cell_split/Wortel.cpp

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/*
 * Copyright 2011-2016 Universiteit Antwerpen
 *
 * Licensed under the EUPL, Version 1.1 or  as soon they will be approved by
 * the European Commission - subsequent versions of the EUPL (the "Licence");
 * You may not use this work except in compliance with the Licence.
 * You may obtain a copy of the Licence at: http://ec.europa.eu/idabc/eupl5
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the Licence is distributed on an "AS IS" basis,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the Licence for the specific language governing
 * permissions and limitations under the Licence.
 */
#include "Wortel.h"

#include "bio/Cell.h"
#include "math/RandomEngine.h"

#include <trng/uniform01_dist.hpp>
#include <cmath>
#include <iostream>

namespace SimPT_Default {
namespace CellSplit {

using namespace std;
using namespace boost::property_tree;

Wortel::Wortel(const CoreData& cd)
{
        Initialize(cd);
}

void Wortel::Initialize(const CoreData& cd)
{
        m_cd = cd;
        const trng::uniform01_dist<double> dist;
        m_uniform_generator = m_cd.m_random_engine->GetGenerator(dist);

        const auto& p            = m_cd.m_parameters;
        m_ga_threshold           = p->get<double>("wortel.ga_threshold");
        m_shy2_threshold         = p->get<double>("wortel.shy2_threshold");
        //m_cell_base_area       = p->get<double>("cell_mechanics.base_area");
        //m_division_ratio       = p->get<double>("cell_mechanics.division_ratio");
        m_fixed_division_axis  = p->get<bool>("cell_mechanics.fixed_division_axis", false);

        //m_div_area             = m_division_ratio * m_cell_base_area;
}

std::tuple<bool, bool, std::array<double, 3>> Wortel::operator()(Cell* cell)
{
        const double chem2      = cell->GetChemical(2);
        const double chem3      = cell->GetChemical(3);
        const int celltype      = cell->GetCellType();
        const double a_area     = cell->GetArea();
        bool must_divide        = false;

        double time_now = m_cd.m_time_data->m_sim_time;
        double time_start = 0;//DDV: How fetch from xml file?

        if (cell->GetBoundaryType() == BoundaryType::None) {
                double CCnoise = 1 + (m_uniform_generator() - 0.5) / 5;

                if ( cell->GetIndex() > 60 ) {
                        if ( (( chem2 / a_area ) < m_shy2_threshold) && (( chem3 / a_area ) >= m_ga_threshold)) {
                                if ( ( celltype > 2 && celltype < 8 ) && ( a_area >= ( 200. * CCnoise) )
                                        // JB: changed 10. to 40. to reflect change in time management
                                        && ( ( time_now - time_start ) >= 40. ) ) {
                                        must_divide = true;
                                }
                                if ( celltype != 0 && ( celltype > 7 || celltype < 3 ) && ( a_area >= ( 400.* CCnoise) )
                                        // JB: changed 10. to 40. to reflect change in time management
                                        && ( ( time_now - time_start ) >= 40.) ) {
                                        must_divide = true;
                                }
                        }
                }
        }

        return std::make_tuple(must_divide, true, array<double, 3> {{1.0, 0.0, 0.0}});

}

} // namespace
} // namespace