Merge pull request #405 from int-brain-lab/hotfix/2.3.2

bugfix: training wheel extraction more robust

ibllib/io/extractors/training_wheel.py

@@ -4,6 +4,7 @@
 import numpy as np
 from scipy import interpolate
 
+from ibllib.dsp.utils import sync_timestamps
 from ibllib.io.extractors import training_trials
 from ibllib.io.extractors.base import BaseBpodTrialsExtractor, run_extractor_classes
 import ibllib.io.raw_data_loaders as raw
@@ -73,6 +74,12 @@ def sync_rotary_encoder(session_path, bpod_data=None, re_events=None):
     else:
         bp, re = raw.sync_trials_robust(bpod['closed_loop'], rote['closed_loop'],
                                         diff_threshold=DIFF_THRESHOLD, max_shift=5)
+        # we dont' want to change the extractor, but in rare cases the following method may save the day
+        if len(bp) == 0:
+            _, _, ib, ir = sync_timestamps(bpod['closed_loop'], rote['closed_loop'], return_indices=True)
+            bp = bpod['closed_loop'][ib]
+            re = rote['closed_loop'][ir]
+
         indko = np.array([])
         # raise ValueError("Can't sync bpod and rotary encoder: non-contiguous sync pulses")
     # remove faulty indices due to missing or bad syncs

ibllib/pipes/tasks.py

@@ -95,8 +95,8 @@ def run(self, **kwargs):
             _logger.info(f"Running on machine: {self.machine}")
         _logger.info(f"running ibllib version {version.ibllib()}")
         # setup
+        start_time = time.time()
         try:
-            start_time = time.time()
             setup = self.setUp(**kwargs)
             _logger.info(f"Setup value is: {setup}")
             self.status = 0
@@ -117,7 +117,8 @@ def run(self, **kwargs):
             _logger.error(traceback.format_exc())
             _logger.info(f"Job {self.__class__} errored")
             self.status = -1
-            self.time_elapsed_secs = time.time() - start_time
+
+        self.time_elapsed_secs = time.time() - start_time
 
         # log the outputs
         if isinstance(self.outputs, list):

ibllib/pipes/training_preprocessing.py

@@ -25,6 +25,31 @@ def _run(self, overwrite=False):
 class TrainingTrials(tasks.Task):
     priority = 90
     level = 0
+    force = False
+    signature = {
+        'input_files': [('_iblrig_taskData.raw.*', 'raw_behavior_data', True),
+                        ('_iblrig_taskSettings.raw.*', 'raw_behavior_data', True),
+                        ('_iblrig_encoderEvents.raw*', 'raw_behavior_data', True),
+                        ('_iblrig_encoderPositions.raw*', 'raw_behavior_data', True)],
+        'output_files': [('*trials.choice.npy', 'alf', True),
+                         ('*trials.contrastLeft.npy', 'alf', True),
+                         ('*trials.contrastRight.npy', 'alf', True),
+                         ('*trials.feedbackType.npy', 'alf', True),
+                         ('*trials.feedback_times.npy', 'alf', True),
+                         ('*trials.firstMovement_times.npy', 'alf', True),
+                         ('*trials.goCueTrigger_times.npy', 'alf', True),
+                         ('*trials.goCue_times.npy', 'alf', True),
+                         ('*trials.intervals.npy', 'alf', True),
+                         ('*trials.itiDuration.npy', 'alf', False),
+                         ('*trials.probabilityLeft.npy', 'alf', True),
+                         ('*trials.response_times.npy', 'alf', True),
+                         ('*trials.rewardVolume.npy', 'alf', True),
+                         ('*trials.stimOn_times.npy', 'alf', True),
+                         ('*wheel.position.npy', 'alf', True),
+                         ('*wheel.timestamps.npy', 'alf', True),
+                         ('*wheelMoves.intervals.npy', 'alf', True),
+                         ('*wheelMoves.peakAmplitude.npy', 'alf', True)]
+    }
 
     def _run(self):
         """

release_notes.md

@@ -1,4 +1,8 @@
 ## Release Notes 2.3
+### Release Notes 2.3.1 2021-11-08
+- Trial wheel extraction: use alternative sync method when first on fails
+- bugfix: timer for tasks was returning None
+
 ### Release Notes 2.3.1 2021-11-5
 - Add setup method in tasks.py into try except to catch globus download errors
 

setup.py

@@ -24,7 +24,7 @@
 
 setup(
     name='ibllib',
-    version='2.3.1',
+    version='2.3.2',
     python_requires='>={}.{}'.format(*REQUIRED_PYTHON),
     description='IBL libraries',
     license="MIT",