PseudoEcgCalculator.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2011
00004 
00005 University of Oxford means the Chancellor, Masters and Scholars of the
00006 University of Oxford, having an administrative office at Wellington
00007 Square, Oxford OX1 2JD, UK.
00008 
00009 This file is part of Chaste.
00010 
00011 Chaste is free software: you can redistribute it and/or modify it
00012 under the terms of the GNU Lesser General Public License as published
00013 by the Free Software Foundation, either version 2.1 of the License, or
00014 (at your option) any later version.
00015 
00016 Chaste is distributed in the hope that it will be useful, but WITHOUT
00017 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00018 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00019 License for more details. The offer of Chaste under the terms of the
00020 License is subject to the License being interpreted in accordance with
00021 English Law and subject to any action against the University of Oxford
00022 being under the jurisdiction of the English Courts.
00023 
00024 You should have received a copy of the GNU Lesser General Public License
00025 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00026 
00027 */
00028 
00029 #ifndef _PSEUDOECGALCALCULATOR_HPP_
00030 #define _PSEUDOECGALCALCULATOR_HPP_
00031 
00032 #include "AbstractFunctionalCalculator.hpp"
00033 #include "AbstractTetrahedralMesh.hpp"
00034 #include "ChastePoint.hpp"
00035 #include "UblasCustomFunctions.hpp"
00036 #include "Hdf5DataReader.hpp"
00037 
00053 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
00054 class PseudoEcgCalculator : public AbstractFunctionalCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>
00055 {
00056 private:
00057 
00058     friend class TestPseudoEcgCalculator;//for testing
00059 
00060     Hdf5DataReader* mpDataReader; 
00061     unsigned mNumberOfNodes; 
00062     unsigned mNumTimeSteps;
00063     AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& mrMesh;
00064     ChastePoint<SPACE_DIM> mProbeElectrode; 
00065     double mDiffusionCoefficient;
00066     std::string mVariableName;
00078     double GetIntegrand(ChastePoint<SPACE_DIM>& rX,
00079                                 c_vector<double,PROBLEM_DIM>& rU,
00080                                 c_matrix<double,PROBLEM_DIM,SPACE_DIM>& rGradU);
00081 
00082 
00090     double ComputePseudoEcgAtOneTimeStep (unsigned timeStep);
00091 
00092 public:
00093 
00105     PseudoEcgCalculator (AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& rMesh,
00106                          const ChastePoint<SPACE_DIM>& rProbeElectrode,
00107                          std::string directory,
00108                          std::string hdf5File,
00109                          std::string variableName = "V",
00110                          bool makeAbsolute = true);
00111 
00115     ~PseudoEcgCalculator();
00116 
00117 
00124     void SetDiffusionCoefficient(double diffusionCoefficient);
00125 
00135     void WritePseudoEcg();
00136 
00137 };
00138 
00139 #endif //_PSEUDOECGALCALCULATOR_HPP_
00140 
00141 

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