StreeterFibreGenerator.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 #ifndef STREETERFIBREGENERATOR_HPP_
00029 #define STREETERFIBREGENERATOR_HPP_
00030 
00031 #include <vector>
00032 #include <string>
00033 #include <set>
00034 #include "DistanceMapCalculator.hpp"
00035 #include "AbstractTetrahedralMesh.hpp"
00036 #include "HeartGeometryInformation.hpp"
00037 
00044 template<unsigned SPACE_DIM>
00045 class StreeterFibreGenerator
00046 {
00047 private:
00048     AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>& mrMesh; 
00050     HeartGeometryInformation<SPACE_DIM>* mpGeometryInfo; 
00052     c_vector <double, SPACE_DIM> mApexToBase; 
00062     double GetAveragedThicknessLocalNode(const unsigned nodeIndex, const std::vector<double>& wallThickness) const;
00063 
00069    double GetFibreMaxAngle(const c_vector<HeartRegionType, SPACE_DIM+1>& nodesRegionsForElement) const;
00070 
00071 public:
00077     StreeterFibreGenerator(AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>& rMesh);
00078 
00082     ~StreeterFibreGenerator();
00083 
00093     void SetSurfaceFiles(const std::string &epicardiumFile,
00094                          const std::string &rightVentricleFile,
00095                          const std::string &leftVentricleFile,
00096                          bool indexFromZero);
00097 
00109     void GenerateOrthotropicFibreOrientation(std::string outputDirectory, std::string fibreOrientationFile, bool logInfo=false);
00110 
00115     void SetApexToBase(const c_vector<double, SPACE_DIM>& apexToBase);
00116 
00121     void SetApexToBase(unsigned axis);
00122 };
00123 
00124 #endif /*STREETERFIBREGENERATOR_HPP_*/

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