1 | /* |
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2 | Copyright 2006 by Sean Luke and George Mason University |
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3 | Licensed under the Academic Free License version 3.0 |
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4 | See the file "LICENSE" for more information |
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5 | */ |
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6 | |
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7 | |
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8 | package ec.vector; |
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9 | |
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10 | import ec.*; |
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11 | import ec.util.*; |
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12 | import java.io.*; |
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13 | |
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14 | /* |
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15 | * ByteVectorIndividual.java |
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16 | * Created: Tue Mar 13 15:03:12 EST 2001 |
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17 | */ |
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18 | |
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19 | /** |
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20 | * ByteVectorIndividual is a VectorIndividual whose genome is an array of bytes. |
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21 | * Gene values may range from species.mingene(x) to species.maxgene(x), inclusive. |
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22 | * The default mutation method randomizes genes to new values in this range, |
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23 | * with <tt>species.mutationProbability</tt>. |
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24 | |
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25 | * <P><b>From ec.Individual:</b> |
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26 | * |
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27 | * <p>In addition to serialization for checkpointing, Individuals may read and write themselves to streams in three ways. |
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28 | * |
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29 | * <ul> |
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30 | * <li><b>writeIndividual(...,DataOutput)/readIndividual(...,DataInput)</b> This method |
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31 | * transmits or receives an individual in binary. It is the most efficient approach to sending |
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32 | * individuals over networks, etc. These methods write the evaluated flag and the fitness, then |
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33 | * call <b>readGenotype/writeGenotype</b>, which you must implement to write those parts of your |
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34 | * Individual special to your functions-- the default versions of readGenotype/writeGenotype throw errors. |
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35 | * You don't need to implement them if you don't plan on using read/writeIndividual. |
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36 | * |
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37 | * <li><b>printIndividual(...,PrintWriter)/readIndividual(...,LineNumberReader)</b> This |
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38 | * approach transmits or receives an indivdual in text encoded such that the individual is largely readable |
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39 | * by humans but can be read back in 100% by ECJ as well. To do this, these methods will encode numbers |
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40 | * using the <tt>ec.util.Code</tt> class. These methods are mostly used to write out populations to |
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41 | * files for inspection, slight modification, then reading back in later on. <b>readIndividual</b> reads |
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42 | * in the fitness and the evaluation flag, then calls <b>parseGenotype</b> to read in the remaining individual. |
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43 | * You are responsible for implementing parseGenotype: the Code class is there to help you. |
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44 | * <b>printIndividual</b> writes out the fitness and evaluation flag, then calls <b>genotypeToString</b> |
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45 | * and printlns the resultant string. You are responsible for implementing the genotypeToString method in such |
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46 | * a way that parseGenotype can read back in the individual println'd with genotypeToString. The default form |
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47 | * of genotypeToString simply calls <b>toString</b>, which you may override instead if you like. The default |
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48 | * form of <b>parseGenotype</b> throws an error. You are not required to implement these methods, but without |
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49 | * them you will not be able to write individuals to files in a simultaneously computer- and human-readable fashion. |
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50 | * |
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51 | * <li><b>printIndividualForHumans(...,PrintWriter)</b> This |
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52 | * approach prints an individual in a fashion intended for human consumption only. |
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53 | * <b>printIndividualForHumans</b> writes out the fitness and evaluation flag, then calls <b>genotypeToStringForHumans</b> |
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54 | * and printlns the resultant string. You are responsible for implementing the genotypeToStringForHumans method. |
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55 | * The default form of genotypeToStringForHumans simply calls <b>toString</b>, which you may override instead if you like |
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56 | * (though note that genotypeToString's default also calls toString). You should handle one of these methods properly |
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57 | * to ensure individuals can be printed by ECJ. |
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58 | * </ul> |
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59 | |
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60 | * <p>In general, the various readers and writers do three things: they tell the Fitness to read/write itself, |
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61 | * they read/write the evaluated flag, and they read/write the gene array. If you add instance variables to |
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62 | * a VectorIndividual or subclass, you'll need to read/write those variables as well. |
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63 | <p><b>Default Base</b><br> |
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64 | vector.byte-vect-ind |
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65 | |
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66 | * @author Liviu Panait |
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67 | * @author Sean Luke |
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68 | * @version 1.0 |
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69 | */ |
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70 | |
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71 | public class ByteVectorIndividual extends VectorIndividual |
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72 | { |
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73 | public static final String P_BYTEVECTORINDIVIDUAL = "byte-vect-ind"; |
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74 | public byte[] genome; |
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75 | |
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76 | public Parameter defaultBase() |
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77 | { |
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78 | return VectorDefaults.base().push(P_BYTEVECTORINDIVIDUAL); |
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79 | } |
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80 | |
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81 | public Object clone() |
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82 | { |
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83 | ByteVectorIndividual myobj = (ByteVectorIndividual) (super.clone()); |
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84 | |
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85 | // must clone the genome |
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86 | myobj.genome = (byte[])(genome.clone()); |
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87 | |
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88 | return myobj; |
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89 | } |
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90 | |
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91 | public void setup(final EvolutionState state, final Parameter base) |
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92 | { |
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93 | super.setup(state,base); // actually unnecessary (Individual.setup() is empty) |
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94 | |
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95 | // since IntegerVectorSpecies set its constraint values BEFORE it called |
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96 | // super.setup(...) [which in turn called our setup(...)], we know that |
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97 | // stuff like genomeSize has already been set... |
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98 | |
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99 | Parameter def = defaultBase(); |
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100 | |
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101 | if (!(species instanceof IntegerVectorSpecies)) |
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102 | state.output.fatal("ByteVectorIndividual requires an IntegerVectorSpecies", base, def); |
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103 | IntegerVectorSpecies s = (IntegerVectorSpecies) species; |
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104 | |
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105 | genome = new byte[s.genomeSize]; |
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106 | } |
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107 | |
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108 | public void defaultCrossover(EvolutionState state, int thread, VectorIndividual ind) |
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109 | { |
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110 | IntegerVectorSpecies s = (IntegerVectorSpecies) species; |
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111 | ByteVectorIndividual i = (ByteVectorIndividual) ind; |
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112 | byte tmp; |
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113 | int point; |
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114 | |
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115 | if (genome.length != i.genome.length) |
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116 | state.output.fatal("Genome lengths are not the same for fixed-length vector crossover"); |
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117 | switch(s.crossoverType) |
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118 | { |
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119 | case VectorSpecies.C_ONE_POINT: |
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120 | point = state.random[thread].nextInt((genome.length / s.chunksize)+1); |
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121 | for(int x=0;x<point*s.chunksize;x++) |
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122 | { |
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123 | tmp = i.genome[x]; |
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124 | i.genome[x] = genome[x]; |
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125 | genome[x] = tmp; |
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126 | } |
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127 | break; |
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128 | case VectorSpecies.C_TWO_POINT: |
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129 | int point0 = state.random[thread].nextInt((genome.length / s.chunksize)+1); |
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130 | point = state.random[thread].nextInt((genome.length / s.chunksize)+1); |
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131 | if (point0 > point) { int p = point0; point0 = point; point = p; } |
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132 | for(int x=point0*s.chunksize;x<point*s.chunksize;x++) |
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133 | { |
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134 | tmp = i.genome[x]; |
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135 | i.genome[x] = genome[x]; |
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136 | genome[x] = tmp; |
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137 | } |
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138 | break; |
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139 | case VectorSpecies.C_ANY_POINT: |
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140 | for(int x=0;x<genome.length/s.chunksize;x++) |
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141 | if (state.random[thread].nextBoolean(s.crossoverProbability)) |
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142 | for(int y=x*s.chunksize;y<(x+1)*s.chunksize;y++) |
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143 | { |
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144 | tmp = i.genome[y]; |
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145 | i.genome[y] = genome[y]; |
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146 | genome[y] = tmp; |
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147 | } |
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148 | break; |
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149 | case VectorSpecies.C_LINE_RECOMB: |
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150 | { |
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151 | double alpha = state.random[thread].nextDouble() * (1 + 2*s.lineDistance) - s.lineDistance; |
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152 | double beta = state.random[thread].nextDouble() * (1 + 2*s.lineDistance) - s.lineDistance; |
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153 | long t,u; |
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154 | long min, max; |
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155 | for (int x = 0; x < genome.length; x++) |
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156 | { |
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157 | min = s.minGene(x); |
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158 | max = s.maxGene(x); |
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159 | t = (long) Math.floor(alpha * genome[x] + (1 - alpha) * i.genome[x] + 0.5); |
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160 | u = (long) Math.floor(beta * i.genome[x] + (1 - beta) * genome[x] + 0.5); |
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161 | if (!(t < min || t > max || u < min || u > max)) |
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162 | { |
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163 | genome[x] = (byte) t; |
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164 | i.genome[x] = (byte) u; |
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165 | } |
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166 | } |
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167 | } |
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168 | break; |
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169 | case VectorSpecies.C_INTERMED_RECOMB: |
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170 | { |
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171 | long t,u; |
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172 | long min, max; |
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173 | for (int x = 0; x < genome.length; x++) |
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174 | { |
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175 | do |
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176 | { |
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177 | double alpha = state.random[thread].nextDouble() * (1 + 2*s.lineDistance) - s.lineDistance; |
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178 | double beta = state.random[thread].nextDouble() * (1 + 2*s.lineDistance) - s.lineDistance; |
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179 | min = s.minGene(x); |
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180 | max = s.maxGene(x); |
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181 | t = (long) Math.floor(alpha * genome[x] + (1 - alpha) * i.genome[x] + 0.5); |
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182 | u = (long) Math.floor(beta * i.genome[x] + (1 - beta) * genome[x] + 0.5); |
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183 | } while (t < min || t > max || u < min || u > max); |
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184 | genome[x] = (byte) t; |
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185 | i.genome[x] = (byte) u; |
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186 | } |
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187 | } |
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188 | break; |
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189 | } |
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190 | } |
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191 | |
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192 | /** Splits the genome into n pieces, according to points, which *must* be sorted. |
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193 | pieces.length must be 1 + points.length */ |
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194 | public void split(int[] points, Object[] pieces) |
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195 | { |
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196 | int point0, point1; |
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197 | point0 = 0; point1 = points[0]; |
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198 | for(int x=0;x<pieces.length;x++) |
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199 | { |
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200 | pieces[x] = new byte[point1-point0]; |
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201 | System.arraycopy(genome,point0,pieces[x],0,point1-point0); |
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202 | point0 = point1; |
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203 | if (x >=pieces.length-2) |
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204 | point1 = genome.length; |
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205 | else point1 = points[x+1]; |
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206 | } |
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207 | } |
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208 | |
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209 | /** Joins the n pieces and sets the genome to their concatenation.*/ |
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210 | public void join(Object[] pieces) |
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211 | { |
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212 | int sum=0; |
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213 | for(int x=0;x<pieces.length;x++) |
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214 | sum += ((byte[])(pieces[x])).length; |
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215 | |
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216 | int runningsum = 0; |
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217 | byte[] newgenome = new byte[sum]; |
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218 | for(int x=0;x<pieces.length;x++) |
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219 | { |
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220 | System.arraycopy(pieces[x], 0, newgenome, runningsum, ((byte[])(pieces[x])).length); |
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221 | runningsum += ((byte[])(pieces[x])).length; |
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222 | } |
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223 | // set genome |
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224 | genome = newgenome; |
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225 | } |
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226 | |
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227 | /** Destructively mutates the individual in some default manner. The default form |
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228 | simply randomizes genes to a uniform distribution from the min and max of the gene values. */ |
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229 | public void defaultMutate(EvolutionState state, int thread) |
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230 | { |
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231 | IntegerVectorSpecies s = (IntegerVectorSpecies) species; |
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232 | if (s.mutationProbability>0.0) |
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233 | for(int x=0;x<genome.length;x++) |
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234 | if (state.random[thread].nextBoolean(s.mutationProbability)) |
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235 | genome[x] = (byte)((int)s.minGene(x) + state.random[thread].nextInt((int)s.maxGene(x)-(int)s.minGene(x)+1)); |
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236 | } |
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237 | |
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238 | |
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239 | |
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240 | /** Initializes the individual by randomly choosing Bytes uniformly from mingene to maxgene. */ |
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241 | public void reset(EvolutionState state, int thread) |
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242 | { |
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243 | IntegerVectorSpecies s = (IntegerVectorSpecies) species; |
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244 | for(int x=0;x<genome.length;x++) |
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245 | genome[x] = (byte)((int)s.minGene(x) + state.random[thread].nextInt((int)s.maxGene(x)-(int)s.minGene(x)+1)); |
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246 | } |
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247 | |
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248 | public int hashCode() |
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249 | { |
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250 | // stolen from GPIndividual. It's a decent algorithm. |
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251 | int hash = this.getClass().hashCode(); |
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252 | |
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253 | hash = ( hash << 1 | hash >>> 31 ); |
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254 | for(int x=0;x<genome.length;x++) |
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255 | hash = ( hash << 1 | hash >>> 31 ) ^ genome[x]; |
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256 | |
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257 | return hash; |
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258 | } |
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259 | |
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260 | public String genotypeToStringForHumans() |
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261 | { |
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262 | String s = ""; |
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263 | for( int i = 0 ; i < genome.length ; i++ ) |
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264 | s = s + " " + genome[i]; |
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265 | return s; |
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266 | } |
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267 | |
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268 | public String genotypeToString() |
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269 | { |
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270 | StringBuffer s = new StringBuffer(); |
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271 | s.append( Code.encode( genome.length ) ); |
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272 | for( int i = 0 ; i < genome.length ; i++ ) |
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273 | s.append( Code.encode( genome[i] ) ); |
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274 | return s.toString(); |
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275 | } |
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276 | |
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277 | protected void parseGenotype(final EvolutionState state, |
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278 | final LineNumberReader reader) throws IOException |
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279 | { |
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280 | // read in the next line. The first item is the number of genes |
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281 | String s = reader.readLine(); |
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282 | DecodeReturn d = new DecodeReturn(s); |
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283 | Code.decode( d ); |
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284 | int lll = (int)(d.l); |
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285 | |
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286 | genome = new byte[ lll ]; |
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287 | |
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288 | // read in the genes |
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289 | for( int i = 0 ; i < genome.length ; i++ ) |
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290 | { |
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291 | Code.decode( d ); |
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292 | genome[i] = (byte)(d.l); |
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293 | } |
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294 | } |
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295 | |
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296 | public boolean equals(Object ind) |
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297 | { |
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298 | if (!(this.getClass().equals(ind.getClass()))) return false; // SimpleRuleIndividuals are special. |
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299 | ByteVectorIndividual i = (ByteVectorIndividual)ind; |
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300 | if( genome.length != i.genome.length ) |
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301 | return false; |
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302 | for( int j = 0 ; j < genome.length ; j++ ) |
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303 | if( genome[j] != i.genome[j] ) |
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304 | return false; |
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305 | return true; |
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306 | } |
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307 | |
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308 | public Object getGenome() |
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309 | { return genome; } |
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310 | public void setGenome(Object gen) |
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311 | { genome = (byte[]) gen; } |
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312 | public int genomeLength() |
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313 | { return genome.length; } |
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314 | |
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315 | public void writeGenotype(final EvolutionState state, |
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316 | final DataOutput dataOutput) throws IOException |
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317 | { |
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318 | dataOutput.writeInt(genome.length); |
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319 | for(int x=0;x<genome.length;x++) |
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320 | dataOutput.writeByte(genome[x]); |
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321 | } |
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322 | |
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323 | public void readGenotype(final EvolutionState state, |
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324 | final DataInput dataInput) throws IOException |
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325 | { |
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326 | int len = dataInput.readInt(); |
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327 | if (genome==null || genome.length != len) |
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328 | genome = new byte[len]; |
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329 | for(int x=0;x<genome.length;x++) |
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330 | genome[x] = dataInput.readByte(); |
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331 | } |
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332 | |
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333 | /** Clips each gene value to be within its specified [min,max] range. */ |
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334 | public void clamp() |
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335 | { |
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336 | IntegerVectorSpecies _species = (IntegerVectorSpecies)species; |
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337 | for (int i = 0; i < genomeLength(); i++) |
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338 | { |
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339 | byte minGene = (byte)_species.minGene(i); |
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340 | if (genome[i] < minGene) |
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341 | genome[i] = minGene; |
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342 | else |
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343 | { |
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344 | byte maxGene = (byte)_species.maxGene(i); |
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345 | if (genome[i] > maxGene) |
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346 | genome[i] = maxGene; |
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347 | } |
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348 | } |
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349 | } |
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350 | |
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351 | public void setGenomeLength(int len) |
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352 | { |
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353 | byte[] newGenome = new byte[len]; |
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354 | System.arraycopy(genome, 0, newGenome, 0, |
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355 | genome.length < newGenome.length ? genome.length : newGenome.length); |
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356 | genome = newGenome; |
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357 | } |
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358 | |
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359 | /** Returns true if each gene value is within is specified [min,max] range. */ |
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360 | public boolean isInRange() |
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361 | { |
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362 | IntegerVectorSpecies _species = (IntegerVectorSpecies)species; |
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363 | for (int i = 0; i < genomeLength(); i++) |
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364 | if (genome[i] < _species.minGene(i) || |
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365 | genome[i] > _species.maxGene(i)) return false; |
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366 | return true; |
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367 | } |
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368 | |
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369 | public double distanceTo(Individual otherInd) |
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370 | { |
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371 | if (!(otherInd instanceof ByteVectorIndividual)) |
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372 | return super.distanceTo(otherInd); // will return infinity! |
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373 | |
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374 | ByteVectorIndividual other = (ByteVectorIndividual) otherInd; |
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375 | byte[] otherGenome = other.genome; |
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376 | double sumSquaredDistance =0.0; |
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377 | for(int i=0; i < other.genomeLength(); i++) |
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378 | { |
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379 | long dist = this.genome[i] - (long)otherGenome[i]; |
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380 | sumSquaredDistance += dist*dist; |
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381 | } |
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382 | return StrictMath.sqrt(sumSquaredDistance); |
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383 | } |
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384 | } |
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