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# -*- coding: utf-8 -*-
"""Test reading of BrainVision format."""
# Author: Teon Brooks <teon.brooks@gmail.com>
# Stefan Appelhoff <stefan.appelhoff@mailbox.org>
#
# License: BSD (3-clause)
import os.path as op
from os import unlink
import shutil
import numpy as np
from numpy.testing import (assert_array_almost_equal, assert_array_equal,
assert_allclose, assert_equal)
import pytest
from tempfile import NamedTemporaryFile
from mne.utils import _TempDir, run_tests_if_main
from mne import pick_types, read_annotations, concatenate_raws
from mne.io.constants import FIFF
from mne.io import read_raw_fif, read_raw_brainvision
from mne.io.tests.test_raw import _test_raw_reader
from mne.datasets import testing
from mne.annotations import events_from_annotations
data_dir = op.join(op.dirname(__file__), 'data')
vhdr_path = op.join(data_dir, 'test.vhdr')
vmrk_path = op.join(data_dir, 'test.vmrk')
eeg_path = op.join(data_dir, 'test.eeg')
vhdr_partially_disabled_hw_filter_path = op.join(data_dir,
'test_partially_disabled'
'_hw_filter.vhdr')
vhdr_old_path = op.join(data_dir,
'test_old_layout_latin1_software_filter.vhdr')
vhdr_v2_path = op.join(data_dir, 'testv2.vhdr')
vhdr_highpass_path = op.join(data_dir, 'test_highpass.vhdr')
vhdr_mixed_highpass_path = op.join(data_dir, 'test_mixed_highpass.vhdr')
vhdr_highpass_hz_path = op.join(data_dir, 'test_highpass_hz.vhdr')
vhdr_mixed_highpass_hz_path = op.join(data_dir, 'test_mixed_highpass_hz.vhdr')
# Not a typo: we can reuse the highpass file for the lowpass (Hz) test
vhdr_lowpass_path = op.join(data_dir, 'test_highpass.vhdr')
vhdr_mixed_lowpass_path = op.join(data_dir, 'test_mixed_lowpass.vhdr')
vhdr_lowpass_s_path = op.join(data_dir, 'test_lowpass_s.vhdr')
vhdr_mixed_lowpass_s_path = op.join(data_dir, 'test_mixed_lowpass_s.vhdr')
# VHDR exported with neuroone
data_path = testing.data_path(download=False)
neuroone_vhdr = op.join(data_path, 'Brainvision', 'test_NO.vhdr')
# Test for nanovolts as unit
vhdr_nV_path = op.join(data_dir, 'test_nV.vhdr')
# Test bad date
vhdr_bad_date = op.join(data_dir, 'test_bad_date.vhdr')
eeg_bin = op.join(data_dir, 'test_bin_raw.fif')
eog = ['HL', 'HR', 'Vb']
# XXX: BUG we cannot parse test.hpts FastSCAN file to create a DigMontage
# (plus I've removed montage from all the read_raw_brainvision and nothing
# broke, so we were not testing that set_montage in brainvision was
# working)
# This should be amend in its own PR.
montage = op.join(data_dir, 'test.hpts')
def test_orig_units(recwarn):
"""Test exposure of original channel units."""
raw = read_raw_brainvision(vhdr_path)
orig_units = raw._orig_units
assert len(orig_units) == 32
assert orig_units['FP1'] == u'µV'
assert orig_units['CP5'] == 'n/a' # originally BS, not a valid unit
assert orig_units['CP6'] == u'µS'
assert orig_units['HL'] == 'n/a' # originally ARU, not a valid unit
assert orig_units['HR'] == 'n/a' # originally uS ...
assert orig_units['Vb'] == 'S'
assert orig_units['ReRef'] == 'C'
DATE_TEST_CASES = np.array([
('Mk1=New Segment,,1,1,0,20131113161403794232\n', # content
[1384359243, 794231], # meas_date internal representation
'2013-11-13 16:14:03 GMT'), # meas_date representation
(('Mk1=New Segment,,1,1,0,20070716122240937454\n'
'Mk2=New Segment,,2,1,0,20070716122240937455\n'),
[1184588560, 937453],
'2007-07-16 12:22:40 GMT'),
('Mk1=New Segment,,1,1,0,\nMk2=New Segment,,2,1,0,20070716122240937454\n',
[1184588560, 937453],
'2007-07-16 12:22:40 GMT'),
('Mk1=STATUS,,1,1,0\n', None, 'unspecified'),
('Mk1=New Segment,,1,1,0,\n', None, 'unspecified'),
('Mk1=New Segment,,1,1,0\n', None, 'unspecified'),
('Mk1=New Segment,,1,1,0,00000000000304125000', None, 'unspecified'),
], dtype=np.dtype({
'names': ['content', 'meas_date', 'meas_date_repr'],
'formats': [object, object, 'U22']
}))
@pytest.fixture(scope='session')
def _mocked_meas_date_data(tmpdir_factory):
"""Prepare files for mocked_meas_date_file fixture."""
# Prepare the files
tmpdir = str(tmpdir_factory.mktemp('brainvision_mocked_meas_date'))
vhdr_fname, vmrk_fname, eeg_fname = [
op.join(tmpdir, op.basename(ff))
for ff in [vhdr_path, vmrk_path, eeg_path]
]
for orig, dest in zip([vhdr_path, eeg_path], [vhdr_fname, eeg_fname]):
shutil.copyfile(orig, dest)
# Get the marker information
with open(vmrk_path, 'r') as fin:
lines = fin.readlines()
return vhdr_fname, vmrk_fname, lines
@pytest.fixture(scope='session', params=[tt for tt in DATE_TEST_CASES])
def mocked_meas_date_file(_mocked_meas_date_data, request):
"""Prepare a generator for use in test_meas_date."""
MEAS_DATE_LINE = 11 # see test.vmrk file
vhdr_fname, vmrk_fname, lines = _mocked_meas_date_data
lines[MEAS_DATE_LINE] = request.param['content']
with open(vmrk_fname, 'w') as fout:
fout.writelines(lines)
yield (
vhdr_fname, request.param['meas_date'], request.param['meas_date_repr']
)
def test_meas_date(mocked_meas_date_file):
"""Test successful extraction of measurement date."""
vhdr_f, expected_meas, expected_meas_repr = mocked_meas_date_file
raw = read_raw_brainvision(vhdr_f)
assert expected_meas_repr in repr(raw.info)
if expected_meas is None:
assert raw.info['meas_date'] is None
else:
assert_allclose(raw.info['meas_date'], expected_meas)
def test_vhdr_codepage_ansi():
"""Test BV reading with ANSI codepage."""
raw_init = read_raw_brainvision(vhdr_path)
data_expected, times_expected = raw_init[:]
tempdir = _TempDir()
ansi_vhdr_path = op.join(tempdir, op.split(vhdr_path)[-1])
ansi_vmrk_path = op.join(tempdir, op.split(vmrk_path)[-1])
ansi_eeg_path = op.join(tempdir, op.split(eeg_path)[-1])
# copy data file
shutil.copy(eeg_path, ansi_eeg_path)
# modify header file
with open(ansi_vhdr_path, 'wb') as fout:
with open(vhdr_path, 'rb') as fin:
for line in fin:
# Common Infos section
if line.startswith(b'Codepage'):
line = b'Codepage=ANSI\n'
fout.write(line)
# modify marker file
with open(ansi_vmrk_path, 'wb') as fout:
with open(vmrk_path, 'rb') as fin:
for line in fin:
# Common Infos section
if line.startswith(b'Codepage'):
line = b'Codepage=ANSI\n'
fout.write(line)
raw = read_raw_brainvision(ansi_vhdr_path)
data_new, times_new = raw[:]
assert_equal(raw_init.ch_names, raw.ch_names)
assert_allclose(data_new, data_expected, atol=1e-15)
assert_allclose(times_new, times_expected, atol=1e-15)
def test_ascii():
"""Test ASCII BV reading."""
raw = read_raw_brainvision(vhdr_path)
tempdir = _TempDir()
ascii_vhdr_path = op.join(tempdir, op.split(vhdr_path)[-1])
# copy marker file
shutil.copy(vhdr_path.replace('.vhdr', '.vmrk'),
ascii_vhdr_path.replace('.vhdr', '.vmrk'))
# modify header file
skipping = False
with open(ascii_vhdr_path, 'wb') as fout:
with open(vhdr_path, 'rb') as fin:
for line in fin:
# Common Infos section
if line.startswith(b'DataFormat'):
line = b'DataFormat=ASCII\n'
elif line.startswith(b'DataFile='):
line = b'DataFile=test.dat\n'
# Replace the "'Binary Infos'" section
elif line.startswith(b'[Binary Infos]'):
skipping = True
fout.write(b'[ASCII Infos]\nDecimalSymbol=.\nSkipLines=1\n'
b'SkipColumns=0\n\n')
elif skipping and line.startswith(b'['):
skipping = False
if not skipping:
fout.write(line)
# create the .dat file
data, times = raw[:]
with open(ascii_vhdr_path.replace('.vhdr', '.dat'), 'wb') as fid:
fid.write(b' '.join(ch_name.encode('ASCII')
for ch_name in raw.ch_names) + b'\n')
fid.write(b'\n'.join(b' '.join(b'%.3f' % dd for dd in d)
for d in data.T / raw._cals))
raw = read_raw_brainvision(ascii_vhdr_path)
data_new, times_new = raw[:]
assert_allclose(data_new, data, atol=1e-15)
assert_allclose(times_new, times)
def test_brainvision_data_highpass_filters():
"""Test reading raw Brain Vision files with amplifier filter settings."""
# Homogeneous highpass in seconds (default measurement unit)
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_highpass_path, eog=eog
)
assert_equal(raw.info['highpass'], 1. / (2 * np.pi * 10))
assert_equal(raw.info['lowpass'], 250.)
# Heterogeneous highpass in seconds (default measurement unit)
with pytest.warns(RuntimeWarning, match='different .*pass filters') as w:
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_mixed_highpass_path,
eog=eog)
lowpass_warning = ['different lowpass filters' in str(ww.message)
for ww in w]
highpass_warning = ['different highpass filters' in str(ww.message)
for ww in w]
expected_warnings = zip(lowpass_warning, highpass_warning)
assert (all(any([lp, hp]) for lp, hp in expected_warnings))
assert_equal(raw.info['highpass'], 1. / (2 * np.pi * 10))
assert_equal(raw.info['lowpass'], 250.)
# Homogeneous highpass in Hertz
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_highpass_hz_path,
eog=eog)
assert_equal(raw.info['highpass'], 10.)
assert_equal(raw.info['lowpass'], 250.)
# Heterogeneous highpass in Hertz
with pytest.warns(RuntimeWarning, match='different .*pass filters') as w:
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_mixed_highpass_hz_path,
eog=eog)
trigger_warning = ['will be dropped' in str(ww.message)
for ww in w]
lowpass_warning = ['different lowpass filters' in str(ww.message)
for ww in w]
highpass_warning = ['different highpass filters' in str(ww.message)
for ww in w]
expected_warnings = zip(trigger_warning, lowpass_warning, highpass_warning)
assert (all(any([trg, lp, hp]) for trg, lp, hp in expected_warnings))
assert_equal(raw.info['highpass'], 5.)
assert_equal(raw.info['lowpass'], 250.)
def test_brainvision_data_lowpass_filters():
"""Test files with amplifier LP filter settings."""
# Homogeneous lowpass in Hertz (default measurement unit)
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_lowpass_path, eog=eog
)
assert_equal(raw.info['highpass'], 1. / (2 * np.pi * 10))
assert_equal(raw.info['lowpass'], 250.)
# Heterogeneous lowpass in Hertz (default measurement unit)
with pytest.warns(RuntimeWarning) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_mixed_lowpass_path, eog=eog
)
lowpass_warning = ['different lowpass filters' in str(ww.message)
for ww in w]
highpass_warning = ['different highpass filters' in str(ww.message)
for ww in w]
expected_warnings = zip(lowpass_warning, highpass_warning)
assert (all(any([lp, hp]) for lp, hp in expected_warnings))
assert_equal(raw.info['highpass'], 1. / (2 * np.pi * 10))
assert_equal(raw.info['lowpass'], 250.)
# Homogeneous lowpass in seconds
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_lowpass_s_path, eog=eog
)
assert_equal(raw.info['highpass'], 1. / (2 * np.pi * 10))
assert_equal(raw.info['lowpass'], 1. / (2 * np.pi * 0.004))
# Heterogeneous lowpass in seconds
with pytest.warns(RuntimeWarning) as w: # filter settings
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_mixed_lowpass_s_path, eog=eog
)
lowpass_warning = ['different lowpass filters' in str(ww.message)
for ww in w]
highpass_warning = ['different highpass filters' in str(ww.message)
for ww in w]
expected_warnings = zip(lowpass_warning, highpass_warning)
assert (all(any([lp, hp]) for lp, hp in expected_warnings))
assert_equal(raw.info['highpass'], 1. / (2 * np.pi * 10))
assert_equal(raw.info['lowpass'], 1. / (2 * np.pi * 0.004))
def test_brainvision_data_partially_disabled_hw_filters():
"""Test heterogeneous filter settings including non-numeric values."""
with pytest.warns(RuntimeWarning) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision,
vhdr_fname=vhdr_partially_disabled_hw_filter_path, eog=eog
)
trigger_warning = ['will be dropped' in str(ww.message)
for ww in w]
lowpass_warning = ['different lowpass filters' in str(ww.message)
for ww in w]
highpass_warning = ['different highpass filters' in str(ww.message)
for ww in w]
expected_warnings = zip(trigger_warning, lowpass_warning, highpass_warning)
assert (all(any([trg, lp, hp]) for trg, lp, hp in expected_warnings))
assert_equal(raw.info['highpass'], 0.)
assert_equal(raw.info['lowpass'], 500.)
def test_brainvision_data_software_filters_latin1_global_units():
"""Test reading raw Brain Vision files."""
with pytest.warns(RuntimeWarning, match='software filter'):
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_old_path,
eog=("VEOGo", "VEOGu", "HEOGli", "HEOGre"), misc=("A2",))
assert_equal(raw.info['highpass'], 1. / (2 * np.pi * 0.9))
assert_equal(raw.info['lowpass'], 50.)
def test_brainvision_data():
"""Test reading raw Brain Vision files."""
pytest.raises(IOError, read_raw_brainvision, vmrk_path)
pytest.raises(ValueError, read_raw_brainvision, vhdr_path,
preload=True, scale="foo")
raw_py = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_path, eog=eog, misc='auto'
)
assert ('RawBrainVision' in repr(raw_py))
assert_equal(raw_py.info['highpass'], 0.)
assert_equal(raw_py.info['lowpass'], 250.)
picks = pick_types(raw_py.info, meg=False, eeg=True, exclude='bads')
data_py, times_py = raw_py[picks]
# compare with a file that was generated using MNE-C
raw_bin = read_raw_fif(eeg_bin, preload=True)
picks = pick_types(raw_py.info, meg=False, eeg=True, exclude='bads')
data_bin, times_bin = raw_bin[picks]
assert_array_almost_equal(data_py, data_bin)
assert_array_almost_equal(times_py, times_bin)
# Make sure EOG channels are marked correctly
for ch in raw_py.info['chs']:
if ch['ch_name'] in eog:
assert_equal(ch['kind'], FIFF.FIFFV_EOG_CH)
elif ch['ch_name'] == 'STI 014':
assert_equal(ch['kind'], FIFF.FIFFV_STIM_CH)
elif ch['ch_name'] in ('CP5', 'CP6'):
assert_equal(ch['kind'], FIFF.FIFFV_MISC_CH)
assert_equal(ch['unit'], FIFF.FIFF_UNIT_NONE)
elif ch['ch_name'] == 'ReRef':
assert_equal(ch['kind'], FIFF.FIFFV_MISC_CH)
assert_equal(ch['unit'], FIFF.FIFF_UNIT_CEL)
elif ch['ch_name'] in raw_py.info['ch_names']:
assert_equal(ch['kind'], FIFF.FIFFV_EEG_CH)
assert_equal(ch['unit'], FIFF.FIFF_UNIT_V)
else:
raise RuntimeError("Unknown Channel: %s" % ch['ch_name'])
# test loading v2
read_raw_brainvision(vhdr_v2_path, eog=eog, preload=True,
verbose='error')
# For the nanovolt unit test we use the same data file with a different
# header file.
raw_nV = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_nV_path, eog=eog, misc='auto'
)
assert_equal(raw_nV.info['chs'][0]['ch_name'], 'FP1')
assert_equal(raw_nV.info['chs'][0]['kind'], FIFF.FIFFV_EEG_CH)
data_nanovolt, _ = raw_nV[0]
assert_array_almost_equal(data_py[0, :], data_nanovolt[0, :])
def test_brainvision_vectorized_data():
"""Test reading BrainVision data files with vectorized data."""
with pytest.warns(RuntimeWarning, match='software filter'):
raw = read_raw_brainvision(vhdr_old_path, preload=True)
assert_array_equal(raw._data.shape, (29, 251))
first_two_samples_all_chs = np.array([[+5.22000008e-06, +5.10000000e-06],
[+2.10000000e-06, +2.27000008e-06],
[+1.15000000e-06, +1.33000002e-06],
[+4.00000000e-07, +4.00000000e-07],
[-3.02999992e-06, -2.82000008e-06],
[+2.71000004e-06, +2.45000000e-06],
[+2.41000004e-06, +2.36000004e-06],
[+1.01999998e-06, +1.18000002e-06],
[-1.33999996e-06, -1.25000000e-06],
[-2.60000000e-06, -2.46000004e-06],
[+6.80000019e-07, +8.00000000e-07],
[+1.48000002e-06, +1.48999996e-06],
[+1.61000004e-06, +1.51000004e-06],
[+7.19999981e-07, +8.60000038e-07],
[-3.00000000e-07, -4.00000006e-08],
[-1.20000005e-07, +6.00000024e-08],
[+8.19999981e-07, +9.89999962e-07],
[+1.13000002e-06, +1.28000002e-06],
[+1.08000002e-06, +1.33999996e-06],
[+2.20000005e-07, +5.69999981e-07],
[-4.09999990e-07, +4.00000006e-08],
[+5.19999981e-07, +9.39999962e-07],
[+1.01000004e-06, +1.51999998e-06],
[+1.01000004e-06, +1.55000000e-06],
[-1.43000002e-06, -1.13999996e-06],
[+3.65000000e-06, +3.65999985e-06],
[+4.15999985e-06, +3.79000015e-06],
[+9.26999969e-06, +8.95999985e-06],
[-7.35999985e-06, -7.18000031e-06],
])
assert_array_almost_equal(raw._data[:, :2], first_two_samples_all_chs)
def test_coodinates_extraction():
"""Test reading of [Coordinates] section if present."""
# vhdr 2 has a Coordinates section
with pytest.warns(RuntimeWarning, match='coordinate information'):
raw = read_raw_brainvision(vhdr_v2_path)
# Basic check of extracted coordinates
assert raw.info['dig'] is not None
diglist = raw.info['dig']
coords = np.array([dig['r'] for dig in diglist])
EXPECTED_SHAPE = (
len(raw.ch_names) - 4, # HL, HR, Vb, ReRef are not set in dig
3,
)
assert coords.shape == EXPECTED_SHAPE
# Make sure the scaling seems right
# a coordinate more than 20cm away from origin is implausible
assert coords.max() < 0.2
# vhdr 1 does not have a Coordinates section
raw2 = read_raw_brainvision(vhdr_path)
assert raw2.info['dig'] is None
@testing.requires_testing_data
def test_brainvision_neuroone_export():
"""Test Brainvision file exported with neuroone system."""
raw = read_raw_brainvision(neuroone_vhdr, verbose='error')
assert raw.info['meas_date'] is None
assert len(raw.info['chs']) == 65
assert raw.info['sfreq'] == 5000.
@testing.requires_testing_data
def test_read_vmrk_annotations():
"""Test load brainvision annotations."""
sfreq = 1000.0
# Test vmrk file without annotations
# delete=False is for Windows compatibility
with open(vmrk_path) as myfile:
head = [next(myfile) for x in range(6)]
with NamedTemporaryFile(mode='w+', suffix='.vmrk', delete=False) as temp:
for item in head:
temp.write(item)
temp.seek(0)
read_annotations(temp.name, sfreq=sfreq)
try:
temp.close()
unlink(temp.name)
except IOError:
pass
@testing.requires_testing_data
def test_read_vhdr_annotations_and_events():
"""Test load brainvision annotations and parse them to events."""
sfreq = 1000.0
expected_orig_time = 1384359243.794231
expected_onset_latency = np.array(
[0, 486., 496., 1769., 1779., 3252., 3262., 4935., 4945., 5999., 6619.,
6629., 7629., 7699.]
)
expected_annot_description = [
'New Segment/', 'Stimulus/S253', 'Stimulus/S255', 'Event/254',
'Stimulus/S255', 'Event/254', 'Stimulus/S255', 'Stimulus/S253',
'Stimulus/S255', 'Response/R255', 'Event/254', 'Stimulus/S255',
'SyncStatus/Sync On', 'Optic/O 1'
]
expected_events = np.stack([
expected_onset_latency,
np.zeros_like(expected_onset_latency),
[99999, 253, 255, 254, 255, 254, 255, 253, 255, 1255, 254, 255, 99998,
2001],
]).astype('int64').T
expected_event_id = {'New Segment/': 99999, 'Stimulus/S253': 253,
'Stimulus/S255': 255, 'Event/254': 254,
'Response/R255': 1255, 'SyncStatus/Sync On': 99998,
'Optic/O 1': 2001}
raw = read_raw_brainvision(vhdr_path, eog=eog)
# validate annotations
assert raw.annotations.orig_time == expected_orig_time
assert_allclose(raw.annotations.onset, expected_onset_latency / sfreq)
assert_array_equal(raw.annotations.description, expected_annot_description)
# validate event extraction
events, event_id = events_from_annotations(raw)
assert_array_equal(events, expected_events)
assert event_id == expected_event_id
# validate that None gives us a sorted list
expected_none_event_id = {desc: idx + 1 for idx, desc in enumerate(sorted(
event_id.keys()))}
events, event_id = events_from_annotations(raw, event_id=None)
assert event_id == expected_none_event_id
# Add some custom ones, plus a 2-digit one
s_10 = 'Stimulus/S 10'
raw.annotations.append([1, 2, 3], 10, ['ZZZ', s_10, 'YYY'])
expected_event_id.update(YYY=10001, ZZZ=10002) # others starting at 10001
expected_event_id[s_10] = 10
_, event_id = events_from_annotations(raw)
assert event_id == expected_event_id
# Concatenating two shouldn't change the resulting event_id
# (BAD and EDGE should be ignored)
with pytest.warns(RuntimeWarning, match='expanding outside'):
raw_concat = concatenate_raws([raw.copy(), raw.copy()])
_, event_id = events_from_annotations(raw_concat)
assert event_id == expected_event_id
@testing.requires_testing_data
def test_automatic_vmrk_sfreq_recovery():
"""Test proper sfreq inference by checking the onsets."""
assert_array_equal(read_annotations(vmrk_path, sfreq='auto'),
read_annotations(vmrk_path, sfreq=1000.0))
@testing.requires_testing_data
def test_event_id_stability_when_save_and_fif_reload(tmpdir):
"""Test load events from brainvision annotations when read_raw_fif."""
fname = op.join(str(tmpdir), 'bv-raw.fif')
raw = read_raw_brainvision(vhdr_path, eog=eog)
original_events, original_event_id = events_from_annotations(raw)
raw.save(fname)
raw = read_raw_fif(fname)
events, event_id = events_from_annotations(raw)
assert event_id == original_event_id
assert_array_equal(events, original_events)
run_tests_if_main()
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