def run():
t0 = time.time()
parser = get_optparser(__file__)
parser.add_option("--raw",
dest="raw_in",
help="Input raw FIF file",
metavar="FILE")
parser.add_option("--pos",
dest="pos",
default=None,
help="Position definition text file. Can be 'constant' "
"to hold the head position fixed",
metavar="FILE")
parser.add_option("--dipoles",
dest="dipoles",
default=None,
help="Dipole definition file",
metavar="FILE")
parser.add_option("--cov",
dest="cov",
help="Covariance to use for noise generation. Can be "
"'simple' to use a diagonal covariance, or 'off' to "
"omit noise",
metavar="FILE",
default='simple')
parser.add_option("--duration",
dest="duration",
default=None,
help="Duration of each epoch (sec). If omitted, the last"
" time point in the dipole definition file plus 200 ms "
"will be used",
type="float")
parser.add_option("-j",
"--jobs",
dest="n_jobs",
help="Number of jobs to"
" run in parallel",
type="int",
default=1)
parser.add_option("--out",
dest="raw_out",
help="Output raw filename",
metavar="FILE")
parser.add_option("--plot-dipoles",
dest="plot_dipoles",
help="Plot "
"input dipole positions",
action="store_true")
parser.add_option("--plot-raw",
dest="plot_raw",
help="Plot the resulting "
"raw traces",
action="store_true")
parser.add_option("--plot-evoked",
dest="plot_evoked",
help="Plot evoked "
"data",
action="store_true")
parser.add_option("-p",
"--plot",
dest="plot",
help="Plot dipoles, raw, "
"and evoked",
action="store_true")
parser.add_option("--overwrite",
dest="overwrite",
help="Overwrite the"
"output file if it exists",
action="store_true")
options, args = parser.parse_args()
raw_in = options.raw_in
pos = options.pos
raw_out = options.raw_out
dipoles = options.dipoles
n_jobs = options.n_jobs
plot = options.plot
plot_dipoles = options.plot_dipoles or plot
plot_raw = options.plot_raw or plot
plot_evoked = options.plot_evoked or plot
overwrite = options.overwrite
duration = options.duration
cov = options.cov
# check parameters
if not (raw_out or plot_raw or plot_evoked):
raise ValueError('data must either be saved (--out) or '
'plotted (--plot-raw or --plot_evoked)')
if raw_out and op.isfile(raw_out) and not overwrite:
raise ValueError('output file exists, use --overwrite (%s)' % raw_out)
if raw_in is None or pos is None or dipoles is None:
parser.print_help()
sys.exit(1)
s = 'Simulate raw data with head movements'
print('\n%s\n%s\n%s\n' % ('-' * len(s), s, '-' * len(s)))
# setup the simulation
with printer('Reading dipole definitions'):
if not op.isfile(dipoles):
raise IOError('dipole file not found:\n%s' % dipoles)
dipoles = np.loadtxt(dipoles, skiprows=1, dtype=float)
n_dipoles = dipoles.shape[0]
if dipoles.shape[1] != 8:
raise ValueError('dipoles must have 8 columns')
rr = dipoles[:, :3] * 1e-3
nn = dipoles[:, 3:6]
t = dipoles[:, 6:8]
duration = t.max() + 0.2 if duration is None else duration
if (t[:, 0] > t[:, 1]).any():
raise ValueError('found tmin > tmax in dipole file')
if (t < 0).any():
raise ValueError('found t < 0 in dipole file')
if (t > duration).any():
raise ValueError('found t > duration in dipole file')
amp = np.sqrt(np.sum(nn * nn, axis=1)) * 1e-9
mne.surface._normalize_vectors(nn)
nn[(nn == 0).all(axis=1)] = (1, 0, 0)
src = mne.SourceSpaces([
dict(rr=rr,
nn=nn,
inuse=np.ones(n_dipoles, int),
coord_frame=FIFF.FIFFV_COORD_HEAD)
])
for key in ['pinfo', 'nuse_tri', 'use_tris', 'patch_inds']:
src[0][key] = None
trans = {
'from': FIFF.FIFFV_COORD_HEAD,
'to': FIFF.FIFFV_COORD_MRI,
'trans': np.eye(4)
}
if (amp > 100e-9).any():
print('')
warnings.warn('Largest dipole amplitude %0.1f > 100 nA' %
(amp.max() * 1e9))
if pos == 'constant':
print('Holding head position constant')
pos = None
else:
with printer('Loading head positions'):
pos = mne.get_chpi_positions(pos)
with printer('Loading raw data file'):
with warnings.catch_warnings(record=True):
raw = mne.io.Raw(raw_in,
preload=False,
allow_maxshield=True,
verbose=False)
if cov == 'simple':
print('Using diagonal covariance for brain noise')
elif cov == 'off':
print('Omitting brain noise in the simulation')
cov = None
else:
with printer('Loading covariance file for brain noise'):
cov = mne.read_cov(cov)
with printer('Setting up spherical model'):
bem = mne.bem.make_sphere_model('auto',
'auto',
raw.info,
verbose=False)
# check that our sources are reasonable
rad = bem['layers'][0]['rad']
r0 = bem['r0']
outside = np.sqrt(np.sum((rr - r0)**2, axis=1)) >= rad
n_outside = outside.sum()
if n_outside > 0:
print('')
raise ValueError(
'%s dipole%s outside the spherical model, are your positions '
'in mm?' % (n_outside, 's were' if n_outside != 1 else ' was'))
with printer('Constructing source estimate'):
tmids = t.mean(axis=1)
t = np.round(t * raw.info['sfreq']).astype(int)
t[:, 1] += 1 # make it inclusive
n_samp = int(np.ceil(duration * raw.info['sfreq']))
data = np.zeros((n_dipoles, n_samp))
for di, (t_, amp_) in enumerate(zip(t, amp)):
data[di, t_[0]:t_[1]] = amp_ * np.hanning(t_[1] - t_[0])
stc = mne.VolSourceEstimate(data, np.arange(n_dipoles), 0,
1. / raw.info['sfreq'])
# do the simulation
print('')
raw_mv = simulate_raw(raw,
stc,
trans,
src,
bem,
cov=cov,
head_pos=pos,
chpi=True,
n_jobs=n_jobs,
verbose=True)
print('')
if raw_out:
with printer('Saving data'):
raw_mv.save(raw_out, overwrite=overwrite)
# plot results -- must be *after* save because we low-pass filter
if plot_dipoles:
with printer('Plotting dipoles'):
fig, axs = plt.subplots(1, 3, figsize=(10, 3), facecolor='w')
fig.canvas.set_window_title('Dipoles')
meg_info = mne.pick_info(
raw.info, mne.pick_types(raw.info, meg=True, eeg=False))
helmet_rr = [
ch['coil_trans'][:3, 3].copy() for ch in meg_info['chs']
]
helmet_nn = np.zeros_like(helmet_rr)
helmet_nn[:, 2] = 1.
surf = dict(rr=helmet_rr,
nn=helmet_nn,
coord_frame=FIFF.FIFFV_COORD_DEVICE)
helmet_rr = mne.surface.transform_surface_to(
surf, 'head', meg_info['dev_head_t'])['rr']
p = np.linspace(0, 2 * np.pi, 40)
x_sphere, y_sphere = rad * np.sin(p), rad * np.cos(p)
for ai, ax in enumerate(axs):
others = np.setdiff1d(np.arange(3), [ai])
ax.plot(helmet_rr[:, others[0]],
helmet_rr[:, others[1]],
marker='o',
linestyle='none',
alpha=0.1,
markeredgecolor='none',
markerfacecolor='b',
zorder=-2)
ax.plot(x_sphere + r0[others[0]],
y_sphere + r0[others[1]],
color='y',
alpha=0.25,
zorder=-1)
ax.quiver(rr[:, others[0]],
rr[:, others[1]],
amp * nn[:, others[0]],
amp * nn[:, others[1]],
angles='xy',
units='x',
color='k',
alpha=0.5)
ax.set_aspect('equal')
ax.set_xlabel(' - ' + 'xyz'[others[0]] + ' + ')
ax.set_ylabel(' - ' + 'xyz'[others[1]] + ' + ')
ax.set_xticks([])
ax.set_yticks([])
plt.setp(list(ax.spines.values()), color='none')
plt.tight_layout()
if plot_raw or plot_evoked:
with printer('Low-pass filtering simulated data'):
events = mne.find_events(raw_mv, 'STI101', verbose=False)
b, a = signal.butter(4,
40. / (raw.info['sfreq'] / 2.),
'low',
analog=False)
raw_mv.filter(None,
40.,
method='iir',
iir_params=dict(b=b, a=a),
verbose=False,
n_jobs=n_jobs)
if plot_raw:
with printer('Plotting raw data'):
raw_mv.plot(clipping='transparent', events=events, show=False)
if plot_evoked:
with printer('Plotting evoked data'):
picks = mne.pick_types(raw_mv.info, meg=True, eeg=True)
events[:, 2] = 1
evoked = mne.Epochs(raw_mv, events, {
'Simulated': 1
}, 0, duration, None, picks).average()
evoked.plot_topomap(np.unique(tmids), show=False)
print('\nTotal time: %0.1f sec' % (time.time() - t0))
sys.stdout.flush()
if any([plot_dipoles, plot_raw, plot_evoked]):
plt.show(block=True)
def run():
t0 = time.time()
parser = get_optparser(__file__)
parser.add_option("--raw", dest="raw_in",
help="Input raw FIF file", metavar="FILE")
parser.add_option("--pos", dest="pos", default=None,
help="Position definition text file. Can be 'constant' "
"to hold the head position fixed", metavar="FILE")
parser.add_option("--dipoles", dest="dipoles", default=None,
help="Dipole definition file", metavar="FILE")
parser.add_option("--cov", dest="cov",
help="Covariance to use for noise generation. Can be "
"'simple' to use a diagonal covariance, or 'off' to "
"omit noise",
metavar="FILE", default='simple')
parser.add_option("--duration", dest="duration", default=None,
help="Duration of each epoch (sec). If omitted, the last"
" time point in the dipole definition file plus 200 ms "
"will be used", type="float")
parser.add_option("-j", "--jobs", dest="n_jobs", help="Number of jobs to"
" run in parallel", type="int", default=1)
parser.add_option("--out", dest="raw_out",
help="Output raw filename", metavar="FILE")
parser.add_option("--plot-dipoles", dest="plot_dipoles", help="Plot "
"input dipole positions", action="store_true")
parser.add_option("--plot-raw", dest="plot_raw", help="Plot the resulting "
"raw traces", action="store_true")
parser.add_option("--plot-evoked", dest="plot_evoked", help="Plot evoked "
"data", action="store_true")
parser.add_option("-p", "--plot", dest="plot", help="Plot dipoles, raw, "
"and evoked", action="store_true")
parser.add_option("--overwrite", dest="overwrite", help="Overwrite the"
"output file if it exists", action="store_true")
options, args = parser.parse_args()
raw_in = options.raw_in
pos = options.pos
raw_out = options.raw_out
dipoles = options.dipoles
n_jobs = options.n_jobs
plot = options.plot
plot_dipoles = options.plot_dipoles or plot
plot_raw = options.plot_raw or plot
plot_evoked = options.plot_evoked or plot
overwrite = options.overwrite
duration = options.duration
cov = options.cov
# check parameters
if not (raw_out or plot_raw or plot_evoked):
raise ValueError('data must either be saved (--out) or '
'plotted (--plot-raw or --plot_evoked)')
if raw_out and op.isfile(raw_out) and not overwrite:
raise ValueError('output file exists, use --overwrite (%s)' % raw_out)
if raw_in is None or pos is None or dipoles is None:
parser.print_help()
sys.exit(1)
s = 'Simulate raw data with head movements'
print('\n%s\n%s\n%s\n' % ('-' * len(s), s, '-' * len(s)))
# setup the simulation
with printer('Reading dipole definitions'):
if not op.isfile(dipoles):
raise IOError('dipole file not found:\n%s' % dipoles)
dipoles = np.loadtxt(dipoles, skiprows=1, dtype=float)
n_dipoles = dipoles.shape[0]
if dipoles.shape[1] != 8:
raise ValueError('dipoles must have 8 columns')
rr = dipoles[:, :3] * 1e-3
nn = dipoles[:, 3:6]
t = dipoles[:, 6:8]
duration = t.max() + 0.2 if duration is None else duration
if (t[:, 0] > t[:, 1]).any():
raise ValueError('found tmin > tmax in dipole file')
if (t < 0).any():
raise ValueError('found t < 0 in dipole file')
if (t > duration).any():
raise ValueError('found t > duration in dipole file')
amp = np.sqrt(np.sum(nn * nn, axis=1)) * 1e-9
mne.surface._normalize_vectors(nn)
nn[(nn == 0).all(axis=1)] = (1, 0, 0)
src = mne.SourceSpaces([
dict(rr=rr, nn=nn, inuse=np.ones(n_dipoles, int),
coord_frame=FIFF.FIFFV_COORD_HEAD)])
for key in ['pinfo', 'nuse_tri', 'use_tris', 'patch_inds']:
src[0][key] = None
trans = {'from': FIFF.FIFFV_COORD_HEAD, 'to': FIFF.FIFFV_COORD_MRI,
'trans': np.eye(4)}
if (amp > 100e-9).any():
print('')
warnings.warn('Largest dipole amplitude %0.1f > 100 nA'
% (amp.max() * 1e9))
if pos == 'constant':
print('Holding head position constant')
pos = None
else:
with printer('Loading head positions'):
pos = mne.get_chpi_positions(pos)
with printer('Loading raw data file'):
with warnings.catch_warnings(record=True):
raw = mne.io.Raw(raw_in, preload=False, allow_maxshield=True,
verbose=False)
if cov == 'simple':
print('Using diagonal covariance for brain noise')
elif cov == 'off':
print('Omitting brain noise in the simulation')
cov = None
else:
with printer('Loading covariance file for brain noise'):
cov = mne.read_cov(cov)
with printer('Setting up spherical model'):
bem = mne.bem.make_sphere_model('auto', 'auto', raw.info,
verbose=False)
# check that our sources are reasonable
rad = bem['layers'][0]['rad']
r0 = bem['r0']
outside = np.sqrt(np.sum((rr - r0) ** 2, axis=1)) >= rad
n_outside = outside.sum()
if n_outside > 0:
print('')
raise ValueError(
'%s dipole%s outside the spherical model, are your positions '
'in mm?' % (n_outside, 's were' if n_outside != 1 else ' was'))
with printer('Constructing source estimate'):
tmids = t.mean(axis=1)
t = np.round(t * raw.info['sfreq']).astype(int)
t[:, 1] += 1 # make it inclusive
n_samp = int(np.ceil(duration * raw.info['sfreq']))
data = np.zeros((n_dipoles, n_samp))
for di, (t_, amp_) in enumerate(zip(t, amp)):
data[di, t_[0]:t_[1]] = amp_ * np.hanning(t_[1] - t_[0])
stc = mne.VolSourceEstimate(data, np.arange(n_dipoles),
0, 1. / raw.info['sfreq'])
# do the simulation
print('')
raw_mv = simulate_raw(raw, stc, trans, src, bem, cov=cov, head_pos=pos,
chpi=True, n_jobs=n_jobs, verbose=True)
print('')
if raw_out:
with printer('Saving data'):
raw_mv.save(raw_out, overwrite=overwrite)
# plot results -- must be *after* save because we low-pass filter
if plot_dipoles:
with printer('Plotting dipoles'):
fig, axs = plt.subplots(1, 3, figsize=(10, 3), facecolor='w')
fig.canvas.set_window_title('Dipoles')
meg_info = mne.pick_info(raw.info,
mne.pick_types(raw.info,
meg=True, eeg=False))
helmet_rr = [ch['coil_trans'][:3, 3].copy()
for ch in meg_info['chs']]
helmet_nn = np.zeros_like(helmet_rr)
helmet_nn[:, 2] = 1.
surf = dict(rr=helmet_rr, nn=helmet_nn,
coord_frame=FIFF.FIFFV_COORD_DEVICE)
helmet_rr = mne.surface.transform_surface_to(
surf, 'head', meg_info['dev_head_t'])['rr']
p = np.linspace(0, 2 * np.pi, 40)
x_sphere, y_sphere = rad * np.sin(p), rad * np.cos(p)
for ai, ax in enumerate(axs):
others = np.setdiff1d(np.arange(3), [ai])
ax.plot(helmet_rr[:, others[0]], helmet_rr[:, others[1]],
marker='o', linestyle='none', alpha=0.1,
markeredgecolor='none', markerfacecolor='b', zorder=-2)
ax.plot(x_sphere + r0[others[0]], y_sphere + r0[others[1]],
color='y', alpha=0.25, zorder=-1)
ax.quiver(rr[:, others[0]], rr[:, others[1]],
amp * nn[:, others[0]], amp * nn[:, others[1]],
angles='xy', units='x', color='k', alpha=0.5)
ax.set_aspect('equal')
ax.set_xlabel(' - ' + 'xyz'[others[0]] + ' + ')
ax.set_ylabel(' - ' + 'xyz'[others[1]] + ' + ')
ax.set_xticks([])
ax.set_yticks([])
plt.setp(list(ax.spines.values()), color='none')
plt.tight_layout()
if plot_raw or plot_evoked:
with printer('Low-pass filtering simulated data'):
events = mne.find_events(raw_mv, 'STI101', verbose=False)
b, a = signal.butter(4, 40. / (raw.info['sfreq'] / 2.), 'low',
analog=False)
raw_mv.filter(None, 40., method='iir', iir_params=dict(b=b, a=a),
verbose=False, n_jobs=n_jobs)
if plot_raw:
with printer('Plotting raw data'):
raw_mv.plot(clipping='transparent', events=events,
show=False)
if plot_evoked:
with printer('Plotting evoked data'):
picks = mne.pick_types(raw_mv.info, meg=True, eeg=True)
events[:, 2] = 1
evoked = mne.Epochs(raw_mv, events, {'Simulated': 1},
0, duration, None, picks).average()
evoked.plot_topomap(np.unique(tmids), show=False)
print('\nTotal time: %0.1f sec' % (time.time() - t0))
sys.stdout.flush()
if any([plot_dipoles, plot_raw, plot_evoked]):
plt.show(block=True)
# ############################################################################
# Simulate data
# Simulate data with movement
with warnings.catch_warnings(record=True):
raw = Raw(fname_raw, allow_maxshield=True)
raw_movement = simulate_movement(raw, fname_pos_orig, stc, trans, src, bem,
interp='zero', n_jobs=6, verbose=True)
# Simulate data with no movement (use initial head position)
raw_stationary = simulate_movement(raw, None, stc, trans, src, bem,
interp='zero', n_jobs=6, verbose=True)
# Extract positions
trans_move, rot_move, t_move = get_chpi_positions(fname_pos_move)
trans_stat, rot_stat, t_stat = get_chpi_positions(fname_pos_stat)
trans_orig, rot_orig, t_orig = get_chpi_positions(fname_pos_orig)
# ############################################################################
# Let's look at the results, just translation for simplicity
axes = 'XYZ'
fig = plt.figure(dpi=200)
ts = [t_orig, t_stat, t_move]
transs = [trans_orig, trans_stat, trans_move]
labels = ['original', 'stationary', 'simulated']
sizes = [10, 5, 5]
colors = 'kyr'
for ai, axis in enumerate(axes):
ax = plt.subplot(3, 1, ai + 1)
def simulate_movement(raw, pos, stc, trans, src, bem, cov='simple',
mindist=1.0, interp='linear', random_state=None,
n_jobs=1, verbose=None):
"""Simulate raw data with head movements
Parameters
----------
raw : instance of Raw
The raw instance to use. The measurement info, including the
head positions, will be used to simulate data.
pos : str | dict | None
Name of the position estimates file. Should be in the format of
the files produced by maxfilter-produced. If dict, keys should
be the time points and entries should be 4x3 ``dev_head_t``
matrices. If None, the original head position (from
``raw.info['dev_head_t']``) will be used.
stc : instance of SourceEstimate
The source estimate to use to simulate data. Must have the same
sample rate as the raw data.
trans : dict | str
Either a transformation filename (usually made using mne_analyze)
or an info dict (usually opened using read_trans()).
If string, an ending of `.fif` or `.fif.gz` will be assumed to
be in FIF format, any other ending will be assumed to be a text
file with a 4x4 transformation matrix (like the `--trans` MNE-C
option).
src : str | instance of SourceSpaces
If string, should be a source space filename. Can also be an
instance of loaded or generated SourceSpaces.
bem : str
Filename of the BEM (e.g., "sample-5120-5120-5120-bem-sol.fif").
cov : instance of Covariance | 'simple' | None
The sensor covariance matrix used to generate noise. If None,
no noise will be added. If 'simple', a basic (diagonal) ad-hoc
noise covariance will be used.
mindist : float
Minimum distance between sources and the inner skull boundary
to use during forward calculation.
interp : str
Either 'linear' or 'zero', the type of forward-solution
interpolation to use between provided time points.
random_state : None | int | np.random.RandomState
To specify the random generator state.
n_jobs : int
Number of jobs to use.
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose).
Returns
-------
raw : instance of Raw
The simulated raw file.
Notes
-----
Events coded with the number of the forward solution used will be placed
in the raw files in the trigger channel STI101 at the t=0 times of the
SourceEstimates.
The resulting SNR will be determined by the structure of the noise
covariance, and the amplitudes of the SourceEstimate. Note that this
will vary as a function of position.
"""
if isinstance(raw, string_types):
with warnings.catch_warnings(record=True):
raw = Raw(raw, allow_maxshield=True, preload=True, verbose=False)
else:
raw = raw.copy()
if not isinstance(stc, _BaseSourceEstimate):
raise TypeError('stc must be a SourceEstimate')
if not np.allclose(raw.info['sfreq'], 1. / stc.tstep):
raise ValueError('stc and raw must have same sample rate')
rng = check_random_state(random_state)
if interp not in ('linear', 'zero'):
raise ValueError('interp must be "linear" or "zero"')
if pos is None: # use pos from file
dev_head_ts = [raw.info['dev_head_t']] * 2
offsets = np.array([0, raw.n_times])
interp = 'zero'
else:
if isinstance(pos, string_types):
pos = get_chpi_positions(pos, verbose=False)
if isinstance(pos, tuple): # can be an already-loaded pos file
transs, rots, ts = pos
ts -= raw.first_samp / raw.info['sfreq'] # MF files need reref
dev_head_ts = [np.r_[np.c_[r, t[:, np.newaxis]], [[0, 0, 0, 1]]]
for r, t in zip(rots, transs)]
del transs, rots
elif isinstance(pos, dict):
ts = np.array(list(pos.keys()), float)
ts.sort()
dev_head_ts = [pos[float(tt)] for tt in ts]
else:
raise TypeError('unknown pos type %s' % type(pos))
if not (ts >= 0).all(): # pathological if not
raise RuntimeError('Cannot have t < 0 in transform file')
tend = raw.times[-1]
assert not (ts < 0).any()
assert not (ts > tend).any()
if ts[0] > 0:
ts = np.r_[[0.], ts]
dev_head_ts.insert(0, raw.info['dev_head_t']['trans'])
dev_head_ts = [{'trans': d, 'to': raw.info['dev_head_t']['to'],
'from': raw.info['dev_head_t']['from']}
for d in dev_head_ts]
if ts[-1] < tend:
dev_head_ts.append(dev_head_ts[-1])
ts = np.r_[ts, [tend]]
offsets = raw.time_as_index(ts)
offsets[-1] = raw.n_times # fix for roundoff error
assert offsets[-2] != offsets[-1]
del ts
if isinstance(cov, string_types):
assert cov == 'simple'
cov = make_ad_hoc_cov(raw.info, verbose=False)
assert np.array_equal(offsets, np.unique(offsets))
assert len(offsets) == len(dev_head_ts)
approx_events = int((raw.n_times / raw.info['sfreq']) /
(stc.times[-1] - stc.times[0]))
logger.info('Provided parameters will provide approximately %s event%s'
% (approx_events, '' if approx_events == 1 else 's'))
# get HPI freqs and reorder
hpi_freqs = np.array([x['custom_ref'][0]
for x in raw.info['hpi_meas'][0]['hpi_coils']])
n_freqs = len(hpi_freqs)
order = [x['number'] - 1 for x in raw.info['hpi_meas'][0]['hpi_coils']]
assert np.array_equal(np.unique(order), np.arange(n_freqs))
hpi_freqs = hpi_freqs[order]
hpi_order = raw.info['hpi_results'][0]['order'] - 1
assert np.array_equal(np.unique(hpi_order), np.arange(n_freqs))
hpi_freqs = hpi_freqs[hpi_order]
# extract necessary info
picks = pick_types(raw.info, meg=True, eeg=True) # for simulation
meg_picks = pick_types(raw.info, meg=True, eeg=False) # for CHPI
fwd_info = pick_info(raw.info, picks)
fwd_info['projs'] = []
logger.info('Setting up raw data simulation using %s head position%s'
% (len(dev_head_ts), 's' if len(dev_head_ts) != 1 else ''))
raw.preload_data(verbose=False)
if isinstance(stc, VolSourceEstimate):
verts = [stc.vertices]
else:
verts = stc.vertices
src = _restrict_source_space_to(src, verts)
# figure out our cHPI, ECG, and EOG dipoles
dig = raw.info['dig']
assert all([d['coord_frame'] == FIFF.FIFFV_COORD_HEAD
for d in dig if d['kind'] == FIFF.FIFFV_POINT_HPI])
chpi_rrs = [d['r'] for d in dig if d['kind'] == FIFF.FIFFV_POINT_HPI]
R, r0 = fit_sphere_to_headshape(raw.info, verbose=False)[:2]
R /= 1000.
r0 /= 1000.
ecg_rr = np.array([[-R, 0, -3 * R]])
eog_rr = [d['r'] for d in raw.info['dig']
if d['ident'] == FIFF.FIFFV_POINT_NASION][0]
eog_rr = eog_rr - r0
eog_rr = (eog_rr / np.sqrt(np.sum(eog_rr * eog_rr)) *
0.98 * R)[np.newaxis, :]
eog_rr += r0
eog_bem = make_sphere_model(r0, head_radius=R, relative_radii=(0.99, 1.),
sigmas=(0.33, 0.33), verbose=False)
# let's oscillate between resting (17 bpm) and reading (4.5 bpm) rate
# http://www.ncbi.nlm.nih.gov/pubmed/9399231
blink_rate = np.cos(2 * np.pi * 1. / 60. * raw.times)
blink_rate *= 12.5 / 60.
blink_rate += 4.5 / 60.
blink_data = rng.rand(raw.n_times) < blink_rate / raw.info['sfreq']
blink_data = blink_data * (rng.rand(raw.n_times) + 0.5) # vary amplitudes
blink_kernel = np.hanning(int(0.25 * raw.info['sfreq']))
eog_data = np.convolve(blink_data, blink_kernel, 'same')[np.newaxis, :]
eog_data += rng.randn(eog_data.shape[1]) * 0.05
eog_data *= 100e-6
del blink_data,
max_beats = int(np.ceil(raw.times[-1] * 70. / 60.))
cardiac_idx = np.cumsum(rng.uniform(60. / 70., 60. / 50., max_beats) *
raw.info['sfreq']).astype(int)
cardiac_idx = cardiac_idx[cardiac_idx < raw.n_times]
cardiac_data = np.zeros(raw.n_times)
cardiac_data[cardiac_idx] = 1
cardiac_kernel = np.concatenate([
2 * np.hanning(int(0.04 * raw.info['sfreq'])),
-0.3 * np.hanning(int(0.05 * raw.info['sfreq'])),
0.2 * np.hanning(int(0.26 * raw.info['sfreq']))], axis=-1)
ecg_data = np.convolve(cardiac_data, cardiac_kernel, 'same')[np.newaxis, :]
ecg_data += rng.randn(ecg_data.shape[1]) * 0.05
ecg_data *= 3e-4
del cardiac_data
# Add to data file, then rescale for simulation
for data, scale, exg_ch in zip([eog_data, ecg_data],
[1e-3, 5e-4],
['EOG062', 'ECG063']):
ch = pick_channels(raw.ch_names, [exg_ch])
if len(ch) == 1:
raw._data[ch[0], :] = data
data *= scale
evoked = EvokedArray(np.zeros((len(picks), len(stc.times))), fwd_info,
stc.tmin, verbose=False)
stc_event_idx = np.argmin(np.abs(stc.times))
event_ch = pick_channels(raw.info['ch_names'], ['STI101'])[0]
used = np.zeros(raw.n_times, bool)
stc_indices = np.arange(raw.n_times) % len(stc.times)
raw._data[event_ch, ].fill(0)
hpi_mag = 25e-9
last_fwd = last_fwd_chpi = last_fwd_eog = last_fwd_ecg = src_sel = None
for fi, (fwd, fwd_eog, fwd_ecg, fwd_chpi) in \
enumerate(_make_forward_solutions(
fwd_info, trans, src, bem, eog_bem, dev_head_ts, mindist,
chpi_rrs, eog_rr, ecg_rr, n_jobs)):
# must be fixed orientation
fwd = convert_forward_solution(fwd, surf_ori=True,
force_fixed=True, verbose=False)
# just use one arbitrary direction
fwd_eog = fwd_eog['sol']['data'][:, ::3]
fwd_ecg = fwd_ecg['sol']['data'][:, ::3]
fwd_chpi = fwd_chpi[:, ::3]
if src_sel is None:
src_sel = _stc_src_sel(fwd['src'], stc)
if isinstance(stc, VolSourceEstimate):
verts = [stc.vertices]
else:
verts = stc.vertices
diff_ = sum([len(v) for v in verts]) - len(src_sel)
if diff_ != 0:
warnings.warn('%s STC vertices omitted due to fwd calculation'
% (diff_,))
if last_fwd is None:
last_fwd, last_fwd_eog, last_fwd_ecg, last_fwd_chpi = \
fwd, fwd_eog, fwd_ecg, fwd_chpi
continue
n_time = offsets[fi] - offsets[fi-1]
time_slice = slice(offsets[fi-1], offsets[fi])
assert not used[time_slice].any()
stc_idxs = stc_indices[time_slice]
event_idxs = np.where(stc_idxs == stc_event_idx)[0] + offsets[fi-1]
used[time_slice] = True
logger.info(' Simulating data for %0.3f-%0.3f sec with %s event%s'
% (tuple(offsets[fi-1:fi+1] / raw.info['sfreq']) +
(len(event_idxs), '' if len(event_idxs) == 1 else 's')))
# simulate brain data
stc_data = stc.data[:, stc_idxs][src_sel]
data = _interp(last_fwd['sol']['data'], fwd['sol']['data'],
stc_data, interp)
simulated = EvokedArray(data, evoked.info, 0)
if cov is not None:
noise = generate_noise_evoked(simulated, cov, [1, -1, 0.2], rng)
simulated.data += noise.data
assert simulated.data.shape[0] == len(picks)
assert simulated.data.shape[1] == len(stc_idxs)
raw._data[picks, time_slice] = simulated.data
# add ECG, EOG, and CHPI traces
raw._data[picks, time_slice] += \
_interp(last_fwd_eog, fwd_eog, eog_data[:, time_slice], interp)
raw._data[meg_picks, time_slice] += \
_interp(last_fwd_ecg, fwd_ecg, ecg_data[:, time_slice], interp)
this_t = np.arange(offsets[fi-1], offsets[fi]) / raw.info['sfreq']
sinusoids = np.zeros((n_freqs, n_time))
for fi, freq in enumerate(hpi_freqs):
sinusoids[fi] = 2 * np.pi * freq * this_t
sinusoids[fi] = hpi_mag * np.sin(sinusoids[fi])
raw._data[meg_picks, time_slice] += \
_interp(last_fwd_chpi, fwd_chpi, sinusoids, interp)
# add events
raw._data[event_ch, event_idxs] = fi
# prepare for next iteration
last_fwd, last_fwd_eog, last_fwd_ecg, last_fwd_chpi = \
fwd, fwd_eog, fwd_ecg, fwd_chpi
assert used.all()
logger.info('Done')
return raw
head_pos=fname_pos_orig,
n_jobs=6,
verbose=True)
# Simulate data with no movement (use initial head position)
raw_stationary = simulate_raw(raw,
stc,
trans,
src,
bem,
chpi=True,
n_jobs=6,
verbose=True)
# Extract positions
trans_orig, rot_orig, t_orig = get_chpi_positions(fname_pos_orig)
t_orig -= raw.first_samp / raw.info['sfreq']
trans_move, rot_move, t_move = _calculate_chpi_positions(raw_movement)
trans_stat, rot_stat, t_stat = _calculate_chpi_positions(raw_stationary)
# ############################################################################
# Let's look at the results, just translation for simplicity
axes = 'XYZ'
fig = plt.figure(dpi=200)
ts = [t_orig, t_stat, t_move]
transs = [trans_orig, trans_stat, trans_move]
labels = ['original', 'stationary', 'simulated']
sizes = [10, 5, 5]
colors = 'kyr'
for ai, axis in enumerate(axes):
n_jobs=6,
verbose=True)
# Simulate data with no movement (use initial head position)
raw_stationary = simulate_movement(raw,
None,
stc,
trans,
src,
bem,
interp='zero',
n_jobs=6,
verbose=True)
# Extract positions
trans_move, rot_move, t_move = get_chpi_positions(fname_pos_move)
trans_stat, rot_stat, t_stat = get_chpi_positions(fname_pos_stat)
trans_orig, rot_orig, t_orig = get_chpi_positions(fname_pos_orig)
# ############################################################################
# Let's look at the results, just translation for simplicity
axes = 'XYZ'
fig = plt.figure(dpi=200)
ts = [t_orig, t_stat, t_move]
transs = [trans_orig, trans_stat, trans_move]
labels = ['original', 'stationary', 'simulated']
sizes = [10, 5, 5]
colors = 'kyr'
for ai, axis in enumerate(axes):
ax = plt.subplot(3, 1, ai + 1)
def simulate_movement(raw,
pos,
stc,
trans,
src,
bem,
cov='simple',
mindist=1.0,
interp='linear',
random_state=None,
n_jobs=1,
verbose=None):
"""Simulate raw data with head movements
Parameters
----------
raw : instance of Raw
The raw instance to use. The measurement info, including the
head positions, will be used to simulate data.
pos : str | dict | None
Name of the position estimates file. Should be in the format of
the files produced by maxfilter-produced. If dict, keys should
be the time points and entries should be 4x3 ``dev_head_t``
matrices. If None, the original head position (from
``raw.info['dev_head_t']``) will be used.
stc : instance of SourceEstimate
The source estimate to use to simulate data. Must have the same
sample rate as the raw data.
trans : dict | str
Either a transformation filename (usually made using mne_analyze)
or an info dict (usually opened using read_trans()).
If string, an ending of `.fif` or `.fif.gz` will be assumed to
be in FIF format, any other ending will be assumed to be a text
file with a 4x4 transformation matrix (like the `--trans` MNE-C
option).
src : str | instance of SourceSpaces
If string, should be a source space filename. Can also be an
instance of loaded or generated SourceSpaces.
bem : str
Filename of the BEM (e.g., "sample-5120-5120-5120-bem-sol.fif").
cov : instance of Covariance | 'simple' | None
The sensor covariance matrix used to generate noise. If None,
no noise will be added. If 'simple', a basic (diagonal) ad-hoc
noise covariance will be used.
mindist : float
Minimum distance between sources and the inner skull boundary
to use during forward calculation.
interp : str
Either 'linear' or 'zero', the type of forward-solution
interpolation to use between provided time points.
random_state : None | int | np.random.RandomState
To specify the random generator state.
n_jobs : int
Number of jobs to use.
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose).
Returns
-------
raw : instance of Raw
The simulated raw file.
Notes
-----
Events coded with the number of the forward solution used will be placed
in the raw files in the trigger channel STI101 at the t=0 times of the
SourceEstimates.
The resulting SNR will be determined by the structure of the noise
covariance, and the amplitudes of the SourceEstimate. Note that this
will vary as a function of position.
"""
if isinstance(raw, string_types):
with warnings.catch_warnings(record=True):
raw = Raw(raw, allow_maxshield=True, preload=True, verbose=False)
else:
raw = raw.copy()
if not isinstance(stc, _BaseSourceEstimate):
raise TypeError('stc must be a SourceEstimate')
if not np.allclose(raw.info['sfreq'], 1. / stc.tstep):
raise ValueError('stc and raw must have same sample rate')
rng = check_random_state(random_state)
if interp not in ('linear', 'zero'):
raise ValueError('interp must be "linear" or "zero"')
if pos is None: # use pos from file
dev_head_ts = [raw.info['dev_head_t']] * 2
offsets = np.array([0, raw.n_times])
interp = 'zero'
else:
if isinstance(pos, string_types):
pos = get_chpi_positions(pos, verbose=False)
if isinstance(pos, tuple): # can be an already-loaded pos file
transs, rots, ts = pos
ts -= raw.first_samp / raw.info['sfreq'] # MF files need reref
dev_head_ts = [
np.r_[np.c_[r, t[:, np.newaxis]], [[0, 0, 0, 1]]]
for r, t in zip(rots, transs)
]
del transs, rots
elif isinstance(pos, dict):
ts = np.array(list(pos.keys()), float)
ts.sort()
dev_head_ts = [pos[float(tt)] for tt in ts]
else:
raise TypeError('unknown pos type %s' % type(pos))
if not (ts >= 0).all(): # pathological if not
raise RuntimeError('Cannot have t < 0 in transform file')
tend = raw.times[-1]
assert not (ts < 0).any()
assert not (ts > tend).any()
if ts[0] > 0:
ts = np.r_[[0.], ts]
dev_head_ts.insert(0, raw.info['dev_head_t']['trans'])
dev_head_ts = [{
'trans': d,
'to': raw.info['dev_head_t']['to'],
'from': raw.info['dev_head_t']['from']
} for d in dev_head_ts]
if ts[-1] < tend:
dev_head_ts.append(dev_head_ts[-1])
ts = np.r_[ts, [tend]]
offsets = raw.time_as_index(ts)
offsets[-1] = raw.n_times # fix for roundoff error
assert offsets[-2] != offsets[-1]
del ts
if isinstance(cov, string_types):
assert cov == 'simple'
cov = make_ad_hoc_cov(raw.info, verbose=False)
assert np.array_equal(offsets, np.unique(offsets))
assert len(offsets) == len(dev_head_ts)
approx_events = int(
(raw.n_times / raw.info['sfreq']) / (stc.times[-1] - stc.times[0]))
logger.info('Provided parameters will provide approximately %s event%s' %
(approx_events, '' if approx_events == 1 else 's'))
# get HPI freqs and reorder
hpi_freqs = np.array(
[x['custom_ref'][0] for x in raw.info['hpi_meas'][0]['hpi_coils']])
n_freqs = len(hpi_freqs)
order = [x['number'] - 1 for x in raw.info['hpi_meas'][0]['hpi_coils']]
assert np.array_equal(np.unique(order), np.arange(n_freqs))
hpi_freqs = hpi_freqs[order]
hpi_order = raw.info['hpi_results'][0]['order'] - 1
assert np.array_equal(np.unique(hpi_order), np.arange(n_freqs))
hpi_freqs = hpi_freqs[hpi_order]
# extract necessary info
picks = pick_types(raw.info, meg=True, eeg=True) # for simulation
meg_picks = pick_types(raw.info, meg=True, eeg=False) # for CHPI
fwd_info = pick_info(raw.info, picks)
fwd_info['projs'] = []
logger.info('Setting up raw data simulation using %s head position%s' %
(len(dev_head_ts), 's' if len(dev_head_ts) != 1 else ''))
raw.preload_data(verbose=False)
if isinstance(stc, VolSourceEstimate):
verts = [stc.vertices]
else:
verts = stc.vertices
src = _restrict_source_space_to(src, verts)
# figure out our cHPI, ECG, and EOG dipoles
dig = raw.info['dig']
assert all([
d['coord_frame'] == FIFF.FIFFV_COORD_HEAD for d in dig
if d['kind'] == FIFF.FIFFV_POINT_HPI
])
chpi_rrs = [d['r'] for d in dig if d['kind'] == FIFF.FIFFV_POINT_HPI]
R, r0 = fit_sphere_to_headshape(raw.info, verbose=False)[:2]
R /= 1000.
r0 /= 1000.
ecg_rr = np.array([[-R, 0, -3 * R]])
eog_rr = [
d['r'] for d in raw.info['dig']
if d['ident'] == FIFF.FIFFV_POINT_NASION
][0]
eog_rr = eog_rr - r0
eog_rr = (eog_rr / np.sqrt(np.sum(eog_rr * eog_rr)) * 0.98 *
R)[np.newaxis, :]
eog_rr += r0
eog_bem = make_sphere_model(r0,
head_radius=R,
relative_radii=(0.99, 1.),
sigmas=(0.33, 0.33),
verbose=False)
# let's oscillate between resting (17 bpm) and reading (4.5 bpm) rate
# http://www.ncbi.nlm.nih.gov/pubmed/9399231
blink_rate = np.cos(2 * np.pi * 1. / 60. * raw.times)
blink_rate *= 12.5 / 60.
blink_rate += 4.5 / 60.
blink_data = rng.rand(raw.n_times) < blink_rate / raw.info['sfreq']
blink_data = blink_data * (rng.rand(raw.n_times) + 0.5) # vary amplitudes
blink_kernel = np.hanning(int(0.25 * raw.info['sfreq']))
eog_data = np.convolve(blink_data, blink_kernel, 'same')[np.newaxis, :]
eog_data += rng.randn(eog_data.shape[1]) * 0.05
eog_data *= 100e-6
del blink_data,
max_beats = int(np.ceil(raw.times[-1] * 70. / 60.))
cardiac_idx = np.cumsum(
rng.uniform(60. / 70., 60. / 50., max_beats) *
raw.info['sfreq']).astype(int)
cardiac_idx = cardiac_idx[cardiac_idx < raw.n_times]
cardiac_data = np.zeros(raw.n_times)
cardiac_data[cardiac_idx] = 1
cardiac_kernel = np.concatenate([
2 * np.hanning(int(0.04 * raw.info['sfreq'])),
-0.3 * np.hanning(int(0.05 * raw.info['sfreq'])),
0.2 * np.hanning(int(0.26 * raw.info['sfreq']))
],
axis=-1)
ecg_data = np.convolve(cardiac_data, cardiac_kernel, 'same')[np.newaxis, :]
ecg_data += rng.randn(ecg_data.shape[1]) * 0.05
ecg_data *= 3e-4
del cardiac_data
# Add to data file, then rescale for simulation
for data, scale, exg_ch in zip([eog_data, ecg_data], [1e-3, 5e-4],
['EOG062', 'ECG063']):
ch = pick_channels(raw.ch_names, [exg_ch])
if len(ch) == 1:
raw._data[ch[0], :] = data
data *= scale
evoked = EvokedArray(np.zeros((len(picks), len(stc.times))),
fwd_info,
stc.tmin,
verbose=False)
stc_event_idx = np.argmin(np.abs(stc.times))
event_ch = pick_channels(raw.info['ch_names'], ['STI101'])[0]
used = np.zeros(raw.n_times, bool)
stc_indices = np.arange(raw.n_times) % len(stc.times)
raw._data[event_ch, ].fill(0)
hpi_mag = 25e-9
last_fwd = last_fwd_chpi = last_fwd_eog = last_fwd_ecg = src_sel = None
for fi, (fwd, fwd_eog, fwd_ecg, fwd_chpi) in \
enumerate(_make_forward_solutions(
fwd_info, trans, src, bem, eog_bem, dev_head_ts, mindist,
chpi_rrs, eog_rr, ecg_rr, n_jobs)):
# must be fixed orientation
fwd = convert_forward_solution(fwd,
surf_ori=True,
force_fixed=True,
verbose=False)
# just use one arbitrary direction
fwd_eog = fwd_eog['sol']['data'][:, ::3]
fwd_ecg = fwd_ecg['sol']['data'][:, ::3]
fwd_chpi = fwd_chpi[:, ::3]
if src_sel is None:
src_sel = _stc_src_sel(fwd['src'], stc)
if isinstance(stc, VolSourceEstimate):
verts = [stc.vertices]
else:
verts = stc.vertices
diff_ = sum([len(v) for v in verts]) - len(src_sel)
if diff_ != 0:
warnings.warn(
'%s STC vertices omitted due to fwd calculation' %
(diff_, ))
if last_fwd is None:
last_fwd, last_fwd_eog, last_fwd_ecg, last_fwd_chpi = \
fwd, fwd_eog, fwd_ecg, fwd_chpi
continue
n_time = offsets[fi] - offsets[fi - 1]
time_slice = slice(offsets[fi - 1], offsets[fi])
assert not used[time_slice].any()
stc_idxs = stc_indices[time_slice]
event_idxs = np.where(stc_idxs == stc_event_idx)[0] + offsets[fi - 1]
used[time_slice] = True
logger.info(' Simulating data for %0.3f-%0.3f sec with %s event%s' %
(tuple(offsets[fi - 1:fi + 1] / raw.info['sfreq']) +
(len(event_idxs), '' if len(event_idxs) == 1 else 's')))
# simulate brain data
stc_data = stc.data[:, stc_idxs][src_sel]
data = _interp(last_fwd['sol']['data'], fwd['sol']['data'], stc_data,
interp)
simulated = EvokedArray(data, evoked.info, 0)
if cov is not None:
noise = generate_noise_evoked(simulated, cov, [1, -1, 0.2], rng)
simulated.data += noise.data
assert simulated.data.shape[0] == len(picks)
assert simulated.data.shape[1] == len(stc_idxs)
raw._data[picks, time_slice] = simulated.data
# add ECG, EOG, and CHPI traces
raw._data[picks, time_slice] += \
_interp(last_fwd_eog, fwd_eog, eog_data[:, time_slice], interp)
raw._data[meg_picks, time_slice] += \
_interp(last_fwd_ecg, fwd_ecg, ecg_data[:, time_slice], interp)
this_t = np.arange(offsets[fi - 1], offsets[fi]) / raw.info['sfreq']
sinusoids = np.zeros((n_freqs, n_time))
for fi, freq in enumerate(hpi_freqs):
sinusoids[fi] = 2 * np.pi * freq * this_t
sinusoids[fi] = hpi_mag * np.sin(sinusoids[fi])
raw._data[meg_picks, time_slice] += \
_interp(last_fwd_chpi, fwd_chpi, sinusoids, interp)
# add events
raw._data[event_ch, event_idxs] = fi
# prepare for next iteration
last_fwd, last_fwd_eog, last_fwd_ecg, last_fwd_chpi = \
fwd, fwd_eog, fwd_ecg, fwd_chpi
assert used.all()
logger.info('Done')
return raw
stc.data.fill(0)
stc.data[:, (stc.times >= pulse_tmin) & (stc.times <= pulse_tmax)] = 10e-9
# ############################################################################
# Simulate data
# Simulate data with movement
with warnings.catch_warnings(record=True):
raw = Raw(fname_raw, allow_maxshield=True)
raw_movement = simulate_raw(raw, stc, trans, src, bem, chpi=True, head_pos=fname_pos_orig, n_jobs=6, verbose=True)
# Simulate data with no movement (use initial head position)
raw_stationary = simulate_raw(raw, stc, trans, src, bem, chpi=True, n_jobs=6, verbose=True)
# Extract positions
trans_orig, rot_orig, t_orig = get_chpi_positions(fname_pos_orig)
t_orig -= raw.first_samp / raw.info["sfreq"]
trans_move, rot_move, t_move = _calculate_chpi_positions(raw_movement)
trans_stat, rot_stat, t_stat = _calculate_chpi_positions(raw_stationary)
# ############################################################################
# Let's look at the results, just translation for simplicity
axes = "XYZ"
fig = plt.figure(dpi=200)
ts = [t_orig, t_stat, t_move]
transs = [trans_orig, trans_stat, trans_move]
labels = ["original", "stationary", "simulated"]
sizes = [10, 5, 5]
colors = "kyr"
for ai, axis in enumerate(axes):