PapillaryFibreCalculator.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 PAPILLARYFIBRECALCULATOR_HPP_
00029 #define PAPILLARYFIBRECALCULATOR_HPP_
00030 
00031 #include "UblasCustomFunctions.hpp"
00032 #include "TetrahedralMesh.hpp"
00033 
00039 class PapillaryFibreCalculator
00040 {
00041 // Allow the test class to use the private functions.
00042 friend class TestPapillaryFibreCalculator;
00043 
00044 private:
00046     TetrahedralMesh<3,3>& mrMesh;
00048     std::vector< c_vector<double, 3> > mRadiusVectors;
00050     std::vector< c_matrix<double,3,3> > mStructureTensors;
00052     std::vector< c_matrix<double,3,3> > mSmoothedStructureTensors;
00053 
00061     c_vector<double,3> GetRadiusVectorForOneElement(unsigned elementIndex);
00062 
00067     void GetRadiusVectors();
00068 
00069 
00075     void ConstructStructureTensors();
00076 
00086     void SmoothStructureTensors();
00087 
00088 public:
00094     PapillaryFibreCalculator(TetrahedralMesh<3,3>& rMesh);
00095 
00101      std::vector<c_vector<double,3> > CalculateFibreOrientations();
00102 
00103 };
00104 
00105 // PUBLIC METHODS
00106 PapillaryFibreCalculator::PapillaryFibreCalculator(TetrahedralMesh<3,3>& rMesh)
00107     : mrMesh(rMesh)
00108 {
00109     mRadiusVectors.resize(mrMesh.GetNumElements());
00110     mStructureTensors.resize(mrMesh.GetNumElements());
00111     mSmoothedStructureTensors.resize(mrMesh.GetNumElements());
00112 }
00113 
00114 std::vector<c_vector<double,3> > PapillaryFibreCalculator::CalculateFibreOrientations()
00115 {
00116    GetRadiusVectors();
00117 
00118    ConstructStructureTensors();
00119 
00120    SmoothStructureTensors();
00121 
00122    // Calculate eigenvalues
00123    std::vector<c_vector<double,3> > fibre_orientations(mrMesh.GetNumElements());
00124    for(unsigned i=0; i<fibre_orientations.size(); i++)
00125    {
00126        fibre_orientations[i] = CalculateEigenvectorForSmallestNonzeroEigenvalue(mSmoothedStructureTensors[i]);
00127    }
00128 
00129    return fibre_orientations;
00130 }
00131 
00132 // PRIVATE METHODS
00133 c_vector<double,3> PapillaryFibreCalculator::GetRadiusVectorForOneElement(unsigned elementIndex)
00134 {
00135     c_vector<double, 3> centroid = (mrMesh.GetElement(elementIndex))->CalculateCentroid();
00136     // Loops over all papillary face nodes
00137     c_vector<double,3> coordinates;
00138 
00139     double nearest_r_squared=DBL_MAX;
00140     unsigned nearest_face_node = 0;
00141 
00142     TetrahedralMesh<3,3>::BoundaryNodeIterator bound_node_iter = mrMesh.GetBoundaryNodeIteratorBegin();
00143     while (bound_node_iter != mrMesh.GetBoundaryNodeIteratorEnd())
00144     {
00145         unsigned bound_node_index =  (*bound_node_iter)->GetIndex();
00146         coordinates=mrMesh.GetNode(bound_node_index)->rGetLocation();
00147 
00148         // Calculates the distance between the papillary face node and the centroid
00149         double r_squared =  norm_2(centroid-coordinates);
00150         // Checks to see if it is the smallest so far - if it is, update the current smallest distance
00151         if (r_squared < nearest_r_squared)
00152         {
00153             nearest_r_squared = r_squared;
00154             nearest_face_node = bound_node_index;
00155         }
00156         ++bound_node_iter;
00157     }
00158 
00159     coordinates = mrMesh.GetNode(nearest_face_node)->rGetLocation();
00160     c_vector<double,3> radial_vector = coordinates-centroid;
00161     return radial_vector;
00162 }
00163 
00164 void PapillaryFibreCalculator::GetRadiusVectors()
00165 {
00166     // Loops over all elements finding radius vector
00167     for (AbstractTetrahedralMesh<3,3>::ElementIterator iter = mrMesh.GetElementIteratorBegin();
00168          iter != mrMesh.GetElementIteratorEnd();
00169          ++iter)
00170     {
00171         unsigned element_index = iter->GetIndex();
00172         mRadiusVectors[element_index] = GetRadiusVectorForOneElement(element_index);
00173     }
00174 }
00175 
00176 void PapillaryFibreCalculator::ConstructStructureTensors()
00177 {
00178     for(unsigned i=0;i<mRadiusVectors.size();i++)
00179     {
00180         mStructureTensors[i] = outer_prod(mRadiusVectors[i],mRadiusVectors[i]);
00181     }
00182 }
00183 
00184 void PapillaryFibreCalculator::SmoothStructureTensors()
00185 {
00186     const double sigma = 0.05; //cm
00187     const double r_max = 0.1; //cm
00188     double g_factor_sum = 0;
00189     double g_factor = 0;
00190 
00191     for (AbstractTetrahedralMesh<3,3>::ElementIterator elem_iter = mrMesh.GetElementIteratorBegin();
00192          elem_iter != mrMesh.GetElementIteratorEnd();
00193          ++elem_iter)
00194     {
00195         mSmoothedStructureTensors[ elem_iter->GetIndex()] = zero_matrix<double>(3,3);
00196 
00197         c_vector<double, 3> centroid = elem_iter->CalculateCentroid();
00198         g_factor_sum = 0;
00199 
00200         for (AbstractTetrahedralMesh<3,3>::ElementIterator iter_2 = mrMesh.GetElementIteratorBegin();
00201              iter_2 != mrMesh.GetElementIteratorEnd();
00202              ++iter_2)
00203         {
00204             c_vector<double, 3> centroid_2 = iter_2->CalculateCentroid();
00205             double r = norm_2(centroid-centroid_2);
00206             if (r < r_max)
00207             {
00208                 g_factor = exp(-r/(2*sigma*sigma));
00209 
00210                 g_factor_sum += g_factor;
00211 
00212                 mSmoothedStructureTensors[elem_iter->GetIndex()] += g_factor*mStructureTensors[iter_2->GetIndex()];
00213             }
00214         }
00215 
00216         mSmoothedStructureTensors[elem_iter->GetIndex()] /= g_factor_sum;
00217     }
00218 }
00219 
00220 #endif /*PAPILLARYFIBRECALCULATOR_HPP_*/
00221 

Generated on Tue May 31 14:31:41 2011 for Chaste by  doxygen 1.5.5