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 ()

void SetTimestep (double dt)

virtual void SolveAndUpdateState (double tStart, double tEnd)

virtual OdeSolution Compute (double tStart, double tEnd, double tSamp=0.0)

virtual void ComputeExceptVoltage (double tStart, double tEnd)

void SetVoltage (double voltage)

double GetVoltage ()

virtual double GetIntracellularCalciumConcentration ()

virtual void SetStretch (double stretch)

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 ()

Protected Attributes

double mDt

Private Member Functions

template<class Archive>

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

void CheckForArchiveFix ()

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 66 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. The state variables of the cell will be set to AbstractOdeSystemInformation::GetInitialConditions(). Note that calls to SetDefaultInitialConditions() on a particular instance of this class will not modify its state variables. You can modify them directly with rGetStateVariables().

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 36 of file AbstractCardiacCell.cpp.

References AbstractParameterisedSystem< std::vector< double > >::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 AbstractCardiacCellInterface.

Reimplemented in AbstractBackwardEulerCardiacCell< SIZE >, FakeBathCell, and CML_noble_varghese_kohl_noble_1998_basic_with_sac.

Definition at line 78 of file AbstractCardiacCell.hpp.

References CheckForArchiveFix(), mDt, AbstractCardiacCellInterface::mHasDefaultStimulusFromCellML, AbstractCardiacCellInterface::mIsUsedInTissue, AbstractParameterisedSystem< std::vector< double > >::mParameters, AbstractCardiacCellInterface::mSetVoltageDerivativeToZero, and AbstractParameterisedSystem< std::vector< double > >::rGetParameterNames().

void AbstractCardiacCell::CheckForArchiveFix ( ) [private]

The Luo-Rudy 1991 model saved in previous Chaste versions had a different ordering of state variables. If we're loading that model, we'll need to permute the state vector. This can't (easily) be done in the LR91 code itself, since that is auto-generated!

Definition at line 113 of file AbstractCardiacCell.cpp.

References AbstractParameterisedSystem< std::vector< double > >::GetNumberOfStateVariables(), AbstractParameterisedSystem< std::vector< double > >::mParameters, AbstractParameterisedSystem< std::vector< double > >::mStateVariables, and AbstractParameterisedSystem< std::vector< double > >::rGetParameterNames().

Referenced by serialize().

void AbstractCardiacCell::Init ( )

Initialise the cell:

set our state variables to the initial conditions,
resize model parameters vector.

Note:: Must be called by subclass constructors.

Definition at line 52 of file AbstractCardiacCell.cpp.

References AbstractParameterisedSystem< std::vector< double > >::mParameters, AbstractParameterisedSystem< std::vector< double > >::ResetToInitialConditions(), and AbstractParameterisedSystem< std::vector< double > >::rGetParameterNames().

Referenced by CML_noble_varghese_kohl_noble_1998_basic_with_sac::CML_noble_varghese_kohl_noble_1998_basic_with_sac(), FakeBathCell::FakeBathCell(), and FitzHughNagumo1961OdeSystem::FitzHughNagumo1961OdeSystem().

void AbstractCardiacCell::SetTimestep ( double dt ) [virtual]

Set the timestep to use for simulating this cell.

Parameters:

dt

the timestep

Implements AbstractCardiacCellInterface.

Definition at line 58 of file AbstractCardiacCell.cpp.

References mDt.

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

Simulate this cell's behaviour between the time interval [tStart, tEnd], with timestemp mDt, updating the internal state variable values.

Parameters:

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

Implements AbstractCardiacCellInterface.

Reimplemented in AbstractBackwardEulerCardiacCell< SIZE >.

Definition at line 63 of file AbstractCardiacCell.cpp.

References mDt, and AbstractCardiacCellInterface::mpOdeSolver.

OdeSolution AbstractCardiacCell::Compute	(	double	tStart,
		double	tEnd,
		double	tSamp = `0.0`
	)			`[virtual]`

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt, and return state variable values.

Parameters:

	tStart	beginning of the time interval to simulate
	tEnd	end of the time interval to simulate
	tSamp	sampling interval for returned results (defaults to mDt)

Implements AbstractCardiacCellInterface.

Reimplemented in AbstractBackwardEulerCardiacCell< SIZE >.

Definition at line 68 of file AbstractCardiacCell.cpp.

References mDt, AbstractCardiacCellInterface::mpOdeSolver, and AbstractParameterisedSystem< std::vector< double > >::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

Implements AbstractCardiacCellInterface.

Reimplemented in AbstractBackwardEulerCardiacCell< SIZE >, and FakeBathCell.

Definition at line 77 of file AbstractCardiacCell.cpp.

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

void AbstractCardiacCell::SetVoltage ( double voltage ) [virtual]

Set the transmembrane potential

Parameters:

voltage

new value

Implements AbstractCardiacCellInterface.

Definition at line 94 of file AbstractCardiacCell.cpp.

References AbstractCardiacCellInterface::mVoltageIndex, and AbstractParameterisedSystem< std::vector< double > >::SetAnyVariable().

Referenced by ComputeExceptVoltage().

double AbstractCardiacCell::GetVoltage ( ) [virtual]

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

Implements AbstractCardiacCellInterface.

Definition at line 99 of file AbstractCardiacCell.cpp.

References AbstractParameterisedSystem< std::vector< double > >::GetAnyVariable(), and AbstractCardiacCellInterface::mVoltageIndex.

Referenced by ComputeExceptVoltage().

double AbstractCardiacCell::GetIntracellularCalciumConcentration ( ) [virtual]

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

Reimplemented in CML_noble_varghese_kohl_noble_1998_basic_with_sac.

Definition at line 104 of file AbstractCardiacCell.cpp.

References EXCEPTION.

virtual void AbstractCardiacCell::SetStretch ( double stretch ) [inline, virtual]

In electromechanics problems, the stretch is passed back to cell-model in case mechano-electric feedback has been modelled. We define an empty method here. Stretch-dependent cell models should overload this method to use the input stretch accordingly.

Parameters:

stretch

the stretch of the cell in the axial direction

Reimplemented in CML_noble_varghese_kohl_noble_1998_basic_with_sac.

Definition at line 209 of file AbstractCardiacCell.hpp.

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 from AbstractCardiacCellInterface.

Definition at line 219 of file AbstractCardiacCell.hpp.

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

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 139 of file AbstractCardiacCell.cpp.

References EXCEPTION.

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 144 of file AbstractCardiacCell.cpp.

References EXCEPTION.

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 149 of file AbstractCardiacCell.cpp.

References EXCEPTION.

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 154 of file AbstractCardiacCell.cpp.

References EXCEPTION.

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 164 of file AbstractCardiacCell.cpp.

References EXCEPTION.

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 159 of file AbstractCardiacCell.cpp.

References EXCEPTION.

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractCardiacCellInterface.

Reimplemented in AbstractBackwardEulerCardiacCell< SIZE >, FakeBathCell, and CML_noble_varghese_kohl_noble_1998_basic_with_sac.

Definition at line 70 of file AbstractCardiacCell.hpp.

Member Data Documentation

double AbstractCardiacCell::mDt [protected]

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

Definition at line 116 of file AbstractCardiacCell.hpp.

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

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

heart/src/odes/AbstractCardiacCell.hpp
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 ()
void	SetTimestep (double dt)
virtual void	SolveAndUpdateState (double tStart, double tEnd)
virtual OdeSolution	Compute (double tStart, double tEnd, double tSamp=0.0)
virtual void	ComputeExceptVoltage (double tStart, double tEnd)
void	SetVoltage (double voltage)
double	GetVoltage ()
virtual double	GetIntracellularCalciumConcentration ()
virtual void	SetStretch (double stretch)
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 ()
Protected Attributes
double	mDt
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
void	CheckForArchiveFix ()
Friends
class	boost::serialization::access