AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractCellWriter.hpp>

Inheritance diagram for AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	AbstractCellWriter (const std::string &rFileName)
virtual double	GetCellDataForVtkOutput (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)
virtual c_vector< double, SPACE_DIM >	GetVectorCellDataForVtkOutput (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)
virtual void	VisitCell (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)=0
bool	GetOutputScalarData ()
bool	GetOutputVectorData ()
void	SetVtkCellDataName (std::string vtkCellDataName)
void	SetVtkVectorCellDataName (std::string vtkCellDataName)
std::string	GetVtkCellDataName ()
std::string	GetVtkVectorCellDataName ()
Public Member Functions inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractCellBasedWriter (const std::string &rFileName)
virtual	~AbstractCellBasedWriter ()
void	CloseFile ()
virtual void	OpenOutputFile (OutputFileHandler &rOutputFileHandler)
void	OpenOutputFileForAppend (OutputFileHandler &rOutputFileHandler)
virtual void	WriteTimeStamp ()
virtual void	WriteNewline ()
void	SetFileName (std::string fileName)
std::string	GetFileName ()
Public Member Functions inherited from Identifiable
virtual	~Identifiable ()
std::string	GetIdentifier () const

Protected Attributes
bool	mOutputScalarData
bool	mOutputVectorData
std::string	mVtkCellDataName
std::string	mVtkVectorCellDataName
Protected Attributes inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >
std::string	mFileName
out_stream	mpOutStream

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	boost::serialization::access

Detailed Description

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

An abstract class for a writer that visits individual cells of a population and writes their data.

Definition at line 52 of file AbstractCellWriter.hpp.

Constructor & Destructor Documentation

AbstractCellWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::AbstractCellWriter

(

const std::string &

rFileName

)

Default constructor.

Parameters

rFileName

the name of the file to write to.

Definition at line 40 of file AbstractCellWriter.cpp.

Member Function Documentation

GetCellDataForVtkOutput()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput ( CellPtr  pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *  pCellPopulation  )

virtual

Get a double associated with a cell. This method reduces duplication of code between the methods VisitCell() and AddVtkData().

By default this method returns a DOUBLE_UNSET, but it may be overridden in subclasses

Parameters

pCell	a cell
pCellPopulation	a pointer to the cell population owning the cell.

Returns

data associated with the cell

Reimplemented in CellAgesWriter< ELEMENT_DIM, SPACE_DIM >, CellAncestorWriter< ELEMENT_DIM, SPACE_DIM >, CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >, CellDataItemWriter< ELEMENT_DIM, SPACE_DIM >, CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >, CellIdWriter< ELEMENT_DIM, SPACE_DIM >, CellLabelWriter< ELEMENT_DIM, SPACE_DIM >, CellLocationIndexWriter< ELEMENT_DIM, SPACE_DIM >, CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativePhasesWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativeTypesWriter< ELEMENT_DIM, SPACE_DIM >, CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >, CellRosetteRankWriter< ELEMENT_DIM, SPACE_DIM >, CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >, ImmersedBoundaryBoundaryCellWriter< ELEMENT_DIM, SPACE_DIM >, ImmersedBoundaryNeighbourNumberWriter< ELEMENT_DIM, SPACE_DIM >, LegacyCellProliferativeTypesWriter< ELEMENT_DIM, SPACE_DIM >, and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 74 of file AbstractCellWriter.cpp.

References DOUBLE_UNSET.

GetOutputScalarData()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetOutputScalarData

(

)

Get whether to invoke GetCellDataForVtkOutput()

Returns

mOutputScalarData

Definition at line 50 of file AbstractCellWriter.cpp.

GetOutputVectorData()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetOutputVectorData

(

)

Get whether to invoke GetVectorCellDataForVtkOutput()

Returns

mOutputScalarData

Definition at line 56 of file AbstractCellWriter.cpp.

GetVectorCellDataForVtkOutput()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetVectorCellDataForVtkOutput ( CellPtr  pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *  pCellPopulation  )

virtual

Get a c_vector associated with a cell. This method reduces duplication of code between the methods VisitCell() and AddVtkData().

By default this method returns a c_vector of DOUBLE_UNSET, but it may be overridden in subclasses

Parameters

pCell	a cell
pCellPopulation	a pointer to the cell population owning the cell.

Returns

data associated with the cell

Reimplemented in CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 82 of file AbstractCellWriter.cpp.

References DOUBLE_UNSET.

GetVtkCellDataName()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetVtkCellDataName

(

)

Returns

the name of the scalar cell data used in VTK output.

Definition at line 90 of file AbstractCellWriter.cpp.

GetVtkVectorCellDataName()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetVtkVectorCellDataName

(

)

Returns

the name of the vector cell data used in VTK output.

Definition at line 96 of file AbstractCellWriter.cpp.

serialize()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::serialize ( Archive &  archive, const unsigned int  version  )

inlineprivate

Serialize the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 66 of file AbstractCellWriter.hpp.

References AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mOutputScalarData, AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mOutputVectorData, AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mVtkCellDataName, and AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mVtkVectorCellDataName.

SetVtkCellDataName()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::SetVtkCellDataName

(

std::string

vtkCellDataName

)

Set the name of the scalar cell data used in VTK output. This method allows the user to change mVtkCellDataName from its default value, which is set in each subclass's constructor.

Parameters

vtkCellDataName

the name of the VTK field

Definition at line 62 of file AbstractCellWriter.cpp.

SetVtkVectorCellDataName()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::SetVtkVectorCellDataName

(

std::string

vtkCellDataName

)

Set the name of the vector cell data used in VTK output. This method allows the user to change mVtkCellDataName from its default value, which is set in each subclass's constructor.

Parameters

vtkCellDataName

the name of the VTK field

Definition at line 68 of file AbstractCellWriter.cpp.

VisitCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

virtual void AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell ( CellPtr  pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *  pCellPopulation  )

pure virtual

Visit a cell and write its data.

As this method is pure virtual, it must be overridden in subclasses.

Parameters

pCell	a cell
pCellPopulation	a pointer to the cell population owning the cell.

Implemented in CellAgesWriter< ELEMENT_DIM, SPACE_DIM >, CellAncestorWriter< ELEMENT_DIM, SPACE_DIM >, CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >, CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >, CellDataItemWriter< ELEMENT_DIM, SPACE_DIM >, CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >, CellIdWriter< ELEMENT_DIM, SPACE_DIM >, CellLabelWriter< ELEMENT_DIM, SPACE_DIM >, CellLocationIndexWriter< ELEMENT_DIM, SPACE_DIM >, CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativePhasesWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativeTypesWriter< ELEMENT_DIM, SPACE_DIM >, CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >, CellRosetteRankWriter< ELEMENT_DIM, SPACE_DIM >, CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >, ImmersedBoundaryBoundaryCellWriter< ELEMENT_DIM, SPACE_DIM >, ImmersedBoundaryNeighbourNumberWriter< ELEMENT_DIM, SPACE_DIM >, LegacyCellProliferativeTypesWriter< ELEMENT_DIM, SPACE_DIM >, and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >.

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 57 of file AbstractCellWriter.hpp.

Member Data Documentation

mOutputScalarData

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mOutputScalarData

protected

Whether to output scalar data for VTK using GetCellDataForVtkOutput(). Default true.

Definition at line 78 of file AbstractCellWriter.hpp.

Referenced by CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >::CellAppliedForceWriter(), and AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::serialize().

mOutputVectorData

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mOutputVectorData

protected

Whether to output scalar data for VTK using GetVectorCellDataForVtkOutput(). Default false.

Definition at line 81 of file AbstractCellWriter.hpp.

Referenced by CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >::CellAppliedForceWriter(), and AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::serialize().

mVtkCellDataName

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mVtkCellDataName

protected

The name of the cell data used in VTK output.

Definition at line 84 of file AbstractCellWriter.hpp.

Referenced by CellAgesWriter< ELEMENT_DIM, SPACE_DIM >::CellAgesWriter(), CellAncestorWriter< ELEMENT_DIM, SPACE_DIM >::CellAncestorWriter(), CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::CellBetaCateninWriter(), CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::CellCycleModelProteinConcentrationsWriter(), CellDataItemWriter< ELEMENT_DIM, SPACE_DIM >::CellDataItemWriter(), CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >::CellDeltaNotchWriter(), CellIdWriter< ELEMENT_DIM, SPACE_DIM >::CellIdWriter(), CellLabelWriter< ELEMENT_DIM, SPACE_DIM >::CellLabelWriter(), CellLocationIndexWriter< ELEMENT_DIM, SPACE_DIM >::CellLocationIndexWriter(), CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >::CellMutationStatesWriter(), CellProliferativePhasesWriter< ELEMENT_DIM, SPACE_DIM >::CellProliferativePhasesWriter(), CellProliferativeTypesWriter< ELEMENT_DIM, SPACE_DIM >::CellProliferativeTypesWriter(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::CellRadiusWriter(), CellRosetteRankWriter< ELEMENT_DIM, SPACE_DIM >::CellRosetteRankWriter(), CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::CellVolumesWriter(), ImmersedBoundaryBoundaryCellWriter< ELEMENT_DIM, SPACE_DIM >::ImmersedBoundaryBoundaryCellWriter(), ImmersedBoundaryNeighbourNumberWriter< ELEMENT_DIM, SPACE_DIM >::ImmersedBoundaryNeighbourNumberWriter(), LegacyCellProliferativeTypesWriter< ELEMENT_DIM, SPACE_DIM >::LegacyCellProliferativeTypesWriter(), and AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::serialize().

mVtkVectorCellDataName

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::string AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mVtkVectorCellDataName

protected

The name of the vector cell data used in VTK output.

Definition at line 87 of file AbstractCellWriter.hpp.

Referenced by CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >::CellAppliedForceWriter(), and AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::serialize().

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

• cell_based/src/writers/cell_writers/AbstractCellWriter.hpp
• cell_based/src/writers/cell_writers/AbstractCellWriter.cpp