Changeset 418 for experiments/frams/foraminifera

Timestamp:

08/01/15 16:32:10 (9 years ago)

Author:

oriona

Message:

invalid index error fixed

Location:

experiments/frams/foraminifera/data/scripts

Files:

• foraminifera.expdef (modified) (7 diffs)
• foraminifera.inc (modified) (3 diffs)

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

@@ -24 +24 @@
 - added "S" receptor to visualize the difference between diplo and haplo generations
 - signal.value is a MechPart (a reference) so it does not have to be updated after changing the object location
-*/
-
-/* TODO fix
-[ERROR] Population.kill: Invalid index 35 (allowed range is 0..34)
-[ERROR] Population.kill: ... called from reproduce_haploid()  <foraminifera.inc:54>
-[ERROR] Population.kill: ... called from onStep()  <foraminifera.inc:228>
 */
 
@@ -69 +63 @@
         pop.othermask = 0x10000;
 
+        //TODO remove unused params
+
         //radius of the chamber
         ExpParams.rads = [1.2, 0.6];
+        //ExpParams.rads = [2, 2];
         //inital genotypes
         ExpParams.genh = "//0\np:sh=1,sx=" + ExpParams.rads[0] + ",sy=" + ExpParams.rads[0] + ",sz=" + ExpParams.rads[0] + ", rz=3.14159265358979";
@@ -80 +77 @@
         ExpParams.feedtrans = 3;
         ExpParams.creath = -0.99; //just above the bottom
-        ExpParams.foodgen = "//0\np:sh=2,sx=0.1,sy=0.1,sz=0.1\nn:d=T,p=0";
+        ExpParams.foodgen = "//0\np:sh=2,sx=0.1,sy=0.1,sz=0.1\nn:d=T,p=0"; //TODO food size as param
         ExpParams.autorestart = 0;
         ExpParams.psize = 10;
@@ -102 +99 @@
 
         //grwoth speed in time steps
-        ExpParams.growth_step = 50;
+        ExpParams.growth_step = 50; //50
 
         ExpState.totaltestedcr = 0;
@@ -308 +305 @@
                 else
                 {
-                        properSize = cr.user2["Va"] >= cr.user1[0]["vamin"];
+                        properSize = cr.user2["Va"] >= cr.user1[0]["vamin"]; //TODO gene selection
                 }
 
@@ -333 +330 @@
         geno.user1 = cr.user1;
         geno.user2 = cr.user2;
-        Simulator.print("\"" + cr.name + "\" died...");
+        if (ExpParams.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
         ExpState.totaltestedcr++;
 }
@@ -422 +419 @@
 id:growth_step
 name:Growth step
-type:d 10 10000 1000
+type:d -1 10000 1000
 
 prop:

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

@@ -4 +4 @@
 // -------------------------------- step begin --------------------------------
 
-function reproduce_haploid(repro_list)
+function reproduce_haploid(parent, parent2)
 {
-        var len = repro_list.size;
-        if (len % 2 != 0) len = repro_list.size - 1;
+        var number = parent.user2["Va"] / ExpParams.ofnumd + parent2.user2["Va"] / ExpParams.ofnumd;
 
-        for (var i = 0; i < len - 2 ; i = i + 2)
+        for (var j = 0; j < number; j++)
         {
-                var parent = Populations[0].get(repro_list[i]);
-                var parent2 = Populations[0].get(repro_list[i + 1]);
-
-                var number = parent.user2["Va"] / ExpParams.ofnumd + parent2.user2["Va"] / ExpParams.ofnumd;
-
-                for (var j = 0; j < number; j++)
-                {
-                        createOffspring(ExpParams.gend, ExpParams.ofnumd, [parent.user1, parent2.user1], {"Va" : ExpParams.ofnumd, "gen" : 1 , "growth_step" : ExpParams.growth_step, "rsize": ExpParams.rads[1], "vinit": ExpParams.ofnumd}); //TODO genes from both generations in user1
-                }
+                createOffspring(ExpParams.gend, ExpParams.ofnumd, [parent.user1, parent2.user1], {"Va" : ExpParams.ofnumd, "gen" : 1 , "growth_step" : ExpParams.growth_step, "rsize": ExpParams.rads[1], "vinit": ExpParams.ofnumd}); //TODO genes from both generations in user1
         }
-        killParents(repro_list);
 }
 
-function reproduce_diploid(repro_list)
+function reproduce_diploid(parent)
 {
-        for (var i = 0; i < repro_list.size; i++)
+        var number = parent.user2["Va"] / ExpParams.ofnumh;
+        for (var j = 0; j < number / 2; j++)
         {
-                var parent = Populations[0].get(repro_list[i]);
-
-                if (parent.user2["gen"] != 1)
+                var crossed = 0;
+                //crossover
+                if (Math.rnd01 < ExpParams.crossprob)
                 {
-                        Simulator.print("gen: " + parent.user2["gen"]);
+                        crossover(parent, "vamin");
+                        crossed = 1;
                 }
 
-                if (parent.user2["gen"] == 1)
+                for (var k = 0; k < 2; k++)
                 {
-                        var number = parent.user2["Va"] / ExpParams.ofnumh;
-                        for (var j = 0; j < number / 2; j++)
-                        {
-                                var crossed = 0;
-                                //crossover
-                                if (Math.rnd01 < ExpParams.crossprob)
-                                {
-                                        crossover(parent, "vamin");
-                                        crossed = 1;
-                                }
+                        createOffspring(ExpParams.genh, ExpParams.ofnumh, {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h}, {"Va" : ExpParams.ofnumh, "gen" : 0 , "growth_step" : ExpParams.growth_step, "rsize" : ExpParams.rads[0], "vinit": ExpParams.ofnumh});
+                }
 
-                                for (var k = 0; k < 2; k++)
-                                {
-                                        createOffspring(ExpParams.genh, ExpParams.ofnumh, {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h}, {"Va" : ExpParams.ofnumh, "gen" : 0 , "growth_step" : ExpParams.growth_step, "rsize" : ExpParams.rads[0], "vinit": ExpParams.ofnumh});
-                                }
-
-                                //reverse of crossover for fossilization
-                                if (crossed == 1)
-                                {
-                                        crossover(parent, "vamin");
-                                        crossed = 0;
-                                }
-                        }
+                //reverse of crossover for fossilization
+                if (crossed == 1)
+                {
+                        crossover(parent, "vamin");
+                        crossed = 0;
                 }
+                        
         }
-        killParents(repro_list);
 }
 
@@ -72 +49 @@
 }
 
-function killParents(repro_list)
-{
-        for (var j = 0; j < repro_list.size; j++)
-        {
-                Populations[0].kill(repro_list[j]);
-        }
-}
 
 function createOffspring(geno, energy, new_user1, new_user2)
@@ -164 +134 @@
         {
                 reprocounter = 0;
-                var to_repro_h = [];
-                var to_repro_d = [];
-                for (var i = 0; i < Populations[0].size; i++)
+                var parent1 = null;
+                var parent2 = null;
+                var pop = Populations[0];
+                for (var i = pop.size-1; i >= 0; i--)
                 {
-                        var cr = Populations[0].get(i);
-                        if (cr.signals.size > 0)
-                        {
-                                if (cr.user2["gen"] == 0)
+                        if (pop[i].signals.size > 0) 
+                        { 
+                                if (pop[i].user2["gen"]==1)
                                 {
-                                        to_repro_h.add(i);
+                                        reproduce_diploid(pop[i]);
+                                        pop.kill(i);
                                 }
-                                if (cr.user2["gen"] == 1)
+                                else if (parent1 == null)
                                 {
-                                        to_repro_d.add(i);
+                                        parent1 = pop[i];
                                 }
-                        }
-                }
-                if (to_repro_h.size > 1)
-                {
-                        reproduce_haploid(to_repro_h);
-                }
-                if (to_repro_d.size > 0)
-                {
-                        reproduce_diploid(to_repro_d);
+                                else if (parent2 == null)
+                                {
+                                        parent2 = pop[i];
+                                }  
+                                else
+                                {
+                                        reproduce_haploid(parent1, parent2);
+                                        pop.kill(parent1);
+                                        pop.kill(parent2);
+                                        parent1 = null;
+                                        parent2 = null;
+                                }
+                
+                        } 
                 }
         }