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| 50 | <h1>Source code for park.diffev</h1><div class="highlight"><pre> |
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| 51 | <span class="kn">from</span> <span class="nn">random</span> <span class="kn">import</span> <span class="n">randint</span><span class="p">,</span> <span class="n">random</span> |
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| 52 | <span class="kn">import</span> <span class="nn">numpy</span> |
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| 53 | |
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| 54 | <div class="viewcode-block" id="DE"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.DE">[docs]</a><span class="k">class</span> <span class="nc">DE</span><span class="p">:</span> |
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| 55 | <span class="sd">"""</span> |
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| 56 | <span class="sd"> Differential evolution test implementation</span> |
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| 57 | <span class="sd"> Implements the Scheme_DE_rand_1 variant</span> |
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| 58 | |
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| 59 | <span class="sd"> F: float</span> |
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| 60 | <span class="sd"> weighting factor which determines the magnitude of perturbation</span> |
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| 61 | <span class="sd"> occurring in each generation.</span> |
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| 62 | |
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| 63 | <span class="sd"> crossover_rate: float</span> |
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| 64 | <span class="sd"> In general, 0 < crossover_rate < 1. Usually</span> |
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| 65 | <span class="sd"> considerably lower than 1. Convergence slows as the value</span> |
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| 66 | <span class="sd"> increases, but higher crossover rates may be necessary when</span> |
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| 67 | |
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| 68 | <span class="sd"> func: w = f(p)</span> |
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| 69 | <span class="sd"> The function to be minimized, of the form w = f(p), where p</span> |
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| 70 | <span class="sd"> is a vector of length func_dim and w is a scalar</span> |
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| 71 | |
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| 72 | <span class="sd"> func_dim: int</span> |
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| 73 | <span class="sd"> The dimension of the objective function</span> |
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| 74 | |
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| 75 | <span class="sd"> pop: array</span> |
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| 76 | <span class="sd"> The initial population. This should be an iterable composed of</span> |
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| 77 | <span class="sd"> Rank-1 numpy arrays. The population size must be at least 4,</span> |
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| 78 | <span class="sd"> preferably much greater.</span> |
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| 79 | |
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| 80 | <span class="sd"> l_bound, u_bound: vector</span> |
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| 81 | <span class="sd"> arrays of size func_dim representing the upper and lower bounds</span> |
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| 82 | <span class="sd"> for the parameters in the solution vectors</span> |
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| 83 | |
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| 84 | <span class="sd"> tol: float</span> |
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| 85 | <span class="sd"> if (max(pop_values) - min(pop_values) <= conv), the population</span> |
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| 86 | <span class="sd"> has converged and the evolution will stop</span> |
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| 87 | <span class="sd"> """</span> |
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| 88 | |
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| 89 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">F</span><span class="p">,</span> <span class="n">crossover_rate</span><span class="p">,</span> <span class="n">func</span><span class="p">,</span> <span class="n">func_dim</span><span class="p">,</span> <span class="n">pop</span><span class="p">,</span> <span class="n">l_bound</span><span class="p">,</span> |
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| 90 | <span class="n">u_bound</span><span class="p">,</span> <span class="n">tol</span><span class="o">=</span><span class="mf">1e-7</span><span class="p">):</span> |
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| 91 | <span class="bp">self</span><span class="o">.</span><span class="n">pop_size</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">pop</span><span class="p">)</span> |
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| 92 | <span class="bp">self</span><span class="o">.</span><span class="n">dimension</span> <span class="o">=</span> <span class="n">func_dim</span> |
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| 93 | <span class="bp">self</span><span class="o">.</span><span class="n">F_orig</span> <span class="o">=</span> <span class="n">F</span> |
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| 94 | <span class="bp">self</span><span class="o">.</span><span class="n">F</span> <span class="o">=</span> <span class="n">F</span> |
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| 95 | <span class="bp">self</span><span class="o">.</span><span class="n">crossover_rate</span> <span class="o">=</span> <span class="n">crossover_rate</span> |
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| 96 | <span class="bp">self</span><span class="o">.</span><span class="n">func</span> <span class="o">=</span> <span class="n">func</span> |
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| 97 | <span class="bp">self</span><span class="o">.</span><span class="n">tol</span> <span class="o">=</span> <span class="n">tol</span> |
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| 98 | <span class="bp">self</span><span class="o">.</span><span class="n">l_bound</span> <span class="o">=</span> <span class="n">l_bound</span> |
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| 99 | <span class="bp">self</span><span class="o">.</span><span class="n">u_bound</span> <span class="o">=</span> <span class="n">u_bound</span> |
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| 100 | <span class="bp">self</span><span class="o">.</span><span class="n">population</span> <span class="o">=</span> <span class="n">pop</span> |
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| 101 | <span class="bp">self</span><span class="o">.</span><span class="n">generations</span> <span class="o">=</span> <span class="mi">0</span> |
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| 102 | <span class="bp">self</span><span class="o">.</span><span class="n">pop_values</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">func</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">population</span><span class="p">]</span> |
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| 103 | <span class="bp">self</span><span class="o">.</span><span class="n">best_gene</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">best_value</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_best_gene</span><span class="p">()</span> |
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| 104 | <span class="bp">self</span><span class="o">.</span><span class="n">best_gene_history</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">best_gene</span><span class="p">]</span> |
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| 105 | <span class="bp">self</span><span class="o">.</span><span class="n">best_val_history</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">best_value</span><span class="p">]</span> |
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| 106 | <span class="bp">self</span><span class="o">.</span><span class="n">ncalls</span> <span class="o">=</span> <span class="mi">0</span> |
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| 107 | |
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| 108 | <span class="c">#//////////////////////////////////////////////////</span> |
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| 109 | <div class="viewcode-block" id="DE.evolve"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.DE.evolve">[docs]</a> <span class="k">def</span> <span class="nf">evolve</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">numgens</span><span class="o">=</span><span class="mi">1000</span><span class="p">,</span> <span class="n">monitor</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
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| 110 | <span class="sd">'''Evolve the population for numgens generations, or until it converges.</span> |
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| 111 | <span class="sd"> Returns the best vector from the run'''</span> |
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| 112 | <span class="k">try</span><span class="p">:</span> |
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| 113 | <span class="kn">import</span> <span class="nn">psyco</span> |
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| 114 | <span class="n">psyco</span><span class="o">.</span><span class="n">full</span><span class="p">()</span> |
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| 115 | <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span> |
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| 116 | <span class="k">pass</span> |
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| 117 | |
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| 118 | <span class="n">start_gen</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">generations</span> |
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| 119 | <span class="k">for</span> <span class="n">gen</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">generations</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">generations</span> <span class="o">+</span> <span class="n">numgens</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span> |
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| 120 | <span class="n">candidate_pop</span> <span class="o">=</span> <span class="p">[]</span> |
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| 121 | |
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| 122 | <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pop_size</span><span class="p">):</span> |
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| 123 | <span class="p">(</span><span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="p">,</span> <span class="n">r3</span><span class="p">)</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">select_participants</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> |
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| 124 | |
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| 125 | <span class="c">#perturbation/mutation</span> |
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| 126 | <span class="n">candidate</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">population</span><span class="p">[</span><span class="n">r1</span><span class="p">]</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">F</span><span class="o">*</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">population</span><span class="p">[</span><span class="n">r2</span><span class="p">]</span> |
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| 127 | <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">population</span><span class="p">[</span><span class="n">r3</span><span class="p">])</span> |
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| 128 | |
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| 129 | <span class="c">#crossover</span> |
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| 130 | <span class="n">candidate</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">crossover</span><span class="p">(</span><span class="n">candidate</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> |
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| 131 | |
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| 132 | <span class="c">#check bound constraints</span> |
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| 133 | <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_within_bounds</span><span class="p">(</span><span class="n">candidate</span><span class="p">):</span> |
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| 134 | <span class="n">candidate</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_random_gene</span><span class="p">()</span> |
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| 135 | |
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| 136 | <span class="c">#test fitness to determine membership in next gen</span> |
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| 137 | <span class="n">candidate_val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">func</span><span class="p">(</span><span class="n">candidate</span><span class="p">)</span> |
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| 138 | <span class="k">if</span> <span class="n">candidate_val</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">pop_values</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span> |
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| 139 | <span class="n">candidate_pop</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">candidate</span><span class="p">)</span> |
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| 140 | <span class="bp">self</span><span class="o">.</span><span class="n">pop_values</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">candidate_val</span><span class="p">)</span> |
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| 141 | <span class="k">else</span><span class="p">:</span> |
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| 142 | <span class="n">candidate_pop</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">population</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> |
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| 143 | <span class="bp">self</span><span class="o">.</span><span class="n">ncalls</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pop_size</span> |
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| 144 | |
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| 145 | <span class="bp">self</span><span class="o">.</span><span class="n">population</span> <span class="o">=</span> <span class="n">candidate_pop</span> |
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| 146 | <span class="n">x</span><span class="p">,</span><span class="n">fx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_best_gene</span><span class="p">()</span> |
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| 147 | <span class="k">if</span> <span class="n">fx</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_value</span><span class="p">:</span> |
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| 148 | <span class="bp">self</span><span class="o">.</span><span class="n">best_gene</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_value</span> <span class="o">=</span> <span class="n">x</span><span class="p">,</span><span class="n">fx</span> |
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| 149 | <span class="k">if</span> <span class="n">monitor</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
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| 150 | <span class="n">monitor</span><span class="o">.</span><span class="n">improvement</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">ncalls</span><span class="p">)</span> |
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| 151 | <span class="bp">self</span><span class="o">.</span><span class="n">best_val_history</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">best_value</span><span class="p">)</span> |
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| 152 | <span class="bp">self</span><span class="o">.</span><span class="n">best_gene_history</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">best_gene</span><span class="p">)</span> |
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| 153 | <span class="bp">self</span><span class="o">.</span><span class="n">generations</span> <span class="o">=</span> <span class="n">gen</span> |
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| 154 | |
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| 155 | <span class="k">if</span> <span class="n">monitor</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
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| 156 | <span class="n">monitor</span><span class="o">.</span><span class="n">progress</span><span class="p">(</span><span class="n">gen</span><span class="o">-</span><span class="n">start_gen</span><span class="p">,</span><span class="n">numgens</span><span class="p">)</span> |
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| 157 | |
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| 158 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_converged</span><span class="p">():</span> |
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| 159 | <span class="k">break</span> |
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| 160 | |
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| 161 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_gene</span> |
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| 162 | |
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| 163 | |
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| 164 | <span class="c">#////////////////////////////////////////////////</span></div> |
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| 165 | <div class="viewcode-block" id="DE.get_random_gene"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.DE.get_random_gene">[docs]</a> <span class="k">def</span> <span class="nf">get_random_gene</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 166 | <span class="sd">'''Generate a random gene within the bounds constraints.</span> |
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| 167 | <span class="sd"> Used to replace out-of-bounds genes'''</span> |
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| 168 | <span class="n">result</span> <span class="o">=</span> <span class="p">[</span><span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">uniform</span><span class="p">(</span><span class="n">low</span><span class="p">,</span> <span class="n">high</span><span class="p">)</span> |
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| 169 | <span class="k">for</span> <span class="n">low</span><span class="p">,</span> <span class="n">high</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">l_bound</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">u_bound</span><span class="p">)]</span> |
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| 170 | <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">result</span><span class="p">)</span> |
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| 171 | |
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| 172 | <span class="c">#////////////////////////////////////////////////</span></div> |
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| 173 | <div class="viewcode-block" id="DE.is_within_bounds"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.DE.is_within_bounds">[docs]</a> <span class="k">def</span> <span class="nf">is_within_bounds</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">gene</span><span class="p">):</span> |
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| 174 | <span class="sd">'''Determine whether the gene meets the bounds constraints'''</span> |
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| 175 | <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">all</span><span class="p">(</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">l_bound</span> <span class="o"><</span> <span class="n">gene</span><span class="p">)</span> <span class="o">&</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">u_bound</span> <span class="o">></span> <span class="n">gene</span><span class="p">)</span> <span class="p">)</span> |
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| 176 | |
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| 177 | <span class="c">#////////////////////////////////////////////////</span> |
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| 178 | <span class="c">#This appears to be a total failure. I'll leave the code in,</span> |
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| 179 | <span class="c">#but it's not called from the main evolution loop anymore.</span></div> |
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| 180 | <div class="viewcode-block" id="DE.adjust_F"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.DE.adjust_F">[docs]</a> <span class="k">def</span> <span class="nf">adjust_F</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 181 | <span class="sd">'''Adjust F to account for stagnation of the population '''</span> |
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| 182 | <span class="c">#has the best vector improved this generation?</span> |
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| 183 | <span class="n">idx</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">best_val_history</span><span class="p">)</span> |
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| 184 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_val_history</span><span class="p">[</span><span class="n">idx</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">best_val_history</span><span class="p">[</span><span class="n">idx</span> <span class="o">-</span> <span class="mi">2</span><span class="p">]:</span> |
---|
| 185 | <span class="bp">self</span><span class="o">.</span><span class="n">stagnant_gens</span> <span class="o">+=</span> <span class="mi">1</span> |
---|
| 186 | <span class="k">else</span><span class="p">:</span> |
---|
| 187 | <span class="bp">self</span><span class="o">.</span><span class="n">stagnant_gens</span> <span class="o">=</span> <span class="mi">0</span> |
---|
| 188 | |
---|
| 189 | <span class="c">#adapt F to account for stagnation</span> |
---|
| 190 | <span class="bp">self</span><span class="o">.</span><span class="n">F</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">F_orig</span> <span class="o">+</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stagnant_gens</span> <span class="o">*</span> <span class="mf">0.01</span><span class="p">)),</span> <span class="mf">2.0</span><span class="p">)</span> |
---|
| 191 | |
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| 192 | <span class="c">#////////////////////////////////////////////////</span></div> |
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| 193 | <div class="viewcode-block" id="DE.get_best_gene"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.DE.get_best_gene">[docs]</a> <span class="k">def</span> <span class="nf">get_best_gene</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
| 194 | <span class="sd">'''find the most fit gene in the current population'''</span> |
---|
| 195 | <span class="c">#print "pop", self.pop_values</span> |
---|
| 196 | |
---|
| 197 | <span class="n">best_index</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">argmin</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pop_values</span><span class="p">)</span> |
---|
| 198 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">population</span><span class="p">[</span><span class="n">best_index</span><span class="p">],</span><span class="bp">self</span><span class="o">.</span><span class="n">pop_values</span><span class="p">[</span><span class="n">best_index</span><span class="p">],</span> |
---|
| 199 | |
---|
| 200 | <span class="c">#////////////////////////////////////////////////</span></div> |
---|
| 201 | <div class="viewcode-block" id="DE.select_participants"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.DE.select_participants">[docs]</a> <span class="k">def</span> <span class="nf">select_participants</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span> |
---|
| 202 | <span class="sd">'''generate r1, r2, and r3 randomly from the range [0, NP-1]</span> |
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| 203 | <span class="sd"> such that they are distinct values not equal to i'''</span> |
---|
| 204 | <span class="n">choices</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="p">]</span> |
---|
| 205 | <span class="k">for</span> <span class="n">choice</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span> |
---|
| 206 | <span class="k">while</span> <span class="bp">True</span><span class="p">:</span> |
---|
| 207 | <span class="n">j</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pop_size</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span> |
---|
| 208 | <span class="k">if</span> <span class="n">j</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">choices</span><span class="p">:</span> |
---|
| 209 | <span class="k">break</span> |
---|
| 210 | <span class="n">choices</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">j</span><span class="p">)</span> |
---|
| 211 | <span class="k">return</span> <span class="n">choices</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span> |
---|
| 212 | <span class="c">#////////////////////////////////////////////////</span></div> |
---|
| 213 | <div class="viewcode-block" id="DE.crossover"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.DE.crossover">[docs]</a> <span class="k">def</span> <span class="nf">crossover</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">candidate</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span> |
---|
| 214 | <span class="sd">'''Perform a crossover between the candidate and the ith member of</span> |
---|
| 215 | <span class="sd"> the previous generation.'''</span> |
---|
| 216 | <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span> |
---|
| 217 | |
---|
| 218 | <span class="c">#generate lower bound of crossover (this bound is inclusive)</span> |
---|
| 219 | <span class="n">low</span> <span class="o">=</span> <span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dimension</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span> |
---|
| 220 | |
---|
| 221 | <span class="c">#determine the size of the crossover</span> |
---|
| 222 | <span class="n">L</span> <span class="o">=</span> <span class="mi">0</span> |
---|
| 223 | <span class="k">while</span> <span class="n">random</span><span class="p">()</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">crossover_rate</span> <span class="ow">and</span> <span class="n">L</span> <span class="o"><</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dimension</span> <span class="o">-</span> <span class="n">low</span><span class="p">):</span> |
---|
| 224 | <span class="n">L</span> <span class="o">+=</span> <span class="mi">1</span> |
---|
| 225 | |
---|
| 226 | <span class="c">#calculate the upper bound of crossover (this bound is exclusive)</span> |
---|
| 227 | <span class="n">high</span> <span class="o">=</span> <span class="n">low</span> <span class="o">+</span> <span class="n">L</span> |
---|
| 228 | |
---|
| 229 | <span class="n">high</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">repeat</span><span class="p">(</span><span class="n">high</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dimension</span><span class="p">)</span> |
---|
| 230 | <span class="n">low</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">repeat</span><span class="p">(</span><span class="n">low</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dimension</span><span class="p">)</span> |
---|
| 231 | <span class="n">seq</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dimension</span><span class="p">)</span> |
---|
| 232 | |
---|
| 233 | <span class="n">result</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">choose</span><span class="p">(</span> <span class="p">((</span><span class="n">seq</span> <span class="o">>=</span> <span class="n">low</span><span class="p">)</span><span class="o">&</span><span class="p">(</span><span class="n">seq</span> <span class="o"><</span> <span class="n">high</span><span class="p">)),</span> |
---|
| 234 | <span class="p">[</span><span class="n">candidate</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">population</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> <span class="p">)</span> |
---|
| 235 | <span class="k">return</span> <span class="n">result</span> |
---|
| 236 | </div> |
---|
| 237 | <div class="viewcode-block" id="DE.is_converged"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.DE.is_converged">[docs]</a> <span class="k">def</span> <span class="nf">is_converged</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
| 238 | <span class="sd">'''check for convergence'''</span> |
---|
| 239 | <span class="k">return</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pop_values</span><span class="p">)</span> <span class="o">-</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pop_values</span><span class="p">)</span> <span class="o"><=</span> <span class="bp">self</span><span class="o">.</span><span class="n">tol</span> |
---|
| 240 | </div></div> |
---|
| 241 | <div class="viewcode-block" id="diffev"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.diffev">[docs]</a><span class="k">def</span> <span class="nf">diffev</span><span class="p">(</span><span class="n">fn</span><span class="p">,</span> <span class="n">bounds</span><span class="p">,</span> <span class="n">x0</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">pop_scale</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span> <span class="n">crossover_rate</span><span class="o">=</span><span class="mf">0.8</span><span class="p">,</span> |
---|
| 242 | <span class="n">Fscale</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">tolerance</span><span class="o">=</span><span class="mf">1e-5</span><span class="p">,</span> <span class="n">maxiter</span><span class="o">=</span><span class="mi">1000</span><span class="p">,</span> <span class="n">monitor</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
---|
| 243 | <span class="sd">"""</span> |
---|
| 244 | <span class="sd"> Run differential evolution, returning x,fx,ncalls</span> |
---|
| 245 | <span class="sd"> """</span> |
---|
| 246 | <span class="n">lo</span><span class="p">,</span> <span class="n">hi</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">bounds</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="n">numpy</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">bounds</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> |
---|
| 247 | <span class="n">dim</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">lo</span><span class="p">)</span> |
---|
| 248 | <span class="n">pop</span> <span class="o">=</span> <span class="n">gen_pop</span><span class="p">(</span><span class="n">dim</span><span class="o">*</span><span class="n">pop_scale</span><span class="p">,</span> <span class="n">lo</span><span class="p">,</span> <span class="n">hi</span><span class="p">,</span> <span class="n">dim</span><span class="p">)</span> |
---|
| 249 | <span class="k">if</span> <span class="n">x0</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
| 250 | <span class="n">pop</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">x0</span><span class="p">)</span> |
---|
| 251 | <span class="n">evolver</span> <span class="o">=</span> <span class="n">DE</span><span class="p">(</span><span class="n">Fscale</span><span class="p">,</span> <span class="n">crossover_rate</span><span class="p">,</span> <span class="n">fn</span><span class="p">,</span> <span class="n">dim</span><span class="p">,</span> <span class="n">pop</span><span class="p">,</span> <span class="n">lo</span><span class="p">,</span> <span class="n">hi</span><span class="p">,</span> <span class="n">tolerance</span><span class="p">)</span> |
---|
| 252 | <span class="n">evolver</span><span class="o">.</span><span class="n">evolve</span><span class="p">(</span><span class="n">maxiter</span><span class="p">,</span> <span class="n">monitor</span><span class="o">=</span><span class="n">monitor</span><span class="p">)</span> |
---|
| 253 | <span class="k">return</span> <span class="n">evolver</span><span class="o">.</span><span class="n">best_gene</span><span class="p">,</span> <span class="n">evolver</span><span class="o">.</span><span class="n">best_value</span><span class="p">,</span> <span class="n">evolver</span><span class="o">.</span><span class="n">ncalls</span> |
---|
| 254 | |
---|
| 255 | |
---|
| 256 | |
---|
| 257 | |
---|
| 258 | <span class="c">########################################################################</span> |
---|
| 259 | <span class="c">#end DE def</span> |
---|
| 260 | <span class="c">########################################################################</span></div> |
---|
| 261 | <div class="viewcode-block" id="gen_pop"><a class="viewcode-back" href="../../dev/api/park.html#park.diffev.gen_pop">[docs]</a><span class="k">def</span> <span class="nf">gen_pop</span><span class="p">(</span><span class="n">size</span><span class="p">,</span> <span class="n">l_bound</span><span class="p">,</span> <span class="n">u_bound</span><span class="p">,</span> <span class="n">dimension</span><span class="p">):</span> |
---|
| 262 | <span class="sd">'''generate a random population of vectors within the given bounds. dimension</span> |
---|
| 263 | <span class="sd"> indicates the length of the vectors. l_bound and u_bound should be vectors</span> |
---|
| 264 | <span class="sd"> of length dimension (any iterable container should work)'''</span> |
---|
| 265 | <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span> |
---|
| 266 | <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="n">size</span><span class="p">):</span> |
---|
| 267 | <span class="n">entry</span> <span class="o">=</span> <span class="p">[]</span> |
---|
| 268 | <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="n">dimension</span><span class="p">):</span> |
---|
| 269 | <span class="n">entry</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">((</span><span class="n">u_bound</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="o">-</span> <span class="n">l_bound</span><span class="p">[</span><span class="n">j</span><span class="p">])</span> <span class="o">*</span> <span class="n">random</span><span class="p">())</span> <span class="o">+</span> <span class="n">l_bound</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="p">)</span> |
---|
| 270 | <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">entry</span><span class="p">))</span> |
---|
| 271 | <span class="k">return</span> <span class="n">result</span></div> |
---|
| 272 | </pre></div> |
---|
| 273 | |
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| 274 | </div> |
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| 275 | </div> |
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| 276 | </div> |
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| 277 | <div class="sphinxsidebar"> |
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| 288 | Enter search terms or a module, class or function name. |
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| 297 | <h3>Navigation</h3> |
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