% EEG_CHECKCHANLOCS - Check the consistency of the channel locations structure
% of an EEGLAB dataset.
%
% Usage:
% >> EEG = eeg_checkchanlocs(EEG);
% >> [chanlocs chaninfo] = eeg_checkchanlocs( chanlocs, chaninfo);
%
% Inputs:
% EEG - EEG dataset
% chanlocs - EEG.chanlocs structure
% chaninfo - EEG.chaninfo structure
%
% Outputs:
% EEG - new EEGLAB dataset with updated channel location structures
% EEG.chanlocs, EEG.urchanlocs, EEG.chaninfo
% chanlocs - updated channel location structure
% chaninfo - updated chaninfo structure
%
% Author: Arnaud Delorme, SCCN/INC/UCSD, March 2, 2011
% Copyright (C) SCCN/INC/UCSD, March 2, 2011, arno@salk.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.
% Hey Arno -- this is a quick fix to make an analysis work for Makoto
% I think the old version had a bug...
function [chans, chaninfo, chanedit]= eeg_checkchanlocs(chans, chaninfo)
if nargin < 1
help eeg_checkchanlocs;
return;
end
if nargin < 2
chaninfo = [];
end
processingEEGstruct = 0;
if isfield(chans, 'data')
processingEEGstruct = 1;
tmpEEG = chans;
[chans, chaninfo] = insertchans(tmpEEG.chanlocs, tmpEEG.chaninfo);
% force Nosedir to +X (done here because of DIPFIT)
% -------------------
if isfield(tmpEEG.chaninfo, 'nosedir')
if ~strcmpi(tmpEEG.chaninfo.nosedir, '+x') && all(isfield(tmpEEG.chanlocs,{'X','Y','theta','sph_theta'}))
disp(['Note for expert users: Nose direction is now set from ''' upper(tmpEEG.chaninfo.nosedir) ''' to default +X in EEG.chanlocs']);
[~, chaninfo, chans] = eeg_checkchanlocs(tmpEEG.chanlocs, tmpEEG.chaninfo); % Merge all channels for rotation (FID and data channels)
if strcmpi(chaninfo.nosedir, '+y')
rotate = 270;
elseif strcmpi(chaninfo.nosedir, '-x')
rotate = 180;
else
rotate = 90;
end
for index = 1:length(chans)
rotategrad = rotate/180*pi;
coord = (chans(index).Y + chans(index).X*sqrt(-1))*exp(sqrt(-1)*-rotategrad);
chans(index).Y = real(coord);
chans(index).X = imag(coord);
if ~isempty(chans(index).theta)
chans(index).theta = chans(index).theta -rotate;
chans(index).sph_theta = chans(index).sph_theta+rotate;
if chans(index).theta <-180, chans(index).theta =chans(index).theta +360; end
if chans(index).sph_theta>180 , chans(index).sph_theta=chans(index).sph_theta-360; end
end
end
if isfield(tmpEEG, 'dipfit')
if isfield(tmpEEG.dipfit, 'coord_transform')
if isempty(tmpEEG.dipfit.coord_transform)
tmpEEG.dipfit.coord_transform = [0 0 0 0 0 0 1 1 1];
end
tmpEEG.dipfit.coord_transform(6) = tmpEEG.dipfit.coord_transform(6)+rotategrad;
end
end
chaninfo.originalnosedir = chaninfo.nosedir;
chaninfo.nosedir = '+X';
end
end
chanedit = chans;
complicated = true;
else
if ~isfield(chans, 'datachan')
[chanedit,dummy,complicated] = insertchans(chans, chaninfo);
else
chanedit = chans;
complicated = true;
end
end
nosevals = { '+X' '-X' '+Y' '-Y' };
if ~isfield(chaninfo, 'plotrad'), chaninfo.plotrad = []; end
if ~isfield(chaninfo, 'shrink'), chaninfo.shrink = []; end
if ~isfield(chaninfo, 'nosedir'), chaninfo.nosedir = nosevals{1}; end
% handles deprecated fields
% -------------------------
plotrad = [];
if isfield(chanedit, 'plotrad'),
plotrad = chanedit(1).plotrad;
chanedit = rmfield(chanedit, 'plotrad');
if ischar(plotrad) && ~isempty(str2num(plotrad)), plotrad = str2num(plotrad); end
chaninfo.plotrad = plotrad;
end
if isfield(chanedit, 'shrink') && ~isempty(chanedit(1).shrink)
shrinkorskirt = 1;
if ~ischar(chanedit(1).shrink)
plotrad = 0.5/(1-chanedit(1).shrink); % convert old values
end
chanedit = rmfield(chanedit, 'shrink');
chaninfo.plotrad = plotrad;
end
% set non-existent fields to []
% -----------------------------
fields = { 'labels' 'theta' 'radius' 'X' 'Y' 'Z' 'sph_theta' 'sph_phi' 'sph_radius' 'type' 'ref' 'urchan' };
fieldtype = { 'str' 'num' 'num' 'num' 'num' 'num' 'num' 'num' 'num' 'str' 'str' 'num' };
check_newfields = true; %length(fieldnames(chanedit)) < length(fields);
if ~isempty(chanedit)
for index = 1:length(fields)
if check_newfields && ~isfield(chanedit, fields{index})
% new field
% ---------
if strcmpi(fieldtype{index}, 'num')
chanedit = setfield(chanedit, {1}, fields{index}, []);
else
for indchan = 1:length(chanedit)
chanedit = setfield(chanedit, {indchan}, fields{index}, '');
end
end
else
% existing fields
% ---------------
allvals = {chanedit.(fields{index})};
if isnumeric(allvals{1}) && any(cellfun(@(x)~isempty(x) & all(isnan(x)), allvals))
posNaNs = find(cellfun(@(x)~isempty(x) & all(isnan(x)), allvals));
for iPos = 1:length(posNaNs)
chanedit = setfield(chanedit, {posNaNs(iPos)}, fields{index}, []);
end
end
if strcmpi(fieldtype{index}, 'num')
if ~all(cellfun('isclass',allvals,'double'))
nomconvert = cellfun(@isinteger, allvals);
if any(nomconvert)
for indConvert = find(nomconvert)
chanedit = setfield(chanedit, {indConvert}, fields{index}, double(allvals{indConvert}));
end
end
allvals = {chanedit.(fields{index})};
numok = cellfun(@isfloat, allvals);
if any(numok == 0)
for indConvert = find(numok == 0)
chanedit = setfield(chanedit, {indConvert}, fields{index}, []);
end
end
end
else
strok = cellfun('isclass', allvals,'char');
if strcmpi(fields{index}, 'labels'), prefix = 'E'; else prefix = ''; end
if any(strok == 0)
for indConvert = find(strok == 0)
try
strval = [ prefix num2str(getfield(chanedit, {indConvert}, fields{index})) ];
chanedit = setfield(chanedit, {indConvert}, fields{index}, strval);
catch
chanedit = setfield(chanedit, {indConvert}, fields{index}, '');
end
end
end
end
end
end
end
if ~isequal(fieldnames(chanedit)',fields)
try
chanedit = orderfields(chanedit, fields);
catch, end
end
% check channel labels
if isfield(chanedit, 'labels')
% prefix (EDF format specification)?
if strfind([chanedit.labels], 'EEG') % `contains() is not back compatible
chanprefixes = {'EEG-', 'EEG ', 'EEG' }; % order matters
tmp = {chanedit.labels};
if sum(~isnan(str2double( strrep(tmp, 'EEG', '')))) < 30 % more than 30 numerical channels, i.e., EEG001, do nothing
disp('Detected/removing ''EEG'' prefix from channel labels')
for idx = 1:length(chanprefixes)
tmp = strrep(tmp, chanprefixes(idx), '');
end
[chanedit.labels] = deal(tmp{:});
end
end
if strfind([chanedit.labels], 'RDA_') % `contains() is not back compatible
chanprefixes = { 'BrainVision RDA_' 'RDA_' }; % order matters
tmp = {chanedit.labels};
disp('Detected/removing prefix from channel labels')
for idx = 1:length(chanprefixes)
tmp = strrep(tmp, chanprefixes(idx), '');
end
[chanedit.labels] = deal(tmp{:});
end
% remove simple quotes or double quotes from channel labels
if sum(chanedit(1).labels == '''') == 2
tmp = {chanedit.labels};
tmp = strrep(tmp, '''', '');
[chanedit.labels] = deal(tmp{:});
end
if sum(chanedit(1).labels == '"') == 2
tmp = {chanedit.labels};
tmp = strrep(tmp, '"', '');
[chanedit.labels] = deal(tmp{:});
end
% duplicate labels?
tmp = sort({chanedit.labels});
if any(strcmp(tmp(1:end-1),tmp(2:end)))
disp('Warning: some channels have the same label');
end
% empty labels?
indEmpty = find(cellfun(@isempty, {chanedit.labels}));
if ~isempty(indEmpty)
tmpWarning = warning('backtrace');
warning backtrace off;
warning('channel labels should not be empty, creating unique labels');
warning(tmpWarning);
for index = indEmpty
chanedit(index).labels = sprintf('E%d', index);
end
end
% handle MEG
if ~isfield(chaninfo, 'topoplot')
if ~isempty(strfind([chanedit(1).labels], 'MLC11')) || (isfield(chanedit, 'type') && ~isempty(strfind(chanedit(1).type, 'meg')))
disp('MEG data detected and topoplot options not set, so setting them in EEG.chaninfo')
chaninfo.topoplot = { 'conv' 'on' 'headrad' 0.3 };
end
end
end
% remove fields
% -------------
if isfield(chanedit, 'sph_phi_besa' ), chanedit = rmfield(chanedit, 'sph_phi_besa'); end
if isfield(chanedit, 'sph_theta_besa'), chanedit = rmfield(chanedit, 'sph_theta_besa'); end
% Check if some channels need conversion
% --------------------------------------
chanX = cellfun('isempty',{ chanedit.X });
chanTheta = cellfun('isempty',{ chanedit.theta });
chanSphTheta = cellfun('isempty',{ chanedit.sph_theta });
if any(~chanX & chanTheta) || any(~chanSphTheta & chanTheta) || any(~chanX & chanSphTheta)
try
% convert them all
chanedit = convertlocs(chanedit,'auto');
catch
disp('eeg_checkchanlocs: Unable to convert electrode locations between coordinate systems');
end
end
% reconstruct the chans structure
% -------------------------------
if complicated
[chans, chaninfo.nodatchans] = getnodatchan( chanedit );
if ~isfield(chaninfo, 'nodatchans'), chaninfo.nodatchans = []; end
if isempty(chanedit)
for iField = 1:length(fields)
chanedit = setfield(chanedit, fields{iField}, []);
end
end
else
chans = rmfield(chanedit,'datachan');
chaninfo.nodatchans = [];
end
if processingEEGstruct
tmpEEG.chanlocs = chans;
tmpEEG.chaninfo = chaninfo;
chans = tmpEEG;
end
% ---------------------------------------------
% separate data channels from non-data channels
% ---------------------------------------------
function [chans, fidsval] = getnodatchan(chans)
if isfield(chans,'datachan')
[chans(cellfun('isempty',{chans.datachan})).datachan] = deal(0);
fids = [chans.datachan] == 0;
fidsval = chans(fids);
chans = rmfield(chans(~fids),'datachan');
else
fids = [];
end
% ----------------------------------------
% fuse data channels and non-data channels
% ----------------------------------------
function [chans, chaninfo,complicated] = insertchans(chans, chaninfo, nchans)
if nargin < 3, nchans = length(chans); end
[chans.datachan] = deal(1);
complicated = false; % whether we need complicated treatment of datachans & co further down the road.....
if isfield(chans,'type')
mask = strcmpi({chans.type},'FID') | strcmpi({chans.type},'IGNORE');
if any(mask)
[chans(mask).datachan] = deal(0);
complicated = true;
end
end
if length(chans) > nchans && nchans ~= 0 % reference at the end of the structure
chans(end).datachan = 0;
complicated = true;
end
if isfield(chaninfo, 'nodatchans')
if ~isempty(chaninfo.nodatchans) && isstruct(chaninfo.nodatchans)
chanlen = length(chans);
for index = 1:length(chaninfo.nodatchans)
fields = fieldnames( chaninfo.nodatchans );
ind = chanlen+index;
for f = 1:length( fields )
chans = setfield(chans, { ind }, fields{f}, getfield( chaninfo.nodatchans, { index }, fields{f}));
end
chans(ind).datachan = 0;
complicated = true;
end
chaninfo = rmfield(chaninfo, 'nodatchans');
% put these channels first
% ------------------------
% tmp = chans(chanlen+1:end);
% chans(length(tmp)+1:end) = chans(1:end-length(tmp));
% chans(1:length(tmp)) = tmp;
end
end
Datasets
Models
