HeterotypicBoundaryLengthWriter.cpp

/*

Copyright (c) 2005-2017, University of Oxford.
All rights reserved.

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#include "HeterotypicBoundaryLengthWriter.hpp"

#include "AbstractCellPopulation.hpp"
#include "MeshBasedCellPopulation.hpp"
#include "CaBasedCellPopulation.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "PottsBasedCellPopulation.hpp"
#include "VertexBasedCellPopulation.hpp"

#include "CellLabel.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
HeterotypicBoundaryLengthWriter<ELEMENT_DIM, SPACE_DIM>::HeterotypicBoundaryLengthWriter()
    : AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM>("heterotypicboundary.dat")
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void HeterotypicBoundaryLengthWriter<ELEMENT_DIM, SPACE_DIM>::Visit(MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
{
    // Initialise helper variables
    double heterotypic_boundary_length = 0.0;
    double total_shared_edges_length = 0.0;
    double num_heterotypic_pairs = 0.0;
    double total_num_pairs = 0.0;

    // Make sure the Voronoi tessellation has been created
    pCellPopulation->CreateVoronoiTessellation();

    // Iterate over cells
    for (typename AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator cell_iter = pCellPopulation->Begin();
         cell_iter != pCellPopulation->End();
         ++cell_iter)
    {
        // Get the location index corresponding to this cell
        unsigned index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);

        // Store whether this cell is labelled
        bool cell_is_labelled = cell_iter->template HasCellProperty<CellLabel>();

        // Get the set of neighbouring location indices
        std::set<unsigned> neighbour_indices = pCellPopulation->GetNeighbouringNodeIndices(index);

        // Iterate over these neighbours
        for (std::set<unsigned>::iterator neighbour_iter = neighbour_indices.begin();
             neighbour_iter != neighbour_indices.end();
             ++neighbour_iter)
        {
            // Get the length of the edge shared with this neighbour
            unsigned neighbour_index = *neighbour_iter;
            double edge_length = pCellPopulation->GetVoronoiEdgeLength(index,neighbour_index);

            // Ignore ghost nodes (in the case of a MeshBasedCellPopulationWithGhostNodes)
            if (!pCellPopulation->IsGhostNode(neighbour_index))
            {
                total_shared_edges_length += edge_length;
                total_num_pairs += 1.0;

                // Store whether this neighbour is labelled
                CellPtr p_neighbour_cell = pCellPopulation->GetCellUsingLocationIndex(neighbour_index);
                bool neighbour_is_labelled = p_neighbour_cell->template HasCellProperty<CellLabel>();

                // If this cell is labelled and its neighbour is not, or vice versa...
                if (cell_is_labelled != neighbour_is_labelled)
                {
                    // ... then increment the fractional boundary length
                    heterotypic_boundary_length += edge_length;
                    num_heterotypic_pairs += 1.0;
                }
            }
        }
    }

    // We have counted each cell-cell edge twice
    heterotypic_boundary_length *= 0.5;
    total_shared_edges_length *= 0.5;

    // We have counted each pair of neighbouring cells twice
    num_heterotypic_pairs *= 0.5;
    total_num_pairs *= 0.5;

    *this->mpOutStream << heterotypic_boundary_length << "\t" << total_shared_edges_length << "\t" << num_heterotypic_pairs << "\t" << total_num_pairs;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void HeterotypicBoundaryLengthWriter<ELEMENT_DIM, SPACE_DIM>::Visit(CaBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{
    // Initialise helper variables
    double heterotypic_boundary_length = 0.0;
    double total_shared_edges_length = 0.0;
    double num_heterotypic_pairs = 0.0;
    double total_num_pairs = 0.0;

    // Iterate over cells
    for (typename AbstractCellPopulation<SPACE_DIM>::Iterator cell_iter = pCellPopulation->Begin();
         cell_iter != pCellPopulation->End();
         ++cell_iter)
    {
        // Get the location index corresponding to this cell
        unsigned index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);

        // Store whether this cell is labelled
        bool cell_is_labelled = cell_iter->template HasCellProperty<CellLabel>();

        // Get this node's von Neumann neighbours (not Moore neighbours, since they must share an edge)
        std::set<unsigned> neighbour_node_indices = pCellPopulation->rGetMesh().GetVonNeumannNeighbouringNodeIndices(index);

        // Iterate over these neighbours
        for (std::set<unsigned>::iterator neighbour_iter = neighbour_node_indices.begin();
             neighbour_iter != neighbour_node_indices.end();
             ++neighbour_iter)
        {
            // Assume the lattice is comprised of uniform unit lattice sites
            double edge_length = 1.0;

            unsigned neighbour_index = *neighbour_iter;

            if (pCellPopulation->IsCellAttachedToLocationIndex(neighbour_index))
            {
                CellPtr p_neighbour_cell = pCellPopulation->GetCellUsingLocationIndex(neighbour_index);

                total_shared_edges_length += edge_length;
                total_num_pairs += 1.0;

                // Store whether this neighbour is labelled
                bool neighbour_is_labelled = p_neighbour_cell->template HasCellProperty<CellLabel>();

                // If this cell is labelled and its neighbour is not, or vice versa...
                if (cell_is_labelled != neighbour_is_labelled)
                {
                    // ... then increment the fractional boundary length
                    heterotypic_boundary_length += edge_length;
                    num_heterotypic_pairs += 1.0;
                }
            }
        }
    }

    // We have counted each cell-cell edge twice
    heterotypic_boundary_length *= 0.5;
    total_shared_edges_length *= 0.5;

    // We have counted each pair of neighbouring cells twice
    num_heterotypic_pairs *= 0.5;
    total_num_pairs *= 0.5;

    *this->mpOutStream << heterotypic_boundary_length << "\t" << total_shared_edges_length << "\t" << num_heterotypic_pairs << "\t" << total_num_pairs;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void HeterotypicBoundaryLengthWriter<ELEMENT_DIM, SPACE_DIM>::Visit(NodeBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{
    // Make sure the cell population is updated so that mNodeNeighbours is set up
    pCellPopulation->Update();

    // Initialise helper variables
    double heterotypic_boundary_length = 0.0;
    double total_shared_edges_length = 0.0;
    double num_heterotypic_pairs = 0.0;
    double total_num_pairs = 0.0;

    // Loop over cells
    for (typename AbstractCellPopulation<SPACE_DIM>::Iterator cell_iter = pCellPopulation->Begin();
         cell_iter != pCellPopulation->End();
         ++cell_iter)
    {
        // Store whether this cell is labelled
        bool cell_is_labelled = cell_iter->template HasCellProperty<CellLabel>();

        // Store the radius of the node corresponding to this cell
        unsigned node_index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);
        double node_radius = pCellPopulation->GetNode(node_index)->GetRadius();

        // Get the set of neighbouring node indices
        std::set<unsigned> neighbour_indices = pCellPopulation->GetNeighbouringNodeIndices(node_index);

        if (!neighbour_indices.empty())
        {
            // Iterate over these neighbours
            for (std::set<unsigned>::iterator neighbour_iter = neighbour_indices.begin();
                 neighbour_iter != neighbour_indices.end();
                 ++neighbour_iter)
            {
                // Store the radius of the node corresponding to this neighbour
                double neighbour_radius = pCellPopulation->GetNode(*neighbour_iter)->GetRadius();

                // Get the (approximate) length of the edge shared with this neighbour
                double separation = pCellPopulation->rGetMesh().GetDistanceBetweenNodes(node_index, *neighbour_iter);
                double sum_of_radii = node_radius + neighbour_radius;

                // If the neighbours are close enough, then approximate their 'edge length'
                if (separation < sum_of_radii)
                {
                    // Use Heron's formula to compute the edge length
                    double a = node_radius;
                    double b = neighbour_radius;
                    double c = separation;
                    double s = 0.5*(a + b + c);
                    double A = sqrt(s*(s-a)*(s-b)*(s-c));
                    double edge_length = 4.0*A/c;

                    total_shared_edges_length += edge_length;
                    total_num_pairs += 1.0;

                    // Store whether this neighbour is labelled
                    CellPtr p_neighbour_cell = pCellPopulation->GetCellUsingLocationIndex(*neighbour_iter);
                    bool neighbour_is_labelled = p_neighbour_cell->template HasCellProperty<CellLabel>();

                    // If this cell is labelled and its neighbour is not, or vice versa...
                    if (cell_is_labelled != neighbour_is_labelled)
                    {
                        // ... then increment the fractional boundary length
                        heterotypic_boundary_length += edge_length;
                        num_heterotypic_pairs += 1.0;
                    }
                }
            }
        }
    }

    // We have counted each cell-cell edge twice
    heterotypic_boundary_length *= 0.5;
    total_shared_edges_length *= 0.5;

    // We have counted each pair of neighbouring cells twice
    num_heterotypic_pairs *= 0.5;
    total_num_pairs *= 0.5;

    *this->mpOutStream << heterotypic_boundary_length << "\t" << total_shared_edges_length << "\t" << num_heterotypic_pairs << "\t" << total_num_pairs;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void HeterotypicBoundaryLengthWriter<ELEMENT_DIM, SPACE_DIM>::Visit(PottsBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{

    // Initialise helper variables
    double heterotypic_boundary_length = 0.0;
    double total_shared_edges_length = 0.0;
    double num_heterotypic_pairs = 0.0;
    double total_num_pairs = 0.0;

    // Iterate over cells
    for (typename AbstractCellPopulation<SPACE_DIM>::Iterator cell_iter = pCellPopulation->Begin();
         cell_iter != pCellPopulation->End();
         ++cell_iter)
    {
        // Store whether this cell is labelled
        bool cell_is_labelled = cell_iter->template HasCellProperty<CellLabel>();

        unsigned elem_index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);
        unsigned num_nodes_in_elem = pCellPopulation->rGetMesh().GetElement(elem_index)->GetNumNodes();

        // Iterate over nodes contained in the element corresponding to this cell
        for (unsigned local_index=0; local_index<num_nodes_in_elem; local_index++)
        {
            // Get this node's von Neumann neighbours (not Moore neighbours, since they must share an edge)
            unsigned global_index = pCellPopulation->rGetMesh().GetElement(elem_index)->GetNodeGlobalIndex(local_index);
            std::set<unsigned> neighbour_node_indices = pCellPopulation->rGetMesh().GetVonNeumannNeighbouringNodeIndices(global_index);

            // Iterate over these neighbours
            for (std::set<unsigned>::iterator neighbour_iter = neighbour_node_indices.begin();
                 neighbour_iter != neighbour_node_indices.end();
                 ++neighbour_iter)
            {
                // Get the elements containing this neighbour
                std::set<unsigned> neighbour_elem_indices = pCellPopulation->GetNode(*neighbour_iter)->rGetContainingElementIndices();

                if (neighbour_elem_indices.size() == 1)
                {
                    unsigned neigbour_elem_index = *(neighbour_elem_indices.begin());

                    if (neigbour_elem_index != elem_index)
                    {
                        // Edge is between two different elements
                        total_shared_edges_length += 1.0;

                        // Store whether the cell corresponding to this element index is labelled
                        CellPtr p_neighbour_cell = pCellPopulation->GetCellUsingLocationIndex(neigbour_elem_index);
                        bool neighbour_is_labelled = p_neighbour_cell->template HasCellProperty<CellLabel>();

                        // If this cell is labelled and its neighbour is not, or vice versa...
                        if (cell_is_labelled != neighbour_is_labelled)
                        {
                            // ... then increment the fractional boundary length
                            heterotypic_boundary_length += 1.0;
                        }
                    }
                }
                else
                {
                    // Original node is on boundary of mesh so don't include in the edge calculation.
                }
            }
        }

        std::set<unsigned> neighbour_node_indices = pCellPopulation->GetNeighbouringLocationIndices(*cell_iter);

        // Iterate over these neighbours
        for (std::set<unsigned>::iterator neighbour_iter = neighbour_node_indices.begin();
             neighbour_iter != neighbour_node_indices.end();
             ++neighbour_iter)
        {
            total_num_pairs += 1.0;

            CellPtr p_neighbour_cell = pCellPopulation->GetCellUsingLocationIndex(*neighbour_iter);
            bool neighbour_is_labelled = p_neighbour_cell->template HasCellProperty<CellLabel>();

            // If this cell is labelled and its neighbour is not, or vice versa...
            if (cell_is_labelled != neighbour_is_labelled)
            {
                // ... then increment the fractional boundary length
                num_heterotypic_pairs += 1.0;
            }
        }
    }

    // We have counted each cell-cell edge twice
    heterotypic_boundary_length *= 0.5;
    total_shared_edges_length *= 0.5;

    // We have counted each pair of neighbouring cells twice
    num_heterotypic_pairs *= 0.5;
    total_num_pairs *= 0.5;

    *this->mpOutStream << heterotypic_boundary_length << "\t" << total_shared_edges_length << "\t" << num_heterotypic_pairs << "\t" << total_num_pairs;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void HeterotypicBoundaryLengthWriter<ELEMENT_DIM, SPACE_DIM>::Visit(VertexBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{
    // Make sure the cell population is updated
    pCellPopulation->Update();

    // Initialise helper variables
    double heterotypic_boundary_length = 0.0;
    double total_shared_edges_length = 0.0;
    double num_heterotypic_pairs = 0.0;
    double total_num_pairs = 0.0;

    // Iterate over cells
    for (typename AbstractCellPopulation<SPACE_DIM>::Iterator cell_iter = pCellPopulation->Begin();
         cell_iter != pCellPopulation->End();
         ++cell_iter)
    {
        // Store whether this cell is labelled
        bool cell_is_labelled = cell_iter->template HasCellProperty<CellLabel>();

        // Get the set of neighbouring element indices
        unsigned elem_index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);
        std::set<unsigned> neighbour_elem_indices = pCellPopulation->rGetMesh().GetNeighbouringElementIndices(elem_index);

        // Iterate over these neighbours
        for (std::set<unsigned>::iterator neighbour_iter = neighbour_elem_indices.begin();
             neighbour_iter != neighbour_elem_indices.end();
             ++neighbour_iter)
        {
            // Get the length of the edge shared with this neighbour
            unsigned neighbour_index = *neighbour_iter;
            double edge_length = pCellPopulation->rGetMesh().GetEdgeLength(elem_index, neighbour_index);

            total_shared_edges_length += edge_length;
            total_num_pairs += 1.0;

            // Store whether this neighbour is labelled
            CellPtr p_neighbour_cell = pCellPopulation->GetCellUsingLocationIndex(*neighbour_iter);
            bool neighbour_is_labelled = p_neighbour_cell->template HasCellProperty<CellLabel>();

            // If this cell is labelled and its neighbour is not, or vice versa...
            if (cell_is_labelled != neighbour_is_labelled)
            {
                // ... then increment the fractional boundary length
                heterotypic_boundary_length += edge_length;
                num_heterotypic_pairs += 1.0;
            }
        }
    }

    // We have counted each cell-cell edge twice
    heterotypic_boundary_length *= 0.5;
    total_shared_edges_length *= 0.5;

    // We have counted each pair of neighbouring cells twice
    num_heterotypic_pairs *= 0.5;
    total_num_pairs *= 0.5;

    *this->mpOutStream << heterotypic_boundary_length << "\t" << total_shared_edges_length << "\t" << num_heterotypic_pairs << "\t" << total_num_pairs;
}

// Explicit instantiation
template class HeterotypicBoundaryLengthWriter<1,1>;
template class HeterotypicBoundaryLengthWriter<1,2>;
template class HeterotypicBoundaryLengthWriter<2,2>;
template class HeterotypicBoundaryLengthWriter<1,3>;
template class HeterotypicBoundaryLengthWriter<2,3>;
template class HeterotypicBoundaryLengthWriter<3,3>;

#include "SerializationExportWrapperForCpp.hpp"
// Declare identifier for the serializer
EXPORT_TEMPLATE_CLASS_ALL_DIMS(HeterotypicBoundaryLengthWriter)