allensdk.internal.brain_observatory.time_sync module¶
-
class
allensdk.internal.brain_observatory.time_sync.
OphysTimeAligner
(sync_file, scanner=None, dff_file=None, stimulus_pkl=None, eye_video=None, behavior_video=None, long_stim_threshold=0.2)[source]¶ Bases:
object
-
behavior_video_timestamps
¶
-
clipped_stim_timestamps
¶ Return the stimulus timestamps with the erroneous initial spike removed (if relevant)
Returns: - timestamps: np.ndarray
An array of stimulus timestamps in seconds with th emonitor delay added
- delta: int
Difference between the length of timestamps and the number of frames reported in the stimulus pickle file, i.e. len(timestamps) - len(pkl_file[‘items’][‘behavior’][‘intervalsms’]
-
corrected_behavior_video_timestamps
¶
-
corrected_eye_video_timestamps
¶
-
corrected_ophys_timestamps
¶
-
corrected_stim_timestamps
¶ The stimulus timestamps corrected for monitor delay
Returns: - timestamps: np.ndarray
An array of stimulus timestamps in seconds with th emonitor delay added
- delta: int
Difference between the length of timestamps and the number of frames reported in the stimulus pickle file, i.e. len(timestamps) - len(pkl_file[‘items’][‘behavior’][‘intervalsms’]
- delay: float
The monitor delay in seconds
-
dataset
¶
-
eye_video_timestamps
¶
-
monitor_delay
¶ The monitor delay (in seconds) associated with the session
-
ophys_timestamps
¶ Get the timestamps for the ophys data.
-
stim_timestamps
¶
-
-
allensdk.internal.brain_observatory.time_sync.
calculate_monitor_delay
(sync_dset, stim_times, photodiode_key, transition_frame_interval=60, max_monitor_delay=0.07)[source]¶ Calculate monitor delay.
-
allensdk.internal.brain_observatory.time_sync.
corrected_video_timestamps
(video_name, timestamps, data_length)[source]¶
-
allensdk.internal.brain_observatory.time_sync.
get_alignment_array
(ref, other, int_method=<ufunc 'floor'>)[source]¶ Generate an alignment array
-
allensdk.internal.brain_observatory.time_sync.
get_keys
(sync_dset: allensdk.brain_observatory.sync_dataset.Dataset) → dict[source]¶ Gets the correct keys for the sync file by searching the sync file line labels. Removes key from the dictionary if it is not in the sync dataset line labels. Args:
sync_dset: The sync dataset to search for keys within- Returns:
- key_dict: dictionary of key value pairs for finding data in the
- sync file
-
allensdk.internal.brain_observatory.time_sync.
get_photodiode_events
(sync_dset, photodiode_key)[source]¶ Returns the photodiode events with the start/stop indicators and the window init flash stripped off. These transitions occur roughly ~1.0s apart, since the sync square changes state every N frames (where N = 60, and frame rate is 60 Hz). Because there are no markers for when the first transition of this type started, we estimate based on the event intervals. For the first valid event, find the first two events that both meet the following criteria:
The next event occurs ~1.0s laterFirst the last valid event, find the first two events that both meet the following criteria:
The last valid event occured ~1.0s before
-
allensdk.internal.brain_observatory.time_sync.
get_real_photodiode_events
(sync_dset, photodiode_key, anomaly_threshold=0.5)[source]¶ Gets the photodiode events with the anomalies removed.