U f{j&@spdZddlmZddlmZddlZddlmZddl m Z ddl m Z ddl mZddlZdd lmZmZmZd d lmZd d lmZmZd d lmZmZmZmZd dlm Z d dl!m"Z"m#Z#m$Z$m%Z%m&Z&d dl'm(Z(d dl)m*Z*m+Z+d dl,m-Z-m.Z.m/Z/m0Z0m1Z1d dl2m3Z3m4Z4m5Z5m6Z6m7Z7m8Z8d dl9m:Z:m;Z;mZ>m?Z?m@Z@mAZAmBZBmCZCmDZDmEZEmFZFd dlGmHZHmIZImJZJmKZKmLZLmMZMmNZNmOZOmPZPmQZQmRZRmSZSmTZTmUZUddlVmWZWddlGmXZXmYZYmZZZm[Z[m\Z\m]Z]d dl^m_Z_m`Z`maZaeKZbe(jce(jde(jefZfdddZgeOdd d!Zhd"d#ZieKdd&dd'd(d)ZjeKdd-d.Zkd/d0ZleKdd1d2Zmdd3d4Zndd6d7Zod8d9Zpd:d;Zqd?s z$_fiducial_coords..cSs$i|]}|dtjkr|d|qS)kindident)rZFIFFV_POINT_CARDINALrOrNrNrR @sz$_fiducial_coords..csg|]}|dqS)rrNrPi)points_rNrRrSCsr\rTrWrrgư>)Zatolr ) nparrayFIDUCIAL_ORDERrFIFFV_COORD_HEADemptyfillnanFIFFV_POINT_HPIiscloseallisfinite)pointsrMoutrQrN)rMrZrR_fiducial_coords;s$   ""rjtracesviridiszTkc A s^ ddlm} ddlm} ddlm} td|ddgdkrFtdd n} | || d d }|dk rt|d d }|ddd }|dddfd9<t |t t fs|g}t |D]z\} }t|t}|jdks|jddkrtd|jf| dkr&|dddf|| dd|d7<||| <qtdd|D}tj|dd}| |\}}}td|ddddddfdddg| d|dddg}|ddddf }d}}dk rbtd ddd}t|dkrbdtfdd|Dt}|dkr6t|d|dfjn,t}t|d ddd |d!d"9<td#d$}|dkr|dkr| j ddd d%d}n t|}|jd&krtd'|jf|dj!}d(d)g}t t"|jjD]\} \}}|| dfj#|||d*dd+|| dfj$|d| |dd,gd-|| dfj#|||d*dd+|| dfj$|d| |dd,gd-|dd,D]0}t%dD] }|| |fj&||d.d/qq~qt d0D]2\} }|d| fj$|d1|d,| fj$d2d3q|dk rtj'fd4dt%dDdd} t%dD]} t t%| t t%| dd}!dd5l(m)}"|"|dd|!fdd|!f}#|dd| gfdd| fk}$|# }%tj*|%|$<| dkr,t+|%'r,tj,|%dd}&||&| f}'t+|%|&t-t|&f| B}(tj.|'|(<|| dfj#||'|d6d7dd8n$|| dfj/| d|d6d7dd8|#})tj*|)|$<t+|)'rtj,|)dd}&||&| f}*t+|)|&t-t|&f| B}(tj.|*|(<|| dfj#||*|d6d7dd8n$|| dfj/| d|d6d7dd8q$t%dD]} || dfj$d,dgd9q|dk rHt|dddft0|ddddfgj1}+t"|j2|+D]\},}-|,j/|-d.d:dd*d;qnnddl7m8}0| j dtd?d@dA\}},ddtj9f}1tj|1dd,|1ddgdd}2|.|d|dB}3|/|2||3dC}4|4:|dd,|,;|4tddddD}5tdEdF}6t"|dGdHd*gD]\}7}8|dddd|5|7f}9t|t<|df}:|,j=dddfdddfdddf|9dddf|9dddf|9dddff|3||:|8dI|6|dk rf|,j=|dJ|dK|dL||5|7df||5|7df||5|7dff||8dM|6qfd};d}<|dk r|,j>|d!j|dN|dOddP|,j?|jd|dQt@|;|d};tA|<|d}<|<|;dR}=|<|;ddtj9fdR|= |=g\}>}?}@|,j$dSdTdU|>|?|@dVtB|,|,CdWdXtD|dYtE||S)ZaPlot head positions. Parameters ---------- pos : ndarray, shape (n_pos, 10) | list of ndarray The head position data. Can also be a list to treat as a concatenation of runs. mode : str Can be 'traces' (default) to show position and quaternion traces, or 'field' to show the position as a vector field over time. cmap : colormap Colormap to use for the trace plot, default is "viridis". direction : str Can be any combination of "x", "y", or "z" (default: "z") to show directional axes in "field" mode. show : bool Show figure if True. Defaults to True. destination : str | array-like, shape (3,) | None The destination location for the head, assumed to be in head coordinates. See :func:`mne.preprocessing.maxwell_filter` for details. .. versionadded:: 0.16 %(info)s If provided, will be used to show the destination position when ``destination is None``, and for showing the MEG sensors. .. versionadded:: 0.16 color : color object The color to use for lines in ``mode == 'traces'`` and quiver arrows in ``mode == 'field'``. .. versionadded:: 0.16 axes : array-like, shape (3, 2) The matplotlib axes to use. Only used for ``mode == 'traces'``. .. versionadded:: 0.16 Returns ------- fig : instance of matplotlib.figure.Figure The figure. r )head_pos_to_trans_rot_t)_check_destinationrNmoderkfield) dev_head_tT)Z head_frameheadmegtransr\r zFpos (or each entry in pos if a list) must be dimension (N, 10), got %s)rrrcSsg|] }t|qSrNlen)rPpprNrNrRrSsz'plot_head_positions..axisz ijk,ik->ijFrN)ruref_megexcludecs$g|]}d|dddqS)chslocNr\rN)rPpick)inforNrRrSsrscopyrr@@coreg helmet_color)Zsharex)r\r z#axes must have shape (3, 2), got %sxyz)z$q_1$z$q_2$z$q_3$?)lwzorderry)ylabelxlimrWcolor)z Position (mm)zRotation (quat)titleTime (s))xlabelcsDg|]<}dd|f|dfkdd|f|dfkBqS)NrrrNrPii)lims use_transrNrRrSs)cdist-?rlsrrylim:)rrrr Normalize)Line3DCollectionAxes3D3dZ projectionZ subplot_kwcmapnormxyrmtail)pivotg@g@)rrr^length)rr\)rr\)r r\)rrtris皙?) trianglesralphaZshade)sr@rrrm)rrZzlabelrrzlim-)fig)FZchpiroZpreprocessing.maxwellrpmatplotlib.pyplotpyplotr@dictr+r isinstancelisttuple enumerater]r^floatndimshape ValueErrorZcumsum concatenateZeinsumZ transposerr|minmaxTr!r1r subplotsfigurezipplotsetrangeaxvlineanyZscipy.spatial.distancerinfrgargminarangercaxhliner(ravelaxesmatplotlib.colorsrZmpl_toolkits.mplot3d.art3drmpl_toolkits.mplot3drnewaxis set_arrayZadd_collectionrepeatquiver plot_trisurfscatterminimummaximum_set_aspect_equal view_initrFrE)Aposrqr directionshow destinationrrrrorppltZ dest_inforrQZbordersrvZrottZuse_rotZ use_quatssurfrrsZ meg_picksrrlabelsZquatZcoordbZjjrZpos_badsZoidxrdistsleftZleft_dists_allidxZ left_distsZbadsZright_dists_allZ right_distsvalsaxvalrrrptssegmentsrlcZdir_idxkwargsdrZuse_dirr^ZminsZmaxsscalerrrrN)rrrrRplot_head_positionsUs.      , *          && &  ""             "  .      *   rcCs(z|dWntk r"YnXdS)Nequal)Z set_aspectNotImplementedError)rrNrNrRr)sr t = %0.0f msterrain) interactionr7c$ sXddlm} fdddD} t|ddt|d}td |d d gd } |d krhtfd d| D}~ jd|krjdksntd|t t j|} ddg} ddg}t dd}t t ddddgdt ddddgdt ddddgdg}| |ddd}||t|D]\}}|d}|d}|d }|d!}|d"krntjd#d$d%}ntjd$d#d#d&}fd'd|D}t|}t|}||krd(g}||}t|r|d)t|g7}||}t|r|d*t|g7}td+|t|j|| f}|d kr8tt |}t|}| |}t||d,|d-|d.d/} | t||d$d0}!td1|!g}"t|"d2 tj!}#| j"t#t||#ddg|dd3| j"||| |gdd4d3|dkr(|j$|||| |||d5q(|d k r:d6|kr*|d7j| ;}|j%d8d8|d9|j&d:d;d<|'|(S)=a:Plot MEG/EEG fields on head surface and helmet in 3D. Parameters ---------- evoked : instance of mne.Evoked The evoked object. surf_maps : list The surface mapping information obtained with make_field_map. time : float | None The time point at which the field map shall be displayed. If None, the average peak latency (across sensor types) is used. time_label : str | None How to print info about the time instant visualized. %(n_jobs)s fig : instance of Figure3D | None If None (default), a new figure will be created, otherwise it will plot into the given figure. .. versionadded:: 0.20 vmax : float | None Maximum intensity. Can be None to use the max(abs(data)). .. versionadded:: 0.21 n_contours : int The number of contours. .. versionadded:: 0.21 %(interaction_scene)s Defaults to ``'terrain'``. .. versionadded:: 1.1 %(verbose)s Returns ------- fig : instance of Figure3D The figure. r _get_renderercsg|]}|kr|qSrNrNrPrevokedrNrRrS^sz%plot_evoked_field..)eegZgradmagNnumericvmax n_contoursr trackballrNcsg|]}j|ddqS))ch_typer)Zget_peakr r rNrRrSesrryz,`time` (%0.3f) must be inside `evoked.times`rr333333?rr)rrrZvtkformatgo@)r)r rrrrXr)bgcolorsizerdatarTch_namesr FT)rur )rur rcsg|]}j|qSrNr )rPrnr rNrRrSsz&Channels in map and data do not match.z%s not in data file. z%s not in map file. rrnn)rendererverticesrnormalsr)rrrr)scalarscolormaprngopacitynamerr)surfacer)Zcontoursvminrr,r*%r{Gz?)Zx_windowZy_windowtextrx<)azimuth elevation))backends.rendererrr?r>r@r]meantimesrrabsrCrtileset_interactionrrrrr|r RuntimeErrorjoindotrrrrBmaprAr^roundastypeZuint8Z add_overlayonesZcontourZtext2d set_camerarscene)$r Z surf_mapstime time_labelZn_jobsrrrrr7rtypestime_idxalphascolorsr*Zcolormap_linesr$rZthis_maprZmap_dataZmap_typeZ map_ch_namesrr Z set_ch_namesZset_map_ch_namesmessagediffrrmeshrrZctablerNr rRplot_evoked_field2s+   "              rNautooriginalFcDs ddlm}t|||\}}}}td|ddg|dkrDtdddn|}t|d |d krh|dkrht}t|trx|g}t|t r| }| D]~\}}t|d d t |t|d dt |d|dk rt |||<d||krdksntdt |d|dqni}t|}t|D]\}}t|d d|dq*t| tdfd} t| tst| dkstttd|dddd g|d kr|dkrdnd}| dk rt| } | j}|dkr|n|}|dk r||krtd|d|d|d krt|dd}t||}t|d|kd|kt|dk| ||t|dkd}|dkrd |d!}|dk rt|d}||krt|d"|d#| dk rt| dd} | |krt|d"| d$| d%k r|dkrt|d&|jr|dkrt|d| dk r\| d's4|dkrZt|d(n&|d)ggfkrt|d*|d+n.t|dkr|dkrt|d*|d+tdd}t|ddd}!t||!|d,}"t }#tt |t d)d-d.d/g@}$t|$dkrtd0|$d1|$r|$dnd%}$|$d%k r|!|"|$| dk rL| d'rL|$d)krLt#| d)|#d2<nr|$d)krZd-n|$}$t|dd}d3D]N}%t$||d4|%d1|$}&t$%|&st&d5|d6|&d7t'|&|#|%<qnd8fd9d:|D}'t|'dkrtd;|'|'r|'dnd%}'|'d%k r|!|"|'nd<|kr0td=d>d:|D}(|(D]@})|!|"|)t(|))d?d||| d@}*|)|*dA<|*|#|)<qBt|dkrtdBt*|dC|t+dD|p| pt|dddEjdk}+|+rdFndG},dH}-| dks |$rt,dIdJ| Dr|,}-t-.|,dKddLdt|(d}.| dkr^|$d%kr^t|(dkr^|s^|,}/n|.d}/t |-|-d3}0t dMdMd3}1t|(D]8\}2}3|.|2d|0|3<dN|2dOdPdN|2dOf|1|3<q|$d%k r|$|kr|!|$|0d2<|0dQ<| D]4\}4}5|5dk r |5|0|4<|4kr|5dk r|5}/qt/fdRdJdSD}6||dT|dMdUdV}7|70|t1|7|'||| ||"|/dW\}8}8}9dX|krt|ddYjdkrt2|7||"|!|\}8}8}:|$rd2|#kr| dt3j4kst| dZ };t5|"d|;};|7j6|;d[|1d2|0d2d\|rt7|7||"|!td]| d^| r^| dkrPt8|7||"t9|7||"t:|7||"|6| rvt;|7| |||"|6|# D]f\}}|<|1||0||dXkd`q~|jdk r t?|7||"||||||9da | dk r^t@\}=}1| D]6}>|>db|>dcAtB}?|>dd|>dcAtB}@|"t| dd}At5|A|?}?t5|A|@d%de}@|>dfdgk r|>Cdhd}B|Bdk r|B|1k r|1|Bddi}Ct/djdJ|CD}Cndk}Cndk}Ct|?dk r$|7jD|?dddf|?dddf|?dddlf|@dddf|@dddf|@dddlf|CdmdndGdodpdqddr q$|dk rtE|7||"t|d|7jFdsdsdtdpdu|7G|7HS)va9Plot head, sensor, and source space alignment in 3D. Parameters ---------- %(info)s If None (default), no sensor information will be shown. %(trans)s %(subject)s Can be omitted if ``src`` is provided. %(subjects_dir)s surfaces : str | list | dict Surfaces to plot. Supported values: * scalp: one of 'head', 'outer_skin' (alias for 'head'), 'head-dense', or 'seghead' (alias for 'head-dense') * skull: 'outer_skull', 'inner_skull', 'brain' (alias for 'inner_skull') * brain: one of 'pial', 'white', 'inflated', or 'brain' (alias for 'pial'). Can be dict to specify alpha values for each surface. Use None to specify default value. Specified values must be between 0 and 1. for example:: surfaces=dict(brain=0.4, outer_skull=0.6, head=None) Defaults to 'auto', which will look for a head surface and plot it if found. .. note:: For single layer BEMs it is recommended to use ``'brain'``. coord_frame : 'auto' | 'head' | 'meg' | 'mri' The coordinate frame to use. If ``'auto'`` (default), chooses ``'mri'`` if ``trans`` was passed, and ``'head'`` otherwise. .. versionchanged:: 1.0 Defaults to ``'auto'``. %(meg)s %(eeg)s %(fwd)s dig : bool | 'fiducials' If True, plot the digitization points; 'fiducials' to plot fiducial points only. %(ecog)s src : instance of SourceSpaces | None If not None, also plot the source space points. mri_fiducials : bool | str Plot MRI fiducials (default False). If ``True``, look for a file with the canonical name (``bem/{subject}-fiducials.fif``). If ``str``, it can be ``'estimated'`` to use :func:`mne.coreg.get_mni_fiducials`, otherwise it should provide the full path to the fiducials file. .. versionadded:: 0.22 Support for ``'estimated'``. bem : list of dict | instance of ConductorModel | None Can be either the BEM surfaces (list of dict), a BEM solution or a sphere model. If None, we first try loading ``'$SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-$SOURCE.fif'``, and then look for ``'$SUBJECT*$SOURCE.fif'`` in the same directory. For ``'outer_skin'``, the subjects bem and bem/flash folders are searched. Defaults to None. %(seeg)s %(fnirs)s .. versionadded:: 0.20 show_axes : bool If True (default False), coordinate frame axis indicators will be shown: * head in pink. * MRI in gray (if ``trans is not None``). * MEG in blue (if MEG sensors are present). .. versionadded:: 0.16 %(dbs)s fig : Figure3D | None PyVista scene in which to plot the alignment. If ``None``, creates a new 600x600 pixel figure with black background. .. versionadded:: 0.16 %(interaction_scene)s .. versionadded:: 0.16 .. versionchanged:: 1.0 Defaults to ``'terrain'``. %(verbose)s Returns ------- fig : instance of Figure3D The figure. See Also -------- mne.viz.plot_bem Notes ----- This function serves the purpose of checking the validity of the many different steps of source reconstruction: - Transform matrix (keywords ``trans``, ``meg`` and ``mri_fiducials``), - BEM surfaces (keywords ``bem`` and ``surfaces``), - sphere conductor model (keywords ``bem`` and ``surfaces``) and - source space (keywords ``surfaces`` and ``src``). .. versionadded:: 0.15 rrrrrNrmiscrrOstrz surfaces key rz surfaces[]rz] (z) must be between 0 and 1)Z extra_allowrMrtrumriz subject ("z+") did not match the subject name in src ("z")T raise_errorsensorsref)rurr ecogseegdbsfnirszEA head<->mri transformation matrix (trans) is required to plot %s in z) coordinates, `trans=None` is not allowedza z-coordinate forward solutionz-coordinate source spaceFz mri fiducialsZ is_sphereza BEMbrain, z surfacesrLpialwhiteinflatedz+Only one brain surface can be plotted, got .lhrcrhrz#No brain surface found for subject z , expected z to exist)rOrtZ outer_skinz head-densesegheadcsg|]}|kr|qSrNrNrPr) head_keysrNrRrSsz"plot_alignment..z0Can only supply one head-like surface name, got projectedzA head surface is required to project EEG, "head", "outer_skin", "head-dense" or "seghead" must be in surfaces or surfaces must be "auto"cSsg|]}|dkr|qS))Z outer_skullZ inner_skullrNrgrNrNrRrSs_bemr-zUnknown surface type: r)r[rZr?rcss|]}|ddkVqdS)typerNrNrgrNrNrR sz!plot_alignment..r)rrrffffff?皙?g333333?rec3s|]}|dVqdS)_colorNrN)rPkey)defaultsrNrRrps)ZlpaZnasionZrpazSensor alignment: ) rw)r-rrr'helmetruZr0r1)rrr,dig)TFZ fiducialsrr.rr,backface_cullingmrinuser#moverovolseg_namer\css|]}|dVqdS)gp@NrNrXrNrNrRrps)rrrr cylinder~jth??rrrrmuvwrrqrr, glyph_height glyph_centerglyph_resolutionr|Zr)r4r5ZdistanceZ focalpoint)Ir6r_handle_sensor_typesr@rr?rrrRrritemsreprrrrrKrIAssertionErrorr_subjectr4r0rr|r2rr=r,r*r3sortedrpopindexrJopisfiler<r"rsplitr<r rr]linspacerr;_plot_head_surface _plot_helmetrr`r'sphere _plot_axes_plot_hpi_coils_plot_head_shape_points_plot_head_fiducials_plot_mri_fiducialsror1r. _plot_sensorsr rAboolgetquiver3d _plot_forwardrCrrD)Drrvsubject subjects_dirZsurfacesrMrur fwdrzrYsrc mri_fiducialsrlrZr\Z show_axesr[rrr7rwarn_megZ user_alpharursir src_subjectpicksmsgZ fwd_frameZ src_frame head_mri_tto_cf_tZsurfsr]hemiZ brain_fnamertZskullsZ skull_nameskullZno_deepZ max_alphaZhemi_valZ alpha_rangeZ head_alpharIrJrr-rnr fid_colorsr$rj head_surfsrc_surfcenterrZ atlas_idsssZsrc_rrZsrc_nnZ src_transrrrN)rvrhrRplot_alignmentsp                                   $"(  "            "          rcCs||dkrdg}n|dkrt}|dk }|dkr:dddg}n |dkrLddg}n|dkrZt}|dkrjdg}n|dkrxt}t|tr|g}t|tr|g}t|tr|g}td |||fD]>\}}t|ttfrtd d |Dst|d t|qt|D]\}}t d |d|dqt|D]\}}t d|d|dq(t|D]\}}t d|d|dqP||||fS)z)Handle plotting inputs for sensors types.TrPFNrxrWrXpairs)r rur\css|]}t|tVqdSN)rrR)rPrrNrNrRrpWsz'_handle_sensor_types..z# must be list or tuple of str, got zmeg[rS)rxrWrXzeeg[)rPrizfnirs[)channelsrsources detectors) rrrRrrrf TypeErrorrorr@)rur r\rrTvarxirrNrNrRr:sF     rc Cstddlm}ttttd}t}t}t|dD]}t||} | |krb|| d7<nd|| <ttddd} | tkr| jtdd td d d | D]|\} } | t d kr\t |d |d} |d |g}z||ddd}Wn&t k r||ddd}YnXt |\}}t| |}t|dkrp|rptd|j|dn|d |d| }|d |d}|tjtjtjtjfkrt d|j|d|d|tjkr||j|tj}t|t||}| t d kr||f|| |j|<q||| |j|<qq8|r.rrr)forwardrrrrrslicerupdaterrrr< _sensor_shaper'r|r8r rZFIFFV_COORD_UNKNOWNZFIFFV_COORD_DEVICEr`FIFFV_COORD_MRIappendr2r5rr=)rrrr7rrZ unknown_chsZ type_countsrrZ type_slices type_nameZ type_sliceZ coil_transZ this_coilcoilch_coordrZch_coord_framerNrNrR_ch_pos_in_coord_framedsd       rc Csx|dkrtddn|}d} d} } |dk rnt||||d} t| ||d|dgdd } |j| ||dd \} } | | | fS) z$Render a head surface in a 3D scene.NrZ head_colorFrkrTrtTrr{)r rr1r.) r$rtrrrlrMrrractorrdst_surfrNrNrRrs$ rrc Csp|dkrtddn|}t||}|dtjks4tt|||d|dgdd}|j|||dd \}} || |fS) NrrrMrTrtTrFr{)r r!rrrr1r.) r$rrrrMrrrrrrNrNrRrs   rcCs2|ddfg}t|dtds6||ddft|ddjd krZ||d d ft}|D]}t|d dd d d fd dj \}}} |d dd d d d f\} } } |j t |d |d | d f|ddd\} }|| |j ||| | | | dd|ddddddgd \} }|| qd|S)z!Render different axes a 3D scene.rt)g?333333?rrvrrTrTryrru)rrrNr\r[rr)rrrarrowg{Gz?scalarrQ?Q?r) rrrmrrrrqrr scale_mode resolutionr)) r]allcloseeyerrrrr:reshaperrZ column_stackr)r$rrrractorsrrrrmrrrrrjrNrNrRrs0."    rc Cstd}t|dtj}t|d|}t|dkr:tdt}t||D]2\}}|j |||d|ddd \} } | | qJ|S) Nrrzrtrz8Digitization points not found. 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Parameters ---------- brains : list, tuple or np.ndarray The collection of brains to plot. time : bool If True, link the time controllers. Defaults to True. camera : bool If True, link the camera controls. Defaults to False. colorbar : bool If True, link the colorbar controllers. Defaults to True. picking : bool If True, link the vertices picked with the mouse. Defaults to False. r)_get_3d_backend pyvistaqtz2Expected 3d backend is pyvistaqt but {} was given.)Brain _LinkViewerrz"The collection of brains is empty.z(Expected type is Brain but {} was given.cSsg|] }|jqSrN)Z _subject_id)rPr]rNrNrRrSszlink_brains..z+Cannot link brains from different subjects.)brainsrEcamerarpickingN)r6rrrZ_brainrrrrr|rrrosetup_time_viewerrr<) rrErrrrrrr]ZsubjectsrNrNrR link_brainss4      rcCsNddlm}m}t||rdSt|tddt||rFtd|ddd d SdS) Nr )_BaseSurfaceSourceEstimate_BaseMixedSourceEstimateFrz1src when stc is a mixed or volume source estimater.)r`r_z%when plotting a mixed source estimateextraT)source_estimaterrrr?rr@)rLrr. backend_namerrrNrNrR _check_volumes  rrclassicrwverticalc%Cs4ddlm}m} ddlm}!m}"|"||t||!ddt| dd} t|j |}t d |d d d d g|d k}#|#s|d krz |}Wn$t t fk rt dd}#YnXt||||||| | || |||| | |d}$|#rt|fd|i|$S| |:t|f||||||d||||||d |$W5QRSQRXdS)aXPlot SourceEstimate. Parameters ---------- stc : SourceEstimate The source estimates to plot. %(subject_none)s If ``None``, ``stc.subject`` will be used. surface : str The type of surface (inflated, white etc.). hemi : str Hemisphere id (ie 'lh', 'rh', 'both', or 'split'). In the case of 'both', both hemispheres are shown in the same window. In the case of 'split' hemispheres are displayed side-by-side in different viewing panes. %(colormap)s The default ('auto') uses 'hot' for one-sided data and 'mne' for two-sided data. %(time_label)s smoothing_steps : int The amount of smoothing. %(transparent)s alpha : float Alpha value to apply globally to the overlay. Has no effect with mpl backend. time_viewer : bool | str Display time viewer GUI. Can also be 'auto', which will mean True for the PyVista backend and False otherwise. .. versionchanged:: 0.20.0 "auto" mode added. %(subjects_dir)s figure : instance of Figure3D | instance of matplotlib.figure.Figure | list | int | None If None, a new figure will be created. If multiple views or a split view is requested, this must be a list of the appropriate length. If int is provided it will be used to identify the PyVista figure by it's id or create a new figure with the given id. If an instance of matplotlib figure, mpl backend is used for plotting. %(views)s When plotting a standard SourceEstimate (not volume, mixed, or vector) and using the PyVista backend, ``views='flat'`` is also supported to plot cortex as a flatmap. Using multiple views (list) is not supported by the matplotlib backend. .. versionchanged:: 0.21.0 Support for flatmaps. colorbar : bool If True, display colorbar on scene. %(clim)s cortex : str or tuple Specifies how binarized curvature values are rendered. Either the name of a preset Brain cortex colorscheme (one of 'classic', 'bone', 'low_contrast', or 'high_contrast'), or the name of a colormap, or a tuple with values (colormap, min, max, reverse) to fully specify the curvature colors. Has no effect with mpl backend. size : float or tuple of float The size of the window, in pixels. can be one number to specify a square window, or the (width, height) of a rectangular window. Has no effect with mpl backend. background : matplotlib color Color of the background of the display window. foreground : matplotlib color | None Color of the foreground of the display window. Has no effect with mpl backend. None will choose white or black based on the background color. initial_time : float | None The time to display on the plot initially. ``None`` to display the first time sample (default). time_unit : 's' | 'ms' Whether time is represented in seconds ("s", default) or milliseconds ("ms"). backend : 'auto' | 'pyvistaqt' | 'matplotlib' Which backend to use. If ``'auto'`` (default), tries to plot with pyvistaqt, but resorts to matplotlib if no 3d backend is available. .. versionadded:: 0.15.0 spacing : str Only affects the matplotlib backend. The spacing to use for the source space. Can be ``'ico#'`` for a recursively subdivided icosahedron, ``'oct#'`` for a recursively subdivided octahedron, or ``'all'`` for all points. In general, you can speed up the plotting by selecting a sparser source space. Defaults to 'oct6'. .. versionadded:: 0.15.0 title : str | None Title for the figure. If None, the subject name will be used. .. versionadded:: 0.17.0 %(show_traces)s %(src_volume_options)s %(view_layout)s %(add_data_kwargs)s %(brain_kwargs)s %(verbose)s Returns ------- figure : instance of mne.viz.Brain | matplotlib.figure.Figure An instance of :class:`mne.viz.Brain` or matplotlib figure. Notes ----- Flatmaps are available by default for ``fsaverage`` but not for other subjects reconstructed by FreeSurfer. We recommend using :func:`mne.compute_source_morph` to morph source estimates to ``fsaverage`` for flatmap plotting. If you want to construct your own flatmap for a given subject, these links might help: - https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch - https://openwetware.org/wiki/Beauchamp:FreeSurfer r)ruse_3d_backendr )_BaseSourceEstimate_check_stc_srcrLzsource estimateTrrVbackendrOr(rnotebookz0No 3D backend found. Resorting to matplotlib 3d.)rr.rr*rFrXrrsrrrrHrrSrr4rN) overlay_alpha brain_alpha vector_alphacortex foregroundr scale_factor show_tracesrvolume_options view_layoutadd_data_kwargs brain_kwargs)r6rrrrrr?r4r6rr@rModuleNotFoundErrorr8rr _plot_stc)%rLrr.rr*rFrXr4rrSrrrsrrrrrrrrHrrrrrrrrrr7rrrrZplot_mplrrNrNrRplot_source_estimatessv~      rc1s0ddlm}m}ddlm} |jdk}!t|dd}t|j|}|}"~|}#t |||||"}t d|d d d d gt d |dt || |j \}}$t |||$\}}|!r|jn|j}%t| |||%|! d}&t||||"}'t|&|&d}d|&dk}(|&d|(rdnd})|&d}~&|dkr"d d g}*n|g}*|dkr6|}|dkrDd}t|*dkrV|nd||*df}+||||+||| || |||d },|dk r|,|d|,d<||,d <tjdd|#f|,W5QRX~,|dkrtfdd|*D}-d|-|)d}|dkr d}|(rd nd}.||||$|||||| ||.|)d|)d|)d| ||dd!},|dk rf|,||*D]z}t|| rq|j|d krdnd}/t|/dkrqj|,}0|0j|d"tjddjf|0W5QRXqj|'r |,}0|0jd#d"jf|0~,|r$j||d$nS)%Nr)rget_brain_classr )_BaseVolSourceEstimater\Trrrcrerbothr)rr)r5r*r.rrr4)rrrz%s - %s) Z subject_idrrrrrrrrrrsrFrrecordcs4g|],}|jkrtj|jdddfqS)Nr)Zgeor]Zptpr\)rPrr]rNrRrSs z_plot_stc..g?ryr)r^r*rXrErFrrrrrr4rZfminZfmidZfmaxrrrr7)rr)rSr)r6rrrrZ _data_ndimr4r6r _check_viewsr@rIr8 _check_st_tvZ magnituderr9rr:r|rwarningscatch_warningsr]r7rr%rZadd_datarr)1rLrr.rr*rFrXrrsrrrrHrrSrr4rrrrrrrrrrrrrrrrrrrr8Zuser8volumer6r=Zhemisrrrrr%Z use_kwargsrNrrRrs          "          rcCs|td|dt|ttdfdt|tr8td|ddd|dkrDd }|dkrd|ob|dk obt|d k}|rt|sttd ||fS) NrS)TFrOrr)rOZseparateZvertexrwz when a stringrrOTrz1show_traces cannot be used when time_viewer=False)r@r?rRrrr|r)rrSr8rNrNrRr#s$   rcCsT|d||f|d||f|d||ffD]&\}}}|j|dd|j|ddq(dS)Nax_yax_xax_zz0.75r)rr)rQrrrmrarrNrNrR_glass_brain_crosshairs8s    rc CsFttj|j|}tt|tdt |j ddd}|S)Nrr\r) r'r]rraffinerr@rArr^r) cut_coordsimgijkrNrNrR_cut_coords_to_ijk@s.rcCs t|j|Sr)r'r)rrrNrNrR_ijk_to_cut_coordsFsrcCsPddl}ddlm}t|d|f|t|trLt|j|}|t |||}|S)Nr) SpatialImagez path-like) rZnibabel.spatialimagesrr?rrRr6rloadr)rTrLrrr-rrrNrNrR_load_subject_mriJs   rstat_mapT1.mgzc- sddlm}m}ddl ddlm}ddlm}tddsBt d dd l m }m }dd l m td d t||d  t|dt||r|jdddd |jdddd|j}}n(t|ddd}j|dd d|j}}~ttdd jddddt|||d}ttjjd j ddd d!j!}|j t"jddfksXt#~t$|d"d#fd$d%td&d'd(d) fd*d+fd,d-} fd.d/fd0d1t%dgfd2d3 } d4krHtj&|}t'||}t(|d5t)d6sBt|d7dd8t*+d9 , j-t.|d5 j d}n|dkrVd:}t/|||d;}| dkr|t0dd}nkr.t8d?| j f| d@9} t*+dA| 9f| }| dk rf|j7}nt6t3j5|} |}|j j ddkst#~ ~ ||}t:||}tj;|t>|jd|f~|?d\} \j@ggdCt"j4d=kr6dDnd}!j5|}"jAj4|"dE|!dFd}#t"j4d=krj@j4ddGgdHj@dIdJdKjB|#gd9gdLdM|jCj4|dNdO}$| D d4k}%tE||| j5|%}&tF|&dP|&dQktG|&}'tH|&\}~&tId|"IftJdG|"Jfg}(t|(tdGd=gdRtK|(d}(d})j5IdkrjLdSdTdUdVddW })tM|'}*|)r|*dgtMt|' 7}*tN|*}*j@|*dXj@|(dY~*s2dkOrt8dZ|P|}|tQtRdGd=d[dddVd=g}|S|}dG}+tdd\|+| |||d"d"d]  fd^d_},t|,|| |$ |'d` |, dad9|db| r|T| jUVdctW| | dd| jUVdetW| df| S)ha Plot Nutmeg style volumetric source estimates using nilearn. Parameters ---------- stc : VectorSourceEstimate The vector source estimate to plot. src : instance of SourceSpaces | instance of SourceMorph The source space. Can also be a SourceMorph to morph the STC to a new subject (see Examples). .. versionchanged:: 0.18 Support for :class:`~nibabel.spatialimages.SpatialImage`. %(subject_none)s If ``None``, ``stc.subject`` will be used. %(subjects_dir)s mode : str The plotting mode to use. Either 'stat_map' (default) or 'glass_brain'. For "glass_brain", activation absolute values are displayed after being transformed to a standard MNI brain. bg_img : instance of SpatialImage | str The background image used in the nilearn plotting function. Can also be a string to use the ``bg_img`` file in the subject's MRI directory (default is ``'T1.mgz'``). Not used in "glass brain" plotting. colorbar : bool, optional If True, display a colorbar on the right of the plots. %(colormap)s %(clim)s %(transparent)s show : bool Show figures if True. Defaults to True. initial_time : float | None The initial time to plot. Can be None (default) to use the time point with the maximal absolute value activation across all voxels or the ``initial_pos`` voxel (if ``initial_pos is None`` or not, respectively). .. versionadded:: 0.19 initial_pos : ndarray, shape (3,) | None The initial position to use (in m). Can be None (default) to use the voxel with the maximum absolute value activation across all time points or at ``initial_time`` (if ``initial_time is None`` or not, respectively). .. versionadded:: 0.19 %(verbose)s Returns ------- fig : instance of Figure The figure. Notes ----- Click on any of the anatomical slices to explore the time series. Clicking on any time point will bring up the corresponding anatomical map. The left and right arrow keys can be used to navigate in time. To move in time by larger steps, use shift+left and shift+right. In ``'glass_brain'`` mode, values are transformed to the standard MNI brain using the FreeSurfer Talairach transformation ``$SUBJECTS_DIR/$SUBJECT/mri/transforms/talairach.xfm``. .. versionadded:: 0.17 .. versionchanged:: 0.19 MRI volumes are automatically transformed to MNI space in ``'glass_brain'`` mode. Examples -------- Passing a :class:`mne.SourceMorph` as the ``src`` parameter can be useful for plotting in a different subject's space (here, a ``'sample'`` STC in ``'fsaverage'``'s space):: >>> morph = mne.compute_source_morph(src_sample, subject_to='fsaverage') # doctest: +SKIP >>> fig = stc_vol_sample.plot(morph) # doctest: +SKIP r)rrJNr )VolSourceEstimate) SourceMorphZnilearnz0.4z%This function requires nilearn >= 0.4) plot_stat_mapplot_glass_brain) index_imgrq)r glass_brainrLZnifti1F)mri_resolutionZ mri_spacezmorph.subject_torz or SourceMorph)rTr)rz src subjectZ mri_voxelrasz Image affine mmr")prefixrlevel)Z first_kindr\ForderT)Z allow_kdtreecsdt||}~tdt||tj\}}|d|d}}tdjd||f|S)z/Convert voxel coordinates to index in stc.data.z2 Affine remapped cut coords to [%d, %d, %d] idxrz. 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A "glass brain" is drawn and all dipoles defined in the source estimate are shown using arrows, depicting the direction and magnitude of the current moment at the dipole. Additionally, an overlay is plotted on top of the cortex with the magnitude of the current. Parameters ---------- stc : VectorSourceEstimate | MixedVectorSourceEstimate The vector source estimate to plot. %(subject_none)s If ``None``, ``stc.subject`` will be used. hemi : str, 'lh' | 'rh' | 'split' | 'both' The hemisphere to display. %(colormap)s This should be a sequential colormap. %(time_label)s smoothing_steps : int The amount of smoothing. %(transparent)s brain_alpha : float Alpha value to apply globally to the surface meshes. Defaults to 0.4. overlay_alpha : float Alpha value to apply globally to the overlay. Defaults to ``brain_alpha``. vector_alpha : float Alpha value to apply globally to the vector glyphs. Defaults to 1. scale_factor : float | None Scaling factor for the vector glyphs. By default, an attempt is made to automatically determine a sane value. time_viewer : bool | str Display time viewer GUI. Can be "auto", which is True for the PyVista backend and False otherwise. .. versionchanged:: 0.20 Added "auto" option and default. subjects_dir : str The path to the freesurfer subjects reconstructions. It corresponds to Freesurfer environment variable SUBJECTS_DIR. figure : instance of Figure3D | list | int | None If None, a new figure will be created. If multiple views or a split view is requested, this must be a list of the appropriate length. If int is provided it will be used to identify the PyVista figure by it's id or create a new figure with the given id. %(views)s colorbar : bool If True, display colorbar on scene. %(clim_onesided)s cortex : str or tuple Specifies how binarized curvature values are rendered. either the name of a preset Brain cortex colorscheme (one of 'classic', 'bone', 'low_contrast', or 'high_contrast'), or the name of a colormap, or a tuple with values (colormap, min, max, reverse) to fully specify the curvature colors. size : float or tuple of float The size of the window, in pixels. can be one number to specify a square window, or the (width, height) of a rectangular window. background : matplotlib color Color of the background of the display window. foreground : matplotlib color | None Color of the foreground of the display window. None will choose black or white based on the background color. initial_time : float | None The time to display on the plot initially. ``None`` to display the first time sample (default). time_unit : 's' | 'ms' Whether time is represented in seconds ("s", default) or milliseconds ("ms"). %(show_traces)s %(src_volume_options)s %(view_layout)s %(add_data_kwargs)s %(brain_kwargs)s %(verbose)s Returns ------- brain : mne.viz.Brain A instance of :class:`mne.viz.Brain`. Notes ----- .. versionadded:: 0.15 If the current magnitude overlay is not desired, set ``overlay_alpha=0`` and ``smoothing_steps=1``. r )_BaseVectorSourceEstimaterLzvector source estimater`)rr.rr*rFrXrrsrrrrHrrSrr4rrrrrrrrrrrrr)rrr?r)rLrrr*rFrXr4rrrrrSrrrsrrrrrrrrHrrrrrrr7rrNrNrRplot_vector_source_estimates sNh r rzrrrsffffff?r$r$conerrrc0 sddlm}ddlm}ddddd d d d d dddddddgddgt| ttfrhtfdd| Dsptdt|ts|g}| dk rt| ts| g} dkrt t fddt t |D|dd|dd}t j|f}|dd}|dd}t j||f}| r4|dd}|dd}n|dd}|dd}t j|jd|f}|d 9}fd!d|D}t t |}||d"| d#}|jf|dddf|dddf|ddd$f|||d%d%|d& ||| }||d'}t td(t || dk rPfd)dt t t | jDt|D]^\} fd*dt|D}!t |!dk}"| dkrt}#n | |!d||!dk}#|"r| dn| d}$|"r|dn|d}%t|%t jttfrt |t |%kr|%| }%|\}&}'}(|\})}*}+|j|&|'|(|)|*|+t|#|$|%d+ |!D]b},||,}-|-k}.t |.dkszt |,}/|j!d,||,j"d-||,j#|.|#||/d.qRqX|j$d/d0d1|j%d2d0d1| dk r|&| t'||(|)S)3a2Plot source estimates obtained with sparse solver. Active dipoles are represented in a "Glass" brain. If the same source is active in multiple source estimates it is displayed with a sphere otherwise with a cone in 3D. Parameters ---------- src : dict The source space. stcs : instance of SourceEstimate or list of instances of SourceEstimate The source estimates. colors : list List of colors. linewidth : int Line width in 2D plot. fontsize : int Font size. bgcolor : tuple of length 3 Background color in 3D. opacity : float in [0, 1] Opacity of brain mesh. brain_color : tuple of length 3 Brain color. show : bool Show figures if True. high_resolution : bool If True, plot on the original (non-downsampled) cortical mesh. fig_name : str PyVista figure name. fig_number : int Matplotlib figure number. labels : ndarray or list of ndarray Labels to show sources in clusters. Sources with the same label and the waveforms within each cluster are presented in the same color. labels should be a list of ndarrays when stcs is a list ie. one label for each stc. modes : list Should be a list, with each entry being ``'cone'`` or ``'sphere'`` to specify how the dipoles should be shown. The pivot for the glyphs in ``'cone'`` mode is always the tail whereas the pivot in ``'sphere'`` mode is the center. scale_factors : list List of floating point scale factors for the markers. %(verbose)s **kwargs : kwargs Keyword arguments to pass to renderer.mesh. Returns ------- surface : instance of Figure3D The 3D figure containing the triangular mesh surface. rNrr)solidr()dashedr))dottedr*)dashdotr+)zloosely dotted)r)rrx)r*r)rr)zdensely dottedr,)zloosely dashed)r)rqrx)r))r)rqrq)zdensely dashed)r)rqr)zloosely dashdotted)r)r\rxrrx)Z dashdotted)r)r\rqrrq)zdensely dashdotted)r)r\rrr)Z dashdotdotted)r)r\rqrrqrrq)zloosely dashdotdotted)r)r\rxrrxrrx)zdensely dashdotdotted)r)r\rrrrrr&rc3s|]}|kVqdSrrN)rPrq) known_modesrNrRrp sz/plot_sparse_source_estimates..z6mode must be a list containing only "cone" or "sphere"csg|]}tdqS)rnextrPrj) linestylesrNrRrS sz0plot_sparse_source_estimates..rr#rrucs(g|] }tj|jjd|jfqS)r)r]r_Z lh_vertnorZ rh_vertno)rPrL) lh_pointsrNrRrS sr)rrr-r T) rrrmrrr,r|Zshadingr&oz"Total number of active sources: %dcsg|] }tqSrNr.r0)rJrNrRrS scsg|]\}}|kr|qSrNrN)rPrnrt)rrNrRrS s) rrrmrrrrrqrreA)c linewidth linestylez Time (ms)r!)fontsizezSource amplitude (nAm))*rrr6rrrrrfrrDrrr|r]r3rrrrrMrZclfZ add_subplotr5rrrr/rrrAsumrrr8r set_xlabel set_ylabelrfrErrD)0rZstcsrJr8r:rr,Z brain_colorrZhigh_resolutionZfig_nameZ fig_numberrmodesZ scale_factorsr7rrrZ rh_pointsrhZ lh_normalsZ rh_normalsr&Z use_lh_facesZ use_rh_facesZ use_facesZvertnosZunique_vertnosr$rrrindZ is_commonr7rqrrrrmnxnyZnzrnrtrr9rN)rJr-r4r1rrRplot_sparse_source_estimates s>                   $  rB orthoviewrTgofrWrfr_)highlight_colorrr head_sourcerrr7c  Cst|tdt|tdtd|d|dkr8t|dd}t|||||| | | ||d }t|}|dkr~t|f||| d |}nH|d krt|f||| d |}n&|d kst|t |||| || |d }|S)ugPlot dipole locations. If mode is set to 'arrow' or 'sphere', only the location of the first time point of each dipole is shown else use the show_all parameter. Parameters ---------- dipoles : list of instances of Dipole | Dipole The dipoles to plot. trans : dict | None The mri to head trans. Can be None with mode set to '3d'. subject : str | None The FreeSurfer subject name (will be used to set the FreeSurfer environment variable ``SUBJECT``). Can be ``None`` with mode set to ``'3d'``. %(subjects_dir)s mode : str Can be: ``'arrow'`` or ``'sphere'`` Plot in 3D mode using PyVista with the given glyph type. ``'orthoview'`` Plot in matplotlib ``Axes3D`` using matplotlib with MRI slices shown on the sides of a cube, with the dipole(s) shown as arrows extending outward from a dot (i.e., the arrows pivot on the tail). ``'outlines'`` Plot in matplotlib ``Axes`` using a quiver of arrows for the dipoles in three axes (axial, coronal, and sagittal views), with the arrow pivoting in the middle of the arrow. .. versionchanged:: 1.1 Added support for ``'outlines'``. coord_frame : str Coordinate frame to use: 'head' or 'mri'. Can also be 'mri_rotated' when mode equals ``'outlines'``. Defaults to 'mri'. .. versionadded:: 0.14.0 .. versionchanged:: 1.1 Added support for ``'mri_rotated'``. idx : int | 'gof' | 'amplitude' Index of the initially plotted dipole. Can also be 'gof' to plot the dipole with highest goodness of fit value or 'amplitude' to plot the dipole with the highest amplitude. The dipoles can also be browsed through using up/down arrow keys or mouse scroll. Defaults to 'gof'. Only used if mode equals 'orthoview'. .. versionadded:: 0.14.0 show_all : bool Whether to always plot all the dipoles. If ``True`` (default), the active dipole is plotted as a red dot and its location determines the shown MRI slices. The non-active dipoles are plotted as small blue dots. If ``False``, only the active dipole is plotted. Only used if ``mode='orthoview'``. .. versionadded:: 0.14.0 ax : instance of matplotlib Axes3D | list of matplotlib Axes | None Axes to plot into. If None (default), axes will be created. If mode equals ``'orthoview'``, must be a single ``Axes3D``. If mode equals ``'outlines'``, must be a list of three ``Axes``. .. versionadded:: 0.14.0 block : bool Whether to halt program execution until the figure is closed. Defaults to False. Only used if mode equals 'orthoview'. .. versionadded:: 0.14.0 show : bool Show figure if True. Defaults to True. Only used if mode equals 'orthoview'. scale : float The scale (size in meters) of the dipoles if ``mode`` is not ``'orthoview'``. The default is 0.03 when mode is ``'outlines'`` and 0.005 otherwise. color : tuple The color of the dipoles. The default (None) will use ``'y'`` if mode is ``'orthoview'`` and ``show_all`` is True, else 'r'. Can also be a list of colors to use when mode is ``'outlines'``. .. versionchanged:: 0.19.0 Color is now passed in orthoview mode. highlight_color : color The highlight color. Only used in orthoview mode with ``show_all=True``. .. versionadded:: 0.19.0 fig : instance of Figure3D | None 3D figure in which to plot the alignment. If ``None``, creates a new 600x600 pixel figure with black background. Only used when mode is ``'arrow'`` or ``'sphere'``. .. versionadded:: 0.19.0 title : str | None The title of the figure if ``mode='orthoview'`` (ignored for all other modes). If ``None``, dipole number and its properties (amplitude, orientation etc.) will be shown. Defaults to ``None``. .. versionadded:: 0.21.0 %(head_source)s Only used when mode equals ``'outlines'``. .. versionadded:: 1.1 surf : str | None Brain surface to show outlines for, can be ``'white'``, ``'pial'``, or ``None``. Only used when mode is ``'outlines'``. .. versionadded:: 1.1 width : float | None Width of the matplotlib quiver arrow, see :meth:`matplotlib:matplotlib.axes.Axes.quiver`. If None (default), when mode is ``'outlines'`` 0.015 will be used, and when mode is ``'orthoview'`` the matplotlib default is used. %(verbose)s Returns ------- fig : instance of Figure3D or matplotlib.figure.Figure The PyVista figure or matplotlib Figure. Notes ----- .. versionadded:: 0.9.0 rqrM)rCoutlinesrr)rCrGTrU) rvrrrMrblockrrrrrC)rshow_allrErG)rFrr)rr)rvrMrrrrq) r?rRr@r4rr_plot_dipole_mri_orthoviewr rr )ZdipolesrvrrrqrMrrIrrHrrrrErrrFrrr7rrNrNrRplot_dipole_locations< sd    rKc Cs2ddlm}ddlm}ddlm}|dkr4tdt||rb|}t dd | D\}}n|t||rd d |d D}d d |d D}nLt|t rt d d| Dstdt dd | D\}}ntd||dd} t|}| j||d} |dkr| d| } | d| j| fS)aTake a snapshot of a PyVista Scene and project channels onto 2d coords. Note that this will take the raw values for 3d coordinates of each channel, without applying any transforms. If brain images are flipped up/dn upon using `~matplotlib.pyplot.imshow`, check your matplotlib backend as this behavior changes. Parameters ---------- fig : instance of Figure3D The figure on which you've plotted electrodes using :func:`mne.viz.plot_alignment`. montage : instance of DigMontage or Info | dict The digital montage for the electrodes plotted in the scene. If :class:`~mne.Info`, channel positions will be pulled from the ``loc`` field of ``chs``. dict should have ch:xyz mappings. hide_sensors : bool Whether to remove the spheres in the scene before taking a snapshot. The sensors will always be shown in the final figure. If you want an image of just the brain, use :class:`mne.viz.Brain` instead. Returns ------- xy : array, shape (n_channels, 2) The 2d location of each channel on the image of the current scene view. im : array, shape (m, n, 3) The screenshot of the current scene view. r ) DigMontage)InforrNzThe figure must have a scenecSsg|]\}}||fqSrNrNrPichZixyzrNrNrRrS sz*snapshot_brain_montage..cSsg|]}|dddqS)rNr\rNrPrOrNrNrRrS srcSsg|] }|dqS)rrNrPrNrNrRrS scss|]}t|dkVqdS)r\Nr{rrNrNrRrp sz)snapshot_brain_montage..z(All electrode positions must be length 3cSsg|]\}}||fqSrNrNrNrNrNrRrS sz>montage must be an instance of `DigMontage`, `Info`, or `dict`T)r)rr F)rrLrrMr6rrrZ _get_ch_posrrrrfr3rr]ZvstackprojectvisibleZ screenshotZxy) rZmontageZ hide_sensorsrLrMrrr rr$ZprojZimrNrNrRsnapshot_brain_montage s0           rSrtcCsxddlm}ddlm}ts&tdtd|ddg|dkrLt|j }n(|d krhtt |j }n t |d d }t |||||\}}}}t|}|d }|dkr|jd tddd\}}nt||dddd|}tjt| ||t| ||dd\}}|||||||||||| | | | d}tf||jdddtt|d}|jd||jd|t| |d|S)z)Plot dipoles on top of MRI slices in 3-D.rNrzThis function requires nibabel.rMrtrTrD amplituderz%an int or one of ["gof", "amplitude"]r rrrrrrzwhen mode is "orthoview"rZij)Zindexing)rrrdipolevoxgridxgridyr rMrIrrrErrritrqrxZ scroll_eventry)rH)rrrrr9rr@r]rrDr9rTr>_get_dipole_locr|rrr? get_figureZmeshgridr _plot_dipolerr_dipole_changedrNrrE)rUrvrrrMrrIrrHrrrErrrrrVr rrdimsddrrWrXrQZ callback_funcrNrNrRrJ sb         rJrir\)r;r;r;cCsJddl}ddlm}td|ddgt|dd}t||dd }||}t|d d \} } } } } t |ddd d } | d dddfd9<~|j d} |j }t j| d jtjj}|dkrt| | ddd }n"t| | } t| |j dd}| d }t t ||| d }||t|fdd}tt jt| }t|}||| |fS)z*Get the dipole locations and orientations.rN)resample_from_torMrtrTTrrr)r)rrtorvr\rwrrFrr)rZnibabel.processingr_r@r4rr=rrr*rrr r]rZsolver RAS_AFFINEr)r'r> RAS_SHAPErr)rUrvrrrMrr_Zt1_fnamet1Z vox_ras_trjZ mri_ras_trrr ZupsampZ dest_ras_trrVZt1_datarNrNrRrYP sF     rYc# Csddlm}t||t\}}}||}|dd|f}|dddd|f}||}| dkrp| rldnd} tt| dd} tt| ddd} | rtj| tj t |dd }| ||<td t |}d ||<t t |}n | }d }|}t |}| }|j ||df||d f||d fd ||dt|||df|}t|||d f|}t|||d f|}|j|t||d ft |||d fd d| d|jt||dft ||||d fd d| d|jt||dft |t||d ft ||d d| dtd| dd}|dk r0||d<|j||df||d f||d f|d|d |d f|tt |dt |dg}|j| | |d|j||||ddddd|j||||ddddd|j||||dddddtt||t|gd} tdD]"}!|ddg| |!|!|!dgf<q|j| jddi||d kr\d!nd"}"| dkrd#|d t |j|j||j||j|d$|"fd%t||} || |d|d|d| dS)&z Plot dipoles.rNrrWTr'rE)r-rr~rqrrr )ZxsZyszsrr facecolorr)rdrr9r2r)rrrrgrrargrayr)r$Zzdirrrrrmr\rrnrtZHeadZMRIz2Dipole #%s / %s @ %.3fs, GOF: %.1f%%, %.1fnAm %s: r6z(%0.1f, %0.1f, %0.1f) mm)!rrr]r@rArr^rArrr|rrrrrrrrZcontourfrrrr8rDrTrrZZsuptitler<r=Z set_zlabelrg)#rrrVrrUrWrXr rMrIrrrErrrZxidxZyidxZzidxZxsliceZysliceZzslicerJrrRr$rZxxyyzzZq_kwargsr]rrZcoord_frame_namerNrNrRr[ s    (( 6        r[cCs|jdk rH|jdkr&|dd7<qt|jdkrB|dd8<qtdSn,|jdkrd|dd7<n|dd8<ttd|dt|djd|d<|dtf|dS) z'Handle dipole plotter scroll/key event.NuprrZdownrrUr)rurRrrr|rrcr[)rPrQrNrNrRr\ s    & r\rrcCsddlm}ddlm}t|||} t| } t| \}} ~ || d| dd} |||| | ||d} | jj|d| j d| j d d d |d krd ndfD]}|j | dq| S)a'Plot a colorbar that corresponds to a brain activation map. Parameters ---------- ax : instance of Axes The Axes to plot into. %(clim)s %(colormap)s %(transparent)s orientation : str Orientation of the colorbar, can be "vertical" or "horizontal". label : str The colorbar label. bgcolor : color The color behind the colorbar (for alpha blending). Returns ------- cbar : instance of ColorbarBase The colorbar. Notes ----- .. versionadded:: 0.19 r) ColorbarBaserr )r/r)rrrArwr)reFTrr|rr{rK) Zmatplotlib.colorbarrkrrr9rCr@rrrrZ set_frame_onZspines)rrr*r4rrwrrkrr8rArrZcbarrurNrNrRplot_brain_colorbar s&       rlc@s>eZdZUeeed<eeed<eeed<eeed<dS) _3d_Options antialias depth_peelingsmooth_shading multi_samplesN)__name__ __module__ __qualname__rr__annotations__rrNrNrNrRrm s    rmrnrorprqtrue4)rqcCsL|dk rt|t_|dk r$t|t_|dk r6t|t_|dk rHt|t_dS)aeSet 3D rendering options. Parameters ---------- antialias : bool | None If bool, whether to enable or disable full-screen anti-aliasing. False is useful when renderers have problems (such as software MESA renderers). If None, use the default setting. This option can also be controlled using an environment variable, e.g., ``MNE_3D_OPTION_ANTIALIAS=false``. depth_peeling : bool | None If bool, whether to enable or disable accurate transparency. False is useful when renderers have problems (for instance while X forwarding on remote servers). If None, use the default setting. This option can also be controlled using an environment variable, e.g., ``MNE_3D_OPTION_DEPTH_PEELING=false``. smooth_shading : bool | None If bool, whether to enable or disable smooth color transitions between polygons. False is useful on certain configurations where this type of shading is not supported or for performance reasons. This option can also be controlled using an environment variable, e.g., ``MNE_3D_OPTION_SMOOTH_SHADING=false``. multi_samples : int Number of multi-samples. Should be 1 for MESA for volumetric rendering to work properly. .. versionadded:: 1.1 Notes ----- .. versionadded:: 0.21.0 N)r _3d_optionsrnrorprrqrvrNrNrRset_3d_options+ s"   rzcCs^t|ddtt|}|dkrZtt|}td||}|dkrNt|}n |dk}|S)NrRruZMNE_3D_OPTION_rqrw)r?getattrry _3d_defaultr=upperrlower)ruopt default_valuerNrNrR_get_3d_optionW s     r)N)rkrlrmTNNrnN)NrNNNr)NNNNrOrONrPNFTNFNTTFTNrN)TN)N)rN)rNFFNNN)FFNN) rrFFFFNFNN) rFFFNNNNF)rrr)rFFFNNN)rT)NrarcrOrOrxNrirONNrrjrkFTT)TFTF)NrarcrOrOrxTrrONNrOTrOrrwrjNNrrOrkNrONrrNNN) NNrrTrOrONTNNN)NN)Nrcr,rOrxNrNrNrONNrTrOrrwrjNNrrONrrNNN)Nr r!r"rsr#TFNNNr%r'N) NNNrCrTrDTNFTNN)T) NrtrDTNFTNrWNN)rOTrrr)NNN)__doc__ itertoolsros.pathpathrrcollections.abcr functoolsr dataclassesrtypingrnumpyr]Z_dipolerr r rvr fixesr rZ _freesurferrrrriorZio.pickrrrrrZ io.constantsrZ io.meas_inforrZ source_spacerrrrr r.r!r"r#r$r%r&Z transformsr'r(r)r*r+r,r-r.r/r0r1r2r3utilsr4r5r6r7r8r9r:r;r<r=r>r?r@rAZ _3d_overlayrBrCrDrErFrGrHrlrIrJrKrZFIFFV_POINT_LPAZFIFFV_POINT_NASIONZFIFFV_POINT_RPAr_rjrrrNrrrrrrrrrrrrrrrrrr*r9r:r@rCrIrUrhrrrrrrrrrrrrr rBrKrSrJrrarbrYr[r\rlrmryr|rzrrNrNrNrRs~          <@    T  {* =  '    $   ^d C0 ~ . #z    w ; ? 2 2P 0 ,