; k++)
{
const GeoLib::Polyline* ply = (*ply_vec.getVector())[k];
// search nodes on the polyline
MeshGeoToolsLib::MeshNodesAlongPolyline mshNodesAlongPoly(
mesh, *ply, mesh.getMinEdgeLength() * 0.5,
MeshGeoToolsLib::SearchAllNodes::Yes);
auto &vec_nodes_on_ply = mshNodesAlongPoly.getNodeIDs();
if (vec_nodes_on_ply.empty()) {
std::string ply_name;
ply_vec.getNameOfElementByID(k, ply_name);
INFO("No nodes found on polyline %s", ply_name.c_str());
continue;
}
// add line elements
for (std::size_t i=0; i<vec_nodes_on_ply.size()-1; i++) {
std::array<MeshLib::Node*, 2> element_nodes;
element_nodes[0] = vec_new_nodes[vec_nodes_on_ply[i]];
element_nodes[1] = vec_new_nodes[vec_nodes_on_ply[i+1]];
vec_new_eles.push_back(
new MeshLib::Line(element_nodes, vec_new_eles.size()));
new_mat_ids.push_back(max_matID+k+1);
}
}
// generate a mesh
const std::string name = mesh.getName() + "_with_lines";
auto new_mesh =
std::make_unique<MeshLib::Mesh>(name, vec_new_nodes, vec_new_eles);
auto opt_mat_pv = new_mesh->getProperties().createNewPropertyVector<int>(
"MaterialIDs", MeshLib::MeshItemType::Cell);
if (opt_mat_pv) {
auto & mat_pv = *opt_mat_pv;
mat_pv.reserve(new_mat_ids.size());
std::copy(new_mat_ids.cbegin(), new_mat_ids.cend(),
std::back_inserter(mat_pv));
}
return new_mesh;
}
int main (int argc, char* argv[])
{
LOGOG_INITIALIZE();
logog::Cout* logog_cout (new logog::Cout);
BaseLib::LogogSimpleFormatter *custom_format (new BaseLib::LogogSimpleFormatter);
logog_cout->SetFormatter(*custom_format);
TCLAP::CmdLine cmd("Remove mesh elements.", ' ', "0.1");
TCLAP::ValueArg<std::string> mesh_in("i", "mesh-input-file",
"the name of the file containing the input mesh", true,
"", "file name of input mesh");
cmd.add(mesh_in);
TCLAP::ValueArg<std::string> mesh_out("o", "mesh-output-file",
"the name of the file the mesh will be written to", true,
"", "file name of output mesh");
cmd.add(mesh_out);
TCLAP::SwitchArg zveArg("z", "zero-volume", "remove zero volume elements", false);
cmd.add(zveArg);
TCLAP::MultiArg<std::string> eleTypeArg("t", "element-type",
"element type to be removed", false, "element type");
cmd.add(eleTypeArg);
TCLAP::MultiArg<unsigned> matIDArg("m", "material-id",
"material id", false, "material id");
cmd.add(matIDArg);
cmd.parse(argc, argv);
MeshLib::Mesh* mesh (FileIO::readMeshFromFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
// search elements IDs to be removed
std::vector<std::size_t> vec_elementIDs_removed;
if (zveArg.isSet()) {
std::vector<std::size_t> vec_matched = searchByZeroContent(mesh->getElements());
updateUnion(vec_matched, vec_elementIDs_removed);
INFO("%d zero volume elements found.", vec_matched.size());
}
if (eleTypeArg.isSet()) {
std::vector<std::string> eleTypeNames = eleTypeArg.getValue();
for (auto typeName : eleTypeNames) {
MeshElemType type = String2MeshElemType(typeName);
if (type == MeshElemType::INVALID) continue;
std::vector<std::size_t> vec_matched = searchByElementType(mesh->getElements(), type);
updateUnion(vec_matched, vec_elementIDs_removed);
INFO("%d %s elements found.", vec_matched.size(), typeName.c_str());
}
}
if (matIDArg.isSet()) {
std::vector<unsigned> vec_matID = matIDArg.getValue();
for (auto matID : vec_matID) {
std::vector<std::size_t> vec_matched = searchByMaterialID(mesh->getElements(), matID);
updateUnion(vec_matched, vec_elementIDs_removed);
INFO("%d elements with material ID %d found.", vec_matched.size(), matID);
}
}
// remove the elements
INFO("Removing total %d elements...", vec_elementIDs_removed.size());
std::vector<MeshLib::Element*> tmp_eles = excludeElements(mesh->getElements(), vec_elementIDs_removed);
INFO("%d elements remained.", tmp_eles.size());
std::vector<MeshLib::Node*> new_nodes;
std::vector<MeshLib::Element*> new_eles;
copyNodesElements(mesh->getNodes(), tmp_eles, new_nodes, new_eles);
// create a new mesh object. Unsued nodes are removed while construction
MeshLib::Mesh* new_mesh(new MeshLib::Mesh(mesh->getName(), new_nodes, new_eles));
// write into a file
FileIO::Legacy::MeshIO meshIO;
meshIO.setMesh(new_mesh);
meshIO.writeToFile(mesh_out.getValue());
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0;
}
