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# Author: Luke Bloy <bloyl@chop.edu>
#
# License: BSD (3-clause)
import os.path as op
import numpy as np
from numpy.testing import assert_allclose, assert_equal
import pytest
from mne.utils import run_tests_if_main, _TempDir
from mne.io import read_raw_artemis123
from mne.io.tests.test_raw import _test_raw_reader
from mne.datasets import testing
from mne.io.artemis123.utils import _generate_mne_locs_file, _load_mne_locs
from mne import pick_types
from mne.transforms import rot_to_quat, _angle_between_quats
artemis123_dir = op.join(testing.data_path(download=False), 'ARTEMIS123')
short_HPI_dip_fname = op.join(artemis123_dir,
'Artemis_Data_2017-04-04-15h-44m-' +
'22s_Motion_Translation-z.bin')
dig_fname = op.join(artemis123_dir, 'Phantom_040417_dig.pos')
short_hpi_1kz_fname = op.join(artemis123_dir, 'Artemis_Data_2017-04-14-10h' +
'-38m-59s_Phantom_1k_HPI_1s.bin')
def _assert_trans(actual, desired, dist_tol=0.003, angle_tol=5.):
trans_est = actual[0:3, 3]
quat_est = rot_to_quat(actual[0:3, 0:3])
trans = desired[0:3, 3]
quat = rot_to_quat(desired[0:3, 0:3])
angle = 180 * _angle_between_quats(quat_est, quat) / np.pi
dist = np.sqrt(np.sum((trans - trans_est) ** 2))
assert dist <= dist_tol, '%0.3f > %0.3f mm' % (1000 * dist,
1000 * dist_tol)
assert angle <= angle_tol, '%0.3f > %0.3f deg' % (angle, angle_tol)
@testing.requires_testing_data
def test_data():
"""Test reading raw Artemis123 files."""
_test_raw_reader(read_raw_artemis123, input_fname=short_hpi_1kz_fname,
pos_fname=dig_fname, verbose='error')
# test a random selected point
raw = read_raw_artemis123(short_hpi_1kz_fname, preload=True,
add_head_trans=False)
meg_picks = pick_types(raw.info, meg=True, eeg=False)
# checked against matlab reader.
assert_allclose(raw[meg_picks[12]][0][0][123], 1.08239606023e-11)
dev_head_t_1 = np.array([[9.713e-01, 2.340e-01, -4.164e-02, 1.302e-04],
[-2.371e-01, 9.664e-01, -9.890e-02, 1.977e-03],
[1.710e-02, 1.059e-01, 9.942e-01, -8.159e-03],
[0.0, 0.0, 0.0, 1.0]])
dev_head_t_2 = np.array([[9.890e-01, 1.475e-01, -8.090e-03, 4.997e-04],
[-1.476e-01, 9.846e-01, -9.389e-02, 1.962e-03],
[-5.888e-03, 9.406e-02, 9.955e-01, -1.610e-02],
[0.0, 0.0, 0.0, 1.0]])
# test with head loc no digitization
raw = read_raw_artemis123(short_HPI_dip_fname, add_head_trans=True)
_assert_trans(raw.info['dev_head_t']['trans'], dev_head_t_1)
assert_equal(raw.info['sfreq'], 5000.0)
# test with head loc and digitization
with pytest.warns(RuntimeWarning, match='Large difference'):
raw = read_raw_artemis123(short_HPI_dip_fname, add_head_trans=True,
pos_fname=dig_fname)
_assert_trans(raw.info['dev_head_t']['trans'], dev_head_t_1)
# test 1kz hpi head loc (different freq)
raw = read_raw_artemis123(short_hpi_1kz_fname, add_head_trans=True)
_assert_trans(raw.info['dev_head_t']['trans'], dev_head_t_2)
assert_equal(raw.info['sfreq'], 1000.0)
def test_utils():
"""Test artemis123 utils."""
# make a tempfile
tmp_dir = _TempDir()
tmp_fname = op.join(tmp_dir, 'test_gen_mne_locs.csv')
_generate_mne_locs_file(tmp_fname)
installed_locs = _load_mne_locs()
generated_locs = _load_mne_locs(tmp_fname)
assert_equal(set(installed_locs.keys()), set(generated_locs.keys()))
for key in installed_locs.keys():
assert_allclose(installed_locs[key], generated_locs[key], atol=1e-7)
run_tests_if_main()
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