source: cpp/frams/genetics/fS/fS_general.cpp @ 1227

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 2019-2021  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.

#include <float.h>
#include "fS_general.h"
#include "frams/model/geometry/geometryutils.h"
#include "frams/genetics/genooperators.h"
#include "common/Convert.h"
#include "frams/util/rndutil.h"
#include "frams/neuro/neurolibrary.h"
#include "../genooperators.h"
#include "common/nonstd_math.h"
#include <frams/model/geometry/part_distance_estimator.h>
#include <algorithm>

int fS_Genotype::precision = 4;
std::map<string, double> Node::minValues;
std::map<string, double> Node::defaultValues;
std::map<string, double> Node::maxValues;

void Node::prepareParams()
{
        if(minValues.empty())
        {
                minValues = {
                                {INGESTION, Model::getMinPart().ingest},
                                {FRICTION,  Model::getMinPart().friction},
                                {ROT_X,     -M_PI},
                                {ROT_Y,     -M_PI},
                                {ROT_Z,     -M_PI},
                                {RX,        -M_PI},
                                {RY,        -M_PI},
                                {RZ,        -M_PI},
                                {SCALE,      0.01},
                                {SCALE_X,    Model::getMinPart().scale.x},
                                {SCALE_Y,    Model::getMinPart().scale.y},
                                {SCALE_Z,    Model::getMinPart().scale.z}
                };
        }

        if(maxValues.empty())
        {
                maxValues = {
                                {INGESTION, Model::getMaxPart().ingest},
                                {FRICTION,  Model::getMaxPart().friction},
                                {ROT_X,     M_PI},
                                {ROT_Y,     M_PI},
                                {ROT_Z,     M_PI},
                                {RX,        M_PI},
                                {RY,        M_PI},
                                {RZ,        M_PI},
                                {SCALE,      100.0},
                                {SCALE_X,    Model::getMaxPart().scale.x},
                                {SCALE_Y,    Model::getMaxPart().scale.y},
                                {SCALE_Z,    Model::getMaxPart().scale.z}
                };
        }
        if(defaultValues.empty())
        {
                defaultValues = {
                                {INGESTION, Model::getDefPart().ingest},
                                {FRICTION,  Model::getDefPart().friction},
                                {ROT_X,     0.0},
                                {ROT_Y,     0.0},
                                {ROT_Z,     0.0},
                                {RX,        0.0},
                                {RY,        0.0},
                                {RZ,        0.0},
                                {SCALE,      1.0},
                                {SCALE_X,    Model::getDefPart().scale.x},
                                {SCALE_Y,    Model::getDefPart().scale.y},
                                {SCALE_Z,    Model::getDefPart().scale.z}
                };
        }
}

double fS_stod(const string&  str, int start, size_t* size)
{
        try
        {
                return std::stod(str, size);
        }
        catch(const std::invalid_argument&)
        {
                throw fS_Exception("Invalid numeric value", start);
        }
        catch(const std::out_of_range&)
        {
                throw fS_Exception("Invalid numeric value; out of range", start);
        }
}

State::State(State *_state)
{
        location = Pt3D(_state->location);
        v = Pt3D(_state->v);
        fr = _state->fr;
        s = _state->s;
}

State::State(Pt3D _location, Pt3D _v)
{
        location = Pt3D(_location);
        v = Pt3D(_v);
}

void State::addVector(const double length)
{
        location += v * length;
}

void rotateVector(Pt3D &vector, const Pt3D &rotation)
{
        Orient rotmatrix = Orient_1;
        rotmatrix.rotate(rotation);
        vector = rotmatrix.transform(vector);
}

void State::rotate(const Pt3D &rotation)
{
       rotateVector(v, rotation);
       v.normalize();
}

int findEndOfNeuronParamString(SString neuronDefinition)
{
        for(int i=1; i< neuronDefinition.size(); i++)
        {
                if(neuronDefinition[i - 1] == ',' && isdigit(neuronDefinition[i]))
                        return i - 1;
        }

        return neuronDefinition.size();
}

fS_Neuron::fS_Neuron(const char *str, int _start, int length)
{
        start = _start + 1;
        end = start + length;
        if (length == 0)
                return;

        SString neuronDefinition(str, length);
        int endOfNeuronParamString = findEndOfNeuronParamString(neuronDefinition);
        SString neuronParamString = neuronDefinition.substr(0, endOfNeuronParamString);
        SString neuronInputString = neuronDefinition.substr(endOfNeuronParamString + 1);

        SString details = "N";

        SString tmp = neuronParamString;
        if(tmp.indexOf(':') != -1)
                tmp = tmp.substr(0, tmp.indexOf(':'));

        if (NeuroLibrary::staticlibrary.findClassIndex(tmp, true) != -1)
        {
                details = neuronParamString;
        }
        else{
                neuronInputString = neuronParamString;
        }
        setDetails(details);

        vector<SString> inputStrings;
        strSplit(neuronInputString, NEURON_INTERNAL_SEPARATOR, false, inputStrings);
        if (inputStrings.empty() || inputStrings[0] == SString())
                return;
        for (int i = 0; i < int(inputStrings.size()); i++)
        {
                SString keyValue = inputStrings[i];
                int separatorIndex = keyValue.indexOf(NEURON_I_W_SEPARATOR);
                const char *buffer = keyValue.c_str();
                size_t keyLength;
                double value;
                if (separatorIndex == -1)
                {
                        keyLength = keyValue.length();
                        value = DEFAULT_NEURO_CONNECTION_WEIGHT;
                } else
                {
                        keyLength = separatorIndex;
                        size_t valueLength = keyValue.length() - (separatorIndex);
                        value = fS_stod(buffer + separatorIndex + 1, start, &valueLength);
                }
                inputs[fS_stod(buffer, start, &keyLength)] = value;
        }
}

Node::Node(Substring &restOfGeno, Node *_parent, GenotypeParams _genotypeParams)
{
        prepareParams();
        partDescription = new Substring(restOfGeno);
        genotypeParams = _genotypeParams;
        parent = _parent;

        try
        {
                extractModifiers(restOfGeno);
                extractPartType(restOfGeno);
                extractNeurons(restOfGeno);
                extractParams(restOfGeno);

                partDescription->shortenBy(restOfGeno.len);
                if (restOfGeno.len > 0)
                        getChildren(restOfGeno);
        }
        catch(fS_Exception &e)
        {
                cleanUp();
                throw e;
        }
}

Node::~Node()
{
        cleanUp();
}

void Node::cleanUp()
{
        delete partDescription;
        if (state != nullptr)
                delete state;
        for (int i = 0; i < int(neurons.size()); i++)
                delete neurons[i];
        for (int i = 0; i < int(children.size()); i++)
                delete children[i];
}

int Node::getPartPosition(Substring &restOfGenotype)
{
        for (int i = 0; i < restOfGenotype.len; i++)
        {
                if (GENE_TO_SHAPE.find(restOfGenotype.at(i)) != GENE_TO_SHAPE.end())
                        return i;
        }
        return -1;
}

void Node::extractModifiers(Substring &restOfGenotype)
{
        int partShapePosition = getPartPosition(restOfGenotype);
        if (partShapePosition == -1)
                throw fS_Exception("Part type missing", restOfGenotype.start);

        for (int i = 0; i < partShapePosition; i++)
        {
                // Extract modifiers and joint
                char mType = restOfGenotype.at(i);
                if (JOINTS.find(tolower(mType)) != string::npos)
                        joint = tolower(mType);
                else if (MODIFIERS.find(toupper(mType)) != string::npos)
                        modifiers[toupper(mType)] += isupper(mType) ? 1 : -1;
                else
                        throw fS_Exception("Invalid modifier", restOfGenotype.start + i);
        }
        restOfGenotype.startFrom(partShapePosition);
}

void Node::extractPartType(Substring &restOfGenotype)
{
        auto itr = GENE_TO_SHAPE.find(restOfGenotype.at(0));
        if (itr == GENE_TO_SHAPE.end())
                throw fS_Exception("Invalid part type", restOfGenotype.start);

        partShape = itr->second;
        restOfGenotype.startFrom(1);
}

vector<int> getSeparatorPositions(const char *str, int len, char separator, char endSign, int &endIndex)
{
        endIndex = -1;
        vector<int> separators {-1};
        for (int i = 0; i < len; i++)
        {
                if (str[i] == separator)
                        separators.push_back(i);
                else if (str[i] == endSign)
                {
                        endIndex = i;
                        break;
                }
        }
        separators.push_back(endIndex); // End of string as last separator
        return separators;
}

void Node::extractNeurons(Substring &restOfGenotype)
{
        if (restOfGenotype.len == 0 || restOfGenotype.at(0) != NEURON_START)
                return;

        const char *ns = restOfGenotype.c_str() + 1;
        int neuronsEndIndex;
        vector<int> separators = getSeparatorPositions(ns, restOfGenotype.len, NEURON_SEPARATOR, NEURON_END, neuronsEndIndex);
        if(neuronsEndIndex == -1)
                throw fS_Exception("Lacking neuro end sign", restOfGenotype.start);

        for (int i = 0; i < int(separators.size()) - 1; i++)
        {
                int start = separators[i] + 1;
                int length = separators[i + 1] - start;
                fS_Neuron *newNeuron = new fS_Neuron(ns + start, restOfGenotype.start + start, length);
                neurons.push_back(newNeuron);
        }

        restOfGenotype.startFrom(neuronsEndIndex + 2);
}

void Node::extractParams(Substring &restOfGenotype)
{
        if (restOfGenotype.len == 0 || restOfGenotype.at(0) != PARAM_START)
                return;

        const char *paramString = restOfGenotype.c_str() + 1;

        // Find the indexes of the parameter separators
        int paramsEndIndex;
        vector<int> separators = getSeparatorPositions(paramString, restOfGenotype.len, PARAM_SEPARATOR, PARAM_END, paramsEndIndex);
        if(paramsEndIndex == -1)
                throw fS_Exception("Lacking param end sign", restOfGenotype.start);

        for (int i = 0; i < int(separators.size()) - 1; i++)
        {
                int start = separators[i] + 1;
                int length = separators[i + 1] - start;
                const char *buffer = paramString + start;

                // Find the index of key-value separator
                int separatorIndex = -1;
                for (int i = 0; i < length; i++)
                {
                        if (buffer[i] == PARAM_KEY_VALUE_SEPARATOR)
                        {
                                separatorIndex = i;
                                break;
                        }
                }
                if (-1 == separatorIndex)
                        throw fS_Exception("Parameter separator expected", restOfGenotype.start);

                // Compute the value of parameter and assign it to the key
                int valueStartIndex = separatorIndex + 1;
                string key(buffer, separatorIndex);
                if(std::find(PARAMS.begin(), PARAMS.end(), key) == PARAMS.end())
                        throw fS_Exception("Invalid parameter key", restOfGenotype.start + start);

                const char *val = buffer + valueStartIndex;
                size_t len = length - valueStartIndex;
                double value = fS_stod(val, restOfGenotype.start + start + valueStartIndex, &len);
                if((key==SCALE_X || key==SCALE_Y || key==SCALE_Z) && value <= 0.0)
                        throw fS_Exception("Invalid value of radius parameter", restOfGenotype.start + start + valueStartIndex);

                params[key] = value;

        }

        restOfGenotype.startFrom(paramsEndIndex + 2);
}

double Node::getParam(const string &key)
{
        auto item = params.find(key);
        if (item != params.end())
                return item->second;

        auto defaultItem = defaultValues.find(key);
        if(defaultItem == defaultValues.end())
                throw fS_Exception("Default value missing", 0);
        return defaultItem->second;
}

double Node::getParam(const string &key, double defaultValue)
{
        auto item = params.find(key);
        if (item != params.end())
                return item->second;
        return defaultValue;
}


void Node::getState(State *_state, bool calculateLocation)
{
        if (state != nullptr)
                delete state;
        if (parent == nullptr)
                state = _state;
        else
                state = new State(_state);


        // Update state by modifiers
        for (auto it = modifiers.begin(); it != modifiers.end(); ++it)
        {
                char mod = it->first;
                double multiplier = pow(genotypeParams.modifierMultiplier, it->second);
                if (mod == MODIFIERS[0])
                        state->ing *= multiplier;
                else if (mod == MODIFIERS[1])
                        state->fr *= multiplier;
                else if (mod == MODIFIERS[2])
                        state->s *= multiplier;
        }

        if (parent != nullptr && calculateLocation)
        {
                // Rotate
                state->rotate(getVectorRotation());

                double distance = calculateDistanceFromParent();
                state->addVector(distance);
        }
        for (int i = 0; i < int(children.size()); i++)
                children[i]->getState(state, calculateLocation);
}

void Node::getChildren(Substring &restOfGenotype)
{
        vector<Substring> branches = getBranches(restOfGenotype);
        for (int i = 0; i < int(branches.size()); i++)
        {
                children.push_back(new Node(branches[i], this, genotypeParams));
        }
}

vector<Substring> Node::getBranches(Substring &restOfGenotype)
{
        vector<Substring> children;
        if (restOfGenotype.at(0) != BRANCH_START)
        {
                children.push_back(restOfGenotype);  // Only one child
                return children;
        }

        int depth = 0;
        int start = 1;
        char c;
        const char *str = restOfGenotype.c_str();
        bool insideSpecifiation = false;        // True when inside parameter or neuron specification
        for (int i = 0; i < restOfGenotype.len; i++)
        {
                if (depth < 0)
                        throw fS_Exception("The number of branch start signs does not equal the number of branch end signs", restOfGenotype.start + i);
                c = str[i];
                if (c == BRANCH_START)
                        depth++;
                else if (c == PARAM_START || c == NEURON_START)
                        insideSpecifiation = true;
                else if (c == PARAM_END || c == NEURON_END)
                        insideSpecifiation = false;
                else if (!insideSpecifiation && ((c == BRANCH_SEPARATOR && depth == 1) || i + 1 == restOfGenotype.len))
                {
                        Substring substring(restOfGenotype);
                        substring.startFrom(start);
                        substring.len = i - start;
                        children.push_back(substring);
                        start = i + 1;
                } else if (c == BRANCH_END)
                        depth--;
        }
        if (depth != 1)    // T
                throw fS_Exception("The number of branch start signs does not equal the number of branch end signs", restOfGenotype.start);
        return children;
}

void Node::calculateScale(Pt3D &scale)
{
        double scaleMultiplier = getParam(SCALE) * state->s;
        scale.x = getParam(SCALE_X) * scaleMultiplier;
        scale.y = getParam(SCALE_Y) * scaleMultiplier;
        scale.z = getParam(SCALE_Z) * scaleMultiplier;
}

double Node::calculateVolume()
{
        Part *tmpPart = new Part(partShape);
        calculateScale(tmpPart->scale);
        return GeometryUtils::calculateSolidVolume(tmpPart);
}

bool Node::isPartScaleValid()
{
        Pt3D scale;
        calculateScale(scale);
        return GeometryUtils::isSolidPartScaleValid(partShape, scale, true); //2020-12: mac->JS: I set the last argument to true because this is how the original code worked, but I think it should be ensureCircleSection?
}

Pt3D Node::getVectorRotation()
{
        return Pt3D(getParam(ROT_X, 0.0), getParam(ROT_Y, 0.0), getParam(ROT_Z, 0.0));
}

Pt3D Node::getRotation()
{
        Pt3D rotation = Pt3D(getParam(RX, 0.0), getParam(RY, 0.0), getParam(RZ, 0.0));
        if(genotypeParams.turnWithRotation)
                rotation += getVectorRotation();
        return rotation;
}

void Node::buildModel(Model &model, Node *parent)
{
        createPart();
        model.addPart(part);
        if (parent != nullptr)
                addJointsToModel(model, parent);

        for (int i = 0; i < int(neurons.size()); i++)
        {
                Neuro *neuro = new Neuro(*neurons[i]);
                model.addNeuro(neuro);
                neuro->addMapping(MultiRange(IRange(neurons[i]->start, neurons[i]->end)));
                if (neuro->getClass()->preflocation == NeuroClass::PREFER_JOINT && parent != nullptr)
                {
                        neuro->attachToJoint(model.getJoint(model.getJointCount() - 1));
                } else
                        neuro->attachToPart(part);
        }

        model.checkpoint();
        part->addMapping(partDescription->toMultiRange());

        for (int i = 0; i < int(children.size()); i++)
        {
                Node *child = children[i];
                child->buildModel(model, this);
        }
}

void Node::createPart()
{
        part = new Part(partShape);
        part->p = Pt3D(state->location);

        part->friction = getParam(FRICTION) * state->fr;
        part->ingest = getParam(INGESTION) * state->ing;
        calculateScale(part->scale);
        part->setRot(getRotation());
}

void Node::addJointsToModel(Model &model, Node *parent)
{
        Joint *j = new Joint();
        j->attachToParts(parent->part, part);
        switch (joint)
        {
                case HINGE_X:
                        j->shape = Joint::Shape::SHAPE_HINGE_X;
                        break;
                case HINGE_XY:
                        j->shape = Joint::Shape::SHAPE_HINGE_XY;
                        break;
                default:
                        j->shape = Joint::Shape::SHAPE_FIXED;
        }
        model.addJoint(j);
        j->addMapping(partDescription->toMultiRange());
}


void Node::getGeno(SString &result)
{
        if (joint != DEFAULT_JOINT)
                result += joint;
        for (auto it = modifiers.begin(); it != modifiers.end(); ++it)
        {
                char mod = it->first;
                int count = it->second;
                if(it->second < 0)
                {
                        mod = tolower(mod);
                        count = fabs(count);
                }
                result += std::string(count, mod).c_str();
        }
        result += SHAPE_TO_GENE.at(partShape);

        if (!neurons.empty())
        {
                // Add neurons to genotype string
                result += NEURON_START;
                for (int i = 0; i < int(neurons.size()); i++)
                {
                        fS_Neuron *n = neurons[i];
                        if (i != 0)
                                result += NEURON_SEPARATOR;

                        result += n->getDetails();
                        if (!n->inputs.empty())
                                result += NEURON_INTERNAL_SEPARATOR;

                        for (auto it = n->inputs.begin(); it != n->inputs.end(); ++it)
                        {
                                if (it != n->inputs.begin())
                                        result += NEURON_INTERNAL_SEPARATOR;
                                result += SString::valueOf(it->first);
                                if (it->second != DEFAULT_NEURO_CONNECTION_WEIGHT)
                                {
                                        result += NEURON_I_W_SEPARATOR;
                                        result += SString::valueOf(it->second);
                                }
                        }
                }
                result += NEURON_END;
        }

        if (!params.empty())
        {
                // Add parameters to genotype string
                result += PARAM_START;
                for (auto it = params.begin(); it != params.end(); ++it)
                {
                        if (it != params.begin())
                                result += PARAM_SEPARATOR;

                        result += it->first.c_str();                    // Add parameter key to string
                        result += PARAM_KEY_VALUE_SEPARATOR;
                        // Round the value to two decimal places and add to string
                        result += doubleToString(it->second, fS_Genotype::precision).c_str();
                }
                result += PARAM_END;
        }

        if (children.size() == 1)
                children[0]->getGeno(result);
        else if (children.size() > 1)
        {
                result += BRANCH_START;
                for (int i = 0; i < int(children.size()) - 1; i++)
                {
                        children[i]->getGeno(result);
                        result += BRANCH_SEPARATOR;
                }
                children.back()->getGeno(result);
                result += BRANCH_END;
        }
}

void Node::getAllNodes(vector<Node *> &allNodes)
{
        allNodes.push_back(this);
        for (int i = 0; i < int(children.size()); i++)
                children[i]->getAllNodes(allNodes);
}

int Node::getNodeCount()
{
        vector<Node*> allNodes;
        getAllNodes(allNodes);
        return allNodes.size();
}

fS_Genotype::fS_Genotype(const string &geno)
{
        try
        {
                GenotypeParams genotypeParams;
                genotypeParams.modifierMultiplier = 1.1;
                genotypeParams.distanceTolerance = 0.1;
                genotypeParams.relativeDensity = 10.0;
                genotypeParams.turnWithRotation = false;
                genotypeParams.paramMutationStrength = 0.4;

                size_t modeSeparatorIndex = geno.find(MODE_SEPARATOR);
                if (modeSeparatorIndex == string::npos)
                        throw fS_Exception("Genotype parameters missing", 0);

                std::vector<SString> paramStrings;
                strSplit(SString(geno.c_str(), modeSeparatorIndex), ',', false, paramStrings);

                if(paramStrings.size() >= 1 && paramStrings[0] != "")
                {
                        size_t len0 = paramStrings[0].length();
                        genotypeParams.modifierMultiplier = fS_stod(paramStrings[0].c_str(), 0, &len0);
                }
                if(paramStrings.size() >= 2 && paramStrings[1] != "")
                {
                        genotypeParams.turnWithRotation = bool(atoi(paramStrings[1].c_str()));
                }
                if(paramStrings.size() >= 3 && paramStrings[2] != "")
                {
                        size_t len2 = paramStrings[2].length();
                        genotypeParams.paramMutationStrength = fS_stod(paramStrings[2].c_str(), 0, &len2);
                }

                int genoStart = modeSeparatorIndex + 1;
                Substring substring(geno.c_str(), genoStart, int(geno.length()) - genoStart);
                startNode = new Node(substring, nullptr, genotypeParams);
                validateNeuroInputs();
        }
        catch (fS_Exception &e)
        {
                delete startNode;
                throw e;
        }
}

fS_Genotype::~fS_Genotype()
{
        delete startNode;
}

void fS_Genotype::getState(bool calculateLocation)
{
        State *initialState = new State(Pt3D(0), Pt3D(1, 0, 0));
        startNode->getState(initialState, calculateLocation);
}

Model fS_Genotype::buildModel(bool using_checkpoints)
{

        Model model;
        model.open(using_checkpoints);

        getState(true);
        startNode->buildModel(model, nullptr);
        buildNeuroConnections(model);

        model.close();
        return model;
}


void fS_Genotype::buildNeuroConnections(Model &model)
{
        // All the neurons are already created in the model
        vector<fS_Neuron*> allNeurons = getAllNeurons();
        for (int i = 0; i < int(allNeurons.size()); i++)
        {
                fS_Neuron *neuron = allNeurons[i];
                Neuro *modelNeuro = model.getNeuro(i);
                for (auto it = neuron->inputs.begin(); it != neuron->inputs.end(); ++it)
                {
                        Neuro *inputNeuro = model.getNeuro(it->first);
                        modelNeuro->addInput(inputNeuro, it->second);

                }
        }
}

Node *fS_Genotype::getNearestNode(vector<Node *> allNodes, Node *node)
{
        Node *result = nullptr;
        double minDistance = DBL_MAX, distance = DBL_MAX;
        for (int i = 0; i < int(allNodes.size()); i++)
        {
                Node *otherNode = allNodes[i];
                auto v = node->children;
                if (otherNode != node &&
                        find(v.begin(), v.end(), otherNode) == v.end())
                {   // Not the same node and not a child
                        distance = node->state->location.distanceTo(otherNode->state->location);
                        if (distance < minDistance)
                        {
                                minDistance = distance;
                                result = otherNode;
                        }
                }
        }
        return result;
}

SString fS_Genotype::getGeno()
{
        SString geno;
        geno.reserve(100);

        GenotypeParams gp = startNode->genotypeParams;
        geno += doubleToString(gp.modifierMultiplier, precision).c_str();
        geno += ",";
        geno += std::to_string(int(gp.turnWithRotation)).c_str();
        geno += ",";
        geno += doubleToString(gp.paramMutationStrength, precision).c_str();
        geno += MODE_SEPARATOR;

        startNode->getGeno(geno);
        return geno;
}

vector<fS_Neuron *> fS_Genotype::extractNeurons(Node *node)
{
        vector<Node*> allNodes;
        node->getAllNodes(allNodes);

        vector<fS_Neuron*> allNeurons;
        for (int i = 0; i < int(allNodes.size()); i++)
        {
                for (int j = 0; j < int(allNodes[i]->neurons.size()); j++)
                {
                        allNeurons.push_back(allNodes[i]->neurons[j]);
                }
        }
        return allNeurons;
}

int fS_Genotype::getNeuronIndex(vector<fS_Neuron *> neurons, fS_Neuron *changedNeuron)
{
        int neuronIndex = -1;
        for (int i = 0; i < int(neurons.size()); i++)
        {
                if (changedNeuron == neurons[i])
                {
                        neuronIndex = i;
                        break;
                }
        }
        return neuronIndex;
}

void fS_Genotype::shiftNeuroConnections(vector<fS_Neuron *> &neurons, int start, int end, SHIFT shift)
{
        if (start == -1 || end == -1)
                return;
        int shiftValue = end - start + 1;
        if (shift == SHIFT::LEFT)
                shiftValue *= -1;

        for (int i = 0; i < int(neurons.size()); i++)
        {
                fS_Neuron *n = neurons[i];
                std::map<int, double> newInputs;
                for (auto it = n->inputs.begin(); it != n->inputs.end(); ++it)
                {
                        if (start > it->first)
                                newInputs[it->first] = it->second;
                        else if (it->first >= start)
                        {
                                if (end >= it->first)
                                {
                                        if (shift == SHIFT::RIGHT)
                                                newInputs[it->first + shiftValue] = it->second;
                                        // If shift == -1, just delete the input
                                } else if (it->first > end)
                                        newInputs[it->first + shiftValue] = it->second;
                        }
                }
                n->inputs = newInputs;
        }
}

vector<Node *> fS_Genotype::getAllNodes()
{
        vector<Node*> allNodes;
        startNode->getAllNodes(allNodes);
        return allNodes;
}

vector<fS_Neuron *> fS_Genotype::getAllNeurons()
{
        return extractNeurons(startNode);
}

Node *fS_Genotype::chooseNode(int fromIndex)
{
        vector<Node*> allNodes = getAllNodes();
        return allNodes[fromIndex + rndUint(int(allNodes.size()) - fromIndex)];
}

int fS_Genotype::getNodeCount()
{
        return startNode->getNodeCount();
}

int fS_Genotype::checkValidityOfPartSizes()
{
        getState(false);
        vector<Node*> nodes = getAllNodes();
        for (int i = 0; i < int(nodes.size()); i++)
        {
                if (!nodes[i]->isPartScaleValid())
                {
                        return 1 + nodes[i]->partDescription->start;
                }
        }
        return 0;
}


void fS_Genotype::validateNeuroInputs()
{

        // Validate neuro input numbers
        vector<fS_Neuron*> allNeurons = getAllNeurons();
        int allNeuronsSize = allNeurons.size();
        for(int i=0; i<allNeuronsSize; i++)
        {
                fS_Neuron *n = allNeurons[i];
                for (auto it = n->inputs.begin(); it != n->inputs.end(); ++it)
                {
                        if (it->first < 0 || it->first >= allNeuronsSize)
                                throw fS_Exception("Invalid neuron input", 0);
                }
        }
}


void fS_Genotype::rearrangeNeuronConnections(fS_Neuron *changedNeuron, SHIFT shift)
{
        vector<fS_Neuron*> neurons = getAllNeurons();
        int changedNeuronIndex = getNeuronIndex(neurons, changedNeuron);
        shiftNeuroConnections(neurons, changedNeuronIndex, changedNeuronIndex, shift);
}

double Node::calculateDistanceFromParent()
{
        Pt3D scale;
        calculateScale(scale);
        Pt3D parentScale;
        parent->calculateScale(parentScale);    // Here we are sure that parent is not nullptr
        Part *tmpPart = PartDistanceEstimator::buildTemporaryPart(partShape, scale, getRotation());
        Part *parentTmpPart = PartDistanceEstimator::buildTemporaryPart(parent->partShape, parentScale, parent->getRotation());

        tmpPart->p = state->v;
        double result = PartDistanceEstimator::calculateDistance(*tmpPart, *parentTmpPart, genotypeParams.distanceTolerance, genotypeParams.relativeDensity);

        delete tmpPart;
        delete parentTmpPart;
        return result;
}