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import os.path as op
import pytest
import numpy as np
from mne.io import read_raw_fif
from mne import pick_types
from mne.preprocessing import find_ecg_events, create_ecg_epochs
data_path = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
raw_fname = op.join(data_path, 'test_raw.fif')
event_fname = op.join(data_path, 'test-eve.fif')
proj_fname = op.join(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_types(meg=True)
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. / 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)
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.
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
with pytest.warns(RuntimeWarning, match='unit for channel'):
raw.set_channel_types({'MEG 2641': 'ecg'})
create_ecg_epochs(raw)
raw.pick_types(meg=True) # 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.
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))
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