allensdk.internal.brain_observatory.time_sync module¶
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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
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behavior_video_timestamps
¶
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corrected_behavior_video_timestamps
¶
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corrected_eye_video_timestamps
¶
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corrected_ophys_timestamps
¶
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corrected_stim_timestamps
¶
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dataset
¶
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eye_video_timestamps
¶
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ophys_timestamps
¶ Get the timestamps for the ophys data.
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stim_timestamps
¶
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allensdk.internal.brain_observatory.time_sync.
corrected_video_timestamps
(video_name, timestamps, data_length)[source]¶
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allensdk.internal.brain_observatory.time_sync.
get_alignment_array
(ref, other, int_method=<ufunc 'floor'>)[source]¶ Generate an alignment array
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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
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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
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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.