Module: YPetri::Agent::SimulationRelated

Defined in:
lib/y_petri/agent/simulation_related.rb

Overview

Agent instance methods related to simulation (initial marking collections, clamp collections, initial marking collections, management of simulations…)

Defined Under Namespace

Classes: SimulationPoint

Constant Summary collapse

SimulationSelection =

Simulation selection class.

YPetri::Agent::Selection.parametrize( agent: self )
SscSelection =

Simulation settings collection selection class.

YPetri::Agent::Selection.parametrize( agent: self )
CcSelection =

Clamp collection selection class.

YPetri::Agent::Selection.parametrize( agent: self )
ImcSelection =

Initial marking collection selection class.

YPetri::Agent::Selection.parametrize( agent: self )
SscPoint =

Pointer to a collection of simulation settings.

YPetri::Agent::HashKeyPointer.parametrize( agent: self )
CcPoint =

Pointer to a clamp collection.

YPetri::Agent::HashKeyPointer.parametrize( agent: self )
ImcPoint =

Pointer to a collection of initial markings.

YPetri::Agent::HashKeyPointer.parametrize( agent: self )

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#cc_point ⇒ Object (readonly)

Returns the value of attribute cc_point.



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# File 'lib/y_petri/agent/simulation_related.rb', line 62

def cc_point
  @cc_point
end

#cc_selection ⇒ Object (readonly)

Returns the value of attribute cc_selection.



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# File 'lib/y_petri/agent/simulation_related.rb', line 62

def cc_selection
  @cc_selection
end

#imc_point ⇒ Object (readonly)

Returns the value of attribute imc_point.



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# File 'lib/y_petri/agent/simulation_related.rb', line 62

def imc_point
  @imc_point
end

#imc_selection ⇒ Object (readonly)

Returns the value of attribute imc_selection.



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# File 'lib/y_petri/agent/simulation_related.rb', line 62

def imc_selection
  @imc_selection
end

#simulation_point ⇒ Object (readonly)

Returns the value of attribute simulation_point.



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# File 'lib/y_petri/agent/simulation_related.rb', line 62

def simulation_point
  @simulation_point
end

#simulation_selection ⇒ Object (readonly)

Returns the value of attribute simulation_selection.



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# File 'lib/y_petri/agent/simulation_related.rb', line 62

def simulation_selection
  @simulation_selection
end

#ssc_point ⇒ Object (readonly)

Returns the value of attribute ssc_point.



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# File 'lib/y_petri/agent/simulation_related.rb', line 62

def ssc_point
  @ssc_point
end

#ssc_selection ⇒ Object (readonly)

Returns the value of attribute ssc_selection.



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# File 'lib/y_petri/agent/simulation_related.rb', line 62

def ssc_selection
  @ssc_selection
end

Instance Method Details

#clamp(clamp_hash) ⇒ Object

FIXME: This is going to be tested



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# File 'lib/y_petri/agent/simulation_related.rb', line 160

def clamp clamp_hash
  clamp_hash.each_pair do |place, clamp|
    clamp_collection.merge! world.place( place ) => clamp
  end
end

#clamp_collection(id = nil) ⇒ Object Also known as: cc

Returns identified clamp collection, or (if no argument given) one corresponding to cc_point.



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# File 'lib/y_petri/agent/simulation_related.rb', line 133

def clamp_collection id=nil
  if id.nil? then cc_point.get else clamp_collections[ id ] end
end

#initial_marking(*args) ⇒ Object Also known as: im

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.

  • 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.



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# File 'lib/y_petri/agent/simulation_related.rb', line 178

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 ArgumentError, "Too many ordered parameters" end
end

#initial_marking_collection(id = nil) ⇒ Object Also known as: imc

Returns identified initial marking collection, or (if no argument given) one corresponding to imc_point.



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# File 'lib/y_petri/agent/simulation_related.rb', line 141

def initial_marking_collection id=nil
  if id.nil? then imc_point.get else
    initial_marking_collections[ id ]
  end
end

#initialize ⇒ Object

Agent initialziation method.



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# File 'lib/y_petri/agent/simulation_related.rb', line 73

def initialize
  # set up this agent's pointers
  @simulation_point = SimulationPoint.new( hash: simulations,
                                           hash_value_is: "simulation" )
  @ssc_point = SscPoint.new( hash: simulation_settings_collections,
                                   hash_value_is: "simulation settings collection",
                                   default_key: :Base )
  @cc_point = CcPoint.new( hash: clamp_collections,
                           hash_value_is: "clamp collection",
                           default_key: :Base )
  @imc_point = ImcPoint.new( hash: initial_marking_collections,
                             hash_value_is: "initial marking collection",
                             default_key: :Base )
  # set up this manipulator's selections
  @simulation_selection = SimulationSelection.new
  @ssc_selection = SscSelection.new
  @cc_selection = CcSelection.new
  @imc_selection = ImcSelection.new
  # do anything else prescribed
  super
end

#new_simulation(*args, &block) ⇒ Object

Create a new timed simulation and make it available in the simulations table.



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# File 'lib/y_petri/agent/simulation_related.rb', line 242

def new_simulation *args, &block
  instance = world.new_simulation( *args, &block )
  # Set the point to it
  simulation_point.set( simulations.rassoc( instance )[0] )
  return instance
end

#plot(features) ⇒ Object

Plot the recording reduced into the given feature set.



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# File 'lib/y_petri/agent/simulation_related.rb', line 267

def plot features
  ff = simulation.net.state.features( features )
  simulation.recording.reduce_features( ff ).plot
end

#plot_delta(place_ids = nil, except: [], transitions: nil, title: "Delta plot", ylabel: "Delta [µM]", **options) ⇒ Object

Plot delta history of selected places with respect to a set of transitions.



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# File 'lib/y_petri/agent/simulation_related.rb', line 324

def plot_delta( place_ids=nil, except: [], transitions: nil,
                title: "Delta plot", ylabel: "Delta [µM]",
                **options )
  options.may_have :delta_time, syn!: :Δt
  rec = simulation.recording
  pp = simulation.pp( place_ids ) - simulation.ee( except )
  tt = transitions.nil? ? simulation.tt : tranisitions
  tt = simulation.tt( tt )
  tt -= simulation.ee( except )
  rec.delta( pp, transitions: tt, Δt: options[:delta_time] )
    .plot( title: title, ylabel: ylabel, **options )
end

#plot_firing(transition_ids = nil, except: [], title: "Firing plot", ylabel: "Firing [µM]", **options) ⇒ Object

Plot firing history of tS transitions.



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# File 'lib/y_petri/agent/simulation_related.rb', line 297

def plot_firing( transition_ids=nil, except: [],
                 title: "Firing plot", ylabel: "Firing [µM]",
                 **options )
  rec = simulation.recording
  tt = transition_ids.nil? ? simulation.tS_tt : transition_ids
  tt = simulation.tS_tt( tt )
  tt -= simulation.tt( except )
  rec.firing( tt ).plot( title: title, ylabel: ylabel, **options )
end

#plot_flux(transition_ids = nil, except: [], title: "Flux plot", ylabel: "Flux [µM.s⁻¹]", **options) ⇒ Object

Plot flux history of TS transitions.



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# File 'lib/y_petri/agent/simulation_related.rb', line 285

def plot_flux( transition_ids=nil, except: [],
               title: "Flux plot", ylabel: "Flux [µM.s⁻¹]",
               **options )
  rec = simulation.recording
  tt = transition_ids.nil? ? simulation.TS_tt : transition_ids
  tt = simulation.TS_tt( tt )
  tt -= simulation.tt( except )
  rec.flux( tt ).plot( title: title, ylabel: ylabel, **options )
end

#plot_gradient(place_ids = nil, except: [], transitions: nil, title: "Gradient plot", ylabel: "Gradient [µM.s⁻¹]", **options) ⇒ Object

Plot gradient history of selected places with respect to a set of T transitions.



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# File 'lib/y_petri/agent/simulation_related.rb', line 310

def plot_gradient( place_ids=nil, except: [], transitions: nil,
                   title: "Gradient plot", ylabel: "Gradient [µM.s⁻¹]",
                   **options )
  rec = simulation.recording
  pp = simulation.pp( place_ids ) - simulation.ee( place_ids )
  tt = transitions.nil? ? simulation.T_tt : transitions
  tt = simulation.T_tt( tt )
  tt -= simulation.ee( except )
  rec.gradient( pp, transitions: tt )
    .plot( title: title, ylabel: ylabel, **options )
end

#plot_state(place_ids = nil, except: [], title: "State plot", ylabel: "Marking [µM]", **options) ⇒ Object Also known as: plot_marking

Plot system state history.



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# File 'lib/y_petri/agent/simulation_related.rb', line 274

def plot_state( place_ids=nil, except: [],
                title: "State plot", ylabel: "Marking [µM]",
                **options )
  rec = simulation.recording
  pp = simulation.pp( place_ids ) - simulation.pp( except )
  rec.marking( pp ).plot( title: title, ylabel: ylabel, **options )
end

#print_recording(filename = nil, **nn) ⇒ Object

Write the recorded samples in a file (csv).



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# File 'lib/y_petri/agent/simulation_related.rb', line 257

def print_recording( filename=nil, **nn )
  if filename.nil? then
    simulation.recording.print **nn
  else
    File.open filename, "w" do |f| f << print_recording( **nn ) end
  end
end

#run!(*args) ⇒ Object

Create a new timed simulation and run it.



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# File 'lib/y_petri/agent/simulation_related.rb', line 251

def run! *args
  new_simulation.run! *args
end

#set_sampling(Δt) ⇒ Object

Changes the sampling period of the current ssc (ssc = simulation settings collection).



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# File 'lib/y_petri/agent/simulation_related.rb', line 228

def set_sampling Δt
  ssc.update sampling: Δt
end

#set_simulation_method(m) ⇒ Object

Changes the simulation method of the current ssc (ssc = simulation settings collection).



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# File 'lib/y_petri/agent/simulation_related.rb', line 235

def set_simulation_method m
  ssc.update method: m
end

#set_step(Δt) ⇒ Object Also known as: set_step_size

Changes the time step of the current ssc (ssc = simulation settings collection).



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# File 'lib/y_petri/agent/simulation_related.rb', line 207

def set_step Δt
  ssc.update step: Δt
end

#set_target_time(time) ⇒ Object

Sets the time frame of the current ssc to run from zero to the time supplied as the argument.



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# File 'lib/y_petri/agent/simulation_related.rb', line 221

def set_target_time time
  set_time time * 0 .. time
end

#set_time(time_range) ⇒ Object

Sets the time frame of the current ssc (sim. settings collection).



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# File 'lib/y_petri/agent/simulation_related.rb', line 214

def set_time time_range
  ssc.update time: time_range.aT_kind_of( Range )
end

#simulation(*args) ⇒ Object

Returns the simulation identified by the argument, or one at simulation point, if no argument given. The simulation is identified in the same way as for #simulation_point_to method.



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# File 'lib/y_petri/agent/simulation_related.rb', line 125

def simulation *args
  return simulation_point.get if args.empty?
  SimulationPoint.new( hash: simulations, hash_value_is: "simulation" ).get
end

#simulation_settings_collection(id = nil) ⇒ Object Also known as: ssc

Returns identified simulation settings collection, or (if no argument given) one corresponding to ssc_point.



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# File 'lib/y_petri/agent/simulation_related.rb', line 151

def simulation_settings_collection id=nil
  if id.nil? then ssc_point.get else
    simulation_settings_collections[ id ]
  end
end

#state ⇒ Object

Pretty print the state.



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# File 'lib/y_petri/agent/simulation_related.rb', line 116

def state
  pp pm
  return nil
end