allensdk.brain_observatory.behavior.data_objects.licks module

class allensdk.brain_observatory.behavior.data_objects.licks.Licks(licks: DataFrame)

Bases: DataObject, StimulusFileReadableInterface, NwbReadableInterface, NwbWritableInterface

classmethod from_nwb(nwbfile: NWBFile) → Licks | None

Populate a DataObject from a pyNWB file object.

Parameters:

nwbfile:

The file object (NWBFile) of a pynwb dataset file.

Returns:

DataObject:

An instantiated DataObject which has name and value properties

classmethod from_stimulus_file(stimulus_file: BehaviorStimulusFile, stimulus_timestamps: StimulusTimestamps | ndarray) → Licks

Get lick data from pkl file. This function assumes that the first sensor in the list of lick_sensors is the desired lick sensor.

Since licks can occur outside of a trial context, the lick times are extracted from the vsyncs and the frame number in lick_events. Since we don’t have a timestamp for when in “experiment time” the vsync stream starts (from self.get_stimulus_timestamps), we compute it by fitting a linear regression (frame number x time) for the start_trial and end_trial events in the trial_log, to true up these time streams.

Parameters:

stimulus_fileBehaviorStimulusFile

Input Behavior stims loaded from a pickle file.

stimulus_timestampsStimulusTimestamps or np.ndarray

Timestamps containing lick data either in a StimulusTimestamps object or numpy array. Numpy array data must be the SyncFile line named lick_times.

Returns:

Licks instance

to_nwb(nwbfile: NWBFile) → NWBFile

Given an already populated DataObject, return an pyNWB file object that had had DataObject data added.

Parameters:

nwbfileNWBFile

An NWB file object

Returns:

NWBFile

An NWB file object that has had data from the DataObject added to it.