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;
}
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(
"Creates a new file for material properties and sets the material ids in the msh-file to 0",
' ',
"0.1");
TCLAP::ValueArg<std::string> mesh_arg("m",
"mesh",
"the mesh to open from a file",
false,
"",
"filename for mesh input");
cmd.add( mesh_arg );
cmd.parse( argc, argv );
// read mesh
MeshLib::Mesh* mesh(FileIO::readMeshFromFile(mesh_arg.getValue()));
std::vector<MeshLib::Element*> &elems = *(const_cast<std::vector<MeshLib::Element*>*>(&(mesh->getElements())));
std::size_t nElems(elems.size());
std::string name = BaseLib::extractBaseNameWithoutExtension(mesh_arg.getValue());
// create file
std::string new_matname(name + "_prop");
std::ofstream out_prop( new_matname.c_str(), std::ios::out );
if (out_prop.is_open())
{
for (std::size_t i=0; i<nElems; i++)
out_prop << i << "\t" << elems[i]->getValue() << "\n";
out_prop.close();
}
else
{
ERR("Could not create property \"%s\" file.", new_matname.c_str());
return -1;
}
// set mat ids to 0 and write new msh file
for (std::size_t i=0; i<nElems; i++)
elems[i]->setValue(0);
std::string new_mshname(name + "_new.vtu");
INFO("Writing mesh to file \"%s\".", new_mshname.c_str());
FileIO::VtuInterface mesh_io(mesh);
mesh_io.writeToFile (new_mshname);
INFO("New files \"%s\" and \"%s\" written.", new_mshname.c_str(), new_matname.c_str());
std::cout << "Conversion finished." << std::endl;
return 1;
}
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 TIN file into VTU file.", ' ', BaseLib::BuildInfo::git_describe);
TCLAP::ValueArg<std::string> inArg("i", "input-tin-file",
"the name of the file containing the input TIN", true,
"", "string");
cmd.add(inArg);
TCLAP::ValueArg<std::string> outArg("o", "output-vtu-file",
"the name of the file the mesh will be written to", true,
"", "string");
cmd.add(outArg);
cmd.parse(argc, argv);
INFO("reading the TIN file...");
const std::string tinFileName(inArg.getValue());
auto pnt_vec = std::unique_ptr<std::vector<GeoLib::Point*>>(
new std::vector<GeoLib::Point*>);
GeoLib::PointVec point_vec("SurfacePoints", std::move(pnt_vec));
std::unique_ptr<GeoLib::Surface> sfc(FileIO::TINInterface::readTIN(tinFileName, point_vec));
if (!sfc)
return 1;
INFO("TIN read: %d points, %d triangles", pnt_vec->size(), sfc->getNTriangles());
INFO("converting to mesh data");
std::unique_ptr<MeshLib::Mesh> mesh(MeshLib::convertSurfaceToMesh(*sfc, BaseLib::extractBaseNameWithoutExtension(tinFileName), std::numeric_limits<double>::epsilon()));
INFO("Mesh created: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
INFO("Write it into VTU");
FileIO::VtuInterface writer(mesh.get());
writer.writeToFile(outArg.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");
// Bounding box params
TCLAP::ValueArg<double> zLargeArg("", "z-max", "largest allowed extent in z-dimension",
false, std::numeric_limits<double>::max(), "value");
cmd.add(zLargeArg);
TCLAP::ValueArg<double> zSmallArg("", "z-min", "smallest allowed extent in z-dimension",
false, -1 * std::numeric_limits<double>::max(), "value");
cmd.add(zSmallArg);
TCLAP::ValueArg<double> yLargeArg("", "y-max", "largest allowed extent in y-dimension",
false, std::numeric_limits<double>::max(), "value");
cmd.add(yLargeArg);
TCLAP::ValueArg<double> ySmallArg("", "y-min", "smallest allowed extent in y-dimension",
false, -1 * std::numeric_limits<double>::max(), "value");
cmd.add(ySmallArg);
TCLAP::ValueArg<double> xLargeArg("", "x-max", "largest allowed extent in x-dimension",
false, std::numeric_limits<double>::max(), "value");
cmd.add(xLargeArg);
TCLAP::ValueArg<double> xSmallArg("", "x-min", "smallest allowed extent in x-dimension",
false, -1 * std::numeric_limits<double>::max(), "value");
cmd.add(xSmallArg);
// Non-bounding-box params
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);
// I/O params
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::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);
cmd.parse(argc, argv);
MeshLib::Mesh const*const mesh (FileIO::readMeshFromFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
MeshLib::ElementSearch ex(*mesh);
// search elements IDs to be removed
if (zveArg.isSet()) {
const std::size_t n_removed_elements = ex.searchByContent();
INFO("%d zero volume elements found.", n_removed_elements);
}
if (eleTypeArg.isSet()) {
const std::vector<std::string> eleTypeNames = eleTypeArg.getValue();
for (auto typeName : eleTypeNames) {
const MeshLib::MeshElemType type = MeshLib::String2MeshElemType(typeName);
if (type == MeshLib::MeshElemType::INVALID) continue;
const std::size_t n_removed_elements = ex.searchByElementType(type);
INFO("%d %s elements found.", n_removed_elements, typeName.c_str());
}
}
if (matIDArg.isSet()) {
const std::vector<unsigned> vec_matID = matIDArg.getValue();
for (auto matID : vec_matID) {
const std::size_t n_removed_elements = ex.searchByMaterialID(matID);
INFO("%d elements with material ID %d found.", n_removed_elements, matID);
}
}
if (xSmallArg.isSet() || xLargeArg.isSet() ||
ySmallArg.isSet() || yLargeArg.isSet() ||
zSmallArg.isSet() || zLargeArg.isSet())
{
bool aabb_error (false);
if (xSmallArg.getValue() >= xLargeArg.getValue())
{
ERR ("Minimum x-extent larger than maximum x-extent.");
aabb_error = true;
}
if (ySmallArg.getValue() >= yLargeArg.getValue())
{
ERR ("Minimum y-extent larger than maximum y-extent.");
aabb_error = true;
}
if (zSmallArg.getValue() >= zLargeArg.getValue())
{
ERR ("Minimum z-extent larger than maximum z-extent.");
aabb_error = true;
}
if (aabb_error)
return 1;
std::array<MathLib::Point3d, 2> extent({{
MathLib::Point3d(std::array<double,3>{{xSmallArg.getValue(),
ySmallArg.getValue(), zSmallArg.getValue()}}),
MathLib::Point3d(std::array<double,3>{{xLargeArg.getValue(),
yLargeArg.getValue(), zLargeArg.getValue()}})}});
const std::size_t n_removed_elements = ex.searchByBoundingBox(
GeoLib::AABB(extent.begin(), extent.end()));
INFO("%d elements found.", n_removed_elements);
}
// remove the elements and create a new mesh object.
MeshLib::Mesh const*const new_mesh = MeshLib::removeElements(*mesh, ex.getSearchedElementIDs(), mesh->getName());
// 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;
}
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("Simple mesh search 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,"test.msh","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 );
TCLAP::ValueArg<unsigned> number_arg("n","number-of-test-points","the number of test points",true,10000,"positive number");
cmd.add( number_arg );
TCLAP::ValueArg<bool> contiguous_arg("c","use-contiguous-memory","use a contiguous memory for the test",false,true,"yes or no | 1 or 0");
cmd.add( contiguous_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());
INFO ("mem for mesh: %i MB", (mem_with_mesh - mem_without_mesh)/(1024*1024));
#endif
run_time.stop();
INFO ("time for reading: %f s", run_time.elapsed());
// *** preparing test data
std::vector<MeshLib::Node*> const& nodes(mesh->getNodes());
std::vector<GeoLib::Point*> pnts_for_search;
unsigned n(std::min(static_cast<unsigned>(nodes.size()), number_arg.getValue()));
for (size_t k(0); k<n; k++) {
pnts_for_search.push_back(new GeoLib::Point(nodes[k]->getCoords()));
}
std::vector<size_t> idx_found_nodes;
testMeshGridAlgorithm(mesh, pnts_for_search, idx_found_nodes, contiguous_arg.getValue());
for (size_t k(0); k<n; k++) {
delete pnts_for_search[k];
}
delete mesh;
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
}
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("Append line elements into a 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);
TCLAP::ValueArg<std::string> geoFileArg("g", "geo-file",
"the name of the geometry file which contains polylines", true, "", "the name of the geometry file");
cmd.add(geoFileArg);
// parse arguments
cmd.parse(argc, argv);
// read GEO objects
GeoLib::GEOObjects geo_objs;
FileIO::BoostXmlGmlInterface xml(geo_objs);
xml.readFile(geoFileArg.getValue());
std::vector<std::string> geo_names;
geo_objs.getGeometryNames (geo_names);
if (geo_names.empty ())
{
std::cout << "no geometries found" << std::endl;
return -1;
}
const GeoLib::PolylineVec* ply_vec (geo_objs.getPolylineVecObj(geo_names[0]));
if (!ply_vec)
{
std::cout << "could not found polylines" << std::endl;
return -1;
}
// read a mesh
MeshLib::Mesh const*const mesh (FileIO::readMeshFromFile(mesh_in.getValue()));
if (!mesh)
{
ERR("Mesh file %s not found", mesh_in.getValue().c_str());
return 1;
}
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
// add line elements
std::unique_ptr<MeshLib::Mesh> new_mesh =
MeshGeoToolsLib::appendLinesAlongPolylines(*mesh, *ply_vec);
INFO("Mesh created: %d nodes, %d elements.", new_mesh->getNNodes(), new_mesh->getNElements());
// write into a file
FileIO::Legacy::MeshIO meshIO;
meshIO.setMesh(new_mesh.get());
meshIO.writeToFile(mesh_out.getValue());
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 1;
}
int main (int argc, char* argv[])
{
LOGOG_INITIALIZE();
logog::Cout* logog_cout (new logog::Cout);
BaseLib::LogogSimpleFormatter *const custom_format (new BaseLib::LogogSimpleFormatter);
logog_cout->SetFormatter(*custom_format);
TCLAP::CmdLine cmd("Converting a mesh in FEFLOW file format (ASCII, version 5.4) to a vtk unstructured grid file (new OGS file format) or to the old OGS file format - see options.", ' ', "0.1");
TCLAP::ValueArg<std::string> ogs_mesh_arg(
"o",
"out",
"filename for output mesh (if extension is msh, old OGS fileformat is written)",
true,
"",
"filename as string");
cmd.add(ogs_mesh_arg);
TCLAP::ValueArg<std::string> feflow_mesh_arg(
"i",
"in",
"FEFLOW input file (*.fem)",
true,
"",
"filename as string");
cmd.add(feflow_mesh_arg);
cmd.parse(argc, argv);
// *** read mesh
INFO("Reading %s.", feflow_mesh_arg.getValue().c_str());
#ifndef WIN32
BaseLib::MemWatch mem_watch;
unsigned long mem_without_mesh (mem_watch.getVirtMemUsage());
#endif
BaseLib::RunTime run_time;
run_time.start();
FileIO::FEFLOWInterface feflowIO(nullptr);
MeshLib::Mesh const*const mesh(feflowIO.readFEFLOWFile(feflow_mesh_arg.getValue()));
if (mesh == nullptr) {
INFO("Could not read mesh from %s.", feflow_mesh_arg.getValue().c_str());
return -1;
}
#ifndef WIN32
unsigned long mem_with_mesh (mem_watch.getVirtMemUsage());
INFO("Mem for mesh: %i MB", (mem_with_mesh - mem_without_mesh)/(1024*1024));
#endif
run_time.stop();
INFO("Time for reading: %f seconds.", run_time.elapsed());
INFO("Read %d nodes and %d elements.", mesh->getNNodes(), mesh->getNElements());
// *** write mesh in new format
std::string ogs_mesh_fname(ogs_mesh_arg.getValue());
if (BaseLib::getFileExtension(ogs_mesh_fname).compare("msh") == 0) {
INFO("Writing %s.", ogs_mesh_fname.c_str());
FileIO::Legacy::MeshIO mesh_io;
mesh_io.setMesh(mesh);
mesh_io.writeToFile(ogs_mesh_fname);
} else {
if (BaseLib::getFileExtension(ogs_mesh_fname).compare("vtu") != 0) {
ogs_mesh_fname += ".vtu";
}
INFO("Writing %s.", ogs_mesh_fname.c_str());
FileIO::BoostVtuInterface mesh_io;
mesh_io.setMesh(mesh);
mesh_io.writeToFile(ogs_mesh_fname);
}
INFO("\tDone.");
delete 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("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(
"Generates properties for mesh elements of an input mesh deploying a ASC raster file",
' ',
"0.1");
TCLAP::ValueArg<std::string> out_mesh_arg("o",
"out-mesh",
"the mesh is stored to a file of this name",
false,
"",
"filename for mesh output");
cmd.add( out_mesh_arg );
TCLAP::ValueArg<bool> refinement_raster_output_arg("",
"output-refined-raster",
"write refined raster to a new ASC file",
false,
false,
"0");
cmd.add( refinement_raster_output_arg );
TCLAP::ValueArg<unsigned> refinement_arg(
"r",
"refine",
"refinement factor that raises the resolution of the raster data",
false,
1,
"factor (default = 1)");
cmd.add( refinement_arg );
TCLAP::ValueArg<std::string> mapping_arg("",
"mapping-name",
"file name of mapping",
true,
"",
"file name");
cmd.add( mapping_arg );
TCLAP::ValueArg<std::string> raster_arg("",
"raster-file",
"the name of the ASC raster file",
true,
"",
"file name");
cmd.add( raster_arg );
TCLAP::ValueArg<std::string> mesh_arg("m",
"mesh",
"the mesh is read from this file",
true,
"test.msh",
"file name");
cmd.add( mesh_arg );
cmd.parse( argc, argv );
// read mesh
MeshLib::Mesh* dest_mesh(FileIO::readMeshFromFile(mesh_arg.getValue()));
// read raster and if required manipulate it
GeoLib::Raster* raster(FileIO::AsciiRasterInterface::getRasterFromASCFile(
raster_arg.getValue()));
if (refinement_arg.getValue() > 1) {
raster->refineRaster(refinement_arg.getValue());
if (refinement_raster_output_arg.getValue()) {
// write new asc file
std::string new_raster_fname (BaseLib::dropFileExtension(
raster_arg.getValue()));
new_raster_fname += "-" + std::to_string(raster->getNRows()) + "x" +
std::to_string(raster->getNCols()) + ".asc";
FileIO::AsciiRasterInterface::writeRasterAsASC(*raster, new_raster_fname);
}
}
// put raster data in a std::vector
GeoLib::Raster::const_iterator raster_it(raster->begin());
std::size_t n_cols(raster->getNCols()), n_rows(raster->getNRows());
std::size_t size(n_cols * n_rows);
std::vector<double> src_properties(size);
for (unsigned row(0); row<n_rows; row++) {
for (unsigned col(0); col<n_cols; col++) {
src_properties[row * n_cols + col] = *raster_it;
++raster_it;
}
}
{
double mu, var;
std::tie(mu, var) = computeMeanAndVariance(src_properties.begin(), src_properties.end());
INFO("Mean value of source: %f.", mu);
INFO("Variance of source: %f.", var);
}
MeshLib::Mesh* src_mesh(MeshLib::ConvertRasterToMesh(*raster, MeshLib::MeshElemType::QUAD,
MeshLib::UseIntensityAs::MATERIAL).execute());
std::vector<std::size_t> src_perm(size);
std::iota(src_perm.begin(), src_perm.end(), 0);
BaseLib::Quicksort<double>(src_properties, 0, size, src_perm);
// compress the property data structure
const std::size_t mat_map_size(src_properties.size());
std::vector<std::size_t> mat_map(mat_map_size);
mat_map[0] = 0;
std::size_t n_mat(1);
for (std::size_t k(1); k<mat_map_size; ++k) {
if (std::fabs(src_properties[k] - src_properties[k-1]) > std::numeric_limits<double>::epsilon()) {
mat_map[k] = mat_map[k - 1] + 1;
n_mat++;
} else
mat_map[k] = mat_map[k - 1];
}
std::vector<double> compressed_src_properties(n_mat);
compressed_src_properties[0] = src_properties[0];
for (std::size_t k(1), id(1); k<mat_map_size; ++k) {
if (std::fabs(src_properties[k] - src_properties[k-1]) > std::numeric_limits<double>::epsilon()) {
compressed_src_properties[id] = src_properties[k];
id++;
}
}
compressed_src_properties[n_mat - 1] = src_properties[mat_map_size - 1];
// reset materials in source mesh
const std::size_t n_mesh_elements(src_mesh->getNElements());
for (std::size_t k(0); k<n_mesh_elements; k++) {
const_cast<MeshLib::Element*>(src_mesh->getElement(src_perm[k]))->setValue(mat_map[k]);
}
// do the interpolation
MeshLib::Mesh2MeshPropertyInterpolation mesh_interpolation(src_mesh,
&compressed_src_properties);
std::vector<double> dest_properties(dest_mesh->getNElements());
mesh_interpolation.setPropertiesForMesh(const_cast<MeshLib::Mesh*>(dest_mesh),
dest_properties);
const std::size_t n_dest_mesh_elements(dest_mesh->getNElements());
{ // write property file
std::string property_fname(mapping_arg.getValue());
std::ofstream property_out(property_fname.c_str());
if (!property_out)
{
ERR("Could not open file %s for writing the mapping.", property_fname.c_str());
return -1;
}
for (std::size_t k(0); k < n_dest_mesh_elements; k++)
property_out << k << " " << dest_properties[k] << "\n";
property_out.close();
}
{
double mu, var;
std::tie(mu, var) = computeMeanAndVariance(dest_properties.begin(), dest_properties.end());
INFO("Mean value of destination: %f.", mu);
INFO("Variance of destination: %f.", var);
}
if (! out_mesh_arg.getValue().empty()) {
std::vector<std::size_t> dest_perm(n_dest_mesh_elements);
std::iota(dest_perm.begin(), dest_perm.end(), 0);
BaseLib::Quicksort<double>(dest_properties, 0, n_dest_mesh_elements, dest_perm);
// reset materials in destination mesh
for (std::size_t k(0); k<n_dest_mesh_elements; k++) {
const_cast<MeshLib::Element*>(dest_mesh->getElement(dest_perm[k]))->setValue(k);
}
FileIO::Legacy::MeshIO mesh_writer;
mesh_writer.setPrecision(12);
mesh_writer.setMesh(dest_mesh);
mesh_writer.writeToFile(out_mesh_arg.getValue());
}
delete raster;
delete src_mesh;
delete dest_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("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;
}
int main (int argc, char* argv[])
{
LOGOG_INITIALIZE();
logog::Cout* logog_cout (new logog::Cout);
BaseLib::LogogSimpleFormatter *const custom_format (new BaseLib::LogogSimpleFormatter);
logog_cout->SetFormatter(*custom_format);
TCLAP::CmdLine cmd("Converting meshes in gmsh file format (ASCII, version 2.2) to a vtk unstructured grid file (new OGS file format) or to the old OGS file format - see options.", ' ', "0.1");
TCLAP::ValueArg<std::string> ogs_mesh_arg(
"o",
"out",
"filename for output mesh (if extension is msh, old OGS fileformat is written)",
true,
"",
"filename as string");
cmd.add(ogs_mesh_arg);
TCLAP::ValueArg<std::string> gmsh_mesh_arg(
"i",
"in",
"gmsh input file",
true,
"",
"filename as string");
cmd.add(gmsh_mesh_arg);
TCLAP::SwitchArg exclude_lines_arg("e", "exclude-lines",
"if set, lines will not be written to the ogs mesh");
cmd.add(exclude_lines_arg);
cmd.parse(argc, argv);
// *** read mesh
INFO("Reading %s.", gmsh_mesh_arg.getValue().c_str());
#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(FileIO::GMSHInterface::readGMSHMesh(gmsh_mesh_arg.getValue()));
if (mesh == nullptr) {
INFO("Could not read mesh from %s.", gmsh_mesh_arg.getValue().c_str());
return -1;
}
#ifndef WIN32
unsigned long mem_with_mesh (mem_watch.getVirtMemUsage());
INFO("Mem for mesh: %i MB", (mem_with_mesh - mem_without_mesh)/(1024*1024));
#endif
INFO("Time for reading: %f seconds.", run_time.elapsed());
INFO("Read %d nodes and %d elements.", mesh->getNNodes(), mesh->getNElements());
// *** remove line elements on request
if (exclude_lines_arg.getValue()) {
auto ex = MeshLib::ElementSearch(*mesh);
ex.searchByElementType(MeshLib::MeshElemType::LINE);
auto m = MeshLib::removeElements(*mesh, ex.getSearchedElementIDs(), mesh->getName()+"-withoutLines");
if (m != nullptr) {
INFO("Removed %d lines.", mesh->getNElements() - m->getNElements());
std::swap(m, mesh);
delete m;
} else {
INFO("Mesh does not contain any lines.");
}
}
// *** write mesh in new format
std::string ogs_mesh_fname(ogs_mesh_arg.getValue());
if (BaseLib::getFileExtension(ogs_mesh_fname).compare("msh") == 0) {
INFO("Writing %s.", ogs_mesh_fname.c_str());
FileIO::Legacy::MeshIO mesh_io;
mesh_io.setMesh(mesh);
mesh_io.writeToFile(ogs_mesh_fname);
} else {
if (BaseLib::getFileExtension(ogs_mesh_fname).compare("vtu") != 0) {
ogs_mesh_fname += ".vtu";
}
INFO("Writing %s.", ogs_mesh_fname.c_str());
FileIO::VtuInterface mesh_io(mesh);
mesh_io.writeToFile(ogs_mesh_fname);
}
INFO("\tDone.");
delete 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("Query mesh information", ' ', BaseLib::BuildInfo::git_describe);
TCLAP::UnlabeledValueArg<std::string> mesh_arg("mesh-file","input mesh file",true,"","string");
cmd.add( mesh_arg );
TCLAP::MultiArg<std::size_t> eleId_arg("e","element-id","element ID",false,"number");
cmd.add( eleId_arg );
TCLAP::MultiArg<std::size_t> nodeId_arg("n","node-id","node ID",false,"number");
cmd.add( nodeId_arg );
cmd.parse( argc, argv );
const std::string filename(mesh_arg.getValue());
// read the mesh file
const MeshLib::Mesh* mesh = FileIO::readMeshFromFile(filename);
if (!mesh)
return 1;
std::cout << std::scientific << std::setprecision(12);
for (auto ele_id : eleId_arg.getValue())
{
std::cout << "--------------------------------------------------------" << std::endl;
auto* ele = mesh->getElement(ele_id);
std::cout << "# Element " << ele->getID() << std::endl;
std::cout << "Type : " << CellType2String(ele->getCellType()) << std::endl;
std::cout << "Mat ID : " << ele->getValue() << std::endl;
std::cout << "Nodes: " << std::endl;
for (unsigned i=0; i<ele->getNNodes(); i++)
std::cout << ele->getNode(i)->getID() << " " << *ele->getNode(i) << std::endl;
std::cout << "Content: " << ele->getContent() << std::endl;
std::cout << "Neighbors: ";
for (unsigned i=0; i<ele->getNNeighbors(); i++)
{
if (ele->getNeighbor(i))
std::cout << ele->getNeighbor(i)->getID() << " ";
else
std::cout << "none ";
}
std::cout << std::endl;
}
for (auto node_id : nodeId_arg.getValue())
{
std::cout << "--------------------------------------------------------" << std::endl;
auto* node = mesh->getNode(node_id);
std::cout << "# Node" << node->getID() << std::endl;
std::cout << "Coordinates: " << *node << std::endl;
std::cout << "Connected elements: " ;
for (unsigned i=0; i<node->getNElements(); i++)
std::cout << node->getElement(i)->getID() << " ";
std::cout << std::endl;
}
delete mesh;
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
}
