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# Author: Teon Brooks <teon.brooks@gmail.com>
#
# License: BSD (3-clause)
import os.path as op
import warnings
from nose.tools import assert_equal, assert_true, assert_raises
import numpy as np
from numpy.testing import (assert_array_equal, assert_almost_equal,
assert_allclose, assert_array_almost_equal,
assert_array_less)
from mne.tests.common import assert_dig_allclose
from mne.channels.montage import read_montage, _set_montage, read_dig_montage
from mne.utils import _TempDir, run_tests_if_main
from mne import create_info, EvokedArray, read_evokeds
from mne.coreg import fit_matched_points
from mne.transforms import apply_trans, get_ras_to_neuromag_trans
from mne.io.constants import FIFF
from mne.io.meas_info import _read_dig_points
from mne.io.kit import read_mrk
from mne.io import read_raw_brainvision
from mne.datasets import testing
data_path = testing.data_path(download=False)
fif_dig_montage_fname = op.join(data_path, 'montage', 'eeganes07.fif')
evoked_fname = op.join(data_path, 'montage', 'level2_raw-ave.fif')
io_dir = op.join(op.dirname(__file__), '..', '..', 'io')
kit_dir = op.join(io_dir, 'kit', 'tests', 'data')
elp = op.join(kit_dir, 'test_elp.txt')
hsp = op.join(kit_dir, 'test_hsp.txt')
hpi = op.join(kit_dir, 'test_mrk.sqd')
bv_fname = op.join(io_dir, 'brainvision', 'tests', 'data', 'test.vhdr')
def test_montage():
"""Test making montages"""
tempdir = _TempDir()
# no pep8
input_str = [
'FidNz 0.00000 10.56381 -2.05108\nFidT9 -7.82694 0.45386 -3.76056\n'
'very_very_very_long_name 7.82694 0.45386 -3.76056',
'// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa
'E2 44.600 -0.880 1.000 0.7119 0.7021 -0.0154 0.00000000000000000\n' # noqa
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000', # noqa
'# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n'
'NumberPositions= 68\nPositions\n-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n0.0083 86.8110 -39.9830\n'
'Labels\nLPA\nRPA\nNz\n',
'# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n'
'NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n'
'.0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n'
'Labels\nLPA\nRPA\nNz\n',
'Site Theta Phi\nFp1 -92 -72\nFp2 92 72\n'
'very_very_very_long_name -60 -51\n',
'346\n'
'EEG\t F3\t -62.027\t -50.053\t 85\n'
'EEG\t Fz\t 45.608\t 90\t 85\n'
'EEG\t F4\t 62.01\t 50.103\t 85\n',
'eeg Fp1 -95.0 -31.0 -3.0\neeg AF7 -81 -59 -3\neeg AF3 -87 -41 28\n'
]
kinds = ['test.sfp', 'test.csd', 'test_mm.elc', 'test_m.elc', 'test.txt',
'test.elp', 'test.hpts']
for kind, text in zip(kinds, input_str):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
if ".sfp" in kind or ".txt" in kind:
assert_true('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 3)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (3, 3))
assert_equal(montage.kind, op.splitext(kind)[0])
if kind.endswith('csd'):
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
pos2 = np.c_[table['x'], table['y'], table['z']]
assert_array_almost_equal(pos2, montage.pos, 4)
if kind.endswith('elc'):
# Make sure points are reasonable distance from geometric centroid
centroid = np.sum(montage.pos, axis=0) / montage.pos.shape[0]
distance_from_centroid = np.apply_along_axis(
np.linalg.norm, 1,
montage.pos - centroid)
assert_array_less(distance_from_centroid, 0.2)
assert_array_less(0.01, distance_from_centroid)
# test transform
input_str = """
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
"""
kind = 'test_fid.hpts'
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, 'test_fid.hpts'), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index('2')
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index('1')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index('3')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, 'test_fid.hpts')
montage = read_montage(montage_fname, unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
info = create_info(
montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
evoked = EvokedArray(
data=np.zeros((len(montage.ch_names), 1)), info=info, tmin=0)
evoked.set_montage(montage)
pos3 = np.array([c['loc'][:3] for c in evoked.info['chs']])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info['ch_names'])
# Warning should be raised when some EEG are not specified in the montage
with warnings.catch_warnings(record=True) as w:
info = create_info(montage.ch_names + ['foo', 'bar'], 1e3,
['eeg'] * (len(montage.ch_names) + 2))
_set_montage(info, montage)
assert_true(len(w) == 1)
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)
assert_equal(montage.point_names, names)
assert_array_equal(montage.elp, elp_points)
assert_array_equal(montage.hsp, hsp_points)
assert_array_equal(montage.hpi, hpi_points)
assert_array_equal(montage.dev_head_t, np.identity(4))
montage = read_dig_montage(hsp, hpi, elp, names,
transform=True, dev_head_t=True)
# check coordinate transformation
# nasion
assert_almost_equal(montage.nasion[0], 0)
assert_almost_equal(montage.nasion[2], 0)
# lpa and rpa
assert_allclose(montage.lpa[1:], 0, atol=1e-16)
assert_allclose(montage.rpa[1:], 0, atol=1e-16)
# device head transform
dev_head_t = fit_matched_points(tgt_pts=montage.elp,
src_pts=montage.hpi, out='trans')
assert_array_equal(montage.dev_head_t, dev_head_t)
# Digitizer as array
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)
assert_allclose(m3.hsp, montage.hsp)
# test unit parameter
montage_cm = read_dig_montage(hsp, hpi, elp, names, unit='cm')
assert_allclose(montage_cm.hsp, montage.hsp * 10.)
assert_allclose(montage_cm.elp, montage.elp * 10.)
assert_array_equal(montage_cm.hpi, montage.hpi)
assert_raises(ValueError, read_dig_montage, hsp, hpi, elp, names,
unit='km')
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)
hpi_points = read_mrk(hpi)
p0, p1, p2 = elp_points[:3]
nm_trans = get_ras_to_neuromag_trans(p0, p1, p2)
elp_points = apply_trans(nm_trans, elp_points)
nasion_point, lpa_point, rpa_point = elp_points[:3]
hsp_points = apply_trans(nm_trans, hsp_points)
montage = read_dig_montage(hsp, hpi, elp, names, transform=True)
info = create_info(['Test Ch'], 1e3, ['eeg'])
_set_montage(info, montage)
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_array_equal(hs, hsp_points)
assert_array_equal(nasion_dig.ravel(), nasion_point)
assert_array_equal(lpa_dig.ravel(), lpa_point)
assert_array_equal(rpa_dig.ravel(), rpa_point)
assert_array_equal(hpi_dig, hpi_points)
assert_array_equal(montage.dev_head_t, info['dev_head_t']['trans'])
@testing.requires_testing_data
def test_fif_dig_montage():
"""Test FIF dig montage support"""
dig_montage = read_dig_montage(fif=fif_dig_montage_fname)
# Make a BrainVision file like the one the user would have had
with warnings.catch_warnings(record=True) as w:
raw_bv = read_raw_brainvision(bv_fname, preload=True)
assert_true(any('will be dropped' in str(ww.message) for ww in w))
raw_bv_2 = raw_bv.copy()
mapping = dict()
for ii, ch_name in enumerate(raw_bv.ch_names[:-1]):
mapping[ch_name] = 'EEG%03d' % (ii + 1,)
raw_bv.rename_channels(mapping)
for ii, ch_name in enumerate(raw_bv_2.ch_names[:-1]):
mapping[ch_name] = 'EEG%03d' % (ii + 33,)
raw_bv_2.rename_channels(mapping)
raw_bv.drop_channels(['STI 014'])
raw_bv.add_channels([raw_bv_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))
for ch_py, ch_c in zip(raw_bv.info['chs'], evoked.info['chs']):
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)
assert_allclose(ch_py['loc'], ch_c['loc'])
assert_dig_allclose(raw_bv.info, evoked.info)
run_tests_if_main()
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