yinspire 0.1.0 → 0.2.0

data/bin/yinspire

@@ -1,7 +1,5 @@
 #!/usr/bin/env ruby
 
-# TODO: Dump at the end.
-
 begin
   require 'rubygems'
 rescue LoadError
@@ -23,15 +21,24 @@ LOADERS = {
 }
 
 DUMPERS = {
-  :dot => Dumper_Dot
+  :dot => Dumper_Dot,
+  :yin => Dumper_Yin
 }
 
+def parse_file_format(str, formats)
+  file, format = str.split(":")
+  format ||= File.extname(file)[1..-1]
+  raise "invalid FORMAT #{format}" unless format
+  klass = formats[format.to_sym]
+  raise "invalid FORMAT #{format}" unless klass
+  return file, klass
+end
+
 def parse_cmdline
   require 'optparse'
   require 'ostruct'
 
   options = OpenStruct.new 
-  options.current_format = :yin
   options.stop_at = Infinity
   options.tolerance = 0.0
   options.output = nil
@@ -45,7 +52,7 @@ def parse_cmdline
   options.loads = []
 
   opts = OptionParser.new do |opts|
-    opts.banner = "Usage: yinspire [options] [file] [options] [file] ..."
+    opts.banner = "Usage: yinspire [options]"
 
     opts.on("-s", "--stop-at N", Float, "Stop simulation at N (default: #{options.stop_at})") do |n|
       options.stop_at = n
@@ -55,21 +62,15 @@ def parse_cmdline
       options.tolerance = n
     end
 
-    opts.on("-f", "--format FORMAT", LOADERS.keys,
-            "Select format type of files to load",
-            "  (#{LOADERS.keys.join(', ')})") do |t|
-      options.current_format = t
-    end
-
-    opts.on("-l", "--load FILE", "Load file") do |ld|
-      options.loads << [options.current_format, ld]
+    opts.on("-l", "--load FILE[:FORMAT]", "Load file",
+                                        "  (formats: #{LOADERS.keys.join(', ')})") do |ld|
+           
+      options.loads << parse_file_format(ld, LOADERS)
     end
 
-    opts.on("-d", "--dump FILE:FORMAT", "Dump net to file (after simulation)",
-                                        "  (formats: #{DUMPERS.keys.join(', ')})") do |t|
-      file, format = t.split(":")
-      raise "invalid FORMAT" if format.nil? or !DUMPERS.include?(format.to_sym)
-      options.dumps << [file, format.to_sym]
+    opts.on("-d", "--dump FILE[:FORMAT]", "Dump net to file (after simulation)",
+                                        "  (formats: #{DUMPERS.keys.join(', ')})") do |d|
+      options.dumps << parse_file_format(d, DUMPERS)
     end
 
     opts.on("-o", "--output FILE", "Filename to write output to",
@@ -107,9 +108,7 @@ def parse_cmdline
     end
   end
 
-  unparsed = opts.order(ARGV.dup) {|arg|
-    options.loads << [options.current_format, arg]
-  }
+  unparsed = opts.parse!(ARGV.dup)
   if !unparsed.empty? or options.loads.empty? 
     puts opts
     exit
@@ -164,8 +163,8 @@ def run
   sim = Simulator.new
   sim.stimuli_tolerance = options.tolerance
 
-  options.loads.each do |format, file|
-    LOADERS[format].new(sim).load(file)
+  options.loads.each do |file, klass|
+    klass.new(sim).load(file)
   end
 
   sim.run(options.stop_at) unless options.do_not_simulate
@@ -173,8 +172,8 @@ def run
   $yinspire_out.close if options.output and options.output != "-"
 
   # dump nets
-  options.dumps.each do |file, format|
-    dumper = DUMPERS[format].new(sim)
+  options.dumps.each do |file, klass|
+    dumper = klass.new(sim)
     if file == "-"
       dumper.dump(STDOUT)
     else

data/lib/Yinspire/All.rb

@@ -8,3 +8,4 @@ require 'Yinspire/Loaders/Loader_GraphML'
 require 'Yinspire/Loaders/Loader_Yin'
 require 'Yinspire/Loaders/Loader_Spike'
 require 'Yinspire/Dumpers/Dumper_Dot'
+require 'Yinspire/Dumpers/Dumper_Yin'

data/lib/Yinspire/Dumpers/Dumper_Yin.rb

@@ -0,0 +1,80 @@
+require 'Yinspire/Dumpers/Dumper'
+require 'enumerator'
+
+class Dumper_Yin < Dumper
+
+  def initialize(*args)
+    super
+    @verbose = true
+  end
+
+  def dump(out)
+    ekeys = @entities.keys.sort
+    ekeys.each {|key|
+      entity = @entities[key]
+      out << "ENTITY " if @verbose
+      out << to_yin_str(entity.id)
+      out << " = #{to_yin_str(entity.entity_type)} "
+      out << to_yin_str(entity.dump)
+      out << "\n"
+    }
+
+    ekeys.each {|key|
+      entity = @entities[key]
+      targets = []; entity.each_connection {|t| targets << to_yin_str(t.id)}
+      next if targets.empty?
+
+      out << "CONNECT " if @verbose
+      out << "#{to_yin_str(entity.id)} -> #{targets.join(', ')}\n"
+    }
+
+    ekeys.each {|key|
+      entity = @entities[key]
+      next unless entity.respond_to?(:stimuli_pq_to_a)
+      stimuli = entity.stimuli_pq_to_a
+      next if stimuli.empty?
+
+      out << "\n"
+      out << "STIMULATE " if @verbose
+      out << "#{to_yin_str(entity.id)} ! {\n  "
+
+      out << stimuli.to_enum(:each_slice, 2).
+        map {|at, weight| 
+          if weight == Infinity
+            to_yin_str(at)
+          else
+            "#{to_yin_str(weight)}@#{to_yin_str(at)}"
+          end
+        }.to_enum(:each_slice, 5).map {|arr| arr.join(" ")}.join("\n  ")
+
+      out << "\n}\n"
+    }
+  end
+
+  def to_yin_str(obj)
+    case obj
+    when String
+      if obj =~ /^\w+$/
+        obj
+      else
+        '"' + obj + '"'
+      end
+    when Symbol
+      to_yin_str(obj.to_s)
+    when Hash
+      out = ""
+      out << "{\n"
+      obj.keys.sort_by {|k| k.to_s}.each do |k|
+        out << "  " if @verbose
+        out << "#{to_yin_str(k)} = #{to_yin_str(obj[k])}\n"
+      end
+      out << "}\n"
+      out
+    when TrueClass, FalseClass, Float, Fixnum, Bignum
+      obj.to_s
+    else
+      raise "#{obj.class}"
+    end
+  end
+
+end

data/yinspire.gemspec

@@ -2,10 +2,10 @@ require 'rubygems'
 
 spec = Gem::Specification.new do |s|
   s.name = "yinspire"
-  s.version = "0.1.0"
+  s.version = "0.2.0"
   s.summary = "An efficient Spiking Neural Net Simulator"
   s.files = Dir['**/*']
-  s.add_dependency('cplus2ruby', '>= 1.1.1')
+  s.add_dependency('cplus2ruby', '>= 1.1.2')
   s.executables = ['yinspire']
 
   s.author = "Michael Neumann"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: yinspire
 version: !ruby/object:Gem::Version 
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors: 
 - Michael Neumann
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2008-03-31 00:00:00 +02:00
+date: 2008-04-01 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -19,7 +19,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.1.1
+        version: 1.1.2
     version: 
 description: 
 email: mneumann@ntecs.de
@@ -30,102 +30,103 @@ extensions: []
 extra_rdoc_files: []
 
 files: 
-- bench
-- bench/pq
-- bench/pq/bench_pairingheap.h
-- bench/pq/bench_binaryheap.h
-- bench/pq/bench.rb
-- bench/pq/bench_calendarqueue.h
-- bench/pq/Makefile
-- bench/pq/distribution.h
-- bench/pq/make.rb
-- bench/pq/bench_stlpq.h
-- bench/pq/bench.cc
-- bench/pq/benchmark.h
-- yinspire.gemspec
-- pure_cpp
-- pure_cpp/src
-- pure_cpp/src/algo
-- pure_cpp/src/algo/indexed_binary_heap.h
-- pure_cpp/src/algo/binary_heap.h
-- pure_cpp/src/neuron.cc
-- pure_cpp/src/neural_entity.cc
-- pure_cpp/src/neuron.h
-- pure_cpp/src/simulator.h
-- pure_cpp/src/neuron_srm_01.h
-- pure_cpp/src/neural_entity.h
-- pure_cpp/src/memory_allocator.h
-- pure_cpp/src/synapse.h
-- pure_cpp/src/main.cc
-- pure_cpp/src/synapse.cc
-- pure_cpp/src/json
-- pure_cpp/src/json/json_parser.rl
-- pure_cpp/src/json/json_parser.h
-- pure_cpp/src/json/json.cc
-- pure_cpp/src/json/json.h
-- pure_cpp/src/json/json_parser.cc
-- pure_cpp/src/neuron_srm_01.cc
-- pure_cpp/src/simulator.cc
-- pure_cpp/src/types.h
-- pure_cpp/Makefile
-- pure_cpp/README
 - lib
-- lib/Allocators
-- lib/Allocators/MemoryAllocator.h
-- lib/Allocators/ChunkedFreelistAllocator.h
-- lib/Allocators/RubyMemoryAllocator.h
-- lib/Yinspire.rb
+- lib/Algorithms
+- lib/Algorithms/CalendarQueue.h
+- lib/Algorithms/BinaryHeap.h
+- lib/Algorithms/Array.h
+- lib/Algorithms/IndexedBinaryHeap.h
+- lib/Algorithms/PairingHeap.h
 - lib/Yinspire
-- lib/Yinspire/Models
-- lib/Yinspire/Models/Neuron_Base.rb
-- lib/Yinspire/Models/Synapse_Hebb.rb
-- lib/Yinspire/Models/Neuron_Input.rb
-- lib/Yinspire/Models/Neuron_Output.rb
-- lib/Yinspire/Models/Neuron_InputOutput.rb
-- lib/Yinspire/Models/Neuron_SRM01.rb
-- lib/Yinspire/Models/Neuron_SRM02.rb
+- lib/Yinspire/Dumpers
+- lib/Yinspire/Dumpers/Dumper_Yin.rb
+- lib/Yinspire/Dumpers/Dumper.rb
+- lib/Yinspire/Dumpers/Dumper_Dot.rb
+- lib/Yinspire/All.rb
 - lib/Yinspire/Core
-- lib/Yinspire/Core/StimuliMixin.rb
+- lib/Yinspire/Core/Stimulus.rb
+- lib/Yinspire/Core/Simulator.rb
+- lib/Yinspire/Core/Synapse.rb
 - lib/Yinspire/Core/NeuralEntity.rb
+- lib/Yinspire/Core/Neuron.rb
+- lib/Yinspire/Core/StimuliMixin.rb
 - lib/Yinspire/Core/Scheduling
-- lib/Yinspire/Core/Scheduling/Simulator.rb
 - lib/Yinspire/Core/Scheduling/NeuralEntity.rb
-- lib/Yinspire/Core/Synapse.rb
-- lib/Yinspire/Core/Neuron.rb
-- lib/Yinspire/Core/Simulator.rb
-- lib/Yinspire/Core/Stimulus.rb
-- lib/Yinspire/Dumpers
-- lib/Yinspire/Dumpers/Dumper.rb
-- lib/Yinspire/Dumpers/Dumper_Dot.rb
+- lib/Yinspire/Core/Scheduling/Simulator.rb
 - lib/Yinspire/Loaders
 - lib/Yinspire/Loaders/Loader_Yin.rb
 - lib/Yinspire/Loaders/Loader_GraphML.rb
-- lib/Yinspire/Loaders/Loader.rb
-- lib/Yinspire/Loaders/YinScanner.rb
 - lib/Yinspire/Loaders/GraphML.rb
+- lib/Yinspire/Loaders/YinScanner.rb
+- lib/Yinspire/Loaders/Loader.rb
 - lib/Yinspire/Loaders/Loader_Spike.rb
 - lib/Yinspire/Loaders/Loader_JSON.rb
-- lib/Yinspire/All.rb
-- lib/Algorithms
-- lib/Algorithms/IndexedBinaryHeap.h
-- lib/Algorithms/Array.h
-- lib/Algorithms/PairingHeap.h
-- lib/Algorithms/CalendarQueue.h
-- lib/Algorithms/BinaryHeap.h
+- lib/Yinspire/Models
+- lib/Yinspire/Models/Neuron_Input.rb
+- lib/Yinspire/Models/Neuron_Base.rb
+- lib/Yinspire/Models/Neuron_InputOutput.rb
+- lib/Yinspire/Models/Synapse_Hebb.rb
+- lib/Yinspire/Models/Neuron_SRM02.rb
+- lib/Yinspire/Models/Neuron_Output.rb
+- lib/Yinspire/Models/Neuron_SRM01.rb
+- lib/Yinspire.rb
+- lib/Allocators
+- lib/Allocators/RubyMemoryAllocator.h
+- lib/Allocators/ChunkedFreelistAllocator.h
+- lib/Allocators/MemoryAllocator.h
+- tools
+- tools/json_writer.rb
+- tools/conv_jsonc_to_yin.rb
+- tools/converter.rb
+- pure_cpp
+- pure_cpp/src
+- pure_cpp/src/algo
+- pure_cpp/src/algo/binary_heap.h
+- pure_cpp/src/algo/indexed_binary_heap.h
+- pure_cpp/src/synapse.h
+- pure_cpp/src/main.cc
+- pure_cpp/src/memory_allocator.h
+- pure_cpp/src/simulator.h
+- pure_cpp/src/neuron_srm_01.h
+- pure_cpp/src/neuron.cc
+- pure_cpp/src/neural_entity.h
+- pure_cpp/src/simulator.cc
+- pure_cpp/src/json
+- pure_cpp/src/json/json_parser.cc
+- pure_cpp/src/json/json.h
+- pure_cpp/src/json/json_parser.h
+- pure_cpp/src/json/json.cc
+- pure_cpp/src/json/json_parser.rl
+- pure_cpp/src/neural_entity.cc
+- pure_cpp/src/types.h
+- pure_cpp/src/neuron.h
+- pure_cpp/src/neuron_srm_01.cc
+- pure_cpp/src/synapse.cc
+- pure_cpp/README
+- pure_cpp/Makefile
 - bin
 - bin/yinspire
-- README
-- run.rb
+- yinspire.gemspec
 - examples
 - examples/nets
-- examples/nets/gereon2005.c.json
 - examples/nets/spiketrains_angle_180.txt
-- examples/nets/skorpion.graphml
 - examples/nets/gereon2005.yin
-- tools
-- tools/converter.rb
-- tools/json_writer.rb
-- tools/conv_jsonc_to_yin.rb
+- examples/nets/gereon2005.c.json
+- examples/nets/skorpion.graphml
+- README
+- run.rb
+- bench
+- bench/pq
+- bench/pq/distribution.h
+- bench/pq/make.rb
+- bench/pq/bench.cc
+- bench/pq/benchmark.h
+- bench/pq/bench_calendarqueue.h
+- bench/pq/bench_pairingheap.h
+- bench/pq/bench.rb
+- bench/pq/bench_stlpq.h
+- bench/pq/bench_binaryheap.h
+- bench/pq/Makefile
 has_rdoc: false
 homepage: http://www.ntecs.de/projects/yinspire/
 post_install_message: