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function [cfg] = ft_layoutplot(cfg, data)
% FT_LAYOUTPLOT makes a figure with the 2-D layout of the channel positions
% for topoplotting and the individual channel axes (i.e. width and height
% of the subfigures) for multiplotting. A correct 2-D layout is a
% prerequisite for plotting the topographical distribution of the
% potential or field distribution, or for plotting timecourses in a
% topographical arrangement.
%
% This function uses the same configuration options as prepare_layout and
% as the topoplotting and multiplotting functions. The difference is that
% this function plots the layout without any data, which facilitates
% the validation of your 2-D layout.
%
% Use as
% ft_layoutplot(cfg, data)
%
% There are several ways in which a 2-D layout can be made: it can be read
% directly from a *.lay file, it can be created based on 3-D electrode or
% gradiometer positions in the configuration or in the data, or it can be
% created based on the specification of an electrode of gradiometer file.
%
% You can specify either one of the following configuration options
% cfg.layout = filename containg the layout
% cfg.rotate = number, rotation around the z-axis in degrees (default = [], which means automatic)
% cfg.projection = string, 2D projection method can be 'stereographic', 'ortographic', 'polar', 'gnomic' or 'inverse' (default = 'orthographic')
% cfg.elec = structure with electrode positions or filename, see FT_READ_SENS
% cfg.grad = structure with gradiometer definition or filename, see FT_READ_SENS
% cfg.opto = structure with optode definition or filename, see FT_READ_SENS
% cfg.output = filename to which the layout will be written (default = [])
% cfg.montage = 'no' or a montage structure (default = 'no')
% cfg.image = filename, use an image to construct a layout (e.g. usefull for ECoG grids)
% cfg.box = string, 'yes' or 'no' whether box should be plotted around electrode (default = 'yes')
% cfg.mask = string, 'yes' or 'no' whether the mask should be plotted (default = 'yes')
% cfg.visible = string, 'on' or 'off' whether figure will be visible (default = 'on')
% cfg.position = location and size of the figure, specified as a vector of the form [left bottom width height]
% cfg.renderer = string, 'opengl', 'zbuffer', 'painters', see MATLAB Figure Properties. If this function crashes, you should try 'painters'.
%
% Alternatively the layout can be constructed from either
% data.elec structure with electrode positions
% data.grad structure with gradiometer definition
%
% Alternatively, you can specify
% cfg.layout = 'ordered'
% which will give you a 2-D ordered layout. Note that this is only suited
% for multiplotting and not for topoplotting.
%
% To facilitate data-handling and distributed computing you can use
% cfg.inputfile = ...
% If you specify this option the input data will be read from a *.mat
% file on disk. This mat files should contain only a single variable named 'data',
% corresponding to the input structure.
%
% See also FT_PREPARE_LAYOUT, FT_TOPOPLOTER, FT_TOPOPLOTTFR, FT_MULTIPLOTER, FT_MULTIPLOTTFR
% Undocumented options
% cfg.montage
% Copyright (C) 2006-2008, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% FieldTrip is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
% these are used by the ft_preamble/ft_postamble function and scripts
ft_revision = '$Id$';
ft_nargin = nargin;
ft_nargout = nargout;
% do the general setup of the function
ft_defaults
ft_preamble init
ft_preamble debug
ft_preamble loadvar data
ft_preamble provenance data
% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
return
end
% the data can be passed as input argument or can be read from disk
hasdata = exist('data', 'var');
if hasdata
% check if the input data is valid for this function
data = ft_checkdata(data);
end
% check if the input cfg is valid for this function
cfg = ft_checkconfig(cfg, 'renamed', {'elecfile', 'elec'});
cfg = ft_checkconfig(cfg, 'renamed', {'gradfile', 'grad'});
cfg = ft_checkconfig(cfg, 'renamed', {'optofile', 'opto'});
cfg = ft_checkconfig(cfg, 'renamed', {'newfigure', 'figure'});
% set the defaults
cfg.box = ft_getopt(cfg, 'box', 'yes');
cfg.mask = ft_getopt(cfg, 'mask', 'yes');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% extract or generate the layout information
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
tmpcfg = keepfields(cfg, {'layout', 'channel', 'rows', 'columns', 'commentpos', 'skipcomnt', 'scalepos', 'skipscale', 'projection', 'viewpoint', 'rotate', 'width', 'height', 'elec', 'grad', 'opto', 'showcallinfo', 'trackcallinfo', 'trackusage', 'trackdatainfo', 'trackmeminfo', 'tracktimeinfo'});
if hasdata
layout = ft_prepare_layout(tmpcfg, data);
else
layout = ft_prepare_layout(tmpcfg);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% plot all details pertaining to the layout in one figure
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% open a new figure with the specified settings
h = open_figure(keepfields(cfg, {'figure', 'position', 'visible', 'renderer'}));
if isfield(cfg, 'image') && ~isempty(cfg.image)
% start with the background image
fprintf('reading background image from %s\n', cfg.image);
img = imread(cfg.image);
img = flipdim(img, 1); % in combination with "axis xy"
bw = 1;
if bw
% convert to greyscale image
img = mean(img, 3);
imagesc(img);
colormap gray
else
% plot as RGB image
image(img);
end
axis equal
axis off
axis xy
end
ft_plot_layout(layout, 'point', true, 'box', cfg.box, 'label', true, 'mask', cfg.mask, 'outline', true);
% the following code can be used to verify a bipolar montage, given the
% layout of the monopolar channels
if isfield(cfg, 'montage') && ~isempty(cfg.montage)
fprintf('plotting an arrow for each of the bipolar electrode pairs\n');
% the arrow begins at the +1 electrode
% the arrow ends at the -1 electrode
for i=1:length(cfg.montage.labelnew)
begindx = find(cfg.montage.tra(i,:)==+1);
endindx = find(cfg.montage.tra(i,:)==-1);
if ~numel(begindx)==1 || ~numel(endindx)==1
% the re-referenced channel does not seem to be a bipolar pair
continue
end
% find the position of the begin and end of the arrow
beglab = cfg.montage.labelold{begindx};
endlab = cfg.montage.labelold{endindx};
begindx = find(strcmp(layout.label, beglab)); % the index in the layout
endindx = find(strcmp(layout.label, endlab)); % the index in the layout
if ~numel(begindx)==1 || ~numel(endindx)==1
% one of the channels in the bipolar pair does not seem to be in the layout
continue
end
begpos = layout.pos(begindx,:);
endpos = layout.pos(endindx,:);
arrow(begpos, endpos, 'Length', 5)
end % for all re-referenced channels
end % if montage
% this is needed for the figure title
if isfield(cfg, 'dataname') && ~isempty(cfg.dataname)
dataname = cfg.dataname;
elseif isfield(cfg, 'inputfile') && ~isempty(cfg.inputfile)
dataname = cfg.inputfile;
elseif nargin>1
dataname = arrayfun(@inputname, 2:nargin, 'UniformOutput', false);
else
dataname = {};
end
% set the figure window title
if ~isempty(dataname)
set(h, 'Name', sprintf('%d: %s: %s', double(h), mfilename, join_str(', ', dataname)));
else
set(h, 'Name', sprintf('%d: %s', double(h), mfilename));
end
set(h, 'NumberTitle', 'off');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% deal with the output
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble previous data
ft_postamble provenance
ft_postamble savefig
% add a menu to the figure, but only if the current figure does not have subplots
menu_fieldtrip(gcf, cfg, false);
if ~ft_nargout
% don't return anything
clear cfg
end