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topoplot.m
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% TOPOPLOT - plot a topographic map of a scalp data field in a 2-D circular view
% (looking down at the top of the head) using interpolation on a fine
% cartesian grid. Can also show specified channel location(s), or return
% an interpolated value at an arbitrary scalp location (see 'noplot').
% By default, channel locations below head center (arc_length 0.5) are
% shown in a 'skirt' outside the cartoon head (see 'plotrad' and 'headrad'
% options below). Nose is at top of plot; left is left; right is right.
% Using option 'plotgrid', the plot may be one or more rectangular grids.
% Usage:
% >> topoplot(datavector, EEG.chanlocs); % plot a map using an EEG chanlocs structure
% >> topoplot(datavector, 'my_chan.locs'); % read a channel locations file and plot a map
% >> topoplot('example'); % give an example of an electrode location file
% >> [h grid_or_val plotrad_or_grid, xmesh, ymesh]= ...
% topoplot(datavector, chan_locs, 'Input1','Value1', ...);
% Required Inputs:
% datavector - single vector of channel values. Else, if a vector of selected subset
% (int) channel numbers -> mark their location(s) using 'style' 'blank'.
% chan_locs - name of an EEG electrode position file (>> topoplot example).
% Else, an EEG.chanlocs structure (>> help readlocs or >> topoplot example)
% Optional inputs:
% 'maplimits' - 'absmax' -> scale map colors to +/- the absolute-max (makes green 0);
% 'maxmin' -> scale colors to the data range (makes green mid-range);
% [lo.hi] -> use user-definined lo/hi limits
% {default: 'absmax'}
% 'style' - 'map' -> plot colored map only
% 'contour' -> plot contour lines only
% 'both' -> plot both colored map and contour lines
% 'fill' -> plot constant color between contour lines
% 'blank' -> plot electrode locations only {default: 'both'}
% 'electrodes' - 'on','off','labels','numbers','ptslabels','ptsnumbers'. To set the 'pts'
% marker,,see 'Plot detail options' below. {default: 'on' -> mark electrode
% locations with points ('.') unless more than 64 channels, then 'off'}.
% 'plotchans' - [vector] channel numbers (indices) to use in making the head plot.
% {default: [] -> plot all chans}
% 'plotgrid' - [channels] Plot channel data in one or more rectangular grids, as
% specified by [channels], a position matrix of channel numbers defining
% the topographic locations of the channels in the
% grid. Zero values are ignored (given the figure background color);
% negative integers, the color of the polarity-reversed channel values.
% Ex: >> figure; ...
% >> topoplot(values,'chanlocs','plotgrid',[11 12 0; 13 14 15]);
% % Plot a (2,3) grid of data values from channels 11-15 with one empty
% grid cell (top right) {default: no grid plot}
% 'nosedir' - ['+X'|'-X'|'+Y'|'-Y'] direction of nose {default: '+X'}
% 'chaninfo' - [struct] optional structure containing fields 'nosedir', 'plotrad'.
% See these (separate) field definitions above, below.
% {default: nosedir +X, plotrad 0.5, all channels}
% 'plotrad' - [0.15<=float<=1.0] plotting radius = max channel arc_length to plot.
% See >> topoplot example. If plotrad > 0.5, chans with arc_length > 0.5
% (i.e. below ears-eyes) are plotted in a circular 'skirt' outside the
% cartoon head. See 'intrad' below. {default: max(max(chanlocs.radius),0.5);
% If the chanlocs structure includes a field chanlocs.plotrad, its value
% is used by default}.
% 'headrad' - [0.15<=float<=1.0] drawing radius (arc_length) for the cartoon head.
% NOTE: Only headrad = 0.5 is anatomically correct! 0 -> don't draw head;
% 'rim' -> show cartoon head at outer edge of the plot {default: 0.5}
% 'intrad' - [0.15<=float<=1.0] radius of the scalp map interpolation area (square or
% disk, see 'intsquare' below). Interpolate electrodes in this area and use
% this limit to define boundaries of the scalp map interpolated data matrix
% {default: max channel location radius}
% 'intsquare' - ['on'|'off'] 'on' -> Interpolate values at electrodes located in the whole
% square containing the (radius intrad) interpolation disk; 'off' -> Interpolate
% values from electrodes shown in the interpolation disk only {default: 'on'}.
% 'conv' - ['on'|'off'] Show map interpolation only out to the convext hull of
% the electrode locations to minimize extrapolation. Use this option ['on'] when
% plotting pvalues {default: 'off'}. When plotting pvalues in totoplot, set
% 'conv' option to 'on' to minimize interpolation effects
% 'noplot' - ['on'|'off'|[rad theta]] do not plot (but return interpolated data).
% Else, if [rad theta] are coordinates of a (possibly missing) channel,
% returns interpolated value for channel location. For more info,
% see >> topoplot 'example' {default: 'off'}
% 'verbose' - ['on'|'off'] comment on operations on command line {default: 'on'}.
% 'chantype' - deprecated
%
% Plot detail options:
% 'drawaxis' - ['on'|'off'] draw axis on the top left corner.
% 'emarker' - Matlab marker char | {markerchar color size linewidth} char, else cell array
% specifying the electrode 'pts' marker. Ex: {'s','r',32,1} -> 32-point solid
% red square. {default: {'.','k',[],1} where marker size ([]) depends on the number
% of channels plotted}.
% 'emarker2' - {markchans}|{markchans marker color size linewidth} cell array specifying
% an alternate marker for specified 'plotchans'. Ex: {[3 17],'s','g'}
% {default: none, or if {markchans} only are specified, then {markchans,'o','r',10,1}}
% 'scatter' - ['on'|'off'] use scatter3 function instead of plot3 function toplot the electrode location. This
% helps with controlling over the individual size and color of the electrodes.
% If on, you can use {markerchar color size linewidth} convention for emarker and/or emarker2,
% but you can provide a 1byX vector for size and Xby3 vector for color to change.
% {default : 'off'}
% 'hcolor' - color of the cartoon head. Use 'hcolor','none' to plot no head. {default: 'k' = black}
% 'shading' - 'flat','interp' {default: 'flat'}
% 'numcontour' - number of contour lines {default: 6}. You may also enter a vector to set contours
% at specified values.
% 'contourvals' - values for contour {default: same as input values}
% 'pmask' - values for masking topoplot. Array of zeros and 1 of the same size as the input
% value array {default: []}
% 'color' - color of the contours {default: dark grey}
% 'whitebk' - ('on'|'off') make the background color white (e.g., to print empty plotgrid channels)
% {default: 'off'}
% 'gridscale' - [int > 32] size (nrows) of interpolated scalp map data matrix {default: 67}
% 'colormap' - (n,3) any size colormap {default: existing colormap}
% 'circgrid' - [int > 100] number of elements (angles) in head and border circles {201}
% 'emarkercolor' - cell array of colors for 'blank' option.
% 'plotdisk' - ['on'|'off'] plot disk instead of dots for electrodefor 'blank' option. Size of disk
% is controlled by input values at each electrode. If an imaginary value is provided,
% plot partial circle with red for the real value and blue for the imaginary one.
%
% Dipole plotting options:
% 'dipole' - [xi yi xe ye ze] plot dipole on the top of the scalp map
% from coordinate (xi,yi) to coordinates (xe,ye,ze) (dipole head
% model has radius 1). If several rows, plot one dipole per row.
% Coordinates returned by DIPPLOT may be used. Can accept
% an EEG.dipfit.model structure (See >> help dipplot).
% Ex: ,'dipole',EEG.dipfit.model(17) % Plot dipole(s) for comp. 17.
% 'dipnorm' - ['on'|'off'] normalize dipole length {default: 'on'}.
% 'diporient' - [-1|1] invert dipole orientation {default: 1}.
% 'diplen' - [real] scale dipole length {default: 1}.
% 'dipscale' - [real] scale dipole size {default: 1}.
% 'dipsphere' - [real] size of the dipole sphere. {default: 85 mm}.
% 'dipcolor' - [color] dipole color as Matlab code code or [r g b] vector
% {default: 'k' = black}.
% Outputs:
% handle - handle of the colored surface.If
% contour only is plotted, then is the handle of
% the countourgroup. (If no surface or contour is plotted,
% return "gca", the handle of the current plot)
% grid_or_val - [matrix] the interpolated data image (with off-head points = NaN).
% Else, single interpolated value at the specified 'noplot' arg channel
% location ([rad theta]), if any.
% plotrad_or_grid - IF grid image returned above, then the 'plotrad' radius of the grid.
% Else, the grid image
% xmesh, ymesh - x and y values of the returned grid (above)
%
% Chan_locs format:
% See >> topoplot 'example'
%
% Examples:
%
% To plot channel locations only:
% >> figure; topoplot([],EEG.chanlocs,'style','blank','electrodes','labelpoint','chaninfo',EEG.chaninfo);
%
% Notes: - To change the plot map masking ring to a new figure background color,
% >> set(findobj(gca,'type','patch'),'facecolor',get(gcf,'color'))
% - Topoplots may be rotated. From the commandline >> view([deg 90]) {default: [0 90])
% - When plotting pvalues make sure to use the option 'conv' to minimize extrapolation effects
%
% Authors: Andy Spydell, Colin Humphries, Arnaud Delorme & Scott Makeig
% CNL / Salk Institute, 8/1996-/10/2001; SCCN/INC/UCSD, Nov. 2001 -
%
% See also: TIMTOPO, ENVTOPO
% Deprecated options:
% 'shrink' - ['on'|'off'|'force'|factor] Deprecated. 'on' -> If max channel arc_length
% > 0.5, shrink electrode coordinates towards vertex to plot all channels
% by making max arc_length 0.5. 'force' -> Normalize arc_length
% so the channel max is 0.5. factor -> Apply a specified shrink
% factor (range (0,1) = shrink fraction). {default: 'off'}
% 'electcolor' {'k'} ... electrode marking details and their {defaults}.
% 'emarker' {'.'}|'emarkersize' {14}|'emarkersizemark' {40}|'efontsize' {var} -
% electrode marking details and their {defaults}.
% 'ecolor' - color of the electrode markers {default: 'k' = black}
% 'interplimits' - ['electrodes'|'head'] 'electrodes'-> interpolate the electrode grid;
% 'head'-> interpolate the whole disk {default: 'head'}.
% Unimplemented future options:
% Copyright (C) Colin Humphries & Scott Makeig, CNL / Salk Institute, Aug, 1996
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
%
% 1. Redistributions of source code must retain the above copyright notice,
% this list of conditions and the following disclaimer.
%
% 2. Redistributions in binary form must reproduce the above copyright notice,
% this list of conditions and the following disclaimer in the documentation
% and/or other materials provided with the distribution.
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
% THE POSSIBILITY OF SUCH DAMAGE.
% Topoplot Version 2.1
% Early development history:
% Begun by Andy Spydell and Scott Makeig, NHRC, 7-23-96
% 8-96 Revised by Colin Humphries, CNL / Salk Institute, La Jolla CA
% -changed surf command to imagesc (faster)
% -can now handle arbitrary scaling of electrode distances
% -can now handle non integer angles in chan_locs
% 4-4-97 Revised again by Colin Humphries, reformatted by SM
% -added parameters
% -changed chan_locs format
% 2-26-98 Revised by Colin
% -changed image back to surface command
% -added fill and blank styles
% -removed extra background colormap entry (now use any colormap)
% -added parameters for electrode colors and labels
% -now each topoplot axes use the caxis command again.
% -removed OUTPUT parameter
% 3-11-98 changed default emarkersize, improve help msg -sm
% 5-24-01 made default emarkersize vary with number of channels -sm
% 01-25-02 reformated help & license, added link -ad
% 03-15-02 added readlocs and the use of eloc input structure -ad
% 03-25-02 added 'labelpoint' options and allow Values=[] -ad &sm
% 03-25-02 added details to "Unknown parameter" warning -sm & ad
function [handle,Zi,grid,Xi,Yi] = topoplot(Values,loc_file,varargin)
%
%%%%%%%%%%%%%%%%%%%%%%%% Set defaults %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
icadefs % read defaults MAXTOPOPLOTCHANS and DEFAULT_ELOC and BACKCOLOR
if ~exist('BACKCOLOR') % if icadefs.m does not define BACKCOLOR
BACKCOLOR = [.93 .96 1]; % EEGLAB standard
end
whitebk = 'off'; % by default, make gridplot background color = EEGLAB screen background color
persistent warningInterp;
plotgrid = 'off';
plotchans = [];
noplot = 'off';
handle = [];
Zi = [];
chanval = NaN;
rmax = 0.5; % actual head radius - Don't change this!
INTERPLIMITS = 'head'; % head, electrodes
INTSQUARE = 'on'; % default, interpolate electrodes located though the whole square containing
% the plotting disk
default_intrad = 1; % indicator for (no) specified intrad
MAPLIMITS = 'absmax'; % absmax, maxmin, [values]
GRID_SCALE = 67; % plot map on a 67X67 grid
CIRCGRID = 201; % number of angles to use in drawing circles
AXHEADFAC = 1.3; % head to axes scaling factor
CONTOURNUM = 6; % number of contour levels to plot
STYLE = 'both'; % default 'style': both,straight,fill,contour,blank
HEADCOLOR = [0 0 0]; % default head color (black)
CCOLOR = [0.2 0.2 0.2]; % default contour color
ELECTRODES = []; % default 'electrodes': on|off|label - set below
MAXDEFAULTSHOWLOCS = 64;% if more channels than this, don't show electrode locations by default
EMARKER = '.'; % mark electrode locations with small disks
ECOLOR = [0 0 0]; % default electrode color = black
EMARKERSIZE = []; % default depends on number of electrodes, set in code
EMARKERLINEWIDTH = 1; % default edge linewidth for emarkers
EMARKERSIZE1CHAN = 20; % default selected channel location marker size
EMARKERCOLOR1CHAN = 'red'; % selected channel location marker color
EMARKER2CHANS = []; % mark subset of electrode locations with small disks
EMARKER2 = 'o'; % mark subset of electrode locations with small disks
EMARKER2COLOR = 'r'; % mark subset of electrode locations with small disks
EMARKERSIZE2 = 10; % default selected channel location marker size
EMARKER2LINEWIDTH = 1;
SCATTER = 'off'; % plot the electrode locations using scatter plot.
EFSIZE = get(0,'DefaultAxesFontSize'); % use current default fontsize for electrode labels
HLINEWIDTH = 2; % default linewidth for head, nose, ears
BLANKINGRINGWIDTH = .035;% width of the blanking ring
HEADRINGWIDTH = .007;% width of the cartoon head ring
SHADING = 'flat'; % default 'shading': flat|interp
shrinkfactor = []; % shrink mode (deprecated)
intrad = []; % default interpolation square is to outermost electrode (<=1.0)
plotrad = []; % plotting radius ([] = auto, based on outermost channel location)
headrad = []; % default plotting radius for cartoon head is 0.5
squeezefac = 1.0;
MINPLOTRAD = 0.15; % can't make a topoplot with smaller plotrad (contours fail)
VERBOSE = 'off';
MASKSURF = 'off';
CONVHULL = ''; % dont mask outside the electrodes convex hull
DRAWAXIS = 'off';
PLOTDISK = 'off';
ContourVals = Values;
PMASKFLAG = 0;
COLORARRAY = { [1 0 0] [0.5 0 0] [0 0 0] };
%COLORARRAY2 = { [1 0 0] [0.5 0 0] [0 0 0] };
gb = [0 0];
COLORARRAY2 = { [gb 0] [gb 1/4] [gb 2/4] [gb 3/4] [gb 1] };
%%%%%% Dipole defaults %%%%%%%%%%%%
DIPOLE = [];
DIPNORM = 'on';
DIPNORMMAX = 'off';
DIPSPHERE = 85;
DIPLEN = 1;
DIPSCALE = 1;
DIPORIENT = 1;
DIPCOLOR = [0 0 0];
NOSEDIR = '+X';
CHANINFO = [];
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%%%%%%%%%%%%%%%%%%%%%%% Handle arguments %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if nargin< 1
help topoplot;
return
end
% calling topoplot from Fieldtrip
% -------------------------------
fieldtrip = 0;
if nargin < 2, loc_file = []; end
if isstruct(Values) || ~isstruct(loc_file), fieldtrip == 1; end
if ischar(loc_file), if exist(loc_file) ~= 2, fieldtrip == 1; end; end
if fieldtrip
error('Wrong calling format, are you trying to use the topoplot Fieldtrip function?');
end
nargs = nargin;
if nargs == 1
if ischar(Values)
if any(strcmp(lower(Values),{'example','demo'}))
fprintf(['This is an example of an electrode location file,\n',...
'an ascii file consisting of the following four columns:\n',...
' channel_number degrees arc_length channel_name\n\n',...
'Example:\n',...
' 1 -18 .352 Fp1 \n',...
' 2 18 .352 Fp2 \n',...
' 5 -90 .181 C3 \n',...
' 6 90 .181 C4 \n',...
' 7 -90 .500 A1 \n',...
' 8 90 .500 A2 \n',...
' 9 -142 .231 P3 \n',...
'10 142 .231 P4 \n',...
'11 0 .181 Fz \n',...
'12 0 0 Cz \n',...
'13 180 .181 Pz \n\n',...
...
'In topoplot() coordinates, 0 deg. points to the nose, positive\n',...
'angles point to the right hemisphere, and negative to the left.\n',...
'The model head sphere has a circumference of 2; the vertex\n',...
'(Cz) has arc_length 0. Locations with arc_length > 0.5 are below\n',...
'head center and are plotted outside the head cartoon.\n',...
'Option plotrad controls how much of this lower-head "skirt" is shown.\n',...
'Option headrad controls if and where the cartoon head will be drawn.\n',...
'Option intrad controls how many channels will be included in the interpolation.\n',...
])
return
end
end
end
if nargs < 2
loc_file = DEFAULT_ELOC;
if ~exist(loc_file)
fprintf('default locations file "%s" not found - specify chan_locs in topoplot() call.\n',loc_file)
error(' ')
end
end
if isempty(loc_file)
loc_file = 0;
end
if isnumeric(loc_file) && loc_file == 0
loc_file = DEFAULT_ELOC;
end
if nargs > 2
if ~(round(nargs/2) == nargs/2)
error('Odd number of input arguments??')
end
% check for chaninfo
options = varargin;
for i = 1:2:length(options)
if strcmpi(options{i}, 'chaninfo')
chaninfoTmp = options{i+1};
if isfield(chaninfoTmp, 'topoplot')
options = [ options chaninfoTmp.topoplot ];
break;
end
end
end
for i = 1:2:length(options)
Param = options{i};
Value = options{i+1};
if ~ischar(Param)
error('Flag arguments must be strings')
end
Param = lower(Param);
switch Param
case 'conv'
CONVHULL = lower(Value);
if ~strcmp(CONVHULL,'on') && ~strcmp(CONVHULL,'off')
error('Value of ''conv'' must be ''on'' or ''off''.');
end
case 'colormap'
if size(Value,2)~=3
error('Colormap must be a n x 3 matrix')
end
colormap(Value)
case 'plotdisk'
PLOTDISK = lower(Value);
if ~strcmp(PLOTDISK,'on') && ~strcmp(PLOTDISK,'off')
error('Value of ''plotdisk'' must be ''on'' or ''off''.');
end
case 'intsquare'
INTSQUARE = lower(Value);
if ~strcmp(INTSQUARE,'on') && ~strcmp(INTSQUARE,'off')
error('Value of ''intsquare'' must be ''on'' or ''off''.');
end
case 'emarkercolors'
COLORARRAY = Value;
case {'interplimits','headlimits'}
if ~ischar(Value)
error('''interplimits'' value must be a string')
end
Value = lower(Value);
if ~strcmp(Value,'electrodes') && ~strcmp(Value,'head')
error('Incorrect value for interplimits')
end
INTERPLIMITS = Value;
case 'verbose'
VERBOSE = Value;
case 'nosedir'
NOSEDIR = Value;
if isempty(strmatch(lower(NOSEDIR), { '+x', '-x', '+y', '-y' }))
error('Invalid nose direction');
end
case 'chaninfo'
CHANINFO = Value;
if isfield(CHANINFO, 'nosedir'), NOSEDIR = CHANINFO.nosedir; end
if isfield(CHANINFO, 'shrink' ), shrinkfactor = CHANINFO.shrink; end
if isfield(CHANINFO, 'plotrad') && isempty(plotrad), plotrad = CHANINFO.plotrad; end
case 'chantype'
case 'drawaxis'
DRAWAXIS = Value;
case 'maplimits'
MAPLIMITS = Value;
case 'masksurf'
MASKSURF = Value;
case 'circgrid'
CIRCGRID = Value;
if ischar(CIRCGRID) || CIRCGRID<100
error('''circgrid'' value must be an int > 100');
end
case 'style'
STYLE = lower(Value);
case 'numcontour'
CONTOURNUM = Value;
case 'electrodes'
ELECTRODES = lower(Value);
if strcmpi(ELECTRODES,'pointlabels') || strcmpi(ELECTRODES,'ptslabels') ...
| strcmpi(ELECTRODES,'labelspts') | strcmpi(ELECTRODES,'ptlabels') ...
| strcmpi(ELECTRODES,'labelpts')
ELECTRODES = 'labelpoint'; % backwards compatibility
elseif strcmpi(ELECTRODES,'pointnumbers') || strcmpi(ELECTRODES,'ptsnumbers') ...
| strcmpi(ELECTRODES,'numberspts') | strcmpi(ELECTRODES,'ptnumbers') ...
| strcmpi(ELECTRODES,'numberpts') | strcmpi(ELECTRODES,'ptsnums') ...
| strcmpi(ELECTRODES,'numspts')
ELECTRODES = 'numpoint'; % backwards compatibility
elseif strcmpi(ELECTRODES,'nums')
ELECTRODES = 'numbers'; % backwards compatibility
elseif strcmpi(ELECTRODES,'pts')
ELECTRODES = 'on'; % backwards compatibility
elseif ~strcmp(ELECTRODES,'off') ...
& ~strcmpi(ELECTRODES,'on') ...
& ~strcmp(ELECTRODES,'labels') ...
& ~strcmpi(ELECTRODES,'numbers') ...
& ~strcmpi(ELECTRODES,'labelpoint') ...
& ~strcmpi(ELECTRODES,'numpoint')
error('Unknown value for keyword ''electrodes''');
end
case 'dipole'
DIPOLE = Value;
case 'dipsphere'
DIPSPHERE = Value;
case {'dipnorm', 'dipnormmax'}
if strcmp(Param,'dipnorm')
DIPNORM = Value;
if strcmpi(Value,'on')
DIPNORMMAX = 'off';
end
else
DIPNORMMAX = Value;
if strcmpi(Value,'on')
DIPNORM = 'off';
end
end
case 'diplen'
DIPLEN = Value;
case 'dipscale'
DIPSCALE = Value;
case 'contourvals'
ContourVals = Value;
case 'pmask'
ContourVals = Value;
PMASKFLAG = 1;
case 'diporient'
DIPORIENT = Value;
case 'dipcolor'
DIPCOLOR = Value;
case 'emarker'
if ischar(Value)
EMARKER = Value;
elseif ~iscell(Value) || length(Value) > 4
error('''emarker'' argument must be a cell array {marker color size linewidth}')
else
EMARKER = Value{1};
end
if length(Value) > 1
ECOLOR = Value{2};
end
if length(Value) > 2
EMARKERSIZE = Value{3};
end
if length(Value) > 3
EMARKERLINEWIDTH = Value{4};
end
case 'emarker2'
if ~iscell(Value) || length(Value) > 5
error('''emarker2'' argument must be a cell array {chans marker color size linewidth}')
end
EMARKER2CHANS = abs(Value{1}); % ignore channels < 0
if length(Value) > 1
EMARKER2 = Value{2};
end
if length(Value) > 2
EMARKER2COLOR = Value{3};
end
if length(Value) > 3
EMARKERSIZE2 = Value{4};
end
if length(Value) > 4
EMARKER2LINEWIDTH = Value{5};
end
case 'scatter'
SCATTER = Value;
case 'shrink'
shrinkfactor = Value;
case 'intrad'
intrad = Value;
if ischar(intrad) || (intrad < MINPLOTRAD || intrad > 1)
error('intrad argument should be a number between 0.15 and 1.0');
end
case 'plotrad'
plotrad = Value;
if ~isempty(plotrad) && (ischar(plotrad) || (plotrad < MINPLOTRAD || plotrad > 1))
error('plotrad argument should be a number between 0.15 and 1.0');
end
case 'headrad'
headrad = Value;
if ischar(headrad) && ( strcmpi(headrad,'off') || strcmpi(headrad,'none') )
headrad = 0; % undocumented 'no head' alternatives
end
if isempty(headrad) % [] -> none also
headrad = 0;
end
if ~ischar(headrad)
if ~(headrad==0) && (headrad < MINPLOTRAD || headrad>1)
error('bad value for headrad');
end
elseif ~strcmpi(headrad,'rim')
error('bad value for headrad');
end
case {'headcolor','hcolor'}
HEADCOLOR = Value;
case {'contourcolor','ccolor'}
CCOLOR = Value;
case {'electcolor','ecolor'}
ECOLOR = Value;
case {'emarkersize','emsize'}
EMARKERSIZE = Value;
case {'emarkersize1chan','emarkersizemark'}
EMARKERSIZE1CHAN= Value;
case {'efontsize','efsize'}
EFSIZE = Value;
case 'shading'
SHADING = lower(Value);
if ~any(strcmp(SHADING,{'flat','interp'}))
error('Invalid shading parameter')
end
if strcmpi(SHADING,'interp') && isempty(warningInterp)
warning('Using interpolated shading in scalp topographies prevent to export them as vectorized figures');
warningInterp = 1;
end
case 'noplot'
noplot = Value;
if ~ischar(noplot)
if length(noplot) ~= 2
error('''noplot'' location should be [radius, angle]')
else
chanrad = noplot(1);
chantheta = noplot(2);
noplot = 'on';
end
end
case 'gridscale'
GRID_SCALE = Value;
if ischar(GRID_SCALE) || GRID_SCALE ~= round(GRID_SCALE) || GRID_SCALE < 32
error('''gridscale'' value must be integer > 32.');
end
case {'plotgrid','gridplot'}
plotgrid = 'on';
gridchans = Value;
case 'plotchans'
plotchans = Value(:);
if find(plotchans<=0)
error('''plotchans'' values must be > 0');
end
% if max(abs(plotchans))>max(Values) | max(abs(plotchans))>length(Values) -sm ???
case {'whitebk','whiteback','forprint'}
whitebk = Value;
case {'iclabel'} % list of options to ignore
otherwise
error(['Unknown input parameter ''' Param ''' ???'])
end
end
end
if strcmpi(whitebk, 'on')
BACKCOLOR = [ 1 1 1 ];
end
if isempty(find(strcmp(varargin,'colormap')))
if exist('DEFAULT_COLORMAP','var')
cmap = colormap(DEFAULT_COLORMAP);
else
cmap = parula;
end
else
cmap = colormap;
end
cmaplen = size(cmap,1);
if strcmp(STYLE,'blank') % else if Values holds numbers of channels to mark
if length(Values) < length(loc_file)
ContourVals = zeros(1,length(loc_file));
ContourVals(Values) = 1;
Values = ContourVals;
end
end
%
%%%%%%%%%%%%%%%%%%%%%%%%%%% test args for plotting an electrode grid %%%%%%%%%%%%%%%%%%%%%%
%
if strcmp(plotgrid,'on')
STYLE = 'grid';
gchans = sort(find(abs(gridchans(:))>0));
% if setdiff(gchans,unique(gchans))
% fprintf('topoplot() warning: ''plotgrid'' channel matrix has duplicate channels\n');
% end
if ~isempty(plotchans)
if intersect(gchans,abs(plotchans))
fprintf('topoplot() warning: ''plotgrid'' and ''plotchans'' have channels in common\n');
end
end
end
%
%%%%%%%%%%%%%%%%%%%%%%%%%%% misc arg tests %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if isempty(ELECTRODES) % if electrode labeling not specified
if length(Values) > MAXDEFAULTSHOWLOCS % if more channels than default max
ELECTRODES = 'off'; % don't show electrodes
else % else if fewer chans,
ELECTRODES = 'on'; % do
end
end
if isempty(Values)
STYLE = 'blank';
end
[r,c] = size(Values);
if r>1 && c>1,
error('input data must be a single vector');
end
Values = Values(:); % make Values a column vector
ContourVals = ContourVals(:); % values for contour
if ~isempty(intrad) && ~isempty(plotrad) && intrad < plotrad
error('intrad must be >= plotrad');
end
if ~strcmpi(STYLE,'grid') % if not plot grid only
%
%%%%%%%%%%%%%%%%%%%% Read the channel location information %%%%%%%%%%%%%%%%%%%%%%%%
%
if ischar(loc_file)
[tmpeloc labels Th Rd indices] = readlocs( loc_file);
elseif isstruct(loc_file) % a locs struct
[tmpeloc labels Th Rd indices] = readlocs( loc_file );
% Note: Th and Rd correspond to indices channels-with-coordinates only
else
error('loc_file must be a EEG.locs struct or locs filename');
end
Th = pi/180*Th; % convert degrees to radians
allchansind = 1:length(Th);
if ~isempty(plotchans)
if max(plotchans) > length(Th)
error('''plotchans'' values must be <= max channel index');
end
end
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% channels to plot %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if ~isempty(plotchans)
plotchans = intersect_bc(plotchans, indices);
end
if ~isempty(Values) && ~strcmpi( STYLE, 'blank') && isempty(plotchans)
plotchans = indices;
end
if isempty(plotchans) && strcmpi( STYLE, 'blank')
plotchans = indices;
end
%
%%%%%%%%%%%%%%%%%%%%%%%%%%% filter channels used for components %%%%%%%%%%%%%%%%%%%%%
%
if isfield(CHANINFO, 'icachansind') && ~isempty(Values) && length(Values) ~= length(tmpeloc)
% test if ICA component
% ---------------------
if length(CHANINFO.icachansind) == length(Values)
% if only a subset of channels are to be plotted
% and ICA components also use a subject of channel
% we must find the new indices for these channels
plotchans = intersect_bc(CHANINFO.icachansind, plotchans);
tmpvals = zeros(1, length(tmpeloc));
tmpvals(CHANINFO.icachansind) = Values;
Values = tmpvals;
tmpvals = zeros(1, length(tmpeloc));
tmpvals(CHANINFO.icachansind) = ContourVals;
ContourVals = tmpvals;
end
end
%
%%%%%%%%%%%%%%%%%%% last channel is reference? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if length(tmpeloc) == length(Values) + 1 % remove last channel if necessary
% (common reference channel)
if plotchans(end) == length(tmpeloc)
plotchans(end) = [];
end
end
%
%%%%%%%%%%%%%%%%%%% remove infinite and NaN values %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if length(Values) > 1
inds = union_bc(find(isnan(Values)), find(isinf(Values))); % NaN and Inf values
plotchans = setdiff_bc(plotchans, inds);
end
if strcmp(plotgrid,'on')
plotchans = setxor(plotchans,gchans); % remove grid chans from head plotchans
end
[x,y] = pol2cart(Th,Rd); % transform electrode locations from polar to cartesian coordinates
plotchans = abs(plotchans); % reverse indicated channel polarities
allchansind = allchansind(plotchans);
Th = Th(plotchans);
Rd = Rd(plotchans);
x = x(plotchans);
y = y(plotchans);
labels = labels(plotchans); % remove labels for electrodes without locations
labels = strvcat(labels); % make a label string matrix
if ~isempty(Values) && length(Values) > 1
Values = Values(plotchans);
ContourVals = ContourVals(plotchans);
end
%
%%%%%%%%%%%%%%%%%% Read plotting radius from chanlocs %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if isempty(plotrad) && isfield(tmpeloc, 'plotrad'),
plotrad = tmpeloc(1).plotrad;
if ischar(plotrad) % plotrad shouldn't be a string
plotrad = str2num(plotrad) % just checking
end
if plotrad < MINPLOTRAD || plotrad > 1.0
fprintf('Bad value (%g) for plotrad.\n',plotrad);
error(' ');
end
if strcmpi(VERBOSE,'on') && ~isempty(plotrad)
fprintf('Plotting radius plotrad (%g) set from EEG.chanlocs.\n',plotrad);
end
end
if isempty(plotrad)
plotrad = min(1.0,max(Rd)*1.02); % default: just outside the outermost electrode location
plotrad = max(plotrad,0.5); % default: plot out to the 0.5 head boundary
end % don't plot channels with Rd > 1 (below head)
if isempty(intrad)
default_intrad = 1; % indicator for (no) specified intrad
intrad = min(1.0,max(Rd)*1.02); % default: just outside the outermost electrode location
else
default_intrad = 0; % indicator for (no) specified intrad
if plotrad > intrad
plotrad = intrad;
end
end % don't interpolate channels with Rd > 1 (below head)
if ischar(plotrad) || plotrad < MINPLOTRAD || plotrad > 1.0
error('plotrad must be between 0.15 and 1.0');
end
%
%%%%%%%%%%%%%%%%%%%%%%% Set radius of head cartoon %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if isempty(headrad) % never set -> defaults
if plotrad >= rmax
headrad = rmax; % (anatomically correct)
else % if plotrad < rmax
headrad = 0; % don't plot head
if strcmpi(VERBOSE, 'on')
fprintf('topoplot(): not plotting cartoon head since plotrad (%5.4g) < 0.5\n',...
plotrad);
end
end
elseif strcmpi(headrad,'rim') % force plotting at rim of map
headrad = plotrad;
end
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Shrink mode %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if ~isempty(shrinkfactor) || isfield(tmpeloc, 'shrink'),
if isempty(shrinkfactor) && isfield(tmpeloc, 'shrink'),
shrinkfactor = tmpeloc(1).shrink;
if strcmpi(VERBOSE,'on')
if ischar(shrinkfactor)
fprintf('Automatically shrinking coordinates to lie above the head perimter.\n');
else
fprintf('Automatically shrinking coordinates by %3.2f\n', shrinkfactor);
end
end
end
if ischar(shrinkfactor)
if strcmpi(shrinkfactor, 'on') || strcmpi(shrinkfactor, 'force') || strcmpi(shrinkfactor, 'auto')
if abs(headrad-rmax) > 1e-2
fprintf(' NOTE -> the head cartoon will NOT accurately indicate the actual electrode locations\n');
end
if strcmpi(VERBOSE,'on')
fprintf(' Shrink flag -> plotting cartoon head at plotrad\n');
end
headrad = plotrad; % plot head around outer electrodes, no matter if 0.5 or not
end
else % apply shrinkfactor
plotrad = rmax/(1-shrinkfactor);
headrad = plotrad; % make deprecated 'shrink' mode plot
if strcmpi(VERBOSE,'on')
fprintf(' %g%% shrink applied.');
if abs(headrad-rmax) > 1e-2
fprintf(' Warning: With this "shrink" setting, the cartoon head will NOT be anatomically correct.\n');
else
fprintf('\n');
end
end
end
end; % if shrink
%
%%%%%%%%%%%%%%%%% Issue warning if headrad ~= rmax %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if headrad ~= 0.5 && strcmpi(VERBOSE, 'on')
fprintf(' NB: Plotting map using ''plotrad'' %-4.3g,',plotrad);
fprintf( ' ''headrad'' %-4.3g\n',headrad);
fprintf('Warning: The plotting radius of the cartoon head is NOT anatomically correct (0.5).\n')
end
%
%%%%%%%%%%%%%%%%%%%%% Find plotting channels %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
pltchans = find(Rd <= plotrad); % plot channels inside plotting circle
if strcmpi(INTSQUARE,'on') % interpolate channels in the radius intrad square
intchans = find(x <= intrad & y <= intrad); % interpolate and plot channels inside interpolation square
else
intchans = find(Rd <= intrad); % interpolate channels in the radius intrad circle only
end
%
%%%%%%%%%%%%%%%%%%%%% Eliminate channels not plotted %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
allx = x;
ally = y;
intchans; % interpolate using only the 'intchans' channels
pltchans; % plot using only indicated 'plotchans' channels
if length(pltchans) < length(Rd) && strcmpi(VERBOSE, 'on')
fprintf('Interpolating %d and plotting %d of the %d scalp electrodes.\n', ...
length(intchans),length(pltchans),length(Rd));
end;
% fprintf('TOPOPLOT: plotting %d channels\n',length(pltchans));
if ~isempty(EMARKER2CHANS)
if strcmpi(STYLE,'blank')
error('emarker2 not defined for style ''blank'' - use marking channel numbers in place of data');
else % mark1chans and mark2chans are subsets of pltchans for markers 1 and 2
[tmp1, mark1chans, tmp2] = setxor(pltchans,EMARKER2CHANS);
[tmp3, tmp4, mark2chans] = intersect_bc(EMARKER2CHANS,pltchans);
end
end
if ~isempty(Values)
if length(Values) == length(Th) % if as many map Values as channel locs
intValues = Values(intchans);
intContourVals = ContourVals(intchans);
Values = Values(pltchans);
ContourVals = ContourVals(pltchans);
end;
end; % now channel parameters and values all refer to plotting channels only
allchansind = allchansind(pltchans);
intTh = Th(intchans); % eliminate channels outside the interpolation area
intRd = Rd(intchans);
intx = x(intchans);
inty = y(intchans);
Th = Th(pltchans); % eliminate channels outside the plotting area
Rd = Rd(pltchans);
x = x(pltchans);
y = y(pltchans);
labels= labels(pltchans,:);
%
%%%%%%%%%%%%%%% Squeeze channel locations to <= rmax %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
squeezefac = rmax/plotrad;
intRd = intRd*squeezefac; % squeeze electrode arc_lengths towards the vertex
Rd = Rd*squeezefac; % squeeze electrode arc_lengths towards the vertex
% to plot all inside the head cartoon
intx = intx*squeezefac;
inty = inty*squeezefac;
x = x*squeezefac;
y = y*squeezefac;
allx = allx*squeezefac;
ally = ally*squeezefac;
% Note: Now outermost channel will be plotted just inside rmax
else % if strcmpi(STYLE,'grid')
intx = rmax; inty=rmax;
end % if ~strcmpi(STYLE,'grid')
%
%%%%%%%%%%%%%%%% rotate channels based on chaninfo %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if strcmpi(lower(NOSEDIR), '+x')
rotate = 0;
else
if strcmpi(lower(NOSEDIR), '+y')
rotate = 3*pi/2;
elseif strcmpi(lower(NOSEDIR), '-x')
rotate = pi;
else rotate = pi/2;
end
allcoords = (inty + intx*sqrt(-1))*exp(sqrt(-1)*rotate);
intx = imag(allcoords);
inty = real(allcoords);
allcoords = (ally + allx*sqrt(-1))*exp(sqrt(-1)*rotate);
allx = imag(allcoords);
ally = real(allcoords);
allcoords = (y + x*sqrt(-1))*exp(sqrt(-1)*rotate);
x = imag(allcoords);
y = real(allcoords);
end
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Make the plot %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if ~strcmpi(STYLE,'blank') % if draw interpolated scalp map
if ~strcmpi(STYLE,'grid') % not a rectangular channel grid
%
%%%%%%%%%%%%%%%% Find limits for interpolation %%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if default_intrad % if no specified intrad
if strcmpi(INTERPLIMITS,'head') % intrad is 'head'
xmin = min(-rmax,min(intx)); xmax = max(rmax,max(intx));
ymin = min(-rmax,min(inty)); ymax = max(rmax,max(inty));
else % INTERPLIMITS = rectangle containing electrodes -- DEPRECATED OPTION!
xmin = max(-rmax,min(intx)); xmax = min(rmax,max(intx));
ymin = max(-rmax,min(inty)); ymax = min(rmax,max(inty));
end
else % some other intrad specified
xmin = -intrad*squeezefac; xmax = intrad*squeezefac; % use the specified intrad value
ymin = -intrad*squeezefac; ymax = intrad*squeezefac;