#include <AbstractCellPopulation.hpp>
Inherits Identifiable.
Inherited by AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >, and AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.
Classes | |
class | Iterator |
Public Member Functions | |
AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >()) | |
virtual | ~AbstractCellPopulation () |
void | InitialiseCells () |
void | SetDataOnAllCells (const std::string &dataName, double dataValue) |
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & | rGetMesh () |
std::list< CellPtr > & | rGetCells () |
virtual unsigned | GetNumNodes ()=0 |
virtual c_vector< double, SPACE_DIM > | GetLocationOfCellCentre (CellPtr pCell)=0 |
virtual Node< SPACE_DIM > * | GetNode (unsigned index)=0 |
virtual void | SetNode (unsigned nodeIndex, ChastePoint< SPACE_DIM > &rNewLocation)=0 |
virtual bool | IsCellAssociatedWithADeletedLocation (CellPtr pCell)=0 |
virtual CellPtr | AddCell (CellPtr pNewCell, const c_vector< double, SPACE_DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())=0 |
virtual unsigned | RemoveDeadCells ()=0 |
virtual void | Update (bool hasHadBirthsOrDeaths=true)=0 |
std::vector< unsigned > | GetCellMutationStateCount () |
std::vector< unsigned > | GetCellProliferativeTypeCount () |
std::vector< unsigned > | GetCellCyclePhaseCount () |
unsigned | GetNumRealCells () |
unsigned | GetNumAllCells () |
void | SetCellAncestorsToLocationIndices () |
std::set< unsigned > | GetCellAncestors () |
virtual CellPtr | GetCellUsingLocationIndex (unsigned index) |
std::set< CellPtr > | GetCellsUsingLocationIndex (unsigned index) |
bool | IsCellAttachedToLocationIndex (unsigned index) |
void | SetCellUsingLocationIndex (unsigned index, CellPtr pCell) |
virtual void | AddCellUsingLocationIndex (unsigned index, CellPtr pCell) |
virtual void | RemoveCellUsingLocationIndex (unsigned index, CellPtr pCell) |
void | MoveCellInLocationMap (CellPtr pCell, unsigned old_index, unsigned new_index) |
unsigned | GetLocationIndexUsingCell (CellPtr pCell) |
boost::shared_ptr < CellPropertyRegistry > | GetCellPropertyRegistry () |
void | SetDefaultCellMutationStateAndProliferativeTypeOrdering () |
virtual double | GetWidth (const unsigned &rDimension)=0 |
virtual double | GetVolumeOfCell (CellPtr pCell)=0 |
virtual std::set< unsigned > | GetNeighbouringNodeIndices (unsigned index)=0 |
virtual std::set< unsigned > | GetNeighbouringLocationIndices (CellPtr pCell)=0 |
c_vector< double, SPACE_DIM > | GetCentroidOfCellPopulation () |
virtual void | UpdateCellProcessLocation () |
virtual void | OpenWritersFiles (OutputFileHandler &rOutputFileHandler) |
void | CloseWritersFiles () |
virtual void | WriteResultsToFiles (const std::string &rDirectory) |
virtual void | AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter)=0 |
virtual void | AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationCountWriter)=0 |
virtual void | AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter, CellPtr pCell)=0 |
void | OutputCellPopulationInfo (out_stream &rParamsFile) |
virtual void | OutputCellPopulationParameters (out_stream &rParamsFile)=0 |
bool | GetOutputResultsForChasteVisualizer () |
template<template< unsigned, unsigned > class T> | |
void | AddPopulationWriter () |
template<template< unsigned, unsigned > class T> | |
void | AddCellWriter () |
template<template< unsigned, unsigned > class T> | |
void | AddCellPopulationCountWriter () |
void | AddPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter) |
void | AddCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter) |
void | AddCellPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationCountWriter) |
template<template< unsigned, unsigned > class T> | |
bool | HasWriter () const |
void | SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer) |
c_vector< double, SPACE_DIM > | GetSizeOfCellPopulation () |
virtual bool | IsRoomToDivide (CellPtr pCell) |
std::pair< unsigned, unsigned > | CreateOrderedPair (unsigned index1, unsigned index2) |
Iterator | Begin () |
Iterator | End () |
Protected Member Functions | |
virtual void | Validate ()=0 |
virtual void | WriteVtkResultsToFile (const std::string &rDirectory)=0 |
AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | |
Protected Attributes | |
std::map< unsigned, std::set < CellPtr > > | mLocationCellMap |
std::map< Cell *, unsigned > | mCellLocationMap |
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & | mrMesh |
std::list< CellPtr > | mCells |
c_vector< double, SPACE_DIM > | mCentroid |
out_stream | mpVtkMetaFile |
boost::shared_ptr < CellPropertyRegistry > | mpCellPropertyRegistry |
bool | mOutputResultsForChasteVisualizer |
std::vector< boost::shared_ptr < AbstractCellWriter < ELEMENT_DIM, SPACE_DIM > > > | mCellWriters |
std::vector< boost::shared_ptr < AbstractCellPopulationWriter < ELEMENT_DIM, SPACE_DIM > > > | mCellPopulationWriters |
std::vector< boost::shared_ptr < AbstractCellPopulationCountWriter < ELEMENT_DIM, SPACE_DIM > > > | mCellPopulationCountWriters |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
void | OpenRoundRobinWritersFilesForAppend (OutputFileHandler &rOutputFileHandler) |
void | CloseRoundRobinWritersFiles () |
Friends | |
class | boost::serialization::access |
An abstract facade class encapsulating a cell population.
Contains a group of cells and associated methods.
Definition at line 83 of file AbstractCellPopulation.hpp.
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation | ( | AbstractMesh< ELEMENT_DIM, SPACE_DIM > & | rMesh | ) | [inline, protected] |
Constructor that just takes in a mesh.
rMesh | the mesh for the population. |
Definition at line 97 of file AbstractCellPopulation.cpp.
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation | ( | AbstractMesh< ELEMENT_DIM, SPACE_DIM > & | rMesh, | |
std::vector< CellPtr > & | rCells, | |||
const std::vector< unsigned > | locationIndices = std::vector<unsigned>() | |||
) | [inline] |
AbstractCellPopulation Constructor.
rMesh | a reference to the mesh underlying the cell population | |
rCells | a vector of cells. Copies of the cells will be stored in the cell population, and the passed-in vector cleared. | |
locationIndices | an optional vector of location indices that correspond to real cells |
Definition at line 59 of file AbstractCellPopulation.cpp.
References EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCellPropertyRegistry.
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::~AbstractCellPopulation | ( | ) | [inline, virtual] |
Base class with virtual methods needs a virtual destructor.
Definition at line 103 of file AbstractCellPopulation.cpp.
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptCellWriter | ( | boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > | pCellWriter, | |
CellPtr | pCell | |||
) | [pure virtual] |
A virtual method to accept a cell writer so it can write data from this object to file.
pCellWriter | the population writer. | |
pCell | the cell whose data is being written. |
Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationCountWriter | ( | boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > | pPopulationCountWriter | ) | [pure virtual] |
A virtual method to accept a cell population count writer so it can write data from this object to file.
pPopulationCountWriter | the population count writer. |
Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationWriter | ( | boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > | pPopulationWriter | ) | [pure virtual] |
A virtual method to accept a cell population writer so it can write data from this object to file.
pPopulationWriter | the population writer. |
Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
virtual CellPtr AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell | ( | CellPtr | pNewCell, | |
const c_vector< double, SPACE_DIM > & | rCellDivisionVector, | |||
CellPtr | pParentCell = CellPtr() | |||
) | [pure virtual] |
Add a new cell to the cell population.
As this method is pure virtual, it must be overridden in subclasses.
pNewCell | the cell to add | |
rCellDivisionVector | a vector providing information regarding how the cell division should occur (for cell-centre cell populations, this vector is the position of the daughter cell; for vertex cell populations it can be used by any subclass of CellBasedSimulation to as a means of dictating the axis along which the parent cell divides) | |
pParentCell | pointer to a parent cell (if required) |
Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellPopulationCountWriter | ( | boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > | pCellPopulationCountWriter | ) | [inline] |
Add a cell population count writer through an input argument. This alternative to the templated AddPopulationCountWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.
pCellPopulationCountWriter | shared pointer to a cell population count writer |
Definition at line 681 of file AbstractCellPopulation.hpp.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellPopulationCountWriter | ( | ) | [inline] |
Add a cell population count writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.
Definition at line 639 of file AbstractCellPopulation.hpp.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex | ( | unsigned | index, | |
CellPtr | pCell | |||
) | [inline, virtual] |
Adds a cell to a given location index.
index | the location index | |
pCell | the cell. |
Reimplemented in CaBasedCellPopulation< DIM >.
Definition at line 350 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap.
Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation(), NodeBasedCellPopulation< DIM >::AddMovedCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::DivideLongSprings(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::MoveCellInLocationMap().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellWriter | ( | boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > | pCellWriter | ) | [inline] |
Add a cell writer through an input argument. This alternative to the templated AddCellWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.
pCellWriter | shared pointer to a cell writer |
Definition at line 667 of file AbstractCellPopulation.hpp.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellWriter | ( | ) | [inline] |
Add a cell writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.
Definition at line 627 of file AbstractCellPopulation.hpp.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddPopulationWriter | ( | boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > | pPopulationWriter | ) | [inline] |
Add a cell population writer through an input argument. This alternative to the templated AddPopulationWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.
pPopulationWriter | shared pointer to a cell population writer |
Definition at line 653 of file AbstractCellPopulation.hpp.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddPopulationWriter | ( | ) | [inline] |
Add a cell population writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.
Definition at line 615 of file AbstractCellPopulation.hpp.
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin | ( | ) | [inline] |
Definition at line 908 of file AbstractCellPopulation.hpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells.
Referenced by CryptProjectionForce::AddForceContribution(), DiffusionForce< DIM >::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), SloughingCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), RadialSloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath(), RandomCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), PlaneBasedCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), IsolatedLabelledCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), ApoptoticCellKiller< SPACE_DIM >::CheckAndLabelCellsForApoptosisOrDeath(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellAncestors(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellCyclePhaseCount(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation(), CryptStatistics::GetCryptSection(), CryptProjectionStatistics::GetCryptSection(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSizeOfCellPopulation(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::ImposeBoundaryCondition(), PlaneBoundaryCondition< DIM >::ImposeBoundaryCondition(), CellBasedPdeHandler< DIM >::InitialiseCellPdeElementMap(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::InitialiseCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationInfo(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellAncestorsToLocationIndices(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDataOnAllCells(), CellwiseDataGradient< DIM >::SetupGradients(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), AveragedSourcePde< DIM >::SetupSourceTerms(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), NodeBasedCellPopulation< DIM >::Update(), VolumeTrackingModifier< DIM >::UpdateCellData(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), CellBasedPdeHandler< DIM >::UpdateCellPdeElementMap(), CryptProjectionForce::UpdateNode3dLocationMap(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations(), NodeBasedCellPopulationWithParticles< DIM >::Validate(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate(), CryptSimulationBoundaryCondition< DIM >::VerifyBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::VerifyBoundaryCondition(), PlaneBoundaryCondition< DIM >::VerifyBoundaryCondition(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellBasedPdeHandler< DIM >::WriteAverageRadialPdeSolution(), CellBasedPdeHandler< DIM >::WritePdeSolution(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseRoundRobinWritersFiles | ( | ) | [inline, private] |
Close all files in mCellPopulationWriters and mCellWriters.
Files in mCellPopulationCountWriters are NOT closed in this call since they are not written in a round-robin fashion
Definition at line 438 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationWriters, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseWritersFiles | ( | ) | [inline] |
Close output files associated with any writers in the members mCellPopulationCountWriters, mCellPopulationWriters and mCellWriters.
The method also closes the .pvd output file if VTK is available.
Definition at line 454 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationWriters, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVtkMetaFile.
std::pair< unsigned, unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair | ( | unsigned | index1, | |
unsigned | index2 | |||
) | [inline] |
index1 | a node index | |
index2 | a node index |
Definition at line 737 of file AbstractCellPopulation.cpp.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::DivideLongSprings(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength().
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End | ( | ) | [inline] |
Definition at line 914 of file AbstractCellPopulation.hpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells.
Referenced by CryptProjectionForce::AddForceContribution(), DiffusionForce< DIM >::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), SloughingCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), RadialSloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath(), RandomCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), PlaneBasedCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), IsolatedLabelledCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), ApoptoticCellKiller< SPACE_DIM >::CheckAndLabelCellsForApoptosisOrDeath(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellAncestors(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellCyclePhaseCount(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation(), CryptStatistics::GetCryptSection(), CryptProjectionStatistics::GetCryptSection(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSizeOfCellPopulation(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::ImposeBoundaryCondition(), PlaneBoundaryCondition< DIM >::ImposeBoundaryCondition(), CellBasedPdeHandler< DIM >::InitialiseCellPdeElementMap(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::InitialiseCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationInfo(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellAncestorsToLocationIndices(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDataOnAllCells(), CellwiseDataGradient< DIM >::SetupGradients(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), AveragedSourcePde< DIM >::SetupSourceTerms(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), NodeBasedCellPopulation< DIM >::Update(), VolumeTrackingModifier< DIM >::UpdateCellData(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), CellBasedPdeHandler< DIM >::UpdateCellPdeElementMap(), CryptProjectionForce::UpdateNode3dLocationMap(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations(), NodeBasedCellPopulationWithParticles< DIM >::Validate(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate(), CryptSimulationBoundaryCondition< DIM >::VerifyBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::VerifyBoundaryCondition(), PlaneBoundaryCondition< DIM >::VerifyBoundaryCondition(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellBasedPdeHandler< DIM >::WriteAverageRadialPdeSolution(), CellBasedPdeHandler< DIM >::WritePdeSolution(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().
std::set< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellAncestors | ( | ) | [inline] |
Loops over cells and makes a list of the ancestors that are part of the cell population.
Definition at line 171 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End().
std::vector< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellCyclePhaseCount | ( | ) | [inline] |
Find out how many cells in each cell cycle phase there are.
Definition at line 251 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), PetscTools::GetWorld(), PetscTools::IsParallel(), and NEVER_REACHED.
Referenced by CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().
std::vector< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellMutationStateCount | ( | ) | [inline] |
Find out how many cells of each mutation state there are
Definition at line 182 of file AbstractCellPopulation.cpp.
References PetscTools::GetWorld(), PetscTools::IsParallel(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCellPropertyRegistry.
Referenced by CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().
std::vector< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellProliferativeTypeCount | ( | ) | [inline] |
Find out how many cells of each type there are.
Definition at line 216 of file AbstractCellPopulation.cpp.
References PetscTools::GetWorld(), PetscTools::IsParallel(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCellPropertyRegistry.
Referenced by CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().
boost::shared_ptr< CellPropertyRegistry > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellPropertyRegistry | ( | ) | [inline] |
Definition at line 392 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCellPropertyRegistry.
Referenced by IsolatedLabelledCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDefaultCellMutationStateAndProliferativeTypeOrdering(), and CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::WriteHeader().
std::set< CellPtr > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellsUsingLocationIndex | ( | unsigned | index | ) | [inline] |
Get the set of cells corresponding to a given location index.
Note that the set may be empty.
index | the location index |
Definition at line 319 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap.
CellPtr AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex | ( | unsigned | index | ) | [inline, virtual] |
Get the cell corresponding to a given location index.
This method assumes that there is at most one cell attached to a location index and an assertion fails if not.
index | the location index |
Reimplemented in NodeBasedCellPopulation< DIM >.
Definition at line 298 of file AbstractCellPopulation.cpp.
References EXCEPTION, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap.
Referenced by CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes(), TargetedCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), T2SwapCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), IsolatedLabelledCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers(), CellwiseSourcePde< DIM >::ComputeLinearInUCoeffInSourceTermAtNode(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::DivideLongSprings(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstant(), CellwiseDataGradient< DIM >::SetupGradients(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().
c_vector< double, SPACE_DIM > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation | ( | ) | [inline] |
Definition at line 418 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCentroid.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSizeOfCellPopulation(), CellBasedPdeHandler< DIM >::UseCoarsePdeMesh(), and CellBasedPdeHandler< DIM >::WriteAverageRadialPdeSolution().
unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell | ( | CellPtr | pCell | ) | [inline] |
Get the location index corresponding to a given cell.
Assumes there is one location index for each cell and an assertion fails if not.
pCell | the cell |
Definition at line 383 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap.
Referenced by NodeBasedCellPopulationWithParticles< DIM >::AddCell(), NodeBasedCellPopulation< DIM >::AddCell(), MeshBasedCellPopulationWithGhostNodes< DIM >::AddCell(), CryptProjectionForce::AddForceContribution(), DiffusionForce< DIM >::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), CryptSimulation1d::CalculateCellDivisionVector(), IsolatedLabelledCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers(), NodeBasedCellPopulation< DIM >::DeleteMovedCell(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput(), MeshBasedCellPopulationWithGhostNodes< DIM >::GetNeighbouringLocationIndices(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNodeCorrespondingToCell(), NodeBasedCellPopulation< DIM >::GetVolumeOfCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::ImposeBoundaryCondition(), PlaneBoundaryCondition< DIM >::ImposeBoundaryCondition(), NodeBasedCellPopulation< DIM >::RemoveDeadCells(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells(), CellwiseDataGradient< DIM >::SetupGradients(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), NodeBasedCellPopulation< DIM >::Update(), CryptProjectionForce::UpdateNode3dLocationMap(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations(), NodeBasedCellPopulationWithParticles< DIM >::Validate(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate(), CryptSimulationBoundaryCondition< DIM >::VerifyBoundaryCondition(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellLocationIndexWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellLabelWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellIdWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellAgesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellBasedPdeHandler< DIM >::WritePdeSolution(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().
virtual c_vector<double, SPACE_DIM> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre | ( | CellPtr | pCell | ) | [pure virtual] |
Find where a given cell is in space.
As this method is pure virtual, it must be overridden in subclasses.
pCell | the cell |
Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< DIM >, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.
Referenced by SloughingCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), RadialSloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath(), PlaneBasedCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), CellBasedPdeHandler< DIM >::FindCoarseElementContainingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSizeOfCellPopulation(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), SphereGeometryBoundaryCondition< DIM >::ImposeBoundaryCondition(), CellBasedPdeHandler< DIM >::InitialiseCellPdeElementMap(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), AveragedSourcePde< DIM >::SetupSourceTerms(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), CellBasedPdeHandler< DIM >::UpdateCellPdeElementMap(), CryptProjectionForce::UpdateNode3dLocationMap(), SphereGeometryBoundaryCondition< DIM >::VerifyBoundaryCondition(), PlaneBoundaryCondition< DIM >::VerifyBoundaryCondition(), CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellLabelWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellIdWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellAgesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellBasedPdeHandler< DIM >::WriteAverageRadialPdeSolution(), and CellBasedPdeHandler< DIM >::WritePdeSolution().
virtual std::set<unsigned> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices | ( | CellPtr | pCell | ) | [pure virtual] |
Given a cell, returns the set of location indices corresponding to neighbouring cells.
As this method is pure virtual, it must be overridden in subclasses.
pCell | a cell |
Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< DIM >, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.
Referenced by DeltaNotchTrackingModifier< DIM >::UpdateCellData().
virtual std::set<unsigned> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices | ( | unsigned | index | ) | [pure virtual] |
Given a node index, returns the set of neighbouring node indices.
As this method is pure virtual, it must be overridden in subclasses.
index | the node index |
Implemented in AbstractOnLatticeCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices().
virtual Node<SPACE_DIM>* AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode | ( | unsigned | index | ) | [pure virtual] |
Get a pointer to the node with a given index.
As this method is pure virtual, it must be overridden in subclasses.
index | global index of the specified node |
Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Referenced by CryptProjectionForce::AddForceContribution(), DiffusionForce< DIM >::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes(), BuskeElasticForce< DIM >::CalculateForceBetweenNodes(), BuskeAdhesiveForce< DIM >::CalculateForceBetweenNodes(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNodeCorrespondingToCell(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::ImposeBoundaryCondition(), PlaneBoundaryCondition< DIM >::ImposeBoundaryCondition(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodeLocations(), CryptSimulationBoundaryCondition< DIM >::VerifyBoundaryCondition(), and CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().
unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumAllCells | ( | ) | [inline] |
This returns the number of cells that are present in the internal mCells vector. It also includes dead cells and cells that are associated with a deleted location in the mesh.
Definition at line 155 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().
virtual unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumNodes | ( | ) | [pure virtual] |
As this method is pure virtual, it must be overridden in subclasses.
Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), and CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition().
unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells | ( | ) | [inline] |
This counts the number of cells that the cell iterator covers. It does not include dead cells or cells that are associated with a deleted location in the mesh.
Definition at line 142 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End().
Referenced by CellBasedPdeHandler< DIM >::CellBasedPdeHandler(), TargetedCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation().
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputResultsForChasteVisualizer | ( | ) | [inline] |
Definition at line 689 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputResultsForChasteVisualizer.
c_vector< double, SPACE_DIM > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSizeOfCellPopulation | ( | ) | [inline] |
Reimplemented in NodeBasedCellPopulation< DIM >.
Definition at line 707 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre().
virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell | ( | CellPtr | pCell | ) | [pure virtual] |
As this method is pure virtual, it must be overridden in subclasses.
pCell | boost shared pointer to a cell |
Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Referenced by CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput(), VolumeTrackingModifier< DIM >::UpdateCellData(), and CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().
virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWidth | ( | const unsigned & | rDimension | ) | [pure virtual] |
Calculate the 'width' of any dimension of the cell population.
As this method is pure virtual, it must be overridden in subclasses.
rDimension | a dimension (0,1 or 2) |
Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::HasWriter | ( | ) | const [inline] |
Get whether the population has a writer of the specified type.
Definition at line 692 of file AbstractCellPopulation.hpp.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::InitialiseCells | ( | ) | [inline] |
Initialise each cell's cell-cycle model.
Definition at line 108 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End().
virtual bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAssociatedWithADeletedLocation | ( | CellPtr | pCell | ) | [pure virtual] |
Helper method for establishing if a cell is real.
As this method is pure virtual, it must be overridden in subclasses.
pCell | the cell |
Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< DIM >, and AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator::IsRealCell().
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAttachedToLocationIndex | ( | unsigned | index | ) | [inline] |
Returns whether or not a cell is associated with a location index
index | the location index |
Definition at line 326 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap.
Referenced by CellwiseSourcePde< DIM >::ComputeLinearInUCoeffInSourceTermAtNode(), and CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit().
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsRoomToDivide | ( | CellPtr | pCell | ) | [inline, virtual] |
pCell | pointer to a cell |
Reimplemented in CaBasedCellPopulation< DIM >.
Definition at line 701 of file AbstractCellPopulation.cpp.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::MoveCellInLocationMap | ( | CellPtr | pCell, | |
unsigned | old_index, | |||
unsigned | new_index | |||
) | [inline] |
Change the location index of a cell in mLocationCellMap and mCellLocationMap
pCell | the cell to move | |
old_index | the old location index | |
new_index | the new location index |
Definition at line 373 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenRoundRobinWritersFilesForAppend | ( | OutputFileHandler & | rOutputFileHandler | ) | [inline, private] |
Open all files in mCellPopulationWriters and mCellWriters in append mode for writing.
Files in mCellPopulationCountWriters are NOT opened in this call since they are not written in a round-robin fashion.
rOutputFileHandler | handler for the directory in which to open this file. |
Definition at line 526 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationWriters, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles | ( | OutputFileHandler & | rOutputFileHandler | ) | [inline, virtual] |
Open output files (and, if required, write headers) for any writers in the members mCellPopulationCountWriters, mCellPopulationWriters and mCellWriters.
The method also writes the header for the .pvd output file if VTK is available.
Before doing this, the method also creates appropriate writer objects if mOutputResultsForChasteVisualizer is set to true.
This method is public because it is called by the simulation class at the start of the Solve() call.
rOutputFileHandler | handler for the directory in which to open this file. |
Reimplemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Definition at line 476 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationCountWriters, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationWriters, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputResultsForChasteVisualizer, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVtkMetaFile, and OutputFileHandler::OpenOutputFile().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationInfo | ( | out_stream & | rParamsFile | ) | [inline] |
Outputs CellPopulation used in the simulation to file and then calls OutputCellPopulationParameters to output all relevant parameters.
rParamsFile | the file stream to which the parameters are output |
Loop over cells and generate a set of cell-cycle model classes that are present in the population.
Definition at line 642 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), Identifiable::GetIdentifier(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters | ( | out_stream & | rParamsFile | ) | [inline, pure virtual] |
Outputs CellPopulation parameters to file
As this method is pure virtual, it must be overridden in subclasses.
rParamsFile | the file stream to which the parameters are output |
Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractOnLatticeCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, NodeBasedCellPopulationWithParticles< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >, AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >, AbstractOffLatticeCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Definition at line 683 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputResultsForChasteVisualizer.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationInfo().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex | ( | unsigned | index, | |
CellPtr | pCell | |||
) | [inline, virtual] |
Removes a cell from a given location index.
index | the location index | |
pCell | the cell. |
Reimplemented in CaBasedCellPopulation< DIM >.
Definition at line 357 of file AbstractCellPopulation.cpp.
References EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap.
Referenced by NodeBasedCellPopulation< DIM >::DeleteMovedCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::MoveCellInLocationMap(), NodeBasedCellPopulation< DIM >::RemoveDeadCells(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells().
virtual unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells | ( | ) | [pure virtual] |
Remove all cells labelled as dead.
As this method is pure virtual, it must be overridden in subclasses.
Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
std::list< CellPtr > & AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetCells | ( | ) | [inline] |
Definition at line 136 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator::IsAtEnd(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator::Iterator(), and AbstractTargetAreaModifier< DIM >::UpdateTargetAreas().
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh | ( | ) | [inline] |
Reimplemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Definition at line 130 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.
Referenced by GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes(), T2SwapCellKiller< DIM >::CheckAndLabelCellsForApoptosisOrDeath(), CellBasedPdeHandler< DIM >::OpenResultsFiles(), NodeLocationWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), and BoundaryNodeWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize | ( | Archive & | archive, | |
const unsigned int | version | |||
) | [inline, private] |
Serialize the object and its member variables.
archive | the archive | |
version | the current version of this class |
Reimplemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractOnLatticeCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, NodeBasedCellPopulationWithParticles< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >, AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >, AbstractOffLatticeCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Definition at line 97 of file AbstractCellPopulation.hpp.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellAncestorsToLocationIndices | ( | ) | [inline] |
Sets the Ancestor index of all the cells at this time to be the same as their location index, can be used to trace clonal populations.
Definition at line 161 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), MAKE_PTR_ARGS, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellUsingLocationIndex | ( | unsigned | index, | |
CellPtr | pCell | |||
) | [inline] |
Set the cell corresponding to a given location index.
Assumes there is one cell for each location index and replaces any existing cell attached to the location index. If you wish to attach an additional cell to a location index use AddCellUsingLocaitonIndex as SetCellUsingLocation Index will overwrite cells attached to this index.
index | the location index | |
pCell | the cell. |
Definition at line 336 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap.
Referenced by AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), and NodeBasedCellPopulation< DIM >::UpdateMapsAfterRemesh().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDataOnAllCells | ( | const std::string & | dataName, | |
double | dataValue | |||
) | [inline] |
Add an item of cell data to every cell in the population
dataName | is the name associated with the data | |
dataValue | is the value of the data, initially the same for each cell |
Definition at line 119 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDefaultCellMutationStateAndProliferativeTypeOrdering | ( | ) | [inline] |
Set a default ordering on cell mutation states and cell proliferative types, so that existing tests don't need to specify the old ordering explicitly.
Definition at line 398 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellPropertyRegistry().
Referenced by CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::WriteHeader(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode | ( | unsigned | nodeIndex, | |
ChastePoint< SPACE_DIM > & | rNewLocation | |||
) | [pure virtual] |
Move the node with a given index to a new point in space.
As this method is pure virtual, it must be overridden in subclasses.
nodeIndex | the index of the node to be moved | |
rNewLocation | the new target location of the node |
Implemented in AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, and AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputResultsForChasteVisualizer | ( | bool | outputResultsForChasteVisualizer | ) | [inline] |
Set mOutputResultsForChasteVisualizer.
outputResultsForChasteVisualizer | the new value of mOutputResultsForChasteVisualizer |
Definition at line 695 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputResultsForChasteVisualizer.
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update | ( | bool | hasHadBirthsOrDeaths = true |
) | [pure virtual] |
Remove the Nodes (for cell-centre) or VertexElements (for cell-vertex) which have been marked as deleted and update the correspondence with Cells.
hasHadBirthsOrDeaths | - a bool saying whether cell population has had Births Or Deaths |
Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Referenced by CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), VolumeTrackingModifier< DIM >::UpdateCellData(), and DeltaNotchTrackingModifier< DIM >::UpdateCellData().
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellProcessLocation | ( | ) | [inline, virtual] |
Update the ownership of cell in a parallel cell-based simulation.
Reimplemented in NodeBasedCellPopulation< DIM >.
Definition at line 433 of file AbstractCellPopulation.cpp.
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Validate | ( | ) | [protected, pure virtual] |
Check consistency of our internal data structures.
As this method is pure virtual, it must be overridden in subclasses.
Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithParticles< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles | ( | const std::string & | rDirectory | ) | [inline, virtual] |
Write results from the current cell population state to output files.
rDirectory | pathname of the output directory, relative to where Chaste output is stored |
Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, PottsBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Definition at line 541 of file AbstractCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptCellWriter(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationCountWriter(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationWriter(), PetscTools::AmMaster(), PetscTools::AmTopMost(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), PetscTools::BeginRoundRobin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseRoundRobinWritersFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), PetscTools::EndRoundRobin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationCountWriters, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationWriters, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenRoundRobinWritersFilesForAppend(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDefaultCellMutationStateAndProliferativeTypeOrdering(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile | ( | const std::string & | rDirectory | ) | [protected, pure virtual] |
Write the current results to mpVtkMetaFile.
As this method is pure virtual, it must be overridden in subclasses.
rDirectory | pathname of the output directory, relative to where Chaste output is stored |
Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithParticles< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractOnLatticeCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, NodeBasedCellPopulationWithParticles< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >, AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >, AbstractOffLatticeCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.
Definition at line 88 of file AbstractCellPopulation.hpp.
std::map<Cell*, unsigned> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap [protected] |
Map cells to location (node or VertexElement) indices.
Definition at line 134 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex(), AbstractCellPopulation< DIM, DIM >::serialize(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellAncestorsToLocationIndices(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellUsingLocationIndex(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), and NodeBasedCellPopulation< DIM >::UpdateMapsAfterRemesh().
std::vector<boost::shared_ptr<AbstractCellPopulationCountWriter<ELEMENT_DIM, SPACE_DIM> > > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationCountWriters [protected] |
A list of cell population count writers.
Definition at line 161 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< DIM, DIM >::AddCellPopulationCountWriter(), AbstractCellPopulation< DIM, DIM >::HasWriter(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles(), AbstractCellPopulation< DIM, DIM >::serialize(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
std::vector<boost::shared_ptr<AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM> > > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationWriters [protected] |
A list of cell population writers.
Definition at line 158 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< DIM, DIM >::AddPopulationWriter(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseRoundRobinWritersFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseWritersFiles(), AbstractCellPopulation< DIM, DIM >::HasWriter(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenRoundRobinWritersFilesForAppend(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles(), AbstractCellPopulation< DIM, DIM >::serialize(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().
std::list<CellPtr> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells [protected] |
List of cells.
Definition at line 140 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCentreBasedCellPopulation(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell(), NodeBasedCellPopulation< DIM >::AddMovedCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers(), NodeBasedCellPopulation< DIM >::DeleteMovedCell(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::DivideLongSprings(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumAllCells(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), NodeBasedCellPopulation< DIM >::RemoveDeadCells(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetCells(), AbstractCellPopulation< DIM, DIM >::serialize(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), and NodeBasedCellPopulation< DIM >::UpdateMapsAfterRemesh().
std::vector<boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters [protected] |
A list of cell writers.
Definition at line 155 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< DIM, DIM >::AddCellWriter(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseRoundRobinWritersFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseWritersFiles(), AbstractCellPopulation< DIM, DIM >::HasWriter(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenRoundRobinWritersFilesForAppend(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles(), AbstractCellPopulation< DIM, DIM >::serialize(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().
c_vector<double, SPACE_DIM> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCentroid [protected] |
Population centroid.
Definition at line 143 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation().
std::map<unsigned, std::set<CellPtr> > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap [protected] |
Map location (node or VertexElement) indices back to cells.
Definition at line 131 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellsUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAttachedToLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex(), AbstractCellPopulation< DIM, DIM >::serialize(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellUsingLocationIndex(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), and NodeBasedCellPopulation< DIM >::UpdateMapsAfterRemesh().
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputResultsForChasteVisualizer [protected] |
Whether to write results to file for visualization using the Chaste java visualizer (defaults to true).
Definition at line 152 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputResultsForChasteVisualizer(), MeshBasedCellPopulationWithGhostNodes< DIM >::OpenWritersFiles(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< DIM, DIM >::serialize(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputResultsForChasteVisualizer().
boost::shared_ptr<CellPropertyRegistry> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCellPropertyRegistry [protected] |
Cell property registry.
Definition at line 149 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellMutationStateCount(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellProliferativeTypeCount(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellPropertyRegistry(), and AbstractCellPopulation< DIM, DIM >::serialize().
out_stream AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVtkMetaFile [protected] |
Meta results file for VTK.
Definition at line 146 of file AbstractCellPopulation.hpp.
Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseWritersFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().
AbstractMesh<ELEMENT_DIM, SPACE_DIM>& AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh [protected] |
Reference to the mesh.
Definition at line 137 of file AbstractCellPopulation.hpp.
Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::CalculateForceBetweenGhostNodes(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateVoronoiTessellation(), MeshBasedCellPopulation< 2 >::CreateVoronoiTessellation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), NodeBasedCellPopulationWithParticles< DIM >::GetParticleIndices(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWidth(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::MeshBasedCellPopulation(), NodeBasedCellPopulation< DIM >::NodeBasedCellPopulation(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetMesh(), MeshBasedCellPopulationWithGhostNodes< DIM >::SetGhostNodes(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode(), NodeBasedCellPopulationWithParticles< DIM >::SetParticles(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsEnd(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions(), NodeBasedCellPopulationWithParticles< DIM >::UpdateParticlePositions(), NodeBasedCellPopulationWithParticles< DIM >::Validate(), NodeBasedCellPopulation< DIM >::Validate(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::~MeshBasedCellPopulation(), and NodeBasedCellPopulation< DIM >::~NodeBasedCellPopulation().