Chaste Release::3.1
Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | Friends
ElectrodesStimulusFactory< DIM > Class Template Reference

#include <ElectrodesStimulusFactory.hpp>

Inheritance diagram for ElectrodesStimulusFactory< DIM >:
Collaboration diagram for ElectrodesStimulusFactory< DIM >:

List of all members.

Public Member Functions

 ElectrodesStimulusFactory (std::vector< std::pair< AbstractChasteRegion< DIM > *, AbstractChasteRegion< DIM > * > > &rElectrodePairs, std::vector< double > &rStimulusMagnitudes, std::vector< double > &rDurations, std::vector< double > &rPeriods, std::vector< double > &rStarts, std::vector< double > &rEnds)
boost::shared_ptr
< AbstractStimulusFunction > 		CreateStimulusForNode (unsigned nodeIndex)
 ~ElectrodesStimulusFactory ()
void SetCompatibleExtracellularStimulus ()
void GroundSecondElectrode (bool grounded)

Protected Types

typedef LinearBasisFunction< DIM > BasisFunction

Protected Member Functions

void CheckForElectrodesIntersection ()
double ComputeElectrodeTotalFlux (AbstractChasteRegion< DIM > *pRegion, double stimulusMagnitude)

Protected Attributes

std::vector< std::pair
< AbstractChasteRegion< DIM >
*, AbstractChasteRegion< DIM > * > > & 		mrElectrodePairs
std::vector< double > & mrMagnitudes
std::vector< double > & mrDurations
std::vector< double > & mrPeriods
std::vector< double > & mrStarts
std::vector< double > & mrEnds
std::vector< double > mMagnitudesElectrode1
std::vector< double > mMagnitudesElectrode2
bool mGroundSecondElectrode

Friends

class TestStimulusFactory

Detailed Description

template<unsigned DIM>
class ElectrodesStimulusFactory< DIM >

This class implements the specification of tow electrodes with a RegularStimulus applied to them. It makes sure the compatibility conditions is verified by scaling the magnitude of the second electrode according to the flux flowing thorugh each of them.

User needs to pass in a vector of pairs of electrodes and, for each pair, the stimulation parameters. This class will then implement the CreateStimulusForNode accordingly by creating a RegularStimulus object for each node. Each node belonging to any "first electrode" will have an extracellular volume stimulus equals to the value that is passed in, while each node belonging to any "second elecrode" will have an extracellular volume stimulus corrected by the flux (proportional to electrode volume) in such a way that compatibility conditions of the extended bidomain equations are followed.

It is possible to ground all second electrodes by calling GroundSecondElectrode. In this case, the member variable mGroundSecondElectrode will have size > 0 and other classes can behave accordingly (e.g., problem class will set Dirichlet boundary conditions accordingly).

Definition at line 67 of file ElectrodesStimulusFactory.hpp.

Member Typedef Documentation

template<unsigned DIM>
typedef LinearBasisFunction<DIM> ElectrodesStimulusFactory< DIM >::BasisFunction [protected]

typedef for basis function

Definition at line 121 of file ElectrodesStimulusFactory.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
ElectrodesStimulusFactory< DIM >::ElectrodesStimulusFactory ( std::vector< std::pair< AbstractChasteRegion< DIM > *, AbstractChasteRegion< DIM > * > > &  rElectrodePairs,
std::vector< double > &  rStimulusMagnitudes,
std::vector< double > &  rDurations,
std::vector< double > &  rPeriods,
std::vector< double > &  rStarts,
std::vector< double > &  rEnds 
)

Constructor. Electrodes and stimulation parameters need to be passed in.

Parameters:
rElectrodePairsthe pairs of electrodes
rStimulusMagnitudesthe magnitudes of the stimuli (microA / cm^3). First electrode will have magnitude value and second electrode will have -magnitude (before being corrected to ensure equal flux).
rDurationsthe duration of each stimulus (ms)
rPeriodsthe period of each stimulus (ms)
rStartsthe start time of each stimulus (ms).
rEndsthe end of each stimulation (ms)

Definition at line 43 of file ElectrodesStimulusFactory.cpp.

References EXCEPTION, ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode1, ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode2, and ElectrodesStimulusFactory< DIM >::mrMagnitudes.

template<unsigned DIM>
ElectrodesStimulusFactory< DIM >::~ElectrodesStimulusFactory ( )

Destructor

Definition at line 72 of file ElectrodesStimulusFactory.cpp.

Member Function Documentation

template<unsigned DIM>
void ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection ( ) [protected]

Helper method to check if any of the electrodes intersects with the other. it needs to check whether any element that conatins any node of electrode 1 does not conatin also nodes of eledtrode 2

Definition at line 77 of file ElectrodesStimulusFactory.cpp.

References PetscTools::Barrier(), and EXCEPTION.

template<unsigned DIM>
double ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux ( AbstractChasteRegion< DIM > *  pRegion,
double  stimulusMagnitude 
) [protected]

Helper method to compute electrode flux. This method is the main functionality of this class.

It essentially computes the contribution of each electrode to the RHS vector of the linear system. The loops over elements and gauss points mimicks the ones in AssembleOnElement. Interpolation is done for the value of the magnitude of the electrode.

NOTE that this method assumes the use of a GaussianQuadratureRule with 2 Gauss points (the default value of Chaste FE assemblers).

Parameters:
pRegionthe electrode
stimulusMagnitudethe stimulus magnitude

Definition at line 185 of file ElectrodesStimulusFactory.cpp.

References AbstractChasteRegion< SPACE_DIM >::DoesContain(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), GaussianQuadratureRule< ELEMENT_DIM >::GetNumQuadPoints(), GaussianQuadratureRule< ELEMENT_DIM >::GetWeight(), and GaussianQuadratureRule< ELEMENT_DIM >::rGetQuadPoint().

template<unsigned DIM>
boost::shared_ptr< AbstractStimulusFunction > ElectrodesStimulusFactory< DIM >::CreateStimulusForNode ( unsigned  nodeIndex) [virtual]

Creates an appropriate stimuus for each node as to abide compatibility conditions.

Parameters:
nodeIndexthe node index for which to create the stimulus

Reimplemented from AbstractStimulusFactory< DIM >.

Reimplemented in ZeroNetChargeElectrodes< DIM >.

Definition at line 161 of file ElectrodesStimulusFactory.cpp.

template<unsigned DIM>
void ElectrodesStimulusFactory< DIM >::GroundSecondElectrode ( bool  grounded)

Allow the user to ground the second electrode

Parameters:
grounded: true if second electrode is grounded

Definition at line 116 of file ElectrodesStimulusFactory.cpp.

template<unsigned DIM>
void ElectrodesStimulusFactory< DIM >::SetCompatibleExtracellularStimulus ( ) [virtual]

This method checks whether the users wanted a grounded electrode. If so, it fills in mGroundedRegions accordingly.

If not, it calls ComputeElectrodeTotalFlux and scales the magnitudes of the electrodes stimuli accordingly

Reimplemented from AbstractStimulusFactory< DIM >.

Definition at line 122 of file ElectrodesStimulusFactory.cpp.

References PetscTools::ReplicateException().

Member Data Documentation

template<unsigned DIM>
bool ElectrodesStimulusFactory< DIM >::mGroundSecondElectrode [protected]

Whether the second electrode is grounded

Definition at line 111 of file ElectrodesStimulusFactory.hpp.

template<unsigned DIM>
std::vector<double> ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode1 [protected]

Used to store temporarily magnitudes of electrode 1 for correction

Definition at line 102 of file ElectrodesStimulusFactory.hpp.

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

template<unsigned DIM>
std::vector<double> ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode2 [protected]

Used to store temporarily magnitudes of electrode 2 for correction

Definition at line 107 of file ElectrodesStimulusFactory.hpp.

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

template<unsigned DIM>
std::vector<double>& ElectrodesStimulusFactory< DIM >::mrDurations [protected]

Vector of stimuli durations (ms). Must be the same size as mrElectrodePairs.

Definition at line 85 of file ElectrodesStimulusFactory.hpp.

template<unsigned DIM>
std::vector<std::pair<AbstractChasteRegion<DIM>*, AbstractChasteRegion<DIM>*> >& ElectrodesStimulusFactory< DIM >::mrElectrodePairs [protected]

Vector of pairs, each pair representing a pair of electrodes.

Definition at line 76 of file ElectrodesStimulusFactory.hpp.

template<unsigned DIM>
std::vector<double>& ElectrodesStimulusFactory< DIM >::mrEnds [protected]

Vector of stimuli end times (ms). Must be the same size as mrElectrodePairs.

Definition at line 97 of file ElectrodesStimulusFactory.hpp.

template<unsigned DIM>
std::vector<double>& ElectrodesStimulusFactory< DIM >::mrMagnitudes [protected]

Vector of stimuli magnitudes (microA / cm^3). Must be the same size as mrElectrodePairs.

Definition at line 81 of file ElectrodesStimulusFactory.hpp.

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

template<unsigned DIM>
std::vector<double>& ElectrodesStimulusFactory< DIM >::mrPeriods [protected]

Vector of stimuli periods (ms). Must be the same size as mrElectrodePairs.

Definition at line 89 of file ElectrodesStimulusFactory.hpp.

template<unsigned DIM>
std::vector<double>& ElectrodesStimulusFactory< DIM >::mrStarts [protected]

Vector of stimuli start times (ms). Must be the same size as mrElectrodePairs.

Definition at line 93 of file ElectrodesStimulusFactory.hpp.

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