Changeset 847 for experiments/frams/foraminifera/data/scripts/foraminifera.inc

Timestamp:

01/31/19 03:43:35 (5 years ago)

Author:

Maciej Komosinski

Message:

Code formatting

File:

• experiments/frams/foraminifera/data/scripts/foraminifera.inc (modified) (16 diffs)

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

@@ -2 +2 @@
 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\nm:Vstyle=foram\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) //last chamber
-                {
-                        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
-                        if (lastchambergrowth<1)
-                                rgbstring="0.9,0.9,0.9,i=\"growing=%g\"" % lastchambergrowth; //when the last chamber is growing, make it bright gray and add extra information in its "i" field
+        const shift = 0.7;
+        const angle_delta = 0.8;
+        const angle_delta_delta = -0.01;
+        const growing = 1.07; //7% growth
+
+        var str = "//0\nm:Vstyle=foram\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) //last chamber
+                {
+                        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
+                        if (lastchambergrowth < 1)
+                                rgbstring = "0.9,0.9,0.9,i=\"growing=%g\"" % lastchambergrowth; //when the last chamber is growing, make it bright gray and add extra information in its "i" field
                 }
                 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;
+                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;
@@ -38 +38 @@
         {
                 foram_uid += 1;
-                var new_id = "c"+string(foram_uid);
+                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};    
+                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";
                 var inherit = [1.0];
                 if (mode->parentsuids.size > 1)
-                {       
+                {
                         oper = "cross-over";
                         inherit = [0.5, 0.5];
                 }
-                
-                var dict={"Time":Simulator.stepNumber,"FromIDs":mode->parentsuids,"ID":new_id, "Inherited":inherit, "Operation": oper, "Kind" : mode->gen};
-                Simulator.print("[OFFSPRING] " + String.serialize(dict));               
+
+                var dict = {"Time": Simulator.stepNumber, "FromIDs": mode->parentsuids, "ID": new_id, "Inherited": inherit, "Operation": oper, "Kind" : mode->gen};
+                Simulator.print("[OFFSPRING] " + String.serialize(dict));
         }
 }
@@ -57 +57 @@
 function getEnergy0(radius)
 {
-        return energyFromVolume(micronsToFrams(radius),1);
+        return energyFromVolume(micronsToFrams(radius), 1);
 }
 
@@ -64 +64 @@
         var number = 1;
         var result = parent_energy;
-        while ((result-ExpProperties.divisionCost) >= energy0)
-        {
-                result = (result-ExpProperties.divisionCost)/2;
+        while ((result - ExpProperties.divisionCost) >= energy0)
+        {
+                result = (result - ExpProperties.divisionCost) / 2;
                 number *= 2;
         }
@@ -74 +74 @@
 
 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])); 
+                var offspring = gametsDivision(parent.energy, getEnergy0(getGene(parent, "energies0", 0)[0]));
                 energy0 = offspring->energy;
                 number = offspring->number;
@@ -87 +87 @@
         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;
+                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;
@@ -96 +96 @@
                 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");
-                }       
+                        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");
+                }
         }
 
@@ -114 +114 @@
 function reproduce_diploid(parent)
 {
-        var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[0]));
-        var energy0 = offspring->energy; 
+        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");
-                }       
+        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);
@@ -139 +139 @@
                 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]); 
+                        createOffspring(create_genotype(ExpProperties.chamber_proculus_haplo, 1, colors[0], 1), energy0, parent.data->genes[0], parent.data->lifeparams, [parent.data->lifeparams->uid]);
                 }
 
@@ -148 +148 @@
                         crossed = 0;
                 }
-                        
+
         }
 }
@@ -154 +154 @@
 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))
+        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)
                                 {
-                                        continue;
+                                        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);
                                 }
-                                else if (parent1 == null)
+                                //when gametogenesis is finished fuse gamets
+                                else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0)
                                 {
-                                        parent1 = pop[i];
+                                        reproduce_haploid(parent1, parent2, 0);
+                                        //print_repro_info(parent1);
+                                        //print_repro_info(parent2);
+                                        pop.kill(parent1);
+                                        pop.kill(parent2);
+                                        parent1 = null;
+                                        parent2 = null;
                                 }
-                                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;
-                                        }
-                                }       
-                        } 
-                }
+                        }
+                }
+        }
 }
 
@@ -219 +219 @@
                 if (cr.signals.size == 0)
                 {
-                        cr.signals.add("repro"+cr.data->lifeparams->species);
+                        cr.signals.add("repro" + cr.data->lifeparams->species);
                         cr.signals[0].power = 1;
                 }
@@ -237 +237 @@
 function foramReproduce(cr)
 {
-        var properEnergy = cr.energy >= getGene(cr, "min_repro_energies",0)[cr.data->lifeparams->gen];
-        var reproduced = 0;     
+        var properEnergy = cr.energy >= getGene(cr, "min_repro_energies", 0)[cr.data->lifeparams->gen];
+        var reproduced = 0;
 
         //if creature has proper energy
@@ -248 +248 @@
                         reproduced = readyToRepro(cr);
                 }
-                else if (cr.signals.receive("repro"+cr.data->lifeparams->species) > 0)
+                else if (cr.signals.receive("repro" + cr.data->lifeparams->species) > 0)
                 {
                         reproduced = readyToRepro(cr);
                 }
                 if (reproduced == 1)
-                                return 1;
+                        return 1;
         }
 
@@ -259 +259 @@
         {
                 cr.signals.clear();
-                cr.data->lifeparams->reproduce = 0; 
+                cr.data->lifeparams->reproduce = 0;
         }
 
@@ -274 +274 @@
 function createOffspring(geno, energy, parent_genes, parent_lifeparams, parentsuids)
 {
-        curColor = colors[1-parent_lifeparams->gen];
-        var cr = createAndRotate(geno, 0, 2*Math.pi, 0);
+        curColor = colors[1 - parent_lifeparams->gen];
+        var cr = createAndRotate(geno, 0, 2 * Math.pi, 0);
         cr.energy0 = energy;
         cr.energy = cr.energy0;