Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM > Class Template Reference
#include <Hdf5ToCmguiConverter.hpp>
Public Member Functions | |
| Hdf5ToCmguiConverter (std::string inputDirectory, std::string fileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, bool hasBath=false) | |
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
| Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter | ( | std::string | inputDirectory, | |
| std::string | fileBaseName, | |||
| AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | pMesh, | |||
| bool | hasBath = false | |||
| ) | [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. hasBath whether the mesh has a bath or not. Defaults to false.
- Todo:
- What if the mesh has been scaled, translated or rotated?
Definition at line 123 of file Hdf5ToCmguiConverter.cpp.
References PetscTools::Barrier(), HeartConfig::GetOutputDirectory(), Hdf5DataReader::GetVariableNames(), HeartConfig::Instance(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpMesh, AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::mpReader, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetAdditionalFieldNames(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetRegionNames(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMeshReader().
Member Function Documentation
| 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 43 of file Hdf5ToCmguiConverter.cpp.
References PetscTools::AmMaster(), DistributedVectorFactory::CreateVec(), Hdf5DataReader::GetNumberOfRows(), ChasteBuildInfo::GetProvenanceString(), ReplicatableVector::GetSize(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableNames(), 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:
- heart/src/postprocessing/Hdf5ToCmguiConverter.hpp
- heart/src/postprocessing/Hdf5ToCmguiConverter.cpp
