#include <PseudoEcgCalculator.hpp>

Inheritance diagram for PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >:

Collaboration diagram for PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >:

Public Member Functions
	PseudoEcgCalculator (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, const ChastePoint< SPACE_DIM > &rProbeElectrode, const FileFinder &rDirectory, const std::string &rHdf5FileName, const std::string &rVariableName="V", unsigned timestepStride=1)

	~PseudoEcgCalculator ()

void	SetDiffusionCoefficient (double diffusionCoefficient)

void	WritePseudoEcg ()

Public Member Functions inherited from AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
virtual	~AbstractFunctionalCalculator ()

double	Calculate (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, Vec solution)

double	CalculateOnElement (Element< ELEMENT_DIM, SPACE_DIM > &rElement)

Private Member Functions
double	GetIntegrand (ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU)

double	ComputePseudoEcgAtOneTimeStep (unsigned timeStep)

bool	ShouldSkipThisElement (Element< ELEMENT_DIM, SPACE_DIM > &rElement)

Private Attributes
Hdf5DataReader *	mpDataReader

unsigned	mNumberOfNodes

unsigned	mNumTimeSteps

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &	mrMesh

ChastePoint< SPACE_DIM >	mProbeElectrode

double	mDiffusionCoefficient

std::string	mVariableName

unsigned	mTimestepStride

Friends
class	TestPseudoEcgCalculator

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

This class implements a pseudo-ECG calculator. It is a concrete class of AbstractFunctionalCalculator. The pseudo-ECG is defined as the integral over the mesh of the following integrand:

D * grad (solution) dot grad (1/r)

where D is a diffusion coefficient and r is the distance between a recording electrode and a given point in the mesh.

References for the formula that defines the pseudo-ECG:

Gima K, Rudy Y Circ Res (2002) 90:889-896 (equation 1) Baher et al. Am J Physiol (2007) 292:H180-H189 (equation 5)

Definition at line 71 of file PseudoEcgCalculator.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator	(	AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &	rMesh,
		const ChastePoint< SPACE_DIM > &	rProbeElectrode,
		const FileFinder &	rDirectory,
		const std::string &	rHdf5FileName,
		const std::string &	rVariableName = `"V"`,
		unsigned	timestepStride = `1`
	)

Constructor

Parameters

rMesh	A reference to the mesh
rProbeElectrode	The location of the recording electrode
rDirectory	The directory where the simulation results are stored
rHdf5FileName	The file name where the simulation results are stored
rVariableName	The name of the voltage variable (is V by default)
timestepStride	The number of timesteps in a stride (so that we don't have to compute all the ECGs). This defaults to 1.

Definition at line 62 of file PseudoEcgCalculator.cpp.

References Hdf5DataReader::GetNumberOfRows(), Hdf5DataReader::GetVariableOverTime(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDiffusionCoefficient, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumberOfNodes, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumTimeSteps, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDataReader, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mrMesh, and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVariableName.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~PseudoEcgCalculator ( )

Destructor.

Definition at line 94 of file PseudoEcgCalculator.cpp.

References PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDataReader.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep ( unsigned timeStep )

private

Calculates the pseudo-ECG and returns its value at the given time step.

Parameters

timeStep the time step where we want to calculate the pseudo-ecg

Returns: the pseudo ECG at the given time step.

Definition at line 107 of file PseudoEcgCalculator.cpp.

References AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), PetscTools::CreateVec(), PetscTools::Destroy(), Hdf5DataReader::GetVariableOverNodes(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumberOfNodes, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDataReader, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mrMesh, and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVariableName.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetIntegrand	(	ChastePoint< SPACE_DIM > &	rX,
		c_vector< double, PROBLEM_DIM > &	rU,
		c_matrix< double, PROBLEM_DIM, SPACE_DIM > &	rGradU
	)

privatevirtual

Returns: the integrand. The pseudo-ECG is defined as the integral over the mesh of the following integrand:

D * grad (solution) dot grad (1/r)

Parameters

rX	The point in space
rU	The unknown as a vector, u(i) = u_i
rGradU	The gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)

Implements AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 44 of file PseudoEcgCalculator.cpp.

References EXCEPTION, ChastePoint< DIM >::rGetLocation(), and SmallPow().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetDiffusionCoefficient ( double diffusionCoefficient )

Sets the value of the diffusion coefficient (D)

Parameters

diffusionCoefficient The desired value of the diffusion coefficient

Definition at line 100 of file PseudoEcgCalculator.cpp.

References PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDiffusionCoefficient.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ShouldSkipThisElement ( Element< ELEMENT_DIM, SPACE_DIM > & rElement )

privatevirtual

Whether we should not calculate the Pseudo ECG on this element.

This method returns true if we are integrating voltage and the tissue element is in the bath.

Parameters

rElement the element of interest

Returns: whether we should skip this element.

Reimplemented from AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 82 of file PseudoEcgCalculator.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetUnsignedAttribute(), HeartRegionCode::IsRegionBath(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVariableName.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg ( )

Calculates and writes the pseudo-ECG to file. the file will be named PseudoEcgFromElectrodeAt_x_y_z.dat, where x,y,z are replaced by the location of the electrode. It will contain one column of numbers, each being the pseudoECG at each time step. It will be created by the master processor into /output relaitive to where the output directory is set (by the HeartConfig or by default)

Definition at line 127 of file PseudoEcgCalculator.cpp.

References PetscTools::AmMaster(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), ChasteBuildInfo::GetProvenanceString(), Hdf5DataReader::GetUnlimitedDimensionValues(), ChastePoint< DIM >::GetWithDefault(), HeartConfig::Instance(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumTimeSteps, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDataReader, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mProbeElectrode, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mTimestepStride, and OutputFileHandler::OpenOutputFile().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDiffusionCoefficient

private

The diffusion coefficient D

Definition at line 82 of file PseudoEcgCalculator.hpp.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetDiffusionCoefficient().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

unsigned PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumberOfNodes

private

Number of nodes in the mesh (got from the data reader)

Definition at line 78 of file PseudoEcgCalculator.hpp.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

unsigned PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumTimeSteps

private

Number of time steps in the simulation (got from the data reader)

Definition at line 79 of file PseudoEcgCalculator.hpp.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Hdf5DataReader* PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDataReader

private

An HDF5 reader from which to get the solution

Definition at line 77 of file PseudoEcgCalculator.hpp.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~PseudoEcgCalculator().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

ChastePoint<SPACE_DIM> PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mProbeElectrode

private

The point from where we want to calculate the pseudoECG

Definition at line 81 of file PseudoEcgCalculator.hpp.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mrMesh

private

A mesh used by the calculator

Definition at line 80 of file PseudoEcgCalculator.hpp.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

unsigned PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mTimestepStride

private

The number of timesteps in a stride (so that we don't have to compute all the ECGs). This defaults to 1.

Definition at line 84 of file PseudoEcgCalculator.hpp.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::string PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVariableName

private

the variable for which we want to calculate the pseudo ecg, defaults to "V"

Definition at line 83 of file PseudoEcgCalculator.hpp.

Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ShouldSkipThisElement().

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

heart/src/postprocessing/PseudoEcgCalculator.hpp
heart/src/postprocessing/PseudoEcgCalculator.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM> class PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >