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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from pathlib import Path
import numpy as np
import pytest
from mne import pick_types
from mne.io import read_raw_fif
from mne.preprocessing import create_ecg_epochs, find_ecg_events
data_path = Path(__file__).parents[2] / "io" / "tests" / "data"
raw_fname = data_path / "test_raw.fif"
event_fname = data_path / "test-eve.fif"
proj_fname = data_path / "test-proj.fif"
def test_find_ecg():
"""Test find ECG peaks."""
# Test if ECG analysis will work on data that is not preloaded
raw = read_raw_fif(raw_fname, preload=False).pick(picks="meg")
raw.pick(raw.ch_names[::10] + ["MEG 2641"])
raw.info.normalize_proj()
# once with mag-trick
# once with characteristic channel
raw_bad = raw.copy().load_data()
ecg_idx = raw.ch_names.index("MEG 1531")
raw_bad._data[ecg_idx, :1] = 1e6 # this will break the detector
raw_bad.annotations.append(
raw.first_samp / raw.info["sfreq"], 1.0 / raw.info["sfreq"], "BAD_values"
)
raw_noload = raw.copy()
raw.resample(100)
for ch_name, tstart in zip(["MEG 1531", None], [raw.times[-1] / 2, 0]):
events, ch_ECG, average_pulse, ecg = find_ecg_events(
raw, event_id=999, ch_name=ch_name, tstart=tstart, return_ecg=True
)
if ch_name is None:
assert ch_ECG is None
else:
assert raw.ch_names[ch_ECG] == ch_name
assert raw.n_times == ecg.shape[-1]
assert 40 < average_pulse < 60
n_events = len(events)
# with annotations
average_pulse = find_ecg_events(
raw_bad, ch_name=ch_name, tstart=tstart, reject_by_annotation=False
)[2]
assert average_pulse < 1.0
average_pulse = find_ecg_events(
raw_bad, ch_name=ch_name, tstart=tstart, reject_by_annotation=True
)[2]
assert 55 < average_pulse < 60
picks = pick_types(
raw.info,
meg="grad",
eeg=False,
stim=False,
eog=False,
ecg=True,
emg=False,
ref_meg=False,
exclude="bads",
)
# There should be no ECG channels, or else preloading will not be
# tested
assert "ecg" not in raw
ecg_epochs = create_ecg_epochs(raw_noload, picks=picks, keep_ecg=True)
assert len(ecg_epochs.events) == n_events
assert "ECG-SYN" not in raw.ch_names
assert "ECG-SYN" in ecg_epochs.ch_names
assert len(ecg_epochs) == 23
picks = pick_types(
ecg_epochs.info,
meg=False,
eeg=False,
stim=False,
eog=False,
ecg=True,
emg=False,
ref_meg=False,
exclude="bads",
)
assert len(picks) == 1
ecg_epochs = create_ecg_epochs(raw, ch_name="MEG 2641")
assert "MEG 2641" in ecg_epochs.ch_names
# test with user provided ecg channel
raw.del_proj()
assert "MEG 2641" in raw.ch_names
raw.set_channel_types({"MEG 2641": "ecg"}, on_unit_change="ignore")
create_ecg_epochs(raw)
raw.pick(picks="meg") # remove ECG
assert "MEG 2641" not in raw.ch_names
ecg_epochs = create_ecg_epochs(raw, keep_ecg=False)
assert len(ecg_epochs.events) == n_events
assert "ECG-SYN" not in raw.ch_names
assert "ECG-SYN" not in ecg_epochs.ch_names
# Test behavior if no peaks can be found -> achieve this by providing
# all-zero'd data
raw._data[ecg_idx] = 0.0
ecg_events, _, average_pulse, ecg = find_ecg_events(
raw, ch_name=raw.ch_names[ecg_idx], return_ecg=True
)
assert ecg_events.size == 0
assert average_pulse == 0
assert np.allclose(ecg, np.zeros_like(ecg))
# Needs MEG
with pytest.raises(ValueError, match="Generating an artificial"):
find_ecg_events(read_raw_fif(raw_fname, preload=False).pick("eeg"))
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