U f»{j„Z"d?d@„Z#dAdB„Z$dCdD„Z%dEdF„Z&dGdH„Z'‡fdIdJ„Z(‡Z)S)VÚIntracranialElectrodeLocatorz:Locate electrode contacts using a coregistered MRI and CT.NTc sH|jstdƒ‚|ˆ_tˆjdddˆ_|ˆ_dˆ_ttdƒˆ_ dˆ_ t |dd ƒdˆ_ t ˆj ƒˆ_‡fd d „t|j|d ƒDƒˆ_tˆj ¡ƒˆ_ˆ |¡ttˆƒj|||d t ˆjˆjˆj ¡ ¡sìˆjˆjˆjˆj ddˆ ¡tƒˆ_tƒˆ_t ˆj! "¡ƒD]} ˆ #| ¡qˆ $¡ˆj% &¡|rDˆ '¡dS)aGUI for locating intracranial electrodes. .. note:: Images will be displayed using orientation information obtained from the image header. Images will be resampled to dimensions [256, 256, 256] for display. z%No channels found in `info` to locateFT)ZmegZseegçà?édrÚheadÚmrics.i|]&\}}|tˆj|ddd…ƒd“qS)ÚlocNééè)rÚ _head_mri_t)Ú.0ÚnameÚchr3r7r8Ú Xsÿz9IntracranialElectrodeLocator.__init__..Úchs)Z base_imageÚsubjectÚ subjects_dir)Z update_plotsN)(Úch_namesÚ ValueErrorÚ_inforÚ _seeg_idxZ_verboseÚ _ch_alphaÚintÚ _CH_PLOT_SIZEÚ_radiusÚ _ch_indexrrFrÚ _mri_head_tÚzipÚ_chsÚlistÚkeysÚ _ch_namesÚ_group_channelsr1r>Ú__init__ÚnpÚisnanÚanyÚ_set_rasÚ_plot_ch_imagesÚdictÚ_linesÚ _lines_2DÚsetÚ_groupsÚvaluesÚ _update_linesÚ_move_cursors_to_posÚ_ch_listÚsetFocusÚshow) r4ÚinfoZtransZ aligned_ctrLrMÚgroupsrnrÚgroupr5r3r8r^>sB  ÿ  ÿÿ z%IntracranialElectrodeLocator.__init__cCsª|j|_|jd|jd<d|_| ¡}| ¡}| ¡}| ¡|_t ƒ}|  |j ¡|  |j¡t ƒ}|  |¡|  |¡|  |¡|  |¡tƒ}| |¡| |¡dS)NÚbaseÚct)Z _base_dataÚ_ct_dataÚ_imagesÚ _ct_maximaÚ_configure_toolbarÚ_configure_slidersÚ_configure_status_barÚ_configure_channel_sidebarrlrÚ addLayoutZ _plt_gridÚ addWidgetrr Z setLayoutZsetCentralWidget)r4ZtoolbarZ slider_barZ status_barZ plot_layoutZ main_vboxZcentral_widgetr7r7r8Ú _configure_uivs$        z*IntracranialElectrodeLocator._configure_uicCs´tƒ}| tj¡tdd„|jDƒƒ}| |t¡| |t¡t   |¡|_ |j D]"}|j   t  |¡¡|j|dqT| |j ¡|j |j¡| |j  |jd¡¡|j|_|S)z2Configure the sidebar to select channels/contacts.cSsg|] }t|ƒ‘qSr7)Úlen)rGrHr7r7r8Ú “szKIntracranialElectrodeLocator._configure_channel_sidebar..)rHr)r ZsetSelectionModer ZSingleSelectionÚmaxrYZsetMinimumWidthÚ_CH_MENU_WIDTHÚsetMaximumWidthrZQStandardItemModelÚ_ch_list_modelr\Z appendRowZ QStandardItemÚ_color_list_itemZsetModelr/ÚconnectÚ _go_to_chÚsetCurrentIndexÚindexrVÚ_key_press_eventÚ keyPressEvent)r4Zch_listZmax_ch_name_lenrHr7r7r8rzs     ÿz7IntracranialElectrodeLocator._configure_channel_sidebarFcCsÎt ttf¡tj}|j}dd„}|j ¡D]œ\}}t |¡ ¡rDq,t |j |ƒ}tj   ||j ¡} |sp| |jkr,|j|} |r„|jn|jt t| ƒ¡ t¡} ||t|j|ƒ\} } ||| | | | ƒ}q,|S)z-Make a plot to display the channel locations.c SsŠt t ||g¡t¡ t¡\}}t | |d¡}||}t ||dd…tjf||k¡} ||||| d ||| df<|S)Nrr) r_ÚroundÚarrayrTÚastyperSZarangeÚwhereZnewaxis) Úch_imageÚxfÚyfrqÚradiusÚexZeyÚiiZii_sqÚidxr7r7r8Úcolor_ch_radius§s "$&zDIntracranialElectrodeLocator._make_ch_image..color_ch_radius)r_ZzerosrTÚnanÚ _voxel_sizesrYÚitemsr`rarÚ _ras_vox_tÚlinalgÚnormÚ_current_slicerUrhr‹ÚabsrrSrZÚ_xy_idx)r4ÚaxisÚprojrZvxyzr–rHÚrasÚxyzÚdistrqÚrrr‘r7r7r8Ú_make_ch_image¡s     ÿz+IntracranialElectrodeLocator._make_ch_imagec Cs|t d¡|dkr|j}| ¡Rt|j|dƒD]:\}}|d ¡}t|j|j |dƒ|dd…<||d<q2W5QRXdS)z,Save the location of the electrode contacts.z"Saving channel positions to `info`NrKrCrErD) rrorPZ_unlockrXrNÚcopyrrWrY)r4rorrHrIrCr7r7r8Ú_save_ch_coordsÃs    ÿ z,IntracranialElectrodeLocator._save_ch_coordsc sÄd‰t‡‡fdd„tdƒDƒƒ}t‡fdd„tˆj|ƒDƒƒˆ_tƒˆjd<tdƒD]L}ˆj|}|jd}ˆjd |j ˆ  |¡dˆj|dt ˆj dt d ¡qTtƒˆ_ˆjD]}ˆ |¡q°dS) Nr?c3s |]}ˆˆj|tVqdS©N)r˜rT)rGr”©Z img_deltar4r7r8Ú Òsÿz?IntracranialElectrodeLocator._plot_ch_images..rDc3s>|]6\}}| ˆj|d|| ˆj|d|gVqdS)rrN)r˜)rGr•Zch_deltar3r7r8r«Ôs þÿrKrÚauto©ÚaspectZextentÚzorderÚcmapÚalphaÚvminÚvmax)rZÚrangerXrŸÚ _ch_extentsruÚ_figsÚaxesÚappendÚimshowr¦Ú_CMAPrRÚ _N_COLORSrdÚ_3d_chsrYÚ _plot_3d_ch)r4Z ch_deltasr ZfigZaxrHr7rªr8rcÐs0ÿ  ý     ý  z,IntracranialElectrodeLocator._plot_ch_imagescCs²||jkr$|jjj|j |¡ddtt |j|¡ƒs |jj t |j|ƒdt |j |ƒdd…|j dd|j|<|j| |j|¡|j| |jt¡|r®|j ¡dS)zPlot a single 3D channel.F©ÚrenderrNrD)ÚscaleÚcolorZopacityr)r¼Ú _rendererÚplotterÚ remove_actorÚpoprar_r`rYZsphereÚtuplerºrhrRÚ SetOriginÚSetScalerUÚ_RADIUS_SCALARÚ_update)r4rHr¿r7r7r8r½äs$  ÿ þþ z(IntracranialElectrodeLocator._plot_3d_chc Cs´tƒ}tdƒ}|j |j¡| |¡| d¡| tdƒ¡tdƒ|_|j  d¡| |j¡|jj |j ¡|  ¡| d¡tdƒ|_ |j j |j ¡| |j ¡| d¡tdƒ}| |¡|j |j ¡td ƒ}| |¡|j |j¡tƒ|_|j ¡}ttƒD]n}|j d ¡t ¡}|jd t t|ƒ¡ ¡ t¡Žt |¡}| t j!j"¡| #| $|d ¡|t j!j%¡q |jj& |j'¡|jj( |j'¡| |j¡| )¡|S) z.Make a bar with buttons for user interactions.ÚHelpézSnap to CenterÚOfférú Show BrainZMarkZRemoveú éÿr)*rrÚreleasedr…Ú _show_helpr|Ú addStretchr Ú _snap_buttonr‚Ú _toggle_snapÚ_toggle_brain_buttonÚ_toggle_show_brainÚ_mark_chÚ _remove_chr.Ú_group_selectorÚmodelr´r»ZaddItemrÚQColorÚsetRgbr_rŒrºr‹rrSÚQBrushÚsetStylerÚQtÚ SolidPatternÚsetDatarˆÚBackgroundRoler/Ú _select_groupZcurrentIndexChangedÚ _update_group) r4ÚhboxZ help_buttonZ mark_buttonZ remove_buttonZ group_modelÚirÁÚbrushr7r7r8rwôsR              " ÿÿ z/IntracranialElectrodeLocator._configure_toolbarc sHdd„}d ‡fdd„ }tƒ}tƒ}| |dƒ¡| |dƒ¡| |¡tƒ}|dd ˆjd ˆjƒˆ_td }| ˆj¡|d|ˆjˆj ƒˆ_ | ˆj ¡| |¡tƒ}| |d ƒ¡| |d ƒ¡| |¡tƒ}t t t  ˆj¡ƒƒ} t t t  ˆj¡ƒƒ} || | | ˆjƒˆ_| ˆj¡|| | | ˆjƒˆ_| ˆj¡| |¡|S)zMake a bar with sliders on it.cSst|ƒ}| tjj¡|Sr©)r Z setAlignmentrráZ AlignCenter)rHÚlabelr7r7r8Ú make_label-szCIntracranialElectrodeLocator._configure_sliders..make_labelNcslttjjƒ}| tt|ƒƒ¡| tt|ƒƒ¡| tt|ƒƒ¡|  d¡|dk r`|j   |¡ˆj |_ |S)NF)rrráZ HorizontalZ setMinimumrSr‹Z setMaximumÚsetValueZ setTrackingZ valueChangedr…r‰rŠ)ZsminZsmaxZsvalZsfunZsliderr3r7r8Ú make_slider2s   zDIntracranialElectrodeLocator._configure_sliders..make_sliderzch alphaz ch radiusrr@é2zCT minzCT max)N)rrr|r{rRÚ_update_ch_alphaÚ _alpha_sliderrTrUÚ_update_radiusÚ_radius_sliderrSr‹r_ÚnanminrtÚnanmaxÚ_update_ct_scaleÚ_ct_min_sliderÚ_ct_max_slider) r4rëríZ slider_hboxZch_vboxZch_slider_vboxZ ch_plot_maxZct_vboxZct_slider_vboxÚct_minÚct_maxr7r3r8rx*sR  ÿ  ÿ   ÿ ÿ  z/IntracranialElectrodeLocator._configure_sliderscs”|dkrtƒn|}| d¡tdƒ|_|jj |j¡| |j¡tdƒ|_|jj |j ¡| |j¡t dƒ|_ | |j ¡t t |ƒj|d|S)NrDúShow Max Intensity Projú Show MaximaÚ)rç)rrÔrÚ_toggle_show_mip_buttonrÒr…Ú_toggle_show_mipr|Ú_toggle_show_max_buttonÚ_toggle_show_maxr Z_intensity_labelr1r>ry)r4rçr5r7r8ry_s$  ÿ  ÿ    ÿz2IntracranialElectrodeLocator._configure_status_barcstt|ƒ ¡|j ¡dSr©)r1r>rkrlrmr3r5r7r8rkvsz1IntracranialElectrodeLocator._move_cursors_to_poscCs¶|dk rN|jD]6}||kr(t|›dƒ‚t||ttfd|›dƒq||_ndd}tƒ|_tƒ}|jD]J}d dd„|Dƒ¡}||kr–|||j|<qf||j|<|||<|d 7}qfdS) z.r) r\rOrÚfloatrSrprdrhÚjoin)r4rprHrèZ base_namesÚ base_namer7r7r8r]zs    z,IntracranialElectrodeLocator._group_channelsc söˆˆjkr.ˆjˆD] }| ¡qˆj ˆ¡|rFˆj ¡dkrhdSn"ˆˆjkrhˆjjjˆjˆddt   ‡‡fdd„t ˆj ƒDƒ¡}t |ƒdkr˜dSt  t jj|t   dd dg¡dd ¡}t  t jj|||dd ¡}||||}|t j |¡}|sFˆjj||g|||tgˆjttˆƒdd …d d ˆjˆ<ˆj ¡dkròtˆj||ƒ}tˆj|||tƒ} tƒ} td ƒD]Z} ˆj| \} } |  ˆj| jd j|| | | g|| | | gtˆƒdddd ¡qŒ| ˆjˆ<dS)z.Draw lines that connect the points in a group.rúNFr¾csFg|]>\}}ˆj|ˆkr|ˆjkrt ˆj|¡ ¡sˆj|‘qSr7)rhrQr_r`rYra)rGrèrI©rqr4r7r8rŸs  þz>IntracranialElectrodeLocator._update_lines..rrr,©r rD)r’rÁrúHide Max Intensity ProjçÐ?é)rÁZ linewidthr¯)rfÚremoverÅrýÚtextrerÂrÃrÄr_rŒÚ enumerater\r~Zargmaxr›rœZtubeÚ _BOLT_SCALARrUÚ _TUBE_SCALARrºrršrZr´rŸr¸r¶r·Zplot)r4rqÚonly_2DÚlineÚposZ insert_idxZ target_idxZelec_vZ target_voxZ insert_voxZlines_2Dr ÚxÚyr7rr8rj’sh   ÿ ÿÿ ÿþþ ÿ ýý z*IntracranialElectrodeLocator._update_linescCs:|j ¡}||j|j|j<| |j|j¡| ¡dS)z(Change the group label to the selection.N)rÛÚ currentIndexrhr\rVr„ræ)r4rqr7r7r8råÀs z*IntracranialElectrodeLocator._select_groupcCsF|j ¡}dt t|ƒ¡ ¡ t¡}|j dj |Ž¡|j  ¡dS)z%Set background for closed group menu.rÑz%background-color: rgb({:d},{:d},{:d})N) rÛrr_rŒrºr‹rrSÚ setStyleSheetÚformatÚupdate)r4rqÚrgbr7r7r8ræÈs  ÿz*IntracranialElectrodeLocator._update_groupcCsz|j|j}|j |j |jd¡¡|j |j|¡| ¡t   |j |¡  ¡sv|  |j |¡|jdd| ¡dS)z!Update which channel is selected.rTr¾N)r\rVrlr‡rƒrˆrÛrhrær_r`rYrarbZ_update_cameraÚ_draw©r4rHr7r7r8Ú_update_ch_selectionÐs ÿ z1IntracranialElectrodeLocator._update_ch_selectioncCs| ¡|_| ¡dS)z,Change current channel to the item selected.N)ÚrowrVr)r4rˆr7r7r8r†Üs z&IntracranialElectrodeLocator._go_to_chcCs"|jdt|jƒ|_| ¡dS)z.Increment the current channel selection index.rN)rVr~r\rr3r7r7r8Ú_next_chász%IntracranialElectrodeLocator._next_chcCsâ|dkr|j|jn|}t d¡}t |j|¡ ¡sX|j|}|j dd„t |ƒDƒŽt  |¡}|  t jj¡|j |j |j |¡d¡|t jj¡t d¡}t  |¡}|  t jj¡|j |j |j |¡d¡|t jj¡dS)z?Color the item in the view list for easy id of marked channels.NÚwhitecSsg|]}t|dƒ‘qS)rÑ)rS)rGÚcr7r7r8ríszAIntracranialElectrodeLocator._color_list_item..rÚblack)r\rVrrÝr_r`rYrarhrÞrºrßràrrárârƒrãrˆräZForegroundRole)r4rHrÁrqrér7r7r8r„çs(   þ  þz-IntracranialElectrodeLocator._color_list_itemcCsD|j ¡dkr(|j d¡|j d¡n|j d¡|j d¡dS)z;Toggle snapping the contact location to the center of mass.rÍZOnzbackground-color: greenzbackground-color: redN)rÕr ÚsetTextrr3r7r7r8rÖûs   z)IntracranialElectrodeLocator._toggle_snapcCsð|j|j}|j ¡dkr0|j|j|dd…<npt |jj ¡}t dtj ||j t dƒ}t|j|jd|dd}t|jt t|ƒ¡jdd ƒ|j|dd…<| ¡| |j|¡|jdd |j|dd | ¡| ¡|j ¡dS) z;Mark the current channel as being located at the crosshair.rÍNgUUUUUUõ?rDr?T)ZthreshÚ voxels_maxZ use_relativerr©Údrawr¾)r\rVrÕr Z_rasrYr_ZmeanÚ _mri_dataÚshaperSÚpirUrTrÚ_voxrtrZ _vox_ras_trŒrZr„rjrhÚ_update_ch_imagesr½r¨rrlrm)r4rHr(r$Z neighborsr7r7r8rÙs2 ÿþÿ z%IntracranialElectrodeLocator._mark_chcCsp|j|j}|j|tj9<| ¡| ¡| |j|¡|j dd|j |dd|  ¡|j   ¡dS)z1Remove the location data for the current channel.Tr%r¾N)r\rVrYr_r—r„r¨rjrhr+r½rrlrmrr7r7r8rÚs  z'IntracranialElectrodeLocator._remove_chcCst|dkrtdƒn|gD]X}|jd| | |¡¡|j ¡dkr`|jd| |j|dd¡|r| |¡qdS)zUpdate the channel image(s).NrDrKr Úmip_chsT©r¡)r´ruÚset_datar¦rýr r©r4r r&r7r7r8r+)sÿÿ ÿz.IntracranialElectrodeLocator._update_ch_imagescCs¼|dkrtdƒn|gD] }tj|j|j||dj}tj|||j ¡k<tj|||j  ¡k<|j d|  |¡d|j kr¨tj|j |j||dj}|j d|  |¡|r|  |¡qdS)úUpdate the CT image(s).NrDrrsÚ local_max)r´r_ÚtakertrÚTr—röÚvaluer÷rur.rvr)r4r r&Zct_dataÚ ct_max_datar7r7r8Ú_update_ct_images5s ÿ ÿz.IntracranialElectrodeLocator._update_ct_imagescCsbd|jkr^|dkrtdƒn|gD]<}|jd| tj|j|j||dj¡|r | |¡q dS)r0rBNrDr) rur´r.r_r2r'rr3rr/r7r7r8Ú_update_mri_imagesEs ÿÿz/IntracranialElectrodeLocator._update_mri_imagescs&|j|d|j|dtƒ ¡dS)z9Update CT and channel images when general changes happen.rN)r+r7r1Ú_update_imagesr/r5r7r8r8Os  z+IntracranialElectrodeLocator._update_imagescCsL|j ¡}|j ¡}|j t||gƒ¡|j t||gƒ¡|jdddS)zUpdate CT min slider value.Tr%N)rör4r÷rìÚminr€r6)r4Znew_minZnew_maxr7r7r8rõUs   z-IntracranialElectrodeLocator._update_ct_scalecCsªt |j ¡¡ t¡|_|j ¡dkr8|  ¡|  ¡nd|_ |j dd|j  ¡D]<\}}t |j|¡ ¡sT| |j|¡| |jt¡qT|j ¡|j ¡dS)zUpdate channel plot radius.ú Hide MaximaNTr%)r_r‹ròr4rrSrUrÿr Ú_update_ct_maximar6rvr+r¼r™r`rYrarÇrÈrÉrÂrÊrlrm)r4rHÚactorr7r7r8rñ^s   z+IntracranialElectrodeLocator._update_radiuscCst|j ¡d|_tdƒD]}|jd| |j¡q| ¡|j ¡D]}|  ¡  |j¡qF|j   ¡|j  ¡dS)zUpdate channel plot alpha.r@rDrKN)rðr4rRr´ruZ set_alpharr¼riZ GetPropertyZ SetOpacityrÂrÊrlrm)r4r r<r7r7r8rïns  z-IntracranialElectrodeLocator._update_ch_alphacCst |dd¡dS)zShow the help menu.rËzçHelp: 'm': mark channel location 'r': remove channel location 'b': toggle viewing of brain in T1 '+'/'-': zoom left/right arrow: left/right up/down arrow: superior/inferior left angle bracket/right angle bracket: anterior/posteriorN)r Ú informationr3r7r7r8rÓys þz'IntracranialElectrodeLocator._show_helpcCsLt|j|jfdƒ|jk|_d|j|jt |j¡k<t |jdtj¡|_dS)z7Compute the maximum voxels based on the current radius.rDFrN)rrtrUrvr_ZmedianrŽr—r3r7r7r8r;„s ÿÿÿz.IntracranialElectrodeLocator._update_ct_maximac Csð|j ¡dkrx|j d¡tƒ|jd<tƒ|jd<t |j¡t |j¡}}t dƒD]ú}tj |j|dj }|jd  |j |jdj|dd ||d d ¡tƒtƒtƒ}}}|j ¡D]R\}} |j} |  | |j|d¡|  | |j|d ¡|  t|j|ƒ¡qº|jd  |j |jdj|j|d dd |j|dtd dtd¡qVt|j ¡ƒD]} |j| d dq`nl|jd|jdD]} |  ¡qŒ|j d¡|j d¡|j d¡t|j ¡ƒD]} |j| d dqÎ| ¡dS)z9Toggle whether the maximum-intensity projection is shown.rúr Zmipr,rDrrÚgrayr¬é©r°r®r²r³r¯rTr-ér­)rN)rýr r#rZrur_rórtrôr´r€r3r¸r¶r·r¹rYr™r*rŸrºrhr¦rµr»rgrirjr rÅr) r4rørùr Z ct_mip_dataZxsZysÚcolorsrHr¢r£rqÚimgr7r7r8rþŒsZ     þÿ  ýÿ    z-IntracranialElectrodeLocator._toggle_show_mipc CsÌ|j ¡dkr|j d¡|jdkr,| ¡tƒ|jd<tdƒD]L}tj |j|j ||dj }|jd  |j |jdj|dd dd d d ¡q@n0|jdD] }| ¡qš|j d¡|j d¡| ¡dS) z1Toggle whether to color local maxima differently.rûr:Nr1rDrrÚautumnr¬rér@)rÿr r#rvr;rZrur´r_r2rr3r¸r¶r·r¹r rÅr)r4r r5rCr7r7r8r±s2    ÿ þÿ   z-IntracranialElectrodeLocator._toggle_show_maxc Cs´d|jkr<|jdD] }| ¡q|j d¡|j d¡nltƒ|jd<tdƒD]J}tj|j |j ||dj }|jd  |j |jdj|dddd d ¡qP|j d ¡| ¡d S) z,Toggle whether the brain/MRI is being shown.rBrÏrDrrZhotr¬r r)r°r®r±r¯z Hide BrainN)rur rÅr×r#rZr´r_r2r'rr3r¸r¶r·r¹r)r4rCr Zmri_datar7r7r8rØÇs(     ÿÿ  z/IntracranialElectrodeLocator._toggle_show_braincsPtt|ƒ |¡| ¡dkr$| ¡| ¡dkr8| ¡| ¡dkrL| ¡dS)z.Execute functions when the user presses a key.Úmr¥ÚbN)r1r>r‰r rÙrÚrØ)r4Úeventr5r7r8r‰Øs   z-IntracranialElectrodeLocator._key_press_event)NNNTN)F)NN)F)N)F)N)NF)NF)NF)NT)*r9r:r;r<r^r}rzr¦rr¨rcr½rwrxryrkr]rjrårærr†rrr„rÖrÙrÚr+r6r7r8rõrñrïrÓr;rþrrØr‰r=r7r7r5r8r>;s\ÿ8 "  65  .          %r>)4r<Únumpyr_ÚplatformZ scipy.ndimagerZqtpyrrZ qtpy.QtCorerrZqtpy.QtWidgetsrrr r r r r rrrZmatplotlib.colorsrZ_corerZsurfacerZ transformsrrrÚutilsrrrrürrTrÉrrÚsystemrZ_UNIQUE_COLORSr~r»Ú from_listrºr.r>r7r7r7r8ÚsX 0    úÿ