source: cpp/frams/genetics/fH/fH_general.cpp @ 780

#include <string>
#include <limits>
#include <algorithm>
#include <frams/util/multirange.h>
#include <utility>
#include "fH_general.h"

using namespace std;
#undef max //this macro is not needed here and it clashes with numeric_limits<>::max()



// Methods for loading handles

const char *fH_part_names[PART_PROPS_COUNT] = { "dn", "fr", "ing", "as" };

const char *fH_joint_names[JOINT_PROPS_COUNT] = { "stif", "rotstif", "stam" };

void fH_Handle::loadProperties(Param par)
{
        // loading values for vectors
        for (int i = 0; i < dimensions; i++)
        {
                first[i] = par.getDouble(i);
                second[i] = par.getDouble(dimensions + i);
        }
        obj = par.getSelected();
}

void fH_Builder::addHandle(fH_Handle *handle)
{
        switch (handle->type)
        {
        case fHBodyType::JOINT:
                sticks.push_back((fH_StickHandle*)handle);
                break;
        case fHBodyType::NEURON:
                neurons.push_back((fH_NeuronHandle*)handle);
                break;
        case fHBodyType::CONNECTION:
                connections.push_back((fH_ConnectionHandle*)handle);
                break;
        }
}

// Methods for saving properties of handles in params

void fH_Handle::saveProperties(Param &par)
{
        par.select(obj);
        for (int i = 0; i < dimensions; i++)
        {
                par.setDouble(i, first[i]);
                par.setDouble(dimensions + i, second[i]);
        }
}

// Destructor of Builder

fH_Builder::~fH_Builder()
{
        for (fH_StickHandle *obj : sticks)
        {
                delete obj;
        }
        sticks.clear();
        for (fH_NeuronHandle *obj : neurons)
        {
                delete obj;
        }
        neurons.clear();
        for (fH_ConnectionHandle *obj : connections)
        {
                delete obj;
        }
        connections.clear();

        if (stickparamtab) ParamObject::freeParamTab(stickparamtab);
        if (neuronparamtab) ParamObject::freeParamTab(neuronparamtab);
        if (connectionparamtab) ParamObject::freeParamTab(connectionparamtab);

}

// Methods for parsing genotype

void fH_Builder::prepareParams()
{
        for (int i = 0; i < dimensions; i++) // preparing first vector fields
        {
                string x = "x";
                x += to_string(i);
                stickmut.addProperty(NULL, x.c_str(), HANDLE_VECTOR_TYPE, x.c_str(), "", PARAM_CANOMITNAME, 0, -1);
                neuronmut.addProperty(NULL, x.c_str(), HANDLE_VECTOR_TYPE, x.c_str(), "", PARAM_CANOMITNAME, 0, -1);
                connectionmut.addProperty(NULL, x.c_str(), HANDLE_VECTOR_TYPE, x.c_str(), "", PARAM_CANOMITNAME, 0, -1);

        }
        for (int i = 0; i < dimensions; i++) // preparing second vector fields
        {
                string y = "y";
                y += to_string(i);
                stickmut.addProperty(NULL, y.c_str(), HANDLE_VECTOR_TYPE, y.c_str(), "", PARAM_CANOMITNAME, 0, -1);
                neuronmut.addProperty(NULL, y.c_str(), HANDLE_VECTOR_TYPE, y.c_str(), "", PARAM_CANOMITNAME, 0, -1);
                connectionmut.addProperty(NULL, y.c_str(), HANDLE_VECTOR_TYPE, y.c_str(), "", PARAM_CANOMITNAME, 0, -1);

        }

        Part p;
        for (int i = 0; i < PART_PROPS_COUNT; i++)
        {
                stickmut.addProperty(&p.properties().getParamTab()[p.properties().findId(fH_part_names[i]) + p.properties().getGroupCount()], -1);
        }

        Joint j;
        for (int i = 0; i < JOINT_PROPS_COUNT; i++)
        {
                stickmut.addProperty(&j.properties().getParamTab()[j.properties().findId(fH_joint_names[i]) + j.properties().getGroupCount()], -1);
        }
        stickmut.addProperty(NULL, "l", STICKH_LENGTH_TYPE, "length", "", 0, 0, -1);

        Neuro n;
        neuronmut.addProperty(&n.properties().getParamTab()[n.properties().findId(PE_NEURO_DET) + n.properties().getGroupCount()], -1);

        Param tmp(f0_neuroconn_paramtab, NULL);
        connectionmut.addProperty(&tmp.getParamTab()[tmp.findId(PE_CONN_WEIGHT) + tmp.getGroupCount()], -1);

        stickparamtab = ParamObject::makeParamTab((ParamInterface *)&stickmut, 0, 0, stickmut.firstMutableIndex());
        neuronparamtab = ParamObject::makeParamTab((ParamInterface *)&neuronmut, 0, 0, neuronmut.firstMutableIndex());
        connectionparamtab = ParamObject::makeParamTab((ParamInterface *)&connectionmut, 0, 0, connectionmut.firstMutableIndex());
}

int fH_Builder::processLine(SString line, int linenumber, int begin, int end)
{
        // Firstly, method determines if line describes joint, neuron or neural connection
        // and prepares corresponding ParamTab
        fH_Handle *handle = NULL;
        ParamEntry *tab = NULL;
        if (line.startsWith("j:")) //joint
        {
                handle = new fH_StickHandle(dimensions, begin, end);
                tab = stickparamtab;
        }
        else if (line.startsWith("n:")) //neuron
        {
                handle = new fH_NeuronHandle(dimensions, begin, end);
                tab = neuronparamtab;
        }
        else if (line.startsWith("c:")) //connection
        {
                handle = new fH_ConnectionHandle(dimensions, begin, end);
                tab = connectionparamtab;
        }
        else // could not determine type of a handle
        {
                string message = "Cannot determine handle type at line:  " + to_string(linenumber);
                logMessage("fH_Builder", "processLine", LOG_ERROR, message.c_str());
                return begin;
        }
        line = line.substr(2); // skip of "j:", "c:" or "n:"

        // Secondly, ParamObject for holding handle properties is created
        void *obj = ParamObject::makeObject(tab);
        Param par(tab, obj);
        par.setDefault();
        ParamInterface::LoadOptions opts;

        // After preparing Param objects, vector values and body properties are parsed
        par.load(ParamInterface::FormatSingleLine, line, &opts);

        // If parsing failed, method writes error message and ends processing
        if (opts.parse_failed)
        {
                string message = "Error in parsing handle parameters at line:  " + to_string(linenumber);
                logMessage("fH_Builder", "processLine", LOG_ERROR, message.c_str());
                delete handle;
                ParamObject::freeObject(obj);
                return begin;
        }

        // If parsing ended successfully, parsed properties are loaded into handle fields
        handle->loadProperties(par);

        // In the end, ready handle is stored in an appropriate vector
        addHandle(handle);
        return 0;
}

int fH_Builder::parseGenotype(SString genotype)
{
        // Firstly, number of dimensions is parsed
        int pos = 0;
        SString numdimensions;
        genotype.getNextToken(pos, numdimensions, '\n');
        if (!ExtValue::parseInt(numdimensions.c_str(), dimensions, true, false))
        {
                logMessage("fH_Builder", "parseGenotype", LOG_ERROR, "Could not parse number of dimensions");
                return 1;
        }
        if (dimensions < 1)
        {
                logMessage("fH_Builder", "parseGenotype", LOG_ERROR, "Number of dimensions cannot be lower than 1");
                return 1;
        }
        SString line;
        int linenumber = 2;

        // With known number of dimensions ParamTabs for handles are prepared
        prepareParams();

        // After preparing Builder for parsing, each line is processed with processLine
        int lastpos = pos;
        while (genotype.getNextToken(pos, line, '\n'))
        {
                if (line.len() > 0)
                {
                        int res = processLine(line, linenumber, lastpos, pos - 1);
                        if (res != 0)
                        {
                                return res;
                        }
                }
                lastpos = pos;
                linenumber++;
        }
        if (sticks.size() == 0)
        {
                logMessage("fH_Builder", "parseGenotype", LOG_ERROR, "Genotype does not contain any stick");
                return 1;
        }
        return 0;
}

// Distance calculations

double fH_Handle::dist(vector<double> left, vector<double> right)
{
        double sum = 0;
        for (unsigned int i = 0; i < left.size(); i++)
        {
                sum += (left[i] - right[i]) * (left[i] - right[i]);
        }
        return sqrt(sum);
}

vector<double> fH_Handle::getVectorsAverage()
{
        vector<double> result(dimensions, 0);
        for (int i = 0; i < dimensions; i++)
        {
                result[i] = (first[i] + second[i]) / 2;
        }
        return result;
}

double fH_StickHandle::distance(fH_Handle *right)
{
        double distance = 0;
        switch (right->type)
        {
        case fHBodyType::JOINT:
                // distance is computed between second vector of current handle and first
                // vector of second handle
                distance = dist(second, right->first);
                break;
        case fHBodyType::NEURON:
        {
                // if neuron has to be connected to joint, then distance is calculated
                // between averages of both handles
                vector<double> avgs = getVectorsAverage();
                vector<double> avgn = right->getVectorsAverage();
                distance = dist(avgs, avgn);
                break;
        }
        case fHBodyType::CONNECTION:
                // it is impossible to calculate distance between Joint and Connection
                return numeric_limits<double>::quiet_NaN();
        }
        return distance;
}

double fH_NeuronHandle::distance(fH_Handle *right)
{
        double distance = 0;
        switch (right->type)
        {
        case fHBodyType::JOINT:
        {
                // if neuron has to be connected to joint, then distance is calculated
                // between averages of both handles
                vector<double> avgs = right->getVectorsAverage();
                vector<double> avgn = getVectorsAverage();
                distance = dist(avgs, avgn);
                break;
        }
        case fHBodyType::CONNECTION:
                // this calculation is meant for input neuron - it compares second vector
                // of neuron and first vector of connection
                distance = dist(second, right->first);
                break;
        case fHBodyType::NEURON:
                // it is impossible to calculate distance between two Neurons
                return numeric_limits<double>::quiet_NaN();
        }
        return distance;
}

double fH_NeuronHandle::distance(fH_StickHandle *right, bool first)
{
        vector<double> avgn = getVectorsAverage();
        double distance = 0;
        if (first)
        {
                distance = dist(avgn, right->firstparthandle);
        }
        else
        {
                distance = dist(avgn, right->secondparthandle);
        }
        return distance;
}

double fH_ConnectionHandle::distance(fH_Handle *right)
{
        double distance = 0;
        switch (right->type)
        {
        case fHBodyType::NEURON:
                // this calculation is meant for output neuron - it compares second vector
                // of connection and first vector of neuron
                distance = dist(second, right->first);
                break;
        case fHBodyType::JOINT:
        case fHBodyType::CONNECTION:
                // it is impossible to calculate distance between Connection and other
                // Connection or Joint
                return numeric_limits<double>::quiet_NaN();
        }
        return distance;
}

// Creature build functions

Part * fH_StickHandle::createPart(ParamEntry *tab, std::vector<fH_StickHandle *> children, Model *model, bool createmapping)
{
        Param par(tab, obj);
        double partprops[PART_PROPS_COUNT];
        for (int i = 0; i < PART_PROPS_COUNT; i++)
        {
                partprops[i] = par.getDouble(2 * getDimensions() + i);
        }

        unsigned int stickscount = children.size() + 1;

        MultiRange ranges;
        ranges.add(begin, end);

        for (fH_StickHandle *child : children)
        {
                par.select(child->obj);
                for (int i = 0; i < PART_PROPS_COUNT; i++)
                {
                        partprops[i] += par.getDouble(2 * getDimensions() + i);
                }
                ranges.add(child->begin, child->end);
        }

        for (int i = 0; i < PART_PROPS_COUNT; i++)
        {
                partprops[i] /= stickscount;
        }

        Part *newpart = new Part();

        model->addPart(newpart);

        newpart->density = partprops[0];
        newpart->friction = partprops[1];
        newpart->ingest = partprops[2];
        newpart->assim = partprops[3];

        if (createmapping) newpart->addMapping(ranges);

        return newpart;
}

Joint* fH_StickHandle::createJoint(ParamEntry *tab, Model *model, bool createmapping)
{
        Param par(tab, obj);
        if (firstpart == NULL || secondpart == NULL)
        {
                return NULL;
        }
        Joint *newjoint = new Joint();

        model->addJoint(newjoint);

        newjoint->stif = par.getDoubleById("stif");
        newjoint->rotstif = par.getDoubleById("rotstif");
        newjoint->stamina = par.getDoubleById("stam");
        newjoint->attachToParts(firstpart, secondpart);
        if (createmapping) newjoint->addMapping(IRange(begin, end));
        return newjoint;
}

void fH_Builder::buildBody()
{
        // stickconnections vector holds information about connections between sticks.
        // Left side of pair should hold pointer to stick that is connected with second
        // vector, and right side of pair should hold pointer to stick that is connected
        // with first vector
        stickconnections.clear();

        // if body consists of single stick, just add it to body
        if (sticks.size() == 1)
        {
                stickconnections.push_back(pair<fH_StickHandle *, fH_StickHandle *>(NULL, sticks[0]));
                sticksorder.push_back(0);
                return;
        }

        vector<bool> remainingsticks(sticks.size(), true);

        // first we find two handles that have minimal distances between their second
        // and first vector
        fH_StickHandle *left = sticks[0];
        fH_StickHandle *right = sticks[1];
        double mindist = left->distance(right);
        int leftid = 0;
        int rightid = 1;
        for (unsigned int i = 0; i < sticks.size(); i++)
        {
                for (unsigned int j = i + 1; j < sticks.size(); j++)
                {
                        double distance = sticks[i]->distance(sticks[j]);
                        if (distance < mindist)
                        {
                                mindist = distance;
                                left = sticks[i];
                                right = sticks[j];
                                leftid = i;
                                rightid = j;
                        }
                        distance = sticks[j]->distance(sticks[i]);
                        if (distance < mindist)
                        {
                                mindist = distance;
                                left = sticks[j];
                                right = sticks[i];
                                leftid = j;
                                rightid = i;
                        }
                }
        }

        // two found handles are the beginning of creature body
        stickconnections.push_back(pair<fH_StickHandle *, fH_StickHandle *>(NULL, left));
        stickconnections.push_back(pair<fH_StickHandle *, fH_StickHandle *>(left, right));

        // after selecting two handles as beginning of body, they are marked as used
        // in the list of remaining sticks
        remainingsticks[leftid] = false;
        remainingsticks[rightid] = false;

        sticksorder.push_back(leftid);
        sticksorder.push_back(rightid);

        // next stick is selected by minimum distance between first vector of its handle
        // and second vector of any existing StickHandle in body
        int remaining = sticks.size() - 2;
        while (remaining > 0)
        {
                leftid = -1;
                rightid = -1;
                mindist = numeric_limits<double>::max();
                for (unsigned int i = 0; i < sticks.size(); i++)
                {
                        // if stick is not already in
                        if (remainingsticks[i])
                        {
                                for (int stickid : sticksorder)
                                {
                                        double distance = sticks[stickid]->distance(sticks[i]);
                                        if (distance < mindist)
                                        {
                                                mindist = distance;
                                                leftid = stickid;
                                                rightid = i;
                                        }
                                }
                        }
                }
                stickconnections.push_back(pair<fH_StickHandle *, fH_StickHandle *>(sticks[leftid], sticks[rightid]));
                remainingsticks[rightid] = false;
                sticksorder.push_back(rightid);
                remaining--;
        }
}

int fH_Builder::developBrain(Model *model, bool createmapping)
{
        Param par(neuronparamtab, NULL);
        // First of all, neurons are attached to body
        for (fH_NeuronHandle *currneu : neurons)
        {
                par.select(currneu->obj);
                // create Neuro object and set details
                currneu->neuron = new Neuro();
                SString det = par.getStringById("d");
                if (det != "")
                {
                        currneu->neuron->setDetails(det);
                }
                else
                {
                        currneu->neuron->setDetails("N");
                }

                // get class of neuron. If class with given name does not exist - return error
                NeuroClass *nclass = currneu->neuron->getClass();
                if (!nclass)
                {
                        SString msg = "NeuroClass given in details \"";
                        msg += det + "\" does not exist";
                        logMessage("fH_Builder", "developBrain", LOG_ERROR, msg.c_str());
                        return -1;
                }
                // add neuron to model -> required before attaching to body part
                model->addNeuro(currneu->neuron);
                if (nclass->getPreferredLocation() == 2) // attach to Joint
                {
                        // find stick that has closest average handle to average handle of
                        // neuron
                        double mindist = currneu->distance(sticks[0]);
                        fH_StickHandle *minstick = sticks[0];
                        for (unsigned int i = 1; i < sticks.size(); i++)
                        {
                                double distance = currneu->distance(sticks[i]);
                                if (distance < mindist)
                                {
                                        mindist = distance;
                                        minstick = sticks[i];
                                }
                        }
                        currneu->neuron->attachToJoint(minstick->joint);
                }
                else if (nclass->getPreferredLocation() == 1) // attach to Part
                {
                        // in the beginning we take first part of first stick to calculate
                        // distance between them as initial minimal distance
                        double mindist = currneu->distance(sticks[0], true);
                        Part *minpart = sticks[0]->firstpart;
                        for (unsigned int i = 0; i < sticks.size(); i++)
                        {
                                // after this we take only second parts of following sticks to
                                // avoid repetition (thats why we start from i = 0)
                                double distance = currneu->distance(sticks[i], false);
                                if (distance < mindist)
                                {
                                        mindist = distance;
                                        minpart = sticks[i]->secondpart;
                                }
                        }
                        currneu->neuron->attachToPart(minpart);
                }
                if (createmapping) currneu->neuron->addMapping(IRange(currneu->begin, currneu->end));
                model->checkpoint();
        }

        par.setParamTab(connectionparamtab);
        // Secondly, connections are created
        for (fH_ConnectionHandle *currcon : connections)
        {
                par.select(currcon->obj);
                // Connection is created as follows:
                //   beginneu ---> endneu
                // distance between beginneu and connection is calculated as distance
                // between second handle of beginneu and first handle of connection.
                // This is why calculation is written as beginneu->distance(currcon).
                // In case of connection and endneu distance between them is calculated
                // as distance between second handle of connection and first handle of
                // endneu. This is why calculation is written as currcon->distance(endneu).

                fH_NeuronHandle *beginneu = NULL;
                double mindist = numeric_limits<double>::max();
                // find beginning of connection
                for (fH_NeuronHandle *neuron : neurons)
                {
                        // These method checked earlier if all neurons have valid classes.
                        // If a neuron does not have output, then it's skipped from comparison.
                        // Otherwise:
                        if (neuron->neuron->getClass()->getPreferredOutput() > 0)
                        {
                                double distance = neuron->distance(currcon);
                                if (distance < mindist)
                                {
                                        mindist = distance;
                                        beginneu = neuron;
                                }
                        }
                }
                // if there was no neuron that could begin connection, then return warning
                if (!beginneu)
                {
                        logMessage("fH_Builder", "developBrain", LOG_WARN, "There are no available neurons with outputs, connection could not be established");
                        continue;
                }

                fH_NeuronHandle *endneu = NULL;
                mindist = numeric_limits<double>::max();
                // find ending of connection
                for (fH_NeuronHandle *neuron : neurons)
                {
                        // Method checked earlier if all neurons have valid classes.
                        // If neuron does not accept input or all inputs are already connected,
                        // then it's skipped from comparison.
                        // Otherwise:
                        if (neuron->neuron->getClass()->getPreferredInputs() == -1 ||
                                neuron->neuron->getClass()->getPreferredInputs() > neuron->neuron->getInputCount())
                        {
                                double distance = currcon->distance(neuron);
                                if (distance < mindist)
                                {
                                        mindist = distance;
                                        endneu = neuron;
                                }
                        }
                }
                // if there was no neuron that could end connection, then return warning
                if (!endneu)
                {
                        logMessage("fH_Builder", "developBrain", LOG_WARN, "There are no available neurons with free inputs, connection could not be established");
                        continue;
                }
                endneu->neuron->addInput(beginneu->neuron, par.getDoubleById("w"));
                if (createmapping) endneu->neuron->addMapping(IRange(currcon->begin, currcon->end));
                model->checkpoint();
        }
        return 0;
}

Pt3D fH_Builder::getNextDirection(int count, int number)
{
        // In order to get evenly distributed sticks coming from the same Part method
        // uses algorithm for even distribution of points on a sphere. There are several
        // methods to perform this, usually they are iterative. This method introduced
        // below offers not fully accurate, yet quite satisfying results. This is
        // RSZ method (Rakhmanov, Saff and Zhou method), with use of the golden angle.
        // This method is based on distribution of points along spiral that covers sphere
        // surface.

        // Following method works partially on spherical coordinates (r and theta is used).
        // The Z coordinate is from Cartesian coordinate system. The golden angle is used
        // to "iterate" along spiral, while Z coordinate is used to move down the
        // sphere.

        double golden_angle = M_PI * (3.0 - sqrt(5));
        double dz = 2.0 / (double)count;
        double z = 1 - ((double)number + 0.5) * dz;
        double r = sqrt(1 - z * z);
        double theta = golden_angle * number;
        Pt3D vec;
        // In the end X and Y coordinates are calculated with current values of
        // r and theta. Value z is already calculated
        vec.x = r * cos(theta);
        vec.y = r * sin(theta);
        vec.z = z;
        vec.normalize();
        return vec;
}

Orient fH_Builder::getRotationMatrixToFitVector(Pt3D currdir, Pt3D expecteddir)
{
        Orient res;
        // first method normalizes vectors for easy calculations
        currdir.normalize();
        expecteddir.normalize();
        double c = currdir.dotProduct(expecteddir); // dot product of both vectors
        // if the dot product of both vectors equals 0
        if (c == 0)
        {
                res.x.x = -1;
                res.x.y = 0;
                res.x.z = 0;

                res.y.x = 0;
                res.y.y = -1;
                res.y.z = 0;

                res.z.x = 0;
                res.z.y = 0;
                res.z.z = -1;
        }
        Pt3D v = Pt3D(0); // cross product of both vectors
        v.x = currdir.y * expecteddir.z - currdir.z * expecteddir.y;
        v.y = currdir.z * expecteddir.x - currdir.x * expecteddir.z;
        v.z = currdir.x * expecteddir.y - currdir.y * expecteddir.x;

        // Rotation matrix that enables aligning currdir to expecteddir comes from
        // following calculation
        // R = I + [v]_x + ([v]_x)^2 / (1+c)
        // where [v]_x is the skew-symmetric cross-product matrix of v
        res.x.x = 1 - (v.y * v.y + v.z * v.z) / (1 + c);
        res.x.y = v.z + (v.x * v.y) / (1 + c);
        res.x.z = -v.y + (v.x * v.z) / (1 + c);
        res.y.x = -v.z + (v.x * v.y) / (1 + c);
        res.y.y = 1 - (v.x * v.x + v.z * v.z) / (1 + c);
        res.y.z = v.x + (v.y * v.z) / (1 + c);
        res.z.x = v.y + (v.x * v.z) / (1 + c);
        res.z.y = -v.x + (v.y * v.z) / (1 + c);
        res.z.z = 1 - (v.x * v.x + v.y * v.y) / (1 + c);

        return res;
}

Model* fH_Builder::buildModel(bool using_checkpoints)
{
        Model *model = new Model();

        // At first, floating sticks are connected
        buildBody();

        model->open(using_checkpoints);

        // Secondly, parts and joints are created
        // For every stick in body, starting with initial
        Param par(stickparamtab, NULL);
        for (int currid : sticksorder)
        {
                fH_StickHandle *currstick = sticks[currid];
                fH_StickHandle *parent = NULL;
                // find parent of current stick - it is first element of pair, in which
                // current stick is second
                for (pair<fH_StickHandle *, fH_StickHandle *> conn : stickconnections)
                {
                        if (conn.second == currstick)
                        {
                                parent = conn.first;
                                break;
                        }
                }

                // if parent is NULL, then create Part with current stick properties and
                // location at (0,0,0)
                if (!parent)
                {
                        vector<fH_StickHandle *> emptylist;
                        Part *firstpart = currstick->createPart(stickparamtab, emptylist, model, createmapping);
                        firstpart->p = Pt3D(0);
                        currstick->firstpart = firstpart;
                        currstick->firstparthandle = currstick->first; // this is used to calculate later distance between
                        model->checkpoint();
                }
                else //otherwise first part of current stick is the second part of previous stick
                {
                        currstick->firstpart = parent->secondpart;
                        currstick->firstparthandle = parent->secondparthandle;
                }
                // position of second part depends on two things
                //  1. direction of previous joint
                //  2. how many sticks are connected to the same parent
                // default direction of growth (without parent) is (1,0,0)
                Pt3D direction(1, 0, 0);
                Pt3D secondposition(currstick->firstpart->p);
                // if parent does exist, then determine how many sticks are connected to
                // parent and distribute them evenly on a sphere surrounding second part
                if (parent)
                {
                        // improved RSZ method creates vectors that starts in
                        // center of sphere (which will act as shared part), so direction
                        // calculated below should point from shared part to previous part
                        // in order to perform proper aligning
                        direction = parent->secondpart->p - parent->firstpart->p;
                        direction.normalize();
                        // determine how many sticks are connected to parent and when connection
                        // between parent and current stick appear
                        int count = 0;
                        int id = -1;
                        for (unsigned int i = 0; i < stickconnections.size(); i++)
                        {
                                if (stickconnections[i].first == parent)
                                {
                                        if (stickconnections[i].second == currstick)
                                        {
                                                id = count;
                                        }
                                        count++;
                                }
                        }
                        if (id == -1)
                        {
                                logMessage("fH_Builder", "buildModel", LOG_ERROR, "Invalid behaviour");
                                delete model;
                                return NULL;
                        }

                        // if there is only one child, then don't change direction - continue
                        // along axis of parent. Otherwise calculate direction of id-th stick
                        // (that is currstick) with use of RSZ/Vogel method of distributing points
                        // evenly on a sphere
                        if (count > 1)
                        {
                                direction = parent->firstpart->p - parent->secondpart->p;
                                direction.normalize();
                                // there has to be count+1 directions, so method needs to generate
                                // count+1 evenly distributed points on a sphere to make vectors
                                // from point (0,0,0) to those points. First generated vector
                                // will act as parent joint direction vector
                                Pt3D sphere0direction = getNextDirection(count + 1, 0);

                                // First generated vector needs to be aligned to parent vector
                                Orient rotmatrix = getRotationMatrixToFitVector(sphere0direction, direction);

                                // Calculation of direction from sphere for currstick
                                direction = getNextDirection(count + 1, id + 1);
                                // Rotation matrix aligning
                                direction = rotmatrix.transform(direction);
                                direction.normalize();
                        }
                }

                // calculate second position
                par.select(currstick->obj);
                secondposition += direction * par.getDoubleById("l");

                // find every stick connected to current stick in order to calculate second
                // part properties
                vector<fH_StickHandle *> children;
                currstick->secondparthandle = currstick->second;
                for (pair<fH_StickHandle *, fH_StickHandle *> conn : stickconnections)
                {
                        if (conn.first == currstick)
                        {
                                children.push_back(conn.second);
                                for (int i = 0; i < dimensions; i++)
                                {
                                        currstick->secondparthandle[i] += conn.second->first[i];
                                }
                        }
                }
                // create part from current stick and other sticks connected to this part
                Part *secondpart = currstick->createPart(stickparamtab, children, model, createmapping);
                secondpart->p = secondposition;
                currstick->secondpart = secondpart;
                double count = (double)children.size() + 1;
                for (int i = 0; i < dimensions; i++)
                {
                        currstick->secondparthandle[i] /= count;
                }

                //after creating second part connect two parts with joint
                Joint * joint = currstick->createJoint(stickparamtab, model, createmapping);
                if (!joint)
                {
                        logMessage("fH_Builder", "buildModel", LOG_ERROR, "Joint cannot be created");
                        delete model;
                        return NULL;

                }
                currstick->joint = joint;
                model->checkpoint();
        }
        // after creating a body, attach neurons to body and link them according to
        // connections
        if (developBrain(model, createmapping) == -1)
        {
                delete model;
                return NULL;
        }
        model->close();
        return model;
}

int fH_Builder::removeNeuronsWithInvalidClasses()
{
        int count = neurons.size();
        if (count == 0)
        {
                return 0;
        }
        vector<fH_NeuronHandle *>::iterator it = neurons.begin();
        Param par(neuronparamtab, NULL);
        while (it != neurons.end())
        {
                par.select((*it)->obj);
                SString det = par.getStringById("d");
                if (det == "")
                {
                        it++;
                }
                else
                {
                        Neuro *neu = new Neuro();
                        neu->setDetails(det);
                        if (neu->getClass())
                        {
                                it++;
                        }
                        else
                        {
                                fH_NeuronHandle *tmp = (*it);
                                it = neurons.erase(it);
                                delete tmp;
                        }
                        delete neu;
                }

        }
        return count - neurons.size();
}

SString fH_Builder::toString()
{
        SString result = "";
        result += to_string(dimensions).c_str();
        result += "\n";
        // first method stringifies parts
        Param par(stickparamtab, NULL);
        void *def = ParamObject::makeObject(stickparamtab);
        par.select(def);
        par.setDefault();
        for (fH_StickHandle *currstick : sticks)
        {
                currstick->saveProperties(par);
                SString props;
                par.saveSingleLine(props, def, true, false);
                result += "j:";
                result += props;
        }
        ParamObject::freeObject(def);
        par.setParamTab(neuronparamtab);
        def = ParamObject::makeObject(neuronparamtab);
        par.select(def);
        par.setDefault();
        for (fH_NeuronHandle *currneuron : neurons)
        {
                currneuron->saveProperties(par);
                SString props;
                par.saveSingleLine(props, def, true, false);
                result += "n:";
                result += props;
        }
        ParamObject::freeObject(def);
        par.setParamTab(connectionparamtab);
        def = ParamObject::makeObject(connectionparamtab);
        par.select(def);
        par.setDefault();
        for (fH_ConnectionHandle *currconnection : connections)
        {
                currconnection->saveProperties(par);
                SString props;
                par.saveSingleLine(props, def, true, false);
                result += "c:";
                result += props;
        }
        ParamObject::freeObject(def);
        return result;
}

ParamEntry* fH_Builder::getParamTab(fHBodyType type)
{
        switch (type)
        {
        case fHBodyType::JOINT:
                return stickparamtab;
                break;
        case fHBodyType::NEURON:
                return neuronparamtab;
                break;
        default:
                return connectionparamtab;
                break;
        }
}