mne_bti2fiff.py

"""Import BTi / 4D MagnesWH3600 data to fif file.

Notes
-----
1. Currently direct inclusion of reference channel weights
   is not supported. Please use 'mne_create_comp_data' to include
   the weights or use the low level functions from this module to
   include them by yourself.
2. The informed guess for the 4D name is E31 for the ECG channel and
   E63, E63 for the EOG channels. Please check and adjust if those channels
   are present in your dataset but 'ECG 01' and 'EOG 01', 'EOG 02' don't
   appear in the channel names of the raw object.

Examples
--------
.. code-block:: console

     $ mne bti2fiff --pdf C,rfDC -o my_raw.fif

"""

# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import sys

import mne
from mne.io import read_raw_bti


def run():
    """Run command."""
    from mne.commands.utils import get_optparser

    parser = get_optparser(__file__)

    parser.add_option(
        "-p", "--pdf", dest="pdf_fname", help="Input data file name", metavar="FILE"
    )
    parser.add_option(
        "-c",
        "--config",
        dest="config_fname",
        help="Input config file name",
        metavar="FILE",
        default="config",
    )
    parser.add_option(
        "--head_shape",
        dest="head_shape_fname",
        help="Headshape file name",
        metavar="FILE",
        default="hs_file",
    )
    parser.add_option(
        "-o",
        "--out_fname",
        dest="out_fname",
        help="Name of the resulting fiff file",
        default="as_data_fname",
    )
    parser.add_option(
        "-r",
        "--rotation_x",
        dest="rotation_x",
        type="float",
        help="Compensatory rotation about Neuromag x axis, deg",
        default=2.0,
    )
    parser.add_option(
        "-T",
        "--translation",
        dest="translation",
        type="str",
        help="Default translation, meter",
        default=(0.00, 0.02, 0.11),
    )
    parser.add_option(
        "--ecg_ch", dest="ecg_ch", type="str", help="4D ECG channel name", default="E31"
    )
    parser.add_option(
        "--eog_ch",
        dest="eog_ch",
        type="str",
        help="4D EOG channel names",
        default="E63,E64",
    )

    options, args = parser.parse_args()

    pdf_fname = options.pdf_fname
    if pdf_fname is None:
        parser.print_help()
        sys.exit(1)

    config_fname = options.config_fname
    head_shape_fname = options.head_shape_fname
    out_fname = options.out_fname
    rotation_x = options.rotation_x
    translation = options.translation
    ecg_ch = options.ecg_ch
    eog_ch = options.ecg_ch.split(",")

    if out_fname == "as_data_fname":
        out_fname = pdf_fname + "_raw.fif"

    raw = read_raw_bti(
        pdf_fname=pdf_fname,
        config_fname=config_fname,
        head_shape_fname=head_shape_fname,
        rotation_x=rotation_x,
        translation=translation,
        ecg_ch=ecg_ch,
        eog_ch=eog_ch,
    )

    raw.save(out_fname)
    raw.close()


mne.utils.run_command_if_main()