U f{jw@sddlmZddlmZddlZddlmZddlZ ddl m Z ddl m Z mZddlmZddlmZmZdd lmZdd lmZmZmZmZmZmZmZmZmZm Z dd l!m"Z"m#Z#dd l$m%Z%m&Z&dd l'm(Z(ddl)m*Z*m+Z+m,Z,m-Z-m.Z.m/Z/m0Z0m1Z1m2Z2m3Z3m4Z4m5Z5ddl6m7Z7m8Z8m9Z9m:Z:m;Z;ddlZ>m?Z?m@Z@mAZAmBZBmCZCmDZDmEZEmFZFmGZGmHZHmIZImJZJmKZKmLZLmMZMmNZNmOZOddlPmQZQddlRmSZSmTZTmUZUmVZVmWZWmXZXmYZYmZZZm[Z[ddddZ\Gddde]Z^ddZ_e@d}ddZ`e@d~ddZad d!Zbe@dd"d#Zcd$d%Zdd&d'Zed(d)Zfe@dd*d+Zge@ddd,d-d.Zhd/d0Zidd1d2Zje@dd3d4Zke@ddd8d9d:Zlddsz$SourceSpaces.kind..rKmixedrcss|]}|dkVqdS)rLNrZr_rZrZr[rbsrLrJcss|]}|dkVqdSr^rZr_rZrZr[rbsz"Invalid source space with kinds %s) rQ enumerater9rUappendgetr:alllenany RuntimeError)rWtypessisZ surf_checkrTrZrZr[rTs(  zSourceSpaces.kindFcCsrddlm}t}d} |dkr8tdd|Dr4dnd}t|trN||n|r\|d|dkrv|jd krrdnd }t|tr||nx|d kr|d nd|dk rt|d trt j d t j d t j di} |D]} || | dq|} n|D]} || q|r|d|d dt j kr@d} |dkrDtdnd} td dd}||||j||| dddd| |d S)aPlot the source space. Parameters ---------- head : bool If True, show head surface. brain : bool | str If True, show the brain surfaces. Can also be a str for surface type (e.g., 'pial', same as True). Default is None, which means 'white' for surface source spaces and False otherwise. skull : bool | str | list of str | list of dict | None Whether to plot skull surface. If string, common choices would be 'inner_skull', or 'outer_skull'. Can also be a list to plot multiple skull surfaces. If a list of dicts, each dict must contain the complete surface info (such as you get from :func:`mne.make_bem_model`). True is an alias of 'outer_skull'. The subjects bem and bem/flash folders are searched for the 'surf' files. Defaults to None, which is False for surface source spaces, and True otherwise. subjects_dir : str | None Path to SUBJECTS_DIR if it is not set in the environment. trans : str | 'auto' | dict | None The full path to the head<->MRI transform ``*-trans.fif`` file produced during coregistration. If trans is None, an identity matrix is assumed. This is only needed when the source space is in head coordinates. %(verbose)s Returns ------- fig : instance of Figure3D The figure. r)plot_alignmentNcss|]}|ddkVqdS)r\rNNrZ)r`ssrZrZr[rbsz$SourceSpaces.plot..whiteFbrainrKTZ outer_skullrZ inner_skullZ outer_skinidhead coord_framezSource space is in head coordinates, but no head<->MRI transform was given. Please specify the full path to the appropriate *-trans.fif file as the "trans" parameter.mri@@eegrZ) transsubject subjects_dirsurfacesrumegrxdigZecogbemsrc)ZvizrorQrj isinstancestrrfrTrUrFIFFV_BEM_SURF_ID_BRAINZFIFFV_BEM_SURF_ID_SKULLZFIFFV_BEM_SURF_ID_HEADFIFFV_COORD_HEAD ValueErrorr_subject)rWrtrrskullr{ryr0ror|rZ skull_mapZ this_skullrNrurVrZrZr[plotsl$              zSourceSpaces.plotcs$tj||}t|tr t|}|S)z Get an item.)rR __getitem__rrQrO)rWargskwargsoutrXrZr[rDs zSourceSpaces.__getitem__c Cs$g}g}t|D]\}}|d}t|}|dkr`d|krL|d|df7}q|d|df7}n$|dkr|dt|d |d f7}|d |d f7}|d kr|d tt|dg7}|d|q|j}|dk r|d|fg7}t|}|dk r |dt|g7}dd |d |fS)Nr\rMseg_namez (%s)z , shape=%sshaperNz (%s), n_vertices=%irnpz , n_used=%inusez %s coordsruz<%s>z subject %r~zz, ) re_src_kind_dict _get_hemirFintrfrr>r?join) rWZss_reprextrarmrpZss_typerZsubjszrZrZr[__repr__Ks6 zSourceSpaces.__repr__cCs|dddS)Nrsubject_his_id)rgrWrZrZr[rfszSourceSpaces._subjectcCs|}||7}t|S)zCombine source spaces.)copyrO)rWotherrrZrZr[__add__jszSourceSpaces.__add__cCst|S)zMake a copy of the source spaces. Returns ------- src : instance of SourceSpaces The copied source spaces. rrrZrZr[rpszSourceSpaces.copycCspt|j|}t}|D]N}dD]4}||kr||}t|}||kr|jjs|||<q|t||qt||S)zMake a deepcopy.rrnn)rrVrQrsflagsZ writeablerfrO)rWmemodictrVrprnkeyarrid_rZrZr[ __deepcopy__zs  zSourceSpaces.__deepcopy__r0cCst|||ddS)zSave the source spaces to a fif file. Parameters ---------- fname : str File to write. %(overwrite)s %(verbose)s  overwriteN)write_source_spaces)rWfnamerr0rZrZr[saves zSourceSpaces.saveTrvc )Cs2t||t|ttfdt|tr8td|dgddnt|}t|}z ddl} Wntk rptdYnXt dd |D} | t j k rd } |r|r|dkrt d q|dk rtd n.| t jk rd } |dk rtdnt dtdt\} }tggd}|D]R}|ddkr:|d|n.|ddkrX|d|nt d|dqt|ddkrt d|dd}d}|r|dkrt| |d}|d|d|df}n|d}|r|d}n|d }t|}|d!}| d kr*t|d d d}t||d |}n|}t|}t|dD]\}}d"|kr^t d#d$}|dksr|r| |d"}|r|}|dkrt||d%|d&}t|t j!}n:|dkr||k}n&|d'kst"|d(j#|d)d*t}|||<qD|dD]j}d+}|dd,krZ|s.q |rt j$d-t j%d.i|d/d0}| |}n,|dd1kslt"|svq |rtd2|dkr|d%}n(|d'ks|dkst"|d%|d&}t|d3|}|j!t \} }!}"t&| d|dd+f}#t&|!d|d+d+}$t&|"d|d4d+}%| |#k|!|$kB|"|%kB'}&|&dkrht(|&d5|dd6|||#|$|%f<q |d krt||d7|d8|d7d!}|d3)}'|'dd9d:9<|*d;r| +}(|(,d<| j-||'|(d=}n0|*d>r|d?}| j.j/0||'}nt d@| 1||dS)Aa0Export source spaces to nifti or mgz file. Parameters ---------- fname : str Name of nifti or mgz file to write. include_surfaces : bool If True, include surface source spaces. include_discrete : bool If True, include discrete source spaces. dest : 'mri' | 'surf' If 'mri' the volume is defined in the coordinate system of the original T1 image. If 'surf' the coordinate system of the FreeSurfer surface is used (Surface RAS). trans : dict, str, or 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. Must be provided if source spaces are in head coordinates and include_surfaces and mri_resolution are True. mri_resolution : bool | str If True, the image is saved in MRI resolution (e.g. 256 x 256 x 256), and each source region (surface or segmentation volume) filled in completely. If "sparse", only a single voxel in the high-resolution MRI is filled in for each source point. .. versionchanged:: 0.21.0 Support for "sparse" was added. use_lut : bool If True, assigns a numeric value to each source space that corresponds to a color on the freesurfer lookup table. %(overwrite)s .. versionadded:: 0.19 %(verbose)s Notes ----- This method requires nibabel. mri_resolutionsparsezwhen mri_resolution is a string)rrNzThis function requires nibabel.cSsg|] }|dqS)rurZr`rnrZrZr[ sz.SourceSpaces.export_volume..rtztrans containing mri to head transform must be provided if mri_resolution and include_surfaces are true and surfaces are in head coordinatesz]trans is not needed and will not be used unless include_surfaces and mri_resolution are True.rvzPtrans is not needed and will not be used unless sources are in head coordinates.zRAll sources must be in head coordinates or all sources must be in mri coordinates.zReading FreeSurfer lookup table)rJsurface_discreter\rMrJ)rNrLrzUnrecognized source type: %s.z/Source spaces must contain at least one volume.Tmri_file mri_width mri_depth mri_heightr vox_mri_t src_mri_ttorz9Volume sources should be segments, not the entire volume.?rvertnoFinuseF)orderrrNZLeftZRightrsz-Cerebral-CortexrLzIDiscrete sources do not have values on the lookup table. 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Consider using a larger volume space. mri_ras_tfromrw)z.niiz.nii.gzmm)headerz.mgzfloat32zUnrecognized file extension)2r6r9boolrrr:Znibabel ImportErrorrarrayrrrhrr/rVFIFFV_COORD_MRIr*rUrfrirloadrArErDzerosrerBtupleroundastyperTAssertionErrorreshapeFIFFV_MNE_SURF_LEFT_HEMIFIFFV_MNE_SURF_RIGHT_HEMIZclipsumr5rendswithZ Nifti1HeaderZset_xyzt_unitsZ Nifti1ImageZ freesurferZ mghformatZMGHImager))rWrZinclude_surfacesZinclude_discretedestryrZuse_lutrr0ZnibZ coord_framesZcoordslut_Z src_typesrZ aseg_dataZshape3dZ transformZ fro_dst_tZ head_mri_tZimgiivsZuse_idridxvalZ surf_nameZuse_rrZsrf_voxZix_Ziy_Ziz_ZixZiyZizZn_diffZaffinehdrrZrZr[ export_volumes0                                  zSourceSpaces.export_volume)N)FNNNNN)F)TTrvNFTFN)__name__ __module__ __qualname____doc__rSpropertyrTr0rrrrrrrrr __classcell__rZrZrXr[rO7s:   Z    rOc Cs|d}|dkr$d|d<d|d<dStdt|}||}t|dd|ddkdd}tjdg|f}tj|t|gf}t}t||D] \}} | t ||| q||d<||d} t | |d |d<td dS) a>Patch information in a source space. Generate the patch information from the 'nearest' vector in a source space. For vertex in the source space it provides the list of neighboring vertices in the high resolution triangulation. Parameters ---------- s : dict The source space. nearestNpinfo patch_indsz! Computing patch statistics...rr]rrz Patch information added...) r/rVrargsortwherer_rirQziprfsort searchsorted) rnrZindnZnearest_sortedZstepsZstartiZstopirstartstopZ patch_vertsrZrZr[_add_patch_infos$   & rFcCs~t|tj}t|dkr tdt}|D]8}tdt||}td|rXt || |q*tdt|t |S)aRead the source spaces from a FIF file. Parameters ---------- fid : file descriptor An open file descriptor. tree : dict The FIF tree structure if source is a file id. patch_stats : bool, optional (default False) Calculate and add cortical patch statistics to the surfaces. %(verbose)s Returns ------- src : SourceSpaces The source spaces. rzNo source spaces foundz Reading a source space... [done]z %d source spaces read) r rFIFFB_MNE_SOURCE_SPACErirrQr/rV_read_one_source_space_complete_source_space_inforfrO)fidtree patch_statsr0spacesrrnthisrZrZr[_read_source_spaces_from_trees      rc Cst|ddd}t|ddt|\}}}|}t||||d}||jd<t|tj}|r|d}t|d D]X} |d | j } |d | j } t || } | tj kr| j |jd <ql| tjkrl| j |jd <qlW5QRX|S) aRead the source spaces from a FIF file. Parameters ---------- fname : str The name of the file, which should end with -src.fif or -src.fif.gz. patch_stats : bool, optional (default False) Calculate and add cortical patch statistics to the surfaces. %(verbose)s Returns ------- src : SourceSpaces The source spaces. See Also -------- write_source_spaces, setup_source_space, setup_volume_source_space readTr must_exist source space) -src.fif -src.fif.gz_src.fif _src.fif.gzz-fwd.fifz -fwd.fif.gzz_fwd.fifz _fwd.fif.gzz-inv.fifz -inv.fif.gzz_inv.fifz _inv.fif.gz)rr0rrZnent directory working_dir command_line)r6r.r rrVr r FIFFB_MNE_ENVrangerTposr FIFF_MNE_ENV_WORKING_DIRdataFIFF_MNE_ENV_COMMAND_LINE) rrr0ffrrrrnodeprTrtagrZrZr[read_source_spacess(      rcCst}t||tj}|dkr,ttj|d<nt|j|d<t||tj}|dkrZtdnRt|j}|tj krxd|d<n4|tj krd|d<n |tj krd|d<n td||ddkr t||tj }|dk rt |j|d <t||tj}|dk r|j|d <t|tj}t|d kr td |d }|d D]V}|jtjkr0t||j}|j}|dtjkrl||d<|dtjkr0||d<q0t||tj}|dk r|j|d<|jjjd kr|d=n tdt||tj}|dk r|j|d<t||tj}|dk rt|j|d<t||tj}|dk r:t|j|d<t||tj}|dk r`t|j|d<t||tj}|dk r|j|d<t||tj }|dk r|j} t||tj!}d } g} | D]&} | "|j| | | | | 7} q| |d<t||tj#}|dk r |j|d<t||tj$}|dkr,tdt|j|d<t||tj%}|dkrt||tj&}|dkrtd |d<nt|j|d<n |j|d<t||tj'}|dkrtd|jd |d<t||tj(}|dkrtd |j)t*j+|d!<|d!j,d |dkrtd"t||tj-}|dkr.td#|j.|d$<|d$j,d |dkr\td%|dd krt||tj/}|dkrt||tj0}|dkrtd&n|jd'|d(<n|jd'|d(<|d(j,d |dkrtd)nd|d(<t||tj1}|dkr.d |d*<t*j2|d*t*j3d+|d,<d|d-<nvt|j|d*<t||tj4}|dkr\td.|j)t*j3j5|d,<t|d,|dkrtd/t*6|d,d |d-<t||tj7} t||tj8}| dks|dkrd |d0<d|d1<n| j|d0<|jd'|d1<t||tj9} t||tj:}| dks.|dkr@d|d2<d|d3<n| j|d2<|jj5|d3<t;|t||tj<} t||tj=}| dks|dkrd|d4<d|d5<n*| j|d4<|j|d5<|d4|d4j5|d4<|d4dk rtd6t||tj>}|dkrd|d7<n |j|d7<|S)8zRead one source space.NrszUnknown source space typerNr\rMrLzUnknown source space type (%d)rrrzCan not find parent MRI location. The volume source space may have been made with an MNE version that is too old (<= 2.7.3). Consider updating and regenerating the inverse.rrrrr interpolatorz'Interpolation matrix for MRI not found.rrrrmri_volume_name neighbor_vertrzNumber of vertices not foundrntriz&Coordinate frame information not foundruzVertex data not foundrzVertex information is incorrectzVertex normals not foundrz&Vertex normal information is incorrectzTriangulation not foundrtrisz&Triangulation information is incorrectr)dtyperrz$Source selection information missingz5Incorrect number of entries in source space selectionnuse_triuse_trisr nearest_distdist dist_limitz! Distance information added...r)?rUr rFIFF_MNE_SOURCE_SPACE_IDrFIFFV_MNE_SURF_UNKNOWNr FIFF_MNE_SOURCE_SPACE_TYPErFIFFV_MNE_SPACE_SURFACEFIFFV_MNE_SPACE_VOLUMEFIFFV_MNE_SPACE_DISCRETE FIFF_MNE_SOURCE_SPACE_VOXEL_DIMSrZFIFF_COORD_TRANSr FIFFB_MNE_PARENT_MRI_FILErirTr rZFIFFV_MNE_COORD_MRI_VOXELZFIFFV_MNE_COORD_RAS"FIFF_MNE_SOURCE_SPACE_INTERPOLATORsizer/rVFIFF_MNE_SOURCE_SPACE_MRI_FILEFIFF_MRI_WIDTHFIFF_MRI_HEIGHTFIFF_MRI_DEPTHFIFF_MNE_FILE_NAME FIFF_MNE_SOURCE_SPACE_NNEIGHBORSFIFF_MNE_SOURCE_SPACE_NEIGHBORSrf FIFF_COMMENTFIFF_MNE_SOURCE_SPACE_NPOINTSZFIFF_BEM_SURF_NTRIFIFF_MNE_SOURCE_SPACE_NTRIFIFF_MNE_COORD_FRAMEFIFF_MNE_SOURCE_SPACE_POINTSrrfloat64rFIFF_MNE_SOURCE_SPACE_NORMALSrZFIFF_BEM_SURF_TRIANGLESFIFF_MNE_SOURCE_SPACE_TRIANGLESFIFF_MNE_SOURCE_SPACE_NUSErint64FIFF_MNE_SOURCE_SPACE_SELECTIONrrFIFF_MNE_SOURCE_SPACE_NUSE_TRI#FIFF_MNE_SOURCE_SPACE_USE_TRIANGLESFIFF_MNE_SOURCE_SPACE_NEAREST"FIFF_MNE_SOURCE_SPACE_NEAREST_DISTrFIFF_MNE_SOURCE_SPACE_DIST FIFF_MNE_SOURCE_SPACE_DIST_LIMITFIFF_SUBJ_HIS_ID)rrresrsrc_typeZ parent_mrirvdry nneighborsoffset neighborsnZtag1Ztag2rZrZr[rs,                                                       rcCstdt|d|d<|d|ddddfddf}|d|ddddfddf}|d|dddd fddf}|||d |d <t|||||d <t|d d |d<tdtd|ddkr|d|ddddfddf}|d|ddddfddf}|d|dddd fddf}|||d |d<t|||||d<tjj|dddd |d<tddS)zAdd more info on surface.z$ Completing triangulation info...rtri_arearrNrrrcg@tri_centtri_nng@[done]z. Completing selection triangulation info...rrZ use_tri_centZ use_tri_nnaxisZ use_tri_area)r/rVrrr&r!linalgnorm)rr0r1r2Zr3rZrZr[rs$ $$$  $$$rcCs:|ddddf}|dkr,ttj}n ttj}|S)zReturn the hemisphere id for a source space. Parameters ---------- src : dict The source space to investigate. Returns ------- hemi : int Deduced hemisphere id. rNr)rrrrr)rZxavehemirZrZr[find_source_space_hemis   rQc CsP|dddkrtdS|dd|ddg}|jdkrvt|d|j}t|d|}||d<tgt|d<n|jdkrt|d|j}t|d|t|d}tgt|d<||d<n|jd kr@t|d|j j}t|d|}t|d|j j}t|d|t|d}t ||f}||g}ntd ||fS) aFind vertex numbers and indices from label. Parameters ---------- label : Label Source space label. src : dict Source space. Returns ------- vertices : list of length 2 Vertex numbers for lh and rh. src_sel : array of int (len(idx) = len(vertices[0]) + len(vertices[1])) Indices of the selected vertices in sourse space. rr\rNz4Labels are only supported with surface source spacesrrlhrhbothzUnknown hemisphere type) ExceptionrPrZ intersect1dverticesrrrrirRrSZhstack) labelrrZ vertno_selZsrc_selZ vertno_sel_lhZ src_sel_lhZ vertno_sel_rhZ src_sel_rhrZrZr[label_src_vertno_sels,     rXcCsdd|DS)NcSsg|] }|dqS)rrZrrZrZr[rJsz_get_vertno..rZ)rrZrZr[ _get_vertnoIsrYcCsX|D]<}tdt|tjt|||t|tjtdqtdt|dS)zWrite the source spaces to a FIF file. Parameters ---------- fid : file descriptor An open file descriptor. src : list The list of source spaces. %(verbose)s z Write a source space...rz %d source spaces writtenN)r/rVr rr_write_one_source_spacerri)rrr0rnrZrZr[_write_source_spaces_to_fidPs      r[)rr0c CsFt|tdt|ddt||dt|}t||W5QRXdS)a]Write source spaces to a file. Parameters ---------- fname : str The name of the file, which should end with -src.fif or -src.fif.gz. src : instance of SourceSpaces The source spaces (as returned by read_source_spaces). %(overwrite)s %(verbose)s See Also -------- read_source_spaces rr)rrrrrN)r9rOr.r6r_write_source_spaces)rrrr0rrZrZr[res     rcCst|tj|jrvt|tjt|tj|jdd}|rJt|tj ||jdd}|rjt|tj |t |tjt ||t |tjdS)Nrr) r rZ FIFFB_MNErVrrZ FIFF_BLOCK_IDrgrr r rr[)rrr rZrZr[r\s     r\cCsddlm}|ddkr tj}n8|ddkr4tj}n$|ddkrHtj}ntd|dt|tj||ddkrt|tj |d| d d }|rt |tj |t|tj |d t|tj|d t|tj|d t|tj|dt|tj|dt|tj|d|ddkrDt|tj|dt|tj|dd|ddkr|dd k rt|tj|dt|tj|dd|ddkr| dd }|d k rtdd|D}t|}t|tj|t|tj|t||dt|tj|dt |tj!t||dt||d| dd } | d k rRt |tj"| t#|\} } } } | d}|d kr|$| |d f}t%|tj&|d|kr|dd k rt |tj'|dt|tj(| t|tj)| t|tj*| t+|tj!|d d k r(t|tj,|d t|tj-|d!|d"d k rr|d".}|j/||j0d#}t%|tj1|t|tj2|d$|ddkrd%|krt |tj3|d%d S)&zWrite one source space.rrr\rNrMrLzUnknown source space type (%s)rsrNrurrrrrrrrrrrcSsg|] }t|qSrZri)r`rErZrZr[rsz+_write_one_source_space..rrrrrrrrrr)formatrr)4scipyrrrr r!rrrrrgrr>r0r.rr1r3r7r5r/rr4r8r9rr concatenater+r,rr"r r#r* _src_vol_dims csr_matrixrr$r&r'r(r)rr:r;rZtriur_r<r=r-)rrr0rr@r rrBrDrrrrnvoxrdistsrZrZr[rZs                  rZc Csd}d|t||f}t|tr|dkr2d}d}qt|tr|dddkr|dd}|dd}z t|}Wn$tk rtd||fYnX|d krd nd }||krtd |||fqt|n&d }t|d |}|dkrtd|f|dkrtdd}d}npd||f}|d kr>td|t |}nB|dkr`td|t |}n |d ksnt td||}||||fS)zCheck spacing parameter.z:a string with values "ico#", "oct#", "all", or an int >= 2z&"spacing" must be %s, got type %s (%r)rhNricooctz)%s subdivision must be an integer, got %rrhrrz$%s subdivision must be >= %s, got %sspacingrczspacing must be >= 2, got %dzInclude all verticesz%s = %sz Icosahedron subdivision grade %srizOctahedron subdivision grade %szApproximate spacing %s mm) r\rrrrUrr2r/rVrrr) rjr0rlZ space_errstypesvalZlimico_surf src_type_strrZrZr[_check_spacingsT               rooct6rqTrcsBd|||f}tddfdddD}t|ddgD]*\} } | d k rDt| sDtd | | fqDtd td td tdt|\} } } }td~tdg}| dkrtdtddd| ftddg|D]\} } td| | dkr6td| | | ft | | | | }tdt | d|d|d|f| |tdqt j t jg}t||D]T\}}|td d d dd d d |t jd |d!d"<|d#=|d$=|d%=|d&=qt|tt|d'}|r4|d(krd)ntj}t||||d*td+|S),aHSet up bilateral hemisphere surface-based source space with subsampling. Parameters ---------- %(subject)s spacing : str The spacing to use. Can be ``'ico#'`` for a recursively subdivided icosahedron, ``'oct#'`` for a recursively subdivided octahedron, ``'all'`` for all points, or an integer to use approximate distance-based spacing (in mm). .. versionchanged:: 0.18 Support for integers for distance-based spacing. surface : str The surface to use. %(subjects_dir)s add_dist : bool | str Add distance and patch information to the source space. This takes some time so precomputing it is recommended. Can also be 'patch' to only compute patch information (requires SciPy 1.3+). .. versionchanged:: 0.20 Support for add_dist='patch'. %(n_jobs)s Ignored if ``add_dist=='patch'``. %(verbose)s Returns ------- src : SourceSpaces The source space for each hemisphere. See Also -------- setup_volume_source_space zXsetup_source_space(%s, spacing=%s, surface=%s, subjects_dir=%s, add_dist=%s, verbose=%s)TZ raise_errorc s g|]}td|qS)rNopr)r`rPrzr{rKrZr[rXsz&setup_source_space..)zlh.zrh.ZLHZRHNz Could not find the %s surface %sz;Setting up the source space with the following parameters: zSUBJECTS_DIR = %szSubject = %szSurface = %srfz$>>> 1. Creating the source space... )rjrhz$Doing the %shedral vertex picking...ZicosaZoctargrRrSz Loading %s...rhzMapping %s %s -> %s (%d) ...z-loaded %s %d/%d selected to source space (%s)rrrrN) rrrr\rrrrsrurrwrFrGrH neighbor_trirrpatch)rn_jobsr0z8You are now one step closer to computing the gain matrix)r-rrsisfileIOErrorr/rVrorUrsplitrfrrrupdaterrOosgetcwdrinfadd_source_space_distances)rzrjrKr{Zadd_distryr0cmdsurfsrNrPrkrlrmrnrrnZhemi_idss_idrrZrtr[setup_source_space+s|(           r volume_labelcCst|dd|ft|ddd}t|tr0|g}t|tttf|t|ts|dsltd|t |ft \}}t}|D]0}||krt d||t ||f||||<q|}|D]&\}}t|td t|d d |fqd d |D}|S)N path-likezmri when %s is not NonerTraseg.mgzz5Must use a *aseg.mgz file unless %s is a dict, got %szGVolume %r not found in file %s. Double check FreeSurfer lookup table.%szvolume_label keyszint-likezvolume_labels[%r]cSsi|]\}}|t|qSrZ)r2)r`ravrZrZr[ sz(_check_volume_labels..)r9r6rrrQrrUrrkrsbasenamer*rr=items)rrvnamerrZuse_volume_labelrWrrZrZr[_check_volume_labelss8      r@rxmc svt|}t| ttttdfdt|dtdfdtdtdfd|dk rdt|tsdt|dddd }dk rttstddd d |dk rdk rt d |dkr|dk r| dk rd }n t rd }|dk rt |||}ttrt d| dk rt | |} | dkst| tst t|| d}|dk r@td|ndk rttrtfdddDsvtdtdddd}ntstd}td|nDtdd|dd|dd|dftdd|d fttr*tfd!dd"Ds$td#d}n0z tWn"tt fk rXt d$YnXttstd%|td&td'ttrtd(td)|d*|d+krtd,|t}|dk rtd-|td.td/|t|| dk d0}|d*}td.tts@tg}nrt|trvt|tjdd1}td2||d3fn$|dk r|d4dkrt d5d6|d7Dd}t!|dkrt d8|d7|d}|d9tjkst |d:tj"kr t d;t#|d:ftd<|n~dk rxttrDt$dd=d>}n}td?|d3ft%|}|d@dA9<n"tdBt|d |dd dC}t&||||| || dD}~t|tst | dks| rt!|dksn t!| st |dk r | r*t'|n|ddEdFkr*dG|ddE<| dkrLdH|dkrL|ddH=|D]}dI|krP|dI=qPt(||}|S)JaSet up a volume source space with grid spacing or discrete source space. Parameters ---------- subject : str | None Subject to process. If None, the path to the MRI volume must be absolute to get a volume source space. If a subject name is provided the T1.mgz file will be found automatically. Defaults to None. pos : float | dict Positions to use for sources. If float, a grid will be constructed with the spacing given by ``pos`` in mm, generating a volume source space. If dict, pos['rr'] and pos['nn'] will be used as the source space locations (in meters) and normals, respectively, creating a discrete source space. .. note:: For a discrete source space (``pos`` is a dict), ``mri`` must be None. mri : str | None The filename of an MRI volume (mgh or mgz) to create the interpolation matrix over. Source estimates obtained in the volume source space can then be morphed onto the MRI volume using this interpolator. If pos is a dict, this cannot be None. If subject name is provided, ``pos`` is a float or ``volume_label`` are not provided then the ``mri`` parameter will default to 'T1.mgz' or ``aseg.mgz``, respectively, else it will stay None. sphere : ndarray, shape (4,) | ConductorModel | None Define spherical source space bounds using origin and radius given by (ox, oy, oz, rad) in ``sphere_units``. Only used if ``bem`` and ``surface`` are both None. Can also be a spherical ConductorModel, which will use the origin and radius. None (the default) uses a head-digitization fit. bem : path-like | None | ConductorModel Define source space bounds using a BEM file (specifically the inner skull surface) or a ConductorModel for a 1-layer of 3-layers BEM. surface : path-like | dict | None Define source space bounds using a FreeSurfer surface file. Can also be a dictionary with entries ``'rr'`` and ``'tris'``, such as those returned by :func:`mne.read_surface`. mindist : float Exclude points closer than this distance (mm) to the bounding surface. exclude : float Exclude points closer than this distance (mm) from the center of mass of the bounding surface. %(subjects_dir)s volume_label : str | dict | list | None Region(s) of interest to use. None (default) will create a single whole-brain source space. Otherwise, a separate source space will be created for each entry in the list or dict (str will be turned into a single-element list). If list of str, standard Freesurfer labels are assumed. If dict, should be a mapping of region names to atlas id numbers, allowing the use of other atlases. .. versionchanged:: 0.21.0 Support for dict added. add_interpolator : bool If True and ``mri`` is not None, then an interpolation matrix will be produced. sphere_units : str Defaults to ``"m"``. .. versionadded:: 0.20 single_volume : bool If True, multiple values of ``volume_label`` will be merged into a a single source space instead of occupying multiple source spaces (one for each sub-volume), i.e., ``len(src)`` will be ``1`` instead of ``len(volume_label)``. This can help conserve memory and disk space when many labels are used. .. versionadded:: 0.21 %(verbose)s Returns ------- src : SourceSpaces A :class:`SourceSpaces` object containing one source space for each entry of ``volume_labels``, or a single source space if ``volume_labels`` was not specified. See Also -------- setup_source_space Notes ----- Volume source spaces are related to an MRI image such as T1 and allow to visualize source estimates overlaid on MRIs and to morph estimates to a template brain for group analysis. Discrete source spaces don't allow this. If you provide a subject name the T1 MRI will be used by default. When you work with a source space formed from a grid you need to specify the domain in which the grid will be defined. There are three ways of specifying this: (i) sphere, (ii) bem model, and (iii) surface. The default behavior is to use sphere model (``sphere=(0.0, 0.0, 0.0, 90.0)``) if ``bem`` or ``surface`` is not ``None`` then ``sphere`` is ignored. If you're going to use a BEM conductor model for forward model it is recommended to pass it here. To create a discrete source space, ``pos`` must be a dict, ``mri`` must be None, and ``volume_label`` must be None. To create a whole brain volume source space, ``pos`` must be a float and 'mri' must be provided. To create a volume source space from label, ``pos`` must be a float, ``volume_label`` must be provided, and 'mri' must refer to a .mgh or .mgz file with values corresponding to the freesurfer lookup-table (typically ``aseg.mgz``). NrrrrKrTz bem filename)rrrzsurface filenamez3Only one of "bem" and "surface" should be specifiedrzT1.mgzz_Cannot create interpolation matrix for discrete source space, mri must be None if pos is a dict) sphere_unitszBEM : %sc3s|]}|kVqdSNrZr`r)rKrZr[rbQsz,setup_volume_source_space..)rrz3surface, if dict, must have entries "rr" and "tris"F)rr0zdict()zsurface file "%s" not foundzBoundary surface file : %sz5Sphere : origin at (%.1f %.1f %.1f) mmrrrcz radius : %.1f mmrc3s|]}|kVqdSrrZr)rrZr[rbcsrz(pos, if dict, must contain "rr" and "nn"z.rz*Could not get inner skull surface from BEMrsruz%BEM is not in MRI coordinates, got %szTaking inner skull from %s return_dictr]z*Loaded bounding surface from %s (%d nodes)rMbP?zSetting up the sphere...)Rr0)vol_info single_volumer\rMrLrvol_dims))r-r9rrQrrUrrr6rr;r,rrr8r/rVrhKeyErrorr$rsrzr{float TypeErrorr(_make_discrete_source_spacerrrrgrrrirrFrr_make_volume_source_space_add_interpolator_complete_vol_src)rzrrvZsphererrKmindistexcluder{rZadd_interpolatorrrr0Z surf_extraZ pos_extrarsprNwhichrnrZ)rrKr[setup_volume_source_spacesu                                        rcCsH|D](}|tdddddddddd|d qt|ttdd}|S)Nr) rrrrrrrrrrrNonerv)r}rUrOr~r)rrzrnrZrZr[rs rcCs|jdkst|jdkst|j|tjddf}|jdksBt|jddksTt|jddksfttjtj|t dftj|dff}t dd |}|S) zCMake a transformation from MRI_VOXEL to MRI surface RAS (i.e. MRI).rrNrcr)rrr mri_voxelrv) ndimrr%rrZnewaxisrZc_rrrG)moveras voxel_sizeZrotrytrZrZr[_make_voxel_ras_transs( rrvc Cs8|tkr tdtt|ft|}t|dt}t|dt}|j|jkr`dkrnnD|jd|jdkr|jd|jdkrt | rt | st d|jd}t |t tj ||dddk}|dkrt d |td td |t|d ||t|tt|||tjd }|S)aUse a discrete set of source locs/oris to make src space. Parameters ---------- pos : dict Must have entries "rr" and "nn". Data should be in meters. coord_frame : str The coordinate frame in which the positions are given; default: 'mri'. The frame must be one defined in transforms.py:_str_to_frame Returns ------- src : dict The source space. z'coord_frame must be one of %s, not "%s"rrrcrrzV"rr" and "nn" must both be finite 2D arrays with the same number of rows and 3 columnsrJz"%d sources have zero length normalz&Positions (in meters) and orientationsz %d sourcesrL) rur\rrrrrrrs)rHrrQkeysrrrrrisfiniterhrkr!rr/rVrUonesrarangerr)rrurrnptsZnzrrZrZr[rs<0       rc ; sn d|kr\tj|ddd} tj|ddd} tj|ddd} tjj|d| dd} n4|d|d} |d|d} |d} |d} tdd| dd| dd| d ftd d| td t d | | D]&\}}}td |d|d|fqt fdd| Dt }t fdd| Dt }tdt d ||D]0\}}}td |d|d|fqVt ||d}t |}|d}|d}||}tjt|d |d dt|d|ddt|d|dddd}|d |d|d}}}t |||gj}t|t|df|t|td|tjtj|d }d|dddd f<|djd|ksttd|dtjj|d| dd}tt||k|| kd}d|d|<|dt|8<td|dd|d| d|krJt||d|g|n~t|dd}tjj|d||ddd|d|d k}|d|8<d|d||<t|dd|d!<~~td"|d|f|dkrd#|d$<|g} n|s t d%t!} |}!|"D]\}"}#t}$d&D]$}%|%|!kr.|!|%}&|&|$t#|&<q.t$|!|$}t%||d|d!|#k}'|'}(td'|(t&|(|"f|(dkrt'd(t(|"d)|#d*dd+d,d|d|d!|'<|d!|'|d!<|d|d<|"|d$<||d-<| )|q~!t| t|ks4t| r| ddD]}d.| dd|d!<qF| d}d/*d0d1| D|d$<| dd} t|dd|d!<t|d!|d<~~|s| St|})t+d2|ft }*|*,d||d k||dk||dk||dk||dk||d kg}+| d|d| |g},t |*dd3|+|,D]\}-}.}/|)|.|/|-|.<qN||d k}0t-|0||dk}1|)|1d||*d3|1f<t-|1||dk}2|)|2d|||*d4|2f<t-|0||dk}1|)|1|||*d5|1f<t-|0||dk}1t-|1||dk}2|)|2d|||*d6|2f<|)|1d||*d7|1f<t-|1||dk}2|)|2d|||*d8|2f<t-|0||dk}1|)|1|||*d9|1f<t-|1||dk}2|)|2d|||*d:|2f<t-||dk||dk}0|)|0d||*d;|0f<||dk}0t-|0||dk}1|)|1d||*d<|1f<t-|0||dk}1|)|1d||*d=|1f<t-||dk||dk}0|)|0d|||*d>|0f<||d k}0t-|0||dk}1|)|1d||*d?|1f<t-|1||dk}2|)|2d|||*d@|2f<t-|0||dk}1|)|1|||*dA|1f<t-|0||dk}1t-|1||dk}2|)|2d|||*dB|2f<|)|1d||*dC|1f<t-|1||dk}2|)|2d|||*dD|2f<t-|0||dk}1|)|1|||*dE|1f<t-|1||dk}2|)|2d|||*dF|2f<tdG|}3td}4t.d}5t/|3|5|4}6|*}7| D]}|7}*d|*ddt0|df<|*j}8|*}*t|*dkd}9t0t1|9|d!}:d|*|9|:<|8|*_|*j}*|*|dH<|6|dI<||d|dJ<dKD]}%|%|k r ||%||%< q qrt2| ddIdLdMD]&}%|%| dk rBt2| d|%dN qB| S)Oz}|dkr(tt|dntt| dqSrrrfloorabsr`rgridrZr[r s  z-_make_volume_source_space..csFg|]>}|dkr(tt|dntt| dqSrrrrrZr[r"s  z Grid extent:Zij)ZindexingrrM) rrrrr\rrursrrrNz%d sources before omitting any.rFrzI%d sources after omitting infeasible sources not within %0.1f - 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This function will also try to add patch info for the source space. It will only occur if the ``dist_limit`` is sufficiently high that all points on the surface are within ``dist_limit`` of a point in the source space. Parameters ---------- src : instance of SourceSpaces The source spaces to compute distances for. dist_limit : float The upper limit of distances to include (in meters). Note: if limit < np.inf, scipy > 0.13 (bleeding edge as of 10/2013) must be installed. If 0, then only patch (nearest vertex) information is added. %(n_jobs)s Ignored if ``dist_limit==0.``. %(verbose)s Returns ------- src : instance of SourceSpaces The original source spaces, with distance information added. The distances are stored in src[n]['dist']. Note: this function operates in-place. Notes ----- This function can be memory- and CPU-intensive. On a high-end machine (2012) running 6 jobs in parallel, an ico-5 (10242 per hemi) source space takes about 10 minutes to compute all distances (``dist_limit = np.inf``). With ``dist_limit = 0.007``, computing distances takes about 1 minute. We recommend computing distances once per source space and then saving the source space to disk, as the computed distances will automatically be stored along with the source space data for future use. r)rcdijkstraz'dist_limit must be non-negative, got %sr`z1.3zscipy >= 1.3 is required to calculate patch information only, consider upgrading SciPy or using dist_limit=np.inf when running add_source_space_distancesrKz3Currently all source spaces must be of surface typezpatch informationzsource space distanceszCalculating %s (limit=%s mm)...rcss|]}|dVqdS)rNrZrrZrZr[rb| sz-add_source_space_distances..zsComputing distances for %d source space points (in one hemisphere) will be very slow, consider using add_dist=FalserrrT)rZmin_onlyZreturn_predecessors)rrNc3s |]}d|VqdS)rNrZr`rZ adjacencyrZp_funrnrZr[rb scSsg|] }|dqS)rrZr`ddrZrZr[r sz.add_source_space_distances..cSsg|] }|dqS)rcrZrrZrZr[r srJcSsg|] }|dqS)rrZrrZrZr[r sr)rrrrcss|]}tt|VqdSr)rrjisinf)r`mdrZrZr[rb srrz2Not adding patch information, dist_limit too small)"Z scipy.sparsercscipy.sparse.csgraphrrrrr3rkrTr@_do_src_distancesrQr/rVr_DIST_WARN_LIMITr5r#rfrrrZ array_splitrrirargminrarrrjrr)rrryr0rcrZ patch_onlyparallelZ min_distsZmin_idxsrZmax_nmin_distrmin_idxrrAmidx range_idxrijrZrr[r= s)                 rcCsfddlm}t||d}d}tjtdt||t|f}t|d}tt|t|ftj} t||j df} t||j dftj } t|j d} t t |dd|ddD]j\} \}}||||}|||d}tj |dd }||| | <||| f| | <|dd|f| ||<qtj | dd }| || f} | || f} d| | tjk<| | | fS) z)Compute source space distances in chunks.rr)rrrNr])rrJ)r!rrrrrrirrrrrerr$r)conrZrun_indsrrfunc chunk_sizeZlimsZn_chunksrAr&r'r)Zlil1l2rrr(rZrZr[r" s*    *    r"c Cshddlm}ddlm}t||dd}||dd}t|dkrHtd td d |dd Drjtd t }t dt|D]}||d} ||d||dd d f} ||d} z(|d | } t |d| d} Wntk rYnXd| krd}| ddd} n(d| kr@d}| ddd} nd}|| | || | |d}||q~|S)aReturn a list of Label of segmented volumes included in the src space. Parameters ---------- src : instance of SourceSpaces The source space containing the volume regions. %(subject)s subjects_dir : str Freesurfer folder of the subjects. Returns ------- labels_aseg : list of Label List of Label of segmented volumes included in src space. r)Label)get_volume_labels_from_asegrvrT)Z return_colorsrczNo vol src space in srccss |]}t|ddkVqdS)r\rMN)rrjrrZrZr[rb sz-get_volume_labels_from_src..Nz$source spaces have to be of vol typerrrrleftrRzLeft-rfz-lhrightrSzRight-z-rhrT)rVrrPrcolorrz)rfr1 _freesurferr2rsrrirrjrQrindexrrlowerreplacerf)rrzr{r1r2Z aseg_fnameZall_labels_asegZ labels_asegnrrVrZroi_strindr6rPrWrZrZr[get_volume_labels_from_src sF       r=cCs`|ddkrtd|dtjkr0dd|dfS|dtjkrLdd|dfStd |dd S) z+Get a hemisphere from a given source space.r\rNz$Only surface source spaces supportedrsrRrrSrzunknown surface ID %sN)rkrrrrrrZrZr[r s rcs:td||ffdd||fD}dd|D\}}|dk rN||d<d|krlt|d|d|d<tt|d t} t|dt} t|d |d |d } t|d | D]|\} } | | r$t || }| }|t | |d } t| d kr t d | | d } td || f| | | <d| | <q| S)zGet a nearest-neigbor vertex match for a given hemi src. The to_neighbor_tri can optionally be passed in to avoid recomputation if it's already available. z)Mapping %s %s -> %s (nearest neighbor)...c s g|]}t|ddqS)rNz %s.sphere.regrrrrPr{rZr[r! sz&_get_vertex_map_nn..cSsg|]}t|dddqS)Trr])rrrZrZr[r# sNrurrrrrz'vertex %d would be used multiple times.zESource space vertex moved from %d to %d because of double occupation.T) r/rVr"rrrirr%rr rrk)Zfro_src subject_from subject_torPr{Zto_neighbor_triregsZreg_froZreg_toZ morph_inusebestrronerwasrZr>r[_get_vertex_map_nn s@     rEcCsht|}t||}t|dd}t}|D]}t|\}} } t||dd||f} td| ft | dddd} t | dd t |||||| d } d D] } | | =qt | |d | d <t t| d t| d<d| d| d <| |d| d<| jt| d t| dddddd| ddtj|| d dd || tdq(tttd}t||dS)aMorph an existing source space to a different subject. .. warning:: This can be used in place of morphing source estimates for multiple subjects, but there may be consequences in terms of dipole topology. Parameters ---------- src_from : instance of SourceSpaces Surface source spaces to morph. subject_to : str The destination subject. surf : str The brain surface to use for the new source space. subject_from : str | None The "from" subject. For most source spaces this shouldn't need to be provided, since it is stored in the source space itself. subjects_dir : str | None Path to SUBJECTS_DIR if it is not set in the environment. %(verbose)s Returns ------- src : instance of SourceSpaces The morphed source spaces. Notes ----- .. versionadded:: 0.10.0 TrqrNz%s.%szReading destination surface %sF)rr0r])rru)rurFrGrHrrrrrNrw) rrrrrrrrsrr\rurrz[done] rv)rV)rrr-rQrrsrr/rVrr$rErrrrirr}rrrfrUr~rr4rO)src_fromr@rNr?r{r0Zsrc_outZfrorPrrrrBrrVrZrZr[morph_source_spacesB sJ"       rGcCs&t|dd}t}t}d}tdD]\} } t|| ||| |} | || d} t| || } ||| d| | | }tt||| rt|| |  st d|t |}t |}||7}|||t |7}q$t |}tt|ttdd|Dst||fS) aWGet the reordering indices for a morphed source space. Parameters ---------- vertices : list The vertices for the left and right hemispheres. src_from : instance of SourceSpaces The original source space. subject_from : str The source subject. subject_to : str The destination subject. %(subjects_dir)s %(verbose)s Returns ------- data_idx : ndarray, shape (n_vertices,) The array used to reshape the data. from_vertices : list The right and left hemisphere vertex numbers for the "from" subject. Trqr)rRrSrzDCould not map vertices, perhaps the wrong subject "%s" was provided?css|]}t|VqdSrr^)r`rrZrZr[rb sz,_get_morph_src_reordering..)r-rQrerErrrfrrrhrkrrirarrr)rVrFr?r@r{r0Z from_verticesZ data_idxsrCrrPrBZ full_mappingZ used_verticesZremaining_mappingZimplicit_mappingZdata_idxrZrZr[_get_morph_src_reordering s:        rHexact~jtX?c Csddlm}m}m}m}m} ddlm} |dkrDd|krDtd|t t ||D]\} \} } t | t | }}|||t ||AdD]<}| || |}}|dkrt|t|}}||||qd D](}|| ks|| kr|| || ||qd D]}|| ks|| kr|| ks2t|d || ksJt|d t| d j}| d | d j}t|dkrd |kr| tt|||d|ddqdD]t}| |dkr|| |dk|nL|dkr|| || ||n,|dkrdnd}|| || |d||dqdD].}|| ksF|| kr.|| || ||q.|r8dD]R}| |dkr|| |dk|n*|dkrdnd}|| || |||dqhdD]v}| |dkr|| |dk|nN|t| |t| |k|t | || |D]\}}|t||k|qq|dkrdD]}|| || ||dqFdD]}|| || |k|qhdD]H}| |dk r|| |j| |j|t| d| djdkqqRt | | fD]4\}}||dt|d dd!|| || fq|t| dt| dt| d | d k}||d"kd#||d$krt| d| d}t| d| d}| | d%|| d%|}|tj|d&d'tt||d(d| d)dk r|| d)j| d)jn|| d)dk|t| d)| d)kd"kqRd*D]^}|dkrJ||j||j|n6||jkrl|||jkd+|n|||jkd,|q$dS)-zkCompare two source spaces. Note: this function is also used by forward/tests/test_make_forward.py r)assert_allcloseassert_array_equal assert_equalassert_assert_array_lesscdistrIZapproxzunknown mode %s)rrrr\rsrs)r)rz in s1 but not s0rZnointerprz > 0.1%)err_msg)rrrrurNrg-C6?)ZrtolatolrR)r)rrrgư>)rSrR)r)rrr)r)rrrrz6src%s[%s]["vertno"] != np.where(src%s[%s]["inuse"])[0]gGz?z %s < 0.99rrrrJzmismatched vertnorrvz "%s" missingz"%s" should not exist)Z numpy.testingrKrLrMrNrOscipy.spatial.distancerQrkrersetrrrrrrrr risqrtrrhrrZ setdiff1drrrV)Zsrc0Zsrc1moderZdist_tolrKrLrMrNrOrQrms0s1abrrEZdiffsrSp1Zp2rrnZ agreementZv0Zv1rerZrZr[_compare_source_spaces s       $     r]cCst|t|kstt||D]n\}}|ddt||d<t||d<d|d|d<tggt|d<tdg|d<t|dd q|S) z(Reset the list of source space vertices.rrrrrrrFr)rirrrrrrr)rrVrnrrZrZr[_set_source_space_vertices4 s r^cCs|dkr|dn|}|r|ddk rtt|df}tt|d|D]R\}}|d|||kslttj|d|d|d|ddfdd||<qL|tjj |dd d }n|d|ddf}|S) NrrrrrrrJr]T)rKZkeepdims) rgrrrirerrrrLrM)rnZuse_cpsrVrZvprrZrZr[ _get_src_nnC s" r_c sddlm}t|tstt|tfd|ddtjkrLt |dd\}n t ddt fdd |D}t ||d d d }g}d } |D]n} t|| dkr| d krt|ddd} |t| |d| dd dq||d| dd dqt |}|||} | S)aCompute distances between vertices and sensors. Parameters ---------- src : instance of SourceSpaces The object with vertex positions for which to compute distances to sensors. %(info)s Must contain sensor positions to which distances shall be computed. %(picks_good_data)s %(trans_not_none)s %(verbose)s Returns ------- depth : array of shape (n_vertices, n_channels) The Euclidean distances of source space vertices with respect to sensors. rrPrVruF) allow_nonertcs(g|] }t|d|dtqS)rr)rBrrrZ src_transrZr[rt sz/compute_distance_to_sensors..r rZ)rN)magZgradZ dev_head_tr}Zchslocr)rTrQrrOrr9rrrrErGrZvstackrrrIrfrBr) rrVZpicksryr0rQrZsrc_posZ sensor_posZ dev_to_headchZdepthsrZrar[compute_distance_to_sensorsR s4     recCst|}g}|D]}|ddkr"q|d}|d}|d}i}|||d<tt|dt}tt|||<|||d<|ddkst||q|S) aGet the decimated surfaces from a source space. Parameters ---------- src : instance of SourceSpaces | path-like The source space with decimated surfaces. Returns ------- surfaces : list of dict The decimated surfaces present in the source space. Each dict which contains 'rr' and 'tris' keys for vertices positions and triangle indices. Notes ----- .. versionadded:: 1.0 r\rNrrrr]rr) rrfullrirrrhrrf)rr|rnrrrrpZreindexrZrZr[get_decimated_surfaces s     rg)FN)FN)N)N)N)N)rprqNTN)r)NrNNNNrrxNNTrFN)N)rv)rN)r )NN)N)NrfN)N)rqNNN)NN)rITrJ)TN)NNN)rr functoolsrr~os.pathpathrsnumpyrZ io.constantsrZ io.meas_inforrZio.treer Zio.tagr r Zio.openr Zio.writer rrrrrrrrrZio.pickrrrrrfixesrrKrrrrr r!r"r#r$r%r&r'r7r(r)r*r+r,utilsr-r.r/r0r1r2r3r4r5r6r7r8r9r:r;r<r=r>r?r%r@Z transformsrArBrCrDrErFrGrHrIrrQrOrrrrrrQrXrYr[rr\rZrorrrrrrrrrbrrrrrrrrr#rrr"r=rrErGrHr]r^r_rergrZrZrZr[ s      0 8T ,\( % 1\ .  d 0k    - o6 j  K  q < , H = k  <