def test_fiducials_io(tmpdir):
"""Test fiducials i/o."""
pts, coord_frame = read_fiducials(fiducials_fname)
assert pts[0]['coord_frame'] == FIFF.FIFFV_COORD_MRI
assert pts[0]['ident'] == FIFF.FIFFV_POINT_CARDINAL
temp_fname = tmpdir.join('test.fif')
write_fiducials(temp_fname, pts, coord_frame)
pts_1, coord_frame_1 = read_fiducials(temp_fname)
assert coord_frame == coord_frame_1
for pt, pt_1 in zip(pts, pts_1):
assert pt['kind'] == pt_1['kind']
assert pt['ident'] == pt_1['ident']
assert pt['coord_frame'] == pt_1['coord_frame']
assert_array_equal(pt['r'], pt_1['r'])
# test safeguards
pts[0]['coord_frame'] += 1
pytest.raises(ValueError, write_fiducials, temp_fname, pts, coord_frame)
def test_fiducials_io():
"""Test fiducials i/o"""
pts, coord_frame = read_fiducials(fiducials_fname)
assert_equal(pts[0]['coord_frame'], FIFF.FIFFV_COORD_MRI)
assert_equal(pts[0]['ident'], FIFF.FIFFV_POINT_CARDINAL)
temp_fname = op.join(tempdir, 'test.fif')
write_fiducials(temp_fname, pts, coord_frame)
pts_1, coord_frame_1 = read_fiducials(temp_fname)
assert_equal(coord_frame, coord_frame_1)
for pt, pt_1 in zip(pts, pts_1):
assert_equal(pt['kind'], pt_1['kind'])
assert_equal(pt['ident'], pt_1['ident'])
assert_equal(pt['coord_frame'], pt_1['coord_frame'])
assert_array_equal(pt['r'], pt_1['r'])
# test safeguards
pts[0]['coord_frame'] += 1
assert_raises(ValueError, write_fiducials, temp_fname, pts, coord_frame)
def test_fiducials_io():
"""Test fiducials i/o."""
tempdir = _TempDir()
pts, coord_frame = read_fiducials(fiducials_fname)
assert pts[0]['coord_frame'] == FIFF.FIFFV_COORD_MRI
assert pts[0]['ident'] == FIFF.FIFFV_POINT_CARDINAL
temp_fname = op.join(tempdir, 'test.fif')
write_fiducials(temp_fname, pts, coord_frame)
pts_1, coord_frame_1 = read_fiducials(temp_fname)
assert coord_frame == coord_frame_1
for pt, pt_1 in zip(pts, pts_1):
assert pt['kind'] == pt_1['kind']
assert pt['ident'] == pt_1['ident']
assert pt['coord_frame'] == pt_1['coord_frame']
assert_array_equal(pt['r'], pt_1['r'])
# test safeguards
pts[0]['coord_frame'] += 1
pytest.raises(ValueError, write_fiducials, temp_fname, pts, coord_frame)
def test_fiducials_io():
"""Test fiducials i/o."""
tempdir = _TempDir()
pts, coord_frame = read_fiducials(fiducials_fname)
assert_equal(pts[0]["coord_frame"], FIFF.FIFFV_COORD_MRI)
assert_equal(pts[0]["ident"], FIFF.FIFFV_POINT_CARDINAL)
temp_fname = op.join(tempdir, "test.fif")
write_fiducials(temp_fname, pts, coord_frame)
pts_1, coord_frame_1 = read_fiducials(temp_fname)
assert_equal(coord_frame, coord_frame_1)
for pt, pt_1 in zip(pts, pts_1):
assert_equal(pt["kind"], pt_1["kind"])
assert_equal(pt["ident"], pt_1["ident"])
assert_equal(pt["coord_frame"], pt_1["coord_frame"])
assert_array_equal(pt["r"], pt_1["r"])
# test safeguards
pts[0]["coord_frame"] += 1
assert_raises(ValueError, write_fiducials, temp_fname, pts, coord_frame)
def test_fiducials_io(tmp_path):
"""Test fiducials i/o."""
pts, coord_frame = read_fiducials(fiducials_fname)
assert pts[0]['coord_frame'] == FIFF.FIFFV_COORD_MRI
assert pts[0]['ident'] == FIFF.FIFFV_POINT_CARDINAL
temp_fname = tmp_path / 'test.fif'
write_fiducials(temp_fname, pts, coord_frame)
pts_1, coord_frame_1 = read_fiducials(temp_fname)
assert coord_frame == coord_frame_1
for pt, pt_1 in zip(pts, pts_1):
assert pt['kind'] == pt_1['kind']
assert pt['ident'] == pt_1['ident']
assert pt['coord_frame'] == pt_1['coord_frame']
assert_array_equal(pt['r'], pt_1['r'])
assert isinstance(pt, DigPoint)
assert isinstance(pt_1, DigPoint)
# test safeguards
pts[0]['coord_frame'] += 1
with pytest.raises(ValueError, match='coord_frame entries that are incom'):
write_fiducials(temp_fname, pts, coord_frame, overwrite=True)
RAS_lpa = vox2ras.dot(lpa_fs)
print('LEFT_EAR: {} '.format(RAS_lpa))
RAS_rpa = vox2ras.dot(rpa_fs)
print('RIGHT_EAR: {}'.format(RAS_rpa))
# FIFF.FIFFV_POINT_LPA = 1
# FIFF.FIFFV_POINT_NASION = 2
# FIFF.FIFFV_POINT_RPA = 3
# Write new fiducial points to fsaverage-fiducials
fiducials = [{'kind': FIFF.FIFFV_POINT_CARDINAL,
'ident': FIFF.FIFFV_POINT_LPA,
'r': np.float32(RAS_lpa)/1000},
{'kind': FIFF.FIFFV_POINT_CARDINAL,
'ident': FIFF.FIFFV_POINT_NASION,
'r': np.float32(RAS_nas)/1000},
{'kind': FIFF.FIFFV_POINT_CARDINAL,
'ident': FIFF.FIFFV_POINT_RPA,
'r': np.float32(RAS_rpa)/1000}]
fiducials_file = op.join(sbj_dir, sbj_FS, 'bem',
sbj_FS + '-fiducials.fif')
write_fiducials(fiducials_file, fiducials, FIFF.FIFFV_COORD_MRI)
print('fsaverage fiducial points \n {} saved in \n {}'.format(
fiducials, fiducials_file))
else:
print('!!! No Freesurfer folder for {}'.format(sbj_FS))
else:
print('!!! No DS folder for {}'.format(sbj_FS))