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)[source]

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)[source]
Returns:

dict of numpy.array, list of filenames

class BaseBpodTrialsExtractor(session_path=None)[source]

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)[source]
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)[source]

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')[source]
get_task_extractor_type(task_name)[source]

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')[source]

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')[source]

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')[source]

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)[source]

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