CryptStatistics.cpp

/*

Copyright (C) University of Oxford, 2005-2009

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.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#include "CryptStatistics.hpp"

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

/*
 * PRIVATE FUNCTIONS -----------------------------------------------------------------
 */

bool CryptStatistics::CellIsInSection(double xBottom, double xTop, double yTop, const c_vector<double,2>& cellPosition, double widthOfSection)
{
    c_vector<double,2> intercept;

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

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

    c_vector<double,2> vec_from_A_to_B = mrCrypt.rGetMesh().GetVectorFromAtoB(intercept, cellPosition);
    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>& cellPosition, double widthOfSection)
{
    bool is_in_section=false;

    c_vector<double,2> intercept;
    double crypt_width = CancerParameters::Instance()->GetCryptWidth();

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

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

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

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

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

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

    return is_in_section;
}

/*
 * PUBLIC FUNCTIONS -----------------------------------------------------------------
 */
std::vector<TissueCell*> CryptStatistics::GetCryptSection(double xBottom, double xTop, double yTop, bool periodic)
{
    //Fill in the default values - in a sequential manner
    if (xBottom == DBL_MAX)
    {
        xBottom = RandomNumberGenerator::Instance()->ranf()*CancerParameters::Instance()->GetCryptWidth();
    }

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


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

    if (fabs(xTop-xBottom)<0.5*CancerParameters::Instance()->GetCryptWidth())
    {
        // 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 (AbstractTissue<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<TissueCell*, 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<TissueCell*, 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<TissueCell*> ordered_cells;
    for (std::list<std::pair<TissueCell*, double> >::iterator iter = cells_list.begin();
        iter!=cells_list.end();
        iter++)
    {
        ordered_cells.push_back(iter->first);
    }

    return ordered_cells;
}

std::vector<TissueCell*> CryptStatistics::GetCryptSectionPeriodic(double xBottom, double xTop, double yTop)
{
   return GetCryptSection(xBottom,xTop,yTop,true);
}

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