Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <AbstractOnLatticeCellPopulation.hpp>
Public Member Functions | |
AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false) | |
virtual | ~AbstractOnLatticeCellPopulation () |
virtual void | UpdateCellLocations (double dt)=0 |
bool | GetUpdateNodesInRandomOrder () |
void | SetUpdateNodesInRandomOrder (bool updateNodesInRandomOrder) |
void | SetIterateRandomlyOverUpdateRuleCollection (bool iterateRandomly) |
bool | GetIterateRandomlyOverUpdateRuleCollection () |
void | SetNode (unsigned index, ChastePoint< DIM > &rNewLocation) |
std::set< unsigned > | GetNeighbouringNodeIndices (unsigned index) |
virtual void | OutputCellPopulationParameters (out_stream &rParamsFile) |
virtual double | GetDefaultTimeStep () |
virtual void | AddUpdateRule (boost::shared_ptr< AbstractUpdateRule< DIM > > pUpdateRule)=0 |
virtual void | RemoveAllUpdateRules () |
virtual const std::vector< boost::shared_ptr< AbstractUpdateRule< DIM > > > | GetUpdateRuleCollection () const |
Public Member Functions inherited from AbstractCellPopulation< DIM > | |
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 &rDataName, double dataValue) |
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & | rGetMesh () |
virtual TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * | GetTetrahedralMeshForPdeModifier ()=0 |
virtual bool | IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex) |
virtual double | GetCellDataItemAtPdeNode (unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)=0 |
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 void | WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile) |
virtual CellPtr | AddCell (CellPtr pNewCell, 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) |
virtual 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 > | GetNeighbouringLocationIndices (CellPtr pCell)=0 |
virtual std::set< std::pair< unsigned, unsigned > > | GetNeighbouringEdgeIndices (CellPtr pCell, unsigned pEdgeIndex) |
c_vector< double, SPACE_DIM > | GetCentroidOfCellPopulation () |
virtual void | UpdateCellProcessLocation () |
virtual void | OpenWritersFiles (OutputFileHandler &rOutputFileHandler) |
virtual 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 | AcceptPopulationEventWriter (boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationEventWriter)=0 |
virtual void | AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter, CellPtr pCell)=0 |
std::vector< std::string > | GetDivisionsInformation () |
void | AddDivisionInformation (std::string divisionInformation) |
void | ClearDivisionsInformation () |
std::vector< std::string > | GetRemovalsInformation () |
void | AddRemovalInformation (std::string removalInformation) |
void | ClearRemovalsInformation () |
void | GenerateRemovalInformation (CellPtr pCell, std::string killerInfo) |
void | KillCell (CellPtr pCell, std::string killerInfo) |
void | StartApoptosisOnCell (CellPtr pCell, std::string killerInfo) |
void | OutputCellPopulationInfo (out_stream &rParamsFile) |
virtual void | SimulationSetupHook (AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM > *pSimulation) |
bool | GetOutputResultsForChasteVisualizer () |
void | AddPopulationWriter () |
void | AddPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter) |
void | AddCellWriter () |
void | AddCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter) |
void | AddCellPopulationCountWriter () |
void | AddCellPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationCountWriter) |
void | AddCellPopulationEventWriter () |
void | AddCellPopulationEventWriter (boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationEventWriter) |
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 () |
Public Member Functions inherited from Identifiable | |
virtual | ~Identifiable () |
std::string | GetIdentifier () const |
Protected Member Functions | |
AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh) | |
Protected Member Functions inherited from AbstractCellPopulation< DIM > | |
virtual void | Validate ()=0 |
virtual void | WriteVtkResultsToFile (const std::string &rDirectory)=0 |
AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | |
virtual void | AcceptCellWritersAcrossPopulation () |
Protected Attributes | |
std::vector< boost::shared_ptr< AbstractUpdateRule< DIM > > > | mUpdateRuleCollection |
bool | mDeleteMesh |
bool | mUpdateNodesInRandomOrder |
bool | mIterateRandomlyOverUpdateRuleCollection |
Protected Attributes inherited from AbstractCellPopulation< DIM > | |
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 |
std::vector< boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > > | mCellPopulationEventWriters |
std::vector< std::string > | mDivisionsInformation |
std::vector< std::string > | mRemovalsInformation |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Friends | |
class | boost::serialization::access |
An abstract class for on-lattice cell populations.
Definition at line 46 of file AbstractOnLatticeCellPopulation.hpp.
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protected |
Constructor that just takes in a mesh.
rMesh | the mesh for the cell population. |
Definition at line 57 of file AbstractOnLatticeCellPopulation.cpp.
AbstractOnLatticeCellPopulation< DIM >::AbstractOnLatticeCellPopulation | ( | AbstractMesh< DIM, DIM > & | rMesh, |
std::vector< CellPtr > & | rCells, | ||
const std::vector< unsigned > | locationIndices = std::vector<unsigned>() , |
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bool | deleteMesh = false |
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Default constructor.
rMesh | a refernce to the mesh underlying the cell population |
rCells | a vector of cells |
locationIndices | an optional vector of location indices that correspond to real cells |
deleteMesh | set to true if you want the cell population to free the mesh memory on destruction (defaults to false) |
Definition at line 39 of file AbstractOnLatticeCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), and AbstractCellPopulation< DIM >::mCells.
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virtual |
Destructor.
Definition at line 66 of file AbstractOnLatticeCellPopulation.cpp.
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pure virtual |
Add an update rule to be used with this population.
As this method is pure virtual, it must be overridden in subclasses.
pUpdateRule | pointer to an update rule |
Implemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.
Referenced by OnLatticeSimulation< DIM >::AddUpdateRule().
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virtual |
Overridden GetDefaultTimeStep() method.
A hard-coded value of 0.1 is returned. However, note that the time step can be reset by calling SetDt() on the simulation object used to simulate the cell population.
Implements AbstractCellPopulation< DIM >.
Definition at line 119 of file AbstractOnLatticeCellPopulation.cpp.
bool AbstractOnLatticeCellPopulation< DIM >::GetIterateRandomlyOverUpdateRuleCollection | ( | ) |
Definition at line 89 of file AbstractOnLatticeCellPopulation.cpp.
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virtual |
Overridden GetNeighbouringNodeIndices() method.
This method currently returns an exception as the two types of neighbourhood (Moore and Von Neumann) are defined in the PottsMesh.
index | the node index |
Implements AbstractCellPopulation< DIM >.
Definition at line 101 of file AbstractOnLatticeCellPopulation.cpp.
References EXCEPTION.
bool AbstractOnLatticeCellPopulation< DIM >::GetUpdateNodesInRandomOrder | ( | ) |
Get whether we update nodes in a random order.
Definition at line 71 of file AbstractOnLatticeCellPopulation.cpp.
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virtual |
Get the collection of update rules to be used with this population.
Reimplemented in CaBasedCellPopulation< DIM >.
Definition at line 125 of file AbstractOnLatticeCellPopulation.cpp.
Referenced by OnLatticeSimulation< DIM >::OutputAdditionalSimulationSetup().
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virtual |
Outputs parameters to file.
rParamsFile | the file stream to which the parameters are output |
Implements AbstractCellPopulation< DIM >.
Reimplemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.
Definition at line 109 of file AbstractOnLatticeCellPopulation.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().
Referenced by CaBasedCellPopulation< DIM >::OutputCellPopulationParameters(), and PottsBasedCellPopulation< DIM >::OutputCellPopulationParameters().
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virtual |
Remove any update rules previously passed to this population.
Reimplemented in CaBasedCellPopulation< DIM >.
Definition at line 131 of file AbstractOnLatticeCellPopulation.cpp.
Referenced by CaBasedCellPopulation< DIM >::RemoveAllUpdateRules(), and OnLatticeSimulation< DIM >::RemoveAllUpdateRules().
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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 59 of file AbstractOnLatticeCellPopulation.hpp.
References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection, AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder, and AbstractOnLatticeCellPopulation< DIM >::mUpdateRuleCollection.
void AbstractOnLatticeCellPopulation< DIM >::SetIterateRandomlyOverUpdateRuleCollection | ( | bool | iterateRandomly | ) |
Set mIterateRandomlyOverUpdateRuleCollection.
iterateRandomly | whether to iterate randomly over mUpdateRuleCollection |
Definition at line 83 of file AbstractOnLatticeCellPopulation.cpp.
void AbstractOnLatticeCellPopulation< DIM >::SetNode | ( | unsigned | index, |
ChastePoint< DIM > & | rNewLocation | ||
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Overridden SetNode() method.
This method throws an exception if called on a subclass of AbstractOnLatticeCellPopulation, since in such classes the lattice is assumed to be fixed.
index | the index of the node to be moved |
rNewLocation | the new target location of the node |
Definition at line 95 of file AbstractOnLatticeCellPopulation.cpp.
References EXCEPTION.
void AbstractOnLatticeCellPopulation< DIM >::SetUpdateNodesInRandomOrder | ( | bool | updateNodesInRandomOrder | ) |
Get whether we update nodes in a random order.
updateNodesInRandomOrder | Whether to update nodes in a random order. |
Definition at line 77 of file AbstractOnLatticeCellPopulation.cpp.
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pure virtual |
Update cell locations over the course of a time step of specified length.
As this method is pure virtual, it must be overridden in subclasses.
dt | time step |
Implemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.
Referenced by OnLatticeSimulation< DIM >::UpdateCellLocationsAndTopology().
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friend |
Needed for serialization.
Definition at line 51 of file AbstractOnLatticeCellPopulation.hpp.
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protected |
Whether to delete the mesh when we are destroyed. Needed if this cell population has been de-serialized.
Definition at line 79 of file AbstractOnLatticeCellPopulation.hpp.
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protected |
Whether to iterate randomly over mUpdateRuleCollection when updating cell locations. Initialized to false in the constructor.
Definition at line 91 of file AbstractOnLatticeCellPopulation.hpp.
Referenced by AbstractOnLatticeCellPopulation< DIM >::serialize().
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protected |
Whether to update nodes in random order. Initialized to true in the constructor.
Definition at line 85 of file AbstractOnLatticeCellPopulation.hpp.
Referenced by AbstractOnLatticeCellPopulation< DIM >::serialize().
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protected |
The update rules used to determine the new location of the cells. These rules specify how individual cells move into free spaces.
Definition at line 73 of file AbstractOnLatticeCellPopulation.hpp.
Referenced by AbstractOnLatticeCellPopulation< DIM >::serialize().