Names/log/set log conditions (#590)

* • System - show_graph(): fixed bug producing empty image for graphs with just one Mechanism added auto-recurrent projections * • Log - added numpy_array output method * - * - * - * - * - * - * - * - * - * - * - * - * - * • Log - fixed bugs preventing logging during INITIALIZATION * • Log - fixed bugs preventing logging during INITIALIZATION * - * - * - * - * - * • Log - logged_item, print_entries: corrected to use 'value' rather than owner's name in reports * • Log - logged_item, print_entries: corrected to use 'value' rather than owner's name in reports • Tests test_log: added test_log_initialization * • Log - _alias_owner_name: added to used 'value' rather than owner's name in reports - nparray: bug fix to handle None values • Tests test_log: added test_log_initialization * • Log - log_value: added • Tests - test_multilayer: added test of log_value * • Log - log_value: implemented - logged_item, print_entries: corrected to use 'value' rather than owner's name in reports • Tests - test_multilayer: added test of log_value * • Log - log_value: implemented - logged_item, print_entries: corrected to use 'value' rather than owner's name in reports • Tests - test_multilayer: added test of log_value * Merge branch 'feat/Log/add_entry' into devel # Conflicts: # Scripts/Scratch Pad.py # psyneulink/globals/log.py * Merge branch 'feat/Log/add_entry' into devel # Conflicts: # Scripts/Scratch Pad.py # psyneulink/globals/log.py * Merge branch 'feat/Log/add_entry' into devel # Conflicts: # Scripts/Scratch Pad.py # psyneulink/globals/log.py * Merge branch 'feat/Log/add_entry' into devel # Conflicts: # Scripts/Scratch Pad.py # psyneulink/globals/log.py * • Log - print_entries(): fixed field widths * • Log - print_entries(): fixed field widths * • Log - print_entries(): fixed field widths * • Log - clear_entries: option added for deleting entry or just the data * • Log - LogLevels -> LogConditions - set_log_levels -> set_log_conditions * • Log - LogLevels -> LogConditions - set_log_levels -> set_log_conditions * • Log - LogLevels -> LogConditions - set_log_levels -> set_log_conditions * - * - * -
PrincetonUniversity · Dec 12, 2017 · a245271 · a245271
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diff --git a/.idea/runConfigurations/Make_HTML.xml b/.idea/runConfigurations/Make_HTML.xml
diff --git a/Scripts/Examples/Multilayer-Learning.py b/Scripts/Examples/Multilayer-Learning.py
@@ -104,8 +104,8 @@ def show_target(system):
 )
 
 # Log Middle_Weights of MappingProjection to Hidden_Layer_2
-# Hidden_Layer_2.log_items('Middle Weights')
-Middle_Weights.log_items('matrix')
+# Hidden_Layer_2.set_log_conditions('Middle Weights')
+Middle_Weights.set_log_conditions('matrix')
 
 mySystem.reportOutputPref = True
 # Shows graph will full information:

diff --git a/Scripts/Scratch Pad.py b/Scripts/Scratch Pad.py
@@ -2237,9 +2237,9 @@ def __init__(self, error_value):
 #     assert PJ.loggable_items == {'matrix': 'OFF',
 #                                  'value': 'OFF'}
 #
-#     T_1.log_items(pnl.NOISE)
-#     T_1.log_items(pnl.RESULTS)
-#     PJ.log_items(pnl.MATRIX)
+#     T_1.set_log_conditions(pnl.NOISE)
+#     T_1.set_log_conditions(pnl.RESULTS)
+#     PJ.set_log_conditions(pnl.MATRIX)
 #
 #     assert T_1.loggable_items == {'InputState-0': 'OFF',
 #                                  'slope': 'OFF',
@@ -2312,7 +2312,7 @@ def __init__(self, error_value):
 #
 # def test_log_initialization():
 #     T = pnl.TransferMechanism(
-#             prefs={pnl.LOG_PREF: pnl.PreferenceEntry(pnl.LogLevel.INITIALIZATION, pnl.PreferenceLevel.INSTANCE)}
+#             prefs={pnl.LOG_PREF: pnl.PreferenceEntry(pnl.LogCondition.INITIALIZATION, pnl.PreferenceLevel.INSTANCE)}
 #     )
 #     print(T.logged_items)
 #     print(T.log.nparray())
@@ -2325,12 +2325,12 @@ def __init__(self, error_value):
 
 #region TEST LOG MISC @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 # print("TEST LOG MISC")
-
+#
 # T = pnl.TransferMechanism()
 #
 # P = pnl.Process(pathway=[T])
 # S = pnl.System(processes=P)
-# T.log_items(pnl.RESULTS)
+# T.set_log_conditions(pnl.RESULTS)
 # S.execute()
 # S.execute()
 # S.execute()
@@ -2342,13 +2342,13 @@ def __init__(self, error_value):
 # assert True
 
 # T = pnl.TransferMechanism(size=3, name='My_T'
-#     # prefs={pnl.LOG_PREF:pnl.PreferenceEntry(pnl.LogLevel.INITIALIZATION, pnl.PreferenceLevel.INSTANCE)}
+#     # prefs={pnl.LOG_PREF:pnl.PreferenceEntry(pnl.LogCondition.INITIALIZATION, pnl.PreferenceLevel.INSTANCE)}
 # )
 # T2 = pnl.TransferMechanism(size=4, input_states=[T])
-# # T.parameter_states['slope'].logPref=pnl.PreferenceEntry(pnl.LogLevel.EXECUTION, pnl.PreferenceLevel.INSTANCE)
+# # T.parameter_states['slope'].logPref=pnl.PreferenceEntry(pnl.LogCondition.EXECUTION, pnl.PreferenceLevel.INSTANCE)
 # print(T.loggable_items)
-# T.log_items(('noise'))
-# T.log_items('RESULTS')
+# T.set_log_conditions(('noise'))
+# T.set_log_conditions('RESULTS')
 # print(T.loggable_items)
 #
 # T.execute()
@@ -2369,9 +2369,9 @@ def __init__(self, error_value):
 # PJ = T2.path_afferents[0]
 # print(PJ.loggable_items)
 #
-# T1.log_items('noise')
-# T1.log_items('RESULTS')
-# PJ.log_items('matrix')
+# T1.set_log_conditions('noise')
+# T1.set_log_conditions('RESULTS')
+# PJ.set_log_conditions('matrix')
 #
 # # Execute each Process twice (to generate some values in the logs):
 # PS.execute()
@@ -2403,9 +2403,9 @@ def __init__(self, error_value):
 # print(my_mech_B.loggable_items) # doctest: +SKIP
 # print(proj_A_to_B.loggable_items) # doctest: +SKIP
 #
-# my_mech_A.log_items('noise')
-# my_mech_A.log_items('RESULTS')
-# proj_A_to_B.log_items(pnl.MATRIX)
+# my_mech_A.set_log_conditions('noise')
+# my_mech_A.set_log_conditions('RESULTS')
+# proj_A_to_B.set_log_conditions(pnl.MATRIX)
 #
 #
 # my_process.execute()
@@ -2517,7 +2517,7 @@ def test_multilayer():
         },
     )
 
-    Middle_Weights.log_items(('matrix', pnl.EXECUTION))
+    Middle_Weights.set_log_conditions(('matrix', pnl.EXECUTION))
 
     stim_list = {Input_Layer: [[-1, 30]]}
     target_list = {Output_Layer: [[0, 0, 1]]}
@@ -2673,14 +2673,16 @@ def show_target():
                                            atol=1e-08,
                                            err_msg='Failed on test of logged values')
 
-    Middle_Weights.log.print_entries()
+    Middle_Weights.log.print_entries(width=200, display=[pnl.TIME, pnl.CONTEXT, pnl.VALUE])
 
     # Test Programatic logging
-    # Test Programatic logging
-    Hidden_Layer_2.log.log_value(pnl.VALUE)
+    Hidden_Layer_2.log.log_values(pnl.VALUE)
+
     log_val = Hidden_Layer_2.log.nparray(header=False)
     expected_log_val = np.array(
             [
+                [[0]],
+                [[10]],
                 [[0]],
                 [[[0.8565238418942037, 0.8601053239957609, 0.8662098921116546, 0.8746933736954071]]]
             ], dtype=object
@@ -2698,7 +2700,7 @@ def show_target():
 
     # Clear log and test with logging of weights set to LEARNING for another 5 trials of learning
     Middle_Weights.log.clear_entries(entries=None, confirm=False)
-    Middle_Weights.log_items(('matrix', pnl.LEARNING))
+    Middle_Weights.set_log_conditions(('matrix', pnl.LEARNING))
     s.run(
             num_trials=5,
             inputs=stim_list,
@@ -2749,10 +2751,9 @@ def show_target():
                                            err_msg='Failed on test of logged values')
 test_multilayer()
 
-#endregion
+# endregion
 
 #region TEST OVER-WRITING OF LOG @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
-#
 
 # class a:
 #

diff --git a/psyneulink/components/component.py b/psyneulink/components/component.py
@@ -139,9 +139,9 @@
 
 * **log** - the `log <Component.log>` attribute contains the Component's `Log`, that can be used to record its
   `value <Component.value>`, as well as that of Components that belong to it, during initialization, validation,
-  execution and learning.  It also has three convenience methods -- `loggable_items <Log.loggable_items>`, `log_items
-  <Log.log_items>`, and `logged_items <Log.logged_items>` -- that provide access to the corresponding methods of its
-  Log, used to identify, configure and track items for logging.
+  execution and learning.  It also has four convenience methods -- `loggable_items <Log.loggable_items>`, `set_log_conditions
+  <Log.set_log_conditions>`, `log_values <Log.log_values>` and `logged_items <Log.logged_items>` -- that provide access to the
+  corresponding methods of its Log, used to identify, configure and track items for logging.
 ..
 
 .. _Component_Name:
@@ -361,7 +361,7 @@ class `UserList <https://docs.python.org/3.6/library/collections.html?highlight=
     INIT_FULL_EXECUTE_METHOD, INPUT_STATES, LEARNING, LEARNING_PROJECTION, MAPPING_PROJECTION, NAME, OUTPUT_STATES, \
     PARAMS, PARAMS_CURRENT, PARAM_CLASS_DEFAULTS, PARAM_INSTANCE_DEFAULTS, PREFS_ARG, SEPARATOR_BAR, SET_ATTRIBUTE, \
     SIZE, USER_PARAMS, VALUE, VARIABLE, MODULATORY_SPEC_KEYWORDS, kwComponentCategory
-# from psyneulink.globals.log import Log, LogLevel
+# from psyneulink.globals.log import Log, LogCondition
 from psyneulink.globals.preferences.componentpreferenceset import ComponentPreferenceSet, kpVerbosePref
 from psyneulink.globals.preferences.preferenceset import PreferenceEntry, PreferenceLevel, PreferenceSet
 from psyneulink.globals.utilities import ContentAddressableList, ReadOnlyOrderedDict, convert_all_elements_to_np_array, convert_to_np_array, is_matrix, is_same_function_spec, iscompatible, kwCompatibilityLength
@@ -2834,28 +2834,42 @@ def runtimeParamStickyAssignmentPref(self, setting):
 
     @property
     def loggable_items(self):
-        """Diciontary of items that can be logged in the Component's `log <Component.log>` and their current `LogLevel`.
+        """Diciontary of items that can be logged in the Component's `log <Component.log>` and their current `LogCondition`.
         This is a convenience method that calls the `loggable_items <Log.loggable_items>` property of the Component's
         `log <Component.log>`.
         """
         return self.log.loggable_items
 
-    from psyneulink.globals.log import LogLevel
-    def log_items(self, items, log_level=LogLevel.EXECUTION):
+    from psyneulink.globals.log import LogCondition
+    def set_log_conditions(self, items, log_condition=LogCondition.EXECUTION):
         """
-        log_items(               \
+        set_log_conditions(               \
             items                \
-            log_level=EXECUTION  \
+            log_condition=EXECUTION  \
         )
 
-        Specifies items to be logged. This is a convenience method that calls the `log_items <Log.logged_items>` method
+        Specifies items to be logged; these must be be `loggable_items <Component.loggable_items>` of the Component's
+        `log <Component.log>`. This is a convenience method that calls the `set_log_conditions <Log.set_log_conditions>` method
         of the Component's `log <Component.log>`.
         """
-        self.log.log_items(items=items, log_level=log_level)
+        self.log.set_log_conditions(items=items, log_condition=log_condition)
+
+    def log_values(self, entries):
+        """
+        log_values(              \
+            entries              \
+        )
+
+        Specifies items to be logged; ; these must be be `loggable_items <Component.loggable_items>` of the Component's
+        `log <Component.log>`. This is a convenience method that calls the `log_values <Log.log_values>` method
+        of the Component's `log <Component.log>`.
+        """
+        self.log.log_values(entries)
+
 
     @property
     def logged_items(self):
-        """Dictionary of all items that have entries in the log, and their currently assigned `LogLevel`\\s
+        """Dictionary of all items that have entries in the log, and their currently assigned `LogCondition`\\s
         This is a convenience method that calls the `logged_items <Log.logged_items>` property of the Component's
         `log <Component.log>`.
         """

diff --git a/psyneulink/components/mechanisms/processing/transfermechanism.py b/psyneulink/components/mechanisms/processing/transfermechanism.py
@@ -140,6 +140,15 @@
 <OutputState.value>` of each of its `OutputStates <OutputState>`, and to the 1st item of the Mechanism's
 `output_values <TransferMechanism.output_values>` attribute.
 
+COMMENT:
+.. _Transfer_Examples:
+
+Examples
+--------
+
+EXAMPLES HERE
+COMMENT
+
 .. _Transfer_Class_Reference:
 
 Class Reference

diff --git a/psyneulink/components/projections/modulatory/modulatoryprojection.py b/psyneulink/components/projections/modulatory/modulatoryprojection.py
@@ -86,7 +86,7 @@
 from psyneulink.components.component import InitStatus
 from psyneulink.components.projections.projection import Projection_Base
 from psyneulink.globals.keywords import EXECUTING, INITIALIZING, MODULATORY_PROJECTION, NAME, kwAssign
-from psyneulink.globals.log import LogEntry, LogLevel
+from psyneulink.globals.log import LogEntry, LogCondition
 
 
 __all__ = [

diff --git a/psyneulink/components/projections/pathway/mappingprojection.py b/psyneulink/components/projections/pathway/mappingprojection.py
@@ -265,7 +265,7 @@
 from psyneulink.components.projections.projection import ProjectionError, Projection_Base, projection_keywords
 from psyneulink.components.states.outputstate import OutputState
 from psyneulink.globals.keywords import AUTO_ASSIGN_MATRIX, CHANGED, DEFAULT_MATRIX, EXECUTING, FULL_CONNECTIVITY_MATRIX, FUNCTION, FUNCTION_PARAMS, HOLLOW_MATRIX, IDENTITY_MATRIX, INITIALIZING, INPUT_STATE, LEARNING, LEARNING_PROJECTION, MAPPING_PROJECTION, MATRIX, OUTPUT_STATE, PROCESS_INPUT_STATE, PROJECTION_SENDER, PROJECTION_SENDER_VALUE, SYSTEM_INPUT_STATE, VALUE, kwAssign
-from psyneulink.globals.log import LogEntry, LogLevel
+from psyneulink.globals.log import LogEntry, LogCondition
 from psyneulink.globals.preferences.componentpreferenceset import is_pref_set
 from psyneulink.globals.preferences.preferenceset import PreferenceEntry, PreferenceLevel
 

diff --git a/psyneulink/components/projections/projection.py b/psyneulink/components/projections/projection.py
@@ -396,7 +396,7 @@
 from psyneulink.globals.registry import register_category
 from psyneulink.globals.utilities import ContentAddressableList, is_matrix, is_numeric, iscompatible, type_match
 from psyneulink.globals.utilities import ContentAddressableList, iscompatible, is_numeric, is_matrix, type_match
-from psyneulink.globals.log import LogLevel, LogEntry, _get_log_context
+from psyneulink.globals.log import LogCondition, LogEntry, _get_log_context
 
 __all__ = [
     'kpProjectionTimeScaleLogEntry', 'Projection_Base', 'projection_keywords', 'PROJECTION_SPEC_KEYWORDS', 'ProjectionError',

diff --git a/psyneulink/components/states/modulatorysignals/controlsignal.py b/psyneulink/components/states/modulatorysignals/controlsignal.py
@@ -304,7 +304,7 @@
 from psyneulink.components.states.state import State_Base
 from psyneulink.globals.defaults import defaultControlAllocation
 from psyneulink.globals.keywords import ALLOCATION_SAMPLES, AUTO, COMMAND_LINE, CONTROLLED_PARAMS, CONTROL_PROJECTION, CONTROL_SIGNAL, EXECUTING, FUNCTION, FUNCTION_PARAMS, INTERCEPT, OFF, ON, OUTPUT_STATE_PARAMS, PARAMETER_STATE, PARAMETER_STATES, PROJECTION_TYPE, RECEIVER, SEPARATOR_BAR, SLOPE, SUM, kwAssign
-from psyneulink.globals.log import LogEntry, LogLevel
+from psyneulink.globals.log import LogEntry, LogCondition
 from psyneulink.globals.preferences.componentpreferenceset import is_pref_set
 from psyneulink.globals.preferences.preferenceset import PreferenceLevel
 from psyneulink.globals.utilities import is_numeric, iscompatible, kwCompatibilityLength, kwCompatibilityNumeric, kwCompatibilityType
@@ -975,9 +975,9 @@ def update(self, params=None, time_scale=TimeScale.TRIAL, context=None):
             context = context + SEPARATOR_BAR + self.name + kwAssign
 
         # If context is consistent with log_pref:
-        if (log_pref is LogLevel.ALL_ASSIGNMENTS or
-                (log_pref is LogLevel.EXECUTION and EXECUTING in context) or
-                (log_pref is LogLevel.VALUE_ASSIGNMENT and (EXECUTING in context))):
+        if (log_pref is LogCondition.ALL_ASSIGNMENTS or
+                (log_pref is LogCondition.EXECUTION and EXECUTING in context) or
+                (log_pref is LogCondition.VALUE_ASSIGNMENT and (EXECUTING in context))):
             # record info in log
 
 # FIX: ENCODE ALL OF THIS AS 1D ARRAYS IN 2D PROJECTION VALUE, AND PASS TO .value FOR LOGGING

diff --git a/psyneulink/components/system.py b/psyneulink/components/system.py
@@ -198,10 +198,11 @@
 The `scheduler_processing` can be assigned in the **scheduler** argument of the System's constructor;  if it is not
 specified, a default `Scheduler` is created automatically.   The `scheduler_learning` is always assigned automatically.
 The System's Schedulers base the ordering of execution of its Components based on the order in which they are listed
-in the `pathway <Process.pathway>`\\s of the `Proceses <Process>` used to construct the System, constrained by any
+in the `pathway <Process.pathway>`\\s of the `Processes <Process>` used to construct the System, constrained by any
 `Conditions <Condition>` that have been created for individual Components and assigned to the System's Schedulers (see
 `Scheduler`, `Condition <Condition_Creation>`, `System_Execution_Processing`, and `System_Execution_Learning` for
-additional details).
+additional details).  Both schedulers maintain a `Clock` that can be used to access their current `time
+<Time_Overview>`.
 
 .. _System_Control:
 

diff --git a/psyneulink/globals/keywords.py b/psyneulink/globals/keywords.py
@@ -52,7 +52,7 @@
     'INTEGRATOR_MECHANISM', 'INTERCEPT', 'INTERNAL', 'K_VALUE', 'kpMechanismControlAllocationsLogEntry',
     'kpMechanismExecutedLogEntry', 'kpMechanismInputLogEntry', 'kpMechanismOutputLogEntry', 'kpMechanismTimeScaleLogEntry',
     'kwAddInputState', 'kwAddOutputState', 'kwAggregate', 'kwAssign', 'kwComponentCategory', 'kwComponentPreferenceSet',
-    'kwContext', 'kwDefaultPreferenceSetOwner', 'kwInitialPoint', 'kwInstantiate', 'kwMechanismAdjustFunction',
+    'kwDefaultPreferenceSetOwner', 'kwInitialPoint', 'kwInstantiate', 'kwMechanismAdjustFunction',
     'kwMechanismComponentCategory', 'kwMechanismConfidence', 'kwMechanismDefault', 'kwMechanismDefaultInputValue',
     'kwMechanismDefaultParams', 'kwMechanismDuration', 'kwMechanismExecuteFunction', 'kwMechanismExecutionSequenceTemplate',
     'kwMechanismInterrogateFunction', 'kwMechanismName', 'kwMechanismOutputValue', 'kwMechanismParams',
@@ -61,7 +61,7 @@
     'kwPrefsOwner', 'kwProcessComponentCategory', 'kwProcessDefaultMechanism', 'kwProcessDefaultProjectionFunction',
     'kwProcessExecute', 'kwProgressBarChar', 'kwProjectionComponentCategory', 'kwProjectionReceiver', 'kwProjections',
     'kwReceiverArg', 'kwSeparator', 'kwStateComponentCategory', 'kwStateContext', 'kwStateName', 'kwStatePrefs',
-    'kwSystemComponentCategory', 'KWTA', 'kwThreshold', 'kwTime', 'kwValue', 'LCA', 'LEARNED_PARAM', 'LEARNING',
+    'kwSystemComponentCategory', 'KWTA', 'kwThreshold', 'LCA', 'LEARNED_PARAM', 'LEARNING',
     'LEARNING_FUNCTION_TYPE', 'LEARNING_MECHANISM', 'LEARNING_PROJECTION', 'LEARNING_PROJECTION_PARAMS', 'LEARNING_RATE',
     'LEARNING_SIGNAL', 'LEARNING_SIGNAL_SPECS', 'LEARNING_SIGNALS', 'LINEAR', 'LINEAR_COMBINATION_FUNCTION',
     'LINEAR_FUNCTION', 'LINEAR_MATRIX_FUNCTION', 'LOG_ENTRIES', 'LOGISTIC_FUNCTION', 'LOW',
@@ -84,7 +84,7 @@
     'SIMPLE', 'SIMPLE_INTEGRATOR_FUNCTION', 'SINGLETON', 'SIZE', 'SLOPE', 'SOFT_CLAMP', 'SOFTMAX_FUNCTION',
     'STABILITY_FUNCTION', 'STANDARD_ARGS','STANDARD_DEVIATION', 'STANDARD_OUTPUT_STATES', 'STATE', 'STATE_PARAMS',
     'STATE_TYPE', 'STATE_VALUE', 'STATES', 'SUBTRACTION', 'SUM', 'SYSTEM', 'SYSTEM_DEFAULT_CONTROLLER',
-    'SYSTEM_INIT', 'TARGET', 'TERMINAL', 'THRESHOLD', 'TIME_SCALE', 'TIME_STEP_SIZE', 'TIME_STEPS_DIM',
+    'SYSTEM_INIT', 'TARGET', 'TERMINAL', 'THRESHOLD', 'TIME', 'TIME_SCALE', 'TIME_STEP_SIZE', 'TIME_STEPS_DIM',
     'TRANSFER_FUNCTION_TYPE', 'TRANSFER_MECHANISM', 'TRIALS_DIM', 'UNCHANGED', 'UNIFORM_DIST_FUNCTION',
     'USER_DEFINED_FUNCTION', 'USER_DEFINED_FUNCTION_TYPE', 'USER_PARAMS', 'UTILITY_INTEGRATOR_FUNCTION',
     'VALIDATE', 'VALIDATION', 'VALUE', 'VALUE_ASSIGNMENT', 'VALUE_FUNCTION', 'VARIABLE', 'VARIANCE', 'VECTOR',
@@ -378,9 +378,7 @@ def _is_metric(metric):
 
 #region ------------------------------------------------   LOG    ------------------------------------------------------
 
-kwTime = 'Time'
-kwContext = 'Context'
-kwValue = 'Value'
+TIME = 'time'
 LOG_ENTRIES = 'LOG_ENTRIES'
 INITIALIZATION = 'INITIALIZATION'
 VALIDATION = 'VALIDATION'