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Sess load improv #516

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Merged
juhuntenburg merged 3 commits into from
Sep 26, 2022
Merged

Sess load improv #516

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e980a1e
Bug in pupil loading
juhuntenburg Sep 23, 2022
fae06f5
Don't catch errors in indv loading funcs
juhuntenburg Sep 23, 2022
12ef814
Release notes
juhuntenburg Sep 23, 2022
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41 changes: 17 additions & 24 deletions brainbox/io/one.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1280,16 +1280,12 @@ def load_pose(self, likelihood_thr=0.9, views=['left', 'right', 'body']):
# empty the dictionary so that if one loads only one view, after having loaded several, the others don't linger
self.pose = {}
for view in views:
try:
pose_raw = self.one.load_object(self.eid, f'{view}Camera', attribute=['dlc', 'times'])
# Double check if video timestamps are correct length or can be fixed
times_fixed, dlc = self._check_video_timestamps(view, pose_raw['times'], pose_raw['dlc'])
self.pose[f'{view}Camera'] = likelihood_threshold(dlc, likelihood_thr)
self.pose[f'{view}Camera'].insert(0, 'times', times_fixed)
self.data_info.loc[self.data_info['name'] == 'pose', 'is_loaded'] = True
except BaseException as e:
_logger.warning(f'Could not load pose data for {view}Camera. Skipping camera.')
_logger.debug(e)
pose_raw = self.one.load_object(self.eid, f'{view}Camera', attribute=['dlc', 'times'])
# Double check if video timestamps are correct length or can be fixed
times_fixed, dlc = self._check_video_timestamps(view, pose_raw['times'], pose_raw['dlc'])
self.pose[f'{view}Camera'] = likelihood_threshold(dlc, likelihood_thr)
self.pose[f'{view}Camera'].insert(0, 'times', times_fixed)
self.data_info.loc[self.data_info['name'] == 'pose', 'is_loaded'] = True

def load_motion_energy(self, views=['left', 'right', 'body']):
"""
Expand All @@ -1311,17 +1307,13 @@ def load_motion_energy(self, views=['left', 'right', 'body']):
# empty the dictionary so that if one loads only one view, after having loaded several, the others don't linger
self.motion_energy = {}
for view in views:
try:
me_raw = self.one.load_object(self.eid, f'{view}Camera', attribute=['ROIMotionEnergy', 'times'])
# Double check if video timestamps are correct length or can be fixed
times_fixed, motion_energy = self._check_video_timestamps(
view, me_raw['times'], me_raw['ROIMotionEnergy'])
self.motion_energy[f'{view}Camera'] = pd.DataFrame(columns=[names[view]], data=motion_energy)
self.motion_energy[f'{view}Camera'].insert(0, 'times', times_fixed)
self.data_info.loc[self.data_info['name'] == 'motion_energy', 'is_loaded'] = True
except BaseException as e:
_logger.warning(f'Could not load motion energy data for {view}Camera. Skipping camera.')
_logger.debug(e)
me_raw = self.one.load_object(self.eid, f'{view}Camera', attribute=['ROIMotionEnergy', 'times'])
# Double check if video timestamps are correct length or can be fixed
times_fixed, motion_energy = self._check_video_timestamps(
view, me_raw['times'], me_raw['ROIMotionEnergy'])
self.motion_energy[f'{view}Camera'] = pd.DataFrame(columns=[names[view]], data=motion_energy)
self.motion_energy[f'{view}Camera'].insert(0, 'times', times_fixed)
self.data_info.loc[self.data_info['name'] == 'motion_energy', 'is_loaded'] = True

def load_licks(self):
"""
Expand All @@ -1342,7 +1334,7 @@ def load_pupil(self, snr_thresh=5.):
# Try to load from features
feat_raw = self.one.load_object(self.eid, 'leftCamera', attribute=['times', 'features'])
if 'features' in feat_raw.keys():
times_fixed, feats = self._check_video_timestamps(feat_raw['times'], feat_raw['features'])
times_fixed, feats = self._check_video_timestamps('left', feat_raw['times'], feat_raw['features'])
self.pupil = feats.copy()
self.pupil.insert(0, 'times', times_fixed)

Expand All @@ -1364,7 +1356,8 @@ def load_pupil(self, snr_thresh=5.):
try:
self.pupil['pupilDiameter_smooth'] = get_smooth_pupil_diameter(self.pupil['pupilDiameter_raw'], 'left')
except BaseException as e:
_logger.error("Computing smooth pupil diameter failed, saving all NaNs.")
_logger.error("Loaded raw pupil diameter but computing smooth pupil diameter failed. "
"Saving all NaNs for pupilDiameter_smooth.")
_logger.debug(e)
self.pupil['pupilDiameter_smooth'] = np.nan

Expand All @@ -1375,7 +1368,7 @@ def load_pupil(self, snr_thresh=5.):
(np.var(self.pupil['pupilDiameter_smooth'][good_idxs] - self.pupil['pupilDiameter_raw'][good_idxs])))
if snr < snr_thresh:
self.pupil = pd.DataFrame()
_logger.error(f'Pupil diameter SNR ({snr:.2f}) below threshold SNR ({snr_thresh}), removing data.')
raise ValueError(f'Pupil diameter SNR ({snr:.2f}) below threshold SNR ({snr_thresh}), removing data.')

def _check_video_timestamps(self, view, video_timestamps, video_data):
"""
Expand Down
3 changes: 3 additions & 0 deletions release_notes.md
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Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
## Release Notes 2.15
### Release Notes NOT YET RELEASED
- SessionLoader error handling and bug fix

### Release Notes 2.15.2 - 2022-09-22
- extraction pipeline: fix unpacking of empty arguments field from alyx dict that prevents running task

Expand Down