CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#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 515 of file CmguiMeshWriter.hpp.

Constructor & Destructor Documentation

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.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

inlinevirtual

Destructor.

Definition at line 658 of file CmguiMeshWriter.hpp.

Member Function Documentation

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.

References AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNodesPerElement, AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpDistributedMesh, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mRegionNames, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenElementFiles(), and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenNodeFile().

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.

References CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenElementFiles(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenNodeFile(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteElementsFileHeader(), and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNodeFileHeader().

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.

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

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, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetOpenMode(), OutputFileHandler::GetOutputDirectoryFullPath(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBaseName, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mRegionNames.

Referenced by CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::AppendLocalDataToFiles(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::CreateFilesWithHeaders(), and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles().

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.

References CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetOpenMode(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mBaseName, AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::mpOutputFileHandler, and OutputFileHandler::OpenOutputFile().

Referenced by CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::AppendLocalDataToFiles(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::CreateFilesWithHeaders(), and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles().

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.

References CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mAdditionalFieldNames.

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

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.

References CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mRegionNames.

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

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(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mAdditionalFieldHeader, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mAdditionalFieldNames, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mCoordinatesFileHeader, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mElementFileHeader, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mGroupName, and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mRegionNames.

Referenced by CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::CreateFilesWithHeaders(), and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::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, AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextElement(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mNumNodesPerElement, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mRegionNames, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mReordering, ElementData::NodeIndices, CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenElementFiles(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenNodeFile(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteElementsFileHeader(), and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNodeFileHeader().

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.

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(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::mGroupName, and NEVER_REACHED.

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

Member Data Documentation

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 556 of file CmguiMeshWriter.hpp.

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

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 522 of file CmguiMeshWriter.hpp.

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

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 550 of file CmguiMeshWriter.hpp.

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

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 543 of file CmguiMeshWriter.hpp.

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

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 537 of file CmguiMeshWriter.hpp.

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

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 562 of file CmguiMeshWriter.hpp.

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

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 529 of file CmguiMeshWriter.hpp.

Referenced by CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::AppendLocalDataToFiles(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenElementFiles(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetRegionNames(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteElementsFileHeader(), and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFiles().

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 567 of file CmguiMeshWriter.hpp.

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

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

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