Hdf5DataReader Class Reference

#include <Hdf5DataReader.hpp>

Collaboration diagram for Hdf5DataReader:

Public Member Functions
	Hdf5DataReader (const std::string &rDirectory, const std::string &rBaseName, bool makeAbsolute=true)
std::vector< double >	GetVariableOverTime (const std::string &rVariableName, unsigned nodeIndex)
void	GetVariableOverNodes (Vec data, const std::string &rVariableName, unsigned timestep=0)
std::vector< double >	GetUnlimitedDimensionValues ()
unsigned	GetNumberOfRows ()
std::vector< std::string >	GetVariableNames ()
std::string	GetUnit (const std::string &rVariableName)
bool	IsDataComplete ()
std::vector< unsigned >	GetIncompleteNodeMap ()
void	Close ()
	~Hdf5DataReader ()
Private Attributes
std::string	mDirectory
std::string	mBaseName
hid_t	mFileId
hid_t	mVariablesDatasetId
unsigned	mVariablesDatasetRank
hsize_t	mVariablesDatasetSizes [MAX_DATASET_RANK]
bool	mIsUnlimitedDimensionSet
hid_t	mTimeDatasetId
hsize_t	mNumberTimesteps
std::vector< std::string >	mVariableNames
std::map< std::string, unsigned >	mVariableToColumnIndex
std::map< std::string, std::string >	mVariableToUnit
bool	mIsDataComplete
std::vector< unsigned >	mIncompleteNodeIndices
Static Private Attributes
static const unsigned	MAX_DATASET_RANK = 3

Detailed Description

Todo:: : magic number

A concrete HDF5 data reader class.

Definition at line 45 of file Hdf5DataReader.hpp.

Constructor & Destructor Documentation

Hdf5DataReader::Hdf5DataReader	(	const std::string &	rDirectory,
		const std::string &	rBaseName,
		bool	makeAbsolute = `true`
	)

Read data from the given files into memory.

Parameters:

	rDirectory	The directory the files are stored in
	rBaseName	The base name of the files to read (i.e. without the extensions)
	makeAbsolute	Whether to convert directory to an absolute path using the OutputFileHandler (defaults to true)

Definition at line 35 of file Hdf5DataReader.cpp.

References OutputFileHandler::GetOutputDirectoryFullPath(), MAX_DATASET_RANK, mBaseName, mFileId, mIncompleteNodeIndices, mIsDataComplete, mIsUnlimitedDimensionSet, mNumberTimesteps, mTimeDatasetId, mVariableNames, mVariablesDatasetId, mVariablesDatasetRank, mVariablesDatasetSizes, mVariableToColumnIndex, and mVariableToUnit.

Hdf5DataReader::~Hdf5DataReader ( )

Destructor just calls Close.

Definition at line 347 of file Hdf5DataReader.cpp.

References Close().

Member Function Documentation

void Hdf5DataReader::Close ( )

Close any open files.

Todo:: : move code to the destructor???

Definition at line 334 of file Hdf5DataReader.cpp.

References mFileId, mIsUnlimitedDimensionSet, mTimeDatasetId, and mVariablesDatasetId.

Referenced by ~Hdf5DataReader().

std::vector< unsigned > Hdf5DataReader::GetIncompleteNodeMap ( )

Get method for mIncompleteNodeIndices.

Definition at line 372 of file Hdf5DataReader.cpp.

References mIncompleteNodeIndices.

unsigned Hdf5DataReader::GetNumberOfRows ( )

Get the number of rows in the data file.

Definition at line 352 of file Hdf5DataReader.cpp.

References mVariablesDatasetSizes.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), and Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write().

std::string Hdf5DataReader::GetUnit ( const std::string & rVariableName )

Get the units in which a given variable is measured.

Parameters:

rVariableName

name of a variable in the data file

Definition at line 362 of file Hdf5DataReader.cpp.

References mVariableToUnit.

std::vector< double > Hdf5DataReader::GetUnlimitedDimensionValues ( )

Get the unlimited dimension values.

Definition at line 307 of file Hdf5DataReader.cpp.

References mIsUnlimitedDimensionSet, mNumberTimesteps, and mTimeDatasetId.

std::vector< std::string > Hdf5DataReader::GetVariableNames ( )

Get the variable names.

Definition at line 357 of file Hdf5DataReader.cpp.

References mVariableNames.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter().

void Hdf5DataReader::GetVariableOverNodes	(	Vec	data,
		const std::string &	rVariableName,
		unsigned	timestep = `0`
	)

Get the values of a given variable at each node at a given time step.

Parameters:

	data	Petsc vec to hold the data
	rVariableName	name of a variable in the data file
	timestep	the time step for which the data is obtained (defaults to 0)