#include <Hdf5ToCmguiConverter.hpp>

Inheritance diagram for Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	Hdf5ToCmguiConverter (const FileFinder &rInputDirectory, const std::string &rFileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, bool hasBath=false, unsigned precision=0u)

Public Member Functions inherited from 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)

void	WriteInfoFile ()

	~AbstractHdf5Converter ()

std::string	GetSubdirectory ()

Private Member Functions
void	Write (std::string type)

void	WriteCmguiScript ()

Additional Inherited Members
Protected Member Functions inherited from AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >
bool	MoveOntoNextDataset ()

Protected Attributes inherited from AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >
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

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 64 of file Hdf5ToCmguiConverter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter	(	const FileFinder &	rInputDirectory,
		const std::string &	rFileBaseName,
		AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		bool	hasBath = `false`,
		unsigned	precision = `0u`
	)

Constructor, which does the conversion.

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

Parameters

rInputDirectory	The input directory, relative to CHASTE_TEST_OUTPUT, where the .h5 file has been written
rFileBaseName	The base name of the data file.
pMesh	Pointer to the mesh.
hasBath	whether the mesh has a bath or not. Defaults to false.
precision	The number of digits to use when printing to file (0u = default).

Todo:: #1660 at present this converter is hardcoded to work with "Data" using the below statement

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

Definition at line 136 of file Hdf5ToCmguiConverter.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write ( std::string type )

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 49 of file Hdf5ToCmguiConverter.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::WriteCmguiScript ( )

private

Writes a basic script for visualization of mesh and data.

It loads the nodes and elements. It also asks cmgui to create faces and lines (because our output files don't have the information). Data are loaded by means of a 'for' loop.

After loading the script, nodes (seen as small dots) and lines connecting them will be displayed. Both nodes and lines will be coloured according to the first variable in the Hdf5 file (usually Vm). The Cmgui default spectrum (0 to 1, blue to red) is used. This can be changed by clicking on 'graphics->spectrum editor'. Other manual modification can be made by clicking on 'graphics->scene editor'.

Definition at line 191 of file Hdf5ToCmguiConverter.cpp.

References PetscTools::AmMaster(), HeartConfig::GetOutputFilenamePrefix(), ChasteBuildInfo::GetProvenanceString(), HeartConfig::Instance(), 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

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

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