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