void MeshElementRemovalDialog::on_materialIDCheckBox_toggled(bool is_checked)
{
materialListWidget->setEnabled(is_checked);
if (is_checked && (_currentIndex != _matIDIndex))
{
materialListWidget->clear();
_matIDIndex = _currentIndex;
auto mesh = _project.getMesh(meshNameComboBox->currentText().toStdString());
auto const opt_mat_ids = mesh->getProperties().getPropertyVector<int>("MaterialIDs");
if (!opt_mat_ids) {
INFO("Properties \"MaterialIDs\" not found in the mesh \"%s\".",
mesh->getName().c_str());
return;
}
auto const& mat_ids = opt_mat_ids.get();
if (mat_ids.size() != mesh->getNElements()) {
INFO("Size mismatch: Properties \"MaterialIDs\" contains %u values,"
" the mesh \"%s\" contains %u elements.", mat_ids.size(),
mesh->getName().c_str(), mesh->getNElements());
return;
}
auto max_material = std::max_element(mat_ids.cbegin(), mat_ids.cend());
for (unsigned i=0; i <= static_cast<unsigned>(*max_material); ++i)
materialListWidget->addItem(QString::number(i));
}
}
struct slName *randomBigBedIds(char *table, struct sqlConnection *conn, int count)
/* Return some arbitrary IDs from a bigBed file. */
{
/* Figure out bigBed file name and open it. Get contents for first chromosome as an example. */
struct slName *idList = NULL;
char *fileName = bigBedFileName(table, conn);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct bbiChromInfo *chromList = bbiChromList(bbi);
struct lm *lm = lmInit(0);
int orderedCount = count * 4;
if (orderedCount < 100)
orderedCount = 100;
struct bigBedInterval *iv, *ivList = getNElements(bbi, chromList, lm, orderedCount);
shuffleList(&ivList);
// Make a list of item names from intervals.
int outCount = 0;
for (iv = ivList; iv != NULL && outCount < count; iv = iv->next)
{
char *row[bbi->fieldCount];
char startBuf[16], endBuf[16];
bigBedIntervalToRow(iv, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
if (idList == NULL || differentString(row[3], idList->name))
{
slAddHead(&idList, slNameNew(row[3]));
outCount++;
}
}
lmCleanup(&lm);
bbiFileClose(&bbi);
freeMem(fileName);
return idList;
}
void MeshElementRemovalDialog::on_meshNameComboBox_currentIndexChanged(int idx)
{
Q_UNUSED(idx);
this->_currentIndex = this->meshNameComboBox->currentIndex();
this->newMeshNameEdit->setText(this->meshNameComboBox->currentText() + "_new");
this->elementTypeListWidget->clearSelection();
this->materialListWidget->clearSelection();
if (this->boundingBoxCheckBox->isChecked()) this->on_boundingBoxCheckBox_toggled(true);
auto mesh = _project.getMesh(meshNameComboBox->currentText().toStdString());
auto materialIds = mesh->getProperties().getPropertyVector<int>("MaterialIDs");
if (materialIds)
{
if (materialIds->size() != mesh->getNElements())
{
ERR ("Incorrect mesh structure: Number of Material IDs does not match number of mesh elements.");
OGSError::box("Incorrect mesh structure detected.\n Number of Material IDs does not match number of mesh elements");
QMetaObject::invokeMethod(this, "close", Qt::QueuedConnection);
}
materialIDCheckBox->setEnabled(true);
if (materialIDCheckBox->isChecked())
on_materialIDCheckBox_toggled(true);
}
else
materialIDCheckBox->setEnabled(false);
}
TEST(MeshLib, RemoveElements)
{
auto mesh = std::unique_ptr<MeshLib::Mesh>{
MeshLib::MeshGenerator::generateLineMesh(1.0, 9)};
std::vector<std::size_t> removed_ele_ids;
for (std::size_t i=0; i<5; i++)
removed_ele_ids.push_back(i);
auto new_mesh = std::unique_ptr<MeshLib::Mesh>{
MeshLib::removeElements(*mesh, removed_ele_ids, "")};
ASSERT_EQ(5u, new_mesh->getNNodes());
ASSERT_EQ(5u, new_mesh->getNBaseNodes());
ASSERT_EQ(4u, new_mesh->getNElements());
for (std::size_t i=0; i<new_mesh->getNNodes(); i++)
ASSERT_TRUE(*mesh->getNode(5+i) == *new_mesh->getNode(i));
}
TEST_F(TestVtkMeshConverter, Conversion)
{
auto mesh = std::unique_ptr<MeshLib::Mesh>(
MeshLib::VtkMeshConverter::convertUnstructuredGrid(vtu));
ASSERT_EQ(mesh->getNNodes(), vtu->GetNumberOfPoints());
ASSERT_EQ(mesh->getNElements(), vtu->GetNumberOfCells());
ASSERT_EQ(mesh->getElement(0)->getCellType(), MeshLib::CellType::HEX8);
auto meshProperties = mesh->getProperties();
// MaterialIDs are converted to an int property
auto materialIds = meshProperties.getPropertyVector<int>("MaterialIDs");
ASSERT_TRUE(static_cast<bool>(materialIds));
auto vtkMaterialIds = vtu->GetCellData()->GetArray("MaterialIDs");
ASSERT_EQ((*materialIds).size(), vtkMaterialIds->GetNumberOfTuples());
for(std::size_t i = 0; i < (*materialIds).size(); i++)
ASSERT_EQ((*materialIds)[i], vtkMaterialIds->GetTuple1(i));
}
void showSchemaBigBed(char *table, struct trackDb *tdb)
/* Show schema on bigBed. */
{
/* Figure out bigBed file name and open it. Get contents for first chromosome as an example. */
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(database);
char *fileName = bigBedFileName(table, conn);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct bbiChromInfo *chromList = bbiChromList(bbi);
struct lm *lm = lmInit(0);
struct bigBedInterval *ivList = getNElements(bbi, chromList, lm, 10);
/* Get description of columns, making it up from BED records if need be. */
struct asObject *as = bigBedAsOrDefault(bbi);
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>Big Bed File:</B> %s", fileName);
if (bbi->version >= 2)
{
hPrintf("<BR><B>Item Count:</B> ");
printLongWithCommas(stdout, bigBedItemCount(bbi));
}
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
if (ivList != NULL)
hPrintf("<TH>example</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
char *row[bbi->fieldCount];
char startBuf[16], endBuf[16];
if (ivList != NULL)
{
char *dupeRest = lmCloneString(lm, ivList->rest); /* Manage rest-stomping side-effect */
bigBedIntervalToRow(ivList, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
ivList->rest = dupeRest;
}
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
if (ivList != NULL)
hPrintf("<TD>%s</TD>", row[colCount]);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
/* If more fields than descriptions put up minimally helpful info (at least has example). */
for ( ; colCount < bbi->fieldCount; ++colCount)
{
hPrintf("<TR><TD><TT>column%d</TT></TD>", colCount+1);
if (ivList != NULL)
hPrintf("<TD>%s</TD>", row[colCount]);
hPrintf("<TD>n/a</TD></TR>\n");
}
hTableEnd();
if (ivList != NULL)
{
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Print field names as column headers for example */
hPrintf("<TR>");
int colIx = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TH>%s</TH>", col->name);
++colIx;
}
for (; colIx < colCount; ++colIx)
hPrintf("<TH>column%d</TH>", colIx+1);
hPrintf("</TR>\n");
/* Print sample lines. */
struct bigBedInterval *iv;
for (iv=ivList; iv != NULL; iv = iv->next)
{
bigBedIntervalToRow(iv, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
hPrintf("<TR>");
for (colIx=0; colIx<colCount; ++colIx)
{
writeHtmlCell(row[colIx]);
}
hPrintf("</TR>\n");
}
hTableEnd();
}
printTrackHtml(tdb);
/* Clean up and go home. */
lmCleanup(&lm);
bbiFileClose(&bbi);
freeMem(fileName);
hFreeConn(&conn);
}
// Writes the mesh into a vtk file, reads the file back and converts it into a
// OGS mesh
TEST_F(InSituMesh, MappedMeshSourceRoundtrip)
{
// TODO Add more comparison criteria
ASSERT_TRUE(mesh != nullptr);
std::string test_data_file(BaseLib::BuildInfo::tests_tmp_path + "/MappedMeshSourceRoundtrip.vtu");
// -- Test VtkMappedMeshSource, i.e. OGS mesh to VTK mesh
vtkNew<InSituLib::VtkMappedMeshSource> vtkSource;
vtkSource->SetMesh(mesh);
vtkSource->Update();
vtkUnstructuredGrid* output = vtkSource->GetOutput();
// Point and cell numbers
ASSERT_EQ((subdivisions+1)*(subdivisions+1)*(subdivisions+1), output->GetNumberOfPoints());
ASSERT_EQ(subdivisions*subdivisions*subdivisions, output->GetNumberOfCells());
// Point data arrays
vtkDataArray* pointDoubleArray = output->GetPointData()->GetScalars("PointDoubleProperty");
ASSERT_EQ(pointDoubleArray->GetSize(), mesh->getNNodes());
ASSERT_EQ(pointDoubleArray->GetComponent(0, 0), 1.0);
double* range = pointDoubleArray->GetRange(0);
ASSERT_EQ(range[0], 1.0);
ASSERT_EQ(range[1], 1.0 + mesh->getNNodes() - 1.0);
vtkDataArray* pointIntArray = output->GetPointData()->GetScalars("PointIntProperty");
ASSERT_EQ(pointIntArray->GetSize(), mesh->getNNodes());
ASSERT_EQ(pointIntArray->GetComponent(0, 0), 1.0);
range = pointIntArray->GetRange(0);
ASSERT_EQ(range[0], 1.0);
ASSERT_EQ(range[1], 1 + mesh->getNNodes() - 1);
vtkDataArray* pointUnsignedArray = output->GetPointData()->GetScalars("PointUnsignedProperty");
ASSERT_EQ(pointUnsignedArray->GetSize(), mesh->getNNodes());
ASSERT_EQ(pointUnsignedArray->GetComponent(0, 0), 1.0);
range = pointUnsignedArray->GetRange(0);
ASSERT_EQ(range[0], 1.0);
ASSERT_EQ(range[1], 1 + mesh->getNNodes() - 1);
// Cell data arrays
vtkDataArray* cellDoubleArray = output->GetCellData()->GetScalars("CellDoubleProperty");
ASSERT_EQ(cellDoubleArray->GetSize(), mesh->getNElements());
ASSERT_EQ(cellDoubleArray->GetComponent(0, 0), 1.0);
range = cellDoubleArray->GetRange(0);
ASSERT_EQ(range[0], 1.0);
ASSERT_EQ(range[1], 1.0 + mesh->getNElements() - 1.0);
vtkDataArray* cellIntArray = output->GetCellData()->GetScalars("CellIntProperty");
ASSERT_EQ(cellIntArray->GetSize(), mesh->getNElements());
ASSERT_EQ(cellIntArray->GetComponent(0, 0), 1.0);
range = cellIntArray->GetRange(0);
ASSERT_EQ(range[0], 1.0);
ASSERT_EQ(range[1], 1 + mesh->getNElements() - 1);
vtkDataArray* cellUnsignedArray = output->GetCellData()->GetScalars("CellUnsignedProperty");
ASSERT_EQ(cellUnsignedArray->GetSize(), mesh->getNElements());
ASSERT_EQ(cellUnsignedArray->GetComponent(0, 0), 1.0);
range = cellUnsignedArray->GetRange(0);
ASSERT_EQ(range[0], 1.0);
ASSERT_EQ(range[1], 1 + mesh->getNElements() - 1);
// -- Write VTK mesh to file (in all combinations of binary, appended and compressed)
// atm vtkXMLWriter::Appended does not work, see http://www.paraview.org/Bug/view.php?id=13382
for(int dataMode : { vtkXMLWriter::Ascii, vtkXMLWriter::Binary })
{
for(bool compressed : { true, false })
{
if(dataMode == vtkXMLWriter::Ascii && compressed)
continue;
FileIO::VtuInterface vtuInterface(mesh, dataMode, compressed);
ASSERT_TRUE(vtuInterface.writeToFile(test_data_file));
// -- Read back VTK mesh
vtkSmartPointer<vtkXMLUnstructuredGridReader> reader =
vtkSmartPointer<vtkXMLUnstructuredGridReader>::New();
reader->SetFileName(test_data_file.c_str());
reader->Update();
vtkUnstructuredGrid *vtkMesh = reader->GetOutput();
// Both VTK meshes should be identical
ASSERT_EQ(vtkMesh->GetNumberOfPoints(), output->GetNumberOfPoints());
ASSERT_EQ(vtkMesh->GetNumberOfCells(), output->GetNumberOfCells());
ASSERT_EQ(vtkMesh->GetPointData()->GetScalars("PointDoubleProperty")->GetNumberOfTuples(),
pointDoubleArray->GetNumberOfTuples());
ASSERT_EQ(vtkMesh->GetPointData()->GetScalars("PointIntProperty")->GetNumberOfTuples(),
pointIntArray->GetNumberOfTuples());
ASSERT_EQ(vtkMesh->GetPointData()->GetScalars("PointUnsignedProperty")->GetNumberOfTuples(),
pointUnsignedArray->GetNumberOfTuples());
ASSERT_EQ(vtkMesh->GetCellData()->GetScalars("CellDoubleProperty")->GetNumberOfTuples(),
cellDoubleArray->GetNumberOfTuples());
ASSERT_EQ(vtkMesh->GetCellData()->GetScalars("CellIntProperty")->GetNumberOfTuples(),
cellIntArray->GetNumberOfTuples());
ASSERT_EQ(vtkMesh->GetCellData()->GetScalars("CellUnsignedProperty")->GetNumberOfTuples(),
cellUnsignedArray->GetNumberOfTuples());
// Both OGS meshes should be identical
auto newMesh = std::unique_ptr<MeshLib::Mesh>{MeshLib::VtkMeshConverter::convertUnstructuredGrid(vtkMesh)};
ASSERT_EQ(mesh->getNNodes(), newMesh->getNNodes());
ASSERT_EQ(mesh->getNElements(), newMesh->getNElements());
// Both properties should be identical
auto meshProperties = mesh->getProperties();
auto newMeshProperties = newMesh->getProperties();
ASSERT_EQ(newMeshProperties.hasPropertyVector("PointDoubleProperty"),
meshProperties.hasPropertyVector("PointDoubleProperty"));
ASSERT_EQ(newMeshProperties.hasPropertyVector("PointIntProperty"),
meshProperties.hasPropertyVector("PointIntProperty"));
ASSERT_EQ(newMeshProperties.hasPropertyVector("PointUnsignedProperty"),
meshProperties.hasPropertyVector("PointUnsignedProperty"));
ASSERT_EQ(newMeshProperties.hasPropertyVector("CellDoubleProperty"),
meshProperties.hasPropertyVector("CellDoubleProperty"));
ASSERT_EQ(newMeshProperties.hasPropertyVector("CellIntProperty"),
meshProperties.hasPropertyVector("CellIntProperty"));
ASSERT_EQ(newMeshProperties.hasPropertyVector("CellUnsignedProperty"),
meshProperties.hasPropertyVector("CellUnsignedProperty"));
ASSERT_EQ(newMeshProperties.hasPropertyVector("MaterialIDs"),
meshProperties.hasPropertyVector("MaterialIDs"));
// Check some properties on equality
auto doubleProps = meshProperties.getPropertyVector<double>("PointDoubleProperty");
auto newDoubleProps = newMeshProperties.getPropertyVector<double>("PointDoubleProperty");
ASSERT_EQ((*newDoubleProps).getTupleSize(), (*doubleProps).getTupleSize());
ASSERT_EQ((*newDoubleProps).getNumberOfTuples(), (*doubleProps).getNumberOfTuples());
ASSERT_EQ((*newDoubleProps).size(), (*doubleProps).size());
for(std::size_t i = 0; i < (*doubleProps).size(); i++)
ASSERT_EQ((*newDoubleProps)[i], (*doubleProps)[i]);
auto unsignedProps = meshProperties.getPropertyVector<unsigned>("CellUnsignedProperty");
auto newUnsignedIds = newMeshProperties.getPropertyVector<unsigned>("CellUnsignedProperty");
ASSERT_EQ((*newUnsignedIds).getTupleSize(), (*unsignedProps).getTupleSize());
ASSERT_EQ((*newUnsignedIds).getNumberOfTuples(), (*unsignedProps).getNumberOfTuples());
ASSERT_EQ((*newUnsignedIds).size(), (*unsignedProps).size());
for(std::size_t i = 0; i < (*unsignedProps).size(); i++)
ASSERT_EQ((*newUnsignedIds)[i], (*unsignedProps)[i]);
auto materialIds = meshProperties.getPropertyVector<int>("MaterialIDs");
auto newMaterialIds = newMeshProperties.getPropertyVector<int>("MaterialIDs");
ASSERT_EQ((*newMaterialIds).getTupleSize(), (*materialIds).getTupleSize());
ASSERT_EQ((*newMaterialIds).getNumberOfTuples(), (*materialIds).getNumberOfTuples());
ASSERT_EQ((*newMaterialIds).size(), (*materialIds).size());
for(std::size_t i = 0; i < (*materialIds).size(); i++)
ASSERT_EQ((*newMaterialIds)[i], (*materialIds)[i]);
}
}
}
int main (int argc, char* argv[])
{
ApplicationsLib::LogogSetup logog_setup;
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
MeshLib::IO::writeMeshToFile(*mesh, ogs_mesh_arg.getValue());
delete mesh;
}
