def test_snirf_nirsport2():
"""Test reading SNIRF files."""
raw = read_raw_snirf(nirx_nirsport2_103, preload=True)
# Test data import
assert raw._data.shape == (92, 84)
assert_almost_equal(raw.info['sfreq'], 7.6, decimal=1)
# Test channel naming
assert raw.info['ch_names'][:4] == ['S1_D1 760', 'S1_D1 850',
'S1_D3 760', 'S1_D3 850']
assert raw.info['ch_names'][24:26] == ['S6_D4 760', 'S6_D4 850']
# Test frequency encoding
assert raw.info['chs'][0]['loc'][9] == 760
assert raw.info['chs'][1]['loc'][9] == 850
assert sum(short_channels(raw.info)) == 16
def test_snirf_nirsport2_w_positions():
"""Test reading SNIRF files with known positions."""
raw = read_raw_snirf(nirx_nirsport2_103_2,
preload=True,
optode_frame="mri")
# Test data import
assert raw._data.shape == (40, 128)
assert_almost_equal(raw.info['sfreq'], 10.2, decimal=1)
# Test channel naming
assert raw.info['ch_names'][:4] == [
'S1_D1 760', 'S1_D1 850', 'S1_D6 760', 'S1_D6 850'
]
assert raw.info['ch_names'][24:26] == ['S6_D4 760', 'S6_D4 850']
# Test frequency encoding
assert raw.info['chs'][0]['loc'][9] == 760
assert raw.info['chs'][1]['loc'][9] == 850
assert sum(short_channels(raw.info)) == 16
# Test distance between optodes matches values from
# nirsite https://github.com/mne-tools/mne-testing-data/pull/86
# figure 3
allowed_distance_error = 0.005
distances = source_detector_distances(raw.info)
assert_allclose(distances[::2][:14], [
0.0304, 0.0411, 0.008, 0.0400, 0.008, 0.0310, 0.0411, 0.008, 0.0299,
0.008, 0.0370, 0.008, 0.0404, 0.008
],
atol=allowed_distance_error)
# Test location of detectors
# The locations of detectors can be seen in the first
# figure on this page...
# https://github.com/mne-tools/mne-testing-data/pull/86
allowed_dist_error = 0.0002
locs = [ch['loc'][6:9] for ch in raw.info['chs']]
head_mri_t, _ = _get_trans('fsaverage', 'head', 'mri')
mni_locs = apply_trans(head_mri_t, locs)
assert raw.info['ch_names'][0][3:5] == 'D1'
assert_allclose(mni_locs[0], [-0.0841, -0.0464, -0.0129],
atol=allowed_dist_error)
assert raw.info['ch_names'][2][3:5] == 'D6'
assert_allclose(mni_locs[2], [-0.0841, -0.0138, 0.0248],
atol=allowed_dist_error)
assert raw.info['ch_names'][34][3:5] == 'D5'
assert_allclose(mni_locs[34], [0.0845, -0.0451, -0.0123],
atol=allowed_dist_error)
# Test location of sensors
# The locations of sensors can be seen in the second
# figure on this page...
# https://github.com/mne-tools/mne-testing-data/pull/86
allowed_dist_error = 0.0002
locs = [ch['loc'][3:6] for ch in raw.info['chs']]
head_mri_t, _ = _get_trans('fsaverage', 'head', 'mri')
mni_locs = apply_trans(head_mri_t, locs)
assert raw.info['ch_names'][0][:2] == 'S1'
assert_allclose(mni_locs[0], [-0.0848, -0.0162, -0.0163],
atol=allowed_dist_error)
assert raw.info['ch_names'][9][:2] == 'S2'
assert_allclose(mni_locs[9], [-0.0, -0.1195, 0.0142],
atol=allowed_dist_error)
assert raw.info['ch_names'][34][:2] == 'S8'
assert_allclose(mni_locs[34], [0.0828, -0.046, 0.0285],
atol=allowed_dist_error)
mon = raw.get_montage()
assert len(mon.dig) == 43
def test_nirx_15_3_short():
"""Test reading NIRX files."""
raw = read_raw_nirx(fname_nirx_15_3_short, preload=True)
# Test data import
assert raw._data.shape == (26, 220)
assert raw.info['sfreq'] == 12.5
# Test channel naming
assert raw.info['ch_names'][:4] == [
"S1_D2 760", "S1_D2 850", "S1_D9 760", "S1_D9 850"
]
assert raw.info['ch_names'][24:26] == ["S5_D13 760", "S5_D13 850"]
# Test frequency encoding
assert raw.info['chs'][0]['loc'][9] == 760
assert raw.info['chs'][1]['loc'][9] == 850
# Test info import
assert raw.info['subject_info'] == dict(birthday=(2020, 8, 18),
sex=0,
first_name="testMontage\\0A"
"TestMontage",
his_id="testMontage\\0A"
"TestMontage")
# Test distance between optodes matches values from
# https://github.com/mne-tools/mne-testing-data/pull/72
allowed_distance_error = 0.001
distances = source_detector_distances(raw.info)
assert_allclose(distances[::2], [
0.0304, 0.0078, 0.0310, 0.0086, 0.0416, 0.0072, 0.0389, 0.0075, 0.0558,
0.0562, 0.0561, 0.0565, 0.0077
],
atol=allowed_distance_error)
# Test which channels are short
# These are the ones marked as red at
# https://github.com/mne-tools/mne-testing-data/pull/72
is_short = short_channels(raw.info)
assert_array_equal(is_short[:9:2], [False, True, False, True, False])
is_short = short_channels(raw.info, threshold=0.003)
assert_array_equal(is_short[:3:2], [False, False])
is_short = short_channels(raw.info, threshold=50)
assert_array_equal(is_short[:3:2], [True, True])
# Test trigger events
assert_array_equal(raw.annotations.description, ['4.0', '2.0', '1.0'])
# Test location of detectors
# The locations of detectors can be seen in the first
# figure on this page...
# https://github.com/mne-tools/mne-testing-data/pull/72
# And have been manually copied below
allowed_dist_error = 0.0002
locs = [ch['loc'][6:9] for ch in raw.info['chs']]
head_mri_t, _ = _get_trans('fsaverage', 'head', 'mri')
mni_locs = apply_trans(head_mri_t, locs)
assert raw.info['ch_names'][0][3:5] == 'D2'
assert_allclose(mni_locs[0], [-0.0841, -0.0464, -0.0129],
atol=allowed_dist_error)
assert raw.info['ch_names'][4][3:5] == 'D1'
assert_allclose(mni_locs[4], [0.0846, -0.0142, -0.0156],
atol=allowed_dist_error)
assert raw.info['ch_names'][8][3:5] == 'D3'
assert_allclose(mni_locs[8], [0.0207, -0.1062, 0.0484],
atol=allowed_dist_error)
assert raw.info['ch_names'][12][3:5] == 'D4'
assert_allclose(mni_locs[12], [-0.0196, 0.0821, 0.0275],
atol=allowed_dist_error)
assert raw.info['ch_names'][16][3:5] == 'D5'
assert_allclose(mni_locs[16], [-0.0360, 0.0276, 0.0778],
atol=allowed_dist_error)
assert raw.info['ch_names'][19][3:5] == 'D6'
assert_allclose(mni_locs[19], [0.0388, -0.0477, 0.0932],
atol=allowed_dist_error)
assert raw.info['ch_names'][21][3:5] == 'D7'
assert_allclose(mni_locs[21], [-0.0394, -0.0483, 0.0928],
atol=allowed_dist_error)
def test_nirx_15_2_short():
"""Test reading NIRX files."""
raw = read_raw_nirx(fname_nirx_15_2_short, preload=True)
# Test data import
assert raw._data.shape == (26, 145)
assert raw.info['sfreq'] == 12.5
assert raw.info['meas_date'] == dt.datetime(2019,
8,
23,
7,
37,
4,
540000,
tzinfo=dt.timezone.utc)
# Test channel naming
assert raw.info['ch_names'][:4] == [
"S1_D1 760", "S1_D1 850", "S1_D9 760", "S1_D9 850"
]
assert raw.info['ch_names'][24:26] == ["S5_D13 760", "S5_D13 850"]
# Test frequency encoding
assert raw.info['chs'][0]['loc'][9] == 760
assert raw.info['chs'][1]['loc'][9] == 850
# Test info import
assert raw.info['subject_info'] == dict(sex=1,
first_name="MNE",
middle_name="Test",
last_name="Recording",
birthday=(2014, 8, 23),
his_id="MNE_Test_Recording")
# Test distance between optodes matches values from
# nirsite https://github.com/mne-tools/mne-testing-data/pull/51
# step 4 figure 2
allowed_distance_error = 0.0002
distances = source_detector_distances(raw.info)
assert_allclose(distances[::2], [
0.0304, 0.0078, 0.0310, 0.0086, 0.0416, 0.0072, 0.0389, 0.0075, 0.0558,
0.0562, 0.0561, 0.0565, 0.0077
],
atol=allowed_distance_error)
# Test which channels are short
# These are the ones marked as red at
# https://github.com/mne-tools/mne-testing-data/pull/51 step 4 figure 2
is_short = short_channels(raw.info)
assert_array_equal(is_short[:9:2], [False, True, False, True, False])
is_short = short_channels(raw.info, threshold=0.003)
assert_array_equal(is_short[:3:2], [False, False])
is_short = short_channels(raw.info, threshold=50)
assert_array_equal(is_short[:3:2], [True, True])
# Test trigger events
assert_array_equal(raw.annotations.description, ['3.0', '2.0', '1.0'])
# Test location of detectors
# The locations of detectors can be seen in the first
# figure on this page...
# https://github.com/mne-tools/mne-testing-data/pull/51
# And have been manually copied below
# These values were reported in mm, but according to this page...
# https://mne.tools/stable/auto_tutorials/intro/plot_40_sensor_locations.html
# 3d locations should be specified in meters, so that's what's tested below
# Detector locations are stored in the third three loc values
allowed_dist_error = 0.0002
locs = [ch['loc'][6:9] for ch in raw.info['chs']]
head_mri_t, _ = _get_trans('fsaverage', 'head', 'mri')
mni_locs = apply_trans(head_mri_t, locs)
assert raw.info['ch_names'][0][3:5] == 'D1'
assert_allclose(mni_locs[0], [-0.0841, -0.0464, -0.0129],
atol=allowed_dist_error)
assert raw.info['ch_names'][4][3:5] == 'D3'
assert_allclose(mni_locs[4], [0.0846, -0.0142, -0.0156],
atol=allowed_dist_error)
assert raw.info['ch_names'][8][3:5] == 'D2'
assert_allclose(mni_locs[8], [0.0207, -0.1062, 0.0484],
atol=allowed_dist_error)
assert raw.info['ch_names'][12][3:5] == 'D4'
assert_allclose(mni_locs[12], [-0.0196, 0.0821, 0.0275],
atol=allowed_dist_error)
assert raw.info['ch_names'][16][3:5] == 'D5'
assert_allclose(mni_locs[16], [-0.0360, 0.0276, 0.0778],
atol=allowed_dist_error)
assert raw.info['ch_names'][19][3:5] == 'D6'
assert_allclose(mni_locs[19], [0.0352, 0.0283, 0.0780],
atol=allowed_dist_error)
assert raw.info['ch_names'][21][3:5] == 'D7'
assert_allclose(mni_locs[21], [0.0388, -0.0477, 0.0932],
atol=allowed_dist_error)
