source: experiments/frams/foraminifera/data/scripts/foraminifera.inc @ 559

Last change on this file since 559 was 559, checked in by Maciej Komosinski, 8 years ago

Foram genotype generator can produce genotypes with the last chamber smaller ("growing" from 0 to 1)

File size: 11.1 KB
RevLine 
[401]1
[559]2function create_genotype(proculus_size, number_of_chambers, rgbstring, lastchambergrowth) //lastchambergrowth is 0..1
[557]3{
[558]4        const shift=0.7;
5        const angle_delta=0.8;
6        const angle_delta_delta=-0.015;
[557]7        const growing=1.05;
8       
9        var str="//0\n";
10        var size=proculus_size;
11        for(var i=0;i<number_of_chambers;i++)
12        {
[559]13                var effectivesize=size; //'effectivesize' is introduced only to consider the last chamber
14                if (i==number_of_chambers-1)
15                {
16                        effectivesize*=lastchambergrowth;
17                        size=size*(1.35-0.35*lastchambergrowth); //last interation: 'size' is only used for shifting (dx). The last chamber emerges at the surface of the previous one
18                }
19                str+="p:sh=1,sx=%g,sy=%g,sz=%g,vr=%s\n" % effectivesize % effectivesize % effectivesize % rgbstring;
[557]20                if (i>0)
21                        str+="j:%d,%d,sh=1,dx=%g,ry=%g\n" % (i-1) % i % (size*shift) % (angle_delta+i*angle_delta_delta);
22                size*=growing;
23        }
24        return str;
25}
26
[422]27function init_chambers()
28{
29        colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
[552]30        retColors = ["1.0,1.0,1.0", "1.0,1.0,0.0"];
[496]31        chambers = [ ["p:sh=1, sx=0.2, sy=0.2, sz=0.2, rz=3.14159265358979,",
32"p:0.18421219587326, 0.13, sh=1, sx=0.21, sy=0.21, sz=0.21,",
33"p:0.323935478925705, 0.195192575454712, -0.0246672090142965, sh=1, sx=0.2205, sy=0.2205, sz=0.2205,",
34"p:0.467822402715683, 0.258204102516174, -0.0246672090142965, sh=1, sx=0.231525, sy=0.231525, sz=0.231525,",
35"p:0.664101362228394, 0.309014827013016, -0.0246672090142965, sh=1, sx=0.24310125, sy=0.24310125, sz=0.24310125,",
36"p:0.860512733459473, 0.274790525436401, -0.0246672090142965, sh=1, sx=0.2552563125, sy=0.2552563125, sz=0.2552563125,",
37"p:1.0273220539093, 0.1655353307724, -0.0246672090142965, sh=1, sx=0.268019128125, sy=0.268019128125, sz=0.268019128125,",
38"p:1.13825333118439, -0.000509921927005053, -0.0246672090142965, sh=1, sx=0.28142008453125, sy=0.28142008453125, sz=0.28142008453125,",
39"p:1.17569863796234, -0.196833491325378, -0.0246672090142965, sh=1, sx=0.295491088757813, sy=0.295491088757813, sz=0.295491088757813,",
40"p:1.13369226455688, -0.392314255237579, -0.0246672090142965, sh=1, sx=0.310265643195703, sy=0.310265643195703, sz=0.310265643195703,"],
41        ["p:sh=1, sx=0.1, sy=0.1, sz=0.1, rz=3.14159265358979,",
42"p:0.110527315735817, -0.0167302016913891, sh=1, sx=0.105, sy=0.105, sz=0.105, rx=3.63519277003091e-33,",
43"p:0.207026958465576, -0.080698736011982, 1.17627548103266e-17, sh=1, sx=0.11025, sy=0.11025, sz=0.11025,",
44"p:0.271191358566284, -0.169948443770409, 1.17627548103266e-17, sh=1, sx=0.1157625, sy=0.1157625, sz=0.1157625,",
45"p:0.291628688573837, -0.286643952131271, 1.17627548103266e-17, sh=1, sx=0.121550625, sy=0.121550625, sz=0.121550625,",
46"p:0.264833927154541, -0.403534322977066, 1.17627548103266e-17, sh=1, sx=0.12762815625, sy=0.12762815625, sz=0.12762815625,",
47"p:0.194418027997017, -0.500668346881866, 1.17627548103266e-17, sh=1, sx=0.1340095640625, sy=0.1340095640625, sz=0.1340095640625,",
48"p:0.091719962656498, -0.562735974788666, 1.17627548103266e-17, sh=1, sx=0.140710042265625, sy=0.140710042265625, sz=0.140710042265625,",
49"p:-0.0270438715815544, -0.57991486787796, 1.17627548103266e-17, sh=1, sx=0.147745544378906, sy=0.147745544378906, sz=0.147745544378906,",
50"p:-0.143122747540474, -0.549489378929138, 1.17627548103266e-17, sh=1, sx=0.155132821597852, sy=0.155132821597852, sz=0.155132821597852,"]];
[422]51}
[401]52
[487]53function createForamMorphology(morphotype, gen, chamber_num)
[401]54{
[496]55        var geno = "//0\nm:Vstyle=foram\n" + chambers[morphotype][0] + "vr=" + colors[gen];
[401]56
[487]57        chamber_num = Math.min(chamber_num, chambers[morphotype].size - 1);
[422]58
59        for (var i = 0; i < chamber_num; i++)
60        {
[496]61                geno += "\n" + chambers[morphotype][i+1]  + "vr=" +  colors[gen];
[422]62        }
63
64        for (var i = 0; i < chamber_num; i++)
65        {
66                geno += "\n" +  "j:"+ i +", "+ (i+1) +", sh=1";
67        }
[430]68
[422]69        return geno;
70}
71
72function setGenotype(mode)
73{
[554]74        if (mode->opt == "growth")
[422]75        {
[554]76                mode->cr.data->genes = mode->parent_genes;
77                mode->cr.data->lifeparams = mode->parent_lifeparams;
[422]78        }
[554]79
80        else if (mode->opt == "birth")
[422]81        {
[554]82                mode->cr.data->genes = String.deserialize(String.serialize(mode->genes));
83                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};                   
84
[422]85        }
86}
87
[479]88function gametsDivision(parent_energy, energy0)
89{
90        var number = 1;
91        var result = parent_energy;
[486]92        while ((result-ExpProperties.divisionCost) >= energy0)
[479]93        {
[486]94                result = (result-ExpProperties.divisionCost)/2;
[479]95                number *= 2;
96        }
97        //Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number);
98        return {"energy" : result, "number" : number};
99}
100
[487]101function getEnergy0(radius)
102{
103        return energyFromVolume(micronsToFrams(radius),1);
104}
105
[422]106function reproduce_haploid(parent, parent2, clone)
107{       
[476]108        var number, energy0, new_genes, gen;
[422]109        if (clone == 1)
110        {
[487]111                var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0",0)[0]));
[479]112                energy0 = offspring->energy;
113                number = offspring->number;
[476]114                new_genes = parent.data->genes;
115                parent.data->lifeparams->gen = 1 - parent.data->lifeparams->gen; //because of reversal of "gen" in createOffspring function
116                gen = parent.data->lifeparams->gen;
[422]117        }
118        else
119        {
[487]120                var offspring1 = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[1]));
121                var offspring2 = gametsDivision(parent2.energy,getEnergy0(getGene(parent2,"energies0", 0)[1]));
[479]122                energy0 = (offspring1->energy+offspring2->energy);
[486]123                number = ExpProperties.gametSuccessRate*(offspring1->number+offspring2->number)/2;
[476]124                new_genes = [parent.data->genes, parent2.data->genes];
125                gen = 1 - parent.data->lifeparams->gen;
[493]126
127                if (ExpProperties.logging == 1)
128                {
129                                log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
130                                log(createLogVector(parent2, parent2.energy),ExpProperties.logPref+"repro_energies_log.txt");
131                                log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
[552]132                                log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
133                                log(createLogVector(parent2, parent2.lifespan),ExpProperties.logPref+"lifespan_log.txt");
[493]134                }       
[422]135        }
136
[430]137        Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0);
[422]138
[418]139        for (var j = 0; j < number; j++)
[401]140        {
[496]141                createOffspring(createForamMorphology(gen, gen, 0), energy0, new_genes, parent.data->lifeparams);
[401]142        }
143}
144
[418]145function reproduce_diploid(parent)
[401]146{
[510]147        var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[0]));
148        var energy0 = offspring->energy;
149        var number = offspring->number;
[422]150
[493]151                if (ExpProperties.logging == 1)
152                {
153                        log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
154                        log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
[552]155                        log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
[493]156                }       
157
[430]158        Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);
[422]159
[418]160        for (var j = 0; j < number / 2; j++)
[401]161        {
[418]162                var crossed = 0;
163                //crossover
[486]164                if (Math.rnd01 < ExpProperties.crossprob)
[418]165                {
[422]166                        crossover(parent, "min_repro_energies");
[418]167                        crossed = 1;
168                }
[401]169
[418]170                for (var k = 0; k < 2; k++)
[404]171                {
[496]172                        createOffspring(createForamMorphology(1 - parent.data->lifeparams->gen, 1 - parent.data->lifeparams->gen, 0), energy0, parent.data->genes[0], parent.data->lifeparams);
[404]173                }
174
[418]175                //reverse of crossover for fossilization
176                if (crossed == 1)
[401]177                {
[422]178                        crossover(parent, "min_repro_energies");
[418]179                        crossed = 0;
[401]180                }
[418]181                       
[401]182        }
[404]183}
184
[422]185function reproduce_parents(species)
[404]186{
[418]187                var parent1 = null;
188                var parent2 = null;
189                var pop = Populations[0];
190                for (var i = pop.size-1; i >= 0; i--)
[401]191                {
[476]192                        if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species)
[418]193                        {
[486]194                                if ((pop[i].data->lifeparams->gen==1) || ((pop[i].data->lifeparams->gen==0) && ExpProperties.stress == 0))
[401]195                                {
[422]196                                        continue;
[401]197                                }
[418]198                                else if (parent1 == null)
[401]199                                {
[418]200                                        parent1 = pop[i];
[401]201                                }
[418]202                                else if (parent2 == null)
203                                {
204                                        parent2 = pop[i];
205                                } 
[430]206                                if (parent1 != null && parent2 != null)
[418]207                                {
[479]208                                        //when parents are ready for reproduction start gametogenesis
209                                        if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1)
210                                        {
[554]211                                                var time = int(secToSimSteps(ExpProperties.gametoPeriodSec));
[479]212                                                parent1.data->lifeparams->division_time = time;
213                                                parent2.data->lifeparams->division_time = time;
214                                                parent1.idleen = 0;
215                                                parent2.idleen = 0;
216                                                //Simulator.print("parents "+parent1.uid + " " + parent2.uid + " ready to repro: "+Simulator.stepNumber);
217                                        }
218                                        //when gametogenesis is finished fuse gamets
219                                        else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0)
220                                        {
221                                                reproduce_haploid(parent1, parent2, 0);
222                                                print_repro_info(parent1);
223                                                print_repro_info(parent2);
224                                                pop.kill(parent1);
225                                                pop.kill(parent2);
226                                                parent1 = null;
227                                                parent2 = null;
228                                        }
[430]229                                }       
[418]230                        }
[401]231                }
[422]232}
233
234function readyToRepro(cr)
235{
236        var reproduced = 1;
237       
238       
[476]239        if (cr.data->lifeparams->gen == 1)
[422]240        {
241                reproduce_diploid(cr);
[401]242        }
243
[486]244        else if (ExpProperties.stress == 0)
[401]245        {
[422]246                reproduce_haploid(cr, null, 1);
247        }
248
249        else
250        {
251                if (cr.signals.size == 0)
[401]252                {
[476]253                        cr.signals.add("repro"+cr.data->lifeparams->species);
[422]254                        cr.signals[0].power = 1;
[401]255                }
[422]256                reproduced = 0;
[476]257                cr.data->lifeparams->reproduce = 1;
[401]258        }
[422]259
260        if (reproduced == 1)
261        {
262                print_repro_info(cr);
263                Populations[0].kill(cr);
264        }
265
266        return reproduced;
[401]267}
268
[422]269function print_repro_info(cr)
[421]270{
[476]271        Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy);
[422]272}
[421]273
[422]274function foramReproduce(cr)
275{
[488]276        var properEnergy = cr.energy >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][getGene(cr, "min_repro_energies",0)[cr.data->lifeparams->gen]],0);
[487]277        var reproduced = 0;     
[422]278
279        //if creature has proper energy
280        if ( properEnergy && cr.signals.size == 0)
281        {
282                //reproduce with probability repro_prob
[486]283                if (Math.rnd01 <= ExpProperties.repro_prob) //TODO env trigger
[421]284                {
[422]285                        reproduced = readyToRepro(cr);
[421]286                }
[476]287                else if (cr.signals.receive("repro"+cr.data->lifeparams->species) > 0)
[421]288                {
[422]289                        reproduced = readyToRepro(cr);
[421]290                }
[422]291                if (reproduced == 1)
[430]292                                return 1;
[421]293        }
294
[422]295        else if (!properEnergy)
[421]296        {
[422]297                cr.signals.clear();
[476]298                cr.data->lifeparams->reproduce = 0;
[421]299        }
[430]300
301        return 0;
[422]302}
[421]303
[422]304function crossover(parent, gene)
305{
[476]306        var tmp = parent.data->genes[0][gene];
307        parent.data->genes[0][gene] = parent.data->genes[1][gene];
308        parent.data->genes[1][gene] = tmp;
[422]309}
[421]310
[476]311function createOffspring(geno, energy, parent_genes, parent_lifeparams)
[422]312{
[493]313        curColor = retColors[1-parent_lifeparams->gen];
[422]314        var cr = Populations[0].add(geno);
315        cr.energy0 = energy;
316        cr.energy = cr.energy0;
[554]317        setGenotype({"opt" : "birth", "cr" : cr, "gen" : 1 - parent_lifeparams->gen, "species" : parent_lifeparams->species, "energy0" : cr.energy0, "genes" : parent_genes});
[422]318        placeRandomlyNotColliding(cr);
[421]319}
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