def test_ch_loc():
"""Test raw kit loc."""
raw_py = read_raw_kit(sqd_path, mrk_path, elp_txt_path, hsp_txt_path,
stim='<')
raw_bin = read_raw_fif(op.join(data_dir, 'test_bin_raw.fif'))
ch_py = np.array([ch['loc'] for ch in
raw_py._raw_extras[0]['channels'][:160]])
# ch locs stored as m, not mm
ch_py[:, :3] *= 1e3
ch_sns = read_sns(op.join(data_dir, 'sns.txt'))
assert_array_almost_equal(ch_py, ch_sns, 2)
assert_array_almost_equal(raw_py.info['dev_head_t']['trans'],
raw_bin.info['dev_head_t']['trans'], 4)
for py_ch, bin_ch in zip(raw_py.info['chs'], raw_bin.info['chs']):
if bin_ch['ch_name'].startswith('MEG'):
# the stored ch locs have more precision than the sns.txt
assert_array_almost_equal(py_ch['loc'], bin_ch['loc'], decimal=2)
# test when more than one marker file provided
mrks = [mrk_path, mrk2_path, mrk3_path]
read_raw_kit(sqd_path, mrks, elp_txt_path, hsp_txt_path, preload=False)
# this dataset does not have the equivalent set of points :(
raw_bin.info['dig'] = raw_bin.info['dig'][:8]
raw_py.info['dig'] = raw_py.info['dig'][:8]
assert_dig_allclose(raw_py.info, raw_bin.info)
def test_ch_loc():
"""Test raw kit loc."""
raw_py = read_raw_kit(sqd_path, mrk_path, elp_txt_path, hsp_txt_path,
stim='<')
raw_bin = read_raw_fif(op.join(data_dir, 'test_bin_raw.fif'))
ch_py = np.array([ch['loc'] for ch in
raw_py._raw_extras[0]['channels'][:160]])
# ch locs stored as m, not mm
ch_py[:, :3] *= 1e3
ch_sns = read_sns(op.join(data_dir, 'sns.txt'))
assert_array_almost_equal(ch_py, ch_sns, 2)
assert_array_almost_equal(raw_py.info['dev_head_t']['trans'],
raw_bin.info['dev_head_t']['trans'], 4)
for py_ch, bin_ch in zip(raw_py.info['chs'], raw_bin.info['chs']):
if bin_ch['ch_name'].startswith('MEG'):
# the stored ch locs have more precision than the sns.txt
assert_array_almost_equal(py_ch['loc'], bin_ch['loc'], decimal=2)
# test when more than one marker file provided
mrks = [mrk_path, mrk2_path, mrk3_path]
read_raw_kit(sqd_path, mrks, elp_txt_path, hsp_txt_path, preload=False)
# this dataset does not have the equivalent set of points :(
raw_bin.info['dig'] = raw_bin.info['dig'][:8]
raw_py.info['dig'] = raw_py.info['dig'][:8]
assert_dig_allclose(raw_py.info, raw_bin.info)
def test_egi_dig_montage():
"""Test EGI MFF XML dig montage support."""
dig_montage = read_dig_montage(egi=egi_dig_montage_fname, unit='m')
# # test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'egi_test.fif')
_check_roundtrip(dig_montage, fname_temp)
# Test coordinate transform
dig_montage.transform_to_head()
# nasion
assert_almost_equal(dig_montage.nasion[0], 0)
assert_almost_equal(dig_montage.nasion[2], 0)
# lpa and rpa
assert_allclose(dig_montage.lpa[1:], 0, atol=1e-16)
assert_allclose(dig_montage.rpa[1:], 0, atol=1e-16)
# Test accuracy and embedding within raw object
raw_egi = read_raw_egi(egi_raw_fname, channel_naming='EEG %03d')
raw_egi.set_montage(dig_montage)
test_raw_egi = read_raw_fif(egi_fif_fname)
assert_equal(len(raw_egi.ch_names), len(test_raw_egi.ch_names))
for ch_raw, ch_test_raw in zip(raw_egi.info['chs'],
test_raw_egi.info['chs']):
assert_equal(ch_raw['ch_name'], ch_test_raw['ch_name'])
assert_equal(ch_raw['coord_frame'], FIFF.FIFFV_COORD_HEAD)
assert_allclose(ch_raw['loc'], ch_test_raw['loc'], atol=1e-7)
assert_dig_allclose(raw_egi.info, test_raw_egi.info)
def test_egi_dig_montage():
"""Test EGI MFF XML dig montage support."""
dig_montage = read_dig_montage(egi=egi_dig_montage_fname, unit='m')
# # test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'egi_test.fif')
_check_roundtrip(dig_montage, fname_temp)
# Test coordinate transform
dig_montage.transform_to_head()
# nasion
assert_almost_equal(dig_montage.nasion[0], 0)
assert_almost_equal(dig_montage.nasion[2], 0)
# lpa and rpa
assert_allclose(dig_montage.lpa[1:], 0, atol=1e-16)
assert_allclose(dig_montage.rpa[1:], 0, atol=1e-16)
# Test accuracy and embedding within raw object
raw_egi = read_raw_egi(egi_raw_fname, channel_naming='EEG %03d')
raw_egi.set_montage(dig_montage)
test_raw_egi = read_raw_fif(egi_fif_fname)
assert_equal(len(raw_egi.ch_names), len(test_raw_egi.ch_names))
for ch_raw, ch_test_raw in zip(raw_egi.info['chs'],
test_raw_egi.info['chs']):
assert_equal(ch_raw['ch_name'], ch_test_raw['ch_name'])
assert_equal(ch_raw['coord_frame'], FIFF.FIFFV_COORD_HEAD)
assert_allclose(ch_raw['loc'], ch_test_raw['loc'], atol=1e-7)
assert_dig_allclose(raw_egi.info, test_raw_egi.info)
def test_raw():
"""Test bti conversion to Raw object."""
for pdf, config, hs, exported in zip(pdf_fnames, config_fnames, hs_fnames,
exported_fnames):
# rx = 2 if 'linux' in pdf else 0
pytest.raises(ValueError, read_raw_bti, pdf, 'eggs', preload=False)
pytest.raises(ValueError,
read_raw_bti,
pdf,
config,
'spam',
preload=False)
if op.exists(tmp_raw_fname):
os.remove(tmp_raw_fname)
ex = read_raw_fif(exported, preload=True)
ra = read_raw_bti(pdf, config, hs, preload=False)
assert ('RawBTi' in repr(ra))
assert_equal(ex.ch_names[:NCH], ra.ch_names[:NCH])
assert_array_almost_equal(ex.info['dev_head_t']['trans'],
ra.info['dev_head_t']['trans'], 7)
assert len(ex.info['dig']) in (3563, 5154)
assert_dig_allclose(ex.info, ra.info, limit=100)
coil1, coil2 = [
np.concatenate([d['loc'].flatten() for d in r_.info['chs'][:NCH]])
for r_ in (ra, ex)
]
assert_array_almost_equal(coil1, coil2, 7)
loc1, loc2 = [
np.concatenate([d['loc'].flatten() for d in r_.info['chs'][:NCH]])
for r_ in (ra, ex)
]
assert_allclose(loc1, loc2)
assert_allclose(ra[:NCH][0], ex[:NCH][0])
assert_array_equal([c['range'] for c in ra.info['chs'][:NCH]],
[c['range'] for c in ex.info['chs'][:NCH]])
assert_array_equal([c['cal'] for c in ra.info['chs'][:NCH]],
[c['cal'] for c in ex.info['chs'][:NCH]])
assert_array_equal(ra._cals[:NCH], ex._cals[:NCH])
# check our transforms
for key in ('dev_head_t', 'dev_ctf_t', 'ctf_head_t'):
if ex.info[key] is None:
pass
else:
assert (ra.info[key] is not None)
for ent in ('to', 'from', 'trans'):
assert_allclose(ex.info[key][ent], ra.info[key][ent])
ra.save(tmp_raw_fname)
re = read_raw_fif(tmp_raw_fname)
print(re)
for key in ('dev_head_t', 'dev_ctf_t', 'ctf_head_t'):
assert (isinstance(re.info[key], dict))
this_t = re.info[key]['trans']
assert_equal(this_t.shape, (4, 4))
# check that matrix by is not identity
assert (not np.allclose(this_t, np.eye(4)))
os.remove(tmp_raw_fname)
def test_bvct_dig_montage_old_api(): # XXX: to remove in 0.20
"""Test BrainVision CapTrak XML dig montage support."""
with pytest.warns(RuntimeWarning, match='Using "m" as unit for BVCT file'):
read_dig_montage(bvct=bvct_dig_montage_fname, unit='m')
with pytest.deprecated_call():
dig_montage = read_dig_montage(bvct=bvct_dig_montage_fname)
# test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'bvct_test.fif')
_check_roundtrip(dig_montage, fname_temp)
with pytest.deprecated_call():
# nasion
assert_almost_equal(dig_montage.nasion[0], 0)
assert_almost_equal(dig_montage.nasion[2], 0)
# lpa and rpa
assert_allclose(dig_montage.lpa[1:], 0, atol=1e-16)
assert_allclose(dig_montage.rpa[1:], 0, atol=1e-16)
# Test accuracy and embedding within raw object
raw_bv = read_raw_brainvision(bv_raw_fname)
with pytest.warns(RuntimeWarning, match='Did not set.*channel pos'):
raw_bv.set_montage(dig_montage)
test_raw_bv = read_raw_fif(bv_fif_fname)
assert_equal(len(raw_bv.ch_names), len(test_raw_bv.ch_names))
for ch_raw, ch_test_raw in zip(raw_bv.info['chs'],
test_raw_bv.info['chs']):
assert_equal(ch_raw['ch_name'], ch_test_raw['ch_name'])
assert_equal(ch_raw['coord_frame'], FIFF.FIFFV_COORD_HEAD)
assert_allclose(ch_raw['loc'], ch_test_raw['loc'], atol=1e-7)
assert_dig_allclose(raw_bv.info, test_raw_bv.info)
def test_fif_dig_montage():
"""Test FIF dig montage support."""
dig_montage = read_dig_fif(fif_dig_montage_fname)
# test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'test.fif')
_check_roundtrip(dig_montage, fname_temp)
# Make a BrainVision file like the one the user would have had
raw_bv = read_raw_brainvision(bv_fname, preload=True)
raw_bv_2 = raw_bv.copy()
mapping = dict()
for ii, ch_name in enumerate(raw_bv.ch_names):
mapping[ch_name] = 'EEG%03d' % (ii + 1,)
raw_bv.rename_channels(mapping)
for ii, ch_name in enumerate(raw_bv_2.ch_names):
mapping[ch_name] = 'EEG%03d' % (ii + 33,)
raw_bv_2.rename_channels(mapping)
raw_bv.add_channels([raw_bv_2])
for ch in raw_bv.info['chs']:
ch['kind'] = FIFF.FIFFV_EEG_CH
# Set the montage
raw_bv.set_montage(dig_montage)
# Check the result
evoked = read_evokeds(evoked_fname)[0]
# check info[chs] matches
assert_equal(len(raw_bv.ch_names), len(evoked.ch_names) - 1)
for ch_py, ch_c in zip(raw_bv.info['chs'], evoked.info['chs'][:-1]):
assert_equal(ch_py['ch_name'],
ch_c['ch_name'].replace('EEG ', 'EEG'))
# C actually says it's unknown, but it's not (?):
# assert_equal(ch_py['coord_frame'], ch_c['coord_frame'])
assert_equal(ch_py['coord_frame'], FIFF.FIFFV_COORD_HEAD)
c_loc = ch_c['loc'].copy()
c_loc[c_loc == 0] = np.nan
assert_allclose(ch_py['loc'], c_loc, atol=1e-7)
# check info[dig]
assert_dig_allclose(raw_bv.info, evoked.info)
# Roundtrip of non-FIF start
montage = make_dig_montage(hsp=read_polhemus_fastscan(hsp),
hpi=read_mrk(hpi))
elp_points = read_polhemus_fastscan(elp)
ch_pos = {"EEG%03d" % (k + 1): pos for k, pos in enumerate(elp_points[8:])}
montage += make_dig_montage(nasion=elp_points[0],
lpa=elp_points[1],
rpa=elp_points[2],
ch_pos=ch_pos)
pytest.raises(RuntimeError, montage.save, fname_temp) # must be head coord
montage = transform_to_head(montage)
_check_roundtrip(montage, fname_temp)
def test_raw():
"""Test bti conversion to Raw object."""
for pdf, config, hs, exported in zip(pdf_fnames, config_fnames, hs_fnames,
exported_fnames):
# rx = 2 if 'linux' in pdf else 0
pytest.raises(ValueError, read_raw_bti, pdf, 'eggs', preload=False)
pytest.raises(ValueError, read_raw_bti, pdf, config, 'spam',
preload=False)
if op.exists(tmp_raw_fname):
os.remove(tmp_raw_fname)
ex = read_raw_fif(exported, preload=True)
ra = read_raw_bti(pdf, config, hs, preload=False)
assert ('RawBTi' in repr(ra))
assert_equal(ex.ch_names[:NCH], ra.ch_names[:NCH])
assert_array_almost_equal(ex.info['dev_head_t']['trans'],
ra.info['dev_head_t']['trans'], 7)
assert len(ex.info['dig']) in (3563, 5154)
assert_dig_allclose(ex.info, ra.info, limit=100)
coil1, coil2 = [np.concatenate([d['loc'].flatten()
for d in r_.info['chs'][:NCH]])
for r_ in (ra, ex)]
assert_array_almost_equal(coil1, coil2, 7)
loc1, loc2 = [np.concatenate([d['loc'].flatten()
for d in r_.info['chs'][:NCH]])
for r_ in (ra, ex)]
assert_allclose(loc1, loc2)
assert_allclose(ra[:NCH][0], ex[:NCH][0])
assert_array_equal([c['range'] for c in ra.info['chs'][:NCH]],
[c['range'] for c in ex.info['chs'][:NCH]])
assert_array_equal([c['cal'] for c in ra.info['chs'][:NCH]],
[c['cal'] for c in ex.info['chs'][:NCH]])
assert_array_equal(ra._cals[:NCH], ex._cals[:NCH])
# check our transforms
for key in ('dev_head_t', 'dev_ctf_t', 'ctf_head_t'):
if ex.info[key] is None:
pass
else:
assert (ra.info[key] is not None)
for ent in ('to', 'from', 'trans'):
assert_allclose(ex.info[key][ent],
ra.info[key][ent])
ra.save(tmp_raw_fname)
re = read_raw_fif(tmp_raw_fname)
print(re)
for key in ('dev_head_t', 'dev_ctf_t', 'ctf_head_t'):
assert (isinstance(re.info[key], dict))
this_t = re.info[key]['trans']
assert_equal(this_t.shape, (4, 4))
# check that matrix by is not identity
assert (not np.allclose(this_t, np.eye(4)))
os.remove(tmp_raw_fname)
def test_fif_dig_montage():
"""Test FIF dig montage support."""
with pytest.deprecated_call():
dig_montage = read_dig_montage(fif=fif_dig_montage_fname)
# test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'test.fif')
_check_roundtrip(dig_montage, fname_temp)
# Make a BrainVision file like the one the user would have had
raw_bv = read_raw_brainvision(bv_fname, preload=True)
raw_bv_2 = raw_bv.copy()
mapping = dict()
for ii, ch_name in enumerate(raw_bv.ch_names):
mapping[ch_name] = 'EEG%03d' % (ii + 1, )
raw_bv.rename_channels(mapping)
for ii, ch_name in enumerate(raw_bv_2.ch_names):
mapping[ch_name] = 'EEG%03d' % (ii + 33, )
raw_bv_2.rename_channels(mapping)
raw_bv.add_channels([raw_bv_2])
for ii in range(2):
# Set the montage
raw_bv.set_montage(dig_montage)
# Check the result
evoked = read_evokeds(evoked_fname)[0]
assert_equal(len(raw_bv.ch_names), len(evoked.ch_names) - 1)
for ch_py, ch_c in zip(raw_bv.info['chs'], evoked.info['chs'][:-1]):
assert_equal(ch_py['ch_name'],
ch_c['ch_name'].replace('EEG ', 'EEG'))
# C actually says it's unknown, but it's not (?):
# assert_equal(ch_py['coord_frame'], ch_c['coord_frame'])
assert_equal(ch_py['coord_frame'], FIFF.FIFFV_COORD_HEAD)
c_loc = ch_c['loc'].copy()
c_loc[c_loc == 0] = np.nan
assert_allclose(ch_py['loc'], c_loc, atol=1e-7)
assert_dig_allclose(raw_bv.info, evoked.info)
# Roundtrip of non-FIF start
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
montage = read_dig_montage(hsp, hpi, elp, names, transform=False)
pytest.raises(RuntimeError, montage.save, fname_temp) # must be head coord
montage = read_dig_montage(hsp, hpi, elp, names)
_check_roundtrip(montage, fname_temp)
# Test old way matches new way
with pytest.deprecated_call():
dig_montage = read_dig_montage(fif=fif_dig_montage_fname)
dig_montage_fif = read_dig_fif(fif_dig_montage_fname)
assert dig_montage.dig == dig_montage_fif.dig
assert object_diff(dig_montage.ch_names, dig_montage_fif.ch_names) == ''
def test_fif_dig_montage():
"""Test FIF dig montage support."""
dig_montage = read_dig_montage(fif=fif_dig_montage_fname)
# test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'test.fif')
_check_roundtrip(dig_montage, fname_temp)
# Make a BrainVision file like the one the user would have had
raw_bv = read_raw_brainvision(bv_fname, preload=True)
raw_bv_2 = raw_bv.copy()
mapping = dict()
for ii, ch_name in enumerate(raw_bv.ch_names):
mapping[ch_name] = 'EEG%03d' % (ii + 1,)
raw_bv.rename_channels(mapping)
for ii, ch_name in enumerate(raw_bv_2.ch_names):
mapping[ch_name] = 'EEG%03d' % (ii + 33,)
raw_bv_2.rename_channels(mapping)
raw_bv.add_channels([raw_bv_2])
for ii in range(2):
if ii == 1:
dig_montage.transform_to_head() # should have no meaningful effect
# Set the montage
raw_bv.set_montage(dig_montage)
# Check the result
evoked = read_evokeds(evoked_fname)[0]
assert_equal(len(raw_bv.ch_names), len(evoked.ch_names) - 1)
for ch_py, ch_c in zip(raw_bv.info['chs'], evoked.info['chs'][:-1]):
assert_equal(ch_py['ch_name'],
ch_c['ch_name'].replace('EEG ', 'EEG'))
# C actually says it's unknown, but it's not (?):
# assert_equal(ch_py['coord_frame'], ch_c['coord_frame'])
assert_equal(ch_py['coord_frame'], FIFF.FIFFV_COORD_HEAD)
c_loc = ch_c['loc'].copy()
c_loc[c_loc == 0] = np.nan
assert_allclose(ch_py['loc'], c_loc, atol=1e-7)
assert_dig_allclose(raw_bv.info, evoked.info)
# Roundtrip of non-FIF start
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
montage = read_dig_montage(hsp, hpi, elp, names, transform=False)
pytest.raises(RuntimeError, montage.save, fname_temp) # must be head coord
montage = read_dig_montage(hsp, hpi, elp, names)
_check_roundtrip(montage, fname_temp)
def test_egi_dig_montage():
"""Test EGI MFF XML dig montage support."""
dig_montage = read_dig_egi(egi_dig_montage_fname)
fid, coord = _get_fid_coords(dig_montage.dig)
assert coord == FIFF.FIFFV_COORD_UNKNOWN
assert_allclose(
actual=np.array([fid[key] for key in ['nasion', 'lpa', 'rpa']]),
desired=[
[0., 10.564, -2.051], # noqa
[-8.592, 0.498, -4.128], # noqa
[8.592, 0.498, -4.128]
], # noqa
)
# Test accuracy and embedding within raw object
raw_egi = read_raw_egi(egi_raw_fname, channel_naming='EEG %03d')
raw_egi.set_montage(dig_montage)
test_raw_egi = read_raw_fif(egi_fif_fname)
assert_equal(len(raw_egi.ch_names), len(test_raw_egi.ch_names))
for ch_raw, ch_test_raw in zip(raw_egi.info['chs'],
test_raw_egi.info['chs']):
assert_equal(ch_raw['ch_name'], ch_test_raw['ch_name'])
assert_equal(ch_raw['coord_frame'], FIFF.FIFFV_COORD_HEAD)
assert_allclose(ch_raw['loc'], ch_test_raw['loc'], atol=1e-7)
assert_dig_allclose(raw_egi.info, test_raw_egi.info)
dig_montage_in_head = transform_to_head(dig_montage.copy())
fid, coord = _get_fid_coords(dig_montage_in_head.dig)
assert coord == FIFF.FIFFV_COORD_HEAD
assert_allclose(
actual=np.array([fid[key] for key in ['nasion', 'lpa', 'rpa']]),
desired=[[0., 10.278, 0.], [-8.592, 0., 0.], [8.592, 0., 0.]],
atol=1e-4,
)
# test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'egi_test.fif')
_check_roundtrip(dig_montage_in_head, fname_temp) # XXX: write forces head
def test_read_dig_captrack(tmpdir):
"""Test reading a captrack montage file."""
EXPECTED_CH_NAMES = [
'AF3', 'AF4', 'AF7', 'AF8', 'C1', 'C2', 'C3', 'C4', 'C5', 'C6', 'CP1',
'CP2', 'CP3', 'CP4', 'CP5', 'CP6', 'CPz', 'Cz', 'F1', 'F2', 'F3', 'F4',
'F5', 'F6', 'F7', 'F8', 'FC1', 'FC2', 'FC3', 'FC4', 'FC5', 'FC6',
'FT10', 'FT7', 'FT8', 'FT9', 'Fp1', 'Fp2', 'Fz', 'O1', 'O2', 'Oz',
'P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'PO10', 'PO3', 'PO4',
'PO7', 'PO8', 'PO9', 'POz', 'Pz', 'T7', 'T8', 'TP10', 'TP7', 'TP8',
'TP9'
]
montage = read_dig_captrack(
fname=op.join(data_path, 'montage', 'captrak_coords.bvct')
)
assert montage.ch_names == EXPECTED_CH_NAMES
assert montage.__repr__() == (
'<DigMontage | '
'0 extras (headshape), 0 HPIs, 3 fiducials, 64 channels>'
)
montage = transform_to_head(montage) # transform_to_head has to be tested
_check_roundtrip(montage=montage, fname=str(tmpdir.join('bvct_test.fif')))
with pytest.deprecated_call():
assert_allclose(
actual=np.array([montage.nasion, montage.lpa, montage.rpa]),
desired=[[0, 0.11309, 0], [-0.09189, 0, 0], [0.09240, 0, 0]],
atol=1e-5,
)
# I think that comparing dig should be enough. cc: @sappelhoff
raw_bv = read_raw_brainvision(bv_raw_fname)
with pytest.warns(RuntimeWarning, match='Did not set 3 channel pos'):
raw_bv.set_montage(montage)
test_raw_bv = read_raw_fif(bv_fif_fname)
assert_dig_allclose(raw_bv.info, test_raw_bv.info)
def test_handle_ieeg_coords_reading(bids_basename):
"""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_basename.copy().update(suffix='ieeg.edf')
raw = mne.io.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_basename,
bids_root,
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_basename=bids_basename,
bids_root=bids_root,
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_basename,
bids_root,
overwrite=True,
verbose=False)
# obtain the sensor positions and assert ch_coords are same
raw_test = read_raw_bids(bids_basename=bids_basename,
bids_root=bids_root,
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}
coordsystem_fname = _find_matching_sidecar(bids_fname,
bids_root,
suffix='coordsystem.json',
allow_fail=True)
electrodes_fname = _find_matching_sidecar(bids_fname,
bids_root,
"electrodes.tsv",
allow_fail=True)
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_basename=bids_basename,
bids_root=bids_root,
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_basename=bids_basename,
bids_root=bids_root,
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_basename=bids_basename,
bids_root=bids_root,
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_basename=bids_basename,
bids_root=bids_root,
verbose=False)
coord_frame_int = MNE_STR_TO_FRAME['ras']
for digpoint in raw_test.info['dig']:
assert digpoint['coord_frame'] == coord_frame_int
# test error message if electrodes don't match
write_raw_bids(raw, bids_basename, bids_root, 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_basename=bids_basename,
bids_root=bids_root,
verbose=False)
# make sure montage is set if there are coordinates w/ 'n/a'
raw.info['bads'] = []
write_raw_bids(raw,
bids_basename,
bids_root,
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_basename=bids_basename,
bids_root=bids_root,
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_ieeg_coords_reading(bids_path, tmpdir):
"""Test reading iEEG coordinates from BIDS files."""
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=tmpdir)
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 = ['mni_tal']
for coord_frame in coordinate_frames:
# XXX: mne-bids doesn't support multiple electrodes.tsv files
sh.rmtree(tmpdir)
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(tmpdir)
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=tmpdir)
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 = ['Other']
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="Defaulting coordinate "
"frame to unknown"):
raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
assert raw_test.info['dig'] is not None
# check that standard template identifiers that are unsupported in
# mne-python coordinate frames, still get read in, but produce a warning
coordinate_frames = [
'individual', 'fsnative', 'scanner', 'ICBM452AirSpace', 'NIHPD'
]
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=f"iEEG Coordinate frame {coord_frame} "
f"is not a readable BIDS keyword "):
raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
assert raw_test.info['dig'] is not 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['mri']
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 is not a subset of Raw
bids_path.update(root=tmpdir)
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)
# popping off channels should not result in an error
# however, a warning will be raised through mne-python
with pytest.warns(RuntimeWarning,
match='DigMontage is '
'only a subset of info'):
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']
