1 | // This file is a part of Framsticks SDK. http://www.framsticks.com/ |
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2 | // Copyright (C) 1999-2020 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 | #include "genman.h" |
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6 | #include <frams/vm/classes/genoobj.h> |
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7 | #include GEN_CONFIG_FILE //configuration of active genetic operators |
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8 | #include "common/log.h" |
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9 | #include "common/nonstd_math.h" |
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10 | #include "common/util-string.h" |
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11 | #include <common/loggers/loggers.h> |
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12 | |
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13 | |
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14 | #define GENMAN_REPEAT_FAILED 100 //how many times GenMan tries to repeat a mutation or crossover when the operator does not return acceptable genotype |
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15 | #define STRINGIFY_1(x) #x |
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16 | #define STRINGIFY(x) STRINGIFY_1(x) //this second-level macro allows the parameter to be a macro itself and to stringify its value, not its name |
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17 | #define GENMAN_REPEAT_FAILED_STR STRINGIFY(GENMAN_REPEAT_FAILED) |
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18 | |
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19 | |
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20 | #ifdef USE_GENMAN_f0 |
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21 | #include "f0/f0_oper.h" |
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22 | #endif |
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23 | #ifdef USE_GENMAN_f0FUZZY |
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24 | #include "f0/f0Fuzzy_oper.h" |
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25 | #endif |
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26 | #ifdef USE_GENMAN_f1 |
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27 | #include "f1/f1_oper.h" |
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28 | #endif |
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29 | #ifdef USE_GENMAN_f2 |
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30 | #include "f2/f2_oper.h" |
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31 | #endif |
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32 | #ifdef USE_GENMAN_f2 |
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33 | #include "f3/f3_oper.h" |
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34 | #endif |
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35 | #ifdef USE_GENMAN_f4 |
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36 | #include "f4/f4_oper.h" |
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37 | #endif |
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38 | #ifdef USE_GENMAN_f5 |
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39 | #include "f5/f5_oper.h" |
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40 | #endif |
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41 | #ifdef USE_GENMAN_f6 |
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42 | #include "f6/f6_oper.h" |
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43 | #endif |
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44 | #ifdef USE_GENMAN_f7 |
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45 | #include "f7/f7_oper.h" |
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46 | #endif |
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47 | #ifdef USE_GENMAN_f8 |
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48 | #include "f8/f8_oper.h" |
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49 | #endif |
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50 | #ifdef USE_GENMAN_f9 |
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51 | #include "f9/f9_oper.h" |
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52 | #endif |
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53 | #ifdef USE_GENMAN_fF |
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54 | #include "fF/fF_oper.h" |
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55 | #endif |
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56 | #ifdef USE_GENMAN_fn |
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57 | #include "fn/fn_oper.h" |
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58 | #endif |
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59 | #ifdef USE_GENMAN_fT |
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60 | #include "fT/fTest_oper.h" |
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61 | #endif |
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62 | #ifdef USE_GENMAN_fB |
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63 | #include "fB/fB_oper.h" |
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64 | #endif |
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65 | #ifdef USE_GENMAN_fH |
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66 | #include "fH/fH_oper.h" |
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67 | #endif |
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68 | #ifdef USE_GENMAN_fL |
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69 | #include "fL/fL_oper.h" |
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70 | #endif |
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71 | #ifdef USE_GENMAN_fS |
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72 | #include "fS/fS_oper.h" |
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73 | #endif |
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74 | |
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75 | using namespace std; //string, vector |
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76 | |
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77 | //old code needs update: |
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78 | //#include "gengroups.h" |
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79 | //extern GenGroup *listaGen; |
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80 | // GENGROUP(0)->l_del.add(sim->GM.onDelGen,&sim->GM); //before delete |
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81 | // GENGROUP(0)->l_del.remove(sim->GM.onDelGen,&sim->GM); //before delete |
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82 | |
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83 | |
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84 | #define FIELDSTRUCT GenMan |
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85 | |
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86 | static ParamEntry GMparam_tab[] = |
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87 | { |
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88 | { "Genetics", 1, 11, "GenMan", }, |
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89 | { "gen_hist", 0, PARAM_DONTSAVE, "Remember history of genetic operations", "d 0 1 0", FIELD(history), "Required for phylogenetic analysis", }, |
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90 | { "gen_hilite", 0, 0, "Use syntax highlighting", "d 0 1 1", FIELD(hilite), "Use colors for genes?\n(slows down viewing/editing of huge genotypes)", }, |
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91 | { "gen_extmutinfo", 0, 0, "Extended mutation info", "d 0 2 0 ~Off~Method ID~Method description", FIELD(extmutinfo), "If active, information about employed mutation method will be stored in the 'info' field of each mutated genotype.", }, |
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92 | { "operReport", 0, PARAM_DONTSAVE, "Operators report", "p()", PROCEDURE(p_report), "Show available genetic operators", }, |
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93 | { "toHTML", 0, PARAM_DONTSAVE, "HTMLize a genotype", "p s(s)", PROCEDURE(p_htmlize), "returns genotype expressed as colored HTML", }, |
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94 | { "toHTMLshort", 0, PARAM_DONTSAVE, "HTMLize a genotype, shorten if needed", "p s(s)", PROCEDURE(p_htmlizeshort), "returns genotype (abbreviated if needed) in colored HTML format", }, |
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95 | { "toLaTeX", 0, PARAM_DONTSAVE, "LaTeXize a genotype", "p s(s)", PROCEDURE(p_latexize), "returns genotype in colored LaTeX format", }, |
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96 | { "validate", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Validate", "p oGeno(oGeno)", PROCEDURE(p_validate), "returns validated (if possible) Geno object from supplied Geno", }, |
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97 | { "mutate", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Mutate", "p oGeno(oGeno)", PROCEDURE(p_mutate), "returns mutated Geno object from supplied Geno", }, |
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98 | { "crossOver", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Crossover", "p oGeno(oGeno,oGeno)", PROCEDURE(p_crossover), "returns crossed over genotype", }, |
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99 | { "getSimplest", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Get simplest genotype", "p oGeno(s format)", PROCEDURE(p_getsimplest), "returns the simplest genotype for a given encoding (format). \"0\" means f0, \"4\" means f4, etc.", }, |
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100 | { 0, }, |
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101 | }; |
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102 | |
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103 | static ParamEntry GMstats_tab[] = |
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104 | { |
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105 | { "Genetics", 1, 12, "GenManStats", "Statistics for genetic operations." }, |
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106 | { "gen_count", 0, PARAM_READONLY, "Number of genetic operations so far", "d", FIELD(count), "", }, |
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107 | { "gen_mvalid", 0, PARAM_READONLY, "Mutations valid", "d", FIELD(valid_m), "", }, |
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108 | { "gen_mvalidated", 0, PARAM_READONLY, "Mutations validated", "d", FIELD(validated_m), "", }, |
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109 | { "gen_minvalid", 0, PARAM_READONLY, "Mutations invalid", "d", FIELD(invalid_m), "couldn't be repaired", }, |
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110 | { "gen_mfailed", 0, PARAM_READONLY, "Mutations failed", "d", FIELD(failed_m), "couldn't be performed", }, |
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111 | { "gen_xovalid", 0, PARAM_READONLY, "Crossovers valid", "d", FIELD(valid_xo), "", }, |
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112 | { "gen_xovalidated", 0, PARAM_READONLY, "Crossovers validated", "d", FIELD(validated_xo), "", }, |
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113 | { "gen_xoinvalid", 0, PARAM_READONLY, "Crossovers invalid", "d", FIELD(invalid_xo), "couldn't be repaired", }, |
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114 | { "gen_xofailed", 0, PARAM_READONLY, "Crossovers failed", "d", FIELD(failed_xo), "couldn't be performed", }, |
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115 | { "gen_mutimpr", 0, PARAM_READONLY, "Mutations total effect", "f", FIELD(mutchg), "total cumulative mutation change", }, |
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116 | { "gen_xoimpr", 0, PARAM_READONLY, "Crossovers total effect", "f", FIELD(xochg), "total cumulative crossover change", }, |
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117 | { "clrstats", 0, PARAM_DONTSAVE, "Clear stats and history", "p()", PROCEDURE(p_clearStats), "", }, |
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118 | { 0, }, |
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119 | }; |
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120 | |
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121 | #undef FIELDSTRUCT |
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122 | |
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123 | GenMan::GenMan() : localpar(GMparam_tab, this), localstats(GMstats_tab, this), |
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124 | seloperpar("GenOperators", "Genetics: Active operators"), |
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125 | neuronsparam("Genetics: Neurons to add", "neuronsAdd", "neuadd_"), |
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126 | par("GenMan", "Manages various genetic operations, using appropriate operators for the argument genotype format.") |
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127 | { |
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128 | history = 0; |
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129 | hilite = 1; |
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130 | clearStats(); |
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131 | |
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132 | #ifdef USE_GENMAN_f0 |
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133 | oper_fx_list.push_back(new Geno_f0); |
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134 | #endif |
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135 | #ifdef USE_GENMAN_f0FUZZY |
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136 | oper_fx_list.push_back(new Geno_f0Fuzzy); |
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137 | #endif |
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138 | #ifdef USE_GENMAN_f1 |
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139 | oper_fx_list.push_back(new Geno_f1); |
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140 | #endif |
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141 | #ifdef USE_GENMAN_f2 |
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142 | oper_fx_list.push_back(new Geno_f2); |
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143 | #endif |
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144 | #ifdef USE_GENMAN_f3 |
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145 | oper_fx_list.push_back(new Geno_f3); |
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146 | #endif |
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147 | #ifdef USE_GENMAN_f4 |
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148 | oper_fx_list.push_back(new Geno_f4); |
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149 | #endif |
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150 | #ifdef USE_GENMAN_f5 |
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151 | oper_fx_list.push_back(new Geno_f5); |
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152 | #endif |
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153 | #ifdef USE_GENMAN_f6 |
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154 | oper_fx_list.push_back(new Geno_f6); |
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155 | #endif |
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156 | #ifdef USE_GENMAN_f7 |
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157 | oper_fx_list.push_back(new Geno_f7); |
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158 | #endif |
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159 | #ifdef USE_GENMAN_f8 |
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160 | oper_fx_list.push_back(new Geno_f8); |
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161 | #endif |
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162 | #ifdef USE_GENMAN_f9 |
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163 | oper_fx_list.push_back(new GenoOper_f9); |
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164 | #endif |
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165 | #ifdef USE_GENMAN_fF |
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166 | oper_fx_list.push_back(new GenoOper_fF); |
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167 | #endif |
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168 | #ifdef USE_GENMAN_fn |
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169 | oper_fx_list.push_back(new GenoOper_fn); |
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170 | #endif |
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171 | #ifdef USE_GENMAN_fT |
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172 | oper_fx_list.push_back(new GenoOper_fTest); |
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173 | #endif |
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174 | #ifdef USE_GENMAN_fB |
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175 | oper_fx_list.push_back(new Geno_fB); |
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176 | #endif |
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177 | #ifdef USE_GENMAN_fH |
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178 | oper_fx_list.push_back(new Geno_fH); |
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179 | #endif |
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180 | #ifdef USE_GENMAN_fL |
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181 | oper_fx_list.push_back(new Geno_fL); |
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182 | #endif |
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183 | #ifdef USE_GENMAN_fS |
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184 | oper_fx_list.push_back(new GenoOper_fS); |
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185 | #endif |
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186 | |
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187 | seloper = new int[oper_fx_list.size()]; //may result in a little overhead if some of the operators on the oper_fx_list concern the same genetic format |
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188 | int selopercount = 0; |
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189 | for (unsigned int i = 0; i < oper_fx_list.size(); i++) |
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190 | { |
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191 | if (findOperFormatIndex(oper_fx_list[i]->supported_format) != -1) continue; |
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192 | string type = string("~") + oper_fx_list[i]->name; |
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193 | int dup = 0; |
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194 | for (unsigned int j = i + 1; j < oper_fx_list.size(); j++) |
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195 | if (oper_fx_list[i]->supported_format == oper_fx_list[j]->supported_format) |
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196 | { |
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197 | type += "~"; |
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198 | type += oper_fx_list[j]->name; |
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199 | dup++; |
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200 | } |
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201 | type = ssprintf("d 0 %d ", dup) + type; |
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202 | string id = ssprintf("genoper_f%s", oper_fx_list[i]->supported_format.c_str()); |
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203 | string name = ssprintf("Operators for f%s", oper_fx_list[i]->supported_format.c_str()); |
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204 | seloper[selopercount] = 0; |
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205 | operformats += &oper_fx_list[i]->supported_format; |
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206 | //printf("%x %s %s %s\n",&seloper[selopercount],(const char*)id,(const char*)type,(const char*)name); |
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207 | seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY * (dup == 0)); |
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208 | } |
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209 | |
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210 | par += &localpar; |
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211 | par += &seloperpar; |
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212 | par += &neuronsparam; |
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213 | for (unsigned int i = 0; i < oper_fx_list.size(); i++) |
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214 | if (oper_fx_list[i]->par.getParamTab()) par += &oper_fx_list[i]->par; |
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215 | |
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216 | setDefaults(); //use Param to initialize all values of fields in the paramtab of this object and genetic operators on oper_fx_list |
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217 | } |
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218 | |
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219 | GenMan::~GenMan() |
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220 | { |
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221 | for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i]; |
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222 | delete[] seloper; |
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223 | } |
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224 | |
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225 | int GenMan::findOperFormatIndex(const SString& format) |
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226 | { |
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227 | for (int i = 0; i < operformats.size(); i++) |
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228 | if (*operformats(i) == format) |
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229 | return i; |
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230 | return -1; |
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231 | } |
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232 | |
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233 | void GenMan::setDefaults() |
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234 | { |
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235 | for (unsigned int i = 0; i < oper_fx_list.size(); i++) |
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236 | { |
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237 | oper_fx_list[i]->par.setDefault(); |
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238 | oper_fx_list[i]->setDefaults(); |
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239 | } |
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240 | localpar.setDefault(); |
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241 | //...and we do not reset others that are linked to 'par', |
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242 | //because there quite a few of them, and not every of them defines defaults for each of its parameters. |
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243 | } |
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244 | |
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245 | int GenMan::testValidity(Geno &g, bool &canvalidate) |
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246 | { |
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247 | SString ggs = g.getGenes(); |
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248 | const char *gg = ggs.c_str(); |
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249 | GenoOperators *gf = getOper_f(g.getFormat()); |
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250 | int check1; |
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251 | if (!gf) { canvalidate = false; return GENOPER_NOOPER; } |
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252 | else check1 = gf->checkValidity(gg, g.getName().c_str()); |
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253 | if (!canvalidate) return check1; //just checking |
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254 | if (check1 == GENOPER_OK) { canvalidate = false; return check1; } |
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255 | char *g2 = strdup(gg); |
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256 | if (gf->validate(g2, g.getName().c_str()) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; } |
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257 | if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator |
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258 | { |
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259 | g.setGenesAssumingSameFormat(g2); free(g2); canvalidate = false; return GENOPER_NOOPER; |
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260 | } |
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261 | int check2 = gf->checkValidity(g2, "validated"); |
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262 | if (check2 == GENOPER_OK) g.setGenesAssumingSameFormat(g2); |
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263 | free(g2); |
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264 | if (check2 == GENOPER_OK) return check1; |
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265 | canvalidate = false; |
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266 | return check1; //could not validate. |
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267 | } |
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268 | |
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269 | int GenMan::testGenoValidity(Geno& g) |
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270 | { |
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271 | bool fix = false; |
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272 | switch (testValidity(g, fix)) |
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273 | { |
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274 | case GENOPER_OK: return 1; |
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275 | case GENOPER_NOOPER: return -1; |
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276 | default: return 0; |
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277 | } |
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278 | } |
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279 | |
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280 | Geno GenMan::validate(const Geno& geny) |
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281 | { |
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282 | SString format = geny.getFormat(); |
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283 | GenoOperators *gf = getOper_f(format); |
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284 | if (gf == NULL) |
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285 | return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %s", format.c_str())); |
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286 | char *g2 = strdup(geny.getGenes().c_str()); //copy for validation |
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287 | int res = gf->validate(g2, geny.getName().c_str()); |
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288 | SString sg2 = g2; |
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289 | free(g2); |
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290 | if (res == GENOPER_OK) |
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291 | return Geno(sg2, format, geny.getName(), geny.getComment()); |
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292 | else |
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293 | return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: validate() for format %s returned invalid value", format.c_str())); |
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294 | } |
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295 | |
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296 | Geno GenMan::mutate(const Geno& g) |
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297 | { |
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298 | float chg; //how many changes |
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299 | int method; //mutation method |
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300 | SString format = g.getFormat(); |
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301 | GenoOperators *gf = getOper_f(format); |
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302 | if (gf == NULL) |
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303 | return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %s", format.c_str())); |
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304 | Geno gv = g; |
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305 | bool canvalidate = true; |
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306 | if (testValidity(gv, canvalidate) > 0 && canvalidate == false) |
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307 | return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype"); |
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308 | bool ok = false; |
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309 | int pcount = count; |
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310 | while (!ok) |
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311 | { |
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312 | char *gn = strdup(gv.getGenes().c_str()); //copy for mutation |
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313 | chg = 0; |
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314 | if (gf->mutate(gn, chg, method) == GENOPER_OK) |
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315 | { |
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316 | LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity() |
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317 | Geno G(gn, gv.getFormat(), "", ""); |
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318 | canvalidate = true; |
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319 | int res = testValidity(G, canvalidate); |
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320 | if (res == GENOPER_OK && canvalidate == false) { valid_m++; ok = true; } |
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321 | else |
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322 | if (res > 0 && canvalidate == false) invalid_m++; else |
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323 | { |
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324 | validated_m++; ok = true; |
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325 | } |
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326 | if (ok) gv = G; |
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327 | } |
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328 | else failed_m++; |
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329 | free(gn); |
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330 | count++; |
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331 | if (!ok && (count - pcount > GENMAN_REPEAT_FAILED)) |
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332 | { |
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333 | logPrintf("GenMan", "Mutate", LOG_WARN, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s", g.getGenes().c_str()); |
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334 | return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried " GENMAN_REPEAT_FAILED_STR "x and failed"); |
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335 | } |
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336 | } |
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337 | mutchg += chg; |
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338 | if (history) saveLink(g.getGenes().c_str(), "", gv.getGenes().c_str(), chg); |
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339 | SString mutinfo; |
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340 | if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else |
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341 | if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, g.getName().c_str()); else |
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342 | mutinfo = SString::sprintf("%.2f%% mutation(%s) of '%s'", 100 * chg, gf->mutation_method_names ? gf->mutation_method_names[method] : "unspecified method name", g.getName().c_str()); |
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343 | gv.setComment(mutinfo); |
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344 | return gv; |
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345 | } |
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346 | |
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347 | Geno GenMan::crossOver(const Geno& g1, const Geno& g2) |
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348 | { |
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349 | SString format = g1.getFormat(); |
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350 | if (format != g2.getFormat()) return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): does not work for parents with differing genetic formats (%s and %s)", format.c_str(), g2.getFormat().c_str())); |
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351 | GenoOperators *gf = getOper_f(format); |
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352 | if (gf == NULL) |
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353 | return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %s", format.c_str())); |
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354 | Geno g1v = g1, g2v = g2; |
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355 | |
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356 | { |
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357 | LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity() |
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358 | bool canvalidate = true; |
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359 | if (testValidity(g1v, canvalidate) > 0 && canvalidate == false) |
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360 | return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1"); |
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361 | canvalidate = true; |
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362 | if (testValidity(g2v, canvalidate) > 0 && canvalidate == false) |
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363 | return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2"); |
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364 | } |
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365 | |
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366 | float chg; |
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367 | bool ok = false; |
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368 | int pcount = count; |
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369 | |
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370 | while (!ok) |
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371 | { |
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372 | float chg1, chg2; |
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373 | char *g1n = strdup(g1.getGenes().c_str()); //copy for crossover |
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374 | char *g2n = strdup(g2.getGenes().c_str()); //copy for crossover |
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375 | chg1 = chg2 = 0; |
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376 | if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK) |
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377 | { |
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378 | char *gn; |
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379 | if (g1n[0] && g2n[0]) if (rndUint(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one |
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380 | if (g1n[0]) { gn = g1n; chg = chg1; } |
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381 | else { gn = g2n; chg = chg2; } |
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382 | LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity() |
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383 | Geno G(gn, g1v.getFormat(), "", ""); |
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384 | bool canvalidate = true; |
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385 | int res = testValidity(G, canvalidate); |
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386 | if (res == GENOPER_OK && canvalidate == false) { valid_xo++; ok = true; } |
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387 | else |
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388 | if (res > 0 && canvalidate == false) invalid_xo++; else |
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389 | { |
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390 | validated_xo++; ok = true; |
---|
391 | } |
---|
392 | if (ok) g1v = G; |
---|
393 | } |
---|
394 | else failed_xo++; |
---|
395 | free(g1n); |
---|
396 | free(g2n); |
---|
397 | count++; |
---|
398 | if (!ok && (count - pcount > GENMAN_REPEAT_FAILED)) |
---|
399 | { |
---|
400 | logPrintf("GenMan", "CrossOver", LOG_WARN, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str()); |
---|
401 | return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver() tried " GENMAN_REPEAT_FAILED_STR "x and failed"); |
---|
402 | } |
---|
403 | } |
---|
404 | // result in g1v |
---|
405 | xochg += chg; |
---|
406 | if (history) saveLink(g1.getGenes().c_str(), g2.getGenes().c_str(), g1v.getGenes().c_str(), chg); |
---|
407 | SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)", |
---|
408 | g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg)); |
---|
409 | g1v.setComment(xoinfo); |
---|
410 | return g1v; |
---|
411 | } |
---|
412 | |
---|
413 | float GenMan::similarity(const Geno& g1, const Geno& g2) |
---|
414 | { |
---|
415 | SString format = g1.getFormat(); |
---|
416 | if (format != g2.getFormat()) return GENOPER_NOOPER; |
---|
417 | GenoOperators *gf = getOper_f(format); |
---|
418 | if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGenes().c_str(), g2.getGenes().c_str()); |
---|
419 | } |
---|
420 | |
---|
421 | uint32_t GenMan::getStyle(const char *g, const Geno *G, int pos) |
---|
422 | { |
---|
423 | SString format = G->getFormat(); |
---|
424 | if (format == Geno::INVALID_FORMAT) |
---|
425 | return GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not) |
---|
426 | if ((pos = G->mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT; |
---|
427 | GenoOperators *gf = getOper_f(format); |
---|
428 | if (!gf) return GENSTYLE_CS(0, 0); //black & valid |
---|
429 | else return gf->style(G->getGenes().c_str(), pos); |
---|
430 | } |
---|
431 | |
---|
432 | uint32_t GenMan::getStyle(const char *g, int pos) |
---|
433 | { |
---|
434 | Geno G(g); |
---|
435 | return getStyle(g, &G, pos); |
---|
436 | } |
---|
437 | |
---|
438 | void GenMan::getFullStyle(const char *g, const Geno *G, uint32_t *styletab) |
---|
439 | { |
---|
440 | SString format = G->getFormat(); |
---|
441 | if (format == Geno::INVALID_FORMAT) |
---|
442 | { |
---|
443 | for (unsigned int pos = 0; pos < strlen(g); pos++) |
---|
444 | styletab[pos] = GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not) |
---|
445 | return; |
---|
446 | } |
---|
447 | GenoOperators *gf = getOper_f(format); |
---|
448 | SString geny = G->getGenes(); |
---|
449 | for (unsigned int pos = 0; pos < strlen(g); pos++) |
---|
450 | { |
---|
451 | int posmapped = G->mapStringToGen(pos); |
---|
452 | if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT; |
---|
453 | else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid |
---|
454 | else styletab[pos] = gf->style(geny.c_str(), posmapped); |
---|
455 | //logPrintf("GenMan", "getFullStyle", LOG_INFO, "%d char='%c' (%d) format=0x%08x", pos, g[pos], g[pos], styletab[pos]); |
---|
456 | } |
---|
457 | } |
---|
458 | |
---|
459 | void GenMan::getFullStyle(const char *g, uint32_t *styletab) |
---|
460 | { |
---|
461 | Geno G(g); |
---|
462 | getFullStyle(g, &G, styletab); |
---|
463 | } |
---|
464 | |
---|
465 | string GenMan::HTMLize(const char *g) { return HTMLize(g, false); } |
---|
466 | |
---|
467 | string GenMan::HTMLizeShort(const char *g) { return HTMLize(g, true); } |
---|
468 | |
---|
469 | string GenMan::HTMLize(const char *g, bool shorten) |
---|
470 | { |
---|
471 | char buf[50]; |
---|
472 | int len = strlen(g); |
---|
473 | int chars = 0, lines = 0; |
---|
474 | bool shortened = false; |
---|
475 | uint32_t *styletab = new uint32_t[len]; |
---|
476 | getFullStyle(g, styletab); |
---|
477 | string html = "\n<div style=\"background:white;padding:0.2em;font-family:arial,helvetica,sans-serif;font-size:90%\">"; |
---|
478 | uint32_t prevstyle, prevcolor, style = 0, color = 0; |
---|
479 | for (int i = 0; i < len; i++) |
---|
480 | { |
---|
481 | if (shorten && ((lines == 0 && chars > 160) || (lines > 5 || chars > 300))) { shortened = true; break; } |
---|
482 | if (g[i] == '\r') continue; |
---|
483 | if (g[i] == '\n') { html += "<br>\n"; lines++; continue; } |
---|
484 | chars++; |
---|
485 | prevstyle = style; |
---|
486 | prevcolor = color; |
---|
487 | style = GENGETSTYLE(styletab[i]); |
---|
488 | color = GENGETCOLOR(styletab[i]); |
---|
489 | if ((i != 0 && (color != prevcolor))) html += "</font>"; |
---|
490 | if ((style & GENSTYLE_INVALID) != (prevstyle & GENSTYLE_INVALID)) |
---|
491 | { |
---|
492 | html += "<"; if (!(style & GENSTYLE_INVALID)) html += "/"; html += "u>"; |
---|
493 | } |
---|
494 | if ((style & GENSTYLE_BOLD) != (prevstyle & GENSTYLE_BOLD)) |
---|
495 | { |
---|
496 | html += "<"; if (!(style & GENSTYLE_BOLD)) html += "/"; html += "b>"; |
---|
497 | } |
---|
498 | if ((style & GENSTYLE_ITALIC) != (prevstyle & GENSTYLE_ITALIC)) |
---|
499 | { |
---|
500 | html += "<"; if (!(style & GENSTYLE_ITALIC)) html += "/"; html += "i>"; |
---|
501 | } |
---|
502 | if ((i == 0 || (color != prevcolor))) |
---|
503 | { |
---|
504 | sprintf(buf, "<font color=#%02x%02x%02x>", GENGET_R(color), GENGET_G(color), GENGET_B(color)); html += buf; |
---|
505 | } |
---|
506 | if (g[i] == '<') html += "<"; else if (g[i] == '>') html += ">"; else html += g[i]; |
---|
507 | if ((i % 3) == 0 && g[i] == ' ') html += "\n"; //for readability, insert some newlines into html... |
---|
508 | } |
---|
509 | delete[] styletab; |
---|
510 | html += "</u></b></i></font>"; |
---|
511 | if (shortened) html += " [etc...]"; |
---|
512 | html += "</div>\n"; |
---|
513 | return html; |
---|
514 | } |
---|
515 | |
---|
516 | void GenMan::p_htmlize(ExtValue *args, ExtValue *ret) |
---|
517 | { |
---|
518 | ret->setString(HTMLize(args->getString().c_str()).c_str()); |
---|
519 | } |
---|
520 | |
---|
521 | void GenMan::p_htmlizeshort(ExtValue *args, ExtValue *ret) |
---|
522 | { |
---|
523 | ret->setString(HTMLizeShort(args->getString().c_str()).c_str()); |
---|
524 | } |
---|
525 | |
---|
526 | string GenMan::LaTeXize(const char *g) |
---|
527 | { |
---|
528 | char buf[50]; |
---|
529 | int len = strlen(g); |
---|
530 | int chars = 0, lines = 0; //currently not used |
---|
531 | uint32_t *styletab = new uint32_t[len]; |
---|
532 | getFullStyle(g, styletab); |
---|
533 | string latex = "\\usepackage{xcolor}\n% Using \\texttt{} may be beneficial for some genetic encodings, but then you may lose bold/italic.\n\\noindent \\sloppy"; |
---|
534 | uint32_t prevstyle, prevcolor, style = 0, color = 0; |
---|
535 | for (int i = 0; i < len; i++) |
---|
536 | { |
---|
537 | if (g[i] == '\r') continue; |
---|
538 | if (g[i] == '\n') { latex += "\\\\\n"; lines++; continue; } |
---|
539 | chars++; |
---|
540 | prevstyle = style; |
---|
541 | prevcolor = color; |
---|
542 | style = GENGETSTYLE(styletab[i]); |
---|
543 | color = GENGETCOLOR(styletab[i]); |
---|
544 | |
---|
545 | // Unfortunately, LaTeX (as opposed to HTML) uses the same closing tags "}" for color, bold, italic, underline - so they cannot intersect. |
---|
546 | // Therefore we have to "turn off" everything on every change of style or color, and then "turn on" (to avoid problems with e.g. red-bold-blue-unbold or bold-italic-unbold-unitalic). |
---|
547 | // This could be optimized by a more complex logic and tracking which color/style section starts and ends within another section. |
---|
548 | |
---|
549 | if (((style & GENSTYLE_INVALID) != (prevstyle & GENSTYLE_INVALID)) |
---|
550 | || |
---|
551 | ((style & GENSTYLE_BOLD) != (prevstyle & GENSTYLE_BOLD)) |
---|
552 | || |
---|
553 | ((style & GENSTYLE_ITALIC) != (prevstyle & GENSTYLE_ITALIC)) |
---|
554 | || |
---|
555 | ((i == 0 || (color != prevcolor)))) |
---|
556 | { |
---|
557 | if (prevstyle & GENSTYLE_INVALID) latex += "}"; |
---|
558 | if (prevstyle & GENSTYLE_BOLD) latex += "}"; |
---|
559 | if (prevstyle & GENSTYLE_ITALIC) latex += "}"; |
---|
560 | if (i != 0) latex += "}"; //for color |
---|
561 | if (style & GENSTYLE_INVALID) latex += "\\underline{"; |
---|
562 | if (style & GENSTYLE_BOLD) latex += "\\textbf{"; |
---|
563 | if (style & GENSTYLE_ITALIC) latex += "\\textit{"; |
---|
564 | sprintf(buf, "\\textcolor[rgb]{%.2g,%.2g,%.2g}{", GENGET_R(color) / 255.0, GENGET_G(color) / 255.0, GENGET_B(color) / 255.0); latex += buf; |
---|
565 | } |
---|
566 | if (g[i] == '<') latex += "$<$"; else if (g[i] == '>') latex += "$>$"; else |
---|
567 | if (g[i] == '-') latex += "$-$"; else if (g[i] == '|') latex += "$|$"; else |
---|
568 | if (g[i] == '$') latex += "\\$"; else if (g[i] == '%') latex += "\\%"; else latex += g[i]; |
---|
569 | if ((i % 3) == 0 && g[i] == ' ') latex += "\n"; //for readability, insert some newlines into latex... |
---|
570 | if (i % 10 == 0) latex += "{\\hskip 0pt}"; // https://tex.stackexchange.com/questions/33526/automatic-line-breaking-of-long-lines-of-text |
---|
571 | } |
---|
572 | delete[] styletab; |
---|
573 | latex += "}"; //for color (it was used at least once) |
---|
574 | if (style & GENSTYLE_INVALID) latex += "}"; |
---|
575 | if (style & GENSTYLE_BOLD) latex += "}"; |
---|
576 | if (style & GENSTYLE_ITALIC) latex += "}"; |
---|
577 | latex += "\n"; |
---|
578 | return latex; |
---|
579 | } |
---|
580 | |
---|
581 | void GenMan::p_latexize(ExtValue *args, ExtValue *ret) |
---|
582 | { |
---|
583 | ret->setString(LaTeXize(args->getString().c_str()).c_str()); |
---|
584 | } |
---|
585 | |
---|
586 | Geno GenMan::getSimplest(const SString& format) |
---|
587 | { |
---|
588 | GenoOperators *gf = getOper_f(format); |
---|
589 | if (!gf) return Geno(); |
---|
590 | string info = "The simplest genotype of format f"; info += format.c_str(); |
---|
591 | info += " for operators '"; info += gf->name; info += "'."; |
---|
592 | return Geno(gf->getSimplest(), format, "Root", info.c_str()); |
---|
593 | } |
---|
594 | |
---|
595 | void GenMan::p_getsimplest(ExtValue *args, ExtValue *ret) |
---|
596 | { |
---|
597 | SString format = GenoObj::formatFromExtValue(args[0]); |
---|
598 | if (!getOper_f(format)) |
---|
599 | ret->setEmpty(); |
---|
600 | else |
---|
601 | *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(getSimplest(format))); |
---|
602 | } |
---|
603 | |
---|
604 | const char *GenMan::getOpName(const SString& format) |
---|
605 | { |
---|
606 | GenoOperators *gf = getOper_f(format); |
---|
607 | if (!gf) return "n/a"; else return gf->name.c_str(); |
---|
608 | } |
---|
609 | |
---|
610 | GenoOperators* GenMan::getOper_f(const SString& format) |
---|
611 | { |
---|
612 | int ind = findOperFormatIndex(format); |
---|
613 | if (ind == -1) return NULL; |
---|
614 | int which_oper_of_format = seloper[ind]; |
---|
615 | for (unsigned int i = 0; i < oper_fx_list.size(); i++) |
---|
616 | if (oper_fx_list[i]->supported_format == format) |
---|
617 | if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--; |
---|
618 | return NULL; //should never happen |
---|
619 | } |
---|
620 | |
---|
621 | void GenMan::saveLink(const string parent1, const string parent2, const string child, const float chg) |
---|
622 | { |
---|
623 | GenoLink l; |
---|
624 | l.count = count; |
---|
625 | l.parent1 = parent1; |
---|
626 | l.parent2 = parent2; |
---|
627 | l.child = child; |
---|
628 | l.chg = chg; |
---|
629 | l.fit = 0; //temporarily. Will be set when the genotype dies |
---|
630 | //logPrintf("GenMan","saveLink",0,"#%d: [%d] '%s' + '%s' -> '%s'",GenoLinkList.size(),count,parent1.c_str(),parent2.c_str(),child.c_str()); |
---|
631 | GenoLinkList.push_back(l); |
---|
632 | } |
---|
633 | |
---|
634 | void GenMan::onDelGen(void *obj, intptr_t n) |
---|
635 | { |
---|
636 | //old code needs update: |
---|
637 | // ((SpeciesList*)obj)->przyDodaniu(i); |
---|
638 | /* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
---|
639 | GenMan *gm=(GenMan*)obj; |
---|
640 | Genotype *gt=(Genotype*)(*listaGen)(n); //there is no more "listaGen" |
---|
641 | string g=(const char*)gt->genotype.getGene(); |
---|
642 | float fit=gt->getFinalFitness(); |
---|
643 | for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype |
---|
644 | if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;} |
---|
645 | */ |
---|
646 | } |
---|
647 | |
---|
648 | void GenMan::clearStats() |
---|
649 | { |
---|
650 | count = 0; |
---|
651 | valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0; |
---|
652 | mutchg = xochg = 0; |
---|
653 | GenoLinkList.clear(); |
---|
654 | } |
---|
655 | |
---|
656 | void GenMan::p_clearStats(ExtValue *args, ExtValue *ret) { clearStats(); } |
---|
657 | |
---|
658 | void GenMan::p_report(ExtValue *args, ExtValue *ret) |
---|
659 | { //should be updated to handle multiple operators for a single format |
---|
660 | char *g, *g2; |
---|
661 | float f1, f2; |
---|
662 | int m; |
---|
663 | logMessage("GenMan", "Report", 0, "The following genetic operators are available:"); |
---|
664 | for (unsigned int i = 0; i < oper_fx_list.size(); i++) |
---|
665 | { |
---|
666 | string l; |
---|
667 | if (oper_fx_list[i]->checkValidity("", "") != GENOPER_NOOPER) l += " checkValidity"; |
---|
668 | if (oper_fx_list[i]->getSimplest()) |
---|
669 | { |
---|
670 | g = strdup(oper_fx_list[i]->getSimplest()); |
---|
671 | g2 = strdup(g); |
---|
672 | if (oper_fx_list[i]->validate(g, "") != GENOPER_NOOPER) l += " validate"; |
---|
673 | if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate"; |
---|
674 | if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover"; |
---|
675 | l += " getSimplest"; |
---|
676 | free(g); free(g2); |
---|
677 | } |
---|
678 | // if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity"; |
---|
679 | logPrintf("GenMan", "Report", LOG_INFO, "format f%s (%s):%s", |
---|
680 | oper_fx_list[i]->supported_format.c_str(), oper_fx_list[i]->name.c_str(), l.c_str()); |
---|
681 | } |
---|
682 | } |
---|
683 | |
---|
684 | void GenMan::p_validate(ExtValue *args, ExtValue *ret) |
---|
685 | { |
---|
686 | Geno *g = GenoObj::fromObject(args[0]); |
---|
687 | if (g == NULL) |
---|
688 | ret->setEmpty(); |
---|
689 | else |
---|
690 | *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(validate(*g))); |
---|
691 | } |
---|
692 | |
---|
693 | void GenMan::p_mutate(ExtValue *args, ExtValue *ret) |
---|
694 | { |
---|
695 | Geno *g = GenoObj::fromObject(args[0]); |
---|
696 | if (g == NULL) |
---|
697 | ret->setEmpty(); |
---|
698 | else |
---|
699 | *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(mutate(*g))); |
---|
700 | } |
---|
701 | |
---|
702 | void GenMan::p_crossover(ExtValue *args, ExtValue *ret) |
---|
703 | { |
---|
704 | Geno *g1 = GenoObj::fromObject(args[1]); |
---|
705 | Geno *g2 = GenoObj::fromObject(args[0]); |
---|
706 | if (g1 == NULL || g2 == NULL) |
---|
707 | ret->setEmpty(); |
---|
708 | else |
---|
709 | *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(crossOver(*g1, *g2))); |
---|
710 | } |
---|
711 | |
---|