U f{j1@sdZddlZddlZddlmZmZddlZddlmZddl Z ddl Z ddl Z ddl Z ddl mZddlZddlmZmZmZddlmZddlmZdd lmZdd lmZmZmZdd lm Z m!Z!dd l"m#Z#m$Z$m%Z%dd l&m'Z'm(Z(m)Z)m*Z*m+Z+m,Z,ddl-m.Z.m/Z/ddl0m1Z1m2Z2m3Z3m4Z4m5Z5m6Z6m7Z7m8Z8m9Z9m:Z:m;Z;mZ>ddl?m@Z@ddlAmBZBmCZCmDZDmEZEmFZFmGZGmHZHmIZImJZJmKZKmLZLddlMmNZNejOddZPejOddZQejOeQdZRejOeQdZSejOeQddZTejOeQdZUejOeRdZVeEeVddZWeEeVddZXeEeVddZYejOeRd ZZejOeRd!Z[ejOeRd"eXeWfZ\ejOeRd#ejOeUd$ejOeUd%fZ]e^e_d&d'd(Z`d)d*Zad+d,Zbded.d/ZceIdfd1d2ZdeFdgd3d4Zedhd6d7Zfd8d9Zgd:Zhdidd?ZjdjdAdBZkdCdDZldEdFZmdkdGdHZndldIdJZodmdKdLZpdndMdNZqdOdPZrdQdRZseFdodSddTdUdVZtdpdWdXZueFdqdSddTdYdZZveFdrd[d\Zwd]d^Zxd_d`ZydadbZzeIGdcdddde{Z|dS)sz3Coregistration between different coordinate frames.N)globiglob)reduce)read_fiducialswrite_fiducials read_info)FIFF)Info)_get_data_as_dict_from_dig)_read_mri_infoget_mni_fiducialsestimate_head_mri_t) read_labelLabel)add_source_space_distancesread_source_spaceswrite_source_spaces) read_surface write_surface_normalize_vectorscomplete_surface_infodecimate_surface_DistanceQuery)read_bem_surfaceswrite_bem_surfaces)rotation rotation3dscaling translation Transform _read_fs_xfm _write_fs_xfminvert_transformcombine_transforms_quat_to_euler_fit_matched_points apply_trans rot_to_quat_angle_between_quats)make_dig_montage) get_configget_subjects_dirloggerpformatverbosewarn has_nibabelfill_doc_validate_type_check_subject _check_option)_fiducial_coordsz {raw_dir}z{subject}-trans.fifz{subjects_dir} {subject}bemmri transformssurfz{subject}-{name}.fifheadnamez head-sparse fiducialsz{head}-fiducials.fifz{subject}-{spacing}-src.fifouter_skin.surfz{subject}-head-dense.fifz lh.segheadz lh.smseghead)r>returncCs4|}|dkrdS|dkr dS|dks,tdSdS)z3Map a fiducial name to its index in the DigMontage.lparnasionrrpaN)lowerAssertionErrorr=rHH/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/coreg.py_map_fid_name_to_idxDs rJcCs&t|tt|tjdBdS)zMake a file writable.N)oschmodstatS_IMODElstatST_MODE)fnamerHrHrI_make_writableQsrScCsNtjdrdStj|ddD]*\}}}||D]}ttj||q0qdS)zRecursively set writable.winNF)topdown)sysplatform startswithrLwalkrSpathjoin)rZrootdirsfilesfrHrHrI_make_writable_recursiveVs   r`FcCs<|rtnt}|D]&}|j||d}tj|r|SqdS)zFind a high resolution head. subjects_dirsubjectN)_high_res_head_fnames _head_fnamesformatrLrZexists)rcrbhigh_resfnamesrRrZrHrHrI_find_head_bem_s   rj{Gz?c Cst|trt|}t|tr*t|\}}ntj}dd|dD}t|dkrXtdn|}t |d}t ||}t |||d}t |||S)aCreate a head-MRI transform by aligning 3 fiducial points. Parameters ---------- %(info_not_none)s fiducials : str | list of dict Fiducials in MRI coordinate space (either path to a ``*-fiducials.fif`` file or list of fiducials as returned by :func:`read_fiducials`. Returns ------- trans : Transform The device-MRI transform. .. note:: The :class:`mne.Info` object fiducials must be in the head coordinate space. cSsh|] }|dqS) coord_framerH).0drHrHrI sz'coregister_fiducials..digrz8info contains fiducials from different coordinate frames)tol) isinstancestrrrr ZFIFFV_COORD_MRIlen ValueErrorpopr6fit_matched_pointsr ) infor?rqZcoord_frame_toZ frames_fromZcoord_frame_fromZ coords_fromZ coords_totransrHrHrIcoregister_fiducialsis      rzc Cst|dd}|dkr.td|}|dkr.tdtj|dd}tj|sVtd|d D].}tj||}tj|sZtd ||fqZtj|d}||krtd |n |stj|rtd d|ft d |rtj|st ||t |tjtjtddd}tj|d} tj| srdestZ source_fnameZdest_bemZ dest_fnamerHrHrIcreate_default_subjects^        r c Csddlm}t|}|d|d\}}}|d|\}}}t|||} t|||} t|||} tj|| | | fdd\} } t| \}}}| |}| |}| |}tj |||f|d}t |dd}| |\} }t |}t tdgtj|t|dg}t|t|d ks(tt}t|D]p\}}||||||d }t|sx|tjgd n,||t|||tjd d dfq6t|td d }|t||jd d |dk}|S)aDecimate the number of points using a voxel grid. Create a voxel grid with a specified resolution and retain at most one point per voxel. For each voxel, the point closest to its center is retained. Parameters ---------- pts : array, shape (n_points, 3) The points making up the head shape. res : scalar The resolution of the voxel space (side length of each voxel). Returns ------- pts : array, shape = (n_points, 3) The decimated points. r)cdistg@F)ZbinsZdensityZcKDTree)method)Z minlengthrNZaxis)Zscipy.spatial.distancernpasarrayminmaxZarangeZ histogramddZnonzeroZc_rqueryZargsortZcumsum concatenateZbincountrtrGlist enumerateappendinfZargminnewaxisarrayfloatreshapeabs)ptsresrZxminZyminZzminZxmaxZymaxZzmaxZxaxZyaxZzaxH_ZxbinsZybinsZzbinsxyzZmidstreeZmid_idxZsort_idxZboundsoutmimidZuse_ptsrHrHrI_decimate_pointss>     $"rc Cs|\}}}d}g}|rB|dd\}}} |t||| |d7}|rx|||d\}}} |dt||| |d7}|dkr||} |t| | | n0|dkr|||d\}}} |t||| ttj|}|S)z?Convert transformation parameters into a transformation matrix.rNrr)rrinsertrrrrdot) param_infoparamsZ do_rotateZ do_translateZdo_scaleiryrrrsrHrHrI_trans_from_params*s&  rTryc Cst|}t|}|j|jkr4td|j|j|dk rt||j}|jdksh|j|jddfkrtd|j|jdf|ddtj f}t |t |t |f} ~~~| dkr.error)rrrrc sj|\}}}}}}tt|||t|||}t|jddddf}|} dk rb| 9} | SNr)rrrrrr) rrrrtxtytzryrrnrrHrIrs)rrrrrrrc sz|\}}}}}}}ttjt|||t|||t|||f}t|jddddf} | } dk rr| 9} | Srrrrrrrrr) rrrrrrrrryrrnrrHrIrs  )rrrrrrr)TTrc s~|\ }}}}}}}}} ttjt|||t|||t||| f} t| jddddf} | } dk rv| 9} | Srr) rrrrrrrsxZsyszryrrnrrHrIrs  ) rrrrrrrrrzYThe specified parameter combination is not implemented: rotate=%r, translate=%r, scale=%rT)Z full_output)Zscipy.optimizerrrrrtNotImplementedError) rrrrrrrrrrHrrIrs4   rr|c st|dd}tj||}tj|d|dkrg}tD]B\}}}tj|}t|dD]} tj|| } || qbq>nfddt |D}|S)asFind paths to label files in a subject's label directory. Parameters ---------- subject : str Name of the mri subject. pattern : str | None Pattern for finding the labels relative to the label directory in the MRI subject directory (e.g., "aparc/*.label" will find all labels in the "subject/label/aparc" directory). With None, find all labels. subjects_dir : None | str Override the SUBJECTS_DIR environment variable (sys.environ['SUBJECTS_DIR']) Returns ------- paths : list List of paths relative to the subject's label directory Tr{r}Nz*.labelcsg|]}tj|qSrH)rLrZrelpath)rmrZZlbl_dirrHrI sz%_find_label_paths..) r,rLrZr[rYrfnmatchfilterrr) rcpatternrbZ subject_dirpathsdirpathr filenamesZrel_dirfilenamerZrHrrI_find_label_pathss rcs>t|dd}i}ttg|d<g|d<tjtd}d}tddd krR|d d }|D]H}d D]>}||}|j|||d } tj| r^|d t ||dq^qVtjtd}d}|D]6}|j|||d } tj| r|d t ||dq~~~ ~g|d<} t j||d} tj| r(| dt t ||dd } t t ||dd  dd} t| D]&} t| | } | d}| |qX~ ~ ~ ~ |rg|d<n,t|||d<t|ddkrtd|g|d<tjtd} tjtd}d}|D]N}d D]B}||}|j|||d } tj| r|d t ||dqq~~~ ~g|d<tjtd}|j||d} tj| r|d |~~ g|d<}tj||d}tt|d }|d!}|D]>}||rd"|t|d }tjt|} | | qtj||dttd#}fd$d%|D|d&<|S)'a8Find all files of an mri relevant for source transformation. Parameters ---------- subject : str Name of the mri subject. skip_fiducials : bool Do not scale the MRI fiducials. If False, an IOError will be raised if no fiducials file can be found. subjects_dir : None | str Override the SUBJECTS_DIR environment variable (sys.environ['SUBJECTS_DIR']) Returns ------- paths : dict Dictionary whose keys are relevant file type names (str), and whose values are lists of paths. Tr{r]r;z{name}) ZinflatedwhiteorigZorig_avgZ inflated_avgZ inflated_preZpialZpial_avgZsmoothwmZ white_avgZsegheadZ smsegheadZ_MNE_FEW_SURFACEStrueN)zlh.zrh.rbrcr>r=)zinner_skull.surfzouter_skull.surfr@r8rar<*-bem(.+)\\\rfidrzNo fiducials file found for %s. The fiducials file should be named {subject}/bem/{subject}-fiducials.fif. In order to scale an MRI without fiducials set skip_fiducials=True. duplicate)ZcurvZspherez sphere.regzsphere.reg.avgr:z talairach.xfmsrcz *-src.fif-z {subject}-%sz*.mgzcsg|]}tj|qSrH)rLrZr[)rmr_Zmri_dirrHrIr|sz#_find_mri_paths..r9)r, bem_dirname surf_dirnamerLrZr[getenvrfrgrr.head_bem_fname bem_fnamereplacerrematchgroup_find_fiducials_filesrtrmri_transforms_dirnamerrlistdirrX mri_dirname)rcskip_fiducialsrbrZ surf_fnameZ surf_namesZ surf_namehemir>rZr8Z bem_patternZ re_patternrZsurf_dup_namesZ surf_dup_nameZtransform_fnamerZbem_dirriprefixrRrHrrI_find_mri_paths s             rcCsg}tjtj||dr$|ttt||dd}tt||dddd}t |D]4}t ||}| d|d}|tt|d qT|S) zFind fiducial files.ra*)rbrcr<rrrrr7)r<) rLrZrg fid_fnamerfrr.fid_fname_generalrrrrr)rcrbrrregexrZrr<rHrHrIrs*    rcCs(t|dd}tt||p$t||ddS)aeCheck whether a directory in subjects_dir is an mri subject directory. Parameters ---------- subject : str Name of the potential subject/directory. subjects_dir : None | str Override the SUBJECTS_DIR environment variable. Returns ------- is_mri_subject : bool Whether ``subject`` is an mri subject. Tr{rh)r,rrjrcrbrHrHrI_is_mri_subjects   r cCs6t|dd}t||sdStj||d}tj|S)anCheck whether a directory in subjects_dir is a scaled mri subject. Parameters ---------- subject : str Name of the potential subject/directory. subjects_dir : None | str Override the SUBJECTS_DIR environment variable. Returns ------- is_scaled_mri_subject : bool Whether ``subject`` is a scaled mri subject. Tr{FMRI scaling parameters.cfg)r,r rLrZr[rg)rcrbrRrHrHrI_is_scaled_mri_subjects   rcCs0t|dd}tj||dd}t|}tt|S)aGCheck whether an mri subject has a file matching the bem pattern. Parameters ---------- subject : str Name of the subject. subjects_dir : None | str Override the SUBJECTS_DIR environment variable. Returns ------- has_bem_file : bool Whether ``subject`` has a bem file. Tr{rr)r,rrfrrrt)rcrbrrirHrHrI_mri_subject_has_bems  rcCst|dd}tj||d}tj|s8td||ftd|t }| || dd}|dkrz| dd }n:|d kr| dd }td d |D}n td || dd||d}|S)aNRead information from the cfg file of a scaled MRI brain. Parameters ---------- subject : str Name of the scaled MRI subject. subjects_dir : None | str Override the SUBJECTS_DIR environment variable. Returns ------- cfg : dict Dictionary with entries from the MRI's cfg file. Tr{rz?%r does not seem to be a scaled mri subject: %r does not exist.zReading MRI cfg file %s MRI Scalingn_paramsrrrcSsg|] }t|qSrH)rrmrrHrHrIrsz read_mri_cfg..z%Invalid n_params value in MRI cfg: %i subject_from)rrr)r,rLrZr[rgrr-rx configparserRawConfigParserreadgetintgetfloatgetrrsplitru)rcrbrRconfigrrZ scale_strrrHrHrI read_mri_cfgs*       rc Cst|}t|s|jdkr$d}nd}t}|d|dd||dd||ddt||dkr|ddt|n|ddd d d |D|dd d t |d}| |W5QRXdS)aDWrite the cfg file describing a scaled MRI subject. Parameters ---------- fname : str Target file. subject_from : str Name of the source MRI subject. subject_to : str Name of the scaled MRI subject. scale : float | array_like, shape = (3,) The scaling parameter. rHrrrr subject_torr cSsg|] }t|qSrH)rsrrHrHrIrsz%_write_mri_config..version1wN) rrZisscalarrrr add_sectionsetrsr[openwrite)rRrrrrrrrHrHrI_write_mri_configs   r'cCst|dd}|dk|dkkr$td|dkrZt||}|d}|d}|dksRt|d}t|}|jd ks||jd dkrtd |jft |}||||d kfS) a`Assemble parameters for scaling. Returns ------- subjects_dir : str Subjects directory. subject_from : str Name of the source subject. scale : array Scaling factor, either shape=() for uniform scaling or shape=(3,) for non-uniform scaling. uniform : bool Whether scaling is uniform. Tr{NzJNeed to provide either both subject_from and scale parameters, or neither.rrrrrrrzQInvalid shape for scale parameer. Need scalar or array of length 3. Got shape %s.) r, TypeErrorrrGr atleast_1drrrurt)rrrrbcfgrrHrHrI _scale_paramss     r,raise on_defectsr/c Cst||||\}}}}tj|||d}tj|||d} tj| rNtd| t||d} | D]H} | d|9<|s^t| ddkst | d|<t | dq^t | | dS)aScale a bem file. Parameters ---------- subject_to : str Name of the scaled MRI subject (the destination mri subject). bem_name : str Name of the bem file. For example, to scale ``fsaverage-inner_skull-bem.fif``, the bem_name would be "inner_skull-bem". subject_from : None | str The subject from which to read the source space. If None, subject_from is read from subject_to's config file. scale : None | float | array, shape = (3,) Scaling factor. Has to be specified if subjects_from is specified, otherwise it is read from subject_to's config file. subjects_dir : None | str Override the SUBJECTS_DIR environment variable. %(on_defects)s .. versionadded:: 1.0 %(verbose)s rzFile already exists: %sr/rrnnrN) r,rrfrLrZrgrrrtrGrr) rbem_namerrrbr/r/uniformrdstZsurfsr;rHrHrI scale_bem@s$    r6c Cst||||\}}}}t|||}|s*dSt|dd}tj||d}tj||d} |D]} tj| | } |s~tj| r~qZtj| } tj| st| tj|| } t | }|j |}t |j ||j |j|j|d}|| qZdS)a*Scale labels to match a brain that was previously created by scaling. Parameters ---------- subject_to : str Name of the scaled MRI subject (the destination brain). pattern : str | None Pattern for finding the labels relative to the label directory in the MRI subject directory (e.g., "lh.BA3a.label" will scale "fsaverage/label/lh.BA3a.label"; "aparc/\*.label" will find all labels in the "fsaverage/label/aparc" directory). With None, scale all labels. overwrite : bool Overwrite any label file that already exists for subject_to (otherwise existing labels are skipped). subject_from : None | str Name of the original MRI subject (the brain that was scaled to create subject_to). If None, the value is read from subject_to's cfg file. scale : None | float | array_like, shape = (3,) Scaling parameter. If None, the value is read from subject_to's cfg file. subjects_dir : None | str Override the SUBJECTS_DIR environment variable. NTr{r})rc)r,rr,rLrZr[rgrmakedirsrposrZverticesvaluesrcommentsave)rr overwriterrrbrrZsrc_rootZdst_rootrRr5rrZl_oldr8Zl_newrHrHrI scale_labelsos6       r=c Cst|dd}t|||} t|}|jdkr^t|d|drxt|d|drx|d}n|jdkrxtd|jftj||d } t j | r|st d || ft | td | d D]} | j||d } t | qtd t j | d}t||||td| dD]J}|j||d }t j |}|j||d } t|\}}t| |||qtd| dD]}t||||||ddqvtd| dD]l}|j||d }t j |}t|dd\}}|D]}|d||d<q|j||d } t| ||dddqtdt tj||d| dD]"}t j |}t|||||q:td| dD]Z}|drpt tj||d| dD]$}t j |}t ||||||qq̐qptd | d!D].}|j||d }|j||d } t !|| qtd"| d#D]&}t j |}t"|||||ddq td$t t j ||d%|r~t#||||d&td'|rt j ||d%d(}t j ||d%}t$|D]}t %||qd)S)*aCreate a scaled copy of an MRI subject. Parameters ---------- subject_from : str Name of the subject providing the MRI. subject_to : str New subject name for which to save the scaled MRI. scale : float | array_like, shape = (3,) The scaling factor (one or 3 parameters). overwrite : bool If an MRI already exists for subject_to, overwrite it. subjects_dir : None | str Override the SUBJECTS_DIR environment variable. skip_fiducials : bool Do not scale the MRI fiducials. If False (default), an IOError will be raised if no fiducials file can be found. labels : bool Also scale all labels (default True). annot : bool Copy ``*.annot`` files to the new location (default False). %(on_defects)s .. versionadded:: 1.0 %(verbose)s See Also -------- scale_bem : Add a scaled BEM to a scaled MRI. scale_labels : Add labels to a scaled MRI. scale_source_space : Add a source space to a scaled MRI. Notes ----- This function will automatically call :func:`scale_bem`, :func:`scale_labels`, and :func:`scale_source_space` based on expected filename patterns in the subject directory. Tr{)rrrrE)rz*scale must have shape (3,) or (1,), got %sr z+Subject directory for %s already exists: %rz create empty directory structurer]zsave MRI scaling parametersrzsurf files [in mm]r;zBEM files [in m]r8Fr.zfiducials [in m]r)r/r)r<r/zMRIs [nibabel]rar9Z TransformszT1.mgzr:zduplicate filesrz source spacesrz labels [in m]r})rrrbzcopy *.annot filesz*.annotN)&r,rrr*riscloserusubject_dirnamerfrLrZrgrrrmtreer-debugr7r[r'realpathrrr6rrrrbasename _scale_mriendswithr _scale_xfmcopyfilescale_source_spacer=rr)rrrr<rbrlabelsZannotr/r/rrrZdir_rRrrZtrir3Zcframeptmri_nameZxfm_namesrc_name src_patternZdst_dirZsrc_filerHrHrI scale_mris*    (                                         rOcCst||||\}}}}|r(|}t} n6td|} | rLd| }t} nd}tjt |} | j |||d} | j |||d} t | } t d|||t d|d}| D]}||d<|d |9<d D]6}||kr||d dd |ddtjf9<q|rN|d dk r|d |d9<|d||d<|d||d<q|d|<t|d|d dk rd}tt| dd}q|ddk rd}d}q|rt dt| ||t| | dS)aScale a source space for an mri created with scale_mri(). Parameters ---------- subject_to : str Name of the scaled MRI subject (the destination mri subject). src_name : str Source space name. Can be a spacing parameter (e.g., ``'7'``, ``'ico4'``, ``'oct6'``) or a file name of a source space file relative to the bem directory; if the file name contains the subject name, it should be indicated as "{subject}" in ``src_name`` (e.g., ``"{subject}-my_source_space-src.fif"``). subject_from : None | str The subject from which to read the source space. If None, subject_from is read from subject_to's config file. scale : None | float | array, shape = (3,) Scaling factor. Has to be specified if subjects_from is specified, otherwise it is read from subject_to's config file. subjects_dir : None | str Override the SUBJECTS_DIR environment variable. n_jobs : int Number of jobs to run in parallel if recomputing distances (only applies if scale is an array of length 3, and will not use more cores than there are source spaces). %(verbose)s Notes ----- When scaling volume source spaces, the source (vertex) locations are scaled, but the reference to the MRI volume is left unchanged. Transforms are updated so that source estimates can be plotted on the original MRI volume. z(oct|ico|vol)-?(\d+)$rN)rbrcspacingz"scaling source space %s: %s -> %szScale factor: %sFZsubject_his_idr1)Z vox_mri_tZ src_mri_tryrdistrZ nearest_dist dist_limitr2Tnearestz.Recomputing distances, this might take a while)r,isdigit src_fnamerrr[groupsrLrZrrfrr-rxrrrrrrr)rrMrrrbZn_jobsr/r4rPrNrrr5ZsssZadd_distsskeyrRrHrHrIrI1s\%     ,    rIc Cst||||\}}}}ts(tddSddl}ttj||d|}ttj||d|}||} t | j } | dddg|9<| j | | j | _|| |dS)z#Scale an MRI by setting its affine.z3Skipping MRI scaling for %s, please install nibabelNrrarEr)r,r1r0nibabelopr[rrfloadrrheaderZ get_zoomsZ set_zoomsZ get_affineZ_affiner;) rZ mri_fnamerrrbrrY fname_fromfname_toZimgZzoomsrHrHrIrEs8    rEcCslt||||\}}}}ts dStjtj||d|}ttj||d|}t|s`t |t t |s~t t |t |}t|dkrt |dn|}tddt|} t|\} } | dkst | t|dd\}}} }}td d | } ~ ttj||dt|}t|dd\}}}}}t|}~~ttt|t| d d| d d | d d }t||d | dS) zScale a transform.Nrarrr9zMNI Transform Filemm)ZunitsZrasZmni_talry)r,r1rLrZr[rrfrZisfilerGrrrr*rtZtiler rr!r rrDr#r$r")rZ xfm_fnamerLrrrbrr]r^SZxfmkindZ F_mri_rasZ F_ras_mniZ T_mri_rasZ T_ras_mriZ T_ras_mnirHrHrIrGsv    rGcCst}|dk rt|r|dr6t||ddd}nRz0t|ddd}|dd 9<t|dd Wn tk rtd |YnX|S) Nz.fifFr.rT)Z return_dictrEr1MbP?)rz9Error loading surface from %s (see Terminal for details).) dictrZrgrFrrr Exceptionru)rr/r8rHrHrI _read_surfaces*  rfc @seZdZdZdbddddZdd Zd d Zd d ZddZdcddZ ddZ ddZ ddZ ddZ ddZddZedd Zed!d"Zed#d$Zed%d&Zed'd(Zed)d*Zed+d,Zed-d.Zed/d0Zed1d2Zed3d4Zed5d6Zed7d8Zd9d:Zed;d<Zed=d>Z ed?d@Z!dAdBZ"edCdDZ#e$dddGdHZ%dIdJZ&dKdLZ'e$dedNdOZ(edPdQZ)dRdSZ*dTdUZ+edVdWZ,dXdYZ-dZd[Z.d\d]Z/d^d_Z0d`daZ1dS)fCoregistrationa.Class for MRI<->head coregistration. Parameters ---------- info : instance of Info | None The measurement info. %(subject)s %(subjects_dir)s %(fiducials)s %(on_defects)s .. versionadded:: 1.0 Attributes ---------- fiducials : instance of DigMontage A montage containing the MRI fiducials. trans : instance of Transform MRI<->Head coordinate transformation. See Also -------- mne.scale_mri Notes ----- Internal computation quantities parameters are in the following units: - rotation are in radians - translation are in m - scale are in scale proportion If using a scale mode, the :func:`~mne.scale_mri` should be used to create a surrogate MRI subject with the proper scale factors. Nautor-r0c Cst|tdfd||_t|||_t|dd|_d|_||_d|_ t dddddddddg |_ |j dd|_ |j dd|_|j dd|_d |_d |_d |_d |_d |_|jd |_d|_d |_d|_d|_d|_d|_d|_||d|_| ||!dS)NrxTr{?r g?)rSmatchedr$@)"r3r _infor4_subjectr, _subjects_dir _scale_mode _on_defectsZ _rot_transrr_default_parameters _rotation _translation_scaleZ_icp_iterations _icp_angle _icp_distance _icp_scale_icp_fid_matches_icp_fid_match _lpa_weight_nasion_weight _rpa_weight _hsp_weight _eeg_weight _hpi_weight_extra_points_filter _setup_digs _setup_bem _fid_filename_setup_fiducialsreset)selfrxrcrbr?r/rHrHrI__init__/s<   zCoregistration.__init__c Cs|jdkrFttdtdtdtdtdtdd|_nt|jddd|_tdddd d gd d d ddgD]V\}}|j|dkrtd|j|<t||dqx|dkrxt|j|gt |j|<qxdS)Nr()hpidig_ch_pos_locationhsprDrCrBrpF)rpZexclude_ref_channelrCrBrDrrrr~rrr)rrr)rDrCrB) rprdrZzeros _dig_dictr zipsetattrrr)rkZw_atrrHrHrIrTs2   zCoregistration._setup_digscCst|j|jdd}t|j|jdd}|dkrD|dkrDtd|j|dk rnt||jd|_td|n t||jd|_td||dkrt dt |jd |ft |jd |jd d d \}}t t ||d ddd|_nt||jd|_dS)NTr Fz-No standard head model was found for subject r0z$Using high resolution head model in z#Using low resolution head model in zONo low-resolution head found, decimating high resolution mesh (%d vertices): %sr1trisi)Z n_triangles)r1r)rr/)rjrqrrrrfrt _bem_high_resr-rxr0rtrrrd _bem_low_res)rZ high_res_pathZ low_res_pathr1rrHrHrIrosL       zCoregistration._setup_bemcCst|tttfd}|dkrzt|j|j}t|dkrv|dj|j|jd}t d|dt |\}}d}||_ nd}|dkrt dd }t |j|j}|dkrdn|}t|trt|}n.t|tsttj|d |d |d gtd }||_||_|dS)NrhrrazUsing fiducials from: .TZ estimatedz$Estimating fiducials from fsaverage.FrBrCrD)r)r3rsrdrrrqrrrtrfr-rxrrr rrr6rGrrr _fid_pointsZ _fid_accurate_reset_fiducials)rZfidsZ fid_accurateZ fid_filesZ fid_filenamerZ fid_coordsrHrHrIrs<     zCoregistration._setup_fiducialscCs,t|jd|jd|jddd}||_dS)NrrrEr9)rBrCrDrl)r*rr?)rZ dig_montagerHrHrIrszCoregistration._reset_fiducialsFcCs0|r|dkr|j}d}|dk r4d}|j|_||_d}|sF|dk r|dkrT|j}d}|j|_||_t|jj|_t |jddddf| |jdddf<t |j|j d|_ t |j|j d|_ t |j|j|_t |j|j d|_t|j|_t||jdddf<|s&|dk r|dkr6|j}|j|_||_td|_|jddddf|9<t |j|j|_||r,|j|jd|_|j|j d|_|j|j d|_|jt |j|j d d|_|jt |j|j d d|_ |jt |j|j d d|_!dS) NFTrrrrrrrDrCrB)"rwrvr_last_rotation_last_translationrr _head_mri_trrr'r_transformed_dig_hpi_transformed_dig_eeg_filtered_extra_points_transformed_dig_extra_transformed_orig_dig_extraZ _mri_head_trrx _last_scaleeye _mri_trans_processed_high_res_mri_points _transformed_high_res_mri_points_update_nearest_calc _nearest_calcr._nearest_transformed_high_res_mri_idx_orig_hsp)_nearest_transformed_high_res_mri_idx_hpi)_nearest_transformed_high_res_mri_idx_eegZ)_nearest_transformed_high_res_mri_idx_rpaZ,_nearest_transformed_high_res_mri_idx_nasionZ)_nearest_transformed_high_res_mri_idx_lpa)rrottrasca force_updateZ rot_changedZ tra_changedrHrHrI_update_paramss       zCoregistration._update_paramscCs ||_|S)aSelect how to fit the scale parameters. Parameters ---------- scale_mode : None | str The scale mode can be 'uniform', '3-axis' or disabled. Defaults to None. * 'uniform': 1 scale factor is recovered. * '3-axis': 3 scale factors are recovered. * None: do not scale the MRI. Returns ------- self : Coregistration The modified Coregistration object. rs)rZ scale_moderHrHrIset_scale_modeszCoregistration.set_scale_modecCs||_|jdd|S)a+Compensate for hair on the digitizer head shape. Parameters ---------- value : float Move the back of the MRI head outwards by ``value`` (mm). Returns ------- self : Coregistration The modified Coregistration object. Tr) _grow_hairr)rvaluerHrHrI set_grow_hairs  zCoregistration.set_grow_haircCs|jt|d|S)a Set the rotation parameter. Parameters ---------- rot : array, shape (3,) The rotation parameter (in radians). Returns ------- self : Coregistration The modified Coregistration object. )rrrr)rrrHrHrI set_rotation#s zCoregistration.set_rotationcCs|jt|d|S)a Set the translation parameter. 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Returns ------- self : Coregistration The modified Coregistration object. )rr)rrrHrHrI set_scaleCs zCoregistration.set_scalecCst|j|j|_dSr)rrrxrrrHrHrIrSs z#Coregistration._update_nearest_calccCs(|jdkr|jdS|jd|jSdS)Nr)rrrrHrHrIrWs  z%Coregistration._filtered_extra_pointscCst|j|j|jfSr)rrrvrwrxrrHrHrI _parameters^szCoregistration._parameterscCst|j|j|jfSr)rrrrrrrHrHrI_last_parametersbszCoregistration._last_parametersc Cs|tj|j|jd}tttt|j ddddftt|j ddddf}d|j |j |j }|||fS)N@@rd) rlinalgnormrrwZrad2degr)r(rrvrrxr)rmoveangleZpercsrHrHrI_changesgszCoregistration._changescCs|jt|j|jdS)Nr)rrr'rrrrHrHrI)_nearest_transformed_high_res_mri_idx_hspps  z8Coregistration._nearest_transformed_high_res_mri_idx_hspcCs|jot|jdkSNr _has_mri_datartrrrHrHrI _has_hsp_dataus zCoregistration._has_hsp_datacCs|jot|jdkSr)rrtrrrHrHrI _has_hpi_datazs zCoregistration._has_hpi_datacCs|jot|jdkSr)rrtrrrHrHrI _has_eeg_datas zCoregistration._has_eeg_datacCsH|jjtd}|dtjks"tt|d}t|jd}|oF|S)NrBidentr>) r?rprJr ZFIFFV_POINT_LPArGrrrrZ mri_pointZ has_mri_dataZ has_head_datarHrHrI _has_lpa_datas zCoregistration._has_lpa_datacCsH|jjtd}|dtjks"tt|d}t|jd}|oF|S)NrCrr>) r?rprJr ZFIFFV_POINT_NASIONrGrrrrrHrHrI_has_nasion_datas zCoregistration._has_nasion_datacCsH|jjtd}|dtjks"tt|d}t|jd}|oF|S)NrDrr>) r?rprJr ZFIFFV_POINT_RPArGrrrrrHrHrI _has_rpa_datas zCoregistration._has_rpa_datacCs |dS)Nhigh_get_processed_mri_pointsrrHrHrIrsz-Coregistration._processed_high_res_mri_pointscCs |dS)NlowrrrHrHrI_processed_low_res_mri_pointssz,Coregistration._processed_low_res_mri_pointscCs|dkr|jn|j}|d}|jrt|ds6td|jt|j}|dddf|dddfk}|||d||7<|S)Nrr1r2rcrEr) rrrrrtrGrrrx)rrr8ZpointsZscaled_hair_distZhairrHrHrIrs   z(Coregistration._get_processed_mri_pointscCst|jdkSr)rtrrrHrHrIrszCoregistration._has_mri_datacCs|jot|jdkSrrrrHrHrI _has_dig_datas zCoregistration._has_dig_datacCs&|j|j}|j}tjj||ddS)Nrr)rrrrrrr mri_points hsp_pointsrHrHrI_orig_hsp_point_distances z'Coregistration._orig_hsp_point_distancecCs.|}t|dt|ddddS)Nz median distance: iz6.2f mm)compute_dig_mri_distancesr-rxrZmedian)rrZ errs_nearestrHrHrI_log_dig_mri_distancesz$Coregistration._log_dig_mri_distancecCs |jS)zGet the current scale factor. Returns ------- scale : ndarray, shape (3,) The scale factors. )rxrrrHrHrIrs zCoregistration.scalerjroc Csvtd|d|j}|dkr0tdd}||_||_||_t|j d|j d|j df}t|j j d d |j j dd |j j d d f}|||g}|d kr||j 9}|j } | d d |} t||| d||d} |d kr|j| d d| dd dn`| jdkstt| | dgd g} | jdks@t|j| d d| dd | d dd|d|S)aFind rotation and translation to fit all 3 fiducials. Parameters ---------- lpa_weight : float Relative weight for LPA. The default value is 1. nasion_weight : float Relative weight for nasion. The default value is 10. rpa_weight : float Relative weight for RPA. The default value is 1. %(verbose)s Returns ------- self : Coregistration The modified Coregistration object. zAligning using fiducialsZStartrz5Enforcing 1 scaling parameter for fit with fiducials.rrBrCrDrr>rENrkr)rrrrrrrrlrrrzEnd )r-rxr_n_scale_paramsr~rrrZvstackrr?rprxrrwrrrGr) r lpa_weight nasion_weight rpa_weightr/n_scale_paramshead_ptsmri_ptsrrrrHrHrI fit_fiducialssH         ( zCoregistration.fit_fiducialsc Cst}t}t}|jr\|jdkr\||j||j|j|tt |d|jdD]}t |d|dr`||j ||j dkrt |d}|jj|dd d}||n*|j d kst||jt |d |f|tt |dt |d |q`|jr`|jdkr`||j d ||j|j|tt |d|j|jr|jdkr||j d||j|j|tt |d|jt|}t|}t|}|dkr||j9}|||fS)NrrrBrCrDZ_has__datarnr=r>rrSz(_nearest_transformed_high_res_mri_idx_%sz _%s_weightrr)rrrrrrrrfullrtgetattrrr}rJr?rprrGrrrrrrrrx)rrrrrrXidxprHrHrI _setup_icp s\          zCoregistration._setup_icpcCstd||j||_|S)aSet the strategy for fitting anatomical landmark (fiducial) points. Parameters ---------- match : 'nearest' | 'matched' Alignment strategy; ``'nearest'`` aligns anatomical landmarks to any point on the head surface; ``'matched'`` aligns to the fiducial points in the MRI. Returns ------- self : Coregistration The modified Coregistration object. r)r5r|r})rrrHrHrI set_fid_match3szCoregistration.set_fid_matchrmc  Cstd|d|j} ||_||_||_||_||_||_|j } | dddddg| } t |D](} | | \} }}t || | | d|d} | d kr|j | dd | d dd nx| d krtt| | d gd} |j | dd | d d| dddn(|j | dd | d d| ddd|j\}}}|d| d dd|dk rf|| |||jkrd||jkrdt||jkrdqqd|d|S)a$Find MRI scaling, translation, and rotation to match HSP. Parameters ---------- n_iterations : int Maximum number of iterations. lpa_weight : float Relative weight for LPA. The default value is 1. nasion_weight : float Relative weight for nasion. The default value is 10. rpa_weight : float Relative weight for RPA. The default value is 1. hsp_weight : float Relative weight for HSP. The default value is 1. eeg_weight : float Relative weight for EEG. The default value is 1. hpi_weight : float Relative weight for HPI. The default value is 1. callback : callable | None A function to call on each iteration. Useful for status message updates. It will be passed the keyword arguments ``iteration`` and ``n_iterations``. %(verbose)s Returns ------- self : Coregistration The modified Coregistration object. zAligning using ICPz Start Nrkrrlr)rrrrrrrrrrErz ICP Z2drz End )r-rxrrr~rrrrrrangerrwrrrrrryrzallr{)rZ n_iterationsrrrZ hsp_weightZ eeg_weightZ hpi_weightcallbackr/rr iterationrrrrrrrHrHrIfit_icpFsD!    *(     zCoregistration.fit_icpcCs(|jdkrd}n|jdkr d}nd}|S)Nrr4rrr)rrrHrHrIrs   zCoregistration._n_scale_paramscCsNt|}|dkrdS|j|k}t|}td||||_|jdd|S)aExclude head shape points that are far away from the MRI head. Parameters ---------- distance : float Exclude all points that are further away from the MRI head than this distance (in m.). A value of distance <= 0 excludes nothing. Returns ------- self : Coregistration The modified Coregistration object. rNzGCoregistration: Excluding %i head shape points with distance >= %.3f m.Tr)rrrrr-rxrr)rdistancemaskZ n_excludedrHrHrIomit_head_shape_pointss   z%Coregistration.omit_head_shape_pointscCs0|d\}}}t|j|}tjj||ddS)aCompute distance between head shape points and MRI skin surface. Returns ------- dist : array, shape (n_points,) The distance of the head shape points to the MRI skin surface. See Also -------- mne.dig_mri_distances rrr)rr'rrrr)rrrrrHrHrIrs z(Coregistration.compute_dig_mri_distancescCstdd|jS)z1The head->mri :class:`~mne.transforms.Transform`.r<r9)r rrrHrHrIryszCoregistration.transcCsTd|_||jdd||jdd||jddd|_||S)zReset all the parameters affecting the coregistration. 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