U f{jHw@sddlmZddlZddlmZddlmZddlm Z m Z m Z m Z ddl mZmZmZddlmZmZmZdd lmZmZmZdd lmZmZmZmZdd lmZdd l m!Z!m"Z"m#Z#m$Z$m%Z%m&Z&m'Z'm(Z(m)Z)m*Z*dd l+m,Z,m-Z-ddl.m/Z/m0Z0m1Z1ddl2m3Z3ddl4m5Z5ddl6m7Z7m8Z8m9Z9m:Z:m;Z;mZ>ddZ?ddZ@ddZAd2ddZBe8d3d d!ZCe8d4d"d#ZDe8d5d$d%ZEd&d'ZFe8d6d(d)ZGGd*d+d+eHZId7d,d-ZJGd.d/d/eHZKd0d1ZLdS)8)IterableN)_get_stim_channel)_Interp2) pick_types pick_info pick_channelspick_channels_forward)make_ad_hoc_covread_cov Covariance)fit_sphere_to_headshapemake_sphere_modelread_bem_solution)RawArrayBaseRawInfo) read_head_poshead_pos_to_trans_rot_t get_chpi_info_get_hpi_initial_fit)FIFF) _magnetic_dipole_field_vec_merge_meg_eeg_fwds _stc_src_selconvert_forward_solution_prepare_for_forward_transform_orig_meg_coils_compute_forwards_to_forward_dictrestrict_forward_to_stc_prep_meg_channels) _get_transtransform_surface_to) _ensure_src_set_source_space_verticessetup_volume_source_space)_BaseSourceEstimate) _CheckInside)loggerverbosecheck_random_state_pl_validate_type_check_preload)SourceSimulatorcCslt|tdttdfdt|tsh|dkr*n>t|trDt||dd}n$|dkr\t|ddd}n t|dd}|S)zECheck that the user provided a valid covariance matrix for the noise.Nz path-likecovFr*simple)r-r dictstr isinstancer r )infor1r8Q/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/simulation/raw.py _check_cov%s  r:cCspt|tr|g}t|tdt|}~z t|}Wntk rNtdYnXt|d|d\}}}|||fS)Nz"SourceEstimate, tuple, or iterablezIterable did not provide stc[0]r/sfreq) r6r'r-r enumeratenext StopIteration RuntimeError_stc_data_event)stcr7stc_enum stc_counted_vertsr8r8r9_check_stc_iterable4s   rFcCsH|dk r"dd|d|}}}n d\}}}t||||dS)zLog channel information.Nz stored on channel:2ch_names)z not storedr)r)r7ljust)startr7chextraZjustr8r8r9_log_chFs rNc sdkrtttr tttjr4tttrv\}}}|d}||}ddt||D}~~nJttrt t t }| fdd|D}ntdt|dk} | rtd| t| f|dk r&||dk} | r&td |d| t| ft|dkrT|dd dkrTd |d<n@t|dksp|ddkrtjd g|f}|dd d fdd|D}t|dt} t| t| stt| t|kstt | } || fS)Nr;cSs@g|]8\}}tjtj||ddtjffddddggfqS)Nrr/)npr_Zc_newaxis).0rtr8r8r9 Zsz#_check_head_pos..csg|]}t|qSr8)float)rRtt)head_posr8r9rU`szunknown head_pos type %srz/All position times must be >= 0, found %s/%s< 0z_All position times must be <= t_end (%0.1f sec), found %s/%s bad values (is this a split file?)? dev_head_ttranscs(g|] }|dddddqS)r\tofrom)r]r^r_r8)rRd)r7r8r9rUts  )r4r6r5rrOndarrayrtupleziparraylistkeysrVsort TypeErrortypeanyr?sumlenrPinsertroundastypeint array_equaluniqueAssertionError) rXr7 first_samptimesZtranssZrotstsZ first_time dev_head_tsbadoffsetsr8)rXr7r9_check_head_posOsV         $  rz?cos2T'c% Csdt|tdtt|ddddkr(d}nt|dtd|d}| dk rtdd ||||fDrjtd tj | dd d |d d d dstd| d}t ||| d\}}t |dd}t |t rt|dd}t|ddgd}tdt|t||ft |tr |j| kr tdt||\}}}| dk rNt| |} | d}nt||dddt||}t}td||d}t|||||||||| | }t|||}d}t| D]d}t |dttfr|ddjj d}n|djj d}||}td||d||df||}|dks6t!t"t|d|f}|#||$||\}}|d}t%|||d|j&|dkrdn|\} }!}"|dk r|!d|||ddf<t'd|| ||<z t(|}Wn<t)k rtd|dt|dfYq,YnX~qt*d|ftj+|dd }#t,|#|| dd!}$|$-|$j.td"|$S)#uSimulate raw data. Head movements can optionally be simulated using the ``head_pos`` parameter. Parameters ---------- %(info_not_none)s Used for simulation. .. versionchanged:: 0.18 Support for :class:`mne.Info`. stc : iterable | SourceEstimate | SourceSimulator The source estimates to use to simulate data. Each must have the same sample rate as the raw data, and the vertices of all stcs in the iterable must match. Each entry in the iterable can also be a tuple of ``(SourceEstimate, ndarray)`` to allow specifying the stim channel (e.g., STI001) data accompany the source estimate. See Notes for details. .. versionchanged:: 0.18 Support for tuple, iterable of tuple or `~mne.SourceEstimate`, or `~mne.simulation.SourceSimulator`. 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 | None Source space corresponding to the stc. If string, should be a source space filename. Can also be an instance of loaded or generated SourceSpaces. Can be None if ``forward`` is provided. bem : str | dict | None BEM solution corresponding to the stc. If string, should be a BEM solution filename (e.g., "sample-5120-5120-5120-bem-sol.fif"). Can be None if ``forward`` is provided. %(head_pos)s See for example :footcite:`LarsonTaulu2017`. mindist : float Minimum distance between sources and the inner skull boundary to use during forward calculation. %(interp)s %(n_jobs)s %(use_cps)s forward : instance of Forward | None The forward operator to use. If None (default) it will be computed using ``bem``, ``trans``, and ``src``. If not None, ``bem``, ``trans``, and ``src`` are ignored. .. versionadded:: 0.17 first_samp : int The first_samp property in the output Raw instance. .. versionadded:: 0.18 max_iter : int The maximum number of STC iterations to allow. This is a sanity parameter to prevent accidental blowups. .. versionadded:: 0.18 %(verbose)s Returns ------- raw : instance of Raw The simulated raw file. See Also -------- mne.chpi.read_head_pos add_chpi add_noise add_ecg add_eog simulate_evoked simulate_stc simulate_sparse_stc Notes ----- **Stim channel encoding** By default, the stimulus channel will have the head position number (starting at 1) stored in the trigger channel (if available) at the t=0 point in each repetition of the ``stc``. If ``stc`` is a tuple of ``(SourceEstimate, ndarray)`` the array values will be placed in the stim channel aligned with the :class:`mne.SourceEstimate`. **Data simulation** In the most advanced case where ``stc`` is an iterable of tuples the output will be concatenated in time as: .. table:: Data alignment and stim channel encoding +---------+--------------------------+--------------------------+---------+ | Channel | Data | +=========+==========================+==========================+=========+ | M/EEG | ``fwd @ stc[0][0].data`` | ``fwd @ stc[1][0].data`` | ``...`` | +---------+--------------------------+--------------------------+---------+ | STIM | ``stc[0][1]`` | ``stc[1][1]`` | ``...`` | +---------+--------------------------+--------------------------+---------+ | | *time →* | +---------+--------------------------+--------------------------+---------+ .. versionadded:: 0.10.0 References ---------- .. footbibliography:: r7FT)megZstimrNrHcss|]}|dk VqdSNr8)rRxr8r8r9 szsimulate_raw..zJIf forward is not None then trans, src, bem, and head_pos must all be Noner\r]gư>)ZatolzoThe forward meg<->head transform forward["info"]["dev_head_t"] does not match the one in raw.info["dev_head_t"]srcr2r~eegexcludezstz %d STC iteration%s providedz.Maximum number of STC iterations (%d) exceededrYaxis)rtr*z[done])/r-rrlrrrrj ValueErrorrOallcloserzr$r6r5rr)r7r,r0rtrFr rr%copyrerN _SimForwardsrrangerbdatashaperszerosappendfeedr@reinsumr=r>r? concatenaterZset_annotations annotations)%r7rAr]rbemrXmindistinterpn_jobsuse_cpsforwardrtZmax_iterr*Zevent_chrwry meeg_picksrBrCrEZ raw_datasnget_fwdinterperZ this_startZthis_nZ this_stopZn_doingZ this_datafwdfistc_data stim_datarDraw_datarawr8r8r9 simulate_raw~ss                   rcCst|d||||S)uvAdd blink noise to raw data. Parameters ---------- raw : instance of Raw The raw instance to modify. %(head_pos)s %(interp)s %(n_jobs)s %(random_state)s The random generator state used for blink, ECG, and sensor noise randomization. %(verbose)s Returns ------- raw : instance of Raw The instance, modified in place. See Also -------- add_chpi add_ecg add_noise simulate_raw Notes ----- The blink artifacts are generated by: 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 :footcite:`BentivoglioEtAl1997`. 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. The scale-factor of the activation function was chosen based on visual inspection to yield amplitudes generally consistent with those seen in experimental data. Noisy versions of the activation will be stored in the first EOG channel in the raw instance, if it exists. References ---------- .. footbibliography:: blink_add_exgrrXrr random_stater*r8r8r9add_eogLs3rcCst|d||||S)abAdd ECG noise to raw data. Parameters ---------- raw : instance of Raw The raw instance to modify. %(head_pos)s %(interp)s %(n_jobs)s %(random_state)s The random generator state used for blink, ECG, and sensor noise randomization. %(verbose)s Returns ------- raw : instance of Raw The instance, modified in place. See Also -------- add_chpi add_eog add_noise simulate_raw Notes ----- The ECG artifacts are generated by: 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. The scale-factor of the activation function was chosen based on visual inspection to yield amplitudes generally consistent with those seen in experimental data. Noisy versions of the activation will be stored in the first EOG channel in the raw instance, if it exists. .. versionadded:: 0.18 ecgrrr8r8r9add_ecgs1rc) Cst|tr|dkstt|tdt|d|ft|}|j|j|j }}} |j } t |dddd} t |dddd} t |ddd dd \} }t || d d dd }d}t||| |\}}|dkrtttjdttjddgttjd ttjddgg}|ttj||ddd}|d| 9}||7}tdddgdddgg}dtd tjdd|d}|d9}|d7}|jt|d||dk}||jt|dd}ttd|d}t||dtjddfd}t |dddd }| }~~~n)r~rZeogrz;Can only add ECG artifacts if MEG data channels are presentrYgT@g?g?g{Gz?g333333ӿg?g?gp= ף?rgv !>)r~rrgh㈵>g@@)rrnnmm)posZ sphere_unitsz%s simulated and traceg{Gzt?r}r)1r6r5rsr-rr.r+r7rurt_datarr rrzrOrdcospisinsqrtrkuniformrlZhanningrpZconvolverQr?ceilZcumsumrorrZ zeros_likeZstandard_normalrr&r4rNboolrrarangercrrrjall))rkindrXrrrrngr7rurtr meg_picksrRr0rr]rwryZexg_rrrZ blink_rateZ blink_dataZ blink_kernelZexg_datarLpicksZ max_beatsZ cardiac_idxZ cardiac_dataZcardiac_kernelnoiserusedrrZ proc_limsrKstoprrDr8r8r9rs  $" $      ""rc Cs:t|tdt|d|j|j|j}}}t|ddgd}t|dkrPtdt ||||\} } t |dd \} } } t |d d }|t t j||d d ddt jf}|j}| || ddf<td|| dt dt j| ddt jft t||d}t||}||jggdW5QRXt|dd\}}}}t t|jt}| | dt| | |||}t| ||}t | t|jgg}t|dd|d dD]n\}}| ||\}||||ft !d||dd||f7<|||"rt#d|||<q|$s6t#|S)aSAdd cHPI activations to raw data. 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