CryptStatistics.cpp

/*

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*/
#include "CryptStatistics.hpp"
#include "RandomNumberGenerator.hpp"

bool CellsHeightComparison(const std::pair<CellPtr, double> lhs, const std::pair<CellPtr, double> rhs)
{
    return lhs.second < rhs.second;
}

CryptStatistics::CryptStatistics(MeshBasedCellPopulation<2>& rCrypt)
    : AbstractCryptStatistics(rCrypt)
{
}

std::vector<CellPtr> CryptStatistics::GetCryptSection(double yTop, double xBottom, double xTop, bool periodic)
{
    double crypt_width = mrCrypt.rGetMesh().GetWidth(0);

    // Fill in the default values - in a sequential manner
    if (xBottom == DBL_MAX)
    {
        xBottom = RandomNumberGenerator::Instance()->ranf()*crypt_width;
    }

    if (xTop == DBL_MAX)
    {
        xTop = RandomNumberGenerator::Instance()->ranf()*crypt_width;
    }

    assert(yTop>0.0);
    std::list<std::pair<CellPtr, double> > cells_list; // the second entry is the y value (needed for sorting)

    if (fabs(xTop-xBottom)<0.5*crypt_width)
    {
        // The periodic version isn't needed, ignore even if periodic was set to true
        periodic = false;
    }

    // Loop over cells and add to the store if they are within a cell's radius of the specified line
    for (AbstractCellPopulation<2>::Iterator cell_iter = mrCrypt.Begin();
         cell_iter != mrCrypt.End();
         ++cell_iter)
    {
        if (periodic)
        {
            if (CellIsInSectionPeriodic(xBottom, xTop, yTop, mrCrypt.GetLocationOfCellCentre(*cell_iter)))
            {
                // Set up a pair, equal to (cell,y_val) and insert
                std::pair<CellPtr, double> pair(*cell_iter, mrCrypt.GetLocationOfCellCentre(*cell_iter)[1]);
                cells_list.push_back(pair);
            }
        }
        else
        {
            if (CellIsInSection(xBottom, xTop, yTop, mrCrypt.GetLocationOfCellCentre(*cell_iter)))
            {
                // Set up a pair, equal to (cell,y_val) and insert
                std::pair<CellPtr, double> pair(*cell_iter, mrCrypt.GetLocationOfCellCentre(*cell_iter)[1]);
                cells_list.push_back(pair);
            }
        }
    }

    // Sort the list
    cells_list.sort(CellsHeightComparison);

    // Copy to a vector
    std::vector<CellPtr> ordered_cells;
    for (std::list<std::pair<CellPtr, double> >::iterator iter = cells_list.begin();
         iter!=cells_list.end();
         ++iter)
    {
        ordered_cells.push_back(iter->first);
    }

    return ordered_cells;
}

std::vector<CellPtr> CryptStatistics::GetCryptSectionPeriodic(double yTop, double xBottom, double xTop)
{
   return GetCryptSection(yTop, xBottom, xTop, true);
}
bool CryptStatistics::CellIsInSection(double xBottom, double xTop, double yTop, const c_vector<double,2>& rCellPosition, double widthOfSection)
{
    c_vector<double,2> intercept;

    if (xBottom == xTop)
    {
        intercept[0] = xTop;
        intercept[1] = rCellPosition[1];
    }
    else
    {
        double m = (yTop)/(xTop-xBottom); // gradient of line

        intercept[0] = (m*m*xBottom + rCellPosition[0] + m*rCellPosition[1])/(1+m*m);
        intercept[1] = m*(intercept[0] - xBottom);
    }

    c_vector<double,2> vec_from_A_to_B = mrCrypt.rGetMesh().GetVectorFromAtoB(intercept, rCellPosition);
    double dist = norm_2(vec_from_A_to_B);

    return (dist <= widthOfSection);
}

bool CryptStatistics::CellIsInSectionPeriodic(double xBottom, double xTop, double yTop, const c_vector<double,2>& rCellPosition, double widthOfSection)
{
    bool is_in_section = false;

    c_vector<double,2> intercept;
    double crypt_width = mrCrypt.rGetMesh().GetWidth(0u);

    double m; // gradient of line
    double offset;

    if (xBottom < xTop)
    {
        offset = -crypt_width;
    }
    else
    {
        offset = crypt_width;
    }

    m = (yTop)/(xTop-xBottom+offset); // gradient of line

    // 1st line
    intercept[0] = (m*m*xBottom + rCellPosition[0] + m*rCellPosition[1])/(1+m*m);
    intercept[1] = m*(intercept[0] - xBottom);

    c_vector<double,2> vec_from_A_to_B = mrCrypt.rGetMesh().GetVectorFromAtoB(intercept, rCellPosition);
    double dist = norm_2(vec_from_A_to_B);

    if (dist < widthOfSection)
    {
        is_in_section = true;
    }

    // 2nd line
    intercept[0] = (m*m*(xBottom-offset) + rCellPosition[0] + m*rCellPosition[1])/(1+m*m);
    intercept[1] = m*(intercept[0] - (xBottom-offset));

    vec_from_A_to_B = mrCrypt.rGetMesh().GetVectorFromAtoB(intercept, rCellPosition);
    dist = norm_2(vec_from_A_to_B);

    if (dist < widthOfSection)
    {
        is_in_section = true;
    }

    return is_in_section;
}