Chaste  Release::2018.1
PseudoEcgCalculator.hpp
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35 
36 #ifndef _PSEUDOECGALCALCULATOR_HPP_
37 #define _PSEUDOECGALCALCULATOR_HPP_
38 
39 #include "AbstractFunctionalCalculator.hpp"
40 #include "AbstractTetrahedralMesh.hpp"
41 #include "ChastePoint.hpp"
42 #include "UblasCustomFunctions.hpp"
43 #include "Hdf5DataReader.hpp"
44 
59 /*
60  * NB I don't think that this class needs to be templated over PROBLEM_DIM,
61  * since even when working with Bidomain we only integrate one thing at once,
62  * and hence still need to call AbstractFunctionalCalculator<ELEMENT_DIM, SPACE_DIM, 1>.
63  * See PostProcessingWriter.cpp line ~141. The fact that it is only explicitly
64  * instantiated (at the bottom of the cpp) for cases with 1, would agree with this.
65  *
66  * But at the same time it probably isn't worth breaking users' code by changing it.
67  * Might also make it easier to copy and paste for any new class that does a
68  * fancier integral with more quantities.
69  */
70 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
71 class PseudoEcgCalculator : public AbstractFunctionalCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>
72 {
73 private:
74 
75  friend class TestPseudoEcgCalculator;//for testing
76 
78  unsigned mNumberOfNodes;
79  unsigned mNumTimeSteps;
83  std::string mVariableName;
84  unsigned mTimestepStride;
96  c_vector<double,PROBLEM_DIM>& rU,
97  c_matrix<double,PROBLEM_DIM,SPACE_DIM>& rGradU);
98 
99 
107  double ComputePseudoEcgAtOneTimeStep(unsigned timeStep);
108 
119 
120 public:
121 
135  const ChastePoint<SPACE_DIM>& rProbeElectrode,
136  const FileFinder& rDirectory,
137  const std::string& rHdf5FileName,
138  const std::string& rVariableName = "V",
139  unsigned timestepStride = 1);
140 
145 
146 
153  void SetDiffusionCoefficient(double diffusionCoefficient);
154 
164  void WritePseudoEcg();
165 };
166 
167 #endif //_PSEUDOECGALCALCULATOR_HPP_
void SetDiffusionCoefficient(double diffusionCoefficient)
double GetIntegrand(ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU)
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & mrMesh
bool ShouldSkipThisElement(Element< ELEMENT_DIM, SPACE_DIM > &rElement)
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)
ChastePoint< SPACE_DIM > mProbeElectrode
Hdf5DataReader * mpDataReader
double ComputePseudoEcgAtOneTimeStep(unsigned timeStep)