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 
00049 template<unsigned SPACE_DIM>
00050 class StreeterFibreGenerator
00051 {
00052 private:
00053     AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>& mrMesh; 
00055     HeartGeometryInformation<SPACE_DIM>* mpGeometryInfo; 
00057     c_vector <double, SPACE_DIM> mApexToBase; 
00067     double GetAveragedThicknessLocalNode(const unsigned nodeIndex, const std::vector<double>& wallThickness) const;
00068 
00074    double GetFibreMaxAngle(const c_vector<HeartRegionType, SPACE_DIM+1>& nodesRegionsForElement) const;
00075 
00076 public:
00082     StreeterFibreGenerator(AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>& rMesh);
00083 
00087     ~StreeterFibreGenerator();
00088 
00102     void SetSurfaceFiles(const std::string &rEpicardiumFile,
00103                          const std::string &rRightVentricleFile,
00104                          const std::string &rLeftVentricleFile,
00105                          bool indexFromZero);
00106 
00118     void GenerateOrthotropicFibreOrientation(std::string outputDirectory, std::string fibreOrientationFile, bool logInfo=false);
00119 
00124     void SetApexToBase(const c_vector<double, SPACE_DIM>& apexToBase);
00125 
00130     void SetApexToBase(unsigned axis);
00131 };
00132 
00133 #endif /*STREETERFIBREGENERATOR_HPP_*/