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# -*- coding: utf-8 -*-
# Authors: Denis A. Engemann <denis.engemann@gmail.com>
# 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()
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