Changeset 145 for cpp/frams/genetics/fF

Timestamp:

02/26/14 20:21:22 (11 years ago)

Author:

sz

Message:

Genetics reorganization (affects ALL applications!):

• Converters/Validators? are now configured/initialized in a more verbose but also less confusing way
• At the same time, the PreconfiguredGenetics? object will help you avoid the increased complexity by creating the ready-to-use environment that is sufficient in 99% of cases (see the demos)
• Format F genetics updated (work in progress)

Location:

cpp/frams/genetics/fF

Files:

• fF_genotype.cpp (added)
• fF_genotype.h (modified) (2 diffs)
• oper_fF.cpp (modified) (3 diffs)
• oper_fF.h (modified) (1 diff)

cpp/frams/genetics/fF/fF_genotype.h

@@ -8 +8 @@
 #include <stdio.h>
 #include "common/stl-util.h"
-
+#include <frams/param/param.h>
 
 struct fF_growth_params
 {
         int number_of_chambers;
-        double scalex, scaley, scalez; //scaling factors
-        double translation; //translation factor, TF range [−1; 1]
+        double scalex, scaley, scalez;
+        double translation;
         double angle1, angle2;
 
+        static ParamEntry paramtab[];
+        Param param;
+
         fF_growth_params()
+                :param(paramtab, this)
         {
                 reset();
@@ -24 +28 @@
         void reset()
         {
-                number_of_chambers = 1;
-                scalex = scaley = scalez = 1;
-                translation = 1;
-                angle1 = angle2 = 0;
+                param.setDefault();
         }
 
         bool load(const char* serialized)
         {
-                return sscanf(serialized, "%d %lf %lf %lf %lf %lf %lf", &number_of_chambers, &scalex, &scaley, &scalez, &translation, &angle1, &angle2) == 7;
+                SString s = serialized;
+                int p = 0; //position in string
+                return ((param.load2(s, p)==7) && (p==s.len()));
         }
 
         string save()
         {
-                return ssprintf("%d %f %f %f %f %f %f", number_of_chambers, scalex, scaley, scalez, translation, angle1, angle2);
+                SString tmp;
+                param.save2(tmp, NULL/*object containing default values for comparison*/, false/*add CR*/, false/*force field names*/);
+                return string((const char*)tmp);
         }
 };

cpp/frams/genetics/fF/oper_fF.cpp

@@ -4 +4 @@
 
 #include "oper_fF.h"
-#include <frams/genetics/f9/conv_f9.h>
+#include "fF_genotype.h"
 #include <common/nonstd.h> //randomN, rnd01
 
 
-//THIS FILE NEEDS UPDATE. OLD, UNRELATED SOURCES BELOW (COPIED FROM f9).
-
 #define FIELDSTRUCT GenoOper_fF
-static ParamEntry GENOf9param_tab[]=
+static ParamEntry GENOfFparam_tab[] =
 {
-        {"Genetics: fF",1,1,},
-        {"fF_mut",0,0,"Mutation probability","f 0 1 0.1",FIELD(mut_prob),"How many genes should be mutated during single mutation (1=all genes, 0.1=ten percent)",},
-        {0,},
+        { "Genetics: fF", 1, 1, },
+        { "fF_xover", 0, 0, "Averaging crossover proportion", "f 0 0.5 0.5", FIELD(xover_proportion), "0.5 => children are averaged parents.\n0.2 => children are only 20% different from parents.\n0 => each child is identical to one parent (no crossover).", },
+        { 0, },
 };
 #undef FIELDSTRUCT
@@ -22 +20 @@
 GenoOper_fF::GenoOper_fF()
 {
-        par.setParamTab(GENOf9param_tab);
+        par.setParamTab(GENOfFparam_tab);
         par.select(this);
         par.setDefault();
-        supported_format='F';
+        supported_format = 'F';
 }
 
 int GenoOper_fF::checkValidity(const char* gene)
 {
-        return GENOPER_OK;
-        if (!gene[0]) return 1; //empty is not valid
-        bool ok=true;
-        int i;
-        for(i=0;i<strlen(gene);i++) if (!strchr(turtle_commands_f9,gene[i])) {ok=false; break;}
-        return ok ? GENOPER_OK : i+1;
+        fF_growth_params par;
+        return par.load(gene) ? GENOPER_OK : 1;
 }
 
-///Remove all invalid letters from the genotype
 int GenoOper_fF::validate(char *&gene)
 {
-        SString validated; //new genotype (everything except turtle_commands_f9 is skipped)
-        for(int i=0;i<strlen(gene);i++)
-                if (strchr(turtle_commands_f9,gene[i])) validated+=gene[i];  //validated contains only turtle_commands_f9
+        fF_growth_params par; //is initialized with default values
+        par.load(gene); //loads as much as possible, other fields remain with default values
+        string validated = par.save();
         free(gene);
-        gene=strdup(validated); //reallocate
+        gene = strdup(validated.c_str()); //reallocate
         return GENOPER_OK;
 }
 
-///Very simple mutation
-int GenoOper_fF::mutate(char *&gene,float &chg,int &method)
+//Creep-mutate one property
+int GenoOper_fF::mutate(char *&gene, float &chg, int &method)
 {
-        method=0;
-        int changes=0,len=strlen(gene);
-        int symbols=strlen(turtle_commands_f9);
-
-        for(int i=0;i<len;i++)
+        method = 0;
+        fF_growth_params par;
+        par.load(gene);
+        int which = randomN(par.param.getPropCount());
+        bool mutated_ok = GenoOperators::mutatePropertyNaive(par.param, which);
+        if (mutated_ok)
         {
-                if (rnd01<mut_prob) //normalize prob with the length of the genotype
-                {
-                        char oldgene=gene[i];
-                        gene[i]=turtle_commands_f9[randomN(symbols)];
-                        if (gene[i]!=oldgene) changes++;
-                }
+                string saved = par.save();
+                free(gene);
+                gene = strdup(saved.c_str()); //reallocate
+                chg = 1.0f / par.param.getPropCount();
+                return GENOPER_OK;
         }
-
-        if (rnd01<mut_prob) //add or delete a random char
+        else
         {
-                SString newgeno(gene);
-                if (randomN(2)==0) //add
-                {
-                        int symbols=strlen(turtle_commands_f9);
-                        int p=randomN(len+1);  //random location
-                        //printf("before add: %s\n",(const char*)newgeno);
-                        newgeno=newgeno.substr(0,p)+SString(turtle_commands_f9+randomN(symbols),1)+newgeno.substr(p);
-                        //printf("after add: %s\n",(const char*)newgeno);
-                        changes++;
-                } else if (len>1) //delete
-                {
-                        int p=randomN(len);  //random location
-                        //printf("before delete: %s\n",(const char*)newgeno);
-                        newgeno=newgeno.substr(0,p)+newgeno.substr(p+1);
-                        //printf("after delete: %s\n",(const char*)newgeno);
-                        changes++;
-                }
-                free(gene);
-                gene=strdup(newgeno); //reallocate
+                chg = 0;
+                return GENOPER_OPFAIL;
         }
-
-        chg=(float)changes/len;
-        return changes>0?GENOPER_OK:GENOPER_OPFAIL; //no changes => OPFAIL so that genman will call mutate again
 }
 
-///A simple one-point crossover
-int GenoOper_fF::crossOver(char *&g1,char *&g2,float& chg1,float& chg2)
+///Averaging crossover
+int GenoOper_fF::crossOver(char *&g1, char *&g2, float& chg1, float& chg2)
 {
-        int len1=strlen(g1),len2=strlen(g2);
-        int p1=randomN(len1);  //random cut point for first genotype
-        int p2=randomN(len2);  //random cut point for second genotype
-        char *child1=(char*)malloc(p1+len2-p2+1);
-        char *child2=(char*)malloc(p2+len1-p1+1);
-        strncpy(child1,g1,p1);   strcpy(child1+p1,g2+p2);
-        strncpy(child2,g2,p2);   strcpy(child2+p2,g1+p1);
-        free(g1); g1=child1;
-        free(g2); g2=child2;
-        chg1=(float)p1/strlen(child1);
-        chg2=(float)p2/strlen(child2);
+        //g1 = strdup("1,0.5,0.5,0.5,0.5,1,1"); //testing...
+        //g2 = strdup("4,1,  1,  1,  1,  2,2"); //testing...
+        //xover_proportion = 0.1; //testing...
+        fF_growth_params par1;
+        par1.load(g1);
+        fF_growth_params par2;
+        par2.load(g2);
+        chg1 = xover_proportion;
+        chg2 = 1 - xover_proportion;
+        for (int i = 0; i < par1.param.getPropCount(); i++)
+                GenoOperators::linearMix(par1.param, i, par2.param, i, xover_proportion);
+        string saved = par1.save();
+        free(g1);
+        g1 = strdup(saved.c_str()); //reallocate
+        saved = par2.save();
+        free(g2);
+        g2 = strdup(saved.c_str()); //reallocate
         return GENOPER_OK;
 }
@@ -113 +91 @@
 unsigned long GenoOper_fF::style(const char *g, int pos)
 {
-        char ch=g[pos];
-        unsigned long style=GENSTYLE_CS(0,GENSTYLE_INVALID); //default, should be changed below
-        char *ptr=strchr((char*)turtle_commands_f9,ch);
-        if (ptr)
-        {
-                int pos=ptr-turtle_commands_f9;
-                int axis=pos/2;
-                style=GENSTYLE_RGBS(axis==0?200:0,axis==1?200:0,axis==2?200:0,GENSTYLE_NONE);
-        }
+        char ch = g[pos];
+        unsigned long style = GENSTYLE_CS(0, GENSTYLE_INVALID); //default, should be changed below
+        if (strchr("-.e 0123456789", ch) != NULL)
+                style = GENSTYLE_CS(GENCOLOR_NUMBER, GENSTYLE_NONE);
+        else if (ch == ',')
+                style = GENSTYLE_RGBS(0, 0, 0, GENSTYLE_BOLD);
         return style;
 }

cpp/frams/genetics/fF/oper_fF.h

@@ -18 +18 @@
         int crossOver(char *&g1, char *&g2, float& chg1, float& chg2);
         unsigned long style(const char *g, int pos);
-        const char* getSimplest() { return "5 0.9 0.8 0.7 0.7 0.3 0.7"; }
+        const char* getSimplest() { return "6,0.8,0.85,0.9,0.6,0.3,0.7"; }
 
-        double mut_prob; //mutation probability
+        double xover_proportion;
 };