Merge pull request #849 from int-brain-lab/camera_fixes

Camera fixes

Author: mayofaulkner

ibllib/io/extractors/video_motion.py

@@ -442,7 +442,6 @@ def fix_keys(alf_object):
         # Compute wheel velocity
         self.wheel_vel, _ = wh.velocity_filtered(wheel_pos, 1000)
         # Load in original camera times
-        self.camera_times = alfio.load_file_content(next(alf_path.rglob(f'_ibl_{self.label}Camera.times*.npy')))
         self.camera_path = str(next(self.session_path.joinpath('raw_video_data').glob(f'_iblrig_{self.label}Camera.raw*.mp4')))
         self.camera_meta = vidio.get_video_meta(self.camera_path)
 
@@ -461,17 +460,25 @@ def fix_keys(alf_object):
         # Check if the ttl and video sizes match up
         self.tdiff = self.ttls.size - self.camera_meta['length']
 
+        # Load in original camera times if available otherwise set to ttls
+        camera_times = next(alf_path.rglob(f'_ibl_{self.label}Camera.times*.npy'), None)
+        self.camera_times = alfio.load_file_content(camera_times) if camera_times else self.ttls
+
         if self.tdiff < 0:
             # In this case there are fewer ttls than camera frames. This is not ideal, for now we pad the ttls with
             # nans but if this is too many we reject the wheel alignment based on the qc
             self.ttl_times = self.ttls
             self.times = np.r_[self.ttl_times, np.full((np.abs(self.tdiff)), np.nan)]
+            if self.camera_times.size != self.camera_meta['length']:
+                self.camera_times = np.r_[self.camera_times, np.full((np.abs(self.tdiff)), np.nan)]
             self.short_flag = True
         elif self.tdiff > 0:
             # In this case there are more ttls than camera frames. This happens often, for now we remove the first
             # tdiff ttls from the ttls
             self.ttl_times = self.ttls[self.tdiff:]
             self.times = self.ttls[self.tdiff:]
+            if self.camera_times.size != self.camera_meta['length']:
+                self.camera_times = self.camera_times[self.tdiff:]
             self.short_flag = False
 
         # Compute the frame rate of the camera

ibllib/pipes/video_tasks.py

@@ -190,7 +190,8 @@ def run_qc(self, camera_data=None, update=True):
         if camera_data is None:
             camera_data, _ = self.extract_camera(save=False)
         qc = run_camera_qc(
-            self.session_path, self.cameras, one=self.one, camlog=True, sync_collection=self.sync_collection, sync_type=self.sync)
+            self.session_path, self.cameras, one=self.one, camlog=True, sync_collection=self.sync_collection, sync_type=self.sync,
+            update=update)
         return qc
 
     def _run(self, update=True, **kwargs):
@@ -284,7 +285,8 @@ def signature(self):
                            [(f'_{self.sync_namespace}_sync.channels.npy', self.sync_collection, True),
                             (f'_{self.sync_namespace}_sync.polarities.npy', self.sync_collection, True),
                             (f'_{self.sync_namespace}_sync.times.npy', self.sync_collection, True),
-                            ('*.wiring.json', self.sync_collection, True),
+                            (f'_{self.sync_namespace}_*.wiring.json', self.sync_collection, False),
+                            (f'_{self.sync_namespace}_*.meta', self.sync_collection, True),
                             ('*wheel.position.npy', 'alf', False),
                             ('*wheel.timestamps.npy', 'alf', False),
                             ('*experiment.description*', '', False)],
@@ -308,7 +310,8 @@ def run_qc(self, camera_data=None, update=True):
         if camera_data is None:
             camera_data, _ = self.extract_camera(save=False)
         qc = run_camera_qc(
-            self.session_path, self.cameras, one=self.one, sync_collection=self.sync_collection, sync_type=self.sync)
+            self.session_path, self.cameras, one=self.one, sync_collection=self.sync_collection, sync_type=self.sync,
+            update=update)
         return qc
 
     def _run(self, update=True, **kwargs):
@@ -347,7 +350,7 @@ def signature(self):
             'input_files': [(f'_iblrig_{cam}Camera.raw.mp4', self.device_collection, True) for cam in self.cameras],
             'output_files': [(f'_ibl_{cam}Camera.dlc.pqt', 'alf', True) for cam in self.cameras] +
                             [(f'{cam}Camera.ROIMotionEnergy.npy', 'alf', True) for cam in self.cameras] +
-                            [(f'{cam}ROIMotionEnergy.position.npy', 'alf', True)for cam in self.cameras]
+                            [(f'{cam}ROIMotionEnergy.position.npy', 'alf', True) for cam in self.cameras]
         }
 
         return signature
@@ -504,8 +507,11 @@ def signature(self):
             # In particular the raw videos don't need to be downloaded as they can be streamed
                            [(f'_iblrig_{cam}Camera.raw.mp4', self.device_collection, True) for cam in self.cameras] +
                            [(f'{cam}ROIMotionEnergy.position.npy', 'alf', False) for cam in self.cameras] +
+                           [(f'{cam}Camera.ROIMotionEnergy.npy', 'alf', False) for cam in self.cameras] +
             # The trials table is used in the DLC QC, however this is not an essential dataset
-                           [('_ibl_trials.table.pqt', self.trials_collection, False)],
+                           [('_ibl_trials.table.pqt', self.trials_collection, False),
+                            ('_ibl_wheel.position.npy', self.trials_collection, False),
+                            ('_ibl_wheel.timestamps.npy', self.trials_collection, False)],
             'output_files': [(f'_ibl_{cam}Camera.features.pqt', 'alf', True) for cam in self.cameras] +
                             [('licks.times.npy', 'alf', True)]
         }
@@ -522,7 +528,7 @@ def _run(self, overwrite=True, run_qc=True, plot_qc=True):
 
         """
         # Check if output files exist locally
-        exist, output_files = self.assert_expected(self.signature['output_files'], silent=True)
+        exist, output_files = self.assert_expected(self.output_files, silent=True)
         if exist and not overwrite:
             _logger.warning('EphysPostDLC outputs exist and overwrite=False, skipping computations of outputs.')
         else:

ibllib/qc/camera.py

@@ -420,10 +420,15 @@ def is_metric(x):
         outcome = max(map(spec.QC.validate, values))
 
         if update:
-            extended = {
-                k: spec.QC.NOT_SET if v is None else v
-                for k, v in self.metrics.items()
-            }
+            extended = dict()
+            for k, v in self.metrics.items():
+                if v is None:
+                    extended[k] = spec.QC.NOT_SET.name
+                elif isinstance(v, tuple):
+                    extended[k] = tuple(i.name if isinstance(i, spec.QC) else i for i in v)
+                else:
+                    extended[k] = v.name
+
             self.update_extended_qc(extended)
             self.update(outcome, namespace)
         return outcome, self.metrics