Changeset 797 for cpp

Timestamp:

06/06/18 01:45:18 (6 years ago)

Author:

Maciej Komosinski

Message:

A more complete implementation of fB, fH, fL

Location:

cpp/frams/genetics

Files:

• fB/fB_conv.cpp (modified) (6 diffs)
• fB/fB_conv.h (modified) (2 diffs)
• fB/fB_general.h (modified) (4 diffs)
• fB/fB_oper.cpp (modified) (8 diffs)
• fB/fB_oper.h (modified) (3 diffs)
• fH/fH_conv.cpp (modified) (1 diff)
• fH/fH_conv.h (modified) (1 diff)
• fH/fH_general.cpp (modified) (11 diffs)
• fH/fH_general.h (modified) (2 diffs)
• fH/fH_oper.cpp (modified) (3 diffs)
• fH/fH_oper.h (modified) (2 diffs)
• fL/fL_conv.cpp (modified) (1 diff)
• fL/fL_conv.h (modified) (1 diff)
• fL/fL_general.cpp (modified) (36 diffs)
• fL/fL_general.h (modified) (19 diffs)
• fL/fL_matheval.cpp (modified) (11 diffs)
• fL/fL_matheval.h (modified) (6 diffs)
• fL/fL_oper.cpp (modified) (1 diff)
• fL/fL_oper.h (modified) (1 diff)

cpp/frams/genetics/fB/fB_conv.cpp

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #include "fB_conv.h"
 
@@ -89 +93 @@
                         continue;
                 }
-                fH_Handle *handle = convertCharacterToHandle(gene[2], dims, start, end, ranges);
+                int hclasspos = 2;
+                if (gene[2] == '"')
+                {
+                        hclasspos--;
+                        if (!getNextCharId(gene, hclasspos))
+                        {
+                                return "";
+                        }
+                }
+                fH_Handle *handle = convertCharacterToHandle(gene[hclasspos], dims, start, end, ranges);
                 ParamEntry *tab = creature.getParamTab(handle->type);
                 void *obj = ParamObject::makeObject(tab);
@@ -97 +110 @@
 
                 int propindex = 0;
-                int z = 3;
+                int z = hclasspos;
+                if (gene[z] == '"')
+                {
+                        z--;
+                        if (!getNextCharId(gene, z))
+                        {
+                                delete handle;
+                                ParamObject::freeObject(obj);
+                                return "";
+                        }
+                }
                 endoffset = 0;
                 if (gene.indexOf("zz", 0) != -1) endoffset = 2;
+                int nclassdefcount = 1;
                 while (z < gene.len() - endoffset)
                 {
-                        if (processNextLetter(creature, handle, par, gene, propindex, z, ranges) == -1)
-                        {
-                                logMessage("GenoConv_fBH", "convert", LOG_WARN, "Property of fH could not be parsed");
-                        }
+                        if (processNextLetter(creature, handle, par, gene, propindex, z, ranges, nclassdefcount) == -1)
+                        {
+                                logMessage("GenoConv_fBH", "convert", LOG_ERROR, "Property of fH could not be parsed");
+                                delete handle;
+                                ParamObject::freeObject(obj);
+                                return "";
+                        }
+                }
+                if (handle->type == fHBodyType::NEURON && propindex < par.getPropCount())
+                {
+                        SString nclass;
+                        if (!getNeuroClass(gene, nclass, nclassdefcount))
+                        {
+                                delete handle;
+                                ParamObject::freeObject(obj);
+                                return "";
+                        }
+                        par.setStringById(FH_PE_NEURO_DET, nclass);
                 }
                 handle->loadProperties(par);
@@ -132 +170 @@
 }
 
-int GenoConv_fBH::processNextLetter(fH_Builder &creature, fH_Handle *&currhandle, Param &par, SString gene, int &propindex, int &i, std::vector<IRange> ranges[3])
+bool GenoConv_fBH::getNextCharId(SString genotype, int &i)
+{
+        i++;
+        if (genotype[i] == '"')
+        {
+                int nextid = i + 1;
+                do
+                {
+                        nextid = genotype.indexOf('"', nextid);
+                        if (nextid == -1)
+                        {
+                                return false;
+                        }
+                        nextid++;
+                }
+                while (genotype[nextid] == '"');
+                i = nextid;
+        }
+        return true;
+}
+
+bool GenoConv_fBH::getNeuroClass(SString gene, SString &def, int nclassdefcount)
+{
+        SString lastdef = "N";
+        int nclass = 0;
+        int pos = 0;
+        while (nclass < nclassdefcount)
+        {
+                pos = gene.indexOf('\"', pos);
+                if (pos == -1)
+                {
+                        def = lastdef;
+                        return true;
+                }
+                pos++;
+                SString currdef;
+                if (gene.indexOf('\"', pos) == -1 || !gene.getNextToken(pos, currdef, '\"'))
+                {
+                        def = lastdef;
+                        return false;
+                }
+                lastdef = currdef;
+                nclass++;
+        }
+        def = lastdef;
+        return true;
+}
+
+int GenoConv_fBH::processNextLetter(fH_Builder &creature, fH_Handle *&currhandle, Param &par, SString gene, int &propindex, int &i, std::vector<IRange> ranges[3], int &nclassdefcount)
 {
         if (propindex >= par.getPropCount())
@@ -147 +233 @@
                 par.setDefault();
                 propindex = 0;
-                i++;
+                if (!getNextCharId(gene, i))
+                        return -1;
                 return 0;
         }
@@ -166 +253 @@
                         }
                         propindex++;
-                        i++;
+                        if (!getNextCharId(gene, i))
+                                return -1;
                         return 0;
                 }
                 else if (currhandle->type == fHBodyType::NEURON && *par.id(propindex) == 'd')
                 {
-                        //TODO: handle neuron classes and properties
+                        //When 'd' property appears for i-th element in gene, the method
+                        //looks for i-th neuron definition
+                        SString nclass;
+                        if (!getNeuroClass(gene, nclass, nclassdefcount)) return -1;
+                        par.setString(propindex, nclass);
                         propindex++;
-                        i++;
+                        nclassdefcount++;
+                        if (!getNextCharId(gene, i))
+                                return -1;
                         return 0;
                 }

cpp/frams/genetics/fB/fB_conv.h

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #ifndef _FB_CONV_H_
 #define _FB_CONV_H_
@@ -8 +12 @@
 {
 private:
+        bool getNextCharId(SString genotype, int &i);
         double convertCharacterTo01(char c);
         double convertCharacterToWeight(char c);
         static fH_Handle* convertCharacterToHandle(char c, int dims, int start, int end, std::vector<IRange> ranges[3]);
-        int processNextLetter(fH_Builder &creature, fH_Handle *&currhandle, Param &par, SString gene, int &propindex, int &i, std::vector<IRange> ranges[3]);
+        int processNextLetter(fH_Builder &creature, fH_Handle *&currhandle, Param &par, SString gene, int &propindex, int &i, std::vector<IRange> ranges[3], int &nclassdefcount);
+        bool getNeuroClass(SString gene, SString &def, int nclassdefcount);
 
 public:

cpp/frams/genetics/fB/fB_general.h

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #ifndef _FB_GENERAL_H_
 #define _FB_GENERAL_H_
@@ -10 +14 @@
         {
                 int start = 0;
+                int prev = 0;
                 int count = -1;
                 do {
                         count++;
                         start = geno.indexOf("aa", start) + 1; // +1 is for progress, starting codons can overlap
+                        int quotecount = 0;
+                        for (int q = prev; q < start; q++) if (geno[q] == '\"') quotecount++;
+                        prev = start;
+                        if (quotecount % 2 != 0) count--; // 'aa' sequence is within quotes
                 } while (start - 1 != -1);
                 return count;
@@ -25 +34 @@
                         count++;
                         start = genotype.indexOf("aa", start) + 1;
+                        int quotecount = 0;
+                        for (int q = 0; q < start; q++) if (genotype[q] == '\"') quotecount++;
+                        if (quotecount % 2 != 0) count--; // 'aa' sequence is within quotes
                 } while (start - 1 != -1 && count != i);
                 if (start - 1 == -1) // there is no gene with a given "i"
@@ -33 +45 @@
                 }
                 end = start;
-                end = genotype.indexOf("zz", end);
+                int quotecount = 0;
+                do {
+                        quotecount = 0;
+                        end = genotype.indexOf("zz", end);
+                        if (end != -1)
+                        {
+                                for (int q = start; q < end; q++) if (genotype[q] == '\"') quotecount++;
+                                if (quotecount % 2 != 0) end++;
+                        }
+                } while (quotecount % 2 != 0 && end != -1);
+
                 if (end == -1) end = genotype.len();
                 else end += 2;

cpp/frams/genetics/fB/fB_oper.cpp

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #include <frams/util/sstring.h>
 #include <vector>
@@ -5 +9 @@
 #include "fB_general.h"
 #include "fB_oper.h"
+#include "../fH/fH_oper.h"
 
 #define FIELDSTRUCT Geno_fB
@@ -10 +15 @@
 static ParamEntry GENOfBparam_tab[] =
 {
-        { "Genetics: fB", 3, FB_MUT_COUNT + FB_XOVER_COUNT, }, // ask about it
+        { "Genetics: fB", 3, FB_MUT_COUNT + FB_XOVER_COUNT, },
         { "Genetics: fB: Mutation", },
         { "Genetics: fB: Crossover", },
         { "fB_mut_substitution", 1, 0, "Substitution", "f 0 1 0.6", FIELD(mutationprobs[FB_SUBSTITUTION]), "Probability of mutation by changing single random letter in genotype", },
-        { "fB_mut_insertion", 1, 0, "Insertion", "f 0 1 0.1", FIELD(mutationprobs[FB_INSERTION]), "Probability of mutation by inserting characters in random place of genotype", },
+        { "fB_mut_insertion", 1, 0, "Insertion", "f 0 1 0.95", FIELD(mutationprobs[FB_INSERTION]), "Probability of mutation by inserting characters in random place of genotype", },
+        { "fB_mut_nclassins", 1, 0, "Insertion of neuron class definition", "f 0 1 0.05", FIELD(mutationprobs[FB_NCLASSINS]), "Probability of mutation by inserting neuron class definition in random place of genotype", },
         { "fB_mut_deletion", 1, 0, "Deletion", "f 0 1 0.1", FIELD(mutationprobs[FB_DELETION]), "Probability of mutation by deleting random characters in genotype", },
         { "fB_mut_duplication", 1, 0, "Duplication", "f 0 1 0.05", FIELD(mutationprobs[FB_DUPLICATION]), "Probability of mutation by copying single *gene* of genotype and appending it to the beginning of this genotype", },
@@ -81 +87 @@
                 if (!islower(genotype[i]))
                 {
-                        return i + 1;
+                        if (genotype[i] == '"')
+                        {
+                                SString neuclassdef;
+                                int nextid = i + 1;
+                                if (!genotype.getNextToken(nextid, neuclassdef, '"'))
+                                {
+                                        return i + 1;
+                                }
+                                Neuro *neu = new Neuro();
+                                neu->setDetails(neuclassdef);
+
+                                bool isclass = neu->getClass() ? true : false;
+                                delete neu;
+                                if (!isclass)
+                                {
+                                        return i + 1;
+                                }
+                                i = nextid;
+                        }
+                        else
+                        {
+                                return i + 1;
+                        }
                 }
         }
@@ -121 +149 @@
                 if (!isalpha(genotype[i]))
                 {
-                        return GENOPER_OPFAIL;
+                        if (genotype[i] == '"')
+                        {
+                                SString neuclassdef;
+                                int nextid = i + 1;
+                                if (!genotype.getNextToken(nextid, neuclassdef, '"'))
+                                {
+                                        return i + 1;
+                                }
+                                Neuro *neu = new Neuro();
+                                neu->setDetails(neuclassdef);
+
+                                bool isclass = neu->getClass() ? true : false;
+                                delete neu;
+                                if (!isclass)
+                                {
+                                        return i + 1;
+                                }
+                                i = nextid;
+                        }
+                        else
+                        {
+                                return GENOPER_OPFAIL;
+                        }
                 }
                 // if character is uppercase, then convert it to lowercase
-                if (isupper(genotype[i]))
+                else if (isupper(genotype[i]))
                 {
                         genotype.directWrite()[i] = tolower(genotype[i]);
@@ -142 +192 @@
         }
         return GENOPER_OK;
+}
+
+SString Geno_fB::detokenizeSequence(std::list<SString> tokenlist)
+{
+        SString res = "";
+        for (std::list<SString>::iterator it = tokenlist.begin(); it != tokenlist.end(); it++)
+        {
+                res += (*it);
+        }
+        return res;
+}
+
+std::list<SString> Geno_fB::tokenizeSequence(SString genotype)
+{
+        std::list<SString> res;
+        int i = 0;
+        while (i < genotype.len())
+        {
+                // if character is not alphabetic - error
+                if (isalpha(genotype[i]))
+                {
+                        SString el = "";
+                        el += genotype[i];
+                        res.push_back(el);
+                        i++;
+                }
+                else
+                {
+                        SString neuclassdef;
+                        i++;
+                        genotype.getNextToken(i, neuclassdef, '"');
+                        SString ndef = "\"";
+                        ndef += neuclassdef;
+                        ndef += "\"";
+                        res.push_back(ndef);
+                }
+        }
+        return res;
 }
 
@@ -157 +245 @@
         case FB_SUBSTITUTION:
         {
-                int rndid = randomN(line.len()); // select random letter from genotype
+                std::list<SString> tokenized = tokenizeSequence(line);
+                int rndid = randomN(tokenized.size()); // select random letter from genotype
                 // increment/decrement character - when overflow happens, this method
                 // uses reflect method
-                if (randomN(2) == 0)
-                {
-                        if (line[rndid] == 'a') line.directWrite()[rndid] = 'b';
-                        else line.directWrite()[rndid] = line[rndid] - 1;
+                std::list<SString>::iterator it = tokenized.begin();
+                std::advance(it, rndid);
+                SString t = (*it);
+                if ((*it).len() == 1)
+                {
+                        if (randomN(2) == 0)
+                        {
+                                if ((*it)[0] == 'a') (*it).directWrite()[0] = 'b';
+                                else (*it).directWrite()[0] = (*it)[0] - 1;
+                        }
+                        else
+                        {
+                                if ((*it)[0] == 'z') (*it).directWrite()[0] = 'y';
+                                else (*it).directWrite()[0] = (*it)[0] + 1;
+                        }
+                        chg = 1.0 / line.len();
                 }
                 else
                 {
-                        if (line[rndid] == 'z') line.directWrite()[rndid] = 'y';
-                        else line.directWrite()[rndid] = line[rndid] + 1;
-                }
+                        // first method needs to extract quotes
+                        SString def = (*it);
+                        def = def.substr(1, def.len() - 2);
+                        Geno_fH::mutateNeuronProperties(def);
+                        SString res = "\"";
+                        res += def;
+                        res += "\"";
+                        (*it) = res;
+                        chg = (double)def.len() / line.len();
+                }
+                line = detokenizeSequence(tokenized);
+                break;
+        }
+        case FB_INSERTION:
+        {
                 chg = 1.0 / line.len();
-                break;
-        }
-        case FB_INSERTION:
+                std::list<SString> tokenized = tokenizeSequence(line);
+                int rndid = randomN(tokenized.size()); // select random insertion point
+                std::list<SString>::iterator it = tokenized.begin();
+                std::advance(it, rndid);
+                SString letter = "a";
+                letter.directWrite()[0] = 'a' + randomN(26);
+                tokenized.insert(it, letter);
+                line = detokenizeSequence(tokenized);
+                break;
+        }
+        case FB_NCLASSINS:
+        {
+                std::list<SString> tokenized = tokenizeSequence(line);
+                std::list<SString>::iterator it = tokenized.begin();
+                int rndid = randomN(tokenized.size()); // select random insertion point
+                std::advance(it, rndid);
+                NeuroClass *cls = getRandomNeuroClass();
+                SString classdef = cls->getName();
+                Geno_fH::mutateNeuronProperties(classdef);
+                SString res = "\"";
+                res += classdef;
+                res += "\"";
+                tokenized.insert(it, res);
+                chg = (double)classdef.len() / line.len();
+                line = detokenizeSequence(tokenized);
+                break;
+        }
+        case FB_DELETION:
         {
                 chg = 1.0 / line.len();
-                int rndid = randomN(genotype.len()); // select random insertion point
-                char letter = 'a' + randomN(26);
-                SString result = line.substr(0, rndid);
-                result += letter;
-                result += line.substr(rndid);
-                line = result;
-                break;
-        }
-        case FB_DELETION:
-        {
-                chg = 1.0 / line.len();
-                int rndid = randomN(line.len()); // select random insertion point
-                if (rndid == line.len() - 1)
-                {
-                        line = line.substr(0, line.len() - 1);
-                }
-                else
-                {
-                        line = line.substr(0, rndid) + line.substr(rndid + 1);
-                }
+                std::list<SString> tokenized = tokenizeSequence(line);
+                std::list<SString>::iterator it = tokenized.begin();
+                int rndid = randomN(tokenized.size()); // select random deletion point
+                std::advance(it, rndid);
+                tokenized.erase(it);
+                line = detokenizeSequence(tokenized);
                 break;
         }
@@ -210 +334 @@
         case FB_TRANSLOCATION:
         {
-                std::vector<int> cuts(4);
+                std::list<SString> tokenized = tokenizeSequence(line);
+                std::vector<unsigned int> cuts(4);
                 for (int i = 0; i < 4; i++)
                 {
-                        cuts[i] = randomN(line.len());
+                        cuts[i] = randomN(tokenized.size());
                 }
                 std::sort(cuts.begin(), cuts.end());
-                SString first = line.substr(cuts[0], cuts[1] - cuts[0]);
-                SString second = line.substr(cuts[2], cuts[3] - cuts[2]);
-                SString result = line.substr(0, cuts[0]) + second +
-                        line.substr(cuts[1], cuts[2] - cuts[1]) + first + line.substr(cuts[3]);
-                line = result;
+                std::vector<std::list<SString>::iterator> iters(4);
+                for (int i = 0; i < 4; i++)
+                {
+                        iters[i] = tokenized.begin();
+                        std::advance(iters[i], cuts[i]);
+                }
+
+                std::list<SString> res;
+                res.insert(res.end(), tokenized.begin(), iters[0]);
+                res.insert(res.end(), iters[2], iters[3]);
+                res.insert(res.end(), iters[1], iters[2]);
+                res.insert(res.end(), iters[0], iters[1]);
+                res.insert(res.end(), iters[3], tokenized.end());
+
+//              SString first = line.substr(cuts[0], cuts[1] - cuts[0]);
+//              SString second = line.substr(cuts[2], cuts[3] - cuts[2]);
+//              SString result = line.substr(0, cuts[0]) + second +
+//                      line.substr(cuts[1], cuts[2] - cuts[1]) + first + line.substr(cuts[3]);
+                line = detokenizeSequence(res);
                 chg = (float)(cuts[3] - cuts[2] + cuts[1] - cuts[0]) / line.len();
                 break;

cpp/frams/genetics/fB/fB_oper.h

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #ifndef _FB_OPER_H_
 #define _FB_OPER_H_
 
 #include "../genooperators.h"
+#include <list>
 
 /** @name Codes for general fB mutation types */
@@ -8 +13 @@
 #define FB_SUBSTITUTION  0 ///<Relative probability of mutation by changing single random letter in genotype (substitution)
 #define FB_INSERTION     1 ///<Relative probability of mutation by inserting characters in random place of genotype
-#define FB_DELETION      2 ///<Relative probability of mutation by deleting random characters in genotype
-#define FB_DUPLICATION   3 ///<Relative probability of mutation by copying single *gene* of genotype and appending it to the beginning of this genotype
-#define FB_TRANSLOCATION 4 ///<Relative probability of mutation by replacing two substrings in genotype
-#define FB_MUT_COUNT     5 ///<Count of mutation types
+#define FB_NCLASSINS     2 ///<Relative probability of mutation by inserting neuron class definition in random place of genotype
+#define FB_DELETION      3 ///<Relative probability of mutation by deleting random characters in genotype
+#define FB_DUPLICATION   4 ///<Relative probability of mutation by copying single *gene* of genotype and appending it to the beginning of this genotype
+#define FB_TRANSLOCATION 5 ///<Relative probability of mutation by replacing two substrings in genotype
+#define FB_MUT_COUNT     6 ///<Count of mutation types
 //@}
 
@@ -25 +31 @@
 private:
         bool hasStick(SString genotype);
+        SString detokenizeSequence(std::list<SString> tokenlist);
+        std::list<SString> tokenizeSequence(SString genotype);
 
 public:

cpp/frams/genetics/fH/fH_conv.cpp

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #include "fH_conv.h"
 

cpp/frams/genetics/fH/fH_conv.h

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #ifndef _FH_CONV_H_
 #define _FH_CONV_H_

cpp/frams/genetics/fH/fH_general.cpp

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #include <string>
 #include <limits>
@@ -13 +17 @@
 // Methods for loading handles
 
-const char *fH_part_names[PART_PROPS_COUNT] = { "dn", "fr", "ing", "as" };
-
-const char *fH_joint_names[JOINT_PROPS_COUNT] = { "stif", "rotstif", "stam" };
+const char *fH_part_names[FH_PART_PROPS_COUNT] = { "dn", "fr", "ing", "as" };
+
+const char *fH_joint_names[FH_JOINT_PROPS_COUNT] = { "stif", "rotstif", "stam" };
 
 void fH_Handle::loadProperties(Param par)
@@ -106 +110 @@
 
         Part p;
-        for (int i = 0; i < PART_PROPS_COUNT; i++)
+        for (int i = 0; i < FH_PART_PROPS_COUNT; i++)
         {
                 stickmut.addProperty(&p.properties().getParamTab()[p.properties().findId(fH_part_names[i]) + p.properties().getGroupCount()], -1);
@@ -112 +116 @@
 
         Joint j;
-        for (int i = 0; i < JOINT_PROPS_COUNT; i++)
+        for (int i = 0; i < FH_JOINT_PROPS_COUNT; i++)
         {
                 stickmut.addProperty(&j.properties().getParamTab()[j.properties().findId(fH_joint_names[i]) + j.properties().getGroupCount()], -1);
@@ -119 +123 @@
 
         Neuro n;
-        neuronmut.addProperty(&n.properties().getParamTab()[n.properties().findId(PE_NEURO_DET) + n.properties().getGroupCount()], -1);
+        neuronmut.addProperty(&n.properties().getParamTab()[n.properties().findId(FH_PE_NEURO_DET) + n.properties().getGroupCount()], -1);
 
         Param tmp(f0_neuroconn_paramtab, NULL);
-        connectionmut.addProperty(&tmp.getParamTab()[tmp.findId(PE_CONN_WEIGHT) + tmp.getGroupCount()], -1);
+        connectionmut.addProperty(&tmp.getParamTab()[tmp.findId(FH_PE_CONN_WEIGHT) + tmp.getGroupCount()], -1);
 
         stickparamtab = ParamObject::makeParamTab((ParamInterface *)&stickmut, 0, 0, stickmut.firstMutableIndex());
@@ -343 +347 @@
 {
         Param par(tab, obj);
-        double partprops[PART_PROPS_COUNT];
-        for (int i = 0; i < PART_PROPS_COUNT; i++)
+        double partprops[FH_PART_PROPS_COUNT];
+        for (int i = 0; i < FH_PART_PROPS_COUNT; i++)
         {
                 partprops[i] = par.getDouble(2 * getDimensions() + i);
@@ -357 +361 @@
         {
                 par.select(child->obj);
-                for (int i = 0; i < PART_PROPS_COUNT; i++)
+                for (int i = 0; i < FH_PART_PROPS_COUNT; i++)
                 {
                         partprops[i] += par.getDouble(2 * getDimensions() + i);
@@ -364 +368 @@
         }
 
-        for (int i = 0; i < PART_PROPS_COUNT; i++)
+        for (int i = 0; i < FH_PART_PROPS_COUNT; i++)
         {
                 partprops[i] /= stickscount;
@@ -522 +526 @@
                         msg += det + "\" does not exist";
                         logMessage("fH_Builder", "developBrain", LOG_ERROR, msg.c_str());
+                        delete currneu->neuron;
                         return -1;
                 }
@@ -601 +606 @@
                 if (!beginneu)
                 {
-                        logMessage("fH_Builder", "developBrain", LOG_WARN, "There are no available neurons with outputs, connection could not be established");
+                        // due to often appearance of connection genes in fB encoding, this
+                        // log message is commented
+                        // logMessage("fH_Builder", "developBrain", LOG_DEBUG, "There are no available neurons with outputs, connection could not be established");
                         continue;
                 }
@@ -628 +635 @@
                 if (!endneu)
                 {
-                        logMessage("fH_Builder", "developBrain", LOG_WARN, "There are no available neurons with free inputs, connection could not be established");
+                        // due to often appearance of connection genes in fB encoding, this
+                        // log message is commented
+                        // logMessage("fH_Builder", "developBrain", LOG_DEBUG, "There are no available neurons with free inputs, connection could not be established");
                         continue;
                 }

cpp/frams/genetics/fH/fH_general.h

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #ifndef _FH_GENERAL_H_
 #define _FH_GENERAL_H_
@@ -14 +18 @@
 #define HANDLE_VECTOR_TYPE "f -1.0 1.0 0.0" ///<Vector values type definition
 #define STICKH_LENGTH_TYPE "f 0.001 1.999 1.0" ///<Length of stick handle. Minimum should not be equal to 0, because calculating direction of next part from current stick with length 0 would be impossible
-#define PART_PROPS_COUNT   4 ///<Count of part properties
-#define JOINT_PROPS_COUNT  3 ///<Count of joint properties
-#define PE_NEURO_DET       "d" ///<Id of details type definition in f0_neuro_paramtab
-#define PE_CONN_WEIGHT     "w" ///<Id of weight type definition in f0_neuroconn_paramtab
+#define FH_PART_PROPS_COUNT   4 ///<Count of part properties
+#define FH_JOINT_PROPS_COUNT  3 ///<Count of joint properties
+#define FH_PE_NEURO_DET       "d" ///<Id of details type definition in f0_neuro_paramtab
+#define FH_PE_CONN_WEIGHT     "w" ///<Id of weight type definition in f0_neuroconn_paramtab
 //@}
 

cpp/frams/genetics/fH/fH_oper.cpp

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #include "fH_oper.h"
 
@@ -421 +425 @@
 }
 
-void Geno_fH::mutateNeuronHandleProperties(fH_NeuronHandle *handle, ParamEntry *tab, bool userandomclass)
+void Geno_fH::mutateNeuronProperties(SString &det)
 {
         Neuro neu;
-        Param hpar(tab, handle->obj);
-        SString det = hpar.getStringById("d");
+        det = det == "" ? "N" : det;
         neu.setDetails(det == "" ? "N" : det);
-        NeuroClass *nc = neu.getClass();
-
-        if (userandomclass)
-        {
-                nc = getRandomNeuroClass();
-                if (!nc) nc = Neuro::getClass("N");
-        }
-
-        det = nc->getName();
-        neu.setDetails(det);
 
         SyntParam par = neu.classProperties();
@@ -455 +448 @@
                 if (props != "")
                 {
+                        det = neu.getClass()->name;
                         det += ": ";
                         det += props;
-                        hpar.setStringById("d", det);
-                }
-        }
-}
-
-uint32_t Geno_fH::style(const char *geno, int pos)
-{
-        char ch = geno[pos];
-        uint32_t style = GENSTYLE_CS(0, GENSTYLE_STRIKEOUT);
-        if (pos == 0 || geno[pos - 1] == '\n' || ch == ':') // single-character handle type and all colons
-        {
-                style = GENSTYLE_CS(GENCOLOR_TEXT, GENSTYLE_BOLD);
-        }
-        else if (isalpha(ch)) // properties name
-        {
-                style = GENSTYLE_RGBS(0, 200, 0, GENSTYLE_BOLD);
-        }
-        else if (isdigit(ch) || strchr(",.=", ch)) // properties values
-        {
-                style = GENSTYLE_CS(GENCOLOR_TEXT, GENSTYLE_NONE);
-        }
-        else if (ch == '\"')
-        {
-                style = GENSTYLE_RGBS(200, 0, 0, GENSTYLE_BOLD);
-        }
-
-        return style;
-}
+                }
+        }
+}
+
+void Geno_fH::mutateNeuronHandleProperties(fH_NeuronHandle *handle, ParamEntry *tab, bool userandomclass)
+{
+        Neuro neu;
+        Param hpar(tab, handle->obj);
+        SString det = hpar.getStringById("d");
+        neu.setDetails(det == "" ? "N" : det);
+        NeuroClass *nc = neu.getClass();
+
+        if (userandomclass)
+        {
+                nc = getRandomNeuroClass();
+                if (!nc) nc = Neuro::getClass("N");
+        }
+
+        det = nc->getName();
+
+        mutateNeuronProperties(det);
+
+        hpar.setStringById("d", det);
+}
+
+//uint32_t Geno_fH::style(const char *geno, int pos)
+//{
+//      char ch = geno[pos];
+//      uint32_t style = GENSTYLE_CS(0, GENSTYLE_STRIKEOUT);
+//      if (pos == 0 || geno[pos - 1] == '\n' || ch == ':') // single-character handle type and all colons
+//      {
+//              style = GENSTYLE_CS(GENCOLOR_TEXT, GENSTYLE_BOLD);
+//      }
+//      else if (isalpha(ch)) // properties name
+//      {
+//              style = GENSTYLE_RGBS(0, 200, 0, GENSTYLE_BOLD);
+//      }
+//      else if (isdigit(ch) || strchr(",.=", ch)) // properties values
+//      {
+//              style = GENSTYLE_CS(GENCOLOR_TEXT, GENSTYLE_NONE);
+//      }
+//      else if (ch == '\"')
+//      {
+//              style = GENSTYLE_RGBS(200, 0, 0, GENSTYLE_BOLD);
+//      }
+//
+//      return style;
+//}
+
+uint32_t Geno_fH::style(const char *g, int pos)
+{
+   char ch=g[pos];
+   uint32_t style=GENSTYLE_CS(0,GENSTYLE_NONE); //default, should be changed below
+
+   int pp=pos; //detect comment line
+   while (pp>1 && g[pp-1]!='\n') pp--;
+   if (g[pp]=='#') return GENSTYLE_RGBS(0,220,0,GENSTYLE_NONE); //comment line
+
+   if (pos==0 || g[pos-1]=='\n' || ch==':' || ch==',') style=GENSTYLE_CS(0,GENSTYLE_BOLD); else
+     if (ch=='\"') style=GENSTYLE_RGBS(150,0,0,GENSTYLE_BOLD); else
+     {
+      int cudz=0,neuclass=1; //ile cudz. do poczatku linii; czy w nazwie neuroklasy?
+      while (pos>0)
+      {
+         pos--;
+         if (g[pos]=='\"') cudz++;
+         if (cudz==0 && (g[pos]==':' || g[pos]==',')) neuclass=0;
+         if (g[pos]=='\n') break;
+      }
+      if (cudz%2)
+      {
+         if (neuclass) style=GENSTYLE_RGBS(150,0,150,GENSTYLE_BOLD); else //neuroclass
+           if (isalpha(ch)) style=GENSTYLE_RGBS(255,140,0,GENSTYLE_BOLD); else //property
+             style=GENSTYLE_RGBS(200,0,0,GENSTYLE_NONE);
+      } else
+        if (isalpha(ch)) style=GENSTYLE_RGBS(0,0,200,GENSTYLE_BOLD);
+     }
+   return style;
+}

cpp/frams/genetics/fH/fH_oper.h

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #ifndef _FH_OPER_H_
 #define _FH_OPER_H_
@@ -87 +91 @@
         double addoperations[FH_ADD_OPCOUNT]; ///<relative probabilities of selecting mutation addition subtypes
 
+        // TODO add to GenoOperators?
+        /**
+         * Mutates properties of neuron and returns full neuron class description.
+         * @param det current neuron class definition with its parameters
+         */
+        static void mutateNeuronProperties(SString &det);
+
         Geno_fH();
 

cpp/frams/genetics/fL/fL_conv.cpp

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #include "fL_conv.h"
+#include "fL_general.h"
 
 SString GenoConv_fL0::convert(SString &i, MultiMap *map, bool using_checkpoints)
 {
-        return "";
+        fL_Builder builder(NULL != map, using_checkpoints);
+        if (builder.parseGenotype(i) != 0)  return "";
+        double neededtime;
+        Model *m = builder.developModel(neededtime);
+        if (!m) return SString();
+        if (NULL != map)
+                m->getCurrentToF0Map(*map);
+        SString gen = m->getF0Geno().getGenes();
+        delete m;
+        return gen;
 }

cpp/frams/genetics/fL/fL_conv.h

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #ifndef _FL_CONV_
 #define _FL_CONV_

cpp/frams/genetics/fL/fL_general.cpp

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #include <algorithm>
 #include <stack>
 #include "fL_general.h"
-
-const char *fL_part_names[PART_PROPS_COUNT] = { "dn", "fr", "ing", "as" };
-const char *fL_part_fullnames[PART_PROPS_COUNT] = { "details", "friction", "ingestion", "assimilation" };
-
-const char *fL_joint_names[JOINT_PROPS_COUNT] = { "stif", "rotstif", "stam" };
-const char *fL_joint_fullnames[JOINT_PROPS_COUNT] = { "stiffness", "rotation stiffness", "stamina" };
+#include <frams/util/multirange.h>
+#include <iterator>
+
+const char *fL_part_names[FL_PART_PROPS_COUNT] = { "dn", "fr", "ing", "as" };
+const char *fL_part_fullnames[FL_PART_PROPS_COUNT] = { "details", "friction", "ingestion", "assimilation" };
+
+const char *fL_joint_names[FL_JOINT_PROPS_COUNT] = { "stif", "rotstif", "stam" };
+const char *fL_joint_fullnames[FL_JOINT_PROPS_COUNT] = { "stiffness", "rotation stiffness", "stamina" };
 
 #define FIELDSTRUCT fL_Word
@@ -14 +20 @@
         { "Word", 1, 2, "w" },
         { "name", 0, PARAM_CANOMITNAME, "word name", "s", FIELD(name), },
-        { "npar", 0, PARAM_CANOMITNAME, "number of parameters", "d 0 3 0", FIELD(npar), },
+        { "npar", 0, PARAM_CANOMITNAME, "number of parameters", "d 0 " FL_MAXPARAMS " 0", FIELD(npar), },
         { 0, 0, 0, }
 };
@@ -23 +29 @@
 {
         { "Rule", 1, 3, "r" },
-        { "pred", 0, PARAM_CANOMITNAME, "predecessor", "s", FIELD(predecessor), },
-        { "cond", 0, PARAM_CANOMITNAME, "parameter condition", "s", FIELD(condition), },
-        { "succ", 0, PARAM_CANOMITNAME, "successor", "s", FIELD(successor), },
+        { "pred", 0, 0, "predecessor", "s", FIELD(predecessor), },
+        { "cond", 0, 0, "parameter condition", "s", FIELD(condition), },
+        { "succ", 0, 0, "successor", "s", FIELD(successor), },
         { 0, 0, 0, }
 };
@@ -33 +39 @@
 ParamEntry fL_builder_paramtab[] =
 {
-        { "LSystemInfo", 1, 3, "i" },
-        { "axiom", 0, PARAM_CANOMITNAME, "starting sequence of L-System", "s", FIELD(axiom), },
-        { "time", 0, PARAM_CANOMITNAME, "development time", "f 1.0 100.0 1.0", FIELD(time), },
-        { "numckp", 0, PARAM_CANOMITNAME, "number of checkpoints", "d 1 50 1", FIELD(numckp), },
-        { 0, 0, 0, }
+                {"LSystemInfo", 1, 4, "i"},
+                {"axiom", 0, 0, "starting sequence of L-System", "s", FIELD(axiom),},
+                {"time", 0, PARAM_CANOMITNAME, "development time", "f 0.0 " FL_MAXITER " 1.0", FIELD(time),},
+                {"numckp", 0, PARAM_CANOMITNAME, "number of checkpoints", "d 1 50 1", FIELD(numckp),},
+                {"maxwords", 0, PARAM_CANOMITNAME, "Maximum number of words within genotype sequence", "d -1 9999 -1", FIELD(maxwords),},
+                {0,0,0,}
 };
 #undef FIELDSTRUCT
@@ -134 +141 @@
 }
 
-int fL_Builder::tokenize(SString sequence, std::list<fL_Word *> &result, int numparams)
+int fL_Builder::createWord(SString token, fL_Word *&word, int numparams, int begin, int end)
+{
+        SString wordn;
+        int tokpos = 0;
+        // if word name cannot be extracted, then return error
+        if (!token.getNextToken(tokpos, wordn, '('))
+        {
+                return 1;
+        }
+        std::string wordname = fL_Builder::trimSpaces(wordn.c_str());
+        // if word cannot be found in available words, then return error
+        if (words.find(wordname) == words.end())
+        {
+                SString message = "Word '";
+                message += wordname.c_str();
+                message += "' in sequence does not exist";
+                logMessage("fL_Builder", "createWord", LOG_ERROR, message.c_str());
+                return 1;
+        }
+
+        if (word) delete word;
+        // create new word and assign parameters
+        word = new fL_Word(false, begin, end);
+
+        *word = *words[wordname];
+
+        SString temp;
+        temp = token.substr(tokpos);
+        temp = temp.substr(0, temp.len() - 1);
+
+        // if word has parameters
+        if (word->npar > 0)
+        {
+                // create ParamObject that will hold parameter data
+                word->data = ParamObject::makeObject(word->tab);
+                Param par(word->tab);
+                par.select(word->data);
+                par.setDefault();
+                ParamInterface::LoadOptions opts;
+
+                // load parameters from string
+                par.load(ParamInterface::FormatSingleLine, temp, &opts);
+                for (int i = 0; i < par.getPropCount(); i++)
+                {
+                        SString t(par.id(i));
+                        if (word->builtin && (t == SString("d") || t == SString(FL_PE_CONN_ATTR)))
+                        {
+                                word->parevals.push_back(NULL);
+                        }
+                        else
+                        {
+                                // create MathEvaluation object to check if string contained by
+                                // parameter is valid
+                                double tmp;
+                                MathEvaluation *eval = NULL;
+                                SString seq = par.getString(i);
+                                // if string is empty, then evaluate this with 0
+                                // if sequence could not be evaluated, then return error
+                                if (seq.len() > 0)
+                                {
+                                        eval = new MathEvaluation(numparams);
+                                        if (eval->evaluate(seq.c_str(), tmp) != 0)
+                                        {
+                                                SString message = "Word in sequence has invalid parameter:  ";
+                                                message += temp;
+                                                logMessage("fL_Builder", "createWord", LOG_ERROR, message.c_str());
+                                                delete eval;
+                                                delete word;
+                                                word = NULL;
+                                                return 1;
+                                        }
+                                }
+                                word->parevals.push_back(eval);
+                        }
+                }
+        }
+        else if (word->npar == 0 && temp.len() > 0)
+        {
+                SString message = "Too many parameters for word:  ";
+                message += token;
+                logMessage("fL_Builder", "createWord", LOG_ERROR, message.c_str());
+                delete word;
+                word = NULL;
+                return 1;
+        }
+        return 0;
+}
+
+int fL_Builder::tokenize(SString sequence, std::list<fL_Word *> &result, int numparams, int begin, int end)
 {
         int pos = 0;
@@ -153 +248 @@
                 if (token.indexOf("[", 0) != -1)
                 {
-                        fL_Branch *word = new fL_Branch(fL_Branch::BranchType::OPEN);
+                        fL_Branch *word = new fL_Branch(fL_Branch::BranchType::OPEN, begin, end);
                         result.push_back(word);
                         branchcount++;
@@ -168 +263 @@
                                 return 1;
                         }
-                        fL_Branch *word = new fL_Branch(fL_Branch::BranchType::CLOSE);
+                        fL_Branch *word = new fL_Branch(fL_Branch::BranchType::CLOSE, begin, end);
                         result.push_back(word);
                         branchcount--;
                         continue;
                 }
-                SString wordn;
-                int tokpos = 0;
-                // if word name cannot be extracted, then return error
-                if (!token.getNextToken(tokpos, wordn, '('))
+                fL_Word *word = NULL;
+                if (createWord(token, word, numparams, begin, end) != 0)
                 {
                         SString message = "Error during parsing words sequence:  ";
@@ -183 +276 @@
                         return 1;
                 }
-                std::string wordname = fL_Builder::trimSpaces(wordn.c_str());
-                // if word cannot be found in available words, then return error
-                if (words.find(wordname) == words.end())
-                {
-                        SString message = "Word '";
-                        message += wordname.c_str();
-                        message += "' in sequence does not exist";
-                        logMessage("fL_Builder", "tokenize", LOG_ERROR, message.c_str());
-                        return 1;
-                }
-
-                // create new word and assign parameters
-                fL_Word *word = new fL_Word();
-
-                *word = *words[wordname];
-
-                // if word has parameters
-                if (word->npar > 0)
-                {
-                        // create ParamObject that will hold parameter data
-                        word->data = ParamObject::makeObject(word->tab);
-                        Param par(word->tab);
-                        par.select(word->data);
-                        par.setDefault();
-                        ParamInterface::LoadOptions opts;
-
-                        SString temp;
-                        temp = token.substr(tokpos);
-                        temp = temp.substr(0, temp.len() - 1);
-                        // load parameters from string
-                        par.load(ParamInterface::FormatSingleLine, temp, &opts);
-                        for (int i = 0; i < par.getPropCount(); i++)
-                        {
-                                // create MathEvaluation object to check if string contained by
-                                // parameter is valid
-                                double tmp;
-                                MathEvaluation *eval = new MathEvaluation(numparams);
-                                SString seq = par.getString(i);
-                                // if string is empty, then evaluate this with 0
-                                if (seq.len() == 0)
-                                {
-                                        eval->evaluate("0", tmp);
-                                }
-                                // if sequence could not be evaluated, then return error
-                                else if (eval->evaluate(seq.c_str(), tmp) != 0)
-                                {
-                                        SString message = "Word in sequence has invalid parameter:  ";
-                                        message += temp;
+                if (word->name == "C")
+                {
+                        Param par(word->tab, word->data);
+                        SString attr = par.getStringById(FL_PE_CONN_ATTR);
+                        if (attr.indexOf("$t", 0) != -1)
+                        {
+                                logMessage("fL_Builder", "tokenize", LOG_ERROR, "Attractor definition cannot contain time variable");
+                                delete word;
+                                return 1;
+
+                        }
+                        if (attr != "")
+                        {
+                                fL_Word *attrword = NULL;
+                                if (createWord(attr, attrword, numparams, begin, end) != 0)
+                                {
+                                        SString message = "Error during parsing attractor word:  ";
+                                        message += attr;
                                         logMessage("fL_Builder", "tokenize", LOG_ERROR, message.c_str());
-                                        delete eval;
                                         delete word;
+                                        if (attrword) delete attrword;
                                         return 1;
                                 }
-                                word->parevals.push_back(eval);
+                                if (attrword->builtin)
+                                {
+                                        logMessage("fL_Builder", "tokenize", LOG_ERROR, "Attractor words cannot be built-in");
+                                        delete word;
+                                        delete attrword;
+                                        return 1;
+                                }
+                                delete attrword;
                         }
                 }
@@ -272 +342 @@
                 parevals = src.parevals;
 
+                builtin = src.builtin;
+
                 data = NULL; // properties cannot be copied
         }
@@ -303 +375 @@
 
         builder->words[this->name.c_str()] = this;
+        builder->wordnames.push_back(this->name.c_str());
         return 0;
 }
@@ -318 +391 @@
         *objpred = *builder->words[predecessor.c_str()];
 
+        if (objpred->builtin)
+        {
+                logMessage("fL_Rule", "processDefinition", LOG_ERROR, "Builtin words cannot be predecessors");
+                return 1;
+        }
+
         // parse condition
         if (condition != "")
         {
+                if (objpred->builtin && (objpred->name == "N" || objpred->name == "C"))
+                {
+                        logMessage("fL_Rule", "processDefinition", LOG_ERROR, "Rules with neuron/connection word predecessors cannot contain conditions");
+                        return 1;
+                }
                 std::string cond = condition.c_str();
                 condeval = new MathEvaluation(objpred->npar);
@@ -340 +424 @@
         }
 
-        if (builder->tokenize(successor, objsucc, objpred->npar) != 0)
+        if (builder->tokenize(successor, objsucc, objpred->npar, begin, end) != 0)
         {
                 logMessage("fL_Rule", "processDefinition", LOG_ERROR, "Unable to process successor sequence");
@@ -353 +437 @@
 {
         // tokenize axiom
-        if (tokenize(axiom, genotype, 0) != 0)
+        if (tokenize(axiom, genotype, 0, begin, end) != 0)
         {
                 logMessage("fL_Builder", "processDefinition", LOG_ERROR, "Unable to process axiom sequence");
@@ -372 +456 @@
         switch (type)
         {
-        case fLElementType::TERM:
-        {
-                tab = fL_word_paramtab;
-                obj = new fL_Word();
-                break;
-        }
-        case fLElementType::INFO:
-        {
-                tab = fL_builder_paramtab;
-                obj = this;
-                break;
-        }
-        case fLElementType::RULE:
-        {
-                tab = fL_rule_paramtab;
-                obj = new fL_Rule(begin, end);
-                break;
-        }
-        default:
-                break;
+                case fLElementType::TERM:
+                {
+                        tab = fL_word_paramtab;
+                        obj = new fL_Word();
+                        break;
+                }
+                case fLElementType::INFO:
+                {
+                        tab = fL_builder_paramtab;
+                        obj = this;
+                        break;
+                }
+                case fLElementType::RULE:
+                {
+                        tab = fL_rule_paramtab;
+                        obj = new fL_Rule(begin, end);
+                        break;
+                }
+                default:
+                        break;
         }
         Param par(tab);
@@ -417 +501 @@
         stick->name = "S";
         stick->npar = 8;
-        for (int i = 0; i < PART_PROPS_COUNT; i++)
+        for (int i = 0; i < FL_PART_PROPS_COUNT; i++)
         {
                 stick->mut.addProperty(NULL, fL_part_names[i], "s", fL_part_fullnames[i], fL_part_fullnames[i], PARAM_CANOMITNAME, 0, -1);
         }
 
-        for (int i = 0; i < JOINT_PROPS_COUNT; i++)
+        for (int i = 0; i < FL_JOINT_PROPS_COUNT; i++)
         {
                 stick->mut.addProperty(NULL, fL_joint_names[i], "s", fL_joint_fullnames[i], fL_joint_fullnames[i], PARAM_CANOMITNAME, 0, -1);
@@ -430 +514 @@
         stick->tab = ParamObject::makeParamTab((ParamInterface *)&stick->mut, 0, 0, stick->mut.firstMutableIndex());
         words["S"] = stick;
+        wordnames.push_back("S");
 
         // neuron N
@@ -435 +520 @@
         neuron->name = "N";
         neuron->npar = 1;
-        neuron->mut.addProperty(NULL, "d", "s", "details", "details", PARAM_CANOMITNAME, 0, -1);
+        neuron->mut.addProperty(NULL, "d", "s", "details", "details", 0, 0, -1);
         neuron->tab = ParamObject::makeParamTab((ParamInterface *)&neuron->mut, 0, 0, neuron->mut.firstMutableIndex());
         words["N"] = neuron;
+        wordnames.push_back("N");
 
         // connection C
@@ -443 +529 @@
         connection->name = "C";
         connection->npar = 2;
-        connection->mut.addProperty(NULL, "w", "s", "weight", "weight", PARAM_CANOMITNAME, 0, -1);
-        connection->mut.addProperty(NULL, "attr", "s", "attractor", "connection attractor", PARAM_CANOMITNAME, 0, -1);
+        connection->mut.addProperty(NULL, FL_PE_CONN_WEIGHT, "s", "weight", "weight", PARAM_CANOMITNAME, 0, -1);
+        connection->mut.addProperty(NULL, FL_PE_CONN_ATTR, "s", "attractor", "connection attractor", PARAM_CANOMITNAME, 0, -1);
         connection->tab = ParamObject::makeParamTab((ParamInterface *)&connection->mut, 0, 0, connection->mut.firstMutableIndex());
         words["C"] = connection;
+        wordnames.push_back("C");
 
         // rotation objects
@@ -463 +550 @@
         rotz->npar = 1;
         rotz->processDefinition(this);
+
+        //fL_Branch *branch = new fL_Branch(fL_Branch::BranchType::OPEN, 0, 0);
+        //branch->processDefinition(this);
+
+        builtincount = words.size();
 }
 
@@ -521 +613 @@
                                 return res;
                         }
+                        if (obj == this)
+                        {
+                                begin = lastpos;
+                                end = pos - 1;
+                        }
                         res = obj->processDefinition(this);
                         if (res != 0)
@@ -546 +643 @@
                 for (int i = 0; i < npar; i++)
                 {
+                        SString t(par.id(i));
                         if (parevals[i] != NULL)
                         {
@@ -667 +765 @@
         }
         getStringifiedProducts();
+        removeRedundantRules();
         Param par(fL_builder_paramtab);
         fL_Builder *obj = new fL_Builder();
@@ -681 +780 @@
 }
 
-int fL_Rule::deploy(fL_Word *in, std::list<fL_Word *>::iterator &it, std::list<fL_Word *> &genotype, double currtime)
+int fL_Rule::deploy(fL_Builder *builder, fL_Word *in, std::list<fL_Word *>::iterator &it, double currtime)
 {
         // if predecessor and given word differ, then rule is not applicable
@@ -720 +819 @@
 
         // remove predecessor word from genotype and replace it with successor
-        it = genotype.erase(it);
+        it = builder->genotype.erase(it);
         for (std::list<fL_Word *>::iterator word = objsucc.begin(); word != objsucc.end(); word++)
         {
                 // create new word and copy properties from word definition
-                fL_Word *nword = new fL_Word();
+                fL_Word *nword = new fL_Word(false, begin, end);
                 *nword = **word;
                 // store information about when word has been created
@@ -735 +834 @@
                 // calculate word parameters and store MathEvaluation objects for further
                 // time manipulations.
+                Param par((*word)->tab, (*word)->data);
+                Param npar(nword->tab, nword->data);
                 for (int q = 0; q < nword->npar; q++)
                 {
                         if ((*word)->parevals[q] == NULL)
                         {
-                                MathEvaluation *ev = new MathEvaluation(0);
-                                ev->convertString("0");
-                                nword->parevals.push_back(ev);
+                                if ((*word)->builtin && (strcmp(npar.id(q), "d") == 0))
+                                {
+                                        SString t = par.getString(q);
+                                        npar.setString(q, t);
+                                        nword->parevals.push_back(NULL);
+                                }
+                                if ((*word)->builtin && (strcmp(npar.id(q), FL_PE_CONN_ATTR) == 0))
+                                {
+                                        SString t = par.getString(q);
+                                        if (t.len() > 0)
+                                        {
+                                                fL_Word *attrword = NULL;
+                                                builder->createWord(t, attrword, in->npar, begin, end);
+                                                for (int j = 0; j < attrword->npar; j++)
+                                                {
+                                                        if (attrword->parevals[j])
+                                                        {
+                                                                for (int i = 0; i < in->npar; i++)
+                                                                {
+                                                                        attrword->parevals[j]->modifyVariable(i, inwordvalues[i]);
+                                                                }
+                                                        }
+                                                }
+                                                SString res = attrword->stringify(false);
+                                                npar.setString(q, res);
+                                                nword->parevals.push_back(NULL);
+                                                delete attrword;
+                                        }
+                                }
+                                else
+                                {
+                                        //MathEvaluation *ev = new MathEvaluation(0);
+                                        //ev->convertString("0");
+                                        //nword->parevals.push_back(ev);
+                                        nword->parevals.push_back(NULL);
+                                }
                         }
                         else
@@ -757 +891 @@
                         }
                 }
-                genotype.insert(it, nword);
+                builder->genotype.insert(it, nword);
         }
         delete[] inwordvalues;
@@ -773 +907 @@
                 for (fL_Rule * rule : rules)
                 {
-                        if (rule->deploy((*word), word, genotype, currtime) == 0)
+                        if (rule->deploy(this, (*word), word, currtime) == 0)
                         {
                                 deployed = true;
@@ -806 +940 @@
         Param par(stickword->tab, stickword->data);
         Param ppar = part->properties();
-        for (int i = 0; i < PART_PROPS_COUNT; i++)
-        {
-                double partprop;
+        for (int i = 0; i < FL_PART_PROPS_COUNT; i++)
+        {
+                double mn, mx, df;
+                ppar.getMinMaxDouble(ppar.findId(fL_part_names[i]), mn, mx, df);
                 double currval;
-                if (!ExtValue::parseDouble(par.getStringById(fL_part_names[i]).c_str(), currval, false))
-                {
-                        logMessage("fL_Builder", "alterPartProperties", LOG_ERROR,
-                                "Error parsing word parameter");
-                        return 1;
-                }
-                partprop = (ppar.getDoubleById(fL_part_names[i]) * alterationcount +
-                        currval) / (alterationcount + 1.0);
+                if (!stickword->parevals[i])
+                {
+                        currval = df;
+                }
+                else
+                {
+                        stickword->parevals[i]->evaluateRPN(currval);
+                        currval = sigmoidTransform(currval, mn, mx);
+                }
+                double partprop = (ppar.getDoubleById(fL_part_names[i]) * alterationcount +
+                                currval) / (alterationcount + 1.0);
                 ppar.setDoubleById(fL_part_names[i], partprop);
         }
@@ -823 +961 @@
 }
 
-bool fL_Word::operator==(const fL_Word& other) const
-{
-        if (name == other.name) return false;
-        if (npar == other.npar) return false;
+double fL_Word::distance(fL_Word *right)
+{
+        if (name != right->name || npar != right->npar)
+        {
+                return -1;
+        }
+        double distance = 0;
         for (int i = 0; i < npar; i++)
         {
-                if (parevals[i] && other.parevals[i])
-                {
-                        double first;
-                        double second;
-                        parevals[i]->evaluateRPN(first);
-                        other.parevals[i]->evaluateRPN(second);
-                        if (first != second)
-                        {
-                                return false;
-                        }
-                }
-                else
-                {
-                        return false;
-                }
-        }
-        return true;
-}
-
-void fL_Builder::findNext(fL_Word *word, std::list<fL_Word *> genotype, std::list<fL_Word *>::iterator &it)
-{
-        int rightdist = 0;
-        std::list<fL_Word *>::iterator iter(it);
-        for (; iter != genotype.end(); iter++)
-        {
-                if (*word == **iter)
-                {
-                        break;
-                }
-                rightdist++;
-        }
-        int leftdist = 0;
-        std::list<fL_Word *>::reverse_iterator riter(it);
-        for (; riter != genotype.rend(); riter++)
-        {
-                if (*word == **riter)
-                {
-                        break;
-                }
-                leftdist++;
-        }
-        if (iter == genotype.end())
-        {
-                it = riter.base();
-        }
-        else if (riter == genotype.rend())
-        {
-                it = iter;
-        }
-        else if (leftdist < rightdist)
-        {
-                it = riter.base();
+                double l = 0;
+                double r = 0;
+                if (parevals[i]) parevals[i]->evaluateRPN(l);
+                if (right->parevals[i]) right->parevals[i]->evaluateRPN(r);
+                distance += (l - r) * (l - r);
+        }
+        return sqrt(distance);
+}
+
+Neuro *fL_Builder::findInputNeuron(std::pair<std::list<fL_Word *>::iterator, Neuro *> currneu, fL_Word *attractor)
+{
+        if (!attractor)
+        {
+                std::list<fL_Word *>::reverse_iterator riter(currneu.first);
+                std::list<fL_Word *>::iterator iter(currneu.first);
+                iter++;
+                while (riter != genotype.rend() || iter != genotype.end())
+                {
+                        if (iter != genotype.end())
+                        {
+                                if ((*iter)->name == "N" && (*iter)->bodyelementpointer != currneu.second)
+                                {
+                                        return (Neuro *)(*iter)->bodyelementpointer;
+                                }
+                                iter++;
+                        }
+                        if (riter != genotype.rend())
+                        {
+                                if ((*riter)->name == "N" && (*riter)->bodyelementpointer != currneu.second)
+                                {
+                                        return (Neuro *)(*riter)->bodyelementpointer;
+                                }
+                                riter++;
+                        }
+                }
+                return NULL;
         }
         else
         {
-                it = iter;
-        }
-}
-
-Neuro *fL_Builder::findInputNeuron(std::list<fL_Word *> genotype, std::list<fL_Word *>::iterator it, fL_Word *attractor)
-{
-        if (!attractor)
-        {
-                attractor = new fL_Word();
-                *attractor = *(*it);
-                attractor->data = NULL;
-                // TODO implement
+                double mindistance = -1;
+                std::list<fL_Word *>::iterator minit = genotype.end();
+                for (std::list<fL_Word *>::iterator it = genotype.begin(); it != genotype.end(); it++)
+                {
+                        double currdist = attractor->distance((*it));
+                        if (currdist != -1 && (currdist < mindistance || mindistance == -1))
+                        {
+                                mindistance = currdist;
+                                minit = it;
+                        }
+                }
+                if (minit != genotype.end())
+                {
+                        for (; minit != genotype.end(); minit++)
+                        {
+                                if ((*minit)->name == "N" && (*minit)->bodyelementpointer)
+                                {
+                                        Neuro *n = (Neuro *)(*minit)->bodyelementpointer;
+                                        if (n->getClass()->getPreferredOutput() != 0)
+                                        {
+                                                return n;
+                                        }
+                                }
+                        }
+                }
         }
         return NULL;
 }
 
-int fL_Builder::developModel(Model &model)
-{
-        // TODO implement
+double fL_Builder::sigmoidTransform(double input, double mn, double mx)
+{
+        return mn + (mx - mn) * (1.0 / (1.0 + exp(-input)));
+}
+
+int fL_Builder::buildModelFromSequence(Model *model)
+{
         fL_State currstate;
         std::unordered_map<Part *, double> counters;
@@ -923 +1065 @@
                                                 firstpart->p = Pt3D_0;
                                                 counters[firstpart] = 0;
-                                                model.addPart(firstpart);
+                                                model->addPart(firstpart);
+                                                if (using_mapping) firstpart->addMapping(IRange(word->begin, word->end));
                                         }
                                         currstate.currpart = firstpart;
@@ -941 +1084 @@
                                 Param par(word->tab, word->data);
                                 double length;
-                                if (!ExtValue::parseDouble(par.getStringById("l").c_str(), length, false))
-                                {
-                                        delete newpart;
-                                        logMessage("fL_Builder", "alterPartProperties", LOG_ERROR,
-                                                "Error parsing word parameter");
-                                        return 1;
+                                if (!word->parevals[FL_PART_PROPS_COUNT + FL_JOINT_PROPS_COUNT])
+                                {
+                                        length = FL_DEFAULT_LENGTH; // default length value
+                                }
+                                else
+                                {
+                                        double parsedval = 0.0;
+                                        if (word->parevals[FL_PART_PROPS_COUNT + FL_JOINT_PROPS_COUNT]->evaluateRPN(parsedval) != 0)
+                                        {
+                                                delete newpart;
+                                                logMessage("fL_Builder", "developModel", LOG_ERROR,
+                                                                "Error parsing word parameter");
+                                                return 1;
+                                        }
+                                        length = sigmoidTransform(parsedval, FL_MINIMAL_LENGTH, FL_MAXIMAL_LENGTH);
                                 }
                                 newpart->p = currstate.currpart->p + currstate.direction * length;
                                 counters[newpart] += 1;
-                                model.addPart(newpart);
-
+                                model->addPart(newpart);
+                                if (using_mapping) newpart->addMapping(IRange(word->begin, word->end));
                                 Joint *newjoint = new Joint();
                                 newjoint->attachToParts(currstate.currpart, newpart);
 
                                 Param jpar = newjoint->properties();
-                                for (int i = 0; i < JOINT_PROPS_COUNT; i++)
-                                {
+                                for (int i = 0; i < FL_JOINT_PROPS_COUNT; i++)
+                                {
+                                        double mn, mx, df;
+                                        jpar.getMinMaxDouble(jpar.findId(fL_joint_names[i]), mn, mx, df);
                                         double jointprop;
-                                        if (!ExtValue::parseDouble(par.getStringById(fL_joint_names[i]).c_str(), jointprop, false))
+                                        if (!word->parevals[FL_PART_PROPS_COUNT + i])
                                         {
-                                                logMessage("fL_Builder", "developModel", LOG_ERROR,
-                                                        "Error parsing word parameter");
-                                                delete newjoint;
-                                                return 1;
+                                                jointprop = df; // assign default value
+                                        }
+                                        else
+                                        {
+                                                if (word->parevals[FL_PART_PROPS_COUNT + i]->evaluateRPN(jointprop) != 0)
+                                                {
+                                                        logMessage("fL_Builder", "developModel", LOG_ERROR,
+                                                                        "Error parsing word parameter");
+                                                        delete newjoint;
+                                                        return 1;
+                                                }
+                                                jointprop = sigmoidTransform(jointprop, mn, mx);
                                         }
                                         jpar.setDoubleById(fL_joint_names[i], jointprop);
                                 }
-                                model.addJoint(newjoint);
+                                model->addJoint(newjoint);
+                                if (using_mapping) newjoint->addMapping(IRange(word->begin, word->end));
                                 currstate.currpart = newpart;
                         }
@@ -975 +1138 @@
                                 Param npar(word->tab, word->data);
                                 Neuro *neu = new Neuro();
-                                neu->setDetails(npar.getStringById("d"));
+                                SString details = npar.getStringById("d");
+                                if (details == "")
+                                {
+                                        details = "N";
+                                }
+                                neu->setDetails(details);
                                 if (!neu->getClass())
                                 {
@@ -982 +1150 @@
                                         return 1;
                                 }
-                                model.addNeuro(neu);
-                                currstate.currneuron = neu;
+                                model->addNeuro(neu);
+                                if (using_mapping) neu->addMapping(IRange(word->begin, word->end));
+                                if (neu->getClass()->getPreferredInputs() != 0)
+                                {
+                                        currstate.currneuron = neu;
+                                }
+                                word->bodyelementpointer = neu;
                         }
                         else if (word->name == "C")
                         {
-                                connsbuffer.push_back({ w, currstate.currneuron });
+                                connsbuffer.push_back({w, currstate.currneuron});
                         }
                         else if (word->name.startsWith("rot"))
                         {
-                                Orient rotmatrix;
+                                Orient rotmatrix = Orient_1;
                                 double rot;
-                                if (word->parevals[0]->evaluateRPN(rot) != 0)
-                                {
-                                        logMessage("fL_Builder", "developModel", LOG_ERROR, "Error parsing neuron class");
+                                if (!word->parevals[0])
+                                {
+                                        rot = 0;
+                                }
+                                else if (word->parevals[0]->evaluateRPN(rot) != 0)
+                                {
+                                        logMessage("fL_Builder", "developModel", LOG_ERROR, "Error parsing rotation word");
                                         return 1;
                                 }
+
+                                rot = sigmoidTransform(rot, -M_PI, M_PI);
+
                                 if (word->name == "rotX")
                                 {
-                                        rotmatrix.rotate(Pt3D(rot, 0.0, 0.0));
+                                        rotmatrix.rotate(Pt3D(rot,0,0));
                                 }
                                 else if (word->name == "rotY")
                                 {
-                                        rotmatrix.rotate(Pt3D(0.0, rot, 0.0));
+                                        rotmatrix.rotate(Pt3D(0,rot,0));
                                 }
                                 else if (word->name == "rotZ")
                                 {
-                                        rotmatrix.rotate(Pt3D(0.0, 0.0, rot));
+                                        rotmatrix.rotate(Pt3D(0,0,rot));
                                 }
                                 currstate.direction = rotmatrix.transform(currstate.direction);
+                                currstate.direction.normalize();
                         }
                         else if (word->name == "[")
@@ -1025 +1206 @@
 
         // connections need
-        //      for (std::pair<std::list<fL_Word *>::iterator, Neuro *> conndata : connsbuffer)
-        //      {
-        //
-        //      }
+        // std::pair<std::list<fL_Word *>::iterator, Neuro *> conndata : connsbuffer
+        for (unsigned int i = 0; i < connsbuffer.size(); i++)
+        {
+                if (connsbuffer[i].second == NULL ||
+                                (connsbuffer[i].second->getClass()->getPreferredInputs() != -1 &&
+                                connsbuffer[i].second->getInputCount() >=
+                                connsbuffer[i].second->getClass()->getPreferredInputs()))
+                {
+                        // since connections are separated entities from neurons, it may happen
+                        // that there will be no neuron to connect to
+                        // logMessage("fL_Builder", "developModel", LOG_DEBUG, "Connection could not be established");
+                }
+                else
+                {
+                        Param par((*connsbuffer[i].first)->tab, (*connsbuffer[i].first)->data);
+                        SString attr = par.getStringById(FL_PE_CONN_ATTR);
+                        fL_Word *attractor = NULL;
+                        if (attr.len() > 0)
+                        {
+                                createWord(attr, attractor, 0, (*connsbuffer[i].first)->begin, (*connsbuffer[i].first)->end);
+                        }
+                        Neuro *neu = findInputNeuron(connsbuffer[i], attractor);
+                        double weight = 0.0;
+                        if ((*connsbuffer[i].first)->parevals[0])
+                        {
+                                if ((*connsbuffer[i].first)->parevals[0]->evaluateRPN(weight) != 0)
+                                {
+                                        logMessage("fL_Builder", "developModel", LOG_ERROR,
+                                                        "Error parsing word parameter");
+                                        delete attractor;
+                                        return 1;
+                                }
+                        }
+                        if (neu)
+                        {
+                                connsbuffer[i].second->addInput(neu, weight);
+                                if (using_mapping) neu->addMapping(
+                                                IRange((*connsbuffer[i].first)->begin,
+                                                                (*connsbuffer[i].first)->end));
+                        }
+                        else
+                        {
+                                connsbuffer[i].second->addInput(connsbuffer[i].second, weight);
+                                if (using_mapping) neu->addMapping(
+                                                IRange((*connsbuffer[i].first)->begin,
+                                                                (*connsbuffer[i].first)->end));
+                        }
+                        delete attractor;
+                }
+        }
         return 0;
 }
 
-int fL_Builder::develop()
-{
-        Model m;
+void fL_Builder::clearModelElements(Model *m)
+{
+        for (int i = 0; i < m->getJointCount(); i++)
+        {
+                m->removeJoint(i, 0);
+        }
+        for (int i = 0; i < m->getNeuroCount(); i++)
+        {
+                m->removeNeuro(i, true);
+        }
+        for (int i = 0; i < m->getNeuroCount(); i++)
+        {
+                m->removePart(i, 0, 0);
+        }
+        m->clearMap();
+}
+
+Model* fL_Builder::developModel(double &neededtime)
+{
         double curriter = 0;
         double timestamp = 1.0 / numckp;
         double t = 0;
-        for (; t <= time; t += timestamp)
+        Model *m = new Model();
+        m->open(using_checkpoints);
+        bool wordsexceeded = false;
+        for (; t <= time; t+= timestamp)
         {
                 alterTimedProperties(t); // always alter timed properties in the beginning
@@ -1045 +1291 @@
                 {
                         iterate(t);
-                        curriter += 1.0;
-                }
-        }
+                        curriter+=1.0;
+                }
+                if (using_checkpoints)
+                {
+                        clearModelElements(m);
+                        if (buildModelFromSequence(m) != 0)
+                        {
+                                delete m;
+                                return NULL;
+                        }
+                        m->checkpoint();
+                }
+                if (maxwords != -1 && genotype.size() > (unsigned int)maxwords)
+                {
+                        wordsexceeded = true;
+                        break;
+                }
+        }
+
+        if (wordsexceeded)
+        {
+                neededtime = t;
+        }
+        else
+        {
+                neededtime = time;
+        }
+
         // if exact time of development was not reached due to floating point errors,
         // then alter timed properties
@@ -1054 +1325 @@
                 alterTimedProperties(time);
         }
-        return 0;
-}
+        clearModelElements(m);
+        if (buildModelFromSequence(m) != 0)
+        {
+                delete m;
+                return NULL;
+        }
+        if (using_checkpoints)
+        {
+                m->checkpoint();
+        }
+        m->close();
+        return m;
+}
+
+int fL_Builder::countSticksInSequence(std::list<fL_Word *> sequence)
+{
+        int count = 0;
+        for (std::list<fL_Word *>::iterator it = sequence.begin(); it != sequence.end(); it++)
+        {
+                if ((*it)->builtin && (*it)->name == "S")
+                {
+                        count++;
+                }
+        }
+        return count;
+}
+
+int fL_Builder::countDefinedWords()
+{
+        return words.size() - builtincount;
+}
+
+int fL_Builder::countWordsInLSystem()
+{
+        int count = genotype.size();
+        for (fL_Rule *rul: rules)
+        {
+                count += rul->objsucc.size();
+        }
+        count += words.size();
+        return count;
+}
+
+void fL_Builder::removeRedundantRules()
+{
+        for (std::vector<fL_Rule *>::iterator it = rules.begin();
+                        it != rules.end(); it++)
+        {
+                std::vector<fL_Rule *>::iterator it2 = it;
+                it2++;
+                while (it2 != rules.end())
+                {
+                        bool todelete = false;
+                        if ((*it)->objpred->name == (*it2)->objpred->name)
+                        {
+                                if ((*it)->condeval == NULL && (*it2)->condeval == NULL)
+                                {
+                                        todelete = true;
+                                }
+                                else if ((*it)->condeval == NULL && (*it2)->condeval != NULL)
+                                {
+                                        std::iter_swap(it, it2);
+                                }
+                                else if ((*it)->condeval != NULL && (*it2)->condeval != NULL)
+                                {
+                                        if ((*it)->condeval->getStringifiedRPN() ==
+                                                        (*it2)->condeval->getStringifiedRPN())
+                                        {
+                                                todelete = true;
+                                        }
+                                }
+                        }
+                        if (todelete)
+                        {
+                                delete (*it2);
+                                it2 = rules.erase(it2);
+                        }
+                        else
+                        {
+                                it2++;
+                        }
+                }
+        }
+}

cpp/frams/genetics/fL/fL_general.h

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #ifndef _FL_GENERAL_
-
 #define _FL_GENERAL_
 
@@ -22 +25 @@
 /** @name Constants used in fL methods */
 //@{
-#define PART_PROPS_COUNT   4 ///<Count of part properties
-#define JOINT_PROPS_COUNT  3 ///<Count of joint properties
-#define PE_NEURO_DET       "d" ///<Id of details type definition in f0_neuro_paramtab
-#define PE_CONN_WEIGHT     "w" ///<Id of weight type definition in f0_neuroconn_paramtab
+#define FL_PART_PROPS_COUNT   4 ///<Count of part properties
+#define FL_JOINT_PROPS_COUNT  3 ///<Count of joint properties
+#define FL_PE_NEURO_DET       "d" ///<Id of details type definition in f0_neuro_paramtab
+#define FL_PE_CONN_WEIGHT     "w" ///<Id of weight type definition in f0_neuroconn_paramtab
+#define FL_PE_CONN_ATTR       "attr" ///<Id of attractor of neural connection
+#define FL_DEFAULT_LENGTH     1.0 ///<Default length of a stick in fL encoding
+#define FL_MINIMAL_LENGTH     0.0 ///<Minimal length of a stick in fL encoding
+#define FL_MAXIMAL_LENGTH     2.0 ///<Maximal length of a stick in fL encoding
+#define FL_MAXITER           "100.0" ///<Maximal iteration available in fL
+#define FL_MAXPARAMS          "3" ///<Maximal number of user-parameters
 //@}
 
 extern const char *fL_part_names[];
 extern const char *fL_joint_names[];
-extern const char *fL_joint_fullnames[JOINT_PROPS_COUNT];
-extern const char *fL_part_fullnames[PART_PROPS_COUNT];
+extern const char *fL_joint_fullnames[FL_JOINT_PROPS_COUNT];
+extern const char *fL_part_fullnames[FL_PART_PROPS_COUNT];
 
 #define LSYSTEM_PARAM_TYPE "s" ///< standard type of L-System elements
@@ -46 +55 @@
         fLElementType type; ///< type of fL_Element
 
-        fL_Element(fLElementType type) : type(type) {}
+        int begin; ///<beginning of the element definition in genotype
+        int end; ///<end of the element definition in genotype
+
+
+        fL_Element(fLElementType type) : type(type) { begin = end = 0; }
         virtual ~fL_Element() { }
 
@@ -78 +91 @@
         void *data; ///<pointer to properties of word
         bool builtin; ///<determines if word is built-in (true) or not (false).
+        PartBase *bodyelementpointer; ///<helper field for built-in words
         std::vector<MathEvaluation *> parevals; ///<stores MathEvaluation objects with parameter functions
         double creationiter; ///<this helper field is used during L-System iterations and determines when word was created
-        fL_Word(bool builtin = false) :
-                fL_Element(fLElementType::TERM), mut("Word", "Properties"), //TODO change Word to Term everywhere
+        fL_Word(bool builtin = false, int begin = 0, int end = 0) :
+                fL_Element(fLElementType::TERM), mut("Word", "Properties"),
                 builtin(builtin)
         {
@@ -89 +103 @@
                 data = NULL;
                 creationiter = 0;
+                this->begin = begin;
+                this->end = end;
+                bodyelementpointer = NULL;
         }
 
@@ -102 +119 @@
                 for (MathEvaluation *ev : parevals)
                 {
-                        delete ev;
+                        if (ev) delete ev;
                 }
                 parevals.clear();
@@ -125 +142 @@
 
         /**
-         * TODO
-         */
-        bool operator==(const fL_Word& other) const;
-
-        /**
          * Returns 'w:' line defining word in genotype.
          * @return string representation of word definition
@@ -150 +162 @@
          */
         int saveEvals(bool keepformulas);
+
+        /**
+         * Computes distance between two L-System words in genotype. Distance has sense
+         * only when two words have the same name. Otherwise, returned value equals -1.
+         * The distance is computed as Euclidean distance between words arguments.
+         * @param right the second word
+         * @return Euclidean distance between words in genotype or -1 if words have different name
+         */
+        double distance(fL_Word *right);
 };
 
@@ -164 +185 @@
         };
         BranchType btype; ///< branch parenthesis type
-        fL_Branch(BranchType branchtype) : fL_Word()
+        fL_Branch(BranchType branchtype, int begin, int end) : fL_Word(true, begin, end)
         {
                 type = fLElementType::BRANCH;
@@ -192 +213 @@
         std::list<fL_Word *> objsucc; ///<objec representation of successors
 
-        int start; ///<beginning of the rule definition in genotype
-        int end; ///<end of the rule definition in genotype
-
-        fL_Rule(int start, int end) : fL_Element(fLElementType::RULE),
-                start(start), end(end)
+        fL_Rule(int begin, int end)  : fL_Element(fLElementType::RULE)
         {
                 predecessor = "";
@@ -203 +220 @@
                 objpred = NULL;
                 condeval = NULL;
+                this->begin = begin;
+                this->end = end;
         }
 
@@ -231 +250 @@
          * pointer and iterator of list and inserting successor sequence into list.
          * Final iterator value points to the first word after processed word.
+         * @param builder builder containing current genotype
          * @param in word that is currently processed
          * @param it iterator of genotype list which determines position of current analysis
-         * @param genotype current genotype. Words on the left of genotype are processed and possibly replaced by previous rules
          * @param currtime value representing continuous time value for rule
          * @return 0 if rule processed current word, 1 if rule is no applicable
          */
-        int deploy(fL_Word *in, std::list<fL_Word *>::iterator &it, std::list<fL_Word *> &genotype, double currtime);
-};
-
+        int deploy(fL_Builder *builder, fL_Word *in, std::list<fL_Word *>::iterator &it, double currtime);
+};
+
+/**
+ * Structure for holding current Turtle state.
+ */
 struct fL_State
 {
@@ -245 +267 @@
         Part *currpart; ///<Latest created part
         Neuro *currneuron; ///<Latest created neuron
-        fL_State() : direction(1, 0, 0), currpart(NULL), currneuron(NULL)
+        fL_State() : direction(1,0,0), currpart(NULL), currneuron(NULL)
         { }
 };
@@ -266 +288 @@
         double time; ///<time of creature development
         int numckp; ///<number of checkpoints per growth step - checkpoints are always created after rules deployment in integer steps, numckp determines how many checkpoints should be created within single step (to watch changes of parameters)
+        int maxwords; ///<maximum number of words that can
+        bool using_checkpoints; ///<true if checkpoints should be created, or false
+        bool using_mapping; ///<true if mappings should be created, or false
+
+        int builtincount; ///<number of built-in words
 
         std::list<fL_Word *> genotype; ///<list of current words of genotype
         std::unordered_map<std::string, fL_Word *> words; ///<map from string to words existing in L-System
+        std::vector<std::string> wordnames;
         std::vector<fL_Rule *> rules; ///<rules available in system
 
-        fL_Builder() : fL_Element(fLElementType::INFO)
+        fL_Builder(bool using_mapping = false, bool using_checkpoints = false) : fL_Element(fLElementType::INFO),
+                        using_checkpoints(using_checkpoints), using_mapping(using_mapping)
         {
                 axiom = "";
                 time = 1.0;
                 numckp = 1;
+                builtincount = 0;
+                maxwords = -1;
         }
         ~fL_Builder();
@@ -337 +368 @@
 
         /**
+         * Creates fL_Word object for a given token.
+         * @param worddef string representing single word object in sequence
+         * @param word a reference to a pointer of created word by this method
+         * @param numparams number of parameters for a given sequence (usually number of rule predecessor's arguments)
+         * @param begin the begin of word definition in genotype
+         * @param end the end of word definition in genotype
+         * @return 0 if conversion went successfully, 1 when there is a problem with parsing
+         */
+        int createWord(SString worddef, fL_Word *&word, int numparams, int begin, int end);
+
+        /**
          * Helper function that converts input sequence into list of L-System words.
          * @param sequence input sequence of stringified word objects
@@ -343 +385 @@
          * @return 0 if tokenizing finished successfully, 1 otherwise
          */
-        int tokenize(SString sequence, std::list<fL_Word *> &result, int numparams);
+        int tokenize(SString sequence, std::list<fL_Word *> &result, int numparams, int begin, int end);
 
         /**
@@ -363 +405 @@
         /**
          * Developes L-System from given genotype and builds Framsticks Model from it.
-         */
-        int develop();
+         * When using_checkpoints is enabled, method generates checkpoint for each
+         * step defined in timestamp.
+         * @param neededtime reference to a time value after stopping development (usually it will be equal to time specified in the time field, unless the number of allowed words will be exceeded earlier)
+         * @return final model from a fL genotype
+         */
+        Model* developModel(double &neededtime);
 
         /**
@@ -371 +417 @@
          * @return 0 if developing went successfully, 1 otherwise
          */
-        int developModel(Model &model);
+        int buildModelFromSequence(Model *model);
 
         /**
@@ -386 +432 @@
 
         /**
-         * TODO
+         * Alters part properties according to informations stored in stickword.
+         * Method takes current values of part's properties computed from previous
+         * calls of the alterPartProperties and computes mean according to upcoming
+         * values of properties.
+         * @param part analysed part
+         * @param stickword the L-System word that affects current part
+         * @param alterationcount the number of times of part modifications - used to compute mean of every word properties
+         * @return always 0
          */
         int alterPartProperties(Part *part, fL_Word *stickword, double &alterationcount);
 
         /**
-         * TODO
-         */
-        Neuro *findInputNeuron(std::list<fL_Word *> genotype, std::list<fL_Word *>::iterator it, fL_Word *attractor);
-
-        /**
-         * TODO
-         */
-        void findNext(fL_Word *word, std::list<fL_Word *> genotype, std::list<fL_Word *>::iterator &it);
+         * Finds input neuron that is nearest to attractor or connection definition.
+         * When attractor object is given, then the word with name matching attractor and
+         * with nearest values of parameters is chosen as the point, from which input
+         * neuron is looked for. The searching goes both sides.
+         * @param currneu object storing informations about connection word iterator and current neuron
+         * @param attractor pointer to an attractor definition presented in connection word
+         * @return pointer to the input neuron, or NULL if no neuron could be found
+         */
+        Neuro *findInputNeuron(std::pair<std::list<fL_Word *>::iterator, Neuro *> currneu, fL_Word *attractor);
+
+        /**
+         * Removes joints, parts and neurons with its connections from current model, without
+         * removing checkpoint data.
+         * @param m model to clear
+         */
+        void clearModelElements(Model *m);
+
+        /**
+         * Converts parameters defined in built-in words into desired
+         * range with use of sigmoid function, which ensures staying
+         * within min and max value.
+         * @param input the value from evaluation of parameter
+         * @param min minimal value of property
+         * @param max maximal value of property
+         * @return value of body element property
+         */
+        double sigmoidTransform(double input, double min, double max);
+
+        /**
+         * Counts words defined in the genotype.
+         * @return number of defined words
+         */
+        int countDefinedWords();
+
+        /**
+         * Counts number of sticks in a given sequence
+         * @return number of sticks in sequence
+         */
+        int countSticksInSequence(std::list<fL_Word *> sequence);
+
+        /**
+         * Counts all definitions of words, all words in axiom and rule successors in a genotype.
+         * Used for computing change between original genotype and mutation.
+         * @return number of words in definitions, axiom and rule successors
+         */
+        int countWordsInLSystem();
+
+        /**
+         * Sorts rules and removes rules that will not be used. The "sorting" is
+         * done in such way that all rules with conditions are first, and rules
+         * without conditions go to the end. If there are more than one rule
+         * for the same word with no condition or same condition, than the
+         * second one is removed.
+         */
+        void removeRedundantRules();
 };
 

cpp/frams/genetics/fL/fL_matheval.cpp

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #include <frams/util/extvalue.h>
 #include <frams/util/sstring.h>
 #include <stack>
 #include "fL_matheval.h"
+#include <frams/genetics/genooperators.h>
 
 // Used available operators in MathEvaluation
@@ -94 +99 @@
 }
 
+void MathEvaluation::registerOperator(double(*operation)(double left, double right), int precedence, MathEvaluation::Associativity assoc, std::string opsymbol)
+{
+        operators[opsymbol] = new Operator(operation, precedence, assoc, opsymbol);
+        operatorstrings.push_back(opsymbol);
+}
+
 void MathEvaluation::registerOperators()
 {
         // list of available operators in MathEvaluation
-        operators["+"] = new Operator(madd, 2, Associativity::LEFT, "+");
-        operators["-"] = new Operator(msub, 2, Associativity::LEFT, "-");
-        operators["*"] = new Operator(mmul, 3, Associativity::LEFT, "*");
-        operators["&"] = new Operator(mand, 0, Associativity::LEFT, "&");
-        operators["|"] = new Operator(mor, 0, Associativity::LEFT, "|");
-        operators[">"] = new Operator(mgreater, 1, Associativity::LEFT, ">");
-        operators["<"] = new Operator(mless, 1, Associativity::LEFT, "<");
-        operators[">="] = new Operator(meqgreater, 1, Associativity::LEFT, ">=");
-        operators["<="] = new Operator(meqless, 1, Associativity::LEFT, "<=");
-        operators["="] = new Operator(mequal, 1, Associativity::RIGHT, "=");
-        operators["~"] = new Operator(mnotequal, 1, Associativity::RIGHT, "~");
+        registerOperator(madd, 2, Associativity::LEFT, "+");
+        registerOperator(msub, 2, Associativity::LEFT, "-");
+        registerOperator(mmul, 3, Associativity::LEFT, "*");
+        registerOperator(mgreater, 1, Associativity::LEFT, ">");
+        registerOperator(mless, 1, Associativity::LEFT, "<");
+        registerOperator(meqgreater, 1, Associativity::LEFT, ">=");
+        registerOperator(meqless, 1, Associativity::LEFT, "<=");
+        registerOperator(mequal, 1, Associativity::RIGHT, "=");
+        registerOperator(mnotequal, 1, Associativity::RIGHT, "~");
+        registerOperator(mand, 0, Associativity::LEFT, "&");
+        registerOperator(mor, 0, Associativity::LEFT, "|");
+        arithmeticoperatorscount = 3;
+        comparisonoperatorscount = 6;
 }
 
@@ -159 +172 @@
 int MathEvaluation::convertString(std::string expression)
 {
+        originalexpression = expression;
         clearPostfix(); //clear previous objects
         ExtValue val;
@@ -193 +207 @@
                                         {
                                                 delete operatorstack.back();
-                                                operatorstack.pop_back();
-                                        }
+                                        }
+                                        operatorstack.pop_back();
                                 }
                                 return -1;
@@ -247 +261 @@
                                         {
                                                 delete operatorstack.back();
-                                                operatorstack.pop_back();
-                                        }
+                                        }
+                                        operatorstack.pop_back();
                                 }
                                 return -1;
@@ -407 +421 @@
                                         {
                                                 delete operatorstack.back();
-                                                operatorstack.pop_back();
-                                        }
+                                        }
+                                        operatorstack.pop_back();
                                 }
                                 return -1;
@@ -434 +448 @@
                                 {
                                         delete operatorstack.back();
-                                        operatorstack.pop_back();
-                                }
+                                }
+                                operatorstack.pop_back();
                         }
                         return -1;
@@ -448 +462 @@
         // stack holds number used during operator execution
         std::stack<Number *> numberstack;
-
         for (std::list<Token *>::iterator it = postfixlist.begin(); it != postfixlist.end(); it++)
         {
@@ -532 +545 @@
 int MathEvaluation::RPNToInfix(std::string &result)
 {
+        if (postfixlist.size() == 0)
+        {
+                result = "";
+                return 0;
+        }
         // stack holds stringified chunk and its precedence
         std::stack<std::pair<std::string, int>> chunks;
@@ -585 +603 @@
         {
                 logMessage("MathEvaluation", "RPNToInfix", LOG_ERROR,
-                        "Could not convert RPN notation to infix notation");
+                        "Could not convert RPN notation to infix notation - formula is not complete");
                 return -1;
         }
@@ -592 +610 @@
         return 0;
 }
+
+void MathEvaluation::mutateValueOrVariable(MathEvaluation::Number *&currval, bool usetime)
+{
+        if (randomN(2) == 0 && varcount > 0) // use variable
+        {
+                if (currval && currval->type == TokenType::NUMBER)
+                {
+                        delete currval;
+                }
+                int var = randomN(varcount + (usetime ? 1 : 0));
+                if (varcount == var) // time is used
+                {
+                        currval = t;
+                }
+                else
+                {
+                        currval = vars[var];
+                }
+        }
+        else
+        {
+                if (!currval || currval->type == TokenType::VARIABLE)
+                {
+                        currval = new Number(rnd01);
+                }
+                else
+                {
+                        currval->value = rnd01;
+                }
+        }
+}
+
+MathEvaluation::Operator* MathEvaluation::getRandomOperator(int type)
+{ // 0 for all, 1 for arithmetic only, 2 for logical only
+        int randop = type == 2 ? arithmeticoperatorscount : 0;
+        int count = arithmeticoperatorscount;
+        if (type == 0)
+        {
+                count = operatorstrings.size();
+        }
+        else if (type == 2)
+        {
+                count = operatorstrings.size() - arithmeticoperatorscount;
+        }
+        randop += randomN(count);
+        return operators[operatorstrings[randop]];
+}
+
+void MathEvaluation::mutateConditional()
+{
+        if (varcount > 0)
+        {
+                int currsize = postfixlist.size();
+                int varid = randomN(varcount);
+                postfixlist.push_back(vars[varid]);
+                if (randomN(2) == 0 && varcount > 1)
+                {
+                        int varid2 = randomN(varcount - 1);
+                        if (varid2 >= varid) varid2++;
+                        postfixlist.push_back(vars[varid2]);
+                }
+                else
+                {
+                        Number *num = new Number(rnd01);
+                        postfixlist.push_back(num);
+                }
+                int opid = arithmeticoperatorscount + randomN(comparisonoperatorscount);
+                postfixlist.push_back(operators[operatorstrings[opid]]);
+                if (currsize > 0)
+                {
+                        postfixlist.push_back(operators["&"]);
+                }
+        }
+}
+
+int MathEvaluation::mutate(bool logical, bool usetime)
+{
+        if (postfixlist.size() == 0)
+        {
+                Number *val = new Number(rnd01);
+                postfixlist.push_back(val);
+                return -1;
+        }
+        int method = randomN(postfixlist.size() < MAX_MUT_FORMULA_SIZE ? MATH_MUT_COUNT : MATH_MUT_COUNT - 1);
+        switch (method)
+        {
+        case MATH_MUT_INSERTION:
+        {
+                std::list<Token *> insertpair;
+                Number *val = NULL;
+                mutateValueOrVariable(val, usetime);
+                insertpair.push_back(val);
+                std::list<Token *>::iterator it = postfixlist.begin();
+                // insertion can be applied from 1st occurrence
+                int insertlocation = 1 + randomN(postfixlist.size() - 1);
+                std::advance(it, insertlocation);
+                Operator *rndop;
+                if (insertlocation == (int)postfixlist.size() - 1)
+                {
+                        rndop = getRandomOperator(logical ? 2 : 1);
+                }
+                else
+                {
+                        rndop = getRandomOperator(logical ? 0 : 1);
+
+                }
+                insertpair.push_back(rndop);
+                postfixlist.insert(it, insertpair.begin(), insertpair.end());
+                break;
+        }
+        case MATH_MUT_CHANGEVAL:
+        {
+                std::vector<std::list<Token *>::iterator> numbersineval;
+                int id = 0;
+                for (std::list<Token *>::iterator it = postfixlist.begin(); it != postfixlist.end(); it++)
+                {
+                        if ((*it)->type == TokenType::NUMBER || (*it)->type == TokenType::VARIABLE)
+                        {
+                                numbersineval.push_back(it);
+                        }
+                        id++;
+                }
+                int randid = randomN(numbersineval.size());
+                Number *numptr = (Number *)(*numbersineval[randid]);
+                mutateValueOrVariable(numptr, usetime);
+                (*numbersineval[randid]) = numptr;
+                break;
+        }
+        case MATH_MUT_CHANGEOPER:
+        {
+                std::vector<std::list<Token *>::iterator> ops;
+                for (std::list<Token *>::iterator it = postfixlist.begin(); it != postfixlist.end(); it++)
+                {
+                        if ((*it)->type == TokenType::OPERATOR)
+                        {
+                                ops.push_back(it);
+                        }
+                }
+                if (ops.size() > 0)
+                {
+                        int randid = randomN(ops.size());
+                        Operator *rndop;
+                        if (randid == (int)ops.size() - 1)
+                        {
+                                rndop = getRandomOperator(logical ? 2 : 1);
+                        }
+                        else
+                        {
+                                rndop = getRandomOperator(logical ? 0 : 1);
+                        }
+                        (*ops[randid]) = rndop;
+                }
+                break;
+        }
+        case MATH_MUT_DELETION:
+        {
+                std::list<Token *>::iterator it = postfixlist.begin();
+                std::vector<std::list<Token *>::iterator> firstofpairs;
+                while (it != postfixlist.end())
+                {
+                        if ((*it)->type == TokenType::NUMBER || (*it)->type == TokenType::VARIABLE)
+                        {
+                                std::list<Token *>::iterator next = it;
+                                next++;
+                                if (next != postfixlist.end() && (*next)->type == TokenType::OPERATOR)
+                                {
+                                        firstofpairs.push_back(it);
+                                }
+                        }
+                        it++;
+                }
+                if (firstofpairs.size() > 0)
+                {
+                        int rndid = randomN(firstofpairs.size());
+                        if ((*firstofpairs[rndid])->type == TokenType::NUMBER)
+                        {
+                                delete (*firstofpairs[rndid]);
+                        }
+                        firstofpairs[rndid] = postfixlist.erase(firstofpairs[rndid]);
+                        postfixlist.erase(firstofpairs[rndid]);
+                }
+                break;
+        }
+        }
+        return method;
+}
+
+std::string MathEvaluation::getStringifiedRPN()
+{
+        std::string res = "";
+        for (Token *el: postfixlist)
+        {
+                res += el->toString();
+                res += " ";
+        }
+        return res;
+}

cpp/frams/genetics/fL/fL_matheval.h

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #ifndef _FL_MATHEVAL_H_
 #define _FL_MATHEVAL_H_
@@ -8 +12 @@
 
 #define VARIABLEPREFIX '$'
+
+#define MATH_MUT_DELETION   0
+#define MATH_MUT_CHANGEVAL  1
+#define MATH_MUT_CHANGEOPER 2
+#define MATH_MUT_INSERTION  3
+#define MATH_MUT_COUNT      4
+
+#define MAX_MUT_FORMULA_SIZE 7
+#define XOVER_MAX_MIGRATED_RULES 3
 
 /** @name Available operators for MathEvaluation */
@@ -171 +184 @@
         void registerOperators();
 
+        std::string originalexpression;
         std::unordered_map<std::string, Operator *> operators; ///<map containing available operators for MathEvaluation
         std::list<Token *> postfixlist; ///<list with tokens ordered as postfix (RPN) notation of the given string
@@ -176 +190 @@
         std::vector<Variable *> vars; ///<vector of variables, default values are 0
         Variable *t; ///<additional t variable, that can act as time for evaluation
+        std::vector<std::string> operatorstrings; ///<list of registered operators
+        int arithmeticoperatorscount; ///<count of arithmetic operators
+        int comparisonoperatorscount;
 public:
 
@@ -226 +243 @@
 
         /**
+         * Registers new operator for MathEvaluation object.
+         * @param operation function that needs to be called during evaluation
+         * @param precedence precedence of operator
+         * @param assoc associativity of the operator
+         * @param opsymbol symbol of the operator
+         */
+        void registerOperator(double(*operation)(double left, double right), int precedence, MathEvaluation::Associativity assoc, std::string opsymbol);
+
+        /**
          * Converts stored RPN list to infix string.
          * @param result reference to variable that will hold the result
@@ -231 +257 @@
          */
         int RPNToInfix(std::string &result);
+
+        /**
+         * Mutates formula.
+         * @param logical if true, method uses logical operators only
+         * @param usetime if true, method may use time variable during mutation
+         * @param 0 if mutation could be performed, -1 if postfixlist is empty
+         */
+        int mutate(bool logical, bool usetime);
+
+        /**
+         * Mutates formula so it creates conjuctive of comparisons.
+         */
+        void mutateConditional();
+
+        /**
+         * Mutates number by using random value or one of variables.
+         * @param currval current value of number
+         * @param usetime if true, then time variable may be used
+         */
+        void mutateValueOrVariable(Number *&currval, bool usetime);
+
+        /**
+         * Returns formula in RPN notation
+         * @param RPN notation string
+         */
+        std::string getStringifiedRPN();
+
+        /**
+         * Returns random operator available in object.
+         * @param type 0 for all operators, 1 for arithmetic only, 2 for logical only
+         * @return pointer to random operator
+         */
+        Operator* getRandomOperator(int type);
 };
 

cpp/frams/genetics/fL/fL_oper.cpp

@@ +1 @@
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
 #include "fL_oper.h"
+#include <common/loggers/loggers.h>
+#include "../fH/fH_oper.h"
+#include <algorithm>
+
+#define FIELDSTRUCT Geno_fL
+static ParamEntry GENOfLparam_tab[] =
+{
+        {"Genetics: fL", 3, FL_OPCOUNT + FL_MUTGROUPSCOUNT + FL_CHG_COUNT + 2 + FL_ADD_COUNT, },
+        {"Genetics: fL: Probabilities of mutating axiom and rules", },
+        {"Genetics: fL: Probabilities of mutation types", },
+        {"fL_maxdefinedwords", 0, 0, "Maximum number of defined words", "d 0 100 10", FIELD(maxdefinedwords), "Maximum number of words that can be defined in L-System", },
+
+        {"fL_axm_mut_prob", 1, 0, "Axiom mutation", "f 0 1 0.2", FIELD(groupprobabilities[FL_AXM_WORD_MUT_PROB]), "Probability of performing mutation operations on axiom", },
+        {"fL_rul_mut_prob", 1, 0, "Rule's successor mutation", "f 0 1 0.8", FIELD(groupprobabilities[FL_RUL_WORD_MUT_PROB]), "Probability of performing mutation operations on the successor of random rule", },
+
+        {"fL_mut_addition", 2, 0, "Addition of word to sequence", "f 0 1 0.2", FIELD(operations[FL_ADD_WORD]), "Probability of adding random existing word to the axiom or one of successors", },
+
+        {"fL_mut_add_stick", 2, 0, " - addition of stick", "f 0 1 0.2", FIELD(addtypes[FL_ADD_STICK]), "Probability of adding stick", },
+        {"fL_mut_add_neuro", 2, 0, " - addition of neuron", "f 0 1 0.2", FIELD(addtypes[FL_ADD_NEURO]), "Probability of adding neuron", },
+        {"fL_mut_add_conn", 2, 0, " - addition of neuron connection", "f 0 1 0.2", FIELD(addtypes[FL_ADD_CONN]), "Probability of adding connection", },
+        {"fL_mut_add_rot", 2, 0, " - addition of rotation words", "f 0 1 0.2", FIELD(addtypes[FL_ADD_ROT]), "Probability of adding one of rotation words", },
+        {"fL_mut_add_branch", 2, 0, " - addition of branched stick", "f 0 1 0.2", FIELD(addtypes[FL_ADD_BRANCH]), "Probability of adding branch with rotation and stick", },
+        {"fL_mut_add_other", 2, 0, " - addition of defined words", "f 0 1 0.4", FIELD(addtypes[FL_ADD_OTHER]), "Probability of adding other word, defined in genotype", },
+
+        {"fL_mut_worddefaddition", 2, 0, "Addition of new word definition", "f 0 1 0.05", FIELD(operations[FL_ADD_WDEF]), "Probability of adding new word definition to the genotype", },
+        {"fL_mut_ruleaddition", 2, 0, "Addition of new rule definition", "f 0 1 0.1", FIELD(operations[FL_ADD_RULE]), "Probability of adding new rule definition for existing word", },
+        {"fL_mut_rulecond", 2, 0, "Modification of rule condition", "f 0 1 0.1", FIELD(operations[FL_CHG_COND]), "Probability of modifying random rule condition", },
+
+        {"fL_mut_changeword", 2, 0, "Change of random word", "f 0 1 0.3", FIELD(operations[FL_CHG_WORD]), "Probability of changing word name or formula of a random word from axiom or one of successors", },
+        {"fL_mut_changeword_formula", 2, 0, " - change of formula", "f 0 1 0.7", FIELD(chgoperations[FL_CHG_WORD_FORMULA]), "Probability of changing formula in word", },
+        {"fL_mut_changeword_name", 2, 0, " - change of name", "f 0 1 0.3", FIELD(chgoperations[FL_CHG_WORD_NAME]), "Probability of changing name in word", },
+
+        {"fL_mut_changeiter", 2, 0, "Change of L-System iteration", "f 0 1 0.3", FIELD(operations[FL_CHG_ITER]), "Probability of changing number of iterations of L-Systems", },
+        {"fL_mut_changeiter_step", 2, 0, "Step of iteration changing", "f 0 1 1.0", FIELD(iterchangestep), "Minimal step that should be used for changing iterations in L-Systems", },
+        {"fL_mut_deletion", 2, 0, "Deletion of random word", "f 0 1 0.2", FIELD(operations[FL_DEL_WORD]), "Probability of deleting random word from axiom or random successor (also deletes rule if there is only one word in successor)", },
+        { 0, },
+};
+#undef FIELDSTRUCT
 
 Geno_fL::Geno_fL()
 {
-        //      par.setParamTab(GENOfHparam_tab);
-        //      par.select(this);
-        //      par.setDefault();
-        supported_format = 'H';
-}
+        par.setParamTab(GENOfLparam_tab);
+        par.select(this);
+        par.setDefault();
+        supported_format = 'L';
+        iterchangestep = 1.0;
+        maxdefinedwords = 10;
+}
+
+int Geno_fL::checkValidity(const char *geno, const char *genoname)
+{
+        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreAllMessages, LOG_WARN);
+        fL_Builder builder(false, false);
+
+        int err = builder.parseGenotype(geno);
+        if (err != 0)
+        {
+                return err;
+        }
+
+        if (builder.countSticksInSequence(builder.genotype) == 0)
+        {
+                return GENOPER_OPFAIL;
+        }
+        double neededtime = 0;
+        Model *m = builder.developModel(neededtime);
+        if (!m)
+        {
+                return GENOPER_OPFAIL;
+        }
+        if (!m->isValid())
+        {
+                delete m;
+                return GENOPER_OPFAIL;
+        }
+        delete m;
+
+
+        return GENOPER_OK;
+}
+
+int Geno_fL::validate(char *&geno, const char *genoname)
+{
+        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreAllMessages, LOG_WARN);
+        fL_Builder builder(false, false);
+
+        int err = builder.parseGenotype(geno);
+        if (err != 0)
+        {
+                return err;
+        }
+        double neededtime = 0;
+        Model *m = builder.developModel(neededtime);
+        if (!m->isValid())
+        {
+                delete m;
+                return GENOPER_OPFAIL;
+        }
+        if (neededtime != builder.time)
+        {
+                builder.time = neededtime;
+                free(geno);
+                geno = strdup(builder.toString().c_str());
+                delete m;
+                return GENOPER_OK;
+        }
+        delete m;
+        return GENOPER_OK;
+}
+
+bool Geno_fL::addWord(std::list<fL_Word *>* list, fL_Word *definition, std::list<fL_Word *>::iterator it)
+{
+        fL_Word *newword = new fL_Word();
+        *newword = *definition;
+
+        // if word has parameters
+        if (newword->npar > 0)
+        {
+                // create ParamObject that will hold parameter data
+                newword->data = ParamObject::makeObject(newword->tab);
+                Param par(newword->tab);
+                par.select(newword->data);
+                par.setDefault();
+                for (int i = 0; i < par.getPropCount(); i++)
+                {
+                        newword->parevals.push_back(NULL);
+                }
+                if (newword->name.startsWith("rot"))
+                {
+                        double rot = 2 * rnd01;
+                        MathEvaluation *eval = new MathEvaluation(0);
+                        eval->convertString(SString::valueOf(rot).c_str());
+                        newword->parevals[0] = eval;
+                }
+                else if (newword->name == "N")
+                {
+                        SString det;
+                        NeuroClass *cls = getRandomNeuroClass();
+                        if (!cls) cls = Neuro::getClass("N");
+                        det = cls->getName();
+                        Geno_fH::mutateNeuronProperties(det);
+                        par.setStringById(FL_PE_NEURO_DET, det);
+                }
+                else if (newword->name == "C")
+                {
+                        MathEvaluation *eval = new MathEvaluation(0);
+                        eval->convertString(SString::valueOf(2 * rnd01 - 1).c_str());
+                        newword->parevals[0] = eval;
+                }
+        }
+
+        list->insert(it, newword);
+        return true;
+}
+
+std::list<fL_Word *>* Geno_fL::selectRandomSequence(fL_Builder *creature, int &numparams, int &ruleid)
+{
+        std::list<fL_Word *> *list = NULL;
+        int axiomorrules = roulette(groupprobabilities, FL_MUTGROUPSCOUNT);
+        bool axiomused = axiomorrules == FL_AXM_WORD_MUT_PROB || creature->rules.size() == 0;
+        if (axiomused)
+        {
+                list = &creature->genotype;
+                numparams = 0;
+                ruleid = -1;
+        }
+        else
+        {
+                int rid = randomN(creature->rules.size());
+                list = &creature->rules[rid]->objsucc;
+                numparams = creature->rules[rid]->objpred->npar;
+                ruleid = rid;
+        }
+        return list;
+}
+
+fL_Word* Geno_fL::randomWordDefinition(fL_Builder *creature, int method)
+{
+        if (method == FL_ADD_OTHER && creature->builtincount < (int)creature->words.size())
+        {
+                return creature->words[creature->wordnames[creature->builtincount + randomN((int)creature->words.size() - creature->builtincount)]];
+        }
+        else
+        {
+                if (method == FL_ADD_OTHER) // we should be able to select stick, neuro or conn
+                {
+                        double alttypes[FL_ADD_COUNT - 2];
+                        alttypes[FL_ADD_STICK] = addtypes[FL_ADD_STICK];
+                        alttypes[FL_ADD_NEURO] = addtypes[FL_ADD_NEURO];
+                        alttypes[FL_ADD_CONN] = addtypes[FL_ADD_CONN];
+                        alttypes[FL_ADD_ROT] = addtypes[FL_ADD_ROT];
+                        method = roulette(alttypes, FL_ADD_COUNT - 2);
+                }
+                switch (method)
+                {
+                case FL_ADD_STICK:
+                        return creature->words["S"];
+                case FL_ADD_NEURO:
+                        return creature->words["N"];
+                case FL_ADD_CONN:
+                        return creature->words["C"];
+                case FL_ADD_ROT:
+                {
+                        int rottype = randomN(3);
+                        switch (rottype)
+                        {
+                        case 0:
+                                return creature->words["rotX"];
+                        case 1:
+                                return creature->words["rotY"];
+                        case 2:
+                                return creature->words["rotZ"];
+                        }
+                        break;
+                }
+                case FL_ADD_BRANCH:
+                        // return NULL
+                        break;
+                }
+        }
+        return NULL;
+}
+
+void Geno_fL::deleteBranch(std::list<fL_Word *> *list, std::list<fL_Word *>::iterator openbranchposition)
+{
+        fL_Branch *branch = (fL_Branch *)(*openbranchposition);
+        if (branch->btype == fL_Branch::BranchType::OPEN)
+        {
+                int bcount = 1;
+                delete (*openbranchposition);
+                openbranchposition = list->erase(openbranchposition);
+                for (; openbranchposition != list->end(); openbranchposition++)
+                {
+                        if ((*openbranchposition)->type == fLElementType::BRANCH)
+                        {
+                                branch = (fL_Branch *)(*openbranchposition);
+                                if (branch->btype == fL_Branch::BranchType::OPEN)
+                                {
+                                        bcount++;
+                                }
+                                else
+                                {
+                                        bcount--;
+                                        if (bcount == 0)
+                                        {
+                                                delete branch;
+                                                list->erase(openbranchposition);
+                                                break;
+                                        }
+                                }
+                        }
+                }
+        }
+        else
+        {
+                openbranchposition++;
+                if (openbranchposition != list->end())
+                {
+                        delete (*openbranchposition);
+                        list->erase(openbranchposition);
+                }
+        }
+}
+
+int Geno_fL::mutate(char *&geno, float& chg, int &method)
+{
+        fL_Builder *creature = new fL_Builder(false, false);
+
+        if (creature->parseGenotype(geno) != 0)
+        {
+                delete creature;
+                return GENOPER_OPFAIL;
+        }
+
+        int before = creature->countWordsInLSystem();
+
+        method = roulette(operations, FL_OPCOUNT);
+        switch (method)
+        {
+                case FL_CHG_ITER:
+                {
+                        if (randomN(2) == 0)
+                        {
+                                creature->time = creature->time + iterchangestep <= ExtValue::getDouble(FL_MAXITER) ?
+                                                creature->time + iterchangestep : creature->time - iterchangestep;
+                        }
+                        else
+                        {
+                                creature->time = creature->time - iterchangestep >= 0 ?
+                                                creature->time - iterchangestep : creature->time + iterchangestep;
+                        }
+                        break;
+                }
+                case FL_CHG_COND:
+                {
+                        if (creature->rules.size() > 0)
+                        {
+                                int ruleid = randomN(creature->rules.size());
+                                if (!creature->rules[ruleid]->condeval)
+                                {
+                                        creature->rules[ruleid]->condeval = new MathEvaluation(creature->rules[ruleid]->objpred->npar);
+                                }
+                                creature->rules[ruleid]->condeval->mutateConditional();
+                                break;
+                        }
+                        // if there are no rules - create one
+                }
+                /* no break */
+                case FL_ADD_RULE:
+                {
+                        std::unordered_map<std::string, fL_Word *>::iterator pred = creature->words.begin();
+                        std::vector<fL_Word *> wordswithnorules;
+                        for (; pred != creature->words.end(); pred++)
+                        {
+                                if (!pred->second->builtin)
+                                {
+                                        bool norules = true;
+                                        for (fL_Rule * r : creature->rules)
+                                        {
+                                                if (pred->second->name == r->objpred->name &&
+                                                                pred->second->npar == r->objpred->npar)
+                                                {
+                                                        norules = false;
+                                                        break;
+                                                }
+                                        }
+                                        if (norules)
+                                        {
+                                                wordswithnorules.push_back(pred->second);
+                                        }
+                                }
+                        }
+                        if (wordswithnorules.size() > 0)
+                        {
+                                int predid = randomN(wordswithnorules.size());
+                                fL_Rule *newrule = new fL_Rule(0,0);
+                                fL_Word *pred = new fL_Word();
+                                *pred = *wordswithnorules[predid];
+                                newrule->objpred = pred;
+                                fL_Word *initdef = randomWordDefinition(creature, roulette(addtypes, FL_ADD_COUNT - 1)); // -1 to avoid branching
+                                addWord(&newrule->objsucc, initdef, newrule->objsucc.begin());
+                                creature->rules.push_back(newrule);
+                                break;
+                        }
+                        else if (creature->rules.size() > 0)
+                        {
+                                int ruleid = randomN(creature->rules.size());
+                                fL_Rule *newrule = new fL_Rule(0, 0);
+                                fL_Word *pred = new fL_Word();
+                                *pred = *creature->rules[ruleid]->objpred;
+                                newrule->objpred = pred;
+                                if (creature->rules[ruleid]->condeval)
+                                {
+                                        std::string formula = "";
+                                        creature->rules[ruleid]->condeval->RPNToInfix(formula);
+                                        if (formula.find("1.0-(") != 0)
+                                        {
+                                                std::string res = "1.0-(";
+                                                res += formula;
+                                                res += ")";
+                                                newrule->condeval = new MathEvaluation(pred->npar);
+                                                newrule->condeval->convertString(res);
+                                        }
+                                        else
+                                        {
+                                                newrule->condeval = new MathEvaluation(pred->npar);
+                                                newrule->condeval->mutateConditional();
+                                        }
+                                }
+                                else
+                                {
+                                        newrule->condeval = new MathEvaluation(pred->npar);
+                                        newrule->condeval->mutateConditional();
+                                }
+                                fL_Word *worddef = randomWordDefinition(creature, roulette(addtypes, FL_ADD_COUNT - 1));
+                                addWord(&newrule->objsucc, worddef, newrule->objsucc.begin());
+                                creature->rules.push_back(newrule);
+                                break;
+                        }
+                        // if there are no words, from which rules can be formed, then add one
+                }
+                /* no break */
+                case FL_ADD_WDEF:
+                {
+                        if (creature->countDefinedWords() <= maxdefinedwords)
+                        {
+                                int npar = randomN(ExtValue::getInt(FL_MAXPARAMS, false));
+                                for (int i = 0; i < maxdefinedwords; i++)
+                                {
+                                        std::string name = "w";
+                                        name += std::to_string(i);
+                                        if (creature->words.find(name) == creature->words.end())
+                                        {
+                                                fL_Word *word = new fL_Word(false, 0, 0);
+                                                word->npar = npar;
+                                                word->name = name.c_str();
+                                                word->processDefinition(creature);
+                                                break;
+                                        }
+                                }
+                                break;
+                        }
+                        //no break at the end of case - if there is too many words, then
+                        // deletion should be performed
+                }
+                /* no break */
+                case FL_DEL_WORD:
+                {
+                        int numpars = 0;
+                        int ruleid = 0;
+                        std::list<fL_Word *> *list = selectRandomSequence(creature, numpars, ruleid);
+                        if (ruleid == -1 && creature->countSticksInSequence((*list)) == 1)
+                        {
+                                if (list->size() > 1)
+                                {
+                                        int rndid = randomN(list->size() - 1);
+                                        int j = 0;
+                                        std::list<fL_Word *>::iterator it = list->begin();
+                                        if ((*it)->name == "S")
+                                        {
+                                                it++;
+                                        }
+                                        while (it != list->end() && j < rndid && ((*it)->name == "S"))
+                                        {
+                                                if ((*it)->name != "S")
+                                                {
+                                                        j++;
+                                                }
+                                                it++;
+                                        }
+                                        if (it != list->end())
+                                        {
+                                                if ((*it)->type == fLElementType::BRANCH)
+                                                {
+                                                        deleteBranch(list, it);
+                                                }
+                                                else
+                                                {
+                                                        delete (*it);
+                                                        list->erase(it);
+                                                }
+                                                break;
+                                        }
+                                        // else add word
+                                }
+                                // else add word
+                        }
+                        else
+                        {
+                                int rndid = randomN(list->size());
+                                std::list<fL_Word *>::iterator it = list->begin();
+                                std::advance(it, rndid);
+                                if ((*it)->type == fLElementType::BRANCH)
+                                {
+                                        deleteBranch(list, it);
+                                }
+                                else
+                                {
+                                        delete (*it);
+                                        list->erase(it);
+                                }
+                                if (ruleid > -1 && creature->rules[ruleid]->objsucc.size() == 0)
+                                {
+                                        delete creature->rules[ruleid];
+                                        creature->rules.erase(creature->rules.begin() + ruleid);
+                                }
+                                break;
+                        }
+                        // if no words available, then add word
+                }
+                /* no break */
+                case FL_ADD_WORD:
+                {
+                        int numpars = 0;
+                        int tmp = 0;
+                        std::list<fL_Word *> *list = selectRandomSequence(creature, numpars, tmp);
+                        int rndid = randomN(list->size());
+                        std::list<fL_Word *>::iterator it = list->begin();
+                        std::advance(it, rndid);
+                        int meth = roulette(addtypes, FL_ADD_COUNT);
+                        if (tmp == -1)
+                        { // if sequence is axiom and it does not have non-builtin words
+                                bool hasdefined = false;
+                                for (std::list<fL_Word *>::iterator elem = list->begin(); elem != list->end(); elem++)
+                                {
+                                        if (!(*elem)->builtin)
+                                        {
+                                                hasdefined = true;
+                                                break;
+                                        }
+                                }
+                                if (!hasdefined)
+                                {
+                                        meth = FL_ADD_OTHER;
+                                }
+
+                        }
+                        if (meth != FL_ADD_BRANCH)
+                        {
+                                fL_Word *worddef = randomWordDefinition(creature, meth);
+                                addWord(list, worddef, it);
+                        }
+                        else
+                        {
+                                fL_Branch *start = new fL_Branch(fL_Branch::BranchType::OPEN, 0, 0);
+                                list->insert(it, start);
+                                int rottype = randomN(2);
+                                switch (rottype)
+                                {
+                                case 0:
+                                        addWord(list, creature->words["rotY"], it);
+                                case 1:
+                                        addWord(list, creature->words["rotZ"], it);
+                                }
+                                addWord(list, creature->words["S"], it);
+                                fL_Branch *end = new fL_Branch(fL_Branch::BranchType::CLOSE, 0, 0);
+                                list->insert(it, end);
+                        }
+                        break;
+                }
+                case FL_CHG_WORD:
+                {
+                        int numpars = 0;
+                        int tmp = 0;
+                        std::list<fL_Word *> *list = selectRandomSequence(creature, numpars, tmp);
+                        int rndid = randomN(list->size());
+                        std::list<fL_Word *>::iterator selectedword = list->begin();
+                        std::advance(selectedword, rndid);
+                        if ((*selectedword)->type == fLElementType::BRANCH)
+                        {
+                                break;
+                        }
+                        int chgtype = roulette(chgoperations, FL_CHG_COUNT);
+                        if (creature->countSticksInSequence((*list)) == 1 && tmp == -1) // if sequence is axiom
+                        {
+                                fL_Word *worddef = randomWordDefinition(creature, roulette(addtypes, FL_ADD_COUNT - 1));
+
+                                int numpars = 0;
+                                std::list<fL_Word *> *list = selectRandomSequence(creature, numpars, tmp);
+                                int rndid = randomN(list->size());
+                                std::list<fL_Word *>::iterator it = list->begin();
+                                std::advance(it, rndid);
+
+                                addWord(list, worddef, it);
+
+                                break;
+                        }
+                        else if (chgtype == FL_CHG_WORD_NAME)
+                        {
+                                if ((*selectedword)->builtin)
+                                {
+                                        delete (*selectedword);
+                                        selectedword = list->erase(selectedword);
+                                        fL_Word *worddef = randomWordDefinition(creature, roulette(addtypes, FL_ADD_COUNT - 1));
+                                        addWord(list, worddef, selectedword);
+                                }
+                                else
+                                {
+                                        std::vector<fL_Word *> available;
+                                        for (std::unordered_map<std::string, fL_Word *>::iterator wit = creature->words.begin();
+                                                        wit != creature->words.end(); wit++)
+                                        {
+                                                if ((*selectedword)->npar == wit->second->npar &&
+                                                                (*selectedword)->name != wit->second->name &&
+                                                                !wit->second->builtin)
+                                                {
+                                                        available.push_back(wit->second);
+                                                }
+                                        }
+                                        if (available.size() > 0)
+                                        {
+                                                int newnameid = randomN(available.size());
+                                                (*selectedword)->name = available[newnameid]->name;
+                                        }
+                                        else
+                                        {
+                                                delete (*selectedword);
+                                                selectedword = list->erase(selectedword);
+                                                fL_Word *worddef = randomWordDefinition(creature, roulette(addtypes, FL_ADD_COUNT - 1));
+                                                addWord(list, worddef, selectedword);
+                                        }
+                                }
+                        }
+                        else
+                        {
+                                if ((*selectedword)->npar > 0)
+                                {
+                                        int randeval = randomN((*selectedword)->npar);
+                                        Param par((*selectedword)->tab, (*selectedword)->data);
+                                        if ((*selectedword)->builtin && (*selectedword)->name == "N"
+                                                        && strcmp(par.id(randeval), FL_PE_NEURO_DET) == 0)
+                                        {
+                                                SString res = par.getStringById(FL_PE_NEURO_DET);
+                                                Geno_fH::mutateNeuronProperties(res);
+                                                par.setStringById(FL_PE_NEURO_DET, res);
+                                        }
+                                        else if ((*selectedword)->builtin &&
+                                                        (*selectedword)->name == "C" &&
+                                                        strcmp(par.id(randeval), FL_PE_CONN_ATTR) == 0)
+                                        {
+                                                SString strattractor = par.getStringById(FL_PE_CONN_ATTR);
+                                                if (strattractor.len() > 0)
+                                                {
+                                                        fL_Word *w = NULL;
+                                                        creature->createWord(strattractor, w, numpars, 0, 0);
+                                                        // mutate attractor parameter
+                                                        if (w->npar > 0)
+                                                        {
+                                                                int rndattr = randomN(w->npar);
+                                                                if (!w->parevals[rndattr])
+                                                                {
+                                                                        w->parevals[rndattr] = new MathEvaluation(numpars);
+                                                                }
+                                                                w->parevals[rndattr]->mutate(false, false);
+                                                        }
+                                                        strattractor = w->stringify(true);
+                                                        par.setStringById(FL_PE_CONN_ATTR, strattractor);
+                                                        delete w;
+                                                }
+                                                else
+                                                {
+                                                        if (creature->builtincount < (int)creature->words.size())
+                                                        {
+                                                                fL_Word *wdef = randomWordDefinition(creature, FL_ADD_OTHER);
+                                                                fL_Word *w = new fL_Word();
+                                                                *w = *wdef;
+                                                                w->data = ParamObject::makeObject(w->tab);
+                                                                Param apar(w->tab);
+                                                                apar.select(w->data);
+                                                                apar.setDefault();
+                                                                if (w->npar > 0)
+                                                                {
+                                                                        int rndattr = randomN(w->npar);
+                                                                        for (int i = 0; i < w->npar; i++)
+                                                                        {
+                                                                                if (i == rndattr)
+                                                                                {
+                                                                                        MathEvaluation *ev = new MathEvaluation(numpars);
+                                                                                        ev->mutate(false, false);
+                                                                                        w->parevals.push_back(ev);
+                                                                                }
+                                                                                else
+                                                                                {
+                                                                                        w->parevals.push_back(NULL);
+                                                                                }
+                                                                        }
+
+                                                                }
+                                                                strattractor = w->stringify(false);
+                                                                par.setStringById(FL_PE_CONN_ATTR, strattractor);
+                                                                delete w;
+                                                        }
+                                                }
+                                        }
+                                        else
+                                        {
+                                                if (!(*selectedword)->parevals[randeval])
+                                                {
+                                                        (*selectedword)->parevals[randeval] = new MathEvaluation(numpars);
+                                                }
+                                                (*selectedword)->parevals[randeval]->mutate(false, iterchangestep != 1.0);
+                                        }
+                                }
+                        }
+                        break;
+                }
+        }
+
+        free(geno);
+        geno = strdup(creature->toString().c_str());
+        chg = (double)abs(before - creature->countWordsInLSystem()) / before;
+        delete creature;
+
+        return GENOPER_OK;
+}
+
+fL_Word* Geno_fL::getAppropriateWord(fL_Builder *from, fL_Builder *to, fL_Word *fromword, std::unordered_map<std::string, std::string> &map)
+{
+        if (fromword->name == "[" || fromword->name == "]") // if words are branching words
+        {
+                fL_Branch *newword = new fL_Branch(fromword->name == "[" ? fL_Branch::BranchType::OPEN : fL_Branch::BranchType::CLOSE, 0, 0);
+                return newword;
+        }
+        if (fromword->builtin)
+        {
+                fL_Word *newword = new fL_Word();
+                (*newword) = (*to->words[fromword->name.c_str()]);
+                return newword;
+        }
+        if (map.find(fromword->name.c_str()) != map.end()) // if word is already mapped
+        {
+                fL_Word *newword = new fL_Word();
+                (*newword) = (*to->words[map[fromword->name.c_str()]]);
+                return newword;
+        }
+        else if (to->words.find(fromword->name.c_str()) != to->words.end() &&
+                        to->words[fromword->name.c_str()]->npar == fromword->npar) // if there is already same word with same number of parameters
+        {
+                fL_Word *newword = new fL_Word();
+                map[fromword->name.c_str()] = fromword->name.c_str();
+                (*newword) = (*to->words[map[fromword->name.c_str()]]);
+                return newword;
+        }
+        for (std::unordered_map<std::string, fL_Word *>::iterator it = to->words.begin();
+                        it != to->words.end(); it++)
+        { // find word with same number of parameters
+                if (fromword->npar == it->second->npar && map.find(fromword->name.c_str()) == map.end() && !it->second->builtin)
+                { // if there is a word with same number of parameters
+                        map[fromword->name.c_str()] = it->second->name.c_str();
+                        fL_Word *newword = new fL_Word();
+                        (*newword) = (*it->second);
+                        return newword;
+                }
+        }
+        fL_Word *newworddef = new fL_Word();
+        (*newworddef) = (*fromword);
+        newworddef->parevals.clear();
+        if (to->words.find(newworddef->name.c_str()) != to->words.end())
+        {
+                int i = 0;
+                while (true)
+                {
+                        std::string name = "w";
+                        name += std::to_string(i);
+                        if (to->words.find(name) == to->words.end())
+                        {
+                                newworddef->name = name.c_str();
+                                break;
+                        }
+                        i++;
+                }
+        }
+        newworddef->processDefinition(to);
+        map[fromword->name.c_str()] = newworddef->name.c_str();
+        fL_Word *newword = new fL_Word();
+        (*newword) = (*to->words[map[fromword->name.c_str()]]);
+        return newword;
+}
+
+void Geno_fL::migrateRandomRules(fL_Builder *from, fL_Builder *to, int numselrules)
+{
+        std::unordered_map<std::string, std::string> map;
+        if (from->rules.size() > 0)
+        {
+                for (int i = 0; i < numselrules; i++)
+                {
+                        int rulid = randomN(from->rules.size());
+                        fL_Rule *rul = from->rules[rulid];
+                        fL_Rule *newrule = new fL_Rule(0, 0);
+                        newrule->objpred = getAppropriateWord(from, to, rul->objpred, map);
+                        for (fL_Word *w : rul->objsucc)
+                        {
+                                fL_Word *el = getAppropriateWord(from, to, w, map);
+                                if (el->type == fLElementType::BRANCH)
+                                {
+                                        newrule->objsucc.push_back(el);
+                                        continue;
+                                }
+                                Param origpar(w->tab);
+                                origpar.select(w->data);
+                                el->data = ParamObject::makeObject(el->tab);
+                                Param par(el->tab);
+                                par.select(el->data);
+                                par.setDefault();
+                                for (int i = 0; i < el->npar; i++)
+                                {
+                                        std::string form;
+                                        if (w->builtin && w->name == "N"
+                                                        && strcmp(par.id(i), FL_PE_NEURO_DET) == 0)
+                                        {
+                                                SString res = origpar.getStringById(FL_PE_NEURO_DET);
+                                                par.setStringById(FL_PE_NEURO_DET, res);
+                                                el->parevals.push_back(NULL);
+                                        }
+                                        else if (w->builtin && w->name == "C"
+                                                        && strcmp(par.id(i), FL_PE_CONN_ATTR) == 0)
+                                        {
+                                                SString strattractor = origpar.getStringById(FL_PE_CONN_ATTR);
+                                                if (strattractor.len() > 0)
+                                                {
+                                                        fL_Word *tmp = NULL;
+                                                        from->createWord(strattractor, tmp, newrule->objpred->npar, 0, 0);
+                                                        fL_Word *newsuccword = getAppropriateWord(from, to, tmp, map);
+                                                        newsuccword->data = ParamObject::makeObject(el->tab);
+                                                        newsuccword->parevals = tmp->parevals;
+                                                        tmp->parevals.clear();
+                                                        strattractor = newsuccword->stringify(true);
+                                                        par.setStringById(FL_PE_CONN_ATTR, strattractor);
+                                                        delete newsuccword;
+                                                        delete tmp;
+                                                }
+                                                par.setStringById(FL_PE_CONN_ATTR, strattractor);
+                                                el->parevals.push_back(NULL);
+                                        }
+                                        else if (w->parevals[i])
+                                        {
+                                                MathEvaluation *eval = new MathEvaluation(newrule->objpred->npar);
+                                                w->parevals[i]->RPNToInfix(form);
+                                                eval->convertString(form);
+                                                el->parevals.push_back(eval);
+                                        }
+                                        else
+                                        {
+                                                el->parevals.push_back(NULL);
+                                        }
+                                }
+                                newrule->objsucc.push_back(el);
+                        }
+                        to->rules.push_back(newrule);
+                }
+        }
+}
+
+int Geno_fL::crossOver(char *&g1, char *&g2, float& chg1, float& chg2)
+{
+        fL_Builder *creature1 = new fL_Builder(false, false);
+        fL_Builder *creature1template = new fL_Builder(false, false);
+        fL_Builder *creature2 = new fL_Builder(false, false);
+        fL_Builder *creature2template = new fL_Builder(false, false);
+
+        int count1 = creature1->countWordsInLSystem();
+        int count2 = creature2->countWordsInLSystem();
+
+        if (creature1->parseGenotype(g1) != 0 || creature2->parseGenotype(g2) != 0)
+        {
+                delete creature1;
+                delete creature2;
+                delete creature1template;
+                delete creature2template;
+                return GENOPER_OPFAIL;
+        }
+
+        creature1template->parseGenotype(g1);
+        creature2template->parseGenotype(g2);
+
+        int numselrules = 1 + randomN(XOVER_MAX_MIGRATED_RULES);
+        numselrules = numselrules < (int)creature1->rules.size() ? numselrules : (int)creature1->rules.size();
+
+        migrateRandomRules(creature1template, creature2, numselrules);
+
+        numselrules = 1 + randomN(XOVER_MAX_MIGRATED_RULES);
+        numselrules = numselrules < (int)creature1->rules.size() ? numselrules : (int)creature1->rules.size();
+
+        migrateRandomRules(creature2template, creature1, numselrules);
+
+        free(g1);
+        free(g2);
+
+        g1 = strdup(creature1->toString().c_str());
+        g2 = strdup(creature2->toString().c_str());
+
+        chg1 = (double)count1 / creature1->countWordsInLSystem();
+        chg1 = (double)count2 / creature2->countWordsInLSystem();
+
+        delete creature1;
+        delete creature2;
+        delete creature1template;
+        delete creature2template;
+
+        return GENOPER_OK;
+}
+
+uint32_t Geno_fL::style(const char *geno, int pos)
+{
+        char ch = geno[pos];
+        uint32_t style = GENSTYLE_CS(0, GENSTYLE_STRIKEOUT);
+        if (pos == 0 || geno[pos - 1] == '\n' || ch == ':') // single-character line definition
+        {
+                style = GENSTYLE_CS(GENCOLOR_TEXT, GENSTYLE_BOLD);
+        }
+        else if (strchr("()", ch) != NULL)
+        {
+                style = GENSTYLE_RGBS(50, 50, 50, GENSTYLE_BOLD);
+        }
+        else if (isalpha(ch)) // properties name
+        {
+                style = GENSTYLE_RGBS(0, 200, 0, GENSTYLE_BOLD);
+        }
+        else if (isdigit(ch) || strchr(",.=", ch)) // properties values
+        {
+                style = GENSTYLE_CS(GENCOLOR_TEXT, GENSTYLE_NONE);
+        }
+        else if (ch == '\"')
+        {
+                style = GENSTYLE_RGBS(200, 0, 0, GENSTYLE_BOLD);
+        }
+
+        return style;
+}

cpp/frams/genetics/fL/fL_oper.h

@@ -1 @@
-#ifndef _FL_OPER_
-#define _FL_OPER_
+// This file is a part of Framsticks SDK.  http://www.framsticks.com/
+// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// See LICENSE.txt for details.
+
+#ifndef _FL_OPER_H_
+#define _FL_OPER_H_
 
 #include "../genooperators.h"
+#include "fL_general.h"
+
+/** @name Codes for general fL mutation types */
+//@{
+#define FL_ADD_WORD 0 ///<probability of adding word to axiom or rule successor
+#define FL_ADD_WDEF 1 ///<probability of adding word definition
+#define FL_ADD_RULE 2 ///<probability of adding new rule
+#define FL_CHG_COND 3 ///<probability of modification or rule condition
+#define FL_CHG_WORD 4 ///<probability of changing word name or formula in axiom or rule successor
+#define FL_CHG_ITER 5 ///<probability of changing iteration of genotype
+#define FL_DEL_WORD 6 ///<probability of deleting word from axiom or rule. Deleting all occurrences of word deletes word definition. Deleting all words in rule deletes this rule
+#define FL_OPCOUNT 7 ///<count of mutation operators
+//@}
+
+/** @name Codes for probabilities of mutating axiom words or rule words */
+//@{
+#define FL_AXM_WORD_MUT_PROB 0 ///<probability of performing addition, substitution or deletion of word in axiom
+#define FL_RUL_WORD_MUT_PROB 1 ///<probability of performing addition, substitution or deletion of word in rule's successor
+#define FL_MUTGROUPSCOUNT 2 ///<count of possible groups for mutations
+//@}
+
+/** @name Codes for probabilities of mutating word names or formula during change */
+//@{
+#define FL_CHG_WORD_FORMULA 0 ///<probability of changing formula of one of parameters
+#define FL_CHG_WORD_NAME 1 ///<probability of changing word name to other word name with <= number of parameters
+#define FL_CHG_COUNT 2 ///<count of possible changes in words
+//@}
+
+/** @name Codes for probabilities of choosing one of word types for addition */
+//@{
+#define FL_ADD_STICK  0 ///<probability of adding stick
+#define FL_ADD_NEURO  1 ///<probability of adding neuron
+#define FL_ADD_CONN   2 ///<probability of adding connection
+#define FL_ADD_ROT    3 ///<probability of adding one of rotation words
+#define FL_ADD_OTHER  4 ///<probability of adding word defined in the genotype
+#define FL_ADD_BRANCH 5 ///<probability of adding a branch
+#define FL_ADD_COUNT  6 ///<count of possible additions
+//@}
 
 class Geno_fL : public GenoOperators
 {
+private:
+
+        /**
+         * Adds word with a given definition to the list in place pointed by an iterator.
+         * @param list list, to which new word will be added
+         * @param definition temporal object that will act as pattern for newly created word
+         * @param it the iterator pointing to addition point
+         * @return true
+         */
+        bool addWord(std::list<fL_Word *>* list, fL_Word *definition, std::list<fL_Word *>::iterator it);
+
+        /**
+         * Selects axiom or one of rule's successors.
+         * @param creature the object with defined axiom and rules
+         * @param numparams reference holding the number of parameters that are available for this list, 0 for axiom
+         * @param ruleid the index of the rule in rules structure or -1 if selected sequence is the axiom
+         * @return pointer to a selected sequence
+         */
+        std::list<fL_Word *>* selectRandomSequence(fL_Builder *creature, int &numparams, int &ruleid);
+
+        /**
+         * Selects word definition according to a method. Method is one of
+         * values FL_ADD_STICK, FL_ADD_NEURO, FL_ADD_CONN, FL_ADD_ROT, FL_ADD_OTHER
+         * etc. If FL_ADD_OTHER is chosen, then one of defined words is chosen. If
+         * there are no defined words, then one of built-in words is chosen.
+         * If FL_ADD_BRANCH is selected, then method returns NULL.
+         * @param creature current genotype
+         * @param method one of methods of addition
+         * @return object defining one of genotype words, or NULL if branching method is used
+         */
+        fL_Word* randomWordDefinition(fL_Builder *creature, int method);
+
+        /**
+         * Tries to find appropriate word in second creature that matches the word in first creature.
+         * Firstly, it tries to check if some word is not already assigned to a word in second creature.
+         * If the searching is successful, then appropriate word is used. Otherwise, method tries to find
+         * word that matches by name and number of parameters, or at least by number of parameters and hasn't
+         * been used already for other translation. If this is impossible, method creates new word definition
+         * for the second creature.
+         * @param from creature, from rule is taken
+         * @param to creature, which takes the rule
+         * @param fromword word from the first creature that needs to be translated
+         * @param map hashmap for current assignments
+         * @return word instance that need to be used by generated rule for the second genotype
+         */
+        fL_Word* getAppropriateWord(fL_Builder *from, fL_Builder *to, fL_Word *fromword, std::unordered_map<std::string, std::string> &map);
+
+        /**
+         * Migrates random rule from one creature to the other creature.
+         * @param from creature, from rule is taken
+         * @param to creature, which takes the rule
+         * @param numselrules number of rules that need to be moved
+         */
+        void migrateRandomRules(fL_Builder *from, fL_Builder *to, int numselrules);
+
+        /**
+         * Deletes branch from a given sequence starting from iterator. The deletion
+         * removes only braces, not whole branch.
+         * @param list current list that needs to be modified
+         * @param openbranchposition the iterator pointing to the open branch word
+         */
+        void deleteBranch(std::list<fL_Word *> *list, std::list<fL_Word *>::iterator openbranchposition);
 public:
+        double operations[FL_OPCOUNT]; ///<Relative probabilities of mutation types
+        double groupprobabilities[FL_MUTGROUPSCOUNT]; ///<Relative probabilities of changing elements in rules or axioms
+        double chgoperations[FL_CHG_COUNT]; ///<Relative probabilities of changing word names or parameters of word during change mutation
+        double addtypes[FL_ADD_COUNT]; ///<Relative probabilities of selecting special word types
+
+        double iterchangestep; ///<minimal value, by which time of development is modified
+        int maxdefinedwords; ///<maximal number of defined words for single fL genotype
+
         Geno_fL();
 
-        //      int checkValidity(const char *geno, const char *genoname);
+        int checkValidity(const char *geno, const char *genoname);
 
-        //      int validate(char *&geno, const char *genoname);
+        int validate(char *&geno, const char *genoname);
 
-        //      int mutate(char *&geno, float& chg, int &method);
+        int mutate(char *&geno, float& chg, int &method);
 
-        //      int crossOver(char *&g1, char *&g2, float& chg1, float& chg2);
+        int crossOver(char *&g1, char *&g2, float& chg1, float& chg2);
 
-        //      virtual const char* getSimplest() { return "5\naaazz"; }
+        const char* getSimplest() { return "i:axiom=\"S()\", time=0, maxwords=300"; }
 
-        //      uint32_t style(const char *geno, int pos);
+        uint32_t style(const char *geno, int pos);
 };
 
-#endif // _FL_OPER_
+#endif // _FL_OPER_H_