rubyneat 0.3.5.alpha.3 → 0.3.5.alpha.5
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<p>Instantiations of neural inputs and outputs</p>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">critter</span>, <span class="ruby-identifier">mating</span> = <span class="ruby-keyword">false</span>, <span class="ruby-operator">&</span><span class="ruby-identifier">block</span>)
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<span class="ruby-ivar">@neural_inputs</span> = <span class="ruby-constant">Hash</span>[<span class="ruby-ivar">@critter</span>.<span class="ruby-identifier">population</span>.<span class="ruby-identifier">input_neurons</span>.<span class="ruby-identifier">map</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">sym</span>, <span class="ruby-identifier">ineu</span><span class="ruby-operator">|</span>
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[<span class="ruby-identifier">sym</span>, <span class="ruby-identifier">ineu</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@controller</span>, <span class="ruby-identifier">sym</span>)]
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<span class="ruby-ivar">@neural_outputs</span> = <span class="ruby-constant">Hash</span>[<span class="ruby-ivar">@critter</span>.<span class="ruby-identifier">population</span>.<span class="ruby-identifier">output_neurons</span>.<span class="ruby-identifier">map</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">sym</span>, <span class="ruby-identifier">ineu</span><span class="ruby-operator">|</span>
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[<span class="ruby-identifier">sym</span>, <span class="ruby-identifier">ineu</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@controller</span>, <span class="ruby-identifier">sym</span>)]
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<span class="ruby-ivar">@neurons</span> = <span class="ruby-ivar">@neural_inputs</span>.<span class="ruby-identifier">clone</span> <span class="ruby-comment"># this must be a shallow clone!</span>
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<span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">merge!</span> <span class="ruby-ivar">@neural_outputs</span>
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<span class="ruby-ivar">@controller</span>.<span class="ruby-identifier">evolver</span>.<span class="ruby-identifier">gen_initial_genes!</span>(<span class="ruby-keyword">self</span>) <span class="ruby-keyword">unless</span> <span class="ruby-identifier">mating</span>
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<span class="ruby-identifier">block</span>.(<span class="ruby-keyword">self</span>) <span class="ruby-keyword">unless</span> <span class="ruby-identifier">block</span>.<span class="ruby-identifier">nil?</span>
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<p>Genes added here MUST correspond to pre-existing neurons. Be sure to do <a
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|
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<span class="ruby-identifier">genes</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gene</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-constant">NeatException</span>.<span class="ruby-identifier">new</span> <span class="ruby-node">"Neuron #{gene.in_neuron} missing"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">member?</span> <span class="ruby-identifier">gene</span>.<span class="ruby-identifier">in_neuron</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-constant">NeatException</span>.<span class="ruby-identifier">new</span> <span class="ruby-node">"Neuron #{gene.out_neuron} missing"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">member?</span> <span class="ruby-identifier">gene</span>.<span class="ruby-identifier">out_neuron</span>
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<span class="ruby-ivar">@genes</span>[<span class="ruby-identifier">gene</span>.<span class="ruby-identifier">innovation</span>] = <span class="ruby-identifier">gene</span>
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class="method-args">(*neus)</span>
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<p>Add new neurons to the fold</p>
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<pre><span class="ruby-comment"># File lib/rubyneat/critter.rb, line 155</span>
|
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|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">add_neurons</span>(<span class="ruby-operator">*</span><span class="ruby-identifier">neus</span>)
|
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<span class="ruby-identifier">neus</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">neu</span><span class="ruby-operator">|</span>
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<span class="ruby-ivar">@neurons</span>[<span class="ruby-identifier">neu</span>.<span class="ruby-identifier">name</span>] = <span class="ruby-identifier">neu</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">end</span></pre>
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<pre><span class="ruby-comment"># File lib/rubyneat/critter.rb, line 218</span>
|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">dump_s</span>
|
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<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-string">"\ngenes:\n"</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@genes</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">k</span>, <span class="ruby-identifier">gene</span><span class="ruby-operator">|</span>
|
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<span class="ruby-identifier">gene</span>.<span class="ruby-identifier">to_s</span>}.<span class="ruby-identifier">join</span>(<span class="ruby-string">"\n"</span>) <span class="ruby-operator">+</span> <span class="ruby-string">"\nneurons:\n"</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">k</span>, <span class="ruby-identifier">neu</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">neu</span>.<span class="ruby-identifier">to_s</span>}.<span class="ruby-identifier">join</span>(<span class="ruby-string">"\n"</span>)
|
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<span class="ruby-keyword">end</span></pre>
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<div id="method-i-fitness_cost" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">fitness_cost</span><span
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class="method-args">()</span>
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</div>
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<p>Calculate the cost of this genotype.</p>
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<div class="method-source-code" id="fitness_cost-source">
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<pre><span class="ruby-comment"># File lib/rubyneat/critter.rb, line 213</span>
|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">fitness_cost</span>
|
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<span class="ruby-identifier">p</span> = <span class="ruby-ivar">@controller</span>.<span class="ruby-identifier">parms</span>
|
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<span class="ruby-identifier">p</span>.<span class="ruby-identifier">fitness_cost_per_neuron</span> <span class="ruby-operator">*</span> <span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">p</span>.<span class="ruby-identifier">fitness_cost_per_gene</span> <span class="ruby-operator">*</span> <span class="ruby-ivar">@genes</span>.<span class="ruby-identifier">size</span>
|
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<span class="ruby-keyword">end</span></pre>
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<div id="method-i-forget-21" class="method-detail ">
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<div class="method-heading">
|
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<span class="method-name">forget!</span><span
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class="method-args">()</span>
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<div class="method-description">
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|
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<p>Make the neurons forget their wiring.</p>
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<div class="method-source-code" id="forget-21-source">
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|
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<pre><span class="ruby-comment"># File lib/rubyneat/critter.rb, line 134</span>
|
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|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">forget!</span>
|
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|
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<span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">name</span>, <span class="ruby-identifier">neu</span><span class="ruby-operator">|</span> <span class="ruby-identifier">neu</span>.<span class="ruby-identifier">clear_graph</span> }
|
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|
-
<span class="ruby-ivar">@neural_gene_map</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">h</span>, <span class="ruby-identifier">k</span><span class="ruby-operator">|</span> <span class="ruby-identifier">h</span>[<span class="ruby-identifier">k</span>] = [] }
|
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|
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<span class="ruby-keyword">end</span></pre>
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</div>
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</div>
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<div id="method-i-innervate-21" class="method-detail ">
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|
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<div class="method-heading">
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<span class="method-name">innervate!</span><span
|
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class="method-args">(*hneus)</span>
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</div>
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<div class="method-description">
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<p>We take the neural hashes (presumably from other neurons), and innervate
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them. We do this in distinctions based on the neuron's names. FIXME We
|
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need to randomly select a neuron in the case of clashes. @param [Hash]
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hneus – hashes of neurons to innervate</p>
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<div class="method-source-code" id="innervate-21-source">
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|
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<pre><span class="ruby-comment"># File lib/rubyneat/critter.rb, line 175</span>
|
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|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">innervate!</span>(<span class="ruby-operator">*</span><span class="ruby-identifier">hneus</span>)
|
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|
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<span class="ruby-identifier">hneus</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">neus</span><span class="ruby-operator">|</span>
|
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|
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<span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">merge!</span> <span class="ruby-identifier">neus</span>.<span class="ruby-identifier">dclone</span>
|
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|
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">end</span></pre>
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</div>
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</div>
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</div>
|
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|
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<div id="method-i-neucleate" class="method-detail ">
|
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|
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|
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|
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<div class="method-heading">
|
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|
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<span class="method-name">neucleate</span><span
|
548
|
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class="method-args">(clean: true, &block)</span>
|
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|
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|
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<span class="method-click-advice">click to toggle source</span>
|
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|
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</div>
|
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|
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|
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|
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<div class="method-description">
|
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|
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|
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|
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<p>We add genes given here to the genome. An array of genes is returned from
|
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|
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the block and we simply add them in. @param [boolean] clean @param [Proc]
|
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|
-
block</p>
|
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|
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|
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|
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<div class="method-source-code" id="neucleate-source">
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|
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<pre><span class="ruby-comment"># File lib/rubyneat/critter.rb, line 113</span>
|
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|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">neucleate</span>(<span class="ruby-identifier">clean</span><span class="ruby-operator">:</span> <span class="ruby-keyword">true</span>, <span class="ruby-operator">&</span><span class="ruby-identifier">block</span>)
|
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|
-
<span class="ruby-identifier">genes</span> = <span class="ruby-constant">Hash</span>[<span class="ruby-identifier">block</span>.(<span class="ruby-keyword">self</span>).<span class="ruby-identifier">map</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span>
|
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|
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<span class="ruby-identifier">g</span>.<span class="ruby-identifier">genotype</span> = <span class="ruby-keyword">self</span>
|
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|
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[<span class="ruby-identifier">g</span>.<span class="ruby-identifier">innovation</span>, <span class="ruby-identifier">g</span>] }]
|
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|
-
<span class="ruby-keyword">if</span> <span class="ruby-identifier">clean</span>
|
571
|
-
<span class="ruby-ivar">@genes</span> = <span class="ruby-identifier">genes</span>
|
572
|
-
<span class="ruby-keyword">else</span>
|
573
|
-
<span class="ruby-ivar">@genes</span>.<span class="ruby-identifier">merge!</span> <span class="ruby-identifier">genes</span>
|
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|
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<span class="ruby-keyword">end</span>
|
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|
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<span class="ruby-identifier">nuke_redundancies!</span>
|
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|
-
<span class="ruby-keyword">end</span></pre>
|
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</div>
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</div>
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|
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|
-
<div id="method-i-nuke_redundancies-21" class="method-detail ">
|
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|
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|
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|
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<div class="method-heading">
|
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|
-
<span class="method-name">nuke_redundancies!</span><span
|
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|
-
class="method-args">()</span>
|
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|
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|
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|
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<span class="method-click-advice">click to toggle source</span>
|
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|
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|
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|
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</div>
|
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|
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|
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<div class="method-description">
|
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|
-
|
600
|
-
<p>Remove any redundancies in the genome, any genes refering to the same two
|
601
|
-
neurons. Simply choose one and delete the rest. TODO: implement
|
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|
-
nuke_redundancies!</p>
|
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|
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|
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|
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<div class="method-source-code" id="nuke_redundancies-21-source">
|
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|
-
<pre><span class="ruby-comment"># File lib/rubyneat/critter.rb, line 129</span>
|
609
|
-
<span class="ruby-keyword">def</span> <span class="ruby-identifier">nuke_redundancies!</span>
|
610
|
-
<span class="ruby-identifier">log</span>.<span class="ruby-identifier">warn</span> <span class="ruby-string">'nuke_redundancies! NIY'</span>
|
611
|
-
<span class="ruby-keyword">end</span></pre>
|
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|
-
</div>
|
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|
-
|
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</div>
|
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-
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|
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</div>
|
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|
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|
-
<div id="method-i-prune-21" class="method-detail ">
|
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|
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|
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|
-
<div class="method-heading">
|
625
|
-
<span class="method-name">prune!</span><span
|
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|
-
class="method-args">()</span>
|
627
|
-
|
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|
-
<span class="method-click-advice">click to toggle source</span>
|
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|
630
|
-
</div>
|
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-
|
632
|
-
|
633
|
-
<div class="method-description">
|
634
|
-
|
635
|
-
<p>Go through the list of neurons and drop any neurons not referenced by the
|
636
|
-
genes.</p>
|
637
|
-
|
638
|
-
<p>Then go through the genes and drop any that are dangling (i.e. no matching
|
639
|
-
neurons)</p>
|
640
|
-
|
641
|
-
<p>Then make sure that @neural_inputs and @neural_outputs reference the actual
|
642
|
-
instance neurons in @neurons</p>
|
643
|
-
|
644
|
-
<p>TODO add this circularity check to prune!</p>
|
645
|
-
|
646
|
-
|
647
|
-
|
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|
-
|
649
|
-
<div class="method-source-code" id="prune-21-source">
|
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|
-
<pre><span class="ruby-comment"># File lib/rubyneat/critter.rb, line 191</span>
|
651
|
-
<span class="ruby-keyword">def</span> <span class="ruby-identifier">prune!</span>
|
652
|
-
<span class="ruby-comment"># Take care of dangling neurons</span>
|
653
|
-
<span class="ruby-identifier">neunames</span> = <span class="ruby-ivar">@genes</span>.<span class="ruby-identifier">values</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> [<span class="ruby-identifier">g</span>.<span class="ruby-identifier">in_neuron</span>, <span class="ruby-identifier">g</span>.<span class="ruby-identifier">out_neuron</span>]}.<span class="ruby-identifier">flatten</span>.<span class="ruby-identifier">to_set</span>
|
654
|
-
<span class="ruby-ivar">@neurons</span> = <span class="ruby-constant">Hash</span>[<span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">values</span>.<span class="ruby-identifier">reject</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span>
|
655
|
-
<span class="ruby-keyword">not</span> <span class="ruby-identifier">neunames</span>.<span class="ruby-identifier">member?</span> <span class="ruby-identifier">n</span>.<span class="ruby-identifier">name</span>
|
656
|
-
<span class="ruby-keyword">end</span>.<span class="ruby-identifier">map</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span>
|
657
|
-
[<span class="ruby-identifier">n</span>.<span class="ruby-identifier">name</span>, <span class="ruby-identifier">n</span>]
|
658
|
-
<span class="ruby-keyword">end</span>]
|
659
|
-
|
660
|
-
<span class="ruby-comment"># Take care of dangling genes</span>
|
661
|
-
<span class="ruby-ivar">@genes</span> = <span class="ruby-constant">Hash</span>[<span class="ruby-ivar">@genes</span>.<span class="ruby-identifier">values</span>.<span class="ruby-identifier">reject</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gene</span><span class="ruby-operator">|</span>
|
662
|
-
<span class="ruby-keyword">not</span> (<span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">member?</span>(<span class="ruby-identifier">gene</span>.<span class="ruby-identifier">in_neuron</span>) <span class="ruby-keyword">and</span> <span class="ruby-ivar">@neurons</span>.<span class="ruby-identifier">member?</span>(<span class="ruby-identifier">gene</span>.<span class="ruby-identifier">out_neuron</span>))
|
663
|
-
<span class="ruby-keyword">end</span>.<span class="ruby-identifier">map</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gene</span><span class="ruby-operator">|</span>
|
664
|
-
[<span class="ruby-identifier">gene</span>.<span class="ruby-identifier">name</span>, <span class="ruby-identifier">gene</span>]
|
665
|
-
<span class="ruby-keyword">end</span>]
|
666
|
-
|
667
|
-
<span class="ruby-comment"># Make sure @neural_inputs and @neural_outputs are consistent</span>
|
668
|
-
<span class="ruby-ivar">@neural_inputs</span> = <span class="ruby-constant">Hash</span>[<span class="ruby-ivar">@neural_inputs</span>.<span class="ruby-identifier">values</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span> [<span class="ruby-identifier">n</span>.<span class="ruby-identifier">name</span>, <span class="ruby-ivar">@neurons</span>[<span class="ruby-identifier">n</span>.<span class="ruby-identifier">name</span>]]}]
|
669
|
-
<span class="ruby-ivar">@neural_outputs</span> = <span class="ruby-constant">Hash</span>[<span class="ruby-ivar">@neural_outputs</span>.<span class="ruby-identifier">values</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span> [<span class="ruby-identifier">n</span>.<span class="ruby-identifier">name</span>, <span class="ruby-ivar">@neurons</span>[<span class="ruby-identifier">n</span>.<span class="ruby-identifier">name</span>]]}]
|
670
|
-
<span class="ruby-keyword">end</span></pre>
|
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|
-
</div>
|
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|
-
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673
|
-
</div>
|
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|
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<div id="method-i-wire-21" class="method-detail ">
|
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|
-
<div class="method-heading">
|
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|
-
<span class="method-name">wire!</span><span
|
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|
-
class="method-args">()</span>
|
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-
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687
|
-
<span class="method-click-advice">click to toggle source</span>
|
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|
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-
</div>
|
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-
|
691
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-
|
692
|
-
<div class="method-description">
|
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-
|
694
|
-
<p>Wire up the neurons based on the genes.</p>
|
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696
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-
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|
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|
699
|
-
<div class="method-source-code" id="wire-21-source">
|
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|
-
<pre><span class="ruby-comment"># File lib/rubyneat/critter.rb, line 140</span>
|
701
|
-
<span class="ruby-keyword">def</span> <span class="ruby-identifier">wire!</span>
|
702
|
-
<span class="ruby-identifier">forget!</span>
|
703
|
-
<span class="ruby-ivar">@genes</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">innov</span>, <span class="ruby-identifier">gene</span><span class="ruby-operator">|</span>
|
704
|
-
<span class="ruby-keyword">if</span> <span class="ruby-identifier">gene</span>.<span class="ruby-identifier">enabled?</span>
|
705
|
-
<span class="ruby-identifier">raise</span> <span class="ruby-constant">NeatException</span>.<span class="ruby-identifier">new</span> <span class="ruby-node">"Can't find #{gene.out_neuron}"</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@neurons</span>[<span class="ruby-identifier">gene</span>.<span class="ruby-identifier">out_neuron</span>].<span class="ruby-identifier">nil?</span>
|
706
|
-
<span class="ruby-ivar">@neurons</span>[<span class="ruby-identifier">gene</span>.<span class="ruby-identifier">out_neuron</span>] <span class="ruby-operator"><<</span> <span class="ruby-ivar">@neurons</span>[<span class="ruby-identifier">gene</span>.<span class="ruby-identifier">in_neuron</span>]
|
707
|
-
<span class="ruby-ivar">@neural_gene_map</span>[<span class="ruby-identifier">gene</span>.<span class="ruby-identifier">out_neuron</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">gene</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">gene</span>.<span class="ruby-identifier">in_neuron</span>.<span class="ruby-identifier">nil?</span>
|
708
|
-
<span class="ruby-keyword">end</span>
|
709
|
-
<span class="ruby-keyword">end</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@genes</span>.<span class="ruby-identifier">nil?</span>
|
710
|
-
<span class="ruby-keyword">if</span> <span class="ruby-ivar">@genes</span>.<span class="ruby-identifier">nil?</span>
|
711
|
-
<span class="ruby-identifier">$log</span>.<span class="ruby-identifier">error</span> <span class="ruby-string">'Genes Not Present'</span>
|
712
|
-
<span class="ruby-keyword">end</span>
|
713
|
-
<span class="ruby-keyword">end</span></pre>
|
714
|
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|
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|
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</section>
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</main>
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<p><a href="http://validator.w3.org/check/referer">Validate</a>
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<p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
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<p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
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