AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractHdf5Converter.hpp>

Inherited by Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >, Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >, Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >, Hdf5ToVtkConverter< ELEMENT_DIM, SPACE_DIM >, and Hdf5ToXdmfConverter< ELEMENT_DIM, SPACE_DIM >.

Collaboration diagram for AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >:

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List of all members.

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
	)			`[inline]`

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 52 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 ( ) [inline]

Destructor.

Definition at line 111 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
	)			`[inline, 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 159 of file AbstractHdf5Converter.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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

Definition at line 117 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 ( ) [inline, 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 123 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 ( ) [inline]

Wrtie the unlimited dimension information to file.

Definition at line 74 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(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), 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(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write(), 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(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), 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(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write(), 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.

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

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

AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

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 >