Changeset 430 for experiments/frams/foraminifera/data/scripts/foraminifera.inc

Timestamp:

09/08/15 01:03:24 (10 years ago)

Author:

oriona

Message:

new reticulopodia range implemented, visualization of reticulopodia

File:

• experiments/frams/foraminifera/data/scripts/foraminifera.inc (modified) (13 diffs)

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

@@ -5 +5 @@
 {
         colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
-        chambers = [ ["//0\np:sh=1,",
-        "p:0.98089325428009, 0.00591040402650833, 0.00389722990803421,",
-        "p:1.90962779521942, -0.256769120693207, -0.16194811463356,",
-        "p:2.63965249061584, -0.727959632873535, -0.609036147594452,",
-        "p:3.17575979232788, -1.34843015670776, -1.14828503131866,",
-        "p:3.55273032188416, -2.22369408607483, -1.3917418718338,",
-        "p:3.64916682243347, -3.11888360977173, -1.01666414737701,",
-        "p:3.50461649894714, -3.84039807319641, -0.377427101135254,",
-        "p:3.15921688079834, -4.50001525878906, 0.261153399944305,",
-        "p:2.51528453826904, -5.16421365737915, 0.59241509437561,"],
-        ["//0\np:sh=1,",
-        "p:1.08020961284637, -0.0597195439040661, -0.0393781512975693,",
-        "p:1.08020961284637, -0.0597195439040661, -0.0393781512975693,",
-        "p:0.615013539791107, 0.778662621974945, 0.535521030426025,",
-        "p:0.488581955432892, 0.826426684856415, -0.381044268608093,",
-        "p:0.732419908046722, -0.0084995785728097, -1.02214300632477,",
-        "p:1.35288727283478, 0.875738024711609, -1.03719782829285,",
-        "p:0.342692613601685, 0.938660383224487, -1.45657968521118,",
-        "p:1.0958571434021, 0.316927701234818, -1.813929438591,",
-        "p:0.903768002986908, 1.11856341362, -2.53161096572876,",
-        "p:0.21014116704464, 0.295340299606323, -2.45328187942505,"] ];
+        chambers = [ ["0.0,0.0,0.0,", //longitudal
+        "0.98089325428009, 0.00591040402650833, 0.00389722990803421,",
+        "1.90962779521942, -0.256769120693207, -0.16194811463356,",
+        "2.63965249061584, -0.727959632873535, -0.609036147594452,",
+        "3.17575979232788, -1.34843015670776, -1.14828503131866,",
+        "3.55273032188416, -2.22369408607483, -1.3917418718338,",
+        "3.64916682243347, -3.11888360977173, -1.01666414737701,",
+        "3.50461649894714, -3.84039807319641, -0.377427101135254,",
+        "3.15921688079834, -4.50001525878906, 0.261153399944305,",
+        "2.51528453826904, -5.16421365737915, 0.59241509437561,"],
+        ["0.0,0.0,0.0,",  //coiled
+        "1.08020961284637, -0.0597195439040661, -0.0393781512975693,",
+        "1.08020961284637, -0.0597195439040661, -0.0393781512975693,",
+        "0.615013539791107, 0.778662621974945, 0.535521030426025,",
+        "0.488581955432892, 0.826426684856415, -0.381044268608093,",
+        "0.732419908046722, -0.0084995785728097, -1.02214300632477,",
+        "1.35288727283478, 0.875738024711609, -1.03719782829285,",
+        "0.342692613601685, 0.938660383224487, -1.45657968521118,",
+        "1.0958571434021, 0.316927701234818, -1.813929438591,",
+        "0.903768002986908, 1.11856341362, -2.53161096572876,",
+        "0.21014116704464, 0.295340299606323, -2.45328187942505,"] ];
 }
 
@@ -31 +31 @@
 {
         var rad = getProperty(gen, "chamber_proculus"); 
-        var geno = chambers[species][0] + "sx=" + rad + ",sy=" + rad + ",sz=" + rad + ", rz=3.14159265358979,vr=" + colors[gen];
+        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);
@@ -38 +38 @@
         {
                 rad = getProperty(gen, "chamber_proculus") + getProperty(gen, "chamber_difference") * (i + 1); 
-                geno += "\n" +  chambers[species][i+1] + "sh=1,sx=" + rad + ",sy=" + rad + ",sz=" + rad + ",vr=" + colors[gen];
+                geno += "\n" + "p:" + chambers[species][i+1] + "sh=1,sx=" + rad + ",sy=" + rad + ",sz=" + rad + ",vr=" + colors[gen];
         }
 
@@ -45 +45 @@
                 geno += "\n" +  "j:"+ i +", "+ (i+1) +", sh=1";
         }
+
         if (species == 1) geno += "\nn:p=0,d=\"S\"";
 
@@ -54 +55 @@
         if (mode["opt"] == 0) //initial
         {
-                mode["cr"].user1 = {"min_repro_energies" : [getProperty(0, "min_repro_energ"), getProperty(1, "min_repro_energ")], "hibernation" : 1 - mode["species"]};
+                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" : 1 - mode["species"]};
                 mode["cr"].user2 = {"max_energy_level" : getProperty(0,"energies0"), "gen" : 0,  "hibernated" : 0, "species" : mode["species"], "reproduce" : 0};
         }
@@ -75 +76 @@
         {
                 energy0 = getProperty(0,"energies0");
-                number = getProperty(1, "e_repro_cost") * parent.energy / energy0;
+                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
@@ -83 +84 @@
         {
                 energy0 = getProperty(1,"energies0"); 
-                number = getProperty(parent.user2["gen"], "e_repro_cost") * parent.energy / energy0 + getProperty(parent.user2["gen"], "e_repro_cost") * parent2.energy / energy0;
+                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"];
         }
 
-        Simulator.print("number of offspring: " + number);
+        Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0);
 
         for (var j = 0; j < number; j++)
@@ -99 +100 @@
 {
         var energy0 = getProperty(0,"energies0");
-        var number = getProperty(parent.user2["gen"], "e_repro_cost") * parent.energy / energy0;
-
-        Simulator.print("number of offspring: " + number);
+        var number = ((1 - (getProperty(parent.user2["gen"], "e_repro_cost"))) * parent.energy) / energy0;
+
+        Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);
 
         for (var j = 0; j < number / 2; j++)
@@ -149 +150 @@
                                         parent2 = pop[i];
                                 }  
-                                else
+                                if (parent1 != null && parent2 != null)
                                 {
                                         reproduce_haploid(parent1, parent2, 0);
@@ -158 +159 @@
                                         parent1 = null;
                                         parent2 = null;
-                                }
-                
+                                }       
                         } 
                 }
@@ -204 +204 @@
 }
 
+
+
 function foramReproduce(cr)
 {
@@ -231 +233 @@
                 }
                 if (reproduced == 1)
-                                return;
+                                return 1;
         }
 
@@ -239 +241 @@
                 cr.user2["reproduce"] = 0; 
         }
+
+        return 0;
 }