oneibl.one

Functions

Listable
ONE
parse_id	Ensures the input experiment identifier is an experiment UUID string :param method: An ONE method whose second arg is an experiment id :return: A wrapper function that parses the id to the expected string

Classes

OneAbstract
OneAlyx
OneOffline

Listable(t)

parse_id(method)

Ensures the input experiment identifier is an experiment UUID string :param method: An ONE method whose second arg is an experiment id :return: A wrapper function that parses the id to the expected string

class OneAbstract(username=None, password=None, base_url=None, cache_dir=None, silent=None)

Bases: abc.ABC

path_from_eid(eid: str) → Optional[Union[pathlib.Path, Sequence[pathlib.Path]]]

From an experiment id or a list of experiment ids, gets the local cache path :param eid: eid (UUID) or list of UUIDs :return: eid or list of eids

eid_from_path(path_obj)

From a local path, gets the experiment id :param path_obj: local path or list of local paths :return: eid or list of eids

abstract load(**kwargs)

abstract list(**kwargs)

abstract search(**kwargs)

ONE(offline=False, **kwargs)

class OneOffline(username=None, password=None, base_url=None, cache_dir=None, silent=None)

Bases: oneibl.one.OneAbstract

load(eid, **kwargs)

list(**kwargs)

search(**kwargs)

class OneAlyx(**kwargs)

Bases: oneibl.one.OneAbstract

property alyx

help(dataset_type=None)

list(eid: Optional[Union[str, pathlib.Path, uuid.UUID]] = None, details=False) → Union[List, Dict[str, str]]

From a Session ID, queries Alyx database for datasets related to a session.

Parameters

• eid (bool) – Experiment session uuid str

• details – If false returns a list of path, otherwise returns the REST dictionary

Returns

list of strings or dict of lists if details is True

Return type

list, dict

load(eid, dataset_types=None, dclass_output=False, dry_run=False, cache_dir=None, download_only=False, clobber=False, offline=False, keep_uuid=False)

From a Session ID and dataset types, queries Alyx database, downloads the data from Globus, and loads into numpy array.

Parameters

• eid (str) – Experiment ID, for IBL this is the UUID of the Session as per Alyx database. Could be a full Alyx URL: ‘http://localhost:8000/sessions/698361f6-b7d0-447d-a25d-42afdef7a0da’ or only the UUID: ‘698361f6-b7d0-447d-a25d-42afdef7a0da’. Can also be a list of the above for multiple eids.

• dataset_types (list) – [None]: Alyx dataset types to be returned.

• dclass_output (bool If None or an empty dataset_type is specified, the output will be a dictionary by default.) – [False]: forces the output as dataclass to provide context.

• cache_dir (str) – temporarly overrides the cache_dir from the parameter file

• download_only (bool) – do not attempt to load data in memory, just download the files

• clobber (bool) – force downloading even if files exists locally

• keep_uuid (bool) – keeps the UUID at the end of the filename (defaults to False)

Returns

List of numpy arrays matching the size of dataset_types parameter, OR a dataclass containing arrays and context data.

Return type

list, dict, dataclass SessionDataInfo

load_dataset(eid: Union[str, pathlib.Path, uuid.UUID], dataset: str, collection: Optional[str] = None, download_only: bool = False) → Any

Load a single dataset from a Session ID and a dataset type.

Parameters

eid – Experiment session identifier; may be a UUID, URL, experiment reference string

details dict or Path :param dataset: The ALF dataset to load. Supports asterisks as wildcards. :param collection: The collection to which the object belongs, e.g. ‘alf/probe01’. For IBL this is the relative path of the file from the session root. Supports asterisks as wildcards. :param download_only: When true the data are downloaded and the file path is returned :return: dataset or a Path object if download_only is true

Examples

intervals = one.load_dataset(eid, ‘_ibl_trials.intervals.npy’) intervals = one.load_dataset(eid, ‘trials.intervals’) filepath = one.load_dataset(eid ‘_ibl_trials.intervals.npy’, download_only=True) spikes = one.load_dataset(eid ‘spikes.times.npy’, collection=’alf/probe01’)

load_object(eid: Union[str, pathlib.Path, uuid.UUID], obj: str, collection: Optional[str] = 'alf', download_only: bool = False, **kwargs) → Union[alf.io.AlfBunch, List[pathlib.Path]]

Load all attributes of an ALF object from a Session ID and an object name.

Parameters

eid – Experiment session identifier; may be a UUID, URL, experiment reference string

details dict or Path :param obj: The ALF object to load. Supports asterisks as wildcards. :param collection: The collection to which the object belongs, e.g. ‘alf/probe01’. Supports asterisks as wildcards. :param download_only: When true the data are downloaded and the file paths are returned :param kwargs: Optional filters for the ALF objects, including namespace and timescale :return: An ALF bunch or if download_only is True, a list of Paths objects

Examples: load_object(eid, ‘*moves’) load_object(eid, ‘trials’) load_object(eid, ‘spikes’, collection=’*probe01’)

to_eid(id: Union[str, pathlib.Path, uuid.UUID, dict, Sequence[Union[str, pathlib.Path, uuid.UUID, dict]]] = None, cache_dir: Optional[Union[str, pathlib.Path]] = None) → Union[str, Sequence[str]]

search(details=False, limit=None, **kwargs)

Applies a filter to the sessions (eid) table and returns a list of json dictionaries

corresponding to sessions.

For a list of search terms, use the methods

>>> one.search_terms()

Parameters

• dataset_types (list of str) – list of dataset_types

• date_range (list) – list of 2 strings or list of 2 dates that define the range

• details (bool) – default False, returns also the session details as per the REST response

• lab (list or str) – a str or list of lab names

• limit (int List of possible search terms) – default None, limits results (if pagination enabled on server)

• location (str) – a str or list of lab location (as per Alyx definition) name Note: this corresponds to the specific rig, not the lab geographical location per se

• number (str or int) – number of session to be returned; will take the first n sessions found

• / performance_gte (performance_lte) – search only for sessions whose performance is

less equal or greater equal than a pre-defined threshold as a percentage (0-100) :type performance_gte: float

Parameters

• subjects (list or str) – a list of subjects nickname

• task_protocol (str) – a str or list of task protocol name (can be partial, i.e. any task protocol containing that str will be found)

• users (list or str) – a list of users

Returns

list of eids, if details is True, also returns a list of json dictionaries, each entry corresponding to a matching session

Return type

list, list

download_datasets(dsets, **kwargs)

Download several datsets through a list of alyx REST dictionaries :param dset: list of dataset dictionaries from an Alyx REST query OR list of URL strings :return: local file path

download_dataset(dset, cache_dir=None, **kwargs)

Download a dataset from an alyx REST dictionary :param dset: single dataset dictionary from an Alyx REST query OR URL string :param cache_dir (optional): root directory to save the data in (home/downloads by default) :return: local file path

static search_terms()

Returns possible search terms to be used in the one.search method.

Returns

a tuple containing possible search terms:

Return type

tuple

static keywords()

Returns possible keywords to be used in the one.list method

Returns

a tuple containing possible search terms:

Return type

tuple

static setup()

Interactive command tool that populates parameter file for ONE IBL.

path_from_eid(eid: str, use_cache: bool = True) → Union[pathlib.Path, Sequence[pathlib.Path]]

From an experiment id or a list of experiment ids, gets the local cache path :param eid: eid (UUID) or list of UUIDs :param use_cache: if set to False, will force database connection :return: eid or list of eids

eid_from_path(path_obj: Union[str, pathlib.Path], use_cache: bool = True) → Union[pathlib.Path, Sequence[pathlib.Path]]

From a local path, gets the experiment id :param path_obj: local path or list of local paths :param use_cache: if set to False, will force database connection :return: eid or list of eids

url_from_path(filepath)

Given a local file path, returns the URL of the remote file. :param filepath: A local file path :return: A URL string

datasets_from_type(eid, dataset_type, full=False)

Get list of datasets belonging to a given dataset type for a given session :param eid: Experiment session identifier; may be a UUID, URL, experiment reference string details dict or Path :param dataset_type: A dataset type, e.g. camera.times :param full: If True, a dictionary of details is returned for each dataset :return: A list of datasets belonging to that session’s dataset type

get_details(eid: str, full: bool = False)

Returns details of eid like from one.search, optional return full session details.

download_raw_partial(url_cbin, url_ch, first_chunk=0, last_chunk=0)