source: experiments/frams/foraminifera/data/scripts/foraminifera.inc @ 567

function create_genotype(proculus_size, number_of_chambers, rgbstring, lastchambergrowth) //lastchambergrowth is 0..1
{
        const shift=0.7;
        const angle_delta=0.8;
        const angle_delta_delta=-0.01;
        const growing=1.07; //7% growth
        
        var str="//0\n";
        var size=proculus_size;
        for(var i=0;i<number_of_chambers;i++)
        {
                var effectivesize=size; //'effectivesize' is introduced only to consider the last chamber
                if (i==number_of_chambers-1)
                {
                        effectivesize*=lastchambergrowth;
                        size=size*(1.35-0.35*lastchambergrowth); //last iteration: 'size' is only used for shifting (dx). The last chamber emerges at the surface of the previous one
                }
                str += "p:sh=1,sx=%g,sy=%g,sz=%g,rz=3.14159265358979,vr=%s\n" % effectivesize % effectivesize % effectivesize % rgbstring;
                if (i>0)
                        str+="j:%d,%d,sh=1,dx=%g,rz=%g\n" % (i-1) % i % (size*shift) % (angle_delta+i*angle_delta_delta);
                size*=growing;
        }
        return str;
}

function setGenotype(mode)
{
        if (mode->opt == "growth")
        {
                mode->cr.data->genes = mode->parent_genes;
                mode->cr.data->lifeparams = mode->parent_lifeparams;
        }

        else if (mode->opt == "birth")
        {
                foram_uid += 1;
                var new_id = "c"+string(foram_uid);
                mode->cr.data->genes = String.deserialize(String.serialize(mode->genes));
                mode->cr.data->lifeparams = {"max_energy_level" : mode->energy0, "gen" : mode->gen,  "hibernated" : 0, "species" : mode->species, "reproduce" : 0, "dir" : randomDir(), "dir_counter" : Math.random(int(secToSimSteps(ExpProperties.dir_change_sec))), "chamber_growth" : -1, "division_time" : -1, "uid" : new_id};    

                var oper = "cloning";
                if (mode->parentsuids.size > 1)
                {       
                        oper = "cross-over";
                }
                
                var dict={"Time":Simulator.stepNumber,"FromIDs":mode->parentsuids,"ID":new_id, "Inherited":[1.0], "Operation": oper, "Kind" : mode->gen};
                Simulator.print("[OFFSPRING] " + String.serialize(dict));               
        }
}

function getEnergy0(radius)
{
        return energyFromVolume(micronsToFrams(radius),1);
}

function gametsDivision(parent_energy, energy0)
{
        var number = 1;
        var result = parent_energy;
        while ((result-ExpProperties.divisionCost) >= energy0)
        {
                result = (result-ExpProperties.divisionCost)/2;
                number *= 2;
        }
        //Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number);
        return {"energy" : result, "number" : number};
}

function reproduce_haploid(parent, parent2, clone)
{       
        var number, energy0, new_genes, gen;
        if (clone == 1)
        {
                var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0",0)[0])); 
                energy0 = offspring->energy;
                number = offspring->number;
                new_genes = parent.data->genes;
                parent.data->lifeparams->gen = 1 - parent.data->lifeparams->gen; //because of reversal of "gen" in createOffspring function
                gen = parent.data->lifeparams->gen;
        }
        else
        {
                var offspring1 = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[1])); 
                var offspring2 = gametsDivision(parent2.energy,getEnergy0(getGene(parent2,"energies0", 0)[1])); 
                energy0 = (offspring1->energy+offspring2->energy); 
                number = ExpProperties.gametSuccessRate*(offspring1->number+offspring2->number)/2;
                new_genes = [parent.data->genes, parent2.data->genes];
                gen = 1 - parent.data->lifeparams->gen;

                if (ExpProperties.logging == 1)
                {
                                log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
                                log(createLogVector(parent2, parent2.energy),ExpProperties.logPref+"repro_energies_log.txt");
                                log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
                                log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
                                log(createLogVector(parent2, parent2.lifespan),ExpProperties.logPref+"lifespan_log.txt");
                }       
        }

        //Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0);

        for (var j = 0; j < number; j++)
        {
                createOffspring(create_genotype(ExpProperties.chamber_proculus_diplo, 1, colors[1], 1), energy0, new_genes, parent.data->lifeparams, [parent.data->lifeparams->uid, parent2.data->lifeparams->uid]);
        }
}

function reproduce_diploid(parent)
{
        var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[0]));
        var energy0 = offspring->energy; 
        var number = offspring->number;

                if (ExpProperties.logging == 1)
                {
                        log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
                        log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
                        log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
                }       

        //Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);

        for (var j = 0; j < number / 2; j++)
        {
                var crossed = 0;
                //crossover
                if (Math.rnd01 < ExpProperties.crossprob)
                {
                        crossover(parent, "min_repro_energies");
                        crossed = 1;
                }

                for (var k = 0; k < 2; k++)
                {
                        createOffspring(create_genotype(ExpProperties.chamber_proculus_haplo, 1, colors[0], 1), energy0, parent.data->genes[0], parent.data->lifeparams, [parent.data->lifeparams->uid]); 
                }

                //reverse of crossover for fossilization
                if (crossed == 1)
                {
                        crossover(parent, "min_repro_energies");
                        crossed = 0;
                }
                        
        }
}

function reproduce_parents(species)
{
                var parent1 = null;
                var parent2 = null;
                var pop = Populations[0];
                for (var i = pop.size-1; i >= 0; i--)
                {
                        if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species) 
                        { 
                                if ((pop[i].data->lifeparams->gen==1) || ((pop[i].data->lifeparams->gen==0) && ExpProperties.stress == 0))
                                {
                                        continue;
                                }
                                else if (parent1 == null)
                                {
                                        parent1 = pop[i];
                                }
                                else if (parent2 == null)
                                {
                                        parent2 = pop[i];
                                }  
                                if (parent1 != null && parent2 != null)
                                {
                                        //when parents are ready for reproduction start gametogenesis
                                        if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1)
                                        {
                                                var time = int(secToSimSteps(ExpProperties.gametoPeriodSec));
                                                parent1.data->lifeparams->division_time = time;
                                                parent2.data->lifeparams->division_time = time;
                                                parent1.idleen = 0;
                                                parent2.idleen = 0;
                                                //Simulator.print("parents "+parent1.uid + " " + parent2.uid + " ready to repro: "+Simulator.stepNumber);
                                        }
                                        //when gametogenesis is finished fuse gamets 
                                        else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0)
                                        {
                                                reproduce_haploid(parent1, parent2, 0);
                                                //print_repro_info(parent1);
                                                //print_repro_info(parent2);
                                                pop.kill(parent1);
                                                pop.kill(parent2);
                                                parent1 = null;
                                                parent2 = null;
                                        }
                                }       
                        } 
                }
}

function readyToRepro(cr)
{
        var reproduced = 1;

        if (cr.data->lifeparams->gen == 1)
        {
                reproduce_diploid(cr);
        }

        else if (ExpProperties.stress == 0)
        {
                reproduce_haploid(cr, null, 1);
        }

        else
        {
                if (cr.signals.size == 0)
                {
                        cr.signals.add("repro"+cr.data->lifeparams->species);
                        cr.signals[0].power = 1;
                }
                reproduced = 0;
                cr.data->lifeparams->reproduce = 1;
        }

        if (reproduced == 1)
        {
                //print_repro_info(cr);
                Populations[0].kill(cr);
        }

        return reproduced;
}

function foramReproduce(cr)
{
        var properEnergy = cr.energy >= getGene(cr, "min_repro_energies",0)[cr.data->lifeparams->gen];
        var reproduced = 0;     

        //if creature has proper energy
        if ( properEnergy && cr.signals.size == 0)
        {
                //reproduce with probability repro_prob
                if (Math.rnd01 <= ExpProperties.repro_prob) //TODO env trigger
                {
                        reproduced = readyToRepro(cr);
                }
                else if (cr.signals.receive("repro"+cr.data->lifeparams->species) > 0)
                {
                        reproduced = readyToRepro(cr);
                }
                if (reproduced == 1)
                                return 1;
        }

        else if (!properEnergy)
        {
                cr.signals.clear();
                cr.data->lifeparams->reproduce = 0; 
        }

        return 0;
}

function crossover(parent, gene)
{
        var tmp = parent.data->genes[0][gene];
        parent.data->genes[0][gene] = parent.data->genes[1][gene];
        parent.data->genes[1][gene] = tmp;
}

function createOffspring(geno, energy, parent_genes, parent_lifeparams, parentsuids)
{
        curColor = retColors[1-parent_lifeparams->gen];
        var cr = Populations[0].add(geno);
        cr.energy0 = energy;
        cr.energy = cr.energy0;
        setGenotype({"opt" : "birth", "cr" : cr, "gen" : 1 - parent_lifeparams->gen, "species" : parent_lifeparams->species, "energy0" : cr.energy0, "genes" : parent_genes, "parentsuids" : parentsuids});
        placeRandomlyNotColliding(cr);
}

function print_repro_info(cr)
{
        Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy);
}