StreeterFibreGenerator.cpp

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*/

#include "UblasCustomFunctions.hpp"

#include "StreeterFibreGenerator.hpp"

#include <cmath>
#include <fstream>
#include <sstream>
#include "OutputFileHandler.hpp"
#include "Exception.hpp"
//#include "HeartRegionCodes.hpp"

template<unsigned SPACE_DIM>
double StreeterFibreGenerator<SPACE_DIM>::GetAveragedThicknessLocalNode(
        const unsigned nodeIndex, const std::vector<double>& wallThickness) const
{
    if (nodeIndex < mrMesh.GetDistributedVectorFactory()->GetLow() ||
        nodeIndex >= mrMesh.GetDistributedVectorFactory()->GetHigh() )
    {
        return 0.0;  //Don't calculate this for nodes which aren't local
    }

    // Initialise the average with the value corresponding to the current node
    double average = wallThickness[nodeIndex];
    unsigned nodes_visited = 1;

    // Use a set to store visited nodes
    std::set<unsigned> visited_nodes;
    visited_nodes.insert(nodeIndex);

    Node<SPACE_DIM>* p_current_node = mrMesh.GetNode(nodeIndex);

    // Loop over the elements containing the given node
    for(typename Node<SPACE_DIM>::ContainingElementIterator element_iterator = p_current_node->ContainingElementsBegin();
        element_iterator != p_current_node->ContainingElementsEnd();
        ++element_iterator)
    {
        // Get a pointer to the container element
        Element<SPACE_DIM,SPACE_DIM>* p_containing_element = mrMesh.GetElement(*element_iterator);

       // Loop over the nodes of the element
       for(unsigned node_local_index=0;
           node_local_index<p_containing_element->GetNumNodes();
           node_local_index++)
       {
            Node<SPACE_DIM>* p_neighbour_node = p_containing_element->GetNode(node_local_index);
            unsigned neighbour_node_index = p_neighbour_node->GetIndex();

            // Check if the neighbour node has already been visited
            if (visited_nodes.find(neighbour_node_index) == visited_nodes.end())
            {
                average += wallThickness[neighbour_node_index];
                visited_nodes.insert(neighbour_node_index);
                nodes_visited++;
            }
       }
    }

    return average/nodes_visited;
}




template<unsigned SPACE_DIM>
double StreeterFibreGenerator<SPACE_DIM>::GetFibreMaxAngle(
        const c_vector<HeartRegionType, SPACE_DIM+1>& nodesRegionsForElement) const
{
    unsigned lv=0, rv=0;

    for (unsigned index=0; index<SPACE_DIM+1; index++)
    {
        switch (nodesRegionsForElement[index])
        {
            case HeartGeometryInformation<SPACE_DIM>::LEFT_VENTRICLE_SURFACE:
            case HeartGeometryInformation<SPACE_DIM>::LEFT_VENTRICLE_WALL:
            case HeartGeometryInformation<SPACE_DIM>::LEFT_SEPTUM:
                lv++;
                break;

            case HeartGeometryInformation<SPACE_DIM>::RIGHT_VENTRICLE_SURFACE:
            case HeartGeometryInformation<SPACE_DIM>::RIGHT_VENTRICLE_WALL:
            case HeartGeometryInformation<SPACE_DIM>::RIGHT_SEPTUM:
                rv++;
                break;

            case HeartGeometryInformation<SPACE_DIM>::UNKNOWN:
            default:
                NEVER_REACHED;
        }
    }

    // If most of the nodes are in the right ventricle
    if (rv>lv)
    {
        return M_PI/4.0;
    }

    // Anywhere else
    return M_PI/3.0;
}

template<unsigned SPACE_DIM>
StreeterFibreGenerator<SPACE_DIM>::StreeterFibreGenerator(AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>& rMesh)
    : mrMesh(rMesh),
      mpGeometryInfo(NULL),
      mApexToBase(zero_vector<double>(SPACE_DIM))
{
}

template<unsigned SPACE_DIM>
StreeterFibreGenerator<SPACE_DIM>::~StreeterFibreGenerator()
{
    delete mpGeometryInfo;
}

template<unsigned SPACE_DIM>
void StreeterFibreGenerator<SPACE_DIM>::SetSurfaceFiles(
            const std::string &rEpicardiumFile,
            const std::string &rRightVentricleFile,
            const std::string &rLeftVentricleFile,
            bool indexFromZero)
{
    // Compute the distance map of each surface
     mpGeometryInfo = new HeartGeometryInformation<SPACE_DIM>(mrMesh, rEpicardiumFile, rLeftVentricleFile, rRightVentricleFile, indexFromZero);
}

template<unsigned SPACE_DIM>
void StreeterFibreGenerator<SPACE_DIM>::GenerateOrthotropicFibreOrientation(
            std::string outputDirectory,
            std::string fibreOrientationFile,
            bool logInfo)
{
    assert(SPACE_DIM == 3);
    if (mpGeometryInfo == NULL)
    {
        EXCEPTION("Files defining the heart surfaces not set");
    }
    unsigned num_elements = mrMesh.GetNumElements();

    // Open files
    OutputFileHandler handler(outputDirectory, false);
    out_stream p_fibre_file, p_regions_file, p_thickness_file, p_ave_thickness_file;

    //Make sure that only the master process makes an empty output file
    //and writes the log files
    if (PetscTools::AmMaster())
    {
        //Open file and close it, but don't write to it yet
        p_fibre_file=handler.OpenOutputFile(fibreOrientationFile);
        // First line of the fibre file: number of elements of the mesh
        *p_fibre_file << num_elements << std::endl;
        p_fibre_file->close();
    }
    else
    {
        logInfo=false;
    }

    if (logInfo)
    {
        p_regions_file  = handler.OpenOutputFile("node_regions.data");
        p_thickness_file = handler.OpenOutputFile("wall_thickness.data");
        p_ave_thickness_file = handler.OpenOutputFile("averaged_thickness.data");
    }


    //We expect that the apex to base has been set
    if (fabs(norm_2(mApexToBase)) < DBL_EPSILON)
    {
        EXCEPTION("Apex to base vector has not been set");
    }

    // Compute wall thickness parameter
    unsigned num_nodes = mrMesh.GetNumNodes();
    std::vector<double> wall_thickness(num_nodes);
    for (unsigned node_index=0; node_index<num_nodes; node_index++)
    {
        double dist_epi, dist_endo;

        HeartRegionType node_region = mpGeometryInfo->GetHeartRegion(node_index);

        switch(node_region)
        {
            case HeartGeometryInformation<SPACE_DIM>::LEFT_VENTRICLE_SURFACE:
            case HeartGeometryInformation<SPACE_DIM>::LEFT_VENTRICLE_WALL:
                dist_epi = mpGeometryInfo->rGetDistanceMapEpicardium()[node_index];
                dist_endo = mpGeometryInfo->rGetDistanceMapLeftVentricle()[node_index];
                break;

            case HeartGeometryInformation<SPACE_DIM>::RIGHT_VENTRICLE_SURFACE:
            case HeartGeometryInformation<SPACE_DIM>::RIGHT_VENTRICLE_WALL:
                dist_epi = mpGeometryInfo->rGetDistanceMapEpicardium()[node_index];
                dist_endo = mpGeometryInfo->rGetDistanceMapRightVentricle()[node_index];
                break;

            case HeartGeometryInformation<SPACE_DIM>::LEFT_SEPTUM:
                dist_epi = mpGeometryInfo->rGetDistanceMapRightVentricle()[node_index];
                dist_endo = mpGeometryInfo->rGetDistanceMapLeftVentricle()[node_index];
                break;

            case HeartGeometryInformation<SPACE_DIM>::RIGHT_SEPTUM:
                dist_epi = mpGeometryInfo->rGetDistanceMapLeftVentricle()[node_index];
                dist_endo = mpGeometryInfo->rGetDistanceMapRightVentricle()[node_index];
                break;

            case HeartGeometryInformation<SPACE_DIM>::UNKNOWN:
                #define COVERAGE_IGNORE
                std::cerr << "Wrong distances node: " << node_index << "\t"
                          << "Epi " << mpGeometryInfo->rGetDistanceMapEpicardium()[node_index] << "\t"
                          << "RV " << mpGeometryInfo->rGetDistanceMapRightVentricle()[node_index] << "\t"
                          << "LV " << mpGeometryInfo->rGetDistanceMapLeftVentricle()[node_index]
                          << std::endl;

                // Make wall_thickness=0 as in Martin's code
                dist_epi = 1;
                dist_endo = 0;
                break;
                #undef COVERAGE_IGNORE

            default:
                NEVER_REACHED;
        }

        wall_thickness[node_index] = dist_endo / (dist_endo + dist_epi);

        if (std::isnan(wall_thickness[node_index]))
        {
            #define COVERAGE_IGNORE
            /*
             *  A node contained on both epicardium and lv (or rv) surfaces has wall thickness 0/0.
             *  By setting its value to 0 we consider it contained only on the lv (or rv) surface.
             */
            wall_thickness[node_index] = 0;
            #undef COVERAGE_IGNORE
        }

        if (logInfo)
        {
            *p_regions_file << node_region*100 << "\n";
            *p_thickness_file << wall_thickness[node_index] << "\n";
        }
    }

    /*
     *  For each node, average its value of e with the values of all the neighbours
     */
    std::vector<double> my_averaged_wall_thickness(num_nodes);
    std::vector<double> averaged_wall_thickness(num_nodes);
    for (unsigned node_index=0; node_index<num_nodes; node_index++)
    {
        my_averaged_wall_thickness[node_index] = GetAveragedThicknessLocalNode(node_index, wall_thickness);
    }

    //Non-local information appear as zeros in the vector
    MPI_Allreduce(&my_averaged_wall_thickness[0], &averaged_wall_thickness[0], num_nodes,
                  MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
    if (logInfo)
    {
        for (unsigned node_index=0; node_index<num_nodes; node_index++)
        {
             *p_ave_thickness_file << averaged_wall_thickness[node_index] << "\n";
        }

    }

    /*
     *  Compute the gradient of the averaged wall thickness at the centroid of each tetrahedron
     */
    c_vector<double,SPACE_DIM> grad_ave_wall_thickness;

    bool fibre_file_is_open= false;
    for (unsigned element_index=0; element_index<num_elements; element_index++)
    {
        //PRINT_VARIABLE(element_index);
        if (mrMesh.CalculateDesignatedOwnershipOfElement(element_index))
        {
            //PRINT_VARIABLE(element_index);
            //Locally own this element
            //Make sure that writing will proceed
            //The same file is written to by multiple processes, therefore we need
            //this barrier - Barrier happens BEFORE opening and AFTER closing

            PetscTools::Barrier("GenerateOrthotropicFibreOrientation");
            if (fibre_file_is_open != true)
            {
                //Open and append
                p_fibre_file = handler.OpenOutputFile(fibreOrientationFile, std::ios::app);
                fibre_file_is_open=true;
            }


            Element<SPACE_DIM,SPACE_DIM>* p_element = mrMesh.GetElement(element_index);

            /*
             *  The gradient of the averaged thickness at the element is:
             *
             *     grad_ave_wall_thickness[element_index] = ave' * BF * inv(J)
             *
             *  being : ave, averaged thickness values of the nodes defining the element
             *          J,   the Jacobian of the element as defined in class Element.
             *                               (-1 -1 -1)
             *          BF,  basis functions ( 1  0  0)
             *                               ( 0  1  0)
             *                               ( 0  0  1)
             *
             *  Defined as u in Streeter paper
             */

            c_vector<double, SPACE_DIM+1> elem_nodes_ave_thickness;
            double element_averaged_thickness = 0.0;
            c_vector<HeartRegionType, SPACE_DIM+1> elem_nodes_region;

            for (unsigned local_node_index=0; local_node_index<SPACE_DIM+1; local_node_index++)
            {
                // Get node's global index
                unsigned global_node_index = p_element->GetNode(local_node_index)->GetIndex();

                elem_nodes_ave_thickness[local_node_index] = averaged_wall_thickness[global_node_index];
                elem_nodes_region[local_node_index] = mpGeometryInfo->GetHeartRegion(global_node_index);

                // Calculate wall thickness averaged value for the element
                element_averaged_thickness +=  wall_thickness[global_node_index];
            }

            element_averaged_thickness /= SPACE_DIM+1;

            c_matrix<double, SPACE_DIM+1, SPACE_DIM> basis_functions( zero_matrix<double>(4u,3u) );
            basis_functions(0,0) = basis_functions(0,1) = basis_functions(0,2) = -1.0;
            basis_functions(1,0) = basis_functions(2,1) = basis_functions(3,2) =  1.0;

            c_matrix<double, SPACE_DIM+1, SPACE_DIM> temp;
            c_matrix<double, SPACE_DIM, SPACE_DIM> jacobian, inverse_jacobian;
            double jacobian_det;
            mrMesh.GetInverseJacobianForElement(element_index, jacobian, jacobian_det, inverse_jacobian);
            noalias(temp) = prod (basis_functions, inverse_jacobian);
            noalias(grad_ave_wall_thickness) = prod(elem_nodes_ave_thickness, temp);

            grad_ave_wall_thickness /= norm_2(grad_ave_wall_thickness);

            /*
             *   Normal to the gradient (v in Streeter paper) which is then the circumferential direction
             * (it will be the fibre direction after rotation)
             *
             *  Computed as the cross product with the base-apex direction (originally assumed base-apex axis is x). The output vector is not normal,
             * since the angle between them may be != 90, normalise it.
             */
            c_vector<double, SPACE_DIM> fibre_direction = VectorProduct(grad_ave_wall_thickness, mApexToBase);
            fibre_direction /= norm_2(fibre_direction);

            /*
             *  Longitude direction (w in Streeter paper)
             */
            c_vector<double, SPACE_DIM> longitude_direction = VectorProduct(grad_ave_wall_thickness, fibre_direction);

            /*
             *  Compute fibre to v angle: alpha = R*(1-2e)^3
             *
             *    R is the maximum angle between the fibre and the v axis (heart region dependant)
             *    (1 - 2e)^3 scales it by a value in [-1, 1] defining the rotation of the fibre based
             *       on the position in the wall
             */
            double alpha = GetFibreMaxAngle(elem_nodes_region) * SmallPow( (1 - 2*element_averaged_thickness), 3 );

            /*
             *  Apply alpha rotation about the u axis to the orthonormal basis
             *
             *               ( u(1) v(1) w(1) )
             *   (u, v, w) = ( u(2) v(2) w(2) )
             *               ( u(3) v(3) w(3) )
             *
             *  The following matrix defines a rotation about the u axis
             *
             *                 ( 1        0           0      ) (u')
             *   R = (u, v, w) ( 0    cos(alpha) -sin(alpha) ) (v')
             *                 ( 0    sin(alpha)  cos(alpha) ) (w')
             *
             *  The rotated basis is computed like:
             *
             *                                             ( 1        0           0      )
             *  (u, v_r, w_r ) = R * (u, v, w) = (u, v, w) ( 0    cos(alpha) -sin(alpha) )
             *                                             ( 0    sin(alpha)  cos(alpha) )
             *
             *  Which simplifies to:
             *
             *   v_r =  v*cos(alpha) + w*sin(alpha)
             *   w_r = -v*sin(alpha) + w*cos(alpha)
             */
            c_vector<double, SPACE_DIM> rotated_fibre_direction = fibre_direction*cos(alpha) + longitude_direction*sin(alpha);
            c_vector<double, SPACE_DIM> rotated_longitude_direction = -fibre_direction*sin(alpha) + longitude_direction*cos(alpha);


            /*
             * Test the orthonormality of the basis
             */
            assert( fabs(norm_2(rotated_fibre_direction) - 1) < 100*DBL_EPSILON );
            assert( fabs(norm_2(grad_ave_wall_thickness) - 1) < 100*DBL_EPSILON );
            assert( fabs(norm_2(rotated_longitude_direction) - 1) < 100*DBL_EPSILON );

            assert( fabs(inner_prod(rotated_fibre_direction, grad_ave_wall_thickness)) < 100*DBL_EPSILON );
            assert( fabs(inner_prod(rotated_fibre_direction, rotated_longitude_direction)) < 100*DBL_EPSILON);
            assert( fabs(inner_prod(grad_ave_wall_thickness, rotated_longitude_direction)) < 100*DBL_EPSILON);

            /*
             *  Output the direction of the myofibre, the transverse to it in the plane of the myocite laminae and the normal to this laminae (in that order)
             *
             *  See Fig. 1 "Laminar Structure of the Heart: a mathematical model" LeGrice et al. 97
             *
             */
            *p_fibre_file << rotated_fibre_direction[0]     << " " << rotated_fibre_direction[1]     << " "  << rotated_fibre_direction[2]     << " "
                          << grad_ave_wall_thickness[0]     << " " << grad_ave_wall_thickness[1]     << " "  << grad_ave_wall_thickness[2]     << " "
                          << rotated_longitude_direction[0] << " " << rotated_longitude_direction[1] << " "  << rotated_longitude_direction[2] << std::endl;
        }
        else
        {
            //We don't locally own this element
            //Give up the file pointer
            if (fibre_file_is_open)
            {
                p_fibre_file->close();
                fibre_file_is_open=false;
            }
            PetscTools::Barrier("GenerateOrthotropicFibreOrientation");

        }
    }

    if (fibre_file_is_open)
    {
        p_fibre_file->close();
    }

    if (logInfo)
    {
        p_regions_file->close();
        p_thickness_file->close();
        p_ave_thickness_file->close();
    }

}


template<unsigned SPACE_DIM>
void StreeterFibreGenerator<SPACE_DIM>::SetApexToBase(const c_vector<double, SPACE_DIM>& apexToBase)
{
    double norm = norm_2(apexToBase);
    if (norm < DBL_EPSILON)
    {
        EXCEPTION("Apex to base vector should be non-zero");
    }
    mApexToBase = apexToBase / norm;
}
template<unsigned SPACE_DIM>
void StreeterFibreGenerator<SPACE_DIM>::SetApexToBase(unsigned axis)
{
    if (axis >= SPACE_DIM)
    {
        EXCEPTION("Apex to base coordinate axis was out of range");
    }
    mApexToBase = zero_vector<double>(SPACE_DIM);
    mApexToBase[axis] = 1.0;
}

// Explicit instantiation
#define COVERAGE_IGNORE
template class StreeterFibreGenerator<3>;
#undef COVERAGE_IGNORE