source: experiments/frams/foraminifera/data/scripts/foraminifera.inc @ 493

//size versus energy
//real proportions

function init_chambers()
{
        colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
        retColors = ["1.0,1.0,1.0", "1.0,0.0,0.0"];
        chambers = [ ["0.0,0.0,0.0,",  //coiled
        "1.08020961284637, -0.0597195439040661, -0.0393781512975693,",
        "1.08020961284637, -0.0597195439040661, -0.0393781512975693,",
        "0.615013539791107, 0.778662621974945, 0.535521030426025,",
        "0.488581955432892, 0.826426684856415, -0.381044268608093,",
        "0.732419908046722, -0.0084995785728097, -1.02214300632477,",
        "1.35288727283478, 0.875738024711609, -1.03719782829285,",
        "0.342692613601685, 0.938660383224487, -1.45657968521118,",
        "1.0958571434021, 0.316927701234818, -1.813929438591,",
        "0.903768002986908, 1.11856341362, -2.53161096572876,",
        "0.21014116704464, 0.295340299606323, -2.45328187942505,"],
        ["0.0,0.0,0.0,", //longitudal
        "0.98089325428009, 0.00591040402650833, 0.00389722990803421,",
        "1.90962779521942, -0.256769120693207, -0.16194811463356,",
        "2.63965249061584, -0.727959632873535, -0.609036147594452,",
        "3.17575979232788, -1.34843015670776, -1.14828503131866,",
        "3.55273032188416, -2.22369408607483, -1.3917418718338,",
        "3.64916682243347, -3.11888360977173, -1.01666414737701,",
        "3.50461649894714, -3.84039807319641, -0.377427101135254,",
        "3.15921688079834, -4.50001525878906, 0.261153399944305,",
        "2.51528453826904, -5.16421365737915, 0.59241509437561,"]];
}

function createForamMorphology(morphotype, gen, chamber_num)
{
        var rad = getProperty(gen, "chamber_proculus"); 
        var geno = "//0\np:" + chambers[morphotype][0] + "sh=1,sx=" + rad + ",sy=" + rad + ",sz=" + rad + ", rz=3.14159265358979,vr=" + colors[gen];

        chamber_num = Math.min(chamber_num, chambers[morphotype].size - 1);

        for (var i = 0; i < chamber_num; i++)
        {
                rad = getProperty(gen, "chamber_proculus") + getProperty(gen, "chamber_difference") * (i + 1);
                geno += "\n" + "p:" + chambers[morphotype][i+1] + "sh=1,sx=" + rad + ",sy=" + rad + ",sz=" + rad + ",vr=" + colors[gen];
        }

        for (var i = 0; i < chamber_num; i++)
        {
                geno += "\n" +  "j:"+ i +", "+ (i+1) +", sh=1";
        }

        if (morphotype == 0) geno += "\nn:p=0,d=\"S\"";

        return geno;
}

function setGenotype(mode)
{
        if (mode->opt == 0) //initial
        {
                mode->cr.data->genes = String.deserialize(String.serialize(mode->genes)); 
                mode->cr.data->lifeparams = {"max_energy_level" : mode->energy0, "gen" : 0,  "hibernated" : 0, "species" : mode->species, "reproduce" : 0, "dir" : randomDir(), "chamber_growth" : -1, "division_time" : -1};
        }
        else if (mode->opt  == 1) //child
        {
                mode->cr.data->lifeparams = {"max_energy_level" : mode->energy0, "gen" : 1 - mode->parent_lifeparams->gen,  "hibernated" : 0, "species" : mode->parent_lifeparams->species, "reproduce" : 0, "dir" : randomDir(), "chamber_growth" : -1, "division_time" : -1};
                mode->cr.data->genes = String.deserialize(String.serialize(mode->parent_genes));
        }
        else //grow
        {
                mode->cr.data->genes = mode->parent_genes;
                mode->cr.data->lifeparams = mode->parent_lifeparams;
        }
}

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

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");
                }       
        }

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

        for (var j = 0; j < number; j++)
        {
                createOffspring(createForamMorphology(getGene(parent, "morphotype", 0), gen, 0), energy0, new_genes, parent.data->lifeparams); 
        }
}

function reproduce_diploid(parent)
{
        var energy0 =getEnergy0( getGene(parent,"energies0", 0)[0]); 
        var number = ((1 - (getProperty(parent.data->lifeparams->gen, "e_repro_cost"))) * parent.energy) / energy0;

                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");
                }       

        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(createForamMorphology(getGene(parent, "morphotype", 0), 1 - parent.data->lifeparams->gen, 0), energy0, parent.data->genes[0], parent.data->lifeparams); 
                }

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

function foramReproduce(cr)
{
        var properEnergy = cr.energy >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][getGene(cr, "min_repro_energies",0)[cr.data->lifeparams->gen]],0);
        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)
{
        curColor = retColors[1-parent_lifeparams->gen];
        var cr = Populations[0].add(geno);
        cr.energy0 = energy;
        cr.energy = cr.energy0;
        setGenotype({"cr" : cr, "parent_genes" : parent_genes, "parent_lifeparams" : parent_lifeparams, "opt" : 1, "energy0" : cr.energy0});
        placeRandomlyNotColliding(cr);
}