allensdk.brain_observatory.behavior.data_files.stimulus_file module

class allensdk.brain_observatory.behavior.data_files.stimulus_file.BehaviorStimulusFile(filepath: str | Path)

Bases: _StimulusFile

property behavior_session_uuid: UUID | None

Return the behavior session UUID either from the uuid field or foraging_id field.

property date_of_acquisition: datetime

Return the date_of_acquisition as a datetime.datetime.

This will be read from self.data[‘start_time’]

classmethod file_path_key() → str

The key in the dict_repr that maps to the path to this StimulusFile’s pickle file on disk.

classmethod from_lims(db: PostgresQueryMixin, behavior_session_id: int | str) → BehaviorStimulusFile

Populate a DataFile from an internal database (likely LIMS)

Returns:

DataFile:

An instantiated DataFile which has data and filepath properties

property mouse_id: str

Retrieve the mouse_id value from the stimulus pickle file.

This can be read either from:

data[‘items’][‘behavior’][‘params’][‘stage’] or data[‘items’][‘behavior’][‘cl_params’][‘stage’]

if both are present and they disagree, raise an exception.

property num_frames: int

Return the number of frames associated with this StimulusFile

property session_duration: float

Gets session duration in seconds

Returns:

session duration in seconds

property session_type: str

Return the session type as read from the pickle file. This can be read either from

data[‘items’][‘behavior’][‘params’][‘stage’] or data[‘items’][‘behavior’][‘cl_params’][‘stage’]

if both are present and they disagree, raise an exception

property stimuli: Dict[str, Tuple[str, str | int, int, int]]

Stimuli shown during session

Returns:

stimuli:

(stimulus type (‘Image’ or ‘Grating’),

stimulus descriptor (image_name or orientation of grating in

degrees),

nonsynced time of display, display frame (frame that stimuli was displayed))

property stimulus_name: str

Get the image stimulus name by parsing the file path of the image set.

If no image set, check for gratings and return “behavior” if not found.

Parameters:

stimulus_fileBehaviorStimulusFile

Stimulus pickle file to parse.

Returns:

stimulus_namestr

Name of the image stimulus from the image file path set shown to the mouse.

validate() → BehaviorStimulusFile

exception allensdk.brain_observatory.behavior.data_files.stimulus_file.MalformedStimulusFileError

Bases: RuntimeError

Malformed stimulus file

class allensdk.brain_observatory.behavior.data_files.stimulus_file.MappingStimulusFile(filepath: str | Path)

Bases: _StimulusFile

classmethod file_path_key() → str

The key in the dict_repr that maps to the path to this StimulusFile’s pickle file on disk.

class allensdk.brain_observatory.behavior.data_files.stimulus_file.ReplayStimulusFile(filepath: str | Path)

Bases: _StimulusFile

classmethod file_path_key() → str

The key in the dict_repr that maps to the path to this StimulusFile’s pickle file on disk.

class allensdk.brain_observatory.behavior.data_files.stimulus_file.StimulusFileLookup

Bases: object

A container class to carry around the StimulusFile(s) associated with a BehaviorSession

property behavior_stimulus_file: BehaviorStimulusFile

property mapping_stimulus_file: MappingStimulusFile

property replay_stimulus_file: ReplayStimulusFile

class allensdk.brain_observatory.behavior.data_files.stimulus_file.StimulusFileReadableInterface

Bases: ABC

Marks a data object as readable from stimulus file

abstractmethod classmethod from_stimulus_file(stimulus_file: BehaviorStimulusFile) → DataObject

Populate a DataObject from the stimulus file

Returns:

DataObject:

An instantiated DataObject which has name and value properties

allensdk.brain_observatory.behavior.data_files.stimulus_file.from_json_cache_key(cls, stimulus_file_path: str)

allensdk.brain_observatory.behavior.data_files.stimulus_file.from_lims_cache_key(cls, db, behavior_session_id: int)

allensdk.brain_observatory.behavior.data_files.stimulus_file.stimulus_lookup_from_json(dict_repr: dict) → StimulusFileLookup

Load a lookup table of the stimulus files associated with a BehaviorSession from the dict representation of that session’s session_data