source: cpp/frams/model/similarity/simil_model.h @ 817

Last change on this file since 817 was 817, checked in by oriona, 4 years ago

MDS procedure replaced with weighted MDS procedure.

  • Property svn:eol-style set to native
File size: 5.6 KB
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1// This file is a part of Framsticks SDK.  http://www.framsticks.com/
2// Copyright (C) 1999-2016  Maciej Komosinski and Szymon Ulatowski.
3// See LICENSE.txt for details.
4
5
6#ifndef _SIMIL_MODEL_H_
7#define _SIMIL_MODEL_H_
8
9#include "frams/genetics/geno.h"
10#include "frams/model/model.h"
11#include "frams/util/3d.h"
12#include "simil_match.h"
13
14#define TDN_SIZE 5
15
16enum TDNELEMS
17{
18        ORIG_IND = 0,
19        DEGREE = 1,
20        NEURO_CONNS = 2,
21        NEURONS = 3,
22        FUZZ_DEG = 4
23};
24
25/** This class defines similarity measure for Framsticks organisms.
26 * Authors:
27 * Marek Kubiak (concept, implementation)
28 * Maciej Komosinski (concept, Framsticks interface)
29 * Agnieszka Mensfelt (refactoring)
30 */
31class ModelSimil
32{
33public:
34        ModelSimil();
35        virtual ~ModelSimil();
36        double EvaluateDistance(const Geno *G0, const Geno *G1);
37
38        static int CompareDegrees(const void *pElem1, const void *pElem2);
39        static int CompareConnsNo(const void *pElem1, const void *pElem2);
40        static int GetNOFactors();
41#define STATRICKCLASS ModelSimil
42        PARAMPROCDEF(p_evaldistance);
43#undef STATRICKCLASS
44
45protected:
46        void _PrintSeamnessTable(std::vector<int> *pVector, int iCount);
47        //matching function
48        int MatchPartsGeometry();
49        void ComputeMatching();
50        void _PrintPartsMatching();
51        void SaveIntermediateFiles();
52
53        static int CheckPartsIdentity(Part *P1, Part *P2);
54        int SortPartInfoTables();
55        int CountPartNeurons();
56        bool ComputePartsPositionsBySVD();
57        int GetPartPositions();
58        int CountPartDegrees();
59
60        int SortPartInfoFuzzy();
61        void CountFuzzyNeighb();
62        void SortFuzzyNeighb();
63        void GetNeighbIndexes(int mod, int partInd, std::vector<int> &indexes);
64        void CheckFuzzyIdentity();
65
66        int CreatePartInfoTables();
67        void _PrintDegrees(int i);
68        void _PrintArray(int *array, int base, int size);
69        void _PrintNeighbourhood(int i);
70        void _PrintArrayDouble(double *array, int base, int size);
71        int CountPartsDistance();
72
73
74public:
75        /// Table of weights for weighted distance function.
76        /// Weights are for factors in the following order:
77        /// [0]: m_iDV (difference in the number of vertices)
78        /// [1]: m_iDD (difference in degrees over matching)
79        /// [2]: m_iDN (difference in neurons over matching)
80        /// [3]: m_dDG (difference in geometry over matching)
81        /// @sa EvaluateDistance
82        double m_adFactors[4];
83
84        //for Zfixed = 1, the "z" (vertical) coordinates are not taken into account during PCA alignment
85        int fixedZaxis;
86
87        //Controls the depth of fuzzy neighbourhood
88        int fuzzyDepth;
89        int isFuzzy;
90       
91        //For wMDS = 1 weighted MDS with vertex degrees as weights is used for the alignment.
92        int wMDS;
93
94        /// Interface to local parameters
95        Param localpar;
96
97protected:
98
99        /// Between these genotypes distance is evaluated.
100        const Geno *m_Gen[2];
101
102        /// These models will be created to get the information about creatures
103        /// from their genotypes.
104        Model *m_Mod[2];
105
106        /// Index (0 or 1) of the smaler creature (in the meaning of parts).
107        /// Index of the bigger one is (1-m_iSmaller).
108        int m_iSmaller;
109
110        /// Number of parts of two creatures (index the same as for m_Mod).
111        int m_aiPartCount[2];
112
113        /// Difference between number of parts in organisms
114        int m_iDV;
115
116        /// Sum of absolute values of differences between matched part degrees
117        int m_iDD;
118
119        /// Sum of absolute values of differences between matched part
120        /// in neurons number.
121        int m_iDN;
122        //2 matrices of neighbourhood of parts - one for each genotype
123
124        /// Sum of Euclidean distances between matched parts
125        /// Unmatched Parts have the distance measured to (0,0,0) (the middle of
126        /// an organism)
127        double m_dDG;
128
129        /// Object that holds the matching of Parts.
130        // It is not clear now whether the matching function is
131        // created for orginal indices of Parts, or for sorted Parts
132        // Most probably it is for sorted Parts.
133        SimilMatching *m_pMatching;
134
135        /// Type of 4 ints - describing one Part of the creature in
136        /// its sorted table of degrees
137        /// TDN[0] - original index of creature's Part (that is "i" from GetPart(i))
138        /// TDN[1] - degree (number of adjacent joints) of one Part
139        /// TDN[2] - number of NeuroConnections and Neurons belonging to one Part
140        /// TDN[3] - number of Neurons of the Part
141        /// TDN[4] - fuzzy degree
142        typedef int TDN[5];
143
144        /** 2 arrays holding information about compared organisms (one for each
145        creature) of degree and neuro info for Parts.
146        Index corresponds to the one in m_Mod
147        m_aDegrees[i][j] is a TDN of the j-th Part of the i-th creature in m_Mod
148        */
149        TDN *m_aDegrees[2];
150
151        //std::pair<TDN, double> *m_aDegrees[2];
152        /// Holds information on all on-joint neurons. Only TDN[3] and TDN[4]
153        /// are important (original index and degree are not important).
154        TDN m_aOnJoint[2];
155
156        /// Holds information on all neurons that are not placed neither on
157        /// a joint nor on a part. Only TDN[3] and TDN[4]
158        /// are important (original index and degree are not important).
159        TDN m_aAnywhere[2];
160
161        //array of parts neighbourhood
162        int **m_Neighbours[2];
163        //array of "fuzzy neigbourhood" for each of organisms. Dimensions: parts_num x fuzzyDepth
164        float **m_fuzzyNeighb[2];
165
166        /// Two arrays of points which hold information about positions of Parts
167        /// of both of the compared organisms.
168        /// Matching methods which do not use geometry (MatchPartsOld
169        /// and MatchPartsNew) simply copy these positions from models. The only
170        /// matching method which uses geometry (MatchPartsNewGeometry) makes
171        /// use of these arrays extensively.
172        /// At m_aPositions[ iModel ][ iOriginalPart ] there is a Pt3D of
173        /// a Part with index iOriginalPart of the model iModel.
174        /// iOriginalPart means that this index is the original index of a Part,
175        /// (before sorting).
176        Pt3D *m_aPositions[2];
177
178        /// Number of weights in the function which evaluates distance.
179        static const int iNOFactors;
180
181};
182
183
184#endif
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