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import inspect
import os.path as op
from numpy.testing import assert_array_equal, assert_equal
import pytest
import numpy as np
from mne import (pick_channels_regexp, pick_types, Epochs,
read_forward_solution, rename_channels,
pick_info, pick_channels, create_info)
from mne import __file__ as _root_init_fname
from mne.io import (read_raw_fif, RawArray, read_raw_bti, read_raw_kit,
read_info)
from mne.io.pick import (channel_indices_by_type, channel_type,
pick_types_forward, _picks_by_type)
from mne.io.constants import FIFF
from mne.datasets import testing
from mne.utils import run_tests_if_main, catch_logging
io_dir = op.join(op.dirname(inspect.getfile(inspect.currentframe())), '..')
data_path = testing.data_path(download=False)
fname_meeg = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif')
fname_mc = op.join(data_path, 'SSS', 'test_move_anon_movecomp_raw_sss.fif')
def test_pick_refs():
"""Test picking of reference sensors."""
infos = list()
# KIT
kit_dir = op.join(io_dir, 'kit', 'tests', 'data')
sqd_path = op.join(kit_dir, 'test.sqd')
mrk_path = op.join(kit_dir, 'test_mrk.sqd')
elp_path = op.join(kit_dir, 'test_elp.txt')
hsp_path = op.join(kit_dir, 'test_hsp.txt')
raw_kit = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path)
infos.append(raw_kit.info)
# BTi
bti_dir = op.join(io_dir, 'bti', 'tests', 'data')
bti_pdf = op.join(bti_dir, 'test_pdf_linux')
bti_config = op.join(bti_dir, 'test_config_linux')
bti_hs = op.join(bti_dir, 'test_hs_linux')
raw_bti = read_raw_bti(bti_pdf, bti_config, bti_hs, preload=False)
infos.append(raw_bti.info)
# CTF
fname_ctf_raw = op.join(io_dir, 'tests', 'data', 'test_ctf_comp_raw.fif')
raw_ctf = read_raw_fif(fname_ctf_raw)
raw_ctf.apply_gradient_compensation(2)
for info in infos:
info['bads'] = []
pytest.raises(ValueError, pick_types, info, meg='foo')
pytest.raises(ValueError, pick_types, info, ref_meg='foo')
picks_meg_ref = pick_types(info, meg=True, ref_meg=True)
picks_meg = pick_types(info, meg=True, ref_meg=False)
picks_ref = pick_types(info, meg=False, ref_meg=True)
assert_array_equal(picks_meg_ref,
np.sort(np.concatenate([picks_meg, picks_ref])))
picks_grad = pick_types(info, meg='grad', ref_meg=False)
picks_ref_grad = pick_types(info, meg=False, ref_meg='grad')
picks_meg_ref_grad = pick_types(info, meg='grad', ref_meg='grad')
assert_array_equal(picks_meg_ref_grad,
np.sort(np.concatenate([picks_grad,
picks_ref_grad])))
picks_mag = pick_types(info, meg='mag', ref_meg=False)
picks_ref_mag = pick_types(info, meg=False, ref_meg='mag')
picks_meg_ref_mag = pick_types(info, meg='mag', ref_meg='mag')
assert_array_equal(picks_meg_ref_mag,
np.sort(np.concatenate([picks_mag,
picks_ref_mag])))
assert_array_equal(picks_meg,
np.sort(np.concatenate([picks_mag, picks_grad])))
assert_array_equal(picks_ref,
np.sort(np.concatenate([picks_ref_mag,
picks_ref_grad])))
assert_array_equal(picks_meg_ref, np.sort(np.concatenate(
[picks_grad, picks_mag, picks_ref_grad, picks_ref_mag])))
for pick in (picks_meg_ref, picks_meg, picks_ref,
picks_grad, picks_ref_grad, picks_meg_ref_grad,
picks_mag, picks_ref_mag, picks_meg_ref_mag):
if len(pick) > 0:
pick_info(info, pick)
# test CTF expected failures directly
info = raw_ctf.info
info['bads'] = []
picks_meg_ref = pick_types(info, meg=True, ref_meg=True)
picks_meg = pick_types(info, meg=True, ref_meg=False)
picks_ref = pick_types(info, meg=False, ref_meg=True)
picks_mag = pick_types(info, meg='mag', ref_meg=False)
picks_ref_mag = pick_types(info, meg=False, ref_meg='mag')
picks_meg_ref_mag = pick_types(info, meg='mag', ref_meg='mag')
for pick in (picks_meg_ref, picks_ref, picks_ref_mag, picks_meg_ref_mag):
if len(pick) > 0:
pick_info(info, pick)
for pick in (picks_meg, picks_mag):
if len(pick) > 0:
with catch_logging() as log:
pick_info(info, pick, verbose=True)
assert ('Removing {} compensators'.format(len(info['comps']))
in log.getvalue())
def test_pick_channels_regexp():
"""Test pick with regular expression."""
ch_names = ['MEG 2331', 'MEG 2332', 'MEG 2333']
assert_array_equal(pick_channels_regexp(ch_names, 'MEG ...1'), [0])
assert_array_equal(pick_channels_regexp(ch_names, 'MEG ...[2-3]'), [1, 2])
assert_array_equal(pick_channels_regexp(ch_names, 'MEG *'), [0, 1, 2])
def test_pick_seeg_ecog():
"""Test picking with sEEG and ECoG."""
names = 'A1 A2 Fz O OTp1 OTp2 E1 OTp3 E2 E3'.split()
types = 'mag mag eeg eeg seeg seeg ecog seeg ecog ecog'.split()
info = create_info(names, 1024., types)
idx = channel_indices_by_type(info)
assert_array_equal(idx['mag'], [0, 1])
assert_array_equal(idx['eeg'], [2, 3])
assert_array_equal(idx['seeg'], [4, 5, 7])
assert_array_equal(idx['ecog'], [6, 8, 9])
assert_array_equal(pick_types(info, meg=False, seeg=True), [4, 5, 7])
for i, t in enumerate(types):
assert_equal(channel_type(info, i), types[i])
raw = RawArray(np.zeros((len(names), 10)), info)
events = np.array([[1, 0, 0], [2, 0, 0]])
epochs = Epochs(raw, events, {'event': 0}, -1e-5, 1e-5)
evoked = epochs.average(pick_types(epochs.info, meg=True, seeg=True))
e_seeg = evoked.copy().pick_types(meg=False, seeg=True)
for l, r in zip(e_seeg.ch_names, [names[4], names[5], names[7]]):
assert_equal(l, r)
# Deal with constant debacle
raw = read_raw_fif(op.join(io_dir, 'tests', 'data',
'test_chpi_raw_sss.fif'))
assert_equal(len(pick_types(raw.info, meg=False, seeg=True, ecog=True)), 0)
def test_pick_chpi():
"""Test picking cHPI."""
# Make sure we don't mis-classify cHPI channels
info = read_info(op.join(io_dir, 'tests', 'data', 'test_chpi_raw_sss.fif'))
channel_types = set([channel_type(info, idx)
for idx in range(info['nchan'])])
assert 'chpi' in channel_types
assert 'seeg' not in channel_types
assert 'ecog' not in channel_types
def test_pick_bio():
"""Test picking BIO channels."""
names = 'A1 A2 Fz O BIO1 BIO2 BIO3'.split()
types = 'mag mag eeg eeg bio bio bio'.split()
info = create_info(names, 1024., types)
idx = channel_indices_by_type(info)
assert_array_equal(idx['mag'], [0, 1])
assert_array_equal(idx['eeg'], [2, 3])
assert_array_equal(idx['bio'], [4, 5, 6])
def test_pick_fnirs():
"""Test picking fNIRS channels."""
names = 'A1 A2 Fz O hbo1 hbo2 hbr1'.split()
types = 'mag mag eeg eeg hbo hbo hbr'.split()
info = create_info(names, 1024., types)
idx = channel_indices_by_type(info)
assert_array_equal(idx['mag'], [0, 1])
assert_array_equal(idx['eeg'], [2, 3])
assert_array_equal(idx['hbo'], [4, 5])
assert_array_equal(idx['hbr'], [6])
def _check_fwd_n_chan_consistent(fwd, n_expected):
n_ok = len(fwd['info']['ch_names'])
n_sol = fwd['sol']['data'].shape[0]
assert_equal(n_expected, n_sol)
assert_equal(n_expected, n_ok)
@testing.requires_testing_data
def test_pick_forward_seeg_ecog():
"""Test picking forward with SEEG and ECoG."""
fwd = read_forward_solution(fname_meeg)
counts = channel_indices_by_type(fwd['info'])
for key in counts.keys():
counts[key] = len(counts[key])
counts['meg'] = counts['mag'] + counts['grad']
fwd_ = pick_types_forward(fwd, meg=True)
_check_fwd_n_chan_consistent(fwd_, counts['meg'])
fwd_ = pick_types_forward(fwd, meg=False, eeg=True)
_check_fwd_n_chan_consistent(fwd_, counts['eeg'])
# should raise exception related to emptiness
pytest.raises(ValueError, pick_types_forward, fwd, meg=False, seeg=True)
pytest.raises(ValueError, pick_types_forward, fwd, meg=False, ecog=True)
# change last chan from EEG to sEEG, second-to-last to ECoG
ecog_name = 'E1'
seeg_name = 'OTp1'
rename_channels(fwd['info'], {'EEG 059': ecog_name})
rename_channels(fwd['info'], {'EEG 060': seeg_name})
for ch in fwd['info']['chs']:
if ch['ch_name'] == seeg_name:
ch['kind'] = FIFF.FIFFV_SEEG_CH
ch['coil_type'] = FIFF.FIFFV_COIL_EEG
elif ch['ch_name'] == ecog_name:
ch['kind'] = FIFF.FIFFV_ECOG_CH
ch['coil_type'] = FIFF.FIFFV_COIL_EEG
fwd['sol']['row_names'][-1] = fwd['info']['chs'][-1]['ch_name']
fwd['sol']['row_names'][-2] = fwd['info']['chs'][-2]['ch_name']
counts['eeg'] -= 2
counts['seeg'] += 1
counts['ecog'] += 1
# repick & check
fwd_seeg = pick_types_forward(fwd, meg=False, seeg=True)
assert_equal(fwd_seeg['sol']['row_names'], [seeg_name])
assert_equal(fwd_seeg['info']['ch_names'], [seeg_name])
# should work fine
fwd_ = pick_types_forward(fwd, meg=True)
_check_fwd_n_chan_consistent(fwd_, counts['meg'])
fwd_ = pick_types_forward(fwd, meg=False, eeg=True)
_check_fwd_n_chan_consistent(fwd_, counts['eeg'])
fwd_ = pick_types_forward(fwd, meg=False, seeg=True)
_check_fwd_n_chan_consistent(fwd_, counts['seeg'])
fwd_ = pick_types_forward(fwd, meg=False, ecog=True)
_check_fwd_n_chan_consistent(fwd_, counts['ecog'])
def test_picks_by_channels():
"""Test creating pick_lists."""
rng = np.random.RandomState(909)
test_data = rng.random_sample((4, 2000))
ch_names = ['MEG %03d' % i for i in [1, 2, 3, 4]]
ch_types = ['grad', 'mag', 'mag', 'eeg']
sfreq = 250.0
info = create_info(ch_names=ch_names, sfreq=sfreq, ch_types=ch_types)
raw = RawArray(test_data, info)
pick_list = _picks_by_type(raw.info)
assert_equal(len(pick_list), 3)
assert_equal(pick_list[0][0], 'mag')
pick_list2 = _picks_by_type(raw.info, meg_combined=False)
assert_equal(len(pick_list), len(pick_list2))
assert_equal(pick_list2[0][0], 'mag')
pick_list2 = _picks_by_type(raw.info, meg_combined=True)
assert_equal(len(pick_list), len(pick_list2) + 1)
assert_equal(pick_list2[0][0], 'meg')
test_data = rng.random_sample((4, 2000))
ch_names = ['MEG %03d' % i for i in [1, 2, 3, 4]]
ch_types = ['mag', 'mag', 'mag', 'mag']
sfreq = 250.0
info = create_info(ch_names=ch_names, sfreq=sfreq, ch_types=ch_types)
raw = RawArray(test_data, info)
# This acts as a set, not an order
assert_array_equal(pick_channels(info['ch_names'], ['MEG 002', 'MEG 001']),
[0, 1])
# Make sure checks for list input work.
pytest.raises(ValueError, pick_channels, ch_names, 'MEG 001')
pytest.raises(ValueError, pick_channels, ch_names, ['MEG 001'], 'hi')
pick_list = _picks_by_type(raw.info)
assert_equal(len(pick_list), 1)
assert_equal(pick_list[0][0], 'mag')
pick_list2 = _picks_by_type(raw.info, meg_combined=True)
assert_equal(len(pick_list), len(pick_list2))
assert_equal(pick_list2[0][0], 'mag')
# pick_types type check
pytest.raises(ValueError, raw.pick_types, eeg='string')
# duplicate check
names = ['MEG 002', 'MEG 002']
assert len(pick_channels(raw.info['ch_names'], names)) == 1
assert len(raw.copy().pick_channels(names)[0][0]) == 1
def test_clean_info_bads():
"""Test cleaning info['bads'] when bad_channels are excluded."""
raw_file = op.join(op.dirname(_root_init_fname), 'io', 'tests', 'data',
'test_raw.fif')
raw = read_raw_fif(raw_file)
# select eeg channels
picks_eeg = pick_types(raw.info, meg=False, eeg=True)
# select 3 eeg channels as bads
idx_eeg_bad_ch = picks_eeg[[1, 5, 14]]
eeg_bad_ch = [raw.info['ch_names'][k] for k in idx_eeg_bad_ch]
# select meg channels
picks_meg = pick_types(raw.info, meg=True, eeg=False)
# select randomly 3 meg channels as bads
idx_meg_bad_ch = picks_meg[[0, 15, 34]]
meg_bad_ch = [raw.info['ch_names'][k] for k in idx_meg_bad_ch]
# simulate the bad channels
raw.info['bads'] = eeg_bad_ch + meg_bad_ch
# simulate the call to pick_info excluding the bad eeg channels
info_eeg = pick_info(raw.info, picks_eeg)
# simulate the call to pick_info excluding the bad meg channels
info_meg = pick_info(raw.info, picks_meg)
assert_equal(info_eeg['bads'], eeg_bad_ch)
assert_equal(info_meg['bads'], meg_bad_ch)
info = pick_info(raw.info, picks_meg)
info._check_consistency()
info['bads'] += ['EEG 053']
pytest.raises(RuntimeError, info._check_consistency)
with pytest.raises(ValueError, match='unique'):
pick_info(raw.info, [0, 0])
run_tests_if_main()
|
