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::string datasetName="Data")
	Hdf5DataReader (const FileFinder &rDirectory, const std::string &rBaseName, std::string datasetName="Data")
std::vector< double >	GetVariableOverTime (const std::string &rVariableName, unsigned nodeIndex)
std::vector< std::vector < double > >	GetVariableOverTimeOverMultipleNodes (const std::string &rVariableName, unsigned lowerIndex, unsigned upperIndex)
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)
void	Close ()
	~Hdf5DataReader ()
Private Member Functions
void	CommonConstructor ()
Private Attributes
unsigned	mVariablesDatasetRank
hsize_t	mNumberTimesteps
std::vector< std::string >	mVariableNames
std::map< std::string, unsigned >	mVariableToColumnIndex
std::map< std::string, std::string >	mVariableToUnit
bool	mClosed

Detailed Description

A concrete HDF5 data reader class.

Todo:: Add to documentation whether we can call this in serial/parallel, whether we can call it when file is open already etc...

Definition at line 55 of file Hdf5DataReader.hpp.

Constructor & Destructor Documentation

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

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 the h5 file should be treated as relative to Chaste test output, and converted to absolute, the file is otherwise treated as relative to current working directory.
	datasetName	The name of the HDF5 dataset to read, defaults to "Data".

Definition at line 44 of file Hdf5DataReader.cpp.

References CommonConstructor().

Hdf5DataReader::Hdf5DataReader	(	const FileFinder &	rDirectory,
		const std::string &	rBaseName,
		std::string	datasetName = `"Data"`
	)

Alternative constructor taking a FileFinder to specify the directory.

Parameters:

	rDirectory	The directory the files are stored in
	rBaseName	The base name of the files to read (i.e. without the extensions)
	datasetName	The name of the HDF5 dataset to read, defaults to "Data".

Definition at line 55 of file Hdf5DataReader.cpp.

References CommonConstructor().

Hdf5DataReader::~Hdf5DataReader ( )

Destructor just calls Close.

Definition at line 437 of file Hdf5DataReader.cpp.

References Close().

Member Function Documentation

void Hdf5DataReader::Close ( )

Close any open files.

Definition at line 423 of file Hdf5DataReader.cpp.

References mClosed, AbstractHdf5Access::mFileId, AbstractHdf5Access::mIsUnlimitedDimensionSet, AbstractHdf5Access::mUnlimitedDatasetId, and AbstractHdf5Access::mVariablesDatasetId.

Referenced by ~Hdf5DataReader().

void Hdf5DataReader::CommonConstructor ( ) [private]

unsigned Hdf5DataReader::GetNumberOfRows ( )

Returns:: the number of rows in the data file.

Definition at line 442 of file Hdf5DataReader.cpp.

References AbstractHdf5Access::mDatasetDims.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::PostProcessingWriter(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator().

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

Returns:: the units in which a given variable is measured.

Parameters:

rVariableName

name of a variable in the data file

Definition at line 452 of file Hdf5DataReader.cpp.

References mVariableToUnit.

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

Returns:: the unlimited dimension values.

Definition at line 404 of file Hdf5DataReader.cpp.

References AbstractHdf5Access::mIsUnlimitedDimensionSet, mNumberTimesteps, and AbstractHdf5Access::mUnlimitedDatasetId.

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg(), and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes().

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

Returns:: the variable names.

Definition at line 447 of file Hdf5DataReader.cpp.

References mVariableNames.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes().

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

Returns:: 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)

Definition at line 343 of file Hdf5DataReader.cpp.

References EXCEPTION, AbstractHdf5Access::mDatasetDims, AbstractHdf5Access::mDatasetName, AbstractHdf5Access::mIsDataComplete, AbstractHdf5Access::mIsUnlimitedDimensionSet, mNumberTimesteps, AbstractHdf5Access::mVariablesDatasetId, mVariableToColumnIndex, and UNUSED_OPT.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), ExtendedBidomainProblem< DIM >::load(), AbstractCardiacProblem< DIM, DIM, 1 >::load(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

std::vector< double > Hdf5DataReader::GetVariableOverTime	(	const std::string &	rVariableName,
		unsigned	nodeIndex
	)

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

Parameters:

	rVariableName	name of a variable in the data file
	nodeIndex	the index of the node for which the data is obtained

Definition at line 219 of file Hdf5DataReader.cpp.

References EXCEPTION, AbstractHdf5Access::mDatasetDims, AbstractHdf5Access::mDatasetName, AbstractHdf5Access::mIncompleteNodeIndices, AbstractHdf5Access::mIsDataComplete, AbstractHdf5Access::mIsUnlimitedDimensionSet, AbstractHdf5Access::mVariablesDatasetId, and mVariableToColumnIndex.

Referenced by PropagationPropertiesCalculator::CalculateAllConductionVelocities(), PropagationPropertiesCalculator::CalculateConductionVelocity(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), PropagationPropertiesCalculator::rGetCachedVoltages(), and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes().

std::vector< std::vector< double > > Hdf5DataReader::GetVariableOverTimeOverMultipleNodes	(	const std::string &	rVariableName,
		unsigned	lowerIndex,
		unsigned	upperIndex
	)

Returns:: the values of a given variable at each time step over multiple nodes.

Parameters:

	rVariableName	name of a variable in the data file
	lowerIndex	the index of the lower node for which the data is obtained
	upperIndex	one past the index of the upper node for which the data is obtained

Definition at line 277 of file Hdf5DataReader.cpp.

References EXCEPTION, AbstractHdf5Access::mDatasetDims, AbstractHdf5Access::mDatasetName, AbstractHdf5Access::mIsDataComplete, AbstractHdf5Access::mIsUnlimitedDimensionSet, AbstractHdf5Access::mVariablesDatasetId, and mVariableToColumnIndex.

Referenced by PropagationPropertiesCalculator::CalculateAllActionPotentialDurationsForNodeRange().