// This file is a part of Framsticks SDK. http://www.framsticks.com/
// Copyright (C) 1999-2019 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 "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, improvements)
*/
class ModelSimil
{
public:
ModelSimil();
virtual ~ModelSimil();
double EvaluateDistance(const Geno *G0, const Geno *G1); //chooses greedy or hungarian
double EvaluateDistanceGreedy(const Geno *G0, const Geno *G1);
double EvaluateDistanceHungarian(const Geno *G0, const Geno *G1);
static int CompareDegrees(const void *pElem1, const void *pElem2);
static int CompareFuzzyDegrees(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 *pVector, int iCount);
//matching function
int MatchPartsGeometry();
void ComputeMatching();
void FillPartsDistances(double *&dist, int bigger, int smaller, bool geo);
void _PrintPartsMatching();
void SaveIntermediateFiles();
int SortPartInfoTables();
int CountPartNeurons();
bool ComputePartsPositionsBySVD();
int GetPartPositions();
int CountPartDegrees();
void CountFuzzyNeighb();
void SortFuzzyNeighb();
void GetNeighbIndexes(int mod, int partInd, std::vector &indexes);
void FuzzyOrder();
int CreatePartInfoTables();
void _PrintDegrees(int i);
void _PrintArray(int *array, int base, int size);
void _PrintNeighbourhood(int i);
void _PrintFuzzyNeighbourhood(int i);
void _PrintArrayDouble(double *array, int base, int size);
int CountPartsDistance();
public:
/// Currently selected matching algorithm. Allowed values: 0 (more exact, slower), 1 (more greedy, faster). Details in https://doi.org/10.1007/978-3-030-16692-2_8
/// @sa EvaluateDistance
int matching_method;
/// 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;
//For saveMatching = 1 the best matching found will be saved.
int saveMatching;
/// 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 *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