% CheckEventCodes.m
% This program checks the event codes count, timing, and counterbalancing.
% Reads in cnt file
% Writes output dat file with all event code checks for you to evaluate
% 2010-11-20:  JTK & JJC v1
% 2012-02-03:  Updated to use Subject 0982 in DemoSTIM in Demos folder by JJC 

%% Variables to set
% Edit the variables in this cell for your current study
% No variables should typically need to be edited below this cell

PathName = 'P:\Methods\Matlab\PhysBox\Demos\DemoSTIM\RawData\0982\';  %Change path to folder with input cnt file
InFileName = 'stim1_maintask_0982.cnt'; % Change input cnt file name
OutFileName = 'EventCodeChecks.dat'; % Change output dat file name

% Edit the following event codes to match your study
cues = [1 2]; % Event codes for cue onset
habituation = [100]; % 100 is the even code for the first 3 habituation startles in most Curtin Lab studies
probes = [101   102   103   111   112   113   121   122   123]; % Enter event codes for startle probes
shocks = [254]; % Event code for shock. This is 1 in all Curtin Lab studies

%% Open File
EEG = pop_LoadCnt('0982', InFileName, PathName, 'int32'); % loads cnt file

%% Event Count

% Creates output file named (OutFileName) in the folder (PathName)
% (e.g.,: P:\Methods\Matlab\PhysBox\Demos\DemoSTIM\RawData\0982\)
% IMPORTANT: if there is already a file with the same name it will be deleted
% and written over without prompting the user to check that is ok!!!
% Outputs all event codes in study and the number of times they appear in
% the cnt file
% Do not need to modify anything in this cell
[EventCountAll] = pop_EventCheck(EEG, [], [], [], [] );
fid = fopen([PathName OutFileName],'w'); % 'w' = open file for writing
fprintf(fid,'Check Event Codes: Count, Timing/Spacing, Counterbalancing\n\nColumn 1 = Event\nColumn 2 = Counts\n\n');
fclose(fid);
dlmwrite([PathName OutFileName] ,EventCountAll,'-append', 'delimiter','\t', 'newline','pc', 'precision',5)

%% Overall Timing/Spacing

%Startle probe spacing
% Check timing in column 4 makes sense for your study
[~,TimingArrayAll] = pop_EventCheck(EEG, probes, [], [], [] );
TimingArrayAll(:,3) = TimingArrayAll(:,3)/1000; % divided by 1000 for display purposes
TimingArrayAll(:,4) = TimingArrayAll(:,4)/1000;
fid = fopen([PathName OutFileName],'a'); % 'a' = open file for writing and append to end of file
fprintf(fid,'\n\nOverall Timing/Spacing\n\nTiming for Startle Probes\n\nColumn 1 = Trial #\nColumn 2 = Event Code\nColumn 3 = Time from start of exp (sec)\nColumn 4 = ISI to next event (sec)\n\n');
fclose(fid);
dlmwrite([PathName OutFileName] ,TimingArrayAll,'-append', 'delimiter','\t', 'newline','pc', 'precision',7)

% Display ISI between startle probes sorted from min to max
% Check that min is large enough (usually 13 or 15 sec)
% Check max value makes sense (eg: breaks between blocks)
ProbeSort = (sort(TimingArrayAll(:,4)));
fid = fopen([PathName OutFileName],'a');
fprintf(fid,'\n\nISI time between Startle Probes, sorted min to max (sec):\n\n');
fclose(fid);
dlmwrite([PathName OutFileName] , ProbeSort,'-append', 'delimiter','\t', 'newline','pc', 'precision',7)

%Cue spacing
% This section is often not necessary to check
[EventCountAll,TimingArrayAll] = pop_EventCheck(EEG, cues, [], [], [] );
fid = fopen([PathName OutFileName],'a');
fprintf(fid,'\n\nISI for Cues\n');
fclose(fid);
dlmwrite([PathName OutFileName] ,TimingArrayAll,'-append', 'delimiter','\t', 'newline','pc', 'precision',7)

%% S1-S2 Checks
% Cue to Startle
% Confirm time in column 4 is the correct time between cue onset and
% that startle probe
[~,~, S1S2ArrayAll] = pop_EventCheck(EEG, [], cues, probes, [] );
S1S2ArrayAll(:,4) = S1S2ArrayAll(:,4)/1000;
fid = fopen([PathName OutFileName],'a');
fprintf(fid,'\n\nS1-S2 Spacing\n\nTiming/ISI between Cue and Startle Probes\n\nColumn 1 = Trial #\nColumn 2 = Cue Event Code\nColumn 3 = Startle Probe Event Code\nColumn 4 = Cue-Probe ISI\n\n');
fclose(fid);
dlmwrite([PathName OutFileName] ,S1S2ArrayAll,'-append', 'delimiter','\t', 'newline','pc', 'precision',7)

%Cue to Shock
% Confirm only shock cue event codes appear in column 2
% Confirm time in column 4 is the correct time between cue onset and shock
[~,~, S1S2ArrayAll] = pop_EventCheck(EEG, [], cues, shocks, [] );
S1S2ArrayAll(:,4) = S1S2ArrayAll(:,4)/1000;
fid = fopen([PathName OutFileName],'a'); 
fprintf(fid,'\n\nTiming/ISI between Cue and Shocks\n\nColumn 1 = Trial #\nColumn 2 = Cue Event Code\nColumn 3 = Shock Event Code\nColumn 4 = Cue-Shock ISI\n\n');
fclose(fid);
dlmwrite([PathName OutFileName] ,S1S2ArrayAll,'-append', 'delimiter','\t', 'newline','pc', 'precision',7)

%Shock to Startle
% Confirm no startle probes occur too soon after a shock
[~,~, S1S2ArrayAll] = pop_EventCheck(EEG, [], shocks, probes, [] );
S1S2ArrayAll(:,4) = S1S2ArrayAll(:,4)/1000;
fid = fopen([PathName OutFileName],'a');
fprintf(fid,'\n\nTiming/ISI betewen Shock and Startle Probes\n\nColumn 1 = Trial #\nColumn 2 = Shocks Event Code\nColumn 3 = Startle Probe Event Code\nColumn 4 = Shock-Probe ISI\n\n');
fclose(fid);
dlmwrite([PathName OutFileName] ,S1S2ArrayAll,'-append', 'delimiter','\t', 'newline','pc', 'precision',7)

%% Counterbalancing

%Startle
% Values in column 3 should be very close (low variance)
[~,~,~,AvePosArrayAll] = pop_EventCheck(EEG, [], [], [], probes);
fid = fopen([PathName OutFileName],'a'); 
fprintf(fid,'\n\nCounterbalancing\n\nStartle Probes\n\nColumn 1 = Startle Probe Event Code\nColumn 2 = Count\nColumn 3 = Average Serial Position\n\n');
fclose(fid);
dlmwrite([PathName OutFileName] ,AvePosArrayAll,'-append', 'delimiter','\t', 'newline','pc', 'precision',7)

%Cue
% Values in column 3 should be very close (low variance)
[~,~,~,AvePosArrayAll] = pop_EventCheck(EEG, [], [], [], cues);
fid = fopen([PathName OutFileName],'a');
fprintf(fid,'\n\nCues\n\nColumn 1 = Cue Event Code\nColumn 2 = Count\nColumn 3 = Average Serial Position\n\n');
fclose(fid);
dlmwrite([PathName OutFileName] ,AvePosArrayAll,'-append', 'delimiter','\t', 'newline','pc', 'precision',7)

fprintf('\n\nYour Output File is Here: %s%s \n', PathName, OutFileName);
fprintf('\nCheckEventCodes Complete!\n');