PluginGrimesOxygen.hpp

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#ifndef PLUGINGRIMESOXYGEN_HPP
#define PLUGINGRIMESOXYGEN_HPP
 
#include <vector>
#include <mecacell/mecacell.h>
#include "../SpheroidManager/PluginSpheroidManager.hpp"
#include <math.h>
 
namespace GrimesOxygen {
 
    template<typename cell_t>
    class PluginGrimesOxygen {
 
    private:
        double a = 5.634224/10.0; 
        double omega = 10.0*3.0318; 
        double D = 2000.0; 
        double po = 37.50319; 
        SpheroidManager::PluginSpheroidManager<cell_t> *spheroidManager = nullptr;
 
        void updateOxygen(std::vector<cell_t*> cells) {
            double rl = sqrt(6. * D * po / (a * omega)); // Limit radius in µm
            double rn = 0; // Necrotic radius in µm
            double cstConsoDiff = a * omega / (6. * D); // in mmHg/µm^2
            if (spheroidManager->getSpheroidRadius() > rl)
                rn = (spheroidManager->getSpheroidRadius() * (1.0f / 2.0f - cos((acos(1.0f - 2.0f * pow(rl, 2) / pow(spheroidManager->getSpheroidRadius(), 2)) - 2.0f * M_PI) / 3.0f)));
 
            for (auto &c : cells) {
                c->getBody().setOxygen(eqOxygen(cstConsoDiff, rn, c->getBody().getDistanceFromCentroid()));
            }
        }
 
        double eqOxygen(double cstConsoDiff, double rn, double r) {
            double pr = 0;
            if (r < rn) {
                return 0.0;
            } else if (r >= spheroidManager->getSpheroidRadius()) {
                return po;
            } else {
                if (r == 0)
                    pr = po + cstConsoDiff * (pow(r, 2) - pow(spheroidManager->getSpheroidRadius(), 2));
                else
                    pr = po + cstConsoDiff * (pow(r, 2) - pow(spheroidManager->getSpheroidRadius(), 2) + 2.0f * pow(rn, 3) * ((1 / r) - (1 / spheroidManager->getSpheroidRadius())));
                if (pr >= 0)
                    return pr;
                else
                    return 0.0;
            }
        }
 
    public:
        inline PluginGrimesOxygen() = default;
 
        inline PluginGrimesOxygen(SpheroidManager::PluginSpheroidManager<cell_t> *sm) : spheroidManager(sm) {}
 
        inline void setPo(double p) { po = p; }
 
        inline void setOxygenConsumption(double c) { a = c; }
 
        inline void setDiffusionConstant(double d) { D = d; }
 
        inline void setOmega(double om) { omega = om; }
 
        template<typename world_t>
        void preBehaviorUpdate(world_t *w) {
            if(!spheroidManager) spheroidManager = &w->cellPlugin.pluginSpheroidManager;
            if (w->cells.size() > 5) {
                updateOxygen(w->cells);
            }
        }
    };
}
 
#endif // PLUGINGRIMESOXYGEN_HPP