PapillaryFibreCalculator.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
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*/
#ifndef PAPILLARYFIBRECALCULATOR_HPP_
#define PAPILLARYFIBRECALCULATOR_HPP_

#include "UblasCustomFunctions.hpp"
#include "TetrahedralMesh.hpp"

class PapillaryFibreCalculator
{
// Allow the test class to use the private functions.
friend class TestPapillaryFibreCalculator;

private:
    TetrahedralMesh<3,3>& mrMesh;
    std::vector< c_vector<double, 3> > mRadiusVectors;
    std::vector< c_matrix<double,3,3> > mStructureTensors;
    std::vector< c_matrix<double,3,3> > mSmoothedStructureTensors;

    c_vector<double,3> GetRadiusVectorForOneElement(unsigned elementIndex);

    void GetRadiusVectors();


    void ConstructStructureTensors();

    void SmoothStructureTensors();

public:
    PapillaryFibreCalculator(TetrahedralMesh<3,3>& rMesh);

     std::vector<c_vector<double,3> > CalculateFibreOrientations();

};

// PUBLIC METHODS
PapillaryFibreCalculator::PapillaryFibreCalculator(TetrahedralMesh<3,3>& rMesh)
    : mrMesh(rMesh)
{
    mRadiusVectors.resize(mrMesh.GetNumElements());
    mStructureTensors.resize(mrMesh.GetNumElements());
    mSmoothedStructureTensors.resize(mrMesh.GetNumElements());
}

std::vector<c_vector<double,3> > PapillaryFibreCalculator::CalculateFibreOrientations()
{
   GetRadiusVectors();

   ConstructStructureTensors();

   SmoothStructureTensors();

   // Calculate eigenvalues
   std::vector<c_vector<double,3> > fibre_orientations(mrMesh.GetNumElements());
   for(unsigned i=0; i<fibre_orientations.size(); i++)
   {
       fibre_orientations[i] = CalculateEigenvectorForSmallestNonzeroEigenvalue(mSmoothedStructureTensors[i]);
   }

   return fibre_orientations;
}

// PRIVATE METHODS
c_vector<double,3> PapillaryFibreCalculator::GetRadiusVectorForOneElement(unsigned elementIndex)
{
    c_vector<double, 3> centroid = (mrMesh.GetElement(elementIndex))->CalculateCentroid();
    // Loops over all papillary face nodes
    c_vector<double,3> coordinates;

    double nearest_r_squared=DBL_MAX;
    unsigned nearest_face_node = 0;

    TetrahedralMesh<3,3>::BoundaryNodeIterator bound_node_iter = mrMesh.GetBoundaryNodeIteratorBegin();
    while (bound_node_iter != mrMesh.GetBoundaryNodeIteratorEnd())
    {
        unsigned bound_node_index =  (*bound_node_iter)->GetIndex();
        coordinates=mrMesh.GetNode(bound_node_index)->rGetLocation();

        // Calculates the distance between the papillary face node and the centroid
        double r_squared =  norm_2(centroid-coordinates);
        // Checks to see if it is the smallest so far - if it is, update the current smallest distance
        if (r_squared < nearest_r_squared)
        {
            nearest_r_squared = r_squared;
            nearest_face_node = bound_node_index;
        }
        ++bound_node_iter;
    }

    coordinates = mrMesh.GetNode(nearest_face_node)->rGetLocation();
    c_vector<double,3> radial_vector = coordinates-centroid;
    return radial_vector;
}

void PapillaryFibreCalculator::GetRadiusVectors()
{
    // Loops over all elements finding radius vector
    for (AbstractTetrahedralMesh<3,3>::ElementIterator iter = mrMesh.GetElementIteratorBegin();
         iter != mrMesh.GetElementIteratorEnd();
         ++iter)
    {
        unsigned element_index = iter->GetIndex();
        mRadiusVectors[element_index] = GetRadiusVectorForOneElement(element_index);
    }
}

void PapillaryFibreCalculator::ConstructStructureTensors()
{
    for(unsigned i=0;i<mRadiusVectors.size();i++)
    {
        mStructureTensors[i] = outer_prod(mRadiusVectors[i],mRadiusVectors[i]);
    }
}

void PapillaryFibreCalculator::SmoothStructureTensors()
{
    const double sigma = 0.05; //cm
    const double r_max = 0.1; //cm
    double g_factor_sum = 0;
    double g_factor = 0;

    for (AbstractTetrahedralMesh<3,3>::ElementIterator elem_iter = mrMesh.GetElementIteratorBegin();
         elem_iter != mrMesh.GetElementIteratorEnd();
         ++elem_iter)
    {
        mSmoothedStructureTensors[ elem_iter->GetIndex()] = zero_matrix<double>(3,3);

        c_vector<double, 3> centroid = elem_iter->CalculateCentroid();
        g_factor_sum = 0;

        for (AbstractTetrahedralMesh<3,3>::ElementIterator iter_2 = mrMesh.GetElementIteratorBegin();
             iter_2 != mrMesh.GetElementIteratorEnd();
             ++iter_2)
        {
            c_vector<double, 3> centroid_2 = iter_2->CalculateCentroid();
            double r = norm_2(centroid-centroid_2);
            if (r < r_max)
            {
                g_factor = exp(-r/(2*sigma*sigma));

                g_factor_sum += g_factor;

                mSmoothedStructureTensors[elem_iter->GetIndex()] += g_factor*mStructureTensors[iter_2->GetIndex()];
            }
        }

        mSmoothedStructureTensors[elem_iter->GetIndex()] /= g_factor_sum;
    }
}

#endif /*PAPILLARYFIBRECALCULATOR_HPP_*/