source: cpp/frams/genetics/f4/f4_general.cpp @ 1230

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2023  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.

// Copyright (C) 1999,2000  Adam Rotaru-Varga (adam_rotaru@yahoo.com), GNU LGPL
// 2018, Grzegorz Latosinski, added support for new API for neuron types and their properties

#include "f4_general.h"
#include "../genooperators.h" //for GENOPER_ constants
#include <common/nonstd_stl.h>
#include <common/log.h>
#include <frams/model/model.h> // for min and max attributes
#include <common/nonstd_math.h>

#ifdef DMALLOC
#include <dmalloc.h>
#endif


#define BREAK_WHEN_REP_COUNTER_NULL //see comments where it is used
#define EXTRA_STEP_CELL_DEVELOPMENT //see comments where it is used
#define TREAT_BAD_CONNECTIONS_AS_INVALID_GENO //see comments where it is used


void rolling_dec(double *v)
{
        *v -= 0.7853;  // 0.7853981  45 degrees = pi/4 like in f1
}

void rolling_inc(double *v)
{
        *v += 0.7853;  // 0.7853981  45 degrees
}


f4_Cell::f4_Cell(int nnr, f4_Cell *ndad, int nangle, GeneProps newP)
{
        nr = nnr;
        type = CELL_UNDIFF;
        dadlink = ndad;
        org = NULL;
        genot = NULL;
        gcur = NULL;
        active = true;
        repeat.clear();
        //genoRange.clear(); -- implicit

        anglepos = nangle;
        commacount = 0;
        childcount = 0;
        P = newP;
        rolling = 0;
        xrot = 0;
        zrot = 0;
        //OM = Orient_1;
        inertia = 0.8;
        force = 0.04;
        sigmo = 2;
        conns_count = 0;

        // adjust firstend and OM if there is a stick dad
        if (ndad != NULL)
        {
                // make sure it is a stick (and not a stick f4_Cell!)
                if (ndad->type == CELL_STICK)
                {
                        //firstend = ndad->lastend;
                        //OM = ndad->OM;
                        ndad->childcount++;
                }
                if (ndad->type == CELL_NEURON)
                {
                        inertia = ndad->inertia;
                        force = ndad->force;
                        sigmo = ndad->sigmo;
                }
        }
        // adjust lastend
        //lastend = firstend + ((Orient)OM * (Pt3D(1,0,0) * P.len));
        mz = 1;
}


f4_Cell::f4_Cell(f4_Cells *nO, int nnr, f4_Node *ngeno, f4_Node *ngcur, f4_Cell *ndad, int nangle, GeneProps newP)
{
        nr = nnr;
        type = CELL_UNDIFF;
        dadlink = ndad;
        org = nO;
        genot = ngeno;
        gcur = ngcur;
        active = true;
        repeat.clear();
        //genoRange.clear(); -- implicit
        // preserve geno range of parent cell
        if (NULL != ndad)
                genoRange.add(ndad->genoRange);

        anglepos = nangle;
        commacount = 0;
        childcount = 0;
        P = newP;
        rolling = 0;
        xrot = 0;
        zrot = 0;
        //OM = Orient_1;
        inertia = 0.8;
        force = 0.04;
        sigmo = 2;
        conns_count = 0;

        // adjust firstend and OM if there is a stick dad
        if (ndad != NULL)
        {
                // make sure it is a stick (and not a stick f4_Cell!)
                if (ndad->type == CELL_STICK)
                {
                        //firstend = ndad->lastend;
                        //OM = ndad->OM;
                        ndad->childcount++;
                }
                if (ndad->type == CELL_NEURON)
                {
                        inertia = ndad->inertia;
                        force = ndad->force;
                        sigmo = ndad->sigmo;
                }
        }
        // adjust lastend
        //lastend = firstend + ((Orient)OM * (Pt3D(1,0,0) * P.len));
        mz = 1;
}


f4_Cell::~f4_Cell()
{
        // remove connections
        if (conns_count)
        {
                int i;
                for (i = conns_count - 1; i >= 0; i--)
                        delete conns[i];
                conns_count = 0;
        }
}


/* return codes:
        1 error at pos
        0  halt development (yield) for a cycle
        */
int f4_Cell::oneStep()
{
        while (gcur != NULL)
        {
                //DB( printf("  %d (%d) executing '%c' %d\n", name, type, gcur->name, gcur->pos); )
                // currently this is the last one processed
                // the current genotype code is processed
                //genoRange.add(gcur->pos,gcur->pos+gcur->name.length()-1);

                // To detect what genes are valid neuroclass names, but do NOT have is_neuroclass==true
                // (just as a curiosity to ensure we properly distinguish between, for example, the "G" neuron and the "G" modifier):
                //char *TMP = (char*)gcur->name.c_str();
                //if (gcur->is_neuroclass==false && GenoOperators::parseNeuroClass(TMP, ModelEnum::SHAPETYPE_BALL_AND_STICK))
                //      printf("Could be a valid neuroclass, but is_neuroclass==false: %s\n", gcur->name.c_str());

                if (gcur->neuclass == NULL) //not a neuron
                {
                        if (gcur->name.length() > 1)
                                logPrintf("f4_Cell", "oneStep", LOG_WARN, "Multiple-character code that is not a neuron class name: '%s'", gcur->name.c_str()); //let's see an example of such a code...

                        genoRange.add(gcur->pos, gcur->pos);
                        char name = gcur->name[0];
                        switch (name)
                        {
                        case '<':
                        {
                                // cell division!
                                //DB( printf("  div! %d\n", name); )

                                // error: sticks cannot divide
                                if (type == CELL_STICK)
                                {
                                        // cannot fix
                                        org->setError(gcur->pos);
                                        return 1;  // stop
                                }

                                // undiff divides
                                if (type == CELL_UNDIFF)
                                {
                                        // commacount is set only when daughter turns into X
                                        // daughter cell
                                        // adjust new len
                                        GeneProps newP = P;
                                        newP.propagateAlong(false);
                                        f4_Cell *tmp = new f4_Cell(org, org->cell_count, genot, gcur->child2, this, commacount, newP);
                                        tmp->repeat = repeat;
                                        repeat.clear();
                                        org->addCell(tmp);
                                }
                                // a neuron divides: create a new, duplicate connections
                                if (type == CELL_NEURON)
                                {
                                        // daughter cell
                                        f4_Cell *tmp = new f4_Cell(org, org->cell_count, genot, gcur->child2,
                                                // has the same dadlink
                                                this->dadlink, commacount, P);
                                        tmp->repeat = repeat;
                                        repeat.clear();
                                        // it is a neuron from start
                                        tmp->type = CELL_NEURON;
                                        // it has the same type as the parent neuron
                                        tmp->neuclass = neuclass;
                                        // duplicate connections
                                        f4_CellConn *conn;
                                        for (int i = 0; i < conns_count; i++)
                                        {
                                                conn = conns[i];
                                                tmp->addConnection(conn->from, conn->weight);
                                        }
                                        org->addCell(tmp);
                                }
                                // adjustments for this cell
                                gcur = gcur->child;
                                // halt development
                                return 0;
                        }
                        case '>':
                        {
                                // finish
                                // see if there is a repeat count
                                if (repeat.top > 0)
                                { // there is a repeat counter
                                        if (!repeat.first()->isNull())
                                        { // repeat counter is not null
                                                repeat.first()->dec();
                                                if (repeat.first()->count > 0)
                                                {
                                                        // return to repeat
                                                        gcur = repeat.first()->node->child;
                                                }
                                                else
                                                {
                                                        // continue
                                                        gcur = repeat.first()->node->child2;
                                                        repeat.pop();
                                                }
                                                break;
                                        }
                                        else
                                        {
                                                repeat.pop();
                                                // MacKo 2023-04: originally, there was no "break" nor "return" here (hence [[fallthrough]]; needed below for modern compilers) - not sure if this was intentional or overlooking.
                                                // This case can be tested with "#0" in the genotype. Anyway, there seems to be no difference in outcomes with and without "break".
                                                // However, falling through [[fallthrough]] below for count==0 causes performing repeat.push(repeat_ptr(gcur, 0)) while the very reason
                                                // we are here is that repeat count==0 (one of the conditions for isNull()), so I opted to add "break", but marked this tentative decision using #define.
                                                // The ultimate informed decision would require understanding all the logic and testing all the edge cases.
#ifdef BREAK_WHEN_REP_COUNTER_NULL
                                                break;
#endif
                                        }
                                }
                                else
                                {
                                        // error: still undiff
                                        if (type == CELL_UNDIFF)
                                        {
                                                // fix it: insert an 'X'
                                                f4_Node *insertnode = new f4_Node("X", NULL, gcur->pos);
                                                if (org->setRepairInsert(gcur->pos, gcur, insertnode)) // not in repair mode, release
                                                        delete insertnode;
                                                return 1;
                                        }
                                        repeat.clear();
                                        active = false;  // stop
                                        // eat up rest
                                        int remaining_nodes = gcur->count() - 1;
                                        if (remaining_nodes > 0)
                                                logPrintf("f4_Cell", "oneStep", LOG_WARN, "Ignoring junk genetic code: %d node(s) at position %d", remaining_nodes, gcur->child->pos); //let's see an example of such a genotype...
                                        gcur = NULL;
                                        return 0;
                                }
                        }
#ifndef BREAK_WHEN_REP_COUNTER_NULL
                        [[fallthrough]];
#endif
                        case '#':
                        {
                                // repetition marker
                                if (repeat.top >= repeat_stack::stackSize)
                                {
                                        // repeat pointer stack is full, cannot remember this one.
                                        // fix: delete it
                                        org->setRepairRemove(gcur->pos, gcur);
                                        return 1;  // stop
                                }
                                repeat.push(repeat_ptr(gcur, gcur->reps));
                                gcur = gcur->child;
                                break;
                        }
                        case ',':
                        {
                                commacount++;
                                gcur = gcur->child;
                                break;
                        }
                        case 'r':  case 'R':
                        {
                                // error: if neuron
                                if (type == CELL_NEURON)
                                {
                                        // fix: delete it
                                        org->setRepairRemove(gcur->pos, gcur);
                                        return 1;  // stop
                                }
                                switch (name)
                                {
                                case 'r':   rolling_dec(&rolling); break;
                                case 'R':   rolling_inc(&rolling); break;
                                }
                                gcur = gcur->child;
                                break;
                        }
                        case 'l':  case 'L':
                        case 'c':  case 'C':
                        case 'q':  case 'Q':
                        case 'a':  case 'A':
                        case 'i':  case 'I':
                        case 's':  case 'S':
                        case 'm':  case 'M':
                        case 'f':  case 'F':
                        case 'w':  case 'W':
                        case 'e':  case 'E':
                        case 'd':  case 'D':
                        case 'g':  case 'G':
                        case 'b':  case 'B':
                        case 'h':  case 'H':
                        {
                                // error: if neuron
                                if (type == CELL_NEURON) //some neurons have the same single-letter names as modifiers (for example G,S,D), but they are supposed to have is_neuroclass==true so they should indeed not be handled here
                                {//however, what we see here is actually modifiers such as IdqEbWL (so not valid neuroclasses) that occurred within an already differentiated cell type==CELL_NEURON.
                                        //printf("Handled as a modifier, but type==CELL_NEURON: '%c'\n", name);
                                        // fix: delete it
                                        org->setRepairRemove(gcur->pos, gcur);
                                        return 1;  // stop
                                }
                                P.executeModifier(name);
                                gcur = gcur->child;
                                break;
                        }
                        case 'X':
                        {
                                // turn undiff. cell into a stick
                                // error: already differentiated
                                if (type != CELL_UNDIFF)
                                {
                                        // fix: delete this node
                                        org->setRepairRemove(gcur->pos, gcur);
                                        return 1;  // stop
                                }
                                type = CELL_STICK;
                                // fix dad commacount and own anglepos
                                if (NULL != dadlink)
                                {
                                        dadlink->commacount++;
                                        anglepos = dadlink->commacount;
                                }
                                // change of type halts developments, see comment at 'neuclasshandler' below
                                gcur = gcur->child;
                                return 0;
                        }
                        case '[':
                        {
                                // connection to neuron
                                // error: not a neuron
                                if (type != CELL_NEURON)
                                {
                                        // fix: delete it
                                        org->setRepairRemove(gcur->pos, gcur);
                                        return 1;  // stop
                                }
                                // input [%d:%g]
                                int relfrom = gcur->conn_from;
                                double weight = gcur->conn_weight;
                                f4_Cell *neu_from = NULL;

                                // input from other neuron
                                // find neuron at relative i
                                // find own index
                                int this_index = 0, neu_counter = 0;
                                for (int i = 0; i < org->cell_count; i++)
                                {
                                        if (org->C[i]->type == CELL_NEURON) neu_counter++;
                                        if (org->C[i] == this) { this_index = neu_counter - 1; break; }
                                }
                                // find index of incoming
                                int from_index = this_index + relfrom;

                                if (from_index < 0) goto wait_conn;
                                if (from_index >= org->cell_count) goto wait_conn;

                                // find that neuron
                                neu_counter = 0;
                                int from;
                                for (from = 0; from < org->cell_count; from++)
                                {
                                        if (org->C[from]->type == CELL_NEURON) neu_counter++;
                                        if (from_index == (neu_counter - 1)) break;
                                }
                                if (from >= org->cell_count) goto wait_conn;
                                neu_from = org->C[from];

                                // add connection
                                // error: could not add connection (too many?)
                                if (addConnection(neu_from, weight))
                                {
                                        // cannot fix
                                        org->setError(gcur->pos);
                                        return 1;  // stop
                                }
                                gcur = gcur->child;
                                break;
                        }
                wait_conn:
                        {
                                // wait for other neurons to develop
                                // if there are others still active

                                int active_count = 0;
                                for (int i = 0; i < org->cell_count; i++)
                                        if (org->C[i]->active) active_count++;
                                active = false; // next time when we reach wait_conn, we will not count ourselves as active (if we were the last active cell, we got a chance to continue development for one development step only)
                                if (active_count > 0)
                                        return 0;  // there is at least one active (including ourselves), halt, try again

#ifdef TREAT_BAD_CONNECTIONS_AS_INVALID_GENO // MacKo 2023-04: there were so many invalid connections accumulating in the genotype (and stopping processing of the chain of gcur->child) that it looks like treating them as errors is better... in 2000's, Framsticks neurons were flexible when it comes to inputs and outputs (for example, when asked, muscles would provide an output too, and neurons that ignored inputs would still accept them when connected) so f4 could create connections pretty randomly, but after 2000's we attempt to respect neurons' getPreferredInputs() and getPreferredOutput() so the network of connections has more constraints.
                                if (gcur->parent->name == "#")
                                {
                                        // MacKo 2023-04: Unfortunately the logic of multiplicating connections is not ideal...
                                        //TREAT_BAD_CONNECTIONS_AS_INVALID_GENO without this "#" exception would break /*4*/<X>N:N#5<[1:1]>
                                        // because every neuron wants to get an input from the neuron that will be created next
                                        // and all is fine until the last created neuron, which wants to get an input from another one which will not be created
                                        // (3 gets from 4, 4 gets from 5, 5 wants to get from 6 (relative connection offset for each of them is 1),
                                        // but 6 will not get created and if we want to TREAT_BAD_CONNECTIONS_AS_INVALID_GENO, we produce an error...
                                        // We would like to have this multiplication working, but OTAH we don't want to accept bad connections because then they tend to multiply as junk genes and bloat the genotype also causing more and more neutral mutations...
                                        //so this condition and checking for "#" is a simple way to be kind to some, but not all, bad connections, and not raise errors. Perhaps too kind and we open the door for too many cases with invalid connections.
                                        //Maybe it would be better to perform this check before addConnection(), seeing that for example we process the last iteration of the repetition counter? But how would we know that the (needed here) input neuron will not be developed later by other dividing cells...
                                        active = true; //not sure if needed, but let this cell have the chance to continue for as long as many children in the tree are left
                                        gcur = gcur->child;
                                        return 0;
                                }
                                else
                                {
                                        //org->setError(gcur->pos); //in case setRepairRemove() would not always produce reasonable results
                                        org->setRepairRemove(gcur->pos, gcur); //produces unexpected results? or NOT? TODO verify, some genotypes earlier produced strange outcomes of this repair (produced a valid genotype, but some neurons were multiplied/copied after repair - maybe because when a branch of '<' (or something else) is missing, the other branch is copied?)
                                        return 1;  // stop
                                }
#else
                                // no more actives, cannot add connection, ignore, but treat not as an error - before 2023-04
                                gcur = gcur->child;
#endif
                        }
                        break;
                        case ':':
                        {
                                // neuron parameter
                                // error: not a neuron
                                if (type != CELL_NEURON)
                                {
                                        // fix: delete it
                                        org->setRepairRemove(gcur->pos, gcur);
                                        return 1;  // stop
                                }
                                switch (gcur->prop_symbol)
                                {
                                case '!':
                                        if (gcur->prop_increase)
                                                force += (1.0 - force) * 0.2;
                                        else
                                                force -= force * 0.2;
                                        break;
                                case '=':
                                        if (gcur->prop_increase)
                                                inertia += (1.0 - inertia) * 0.2;
                                        else
                                                inertia -= inertia * 0.2;
                                        break;
                                case '/':
                                        if (gcur->prop_increase)
                                                sigmo *= 1.4;
                                        else
                                                sigmo /= 1.4;
                                        break;
                                default:
                                        org->setRepairRemove(gcur->pos, gcur);
                                        return 1;  // stop
                                }
                                gcur = gcur->child;
                                break;
                        }
                        case ' ':
                        {
                                // space has no effect, should not occur
                                // fix: delete it
                                org->setRepairRemove(gcur->pos, gcur);
                                gcur = gcur->child;
                                break;
                        }
                        default:
                        {
                                // error: unknown code
                                string buf = "Unknown code '" + gcur->name + "'";
                                logMessage("f4_Cell", "oneStep", LOG_ERROR, buf.c_str());
                                org->setRepairRemove(gcur->pos, gcur);
                                return 1;
                        }
                        }
                }
                else
                {
                        genoRange.add(gcur->pos, gcur->pos + int(gcur->name.length()) + 2 - 1); // +2 for N:
                        if (type != CELL_UNDIFF)
                        {
                                // fix: delete this node
                                org->setRepairRemove(gcur->pos, gcur);
                                return 1;  // stop
                        }
                        // error: if no previous
                        if (dadlink == NULL)
                        {
                                // fix: delete it
                                org->setRepairRemove(gcur->pos, gcur);
                                return 1;  // stop
                        }
                        neuclass = gcur->neuclass;
                        type = CELL_NEURON;
                        // change of type also halts development, to give other
                        // cells a chance for adjustment.  Namely, it is important
                        // to wait for other cells to turn to neurons before adding connections
                        gcur = gcur->child;
                        return 0; //stop
                }
        }
        active = false;  // done
        return 0;
}


int f4_Cell::addConnection(f4_Cell *nfrom, double nweight)
{
        if (nfrom->neuclass->getPreferredOutput() == 0) return -1; // if incoming neuron does not produce output, return error
        if (neuclass->getPreferredInputs() != -1 && conns_count >= neuclass->getPreferredInputs()) return -1; //cannot add more inputs to this neuron
        if (conns_count >= F4_MAX_CELL_INPUTS - 1) return -1; // over hardcoded limit
        conns[conns_count] = new f4_CellConn(nfrom, nweight);
        conns_count++;
        return 0;
}


void f4_Cell::adjustRec()
{
        //f4_OrientMat rot;
        int i;

        if (recProcessedFlag)
                // already processed
                return;

        // mark it processed
        recProcessedFlag = 1;

        // make sure its parent is processed first
        if (dadlink != NULL)
                dadlink->adjustRec();

        // count children
        childcount = 0;
        for (i = 0; i < org->cell_count; i++)
        {
                if (org->C[i]->dadlink == this)
                        if (org->C[i]->type == CELL_STICK)
                                childcount++;
        }

        if (type == CELL_STICK)
        {
                if (dadlink == NULL)
                {
                        //firstend = Pt3D_0;
                        // rotation due to rolling
                        xrot = rolling;
                        mz = 1;
                }
                else
                {
                        //firstend = dadlink->lastend;
                        GeneProps Pdad = dadlink->P;
                        GeneProps Padj = Pdad;
                        Padj.propagateAlong(false);

                        //rot = Orient_1;

                        // rotation due to rolling
                        xrot = rolling +
                                // rotation due to twist
                                Pdad.twist;
                        if (dadlink->commacount <= 1)
                        {
                                // rotation due to curvedness
                                zrot = Padj.curvedness;
                        }
                        else
                        {
                                zrot = Padj.curvedness + (anglepos * 1.0 / (dadlink->commacount + 1) - 0.5) * M_PI * 2.0;
                        }

                        //rot = rot * f4_OrientMat(yOz, xrot);
                        //rot = rot * f4_OrientMat(xOy, zrot);
                        // rotation relative to parent stick
                        //OM = rot * OM;

                        // rotation in world coordinates
                        //OM =  ((f4_OrientMat)dadlink->OM) * OM;
                        mz = dadlink->mz / dadlink->childcount;
                }
                //Pt3D lastoffset = (Orient)OM * (Pt3D(1,0,0)*P.len);
                //lastend = firstend + lastoffset;
        }
}



f4_CellConn::f4_CellConn(f4_Cell *nfrom, double nweight)
{
        from = nfrom;
        weight = nweight;
}



f4_Cells::f4_Cells(f4_Node *genome, int nrepair)
{
        // create ancestor cell
        repair = nrepair;
        errorcode = GENOPER_OK;
        errorpos = -1;
        repair_remove = NULL;
        repair_parent = NULL;
        repair_insert = NULL;
        tmpcel = NULL;
        f4rootnode = NULL;
        C[0] = new f4_Cell(this, 0, genome, genome, NULL, 0, GeneProps::standard_values);
        cell_count = 1;
}


f4_Cells::f4_Cells(SString & genome, int nrepair)
{
        repair = nrepair;
        errorcode = GENOPER_OK;
        errorpos = -1;
        repair_remove = NULL;
        repair_parent = NULL;
        repair_insert = NULL;
        tmpcel = NULL;
        f4rootnode = NULL;

        // transform geno from string to nodes
        f4rootnode = new f4_Node();
        int _ = 0;
        int res = f4_processRecur(genome.c_str(), _, f4rootnode);
        if (res || (f4rootnode->childCount() != 1))
        {
                errorcode = GENOPER_OPFAIL;
                errorpos = -1;
        }

        // create ancestor cell
        C[0] = new f4_Cell(this, 0, f4rootnode->child, f4rootnode->child, NULL, 0, GeneProps::standard_values);
        cell_count = 1;
}

f4_Cells::~f4_Cells()
{
        // release cells
        int i;
        if (cell_count)
        {
                for (i = cell_count - 1; i >= 0; i--)
                        delete C[i];
                cell_count = 0;
        }
        if (f4rootnode)
                delete f4rootnode;
}


bool f4_Cells::oneStep()
{
        int old_cell_count = cell_count; //cell_count may change in the loop as new cells may be appended because cells may be dividing
        for (int i = 0; i < old_cell_count; i++)
        {
                int cellstep_ret = C[i]->oneStep(); //keeps calling independently of C[i]->active
                if (cellstep_ret > 0)
                {
                        // error
                        C[i]->active = false;  // stop
                        return false;
                }
        }
        for (int i = 0; i < cell_count; i++) //we check all cells, including newly created ones
                if (C[i]->active)
                        return true; //at least one cell is still active. TODO maybe the development should stop NOT because of the "active" field (there is this strange "yielding" state too), but by observing the progress of all cells and continuing the development while (errorcode==0 AND (gcur of at least one cell changed OR cell_count changed)) ? Also get rid of return 1/return 0, just observe error.
        return false;
}


int f4_Cells::simulate()
{
        constexpr bool print_debugging = false; //print the state of cells during development
        errorcode = GENOPER_OK;

        for (int i = 0; i < cell_count; i++)  C[i]->active = true;

        if (print_debugging) f4_Node::print_tree(C[0]->genot, 0);
        if (print_debugging) print_cells("Initialization");

        // execute oneStep() in a cycle
        while (oneStep()) if (print_debugging) print_cells("Development step");
        if (print_debugging) print_cells("After last development step");

#ifdef EXTRA_STEP_CELL_DEVELOPMENT
        if (errorcode == GENOPER_OK)
        {
                oneStep(); if (print_debugging) print_cells("After extra step"); //for these "halted" (yielding) cells (they have active==false) that wait for other cells to develop. Without this step, the last, recently halted one(s) may miss the "retrying" step if all active==true cells became active==false in the last step.
        }
#endif

        if (errorcode != GENOPER_OK) return errorcode;

        // fix neuron attachements
        for (int i = 0; i < cell_count; i++)
        {
                if (C[i]->type == CELL_NEURON)
                {
                        while (C[i]->dadlink->type == CELL_NEURON)
                        {
                                C[i]->dadlink = C[i]->dadlink->dadlink;
                        }
                }
        }

        // there should be no undiff. cells
        // make undifferentiated cells sticks
        for (int i = 0; i < cell_count; i++)
        {
                if (C[i]->type == CELL_UNDIFF)
                {
                        C[i]->type = CELL_STICK;
                        //setError();
                }
        }

        // recursive adjust
        // reset recursive traverse flags
        for (int i = 0; i < cell_count; i++)
                C[i]->recProcessedFlag = 0;
        // process every cell
        for (int i = 0; i < cell_count; i++)
                C[i]->adjustRec();

        //DB( printf("Cell simulation done, %d cells. \n", nc); )

        if (print_debugging) print_cells("Final");

        return errorcode;
}


void f4_Cells::print_cells(const char* description)
{
        printf("------ %-55s ------ errorcode=%d, errorpos=%d\n", description, getErrorCode(), getErrorPos());
        for (int i = 0; i < cell_count; i++)
        {
                f4_Cell *c = C[i];
                string type;
                switch (c->type)
                {
                case CELL_UNDIFF: type = "undiff"; break;
                case CELL_STICK:  type = "STICK"; break;
                case CELL_NEURON: type = string("NEURON:") + c->neuclass->name.c_str(); break;
                default: type = std::to_string(c->type);
                }
                const char *status = c->active ? "active" : (c->gcur != NULL ? "yielding" : ""); //yielding = not active but waiting for other cells
                printf("%2d(%-8s)  nr=%d \t type=%-15s \t genot=%s \t gcurrent=%s", i, status, c->nr, type.c_str(), c->genot->name.c_str(), c->gcur ? c->gcur->name.c_str() : "null");
                if (c->gcur && c->gcur->name == "[")
                        printf("\tfrom=%d  weight=%g", c->gcur->conn_from, c->gcur->conn_weight);
                printf("\n");
                for (int l = 0; l < c->conns_count; l++)
                        printf("\tconn:%d from=%d weight=%g\n", l, c->conns[l]->from->nr, c->conns[l]->weight);
        }
        printf("\n");
}


void f4_Cells::addCell(f4_Cell *newcell)
{
        if (cell_count >= F4_MAX_CELLS - 1)
        {
                delete newcell;
                return;
        }
        C[cell_count] = newcell;
        cell_count++;
}


void f4_Cells::setError(int nerrpos)
{
        errorcode = GENOPER_OPFAIL;
        errorpos = nerrpos;
}

void f4_Cells::setRepairRemove(int nerrpos, f4_Node *rem)
{
        if (!repair)
        {
                // not in repair mode, treat as repairable error
                errorcode = GENOPER_REPAIR;
                errorpos = nerrpos;
        }
        else
        {
                errorcode = GENOPER_REPAIR;
                errorpos = nerrpos;
                repair_remove = rem;
        }
}

int f4_Cells::setRepairInsert(int nerrpos, f4_Node *parent, f4_Node *insert)
{
        if (!repair)
        {
                // not in repair mode, treat as repairable error
                errorcode = GENOPER_REPAIR;
                errorpos = nerrpos;
                return -1;
        }
        else
        {
                errorcode = GENOPER_REPAIR;
                errorpos = nerrpos;
                repair_parent = parent;
                repair_insert = insert;
                return 0;
        }
}

void f4_Cells::repairGeno(f4_Node *geno, int whichchild)
{
        // assemble repaired geno, if the case
        if (!repair) return;
        if ((repair_remove == NULL) && (repair_insert == NULL)) return;
        // traverse genotype tree, remove / insert node
        f4_Node *g2;
        if (whichchild == 1)
                g2 = geno->child;
        else
                g2 = geno->child2;
        if (g2 == NULL)
                return;
        if (g2 == repair_remove)
        {
                f4_Node *oldgeno;
                geno->removeChild(g2);
                if (g2->child)
                {
                        // add g2->child as child to geno
                        if (whichchild == 1)
                                geno->child = g2->child;
                        else
                                geno->child2 = g2->child;
                        g2->child->parent = geno;
                }
                oldgeno = g2;
                oldgeno->child = NULL;
                delete oldgeno;
                if (geno->child == NULL) return;
                // check this new
                repairGeno(geno, whichchild);
                return;
        }
        if (g2 == repair_parent)
        {
                geno->removeChild(g2);
                geno->addChild(repair_insert);
                repair_insert->parent = geno;
                repair_insert->child = g2;
                repair_insert->child2 = NULL;
                g2->parent = repair_insert;
        }
        // recurse
        if (g2->child)  repairGeno(g2, 1);
        if (g2->child2) repairGeno(g2, 2);
}


void f4_Cells::toF1Geno(SString &out)
{
        if (tmpcel) delete tmpcel;
        tmpcel = new f4_Cell(-1, NULL, 0, GeneProps::standard_values);
        out = "";
        toF1GenoRec(0, out);
        delete tmpcel;
}


void f4_Cells::toF1GenoRec(int curc, SString &out)
{
        int i, j, ccount;
        f4_Cell *thisti;
        f4_Cell *thneu;
        char buf[200];

        if (curc >= cell_count) return;

        if (C[curc]->type != CELL_STICK) return;

        thisti = C[curc];
        if (thisti->dadlink != NULL)
                *tmpcel = *(thisti->dadlink);

        // adjust length, curvedness, etc.
        tmpcel->P.propagateAlong(false);
        while (tmpcel->P.length > thisti->P.length)
        {
                tmpcel->P.executeModifier('l');
                out += "l";
        }
        while (tmpcel->P.length < thisti->P.length)
        {
                tmpcel->P.executeModifier('L');
                out += "L";
        }
        while (tmpcel->P.curvedness > thisti->P.curvedness)
        {
                tmpcel->P.executeModifier('c');
                out += "c";
        }
        while (tmpcel->P.curvedness < thisti->P.curvedness)
        {
                tmpcel->P.executeModifier('C');
                out += "C";
        }
        while (thisti->rolling > 0.0f)
        {
                rolling_dec(&(thisti->rolling));
                out += "R";
        }
        while (thisti->rolling < 0.0f)
        {
                rolling_inc(&(thisti->rolling));
                out += "r";
        }

        // output X for this stick
        out += "X";

        // neurons attached to it
        for (i = 0; i < cell_count; i++)
        {
                if (C[i]->type == CELL_NEURON)
                {
                        if (C[i]->dadlink == thisti)
                        {
                                thneu = C[i];
                                out += "[";
                                // ctrl
                                //if (1 == thneu->ctrl) out += "@"; // old code; this can be easily generalized to any neuroclass if ever needed
                                //if (2 == thneu->ctrl) out += "|";
                                out += thneu->neuclass->name.c_str(); // not tested, but something like that
                                // connections
                                for (j = 0; j < thneu->conns_count; j++)
                                {
                                        if (j) out += ",";
                                        sprintf(buf, "%d", thneu->conns[j]->from->nr - thneu->nr);
                                        out += buf;
                                        out += ":";
                                        // connection weight
                                        sprintf(buf, "%g", thneu->conns[j]->weight);
                                        out += buf;
                                }
                                out += "]";
                        }
                }
        }

        // sticks connected to it
        if (thisti->commacount >= 2)
                out += "(";

        ccount = 1;
        for (i = 0; i < cell_count; i++)
        {
                if (C[i]->type == CELL_STICK)
                {
                        if (C[i]->dadlink == thisti)
                        {
                                while (ccount < (C[i])->anglepos)
                                {
                                        ccount++;
                                        out += ",";
                                }
                                toF1GenoRec(i, out);
                        }
                }
        }

        while (ccount < thisti->commacount)
        {
                ccount++;
                out += ",";
        }

        if (thisti->commacount >= 2)
                out += ")";
}



// to organize an f4 genotype in a tree structure

f4_Node::f4_Node()
{
        name = "?";
        parent = NULL;
        child = NULL;
        child2 = NULL;
        pos = -1;

        reps = 0;
        prop_symbol = '\0';
        prop_increase = false;
        conn_from = 0;
        conn_weight = 0.0;
        neuclass = NULL;
}

f4_Node::f4_Node(string nname, f4_Node *nparent, int npos)
{
        name = nname;
        parent = nparent;
        child = NULL;
        child2 = NULL;
        pos = npos;
        if (parent) parent->addChild(this);

        reps = 0;
        prop_symbol = '\0';
        prop_increase = false;
        conn_from = 0;
        conn_weight = 0.0;
        neuclass = NULL;
}

f4_Node::f4_Node(char nname, f4_Node *nparent, int npos)
{
        name = nname;
        parent = nparent;
        child = NULL;
        child2 = NULL;
        pos = npos;
        if (parent) parent->addChild(this);

        reps = 0;
        prop_symbol = '\0';
        prop_increase = false;
        conn_from = 0;
        conn_weight = 0.0;
        neuclass = NULL;
}

f4_Node::~f4_Node()
{
        destroy();
}

void f4_Node::print_tree(const f4_Node *root, int indent)
{
        for (int i = 0; i < indent; i++) printf(" ");
        printf("%s (%d)", root->name.c_str(), root->count());
        if (root->name == "[")
                printf("     from=%-3d  weight=%g", root->conn_from, root->conn_weight);
        printf("\n");
        if (root->child) print_tree(root->child, indent + 1);
        if (root->child2) print_tree(root->child2, indent + 1);
}

int f4_Node::addChild(f4_Node *nchi)
{
        if (child == NULL)
        {
                child = nchi;
                return 0;
        }
        if (child2 == NULL)
        {
                child2 = nchi;
                return 0;
        }
        return -1;
}

int f4_Node::removeChild(f4_Node *nchi)
{
        if (nchi == child2)
        {
                child2 = NULL;
                return 0;
        }
        if (nchi == child)
        {
                child = NULL;
                return 0;
        }
        return -1;
}

int f4_Node::childCount()
{
        if (child != NULL)
        {
                if (child2 != NULL) return 2;
                else return 1;
        }
        else
        {
                if (child2 != NULL) return 1;
                else return 0;
        }
}

int f4_Node::count() const
{
        int c = 1;
        if (child != NULL)  c += child->count();
        if (child2 != NULL) c += child2->count();
        return c;
}

f4_Node* f4_Node::ordNode(int n)
{
        int n1;
        if (n == 0) return this;
        n--;
        if (child != NULL)
        {
                n1 = child->count();
                if (n < n1) return child->ordNode(n);
                n -= n1;
        }
        if (child2 != NULL)
        {
                n1 = child2->count();
                if (n < n1) return child2->ordNode(n);
                n -= n1;
        }
        return NULL;
}

f4_Node* f4_Node::randomNode()
{
        int n = count();
        // pick a random node between 0 and n-1
        return ordNode(rndUint(n));
}

f4_Node* f4_Node::randomNodeWithSize(int mn, int mx)
{
        // try random nodes, and accept if size in range
        // limit to maxlim tries
        int i, n, maxlim;
        f4_Node *nod = NULL;
        maxlim = count();
        for (i = 0; i < maxlim; i++)
        {
                nod = randomNode();
                n = nod->count();
                if ((n >= mn) && (n <= mx)) return nod;
        }
        // failed, doesn't matter
        return nod;
}

void f4_Node::sprint(SString& out)
{
        char buf2[20];
        // special case: repetition code
        if (name == "#")
        {
                out += "#";
                sprintf(buf2, "%d", reps);
                out += buf2;
        }
        else {
                // special case: neuron connection
                if (name == "[")
                {
                        out += "[";
                        sprintf(buf2, "%d", conn_from);
                        out += buf2;
                        sprintf(buf2, ":%g]", conn_weight);
                        out += buf2;
                }
                else if (name == ":")
                {
                        sprintf(buf2, ":%c%c:", prop_increase ? '+' : '-', prop_symbol);
                        out += buf2;
                }
                else if (neuclass != NULL)
                {
                        out += "N:";
                        out += neuclass->name.c_str();
                }
                else
                {
                        out += name.c_str();
                }
        }

        if (child != NULL)
                child->sprint(out);
        // if two children, make sure last char is a '>'
        if (childCount() == 2)
                if (out[0] == 0) out += ">"; else
                        if (out[out.length() - 1] != '>') out += ">";

        if (child2 != NULL)
                child2->sprint(out);
        // make sure last char is a '>'
        if (out[0] == 0) out += ">"; else
                if (out[out.length() - 1] != '>') out += ">";
}

void f4_Node::sprintAdj(char *& buf)
{
        unsigned int len;
        // build in a SString, with initial size
        SString out;
        out.reserve(int(strlen(buf)) + 2000);

        sprint(out);

        // very last '>' can be omitted
        len = out.length();
        if (len > 1)
                if (out[len - 1] == '>') { (out.directWrite())[len - 1] = 0; out.endWrite(); }; //Macko 2023-04 TODO "can be omitted", but should we remove it as a rule even in generated genotypes? see if I can somehow detect junk characters after top-level '>' ends properly: /*4*/<X>N:N>whatever
        // copy back to string
        // if new is longer, reallocate buf
        if (len + 1 > strlen(buf))
        {
                buf = (char*)realloc(buf, len + 1);
        }
        strcpy(buf, out.c_str());
}

f4_Node* f4_Node::duplicate()
{
        f4_Node *copy;
        copy = new f4_Node(*this);
        copy->parent = NULL;  // set later
        copy->child = NULL;
        copy->child2 = NULL;
        if (child != NULL)
        {
                copy->child = child->duplicate();
                copy->child->parent = copy;
        }
        if (child2 != NULL)
        {
                copy->child2 = child2->duplicate();
                copy->child2->parent = copy;
        }
        return copy;
}


void f4_Node::destroy()
{
        // children are destroyed (recursively) through the destructor
        if (child2 != NULL) delete child2;
        if (child != NULL) delete child;
}

// scan genotype string and build tree
// return >1 for error (errorpos)
int f4_processRecur(const char* genot, int &pos_inout, f4_Node *parent)
{
        f4_Node *par = parent;

        if (pos_inout >= (int)strlen(genot))
                return (int)strlen(genot) + 1;

        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 '<':
                {
                        f4_Node *node = new f4_Node("<", par, pos_inout);
                        par = node;
                        pos_inout++; //move after '<'
                        int res = f4_processRecur(genot, pos_inout, par);
                        if (res) return res;
                        if (pos_inout < (int)strlen(genot))
                        {
                                res = f4_processRecur(genot, pos_inout, par);
                                if (res) return res;
                        }
                        else // ran out
                        {
                                //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 (int)strlen(genot) + 1;
                                //old silent repair:
                                //node = new f4_Node(">", par, int(strlen(genot)) - 1);
                        }
                        return 0;  // OK
                }
                case '>':
                {
                        new f4_Node(">", par, pos_inout);
                        pos_inout++; //move after '>'
                        return 0;  // OK
                }
                case '#':
                {
                        // repetition marker, 1 by default
                        ExtValue val;
                        const char* end = val.parseNumber(genot + pos_inout + 1, ExtPType::TInt);
                        //TODO end==NULL? -> error!
                        int reps = (end == NULL) ? 1 : val.getInt();
                        f4_Node *node = new f4_Node("#", par, pos_inout);
                        node->reps = reps;
                        // skip number
                        pos_inout += end - (genot + pos_inout);
                        int res = f4_processRecur(genot, pos_inout, node);
                        if (res) return res;
                        if (pos_inout < (int)strlen(genot))
                        {
                                res = f4_processRecur(genot, pos_inout, node);
                                if (res) return res;
                        }
                        else // ran out
                        {
                                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)
                        }
                        return 0;  // OK
                }
                case ' ':
                case '\n':
                case '\r':
                case '\t':
                {
                        // whitespace: ignore
                        pos_inout++;
                        break;
                }
                case 'N':
                {
                        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 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;
                        par = node;
                        // if it continues with a colon that determines a neuron parameter (e.g. N:N:+=: ), then let the switch case for colon handle this
                        break;
                }
                case ':':
                {
                        // neuron parameter  +! -! += -= +/ or -/
                        // 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 + pos_inout, ":%c%c%1[:]", &prop_dir, &prop_symbol, &prop_end) != 3)
                                // error: incorrect format
                                return pos_inout + 1 + 1;
                        if (prop_dir != '-' && prop_dir != '+')
                                return pos_inout + 1 + 1; //error
                        switch (prop_symbol)
                        {
                        case '!':  case '=':  case '/':  break;
                        default:
                                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;
                        pos_inout += 4; //skipping :ds:
                        break;
                }
                case '[':
                {
                        double weight = 0;
                        int relfrom;
                        const char *end = parseConnection(genot + pos_inout, relfrom, weight);
                        if (end == NULL)
                                return pos_inout + 1; //error

                        f4_Node *node = new f4_Node("[", par, pos_inout);
                        node->conn_from = relfrom;
                        node->conn_weight = weight;
                        par = node;
                        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[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;
                        pos_inout++;
                        break;
                }
                }
        }

        // should end with a '>'
        if (par && par->name != ">")
        {
                //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
}

const char* parseConnection(const char *fragm, int& relfrom, double &weight)
{
        const char *parser = fragm;
        if (*parser != '[') return NULL;
        parser++;
        ExtValue val;
        parser = val.parseNumber(parser, ExtPType::TInt);
        if (parser == NULL) return NULL;
        relfrom = val.getInt();
        if (*parser != ':') return NULL;
        parser++;
        parser = val.parseNumber(parser, ExtPType::TDouble);
        if (parser == NULL) return NULL;
        weight = val.getDouble();
        if (*parser != ']') return NULL;
        parser++;
        return parser;
}

/*
f4_Node* f4_processTree(const char* geno)
{
        f4_Node *root = new f4_Node();
        int res = f4_processRecur(geno, 0, root);
        if (res) return NULL;
        //DB( printf("test f4  "); )
        DB(
                if (root->child)
                {
                        char* buf = (char*)malloc(300);
                        DB(printf("(%d) ", root->child->count());)
                                buf[0] = 0;
                        root->child->sprintAdj(buf);
                        DB(printf("%s\n", buf);)
                                free(buf);
                }
        )
                return root->child;
}
*/