TissueSimulation< DIM > Class Template Reference

#include <TissueSimulation.hpp>

Inheritance diagram for TissueSimulation< DIM >:

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List of all members.

Public Member Functions

 TissueSimulation (AbstractTissue< DIM > &rTissue, std::vector< AbstractForce< DIM > * > forceCollection, bool deleteTissueAndForceCollection=false, bool initialiseCells=true)
virtual ~TissueSimulation ()
std::vector< double > GetNodeLocation (const unsigned &rNodeIndex)
double GetDt ()
unsigned GetNumBirths ()
unsigned GetNumDeaths ()
std::string GetOutputDirectory ()
void SetDt (double dt)
void SetEndTime (double endTime)
void SetOutputDirectory (std::string outputDirectory)
void SetSamplingTimestepMultiple (unsigned samplingTimestepMultiple)
void SetNoBirth (bool noBirth)
void SetUpdateTissueRule (bool updateTissue)
void AddCellKiller (AbstractCellKiller< DIM > *pCellKiller)
void Solve ()
AbstractTissue< DIM > & rGetTissue ()
const AbstractTissue< DIM > & rGetTissue () const
const std::vector
< AbstractForce< DIM > * > 		rGetForceCollection () const

Protected Member Functions

template<class Archive>
void serialize (Archive &archive, const unsigned int version)
virtual void WriteVisualizerSetupFile ()
unsigned DoCellBirth ()
virtual c_vector< double, DIM > CalculateDividingCellCentreLocations (TissueCell *pParentCell)
unsigned DoCellRemoval ()
virtual void UpdateNodePositions (const std::vector< c_vector< double, DIM > > &rNodeForces)
virtual void ApplyTissueBoundaryConditions (const std::vector< c_vector< double, DIM > > &rOldLocations)
virtual void PostSolve ()
virtual void SetupSolve ()
virtual void AfterSolve ()
virtual bool StoppingEventHasOccurred ()
void UpdateTissue ()

Protected Attributes

double mDt
double mEndTime
AbstractTissue< DIM > & mrTissue
bool mDeleteTissue
bool mAllocatedMemoryForForceCollection
bool mInitialiseCells
bool mNoBirth
bool mUpdateTissue
std::string mOutputDirectory
std::string mSimulationOutputDirectory
out_stream mpSetupFile
TissueConfig * mpConfig
RandomNumberGenerator * mpRandomGenerator
unsigned mNumBirths
unsigned mNumDeaths
unsigned mSamplingTimestepMultiple
std::vector
< AbstractCellKiller< DIM > * > 		mCellKillers
std::vector< AbstractForce
< DIM > * > 		mForceCollection

Friends

class TestCryptSimulation2d
class TestTissueSimulation3d
class boost::serialization::access

Detailed Description

template<unsigned DIM>
class TissueSimulation< DIM >

Run an off-lattice 2D or 3D cell-based simulation using a cell-centre- or vertex-based tissue.

In cell-centre-based tissues, each cell is represented by a single node (corresponding to its centre), and connectivity is defined either by a Delaunay triangulation or a radius of influence. In vertex-based tissues, each cell is represented by a polytope (corresponding to its membrane) with a variable number of vertices.

The TissueSimulation is constructed with a Tissue, which updates the correspondence between each TissueCell and its spatial representation and handles cell division (governed by the CellCycleModel associated with each cell); and one or more Force laws, which define the mechanical properties of the Tissue. It is also possible to add one or more CellKiller objects to the TissueSimulation, which specify the conditions under which a TissueCell dies.

Definition at line 61 of file TissueSimulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
TissueSimulation< DIM >::TissueSimulation ( AbstractTissue< DIM > &  rTissue,
std::vector< AbstractForce< DIM > * >  forceCollection,
bool  deleteTissueAndForceCollection = false,
bool  initialiseCells = true 
) [inline]

Constructor.

Parameters:
rTissue A tissue facade class (contains a mesh and cells)
forceCollection The mechanics to use in the simulation
deleteTissueAndForceCollection Whether to delete the tissue and force collection on destruction to free up memory
initialiseCells Whether to initialise cells (set to false when loading from an archive)

Definition at line 40 of file TissueSimulation.cpp.

References RandomNumberGenerator::Instance(), TissueConfig::Instance(), TissueSimulation< DIM >::mInitialiseCells, TissueSimulation< DIM >::mpConfig, TissueSimulation< DIM >::mpRandomGenerator, and TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
TissueSimulation< DIM >::~TissueSimulation (  )  [inline, virtual]

Destructor.

This frees the tissue and cell killers, if they were created by de-serialization.

Definition at line 72 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mAllocatedMemoryForForceCollection, TissueSimulation< DIM >::mCellKillers, TissueSimulation< DIM >::mDeleteTissue, TissueSimulation< DIM >::mForceCollection, and TissueSimulation< DIM >::mrTissue.

Member Function Documentation

template<unsigned DIM>
template<class Archive>
void TissueSimulation< DIM >::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, protected]

Archive the member variables.

Serialization of singleton objects must be done with care. Before the object is serialized via a pointer, it *MUST* be serialized directly, or an assertion will trip when a second instance of the class is created on de-serialization.

Parameters:
archive the archive
version the current version of this class

Reimplemented in CryptSimulation2d.

Definition at line 141 of file TissueSimulation.hpp.

template<unsigned DIM>
virtual void TissueSimulation< DIM >::WriteVisualizerSetupFile (  )  [inline, protected, virtual]

Writes out special information about the mesh to the visualizer.

Reimplemented in CryptSimulation2d.

Definition at line 168 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::DoCellBirth (  )  [inline, protected]

During a simulation time step, process any cell divisions that need to occur. If the simulation includes cell birth, causes (almost) all cells that are ready to divide to produce daughter cells.

Returns:
the number of births that occurred.

Todo:
This is specific to cell-centre based models, the location isn't used in a vertex simulation, move it down to AbstractCellCentreBasedTissue??

Definition at line 98 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::CalculateDividingCellCentreLocations(), TissueSimulation< DIM >::mNoBirth, and TissueSimulation< DIM >::mrTissue.

Referenced by TissueSimulation< DIM >::UpdateTissue().

template<unsigned DIM>
c_vector< double, DIM > TissueSimulation< DIM >::CalculateDividingCellCentreLocations ( TissueCell *  pParentCell  )  [inline, protected, virtual]

Calculate the new locations of the cell centres of a dividing cell, move the parent cell and return the location of the daughter cell.

The new locations are found by picking a random direction and placing the parent and daughter in opposing directions along this axis.

Parameters:
pParentCell pointer to the parent cell
Returns:
daughter_coords The coordinates for the daughter cell.

Reimplemented in CryptSimulation2d.

Definition at line 167 of file TissueSimulation.cpp.

References TissueConfig::GetDivisionSeparation(), RandomNumberGenerator::Instance(), TissueConfig::Instance(), TissueSimulation< DIM >::mrTissue, and RandomNumberGenerator::ranf().

Referenced by TissueSimulation< DIM >::DoCellBirth().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::DoCellRemoval (  )  [inline, protected]

During a simulation time step, process any cell sloughing or death

This uses the cell killers to remove cells and associated nodes from the facade class.

Returns:
the number of deaths that occurred.

Definition at line 140 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mCellKillers, and TissueSimulation< DIM >::mrTissue.

Referenced by TissueSimulation< DIM >::UpdateTissue().

template<unsigned DIM>
void TissueSimulation< DIM >::UpdateNodePositions ( const std::vector< c_vector< double, DIM > > &  rNodeForces  )  [inline, protected, virtual]

Moves each node to a new position for this timestep by calling the tissue UpdateNodeLocations() method then applying any boundary conditions.

Parameters:
rNodeForces the forces on nodes

Definition at line 229 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::ApplyTissueBoundaryConditions(), TissueSimulation< DIM >::mDt, and TissueSimulation< DIM >::mrTissue.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
virtual void TissueSimulation< DIM >::ApplyTissueBoundaryConditions ( const std::vector< c_vector< double, DIM > > &  rOldLocations  )  [inline, protected, virtual]

Apply any tissue boundary conditions. Can be overridden in subclasses.

Parameters:
rOldLocations the node locations before any boundary conditions are applied

Definition at line 219 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::UpdateNodePositions().

template<unsigned DIM>
virtual void TissueSimulation< DIM >::PostSolve (  )  [inline, protected, virtual]

A method for subclasses to do something at the end of each timestep

Reimplemented in CryptSimulation2d.

Definition at line 226 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
virtual void TissueSimulation< DIM >::SetupSolve (  )  [inline, protected, virtual]

A method for subclasses to do something at before the start of the time loop

Reimplemented in CryptSimulation2d.

Definition at line 233 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
virtual void TissueSimulation< DIM >::AfterSolve (  )  [inline, protected, virtual]

This method may be overridden in subclasses to do something at the end of each time loop.

Reimplemented in CryptSimulation2d.

Definition at line 241 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
bool TissueSimulation< DIM >::StoppingEventHasOccurred (  )  [inline, protected, virtual]

A child class can overload this if they want the simulation to stop based on certain conditions before the specified end time (for example, run until a crypt becomes monoclonal).

Definition at line 522 of file TissueSimulation.cpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
void TissueSimulation< DIM >::UpdateTissue (  )  [inline, protected]

Calls the deaths, births and (if mUpdateTissue is true) Tissue::Update() methods.

Definition at line 529 of file TissueSimulation.cpp.

References GenericEventHandler< 9, CancerEventHandler >::BeginEvent(), TissueSimulation< DIM >::DoCellBirth(), TissueSimulation< DIM >::DoCellRemoval(), GenericEventHandler< 9, CancerEventHandler >::EndEvent(), TissueSimulation< DIM >::mNumBirths, TissueSimulation< DIM >::mNumDeaths, TissueSimulation< DIM >::mrTissue, and TissueSimulation< DIM >::mUpdateTissue.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
std::vector< double > TissueSimulation< DIM >::GetNodeLocation ( const unsigned &  rNodeIndex  )  [inline]

Get a node's location (ONLY FOR TESTING).

Parameters:
rNodeIndex the node index
Returns:
the co-ordinates of this node.

Definition at line 345 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
double TissueSimulation< DIM >::GetDt (  )  [inline]

Returns:
the timestep of the simulation

Definition at line 258 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mDt.

template<unsigned DIM>
unsigned TissueSimulation< DIM >::GetNumBirths (  )  [inline]

Returns:
the number of births that have occurred in the entire simulation (since t=0)

Definition at line 265 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mNumBirths.

template<unsigned DIM>
unsigned TissueSimulation< DIM >::GetNumDeaths (  )  [inline]

Returns:
the number of deaths that have occurred in the entire simulation (since t=0).

Definition at line 272 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mNumDeaths.

template<unsigned DIM>
std::string TissueSimulation< DIM >::GetOutputDirectory (  )  [inline]

Get the output directory of the simulation.

Definition at line 295 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputDirectory.

template<unsigned DIM>
void TissueSimulation< DIM >::SetDt ( double  dt  )  [inline]

Set the timestep of the simulation.

Parameters:
dt the timestep to use

Definition at line 250 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mDt.

template<unsigned DIM>
void TissueSimulation< DIM >::SetEndTime ( double  endTime  )  [inline]

Set the end time and resets the timestep to be endtime/100.

Parameters:
endTime the end time to use

Definition at line 279 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mEndTime.

template<unsigned DIM>
void TissueSimulation< DIM >::SetOutputDirectory ( std::string  outputDirectory  )  [inline]

Set the output directory of the simulation.

Parameters:
outputDirectory the output directory to use

Definition at line 287 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mOutputDirectory, and TissueSimulation< DIM >::mSimulationOutputDirectory.

template<unsigned DIM>
void TissueSimulation< DIM >::SetSamplingTimestepMultiple ( unsigned  samplingTimestepMultiple  )  [inline]

Set the ratio of the number of actual timesteps to the number of timesteps at which results are written to file. Default value is set to 1 by the constructor.

Parameters:
samplingTimestepMultiple the ratio to use

Definition at line 302 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mSamplingTimestepMultiple.

template<unsigned DIM>
void TissueSimulation< DIM >::SetNoBirth ( bool  noBirth  )  [inline]

Set the simulation to run with no birth.

Parameters:
noBirth whether to run with no birth

Definition at line 331 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mNoBirth.

template<unsigned DIM>
void TissueSimulation< DIM >::SetUpdateTissueRule ( bool  updateTissue  )  [inline]

Set whether to update the topology of the tissue at each time step.

Parameters:
updateTissue whether to update the tissue each time step

Definition at line 324 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mUpdateTissue.

template<unsigned DIM>
void TissueSimulation< DIM >::AddCellKiller ( AbstractCellKiller< DIM > *  pCellKiller  )  [inline]

Add a cell killer to be used in this simulation.

Parameters:
pCellKiller pointer to a cell killer

Definition at line 338 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mCellKillers.

template<unsigned DIM>
void TissueSimulation< DIM >::Solve (  )  [inline]

Main solve method.

This method sets up the simulation time, creates output files, and initialises the tissue. It then iterates through a time loop. At each time step, first any cell death or birth is implemented, then the tissue topology is updated, then the forces are recalculated and the tissue evolved according to whatever force laws are present in the simulation, and finally the results for that time step are output to file. At the end of the time loop, the method closes any output files.

This function calls: DoCellRemoval() DoCellBirth() Tissue::Update()

Definition at line 357 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::AfterSolve(), GenericEventHandler< 9, CancerEventHandler >::BeginEvent(), GenericEventHandler< 9, CancerEventHandler >::EndEvent(), SimulationTime::GetTime(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::IncrementTimeOneStep(), SimulationTime::Instance(), TissueSimulation< DIM >::mDt, TissueSimulation< DIM >::mEndTime, TissueSimulation< DIM >::mForceCollection, TissueSimulation< DIM >::mOutputDirectory, TissueSimulation< DIM >::mpSetupFile, TissueSimulation< DIM >::mrTissue, TissueSimulation< DIM >::mSamplingTimestepMultiple, TissueSimulation< DIM >::mSimulationOutputDirectory, OutputFileHandler::OpenOutputFile(), TissueSimulation< DIM >::PostSolve(), SimulationTime::ResetEndTimeAndNumberOfTimeSteps(), SimulationTime::SetEndTimeAndNumberOfTimeSteps(), TissueSimulation< DIM >::SetupSolve(), TissueSimulation< DIM >::StoppingEventHasOccurred(), TissueSimulation< DIM >::UpdateNodePositions(), TissueSimulation< DIM >::UpdateTissue(), and TissueSimulation< DIM >::WriteVisualizerSetupFile().

template<unsigned DIM>
AbstractTissue< DIM > & TissueSimulation< DIM >::rGetTissue (  )  [inline]

Returns:
reference to the tissue.

Definition at line 310 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
const AbstractTissue< DIM > & TissueSimulation< DIM >::rGetTissue (  )  const [inline]

Returns:
const reference to the tissue (used in archiving).

Definition at line 317 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mrTissue.

template<unsigned DIM>
const std::vector< AbstractForce< DIM > * > TissueSimulation< DIM >::rGetForceCollection (  )  const [inline]

Returns:
const reference to mForceCollection (used in archiving).

Definition at line 160 of file TissueSimulation.cpp.

References TissueSimulation< DIM >::mForceCollection.

Friends And Related Function Documentation

template<unsigned DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented in CryptSimulation2d.

Definition at line 128 of file TissueSimulation.hpp.

Member Data Documentation

template<unsigned DIM>
double TissueSimulation< DIM >::mDt [protected]

Time step.

Definition at line 71 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::GetDt(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetDt(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::UpdateNodePositions().

template<unsigned DIM>
double TissueSimulation< DIM >::mEndTime [protected]

Time to run the Solve() method up to.

Definition at line 74 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetEndTime(), and TissueSimulation< DIM >::Solve().

template<unsigned DIM>
AbstractTissue<DIM>& TissueSimulation< DIM >::mrTissue [protected]

Facade encapsulating cells in the tissue being simulated.

Definition at line 77 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::CalculateDividingCellCentreLocations(), TissueSimulation< DIM >::DoCellBirth(), TissueSimulation< DIM >::DoCellRemoval(), TissueSimulation< DIM >::GetNodeLocation(), TissueSimulation< DIM >::rGetTissue(), TissueSimulation< DIM >::Solve(), TissueSimulation< DIM >::TissueSimulation(), TissueSimulation< DIM >::UpdateNodePositions(), TissueSimulation< DIM >::UpdateTissue(), and TissueSimulation< DIM >::~TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mDeleteTissue [protected]

Whether to delete the tissue facade in the destructor.

Definition at line 80 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::~TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mAllocatedMemoryForForceCollection [protected]

Whether delete the collection of force laws in the destructor.

Definition at line 83 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::~TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mInitialiseCells [protected]

Whether to initialise the cells.

Definition at line 86 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
bool TissueSimulation< DIM >::mNoBirth [protected]

Whether to run the simulation with no birth (defaults to false).

Definition at line 89 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::DoCellBirth(), TissueSimulation< 2 >::serialize(), and TissueSimulation< DIM >::SetNoBirth().

template<unsigned DIM>
bool TissueSimulation< DIM >::mUpdateTissue [protected]

Whether to update the topology of the tissue at each time step (defaults to true).

Definition at line 92 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetUpdateTissueRule(), and TissueSimulation< DIM >::UpdateTissue().

template<unsigned DIM>
std::string TissueSimulation< DIM >::mOutputDirectory [protected]

Output directory (a subfolder of tmp/[USERNAME]/testoutput)

Definition at line 95 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::GetOutputDirectory(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetOutputDirectory(), and TissueSimulation< DIM >::Solve().

template<unsigned DIM>
std::string TissueSimulation< DIM >::mSimulationOutputDirectory [protected]

Simulation Output directory either the same as mOutputDirectory or includes mOutputDirectory/results_from_time_[TIME]

Definition at line 98 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::SetOutputDirectory(), and TissueSimulation< DIM >::Solve().

template<unsigned DIM>
out_stream TissueSimulation< DIM >::mpSetupFile [protected]

Visualiser setup file

Definition at line 101 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::Solve().

template<unsigned DIM>
TissueConfig* TissueSimulation< DIM >::mpConfig [protected]

The cancer tissue configuration

Definition at line 104 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
RandomNumberGenerator* TissueSimulation< DIM >::mpRandomGenerator [protected]

The singleton RandomNumberGenerator

Definition at line 107 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), and TissueSimulation< DIM >::TissueSimulation().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::mNumBirths [protected]

Counts the number of births during the simulation

Definition at line 110 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::GetNumBirths(), TissueSimulation< 2 >::serialize(), and TissueSimulation< DIM >::UpdateTissue().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::mNumDeaths [protected]

Counts the number of deaths during the simulation

Definition at line 113 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::GetNumDeaths(), TissueSimulation< 2 >::serialize(), and TissueSimulation< DIM >::UpdateTissue().

template<unsigned DIM>
unsigned TissueSimulation< DIM >::mSamplingTimestepMultiple [protected]

The ratio of the number of actual timesteps to the number of timesteps at which results are written to file

Definition at line 119 of file TissueSimulation.hpp.

Referenced by TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::SetSamplingTimestepMultiple(), and TissueSimulation< DIM >::Solve().

template<unsigned DIM>
std::vector<AbstractCellKiller<DIM>*> TissueSimulation< DIM >::mCellKillers [protected]

List of cell killers

Definition at line 122 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::AddCellKiller(), TissueSimulation< DIM >::DoCellRemoval(), TissueSimulation< 2 >::serialize(), and TissueSimulation< DIM >::~TissueSimulation().

template<unsigned DIM>
std::vector<AbstractForce<DIM>*> TissueSimulation< DIM >::mForceCollection [protected]

The mechanics used to determine the new location of the cells

Definition at line 125 of file TissueSimulation.hpp.

Referenced by TissueSimulation< DIM >::rGetForceCollection(), TissueSimulation< 2 >::serialize(), TissueSimulation< DIM >::Solve(), and TissueSimulation< DIM >::~TissueSimulation().

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