# -*- coding: utf-8 -*- # Authors: Denis A. Engemann # simplified BSD-3 license import os.path as op import inspect import numpy as np from numpy.testing import assert_array_equal, assert_allclose, assert_equal import pytest from scipy import io as sio from mne import find_events, pick_types from mne.io import read_raw_egi from mne.io.tests.test_raw import _test_raw_reader from mne.io.egi.egi import _combine_triggers from mne.utils import run_tests_if_main from mne.datasets.testing import data_path, requires_testing_data FILE = inspect.getfile(inspect.currentframe()) base_dir = op.join(op.dirname(op.abspath(FILE)), 'data') egi_fname = op.join(base_dir, 'test_egi.raw') egi_txt_fname = op.join(base_dir, 'test_egi.txt') @requires_testing_data def test_io_egi_mff(): """Test importing EGI MFF simple binary files.""" egi_fname_mff = op.join(data_path(), 'EGI', 'test_egi.mff') raw = read_raw_egi(egi_fname_mff, include=None) assert ('RawMff' in repr(raw)) include = ['DIN1', 'DIN2', 'DIN3', 'DIN4', 'DIN5', 'DIN7'] raw = _test_raw_reader(read_raw_egi, input_fname=egi_fname_mff, include=include, channel_naming='EEG %03d') assert_equal('eeg' in raw, True) eeg_chan = [c for c in raw.ch_names if 'EEG' in c] assert_equal(len(eeg_chan), 129) picks = pick_types(raw.info, eeg=True) assert_equal(len(picks), 129) assert_equal('STI 014' in raw.ch_names, True) events = find_events(raw, stim_channel='STI 014') assert_equal(len(events), 8) assert_equal(np.unique(events[:, 1])[0], 0) assert (np.unique(events[:, 0])[0] != 0) assert (np.unique(events[:, 2])[0] != 0) pytest.raises(ValueError, read_raw_egi, egi_fname_mff, include=['Foo'], preload=False) pytest.raises(ValueError, read_raw_egi, egi_fname_mff, exclude=['Bar'], preload=False) for ii, k in enumerate(include, 1): assert (k in raw.event_id) assert (raw.event_id[k] == ii) def test_io_egi(): """Test importing EGI simple binary files.""" # test default with open(egi_txt_fname) as fid: data = np.loadtxt(fid) t = data[0] data = data[1:] data *= 1e-6 # μV with pytest.warns(RuntimeWarning, match='Did not find any event code'): raw = read_raw_egi(egi_fname, include=None) assert 'RawEGI' in repr(raw) data_read, t_read = raw[:256] assert_allclose(t_read, t) assert_allclose(data_read, data, atol=1e-10) include = ['TRSP', 'XXX1'] raw = _test_raw_reader(read_raw_egi, input_fname=egi_fname, include=include) assert_equal('eeg' in raw, True) eeg_chan = [c for c in raw.ch_names if c.startswith('E')] assert_equal(len(eeg_chan), 256) picks = pick_types(raw.info, eeg=True) assert_equal(len(picks), 256) assert_equal('STI 014' in raw.ch_names, True) events = find_events(raw, stim_channel='STI 014') assert_equal(len(events), 2) # ground truth assert_equal(np.unique(events[:, 1])[0], 0) assert (np.unique(events[:, 0])[0] != 0) assert (np.unique(events[:, 2])[0] != 0) triggers = np.array([[0, 1, 1, 0], [0, 0, 1, 0]]) # test trigger functionality triggers = np.array([[0, 1, 0, 0], [0, 0, 1, 0]]) events_ids = [12, 24] new_trigger = _combine_triggers(triggers, events_ids) assert_array_equal(np.unique(new_trigger), np.unique([0, 12, 24])) pytest.raises(ValueError, read_raw_egi, egi_fname, include=['Foo'], preload=False) pytest.raises(ValueError, read_raw_egi, egi_fname, exclude=['Bar'], preload=False) for ii, k in enumerate(include, 1): assert (k in raw.event_id) assert (raw.event_id[k] == ii) @requires_testing_data def test_io_egi_pns_mff(): """Test importing EGI MFF with PNS data.""" egi_fname_mff = op.join(data_path(), 'EGI', 'test_egi_pns.mff') raw = read_raw_egi(egi_fname_mff, include=None, preload=True, verbose='error') assert ('RawMff' in repr(raw)) pns_chans = pick_types(raw.info, ecg=True, bio=True, emg=True) assert_equal(len(pns_chans), 7) names = [raw.ch_names[x] for x in pns_chans] pns_names = ['Resp. Temperature'[:15], 'Resp. Pressure', 'ECG', 'Body Position', 'Resp. Effort Chest'[:15], 'Resp. Effort Abdomen'[:15], 'EMG-Leg'] _test_raw_reader(read_raw_egi, input_fname=egi_fname_mff, channel_naming='EEG %03d', verbose='error') assert_equal(names, pns_names) mat_names = [ 'Resp_Temperature'[:15], 'Resp_Pressure', 'ECG', 'Body_Position', 'Resp_Effort_Chest'[:15], 'Resp_Effort_Abdomen'[:15], 'EMGLeg' ] egi_fname_mat = op.join(data_path(), 'EGI', 'test_egi_pns.mat') mc = sio.loadmat(egi_fname_mat) for ch_name, ch_idx, mat_name in zip(pns_names, pns_chans, mat_names): print('Testing {}'.format(ch_name)) mc_key = [x for x in mc.keys() if mat_name in x][0] cal = raw.info['chs'][ch_idx]['cal'] mat_data = mc[mc_key] * cal raw_data = raw[ch_idx][0] assert_array_equal(mat_data, raw_data) @requires_testing_data def test_io_egi_pns_mff_bug(): """Test importing EGI MFF with PNS data (BUG).""" egi_fname_mff = op.join(data_path(), 'EGI', 'test_egi_pns_bug.mff') with pytest.warns(RuntimeWarning, match='EGI PSG sample bug'): raw = read_raw_egi(egi_fname_mff, include=None, preload=True, verbose='warning') egi_fname_mat = op.join(data_path(), 'EGI', 'test_egi_pns.mat') mc = sio.loadmat(egi_fname_mat) pns_chans = pick_types(raw.info, ecg=True, bio=True, emg=True) pns_names = ['Resp. Temperature'[:15], 'Resp. Pressure', 'ECG', 'Body Position', 'Resp. Effort Chest'[:15], 'Resp. Effort Abdomen'[:15], 'EMG-Leg'] mat_names = [ 'Resp_Temperature'[:15], 'Resp_Pressure', 'ECG', 'Body_Position', 'Resp_Effort_Chest'[:15], 'Resp_Effort_Abdomen'[:15], 'EMGLeg' ] for ch_name, ch_idx, mat_name in zip(pns_names, pns_chans, mat_names): print('Testing {}'.format(ch_name)) mc_key = [x for x in mc.keys() if mat_name in x][0] cal = raw.info['chs'][ch_idx]['cal'] mat_data = mc[mc_key] * cal mat_data[:, -1] = 0 # The MFF has one less sample, the last one raw_data = raw[ch_idx][0] assert_array_equal(mat_data, raw_data) run_tests_if_main()