def test_handle_info_reading():
"""Test reading information from a BIDS sidecar.json file."""
bids_root = _TempDir()
# read in USA dataset, so it should find 50 Hz
raw = _read_raw_fif(raw_fname)
# write copy of raw with line freq of 60
# bids basename and fname
bids_path = BIDSPath(subject='01',
session='01',
task='audiovisual',
run='01',
root=bids_root)
suffix = "meg"
bids_fname = bids_path.copy().update(suffix=suffix, extension='.fif')
write_raw_bids(raw, bids_path, overwrite=True)
# find sidecar JSON fname
bids_fname.update(datatype=suffix)
sidecar_fname = _find_matching_sidecar(bids_fname,
suffix=suffix,
extension='.json')
# assert that we get the same line frequency set
raw = read_raw_bids(bids_path=bids_path)
assert raw.info['line_freq'] == 60
# 2. if line frequency is not set in raw file, then ValueError
raw.info['line_freq'] = None
with pytest.raises(ValueError, match="PowerLineFrequency .* required"):
write_raw_bids(raw, bids_path, overwrite=True)
# make a copy of the sidecar in "derivatives/"
# to check that we make sure we always get the right sidecar
# in addition, it should not break the sidecar reading
# in `read_raw_bids`
deriv_dir = op.join(bids_root, "derivatives")
sidecar_copy = op.join(deriv_dir, op.basename(sidecar_fname))
os.mkdir(deriv_dir)
with open(sidecar_fname, "r", encoding='utf-8') as fin:
sidecar_json = json.load(fin)
sidecar_json["PowerLineFrequency"] = 45
_write_json(sidecar_copy, sidecar_json)
raw = read_raw_bids(bids_path=bids_path)
assert raw.info['line_freq'] == 60
# 3. assert that we get an error when sidecar json doesn't match
_update_sidecar(sidecar_fname, "PowerLineFrequency", 55)
with pytest.raises(ValueError, match="Line frequency in sidecar json"):
raw = read_raw_bids(bids_path=bids_path)
assert raw.info['line_freq'] == 55
def test_handle_ieeg_coords_reading(bids_path):
"""Test reading iEEG coordinates from BIDS files."""
bids_root = _TempDir()
data_path = op.join(testing.data_path(), 'EDF')
raw_fname = op.join(data_path, 'test_reduced.edf')
bids_fname = bids_path.copy().update(datatype='ieeg',
suffix='ieeg',
extension='.edf',
root=bids_root)
raw = _read_raw_edf(raw_fname)
# ensure we are writing 'ecog'/'ieeg' data
raw.set_channel_types({ch: 'ecog' for ch in raw.ch_names})
# coordinate frames in mne-python should all map correctly
# set a `random` montage
ch_names = raw.ch_names
elec_locs = np.random.random((len(ch_names), 3)).astype(float)
ch_pos = dict(zip(ch_names, elec_locs))
coordinate_frames = ['mri', 'ras']
for coord_frame in coordinate_frames:
# XXX: mne-bids doesn't support multiple electrodes.tsv files
sh.rmtree(bids_root)
montage = mne.channels.make_dig_montage(ch_pos=ch_pos,
coord_frame=coord_frame)
raw.set_montage(montage)
write_raw_bids(raw, bids_fname, overwrite=True, verbose=False)
# read in raw file w/ updated coordinate frame
# and make sure all digpoints are correct coordinate frames
raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
coord_frame_int = MNE_STR_TO_FRAME[coord_frame]
for digpoint in raw_test.info['dig']:
assert digpoint['coord_frame'] == coord_frame_int
# start w/ new bids root
sh.rmtree(bids_root)
write_raw_bids(raw, bids_fname, overwrite=True, verbose=False)
# obtain the sensor positions and assert ch_coords are same
raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
orig_locs = raw.info['dig'][1]
test_locs = raw_test.info['dig'][1]
assert orig_locs == test_locs
assert not object_diff(raw.info['chs'], raw_test.info['chs'])
# read in the data and assert montage is the same
# regardless of 'm', 'cm', 'mm', or 'pixel'
scalings = {'m': 1, 'cm': 100, 'mm': 1000}
bids_fname.update(root=bids_root)
coordsystem_fname = _find_matching_sidecar(bids_fname,
suffix='coordsystem',
extension='.json')
electrodes_fname = _find_matching_sidecar(bids_fname,
suffix='electrodes',
extension='.tsv')
orig_electrodes_dict = _from_tsv(electrodes_fname,
[str, float, float, float, str])
# not BIDS specified should not be read
coord_unit = 'km'
scaling = 0.001
_update_sidecar(coordsystem_fname, 'iEEGCoordinateUnits', coord_unit)
electrodes_dict = _from_tsv(electrodes_fname,
[str, float, float, float, str])
for axis in ['x', 'y', 'z']:
electrodes_dict[axis] = \
np.multiply(orig_electrodes_dict[axis], scaling)
_to_tsv(electrodes_dict, electrodes_fname)
with pytest.warns(RuntimeWarning,
match='Coordinate unit is not '
'an accepted BIDS unit'):
raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
# correct BIDS units should scale to meters properly
for coord_unit, scaling in scalings.items():
# update coordinate SI units
_update_sidecar(coordsystem_fname, 'iEEGCoordinateUnits', coord_unit)
electrodes_dict = _from_tsv(electrodes_fname,
[str, float, float, float, str])
for axis in ['x', 'y', 'z']:
electrodes_dict[axis] = \
np.multiply(orig_electrodes_dict[axis], scaling)
_to_tsv(electrodes_dict, electrodes_fname)
# read in raw file w/ updated montage
raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
# obtain the sensor positions and make sure they're the same
assert_dig_allclose(raw.info, raw_test.info)
# XXX: Improve by changing names to 'unknown' coordframe (needs mne PR)
# check that coordinate systems other coordinate systems should be named
# in the file and not the CoordinateSystem, which is reserved for keywords
coordinate_frames = ['lia', 'ria', 'lip', 'rip', 'las']
for coord_frame in coordinate_frames:
# update coordinate units
_update_sidecar(coordsystem_fname, 'iEEGCoordinateSystem', coord_frame)
# read in raw file w/ updated coordinate frame
# and make sure all digpoints are MRI coordinate frame
with pytest.warns(RuntimeWarning,
match="iEEG Coordinate frame is "
"not accepted BIDS keyword"):
raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
assert raw_test.info['dig'] is None
# ACPC should be read in as RAS for iEEG
_update_sidecar(coordsystem_fname, 'iEEGCoordinateSystem', 'acpc')
raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
coord_frame_int = MNE_STR_TO_FRAME['ras']
for digpoint in raw_test.info['dig']:
assert digpoint['coord_frame'] == coord_frame_int
# if we delete the coordsystem.json file, an error will be raised
os.remove(coordsystem_fname)
with pytest.raises(RuntimeError,
match='BIDS mandates that '
'the coordsystem.json'):
raw = read_raw_bids(bids_path=bids_fname, verbose=False)
# test error message if electrodes don't match
bids_path.update(root=bids_root)
write_raw_bids(raw, bids_path, overwrite=True)
electrodes_dict = _from_tsv(electrodes_fname)
# pop off 5 channels
for key in electrodes_dict.keys():
for i in range(5):
electrodes_dict[key].pop()
_to_tsv(electrodes_dict, electrodes_fname)
with pytest.raises(RuntimeError, match='Channels do not correspond'):
raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
# make sure montage is set if there are coordinates w/ 'n/a'
raw.info['bads'] = []
write_raw_bids(raw, bids_path, overwrite=True, verbose=False)
electrodes_dict = _from_tsv(electrodes_fname)
for axis in ['x', 'y', 'z']:
electrodes_dict[axis][0] = 'n/a'
electrodes_dict[axis][3] = 'n/a'
_to_tsv(electrodes_dict, electrodes_fname)
# test if montage is correctly set via mne-bids
# electrode coordinates should be nan
# when coordinate is 'n/a'
nan_chs = [electrodes_dict['name'][i] for i in [0, 3]]
with pytest.warns(RuntimeWarning,
match='There are channels '
'without locations'):
raw = read_raw_bids(bids_path=bids_fname, verbose=False)
for idx, ch in enumerate(raw.info['chs']):
if ch['ch_name'] in nan_chs:
assert all(np.isnan(ch['loc'][:3]))
else:
assert not any(np.isnan(ch['loc'][:3]))
assert ch['ch_name'] not in raw.info['bads']
def test_handle_eeg_coords_reading():
"""Test reading iEEG coordinates from BIDS files."""
bids_root = _TempDir()
bids_path = BIDSPath(subject=subject_id,
session=session_id,
run=run,
acquisition=acq,
task=task,
root=bids_root)
data_path = op.join(testing.data_path(), 'EDF')
raw_fname = op.join(data_path, 'test_reduced.edf')
raw = _read_raw_edf(raw_fname)
# ensure we are writing 'eeg' data
raw.set_channel_types({ch: 'eeg' for ch in raw.ch_names})
# set a `random` montage
ch_names = raw.ch_names
elec_locs = np.random.random((len(ch_names), 3)).astype(float)
ch_pos = dict(zip(ch_names, elec_locs))
# # create montage in 'unknown' coordinate frame
# # and assert coordsystem/electrodes sidecar tsv don't exist
montage = mne.channels.make_dig_montage(ch_pos=ch_pos,
coord_frame="unknown")
raw.set_montage(montage)
with pytest.warns(RuntimeWarning, match="Skipping EEG electrodes.tsv"):
write_raw_bids(raw, bids_path, overwrite=True)
bids_path.update(root=bids_root)
coordsystem_fname = _find_matching_sidecar(bids_path,
suffix='coordsystem',
extension='.json',
on_error='warn')
electrodes_fname = _find_matching_sidecar(bids_path,
suffix='electrodes',
extension='.tsv',
on_error='warn')
assert coordsystem_fname is None
assert electrodes_fname is None
# create montage in head frame and set should result in
# warning if landmarks not set
montage = mne.channels.make_dig_montage(ch_pos=ch_pos, coord_frame="head")
raw.set_montage(montage)
with pytest.warns(RuntimeWarning,
match='Setting montage not possible '
'if anatomical landmarks'):
write_raw_bids(raw, bids_path, overwrite=True)
montage = mne.channels.make_dig_montage(ch_pos=ch_pos,
coord_frame="head",
nasion=[1, 0, 0],
lpa=[0, 1, 0],
rpa=[0, 0, 1])
raw.set_montage(montage)
write_raw_bids(raw, bids_path, overwrite=True)
# obtain the sensor positions and assert ch_coords are same
raw_test = read_raw_bids(bids_path, verbose=True)
assert not object_diff(raw.info['chs'], raw_test.info['chs'])
# modify coordinate frame to not-captrak
coordsystem_fname = _find_matching_sidecar(bids_path,
suffix='coordsystem',
extension='.json')
_update_sidecar(coordsystem_fname, 'EEGCoordinateSystem', 'besa')
with pytest.warns(RuntimeWarning,
match='EEG Coordinate frame is not '
'accepted BIDS keyword'):
raw_test = read_raw_bids(bids_path)
assert raw_test.info['dig'] is None
def test_handle_info_reading(tmpdir):
"""Test reading information from a BIDS sidecar JSON file."""
# read in USA dataset, so it should find 50 Hz
raw = _read_raw_fif(raw_fname)
# write copy of raw with line freq of 60
# bids basename and fname
bids_path = BIDSPath(subject='01',
session='01',
task='audiovisual',
run='01',
root=tmpdir)
suffix = "meg"
bids_fname = bids_path.copy().update(suffix=suffix, extension='.fif')
write_raw_bids(raw, bids_path, overwrite=True)
# find sidecar JSON fname
bids_fname.update(datatype=suffix)
sidecar_fname = _find_matching_sidecar(bids_fname,
suffix=suffix,
extension='.json')
# assert that we get the same line frequency set
raw = read_raw_bids(bids_path=bids_path)
assert raw.info['line_freq'] == 60
# setting line_freq to None should produce 'n/a' in the JSON sidecar
raw.info['line_freq'] = None
write_raw_bids(raw, bids_path, overwrite=True)
raw = read_raw_bids(bids_path=bids_path)
assert raw.info['line_freq'] is None
with open(sidecar_fname, 'r', encoding='utf-8') as fin:
sidecar_json = json.load(fin)
assert sidecar_json["PowerLineFrequency"] == 'n/a'
# 2. if line frequency is not set in raw file, then ValueError
del raw.info['line_freq']
with pytest.raises(ValueError, match="PowerLineFrequency .* required"):
write_raw_bids(raw, bids_path, overwrite=True)
# check whether there are "Extra points" in raw.info['dig'] if
# DigitizedHeadPoints is set to True and not otherwise
n_dig_points = 0
for dig_point in raw.info['dig']:
if dig_point['kind'] == FIFF.FIFFV_POINT_EXTRA:
n_dig_points += 1
if sidecar_json['DigitizedHeadPoints']:
assert n_dig_points > 0
else:
assert n_dig_points == 0
# check whether any of NAS/LPA/RPA are present in raw.info['dig']
# DigitizedLandmark is set to True, and False otherwise
landmark_present = False
for dig_point in raw.info['dig']:
if dig_point['kind'] in [
FIFF.FIFFV_POINT_LPA, FIFF.FIFFV_POINT_RPA,
FIFF.FIFFV_POINT_NASION
]:
landmark_present = True
break
if landmark_present:
assert sidecar_json['DigitizedLandmarks'] is True
else:
assert sidecar_json['DigitizedLandmarks'] is False
# make a copy of the sidecar in "derivatives/"
# to check that we make sure we always get the right sidecar
# in addition, it should not break the sidecar reading
# in `read_raw_bids`
raw.info['line_freq'] = 60
write_raw_bids(raw, bids_path, overwrite=True)
deriv_dir = tmpdir.mkdir("derivatives")
sidecar_copy = deriv_dir / op.basename(sidecar_fname)
with open(sidecar_fname, "r", encoding='utf-8') as fin:
sidecar_json = json.load(fin)
sidecar_json["PowerLineFrequency"] = 45
_write_json(sidecar_copy, sidecar_json)
raw = read_raw_bids(bids_path=bids_path)
assert raw.info['line_freq'] == 60
# 3. assert that we get an error when sidecar json doesn't match
_update_sidecar(sidecar_fname, "PowerLineFrequency", 55)
with pytest.warns(RuntimeWarning, match="Defaulting to .* sidecar JSON"):
raw = read_raw_bids(bids_path=bids_path)
assert raw.info['line_freq'] == 55
