ElectrodesStimulusFactory< DIM > Class Template Reference

#include <ElectrodesStimulusFactory.hpp>

Inherits AbstractStimulusFactory< DIM >.

Inherited by ZeroNetChargeElectrodes< DIM >.

Collaboration diagram for ElectrodesStimulusFactory< DIM >:
Collaboration graph
[legend]

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 60 of file ElectrodesStimulusFactory.hpp.

Member Typedef Documentation

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

typedef for basis function

Definition at line 114 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 
) [inline]

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

Parameters:
rElectrodePairs the pairs of electrodes
rStimulusMagnitudes the 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).
rDurations the duration of each stimulus (ms)
rPeriods the period of each stimulus (ms)
rStarts the start time of each stimulus (ms).
rEnds the end of each stimulation (ms)

Definition at line 36 of file ElectrodesStimulusFactory.cpp.

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

template<unsigned DIM>
ElectrodesStimulusFactory< DIM >::~ElectrodesStimulusFactory (  )  [inline]

Destructor

Definition at line 65 of file ElectrodesStimulusFactory.cpp.

Member Function Documentation

template<unsigned DIM>
void ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection (  )  [inline, 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 70 of file ElectrodesStimulusFactory.cpp.

References PetscTools::Barrier(), EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), DistributedVectorFactory::IsGlobalIndexLocal(), AbstractStimulusFactory< DIM >::mpMesh, and ElectrodesStimulusFactory< DIM >::mrElectrodePairs.

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

template<unsigned DIM>
double ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux ( AbstractChasteRegion< DIM > *  pRegion,
double  stimulusMagnitude 
) [inline, 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:
pRegion the electrode
stimulusMagnitude the stimulus magnitude

Definition at line 178 of file ElectrodesStimulusFactory.cpp.

References LinearBasisFunction< ELEMENT_DIM >::ComputeBasisFunctions(), AbstractChasteRegion< SPACE_DIM >::DoesContain(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), GaussianQuadratureRule< ELEMENT_DIM >::GetNumQuadPoints(), GaussianQuadratureRule< ELEMENT_DIM >::GetWeight(), AbstractStimulusFactory< DIM >::mpMesh, and GaussianQuadratureRule< ELEMENT_DIM >::rGetQuadPoint().

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

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

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

Parameters:
nodeIndex the node index for which to create the stimulus

Reimplemented from AbstractStimulusFactory< DIM >.

Reimplemented in ZeroNetChargeElectrodes< DIM >.

Definition at line 154 of file ElectrodesStimulusFactory.cpp.

References ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode1, ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode2, ElectrodesStimulusFactory< DIM >::mrDurations, ElectrodesStimulusFactory< DIM >::mrElectrodePairs, ElectrodesStimulusFactory< DIM >::mrEnds, ElectrodesStimulusFactory< DIM >::mrPeriods, and ElectrodesStimulusFactory< DIM >::mrStarts.

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

Allow the user to ground the second electrode

Parameters:
grounded : true if second electrode is grounded

Definition at line 109 of file ElectrodesStimulusFactory.cpp.

References ElectrodesStimulusFactory< DIM >::mGroundSecondElectrode.

template<unsigned DIM>
void ElectrodesStimulusFactory< DIM >::SetCompatibleExtracellularStimulus (  )  [inline, 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 115 of file ElectrodesStimulusFactory.cpp.

References ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection(), ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux(), AbstractStimulusFactory< DIM >::mGroundedRegions, ElectrodesStimulusFactory< DIM >::mGroundSecondElectrode, ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode1, ElectrodesStimulusFactory< DIM >::mMagnitudesElectrode2, AbstractStimulusFactory< DIM >::mpMesh, ElectrodesStimulusFactory< DIM >::mrElectrodePairs, and PetscTools::ReplicateException().

Member Data Documentation

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

Whether the second electrode is grounded

Definition at line 104 of file ElectrodesStimulusFactory.hpp.

Referenced by ElectrodesStimulusFactory< DIM >::GroundSecondElectrode(), and ElectrodesStimulusFactory< DIM >::SetCompatibleExtracellularStimulus().

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

Used to store temporarily magnitudes of electrode 1 for correction

Definition at line 95 of file ElectrodesStimulusFactory.hpp.

Referenced by ZeroNetChargeElectrodes< DIM >::CreateStimulusForNode(), ElectrodesStimulusFactory< DIM >::CreateStimulusForNode(), ElectrodesStimulusFactory< DIM >::ElectrodesStimulusFactory(), and ElectrodesStimulusFactory< DIM >::SetCompatibleExtracellularStimulus().

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

Used to store temporarily magnitudes of electrode 2 for correction

Definition at line 100 of file ElectrodesStimulusFactory.hpp.

Referenced by ZeroNetChargeElectrodes< DIM >::CreateStimulusForNode(), ElectrodesStimulusFactory< DIM >::CreateStimulusForNode(), ElectrodesStimulusFactory< DIM >::ElectrodesStimulusFactory(), and ElectrodesStimulusFactory< DIM >::SetCompatibleExtracellularStimulus().

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 78 of file ElectrodesStimulusFactory.hpp.

Referenced by ZeroNetChargeElectrodes< DIM >::CreateStimulusForNode(), and ElectrodesStimulusFactory< DIM >::CreateStimulusForNode().

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 69 of file ElectrodesStimulusFactory.hpp.

Referenced by ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection(), ZeroNetChargeElectrodes< DIM >::CreateStimulusForNode(), ElectrodesStimulusFactory< DIM >::CreateStimulusForNode(), and ElectrodesStimulusFactory< DIM >::SetCompatibleExtracellularStimulus().

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 90 of file ElectrodesStimulusFactory.hpp.

Referenced by ZeroNetChargeElectrodes< DIM >::CreateStimulusForNode(), and ElectrodesStimulusFactory< DIM >::CreateStimulusForNode().

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 74 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 82 of file ElectrodesStimulusFactory.hpp.

Referenced by ZeroNetChargeElectrodes< DIM >::CreateStimulusForNode(), and ElectrodesStimulusFactory< DIM >::CreateStimulusForNode().

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 86 of file ElectrodesStimulusFactory.hpp.

Referenced by ZeroNetChargeElectrodes< DIM >::CreateStimulusForNode(), and ElectrodesStimulusFactory< DIM >::CreateStimulusForNode().

The documentation for this class was generated from the following files:
Generated on Thu Dec 22 13:04:28 2011 for Chaste by  doxygen 1.6.3