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ctf_eog.m
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ctf_eog.m
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function [ctf,GUI] = ctf_eog(command);
% ctf_eog - GUI interface to check EOG data in a CTF .ds folder
%
% [ctf,FIG] = ctf_eog( [command] );
%
% eg,
% ctf = ctf_eog;
%
% <>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> %
% < > %
% < DISCLAIMER: > %
% < > %
% < THIS PROGRAM IS INTENDED FOR RESEARCH PURPOSES ONLY. > %
% < THIS PROGRAM IS IN NO WAY INTENDED FOR CLINICAL OR > %
% < OFFICIAL USE. > %
% < > %
% <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<> %
%
% $Revision: 1.1 $ $Date: 2009-01-30 03:49:26 $
% Copyright (C) 2006 Darren L. Weber
%
% This program is free software; you can redistribute it and/or
% modify it under the terms of the GNU General Public License
% as published by the Free Software Foundation; either version 2
% of the License, or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
% Created: 01/2006, Darren.Weber_at_radiology.ucsf.edu
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~exist('command','var'), command = 'init'; end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Paint the GUI
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
switch command,
case 'init',
[ctf,GUI] = INIT;
case 'update',
CTFeog = get(gcbf,'Userdata');
ctf = CTFeog.ctf;
CTFeog.CHANNELS = 1:ctf.setup.number_channels;
CTFeog.TIME = ctf.setup.time_sec;
CTFeog.TRIALS = 1:ctf.setup.number_trials;
set(gcbf,'Userdata',CTFeog);
case 'return',
CTFeog = get(gcbf,'Userdata');
ctf = CTFeog.ctf;
close gcbf;
case 'plot',
fprintf('\nCTF_EOG: Plot not implemented yet.\n');
case 'save',
fprintf('\nCTF_EOG: Save not implemented yet.\n');
otherwise,
CTFeog = get(gcbf,'Userdata');
GUI.parent = CTFeog.parent;
gui_updateparent(GUI);
close gcbf;
end
return
% -------------------------------------------
fig = figure;
for e = allTrials,
set(fig,'Name',sprintf('Trial %04d',e))
veogData = ctf.data(:,veog,e);
heogData = ctf.data(:,heog,e);
veogBaseline = mean(veogData(1:blPoints));
heogBaseline = mean(heogData(1:blPoints));
veogDataBaselined = veogData - veogBaseline;
heogDataBaselined = heogData - heogBaseline;
%plot(timeSec,[veogDataBaselined,heogDataBaselined]);
%legend('VEOG','HEOG')
% EEG differential must be normalized by the sample rate (sec)
veogDataDiff = [0; diff(veogDataBaselined)] / ctf.setup.sample_sec;
heogDataDiff = [0; diff(heogDataBaselined)] / ctf.setup.sample_sec;
% check if this is an artifact trial
EYEBLINKaTrial = find(EYEBLINKaTrials == e);
EYEBLINKdTrial = find(EYEBLINKdTrials == e);
EYEMVMTaTrial = find(EYEMVMTaTrials == e);
EYEMVMTdTrial = find(EYEMVMTdTrials == e);
% -------------------------------
% VEOG check
% amplitude threshold
t = thresholdDetect.veog.amp; % 80 uV
% detect values above threshold
eyeblinkA = find(abs(veogDataBaselined) > t);
eyeblinkWave = veogDataBaselined * 0;
eyeblinkWave(eyeblinkA) = max(abs(veogDataBaselined));
veogAxisAmp = subplot(2,2,1);
plot(timeSec, [veogDataBaselined, eyeblinkWave]); hold on
legend('VEOG', 'VEOG Blink (Amp)')
plot(timeSec, [veogData*0, (veogData*0)+t, (veogData*0)-t],'k:'); hold off
ylabel('Volt')
xlabel('Time (sec)')
set(veogAxisAmp,'XLim',[ctf.setup.start_sec, ctf.setup.end_sec]);
ampLimit = thresholdDetect.veog.amp + (thresholdDetect.veog.amp * 0.5);
set(veogAxisAmp,'YLim',[-ampLimit, ampLimit])
set(veogAxisAmp,'YTick',-ampLimit:10e-6:ampLimit)
if EYEBLINKaTrial,
set(veogAxisAmp,'color',[1 0.75 0.75])
else
set(veogAxisAmp,'color',[1 1 1])
end
% detect derivatives above 20 mV/sec
t = thresholdDetect.veog.der;
eyeblinkD = find(abs(veogDataDiff) > t);
eyeblinkWave = veogDataDiff * 0;
eyeblinkWave(eyeblinkD) = max(abs(veogDataDiff));
veogAxisDer = subplot(2,2,3);
plot(timeSec,[veogDataDiff, eyeblinkWave]); hold on
legend('diff(VEOG)/sec', 'VEOG Blink (Der)')
plot(timeSec, [veogData*0, (veogData*0)+t, (veogData*0)-t],'k:'); hold off
ylabel('Volt / sec')
xlabel('Time (sec)')
set(veogAxisDer,'XLim',[ctf.setup.start_sec, ctf.setup.end_sec]);
ampLimit = thresholdDetect.veog.der + (thresholdDetect.veog.der * 0.5);
set(veogAxisDer,'YLim',[-ampLimit, ampLimit])
%set(veogAxisDer,'YTick',-ampLimit:10e-6:ampLimit)
if EYEBLINKdTrial,
set(veogAxisDer,'color',[1 0.75 0.75])
else
set(veogAxisDer,'color',[1 1 1])
end
% -------------------------------
% HEOG check
% amplitude threshold
t = thresholdDetect.heog.amp;
% detect values above threshold
eyeMoveA = find(abs(heogDataBaselined) > t);
eyeMoveWave = heogDataBaselined * 0;
eyeMoveWave(eyeMoveA) = max(abs(heogDataBaselined));
heogAxisAmp = subplot(2,2,2);
plot(timeSec, [heogDataBaselined, eyeMoveWave]); hold on
legend('HEOG', 'HEOG Move (Amp)')
plot(timeSec, [heogData*0, (heogData*0)+t, (heogData*0)-t],'k:'); hold off
ylabel('Volt')
xlabel('Time (sec)')
set(heogAxisAmp,'XLim',[ctf.setup.start_sec, ctf.setup.end_sec]);
ampLimit = thresholdDetect.heog.amp + (thresholdDetect.heog.amp * 0.5);
set(heogAxisAmp,'YLim',[-ampLimit, ampLimit])
set(heogAxisAmp,'YTick',-ampLimit:10e-6:ampLimit)
if EYEMVMTaTrial,
set(heogAxisAmp,'color',[1 0.75 0.75])
else
set(heogAxisAmp,'color',[1 1 1])
end
% HEOG movements may accelerate at about 20 mV/sec
t = thresholdDetect.heog.der;
eyeMoveD = find(abs(heogDataDiff) > t);
eyeMoveWave = heogDataDiff * 0;
eyeMoveWave(eyeMoveD) = max(abs(heogDataDiff));
heogAxisDer = subplot(2,2,4);
plot(timeSec, [heogDataDiff, eyeMoveWave]); hold on
legend('diff(HEOG)/sec', 'HEOG Move (Der)')
plot(timeSec, [heogData*0, (heogData*0)+t, (heogData*0)-t],'k:'); hold off
ylabel('Volt / sec')
xlabel('Time (sec)')
set(heogAxisDer,'XLim',[ctf.setup.start_sec, ctf.setup.end_sec]);
ampLimit = thresholdDetect.heog.der + (thresholdDetect.heog.der * 0.5);
set(heogAxisDer,'YLim',[-ampLimit, ampLimit])
%set(heogAxisDer,'YTick',-ampLimit:10e-6:ampLimit)
if EYEMVMTdTrial,
set(heogAxisDer,'color',[1 0.75 0.75])
else
set(heogAxisDer,'color',[1 1 1])
end
pause(10)
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ctf,GUI] = INIT
% GUI General Parameters
ctf = ctf_folder;
ctf = ctf_read_res4(ctf.folder);
thresholdDetect.veog.amp = 50e-6; % 50 uV
thresholdDetect.veog.der = 25e-3; % 25 mV/sec
thresholdDetect.heog.amp = 25e-6; % 25 uV
thresholdDetect.heog.der = 25e-3; % 25 mV/sec
CTFeog.CHANNELS = 1:ctf.setup.number_channels;
CTFeog.TIME = ctf.setup.time_sec;
CTFeog.TRIALS = 1:ctf.setup.number_trials;
GUIwidth = 800;
GUIheight = 600;
ver = '$Revision: 1.1 $';
name = sprintf('CTF EOG [v %s]\n',ver(11:15));
GUI = figure('Name',name,'Tag','CTF_EOG',...
'NumberTitle','off',...
'MenuBar','none','Position',[1 1 GUIwidth GUIheight]);
movegui(GUI,'center');
%Font.FontName = 'Helvetica';
Font.FontUnits = 'Pixels';
Font.FontSize = 12;
Font.FontWeight = 'normal';
Font.FontAngle = 'normal';
boxdepth = 0.15;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% CTF Data Selection and Parameters
Font.FontWeight = 'bold';
% BROWSE for a .ds folder
browsecommand = strcat('CTFeog = get(gcbf,''Userdata'');',...
'ctf = CTFeog.ctf; ',...
'ctf = ctf_folder([],ctf); ',...
'ctf = ctf_read_res4(ctf.folder); ',...
'CTFeog.ctf = ctf; ',...
'set(CTFeog.handles.EctfFolder,''String'',ctf.folder); ',...
'set(gcbf,''Userdata'',CTFeog);',...
'clear CTFeog; ctf = ctf_read_gui(''update'');');
G.BctfFile = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized',Font, ...
'Position',[.01 .80 .17 boxdepth], 'String','CTF Folder (*.ds)',...
'BackgroundColor',[0.8 0.8 0.0], 'ForegroundColor', [1 1 1], ...
'HorizontalAlignment', 'center', ...
'TooltipString','Browse for CTF folder', ...
'Callback', browsecommand );
Font.FontWeight = 'normal';
% EDIT the .ds folder name
editcommand = strcat('CTFeog = get(gcbf,''Userdata'');',...
'CTFeog.ctf.folder = get(CTFeog.handles.EctfFolder,''String''); ',...
'ctf = CTFeog.ctf; ',...
'ctf = ctf_folder(ctf.folder,ctf); ',...
'ctf = ctf_read_res4(ctf.folder); ',...
'CTFeog.ctf = ctf; ',...
'set(CTFeog.handles.EctfFolder,''String'',ctf.folder); ',...
'set(gcbf,''Userdata'',CTFeog);',...
'clear CTFeog; ctf = ctf_read_gui(''update'');');
G.EctfFolder = uicontrol('Parent',GUI,'Style','edit','Units','Normalized',Font, ...
'Position',[.20 .80 .75 boxdepth], 'String',ctf.folder,...
'Callback', editcommand );
%---------------------------------------------------------------
% Channels
height = 0.6;
G.Title_channels = uicontrol('Parent',GUI,'Style','text','Units','Normalized',Font, ...
'Position',[.01 height .17 boxdepth],'HorizontalAlignment', 'center','String','Channels:');
% Channel types
CTFeog.channeltypes = {'all', 'eeg', 'meg', 'ref', 'other', '[array]'};
channelpopup = strcat('CTFeog = get(gcbf,''Userdata'');',...
'channelvalue = get(CTFeog.handles.PctfCHANNELS,''Value''); ',...
'channeltype = CTFeog.channeltypes{channelvalue}; ',...
'switch channeltype, ',...
' case ''all'', CTFeog.CHANNELS = 1:CTFeog.ctf.setup.number_channels; ',...
' case ''eeg'', CTFeog.CHANNELS = CTFeog.ctf.sensor.index.eeg; ',...
' case ''meg'', CTFeog.CHANNELS = CTFeog.ctf.sensor.index.meg; ',...
' case ''ref'', CTFeog.CHANNELS = CTFeog.ctf.sensor.index.ref; ',...
' case ''other'', CTFeog.CHANNELS = CTFeog.ctf.sensor.index.other; ',...
' otherwise, CTFeog.CHANNELS = []; ',...
'end; ',...
'set(CTFeog.handles.EctfCHANNELS,''Value'',CTFeog.CHANNELS); ',...
'set(CTFeog.handles.EctfCHANNELS,''string'',num2str(CTFeog.CHANNELS)); ',...
'set(gcbf,''Userdata'',CTFeog);',...
'clear CTFeog channelvalue channeltype;');
G.PctfCHANNELS = uicontrol('Parent',GUI,'Style','popup','Units','Normalized',Font, ...
'Position',[.20 height .20 boxdepth], ...
'String',CTFeog.channeltypes,...
'Value',1, ...
'TooltipString','Channel selection - enter values for [array]', ...
'Callback', channelpopup );
% Channels array
channelarray = strcat('CTFeog = get(gcbf,''Userdata'');',...
'CTFeog.CHANNELS = str2num(get(CTFeog.handles.EctfCHANNELS,''String'')); ',...
'set(CTFeog.handles.EctfCHANNELS,''Value'',CTFeog.CHANNELS); ',...
'set(gcbf,''Userdata'',CTFeog); clear CTFeog;');
G.EctfCHANNELS = uicontrol('Parent',GUI,'Style','edit','Units','Normalized',Font, ...
'Position',[.40 height .50 boxdepth], ...
'String',num2str(CTFeog.CHANNELS),'Value',CTFeog.CHANNELS,...
'TooltipString','Channels array - enter values for [array] selection', ...
'Callback', channelarray );
G.EctfCHANNELSCLEAR = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized',Font, ...
'Position',[.90 height .05 boxdepth], ...
'String','Clear',...
'TooltipString','Clear channels array', ...
'Callback', strcat('CTFeog = get(gcbf,''Userdata'');',...
'CTFeog.CHANNELS = []; ',...
'set(CTFeog.handles.EctfCHANNELS,''String'',''''); ',...
'set(CTFeog.handles.EctfCHANNELS,''Value'',CTFeog.CHANNELS); ',...
'set(gcbf,''Userdata'',CTFeog); clear CTFeog;') );
%---------------------------------------------------------------
% Time
height = 0.4;
G.Title_channels = uicontrol('Parent',GUI,'Style','text','Units','Normalized',Font, ...
'Position',[.01 height .17 boxdepth],'HorizontalAlignment', 'center','String','Time (sec):');
% Time array
start = sprintf('%6.5f', CTFeog.TIME(1));
step = sprintf('%6.5f',[CTFeog.TIME(2) - CTFeog.TIME(1)]);
stop = sprintf('%6.5f', CTFeog.TIME(end));
timestring = [start,':',step,':',stop];
G.TctfTIME = uicontrol('Parent',GUI,'Style','text','Units','Normalized',Font, ...
'Position',[.20 height .20 boxdepth],'HorizontalAlignment', 'center',...
'TooltipString','Time array (sec)', ...
'String',timestring);
timearray = strcat('CTFeog = get(gcbf,''Userdata'');',...
'CTFeog.TIME = str2num(get(CTFeog.handles.EctfTIME,''String''))''; ',...
'set(CTFeog.handles.EctfTIME,''Value'',CTFeog.TIME); ',...
'set(gcbf,''Userdata'',CTFeog); clear CTFeog;');
G.EctfTIME = uicontrol('Parent',GUI,'Style','edit','Units','Normalized',Font, ...
'Position',[.40 height .50 boxdepth], ...
'String',num2str(CTFeog.TIME'),'Value',CTFeog.TIME,...
'TooltipString','Time array (sec)', ...
'Callback', timearray );
G.EctfTIMECLEAR = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized',Font, ...
'Position',[.90 height .05 boxdepth], ...
'String','Clear',...
'TooltipString','Clear time array', ...
'Callback', strcat('CTFeog = get(gcbf,''Userdata'');',...
'CTFeog.TIME = []; ',...
'set(CTFeog.handles.EctfTIME,''String'',''''); ',...
'set(CTFeog.handles.EctfTIME,''Value'',CTFeog.TIME); ',...
'set(gcbf,''Userdata'',CTFeog); clear CTFeog;') );
%---------------------------------------------------------------
% Trials
height = 0.2;
G.Title_trials = uicontrol('Parent',GUI,'Style','text','Units','Normalized',Font, ...
'Position',[.01 height .17 boxdepth],'HorizontalAlignment', 'center','String','Trials:');
start = num2str(CTFeog.TRIALS(1));
stop = num2str(CTFeog.TRIALS(end));
trialstring = [start,':',stop];
G.TctfTRIALS = uicontrol('Parent',GUI,'Style','text','Units','Normalized',Font, ...
'Position',[.20 height .20 boxdepth],'HorizontalAlignment', 'center',...
'String',trialstring);
% Trials array
trialsarray = strcat('CTFeog = get(gcbf,''Userdata'');',...
'CTFeog.TRIALS = str2num(get(CTFeog.handles.EctfTRIALS,''String'')); ',...
'set(CTFeog.handles.EctfTRIALS,''Value'',CTFeog.TRIALS); ',...
'set(gcbf,''Userdata'',CTFeog); clear CTFeog;');
G.EctfTRIALS = uicontrol('Parent',GUI,'Style','edit','Units','Normalized',Font, ...
'Position',[.40 height .50 boxdepth], ...
'String',num2str(CTFeog.TRIALS),'Value',CTFeog.TRIALS,...
'TooltipString','Trials array', ...
'Callback', trialsarray );
G.EctfTRIALSCLEAR = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized',Font, ...
'Position',[.90 height .05 boxdepth], ...
'String','Clear',...
'TooltipString','Clear trials array', ...
'Callback', strcat('CTFeog = get(gcbf,''Userdata'');',...
'CTFeog.TRIALS = []; ',...
'set(CTFeog.handles.EctfTRIALS,''String'',''''); ',...
'set(CTFeog.handles.EctfTRIALS,''Value'',CTFeog.TRIALS); ',...
'set(gcbf,''Userdata'',CTFeog); clear CTFeog;') );
% % PLOT: Load & plot the data!
% G.Bplot = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
% 'Position',[.20 .01 .18 .2],...
% 'String','PLOT','BusyAction','queue',...
% 'TooltipString','Plot the EEG data and return p struct.',...
% 'BackgroundColor',[0.0 0.5 0.0],...
% 'ForegroundColor', [1 1 1], 'HorizontalAlignment', 'center',...
% 'Callback',strcat('CTFeog = get(gcbf,''Userdata'');',...
% 'p = ctf_read_gui(CTFeog.p,''plot'');',...
% 'clear CTFeog;'));
%
% % Save As
% G.Bsave = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
% 'Position',[.40 .01 .18 .2],'HorizontalAlignment', 'center',...
% 'String','SAVE AS','TooltipString','EEG File Conversion Tool (not implemented yet)',...
% 'BusyAction','queue',...
% 'Visible','off',...
% 'BackgroundColor',[0.0 0.0 0.75],...
% 'ForegroundColor', [1 1 1], 'HorizontalAlignment', 'center',...
% 'Callback',strcat('CTFeog = get(gcbf,''Userdata'');',...
% 'p = ctf_read_gui(CTFeog.p,''save'');',...
% 'clear CTFeog;'));
Font.FontWeight = 'bold';
% Quit, return file parameters
G.Breturn = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
'Position',[.70 .01 .10 boxdepth],...
'String','RETURN','BusyAction','queue',...
'TooltipString','Return p struct to workspace and parent GUI.',...
'BackgroundColor',[0.0 0.75 0.0],...
'ForegroundColor', [1 1 1], 'HorizontalAlignment', 'center',...
'Callback','ctf = ctf_read_gui(''return'');' );
% Cancel
G.Bcancel = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
'Position',[.85 .01 .10 boxdepth],...
'String','CANCEL','BusyAction','queue',...
'TooltipString','Close, do not read data.',...
'BackgroundColor',[0.75 0.0 0.0],...
'ForegroundColor', [1 1 1], 'HorizontalAlignment', 'center',...
'Callback','close(gcbf);');
% Store userdata
CTFeog.gui = GUI;
CTFeog.handles = G;
CTFeog.ctf = ctf;
set(GUI,'Userdata',CTFeog);
set(GUI,'HandleVisibility','callback');
return
% ---------------------------------------------------------
function classTrials = extract_classTrials(CTFeog),
ctf = CTFeog.ctf;
ctf.class = ctf_read_classfile(ctf);
if ctf.class.number,
classNames = {ctf.class.data(:).name};
classTrials = cell(1,ctf.class.number);
for c = 1:ctf.class.number,
classTrials{c} = ctf.class.data(c).trials;
end
% ------------------------------
cd(ctf.folder)
% -----------------------------
% This section here is based on prior extraction of the STIM, EEG121 and
% EEG122 channels, it could be replaced with the ctf_read_meg4 function
% to do this directly
stimeegFile = fullfile(ctf.folder,'WA_HiN_alltrials_1250msec_stimeeg.mat');
stimeegData = load(stimeegFile);
ctf.data = stimeegData.data;
ctf.sensor.label = stimeegData.labels
% -----------------------------
stim = strmatch('STIM',ctf.sensor.label);
veog = strmatch('EEG121',ctf.sensor.label);
heog = strmatch('EEG122',ctf.sensor.label);
blPoints = ctf.setup.pretrigger_samples;
timeSec = ctf.setup.time_sec;
epochs = size(ctf.data,3);
end
% For continuous data, use arbitrary epoch lengths for viewing
%i = 1;
%epochs(i,:) = 1:10000;
%timeSec = epochs(i,:) * ctf.setup.sample_sec;
%while (i * 10000) < size(ctf.data,1),
% epochs(i,:) = (i * 10000) + epochs(1,:);
% i = i + 1;
%end
return