ibllib.tests.fixtures.utils

Functions

create_fake_alf_folder_dlc_data
create_fake_complete_ephys_session
create_fake_ephys_recording_bad_passive_transfer_sessions
create_fake_raw_behavior_data_folder	Create the folder structure for a raw behaviour session.
create_fake_raw_ephys_data_folder	create_fake_raw_ephys_data_folder creates raw_ephys_data folder can populate with empty files with expected names
create_fake_raw_video_data_folder	Create the folder structure for a raw video session with three cameras.
create_fake_session_folder
populate_raw_spikeglx	Touch file tree to emulate files saved by SpikeGLX
populate_task_settings	Populate a task settings JSON file.
register_new_session	Register a new test session.

create_fake_session_folder(root_data_path, lab='fakelab', mouse='fakemouse', date='1900-01-01', num='001', increment=True)

create_fake_raw_ephys_data_folder(session_path, populate=True)

create_fake_raw_ephys_data_folder creates raw_ephys_data folder can populate with empty files with expected names

Parameters:

• session_path ([type]) – [description]

• populate (bool, optional) – [description], defaults to True

Returns:

[description]

Return type:

[type]

populate_raw_spikeglx(session_path, model='3B', legacy=False, user_label='my_run', n_probes=2)

Touch file tree to emulate files saved by SpikeGLX

Parameters:

• session_path – The raw ephys data path to place files

• model – Probe model file structure (‘3A’ or ‘3B’)

• legacy – If true, emulate older SpikeGLX version where all files are saved

into a single folder :param user_label: User may input any name into SpikeGLX and filenames will include this :param n_probes: Number of probe datafiles to touch :return:

Examples

populate_raw_spikeglx(‘3A_folder’, model=’3A’, legacy=True, n_probes=1) 3A_folder

└───raw_ephys_folder

my_run_probe00_g0_t0.imec.ap.bin my_run_probe00_g0_t0.imec.ap.meta my_run_probe00_g0_t0.imec.lf.bin my_run_probe00_g0_t0.imec.lf.meta

populate_raw_spikeglx(‘3B_folder’, model=’3B’, n_probes=3) 3B_folder

└───my_run_g0_t0

my_run_g0_t0.imec0.ap.bin my_run_g0_t0.imec0.ap.meta my_run_g0_t0.imec0.lf.bin my_run_g0_t0.imec0.lf.meta my_run_g0_t0.imec1.ap.bin my_run_g0_t0.imec1.ap.meta my_run_g0_t0.imec1.lf.bin my_run_g0_t0.imec1.lf.meta my_run_g0_t0.imec2.ap.bin my_run_g0_t0.imec2.ap.meta my_run_g0_t0.imec2.lf.bin my_run_g0_t0.imec2.lf.meta my_run_g0_t0.nidq.bin my_run_g0_t0.nidq.meta

populate_raw_spikeglx(‘3B_folder’, model=’3B’, n_probes=0) 3B_folder

└───my_run_g0_t0

my_run_g0_t0.nidq.bin my_run_g0_t0.nidq.meta

See also: http://billkarsh.github.io/SpikeGLX/help/parsing/

create_fake_raw_video_data_folder(session_path, populate=True, write_pars_stub=False)

Create the folder structure for a raw video session with three cameras. Creates a raw_video_data folder and optionally, touches some files and writes a experiment description stub to a _devices folder.

Parameters:

• session_path (str, pathlib.Path) – The session path in which to create the folders.

• populate (bool) – If true, touch some raw video files.

• write_pars_stub (bool, str, dict) – If true, write an experiment description stub containing behaviour settings. If a string, the stub filename will contain this. If a dict, the key is used as the filename; the value, the file contents.

Example

>>> create_fake_raw_video_data_folder(session_path, populate=False, write_pars_stub=False)
>>> create_fake_raw_video_data_folder(session_path, write_pars_stub='hostname_19826354')

create_fake_alf_folder_dlc_data(session_path, populate=True)

create_fake_raw_behavior_data_folder(session_path, populate=True, task='ephysCW', folder='raw_behavior_data', write_pars_stub=False)

Create the folder structure for a raw behaviour session.

Creates a raw_behavior_data folder and optionally, touches some files and writes an experiment description stub to a _devices folder.

Parameters:

• session_path (pathlib.Path) – The session path in which to create the folders.

• populate (bool) – If true, touch some raw behaviour files.

• task (str) – The name of the task protocol, if ‘ephys’ or ‘passive’ extra files are touched.

• write_pars_stub (bool, str, dict) – If true, write an experiment description stub containing behaviour settings. If a string, the stub will be named as such. If a dict, the key is used as the filename; the value, the file contents.

Returns:

The raw behaviour data path.

Return type:

pathlib.Path

populate_task_settings(fpath: Path, patch: dict)

Populate a task settings JSON file.

Parameters:

• fpath (pathlib.Path) – A path to a raw task settings folder or the full settings file path.

• patch (dict) – The settings dict to write to file.

Returns:

The full settings file path.

Return type:

pathlib.Path

create_fake_complete_ephys_session(root_data_path, lab='fakelab', mouse='fakemouse', date='1900-01-01', num='001', increment=True)

create_fake_ephys_recording_bad_passive_transfer_sessions(root_data_path, lab='fakelab', mouse='fakemouse', date='1900-01-01', num='001', increment=True)

register_new_session(one, subject=None, date=None)

Register a new test session.

NB: This creates the session path on disk, using one.cache_dir.

Parameters:

• one (one.api.OneAlyx) – An instance of ONE.

• subject (str) – The subject name. If None, a new random subject is created.

• date (str) – An ISO date string. If None, a random one is created.

Returns:

• pathlib.Path – New local session path.

• uuid.UUID – The experiment UUID.