def test_make_dig_points():
"""Test application of Polhemus HSP to info."""
extra_points = _read_dig_points(hsp_fname)
info = create_info(ch_names=['Test Ch'], sfreq=1000., ch_types=None)
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_dig_points(elp_fname)
nasion, lpa, rpa = elp_points[:3]
info = create_info(ch_names=['Test Ch'], sfreq=1000., ch_types=None)
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_array_equal(info['dig'][idx]['r'],
np.array([.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 _read_dig_montage(
hsp=None, hpi=None, elp=None, point_names=None, unit='auto',
fif=None, egi=None, bvct=None, transform=True, dev_head_t=False,
):
"""Unfolds the `read_dig_montage` old behavior of the call below.
montage = read_dig_montage(hsp, hpi, elp, names,
transform=True, dev_head_t=False)
"""
assert isinstance(hsp, str), 'original call hsp was string'
assert op.splitext(hpi)[-1] == '.sqd', 'original call hpi was .sqd'
assert isinstance(elp, str), 'original call elp was string'
hsp = _read_dig_points(hsp, unit=unit)
hpi = read_mrk(hpi)
elp = _read_dig_points(elp, unit=unit)
data = Bunch(nasion=None, lpa=None, rpa=None,
hsp=hsp, hpi=hpi, elp=elp, coord_frame='unknown',
point_names=point_names, dig_ch_pos=None)
data = _fix_data_fiducials(data)
data = _transform_to_head_call(data)
with pytest.deprecated_call():
montage = DigMontage(**data)
return montage
def test_set_dig_montage():
"""Test applying DigMontage to inst."""
# Extensive testing of applying `dig` to info is done in test_meas_info
# with `test_make_dig_points`.
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
hsp_points = _read_dig_points(hsp)
elp_points = _read_dig_points(elp)
nasion, lpa, rpa = elp_points[:3]
nm_trans = get_ras_to_neuromag_trans(nasion, lpa, rpa)
elp_points = apply_trans(nm_trans, elp_points)
nasion, lpa, rpa = elp_points[:3]
hsp_points = apply_trans(nm_trans, hsp_points)
montage = read_dig_montage(hsp,
hpi,
elp,
names,
transform=True,
dev_head_t=True)
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'test.fif')
montage.save(fname_temp)
with pytest.deprecated_call():
montage_read = read_dig_montage(fif=fname_temp)
for use_mon in (montage, montage_read):
info = create_info(['Test Ch'], 1e3, ['eeg'])
with pytest.warns(None): # warns on one run about not all positions
_set_montage(info, use_mon)
hs = np.array([
p['r'] for i, p in enumerate(info['dig'])
if p['kind'] == FIFF.FIFFV_POINT_EXTRA
])
nasion_dig = np.array([
p['r'] for p in info['dig'] if all([
p['ident'] == FIFF.FIFFV_POINT_NASION, p['kind'] ==
FIFF.FIFFV_POINT_CARDINAL
])
])
lpa_dig = np.array([
p['r'] for p in info['dig'] if all([
p['ident'] == FIFF.FIFFV_POINT_LPA, p['kind'] ==
FIFF.FIFFV_POINT_CARDINAL
])
])
rpa_dig = np.array([
p['r'] for p in info['dig'] if all([
p['ident'] == FIFF.FIFFV_POINT_RPA, p['kind'] ==
FIFF.FIFFV_POINT_CARDINAL
])
])
hpi_dig = np.array(
[p['r'] for p in info['dig'] if p['kind'] == FIFF.FIFFV_POINT_HPI])
assert_allclose(hs, hsp_points, atol=1e-7)
assert_allclose(nasion_dig.ravel(), nasion, atol=1e-7)
assert_allclose(lpa_dig.ravel(), lpa, atol=1e-7)
assert_allclose(rpa_dig.ravel(), rpa, atol=1e-7)
assert_allclose(hpi_dig, elp_points[3:], atol=1e-7)
def test_io_dig_points():
"""Test Writing for dig files."""
tempdir = _TempDir()
points = _read_dig_points(hsp_fname)
dest = op.join(tempdir, 'test.txt')
dest_bad = op.join(tempdir, 'test.mne')
pytest.raises(ValueError, _write_dig_points, dest, points[:, :2])
pytest.raises(ValueError, _write_dig_points, dest_bad, points)
_write_dig_points(dest, points)
points1 = _read_dig_points(dest, unit='m')
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')
pytest.raises(ValueError, _read_dig_points, dest)
def test_io_dig_points(tmpdir):
"""Test Writing for dig files."""
points = _read_dig_points(hsp_fname)
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_dig_points(dest, unit='m')
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'):
_read_dig_points(dest)
def test_read_dig_montage():
"""Test read_dig_montage."""
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
montage = read_dig_montage(hsp, hpi, elp, names, transform=False)
elp_points = _read_dig_points(elp)
hsp_points = _read_dig_points(hsp)
hpi_points = read_mrk(hpi)
with pytest.deprecated_call():
assert_equal(montage.point_names, names)
assert_array_equal(montage.elp, elp_points)
assert_array_equal(montage.hsp, hsp_points)
assert (montage.dev_head_t is None)
montage = read_dig_montage(hsp,
hpi,
elp,
names,
transform=True,
dev_head_t=True)
# check coordinate transformation
# nasion
with pytest.deprecated_call():
assert_almost_equal(montage.nasion[0], 0)
assert_almost_equal(montage.nasion[2], 0)
# lpa and rpa
with pytest.deprecated_call():
assert_allclose(montage.lpa[1:], 0, atol=1e-16)
assert_allclose(montage.rpa[1:], 0, atol=1e-16)
# device head transform
EXPECTED_DEV_HEAD_T = np.array(
[[-3.72201691e-02, -9.98212167e-01, -4.67667497e-02, -7.31583414e-04],
[8.98064989e-01, -5.39382685e-02, 4.36543170e-01, 1.60134431e-02],
[-4.38285221e-01, -2.57513699e-02, 8.98466990e-01, 6.13035748e-02],
[0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.00000000e+00]])
assert_allclose(montage.dev_head_t, EXPECTED_DEV_HEAD_T, atol=1e-7)
# Digitizer as array
with pytest.deprecated_call():
m2 = read_dig_montage(hsp_points,
hpi_points,
elp_points,
names,
unit='m')
assert_array_equal(m2.hsp, montage.hsp)
m3 = read_dig_montage(hsp_points * 1000, hpi_points, elp_points * 1000,
names)
with pytest.deprecated_call():
assert_allclose(m3.hsp, montage.hsp)
# test unit parameter and .mat support
tempdir = _TempDir()
mat_hsp = op.join(tempdir, 'test.mat')
savemat(mat_hsp, dict(Points=(1000 * hsp_points).T), oned_as='row')
montage_cm = read_dig_montage(mat_hsp, hpi, elp, names, unit='cm')
with pytest.deprecated_call():
assert_allclose(montage_cm.hsp, montage.hsp * 10.)
assert_allclose(montage_cm.elp, montage.elp * 10.)
pytest.raises(ValueError,
read_dig_montage,
hsp,
hpi,
elp,
names,
unit='km')
# extra columns
extra_hsp = op.join(tempdir, 'test.txt')
with open(hsp, 'rb') as fin:
with open(extra_hsp, 'wb') as fout:
for line in fin:
if line.startswith(b'%'):
fout.write(line)
else:
# extra column
fout.write(line.rstrip() + b' 0.0 0.0 0.0\n')
with pytest.warns(RuntimeWarning, match='Found .* columns instead of 3'):
montage_extra = read_dig_montage(extra_hsp, hpi, elp, names)
with pytest.deprecated_call():
assert_allclose(montage_extra.hsp, montage.hsp)
assert_allclose(montage_extra.elp, montage.elp)