Merge pull request #12 from int-brain-lab/cuedBiasedQC

Fix cuedBiasedChoiceWorld QC and task extractor bug

Author: k1o0

iblrig_custom_tasks/samuel_cuedBiasedChoiceWorld/task.py

@@ -17,15 +17,17 @@ class Session(BiasedChoiceWorldSession):
 
     protocol_name = 'samuel_cuedBiasedChoiceWorld'
 
-    def __init__(self, *args, delay_secs=0, **kwargs):  #SP _init_ should be the same as biasedChoiceWorld, so should it be specified?
+    def __init__(self, *args, delay_secs=0, **kwargs):
         super().__init__(**kwargs)
 
         # loads in the settings in order to determine the main sync and thus the pipeline extractor tasks
         is_main_sync = self.hardware_settings.get('MAIN_SYNC', False)
         trials_task = 'CuedBiasedTrials' if is_main_sync else 'CuedBiasedTrialsTimeline'
         self.extractor_tasks = ['TrialRegisterRaw', trials_task, 'TrainingStatus']
+        # Update experiment description which was created by superclass init
+        next(iter(self.experiment_description['tasks']))['extractors'] = self.extractor_tasks
 
-        self.task_params["SESSION_DELAY_START"] = delay_secs
+        self.task_params['SESSION_DELAY_START'] = delay_secs
         # init behaviour data
         self.movement_left = self.device_rotary_encoder.THRESHOLD_EVENTS[
             self.task_params.QUIESCENCE_THRESHOLDS[0]]

projects/samuel_cuedBiasedChoiceWorld.py

@@ -1,7 +1,8 @@
 """Task QC for samuel_cuedBiasedChoiceWorld.
 
 The task itself is identical to the biasedChoiceWorld except that there is an interactive delay
-between stimOn and goCue.
+between stimOn and goCue.  Critically, the tone plays **before** the visual stimulus onset and is
+therefore not strictly a 'go cue' tone and the delay is not strictly an 'interactive' one.
 
 Mapping the correct Bpod trials extractor is done in `projects.task_extractor_map.json`. The trial
 alignment to the DAQ remains unchanged. The
@@ -27,7 +28,9 @@ def check_stimOn_goCue_delays(self, data, audio_output='harp', **_):
         """
         Verify time delay between audio cue and stimOn is ~equal to the INTERACTIVE_DELAY specified.
 
-        Metric: M = stimOn_times - goCue_times - interactive_delay
+        The so-called goCue is expected to occur before the stimulus onset.
+
+        Metric: M = goCue_times - stimOn_times - interactive_delay
         Criteria: 0 < M < 0.010 s
         Units: seconds [s]
 
@@ -55,7 +58,7 @@ def check_stimOn_goCue_delays(self, data, audio_output='harp', **_):
         # If either are NaN, the result will be Inf to ensure that it crosses the failure threshold.
         threshold = 0.01 if audio_output.lower() == 'harp' else 0.053
         delay = self.extractor.settings['INTERACTIVE_DELAY']
-        metric = np.nan_to_num(data['goCue_times'] - data['stimOn_times'] - delay, nan=np.inf)
+        metric = np.nan_to_num(data['stimOn_times'] - data['goCue_times'] - delay, nan=np.inf)
         passed = (metric < threshold) & (metric > 0)
         assert data['intervals'].shape[0] == len(metric) == len(passed)
         return metric, passed

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name            = "project_extraction"
-version         = "0.2.5"
+version         = "0.2.6"
 description     = "Custom extractors for satellite tasks"
 dynamic         = [ "readme" ]
 keywords        = [ "IBL", "neuro-science" ]