#include <AbstractHdf5Converter.hpp>

Inheritance diagram for AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	AbstractHdf5Converter (const FileFinder &rInputDirectory, const std::string &rFileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, const std::string &rSubdirectoryName, unsigned precision)

void	WriteInfoFile ()

	~AbstractHdf5Converter ()

std::string	GetSubdirectory ()

Protected Member Functions
bool	MoveOntoNextDataset ()

Protected Attributes
const FileFinder &	mrH5Folder

boost::shared_ptr< Hdf5DataReader >	mpReader

unsigned	mNumVariables

std::string	mFileBaseName

std::vector< std::string >	mDatasetNames

unsigned	mOpenDatasetIndex

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

OutputFileHandler *	mpOutputFileHandler

std::string	mRelativeSubdirectory

unsigned	mPrecision

Private Member Functions
void	GenerateListOfDatasets (const FileFinder &rH5Folder, const std::string &rFileName)

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >

The derived children of this class convert output from Hdf5 format to a range of other formats for postprocessing.

Definition at line 50 of file AbstractHdf5Converter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter	(	const FileFinder &	rInputDirectory,
		const std::string &	rFileBaseName,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		const std::string &	rSubdirectoryName,
		unsigned	precision
	)

Constructor, which does the conversion and writes the .info file.

Note: This method is collective, and must be called by all processes.

Parameters

rInputDirectory	The input directory, where the .h5 file to post-process is.
rFileBaseName	The base name of the data file.
pMesh	Pointer to the mesh.
rSubdirectoryName	Name for the output directory to be created (relative to inputDirectory).
precision	The number of digits to use in numerical output to file.

Definition at line 50 of file AbstractHdf5Converter.cpp.

References AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::GenerateListOfDatasets(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mFileBaseName, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mRelativeSubdirectory, and AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mrH5Folder.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::~AbstractHdf5Converter ( )

Destructor.

Definition at line 109 of file AbstractHdf5Converter.cpp.

References AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::GenerateListOfDatasets	(	const FileFinder &	rH5Folder,
		const std::string &	rFileName
	)

private

Have a look in the HDF5 file and generate a list of the datasets that it contains.

Parameters

rH5Folder	The directory the h5 file is in.
rFileName	The name of the h5 file.

Definition at line 157 of file AbstractHdf5Converter.cpp.

References FileFinder::GetAbsolutePath(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mDatasetNames, and NEVER_REACHED.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::GetSubdirectory ( )

Returns: the relative path of the sub-directory in which the converted output is stored.

Definition at line 115 of file AbstractHdf5Converter.cpp.

References AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mRelativeSubdirectory.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CloseFilesAndPostProcess().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset ( )

protected

Close the existing dataset and open a new one.

This method deletes the existing mpDataReader, and opens a new one for the new dataset.

Returns: whether a new dataset is open, false if we have run out of them.

Definition at line 121 of file AbstractHdf5Converter.cpp.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), and Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::WriteInfoFile ( )

Wrtie the unlimited dimension information to file.

Definition at line 72 of file AbstractHdf5Converter.cpp.

References PetscTools::AmMaster(), DOUBLE_UNSET, ChasteBuildInfo::GetProvenanceString(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mDatasetNames, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mFileBaseName, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mOpenDatasetIndex, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpReader, and OutputFileHandler::OpenOutputFile().

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<std::string> AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mDatasetNames

protected

The datasets that we are working with.

'Data' is a special case and handled slightly differently as all variables use the same 'time'.

Definition at line 81 of file AbstractHdf5Converter.hpp.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::GenerateListOfDatasets(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset(), and AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::WriteInfoFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mFileBaseName

protected

Base name for the files: [basename].vtu, [basename].dat etc.

Definition at line 73 of file AbstractHdf5Converter.hpp.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::WriteCmguiScript(), and AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::WriteInfoFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mNumVariables

protected

Number of variables to output. Read from the reader.

Definition at line 70 of file AbstractHdf5Converter.hpp.

Referenced by Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >::AddDataOnNodes(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), and AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mOpenDatasetIndex

protected

The index of the dataset that is currently open.

Definition at line 86 of file AbstractHdf5Converter.hpp.

Referenced by Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset(), and AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::WriteInfoFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpMesh

protected

Pointer to a mesh.

Definition at line 89 of file AbstractHdf5Converter.hpp.

Referenced by Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter(), and AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

OutputFileHandler* AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler

protected

Initialised as the directory in which to store the results.

Definition at line 92 of file AbstractHdf5Converter.hpp.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::WriteCmguiScript(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::WriteInfoFile(), and AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::~AbstractHdf5Converter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

boost::shared_ptr<Hdf5DataReader> AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpReader

protected

Pointer to reader of the dataset to be converted.

Definition at line 67 of file AbstractHdf5Converter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mPrecision

protected

The precision with which to write files: that is, the number of digits to use in numerical output.

Definition at line 104 of file AbstractHdf5Converter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mRelativeSubdirectory

protected

Get the subdirectory in which the converted output is stored, relative to the input directory.

Definition at line 98 of file AbstractHdf5Converter.hpp.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::GetSubdirectory(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), and Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToVtkConverter().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

const FileFinder& AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mrH5Folder

protected

Folder that the h5 file to convert resides in

Definition at line 64 of file AbstractHdf5Converter.hpp.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), and AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::MoveOntoNextDataset().

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

pde/src/postprocessing/AbstractHdf5Converter.hpp
pde/src/postprocessing/AbstractHdf5Converter.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >