Changeset 476 for experiments

Timestamp:

03/13/16 02:45:09 (9 years ago)

Author:

sz

Message:

• use arrow syntax (dict->key instead of dictkey?)
• use creature/genotype.data instead of user1/2/3 (user1=>genes, user2->lifeparams, user3=reticulopodiacreature)

Location:

experiments/frams/foraminifera/data/scripts

Files:

• foraminifera.expdef (modified) (20 diffs)
• foraminifera.inc (modified) (13 diffs)

experiments/frams/foraminifera/data/scripts/foraminifera.expdef

@@ -6 +6 @@
 
 Technical information:
-Genes and parameter values which control reproduction are stored in user1 and user2 fields.
-
-user1:
+Genes and parameter values which control reproduction are stored in data->genes and data->lifeparams fields.
+
+genes:
 genes which are not encoded in Ff genotype:
 min_repro_energy - Minimum energy necessary for reproduction
 hibernation - Defines foram behavior in the case of no nutrients
 
-user2:
+lifeparams:
 Physiological parameters of foraminifera:
 max_energy_level - maximum energy level reached so far
@@ -220 +220 @@
                 {
                         //cr.rotate(0,0,Math.rnd01*Math.twopi);
-                        if ((typeof(g.user1) == "Vector") && (g.user1.size >= 3))
+                        if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
                         {
                                 // [x,y,energy]
-                                cr.move(g.user1[0] - cr.center_x, g.user1[1] - cr.center_y, 0);
-                                cr.energy = g.user1[2];
+                                cr.move(g.data->genes[0] - cr.center_x, g.data->genes[1] - cr.center_y, 0);
+                                cr.energy = g.data->genes[2];
                         }
                         else
@@ -278 +278 @@
         {
                 var ret = Populations[2].add("//0\np:sh=3,sx=0.01,sy="+ExpParams.zone1_range+",sz="+ExpParams.zone1_range+",ry=1.57,vr=1.0,1.0,1.0");
-                cr.user3 = ret;
+                cr.data->reticulopodiacreature = ret;
         }
 }
@@ -299 +299 @@
         var has_ret = 0;
 
-        if (cr.user3 != null)
-        {
-                if (Populations[2].findUID(cr.user3.uid) != null)
+        if (cr.data->reticulopodiacreature != null)
+        {
+                if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
                 {
                         has_ret = 1;
@@ -312 +312 @@
 function foramGrow(cr, chamber_num)
 {
-        if ((chamber_num+1) < chambers[cr.user2["species"]].size)
-        {
-                var geno = createForamGenotype(cr.user2["gen"], cr.user2["species"], chamber_num+1);
+        if ((chamber_num+1) < chambers[cr.data->lifeparams->species].size)
+        {
+                var geno = createForamGenotype(cr.data->lifeparams->gen, cr.data->lifeparams->species, chamber_num+1);
                 var cr2 = Populations[0].add(geno);
 
@@ -320 +320 @@
                 cr2.energy = cr2.energy0;
 
-                setGenotype({"cr" : cr2, "parent_user1" : cr.user1, "parent_user2" : cr.user2, "opt" : 2});
+                setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : 2});
                 cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
-                setForamMeta(cr2, cr2.user2["gen"]);
+                setForamMeta(cr2, cr2.data->lifeparams->gen);
 
                 if (visualization(cr))
                 {
-                        Populations[2].delete(cr.user3);
+                        Populations[2].delete(cr.data->reticulopodiacreature);
                 }
                 Populations[0].delete(cr);
@@ -362 +362 @@
                                 }
                         }
-                        else if (eating == 0 && cr.user2["hibernated"] == 0 && dist < mindist)
+                        else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
                         {
                                 mindist = dist;
@@ -369 +369 @@
                 }
 
-                if (!eating && cr.user2["hibernated"] == 0)
+                if (!eating && cr.data->lifeparams->hibernated == 0)
                 {
                         mindistvec.normalize();
@@ -388 +388 @@
 function moveEnergyDec(cr)
 {
-        if (cr.user2["hibernated"] == 0)
-        {
-                //cr.energy_m += (ExpParams.energy_move * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)])*ExpParams.secPerStep;
+        if (cr.data->lifeparams->hibernated == 0)
+        {
+                //cr.energy_m += (ExpParams.energy_move * max_chamber_energ[cr.data->lifeparams->gen][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.data->lifeparams->gen].size)-1)])*ExpParams.secPerStep;
                 cr.energy_m += (ExpParams.energy_move * cr.energy)*ExpParams.secPerStep;
         }
@@ -413 +413 @@
         //no nutrients in zone 2
         var hibernation = 0;
-        if (cr.user2["gen"] == 0) hibernation =  cr.user1["hibernation"];
-        else hibernation =  cr.user1[0]["hibernation"];
+        if (cr.data->lifeparams->gen == 0) hibernation =  cr.data->genes->hibernation;
+        else hibernation =  cr.data->genes[0]->hibernation;
         //hibernation
         if (hibernation == 1)
@@ -424 +424 @@
         else if (cr.lifespan%(dir_change/ExpParams.secPerStep) == 0)
         {
-                cr.user2["dir"] = randomDir();
-                cr.localDrive = cr.user2["dir"];
+                cr.data->lifeparams->dir = randomDir();
+                cr.localDrive = cr.data->lifeparams->dir;
                 moveEnergyDec(cr);
         }
         else
         {
-                cr.localDrive = cr.user2["dir"];
+                cr.localDrive = cr.data->lifeparams->dir;
         }
 }
@@ -450 +450 @@
         cr2.energy_m = cr2.energy_m + e;
         cr1.energy_p = cr1.energy_p + e;
-        if (cr1.user2["hibernated"] == 1)
+        if (cr1.data->lifeparams->hibernated == 1)
         {
                 reverseHib(cr1);
@@ -458 +458 @@
 function reverseHib(cr)
 {
-        if (cr.user2["hibernated"] == 1)
-        {
-                setForamMeta(cr, cr.user2["gen"]); //unhibernate
+        if (cr.data->lifeparams->hibernated == 1)
+        {
+                setForamMeta(cr, cr.data->lifeparams->gen); //unhibernate
         } 
         else
         {
-                //cr.idleen = (ExpParams.energy_hib * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)])*ExpParams.secPerStep; //hibernate
+                //cr.idleen = (ExpParams.energy_hib * max_chamber_energ[cr.data->lifeparams->gen][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.data->lifeparams->gen].size)-1)])*ExpParams.secPerStep; //hibernate
                 cr.idleen = (ExpParams.energy_hib * cr.energy)*ExpParams.secPerStep; //hibernate
         }
-        cr.user2["hibernated"] = 1 - cr.user2["hibernated"];
+        cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
 }
 
@@ -475 +475 @@
         if (visualization(cr))
         {
-                cr.user3.moveAbs(cr.center_x-ExpParams.zone1_range, cr.center_y-ExpParams.zone1_range, cr.center_z-ExpParams.zone1_range-getProperty(cr.user2["gen"], "chamber_proculus"));
+                cr.data->reticulopodiacreature.moveAbs(cr.center_x-ExpParams.zone1_range, cr.center_y-ExpParams.zone1_range, cr.center_z-ExpParams.zone1_range-getProperty(cr.data->lifeparams->gen, "chamber_proculus"));
         }
 
@@ -492 +492 @@
         }
 
-        cr.user2["max_energy_level"] = Math.max(cr.energy, cr.user2["max_energy_level"]);
+        cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
         if  (lastChamberNum(cr) <= chambers[0].size-1)
         {
-                if ((cr.user2["max_energy_level"] >= max_chamber_energ[cr.user2["gen"]][lastChamberNum(cr)]))   
+                if ((cr.data->lifeparams->max_energy_level >= max_chamber_energ[cr.data->lifeparams->gen][lastChamberNum(cr)]))         
                 {
                         foramGrow(cr, lastChamberNum(cr)); 
@@ -504 +504 @@
 function deathConditions(cr)
 {
-        if ((cr.energy <= getProperty(cr.user2["species"],"e_death_level")) || (Math.rnd01 < ExpParams.hunted_prob))
+        if ((cr.energy <= getProperty(cr.data->lifeparams->species,"e_death_level")) || (Math.rnd01 < ExpParams.hunted_prob))
                 return 1;
         else
@@ -514 +514 @@
         if (visualization(cr))
         {
-                Populations[2].delete(cr.user3);
+                Populations[2].delete(cr.data->reticulopodiacreature);
         }
         //fossilization
         var geno = GenePools[0].add(cr.genotype);
-        geno.user1 = cr.user1;
-        geno.user2 = cr.user2;
+        geno.data->genes = cr.data->genes;
+        geno.data->lifeparams = cr.data->lifeparams;
         if (ExpParams.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
         ExpState.totaltestedcr++;
@@ -555 +555 @@
                 var nutsize = ExpParams.nutrientsize*10;
                 var nut = Populations[2].add("//0\np:sh=2,sx="+nutsize+",sy="+nutsize+",sz="+nutsize+",ry=1.5,vr=0.0,1.0,0.0");
-                cr.user3 = nut;
+                cr.data->reticulopodiacreature = nut;
                 nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
         }
@@ -564 +564 @@
         if (visualization(cr))
         {
-                Populations[2].delete(cr.user3);
+                Populations[2].delete(cr.data->reticulopodiacreature);
         }
 }
@@ -635 +635 @@
         {
                 var cr = Populations[0].get(i);
-                var gen = cr.user2["gen"];
-                var species = cr.user2["species"];
+                var gen = cr.data->lifeparams->gen;
+                var species = cr.data->lifeparams->species;
 
                 number[species][gen] = number[species][gen] + 1; 

experiments/frams/foraminifera/data/scripts/foraminifera.inc

@@ -53 +53 @@
 function setGenotype(mode)
 {
-        if (mode["opt"] == 0) //initial
-        {
-                mode["cr"].user1 = {"min_repro_energies" : [max_chamber_energ[0][getProperty(0, "min_repro_energ")], max_chamber_energ[1][getProperty(1, "min_repro_energ")]], "hibernation" : mode["species"]};
-                mode["cr"].user2 = {"max_energy_level" : getProperty(0,"energies0"), "gen" : 0,  "hibernated" : 0, "species" : mode["species"], "reproduce" : 0, "dir" : randomDir()};
-        }
-        else if (mode["opt"]  == 1) //child
-        {
-                mode["cr"].user2 = {"max_energy_level" : getProperty(1 - mode["parent_user2"]["gen"],"energies0"), "gen" : 1 - mode["parent_user2"]["gen"],  "hibernated" : 0, "species" : mode["parent_user2"]["species"], "reproduce" : 0, "dir" : randomDir()};
-                mode["cr"].user1 = mode["parent_user1"];
+        if (mode->opt == 0) //initial
+        {
+                mode->cr.data->genes = {"min_repro_energies" : [max_chamber_energ[0][getProperty(0, "min_repro_energ")], max_chamber_energ[1][getProperty(1, "min_repro_energ")]], "hibernation" : mode->species};
+                mode->cr.data->lifeparams = {"max_energy_level" : getProperty(0,"energies0"), "gen" : 0,  "hibernated" : 0, "species" : mode->species, "reproduce" : 0, "dir" : randomDir()};
+        }
+        else if (mode->opt  == 1) //child
+        {
+                mode->cr.data->lifeparams = {"max_energy_level" : getProperty(1 - mode->parent_lifeparams->gen,"energies0"), "gen" : 1 - mode->parent_lifeparams->gen,  "hibernated" : 0, "species" : mode->parent_lifeparams->species, "reproduce" : 0, "dir" : randomDir()};
+                mode->cr.data->genes = mode->parent_genes;
         }
         else //grow
         {
-                mode["cr"].user1 = mode["parent_user1"];
-                mode["cr"].user2 = mode["parent_user2"];
+                mode->cr.data->genes = mode->parent_genes;
+                mode->cr.data->lifeparams = mode->parent_lifeparams;
         }
 }
@@ -72 +72 @@
 function reproduce_haploid(parent, parent2, clone)
 {       
-        var number, energy0, new_user1, gen;
+        var number, energy0, new_genes, gen;
         if (clone == 1)
         {
                 energy0 = getProperty(0,"energies0");
                 number = (( 1 - getProperty(1, "e_repro_cost")) * parent.energy) / energy0;
-                new_user1 = parent.user1;
-                parent.user2["gen"] = 1 - parent.user2["gen"]; //because of reversal of "gen" in createOffspring function
-                gen = parent.user2["gen"];
+                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
         {
                 energy0 = getProperty(1,"energies0"); 
-                number = (((1 - getProperty(parent.user2["gen"], "e_repro_cost")) * parent.energy) + ((1 -(getProperty(parent.user2["gen"], "e_repro_cost"))) * parent2.energy)) / energy0;
-                new_user1 = [parent.user1, parent2.user1];
-                gen = 1 - parent.user2["gen"];
+                number = (((1 - getProperty(parent.data->lifeparams->gen, "e_repro_cost")) * parent.energy) + ((1 -(getProperty(parent.data->lifeparams->gen, "e_repro_cost"))) * parent2.energy)) / energy0;
+                new_genes = [parent.data->genes, parent2.data->genes];
+                gen = 1 - parent.data->lifeparams->gen;
         }
 
@@ -93 +93 @@
         for (var j = 0; j < number; j++)
         {
-                createOffspring(createForamGenotype(gen, parent.user2["species"], 0), energy0, new_user1, parent.user2); 
+                createOffspring(createForamGenotype(gen, parent.data->lifeparams->species, 0), energy0, new_genes, parent.data->lifeparams); 
         }
 }
@@ -100 +100 @@
 {
         var energy0 = getProperty(0,"energies0");
-        var number = ((1 - (getProperty(parent.user2["gen"], "e_repro_cost"))) * parent.energy) / energy0;
+        var number = ((1 - (getProperty(parent.data->lifeparams->gen, "e_repro_cost"))) * parent.energy) / energy0;
 
         Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);
@@ -116 +116 @@
                 for (var k = 0; k < 2; k++)
                 {
-                        createOffspring(createForamGenotype(1 - parent.user2["gen"], parent.user2["species"], 0), energy0, parent.user1[0], parent.user2); 
+                        createOffspring(createForamGenotype(1 - parent.data->lifeparams->gen, parent.data->lifeparams->species, 0), energy0, parent.data->genes[0], parent.data->lifeparams); 
                 }
 
@@ -136 +136 @@
                 for (var i = pop.size-1; i >= 0; i--)
                 {
-                        if (pop[i].user2["reproduce"] == 1 && pop[i].user2["species"] == species) 
+                        if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species) 
                         { 
-                                if ((pop[i].user2["gen"]==1) || ((pop[i].user2["gen"]==0) && ExpParams.stress == 0))
+                                if ((pop[i].data->lifeparams->gen==1) || ((pop[i].data->lifeparams->gen==0) && ExpParams.stress == 0))
                                 {
                                         continue;
@@ -169 +169 @@
         
         
-        if (cr.user2["gen"] == 1)
+        if (cr.data->lifeparams->gen == 1)
         {
                 reproduce_diploid(cr);
@@ -183 +183 @@
                 if (cr.signals.size == 0)
                 {
-                        cr.signals.add("repro"+cr.user2["species"]);
+                        cr.signals.add("repro"+cr.data->lifeparams->species);
                         cr.signals[0].power = 1;
                 }
                 reproduced = 0;
-                cr.user2["reproduce"] = 1;
+                cr.data->lifeparams->reproduce = 1;
         }
 
@@ -201 +201 @@
 function print_repro_info(cr)
 {
-        Simulator.print("Reproduced " + cr.user2["gen"] + " of species " + cr.user2["species"] + " energy: " + cr.energy);
+        Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy);
 }
 
@@ -211 +211 @@
         var reproduced = 0;
 
-        if (cr.user2["gen"] == 0)
-        {
-                properEnergy = ( cr.energy >= cr.user1["min_repro_energies"][cr.user2["gen"]] );
+        if (cr.data->lifeparams->gen == 0)
+        {
+                properEnergy = ( cr.energy >= cr.data->genes->min_repro_energies[cr.data->lifeparams->gen] );
         }
         else
         {
-                properEnergy = ( cr.energy >= cr.user1[0]["min_repro_energies"][cr.user2["gen"]] ); //TODO gene selection
+                properEnergy = ( cr.energy >= cr.data->genes[0]->min_repro_energies[cr.data->lifeparams->gen] ); //TODO gene selection
         }
 
@@ -228 +228 @@
                         reproduced = readyToRepro(cr);
                 }
-                else if (cr.signals.receive("repro"+cr.user2["species"]) > 0)
+                else if (cr.signals.receive("repro"+cr.data->lifeparams->species) > 0)
                 {
                         reproduced = readyToRepro(cr);
@@ -239 +239 @@
         {
                 cr.signals.clear();
-                cr.user2["reproduce"] = 0; 
+                cr.data->lifeparams->reproduce = 0; 
         }
 
@@ -247 +247 @@
 function crossover(parent, gene)
 {
-        var tmp = parent.user1[0][gene];
-        parent.user1[0][gene] = parent.user1[1][gene];
-        parent.user1[1][gene] = tmp;
-}
-
-function createOffspring(geno, energy, parent_user1, parent_user2)
+        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)
 {
         var cr = Populations[0].add(geno);
         cr.energy0 = energy;
         cr.energy = cr.energy0;
-        setGenotype({"cr" : cr, "parent_user1" : parent_user1, "parent_user2" : parent_user2, "opt" : 1});
+        setGenotype({"cr" : cr, "parent_genes" : parent_genes, "parent_lifeparams" : parent_lifeparams, "opt" : 1});
         placeRandomlyNotColliding(cr);
 }