U f{j@stddlZddlmZddlmZddlmZddlZ ddl m Z m Z ddl mZmZmZddlmZddlmZdd lmZmZmZmZmZmZmZd d lmZGd d d eZ ddZ!ddZ"dddZ%ed?ddZ&eddZ'd@d!d"Z(edAd#d$Z)ed%d&Z*d'd(Z+edBd)d*Z,d+d,Z-d-d.Z.dCd0d1Z/dDd2d3Z0d4d5Z1dEd:d;Z2dS)FN) defaultdict) combinations) _pol_to_cart _cart_to_sph) pick_types _picks_to_idx_FNIRS_CH_TYPES_SPLIT)FIFF)Info) _clean_nameswarn_check_ch_locsfill_doc _check_option _check_spherelogger) _get_ch_infoc@s6eZdZdZddZddZddZed d d ZdS)LayoutaASensor layouts. Layouts are typically loaded from a file using :func:`~mne.channels.read_layout`. Only use this class directly if you're constructing a new layout. Parameters ---------- box : tuple of length 4 The box dimension (x_min, x_max, y_min, y_max). pos : array, shape=(n_channels, 4) The unit-normalized positions of the channels in 2d (x, y, width, height). names : list The channel names. ids : list The channel ids. kind : str The type of Layout (e.g. 'Vectorview-all'). cCs"||_||_||_||_||_dS)N)boxposnamesidskind)selfrrrrrrR/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/channels/layout.py__init__2s zLayout.__init__c Cs|jdddf}|jdddf}|jdddf}|jdddf}|dr^d|j}n|drnd }ntd t|jdD]8}|d |j||||||||||j|f7}qt|d }| || dS) zSave Layout to disk. Parameters ---------- fname : str The file name (e.g. 'my_layout.lout'). See Also -------- read_layout Nrrr.loutz%8.2f %8.2f %8.2f %8.2f .lay5Unknown layout type. Should be of type .lout or .lay.z %03d %8.2f %8.2f %8.2f %8.2f %s w) rendswithr ValueErrorrangeshaperropenwriteclose) rfnamexywidthheightZout_striifrrrsave9s(      z Layout.savecCsd|jd|jddfS)z!Return the string representation.z , Nr)rjoinr)rrrr__repr__ZszLayout.__repr__NFTcCsddlm}|||||dS)aPlot the sensor positions. Parameters ---------- %(picks_nostr)s show_axes : bool Show layout axes if True. Defaults to False. show : bool Show figure if True. Defaults to True. Returns ------- fig : instance of matplotlib.figure.Figure Figure containing the sensor topography. Notes ----- .. versionadded:: 0.12.0 r) plot_layout)picks show_axesshow)Z viz.topomapr7)rr8r9r:r7rrrplot_s z Layout.plot)NFT) __name__ __module__ __qualname____doc__rr3r6rr;rrrrrs !rc Cst|}|}ttt|}ggg}}}|D]~}|}t|dkrp|\} } } } } }}|d|}n|\} } } } } }|tj | | | | gtj d|||t | q8W5QRXt |}||||fS) Aux function. Zdtype) r)readlinetuplemapfloatsplitlenappendnparrayfloat64int)r,r2Zbox_linerrrrlinesplitscidr-r.dxdychkindnbnamerrr _read_loutxs    rWc Cst|}d}ggg}}}|D]~}|}t|dkrZ|\}} } } } } }| d|}n|\}} } } } }|tj| | | | gtjd|||t|q"W5QRXt|}||||fS)r@NrArBrC)r)rHrIrJrKrLrMrN)r,r2rrrrrOrPrQr-r.rRrSrTrUrVrrr _read_lays    rXTc Cs|dkrtttdd}|dsFtt||drF|d7}n(|dsntt||drn|d7}|drt||}|dd}t|\}}}}nF|drt||}|dd}t|\}}}}|dntd|r|ddd ft |ddd f8<|ddd ft |ddd f8<t t |ddd ft |ddd f|d }||}|dddd fd 7<|dddd fd9<|ddd dfd9<t |||||dS)aRead layout from a file. Parameters ---------- kind : str The name of the .lout file (e.g. kind='Vectorview-all' for 'Vectorview-all.lout'). path : str | None The path of the folder containing the Layout file. Defaults to the mne/channels/data/layouts folder inside your mne-python installation. scale : bool Apply useful scaling for out the box plotting using layout.pos. Defaults to True. Returns ------- layout : instance of Layout The layout. See Also -------- Layout.save Notes ----- Valid ``kind`` arguments are: .. table:: :widths: auto +----------------------+ | Kind | +======================+ | biosemi | +----------------------+ | CTF151 | +----------------------+ | CTF275 | +----------------------+ | CTF-275 | +----------------------+ | EEG1005 | +----------------------+ | EGI256 | +----------------------+ | GeodesicHeadWeb-130 | +----------------------+ | GeodesicHeadWeb-280 | +----------------------+ | KIT-125 | +----------------------+ | KIT-157 | +----------------------+ | KIT-160 | +----------------------+ | KIT-AD | +----------------------+ | KIT-AS-2008 | +----------------------+ | KIT-UMD-3 | +----------------------+ | magnesWH3600 | +----------------------+ | Neuromag_122 | +----------------------+ | Vectorview-all | +----------------------+ | Vectorview-grad | +----------------------+ | Vectorview-grad_norm | +----------------------+ | Vectorview-mag | +----------------------+ NdataZlayoutsr r!r#rr)rrrgQ?g'J"?gGz?rrrrr) opr5dirname__file__r%existsrWrXr&rKminmaxr) rpathscaler,rrrrscalingrrr read_layouts2M          **6rf?badsFcsd|krdksntd|dk rDd|kr:dksDntd|dk rjd|kr`dksjntdtdd d|d }|r|jd dd tf|}t|}fd d |D} ttj|dd tj|ddd} || }|dks|dkr t |||dd\}}|d|9}tdd|dd|} || 9}|| 9}|| 9}|d7}|j d} tj |dddfd||dddfd||t | |t | f} d}dt | }t|| | d|d}|S)aCreate .lout file from EEG electrode digitization. Parameters ---------- %(info_not_none)s radius : float Viewport radius as a fraction of main figure height. Defaults to 0.5. width : float | None Width of sensor axes as a fraction of main figure height. By default, this will be the maximum width possible without axes overlapping. height : float | None Height of sensor axes as a fraction of main figure height. By default, this will be the maximum height possible without axes overlapping. exclude : list of str | str List of channels to exclude. If empty do not exclude any. If 'bads', exclude channels in info['bads'] (default). csd : bool Whether the channels contain current-source-density-transformed data. Returns ------- layout : Layout The generated Layout. See Also -------- make_grid_layout, generate_2d_layout rrgz1The radius parameter should be between 0 and 0.5.N?z.The width parameter should be between 0 and 1.z/The height parameter should be between 0 and 1.FT)megeegref_megexclude)csdrkcsg|]}d|dqSchsch_namer.0iinforr ;sz#make_eeg_layout..Zaxisr皙?paddingrrrrrZEEGr\)r&dictupdater_find_topomap_coordsrKmaximumrarb _box_sizer(c_onesaranger)rvZradiusr/r0rmrnZ pick_kwargsr8Zloc2drrdreZ n_channelsrrrlayoutrrurmake_eeg_layouts@  *    rcst|d}fdd|D}|s*tdttt|}t|}|dkrt|}}|drvt|dt|}}|||kr|d7}ntt|t |}t t dd|t dd|\}}| d|| d|}}t tj||fd d \} } d \} } dd | | } dd | | }|| }||}| | 9} | |9} |d7}|d7}tj|d| |d| | t|| t|f}d }t|||d|d}|S)aGenerate .lout file for custom data, i.e., ICA sources. Parameters ---------- %(info_not_none)s %(picks_base)s all good misc channels. n_col : int | None Number of columns to generate. If None, a square grid will be produced. Returns ------- layout : Layout The generated layout. See Also -------- make_eeg_layout, generate_2d_layout misccsg|]}d|dqSror)rskrurrrwvsz$make_grid_layout..zNo misc data channels found.Nrgrgryrz){Gz?rrir|z grid-miscr\)rr&listr'rIrKsqrtrNceilrGZmeshgridZlinspaceZravelrrrr)rvr8Zn_colrrsizeZn_rowr-r.r/r0Zborder_xZborder_yZ x_scalingZ y_scalingrrrrrurmake_grid_layout`sD    " rc sdtd|ddddddgt\ }}}}}}} } } } } }}|o@|}|oJ| }|oT| }|dkrj| sjtd|dkr~| s~td d}|r|dkst||gr|dkrd }n|s|r|dkrd }n|s|r|dkrd d drd}nd}n|rd}n| r|dks| r:|dkr:tttfs.tdtdS|rX|dkrXtddS|rdd}n |rpd}n| d krt | }|dkrt dddd}fdd|D}t |dd }t ||d!dd"St ||stjdd#_|rtjdd$_d%krd%fd&dtjD}fd'd|D_j|_fd(d|D_S))aChoose a layout based on the channels in the info 'chs' field. Parameters ---------- %(info_not_none)s ch_type : {'mag', 'grad', 'meg', 'eeg'} | None The channel type for selecting single channel layouts. Defaults to None. Note, this argument will only be considered for VectorView type layout. Use ``'meg'`` to force using the full layout in situations where the info does only contain one sensor type. exclude : list of str | str List of channels to exclude. If empty do not exclude any. If 'bads', exclude channels in info['bads'] (default). Returns ------- layout : Layout instance | None None if layout not found. ch_typeNmaggradrjrkrnz0No MEG channels present. Cannot find MEG layout.z0No EEG channels present. Cannot find EEG layout.zVectorview-allzVectorview-magch_namesrXzVectorview-grad_normzVectorview-gradZ Neuromag_122)NrkzGCannot make EEG layout, no measurement info was passed to `find_layout`rm)NrnT)rmrnZ magnesWH3600zCTF-275rYrF)rmZ with_ref_megcsg|]}d|qSrr)rspickrurrrwszfind_layout..)r8ignore_overlapZcustom)rrV normalize)Zremove_whitespace)Z before_dashrhcsg|]\}}|kr|qSrr)rsr1rVrrrrwscsg|]}j|qSr)rrsr1rrrrwscsg|]}j|qSr)rrrrrrws)rr RuntimeErroranyr% isinstancer}r r_find_kit_layoutrrgenerate_2d_layoutrfr r enumeraterr)rvrrmZ has_vv_mag has_vv_gradZ is_old_vvZ has_4D_magZctf_other_typesZ has_CTF_gradZ n_kit_gradsZ has_any_megZ has_eeg_coilsZhas_eeg_coils_and_megZhas_eeg_coils_onlyhas_neuromag_122_gradZ has_csd_coilsZ has_vv_megZhas_vv_only_magZhas_vv_only_gradZ layout_namer8rxyidxr)rmrvrr find_layouts             rcs|ddk r&ddlm}||dS|dkr2dS|dkr>dS|d krJd Sd fd d |dD}t|rrdStt|rtdntddS)aDetermine the KIT layout. Parameters ---------- %(info_not_none)s n_grads : int Number of KIT-gradiometers in the info. Returns ------- kit_layout : str | None String naming the detected KIT layout or ``None`` if layout is missing. Z kit_system_idNr) KIT_LAYOUTzKIT-160}zKIT-125zKIT-AD)&zMEG 13zMEG 14zMEG 15zMEG 16zMEG 25zMEG 26zMEG 27zMEG 28zMEG 29zMEG 30zMEG 31zMEG 32zMEG 57zMEG 60zMEG 61zMEG 62zMEG 63zMEG 64zMEG 73zMEG 90zMEG 93zMEG 95zMEG 96zMEG 105zMEG 112zMEG 120zMEG 121zMEG 122zMEG 123zMEG 124zMEG 125zMEG 126zMEG 142zMEG 144zMEG 153zMEG 154zMEG 155zMEG 156cs(g|] }|dkr|dddkqS)rqlocrrrschZtest_chsrrrw$s z$_find_kit_layout..rpzKIT-157zzGuessing sensor layout for legacy UMD files is not implemented. Please convert your files using MNE-Python 0.13 or higher.z+KIT system could not be determined for data)Zio.kit.constantsrgetrKallinvertNotImplementedErrorr)rvZn_gradsrr-rrrrs     rc sfddlm}ddddt|}tt|ddkrdkrt|d krZd d n>t||\}}||||}}||kr|n|dkr||} fd d t| D} t| dkrd nt fd d | DnXdkrF||} fdd t| D} t| dkr.d nt fdd | Dd |9d |9fS)aTGiven a series of points, calculate an appropriate box size. Parameters ---------- points : array, shape (n_points, 2) The centers of the axes as a list of (x, y) coordinate pairs. Normally these are points in the range [0, 1] centered at 0.5. width : float | None An optional box width to enforce. When set, only the box height will be calculated by the function. height : float | None An optional box height to enforce. When set, only the box width will be calculated by the function. padding : float Portion of the box to reserve for padding. The value can range between 0.0 (boxes will touch, default) to 1.0 (boxes consist of only padding). Returns ------- width : float Width of the box height : float Height of the box r)pdistcSst|d|dS)NrrKabsabrrrxdiffKsz_box_size..xdiffcSst|d|dS)NrrrrrrydiffNsz_box_size..ydiffrNrrics g|]\}}|kr|qSrrrsrtd)all_combinationsr/rrrwhsz_box_size..csg|] }|qSrrrsc)rrrrwqscs g|]\}}|kr|qSrrr)rr0rrrwvscsg|] }|qSrrr)rrrrws) scipy.spatial.distancerrKasarrayrrrIZargminrra) Zpointsr/r0r{rrrr$hZhdist candidatesZvdistr)rr0r/rrrr0s:         rcs`t|dddd}dk rJfdd|D}fdd|D}t|}nt||||d }|S) a[Guess the E/MEG layout and return appropriate topomap coordinates. Parameters ---------- %(info_not_none)s picks : str | list | slice | None None will choose all channels. layout : None | instance of Layout Enforce using a specific layout. With None, a new map is generated and a layout is chosen based on the channels in the picks parameter. sphere : array-like | str Definition of the head sphere. Returns ------- coords : array, shape = (n_chs, 2) 2 dimensional coordinates for each sensor for a topomap plot. rrFrmZ allow_emptyNcsg|]}d|qSrprrrrurrrwsz(_find_topomap_coords..cs"g|]}jj|dqSrq)rrindexrrrrrws)r to_spheresphere)rrKr_auto_topomap_coords)rvr8rrrrrprr)rvrrrs rcsVddlm}m}t|}td|t|dddd}fdd |Dtd d D}t |d sTt d D]}|d t j kr~tdq~dd dD} ddkstddkrtdtdd dD}t|dkrtdt jt|t| kr.tdt|t| ftt| |tfdd D}d|t|<||} t|dkrt| dkr|ṡfdd || dkjdddD} tdd| |rF||dd8}t|} t| ddddfddddd f} | | dddgftjd!9} | |dd"7} n tt|} | S)#aMake a 2 dimensional sensor map from sensor positions in an info dict. The default is to use the electrode locations. The fallback option is to attempt using digitization points of kind FIFFV_POINT_EEG. This only works with EEG and requires an equal number of digitization points and sensors. Parameters ---------- %(info_not_none)s picks : list | str | slice | None None will pick all channels. ignore_overlap : bool Whether to ignore overlapping positions in the layout. If False and positions overlap, an error is thrown. to_sphere : bool If True, the radial distance of spherical coordinates is ignored, in effect fitting the xyz-coordinates to a sphere. sphere : array-like | str The head sphere definition. Returns ------- locs : array, shape = (n_sensors, 2) An array of positions of the 2 dimensional map. r)r squareformzGenerating coords using: rrFrcsg|]}d|qSrrrrrurrrwsz(_auto_topomap_coords..cSsg|]}|dddqS)rNrrrrrrrws)rvr8aDid not find any electrode locations (in the info object), will attempt to use digitization points instead. However, if digitization points do not correspond to the EEG electrodes, this will lead to bad results. Please verify that the sensor locations in the plot are accurate.rzLCannot determine location of MEG/EOG/ECG channels using digitization points.cSs"g|]}|dtjkr|dqS)rrq)r FIFFV_EEG_CHrrrrrwsrpdigNzNo digitization points found.cSs"g|]}|dtjkr|dqS)rr)r FIFFV_POINT_EEG)rspointrrrrwszNDid not find any digitization points of kind FIFFV_POINT_EEG (%d) in the info.zTNumber of EEG digitization points (%d) doesn't match the number of EEG channels (%d)csg|]}|dqSrrr) eeg_ch_locsrrrwsrrg|=csg|]}|dqSrr)rsZelec_irrrrwsrxzaThe following electrodes have overlapping positions, which causes problems during visualization: r4r@r)rrrrrdebugrrKrLrloggingwarningr rr&rIrrr}zipisfiniterarZnonzeror5rrpi)rvr8rrrrrZlocs3drZ eeg_ch_namesdistZproblematic_electrodesZ cart_coordsoutr)rprrvrrsT    $ *  rcCst|j\}}tt||d||d}||}||}|dt||7}|dt||7}|dd}|dd}tt|d|ddd}t|}t|}t |||gS)aYTransform xy-coordinates to sphere. Parameters ---------- pos : array-like, shape (n_channels, 2) xy-oordinates to transform. eegs : list of int Indices of EEG channels that are included when calculating the sphere. Returns ------- coords : array, shape (n_channels, 3) xyz-coordinates. rrgrrir) rKrLTrbrmeanZclipZarccossinZ column_stack)rZeegsZxsZysZsqsrsZalphasZzsrrr_topo_to_spheres$     rcsLtt}t|dd|d}t|^}}}} }|D]~} |d| } | d} |rz| drz| drz| dd } || | | r0| dr0t| d d d d } || | q0dd|D}t |dkr|rt dnt dtSt |g}|dfdd|D}|rDt |d d f}t ||||jd d}||fS|Sd S)apFind the picks for pairing grad channels. Parameters ---------- %(info_not_none)s layout : Layout | None The layout if available. Defaults to None. topomap_coords : bool Return the coordinates for a topomap plot along with the picks. If False, only picks are returned. Defaults to True. exclude : list of str | str List of channels to exclude. If empty, do not exclude any. If 'bads', exclude channels in info['bads']. Defaults to 'bads'. raise_error : bool Whether to raise an error when no pairs are found. If False, raises a warning. Returns ------- picks : array of int Picks for the grad channels, ordered in pairs. coords : array, shape = (n_grad_channels, 3) Coordinates for a topomap plot (optional, only returned if topomap_coords == True). rF)rjrlrmrprqMEG23r[rNrrcSsg|]}t|dkr|qSrrIrsprrrrwhs z&_pair_grad_sensors..rzNo 'grad' channel pairs found.rcsg|]}|dqSr)rrrrrrwssrx)rrrr startswithr%rJrNvaluesrIr&r sumrreshaper)rvrZtopomap_coordsrmZ raise_errorpairsZ grad_picks_rrrtrrVkeygrad_chsr8r(Zcoordsrrr_pair_grad_sensors;s>       rcCshtt}t|D]6\}}|dr|dr|dd}|||qdd|D}t|g}|S)a Find the indices for pairing grad channels in a Vectorview system. Parameters ---------- ch_names : list of str A list of channel names. Returns ------- indexes : list of int Indices of the grad channels, ordered in pairs. rrr[rcSsg|]}t|dkr|qSrrrrrrrws z:_pair_grad_sensors_ch_names_vectorview..)rrrrr%rJrrrrrtrVrrrrr&_pair_grad_sensors_ch_names_vectorviews     rcCsjtt}t|D]8\}}|drt|dddd}|||qdd|D}t|g}|S)aFind the indices for pairing grad channels in a Neuromag 122 system. Parameters ---------- ch_names : list of str A list of channel names. Returns ------- indexes : list of int Indices of the grad channels, ordered in pairs. rrNrrcSsg|]}t|dkr|qSrrrrrrrws z;_pair_grad_sensors_ch_names_neuromag122..)rrrrrNrJrrrrrr'_pair_grad_sensors_ch_names_neuromag122s   rrmscCs6|dkrt||}n|tks tt||\}}||fS)aMerge data from channel pairs. Parameters ---------- data : array, shape = (n_channels, ..., n_times) Data for channels, ordered in pairs. ch_type : str Channel type. names : list List of channel names. method : str Can be 'rms' or 'mean'. Returns ------- data : array, shape = (n_channels / 2, ..., n_times) The root mean square or mean for each pair. names : list List of channel names. r)_merge_grad_datar AssertionError_merge_nirs_data)rYrrmethodrrr_merge_ch_datas   rcCs|t|dddf|j}}|dkr8tj|dd}n2|dkr^ttj|dddd}n td|||jdd|ddS) aqMerge data from channel pairs using the RMS or mean. Parameters ---------- data : array, shape = (n_channels, ..., n_times) Data for channels, ordered in pairs. method : str Can be 'rms' or 'mean'. Returns ------- data : array, shape = (n_channels / 2, ..., n_times) The root mean square or mean for each pair. rrrrrxrz'method must be "rms" or "mean", got %s.N)rrIr(rKrrrr&)rYrZ orig_shaperrrrs  rc Cstjdtjd}t|D]x\}}d|krtjdtjd}|d}|ddD]}t|||}qNtj|t||dd||<t||}qt|}t |ddD]}||=t ||d}q||fS) aMerge data from multiple nirs channel using the mean. Channel names that have an x in them will be merged. The first channel in the name is replaced with the mean of all listed channels. The other channels are removed. Parameters ---------- data : array, shape = (n_channels, ..., n_times) Data for channels. merged_names : list List of strings containing the channel names. Channels that are to be merged contain an x between them. Returns ------- data : array Data for channels with requested channels merged. Channels used in the merge are removed from the array. rrCr-rNrxT)reverse) rKemptyZint32rrHrJrruniquesorteddelete) rYZ merged_namesZ to_removerrindiceschannelsZsub_chremrrrrs  rQ?皙?{Gz?ecogc sbddlm} |dkr$t|jd}|dkr:dd|D}t|t|krRtdt|t|krjtd|t j \} |dk rt |t r| |n|} | jd| | jd} n8|r| fD]*} | | d8} | | d| d} qtt| gj |d} dd| d| df} fd d||fD\}}t| ||gj }t| ||||}|S) aGenerate a custom 2D layout from xy points. Generates a 2-D layout for plotting with plot_topo methods and functions. XY points will be normalized between 0 and 1, where normalization extremes will be either the min/max of xy, or the width/height of bg_image. Parameters ---------- xy : ndarray, shape (N, 2) The xy coordinates of sensor locations. w : float The width of each sensor's axis (between 0 and 1). h : float The height of each sensor's axis (between 0 and 1). pad : float Portion of the box to reserve for padding. The value can range between 0.0 (boxes will touch, default) to 1.0 (boxes consist of only padding). ch_names : list The names of each channel. Must be a list of strings, with one string per channel. ch_indices : list Index of each channel - must be a collection of unique integers, one index per channel. name : str The name of this layout type. bg_image : str | ndarray The image over which sensor axes will be plotted. Either a path to an image file, or an array that can be plotted with plt.imshow. If provided, xy points will be normalized by the width/height of this image. If not, xy points will be normalized by their own min/max. normalize : bool Whether to normalize the coordinates to run from 0 to 1. Defaults to True. Returns ------- layout : Layout A Layout object that can be plotted with plot_topo functions and methods. See Also -------- make_eeg_layout, make_grid_layout Notes ----- .. versionadded:: 0.9.0 rNcSsg|]}d|qS)z{})formatrrrrrrwHsz&generate_2d_layout..z)# channel names and indices must be equalz)# channel names and xy vals must be equalrrzcs"g|]}t|gjdqS)r)rKrLr(rrr-rrrw`s)Zmatplotlib.pyplotZpyplotrKrr(rIr&copyZastyperGrrstrZimreadrarbrZvstackr)rr$rpadrZ ch_indicesrVZbg_imagerZpltr.ZimgZi_dimrZ loc_paramsrrr rrs04  r)NT)rgNNrhF)NN)Nrh)NNr)NFTN)NTrhT)r)r)rrrNNrNT)3r collectionsr itertoolsros.pathrcr]numpyrKZ transformsrrZio.pickrrr Z io.constantsr Z io.meas_infor utilsr r rrrrrrrobjectrrWrXrfrrrrrrrrrrrrrrrrrrr s`     $ \ m O F Y . X # m! D  %