% POP_STUDYDESIGN - create a STUDY design structure.
%
% Usage:
% >> [STUDY, ALLEEG] = pop_studydesign(STUDY, ALLEEG, key1, val1, ...);
%
% Inputs:
% STUDY - EEGLAB STUDY set
% ALLEEG - vector of the EEG datasets included in the STUDY structure
%
% Optional inputs:
%
% Authors: Arnaud Delorme, April 2010
% Copyright (C) Arnaud Delorme & Scott Makeig, SCCN/INC/UCSD, October 11, 2004, smakeig@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 [STUDY allcom] = pop_studydesign(STUDY, ALLEEG, designind, varargin);
allcom = '';
if nargin < 2
help pop_studydesign;
return;
end
if ~ischar(STUDY) && isfield(STUDY, 'currentdesign') && STUDY.currentdesign > length(STUDY.design)
STUDY.currentdesign = length(STUDY.design);
end
if nargin < 3 && ~ischar(STUDY)
%% create GUI
[ usrdat.factors usrdat.factorvals usrdat.factsubj usrdat.pairing] = std_getindvar(STUDY, 'both', 1);
usrdat.factors = { 'None' usrdat.factors{:} };
usrdat.factorvals = { {} usrdat.factorvals{:} };
usrdat.factsubj = { {} usrdat.factsubj{:} };
usrdat.subjects = STUDY.subject;
usrdat.datasetinfo = STUDY.datasetinfo;
usrdat.design = STUDY.design;
usrdat.filepath = STUDY.filepath;
for ind = 1:length(usrdat.design)
for iVar = length(usrdat.design(ind).variable):-1:1
if isempty(usrdat.design(ind).variable(iVar).label)
usrdat.design(ind).variable(iVar) = [];
end
end
end
% check numerical variables
for ind1 = 1:length(usrdat.factors)
if all(cellfun(@isnumeric, usrdat.factorvals{ind1}))
usrdat.numerical(ind1) = 1;
else usrdat.numerical(ind1) = 0;
end
end
cb_selectsubj = 'pop_studydesign(''selectsubj'', gcbf);';
cb_setsubj = 'pop_studydesign(''setsubj'', gcbf);';
cb_rename = 'pop_studydesign(''rename'', gcbf);';
cb_add = 'pop_studydesign(''add'', gcbf);';
cb_del = 'pop_studydesign(''del'', gcbf);';
cb_listboxfact1 = 'pop_studydesign(''selectfact'', gcf, 0);';
cb_listboxfact2 = 'pop_studydesign(''selectfact'', gcf, 1);';
cb_lbval = 'pop_studydesign(''updategui'', gcbf);';
cb_selectdesign = 'pop_studydesign(''selectdesign'', gcbf);';
cb_selectdata = 'pop_studydesign(''selectdatatrials'', gcbf);';
cb_selectfolder = 'pop_studydesign(''selectfolder'', gcbf);';
cb_setfolder = 'pop_studydesign(''updategui'', gcbf);';
cb_newvar = 'pop_studydesign(''newvar'', gcbf);';
cb_editvar = 'pop_studydesign(''editvar'', gcbf);';
cb_delvar = 'pop_studydesign(''delvar'', gcbf);';
cb_list = 'pop_studydesign(''list'', gcbf);';
cb_plotdmat = 'pop_studydesign(''plotdmat'', gcbf);';
cb_importgvar = 'pop_studydesign(''importgvar'', gcbf);';
icadefs;
% { 'style' 'text' 'string' 'Subjects' 'fontweight' 'bold' } ...
% { 'style' 'listbox' 'string' usrdat.subjects 'tag' 'lbsubj' 'min' 0 'max' 2 'value' 1 'callback' cb_selectsubj } ...
uilist = { ...
{ 'style' 'text' 'string' 'Include these subjects (default: all)' 'fontweight' 'bold' } ...
{ 'style' 'edit' 'string' '' 'tag' 'subjects' 'callback' cb_setsubj } ...
{ 'style' 'pushbutton' 'string' '...' 'callback' cb_selectsubj } ...
{ 'style' 'text' 'string' 'Design name' 'fontweight' 'bold' } ...
{ 'style' 'listbox' 'string' { usrdat.design.name } 'tag' 'listboxdesign' 'callback' cb_selectdesign 'value' STUDY.currentdesign } ...
{ 'style' 'pushbutton' 'string' 'New' 'callback' cb_add } ...
{ 'style' 'pushbutton' 'string' 'Rename' 'callback' cb_rename } ...
{ 'style' 'pushbutton' 'string' 'Delete' 'callback' cb_del } ...
...
{ 'panel' 'title' 'Edit the independent variables for this design' 'fontweight' 'bold' 'backgroundcolor' GUIBACKCOLOR } ...
{ 'style' 'text' 'string' '' 'fontweight' 'bold' } ...
{ 'style' 'pushbutton' 'string' 'New' 'callback' cb_newvar } ...
{ 'style' 'pushbutton' 'string' 'Edit' 'callback' cb_editvar } ...
{ 'style' 'pushbutton' 'string' 'Delete' 'callback' cb_delvar } ...
{ 'style' 'pushbutton' 'string' 'List factors' 'callback' cb_list } ...
{ 'style' 'listbox' 'string' '' 'tag' 'lbfact0' 'value' 2 } ...
{ 'style' 'checkbox' 'string' ' Re-save STUDY file (if saved previously)' 'tag' 'chk_save' 'value' 1 } };
% { 'style' 'checkbox' 'string' 'Delete all pre-computed datafiles' 'tag' 'chk_del' 'callback' cb_lbval } };
% { 'style' 'checkbox' 'string' 'Paired statistics' 'tag' 'lbpair0' 'callback' cb_lbval } ...
% { 'style' 'checkbox' 'string' 'Paired statistics' 'tag' 'lbpair1' 'callback' cb_lbval } ...
% { 'style' 'pushbutton' 'string' 'Plot' 'callback' cb_plotdmat} ...
ht = 11.5;
h2 = 1.1;
h1 = 1.5;
geometry = { {3 ht [1 1] [2 1] } ...
{3 ht [2.55 1] [1 1] } ...
{3 ht [3.6 1] [0.4 1] } ...
...
{3 ht [1 h1+1] [1 1] } ...
{3 ht [1 h1+2] [3 2.6] } ...
{3 ht [2.85 h1+1.15] [0.4 1] } ... % Edit
{3 ht [3.15 h1+1.15] [0.5 1] } ... % Raname
{3 ht [3.55 h1+1.15] [0.45 1] } ... % Delete
...
{3 ht [1 h2+5.4] [3 5.1] } ...
{3 ht [1.07 h2+6 ] [1 1] } ... % Indep variables
{3 ht [2.20 h2+6.2] [0.4 1] } ... % New
{3 ht [2.50 h2+6.2] [0.4 1] } ... % Edit
{3 ht [2.80 h2+6.2] [0.45 1] } ... % Delete
{3 ht [3.15 h2+6.2] [0.75 1] } ... % List var
{3 ht [1.07 h2+7 ] [2.85 3] } ... % listbox variable
{3 ht [1 h2+11 ] [3 1] } ...
};
% {3 ht [3.3 6+h2] [0.5 1] } ... % Subject text
% {3 ht [3.3 7+h2 ] [0.7 3] } ... % listbox subject
% {3 ht [1 9.8+h2] [3 1] } ...
for i = 1:length(geometry), geometry{i}{3} = geometry{i}{3}-1; end;
streval = [ 'pop_studydesign(''selectdesign'', gcf);' ];
[tmp usrdat tmp2 result] = inputgui('uilist', uilist, 'title', 'Edit STUDY design -- pop_studydesign()', 'helpbut', 'Web help', 'helpcom', 'web(''http://sccn.ucsd.edu/wiki/Chapter_03:_Working_with_STUDY_designs'', ''-browser'')', 'geom', geometry, 'userdata', usrdat, 'eval', streval);
if isempty(tmp), return; end
% call std_makedesign
% -------------------
des = usrdat.design;
allcom = '';
if length(des) < length(STUDY.design)
for index = length(STUDY.design):-1:length(des)+1
fprintf('Deleting STUDY design %d\n', index);
com = 'STUDY.design(index) = [];'; eval(com);
allcom = [ allcom 10 com ];
end
end
for index = 1:length(des)
tmpdes = des(index);
if ~isfield(tmpdes.variable, 'vartype'), tmpdes.variable(1).vartype = []; end;
if index > length(STUDY.design) || ~isequal(STUDY.design(index), tmpdes)
fprintf('Updating/creating STUDY design %d\n', index);
if isfield(tmpdes, 'variable')
for iVar = 1:length(tmpdes.variable)
if isempty(tmpdes.variable(iVar).vartype)
tmpdes.variable(iVar).vartype = 'categorical';
end
end
end
[STUDY com] = std_makedesign(STUDY, ALLEEG, index, tmpdes);
allcom = [ allcom 10 com ];
else
fprintf('STUDY design %d not modified\n', index);
end
end
if result.listboxdesign ~= STUDY.currentdesign
fprintf('Selecting STUDY design %d\n', result.listboxdesign);
com = sprintf('STUDY = std_selectdesign(STUDY, ALLEEG, %d);', result.listboxdesign); eval(com);
allcom = [ allcom 10 com ];
end
if result.chk_save == 1 && ~isempty(STUDY.filename)
fprintf('Resaving STUDY\n');
[STUDY ALLEEG com] = pop_savestudy(STUDY, ALLEEG, 'savemode', 'resave');
allcom = [ allcom 10 com ];
end
if ~isempty(allcom), allcom(1) = []; end
elseif ischar(STUDY)
com = STUDY;
fig = ALLEEG;
usrdat = get(fig, 'userdata');
datinfo = usrdat.datasetinfo;
des = usrdat.design;
subjects = usrdat.subjects;
filepath = usrdat.filepath;
val = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
switch com
% summary of callbacks
% case 'add', Add new study design
% case 'del', Delete study design
% case 'rename', Rename study design
%
% case 'selectdesign', select a specific design
% case 'updategui', update the study information (whenever the
% user click on a button
%
% case 'selectdatatrials', new GUI to select specific dataset and trials
% case 'selectdatatrialssel', % select in the GUI above
% case 'selectdatatrialsadd', % add new selection in the GUI above
case 'selectsubj'
strSubj = get(findobj(fig, 'tag', 'subjects'), 'string');
if ~isempty(strSubj)
res = str2cell(strSubj);
selected = eeg_chaninds(struct('labels', subjects), res);
else
selected = 1:length(subjects);
end
[inds, strSubj, cellSubj] = pop_chansel(struct('labels', subjects), 'select', selected);
if ~isempty(inds)
if length(inds) == length(subjects)
strSubj = '';
end
set(findobj(fig, 'tag', 'subjects'), 'string', strSubj);
disp('Warning: setting subjects for all designs');
for iDes = 1:length(des)
des(iDes).cases.value = cellSubj;
end
end
case 'setsubj'
strSubj = get(findobj(fig, 'tag', 'subjects'), 'string');
res = str2cell(strSubj);
if ~isempty(setdiff(res, subjects))
set(findobj(fig, 'tag', 'subjects'), 'string', '');
warndlg2('Unknown subject(s) - check syntax');
res = subjects';
end
for iDes = 1:length(des)
des(iDes).cases.value = res;
end
case 'add' % Add new study design
des(end+1) = des(val);
des(end).variable = [];
des(end).limo = [];
des(end).name = sprintf('Design %d', length(des));
set(findobj(fig, 'tag', 'listboxdesign'), 'string', { des.name }, 'value', length(des));
case 'del' % Delete study design
val = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
if val == 1
warndlg2('The first STUDY design cannot be removed, only modified');
return;
end
des(val) = [];
case 'rename' % Rename study design
val = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
strs = get(findobj(fig, 'tag', 'listboxdesign'), 'string');
result = inputdlg2( { 'Study design name: ' }, ...
'Rename Study Design', 1, { strs{val} }, 'pop_studydesign');
if isempty(result), return; end
des(val).name = result{1};
case 'updategui' % update the study information (whenever the user click on a button)
val = min(val, length(des));
set(findobj(fig, 'tag', 'listboxdesign'), 'string', { des.name }, 'value', val );
set(findobj(fig, 'tag', 'edit_storedir'), 'string', des(val).filepath);
set(findobj(fig, 'tag', 'edit_selectdattrials'), 'string', vararg2str( des(val).include ));
% update subjects
if length(des(val).cases.value) ~= length(subjects)
tmp = des(val).cases.value;
tmp = cellfun(@(x) [ x ' ' ], tmp, 'uniformoutput', false);
subjectStr = [tmp{:}];
set(findobj(fig, 'tag', 'subjects'), 'string', subjectStr);
end
% categorical var
curVal = {};
for iVar = 1:length(des(val).variable)
if ~isempty(des(val).variable(iVar).value) && strcmpi(des(val).variable(iVar).vartype, 'categorical')
valStr = '';
valStrCell = encodevals(des(val).variable(iVar).value);
for iVal = 1:length(valStrCell)
valStr = [ valStr sprintf('%s - ', valStrCell{iVal}) ];
end
valStr(end-2:end) = [];
strCond = sprintf('Categorical variable: %s - Values (%s)', des(val).variable(iVar).label, valStr);
else
strCond = sprintf('Continuous variable: %s', des(val).variable(iVar).label);
end
curVal{end+1} = strCond;
end
curValLbfact = get(findobj(fig, 'tag', 'lbfact0'), 'value');
valVar = min(curValLbfact, length(des(val).variable(iVar)));
if isequal(valVar, 0), valVar = []; end
if isempty(valVar) && ~isempty(curVal), valVar = 1; end
set(findobj(fig, 'tag', 'lbfact0'), 'string', curVal, 'value', valVar);
return;
case 'selectdatatrials' % select specific dataset and trials
usrdat.parent = fig;
cb_sel = 'pop_studydesign(''selectdatatrialssel'',gcbf);';
cb_add = 'pop_studydesign(''selectdatatrialsadd'',gcbf);';
uilist = { { 'style' 'text' 'string' strvcat('Press ''Add'' to add data', 'selection. Multiple variables', 'are combined using AND.') } ...
{ 'style' 'text' 'string' 'Select data based on variable', 'fontweight' 'bold' } ...
{ 'style' 'listbox' 'string' usrdat.factors 'tag' 'lbfact2' 'callback' cb_sel 'value' 1 } ...
{ 'style' 'text' 'string' 'Select data based on value(s)' 'fontweight' 'bold' } ...
{ 'style' 'listbox' 'string' encodevals(usrdat.factorvals{1}) 'tag' 'lbval2' 'min' 0 'max' 2} };
cb_renamehelp = [ 'set(findobj(gcf, ''tag'', ''help''), ''string'', ''Add'');' ...
'set(findobj(gcf, ''tag'', ''cancel''), ''string'', ''Erase'', ''callback'', ''set(findobj(''''tag'''', ''''edit_selectdattrials''''), ''''string'''', '''''''');'');' ...
'set(findobj(gcf, ''tag'', ''ok''), ''string'', ''Close'');' ];
usrdat.fig = fig;
inputgui('uilist', uilist, 'geometry', { [1] [1] [1] [1] [1] }, 'geomvert', [2 1 2.5 1 2.5], ...
'helpcom', cb_add, 'userdata', usrdat, 'eval', cb_renamehelp);
return;
case 'selectdatatrialssel' % select in the GUI above
val1 = get(findobj(fig, 'tag', 'lbfact2'), 'value');
valfact = [1:length(usrdat.factorvals{val1})];
tmpval = get(findobj(fig, 'tag', 'lbval2'), 'value');
if max(tmpval) > max(valfact)
set(findobj(fig, 'tag', 'lbval2'), 'value', valfact, 'string', encodevals(usrdat.factorvals{val1}));
else
set(findobj(fig, 'tag', 'lbval2'), 'string', encodevals(usrdat.factorvals{val1}), 'value', valfact);
end
return;
case 'selectdatatrialsadd' % Add button in the GUI above
val1 = get(findobj(fig, 'tag', 'lbfact2'), 'value');
val2 = get(findobj(fig, 'tag', 'lbval2') , 'value');
%close(fig);
fig = usrdat.parent;
val = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
des(val).include{end+1} = { usrdat.factors{val1} usrdat.factorvals{val1}(val2) };
case 'updateinclude' % Add button in the GUI above
try
des(val).include = eval( get(findobj(fig, 'tag', 'lbfact2'), 'string') );
catch,
warndlg2('Syntax error');
end
case 'selectfolder'
res = uigetdir;
if ~isempty(findstr(filepath, res)) && findstr(filepath, res) == 1 && ~isequal(filepath, res)
res = res(length(filepath)+2:end);
end
if res(1) == 0, return; end
des(val).filepath = res;
case 'list'
val1 = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
val2 = get(findobj(fig, 'tag', 'lbfact0'), 'value');
STD.datasetinfo = datinfo;
STD.design = des(val1);
STD = std_addvarlevel(STD, 1);
pop_listfactors(STD.design);
case 'delvar'
val1 = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
val2 = get(findobj(fig, 'tag', 'lbfact0'), 'value');
des(val1).variable(val2) = [];
case 'newvar'
val = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
[tmpVar tmpVarList cat] = pop_addindepvar(usrdat);
if ~isempty(tmpVar) && ~strcmp(tmpVar,'None')
des(val).variable(end+1).label = tmpVar;
des(val).variable(end ).value = tmpVarList; % empty for cont var
if cat, des(val).variable(end).vartype = 'categorical'; else des(val).variable(end).vartype = 'continuous'; end
end
% update var list
[ usrdat.factors usrdat.factorvals usrdat.factsubj usrdat.pairing] = std_getindvar(struct('design', des, 'datasetinfo', datinfo), 'both', 1);
usrdat.factors = { 'None' usrdat.factors{:} };
usrdat.factorvals = { {} usrdat.factorvals{:} };
usrdat.factsubj = { {} usrdat.factsubj{:} };
case 'editvar'
val = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
val2 = get(findobj(fig, 'tag', 'lbfact0'), 'value');
if isempty(val2), return; end
tmpval = des(val).variable(val2).value;
if strcmpi(des(val).variable(val2).vartype, 'continuous'), tmpval = []; end
[tmpVar tmpVarList cat] = pop_addindepvar(usrdat, [], des(val).variable(val2).label, tmpval);
if ~isempty(tmpVar) && ~strcmp(tmpVar,'None')
des(val).variable(val2).label = tmpVar;
des(val).variable(val2).value = tmpVarList; % empty for cont var
if cat, des(val).variable(val2).vartype = 'categorical'; else des(val).variable(val2).vartype = 'continuous'; end
end
% update var list
[ usrdat.factors usrdat.factorvals usrdat.factsubj usrdat.pairing] = std_getindvar(struct('design', des, 'datasetinfo', datinfo), 'both', 1);
usrdat.factors = { 'None' usrdat.factors{:} };
usrdat.factorvals = { {} usrdat.factorvals{:} };
usrdat.factsubj = { {} usrdat.factsubj{:} };
case 'plotdmat'
val = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
std_plotdmat(usrdat.design(val),usrdat.datasetinfo);
case 'importgvar'
val = get(findobj(fig, 'tag', 'listboxdesign'), 'value');
usrdat = pop_importgroupvar(usrdat,val);
end
usrdat.design = des;
set(fig, 'userdata', usrdat);
pop_studydesign( 'updategui', fig);
if strcmpi(com, 'newvar')
set(findobj(fig, 'tag', 'lbfact0'), 'value', length(des(val).variable));
end
end
function res = str2cell(strSubj)
res = textscan(strSubj, '%s');
res = res{1};
for iRes = 1:length(res)
res{iRes}(res{iRes} == '''') = [];
end
res = res';
function res = strmatchmult(a, b)
if isempty(b), res = []; return; end
res = zeros(1,length(a));
for index = 1:length(a)
tmpi = std_indvarmatch(a{index}, b);
res(index) = tmpi(1); % in case there is a duplicate
end
%[tmp ind] = mysetdiff(b, a);
%res = setdiff_bc([1:length(b)], ind);
function cellarray = mysort(cellarray)
return; % was crashing for combinations of selection
% also there is no reason the order should be different
if ~isempty(cellarray) && ischar(cellarray{1})
cellarray = sort(cellarray);
end
function [cellout inds ] = mysetdiff(cell1, cell2)
if (~isempty(cell1) && ischar(cell1{1})) || (~isempty(cell2) && ischar(cell2{1}))
[ cellout inds ] = setdiff_bc(cell1, cell2);
else [ cellout inds ] = setdiff_bc([ cell1{:} ], [ cell2{:} ]);
cellout = mattocell(cellout);
end
% encode string an numerical values for list boxes
function cellout = encodevals(cellin)
if isempty(cellin)
cellout = {};
elseif ~iscell(cellin)
cellout = { num2str(cellin) };
elseif ischar(cellin{1}) || iscell(cellin{1})
for index = 1:length(cellin)
if ischar(cellin{index})
cellout{index} = cellin{index};
else
cellout{index} = cellin{index}{1};
for indcell = 2:length(cellin{index})
cellout{index} = [ cellout{index} ' & ' cellin{index}{indcell} ];
end
end
end
else
for index = 1:length(cellin)
if length(cellin{index}) == 1
cellout{index} = num2str(cellin{index});
else
cellout{index} = num2str(cellin{index}(1));
for indcell = 2:length(cellin{index})
cellout{index} = [ cellout{index} ' & ' num2str(cellin{index}(indcell)) ];
end
end
end
end
Datasets
Models
