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# Author: Teon Brooks <teon.brooks@gmail.com>
# Stefan Appelhoff <stefan.appelhoff@mailbox.org>
#
# License: BSD (3-clause)
import os
import os.path as op
import pytest
import numpy as np
from scipy.io import savemat
from copy import deepcopy
from functools import partial
from string import ascii_lowercase
from numpy.testing import (assert_array_equal, assert_almost_equal,
assert_allclose, assert_array_almost_equal,
assert_array_less, assert_equal)
from mne import create_info, EvokedArray, read_evokeds, __file__ as _mne_file
from mne.channels import (read_montage, read_dig_montage,
get_builtin_montages, DigMontage,
read_dig_egi, read_dig_captrack, read_dig_fif,
make_standard_montage, read_custom_montage,
compute_dev_head_t, make_dig_montage,
read_dig_polhemus_isotrak,
read_polhemus_fastscan,
read_dig_hpts)
from mne.channels.montage import (_set_montage, transform_to_head,
HEAD_SIZE_DEFAULT)
from mne.channels._dig_montage_utils import _transform_to_head_call
from mne.channels._dig_montage_utils import _fix_data_fiducials
from mne.utils import (_TempDir, run_tests_if_main, assert_dig_allclose,
object_diff, Bunch)
from mne.bem import _fit_sphere
from mne.transforms import apply_trans, get_ras_to_neuromag_trans
from mne.io.constants import FIFF
from mne._digitization import Digitization
from mne._digitization._utils import _read_dig_points, _format_dig_points
from mne._digitization._utils import _get_fid_coords
from mne._digitization.base import _get_dig_eeg, _count_points_by_type
from mne.viz._3d import _fiducial_coords
from mne.io.kit import read_mrk
from mne.io import (read_raw_brainvision, read_raw_egi, read_raw_fif,
read_raw_cnt, read_raw_edf, read_raw_nicolet, read_raw_bdf,
read_raw_eeglab, read_fiducials, __file__ as _MNE_IO_FILE)
from mne.io import RawArray
from mne.datasets import testing
from mne.io.brainvision import __file__ as _BRAINVISON_FILE
data_path = testing.data_path(download=False)
fif_dig_montage_fname = op.join(data_path, 'montage', 'eeganes07.fif')
egi_dig_montage_fname = op.join(data_path, 'montage', 'coordinates.xml')
egi_raw_fname = op.join(data_path, 'montage', 'egi_dig_test.raw')
egi_fif_fname = op.join(data_path, 'montage', 'egi_dig_raw.fif')
bvct_dig_montage_fname = op.join(data_path, 'montage', 'captrak_coords.bvct')
bv_raw_fname = op.join(data_path, 'montage', 'bv_dig_test.vhdr')
bv_fif_fname = op.join(data_path, 'montage', 'bv_dig_raw.fif')
locs_montage_fname = op.join(data_path, 'EEGLAB', 'test_chans.locs')
evoked_fname = op.join(data_path, 'montage', 'level2_raw-ave.fif')
eeglab_fname = op.join(data_path, 'EEGLAB', 'test_raw.set')
bdf_fname1 = op.join(data_path, 'BDF', 'test_generator_2.bdf')
bdf_fname2 = op.join(data_path, 'BDF', 'test_bdf_stim_channel.bdf')
egi_fname1 = op.join(data_path, 'EGI', 'test_egi.mff')
cnt_fname = op.join(data_path, 'CNT', 'scan41_short.cnt')
io_dir = op.dirname(_MNE_IO_FILE)
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')
fif_fname = op.join(io_dir, 'tests', 'data', 'test_raw.fif')
edf_path = op.join(io_dir, 'edf', 'tests', 'data', 'test.edf')
bdf_path = op.join(io_dir, 'edf', 'tests', 'data', 'test_bdf_eeglab.mat')
egi_fname2 = op.join(io_dir, 'egi', 'tests', 'data', 'test_egi.raw')
vhdr_path = op.join(io_dir, 'brainvision', 'tests', 'data', 'test.vhdr')
ctf_fif_fname = op.join(io_dir, 'tests', 'data', 'test_ctf_comp_raw.fif')
nicolet_fname = op.join(io_dir, 'nicolet', 'tests', 'data',
'test_nicolet_raw.data')
def _make_toy_raw(n_channels):
return RawArray(
data=np.empty([n_channels, 1]),
info=create_info(
ch_names=list(ascii_lowercase[:n_channels]),
sfreq=1, ch_types='eeg'
)
)
def _make_toy_dig_montage(n_channels, **kwargs):
return make_dig_montage(
ch_pos=dict(zip(
list(ascii_lowercase[:n_channels]),
np.arange(n_channels * 3).reshape(n_channels, 3),
)),
**kwargs
)
def _get_dig_montage_pos(montage):
return np.array([d['r'] for d in _get_dig_eeg(montage.dig)])
def test_fiducials():
"""Test handling of fiducials."""
# Eventually the code used here should be unified with montage.py, but for
# now it uses code in odd places
for fname in (fif_fname, ctf_fif_fname):
fids, coord_frame = read_fiducials(fname)
points = _fiducial_coords(fids, coord_frame)
assert points.shape == (3, 3)
# Fids
assert_allclose(points[:, 2], 0., atol=1e-6)
assert_allclose(points[::2, 1], 0., atol=1e-6)
assert points[2, 0] > 0 # RPA
assert points[0, 0] < 0 # LPA
# Nasion
assert_allclose(points[1, 0], 0., atol=1e-6)
assert points[1, 1] > 0
def test_documented():
"""Test that montages are documented."""
docs = read_montage.__doc__
lines = [line[4:] for line in docs.splitlines()]
start = stop = None
for li, line in enumerate(lines):
if line.startswith('====') and li < len(lines) - 2 and \
lines[li + 1].startswith('Kind') and\
lines[li + 2].startswith('===='):
start = li + 3
elif start is not None and li > start and line.startswith('===='):
stop = li
break
assert (start is not None)
assert (stop is not None)
kinds = [line.split(' ')[0] for line in lines[start:stop]]
kinds = [kind for kind in kinds if kind != '']
montages = os.listdir(op.join(op.dirname(_mne_file), 'channels', 'data',
'montages'))
montages = sorted(op.splitext(m)[0] for m in montages)
assert_equal(len(set(montages)), len(montages))
assert_equal(len(set(kinds)), len(kinds), err_msg=str(sorted(kinds)))
assert_equal(set(montages), set(kinds))
# XXX: This function tests read_montage and Montage. Should be removed in 0.20
def test_montage():
"""Test making montages."""
tempdir = _TempDir()
inputs = dict(
sfp='FidNz 0 9.071585155 -2.359754454\n'
'FidT9 -6.711765 0.040402876 -3.251600355\n'
'very_very_very_long_name -5.831241498 -4.494821698 4.955347697\n'
'Cz 0 0 8.899186843',
csd='// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa: E501
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa: E501
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n' # noqa: E501
'E31 90.000 -11.000 1.000 0.0000 0.9816 -0.1908 0.00000000000000000\n' # noqa: E501
'E61 158.000 -17.200 1.000 -0.8857 0.3579 -0.2957 -0.00000000000000022', # noqa: E501
mm_elc='# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n' # noqa:E501
'NumberPositions= 68\n'
'Positions\n'
'-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n'
'0.0083 86.8110 -39.9830\n'
'-86.0761 -24.9897 -67.9860\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
m_elc='# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n'
'NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n' # noqa:E501
'.0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n'
'.08 -.02 -.04\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
txt='Site Theta Phi\n'
'Fp1 -92 -72\n'
'Fp2 92 72\n'
'very_very_very_long_name -92 72\n'
'O2 92 -90\n',
elp='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\t FCz\t 68.01\t 58.103\t 85\n',
hpts='eeg Fp1 -95.0 -3. -3.\n'
'eeg AF7 -1 -1 -3\n'
'eeg A3 -2 -2 2\n'
'eeg A 0 0 0',
bvef='<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n'
'<!-- Generated by EasyCap Configurator 19.05.2014 -->\n'
'<Electrodes defaults="false">\n'
' <Electrode>\n'
' <Name>Fp1</Name>\n'
' <Theta>-90</Theta>\n'
' <Phi>-72</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>1</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>Fz</Name>\n'
' <Theta>45</Theta>\n'
' <Phi>90</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>2</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>F3</Name>\n'
' <Theta>-60</Theta>\n'
' <Phi>-51</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>3</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>F7</Name>\n'
' <Theta>-90</Theta>\n'
' <Phi>-36</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>4</Number>\n'
' </Electrode>\n'
'</Electrodes>',
)
# Get actual positions and save them for checking
# csd comes from the string above, all others come from commit 2fa35d4
poss = dict(
sfp=[[0.0, 9.07159, -2.35975], [-6.71176, 0.0404, -3.2516],
[-5.83124, -4.49482, 4.95535], [0.0, 0.0, 8.89919]],
mm_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.08681, -0.03998], [-0.08608, -0.02499, -0.06799]],
m_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.00868, -0.03998], [0.08, -0.02, -0.04]],
txt=[[-26.25044, 80.79056, -2.96646], [26.25044, 80.79056, -2.96646],
[-26.25044, -80.79056, -2.96646], [0.0, -84.94822, -2.96646]],
elp=[[-48.20043, 57.55106, 39.86971], [0.0, 60.73848, 59.4629],
[48.1426, 57.58403, 39.89198], [41.64599, 66.91489, 31.8278]],
hpts=[[-95, -3, -3], [-1, -1., -3.], [-2, -2, 2.], [0, 0, 0]],
bvef=[[-2.62664445e-02, 8.08398039e-02, 5.20474890e-18],
[3.68031324e-18, 6.01040764e-02, 6.01040764e-02],
[-4.63256329e-02, 5.72073923e-02, 4.25000000e-02],
[-6.87664445e-02, 4.99617464e-02, 5.20474890e-18]],
)
for key, text in inputs.items():
kind = key.split('_')[-1]
fname = op.join(tempdir, 'test.' + kind)
with open(fname, 'w') as fid:
fid.write(text)
unit = 'mm' if kind == 'bvef' else 'm'
with pytest.deprecated_call():
montage = read_montage(fname, unit=unit)
if kind in ('sfp', 'txt'):
assert ('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 4)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (4, 3))
assert_equal(montage.kind, 'test')
if kind == '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)
poss['csd'] = np.c_[table['x'], table['y'], table['z']]
if kind == '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)
assert_array_almost_equal(poss[key], montage.pos, 4, err_msg=key)
# Bvef is either auto or mm in terms of "units"
with pytest.raises(ValueError, match='be "auto" or "mm" for .bvef files.'):
bvef_file = op.join(tempdir, 'test.' + 'bvef')
with pytest.deprecated_call():
read_montage(bvef_file, unit='m')
# test transform
input_strs = ["""
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
""", """
Fp1 -95.0 -31.0 -3.0
AF7 -81 -59 -3
AF3 -87 -41 28
FidNz -91 0 -42
FidT9 0 -91 -42
FidT10 0 91 -42
"""]
# sfp files seem to have Nz, T9, and T10 as fiducials:
# https://github.com/mne-tools/mne-python/pull/4482#issuecomment-321980611
kinds = ['test_fid.hpts', 'test_fid.sfp']
for kind, input_str in zip(kinds, input_strs):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
with pytest.deprecated_call():
montage = read_montage(op.join(tempdir, kind), 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)
assert_array_equal(montage.nasion[[0, 2]], [0, 0])
assert_array_equal(montage.lpa[[1, 2]], [0, 0])
assert_array_equal(montage.rpa[[1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, kind)
with pytest.deprecated_call():
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))
with pytest.deprecated_call():
_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)
# test return type as well as set montage
with pytest.deprecated_call():
assert (isinstance(evoked.set_montage(montage), type(evoked)))
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 montage
info = create_info(montage.ch_names + ['foo', 'bar'], 1e3,
['eeg'] * (len(montage.ch_names) + 2))
with pytest.warns(RuntimeWarning, match='position specified'):
_set_montage(info, montage)
# Channel names can be treated case insensitive
info = create_info(['FP1', 'af7', 'AF3'], 1e3, ['eeg'] * 3)
with pytest.deprecated_call():
_set_montage(info, montage)
# Unless there is a collision in names
info = create_info(['FP1', 'Fp1', 'AF3'], 1e3, ['eeg'] * 3)
assert (info['dig'] is None)
with pytest.warns(RuntimeWarning, match='position specified'):
_set_montage(info, montage)
assert len(info['dig']) == 5 # 2 EEG w/pos, 3 fiducials
montage.ch_names = ['FP1', 'Fp1', 'AF3']
info = create_info(['fp1', 'AF3'], 1e3, ['eeg', 'eeg'])
assert (info['dig'] is None)
with pytest.warns(RuntimeWarning, match='position specified'):
_set_montage(info, montage, set_dig=False)
assert (info['dig'] is None)
# test get_builtin_montages function
montages = get_builtin_montages()
assert (len(montages) > 0) # MNE should always ship with montages
assert ("standard_1020" in montages) # 10/20 montage
assert ("standard_1005" in montages) # 10/05 montage
@pytest.mark.parametrize('reader, file_content, expected_dig, ext', [
pytest.param(
partial(read_custom_montage, head_size=None, unit='m'),
('FidNz 0 9.071585155 -2.359754454\n'
'FidT9 -6.711765 0.040402876 -3.251600355\n'
'very_very_very_long_name -5.831241498 -4.494821698 4.955347697\n'
'Cz 0 0 8.899186843'),
make_dig_montage(
ch_pos={
'very_very_very_long_name': [-5.8312416, -4.4948215, 4.9553475], # noqa
'Cz': [0., 0., 8.899187],
},
nasion=[0., 9.071585, -2.3597546],
lpa=[-6.711765, 0.04040287, -3.2516003],
rpa=None,
),
'sfp', id='sfp'),
pytest.param(
partial(read_custom_montage, head_size=1, unit='n/a'),
('1 0 0.50669 FPz\n'
'2 23 0.71 EOG1\n'
'3 -39.947 0.34459 F3\n'
'4 0 0.25338 Fz\n'),
make_dig_montage(
ch_pos={
'EOG1': [0.30873816, 0.72734152, -0.61290705],
'F3': [-0.56705965, 0.67706631, 0.46906776],
'FPz': [0., 0.99977915, -0.02101571],
'Fz': [0., 0.71457525, 0.69955859],
},
nasion=None, lpa=None, rpa=None,
),
'loc', id='EEGLAB'),
pytest.param(
partial(read_custom_montage, head_size=None, unit='m'),
('// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa: E501
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa: E501
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n' # noqa: E501
'E31 90.000 -11.000 1.000 0.0000 0.9816 -0.1908 0.00000000000000000\n' # noqa: E501
'E61 158.000 -17.200 1.000 -0.8857 0.3579 -0.2957 -0.00000000000000022'), # noqa: E501
make_dig_montage(
ch_pos={
'E1': [0.7677, 0.5934, -0.2419],
'E3': [0.6084, 0.7704, 0.1908],
'E31': [0., 0.9816, -0.1908],
'E61': [-0.8857, 0.3579, -0.2957],
},
nasion=None, lpa=None, rpa=None,
),
'csd', id='matlab'),
pytest.param(
partial(read_custom_montage, head_size=None, unit='not_used'),
('# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n'
'NumberPositions= 68\n'
'Positions\n'
'-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n'
'0.0083 86.8110 -39.9830\n'
'-86.0761 -24.9897 -67.9860\n'
'Labels\nLPA\nRPA\nNz\nDummy\n'),
make_dig_montage(
ch_pos={
'Dummy': [-0.0860761, -0.0249897, -0.067986],
},
nasion=[8.3000e-06, 8.6811e-02, -3.9983e-02],
lpa=[-0.0860761, -0.0199897, -0.047986],
rpa=[0.0857939, -0.0200093, -0.048031],
),
'elc', id='ASA electrode'),
pytest.param(
partial(read_custom_montage, head_size=1, unit='n/a'),
('Site Theta Phi\n'
'Fp1 -92 -72\n'
'Fp2 92 72\n'
'very_very_very_long_name -92 72\n'
'O2 92 -90\n'),
make_dig_montage(
ch_pos={
'Fp1': [-0.30882875, 0.95047716, -0.0348995],
'Fp2': [0.30882875, 0.95047716, -0.0348995],
'very_very_very_long_name': [-0.30882875, -0.95047716, -0.0348995], # noqa
'O2': [6.11950389e-17, -9.99390827e-01, -3.48994967e-02]
},
nasion=None, lpa=None, rpa=None,
),
'txt', id='generic theta-phi (txt)'),
pytest.param(
partial(read_custom_montage, head_size=None, unit='n/a'),
('346\n' # XXX: this should actually race an error 346 != 4
'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\t FCz\t 68.01\t 58.103\t 85\n'),
make_dig_montage(
ch_pos={
'F3': [-0.48200427, 0.57551063, 0.39869712],
'Fz': [3.71915931e-17, 6.07384809e-01, 5.94629038e-01],
'F4': [0.48142596, 0.57584026, 0.39891983],
'FCz': [0.41645989, 0.66914889, 0.31827805],
},
nasion=None, lpa=None, rpa=None,
),
'elp', id='BESA spherical model'),
pytest.param(
partial(read_dig_hpts, unit='m'),
('eeg Fp1 -95.0 -3. -3.\n'
'eeg AF7 -1 -1 -3\n'
'eeg A3 -2 -2 2\n'
'eeg A 0 0 0'),
make_dig_montage(
ch_pos={
'A': [0., 0., 0.], 'A3': [-2., -2., 2.],
'AF7': [-1., -1., -3.], 'Fp1': [-95., -3., -3.],
},
nasion=None, lpa=None, rpa=None,
),
'hpts', id='legacy mne-c'),
pytest.param(
partial(read_custom_montage, head_size=None, unit='mm'),
('<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n'
'<!-- Generated by EasyCap Configurator 19.05.2014 -->\n'
'<Electrodes defaults="false">\n'
' <Electrode>\n'
' <Name>Fp1</Name>\n'
' <Theta>-90</Theta>\n'
' <Phi>-72</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>1</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>Fz</Name>\n'
' <Theta>45</Theta>\n'
' <Phi>90</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>2</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>F3</Name>\n'
' <Theta>-60</Theta>\n'
' <Phi>-51</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>3</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>F7</Name>\n'
' <Theta>-90</Theta>\n'
' <Phi>-36</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>4</Number>\n'
' </Electrode>\n'
'</Electrodes>'),
make_dig_montage(
ch_pos={
'Fp1': [-3.09016994e-01, 9.51056516e-01, 6.12323400e-17],
'Fz': [4.32978028e-17, 7.07106781e-01, 7.07106781e-01],
'F3': [-0.54500745, 0.67302815, 0.5],
'F7': [-8.09016994e-01, 5.87785252e-01, 6.12323400e-17],
},
nasion=None, lpa=None, rpa=None,
),
'bvef', id='brainvision'),
])
def test_montage_readers(
reader, file_content, expected_dig, ext, tmpdir
):
"""Test that we have an equivalent of read_montage for all file formats."""
fname = op.join(str(tmpdir), 'test.{ext}'.format(ext=ext))
with open(fname, 'w') as fid:
fid.write(file_content)
dig_montage = reader(fname)
assert isinstance(dig_montage, DigMontage)
actual_ch_pos = dig_montage._get_ch_pos()
expected_ch_pos = expected_dig._get_ch_pos()
for kk in actual_ch_pos:
assert_allclose(actual_ch_pos[kk], expected_ch_pos[kk], atol=1e-5)
@testing.requires_testing_data
def test_read_locs():
"""Test reading EEGLAB locs."""
data = read_custom_montage(locs_montage_fname)._get_ch_pos()
assert_allclose(
actual=np.stack(
[data[kk] for kk in ('FPz', 'EOG1', 'F3', 'Fz')] # 4 random chs
),
desired=[[0., 0.094979, -0.001996],
[0.02933, 0.069097, -0.058226],
[-0.053871, 0.064321, 0.044561],
[0., 0.067885, 0.066458]],
atol=1e-6
)
def test_read_dig_montage():
"""Test read_dig_montage."""
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
with pytest.deprecated_call():
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)
with pytest.deprecated_call():
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')
with pytest.deprecated_call():
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.)
with pytest.deprecated_call():
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)
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_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_polhemus_isotrak_hsp():
"""Test reading Polhemus IsoTrak HSP file."""
EXPECTED_FID_IN_POLHEMUS = {
'nasion': np.array([1.1056e-01, -5.4210e-19, 0]),
'lpa': np.array([-2.1075e-04, 8.0793e-02, -7.5894e-19]),
'rpa': np.array([2.1075e-04, -8.0793e-02, -2.8731e-18]),
}
montage = read_dig_polhemus_isotrak(fname=op.join(kit_dir, 'test.hsp'),
ch_names=None)
assert repr(montage) == (
'<DigMontage | '
'500 extras (headshape), 0 HPIs, 3 fiducials, 0 channels>'
)
fiducials, fid_coordframe = _get_fid_coords(montage.dig)
assert fid_coordframe == FIFF.FIFFV_COORD_UNKNOWN
for kk, val in fiducials.items():
assert_array_equal(val, EXPECTED_FID_IN_POLHEMUS[kk])
def test_read_dig_polhemus_isotrak_elp():
"""Test reading Polhemus IsoTrak ELP file."""
EXPECTED_FID_IN_POLHEMUS = {
'nasion': np.array([1.1056e-01, -5.4210e-19, 0]),
'lpa': np.array([-2.1075e-04, 8.0793e-02, -7.5894e-19]),
'rpa': np.array([2.1075e-04, -8.0793e-02, -2.8731e-18]),
}
montage = read_dig_polhemus_isotrak(fname=op.join(kit_dir, 'test.elp'),
ch_names=None)
assert repr(montage) == (
'<DigMontage | '
'0 extras (headshape), 5 HPIs, 3 fiducials, 0 channels>'
)
fiducials, fid_coordframe = _get_fid_coords(montage.dig)
assert fid_coordframe == FIFF.FIFFV_COORD_UNKNOWN
for kk, val in fiducials.items():
assert_array_equal(val, EXPECTED_FID_IN_POLHEMUS[kk])
@pytest.fixture(scope='module')
def isotrak_eeg(tmpdir_factory):
"""Mock isotrak file with EEG positions."""
_SEED = 42
N_ROWS, N_COLS = 5, 3
content = np.random.RandomState(_SEED).randn(N_ROWS, N_COLS)
fname = tmpdir_factory.mktemp('data').join('test.eeg')
with open(str(fname), 'w') as fid:
fid.write((
'3 200\n'
'//Shape file\n'
'//Minor revision number\n'
'2\n'
'//Subject Name\n'
'%N Name \n'
'////Shape code, number of digitized points\n'
))
fid.write('0 {rows:d}\n'.format(rows=N_ROWS))
fid.write((
'//Position of fiducials X+, Y+, Y- on the subject\n'
'%F 0.11056 -5.421e-19 0 \n'
'%F -0.00021075 0.080793 -7.5894e-19 \n'
'%F 0.00021075 -0.080793 -2.8731e-18 \n'
'//No of rows, no of columns; position of digitized points\n'
))
fid.write('{rows:d} {cols:d}\n'.format(rows=N_ROWS, cols=N_COLS))
for row in content:
fid.write('\t'.join('%0.18e' % cell for cell in row) + '\n')
return str(fname)
def test_read_dig_polhemus_isotrak_eeg(isotrak_eeg):
"""Test reading Polhemus IsoTrak EEG positions."""
N_CHANNELS = 5
_SEED = 42
EXPECTED_FID_IN_POLHEMUS = {
'nasion': np.array([1.1056e-01, -5.4210e-19, 0]),
'lpa': np.array([-2.1075e-04, 8.0793e-02, -7.5894e-19]),
'rpa': np.array([2.1075e-04, -8.0793e-02, -2.8731e-18]),
}
ch_names = ['eeg {:01d}'.format(ii) for ii in range(N_CHANNELS)]
EXPECTED_CH_POS = dict(zip(
ch_names, np.random.RandomState(_SEED).randn(N_CHANNELS, 3)))
montage = read_dig_polhemus_isotrak(fname=isotrak_eeg, ch_names=ch_names)
assert repr(montage) == (
'<DigMontage | '
'0 extras (headshape), 0 HPIs, 3 fiducials, 5 channels>'
)
fiducials, fid_coordframe = _get_fid_coords(montage.dig)
assert fid_coordframe == FIFF.FIFFV_COORD_UNKNOWN
for kk, val in fiducials.items():
assert_array_equal(val, EXPECTED_FID_IN_POLHEMUS[kk])
for kk, dig_point in zip(montage.ch_names, _get_dig_eeg(montage.dig)):
assert_array_equal(dig_point['r'], EXPECTED_CH_POS[kk])
assert dig_point['coord_frame'] == FIFF.FIFFV_COORD_UNKNOWN
def test_read_dig_polhemus_isotrak_error_handling(isotrak_eeg, tmpdir):
"""Test errors in reading Polhemus IsoTrak files.
1 - matching ch_names and number of points in isotrak file.
2 - error for unsupported file extensions.
"""
# Check ch_names
N_CHANNELS = 5
EXPECTED_ERR_MSG = "not match the number of points.*Expected.*5, given 47"
with pytest.raises(ValueError, match=EXPECTED_ERR_MSG):
_ = read_dig_polhemus_isotrak(
fname=isotrak_eeg,
ch_names=['eeg {:01d}'.format(ii) for ii in range(N_CHANNELS + 42)]
)
# Check fname extensions
fname = op.join(tmpdir, 'foo.bar')
with pytest.raises(
ValueError,
match="Allowed val.*'.hsp', '.elp' and '.eeg', but got '.bar' instead"
):
_ = read_dig_polhemus_isotrak(fname=fname, ch_names=None)
def test_combining_digmontage_objects():
"""Test combining different DigMontage objects."""
rng = np.random.RandomState(0)
fiducials = dict(zip(('nasion', 'lpa', 'rpa'), rng.rand(3, 3)))
# hsp positions are [1X, 1X, 1X]
hsp1 = make_dig_montage(**fiducials, hsp=np.full((2, 3), 11.))
hsp2 = make_dig_montage(**fiducials, hsp=np.full((2, 3), 12.))
hsp3 = make_dig_montage(**fiducials, hsp=np.full((2, 3), 13.))
# hpi positions are [2X, 2X, 2X]
hpi1 = make_dig_montage(**fiducials, hpi=np.full((2, 3), 21.))
hpi2 = make_dig_montage(**fiducials, hpi=np.full((2, 3), 22.))
hpi3 = make_dig_montage(**fiducials, hpi=np.full((2, 3), 23.))
# channels have positions at 40s, 50s, and 60s.
ch_pos1 = make_dig_montage(
**fiducials,
ch_pos={'h': [41, 41, 41], 'b': [42, 42, 42], 'g': [43, 43, 43]}
)
ch_pos2 = make_dig_montage(
**fiducials,
ch_pos={'n': [51, 51, 51], 'y': [52, 52, 52], 'p': [53, 53, 53]}
)
ch_pos3 = make_dig_montage(
**fiducials,
ch_pos={'v': [61, 61, 61], 'a': [62, 62, 62], 'l': [63, 63, 63]}
)
montage = (
DigMontage() + hsp1 + hsp2 + hsp3 + hpi1 + hpi2 + hpi3 + ch_pos1 +
ch_pos2 + ch_pos3
)
assert repr(montage) == (
'<DigMontage | '
'6 extras (headshape), 6 HPIs, 3 fiducials, 9 channels>'
)
EXPECTED_MONTAGE = make_dig_montage(
**fiducials,
hsp=np.concatenate([np.full((2, 3), 11.), np.full((2, 3), 12.),
np.full((2, 3), 13.)]),
hpi=np.concatenate([np.full((2, 3), 21.), np.full((2, 3), 22.),
np.full((2, 3), 23.)]),
ch_pos={
'h': [41, 41, 41], 'b': [42, 42, 42], 'g': [43, 43, 43],
'n': [51, 51, 51], 'y': [52, 52, 52], 'p': [53, 53, 53],
'v': [61, 61, 61], 'a': [62, 62, 62], 'l': [63, 63, 63],
}
)
# Do some checks to ensure they are the same DigMontage
assert len(montage.ch_names) == len(EXPECTED_MONTAGE.ch_names)
assert all([c in montage.ch_names for c in EXPECTED_MONTAGE.ch_names])
actual_occurrences = _count_points_by_type(montage.dig)
expected_occurrences = _count_points_by_type(EXPECTED_MONTAGE.dig)
assert actual_occurrences == expected_occurrences
def test_combining_digmontage_forbiden_behaviors():
"""Test combining different DigMontage objects with repeated names."""
rng = np.random.RandomState(0)
fiducials = dict(zip(('nasion', 'lpa', 'rpa'), rng.rand(3, 3)))
dig1 = make_dig_montage(
**fiducials,
ch_pos=dict(zip(list('abc'), rng.rand(3, 3))),
)
dig2 = make_dig_montage(
**fiducials,
ch_pos=dict(zip(list('bcd'), rng.rand(3, 3))),
)
dig2_wrong_fid = make_dig_montage(
nasion=rng.rand(3), lpa=rng.rand(3), rpa=rng.rand(3),
ch_pos=dict(zip(list('ghi'), rng.rand(3, 3))),
)
dig2_wrong_coordframe = make_dig_montage(
**fiducials,
ch_pos=dict(zip(list('ghi'), rng.rand(3, 3))),
coord_frame='meg'
)
EXPECTED_ERR_MSG = "Cannot.*duplicated channel.*found: \'b\', \'c\'."
with pytest.raises(RuntimeError, match=EXPECTED_ERR_MSG):
_ = dig1 + dig2
with pytest.raises(RuntimeError, match='fiducial locations do not match'):
_ = dig1 + dig2_wrong_fid
with pytest.raises(RuntimeError, match='not in the same coordinate '):
_ = dig1 + dig2_wrong_coordframe
def test_set_dig_montage_old():
"""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)
with pytest.deprecated_call():
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():
_ = read_dig_montage(fif=fname_temp)
def test_set_dig_montage():
"""Test setting DigMontage with toy understandable points."""
N_CHANNELS, N_HSP, N_HPI = 3, 2, 1
ch_names = list(ascii_lowercase[:N_CHANNELS])
ch_pos = dict(zip(
ch_names,
np.arange(N_CHANNELS * 3).reshape(N_CHANNELS, 3),
))
montage_ch_only = make_dig_montage(ch_pos=ch_pos, coord_frame='head')
assert repr(montage_ch_only) == (
'<DigMontage | 0 extras (headshape), 0 HPIs, 0 fiducials, 3 channels>'
)
info = create_info(ch_names, sfreq=1, ch_types='eeg',
montage=montage_ch_only)
assert len(info['dig']) == len(montage_ch_only.dig)
assert_allclose(actual=np.array([ch['loc'][:6] for ch in info['chs']]),
desired=[[0., 1., 2., 0., 0., 0.],
[3., 4., 5., 0., 0., 0.],
[6., 7., 8., 0., 0., 0.]])
montage_full = make_dig_montage(
ch_pos=dict(**ch_pos, EEG000=np.full(3, 42)), # 4 = 3 egg + 1 eeg_ref
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 repr(montage_full) == (
'<DigMontage | 2 extras (headshape), 1 HPIs, 3 fiducials, 4 channels>'
)
info = create_info(ch_names, sfreq=1, ch_types='eeg', montage=montage_full)
EXPECTED_LEN = sum({'hsp': 2, 'hpi': 1, 'fid': 3, 'eeg': 4}.values())
assert len(info['dig']) == EXPECTED_LEN
assert_allclose(actual=np.array([ch['loc'][:6] for ch in info['chs']]),
desired=[[0., 1., 2., 42., 42., 42.],
[3., 4., 5., 42., 42., 42.],
[6., 7., 8., 42., 42., 42.]])
@testing.requires_testing_data
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)
# 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) == ''
@testing.requires_testing_data
def test_egi_dig_montage():
"""Test EGI MFF XML dig montage support."""
dig_montage = read_dig_egi(egi_dig_montage_fname)
fid, coord = _get_fid_coords(dig_montage.dig)
assert coord == FIFF.FIFFV_COORD_UNKNOWN
assert_allclose(
actual=np.array([fid[key] for key in ['nasion', 'lpa', 'rpa']]),
desired=[[ 0. , 10.564, -2.051], # noqa
[-8.592, 0.498, -4.128], # noqa
[ 8.592, 0.498, -4.128]], # noqa
)
# Test accuracy and embedding within raw object
raw_egi = read_raw_egi(egi_raw_fname, channel_naming='EEG %03d')
raw_egi.set_montage(dig_montage)
test_raw_egi = read_raw_fif(egi_fif_fname)
assert_equal(len(raw_egi.ch_names), len(test_raw_egi.ch_names))
for ch_raw, ch_test_raw in zip(raw_egi.info['chs'],
test_raw_egi.info['chs']):
assert_equal(ch_raw['ch_name'], ch_test_raw['ch_name'])
assert_equal(ch_raw['coord_frame'], FIFF.FIFFV_COORD_HEAD)
assert_allclose(ch_raw['loc'], ch_test_raw['loc'], atol=1e-7)
assert_dig_allclose(raw_egi.info, test_raw_egi.info)
dig_montage_in_head = transform_to_head(dig_montage.copy())
fid, coord = _get_fid_coords(dig_montage_in_head.dig)
assert coord == FIFF.FIFFV_COORD_HEAD
assert_allclose(
actual=np.array([fid[key] for key in ['nasion', 'lpa', 'rpa']]),
desired=[[0., 10.278, 0.], [-8.592, 0., 0.], [8.592, 0., 0.]],
atol=1e-4,
)
# test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'egi_test.fif')
_check_roundtrip(dig_montage_in_head, fname_temp) # XXX: write forces head
# Test old way matches new way
with pytest.deprecated_call():
dig_montage = read_dig_montage(egi=egi_dig_montage_fname, unit='m')
dig_montage_egi = read_dig_egi(egi_dig_montage_fname)
dig_montage_egi = transform_to_head(dig_montage_egi)
assert dig_montage.dig == dig_montage_egi.dig
assert object_diff(dig_montage.ch_names, dig_montage_egi.ch_names) == ''
def _pop_montage(dig_montage, ch_name):
# remove reference that was not used in old API
name_idx = dig_montage.ch_names.index(ch_name)
dig_idx = dig_montage._get_dig_names().index(ch_name)
del dig_montage.dig[dig_idx]
del dig_montage.ch_names[name_idx]
for k in range(dig_idx, len(dig_montage.dig)):
dig_montage.dig[k]['ident'] -= 1
@testing.requires_testing_data
def test_bvct_dig_montage_old_api(): # XXX: to remove in 0.20
"""Test BrainVision CapTrak XML dig montage support."""
with pytest.warns(RuntimeWarning, match='Using "m" as unit for BVCT file'):
read_dig_montage(bvct=bvct_dig_montage_fname, unit='m')
with pytest.deprecated_call():
dig_montage = read_dig_montage(bvct=bvct_dig_montage_fname)
_pop_montage(dig_montage, 'REF')
_pop_montage(dig_montage, 'GND')
# test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'bvct_test.fif')
_check_roundtrip(dig_montage, fname_temp)
with pytest.deprecated_call():
# nasion
assert_almost_equal(dig_montage.nasion[0], 0)
assert_almost_equal(dig_montage.nasion[2], 0)
# lpa and rpa
assert_allclose(dig_montage.lpa[1:], 0, atol=1e-16)
assert_allclose(dig_montage.rpa[1:], 0, atol=1e-16)
# Test accuracy and embedding within raw object
raw_bv = read_raw_brainvision(bv_raw_fname)
with pytest.warns(RuntimeWarning, match='Did not set 3 channel positions'):
raw_bv.set_montage(dig_montage, raise_if_subset=False)
test_raw_bv = read_raw_fif(bv_fif_fname)
assert_equal(len(raw_bv.ch_names), len(test_raw_bv.ch_names))
for ch_raw, ch_test_raw in zip(raw_bv.info['chs'],
test_raw_bv.info['chs']):
assert_equal(ch_raw['ch_name'], ch_test_raw['ch_name'])
assert_equal(ch_raw['coord_frame'], FIFF.FIFFV_COORD_HEAD)
assert_allclose(ch_raw['loc'][:3], ch_test_raw['loc'][:3], atol=1e-7)
assert_dig_allclose(raw_bv.info, test_raw_bv.info)
@testing.requires_testing_data
def test_read_dig_captrack(tmpdir):
"""Test reading a captrack montage file."""
EXPECTED_CH_NAMES = [
'AF3', 'AF4', 'AF7', 'AF8', 'C1', 'C2', 'C3', 'C4', 'C5', 'C6', 'CP1',
'CP2', 'CP3', 'CP4', 'CP5', 'CP6', 'CPz', 'Cz', 'F1', 'F2', 'F3', 'F4',
'F5', 'F6', 'F7', 'F8', 'FC1', 'FC2', 'FC3', 'FC4', 'FC5', 'FC6',
'FT10', 'FT7', 'FT8', 'FT9', 'Fp1', 'Fp2', 'Fz', 'GND', 'O1', 'O2',
'Oz', 'P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'PO10', 'PO3',
'PO4', 'PO7', 'PO8', 'PO9', 'POz', 'Pz', 'REF', 'T7', 'T8', 'TP10',
'TP7', 'TP8', 'TP9'
]
montage = read_dig_captrack(
fname=op.join(data_path, 'montage', 'captrak_coords.bvct')
)
assert montage.ch_names == EXPECTED_CH_NAMES
assert repr(montage) == (
'<DigMontage | '
'0 extras (headshape), 0 HPIs, 3 fiducials, 66 channels>'
)
montage = transform_to_head(montage) # transform_to_head has to be tested
_check_roundtrip(montage=montage, fname=str(tmpdir.join('bvct_test.fif')))
with pytest.deprecated_call():
assert_allclose(
actual=np.array([montage.nasion, montage.lpa, montage.rpa]),
desired=[[0, 0.11309, 0], [-0.09189, 0, 0], [0.09240, 0, 0]],
atol=1e-5,
)
raw_bv = read_raw_brainvision(bv_raw_fname)
raw_bv.set_channel_types({"HEOG": 'eog', "VEOG": 'eog', "ECG": 'ecg'})
raw_bv.set_montage(montage)
test_raw_bv = read_raw_fif(bv_fif_fname)
# compare after set_montage using chs loc.
for actual, expected in zip(raw_bv.info['chs'], test_raw_bv.info['chs']):
assert_allclose(actual['loc'][:3], expected['loc'][:3])
if actual['kind'] == FIFF.FIFFV_EEG_CH:
assert_allclose(actual['loc'][3:6],
[-0.005103, 0.05395, 0.144622], rtol=1e-04)
def test_set_montage():
"""Test setting 'mgh60' montage to old fif."""
raw = read_raw_fif(fif_fname)
raw.rename_channels(lambda x: x.replace('EEG ', 'EEG'))
orig_pos = np.array([ch['loc'][:3] for ch in raw.info['chs']
if ch['ch_name'].startswith('EEG')])
raw.set_montage('mgh60') # test loading with string argument
new_pos = np.array([ch['loc'][:3] for ch in raw.info['chs']
if ch['ch_name'].startswith('EEG')])
assert ((orig_pos != new_pos).all())
r0 = _fit_sphere(new_pos)[1]
assert_allclose(r0, [0.000775, 0.006881, 0.047398], atol=1e-3)
# XXX: this does not check ch_names + it cannot work because of write_dig
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 _fake_montage(ch_names):
pos = np.random.RandomState(42).randn(len(ch_names), 3)
return make_dig_montage(ch_pos=dict(zip(ch_names, pos)),
coord_frame='head')
cnt_ignore_warns = [
pytest.mark.filterwarnings(
'ignore:.*Could not parse meas date from the header. Setting to None.'
),
pytest.mark.filterwarnings((
'ignore:.*Could not define the number of bytes automatically.'
' Defaulting to 2.')
),
]
@testing.requires_testing_data
@pytest.mark.parametrize('read_raw,fname', [
pytest.param(partial(read_raw_nicolet, ch_type='eeg'),
nicolet_fname,
id='nicolet'),
pytest.param(read_raw_eeglab, eeglab_fname, id='eeglab'),
pytest.param(read_raw_edf, edf_path, id='edf'),
pytest.param(read_raw_bdf, bdf_path,
marks=pytest.mark.xfail(raises=NotImplementedError),
id='bdf 1'),
pytest.param(read_raw_bdf, bdf_fname1, id='bdf 2'),
pytest.param(read_raw_bdf, bdf_fname2, id='bdf 3'),
pytest.param(read_raw_egi, egi_fname1, id='egi mff'),
pytest.param(read_raw_egi, egi_fname2,
marks=pytest.mark.filterwarnings('ignore:.*than one event'),
id='egi raw'),
pytest.param(partial(read_raw_cnt, eog='auto', misc=['NA1', 'LEFT_EAR']),
cnt_fname, marks=cnt_ignore_warns, id='cnt'),
pytest.param(read_raw_brainvision, vhdr_path, id='brainvision'),
])
def test_montage_when_reading_and_setting(read_raw, fname):
"""Test montage.
This is a regression test to help refactor Digitization.
"""
with pytest.deprecated_call():
raw_none = read_raw(fname, montage=None, preload=False)
# raw_none_copy = deepcopy(raw_none)
montage = _fake_montage(raw_none.info['ch_names'])
with pytest.deprecated_call():
raw_montage = read_raw(fname, montage=montage, preload=False)
raw_none.set_montage(montage)
# Check that reading with montage or setting the montage is the same
assert_array_equal(raw_none.get_data(), raw_montage.get_data())
assert object_diff(raw_none.info['dig'], raw_montage.info['dig']) == ''
assert object_diff(raw_none.info['chs'], raw_montage.info['chs']) == ''
@testing.requires_testing_data
@pytest.mark.parametrize('read_raw,fname', [
pytest.param(partial(read_raw_nicolet, ch_type='eeg'),
nicolet_fname,
marks=pytest.mark.skip,
id='nicolet'),
pytest.param(read_raw_eeglab, eeglab_fname,
marks=pytest.mark.skip,
id='eeglab'),
pytest.param(read_raw_edf, edf_path, id='edf'),
pytest.param(read_raw_bdf, bdf_path,
marks=pytest.mark.xfail(raises=NotImplementedError),
id='bdf 1'),
pytest.param(read_raw_bdf, bdf_fname1, id='bdf 2'),
pytest.param(read_raw_bdf, bdf_fname2, id='bdf 3'),
pytest.param(read_raw_egi, egi_fname1,
marks=pytest.mark.skip,
id='egi mff'),
pytest.param(read_raw_egi, egi_fname2,
marks=pytest.mark.filterwarnings('ignore:.*than one event'),
id='egi raw'),
pytest.param(partial(read_raw_cnt, eog='auto', misc=['NA1', 'LEFT_EAR']),
cnt_fname,
marks=[*cnt_ignore_warns, pytest.mark.skip],
id='cnt'),
pytest.param(read_raw_brainvision, vhdr_path,
marks=pytest.mark.skip,
id='brainvision'),
])
def test_montage_when_reading_and_setting_more(read_raw, fname):
"""Test montage.
This is a regression test to help refactor Digitization.
"""
with pytest.deprecated_call():
raw_none = read_raw(fname, montage=None, preload=False)
raw_none_copy = deepcopy(raw_none)
# check consistency between reading and setting with montage=None
assert raw_none_copy.info['dig'] is None
original_chs = deepcopy(raw_none_copy.info['chs'])
original_loc = np.array([ch['loc'] for ch in original_chs])
assert_array_equal(original_loc, np.zeros_like(original_loc))
raw_none_copy.set_montage(montage=None)
loc = np.array([ch['loc'] for ch in raw_none_copy.info['chs']])
assert_array_equal(loc, np.full_like(loc, np.NaN))
# XXX: deprecated to remove in 0.20, we are testing DigMontages somewhere else
# plus the positions are off. They don't fit HEAD_SIZE_DEFAULT
EXPECTED_DIG_RPR = [
'<DigPoint | LPA : (-6.7, 0.0, -3.3) mm : head frame>', # FidT9 [-6.711765 0.04040288 -3.25160035] # noqa
'<DigPoint | Nasion : (0.0, 9.1, -2.4) mm : head frame>', # FidNz [ 0. 9.07158515 -2.35975445] # noqa
'<DigPoint | RPA : (6.7, 0.0, -3.3) mm : head frame>', # FidT10 [ 6.711765 0.04040288 -3.25160035] # noqa
'<DigPoint | EEG #1 : (-2.7, 8.9, 1.1) mm : head frame>', # E1 [-2.69540556 8.88482032 1.08830814] # noqa
'<DigPoint | EEG #2 : (2.7, 8.9, 1.1) mm : head frame>', # E2 [2.69540556 8.88482032 1.08830814] # noqa
'<DigPoint | EEG #3 : (-4.5, 6.0, 4.4) mm : head frame>', # E3 [-4.45938719 6.02115996 4.36532148] # noqa
'<DigPoint | EEG #4 : (4.5, 6.0, 4.4) mm : head frame>', # E4 [4.45938719 6.02115996 4.36532148] # noqa
'<DigPoint | EEG #5 : (-5.5, 0.3, 6.4) mm : head frame>', # E5 [-5.47913021 0.28494865 6.38332782] # noqa
'<DigPoint | EEG #6 : (5.5, 0.3, 6.4) mm : head frame>', # E6 [5.47913021 0.28494865 6.38332782] # noqa
'<DigPoint | EEG #7 : (-5.8, -4.5, 5.0) mm : head frame>', # E7 [-5.8312415 -4.4948217 4.9553477] # noqa
'<DigPoint | EEG #8 : (5.8, -4.5, 5.0) mm : head frame>', # E8 [ 5.8312415 -4.4948217 4.9553477] # noqa
'<DigPoint | EEG #9 : (-2.7, -8.6, 0.2) mm : head frame>', # E9 [-2.73883802 -8.60796685 0.23936822] # noqa
'<DigPoint | EEG #10 : (2.7, -8.6, 0.2) mm : head frame>', # E10 [ 2.73883802 -8.60796685 0.23936822] # noqa
'<DigPoint | EEG #11 : (-6.4, 4.1, -0.4) mm : head frame>', # E11 [-6.3990872 4.12724888 -0.35685224] # noqa
'<DigPoint | EEG #12 : (6.4, 4.1, -0.4) mm : head frame>', # E12 [ 6.3990872 4.12724888 -0.35685224] # noqa
'<DigPoint | EEG #13 : (-7.3, -1.9, -0.6) mm : head frame>', # E13 [-7.3046251 -1.86623801 -0.62918201] # noqa
'<DigPoint | EEG #14 : (7.3, -1.9, -0.6) mm : head frame>', # E14 [ 7.3046251 -1.86623801 -0.62918201] # noqa
'<DigPoint | EEG #15 : (-6.0, -5.8, 0.1) mm : head frame>', # E15 [-6.03474684 -5.7557822 0.05184301] # noqa
'<DigPoint | EEG #16 : (6.0, -5.8, 0.1) mm : head frame>', # E16 [ 6.03474684 -5.7557822 0.05184301] # noqa
'<DigPoint | EEG #17 : (0.0, 8.0, 5.0) mm : head frame>', # E17 [0. 7.96264703 5.044718 ] # noqa
'<DigPoint | EEG #18 : (0.0, 9.3, -2.2) mm : head frame>', # E18 [ 0. 9.2711397 -2.21151643] # noqa
'<DigPoint | EEG #19 : (0.0, -6.7, 6.5) mm : head frame>', # E19 [ 0. -6.67669403 6.46520826] # noqa
'<DigPoint | EEG #20 : (0.0, -9.0, 0.5) mm : head frame>', # E20 [ 0. -8.9966865 0.48795205] # noqa
'<DigPoint | EEG #21 : (-6.5, 2.4, -5.3) mm : head frame>', # E21 [-6.51899513 2.4172994 -5.25363707] # noqa
'<DigPoint | EEG #22 : (6.5, 2.4, -5.3) mm : head frame>', # E22 [ 6.51899513 2.4172994 -5.25363707] # noqa
'<DigPoint | EEG #23 : (-6.2, -2.5, -5.6) mm : head frame>', # E23 [-6.17496939 -2.45813888 -5.637381 ] # noqa
'<DigPoint | EEG #24 : (6.2, -2.5, -5.6) mm : head frame>', # E24 [ 6.17496939 -2.45813888 -5.637381 ] # noqa
'<DigPoint | EEG #25 : (-3.8, -6.4, -5.3) mm : head frame>', # E25 [-3.78498391 -6.40101441 -5.26004069] # noqa
'<DigPoint | EEG #26 : (3.8, -6.4, -5.3) mm : head frame>', # E26 [ 3.78498391 -6.40101441 -5.26004069] # noqa
'<DigPoint | EEG #27 : (0.0, 9.1, 1.3) mm : head frame>', # E27 [0. 9.08744089 1.33334501] # noqa
'<DigPoint | EEG #28 : (0.0, 3.8, 7.9) mm : head frame>', # E28 [0. 3.80677022 7.89130496] # noqa
'<DigPoint | EEG #29 : (-3.7, 6.6, -6.5) mm : head frame>', # E29 [-3.74350495 6.64920491 -6.53024307] # noqa
'<DigPoint | EEG #30 : (3.7, 6.6, -6.5) mm : head frame>', # E30 [ 3.74350495 6.64920491 -6.53024307] # noqa
'<DigPoint | EEG #31 : (-6.1, 4.5, -4.4) mm : head frame>', # E31 [-6.11845814 4.52387011 -4.40917443] # noqa
'<DigPoint | EEG #32 : (6.1, 4.5, -4.4) mm : head frame>', # E32 [ 6.11845814 4.52387011 -4.40917443] # noqa
]
# XXX : to remove in 0.20 (tested separately in test_montage_readers and
# test_set_montage functions)
def test_setting_hydrocel_montage():
"""Test set_montage using GSN-HydroCel-32."""
with pytest.deprecated_call():
montage = read_montage('GSN-HydroCel-32')
ch_names = [name for name in montage.ch_names if name.startswith('E')]
montage.pos /= 1e3
raw = RawArray(
data=np.empty([len(ch_names), 1]),
info=create_info(ch_names=ch_names, sfreq=1, ch_types='eeg')
)
with pytest.deprecated_call():
raw.set_montage(montage)
# test info['chs']
_slice = [name.startswith('E') for name in montage.ch_names]
_slice = np.array(_slice, dtype=bool)
EXPECTED_CHS_POS = montage.pos[_slice, :] # Shall this be in the same units as info['dig'] ?? # noqa
actual_pos = np.array([ch['loc'][:3] for ch in raw.info['chs']])
assert_array_equal(actual_pos, EXPECTED_CHS_POS)
# test info['dig']
for actual, expected in zip([str(d) for d in raw.info['dig']],
EXPECTED_DIG_RPR):
assert actual == expected
def test_dig_dev_head_t_regression():
"""Test deprecated compute_dev_head_t behavior."""
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)
del data['coord_frame']
with pytest.deprecated_call():
montage = DigMontage(**data)
return montage
EXPECTED_DEV_HEAD_T = \
[[-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]]
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
montage = _read_dig_montage(
hsp, hpi, elp, names, transform=True, dev_head_t=False)
assert montage.dev_head_t is None
with pytest.deprecated_call():
montage.compute_dev_head_t()
assert_allclose(montage.dev_head_t, EXPECTED_DEV_HEAD_T, atol=1e-7)
def test_digmontage_constructor_errors():
"""Test proper error messaging."""
with pytest.raises(ValueError, match='does not match the number'):
_ = DigMontage(ch_names=['foo', 'bar'], dig=Digitization())
def test_transform_to_head_and_compute_dev_head_t():
"""Test transform_to_head and compute_dev_head_t."""
EXPECTED_DEV_HEAD_T = \
[[-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]]
EXPECTED_FID_IN_POLHEMUS = {
'nasion': np.array([0.001393, 0.0131613, -0.0046967]),
'lpa': np.array([-0.0624997, -0.0737271, 0.07996]),
'rpa': np.array([-0.0748957, 0.0873785, 0.0811943]),
}
EXPECTED_FID_IN_HEAD = {
'nasion': np.array([-8.94466792e-18, 1.10559624e-01, -3.85185989e-34]),
'lpa': np.array([-8.10816716e-02, 6.56321671e-18, 0]),
'rpa': np.array([8.05048781e-02, -6.47441364e-18, 0]),
}
hpi_dev = np.array(
[[ 2.13951493e-02, 8.47444056e-02, -5.65431188e-02], # noqa
[ 2.10299433e-02, -8.03141101e-02, -6.34420259e-02], # noqa
[ 1.05916829e-01, 8.18485672e-05, 1.19928083e-02], # noqa
[ 9.26595105e-02, 4.64804385e-02, 8.45141253e-03], # noqa
[ 9.42554419e-02, -4.35206589e-02, 8.78999363e-03]] # noqa
)
hpi_polhemus = np.array(
[[-0.0595004, -0.0704836, 0.075893 ], # noqa
[-0.0646373, 0.0838228, 0.0762123], # noqa
[-0.0135035, 0.0072522, -0.0268405], # noqa
[-0.0202967, -0.0351498, -0.0129305], # noqa
[-0.0277519, 0.0452628, -0.0222407]] # noqa
)
montage_polhemus = make_dig_montage(
**EXPECTED_FID_IN_POLHEMUS, hpi=hpi_polhemus, coord_frame='unknown'
)
montage_meg = make_dig_montage(hpi=hpi_dev, coord_frame='meg')
# Test regular worflow to get dev_head_t
montage = montage_polhemus + montage_meg
fids, _ = _get_fid_coords(montage.dig)
for kk in fids:
assert_allclose(fids[kk], EXPECTED_FID_IN_POLHEMUS[kk], atol=1e-5)
with pytest.raises(ValueError, match='set to head coordinate system'):
_ = compute_dev_head_t(montage)
montage = transform_to_head(montage)
fids, _ = _get_fid_coords(montage.dig)
for kk in fids:
assert_allclose(fids[kk], EXPECTED_FID_IN_HEAD[kk], atol=1e-5)
dev_head_t = compute_dev_head_t(montage)
assert_allclose(dev_head_t['trans'], EXPECTED_DEV_HEAD_T, atol=1e-7)
# Test errors when number of HPI points do not match
EXPECTED_ERR_MSG = 'Device-to-Head .*Got 0 .*device and 5 points in head'
with pytest.raises(ValueError, match=EXPECTED_ERR_MSG):
_ = compute_dev_head_t(transform_to_head(montage_polhemus))
EXPECTED_ERR_MSG = 'Device-to-Head .*Got 5 .*device and 0 points in head'
with pytest.raises(ValueError, match=EXPECTED_ERR_MSG):
_ = compute_dev_head_t(transform_to_head(
montage_meg + make_dig_montage(**EXPECTED_FID_IN_POLHEMUS)
))
EXPECTED_ERR_MSG = 'Device-to-Head .*Got 3 .*device and 5 points in head'
with pytest.raises(ValueError, match=EXPECTED_ERR_MSG):
_ = compute_dev_head_t(transform_to_head(
DigMontage(dig=_format_dig_points(montage_meg.dig[:3])) +
montage_polhemus
))
def test_set_montage_with_mismatching_ch_names():
"""Test setting a DigMontage with mismatching ch_names."""
raw = read_raw_fif(fif_fname)
montage = make_standard_montage('mgh60')
# 'EEG 001' and 'EEG001' won't match
with pytest.warns(RuntimeWarning, match='not set 60 channel positions'):
raw.set_montage(montage, raise_if_subset=False)
montage.ch_names = [ # modify the names in place
name.replace('EEG', 'EEG ') for name in montage.ch_names
]
raw.set_montage(montage) # does not raise
def test_set_montage_with_sub_super_set_of_ch_names():
"""Test info and montage ch_names matching criteria."""
N_CHANNELS = len('abcdef')
montage = _make_toy_dig_montage(N_CHANNELS, coord_frame='head')
# Montage and info match
_ = create_info(
ch_names=list('abcdef'), sfreq=1, ch_types='eeg', montage=montage
)
# Montage is a SUPERset of info
info = create_info(
ch_names=list('abc'), sfreq=1, ch_types='eeg', montage=montage
)
assert len(info['dig']) == len(list('abc'))
# Montage is a SUBset of info
_MSG = 'subset of info. There are 2 .* not present it the DigMontage'
with pytest.raises(ValueError, match=_MSG):
_ = create_info(
ch_names=list('abcdfgh'), sfreq=1, ch_types='eeg', montage=montage
)
def test_heterogeneous_ch_type():
"""Test ch_names matching criteria with heterogeneous ch_type."""
VALID_MONTAGE_NAMED_CHS = ('eeg', 'ecog', 'seeg')
montage = _make_toy_dig_montage(
n_channels=len(VALID_MONTAGE_NAMED_CHS),
coord_frame='head',
)
# Montage and info match
_ = create_info(
ch_names=montage.ch_names,
ch_types=list(VALID_MONTAGE_NAMED_CHS),
montage=montage,
sfreq=1,
)
def test_set_montage_coord_frame_in_head_vs_unknown():
"""Test set montage using head and unknown only."""
N_CHANNELS, NaN = 3, np.nan
raw = _make_toy_raw(N_CHANNELS)
montage_in_head = _make_toy_dig_montage(N_CHANNELS, coord_frame='head')
montage_in_unknown = _make_toy_dig_montage(
N_CHANNELS, coord_frame='unknown'
)
montage_in_unknown_with_fid = _make_toy_dig_montage(
N_CHANNELS, coord_frame='unknown',
nasion=[0, 1, 0], lpa=[1, 0, 0], rpa=[-1, 0, 0],
)
assert_allclose(
actual=np.array([ch['loc'] for ch in raw.info['chs']]),
desired=np.full((N_CHANNELS, 12), np.nan)
)
raw.set_montage(montage_in_head)
assert_allclose(
actual=np.array([ch['loc'] for ch in raw.info['chs']]),
desired=[
[0., 1., 2., 0., 0., 0., NaN, NaN, NaN, NaN, NaN, NaN],
[3., 4., 5., 0., 0., 0., NaN, NaN, NaN, NaN, NaN, NaN],
[6., 7., 8., 0., 0., 0., NaN, NaN, NaN, NaN, NaN, NaN],
]
)
_MSG = 'Points have to be provided as one dimensional arrays of length 3.'
with pytest.raises(ValueError, match=_MSG):
raw.set_montage(montage_in_unknown)
raw.set_montage(montage_in_unknown_with_fid)
assert_allclose(
actual=np.array([ch['loc'] for ch in raw.info['chs']]),
desired=[
[-0., 1., -2., 0., 0., 0., NaN, NaN, NaN, NaN, NaN, NaN],
[-3., 4., -5., 0., 0., 0., NaN, NaN, NaN, NaN, NaN, NaN],
[-6., 7., -8., 0., 0., 0., NaN, NaN, NaN, NaN, NaN, NaN],
]
)
# check no collateral effects from transforming montage
assert montage_in_unknown_with_fid._coord_frame == 'unknown'
assert_array_equal(
_get_dig_montage_pos(montage_in_unknown_with_fid),
[[0, 1, 2], [3, 4, 5], [6, 7, 8]],
)
def test_set_dig_montage_parameters_deprecation():
"""Test parameter deprecation for set_montage."""
N_CHANNELS = 3
raw = _make_toy_raw(N_CHANNELS)
montage = _make_toy_dig_montage(N_CHANNELS, coord_frame='head')
# ok
raw.set_montage(montage)
with pytest.deprecated_call():
raw.set_montage(montage, set_dig=True)
with pytest.deprecated_call():
_set_montage(raw.info, montage, update_ch_names=False)
def test_read_dig_hpts():
"""Test reading .hpts file (from MNE legacy)."""
fname = op.join(
op.dirname(_BRAINVISON_FILE), 'tests', 'data', 'test.hpts'
)
montage = read_dig_hpts(fname)
assert repr(montage) == (
'<DigMontage | '
'0 extras (headshape), 5 HPIs, 3 fiducials, 34 channels>'
)
# XXX should be removed in 0.20
@testing.requires_testing_data
def test_read_custom_montage_vs_old_on_loc_eeglab():
"""Test reading EEGLAB locations data."""
with pytest.deprecated_call():
old = read_montage(locs_montage_fname)
old.pos *= HEAD_SIZE_DEFAULT # read_montage was not scaling for loc files
new = read_custom_montage(locs_montage_fname)
# compare montages
old_ch_pos = {kk: vv for kk, vv in zip(old.ch_names, old.pos)}
new_ch_pos = new._get_ch_pos()
for kk in old.ch_names:
assert_allclose(new_ch_pos[kk], old_ch_pos[kk])
run_tests_if_main()
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