Loading with ONE

Once a session and datasets of interest have been identified, the ONE load methods can be used to load in the relevant data

To load all datasets for a given object we can use the load_object method

from one.api import ONE
one = ONE(base_url='https://openalyx.internationalbrainlab.org', silent=True)

eid = 'CSH_ZAD_029/2020-09-19/001'
trials = one.load_object(eid, 'trials')

The attributes of returned object mirror the datasets

print(trials.keys())

dict_keys(['intervals', 'rewardVolume', 'contrastRight', 'response_times', 'choice', 'stimOn_times', 'probabilityLeft', 'goCueTrigger_times', 'intervals_bpod', 'goCue_times', 'firstMovement_times', 'stimOff_times', 'contrastLeft', 'feedbackType', 'feedback_times'])

If we only want to load in certain attributes of an object we can use the following

trials = one.load_object(eid, 'trials', attribute=['intervals', 'rewardVolume', 'probabilityLeft'])
print(trials.keys())

dict_keys(['intervals', 'rewardVolume', 'probabilityLeft', 'intervals_bpod'])

If an object belongs to more than one collection, for example the clusters object, the collection must be specified

clusters = one.load_object(eid, 'clusters', collection='alf/probe01')

By default, the load_object method downloads and loads the data into memory, if you only want to download the data you can specify a download only flag. In this case the returned object will be a list of paths to the datasets on your local system

files = one.load_object(eid, 'clusters', collection='alf/probe01', download_only=True)

To load a single dataset we can use the load_dataset method

reward_volume = one.load_dataset(eid, '_ibl_trials.rewardVolume.npy')

Once again if the same dataset exists in more than one collection, the collection must be specified

waveforms = one.load_dataset(eid, 'clusters.waveforms.npy', collection='alf/probe01')

We can use the load_datasets method to load multiple datasets at once. This method returns two lists, the first which contains the data for each dataset and the second which contains meta information about the data.

data, info = one.load_datasets(eid, datasets=['_ibl_trials.rewardVolume.npy',
                                              '_ibl_trials.probabilityLeft.npy'])

It is also possible to load datasets from different collections. For example if we want to simultaneously load a trials dataset and a clusters dataset we would type,

data, info = one.load_datasets(eid, datasets=['_ibl_trials.rewardVolume.npy',
                                              'clusters.waveforms.npy'],
                               collections=['alf', 'alf/probe01'])

More information about these methods can be found using the help command

help(one.load_dataset)

Help on method load_dataset in module one.api:

load_dataset(eid: Union[str, pathlib.Path, uuid.UUID], dataset: str, collection: Optional[str] = None, revision: Optional[str] = None, query_type: Optional[str] = None, download_only: bool = False, **kwargs) -> Any method of one.api.OneAlyx instance
    Load a single dataset for a given session id and dataset name

    Parameters
    ----------
    eid : str, UUID, pathlib.Path, dict
        Experiment session identifier; may be a UUID, URL, experiment reference string
        details dict or Path.
    dataset : str, dict
        The ALF dataset to load.  May be a string or dict of ALF parts.  Supports asterisks as
        wildcards.
    collection : str
        The collection to which the object belongs, e.g. 'alf/probe01'.
        This is the relative path of the file from the session root.
        Supports asterisks as wildcards.
    revision : str
        The dataset revision (typically an ISO date).  If no exact match, the previous
        revision (ordered lexicographically) is returned.  If None, the default revision is
        returned (usually the most recent revision).  Regular expressions/wildcards not
        permitted.
    query_type : str
        Query cache ('local') or Alyx database ('remote')
    download_only : bool
        When true the data are downloaded and the file path is returned.

    Returns
    -------
    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)
    spike_times = one.load_dataset(eid 'spikes.times.npy', collection='alf/probe01')
    old_spikes = one.load_dataset(eid, ''spikes.times.npy',
                                  collection='alf/probe01', revision='2020-08-31')