source: cpp/frams/model/model.cpp @ 1311

// 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.

#include <common/nonstd_math.h>
#include "model.h"
#include <common/log.h>
#include <frams/util/multimap.h>
#include <common/loggers/loggers.h>

#define F0_CHECKPOINT_LINE "checkpoint:"

Model::Model(ShapeType sh)
{
        autobuildmaps = false;
        init(sh);
}

void Model::init(ShapeType shtype)
{
        partmappingchanged = 0;
        using_checkpoints = false;
        is_checkpoint = false;
        buildstatus = empty;
        modelfromgenotype = 0;
        startenergy = 1.0;
        checklevel = 1;
        map = 0;
        f0map = 0;
        f0genoknown = 1;
        shapetype = SHAPETYPE_UNKNOWN;
        declared_shapetype = shtype;
}

void Model::declareShapeType(ShapeType shtype)
{
        declared_shapetype = shtype;
}

void Model::moveElementsFrom(Model &source)
{
        int i;
        open();
        for (i = 0; i < source.getPartCount(); i++)
                addPart(source.getPart(i));
        for (i = 0; i < source.getJointCount(); i++)
                addJoint(source.getJoint(i));
        for (i = 0; i < source.getNeuroCount(); i++)
                addNeuro(source.getNeuro(i));
        source.parts.clear(); source.joints.clear(); source.neurons.clear();
        source.clear();
}

void Model::internalCopy(const Model &mod)
{
        geno = mod.geno;
        f0genoknown = 0;
        shapetype = mod.shapetype;
        declared_shapetype = mod.declared_shapetype;
        startenergy = mod.startenergy;
        modelfromgenotype = mod.modelfromgenotype;
        for (int i = 0; i < mod.getPartCount(); i++)
                addPart(new Part(*mod.getPart(i)));
        for (int i = 0; i < mod.getJointCount(); i++)
        {
                Joint *oldj = mod.getJoint(i);
                Joint *j = new Joint(*oldj);
                addJoint(j);
                j->attachToParts(oldj->part1->refno, oldj->part2->refno);
        }
        for (int i = 0; i < mod.getNeuroCount(); i++)
        {
                Neuro *oldn = mod.getNeuro(i);
                Neuro *n = new Neuro(*oldn);
                addNeuro(n);
                if (oldn->part_refno >= 0) n->attachToPart(oldn->part_refno);
                else n->attachToJoint(oldn->joint_refno);
        }
        for (int i = 0; i < mod.getNeuroCount(); i++)
        {
                Neuro *oldn = mod.getNeuro(i);
                Neuro *n = getNeuro(i);
                for (int ni = 0; ni < oldn->getInputCount(); ni++)
                {
                        double w;
                        Neuro *oldinput = oldn->getInput(ni, w);
                        SString info = n->getInputInfo(ni);
                        n->addInput(getNeuro(oldinput->refno), w, &info);
                }
        }
        updateRefno();
        if (using_checkpoints)
                for (vector<Model *>::const_iterator it = mod.checkpoints.begin(); it != mod.checkpoints.end(); it++)
                {
                        Model *m = *it;
                        Model *n = new Model(*m, m->autobuildmaps, false, true);
                        checkpoints.push_back(n);
                }
}


Model::Model(const Geno &src, ShapeType st, bool buildmaps, bool _using_checkpoints, bool _is_checkpoint)
        :autobuildmaps(buildmaps)
{
        init(src, st, _using_checkpoints, _is_checkpoint);
}

void Model::operator=(const Model &mod)
{
        clear();
        open(mod.isUsingCheckpoints(), mod.isCheckpoint());
        internalCopy(mod);
        buildstatus = mod.buildstatus;
}

Model::Model(const Model &mod, bool buildmaps, bool _using_checkpoints, bool _is_checkpoint)
        :autobuildmaps(buildmaps)
{
        init(mod.declared_shapetype);
        open(_using_checkpoints, _is_checkpoint);
        internalCopy(mod);
        if (is_checkpoint)
                close();
        else
                buildstatus = mod.buildstatus;
        if (mod.map)
                map = new MultiMap(*mod.map);
        if (mod.f0map)
                f0map = new MultiMap(*mod.f0map);
}

void Model::init(const Geno &src, ShapeType sh, bool _using_checkpoints, bool _is_checkpoint)
{
        init(sh);
        using_checkpoints = _using_checkpoints;
        is_checkpoint = _is_checkpoint;
        modelfromgenotype = 1;
        geno = src;
        build();
}

void Model::resetAllDelta()
{
        for (int i = 0; i < getJointCount(); i++)
                getJoint(i)->resetDelta();
}

void Model::useAllDelta(bool yesno)
{
        for (int i = 0; i < getJointCount(); i++)
                getJoint(i)->useDelta(yesno);
}

Model::~Model()
{
        delmodel_list.action((intptr_t)this);
        clear();
}

void Model::clear()
{
        FOREACH(Part *, p, parts)
                delete p;
        FOREACH(Joint *, j, joints)
                delete j;
        FOREACH(Neuro *, n, neurons)
                delete n;
        parts.clear(); joints.clear(); neurons.clear();
        delMap();
        delF0Map();
        init(declared_shapetype);
        geno = Geno();
        f0geno = Geno();
        for (vector<Model *>::iterator it = checkpoints.begin(); it != checkpoints.end(); it++)
                delete *it;
        checkpoints.clear();
}

Part *Model::addPart(Part *p)
{
        p->owner = this;
        p->refno = parts.size();
        parts += p;
        return p;
}

Joint *Model::addJoint(Joint *j)
{
        j->owner = this;
        j->refno = joints.size();
        joints += j;
        return j;
}

Neuro *Model::addNeuro(Neuro *n)
{
        n->owner = this;
        n->refno = neurons.size();
        neurons += n;
        return n;
}

void Model::removeNeuros(SList &nlist)
{
        FOREACH(Neuro *, nu, nlist)
        {
                int i = findNeuro(nu);
                if (i >= 0) removeNeuro(i);
        }
}

void Model::removePart(int partindex, int removeattachedjoints, int removeattachedneurons)
{
        Part *p = getPart(partindex);
        if (removeattachedjoints)
        {
                SList jlist;
                findJoints(jlist, p);
                FOREACH(Joint *, j, jlist)
                {
                        int i = findJoint(j);
                        if (i >= 0) removeJoint(i, removeattachedneurons);
                }
        }
        if (removeattachedneurons)
        {
                SList nlist;
                findNeuros(nlist, 0, p);
                removeNeuros(nlist);
        }
        parts -= partindex;
        delete p;
}

void Model::removeJoint(int jointindex, int removeattachedneurons)
{
        Joint *j = getJoint(jointindex);
        if (removeattachedneurons)
        {
                SList nlist;
                findNeuros(nlist, 0, 0, j);
                removeNeuros(nlist);
        }
        joints -= jointindex;
        delete j;
}

void Model::removeNeuro(int neuroindex, bool removereferences)
{
        Neuro *thisN = getNeuro(neuroindex);

        if (removereferences)
        {
                Neuro *n;
                // remove all references to thisN
                for (int i = 0; n = (Neuro *)neurons(i); i++)
                {
                        Neuro *inp;
                        for (int j = 0; inp = n->getInput(j); j++)
                                if (inp == thisN)
                                {
                                        n->removeInput(j);
                                        j--;
                                }
                }
        }

        neurons -= neuroindex;
        delete thisN;
}

MultiMap &Model::getMap()
{
        if (!map) map = new MultiMap();
        return *map;
}

void Model::delMap()
{
        if (map) { delete map; map = 0; }
}
void Model::delF0Map()
{
        if (f0map) { delete f0map; f0map = 0; }
}

void Model::makeGenToGenMap(MultiMap &result, const MultiMap &gen1tomodel, const MultiMap &gen2tomodel)
{
        result.clear();
        MultiMap m;
        m.addReversed(gen2tomodel);
        result.addCombined(gen1tomodel, m);
}

void Model::getCurrentToF0Map(MultiMap &result)
{
        result.clear();
        if (!map) return;
        const MultiMap &f0m = getF0Map();
        makeGenToGenMap(result, *map, f0m);
}

void Model::rebuild(bool buildm)
{
        autobuildmaps = buildm;
        clear();
        build();
}

void Model::initMap()
{
        if (!map) map = new MultiMap();
        else map->clear();
}

void Model::initF0Map()
{
        if (!f0map) f0map = new MultiMap();
        else f0map->clear();
}

Model::ItemType Model::itemTypeFromLinePrefix(const char *line)
{
        struct PrefixAndItem { const char *prefix; ItemType type; };
        static const PrefixAndItem types[] = { { "m:", ModelType }, { "p:", PartType }, { "j:", JointType }, { "n:", NeuronType }, { "c:", NeuronConnectionType }, { F0_CHECKPOINT_LINE, CheckpointType }, { NULL } };
        for (const PrefixAndItem *t = types; t->prefix != NULL; t++)
        {
                const char *in = line;
                const char *pattern = t->prefix;
                for (; *in == *pattern; in++, pattern++)
                        if (*pattern == ':')
                                return t->type;
        }
        return UnknownType;
}

void Model::build()
{
        f0errorposition = -1;
        f0warnposition = -1;
        MultiMap *convmap = autobuildmaps ? new MultiMap() : NULL;
        if (declared_shapetype == SHAPETYPE_UNKNOWN)
                f0geno = geno.getConverted(Geno::F0_FORMAT_LIST, convmap, using_checkpoints);
        else
                f0geno = geno.getConverted(genoFormatForShapeType(declared_shapetype), convmap, using_checkpoints);
        f0genoknown = 1;
        if (f0geno.isInvalid())
        {
                buildstatus = invalid;
                if (convmap) delete convmap;
                return;
        }
        if (declared_shapetype == SHAPETYPE_UNKNOWN)
                declareShapeType(shapeTypeForGenoFormat(f0geno.getFormat()));
        SString f0txt = f0geno.getGenes();
        buildstatus = building; // was: open();
        if (autobuildmaps)
        {
                partmappingchanged = 0;
                initMap();
                initF0Map();
        }
        int pos = 0, lnum = 1, lastpos = 0;
        SString line;
        MultiRange frommap;
        LoggerToMemory mh(LoggerBase::Enable | LoggerBase::DontBlock);
        Model *current_model = this;
        for (; f0txt.getNextToken(pos, line, '\n'); lnum++)
        {
                const char *line_ptr = line.c_str();
                for (; *line_ptr; line_ptr++)
                        if (!strchr(" \r\t", *line_ptr)) break;
                if (*line_ptr == '#') continue;
                if (!*line_ptr) continue;

                const char *colon = strchr(line_ptr, ':');
                ItemType type = UnknownType;
                SString excluding_prefix;
                if (colon != NULL)
                {
                        colon++;
                        type = itemTypeFromLinePrefix(line_ptr);
                        for (; *colon; colon++)
                                if (!strchr(" \r\t", *colon)) break;
                        excluding_prefix = colon;
                }

                if (autobuildmaps)
                {
                        frommap.clear();
                        frommap.add(lastpos, pos - 1);
                }
                mh.reset();
                if (type == CheckpointType)
                {
                        current_model->close();
                        current_model = new Model;
                        current_model->open(false, true);
                        checkpoints.push_back(current_model);
                }
                else if (current_model->addFromString(type, excluding_prefix, lnum, autobuildmaps ? (&frommap) : 0) == -1)
                {
                        buildstatus = invalid;
                        f0errorposition = lastpos;
                        if (convmap) delete convmap;
                        return;
                }
                if (mh.getErrorWarningCount())
                {
                        if (f0warnposition < 0) f0warnposition = lastpos;
                }
                lastpos = pos;
        }
        mh.disable();
        current_model->close();
        if (convmap)
        {
                *f0map = *map;
                if (!Geno::formatIsOneOf(geno.getFormat(), Geno::F0_FORMAT_LIST))
                {
                        MultiMap tmp;
                        tmp.addCombined(*convmap, getMap());
                        *map = tmp;
                }
                delete convmap;
        }
}

const MultiMap &Model::getF0Map()
{
        if (!f0map)
        {
                f0map = new MultiMap();
                makeGeno(f0geno, f0map);
                f0genoknown = 1;
        }
        return *f0map;
}

Geno Model::rawGeno()
{
        Geno tmpgen;
        makeGeno(tmpgen, NULL, true, true);
        return tmpgen;
}

void Model::makeGeno(Geno &g, MultiMap *map, bool handle_defaults, bool can_be_invalid)
{
        if ((buildstatus != valid) && (!can_be_invalid))
        {
                g = Geno("", Geno::FORMAT_INVALID, "", "invalid model");
                return;
        }

        SString gen;

        Param modelparam(f0_model_paramtab);
        Param partparam(f0_part_paramtab);
        Param jointparam(f0_joint_paramtab);
        Param neuroparam(f0_neuro_paramtab);
        Param connparam(f0_neuroconn_paramtab);

        static Part defaultpart;
        static Joint defaultjoint;
        static Neuro defaultneuro;
        static Model defaultmodel;
        static NeuroConn defaultconn;
        //static NeuroItem defaultneuroitem;

        Part *p;
        Joint *j;
        Neuro *n;
        int i;
        int len;
        int a, b;
        //NeuroItem *ni;

        SString mod_props;
        modelparam.select(this);
        modelparam.saveSingleLine(mod_props, handle_defaults ? &defaultmodel : NULL, true, !handle_defaults);
        if (mod_props.length() > 1) //are there any non-default values? ("\n" is empty)
        {
                gen += "m:";
                gen += mod_props;
        }

        for (i = 0; p = (Part *)parts(i); i++)
        {
                partparam.select(p);
                len = gen.length();
                gen += "p:";
                partparam.saveSingleLine(gen, handle_defaults ? &defaultpart : NULL, true, !handle_defaults);
                if (map)
                        map->add(len, gen.length() - 1, partToMap(i));
        }
        for (i = 0; j = (Joint *)joints(i); i++)
        {
                jointparam.select(j);
                len = gen.length();
                jointparam.setParamTab(j->usedelta ? f0_joint_paramtab : f0_nodeltajoint_paramtab);
                gen += "j:";
                jointparam.saveSingleLine(gen, handle_defaults ? &defaultjoint : NULL, true, !handle_defaults);
                if (map)
                        map->add(len, gen.length() - 1, jointToMap(i));
        }
        for (i = 0; n = (Neuro *)neurons(i); i++)
        {
                neuroparam.select(n);
                len = gen.length();
                gen += "n:";
                neuroparam.saveSingleLine(gen, handle_defaults ? &defaultneuro : NULL, true, !handle_defaults);
                if (map)
                        map->add(len, gen.length() - 1, neuroToMap(i));
        }
        for (a = 0; a < neurons.size(); a++)
        { // inputs
                n = (Neuro *)neurons(a);
                //      if ((n->getInputCount()==1)&&(n->getInput(0).refno <= n->refno))
                //              continue; // already done with Neuro::conn_refno

                for (b = 0; b < n->getInputCount(); b++)
                {
                        double w;
                        NeuroConn nc;
                        Neuro *n2 = n->getInput(b, w);
                        //              if (((n2.parentcount==1)&&(n2.parent)&&(n2.parent->refno < n2.refno)) ^ 
                        //                  (n2.neuro_refno>=0))
                        //                      printf("!!!! bad Neuro::neuro_refno ?!\n");

                        //              if ((n2.parentcount==1)&&(n2.parent)&&(n2.parent->refno < n2.refno))
                        //              if (n2.neuro_refno>=0)
                        //                      continue; // already done with Neuro::neuro_refno

                        nc.n1_refno = n->refno; nc.n2_refno = n2->refno;
                        nc.weight = w;
                        SString **s = n->inputInfo(b);
                        if ((s) && (*s))
                                nc.info = **s;
                        connparam.select(&nc);
                        len = gen.length();
                        gen += "c:";
                        connparam.saveSingleLine(gen, handle_defaults ? &defaultconn : NULL, true, !handle_defaults);
                        if (map)
                                map->add(len, gen.length() - 1, neuroToMap(n->refno));
                }
        }

        for (vector<Model *>::const_iterator it = checkpoints.begin(); it != checkpoints.end(); it++)
        {
                Geno g = (*it)->getF0Geno();
                gen += F0_CHECKPOINT_LINE "\n";
                gen += g.getGenes();
        }

        g = Geno(gen.c_str(), genoFormatForShapeType(getShapeType()), "", "");
}

SString Model::genoFormatForShapeType(ShapeType st)
{
        switch (st)
        {
        case SHAPETYPE_BALL_AND_STICK:
                return "0";
        case SHAPETYPE_SOLIDS:
                return "0s";
        default:
                return Geno::FORMAT_INVALID;
        }
}

Model::ShapeType Model::shapeTypeForGenoFormat(const SString& format)
{
        if (format == "0")
                return SHAPETYPE_BALL_AND_STICK;
        else if (format == "0s")
                return SHAPETYPE_SOLIDS;
        else
                return SHAPETYPE_UNKNOWN;

}

const char* Model::getShapeTypeName(ShapeType sh)
{
        switch (sh)
        {
        case SHAPETYPE_BALL_AND_STICK: return "ball-and-stick";
        case SHAPETYPE_SOLIDS: return "solid shapes";
        case SHAPETYPE_UNKNOWN: return "unknown";

        case SHAPETYPE_ILLEGAL:
        default:
                return "illegal";
        }
}

//////////////

void Model::open(bool _using_checkpoints, bool _is_checkpoint)
{
        if (buildstatus == building) return;
        using_checkpoints = _using_checkpoints;
        is_checkpoint = _is_checkpoint;
        buildstatus = building;
        modelfromgenotype = 0;
        partmappingchanged = 0;
        f0genoknown = 0;
        delMap();
}

int Model::getCheckpointCount()
{
        return (int)checkpoints.size();
}

Model *Model::getCheckpoint(int i)
{
        return checkpoints[i];
}

void Model::checkpoint()
{
        if (!using_checkpoints) return;
        updateRefno();
        Model *m = new Model(*this, false, false, true);
        checkpoints.push_back(m);
}

void Model::setGeno(const Geno &newgeno)
{
        geno = newgeno;
}

void Model::clearMap()
{
        Part *p; Joint *j; Neuro *n;
        int i;
        delMap();
        delF0Map();
        for (i = 0; p = (Part *)parts(i); i++)
                p->clearMapping();
        for (i = 0; j = (Joint *)joints(i); i++)
                j->clearMapping();
        for (i = 0; n = (Neuro *)neurons(i); i++)
                n->clearMapping();
}

int Model::close(bool building_live_model)
{
        if (buildstatus != building)
                logPrintf("Model", "close", LOG_WARN, "Unexpected close() - no open()");
        if (internalcheck(is_checkpoint ? CHECKPOINT_CHECK : (building_live_model ? LIVE_CHECK : FINAL_CHECK)) > 0)
        {
                buildstatus = valid;

                if (partmappingchanged)
                {
                        getMap();
                        Part *p; Joint *j; Neuro *n;
                        int i;
                        for (i = 0; p = (Part *)parts(i); i++)
                                if (p->getMapping())
                                        map->add(*p->getMapping(), partToMap(i));
                        for (i = 0; j = (Joint *)joints(i); i++)
                                if (j->getMapping())
                                        map->add(*j->getMapping(), jointToMap(i));
                        for (i = 0; n = (Neuro *)neurons(i); i++)
                                if (n->getMapping())
                                        map->add(*n->getMapping(), neuroToMap(i));
                }
        }
        else
                buildstatus = invalid;

        return (buildstatus == valid);
}

int Model::validate()
{
        return internalcheck(EDITING_CHECK);
}

Pt3D Model::whereDelta(const Part &start, const Pt3D &rot, const Pt3D &delta)
{
        Orient roto;
        roto = rot;
        Orient o;
        roto.transform(o, start.o);
        //o.x=start.o/roto.x;
        //o.y=start.o/roto.y;
        //o.z=start.o/roto.z;
        return o.transform(delta) + start.p;
}

int Model::addFromString(ItemType item_type, const SString &singleline, const MultiRange *srcrange)
{
        return addFromString(item_type, singleline, 0, srcrange);
}

int Model::addFromString(ItemType item_type, const SString &singleline, int line_num, const MultiRange *srcrange)
{
        SString error_message;
        int result = addFromStringNoLog(item_type, singleline, error_message, srcrange);
        if (result < 0)
        {
                if (error_message.length() == 0) // generic error when no detailed message is available
                        error_message = "Invalid f0 code";
                if (line_num > 0)
                        error_message += SString::sprintf(", line #%d", line_num);
                error_message += nameForErrors();
                logPrintf("Model", "build", LOG_ERROR, "%s", error_message.c_str());
        }
        return result;
}

int Model::addFromStringNoLog(ItemType item_type, const SString &line, SString &error_message, const MultiRange *srcrange)
{
        error_message = SString::empty();
        ParamInterface::LoadOptions opts;
        switch (item_type)
        {
        case PartType:
        {
                Param partparam(f0_part_paramtab);
                Part *p = new Part();
                partparam.select(p);
                partparam.load(ParamInterface::FormatSingleLine, line, &opts);
                if (opts.parse_failed) { delete p; error_message = "Invalid 'p:'"; return -1; }
                p->o.rotate(p->rot);
                parts += p;
                p->owner = this;
                if (srcrange) p->setMapping(*srcrange);
                return getPartCount() - 1;
        }

        case ModelType:
        {
                Param modelparam(f0_model_paramtab);
                modelparam.select(this);
                modelparam.load(ParamInterface::FormatSingleLine, line, &opts);
                if (opts.parse_failed) { error_message = "Invalid 'm:'"; return -1; }
                return 0;
        }

        case JointType:
        {
                Param jointparam(f0_joint_paramtab);
                Joint *j = new Joint();
                jointparam.select(j);
                j->owner = this;
                jointparam.load(ParamInterface::FormatSingleLine, line, &opts);
                if (opts.parse_failed) { delete j; error_message = "Invalid 'j:'"; return -1; }
                bool p1_ok = false, p2_ok = false;
                if ((p1_ok = ((j->p1_refno >= 0) && (j->p1_refno < getPartCount()))) &&
                        (p2_ok = ((j->p2_refno >= 0) && (j->p2_refno < getPartCount()))))
                {
                        addJoint(j);
                        if ((j->d.x != JOINT_DELTA_MARKER) || (j->d.y != JOINT_DELTA_MARKER) || (j->d.z != JOINT_DELTA_MARKER))
                        {
                                j->useDelta(1);
                                j->resetDeltaMarkers();
                        }
                        j->attachToParts(j->p1_refno, j->p2_refno);
                        if (srcrange) j->setMapping(*srcrange);
                        return j->refno;
                }
                else
                {
                        error_message = SString::sprintf("Invalid reference to Part #%d", p1_ok ? j->p1_refno : j->p2_refno);
                        delete j;
                        return -1;
                }
        }

        case NeuronType:
        {
                Param neuroparam(f0_neuro_paramtab);
                Neuro *nu = new Neuro();
                neuroparam.select(nu);
                neuroparam.load(ParamInterface::FormatSingleLine, line, &opts);
                if (opts.parse_failed) { delete nu; error_message = "Invalid 'n:'"; return -1; }
                {
                        // default class for unparented units: standard neuron
                        if (nu->getClassName().length() == 0) nu->setClassName("N");
                }
                /*
                        if (nu->conn_refno>=0) // input specified...
                        {
                        if (nu->conn_refno >= getNeuroCount()) // and it's illegal
                        {
                        delete nu;
                        return -1;
                        }
                        Neuro *inputNU=getNeuro(nu->conn_refno);
                        nu->addInput(inputNU,nu->weight);
                        }
                        */
                nu->owner = this;
                // attach to part/joint
                if (nu->part_refno >= 0)
                {
                        nu->attachToPart(nu->part_refno);
                        if (nu->part == NULL)
                        {
                                error_message = SString::sprintf("Invalid reference to Part #%d", nu->part_refno); delete nu; return -1;
                        }
                }
                if (nu->joint_refno >= 0)
                {
                        nu->attachToJoint(nu->joint_refno);
                        if (nu->joint == NULL)
                        {
                                error_message = SString::sprintf("Invalid reference to Joint #%d", nu->joint_refno); delete nu; return -1;
                        }
                }
                if (srcrange) nu->setMapping(*srcrange);
                // todo: check part/joint ref# 
                {
                        neurons += nu;
                        return neurons.size() - 1;
                }
        }

        case NeuronConnectionType:
        {
                Param ncparam(f0_neuroconn_paramtab);
                NeuroConn c;
                ncparam.select(&c);
                ncparam.load(ParamInterface::FormatSingleLine, line, &opts);
                if (opts.parse_failed) { error_message = "Invalid 'c:'"; return -1; }
                bool n1_ok = false, n2_ok = false;
                if ((n1_ok = ((c.n1_refno >= 0) && (c.n1_refno < getNeuroCount())))
                        && (n2_ok = ((c.n2_refno >= 0) && (c.n2_refno < getNeuroCount()))))
                {
                        Neuro *na = getNeuro(c.n1_refno);
                        Neuro *nb = getNeuro(c.n2_refno);
                        na->addInput(nb, c.weight, &c.info);
                        if (srcrange)
                                na->addMapping(*srcrange);
                        return 0;
                }
                error_message = SString::sprintf("Invalid reference to Neuro #%d", n1_ok ? c.n2_refno : c.n1_refno);
                return -1;
        }

        case CheckpointType: case UnknownType: //handled by addFromString for uniform error handling
                return -1;
        }
        return -1;
}


/////////////

void Model::updateRefno()
{
        for (int i = 0; i < parts.size(); i++)
                getPart(i)->refno = i;
        for (int i = 0; i < joints.size(); i++)
        {
                Joint *j = getJoint(i);
                j->refno = i;
                if (j->part1 && j->part2 && (j->part1 != j->part2))
                {
                        j->p1_refno = j->part1->refno;
                        j->p2_refno = j->part2->refno;
                }
        }
        for (int i = 0; i < neurons.size(); i++)
                getNeuro(i)->refno = i;
}

#define VALIDMINMAX(var,template,field) \
if (var -> field < getMin ## template () . field) \
        { var->field= getMin ## template () . field; \
        logPrintf("Model","internalCheck",LOG_WARN,# field " too small in " # template " #%d (adjusted)",i);} \
else if (var -> field > getMax ## template () . field) \
        { var->field= getMax ## template ()  . field; \
        logPrintf("Model","internalCheck",LOG_WARN,# field " too big in " # template " #%d (adjusted)",i);}

#define LINKFLAG 0x8000000

SString Model::nameForErrors() const
{
        if (geno.getName().length() > 0)
                return SString::sprintf(" in '%s'", geno.getName().c_str());
        return SString::empty();
}

int Model::internalcheck(CheckType check)
{
        Part *p;
        Joint *j;
        Neuro *n;
        int i, k;
        int ret = 1;
        shapetype = SHAPETYPE_UNKNOWN;
        updateRefno();
        if ((parts.size() == 0) && (neurons.size() == 0)) return 0;
        if (parts.size() == 0)
                size = Pt3D_0;
        else
        {
                Pt3D bbmin = ((Part *)parts(0))->p, bbmax = bbmin;
                for (i = 0; i < parts.size(); i++)
                {
                        p = (Part *)parts(i);
                        p->owner = this;
                        if (checklevel > 0)
                                p->mass = 0.0;
                        //VALIDMINMAX(p,part,mass);//mass is very special
                        // VALIDMINMAX are managed manually when adding part properties in f0-def!
                        // (could be made dynamic but not really worth the effort)
                        VALIDMINMAX(p, Part, size);
                        VALIDMINMAX(p, Part, scale.x);
                        VALIDMINMAX(p, Part, scale.y);
                        VALIDMINMAX(p, Part, scale.z);
                        VALIDMINMAX(p, Part, hollow);
                        VALIDMINMAX(p, Part, density);
                        VALIDMINMAX(p, Part, friction);
                        VALIDMINMAX(p, Part, ingest);
                        VALIDMINMAX(p, Part, assim);
                        VALIDMINMAX(p, Part, vcolor.x);
                        VALIDMINMAX(p, Part, vcolor.y);
                        VALIDMINMAX(p, Part, vcolor.z);
                        p->flags &= ~LINKFLAG; // for delta joint cycle detection
                        if (p->p.x - p->size < bbmin.x) bbmin.x = p->p.x - p->size;
                        if (p->p.y - p->size < bbmin.y) bbmin.y = p->p.y - p->size;
                        if (p->p.z - p->size < bbmin.z) bbmin.z = p->p.z - p->size;
                        if (p->p.x + p->size > bbmax.x) bbmax.x = p->p.x + p->size;
                        if (p->p.y + p->size > bbmax.y) bbmax.y = p->p.y + p->size;
                        if (p->p.z + p->size > bbmax.z) bbmax.z = p->p.z + p->size;
                        if (shapetype == SHAPETYPE_UNKNOWN)
                                shapetype = (p->shape == Part::SHAPE_BALL) ? SHAPETYPE_BALL_AND_STICK : SHAPETYPE_SOLIDS;
                        else if (shapetype != SHAPETYPE_ILLEGAL)
                        {
                                if ((p->shape == Part::SHAPE_BALL) ^ (shapetype == SHAPETYPE_BALL_AND_STICK))
                                {
                                        shapetype = SHAPETYPE_ILLEGAL;
                                        logPrintf("Model", "internalCheck", LOG_WARN, "Inconsistent part shapes (mixed ball-and-stick and solids shape types)%s", nameForErrors().c_str());
                                }
                        }
                }
                size = bbmax - bbmin;
                for (i = 0; i < joints.size(); i++)
                {
                        j = (Joint *)joints(i);
                        // VALIDMINMAX are managed manually when adding joint properties in f0-def!
                        // (could be made dynamic but not really worth the effort)
                        VALIDMINMAX(j, Joint, stamina);
                        VALIDMINMAX(j, Joint, stif);
                        VALIDMINMAX(j, Joint, rotstif);
                        VALIDMINMAX(p, Part, vcolor.x);
                        VALIDMINMAX(p, Part, vcolor.y);
                        VALIDMINMAX(p, Part, vcolor.z);
                        j->refno = i;
                        j->owner = this;
                        if (j->part1 && j->part2 && (j->part1 != j->part2))
                        {
                                j->p1_refno = j->part1->refno;
                                j->p2_refno = j->part2->refno;
                                if (checklevel > 0)
                                {
                                        j->part1->mass += 1.0;
                                        j->part2->mass += 1.0;
                                }
                                if ((j->usedelta) && ((j->d.x != JOINT_DELTA_MARKER) || (j->d.y != JOINT_DELTA_MARKER) || (j->d.z != JOINT_DELTA_MARKER)))
                                { // delta positioning -> calc. orient.
                                        if (j->part2->flags & LINKFLAG)
                                        {
                                                ret = 0;
                                                logPrintf("Model", "internalCheck", LOG_WARN, "A cycle of \"delta Joints\" found at Joint #%d%s", i, nameForErrors().c_str());
                                        }
                                        j->resetDeltaMarkers();
                                        j->o = j->rot;
                                        j->part1->o.transform(j->part2->o, j->o);
                                        //                      j->part2->o.x=j->part1->o/j->o.x;
                                        //                      j->part2->o.y=j->part1->o/j->o.y;
                                        //                      j->part2->o.z=j->part1->o/j->o.z;
                                        j->part2->p = j->part2->o.transform(j->d) + j->part1->p;
                                        j->part2->flags |= LINKFLAG; j->part1->flags |= LINKFLAG; // for delta joint cycle detection
                                }
                                else
                                { // abs.positioning -> calc. delta
                                        if (check != EDITING_CHECK)
                                        {
                                                // calc orient delta
                                                //                      Orient tmpo(j->part2->o);
                                                //                      tmpo*=j->part1->o;
                                                Orient tmpo;
                                                j->part1->o.revTransform(tmpo, j->part2->o);
                                                tmpo.getAngles(j->rot);
                                                j->o = j->rot;
                                                // calc position delta
                                                Pt3D tmpp(j->part2->p);
                                                tmpp -= j->part1->p;
                                                j->d = j->part2->o.revTransform(tmpp);
                                        }
                                }
                                if ((check != LIVE_CHECK) && (check != CHECKPOINT_CHECK))
                                {
                                        if (j->shape == Joint::SHAPE_STICK)
                                        {
                                                if (j->d() > getMaxJoint().d.x)
                                                {
                                                        ret = 0;
                                                        logPrintf("Model", "internalCheck", LOG_WARN, "Joint #%d too long (its length %g exceeds allowed %g)%s", i, j->d(), getMaxJoint().d.x, nameForErrors().c_str());
                                                }
                                                else if (j->d() < getMinJoint().d.x)
                                                {
                                                        ret = 0;
                                                        logPrintf("Model", "internalCheck", LOG_WARN, "Joint #%d too short (its length %g is below allowed %g)%s", i, j->d(), getMinJoint().d.x, nameForErrors().c_str());
                                                }
                                        }
                                }
                        }
                        else
                        {
                                ret = 0;
                                logPrintf("Model", "internalCheck", LOG_WARN, "Illegal Part references in Joint #%d%s", i, nameForErrors().c_str());
                        }
                        if (shapetype != SHAPETYPE_ILLEGAL)
                        {
                                if ((j->shape == Joint::SHAPE_STICK) ^ (shapetype == SHAPETYPE_BALL_AND_STICK))
                                {
                                        shapetype = SHAPETYPE_ILLEGAL;
                                        logPrintf("Model", "internalCheck", LOG_WARN, "Inconsistent Joint shapes (mixed ball-and-stick and solids shape types)%s", nameForErrors().c_str());
                                }
                        }
                }
        }

        for (i = 0; i < neurons.size(); i++)
        {
                n = (Neuro *)neurons(i);
                n->part_refno = (n->part) ? n->part->refno : -1;
                n->joint_refno = (n->joint) ? n->joint->refno : -1;
        }

        if (check != CHECKPOINT_CHECK)
        {

                if (parts.size() && (checklevel > 0))
                {
                        for (i = 0; i < parts.size(); i++)
                        {
                                p = (Part *)parts(i);
                                if (p->mass <= 0.001)
                                        p->mass = 1.0;
                                p->flags &= ~LINKFLAG;
                        }
                        getPart(0)->flags |= LINKFLAG;
                        int change = 1;
                        while (change)
                        {
                                change = 0;
                                for (i = 0; i < joints.size(); i++)
                                {
                                        j = (Joint *)joints(i);
                                        if (j->part1->flags & LINKFLAG)
                                        {
                                                if (!(j->part2->flags & LINKFLAG))
                                                {
                                                        change = 1;
                                                        j->part2->flags |= LINKFLAG;
                                                }
                                        }
                                        else
                                                if (j->part2->flags & LINKFLAG)
                                                {
                                                        if (!(j->part1->flags & LINKFLAG))
                                                        {
                                                                change = 1;
                                                                j->part1->flags |= LINKFLAG;
                                                        }
                                                }
                                }
                        }
                        for (i = 0; i < parts.size(); i++)
                        {
                                p = (Part *)parts(i);
                                if (!(p->flags & LINKFLAG))
                                {
                                        ret = 0;
                                        logPrintf("Model", "internalCheck", LOG_WARN, "Not all Parts connected (e.g., Part #0 and Part #%d)%s", i, nameForErrors().c_str());
                                        break;
                                }
                        }
                }

                for (i = 0; i < joints.size(); i++)
                {
                        j = (Joint *)joints(i);
                        if (j->p1_refno == j->p2_refno)
                        {
                                ret = 0;
                                logPrintf("Model", "internalCheck", LOG_WARN, "Part #%d connected to itself using Joint #%d%s", j->p1_refno, i, nameForErrors().c_str());
                                break;
                        }
                        for (k = i + 1; k < joints.size(); k++)
                        {
                                Joint *j2 = (Joint *)joints(k);
                                if (((j->p1_refno == j2->p1_refno) && (j->p2_refno == j2->p2_refno))
                                        || ((j->p1_refno == j2->p2_refno) && (j->p2_refno == j2->p1_refno)))
                                {
                                        ret = 0;
                                        logPrintf("Model", "internalCheck", LOG_WARN, "Two parallel Joints connect the same Parts: Joint #%d and Joint #%d%s", i, k, nameForErrors().c_str());
                                        break;
                                }
                        }
                }
        }

        if (shapetype == SHAPETYPE_ILLEGAL)
                ret = 0;
        else if ((declared_shapetype != SHAPETYPE_UNKNOWN) && (declared_shapetype != shapetype))
        {
                ret = 0;
                logPrintf("Model", "internalCheck", LOG_WARN, "Model shape type '%s' does not match the declared type '%s'", getShapeTypeName(shapetype), getShapeTypeName(declared_shapetype));
        }

        return ret;
}

/////////////

int Model::getErrorPosition(bool includingwarnings)
{
        return includingwarnings ?
                ((f0errorposition >= 0) ? f0errorposition : f0warnposition)
                :
                f0errorposition;
}

const Geno &Model::getGeno() const
{
        return geno;
}

const Geno Model::getF0Geno()
{
        if (buildstatus == building)
                logPrintf("Model", "getGeno", LOG_WARN, "Model was not completed - missing close()");
        if (buildstatus != valid)
                return Geno("", '0', "", "invalid");
        if (!f0genoknown)
        {
                if (autobuildmaps)
                {
                        initF0Map();
                        makeGeno(f0geno, f0map);
                }
                else
                {
                        delF0Map();
                        makeGeno(f0geno);
                }
                f0genoknown = 1;
        }
        return f0geno;
}

int Model::getPartCount() const
{
        return parts.size();
}

Part *Model::getPart(int i) const
{
        return ((Part *)parts(i));
}

int Model::getJointCount() const
{
        return joints.size();
}

Joint *Model::getJoint(int i) const
{
        return ((Joint *)joints(i));
}

int Model::findJoints(SList &result, const Part *part)
{
        Joint *j;
        int n0 = result.size();
        if (part)
                for (int i = 0; j = (Joint *)joints(i); i++)
                        if ((j->part1 == part) || (j->part2 == part)) result += (void *)j;
        return result.size() - n0;
}

int Model::findNeuro(Neuro *n)
{
        return neurons.find(n);
}

int Model::findPart(Part *p)
{
        return parts.find(p);
}

int Model::findJoint(Joint *j)
{
        return joints.find(j);
}

int Model::findJoint(Part *p1, Part *p2)
{
        Joint *j;
        for (int i = 0; j = getJoint(i); i++)
                if ((j->part1 == p1) && (j->part2 == p2)) return i;
        return -1;
}

///////////////////////

int Model::getNeuroCount() const
{
        return neurons.size();
}

Neuro *Model::getNeuro(int i) const
{
        return (Neuro *)neurons(i);
}

int Model::getConnectionCount() const
{
        int n = 0;
        for (int i = 0; i < getNeuroCount(); i++)
                n += getNeuro(i)->getInputCount();
        return n;
}

int Model::findNeuros(SList &result,
        const char *classname, const Part *part, const Joint *joint)
{
        Neuro *nu;
        SString cn(classname);
        int n0 = result.size();
        for (int i = 0; nu = (Neuro *)neurons(i); i++)
        {
                if (part)
                        if (nu->part != part) continue;
                if (joint)
                        if (nu->joint != joint) continue;
                if (classname)
                        if (nu->getClassName() != cn) continue;
                result += (void *)nu;
        }
        return result.size() - n0;
}

///////////////////

void Model::disturb(double amount)
{
        int i;
        if (amount <= 0) return;
        for (i = 0; i < parts.size(); i++)
        {
                Part *p = getPart(i);
                p->p.x += (rndDouble(1) - 0.5) * amount;
                p->p.y += (rndDouble(1) - 0.5) * amount;
                p->p.z += (rndDouble(1) - 0.5) * amount;
        }
        for (i = 0; i < joints.size(); i++)
        {
                Joint *j = getJoint(i);
                Pt3D tmpp(j->part2->p);
                tmpp -= j->part1->p;
                j->d = j->part2->o.revTransform(tmpp);
        }
}

void Model::move(const Pt3D &shift)
{
        FOREACH(Part *, p, parts)
                p->p += shift;
}

void Model::rotate(const Orient &rotation)
{
        FOREACH(Part *, p, parts)
        {
                p->p = rotation.transform(p->p);
                p->setOrient(rotation.transform(p->o));
        }
}

void Model::buildUsingSolidShapeTypes(const Model &src_ballandstick_shapes, Part::Shape use_shape, double thickness)
{
        for (int i = 0; i < src_ballandstick_shapes.getJointCount(); i++)
        {
                Joint *oj = src_ballandstick_shapes.getJoint(i);
                Part *p = addNewPart(use_shape);
                p->p = (oj->part1->p + oj->part2->p) / 2;
                Orient o;
                o.lookAt(oj->part1->p - oj->part2->p);
                p->setRot(o.getAngles());
                p->scale.x = oj->part1->p.distanceTo(oj->part2->p) / 2;
                p->scale.y = thickness;
                p->scale.z = thickness;
        }
        if (src_ballandstick_shapes.getJointCount() == 0) //single part "ball-and-stick" models are valid so let's make a valid solid shape model
                for (int i = 0; i < src_ballandstick_shapes.getPartCount(); i++)
                {
                        Part *op = src_ballandstick_shapes.getPart(i);
                        Part *p = addNewPart(Part::SHAPE_ELLIPSOID); //always using spherical shape regardless of the 'use_shape' parameter - 'use shape' is meant for sticks!
                        p->p = op->p;
                        p->rot = op->rot;
                        p->scale.x = p->scale.y = p->scale.z = thickness;
                }
        for (int i = 0; i < src_ballandstick_shapes.getPartCount(); i++)
        {
                Part *op = src_ballandstick_shapes.getPart(i);
                for (int j = 0; j < src_ballandstick_shapes.getJointCount(); j++)
                {
                        Joint *oj = src_ballandstick_shapes.getJoint(j);
                        if ((oj->part1 == op) || (oj->part2 == op))
                        {
                                for (int j2 = j + 1; j2 < src_ballandstick_shapes.getJointCount(); j2++)
                                {
                                        Joint *oj2 = src_ballandstick_shapes.getJoint(j2);
                                        if ((oj2->part1 == op) || (oj2->part2 == op))
                                        {
                                                addNewJoint(getPart(j), getPart(j2), Joint::SHAPE_FIXED);
                                        }
                                }
                                break;
                        }
                }
        }
}

SolidsShapeTypeModel::SolidsShapeTypeModel(Model &m, Part::Shape use_shape, double thickness)
{
        using_model = converted_model = NULL;
        if (m.getShapeType() == Model::SHAPETYPE_BALL_AND_STICK)
        {
                converted_model = new Model;
                converted_model->open();
                converted_model->buildUsingSolidShapeTypes(m, use_shape, thickness);
                converted_model->close();
                using_model = converted_model;
        }
        else
        {
                converted_model = NULL;
                using_model = &m;
        }
}

//////////////////////

int Model::elementToMap(ItemType type, int index)
{
        switch (type)
        {
        case PartType: return partToMap(index);
        case JointType: return jointToMap(index);
        case NeuronType: return neuroToMap(index);
        default: return -1;
        }
}

Model::TypeAndIndex Model::mapToElement(int map_index)
{
        if ((map_index >= 0) && (map_index < MODEL_MAPPING_OFFSET))
                return TypeAndIndex(PartType, mapToPart(map_index));
        if ((map_index >= MODEL_MAPPING_OFFSET) && (map_index < 2 * MODEL_MAPPING_OFFSET))
                return TypeAndIndex(JointType, mapToJoint(map_index));
        if ((map_index >= 2 * MODEL_MAPPING_OFFSET) && (map_index < 3 * MODEL_MAPPING_OFFSET))
                return TypeAndIndex(NeuronType, mapToNeuro(map_index));
        return TypeAndIndex();
}

int Model::partToMap(int i) { return MODEL_MAPPING_OFFSET + i; }
int Model::jointToMap(int i) { return 2 * MODEL_MAPPING_OFFSET + i; }
int Model::neuroToMap(int i) { return 3 * MODEL_MAPPING_OFFSET + i; }
int Model::mapToPart(int i) { return i - MODEL_MAPPING_OFFSET; }
int Model::mapToJoint(int i) { return i - 2 * MODEL_MAPPING_OFFSET; }
int Model::mapToNeuro(int i) { return i - 3 * MODEL_MAPPING_OFFSET; }


//////////////////////

class MinPart : public Part_MinMaxDef { public: MinPart() { Param par(f0_part_paramtab, this); par.setMin(); Param par2(f0_part_minmaxdef_paramtab, this); par2.setMin(); } };
class MaxPart : public Part_MinMaxDef { public: MaxPart() { Param par(f0_part_paramtab, this); par.setMax(); Param par2(f0_part_minmaxdef_paramtab, this); par2.setMax(); } };
class MinJoint : public Joint { public: MinJoint() { Param par(f0_joint_paramtab, this); par.setMin(); } };
class MaxJoint : public Joint { public: MaxJoint() { Param par(f0_joint_paramtab, this); par.setMax(); } };
class MinNeuro : public Neuro { public: MinNeuro() { Param par(f0_neuro_paramtab, this); par.setMin(); } };
class MaxNeuro : public Neuro { public: MaxNeuro() { Param par(f0_neuro_paramtab, this); par.setMax(); } };

Part_MinMaxDef &Model::getMinPart() { static MinPart part; return part; }
Part_MinMaxDef &Model::getMaxPart() { static MaxPart part; return part; }
Part_MinMaxDef &Model::getDefPart() { static Part_MinMaxDef part; return part; }
Joint &Model::getMinJoint() { static MinJoint joint; return joint; }
Joint &Model::getMaxJoint() { static MaxJoint joint; return joint; }
Joint &Model::getDefJoint() { static Joint joint; return joint; }
Neuro &Model::getMinNeuro() { static MinNeuro neuro; return neuro; }
Neuro &Model::getMaxNeuro() { static MaxNeuro neuro; return neuro; }
Neuro &Model::getDefNeuro() { static Neuro neuro; return neuro; }