Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <Hdf5ToCmguiConverter.hpp>

Inherits AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >.

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List of all members.

Public Member Functions

 Hdf5ToCmguiConverter (std::string inputDirectory, std::string fileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

Private Member Functions

void Write (std::string type)

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >

This class converts from Hdf5 format to Cmgui format. The output will be one .exnode file per time step. The format that cmgui accepts is (after the headers):

Node: 1 Value_at_node_1 Node:2 Value_at_node_2 .....

For bidomain simulations, we will have two fields, one for Vm and one for Phie. The Cmgui format for two fields is as follows:

Node: 1 Vm_node_1 Phie_at_node_1 Node:2 Vm_at_node_2 Phie_at_node_2 .....

Definition at line 57 of file Hdf5ToCmguiConverter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter ( std::string  inputDirectory,
std::string  fileBaseName,
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *  pMesh 
) [inline]

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.

Definition at line 126 of file Hdf5ToCmguiConverter.cpp.

References PetscTools::Barrier(), HeartConfig::GetOutputDirectory(), HeartConfig::Instance(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mNumVariables, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpMesh, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetAdditionalFieldNames(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write ( std::string  type  )  [inline, private]

A helper method which takes in a string, which must be 'Mono' or 'Bi' and reads the data from the hdf5 file, writing it out in Cmgui format.

Parameters:
type - the type of simulation (Mono or Bi)

Definition at line 45 of file Hdf5ToCmguiConverter.cpp.

References PetscTools::AmMaster(), DistributedVectorFactory::CreateVec(), Hdf5DataReader::GetNumberOfRows(), ChasteBuildInfo::GetProvenanceString(), ReplicatableVector::GetSize(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableOverNodes(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mFileBaseName, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpReader, and OutputFileHandler::OpenOutputFile().

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

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