Class for reading data from HDF5 files. More...

Detailed Description

Definition at line 60 of file hdf5Reader.H.

Public Member Functions
	hdf5Reader (std::string fname, std::string _outputFname, int _verb=0)
	Construct HDF5 reader object. More...

virtual	~hdf5Reader ()

int	openFile ()
	Open HDF5 file. More...

int	closeFile ()
	Close HDF5 file. More...

int	readTopDataSet (std::string dsetName, std::string &buffer)
	Read string data from top level HDF5 DataSet. More...

int	readDataSet (DataSet dset, std::string &buffer)
	Read string data from generic HDF5 DataSet. More...

template<class T >
int	readTopDataSet (std::string dsetName, std::vector< T > &buffer)
	Read numeric data from top level HDF5 DataSet. More...

template<class T >
int	readDataSet (DataSet dset, std::vector< T > &buffer)
	Read numeric data from generic HDF5 DataSet. More...

int	readGroup (std::string groupName, Group &group)
	Read existing HDF5 Group. More...

template<class T >
int	readGroupDataSet (std::string dsetName, Group &group, std::vector< T > &buffer)
	Read numeric data from HDF5 group. More...

std::string	getFileName ()
	Get HDF5 filename. More...

template<class T >
void	flattenBuffer2d (std::vector< std::vector< T >> originalBuffer, std::vector< T > &flatBuffer)
	Flatten 2d data buffer. More...

template<class T >
void	unflattenBuffer2d (std::vector< T > flatBuffer, std::vector< std::vector< T >> &originalBuffer)
	Unflatten 2d data buffer. More...

void	exportToVTKMesh ()
	Export to VTK format. More...

vtkSmartPointer< vtkDataSet >	getVTKMesh ()
	Get VTK mesh object. More...

void	exportToMeshBase ()
	Export HDF5 mesh to meshBase object. More...

meshBase *	getMeshBase ()
	Get meshBase object. More...

void	writeVTK ()
	Write mesh to VTK file. More...

void	setFields (meshBase *myMeshBase, std::vector< std::string > dataNames, std::vector< std::vector< double >> data, int pointOrCell)
	Set meshBase field data. More...

void	setNumberOfVertices (int numVertices)
	Set number of vertices in meshBase. More...

void	setNumberOfElements (int numElements)
	Set number of elements in meshBase. More...

void	setNumberOfDimensions (int numDimensions)
	Set number of spatial dimensions in meshBase. More...

void	setCoordinates (std::vector< double > xCrd)
	Set meshBase 1d coordinate data. More...

void	setCoordinates (std::vector< double > xCrd, std::vector< double > yCrd)
	Set meshBase 2d coordinate data. More...

void	setCoordinates (std::vector< double > xCrd, std::vector< double > yCrd, std::vector< double > zCrd)
	Set meshBase 3d coordinate data. More...

void	setConnectivities (std::vector< std::map< int, std::vector< int >>> elementConnectivity)
	Set meshBase element connectivity table. More...

void	setElementTypes (std::vector< int > vtkElementTypes)
	Set VTK element types for each element. More...

void	setElementTypesList (std::vector< int > vtkElementTypesList)
	Set list of each unique type of VTK element in mesh. More...

std::vector< int >	getElementConnectivity (int elementId)
	Get element connectivity for global element ID. More...

Protected Attributes
std::string	h5FileName
	HDF5 filename. More...

std::string	baseH5FileName
	base of HDF5 filename More...

std::string	outputFname
	VTK output filename. More...

int	verb
	verbosity flag More...

H5File	file
	HDF5 file object. More...

vtkSmartPointer< vtkDataSet >	vtkMesh
	VTK DataSet object. More...

meshBase *	myMeshBase
	meshBase object More...

std::vector< double >	xCrd

std::vector< double >	yCrd

std::vector< double >	zCrd
	vector of coordinates More...

std::vector< std::map< int, std::vector< int > > >	elementConnectivity
	element connectivity table More...

int	numVertices
	number of vertices in mesh More...

int	numElements
	number of elements in mesh More...

int	numDimensions
	number of spatial dimensions More...

std::vector< int >	vtkElementTypes
	vector of VTK element type for each element More...

std::vector< int >	vtkElementTypesList
	vector storing list of each unique VTK element type More...

Inherited by proteusHdf5.

Constructor & Destructor Documentation

◆ hdf5Reader()

hdf5Reader::hdf5Reader	(	std::string	fname,
		std::string	_outputFname,
		int	_verb = `0`
	)

inline

Parameters

fname	HDF5 filename
_outputFName	Filename for VTK output file
_verb	Boolean verbosity flag

Definition at line 67 of file hdf5Reader.H.

       :  // Initialization of class variables
         h5FileName(fname),
         outputFname(_outputFname),
         verb(_verb),
         vtkMesh(0) {
     // Parse filename
     std::size_t _loc = h5FileName.find_last_of(".");
     baseH5FileName = h5FileName.substr(0, _loc);
   };

◆ ~hdf5Reader()

virtual hdf5Reader::~hdf5Reader ( )

inlinevirtual

Definition at line 79 of file hdf5Reader.H.

79 {};

Member Function Documentation

◆ closeFile()

int hdf5Reader::closeFile ( )

Returns: Integer flag: 0 (failure) or 1 (success)

Definition at line 63 of file hdf5Reader.C.

References file, and h5FileName.

Referenced by proteusHdf5::proteusHdf5().

                           {
   std::cout << "Closing HDF5 file " << h5FileName << std::endl;
 
   try {
     // Close HDF5 file
     file.close();
   } catch (FileIException error) {
 #if H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && H5_VERS_RELEASE >= 20
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 10 && H5_VERS_RELEASE >= 2
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 11 && H5_VERS_RELEASE >= 0
       error.printErrorStack();
 #else
     error.printError();
 #endif
     return -1;
   }
   return 0;
 }

◆ exportToMeshBase()

void hdf5Reader::exportToMeshBase ( )

Definition at line 313 of file hdf5Reader.C.

References meshBase::Create(), exportToVTKMesh(), myMeshBase, and outputFname.

Referenced by proteusHdf5::proteusHdf5(), and writeVTK().

                                   {
   std::cout << "Exporting hdf5Reader object to meshBase format..." << std::endl;
   if (!vtkMesh) {
     exportToVTKMesh();
   }
   myMeshBase = meshBase::Create(vtkMesh, outputFname);
 }

◆ exportToVTKMesh()

void hdf5Reader::exportToVTKMesh ( )

Definition at line 241 of file hdf5Reader.C.

References getElementConnectivity(), NEM::MSH::New(), numDimensions, numElements, numVertices, points, vtkElementTypes, xCrd, yCrd, and zCrd.

Referenced by exportToMeshBase(), getVTKMesh(), and proteusHdf5::proteusHdf5().

                                  {
   std::cout << "Exporting hdf5Reader object to VTK format..." << std::endl;
 
   if (!vtkMesh) {
     // declare vtk dataset
     auto dataSet_tmp = vtkSmartPointer<vtkUnstructuredGrid>::New();
 
     // points to be pushed into dataSet
     auto points = vtkSmartPointer<vtkPoints>::New();
     // set double precision points
     points->SetDataTypeToDouble();
 
     // allocate size for vtk point container
     points->SetNumberOfPoints(numVertices);
 
     if (numDimensions == 2) {
       for (int i = 0; i < numVertices; ++i) {
         points->SetPoint(i, xCrd[i], yCrd[i], 0.0);
       }
     } else {
       for (int i = 0; i < numVertices; ++i) {
         points->SetPoint(i, xCrd[i], yCrd[i], zCrd[i]);
       }
     }
     // add points to vtk mesh data structure
     std::cout << "    setting VTK point data..." << std::endl;
     dataSet_tmp->SetPoints(points);
     // allocate space for elements
     std::cout << "    allocating memory for elements..." << std::endl;
     dataSet_tmp->Allocate(numElements);
     // add the elements
     std::cout << "    adding VTK elements..." << std::endl;
     for (int i = 0; i < numElements; ++i) {
       auto vtkElmIds = vtkSmartPointer<vtkIdList>::New();
       std::vector<int> elmIds(getElementConnectivity(i));
       vtkElmIds->SetNumberOfIds(elmIds.size());
       for (int j = 0; j < elmIds.size(); ++j) {
         vtkElmIds->SetId(j, elmIds[j] - 0);
       }
       switch (vtkElementTypes[i]) {
 #if VTK_MAJOR_VERSION > 8 || (VTK_MAJOR_VERSION == 8 && VTK_MINOR_VERSION >= 1)
         case VTK_LAGRANGE_QUADRILATERAL:
           dataSet_tmp->InsertNextCell(VTK_LAGRANGE_QUADRILATERAL, vtkElmIds);
           break;
 #endif
         case VTK_QUAD:
           dataSet_tmp->InsertNextCell(VTK_QUAD, vtkElmIds);
           break;
         case VTK_TRIANGLE:
           dataSet_tmp->InsertNextCell(VTK_TRIANGLE, vtkElmIds);
           break;
         default:
           std::cerr << "Unknown element type " << vtkElementTypes[i]
                     << std::endl;
           break;
       }
     }
     // build links - element incidences
     dataSet_tmp->BuildLinks();
     vtkMesh = dataSet_tmp;
   }
 }

◆ flattenBuffer2d()

template<class T >

void hdf5Reader::flattenBuffer2d	(	std::vector< std::vector< T >>	originalBuffer,
		std::vector< T > &	flatBuffer
	)

inline

Parameters

originalBuffer	Original unflattened data
flatBuffer	Output flattened data

Definition at line 241 of file hdf5Reader.H.

                                                  {
     // Populate flat buffer
     for (auto bufItr1 = originalBuffer.begin(); bufItr1 != originalBuffer.end();
          bufItr1++) {
       for (auto bufItr2 = (*bufItr1).begin(); bufItr2 != (*bufItr1).end();
            bufItr2++) {
         flatBuffer.push_back(*bufItr2);
       }
     }
   }

◆ getElementConnectivity()

std::vector< int > hdf5Reader::getElementConnectivity ( int elementId )

Parameters

elementId Element ID

Returns: Element connectivity table

Definition at line 195 of file hdf5Reader.C.

References elementConnectivity, vtkElementTypes, and vtkElementTypesList.

Referenced by exportToVTKMesh().

                                                                {
   int nVerts;
   int connId = -1;
 #if VTK_MAJOR_VERSION > 8 || (VTK_MAJOR_VERSION == 8 && VTK_MINOR_VERSION >= 1)
   if (vtkElementTypes[elementId] == VTK_LAGRANGE_QUADRILATERAL) {
     nVerts = 16;
     auto itr = std::find(vtkElementTypesList.begin(), vtkElementTypesList.end(),
                          VTK_LAGRANGE_QUADRILATERAL);
     if (itr != vtkElementTypesList.end()) {
       connId = distance(vtkElementTypesList.begin(), itr);
     }
   } else if (vtkElementTypes[elementId] == VTK_QUAD)
 #else
   if (vtkElementTypes[elementId] == VTK_QUAD)
 #endif
   {
     nVerts = 4;
     auto itr = std::find(vtkElementTypesList.begin(), vtkElementTypesList.end(),
                          VTK_QUAD);
     if (itr != vtkElementTypesList.end()) {
       connId = distance(vtkElementTypesList.begin(), itr);
     }
   } else if (vtkElementTypes[elementId] == VTK_TRIANGLE) {
     nVerts = 3;
     auto itr = std::find(vtkElementTypesList.begin(), vtkElementTypesList.end(),
                          VTK_TRIANGLE);
     if (itr != vtkElementTypesList.end()) {
       connId = distance(vtkElementTypesList.begin(), itr);
     }
   } else {
     std::cerr << "Element type not supported: " << vtkElementTypes[elementId]
               << std::endl;
     exit(-1);
   }
   if (connId != -1) {
     std::vector<int> subConnectivity(
         elementConnectivity[connId][elementId].begin(),
         elementConnectivity[connId][elementId].begin() + nVerts);
     return subConnectivity;
   } else {
     std::cerr << "Element type " << vtkElementTypes[elementId]
               << " not found in connectivity table" << std::endl;
     exit(-1);
   }
 }

◆ getFileName()

std::string hdf5Reader::getFileName ( )

Returns: HDF5 filename

Definition at line 39 of file hdf5Reader.C.

References h5FileName.

39 { return h5FileName; }

hdf5Reader::h5FileName

std::string h5FileName

HDF5 filename.

Definition: hdf5Reader.H:372

◆ getMeshBase()

meshBase * hdf5Reader::getMeshBase ( )

Returns: meshBase object

Definition at line 321 of file hdf5Reader.C.

References myMeshBase.

Referenced by proteusHdf5::proteusHdf5().

321 { return myMeshBase; }

hdf5Reader::myMeshBase

meshBase * myMeshBase

meshBase object

Definition: hdf5Reader.H:378

◆ getVTKMesh()

vtkSmartPointer< vtkDataSet > hdf5Reader::getVTKMesh ( )

Returns: Pointer to vtkDataSet

Definition at line 304 of file hdf5Reader.C.

References exportToVTKMesh(), and vtkMesh.

                                                    {
   if (vtkMesh)
     return vtkMesh;
   else {
     exportToVTKMesh();
     return vtkMesh;
   }
 }

◆ openFile()

int hdf5Reader::openFile ( )

Returns: Integer flag: 0 (failure) or 1 (success)

Definition at line 41 of file hdf5Reader.C.

References file, and h5FileName.

Referenced by proteusHdf5::proteusHdf5().

                          {
   std::cout << "Opening HDF5 file " << h5FileName << std::endl;
 
   try {
     // Open HDF5 file
     H5std_string h5FileName_(h5FileName);
     file.openFile(h5FileName_, H5F_ACC_RDWR);
   } catch (FileIException error) {
 #if H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && H5_VERS_RELEASE >= 20
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 10 && H5_VERS_RELEASE >= 2
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 11 && H5_VERS_RELEASE >= 0
       error.printErrorStack();
 #else
     error.printError();
 #endif
     return -1;
   }
   return 0;
 }

◆ readDataSet() [1/2]

int hdf5Reader::readDataSet	(	DataSet	dset,
		std::string &	buffer
	)

Parameters

dset	HDF5 dataset
buffer	Buffer into which data is read

Returns: Integer flag: 0 (failure) or 1 (success)

Definition at line 109 of file hdf5Reader.C.

Referenced by readTopDataSet().

                                                            {
   try {
     // Get type of data
     DataType dtype = dset.getDataType();
     // Read data
     dset.read(buffer, dtype);
     // Close dataset
     dset.close();
   }
   // catch failure caused by the H5File operations
   catch (DataSetIException error) {
 #if H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && H5_VERS_RELEASE >= 20
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 10 && H5_VERS_RELEASE >= 2
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 11 && H5_VERS_RELEASE >= 0
       error.printErrorStack();
 #else
     error.printError();
 #endif
     return -1;
   }
   return 0;
 }

◆ readDataSet() [2/2]

template<class T >

int hdf5Reader::readDataSet	(	DataSet	dset,
		std::vector< T > &	buffer
	)

inline

Parameters

dset	HDF5 dataset
buffer	Buffer into which numeric data is read

Returns: Integer flag: 0 (failure) or 1 (success)

Definition at line 148 of file hdf5Reader.H.

                                                                          {
     try {
       // Get type of data
       DataType dtype = dset.getDataType();
       // Read data
       dset.read(&buffer[0], dtype);
       // Close dataset
       dset.close();
     }
     // catch failure caused by the H5File operations
     catch (DataSetIException error) {
 #if H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && H5_VERS_RELEASE >= 20
       error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 10 && H5_VERS_RELEASE >= 2
       error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 11 && H5_VERS_RELEASE >= 0
       error.printErrorStack();
 #else
       error.printError();
 #endif
       return -1;
     }
 
     return 0;
   }

◆ readGroup()

int hdf5Reader::readGroup	(	std::string	groupName,
		Group &	group
	)

Parameters

groupName	HDF5 group object name
group	HDF5 group object

Returns: Integer flag: 0 (failure) or 1 (success)

Definition at line 135 of file hdf5Reader.C.

References file.

Referenced by proteusHdf5::getBlocks().

                                                            {
   try {
     // Open group
     group = Group(file.openGroup(groupName));
   } catch (FileIException error) {
 #if H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && H5_VERS_RELEASE >= 20
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 10 && H5_VERS_RELEASE >= 2
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 11 && H5_VERS_RELEASE >= 0
       error.printErrorStack();
 #else
     error.printError();
 #endif
     return -1;
   }
   return 0;
 }

◆ readGroupDataSet()

template<class T >

int hdf5Reader::readGroupDataSet	(	std::string	dsetName,
		Group &	group,
		std::vector< T > &	buffer
	)

inline

Parameters

dsetName	DataSet name
group	HDF5 group object
buffer	Buffer into which numeric data is read

Returns: Integer flag: 0 (failure) or 1 (success)

Definition at line 190 of file hdf5Reader.H.

Referenced by proteusHdf5::getBlockElementData(), proteusHdf5::getBlockGlobalID(), proteusHdf5::getBlockInfo(), proteusHdf5::getBlockVertexData(), and proteusHdf5::getBlockXYZ().

                                              {
     try {
       // Open dataset
       DataSet dset = group.openDataSet(dsetName);
       // Get type of data
       DataType dtype = dset.getDataType();
       // Read data
       dset.read(&buffer[0], dtype);
       // Close dataset
       dset.close();
     }
     // catch failure caused by the H5File operations
     catch (GroupIException error) {
 #if H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && H5_VERS_RELEASE >= 20
       error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 10 && H5_VERS_RELEASE >= 2
       error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 11 && H5_VERS_RELEASE >= 0
       error.printErrorStack();
 #else
       error.printError();
 #endif
       return -1;
     } catch (DataSetIException error) {
 #if H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && H5_VERS_RELEASE >= 20
       error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 10 && H5_VERS_RELEASE >= 2
       error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 11 && H5_VERS_RELEASE >= 0
       error.printErrorStack();
 #else
       error.printError();
 #endif
       return -1;
     }
 
     return 0;
   }

◆ readTopDataSet() [1/2]

int hdf5Reader::readTopDataSet	(	std::string	dsetName,
		std::string &	buffer
	)

Parameters

dsetName	Dataset name
buffer	Buffer into which string data is read

Returns: Integer flag: 0 (failure) or 1 (success)

Definition at line 85 of file hdf5Reader.C.

References file, and readDataSet().

Referenced by proteusHdf5::getControlInformation(), and proteusHdf5::getVectorNames().

                                                                     {
   try {
     // Open dataset
     DataSet dset = file.openDataSet(dsetName);
     // Read dataset
     readDataSet(dset, buffer);
   }
   // catch failure caused by the H5File operations
   catch (FileIException error) {
 #if H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && H5_VERS_RELEASE >= 20
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 10 && H5_VERS_RELEASE >= 2
     error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 11 && H5_VERS_RELEASE >= 0
       error.printErrorStack();
 #else
     error.printError();
 #endif
     return -1;
   }
   return 0;
 }

◆ readTopDataSet() [2/2]

template<class T >

int hdf5Reader::readTopDataSet	(	std::string	dsetName,
		std::vector< T > &	buffer
	)

inline

Parameters

dsetName	Dataset name
buffer	Buffer into which numeric data is read

Returns: Integer flag: 0 (failure) or 1 (success)

Definition at line 115 of file hdf5Reader.H.

                                                                {
     try {
       std::cout << "H5_VERS_MAJOR = " << H5_VERS_MAJOR << std::endl;
       std::cout << "H5_VERS_MINOR = " << H5_VERS_MINOR << std::endl;
       std::cout << "H5_VERS_RELEASE = " << H5_VERS_RELEASE << std::endl;
       std::cout << "H5_VERS_SUBRELEASE = " << H5_VERS_SUBRELEASE << std::endl;
       // Open dataset
       DataSet dset = file.openDataSet(dsetName);
       readDataSet(dset, buffer);
     }
     // catch failure caused by the H5File operations
     catch (FileIException error) {
 #if H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 8 && H5_VERS_RELEASE >= 20
       error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 10 && H5_VERS_RELEASE >= 2
       error.printErrorStack();
 #elif H5_VERS_MAJOR >= 1 && H5_VERS_MINOR >= 11 && H5_VERS_RELEASE >= 0
       error.printErrorStack();
 #else
       error.printError();
 #endif
       return -1;
     }
 
     return 0;
   }

◆ setConnectivities()

void hdf5Reader::setConnectivities ( std::vector< std::map< int, std::vector< int >>> elementConnectivity )

Parameters

elementConnectivity Element connectivity table

Definition at line 190 of file hdf5Reader.C.

References elementConnectivity.

Referenced by proteusHdf5::proteusHdf5().

                                                                  {
   elementConnectivity = _elementConnectivity;
 }

◆ setCoordinates() [1/3]

void hdf5Reader::setCoordinates ( std::vector< double > xCrd )

Parameters

xCrd	vector of x-coordinates

Definition at line 166 of file hdf5Reader.C.

References xCrd.

Referenced by proteusHdf5::proteusHdf5().

166 { xCrd = _xCrd; }

◆ setCoordinates() [2/3]

void hdf5Reader::setCoordinates	(	std::vector< double >	xCrd,
		std::vector< double >	yCrd
	)

Parameters

xCrd	vector of x-coordinates
yCrd	vector of y-coordinates

Definition at line 168 of file hdf5Reader.C.

References xCrd, and yCrd.

                                                          {
   xCrd = _xCrd;
   yCrd = _yCrd;
 }

◆ setCoordinates() [3/3]

void hdf5Reader::setCoordinates	(	std::vector< double >	xCrd,
		std::vector< double >	yCrd,
		std::vector< double >	zCrd
	)

Parameters

xCrd	vector of x-coordinates
yCrd	vector of y-coordinates
zCrd	vector of z-coordinates

Definition at line 174 of file hdf5Reader.C.

References xCrd, yCrd, and zCrd.

                                                          {
   xCrd = _xCrd;
   yCrd = _yCrd;
   zCrd = _zCrd;
 }

◆ setElementTypes()

void hdf5Reader::setElementTypes ( std::vector< int > vtkElementTypes )

Parameters

vtkElementTypes Vector of VTK element types for each element

Definition at line 182 of file hdf5Reader.C.

References vtkElementTypes.

Referenced by proteusHdf5::proteusHdf5().

                                                                 {
   vtkElementTypes = _vtkElementTypes;
 }

◆ setElementTypesList()

void hdf5Reader::setElementTypesList ( std::vector< int > vtkElementTypesList )

Parameters

vtkElementTypesList Vector of each unique VTK element type in mesh

Definition at line 186 of file hdf5Reader.C.

References vtkElementTypesList.

Referenced by proteusHdf5::proteusHdf5().

                                                                         {
   vtkElementTypesList = _vtkElementTypesList;
 }

◆ setFields()

void hdf5Reader::setFields	(	meshBase *	myMeshBase,
		std::vector< std::string >	dataNames,
		std::vector< std::vector< double >>	data,
		int	pointOrCell
	)

Parameters

myMeshBase	meshBase object
dataNames	Vector of names of data fields
data	Vector storing data
pointOrCell	Boolean indicating point or cell data

Definition at line 323 of file hdf5Reader.C.

References data, meshBase::setCellDataArray(), and meshBase::setPointDataArray().

Referenced by proteusHdf5::proteusHdf5().

                                             {
   if (pointOrCell == 0) {
     std::cout << "Setting hdf5Reader object point fields..." << std::endl;
   } else if (pointOrCell == 1) {
     std::cout << "Setting hdf5Reader object cell fields..." << std::endl;
   }
 
   // Set element data
   auto dataNameItr = dataNames.begin();
   auto dataItr = data.begin();
   while (dataNameItr != dataNames.end() || dataItr != data.end()) {
     std::cout << "    " << *dataNameItr << std::endl;
 
     if (pointOrCell == 0) {
       myMeshBase->setPointDataArray((*dataNameItr).c_str(), *dataItr);
     } else if (pointOrCell == 1) {
       myMeshBase->setCellDataArray((*dataNameItr).c_str(), *dataItr);
     }
 
     if (dataNameItr != dataNames.end()) {
       dataNameItr++;
     }
     if (dataItr != data.end()) {
       dataItr++;
     }
   }
 }

◆ setNumberOfDimensions()

void hdf5Reader::setNumberOfDimensions ( int numDimensions )

Parameters

numDimensions Number of spatial dimensions

Definition at line 162 of file hdf5Reader.C.

References numDimensions.

Referenced by proteusHdf5::proteusHdf5().

                                                          {
   numDimensions = _numDimensions;
 }

◆ setNumberOfElements()

void hdf5Reader::setNumberOfElements ( int numElements )

Parameters

numElements Number of elements

Definition at line 158 of file hdf5Reader.C.

References numElements.

Referenced by proteusHdf5::proteusHdf5().

                                                      {
   numElements = _numElements;
 }

◆ setNumberOfVertices()

void hdf5Reader::setNumberOfVertices ( int numVertices )

Parameters

numVertices Number of vertices

Definition at line 154 of file hdf5Reader.C.

References numVertices.

Referenced by proteusHdf5::proteusHdf5().

                                                      {
   numVertices = _numVertices;
 }

◆ unflattenBuffer2d()

template<class T >

void hdf5Reader::unflattenBuffer2d	(	std::vector< T >	flatBuffer,
		std::vector< std::vector< T >> &	originalBuffer
	)

inline

Parameters

flatBuffer	Original flattened data
originalBuffer	Output unflattened data

Definition at line 258 of file hdf5Reader.H.

References data.

Referenced by proteusHdf5::getBlockElementData(), and proteusHdf5::getBlockVertexData().

                                                                   {
     // Populate original buffer
     auto flatItr = flatBuffer.begin();
     for (auto bufItr1 = originalBuffer.begin(); bufItr1 != originalBuffer.end();
          bufItr1++) {
       for (auto bufItr2 = (*bufItr1).begin(); bufItr2 != (*bufItr1).end();
            bufItr2++) {
         *bufItr2 = *flatItr;
         flatItr++;
       }
     }
   }

◆ writeVTK()

void hdf5Reader::writeVTK ( )

Definition at line 354 of file hdf5Reader.C.

References exportToMeshBase(), myMeshBase, and meshBase::write().

                           {
   std::cout << "Writing hdf5Reader object to VTK file" << std::endl;
   if (!myMeshBase) {
     exportToMeshBase();
   }
   myMeshBase->write();
 }

Member Data Documentation

◆ baseH5FileName

std::string hdf5Reader::baseH5FileName

protected

Definition at line 373 of file hdf5Reader.H.

◆ elementConnectivity

std::vector<std::map<int, std::vector<int> > > hdf5Reader::elementConnectivity

protected

Definition at line 383 of file hdf5Reader.H.

Referenced by getElementConnectivity(), proteusHdf5::mergeBlocks(), and setConnectivities().

◆ file

H5File hdf5Reader::file

protected

Definition at line 376 of file hdf5Reader.H.

Referenced by closeFile(), openFile(), readGroup(), and readTopDataSet().

◆ h5FileName

std::string hdf5Reader::h5FileName

protected

Definition at line 372 of file hdf5Reader.H.

Referenced by closeFile(), getFileName(), and openFile().

◆ myMeshBase

meshBase* hdf5Reader::myMeshBase

protected

Definition at line 378 of file hdf5Reader.H.

Referenced by exportToMeshBase(), getMeshBase(), proteusHdf5::proteusHdf5(), and writeVTK().

◆ numDimensions

int hdf5Reader::numDimensions

protected

Definition at line 386 of file hdf5Reader.H.

Referenced by exportToVTKMesh(), and setNumberOfDimensions().

◆ numElements

int hdf5Reader::numElements

protected

Definition at line 385 of file hdf5Reader.H.

Referenced by exportToVTKMesh(), and setNumberOfElements().

◆ numVertices

int hdf5Reader::numVertices

protected

Definition at line 384 of file hdf5Reader.H.

Referenced by exportToVTKMesh(), and setNumberOfVertices().

◆ outputFname

std::string hdf5Reader::outputFname

protected

Definition at line 374 of file hdf5Reader.H.

Referenced by exportToMeshBase().

◆ verb

int hdf5Reader::verb

protected

Definition at line 375 of file hdf5Reader.H.

◆ vtkElementTypes

std::vector<int> hdf5Reader::vtkElementTypes

protected

Definition at line 388 of file hdf5Reader.H.

Referenced by exportToVTKMesh(), getElementConnectivity(), and setElementTypes().

◆ vtkElementTypesList

std::vector<int> hdf5Reader::vtkElementTypesList

protected

Definition at line 389 of file hdf5Reader.H.

Referenced by getElementConnectivity(), and setElementTypesList().

◆ vtkMesh

vtkSmartPointer<vtkDataSet> hdf5Reader::vtkMesh

protected

Definition at line 377 of file hdf5Reader.H.

Referenced by getVTKMesh().

◆ xCrd

std::vector<double> hdf5Reader::xCrd

protected

Definition at line 381 of file hdf5Reader.H.

Referenced by exportToVTKMesh(), and setCoordinates().

◆ yCrd

std::vector<double> hdf5Reader::yCrd

protected

Definition at line 381 of file hdf5Reader.H.

Referenced by exportToVTKMesh(), and setCoordinates().

◆ zCrd

std::vector<double> hdf5Reader::zCrd

protected

Definition at line 381 of file hdf5Reader.H.

Referenced by exportToVTKMesh(), and setCoordinates().

The documentation for this class was generated from the following files:

Detailed Description

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ hdf5Reader()

◆ ~hdf5Reader()

Member Function Documentation

◆ closeFile()

◆ exportToMeshBase()

◆ exportToVTKMesh()

◆ flattenBuffer2d()

◆ getElementConnectivity()

◆ getFileName()

◆ getMeshBase()

◆ getVTKMesh()

◆ openFile()

◆ readDataSet() [1/2]

◆ readDataSet() [2/2]

◆ readGroup()

◆ readGroupDataSet()

◆ readTopDataSet() [1/2]

◆ readTopDataSet() [2/2]

◆ setConnectivities()

◆ setCoordinates() [1/3]

◆ setCoordinates() [2/3]

◆ setCoordinates() [3/3]

◆ setElementTypes()

◆ setElementTypesList()

◆ setFields()

◆ setNumberOfDimensions()

◆ setNumberOfElements()

◆ setNumberOfVertices()

◆ unflattenBuffer2d()

◆ writeVTK()

Member Data Documentation

◆ baseH5FileName

◆ elementConnectivity

◆ file

◆ h5FileName

◆ myMeshBase

◆ numDimensions

◆ numElements

◆ numVertices

◆ outputFname

◆ verb

◆ vtkElementTypes

◆ vtkElementTypesList

◆ vtkMesh

◆ xCrd

◆ yCrd

◆ zCrd