mne_compute_proj_ecg.py

r"""Compute SSP/PCA projections for ECG artifacts.

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

    $ mne compute_proj_ecg -i sample_audvis_raw.fif -c "MEG 1531" -a \
                           --l-freq 1 --h-freq 100 \
                           --rej-grad 3000 --rej-mag 4000 --rej-eeg 100

"""

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

import os
import sys

import mne


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

    parser = get_optparser(__file__)

    parser.add_option(
        "-i", "--in", dest="raw_in", help="Input raw FIF file", metavar="FILE"
    )
    parser.add_option(
        "--tmin",
        dest="tmin",
        type="float",
        help="Time before event in seconds",
        default=-0.2,
    )
    parser.add_option(
        "--tmax",
        dest="tmax",
        type="float",
        help="Time after event in seconds",
        default=0.4,
    )
    parser.add_option(
        "-g",
        "--n-grad",
        dest="n_grad",
        type="int",
        help="Number of SSP vectors for gradiometers",
        default=2,
    )
    parser.add_option(
        "-m",
        "--n-mag",
        dest="n_mag",
        type="int",
        help="Number of SSP vectors for magnetometers",
        default=2,
    )
    parser.add_option(
        "-e",
        "--n-eeg",
        dest="n_eeg",
        type="int",
        help="Number of SSP vectors for EEG",
        default=2,
    )
    parser.add_option(
        "--l-freq",
        dest="l_freq",
        type="float",
        help="Filter low cut-off frequency in Hz",
        default=1,
    )
    parser.add_option(
        "--h-freq",
        dest="h_freq",
        type="float",
        help="Filter high cut-off frequency in Hz",
        default=100,
    )
    parser.add_option(
        "--ecg-l-freq",
        dest="ecg_l_freq",
        type="float",
        help="Filter low cut-off frequency in Hz used for ECG event detection",
        default=5,
    )
    parser.add_option(
        "--ecg-h-freq",
        dest="ecg_h_freq",
        type="float",
        help="Filter high cut-off frequency in Hz used for ECG event detection",
        default=35,
    )
    parser.add_option(
        "-p",
        "--preload",
        dest="preload",
        help="Temporary file used during computation (to save memory)",
        default=True,
    )
    parser.add_option(
        "-a",
        "--average",
        dest="average",
        action="store_true",
        help="Compute SSP after averaging",
        default=False,
    )
    parser.add_option(
        "--proj", dest="proj", help="Use SSP projections from a fif file.", default=None
    )
    parser.add_option(
        "--filtersize",
        dest="filter_length",
        type="int",
        help="Number of taps to use for filtering",
        default=2048,
    )
    parser.add_option(
        "-j",
        "--n-jobs",
        dest="n_jobs",
        type="int",
        help="Number of jobs to run in parallel",
        default=1,
    )
    parser.add_option(
        "-c",
        "--channel",
        dest="ch_name",
        help="Channel to use for ECG detection (Required if no ECG found)",
        default=None,
    )
    parser.add_option(
        "--rej-grad",
        dest="rej_grad",
        type="float",
        help="Gradiometers rejection parameter in fT/cm (peak to peak amplitude)",
        default=2000,
    )
    parser.add_option(
        "--rej-mag",
        dest="rej_mag",
        type="float",
        help="Magnetometers rejection parameter in fT (peak to peak amplitude)",
        default=3000,
    )
    parser.add_option(
        "--rej-eeg",
        dest="rej_eeg",
        type="float",
        help="EEG rejection parameter in µV (peak to peak amplitude)",
        default=50,
    )
    parser.add_option(
        "--rej-eog",
        dest="rej_eog",
        type="float",
        help="EOG rejection parameter in µV (peak to peak amplitude)",
        default=250,
    )
    parser.add_option(
        "--avg-ref",
        dest="avg_ref",
        action="store_true",
        help="Add EEG average reference proj",
        default=False,
    )
    parser.add_option(
        "--no-proj",
        dest="no_proj",
        action="store_true",
        help="Exclude the SSP projectors currently in the fiff file",
        default=False,
    )
    parser.add_option(
        "--bad",
        dest="bad_fname",
        help="Text file containing bad channels list (one per line)",
        default=None,
    )
    parser.add_option(
        "--event-id",
        dest="event_id",
        type="int",
        help="ID to use for events",
        default=999,
    )
    parser.add_option(
        "--event-raw",
        dest="raw_event_fname",
        help="raw file to use for event detection",
        default=None,
    )
    parser.add_option(
        "--tstart",
        dest="tstart",
        type="float",
        help="Start artifact detection after tstart seconds",
        default=0.0,
    )
    parser.add_option(
        "--qrsthr",
        dest="qrs_threshold",
        type="string",
        help="QRS detection threshold. Between 0 and 1. Can "
        "also be 'auto' for automatic selection",
        default="auto",
    )

    options, args = parser.parse_args()

    raw_in = options.raw_in

    if raw_in is None:
        parser.print_help()
        sys.exit(1)

    tmin = options.tmin
    tmax = options.tmax
    n_grad = options.n_grad
    n_mag = options.n_mag
    n_eeg = options.n_eeg
    l_freq = options.l_freq
    h_freq = options.h_freq
    ecg_l_freq = options.ecg_l_freq
    ecg_h_freq = options.ecg_h_freq
    average = options.average
    preload = options.preload
    filter_length = options.filter_length
    n_jobs = options.n_jobs
    ch_name = options.ch_name
    reject = dict(
        grad=1e-13 * float(options.rej_grad),
        mag=1e-15 * float(options.rej_mag),
        eeg=1e-6 * float(options.rej_eeg),
        eog=1e-6 * float(options.rej_eog),
    )
    avg_ref = options.avg_ref
    no_proj = options.no_proj
    bad_fname = options.bad_fname
    event_id = options.event_id
    proj_fname = options.proj
    raw_event_fname = options.raw_event_fname
    tstart = options.tstart
    qrs_threshold = options.qrs_threshold
    if qrs_threshold != "auto":
        try:
            qrs_threshold = float(qrs_threshold)
        except ValueError:
            raise ValueError('qrsthr must be "auto" or a float')

    if bad_fname is not None:
        with open(bad_fname) as fid:
            bads = [w.rstrip() for w in fid.readlines()]
        print(f"Bad channels read : {bads}")
    else:
        bads = []

    if raw_in.endswith("_raw.fif") or raw_in.endswith("-raw.fif"):
        prefix = raw_in[:-8]
    else:
        prefix = raw_in[:-4]

    ecg_event_fname = prefix + "_ecg-eve.fif"

    if average:
        ecg_proj_fname = prefix + "_ecg_avg-proj.fif"
    else:
        ecg_proj_fname = prefix + "_ecg-proj.fif"

    raw = mne.io.read_raw_fif(raw_in, preload=preload)

    if raw_event_fname is not None:
        raw_event = mne.io.read_raw_fif(raw_event_fname)
    else:
        raw_event = raw

    flat = None
    projs, events = mne.preprocessing.compute_proj_ecg(
        raw,
        raw_event,
        tmin,
        tmax,
        n_grad,
        n_mag,
        n_eeg,
        l_freq,
        h_freq,
        average,
        filter_length,
        n_jobs,
        ch_name,
        reject,
        flat,
        bads,
        avg_ref,
        no_proj,
        event_id,
        ecg_l_freq,
        ecg_h_freq,
        tstart,
        qrs_threshold,
        copy=False,
    )

    raw.close()

    if raw_event_fname is not None:
        raw_event.close()

    if proj_fname is not None:
        print(f"Including SSP projections from : {proj_fname}")
        # append the ecg projs, so they are last in the list
        projs = mne.read_proj(proj_fname) + projs

    if isinstance(preload, str) and os.path.exists(preload):
        os.remove(preload)

    print(f"Writing ECG projections in {ecg_proj_fname}")
    mne.write_proj(ecg_proj_fname, projs)

    print(f"Writing ECG events in {ecg_event_fname}")
    mne.write_events(ecg_event_fname, events)


mne.utils.run_command_if_main()