1 | // This file is a part of Framsticks SDK. http://www.framsticks.com/ |
---|
2 | // Copyright (C) 1999-2019 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 "simil_match.h" |
---|
12 | |
---|
13 | #define TDN_SIZE 5 |
---|
14 | |
---|
15 | enum TDNELEMS |
---|
16 | { |
---|
17 | ORIG_IND = 0, |
---|
18 | DEGREE = 1, |
---|
19 | NEURO_CONNS = 2, |
---|
20 | NEURONS = 3, |
---|
21 | FUZZ_DEG = 4 |
---|
22 | }; |
---|
23 | |
---|
24 | /** This class defines similarity measure for Framsticks organisms. |
---|
25 | * Authors: |
---|
26 | * Marek Kubiak (concept, implementation) |
---|
27 | * Maciej Komosinski (concept, Framsticks interface) |
---|
28 | * Agnieszka Mensfelt (refactoring, improvements) |
---|
29 | */ |
---|
30 | class ModelSimil |
---|
31 | { |
---|
32 | public: |
---|
33 | ModelSimil(); |
---|
34 | virtual ~ModelSimil(); |
---|
35 | double EvaluateDistance(const Geno *G0, const Geno *G1); //chooses greedy or hungarian |
---|
36 | double EvaluateDistanceGreedy(const Geno *G0, const Geno *G1); |
---|
37 | double EvaluateDistanceHungarian(const Geno *G0, const Geno *G1); |
---|
38 | |
---|
39 | static int CompareDegrees(const void *pElem1, const void *pElem2); |
---|
40 | static int CompareFuzzyDegrees(const void *pElem1, const void *pElem2); |
---|
41 | static int CompareConnsNo(const void *pElem1, const void *pElem2); |
---|
42 | static int GetNOFactors(); |
---|
43 | #define STATRICKCLASS ModelSimil |
---|
44 | PARAMPROCDEF(p_evaldistance); |
---|
45 | #undef STATRICKCLASS |
---|
46 | |
---|
47 | protected: |
---|
48 | void _PrintSeamnessTable(std::vector<int> *pVector, int iCount); |
---|
49 | //matching function |
---|
50 | int MatchPartsGeometry(); |
---|
51 | void ComputeMatching(); |
---|
52 | void FillPartsDistances(double *&dist, int bigger, int smaller, bool geo); |
---|
53 | void _PrintPartsMatching(); |
---|
54 | void SaveIntermediateFiles(); |
---|
55 | |
---|
56 | int SortPartInfoTables(); |
---|
57 | int CountPartNeurons(); |
---|
58 | bool ComputePartsPositionsBySVD(); |
---|
59 | int GetPartPositions(); |
---|
60 | int CountPartDegrees(); |
---|
61 | |
---|
62 | void CountFuzzyNeighb(); |
---|
63 | void SortFuzzyNeighb(); |
---|
64 | void GetNeighbIndexes(int mod, int partInd, std::vector<int> &indexes); |
---|
65 | void FuzzyOrder(); |
---|
66 | |
---|
67 | int CreatePartInfoTables(); |
---|
68 | void _PrintDegrees(int i); |
---|
69 | void _PrintArray(int *array, int base, int size); |
---|
70 | void _PrintNeighbourhood(int i); |
---|
71 | void _PrintFuzzyNeighbourhood(int i); |
---|
72 | void _PrintArrayDouble(double *array, int base, int size); |
---|
73 | int CountPartsDistance(); |
---|
74 | |
---|
75 | |
---|
76 | public: |
---|
77 | /// 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 |
---|
78 | /// @sa EvaluateDistance |
---|
79 | int matching_method; |
---|
80 | |
---|
81 | /// Table of weights for weighted distance function. |
---|
82 | /// Weights are for factors in the following order: |
---|
83 | /// [0]: m_iDV (difference in the number of vertices) |
---|
84 | /// [1]: m_iDD (difference in degrees over matching) |
---|
85 | /// [2]: m_iDN (difference in neurons over matching) |
---|
86 | /// [3]: m_dDG (difference in geometry over matching) |
---|
87 | /// @sa EvaluateDistance |
---|
88 | double m_adFactors[4]; |
---|
89 | |
---|
90 | //for Zfixed = 1, the "z" (vertical) coordinates are not taken into account during PCA alignment |
---|
91 | int fixedZaxis; |
---|
92 | |
---|
93 | //Controls the depth of fuzzy neighbourhood |
---|
94 | int fuzzyDepth; |
---|
95 | int isFuzzy; |
---|
96 | |
---|
97 | //For wMDS = 1 weighted MDS with vertex degrees as weights is used for the alignment. |
---|
98 | int wMDS; |
---|
99 | |
---|
100 | //For saveMatching = 1 the best matching found will be saved. |
---|
101 | int saveMatching; |
---|
102 | |
---|
103 | /// Interface to local parameters |
---|
104 | Param localpar; |
---|
105 | |
---|
106 | protected: |
---|
107 | |
---|
108 | /// Between these genotypes distance is evaluated. |
---|
109 | const Geno *m_Gen[2]; |
---|
110 | |
---|
111 | /// These models will be created to get the information about creatures |
---|
112 | /// from their genotypes. |
---|
113 | Model *m_Mod[2]; |
---|
114 | |
---|
115 | /// Index (0 or 1) of the smaler creature (in the meaning of parts). |
---|
116 | /// Index of the bigger one is (1-m_iSmaller). |
---|
117 | int m_iSmaller; |
---|
118 | |
---|
119 | /// Number of parts of two creatures (index the same as for m_Mod). |
---|
120 | int m_aiPartCount[2]; |
---|
121 | |
---|
122 | /// Difference between number of parts in organisms |
---|
123 | int m_iDV; |
---|
124 | |
---|
125 | /// Sum of absolute values of differences between matched part degrees |
---|
126 | int m_iDD; |
---|
127 | |
---|
128 | /// Sum of absolute values of differences between matched part |
---|
129 | /// in neurons number. |
---|
130 | int m_iDN; |
---|
131 | //2 matrices of neighbourhood of parts - one for each genotype |
---|
132 | |
---|
133 | /// Sum of Euclidean distances between matched parts |
---|
134 | /// Unmatched Parts have the distance measured to (0,0,0) (the middle of |
---|
135 | /// an organism) |
---|
136 | double m_dDG; |
---|
137 | |
---|
138 | /// Object that holds the matching of Parts. |
---|
139 | // It is not clear now whether the matching function is |
---|
140 | // created for orginal indices of Parts, or for sorted Parts |
---|
141 | // Most probably it is for sorted Parts. |
---|
142 | SimilMatching *m_pMatching; |
---|
143 | |
---|
144 | /// Type of 4 ints - describing one Part of the creature in |
---|
145 | /// its sorted table of degrees |
---|
146 | /// TDN[0] - original index of creature's Part (that is "i" from GetPart(i)) |
---|
147 | /// TDN[1] - degree (number of adjacent joints) of one Part |
---|
148 | /// TDN[2] - number of NeuroConnections and Neurons belonging to one Part |
---|
149 | /// TDN[3] - number of Neurons of the Part |
---|
150 | /// TDN[4] - fuzzy degree |
---|
151 | typedef int TDN[5]; |
---|
152 | |
---|
153 | /** 2 arrays holding information about compared organisms (one for each |
---|
154 | creature) of degree and neuro info for Parts. |
---|
155 | Index corresponds to the one in m_Mod |
---|
156 | m_aDegrees[i][j] is a TDN of the j-th Part of the i-th creature in m_Mod |
---|
157 | */ |
---|
158 | TDN *m_aDegrees[2]; |
---|
159 | |
---|
160 | //std::pair<TDN, double> *m_aDegrees[2]; |
---|
161 | /// Holds information on all on-joint neurons. Only TDN[3] and TDN[4] |
---|
162 | /// are important (original index and degree are not important). |
---|
163 | TDN m_aOnJoint[2]; |
---|
164 | |
---|
165 | /// Holds information on all neurons that are not placed neither on |
---|
166 | /// a joint nor on a part. Only TDN[3] and TDN[4] |
---|
167 | /// are important (original index and degree are not important). |
---|
168 | TDN m_aAnywhere[2]; |
---|
169 | |
---|
170 | //array of parts neighbourhood |
---|
171 | int **m_Neighbours[2]; |
---|
172 | //array of "fuzzy neigbourhood" for each of organisms. Dimensions: parts_num x fuzzyDepth |
---|
173 | float **m_fuzzyNeighb[2]; |
---|
174 | |
---|
175 | /// Two arrays of points which hold information about positions of Parts |
---|
176 | /// of both of the compared organisms. |
---|
177 | /// Matching methods which do not use geometry (MatchPartsOld |
---|
178 | /// and MatchPartsNew) simply copy these positions from models. The only |
---|
179 | /// matching method which uses geometry (MatchPartsNewGeometry) makes |
---|
180 | /// use of these arrays extensively. |
---|
181 | /// At m_aPositions[ iModel ][ iOriginalPart ] there is a Pt3D of |
---|
182 | /// a Part with index iOriginalPart of the model iModel. |
---|
183 | /// iOriginalPart means that this index is the original index of a Part, |
---|
184 | /// (before sorting). |
---|
185 | Pt3D *m_aPositions[2]; |
---|
186 | |
---|
187 | /// Number of weights in the function which evaluates distance. |
---|
188 | static const int iNOFactors; |
---|
189 | |
---|
190 | }; |
---|
191 | |
---|
192 | #endif |
---|