ibllib.io.extractors.base

Base Extractor classes. A module for the base Extractor classes. The Extractor, given a session path, will extract the processed data from raw hardware files and optionally save them.

Functions

get_bpod_extractor_class	Get the Bpod trials extractor class associated with a given Bpod session.
get_pipeline	Get the pre-processing pipeline name from a session path
get_session_extractor_type	From a session path, loads the settings file, finds the task and checks if extractors exist task names examples:
get_task_extractor_type	Returns the task type string from the full pybpod task name: _iblrig_tasks_biasedChoiceWorld3.7.0 returns "biased" _iblrig_tasks_trainingChoiceWorld3.6.0 returns "training'
get_task_protocol
protocol2extractor	Get the Bpod trials extractor class associated with a given Bpod task protocol.
run_extractor_classes	Run a set of extractors with the same inputs

Classes

BaseBpodTrialsExtractor	Base (abstract) extractor class for bpod jsonable data set Wrps the _extract private method
BaseExtractor	Base extractor class Writing an extractor checklist: - on the child class, overload the _extract method - this method should output one or several numpy.arrays or dataframe with a consistent shape - save_names is a list or a string of filenames, there should be one per dataset - set save_names to None for a dataset that doesn't need saving (could be set dynamically in the _extract method)

class BaseExtractor(session_path=None)

Bases: ABC

Base extractor class Writing an extractor checklist: - on the child class, overload the _extract method - this method should output one or several numpy.arrays or dataframe with a consistent shape - save_names is a list or a string of filenames, there should be one per dataset - set save_names to None for a dataset that doesn’t need saving (could be set dynamically in the _extract method)

Parameters:

session_path (str/Path) – Absolute path of session folder

save_names = None

var_names = None

default_path = PosixPath('alf')

session_path = None

extract(save=False, path_out=None, **kwargs)

Returns:

dict of numpy.array, list of filenames

class BaseBpodTrialsExtractor(session_path=None)

Bases: BaseExtractor

Base (abstract) extractor class for bpod jsonable data set Wrps the _extract private method

Parameters:

session_path (str) – Absolute path of session folder

:param bpod_trials :param settings

bpod_trials = None

settings = None

task_collection = None

extract(bpod_trials=None, settings=None, **kwargs)

Param:

bpod_trials (optional) bpod trials from jsonable in a dictionary

Param:

settings (optional) bpod iblrig settings json file in a dictionary

Param:

save (bool) write output ALF files, defaults to False

Param:

path_out (pathlib.Path) output path (defaults to {session_path}/alf)

Returns:

numpy.ndarray or list of ndarrays, list of filenames

Return type:

dtype(‘float64’)

run_extractor_classes(classes, session_path=None, **kwargs)

Run a set of extractors with the same inputs

Parameters:

• classes – list of Extractor class

• save – True/False

• path_out – (defaults to alf path)

• kwargs – extractor arguments (session_path…)

Returns:

dictionary of arrays, list of files

get_task_protocol(session_path, task_collection='raw_behavior_data')

get_task_extractor_type(task_name)

Returns the task type string from the full pybpod task name: _iblrig_tasks_biasedChoiceWorld3.7.0 returns “biased” _iblrig_tasks_trainingChoiceWorld3.6.0 returns “training’

Parameters:

task_name –

Returns:

one of [‘biased’, ‘habituation’, ‘training’, ‘ephys’, ‘mock_ephys’, ‘sync_ephys’]

get_session_extractor_type(session_path, task_collection='raw_behavior_data')

From a session path, loads the settings file, finds the task and checks if extractors exist task names examples:

Parameters:

session_path –

Returns:

bool

get_pipeline(session_path, task_collection='raw_behavior_data')

Get the pre-processing pipeline name from a session path

Parameters:

session_path –

Returns:

get_bpod_extractor_class(session_path, task_collection='raw_behavior_data')

Get the Bpod trials extractor class associated with a given Bpod session.

Parameters:

• session_path (str, pathlib.Path) – The session path containing Bpod behaviour data.

• task_collection (str) – The session_path subfolder containing the Bpod settings file.

Returns:

The extractor class name.

Return type:

str

protocol2extractor(protocol)

Get the Bpod trials extractor class associated with a given Bpod task protocol.

The Bpod task protocol can be found in the ‘PYBPOD_PROTOCOL’ field of _iblrig_taskSettings.raw.json.

Parameters:

protocol (str) – A Bpod task protocol name.

Returns:

The extractor class name.

Return type:

str