#include <AbstractHdf5Access.hpp>

Inheritance diagram for AbstractHdf5Access:

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 53 of file AbstractHdf5Access.hpp.

Constructor & Destructor Documentation

◆ AbstractHdf5Access() [1/2]

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 96 of file AbstractHdf5Access.cpp.

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

◆ AbstractHdf5Access() [2/2]

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 117 of file AbstractHdf5Access.cpp.

◆ ~AbstractHdf5Access()

AbstractHdf5Access::~AbstractHdf5Access ( )

virtual

Destructor.

Definition at line 128 of file AbstractHdf5Access.cpp.

Member Function Documentation

◆ DoesDatasetExist()

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().

◆ GetIncompleteNodeMap()

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

Returns: mIncompleteNodeIndices. Vector of node indices for which the data file does not contain data.

Definition at line 137 of file AbstractHdf5Access.cpp.

References mIncompleteNodeIndices.

◆ GetUnlimitedDimensionName()

std::string AbstractHdf5Access::GetUnlimitedDimensionName ( )

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

Definition at line 142 of file AbstractHdf5Access.cpp.

References mUnlimitedDimensionName.

◆ GetUnlimitedDimensionUnit()

std::string AbstractHdf5Access::GetUnlimitedDimensionUnit ( )

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

Definition at line 147 of file AbstractHdf5Access.cpp.

References mUnlimitedDimensionUnit.

◆ IsDataComplete()

bool AbstractHdf5Access::IsDataComplete ( )

Get method for mIsDataComplete. If this is true the data file contains entries for all nodes. If this is false the data file only contains entries for some nodes.

Returns: mIsDataComplete.

Definition at line 132 of file AbstractHdf5Access.cpp.

References mIsDataComplete.

◆ SetMainDatasetRawChunkCache()

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 152 of file AbstractHdf5Access.cpp.

References mFileId, and mVariablesDatasetId.

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

◆ SetUnlimitedDatasetId()

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 46 of file AbstractHdf5Access.cpp.

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

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

Member Data Documentation

◆ DATASET_DIMS

const unsigned AbstractHdf5Access::DATASET_DIMS = 3

staticprotected

The dimensions of each dataset (variable, node, time).

Definition at line 60 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), Hdf5DataWriter::CalculateChunkDims(), Hdf5DataWriter::CalculateNumberOfChunks(), Hdf5DataReader::CommonConstructor(), Hdf5DataWriter::EndDefineMode(), Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutVector(), Hdf5DataWriter::SetChunkSize(), and Hdf5DataWriter::WriteCache().

◆ mBaseName

std::string AbstractHdf5Access::mBaseName

protected

The base name for the data files.

Definition at line 57 of file AbstractHdf5Access.hpp.

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

◆ mDatasetDims

hsize_t AbstractHdf5Access::mDatasetDims[DATASET_DIMS]

protected

The sizes of each dimension of the dataset (variable, node, time).

Definition at line 71 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), Hdf5DataWriter::AdvanceAlongUnlimitedDimension(), Hdf5DataWriter::CalculateChunkDims(), Hdf5DataWriter::CalculateNumberOfChunks(), Hdf5DataReader::CommonConstructor(), Hdf5DataWriter::EmptyDataset(), Hdf5DataWriter::EndDefineMode(), Hdf5DataReader::GetNumberOfRows(), Hdf5DataReader::GetVariableOverNodes(), Hdf5DataReader::GetVariableOverTime(), Hdf5DataReader::GetVariableOverTimeOverMultipleNodes(), Hdf5DataWriter::OpenFile(), Hdf5DataWriter::PossiblyExtend(), Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutVector(), and Hdf5DataWriter::WriteCache().

◆ mDatasetName

std::string AbstractHdf5Access::mDatasetName

protected

The base name for the dataset we are reading/writing.

Definition at line 58 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), Hdf5DataReader::CommonConstructor(), Hdf5DataWriter::EndDefineMode(), Hdf5DataReader::GetVariableOverNodes(), Hdf5DataReader::GetVariableOverTime(), Hdf5DataReader::GetVariableOverTimeOverMultipleNodes(), and SetUnlimitedDatasetId().

◆ mDirectory

FileFinder AbstractHdf5Access::mDirectory

protected

Directory HDF5 file will be, or is, stored in.

Definition at line 59 of file AbstractHdf5Access.hpp.

Referenced by AbstractHdf5Access(), Hdf5DataReader::CommonConstructor(), and Hdf5DataWriter::OpenFile().

◆ mFileId

hid_t AbstractHdf5Access::mFileId

protected

The data file ID.

Definition at line 68 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), Hdf5DataReader::Close(), Hdf5DataWriter::Close(), Hdf5DataReader::CommonConstructor(), DoesDatasetExist(), Hdf5DataWriter::EndDefineMode(), Hdf5DataWriter::OpenFile(), SetMainDatasetRawChunkCache(), and SetUnlimitedDatasetId().

◆ mIncompleteNodeIndices

std::vector<unsigned> AbstractHdf5Access::mIncompleteNodeIndices

protected

Vector of node indices for which the data file does not contain data.

Definition at line 66 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), Hdf5DataReader::CommonConstructor(), Hdf5DataWriter::ComputeIncompleteOffset(), Hdf5DataWriter::DefineFixedDimension(), Hdf5DataWriter::EndDefineMode(), GetIncompleteNodeMap(), and Hdf5DataReader::GetVariableOverTime().

◆ mIsDataComplete

bool AbstractHdf5Access::mIsDataComplete

protected

Whether the data file contains entries for all nodes.

Definition at line 62 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), Hdf5DataReader::CommonConstructor(), Hdf5DataWriter::DefineFixedDimension(), Hdf5DataWriter::EndDefineMode(), Hdf5DataReader::GetVariableOverNodes(), Hdf5DataReader::GetVariableOverTime(), Hdf5DataReader::GetVariableOverTimeOverMultipleNodes(), IsDataComplete(), Hdf5DataWriter::PutStripedVector(), and Hdf5DataWriter::PutVector().

◆ mIsUnlimitedDimensionSet

bool AbstractHdf5Access::mIsUnlimitedDimensionSet

protected

Is the unlimited dimension set up at the moment?

Definition at line 65 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), Hdf5DataWriter::AdvanceAlongUnlimitedDimension(), Hdf5DataReader::Close(), Hdf5DataWriter::Close(), Hdf5DataWriter::DefineUnlimitedDimension(), Hdf5DataWriter::EndDefineMode(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableOverNodes(), Hdf5DataReader::GetVariableOverTime(), Hdf5DataReader::GetVariableOverTimeOverMultipleNodes(), Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutUnlimitedVariable(), Hdf5DataWriter::PutVector(), and SetUnlimitedDatasetId().

◆ mUnlimitedDatasetId

hid_t AbstractHdf5Access::mUnlimitedDatasetId

protected

The dataset ID for the unlimited (independent) variable - usually time.

Definition at line 69 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), Hdf5DataReader::Close(), Hdf5DataWriter::Close(), Hdf5DataReader::CommonConstructor(), Hdf5DataWriter::EndDefineMode(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataWriter::PossiblyExtend(), Hdf5DataWriter::PutUnlimitedVariable(), and SetUnlimitedDatasetId().

◆ mUnlimitedDimensionName

std::string AbstractHdf5Access::mUnlimitedDimensionName

protected

The name of the unlimited dimension.

Definition at line 63 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::DefineUnlimitedDimension(), Hdf5DataWriter::EndDefineMode(), GetUnlimitedDimensionName(), and SetUnlimitedDatasetId().

◆ mUnlimitedDimensionUnit

std::string AbstractHdf5Access::mUnlimitedDimensionUnit

protected

The physical units of the unlimited dimension.

Definition at line 64 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::DefineUnlimitedDimension(), Hdf5DataWriter::EndDefineMode(), GetUnlimitedDimensionUnit(), and SetUnlimitedDatasetId().

◆ mVariablesDatasetId

hid_t AbstractHdf5Access::mVariablesDatasetId

protected

The dataset ID for the dependent variables.

Definition at line 70 of file AbstractHdf5Access.hpp.

Referenced by Hdf5DataWriter::Hdf5DataWriter(), Hdf5DataReader::Close(), Hdf5DataWriter::Close(), Hdf5DataReader::CommonConstructor(), Hdf5DataWriter::EndDefineMode(), Hdf5DataReader::GetVariableOverNodes(), Hdf5DataReader::GetVariableOverTime(), Hdf5DataReader::GetVariableOverTimeOverMultipleNodes(), Hdf5DataWriter::OpenFile(), Hdf5DataWriter::PossiblyExtend(), Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutVector(), SetMainDatasetRawChunkCache(), and Hdf5DataWriter::WriteCache().

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

io/src/common/AbstractHdf5Access.hpp
io/src/common/AbstractHdf5Access.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractHdf5Access() [1/2]

◆ AbstractHdf5Access() [2/2]

◆ ~AbstractHdf5Access()

Member Function Documentation

◆ DoesDatasetExist()

◆ GetIncompleteNodeMap()

◆ GetUnlimitedDimensionName()

◆ GetUnlimitedDimensionUnit()

◆ IsDataComplete()

◆ SetMainDatasetRawChunkCache()

◆ SetUnlimitedDatasetId()

Member Data Documentation

◆ DATASET_DIMS

◆ mBaseName

◆ mDatasetDims

◆ mDatasetName

◆ mDirectory

◆ mFileId

◆ mIncompleteNodeIndices

◆ mIsDataComplete

◆ mIsUnlimitedDimensionSet

◆ mUnlimitedDatasetId

◆ mUnlimitedDimensionName

◆ mUnlimitedDimensionUnit

◆ mVariablesDatasetId