cedalion.io.probe_geometry

Module for reading and writing probe geometry files.

Functions

`export_to_tsv`(tsv_filename, points)	Export optodes, fiducials, landmarks, electrodes, or measurement lists to tsv.
`load_tsv`(tsv_fname[, crs, units])	Load a tsv file containing optodes or landmarks.
`read_digpts`(fname[, units])	Read a file containing digitized 3D points.
`read_einstar_obj`(fname)	Read a textured triangle mesh generated by Einstar 3D scanners.
`read_fieldtrip_elc`(fname)	Read electrode positions from a FieldTrip `.elc` file.
`read_mrk_json`(fname, crs)	Read a JSON file containing landmarks (3D Slicer `.mrk.json` format).
`read_sd`(fname[, crs])	Read optode positions from a Homer/AtlasViewer `.mat` SD file.
`save_mrk_json`(fname, landmarks, crs)	Save landmarks to a 3D Slicer `.mrk.json` file.

cedalion.io.probe_geometry.load_tsv( tsv_fname: str, crs: str = None, units: str = None, ) → DataArray[source]

Load a tsv file containing optodes or landmarks.

This function reads tsv-files with a column layout that differs from the NIRS-BIDS standard.

Parameters:

tsv_fname – Path to the tsv file.
crs – Coordinate reference system of the points if not in the file header.
units – Units of the points if not in the file header.

Returns:

xr.DataArray containing the optodes or landmarks with label, type, and positional dimensions.

cedalion.io.probe_geometry.export_to_tsv(tsv_filename, points)[source]

Export optodes, fiducials, landmarks, electrodes, or measurement lists to tsv.

This function writes tsv-files with a column layout that differs from the NIRS-BIDS standard.

Parameters:

tsv_filename – Path to the output tsv file.
points – Points to save. Either an xr.DataArray (optodes / landmarks / electrodes) or a pd.DataFrame (measurement list).

cedalion.io.probe_geometry.read_mrk_json(fname: str, crs: str) → DataArray[source]

Read a JSON file containing landmarks (3D Slicer .mrk.json format).

Parameters:

fname – Path to the JSON file.
crs – Coordinate reference system of the landmarks.

Returns:

xr.DataArray containing landmark positions with label and type coordinates, quantified with pint units.

cedalion.io.probe_geometry.save_mrk_json(fname: str, landmarks: DataArray, crs: str)[source]

Save landmarks to a 3D Slicer .mrk.json file.

Parameters:

fname – Path to the output JSON file.
landmarks – Landmark positions as an xr.DataArray with label coordinate.
crs – Coordinate reference system name to embed in the file.

cedalion.io.probe_geometry.read_digpts(fname: str, units: str = 'mm') → DataArray[source]

Read a file containing digitized 3D points.

Each line must have the format label: x y z.

Parameters:

fname – Path to the digitized-points file.
units – Physical units of the coordinates (default: "mm").

Returns:

xr.DataArray with dimensions ["label", "pos"], quantified with pint units.

cedalion.io.probe_geometry.read_einstar_obj(fname: str) → TrimeshSurface[source]

Read a textured triangle mesh generated by Einstar 3D scanners.

Parameters:: fname – Path to the .obj mesh file.
Returns:: TrimeshSurface in the "digitized" CRS with millimetre units.

cedalion.io.probe_geometry.read_fieldtrip_elc( fname: Path | str, ) → Annotated[DataArray, DataArraySchema(dims='label', coords='label', 'label', 'type')][source]

Read electrode positions from a FieldTrip .elc file.

Parameters:: fname – Path to the .elc file.
Returns:: LabeledPoints with electrode positions, label and type coordinates, and pint units derived from the file header.

cedalion.io.probe_geometry.read_sd( fname: Path | str, crs='av', ) → Annotated[DataArray, DataArraySchema(dims='label', coords='label', 'label', 'type')][source]

Read optode positions from a Homer/AtlasViewer .mat SD file.

Parameters:

fname – Path to the .mat SD file.
crs – Coordinate reference system label to assign (default: "av").

Returns:

LabeledPoints with source, detector, and landmark positions.