y_petri 2.0.2 → 2.0.3

data/lib/y_petri/manipulator.rb

@@ -3,596 +3,18 @@
 # Public command interface of YPetri.
 # 
 class YPetri::Manipulator
-
-  # Current workspace.
-  # 
-  def workspace;
-    # puts "Manipulator is #{self}, obj. id #{object_id}."
-    @workspace
-  end
+  attr_reader :workspace
 
   def initialize
-    new_workspace_instance = YPetri::Workspace.new
-    @workspace = new_workspace_instance
-    net_point_reset
-    net_selection_clear
-    simulation_point_reset
-    simulation_selection_clear
-    ssc_point_reset
-    ssc_selection_clear
-    cc_point_reset
-    cc_selection_clear
-    imc_point_reset
-    imc_selection_clear
-  end
-
-  delegate :place, :transition, :p, :t,
-           :places, :transitions, :nets, :simulations,
-           :pp, :tt, :nn,
-           :clamp_collections,
-           :initial_marking_collections,
-           :simulation_settings_collections,
-           :clamp_cc, :initial_marking_cc, :simulation_settings_cc,
-           to: :workspace
-
-  # Place constructor: Creates a new place in the current workspace.
-  # 
-  def Place *args, &block
-    workspace.Place.new *args, &block
-  end
-
-  # Transiton constructor: Creates a new transition in the current workspace.
-  # 
-  def Transition *args, &block
-    workspace.Transition.new *args, &block
-  end
-
-  # Net constructor: Creates a new Net instance in the current workspace.
-  # 
-  def Net *args, &block
-    workspace.Net.new *args, &block
-  end
-
-  # ==== Net point
-
-  # Sets net point to workspace.Net::Top
-  # 
-  def net_point_reset
-    net_point_to( workspace.Net::Top )
-  end
-
-  # Sets net point to the one identified in the argument (Net instance or
-  # its name).
-  # 
-  def net_point_to which_net
-    @net_point = workspace.net which_net
-  end
-  alias :net→ :net_point_to
-
-  # Returns the net identified by the argument, or the net at the point, if
-  # none given.
-  # 
-  def net which=nil
-    which.nil? ? @net_point : workspace.net( which )
-  end
-
-  # Returns the name of the net identified by the argument, or the net at the
-  # point (if no argument is given).
-  # 
-  def n which=nil
-    net( which ).name
-  end
-
-  # ==== Simulation point
-
-  # Sets simulation point to the first key of the workspace's collection of
-  # simulations (or nil if there are no simulations yet).
-  # 
-  def simulation_point_reset
-    @simulation_point =
-      workspace.simulations.empty? ? nil :
-      simulation_point_to( workspace.simulations.first[0] )
-  end
-
-  # Sets simulation point to the simulation identified by the argument.
-  # A simulation can be identified either by its name (if named), or by
-  # its parameters and settings (simulated net, clamp collection, initial
-  # marking collection, and simulation settings collection).
-  #
-  # If a single ordered (non-hash) argument is supplied, it is assumed to be
-  # a simulation name. If a hash is supplied, it is expected that it will
-  # contain four pairs with keys :net, :cc, :imc, :ssc, identifying the
-  # simulation by its parameters and settings. Alternatively, use of hash
-  # can be forgone - if exactly 4 ordered arguments are supplied, it is
-  # assumed that they specified the parameter settings in the order set forth
-  # earlier.
-  # 
-  def simulation_point_to *args
-    key = normalize_simulation_identifier *args
-    @simulation_point = if key.nil? then nil
-                        elsif workspace.simulations.has_key? key then key
-                        else raise "No such simulation" end
-  end
-  alias :sim→ :simulation_point_to
-
-  # Returns the simulation identified by the argument, or one indicated by the
-  # simulation point (if no argument was given). The simulation is identified
-  # by the arguments in the same way as for #simulation_point_to method.
-  # 
-  def simulation *args
-    workspace.simulation( normalize_simulation_identifier *args )
-  end
-
-  # TEMPORARY KLUGE - FIXME
-  # 
-  def simulation; @workspace.simulations.values[-1] end
-
-  # Returns the index (position) of the simulation point.
-  # 
-  def simulation_point_position
-    # FIXME: Change @simulations from being a has of { key => simulation } pairs
-    # to be the hash of { simulation => names } pairs, in which simulations are
-    # looked up either by rassoc or by sniffing their parameters and settings.
-    @simulation_point
-  end
-
-  # ==== cc point (cc = clamp collection)
-
-  # Clamp collections are stored in workplace in a hash. The cc point
-  # points to its keys.
-
-  # Resets cc point to :base.
-  # 
-  def cc_point_reset
-    @cc_point = :Base
-  end
-
-  # Sets the cc point to the specified cc.
-  # 
-  def cc_point_to arg
-    if workspace.clamp_collections.has_key? arg
-      @cc_point = arg
-    else
-      raise "No clamp collection #{arg} in this workspace"
-    end
-  end
-  alias :cc→ :cc_point_to
-
-    # Returns clamp collection corresp. to cc point (if no argument), or to
-    # the argument (if this was given).
-    # 
-    def clamp_collection collection_name=nil
-      cɴ = collection_name.nil? ? @cc_point : collection_name
-      workspace.clamp_collections[ cɴ ] or
-        raise AE, "No clamp collection #{cɴ} in this workspace."
-    end
-    alias :cc :clamp_collection
-
-    # Returns the cc point position (cc hash key).
-    # 
-    def cc_point_position; @cc_point end
-
-    # ==== imc point ( imc = initial marking collection )
-
-    # Initial marking collections are stored in a workplace in a hash.
-    # The imc point points to its keys.
-
-    # Resets imc point to :base.
-    # 
-    def imc_point_reset; @imc_point = :Base end
-
-    # Sets the imc point to the specified imc.
-    # 
-    def imc_point_to arg
-      if workspace.initial_marking_collections.has_key? arg
-        @imc_point = arg
-      else
-        raise "No initial marking collection #{arg} in this workspace."
-      end
-    end
-    alias :imc→ :imc_point_to
-
-    # Returns initial marking collection corresp. to imc point (if no
-    # argument), or to the argument (if this was given).
-    # 
-    def initial_marking_collection collection_name=nil
-      cɴ = collection_name.nil? ? @imc_point : collection_name
-      workspace.initial_marking_collections[ cɴ ] or
-        raise AE, "No initial marking collection #{cɴ} in this workspace."
-    end
-    alias :imc :initial_marking_collection
-
-    # Returns the ssc point position (ssc hash key).
-    # 
-    def imc_point_position; @imc_point end
-
-    # ==== ssc point (ssc = simulation settings collection)
-
-    # Simulation settings collections are stored in workplace in a hash.
-    # The ssc point of manipulator points to its keys.
-
-    # Resets ssc point to :base.
-    # 
-    def ssc_point_reset; @ssc_point = :Base end
-
-    # Sets the ssc point to the specified ssc.
-    # 
-    def ssc_point_to arg
-      if workspace.simulation_settings_collections.has_key? arg
-        @ssc_point = arg
-      else raise "No such simulation settings collection: #{arg}" end
-    end
-    alias :ssc→ :ssc_point_to
-
-  # Returns the ssc identified by the argument, or that at ssc point (if no
-  # argument is given).
-  # 
-  def simulation_settings_collection collection_name=nil
-    cɴ = collection_name.nil? ? @ssc_point : collection_name
-    # puts "Target workspace is #{workspace}, obj. id #{workspace.object_id}"
-    workspace.simulation_settings_collections[ cɴ ] or
-      raise AE, "No simulations settings collection #{cɴ} in this workspace."
-  end
-  alias :ssc :simulation_settings_collection
-
-  # Returns the ssc point position (ssc hash key).
-  # 
-  def ssc_point_position; @ssc_point end
-
-
-  # ==== Selection mechanism for net, simulation, cc, imc and ssc
-  # TODO
-
-  # Net selection.
-  # 
-  attr_reader :net_selection
-
-  # Simulation selection.
-  # 
-  attr_reader :simulation_selection
-
-  # Simulation settings collection selection.
-  # 
-  attr_reader :ssc_selection
-
-  # Clamp collection selection.
-  # 
-  attr_reader :cc_selection
-
-  # Initial marking collection selection.
-  # 
-  attr_reader :imc_selection
-
-  # ==== Net selection
-
-  def net_selection_clear
-    @net_selection ||= []
-    @net_selection.clear
-  end
-
-  def net_select! *aa; net_selection_clear; net_select *aa end
-
-  def net_select *aa
-    case aa.size
-    when 0 then ( @net_selection << net ).uniq!
-    when 1 then ( @net_selection << aa[0] ).uniq!
-    else aa.each { |a| net_select a } end
-  end
-
-  def net_unselect *aa
-    if aa.empty? then @net_selection.delete net else
-      aa.each { |arg| @net_selection.delete net( arg ) }
-    end
-  end
-
-  # --- simulation selection ---------------------------------------------
-
-  def simulation_selection_clear
-    @simulation_selection ||= []
-    @simulation_selection.clear
-  end
-
-  def simulation_select! *aa
-    simulation_selection_clear
-    simulation_select *aa
-  end
-
-  def simulation_select *aa
-    # FIXME
-  end
-
-  def simulation_unselect *aa
-    # FIXME
-  end
-
-  # --- cc selection -----------------------------------------------------
-
-  def cc_selection_clear; @cc_selection ||= []; @cc_selection.clear end
-
-  def cc_select! *aa; cc_selection_clear; cc_select *aa end
-
-  def cc_select
-    # FIXME
-  end
-
-  def cc_unselect *aa
-    # FIXME
-  end
-
-  # --- imc selection ----------------------------------------------------
-
-  def imc_selection_clear; @imc_selection ||= []; @imc_selection.clear end
-
-  def imc_select! *aa; imc_selection_clear; imc_select *aa end
-
-  def imc_select
-    # FIXME
-  end
-
-  def imc_unselect *aa
-    # FIXME
+    @workspace = YPetri::Workspace.new
+    super
   end
 
-  # --- ssc selection ----------------------------------------------------
+  require_relative 'manipulator/selection'
+  require_relative 'manipulator/hash_key_pointer'
+  require_relative 'manipulator/petri_net_related_methods'
+  require_relative 'manipulator/simulation_related_methods'
 
-  def ssc_selection_clear; @ssc_selection ||= []; @ssc_selection.clear end
-
-  def ssc_select! *aa; ssc_selection_clear; ssc_select *aa end
-
-  def ssc_select
-    # FIXME
-  end
-
-  def ssc_unselect *aa
-    # FIXME
-  end
-
-  # --- rest of the world ------------------------------------------------
-  # FIXME: This is going to be tested
-
-  def clamp clamp_hash
-    clamp_hash.each_pair { |pl, cl|
-      clamp_collection.merge! workspace.place( pl ) => cl
-    }
-  end
-
-  # 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 teh current imc will be returned.
-  # * A hash: Assumed to be { place_id => im }, current imc is updated with it.
-  # * One ordered argument, and a hash: The imc identified by the ordered
-  #   ordered arg is updated with the hash.
-  # * 2 ordered arguments: First is assumed to identify an imc, second place
-  #   whose im acc. to that imc to return.
-  # 
-  def initial_marking *args;
-    oo = args.extract_options!
-    case args.size
-    when 0 then
-      if oo.empty? then            # no ordered arguments were given,
-        initial_marking_collection # current imc will be returned
-      else # hash was supplied, assumed of pairs { place_id => marking },
-        initial_marking_collection # it will be merged to imc
-          .update( oo.with_keys do |key| place( key ) end )
-      end
-    when 1 then                    # exactly one ordered argument was given,
-      if oo.empty? then            # without any named arguments, it is
-        place = place( args[0] )   # assumed that it identifies a place,
-        initial_marking_collection[ place ] # return its init. marking in imc
-      else # One ordered argument (imc), and one hash (update values) given.
-        im_coll = initial_marking_collection( args[0] )
-        im_coll.update( oo.with_keys do |key| place( key ) end )
-      end
-    when 2 then # 2 ordered arguments (imc, place whose marking to return)
-      im_coll = initial_marking_collection( args[0] )
-      place = place( args[1] )
-      im_coll[ place ]
-    else raise AE, "Too many ordered parameters" end
-  end
-  alias :im :initial_marking
-
-  # Changes the time step of the current ssc (ssc = simulation settings
-  # collection).
-  # 
-  def set_step Δt
-    ssc.update step_size: Δt
-  end
-  alias :set_step_size :set_step
-
-  # Changes the simulation time of the current ssc (ssc = simulation
-  # settings collection).
-  # 
-  def set_time t
-    ssc.update target_time: t
-  end
-  alias :set_target_time :set_time
-
-  # Changes the sampling period of the current ssc (ssc = simulation
-  # settings collection).
-  # 
-  def set_sampling Δt
-    ssc.update sampling_period: Δt
-  end
-
-  # Changes the simulation method of the current ssc (ssc = simulation
-  # settings collection).
-  # 
-  def set_simulation_method m
-    ssc.update method: m
-  end
-
-  # Create a new timed simulation and make it available in the simulations
-  # table.
-  # 
-  def new_timed_simulation *args, &block
-    instance = workspace.new_timed_simulation( *args, &block )
-    # Set the point to it
-    simulation_point_to( simulations.rassoc( instance )[0] )
-    return instance
-  end
-
-  # Create a new timed simulation and run it.
-  # 
-  def run!
-    new_timed_simulation.run!
-  end
-
-  # Write the recorded samples in a file (csv).
-  # 
-  def print_recording( filename = nil )
-    if filename.nil? then
-      puts simulation.recording_csv_string
-    else
-      File.open( filename, "w" ) do |f|
-        f << simulation.recording_csv_string
-      end
-    end
-  end
-
-  # Plot the recorded samples.
-  # 
-  def plot *args
-    oo = args.extract_options!
-    case args.size
-    when 0 then plot_recording oo
-    when 1 then
-      plot_what = args[0]
-      case plot_what
-      when :state then plot_recording oo
-      when :flux then plot_flux oo
-      when :all then plot_all oo
-      else plot_selected *args end
-    else raise "Too many ordered arguments!" end
-  end
-
-  # Plot the selected features.
-  # 
-  def plot_selected *args
-    oo = args.extract_options!
-    collection = Array args[0]
-    return nil unless sim = @workspace.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" )
-  end
-    
-
-  # Plot the recorded samples (system state history).
-  # 
-  def plot_state( *args )
-    oo = args.extract_options!
-    excluded = Array oo[:except]
-    return nil unless sim = @workspace.simulations.values[-1] # sim@point
-    # Decide about the features to plot.
-    features = excluded.each_with_object sim.places.dup do |x, α|
-      i = α.index x
-      α[i] = nil if i
-    end
-    # 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: "State plot", ylabel: "Marking" )
-  end
-
-  # Plot the recorded flux (computed flux history at the sampling points).
-  # 
-  def plot_flux( *args )
-    oo = args.extract_options!
-    excluded = Array oo[:except]
-    return nil unless sim = @workspace.simulations.values[-1] # sim@point
-    # Decide about the features to plot.
-    all = sim.SR_transitions
-    features = excluded.each_with_object all.dup do |x, α|
-      i = α.index x
-      if i then α[i] = nil end
-    end
-    # Get recording.
-    rec = sim.recording
-    # Get flux recording.
-    flux = rec.modify { |ᴛ, ᴍ| [ ᴛ, sim.at( t: ᴛ, m: ᴍ ).flux_for( *all ) ] }
-    # Select a time series for each feature.
-    time_series = features.map.with_index do |feature, i|
-      feature and flux.map { |ᴛ, flux| [ ᴛ, flux[i] ] }.transpose
-    end
-    # Time axis
-    ᴛ = sim.target_time
-    # Gnuplot call
-    gnuplot( ᴛ, features.compact.map( &:name ), time_series.compact,
-             title: "Flux plot", ylabel: "Flux [µMⁿ.s⁻¹]" )
-  end
-
-  private
-
-  # Gnuplots things.
-  # 
-  def gnuplot( time, labels, time_series, *args )
-    labels = labels.dup
-    time_series = time_series.dup
-    oo = args.extract_options!
-
-    Gnuplot.open do |gp|
-      Gnuplot::Plot.new( gp ) do |plot|
-        plot.xrange "[-0:#{SY::Time.magnitude( time ).amount rescue time}]"
-        plot.title oo[:title] || "Simulation plot"
-        plot.ylabel oo[:ylabel] || "Values"
-        plot.xlabel oo[:xlabel] || "Time [s]"
-
-        labels.zip( time_series ).each { |label, series|
-          plot.data << Gnuplot::DataSet.new( series ) do |data_series|
-            data_series.with = "linespoints"
-            data_series.title = label
-          end
-        }
-      end
-    end
-  end
-
-  # Helper method allowing more flexible access to the simulations stored in
-  # the current workspace. A single, non-hash ordered argument is considered
-  # a simulation name. A hash argument is assumed to be have keys :net, :cc,
-  # :imc, :ssc, by which to identify a simulation. Hash keys can be forgone if
-  # 4 ordered arguments are supplied: These are then considered to represent
-  # the values of a hash with the above keys, and are converted to such hash.
-  # Summarizing this, there is a single return value, with which a simulation
-  # can be identified - this return value is either a hash of simulation
-  # parameters and settings, if it is a hash, or a simulation name, if it is
-  # non-hash. 
-  # 
-  def normalize_simulation_identifier *args
-    oo = args.extract_options!
-    if args.empty? then
-      raise AE, "Simulation point position not supplied" if oo.empty?
-      oo
-    else
-      if oo.empty? then
-        case args.size
-        when 1 then args[0]
-        when 4 then Hash[ [:net, :cc, :imc, :ssc].zip( args ) ]
-        else raise AE, "Wrong number of ordered arguments." end
-      else
-        raise AE, "Bad arguments: Can't combine named & ordered args."
-      end
-    end
-  end
+  include YPetri::Manipulator::PetriNetRelatedMethods
+  include YPetri::Manipulator::SimulationRelatedMethods
 end # class YPetri::Manipulator