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# -*- coding: utf-8 -*-
"""Test reading of NEDF format."""
# Author: Tristan Stenner <nedf@nicht.dienstli.ch>
#
# License: BSD-3-Clause
import os.path as op
import pytest
from numpy.testing import assert_allclose, assert_array_equal
from mne import find_events
from mne.io.constants import FIFF
from mne.io.nedf import read_raw_nedf, _parse_nedf_header
from mne.datasets import testing
from mne.io.tests.test_raw import _test_raw_reader
eeg_path = testing.data_path(download=False, verbose=True)
eegfile = op.join(eeg_path, 'nedf', 'testdata.nedf')
stimhdr = b"""
<nedf>
<NEDFversion>1.3</NEDFversion>
<NumberOfChannelsOfAccelerometer>%d</NumberOfChannelsOfAccelerometer>
<EEGSettings>
<TotalNumberOfChannels>4</TotalNumberOfChannels>
<EEGSamplingRate>500</EEGSamplingRate>
<EEGMontage><C>A</C><C>B</C><C>C</C><C>D</C></EEGMontage>
<NumberOfRecordsOfEEG>11</NumberOfRecordsOfEEG>
</EEGSettings>
<STIMSettings/>
</nedf>\x00"""
@pytest.mark.parametrize('nacc', (0, 3))
def test_nedf_header_parser(nacc):
"""Test NEDF header parsing and dtype extraction."""
with pytest.warns(RuntimeWarning, match='stim channels.*ignored'):
info, dt, dt_last, n_samples, n_full = _parse_nedf_header(
stimhdr % nacc)
assert n_samples == 11
assert n_full == 2
nchan = 4
assert info['nchan'] == nchan
assert dt.itemsize == 200 + nacc * 2
if nacc:
assert dt.names[0] == 'acc'
assert dt['acc'].shape == (nacc,)
assert dt['data'].shape == (5,) # blocks of 5 EEG samples each
assert dt_last['data'].shape == (1,) # plus one last extra one
eegsampledt = dt['data'].subdtype[0]
assert eegsampledt.names == ('eeg', 'stim', 'trig')
assert eegsampledt['eeg'].shape == (nchan, 3)
assert eegsampledt['stim'].shape == (2, nchan, 3)
def test_invalid_headers():
"""Test that invalid headers raise exceptions."""
tpl = b"""<nedf>
<NEDFversion>1.3</NEDFversion>
<EEGSettings>
%s
<EEGMontage><C>A</C><C>B</C><C>C</C><C>D</C></EEGMontage>
</EEGSettings>
</nedf>\x00"""
nchan = b'<TotalNumberOfChannels>4</TotalNumberOfChannels>'
sr = b'<EEGSamplingRate>500</EEGSamplingRate>'
hdr = {
'null':
b'No null terminator',
'Unknown additional':
(b'<a><NEDFversion>1.3</NEDFversion>' +
b'<AdditionalChannelStatus>???</AdditionalChannelStatus></a>\x00'), # noqa: E501
'No EEG channels found':
b'<a><NEDFversion>1.3</NEDFversion></a>\x00',
'TotalNumberOfChannels not found':
tpl % b'No nchan.',
'!= channel count':
tpl % (sr + b'<TotalNumberOfChannels>52</TotalNumberOfChannels>'),
'EEGSamplingRate not found':
tpl % nchan,
'NumberOfRecordsOfEEG not found':
tpl % (sr + nchan),
}
for match, invalid_hdr in hdr.items():
with pytest.raises(RuntimeError, match=match):
_parse_nedf_header(invalid_hdr)
sus_hdrs = {
'unsupported': b'<a><NEDFversion>25</NEDFversion></a>\x00',
'tested': (
b'<a><NEDFversion>1.3</NEDFversion><stepDetails>' +
b'<DeviceClass>STARSTIM</DeviceClass></stepDetails></a>\x00'),
}
for match, sus_hdr in sus_hdrs.items():
with pytest.warns(RuntimeWarning, match=match):
with pytest.raises(RuntimeError, match='No EEG channels found'):
_parse_nedf_header(sus_hdr)
@testing.requires_testing_data
def test_nedf_data():
"""Test reading raw NEDF files."""
raw = read_raw_nedf(eegfile)
nsamples = len(raw)
assert nsamples == 32538
events = find_events(raw, shortest_event=1)
assert len(events) == 4
assert_array_equal(events[:, 2], [1, 1, 1, 1])
onsets = events[:, 0] / raw.info['sfreq']
assert raw.info['sfreq'] == 500
data_end = raw.get_data('Fp1', nsamples - 100, nsamples).mean()
assert_allclose(data_end, .0176, atol=.01)
assert_allclose(raw.get_data('Fpz', 0, 100).mean(), .0185, atol=.01)
assert_allclose(onsets, [22.384, 38.238, 49.496, 63.15])
assert raw.info['meas_date'].year == 2019
assert raw.ch_names[2] == 'AF7'
for ch in raw.info['chs'][:-1]:
assert ch['kind'] == FIFF.FIFFV_EEG_CH
assert ch['unit'] == FIFF.FIFF_UNIT_V
assert raw.info['chs'][-1]['kind'] == FIFF.FIFFV_STIM_CH
assert raw.info['chs'][-1]['unit'] == FIFF.FIFF_UNIT_V
# full tests
_test_raw_reader(read_raw_nedf, filename=eegfile)
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