U f{j0@s ddlmZddlmZddlZddlZddlZddlZddlmZ ddl Z ddl m Z m Z ddlmZddlmZdd lmZdd lmZmZdd lmZmZmZdd lmZmZmZmZm Z m!Z!dd l"m#Z#m$Z$m%Z%m&Z&ddl'm(Z(m)Z)m*Z*m+Z+m,Z,m-Z-m.Z.m/Z/ddl0m1Z1ddl2m3Z3m4Z4ddl5m6Z6ddl7m8Z8m9Z9m:Z:m;Z;mm?Z?m@Z@ddlAmBZBddlCmDZDmEZEmFZFddlGmHZHmIZImJZJmKZKmLZLmMZMmNZNmOZOmPZPmQZQmRZRmSZSmTZTmUZUmVZVddlWmXZXGdddeYZZddZ[ddZ\ddZ]ePd d!Z^d"d#Z_eOdZd$d%Z`eOd[d'd(ZaeOd\d+d,ZbeOd]d-d.Zcd/d0Zdd^d1d2ZeePd3d4Zfd_d5d6Zgd`d8d9ZheOdad:d;Zidsz:Forward._get_src_type_and_ori_for_repr..rKsurfzSurface with %d verticesnsourcevolzVolume with %d grid pointsdiscretezDiscrete with %d dipolesz %d surface, z %d volume, z %d discrete, z, zMixed (%s) with %d vertices source_oriUnknownZFixedZFree) nparrayallanysumrstriprZFIFFV_MNE_UNKNOWN_ORIFIFFV_MNE_FIXED_ORIFIFFV_MNE_FREE_ORI)rD src_typessrc_typeZ count_stringsrc_orirErErF_get_src_type_and_ori_for_reprs6         z&Forward._get_src_type_and_ori_for_reprcCsd}tt|dddgd}|dd|7}tt|dddgd}|dd|7}|\}}|d |7}|d |7}|d 7}|S) z/Summarize forward info instead of printing all.z)lenrr_)rDZentrnchanr]r^rErErF__repr__s zForward.__repr__c CsLddlm}|d\}}}}|\}}|d}|j||||d}|S)Nr)repr_templates_envr`zforward.html.jinja)Z good_channelsZ bad_channelsZsource_space_descrZsource_orientation)Zhtml_templatesrhZ_get_chs_for_reprr_Z get_templaterender) rDrhZgood_chsZbad_chs_Z src_descrr^thtmlrErErF _repr_html_s   zForward._repr_html_cCs |ddS)Nr`ch_namesrErCrErErFrnszForward.ch_namesFcCst||g|dddS)aPick channels from this forward operator. Parameters ---------- ch_names : list of str List of channels to include. ordered : bool If true (default False), treat ``include`` as an ordered list rather than a set. Returns ------- fwd : instance of Forward. The modified forward model. Notes ----- Operates in-place. .. versionadded:: 0.20.0 F)rcorderedrGr9)r)rDrnrorErErFrs zForward.pick_channelsN)F) __name__ __module__ __qualname____doc__rGr_rgrmpropertyrnrrErErErFrB6sK  rBc Csddlm}||rtd|j\}}|t|}||dkrHtdtj||tj d ||}t |d|f}| }tj|tj ddddf}|tj |tj ddddf}|j }||j tj||fjf} | S)aConstruct a block diagonal from a packed structure. You have to try it on a matrix to see what it's doing. If A is not sparse, then returns a sparse block diagonal "bd", diagonalized from the elements in "A". "A" is ma x na, comprising bdn=(na/"n") blocks of submatrices. Each submatrix is ma x "n", and these submatrices are placed down the diagonal of the matrix. If A is already sparse, then the operation is reversed, yielding a block row matrix, where each set of n columns corresponds to a block element from the block diagonal. Parameters ---------- A : array The matrix n : int The block size Returns ------- bd : scipy.sparse.spmatrix The block diagonal matrix rsparsez#sparse reversal not implemented yetz'Width of matrix must be a multiple of nZdtypeN)scipyrvissparseNotImplementedErrorshapeint ValueErrorrTarangeZint64reshapetileravelonesTZ coo_matrixZc_Ztocsc) AnrvmanaZbdntmpiiZjjZbdrErErF _block_diags       $rcCs2t|||}|dkr(|t|dt|jS)z!Check we have an appropriate tag.Nz tag not found)r closer~r}data)fidnodenameZid_tagrErErF _get_tag_ints   rcCs|dkr dSt}t||dtj|d<t||dtj|d<t||dtj|d<t||dtj|d <z.t||tjd d |d <|d d  |d<Wn t k rt dYnXz2tj }t|||d d |d<|dd  |d<Wnt k rd|d<YnX|d d jd|d ks\|d d jd|dkrd|d d jdd|dkrdtd|ddk r|dd jd|d ks|dd jdd|dkr|dd jdd|dkrtd|S)z4Read all interesting stuff for one forward solution.NzSource orientationrRzCoordinate frame coord_framezNumber of sourcesrNzNumber of channelsrfT)Z transposesolr _orig_solzForward solution data not foundsol_grad_orig_sol_gradrrxz,Forward solution matrix has wrong dimensions z5Forward solution gradient matrix has wrong dimensions)rBrrFIFF_MNE_SOURCE_ORIENTATIONFIFF_MNE_COORD_FRAMEFIFF_MNE_SOURCE_SPACE_NPOINTS FIFF_NCHANr FIFF_MNE_FORWARD_SOLUTIONrG Exceptionr8errorFIFF_MNE_FORWARD_SOLUTION_GRADr|r~)rroneZfwd_typerErErF _read_ones\   rcstd_t|tj}t|dkr,td|d}t||tj}|dk rP|j ndd<t||tj }|dk rt|j ndd<t|tj }t|dkrtd|d}t||tj}|dk r|j ndd<t||tj }|dk r|j ndd<t d <}t |d D]D}|d |j}|d |j}|tjkrt||}||j qt|||} t||tj}tj} tj} tj} tj} |dkrtd |j }|d | kr|d| kr|d<ntd t||tj}|dkrtd|j }|d | kr|d| kr|d<n.|d | kr>|d| kr>|d<ntdt||| dd<fdddDd<t||tj}|dkrt||d}|dk rt|j ndd<d_S)zRead light measurement info from forward operator. Parameters ---------- tree : tree FIF tree structure. fid : file id The file id. Returns ------- %(info_not_none)s Trz+No parent MEG information found in operatorNmri_filemri_id meas_filemeas_idchsZnent directory,MRI/head coordinate transformation not foundfromto mri_head_tz,MEG/head coordinate transformation not found dev_head_t ctf_head_t)ch_names_mappingbadscsg|]}|dkr|qSrnrE)rJbadr`rErFrLs z+_read_forward_meas_info..FZcustom_ref_applied)rZ _unlockedr rFIFFB_MNE_PARENT_MRI_FILErer~r FIFF_MNE_FILE_NAMErFIFF_PARENT_FILE_IDFIFFB_MNE_PARENT_MEAS_FILElistrangekindposZ FIFF_CH_INFOr appendrZ_update_redundantFIFF_COORD_TRANSFIFFV_COORD_HEADFIFFV_COORD_MRIZFIFFV_COORD_DEVICEZFIFFV_MNE_COORD_CTF_HEADrZFIFF_MNE_CUSTOM_REFr})treer parent_mrirZ parent_megrkrrrZ coord_headZ coord_mriZ coord_deviceZcoord_ctf_headcandrErrF_read_forward_meas_infoKsv               rcCs |djS)z%Get subject id from inverse operator.rK)Z_subject)forwardrErErF_subject_from_forwardsrcCs|dk r|dk r|ddjd|ddjdksh|d|dksh|d|dksh|d|dkrptd|}tj|dd|ddf|dd<tj|d |d f|d <|dd |dd |dd <|dd |dd |dd <|d dk rtj|d d|d df|d d<tj|d |d f|d <|d d |d d |d d <|d d |d d |d d <|d|d|d<tdn|dk r|}n|}|S)z5Merge loaded MEG and EEG forward dicts into one dict.NrrrxrRrNrz.The MEG and EEG forward solutions do not matchrnrow row_namesrrrfz* MEG and EEG forward solutions combined)r|r~rTZr_r8r`)megfwdeegfwdr9fwdrErErF_merge_meg_eeg_fwdssF$&            rrEc CsLt|ddt|ddd}td|t|\}}}|}t|tj}t|dkrbt d|t|tj } t| dkrt d || d} t ||d d } | D]} t | | d <qd } d } d }t t|D]R}t|||tj}|d krt d|jtjkr||} q|jtjkr||}qt|| }|d k rbt|rBd}nd}td|d|d|ft||}|d k rt|rd}nd}td|d|d|ft||} t|| tj}|d krt d|j}|dtjks|dtjkr.t|}|dtjks|dtjkr.|t d|| d<t||| d<t|tj}t|dkr|d}t||tj}|d k r| d|j| dd<W5QRXt||tj}|d k r| d|j| dd<W5QRXW5QRX| dtjtjfkr t dd}| D]X} zt | | d|} Wn0t!k rZ}zt d|W5d }~XYnX|| d7}q|| dkrt d td!| | d"<t"j#d#d$| Ddd%| d&<| d'| d(<t$| ||d d)t| dd*rt"j#d+d$| d"Ddd%| d,<tj%| d'<d| d-<n6t"&t"'| dd.ft"(d/| d,<tj)| d'<d | d-<t*| S)0a^Read a forward solution a.k.a. lead field. Parameters ---------- fname : str The file name, which should end with -fwd.fif or -fwd.fif.gz. include : list, optional List of names of channels to include. If empty all channels are included. exclude : list, optional List of names of channels to exclude. If empty include all channels. %(verbose)s Returns ------- fwd : instance of Forward The forward solution. See Also -------- write_forward_solution, make_forward_solution Notes ----- Forward solutions, which are derived from an original forward solution with free orientation, are always stored on disk as forward solution with free orientation in X/Y/Z RAS coordinates. To apply any transformation to the forward operator (surface orientation, fixed orientation) please apply :func:`convert_forward_solution` after reading the forward solution with :func:`read_forward_solution`. Forward solutions, which are derived from an original forward solution with fixed orientation, are stored on disk as forward solution with fixed surface-based orientations. Please note that the transformation to surface-based, fixed orientation cannot be reverted after loading the forward solution with :func:`read_forward_solution`. rz-fwd.fifz -fwd.fif.gzz_fwd.fifz _fwd.fif.gzTread)fnameZ must_exist overwritez#Reading forward solution from %s...rzNo forward solutions in %szNo parent MRI information in %sF)Z patch_statsidNz3Methods not listed for one of the forward solutionsfixedfreezH Read MEG forward solution (%d sources, %d channels, %s orientations)rNrfzH Read EEG forward solution (%d sources, %d channels, %s orientations)rrrrr` working_dir command_linerzIOnly forward solutions computed in MRI or head coordinates are acceptable%Could not transform source space (%s)nusez0Source spaces do not match the forward solution.zF Source spaces transformed to the forward solution coordinate framerKcSs$g|]}|d|dddfqS)ZrrvertnoNrErJssrErErFrLtsz)read_forward_solution..axis source_rrrR_orig_source_ori)includercrGorigcSs$g|]}|d|dddfqS)nnrNrE)rJZ_srcrErErFrL~s source_nnsurf_orirxr)+r7r2r8r`r r rFIFFB_MNE_FORWARD_SOLUTIONrer~rr&r'rr FIFF_MNE_INCLUDED_METHODSr FIFFV_MNE_MEG FIFFV_MNE_EEGris_fixed_orientrrrrr0rr FIFFB_MNE_ENVFIFF_MNE_ENV_WORKING_DIR_unlockFIFF_MNE_ENV_COMMAND_LINEr/rrT concatenaterrZkronreyer[rB)rrrcr9frrjrfwdsrrKsrZmegnodeZeegnoderrrZorirrZ parent_envrinstrErErFread_forward_solutions(                       "        $ rFTcsddlm}|r|n|}|dkr(d}tdd|dDrJ|rJtd|rrtdd |dDrttd nd td t|dd s|rlsltj fdd|dDdd|d<t|dd sVtdt |dj d}|d| d|dd<|d|dd<|ddk rV| |gd}|d||dd<d|d|dd<tj|d<d|d<n|rZtt|ddftd|d<tdd} |dD]b} | d d!krt| } | d| d"} t| d#d|d| | <| } ~ n| d| d"7} q|r|dd$ddddf|d<t |dj d}|d| d|dd<|d|dd<|ddk r| |gd}|d||dd<d|d|dd<tj|d<d|d<nt |dj d} |d| |dd<d|d|dd<|ddk rF| | gd}|d||dd<d%|d|dd<tj|d<d|d<ntd&ttd|ddf|d<|d|dd<d|d|dd<|ddk r|d|dd<d%|d|dd<tj|d<d |d<td'|S)(a_Convert forward solution between different source orientations. Parameters ---------- fwd : Forward The forward solution to modify. surf_ori : bool, optional (default False) Use surface-based source coordinate system? Note that force_fixed=True implies surf_ori=True. force_fixed : bool, optional (default False) If True, force fixed source orientation mode. copy : bool Whether to return a new instance or modify in place. %(use_cps)s %(verbose)s Returns ------- fwd : Forward The modified forward solution. rruTcSsg|]}|ddkqS)rHrOrErIrErErFrLsz,convert_forward_solution..rKzForward operator was generated with sources from a volume source space. Conversion to fixed orientation is not possible. Consider using a discrete source space if you have meaningful normal orientations.css|]}|ddk VqdS)Z patch_indsN)getrJrrErErF sz+convert_forward_solution..z_ Average patch normals will be employed in the rotation to the local surface coordinates....Fz No patch info available. The standard source space normals will be employed in the rotation to the local surface coordinates....rcsg|]}t|qSrE)r*ruse_cpsrErFrLsrrz\ Changing to fixed-orientation forward solution with surface-based source orientations...rxrZfloat32rrrNncolrNrrrRrz6 Converting to surface-based source orientations...rH)rMrPrrrz$ Cartesian source orientations...z [done])ryrvrGrWr~r8r`rrTrrrZastypeZ block_diagrrZrrrr*r.rr[r)rr force_fixedrGrr9rvZfix_rotxpprrstopZsurf_rotrErrFconvert_forward_solutions        $           rc Cs8t|ddt||}t|}t||W5QRXdS)aWrite forward solution to a file. Parameters ---------- fname : str File name to save the forward solution to. It should end with ``-fwd.fif`` or ``-fwd.fif.gz``. fwd : Forward Forward solution. %(overwrite)s %(verbose)s See Also -------- read_forward_solution Notes ----- Forward solutions, which are derived from an original forward solution with free orientation, are always stored on disk as forward solution with free orientation in X/Y/Z RAS coordinates. Transformations (surface orientation, fixed orientation) will be reverted. To reapply any transformation to the forward operator please apply :func:`convert_forward_solution` after reading the forward solution with :func:`read_forward_solution`. Forward solutions, which are derived from an original forward solution with fixed orientation, are stored on disk as forward solution with fixed surface-based orientations. Please note that the transformation to surface-based, fixed orientation cannot be reverted after loading the forward solution with :func:`read_forward_solution`. rrN)r7r2r _write_forward_solution)rrrr9rrErErFwrite_forward_solutions!   rc st|tjt|tjt|tjddd}|dk rJt|tj|ddd}|dk rpt|tj |t |tjt|tj t|tj dddddk rt|tj ddt|ddt |tj t|dt}dD]d}t|}zt|ddd}Wn0tk rV}ztd |W5d}~XYnX||qt||td d |D}d tjkr|}nd |}d}ddk rƈd} nd} ddkrd tjkrtdtn tdttddddgd} tddddgd} t| } t| } fdd | D}fdd | D}| dkr6t|| | ||gd}t|t|tj t!|tj"tj#t!|tj$dt!|tj%d t!|tj&|t!|tj'| t(|tj)|| dk r*t| | | |d |gd}t|t(|tj*|t |tj | dkrt|| | ||gd}t|t|tj t!|tj"tj+t!|tj$dt!|tj%d t!|tj'| t!|tj&|t(|tj)|| dk rt| | | |d |gd}t|t(|tj*|t |tj t |tjdS)Nr`rrrrrrKrrcSsg|] }|dqS)rrErrErErFrLhsz+_write_forward_solution..rrrrrrTaThe forward solution, which is stored on disk now, is based on a forward solution with fixed orientation. Please note that the transformation to surface-based, fixed orientation cannot be reverted after loading the forward solution with read_forward_solution.aThis forward solution is based on a forward solution with free orientation. The original forward solution is stored on disk in X/Y/Z RAS coordinates. Any transformation (surface orientation or fixed orientation) will be reverted. To reapply any transformation to the forward operator please apply convert_forward_solution after reading the forward solution with read_forward_solution.FrarbZref_megrccsg|]}dd|qSrrrErJprrErFrLscsg|]}dd|qSrrErr rErFrLsr)rrrrZ col_namesr),rrZ FIFFB_MNErr!Z FIFF_BLOCK_IDrrrrrrrrrwrite_forward_meas_inforrr/rr~rr)rXrZrGr5RuntimeWarningrredictrrrrrrrrrrrrr)rrrrKrrZn_vertZn_colrrZ picks_megZ picks_eegZn_megZn_eegZ row_names_megZ row_names_eegZ meg_solutionZmeg_solution_gradZ eeg_solutionZeeg_solution_gradrEr rFr9s                     rcCs&|r|dtjk}n|dtjk}|S)a|Check if the forward operator is fixed orientation. Parameters ---------- forward : instance of Forward The forward. orig : bool If True, consider the original source orientation. If False (default), consider the current source orientation. Returns ------- fixed_ori : bool Whether or not it is fixed orientation. rrR)rrZ)rrZ fixed_orirErErFrsrcCs|t|tjt|tj|d|ddk rDt|tj|d|d|d}|dkrn| t dt ||t }d|krt |d}t|tjt|dt||dd|d |kr t|d d kr t|d |}t|tjt|tj|t|tjt|tjdS) zWrite measurement info stored in forward solution. Parameters ---------- fid : file id The file id %(info_not_none)s rrNrrz"Head<-->sensor transform not foundrFrr)_check_consistencyrrrrrr!ZFIFF_PARENT_BLOCK_IDrrr~rr rrrrerrZFIFFB_MNE_BAD_CHANNELSrZFIFF_MNE_CH_NAME_LISTr)rr`Z meg_head_trrrErErFr s*       r c s|dd}t|tddk rJtdMtdOntddfddd D}tdtdkrtfd d dDstd t|d dt|}td|t||d|d}fdd|D}t|}|d  | ||fS)z-Prepare forward solution for inverse solvers.rrrNnames)rcs,g|]$}|dkr|dkr|dqS)ch_namerE)rJc)all_bads all_ch_namesrErFrL s  z*_select_orient_forward..rc3s|]}|dkVqdS)rNrE)rJb) noise_covrErFrsz)_select_orient_forward..zQinfo["bads"] and noise_cov["bads"] do not match, excluding bad channels from bothr`rz,Computing inverse operator with %d channels.T)rorGcsg|]}d|qSrindexrJrrrErFrLs) setr rerVr8r`r<rrr) rr`rrGZfwd_sol_ch_namesrnZn_chanZinfo_idxZ info_pickedrE)rrr`rrF_select_orient_forwards.     rautocstttdfdt|ttfd}ttr\tdd|dkrJdn|jdkrXdnd td d |D}ttstfd d |Dt }||krt dt |dt ||dkrt dd Dst d|n*|dkrtdd Drt d~D]`\}}|dkrT|dkrTt d|d|d|krldks$nt d|d|q$S)Nnumericlooser)rTsurfaceg??css|]}t|dVqdS)rHN)r+rrErErFr.sz _triage_loose..csi|] }|qSrErErJkeyrrErF 1sz!_triage_loose..zloose, if dict, must have keys z to match the source space, got css|]}|dkVqdSrNrErJvrErErFr:sz7When using fixed=True, loose must be 0. or "auto", got Fcss|]}|dkVqdSr%rEr&rErErFr?sz:If loose==0., then fixed must be True or "auto", got False)rrPrxzYloose parameter has to be 1 or "auto" for non-surface/discrete source spaces, got loose["z"] = rzloose (z) must be between 0 and 1, got )r;strr bool isinstancer=rrfloatkeysr~sortedrVvaluesrWitems)rKrrZ orig_looser\Z loose_keysr"Z this_looserEr#rF _triage_loose$sL     r0c Csjt|td|ddjd}t|d|}tj|tjd}t|rltdd| Drht d |f|St d d| Dr|S|d st d |fd }t }|dD]}t |d}||} ||s | dkrd} n| dkrdnd} td| dd|dd| d||<|d|d} ||| d| 9<||d| d| 9<| }q|S)a/Compute orientation prior. Parameters ---------- forward : instance of Forward Forward operator. %(loose)s %(verbose)s Returns ------- orient_prior : ndarray, shape (n_sources,) Orientation priors. See Also -------- compute_depth_prior rrrrxrKrwcss|]}|dkVqdSr%rEr&rErErFrisz'compute_orient_prior..zEloose must be 0. with forward operator with fixed orientation, got %scss|]}|dkVqdS)r NrEr&rErErFrmsrz]Forward operator is not oriented in surface coordinates. loose parameter should be 1. not %s.rrHr rrrrz Applying z dipole orientations to z source spaces: Trr)r;rBr|r0rTrZfloat64rrWr.r~rVr r+rr8r`ljust) rrr9 n_sourcesZ orient_priorstartZloggedrZ this_typeZ use_looserrrErErFcompute_orient_priorOs@    (r6cCst|d|jdkr4td|jdt|dfdD]B\}}}t|||dgd}t|dkr8tdt||fqq8tdtd }||S) z9Restrict gain matrix entries for optimal depth weighting.rrz;G.shape[0] (%d) and length of info["chs"] (%d) do not match))gradFZplanar)magFz!magnetometer or axial gradiometer)FTZEEGFrz %d %s channelsz:Could not find MEG or EEG channels to limit depth channelsN)rer|r~rr8r`r5slice)Gr`rarbrselrErErF_restrict_gain_matrixs r<皙?$@spectralc  Csddlm} m} t|td|dd} t|} |dd} tdt|| dfd d t|t t fd t |t r|d krt d |ft || st dt |f|dk rtd|d|dkrt| |} n*|d kr| ||d|dd\}}t|| } | s|dkrXtj| ddd}| s<|dks<|ddjdd}t||dk||dk<n>| jdddf| _tjjtd| | ddd}| jddf| _| dk r| s|dkrt| d} || d}tdd|}|dk rt|}|d}|dkrd}|d|}nP|d}t|}|d||dkrbt|||dkdd}||}|}td |dt|t||dfd|}td!||ft||d}||}| s|dkst|d}|S)"aW Compute depth prior for depth weighting. Parameters ---------- forward : instance of Forward The forward solution. %(info_not_none)s exp : float Exponent for the depth weighting, must be between 0 and 1. limit : float | None The upper bound on depth weighting. Can be None to be bounded by the largest finite prior. limit_depth_chs : bool | 'whiten' How to deal with multiple channel types in depth weighting. The default is True, which whitens based on the source sensitivity of the highest-SNR channel type. See Notes for details. .. versionchanged:: 0.18 Added the "whiten" option. combine_xyz : 'spectral' | 'fro' When a loose (or free) orientation is used, how the depth weighting for each triplet should be calculated. If 'spectral', use the squared spectral norm of Gk. If 'fro', use the squared Frobenius norm of Gk. .. versionadded:: 0.18 noise_cov : instance of Covariance | None The noise covariance to use to whiten the gain matrix when ``limit_depth_chs='whiten'``. .. versionadded:: 0.18 %(rank_none)s .. versionadded:: 0.18 %(verbose)s Returns ------- depth_prior : ndarray, shape (n_vertices,) The depth prior. See Also -------- compute_orient_prior Notes ----- The defaults used by the minimum norm code and sparse solvers differ. In particular, the values for MNE are:: compute_depth_prior(..., limit=10., limit_depth_chs=True, combine_xyz='spectral') In sparse solvers and LCMV, the values are:: compute_depth_prior(..., limit=None, limit_depth_chs='whiten', combine_xyz='fro') The ``limit_depth_chs`` argument can take the following values: * :data:`python:True` (default) Use only grad channels in depth weighting (equivalent to MNE C minimum-norm code). If grad channels aren't present, only mag channels will be used (if no mag, then eeg). This makes the depth prior dependent only on the sensor geometry (and relationship to the sources). * ``'whiten'`` Compute a whitener and apply it to the gain matirx before computing the depth prior. In this case ``noise_cov`` must not be None. Whitening the gain matrix makes the depth prior depend on both sensor geometry and the data of interest captured by the noise covariance (e.g., projections, SNR). .. versionadded:: 0.18 * :data:`python:False` Use all channels. Not recommended since the depth weighting will be biased toward whichever channel type has the largest values in SI units (such as EEG being orders of magnitude larger than MEG). r) Covariancecompute_whitenerr patch_areasNrrz&Creating the depth weighting matrix...rzCovariance or Nonelimit_depth_chsZwhitenz1limit_depth_chs, if str, must be "whiten", got %szEWith limit_depth_chs="whiten", noise_cov must be a Covariance, got %sF combine_xyz)fror?T)Zpcarankr9)rEFrrrrrxrz svj,svk->vjk)rxr)ordrz9 Patch areas taken into account in the depth weightingr z limit = %d/%d = %fz scale = %g exp = %g)Zcovr@rAr;rBrrr8r`r(r)r*r~rHr=r<rTdotrXrminr|ZlinalgZnormZeinsumrepeatsortrewheresqrtminimum)rr`explimitrCrDrrFr9r@rArBZ is_fixed_orir:ZwhitenerrjdwwsZ weight_limitZn_limitindscaleZ depth_priorrErErFcompute_depth_priorsS                      rVraise$, likely due to forward calculationscCst|tr|}nt|tst|j}~t|t|ksNtdt|t|fggg}}}d}} t||D]|\} } t | d| } | t | d| ||t| d7}t | | } | | | | t| 7} | t | | qpt |}t |}t|t|kr0tdd|Dks6nttdd|D}t|}||krd|||dkrnd nd |f}t|||||fS) zDSelect the vertex indices of a source space using a source estimate.zCMismatch between number of source spaces (%s) and STC vertices (%s)rrcss|]}t|VqdSNrer&rErErFr_sz_stc_src_sel..css|]}t|VqdSrYrZr&rErErFrasz7Only %i of %i SourceEstimate %s found in source space%srxZvertexvertices)r*rr-AssertionErrorr[re RuntimeErrorziprT intersect1dr searchsortedrUrrXr@)rKstc on_missingextrar[Zsrc_selsZstc_selsZ out_verticesZ src_offsetZ stc_offsetrr'Z joint_selidxsrc_selstc_selZn_stcZn_jointmsgrErErF _stc_src_selGs@     4  rhc st|ddd}t||}g|d<t}t|}d||}|jdd>|jdd |d tt|t|fd |d |gd W5QRXfd d|dD}||}||fS)z4Fill the measurement info of a Raw or Evoked object.rnrrrg.AT)Z check_afterr`rrg@)rZfile_idZ meas_dateZhighpassZlowpasssfreqprojscsg|]}dd|qSrrrr rErFrL}sz*_fill_measurement_info..) rrrrTfloorrupdater?r}) r`rrirr;nowsecZusecorderrEr rF_fill_measurement_infols"   rpcCsNt|tddt|tdt|tr8d}t|ddd}nd}t|sRt|d|d}t|j dkrjt d t |t |d ||d \}} } |d d } t | t |j krtdn| } |j||} |j | d||fdt | } ~|r | t | | jddd} | dd|ft | d} tdt| | }td|| fS)z5Apply forward model and return data, times, ch_names.raZSourceEstimaterTF)rr)rrrzSource estimate only contains currents with positive values. Use pick_ori="normal" when computing the inverse to compute currents not current magnitudes.rKrbrrN.rrxrz-Projecting source estimate to sensor space...z[done])r;r-rBr*r,rrrTrVrr5r>rhrer9timesrGrr|r8r`rH)rrar5rrbrr9ZvectorrerfrjZgainrrZstc_datarrErErF_apply_forwards4       rsc Cst|tdt|td||ddD]}||dkr,td|q,t||||||d\} } td|j} t||| | \}} t | || d d d } | | | | S) aProject source space currents to sensor space using a forward operator. The sensor space data is computed for all channels present in fwd. Use pick_channels_forward or pick_types_forward to restrict the solution to a subset of channels. The function returns an Evoked object, which is constructed from evoked_template. The evoked_template should be from the same MEG system on which the original data was acquired. An exception will be raised if the forward operator contains channels that are not present in the template. Parameters ---------- fwd : Forward Forward operator to use. stc : SourceEstimate The source estimate from which the sensor space data is computed. %(info_not_none)s start : int, optional Index of first time sample (index not time is seconds). stop : int, optional Index of first time sample not to include (index not time is seconds). %(use_cps)s .. versionadded:: 0.15 %(on_missing_fwd)s Default is "raise". .. versionadded:: 0.18 %(verbose)s Returns ------- evoked : Evoked Evoked object with computed sensor space data. See Also -------- apply_forward_raw: Compute sensor space data and return a Raw object. r`rrrrnz>Channel %s of forward operator not present in evoked_template.rbrr rrx)Znave) r;rrBrr~rsr+tsteprpr$Z _set_timesZ_update_first_last) rrar`r5rrrbr9rrrrrievokedrErErF apply_forwards"+      rwc Cs|ddD]}||dkr td|q t||||||d\} } d|j} t||| | \}} |g|d<W5QRXt| |tt| d| d } d | _ | S) aProject source space currents to sensor space using a forward operator. The sensor space data is computed for all channels present in fwd. Use pick_channels_forward or pick_types_forward to restrict the solution to a subset of channels. The function returns a Raw object, which is constructed using provided info. The info object should be from the same MEG system on which the original data was acquired. An exception will be raised if the forward operator contains channels that are not present in the info. Parameters ---------- fwd : Forward Forward operator to use. stc : SourceEstimate The source estimate from which the sensor space data is computed. %(info_not_none)s start : int, optional Index of first time sample (index not time is seconds). stop : int, optional Index of first time sample not to include (index not time is seconds). %(on_missing_fwd)s Default is "raise". .. versionadded:: 0.18 %(use_cps)s .. versionadded:: 0.21 %(verbose)s Returns ------- raw : Raw object Raw object with computed sensor space data. See Also -------- apply_forward: Compute sensor space data and return an Evoked object. rrrnz3Channel %s of forward operator not present in info.rtr rjr)Z first_sampN) r~rsrurprrr}rTroundZ _projector) rrar`r5rrbrr9rrrrrirawrErErFapply_forward_raws,      rzignorecCs<t|tdtd|dt|d||d\}}}~t||S)aRestrict forward operator to active sources in a source estimate. Parameters ---------- fwd : instance of Forward Forward operator. stc : instance of SourceEstimate Source estimate. %(on_missing_fwd)s Default is "ignore". .. versionadded:: 0.18 Returns ------- fwd_out : instance of Forward Restricted forward operator. See Also -------- restrict_forward_to_label rb)r{r5rWrKrq)r;r(r=rh_restrict_forward_to_src_sel)rrarbrerjr[rErErFrestrict_forward_to_stc.s   r}cst|}tjddt|dDddjdkr@jddksDtjd|d ksZtdd|f|d ||d <t||d <t|r|}|d dk rd |dddft d  }nRd |dddft d  }|d dk rd |dddft d  }|d||d<|dddd|f|dd<|d dk rr|d ddd|f|d d<t||dd<t|ddr|}|d dk rd |dddft d  }nRd |dddft d  }|d dk rd |dddft d  }|ddd|f|d<|d dk rV|ddd|f|d<fddt t|dD}t |d||S)NcSs*g|]"\}}|gt|d|dgqS)rrZ)rJsirrErErFrLPsz0_restrict_forward_to_src_sel..rKrrrrrxrNrrrrrrrrTrrrcs g|]}dd|kqS)rxrrE)rJr~Zidx_selrErFrLus) rrTr enumeratendimr|r\rerrrrr()rrefwd_outrdidx_gradr[rErrFr|MsL    $""  $"" r|c Cstgttgtg}t|ts(|g}|D]:}t|tdd|jdkrLdnd}t|||j ||<q,dd|D}t |}t d|d <d|d <t d|d <t |d d j ddf|d d <t |dj ddf|d<|ddk r0t |dd j ddf|dd <t |dj ddf|d<d|d d<|ddd}t dD]}tgt|d|d<d|d|d<|d|d|d|d<|d|ddtggt|d|d<tdg|d|d<t|d|d||}t|d|d|}|d|d|}d|d|d|<|d|dt|7<t|d|dd|d|d<|||7}t|d |d |g|d <|d t|7<t|r|} |ddk rXd|dddftd} nRd|dddftd} |ddk rXd|dddftd} t|d |d | g|d <t|d d |d d dd| fg|d d <|ddk rt|dd |dd dd| fg|dd <|d dt| 7<t|ddrD|} |ddk rd|dddftd} nRd|dddftd} |ddk rd|dddftd} t|d|ddd| fg|d<|ddk rTt|d|ddd| fg|d<qT|S)aQRestrict forward operator to labels. Parameters ---------- fwd : Forward Forward operator. labels : instance of Label | list Label object or list of label objects. Returns ------- fwd_out : dict Restricted forward operator. See Also -------- restrict_forward_to_stc labelz Label or listZlhrrxcSsg|]}t|qSrE)rTunique)rJZ vert_hemirErErFrLsz-restrict_forward_to_label..)rrrrNrrrrrNrrrKrrrZinuseZuse_trisZnuse_trirrZsol_radTr)rTrUr}r*rr;rAZhemirr[rZzerosr|rrGfillr_r`rerLZvstackrrrZhstack) rlabelsr[rirZnuse_lhrerrdrrErErFrestrict_forward_to_label|s $   &    $"""   $"" rc Cststdt}|dkr*t|d}t||t|ddt|t rbt |st d|n6t|t t tfrt|d}t||j|}ntd|dk r|dk rtd |dkr|dkrtd |dk rt|dd t |st d ||dk rxt|t s`t|trXt|}t|d }zt||Wntk rTt dYnXntdt |sxt d|| s| stdt|\}}t|ddkstdt|}|dk rt|t r|dkstddg}n dd|g}t|||fddD](\}}}|dk rt|||d|qdd|d|d |d!|g }|dk rh|d"|g7}|dk r|r~n0td#|}|dkrtd$|d%|}|d&|g7}|dk r||7}|dk r|d'|g7}|dk r|d(d)|g7}|dk r|d*d)|g7}| s&|d+| s6|d,| rF|d-| rV|d.| rf|d/|rv|d0t j!"}t#|d1d2}||d3<zPzt&d5|t'||d6Wntk rYnXt(t||d7d8}W5t$j%|d1d4X|S)9a Calculate a forward solution for a subject using MNE-C routines. This is kept around for testing purposes. This function wraps to mne_do_forward_solution, so the mne command-line tools must be installed and accessible from Python. Parameters ---------- subject : str Name of the subject. meas : Raw | Epochs | Evoked | str If Raw or Epochs, a temporary evoked file will be created and saved to a temporary directory. If str, then it should be a filename to a file with measurement information the mne command-line tools can understand (i.e., raw or evoked). fname : str | None Destination forward solution filename. If None, the solution will be created in a temporary directory, loaded, and deleted. src : str | None Source space name. If None, the MNE default is used. spacing : str The spacing to use. Can be ``'#'`` for spacing in mm, ``'ico#'`` for a recursively subdivided icosahedron, or ``'oct#'`` for a recursively subdivided octahedron (e.g., ``spacing='ico4'``). Default is 7 mm. mindist : float | str | None Minimum distance of sources from inner skull surface (in mm). If None, the MNE default value is used. If string, 'all' indicates to include all points. bem : str | None Name of the BEM to use (e.g., "sample-5120-5120-5120"). If None (Default), the MNE default will be used. mri : str | None The name of the trans file in FIF format. If None, trans must not be None. trans : dict | str | None File name of the trans file in text format. If None, mri must not be None. eeg : bool If True (Default), include EEG computations. meg : bool If True (Default), include MEG computations. fixed : bool If True, make a fixed-orientation forward solution (Default: False). Note that fixed-orientation inverses can still be created from free-orientation forward solutions. grad : bool If True, compute the gradient of the field with respect to the dipole coordinates as well (Default: False). mricoord : bool If True, calculate in MRI coordinates (Default: False) %(overwrite)s %(subjects_dir)s %(verbose)s See Also -------- make_forward_solution Returns ------- fwd : Forward The generated forward solution. z)mne command line tools could not be foundNz temp-fwd.fifr(subjectz(measurement file "%s" could not be foundzinfo.fifz+meas must be string, Raw, Epochs, or Evokedz&trans and mri cannot both be specifiedz%Either trans or mri must be specifiedtransztrans file "%s" not foundz mri-trans.fifzDmri was a dict, but could not be written to disk as a transform filez&trans must be a string or dict (trans)z"trans file "%s" could not be foundz!meg or eeg (or both) must be Truerxz.fifz#Forward name does not end with .fifrVz!mindist, if string, must be "all"z--allz --mindistz%g)rKspacingbem) path-liker(rz %s or NoneZmne_do_forward_solutionz --subjectz--measz--fwdz --destdirz--srcz(oct|ico)-?(\d+)$zInvalid spacing parameter: %r-z --spacingz--bemz--mriz%sz--transz --eegonlyz --megonlyz--fixedz--gradz --mricoordz --overwriteT)Z raise_errorZ SUBJECTS_DIR) ignore_errorsz@Running forward solution generation command with subjects_dir %s)envF)r9))r4r]tempfilemkdtempopjoinr2r;r*r(isfileIOErrorr"r%r#rr`r~r rr1rsplitsplitextabspathlowerr^isdigitrematchgroupsrosenvironrGr3shutilrmtreer8r6r)rZmeasrrKrZmindistrZmrirrbrarr7ZmricoordrZ subjects_dirr9temp_dirrZmri_datarelementrrcmdrrrrErErF_do_forward_solutionsE                                            rc sdttdtdks td|dkr6tt}t|}t|dksVtdt|tksntdt|}|dkstd||}D]Ltt dd d d d d ddddddddg }tfdd|Dst dqt fddddDr tdt fddddDr2tdt d}|dd|d9<|d|d9<t dd|ddD]B\}|dd|dd7<|d|d7<q|d dk r`|d d|d9<|d |d9<t dd|ddD]B\}|d d|d d7<|d |d 7<q|S)!aAverage forward solutions. Parameters ---------- fwds : list of Forward Forward solutions to average. Each entry (dict) should be a forward solution. weights : array | None Weights to apply to each forward solution in averaging. If None, forward solutions will be equally weighted. Weights must be non-negative, and will be adjusted to sum to one. %(verbose)s Returns ------- fwd : Forward The averaged forward solution. rrzfwds must not be emptyNzweights must be non-negativez/weights must be None or the same length as fwdszweights cannot all be zerozeach entry in fwdsr r`rrfrKrrrrRrrrrNc3s|]}|kVqdSrYrEr!r rErFrsz,average_forward_solutions..zQforward solution dict does not have all standard entries, cannot compute average.c3s4|],}dD]"}|d|dd|kVq qdS))rrrrNrErJrrrrErFrsrxz.Forward solutions have incompatible dimensionsc3s,|]$}dD]}||d|kVq qdS))rRrrrNrErrrErFrsz0Forward solutions have incompatible orientationsrrr)r;rrer~rTrZ asanyarrayrVrXr KeyErrorrWrr^)rweightsr9Zw_sumZ check_keysZfwd_averRrE)rrrFaverage_forward_solutionssZ          " " r)N)rErEN)FFTTN)FN)F)NT)r)rN)r=r>Fr?NNN)rWrX)NNrWTN)NNTrWN)NNrWTN)r{)NNNNNNNTTFFFFNN)NN)vrrGrrnumpyrTrrrrriorrZ io.constantsrZio.openr Zio.treer Zio.tagr r Z io.matrixr rrZ io.meas_inforrrrrrZio.pickrrrrZio.writerrrrrrr r!Zio.baser"rvr#r$Zepochsr%Z source_spacer&r'r(r)r*r+Zsource_estimater,r-rr.Z transformsr/r0r1utilsr2r3r4r5r6r7r8r9r:r;r<r=r>r?r@rrAr rBrrrrrrrrrrrr rr0r6r<rVrhrprsrwrzr}r|rrrrErErErF s       (    D ,2 / \ # 8  )  ( " + 9 * % & D > /l H