#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
| 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.
| PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~PseudoEcgCalculator | ( | ) |
Destructor.
Definition at line 94 of file PseudoEcgCalculator.cpp.
Member Function Documentation
|
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 PetscTools::CreateVec(), and PetscTools::Destroy().
|
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().
| 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.
|
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(), and HeartRegionCode::IsRegionBath().
| 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(), ChasteBuildInfo::GetProvenanceString(), HeartConfig::Instance(), and OutputFileHandler::OpenOutputFile().
Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().
Member Data Documentation
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private |
The diffusion coefficient D
Definition at line 82 of file PseudoEcgCalculator.hpp.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator().
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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 >::PseudoEcgCalculator().
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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().
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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 >::PseudoEcgCalculator().
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private |
The point from where we want to calculate the pseudoECG
Definition at line 81 of file PseudoEcgCalculator.hpp.
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private |
A mesh used by the calculator
Definition at line 80 of file PseudoEcgCalculator.hpp.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator().
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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.
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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 >::PseudoEcgCalculator().
The documentation for this class was generated from the following files:
- heart/src/postprocessing/PseudoEcgCalculator.hpp
- heart/src/postprocessing/PseudoEcgCalculator.cpp
