allensdk.brain_observatory.behavior.sync package¶
Submodules¶
Module contents¶
Created on Sunday July 15 2018
@author: marinag
- allensdk.brain_observatory.behavior.sync.get_behavior_monitoring(dataset: Dataset, permissive: bool = False) ndarray | None [source]¶
Report the timestamps of each frame of the behavior monitoring video
- Parameters:
- datasetdescribes experiment timing
- permissiveIf True, None will be returned if timestamps are not found.
If False, a KeyError will be raised
- Returns:
- array of timestamps (floating point; seconds; relative to experiment
- start) or None. If None, no behavior monitoring timestamps were found in
- this sync dataset.
- allensdk.brain_observatory.behavior.sync.get_eye_tracking(dataset: Dataset, permissive: bool = False) ndarray | None [source]¶
Report the timestamps of each frame of the eye tracking video
- Parameters:
- datasetdescribes experiment timing
- permissiveIf True, None will be returned if timestamps are not found.
If False, a KeyError will be raised
- Returns:
- array of timestamps (floating point; seconds; relative to experiment
- start) or None. If None, no eye tracking timestamps were found in this
- sync dataset.
- allensdk.brain_observatory.behavior.sync.get_lick_times(dataset: Dataset, permissive: bool = False) ndarray | None [source]¶
Report the timestamps of each detected lick
- Parameters:
- datasetdescribes experiment timing
- permissiveIf True, None will be returned if timestamps are not found.
If False, a KeyError will be raised
- Returns:
- array of timestamps (floating point; seconds; relative to experiment
- start)
or None. If None, no lick timestamps were found in this sync dataset.
- allensdk.brain_observatory.behavior.sync.get_ophys_frames(dataset: Dataset, permissive: bool = False) ndarray [source]¶
Report the timestamps of each optical physiology video frame
- Parameters:
- datasetdescribes experiment timing
- permissiveIf True, None will be returned if timestamps are not found.
If False, a KeyError will be raised
- Returns:
- array of timestamps (floating point; seconds; relative to experiment
- start).
Notes
use rising edge for Scientifica, falling edge for Nikon http://confluence.corp.alleninstitute.org/display/IT/Ophys+Time+Sync This function uses rising edges
- allensdk.brain_observatory.behavior.sync.get_raw_stimulus_frames(dataset: Dataset, permissive: bool = False) ndarray [source]¶
Report the raw timestamps of each stimulus frame. This corresponds to the time at which the psychopy window’s flip method returned, but not necessarily to the time at which the stimulus frame was displayed.
- Parameters:
- datasetdescribes experiment timing
- permissiveIf True, None will be returned if timestamps are not found.
If False, a KeyError will be raised
- Returns:
- array of timestamps (floating point; seconds; relative to experiment
- start).
- allensdk.brain_observatory.behavior.sync.get_stim_photodiode(dataset: Dataset, permissive: bool = False) List[float] | None [source]¶
Report the timestamps of each detected sync square transition (both black -> white and white -> black) in this experiment.
- Parameters:
- datasetdescribes experiment timing
- permissiveIf True, None will be returned if timestamps are not found.
If False, a KeyError will be raised
- Returns:
- array of timestamps (floating point; seconds; relative to experiment
- start) or None. If None, no photodiode timestamps were found in this sync
- dataset.
- allensdk.brain_observatory.behavior.sync.get_sync_data(sync_path: str, permissive: bool = False) Dict[str, List | ndarray | None] [source]¶
Convenience function for extracting several timestamp arrays from a sync file.
- Parameters:
- sync_pathThe hdf5 file here ought to be a Visual Behavior sync output
- file. See allensdk.brain_observatory.sync_dataset for more details of
- this format.
- permissiveIf True, None will be returned if timestamps are not found.
If False, a KeyError will be raised
- Returns:
- A dictionary with the following keys. All timestamps in seconds:
ophys_frames : timestamps of each optical physiology frame lick_times : timestamps of each detected lick ophys_trigger : The time at which ophys acquisition was started eye_tracking : timestamps of each eye tracking video frame behavior_monitoring : timestamps of behavior monitoring video frame stim_photodiode : timestamps of each photodiode transition stimulus_times_no_delay : raw stimulus frame timestamps
- Some values may be None. This indicates that the corresponding timestamps
- were not located in this sync file.
- allensdk.brain_observatory.behavior.sync.get_trigger(dataset: Dataset, permissive: bool = False) ndarray | None [source]¶
- Returns (as a 1-element array) the time at which optical physiology
acquisition was started.
- Parameters:
- datasetdescribes experiment timing
- permissiveIf True, None will be returned if timestamps are not found.
If False, a KeyError will be raised
- Returns:
- timestamps (floating point; seconds; relative to experiment start)
- or None. If None, no timestamps were found in this sync dataset.
Notes
Ophys frame timestamps can be recorded before acquisition start when experimenters are setting up the recording session. These do not correspond to acquired ophys frames.