def test_plot_montage():
"""Test plotting montages."""
m = make_standard_montage('easycap-M1')
m.plot()
plt.close('all')
m.plot(kind='3d')
plt.close('all')
m.plot(kind='3d', show_names=True)
plt.close('all')
m.plot(kind='topomap')
plt.close('all')
m.plot(kind='topomap', show_names=True)
plt.close('all')
N_HSP, N_HPI = 2, 1
montage = make_dig_montage(nasion=[1, 1, 1],
lpa=[2, 2, 2],
rpa=[3, 3, 3],
hsp=np.full((N_HSP, 3), 4),
hpi=np.full((N_HPI, 3), 4),
coord_frame='head')
assert '0 channels' in repr(montage)
with pytest.raises(RuntimeError, match='No valid channel positions'):
montage.plot()
d = read_dig_fif(fname=fif_fname)
assert '61 channels' in repr(d)
def test_inst_source():
"""Test DigSource."""
from mne.gui._file_traits import DigSource
tempdir = _TempDir()
inst = DigSource()
assert inst.inst_fname == '-'
inst.file = inst_path
assert inst.inst_dir == op.dirname(inst_path)
lpa = array([[-7.13766068e-02, 0.00000000e+00, 5.12227416e-09]])
nasion = array([[3.72529030e-09, 1.02605611e-01, 4.19095159e-09]])
rpa = array([[7.52676800e-02, 0.00000000e+00, 5.58793545e-09]])
assert_allclose(inst.lpa, lpa)
assert_allclose(inst.nasion, nasion)
assert_allclose(inst.rpa, rpa)
montage = read_dig_fif(inst_path) # test reading DigMontage
montage_path = op.join(tempdir, 'temp_montage.fif')
montage.save(montage_path)
inst.file = montage_path
assert_allclose(inst.lpa, lpa)
assert_allclose(inst.nasion, nasion)
assert_allclose(inst.rpa, rpa)
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_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 _check_roundtrip(montage, fname):
"""Check roundtrip writing."""
with pytest.deprecated_call():
assert_equal(montage.coord_frame, 'head')
montage.save(fname)
montage_read = read_dig_fif(fname=fname)
assert_equal(str(montage), str(montage_read))
with pytest.deprecated_call():
for kind in ('elp', 'hsp', 'nasion', 'lpa', 'rpa'):
if getattr(montage, kind, None) is not None:
assert_allclose(getattr(montage, kind),
getattr(montage_read, kind),
err_msg=kind)
with pytest.deprecated_call():
assert_equal(montage_read.coord_frame, 'head')
def _check_roundtrip(montage, fname):
"""Check roundtrip writing."""
montage.save(fname)
montage_read = read_dig_fif(fname=fname)
assert_equal(repr(montage), repr(montage_read))
assert_equal(_check_get_coord_frame(montage_read.dig), 'head')
# XXX: it tests the same as assert_dig_all_close but without info
# This is a possible refactor
dig_py = sorted(montage_read.dig, key=_dig_sort_key)
dig_bin = sorted(montage.dig, key=_dig_sort_key)
assert len(dig_py) == len(dig_bin)
for ii, (d_py, d_bin) in enumerate(zip(dig_py, dig_bin)):
for key in ('ident', 'kind', 'coord_frame'):
assert d_py[key] == d_bin[key]
assert_allclose(d_py['r'], d_bin['r'], rtol=1e-5, atol=1e-5,
err_msg='Failure on %s:\n%s\n%s'
% (ii, d_py['r'], d_bin['r']))
def test_plot_montage():
"""Test plotting montages."""
m = read_montage('easycap-M1')
m.plot()
plt.close('all')
m.plot(kind='3d')
plt.close('all')
m.plot(kind='3d', show_names=True)
plt.close('all')
m.plot(kind='topomap')
plt.close('all')
m.plot(kind='topomap', show_names=True)
plt.close('all')
d = read_dig_montage(hsp, hpi, elp, point_names)
assert '0 channels' in repr(d)
with pytest.raises(RuntimeError, match='No valid channel positions'):
d.plot()
d = read_dig_fif(fname=fif_fname)
assert '61 channels' in repr(d)
def test_digitization_source(tmpdir):
"""Test DigSource."""
from mne.gui._file_traits import DigSource
tempdir = str(tmpdir)
inst = DigSource()
assert inst.inst_fname == '-'
inst.file = inst_path
assert inst.inst_dir == op.dirname(inst_path)
# FIFF
lpa = array([[-7.13766068e-02, 0.00000000e+00, 5.12227416e-09]])
nasion = array([[3.72529030e-09, 1.02605611e-01, 4.19095159e-09]])
rpa = array([[7.52676800e-02, 0.00000000e+00, 5.58793545e-09]])
assert_allclose(inst.lpa, lpa)
assert_allclose(inst.nasion, nasion)
assert_allclose(inst.rpa, rpa)
# DigMontage
montage = read_dig_fif(inst_path)
montage_path = op.join(tempdir, 'temp_montage.fif')
montage.save(montage_path)
inst.file = montage_path
assert_allclose(inst.lpa, lpa)
assert_allclose(inst.nasion, nasion)
assert_allclose(inst.rpa, rpa)
# EGI MFF
inst.file = op.join(data_path, 'EGI', 'test_egi.mff')
assert len(inst.points) == 0
assert len(inst.eeg_points) == 130
assert_allclose(inst.lpa * 1000, [[-67.1, 0, 0]], atol=0.1)
assert_allclose(inst.nasion * 1000, [[0.0, 103.6, 0]], atol=0.1)
assert_allclose(inst.rpa * 1000, [[67.1, 0, 0]], atol=0.1)
# CTF
inst.file = op.join(data_path, 'CTF', 'testdata_ctf.ds')
assert len(inst.points) == 0
assert len(inst.eeg_points) == 8
assert_allclose(inst.lpa * 1000, [[-74.3, 0.0, 0.0]], atol=0.1)
assert_allclose(inst.nasion * 1000, [[0.0, 117.7, 0.0]], atol=0.1)
assert_allclose(inst.rpa * 1000, [[84.9, -0.0, 0.0]], atol=0.1)
