y_petri 2.1.22 → 2.1.24

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/y_petri.rb

@@ -22,6 +22,7 @@ require 'gnuplot'                      # used for graph visualization
 require 'csv'                          # not used at the moment
 require 'graphviz'                     # used for Petri net visualization
 require 'pp'                           # usef for pretty
+require 'distribution'                 # used in the simulation core
 
 require_relative 'y_petri/version'
 require_relative 'y_petri/fixed_assets'

data/lib/y_petri/agent/simulation_related.rb

@@ -9,19 +9,19 @@ module YPetri::Agent::SimulationRelated
 
   # Simulation selection class.
   # 
-  SimulationSelection = YPetri::Agent::Selection.parametrize agent: self
+  SimulationSelection = YPetri::Agent::Selection.parametrize( agent: self )
 
   # Simulation settings collection selection class.
   # 
-  SscSelection = YPetri::Agent::Selection.parametrize agent: self
+  SscSelection = YPetri::Agent::Selection.parametrize( agent: self )
 
   # Clamp collection selection class.
   # 
-  CcSelection = YPetri::Agent::Selection.parametrize agent: self
+  CcSelection = YPetri::Agent::Selection.parametrize( agent: self )
 
   # Initial marking collection selection class.
   # 
-  ImcSelection = YPetri::Agent::Selection.parametrize agent: self
+  ImcSelection = YPetri::Agent::Selection.parametrize( agent: self )
 
   class SimulationPoint < YPetri::Agent::HashKeyPointer
     # Reset to the first simulation, or nil if that is absent.
@@ -49,15 +49,15 @@ module YPetri::Agent::SimulationRelated
 
   # Pointer to a collection of simulation settings.
   # 
-  SscPoint = YPetri::Agent::HashKeyPointer.parametrize agent: self
+  SscPoint = YPetri::Agent::HashKeyPointer.parametrize( agent: self )
 
   # Pointer to a clamp collection.
   # 
-  CcPoint = YPetri::Agent::HashKeyPointer.parametrize agent: self
+  CcPoint = YPetri::Agent::HashKeyPointer.parametrize( agent: self )
 
   # Pointer to a collection of initial markings.
   # 
-  ImcPoint = YPetri::Agent::HashKeyPointer.parametrize agent: self
+  ImcPoint = YPetri::Agent::HashKeyPointer.parametrize( agent: self )
 
   attr_reader :simulation_point,
               :ssc_point,
@@ -68,8 +68,10 @@ module YPetri::Agent::SimulationRelated
               :cc_selection,
               :imc_selection
 
+  # Agent initialziation method.
+  # 
   def initialize
-    # set up this manipulator's pointers
+    # set up this agent's pointers
     @simulation_point = SimulationPoint.new( hash: simulations,
                                              hash_value_is: "simulation" )
     @ssc_point = SscPoint.new( hash: simulation_settings_collections,
@@ -161,6 +163,7 @@ module YPetri::Agent::SimulationRelated
 
   # Returns or modifies current initial marking(s) as indicated by the argument
   # field:
+  # 
   # * No arguments: returns current imc
   # * Exactly one ordered argument: it is assumed to identify a place whose
   #   im in the current imc will be returned.
@@ -257,34 +260,11 @@ module YPetri::Agent::SimulationRelated
     end
   end
 
-  # Plot the recorded samples.
+  # Plot the recording reduced into the given feature set.
   # 
-  def plot **features
-    # --> state feature ids
-    # --> gradient feature ids
-    # --> delta feature ids
-    # --> flux feature ids
-    # --> firing feature ids
-    # take these features together
-    # construct the labels and the time series for each
-    # plot them
-
-    return nil unless sim = world.simulations.values[-1] # sim@point
-    # Decide abnout the features
-    features = sim.places.dup.map { |p|
-      collection.include?( p ) ? p : nil
-    }
-    # Get recording
-    rec = sim.recording
-    # Select a time series for each feature.
-    time_series = features.map.with_index do |feature, i|
-      feature and rec.map { |key, val| [ key, val[i] ] }.transpose
-    end
-    # Time axis
-    ᴛ = sim.target_time
-    # Gnuplot call
-    gnuplot( ᴛ, features.compact.map( &:name ), time_series.compact,
-             title: "Selected features plot", ylabel: "Marking" )
+  def plot features
+    ff = simulation.net.state.features( features )
+    simulation.recording.reduce_features( ff ).plot
   end
 
   # Plot system state history.

data/lib/y_petri/core.rb

@@ -54,13 +54,13 @@ class YPetri::Core
     end
   end
 
-  # Simlation is not guarded by default.
+  # Simulation is not guarded by default.
   # 
   def guarded?
     false
   end
 
-  # Delta for free places.
+  # Delta for free places from timeless transitions.
   # 
   def delta_timeless
     delta_ts + delta_tS

data/lib/y_petri/core/timed.rb

@@ -3,10 +3,17 @@
 # Timed simulation core.
 # 
 class YPetri::Core::Timed < YPetri::Core
-  require_relative 'timed/euler.rb'
-  require_relative 'timed/pseudo_euler.rb' # timeless fire after each step
-  require_relative 'timed/quasi_euler.rb'  # timeless fire each time tick
-
+  # Euler method.
+  require_relative 'timed/euler'
+  # Euler with timeless transitions firing after each step.
+  require_relative 'timed/pseudo_euler'
+  # Euler with timeless transitions firing each time tick.
+  require_relative 'timed/quasi_euler'
+  # Gillespie stochastic method.
+  require_relative 'timed/gillespie'
+  # Runge-Kutta fifth-order method.
+  require_relative 'timed/runge_kutta'
+  
   # Makes a single step by Δt.
   # 
   def step! Δt=simulation.step
@@ -49,6 +56,7 @@ class YPetri::Core::Timed < YPetri::Core
   def flux_vector_TS
     simulation.TS_rate_closure.call
   end
+  alias propensity_vector_TS flux_vector_TS
 end # class YPetri::Core::Timed
 
 # In general, it is not required that all net elements are simulated with the

data/lib/y_petri/core/timed/gillespie.rb

@@ -0,0 +1,82 @@
+# encoding: utf-8
+
+# Plain Gillespie algorithm.
+#
+# The characteristic of the Gillespie method is, that it does not work starting
+# from Δt towards Δstate. Instead, it makes a random choice weighted by the
+# transition propensities, and the random choice determines both the next timed
+# transition to fire, and the size of Δt to slice off from the time axis.
+# 
+module YPetri::Core::Timed::Gillespie
+  attr_reader :rng
+
+  # Gillespie method initialization.
+  # 
+  def initialize
+    @rng = ::Random
+  end
+
+  # Makes a stochastic number of Gillespie steps necessary to span the period Δt.
+  # 
+  def step! Δt=simulation.step
+    current_time = simulation.time
+    target_time = current_time + Δt
+    @gillespie_time = current_time
+    propensities = propensity_vector_TS
+    puts "Propensity vector TS is:"
+    Kernel::p propensities
+    gillespie_update_next_firing_time( propensities )
+    until ( @gillespie_next_firing_time > target_time )
+      gillespie_step!
+      propensities = propensity_vector_TS
+      gillespie_update_next_firing_time( propensities )
+    end
+  end
+
+  # Name of this method.
+  # 
+  def simulation_method
+    :gillespie
+  end
+
+  # This method updates next firing time given propensities.
+  # 
+  def gillespie_update_next_firing_time( propensities )
+    @gillespie_next_firing_time =
+      @gillespie_time + gillespie_delta_time( propensities )
+  end
+
+  # Step.
+  # 
+  def gillespie_step! propensities
+    t = choose_TS_transition( propensities )
+    fire! t
+  end
+
+  # Computes Δ for the period of Δt.
+  # 
+  def gillespie_delta_time( propensities )
+    sum = Σ propensities
+    mean_period = 1 / sum
+    Distribution::Exponential.p_value( rng.rand, sum )
+  end
+
+  # Chooses the transition to fire.
+  # 
+  def choose_TS_transition( propensities )
+    n = rng.rand
+    propensities.index do |propensity|
+      n -= propensity
+      n <= 0
+    end
+  end
+
+  # Fires a transition.
+  # 
+  def fire!( transition )
+    transition.∇.map { |place, change|
+      mv = simulation.marking_vector
+      mv.set( place, mv.fetch( place ) + change )
+    }
+  end
+end # YPetri::Core::Timed::Euler

data/lib/y_petri/core/timed/runge_kutta.rb

@@ -0,0 +1,22 @@
+# encoding: utf-8
+
+# Gillespie method.
+# 
+module YPetri::Core::Timed::Euler
+  # Name of this method.
+  # 
+  def simulation_method
+    :runge_kutta
+  end
+
+  # FIXME
+
+  # This is from Euler:
+
+  # # Computes Δ for the period of Δt.
+  # # 
+  # def delta Δt
+  #   gradient * Δt
+  # end
+  # alias Δ delta
+end # YPetri::Core::Timed::Euler

data/lib/y_petri/dsl.rb

@@ -56,11 +56,10 @@ module YPetri
            :print_recording,
            :plot,
            :plot_selected,
-  #        :plot_state,
+           :plot_state,
            :plot_flux,
+           :plot_firing,
+           :plot_gradient,
+           :plot_delta,
            to: :y_petri_agent
-
-  def plot_state **nn
-    simulation.recording.marking.plot **nn
-  end
 end

data/lib/y_petri/net/data_set.rb

@@ -253,7 +253,8 @@ class YPetri::Net::DataSet < Hash
     to_s
   end
 
-  # Pretty print the dataset.
+  # Pretty print the dataset. Takes +:precision+ and +:distance+ named arguments,
+  # that control the shape of the printed table.
   # 
   def print precision: 4, distance: precision + 4
     features.labels.print_as_line precision: precision, distance: distance

data/lib/y_petri/version.rb

@@ -1,4 +1,4 @@
 module YPetri
-  VERSION = "2.1.22"
+  VERSION = "2.1.24"
   DEBUG = false
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: y_petri
 version: !ruby/object:Gem::Version
-  version: 2.1.22
+  version: 2.1.24
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-18 00:00:00.000000000 Z
+date: 2013-08-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: y_support
@@ -73,8 +73,10 @@ files:
 - lib/y_petri/core.rb
 - lib/y_petri/core/timed.rb
 - lib/y_petri/core/timed/euler.rb
+- lib/y_petri/core/timed/gillespie.rb
 - lib/y_petri/core/timed/pseudo_euler.rb
 - lib/y_petri/core/timed/quasi_euler.rb
+- lib/y_petri/core/timed/runge_kutta.rb
 - lib/y_petri/core/timeless.rb
 - lib/y_petri/core/timeless/pseudo_euler.rb
 - lib/y_petri/dsl.rb