// 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.


#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;

    /// 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