Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <Hdf5ToMeshalyzerConverter.hpp>

Inheritance diagram for Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >:

List of all members.

Public Member Functions
	Hdf5ToMeshalyzerConverter (std::string inputDirectory, std::string fileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, bool usingOriginalNodeOrdering)
Private Member Functions
void	Write (std::string type)

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Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >

This class converts from Hdf5 format to meshalyzer format, ie, for voltage, one file, which looks like

V_node_0_time_0 .. V_node_N_time_0 V_node_0_time_1 .. V_node_N_time_1 V_node_0_time_2 .. V_node_N_time_M

The files that are written are [base_name]_V.dat or [base_name]_Phi_e.dat, where [base_name] is the base name of the original .h5 file. The new files are written in the same directory as the .h5 file. All paths are relative to the CHASTE_TEST_OUTPUT directory.

Definition at line 61 of file Hdf5ToMeshalyzerConverter.hpp.

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Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter	(	std::string	inputDirectory,
		std::string	fileBaseName,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		bool	usingOriginalNodeOrdering
	)

Constructor, which does the conversion.

Note:

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

Parameters:

inputDirectory	The input directory, relative to CHASTE_TEST_OUTPUT, where the .h5 file has been written
fileBaseName	The base name of the data file.
pMesh	Pointer to the mesh.
usingOriginalNodeOrdering	Whether HDF5 output was written using the original node ordering

Todo:

What if the mesh has been scaled, translated or rotated?

Definition at line 96 of file Hdf5ToMeshalyzerConverter.cpp.

References PetscTools::Barrier(), Hdf5DataReader::GetVariableNames(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpMesh, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpReader, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mRelativeSubdirectory, Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMeshReader().

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Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write

(

std::string

type

)

[private]

A helper method which takes in a string, which must be 'V' or 'Phi_e' and reads the data corresponding to that string, writing it out in meshalyzer format.

Parameters:

type	the type of data stored in this file (V/Phi_e)

Definition at line 49 of file Hdf5ToMeshalyzerConverter.cpp.

References PetscTools::AmMaster(), DistributedVectorFactory::CreateVec(), PetscTools::Destroy(), ChasteBuildInfo::GetProvenanceString(), ReplicatableVector::GetSize(), HeartConfig::GetVisualizerOutputPrecision(), HeartConfig::Instance(), and ReplicatableVector::ReplicatePetscVector().

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

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

• heart/src/postprocessing/Hdf5ToMeshalyzerConverter.hpp
• heart/src/postprocessing/Hdf5ToMeshalyzerConverter.cpp