Changeset 487

Timestamp:

03/27/16 00:12:20 (9 years ago)

Author:

oriona

Message:

Method for definig new species added.

Location:

experiments/frams/foraminifera/data/scripts

Files:

• foraminifera.expdef (modified) (19 diffs)
• foraminifera.inc (modified) (11 diffs)

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

@@ -33 +33 @@
 global changePeriod;
 global phase;
+global species_genes; 
 
 @include "foraminifera.inc"
@@ -52 +53 @@
         pop.death = 1;
         pop.energy = 1;
-        pop.selfmask = 0x10001;
-        pop.othermask = 0x20001;
+        pop.selfmask = 0;
+        pop.othermask = 0;
         //pop.selfmask = 0x20002; pop.othermask = 0x10002;
         pop.perfperiod = 25; 
+        pop.bodysim = 0;
 
         pop = Populations.addGroup("Nutrients");
@@ -62 +64 @@
         pop.death = 1;
         pop.energy = 1;
-        pop.selfmask = 0x20002;
-        pop.othermask = 0x10000;
+        pop.selfmask = 0;
+        pop.othermask = 0;
         //pop.othermask = 0x10002;
+        pop.bodysim = 0;
 
         pop = Populations.addGroup("ReticulopodiaNutrients");
@@ -71 +74 @@
         pop.death = 0;
         pop.energy = 0;
-        pop.selfmask = 0x20002;
-        pop.othermask = 0x10000;
+        pop.selfmask = 0;
+        pop.othermask = 0;
+        pop.bodysim = 0;
 
         //world
@@ -90 +94 @@
         //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
 
-        //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files
+        //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files   
 
         //reproduction
@@ -100 +104 @@
         ExpProperties.divisionCost = 15.6;
         reprocounter = 0;
+
+        species_genes = [];
 
         init_chambers();
@@ -143 +149 @@
         changePeriod = 0;
         phase = "high";
-        ExpProperties.foodperiod = 21600;
+        ExpProperties.foodperiod = 3600;
         ExpProperties.foodPeriodChange = 0;
         ExpProperties.nutrientradius = micronsToFrams(10);
@@ -195 +201 @@
 }
 
+function getGene(cr, gen_id, gen_set)
+{
+        if (cr.data->lifeparams->gen == 0) 
+                return cr.data->genes[gen_id];
+        else 
+                return cr.data->genes[gen_set][gen_id];
+}
+
 function addForam(species, iter, chambernum, ploid)
 {
-        var geno = createForamGenotype(ploid, species, chambernum);
+        var geno = createForamMorphology(species_genes[species]->morphotype, ploid, chambernum);
         var cr = Populations[0].add(geno);
         cr.name = "Initial creature" + species + "_" + iter;
@@ -203 +217 @@
         cr.energy0 = energyFromVolume(max_chamber_volume[ploid][chambernum],0);
         cr.energy = cr.energy0;
-        setGenotype({"opt" : 0, "cr" : cr, "species" : species});
+        setGenotype({"opt" : 0, "cr" : cr, "species" : species, "energy0" : cr.energy0, "genes" : species_genes[species]});
         if (ploid == 1)
         {
@@ -219 +233 @@
         }       
         //add new foram with random energy bewtween starting energy and reproduction treshold
-        addForam(species, iter, Math.rndUni(0,getProperty(ploid, "min_repro_energ")),ploid);
+        addForam(species, iter, Math.rndUni(0,species_genes[species]->min_repro_energies[ploid]),ploid);
+}
+
+//new species can be added as a dictionary with parameter values that are different than default values
+function addSpecies(new_genes)
+{
+        species_genes.add({"min_repro_energies" : [4,6], "energies0" : [20, 1.25], "hibernation" : 0, "morphotype" : 0});
+        for (var i = 0; i < new_genes.size; i++)
+        {
+                var key = new_genes.getKey(i);
+                species_genes[species_genes.size-1][key] = new_genes[key];
+        } 
 }
 
@@ -228 +253 @@
         Populations[2].clear(); //reticulopodia and nutrients
 
-        for (var i = 0; i < ExpProperties.foramPop; i++)
-        {
-                addInitialForam(0, i);  
-                //addInitialForam(1, i);
+        if (species_genes.size == 0)
+        {
+                addSpecies({}); //default
+        }
+
+        for (var spec = 0; spec < species_genes.size; spec++)
+        {
+                for (var i = 0; i < ExpProperties.foramPop; i++)
+                {
+                        addInitialForam(spec, i);       
+                }
         }
         o = Populations[0][0].getMechPart(0).orient.clone();
         ExpState.totaltestedcr = 0;
-        nutrientenergywaiting = ExpProperties.energy_nut;
 }
 
@@ -361 +392 @@
         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 geno = createForamMorphology(getGene(cr, "morphotype", 0), cr.data->lifeparams->gen, chamber_num+1);
                 var cr2 = Populations[0].add(geno);
 
@@ -367 +398 @@
                 cr2.energy = cr2.energy0;
 
-                setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : 2});
+                setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : 2, "energy0" : cr.energy0});
                 cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
                 setForamMeta(cr2);
@@ -442 +473 @@
 }
 
+function fence(pos)
+{
+        return Math.min(Math.max(0,pos),World.wrldsiz);
+}
+
 function foramMove(cr)
 {
@@ -447 +483 @@
 
         //adjustment in z axis
-        cr.moveAbs(cr.pos_x, cr.pos_y, 0);
+        cr.moveAbs(fence(cr.pos_x), fence(cr.pos_y), 0);
 
         //are there any nutrients in zone 1 or 2?
@@ -459 +495 @@
 
         //no nutrients in zone 2
-        var hibernation = 0;
-        if (cr.data->lifeparams->gen == 0) hibernation =  cr.data->genes->hibernation;
-        else hibernation =  cr.data->genes[0]->hibernation;
-        //hibernation
-        if (hibernation == 1)
+        if (getGene(cr, "hibernation",0) == 1)
         {
                 reverseHib(cr);
@@ -469 +501 @@
         }
         //random move
-        else if (cr.lifespan%int(dir_change/ExpProperties.secPerStep) == 0)
+        else if (Simulator.stepNumber%int(dir_change/ExpProperties.secPerStep) == 0)
         {
                 cr.data->lifeparams->dir = randomDir();
@@ -732 +764 @@
 function createStatistics()
 {       
-        var number = [[0, 0],[0,0]]; // [species][gen]
-        var e_inc = [[0, 0],[0,0]];
+        var number = [];
+        var e_inc = [];
         var e_nut = 0.0;
+
+        for (var s = 0; s < species_genes.size; s++)
+        {
+                number.add([0,0]);// [haplo][diplo]
+                e_inc.add([0,0]);
+        }
 
         for (var i = 0; i < Populations[0].size; i++)
@@ -752 +790 @@
         }
 
-        var log_numbers = [number[1][0], number[1][1], number[0][0], number[0][1], Populations[1].size];
-        var log_energies = [e_inc[1][0], e_inc[1][1], e_inc[0][0], e_inc[0][1], e_nut];
+        var log_numbers = [];
+        var log_energies = [];
+
+        for (var s = 0; s < species_genes.size; s++)
+        {
+                for (var p = 0; p < 2; p++)
+                {
+                        log_numbers.add(number[s][p]);
+                        log_energies.add(e_inc[s][p]);
+                }
+        }
+        
+        log_numbers.add(Populations[1].size);
+        log_energies.add(e_nut);
 
         log(log_numbers, "forams_log.txt");

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

@@ -28 +28 @@
 }
 
-function createForamGenotype(gen, species, chamber_num)
+function createForamMorphology(morphotype, gen, chamber_num)
 {
         var rad = getProperty(gen, "chamber_proculus"); 
-        var geno = "//0\np:" + chambers[species][0] + "sh=1,sx=" + rad + ",sy=" + rad + ",sz=" + rad + ", rz=3.14159265358979,vr=" + colors[gen];
-
-        chamber_num = Math.min(chamber_num, chambers[species].size - 1);
+        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[species][i+1] + "sh=1,sx=" + rad + ",sy=" + rad + ",sz=" + rad + ",vr=" + colors[gen];
+                geno += "\n" + "p:" + chambers[morphotype][i+1] + "sh=1,sx=" + rad + ",sy=" + rad + ",sz=" + rad + ",vr=" + colors[gen];
         }
 
@@ -46 +46 @@
         }
 
-        if (species == 0) geno += "\nn:p=0,d=\"S\"";
+        if (morphotype == 0) geno += "\nn:p=0,d=\"S\"";
 
         return geno;
@@ -55 +55 @@
         if (mode->opt == 0) //initial
         {
-                mode->cr.data->genes = {"min_repro_energies" : [energyFromVolume(max_chamber_volume[0][getProperty(0, "min_repro_energ")],0), energyFromVolume(max_chamber_volume[1][getProperty(1, "min_repro_energ")],0)], "hibernation" : mode->species};
-                mode->cr.data->lifeparams = {"max_energy_level" : getProperty(0,"energies0"), "gen" : 0,  "hibernated" : 0, "species" : mode->species, "reproduce" : 0, "dir" : randomDir(), "chamber_growth" : -1, "division_time" : -1};
+                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" : getProperty(1 - mode->parent_lifeparams->gen,"energies0"), "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 = mode->parent_genes;
+                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
@@ -81 +81 @@
         //Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number);
         return {"energy" : result, "number" : number};
+}
+
+function getEnergy0(radius)
+{
+        return energyFromVolume(micronsToFrams(radius),1);
 }
 
@@ -88 +93 @@
         if (clone == 1)
         {
-                var offspring = gametsDivision(parent.energy,getProperty(0,"energies0"));
+                var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0",0)[0])); 
                 energy0 = offspring->energy;
                 number = offspring->number;
@@ -97 +102 @@
         else
         {
-                var offspring1 = gametsDivision(parent.energy,getProperty(1,"energies0"));
-                var offspring2 = gametsDivision(parent2.energy,getProperty(1,"energies0"));
+                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;
@@ -109 +114 @@
         for (var j = 0; j < number; j++)
         {
-                createOffspring(createForamGenotype(gen, parent.data->lifeparams->species, 0), energy0, new_genes, parent.data->lifeparams); 
+                createOffspring(createForamMorphology(getGene(parent, "morphotype", 0), gen, 0), energy0, new_genes, parent.data->lifeparams); 
         }
 }
@@ -115 +120 @@
 function reproduce_diploid(parent)
 {
-        var energy0 = getProperty(0,"energies0");
+        var energy0 =getEnergy0( getGene(parent,"energies0", 0)[0]); 
         var number = ((1 - (getProperty(parent.data->lifeparams->gen, "e_repro_cost"))) * parent.energy) / energy0;
 
@@ -132 +137 @@
                 for (var k = 0; k < 2; k++)
                 {
-                        createOffspring(createForamGenotype(1 - parent.data->lifeparams->gen, parent.data->lifeparams->species, 0), energy0, parent.data->genes[0], parent.data->lifeparams); 
+                        createOffspring(createForamMorphology(getGene(parent, "morphotype", 0), 1 - parent.data->lifeparams->gen, 0), energy0, parent.data->genes[0], parent.data->lifeparams); 
                 }
 
@@ -236 +241 @@
 }
 
-
-
 function foramReproduce(cr)
 {
-        var properEnergy = 0;
-        var reproduced = 0;
-
-        if (cr.data->lifeparams->gen == 0)
-        {
-                properEnergy = ( cr.energy >= cr.data->genes->min_repro_energies[cr.data->lifeparams->gen] );
-        }
-        else
-        {
-                properEnergy = ( cr.energy >= cr.data->genes[0]->min_repro_energies[cr.data->lifeparams->gen] ); //TODO gene selection
-        }
+        var properEnergy = cr.energy >= energyFromVolume(max_chamber_volume[0][getGene(cr, "min_repro_energies",0)[cr.data->lifeparams->gen]],0);
+        var reproduced = 0;     
 
         //if creature has proper energy
@@ -289 +283 @@
         cr.energy0 = energy;
         cr.energy = cr.energy0;
-        setGenotype({"cr" : cr, "parent_genes" : parent_genes, "parent_lifeparams" : parent_lifeparams, "opt" : 1});
+        setGenotype({"cr" : cr, "parent_genes" : parent_genes, "parent_lifeparams" : parent_lifeparams, "opt" : 1, "energy0" : cr.energy0});
         placeRandomlyNotColliding(cr);
 }