source: cpp/frams/model/model.cpp @ 644

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2015  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>

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

void Model::init()
{
        partmappingchanged = 0;
        buildstatus = empty;
        modelfromgenotype = 0;
        startenergy = 1.0;
        checklevel = 1;
#ifdef MODEL_V1_COMPATIBLE
        oldneurocount=-1; // == unknown
        oldconnections=0;
#endif
        map = 0;
        f0map = 0;
        f0genoknown = 1;
        shape = SHAPE_UNKNOWN;
}

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;
        startenergy = mod.startenergy;
        if (mod.getStatus() == valid)
        {
                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);
                        }
                }
        }
}


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

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

Model::Model(const Model &mod, bool buildmaps)
        :autobuildmaps(buildmaps)
{
        init();
        open();
        internalCopy(mod);
        buildstatus = mod.buildstatus;
}

void Model::init(const Geno &src)
{
        init();
        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();
        geno = Geno();
        f0geno = Geno();
}

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();
}

void Model::build()
{
        f0errorposition = -1;
        f0warnposition = -1;
        MultiMap *convmap = autobuildmaps ? new MultiMap() : NULL;
        f0geno = (geno.getFormat() == '0') ? geno : geno.getConverted('0', convmap);
        f0genoknown = 1;
        if (f0geno.isInvalid())
        {
                buildstatus = invalid;
                if (convmap) delete convmap;
                return;
        }
        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);
        for (; f0txt.getNextToken(pos, line, '\n'); lnum++)
        {
                if (autobuildmaps)
                {
                        frommap.clear();
                        frommap.add(lastpos, pos - 1);
                }
                mh.reset();
                if (singleStepBuild(line, lnum, autobuildmaps ? (&frommap) : 0) == -1)
                {
                        buildstatus = invalid;
                        f0errorposition = lastpos;
                        if (convmap) delete convmap;
                        return;
                }
                if (mh.getWarningCount())
                {
                        if (f0warnposition < 0) f0warnposition = lastpos;
                }
                lastpos = pos;
        }
        mh.disable();
        close();
        if (convmap)
        {
                *f0map = *map;
                if (geno.getFormat() != '0')
                {
                        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);
        return tmpgen;
}

void Model::makeGeno(Geno &g, MultiMap *map, bool handle_defaults)
{
        if ((buildstatus != valid) && (buildstatus != building))
        {
                g = Geno(0, 0, 0, "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.save2(mod_props, handle_defaults ? &defaultmodel : NULL, true, !handle_defaults);
        if (mod_props.len() > 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.len();
                gen += "p:";
                partparam.save2(gen, handle_defaults ? &defaultpart : NULL, true, !handle_defaults);
                if (map)
                        map->add(len, gen.len() - 1, partToMap(i));
        }
        for (i = 0; j = (Joint*)joints(i); i++)
        {
                jointparam.select(j);
                len = gen.len();
                jointparam.setParamTab(j->usedelta ? f0_joint_paramtab : f0_nodeltajoint_paramtab);
                gen += "j:";
                jointparam.save2(gen, handle_defaults ? &defaultjoint : NULL, true, !handle_defaults);
                if (map)
                        map->add(len, gen.len() - 1, jointToMap(i));
        }
        for (i = 0; n = (Neuro*)neurons(i); i++)
        {
                neuroparam.select(n);
                len = gen.len();
                gen += "n:";
                neuroparam.save2(gen, handle_defaults ? &defaultneuro : NULL, true, !handle_defaults);
                if (map)
                        map->add(len, gen.len() - 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.len();
                        gen += "c:";
                        connparam.save2(gen, handle_defaults ? &defaultconn : NULL, true, !handle_defaults);
                        if (map)
                                map->add(len, gen.len() - 1, neuroToMap(n->refno));
                }
        }
        g = Geno(gen.c_str(), '0');
}

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

void Model::open()
{
        if (buildstatus == building) return;
        buildstatus = building;
        modelfromgenotype = 0;
        partmappingchanged = 0;
        f0genoknown = 0;
        delMap();
}

void Model::checkpoint()
{}

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(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::singleStepBuild(const SString &singleline, const MultiRange* srcrange)
{
        return singleStepBuild(singleline, 0, srcrange);
}

int Model::singleStepBuild(const SString &singleline, int line_num, const MultiRange* srcrange)
{
        SString error_message;
        int result = singleStepBuildNoLog(singleline, error_message, srcrange);
        if (result < 0)
        {
                if (error_message.len() == 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::singleStepBuildNoLog(const SString &line, SString& error_message, const MultiRange* srcrange)
{
        error_message = SString::empty();
        int pos = 0; const char*t = line.c_str();
        for (; *t; t++, pos++)
                if (!strchr(" \r\t", *t)) break;
        if (*t == '#') return 0;
        if (!*t) return 0;
        if (!strncmp(t, "p:", 2))
        {
                Param partparam(f0_part_paramtab);
                Part *p = new Part();
                partparam.select(p);
                pos += 2;
                if (partparam.load2(line, pos) & ParamInterface::LOAD2_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;
        }
        if (!strncmp(t, "m:", 2))
        {
                Param modelparam(f0_model_paramtab);
                modelparam.select(this);
                pos += 2;
                if (modelparam.load2(line, pos) & ParamInterface::LOAD2_PARSE_FAILED) { error_message = "Invalid 'm:'"; return -1; }
                return 0;
        }
        else if (!strncmp(t, "j:", 2))
        {
                Param jointparam(f0_joint_paramtab);
                Joint *j = new Joint();
                jointparam.select(j);
                pos += 2;
                j->owner = this;
                if (jointparam.load2(line, pos) & ParamInterface::LOAD2_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;
                }
        }
        else if (!strncmp(t, "n:", 2)) // neuro (or the old neuro object as the special case)
        {
                Param neuroparam(f0_neuro_paramtab);
                Neuro *nu = new Neuro();
                neuroparam.select(nu);
                pos += 2;
                if (neuroparam.load2(line, pos) & ParamInterface::LOAD2_PARSE_FAILED) { delete nu; error_message = "Invalid 'n:'"; return -1; }
#ifdef MODEL_V1_COMPATIBLE
                if (nu->neuro_refno>=0) // parent specified...
                {
                        if (nu->neuro_refno >= getNeuroCount()) // and it's illegal
                        {
                                delete nu;
                                return -1;
                        }
                        Neuro *parentNU=getNeuro(nu->neuro_refno);
                        parentNU->addInput(nu,nu->weight);
                        // default class for parented units: n-n link
                        //if (nu->moredata.len()==0) nu->moredata="-";
                }
                else
#endif
                {
                        // default class for unparented units: standard neuron
                        if (nu->getClassName().len() == 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);
                        }
                        */
#ifdef MODEL_V1_COMPATIBLE
                nu->weight=1.0;
#endif
                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# 
#ifdef MODEL_V1_COMPATIBLE
                if (hasOldNeuroLayout())
                {
                        int count=old_getNeuroCount();
                        neurons.insert(count,nu);
                        oldneurocount=count+1;
                        return oldneurocount-1;
                }
                else
#endif
                {
                        neurons += nu;
                        return neurons.size() - 1;
                }
        }
        else if (!strncmp(t, "c:", 2)) // add input
        {
                Param ncparam(f0_neuroconn_paramtab);
                NeuroConn c;
                ncparam.select(&c);
                pos += 2;
                if (ncparam.load2(line, pos) & ParamInterface::LOAD2_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;
        }
#ifdef MODEL_V1_COMPATIBLE
        else if (!strncmp(t,"ni:",3)) // old neuroitem
        {
                // we always use old layout for "ni:"
                Param neuroitemparam(f0_neuroitem_paramtab);
                Neuro *nu=new Neuro();
                neuroitemparam.select(nu);
                pos+=3;
                if (neuroitemparam.load2(line,pos) & ParamInterface::LOAD2_PARSE_FAILED) {delete nu; return -1;}
                // illegal parent?
                if ((nu->neuro_refno<0)||(nu->neuro_refno>=old_getNeuroCount()))
                {
                        delete nu;
                        return -1;
                }
                Neuro *parentN=getNeuro(nu->neuro_refno);
                // copy part/joint refno from parent, if possible
                if ((nu->part_refno<0)&&(parentN->part_refno>=0))
                        nu->part_refno=parentN->part_refno;
                if ((nu->joint_refno<0)&&(parentN->joint_refno>=0))
                        nu->joint_refno=parentN->joint_refno;
                nu->owner=this;
                // attach to part/joint
                if (nu->part_refno>=0)
                        nu->attachToPart(nu->part_refno);
                if (nu->joint_refno>=0)
                        nu->attachToJoint(nu->joint_refno);
                if (srcrange)
                        nu->setMapping(*srcrange);
                // special case: old muscles
                // PARENT neuron will be set up to be the CHILD of the current one (!)
                if (nu->isOldEffector())
                {
                        nu->neuro_refno=parentN->refno;
                        neurons+=nu;
                        nu->owner=this;
                        nu->addInput(parentN,nu->weight); // (!)
                        nu->weight=1.0;
                        parentN->invalidateOldItems();
                        return 0; // !!! -> ...getItemCount()-1;
                }
                parentN->addInput(nu,nu->weight);
                neurons+=nu;
                parentN->invalidateOldItems();
                if (nu->getClassName().len()==0)
                {
                        nu->setClassName("-");
                        // for compatibility, "ni" can define a n-n connection
                        // referring to non-existent neuron (which will be hopefully defined later)
                        // internal check will add the proper input to this unit
                        // if conn_refno >=0 and input count==0
                        oldconnections=1;
                        if (srcrange)
                                parentN->addMapping(*srcrange);
                }
                else
                        nu->weight=1.0;
                return 0; // !!! -> ...getItemCount()-1;
        }
#endif
        else return -1;
}

#ifdef MODEL_V1_COMPATIBLE
int Model::addOldConnectionsInputs()
{
        if (!oldconnections) return 1;
        Neuro* n;
        for (int i=0;i<neurons.size();i++)
        {
                n=(Neuro*)neurons(i);
                if (n->conn_refno>=0)
                        if (n->isNNConnection())
                                if (n->conn_refno < old_getNeuroCount())
                                { // good reference
                        Neuro* parent=n->parent; // nn connection has exactly one parent
                        int inp=parent->findInput(n);
                        Neuro* target=getNeuro(n->conn_refno);
                        parent->setInput(inp,target,n->weight);
                        removeNeuro(i,0); // no need to remove references
                        i--;
                                }
                                else
                                {
                                        logPrintf("Model","internalCheck",LOG_ERROR,
                                                "illegal N-N connection #%d (reference to #%d)%s",
                                                i,n->conn_refno,nameForErrors().c_str());
                                        return 0;
                                }
        }
        oldconnections=0;
        return 1;
}
#endif

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

/** change the sequence of neuro units
        and fix references in "-" objects (n-n connections)  */
void Model::moveNeuro(int oldpos, int newpos)
{
        if (oldpos == newpos) return; // nop!
        Neuro *n = getNeuro(oldpos);
        neurons -= oldpos;
        neurons.insert(newpos, n);
        // conn_refno could be broken -> fix it
#ifdef MODEL_V1_COMPATIBLE
        for (int i=0;i<neurons.size();i++)
        {
                Neuro *n2=getNeuro(i);
                if (n2->isNNConnection())
                        if (n2->conn_refno == oldpos) n2->conn_refno=newpos;
                        else
                        { if (n2->conn_refno > oldpos) n2->conn_refno--;
                if (n2->conn_refno >= newpos) n2->conn_refno++; }
        }
        invalidateOldNeuroCount();
#endif
}

#ifdef MODEL_V1_COMPATIBLE
/** move all old neurons (class "N") to the front of the neurons list.
        @return number of old neurons
        */
int Model::reorderToOldLayout()
{
        Neuro *n;
        int neurocount=0;
        for (int i=0;i<neurons.size();i++)
        {
                n=(Neuro*)neurons(i);
                if (n->isOldNeuron())
                {
                        moveNeuro(i,neurocount);
                        neurocount++;
                        i=neurocount-1;
                }
        }
        return neurocount;
}
#endif
////////////

void Model::updateNeuroRefno()
{
        for (int i = 0; i < neurons.size(); i++)
        {
                Neuro* n = (Neuro*)neurons(i);
                n->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

void Model::updateRefno()
{
        int i;
        for (i = 0; i < getPartCount(); i++) getPart(i)->refno = i;
        for (i = 0; i < getJointCount(); i++) getJoint(i)->refno = i;
        for (i = 0; i < getNeuroCount(); i++) getNeuro(i)->refno = i;
}

SString Model::nameForErrors() const
{
        if (geno.getName().len()>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;
        shape = SHAPE_UNKNOWN;
        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;
                        p->refno = i;
                        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, vsize);
                        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 (shape == SHAPE_UNKNOWN)
                                shape = (p->shape == Part::SHAPE_BALL_AND_STICK) ? SHAPE_BALL_AND_STICK : SHAPE_SOLIDS;
                        else if (shape != SHAPE_ILLEGAL)
                        {
                                if ((p->shape == Part::SHAPE_BALL_AND_STICK) ^ (shape == SHAPE_BALL_AND_STICK))
                                {
                                        shape = SHAPE_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_ERROR,
                                                        "Delta joint cycle detected 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)
                                {
                                        if (j->shape != Joint::SHAPE_FIXED)
                                        {
                                                if (j->d() > getMaxJoint().d.x)
                                                {
                                                        ret = 0;
                                                        logPrintf("Model", "internalCheck", LOG_ERROR, "Joint #%d too long (its length %g exceeds allowed %g)%s", i, j->d(), getMaxJoint().d.x, nameForErrors().c_str());
                                                }
                                        }
                                }
                        }
                        else
                        {
                                logPrintf("Model", "internalCheck", LOG_ERROR, "Illegal part references in Joint #%d%s", i, nameForErrors().c_str());
                                ret = 0;
                        }
                        if (shape != SHAPE_ILLEGAL)
                        {
                                if ((j->shape == Joint::SHAPE_BALL_AND_STICK) ^ (shape == SHAPE_BALL_AND_STICK))
                                {
                                        shape = SHAPE_ILLEGAL;
                                        logPrintf("Model", "internalCheck", LOG_WARN, "Inconsistent joint shapes (mixed old and new shapes)%s", nameForErrors().c_str());
                                }
                        }
                }
        }
#ifdef MODEL_V1_COMPATIBLE
        if (!addOldConnectionsInputs())
                return 0;
#endif

        updateNeuroRefno(); // valid refno is important for n-n connections check (later)

        for (i = 0; i < neurons.size(); i++)
        {
                n = (Neuro*)neurons(i);
#ifdef MODEL_V1_COMPATIBLE
                VALIDMINMAX(n,Neuro,inertia);
                VALIDMINMAX(n,Neuro,force);
                VALIDMINMAX(n,Neuro,sigmo);
                n->conn_refno=-1;
                n->weight=1.0;
                n->neuro_refno=-1;
#endif
                n->part_refno = (n->part) ? n->part->refno : -1;
                n->joint_refno = (n->joint) ? n->joint->refno : -1;
        }

        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))
                        {
                                logPrintf("Model", "internalCheck", LOG_ERROR, "Not all parts connected (eg. Part #0 and Part #%d)%s", i, nameForErrors().c_str());
                                ret = 0;
                                break;
                        }
                }
        }

        for (i = 0; i < joints.size(); i++)
        {
                j = (Joint*)joints(i);
                if (j->p1_refno == j->p2_refno)
                {
                        logPrintf("Model", "internalCheck", LOG_ERROR, "Illegal self connection, Joint #%d%s", i, nameForErrors().c_str());
                        ret = 0;
                        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)))
                        {
                                logPrintf("Model", "internalCheck", LOG_ERROR, "Illegal duplicate Joint #%d and Joint #%d%s", i, k, nameForErrors().c_str());
                                ret = 0;
                                break;
                        }
                }
        }
        if (shape == SHAPE_ILLEGAL)
                ret = 0;
        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;
}


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

#ifdef MODEL_V1_COMPATIBLE
void Model::calcOldNeuroCount()
{
        if (oldneurocount>=0) return;
        oldneurocount=reorderToOldLayout();
}

int Model::old_getNeuroCount()
{ calcOldNeuroCount();
return oldneurocount;}

Neuro* Model::old_getNeuro(int i) 
{calcOldNeuroCount();
return (i<oldneurocount)? (Neuro*)getNeuro(i) : (Neuro*)0;
}

int Model::old_findNeuro(Neuro* n)
{calcOldNeuroCount();
return findNeuro(n);}

Neuro *Model::old_addNewNeuro()
{
        int count=old_getNeuroCount();
        Neuro *nu=addNewNeuro();
        nu->setClassName("N");
        moveNeuro(nu->refno,oldneurocount);
        oldneurocount=count+1;
        return (Neuro*)nu;
}
#endif

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

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 += (rnd01 - 0.5)*amount;
                p->p.y += (rnd01 - 0.5)*amount;
                p->p.z += (rnd01 - 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, float 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->rot = o.getAngles();
                p->scale.x = oj->part1->p.distanceTo(oj->part2->p) / 2;
                p->scale.y = thickness;
                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(const Model& m, Part::Shape use_shape, float thickness)
{
        using_model = converted_model = NULL;
        if (m.getShapeType() == Model::SHAPE_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;
        }
}

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

class MinPart : public Part { public: MinPart() { Param par(f0_part_paramtab, this); par.setMin(); } };
class MaxPart : public Part { public: MaxPart() { Param par(f0_part_paramtab, this); par.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& Model::getMinPart() { static MinPart part; return part; }
Part& Model::getMaxPart() { static MaxPart part; return part; }
Part& Model::getDefPart() { static Part 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; }