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[422372]: / functions / popfunc / pop_icathresh.m

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% POP_ICATHRESH - main menu for choosing threshold for component

%                      rejection in EEGLAB. 

%

% Usage:

%   >> [OUTEEG rej] = pop_icathresh(INEEG, threshval, rejmethod, 

%                                      rejvalue, interact);

%

% Inputs:

%   INEEG      - input dataset

%   threshval  - values of thresholds for each of the 3 statistical

%                measures. Default is [] and the program uses the value

%                in the dataset.

%   rejmethod  - either 'percent', 'dataset' or 'current'. 'percent'

%                will reject a given percentage of components with

%                the highest value in one or several statistical 

%                measure. 'dataset' will use an other dataset for

%                calibration. 'current' will use the current dataset

%                for calibration. Default is 'current'.    

%   rejvalue   - percentage if rejmethod is 'percent', dataset number

%                if rejmethod is 'dataset' (no input if 'current'). If it

%                is a percentage, '25' for instance means that the 25%  

%                independent components with the highest values of one  

%                statistical measure are  rejected. Note that, one can 

%                also enter one percentage per statistical value (such as 

%                25 20 30).

%   interact   - interactive windows or just rejection

%

% Inputs:

%   OUTEEG     - output dataset with updated thresholds 

%   rej        - new rejection array   

%

% Graphic interface:

%   The graphic interface is divided into 3 parts. On the top, the 

% experimenter chooses the basis for the component rejection (see 

% rejmethod input). On the middle panel, the user can tune thresholds

% manually and plot the distribution of statistical values. Each time 

% that setting of one of these two top panels is modified, the curve

% on the third panel are redrawn.   

%   The third panel is composed of 3 graphs, one for each statistical 

% measure. The blue curve on each graph indicates the accuracy of the

% measure to detect artifactual components and non-artifactual 

% components of a dataset. Note that 'artifactual components are 

% defined with the rejection methods fields on the top (if you use 

% the percentage methods, these artifactual components may not actually

% be artifactual). For accurate rejection, one should first reject

% artifactual component manually and then set up the threshold to

% approximate this manual rejection. The green curve indicate the

% rejection when all measure are considered. Points on the blue and 

% on the green curves indicate the position of the current threshold on

% the parametric curve. Not that for the green cumulative curve, this

% point is at the same location for all graphs.

%   How to tune the threshold? To tune the threshold, one should try to 

% maximize the detection of non-artifactual components (because it is

% preferable to miss some artifactual components than to classify as

% artifactual non-artifact components). 

%

% Author: Arnaud Delorme, CNL / Salk Institute, 2001

%

% See also: EEGLAB



% Copyright (C) 2001 Arnaud Delorme, Salk Institute, 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.



%PROBLEM: when the % is set and we change manually the threshold,

% the software comes back to the percentage rejection



% 01-25-02 reformated help & license -ad 



function [EEG, rej, com] = pop_icathresh( EEG, threshval, rejmethod, rejvalue, interact); 



com = [];

rej = EEG.reject.gcompreject;

if nargin < 1

	help pop_icathresh;

	return;	

end



if nargin < 2

	threshval = [];

end

if nargin < 3

	rejmethod = 'current';

end

if nargin < 4

	rejvalue = 25;

end

if nargin < 5

	interact = 1;

end

if ~isempty(threshval)

	EEG.reject.threshentropy = threshval(1);

	EEG.reject.threshkurtact = threshval(2);

	EEG.reject.threshkurtdist = threshval(3);

end



tagmenu = 'pop_icathresh';



if ~isempty( findobj('tag', tagmenu))

	error('cannot open two identical windows, close the first one first');

end



% the current rejection will be stored in userdata of the figure

% --------------------------------------------------------------

gcf = figure('visible', 'off', 'numbertitle', 'off', 'name', 'Choose thresholds', 'tag', tagmenu, 'userdata', rej);

pos = get(gca, 'position');

q = [pos(1) pos(2) 0 0];

s = [pos(3) pos(4) pos(3) pos(4)]./100;

axis off;



% definition of callbacks

% -----------------------



cb_cancel  = [  'userdat = get(gcbo, ''userdata'');' ... % restore thresholds

				'EEG.reject.threshentropy  = userdat{1};' ...

				'EEG.reject.threshkurtact  = userdat{2};' ...

				'EEG.reject.threshkurtdist = userdat{3};' ...

				'clear userdat; close(gcbf);' ];



drawgraphs  = [ 'if isempty( gcbf ), fig = gcf; else fig = gcbf; end;' ... % determine the figure handler

                'if get( findobj(''parent'', fig, ''tag'', ''Ipercent''), ''value'') == 1, ' ... % test if percentage

				'   perc = str2num(get( findobj(''parent'', fig, ''tag'', ''Ipercenttext''), ''String''));' ... 

				'   if length(perc < 2), perc = [perc perc perc]; end;' ...

				'   perc = round((100-perc) * length( EEG.stats.compenta) / 100);' ... % convert the percentage

				'   method = zeros( size( EEG.stats.compenta ) );' ...

				'   [tmprej tmpindex] = sort(EEG.stats.compenta(:));' ...

				'   method( tmpindex(perc(1)+1:end) ) = 1;' ...

				'   set( findobj(''parent'', fig, ''tag'', ''entstring''), ''string'', num2str(tmprej(perc(1)+1)));' ... % update threshold 

				'   [tmprej tmpindex] = sort(EEG.stats.compkurta(:));' ...

				'   method( tmpindex(perc(2)+1:end) ) = 1;' ...

				'   set( findobj(''parent'', fig, ''tag'', ''kurtstring''), ''string'', num2str(tmprej(perc(1)+1)));' ... % update threshold 

				'   [tmprej tmpindex] = sort(EEG.stats.compkurtdist(:));' ...

				'   method( tmpindex(perc(3)+1:end) ) = 1;' ...

				'   set( findobj(''parent'', fig, ''tag'', ''kurtdiststring''), ''string'', num2str(tmprej(perc(1)+1)));' ... % update threshold 

				'   allvalues = [EEG.stats.compenta(:) EEG.stats.compkurta(:) EEG.stats.compkurtdist(:) ];' ...	

				'   clear perc tmprej tmpindex;' ...

                'end;' ...

				'if get( findobj(''parent'', fig, ''tag'', ''Iother''), ''value'') == 1, ' ... % test if other dataset

				'   di = str2num(get( findobj(''parent'', fig, ''tag'', ''Iothertext''), ''String''));' ... 

				'   if isempty( di ), clear fig; return; end;' ...

				'   method    = ALLEEG(di).reject.gcompreject'';' ... 

				'   allvalues = [ALLEEG(di).stats.compenta(:) ALLEEG(di).stats.compkurta(:) ALLEEG(di).stats.compkurtdist(:) ];' ...	

				'   clear di;' ...

                'end;' ...

				'if get( findobj(''parent'', fig, ''tag'', ''Icurrent''), ''value'') == 1, ' ... % test if current dataset

				'   method = EEG.reject.gcompreject'';' ... 

				'   allvalues = [EEG.stats.compenta(:) EEG.stats.compkurta(:) EEG.stats.compkurtdist(:) ];' ...	

                'end;' ...

				'axes( findobj( ''parent'', fig, ''tag'', ''graphent'')); cla;' ...

                '[tmp1 tmp2 tmp3] = drawproba( method, allvalues, [0 EEG.reject.threshkurtact EEG.reject.threshkurtdist ], ' ...

				'   { ''&'' ''|'' }, EEG.reject.threshentropy, ''Entropy of activity'',''Artifact detection (%)'', ''Non-artifact detection (%)'');' ...

				'set(gca, ''tag'', ''graphent'');' ...

				'axes( findobj( ''parent'', fig, ''tag'', ''graphkurt'')); cla;' ...

                '[tmp1 tmp2 tmp3] = drawproba( method, allvalues, [EEG.reject.threshentropy 0 EEG.reject.threshkurtdist ], ' ...

				'   { ''&'' ''|'' }, EEG.reject.threshkurtact, ''Kurtosis of activity'', ''Artifact detection (%)'', '''');' ...

				'set(gca, ''tag'', ''graphkurt'');' ...

				'axes( findobj( ''parent'', fig, ''tag'', ''graphkurtdist'')); cla;' ...

                '[tmp1 tmp2 tmp3] = drawproba( method, allvalues, [EEG.reject.threshentropy EEG.reject.threshkurtact 0 ], ' ...

				'   { ''&'' ''|'' }, EEG.reject.threshkurtdist, ''Kurtosis of topography'', ''Artifact detection (%)'', '''');' ...

				'set(gca, ''tag'', ''graphkurtdist'');' ...

				'clear method allvalues fig;' ...

				];

                                    

cb_percent = [  'if isempty( gcbf ), fig = gcf; else fig = gcbf; end;' ... % determine the figure handler

                'set( findobj(''parent'', fig, ''tag'', ''Ipercent''), ''value'', 1);'...

				'set( findobj(''parent'', fig, ''tag'', ''Iother''), ''value'', 0);' ...

				'set( findobj(''parent'', fig, ''tag'', ''Icurrent''), ''value'', 0);' ...

				'set( findobj(''parent'', fig, ''tag'', ''Ipercenttext''), ''enable'', ''on'');' ...

				'set( findobj(''parent'', fig, ''tag'', ''Iothertext''), ''enable'', ''off''); clear fig;' drawgraphs ];

				

cb_other   = [  'if isempty( gcbf ), fig = gcf; else fig = gcbf; end;' ... % determine the figure handler

                'set( findobj(''parent'', fig, ''tag'', ''Iother''), ''value'', 1);'...

				'set( findobj(''parent'', fig, ''tag'', ''Ipercent''), ''value'', 0);' ...

				'set( findobj(''parent'', fig, ''tag'', ''Icurrent''), ''value'', 0);' ...

				'set( findobj(''parent'', fig, ''tag'', ''Ipercenttext''), ''enable'', ''off'');' ...

				'set( findobj(''parent'', fig, ''tag'', ''Iothertext''), ''enable'', ''on''); clear fig;' drawgraphs ];

				

cb_current = [  'if isempty( gcbf ), fig = gcf; else fig = gcbf; end;' ... % determine the figure handler

                'set( findobj(''parent'', fig, ''tag'', ''Icurrent''), ''value'', 1);'...

				'set( findobj(''parent'', fig, ''tag'', ''Iother''), ''value'', 0);' ...

				'set( findobj(''parent'', fig, ''tag'', ''Ipercent''), ''value'', 0);' ...

				'set( findobj(''parent'', fig, ''tag'', ''Ipercenttext''), ''enable'', ''off'');' ...

				'set( findobj(''parent'', fig, ''tag'', ''Iothertext''), ''enable'', ''off''); clear fig;' drawgraphs ];



cb_entropy  = [ 'EEG.reject.threshentropy = str2num(get(gcbo, ''string''));' ...

				drawgraphs ];

cb_kurtact  = [ 'EEG.reject.threshkurtact = str2num(get(gcbo, ''string''));' ...

				drawgraphs ];

cb_kurtdist  = [ 'EEG.reject.threshkurtdist = str2num(get(gcbo, ''string''));' ...

				drawgraphs ];



if interact

	cb_calrej = [ 'ButtonName=questdlg2( ''This will erase previous projections'', ''Confirmation'', ''CANCEL'', ''OK'', ''OK'');' ]

else

	cb_calrej = [ 'ButtonName= ''OK''' ];	

end

cb_calrej = [ cb_calrej ...

    		  'switch ButtonName,' ...

       	 	  '   case ''OK'',' ... 

			  '    rej1 = find(EEG.stats.compenta > EEG.reject.threshentropy);' ...

			  '    rej2 = find(EEG.stats.compkurta > EEG.reject.threshkurtact);' ...

			  '    rej3 = find(EEG.stats.compkurtdist > EEG.reject.threshkurtdist);' ...

			  '    EEG.reject.gcompreject = (rej1 & rej2) | rej3;' ...

			  '    clear rej1 rej2 rej3;' ...

			  'end; clear ButtonName;' ]; 



% default value for rejection methods

% -----------------------------------

rejvalother = ''; 

rejvalpercent = '25'; 

switch rejmethod

	case 'percent', rejvalpercent = num2str( rejvalue);

	case 'dataset', rejvalother = num2str( rejvalue); 

end

    				

% -----------------------------------------------------

allh = supergui(gcf, { 	[1] ...

					[2 1] [2 1] [2 1] ...

					[1] ... 

					[1] ... 

					[1.5 0.5 1] [1.5 0.5 1] [1.5 0.5 1] ...

					[1] [1] [1] [1] [1] [1] [1] [1] [1] [1] ...

					[1 1 1 1 1] ...

					}, [], ...

	{ 'Style', 'text', 'string', 'Calibration method', 'FontSize', 13, 'fontweight', 'bold' }, ...

	...

	{ 'style', 'checkbox', 'String', '% of artifactual components (can also put one % per rejection)', 'tag', 'Ipercent', 'value', 1, 'callback', cb_percent}, ...

	{ 'style', 'edit', 'String', rejvalpercent, 'tag', 'Ipercenttext', 'callback', drawgraphs }, ...

	...

	{ 'style', 'checkbox', 'String', 'Specific dataset (enter dataset number)', 'tag', 'Iother', 'value', 0, 'callback', cb_other}, ...

	{ 'style', 'edit', 'String', rejvalother, 'tag', 'Iothertext', 'enable', 'off', 'callback', drawgraphs }, ...

	...

	{ 'style', 'checkbox', 'String', 'Current dataset', 'tag', 'Icurrent', 'value', 0, 'callback', cb_current}, ...

	{ }, ...

	...

	{ }, ...

	...

	{ 'Style', 'text', 'string', 'Threshold values', 'FontSize', 13, 'fontweight', 'bold' }, ...

	...

	{ 'style', 'text', 'String', 'Entropy of activity threshold' }, ...

	{ 'style', 'edit', 'String', num2str(EEG.reject.threshentropy), 'tag', 'entstring', 'callback',  cb_entropy }, ...

	{ 'style', 'pushbutton', 'String', 'Histogram', 'callback', 'figure; hist(EEG.stats.compenta,20); title(''Entropy of activity'');' }, ...

	...

	{ 'style', 'text', 'String', 'Kurtosis of activity threshold' }, ...

	{ 'style', 'edit', 'String', num2str(EEG.reject.threshkurtact), 'tag', 'kurtstring', 'callback', cb_kurtact }, ...

	{ 'style', 'pushbutton', 'String', 'Histogram', 'callback', 'figure; hist(EEG.stats.compkurta,200); title(''Kurtosis of activity'');' },  ...

	...

	{ 'style', 'text', 'String', 'Kurtosis of topography threshold' }, ...

	{ 'style', 'edit', 'String', num2str(EEG.reject.threshkurtdist), 'tag', 'kurtdiststring', 'callback', cb_kurtdist }, ...

	{ 'style', 'pushbutton', 'String', 'Histogram', 'callback', 'figure; hist(EEG.stats.compkurtdist,20); title(''Kurtosis of topography'');' }, ...

	...

	{ }, { }, { }, { }, { }, { }, { }, { }, { }, { }, ...

	...

	{ 'style', 'pushbutton', 'String', 'Cancel', 'callback', cb_cancel, 'userdata', { EEG.reject.threshentropy EEG.reject.threshkurtact EEG.reject.threshkurtdist }}, ...

	{ 'style', 'pushbutton', 'String', 'Auto thresh'  , 'callback', '', 'enable', 'off' }, ...

	{ 'style', 'pushbutton', 'String', 'Help'  , 'callback', 'pophelp(''pop_icathresh'');' }, ...

	{ 'style', 'pushbutton', 'String', 'Accept thresh.' , 'callback', 'close(gcbf);' }, ...

	{ 'style', 'pushbutton', 'String', 'Calc. rejection' , 'callback', 'close(gcbf);' } ...

	...

	);



h = axes('position', [0  15 30 30].*s+q, 'tag', 'graphent');

h = axes('position', [35 15 30 30].*s+q, 'tag', 'graphkurt');

h = axes('position', [70 15 30 30].*s+q, 'tag', 'graphkurtdist');



rejmethod

switch rejmethod

	case 'dataset', eval([ 'gcbf = [];' cb_other]);

	case 'current', eval([ 'gcbf = [];' cb_current]);

	otherwise, eval([ 'gcbf = [];' cb_percent]);

end



	

return;