allensdk.brain_observatory.behavior.metadata.behavior_metadata module

class allensdk.brain_observatory.behavior.metadata.behavior_metadata.BehaviorMetadata(extractor: allensdk.brain_observatory.behavior.session_apis.abcs.data_extractor_base.behavior_data_extractor_base.BehaviorDataExtractorBase, stimulus_timestamps: numpy.ndarray, behavior_stimulus_file: dict)

Bases: object

Container class for behavior metadata

age_in_days

Converts the age cod into a numeric days representation

behavior_session_id

behavior_session_uuid

Get the universally unique identifier (UUID)

cre_line

Parses cre_line from full_genotype

date_of_acquisition

Return the timestamp for when experiment was started in UTC

NOTE: This method will only get acquisition datetime from extractor (data from LIMS) methods. As a sanity check, it will also read the acquisition datetime from the behavior stimulus (.pkl) file and raise a warning if the date differs too much from the datetime obtained from the behavior stimulus (.pkl) file.

Return type:datetime

driver_line

equipment_name

full_genotype

get_extractor(self)

mouse_id

reporter_line

There can be multiple reporter lines, so it is returned from LIMS as a list. But there shouldn’t be more than 1 for behavior. This tries to convert to str

Returns:

single reporter line, or None if not possible

session_type

sex

stimulus_frame_rate

to_dict(self) → dict

Returns dict representation of all properties in class

allensdk.brain_observatory.behavior.metadata.behavior_metadata.get_expt_description(session_type: str) → str

Determine a behavior ophys session’s experiment description based on session type. Matches the regex patterns defined as the keys in description_dict

Parameters:

session_type : str

A session description string (e.g. OPHYS_1_images_B )

Returns:

str

A description of the experiment based on the session_type.

Raises:

RuntimeError

Behavior ophys sessions should only have 6 different session types. Unknown session types (or malformed session_type strings) will raise an error.

allensdk.brain_observatory.behavior.metadata.behavior_metadata.get_task_parameters(data: Dict) → Dict

Read task_parameters metadata from the behavior stimulus pickle file.

Parameters:

data: dict

The nested dict read in from the behavior stimulus pickle file. All of the data expected by this method lives under data[‘items’][‘behavior’]

Returns:

dict

A dict containing the task_parameters associated with this session.