% STD_READLIMOFILE- Read limo file into eeglab structure
%
% Usage:
% >> [MeasureData, parameters, MeasureRange1, MeasureRange2] = std_readfilelimo(filestruct,'key', val)
%
% Inputs:
% filestrcuct - Structure with the following fields:
% datasets : Index of he datasets in datasetinfo (real)
% trials : index of the trials to pull out (cell array)
% value : Cell array with the values of the independent variables of the set.
% case : name of the subject /case
% filebase : Full Path and filename of the
%
% Optional inputs:
% 'measure' - ['itcbeta1' | 'itcbeta2' |'itcr2r' |'itcr2f' |'itcr2p' |
% 'erpbeta1' | 'erpbeta2' |'erpr2r' |'erpr2f' |'erpr2p' |
% 'erspbeta1'| 'erspbeta2'|'erspr2r'|'erspr2f'|'erspr2p'|
% 'specbeta1'| 'specbeta2'|'specr2r'|'specr2f'|'specr2p ]
% 'timelimits' - [min max] ERSP time (latency in ms) range of interest
% 'freqlimits' - [min max] ERSP frequency range (in Hz) of interest
% 'channels' - [cell or integer] channel labels - for instance
% { 'cz' 'pz' }
%
% Outputs:
% MeasureData - the multi-channel or multi-component data. The size of this
% output depends on the number of dimension (for ERSP or ERP
% for instance). The last dimension is channels or components.
% parameters - structure containing parameters saved with the data file.
% MeasureRange1 - time points (ERP, ERSP) or frequency points (spectrum)
% MeasureRange2 - frequency points (ERSP, ITCs)
%
%
%
% See also:
%
%
% Authors: Arnaud Delorme, Ramon Martinez-Cancino
%
% Copyright (C) 2014 Ramon Martinez-Cancino,INC, SCCN
%
% 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 [MeasureData, parameters, MeasureRange1, MeasureRange2] = std_readfilelimo(filestruct, varargin)
parameters = [];
try
options = varargin;
if ~isempty( varargin ),
for i = 1:2:numel(options)
g.(options{i}) = options{i+1};
end
else g = []; end
catch
error('std_readfilelimo() error: calling convention {''key'', value, ... } error');
end
try, g.channels; catch, g.channels = []; end; %
try, g.components; catch, g.components = []; end; %
try, g.measure; catch, g.measure = []; end; %
try, g.timelimits; catch, g.timelimits = []; end; %
try, g.triallimits; catch, g.triallimits = []; end; %
try, g.freqlimits; catch, g.freqlimits = []; end; %
try, g.getparamonly; catch, g.getparamonly = 'off'; end; % work on this
% Checking entries
%..........................................................................
% Indetify if components or channels
%..........................................................................
if isempty(g.components)
chanoric = 'Channels';
else
chanoric = 'Components';
end
% Identify type of analysis for limo stuff path
%..........................................................................
if strcmp(g.measure(1:3),'erp') && strcmp(chanoric,'Channels')
type = 'Channels_Time';
elseif strcmp(g.measure(1:3),'erp') && strcmp(chanoric,'Components')
type = 'Components_Time';
elseif strcmp(g.measure(1:3),'spe') && strcmp(chanoric,'Channels')
type = 'Channels_Frequency';
elseif strcmp(g.measure(1:3),'spe') && strcmp(chanoric,'Components')
type = 'Components_Frequency';
elseif strcmp(g.measure(1:3),'ers') && strcmp(chanoric,'Channels')
type = 'Channels_Time-Frequency';
elseif strcmp(g.measure(1:3),'ers') && strcmp(chanoric,'Components')
type = 'Components_Time-Frequency';
end
% Study pathname
%..........................................................................
filebasetemp = filestruct.filebase;
[path, name, tmp] = fileparts(filebasetemp);
[path2study,tmp,tmp]= fileparts(path);
% Getting design index in STUDY
%..........................................................................
designindx = name(7:9);
if isempty(str2num(designindx))
designindx = designindx(1:2);
if isempty(str2num(designindx))
designindx = designindx(1);
if isempty(str2num(designindx))
error('std_readfilelimo(): Fail to detect index of the design in STUDY');
end
end
end
% Creating path to LIMO.mat and loading it
%..........................................................................
filelist = dir(path2study);
fileindxtmp = strmatch('LIMO_', {filelist.name});
limofoldername = filelist(fileindxtmp(1)).name;
path2limofiles = [path2study filesep limofoldername filesep filestruct.case filesep 'GLM' num2str(designindx) '_' type];
structmp = load ([path2limofiles filesep 'LIMO.mat']);
limostruct = structmp.LIMO;
% Identifying condition
%..........................................................................
dims = []; cond_indxs = [];
condtemp = {limostruct.data.studyinfo.value};
for i = 1 : length(condtemp)
dims(i) = length(condtemp{i});
tmp = condtemp{i};
for j = 1: dims(i)
tmp{j} = num2str(tmp{j});
end
condtemp{i} = tmp;
cond_indxs(i) = find(strcmp(condtemp{i},num2str(filestruct.value{i})));
end
% Sub2ind stuff
command = 'sub2ind(dims';
for i = 1: length(dims)
command = [command ',cond_indxs(' num2str(i) ')'];
end
command = [command ')'];
CondIndx = eval(command);
% Checking time and set TimeIndxVec if type = TIME
%..........................................................................
if all([~isempty(g.timelimits),isfield(limostruct.data,'sampling_rate')])
if any([g.timelimits(1) < limostruct.data.start, g.timelimits(2) > limostruct.data.end])
error('std_readfilelimo(): Time indices provided are out of bonds');
else
TimeVec = limostruct.data.start: 1000/limostruct.data.sampling_rate:limostruct.data.end
[tmp,TimeIndx(1)] = min(abs(TimeVec - g.timelimits(1)));
[tmp,TimeIndx(2)] = min(abs(TimeVec - g.timelimits(2)));
TimeIndxVec = TimeIndx(1):TimeIndx(2);
end
elseif all([isempty(g.timelimits),isfield(limostruct.data,'sampling_rate')]) % will use all the timepoints
TimeIndxVec = 1:length(limostruct.data.start: 1000/limostruct.data.sampling_rate:limostruct.data.end);
end
% Checking frequencies and set FreqIndxVec if type = Frequency
%..........................................................................
if all([~isempty(g.freqlimits),isfield(limostruct.data,'freqlist')])
if any([g.freqlimits(1) < limostruct.data.lowf, g.freqlimits(2) > limostruct.data.highf])
error('std_readfilelimo(): Frequency indices provided are out of bonds');
else
[tmp,FreqIndx(1)] = min(abs(limostruct.data.freqlist - g.freqlimits(1)));
[tmp,FreqIndx(2)] = min(abs(limostruct.data.freqlist - g.freqlimits(2)));
FreqIndxVec = FreqIndx(1):FreqIndx(2);
end
elseif all([isempty(g.freqlimits),isfield(limostruct.data,'freqlist')]) % will use all frequencies
FreqIndxVec = 1 : length(limostruct.data.freqlist);
end
% Checking frequencies and time and set FreqIndxVec and TimeIndxVec if type = Time-Frequency
%..........................................................................
if all([isfield(limostruct.data,'tf_times'), isfield(limostruct.data,'tf_freq')])
%1- Time
if ~isempty(g.timelimits)
if any([g.timelimits(1) < limostruct.data.start, g.timelimits(2) > limostruct.data.end])
error('std_readfilelimo(): Time indices provided are out of bonds');
else
[tmp,TimeIndx(1)] = min(abs(limostruct.data.tf_times - g.timelimits(1)));
[tmp,TimeIndx(2)] = min(abs(limostruct.data.tf_times - g.timelimits(2)));
TimeIndxVec = TimeIndx(1):TimeIndx(2);
end
else % will use all timepoints
TimeIndxVec = 1:length(limostruct.data.tf_times);
end
%2- Frequency
if ~isempty(g.freqlimits)
if any([g.freqlimits(1) < limostruct.data.lowf, g.freqlimits(2) > limostruct.data.highf])
error('std_readfilelimo(): Frequency indices provided are out of bonds');
else
[tmp,FreqIndx(1)] = min(abs(limostruct.data.tf_freqs - g.freqlimits(1)));
[tmp,FreqIndx(2)] = min(abs(limostruct.data.tf_freqs - g.freqlimits(2)));
FreqIndxVec = FreqIndx(1):FreqIndx(2);
end
else % will use all frequencies
FreqIndxVec = 1:length(limostruct.data.tf_freqs);
end
end
% Checking channels or ic to load
%..........................................................................
% 1- Channels
if isempty(g.channels) && strcmp(chanoric, 'Channels')
ChanIcIndx = 1:length({limostruct.data.chanlocs.labels});
elseif ~isempty(g.channels) && strcmp(chanoric, 'Channels')
for i = 1 : length(g.channels)
if isempty(find(strcmp(lower(g.channels(i)),lower({limostruct.data.chanlocs.labels}))))
error('std_readfilelimo(): Invalid channel label');
else
ChanIcIndx = find(strcmp(lower(g.channels(i)),lower({limostruct.data.chanlocs.labels})));
end
end
end
% 2- Component
if isempty(g.components) && strcmp(chanoric, 'Components')
ChanIcIndx = 1:length({limostruct.data.chanlocs.labels});
elseif ~isempty(g.channels) && strcmp(chanoric, 'Components')
for i = 1 : length(g.channels)
if isempty(find(strcmp(g.channels(i),{limostruct.data.chanlocs.labels})))
error('std_readfilelimo(): Invalid channel label');
else
ChanIcIndx = find(strcmp(g.channels(i),{limostruct.data.chanlocs.labels}));
end
end
end
% Retrieving data
%..........................................................................
if isfield(limostruct.data,'sampling_rate')
TimeVec = limostruct.data.start: 1000/limostruct.data.sampling_rate:limostruct.data.end
end
switch g.measure
% beta1
%..................................................................
case 'erpbeta1'
datatmp = load([path2limofiles filesep 'Betas.mat']); % PUT THIS OUT OF THE LOOP
data = datatmp.Betas;
MeasureData = data(ChanIcIndx,TimeIndxVec,CondIndx); % Chan/IC x Time x Condition
case 'specbeta1'
datatmp = load([path2limofiles filesep 'Betas.mat']);
data = datatmp.Betas;
MeasureData = data(ChanIcIndx,FreqIndxVec,CondIndx); % Chan/IC x Freq x Condition
case {'erspbeta1','itcbeta1'}
datatmp = load([path2limofiles filesep 'Betas.mat']);
data = datatmp.Betas;
MeasureData = data(FreqIndxVec, TimeIndxVec,CondIndx); % Freq x Time x Condition
% beta2
%..................................................................
case {'erpbeta2','erspbeta2','specbeta2','itcbeta2'}
error('std_readfilelimo(): Invalid option in this realease');
% erpr2
%..................................................................
case 'erpr2r'
datatmp = load([path2limofiles filesep 'R2.mat']);
data = datatmp.R2;
MeasureData = data(ChanIcIndx,TimeIndxVec,1);
case 'erpr2f'
datatmp = load([path2limofiles filesep 'R2.mat']);
data = datatmp.R2;
MeasureData = data(ChanIcIndx,TimeIndxVec,2);
case 'erpr2p'
datatmp = load([path2limofiles filesep 'R2.mat']);
data = datatmp.R2;
MeasureData = data(ChanIcIndx,TimeIndxVec,3);
% erspr2 & itcr2
%..................................................................
case {'erspr2r','itcr2r'}
datatmp = load([path2limofiles filesep 'R2.mat']);
data = datatmp.R2;
MeasureData = data(FreqIndxVec,TimeIndxVec,1);
case {'erspr2f','itcr2f'}
datatmp = load([path2limofiles filesep 'R2.mat']);
data = datatmp.R2;
MeasureData = data(FreqIndxVec,TimeIndxVec,2);
case {'erspr2p','itcr2p'}
datatmp = load([path2limofiles filesep 'R2.mat']);
data = datatmp.R2;
MeasureData = data(FreqIndxVec,TimeIndxVec,3);
%spec
%..................................................................
case {'specr2r'}
datatmp = load([path2limofiles filesep 'R2.mat']);
data = datatmp.R2;
MeasureData = data(ChanIcIndx,FreqIndxVec,1);
case {'specr2f'}
datatmp = load([path2limofiles filesep 'R2.mat']);
data = datatmp.R2;
MeasureData = data(ChanIcIndx,FreqIndxVec,2);
case {'specr2p'}
datatmp = load([path2limofiles filesep 'R2.mat']);
data = datatmp.R2;
MeasureData = data(ChanIcIndx,FreqIndxVec,3);
end
% Measures ranges
%..........................................................................
switch g.measure(1:3)
case 'erp'
MeasureRange1 = TimeVec(TimeIndxVec);
MeasureRange2 = [];
case {'ers','itc'}
MeasureRange1 = limostruct.data.tf_times(TimeIndxVec);
MeasureRange2 = limostruct.data.tf_freqs(FreqIndxVec);
case 'spe'
MeasureRange1 = limostruct.data.freqlist(FreqIndxVec);
MeasureRange2 = [];
end
Datasets
Models
