add quiescence period extracted file (#606)

* add quiescence period extracted file * Extract quiescence period for ephys sessions * add quiescence period to FPGA extractor * Always create new tag in registration test --------- Co-authored-by: Miles Wells <[email protected]>
int-brain-lab · May 15, 2023 · dbb2c4f · dbb2c4f
1 parent 62c0e53
commit dbb2c4f
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Showing 5 changed files with 10 additions and 14 deletions.
diff --git a/ibllib/io/extractors/biased_trials.py b/ibllib/io/extractors/biased_trials.py
@@ -34,7 +34,7 @@ class ProbaContrasts(BaseBpodTrialsExtractor):
     Bpod pre-generated values for probabilityLeft, contrastLR, phase, quiescence
     """
     save_names = ('_ibl_trials.contrastLeft.npy', '_ibl_trials.contrastRight.npy', None, None,
-                  '_ibl_trials.probabilityLeft.npy', None)
+                  '_ibl_trials.probabilityLeft.npy', '_ibl_trials.quiescencePeriod.npy')
     var_names = ('contrastLeft', 'contrastRight', 'phase',
                  'position', 'probabilityLeft', 'quiescence')
 

diff --git a/ibllib/io/extractors/ephys_fpga.py b/ibllib/io/extractors/ephys_fpga.py
@@ -694,7 +694,7 @@ def get_protocol_period(session_path, protocol_number, bpod_sync):
 class FpgaTrials(extractors_base.BaseExtractor):
     save_names = ('_ibl_trials.intervals_bpod.npy',
                   '_ibl_trials.goCueTrigger_times.npy', None, None, None, None, None, None, None,
-                  '_ibl_trials.stimOff_times.npy', None, None, None, None,
+                  '_ibl_trials.stimOff_times.npy', None, None, None, '_ibl_trials.quiescencePeriod.npy',
                   '_ibl_trials.table.pqt', '_ibl_wheel.timestamps.npy',
                   '_ibl_wheel.position.npy', '_ibl_wheelMoves.intervals.npy',
                   '_ibl_wheelMoves.peakAmplitude.npy')

diff --git a/ibllib/io/extractors/training_trials.py b/ibllib/io/extractors/training_trials.py
@@ -649,7 +649,7 @@ class PhasePosQuiescence(BaseBpodTrialsExtractor):
     """Extracts stimulus phase, position and quiescence from Bpod data.
     For extraction of pre-generated events, use the ProbaContrasts extractor instead.
     """
-    save_names = (None, None, None)
+    save_names = (None, None, '_ibl_trials.quiescencePeriod.npy')
     var_names = ('phase', 'position', 'quiescence')
 
     def _extract(self, **kwargs):

diff --git a/ibllib/tests/extractors/test_ephys_trials.py b/ibllib/tests/extractors/test_ephys_trials.py
@@ -127,5 +127,5 @@ def test_get_probabilityLeft(self):
         self.assertTrue(all([x in [0.2, 0.5, 0.8] for x in np.unique(pLeft1)]))
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     unittest.main(exit=False, verbosity=2)
diff --git a/ibllib/tests/test_oneibl.py b/ibllib/tests/test_oneibl.py
@@ -210,13 +210,9 @@ def setUp(self) -> None:
             self.rev = self.one.alyx.rest('revisions', 'read', id=self.revision)
         except HTTPError:
             self.rev = self.one.alyx.rest('revisions', 'create', data={'name': self.revision})
-        # Create a tag if doesn't already exist
-        try:
-            self.tag = next(x for x in self.one.alyx.rest('tags', 'list')
-                            if x['name'] == 'test_tag')
-        except StopIteration:
-            self.tag = self.one.alyx.rest('tags', 'create',
-                                          data={'name': 'test_tag', 'protected': True})
+        # Create a new tag
+        tag_data = {'name': f'test_tag_{np.random.randint(0, 1e3)}', 'protected': True}
+        self.tag = self.one.alyx.rest('tags', 'create', data=tag_data)
 
     def test_registration_datasets(self):
         # registers a single file
@@ -252,7 +248,7 @@ def test_registration_datasets(self):
         dsets = self.one.alyx.rest('datasets', 'list', session=ses['url'][-36:])
         for d in dsets:
             self.one.alyx.rest('datasets', 'partial_update',
-                               id=d['url'][-36:], data={'tags': ['test_tag']})
+                               id=d['url'][-36:], data={'tags': [self.tag['name']]})
 
         # Test registering with a revision already in the file path, should use this rather than create one with today's date
         flist = list(self.rev_path.glob('*.npy'))
@@ -265,7 +261,7 @@ def test_registration_datasets(self):
         dsets = self.one.alyx.rest('datasets', 'list', session=ses['url'][-36:])
         for d in dsets:
             self.one.alyx.rest('datasets', 'partial_update',
-                               id=d['url'][-36:], data={'tags': ['test_tag']})
+                               id=d['url'][-36:], data={'tags': [self.tag['name']]})
 
         # Register again with revision in file path, it should register to self.revision + a
         flist = list(self.rev_path.glob('*.npy'))
@@ -290,7 +286,7 @@ def test_registration_datasets(self):
         dsets = self.one.alyx.rest('datasets', 'list', session=ses['url'][-36:], no_cache=True)
         for d in dsets:
             self.one.alyx.rest('datasets', 'partial_update',
-                               id=d['url'][-36:], data={'tags': ['test_tag']})
+                               id=d['url'][-36:], data={'tags': [self.tag['name']]})
 
         # Same day revision
         # Need to remake the original files