U f{jC> @sddlmZddlmZmZddlmZddlmZddlm Z ddl m Z ddl Z ddlZddlZdd lmZdd lmZmZmZmZmZdd lmZdd lmZdd lmZddlm Z m!Z!m"Z"m#Z#m$Z$m%Z%m&Z&m'Z'ddl(m)Z)m*Z*m+Z+m,Z,m-Z-m.Z.m/Z/m0Z0m1Z1m2Z2m3Z3m4Z4m5Z5m6Z6m7Z7e*dddZ8dddZ9e*dddZ:ddZ;ddZed!d"Z?d#d$Z@ed%d&ZAdd)d*ZBd+d,ZCe*ddd-d.d/ZDd0d1ZEd2d3ZFGd4d5d5eGZHdd7d8ZIdd9d:ZJGd;d<dZLd?d@ZMddAdBZNGdCdDdDeGZOdEdFZPdGdHZQddIdJZRe*ddLdMZSdNdOZTdPdQZUdRdSZVdTdUZWddVdWZXddYdZZYd[d\ZZd]d^Z[d_d`Z\dadbZ]e*ddd-dddeZ^dfdgZ_dhdiZ`e*ddd-dkdlZaedmdnZbdodpZceddqddrdsZdedtduZedvdwZfedxdyddzd{Zgd|d}Zhe*dd~dZieddZjdddZke*dddZlddZmdddZnddZodddZpe*dddZqdZre4dddZsddZtdddZudS))deepcopy)partial lru_cache) OrderedDict)glob)path)packN)_get_meg_system)_serialize_volume_info_get_read_geometryjitprangebincount)FIFF) pick_types) parallel_func)transform_surface_to _pol_to_cart _cart_to_sph _get_trans apply_trans Transform _frame_to_strapply_volume_registration)loggerverboseget_subjects_dirwarn _check_fname _check_option _ensure_int_TempDirrun_subprocess_check_freesurfer_home_hashable_ndarrayfill_doc_validate_type_require_version_plbemheadraisecCst||||dS)aNLoad the subject head surface. Parameters ---------- subject : str Subject name. source : str | list of str Type to load. Common choices would be ``'bem'`` or ``'head'``. We first try loading ``'$SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-$SOURCE.fif'``, and then look for ``'$SUBJECT*$SOURCE.fif'`` in the same directory by going through all files matching the pattern. The head surface will be read from the first file containing a head surface. Can also be a list to try multiple strings. subjects_dir : str, or None Path to the SUBJECTS_DIR. If None, the path is obtained by using the environment variable SUBJECTS_DIR. %(on_defects)s .. versionadded:: 1.0 %(verbose)s Returns ------- surf : dict The head surface. )subjectsource subjects_dir on_defects)_get_head_surface)r.r/r0r1rr3J/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/surface.py get_head_surf(sr5Tc CsTddlm}t|dd}t|ts2tdt|t|trB|g}d}|D]}tt ||dd||f}t |r||dt j |d d }nt ||d} t | std | ttt | d ||f} | D]:}z||dt j |d d }Wntk rYqXq q|dk rJqqJ|dkrB|r>td ||fn|Std||S)zLoad the subject head surface.r read_bem_surfacesT) raise_errorz!subject must be a string, not %s.Nr+z %s-%s.fifF)r1rz*Subject bem directory "%s" does not exist.z %s*%s.fifz=No file matching "%s*%s" and containing a head surface found.zUsing surface from %s.)r+r7r isinstancestr TypeErrortypeoprealpathjoinexistsrZFIFFV_BEM_SURF_ID_HEADisdirIOErrorsortedr ValueErrorrinfo) r.r/r0r1r8r7surfZ this_sourceZ this_headrfilesr3r3r4r2JsZ           r2c sddlm}m}ddlm}m}t\}}|rrtd|t t t ddd|d} || d t jd d } ntfd d td d ddD} td|t| f|| } | t| j} || d d\} }t| |ddddf}tjd|dddfgg}t||f}t|dddddf}||j}||t|dkd}t| |}t| |d} t| d d dt j| d<d}|dkrtdd}t | d||dk rt | d|| S)a+Load the MEG helmet associated with the MEG sensors. Parameters ---------- %(info_not_none)s trans : dict The head<->MRI transformation, usually obtained using read_trans(). Can be None, in which case the surface will be in head coordinates instead of MRI coordinates. %(verbose)s Returns ------- surf : dict The MEG helmet as a surface. Notes ----- A built-in helmet is loaded if possible. If not, a helmet surface will be approximated based on the sensor locations. r) ConvexHullDelaunayr )r7 _fit_spherezGetting helmet for system %sdataZhelmetsz.fif.gzFrcs$g|]}d|dddqS)ZchslocNr3).0pickrEr3r4 sz'get_meg_helmet_surf..Tr3)megZref_megexcludezDGetting helmet for system %s (derived from %d MEG channel locations))ZdispN@rrtris)copyr coord_frame dev_head_trSr,mri)! scipy.spatialrHrIr+r7rJr rrEr=r?split__file__rZFIFFV_MNE_SURF_MEG_HELMETnparrayrlenuniqueZ simplicesrpimax concatenaterall _reorder_ccwdictcomplete_surface_infoZFIFFV_COORD_DEVICErr)rEtransrrHrIr7rJsystemZ have_helmetfnamerFrXZhullRcenterZsphZ front_sphZxyrYr\r3rQr4get_meg_helmet_surf}sN              rqc Cstj|dd}||}tt|dddf|dddf|dddf|dddf|dddf|dt}tddt||DS) z.) rameansigncrosssumastypeintrbzip)rrsrYcomZrr_trisdirsr3r3r4ris&ricCs|jdkst|jdkst|jddks.t|jddks@tt|j|jdkrvtt||j}t||||St ||SdS)a'Compute cross product between list of 3D vectors. Much faster than np.cross() when the number of cross products becomes large (>= 500). This is because np.cross() methods become less memory efficient at this stage. Parameters ---------- x : array Input array 1, shape (..., 3). y : array Input array 2, shape (..., 3). Returns ------- z : array, shape (..., 3) Cross product of x and y along the last dimension. Notes ----- x and y must broadcast against each other. r rVrNiN) ndimAssertionErrorshaperfsizeraempty broadcast _jit_crossrz)xyoutr3r3r4 fast_cross_3ds rcCs|d|d|d<|d|d|d8<|d|d|d<|d|d|d8<|d|d|d<|d|d|d8<dS)N.r .rt.rr3)rrrr3r3r4rs rcCsx|d|d|d|d|d|d|d|d|d|d|d|d|d|d|dS)zFast cross and sum.rrrr3)abcr3r3r4_fast_cross_nd_sums &&&rc Cslt|df}tdD]P}|dd|f}tdD]2}|dd|ft||dd|f|d7<q2q|S)z(Efficiently accumulate triangle normals.rNN)weightsZ minlength)razerosranger)rYtri_nnnptsnnvivertsidxr3r3r4_accumulate_normalss   "rcsddlm}|}ttt|d}tt|}||||ff|t|fdfddt j ddj d dD}t||kst |S) z1Efficiently compute vertex neighboring triangles.r coo_matrixrNrcsg|]\}}j||qSr3)indices)rOstartstopZcsrr3r4rR!sz'_triangle_neighbors..NrVr ) scipy.sparserravelrarepeatarangerconestocsrr~Zindptrr)rYrrrowscolsrK neighbor_trir3rr4_triangle_neighborss   rc Cs||}||} ||}||}||}||}||}||} t| | } t| |} t| |} ||||}|| || |}|| || |}||| fS)z4Get coordinates of a vertex projected to a triangle.)rar{)rbestr1rr12r13rrrrrXzv1v2Zdetrrr3r3r4_triangle_coords'srFaccuratec Cs |dkrt|}tdt}tt|dt}t|||fddi|}|rx|td|d|d|d |df7}|r||d |df7}nr|stt |d|} d d |d| f}|rt|}t |d  t|d t|d} | | } t | || f7}|S) z$Project points onto (scalp) surface.r)rr reprojectTz ij,ijk->ikrrXrYrN) _get_tri_supp_geomrarr}rrc_find_nearest_tri_ptseinsumr_compute_nearestrr|_normalize_vectors) rrFZ project_rrsZ return_nnmethodZ surf_geompt_trispt_lensrrrr3r3r4_project_onto_surface;s6    rc Cs|jdddksttd||}tjtd|\}}|ddddf}tt|dtj ddf|dddf}d||dk<||9}| dd S) z(Compute orthogonal basis given a normal.rVN)rNz...i,...j->...ijrN.r r) rrrarlinalgZeigheyerymatmulnewaxisswapaxes)rprod_uZsignsr3r3r4 _normal_orthWs. rrLc sx|r tdtdd<dtdd<tdd<dddddfddf}dddddfddf}ddddd fddf}|||d d <t||||d <td d d<tddkd}t|dkr*t d|t dt d t d dd<td|rBt ddd<tt} } tdD]P\} } t| dkrt| dkr| | n| | tgt d| <qt| dkrt dddd| Dt| dkrBt dddd| D|dkrtt dfddtdDd<S)aComplete surface information. Parameters ---------- surf : dict The surface. do_neighbor_vert : bool If True (default False), add neighbor vertex information. copy : bool If True (default), make a copy. If False, operate in-place. do_neighbor_tri : bool If True (default), compute triangle neighbors. %(verbose)s Returns ------- surf : dict The transformed surface. ntrirYrarXZtri_areaNrr rtg@Ztri_centrrUz$ Warning: zero size triangles: %sz, Triangle neighbors and vertex normals...rrrNz8 Vertices do not have any neighboring triangles: [%s], css|]}t|VqdSrur:)rOrr3r3r4 sz(complete_surface_info..zR Vertices have fewer than three neighboring triangles, removing neighbors: [%s]css|]}t|VqdSrur)rOfr3r3r4rsTz Vertex neighbors...csg|]}t|qSr3)_get_surf_neighbors)rOkrFr3r4rRsz)complete_surface_info.. neighbor_vert)rgetrcrarrrwhererrErr|r}rlist enumerateappendrbr?r) rFdo_neighbor_vertrZZdo_neighbor_trirrr2Zr3ZzidxzeroZfewerninr3rr4rkdsV$$$        rkcCst}|d|d|jD]}||q||tt|}t||dksZtt |}t |d|}||krt d|n||krt d|||f|S)z7Calculate the surface neighbors based on triangulation.rYrraz Too many neighbors for vertex %dzT Incorrect number of distinct neighbors for vertex %d (%d instead of %d) [fixed].) setZflataddremoverarbrCrhrrc RuntimeErrorrrE)rFrrvZ nneighborsZ nneigh_maxr3r3r4rs"  rcCs6tjj|dd}|dk}||||tjf<|S)zNormalize surface vertices.r rrr)rarnormr)rXrmaskr3r3r4rsrc@s eZdZdZddZddZdS)_CDistz0Wrapper for cdist that uses a Tree-like pattern.cCs ||_dSru)_xhs)selfxhsr3r3r4__init__sz_CDist.__init__cCsvddlm}t}t}|D]D}||tjddf|j}t|}||||d|fqt|t|fS)Nr)cdist) Zscipy.spatial.distancerrrarrargminrrb)rrXrnearestdistsrrvrr3r3r4querys   z _CDist.queryN)__name__ __module__ __qualname____doc__rrr3r3r3r4rsrBallTreecCsj|jdks|jdkr:|r.tgttgfStgtSt||d}||}|rb|dddS|dS)aFind nearest neighbors. Parameters ---------- xhs : array, shape=(n_samples, n_dim) Points of data set. rr : array, shape=(n_query, n_dim) Points to find nearest neighbors for. method : str The query method. If scikit-learn and scipy<1.0 are installed, it will fall back to the slow brute-force search. return_dists : bool If True, return associated distances. Returns ------- nearest : array, shape=(n_query,) Index of nearest neighbor in xhs for every point in rr. distances : array, shape=(n_query,) The distances. Only returned if return_dists is True. rrNrVr )rrarbr}_DistanceQueryr)rrXr return_diststreerr3r3r4rs   rcKs^t|dkr"tgtgtfS||}|rV|ddddf|ddddfgn|}|S)Nrr )rcrarbr})rXfuncreducekwargsrr3r3r4 _safe_querys  0rc@seZdZdZdddZdS)rz"Wrapper for fast distance queries.rFcCs|dks t|dkr`zddlm}Wn"tk rFtdd}YnXtt||jddd|_|dkrzdd l m }Wntk rd }YnX||j|_|d krt |j|_||_ dS) N)rcKDTreerrr)rzTNearest-neighbor searches will be significantly faster if scikit-learn is installed.rT)rrZreturn_distance)rr) rZsklearn.neighborsr ImportErrorrrErrrr^rrrK)rrrZ allow_kdtreerrr3r3r4rs(       z_DistanceQuery.__init__N)rF)rrrrrr3r3r3r4rsrcsxtjddksttt|\}}|fddtd|D}ttj|dddtj d d kS) a@Check whether points are outside a surface. Parameters ---------- rr : ndarray Nx3 array of points to check. surf : dict Surface with entries "rr" and "tris". Returns ------- outside : ndarray 1D logical array of size N for which points are outside the surface. r rNc3s |]}d|VqdS)rXNr3)rOrYZp_funrXrFr3r4r=sz*_points_outside_surface..rYrrrrt?gh㈵>) raZ atleast_2drrr _get_solidsZ array_splitabsr{re)rXrFn_jobsrparallelZ tot_anglesr3rr4_points_outside_surface*s rcCs`ddl}t|d}d|kr(||St|d}tjtt|d|f}|||SdS)NrrXrYrN)pyvistararbPolyDatac_fullrc)rFpvZvertices trianglesr3r3r4_surface_to_polydataBs r cCsXddlm}t||s||}t|j|jddddddfd}|rT|j|d<|S)Nr)rrVr rWr)rrr9rjpointsfacesreshapeZ point_normals)pdnormalsrrr3r3r4_polydata_to_surfaceMs  ( rc@sReZdZdZedddddZddZd d Zedd d Zd dZ ddZ dS) _CheckInsidez1Efficiently check if points are inside a surface.oldN)moderc Csv|dks t||_t}||_|jdkr4|n|td|dt|jddt|ddd dS) N)rrrz Setting up z interior check for rXz points took 0.1f ms) rrtimerF _init_pyvista _init_oldrdebugrc)rrFrrt0r3r3r4rZs   .z_CheckInside.__init__cCszddlm}d|_|jdd|_||jd|_|j|jdkrvtj j |jd|jdd}| |_| |_ dS)Nr)rIrXrVrr)r^rIinner_rrFrxcmdel_tri find_simplexrarrminrfouter_r)rrIrr3r3r4rhs  z_CheckInside._init_oldcCs6t|jts"|j|_t|j|_nt|j|_dSru)r9rFrjpdatarr clean)rr3r3r4rvs z_CheckInside._init_pyvistac Cst|}td|dt|ddt}|jdkrD||}n |||}|}td|d|dt|ddtd t|d d d |S) Nz%Checking surface interior status for  point z...rz Total /z inside the surfacezInterior check completed in rrr) rcrrEr)rr _call_pyvista _call_oldr{)rrXrrn_origrinsiderr3r3r4__call__}s   z_CheckInside.__call__cCs,tt|d}|j|jdd}|dtS)N)rXF)Z check_surfaceZSelectedPoints)r rjZselect_enclosed_pointsr&r|bool)rrXr&rr3r3r4r+sz_CheckInside._call_pyvistac Cs t|}tttt|d}t|t}t|}|j dk r"tj j ||j dd}||j k}| } t| |} td| d|dt| ddd |j d d ||jk} d || <| } t| |} td| d|dt| dd d |jd d || @} || }|| }|j|dk} t | } d ||| <|| }|| }t| |} tt| |}td| d|dt| ddt||j|}t |} t| |} tt||}td| d|dt| ddd |||<|S)N rVrrz Found r*r(r)z& inside an interior sphere of radius rz6.1fz mmFz& outside an exterior sphere of radius rz outside using surface Qhullz outside using solid angles)rcr}raceillog10rfrr0rr rrr!r{r:rjustrrEr)r%r"r#rrF)rrXrr-precr.rrZin_maskrZn_padZout_maskrZ del_outsideZ check_padZ solid_outsider3r3r4r,sR    * *      z_CheckInside._call_old)NN) rrrrrrrrr/r+r,r3r3r3r4rWs  rcCs(t|dd\}}}|d>|d>|S)zRead 3 bytes and adjust.>u1rN)rafromfile)fobjb1b2b3r3r3r4_fread3sr>cCs>t|dd|ddtjj\}}}|d>|d>|S)z1Read 3-byte ints from an open binary file object.r6rNrVr7r8)rar9rr|int64T)r:rr;r<r=r3r3r4 _fread3_manys rAc Cst|dV}t|}|dkr>t|ddd}t|d|}n|}t|t|d|d}W5QRX|rd t|dktjS|Sd S) akLoad in curvature values from the ?h.curv file. Parameters ---------- filepath : str Input path to the .curv file. binary : bool Specify if the output array is to hold binary values. Defaults to True. Returns ------- curv : array, shape=(n_vertices,) The curvature values loaded from the user given file. rbi>i4rNr>f4z>i2dr N)openr>rar9rbr?)filepathbinaryr:magicvnumZcurvr3r3r4read_curvatures rKautocCst|dd}td|dddg|dkrJt|\}}|dkrFd}nd}|dkrbt||d}n |dkrt|}|r|tf7}|r|t|d |d f7}|S) aLoad a Freesurfer surface mesh in triangular format. Parameters ---------- fname : str The name of the file containing the surface. read_metadata : bool Read metadata as key-value pairs. Only works when reading a FreeSurfer surface file. For .obj files this dictionary will be empty. Valid keys: * 'head' : array of int * 'valid' : str * 'filename' : str * 'volume' : array of int, shape (3,) * 'voxelsize' : array of float, shape (3,) * 'xras' : array of float, shape (3,) * 'yras' : array of float, shape (3,) * 'zras' : array of float, shape (3,) * 'cras' : array of float, shape (3,) .. versionadded:: 0.13.0 return_dict : bool If True, a dictionary with surface parameters is returned. file_format : 'auto' | 'freesurfer' | 'obj' File format to use. Can be 'freesurfer' to read a FreeSurfer surface file, or 'obj' to read a Wavefront .obj file (common format for importing in other software), or 'auto' to attempt to infer from the file name. Defaults to 'auto'. .. versionadded:: 0.21.0 %(verbose)s Returns ------- rr : array, shape=(n_vertices, 3) Coordinate points. tris : int array, shape=(n_faces, 3) Triangulation (each line contains indices for three points which together form a face). volume_info : dict-like If read_metadata is true, key-value pairs found in the geometry file. surf : dict The surface parameters. Only returned if ``return_dict`` is True. See Also -------- write_surface read_tri readT file_formatrL freesurferobj.obj) read_metadatarr ) rr r=splitextlowerr _read_wavefront_objrj _rr_tris_dict)rnrR return_dictrNrrextretr3r3r4 read_surfaces 7   rZcCst||t||t|dS)N)rXrYruse_trisra)rjrcrWr3r3r4rVBsrVcCs2t|ddd}|dd<|jtjd|S)NTrWrtrXg@@r[)rZupdaterZFIFFV_COORD_MRI)rnrFr3r3r4_read_mri_surfaceFsr_c Csg}g}t|}|D]}|}t|dks|ddkr.r NrcSsg|]}t|ddqS)r*r)r}r_rcr3r3r4rRhsrNzOnly triangle faces allowed.cSsg|] }|dqSr r3rOrvr3r3r4rRls)rFstriprcr_rrrarb)rncoordsrrliner_Zdatr3r3r4rUMs      rUc s^t}t|dh}tj|dddd}|dkr>td|dtj|dddd}td d d d g}tj|||dW5QRXfd d|jD}|dd8<tt t |t |ddd\}}|}|ddk} |d| } tj t|ftd} d| | <d|| <|| |d}tdddgD]\} } || | || | f<q4|||fS)a!Load a FreeSurfer binary patch file. Parameters ---------- fname : str The filename. Returns ------- rrs : ndarray, shape (n_vertices, 3) The points. tris : ndarray, shape (n_tris, 3) The patches. Not all vertices will be present. rrCr )dtypecountrrVzincorrect version # z (not -1) found)vertnorC)r>f)rrm)rrmcsi|]}||qSr3r3)rOkeyZrecsr3r4 sz_read_patch..rlNrNsphererjTrrr)rjrFrar9rrjfieldskeysrZr=r?dirnamebasenamerrcr0rhr)rnpatchfidverrrjrrYZ orig_trisZis_vertrriirnr3ror4 _read_patchps2  "   r|cCs8ddlm}tttdd}|||d|dd}|S)z3Return an icosahedral surface of the desired grade.r r6rKz icos.fif.gzi(#F)Zs_idr)r+r7r=r?rvr`)ZgradeZ patch_statsr7Z ico_file_nameicor3r3r4_get_ico_surfaces  r~rc CsPt|\}}t|}t|}|}||9}t|||||||t|td}|S)z2Return a surface structure instead of the details.)rXrarYr[rnuserinuse)_tessellate_spherercrZrjrarr})levelradrXrYZnptrrsr3r3r4_tessellate_sphere_surfs  rcCs ||}|||7}t||S)zGet normalized midpoint.)r)ZaiZbirXrr3r3r4 _norm_midpts rc Cstdddgdddgdddgdddgdddgdddggt}tdddgdddgdddgdddgdddgdddgdddgdddggt}|dkrtd|d d dddgf}td|D]p}t|d d df|d d df|}t|d d df|d d df|}t|d d df|d d df|}tt|t|t|t|g}t |d|d}t |d|d} t |d|d} t ||||f}ttj |d d df| |ftj | |d d df| ftj || | ftj || |d d dffft dd}t |t|jd ddf}q|} t|}d} t|D]\} }tdD]t}| ||}t|d | |}t|d kd}t|dkr|d|| |f<n||| <| || |f<| d7} qVqF|d | }||fS) z'Create a tessellation of a unit sphere.r rrVrrtrNzoct subdivision must be >= 1NgwJ?)rarbrbr}rDrrZcumsumrcrrgr rrrrZ empty_likerdotrrZ)ZmylevelrXrYrrrrZlimsZaidxZbidxZcidxZrr_origZnnoderZtrijZcoordZ similarityrr3r3r4rsl$$$$""    rcst|ddd}|dk}t||dd|dkrNt|dt|d <d |d <n|dkrrt||d |d <|d =nt||d |d}t d|t|ddd}t |d|d|dkrt dt |dt |d|dt } t|dt|d <t| D]} |d | rt|| } | } tt|d | d} t | dkrrt d| | fn| | d| <t d| | n0| dks| |dkrt d| d|d | <q t dtfdd|dDtj|d <|d d k r(t |d |d<nd|d<t|d |d<t|d d|d<t |d}d|d |dk<t|d |d<||d<|S)z=Load a surf and use the subdivided icosahedron to get points.Tr\rVspacingFrZrhrarNr[rrFz.spherezLoading geometry from %s...rXzIMismatch between number of surface vertices, possible parcellation error?rz*Could not find neighbor for vertex %d / %dzH Source space vertex moved from %d to %d because of double occupationzMap number out of range (%d), this is probably due to inconsistent surfaces. Parts of the FreeSurfer reconstruction need to be redone.z9Setting up the triangulation for the decimated surface...csg|] }|qSr3r3)rOZistmmapr3r4rRBsz(_create_surf_spacing..rYZnuse_trirrlrZsubject_his_id)rZrkrarr}_decimate_surface_spacingr=r?rrErrrrcrrrrZ logical_notrbZint32r{)rFZhemir.stypeico_surfr0rZ surf_nameZ from_surfZnmaprneighwasindssizesr3rr4_create_surf_spacingsj         rcCst|tst|dksttdt|ddt}t|dD]`}|d|}tt||d||||<|||krd||<t ||||d||<qB|dkr|t|ddddD]J}|d|D]8}t||||d||<t||||d||<qqt|dD]`}||dkr|d|}t ||dk}|d kr\d||<t ||||d||<qt |dt|d <d|d |dk<|S) Nrz Decimating...rai'rr rUrVrtr) r9r}rrrErar rr$minimumr{r)rFrrvrrrr3r3r4rSs2         rc Cs<t||d}td|dddg|dkrJt|\}} | dkrFd}nd}|dkr~zddl} d } Wntk r|d } YnX| r| jjj |||||d dSt | d krt d t |d} | tddddd|dg} dd| D} | | t |}t |}| td||| tj|dd| tj|dd|dk rrt |dkrr| t|W5QRXn|dkr8t |d} | D]}| d|dq|D]0}| d|dd|d d|ddq|D]<}| d|dd d|d d d|dd dqW5QRXdS) aWrite a triangular Freesurfer surface mesh. Accepts the same data format as is returned by read_surface(). Parameters ---------- fname : str File to write. coords : array, shape=(n_vertices, 3) Coordinate points. faces : int array, shape=(n_faces, 3) Triangulation (each line contains indices for three points which together form a face). create_stamp : str Comment that is written to the beginning of the file. Can not contain line breaks. volume_info : dict-like or None Key-value pairs to encode at the end of the file. Valid keys: * 'head' : array of int * 'valid' : str * 'filename' : str * 'volume' : array of int, shape (3,) * 'voxelsize' : array of float, shape (3,) * 'xras' : array of float, shape (3,) * 'yras' : array of float, shape (3,) * 'zras' : array of float, shape (3,) * 'cras' : array of float, shape (3,) .. versionadded:: 0.13.0 file_format : 'auto' | 'freesurfer' | 'obj' File format to use. Can be 'freesurfer' to write a FreeSurfer surface file, or 'obj' to write a Wavefront .obj file (common format for importing in other software), or 'auto' to attempt to infer from the file name. Defaults to 'auto'. .. versionadded:: 0.21.0 %(overwrite)s %(verbose)s See Also -------- read_surface read_tri ) overwriterNrLrOrPrQrNTF) create_stamp volume_infor z&create_stamp can only contain one linewbz>3Bz%s  cSsg|]}|dqS)zutf-8)encode)rOrr3r3r4rRsz!write_surface..z>2irDrrrCwz# zv r)rtzf )rr r=rSrTnibabelrrOioZwrite_geometryrc splitlinesrDrFwriter writelinesrarbtobytesr )rnrhrrrrNrrrrXnibZ has_nibabelrystrsrJZfnumrirrr3r3r4 write_surfacessR1          .rc Csz.rtrNcSsi|]\}}|d|fqS)octr3rr3r3r4rpsr rz when method="sphere")extra)r}rz7Decimating using Freesurfer spherical %s%s downsamplingrYzlh.tempz& Extracting main mesh component ...Zmris_extract_main_componenterrorrLz Smoothing ...z.smoothZ mris_smoothz-nwz Inflating ...z .inflatedZ mris_inflatez -no-save-sulcz Sphere ...z.qsphereZ mris_spherez-qT)rsZkeepdimsrXrrzJCould not reduce to %d triangles using ico, %d/%d vertices were duplicatesz[done])r$r^rrarr rCrjr~rrrErcrr"r=r?rr#rZrrrrdr)rXrYrZmap_Z ico_levelsZ oct_levelsZfunc_mapkindrrtempdirorigsmoothZinflatedZqsphereZ sphere_rrrZnormsrZn_dupr3r3r4_decimate_surface_spheresj                rquadriccCsTt|}tttd}td|t||t|krDtd|t|f|||||S)aDecimate surface data. Parameters ---------- points : ndarray The surface to be decimated, a 3 x number of points array. triangles : ndarray The surface to be decimated, a 3 x number of triangles array. n_triangles : int The desired number of triangles. method : str Can be "quadric" or "sphere". "sphere" will inflate the surface to a sphere using Freesurfer and downsample to an icosahedral or octahedral mesh. .. versionadded:: 0.20 %(verbose)s Returns ------- points : ndarray The decimated points. triangles : ndarray The decimated triangles. Notes ----- **"quadric" mode** This requires VTK. If an odd target number was requested, the ``'decimation'`` algorithm used results in the next even number of triangles. For example a reduction request to 30001 triangles may result in 30000 triangles. **"sphere" mode** This requires Freesurfer to be installed and available in the environment. The destination number of triangles must be one of ``[20, 80, 320, 1280, 5120, 20480]`` for ico (0-5) downsampling or one of ``[8, 32, 128, 512, 2048, 8192, 32768]`` for oct (1-7) downsampling. This mode is slower, but could be more suitable for decimating meshes for BEM creation (recommended ``n_triangles=5120``) due to better topological property preservation. )rrqrzDRequested n_triangles (%s) exceeds number of original triangles (%s))r!rjrrr rCrcrD)rr rrrZ method_mapr3r3r4decimate_surface2s0  rc CsR||}||} |||} | | | |7} | || |7} | ||7} t| S)z$Get the distance to a triangle edge.)rasqrt) pqp0q0rrrdistp1q1rr3r3r4 _get_tri_distps  rc CsD|d|ddddfddf}|d|ddddfddf|}|d|ddddfddf|}tt||gdd}td||}td||}td||}ttt|| g| |ggd}||||} d| | dk<|| ddtjtjf}t||} t| t ||||||||| d S) z=Create supplementary geometry information using tris and rrs.rXrYNrr rtzij,ij->ir) rrrr1213rrrmatr) raascontiguousarrayrbrrZrollaxisrrrrj) rFrrrrrrrrrrr3r3r4r|s($(((   r)rc+ Cstt|df}tt|tj}tt|D]}t||d}|||d\}}||krndkrnn||}|}| }| }d}n4|||}|||}||}| |}| |}d}tt|tj}tt|df}tt|}tj}tdtdtd}}} d}!t t|D]}"t ||"t ||"||"||"<t ||"||"||"<||"\}#}$|#dkr*|$dkr*|#d kr*|$d kr*|#|$d kr*d}!d||"<t ||"t |kr*|#|$|"||"f\}}} }q*|!r|r|| } |!r| rt |d}%|r4||% tj}&n |% tj}&t|&|d||%||%|||\}#}$}'}(t |(t |kr|#|$|'|(f\}}} }d ||||f})| rt|d| |||| ||| }*d|*d|*d |*d|*d f})|)||<| ||<q0||fS) zFind nearest point mapping to a set of triangles. If run_all is False, if the point lies within a triangle, it stops. If run_all is True, edges of other triangles are checked in case those (somehow) are closer. rN)r rNrtrFTrsrr )rarrcr?rrrinfrrrrrr|_nearest_tri_edger)+rZpt_trissrrrrrrrrrrZrun_allrrZtri_idxrirXrrZdrsrZmatsZr1213sZreindexrZusepqsrrrrptfoundr{ppqqrZ use_pt_trisZpttZdisttrrhr3r3r4rsr  "$ 6    " rc Cs||}||}||} |dddf} |dddf} tt| d| | |dd} t| } dd|| d| d|| | ||| }tt|dd}d|}|}tt| d| | |dd}t|}t| | | | ||| |}t| | ||||| |}t| | ||||| |}t| ||f} t| ||f} t|||f}tt|}| || |||t|||f\}}}}||||fS)zDGet nearest location from a point to the edge of a set of triangles.Nrr ?rsrrU) rarmaximumZ zeros_likerrgrrrc)rZto_ptrrrrrZaaZbbccrrrrt1rrq2Zp2Zdist0Zdist1Zdist2rr{rrrr3r3r4rs4$  $ ,rcCst|}t|dS)zReturn sparse matrix with edges as an adjacency matrix. Parameters ---------- tris : array of shape [n_triangles x 3] The triangles. Returns ------- edges : scipy.sparse.spmatrix The adjacency matrix. rY)r% _mesh_edgesrr3r3r4 mesh_edgess rr1)maxsizec Csddlm}t|tt|kr,tdt|d}tdt|}|j\}}}t |||f}t |||f}||||ff||fd} | } | | j} | S)Nrrz5Cannot compute adjacency on a selection of triangles.r rNr) rrrarfrcrdrDrr@rgr) rYrZnpointsZ ones_ntrisrrrrredgesr3r3r4rs   rcCsfddlm}t|}tjj||jddf||jddfdd}|||j|jff|j d}|S)aCompute adjacency matrix weighted by distances. It generates an adjacency matrix where the entries are the distances between neighboring vertices. Parameters ---------- tris : array (n_tris x 3) Mesh triangulation. vert : array (n_vert x 3) Vertex locations. Returns ------- dist_matrix : scipy.sparse.csr_matrix Sparse matrix with distances between adjacent vertices. r) csr_matrixNr rrr) rrrtocoorarrrowcolr)rYZvertrrrZ dist_matrixr3r3r4 mesh_dist+s   0rc s2t|d}|}W5QRXt|d}t||d}t|d}|dkr\tdn|dkrptddntdtfd d |d|dD}tfd d ||d |d |D} |r| d d dd gf| d d d dgf<| d8} t d|||f|dkr"t dnt d|| fS)axRead triangle definitions from an ascii file. Parameters ---------- fname_in : str Path to surface ASCII file (ending with '.tri'). swap : bool Assume the ASCII file vertex ordering is clockwise instead of counterclockwise. %(verbose)s Returns ------- rr : array, shape=(n_vertices, 3) Coordinate points. tris : int array, shape=(n_faces, 3) Triangulation (each line contains indices for three points which together form a face). See Also -------- read_surface write_surface Notes ----- .. versionadded:: 0.13.0 rrr )rNrN)rrrzUnrecognized format of data.cs(g|] }tdd|DqS)cSsg|] }t|qSr3rarOrr3r3r4rRos'read_tri...rarbr_rOrirr3r4rRoszread_tri..cs(g|] }tdd|DqS)cSsg|] }t|qSr3)r}rr3r3r4rRqsrrrrr3r4rRqsrtNz6Loaded surface from %s with %s nodes and %s triangles.)rNrz2Node normals were not included in the source file.zNode normals were not read.) rF readlinesr}rcr_rrBrarbrrEr) Zfname_inZswaprrylinesZn_nodesZn_trisZn_itemsrXrYr3rr4read_triFs4    $  rcCs*tt|}tt|D]}||}||d}||d}||d}t|jddf}t|||tj||dd} ttj||dd} ttj||dd} ttj||dd} | | | tj||dd| tj||dd| tj||dd| } |t | | 8}q|S)z.Compute _sum_solids_div total angle in chunks.rr rtrNrr) rarrcrrrrr{rZarctan2)Ztri_rrsZfrosZ tot_angletiZtri_rrrrZv3Zv4Ztriplel1l2l3rr3r3r4rs*     rcCsT|d|d}|d}t||d}|d|7<|rDt|dd|d|d<|S) z*Convert sphere conductor model to surface.Zlayersrr0)rrXFrr[)rrk)rqrrZcompleterrrFr3r3r4_complete_sphere_surfs   rc Cs`ddlm}t|d||dd} t|dddd }t|| } ||||d } t| | d d d} | S) aCompute distances between head shape points and the scalp surface. This function is useful to check that coregistration is correct. Unless outliers are present in the head shape points, one can assume an average distance around 2-3 mm. Parameters ---------- %(info_not_none)s Must contain the head shape points in ``info['dig']``. trans : str | instance of Transform The head<->MRI transform. If str is passed it is the path to file on disk. subject : str The name of the subject. subjects_dir : str | None Directory containing subjects data. If None use the Freesurfer SUBJECTS_DIR environment variable. %(dig_kinds)s %(exclude_frontal)s Default is False. %(on_defects)s .. versionadded:: 1.0 %(verbose)s Returns ------- dists : array, shape (n_points,) The distances. See Also -------- mne.bem.get_fitting_dig Notes ----- .. versionadded:: 0.19 r )get_fitting_dig)z head-denser,r+)r0r1rXr]r,)Zfrotor)exclude_frontalT)r)r+rr5rrr) rErlr.r0Z dig_kindsrr1rrZptsZinfo_digrr3r3r4dig_mri_distancess *  rcCsNt|tjr|jdkstt|}|}||j||jk}t |j|S)Nr ) r9raZndarrayrrrrrrrd)rYrrZ border_edgesr3r3r4 _mesh_borderss rc Csddlm}m}ddlm}ddlm}ddlm}ddl m } m } ddl m } |jdkrjtd |jt|}|jd ks|jdks|jjd krtd |jd |jd|jd|dk r|}|D]*} || k} |dk}| | ||d} | || <q|j}| |tdd}~|}|}|||d d d g|dddg||| t!|t"|D]\}}|#||qn|$||%t&|'|}|}|$||}|(ddd|j)|j*|}|+|,t-}|D]} z |j.Wn"t/k r |0| | YnX|.| |1| |%|'}| |23}| |456dd}t7|dddddf}t7|dddddf}|8||fq|S)z%Compute marching cubes on a 3D image.r) vtkImageDatavtkDataSetAttributes) vtkThreshold)vtkDiscreteFlyingEdges3D)vtkGeometryFilter) vtk_to_numpyr)binary_dilationrNz3D data must be supplied, got r Zuiz=level must be non-empty numeric or 1D array-like of int, got zD array-like of z with z elementsN)Z iterationsrT)deeprV)9rrr rr Zvtkmodules.vtkFiltersGeneralr Zvtkmodules.vtkFiltersGeometryr rr rZ scipy.ndimagerrrDrrarbrrjrr;rZrr|rbZ SetDimensionsZ SetSpacingZ SetOriginZ GetPointDataZ SetScalarsZSetNumberOfContoursrcrZSetValuerr _vtk_smoothrZSetInputArrayToProcessZFIELD_ASSOCIATION_POINTSZSCALARSZSetInputConnectionZ GetOutputPortrZSetLowerThresholdAttributeErrorZThresholdBetweenZSetUpperThresholdZ GetPointsZGetDataZGetPolysZGetConnectivityArrayrrr)imagerrZfill_hole_sizerr r r r r rrvalZ bin_imagerZ image_shapeZdata_vtkZmcZimdataZliZlevselectorZdsaZgeometryrZpolydatarXrYr3r3r4_marching_cubess               rcCst|d|t|}d|kr(dks8ntd||dkrD|Sddlm}td|d}t|trzt |}d}|}| || d | | |d |d|||||}|rt|dd }|S) Nnumericrr zFsmoothing factor must be between 0 (inclusive) and 1 (exclusive), got )vtkWindowedSincPolyDataFilterz Smoothing by a factor of FTrEg^@r)r'rbrDrrrrEr9rjr rZSetNumberOfIterationsZBoundarySmoothingOffZFeatureEdgeSmoothingOffZSetFeatureAngleZ SetPassBandZNonManifoldSmoothingOnZNormalizeCoordinatesOffrrr)rrrZreturn_ndarrayZsmootherrr3r3r4r7s4       rcsttdtjdttt|j}fdd|D}|r|dkrt dt |dd dd |Dd |rd |nd d S)zWarn that channels are missing.r csg|]}j|dqSre)ch_namesrOrrQr3r4rRZsz%_warn_missing_chs..rZChannelr)rcss|]}t|VqdSru)repr)rOchr3r3r4r\sz$_warn_missing_chs..z not assigned voxels z after applying rN) rrarrcr differencerdrbdataobjrr)r?)rEZ dig_image after_warprmissingZ missing_chr3rQr4_warn_missing_chsUs &r  fsaveragerrEc $sptdddtdddddlm} m}ddlm}d d l}t|| d t||jj d t|t d |d kst|dkrt d|t| t dt| t dt| t d||||d kr|}|||t||jj s||}|t||dd}tj|j|jddstd|ddkr`tdd|jD}ddd|D}td|td}tfdd|D}ttj|j |d}t|j!}| r|d 9}tj"|j#t d!}t$|D]\}}t%|&rqt'|||| | d"}|D]p}||d krjt(|||d|d#)}t(||d#)}||krv|d||<n |d||<qq|j ||j}t*||d$d%|t||dd}t+||||d&d'}|d k rd(nd)}t*|||d%t,|j!} t$|dD]*\}!}tj-t.| |!kdd*|d d <q|t||dd}"t|"j |d}|t/t0||dd+}#|#||fS),az Warp a montage to a template with image volumes using SDR. Find areas of the input volume with intensity greater than a threshold surrounding local extrema near the channel location. Monotonicity from the peak is enforced to prevent channels bleeding into each other. .. note:: This is likely only applicable for channels inside the brain (intracranial electrodes). Parameters ---------- montage : instance of mne.channels.DigMontage The montage object containing the channels. base_image : path-like | nibabel.spatialimages.SpatialImage Path to a volumetric scan (e.g. CT) of the subject. Can be in any format readable by nibabel. Can also be a nibabel image object. Local extrema (max or min) should be nearby montage channel locations. %(reg_affine)s %(sdr_morph)s subject_from : str The name of the subject used for the Freesurfer reconstruction. subject_to : str The name of the subject to use as a template to morph to (e.g. 'fsaverage'). subjects_dir_from : path-like | None The path to the Freesurfer ``recon-all`` directory for the ``subject_from`` subject. The ``SUBJECTS_DIR`` environment variable will be used when ``None``. subjects_dir_to : path-like | None The path to the Freesurfer ``recon-all`` directory for the ``subject_to`` subject. ``subject_dir_from`` will be used when ``None``. thresh : float The threshold relative to the peak to determine the size of the sensors on the volume. max_peak_dist : int The number of voxels away from the channel location to look in the ``image``. This will depend on the accuracy of the channel locations, the default (one voxel in all directions) will work only with localizations that are that accurate. voxels_max : int The maximum number of voxels for each channel. use_min : bool Whether to hypointensities in the volume as channel locations. Default False uses hyperintensities. %(verbose)s Returns ------- montage_warped : mne.channels.DigMontage The modified montage object containing the channels. image_from : nibabel.spatialimages.SpatialImage An image in Freesurfer surface RAS space with voxel values corresponding to the index of the channel. The background is 0s and this index starts at 1. image_to : nibabel.spatialimages.SpatialImage The warped image with voxel values corresponding to the index of the channel. The background is 0s and this index starts at 1. rz SDR morphz2.1.0Zdipyz0.10.1r ) DigMontagemake_dig_montage)_check_subject_dirrNmontage base_imagethreshz&`thresh` must be between 0 and 1, got max_peak_dist voxels_maxuse_minr]z brain.mgzgư>)ZatolzThe `base_image` is not aligned to Freesurfer surface RAS space. This space is required as it is the space where the anatomical segmentation and reconstructed surfaces arer[cSsg|] }|dqSr]r3rfr3r3r4rRsz'warp_montage_volume..rcSs$g|]}|tkrt|nt|qSr3)rr:)rOcfr3r3r4rRs4Coordinate frame not supported, expected "mri", got ch_poscsg|]}d|qS)r-r3)rOnamech_dictr3r4rRsrrVrr)r'r(r)rtF)rr) interpolationzSDR warpzaffine transformationrrr])1r(channelsr"r# _freesurferr$rr'Z spatialimagesZ SpatialImagerbrDr}r0r9loadr=r?raZallcloseZaffiner get_positionsrddigrrurbrrinvheaderget_vox2ras_tkrrrrrisnanany_voxel_neighborsrr{r rZ asanyarrayrxrrjr~)$r%r&Z reg_affineZ sdr_morphZ subject_fromZ subject_toZsubjects_dir_fromZsubjects_dir_tor'r(r)r*rr"r#r$rZ fs_from_imgZbad_coord_framesr ch_coordsZ image_dataZ image_fromich_coordvolumevoxelZdist_oldZdist_newZtemplate_brainZimage_torZ warped_datarZ fs_to_imgZmontage_warpedr3r/r4warp_montage_volumebsB               $ rBr aparc+asegrtcsddlm}ddlm}m}t||dt|ttfd|dksH|dkrPtd||||\}|\}d d | Dt fd d t Dst |j} |} | d dkrtdt| d t t| d} tt j|j| d} t} t|j| D]d\} }t |r6t| | <n>t||| td}t fdd |D}fdd |D| | <qt dd | D}fdd |D}| |fS)a,Get regions of interest near channels from a Freesurfer parcellation. .. note:: This is applicable for channels inside the brain (intracranial electrodes). Parameters ---------- %(montage)s %(subject)s %(subjects_dir)s %(aseg)s dist : float The distance in mm to use for identifying regions of interest. Returns ------- labels : dict The regions of interest labels within ``dist`` of each channel. colors : dict The Freesurfer lookup table colors for the labels. r )r")read_freesurfer_lut _get_asegr%rrr1z`dist` must be between 0 and 10cSsi|]\}}||qSr3r3)rOrrr3r3r4rp6sz-get_montage_volume_labels..csg|] }|kqSr3r3r label_lutr3r4rR9sz-get_montage_volume_labels..r[r]r,r-r)r vox2ras_tkrr)csg|]}t|tqSr3)tupler|r})rOrA) aseg_datar3r4rROscsg|] }|qSr3r3rrFr3r4rRQscSsg|]}|D]}|q qSr3r3)rOrlabelr3r3r4rRSscs*i|]"}|t|ddddqS)NrNr)r)rI)rOrK) fs_colorsr3r4rpTs)!r2r"r3rDrEr'r}rbrDitemsrhrardrr8r9r5rr:rbrvaluesrrr7rr~rr:r;r< _VOXELS_MAXr)r%r.r0Zasegrr"rDrEZlutrHr0r=labelsZch_namer?voxelsZ label_idxsZ all_labelscolorsr3)rJrLrGr4get_montage_volume_labelssR          rSc Cst}tt|D]}dD]}t|}|||7<|dk r|dksLtt|}|||kr||||kr||kr||q|dkst|\} } } t| |d} tj | | | kr|t|qq|S)z6Find all the neighbors above a threshold near a voxel.)rVr Nr) rrrcrarbrrIrrrr) rMrrQr' dist_params neighborsrsr>next_locr seed_fs_rasrHZnext_loc_fs_rasr3r3r4_get_neighborsYs(      rXcs@t|t}|dk |dk dks,t|dk rd}|tfdd|D} ttt| | j |} t t| g} } |r||t| 9}n6|dk stt ||d} || |f}t t|g} } | r.r)rarbroundr|r}rrIZ unravel_indexZargmaxrrrrcrXrunion)seedrr'r(Z use_relativerrHr)rTZ check_gridZpeakrQrUrWZnext_neighborsrVZvoxel_neighborsr3rZr4r<rsH(       r<)r*Nr-N)T)NN)FFr)FTT)rF)F)NN)T)T)FFrLN)F)r)rNrLF)r)TF)N)FN)T)NrLFr-N)rN)N)r!NNrr rEFN)NrCrt)Nr TNNrE)vrZr functoolsrr collectionsrrosrr=structrrrnumpyraZchannels.channelsr fixesr r r rrZ io.constantsrZio.pickrrrZ transformsrrrrrrrrutilsrrrrrr r!r"r#r$r%r&r'r(r)r5r2rqrirrrrrrrrrkrrobjectrrrrrr rrr>rArKrZrVr_rUr|r~rrrrrrrrrrrrrrrrrrrrrrrr rBrOrSrXr<r3r3r3r4 s         (D  " 3 A#      K  &  s  L#2 NC d)1=  S #  8   4 W  , G