def test_saving_picked():
"""Test saving picked CTF instances."""
temp_dir = _TempDir()
out_fname = op.join(temp_dir, 'test_py_raw.fif')
raw = read_raw_ctf(op.join(ctf_dir, ctf_fname_1_trial))
raw.crop(0, 1).load_data()
assert raw.compensation_grade == get_current_comp(raw.info) == 0
assert len(raw.info['comps']) == 5
pick_kwargs = dict(meg=True, ref_meg=False, verbose=True)
for comp_grade in [0, 1]:
raw.apply_gradient_compensation(comp_grade)
with catch_logging() as log:
raw_pick = raw.copy().pick_types(**pick_kwargs)
assert len(raw.info['comps']) == 5
assert len(raw_pick.info['comps']) == 0
log = log.getvalue()
assert 'Removing 5 compensators' in log
raw_pick.save(out_fname, overwrite=True) # should work
raw2 = read_raw_fif(out_fname)
assert (raw_pick.ch_names == raw2.ch_names)
assert_array_equal(raw_pick.times, raw2.times)
assert_allclose(raw2[0:20][0], raw_pick[0:20][0], rtol=1e-6,
atol=1e-20) # atol is very small but > 0
raw2 = read_raw_fif(out_fname, preload=True)
assert (raw_pick.ch_names == raw2.ch_names)
assert_array_equal(raw_pick.times, raw2.times)
assert_allclose(raw2[0:20][0], raw_pick[0:20][0], rtol=1e-6,
atol=1e-20) # atol is very small but > 0
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions
"""
trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
with warnings.catch_warnings(record=True):
raw = Raw(chpi_fif_fname, allow_maxshield=True, preload=True)
t -= raw.first_samp / raw.info['sfreq']
quats = _calculate_chpi_positions(raw, verbose='debug')
trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)
# degenerate conditions
raw_no_chpi = Raw(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1., copy=False)
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, verbose=True)
# ignore HPI info header and [done] footer
for line in log_file.getvalue().strip().split('\n')[4:-1]:
assert_true('0/5 good' in line)
def test_make_inverse_operator():
"""Test MNE inverse computation (precomputed and non-precomputed)."""
# Test old version of inverse computation starting from forward operator
evoked = _get_evoked()
noise_cov = read_cov(fname_cov)
inverse_operator = read_inverse_operator(fname_inv)
fwd_op = convert_forward_solution(read_forward_solution_meg(fname_fwd),
surf_ori=True, copy=False)
with catch_logging() as log:
my_inv_op = make_inverse_operator(evoked.info, fwd_op, noise_cov,
loose=0.2, depth=0.8,
limit_depth_chs=False, verbose=True)
log = log.getvalue()
assert 'rank 302 (3 small eigenvalues omitted)' in log
_compare_io(my_inv_op)
assert_equal(inverse_operator['units'], 'Am')
_compare_inverses_approx(my_inv_op, inverse_operator, evoked,
rtol=1e-2, atol=1e-5, depth_atol=1e-3)
# Test MNE inverse computation starting from forward operator
with catch_logging() as log:
my_inv_op = make_inverse_operator(evoked.info, fwd_op, noise_cov,
loose=0.2, depth=0.8, verbose=True)
log = log.getvalue()
assert 'rank 302 (3 small eigenvalues omitted)' in log
_compare_io(my_inv_op)
_compare_inverses_approx(my_inv_op, inverse_operator, evoked,
rtol=1e-3, atol=1e-5)
assert ('dev_head_t' in my_inv_op['info'])
assert ('mri_head_t' in my_inv_op)
def test_chpi_subtraction():
"""Test subtraction of cHPI signals."""
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True)
raw.info['bads'] = ['MEG0111']
raw.del_proj()
with catch_logging() as log:
filter_chpi(raw, include_line=False, verbose=True)
assert 'No average EEG' not in log.getvalue()
assert '5 cHPI' in log.getvalue()
# MaxFilter doesn't do quite as well as our algorithm with the last bit
raw.crop(0, 16)
# remove cHPI status chans
raw_c = read_raw_fif(sss_hpisubt_fname).crop(0, 16).load_data()
raw_c.pick_types(
meg=True, eeg=True, eog=True, ecg=True, stim=True, misc=True)
assert_meg_snr(raw, raw_c, 143, 624)
# Degenerate cases
raw_nohpi = read_raw_fif(test_fif_fname, preload=True)
pytest.raises(RuntimeError, filter_chpi, raw_nohpi)
# When MaxFliter downsamples, like::
# $ maxfilter -nosss -ds 2 -f test_move_anon_raw.fif \
# -o test_move_anon_ds2_raw.fif
# it can strip out some values of info, which we emulate here:
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes')
raw = raw.crop(0, 1).load_data().resample(600., npad='auto')
raw.info['lowpass'] = 200.
del raw.info['maxshield']
del raw.info['hpi_results'][0]['moments']
del raw.info['hpi_subsystem']['event_channel']
with catch_logging() as log:
filter_chpi(raw, verbose=True)
pytest.raises(ValueError, filter_chpi, raw, t_window=-1)
assert '2 cHPI' in log.getvalue()
def test_head_translation():
"""Test Maxwell filter head translation."""
raw = read_crop(raw_fname, (0., 1.))
# First try with an unchanged destination
raw_sss = maxwell_filter(raw, destination=raw_fname,
origin=mf_head_origin, regularize=None,
bad_condition='ignore')
assert_meg_snr(raw_sss, read_crop(sss_std_fname, (0., 1.)), 200.)
# Now with default
with pytest.warns(RuntimeWarning, match='over 25 mm'):
with catch_logging() as log:
raw_sss = maxwell_filter(raw, destination=mf_head_origin,
origin=mf_head_origin, regularize=None,
bad_condition='ignore', verbose='warning')
assert ('over 25 mm' in log.getvalue())
assert_meg_snr(raw_sss, read_crop(sss_trans_default_fname), 125.)
destination = np.eye(4)
destination[2, 3] = 0.04
assert_allclose(raw_sss.info['dev_head_t']['trans'], destination)
# Now to sample's head pos
with pytest.warns(RuntimeWarning, match='= 25.6 mm'):
with catch_logging() as log:
raw_sss = maxwell_filter(raw, destination=sample_fname,
origin=mf_head_origin, regularize=None,
bad_condition='ignore', verbose='warning')
assert ('= 25.6 mm' in log.getvalue())
assert_meg_snr(raw_sss, read_crop(sss_trans_sample_fname), 350.)
assert_allclose(raw_sss.info['dev_head_t']['trans'],
read_info(sample_fname)['dev_head_t']['trans'])
# Degenerate cases
pytest.raises(RuntimeError, maxwell_filter, raw,
destination=mf_head_origin, coord_frame='meg')
pytest.raises(ValueError, maxwell_filter, raw, destination=[0.] * 4)
def test_fetch_file(url, tmpdir):
"""Test URL retrieval."""
tempdir = str(tmpdir)
archive_name = op.join(tempdir, "download_test")
with catch_logging() as log:
_fetch_file(url, archive_name, timeout=30., verbose='debug')
log = log.getvalue()
assert 'Resuming at' not in log
with open(archive_name, 'rb') as fid:
data = fid.read()
stop = len(data) // 2
assert 0 < stop < len(data)
with open(archive_name + '.part', 'wb') as fid:
fid.write(data[:stop])
with catch_logging() as log:
_fetch_file(url, archive_name, timeout=30., verbose='debug')
log = log.getvalue()
assert 'Resuming at %s' % stop in log
with pytest.raises(Exception, match='unknown url type'):
_fetch_file('NOT_AN_ADDRESS', op.join(tempdir, 'test'), verbose=False)
resume_name = op.join(tempdir, "download_resume")
# touch file
with open(resume_name + '.part', 'w'):
os.utime(resume_name + '.part', None)
_fetch_file(url, resume_name, resume=True, timeout=30.,
verbose=False)
with pytest.raises(ValueError, match='Bad hash value'):
_fetch_file(url, archive_name, hash_='a', verbose=False)
with pytest.raises(RuntimeError, match='Hash mismatch'):
_fetch_file(url, archive_name, hash_='a' * 32, verbose=False)
def test_head_translation():
"""Test Maxwell filter head translation"""
with warnings.catch_warnings(record=True): # maxshield
raw = Raw(raw_fname, allow_maxshield=True).crop(0.0, 1.0, False)
# First try with an unchanged destination
raw_sss = maxwell_filter(raw, destination=raw_fname, origin=mf_head_origin, regularize=None, bad_condition="ignore")
assert_meg_snr(raw_sss, Raw(sss_std_fname).crop(0.0, 1.0, False), 200.0)
# Now with default
with catch_logging() as log:
raw_sss = maxwell_filter(
raw,
destination=mf_head_origin,
origin=mf_head_origin,
regularize=None,
bad_condition="ignore",
verbose="warning",
)
assert_true("over 25 mm" in log.getvalue())
assert_meg_snr(raw_sss, Raw(sss_trans_default_fname), 125.0)
# Now to sample's head pos
with catch_logging() as log:
raw_sss = maxwell_filter(
raw,
destination=sample_fname,
origin=mf_head_origin,
regularize=None,
bad_condition="ignore",
verbose="warning",
)
assert_true("= 25.6 mm" in log.getvalue())
assert_meg_snr(raw_sss, Raw(sss_trans_sample_fname), 350.0)
# Degenerate cases
assert_raises(RuntimeError, maxwell_filter, raw, destination=mf_head_origin, coord_frame="meg")
assert_raises(ValueError, maxwell_filter, raw, destination=[0.0] * 4)
def test_thresholds():
"""Test automatic threshold calculations."""
# within subjects
rng = np.random.RandomState(0)
X = rng.randn(10, 1, 1) + 0.08
want_thresh = -stats.t.ppf(0.025, len(X) - 1)
assert 0.03 < stats.ttest_1samp(X[:, 0, 0], 0)[1] < 0.05
my_fun = partial(ttest_1samp_no_p)
with catch_logging() as log:
with pytest.warns(RuntimeWarning, match='threshold is only valid'):
out = permutation_cluster_1samp_test(X, stat_fun=my_fun,
verbose=True)
log = log.getvalue()
assert str(want_thresh)[:6] in log
assert len(out[1]) == 1 # 1 cluster
assert 0.03 < out[2] < 0.05
# between subjects
Y = rng.randn(10, 1, 1)
Z = rng.randn(10, 1, 1) - 0.7
X = [X, Y, Z]
want_thresh = stats.f.ppf(1. - 0.05, 2, sum(len(a) for a in X) - len(X))
p = stats.f_oneway(*X)[1]
assert 0.03 < p < 0.05
my_fun = partial(f_oneway) # just to make the check fail
with catch_logging() as log:
with pytest.warns(RuntimeWarning, match='threshold is only valid'):
out = permutation_cluster_test(X, tail=1, stat_fun=my_fun,
verbose=True)
log = log.getvalue()
assert str(want_thresh)[:6] in log
assert len(out[1]) == 1 # 1 cluster
assert 0.03 < out[2] < 0.05
with pytest.warns(RuntimeWarning, match='Ignoring argument "tail"'):
permutation_cluster_test(X, tail=0)
def test_chpi_adjust():
"""Test cHPI logging and adjustment"""
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes')
with catch_logging() as log:
_get_hpi_info(raw.info, adjust=True, verbose='debug')
# Ran MaxFilter (with -list, -v, -movecomp, etc.), and got:
msg = ['HPIFIT: 5 coils digitized in order 5 1 4 3 2',
'HPIFIT: 3 coils accepted: 1 2 4',
'Hpi coil moments (3 5):',
'2.08542e-15 -1.52486e-15 -1.53484e-15',
'2.14516e-15 2.09608e-15 7.30303e-16',
'-3.2318e-16 -4.25666e-16 2.69997e-15',
'5.21717e-16 1.28406e-15 1.95335e-15',
'1.21199e-15 -1.25801e-19 1.18321e-15',
'HPIFIT errors: 0.3, 0.3, 5.3, 0.4, 3.2 mm.',
'HPI consistency of isotrak and hpifit is OK.',
'HP fitting limits: err = 5.0 mm, gval = 0.980.',
'Using 5 HPI coils: 83 143 203 263 323 Hz', # actually came earlier
]
log = log.getvalue().splitlines()
assert_true(set(log) == set(msg), '\n' + '\n'.join(set(msg) - set(log)))
# Then took the raw file, did this:
raw.info['dig'][5]['r'][2] += 1.
# And checked the result in MaxFilter, which changed the logging as:
msg = msg[:8] + [
'HPIFIT errors: 0.3, 0.3, 5.3, 999.7, 3.2 mm.',
'Note: HPI coil 3 isotrak is adjusted by 5.3 mm!',
'Note: HPI coil 5 isotrak is adjusted by 3.2 mm!'] + msg[-2:]
with catch_logging() as log:
_get_hpi_info(raw.info, adjust=True, verbose='debug')
log = log.getvalue().splitlines()
assert_true(set(log) == set(msg), '\n' + '\n'.join(set(msg) - set(log)))
def test_make_inverse_operator_loose(evoked):
"""Test MNE inverse computation (precomputed and non-precomputed)."""
# Test old version of inverse computation starting from forward operator
noise_cov = read_cov(fname_cov)
inverse_operator = read_inverse_operator(fname_inv)
fwd_op = convert_forward_solution(read_forward_solution_meg(fname_fwd),
surf_ori=True, copy=False)
with catch_logging() as log:
with pytest.deprecated_call(): # limit_depth_chs
my_inv_op = make_inverse_operator(
evoked.info, fwd_op, noise_cov, loose=0.2, depth=0.8,
limit_depth_chs=False, verbose=True)
log = log.getvalue()
assert 'MEG: rank 302 computed' in log
assert 'limit = 1/%d' % fwd_op['nsource'] in log
_compare_io(my_inv_op)
assert_equal(inverse_operator['units'], 'Am')
_compare_inverses_approx(my_inv_op, inverse_operator, evoked,
rtol=1e-2, atol=1e-5, depth_atol=1e-3)
# Test MNE inverse computation starting from forward operator
with catch_logging() as log:
my_inv_op = make_inverse_operator(evoked.info, fwd_op, noise_cov,
loose='auto', depth=0.8,
fixed=False, verbose=True)
log = log.getvalue()
assert 'MEG: rank 302 computed from 305' in log
_compare_io(my_inv_op)
_compare_inverses_approx(my_inv_op, inverse_operator, evoked,
rtol=1e-3, atol=1e-5)
assert ('dev_head_t' in my_inv_op['info'])
assert ('mri_head_t' in my_inv_op)
def test_chpi_subtraction():
"""Test subtraction of cHPI signals"""
raw = Raw(chpi_fif_fname, allow_maxshield="yes", preload=True)
with catch_logging() as log:
filter_chpi(raw, include_line=False, verbose=True)
assert_true("5 cHPI" in log.getvalue())
# MaxFilter doesn't do quite as well as our algorithm with the last bit
raw.crop(0, 16, copy=False)
# remove cHPI status chans
raw_c = Raw(sss_hpisubt_fname).crop(0, 16, copy=False).load_data()
raw_c.pick_types(meg=True, eeg=True, eog=True, ecg=True, stim=True, misc=True)
assert_meg_snr(raw, raw_c, 143, 624)
# Degenerate cases
raw_nohpi = Raw(test_fif_fname, preload=True)
assert_raises(RuntimeError, filter_chpi, raw_nohpi)
# When MaxFliter downsamples, like::
# $ maxfilter -nosss -ds 2 -f test_move_anon_raw.fif \
# -o test_move_anon_ds2_raw.fif
# it can strip out some values of info, which we emulate here:
raw = Raw(chpi_fif_fname, allow_maxshield="yes")
with warnings.catch_warnings(record=True): # uint cast suggestion
raw = raw.crop(0, 1).load_data().resample(600.0, npad="auto")
raw.info["buffer_size_sec"] = np.float64(2.0)
raw.info["lowpass"] = 200.0
del raw.info["maxshield"]
del raw.info["hpi_results"][0]["moments"]
del raw.info["hpi_subsystem"]["event_channel"]
with catch_logging() as log:
filter_chpi(raw, verbose=True)
assert_true("2 cHPI" in log.getvalue())
def test_chpi_subtraction():
"""Test subtraction of cHPI signals"""
raw = Raw(chpi_fif_fname, allow_maxshield='yes', preload=True)
with catch_logging() as log:
filter_chpi(raw, include_line=False, verbose=True)
assert_true('5 cHPI' in log.getvalue())
# MaxFilter doesn't do quite as well as our algorithm with the last bit
raw.crop(0, 16, copy=False)
raw_c = Raw(sss_hpisubt_fname, preload=True).crop(0, 16, copy=False)
raw_c.pick_types(meg=True, eeg=True, eog=True, ecg=True, stim=True,
misc=True, copy=False) # remove cHPI status chans
assert_meg_snr(raw, raw_c, 143, 624)
# Degenerate cases
raw_nohpi = Raw(test_fif_fname, preload=True)
assert_raises(RuntimeError, filter_chpi, raw_nohpi)
# When MaxFliter downsamples, like::
# $ maxfilter -nosss -ds 2 -f test_move_anon_raw.fif \
# -o test_move_anon_ds2_raw.fif
# it can strip out some values of info, which we emulate here:
raw = Raw(chpi_fif_fname, allow_maxshield='yes')
raw.crop(0, 1, copy=False).load_data()
raw.resample(600., npad='auto')
raw.info['buffer_size_sec'] = np.float64(2.)
raw.info['lowpass'] = 200.
del raw.info['maxshield']
del raw.info['hpi_results'][0]['moments']
del raw.info['hpi_subsystem']['event_channel']
with catch_logging() as log:
filter_chpi(raw, verbose=True)
assert_true('2 cHPI' in log.getvalue())
def test_head_translation():
"""Test Maxwell filter head translation"""
with warnings.catch_warnings(record=True): # maxshield
raw = Raw(raw_fname, allow_maxshield=True).crop(0., 1., False)
# First try with an unchanged destination
raw_sss = maxwell_filter(raw, destination=raw_fname,
origin=mf_head_origin, regularize=None,
bad_condition='ignore')
assert_meg_snr(raw_sss, Raw(sss_std_fname).crop(0., 1., False), 200.)
# Now with default
with warnings.catch_warnings(record=True):
with catch_logging() as log:
raw_sss = maxwell_filter(raw, destination=mf_head_origin,
origin=mf_head_origin, regularize=None,
bad_condition='ignore', verbose='warning')
assert_true('over 25 mm' in log.getvalue())
assert_meg_snr(raw_sss, Raw(sss_trans_default_fname), 125.)
destination = np.eye(4)
destination[2, 3] = 0.04
assert_allclose(raw_sss.info['dev_head_t']['trans'], destination)
# Now to sample's head pos
with warnings.catch_warnings(record=True):
with catch_logging() as log:
raw_sss = maxwell_filter(raw, destination=sample_fname,
origin=mf_head_origin, regularize=None,
bad_condition='ignore', verbose='warning')
assert_true('= 25.6 mm' in log.getvalue())
assert_meg_snr(raw_sss, Raw(sss_trans_sample_fname), 350.)
assert_allclose(raw_sss.info['dev_head_t']['trans'],
read_info(sample_fname)['dev_head_t']['trans'])
# Degenerate cases
assert_raises(RuntimeError, maxwell_filter, raw,
destination=mf_head_origin, coord_frame='meg')
assert_raises(ValueError, maxwell_filter, raw, destination=[0.] * 4)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions."""
# Check to make sure our fits match MF decently
mf_quats = read_head_pos(pos_fname)
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True)
# This is a little hack (aliasing while decimating) to make it much faster
# for testing purposes only. We can relax this later if we find it breaks
# something.
raw_dec = _decimate_chpi(raw, 15)
with catch_logging() as log:
py_quats = _calculate_chpi_positions(raw_dec, t_step_max=1.,
verbose='debug')
assert_true(log.getvalue().startswith('HPIFIT'))
_assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)
# degenerate conditions
raw_no_chpi = read_raw_fif(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
del raw_bad.info['hpi_meas'][0]['hpi_coils'][0]['coil_freq']
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = FIFF.FIFFV_COORD_UNKNOWN
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = FIFF.FIFFV_COORD_HEAD
d['r'] = np.ones(3)
raw_bad.crop(0, 1.)
picks = np.concatenate([np.arange(306, len(raw_bad.ch_names)),
pick_types(raw_bad.info, meg=True)[::16]])
raw_bad.pick_channels([raw_bad.ch_names[pick] for pick in picks])
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, t_step_min=1., verbose=True)
# ignore HPI info header and [done] footer
assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])
# half the rate cuts off cHPI coils
raw.info['lowpass'] /= 2.
assert_raises_regex(RuntimeError, 'above the',
_calculate_chpi_positions, raw)
# test on 5k artemis data
raw = read_raw_artemis123(art_fname, preload=True)
mf_quats = read_head_pos(art_mc_fname)
with catch_logging() as log:
py_quats = _calculate_chpi_positions(raw, t_step_min=2.,
verbose='debug')
_assert_quats(py_quats, mf_quats, dist_tol=0.004, angle_tol=2.5)
def test_manifest_check_download(tmpdir, n_have, monkeypatch):
"""Test our manifest downloader."""
monkeypatch.setattr(datasets.utils, '_fetch_file', _fake_zip_fetch)
destination = op.join(str(tmpdir), 'empty')
manifest_path = op.join(str(tmpdir), 'manifest.txt')
with open(manifest_path, 'w') as fid:
for fname in _zip_fnames:
fid.write('%s\n' % fname)
assert n_have in range(len(_zip_fnames) + 1)
assert not op.isdir(destination)
if n_have > 0:
os.makedirs(op.join(destination, 'foo'))
assert op.isdir(op.join(destination, 'foo'))
for fname in _zip_fnames:
assert not op.isfile(op.join(destination, fname))
for fname in _zip_fnames[:n_have]:
with open(op.join(destination, fname), 'w'):
pass
with catch_logging() as log:
with use_log_level(True):
url = hash_ = '' # we mock the _fetch_file so these are not used
_manifest_check_download(manifest_path, destination, url, hash_)
log = log.getvalue()
n_missing = 3 - n_have
assert ('%d file%s missing from' % (n_missing, _pl(n_missing))) in log
for want in ('Extracting missing', 'Successfully '):
if n_missing > 0:
assert want in log
else:
assert want not in log
assert op.isdir(destination)
for fname in _zip_fnames:
assert op.isfile(op.join(destination, fname))
def test_helmet():
"""Test loading helmet surfaces."""
base_dir = op.join(op.dirname(__file__), '..', 'io')
fname_raw = op.join(base_dir, 'tests', 'data', 'test_raw.fif')
fname_kit_raw = op.join(base_dir, 'kit', 'tests', 'data',
'test_bin_raw.fif')
fname_bti_raw = op.join(base_dir, 'bti', 'tests', 'data',
'exported4D_linux_raw.fif')
fname_ctf_raw = op.join(base_dir, 'tests', 'data', 'test_ctf_raw.fif')
fname_trans = op.join(base_dir, 'tests', 'data',
'sample-audvis-raw-trans.txt')
trans = _get_trans(fname_trans)[0]
new_info = read_info(fname_raw)
artemis_info = new_info.copy()
for pick in pick_types(new_info):
new_info['chs'][pick]['coil_type'] = 9999
artemis_info['chs'][pick]['coil_type'] = \
FIFF.FIFFV_COIL_ARTEMIS123_GRAD
for info, n, name in [(read_info(fname_raw), 304, '306m'),
(read_info(fname_kit_raw), 304, 'KIT'),
(read_info(fname_bti_raw), 304, 'Magnes'),
(read_info(fname_ctf_raw), 342, 'CTF'),
(new_info, 102, 'unknown'),
(artemis_info, 102, 'ARTEMIS123')
]:
with catch_logging() as log:
helmet = get_meg_helmet_surf(info, trans, verbose=True)
log = log.getvalue()
assert name in log
assert_equal(len(helmet['rr']), n)
assert_equal(len(helmet['rr']), len(helmet['nn']))
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions
"""
trans, rot, t = get_chpi_positions(pos_fname)
with warnings.catch_warnings(record=True):
raw = Raw(raw_fif_fname, allow_maxshield=True, preload=True)
t -= raw.first_samp / raw.info['sfreq']
trans_est, rot_est, t_est = _calculate_chpi_positions(raw, verbose='debug')
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est))
# degenerate conditions
raw_no_chpi = Raw(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1., copy=False)
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad)
for line in log_file.getvalue().split('\n')[:-1]:
assert_true('0/5 acceptable' in line)
def test_notch_filters():
"""Test notch filters
"""
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
rng = np.random.RandomState(0)
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a ** 2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, "fft")
assert_raises(ValueError, notch_filter, a, sfreq, None, "iir")
methods = ["spectrum_fit", "spectrum_fit", "fft", "fft", "iir"]
filter_lengths = [None, None, None, 8192, None]
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
with catch_logging() as log_file:
b = notch_filter(a, sfreq, lf, filter_length=fl, method=meth, verbose="INFO")
if lf is None:
out = log_file.getvalue().split("\n")[:-1]
if len(out) != 2:
raise ValueError("Detected frequencies not logged properly")
out = np.fromstring(out[1], sep=", ")
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def test_cache_dir():
"""Test use of cache dir
"""
tempdir = _TempDir()
orig_dir = os.getenv('MNE_CACHE_DIR', None)
orig_size = os.getenv('MNE_MEMMAP_MIN_SIZE', None)
rng = np.random.RandomState(0)
X = rng.randn(9, 2, 10)
try:
os.environ['MNE_MEMMAP_MIN_SIZE'] = '1K'
os.environ['MNE_CACHE_DIR'] = tempdir
# Fix error for #1507: in-place when memmapping
with catch_logging() as log_file:
permutation_cluster_1samp_test(
X, buffer_size=None, n_jobs=2, n_permutations=1,
seed=0, stat_fun=ttest_1samp_no_p, verbose=False)
# ensure that non-independence yields warning
stat_fun = partial(ttest_1samp_no_p, sigma=1e-3)
assert_true('independently' not in log_file.getvalue())
with warnings.catch_warnings(record=True): # independently
permutation_cluster_1samp_test(
X, buffer_size=10, n_jobs=2, n_permutations=1,
seed=0, stat_fun=stat_fun, verbose=False)
assert_true('independently' in log_file.getvalue())
finally:
if orig_dir is not None:
os.environ['MNE_CACHE_DIR'] = orig_dir
else:
del os.environ['MNE_CACHE_DIR']
if orig_size is not None:
os.environ['MNE_MEMMAP_MIN_SIZE'] = orig_size
else:
del os.environ['MNE_MEMMAP_MIN_SIZE']
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions
"""
trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
raw = Raw(chpi_fif_fname, allow_maxshield="yes", preload=True)
t -= raw.first_samp / raw.info["sfreq"]
quats = _calculate_chpi_positions(raw, verbose="debug")
trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)
# degenerate conditions
raw_no_chpi = Raw(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info["dig"]:
if d["kind"] == FIFF.FIFFV_POINT_HPI:
d["coord_frame"] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info["dig"]:
if d["kind"] == FIFF.FIFFV_POINT_HPI:
d["r"] = np.ones(3)
raw_bad.crop(0, 1.0, copy=False)
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, verbose=True)
# ignore HPI info header and [done] footer
for line in log_file.getvalue().strip().split("\n")[4:-1]:
assert_true("0/5 good" in line)
# half the rate cuts off cHPI coils
with warnings.catch_warnings(record=True): # uint cast suggestion
raw.resample(300.0, npad="auto")
assert_raises_regex(RuntimeError, "above the", _calculate_chpi_positions, raw)
def test_notch_filters():
"""Test notch filters."""
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a ** 2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = ['auto', 'auto', 'auto', 8192, 'auto']
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
with catch_logging() as log_file:
with warnings.catch_warnings(record=True):
b = notch_filter(a, sfreq, lf, fl, method=meth, verbose=True)
if lf is None:
out = log_file.getvalue().split('\n')[:-1]
if len(out) != 2 and len(out) != 3: # force_serial: len(out) == 3
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[-1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def test_check_compensation_consistency():
"""Test check picks compensation."""
raw = read_raw_ctf(ctf_fname, preload=False)
events = make_fixed_length_events(raw, 99999)
picks = pick_types(raw.info, meg=True, exclude=[], ref_meg=True)
pick_ch_names = [raw.info['ch_names'][idx] for idx in picks]
for (comp, expected_result) in zip([0, 1], [False, False]):
raw.apply_gradient_compensation(comp)
ret, missing = _bad_chans_comp(raw.info, pick_ch_names)
assert ret == expected_result
assert len(missing) == 0
Epochs(raw, events, None, -0.2, 0.2, preload=False, picks=picks)
picks = pick_types(raw.info, meg=True, exclude=[], ref_meg=False)
pick_ch_names = [raw.info['ch_names'][idx] for idx in picks]
for (comp, expected_result) in zip([0, 1], [False, True]):
raw.apply_gradient_compensation(comp)
ret, missing = _bad_chans_comp(raw.info, pick_ch_names)
assert ret == expected_result
assert len(missing) == 17
with catch_logging() as log:
Epochs(raw, events, None, -0.2, 0.2, preload=False,
picks=picks, verbose=True)
assert'Removing 5 compensators' in log.getvalue()
def test_cuda():
"""Test CUDA-based filtering"""
# NOTE: don't make test_cuda() the last test, or pycuda might spew
# some warnings about clean-up failing
# Also, using `n_jobs='cuda'` on a non-CUDA system should be fine,
# as it should fall back to using n_jobs=1.
sfreq = 500
sig_len_secs = 20
a = rng.randn(sig_len_secs * sfreq)
with catch_logging() as log_file:
for fl in ['auto', '10s', 2048]:
bp = band_pass_filter(a, sfreq, 4, 8, fl, 1.0, 1.0, n_jobs=1,
phase='zero')
bs = band_stop_filter(a, sfreq, 4 - 1.0, 8 + 1.0, fl, 1.0, 1.0,
n_jobs=1, phase='zero')
lp = low_pass_filter(a, sfreq, 8, fl, 1.0, n_jobs=1, phase='zero')
hp = high_pass_filter(lp, sfreq, 4, fl, 1.0, n_jobs=1,
phase='zero')
bp_c = band_pass_filter(a, sfreq, 4, 8, fl, 1.0, 1.0,
n_jobs='cuda', verbose='INFO',
phase='zero')
bs_c = band_stop_filter(a, sfreq, 4 - 1.0, 8 + 1.0, fl, 1.0, 1.0,
n_jobs='cuda', verbose='INFO',
phase='zero')
lp_c = low_pass_filter(a, sfreq, 8, fl, 1.0,
n_jobs='cuda', verbose='INFO',
phase='zero')
hp_c = high_pass_filter(lp, sfreq, 4, fl, 1.0,
n_jobs='cuda', verbose='INFO',
phase='zero')
assert_array_almost_equal(bp, bp_c, 12)
assert_array_almost_equal(bs, bs_c, 12)
assert_array_almost_equal(lp, lp_c, 12)
assert_array_almost_equal(hp, hp_c, 12)
# check to make sure we actually used CUDA
out = log_file.getvalue().split('\n')[:-1]
# triage based on whether or not we actually expected to use CUDA
from mne.cuda import _cuda_capable # allow above funs to set it
tot = 12 if _cuda_capable else 0
assert_true(sum(['Using CUDA for FFT FIR filtering' in o
for o in out]) == tot)
# check resampling
for window in ('boxcar', 'triang'):
for N in (997, 1000): # one prime, one even
a = rng.randn(2, N)
for fro, to in ((1, 2), (2, 1), (1, 3), (3, 1)):
a1 = resample(a, fro, to, n_jobs=1, npad='auto',
window=window)
a2 = resample(a, fro, to, n_jobs='cuda', npad='auto',
window=window)
assert_allclose(a1, a2, rtol=1e-7, atol=1e-14)
assert_array_almost_equal(a1, a2, 14)
assert_array_equal(resample([0, 0], 2, 1, n_jobs='cuda'), [0., 0., 0., 0.])
assert_array_equal(resample(np.zeros(2, np.float32), 2, 1, n_jobs='cuda'),
[0., 0., 0., 0.])
def test_make_sphere_model():
"""Test making a sphere model."""
info = read_info(fname_raw)
pytest.raises(ValueError, make_sphere_model, 'foo', 'auto', info)
pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', None)
pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', info,
relative_radii=(), sigmas=())
pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', info,
relative_radii=(1,)) # wrong number of radii
# here we just make sure it works -- the functionality is actually
# tested more extensively e.g. in the forward and dipole code
with catch_logging() as log:
bem = make_sphere_model('auto', 'auto', info, verbose=True)
log = log.getvalue()
assert ' RV = ' in log
for line in log.split('\n'):
if ' RV = ' in line:
val = float(line.split()[-2])
assert val < 0.01 # actually decent fitting
break
assert '3 layers' in repr(bem)
assert 'Sphere ' in repr(bem)
assert ' mm' in repr(bem)
bem = make_sphere_model('auto', None, info)
assert 'no layers' in repr(bem)
assert 'Sphere ' in repr(bem)
pytest.raises(ValueError, make_sphere_model, sigmas=(0.33,),
relative_radii=(1.0,))
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions."""
trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True,
add_eeg_ref=False)
t -= raw.first_samp / raw.info['sfreq']
quats = _calculate_chpi_positions(raw, verbose='debug')
trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)
# degenerate conditions
raw_no_chpi = read_raw_fif(test_fif_fname, add_eeg_ref=False)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1., copy=False)
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, verbose=True)
# ignore HPI info header and [done] footer
assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])
# half the rate cuts off cHPI coils
with warnings.catch_warnings(record=True): # uint cast suggestion
raw.resample(300., npad='auto')
assert_raises_regex(RuntimeError, 'above the',
_calculate_chpi_positions, raw)
def test_reporting_fir(phase, fir_window, btype):
"""Test FIR filter reporting."""
l_freq = 1. if btype == 'bandpass' else None
fs = 1000.
with catch_logging() as log:
x = create_filter(None, fs, l_freq, 40, method='fir',
phase=phase, fir_window=fir_window, verbose=True)
n_taps = len(x)
log = log.getvalue()
keys = ['FIR',
btype,
fir_window.capitalize(),
'Filter length: %d samples' % (n_taps,),
'passband ripple',
'stopband attenuation',
]
if phase == 'minimum':
keys += [' causal ']
else:
keys += [' non-causal ', ' dB cutoff frequency: 45.00 Hz']
if btype == 'bandpass':
keys += [' dB cutoff frequency: 0.50 Hz']
for key in keys:
assert key in log
if phase == 'zero':
assert '-6 dB cutoff' in log
elif phase == 'zero-double':
assert '-12 dB cutoff' in log
else:
# XXX Eventually we should figure out where the resulting point is,
# since the minimum-phase process will change it. For now we don't
# report it.
assert phase == 'minimum'
# Verify some of the filter properties
if phase == 'zero-double':
x = np.convolve(x, x) # effectively what happens
w, h = freqz(x, worN=10000)
w *= fs / (2 * np.pi)
h = np.abs(h)
# passband
passes = [np.argmin(np.abs(w - f)) for f in (1, 20, 40)]
# stopband
stops = [np.argmin(np.abs(w - 50.))]
# transition
mids = [np.argmin(np.abs(w - 45.))]
# put these where they belong based on filter type
assert w[0] == 0.
idx_0 = 0
idx_0p5 = np.argmin(np.abs(w - 0.5))
if btype == 'bandpass':
stops += [idx_0]
mids += [idx_0p5]
else:
passes += [idx_0, idx_0p5]
assert_allclose(h[passes], 1., atol=0.01)
attenuation = -20 if phase == 'minimum' else -50
assert_allclose(h[stops], 0., atol=10 ** (attenuation / 20.))
if phase != 'minimum': # haven't worked out the math for this yet
expected = 0.25 if phase == 'zero-double' else 0.5
assert_allclose(h[mids], expected, atol=0.01)
def test_inverse_residual():
"""Test MNE inverse application."""
# use fname_inv as it will be faster than fname_full (fewer verts and chs)
evoked = _get_evoked().pick_types()
inv = read_inverse_operator(fname_inv_fixed_depth)
fwd = read_forward_solution(fname_fwd)
fwd = convert_forward_solution(fwd, force_fixed=True, surf_ori=True)
fwd = pick_channels_forward(fwd, evoked.ch_names)
matcher = re.compile(r'.* ([0-9]?[0-9]?[0-9]?\.[0-9])% variance.*')
for method in ('MNE', 'dSPM', 'sLORETA'):
with catch_logging() as log:
stc, residual = apply_inverse(
evoked, inv, method=method, return_residual=True, verbose=True)
log = log.getvalue()
match = matcher.match(log.replace('\n', ' '))
assert match is not None
match = float(match.group(1))
assert 45 < match < 50
if method == 'MNE': # must be first!
recon = apply_forward(fwd, stc, evoked.info)
proj_op = make_projector(evoked.info['projs'], evoked.ch_names)[0]
recon.data[:] = np.dot(proj_op, recon.data)
residual_fwd = evoked.copy()
residual_fwd.data -= recon.data
corr = np.corrcoef(residual_fwd.data.ravel(),
residual.data.ravel())[0, 1]
assert corr > 0.999
with catch_logging() as log:
_, residual = apply_inverse(
evoked, inv, 0., 'MNE', return_residual=True, verbose=True)
log = log.getvalue()
match = matcher.match(log.replace('\n', ' '))
assert match is not None
match = float(match.group(1))
assert match == 100.
assert_array_less(np.abs(residual.data), 1e-15)
# Degenerate: we don't have the right representation for eLORETA for this
with pytest.raises(ValueError, match='eLORETA does not .* support .*'):
apply_inverse(evoked, inv, method="eLORETA", return_residual=True)
def test_inverse_operator_channel_ordering(evoked, noise_cov):
"""Test MNE inverse computation is immune to channel reorderings."""
# These are with original ordering
evoked_orig = evoked.copy()
fwd_orig = make_forward_solution(evoked.info, fname_trans, src_fname,
fname_bem, eeg=True, mindist=5.0)
fwd_orig = convert_forward_solution(fwd_orig, surf_ori=True)
depth = dict(exp=0.8, limit_depth_chs=False)
with catch_logging() as log:
inv_orig = make_inverse_operator(evoked.info, fwd_orig, noise_cov,
loose=0.2, depth=depth, verbose=True)
log = log.getvalue()
assert 'limit = 1/%s' % fwd_orig['nsource'] in log
stc_1 = apply_inverse(evoked, inv_orig, lambda2, "dSPM")
# Assume that a raw reordering applies to both evoked and noise_cov,
# so we don't need to create those from scratch. Just reorder them,
# then try to apply the original inverse operator
new_order = np.arange(len(evoked.info['ch_names']))
randomiser = np.random.RandomState(42)
randomiser.shuffle(new_order)
evoked.data = evoked.data[new_order]
evoked.info['chs'] = [evoked.info['chs'][n] for n in new_order]
evoked.info._update_redundant()
evoked.info._check_consistency()
cov_ch_reorder = [c for c in evoked.info['ch_names']
if (c in noise_cov.ch_names)]
new_order_cov = [noise_cov.ch_names.index(name) for name in cov_ch_reorder]
noise_cov['data'] = noise_cov.data[np.ix_(new_order_cov, new_order_cov)]
noise_cov['names'] = [noise_cov['names'][idx] for idx in new_order_cov]
fwd_reorder = make_forward_solution(evoked.info, fname_trans, src_fname,
fname_bem, eeg=True, mindist=5.0)
fwd_reorder = convert_forward_solution(fwd_reorder, surf_ori=True)
inv_reorder = make_inverse_operator(evoked.info, fwd_reorder, noise_cov,
loose=0.2, depth=depth)
stc_2 = apply_inverse(evoked, inv_reorder, lambda2, "dSPM")
assert_equal(stc_1.subject, stc_2.subject)
assert_array_equal(stc_1.times, stc_2.times)
assert_allclose(stc_1.data, stc_2.data, rtol=1e-5, atol=1e-5)
assert (inv_orig['units'] == inv_reorder['units'])
# Reload with original ordering & apply reordered inverse
evoked = evoked_orig
noise_cov = read_cov(fname_cov)
stc_3 = apply_inverse(evoked, inv_reorder, lambda2, "dSPM")
assert_allclose(stc_1.data, stc_3.data, rtol=1e-5, atol=1e-5)
def test_cuda():
"""Test CUDA-based filtering
"""
# NOTE: don't make test_cuda() the last test, or pycuda might spew
# some warnings about clean-up failing
# Also, using `n_jobs='cuda'` on a non-CUDA system should be fine,
# as it should fall back to using n_jobs=1.
sfreq = 500
sig_len_secs = 20
a = rng.randn(sig_len_secs * sfreq)
with catch_logging() as log_file:
for fl in ['10s', None, 2048]:
bp = band_pass_filter(a, sfreq, 4, 8, n_jobs=1, filter_length=fl)
bs = band_stop_filter(a, sfreq, 4 - 0.5, 8 + 0.5, n_jobs=1,
filter_length=fl)
lp = low_pass_filter(a, sfreq, 8, n_jobs=1, filter_length=fl)
hp = high_pass_filter(lp, sfreq, 4, n_jobs=1, filter_length=fl)
bp_c = band_pass_filter(a, sfreq, 4, 8, n_jobs='cuda',
filter_length=fl, verbose='INFO')
bs_c = band_stop_filter(a, sfreq, 4 - 0.5, 8 + 0.5, n_jobs='cuda',
filter_length=fl, verbose='INFO')
lp_c = low_pass_filter(a, sfreq, 8, n_jobs='cuda',
filter_length=fl, verbose='INFO')
hp_c = high_pass_filter(lp, sfreq, 4, n_jobs='cuda',
filter_length=fl, verbose='INFO')
assert_array_almost_equal(bp, bp_c, 12)
assert_array_almost_equal(bs, bs_c, 12)
assert_array_almost_equal(lp, lp_c, 12)
assert_array_almost_equal(hp, hp_c, 12)
# check to make sure we actually used CUDA
out = log_file.getvalue().split('\n')[:-1]
# triage based on whether or not we actually expected to use CUDA
from mne.cuda import _cuda_capable # allow above funs to set it
tot = 12 if _cuda_capable else 0
assert_true(sum(['Using CUDA for FFT FIR filtering' in o
for o in out]) == tot)
# check resampling
a = rng.randn(3, sig_len_secs * sfreq)
a1 = resample(a, 1, 2, n_jobs=2, npad=0)
a2 = resample(a, 1, 2, n_jobs='cuda', npad=0)
a3 = resample(a, 2, 1, n_jobs=2, npad=0)
a4 = resample(a, 2, 1, n_jobs='cuda', npad=0)
assert_array_almost_equal(a3, a4, 14)
assert_array_almost_equal(a1, a2, 14)
assert_array_equal(resample([0, 0], 2, 1, n_jobs='cuda'), [0., 0., 0., 0.])
assert_array_equal(resample(np.zeros(2, np.float32), 2, 1, n_jobs='cuda'),
[0., 0., 0., 0.])
def test_get_data_reject():
"""Test if reject_by_annotation is working correctly."""
fs = 256
ch_names = ["C3", "Cz", "C4"]
info = create_info(ch_names, sfreq=fs)
raw = RawArray(np.zeros((len(ch_names), 10 * fs)), info)
raw.set_annotations(Annotations(onset=[2, 4], duration=[3, 2],
description="bad"))
with catch_logging() as log:
data = raw.get_data(reject_by_annotation="omit", verbose=True)
msg = ('Omitting 1024 of 2560 (40.00%) samples, retaining 1536' +
' (60.00%) samples.')
assert log.getvalue().strip() == msg
assert data.shape == (len(ch_names), 1536)
with catch_logging() as log:
data = raw.get_data(reject_by_annotation="nan", verbose=True)
msg = ('Setting 1024 of 2560 (40.00%) samples to NaN, retaining 1536' +
' (60.00%) samples.')
assert log.getvalue().strip() == msg
assert data.shape == (len(ch_names), 2560) # shape doesn't change
assert np.isnan(data).sum() == 3072 # but NaNs are introduced instead
def test_cache_dir(tmpdir, numba_conditional):
"""Test use of cache dir."""
tempdir = str(tmpdir)
orig_dir = os.getenv('MNE_CACHE_DIR', None)
orig_size = os.getenv('MNE_MEMMAP_MIN_SIZE', None)
rng = np.random.RandomState(0)
X = rng.randn(9, 2, 10)
try:
os.environ['MNE_MEMMAP_MIN_SIZE'] = '1K'
os.environ['MNE_CACHE_DIR'] = tempdir
# Fix error for #1507: in-place when memmapping
with catch_logging() as log_file:
permutation_cluster_1samp_test(X,
buffer_size=None,
n_jobs=2,
n_permutations=1,
seed=0,
stat_fun=ttest_1samp_no_p,
verbose=False,
out_type='mask')
assert 'independently' not in log_file.getvalue()
# ensure that non-independence yields warning
stat_fun = partial(ttest_1samp_no_p, sigma=1e-3)
if check_version('numpy', '1.17'):
random_state = np.random.default_rng(0)
else:
random_state = 0
with pytest.warns(RuntimeWarning, match='independently'):
permutation_cluster_1samp_test(X,
buffer_size=10,
n_jobs=2,
n_permutations=1,
seed=random_state,
stat_fun=stat_fun,
verbose=False,
out_type='mask')
finally:
if orig_dir is not None:
os.environ['MNE_CACHE_DIR'] = orig_dir
else:
del os.environ['MNE_CACHE_DIR']
if orig_size is not None:
os.environ['MNE_MEMMAP_MIN_SIZE'] = orig_size
else:
del os.environ['MNE_MEMMAP_MIN_SIZE']
def test_make_inverse_operator_fixed():
"""Test MNE inverse computation (fixed orientation)."""
fwd = read_forward_solution_meg(fname_fwd)
evoked = _get_evoked()
noise_cov = read_cov(fname_cov)
# can't make fixed inv with depth weighting without free ori fwd
fwd_fixed = convert_forward_solution(fwd, force_fixed=True,
use_cps=True)
pytest.raises(ValueError, make_inverse_operator, evoked.info, fwd_fixed,
noise_cov, depth=0.8, fixed=True)
# now compare to C solution
# note that the forward solution must not be surface-oriented
# to get equivalency (surf_ori=True changes the normals)
with catch_logging() as log:
inv_op = make_inverse_operator( # test depth=0. alias for depth=None
evoked.info, fwd, noise_cov, depth=0., fixed=True,
use_cps=False, verbose=True)
log = log.getvalue()
assert 'rank 302 (3 small eigenvalues omitted)' in log
assert 'EEG channels: 0' in repr(inv_op)
assert 'MEG channels: 305' in repr(inv_op)
del fwd_fixed
inverse_operator_nodepth = read_inverse_operator(fname_inv_fixed_nodepth)
# XXX We should have this but we don't (MNE-C doesn't restrict info):
# assert 'EEG channels: 0' in repr(inverse_operator_nodepth)
assert 'MEG channels: 305' in repr(inverse_operator_nodepth)
_compare_inverses_approx(inverse_operator_nodepth, inv_op, evoked,
rtol=1e-5, atol=1e-4)
# Inverse has 306 channels - 6 proj = 302
assert (compute_rank_inverse(inverse_operator_nodepth) == 302)
# Now with depth
fwd_surf = convert_forward_solution(fwd, surf_ori=True) # not fixed
for kwargs, use_fwd in zip([dict(fixed=True), dict(loose=0.)],
[fwd, fwd_surf]): # Should be equiv.
inv_op_depth = make_inverse_operator(
evoked.info, use_fwd, noise_cov, depth=0.8, use_cps=True,
**kwargs)
inverse_operator_depth = read_inverse_operator(fname_inv_fixed_depth)
# Normals should be the adjusted ones
assert_allclose(inverse_operator_depth['source_nn'],
fwd_surf['source_nn'][2::3], atol=1e-5)
_compare_inverses_approx(inverse_operator_depth, inv_op_depth, evoked,
rtol=1e-3, atol=1e-4)
def test_plot_volume_source_estimates(mode, stype, init_t, want_t, init_p,
want_p, bg_img):
"""Test interactive plotting of volume source estimates."""
forward = read_forward_solution(fwd_fname)
sample_src = forward['src']
if init_p is not None:
init_p = np.array(init_p) / 1000.
vertices = [s['vertno'] for s in sample_src]
n_verts = sum(len(v) for v in vertices)
n_time = 2
data = np.random.RandomState(0).rand(n_verts, n_time)
if stype == 'vec':
stc = VolVectorSourceEstimate(np.tile(data[:, np.newaxis], (1, 3, 1)),
vertices, 1, 1)
else:
assert stype == 's'
stc = VolSourceEstimate(data, vertices, 1, 1)
with pytest.warns(None): # sometimes get scalars/index warning
with catch_logging() as log:
fig = stc.plot(sample_src,
subject='sample',
subjects_dir=subjects_dir,
mode=mode,
initial_time=init_t,
initial_pos=init_p,
bg_img=bg_img,
verbose=True)
log = log.getvalue()
want_str = 't = %0.3f s' % want_t
assert want_str in log, (want_str, init_t)
want_str = '(%0.1f, %0.1f, %0.1f) mm' % want_p
assert want_str in log, (want_str, init_p)
for ax_idx in [0, 2, 3, 4]:
_fake_click(fig, fig.axes[ax_idx], (0.3, 0.5))
fig.canvas.key_press_event('left')
fig.canvas.key_press_event('shift+right')
if bg_img is not None:
with pytest.raises(FileNotFoundError, match='MRI file .* not found'):
stc.plot(sample_src,
subject='sample',
subjects_dir=subjects_dir,
mode='stat_map',
bg_img='junk.mgz')
def test_make_forward_solution():
"""Test making M-EEG forward solution from python."""
with catch_logging() as log:
fwd_py = make_forward_solution(fname_raw,
fname_trans,
fname_src,
fname_bem,
mindist=5.,
verbose=True)
log = log.getvalue()
assert 'Total 258/258 points inside the surface' in log
assert (isinstance(fwd_py, Forward))
fwd = read_forward_solution(fname_meeg)
assert (isinstance(fwd, Forward))
_compare_forwards(fwd, fwd_py, 366, 1494, meg_rtol=1e-3)
# Homogeneous model
with pytest.raises(RuntimeError, match='homogeneous.*1-layer.*EEG'):
make_forward_solution(fname_raw, fname_trans, fname_src, fname_bem_meg)
def test_plot_alignment_fnirs(renderer, tmp_path):
"""Test fNIRS plotting."""
# Here we use subjects_dir=tmp_path, since no surfaces should actually
# be loaded!
# fNIRS (default is pairs)
info = read_raw_nirx(nirx_fname).info
assert info['nchan'] == 26
kwargs = dict(trans='fsaverage', subject='fsaverage', surfaces=(),
verbose=True, subjects_dir=tmp_path)
with catch_logging() as log:
fig = plot_alignment(info, **kwargs)
log = log.getvalue()
assert f'fnirs_cw_amplitude: {info["nchan"]}' in log
_assert_n_actors(fig, renderer, info['nchan'])
fig = plot_alignment(
info, fnirs=['channels', 'sources', 'detectors'], **kwargs)
_assert_n_actors(fig, renderer, 3)
def test_add_noise():
"""Test noise addition."""
rng = np.random.RandomState(0)
raw = read_raw_fif(raw_fname)
raw.del_proj()
picks = pick_types(raw.info, eeg=True, exclude=())
cov = compute_raw_covariance(raw, picks=picks)
with pytest.raises(RuntimeError, match='to be loaded'):
add_noise(raw, cov)
raw.crop(0, 1).load_data()
with pytest.raises(TypeError, match='Raw, Epochs, or Evoked'):
add_noise(0., cov)
with pytest.raises(TypeError, match='Covariance'):
add_noise(raw, 0.)
# test a no-op (data preserved)
orig_data = raw[:][0]
zero_cov = cov.copy()
zero_cov['data'].fill(0)
add_noise(raw, zero_cov)
new_data = raw[:][0]
assert_allclose(orig_data, new_data, atol=1e-30)
# set to zero to make comparisons easier
raw._data[:] = 0.
epochs = EpochsArray(np.zeros((1, len(raw.ch_names), 100)),
raw.info.copy())
epochs.info['bads'] = []
evoked = epochs.average(picks=np.arange(len(raw.ch_names)))
for inst in (raw, epochs, evoked):
with catch_logging() as log:
add_noise(inst, cov, random_state=rng, verbose=True)
log = log.getvalue()
want = ('to {0}/{1} channels ({0}'.format(len(cov['names']),
len(raw.ch_names)))
assert want in log
if inst is evoked:
inst = EpochsArray(inst.data[np.newaxis], inst.info)
if inst is raw:
cov_new = compute_raw_covariance(inst, picks=picks)
else:
cov_new = compute_covariance(inst)
assert cov['names'] == cov_new['names']
r = np.corrcoef(cov['data'].ravel(), cov_new['data'].ravel())[0, 1]
assert r > 0.99
def test_non_convergence():
"""Test non-convergence of MxNE solver to catch unexpected bugs."""
n, p, t, alpha = 30, 40, 20, 1.
rng = np.random.RandomState(0)
G = rng.randn(n, p)
G /= np.std(G, axis=0)[None, :]
X = np.zeros((p, t))
X[0] = 3
X[4] = -2
M = np.dot(G, X)
# Impossible to converge with only 1 iteration and tol 1e-12
# In case of non-convegence, we test that no error is returned.
args = (M, G, alpha, 1, 1e-12)
with catch_logging() as log:
mixed_norm_solver(*args, active_set_size=None, debias=True,
solver='bcd', verbose=True)
log = log.getvalue()
assert 'Convergence reached' not in log
def test_make_morph_maps():
"""Test reading and creating morph maps."""
# make a new fake subjects_dir
tempdir = _TempDir()
for subject in ('sample', 'sample_ds', 'fsaverage_ds'):
os.mkdir(op.join(tempdir, subject))
os.mkdir(op.join(tempdir, subject, 'surf'))
regs = ('reg',
'left_right') if subject == 'fsaverage_ds' else ('reg', )
for hemi in ['lh', 'rh']:
for reg in regs:
args = [subject, 'surf', hemi + '.sphere.' + reg]
copyfile(op.join(subjects_dir, *args), op.join(tempdir, *args))
for subject_from, subject_to, xhemi in (('fsaverage_ds', 'sample_ds',
False), ('fsaverage_ds',
'fsaverage_ds', True)):
# trigger the creation of morph-maps dir and create the map
with catch_logging() as log:
mmap = read_morph_map(subject_from,
subject_to,
tempdir,
xhemi=xhemi,
verbose=True)
log = log.getvalue()
assert 'does not exist' in log
assert 'Creating' in log
mmap2 = read_morph_map(subject_from,
subject_to,
subjects_dir,
xhemi=xhemi)
assert_equal(len(mmap), len(mmap2))
for m1, m2 in zip(mmap, mmap2):
# deal with sparse matrix stuff
diff = (m1 - m2).data
assert_allclose(diff, np.zeros_like(diff), atol=1e-3, rtol=0)
# This will also trigger creation, but it's trivial
with pytest.warns(None):
mmap = read_morph_map('sample', 'sample', subjects_dir=tempdir)
for mm in mmap:
assert (mm - sparse.eye(mm.shape[0], mm.shape[0])).sum() == 0
def test_apply_function_verbose():
"""Test apply function verbosity
"""
n_chan = 2
n_times = 3
ch_names = [str(ii) for ii in range(n_chan)]
raw = RawArray(np.zeros((n_chan, n_times)),
create_info(ch_names, 1., 'mag'))
# test return types in both code paths (parallel / 1 job)
assert_raises(TypeError, raw.apply_function, bad_1, None, None, 1)
assert_raises(ValueError, raw.apply_function, bad_2, None, None, 1)
assert_raises(TypeError, raw.apply_function, bad_1, None, None, 2)
assert_raises(ValueError, raw.apply_function, bad_2, None, None, 2)
# check our arguments
with catch_logging() as sio:
raw.apply_function(printer, None, None, 1, verbose=False)
assert_equal(len(sio.getvalue()), 0)
raw.apply_function(printer, None, None, 1, verbose=True)
assert_equal(sio.getvalue().count('\n'), n_chan)
def test_apply_function_verbose():
"""Test apply function verbosity."""
n_chan = 2
n_times = 3
ch_names = [str(ii) for ii in range(n_chan)]
raw = RawArray(np.zeros((n_chan, n_times)),
create_info(ch_names, 1., 'mag'))
# test return types in both code paths (parallel / 1 job)
pytest.raises(TypeError, raw.apply_function, bad_1)
pytest.raises(ValueError, raw.apply_function, bad_2)
pytest.raises(TypeError, raw.apply_function, bad_1, n_jobs=2)
pytest.raises(ValueError, raw.apply_function, bad_2, n_jobs=2)
# check our arguments
with catch_logging() as sio:
out = raw.apply_function(printer, verbose=False)
assert len(sio.getvalue()) == 0
assert out is raw
raw.apply_function(printer, verbose=True)
assert sio.getvalue().count('\n') == n_chan
def test_cache_dir():
"""Test use of cache dir
"""
tempdir = _TempDir()
orig_dir = os.getenv('MNE_CACHE_DIR', None)
orig_size = os.getenv('MNE_MEMMAP_MIN_SIZE', None)
rng = np.random.RandomState(0)
X = rng.randn(9, 2, 10)
try:
os.environ['MNE_MEMMAP_MIN_SIZE'] = '1K'
os.environ['MNE_CACHE_DIR'] = tempdir
# Fix error for #1507: in-place when memmapping
with catch_logging() as log_file:
permutation_cluster_1samp_test(X,
buffer_size=None,
n_jobs=2,
n_permutations=1,
seed=0,
stat_fun=ttest_1samp_no_p,
verbose=False)
# ensure that non-independence yields warning
stat_fun = partial(ttest_1samp_no_p, sigma=1e-3)
assert_true('independently' not in log_file.getvalue())
with warnings.catch_warnings(record=True): # independently
permutation_cluster_1samp_test(X,
buffer_size=10,
n_jobs=2,
n_permutations=1,
seed=0,
stat_fun=stat_fun,
verbose=False)
assert_true('independently' in log_file.getvalue())
finally:
if orig_dir is not None:
os.environ['MNE_CACHE_DIR'] = orig_dir
else:
del os.environ['MNE_CACHE_DIR']
if orig_size is not None:
os.environ['MNE_MEMMAP_MIN_SIZE'] = orig_size
else:
del os.environ['MNE_MEMMAP_MIN_SIZE']
def test_plot_volume_source_estimates_morph():
"""Test interactive plotting of volume source estimates with morph."""
forward = read_forward_solution(fwd_fname)
sample_src = forward['src']
vertices = [s['vertno'] for s in sample_src]
n_verts = sum(len(v) for v in vertices)
n_time = 2
data = np.random.RandomState(0).rand(n_verts, n_time)
stc = VolSourceEstimate(data, vertices, 1, 1)
sample_src[0]['subject_his_id'] = 'sample' # old src
morph = compute_source_morph(sample_src,
'sample',
'fsaverage',
zooms=5,
subjects_dir=subjects_dir)
initial_pos = (-0.05, -0.01, -0.006)
# sometimes get scalars/index warning
with _record_warnings():
with catch_logging() as log:
stc.plot(morph,
subjects_dir=subjects_dir,
mode='glass_brain',
initial_pos=initial_pos,
verbose=True)
log = log.getvalue()
assert 't = 1.000 s' in log
assert '(-52.0, -8.0, -7.0) mm' in log
with pytest.raises(ValueError, match='Allowed values are'):
stc.plot(sample_src, 'sample', subjects_dir, mode='abcd')
vertices.append([])
surface_stc = SourceEstimate(data, vertices, 1, 1)
with pytest.raises(TypeError, match='an instance of VolSourceEstimate'):
plot_volume_source_estimates(surface_stc, sample_src, 'sample',
subjects_dir)
with pytest.raises(ValueError, match='Negative colormap limits'):
stc.plot(sample_src,
'sample',
subjects_dir,
clim=dict(lims=[-1, 2, 3], kind='value'))
def test_notch_filters():
"""Test notch filters"""
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a**2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = [None, None, None, 8192, None]
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
with catch_logging() as log_file:
with warnings.catch_warnings(record=True): # filter_length=None
b = notch_filter(a,
sfreq,
lf,
filter_length=fl,
method=meth,
phase='zero',
verbose=True)
if lf is None:
out = log_file.getvalue().split('\n')[:-1]
if len(out) != 2 and len(out) != 3: # force_serial: len(out) == 3
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[-1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def test_cuda_fir():
"""Test CUDA-based filtering."""
# Using `n_jobs='cuda'` on a non-CUDA system should be fine,
# as it should fall back to using n_jobs=None.
rng = np.random.RandomState(0)
sfreq = 500
sig_len_secs = 20
a = rng.randn(sig_len_secs * sfreq)
kwargs = dict(fir_design='firwin')
with catch_logging() as log_file:
for fl in ['auto', '10s', 2048]:
args = [a, sfreq, 4, 8, None, fl, 1.0, 1.0]
bp = filter_data(*args, **kwargs)
bp_c = filter_data(*args, n_jobs='cuda', verbose='info', **kwargs)
assert_array_almost_equal(bp, bp_c, 12)
args = [a, sfreq, 8 + 1.0, 4 - 1.0, None, fl, 1.0, 1.0]
bs = filter_data(*args, **kwargs)
bs_c = filter_data(*args, n_jobs='cuda', verbose='info', **kwargs)
assert_array_almost_equal(bs, bs_c, 12)
args = [a, sfreq, None, 8, None, fl, 1.0]
lp = filter_data(*args, **kwargs)
lp_c = filter_data(*args, n_jobs='cuda', verbose='info', **kwargs)
assert_array_almost_equal(lp, lp_c, 12)
args = [lp, sfreq, 4, None, None, fl, 1.0]
hp = filter_data(*args, **kwargs)
hp_c = filter_data(*args, n_jobs='cuda', verbose='info', **kwargs)
assert_array_almost_equal(hp, hp_c, 12)
# check to make sure we actually used CUDA
out = log_file.getvalue().split('\n')[:-1]
# triage based on whether or not we actually expected to use CUDA
from mne.cuda import _cuda_capable # allow above funs to set it
tot = 12 if _cuda_capable else 0
assert sum(['Using CUDA for FFT FIR filtering' in o for o in out]) == tot
if not _cuda_capable:
pytest.skip('CUDA not enabled')
def test_make_sphere_model():
"""Test making a sphere model."""
info = read_info(fname_raw)
pytest.raises(ValueError, make_sphere_model, 'foo', 'auto', info)
pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', None)
pytest.raises(ValueError,
make_sphere_model,
'auto',
'auto',
info,
relative_radii=(),
sigmas=())
pytest.raises(ValueError,
make_sphere_model,
'auto',
'auto',
info,
relative_radii=(1, )) # wrong number of radii
# here we just make sure it works -- the functionality is actually
# tested more extensively e.g. in the forward and dipole code
with catch_logging() as log:
bem = make_sphere_model('auto', 'auto', info, verbose=True)
log = log.getvalue()
assert ' RV = ' in log
for line in log.split('\n'):
if ' RV = ' in line:
val = float(line.split()[-2])
assert val < 0.01 # actually decent fitting
break
assert '3 layers' in repr(bem)
assert 'Sphere ' in repr(bem)
assert ' mm' in repr(bem)
bem = make_sphere_model('auto', None, info)
assert 'no layers' in repr(bem)
assert 'Sphere ' in repr(bem)
pytest.raises(ValueError,
make_sphere_model,
sigmas=(0.33, ),
relative_radii=(1.0, ))
def test_notch_filters(method, filter_length, line_freq, tol):
"""Test notch filters."""
# let's use an ugly, prime sfreq for fun
rng = np.random.RandomState(0)
sfreq = 487
sig_len_secs = 21
t = np.arange(0, int(round(sig_len_secs * sfreq))) / sfreq
# make a "signal"
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a**2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in line_freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
pytest.raises(ValueError, notch_filter, a, sfreq, None, 'fft')
pytest.raises(ValueError, notch_filter, a, sfreq, None, 'iir')
if method == 'spectrum_fit' and filter_length == 'auto':
ctx = pytest.deprecated_call(match='will change to 10.')
else:
ctx = nullcontext()
with catch_logging() as log_file:
with ctx:
b = notch_filter(a,
sfreq,
line_freq,
filter_length,
method=method,
verbose=True)
if line_freq is None:
out = [
line.strip().split(':')[0]
for line in log_file.getvalue().split('\n') if line.startswith(' ')
]
assert len(out) == 4, 'Detected frequencies not logged properly'
out = np.array(out, float)
assert_array_almost_equal(out, line_freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def test_make_bem_model(tmpdir, kwargs, fname):
"""Test BEM model creation from Python with I/O."""
fname_temp = tmpdir.join('temp-bem.fif')
with catch_logging() as log:
model = make_bem_model('sample', ico=2, subjects_dir=subjects_dir,
verbose=True, **kwargs)
log = log.getvalue()
if len(kwargs.get('conductivity', (0, 0, 0))) == 1:
assert 'distance' not in log
else:
assert re.search(r'urfaces is approximately *3\.4 mm', log) is not None
assert re.search(r'inner skull CM is *0\.65 *-9\.62 *43\.85 mm',
log) is not None
model_c = read_bem_surfaces(fname)
_compare_bem_surfaces(model, model_c)
write_bem_surfaces(fname_temp, model)
model_read = read_bem_surfaces(fname_temp)
_compare_bem_surfaces(model, model_c)
_compare_bem_surfaces(model_read, model_c)
# bad conductivity
with pytest.raises(ValueError, match='conductivity must be'):
make_bem_model('sample', 4, [0.3, 0.006], subjects_dir=subjects_dir)
def test_ica_reject_buffer():
"""Test ICA data raw buffer rejection."""
raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data()
picks = pick_types(raw.info,
meg=True,
stim=False,
ecg=False,
eog=False,
exclude='bads')
ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4)
raw._data[2, 1000:1005] = 5e-12
with catch_logging() as drop_log:
with warnings.catch_warnings(record=True):
ica.fit(raw,
picks[:5],
reject=dict(mag=2.5e-12),
decim=2,
tstep=0.01,
verbose=True)
assert_true(raw._data[:5, ::2].shape[1] - 4 == ica.n_samples_)
log = [l for l in drop_log.getvalue().split('\n') if 'detected' in l]
assert_equal(len(log), 1)
def test_saving_picked():
"""Test saving picked CTF instances."""
temp_dir = _TempDir()
out_fname = op.join(temp_dir, 'test_py_raw.fif')
raw = read_raw_ctf(op.join(ctf_dir, ctf_fname_1_trial))
raw.crop(0, 1).load_data()
assert raw.compensation_grade == get_current_comp(raw.info) == 0
assert len(raw.info['comps']) == 5
pick_kwargs = dict(meg=True, ref_meg=False, verbose=True)
with catch_logging() as log:
raw_pick = raw.copy().pick_types(**pick_kwargs)
assert len(raw.info['comps']) == 5
assert len(raw_pick.info['comps']) == 0
log = log.getvalue()
assert 'Removing 5 compensators' in log
raw_pick.save(out_fname) # should work
read_raw_fif(out_fname)
read_raw_fif(out_fname, preload=True)
# If comp is applied, picking should error
raw.apply_gradient_compensation(1)
assert raw.compensation_grade == get_current_comp(raw.info) == 1
with pytest.raises(RuntimeError, match='Compensation grade 1 has been'):
raw.copy().pick_types(**pick_kwargs)
def test_rap_music_sphere():
"""Test RAP-MUSIC with real data, sphere model, MEG only."""
evoked, noise_cov = _get_data(ch_decim=8)
sphere = mne.make_sphere_model(r0=(0., 0., 0.04))
src = mne.setup_volume_source_space(subject=None,
pos=10.,
sphere=(0.0, 0.0, 40, 65.0),
mindist=5.0,
exclude=0.0,
sphere_units='mm')
forward = mne.make_forward_solution(evoked.info,
trans=None,
src=src,
bem=sphere)
with catch_logging() as log:
dipoles = rap_music(evoked,
forward,
noise_cov,
n_dipoles=2,
verbose=True)
assert_var_exp_log(log.getvalue(), 47, 49)
# Test that there is one dipole on each hemisphere
pos = np.array([dip.pos[0] for dip in dipoles])
assert pos.shape == (2, 3)
assert (pos[:, 0] < 0).sum() == 1
assert (pos[:, 0] > 0).sum() == 1
# Check the amplitude scale
assert (1e-10 < dipoles[0].amplitude[0] < 1e-7)
# Check the orientation
dip_fit = mne.fit_dipole(evoked, noise_cov, sphere)[0]
assert (np.max(np.abs(np.dot(dip_fit.ori, dipoles[0].ori[0]))) > 0.99)
assert (np.max(np.abs(np.dot(dip_fit.ori, dipoles[1].ori[0]))) > 0.99)
idx = dip_fit.gof.argmax()
dist = np.linalg.norm(dipoles[0].pos[idx] - dip_fit.pos[idx])
assert 0.004 <= dist < 0.007
assert_allclose(dipoles[0].gof[idx], dip_fit.gof[idx], atol=3)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions."""
trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
raw = read_raw_fif(chpi_fif_fname,
allow_maxshield='yes',
preload=True,
add_eeg_ref=False)
t -= raw.first_samp / raw.info['sfreq']
quats = _calculate_chpi_positions(raw, verbose='debug')
trans_est, rot_est, t_est = head_pos_to_trans_rot_t(quats)
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est), 0.003)
# degenerate conditions
raw_no_chpi = read_raw_fif(test_fif_fname, add_eeg_ref=False)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1., copy=False)
with warnings.catch_warnings(record=True): # bad pos
with catch_logging() as log_file:
_calculate_chpi_positions(raw_bad, verbose=True)
# ignore HPI info header and [done] footer
assert_true('0/5 good' in log_file.getvalue().strip().split('\n')[-2])
# half the rate cuts off cHPI coils
with warnings.catch_warnings(record=True): # uint cast suggestion
raw.resample(300., npad='auto')
assert_raises_regex(RuntimeError, 'above the', _calculate_chpi_positions,
raw)
def test_read_raw_curry_rfDC(fname, tol, mock_dev_head_t, tmpdir):
"""Test reading CURRY files."""
if mock_dev_head_t:
if 'Curry 7' in fname: # not supported yet
return
# copy files to tmpdir
base = op.splitext(fname)[0]
for ext in ('.cdt', '.cdt.dpa'):
src = base + ext
dst = op.join(tmpdir, op.basename(base) + ext)
copyfile(src, dst)
if ext == '.cdt.dpa':
with open(dst, 'a') as fid:
fid.write(LM_CONTENT)
fname = op.join(tmpdir, op.basename(fname))
with open(fname + '.hpi', 'w') as fid:
fid.write(HPI_CONTENT)
# check data
bti_rfDC = read_raw_bti(pdf_fname=bti_rfDC_file, head_shape_fname=None)
with catch_logging() as log:
raw = read_raw_curry(fname, verbose=True)
log = log.getvalue()
if mock_dev_head_t:
assert 'Composing device' in log
else:
assert 'Leaving device' in log
assert 'no landmark' in log
# test on the eeg chans, since these were not renamed by curry
eeg_names = [
ch["ch_name"] for ch in raw.info["chs"]
if ch["kind"] == FIFF.FIFFV_EEG_CH
]
assert_allclose(raw.get_data(eeg_names),
bti_rfDC.get_data(eeg_names),
rtol=tol)
assert bti_rfDC.info['dev_head_t'] is not None # XXX probably a BTI bug
if mock_dev_head_t:
assert raw.info['dev_head_t'] is not None
assert_allclose(raw.info['dev_head_t']['trans'], WANT_TRANS, atol=1e-5)
else:
assert raw.info['dev_head_t'] is None
# check that most MEG sensors are approximately oriented outward from
# the device origin
n_meg = n_eeg = n_other = 0
pos = list()
nn = list()
for ch in raw.info['chs']:
if ch['kind'] == FIFF.FIFFV_MEG_CH:
assert ch['coil_type'] == FIFF.FIFFV_COIL_CTF_GRAD
t = _loc_to_coil_trans(ch['loc'])
pos.append(t[:3, 3])
nn.append(t[:3, 2])
assert_allclose(np.linalg.norm(nn[-1]), 1.)
n_meg += 1
elif ch['kind'] == FIFF.FIFFV_EEG_CH:
assert ch['coil_type'] == FIFF.FIFFV_COIL_EEG
n_eeg += 1
else:
assert ch['coil_type'] == FIFF.FIFFV_COIL_NONE
n_other += 1
assert n_meg == 148
assert n_eeg == 31
assert n_other == 15
pos = np.array(pos)
nn = np.array(nn)
rad, origin = _fit_sphere(pos, disp=False)
assert 0.11 < rad < 0.13
pos -= origin
pos /= np.linalg.norm(pos, axis=1, keepdims=True)
angles = np.abs(np.rad2deg(np.arccos((pos * nn).sum(-1))))
assert (angles < 20).sum() > 100
def test_other_systems():
"""Test Maxwell filtering on KIT, BTI, and CTF files."""
# 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)
with warnings.catch_warnings(record=True): # head fit
assert_raises(RuntimeError, maxwell_filter, raw_kit)
raw_sss = maxwell_filter(raw_kit, origin=(0., 0., 0.04), ignore_ref=True)
_assert_n_free(raw_sss, 65, 65)
raw_sss_auto = maxwell_filter(raw_kit,
origin=(0., 0., 0.04),
ignore_ref=True,
mag_scale='auto')
assert_allclose(raw_sss._data, raw_sss_auto._data)
# XXX this KIT origin fit is terrible! Eventually we should get a
# corrected HSP file with proper coverage
with warnings.catch_warnings(record=True):
with catch_logging() as log_file:
assert_raises(RuntimeError,
maxwell_filter,
raw_kit,
ignore_ref=True,
regularize=None) # bad condition
raw_sss = maxwell_filter(raw_kit,
origin='auto',
ignore_ref=True,
bad_condition='warning',
verbose='warning')
log_file = log_file.getvalue()
assert_true('badly conditioned' in log_file)
assert_true('more than 20 mm from' in log_file)
# fits can differ slightly based on scipy version, so be lenient here
_assert_n_free(raw_sss, 28, 34) # bad origin == brutal reg
# Let's set the origin
with warnings.catch_warnings(record=True):
with catch_logging() as log_file:
raw_sss = maxwell_filter(raw_kit,
origin=(0., 0., 0.04),
ignore_ref=True,
bad_condition='warning',
regularize=None,
verbose='warning')
log_file = log_file.getvalue()
assert_true('badly conditioned' in log_file)
_assert_n_free(raw_sss, 80)
# Now with reg
with warnings.catch_warnings(record=True):
with catch_logging() as log_file:
raw_sss = maxwell_filter(raw_kit,
origin=(0., 0., 0.04),
ignore_ref=True,
verbose=True)
log_file = log_file.getvalue()
assert_true('badly conditioned' not in log_file)
_assert_n_free(raw_sss, 65)
# 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')
with warnings.catch_warnings(record=True): # weght table
raw_bti = read_raw_bti(bti_pdf, bti_config, bti_hs, preload=False)
picks = pick_types(raw_bti.info, meg='mag', exclude=())
power = np.sqrt(np.sum(raw_bti[picks][0]**2))
raw_sss = maxwell_filter(raw_bti)
_assert_n_free(raw_sss, 70)
_assert_shielding(raw_sss, power, 0.5)
raw_sss_auto = maxwell_filter(raw_bti, mag_scale='auto', verbose=True)
_assert_shielding(raw_sss_auto, power, 0.7)
# CTF
raw_ctf = read_crop(fname_ctf_raw)
assert_equal(raw_ctf.compensation_grade, 3)
assert_raises(RuntimeError, maxwell_filter, raw_ctf) # compensated
raw_ctf.apply_gradient_compensation(0)
assert_raises(ValueError, maxwell_filter, raw_ctf) # cannot fit headshape
raw_sss = maxwell_filter(raw_ctf, origin=(0., 0., 0.04))
_assert_n_free(raw_sss, 68)
_assert_shielding(raw_sss, raw_ctf, 1.8)
raw_sss = maxwell_filter(raw_ctf, origin=(0., 0., 0.04), ignore_ref=True)
_assert_n_free(raw_sss, 70)
_assert_shielding(raw_sss, raw_ctf, 12)
raw_sss_auto = maxwell_filter(raw_ctf,
origin=(0., 0., 0.04),
ignore_ref=True,
mag_scale='auto')
assert_allclose(raw_sss._data, raw_sss_auto._data)
def test_plot_evoked():
"""Test plotting of evoked."""
import matplotlib.pyplot as plt
rng = np.random.RandomState(0)
evoked = _get_epochs().average()
fig = evoked.plot(proj=True, hline=[1], exclude=[], window_title='foo',
time_unit='s')
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(fig, ax,
[line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax,
[ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded & spatial_colors & zorder
evoked.plot(exclude='bads', time_unit='s')
# test selective updating of dict keys is working.
evoked.plot(hline=[1], units=dict(mag='femto foo'), time_unit='s')
evoked_delayed_ssp = _get_epochs_delayed_ssp().average()
evoked_delayed_ssp.plot(proj='interactive', time_unit='s')
evoked_delayed_ssp.apply_proj()
assert_raises(RuntimeError, evoked_delayed_ssp.plot,
proj='interactive', time_unit='s')
evoked_delayed_ssp.info['projs'] = []
assert_raises(RuntimeError, evoked_delayed_ssp.plot,
proj='interactive', time_unit='s')
assert_raises(RuntimeError, evoked_delayed_ssp.plot,
proj='interactive', axes='foo', time_unit='s')
plt.close('all')
# test GFP only
evoked.plot(gfp='only', time_unit='s')
assert_raises(ValueError, evoked.plot, gfp='foo', time_unit='s')
evoked.plot_image(proj=True, time_unit='ms')
# test mask
evoked.plot_image(picks=[1, 2], mask=evoked.data > 0, time_unit='s')
evoked.plot_image(picks=[1, 2], mask_cmap=None, colorbar=False,
mask=np.ones(evoked.data.shape).astype(bool),
time_unit='s')
with warnings.catch_warnings(record=True) as w:
evoked.plot_image(picks=[1, 2], mask=None, mask_style="both",
time_unit='s')
assert len(w) == 2
assert_raises(ValueError, evoked.plot_image, mask=evoked.data[1:, 1:] > 0,
time_unit='s')
# plot with bad channels excluded
evoked.plot_image(exclude='bads', cmap='interactive', time_unit='s')
evoked.plot_image(exclude=evoked.info['bads'], time_unit='s') # same thing
plt.close('all')
assert_raises(ValueError, evoked.plot_image, picks=[0, 0],
time_unit='s') # duplicates
evoked.plot_topo() # should auto-find layout
_line_plot_onselect(0, 200, ['mag', 'grad'], evoked.info, evoked.data,
evoked.times)
plt.close('all')
cov = read_cov(cov_fname)
cov['method'] = 'empirical'
cov['projs'] = [] # avoid warnings
# test rank param.
evoked.plot_white(cov, rank={'mag': 101, 'grad': 201}, time_unit='s')
evoked.plot_white(cov, rank={'mag': 101}, time_unit='s') # test rank param
evoked.plot_white(cov, rank={'grad': 201}, time_unit='s')
assert_raises(
ValueError, evoked.plot_white, cov,
rank={'mag': 101, 'grad': 201, 'meg': 306}, time_unit='s')
assert_raises(
ValueError, evoked.plot_white, cov, rank={'meg': 306}, time_unit='s')
evoked.plot_white([cov, cov], time_unit='s')
# plot_compare_evokeds: test condition contrast, CI, color assignment
plot_compare_evokeds(evoked.copy().pick_types(meg='mag'))
plot_compare_evokeds(
evoked.copy().pick_types(meg='grad'), picks=[1, 2],
show_sensors="upper right", show_legend="upper left")
evokeds = [evoked.copy() for _ in range(10)]
for evoked in evokeds:
evoked.data += (rng.randn(*evoked.data.shape) *
np.std(evoked.data, axis=-1, keepdims=True))
for picks in ([0], [1], [2], [0, 2], [1, 2], [0, 1, 2],):
figs = plot_compare_evokeds([evokeds], picks=picks, ci=0.95)
if not isinstance(figs, list):
figs = [figs]
for fig in figs:
ext = fig.axes[0].collections[0].get_paths()[0].get_extents()
xs, ylim = ext.get_points().T
assert_allclose(xs, evoked.times[[0, -1]])
line = fig.axes[0].lines[0]
xs = line.get_xdata()
assert_allclose(xs, evoked.times)
ys = line.get_ydata()
assert (ys < ylim[1]).all()
assert (ys > ylim[0]).all()
plt.close('all')
evoked.rename_channels({'MEG 2142': "MEG 1642"})
assert len(plot_compare_evokeds(evoked)) == 2
colors = dict(red='r', blue='b')
linestyles = dict(red='--', blue='-')
red, blue = evoked.copy(), evoked.copy()
red.data *= 1.1
blue.data *= 0.9
plot_compare_evokeds([red, blue], picks=3) # list of evokeds
plot_compare_evokeds([red, blue], picks=3, truncate_yaxis=True)
plot_compare_evokeds([[red, evoked], [blue, evoked]],
picks=3) # list of lists
# test picking & plotting grads
contrast = dict()
contrast["red/stim"] = list((evoked.copy(), red))
contrast["blue/stim"] = list((evoked.copy(), blue))
# test a bunch of params at once
for evokeds_ in (evoked.copy().pick_types(meg='mag'), contrast,
[red, blue], [[red, evoked], [blue, evoked]]):
plot_compare_evokeds(evokeds_, picks=0, ci=True) # also tests CI
plt.close('all')
# test styling + a bunch of other params at once
colors, linestyles = dict(red='r', blue='b'), dict(red='--', blue='-')
plot_compare_evokeds(contrast, colors=colors, linestyles=linestyles,
picks=[0, 2], vlines=[.01, -.04], invert_y=True,
truncate_yaxis=False, ylim=dict(mag=(-10, 10)),
styles={"red/stim": {"linewidth": 1}},
show_sensors=True)
# various bad styles
params = [dict(picks=3, colors=dict(fake=1)),
dict(picks=3, styles=dict(fake=1)), dict(picks=3, gfp=True),
dict(picks=3, show_sensors="a"),
dict(colors=dict(red=10., blue=-2))]
for param in params:
assert_raises(ValueError, plot_compare_evokeds, evoked, **param)
assert_raises(TypeError, plot_compare_evokeds, evoked, picks='str')
assert_raises(TypeError, plot_compare_evokeds, evoked, vlines='x')
plt.close('all')
# `evoked` must contain Evokeds
assert_raises(TypeError, plot_compare_evokeds, [[1, 2], [3, 4]])
# `ci` must be float or None
assert_raises(TypeError, plot_compare_evokeds, contrast, ci='err')
# test all-positive ylim
contrast["red/stim"], contrast["blue/stim"] = red, blue
plot_compare_evokeds(contrast, picks=[0], colors=['r', 'b'],
ylim=dict(mag=(1, 10)), ci=_parametric_ci,
truncate_yaxis='max_ticks', show_sensors=False,
show_legend=False)
# sequential colors
evokeds = (evoked, blue, red)
contrasts = {"a{}/b".format(ii): ev for ii, ev in
enumerate(evokeds)}
colors = {"a" + str(ii): ii for ii, _ in enumerate(evokeds)}
contrasts["a1/c"] = evoked.copy()
for split in (True, False):
for linestyles in (["-"], {"b": "-", "c": ":"}):
plot_compare_evokeds(
contrasts, colors=colors, picks=[0], cmap='Reds',
split_legend=split, linestyles=linestyles,
ci=False, show_sensors=False)
colors = {"a" + str(ii): ii / len(evokeds)
for ii, _ in enumerate(evokeds)}
plot_compare_evokeds(
contrasts, colors=colors, picks=[0], cmap='Reds',
split_legend=split, linestyles=linestyles, ci=False,
show_sensors=False)
red.info["chs"][0]["loc"][:2] = 0 # test plotting channel at zero
plot_compare_evokeds(red, picks=[0],
ci=lambda x: [x.std(axis=0), -x.std(axis=0)])
plot_compare_evokeds([red, blue], picks=[0], cmap="summer", ci=None,
split_legend=None)
plot_compare_evokeds([red, blue], cmap=None, split_legend=True)
assert_raises(ValueError, plot_compare_evokeds, [red] * 20)
assert_raises(ValueError, plot_compare_evokeds, contrasts,
cmap='summer')
plt.close('all')
# Hack to test plotting of maxfiltered data
evoked_sss = evoked.copy()
sss = dict(sss_info=dict(in_order=80, components=np.arange(80)))
evoked_sss.info['proc_history'] = [dict(max_info=sss)]
evoked_sss.plot_white(cov, rank={'meg': 64}, time_unit='s')
assert_raises(
ValueError, evoked_sss.plot_white, cov, rank={'grad': 201},
time_unit='s')
evoked_sss.plot_white(cov, time_unit='s')
# plot with bad channels excluded, spatial_colors, zorder & pos. layout
evoked.rename_channels({'MEG 0133': 'MEG 0000'})
evoked.plot(exclude=evoked.info['bads'], spatial_colors=True, gfp=True,
zorder='std', time_unit='s')
evoked.plot(exclude=[], spatial_colors=True, zorder='unsorted',
time_unit='s')
assert_raises(TypeError, evoked.plot, zorder='asdf', time_unit='s')
plt.close('all')
evoked.plot_sensors() # Test plot_sensors
plt.close('all')
evoked.pick_channels(evoked.ch_names[:4])
with catch_logging() as log_file:
evoked.plot(verbose=True, time_unit='s')
assert_true('Need more than one' in log_file.getvalue())
def test_plot_source_estimates(renderer_interactive, all_src_types_inv_evoked,
pick_ori, kind, brain_gc):
"""Test plotting of scalar and vector source estimates."""
backend = renderer_interactive._get_3d_backend()
is_pyvista = backend != 'mayavi'
invs, evoked = all_src_types_inv_evoked
inv = invs[kind]
with pytest.warns(None): # PCA mag
stc = apply_inverse(evoked, inv, pick_ori=pick_ori)
stc.data[1] *= -1 # make it signed
meth_key = 'plot_3d' if isinstance(stc, _BaseVolSourceEstimate) else 'plot'
stc.subject = 'sample'
meth = getattr(stc, meth_key)
kwargs = dict(
subjects_dir=subjects_dir,
time_viewer=False,
show_traces=False, # for speed
smoothing_steps=1,
verbose='error',
src=inv['src'],
volume_options=dict(resolution=None), # for speed
)
if pick_ori != 'vector':
kwargs['surface'] = 'white'
kwargs['backend'] = backend
# Mayavi can't handle non-surface
if kind != 'surface' and not is_pyvista:
with pytest.raises(RuntimeError, match='PyVista'):
meth(**kwargs)
return
brain = meth(**kwargs)
brain.close()
del brain
these_kwargs = kwargs.copy()
these_kwargs['show_traces'] = 'foo'
with pytest.raises(ValueError, match='show_traces'):
meth(**these_kwargs)
del these_kwargs
if pick_ori == 'vector':
with pytest.raises(ValueError, match='use "pos_lims"'):
meth(**kwargs, clim=dict(pos_lims=[1, 2, 3]))
if kind in ('volume', 'mixed'):
with pytest.raises(TypeError, match='when stc is a mixed or vol'):
these_kwargs = kwargs.copy()
these_kwargs.pop('src')
meth(**these_kwargs)
with pytest.raises(ValueError, match='cannot be used'):
these_kwargs = kwargs.copy()
these_kwargs.update(show_traces=True, time_viewer=False)
meth(**these_kwargs)
if not is_pyvista:
with pytest.raises(ValueError, match='view_layout must be'):
meth(view_layout='horizontal', **kwargs)
# flatmaps (mostly a lot of error checking)
these_kwargs = kwargs.copy()
these_kwargs.update(surface='flat',
views='auto',
hemi='both',
verbose='debug')
if kind == 'surface' and pick_ori != 'vector' and is_pyvista:
with catch_logging() as log:
with pytest.raises(FileNotFoundError, match='flatmap'):
meth(**these_kwargs) # sample does not have them
log = log.getvalue()
assert 'offset: 0' in log
fs_stc = stc.copy()
fs_stc.subject = 'fsaverage' # this is wrong, but don't have to care
flat_meth = getattr(fs_stc, meth_key)
these_kwargs.pop('src')
if pick_ori == 'vector':
pass # can't even pass "surface" variable
elif kind != 'surface':
with pytest.raises(TypeError, match='SourceEstimate when a flatmap'):
flat_meth(**these_kwargs)
elif not is_pyvista:
with pytest.raises(RuntimeError, match='PyVista 3D backend.*flatmap'):
flat_meth(**these_kwargs)
else:
brain = flat_meth(**these_kwargs)
brain.close()
del brain
these_kwargs.update(surface='inflated', views='flat')
with pytest.raises(ValueError, match='surface="flat".*views="flat"'):
flat_meth(**these_kwargs)
# just test one for speed
if kind != 'mixed':
return
assert is_pyvista
brain = meth(views=['lat', 'med', 'ven'],
hemi='lh',
view_layout='horizontal',
**kwargs)
brain.close()
assert brain._subplot_shape == (1, 3)
del brain
these_kwargs = kwargs.copy()
these_kwargs['volume_options'] = dict(blending='foo')
with pytest.raises(ValueError, match='mip'):
meth(**these_kwargs)
these_kwargs['volume_options'] = dict(badkey='foo')
with pytest.raises(ValueError, match='unknown'):
meth(**these_kwargs)
# with resampling (actually downsampling but it's okay)
these_kwargs['volume_options'] = dict(resolution=20., surface_alpha=0.)
brain = meth(**these_kwargs)
brain.close()
del brain
def test_plot_alignment_basic(tmpdir, renderer, mixed_fwd_cov_evoked):
"""Test plotting of -trans.fif files and MEG sensor layouts."""
# generate fiducials file for testing
tempdir = str(tmpdir)
fiducials_path = op.join(tempdir, 'fiducials.fif')
fid = [{
'coord_frame': 5,
'ident': 1,
'kind': 1,
'r': [-0.08061612, -0.02908875, -0.04131077]
}, {
'coord_frame': 5,
'ident': 2,
'kind': 1,
'r': [0.00146763, 0.08506715, -0.03483611]
}, {
'coord_frame': 5,
'ident': 3,
'kind': 1,
'r': [0.08436285, -0.02850276, -0.04127743]
}]
write_dig(fiducials_path, fid, 5)
evoked = read_evokeds(evoked_fname)[0]
info = evoked.info
sample_src = read_source_spaces(src_fname)
pytest.raises(TypeError,
plot_alignment,
'foo',
trans_fname,
subject='sample',
subjects_dir=subjects_dir)
pytest.raises(OSError,
plot_alignment,
info,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
src='foo')
pytest.raises(ValueError,
plot_alignment,
info,
trans_fname,
subject='fsaverage',
subjects_dir=subjects_dir,
src=sample_src)
sample_src.plot(subjects_dir=subjects_dir,
head=True,
skull=True,
brain='white')
# mixed source space
mixed_src = mixed_fwd_cov_evoked[0]['src']
assert mixed_src.kind == 'mixed'
plot_alignment(info,
meg=['helmet', 'sensors'],
dig=True,
coord_frame='head',
trans=Path(trans_fname),
subject='sample',
mri_fiducials=fiducials_path,
subjects_dir=subjects_dir,
src=mixed_src)
renderer.backend._close_all()
# no-head version
renderer.backend._close_all()
# trans required
with pytest.raises(ValueError, match='transformation matrix is required'):
plot_alignment(info, trans=None, src=src_fname)
with pytest.raises(ValueError, match='transformation matrix is required'):
plot_alignment(info, trans=None, mri_fiducials=True)
with pytest.raises(ValueError, match='transformation matrix is required'):
plot_alignment(info, trans=None, surfaces=['brain'])
# all coord frames
plot_alignment(info) # works: surfaces='auto' default
for coord_frame in ('meg', 'head', 'mri'):
fig = plot_alignment(info,
meg=['helmet', 'sensors'],
dig=True,
coord_frame=coord_frame,
trans=Path(trans_fname),
subject='sample',
mri_fiducials=fiducials_path,
subjects_dir=subjects_dir,
src=src_fname)
renderer.backend._close_all()
# EEG only with strange options
evoked_eeg_ecog_seeg = evoked.copy().pick_types(meg=False, eeg=True)
evoked_eeg_ecog_seeg.info['projs'] = [] # "remove" avg proj
evoked_eeg_ecog_seeg.set_channel_types({
'EEG 001': 'ecog',
'EEG 002': 'seeg'
})
with catch_logging() as log:
plot_alignment(evoked_eeg_ecog_seeg.info,
subject='sample',
trans=trans_fname,
subjects_dir=subjects_dir,
surfaces=['white', 'outer_skin', 'outer_skull'],
meg=['helmet', 'sensors'],
eeg=['original', 'projected'],
ecog=True,
seeg=True,
verbose=True)
log = log.getvalue()
assert 'ecog: 1' in log
assert 'seeg: 1' in log
renderer.backend._close_all()
sphere = make_sphere_model(info=info, r0='auto', head_radius='auto')
bem_sol = read_bem_solution(
op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem-sol.fif'))
bem_surfs = read_bem_surfaces(
op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem.fif'))
sample_src[0]['coord_frame'] = 4 # hack for coverage
plot_alignment(
info,
trans_fname,
subject='sample',
eeg='projected',
meg='helmet',
bem=sphere,
dig=True,
surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin'])
plot_alignment(info,
subject='sample',
meg='helmet',
subjects_dir=subjects_dir,
eeg='projected',
bem=sphere,
surfaces=['head', 'brain'],
src=sample_src)
# no trans okay, no mri surfaces
plot_alignment(info, bem=sphere, surfaces=['brain'])
with pytest.raises(ValueError, match='A head surface is required'):
plot_alignment(info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
eeg='projected',
surfaces=[])
with pytest.raises(RuntimeError, match='No brain surface found'):
plot_alignment(info,
trans=trans_fname,
subject='foo',
subjects_dir=subjects_dir,
surfaces=['brain'])
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info,
trans_fname,
subject='sample',
meg=[],
subjects_dir=subjects_dir,
bem=bem_sol,
eeg=True,
surfaces=['head', 'inflated', 'outer_skull', 'inner_skull'])
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info,
trans_fname,
subject='sample',
meg=True,
subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'],
bem=bem_surfs)
# single-layer BEM can still plot head surface
assert bem_surfs[-1]['id'] == FIFF.FIFFV_BEM_SURF_ID_BRAIN
bem_sol_homog = read_bem_solution(
op.join(subjects_dir, 'sample', 'bem', 'sample-1280-bem-sol.fif'))
for use_bem in (bem_surfs[-1:], bem_sol_homog):
with catch_logging() as log:
plot_alignment(info,
trans_fname,
subject='sample',
meg=True,
subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'],
bem=use_bem,
verbose=True)
log = log.getvalue()
assert 'not find the surface for head in the provided BEM model' in log
# sphere model
sphere = make_sphere_model('auto', 'auto', info)
src = setup_volume_source_space(sphere=sphere)
plot_alignment(
info,
trans=Transform('head', 'mri'),
eeg='projected',
meg='helmet',
bem=sphere,
src=src,
dig=True,
surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin'])
sphere = make_sphere_model('auto', None, info) # one layer
# if you ask for a brain surface with a 1-layer sphere model it's an error
with pytest.raises(RuntimeError, match='Sphere model does not have'):
fig = plot_alignment(trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['brain'],
bem=sphere)
# but you can ask for a specific brain surface, and
# no info is permitted
fig = plot_alignment(trans=trans_fname,
subject='sample',
meg=False,
coord_frame='mri',
subjects_dir=subjects_dir,
surfaces=['white'],
bem=sphere,
show_axes=True)
renderer.backend._close_all()
if renderer._get_3d_backend() == 'mayavi':
import mayavi # noqa: F401 analysis:ignore
assert isinstance(fig, mayavi.core.scene.Scene)
# 3D coil with no defined draw (ConvexHull)
info_cube = pick_info(info, np.arange(6))
info['dig'] = None
info_cube['chs'][0]['coil_type'] = 9999
info_cube['chs'][1]['coil_type'] = 9998
with pytest.raises(RuntimeError, match='coil definition not found'):
plot_alignment(info_cube, meg='sensors', surfaces=())
coil_def_fname = op.join(tempdir, 'temp')
with open(coil_def_fname, 'w') as fid:
fid.write(coil_3d)
# make sure our other OPMs can be plotted, too
for ii, kind in enumerate(
('QUSPIN_ZFOPM_MAG', 'QUSPIN_ZFOPM_MAG2', 'FIELDLINE_OPM_MAG_GEN1',
'KERNEL_OPM_MAG_GEN1'), 2):
info_cube['chs'][ii]['coil_type'] = getattr(FIFF, f'FIFFV_COIL_{kind}')
with use_coil_def(coil_def_fname):
with catch_logging() as log:
plot_alignment(info_cube,
meg='sensors',
surfaces=(),
dig=True,
verbose='debug')
log = log.getvalue()
assert 'planar geometry' in log
# one layer bem with skull surfaces:
with pytest.raises(RuntimeError, match='Sphere model does not.*boundary'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['brain', 'head', 'inner_skull'],
bem=sphere)
# wrong eeg value:
with pytest.raises(ValueError, match='Invalid value for the .eeg'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
eeg='foo')
# wrong meg value:
with pytest.raises(ValueError, match='Invalid value for the .meg'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
meg='bar')
# multiple brain surfaces:
with pytest.raises(ValueError, match='Only one brain surface can be plot'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['white', 'pial'])
with pytest.raises(TypeError, match='surfaces.*must be'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=[1])
with pytest.raises(ValueError, match='Unknown surface type'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['foo'])
with pytest.raises(TypeError, match="must be an instance of "):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=dict(brain='super clear'))
with pytest.raises(ValueError, match="must be between 0 and 1"):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=dict(brain=42))
fwd_fname = op.join(data_dir, 'MEG', 'sample',
'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif')
fwd = read_forward_solution(fwd_fname)
plot_alignment(subject='sample',
subjects_dir=subjects_dir,
trans=trans_fname,
fwd=fwd,
surfaces='white',
coord_frame='head')
fwd = convert_forward_solution(fwd, force_fixed=True)
plot_alignment(subject='sample',
subjects_dir=subjects_dir,
trans=trans_fname,
fwd=fwd,
surfaces='white',
coord_frame='head')
fwd['coord_frame'] = FIFF.FIFFV_COORD_MRI # check required to get to MRI
with pytest.raises(ValueError, match='transformation matrix is required'):
plot_alignment(info, trans=None, fwd=fwd)
# surfaces as dict
plot_alignment(subject='sample',
coord_frame='head',
trans=trans_fname,
subjects_dir=subjects_dir,
surfaces={
'white': 0.4,
'outer_skull': 0.6,
'head': None
})
def test_plot_evoked():
"""Test evoked.plot."""
epochs = _get_epochs()
evoked = epochs.average()
assert evoked.proj is False
fig = evoked.plot(proj=True,
hline=[1],
exclude=[],
window_title='foo',
time_unit='s')
amplitudes = _get_amplitudes(fig)
assert len(amplitudes) == len(default_picks)
assert evoked.proj is False
# Test a click
ax = fig.get_axes()[0]
line = ax.lines[0]
_fake_click(fig, ax, [line.get_xdata()[0], line.get_ydata()[0]], 'data')
_fake_click(fig, ax, [ax.get_xlim()[0], ax.get_ylim()[1]], 'data')
# plot with bad channels excluded & spatial_colors & zorder
evoked.plot(exclude='bads', time_unit='s')
# test selective updating of dict keys is working.
evoked.plot(hline=[1], units=dict(mag='femto foo'), time_unit='s')
evoked_delayed_ssp = _get_epochs_delayed_ssp().average()
evoked_delayed_ssp.plot(proj='interactive', time_unit='s')
evoked_delayed_ssp.apply_proj()
pytest.raises(RuntimeError,
evoked_delayed_ssp.plot,
proj='interactive',
time_unit='s')
with evoked_delayed_ssp.info._unlock():
evoked_delayed_ssp.info['projs'] = []
pytest.raises(RuntimeError,
evoked_delayed_ssp.plot,
proj='interactive',
time_unit='s')
pytest.raises(RuntimeError,
evoked_delayed_ssp.plot,
proj='interactive',
axes='foo',
time_unit='s')
plt.close('all')
# test `gfp='only'`: GFP (EEG) and RMS (MEG)
fig, ax = plt.subplots(3)
evoked.plot(gfp='only', time_unit='s', axes=ax)
assert len(ax[0].lines) == len(ax[1].lines) == len(ax[2].lines) == 1
assert ax[0].get_title() == 'EEG (3 channels)'
assert ax[0].texts[0].get_text() == 'GFP'
assert ax[1].get_title() == 'Gradiometers (9 channels)'
assert ax[1].texts[0].get_text() == 'RMS'
assert ax[2].get_title() == 'Magnetometers (2 channels)'
assert ax[1].texts[0].get_text() == 'RMS'
plt.close('all')
# Test invalid `gfp`
with pytest.raises(ValueError):
evoked.plot(gfp='foo', time_unit='s')
# plot with bad channels excluded, spatial_colors, zorder & pos. layout
evoked.rename_channels({'MEG 0133': 'MEG 0000'})
evoked.plot(exclude=evoked.info['bads'],
spatial_colors=True,
gfp=True,
zorder='std',
time_unit='s')
evoked.plot(exclude=[],
spatial_colors=True,
zorder='unsorted',
time_unit='s')
pytest.raises(TypeError, evoked.plot, zorder='asdf', time_unit='s')
plt.close('all')
evoked.plot_sensors() # Test plot_sensors
plt.close('all')
evoked.pick_channels(evoked.ch_names[:4])
with catch_logging() as log_file:
evoked.plot(verbose=True, time_unit='s')
assert 'Need more than one' in log_file.getvalue()
def test_reporting_fir(phase, fir_window, btype):
"""Test FIR filter reporting."""
l_freq = 1. if btype == 'bandpass' else None
fs = 1000.
with catch_logging() as log:
x = create_filter(None,
fs,
l_freq,
40,
method='fir',
phase=phase,
fir_window=fir_window,
verbose=True)
n_taps = len(x)
log = log.getvalue()
keys = [
'FIR',
btype,
fir_window.capitalize(),
'Filter length: %d samples' % (n_taps, ),
'passband ripple',
'stopband attenuation',
]
if phase == 'minimum':
keys += [' causal ']
else:
keys += [' non-causal ', ' dB cutoff frequency: 45.00 Hz']
if btype == 'bandpass':
keys += [' dB cutoff frequency: 0.50 Hz']
for key in keys:
assert key in log
if phase == 'zero':
assert '-6 dB cutoff' in log
elif phase == 'zero-double':
assert '-12 dB cutoff' in log
else:
# XXX Eventually we should figure out where the resulting point is,
# since the minimum-phase process will change it. For now we don't
# report it.
assert phase == 'minimum'
# Verify some of the filter properties
if phase == 'zero-double':
x = np.convolve(x, x) # effectively what happens
w, h = freqz(x, worN=10000)
w *= fs / (2 * np.pi)
h = np.abs(h)
# passband
passes = [np.argmin(np.abs(w - f)) for f in (1, 20, 40)]
# stopband
stops = [np.argmin(np.abs(w - 50.))]
# transition
mids = [np.argmin(np.abs(w - 45.))]
# put these where they belong based on filter type
assert w[0] == 0.
idx_0 = 0
idx_0p5 = np.argmin(np.abs(w - 0.5))
if btype == 'bandpass':
stops += [idx_0]
mids += [idx_0p5]
else:
passes += [idx_0, idx_0p5]
assert_allclose(h[passes], 1., atol=0.01)
attenuation = -20 if phase == 'minimum' else -50
assert_allclose(h[stops], 0., atol=10**(attenuation / 20.))
if phase != 'minimum': # haven't worked out the math for this yet
expected = 0.25 if phase == 'zero-double' else 0.5
assert_allclose(h[mids], expected, atol=0.01)
def test_reporting_iir(ftype, btype, order, output):
"""Test IIR filter reporting."""
fs = 1000.
l_freq = 1. if btype == 'bandpass' else None
iir_params = dict(ftype=ftype, order=order, output=output)
rs = 20 if order == 1 else 80
if ftype == 'ellip':
iir_params['rp'] = 3 # dB
iir_params['rs'] = rs # attenuation
pass_tol = np.log10(iir_params['rp']) + 0.01
else:
pass_tol = 0.2
with catch_logging() as log:
x = create_filter(None,
fs,
l_freq,
40.,
method='iir',
iir_params=iir_params,
verbose=True)
order_eff = order * (1 + (btype == 'bandpass'))
if output == 'ba':
assert len(x['b']) == order_eff + 1
log = log.getvalue()
keys = [
'IIR',
'zero-phase',
'two-pass forward and reverse',
'non-causal',
btype,
ftype,
'Filter order %d' % (order_eff * 2, ),
'Cutoff ' if btype == 'lowpass' else 'Cutoffs ',
]
dB_decade = -27.74
if ftype == 'ellip':
dB_cutoff = -6.0
elif order == 1 or ftype == 'butter':
dB_cutoff = -6.02
else:
assert ftype == 'bessel'
assert order == 4
dB_cutoff = -15.16
if btype == 'lowpass':
keys += ['%0.2f dB' % (dB_cutoff, )]
for key in keys:
assert key.lower() in log.lower()
# Verify some of the filter properties
if output == 'ba':
w, h = freqz(x['b'], x['a'], worN=10000)
else:
w, h = sosfreqz(x['sos'], worN=10000)
w *= fs / (2 * np.pi)
h = np.abs(h)
# passband
passes = [np.argmin(np.abs(w - 20))]
# stopband
decades = [np.argmin(np.abs(w - 400.))] # one decade
# transition
edges = [np.argmin(np.abs(w - 40.))]
# put these where they belong based on filter type
assert w[0] == 0.
idx_0p1 = np.argmin(np.abs(w - 0.1))
idx_1 = np.argmin(np.abs(w - 1.))
if btype == 'bandpass':
edges += [idx_1]
decades += [idx_0p1]
else:
passes += [idx_0p1, idx_1]
edge_val = 10**(dB_cutoff / 40.)
assert_allclose(h[edges], edge_val, atol=0.01)
assert_allclose(h[passes], 1., atol=pass_tol)
if ftype == 'butter' and btype == 'lowpass':
attenuation = dB_decade * order
assert_allclose(h[decades], 10**(attenuation / 20.), rtol=0.01)
elif ftype == 'ellip':
assert_array_less(h[decades], 10**(-rs / 20))
def test_coreg_class_gui_match():
"""Test that using Coregistration matches mne coreg."""
fiducials, _ = read_fiducials(fid_fname)
info = read_info(raw_fname)
coreg = Coregistration(info,
subject='sample',
subjects_dir=subjects_dir,
fiducials=fiducials)
assert_allclose(coreg.trans['trans'], np.eye(4), atol=1e-6)
# mne coreg -s sample -d subjects -f MEG/sample/sample_audvis_trunc_raw.fif
# then "Fit Fid.", Save... to get trans, read_trans:
want_trans = [
[9.99428809e-01, 2.94733196e-02, 1.65350307e-02, -8.76054692e-04],
[-1.92420650e-02, 8.98512006e-01, -4.38526988e-01, 9.39774036e-04],
[-2.77817696e-02, 4.37958330e-01, 8.98565888e-01, -8.29207990e-03],
[0, 0, 0, 1]
]
coreg.set_fid_match('matched')
coreg.fit_fiducials(verbose=True)
assert_allclose(coreg.trans['trans'], want_trans, atol=1e-6)
# Set ICP iterations to one, click "Fit ICP"
want_trans = [
[9.99512792e-01, 2.80128177e-02, 1.37659665e-02, 6.08855276e-04],
[-1.91694051e-02, 8.98992002e-01, -4.37545270e-01, 9.66848747e-04],
[-2.46323701e-02, 4.37068194e-01, 8.99091005e-01, -1.44129358e-02],
[0, 0, 0, 1]
]
coreg.fit_icp(1, verbose=True)
assert_allclose(coreg.trans['trans'], want_trans, atol=1e-6)
# Set ICP iterations to 20, click "Fit ICP"
with catch_logging() as log:
coreg.fit_icp(20, verbose=True)
log = log.getvalue()
want_trans = [
[9.97582495e-01, 2.12266613e-02, 6.61706254e-02, -5.07694029e-04],
[1.81089472e-02, 8.39900672e-01, -5.42437911e-01, 7.81218382e-03],
[-6.70908988e-02, 5.42324841e-01, 8.37485850e-01, -2.50057746e-02],
[0, 0, 0, 1]
]
assert_allclose(coreg.trans['trans'], want_trans, atol=1e-6)
assert 'ICP 19' in log
assert 'ICP 20' not in log # converged on 19
# Change to uniform scale mode, "Fit Fiducials" in scale UI
coreg.set_scale_mode('uniform')
coreg.fit_fiducials()
want_scale = [0.975] * 3
want_trans = [
[9.99428809e-01, 2.94733196e-02, 1.65350307e-02, -9.25998494e-04],
[-1.92420650e-02, 8.98512006e-01, -4.38526988e-01, -1.03350170e-03],
[-2.77817696e-02, 4.37958330e-01, 8.98565888e-01, -9.03170835e-03],
[0, 0, 0, 1]
]
assert_allclose(coreg.scale, want_scale, atol=5e-4)
assert_allclose(coreg.trans['trans'], want_trans, atol=1e-6)
# Click "Fit ICP" in scale UI
with catch_logging() as log:
coreg.fit_icp(20, verbose=True)
log = log.getvalue()
assert 'ICP 18' in log
assert 'ICP 19' not in log
want_scale = [1.036] * 3
want_trans = [
[9.98992383e-01, 1.72388796e-02, 4.14364934e-02, 6.19427126e-04],
[6.80460501e-03, 8.54430079e-01, -5.19521892e-01, 5.58008114e-03],
[-4.43605632e-02, 5.19280374e-01, 8.53451848e-01, -2.03358755e-02],
[0, 0, 0, 1]
]
assert_allclose(coreg.scale, want_scale, atol=5e-4)
assert_allclose(coreg.trans['trans'], want_trans, atol=1e-6)
# Change scale mode to 3-axis, click "Fit ICP" in scale UI
coreg.set_scale_mode('3-axis')
with catch_logging() as log:
coreg.fit_icp(20, verbose=True)
log = log.getvalue()
assert 'ICP 7' in log
assert 'ICP 8' not in log
want_scale = [1.025, 1.010, 1.121]
want_trans = [
[9.98387098e-01, 2.04762165e-02, 5.29526398e-02, 4.97257097e-05],
[1.13287698e-02, 8.42087150e-01, -5.39222538e-01, 7.09863892e-03],
[-5.56319728e-02, 5.38952649e-01, 8.40496957e-01, -1.46372067e-02],
[0, 0, 0, 1]
]
assert_allclose(coreg.scale, want_scale, atol=5e-4)
assert_allclose(coreg.trans['trans'], want_trans, atol=1e-6)