def test_make_dig_points():
"""Test application of Polhemus HSP to info."""
extra_points = read_polhemus_fastscan(hsp_fname,
on_header_missing='ignore')
info = create_info(ch_names=['Test Ch'], sfreq=1000.)
assert info['dig'] is None
info['dig'] = _make_dig_points(extra_points=extra_points)
assert (info['dig'])
assert_allclose(info['dig'][0]['r'], [-.10693, .09980, .06881])
elp_points = read_polhemus_fastscan(elp_fname, on_header_missing='ignore')
nasion, lpa, rpa = elp_points[:3]
info = create_info(ch_names=['Test Ch'], sfreq=1000.)
assert info['dig'] is None
info['dig'] = _make_dig_points(nasion, lpa, rpa, elp_points[3:], None)
assert (info['dig'])
idx = [d['ident'] for d in info['dig']].index(FIFF.FIFFV_POINT_NASION)
assert_allclose(info['dig'][idx]['r'], [.0013930, .0131613, -.0046967])
pytest.raises(ValueError, _make_dig_points, nasion[:2])
pytest.raises(ValueError, _make_dig_points, None, lpa[:2])
pytest.raises(ValueError, _make_dig_points, None, None, rpa[:2])
pytest.raises(ValueError, _make_dig_points, None, None, None,
elp_points[:, :2])
pytest.raises(ValueError, _make_dig_points, None, None, None, None,
elp_points[:, :2])
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_read_dig_montage_using_polhemus_fastscan_error_handling(tmpdir):
"""Test reading Polhemus FastSCAN errors."""
with open(op.join(kit_dir, 'test_elp.txt')) as fid:
content = fid.read().replace('FastSCAN', 'XxxxXXXX')
fname = str(tmpdir.join('faulty_FastSCAN.txt'))
with open(fname, 'w') as fid:
fid.write(content)
with pytest.raises(ValueError, match='not contain Polhemus FastSCAN'):
_ = read_polhemus_fastscan(fname)
EXPECTED_ERR_MSG = "allowed value is '.txt', but got '.bar' instead"
with pytest.raises(ValueError, match=EXPECTED_ERR_MSG):
_ = read_polhemus_fastscan(fname=tmpdir.join('foo.bar'))
def test_read_dig_montage_using_polhemus_fastscan():
"""Test FastScan."""
N_EEG_CH = 10
my_electrode_positions = read_polhemus_fastscan(
op.join(kit_dir, 'test_elp.txt')
)
montage = make_dig_montage(
# EEG_CH
ch_pos=dict(zip(ascii_lowercase[:N_EEG_CH],
np.random.RandomState(0).rand(N_EEG_CH, 3))),
# NO NAMED points
nasion=my_electrode_positions[0],
lpa=my_electrode_positions[1],
rpa=my_electrode_positions[2],
hpi=my_electrode_positions[3:],
hsp=read_polhemus_fastscan(op.join(kit_dir, 'test_hsp.txt')),
# Other defaults
coord_frame='unknown'
)
assert repr(montage) == (
'<DigMontage | '
'500 extras (headshape), 5 HPIs, 3 fiducials, 10 channels>'
) # XXX: is this wrong? extra is not in headspace, is it?
assert set([d['coord_frame'] for d in montage.dig]) == {
FIFF.FIFFV_COORD_UNKNOWN
} # XXX: so far we build everything in 'unknown'
EXPECTED_FID_IN_POLHEMUS = {
'nasion': [0.001393, 0.0131613, -0.0046967],
'lpa': [-0.0624997, -0.0737271, 0.07996],
'rpa': [-0.0748957, 0.0873785, 0.0811943],
}
fiducials, fid_coordframe = _get_fid_coords(montage.dig)
assert fid_coordframe == FIFF.FIFFV_COORD_UNKNOWN
for kk, val in fiducials.items():
assert_allclose(val, EXPECTED_FID_IN_POLHEMUS[kk])
def test_io_dig_points(tmpdir):
"""Test Writing for dig files."""
points = read_polhemus_fastscan(hsp_fname, on_header_missing='ignore')
dest = str(tmpdir.join('test.txt'))
dest_bad = str(tmpdir.join('test.mne'))
with pytest.raises(ValueError, match='must be of shape'):
_write_dig_points(dest, points[:, :2])
with pytest.raises(ValueError, match='extension'):
_write_dig_points(dest_bad, points)
_write_dig_points(dest, points)
points1 = read_polhemus_fastscan(
dest, unit='m', on_header_missing='ignore')
err = "Dig points diverged after writing and reading."
assert_array_equal(points, points1, err)
points2 = np.array([[-106.93, 99.80], [99.80, 68.81]])
np.savetxt(dest, points2, delimiter='\t', newline='\n')
with pytest.raises(ValueError, match='must be of shape'):
with pytest.warns(RuntimeWarning, match='FastSCAN header'):
read_polhemus_fastscan(dest, on_header_missing='warn')
