Merge pull request #372 from int-brain-lab/empty_timestamps

Handle empty timestamps in video compression and qc

Author: k1o0

ibllib/io/extractors/camera.py

@@ -123,6 +123,9 @@ def _extract(self, sync=None, chmap=None, video_path=None,
                     count = count[:length]
                 else:
                     assert length == count.size, 'fewer counts than frames'
+                raw_ts = fpga_times[self.label]
+                assert raw_ts.shape[0] > 0, 'no timestamps found in channel indicated for ' \
+                                            f'{self.label} camera'
                 return align_with_audio(raw_ts, audio, gpio, count,
                                         display=display,
                                         extrapolate_missing=extrapolate_missing)

ibllib/qc/camera.py

@@ -347,8 +347,11 @@ def run(self, update: bool = False, **kwargs) -> (str, dict):
         namespace = f'video{self.label.capitalize()}'
         if all(x is None for x in self.data.values()):
             self.load_data(**kwargs)
-        if self.data['frame_samples'] is None:
+        if self.data['frame_samples'] is None or self.data['timestamps'] is None:
             return 'NOT_SET', {}
+        if self.data['timestamps'].shape[0] == 0:
+            _log.error(f'No timestamps for {self.label} camera; setting outcome to CRITICAL')
+            return 'CRITICAL', {}
 
         def is_metric(x):
             return isfunction(x) and x.__name__.startswith('check_')