1 | /* |
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2 | * ---------------------------------------------------------------------- |
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3 | * OPTIMIZER PLUG-IN: Pgapack |
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4 | * |
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5 | * This code connects Pgapack into the Rappture Optimization |
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6 | * infrastructure. |
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7 | * |
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8 | * ====================================================================== |
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9 | * AUTHOR: Michael McLennan, Purdue University |
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10 | * Copyright (c) 2008 Purdue Research Foundation |
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11 | * |
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12 | * See the file "license.terms" for information on usage and |
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13 | * redistribution of this file, and for a DISCLAIMER OF ALL WARRANTIES. |
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14 | * ====================================================================== |
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15 | */ |
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16 | #include "pgapack.h" |
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17 | #include "rp_optimizer.h" |
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18 | |
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19 | typedef struct PgapackData { |
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20 | int operation; /* operation <=> PGA_MINIMIZE/PGA_MAXIMIZE */ |
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21 | int maxRuns; /* maximum runs <=> PGASetMaxGAIterValue() */ |
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22 | int popSize; /* population size <=> PGASetPopSize() */ |
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23 | int popRepl; /* replacement <=> PGASetPopReplacementType() */ |
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24 | int stpcriteria; /*stoppage criteria <=> PGASetStoppingRuleType()*/ |
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25 | int randnumseed; /*Random Number Seed <=> PGASetRandomSeed()*/ |
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26 | double mutnrate; /*Mutation Rate <=> PGASetMutationProb()*/ |
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27 | double crossovrate; /*Crossover Rate <=> PGASetCrossoverProb();*/ |
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28 | } PgapackData; |
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29 | |
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30 | RpCustomTclOptionGet RpOption_GetStpCriteria; |
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31 | RpCustomTclOptionParse RpOption_ParseStpCriteria; |
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32 | RpTclOptionType RpOption_StpCriteria = { |
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33 | "pga_stpcriteria", RpOption_ParseStpCriteria,RpOption_GetStpCriteria,NULL |
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34 | }; |
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35 | |
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36 | RpCustomTclOptionParse RpOption_ParseOper; |
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37 | RpCustomTclOptionGet RpOption_GetOper; |
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38 | RpTclOptionType RpOption_Oper = { |
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39 | "pga_operation", RpOption_ParseOper, RpOption_GetOper, NULL |
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40 | }; |
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41 | |
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42 | RpCustomTclOptionParse RpOption_ParsePopRepl; |
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43 | RpCustomTclOptionGet RpOption_GetPopRepl; |
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44 | RpTclOptionType RpOption_PopRepl = { |
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45 | "pga_poprepl", RpOption_ParsePopRepl, RpOption_GetPopRepl, NULL |
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46 | }; |
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47 | |
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48 | |
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49 | typedef struct PgapackRuntimeDataTable{ |
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50 | double **data; /*Actual data per sample, like values of the genes, fitness of a sample, etc*/ |
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51 | int num_of_rows; /*Number of rows alloced..should be constant for a run*/ |
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52 | int no_of_samples_evaled; /*Number of samples evaluated so far*/ |
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53 | int no_of_columns; /*Number of columns allocated to the data table so far*/ |
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54 | }PgapackRuntimeDataTable; |
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55 | |
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56 | RpTclOption PgapackOptions[] = { |
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57 | {"-maxruns", RP_OPTION_INT, Rp_Offset(PgapackData,maxRuns)}, |
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58 | {"-operation", &RpOption_Oper, Rp_Offset(PgapackData,operation)}, |
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59 | {"-poprepl", &RpOption_PopRepl, Rp_Offset(PgapackData,popRepl)}, |
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60 | {"-popsize", RP_OPTION_INT, Rp_Offset(PgapackData,popSize)}, |
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61 | {"-mutnrate",RP_OPTION_DOUBLE,Rp_Offset(PgapackData,mutnrate)}, |
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62 | {"-crossovrate",RP_OPTION_DOUBLE,Rp_Offset(PgapackData,crossovrate)}, |
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63 | {"-randnumseed",RP_OPTION_INT,Rp_Offset(PgapackData,randnumseed)}, |
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64 | {"-stpcriteria",&RpOption_StpCriteria,Rp_Offset(PgapackData,stpcriteria)}, |
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65 | {NULL, NULL, 0} |
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66 | }; |
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67 | |
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68 | static double PgapEvaluate _ANSI_ARGS_((PGAContext *ctx, int p, int pop)); |
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69 | static void PgapCreateString _ANSI_ARGS_((PGAContext *ctx, int, int, int)); |
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70 | static int PgapMutation _ANSI_ARGS_((PGAContext *ctx, int, int, double)); |
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71 | static void PgapCrossover _ANSI_ARGS_((PGAContext *ctx, int, int, int, |
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72 | int, int, int)); |
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73 | static void PgapPrintString _ANSI_ARGS_((PGAContext *ctx, FILE*, int, int)); |
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74 | static void PgapCopyString _ANSI_ARGS_((PGAContext *ctx, int, int, int, int)); |
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75 | static int PgapDuplicateString _ANSI_ARGS_((PGAContext *ctx, int, int, int, int)); |
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76 | static MPI_Datatype PgapBuildDT _ANSI_ARGS_((PGAContext *ctx, int, int)); |
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77 | |
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78 | static void PgapLinkContext2Env _ANSI_ARGS_((PGAContext *ctx, |
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79 | RpOptimEnv *envPtr)); |
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80 | static RpOptimEnv* PgapGetEnvForContext _ANSI_ARGS_((PGAContext *ctx)); |
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81 | static void PgapUnlinkContext2Env _ANSI_ARGS_((PGAContext *ctx)); |
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82 | void PGARuntimeDataTableInit _ANSI_ARGS_((RpOptimEnv *envPtr)); |
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83 | void PGARuntimeDataTableDeInit(); |
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84 | void GetSampleInformation _ANSI_ARGS_((char *buffer, int sampleNumber)); |
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85 | void PGARuntimeDataTableSetSampleValue _ANSI_ARGS_((RpOptimParam *chrom, double fitness)); |
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86 | static PgapackRuntimeDataTable table; |
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87 | /* |
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88 | * ---------------------------------------------------------------------- |
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89 | * PgapackInit() |
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90 | * |
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91 | * This routine is called whenever a new optimization object is created |
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92 | * to initialize Pgapack. Returns a pointer to PgapackData that is |
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93 | * used in later routines. |
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94 | * ---------------------------------------------------------------------- |
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95 | */ |
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96 | ClientData |
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97 | PgapackInit() |
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98 | { |
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99 | PgapackData *dataPtr; |
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100 | |
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101 | dataPtr = (PgapackData*)malloc(sizeof(PgapackData)); |
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102 | dataPtr->operation = PGA_MINIMIZE; |
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103 | dataPtr->maxRuns = 10000; |
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104 | dataPtr->popRepl = PGA_POPREPL_BEST; |
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105 | dataPtr->popSize = 200; |
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106 | dataPtr->crossovrate = 0.85; |
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107 | dataPtr->mutnrate = 0.05; /*by default in PGAPack 1/stringlength*/ |
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108 | dataPtr->randnumseed = 1; /*should be a number greater than one, PGAPack requires it*/ |
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109 | dataPtr->stpcriteria = PGA_STOP_NOCHANGE; |
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110 | return (ClientData)dataPtr; |
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111 | } |
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112 | |
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113 | int pgapack_abort = 0; |
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114 | |
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115 | /* |
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116 | * ---------------------------------------------------------------------- |
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117 | * PgapackRun() |
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118 | * |
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119 | * This routine is called to kick off an optimization run. Sets up |
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120 | * a PGApack context and starts invoking runs. |
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121 | * ---------------------------------------------------------------------- |
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122 | */ |
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123 | RpOptimStatus |
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124 | PgapackRun(envPtr, evalProc, fitnessExpr) |
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125 | RpOptimEnv *envPtr; /* optimization environment */ |
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126 | RpOptimEvaluator *evalProc; /* call this proc to run tool */ |
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127 | char *fitnessExpr; /* fitness function in string form */ |
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128 | { |
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129 | PgapackData *dataPtr =(PgapackData*)envPtr->pluginData; |
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130 | PGAContext *ctx; |
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131 | |
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132 | /* pgapack requires at least one arg -- the executable name */ |
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133 | /* fake it here by just saying something like "rappture" */ |
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134 | int argc = 1; char *argv[] = {"rappture"}; |
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135 | |
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136 | pgapack_abort = 0; /* FALSE */ |
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137 | PGASetAbortVar(&pgapack_abort); |
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138 | |
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139 | ctx = PGACreate(&argc, argv, PGA_DATATYPE_USER, envPtr->numParams, |
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140 | dataPtr->operation); |
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141 | |
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142 | PGASetMaxGAIterValue(ctx, dataPtr->maxRuns); |
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143 | PGASetPopSize(ctx, dataPtr->popSize); |
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144 | PGASetPopReplaceType(ctx, dataPtr->popRepl); |
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145 | PGASetStoppingRuleType(ctx, dataPtr->stpcriteria); |
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146 | PGASetMutationProb(ctx,dataPtr->mutnrate); |
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147 | PGASetCrossoverProb(ctx,dataPtr->crossovrate); |
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148 | PGASetRandomSeed(ctx,dataPtr->randnumseed); |
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149 | PGASetCrossoverType(ctx, PGA_CROSSOVER_UNIFORM); |
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150 | |
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151 | |
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152 | PGASetUserFunction(ctx, PGA_USERFUNCTION_CREATESTRING, PgapCreateString); |
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153 | PGASetUserFunction(ctx, PGA_USERFUNCTION_MUTATION, PgapMutation); |
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154 | PGASetUserFunction(ctx, PGA_USERFUNCTION_CROSSOVER, PgapCrossover); |
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155 | PGASetUserFunction(ctx, PGA_USERFUNCTION_PRINTSTRING, PgapPrintString); |
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156 | PGASetUserFunction(ctx, PGA_USERFUNCTION_COPYSTRING, PgapCopyString); |
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157 | PGASetUserFunction(ctx, PGA_USERFUNCTION_DUPLICATE, PgapDuplicateString); |
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158 | PGASetUserFunction(ctx, PGA_USERFUNCTION_BUILDDATATYPE, PgapBuildDT); |
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159 | |
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160 | envPtr->evalProc = evalProc; /* plug these in for later during eval */ |
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161 | envPtr->fitnessExpr = fitnessExpr; |
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162 | |
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163 | /* |
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164 | * We need a way to convert from a PGAContext to our RpOptimEnv |
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165 | * data. This happens when Pgapack calls routines like |
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166 | * PgapCreateString, passing in the PGAContext, but nothing else. |
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167 | * Call PgapLinkContext2Env() here, so later on we can figure |
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168 | * out how many parameters, names, types, etc. |
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169 | */ |
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170 | PgapLinkContext2Env(ctx, envPtr); |
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171 | |
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172 | PGASetUp(ctx); |
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173 | PGARun(ctx, PgapEvaluate); |
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174 | PGADestroy(ctx); |
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175 | PgapUnlinkContext2Env(ctx); |
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176 | |
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177 | if (pgapack_abort) { |
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178 | return RP_OPTIM_ABORTED; |
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179 | } |
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180 | return RP_OPTIM_SUCCESS; |
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181 | } |
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182 | |
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183 | /* |
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184 | * ---------------------------------------------------------------------- |
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185 | * PgapackEvaluate() |
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186 | * |
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187 | * Called by PGApack whenever a set of input values needs to be |
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188 | * evaluated. Passes the values on to the underlying Rappture tool, |
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189 | * launches a run, and computes the value of the fitness function. |
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190 | * Returns the value for the fitness function. |
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191 | * ---------------------------------------------------------------------- |
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192 | */ |
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193 | double |
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194 | PgapEvaluate(ctx, p, pop) |
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195 | PGAContext *ctx; /* pgapack context for this optimization */ |
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196 | int p; /* sample #p being run */ |
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197 | int pop; /* identifier for this population */ |
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198 | |
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199 | { |
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200 | double fit = 0.0; |
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201 | RpOptimEnv *envPtr; |
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202 | RpOptimParam *paramPtr; |
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203 | RpOptimStatus status; |
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204 | envPtr = PgapGetEnvForContext(ctx); |
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205 | paramPtr = (RpOptimParam*)PGAGetIndividual(ctx, p, pop)->chrom; |
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206 | status = (*envPtr->evalProc)(envPtr, paramPtr, envPtr->numParams, &fit); |
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207 | |
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208 | if (pgapack_abort) { |
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209 | fprintf(stderr, "==WARNING: run aborted!"); |
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210 | return 0.0; |
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211 | } |
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212 | |
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213 | if (status != RP_OPTIM_SUCCESS) { |
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214 | fprintf(stderr, "==WARNING: run failed!"); |
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215 | PgapPrintString(ctx, stderr, p, pop); |
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216 | } |
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217 | |
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218 | /*populate the table with this sample*/ |
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219 | PGARuntimeDataTableSetSampleValue(paramPtr,fit); |
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220 | return fit; |
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221 | } |
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222 | |
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223 | /* |
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224 | * ---------------------------------------------------------------------- |
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225 | * PgapackCleanup() |
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226 | * |
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227 | * This routine is called whenever an optimization object is deleted |
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228 | * to clean up data associated with the object. Frees the data |
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229 | * allocated in PgapackInit. |
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230 | * ---------------------------------------------------------------------- |
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231 | */ |
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232 | void |
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233 | PgapackCleanup(cdata) |
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234 | ClientData cdata; /* data from to be cleaned up */ |
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235 | { |
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236 | PgapackData *dataPtr = (PgapackData*)cdata; |
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237 | free(dataPtr); |
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238 | } |
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239 | |
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240 | /* |
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241 | * ====================================================================== |
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242 | * ROUTINES FOR MANAGING DATA STRINGS |
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243 | * ====================================================================== |
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244 | * PgapCreateString() |
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245 | * |
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246 | * Called by pgapack to create the so-called "string" of data used for |
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247 | * an evaluation. |
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248 | * ---------------------------------------------------------------------- |
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249 | */ |
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250 | void |
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251 | PgapCreateString(ctx, p, pop, initFlag) |
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252 | PGAContext *ctx; /* pgapack context for this optimization */ |
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253 | int p; /* sample #p being run */ |
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254 | int pop; /* identifier for this population */ |
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255 | int initFlag; /* non-zero => fields should be initialized */ |
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256 | { |
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257 | int n, ival; |
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258 | double dval; |
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259 | RpOptimEnv *envPtr; |
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260 | RpOptimParam *oldParamPtr, *newParamPtr; |
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261 | PGAIndividual *newData; |
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262 | RpOptimParamNumber *numPtr; |
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263 | RpOptimParamString *strPtr; |
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264 | |
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265 | envPtr = PgapGetEnvForContext(ctx); |
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266 | |
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267 | newData = PGAGetIndividual(ctx, p, pop); |
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268 | newData->chrom = malloc(envPtr->numParams*sizeof(RpOptimParam)); |
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269 | newParamPtr = (RpOptimParam*)newData->chrom; |
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270 | |
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271 | for (n=0; n < envPtr->numParams; n++) { |
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272 | oldParamPtr = envPtr->paramList[n]; |
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273 | newParamPtr[n].name = oldParamPtr->name; |
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274 | newParamPtr[n].type = oldParamPtr->type; |
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275 | switch (oldParamPtr->type) { |
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276 | case RP_OPTIMPARAM_NUMBER: |
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277 | newParamPtr[n].value.dval = 0.0; |
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278 | break; |
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279 | case RP_OPTIMPARAM_STRING: |
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280 | newParamPtr[n].value.sval.num = -1; |
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281 | newParamPtr[n].value.sval.str = NULL; |
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282 | break; |
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283 | default: |
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284 | panic("bad parameter type in PgapCreateString()"); |
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285 | } |
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286 | } |
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287 | |
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288 | if (initFlag) { |
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289 | for (n=0; n < envPtr->numParams; n++) { |
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290 | switch (newParamPtr[n].type) { |
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291 | case RP_OPTIMPARAM_NUMBER: |
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292 | numPtr = (RpOptimParamNumber*)envPtr->paramList[n]; |
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293 | if(numPtr->randdist == RAND_NUMBER_DIST_UNIFORM){ |
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294 | dval = PGARandom01(ctx,0); |
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295 | newParamPtr[n].value.dval = |
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296 | (numPtr->max - numPtr->min)*dval + numPtr->min; |
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297 | }else if(numPtr->randdist == RAND_NUMBER_DIST_GAUSSIAN){ |
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298 | dval = PGARandomGaussian(ctx,numPtr->mean,numPtr->stddev); |
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299 | if(numPtr->strictmax){ |
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300 | if(dval>numPtr->max){ |
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301 | dval = numPtr->max; |
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302 | } |
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303 | } |
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304 | if(numPtr->strictmin){ |
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305 | if(dval<numPtr->min){ |
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306 | dval = numPtr->min; |
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307 | } |
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308 | } |
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309 | newParamPtr[n].value.dval = dval; |
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310 | }else{ |
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311 | panic("Incorrect Random Number distribution option in PgapcreateString()"); |
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312 | } |
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313 | break; |
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314 | case RP_OPTIMPARAM_STRING: |
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315 | strPtr = (RpOptimParamString*)envPtr->paramList[n]; |
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316 | ival = (int)floor(PGARandom01(ctx,0) * strPtr->numValues); |
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317 | envPtr->paramList[n]->value.sval.num = ival; |
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318 | envPtr->paramList[n]->value.sval.str = strPtr->values[ival]; |
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319 | break; |
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320 | default: |
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321 | panic("bad parameter type in PgapCreateString()"); |
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322 | } |
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323 | } |
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324 | } |
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325 | } |
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326 | |
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327 | /* |
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328 | * ---------------------------------------------------------------------- |
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329 | * PgapMutation() |
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330 | * |
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331 | * Called by pgapack to perform random mutations on the input data |
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332 | * used for evaluation. |
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333 | * ---------------------------------------------------------------------- |
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334 | */ |
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335 | int |
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336 | PgapMutation(ctx, p, pop, mr) |
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337 | PGAContext *ctx; /* pgapack context for this optimization */ |
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338 | int p; /* sample #p being run */ |
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339 | int pop; /* identifier for this population */ |
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340 | double mr; /* probability of mutation for each gene */ |
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341 | { |
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342 | int count = 0; /* number of mutations */ |
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343 | |
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344 | int n, ival,tempmr; |
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345 | RpOptimEnv *envPtr; |
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346 | RpOptimParam *paramPtr; |
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347 | RpOptimParamNumber *numPtr; |
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348 | RpOptimParamString *strPtr; |
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349 | |
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350 | envPtr = PgapGetEnvForContext(ctx); |
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351 | paramPtr = (RpOptimParam*)PGAGetIndividual(ctx, p, pop)->chrom; |
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352 | |
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353 | for (n=0; n < envPtr->numParams; n++) { |
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354 | |
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355 | |
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356 | switch (paramPtr[n].type) { |
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357 | case RP_OPTIMPARAM_NUMBER: |
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358 | numPtr = (RpOptimParamNumber*)envPtr->paramList[n]; |
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359 | if(numPtr->mutnrate!=PARAM_NUM_UNSPEC_MUTN_RATE){ |
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360 | tempmr = numPtr->mutnrate; |
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361 | }else{ |
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362 | tempmr = mr; |
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363 | } |
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364 | if (PGARandomFlip(ctx, tempmr)) { |
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365 | /* won the coin toss -- change this parameter */ |
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366 | count++; |
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367 | |
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368 | /* bump the value up/down a little, randomly */ |
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369 | if (PGARandomFlip(ctx, 0.5)) { |
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370 | paramPtr[n].value.dval += 0.1*paramPtr[n].value.dval; |
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371 | } else { |
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372 | paramPtr[n].value.dval -= 0.1*paramPtr[n].value.dval; |
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373 | } |
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374 | /* make sure the resulting value is still in bounds */ |
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375 | if(numPtr->randdist == RAND_NUMBER_DIST_UNIFORM || |
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376 | (numPtr->randdist == RAND_NUMBER_DIST_GAUSSIAN && numPtr->strictmax)){ |
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377 | if (paramPtr[n].value.dval > numPtr->max) { |
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378 | paramPtr[n].value.dval = numPtr->max; |
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379 | } |
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380 | } |
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381 | /*also make sure it obeys configured parameters when gaussian*/ |
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382 | if(numPtr->randdist == RAND_NUMBER_DIST_UNIFORM || |
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383 | (numPtr->randdist == RAND_NUMBER_DIST_GAUSSIAN && numPtr->strictmin)){ |
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384 | if (paramPtr[n].value.dval < numPtr->min) { |
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385 | paramPtr[n].value.dval = numPtr->min; |
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386 | } |
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387 | } |
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388 | |
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389 | } |
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390 | break; |
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391 | |
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392 | |
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393 | case RP_OPTIMPARAM_STRING: |
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394 | if (PGARandomFlip(ctx, mr)) { |
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395 | /* won the coin toss -- change this parameter */ |
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396 | count++; |
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397 | |
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398 | ival = paramPtr[n].value.sval.num; |
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399 | if (PGARandomFlip(ctx, 0.5)) { |
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400 | ival += 1; |
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401 | } else { |
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402 | ival -= 1; |
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403 | } |
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404 | strPtr = (RpOptimParamString*)envPtr->paramList[n]; |
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405 | if (ival < 0) ival = 0; |
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406 | if (ival >= strPtr->numValues) ival = strPtr->numValues-1; |
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407 | paramPtr[n].value.sval.num = ival; |
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408 | paramPtr[n].value.sval.str = strPtr->values[ival]; |
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409 | } |
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410 | |
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411 | break; |
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412 | |
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413 | default: |
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414 | panic("bad parameter type in PgapMutation()"); |
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415 | } |
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416 | |
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417 | } |
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418 | return count; |
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419 | } |
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420 | |
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421 | /* |
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422 | * ---------------------------------------------------------------------- |
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423 | * PgapCrossover() |
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424 | * |
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425 | * Called by pgapack to perform cross-over mutations on the input data |
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426 | * used for evaluation. |
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427 | * ---------------------------------------------------------------------- |
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428 | */ |
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429 | void |
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430 | PgapCrossover(ctx, p1, p2, pop1, c1, c2, pop2) |
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431 | PGAContext *ctx; /* pgapack context for this optimization */ |
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432 | int p1; /* sample # for parent of input string1 */ |
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433 | int p2; /* sample # for parent of input string2 */ |
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434 | int pop1; /* population containing p1 and p2 */ |
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435 | int c1; /* sample # for child of input string1 */ |
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436 | int c2; /* sample # for child of input string2 */ |
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437 | int pop2; /* population containing c1 and c2 */ |
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438 | { |
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439 | int n; |
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440 | RpOptimEnv *envPtr; |
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441 | RpOptimParam *parent1, *parent2, *child1, *child2; |
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442 | double pu; |
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443 | |
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444 | envPtr = PgapGetEnvForContext(ctx); |
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445 | parent1 = (RpOptimParam*)PGAGetIndividual(ctx, p1, pop1)->chrom; |
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446 | parent2 = (RpOptimParam*)PGAGetIndividual(ctx, p2, pop1)->chrom; |
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447 | child1 = (RpOptimParam*)PGAGetIndividual(ctx, c1, pop2)->chrom; |
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448 | child2 = (RpOptimParam*)PGAGetIndividual(ctx, c2, pop2)->chrom; |
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449 | |
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450 | pu = PGAGetUniformCrossoverProb(ctx); |
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451 | |
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452 | for (n=0; n < envPtr->numParams; n++) { |
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453 | if (PGARandomFlip(ctx, pu)) { |
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454 | /* child inherits from parent */ |
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455 | memcpy(&child1[n], &parent1[n], sizeof(RpOptimParam)); |
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456 | memcpy(&child2[n], &parent2[n], sizeof(RpOptimParam)); |
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457 | } else { |
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458 | /* crossover */ |
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459 | memcpy(&child1[n], &parent2[n], sizeof(RpOptimParam)); |
---|
460 | memcpy(&child2[n], &parent1[n], sizeof(RpOptimParam)); |
---|
461 | } |
---|
462 | } |
---|
463 | } |
---|
464 | |
---|
465 | /* |
---|
466 | * ---------------------------------------------------------------------- |
---|
467 | * PgapPrintString() |
---|
468 | * |
---|
469 | * Called by pgapack to format the values for a particular string of |
---|
470 | * input data. |
---|
471 | * ---------------------------------------------------------------------- |
---|
472 | */ |
---|
473 | void |
---|
474 | PgapPrintString(ctx, fp, p, pop) |
---|
475 | PGAContext *ctx; /* pgapack context for this optimization */ |
---|
476 | FILE *fp; /* write to this file pointer */ |
---|
477 | int p; /* sample #p being run */ |
---|
478 | int pop; /* identifier for this population */ |
---|
479 | { |
---|
480 | int n; |
---|
481 | RpOptimEnv *envPtr; |
---|
482 | RpOptimParam *paramPtr; |
---|
483 | |
---|
484 | envPtr = PgapGetEnvForContext(ctx); |
---|
485 | paramPtr = (RpOptimParam*)PGAGetIndividual(ctx, p, pop)->chrom; |
---|
486 | |
---|
487 | for (n=0; n < envPtr->numParams; n++) { |
---|
488 | fprintf(fp, "#%4d: ", n); |
---|
489 | switch (paramPtr[n].type) { |
---|
490 | case RP_OPTIMPARAM_NUMBER: |
---|
491 | fprintf(fp, "[%11.7g] (%s)\n", paramPtr[n].value.dval, |
---|
492 | paramPtr[n].name); |
---|
493 | break; |
---|
494 | case RP_OPTIMPARAM_STRING: |
---|
495 | fprintf(fp, "[%d]=\"%s\" (%s)\n", paramPtr[n].value.sval.num, |
---|
496 | paramPtr[n].value.sval.str, paramPtr[n].name); |
---|
497 | break; |
---|
498 | default: |
---|
499 | panic("bad parameter type in PgapPrintString()"); |
---|
500 | } |
---|
501 | } |
---|
502 | } |
---|
503 | |
---|
504 | /* |
---|
505 | * ---------------------------------------------------------------------- |
---|
506 | * PgapCopyString() |
---|
507 | * |
---|
508 | * Called by pgapack to copy one input string to another. |
---|
509 | * ---------------------------------------------------------------------- |
---|
510 | */ |
---|
511 | void |
---|
512 | PgapCopyString(ctx, p1, pop1, p2, pop2) |
---|
513 | PGAContext *ctx; /* pgapack context for this optimization */ |
---|
514 | int p1; /* source sample # being run */ |
---|
515 | int pop1; /* population containing p1 */ |
---|
516 | int p2; /* destination sample # being run */ |
---|
517 | int pop2; /* population containing p1 */ |
---|
518 | { |
---|
519 | int n; |
---|
520 | RpOptimEnv *envPtr; |
---|
521 | RpOptimParam *src, *dst; |
---|
522 | |
---|
523 | envPtr = PgapGetEnvForContext(ctx); |
---|
524 | src = (RpOptimParam*)PGAGetIndividual(ctx, p1, pop1)->chrom; |
---|
525 | dst = (RpOptimParam*)PGAGetIndividual(ctx, p2, pop2)->chrom; |
---|
526 | |
---|
527 | for (n=0; n < envPtr->numParams; n++) { |
---|
528 | dst[n].type = src[n].type; |
---|
529 | switch (src[n].type) { |
---|
530 | case RP_OPTIMPARAM_NUMBER: |
---|
531 | dst[n].value.dval = src[n].value.dval; |
---|
532 | break; |
---|
533 | case RP_OPTIMPARAM_STRING: |
---|
534 | dst[n].value.sval.num = src[n].value.sval.num; |
---|
535 | dst[n].value.sval.str = src[n].value.sval.str; |
---|
536 | break; |
---|
537 | default: |
---|
538 | panic("bad parameter type in PgapCopyString()"); |
---|
539 | } |
---|
540 | } |
---|
541 | } |
---|
542 | |
---|
543 | /* |
---|
544 | * ---------------------------------------------------------------------- |
---|
545 | * PgapDuplicateString() |
---|
546 | * |
---|
547 | * Called by pgapack to compare two input strings. Returns non-zero if |
---|
548 | * the two are duplicates and 0 otherwise. |
---|
549 | * ---------------------------------------------------------------------- |
---|
550 | */ |
---|
551 | int |
---|
552 | PgapDuplicateString(ctx, p1, pop1, p2, pop2) |
---|
553 | PGAContext *ctx; /* pgapack context for this optimization */ |
---|
554 | int p1; /* sample #p being run */ |
---|
555 | int pop1; /* population containing p1 */ |
---|
556 | int p2; /* sample #p being run */ |
---|
557 | int pop2; /* population containing p1 */ |
---|
558 | { |
---|
559 | int n; |
---|
560 | RpOptimEnv *envPtr; |
---|
561 | RpOptimParam *param1, *param2; |
---|
562 | |
---|
563 | envPtr = PgapGetEnvForContext(ctx); |
---|
564 | param1 = (RpOptimParam*)PGAGetIndividual(ctx, p1, pop1)->chrom; |
---|
565 | param2 = (RpOptimParam*)PGAGetIndividual(ctx, p2, pop2)->chrom; |
---|
566 | |
---|
567 | for (n=0; n < envPtr->numParams; n++) { |
---|
568 | if (param1[n].type != param2[n].type) { |
---|
569 | return 0; /* different! */ |
---|
570 | } |
---|
571 | switch (param1[n].type) { |
---|
572 | case RP_OPTIMPARAM_NUMBER: |
---|
573 | if (param1[n].value.dval != param2[n].value.dval) { |
---|
574 | return 0; /* different! */ |
---|
575 | } |
---|
576 | break; |
---|
577 | case RP_OPTIMPARAM_STRING: |
---|
578 | if (param1[n].value.sval.num != param2[n].value.sval.num) { |
---|
579 | return 0; /* different! */ |
---|
580 | } |
---|
581 | break; |
---|
582 | default: |
---|
583 | panic("bad parameter type in PgapDuplicateString()"); |
---|
584 | } |
---|
585 | } |
---|
586 | return 1; |
---|
587 | } |
---|
588 | |
---|
589 | |
---|
590 | |
---|
591 | /* |
---|
592 | * ---------------------------------------------------------------------- |
---|
593 | * PgapCopyString() |
---|
594 | * |
---|
595 | * Called by pgapack to copy one input string to another. |
---|
596 | * ---------------------------------------------------------------------- |
---|
597 | */ |
---|
598 | MPI_Datatype |
---|
599 | PgapBuildDT(ctx, p, pop) |
---|
600 | PGAContext *ctx; /* pgapack context for this optimization */ |
---|
601 | int p; /* sample # being run */ |
---|
602 | int pop; /* population containing sample */ |
---|
603 | { |
---|
604 | panic("MPI support not implemented!"); |
---|
605 | return NULL; |
---|
606 | } |
---|
607 | |
---|
608 | /* |
---|
609 | * ====================================================================== |
---|
610 | * OPTION: -operation <=> PGA_MINIMIZE / PGA_MAXIMIZE |
---|
611 | * ====================================================================== |
---|
612 | */ |
---|
613 | int |
---|
614 | RpOption_ParseOper(interp, valObj, cdata, offset) |
---|
615 | Tcl_Interp *interp; /* interpreter handling this request */ |
---|
616 | Tcl_Obj *valObj; /* set option to this new value */ |
---|
617 | ClientData cdata; /* save in this data structure */ |
---|
618 | int offset; /* save at this offset in cdata */ |
---|
619 | { |
---|
620 | int *ptr = (int*)(cdata+offset); |
---|
621 | char *val = Tcl_GetStringFromObj(valObj, (int*)NULL); |
---|
622 | if (strcmp(val,"minimize") == 0) { |
---|
623 | *ptr = PGA_MINIMIZE; |
---|
624 | } |
---|
625 | else if (strcmp(val,"maximize") == 0) { |
---|
626 | *ptr = PGA_MAXIMIZE; |
---|
627 | } |
---|
628 | else { |
---|
629 | Tcl_AppendStringsToObj(Tcl_GetObjResult(interp), |
---|
630 | "bad value \"", val, "\": should be minimize, maximize", |
---|
631 | (char*)NULL); |
---|
632 | return TCL_ERROR; |
---|
633 | } |
---|
634 | return TCL_OK; |
---|
635 | } |
---|
636 | |
---|
637 | int |
---|
638 | RpOption_GetOper(interp, cdata, offset) |
---|
639 | Tcl_Interp *interp; /* interpreter handling this request */ |
---|
640 | ClientData cdata; /* get from this data structure */ |
---|
641 | int offset; /* get from this offset in cdata */ |
---|
642 | { |
---|
643 | int *ptr = (int*)(cdata+offset); |
---|
644 | switch (*ptr) { |
---|
645 | case PGA_MINIMIZE: |
---|
646 | Tcl_SetResult(interp, "minimize", TCL_STATIC); |
---|
647 | break; |
---|
648 | case PGA_MAXIMIZE: |
---|
649 | Tcl_SetResult(interp, "maximize", TCL_STATIC); |
---|
650 | break; |
---|
651 | default: |
---|
652 | Tcl_SetResult(interp, "???", TCL_STATIC); |
---|
653 | break; |
---|
654 | } |
---|
655 | return TCL_OK; |
---|
656 | } |
---|
657 | |
---|
658 | /* |
---|
659 | * ====================================================================== |
---|
660 | * OPTION: -poprepl <=> PGASetPopReplacementType() |
---|
661 | * ====================================================================== |
---|
662 | */ |
---|
663 | int |
---|
664 | RpOption_ParsePopRepl(interp, valObj, cdata, offset) |
---|
665 | Tcl_Interp *interp; /* interpreter handling this request */ |
---|
666 | Tcl_Obj *valObj; /* set option to this new value */ |
---|
667 | ClientData cdata; /* save in this data structure */ |
---|
668 | int offset; /* save at this offset in cdata */ |
---|
669 | { |
---|
670 | int *ptr = (int*)(cdata+offset); |
---|
671 | char *val = Tcl_GetStringFromObj(valObj, (int*)NULL); |
---|
672 | if (*val == 'b' && strcmp(val,"best") == 0) { |
---|
673 | *ptr = PGA_POPREPL_BEST; |
---|
674 | } |
---|
675 | else if (*val == 'r' && strcmp(val,"random-repl") == 0) { |
---|
676 | *ptr = PGA_POPREPL_RANDOM_REP; |
---|
677 | } |
---|
678 | else if (*val == 'r' && strcmp(val,"random-norepl") == 0) { |
---|
679 | *ptr = PGA_POPREPL_RANDOM_NOREP; |
---|
680 | } |
---|
681 | else { |
---|
682 | Tcl_AppendStringsToObj(Tcl_GetObjResult(interp), |
---|
683 | "bad value \"", val, "\": should be best, random-norepl," |
---|
684 | " or random-repl", (char*)NULL); |
---|
685 | return TCL_ERROR; |
---|
686 | } |
---|
687 | return TCL_OK; |
---|
688 | } |
---|
689 | |
---|
690 | int |
---|
691 | RpOption_GetPopRepl(interp, cdata, offset) |
---|
692 | Tcl_Interp *interp; /* interpreter handling this request */ |
---|
693 | ClientData cdata; /* get from this data structure */ |
---|
694 | int offset; /* get from this offset in cdata */ |
---|
695 | { |
---|
696 | int *ptr = (int*)(cdata+offset); |
---|
697 | switch (*ptr) { |
---|
698 | case PGA_POPREPL_BEST: |
---|
699 | Tcl_SetResult(interp, "best", TCL_STATIC); |
---|
700 | break; |
---|
701 | case PGA_POPREPL_RANDOM_REP: |
---|
702 | Tcl_SetResult(interp, "random-repl", TCL_STATIC); |
---|
703 | break; |
---|
704 | case PGA_POPREPL_RANDOM_NOREP: |
---|
705 | Tcl_SetResult(interp, "random-norepl", TCL_STATIC); |
---|
706 | break; |
---|
707 | default: |
---|
708 | Tcl_SetResult(interp, "???", TCL_STATIC); |
---|
709 | break; |
---|
710 | } |
---|
711 | return TCL_OK; |
---|
712 | } |
---|
713 | |
---|
714 | /* |
---|
715 | * ====================================================================== |
---|
716 | * OPTION: -stpcriteria <=> PGA_STOP_MAXITER / PGA_STOP_NOCHANGE / PGA_STOP_TOOSIMILAR |
---|
717 | * ====================================================================== |
---|
718 | */ |
---|
719 | int |
---|
720 | RpOption_ParseStpCriteria(interp, valObj, cdata, offset) |
---|
721 | Tcl_Interp *interp; /* interpreter handling this request */ |
---|
722 | Tcl_Obj *valObj; /* set option to this new value */ |
---|
723 | ClientData cdata; /* save in this data structure */ |
---|
724 | int offset; /* save at this offset in cdata */ |
---|
725 | { |
---|
726 | int *ptr = (int*)(cdata+offset); |
---|
727 | char *val = Tcl_GetStringFromObj(valObj, (int*)NULL); |
---|
728 | if (strcmp(val,"maxiter") == 0) { |
---|
729 | *ptr = PGA_STOP_MAXITER; |
---|
730 | } |
---|
731 | else if (strcmp(val,"nochange") == 0) { |
---|
732 | *ptr = PGA_STOP_NOCHANGE; |
---|
733 | } |
---|
734 | else if (strcmp(val,"toosimilar") == 0){ |
---|
735 | *ptr = PGA_STOP_TOOSIMILAR; |
---|
736 | } |
---|
737 | else { |
---|
738 | Tcl_AppendStringsToObj(Tcl_GetObjResult(interp), |
---|
739 | "bad value \"", val, "\": should be maxiter, nochange or toosimilar", |
---|
740 | (char*)NULL); |
---|
741 | return TCL_ERROR; |
---|
742 | } |
---|
743 | return TCL_OK; |
---|
744 | } |
---|
745 | |
---|
746 | int |
---|
747 | RpOption_GetStpCriteria(interp, cdata, offset) |
---|
748 | Tcl_Interp *interp; /* interpreter handling this request */ |
---|
749 | ClientData cdata; /* get from this data structure */ |
---|
750 | int offset; /* get from this offset in cdata */ |
---|
751 | { |
---|
752 | int *ptr = (int*)(cdata+offset); |
---|
753 | switch (*ptr) { |
---|
754 | case PGA_STOP_MAXITER: |
---|
755 | Tcl_SetResult(interp, "maxiter", TCL_STATIC); |
---|
756 | break; |
---|
757 | case PGA_STOP_NOCHANGE: |
---|
758 | Tcl_SetResult(interp, "nochange", TCL_STATIC); |
---|
759 | break; |
---|
760 | case PGA_STOP_TOOSIMILAR: |
---|
761 | Tcl_SetResult(interp, "toosimilar", TCL_STATIC); |
---|
762 | break; |
---|
763 | default: |
---|
764 | Tcl_SetResult(interp, "???", TCL_STATIC); |
---|
765 | break; |
---|
766 | } |
---|
767 | return TCL_OK; |
---|
768 | } |
---|
769 | |
---|
770 | /* |
---|
771 | * ====================================================================== |
---|
772 | * ROUTINES FOR CONNECTING PGACONTEXT <=> RPOPTIMENV |
---|
773 | * ====================================================================== |
---|
774 | * PgapLinkContext2Env() |
---|
775 | * This routine is used internally to establish a relationship between |
---|
776 | * a PGAContext token and its corresponding RpOptimEnv data. The |
---|
777 | * PGA routines don't provide a way to pass the RpOptimEnv data along, |
---|
778 | * so we use these routines to find the correspondence. |
---|
779 | * |
---|
780 | * PgapGetEnvForContext() |
---|
781 | * Returns the RpOptimEnv associated with a given PGAContext. If the |
---|
782 | * link has not been established via PgapLinkContext2Env(), then this |
---|
783 | * routine returns NULL. |
---|
784 | * |
---|
785 | * PgapUnlinkContext2Env() |
---|
786 | * Breaks the link between a PGAContext and its RpOptimEnv. Should |
---|
787 | * be called when the PGAContext is destroyed and is no longer valid. |
---|
788 | * ---------------------------------------------------------------------- |
---|
789 | */ |
---|
790 | static Tcl_HashTable *Pgacontext2Rpenv = NULL; |
---|
791 | |
---|
792 | void |
---|
793 | PgapLinkContext2Env(ctx, envPtr) |
---|
794 | PGAContext *ctx; /* pgapack context for this optimization */ |
---|
795 | RpOptimEnv *envPtr; /* corresponding Rappture optimization data */ |
---|
796 | { |
---|
797 | Tcl_HashEntry *ctxEntry; |
---|
798 | int newEntry; |
---|
799 | |
---|
800 | if (Pgacontext2Rpenv == NULL) { |
---|
801 | Pgacontext2Rpenv = (Tcl_HashTable*)malloc(sizeof(Tcl_HashTable)); |
---|
802 | Tcl_InitHashTable(Pgacontext2Rpenv, TCL_ONE_WORD_KEYS); |
---|
803 | } |
---|
804 | ctxEntry = Tcl_CreateHashEntry(Pgacontext2Rpenv, (char*)ctx, &newEntry); |
---|
805 | Tcl_SetHashValue(ctxEntry, (ClientData)envPtr); |
---|
806 | } |
---|
807 | |
---|
808 | RpOptimEnv* |
---|
809 | PgapGetEnvForContext(ctx) |
---|
810 | PGAContext *ctx; |
---|
811 | { |
---|
812 | Tcl_HashEntry *entryPtr; |
---|
813 | |
---|
814 | if (Pgacontext2Rpenv) { |
---|
815 | entryPtr = Tcl_FindHashEntry(Pgacontext2Rpenv, (char*)ctx); |
---|
816 | if (entryPtr) { |
---|
817 | return (RpOptimEnv*)Tcl_GetHashValue(entryPtr); |
---|
818 | } |
---|
819 | } |
---|
820 | return NULL; |
---|
821 | } |
---|
822 | |
---|
823 | void |
---|
824 | PgapUnlinkContext2Env(ctx) |
---|
825 | PGAContext *ctx; |
---|
826 | { |
---|
827 | Tcl_HashEntry *entryPtr; |
---|
828 | |
---|
829 | if (Pgacontext2Rpenv) { |
---|
830 | entryPtr = Tcl_FindHashEntry(Pgacontext2Rpenv, (char*)ctx); |
---|
831 | if (entryPtr) { |
---|
832 | Tcl_DeleteHashEntry(entryPtr); |
---|
833 | } |
---|
834 | } |
---|
835 | } |
---|
836 | /*--------------------------------------------------------------------------------- |
---|
837 | * PGARuntimeDTInit(): It initializes the runtime data table. |
---|
838 | * The table is organized slightly counter-intuitively |
---|
839 | * Instead of a |
---|
840 | * param1|param2|param3 |param4... |
---|
841 | * val11 |val12 |val13 |val14... |
---|
842 | * val12 |val22 |val23 |val24.... |
---|
843 | * orientation, it is organized as |
---|
844 | * param1|val11|val12 |
---|
845 | * param2|val21|val22 |
---|
846 | * param3|val31|val32 |
---|
847 | * param4|val41|val42 |
---|
848 | * Reallocating for additional columns is easier than reallocating additional rows and then |
---|
849 | * reallocating for columns |
---|
850 | * -------------------------------------------------------------------------------- |
---|
851 | */ |
---|
852 | |
---|
853 | void PGARuntimeDataTableInit(envPtr) |
---|
854 | RpOptimEnv *envPtr; |
---|
855 | { |
---|
856 | int i; |
---|
857 | if(envPtr != NULL){ |
---|
858 | table.num_of_rows = (envPtr->numParams)+1; |
---|
859 | table.data = malloc((table.num_of_rows)*sizeof(double*)); |
---|
860 | if(table.data == NULL){ |
---|
861 | panic("\nAllocation for Runtime Data Table failed\n"); |
---|
862 | } |
---|
863 | for(i=0;i<table.num_of_rows;i++){ |
---|
864 | table.data[i] = malloc(PGAPACK_RUNTIME_TABLE_DEFAULT_SIZE*sizeof(double)); |
---|
865 | if(table.data[i] == NULL){ |
---|
866 | panic("\nAllocation for Runtime Data Table failed\n"); |
---|
867 | } |
---|
868 | } |
---|
869 | table.no_of_samples_evaled = 0; |
---|
870 | table.no_of_columns = PGAPACK_RUNTIME_TABLE_DEFAULT_SIZE; |
---|
871 | |
---|
872 | }else{ |
---|
873 | panic("\nError: NULL Environment variable OR Table pointer passed to Data Table Init\n"); |
---|
874 | } |
---|
875 | } |
---|
876 | |
---|
877 | void PGARuntimeDataTableDeInit() |
---|
878 | { |
---|
879 | int i; |
---|
880 | if((&table) == NULL){ |
---|
881 | panic("Error: Table not present, therefore cannot free memory.."); |
---|
882 | } |
---|
883 | for(i=0;i<table.num_of_rows;i++){ |
---|
884 | free(table.data[i]); |
---|
885 | } |
---|
886 | free(table.data); |
---|
887 | } |
---|
888 | |
---|
889 | void PGARuntimeDataTableSetSampleValue(chrom,fitness) |
---|
890 | RpOptimParam *chrom; |
---|
891 | double fitness; |
---|
892 | { |
---|
893 | int i; |
---|
894 | printf("\nSetting sample value.......................\n"); |
---|
895 | if(chrom!=NULL && (&table)!=NULL){ |
---|
896 | (table.no_of_samples_evaled)+=1; |
---|
897 | if((table.no_of_samples_evaled) > table.no_of_columns){ |
---|
898 | /* then Reallocate space for more columns)*/ |
---|
899 | (table.no_of_columns)+=(table.no_of_columns); |
---|
900 | //TODO GTG: Delete printing stuff |
---|
901 | for(i=0;i<(table.num_of_rows);i++){ |
---|
902 | table.data[i] = realloc(table.data[i],table.no_of_columns); |
---|
903 | if(table.data[i]==NULL){ |
---|
904 | panic("\nError: Could not Reallocate more space for the table"); |
---|
905 | } |
---|
906 | } |
---|
907 | }else{ |
---|
908 | if(chrom->type == RP_OPTIMPARAM_NUMBER){ |
---|
909 | for(i=0;i<(table.num_of_rows);i++){ |
---|
910 | if(i==0){ |
---|
911 | table.data[i][(table.no_of_samples_evaled)-1] = fitness; |
---|
912 | printf("\nSample Number %d:- Fitness: %lf\t",table.no_of_samples_evaled,fitness); |
---|
913 | }else{ |
---|
914 | table.data[i][(table.no_of_samples_evaled)-1] = chrom[i-1].value.dval; |
---|
915 | printf("Param %d %lf\t",i,table.data[i][(table.no_of_samples_evaled)-1]); |
---|
916 | } |
---|
917 | } |
---|
918 | }else{ |
---|
919 | panic("\n Chromosome value is RP_OPTIMPARAM_STRING\n"); |
---|
920 | //GTG TODO: find out what happens in this case. Will we be better off handling Tcl_objects? |
---|
921 | } |
---|
922 | } |
---|
923 | }else{ |
---|
924 | panic("\nError:Either Chromosome, or table passed to PGARuntimeDataTableSetSampleValue() is NULL\n"); |
---|
925 | } |
---|
926 | |
---|
927 | } |
---|
928 | |
---|
929 | void GetSampleInformation(buffer,sampleNumber) |
---|
930 | char *buffer; |
---|
931 | int sampleNumber; |
---|
932 | { |
---|
933 | int i; |
---|
934 | char tempBuff[50]; |
---|
935 | printf("\nFetching sample information.........................\n"); |
---|
936 | if((&table) == NULL){ |
---|
937 | panic("Table uninitialized"); |
---|
938 | } |
---|
939 | if(sampleNumber<=0){ |
---|
940 | sprintf(buffer,"\nNumber of Samples Evaluated so far: %d\n",(table.no_of_samples_evaled)+1); |
---|
941 | return; |
---|
942 | } |
---|
943 | if(((table.num_of_rows)-1)*10>SINGLE_SAMPLE_DATA_BUFFER_DEFAULT_SIZE){ |
---|
944 | buffer = realloc(buffer,50+25*(table.num_of_rows)); |
---|
945 | //resizing the buffer, keeping 50 for display related jazz, around 12-15 characs for param names |
---|
946 | //and 10 characs for Fl.pt. display of the value |
---|
947 | if(buffer == NULL){ |
---|
948 | panic("\nError: Could not reallocate space for sample data buffer"); |
---|
949 | } |
---|
950 | } |
---|
951 | for(i=0;i<(table.num_of_rows);i++){ |
---|
952 | if(i==0){ |
---|
953 | sprintf(buffer,"\nSample Number %d ----> Fitness: %lf ",sampleNumber,table.data[i][sampleNumber-1]); |
---|
954 | }else{ |
---|
955 | sprintf(tempBuff,"Param %d: %lf ",i,table.data[i][sampleNumber-1]); |
---|
956 | strcat(buffer,tempBuff); |
---|
957 | } |
---|
958 | } |
---|
959 | strcat(buffer,"\n"); |
---|
960 | } |
---|