Paths for supported data sources#

Path objects describe locations without reading them. All four classes accept a directory root and expose a pathlib.Path through .fpath.

Class	Purpose
`VTKPath`	VneuroTK HDF5 output naming
`EphysPath`	Session-level electrophysiology products
`MNEPath`	Flat MNE-readable filename under `root`
`BIDSPath`	BIDS entities backed by optional `mne-bids`

Electrophysiology paths#

EphysPath uses {root}/sessions/{session_id}/{dtype}_{session_id}[_probeN].ext. Its raw_dir and nwb_path use the same project root.

from pathlib import Path

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

source_root = Path("data")
ephys_path = EphysPath(
    root=source_root,
    session_id="251024_FanFan_nsd1w_MSB",
    dtype="TrialRaster",
    probe=0,
    extension="h5",
)
ephys_file = ephys_path.fpath

MNE versus BIDS#

MNEPath composes a filename directly below root; it does not infer a BIDS hierarchy. BIDSPath delegates entity placement and validation to mne_bids.BIDSPath when vneurotk[mne] is installed. Use BIDSPath for a BIDS dataset and MNEPath when the exact file is directly under the supplied root.

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

VneuroTK output paths#

The VTKPath root is the output directory. The class appends the BIDS-like HDF5 filename; do not pass an existing HDF5 file as its root. Pass existing files directly to vneurotk.read().

output_path = VTKPath(
    root=Path("outputs"),
    subject="01",
    session="ImageNet01",
    task="ImageNet",
    run="01",
)
assert output_path.fpath == Path("outputs/sub-01_ses-ImageNet01_task-ImageNet_run-01.h5")