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<p><h1 id=“label-Genotype+part+of+the+Critter”>Genotype part of the
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<p><p>List of connections, basically.</p></p>
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<p><p>Also, basic phentypic expression (which may be overriden by the
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<pre><strong class="classes">Classes:</strong> <span class='object_link'><a href="Genotype/Gene.html" title="NEAT::Critter::Genotype::Gene (class)">Gene</a></span></pre>
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<p><p>Critter to which we belong.</p> </div></span></p>
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<p><p>This will be set to true if there are dangling neurons.</p>
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<p><p>Genes keyed by innovation numbers.</p>
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<p><p>Map neurons to the genes that marks them as output { oneu_name
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<p><p>Instantiations of neural inputs and outputs.</p>
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<p><p>List of neurons hashed by name.</p>
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<h3 class="inherited">Attributes inherited from <span class='object_link'><a href="../NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></h3>
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<p class="inherited"><span class='object_link'><a href="../NeatOb.html#controller-instance_method" title="NEAT::NeatOb#controller (method)">#controller</a></span>, <span class='object_link'><a href="../NeatOb.html#name-instance_method" title="NEAT::NeatOb#name (method)">#name</a></span></p>
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|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
437
|
+
|
|
438
|
+
<p><p>Genes added here MUST correspond to pre-existing
|
|
439
|
+
neurons.</p> </div></span></p>
|
|
440
|
+
|
|
441
|
+
<p></li></p>
|
|
442
|
+
|
|
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|
+
<pre> <li class="public ">
|
|
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|
+
<span class="summary_signature">
|
|
445
|
+
|
|
446
|
+
<a href="#add_neurons-instance_method" title="#add_neurons (instance method)">- (Object) <strong>add_neurons</strong>(*neus) </a>
|
|
447
|
+
|
|
448
|
+
</span>
|
|
449
|
+
|
|
450
|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
451
|
+
|
|
452
|
+
<p><p>Add new neurons to the fold.</p> </div></span></p>
|
|
453
|
+
|
|
454
|
+
<p></li></p>
|
|
455
|
+
|
|
456
|
+
<pre> <li class="public ">
|
|
457
|
+
<span class="summary_signature">
|
|
458
|
+
|
|
459
|
+
<a href="#dump_s-instance_method" title="#dump_s (instance method)">- (Object) <strong>dump_s</strong> </a>
|
|
460
|
+
|
|
461
|
+
</span>
|
|
462
|
+
|
|
463
|
+
<span class="summary_desc"><div class='inline'></div></span></pre>
|
|
464
|
+
|
|
465
|
+
<p></li></p>
|
|
466
|
+
|
|
467
|
+
<pre> <li class="public ">
|
|
468
|
+
<span class="summary_signature">
|
|
469
|
+
|
|
470
|
+
<a href="#fitness_cost-instance_method" title="#fitness_cost (instance method)">- (Object) <strong>fitness_cost</strong> </a>
|
|
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|
+
|
|
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|
+
</span>
|
|
473
|
+
|
|
474
|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
475
|
+
|
|
476
|
+
<p><p>Calculate the cost of this genotype.</p>
|
|
477
|
+
</div></span></p>
|
|
478
|
+
|
|
479
|
+
<p></li></p>
|
|
480
|
+
|
|
481
|
+
<pre> <li class="public ">
|
|
482
|
+
<span class="summary_signature">
|
|
483
|
+
|
|
484
|
+
<a href="#forget%21-instance_method" title="#forget! (instance method)">- (Object) <strong>forget!</strong> </a>
|
|
485
|
+
|
|
486
|
+
</span>
|
|
487
|
+
|
|
488
|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
489
|
+
|
|
490
|
+
<p><p>Make the neurons forget their wiring.</p>
|
|
491
|
+
</div></span></p>
|
|
492
|
+
|
|
493
|
+
<p></li></p>
|
|
494
|
+
|
|
495
|
+
<pre> <li class="public ">
|
|
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|
+
<span class="summary_signature">
|
|
497
|
+
|
|
498
|
+
<a href="#initialize-instance_method" title="#initialize (instance method)">- (Genotype) <strong>initialize</strong>(critter, mating = false, &amp;block) </a>
|
|
499
|
+
|
|
500
|
+
</span>
|
|
501
|
+
|
|
502
|
+
<span class="note title constructor">constructor</span>
|
|
503
|
+
|
|
504
|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
505
|
+
|
|
506
|
+
<p><p>A new instance of Genotype.</p> </div></span></p>
|
|
507
|
+
|
|
508
|
+
<p></li></p>
|
|
509
|
+
|
|
510
|
+
<pre> <li class="public ">
|
|
511
|
+
<span class="summary_signature">
|
|
512
|
+
|
|
513
|
+
<a href="#innervate%21-instance_method" title="#innervate! (instance method)">- (Object) <strong>innervate!</strong>(*hneus) </a>
|
|
514
|
+
|
|
515
|
+
</span>
|
|
516
|
+
|
|
517
|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
518
|
+
|
|
519
|
+
<p><p>We take the neural hashes (presumably from other neurons), and
|
|
520
|
+
innervate them.</p> </div></span></p>
|
|
521
|
+
|
|
522
|
+
<p></li></p>
|
|
523
|
+
|
|
524
|
+
<pre> <li class="public ">
|
|
525
|
+
<span class="summary_signature">
|
|
526
|
+
|
|
527
|
+
<a href="#neucleate-instance_method" title="#neucleate (instance method)">- (Object) <strong>neucleate</strong>(clean: true, &amp;block) </a>
|
|
528
|
+
|
|
529
|
+
</span>
|
|
530
|
+
|
|
531
|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
532
|
+
|
|
533
|
+
<p><p>We add genes given here to the genome.</p>
|
|
534
|
+
</div></span></p>
|
|
535
|
+
|
|
536
|
+
<p></li></p>
|
|
537
|
+
|
|
538
|
+
<pre> <li class="public ">
|
|
539
|
+
<span class="summary_signature">
|
|
540
|
+
|
|
541
|
+
<a href="#nuke_redundancies%21-instance_method" title="#nuke_redundancies! (instance method)">- (Object) <strong>nuke_redundancies!</strong> </a>
|
|
542
|
+
|
|
543
|
+
</span>
|
|
544
|
+
|
|
545
|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
546
|
+
|
|
547
|
+
<p><p>Remove any redundancies in the genome, any genes refering to the
|
|
548
|
+
same two neurons.</p> </div></span></p>
|
|
549
|
+
|
|
550
|
+
<p></li></p>
|
|
551
|
+
|
|
552
|
+
<pre> <li class="public ">
|
|
553
|
+
<span class="summary_signature">
|
|
554
|
+
|
|
555
|
+
<a href="#prune%21-instance_method" title="#prune! (instance method)">- (Object) <strong>prune!</strong> </a>
|
|
556
|
+
|
|
557
|
+
</span>
|
|
558
|
+
|
|
559
|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
560
|
+
|
|
561
|
+
<p><p>Go through the list of neurons and drop any neurons not referenced
|
|
562
|
+
by the genes.</p> </div></span></p>
|
|
563
|
+
|
|
564
|
+
<p></li></p>
|
|
565
|
+
|
|
566
|
+
<pre> <li class="public ">
|
|
567
|
+
<span class="summary_signature">
|
|
568
|
+
|
|
569
|
+
<a href="#wire%21-instance_method" title="#wire! (instance method)">- (Object) <strong>wire!</strong> </a>
|
|
570
|
+
|
|
571
|
+
</span>
|
|
572
|
+
|
|
573
|
+
<span class="summary_desc"><div class='inline'></pre>
|
|
574
|
+
|
|
575
|
+
<p><p>Wire up the neurons based on the genes.</p>
|
|
576
|
+
</div></span></p>
|
|
577
|
+
|
|
578
|
+
<p></li></p>
|
|
579
|
+
|
|
580
|
+
<pre> </ul>
|
|
581
|
+
|
|
582
|
+
<h3 class="inherited">Methods inherited from <span class='object_link'><a href="../NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></h3>
|
|
583
|
+
<p class="inherited"><span class='object_link'><a href="../NeatOb.html#log-instance_method" title="NEAT::NeatOb#log (method)">#log</a></span>, <span class='object_link'><a href="../NeatOb.html#log-class_method" title="NEAT::NeatOb.log (method)">log</a></span>, <span class='object_link'><a href="../NeatOb.html#to_s-instance_method" title="NEAT::NeatOb#to_s (method)">#to_s</a></span></p>
|
|
584
|
+
|
|
585
|
+
<div id="constructor_details" class="method_details_list">
|
|
586
|
+
<h2>Constructor Details</h2>
|
|
587
|
+
|
|
588
|
+
<div class="method_details first">
|
|
589
|
+
<h3 class="signature first" id="initialize-instance_method">
|
|
590
|
+
|
|
591
|
+
- (<tt><span class='object_link'><a href="" title="NEAT::Critter::Genotype (class)">Genotype</a></span></tt>) <strong>initialize</strong>(critter, mating = false, &amp;block)</pre>
|
|
592
|
+
|
|
593
|
+
<p></h3><div class=“docstring”></p>
|
|
594
|
+
|
|
595
|
+
<pre><div class="discussion"></pre>
|
|
596
|
+
|
|
597
|
+
<p><p>Returns a new instance of Genotype</p></p>
|
|
598
|
+
|
|
599
|
+
<pre></div></pre>
|
|
600
|
+
|
|
601
|
+
<p></div> <div class=“tags”></p>
|
|
602
|
+
|
|
603
|
+
<p></div><table class=“source_code”></p>
|
|
604
|
+
|
|
605
|
+
<pre><tr>
|
|
606
|
+
<td>
|
|
607
|
+
<pre class="lines"></pre>
|
|
608
|
+
|
|
609
|
+
<p>88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106</pre></p>
|
|
610
|
+
|
|
611
|
+
<pre></td>
|
|
612
|
+
<td>
|
|
613
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 88</span></pre>
|
|
614
|
+
|
|
615
|
+
<p><span class='kw'>def</span> <span class='id
|
|
616
|
+
identifier rubyid_initialize'>initialize</span><span
|
|
617
|
+
class='lparen'>(</span><span class='id identifier
|
|
618
|
+
rubyid_critter'>critter</span><span
|
|
619
|
+
class='comma'>,</span> <span class='id identifier
|
|
620
|
+
rubyid_mating'>mating</span> <span
|
|
621
|
+
class='op'>=</span> <span
|
|
622
|
+
class='kw'>false</span><span
|
|
623
|
+
class='comma'>,</span> <span
|
|
624
|
+
class='op'>&amp;</span><span class='id
|
|
625
|
+
identifier rubyid_block'>block</span><span
|
|
626
|
+
class='rparen'>)</span></p>
|
|
627
|
+
|
|
628
|
+
<pre><span class='kw'>super</span> <span class='id identifier rubyid_critter'>critter</span><span class='period'>.</span><span class='id identifier rubyid_controller'>controller</span>
|
|
629
|
+
<span class='ivar'>@critter</span> <span class='op'>=</span> <span class='id identifier rubyid_critter'>critter</span>
|
|
630
|
+
|
|
631
|
+
<span class='comment'># Initialize basic structures</pre>
|
|
632
|
+
|
|
633
|
+
<p></span> <span class='ivar'>@genes</span>
|
|
634
|
+
<span class='op'>=</span> <span
|
|
635
|
+
class='kw'>nil</span></p>
|
|
636
|
+
|
|
637
|
+
<pre><span class='ivar'>@neural_inputs</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@critter</span><span class='period'>.</span><span class='id identifier rubyid_population'>population</span><span class='period'>.</span><span class='id identifier rubyid_input_neurons'>input_neurons</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sym'>sym</span><span class='comma'>,</span> <span class='id identifier rubyid_ineu'>ineu</span><span class='op'>|</span>
|
|
638
|
+
<span class='lbracket'>[</span><span class='id identifier rubyid_sym'>sym</span><span class='comma'>,</span> <span class='id identifier rubyid_ineu'>ineu</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@controller</span><span class='comma'>,</span> <span class='id identifier rubyid_sym'>sym</span><span class='rparen'>)</span><span class='rbracket'>]</span>
|
|
639
|
+
<span class='rbrace'>}</span><span class='rbracket'>]</span>
|
|
640
|
+
|
|
641
|
+
<span class='ivar'>@neural_outputs</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@critter</span><span class='period'>.</span><span class='id identifier rubyid_population'>population</span><span class='period'>.</span><span class='id identifier rubyid_output_neurons'>output_neurons</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sym'>sym</span><span class='comma'>,</span> <span class='id identifier rubyid_ineu'>ineu</span><span class='op'>|</span>
|
|
642
|
+
<span class='lbracket'>[</span><span class='id identifier rubyid_sym'>sym</span><span class='comma'>,</span> <span class='id identifier rubyid_ineu'>ineu</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@controller</span><span class='comma'>,</span> <span class='id identifier rubyid_sym'>sym</span><span class='rparen'>)</span><span class='rbracket'>]</span>
|
|
643
|
+
<span class='rbrace'>}</span><span class='rbracket'>]</span>
|
|
644
|
+
<span class='ivar'>@neurons</span> <span class='op'>=</span> <span class='ivar'>@neural_inputs</span><span class='period'>.</span><span class='id identifier rubyid_clone'>clone</span> <span class='comment'># this must be a shallow clone!</pre>
|
|
645
|
+
|
|
646
|
+
<p></span> <span
|
|
647
|
+
class='ivar'>@neurons</span><span
|
|
648
|
+
class='period'>.</span><span class='id identifier
|
|
649
|
+
rubyid_merge!'>merge!</span> <span
|
|
650
|
+
class='ivar'>@neural_outputs</span></p>
|
|
651
|
+
|
|
652
|
+
<pre><span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_evolver'>evolver</span><span class='period'>.</span><span class='id identifier rubyid_gen_initial_genes!'>gen_initial_genes!</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span> <span class='kw'>unless</span> <span class='id identifier rubyid_mating'>mating</span>
|
|
653
|
+
<span class='id identifier rubyid_block'>block</span><span class='period'>.</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span> <span class='kw'>unless</span> <span class='id identifier rubyid_block'>block</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span></pre>
|
|
654
|
+
|
|
655
|
+
<p><span class='kw'>end</span></pre></p>
|
|
656
|
+
|
|
657
|
+
<pre> </td>
|
|
658
|
+
</tr></pre>
|
|
659
|
+
|
|
660
|
+
<p></table> </div></p>
|
|
661
|
+
|
|
662
|
+
<p></div></p>
|
|
663
|
+
|
|
664
|
+
<pre><div id="instance_attr_details" class="attr_details">
|
|
665
|
+
<h2>Instance Attribute Details</h2>
|
|
666
|
+
|
|
667
|
+
<span id="critter=-instance_method"></span>
|
|
668
|
+
<div class="method_details first">
|
|
669
|
+
<h3 class="signature first" id="critter-instance_method">
|
|
670
|
+
|
|
671
|
+
- (<tt>Object</tt>) <strong>critter</strong></pre>
|
|
672
|
+
|
|
673
|
+
<p></h3><div class=“docstring”></p>
|
|
674
|
+
|
|
675
|
+
<pre><div class="discussion"></pre>
|
|
676
|
+
|
|
677
|
+
<p><p>Critter to which we belong</p></p>
|
|
678
|
+
|
|
679
|
+
<pre></div></pre>
|
|
680
|
+
|
|
681
|
+
<p></div> <div class=“tags”></p>
|
|
682
|
+
|
|
683
|
+
<p></div><table class=“source_code”></p>
|
|
684
|
+
|
|
685
|
+
<pre><tr>
|
|
686
|
+
<td>
|
|
687
|
+
<pre class="lines"></pre>
|
|
688
|
+
|
|
689
|
+
<p>67 68 69</pre></p>
|
|
690
|
+
|
|
691
|
+
<pre></td>
|
|
692
|
+
<td>
|
|
693
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 67</span></pre>
|
|
694
|
+
|
|
695
|
+
<p><span class='kw'>def</span> <span class='id
|
|
696
|
+
identifier rubyid_critter'>critter</span></p>
|
|
697
|
+
|
|
698
|
+
<pre><span class='ivar'>@critter</span></pre>
|
|
699
|
+
|
|
700
|
+
<p><span class='kw'>end</span></pre></p>
|
|
701
|
+
|
|
702
|
+
<pre> </td>
|
|
703
|
+
</tr></pre>
|
|
704
|
+
|
|
705
|
+
<p></table> </div></p>
|
|
706
|
+
|
|
707
|
+
<pre> <span id="dangling_neurons=-instance_method"></span>
|
|
708
|
+
<div class="method_details ">
|
|
709
|
+
<h3 class="signature " id="dangling_neurons-instance_method">
|
|
710
|
+
|
|
711
|
+
- (<tt>Object</tt>) <strong>dangling_neurons</strong>
|
|
712
|
+
|
|
713
|
+
<span class="aliases">Also known as:
|
|
714
|
+
<span class="names"><span id='dangling_neurons?-instance_method'>dangling_neurons?</span></span>
|
|
715
|
+
</span></pre>
|
|
716
|
+
|
|
717
|
+
<p></h3><div class=“docstring”></p>
|
|
718
|
+
|
|
719
|
+
<pre><div class="discussion"></pre>
|
|
720
|
+
|
|
721
|
+
<p><p>This will be set to true if there are dangling neurons.</p></p>
|
|
722
|
+
|
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identifier rubyid_dangling_neurons'>dangling_neurons</span></p>
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<pre> <span id="genes=-instance_method"></span>
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<h3 class="signature " id="genes-instance_method">
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<pre><div class="discussion"></pre>
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<pre></div></pre>
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<pre class="lines"></pre>
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<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 70</span></pre>
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|
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identifier rubyid_genes'>genes</span></p>
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<p><span class='kw'>end</span></pre></p>
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<pre> </td>
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<pre> <span id=""></span>
|
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<div class="method_details ">
|
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|
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<h3 class="signature " id="neural_gene_map-instance_method">
|
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|
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|
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|
+
- (<tt>Object</tt>) <strong>neural_gene_map</strong> <span class="extras">(readonly)</span></pre>
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<p></h3><div class=“docstring”></p>
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|
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<pre><div class="discussion"></pre>
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|
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<p><p>Map neurons to the genes that marks them as output { oneu_name
|
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|
+
=&gt; [ gene_1, gene_2,… gene_n], …} Just take the in_neuron name and
|
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|
+
the weight to do the call to that neuron function with the appropriate
|
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+
weights</p></p>
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<pre></div></pre>
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<p></div> <div class=“tags”></p>
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+
|
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<p></div><table class=“source_code”></p>
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<td>
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<pre class="lines"></pre>
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<p>86 87 88</pre></p>
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|
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<pre></td>
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<td>
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<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 86</span></pre>
|
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|
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|
|
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|
+
<p><span class='kw'>def</span> <span class='id
|
|
823
|
+
identifier rubyid_neural_gene_map'>neural_gene_map</span></p>
|
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|
+
|
|
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|
+
<pre><span class='ivar'>@neural_gene_map</span></pre>
|
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|
+
|
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|
+
<p><span class='kw'>end</span></pre></p>
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|
+
<pre> </td>
|
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|
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</tr></pre>
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|
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<p></table> </div></p>
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|
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|
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<pre> <span id=""></span>
|
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|
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|
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|
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<h3 class="signature " id="neural_inputs-instance_method">
|
|
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|
+
|
|
838
|
+
- (<tt>Object</tt>) <strong>neural_inputs</strong> <span class="extras">(readonly)</span></pre>
|
|
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|
+
|
|
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|
+
<p></h3><div class=“docstring”></p>
|
|
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|
+
|
|
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|
+
<pre><div class="discussion"></pre>
|
|
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|
+
|
|
844
|
+
<p><p>Instantiations of neural inputs and outputs</p></p>
|
|
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|
+
|
|
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|
+
<pre></div></pre>
|
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|
+
|
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|
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<p></div> <div class=“tags”></p>
|
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|
+
|
|
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|
+
<p></div><table class=“source_code”></p>
|
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|
+
|
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|
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<pre><tr>
|
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<td>
|
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|
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<pre class="lines"></pre>
|
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|
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|
|
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|
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<p>76 77 78</pre></p>
|
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|
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|
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|
+
<pre></td>
|
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|
+
<td>
|
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|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 76</span></pre>
|
|
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|
+
|
|
862
|
+
<p><span class='kw'>def</span> <span class='id
|
|
863
|
+
identifier rubyid_neural_inputs'>neural_inputs</span></p>
|
|
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|
+
|
|
865
|
+
<pre><span class='ivar'>@neural_inputs</span></pre>
|
|
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|
+
|
|
867
|
+
<p><span class='kw'>end</span></pre></p>
|
|
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|
+
|
|
869
|
+
<pre> </td>
|
|
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|
+
</tr></pre>
|
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|
+
|
|
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|
+
<p></table> </div></p>
|
|
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|
+
|
|
874
|
+
<pre> <span id=""></span>
|
|
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|
+
<div class="method_details ">
|
|
876
|
+
<h3 class="signature " id="neural_outputs-instance_method">
|
|
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|
+
|
|
878
|
+
- (<tt>Object</tt>) <strong>neural_outputs</strong> <span class="extras">(readonly)</span></pre>
|
|
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|
+
|
|
880
|
+
<p></h3><div class=“docstring”></p>
|
|
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|
+
|
|
882
|
+
<pre><div class="discussion"></pre>
|
|
883
|
+
|
|
884
|
+
<p><p>Instantiations of neural inputs and outputs</p></p>
|
|
885
|
+
|
|
886
|
+
<pre></div></pre>
|
|
887
|
+
|
|
888
|
+
<p></div> <div class=“tags”></p>
|
|
889
|
+
|
|
890
|
+
<p></div><table class=“source_code”></p>
|
|
891
|
+
|
|
892
|
+
<pre><tr>
|
|
893
|
+
<td>
|
|
894
|
+
<pre class="lines"></pre>
|
|
895
|
+
|
|
896
|
+
<p>76 77 78</pre></p>
|
|
897
|
+
|
|
898
|
+
<pre></td>
|
|
899
|
+
<td>
|
|
900
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 76</span></pre>
|
|
901
|
+
|
|
902
|
+
<p><span class='kw'>def</span> <span class='id
|
|
903
|
+
identifier rubyid_neural_outputs'>neural_outputs</span></p>
|
|
904
|
+
|
|
905
|
+
<pre><span class='ivar'>@neural_outputs</span></pre>
|
|
906
|
+
|
|
907
|
+
<p><span class='kw'>end</span></pre></p>
|
|
908
|
+
|
|
909
|
+
<pre> </td>
|
|
910
|
+
</tr></pre>
|
|
911
|
+
|
|
912
|
+
<p></table> </div></p>
|
|
913
|
+
|
|
914
|
+
<pre> <span id="neurons=-instance_method"></span>
|
|
915
|
+
<div class="method_details ">
|
|
916
|
+
<h3 class="signature " id="neurons-instance_method">
|
|
917
|
+
|
|
918
|
+
- (<tt>Object</tt>) <strong>neurons</strong></pre>
|
|
919
|
+
|
|
920
|
+
<p></h3><div class=“docstring”></p>
|
|
921
|
+
|
|
922
|
+
<pre><div class="discussion"></pre>
|
|
923
|
+
|
|
924
|
+
<p><p>List of neurons hashed by name</p></p>
|
|
925
|
+
|
|
926
|
+
<pre></div></pre>
|
|
927
|
+
|
|
928
|
+
<p></div> <div class=“tags”></p>
|
|
929
|
+
|
|
930
|
+
<p></div><table class=“source_code”></p>
|
|
931
|
+
|
|
932
|
+
<pre><tr>
|
|
933
|
+
<td>
|
|
934
|
+
<pre class="lines"></pre>
|
|
935
|
+
|
|
936
|
+
<p>73 74 75</pre></p>
|
|
937
|
+
|
|
938
|
+
<pre></td>
|
|
939
|
+
<td>
|
|
940
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 73</span></pre>
|
|
941
|
+
|
|
942
|
+
<p><span class='kw'>def</span> <span class='id
|
|
943
|
+
identifier rubyid_neurons'>neurons</span></p>
|
|
944
|
+
|
|
945
|
+
<pre><span class='ivar'>@neurons</span></pre>
|
|
946
|
+
|
|
947
|
+
<p><span class='kw'>end</span></pre></p>
|
|
948
|
+
|
|
949
|
+
<pre> </td>
|
|
950
|
+
</tr></pre>
|
|
951
|
+
|
|
952
|
+
<p></table> </div></p>
|
|
953
|
+
|
|
954
|
+
<pre></div>
|
|
955
|
+
|
|
956
|
+
<div id="instance_method_details" class="method_details_list">
|
|
957
|
+
<h2>Instance Method Details</h2>
|
|
958
|
+
|
|
959
|
+
<div class="method_details first">
|
|
960
|
+
<h3 class="signature first" id="add_genes-instance_method">
|
|
961
|
+
|
|
962
|
+
- (<tt>Object</tt>) <strong>add_genes</strong>(*genes)</pre>
|
|
963
|
+
|
|
964
|
+
<p></h3><div class=“docstring”></p>
|
|
965
|
+
|
|
966
|
+
<pre><div class="discussion"></pre>
|
|
967
|
+
|
|
968
|
+
<p><p>Genes added here MUST correspond to pre-existing neurons. Be sure
|
|
969
|
+
to do add_neurons first!!!!</p></p>
|
|
970
|
+
|
|
971
|
+
<pre></div></pre>
|
|
972
|
+
|
|
973
|
+
<p></div> <div class=“tags”></p>
|
|
974
|
+
|
|
975
|
+
<p></div><table class=“source_code”></p>
|
|
976
|
+
|
|
977
|
+
<pre><tr>
|
|
978
|
+
<td>
|
|
979
|
+
<pre class="lines"></pre>
|
|
980
|
+
|
|
981
|
+
<p>163 164 165 166 167 168 169</pre></p>
|
|
982
|
+
|
|
983
|
+
<pre></td>
|
|
984
|
+
<td>
|
|
985
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 163</span></pre>
|
|
986
|
+
|
|
987
|
+
<p><span class='kw'>def</span> <span class='id
|
|
988
|
+
identifier rubyid_add_genes'>add_genes</span><span
|
|
989
|
+
class='lparen'>(</span><span
|
|
990
|
+
class='op'>*</span><span class='id identifier
|
|
991
|
+
rubyid_genes'>genes</span><span
|
|
992
|
+
class='rparen'>)</span></p>
|
|
993
|
+
|
|
994
|
+
<pre><span class='id identifier rubyid_genes'>genes</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_gene'>gene</span><span class='op'>|</span>
|
|
995
|
+
<span class='id identifier rubyid_raise'>raise</span> <span class='const'>NeatException</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Neuron </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span><span class='embexpr_end'>}</span><span class='tstring_content'> missing</span><span class='tstring_end'>&quot;</span></span> <span class='kw'>unless</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span> <span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span>
|
|
996
|
+
<span class='id identifier rubyid_raise'>raise</span> <span class='const'>NeatException</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Neuron </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='embexpr_end'>}</span><span class='tstring_content'> missing</span><span class='tstring_end'>&quot;</span></span> <span class='kw'>unless</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span> <span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span>
|
|
997
|
+
<span class='ivar'>@genes</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_innovation'>innovation</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_gene'>gene</span>
|
|
998
|
+
<span class='kw'>end</span></pre>
|
|
999
|
+
|
|
1000
|
+
<p><span class='kw'>end</span></pre></p>
|
|
1001
|
+
|
|
1002
|
+
<pre> </td>
|
|
1003
|
+
</tr></pre>
|
|
1004
|
+
|
|
1005
|
+
<p></table> </div></p>
|
|
1006
|
+
|
|
1007
|
+
<pre> <div class="method_details ">
|
|
1008
|
+
<h3 class="signature " id="add_neurons-instance_method">
|
|
1009
|
+
|
|
1010
|
+
- (<tt>Object</tt>) <strong>add_neurons</strong>(*neus)</pre>
|
|
1011
|
+
|
|
1012
|
+
<p></h3><div class=“docstring”></p>
|
|
1013
|
+
|
|
1014
|
+
<pre><div class="discussion"></pre>
|
|
1015
|
+
|
|
1016
|
+
<p><p>Add new neurons to the fold</p></p>
|
|
1017
|
+
|
|
1018
|
+
<pre></div></pre>
|
|
1019
|
+
|
|
1020
|
+
<p></div> <div class=“tags”></p>
|
|
1021
|
+
|
|
1022
|
+
<p></div><table class=“source_code”></p>
|
|
1023
|
+
|
|
1024
|
+
<pre><tr>
|
|
1025
|
+
<td>
|
|
1026
|
+
<pre class="lines"></pre>
|
|
1027
|
+
|
|
1028
|
+
<p>155 156 157 158 159</pre></p>
|
|
1029
|
+
|
|
1030
|
+
<pre></td>
|
|
1031
|
+
<td>
|
|
1032
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 155</span></pre>
|
|
1033
|
+
|
|
1034
|
+
<p><span class='kw'>def</span> <span class='id
|
|
1035
|
+
identifier rubyid_add_neurons'>add_neurons</span><span
|
|
1036
|
+
class='lparen'>(</span><span
|
|
1037
|
+
class='op'>*</span><span class='id identifier
|
|
1038
|
+
rubyid_neus'>neus</span><span
|
|
1039
|
+
class='rparen'>)</span></p>
|
|
1040
|
+
|
|
1041
|
+
<pre><span class='id identifier rubyid_neus'>neus</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_neu'>neu</span><span class='op'>|</span>
|
|
1042
|
+
<span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_neu'>neu</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_neu'>neu</span>
|
|
1043
|
+
<span class='kw'>end</span></pre>
|
|
1044
|
+
|
|
1045
|
+
<p><span class='kw'>end</span></pre></p>
|
|
1046
|
+
|
|
1047
|
+
<pre> </td>
|
|
1048
|
+
</tr></pre>
|
|
1049
|
+
|
|
1050
|
+
<p></table> </div></p>
|
|
1051
|
+
|
|
1052
|
+
<pre> <div class="method_details ">
|
|
1053
|
+
<h3 class="signature " id="dump_s-instance_method">
|
|
1054
|
+
|
|
1055
|
+
- (<tt>Object</tt>) <strong>dump_s</strong></pre>
|
|
1056
|
+
|
|
1057
|
+
<p></h3><table class=“source_code”></p>
|
|
1058
|
+
|
|
1059
|
+
<pre><tr>
|
|
1060
|
+
<td>
|
|
1061
|
+
<pre class="lines"></pre>
|
|
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|
+
|
|
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|
+
<p>218 219 220 221 222</pre></p>
|
|
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|
+
|
|
1065
|
+
<pre></td>
|
|
1066
|
+
<td>
|
|
1067
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 218</span></pre>
|
|
1068
|
+
|
|
1069
|
+
<p><span class='kw'>def</span> <span class='id
|
|
1070
|
+
identifier rubyid_dump_s'>dump_s</span></p>
|
|
1071
|
+
|
|
1072
|
+
<pre><span class='id identifier rubyid_to_s'>to_s</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\ngenes:\n</span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_gene'>gene</span><span class='op'>|</span>
|
|
1073
|
+
<span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nneurons:\n</span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_neu'>neu</span><span class='op'>|</span>
|
|
1074
|
+
<span class='id identifier rubyid_neu'>neu</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span></pre>
|
|
1075
|
+
|
|
1076
|
+
<p><span class='kw'>end</span></pre></p>
|
|
1077
|
+
|
|
1078
|
+
<pre> </td>
|
|
1079
|
+
</tr></pre>
|
|
1080
|
+
|
|
1081
|
+
<p></table> </div></p>
|
|
1082
|
+
|
|
1083
|
+
<pre> <div class="method_details ">
|
|
1084
|
+
<h3 class="signature " id="fitness_cost-instance_method">
|
|
1085
|
+
|
|
1086
|
+
- (<tt>Object</tt>) <strong>fitness_cost</strong></pre>
|
|
1087
|
+
|
|
1088
|
+
<p></h3><div class=“docstring”></p>
|
|
1089
|
+
|
|
1090
|
+
<pre><div class="discussion"></pre>
|
|
1091
|
+
|
|
1092
|
+
<p><p>Calculate the cost of this genotype.</p></p>
|
|
1093
|
+
|
|
1094
|
+
<pre></div></pre>
|
|
1095
|
+
|
|
1096
|
+
<p></div> <div class=“tags”></p>
|
|
1097
|
+
|
|
1098
|
+
<p></div><table class=“source_code”></p>
|
|
1099
|
+
|
|
1100
|
+
<pre><tr>
|
|
1101
|
+
<td>
|
|
1102
|
+
<pre class="lines"></pre>
|
|
1103
|
+
|
|
1104
|
+
<p>213 214 215 216</pre></p>
|
|
1105
|
+
|
|
1106
|
+
<pre></td>
|
|
1107
|
+
<td>
|
|
1108
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 213</span></pre>
|
|
1109
|
+
|
|
1110
|
+
<p><span class='kw'>def</span> <span class='id
|
|
1111
|
+
identifier rubyid_fitness_cost'>fitness_cost</span></p>
|
|
1112
|
+
|
|
1113
|
+
<pre><span class='id identifier rubyid_p'>p</span> <span class='op'>=</span> <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_parms'>parms</span>
|
|
1114
|
+
<span class='id identifier rubyid_p'>p</span><span class='period'>.</span><span class='id identifier rubyid_fitness_cost_per_neuron'>fitness_cost_per_neuron</span> <span class='op'>*</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span> <span class='op'>+</span> <span class='id identifier rubyid_p'>p</span><span class='period'>.</span><span class='id identifier rubyid_fitness_cost_per_gene'>fitness_cost_per_gene</span> <span class='op'>*</span> <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span></pre>
|
|
1115
|
+
|
|
1116
|
+
<p><span class='kw'>end</span></pre></p>
|
|
1117
|
+
|
|
1118
|
+
<pre> </td>
|
|
1119
|
+
</tr></pre>
|
|
1120
|
+
|
|
1121
|
+
<p></table> </div></p>
|
|
1122
|
+
|
|
1123
|
+
<pre> <div class="method_details ">
|
|
1124
|
+
<h3 class="signature " id="forget!-instance_method">
|
|
1125
|
+
|
|
1126
|
+
- (<tt>Object</tt>) <strong>forget!</strong></pre>
|
|
1127
|
+
|
|
1128
|
+
<p></h3><div class=“docstring”></p>
|
|
1129
|
+
|
|
1130
|
+
<pre><div class="discussion"></pre>
|
|
1131
|
+
|
|
1132
|
+
<p><p>Make the neurons forget their wiring.</p></p>
|
|
1133
|
+
|
|
1134
|
+
<pre></div></pre>
|
|
1135
|
+
|
|
1136
|
+
<p></div> <div class=“tags”></p>
|
|
1137
|
+
|
|
1138
|
+
<p></div><table class=“source_code”></p>
|
|
1139
|
+
|
|
1140
|
+
<pre><tr>
|
|
1141
|
+
<td>
|
|
1142
|
+
<pre class="lines"></pre>
|
|
1143
|
+
|
|
1144
|
+
<p>134 135 136 137</pre></p>
|
|
1145
|
+
|
|
1146
|
+
<pre></td>
|
|
1147
|
+
<td>
|
|
1148
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 134</span></pre>
|
|
1149
|
+
|
|
1150
|
+
<p><span class='kw'>def</span> <span class='id
|
|
1151
|
+
identifier rubyid_forget!'>forget!</span></p>
|
|
1152
|
+
|
|
1153
|
+
<pre><span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='id identifier rubyid_neu'>neu</span><span class='op'>|</span> <span class='id identifier rubyid_neu'>neu</span><span class='period'>.</span><span class='id identifier rubyid_clear_graph'>clear_graph</span> <span class='rbrace'>}</span>
|
|
1154
|
+
<span class='ivar'>@neural_gene_map</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_h'>h</span><span class='comma'>,</span> <span class='id identifier rubyid_k'>k</span><span class='op'>|</span> <span class='id identifier rubyid_h'>h</span><span class='lbracket'>[</span><span class='id identifier rubyid_k'>k</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span> <span class='rbrace'>}</span></pre>
|
|
1155
|
+
|
|
1156
|
+
<p><span class='kw'>end</span></pre></p>
|
|
1157
|
+
|
|
1158
|
+
<pre> </td>
|
|
1159
|
+
</tr></pre>
|
|
1160
|
+
|
|
1161
|
+
<p></table> </div></p>
|
|
1162
|
+
|
|
1163
|
+
<pre> <div class="method_details ">
|
|
1164
|
+
<h3 class="signature " id="innervate!-instance_method">
|
|
1165
|
+
|
|
1166
|
+
- (<tt>Object</tt>) <strong>innervate!</strong>(*hneus)</pre>
|
|
1167
|
+
|
|
1168
|
+
<p></h3><div class=“docstring”></p>
|
|
1169
|
+
|
|
1170
|
+
<pre><div class="discussion"></pre>
|
|
1171
|
+
|
|
1172
|
+
<p><p>We take the neural hashes (presumably from other neurons), and
|
|
1173
|
+
innervate them. We do this in distinctions based on the neuron&#39;s
|
|
1174
|
+
names. FIXME We need to randomly select a neuron in the case of
|
|
1175
|
+
clashes.</p></p>
|
|
1176
|
+
|
|
1177
|
+
<pre></div></pre>
|
|
1178
|
+
|
|
1179
|
+
<p></div> <div class=“tags”></p>
|
|
1180
|
+
|
|
1181
|
+
<pre><p class="tag_title">Parameters:</p></pre>
|
|
1182
|
+
|
|
1183
|
+
<p><ul class=“param”></p>
|
|
1184
|
+
|
|
1185
|
+
<pre><li>
|
|
1186
|
+
|
|
1187
|
+
<span class='name'>hneus</span>
|
|
1188
|
+
|
|
1189
|
+
<span class='type'>(<tt>Hash</tt>)</span>
|
|
1190
|
+
|
|
1191
|
+
&mdash;
|
|
1192
|
+
<div class='inline'></pre>
|
|
1193
|
+
|
|
1194
|
+
<p><p>– hashes of neurons to innervate</p> </div></p>
|
|
1195
|
+
|
|
1196
|
+
<pre></li></pre>
|
|
1197
|
+
|
|
1198
|
+
<p></ul></p>
|
|
1199
|
+
|
|
1200
|
+
<p></div><table class=“source_code”></p>
|
|
1201
|
+
|
|
1202
|
+
<pre><tr>
|
|
1203
|
+
<td>
|
|
1204
|
+
<pre class="lines"></pre>
|
|
1205
|
+
|
|
1206
|
+
<p>175 176 177 178 179</pre></p>
|
|
1207
|
+
|
|
1208
|
+
<pre></td>
|
|
1209
|
+
<td>
|
|
1210
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 175</span></pre>
|
|
1211
|
+
|
|
1212
|
+
<p><span class='kw'>def</span> <span class='id
|
|
1213
|
+
identifier rubyid_innervate!'>innervate!</span><span
|
|
1214
|
+
class='lparen'>(</span><span
|
|
1215
|
+
class='op'>*</span><span class='id identifier
|
|
1216
|
+
rubyid_hneus'>hneus</span><span
|
|
1217
|
+
class='rparen'>)</span></p>
|
|
1218
|
+
|
|
1219
|
+
<pre><span class='id identifier rubyid_hneus'>hneus</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_neus'>neus</span><span class='op'>|</span>
|
|
1220
|
+
<span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_merge!'>merge!</span> <span class='id identifier rubyid_neus'>neus</span><span class='period'>.</span><span class='id identifier rubyid_dclone'>dclone</span>
|
|
1221
|
+
<span class='kw'>end</span></pre>
|
|
1222
|
+
|
|
1223
|
+
<p><span class='kw'>end</span></pre></p>
|
|
1224
|
+
|
|
1225
|
+
<pre> </td>
|
|
1226
|
+
</tr></pre>
|
|
1227
|
+
|
|
1228
|
+
<p></table> </div></p>
|
|
1229
|
+
|
|
1230
|
+
<pre> <div class="method_details ">
|
|
1231
|
+
<h3 class="signature " id="neucleate-instance_method">
|
|
1232
|
+
|
|
1233
|
+
- (<tt>Object</tt>) <strong>neucleate</strong>(clean: true, &amp;block)</pre>
|
|
1234
|
+
|
|
1235
|
+
<p></h3><div class=“docstring”></p>
|
|
1236
|
+
|
|
1237
|
+
<pre><div class="discussion"></pre>
|
|
1238
|
+
|
|
1239
|
+
<p><p>We add genes given here to the genome. An array of genes is
|
|
1240
|
+
returned from the block and we simply add them in.</p></p>
|
|
1241
|
+
|
|
1242
|
+
<pre></div></pre>
|
|
1243
|
+
|
|
1244
|
+
<p></div> <div class=“tags”></p>
|
|
1245
|
+
|
|
1246
|
+
<pre><p class="tag_title">Parameters:</p></pre>
|
|
1247
|
+
|
|
1248
|
+
<p><ul class=“param”></p>
|
|
1249
|
+
|
|
1250
|
+
<pre><li>
|
|
1251
|
+
|
|
1252
|
+
<span class='name'>clean</span>
|
|
1253
|
+
|
|
1254
|
+
<span class='type'>(<tt>boolean</tt>)</span>
|
|
1255
|
+
|
|
1256
|
+
</li>
|
|
1257
|
+
|
|
1258
|
+
<li>
|
|
1259
|
+
|
|
1260
|
+
<span class='name'>block</span>
|
|
1261
|
+
|
|
1262
|
+
<span class='type'>(<tt>Proc</tt>)</span>
|
|
1263
|
+
|
|
1264
|
+
</li></pre>
|
|
1265
|
+
|
|
1266
|
+
<p></ul></p>
|
|
1267
|
+
|
|
1268
|
+
<p></div><table class=“source_code”></p>
|
|
1269
|
+
|
|
1270
|
+
<pre><tr>
|
|
1271
|
+
<td>
|
|
1272
|
+
<pre class="lines"></pre>
|
|
1273
|
+
|
|
1274
|
+
<p>113 114 115 116 117 118 119 120 121 122 123</pre></p>
|
|
1275
|
+
|
|
1276
|
+
<pre></td>
|
|
1277
|
+
<td>
|
|
1278
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 113</span></pre>
|
|
1279
|
+
|
|
1280
|
+
<p><span class='kw'>def</span> <span class='id
|
|
1281
|
+
identifier rubyid_neucleate'>neucleate</span><span
|
|
1282
|
+
class='lparen'>(</span><span
|
|
1283
|
+
class='label'>clean:</span> <span
|
|
1284
|
+
class='kw'>true</span><span
|
|
1285
|
+
class='comma'>,</span> <span
|
|
1286
|
+
class='op'>&amp;</span><span class='id
|
|
1287
|
+
identifier rubyid_block'>block</span><span
|
|
1288
|
+
class='rparen'>)</span></p>
|
|
1289
|
+
|
|
1290
|
+
<pre><span class='id identifier rubyid_genes'>genes</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='id identifier rubyid_block'>block</span><span class='period'>.</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_g'>g</span><span class='op'>|</span>
|
|
1291
|
+
<span class='id identifier rubyid_g'>g</span><span class='period'>.</span><span class='id identifier rubyid_genotype'>genotype</span> <span class='op'>=</span> <span class='kw'>self</span>
|
|
1292
|
+
<span class='lbracket'>[</span><span class='id identifier rubyid_g'>g</span><span class='period'>.</span><span class='id identifier rubyid_innovation'>innovation</span><span class='comma'>,</span> <span class='id identifier rubyid_g'>g</span><span class='rbracket'>]</span> <span class='rbrace'>}</span><span class='rbracket'>]</span>
|
|
1293
|
+
<span class='kw'>if</span> <span class='id identifier rubyid_clean'>clean</span>
|
|
1294
|
+
<span class='ivar'>@genes</span> <span class='op'>=</span> <span class='id identifier rubyid_genes'>genes</span>
|
|
1295
|
+
<span class='kw'>else</span>
|
|
1296
|
+
<span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_merge!'>merge!</span> <span class='id identifier rubyid_genes'>genes</span>
|
|
1297
|
+
<span class='kw'>end</span>
|
|
1298
|
+
<span class='id identifier rubyid_nuke_redundancies!'>nuke_redundancies!</span></pre>
|
|
1299
|
+
|
|
1300
|
+
<p><span class='kw'>end</span></pre></p>
|
|
1301
|
+
|
|
1302
|
+
<pre> </td>
|
|
1303
|
+
</tr></pre>
|
|
1304
|
+
|
|
1305
|
+
<p></table> </div></p>
|
|
1306
|
+
|
|
1307
|
+
<pre> <div class="method_details ">
|
|
1308
|
+
<h3 class="signature " id="nuke_redundancies!-instance_method">
|
|
1309
|
+
|
|
1310
|
+
- (<tt>Object</tt>) <strong>nuke_redundancies!</strong></pre>
|
|
1311
|
+
|
|
1312
|
+
<p></h3><div class=“docstring”></p>
|
|
1313
|
+
|
|
1314
|
+
<pre><div class="discussion"></pre>
|
|
1315
|
+
|
|
1316
|
+
<p><p>Remove any redundancies in the genome, any genes refering to the
|
|
1317
|
+
same two neurons. Simply choose one and delete the rest. TODO: implement
|
|
1318
|
+
nuke_redundancies!</p></p>
|
|
1319
|
+
|
|
1320
|
+
<pre></div></pre>
|
|
1321
|
+
|
|
1322
|
+
<p></div> <div class=“tags”></p>
|
|
1323
|
+
|
|
1324
|
+
<p></div><table class=“source_code”></p>
|
|
1325
|
+
|
|
1326
|
+
<pre><tr>
|
|
1327
|
+
<td>
|
|
1328
|
+
<pre class="lines"></pre>
|
|
1329
|
+
|
|
1330
|
+
<p>129 130 131</pre></p>
|
|
1331
|
+
|
|
1332
|
+
<pre></td>
|
|
1333
|
+
<td>
|
|
1334
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 129</span></pre>
|
|
1335
|
+
|
|
1336
|
+
<p><span class='kw'>def</span> <span class='id
|
|
1337
|
+
identifier
|
|
1338
|
+
rubyid_nuke_redundancies!'>nuke_redundancies!</span></p>
|
|
1339
|
+
|
|
1340
|
+
<pre><span class='id identifier rubyid_log'>log</span><span class='period'>.</span><span class='id identifier rubyid_warn'>warn</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>nuke_redundancies! NIY</span><span class='tstring_end'>&#39;</span></span></pre>
|
|
1341
|
+
|
|
1342
|
+
<p><span class='kw'>end</span></pre></p>
|
|
1343
|
+
|
|
1344
|
+
<pre> </td>
|
|
1345
|
+
</tr></pre>
|
|
1346
|
+
|
|
1347
|
+
<p></table> </div></p>
|
|
1348
|
+
|
|
1349
|
+
<pre> <div class="method_details ">
|
|
1350
|
+
<h3 class="signature " id="prune!-instance_method">
|
|
1351
|
+
|
|
1352
|
+
- (<tt>Object</tt>) <strong>prune!</strong></pre>
|
|
1353
|
+
|
|
1354
|
+
<p></h3><div class=“docstring”></p>
|
|
1355
|
+
|
|
1356
|
+
<pre><div class="discussion"></pre>
|
|
1357
|
+
|
|
1358
|
+
<p><p>Go through the list of neurons and drop any neurons not referenced
|
|
1359
|
+
by the genes.</p></p>
|
|
1360
|
+
|
|
1361
|
+
<p><p>Then go through the genes and drop any that are dangling (i.e. no
|
|
1362
|
+
matching neurons)</p></p>
|
|
1363
|
+
|
|
1364
|
+
<p><p>Then make sure that @neural_inputs and @neural_outputs reference
|
|
1365
|
+
the actual instance neurons in @neurons</p></p>
|
|
1366
|
+
|
|
1367
|
+
<p><p>TODO add this circularity check to prune!</p></p>
|
|
1368
|
+
|
|
1369
|
+
<pre></div></pre>
|
|
1370
|
+
|
|
1371
|
+
<p></div> <div class=“tags”></p>
|
|
1372
|
+
|
|
1373
|
+
<p></div><table class=“source_code”></p>
|
|
1374
|
+
|
|
1375
|
+
<pre><tr>
|
|
1376
|
+
<td>
|
|
1377
|
+
<pre class="lines"></pre>
|
|
1378
|
+
|
|
1379
|
+
<p>191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209
|
|
1380
|
+
210</pre></p>
|
|
1381
|
+
|
|
1382
|
+
<pre></td>
|
|
1383
|
+
<td>
|
|
1384
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 191</span></pre>
|
|
1385
|
+
|
|
1386
|
+
<p><span class='kw'>def</span> <span class='id
|
|
1387
|
+
identifier rubyid_prune!'>prune!</span></p>
|
|
1388
|
+
|
|
1389
|
+
<pre><span class='comment'># Take care of dangling neurons</pre>
|
|
1390
|
+
|
|
1391
|
+
<p></span> <span class='id identifier
|
|
1392
|
+
rubyid_neunames'>neunames</span> <span
|
|
1393
|
+
class='op'>=</span> <span
|
|
1394
|
+
class='ivar'>@genes</span><span
|
|
1395
|
+
class='period'>.</span><span class='id identifier
|
|
1396
|
+
rubyid_values'>values</span><span
|
|
1397
|
+
class='period'>.</span><span class='id identifier
|
|
1398
|
+
rubyid_map'>map</span><span
|
|
1399
|
+
class='lbrace'>{</span><span
|
|
1400
|
+
class='op'>|</span><span class='id identifier
|
|
1401
|
+
rubyid_g'>g</span><span
|
|
1402
|
+
class='op'>|</span> <span
|
|
1403
|
+
class='lbracket'>[</span><span class='id identifier
|
|
1404
|
+
rubyid_g'>g</span><span
|
|
1405
|
+
class='period'>.</span><span class='id identifier
|
|
1406
|
+
rubyid_in_neuron'>in_neuron</span><span
|
|
1407
|
+
class='comma'>,</span> <span class='id identifier
|
|
1408
|
+
rubyid_g'>g</span><span
|
|
1409
|
+
class='period'>.</span><span class='id identifier
|
|
1410
|
+
rubyid_out_neuron'>out_neuron</span><span
|
|
1411
|
+
class='rbracket'>]</span><span
|
|
1412
|
+
class='rbrace'>}</span><span
|
|
1413
|
+
class='period'>.</span><span class='id identifier
|
|
1414
|
+
rubyid_flatten'>flatten</span><span
|
|
1415
|
+
class='period'>.</span><span class='id identifier
|
|
1416
|
+
rubyid_to_set'>to_set</span></p>
|
|
1417
|
+
|
|
1418
|
+
<pre><span class='ivar'>@neurons</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_values'>values</span><span class='period'>.</span><span class='id identifier rubyid_reject'>reject</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_n'>n</span><span class='op'>|</span>
|
|
1419
|
+
<span class='kw'>not</span> <span class='id identifier rubyid_neunames'>neunames</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span> <span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span>
|
|
1420
|
+
<span class='kw'>end</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_n'>n</span><span class='op'>|</span>
|
|
1421
|
+
<span class='lbracket'>[</span><span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='id identifier rubyid_n'>n</span><span class='rbracket'>]</span>
|
|
1422
|
+
<span class='kw'>end</span><span class='rbracket'>]</span>
|
|
1423
|
+
|
|
1424
|
+
<span class='comment'># Take care of dangling genes</pre>
|
|
1425
|
+
|
|
1426
|
+
<p></span> <span class='ivar'>@genes</span>
|
|
1427
|
+
<span class='op'>=</span> <span
|
|
1428
|
+
class='const'>Hash</span><span
|
|
1429
|
+
class='lbracket'>[</span><span
|
|
1430
|
+
class='ivar'>@genes</span><span
|
|
1431
|
+
class='period'>.</span><span class='id identifier
|
|
1432
|
+
rubyid_values'>values</span><span
|
|
1433
|
+
class='period'>.</span><span class='id identifier
|
|
1434
|
+
rubyid_reject'>reject</span> <span
|
|
1435
|
+
class='kw'>do</span> <span
|
|
1436
|
+
class='op'>|</span><span class='id identifier
|
|
1437
|
+
rubyid_gene'>gene</span><span
|
|
1438
|
+
class='op'>|</span></p>
|
|
1439
|
+
|
|
1440
|
+
<pre> <span class='kw'>not</span> <span class='lparen'>(</span><span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span><span class='lparen'>(</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span><span class='rparen'>)</span> <span class='kw'>and</span> <span class='ivar'>@neurons</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span><span class='lparen'>(</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='rparen'>)</span><span class='rparen'>)</span>
|
|
1441
|
+
<span class='kw'>end</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_gene'>gene</span><span class='op'>|</span>
|
|
1442
|
+
<span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='id identifier rubyid_gene'>gene</span><span class='rbracket'>]</span>
|
|
1443
|
+
<span class='kw'>end</span><span class='rbracket'>]</span>
|
|
1444
|
+
|
|
1445
|
+
<span class='comment'># Make sure @neural_inputs and @neural_outputs are consistent</pre>
|
|
1446
|
+
|
|
1447
|
+
<p></span> <span class='ivar'>@neural_inputs</span>
|
|
1448
|
+
<span class='op'>=</span> <span
|
|
1449
|
+
class='const'>Hash</span><span
|
|
1450
|
+
class='lbracket'>[</span><span
|
|
1451
|
+
class='ivar'>@neural_inputs</span><span
|
|
1452
|
+
class='period'>.</span><span class='id identifier
|
|
1453
|
+
rubyid_values'>values</span><span
|
|
1454
|
+
class='period'>.</span><span class='id identifier
|
|
1455
|
+
rubyid_map'>map</span><span
|
|
1456
|
+
class='lbrace'>{</span><span
|
|
1457
|
+
class='op'>|</span><span class='id identifier
|
|
1458
|
+
rubyid_n'>n</span><span
|
|
1459
|
+
class='op'>|</span> <span
|
|
1460
|
+
class='lbracket'>[</span><span class='id identifier
|
|
1461
|
+
rubyid_n'>n</span><span
|
|
1462
|
+
class='period'>.</span><span class='id identifier
|
|
1463
|
+
rubyid_name'>name</span><span
|
|
1464
|
+
class='comma'>,</span> <span
|
|
1465
|
+
class='ivar'>@neurons</span><span
|
|
1466
|
+
class='lbracket'>[</span><span class='id identifier
|
|
1467
|
+
rubyid_n'>n</span><span
|
|
1468
|
+
class='period'>.</span><span class='id identifier
|
|
1469
|
+
rubyid_name'>name</span><span
|
|
1470
|
+
class='rbracket'>]</span><span
|
|
1471
|
+
class='rbracket'>]</span><span
|
|
1472
|
+
class='rbrace'>}</span><span
|
|
1473
|
+
class='rbracket'>]</span></p>
|
|
1474
|
+
|
|
1475
|
+
<pre><span class='ivar'>@neural_outputs</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='ivar'>@neural_outputs</span><span class='period'>.</span><span class='id identifier rubyid_values'>values</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_n'>n</span><span class='op'>|</span> <span class='lbracket'>[</span><span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='comma'>,</span> <span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_name'>name</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='rbracket'>]</span></pre>
|
|
1476
|
+
|
|
1477
|
+
<p><span class='kw'>end</span></pre></p>
|
|
1478
|
+
|
|
1479
|
+
<pre> </td>
|
|
1480
|
+
</tr></pre>
|
|
1481
|
+
|
|
1482
|
+
<p></table> </div></p>
|
|
1483
|
+
|
|
1484
|
+
<pre> <div class="method_details ">
|
|
1485
|
+
<h3 class="signature " id="wire!-instance_method">
|
|
1486
|
+
|
|
1487
|
+
- (<tt>Object</tt>) <strong>wire!</strong></pre>
|
|
1488
|
+
|
|
1489
|
+
<p></h3><div class=“docstring”></p>
|
|
1490
|
+
|
|
1491
|
+
<pre><div class="discussion"></pre>
|
|
1492
|
+
|
|
1493
|
+
<p><p>Wire up the neurons based on the genes.</p></p>
|
|
1494
|
+
|
|
1495
|
+
<pre></div></pre>
|
|
1496
|
+
|
|
1497
|
+
<p></div> <div class=“tags”></p>
|
|
1498
|
+
|
|
1499
|
+
<p></div><table class=“source_code”></p>
|
|
1500
|
+
|
|
1501
|
+
<pre><tr>
|
|
1502
|
+
<td>
|
|
1503
|
+
<pre class="lines"></pre>
|
|
1504
|
+
|
|
1505
|
+
<p>140 141 142 143 144 145 146 147 148 149 150 151 152</pre></p>
|
|
1506
|
+
|
|
1507
|
+
<pre></td>
|
|
1508
|
+
<td>
|
|
1509
|
+
<pre class="code"><span class="info file"># File 'lib/rubyneat/critter.rb', line 140</span></pre>
|
|
1510
|
+
|
|
1511
|
+
<p><span class='kw'>def</span> <span class='id
|
|
1512
|
+
identifier rubyid_wire!'>wire!</span></p>
|
|
1513
|
+
|
|
1514
|
+
<pre><span class='id identifier rubyid_forget!'>forget!</span>
|
|
1515
|
+
<span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_innov'>innov</span><span class='comma'>,</span> <span class='id identifier rubyid_gene'>gene</span><span class='op'>|</span>
|
|
1516
|
+
<span class='kw'>if</span> <span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_enabled?'>enabled?</span>
|
|
1517
|
+
<span class='id identifier rubyid_raise'>raise</span> <span class='const'>NeatException</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Can&#39;t find </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='embexpr_end'>}</span><span class='tstring_end'>&quot;</span></span> <span class='kw'>if</span> <span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
|
|
1518
|
+
<span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='rbracket'>]</span> <span class='op'>&lt;&lt;</span> <span class='ivar'>@neurons</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span><span class='rbracket'>]</span>
|
|
1519
|
+
<span class='ivar'>@neural_gene_map</span><span class='lbracket'>[</span><span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_out_neuron'>out_neuron</span><span class='rbracket'>]</span> <span class='op'>&lt;&lt;</span> <span class='id identifier rubyid_gene'>gene</span> <span class='kw'>unless</span> <span class='id identifier rubyid_gene'>gene</span><span class='period'>.</span><span class='id identifier rubyid_in_neuron'>in_neuron</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
|
|
1520
|
+
<span class='kw'>end</span>
|
|
1521
|
+
<span class='kw'>end</span> <span class='kw'>unless</span> <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
|
|
1522
|
+
<span class='kw'>if</span> <span class='ivar'>@genes</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
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<span class='gvar'>$log</span><span class='period'>.</span><span class='id identifier rubyid_error'>error</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>Genes Not Present</span><span class='tstring_end'>&#39;</span></span>
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<span class='kw'>end</span></pre>
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<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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0.8.7.3 (ruby-2.1.1).</pre>
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