def _fast_map_meg_channels(inst, pick_from, pick_to, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots.
"""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad,
False,
coils,
my_origin,
'meg',
lut_fun,
n_fact,
n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils, my_origin,
'meg', lut_fun, n_fact).T
return self_dots, cross_dots
_compute_fast_dots = mem.cache(_compute_dots)
info = inst.info.copy()
info['bads'] = [] # if bads is different, hash will be different
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
self_dots, cross_dots = _compute_fast_dots(info, mode=mode)
cross_dots = cross_dots[pick_to, :][:, pick_from]
self_dots = self_dots[pick_from, :][:, pick_from]
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg',
ch_names=ch_names,
origin=my_origin,
noise=noise,
self_dots=self_dots,
surface_dots=cross_dots,
int_rad=int_rad,
miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
return fmd['data']
def _fast_map_meg_channels(info, pick_from, pick_to,
mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
# XXX: hack to silence _compute_mapping_matrix
verbose = mne.get_config('MNE_LOGGING_LEVEL', 'INFO')
mne.set_log_level('WARNING')
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots."""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
_compute_fast_dots = mem.cache(_compute_dots, verbose=0)
info['bads'] = [] # if bads is different, hash will be different
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
# This function needs a clean input. It hates the presence of other
# channels than MEG channels. Make sure all is picked.
self_dots, cross_dots = _compute_fast_dots(
info, mode=mode)
cross_dots = cross_dots[pick_to, :][:, pick_from]
self_dots = self_dots[pick_from, :][:, pick_from]
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg', ch_names=ch_names,
origin=my_origin, noise=noise, self_dots=self_dots,
surface_dots=cross_dots, int_rad=int_rad, miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
mne.set_log_level(verbose)
return fmd['data']
def map_meg_loocv_channels(inst,
pick_from,
pick_to,
self_dots=None,
cross_dots=None,
mode='fast'):
from mne.io.pick import pick_info
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.bem import _check_origin
info_from = pick_info(inst.info, pick_from, copy=True)
info_to = pick_info(inst.info, pick_to, copy=True)
# no need to apply trans because both from and to coils are in device
# coordinates
templates = _read_coil_defs(verbose=False)
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
coils_to = _create_meg_coils(info_to['chs'], 'normal',
info_to['dev_head_t'], templates)
miss = 1e-4 # Smoothing criterion for MEG
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
my_origin = _check_origin((0., 0., 0.04), info_from)
if self_dots is None:
self_dots = _do_self_dots(int_rad,
False,
coils_from,
my_origin,
'meg',
lut_fun,
n_fact,
n_jobs=1)
if cross_dots is None:
cross_dots = _do_cross_dots(int_rad, False, coils_from, coils_to,
my_origin, 'meg', lut_fun, n_fact).T
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg',
ch_names=ch_names,
origin=my_origin,
noise=noise,
self_dots=self_dots,
surface_dots=cross_dots,
int_rad=int_rad,
miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
return fmd['data'], self_dots, cross_dots
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots."""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots.
"""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
def test_utils():
"""Test utils."""
event_id = {'Visual/Left': 3}
tmin, tmax = -0.2, 0.5
events = mne.find_events(raw)
picks = mne.pick_channels(raw.info['ch_names'],
['MEG 2443', 'MEG 2442', 'MEG 2441'])
epochs = mne.Epochs(raw,
events,
event_id,
tmin,
tmax,
picks=picks,
baseline=(None, 0),
reject=None,
preload=True)
this_epoch = epochs.copy()
assert this_epoch.info['bads'] == ['MEG 2443']
epochs_clean = clean_by_interp(this_epoch)
assert this_epoch.info['bads'] == ['MEG 2443']
assert_array_equal(this_epoch.get_data(), epochs.get_data())
pytest.raises(AssertionError, assert_array_equal, epochs_clean.get_data(),
this_epoch.get_data())
picks_meg = mne.pick_types(evoked.info, meg='grad', eeg=False, exclude=[])
picks_eeg = mne.pick_types(evoked.info, meg=False, eeg=True, exclude=[])
picks_bad_meg = mne.pick_channels(evoked.ch_names, include=['MEG 2443'])
picks_bad_eeg = mne.pick_channels(evoked.ch_names, include=['EEG 053'])
evoked_orig = evoked.copy()
for picks, picks_bad in zip([picks_meg, picks_eeg],
[picks_bad_meg, picks_bad_eeg]):
evoked_autoreject = interpolate_bads(evoked,
picks=picks,
reset_bads=False)
evoked.interpolate_bads(reset_bads=False)
assert_array_equal(evoked.data[picks_bad],
evoked_autoreject.data[picks_bad])
pytest.raises(AssertionError, assert_array_equal,
evoked_orig.data[picks_bad], evoked.data[picks_bad])
# test that autoreject EEG interpolation code behaves the same as MNE
evoked_ar = evoked_orig.copy()
evoked_mne = evoked_orig.copy()
origin = _check_origin('auto', evoked_ar.info)
_interpolate_bads_eeg(evoked_ar, picks=None)
mne.channels.interpolation._interpolate_bads_eeg(evoked_mne, origin=origin)
assert_array_almost_equal(evoked_ar.data, evoked_mne.data)
def _fast_map_meg_channels(inst, pick_from, pick_to, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots.
"""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
_compute_fast_dots = mem.cache(_compute_dots)
info = inst.info.copy()
info['bads'] = [] # if bads is different, hash will be different
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
self_dots, cross_dots = _compute_fast_dots(info, mode=mode)
cross_dots = cross_dots[pick_to, :][:, pick_from]
self_dots = self_dots[pick_from, :][:, pick_from]
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg', ch_names=ch_names,
origin=my_origin, noise=noise, self_dots=self_dots,
surface_dots=cross_dots, int_rad=int_rad, miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
return fmd['data']
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots."""
from mne.forward._field_interpolation import _setup_dots
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.bem import _check_origin
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots."""
from mne.forward._field_interpolation import _setup_dots
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.bem import _check_origin
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
def _fast_map_meg_channels(info, pick_from, pick_to, dots=None, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
# XXX: hack to silence _compute_mapping_matrix
verbose = mne.get_config('MNE_LOGGING_LEVEL', 'INFO')
mne.set_log_level('WARNING')
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _patch_setup_dots(
mode, info_from, coils_from, 'meg')
# This function needs a clean input. It hates the presence of other
# channels than MEG channels. Make sure all is picked.
if dots is None:
dots = self_dots, cross_dots = _compute_dots(info, mode=mode)
else:
self_dots, cross_dots = dots
self_dots, cross_dots = _pick_dots(dots, pick_from, pick_to)
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg',
ch_names=ch_names,
origin=my_origin,
noise=noise,
self_dots=self_dots,
surface_dots=cross_dots,
int_rad=int_rad,
miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
mne.set_log_level(verbose)
return fmd['data']
def map_meg_loocv_channels(inst, pick_from, pick_to, self_dots=None,
cross_dots=None, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.bem import _check_origin
info_from = pick_info(inst.info, pick_from, copy=True)
info_to = pick_info(inst.info, pick_to, copy=True)
# no need to apply trans because both from and to coils are in device
# coordinates
templates = _read_coil_defs(verbose=False)
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
coils_to = _create_meg_coils(info_to['chs'], 'normal',
info_to['dev_head_t'], templates)
miss = 1e-4 # Smoothing criterion for MEG
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
my_origin = _check_origin((0., 0., 0.04), info_from)
if self_dots is None:
self_dots = _do_self_dots(int_rad, False, coils_from, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
if cross_dots is None:
cross_dots = _do_cross_dots(int_rad, False, coils_from, coils_to,
my_origin, 'meg', lut_fun, n_fact).T
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg', ch_names=ch_names,
origin=my_origin, noise=noise, self_dots=self_dots,
surface_dots=cross_dots, int_rad=int_rad, miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
return fmd['data'], self_dots, cross_dots
def _fast_map_meg_channels(info, pick_from, pick_to,
dots=None, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
# XXX: hack to silence _compute_mapping_matrix
verbose = mne.get_config('MNE_LOGGING_LEVEL', 'INFO')
mne.set_log_level('WARNING')
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
# This function needs a clean input. It hates the presence of other
# channels than MEG channels. Make sure all is picked.
if dots is None:
dots = self_dots, cross_dots = _compute_dots(info, mode=mode)
else:
self_dots, cross_dots = dots
self_dots, cross_dots = _pick_dots(dots, pick_from, pick_to)
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg', ch_names=ch_names,
origin=my_origin, noise=noise, self_dots=self_dots,
surface_dots=cross_dots, int_rad=int_rad, miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
mne.set_log_level(verbose)
return fmd['data']
