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- property behavior_video_timestamps¶
- property 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’]
- property corrected_behavior_video_timestamps¶
- property corrected_eye_video_timestamps¶
- property corrected_ophys_timestamps¶
- property 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
- property dataset¶
- property eye_video_timestamps¶
- property monitor_delay¶
The monitor delay (in seconds) associated with the session
- property ophys_timestamps¶
Get the timestamps for the ophys data.
- property 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: 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 later
First 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.