yinspire 0.1.0

data/pure_cpp/src/synapse.h

@@ -0,0 +1,60 @@
+#ifndef __YINSPIRE__SYNAPSE__
+#define __YINSPIRE__SYNAPSE__
+
+#include "neural_entity.h"
+
+class Neuron; // forward declaration
+
+class Synapse : public NeuralEntity
+{
+    friend class Neuron;
+    typedef NeuralEntity super; 
+
+  protected:
+
+    /*
+     * The fire weight of a Synapse.
+     */
+    real weight;
+
+    /*
+     * The propagation delay of a Synapse.
+     */
+    simtime delay;
+
+    /*
+     * The pre and post Neurons of the Synapse.
+     */
+    Neuron *pre_neuron;
+    Neuron *post_neuron;
+
+    /*
+     * Those two pointers are part of an internal linked-list that
+     * starts at a Neuron and connects all pre-synapses of an Neuron
+     * together. In the same way it connects all post-synapses of an
+     * Neuron together.
+     */
+    Synapse *next_pre_synapse;
+    Synapse *next_post_synapse;
+
+  public:
+
+    /*
+     * Constructor
+     */
+    Synapse();
+
+  public:
+
+    virtual void dump(jsonHash *into);
+    virtual void load(jsonHash *data);
+
+    virtual void stimulate(simtime at, real weight, NeuralEntity *source);
+    virtual void connect(NeuralEntity *target);
+    virtual void disconnect(NeuralEntity *target);
+    virtual void each_connection(
+      void (*yield)(NeuralEntity *self, NeuralEntity *conn));
+
+};
+
+#endif

data/pure_cpp/src/types.h

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+#ifndef __YINSPIRE__TYPES__
+#define __YINSPIRE__TYPES__
+
+typedef unsigned int uint;
+typedef float real; 
+typedef float simtime;
+
+#define real_exp expf
+#define real_fabs fabsf
+
+#ifndef NULL
+#define NULL 0L
+#endif
+
+#define MIN(a,b) ((a) < (b) ? (a) : (b))
+#define MAX(a,b) ((a) > (b) ? (a) : (b))
+
+#endif

data/run.rb

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+require 'rubygems'
+$LOAD_PATH.unshift "lib"
+
+require 'Yinspire'
+require 'Yinspire/Models/Neuron_Input'
+require 'Yinspire/Models/Neuron_Output'
+require 'Yinspire/Models/Neuron_SRM01'
+require 'Yinspire/Models/Neuron_SRM02'
+require 'Yinspire/Models/Synapse_Hebb'
+require 'Yinspire/Loaders/Loader_JSON'
+require 'Yinspire/Loaders/Loader_GraphML'
+require 'Yinspire/Loaders/Loader_Yin'
+
+def example_net(sim, n)
+  inputs = (0...n).map {|i|
+    Neuron_Input.new("inp_#{i}", sim)
+  }
+
+  outputs = (0...n).map {|i|
+    Neuron_Output.new("out_#{i}", sim)
+  }
+
+  synapses = (0...n).map {|i|
+    Synapse.new("syn_#{i}", sim) {|s|
+      s.delay = 0.4
+      s.weight = 10.0
+    }
+  }
+
+  (0...n).each {|i|
+    inputs[i].connect(synapses[i])
+    synapses[i].connect(outputs[i])
+  }
+
+  (0...n).each {|i|
+    inputs[i].stimulate(0.0+i, 1.0, nil)
+  }
+end
+
+Yinspire.commit('./work/Yinspire')
+
+sim = Simulator.new
+sim.stimuli_tolerance = 0.0 
+
+class Neuron_Output
+  def fire(at, weight)
+    puts "#{id()}\t#{at}\t#{weight}"
+  end
+end
+
+#loader = Loader_GraphML.new(sim)
+#loader.load('examples/nets/skorpion.graphml')
+
+#loader = Loader_JSON.new(sim)
+#loader.load('/tmp/gereon2005.json')
+
+loader = Loader_Yin.new(sim)
+loader.load('./examples/nets/gereon2005.yin')
+
+#require 'pp'
+#pp loader.dump_entities
+#example_net(sim, 10_000)
+
+stop_at = ARGV[0].to_f 
+puts "stop_at: #{stop_at}"
+sim.run(stop_at)
+puts "events: #{sim.event_counter}"
+puts "fires:  #{sim.fire_counter}"

data/tools/conv_jsonc_to_yin.rb

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+require 'yaml'
+require 'enumerator'
+
+class String
+  def to_yin_str
+    if self =~ /^\w+$/
+      self
+    else
+      '"' + self + '"'
+    end
+  end
+end
+
+class TrueClass; alias to_yin_str to_s end
+class FalseClass; alias to_yin_str to_s end
+class Float; alias to_yin_str to_s end
+class Fixnum; alias to_yin_str to_s end
+class Bignum; alias to_yin_str to_s end
+
+class Hash
+  def to_yin_str(out="")
+    out << "{\n"
+    self.keys.sort.each do |k|
+      out << "  " if $verbose
+      out << "#{k.to_yin_str} = #{self[k].to_yin_str}\n"
+    end
+    out << "}\n"
+  end
+end
+
+data = YAML.load(STDIN.read)
+out = STDOUT
+$verbose = true
+
+raise unless data['format'] == 'yinspire.c'
+
+#data['entities'] = nil
+#data['templates'] = nil
+#data['connections'] = nil
+
+#
+# Write out templates
+#
+
+templates = data["templates"] || {}
+if $verbose and !templates.empty?
+  out << "#\n"
+  out << "# Templates\n"
+  out << "#\n\n"
+end
+
+templates.keys.sort.each do |key|
+  base_type, base_data = *templates[key]
+
+  out << "TEMPLATE " if $verbose
+  out << "#{key.to_yin_str} < #{base_type.to_yin_str}"
+  if base_data and not base_data.empty?
+    out << " "
+    base_data.to_yin_str(out)
+  else
+    out << "\n"
+  end
+  out << "\n" if $verbose
+end
+
+
+#
+# Write out entities
+#
+
+entities = data["entities"] || [] 
+if $verbose and !entities.empty?
+  out << "#\n"
+  out << "# Entities\n"
+  out << "#\n\n"
+end
+
+group_by = {}
+entities.each do |id, type, edata|
+  key = [type, edata]
+  group_by[key] ||= []
+  group_by[key] << id
+end
+
+
+group_by.keys.sort_by {|type, _| type}.each do |key|
+  type, edata = *key
+  ids = group_by[key]
+  out << "ENTITY " if $verbose
+  out << ids.sort.map {|id| id.to_yin_str}.enum_for(:each_slice, 8).map {|sl|
+    sl.join(", ")
+  }.join(",\n  ")
+   
+  out << " = #{ type.to_yin_str }"
+
+
+  if edata and not edata.empty?
+    out << " "
+    edata.to_yin_str(out)
+  else
+    out << "\n"
+  end
+  out << "\n" if $verbose
+end
+
+#
+# Write out connections
+#
+
+connections = data["connections"] || []
+if $verbose and !connections.empty?
+  out << "#\n"
+  out << "# Connections\n"
+  out << "#\n\n"
+end
+
+connections.each do |arr|
+  src, *targets = *arr
+  out << "CONNECT " if $verbose
+  out << "#{src.to_yin_str} -> "
+
+  out << targets.map {|t| t.to_yin_str}.enum_for(:each_slice, 8).map {|sl|
+    sl.join(", ")
+  }.join(",\n  ")
+  out << "\n"
+
+  out << "\n" if $verbose
+end
+
+#
+# Write out stimuli
+#
+
+events = data["events"] || {} 
+if $verbose and !events.empty?
+  out << "#\n"
+  out << "# Stimulations\n"
+  out << "#\n\n"
+end
+
+events.keys.sort.each do |key|
+  ev = events[key]
+  next if ev.empty?
+
+  out << "STIMULATE " if $verbose
+  out << "#{key.to_yin_str} ! {\n"
+
+  out << " "
+  char_pos = 1
+
+  ev.each do |e|
+    str = e.to_yin_str 
+    if char_pos > 40 && char_pos+str.size > 75
+      out << "\n "
+      char_pos = 1
+    end
+    out << " "
+    out << str 
+    char_pos += 1 + str.size
+  end
+
+  out << "\n}\n"
+
+  out << "\n" if $verbose
+end

data/tools/converter.rb

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+require 'yaml'
+require 'json_writer'
+
+# format changes:
+#
+# * neuron/synapse type names changed
+# * property names changed
+# * no longer post_neuron, pre_neuron, instead connections.
+# 
+
+old = YAML.load(File.read('/tmp/gereon2005'))
+new = {}
+new['format'] = 'yinspire.1'
+new['templates'] = {}
+entities = new['entities'] = {}
+connections = new['connections'] = {}
+new['events'] = old['events']
+
+#
+# convert templates
+#
+old['templates'].each do |name, hash|
+
+  type =
+  case hash.delete("type") 
+  when 'Synapse_Default' then 'Synapse'
+  when 'Neuron_KernelBasedLIF' then 'Neuron_SRM_01'
+  else
+    raise
+  end
+
+  if abs_ref_duration = hash.delete('abs_ref_duration')
+    hash['abs_refr_duration'] = abs_ref_duration
+  end
+
+  new['templates'][name] = [type, hash] 
+end
+
+
+
+#
+# convert entities and connections
+#
+old['net'].each do |hash|
+  template = hash.delete('_')
+  post_neuron = hash.delete('post_neuron')
+  pre_neuron = hash.delete('pre_neuron')
+  id = hash.delete('id') || raise
+
+  if post_neuron
+    connections[id] ||= []
+    connections[id] << post_neuron 
+  end
+
+  if pre_neuron
+    connections[pre_neuron] ||= []
+    connections[pre_neuron] << id 
+  end
+
+  if hash.empty?
+    entities[id] = template
+  else
+    entities[id] = [template, hash]
+  end
+end
+
+# new2 is efficient for jsonParser/jsonHash which
+# is implemented as a linked list.
+def to_new2(new)
+  new2 = Hash.new
+  new2['format'] = 'yinspire.2'
+  new2['templates'] = new['templates']
+  entities = new2['entities'] = [] 
+  connections = new2['connections'] = []
+  new['entities'].keys.sort.each do |id|
+    v = new['entities'][id]
+    entities << [id, v].flatten
+  end
+
+  new['connections'].keys.sort.each do |from|
+    to = new['connections'][from]
+    #|from, to|
+    connections << [from, to].flatten
+  end
+
+  new2['events'] = new['events']
+
+  return new2
+end
+
+#puts YAML.dump(new)
+#new = to_new2(new)
+json_pp(new)

data/tools/json_writer.rb

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+#
+# Pretty print Ruby objects as JSON
+#
+# Copyright (c) 2007 by Michael Neumann (mneumann@ntecs.de)
+#
+
+require 'prettyprint'
+
+class Hash
+  def to_json(pp)
+    ks = keys
+    pp.group(1, '{', '}') {
+      ks.each_with_index do |k, i|
+        v = self[k]
+
+        pp.group {
+	  pp.text k.to_s.to_json(true) 
+	  pp.text ':'
+	  pp.group(1) {
+	    pp.breakable ' '
+	    case v
+	    when Hash, Array
+	      v.to_json(pp)
+	    else
+	      pp.text v.to_json
+	    end
+	  }
+
+	  if i < ks.size-1
+	    pp.text ","
+	    pp.breakable
+	  end
+	}
+      end
+    }
+  end
+end
+
+class Array
+  def to_json(pp)
+    pp.group(1, "[", "]") {
+      each_with_index do |v, i|
+        pp.group {
+	  case v
+	  when Hash, Array
+	    v.to_json(pp)
+	  else
+	    pp.text v.to_json
+	  end
+
+	  if i < size()-1
+	    pp.text ","
+	    pp.breakable ' '
+	  end
+	}
+      end
+    }
+  end
+end
+
+class TrueClass
+  TRUE = "true".freeze
+  def to_json
+    TRUE
+  end
+end
+
+class FalseClass
+  FALSE = "false".freeze
+  def to_json
+    FALSE
+  end
+end
+
+class NilClass
+  NULL = "null".freeze
+  def to_json
+    NULL
+  end
+end
+
+class Fixnum
+  alias to_json to_s
+end
+
+class Bignum
+  alias to_json to_s
+end
+
+class Float
+  alias to_json to_s
+end
+
+class String
+  def to_json(label=false)
+    label = false # FIXME
+    if label and self =~ /^[A-Za-z_][A-Za-z0-9_]*$/
+      self
+    else
+      inspect
+    end
+  end
+end
+
+class Symbol
+  def to_json(label=false)
+    to_s.to_json(label)
+  end
+end
+
+def json_pp(obj, out=STDOUT, width=79)
+  case obj
+  when Array, Hash
+    q = PrettyPrint.new(out, width)
+    obj.to_json(q)
+    q.flush
+  else
+    out << obj.to_json
+  end
+  out << "\n"
+  return out
+end