Hdf5DataReader Class Reference

#include <Hdf5DataReader.hpp>

Inheritance diagram for Hdf5DataReader:

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 ()
Public Member Functions inherited from AbstractHdf5Access
	AbstractHdf5Access (const std::string &rDirectory, const std::string &rBaseName, const std::string &rDatasetName, bool makeAbsolute=true)
	AbstractHdf5Access (const FileFinder &rDirectory, const std::string &rBaseName, const std::string &rDatasetName)
virtual	~AbstractHdf5Access ()
bool	IsDataComplete ()
std::vector< unsigned >	GetIncompleteNodeMap ()
std::string	GetUnlimitedDimensionName ()
std::string	GetUnlimitedDimensionUnit ()

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

Additional Inherited Members
Protected Member Functions inherited from AbstractHdf5Access
bool	DoesDatasetExist (const std::string &rDatasetName)
void	SetUnlimitedDatasetId ()
void	SetMainDatasetRawChunkCache ()
Protected Attributes inherited from AbstractHdf5Access
std::string	mBaseName
std::string	mDatasetName
FileFinder	mDirectory
bool	mIsDataComplete
std::string	mUnlimitedDimensionName
std::string	mUnlimitedDimensionUnit
bool	mIsUnlimitedDimensionSet
std::vector< unsigned >	mIncompleteNodeIndices
hid_t	mFileId
hid_t	mUnlimitedDatasetId
hid_t	mVariablesDatasetId
hsize_t	mDatasetDims [DATASET_DIMS]
Static Protected Attributes inherited from AbstractHdf5Access
static const unsigned	DATASET_DIMS =3

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

Contains functionality common to both constructors.

Definition at line 65 of file Hdf5DataReader.cpp.

References RelativeTo::Absolute, AbstractHdf5Access::DATASET_DIMS, EXCEPTION, FileFinder::Exists(), FileFinder::GetAbsolutePath(), FileFinder::IsDir(), AbstractHdf5Access::mBaseName, AbstractHdf5Access::mDatasetDims, AbstractHdf5Access::mDatasetName, AbstractHdf5Access::mDirectory, AbstractHdf5Access::mFileId, AbstractHdf5Access::mIncompleteNodeIndices, AbstractHdf5Access::mIsDataComplete, mNumberTimesteps, AbstractHdf5Access::mUnlimitedDatasetId, mVariableNames, AbstractHdf5Access::mVariablesDatasetId, mVariablesDatasetRank, mVariableToColumnIndex, mVariableToUnit, AbstractHdf5Access::SetMainDatasetRawChunkCache(), and AbstractHdf5Access::SetUnlimitedDatasetId().

Referenced by Hdf5DataReader().

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(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

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

(

)

Returns

the variable names.

Definition at line 447 of file Hdf5DataReader.cpp.

References mVariableNames.

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 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(), and PropagationPropertiesCalculator::rGetCachedVoltages().

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().

Member Data Documentation

bool Hdf5DataReader::mClosed

private

Whether we've already closed the file.

Definition at line 67 of file Hdf5DataReader.hpp.

Referenced by Close().

hsize_t Hdf5DataReader::mNumberTimesteps

private

The number of time steps recorded in the data file.

Definition at line 61 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), GetUnlimitedDimensionValues(), and GetVariableOverNodes().

std::vector<std::string> Hdf5DataReader::mVariableNames

private

The variable names.

Definition at line 63 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), and GetVariableNames().

unsigned Hdf5DataReader::mVariablesDatasetRank

private

The rank of the variables data set.

Definition at line 59 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor().

std::map<std::string, unsigned> Hdf5DataReader::mVariableToColumnIndex

private

Map between variable names and data column numbers.

Definition at line 64 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), GetVariableOverNodes(), GetVariableOverTime(), and GetVariableOverTimeOverMultipleNodes().

std::map<std::string, std::string> Hdf5DataReader::mVariableToUnit

private

Map between variable names and variable units.

Definition at line 65 of file Hdf5DataReader.hpp.

Referenced by CommonConstructor(), and GetUnit().

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

• io/src/reader/Hdf5DataReader.hpp
• io/src/reader/Hdf5DataReader.cpp