allensdk.brain_observatory.behavior.session_apis.abcs.session_base.behavior_base module¶
-
class
allensdk.brain_observatory.behavior.session_apis.abcs.session_base.behavior_base.BehaviorBase[source]¶ Bases:
abc.ABCAbstract base class implementing required methods for interacting with behavior session data.
Child classes should be instantiated with a fetch API that implements these methods.
-
get_behavior_session_id(self) → int[source]¶ Returns the behavior_session_id associated with this experiment, if applicable.
-
get_licks(self) → pandas.core.frame.DataFrame[source]¶ Get lick data from pkl file.
Returns: - pd.Dataframe
A dataframe containing lick timestamps.
-
get_metadata(self) → Union[allensdk.brain_observatory.behavior.metadata.behavior_metadata.BehaviorMetadata, dict][source]¶ Get metadata for Session
Returns: - dict if NWB
- BehaviorMetadata otherwise
-
get_rewards(self) → pandas.core.frame.DataFrame[source]¶ Get reward data from pkl file.
Returns: - pd.DataFrame
A dataframe containing timestamps of delivered rewards.
-
get_running_acquisition_df(self) → pandas.core.frame.DataFrame[source]¶ Get running speed acquisition data from a behavior pickle file.
Returns: - pd.DataFrame
- Dataframe with an index of timestamps and the following columns:
“speed”: computed running speed “dx”: angular change, computed during data collection “v_sig”: voltage signal from the encoder “v_in”: the theoretical maximum voltage that the encoder
will reach prior to “wrapping”. This should theoretically be 5V (after crossing 5V goes to 0V, or vice versa). In practice the encoder does not always reach this value before wrapping, which can cause transient spikes in speed at the voltage “wraps”.
-
get_running_speed(self) → pandas.core.frame.DataFrame[source]¶ Get running speed using timestamps from self.get_stimulus_timestamps.
NOTE: Do not correct for monitor delay.
Returns: - pd.DataFrame
- timestamps : np.ndarray
index consisting of timestamps of running speed data samples
- speed : np.ndarray
Running speed of the experimental subject (in cm / s).
-
get_stimulus_presentations(self) → pandas.core.frame.DataFrame[source]¶ Get stimulus presentation data.
NOTE: Uses timestamps that do not account for monitor delay.
Returns: - pd.DataFrame
Table whose rows are stimulus presentations (i.e. a given image, for a given duration, typically 250 ms) and whose columns are presentation characteristics.
-
get_stimulus_templates(self) → allensdk.brain_observatory.behavior.stimulus_processing.stimulus_templates.StimulusTemplate[source]¶ Get stimulus templates (movies, scenes) for behavior session.
Returns: - StimulusTemplate
-
get_stimulus_timestamps(self) → numpy.ndarray[source]¶ Get stimulus timestamps from pkl file.
NOTE: Located with behavior_session_id
Returns: - np.ndarray
Timestamps associated with stimulus presentations on the monitor that do no account for monitor delay.
-