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We suggest using :meth:`mne.viz.plot_source_estimates` with the PyVista backend enabled to obtain a ``Brain`` instance. Parameters ---------- subject_id : str Subject name in Freesurfer subjects dir. 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. surf : str FreeSurfer surface mesh name (ie 'white', 'inflated', etc.). title : str Title for the window. cortex : str, list, dict Specifies how the cortical surface is rendered. Options: 1. The name of one of the preset cortex styles: ``'classic'`` (default), ``'high_contrast'``, ``'low_contrast'``, or ``'bone'``. 2. A single color-like argument to render the cortex as a single color, e.g. ``'red'`` or ``(0.1, 0.4, 1.)``. 3. A list of two color-like used to render binarized curvature values for gyral (first) and sulcal (second). regions, e.g., ``['red', 'blue']`` or ``[(1, 0, 0), (0, 0, 1)]``. 4. A dict containing keys ``'vmin', 'vmax', 'colormap'`` with values used to render the binarized curvature (where 0 is gyral, 1 is sulcal). .. versionchanged:: 0.24 Add support for non-string arguments. alpha : float in [0, 1] Alpha level to control opacity of the cortical surface. size : int | array-like, shape (2,) The size of the window, in pixels. can be one number to specify a square window, or a length-2 sequence to specify (width, height). background : tuple(int, int, int) The color definition of the background: (red, green, blue). foreground : matplotlib color Color of the foreground (will be used for colorbars and text). None (default) will use black or white depending on the value of ``background``. figure : list of Figure | None If None (default), a new window will be created with the appropriate views. subjects_dir : str | None If not None, this directory will be used as the subjects directory instead of the value set using the SUBJECTS_DIR environment variable. %(views)s offset : bool | str If True, shifts the right- or left-most x coordinate of the left and right surfaces, respectively, to be at zero. This is useful for viewing inflated surface where hemispheres typically overlap. Can be "auto" (default) use True with inflated surfaces and False otherwise (Default: 'auto'). Only used when ``hemi='both'``. .. versionchanged:: 0.23 Default changed to "auto". show_toolbar : bool If True, toolbars will be shown for each view. offscreen : bool If True, rendering will be done offscreen (not shown). Useful mostly for generating images or screenshots, but can be buggy. Use at your own risk. interaction : str Can be "trackball" (default) or "terrain", i.e. a turntable-style camera. units : str Can be 'm' or 'mm' (default). %(view_layout)s silhouette : dict | bool As a dict, it contains the ``color``, ``linewidth``, ``alpha`` opacity and ``decimate`` (level of decimation between 0 and 1 or None) of the brain's silhouette to display. If True, the default values are used and if False, no silhouette will be displayed. Defaults to False. %(theme_3d)s show : bool Display the window as soon as it is ready. Defaults to True. block : bool If True, start the Qt application event loop. Default to False. Attributes ---------- geo : dict A dictionary of PyVista surface objects for each hemisphere. overlays : dict The overlays. Notes ----- This table shows the capabilities of each Brain backend ("✓" for full support, and "-" for partial support): .. table:: :widths: auto +-------------------------------------+--------------+---------------+ | 3D function: | surfer.Brain | mne.viz.Brain | +=====================================+==============+===============+ | :meth:`add_annotation` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_data` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_dipole` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_foci` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_forward` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_head` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_label` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_sensors` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_skull` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_text` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_volume_labels` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`close` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | data | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | foci | ✓ | | +-------------------------------------+--------------+---------------+ | labels | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_data` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_dipole` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_forward` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_head` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_labels` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_annotations` | - | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_sensors` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_skull` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_text` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`remove_volume_labels` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`save_image` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`save_movie` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`screenshot` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`show_view` | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | TimeViewer | ✓ | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`get_picked_points` | | ✓ | +-------------------------------------+--------------+---------------+ | :meth:`add_data(volume) ` | | ✓ | +-------------------------------------+--------------+---------------+ | view_layout | | ✓ | +-------------------------------------+--------------+---------------+ | flatmaps | | ✓ | +-------------------------------------+--------------+---------------+ | vertex picking | | ✓ | +-------------------------------------+--------------+---------------+ | label picking | | ✓ | +-------------------------------------+--------------+---------------+ ÚbothÚpialNÚclassicçð?é ÚblackÚautoFÚ trackballÚmmÚverticalTc% CsLddlm}m}|dkrd}|j|dd}|dkr:d|_n|dksFt‚|f|_td |d ƒ|_| dk rxt| t ƒsx|  | ¡|dkrˆ||_ n||_ d |_ t |d d |_| dkrÀt|jƒdkr¼dnd} t | dd |_~~ t|| |ƒ} tdddddd}t| ƒ||f}|jdkr|ddd…}||_tt |¡ d¡ t ¡jƒ}t|ƒdkrRtdƒ‚t|ƒdkrd|n|d}t| ƒ} d|_t ¡|_ ||_!||_"||_#t$|ƒ|_%||_&| |_'| |_(d|_)tƒ|_*tƒ|_+t,ƒt,ƒdœ|_-d|_.t,ƒt,ƒdœ|_/tƒ|_0tƒ|_1ddg|_2d|_3d|_4|jd|ddœ|_5t6|tt7fdƒt|tƒrV|j5 8|¡d|_9n||_9d|_:d|_;i|_d¡| ?|¡}|d  |d!|d }|d"|ƒ|_@t6| tAt7fd#ƒt| tAƒrätd#| d$d%d&|d'k} | rô|d(krødnd)} tB Cd*| ›¡t6|tAdfd+ƒ||j ||j|| d,|_D|jD E|jF¡|jD G|¡|jDjH|_H| I¡dD]x}||jkrzqdtJ|j&|||j'| |j#|jKddd-…fd.}| L¡| M¡||j=|<| N|¡D]\}}} |j0 O|¡dkrXtP|jD|j=|jQ|j=|jR|j=|jSd/}!|! T¡|!jU|j=|jV|d"|d |d!g|d0d1|!|j0|<||!jW_"n|j0|jX}"|jDjHjY|"dd2|j9r¸|j0|}!|jDj5|!jW|j5d3|j5d4|j5d5|j5d6d7|jDjZfddd8œt[|| —ŽqÈqd||_\d|_]|rú| ^¡|jD]0}| N|¡D]\}#}$} |j_| |#|$|d9qq|d:krH|jD `d;¡dS)Ú _bg_colorÚsumÚ _fg_colorrÚdictÚlenÚ_subplot_shapeÚtupleÚnpZ atleast_1dÚroundÚastypernÚ ValueErrorr<Ú time_viewerÚtimeÚtime_nsÚ_hashÚ_blockÚ_hemiÚ_unitsÚfloatZ_alphaÚ _subject_idÚ _subjects_dirÚ_viewsÚ_timesÚ_vertex_to_label_idÚ_annotation_labelsÚlistÚ_labelsÚ_unnamed_label_idÚ_annotsÚ_layered_meshesÚ_actorsÚ_elevation_rngÚ _lut_lockedÚ_cleanedÚ _silhouetter7Úboolr‚rfÚ _scalar_barÚ_time_label_addedÚ_dataÚgeoÚset_time_interpolationÚ_cortex_colormapÚ _brain_colorÚstrr4ÚdebugÚ _rendererZ_window_close_connectÚ_cleanZ_window_set_themeÚplotterÚ_setup_canonical_rotationrÚ_rigidÚ load_geometryZload_curvatureÚ _iter_viewsÚgetrÚcoordsÚfacesÚnnÚmapÚ add_overlayZbin_curvÚ _polydataÚ_actorÚ add_actorÚ set_camerarÚ interactionÚ_closedÚshowÚ show_viewÚset_interaction)%ÚselfZ subject_idr†ÚsurfÚtitleÚcortexrdrqrXr]ÚfigureÚ subjects_dirÚviewsrkZ show_toolbarZ offscreenrÍrurVrfrprÏÚblockrLrMZcol_dictrsZ geo_kwargsÚvalÚhr¶Ú_Úvr€ÚactorÚriÚci©ráúT/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/viz/_brain/_brain.pyÚ__init__ìs ÿ      ü     ý    ÿ    ü û    û ÿ  zBrain.__init__cCsPt d¡|_zt|j|jƒ}Wntk r<t d¡YnX||jdd…<dS)NézCCould not estimate rigid Talairach alignment, using identity matrix) r–ÚeyerÀr&r¢r£Ú Exceptionr4Úinfo)rÒÚxfmrárárâr¿•s  zBrain._setup_canonical_rotationc Csæddlm}|jrdS|js$tdƒ‚||_tt ¡ƒ|_ddg|_ d|_ d|_ t t tdƒƒd ƒ|_d d g|_d d g|_d |_d |_ddgdddgdœ|_d|_d|_d|_d}dd„|Dƒ|_tƒ|_|j d¡t|jƒ|_d|_d|_d|_ dd„|Dƒ|_!dd„|Dƒ|_"t#ƒ|_$tƒ|_%d|_&t#ƒ|_'t#ƒ|_(d|_|j|_)t*|t+t,dfdƒd|_-t.|t,ƒr®d|_/d|_0d |_1|d!krŒd|_0n |d"kržd"|_1n|d ks t2‚n\t.|t+ƒrÂ||_/n¡|j? @¡d%D].}| A|¡D]\}}}|jB|||d&q€qr|j? C¡|j? D¡|j/rÈ|j @¡|jErâ||j?jFjGd'ƒdS)(aaConfigure the time viewer parameters. Parameters ---------- time_viewer : bool If True, enable widgets interaction. Defaults to True. show_traces : bool If True, enable visualization of time traces. Defaults to True. Notes ----- The keyboard shortcuts are the following: '?': Display help window 'i': Toggle interface 's': Apply auto-scaling 'r': Restore original clim 'c': Clear all traces 'n': Shift the time forward by the playback speed 'b': Shift the time backward by the playback speed 'Space': Start/Pause playback 'Up': Decrease camera elevation angle 'Down': Increase camera elevation angle 'Left': Decrease camera azimuth angle 'Right': Increase camera azimuth angle r©Ú _qt_app_execNz'No data to visualize. 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NÚ time_liner›r)rgròrbrÌr‚) rr‹rýr²rIrrzr‘rTZ set_xdatar¤)rÒr‚rhrárárârzs  û zBrain.plot_time_linec Csnddddddddd d d d g }t|Ž\}}d  |¡}d  |¡}|jjdddd|_t|||jj|jjdddS)N)rôzDisplay help window)rzToggle interface)rûzApply auto-scaling)rüzRestore original clim)rýzClear all traces)rþz,Shift the time forward by the playback speed)rz-Shift the time backward by the playback speed)ZSpacezStart/Pause playback)rzDecrease camera elevation angle)rzIncrease camera elevation angle)rzDecrease camera azimuth angle)rzIncrease camera azimuth angleÚ éréP)ÚwidthÚheightÚdpiF)Zcol1Zcol2Zfig_helpZaxrÏ)Úzipr³r¼Z_window_get_simple_canvasrrrtr£)rÒÚpairsZtext1Ztext2rárárâr(s8ô   ÿûzBrain._configure_helpcCs|j ¡dS)zDisplay the help window.N)rrÏrCrárárârò9sz Brain.helpcCsft|dƒsdS|j ¡D]"}|dk rdD]}t||dƒq(q|j ¡t|ddƒdk rb|jj ¡dS)Nr)r¾rqrrr|rr) rrrÒr:r8r7r¾rZclear_key_event_callbacks)rÒrrrõrárárâr5=s  zBrain._clear_callbackscCsJt|dƒsdS|j ¡D]"}|dk rdD]}t||dƒq(q|j ¡dS)Nr)Z triggeredZfloatValueChanged)rrrÒr:r8)rÒr|rõrárárâr6Js zBrain._clear_widgetscCs|jS)zThe interaction style.)rŽrCrárárârÍSszBrain.interactioncCs8t|tdƒtd|dƒ| d¡D]}|j |¡q"dS)zSet the interaction style.rÍ)rIZterrainrNN)r7rºr3rÂr¼rÑ)rÒrÍrÜrárárârÍXs  c Cs.ddlm}ddlm}ttddddtddd dtdd d dtd d ddd}t|ttttfdƒt |tƒrŠ||kr€||}n |gd}t |ttfƒrt dt |ƒdddt |ƒdkrÄ|gd}t|ƒ}t |ƒD]\}}t |dd||<qÔt||ddddd}tt|dƒt|dƒ||dƒd}|S)z0Return the colormap corresponding to the cortex.r)Ú _get_cmapr)ÚListedColormapZGreysr^)rjrhrigš™™™™™¹¿gÍÌÌÌÌÌô?éûÿÿÿrVZbone_rgš™™™™™É¿)rDZ high_contrastZ low_contrastÚbonerÕz len(cortex))rrzwhen cortex is a list or tuplerlrrYz custom binaryrrhrirj)rhrirj)Ú_3dr]Zmatplotlib.colorsr^r’r7rºr¨r•r‹r3r“r×r>r¡)rÒrÕr]r^Z colormap_mapràrýrárárâr¸`sX  ÿÿÿÿú     ÿ   þ   ýzBrain._cortex_colormapcCsl||jkrht dt|j|ƒ›d|›d¡|j|D]}|jjj|ddq6|j |¡|rh|j ¡dS)z&Remove actors from the rendered scene.z Removing rïz actor(s)Fr~N) r­r4r»r“r¼r¾r@rAr*)rÒÚitemrrÞrárárâÚ_remove…s ÿ z Brain._removecCs,||jkr|j| |¡n |g|j|<dS)z&Add an actor to the internal register.N)r­r))rÒrbrÞrárárâÚ _add_actors zBrain._add_actorrçš™™™™™Ù?c& Cst|tdƒt|ddƒt|ddƒtd|dgƒtd|dgƒt|dd ƒ|dk rrt|ƒ}|d krrtd |›ƒ‚|j|d gd }| ||| ¡\}}} t |¡}|dkr¬| n|}||j d<||j d<|j dkrÔd }n¼| dkrît  |j d¡} n8t | ¡} | j |j dfkr&td| j |j dffƒ‚| |j d<|j dkrD| |_n2t| ƒ|j kr^tdƒ‚nt | |j¡svtdƒ‚|dkr†d }n | |¡}t| d| ƒ\} }ddt|ƒ}|j dkrà|j ddkràtd|j dfƒ‚t|||||ƒ\}}}|dkr|dk rdnd}| dkr"d} nH| dkr2d} n8t| tƒrX| d krjtd | ¡ƒ‚ntd t| ƒ¡ƒ‚||j d <||j d!<| |j d"<||j d#<| |j d<||j d$<| |j d%<||j d&<||j d'<||j d<tƒ|j |<d|j |d(<d|j |d)<d|j |d*<||j |d+<| |j |d,<| |j d-<||j d.<||j d/<||j d0<||j d1<||j d2<| ¡d}| |¡D]L}|d3krŽ|j|j}n.|jd4kr¦|d5d…n|}| |||¡\}}qr|dk sÎt ‚| !d6|¡| "|j#¡| $|j d"¡|d7kr|j%d dd f}| |¡D]Ô\} }!}"| |!f|k}#|j&sz| dk rz|#rz|j'j(d8||j)|| |j*ƒd9d:}$|$|j d;<d7|_&|rÎ|j+dkrÎ|#rÎt|d<|j)|j,dd…d=}%|% -|pºi¡|j'j.f|%Ž|_+|j'j/fd>d>d?œt0||"—Žq|j| d@dS)Aa5Display data from a numpy array on the surface or volume. This provides a similar interface to :meth:`surfer.Brain.add_overlay`, but it displays it with a single colormap. It offers more flexibility over the colormap, and provides a way to display four-dimensional data (i.e., a timecourse) or five-dimensional data (i.e., a vector-valued timecourse). .. note:: ``fmin`` sets the low end of the colormap, and is separate from thresh (this is a different convention from :meth:`surfer.Brain.add_overlay`). Parameters ---------- array : numpy array, shape (n_vertices[, 3][, n_times]) Data array. For the data to be understood as vector-valued (3 values per vertex corresponding to X/Y/Z surface RAS), then ``array`` must be have all 3 dimensions. If vectors with no time dimension are desired, consider using a singleton (e.g., ``np.newaxis``) to create a "time" dimension and pass ``time_label=None`` (vector values are not supported). %(fmin_fmid_fmax)s %(thresh)s %(center)s %(transparent)s colormap : str, list of color, or array Name of matplotlib colormap to use, a list of matplotlib colors, or a custom look up table (an n x 4 array coded with RBGA values between 0 and 255), the default "auto" chooses a default divergent colormap, if "center" is given (currently "icefire"), otherwise a default sequential colormap (currently "rocket"). alpha : float in [0, 1] Alpha level to control opacity of the overlay. vertices : numpy array Vertices for which the data is defined (needed if ``len(data) < nvtx``). smoothing_steps : int or None Number of smoothing steps (smoothing is used if len(data) < nvtx) The value 'nearest' can be used too. None (default) will use as many as necessary to fill the surface. time : numpy array Time points in the data array (if data is 2D or 3D). %(time_label)s colorbar : bool Whether to add a colorbar to the figure. Can also be a tuple to give the (row, col) index of where to put the colorbar. hemi : str | None If None, it is assumed to belong to the hemisphere being shown. If two hemispheres are being shown, an error will be thrown. remove_existing : bool Not supported yet. Remove surface added by previous "add_data" call. Useful for conserving memory when displaying different data in a loop. time_label_size : int Font size of the time label (default 14). initial_time : float | None Time initially shown in the plot. ``None`` to use the first time sample (default). scale_factor : float | None (default) The scale factor to use when displaying glyphs for vector-valued data. vector_alpha : float | None Alpha level to control opacity of the arrows. Only used for vector-valued data. If None (default), ``alpha`` is used. clim : dict Original clim arguments. %(src_volume_options)s colorbar_kwargs : dict | None Options to pass to :meth:`pyvista.Plotter.add_scalar_bar` (e.g., ``dict(title_font_size=10)``). %(verbose)s Notes ----- If the data is defined for a subset of vertices (specified by the "vertices" parameter), a smoothing method is used to interpolate the data onto the high resolution surface. If the data is defined for subsampled version of the surface, smoothing_steps can be set to None, in which case only as many smoothing steps are applied until the whole surface is filled with non-zeros. Due to a VTK alpha rendering bug, ``vector_alpha`` is clamped to be strictly < 1. Ú transparent©rüNÚ vector_alphaÚ scale_factorÚthreshNÚremove_existing©NrüÚtime_label_sizerz&time_label_size must be positive, got rNrPrr^z6time has shape %s, but need shape %s (array.shape[-1])r›z.New n_times is different from previous n_timesz=Not all time values are consistent with previously set times.rûrbçš™™™™™¹?rz>If array has 3 dimensions, array.shape[1] must equal 3, got %srHZmneZhotérgzAExpected value of `smoothing_steps` is positive but {} was given.zGExpected type of `smoothing_steps` is int or NoneType but {} was given.rïrðr¹ÚclimrÏrxrOrsÚ glyph_datasetÚ glyph_mapperÚ glyph_actorrárxrdrjr1rùrúrûrRÚmixedrrŠTgffffffî?Úright)Úx_windowÚy_windowrbrqÚtextÚ justificationr0é)ÚsourceZn_labelsrbrrFr©rd)1r7r²r3r¡r™r‡Ú _check_stcr–ÚasarrayrµrãrYrsrZr¥r“Z array_equalÚ_to_time_indexrÚ_update_limitsr‹rŒrPÚ TypeErrorÚtyper’Ú update_lutrÂr¬rÊr®Ú_add_volume_datar‰rdr·Útime_interpolationrºr”r´r¼Útext2dr‘rIr³r¹r‚Z scalarbarrÌr)&rÒrárùrúrûrjr1rfrjrdrxr¹r›rxZcolorbarr†rkrmrÏrirhrprðÚvolume_optionsZcolorbar_kwargsr5rïrsrÜZy_txtrÞZsrc_volrßràrÝÚdor0ÚkwargsrárárâÚadd_data—sø_         þ       ÿÿ      þþ                      û   ÿÿ ÿ zBrain.add_datacCs|jddddS)z#Remove rendered data from the mesh.rŠTr~N©rcrCrárárâÚ remove_data‹szBrain.remove_datac csÎtdgdgdgd}|jdkr2|jdgddgdt|jƒD]Œ\}}t|g|g|gd}|jdkrr|j||gd|jdkrˆ||}}n ||}}t||||ƒD]"\}} |j || ¡|| |fVq¤q.z volume_options got unknown keys zvolume_options["blending"])Z compositeZmiprárrerErorìrnr0Úgrid_volume_posÚgrid_volume_negr1cSsg|]}t |¡‘qSrá)r–rY)rôrûrárárâr‚ãsz*Brain._add_volume_data..rrsZindexingZijrJièrrRrDrEcSsg|]}|jdd‘qS)r-r.)Úravel)rôrýrárárâr‚ës)rÄrxrÐÚ grid_meshrrGrFF)rƒrZÚcullingr)rƒrZr›Zpickabler)r€rbrcrd)/Zbackends._pyvistarr7r-r3r®r’r‰r‹r¡rrºÚreprrÄr“r™Úsortedrµrãr–rùr[rÃZmeshgridrárŒr r ÚTr/r9r¶rsZallcloseZdiagÚzerosÚprodr¼Z_volumer¾rËZSetColorr¹Ú SetOpacityrÂr±ZGetInput)#rÒr†rðr‡rZ allowed_typesrõÚtypesZ extra_keysr’rdr‘r“r”r•Z volume_posZ volume_negr1ZxyzÚ dimensionsÚmultrRrÄrxr r!r{rÐršZ actor_posrÜZ actor_negZ actor_meshÚproprÞrárárâr„³s  ÿ  þ ú  ÿ ÿþ     ÿÿ   "ÿ þÿ þ  þ  þ   ü   zBrain._add_volume_datac CsÔddlm} t|tƒrØ|dkr"d}tj |¡rX|} | | ƒ}|j}tj | ¡  d¡d} nr|  |¡}|} d  || dg¡} |dkr”t   |j |jd| ¡} nt   |j |jd|| ¡} tj | ¡sÂtd| ƒ‚| | ƒ}|j} |j}n¬z‚|j}|j} |jdkrd t|jƒ|_|jd7_t|jƒ} |dkrHt|d ƒrD|jdk rD|j}nd}|dk rX|j}Wntk rxtd ƒ‚YnX|  |¡}|dk rš| ||k} |jr(|jr(|jdkr(|jd }|jd }|j|||jd}|jdkrð|dn|dddd…f}t|j ƒ}|j!j"|jd|| |d}nd}|}t#||dd}t$ %d|g¡}t$ &|d¡ 't$j(¡}t$ )|j*|j+j,d¡}d|| <|r$t-|j*|j.|ƒ}t$j)|j/t$j0d}t|t1ƒrt2|ƒD]R}t$ 3|j*|j. 4¡|¡}|j*|j.j,|_,|j*|j.t$j5|dd}t$ 6|¡}qÀd||<||9}| 7|¡D]–\}}}|j8|}|j9||t$ :|¡t$ ;|¡g|| d|rŠ|j||—Ž|jr²|jr²|jdkr²||_?||_@|jA| B|¡q.|j< C¡dS)a–Add an ROI label to the image. Parameters ---------- label : str | instance of Label Label filepath or name. Can also be an instance of an object with attributes "hemi", "vertices", "name", and optionally "color" and "values" (if scalar_thresh is not None). color : matplotlib-style color | None Anything matplotlib accepts: string, RGB, hex, etc. (default "crimson"). alpha : float in [0, 1] Alpha level to control opacity. scalar_thresh : None | float Threshold the label ids using this value in the label file's scalar field (i.e. label only vertices with scalar >= thresh). borders : bool | int Show only label borders. If int, specify the number of steps (away from the true border) along the cortical mesh to include as part of the border definition. hemi : str | None If None, it is assumed to belong to the hemipshere being shown. subdir : None | str If a label is specified as name, subdir can be used to indicate that the label file is in a sub-directory of the subject's label directory rather than in the label directory itself (e.g. for ``$SUBJECTS_DIR/$SUBJECT/label/aparc/lh.cuneus.label`` ``brain.add_label('cuneus', subdir='aparc')``). reset_camera : bool If True, reset the camera view after adding the label. Defaults to True. Notes ----- To remove previously added labels, run Brain.remove_labels(). r)Ú read_labelNZcrimsonÚ.rròzLabel file %s does not existÚunnamedrbz­Label was not a filename (str), and could not be understood as a class. The class must have attributes "hemi", "vertices", "name", and (if scalar_thresh is not None)"values"rïrð)rðr¥rrr›)ròrbTr|)rrrréÿ©ÚdtyperÉrzr‚F)Dròr¦r‹rºÚosÚpathÚisfiler†ÚbasenamerOr‡r³r²r£r¢Úexistsr™rxrÒrZrªrrbræršrýrrµZextract_label_time_courser rãr2rrrÖr>r–rár—r˜Úuint8rŸr¶rÄrsr*rÅrqÚint64rŒr‹Úin1dr™rÚuniquerÂr¬rÈr[rîr¼rÌrr+r*r©r)r*)rÒròrbrdZ scalar_threshr&r†Úsubdirrƒr¦ÚfilepathZ label_nameZ label_fnameÚidsr{rïrðZtcr8Z orig_colorÚcmapÚctableÚkeep_idxrÏrÜrÝr€rárárâr("sÒ)     ÿ ÿ ÿ        ÿ  ÿ& þ  ÿÿ ûÿzBrain.add_labelc CsÔt|ddddd}~|dkr0|jdkr,dnd }d }|d tkr~t|d }|dkr`tddƒ}q|dkrn|}qt| |¡ƒ‚nt| |d ¡ƒ‚t|j|||jdkr¨d nd ||dD]} | d| ¡q´|j  ¡dS)asAdd a quiver to render positions of dipoles. Parameters ---------- %(fwd)s %(trans_not_none)s %(alpha)s Default 1. scale : None | float The size of the arrow representing the dipoles in :class:`mne.viz.Brain` units. Default 1.5mm. Notes ----- .. versionadded:: 1.0 ÚheadÚmriF©Ú allow_nonerNrJgø?gú~j¼t“X?zEUnexpected forward model coordinate frame {}, must be "head" or "mri"Ú coord_framerEr)Z fwd_scalerñrdÚforward) r1r r0r.Ú RuntimeErrorrPrr¼rdr*) rÒZfwdrDrdrñÚ head_mri_tÚ error_msgZ fwd_frameZ fwd_transrÞrárárâÚ add_forward¶s.   ý zBrain.add_forwardcCs|jddddS)z/Remove forward sources from the rendered scene.rÀTr~Nr‹rCrárárâÚremove_forwardßszBrain.remove_forwardÚredc CsRt|ddddd}~t|ƒ}t|ttfƒs6|g|}t|ƒ|kr\tdt|ƒ›d|›dƒ‚d d „t|ƒDƒ}|d krˆ|jd kr„d nd}t|ttfƒs |g|}t|ƒ|krÆtdt|ƒ›d|›dƒ‚t||j ƒ}||jd krâdnd9}|  d¡D]P} t ||j ||ƒD]:\} } } } |j j| | ž| |d| dœŽ\}} | d|¡qqò|j  ¡d S)a½Add a quiver to render positions of dipoles. Parameters ---------- dipole : instance of Dipole Dipole object containing position, orientation and amplitude of one or more dipoles or in the forward solution. %(trans_not_none)s colors : list | matplotlib-style color | None A single color or list of anything matplotlib accepts: string, RGB, hex, etc. Default red. %(alpha)s Default 1. scales : list | float | None The size of the arrow representing the dipole in :class:`mne.viz.Brain` units. Default 5mm. Notes ----- .. versionadded:: 1.0 r»r¼Fr½rzThe number of colors (z) and dipoles (z ) must matchcSs$g|]\}}t|d|›dd‘qS©zcolors[r–rY©r>©rôràrbrárárâr‚ sÿz$Brain.add_dipole..NrJrVg{®Gázt?zThe number of scales (rErrNÚarrow)rbr}r¥rñÚdipole)r1r“r‹r¨r•r™r×r r/rrÂr[r"r¼Úquiver3drdr*)rÒrËrDÚcolorsrdÚscalesrÂZ n_dipolesrrÜZthis_posZthis_orirbrñrÞrárárâÚ add_dipoleãsH  ÿ   ÿÿþ zBrain.add_dipolecCs|jddddS)z.Remove dipole objects from the rendered scene.rËTr~Nr‹rCrárárâÚ remove_dipole szBrain.remove_dipoleÚgrayr`c Cs’t|r dnd|j|jƒ}|d|d}}||jdkr:dnd9}t|ƒ}| d¡D]0}|jj|j|||d d d œŽ\}}|  d|¡qR|j  ¡d S) aDAdd a mesh to render the outer head surface. Parameters ---------- dense : bool Whether to plot the dense head (``seghead``) or the less dense head (``head``). %(color_matplotlib)s %(alpha)s Notes ----- .. versionadded:: 0.24 Úsegheadr»ÚrrÚtrisrJrErrNF©ryrbr}rƒrN) r$r¢r£r r>rÂr¼r€ržrdr*) rÒZdenserbrdrÓÚvertsryrÜrÞrárárâÚadd_head s$ ÿþ zBrain.add_headcCs|jddddS)z,Remove head objects from the rendered scene.r»Tr~Nr‹rCrárárâÚ remove_head9 szBrain.remove_headc Cs’t|r dnd|j|jƒ}|d|d}}||jdkr:dnd9}t|ƒ}| d¡D]0}|jj|j|||d d d œŽ\}}|  d |¡qR|j  ¡d S) a%Add a mesh to render the skull surface. Parameters ---------- outer : bool Adds the outer skull if ``True``, otherwise adds the inner skull. %(color_matplotlib)s %(alpha)s Notes ----- .. versionadded:: 0.24 ÚouterÚinnerrÓrÔrJrErrNFrÕÚskullN) r%r¢r£r r>rÂr¼r€ržrdr*) rÒrÙrbrdrÓrÖryrÜrÞrárárâÚ add_skull= s$ ÿþ zBrain.add_skullcCs|jddddS)z-Remove skull objects from the rendered scene.rÛTr~Nr‹rCrárárâÚ remove_skullZ szBrain.remove_skullú aparc+asegrac sTddl}| d¡s td|›ƒ‚tt |j|jd|d¡ddd }|} | | ¡}t   |j ¡} |j   ¡} |jd krtd nd } | dd …| 9<~tƒ\‰‰|dkrÈdd„ˆ ¡Dƒ‰‡fdd„tdDƒ}t|tdfdƒt|tdfdƒ|dkrüt|ƒdk}|dkr‡fdd„|Dƒ}nt|ttfƒs8|gt|ƒ}dd„t|ƒDƒ}t| ‡fdd„|Dƒ||d} t||| ƒD]Œ\}}\}}t|ƒdkr¶tdˆ|›dt|ƒ›d| ›ƒqtt| |ƒ}| d¡D]2}|j j!|j"|||dddœŽ\}}| #d |¡qÊqt|st|t$ƒrFt|t$ƒr$|nt$ƒ}|j j%j&tt||ƒƒf|Ž|j  '¡dS)!aÔAdd labels to the rendering from an anatomical segmentation. Parameters ---------- %(aseg)s labels : list Labeled regions of interest to plot. See :func:`mne.get_montage_volume_labels` for one way to determine regions of interest. Regions can also be chosen from the :term:`FreeSurfer LUT`. colors : list | matplotlib-style color | None A list of anything matplotlib accepts: string, RGB, hex, etc. (default :term:`FreeSurfer LUT` colors). %(alpha)s %(smooth)s fill_hole_size : int | None The size of holes to remove in the mesh in voxels. Default is None, no holes are removed. Warning, this dilates the boundaries of the surface by ``fill_hole_size`` number of voxels so use the minimal size. legend : bool | None | dict Add a legend displaying the names of the ``labels``. Default (None) is ``True`` if the number of ``labels`` is 10 or fewer. Can also be a dict of ``kwargs`` to pass to :meth:`pyvista.Plotter.add_legend`. Notes ----- .. versionadded:: 0.24 rNÚasegz+`aseg` file path must end with "aseg", got r¼z.mgzÚreadT)Ú overwriteZ must_existr¬gü©ñÒMbP?rrcSsi|]\}}||“qSrárá)rôr\rÝrárárârö” sz+Brain.add_volume_labels..csg|] }ˆ|‘qSrárá)rôr_)Úlut_rrárâr‚• sz+Brain.add_volume_labels..Zvolume_label_indicesÚfill_hole_sizeÚlegendé csg|]}ˆ|d‘qS)r©rá©rôrò)Ú fs_colorsrárâr‚ scSs$g|]\}}t|d|›dd‘qSrÇrÈrÉrárárâr‚  sÿcsg|] }ˆ|‘qSráráræ)Úlutrárâr‚£ s)rSrãzValue z not found for label z in: rNFrÕÚ volume_labels)(ZnibabelÚendswithrÁr=r²r³r£r¢Úloadr–r~ZdataobjÚheaderZget_vox2ras_tkrr r#Úitemsrr7rŒr²r“r‹r¨r•r×r+r[r;rœr/rÂr¼r€ržrdr’r¾Z add_legendr*)rÒrßÚlabelsrÍrdrSrãräZnibZ aseg_fnameZ aseg_dataZ vox_mri_tr¤ZsurfsròrbrÖryrÜrÞrá)rçrèrârâÚadd_volume_labels^ s~" ÿÿþ      ÿþ" þ  ÿÿzBrain.add_volume_labelscCs|jddd|jj ¡dS)z1Remove the volume labels from the rendered scene.réTr~N)rcr¼r¾Z remove_legendrCrárárâÚremove_volume_labels¹ szBrain.remove_volume_labelsÚwhiteé2c  CsL|j|dgd}|r(|j|j|}d}|dk r”ddlm} t|j|||jd|j|j ddd…fd} |   ¡t j | | j|ƒdd} |j|j| }t |ƒ}|jd kr®|d }| |¡D]:\} } }|jj||d ||| d |jjft||Žq¸|}d |j |g¡kr$t  |j|d |f¡}|j |tƒ¡|j|<||j|d <dS)aAdd spherical foci, possibly mapping to displayed surf. The foci spheres can be displayed at the coordinates given, or mapped through a surface geometry. In other words, coordinates from a volume-based analysis in MNI space can be displayed on an inflated average surface by finding the closest vertex on the white surface and mapping to that vertex on the inflated mesh. Parameters ---------- coords : ndarray, shape (n_coords, 3) Coordinates in stereotaxic space (default) or array of vertex ids (with ``coord_as_verts=True``). coords_as_verts : bool Whether the coords parameter should be interpreted as vertex ids. map_surface : str | None Surface to project the coordinates to, or None to use raw coords. When set to a surface, each foci is positioned at the closest vertex in the mesh. scale_factor : float Controls the size of the foci spheres (relative to 1cm). %(color_matplotlib)s %(alpha)s Default is 1. name : str Internal name to use. hemi : str | None If None, it is assumed to belong to the hemipshere being shown. If two hemispheres are being shown, an error will be thrown. resolution : int The resolution of the spheres. rNrPNr)Úcdistr)rkrurvrÉr¬rEg$@)r1rbrñr}r‘Zfoci)r‡r¶rÄZscipy.spatial.distancerórr¢r£r rÀrÁr–rr>rÂr¼rrÌrrµrÃÚvstackr’)rÒrÄZcoords_as_vertsZ map_surfacerirbrdrZr†r‘róZ foci_surfZ foci_vtxsrÜrÝZ data_focirárárâÚadd_foci¾ s<$  þ  þzBrain.add_fociÚoriginalc  Cs’t|tdƒt|||ƒ\}}}} t|d|kd|kt|ƒdk|||t|ƒdkd} t|dddd d} ~t|| dd } t|d d d jdkr¢d|kr¢td|j |j ƒ}nd}|  d¡D]Ò}| jdkrt |j || | |||| ||jƒ }| ¡D]\}}|D]}| ||¡qòqæd|kr°t|d djdkr°t|| ƒ}|d|jdkr@dnd}|j j|j|dfžtddddddœŽ\}}| d|¡q°|j  ¡dS)aHAdd mesh objects to represent sensor positions. Parameters ---------- %(info_not_none)s %(trans_not_none)s %(meg)s %(eeg)s %(fnirs)s %(ecog)s %(seeg)s %(dbs)s %(verbose)s Notes ----- .. versionadded:: 0.24 rçZsensorsr°r)ÚmegZref_megÚeegÚecogÚseegÚdbsÚfnirsr»r¼Fr½)r¿Trá)røÚexcludeZ projectedrÒNrNÚhelmet)r÷rÓr¬rrErÔZcoregZ helmet_colorrþ)rbr}rƒr)r7r(rr'r“r1r2rqr$r¢r£rÂrr¼r rírdr,r€ržrr*)rÒrçrDr÷rørürùrúrûr5Zwarn_megZpicksrÂZto_cf_tZ head_surfrÜZsensors_actorsrbr<rÞrÓrÖrárárâÚ add_sensors sr    ýÿÿÿ þ ÿ ý zBrain.add_sensorscCshd}|dkr&|D]}|j|ddqn4t|tƒr6|g}|D]}td||ƒq:|j|dd|j ¡dS)a0Remove sensors from the rendered scene. Parameters ---------- kind : str | list | None If None, removes all sensor-related data including the helmet. Can be "meg", "eeg", "fnirs", "ecog", "seeg", "dbs" or "helmet" to remove that item. )r÷rørürùrúrûrþNFr~r®)rcr‹rºr3r¼r*)rÒr®Z all_kindsrbZ this_kindrárárâÚremove_sensorsA s  zBrain.remove_sensorsrc  Cs¾t|tdfdƒ|dkr|n|}d|jkrH||jdkrHtd|›dƒ‚| d¡D]f\} } } |dksl|| krR|dks||| krR|jj||||| | d}d|jkrªtƒ|jd<||jd|<qRdS)a Add a text to the visualization. Parameters ---------- x : float X coordinate. y : float Y coordinate. text : str Text to add. name : str Name of the text (text label can be updated using update_text()). color : tuple Color of the text. Default is the foreground color set during initialization (default is black or white depending on the background color). opacity : float Opacity of the text (default 1.0). row : int | None Row index of which brain to use. Default is the top row. col : int | None Column index of which brain to use. Default is the left-most column. font_size : float | None The font size to use. justification : str | None The text justification. NrZrxzText with the name z already existsrN)rvrwrxrbrqry)r7rºr­r™rÂr¼r†r’)rÒrgrÜrxrZrbr}r„r…Z font_sizeryrßràrÜrÞrárárâÚadd_textW s" þ  zBrain.add_textcCs¸t|tdfdƒ|dkrL|jd ¡D]}|jjj|ddq&|j d¡n^dg}d|jkrr|t|jd  ¡ƒ7}t d||ƒ|jjj|jd|dd|jd |¡|j  ¡dS)z»Remove text from the rendered scene. Parameters ---------- name : str | None Remove specific text by name. If None, all text will be removed. NrZrxFr~) r7rºr­rÒr¼r¾r@rAr¨rr3r*)rÒrZrÞÚnamesrárárâÚ remove_text‚ s   ÿzBrain.remove_textcCsÒddlm}|jsdS|jdkr*| ¡n| ¡d|_|j|jddd|j dd|j  ¡|j D]f}||j |j||j d }t |j|jjd d ¡|j|<||j|<t|ƒD]\}}||j||j<q²qfdS) Nr)Úread_labels_from_annotròr[gè?)rbrdFrÎ)rKZparcr†r×rr^)ròrrýrrÅr3rÚadd_annotationr rzr¤rˆr¢r£r–Úfullr¶rÄrsr¦r§r×rx)rÒrr†rîr_ròrárárâr™ s0      üÿ  z"Brain._configure_label_time_coursec Cs¦ddlm}| |¡}t|tƒrdtj |¡rÚ|} tj | ¡d} tj  | ¡ d¡dd…\} }t |ƒdkrÒ|dd…dkrš| t   | d |dd…¡g} qØ|dd…d krÈt   | d |dd…| ¡g} qØt d ƒ‚n| g} nRg} |D]H}t   |j|jd d  ||dg¡¡} tj | ¡s td| ƒ‚| | g7} qâg} t|| ƒD]&\}} || ƒ\}}}|  ||f¡q:nt |ƒdkrx|gn|} d}t|| ƒD] \}\}}| |||¡d|dd…df<t t |j¡d¡ t¡}d|d<||dd…dfdkdfd7<|||dd…dfdkdd…f<t |dk¡rdt |dd…dfdk¡sdt |t |dgg¡f¡}t |dd…df¡}||}t |dd…df|¡}|dd…dd…f}|dd…df}|d||dk<|dk r t t  t!|ƒd¡¡}| |j"¡|dd…dd…f<| tj#¡}| $|¡D]r}|j%|}|j&||t '|¡t (|¡g||d|j)| |¡|j*rv|j+dkr |j, -|j.| tj/¡d¡q qŠ|j, 0¡dS)a÷Add an annotation file. Parameters ---------- annot : str | tuple Either path to annotation file or annotation name. Alternatively, the annotation can be specified as a ``(labels, ctab)`` tuple per hemisphere, i.e. ``annot=(labels, ctab)`` for a single hemisphere or ``annot=((lh_labels, lh_ctab), (rh_labels, rh_ctab))`` for both hemispheres. ``labels`` and ``ctab`` should be arrays as returned by :func:`nibabel.freesurfer.io.read_annot`. borders : bool | int Show only label borders. If int, specify the number of steps (away from the true border) along the cortical mesh to include as part of the border definition. %(alpha)s Default is 1. hemi : str | None If None, it is assumed to belong to the hemipshere being shown. If two hemispheres are being shown, data must exist for both hemispheres. remove_existing : bool If True (default), remove old annotations. color : matplotlib-style color code If used, show all annotations in the same (specified) color. Probably useful only when showing annotation borders. r)Ú _read_annotrr§Nrrzlh.rTzrh.rSzOTo add both hemispheres simultaneously, filename must begin with "lh." or "rh."ròr z!Annotation file %s does not existr­r©r^räirzrñ)1ròrÚ _check_hemisr‹rºr¬r­r®rOr¯r“r²r³rÁr£r¢r°r™r[r)Ú _to_bordersr–r—rár¹r˜rŒrrôrÑZargsortZ searchsortedÚmultiplyr>r«Zfloat64rÂr¬rÈr[rîr«ršrr¼Ú_set_colormap_rangerÊr±r*)rÒr r&rdr†rkrbrrJr¶r­Z file_hemiZ filepathsZannotsrîr¸rÜrrr/r·Z alpha_vecÚrgbr¹r€rárárârµ sˆ      ýÿ $ ,   û ÿ zBrain.add_annotationcCsd|_|j ¡dS)z-Close all figures and cleanup data structure.TN)rÎr¼ÚcloserCrárárâr ' sz Brain.closecCs2ddlm}|j ¡|jr.||jjjdƒdS)zDisplay the window.rrérN)rrêr¼rÏržrÖr+)rÒrêrárárârÏ, s  z Brain.showcCs\t|dƒ}t|dƒ}|jD]<}| |¡D],\}}}||kr(||kr(|j ¡Sq(qdS)aˆGet the camera orientation for a given subplot display. Parameters ---------- row : int The row to use, default is the first one. col : int The column to check, the default is the first one. Returns ------- %(roll)s %(distance)s %(azimuth)s %(elevation)s %(focalpoint)s r„r…)NNNNN)r?rˆrÂr¼Z get_camera)rÒr„r…rÛrßràrÜrárárâÚget_view3 s   zBrain.get_view)r„r…r†rŽrörøÚ focalpointcCs*t|ddƒt|ddƒ|dkr&|jn|}|dkr`|jdkrD|dksV|jdkr\|dkr\d }nd }t|tdfd ƒt|| ||| d } |dk r²d d„|  ¡Dƒ} tt| |¡f| Ž} |r¼|jnd} |j D]T} |  | ¡D]D\}}}|dksî||krÔ|dks||krÔ|j j f| d| dœ—ŽqÔqÆ|j   ¡dS)aÌOrient camera to display view. Parameters ---------- %(view)s %(roll)s %(distance)s row : int | None The row to set. Default all rows. col : int | None The column to set. Default all columns. hemi : str | None Which hemi to use for view lookup (when in "both" mode). %(align_view)s %(azimuth)s %(elevation)s %(focalpoint)s Notes ----- The builtin string views are the following perspectives, based on the :term:`RAS` convention. If not otherwise noted, the view will have the top of the brain (superior, +Z) in 3D space shown upward in the 2D perspective: ``'lateral'`` From the left or right side such that the lateral (outside) surface of the given hemisphere is visible. ``'medial'`` From the left or right side such that the medial (inside) surface of the given hemisphere is visible (at least when in split or single-hemi mode). ``'rostral'`` From the front. ``'caudal'`` From the rear. ``'dorsal'`` From above, with the front of the brain pointing up. ``'ventral'`` From below, with the front of the brain pointing up. ``'frontal'`` From the front and slightly lateral, with the brain slightly tilted forward (yielding a view from slightly above). ``'parietal'`` From the rear and slightly lateral, with the brain slightly tilted backward (yielding a view from slightly above). ``'axial'`` From above with the brain pointing up (same as ``'dorsal'``). ``'sagittal'`` From the right side. ``'coronal'`` From the rear. Three letter abbreviations (e.g., ``'lat'``) of all of the above are also supported. )zint-likeNr„r…NrOrKrrWrTrSrÿ)rörøÚrollÚdistancercSsi|]\}}|dk r||“qSrƒrá)rôÚparamrÚrárárârö— sÿz#Brain.show_view..F)rƒZrigid)r7rŸrŠrºr’rírrÃrÀrˆrÂr¼rÌr*)rÒrÿrrr„r…r†rŽrörørZ view_paramsrèrÛrßràrÜrárárârÐN s:<  ÿÿÿ "ÿzBrain.show_viewcCsD|jD]8}| |¡D](\}}}|jjft||ddi—ŽqqdS)zReset the camera.rƒFN)rˆrÂr¼rÌr)rÒrÛrÜrÝrárárârR¢ s  ÿzBrain.reset_viewr cCs(|dkrtdƒ}t||j|ddƒdS)zÙSave view from all panels to disk. Parameters ---------- filename : str Path to new image file. mode : str Either 'rgb' or 'rgba' for values to return. Nz.pngT)r¥rš)rrrë)rÒrêr¥rárárârè© s  ÿzBrain.save_imagec sn|dkr dnd}|j |¡}t d|j›¡|rj|jrj|jrj|jsjddlm }|j j j }|  ¡|j j }tƒÂ}| ¡} | ¡‰t‡fdd„| Dƒƒ} | d| d } t d | ›d ˆ›d | ›d | ›d ¡|j|ˆd|jdd| d¡||dddd…dd…d|…f} t t | d¡dd¡ tj¡} W5QRXt |jd|…¡d} t|| g| |d}|S)a'Generate a screenshot of current view. Parameters ---------- mode : str Either 'rgb' or 'rgba' for values to return. %(time_viewer_brain_screenshot)s Returns ------- screenshot : array Image pixel values. r rräzGot screenshot of size r)Úimreadc3s|]}|ˆVqdSrƒrá)rôrg©rZrárârÈÚ sz#Brain.screenshot..rzSaving figure of size z @ z DPI (z = z pixels)ZpngÚnone)rZrPZ facecolorZ edgecolor)rPNr©)rrÚ n_channels)r¼rër4r»rsršrýrZmatplotlib.imagerrrtÚcanvasZ draw_idlerZget_size_inchesZget_dpir•ZsavefigrÚseekr–rùr—r˜r±rár¹r)rÒr¥ršrZimgrrrtÚoutputZsize_inZ want_sizeZn_pixZ trace_imgrrrárrârë¸ sL ÿþ  ÿ ÿ " ÿÿ ÿzBrain.screenshotccs$|j}||_z dVW5||_XdSrƒ)r¯)rÒÚwhyÚorigrárárâÚ_no_lut_updateï s  zBrain._no_lut_updatec s|›d|›d|›d|›}ˆjdk r8t d|›¡dSt d|›¡ˆjd}ˆjd}ˆjd}‡fdd „d Dƒ} t| |||d td d „|  ¡Dƒƒs¢t‚ˆj | ¡t   t |fd ||dœ| —Žd¡  t j ¡ˆjd<ˆj} ˆjd} dD]Ú} ˆj | ¡} | dk rò| ˆjkrRˆj| }|jdˆjd|| dˆj |j| ˆj| ˆj¡|  d¡}|  d¡}||fD]*}|dk rnˆj || | dˆj| ¡qn|  d¡}|dk rò|D]}ˆj || ˆj| ¡q°qòˆjrˆ d|›¡$d D]}ˆj|| |ƒqìW5QRXˆj ¡dS)znUpdate color map. Parameters ---------- %(fmin_fmid_fmax)s %(alpha)s rLNzLUT update postponed with zUpdating LUT with r1rjrfcsi|]}|ˆj|“qSrá©rµrórCrárârö sz$Brain.update_lut..røcss|]}|dk VqdSrƒrá)rôrÚrárárârÈ sz#Brain.update_lut..rE)rdr1rfr©r¹rUrŠ)rZrjr}r|r—r˜rdrsz update_lut )r¯r4r»rµÚ_update_monotonicÚallrÒr‰r‚r–r—rr˜r±Ú _cmap_rangerÃr¬Úupdate_overlayr¼r rÊr³r¹Z_set_volume_rangeršrrr*)rÒrùrúrûrdÚargsr1rjrfÚlimsr|r¹r†rÞr€r—r˜Z grid_volumersZ glyph_actor_rõrárCrârƒø s†       ÿÿþÿý     ýþ    þ ÿ  zBrain.update_lutc Csúddlm}dD]Ê}|j |¡}|dk rt|dƒ|j|jjdkrHq|d}|dkrztdt|ƒ|j|jjdfƒ‚|d kr†d n|}t d ƒ4||j|j t   t|j|j ƒ¡||dd d }W5QRX||j|d <q| |jd¡||jd<dS)zSet the number of smoothing steps. Parameters ---------- n_steps : int Number of smoothing steps. r)Ú _hemi_morphrRNrárrxzClen(data) < nvtx (%s < %s): the vertices parameter must not be Noner^rgF)Úmapsr;rârsr¹)Zmorphr$rµrÃr“r¶rgrsr™r8Ú orig_facesr–rYrÄrJ)rÒZn_stepsr$r†rÞrxZ morph_n_stepsrârárárârº5 s4  þÿ  ýzBrain.set_data_smoothingcCs|jdk rt|jƒSdSrƒ)r¥r“rCrárárârZS szBrain._n_timescCs|jS)zThe interpolation mode.)Ú_time_interpolationrCrárárâr…W szBrain.time_interpolationcCs„td|dƒ|_tƒ|_d|_|jdk r€t |j¡}dD]:}|j   |¡}|dk r6|d}t |||jddd|j|<q6t ||jƒ|_dS) zpSet the interpolation mode. Parameters ---------- %(interpolation_brain_time)s Ú interpolation)ÚlinearrgÚzeroZslinearZ quadraticZcubicNrUrár^T©rÊÚ assume_sorted) r3r'r’Ú_time_interp_funcsÚ_time_interp_invr¥r–rYrZrµrÃÚ_safe_interp1d)rÒr(r_r†rÞrárárárâr·\ s*ý   þzBrain.set_time_interpolationcCsÜtƒ|_|j dd¡}|j dd¡}dD]˜}|j |¡}|dk r(|d}d}|jdkrd|}d|_nD|j||ƒ}| |¡|_|jdkrœ|}tj j |dd }| |¡|_||j|<|dk rÒ|dk rÒ|  ||jƒ¡| d ¡} | dk rB|jd d } |jd } |j } |jd dk rdn| d} t | ƒd | ¡| t | ƒd| <| d¡}|dk r`| |¡}||jkr®|j|}d|jkr’|jd|dn|j||jd|j ddd|dk r(| ||¡q(||jd<|j ¡dS)zìSet the time point shown (can be a float to interpolate). Parameters ---------- time_idx : int | float The time index to use. Can be a float to use interpolation between indices. r0NrxrUrárrrrÉrÐrNrxr1rÒrârŠ)rZr{r¹rzrs)r’Ú_current_act_datarµrÃrãrIr-r.r–rÓrÔrr r ÚfillrOr¬Z _overlaysr!rÈÚ_update_glyphsr¼r*)rÒrsr0rxr†rÞráÚvectorsrÝrÐrxrÒr|r1râr€rárárârJv s\                 û  zBrain.set_time_pointc Csˆ|jdkrtdƒ‚npt|jƒ|kr4t|jƒkr\nn$| t t|ƒ|jt |j ¡¡¡n(td|›dt|jƒ›dt|jƒ›dƒ‚dS)z”Set the time to display (in seconds). Parameters ---------- time : float The time to show, in seconds. Nz0Cannot set time when brain has no defined times.zRequested time (z- s) is outside the range of available times (rdz s).) r¥r™r[rîrJr–r\r¡rYrZ)rÒr›rárárâÚset_time¾ s ÿ$ ÿ"ÿzBrain.set_timecCs°|j |¡}|dk st‚|d}|jd}|jd}|dkrDtdƒn|}t |j|j¡|j\}}} |ddkr‚d} t ƒ|d<nd} d} |  |¡D]} |ddkr|j j ||| |dd…df|dd…d f|dd…d fdd d ||t |ƒd d \} }||d<| |d<n|d}|t|ƒd<|d} | rz|j  | ¡}| ¡}| d¡| |¡|j jj|dd|d |¡n |d| }| d 7} |j j||jdd|jdq”dS)NrxrhrirsTFrrqrrZ2darrowZvectorZ_glyph)rbr¥Z scale_moderñr}rZrrZvecrìr~r¹)rÞr¹Z scalar_barr|)rµrÃr‰Úslicer–rár¶rÄržr¨rÂr¼rÌrºrrÊZ GetPropertyZ SetLineWidthr¡r¾rËr)r r )rÒr†r3rÞrxrhrirgrÜÚzÚaddÚcountrÜrrrqrsr¥rárárâr2Ñ s`       ø       üzBrain._update_glyphscCs8|jd}|jddkr$|jd}nd|}||g}|S)Nrûr1rùr^r)rÒZdt_maxZdt_minr|rárárâr  s   zBrain._cmap_rangecCs>|jd|}|jd|}|jd|}|j|||ddS)zScale the colorbar points.rùrúrûrøN)rµrƒ)rÒZfscalerùrúrûrárárâÚ_update_fscale szBrain._update_fscalec Csè|jd}|dk r d|kr d}nd}|dk r6|r6|}nd}|jd}|jd}t|||t t|j ¡ƒ¡|ƒ}d|dk}|d}|d|rdnd} |d}~| \} } } |r²d nd} | |jd <||jd<||jd<|j| | | d dS) Nrpr#FTrHrjrfZpos_limsror1rø)rµrr–rÑr¨r0rÒrƒ)rÒrEZ user_climZallow_pos_limsrprjrfZmapdataZ divergingZ scale_ptsrùrúrûr1rárárârB s6    ý      zBrain._update_auto_scalingcCs&|jd}t ||t t|ƒ¡¡}|S)z;Return the interpolated time index of the given time value.r›)rµr–r\rYr“)rÒr@r›rárárâr0 s zBrain._to_time_indexcCs|jS)z/Data used by time viewer and color bar widgets.rrCrárárârŠ6 sz Brain.datacCs|jSrƒ)r©rCrárárârî; sz Brain.labelscCs|jSrƒ)r¤rCrárárârØ? sz Brain.viewscCs|jSrƒ)rˆrCrárárârJC sz Brain.hemisr0éc  Ksxddl} |j ¡| |||||| | ¡} W5QRXd| krD|| d<|dk rT|| d<|dk rd|| d<| j|| f| ŽdS)NrZfpsÚcodecÚbitrate)Úimageior¼Z_disabled_interactionÚ_make_movie_framesZmimwrite)rÒrêríÚtminÚtmaxÚ framerater(r;r<rrršr‰r=ÚimagesrárárâÚ _save_movieG s$ þzBrain._save_moviec  s’‡‡fdd„} ˆj ¡} ˆj ˆj d¡¡zRz$ˆjˆ|||||||| | f | ŽWn(ttfk rztdt  ¡ƒYnXW5ˆj | ¡XdS)Ncs¦||kr8ˆj dˆ¡ˆj ¡ˆj ¡ˆj ¡nVˆj d|d|f¡ˆj ¡ˆj ¡ˆj d|dg¡ˆj |¡ˆj ¡ˆj ¡ˆj ¡dS)NzSaving with ImageIO: %sz$Rendering images (frame %d / %d) ...rr) rrmrÏrr r¼Z_status_bar_updateZ set_ranger‚©ÚframeÚn_frames©rêrÒrárâÚframe_callback\ s*ÿÿ    ÿÿ     z,Brain._save_movie_tv..frame_callbackZ WaitCursorzMovie saving aborted: ) r¼Z_window_get_cursorZ_window_set_cursorZ_window_new_cursorrCræÚKeyboardInterruptr;Ú tracebackÚ format_exc)rÒrêrír?r@rAr(r;r<rrršr‰rHZdefault_cursorrárGrâÚ_save_movie_tvX s&  ÿ þþzBrain._save_movie_tvc KsD|dkrtdƒ}|jr|jn|j} | ||||||||| | f | ŽdS)aŽSave a movie (for data with a time axis). The movie is created through the :mod:`imageio` module. The format is determined by the extension, and additional options can be specified through keyword arguments that depend on the format, see :doc:`imageio's format page `. .. Warning:: This method assumes that time is specified in seconds when adding data. If time is specified in milliseconds this will result in movies 1000 times longer than expected. Parameters ---------- filename : str Path at which to save the movie. The extension determines the format (e.g., ``'*.mov'``, ``'*.gif'``, ...; see the :mod:`imageio` documentation for available formats). time_dilation : float Factor by which to stretch time (default 4). For example, an epoch from -100 to 600 ms lasts 700 ms. With ``time_dilation=4`` this would result in a 2.8 s long movie. tmin : float First time point to include (default: all data). tmax : float Last time point to include (default: all data). framerate : float Framerate of the movie (frames per second, default 24). %(interpolation_brain_time)s If None, it uses the current ``brain.interpolation``, which defaults to ``'nearest'``. Defaults to None. codec : str | None The codec to use. bitrate : float | None The bitrate to use. callback : callable | None A function to call on each iteration. Useful for status message updates. It will be passed keyword arguments ``frame`` and ``n_frames``. %(time_viewer_brain_screenshot)s **kwargs : dict Specify additional options for :mod:`imageio`. Nz.mp4)rršrLrC) rÒrêrír?r@rAr(r;r<rrršr‰r»rárárârî s/ þþzBrain.save_moviec sjddlm}|dkr ˆjd}n$|ˆjdkrDtd|ˆjdfƒ‚|dkrXˆjd}n$|ˆjdkr|td|ˆjdfƒ‚|||||ƒ} tj| td} | ||} | |7} t | ˆjt ˆj¡¡} t | ƒ} | dkrâtdƒ‚t   d| | f¡ˆj ˆd ˆj } |dk rˆ |¡z ‡‡fd d „ˆ | |¡Dƒ}W5ˆ | ¡X|dk rf|t | ƒt | ƒd |S) Nr)Úfloorz1tmin=%r is smaller than the first time point (%r)r^z2tmax=%r is greater than the latest time point (%r)rªzNo time points selectedz(Save movie for time points/samples %s %s©ršcsg|]}ˆjˆd‘qS)rN)rë)rôrÜ©rÒršrárâr‚Û sÿz,Brain._make_movie_frames..rD)ÚmathrMr¥r™r–rYr¡r\rZr“r4r»rër…r·Ú _iter_time)rÒrír?r@rAr(rrršrMrFr^rsZn_timesZold_moderBrárOrâr>· sH   ÿ  ÿ ÿ     þ   zBrain._make_movie_framesccsn|jrt|jddd}n|j}|jd}t|ƒD].\}}||ƒ|dk rZ||t|ƒd|Vq2||ƒdS)aÇIterate through time points, then reset to current time. Parameters ---------- time_idx : array_like Time point indexes through which to iterate. callback : callable | None Callback to call before yielding each frame. Yields ------ idx : int | float Current index. Notes ----- Used by movie and image sequence saving functions. r›TrPrsNrD)ršrrrJrµr×r“)rÒrsrrr»Zcurrent_time_idxrr_rárárârQä s ÿ zBrain._iter_timec Csddlm}m}m}m}t||ƒrö|}d} } t||ƒr>|} nXt||ƒrr|dkrX| ¡nd} |dkrl| ¡nd} n$t||ƒrŽ|dkrˆ|nd} ntdƒ‚| dkr®| dkr®t dƒ‚| dk rÚt | |dƒ}| j |dkrÔdnd }| dk rú| j }t  | j ¡}nd}|||fS) Nr)Ú_BaseSourceEstimateÚ_BaseSurfaceSourceEstimateÚ_BaseMixedSourceEstimateÚ_BaseVolSourceEstimaterNzstc not supportedzNo data to be addedrµrSrr)r±rRrSrTrUr‹Úsurfacer™rr™r7rxrŠr–rÑ) rÒr†rárxrRrSrTrUrïZstc_surfZstc_volrárárâr}s,    zBrain._check_stcrácCsHt|dtfdƒ|dkr0|jdkr*tdƒ‚|j}td|dt|ƒƒ|S)z.Check for safe single-hemi input, returns str.Nr†rRz9hemi must not be None when both hemispheres are displayed)r7rºrŸr™r3r•)rÒr†rQrárárâr‡$s zBrain._check_hemicCsX|dkr&|jdkrddg}qT|jg}n.|dkrN|jdkrrQr}r‡rr rXrYrárárárârA6sä5ú * ~ "      ?1>Q 3A Y A  A     % ù t  oþ (2þ Zþ Gÿ : ÿ + ÿ qþS 6 <   H2      þ þ )þ 5-"   rAr)r^FcsBddlm}ˆjˆdkr,‡‡fdd„}|S||ˆ|ˆ|dSdS)z5Work around interp1d not liking singleton dimensions.r)Úinterp1drcs tjˆt t |¡jt¡ˆdS)NrÉ)r–ZtakerŸr~rsrŒ)rg©rÊrÜrárâr»isz_safe_interp1d..funcr+N)Zscipy.interpolaterbrs)rgrÜr®rÊr,rbr»rárcrâr/es  r/cCsÈ|dkrF|dkr&|jdkr"| ¡nd}|dkrz|jdkr@| ¡nd}n4|dkrRd}|dkrz|jdkrvt ||¡ ¡nd}|dkrŽ||d}||kr¦td||fƒ‚||kr¾td||fƒ‚|||fS)Nrrrìz%min must be < mid, got %0.4g >= %0.4gz%mid must be < max, got %0.4g >= %0.4g)rqr[rîr–rÚrÁ)rùrúrûr1rárárárâr€ps(  ÿÿr€cCsÈ|dk rl||d<|d|kr>t d|d›d|›¡||d<|d|krlt d|d›d|›¡||d<|d|dkrŒ|dks’nt‚|dk rþ||d<|d|krÐt d|d›d|›¡||d<|d|krþt d|d›d|›¡||d<|d|dkr"|dks(nt‚|dk rš||d<|d|krjt d|d›d|›¡||d<|d|kršt d|d›d|›¡||d<|d|dkr¾|dksÄnt‚dS)Nrùrûz Bumping fmax = z to rúz Bumping fmid = z Bumping fmin = )r4r»r‰)r#rùrúrûrárárârˆs6  &  * rcCs.t t t|j ¡ƒ¡¡}t |¡t |¡gSrƒ)r–rÚrÑr¨r0rÒr[rî)rqrÚrárárâr–¦sr–c@sDeZdZdd„Zdd„Zdd„Zdd„Zd d „Zd d „Zd d„Z dS)r;cCsdSrƒrárCrárárâÚ EnterEvent¬sz_FakeIren.EnterEventcCsdSrƒrárCrárárâÚMouseMoveEvent¯sz_FakeIren.MouseMoveEventcCsdSrƒrárCrárárâÚ LeaveEvent²sz_FakeIren.LeaveEventcOsdSrƒrá©rÒr"r‰rárárâÚSetEventInformationµsz_FakeIren.SetEventInformationcCsdSrƒrárCrárárâÚ CharEvent¸sz_FakeIren.CharEventcOsdSrƒrárgrárárâÚ KeyPressEvent»sz_FakeIren.KeyPressEventcOsdSrƒrárgrárárâÚKeyReleaseEvent¾sz_FakeIren.KeyReleaseEventN) rZr[r\rdrerfrhrirjrkrárárárâr;«sr;)r)r^F)_r`Ú functoolsrÚiorr¬Úos.pathr­r²r›r rJrÀr¯Únumpyr–rjrrVrrÿrrrrr r r r r ÚutilsrrrrrrrarrrrrrZ _3d_overlayrÚdefaultsrrÚfixesrr Z _freesurferr!r"r#r$r%r&Zio.pickr'Z io.meas_infor(r)r*r+r,Z source_spacer-Z transformsr.r/r0r1r2r3r4r5r6r7r8r9r:r;r<r=r>r?rÚobjectrAr/r€rr–r;rárárárâÚ s|            <J