def test_snirf_nonstandard(tmp_path):
"""Test custom tags."""
from mne.externals.pymatreader.utils import _import_h5py
h5py = _import_h5py()
shutil.copy(sfnirs_homer_103_wShort, str(tmp_path) + "/mod.snirf")
fname = str(tmp_path) + "/mod.snirf"
# Manually mark up the file to match MNE-NIRS custom tags
with h5py.File(fname, "r+") as f:
f.create_dataset("nirs/metaDataTags/middleName",
data=['X'.encode('UTF-8')])
f.create_dataset("nirs/metaDataTags/lastName",
data=['Y'.encode('UTF-8')])
f.create_dataset("nirs/metaDataTags/sex", data=['1'.encode('UTF-8')])
raw = read_raw_snirf(fname, preload=True)
assert raw.info["subject_info"]["middle_name"] == 'X'
assert raw.info["subject_info"]["last_name"] == 'Y'
assert raw.info["subject_info"]["sex"] == 1
with h5py.File(fname, "r+") as f:
del f['nirs/metaDataTags/sex']
f.create_dataset("nirs/metaDataTags/sex", data=['2'.encode('UTF-8')])
raw = read_raw_snirf(fname, preload=True)
assert raw.info["subject_info"]["sex"] == 2
with h5py.File(fname, "r+") as f:
del f['nirs/metaDataTags/sex']
f.create_dataset("nirs/metaDataTags/sex", data=['0'.encode('UTF-8')])
raw = read_raw_snirf(fname, preload=True)
assert raw.info["subject_info"]["sex"] == 0
with h5py.File(fname, "r+") as f:
f.create_dataset("nirs/metaDataTags/MNE_coordFrame", data=[1])
def test_snirf_coordframe():
"""Test reading SNIRF files."""
raw = read_raw_snirf(nirx_nirsport2_103, optode_frame="head").\
info['chs'][3]['coord_frame']
assert raw == FIFF.FIFFV_COORD_HEAD
raw = read_raw_snirf(nirx_nirsport2_103, optode_frame="mri").\
info['chs'][3]['coord_frame']
assert raw == FIFF.FIFFV_COORD_HEAD
raw = read_raw_snirf(nirx_nirsport2_103, optode_frame="unknown").\
info['chs'][3]['coord_frame']
assert raw == FIFF.FIFFV_COORD_UNKNOWN
def test_snirf_write(fname, tmpdir):
"""Test reading NIRX files."""
raw_orig = read_raw_nirx(fname, preload=True)
write_raw_snirf(raw_orig, tmpdir.join('test_raw.snirf'))
raw = read_raw_snirf(tmpdir.join('test_raw.snirf'))
# Check annotations are the same
assert_allclose(raw.annotations.onset, raw_orig.annotations.onset)
assert_allclose([float(d) for d in raw.annotations.description],
[float(d) for d in raw_orig.annotations.description])
assert_allclose(raw.annotations.duration, raw_orig.annotations.duration)
# Check data is the same
assert_allclose(raw.get_data(), raw_orig.get_data())
assert abs(raw_orig.info["meas_date"] - raw.info["meas_date"]) < \
datetime.timedelta(seconds=1)
# Check info object is the same
obj_diff = object_diff(raw.info, raw_orig.info)
diffs = ''
for line in obj_diff.splitlines():
if ('logno' not in line) and ('scanno' not in line) and\
('datetime mismatch' not in line):
# logno and scanno are not used in processing
diffs += f'\n{line}'
assert diffs == ''
def test_snirf_gowerlabs():
"""Test reading SNIRF files."""
raw = read_raw_snirf(lumo110, preload=True)
assert raw._data.shape == (216, 274)
assert raw.info['dig'][0]['coord_frame'] == FIFF.FIFFV_COORD_HEAD
assert len(raw.ch_names) == 216
assert_allclose(raw.info['sfreq'], 10.0)
# we don't force them to be sorted according to a naive split
# (but we do force them to be interleaved, which is tested by beer_lambert
# above)
assert raw.ch_names != sorted(raw.ch_names)
# ... and this file does have a nice logical ordering already
assert raw.ch_names == sorted(
raw.ch_names, # use a key which is (source int, detector int)
key=lambda name: (int(name.split()[0].split('_')[0][1:]),
int(name.split()[0].split('_')[1][1:])))
prefixes = [name.split()[0] for name in raw.ch_names]
# TODO: This is actually not the order on disk -- we reorder to ravel as
# S-D then freq, but gowerlabs order is freq then S-D. So hopefully soon
# we can change these lines to check that the first half of prefixes
# matches the second half of prefixes, rather than every-other matching the
# other every-other
assert prefixes[::2] == prefixes[1::2]
prefixes = prefixes[::2]
assert prefixes == ['S1_D1', 'S1_D2', 'S1_D3', 'S1_D4', 'S1_D5', 'S1_D6', 'S1_D7', 'S1_D8', 'S1_D9', 'S1_D10', 'S1_D11', 'S1_D12', 'S2_D1', 'S2_D2', 'S2_D3', 'S2_D4', 'S2_D5', 'S2_D6', 'S2_D7', 'S2_D8', 'S2_D9', 'S2_D10', 'S2_D11', 'S2_D12', 'S3_D1', 'S3_D2', 'S3_D3', 'S3_D4', 'S3_D5', 'S3_D6', 'S3_D7', 'S3_D8', 'S3_D9', 'S3_D10', 'S3_D11', 'S3_D12', 'S4_D1', 'S4_D2', 'S4_D3', 'S4_D4', 'S4_D5', 'S4_D6', 'S4_D7', 'S4_D8', 'S4_D9', 'S4_D10', 'S4_D11', 'S4_D12', 'S5_D1', 'S5_D2', 'S5_D3', 'S5_D4', 'S5_D5', 'S5_D6', 'S5_D7', 'S5_D8', 'S5_D9', 'S5_D10', 'S5_D11', 'S5_D12', 'S6_D1', 'S6_D2', 'S6_D3', 'S6_D4', 'S6_D5', 'S6_D6', 'S6_D7', 'S6_D8', 'S6_D9', 'S6_D10', 'S6_D11', 'S6_D12', 'S7_D1', 'S7_D2', 'S7_D3', 'S7_D4', 'S7_D5', 'S7_D6', 'S7_D7', 'S7_D8', 'S7_D9', 'S7_D10', 'S7_D11', 'S7_D12', 'S8_D1', 'S8_D2', 'S8_D3', 'S8_D4', 'S8_D5', 'S8_D6', 'S8_D7', 'S8_D8', 'S8_D9', 'S8_D10', 'S8_D11', 'S8_D12', 'S9_D1', 'S9_D2', 'S9_D3', 'S9_D4', 'S9_D5', 'S9_D6', 'S9_D7', 'S9_D8', 'S9_D9', 'S9_D10', 'S9_D11', 'S9_D12'] # noqa: E501
def test_snirf_nobday(fname, tmpdir):
"""Ensure writing works when no birthday is present."""
raw_orig = read_raw_nirx(fname, preload=True)
raw_orig.info['subject_info'].pop('birthday', None)
test_file = tmpdir.join('test_raw.snirf')
write_raw_snirf(raw_orig, test_file)
raw = read_raw_snirf(test_file)
assert_allclose(raw.get_data(), raw_orig.get_data())
def test_snirf_gowerlabs():
"""Test reading SNIRF files."""
raw = read_raw_snirf(lumo110, preload=True)
assert raw._data.shape == (216, 274)
assert raw.info['dig'][0]['coord_frame'] == FIFF.FIFFV_COORD_HEAD
assert len(raw.ch_names) == 216
assert_allclose(raw.info['sfreq'], 10.0)
def test_basic_reading_and_min_process(fname):
"""Test reading SNIRF files and minimum typical processing."""
raw = read_raw_snirf(fname, preload=True)
# SNIRF data can contain several types, so only apply appropriate functions
if 'fnirs_cw_amplitude' in raw:
raw = optical_density(raw)
if 'fnirs_od' in raw:
raw = beer_lambert_law(raw, ppf=6)
assert 'hbo' in raw
def test_nirsport_v2_matches_snirf(fname_nirx, fname_snirf):
"""Test NIRSport2 raw files return same data as snirf."""
raw = read_raw_nirx(fname_nirx, preload=True)
raw_snirf = read_raw_snirf(fname_snirf, preload=True)
assert_allclose(raw._data, raw_snirf._data)
# Check the timing of annotations match (naming is different)
assert_allclose(raw.annotations.onset, raw_snirf.annotations.onset)
assert_array_equal(raw.ch_names, raw_snirf.ch_names)
def test_snirf_fieldtrip_od():
"""Test reading FieldTrip SNIRF files with optical density data."""
raw = read_raw_snirf(ft_od, preload=True)
# Test data import
assert raw._data.shape == (72, 500)
assert raw.copy().pick('fnirs')._data.shape == (72, 500)
assert raw.copy().pick('fnirs_od')._data.shape == (72, 500)
with pytest.raises(ValueError, match='not be interpreted as channel'):
raw.copy().pick('hbo')
with pytest.raises(ValueError, match='not be interpreted as channel'):
raw.copy().pick('hbr')
assert_allclose(raw.info['sfreq'], 50)
def test_snirf_basic():
"""Test reading SNIRF files."""
raw = read_raw_snirf(sfnirs_homer_103_wShort, preload=True)
# Test data import
assert raw._data.shape == (26, 145)
assert raw.info['sfreq'] == 12.5
# 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 source locations
assert_allclose([-8.6765 * 1e-2, 0.0049 * 1e-2, -2.6167 * 1e-2],
raw.info['chs'][0]['loc'][3:6],
rtol=0.02)
assert_allclose([7.9579 * 1e-2, -2.7571 * 1e-2, -2.2631 * 1e-2],
raw.info['chs'][4]['loc'][3:6],
rtol=0.02)
assert_allclose([-2.1387 * 1e-2, -8.8874 * 1e-2, 3.8393 * 1e-2],
raw.info['chs'][8]['loc'][3:6],
rtol=0.02)
assert_allclose([1.8602 * 1e-2, 9.7164 * 1e-2, 1.7539 * 1e-2],
raw.info['chs'][12]['loc'][3:6],
rtol=0.02)
assert_allclose([-0.1108 * 1e-2, 0.7066 * 1e-2, 8.9883 * 1e-2],
raw.info['chs'][16]['loc'][3:6],
rtol=0.02)
# Test detector locations
assert_allclose([-8.0409 * 1e-2, -2.9677 * 1e-2, -2.5415 * 1e-2],
raw.info['chs'][0]['loc'][6:9],
rtol=0.02)
assert_allclose([-8.7329 * 1e-2, 0.7577 * 1e-2, -2.7980 * 1e-2],
raw.info['chs'][3]['loc'][6:9],
rtol=0.02)
assert_allclose([9.2027 * 1e-2, 0.0161 * 1e-2, -2.8909 * 1e-2],
raw.info['chs'][5]['loc'][6:9],
rtol=0.02)
assert_allclose([7.7548 * 1e-2, -3.5901 * 1e-2, -2.3179 * 1e-2],
raw.info['chs'][7]['loc'][6:9],
rtol=0.02)
assert 'fnirs_cw_amplitude' in raw
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_kernel_hb():
"""Test reading Kernel SNIRF files with haemoglobin data."""
raw = read_raw_snirf(kernel_hb, preload=True)
# Test data import
assert raw._data.shape == (180 * 2, 14)
assert raw.copy().pick('hbo')._data.shape == (180, 14)
assert raw.copy().pick('hbr')._data.shape == (180, 14)
assert_allclose(raw.info['sfreq'], 8.257638)
bad_nans = np.isnan(raw.get_data()).any(axis=1)
assert np.sum(bad_nans) == 20
assert len(raw.annotations.description) == 2
assert raw.annotations.onset[0] == 0.036939
assert raw.annotations.onset[1] == 0.874633
assert raw.annotations.description[0] == "StartTrial"
assert raw.annotations.description[1] == "StartIti"
def test_snirf_gowerlabs():
"""Test reading SNIRF files."""
raw = read_raw_snirf(lumo110, preload=True)
assert raw._data.shape == (216, 274)
assert raw.info['dig'][0]['coord_frame'] == FIFF.FIFFV_COORD_HEAD
assert len(raw.ch_names) == 216
assert_allclose(raw.info['sfreq'], 10.0)
# we don't force them to be sorted according to a naive split
assert raw.ch_names != sorted(raw.ch_names)
# ... but this file does have a nice logical ordering already
print(raw.ch_names)
assert raw.ch_names == sorted(
raw.ch_names,
# use a key which is (src triplet, freq, src, freq, det)
key=lambda name: (
(int(name.split()[0].split('_')[0][1:]) - 1) // 3,
int(name.split()[1]), int(name.split()[0].split('_')[0][1:]),
int(name.split()[0].split('_')[1][1:])))
def test_snirf_write(fname, tmpdir):
"""Test reading NIRX files."""
raw_orig = read_raw_nirx(fname, preload=True)
test_file = tmpdir.join('test_raw.snirf')
write_raw_snirf(raw_orig, test_file)
raw = read_raw_snirf(test_file)
result = validateSnirf(str(test_file))
if result.is_valid():
result.display()
assert result.is_valid()
# Check annotations are the same
assert_allclose(raw.annotations.onset, raw_orig.annotations.onset)
assert_allclose([float(d) for d in raw.annotations.description],
[float(d) for d in raw_orig.annotations.description])
assert_allclose(raw.annotations.duration, raw_orig.annotations.duration)
# Check data is the same
assert_allclose(raw.get_data(), raw_orig.get_data())
assert abs(raw_orig.info['meas_date'] - raw.info['meas_date']) < \
datetime.timedelta(seconds=1)
# Check info object is the same
obj_diff = object_diff(raw.info, raw_orig.info)
diffs = ''
for line in obj_diff.splitlines():
if ('logno' not in line) and \
('scanno' not in line) and \
('his_id' not in line) and\
('datetime mismatch' not in line):
# logno and scanno are not used in processing
diffs += f'\n{line}'
assert diffs == ''
_verify_snirf_required_fields(test_file)
_verify_snirf_version_str(test_file)
def test_snirf_against_nirx():
"""Test against file snirf was created from."""
raw = read_raw_snirf(sfnirs_homer_103_wShort, preload=True)
raw_orig = read_raw_nirx(sfnirs_homer_103_wShort_original, preload=True)
# Check annotations are the same
assert_allclose(raw.annotations.onset, raw_orig.annotations.onset)
assert_allclose([float(d) for d in raw.annotations.description],
[float(d) for d in raw_orig.annotations.description])
assert_allclose(raw.annotations.duration, raw_orig.annotations.duration)
# Check names are the same
assert raw.info['ch_names'] == raw_orig.info['ch_names']
# Check frequencies are the same
num_chans = len(raw.ch_names)
new_chs = raw.info['chs']
ori_chs = raw_orig.info['chs']
assert_allclose([new_chs[idx]['loc'][9] for idx in range(num_chans)],
[ori_chs[idx]['loc'][9] for idx in range(num_chans)])
# Check data is the same
assert_allclose(raw.get_data(), raw_orig.get_data())
def test_annotation_description_from_stim_groups():
"""Test annotation descriptions parsed from stim group names."""
raw = read_raw_snirf(nirx_nirsport2_103_2, preload=True)
expected_descriptions = ['1', '2', '6']
assert_equal(expected_descriptions, raw.annotations.description)
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
# %%
# Write data as SNIRF
# -------------------
#
# Now we can write this data back to disk in the SNIRF format.
write_raw_snirf(raw_intensity, 'test_raw.snirf')
# %%
# Read back SNIRF file
# --------------------
#
# Next we can read back the snirf file.
snirf_intensity = read_raw_snirf('test_raw.snirf')
# %%
# Compare files
# -------------
#
# Finally we can compare the data of the original to the SNIRF format and
# ensure that the values are the same.
assert_allclose(raw_intensity.get_data(), snirf_intensity.get_data())
snirf_intensity.plot(n_channels=30, duration=300, show_scrollbars=False)
# %%
def nirx_snirf(request):
"""Return a (raw_nirx, raw_snirf) matched pair."""
pytest.importorskip('h5py')
return (read_raw_nirx(request.param[0], preload=True),
read_raw_snirf(request.param[1], preload=True))