import os.path as op import pytest from numpy.testing import assert_array_almost_equal import numpy as np from mne.io import read_raw_fif, read_raw_ctf from mne.io.proj import make_projector, activate_proj from mne.preprocessing.ssp import compute_proj_ecg, compute_proj_eog from mne.utils import run_tests_if_main from mne.datasets import testing from mne import pick_types data_path = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data') raw_fname = op.join(data_path, 'test_raw.fif') dur_use = 5.0 eog_times = np.array([0.5, 2.3, 3.6, 14.5]) ctf_fname = op.join(testing.data_path(download=False), 'CTF', 'testdata_ctf.ds') def test_compute_proj_ecg(): """Test computation of ECG SSP projectors.""" raw = read_raw_fif(raw_fname).crop(0, 10) raw.load_data() for average in [False, True]: # For speed, let's not filter here (must also not reject then) projs, events = compute_proj_ecg( raw, n_mag=2, n_grad=2, n_eeg=2, ch_name='MEG 1531', bads=['MEG 2443'], average=average, avg_ref=True, no_proj=True, l_freq=None, h_freq=None, reject=None, tmax=dur_use, qrs_threshold=0.5, filter_length=6000) assert len(projs) == 7 # heart rate at least 0.5 Hz, but less than 3 Hz assert (events.shape[0] > 0.5 * dur_use and events.shape[0] < 3 * dur_use) ssp_ecg = [proj for proj in projs if proj['desc'].startswith('ECG')] # check that the first principal component have a certain minimum ssp_ecg = [proj for proj in ssp_ecg if 'PCA-01' in proj['desc']] thresh_eeg, thresh_axial, thresh_planar = .9, .3, .1 for proj in ssp_ecg: if 'planar' in proj['desc']: assert proj['explained_var'] > thresh_planar elif 'axial' in proj['desc']: assert proj['explained_var'] > thresh_axial elif 'eeg' in proj['desc']: assert proj['explained_var'] > thresh_eeg # XXX: better tests # without setting a bad channel, this should throw a warning with pytest.warns(RuntimeWarning, match='No good epochs found'): projs, events, drop_log = compute_proj_ecg( raw, n_mag=2, n_grad=2, n_eeg=2, ch_name='MEG 1531', bads=[], average=average, avg_ref=True, no_proj=True, l_freq=None, h_freq=None, tmax=dur_use, return_drop_log=True) assert projs is None assert len(events) == len(drop_log) def test_compute_proj_eog(): """Test computation of EOG SSP projectors.""" raw = read_raw_fif(raw_fname).crop(0, 10) raw.load_data() for average in [False, True]: n_projs_init = len(raw.info['projs']) projs, events = compute_proj_eog(raw, n_mag=2, n_grad=2, n_eeg=2, bads=['MEG 2443'], average=average, avg_ref=True, no_proj=False, l_freq=None, h_freq=None, reject=None, tmax=dur_use, filter_length=6000) assert (len(projs) == (7 + n_projs_init)) assert (np.abs(events.shape[0] - np.sum(np.less(eog_times, dur_use))) <= 1) ssp_eog = [proj for proj in projs if proj['desc'].startswith('EOG')] # check that the first principal component have a certain minimum ssp_eog = [proj for proj in ssp_eog if 'PCA-01' in proj['desc']] thresh_eeg, thresh_axial, thresh_planar = .9, .3, .1 for proj in ssp_eog: if 'planar' in proj['desc']: assert (proj['explained_var'] > thresh_planar) elif 'axial' in proj['desc']: assert (proj['explained_var'] > thresh_axial) elif 'eeg' in proj['desc']: assert (proj['explained_var'] > thresh_eeg) # XXX: better tests with pytest.warns(RuntimeWarning, match='longer'): projs, events = compute_proj_eog(raw, n_mag=2, n_grad=2, n_eeg=2, average=average, bads=[], avg_ref=True, no_proj=False, l_freq=None, h_freq=None, tmax=dur_use) assert projs is None def test_compute_proj_parallel(): """Test computation of ExG projectors using parallelization.""" raw_0 = read_raw_fif(raw_fname).crop(0, 10) raw_0.load_data() raw = raw_0.copy() projs, _ = compute_proj_eog(raw, n_mag=2, n_grad=2, n_eeg=2, bads=['MEG 2443'], average=False, avg_ref=True, no_proj=False, n_jobs=1, l_freq=None, h_freq=None, reject=None, tmax=dur_use, filter_length=6000) raw_2 = raw_0.copy() projs_2, _ = compute_proj_eog(raw_2, n_mag=2, n_grad=2, n_eeg=2, bads=['MEG 2443'], average=False, avg_ref=True, no_proj=False, n_jobs=2, l_freq=None, h_freq=None, reject=None, tmax=dur_use, filter_length=6000) projs = activate_proj(projs) projs_2 = activate_proj(projs_2) projs, _, _ = make_projector(projs, raw_2.info['ch_names'], bads=['MEG 2443']) projs_2, _, _ = make_projector(projs_2, raw_2.info['ch_names'], bads=['MEG 2443']) assert_array_almost_equal(projs, projs_2, 10) def _check_projs_for_expected_channels(projs, n_mags, n_grads, n_eegs): for p in projs: if 'planar' in p['desc']: assert len(p['data']['col_names']) == n_grads elif 'axial' in p['desc']: assert len(p['data']['col_names']) == n_mags elif 'eeg' in p['desc']: assert len(p['data']['col_names']) == n_eegs @testing.requires_testing_data def test_compute_proj_ctf(): """Test to show that projector code completes on CTF data.""" raw = read_raw_ctf(ctf_fname) raw.load_data() # expected channels per projector type n_mags = len(pick_types(raw.info, meg='mag', ref_meg=False, exclude='bads')) n_grads = len(pick_types(raw.info, meg='grad', ref_meg=False, exclude='bads')) n_eegs = len(pick_types(raw.info, meg=False, eeg=True, ref_meg=False, exclude='bads')) # Test with and without gradient compensation for c in [0, 1]: raw.apply_gradient_compensation(c) for average in [False, True]: n_projs_init = len(raw.info['projs']) projs, events = compute_proj_eog(raw, n_mag=2, n_grad=2, n_eeg=2, average=average, ch_name='EEG059', avg_ref=True, no_proj=False, l_freq=None, h_freq=None, reject=None, tmax=dur_use, filter_length=6000) _check_projs_for_expected_channels(projs, n_mags, n_grads, n_eegs) assert len(projs) == (5 + n_projs_init) projs, events = compute_proj_ecg(raw, n_mag=1, n_grad=1, n_eeg=2, average=average, ch_name='EEG059', avg_ref=True, no_proj=False, l_freq=None, h_freq=None, reject=None, tmax=dur_use, filter_length=6000) _check_projs_for_expected_channels(projs, n_mags, n_grads, n_eegs) assert len(projs) == (4 + n_projs_init) run_tests_if_main()