source: cpp/frams/model/similarity/simil_model.h @ 835

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2016  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.


#ifndef _SIMIL_MODEL_H_
#define _SIMIL_MODEL_H_

#include "frams/genetics/geno.h"
#include "frams/model/model.h"
#include "frams/util/3d.h"
#include "simil_match.h"

#define TDN_SIZE 5

enum TDNELEMS
{
        ORIG_IND = 0,
        DEGREE = 1,
        NEURO_CONNS = 2,
        NEURONS = 3,
        FUZZ_DEG = 4
};

/** This class defines similarity measure for Framsticks organisms.
 * Authors:
 * Marek Kubiak (concept, implementation)
 * Maciej Komosinski (concept, Framsticks interface)
 * Agnieszka Mensfelt (refactoring)
 */
class ModelSimil
{
public:
        ModelSimil();
        virtual ~ModelSimil();
        double EvaluateDistance(const Geno *G0, const Geno *G1);

        static int CompareDegrees(const void *pElem1, const void *pElem2);
        static int CompareConnsNo(const void *pElem1, const void *pElem2);
        static int GetNOFactors();
#define STATRICKCLASS ModelSimil
        PARAMPROCDEF(p_evaldistance);
#undef STATRICKCLASS

protected:
        void _PrintSeamnessTable(std::vector<int> *pVector, int iCount);
        //matching function
        int MatchPartsGeometry();
        void ComputeMatching();
        void _PrintPartsMatching();
        void SaveIntermediateFiles();

        static int CheckPartsIdentity(Part *P1, Part *P2);
        int SortPartInfoTables();
        int CountPartNeurons();
        bool ComputePartsPositionsBySVD();
        int GetPartPositions();
        int CountPartDegrees();

        int SortPartInfoFuzzy();
        void CountFuzzyNeighb();
        void SortFuzzyNeighb();
        void GetNeighbIndexes(int mod, int partInd, std::vector<int> &indexes);
        void CheckFuzzyIdentity();

        int CreatePartInfoTables();
        void _PrintDegrees(int i);
        void _PrintArray(int *array, int base, int size);
        void _PrintNeighbourhood(int i);
        void _PrintArrayDouble(double *array, int base, int size);
        int CountPartsDistance();


public:
        /// Table of weights for weighted distance function.
        /// Weights are for factors in the following order:
        /// [0]: m_iDV (difference in the number of vertices)
        /// [1]: m_iDD (difference in degrees over matching)
        /// [2]: m_iDN (difference in neurons over matching)
        /// [3]: m_dDG (difference in geometry over matching)
        /// @sa EvaluateDistance
        double m_adFactors[4];

        //for Zfixed = 1, the "z" (vertical) coordinates are not taken into account during PCA alignment
        int fixedZaxis;

        //Controls the depth of fuzzy neighbourhood 
        int fuzzyDepth;
        int isFuzzy;
        
        //For wMDS = 1 weighted MDS with vertex degrees as weights is used for the alignment.
        int wMDS;

        /// Interface to local parameters
        Param localpar;

protected:

        /// Between these genotypes distance is evaluated.
        const Geno *m_Gen[2];

        /// These models will be created to get the information about creatures
        /// from their genotypes.
        Model *m_Mod[2];

        /// Index (0 or 1) of the smaler creature (in the meaning of parts).
        /// Index of the bigger one is (1-m_iSmaller).
        int m_iSmaller;

        /// Number of parts of two creatures (index the same as for m_Mod).
        int m_aiPartCount[2];

        /// Difference between number of parts in organisms
        int m_iDV;

        /// Sum of absolute values of differences between matched part degrees
        int m_iDD;

        /// Sum of absolute values of differences between matched part 
        /// in neurons number.
        int m_iDN;
        //2 matrices of neighbourhood of parts - one for each genotype 

        /// Sum of Euclidean distances between matched parts
        /// Unmatched Parts have the distance measured to (0,0,0) (the middle of
        /// an organism)
        double m_dDG;

        /// Object that holds the matching of Parts.
        // It is not clear now whether the matching function is
        // created for orginal indices of Parts, or for sorted Parts
        // Most probably it is for sorted Parts.
        SimilMatching *m_pMatching;

        /// Type of 4 ints - describing one Part of the creature in
        /// its sorted table of degrees
        /// TDN[0] - original index of creature's Part (that is "i" from GetPart(i))
        /// TDN[1] - degree (number of adjacent joints) of one Part
        /// TDN[2] - number of NeuroConnections and Neurons belonging to one Part
        /// TDN[3] - number of Neurons of the Part
        /// TDN[4] - fuzzy degree
        typedef int TDN[5];

        /** 2 arrays holding information about compared organisms (one for each
        creature) of degree and neuro info for Parts.
        Index corresponds to the one in m_Mod
        m_aDegrees[i][j] is a TDN of the j-th Part of the i-th creature in m_Mod
        */
        TDN *m_aDegrees[2];

        //std::pair<TDN, double> *m_aDegrees[2];
        /// Holds information on all on-joint neurons. Only TDN[3] and TDN[4]
        /// are important (original index and degree are not important).
        TDN m_aOnJoint[2];

        /// Holds information on all neurons that are not placed neither on
        /// a joint nor on a part. Only TDN[3] and TDN[4]
        /// are important (original index and degree are not important).
        TDN m_aAnywhere[2];

        //array of parts neighbourhood
        int **m_Neighbours[2];
        //array of "fuzzy neigbourhood" for each of organisms. Dimensions: parts_num x fuzzyDepth
        float **m_fuzzyNeighb[2];

        /// Two arrays of points which hold information about positions of Parts
        /// of both of the compared organisms.
        /// Matching methods which do not use geometry (MatchPartsOld
        /// and MatchPartsNew) simply copy these positions from models. The only
        /// matching method which uses geometry (MatchPartsNewGeometry) makes
        /// use of these arrays extensively.
        /// At m_aPositions[ iModel ][ iOriginalPart ] there is a Pt3D of 
        /// a Part with index iOriginalPart of the model iModel.
        /// iOriginalPart means that this index is the original index of a Part,
        /// (before sorting).
        Pt3D *m_aPositions[2];

        /// Number of weights in the function which evaluates distance.
        static const int iNOFactors;

};


#endif