Merge pull request #367 from int-brain-lab/activate_wheel_period

Active wheel period

Author: oliche

ibllib/io/extractors/ephys_fpga.py

@@ -60,20 +60,37 @@
           }
 
 
+def data_for_keys(keys, data):
+    """Check keys exist in 'data' dict and contain values other than None"""
+    return data is not None and all(k in data and data.get(k, None) is not None for k in keys)
+
+
 def get_ibl_sync_map(ef, version):
     """
     Gets default channel map for the version/binary file type combination
     :param ef: ibllib.io.spikeglx.glob_ephys_file dictionary with field 'ap' or 'nidq'
     :return: channel map dictionary
     """
+    # Determine default channel map
     if version == '3A':
         default_chmap = CHMAPS['3A']['ap']
     elif version == '3B':
         if ef.get('nidq', None):
             default_chmap = CHMAPS['3B']['nidq']
         elif ef.get('ap', None):
             default_chmap = CHMAPS['3B']['ap']
-    return spikeglx.get_sync_map(ef['path']) or default_chmap
+    # Try to load channel map from file
+    chmap = spikeglx.get_sync_map(ef['path'])
+    # If chmap provided but not with all keys, fill up with default values
+    if not chmap:
+        return default_chmap
+    else:
+        if data_for_keys(default_chmap.keys(), chmap):
+            return chmap
+        else:
+            _logger.warning("Keys missing from provided channel map, "
+                            "setting missing keys from default channel map")
+            return {**default_chmap, **chmap}
 
 
 def _sync_to_alf(raw_ephys_apfile, output_path=None, save=False, parts=''):

ibllib/qc/camera.py

@@ -274,6 +274,9 @@ def get_active_wheel_period(wheel, duration_range=(3., 20.), display=False):
         edges = np.c_[on, off]
         indices, _ = np.where(np.logical_and(
             np.diff(edges) > duration_range[0], np.diff(edges) < duration_range[1]))
+        if len(indices) == 0:
+            _log.warning('No period of wheel movement found for motion alignment.')
+            return None
         # Pick movement somewhere in the middle
         i = indices[int(indices.size / 2)]
         if display:
@@ -304,7 +307,7 @@ def ensure_required_data(self):
             # Assert 3A probe model; if so download all probe data
             det = self.one.get_details(self.eid, full=True)
             probe_model = next(x['model'] for x in det['probe_insertion'])
-            assert probe_model == '3A', 'raw ephys data not missing'
+            assert probe_model == '3A', 'raw ephys data missing'
             collections += ('raw_ephys_data/probe00', 'raw_ephys_data/probe01')
             assert_unique = False
         for dstype in dtypes:

ibllib/tests/qc/test_camera_qc.py

@@ -252,6 +252,18 @@ def test_check_wheel_alignment(self):
             outcome = self.qc.check_wheel_alignment()
         self.assertEqual('NOT_SET', outcome)
 
+    def test_get_active_wheel_period(self):
+        """Check that warning is raised, period is returned None, and QC is NOT_SET
+         if there is active wheel period to be found"""
+        wheel_keys = ('timestamps', 'position')
+        wheel_data = (np.arange(1000), np.ones(1000))
+        self.qc.data['wheel'] = Bunch(zip(wheel_keys, wheel_data))
+        with self.assertLogs(logging.getLogger('ibllib'), logging.WARNING):
+            period = self.qc.get_active_wheel_period(self.qc.data['wheel'])
+        self.assertEqual(None, period)
+        outcome = self.qc.check_wheel_alignment()
+        self.assertEqual('NOT_SET', outcome)
+
     def test_ensure_data(self):
         self.qc.eid = self.eid
         self.qc.download_data = False