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from os import path as op
import numpy as np
from numpy.polynomial import legendre
from numpy.testing import (assert_allclose, assert_array_equal, assert_equal,
assert_array_almost_equal)
from scipy.interpolate import interp1d
import pytest
from mne.forward import _make_surface_mapping, make_field_map
from mne.forward._lead_dots import (_comp_sum_eeg, _comp_sums_meg,
_get_legen_table, _do_cross_dots)
from mne.forward._make_forward import _create_meg_coils
from mne.forward._field_interpolation import _setup_dots
from mne.surface import get_meg_helmet_surf, get_head_surf
from mne.datasets import testing
from mne import read_evokeds, pick_types, make_fixed_length_events, Epochs
from mne.io import read_raw_fif
from mne.externals.six.moves import zip
from mne.utils import run_tests_if_main
base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
evoked_fname = op.join(base_dir, 'test-ave.fif')
raw_ctf_fname = op.join(base_dir, 'test_ctf_raw.fif')
data_path = testing.data_path(download=False)
trans_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc-trans.fif')
subjects_dir = op.join(data_path, 'subjects')
@testing.requires_testing_data
def test_field_map_ctf():
"""Test that field mapping can be done with CTF data."""
raw = read_raw_fif(raw_ctf_fname).crop(0, 1)
raw.apply_gradient_compensation(3)
events = make_fixed_length_events(raw, duration=0.5)
evoked = Epochs(raw, events).average()
evoked.pick_channels(evoked.ch_names[:50]) # crappy mapping but faster
# smoke test
make_field_map(evoked, trans=trans_fname, subject='sample',
subjects_dir=subjects_dir)
def test_legendre_val():
"""Test Legendre polynomial (derivative) equivalence."""
rng = np.random.RandomState(0)
# check table equiv
xs = np.linspace(-1., 1., 1000)
n_terms = 100
# True, numpy
vals_np = legendre.legvander(xs, n_terms - 1)
# Table approximation
for nc, interp in zip([100, 50], ['nearest', 'linear']):
lut, n_fact = _get_legen_table('eeg', n_coeff=nc, force_calc=True)
lut_fun = interp1d(np.linspace(-1, 1, lut.shape[0]), lut, interp,
axis=0)
vals_i = lut_fun(xs)
# Need a "1:" here because we omit the first coefficient in our table!
assert_allclose(vals_np[:, 1:vals_i.shape[1] + 1], vals_i,
rtol=1e-2, atol=5e-3)
# Now let's look at our sums
ctheta = rng.rand(20, 30) * 2.0 - 1.0
beta = rng.rand(20, 30) * 0.8
c1 = _comp_sum_eeg(beta.flatten(), ctheta.flatten(), lut_fun, n_fact)
c1.shape = beta.shape
# compare to numpy
n = np.arange(1, n_terms, dtype=float)[:, np.newaxis, np.newaxis]
coeffs = np.zeros((n_terms,) + beta.shape)
coeffs[1:] = (np.cumprod([beta] * (n_terms - 1), axis=0) *
(2.0 * n + 1.0) * (2.0 * n + 1.0) / n)
# can't use tensor=False here b/c it isn't in old numpy
c2 = np.empty((20, 30))
for ci1 in range(20):
for ci2 in range(30):
c2[ci1, ci2] = legendre.legval(ctheta[ci1, ci2],
coeffs[:, ci1, ci2])
assert_allclose(c1, c2, 1e-2, 1e-3) # close enough...
# compare fast and slow for MEG
ctheta = rng.rand(20 * 30) * 2.0 - 1.0
beta = rng.rand(20 * 30) * 0.8
lut, n_fact = _get_legen_table('meg', n_coeff=10, force_calc=True)
fun = interp1d(np.linspace(-1, 1, lut.shape[0]), lut, 'nearest', axis=0)
coeffs = _comp_sums_meg(beta, ctheta, fun, n_fact, False)
lut, n_fact = _get_legen_table('meg', n_coeff=20, force_calc=True)
fun = interp1d(np.linspace(-1, 1, lut.shape[0]), lut, 'linear', axis=0)
coeffs = _comp_sums_meg(beta, ctheta, fun, n_fact, False)
def test_legendre_table():
"""Test Legendre table calculation."""
# double-check our table generation
n = 10
for ch_type in ['eeg', 'meg']:
lut1, n_fact1 = _get_legen_table(ch_type, n_coeff=25, force_calc=True)
lut1 = lut1[:, :n - 1].copy()
n_fact1 = n_fact1[:n - 1].copy()
lut2, n_fact2 = _get_legen_table(ch_type, n_coeff=n, force_calc=True)
assert_allclose(lut1, lut2)
assert_allclose(n_fact1, n_fact2)
@testing.requires_testing_data
def test_make_field_map_eeg():
"""Test interpolation of EEG field onto head."""
evoked = read_evokeds(evoked_fname, condition='Left Auditory')
evoked.info['bads'] = ['MEG 2443', 'EEG 053'] # add some bads
surf = get_head_surf('sample', subjects_dir=subjects_dir)
# we must have trans if surface is in MRI coords
pytest.raises(ValueError, _make_surface_mapping, evoked.info, surf, 'eeg')
evoked.pick_types(meg=False, eeg=True)
fmd = make_field_map(evoked, trans_fname,
subject='sample', subjects_dir=subjects_dir)
# trans is necessary for EEG only
pytest.raises(RuntimeError, make_field_map, evoked, None,
subject='sample', subjects_dir=subjects_dir)
fmd = make_field_map(evoked, trans_fname,
subject='sample', subjects_dir=subjects_dir)
assert len(fmd) == 1
assert_array_equal(fmd[0]['data'].shape, (642, 59)) # maps data onto surf
assert len(fmd[0]['ch_names']) == 59
@testing.requires_testing_data
@pytest.mark.slowtest
def test_make_field_map_meg():
"""Test interpolation of MEG field onto helmet | head."""
evoked = read_evokeds(evoked_fname, condition='Left Auditory')
info = evoked.info
surf = get_meg_helmet_surf(info)
# let's reduce the number of channels by a bunch to speed it up
info['bads'] = info['ch_names'][:200]
# bad ch_type
pytest.raises(ValueError, _make_surface_mapping, info, surf, 'foo')
# bad mode
pytest.raises(ValueError, _make_surface_mapping, info, surf, 'meg',
mode='foo')
# no picks
evoked_eeg = evoked.copy().pick_types(meg=False, eeg=True)
pytest.raises(RuntimeError, _make_surface_mapping, evoked_eeg.info,
surf, 'meg')
# bad surface def
nn = surf['nn']
del surf['nn']
pytest.raises(KeyError, _make_surface_mapping, info, surf, 'meg')
surf['nn'] = nn
cf = surf['coord_frame']
del surf['coord_frame']
pytest.raises(KeyError, _make_surface_mapping, info, surf, 'meg')
surf['coord_frame'] = cf
# now do it with make_field_map
evoked.pick_types(meg=True, eeg=False)
evoked.info.normalize_proj() # avoid projection warnings
fmd = make_field_map(evoked, None,
subject='sample', subjects_dir=subjects_dir)
assert (len(fmd) == 1)
assert_array_equal(fmd[0]['data'].shape, (304, 106)) # maps data onto surf
assert len(fmd[0]['ch_names']) == 106
pytest.raises(ValueError, make_field_map, evoked, ch_type='foobar')
# now test the make_field_map on head surf for MEG
evoked.pick_types(meg=True, eeg=False)
evoked.info.normalize_proj()
fmd = make_field_map(evoked, trans_fname, meg_surf='head',
subject='sample', subjects_dir=subjects_dir)
assert len(fmd) == 1
assert_array_equal(fmd[0]['data'].shape, (642, 106)) # maps data onto surf
assert len(fmd[0]['ch_names']) == 106
pytest.raises(ValueError, make_field_map, evoked, meg_surf='foobar',
subjects_dir=subjects_dir, trans=trans_fname)
@testing.requires_testing_data
def test_make_field_map_meeg():
"""Test making a M/EEG field map onto helmet & head."""
evoked = read_evokeds(evoked_fname, baseline=(-0.2, 0.0))[0]
picks = pick_types(evoked.info, meg=True, eeg=True)
picks = picks[::10]
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.info.normalize_proj()
maps = make_field_map(evoked, trans_fname, subject='sample',
subjects_dir=subjects_dir, n_jobs=1, verbose='debug')
assert_equal(maps[0]['data'].shape, (642, 6)) # EEG->Head
assert_equal(maps[1]['data'].shape, (304, 31)) # MEG->Helmet
# reasonable ranges
maxs = (1.2, 2.0) # before #4418, was (1.1, 2.0)
mins = (-0.8, -1.3) # before #4418, was (-0.6, -1.2)
assert_equal(len(maxs), len(maps))
for map_, max_, min_ in zip(maps, maxs, mins):
assert_allclose(map_['data'].max(), max_, rtol=5e-2)
assert_allclose(map_['data'].min(), min_, rtol=5e-2)
# calculated from correct looking mapping on 2015/12/26
assert_allclose(np.sqrt(np.sum(maps[0]['data'] ** 2)), 19.0903, # 16.6088,
atol=1e-3, rtol=1e-3)
assert_allclose(np.sqrt(np.sum(maps[1]['data'] ** 2)), 19.4748, # 20.1245,
atol=1e-3, rtol=1e-3)
def _setup_args(info):
"""Configure args for test_as_meg_type_evoked."""
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'])
int_rad, noise, lut_fun, n_fact = _setup_dots('fast', coils, 'meg')
my_origin = np.array([0., 0., 0.04])
args_dict = dict(intrad=int_rad, volume=False, coils1=coils, r0=my_origin,
ch_type='meg', lut=lut_fun, n_fact=n_fact)
return args_dict
@testing.requires_testing_data
def test_as_meg_type_evoked():
"""Test interpolation of data on to virtual channels."""
# validation tests
evoked = read_evokeds(evoked_fname, condition='Left Auditory')
pytest.raises(ValueError, evoked.as_type, 'meg')
pytest.raises(ValueError, evoked.copy().pick_types(meg='grad').as_type,
'meg')
# channel names
ch_names = evoked.info['ch_names']
virt_evoked = evoked.copy().pick_channels(ch_names=ch_names[:10:1])
virt_evoked.info.normalize_proj()
virt_evoked = virt_evoked.as_type('mag')
assert (all(ch.endswith('_v') for ch in virt_evoked.info['ch_names']))
# pick from and to channels
evoked_from = evoked.copy().pick_channels(ch_names=ch_names[2:10:3])
evoked_to = evoked.copy().pick_channels(ch_names=ch_names[0:10:3])
info_from, info_to = evoked_from.info, evoked_to.info
# set up things
args1, args2 = _setup_args(info_from), _setup_args(info_to)
args1.update(coils2=args2['coils1'])
args2.update(coils2=args1['coils1'])
# test cross dots
cross_dots1 = _do_cross_dots(**args1)
cross_dots2 = _do_cross_dots(**args2)
assert_array_almost_equal(cross_dots1, cross_dots2.T)
# correlation test
evoked = evoked.pick_channels(ch_names=ch_names[:10:]).copy()
data1 = evoked.pick_types(meg='grad').data.ravel()
data2 = evoked.as_type('grad').data.ravel()
assert (np.corrcoef(data1, data2)[0, 1] > 0.95)
run_tests_if_main()
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