[074d3d]: / mne / forward / tests / test_field_interpolation.py

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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from os import path as op
from pathlib import Path
import numpy as np
import pytest
from numpy.polynomial import legendre
from numpy.testing import (
assert_allclose,
assert_array_almost_equal,
assert_array_equal,
assert_equal,
)
from scipy.interpolate import interp1d
import mne
from mne import Epochs, make_fixed_length_events, pick_types, read_evokeds
from mne.datasets import testing
from mne.forward import _make_surface_mapping, make_field_map
from mne.forward._field_interpolation import _setup_dots
from mne.forward._lead_dots import (
_comp_sum_eeg,
_comp_sums_meg,
_do_cross_dots,
_get_legen_table,
)
from mne.forward._make_forward import _create_meg_coils
from mne.io import read_raw_fif
from mne.surface import get_head_surf, get_meg_helmet_surf
base_dir = op.join(op.dirname(__file__), "..", "..", "io", "tests", "data")
raw_fname = op.join(base_dir, "test_raw.fif")
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(evoked.ch_names[:50]) # crappy mapping but faster
# smoke test - passing trans_fname as pathlib.Path as additional check
make_field_map(
evoked, trans=Path(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(-1.0, 1.0, 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(picks="eeg")
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(picks="eeg")
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(picks="meg")
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(picks="meg")
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([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,
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,
atol=1e-3,
rtol=1e-3,
)
assert_allclose(
np.sqrt(np.sum(maps[1]["data"] ** 2)),
19.4748,
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, _, lut_fun, n_fact = _setup_dots("fast", info, coils, "meg")
my_origin = np.array([0.0, 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
raw = read_raw_fif(raw_fname)
events = mne.find_events(raw)
picks = pick_types(
raw.info,
meg=True,
eeg=True,
stim=True,
ecg=True,
eog=True,
include=["STI 014"],
exclude="bads",
)
epochs = mne.Epochs(raw, events, picks=picks)
evoked = epochs.average()
with pytest.raises(ValueError, match="Invalid value for the 'ch_type'"):
evoked.as_type("meg")
with pytest.raises(ValueError, match="Invalid value for the 'ch_type'"):
evoked.copy().pick(picks="grad").as_type("meg")
# channel names
ch_names = evoked.info["ch_names"]
virt_evoked = evoked.copy().pick(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(ch_names[2:10:3])
evoked_to = evoked.copy().pick(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(ch_names[:10:]).copy()
data1 = evoked.pick("grad").data.ravel()
data2 = evoked.as_type("grad").data.ravel()
assert np.corrcoef(data1, data2)[0, 1] > 0.95
# Do it with epochs
virt_epochs = epochs.copy().load_data().pick(ch_names[:10:1])
virt_epochs.info.normalize_proj()
virt_epochs = virt_epochs.as_type("mag")
assert all(ch.endswith("_v") for ch in virt_epochs.info["ch_names"])
assert_allclose(virt_epochs.get_data(copy=False).mean(0), virt_evoked.data)