#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 ()
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

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 517 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 ( ) [inline, virtual]

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 ( ) [protected, virtual]

Append local mesh data to output files.

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 301 of file CmguiMeshWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::CreateFilesWithHeaders ( ) [protected, virtual]

Create output files and add headers.

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 279 of file CmguiMeshWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Get the mode to use when opening files.

Parameters:

append whether to append to the file, or overwrite it

Definition at line 360 of file CmguiMeshWriter.cpp.

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)

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.

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.

Parameters:

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

Definition at line 163 of file CmguiMeshWriter.cpp.

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().

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().

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().

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.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesFooter ( ) [protected, virtual]

Append footers to output files.

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 354 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(), and NEVER_REACHED.

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 558 of file CmguiMeshWriter.hpp.

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

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 524 of file CmguiMeshWriter.hpp.

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 552 of file CmguiMeshWriter.hpp.

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

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 545 of file CmguiMeshWriter.hpp.

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

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 539 of file CmguiMeshWriter.hpp.

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

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 564 of file CmguiMeshWriter.hpp.

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

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 531 of file CmguiMeshWriter.hpp.

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 569 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

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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