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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <AbstractCellWriter.hpp>
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 () |
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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 () |
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virtual | ~Identifiable () |
std::string | GetIdentifier () const |
Protected Attributes | |
bool | mOutputScalarData |
bool | mOutputVectorData |
std::string | mVtkCellDataName |
std::string | mVtkVectorCellDataName |
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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 |
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.
AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::AbstractCellWriter | ( | const std::string & | rFileName | ) |
Default constructor.
rFileName | the name of the file to write to. |
Definition at line 40 of file AbstractCellWriter.cpp.
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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
pCell | a cell |
pCellPopulation | a pointer to the cell population owning 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.
bool AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetOutputScalarData | ( | ) |
Get whether to invoke GetCellDataForVtkOutput()
Definition at line 50 of file AbstractCellWriter.cpp.
bool AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetOutputVectorData | ( | ) |
Get whether to invoke GetVectorCellDataForVtkOutput()
Definition at line 56 of file AbstractCellWriter.cpp.
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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
pCell | a cell |
pCellPopulation | a pointer to the cell population owning the cell. |
Reimplemented in CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 82 of file AbstractCellWriter.cpp.
References DOUBLE_UNSET.
std::string AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetVtkCellDataName | ( | ) |
Definition at line 90 of file AbstractCellWriter.cpp.
std::string AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::GetVtkVectorCellDataName | ( | ) |
Definition at line 96 of file AbstractCellWriter.cpp.
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inlineprivate |
Serialize the object and its member variables.
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.
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.
vtkCellDataName | the name of the VTK field |
Definition at line 62 of file AbstractCellWriter.cpp.
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.
vtkCellDataName | the name of the VTK field |
Definition at line 68 of file AbstractCellWriter.cpp.
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pure virtual |
Visit a cell and write its data.
As this method is pure virtual, it must be overridden in subclasses.
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 >.
Needed for serialization.
Definition at line 57 of file AbstractCellWriter.hpp.
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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().
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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().
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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().
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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().