% STD_READTOPO - returns the scalp map of a specified ICA component, assumed
% to have been saved in a Matlab file, [dataset_name].icatopo,
% in the same directory as the dataset file. If this file does
% not exist, use STD_TOPO to create it, else a pre-clustering
% function that calls it: POP_PRECLUST or EEG_PRECLUST.
% Usage:
% >> [grid, y, x ] = std_readtopo(ALLEEG, setindx, component);
% >> [grid, y, x ] = std_readtopo(ALLEEG, setindx, component, transform, mode);
%
% Inputs:
% ALLEEG - vector of EEG datasets (can also be one EEG set).
% must contain the dataset of interest (see 'setindx' below).
% setindx - [integer] an index of an EEG dataset in the ALLEEG
% structure, for which to get the component ERP.
% component - [integer] index of the component for which the scalp map
% grid should be returned.
% transform - ['none'!'laplacian'|'gradient'] transform scalp map to
% laplacian or gradient map. Default is 'none'.
% mode - ['2dmap'|'preclust'] return either a 2-D array for direct
% plotting ('2dmap') or an array formatted for preclustering
% with all the NaN values removed (ncomps x points). Default
% is '2dmap' for 1 component and 'preclust' for several.
%
% Outputs:
% grid - square scalp-map color-value grid for the requested ICA component
% in the specified dataset, an interpolated Cartesian grid as output
% by TOPOPLOT.
% y - y-axis values for the interpolated grid
% x - x-axis values of the interpolated grid
%
% See also STD_TOPO, STD_PRECLUST
%
% Authors: Arnaud Delorme, Hilit Serby, SCCN, INC, UCSD, February, 2005
% Copyright (C) Hilit Serby, SCCN, INC, UCSD, October 11, 2004, hilit@sccn.ucsd.edu
%
% 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.
function [X, yi, xi ] = std_readtopo(ALLEEG, abset, comps, option, mode)
X = [];
yi = [];
xi = [];
if nargin < 4
option = 'none';
end
if nargin < 5
mode = '2Dmap';
end
filename = correctfile(fullfile( ALLEEG(abset).filepath,[ ALLEEG(abset).filename(1:end-3) 'icatopo']),ALLEEG(abset).filepath);
tmpfile = which(filename);
if ~isempty(tmpfile), filename = tmpfile; end
% 061411, 2:51pm
% Modified by Joaquin
% while getfield(dir(filename), 'bytes') < 1000
i = 1;
while getfield(dir(filename), 'bytes') < 5000
topo = load( '-mat', filename);
filename = correctfile(topo.file, ALLEEG(abset).filepath);
tmpfile = which(filename);
if ~isempty(tmpfile), filename = tmpfile; end
if(i>100)
error('too many attempts to find valid icatopo');
end
i = i+1;
end
for k = 1:length(comps)
if length(comps) < 3
lastwarn('', '');
warnStruct = warning;
warning('off');
try
topo = load( '-mat', filename, ...
[ 'comp' int2str(comps(k)) '_grid'], ...
[ 'comp' int2str(comps(k)) '_x'], ...
[ 'comp' int2str(comps(k)) '_y'], 'date' );
catch
error( [ 'Cannot read file ''' filename '''' ]);
end
[warnMsg, warnId] = lastwarn();
warning(warnStruct);
if ~isempty(warnId) && ~findstr(warnMsg, 'date')
error( 'Cannot find component %d in file %s', comps(k), filename );
end
elseif k == 1
try
topo = load( '-mat', filename);
catch
error([ 'Missing scalp topography file - also necessary for ERP polarity' 10 'Try recomputing scalp topographies for components' ]);
end
end
if ~isfield(topo, 'date')
fprintf(2, 'You must recompute ICA scalp topographies, see bug https://github.com/sccn/eeglab/issues/767\n')
end
try
tmp = getfield(topo, [ 'comp' int2str(comps(k)) '_grid' ]);
catch
error([ 'Empty scalp topography file - also necessary for ERP polarity' 10 'Try recomputing scalp topographies for components' ]);
end
if strcmpi(option, 'gradient')
[tmpx, tmpy] = gradient(tmp); % Gradient
tmp = tmpx;
tmp(:,:,2) = tmpy;
elseif strcmpi(option, 'laplacian')
tmp = del2(tmp); % Laplacian
end
if length(comps) > 1 || strcmpi(mode, 'preclust')
tmp = tmp(find(~isnan(tmp))); % remove NaN for more than 1 component
end
if k == 1
X = zeros([ length(comps) size(tmp) ]) ;
end
X(k,:,:,:) = tmp;
if k == 1
yi = getfield(topo, [ 'comp' int2str(comps(k)) '_y']);
xi = getfield(topo, [ 'comp' int2str(comps(k)) '_x']);
end
end
X = squeeze(X);
return;
function filename = correctfile(filename, datasetpath)
comp = computer;
if filename(2) == ':' && ~strcmpi(comp(1:2), 'PC')
filename = [filesep filename(4:end) ];
filename(find(filename == '\')) = filesep;
end
if ~exist(filename)
[tmpp tmpf ext] = fileparts(filename);
if exist([tmpf ext])
filename = [tmpf ext];
else
[tmpp2 tmpp1] = fileparts(tmpp);
if exist(fullfile(tmpp1, [ tmpf ext ]))
filename = fullfile(tmpp1, [ tmpf ext ]);
else
filename = fullfile(datasetpath, [ tmpf ext ]);
if ~exist(filename)
error([ 'Cannot load file ''' [ tmpf ext ] '''' 10 'Go back and recompute the data file.' 10 'Note that plotting ICA component ERPs require' 10 'to precompute ICA topographies (see tutorial)']);
end
end
end
end;
Datasets
Models
