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("Converts VTK mesh into OGS mesh.", ' ', "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);
cmd.parse(argc, argv);
MeshLib::Mesh* mesh (FileIO::BoostVtuInterface::readVTUFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
FileIO::Legacy::MeshIO meshIO;
meshIO.setMesh(mesh);
meshIO.writeToFile(mesh_out.getValue());
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0;
}
// Creates a PropertyVector<double> and maps it into a vtkDataArray-equivalent
TEST(InSituLibMappedPropertyVector, Int)
{
const size_t mesh_size = 5;
const double length = 1.0;
MeshLib::Mesh* mesh = MeshLib::MeshGenerator::generateRegularHexMesh(length, mesh_size);
ASSERT_TRUE(mesh != nullptr);
const std::size_t size(mesh_size*mesh_size*mesh_size);
std::string const prop_name("TestProperty");
boost::optional<MeshLib::PropertyVector<int> &> properties(
mesh->getProperties().createNewPropertyVector<int>(prop_name,
MeshLib::MeshItemType::Cell));
(*properties).resize(size);
std::iota((*properties).begin(), (*properties).end(), 1);
vtkNew<InSituLib::VtkMappedPropertyVectorTemplate<int> > dataArray;
dataArray->SetPropertyVector(*properties);
ASSERT_EQ(dataArray->GetNumberOfComponents(), 1);
ASSERT_EQ(dataArray->GetNumberOfTuples(), size);
ASSERT_EQ(dataArray->GetValueReference(0), 1);
double* range = dataArray->GetRange(0);
ASSERT_EQ(range[0], 1);
ASSERT_EQ(range[1], 1 + mesh->getNElements() - 1);
delete mesh;
}
int main(int argc, char *argv[])
{
LOGOG_INITIALIZE();
logog::Cout* logogCout = new logog::Cout;
TCLAP::CmdLine cmd("Simple mesh loading test", ' ', "0.1");
// Define a value argument and add it to the command line.
// A value arg defines a flag and a type of value that it expects,
// such as "-m meshfile".
TCLAP::ValueArg<std::string> mesh_arg("m","mesh","input mesh file",true,"homer","string");
// Add the argument mesh_arg to the CmdLine object. The CmdLine object
// uses this Arg to parse the command line.
cmd.add( mesh_arg );
cmd.parse( argc, argv );
std::string fname (mesh_arg.getValue());
FileIO::MeshIO mesh_io;
#ifndef WIN32
BaseLib::MemWatch mem_watch;
unsigned long mem_without_mesh (mem_watch.getVirtMemUsage());
#endif
BaseLib::RunTime run_time;
run_time.start();
MeshLib::Mesh* mesh = mesh_io.loadMeshFromFile(fname);
#ifndef WIN32
unsigned long mem_with_mesh (mem_watch.getVirtMemUsage());
// std::cout << "mem for mesh: " << (mem_with_mesh - mem_without_mesh)/(1024*1024) << " MB" << std::endl;
INFO ("mem for mesh: %i MB", (mem_with_mesh - mem_without_mesh)/(1024*1024));
#endif
run_time.stop();
// std::cout << "time for reading: " << run_time.elapsed() << " s" << std::endl;
INFO ("time for reading: %f s", run_time.elapsed());
unsigned elem_id = 25000;
const MeshLib::Element* e = mesh->getElement(elem_id);
const size_t nElems = mesh->getNElements();
for (unsigned i=0; i< e->getNNeighbors(); i++)
{
for (unsigned j=0; j< nElems; j++)
if (mesh->getElement(j) == e->getNeighbor(i))
std::cout << "neighbour of element " << elem_id << elem_id << " : " << j << std::endl;
}
delete mesh;
delete logogCout;
LOGOG_SHUTDOWN();
}
TEST(MeshLib, Duplicate)
{
MeshLib::Mesh* mesh (MeshLib::MeshGenerator::generateRegularQuadMesh(10, 5, 1));
std::vector<MeshLib::Node*> new_nodes (MeshLib::copyNodeVector(mesh->getNodes()));
std::vector<MeshLib::Element*> new_elements (MeshLib::copyElementVector(mesh->getElements(), new_nodes));
MeshLib::Mesh new_mesh ("new", new_nodes, new_elements);
ASSERT_EQ (mesh->getNElements(), new_mesh.getNElements());
ASSERT_EQ (mesh->getNNodes(), new_mesh.getNNodes());
std::vector<std::size_t> del_idx(1,1);
MeshLib::removeMeshNodes(*mesh, del_idx);
ASSERT_EQ (mesh->getNElements(), new_mesh.getNElements()-2);
ASSERT_EQ (mesh->getNNodes(), new_mesh.getNNodes()-2);
ASSERT_DOUBLE_EQ (4.0, MathLib::sqrDist(*mesh->getNode(0), *new_mesh.getNode(0)));
ASSERT_DOUBLE_EQ (0.0, MathLib::sqrDist(*mesh->getNode(0), *new_mesh.getNode(2)));
ASSERT_DOUBLE_EQ (4.0, MathLib::sqrDist(*mesh->getElement(0)->getNode(0), *new_mesh.getElement(0)->getNode(0)));
ASSERT_DOUBLE_EQ (0.0, MathLib::sqrDist(*mesh->getElement(0)->getNode(0), *new_mesh.getElement(2)->getNode(0)));
}
bool LayeredVolume::createRasterLayers(const MeshLib::Mesh &mesh,
const std::vector<GeoLib::Raster const*> &rasters,
double minimum_thickness,
double noDataReplacementValue)
{
if (mesh.getDimension() != 2)
return false;
_elevation_epsilon = calcEpsilon(*rasters[0], *rasters.back());
if (_elevation_epsilon <= 0)
return false;
// remove line elements, only tri + quad remain
MeshLib::ElementSearch ex(mesh);
ex.searchByElementType(MeshLib::MeshElemType::LINE);
MeshLib::Mesh* top (removeElements(mesh, ex.getSearchedElementIDs(), "MeshLayer"));
if (top==nullptr)
top = new MeshLib::Mesh(mesh);
if (!MeshLib::MeshLayerMapper::layerMapping(*top, *rasters.back(), noDataReplacementValue))
return false;
MeshLib::Mesh* bottom (new MeshLib::Mesh(*top));
if (!MeshLib::MeshLayerMapper::layerMapping(*bottom, *rasters[0], 0))
{
delete top;
return false;
}
this->_minimum_thickness = minimum_thickness;
_nodes = MeshLib::copyNodeVector(bottom->getNodes());
_elements = MeshLib::copyElementVector(bottom->getElements(), _nodes);
delete bottom;
// map each layer and attach to subsurface mesh
const std::size_t nRasters (rasters.size());
for (std::size_t i=1; i<nRasters; ++i)
this->addLayerToMesh(*top, i, *rasters[i]);
// close boundaries between layers
this->addLayerBoundaries(*top, nRasters);
this->removeCongruentElements(nRasters, top->getNElements());
delete top;
return true;
}
std::vector<ElementErrorCode> MeshValidation::testElementGeometry(const MeshLib::Mesh &mesh, double min_volume)
{
INFO ("Testing mesh element geometry:");
const std::size_t nErrorCodes (static_cast<std::size_t>(ElementErrorFlag::MaxValue));
unsigned error_count[nErrorCodes];
std::fill_n(error_count, 4, 0);
const std::size_t nElements (mesh.getNElements());
const std::vector<MeshLib::Element*> &elements (mesh.getElements());
std::vector<ElementErrorCode> error_code_vector;
error_code_vector.reserve(nElements);
for (std::size_t i=0; i<nElements; ++i)
{
const ElementErrorCode e = elements[i]->validate();
error_code_vector.push_back(e);
if (e.none())
continue;
// increment error statistics
const std::bitset< static_cast<std::size_t>(ElementErrorFlag::MaxValue) > flags (static_cast< std::bitset<static_cast<std::size_t>(ElementErrorFlag::MaxValue)> >(e));
for (unsigned j=0; j<nErrorCodes; ++j)
error_count[j] += flags[j];
}
// if a larger volume threshold is given, evaluate elements again to add them even if they are formally okay
if (min_volume > std::numeric_limits<double>::epsilon())
for (std::size_t i=0; i<nElements; ++i)
if (elements[i]->getContent() < min_volume)
error_code_vector[i].set(ElementErrorFlag::ZeroVolume);
// output
const unsigned error_sum (static_cast<unsigned>(std::accumulate(error_count, error_count+nErrorCodes, 0.0)));
if (error_sum != 0)
{
ElementErrorFlag flags[nErrorCodes] = { ElementErrorFlag::ZeroVolume, ElementErrorFlag::NonCoplanar,
ElementErrorFlag::NonConvex, ElementErrorFlag::NodeOrder };
for (std::size_t i=0; i<nErrorCodes; ++i)
if (error_count[i])
INFO ("%d elements found with %s.", error_count[i], ElementErrorCode::toString(flags[i]).c_str());
}
else
INFO ("No errors found.");
return error_code_vector;
}
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("Add EMI data as a scalar cell array to a 2d mesh.", ' ', "0.1");
// I/O params
TCLAP::ValueArg<std::string> poly_out("o", "polydata-output-file",
"the name of the file the data will be written to", true,
"", "file name of polydata file");
cmd.add(poly_out);
TCLAP::ValueArg<std::string> csv_in("i", "csv-input-file",
"csv-file containing EMI data", true,
"", "name of the csv input file");
cmd.add(csv_in);
TCLAP::ValueArg<std::string> dem_in("s", "DEM-file",
"Surface DEM for mapping ERT data", false,
"", "file name of the Surface DEM");
cmd.add(dem_in);
cmd.parse(argc, argv);
MeshLib::Mesh* mesh (nullptr);
if (dem_in.isSet())
{
mesh = FileIO::VtuInterface::readVTUFile(dem_in.getValue());
if (mesh == nullptr)
{
ERR ("Error reading mesh file.");
return -2;
}
if (mesh->getDimension() != 2)
{
ERR ("This utility can handle only 2d meshes at this point.");
delete mesh;
return -3;
}
INFO("Surface mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
}
GeoLib::GEOObjects geo_objects;
FileIO::XmlGmlInterface xml(geo_objects);
//std::vector<GeoLib::Polyline*> *lines = new std::vector<GeoLib::Polyline*>;
std::array<char, 2> dipol = {{ 'H', 'V' }};
std::array<char,3> const regions = {{'A', 'B', 'C'}};
for (std::size_t j=0; j<dipol.size(); ++j)
{
std::vector<GeoLib::Point*> *points = new std::vector<GeoLib::Point*>;
for (std::size_t i=0; i<regions.size(); ++i)
{
//std::size_t const start_idx (points->size());
getPointsFromFile(*points, csv_in.getValue(), dipol[j], regions[i]);
//std::size_t const end_idx (points->size());
//GeoLib::Polyline* line = new GeoLib::Polyline(*points);
//for (std::size_t j=start_idx; j<end_idx; ++j)
// line->addPoint(j);
//lines->push_back(line);
}
std::string geo_name (std::string("EMI Data ").append(1,dipol[j]));
geo_objects.addPointVec(points, geo_name);
//geo_objects.addPolylineVec(lines, geo_name);
if (mesh != nullptr)
{
GeoMapper mapper(geo_objects, geo_name);
mapper.mapOnMesh(mesh);
}
xml.setNameForExport(geo_name);
std::string const output_name = poly_out.getValue() + "_" + dipol[j] + ".gml";
xml.writeToFile(output_name);
std::vector<double> emi;
for (std::size_t i=0; i<regions.size(); ++i)
getMeasurements(emi, csv_in.getValue(), dipol[j], regions[i]);
writeMeasurementsToFile(emi, poly_out.getValue(), dipol[j]);
std::for_each(points->begin(), points->end(), std::default_delete<GeoLib::Point>());
delete points;
}
delete mesh;
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0;
}
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("Edit material IDs of mesh elements.", ' ', "0.1");
TCLAP::SwitchArg replaceArg("r", "replace", "replace material IDs", false);
TCLAP::SwitchArg condenseArg("c", "condense", "condense material IDs", false);
TCLAP::SwitchArg specifyArg("s", "specify", "specify material IDs by element types (-e)", false);
std::vector<TCLAP::Arg*> vec_xors;
vec_xors.push_back(&replaceArg);
vec_xors.push_back(&condenseArg);
vec_xors.push_back(&specifyArg);
cmd.xorAdd(vec_xors);
TCLAP::ValueArg<std::string> mesh_in("i", "mesh-input-file",
"the name of the file containing the input mesh", true,
"", "file name");
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");
cmd.add(mesh_out);
TCLAP::MultiArg<unsigned> matIDArg("m", "current-material-id",
"current material id to be replaced", false, "number");
cmd.add(matIDArg);
TCLAP::ValueArg<unsigned> newIDArg("n", "new-material-id",
"new material id", false, 0, "number");
cmd.add(newIDArg);
std::vector<std::string> eleList(MeshLib::getMeshElemTypeStringsShort());
TCLAP::ValuesConstraint<std::string> allowedVals(eleList);
TCLAP::ValueArg<std::string> eleTypeArg("e", "element-type",
"element type", false, "", &allowedVals);
cmd.add(eleTypeArg);
cmd.parse(argc, argv);
if (!replaceArg.isSet() && !condenseArg.isSet() && !specifyArg.isSet()) {
INFO("Please select editing mode: -r or -c or -s");
return 0;
} else if (replaceArg.isSet() && condenseArg.isSet()) {
INFO("Please select only one editing mode: -r or -c or -s");
return 0;
} else if (replaceArg.isSet()) {
if (!matIDArg.isSet() || !newIDArg.isSet()) {
INFO("current and new material IDs must be provided for replacement");
return 0;
}
} else if (specifyArg.isSet()) {
if (!eleTypeArg.isSet() || !newIDArg.isSet()) {
INFO("element type and new material IDs must be provided to specify elements");
return 0;
}
}
MeshLib::Mesh* mesh (FileIO::readMeshFromFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
if (condenseArg.isSet()) {
INFO("Condensing material ID...");
MeshLib::ElementValueModification::condense(*mesh);
} else if (replaceArg.isSet()) {
INFO("Replacing material ID...");
const auto vecOldID = matIDArg.getValue();
const unsigned newID = newIDArg.getValue();
for (auto oldID : vecOldID) {
INFO("%d -> %d", oldID, newID);
MeshLib::ElementValueModification::replace(*mesh, oldID, newID, true);
}
} else if (specifyArg.isSet()) {
INFO("Specifying material ID...");
const std::string eleTypeName(eleTypeArg.getValue());
const MeshLib::MeshElemType eleType = MeshLib::String2MeshElemType(eleTypeName);
const unsigned newID = newIDArg.getValue();
unsigned cnt = MeshLib::ElementValueModification::setByElementType(*mesh, eleType, newID);
INFO("updated %d elements", cnt);
}
// write into a file
FileIO::writeMeshToFile(*mesh, mesh_out.getValue());
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0;
}
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;
}