AbstractCardiacCell Class Reference

#include <AbstractCardiacCell.hpp>

Inheritance diagram for AbstractCardiacCell:

Collaboration diagram for AbstractCardiacCell:

List of all members.

Public Member Functions

AbstractCardiacCell (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)

virtual ~AbstractCardiacCell ()

void Init ()

virtual OdeSolution Compute (double tStart, double tEnd)

virtual void ComputeExceptVoltage (double tStart, double tEnd)

virtual double GetIIonic ()=0

void SetVoltage (double voltage)

double GetVoltage ()

unsigned GetVoltageIndex ()

void SetStimulusFunction (boost::shared_ptr< AbstractStimulusFunction > pStimulus)

double GetStimulus (double time)

void SetIntracellularStimulusFunction (boost::shared_ptr< AbstractStimulusFunction > pStimulus)

double GetIntracellularStimulus (double time)

virtual double GetIntracellularCalciumConcentration ()

virtual void VerifyStateVariables ()

virtual void SetState (CellModelState state)

virtual void SetSlowValues (const std::vector< double > &rSlowValues)

virtual void GetSlowValues (std::vector< double > &rSlowValues)

virtual bool IsFastOnly ()

virtual void AdjustOutOfRangeSlowValues (std::vector< double > &rSlowValues)

virtual unsigned GetNumSlowValues ()

const boost::shared_ptr
< AbstractStimulusFunction > GetStimulusFunction () const

const boost::shared_ptr
< AbstractIvpOdeSolver > GetSolver () const

Protected Attributes

unsigned mVoltageIndex

boost::shared_ptr
< AbstractIvpOdeSolver > mpOdeSolver

double mDt

boost::shared_ptr
< AbstractStimulusFunction > mpIntracellularStimulus

bool mSetVoltageDerivativeToZero

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

Friends

class boost::serialization::access

Detailed Description

This is the base class for ode-based cardiac cell models.

It is essentially a cardiac-specific wrapper for ODE systems providing an interface which can interact with the Stimulus classes and the voltage in a mono/bidomain simulation.

Concrete classes can be autogenerated from CellML files by the pyCML package, and will automatically inherit from this class.

Definition at line 62 of file AbstractCardiacCell.hpp.

Constructor & Destructor Documentation

AbstractCardiacCell::AbstractCardiacCell	(	boost::shared_ptr< AbstractIvpOdeSolver >	pOdeSolver,
		unsigned	numberOfStateVariables,
		unsigned	voltageIndex,
		boost::shared_ptr< AbstractStimulusFunction >	pIntracellularStimulus
	)

Create a new cardiac cell.

Parameters:

	pOdeSolver	the ODE solver to use when simulating this cell
	numberOfStateVariables	the size of the ODE system modelling this cell
	voltageIndex	the index of the transmembrane potential within the vector of state variables
	pIntracellularStimulus	the intracellular stimulus current

Definition at line 33 of file AbstractCardiacCell.cpp.

References AbstractOdeSystem::mNumberOfStateVariables.

AbstractCardiacCell::~AbstractCardiacCell ( ) [virtual]

Virtual destructor

Definition at line 48 of file AbstractCardiacCell.cpp.

Member Function Documentation

template<class Archive>

void AbstractCardiacCell::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archive the member variables.

Parameters:

	archive
	version

Reimplemented from AbstractOdeSystem.

Reimplemented in AbstractBackwardEulerCardiacCell< SIZE >, BackwardEulerFoxModel2002Modified, BackwardEulerLuoRudyIModel1991, LuoRudyIModel1991OdeSystem, AbstractBackwardEulerCardiacCell< 12 >, AbstractBackwardEulerCardiacCell< 1 >, and AbstractBackwardEulerCardiacCell< 3 >.

Definition at line 74 of file AbstractCardiacCell.hpp.

References mDt, and mSetVoltageDerivativeToZero.

void AbstractCardiacCell::Init ( )

Initialise the cell:

set our state variables to the initial conditions,
set model parameters to their default values.

Reimplemented in BackwardEulerLuoRudyIModel1991.

Definition at line 52 of file AbstractCardiacCell.cpp.

References AbstractOdeSystem::GetInitialConditions(), and AbstractOdeSystem::SetStateVariables().

Referenced by BackwardEulerFoxModel2002Modified::BackwardEulerFoxModel2002Modified(), DiFrancescoNoble1985OdeSystem::DiFrancescoNoble1985OdeSystem(), FitzHughNagumo1961OdeSystem::FitzHughNagumo1961OdeSystem(), HodgkinHuxleySquidAxon1952OriginalOdeSystem::HodgkinHuxleySquidAxon1952OriginalOdeSystem(), BackwardEulerLuoRudyIModel1991::Init(), LuoRudyIModel1991OdeSystem::LuoRudyIModel1991OdeSystem(), Mahajan2008OdeSystem::Mahajan2008OdeSystem(), and TenTusscher2006OdeSystem::TenTusscher2006OdeSystem().

OdeSolution AbstractCardiacCell::Compute	(	double	tStart,
		double	tEnd
	)			`[virtual]`

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt.

Parameters:

	tStart	beginning of the time interval to simulate
	tEnd	end of the time interval to simulate

Reimplemented in AbstractBackwardEulerCardiacCell< SIZE >, AbstractBackwardEulerCardiacCell< 12 >, AbstractBackwardEulerCardiacCell< 1 >, and AbstractBackwardEulerCardiacCell< 3 >.

Definition at line 58 of file AbstractCardiacCell.cpp.

References mDt, mpOdeSolver, and AbstractOdeSystem::rGetStateVariables().

void AbstractCardiacCell::ComputeExceptVoltage	(	double	tStart,
		double	tEnd
	)			`[virtual]`

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt, but does not update the voltage.

Parameters:

	tStart	beginning of the time interval to simulate
	tEnd	end of the time interval to simulate

Reimplemented in AbstractBackwardEulerCardiacCell< SIZE >, FakeBathCell, AbstractBackwardEulerCardiacCell< 12 >, AbstractBackwardEulerCardiacCell< 1 >, and AbstractBackwardEulerCardiacCell< 3 >.

Definition at line 64 of file AbstractCardiacCell.cpp.

References GetVoltage(), mDt, mpOdeSolver, mSetVoltageDerivativeToZero, SetVoltage(), and VerifyStateVariables().

virtual double AbstractCardiacCell::GetIIonic ( ) [pure virtual]

Computes the total current flowing through the cell membrane, using the current values of the state variables.

Implemented in BackwardEulerFoxModel2002Modified, BackwardEulerLuoRudyIModel1991, DiFrancescoNoble1985OdeSystem, FakeBathCell, FitzHughNagumo1961OdeSystem, FoxModel2002Modified, HodgkinHuxleySquidAxon1952OriginalOdeSystem, LuoRudyIModel1991OdeSystem, Mahajan2008OdeSystem, and TenTusscher2006OdeSystem.

void AbstractCardiacCell::SetVoltage ( double voltage )

Set the transmembrane potential

Parameters:

voltage

new value

Definition at line 77 of file AbstractCardiacCell.cpp.

References mVoltageIndex, and AbstractOdeSystem::rGetStateVariables().

Referenced by ComputeExceptVoltage().

double AbstractCardiacCell::GetVoltage ( )

Get the current value of the transmembrane potential, as given in our state variable vector.

Definition at line 82 of file AbstractCardiacCell.cpp.

References mVoltageIndex, and AbstractOdeSystem::rGetStateVariables().

Referenced by ComputeExceptVoltage().

unsigned AbstractCardiacCell::GetVoltageIndex ( )

Get the index of the transmembrane potential within our state variable vector.

Definition at line 87 of file AbstractCardiacCell.cpp.

References mVoltageIndex.

void AbstractCardiacCell::SetStimulusFunction ( boost::shared_ptr< AbstractStimulusFunction > pStimulus )

Set the intracellular stimulus. Shorthand for SetIntracellularStimulusFunction.

Parameters:

pStimulus

new stimulus function

Definition at line 92 of file AbstractCardiacCell.cpp.

References SetIntracellularStimulusFunction().

double AbstractCardiacCell::GetStimulus ( double time )

Get the value of the intracellular stimulus. Shorthand for GetIntracellularStimulus.

Parameters:

time

the time at which to evaluate the stimulus

Definition at line 97 of file AbstractCardiacCell.cpp.

References GetIntracellularStimulus().

Referenced by TenTusscher2006OdeSystem::EvaluateYDerivatives(), Mahajan2008OdeSystem::EvaluateYDerivatives(), LuoRudyIModel1991OdeSystem::EvaluateYDerivatives(), HodgkinHuxleySquidAxon1952OriginalOdeSystem::EvaluateYDerivatives(), FoxModel2002Modified::EvaluateYDerivatives(), FitzHughNagumo1961OdeSystem::EvaluateYDerivatives(), DiFrancescoNoble1985OdeSystem::EvaluateYDerivatives(), BackwardEulerLuoRudyIModel1991::UpdateTransmembranePotential(), and BackwardEulerFoxModel2002Modified::UpdateTransmembranePotential().

void AbstractCardiacCell::SetIntracellularStimulusFunction ( boost::shared_ptr< AbstractStimulusFunction > pStimulus )

Set the intracellular stimulus.

Parameters:

pStimulus

new stimulus function

Definition at line 102 of file AbstractCardiacCell.cpp.

References mpIntracellularStimulus.

Referenced by SetStimulusFunction().

double AbstractCardiacCell::GetIntracellularStimulus ( double time )

Get the value of the intracellular stimulus.

Parameters:

time

the time at which to evaluate the stimulus

Definition at line 107 of file AbstractCardiacCell.cpp.

References mpIntracellularStimulus.

Referenced by GetStimulus().

double AbstractCardiacCell::GetIntracellularCalciumConcentration ( ) [virtual]

[Ca_i] is needed for mechanics, so we explcitly have a Get method (rather than use a get by name type method, to avoid inefficiency when using different cells types of cells). This method by defaults throws an exception, so should be implemented in the concrete class if IntracellularCalciumConcentration is one of the state variables

Reimplemented in BackwardEulerLuoRudyIModel1991, and LuoRudyIModel1991OdeSystem.

Definition at line 113 of file AbstractCardiacCell.cpp.

virtual void AbstractCardiacCell::VerifyStateVariables ( ) [inline, virtual]

Empty method which can be over-ridden in concrete cell class which should go through the current state vector and go range checking on the values (eg check that concentrations are positive and gating variables are between zero and one). This method is called in the ComputeExceptVoltage method.

Reimplemented in BackwardEulerLuoRudyIModel1991, DiFrancescoNoble1985OdeSystem, LuoRudyIModel1991OdeSystem, and TenTusscher2006OdeSystem.

Definition at line 203 of file AbstractCardiacCell.hpp.

Referenced by AbstractBackwardEulerCardiacCell< SIZE >::Compute(), ComputeExceptVoltage(), and AbstractBackwardEulerCardiacCell< SIZE >::ComputeExceptVoltage().

void AbstractCardiacCell::SetState ( CellModelState state ) [virtual]

This should be implemented by fast/slow cardiac cell subclasses, and

set the state
initialise the cell
SET mNumberOfStateVariables CORRECTLY (as this would not have been known in the constructor.

Note:: This must be implemented by fast/slow cardiac cell subclasses.

Parameters:

state

whether this cell is in fast or slow mode.

Definition at line 122 of file AbstractCardiacCell.cpp.

void AbstractCardiacCell::SetSlowValues ( const std::vector< double > & rSlowValues ) [virtual]

Set the slow variables. Should only be valid in fast mode.

Note:: This must be implemented by fast/slow cardiac cell subclasses.

Parameters:

rSlowValues

values for the slow variables

Definition at line 127 of file AbstractCardiacCell.cpp.

void AbstractCardiacCell::GetSlowValues ( std::vector< double > & rSlowValues ) [virtual]

Get the current values of the slow variables. Should only be valid in slow mode.

Note:: This must be implemented by fast/slow cardiac cell subclasses.

Parameters:

rSlowValues

will be filled in with the values of the slow variables on return.

Definition at line 132 of file AbstractCardiacCell.cpp.

bool AbstractCardiacCell::IsFastOnly ( ) [virtual]

Get whether this cell is a fast or slow version.

Note:: This must be implemented by fast/slow cardiac cell subclasses.

Definition at line 137 of file AbstractCardiacCell.cpp.

void AbstractCardiacCell::AdjustOutOfRangeSlowValues ( std::vector< double > & rSlowValues ) [virtual]

In a multiscale simulation a cut-down cell model can be run:

fast values are calculated according to the CellML definition
slow values are interpolated on synchronisation time-steps. There's a chance that linear interpolation/extrapolation may push some gating variable out of the range [0, 1]. This method alters any values which are out-of-range.

Note:: This must be implemented by fast/slow cardiac cell subclasses.

Parameters:

rSlowValues

A vector of the slow values for a particular cell after they have been interpolated from nearby coarse cells

Definition at line 147 of file AbstractCardiacCell.cpp.

unsigned AbstractCardiacCell::GetNumSlowValues ( ) [virtual]

Get the number of slow variables for the cell model (irrespective of whether in fast or slow mode).

Note:: This must be implemented by fast/slow cardiac cell subclasses.

Definition at line 142 of file AbstractCardiacCell.cpp.

const boost::shared_ptr< AbstractStimulusFunction > AbstractCardiacCell::GetStimulusFunction ( ) const

For boost archiving use only (that's why the 'consts' are required)

Returns:: The Intracellular stimulus pointer

Definition at line 154 of file AbstractCardiacCell.cpp.

References mpIntracellularStimulus.

const boost::shared_ptr< AbstractIvpOdeSolver > AbstractCardiacCell::GetSolver ( ) const

For boost archiving use only (that's why the 'consts' are required)

Returns:: pointer to the ODE solver being used

Definition at line 159 of file AbstractCardiacCell.cpp.

References mpOdeSolver.

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractOdeSystem.

Reimplemented in AbstractBackwardEulerCardiacCell< SIZE >, BackwardEulerFoxModel2002Modified, BackwardEulerLuoRudyIModel1991, LuoRudyIModel1991OdeSystem, AbstractBackwardEulerCardiacCell< 12 >, AbstractBackwardEulerCardiacCell< 1 >, and AbstractBackwardEulerCardiacCell< 3 >.

Definition at line 66 of file AbstractCardiacCell.hpp.

Member Data Documentation

unsigned AbstractCardiacCell::mVoltageIndex [protected]

The index of the voltage within our state variable vector.

Definition at line 87 of file AbstractCardiacCell.hpp.

Referenced by HodgkinHuxleySquidAxon1952OriginalOdeSystem::GetIIonic(), FitzHughNagumo1961OdeSystem::GetIIonic(), GetVoltage(), GetVoltageIndex(), and SetVoltage().

boost::shared_ptr<AbstractIvpOdeSolver> AbstractCardiacCell::mpOdeSolver [protected]

Pointer to the solver used to simulate this cell.

Definition at line 89 of file AbstractCardiacCell.hpp.

Referenced by Compute(), ComputeExceptVoltage(), and GetSolver().

double AbstractCardiacCell::mDt [protected]

The timestep to use when simulating this cell. Set from the HeartConfig object.

Definition at line 91 of file AbstractCardiacCell.hpp.

Referenced by Compute(), AbstractBackwardEulerCardiacCell< SIZE >::Compute(), ComputeExceptVoltage(), AbstractBackwardEulerCardiacCell< SIZE >::ComputeExceptVoltage(), BackwardEulerLuoRudyIModel1991::ComputeJacobian(), BackwardEulerLuoRudyIModel1991::ComputeOneStepExceptVoltage(), BackwardEulerFoxModel2002Modified::ComputeOneStepExceptVoltage(), BackwardEulerLuoRudyIModel1991::ComputeResidual(), serialize(), BackwardEulerLuoRudyIModel1991::UpdateTransmembranePotential(), and BackwardEulerFoxModel2002Modified::UpdateTransmembranePotential().

boost::shared_ptr<AbstractStimulusFunction> AbstractCardiacCell::mpIntracellularStimulus [protected]

The intracellular stimulus current.

Definition at line 93 of file AbstractCardiacCell.hpp.

Referenced by GetIntracellularStimulus(), GetStimulusFunction(), and SetIntracellularStimulusFunction().

bool AbstractCardiacCell::mSetVoltageDerivativeToZero [protected]

Flag set to true if ComputeExceptVoltage is called, to indicate to subclass EvaluateYDerivatives methods that V should be considered fixed, and hence dV/dt set to zero.

Definition at line 100 of file AbstractCardiacCell.hpp.

Referenced by ComputeExceptVoltage(), TenTusscher2006OdeSystem::EvaluateYDerivatives(), Mahajan2008OdeSystem::EvaluateYDerivatives(), LuoRudyIModel1991OdeSystem::EvaluateYDerivatives(), HodgkinHuxleySquidAxon1952OriginalOdeSystem::EvaluateYDerivatives(), FoxModel2002Modified::EvaluateYDerivatives(), FitzHughNagumo1961OdeSystem::EvaluateYDerivatives(), DiFrancescoNoble1985OdeSystem::EvaluateYDerivatives(), and serialize().

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

/tmp/release_1.1/heart/src/odes/AbstractCardiacCell.hpp
/tmp/release_1.1/heart/src/odes/AbstractCardiacCell.cpp


Public Member Functions
	AbstractCardiacCell (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
virtual	~AbstractCardiacCell ()
void	Init ()
virtual OdeSolution	Compute (double tStart, double tEnd)
virtual void	ComputeExceptVoltage (double tStart, double tEnd)
virtual double	GetIIonic ()=0
void	SetVoltage (double voltage)
double	GetVoltage ()
unsigned	GetVoltageIndex ()
void	SetStimulusFunction (boost::shared_ptr< AbstractStimulusFunction > pStimulus)
double	GetStimulus (double time)
void	SetIntracellularStimulusFunction (boost::shared_ptr< AbstractStimulusFunction > pStimulus)
double	GetIntracellularStimulus (double time)
virtual double	GetIntracellularCalciumConcentration ()
virtual void	VerifyStateVariables ()
virtual void	SetState (CellModelState state)
virtual void	SetSlowValues (const std::vector< double > &rSlowValues)
virtual void	GetSlowValues (std::vector< double > &rSlowValues)
virtual bool	IsFastOnly ()
virtual void	AdjustOutOfRangeSlowValues (std::vector< double > &rSlowValues)
virtual unsigned	GetNumSlowValues ()
const boost::shared_ptr < AbstractStimulusFunction >	GetStimulusFunction () const
const boost::shared_ptr < AbstractIvpOdeSolver >	GetSolver () const
Protected Attributes
unsigned	mVoltageIndex
boost::shared_ptr < AbstractIvpOdeSolver >	mpOdeSolver
double	mDt
boost::shared_ptr < AbstractStimulusFunction >	mpIntracellularStimulus
bool	mSetVoltageDerivativeToZero
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access