Fix/input state specs (#521)

* -

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into CURRENT

# Conflicts:
#	tests/mechanisms/test_transfer_mechanism.py

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into CURRENT

# Conflicts:
#	tests/mechanisms/test_transfer_mechanism.py

* • Mechanism, PathwayProjection
  - fixed bugs related to input_state specifications

* • Mechanism, PathwayProjection
  - fixed bugs related to input_state specifications

* • Mechanism
  - _parse_arg_input_states, add_states:  modified to accomdodate deferred_init

* • State
  - _parse_state_spec re: owner name

* • State
  - _parse_state_spec re: owner name

* • State
  - _parse_state_spec re: owner name

* • States
  __init__: now calls add_states to add state to owner if called from COMMAND_LINE

* • States
  __init__: now calls add_states to add state to owner if called from COMMAND_LINE
  add_states works for deferred_init state
  assignment of State to owner now works

* • States
  __init__: now calls add_states to add state to owner if called from COMMAND_LINE
  add_states works for deferred_init state
  assignment of State to owner now works

* -

* -

Scripts/Scratch Pad.py

@@ -412,35 +412,39 @@ def __init__(self, error_value):
 
 # FROM KEVIN: -------------------------------------
 
-# WORKING:
-# I = pnl.InputState(reference_value=[0,0,0])
-# pnl.TransferMechanism(input_states=[I])
 
-# p = pnl.MappingProjection()
-# T = pnl.TransferMechanism(input_states=[{pnl.VARIABLE: [0, 0, 0], pnl.PROJECTIONS:[p]}])
-#
-# p = pnl.MappingProjection()
-# T = pnl.TransferMechanism(default_variable=[0, 0], input_states=[p])
+I = pnl.InputState(reference_value=[0,0,0])
+pnl.TransferMechanism(input_states=[I])
+
+p = pnl.MappingProjection()
+T = pnl.TransferMechanism(input_states=[{pnl.VARIABLE: [0, 0, 0], pnl.PROJECTIONS:[p]}])
+
+p = pnl.MappingProjection()
+T = pnl.TransferMechanism(default_variable=[0, 0], input_states=[p])
 
-#-------------
-# m = pnl.TransferMechanism()
-# i = pnl.InputState(owner=m, variable=[0, 0, 0], reference_value=[0,0,0])
 
-# m = pnl.TransferMechanism(default_variable=[0, 0, 0])
-# i = pnl.InputState(owner=m, reference_value=[0, 0, 0])
 
-# WORKS:
 m = pnl.TransferMechanism()
 i = pnl.InputState(variable=[0,0])
 m.add_states([i])
 m.execute()
-assert True
+assert len(m.input_states) == 2
+assert len(m.variable)==2
+assert len(m.variable[0])==1
+assert len(m.variable[1])==2
+assert m.input_states[0].name == 'INPUT_STATE-0'
+assert m.input_states[1].name == 'INPUT_STATE-1'
 
-# m = pnl.TransferMechanism(default_variable=[0, 0, 0])
-# i = pnl.InputState(owner=m, variable=[0, 0, 0])
-# m.add_states([i])
+m = pnl.TransferMechanism()
+i = pnl.InputState(owner=m, variable=[0, 0, 0])
 m.execute()
-# assert True
+assert len(m.input_states) == 2
+assert m.input_states[0].name == 'INPUT_STATE-0'
+assert m.input_states[1].name == 'INPUT_STATE-1'
+assert len(m.variable)==2
+assert len(m.variable[0])==1
+assert len(m.variable[1])==3
+
 
 # --------------------------------------------------------------------------------------------------
 

psyneulink/components/component.py

@@ -1047,7 +1047,7 @@ def _deferred_init(self, context=None):
             #   the value is stored in paramClassDefaults in assign_ags_to_params_dicts,
             #   and will be restored in _instantiate_function
             try:
-                del self.init_args['function']
+                del self.init_args[FUNCTION]
             except KeyError:
                 pass
 
@@ -1064,7 +1064,7 @@ def _deferred_init(self, context=None):
 
             # If name is None, mark as deferred so that name can be customized
             #    using info that has become available at time of deferred init
-            self.init_args['name'] = (self.init_args['name'] or
+            self.init_args[NAME] = (self.init_args[NAME] or
                                       ('deferred_init_' + self.className) or
                                       DEFERRED_DEFAULT_NAME)
 

psyneulink/components/mechanisms/mechanism.py

@@ -712,7 +712,7 @@ class `UserList <https://docs.python.org/3.6/library/collections.html?highlight=
 from psyneulink.components.states.inputstate import InputState
 from psyneulink.components.states.parameterstate import ParameterState
 from psyneulink.components.states.outputstate import OutputState
-from psyneulink.components.states.state import _parse_state_spec
+from psyneulink.components.states.state import _parse_state_spec, ADD_STATES
 from psyneulink.globals.defaults import timeScaleSystemDefault
 from psyneulink.globals.keywords import \
     CHANGED, COMMAND_LINE, EVC_SIMULATION, EXECUTING, FUNCTION_PARAMS, \
@@ -2000,13 +2000,14 @@ def _get_variable_from_input(self, input):
             # Check if inputs are of different lengths (indicated by dtype == np.dtype('O'))
             num_inputs = np.size(input)
             if isinstance(input, np.ndarray) and input.dtype is np.dtype('O') and num_inputs == num_input_states:
-                pass
+                # Reduce input back down to sequence of arrays (to remove extra dim added by atleast_2d above)
+                input = np.squeeze(input)
             else:
                 num_inputs = np.size(input, 0)  # revert num_inputs to its previous value, when printing the error
                 raise SystemError("Number of inputs ({0}) to {1} does not match "
                                   "its number of input_states ({2})".
                                   format(num_inputs, self.name,  num_input_states ))
-        for i in range(num_input_states):
+        for i, input_state in enumerate(self.input_states):
             # input_state = list(self.input_states.values())[i]
             input_state = self.input_states[i]
             # input_item = np.ndarray(input[i])
@@ -2022,7 +2023,7 @@ def _get_variable_from_input(self, input):
                         input[i],
                         len(input_state.instance_defaults.variable),
                         input_state.name,
-                        append_type_to_name(self),
+                        self.name
                     )
                 )
 
@@ -2190,7 +2191,7 @@ def plot(self, x_range=None):
         plt.show()
 
     @tc.typecheck
-    def add_states(self, states, context=COMMAND_LINE):
+    def add_states(self, states, context=ADD_STATES):
         """
         add_states(states)
 
@@ -2239,6 +2240,7 @@ def add_states(self, states, context=COMMAND_LINE):
         instantiated_output_states = None
 
         for state in states:
+            # FIX: 11/9/17: REFACTOR USING _parse_state_spec
             state_type = _parse_state_type(self, state)
             if (isinstance(state_type, InputState) or
                     (inspect.isclass(state_type) and issubclass(state_type, InputState))):
@@ -2255,15 +2257,14 @@ def add_states(self, states, context=COMMAND_LINE):
                 old_variable = self.instance_defaults.variable.tolist()
                 old_variable.extend(added_variable)
                 self.instance_defaults.variable = np.array(old_variable)
-                # FIX: 11/8/17 - INCLUDE OR NOT:
-                self.function_object.instance_defaults.variable = self.instance_defaults.variable
-                self.function_object.variableClassDefault = self.instance_defaults.variable
-                self.value = self.function()
-                # FIX END
-                instantiated_input_states = _instantiate_input_states(self, input_states,
+                self._update_variable(self.instance_defaults.variable)
+                instantiated_input_states = _instantiate_input_states(self,
+                                                                      input_states,
                                                                       added_variable,
                                                                       context=context)
-                # instantiated_input_states = self._instantiate_input_states(input_states, context=context)
+                for state in instantiated_input_states:
+                    if state.name is state.componentName or state.componentName + '-' in state.name:
+                        state._assign_default_name(context=context)
         if output_states:
             instantiated_output_states = _instantiate_output_states(self, output_states, context=context)
 

psyneulink/components/mechanisms/processing/transfermechanism.py

@@ -712,19 +712,14 @@ def _execute(self,
             if (np.array(noise) != 0).any():
                 current_input = variable[0] + noise
             else:
-
                 current_input = variable[0]
 
         # self.previous_input = current_input
 
         # Apply TransferMechanism function
         output_vector = self.function(variable=current_input, params=runtime_params)
 
-        # # MODIFIED  OLD:
-        # if list(range):
-        # MODIFIED  NEW:
         if range is not None:
-        # MODIFIED  END
             minCapIndices = np.where(output_vector < range[0])
             maxCapIndices = np.where(output_vector > range[1])
             output_vector[minCapIndices] = np.min(range)

psyneulink/components/states/inputstate.py

@@ -388,11 +388,12 @@
 from psyneulink.components.component import InitStatus
 from psyneulink.components.functions.function import Linear, LinearCombination
 from psyneulink.components.mechanisms.mechanism import Mechanism
-from psyneulink.components.states.state import StateError, State_Base, _instantiate_state_list, state_type_keywords
+from psyneulink.components.states.state import \
+    StateError, State_Base, _instantiate_state_list, state_type_keywords, ADD_STATES
 from psyneulink.components.states.outputstate import OutputState
 from psyneulink.globals.keywords import EXPONENT, FUNCTION, INPUT_STATE, INPUT_STATE_PARAMS, MAPPING_PROJECTION, \
     MECHANISM, OUTPUT_STATES, MATRIX, PROJECTIONS, PROJECTION_TYPE, SUM, VARIABLE, WEIGHT, REFERENCE_VALUE, \
-    OUTPUT_STATE, PROCESS_INPUT_STATE, SYSTEM_INPUT_STATE, LEARNING_SIGNAL, GATING_SIGNAL, SENDER
+    OUTPUT_STATE, PROCESS_INPUT_STATE, SYSTEM_INPUT_STATE, LEARNING_SIGNAL, GATING_SIGNAL, SENDER, COMMAND_LINE
 from psyneulink.globals.preferences.componentpreferenceset import is_pref_set
 from psyneulink.globals.preferences.preferenceset import PreferenceLevel
 from psyneulink.globals.utilities import append_type_to_name, iscompatible
@@ -635,17 +636,22 @@ def __init__(self,
                  prefs:is_pref_set=None,
                  context=None):
 
+        if context is None:
+            context = COMMAND_LINE
+        else:
+            context = self
+
         # Assign args to params and functionParams dicts (kwConstants must == arg names)
         params = self._assign_args_to_param_dicts(function=function,
                                                   weight=weight,
                                                   exponent=exponent,
                                                   params=params)
 
         # If owner or reference_value has not been assigned, defer init to State._instantiate_projection()
-        if owner is None or reference_value is None:
+        if owner is None or (variable is None and reference_value is None):
             # Store args for deferred initialization
             self.init_args = locals().copy()
-            self.init_args['context'] = self
+            self.init_args['context'] = context
             self.init_args['name'] = name
             self.init_args['projections'] = projections
 
@@ -664,10 +670,10 @@ def __init__(self,
                                          params=params,
                                          name=name,
                                          prefs=prefs,
-                                         context=self)
+                                         context=context)
 
         if self.name is self.componentName or self.componentName + '-' in self.name:
-            self._assign_default_name()
+            self._assign_default_name(context=context)
 
 
     def _validate_params(self, request_set, target_set=None, context=None):
@@ -730,7 +736,7 @@ def _instantiate_function(self, context=None):
                                              self.function.__self__.componentName, ))
 
         # Insure that self.value is compatible with self.reference_value
-        if not iscompatible(self.value, self.reference_value):
+        if self.reference_value is not None and not iscompatible(self.value, self.reference_value):
             raise InputStateError("Value ({}) of {} {} for {} is not compatible with specified {} ({})".
                                            format(self.value,
                                                   self.componentName,
@@ -773,13 +779,29 @@ def _execute(self, function_params, context):
     def _get_primary_state(self, mechanism):
         return mechanism.input_state
 
-    def _assign_default_name(self):
-        # """Assign index of '-1' to first default  InputState
-        # Subsequent ones are indexed sequentially by Registry starting with '-2'
+    def _assign_default_name(self, context=None):
+        # """Assign 'INPUT_STATE-n' to any InputStates with default name (i.e., name of State: 'InputState'),
+        #    where n is the next index of InputStates with the default name
+        # Returns name assigned to State
         # """
-        # if self.name == self.componentName:
-        #     self.name = self.name+'-1'
-        self.name = self.name.replace(self.componentName, 'INPUT_STATE')
+
+        # Call for State being instantiated in the context of constructing its owner
+        if isinstance(context,State_Base):
+            self.name = self.name.replace(self.componentName, 'INPUT_STATE')
+
+        # Call in the context of adding a state to an existing owner
+        elif ADD_STATES in context:
+            try:
+                i=len([input_state for input_state in self.owner.input_states if 'INPUT_STATE-' in input_state.name])
+                self.name = 'INPUT_STATE-'+str(i)
+            except TypeError:
+                i=0
+                self.name = 'INPUT_STATE-'+str(i)
+
+        else:
+            raise InputStateError("PROGRAM ERROR: unrecognize context ({}) for assigning {} to {}".
+                                  format(context, NAME, InputState.__name__))
+        return self.name
 
 # MODIFIED 9/30/17 NEW:
     @tc.typecheck
@@ -944,12 +966,13 @@ def _instantiate_input_states(owner, input_states=None, reference_value=None, co
                                          state_list=input_states,
                                          state_type=InputState,
                                          state_param_identifier=INPUT_STATE,
-                                         reference_value=reference_value or owner.instance_defaults.variable,
+                                         reference_value=reference_value if reference_value is not None
+                                                                         else owner.instance_defaults.variable,
                                          reference_value_name=VARIABLE,
                                          context=context)
 
     # Call from Mechanism.add_states, so add to rather than assign input_states (i.e., don't replace)
-    if context and 'COMMAND_LINE' in context:
+    if context and 'ADD_STATES' in context:
         owner.input_states.extend(state_list)
     else:
         owner._input_states = state_list

psyneulink/components/states/modulatorysignals/controlsignal.py

@@ -296,7 +296,7 @@
 from psyneulink.globals.defaults import defaultControlAllocation
 from psyneulink.globals.keywords import \
     ALLOCATION_SAMPLES, AUTO, CONTROLLED_PARAMS, CONTROL_PROJECTION, CONTROL_SIGNAL, EXECUTING, \
-    FUNCTION, FUNCTION_PARAMS, INTERCEPT, MECHANISM, MODULATION, NAME, OFF, ON, \
+    FUNCTION, FUNCTION_PARAMS, INTERCEPT, COMMAND_LINE, OFF, ON, \
     PARAMETER_STATE, PARAMETER_STATES, OUTPUT_STATE_PARAMS, \
     PROJECTION_TYPE, RECEIVER, SEPARATOR_BAR, SLOPE, SUM, kwAssign
 from psyneulink.globals.log import LogEntry, LogLevel
@@ -665,6 +665,11 @@ def __init__(self,
                  prefs:is_pref_set=None,
                  context=None):
 
+        if context is None:
+            context = COMMAND_LINE
+        else:
+            context = self
+
         # Note index and calculate are not used by ControlSignal, but included here for consistency with OutputState
         if params and ALLOCATION_SAMPLES in params and params[ALLOCATION_SAMPLES] is not None:
             allocation_samples =  params[ALLOCATION_SAMPLES]
@@ -702,7 +707,7 @@ def __init__(self,
                          params=params,
                          name=name,
                          prefs=prefs,
-                         context=self)
+                         context=context)
 
     def _validate_params(self, request_set, target_set=None, context=None):
         """Validate allocation_samples and control_signal cost functions

psyneulink/components/states/modulatorysignals/gatingsignal.py

@@ -233,7 +233,7 @@
 from psyneulink.components.states.outputstate import OutputState, PRIMARY, SEQUENTIAL
 from psyneulink.components.states.state import State_Base, State
 from psyneulink.globals.keywords import \
-    MECHANISM, NAME, GATING_PROJECTION, GATING_SIGNAL, GATE, RECEIVER, SUM, PROJECTION_TYPE, \
+    COMMAND_LINE, GATING_PROJECTION, GATING_SIGNAL, GATE, RECEIVER, SUM, PROJECTION_TYPE, \
     INPUT_STATE, INPUT_STATES, OUTPUT_STATE, OUTPUT_STATES, OUTPUT_STATE_PARAMS
 from psyneulink.globals.preferences.componentpreferenceset import is_pref_set
 from psyneulink.globals.preferences.preferenceset import PreferenceLevel
@@ -430,6 +430,11 @@ def __init__(self,
                  prefs:is_pref_set=None,
                  context=None):
 
+        if context is None:
+            context = COMMAND_LINE
+        else:
+            context = self
+
         # Note: calculate is not currently used by GatingSignal;
         #       it is included here for consistency with OutputState and possible use by subclasses.
         if index is None and owner is not None:
@@ -459,7 +464,7 @@ def __init__(self,
                          params=params,
                          name=name,
                          prefs=prefs,
-                         context=self)
+                         context=context)
 
     def _execute(self, function_params, context):
         return float(super()._execute(function_params=function_params, context=context))

psyneulink/components/states/modulatorysignals/learningsignal.py

@@ -175,7 +175,7 @@
 from psyneulink.components.states.outputstate import PRIMARY
 from psyneulink.components.states.state import State_Base
 from psyneulink.globals.keywords import \
-    LEARNED_PARAM, LEARNING_SIGNAL, LEARNING_PROJECTION, \
+    COMMAND_LINE, LEARNED_PARAM, LEARNING_SIGNAL, LEARNING_PROJECTION, \
     PROJECTION_TYPE, RECEIVER, OUTPUT_STATE_PARAMS, PARAMETER_STATE, PARAMETER_STATES, SUM
 from psyneulink.globals.preferences.componentpreferenceset import is_pref_set
 from psyneulink.globals.preferences.preferenceset import PreferenceLevel
@@ -375,6 +375,11 @@ def __init__(self,
                  prefs:is_pref_set=None,
                  context=None):
 
+        if context is None:
+            context = COMMAND_LINE
+        else:
+            context = self
+
         # Assign args to params and functionParams dicts (kwConstants must == arg names)
         params = self._assign_args_to_param_dicts(function=function,
                                                   learning_rate=learning_rate,
@@ -397,7 +402,7 @@ def __init__(self,
                          params=params,
                          name=name,
                          prefs=prefs,
-                         context=self)
+                         context=context)
 
     def _get_primary_state(self, projection):
         return projection.parameter_state
@@ -406,12 +411,12 @@ def _get_primary_state(self, projection):
     def learning_signal(self):
         return self.value
 
-    def _assign_default_name(self):
+    def _assign_default_name(self, context=None):
         # Preserve LEARNING_SIGNAL as name of the first LearningSignal
         #    as documented, and as it is used by System._instantiate_learning_graph
         if self.name is self.componentName:
             return self.name
         # Otherwise, allow ModulatorySignal to construct default name as usual
         else:
-            super()._assign_default_name()
+            super()._assign_default_name(context=context)