source: cpp/frams/model/similarity/simil_model.h @ 605

Last change on this file since 605 was 605, checked in by Maciej Komosinski, 8 years ago
  • Added 'fixedZaxis' option to paramtab (so that it is accessible from scripts)
  • Variable renames, improvements in comments
  • Property svn:eol-style set to native
File size: 5.8 KB
Line 
1// This file is a part of Framsticks SDK.  http://www.framsticks.com/
2// Copyright (C) 1999-2015  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    /// Interface to local parameters
92    Param localpar;
93
94protected:
95
96    /// Between these genotypes distance is evaluated.
97    const Geno *m_Gen[2];
98
99    /// These models will be created to get the information about creatures
100    /// from their genotypes.
101    Model *m_Mod[2];
102
103    /// Index (0 or 1) of the smaler creature (in the meaning of parts).
104    /// Index of the bigger one is (1-m_iSmaller).
105    int m_iSmaller;
106
107    /// Number of parts of two creatures (index the same as for m_Mod).
108    int m_aiPartCount[2];
109
110    /// Difference between number of parts in organisms
111    int m_iDV;
112
113    /// Sum of absolute values of differences between matched part degrees
114    int m_iDD;
115
116    /// Sum of absolute values of differences between matched part
117    /// in neurons number.
118    int m_iDN;
119    //2 matrices of neighbourhood of parts - one for each genotype
120
121    /// Sum of Euclidean distances between matched parts
122    /// Unmatched Parts have the distance measured to (0,0,0) (the middle of
123    /// an organism)
124    double m_dDG;
125
126    /// Object that holds the matching of Parts.
127    // It is not clear now whether the matching function is
128    // created for orginal indices of Parts, or for sorted Parts
129    // Most probably it is for sorted Parts.
130    SimilMatching *m_pMatching;
131
132    /// Type of 4 ints - describing one Part of the creature in
133    /// its sorted table of degrees
134    /// TDN[0] - original index of creature's Part (that is "i" from GetPart(i))
135    /// TDN[1] - degree (number of adjacent joints) of one Part
136    /// TDN[2] - number of NeuroConnections and Neurons belonging to one Part
137    /// TDN[3] - number of Neurons of the Part
138    /// TDN[4] - fuzzy degree
139    typedef int TDN[5];
140
141    /** 2 arrays holding information about compared organisms (one for each
142    creature) of degree and neuro info for Parts.
143    Index corresponds to the one in m_Mod
144    m_aDegrees[i][j] is a TDN of the j-th Part of the i-th creature in m_Mod
145     */
146    TDN *m_aDegrees[2];
147
148    //std::pair<TDN, double> *m_aDegrees[2];
149    /// Holds information on all on-joint neurons. Only TDN[3] and TDN[4]
150    /// are important (original index and degree are not important).
151    TDN m_aOnJoint[2];
152
153    /// Holds information on all neurons that are not placed neither on
154    /// a joint nor on a part. Only TDN[3] and TDN[4]
155    /// are important (original index and degree are not important).
156    TDN m_aAnywhere[2];
157
158    //array of parts neighbourhood
159    int **m_Neighbours[2];
160    //array of "fuzzy neigbourhood" for each of organisms. Dimensions: parts_num x fuzzyDepth
161    float **m_fuzzyNeighb[2];
162
163    /// Two arrays of points which hold information about positions of Parts
164    /// of both of the compared organisms.
165    /// Matching methods which do not use geometry (MatchPartsOld
166    /// and MatchPartsNew) simply copy these positions from models. The only
167    /// matching method which uses geometry (MatchPartsNewGeometry) makes
168    /// use of these arrays extensively.
169    /// At m_aPositions[ iModel ][ iOriginalPart ] there is a Pt3D of
170    /// a Part with index iOriginalPart of the model iModel.
171    /// iOriginalPart means that this index is the original index of a Part,
172    /// (before sorting).
173    Pt3D *m_aPositions[2];
174
175    /// Number of weights in the function which evaluates distance.
176    static const int iNOFactors;
177
178};
179
180
181#endif
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