Merge pull request #689 from int-brain-lab/hotfix/2.27.1

Correct handling of missing TTLs in FpgaTrialsHabituation

Author: k1o0

ibllib/__init__.py

@@ -2,7 +2,7 @@
 import logging
 import warnings
 
-__version__ = '2.27'
+__version__ = '2.27.1'
 warnings.filterwarnings('always', category=DeprecationWarning, module='ibllib')
 
 # if this becomes a full-blown library we should let the logging configuration to the discretion of the dev

ibllib/io/extractors/ephys_fpga.py

@@ -1376,7 +1376,6 @@ def build_trials(self, sync, chmap, display=False, **kwargs):
             'intervals_1': bpod_event_intervals['trial_iti'][:, 0],
             'goCue_times': audio_event_intervals['ready_tone'][:, 0]
         })
-        n_trials = self.bpod_trials['intervals'].shape[0]
 
         # Sync the Bpod clock to the DAQ.
         self.bpod2fpga, drift_ppm, ibpod, ifpga = self.sync_bpod_clock(self.bpod_trials, fpga_events, self.sync_field)
@@ -1390,26 +1389,25 @@ def build_trials(self, sync, chmap, display=False, **kwargs):
         # Assigning each event to a trial ensures exactly one event per trial (missing events are NaN)
         assign_to_trial = partial(_assign_events_to_trial, fpga_events['intervals_0'])
         trials = alfio.AlfBunch({
-            'goCue_times': assign_to_trial(fpga_events['goCue_times'], take='first')[:n_trials],
-            'feedback_times': assign_to_trial(fpga_events['feedback_times'])[:n_trials],
-            'stimCenter_times': assign_to_trial(self.frame2ttl['times'], take=-2)[:n_trials],
-            'stimOn_times': assign_to_trial(self.frame2ttl['times'], take='first')[:n_trials],
-            'stimOff_times': assign_to_trial(self.frame2ttl['times'])[:n_trials],
+            'goCue_times': assign_to_trial(fpga_events['goCue_times'], take='first'),
+            'feedback_times': assign_to_trial(fpga_events['feedback_times']),
+            'stimCenter_times': assign_to_trial(self.frame2ttl['times'], take=-2),
+            'stimOn_times': assign_to_trial(self.frame2ttl['times'], take='first'),
+            'stimOff_times': assign_to_trial(self.frame2ttl['times']),
         })
+        out.update({k: trials[k][ifpga] for k in trials.keys()})
 
         # If stim on occurs before trial end, use stim on time. Likewise for trial end and stim off
-        to_correct = ~np.isnan(trials['stimOn_times']) & (trials['stimOn_times'] < out['intervals'][:, 0])
+        to_correct = ~np.isnan(out['stimOn_times']) & (out['stimOn_times'] < out['intervals'][:, 0])
         if np.any(to_correct):
             _logger.warning('%i/%i stim on events occurring outside trial intervals', sum(to_correct), len(to_correct))
-            out['intervals'][to_correct, 0] = trials['stimOn_times'][to_correct]
-        to_correct = ~np.isnan(trials['stimOff_times']) & (trials['stimOff_times'] > out['intervals'][:, 1])
+            out['intervals'][to_correct, 0] = out['stimOn_times'][to_correct]
+        to_correct = ~np.isnan(out['stimOff_times']) & (out['stimOff_times'] > out['intervals'][:, 1])
         if np.any(to_correct):
             _logger.debug(
                 '%i/%i stim off events occurring outside trial intervals; using stim off times as trial end',
                 sum(to_correct), len(to_correct))
-            out['intervals'][to_correct, 1] = trials['stimOff_times'][to_correct]
-
-        out.update({k: trials[k][ifpga] for k in trials.keys()})
+            out['intervals'][to_correct, 1] = out['stimOff_times'][to_correct]
 
         if display:  # pragma: no cover
             width = 0.5

ibllib/tests/qc/test_alignment_qc.py

@@ -266,16 +266,13 @@ class TestAlignmentQcManual(unittest.TestCase):
     @classmethod
     def setUpClass(cls) -> None:
         rng = np.random.default_rng()
-        data = np.load(Path(Path(__file__).parent.parent.
-                            joinpath('fixtures', 'qc', 'data_alignmentqc_manual.npz')),
-                       allow_pickle=True)
+        fixture_path = Path(__file__).parent.parent.joinpath('fixtures', 'qc')
+        data = np.load(fixture_path / 'data_alignmentqc_manual.npz', allow_pickle=True)
         cls.xyz_picks = (data['xyz_picks'] * 1e6).tolist()
         cls.alignments = data['alignments'].tolist()
         cls.cluster_chns = data['cluster_chns']
 
-        data = np.load(Path(Path(__file__).parent.parent.
-                            joinpath('fixtures', 'qc', 'data_alignmentqc_existing.npz')),
-                       allow_pickle=True)
+        data = np.load(fixture_path / 'data_alignmentqc_existing.npz', allow_pickle=True)
         insertion = data['insertion'].tolist()
         insertion['name'] = ''.join(random.choices(string.ascii_letters, k=5))
         insertion['json'] = {'xyz_picks': cls.xyz_picks}

ibllib/tests/test_oneibl.py

@@ -272,9 +272,6 @@ def setUp(self) -> None:
         }
 
         # makes sure tests start without session created
-        eid = self.one.search(subject=self.subject, date_range='2018-04-01', query_type='remote')
-        for ei in eid:
-            self.one.alyx.rest('sessions', 'delete', id=ei)
         self.td = tempfile.TemporaryDirectory()
         self.session_path = Path(self.td.name).joinpath(self.subject, '2018-04-01', '002')
         self.alf_path = self.session_path.joinpath('alf')
@@ -506,12 +503,14 @@ def tearDown(self) -> None:
         # Delete weighings
         for w in self.one.alyx.rest('subjects', 'read', id=self.subject)['weighings']:
             self.one.alyx.rest('weighings', 'delete', id=w['url'].split('/')[-1])
+        # Delete sessions
+        eid = self.one.search(subject=self.subject, date_range='2018-04-01', query_type='remote')
+        for ei in eid:
+            self.one.alyx.rest('sessions', 'delete', id=ei)
 
     @classmethod
     def tearDownClass(cls) -> None:
-        # Note: datasets deleted in cascade
-        for ses in cls.one.alyx.rest('sessions', 'list', subject=cls.subject, no_cache=True):
-            cls.one.alyx.rest('sessions', 'delete', id=ses['url'][-36:])
+        # Note: sessions and datasets deleted in cascade
         cls.one.alyx.rest('subjects', 'delete', id=cls.subject)
 
 

release_notes.md

@@ -16,6 +16,9 @@
 - trainingPhaseChoiceWorld added to Bpod protocol extractor map fixture
 - Last trial of FPGA sessions now correctly extracted
 - Correct dynamic pipeline extraction of passive choice world trials
+#### 2.27.1
+- Correct handling of missing TTLs in FpgaTrialsHabituation
+
 
 ### other
 - Removed deprecated pyschofit module