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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import shutil
from os import remove
import pytest
import scipy.io
from numpy import array, empty, isnan
from numpy.testing import assert_array_almost_equal, assert_array_equal
from mne import pick_types
from mne.datasets import testing
from mne.io import read_raw_fil
from mne.io.fil.sensors import _get_pos_units
fil_path = testing.data_path(download=False) / "FIL"
# TODO: Ignore this warning in all these tests until we deal with this properly
pytestmark = pytest.mark.filterwarnings(
"ignore:.*problems later!:RuntimeWarning",
)
def _set_bads_tsv(chanfile, badchan):
"""Update channels.tsv by setting target channel to bad."""
data = []
with open(chanfile, encoding="utf-8") as f:
for line in f:
columns = line.strip().split("\t")
data.append(columns)
with open(chanfile, "w", encoding="utf-8") as f:
for row in data:
if badchan in row:
row[-1] = "bad"
f.write("\t".join(row) + "\n")
def unpack_mat(matin):
"""Extract relevant entries from unstructred readmat."""
data = matin["data"]
grad = data[0][0]["grad"]
label = list()
coil_label = list()
for ii in range(len(data[0][0]["label"])):
label.append(str(data[0][0]["label"][ii][0][0]))
for ii in range(len(grad[0][0]["label"])):
coil_label.append(str(grad[0][0]["label"][ii][0][0]))
matout = {
"label": label,
"trial": data["trial"][0][0][0][0],
"coil_label": coil_label,
"coil_pos": grad[0][0]["coilpos"],
"coil_ori": grad[0][0]["coilori"],
}
return matout
def _match_str(A_list, B_list):
"""Locate where in a list matches another."""
B_inds = list()
for ii in A_list:
if ii in B_list:
B_inds.append(B_list.index(ii))
return B_inds
def _get_channels_with_positions(info):
"""Parse channel orientation/position."""
ch_list = list()
ch_inds = list()
for ii, ch in enumerate(info["chs"]):
if not (any(isnan(ch["loc"]))):
ch_inds.append(ii)
ch_list.append(ch["ch_name"])
return ch_list, ch_inds
def _fil_megmag(raw_test, raw_mat):
"""Test the magnetometer channels."""
test_inds = pick_types(raw_test.info, meg="mag", ref_meg=False, exclude="bads")
test_list = list(raw_test.info["ch_names"][i] for i in test_inds)
mat_list = raw_mat["label"]
mat_inds = _match_str(test_list, mat_list)
assert len(mat_inds) == len(
test_inds
), "Number of magnetometer channels in RAW does not match .mat file!"
a = raw_test._data[test_inds, :]
b = raw_mat["trial"][mat_inds, :] * 1e-15 # fT to T
assert_array_equal(a, b)
def _fil_stim(raw_test, raw_mat):
"""Test the trigger channels."""
test_inds = pick_types(
raw_test.info, meg=False, ref_meg=False, stim=True, exclude="bads"
)
test_list = list(raw_test.info["ch_names"][i] for i in test_inds)
mat_list = raw_mat["label"]
mat_inds = _match_str(test_list, mat_list)
assert len(mat_inds) == len(
test_inds
), "Number of stim channels in RAW does not match .mat file!"
a = raw_test._data[test_inds, :]
b = raw_mat["trial"][mat_inds, :] # fT to T
assert_array_equal(a, b)
def _fil_sensorpos(raw_test, raw_mat):
"""Test the sensor positions/orientations."""
test_list, test_inds = _get_channels_with_positions(raw_test.info)
grad_list = raw_mat["coil_label"]
grad_inds = _match_str(test_list, grad_list)
assert len(grad_inds) == len(
test_inds
), "Number of channels with position data in RAW does not match .mat file!"
mat_pos = raw_mat["coil_pos"][grad_inds, :]
mat_ori = raw_mat["coil_ori"][grad_inds, :]
_, sf1 = _get_pos_units(mat_pos)
test_pos = empty((len(test_inds), 3))
test_ori = empty((len(test_inds), 3))
for i, ind in enumerate(test_inds):
test_pos[i, :] = raw_test.info["chs"][ind]["loc"][0:3]
test_ori[i, :] = raw_test.info["chs"][ind]["loc"][-3:]
_, sf2 = _get_pos_units(test_pos)
assert_array_almost_equal(test_pos / sf2, mat_pos / sf1)
assert_array_almost_equal(test_ori, mat_ori)
@testing.requires_testing_data
def test_fil_complete():
"""Test FIL reader, match to known answers from .mat file."""
binname = fil_path / "sub-noise_ses-001_task-noise220622_run-001_meg.bin"
matname = fil_path / "sub-noise_ses-001_task-noise220622_run-001_fieldtrip.mat"
raw = read_raw_fil(binname)
raw.load_data(verbose=False)
tmp = scipy.io.loadmat(matname)
mat = unpack_mat(tmp)
_fil_megmag(raw, mat)
_fil_stim(raw, mat)
_fil_sensorpos(raw, mat)
@testing.requires_testing_data
def test_fil_no_positions(tmp_path):
"""Test FIL reader in cases where a position file is missing."""
test_path = tmp_path / "FIL"
shutil.copytree(fil_path, test_path)
posname = test_path / "sub-noise_ses-001_task-noise220622_run-001_positions.tsv"
binname = test_path / "sub-noise_ses-001_task-noise220622_run-001_meg.bin"
remove(posname)
with pytest.warns(RuntimeWarning, match="No sensor position.*"):
raw = read_raw_fil(binname)
chs = raw.info["chs"]
locs = array([ch["loc"][:] for ch in chs])
assert isnan(locs).all()
@testing.requires_testing_data
def test_fil_bad_channel_spec(tmp_path):
"""Test FIL reader when a bad channel is specified in channels.tsv."""
test_path = tmp_path / "FIL"
shutil.copytree(fil_path, test_path)
channame = test_path / "sub-noise_ses-001_task-noise220622_run-001_channels.tsv"
binname = test_path / "sub-noise_ses-001_task-noise220622_run-001_meg.bin"
bad_chan = "G2-OG-Y"
_set_bads_tsv(channame, bad_chan)
raw = read_raw_fil(binname)
bads = raw.info["bads"]
assert bad_chan in bads
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