#include <CmguiMeshWriter.hpp>

Inheritance diagram for CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	CmguiMeshWriter (const std::string &rDirectory, const std::string &rBaseName, bool cleanDirectory=true)

void	WriteFiles ()

void	SetAdditionalFieldNames (std::vector< std::string > &rFieldNames)

void	SetRegionNames (std::vector< std::string > &rRegionNames)

virtual	~CmguiMeshWriter ()

Public Member Functions inherited from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractTetrahedralMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)

virtual	~AbstractTetrahedralMeshWriter ()

virtual void	WriteFilesUsingMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, bool keepOriginalElementIndexing=true)

void	WriteFilesUsingMeshReaderAndMesh (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

std::vector< double >	GetNextNode ()

ElementData	GetNextElement ()

ElementData	GetNextBoundaryElement ()

ElementData	GetNextCableElement ()

Public Member Functions inherited from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)

virtual	~AbstractMeshWriter ()

std::string	GetOutputDirectory ()

virtual unsigned	GetNumNodes ()

unsigned	GetNumElements ()

unsigned	GetNumBoundaryFaces ()

unsigned	GetNumCableElements ()

void	WriteFilesUsingMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)

Protected Member Functions
std::ios_base::openmode	GetOpenMode (bool append)

out_stream	OpenNodeFile (bool append=false)

std::vector< boost::shared_ptr< std::ofstream > >	OpenElementFiles (bool append=false)

void	WriteNodeFileHeader (out_stream &rpNodeFile)

void	WriteElementsFileHeader (std::vector< boost::shared_ptr< std::ofstream > > &rElemFiles)

void	CreateFilesWithHeaders ()

void	AppendLocalDataToFiles ()

void	WriteFilesFooter ()

Protected Attributes
std::vector< std::string >	mAdditionalFieldNames

std::vector< std::string >	mRegionNames

std::string	mGroupName

std::string	mElementFileHeader

std::string	mCoordinatesFileHeader

std::string	mAdditionalFieldHeader

unsigned	mNumNodesPerElement

std::vector< unsigned >	mReordering

Protected Attributes inherited from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
unsigned	mNodesPerElement

unsigned	mNodesPerBoundaryElement

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpDistributedMesh

MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *	mpMixedMesh

MeshWriterIterators< ELEMENT_DIM, SPACE_DIM > *	mpIters

bool	mIndexFromZero

bool	mWriteMetaFile

unsigned	mNodeCounterForParallelMesh

unsigned	mElementCounterForParallelMesh

unsigned	mBoundaryElementCounterForParallelMesh

unsigned	mCableElementCounterForParallelMesh

bool	mFilesAreBinary

Protected Attributes inherited from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
OutputFileHandler *	mpOutputFileHandler

std::string	mBaseName

AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > *	mpMeshReader

unsigned	mNumNodes

unsigned	mNumElements

unsigned	mNumBoundaryElements

unsigned	mNumCableElements

Detailed Description

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

CmguiMeshWriter

Writes a mesh in Cmgui (the visualisation frontend of CMISS) format. Creates an exnode file and a exelem file. Note that the lines and faces are not written in the exelem file, so to load the data in Cmgui, you must use 'generate_faces_and_lines', i.e.

gfx read node base_file gfx read elem base_file generate_faces_and_lines gfx cr win

Definition at line 535 of file CmguiMeshWriter.hpp.

Constructor & Destructor Documentation

◆ CmguiMeshWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::CmguiMeshWriter	(	const std::string &	rDirectory,
		const std::string &	rBaseName,
		bool	cleanDirectory = `true`
	)

Constructor.

Parameters

rDirectory	the directory in which to write the mesh to file
rBaseName	the base name of the files in which to write the mesh data
cleanDirectory	whether to clean the directory (defaults to true)

Definition at line 48 of file CmguiMeshWriter.cpp.

References CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mAdditionalFieldHeader, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBaseName, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mCoordinatesFileHeader, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mElementFileHeader, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mGroupName, AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mIndexFromZero, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumNodesPerElement, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mReordering, and NEVER_REACHED.

◆ ~CmguiMeshWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

virtual CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::~CmguiMeshWriter ( )

inlinevirtual

Destructor.

Definition at line 677 of file CmguiMeshWriter.hpp.

Member Function Documentation

◆ AppendLocalDataToFiles()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::AppendLocalDataToFiles ( )

protectedvirtual

Append local mesh data to output files.

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 301 of file CmguiMeshWriter.cpp.

◆ CreateFilesWithHeaders()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::CreateFilesWithHeaders ( )

protectedvirtual

Create output files and add headers.

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 279 of file CmguiMeshWriter.cpp.

◆ GetOpenMode()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::ios_base::openmode CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetOpenMode ( bool append )

protected

Returns: the mode to use when opening files.

Parameters

append whether to append to the file, or overwrite it

Definition at line 361 of file CmguiMeshWriter.cpp.

◆ OpenElementFiles()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< boost::shared_ptr< std::ofstream > > CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenElementFiles ( bool append = false )

protected

Helper method that open all the elements files (one per region in this case)

Returns: vector of file handlers

Parameters

append whether to clear (append=false) or to append (append=true). False by default. It applies to all files.

Definition at line 170 of file CmguiMeshWriter.cpp.

References EXCEPTION.

◆ OpenNodeFile()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

out_stream CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenNodeFile ( bool append = false )

protected

Open the file node information is written to.

Returns: file handler

Parameters

append whether to clear (append=false) or to append (append=true). False by default.

Definition at line 163 of file CmguiMeshWriter.cpp.

◆ SetAdditionalFieldNames()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetAdditionalFieldNames ( std::vector< std::string > & rFieldNames )

Set any additional field that we want cmgui to visualize (interpolated over) elements and surfaces

Parameters

rFieldNames is a reference to a vector of string containing the names of each additional field name

Definition at line 151 of file CmguiMeshWriter.cpp.

Referenced by Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), and CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve().

◆ SetRegionNames()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetRegionNames ( std::vector< std::string > & rRegionNames )

Set the region names to be used when generating multiple element files

Parameters

rRegionNames is a reference to a vector of string containing the names of each region defined in the mesh

Definition at line 157 of file CmguiMeshWriter.cpp.

Referenced by Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), and CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve().

◆ WriteElementsFileHeader()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteElementsFileHeader ( std::vector< boost::shared_ptr< std::ofstream > > & rElemFiles )

protected

Write the headers of each element file (as many as number of regions defined).

Parameters

rElemFiles vector of pointers to file streams

Definition at line 239 of file CmguiMeshWriter.cpp.

References ChasteBuildInfo::GetProvenanceString().

◆ WriteFiles()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles ( )

virtual

Write mesh data to files.

Todo:: : EXCEPTION maybe...

Implements AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 95 of file CmguiMeshWriter.cpp.

References ElementData::AttributeValue, and ElementData::NodeIndices.

◆ WriteFilesFooter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesFooter ( )

protectedvirtual

Append footers to output files.

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 355 of file CmguiMeshWriter.cpp.

◆ WriteNodeFileHeader()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNodeFileHeader ( out_stream & rpNodeFile )

protected

Write the header part of a node file, depending on the dimension. Short helper method, also called in CmguiDeformedSolutionsWriter. (Note, without the & below this method seg faults).

Parameters

rpNodeFile reference to the out_stream used for the node file

Definition at line 206 of file CmguiMeshWriter.cpp.

References ChasteBuildInfo::GetProvenanceString(), and NEVER_REACHED.

Member Data Documentation

◆ mAdditionalFieldHeader

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mAdditionalFieldHeader

protected

String which is set to either CmguiAdditionalFieldHeader2D or CmguiAdditionalFieldHeader2DQuadratic as appropriate

Definition at line 575 of file CmguiMeshWriter.hpp.

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

◆ mAdditionalFieldNames

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<std::string> CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mAdditionalFieldNames

protected

For storage of names of additional fields.

Definition at line 542 of file CmguiMeshWriter.hpp.

◆ mCoordinatesFileHeader

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mCoordinatesFileHeader

protected

String which is set to either CmguiCoordinatesFileHeader2D or CmguiCoordinatesFileHeader2DQuadratic as appropriate

Definition at line 569 of file CmguiMeshWriter.hpp.

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

◆ mElementFileHeader

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mElementFileHeader

protected

String which is set to either CmguiElementFileHeader2D or CmguiElementFileHeader2DQuadratic as appropriate

Definition at line 563 of file CmguiMeshWriter.hpp.

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

◆ mGroupName

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mGroupName

protected

The group name to give in the output files. Defaults to the same as the base name. The CmguiDeformedSolutionsWriter prepends a counter to the base name (eg "solution_8.exnodes" instead of just "solution.exnodes"), but we would like the group name to stay as "solution", hence this separate variable

Definition at line 557 of file CmguiMeshWriter.hpp.

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

◆ mNumNodesPerElement

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumNodesPerElement

protected

Number of nodes per element, eg, in 2D, 3 for linear visualisation and 6 for quadratic visualisation

Definition at line 581 of file CmguiMeshWriter.hpp.

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

◆ mRegionNames

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<std::string> CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mRegionNames

protected

Stored the names of different regions that we want Cmgui to be able to visualize separately. There will be one .exelem file per region.

Definition at line 549 of file CmguiMeshWriter.hpp.

◆ mReordering

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mReordering

protected

Ordering of the elements nodes, from Chaste convention to CMGUI convention

Definition at line 586 of file CmguiMeshWriter.hpp.

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

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

mesh/src/writer/CmguiMeshWriter.hpp
mesh/src/writer/CmguiMeshWriter.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CmguiMeshWriter()

◆ ~CmguiMeshWriter()

Member Function Documentation

◆ AppendLocalDataToFiles()

◆ CreateFilesWithHeaders()

◆ GetOpenMode()

◆ OpenElementFiles()

◆ OpenNodeFile()

◆ SetAdditionalFieldNames()

◆ SetRegionNames()

◆ WriteElementsFileHeader()

◆ WriteFiles()

◆ WriteFilesFooter()

◆ WriteNodeFileHeader()

Member Data Documentation

◆ mAdditionalFieldHeader

◆ mAdditionalFieldNames

◆ mCoordinatesFileHeader

◆ mElementFileHeader

◆ mGroupName

◆ mNumNodesPerElement

◆ mRegionNames

◆ mReordering