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"""Data Equivalence Tests"""
from __future__ import print_function
# Author: Teon Brooks <teon.brooks@gmail.com>
#
# License: BSD (3-clause)
import os.path as op
import inspect
import warnings
from nose.tools import assert_equal, assert_raises, assert_true
import numpy as np
from numpy.testing import (assert_array_almost_equal, assert_array_equal,
assert_allclose)
from mne.utils import _TempDir, run_tests_if_main
from mne import pick_types, find_events
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
FILE = inspect.getfile(inspect.currentframe())
data_dir = op.join(op.dirname(op.abspath(FILE)), 'data')
vhdr_path = op.join(data_dir, 'test.vhdr')
vmrk_path = op.join(data_dir, 'test.vmrk')
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')
vmrk_old_path = op.join(data_dir,
'test_old_layout_latin1_software_filter.vmrk')
vhdr_v2_path = op.join(data_dir, 'testv2.vhdr')
vmrk_v2_path = op.join(data_dir, 'testv2.vmrk')
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')
montage = op.join(data_dir, 'test.hpts')
eeg_bin = op.join(data_dir, 'test_bin_raw.fif')
eog = ['HL', 'HR', 'Vb']
warnings.simplefilter('always')
def test_brainvision_data_highpass_filters():
"""Test reading raw Brain Vision files with amplifier filter settings."""
# Homogeneous highpass in seconds (default measurement unit)
with warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_highpass_path,
montage=montage, eog=eog)
assert_true(all('parse triggers that' in str(ww.message) for ww in w))
assert_equal(raw.info['highpass'], 0.1)
assert_equal(raw.info['lowpass'], 250.)
# Heterogeneous highpass in seconds (default measurement unit)
with warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_mixed_highpass_path,
montage=montage, eog=eog)
trigger_warning = ['parse triggers that' 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_true(all(any([trg, lp, hp]) for trg, lp, hp in expected_warnings))
assert_equal(raw.info['highpass'], 0.1)
assert_equal(raw.info['lowpass'], 250.)
# Homogeneous highpass in Hertz
with warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_highpass_hz_path,
montage=montage, eog=eog)
assert_true(all('parse triggers that' in str(ww.message) for ww in w))
assert_equal(raw.info['highpass'], 10.)
assert_equal(raw.info['lowpass'], 250.)
# Heterogeneous highpass in Hertz
with warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_mixed_highpass_hz_path,
montage=montage, eog=eog)
trigger_warning = ['parse triggers that' 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_true(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 reading raw Brain Vision files with amplifier LP filter settings"""
# Homogeneous lowpass in Hertz (default measurement unit)
with warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_lowpass_path,
montage=montage, eog=eog)
assert_true(all('parse triggers that' in str(ww.message) for ww in w))
assert_equal(raw.info['highpass'], 0.1)
assert_equal(raw.info['lowpass'], 250.)
# Heterogeneous lowpass in Hertz (default measurement unit)
with warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_mixed_lowpass_path,
montage=montage, eog=eog)
trigger_warning = ['parse triggers that' 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_true(all(any([trg, lp, hp]) for trg, lp, hp in expected_warnings))
assert_equal(raw.info['highpass'], 0.1)
assert_equal(raw.info['lowpass'], 250.)
# Homogeneous lowpass in seconds
with warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_lowpass_s_path,
montage=montage, eog=eog)
assert_true(all('parse triggers that' in str(ww.message) for ww in w))
assert_equal(raw.info['highpass'], 0.1)
assert_equal(raw.info['lowpass'], 250.)
# Heterogeneous lowpass in seconds
with warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_mixed_lowpass_s_path,
montage=montage, eog=eog)
trigger_warning = ['parse triggers that' 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_true(all(any([trg, lp, hp]) for trg, lp, hp in expected_warnings))
assert_equal(raw.info['highpass'], 0.1)
assert_equal(raw.info['lowpass'], 250.)
def test_brainvision_data_partially_disabled_hw_filters():
"""Test reading raw Brain Vision files with heterogeneous amplifier
filter settings including non-numeric values
"""
with warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision,
vhdr_fname=vhdr_partially_disabled_hw_filter_path,
montage=montage, eog=eog)
trigger_warning = ['parse triggers that' 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_true(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 warnings.catch_warnings(record=True) as w: # event parsing
raw = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_old_path,
eog=("VEOGo", "VEOGu", "HEOGli", "HEOGre"), misc=("A2",))
assert_true(all('software filter detected' in str(ww.message) for ww in w))
assert_equal(raw.info['highpass'], 1. / 0.9)
assert_equal(raw.info['lowpass'], 50.)
def test_brainvision_data():
"""Test reading raw Brain Vision files."""
assert_raises(IOError, read_raw_brainvision, vmrk_path)
assert_raises(ValueError, read_raw_brainvision, vhdr_path, montage,
preload=True, scale="foo")
with warnings.catch_warnings(record=True) as w: # event parsing
raw_py = _test_raw_reader(
read_raw_brainvision, vhdr_fname=vhdr_path, montage=montage,
eog=eog, misc='auto')
assert_true(all('parse triggers that' in str(ww.message) for ww in w))
assert_true('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, add_eeg_ref=False)
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,
response_trig_shift=1000)
def test_events():
"""Test reading and modifying events."""
tempdir = _TempDir()
# check that events are read and stim channel is synthesized correcly
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
raw = read_raw_brainvision(vhdr_path, eog=eog, preload=True)
events = raw._get_brainvision_events()
assert_array_equal(events, [[487, 1, 253],
[497, 1, 255],
[1770, 1, 254],
[1780, 1, 255],
[3253, 1, 254],
[3263, 1, 255],
[4936, 1, 253],
[4946, 1, 255],
[6000, 1, 255],
[6620, 1, 254],
[6630, 1, 255]])
assert_equal(len(w), 1) # for dropping Sync & R255 events
# check that events are read and stim channel is synthesized correcly and
# response triggers are shifted like they're supposed to be.
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
raw = read_raw_brainvision(vhdr_path, eog=eog, preload=True,
response_trig_shift=1000)
events = raw._get_brainvision_events()
assert_array_equal(events, [[487, 1, 253],
[497, 1, 255],
[1770, 1, 254],
[1780, 1, 255],
[3253, 1, 254],
[3263, 1, 255],
[4936, 1, 253],
[4946, 1, 255],
[6000, 1, 1255],
[6620, 1, 254],
[6630, 1, 255]])
assert_equal(len(w), 1) # for dropping Sync & R255 events
# check that events are read and stim channel is synthesized correcly and
# response triggers are ignored.
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
raw = read_raw_brainvision(vhdr_path, eog=eog, preload=True,
response_trig_shift=None)
events = raw._get_brainvision_events()
assert_array_equal(events, [[487, 1, 253],
[497, 1, 255],
[1770, 1, 254],
[1780, 1, 255],
[3253, 1, 254],
[3263, 1, 255],
[4936, 1, 253],
[4946, 1, 255],
[6620, 1, 254],
[6630, 1, 255]])
assert_equal(len(w), 1) # for dropping Sync & R255 events
# check that events are read properly when event_id is specified for
# auxiliary events
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
raw = read_raw_brainvision(vhdr_path, eog=eog, preload=True,
response_trig_shift=None,
event_id={'Sync On': 5})
events = raw._get_brainvision_events()
assert_array_equal(events, [[487, 1, 253],
[497, 1, 255],
[1770, 1, 254],
[1780, 1, 255],
[3253, 1, 254],
[3263, 1, 255],
[4936, 1, 253],
[4946, 1, 255],
[6620, 1, 254],
[6630, 1, 255],
[7630, 1, 5]])
assert_equal(len(w), 1) # parsing Sync event, missing R255
assert_raises(TypeError, read_raw_brainvision, vhdr_path, eog=eog,
preload=True, response_trig_shift=0.1)
assert_raises(TypeError, read_raw_brainvision, vhdr_path, eog=eog,
preload=True, response_trig_shift=np.nan)
# Test that both response_trig_shit and event_id can be set
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
read_raw_brainvision(vhdr_path, eog=eog, preload=False,
response_trig_shift=100,
event_id={'Sync On': 5})
mne_events = find_events(raw, stim_channel='STI 014')
assert_array_equal(events[:, [0, 2]], mne_events[:, [0, 2]])
assert_equal(len(w), 0) # parsing the Sync event
# modify events and check that stim channel is updated
index = events[:, 2] == 255
events = events[index]
raw._set_brainvision_events(events)
mne_events = find_events(raw, stim_channel='STI 014')
assert_array_equal(events[:, [0, 2]], mne_events[:, [0, 2]])
# remove events
nchan = raw.info['nchan']
ch_name = raw.info['chs'][-2]['ch_name']
events = np.empty((0, 3))
raw._set_brainvision_events(events)
assert_equal(raw.info['nchan'], nchan)
assert_equal(len(raw._data), nchan)
assert_equal(raw.info['chs'][-2]['ch_name'], ch_name)
assert_equal(len(find_events(raw, 'STI 014')), 0)
assert_allclose(raw[-1][0], 0.)
fname = op.join(tempdir, 'evt_raw.fif')
raw.save(fname)
# add events back in
events = [[10, 1, 2]]
raw._set_brainvision_events(events)
assert_equal(raw.info['nchan'], nchan)
assert_equal(len(raw._data), nchan)
assert_equal(raw.info['chs'][-1]['ch_name'], 'STI 014')
run_tests_if_main()
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