AbstractHdf5Access Class Reference

#include <AbstractHdf5Access.hpp>

Inherited by Hdf5DataReader, and Hdf5DataWriter.

Collaboration diagram for AbstractHdf5Access:

Public Member Functions
	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 ()
Protected Member Functions
bool	DoesDatasetExist (const std::string &rDatasetName)
void	SetUnlimitedDatasetId ()
void	SetMainDatasetRawChunkCache ()
Protected Attributes
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
static const unsigned	DATASET_DIMS = 3

Detailed Description

Todo:: : magic number

An abstract class to get common code for reading and writing HDF5 files into one place.

It doesn't do very much, but provides common member variables.

Definition at line 55 of file AbstractHdf5Access.hpp.

Constructor & Destructor Documentation

AbstractHdf5Access::AbstractHdf5Access	(	const std::string &	rDirectory,
		const std::string &	rBaseName,
		const std::string &	rDatasetName,
		bool	makeAbsolute = `true`
	)

Constructor for directory given as string

Parameters:

	rDirectory	the directory in which to read/write the data to file
	rBaseName	The base name of the HDF5 file (with no extension)
	rDatasetName	The dataset name - default is "Data" for voltage and extracellular potential.
	makeAbsolute	Whether the h5 file should be treated as relative to Chaste test output, otherwise treated as CWD or absolute.

Definition at line 114 of file AbstractHdf5Access.cpp.

References RelativeTo::Absolute, RelativeTo::ChasteTestOutput, mDirectory, and FileFinder::SetPath().

AbstractHdf5Access::AbstractHdf5Access	(	const FileFinder &	rDirectory,
		const std::string &	rBaseName,
		const std::string &	rDatasetName
	)

Constructor for directory given as FileFinder

Parameters:

	rDirectory	the directory in which to read/write the data to file
	rBaseName	The base name of the HDF5 file (with no extension)
	rDatasetName	The dataset name - default is "Data" for voltage and extracellular potential.

Definition at line 135 of file AbstractHdf5Access.cpp.

AbstractHdf5Access::~AbstractHdf5Access ( ) [virtual]

Destructor.

Definition at line 146 of file AbstractHdf5Access.cpp.

Member Function Documentation

bool AbstractHdf5Access::DoesDatasetExist ( const std::string & rDatasetName ) [protected]

Check for the existence of a dataset in an HDF5 file.

Parameters:

rDatasetName

the name of the dataset.

Returns:: whether or not the dataset already exists in the file.

Definition at line 39 of file AbstractHdf5Access.cpp.

References mFileId.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), and SetUnlimitedDatasetId().

std::vector< unsigned > AbstractHdf5Access::GetIncompleteNodeMap ( )

Returns:: mIncompleteNodeIndices.

Definition at line 157 of file AbstractHdf5Access.cpp.

References mIncompleteNodeIndices.

std::string AbstractHdf5Access::GetUnlimitedDimensionName ( )

Returns:: the name of the Unlimited dimension (usually "Time").

Definition at line 162 of file AbstractHdf5Access.cpp.

References mUnlimitedDimensionName.

std::string AbstractHdf5Access::GetUnlimitedDimensionUnit ( )

Returns:: the unit of the Unlimited dimension (usually "msec").

Definition at line 167 of file AbstractHdf5Access.cpp.

References mUnlimitedDimensionUnit.

bool AbstractHdf5Access::IsDataComplete ( )

Get method for mIsDataComplete.

Returns:: mIsDataComplete.

Definition at line 151 of file AbstractHdf5Access.cpp.

References mIsDataComplete.

void AbstractHdf5Access::SetMainDatasetRawChunkCache ( ) [protected]

Sets the raw dataset chunk cache for our main dataset (mVariablesDatasetId). The default in HDF5 is 1 MB, which is too small for many problems, so we've bumped it up to 128 M.

Note: this cache is not currently used with the parallel (MPIO and MPIPOSIX) drivers in read/write mode (as we have in Hdf5DataWriter). However it should be used by the Hdf5DataReader (which uses the default driver).

If system memory is at a premium you may find you need to reduce the size of this cache by reducing max_bytes_in_cache.

Definition at line 172 of file AbstractHdf5Access.cpp.

References mFileId, and mVariablesDatasetId.

Referenced by Hdf5DataReader::CommonConstructor(), and Hdf5DataWriter::EndDefineMode().

void AbstractHdf5Access::SetUnlimitedDatasetId ( ) [protected]

This method sets mUnlimitedDatasetId, the unlimited dataset ID. It does this by looking for a given unlimited dataset name in the file.

Either one of the new format of [mDatasetName + "_Unlimited"], or one of the old format of ["Time"].

Definition at line 64 of file AbstractHdf5Access.cpp.

References DoesDatasetExist(), mDatasetName, mFileId, mIsUnlimitedDimensionSet, mUnlimitedDatasetId, mUnlimitedDimensionName, mUnlimitedDimensionUnit, and NEVER_REACHED.

Referenced by Hdf5DataReader::CommonConstructor(), and Hdf5DataWriter::Hdf5DataWriter().