CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <CmguiMeshWriter.hpp>

Inherits AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Collaboration diagram for CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >:
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List of all members.

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 ()

Static Public Member Functions

static bool CompareCmguiFiles (std::string &rPath1, std::string &rPath2)

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 510 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 
) [inline]

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 41 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 651 of file CmguiMeshWriter.hpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::AppendLocalDataToFiles (  )  [inline, protected, virtual]

Append local mesh data to output files.

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 294 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>
bool CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::CompareCmguiFiles ( std::string &  rPath1,
std::string &  rPath2 
) [inline, static]

Compare two cmgui files, helper methods for tests. It will ignore the provenance lines of the files.

Parameters:
rPath1 path to the first file from calling directory (or full absolute)
rPath2 path to the second file from calling directory (or full absolute)
Returns:
true if the file are the same (except for the provenance lines), false otherwise

Definition at line 368 of file CmguiMeshWriter.cpp.

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

Create output files and add headers.

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 272 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  )  [inline, protected]

Get the mode to use when opening files.

Parameters:
append whether to append to the file, or overwrite it

Definition at line 353 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  )  [inline, 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 163 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  )  [inline, 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 156 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  )  [inline]

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 144 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  )  [inline]

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 150 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  )  [inline, 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 232 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 (  )  [inline, virtual]

Write mesh data to files.

Todo:
: EXCEPTION maybe...

Implements AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 88 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 (  )  [inline, protected, virtual]

Append footers to output files.

Reimplemented from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 347 of file CmguiMeshWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNodeFileHeader ( out_stream &  rpNodeFile  )  [inline, 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 199 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 551 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 517 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 545 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 538 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 532 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 557 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 524 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 562 of file CmguiMeshWriter.hpp.

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

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