Work with VneuroTK paths#

VneuroTK path objects describe locations without performing I/O. They accept str or pathlib.Path roots and produce pathlib.Path values through .fpath.

Class	Use
`VTKPath`	VneuroTK HDF5 recordings and the base naming convention
`EphysPath`	Session-level electrophysiology data
`MNEPath`	MNE-readable MEG/EEG files with a flat filename under `root`
`BIDSPath`	BIDS entities backed by the optional `mne-bids` package

This notebook uses path construction only and does not read files. Full BIDS loading requires vneurotk[mne].

Construct electrophysiology paths#

from pathlib import Path

from vneurotk.io import BIDSPath, EphysPath, MNEPath, VTKPath

root = Path("data")
ephys = EphysPath(
    root=root,
    session_id="251024_FanFan_nsd1w_MSB",
    dtype="TrialRaster",
    extension="h5",
)
ephys.fpath

PosixPath('data/sessions/251024_FanFan_nsd1w_MSB/TrialRaster_251024_FanFan_nsd1w_MSB.h5')

EphysPath supports unit- and channel-level products such as TrialRaster, MeanFr, ChTrialRaster, and ChStimFr. A probe adds the probe suffix; from_components() assembles the session identifier.

multi_probe = EphysPath(
    root=root,
    session_id="251024_FanFan_nsd1w_MSB",
    dtype="TrialRaster",
    probe=0,
    extension="h5",
)
from_parts = EphysPath.from_components(
    root=root,
    date="251024",
    subject="FanFan",
    paradigm="nsd1w",
    region="MSB",
    dtype="TrialRaster",
    extension="h5",
)
from_parts.session_dir, multi_probe.fpath

(PosixPath('data/sessions/251024_FanFan_nsd1w_MSB'),
 PosixPath('data/sessions/251024_FanFan_nsd1w_MSB/TrialRaster_251024_FanFan_nsd1w_MSB_probe0.h5'))

Construct MNE and BIDS paths#

mne_path = MNEPath(
    root=root,
    subject="01",
    session="ImageNet01",
    task="ImageNet",
    run="01",
    suffix="meg_clean",
    extension=".fif",
)

bids_path = BIDSPath(
    root=root,
    subject="01",
    session="01",
    task="images",
    run="01",
    suffix="meg",
    extension=".fif",
)
mne_path.fpath, bids_path.fpath

(PosixPath('data/sub-01_ses-ImageNet01_task-ImageNet_run-01_meg_clean.fif'),
 PosixPath('data/sub-01_ses-01_task-images_run-01_meg.fif'))

MNEPath builds a filename directly under root. BIDSPath delegates BIDS layout and entities to mne_bids.BIDSPath when the extra is installed; otherwise .bids_path is None and .fpath uses the base fallback.

Construct a VneuroTK output path#

output = VTKPath(
    Path("outputs"),
    subject="01",
    session="ImageNet01",
    task="ImageNet",
    run="01",
)
output.fpath

PosixPath('outputs/sub-01_ses-ImageNet01_task-ImageNet_run-01.h5')

Pass a directory as the VTKPath root; the object appends the recording filename. To read an existing HDF5 file, pass that file path directly to vneurotk.read() instead of wrapping it as a VTKPath root.