Changeset 1230 for cpp/frams/genetics

Timestamp:

05/01/23 02:14:27 (19 months ago)

Author:

Maciej Komosinski

Message:

Got rid of the (buggy) look-ahead function, made parsing stricter and simpler

Location:

cpp/frams/genetics/f4

Files:

• f4_general.cpp (modified) (9 diffs)
• f4_general.h (modified) (2 diffs)
• f4_oper.cpp (modified) (5 diffs)

cpp/frams/genetics/f4/f4_general.cpp

@@ -31 +31 @@
 {
         *v += 0.7853;  // 0.7853981  45 degrees
-}
-
-int scanRecur(const char* s, int slen, char stopchar)
-{
-        int i = 0;
-        //DB( printf("    scan('%s', '%c')\n", s, stopchar); )
-        while (1)
-        {
-                if (i >= slen)  // ran out the string, should never happen with a correct string
-                        return 1; //TODO MacKo 2023-04: interesting: why was this situation made undistinguishable from s[1]==stopchar ? does this have any bad consequences or is "1" just used to tell "advance as little as possible"? Anyway, this function can be eliminated when parsing is simplified.
-                if (stopchar == s[i])  // bumped into stopchar
-                        return int(i);
-                if (i < slen - 1) // s[i] is not the last char
-                {
-                        if (s[i] == '(') //not an allowed char in f4, perhaps a remnant of old experiments with code
-                        {
-                                i += 2 + scanRecur(s + i + 1, slen - i - 1, ')');
-                                continue;
-                        }
-                        if (s[i] == '<')
-                        {
-                                i += 2 + scanRecur(s + i + 1, slen - i - 1, '>');
-                                continue;
-                        }
-                        if (s[i] == '#')
-                        {
-                                i += 2 + scanRecur(s + i + 1, slen - i - 1, '>');
-                                continue;
-                        }
-                }
-                // s[i] is a non-special character
-                i++;
-        }
-        return i;
 }
 
@@ -703 +669 @@
         // transform geno from string to nodes
         f4rootnode = new f4_Node();
-        int res = f4_processRecur(genome.c_str(), 0, f4rootnode);
+        int _ = 0;
+        int res = f4_processRecur(genome.c_str(), _, f4rootnode);
         if (res || (f4rootnode->childCount() != 1))
         {
@@ -1329 +1296 @@
 // scan genotype string and build tree
 // return >1 for error (errorpos)
-int f4_processRecur(const char* genot, unsigned int pos0, f4_Node *parent)
-{
-        unsigned int gpos = pos0; //MacKo 2023-04 (TODO): these two variables are often updated before return which has no effect since they are local. Seems like a half step towards making them (or just gpos) in/out parameter which would solve many issues and simplify parsing (getting rid of scanRecur()) while making it more strict.
+int f4_processRecur(const char* genot, int &pos_inout, f4_Node *parent)
+{
         f4_Node *par = parent;
 
-        if (gpos >= strlen(genot))
+        if (pos_inout >= (int)strlen(genot))
                 return (int)strlen(genot) + 1;
 
-        while (gpos < strlen(genot))
-        {
-                // first switch across cell dividers and old semantics
-                switch (genot[gpos])
+        while (pos_inout < (int)strlen(genot))
+        {
+                //#define PRINT_PARSING_LOCATION
+#ifdef PRINT_PARSING_LOCATION
+                printf("%s\n", genot);
+                for (int i = 0; i < pos_inout; i++) printf(" ");
+                printf("^\n");
+#endif
+                switch (genot[pos_inout])
                 {
                 case '<':
                 {
-                        // find out genotype start for child
-                        int stopchar_offset = scanRecur(genot + gpos + 1, (int)strlen(genot + gpos + 1), '>');
-
-                        f4_Node *node = new f4_Node("<", par, gpos);
+                        f4_Node *node = new f4_Node("<", par, pos_inout);
                         par = node;
-                        int res = f4_processRecur(genot, gpos + 1, par);
+                        pos_inout++; //move after '<'
+                        int res = f4_processRecur(genot, pos_inout, par);
                         if (res) return res;
-                        if (gpos + stopchar_offset + 2 < strlen(genot))
-                        {
-                                res = f4_processRecur(genot, gpos + stopchar_offset + 2, par);
+                        if (pos_inout < (int)strlen(genot))
+                        {
+                                res = f4_processRecur(genot, pos_inout, par);
                                 if (res) return res;
                         }
@@ -1359 +1328 @@
                         {
                                 //MacKo 2023-04, more strict behavior: instead of silent repair (no visible effect to the user, genotype stays invalid but is interpreted and reported as valid), we now point out where the error is. For example <X> or <X><X or <X><N:N>
-                                return gpos + 1; //the problem starts here, occurs because second child (branch) <1..>2..> is not completed
+                                return (int)strlen(genot) + 1;
                                 //old silent repair:
                                 //node = new f4_Node(">", par, int(strlen(genot)) - 1);
-                                //par = node;
-                        }
-                        gpos++;
+                        }
                         return 0;  // OK
                 }
                 case '>':
                 {
-                        f4_Node *node = new f4_Node(">", par, gpos);
-                        par = node;
-                        //gpos = (unsigned int)strlen(genot); //MacKo 2023-04: first of all, 'gpos' is a local variable so no effect; second, '>' may be internal (i.e., not the last one in the genotype), so it is a bad hint to assign strlen(). 'par' above is also local...
+                        new f4_Node(">", par, pos_inout);
+                        pos_inout++; //move after '>'
                         return 0;  // OK
                 }
@@ -1378 +1344 @@
                         // repetition marker, 1 by default
                         ExtValue val;
-                        const char* end = val.parseNumber(genot + gpos + 1, ExtPType::TInt);
+                        const char* end = val.parseNumber(genot + pos_inout + 1, ExtPType::TInt);
+                        //TODO end==NULL? -> error!
                         int reps = (end == NULL) ? 1 : val.getInt();
-                        // find out genotype start for continuation
-                        int stopchar_offset = scanRecur(genot + gpos + 1, (int)strlen(genot + gpos + 1), '>');
+                        f4_Node *node = new f4_Node("#", par, pos_inout);
+                        node->reps = reps;
                         // skip number
-                        unsigned int oldpos = gpos;
-                        gpos += end - (genot + gpos);
-                        //gpos++;
-                        //while ((genot[gpos] >= '0') && (genot[gpos] <= '9')) gpos++; node1 = new f4_Node("#", par, oldpos);
-                        f4_Node *node = new f4_Node("#", par, oldpos);
-                        node->reps = reps;
-                        par = node;
-                        int res = f4_processRecur(genot, gpos, node);
+                        pos_inout += end - (genot + pos_inout);
+                        int res = f4_processRecur(genot, pos_inout, node);
                         if (res) return res;
-                        if (oldpos + stopchar_offset + 2 < strlen(genot))
-                        {
-                                res = f4_processRecur(genot, oldpos + stopchar_offset + 2, node);
+                        if (pos_inout < (int)strlen(genot))
+                        {
+                                res = f4_processRecur(genot, pos_inout, node);
                                 if (res) return res;
                         }
                         else // ran out
                         {
-                                return gpos; //MacKo 2023-04: report an error, better to be more strict instead of a silent repair (genotype stays invalid but is interpreted and reported as valid) with non-obvious consequences?
+                                return (int)strlen(genot) + 1; //MacKo 2023-04: report an error, better to be more strict instead of a silent repair (genotype stays invalid but is interpreted and reported as valid) with non-obvious consequences?
                                 //earlier apporach - silently treating this problem (we don't ever see where the error is because it gets corrected in some way here, while parsing the genotype, and error location in the genotype is never reported):
                                 //node = new f4_Node(">", par, int(strlen(genot)) - 1); // check if needed and if this is really the best repair operation; seemed to happen too many times in succession for some genotypes even though they were only a result of f4 operators, not manually created... and the operators should not generate invalid genotypes, right? Or maybe crossover does? Seems like too many #N's for closing >'s; removing #N or adding > helped. Operators somehow don't do it properly sometimes? But F4_ADD_REP adds '>'... (TODO)
@@ -1411 +1372 @@
                 {
                         // whitespace: ignore
-                        gpos++;
+                        pos_inout++;
                         break;
                 }
                 case 'N':
                 {
-                        int forgenorange = gpos;
-                        if (genot[gpos + 1] != ':')
-                                return gpos + 1; //error
-                        gpos += 2; //skipping "N:"
-                        unsigned int begin_index = gpos;
-                        char* end = (char*)genot + begin_index;
-                        NeuroClass *neuclass = GenoOperators::parseNeuroClass(end, ModelEnum::SHAPETYPE_BALL_AND_STICK);
+                        int forgenorange = pos_inout;
+                        if (genot[pos_inout + 1] != ':')
+                                return pos_inout + 1; //error
+                        pos_inout += 2; //skipping "N:"
+                        unsigned int neuroclass_begin = pos_inout;
+                        char* neuroclass_end = (char*)genot + neuroclass_begin;
+                        NeuroClass *neuclass = GenoOperators::parseNeuroClass(neuroclass_end, ModelEnum::SHAPETYPE_BALL_AND_STICK); //advances neuroclass_end
                         if (neuclass == NULL)
-                                return gpos + 1; //error
-                        gpos += end - genot - begin_index;
-                        string neutype = string(genot + begin_index, genot + gpos);
+                                return pos_inout + 1; //error
+                        pos_inout += neuroclass_end - genot - neuroclass_begin;
+                        string neutype = string(genot + neuroclass_begin, genot + pos_inout);
                         f4_Node *node = new f4_Node(neutype, par, forgenorange);
                         node->neuclass = neuclass;
@@ -1438 +1399 @@
                         // in the future this could be generalized to all neuron properties, for example N:|:power:0.6:range:1.4, or can even use '=' or ',' instead of ':' if no ambiguity
                         char prop_dir, prop_symbol, prop_end[2]; // prop_end is only to ensure that neuron parameter definition is completed
-                        if (sscanf(genot + gpos, ":%c%c%1[:]", &prop_dir, &prop_symbol, &prop_end) != 3)
+                        if (sscanf(genot + pos_inout, ":%c%c%1[:]", &prop_dir, &prop_symbol, &prop_end) != 3)
                                 // error: incorrect format
-                                return gpos + 1 + 1;
+                                return pos_inout + 1 + 1;
                         if (prop_dir != '-' && prop_dir != '+')
-                                return gpos + 1 + 1; //error
+                                return pos_inout + 1 + 1; //error
                         switch (prop_symbol)
                         {
                         case '!':  case '=':  case '/':  break;
                         default:
-                                return gpos + 1 + 1; //error
-                        }
-                        f4_Node *node = new f4_Node(":", par, gpos);
+                                return pos_inout + 1 + 1; //error
+                        }
+                        f4_Node *node = new f4_Node(":", par, pos_inout);
                         node->prop_symbol = prop_symbol;
                         node->prop_increase = prop_dir == '+' ? true : false; // + or -
                         par = node;
-                        int stopchar_offset = scanRecur(genot + gpos + 1, (int)strlen(genot + gpos + 1), ':');
-                        gpos += stopchar_offset + 2;
+                        pos_inout += 4; //skipping :ds:
                         break;
                 }
@@ -1461 +1421 @@
                         double weight = 0;
                         int relfrom;
-                        const char *end = parseConnection(genot + gpos, relfrom, weight);
+                        const char *end = parseConnection(genot + pos_inout, relfrom, weight);
                         if (end == NULL)
-                                return gpos + 1; //error
-
-                        f4_Node *node = new f4_Node("[", par, gpos);
+                                return pos_inout + 1; //error
+
+                        f4_Node *node = new f4_Node("[", par, pos_inout);
                         node->conn_from = relfrom;
                         node->conn_weight = weight;
                         par = node;
-                        int stopchar_offset = scanRecur(genot + gpos + 1, (int)strlen(genot + gpos + 1), ']');
-                        gpos += stopchar_offset + 2;
+                        pos_inout += end - (genot + pos_inout);
                         break;
                 }
                 default: // 'X' and ',' and all modifiers and also invalid symbols - add a node, for invalid symbols build will give the error or repair
                 {
-                        //printf("any regular character '%c'\n", genot[gpos]);
-                        f4_Node *node = new f4_Node(genot[gpos], par, gpos);
+                        //printf("any regular character '%c'\n", genot[pos_inout]);
+                        //TODO here: read a continuous sequence of modifiers, sort and optimize ("collapse") it like in f1, then add to tree
+                        f4_Node *node = new f4_Node(genot[pos_inout], par, pos_inout);
                         par = node;
-                        gpos++;
+                        pos_inout++;
                         break;
                 }
@@ -1487 +1447 @@
         if (par && par->name != ">")
         {
-                //happens when gpos == strlen(genot)
-                //return gpos; //MacKo 2023-04: could report an error instead of silent repair, but repair operators only work in Cells (i.e., after the f4_Node tree has been parsed without errors and Cells can start developing) so we don't want to make a fatal error because of missing '>' here. Also after conversions from Cells to text, trailing '>' is deliberately removed... and also the simplest genotype is officially X, not X>.
-                f4_Node *node = new f4_Node('>', par, int(strlen(genot)) - 1);
-                par = node;
-        }
-
-        return 0;
+                //happens when pos_inout == strlen(genot)
+                //return pos_inout; //MacKo 2023-04: could report an error instead of silent repair, but repair operators only work in Cells (i.e., after the f4_Node tree has been parsed without errors and Cells can start developing) so we don't want to make a fatal error because of missing '>' here. Also after conversions from Cells to text, trailing '>' is deliberately removed... and also the simplest genotype is officially X, not X>.
+                new f4_Node('>', par, int(strlen(genot)) - 1);
+        }
+
+        return 0;  // OK
 }
 

cpp/frams/genetics/f4/f4_general.h

@@ -40 +40 @@
 #define CELL_NEURON 42 ///<differentiated to neuron, can divide
 //@}
-
-/**
- * TODO MacKo 2023-04: not sure if this function is needed and if f4_processRecur() would not suffice
- * if it advanced the string pointer (in/out parameter) while processing. Its returned value is always used after
- * f4_processRecur() anyway, and in two cases likely incorrectly (for [...] to detect closing ']'
- * and for :...: to detect closing ':') - we don't need recursion in these cases, a simple linear
- * scan would suffice, but even this would not be needed - since we are parsing the actual characters in these cases,
- * we do scanning anyway. So looks like this function doubles the work already done more thoroughly by f4_processRecur().
- * 
- * Scans f4 genotype string for a stopping character and returns the position of
- * this stopping character or 1 if the end of string was reached. This method is used
- * for closing braces, like ), >, ]. It runs recursively when opening braces
- * like (, <, # are found.
- * @param s string with the f4 genotype
- * @param slen length of a given string
- * @param stopchar character to be found
- * @return 1 if end of string was reached, or position of found character in sequence
- */
-int scanRecur(const char* s, int slen, char stopchar);
 
 
@@ -501 +482 @@
  * @return 0 if processing was successful, otherwise returns the position of an error in the genotype
  */
-int f4_processRecur(const char *genot, unsigned int pos0, f4_Node *parent);
+int f4_processRecur(const char *genot, int &pos_inout, f4_Node *parent);
 
 /**

cpp/frams/genetics/f4/f4_oper.cpp

@@ -16 +16 @@
 //
 // TODO the behavior of neuron input indexes during mutation seems badly implemented (see also TREAT_BAD_CONNECTIONS_AS_INVALID_GENO). Are they kept properly maintained when nodes are added and removed? This could be done well because during mutation we operate on the tree structure with cross-references between nodes (so they should not be affected by local changes in the tree), and then convert the tree back to string. Yet, the f4_Node.conn_from is an integer and these fields in nodes do not seem to be maintained on tree node adding/removal... change these integer offsets to references to node objects? But actually, do the offsets that constitute relative connection references concern the f4_Node tree structure (and all these sophisticated calculations of offsets during mutation are useful) or rather they concern the f4_Cells development? verify all situations in f4_Cell::oneStep(), case '['.
-// TODO add simplifying sequences of modifiers (so capital and small letter cancel out, like in f1) - but seems like each single modifier is a separate f4_Node? and perhaps we don't want to use the repair mechanism for this... maybe mutations, when they add/modify/remove a modifier node, should be "cleaning" the tree by removing nodes when they encounter contradictory modifiers on the same subpath, and also limit the number of modifiers of each type just like in f1? To avoid squences like ...<X>llmlIilImmimiimmimifmfl<fifmmimilimmmiimiliffmfliIfififlliflimfliffififmiffmfliflifmIlimimiflimfiffmllliflmimifllifliliflifmIlimimiflimfiffmllliflmimifllfmIlimimiflimfiffmllliflmimiflliflimimmiflimfliffmiflifmfiffllIlififliffififmiffmfliflifIliflimimflimflfflimimifllfflifllfflimlififfiiffifIr<r<...
+// TODO add simplifying sequences of modifiers (so capital and small letter cancel out, like in f1) - but seems like each single modifier is a separate f4_Node? and perhaps we don't want to use the repair mechanism for this... maybe mutations, when they add/modify/remove a modifier node, should be "cleaning" the tree by removing nodes when they encounter contradictory modifiers on the same subpath, and also limit the number of modifiers of each type just like in f1? To avoid sequences like ...<X>llmlIilImmimiimmimifmfl<fifmmimilimmmiimiliffmfliIfififlliflimfliffififmiffmfliflifmIlimimiflimfiffmllliflmimifllifliliflifmIlimimiflimfiffmllliflmimifllfmIlimimiflimfiffmllliflmimiflliflimimmiflimfliffmiflifmfiffllIlififliffififmiffmfliflifIliflimimflimflfflimimifllfflifllfflimlififfiiffifIr<r<...
 // TODO add support for properties of (any class of) neurons - not just sigmoid/force/intertia (':' syntax) for N
 // TODO add mapping genotype character ranges for neural [connections]
+// TODO change the default branching plane (to match f1) so they do not grow perfectly vertical (cheating vertpos) so easily? (so they require Rr or other modifiers)
 
 
@@ -122 +123 @@
         // convert geno to a tree, then try to validate
         f4_Node root;
-        if (f4_processRecur(geno, 0, &root) || root.childCount() != 1) return GENOPER_OK; // cannot repair
+        int _ = 0;
+        if (f4_processRecur(geno, _, &root) || root.childCount() != 1) return GENOPER_OK; // cannot repair
 
         const int VALIDATE_TRIALS = 20;
@@ -137 +139 @@
 {
         f4_Node root;
-        int res = f4_processRecur(geno, 0, &root);
+        int _ = 0;
+        int res = f4_processRecur(geno, _, &root);
         if (res) return res;  // errorpos, >0
         if (root.childCount() != 1) return 1; //earlier: GENOPER_OPFAIL
@@ -549 +552 @@
 {
         f4_Node *root = new f4_Node;
-        if (f4_processRecur(g, 0, root) || root->childCount() != 1)
+        int _ = 0;
+        if (f4_processRecur(g, _, root) || root->childCount() != 1)
         {
                 delete root;
@@ -673 +677 @@
 
         // convert genotype strings into tree structures
-        if (f4_processRecur(g1, 0, &root1) || (root1.childCount() != 1)) return GENOPER_OPFAIL;
-        if (f4_processRecur(g2, 0, &root2) || (root2.childCount() != 1)) return GENOPER_OPFAIL;
+        int _1 = 0, _2 = 0;
+        if (f4_processRecur(g1, _1, &root1) || (root1.childCount() != 1)) return GENOPER_OPFAIL;
+        if (f4_processRecur(g2, _2, &root2) || (root2.childCount() != 1)) return GENOPER_OPFAIL;
 
         // decide amounts of crossover, 0.1-0.9