Merge branch 'develop' into multiEnv

ibllib/io/extractors/ephys_passive.py

@@ -86,22 +86,39 @@ def _load_passive_session_fixtures(session_path: str, task_collection: str = 'ra
     return fixture
 
 
-def _load_task_protocol(session_path: str, task_collection: str = 'raw_passive_data') -> str:
+def _load_task_version(session_path: str, task_collection: str = 'raw_passive_data') -> str:
     """Find the IBL rig version used for the session
 
     :param session_path: the path to a session
     :type session_path: str
     :return: ibl rig task protocol version
     :rtype: str
 
-    FIXME This function has a misleading name
     """
     settings = rawio.load_settings(session_path, task_collection=task_collection)
     ses_ver = settings["IBLRIG_VERSION"]
 
     return ses_ver
 
 
+def skip_task_replay(session_path: str, task_collection: str = 'raw_passive_data') -> bool:
+    """Find whether the task replay portion of the passive stimulus has been shown
+
+    :param session_path: the path to a session
+    :type session_path: str
+    :param task_collection: collection containing task data
+    :type task_collection: str
+    :return: whether or not the task replay has been run
+    :rtype: bool
+    """
+
+    settings = rawio.load_settings(session_path, task_collection=task_collection)
+    # Attempt to see if SKIP_EVENT_REPLAY is available, if not assume we do have task replay
+    skip_replay = settings.get('SKIP_EVENT_REPLAY', False)
+
+    return skip_replay
+
+
 def _load_passive_stim_meta() -> dict:
     """load_passive_stim_meta Loads the passive protocol metadata
 
@@ -536,7 +553,7 @@ def extract_task_replay(
     bpod = ephys_fpga.get_sync_fronts(sync, sync_map["bpod"], tmin=treplay[0], tmax=treplay[1])
     passiveValve_intervals = _extract_passiveValve_intervals(bpod)
 
-    task_version = _load_task_protocol(session_path, task_collection)
+    task_version = _load_task_version(session_path, task_collection)
     audio = ephys_fpga.get_sync_fronts(sync, sync_map["audio"], tmin=treplay[0], tmax=treplay[1])
     passiveTone_intervals, passiveNoise_intervals = _extract_passiveAudio_intervals(audio, task_version)
 
@@ -588,7 +605,7 @@ def extract_replay_debug(
     passiveValve_intervals = _extract_passiveValve_intervals(bpod)
     plot_valve_times(passiveValve_intervals, ax=ax)
 
-    task_version = _load_task_protocol(session_path, task_collection)
+    task_version = _load_task_version(session_path, task_collection)
     audio = ephys_fpga.get_sync_fronts(sync, sync_map["audio"], tmin=treplay[0])
     passiveTone_intervals, passiveNoise_intervals = _extract_passiveAudio_intervals(audio, task_version)
     plot_audio_times(passiveTone_intervals, passiveNoise_intervals, ax=ax)
@@ -647,13 +664,19 @@ def _extract(self, sync_collection: str = 'raw_ephys_data', task_collection: str
             log.error(f"Failed to extract RFMapping datasets: {e}")
             passiveRFM_times = None
 
-        try:
-            (passiveGabor_df, passiveStims_df,) = extract_task_replay(
-                self.session_path, sync_collection=sync_collection, task_collection=task_collection, sync=sync,
-                sync_map=sync_map, treplay=treplay)
-        except Exception as e:
-            log.error(f"Failed to extract task replay stimuli: {e}")
+        skip_replay = skip_task_replay(self.session_path, task_collection)
+        if not skip_replay:
+            try:
+                (passiveGabor_df, passiveStims_df,) = extract_task_replay(
+                    self.session_path, sync_collection=sync_collection, task_collection=task_collection, sync=sync,
+                    sync_map=sync_map, treplay=treplay)
+            except Exception as e:
+                log.error(f"Failed to extract task replay stimuli: {e}")
+                passiveGabor_df, passiveStims_df = (None, None)
+        else:
+            # If we don't have task replay then we set the treplay intervals to NaN in our passivePeriods_df dataset
             passiveGabor_df, passiveStims_df = (None, None)
+            passivePeriods_df.taskReplay = np.NAN
 
         if plot:
             f, ax = plt.subplots(1, 1)

ibllib/pipes/behavior_tasks.py

@@ -184,17 +184,17 @@ def signature(self):
         signature = {
             'input_files': [],
             'output_files': [('_iblrig_taskSettings.raw.*', self.collection, True),
-                             ('_iblrig_encoderEvents.raw*', self.collection, True),
-                             ('_iblrig_encoderPositions.raw*', self.collection, True),
-                             ('_iblrig_encoderTrialInfo.raw*', self.collection, True),
-                             ('_iblrig_stimPositionScreen.raw*', self.collection, True),
-                             ('_iblrig_syncSquareUpdate.raw*', self.collection, True),
+                             ('_iblrig_encoderEvents.raw*', self.collection, False),
+                             ('_iblrig_encoderPositions.raw*', self.collection, False),
+                             ('_iblrig_encoderTrialInfo.raw*', self.collection, False),
+                             ('_iblrig_stimPositionScreen.raw*', self.collection, False),
+                             ('_iblrig_syncSquareUpdate.raw*', self.collection, False),
                              ('_iblrig_RFMapStim.raw*', self.collection, True)]
         }
         return signature
 
 
-class PassiveTask(base_tasks.BehaviourTask):
+class PassiveTaskNidq(base_tasks.BehaviourTask):
     priority = 90
     job_size = 'small'
 
@@ -208,10 +208,10 @@ def signature(self):
                             (f'_{self.sync_namespace}_sync.times.*', self.sync_collection, True),
                             ('*.wiring.json', self.sync_collection, False),
                             ('*.meta', self.sync_collection, False)],
-            'output_files': [('_ibl_passiveGabor.table.csv', self.output_collection, True),
+            'output_files': [('_ibl_passiveGabor.table.csv', self.output_collection, False),
                              ('_ibl_passivePeriods.intervalsTable.csv', self.output_collection, True),
                              ('_ibl_passiveRFM.times.npy', self.output_collection, True),
-                             ('_ibl_passiveStims.table.csv', self.output_collection, True)]
+                             ('_ibl_passiveStims.table.csv', self.output_collection, False)]
         }
         return signature
 
@@ -240,10 +240,10 @@ def signature(self):
                             (f'_{self.sync_namespace}_sync.channels.*', self.sync_collection, False),
                             (f'_{self.sync_namespace}_sync.polarities.*', self.sync_collection, False),
                             (f'_{self.sync_namespace}_sync.times.*', self.sync_collection, False)],
-            'output_files': [('_ibl_passiveGabor.table.csv', self.output_collection, True),
+            'output_files': [('_ibl_passiveGabor.table.csv', self.output_collection, False),
                              ('_ibl_passivePeriods.intervalsTable.csv', self.output_collection, True),
                              ('_ibl_passiveRFM.times.npy', self.output_collection, True),
-                             ('_ibl_passiveStims.table.csv', self.output_collection, True)]
+                             ('_ibl_passiveStims.table.csv', self.output_collection, False)]
         }
         return signature
 

ibllib/pipes/dynamic_pipeline.py

@@ -279,7 +279,7 @@ def make_pipeline(session_path, **pkwargs):
             # -   choice_world_habituation
             if 'passiveChoiceWorld' in protocol:
                 registration_class = btasks.PassiveRegisterRaw
-                behaviour_class = btasks.PassiveTask
+                behaviour_class = getattr(btasks, 'PassiveTask' + sync_label.capitalize())
                 compute_status = False
             elif 'habituation' in protocol:
                 registration_class = btasks.HabituationRegisterRaw

ibllib/tests/qc/test_task_qc_viewer.py

@@ -8,7 +8,7 @@
 
 from ibllib.pipes.ephys_preprocessing import EphysTrials
 from ibllib.pipes.training_preprocessing import TrainingTrials
-from ibllib.pipes.behavior_tasks import HabituationTrialsBpod, ChoiceWorldTrialsNidq, ChoiceWorldTrialsBpod, PassiveTask
+from ibllib.pipes.behavior_tasks import HabituationTrialsBpod, ChoiceWorldTrialsNidq, ChoiceWorldTrialsBpod, PassiveTaskNidq
 from ibllib.qc.task_qc_viewer.task_qc import get_bpod_trials_task, show_session_task_qc, QcFrame
 from ibllib.qc.task_metrics import TaskQC
 from ibllib.tests import TEST_DB
@@ -65,7 +65,7 @@ def test_show_session_task_qc(self, trials_tasks_mock, run_app_mock):
         self.assertRaises(TypeError, show_session_task_qc, session_path, one=self.one, protocol_number=-2)
         self.assertRaises(ValueError, show_session_task_qc, session_path, one=self.one, protocol_number=1)
 
-        passive_task = PassiveTask('foo/bar', protocol='_iblrig_passiveChoiceWorld', protocol_number=0)
+        passive_task = PassiveTaskNidq('foo/bar', protocol='_iblrig_passiveChoiceWorld', protocol_number=0)
         trials_tasks_mock.return_value = [passive_task]
         self.assertRaises(ValueError, show_session_task_qc, session_path, one=self.one, protocol_number=0)
         self.assertRaises(ValueError, show_session_task_qc, session_path, one=self.one)