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)
	Hdf5DataReader (const FileFinder &rDirectory, const std::string &rBaseName)
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)
bool	IsDataComplete ()
std::vector< unsigned >	GetIncompleteNodeMap ()
void	Close ()
	~Hdf5DataReader ()
Private Member Functions
void	CommonConstructor (const FileFinder &rDirectory, const std::string &rBaseName)
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
bool	mClosed
Static Private Attributes
static const unsigned	MAX_DATASET_RANK = 3

Detailed Description

Todo:: : magic number

A concrete HDF5 data reader class.

Definition at line 49 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 37 of file Hdf5DataReader.cpp.

References RelativeTo::Absolute, RelativeTo::ChasteTestOutput, and CommonConstructor().

Hdf5DataReader::Hdf5DataReader	(	const FileFinder &	rDirectory,
		const std::string &	rBaseName
	)

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)

Definition at line 59 of file Hdf5DataReader.cpp.

References CommonConstructor().

Hdf5DataReader::~Hdf5DataReader ( )

Destructor just calls Close.

Definition at line 424 of file Hdf5DataReader.cpp.

References Close().

Member Function Documentation

void Hdf5DataReader::Close ( )

Close any open files.

Definition at line 410 of file Hdf5DataReader.cpp.

References mClosed, mFileId, mIsUnlimitedDimensionSet, mTimeDatasetId, and mVariablesDatasetId.

Referenced by ~Hdf5DataReader().

void Hdf5DataReader::CommonConstructor	(	const FileFinder &	rDirectory,
		const std::string &	rBaseName
	)			`[private]`

Contains functionality common to both constructors.

Parameters:

	rDirectory	The directory the files are stored in
	rBaseName	The base name of the files to read (i.e. without the extensions)

Definition at line 70 of file Hdf5DataReader.cpp.

References EXCEPTION, FileFinder::Exists(), FileFinder::GetAbsolutePath(), FileFinder::IsDir(), MAX_DATASET_RANK, mBaseName, mDirectory, mFileId, mIncompleteNodeIndices, mIsDataComplete, mIsUnlimitedDimensionSet, mNumberTimesteps, mTimeDatasetId, mVariableNames, mVariablesDatasetId, mVariablesDatasetRank, mVariablesDatasetSizes, mVariableToColumnIndex, and mVariableToUnit.

Referenced by Hdf5DataReader().

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

Get method for mIncompleteNodeIndices.

Definition at line 449 of file Hdf5DataReader.cpp.

References mIncompleteNodeIndices.

unsigned Hdf5DataReader::GetNumberOfRows ( )

Get the number of rows in the data file.

Definition at line 429 of file Hdf5DataReader.cpp.

References mVariablesDatasetSizes.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), 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 439 of file Hdf5DataReader.cpp.

References mVariableToUnit.

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

Get the unlimited dimension values.

Definition at line 383 of file Hdf5DataReader.cpp.

References mIsUnlimitedDimensionSet, mNumberTimesteps, and mTimeDatasetId.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::WriteCmguiScript(), and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes().

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

Get the variable names.

Definition at line 434 of file Hdf5DataReader.cpp.

References mVariableNames.

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)

Definition at line 324 of file Hdf5DataReader.cpp.

References EXCEPTION, mIsDataComplete, mIsUnlimitedDimensionSet, mNumberTimesteps, mVariablesDatasetId, mVariablesDatasetSizes, and mVariableToColumnIndex.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), ExtendedBidomainProblem< DIM >::load(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), and Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write().

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

Get 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 200 of file Hdf5DataReader.cpp.

References EXCEPTION, mIncompleteNodeIndices, mIsDataComplete, mIsUnlimitedDimensionSet, mVariablesDatasetId, mVariablesDatasetSizes, 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::rCacheVoltages(), and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes().

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

Get 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 258 of file Hdf5DataReader.cpp.

References EXCEPTION, mIsDataComplete, mIsUnlimitedDimensionSet, mVariablesDatasetId, mVariablesDatasetSizes, and mVariableToColumnIndex.

Referenced by PropagationPropertiesCalculator::CalculateAllActionPotentialDurationsForNodeRange().

bool Hdf5DataReader::IsDataComplete ( )

Get method for mIsDataComplete.

Definition at line 444 of file Hdf5DataReader.cpp.

References mIsDataComplete.