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# -*- coding: utf-8 -*-
# Authors: Mark Wronkiewicz <wronk@uw.edu>
# Yousra Bekhti <yousra.bekhti@gmail.com>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
from copy import deepcopy
import numpy as np
from .evoked import _generate_noise
from ..event import _get_stim_channel
from ..filter import _Interp2
from ..io.pick import (pick_types, pick_info, pick_channels,
pick_channels_forward)
from ..source_estimate import VolSourceEstimate
from ..cov import make_ad_hoc_cov, read_cov, Covariance
from ..bem import fit_sphere_to_headshape, make_sphere_model, read_bem_solution
from ..io import RawArray, BaseRaw
from ..chpi import (read_head_pos, head_pos_to_trans_rot_t, _get_hpi_info,
_get_hpi_initial_fit)
from ..io.constants import FIFF
from ..forward import (_magnetic_dipole_field_vec, _merge_meg_eeg_fwds,
_stc_src_sel, convert_forward_solution,
_prepare_for_forward, _transform_orig_meg_coils,
_compute_forwards, _to_forward_dict,
restrict_forward_to_stc)
from ..transforms import _get_trans, transform_surface_to
from ..source_space import (_ensure_src, _points_outside_surface,
_adjust_patch_info)
from ..source_estimate import _BaseSourceEstimate
from ..utils import logger, verbose, check_random_state, warn, _pl
from ..parallel import check_n_jobs
from ..externals.six import string_types
def _check_cov(info, cov):
"""Check that the user provided a valid covariance matrix for the noise."""
if isinstance(cov, Covariance) or cov is None:
pass
elif isinstance(cov, dict):
cov = make_ad_hoc_cov(info, cov, verbose=False)
elif isinstance(cov, string_types):
if cov == 'simple':
cov = make_ad_hoc_cov(info, None, verbose=False)
else:
cov = read_cov(cov, verbose=False)
else:
raise TypeError('Covariance matrix type not recognized. Valid input '
'types are: instance of Covariance, dict, str, None. '
', got %s' % (cov,))
return cov
def _log_ch(start, info, ch):
"""Log channel information."""
if ch is not None:
extra, just, ch = ' stored on channel:', 50, info['ch_names'][ch]
else:
extra, just, ch = ' not stored', 0, ''
logger.info((start + extra).ljust(just) + ch)
@verbose
def simulate_raw(raw, stc, trans, src, bem, cov='simple',
blink=False, ecg=False, chpi=False, head_pos=None,
mindist=1.0, interp='cos2', iir_filter=None, n_jobs=1,
random_state=None, use_cps=True, forward=None, verbose=None):
u"""Simulate raw data.
Head movements can optionally be simulated using the ``head_pos``
parameter.
Parameters
----------
raw : instance of Raw
The raw template to use for simulation. The ``info``, ``times``,
and potentially ``first_samp`` properties 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 | None
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). If trans is None, an identity transform will be used.
src : str | instance of SourceSpaces
Source space corresponding to the stc. If string, should be a source
space filename. Can also be an instance of loaded or generated
SourceSpaces.
bem : str | dict
BEM solution corresponding to the stc. If string, should be a BEM
solution filename (e.g., "sample-5120-5120-5120-bem-sol.fif").
cov : instance of Covariance | str | dict of float | None
The sensor covariance matrix used to generate noise. If string, should
be a filename or 'simple'. If 'simple', an ad hoc covariance matrix
will be generated with default values. If dict, an ad hoc covariance
matrix will be generated with the values specified by the dict entries.
If None, no noise will be added.
blink : bool
If true, add simulated blink artifacts. See Notes for details.
ecg : bool
If true, add simulated ECG artifacts. See Notes for details.
chpi : bool
If true, simulate continuous head position indicator information.
Valid cHPI information must encoded in ``raw.info['hpi_meas']``
to use this option.
head_pos : None | str | dict | tuple | array
Name of the position estimates file. Should be in the format of
the files produced by maxfilter. If dict, keys should
be the time points and entries should be 4x4 ``dev_head_t``
matrices. If None, the original head position (from
``info['dev_head_t']``) will be used. If tuple, should have the
same format as data returned by `head_pos_to_trans_rot_t`.
If array, should be of the form returned by
:func:`mne.chpi.read_head_pos`.
mindist : float
Minimum distance between sources and the inner skull boundary
to use during forward calculation.
interp : str
Either 'hann', 'cos2', 'linear', or 'zero', the type of
forward-solution interpolation to use between forward solutions
at different head positions.
iir_filter : None | array
IIR filter coefficients (denominator) e.g. [1, -1, 0.2].
n_jobs : int
Number of jobs to use.
random_state : None | int | np.random.RandomState
The random generator state used for blink, ECG, and sensor
noise randomization.
use_cps : None | bool (default True)
Whether to use cortical patch statistics to define normal
orientations. Only used when surf_ori and/or force_fixed are True.
forward : instance of Forward | None
The forward operator to use. If None (default) it will be computed
using `bem`, `trans`, and `src`.
verbose : bool, str, int, or None
If not None, override default verbose level (see :func:`mne.verbose`
and :ref:`Logging documentation <tut_logging>` for more).
Returns
-------
raw : instance of Raw
The simulated raw file.
See Also
--------
mne.chpi.read_head_pos
simulate_evoked
simulate_stc
simulate_sparse_stc
Notes
-----
Events coded with the position number (starting at 1) will be stored
in the trigger channel (if available) at times corresponding to t=0
in the ``stc``.
The resulting SNR will be determined by the structure of the noise
covariance, the amplitudes of ``stc``, and the head position(s) provided.
The blink and ECG artifacts are generated by 1) placing impulses at
random times of activation, and 2) convolving with activation kernel
functions. In both cases, the scale-factors of the activation functions
(and for the resulting EOG and ECG channel traces) were chosen based on
visual inspection to yield amplitudes generally consistent with those
seen in experimental data. Noisy versions of the blink and ECG
activations will be stored in the first EOG and ECG channel in the
raw file, respectively, if they exist.
For blink artifacts:
1. Random activation times are drawn from an inhomogeneous poisson
process whose blink rate oscillates between 4.5 blinks/minute
and 17 blinks/minute based on the low (reading) and high (resting)
blink rates from [1]_.
2. The activation kernel is a 250 ms Hanning window.
3. Two activated dipoles are located in the z=0 plane (in head
coordinates) at ±30 degrees away from the y axis (nasion).
4. Activations affect MEG and EEG channels.
For ECG artifacts:
1. Random inter-beat intervals are drawn from a uniform distribution
of times corresponding to 40 and 80 beats per minute.
2. The activation function is the sum of three Hanning windows with
varying durations and scales to make a more complex waveform.
3. The activated dipole is located one (estimated) head radius to
the left (-x) of head center and three head radii below (+z)
head center; this dipole is oriented in the +x direction.
4. Activations only affect MEG channels.
If you have a :class:`mne.Info` that you want to use with no associated
:class:`mne.io.Raw` instance, consider creating a dummy one using
:class:`mne.io.RawArray`.
.. versionadded:: 0.10.0
References
----------
.. [1] Bentivoglio et al. "Analysis of blink rate patterns in normal
subjects" Movement Disorders, 1997 Nov;12(6):1028-34.
"""
if not isinstance(raw, BaseRaw):
raise TypeError('raw should be an instance of Raw')
times, info, first_samp = raw.times, raw.info, raw.first_samp
raw_verbose = raw.verbose
# Check for common flag errors and try to override
if not isinstance(stc, _BaseSourceEstimate):
raise TypeError('stc must be a SourceEstimate')
if not np.allclose(info['sfreq'], 1. / stc.tstep):
raise ValueError('stc and info must have same sample rate')
if len(stc.times) <= 2: # to ensure event encoding works
raise ValueError('stc must have at least three time points')
stim = False if len(pick_types(info, meg=False, stim=True)) == 0 else True
n_jobs = check_n_jobs(n_jobs)
rng = check_random_state(random_state)
interper = _Interp2(interp)
if forward is not None:
if any(x is not None for x in (trans, src, bem, head_pos)):
raise ValueError('If forward is not None then trans, src, bem, '
'and head_pos must all be None')
if not np.allclose(forward['info']['dev_head_t']['trans'],
raw.info['dev_head_t']['trans'], atol=1e-6):
raise ValueError('The forward meg<->head transform '
'forward["info"]["dev_head_t"] does not match '
'the one in raw.info["dev_head_t"]')
src = forward['src']
if head_pos is None: # use pos from info['dev_head_t']
head_pos = dict()
if isinstance(head_pos, string_types): # can be a head pos file
head_pos = read_head_pos(head_pos)
if isinstance(head_pos, np.ndarray): # can be head_pos quats
head_pos = head_pos_to_trans_rot_t(head_pos)
if isinstance(head_pos, tuple): # can be quats converted to trans, rot, t
transs, rots, ts = head_pos
ts -= raw._first_time # 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(head_pos, dict):
ts = np.array(list(head_pos.keys()), float)
ts.sort()
dev_head_ts = [head_pos[float(tt)] for tt in ts]
else:
raise TypeError('unknown head_pos type %s' % type(head_pos))
bad = ts < 0
if bad.any():
raise RuntimeError('All position times must be >= 0, found %s/%s'
'< 0' % (bad.sum(), len(bad)))
bad = ts > times[-1]
if bad.any():
raise RuntimeError('All position times must be <= t_end (%0.1f '
'sec), found %s/%s bad values (is this a split '
'file?)' % (times[-1], bad.sum(), len(bad)))
# If it doesn't start at zero, insert one at t=0
if len(ts) == 0 or ts[0] > 0:
ts = np.r_[[0.], ts]
dev_head_ts.insert(0, info['dev_head_t']['trans'])
dev_head_ts = [{'trans': d, 'to': info['dev_head_t']['to'],
'from': info['dev_head_t']['from']}
for d in dev_head_ts]
offsets = raw.time_as_index(ts)
offsets = np.concatenate([offsets, [len(times)]])
assert offsets[-2] != offsets[-1]
assert np.array_equal(offsets, np.unique(offsets))
assert len(offsets) == len(dev_head_ts) + 1
del ts
src = _ensure_src(src, verbose=False)
if isinstance(bem, string_types):
bem = read_bem_solution(bem, verbose=False)
cov = _check_cov(info, cov)
approx_events = int((len(times) / info['sfreq']) /
(stc.times[-1] - stc.times[0]))
logger.info('Provided parameters will provide approximately %s event%s'
% (approx_events, _pl(approx_events)))
# Extract necessary info
meeg_picks = pick_types(info, meg=True, eeg=True, exclude=[]) # for sim
meg_picks = pick_types(info, meg=True, eeg=False, exclude=[]) # for CHPI
fwd_info = pick_info(info, meeg_picks)
fwd_info['projs'] = [] # Ensure no 'projs' applied
logger.info('Setting up raw simulation: %s position%s, "%s" interpolation'
% (len(dev_head_ts), _pl(dev_head_ts), interp))
del interp
verts = stc.vertices
verts = [verts] if isinstance(stc, VolSourceEstimate) else verts
src = _restrict_source_space_to(src, verts)
if forward is not None:
forward = restrict_forward_to_stc(forward, stc)
# array used to store result
raw_data = np.zeros((len(info['ch_names']), len(times)))
# figure out our cHPI, ECG, and blink dipoles
ecg_rr = blink_rrs = exg_bem = hpi_rrs = None
ecg = ecg and len(meg_picks) > 0
chpi = chpi and len(meg_picks) > 0
if chpi:
hpi_freqs, hpi_pick, hpi_ons = _get_hpi_info(info)
hpi_rrs = _get_hpi_initial_fit(info, verbose='error')
hpi_nns = hpi_rrs / np.sqrt(np.sum(hpi_rrs * hpi_rrs,
axis=1))[:, np.newaxis]
# turn on cHPI in file
raw_data[hpi_pick, :] = hpi_ons.sum()
_log_ch('cHPI status bits enbled and', info, hpi_pick)
if blink or ecg:
R, r0 = fit_sphere_to_headshape(info, units='m', verbose=False)[:2]
exg_bem = make_sphere_model(r0, head_radius=R,
relative_radii=(0.97, 0.98, 0.99, 1.),
sigmas=(0.33, 1.0, 0.004, 0.33),
verbose=False)
if blink:
# place dipoles at 45 degree angles in z=0 plane
blink_rrs = np.array([[np.cos(np.pi / 3.), np.sin(np.pi / 3.), 0.],
[-np.cos(np.pi / 3.), np.sin(np.pi / 3), 0.]])
blink_rrs /= np.sqrt(np.sum(blink_rrs *
blink_rrs, axis=1))[:, np.newaxis]
blink_rrs *= 0.96 * R
blink_rrs += r0
# oriented upward
blink_nns = np.array([[0., 0., 1.], [0., 0., 1.]])
# Blink times drawn from an inhomogeneous poisson process
# by 1) creating the rate and 2) pulling random numbers
blink_rate = (1 + np.cos(2 * np.pi * 1. / 60. * times)) / 2.
blink_rate *= 12.5 / 60.
blink_rate += 4.5 / 60.
blink_data = rng.rand(len(times)) < blink_rate / info['sfreq']
blink_data = blink_data * (rng.rand(len(times)) + 0.5) # varying amps
# Activation kernel is a simple hanning window
blink_kernel = np.hanning(int(0.25 * info['sfreq']))
blink_data = np.convolve(blink_data, blink_kernel,
'same')[np.newaxis, :] * 1e-7
# Add rescaled noisy data to EOG ch
ch = pick_types(info, meg=False, eeg=False, eog=True)
noise = rng.randn(blink_data.shape[1]) * 5e-6
if len(ch) >= 1:
ch = ch[-1]
raw_data[ch, :] = blink_data * 1e3 + noise
else:
ch = None
_log_ch('Blinks simulated and trace', info, ch)
del blink_kernel, blink_rate, noise
if ecg:
ecg_rr = np.array([[-R, 0, -3 * R]])
max_beats = int(np.ceil(times[-1] * 80. / 60.))
# activation times with intervals drawn from a uniform distribution
# based on activation rates between 40 and 80 beats per minute
cardiac_idx = np.cumsum(rng.uniform(60. / 80., 60. / 40., max_beats) *
info['sfreq']).astype(int)
cardiac_idx = cardiac_idx[cardiac_idx < len(times)]
cardiac_data = np.zeros(len(times))
cardiac_data[cardiac_idx] = 1
# kernel is the sum of three hanning windows
cardiac_kernel = np.concatenate([
2 * np.hanning(int(0.04 * info['sfreq'])),
-0.3 * np.hanning(int(0.05 * info['sfreq'])),
0.2 * np.hanning(int(0.26 * info['sfreq']))], axis=-1)
ecg_data = np.convolve(cardiac_data, cardiac_kernel,
'same')[np.newaxis, :] * 15e-8
# Add rescaled noisy data to ECG ch
ch = pick_types(info, meg=False, eeg=False, ecg=True)
noise = rng.randn(ecg_data.shape[1]) * 1.5e-5
if len(ch) >= 1:
ch = ch[-1]
raw_data[ch, :] = ecg_data * 2e3 + noise
else:
ch = None
_log_ch('ECG simulated and trace', info, ch)
del cardiac_data, cardiac_kernel, max_beats, cardiac_idx
stc_event_idx = np.argmin(np.abs(stc.times))
if stim:
event_ch = pick_channels(info['ch_names'],
_get_stim_channel(None, info))[0]
raw_data[event_ch, :] = 0.
else:
event_ch = None
_log_ch('Event information', info, event_ch)
used = np.zeros(len(times), bool)
stc_indices = np.arange(len(times)) % len(stc.times)
raw_data[meeg_picks, :] = 0.
if chpi:
sinusoids = 70e-9 * np.sin(2 * np.pi * hpi_freqs[:, np.newaxis] *
(np.arange(len(times)) / info['sfreq']))
zf = None # final filter conditions for the noise
# don't process these any more if no MEG present
for fi, (fwd, fwd_blink, fwd_ecg, fwd_chpi) in \
enumerate(_iter_forward_solutions(
fwd_info, trans, src, bem, exg_bem, dev_head_ts, mindist,
hpi_rrs, blink_rrs, ecg_rr, n_jobs, forward)):
# must be fixed orientation
# XXX eventually we could speed this up by allowing the forward
# solution code to only compute the normal direction
fwd = convert_forward_solution(fwd, surf_ori=True, force_fixed=True,
use_cps=use_cps, verbose=False)
if blink:
fwd_blink = fwd_blink['sol']['data']
for ii in range(len(blink_rrs)):
fwd_blink[:, ii] = np.dot(fwd_blink[:, 3 * ii:3 * (ii + 1)],
blink_nns[ii])
fwd_blink = fwd_blink[:, :len(blink_rrs)]
fwd_blink = fwd_blink.sum(axis=1)[:, np.newaxis]
# just use one arbitrary direction
if ecg:
fwd_ecg = fwd_ecg['sol']['data'][:, [0]]
# align cHPI magnetic dipoles in approx. radial direction
if chpi:
for ii in range(len(hpi_rrs)):
fwd_chpi[:, ii] = np.dot(fwd_chpi[:, 3 * ii:3 * (ii + 1)],
hpi_nns[ii])
fwd_chpi = fwd_chpi[:, :len(hpi_rrs)].copy()
assert fwd['sol']['data'].shape[0] == len(meeg_picks)
interper['fwd'] = fwd['sol']['data']
interper['fwd_blink'] = fwd_blink
interper['fwd_ecg'] = fwd_ecg
interper['fwd_chpi'] = fwd_chpi
if fi == 0:
src_sel = _stc_src_sel(fwd['src'], stc)
verts = stc.vertices
verts = [verts] if isinstance(stc, VolSourceEstimate) else verts
diff_ = sum([len(v) for v in verts]) - len(src_sel)
if diff_ != 0:
warn('%s STC vertices omitted due to fwd calculation' % diff_)
stc_data = stc.data[src_sel]
del stc, src_sel, diff_, verts
continue
del fwd, fwd_blink, fwd_ecg, fwd_chpi
start, stop = offsets[fi - 1:fi + 1]
assert not used[start:stop].any()
event_idxs = np.where(stc_indices[start:stop] ==
stc_event_idx)[0] + start
if stim:
raw_data[event_ch, event_idxs] = fi
logger.info(' Simulating data for %0.3f-%0.3f sec with %s event%s'
% (start / info['sfreq'], stop / info['sfreq'],
len(event_idxs), _pl(event_idxs)))
used[start:stop] = True
time_sl = slice(start, stop)
stc_idxs = stc_indices[time_sl]
# simulate brain data
this_data = raw_data[:, time_sl]
this_data[meeg_picks] = 0.
interper.n_samp = stop - start
interper.interpolate('fwd', stc_data,
this_data, meeg_picks, stc_idxs)
if blink:
interper.interpolate('fwd_blink', blink_data[:, time_sl],
this_data, meeg_picks)
if ecg:
interper.interpolate('fwd_ecg', ecg_data[:, time_sl],
this_data, meg_picks)
if chpi:
interper.interpolate('fwd_chpi', sinusoids[:, time_sl],
this_data, meg_picks)
# add sensor noise, ECG, blink, cHPI
if cov is not None:
noise, zf = _generate_noise(fwd_info, cov, iir_filter, rng,
len(stc_idxs), zi=zf)
raw_data[meeg_picks, time_sl] += noise
this_data[meeg_picks] += noise
assert used[start:stop].all()
assert used.all()
raw = RawArray(raw_data, info, first_samp=first_samp, verbose=False)
raw.verbose = raw_verbose
logger.info('Done')
return raw
def _iter_forward_solutions(info, trans, src, bem, exg_bem, dev_head_ts,
mindist, hpi_rrs, blink_rrs, ecg_rrs, n_jobs,
forward):
"""Calculate a forward solution for a subject."""
logger.info('Setting up forward solutions')
mri_head_t, trans = _get_trans(trans)
megcoils, meg_info, compcoils, megnames, eegels, eegnames, rr, info, \
update_kwargs, bem = _prepare_for_forward(
src, mri_head_t, info, bem, mindist, n_jobs, allow_bem_none=True,
verbose=False)
del (src, mindist)
if forward is None:
eegfwd = _compute_forwards(rr, bem, [eegels], [None],
[None], ['eeg'], n_jobs, verbose=False)[0]
eegfwd = _to_forward_dict(eegfwd, eegnames)
else:
if len(eegnames) > 0:
eegfwd = pick_channels_forward(forward, eegnames, verbose=False)
else:
eegfwd = None
if blink_rrs is not None:
eegblink = _compute_forwards(blink_rrs, exg_bem, [eegels], [None],
[None], ['eeg'], n_jobs,
verbose=False)[0]
eegblink = _to_forward_dict(eegblink, eegnames)
else:
eegblink = None
# short circuit here if there are no MEG channels (don't need to iterate)
if len(pick_types(info, meg=True)) == 0:
eegfwd.update(**update_kwargs)
for _ in dev_head_ts:
yield eegfwd, eegblink, None, None
# extra one to fill last buffer
yield eegfwd, eegblink, None, None
return
coord_frame = FIFF.FIFFV_COORD_HEAD
if bem is not None and not bem['is_sphere']:
idx = np.where(np.array([s['id'] for s in bem['surfs']]) ==
FIFF.FIFFV_BEM_SURF_ID_BRAIN)[0]
assert len(idx) == 1
# make a copy so it isn't mangled in use
bem_surf = transform_surface_to(bem['surfs'][idx[0]], coord_frame,
mri_head_t, copy=True)
for ti, dev_head_t in enumerate(dev_head_ts):
# Could be *slightly* more efficient not to do this N times,
# but the cost here is tiny compared to actual fwd calculation
logger.info('Computing gain matrix for transform #%s/%s'
% (ti + 1, len(dev_head_ts)))
_transform_orig_meg_coils(megcoils, dev_head_t)
_transform_orig_meg_coils(compcoils, dev_head_t)
# Make sure our sensors are all outside our BEM
coil_rr = [coil['r0'] for coil in megcoils]
# Compute forward
if forward is None:
if not bem['is_sphere']:
outside = _points_outside_surface(coil_rr, bem_surf, n_jobs,
verbose=False)
elif bem.radius is not None:
d = coil_rr - bem['r0']
outside = np.sqrt(np.sum(d * d, axis=1)) > bem.radius
else: # only r0 provided
outside = np.ones(len(coil_rr), bool)
if not outside.all():
raise RuntimeError('%s MEG sensors collided with inner skull '
'surface for transform %s'
% (np.sum(~outside), ti))
megfwd = _compute_forwards(rr, bem, [megcoils], [compcoils],
[meg_info], ['meg'], n_jobs,
verbose=False)[0]
megfwd = _to_forward_dict(megfwd, megnames)
else:
megfwd = pick_channels_forward(forward, megnames, verbose=False)
fwd = _merge_meg_eeg_fwds(megfwd, eegfwd, verbose=False)
fwd.update(**update_kwargs)
fwd_blink = fwd_ecg = fwd_chpi = None
if blink_rrs is not None:
megblink = _compute_forwards(blink_rrs, exg_bem, [megcoils],
[compcoils], [meg_info], ['meg'],
n_jobs, verbose=False)[0]
megblink = _to_forward_dict(megblink, megnames)
fwd_blink = _merge_meg_eeg_fwds(megblink, eegblink, verbose=False)
if ecg_rrs is not None:
megecg = _compute_forwards(ecg_rrs, exg_bem, [megcoils],
[compcoils], [meg_info], ['meg'],
n_jobs, verbose=False)[0]
fwd_ecg = _to_forward_dict(megecg, megnames)
if hpi_rrs is not None:
fwd_chpi = _magnetic_dipole_field_vec(hpi_rrs, megcoils).T
yield fwd, fwd_blink, fwd_ecg, fwd_chpi
# need an extra one to fill last buffer
yield fwd, fwd_blink, fwd_ecg, fwd_chpi
def _restrict_source_space_to(src, vertices):
"""Trim down a source space."""
assert len(src) == len(vertices)
src = deepcopy(src)
for s, v in zip(src, vertices):
s['inuse'].fill(0)
s['nuse'] = len(v)
s['vertno'] = v
s['inuse'][s['vertno']] = 1
for key in ('nuse_tri', 'use_tris'):
if key in s:
del s[key]
# This will fix 'patch_info' and 'pinfo'
_adjust_patch_info(s, verbose=False)
return src
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