files = dir('*.not.mat');
k = 1;
clear resampledTrace
clear resampledTraceNorm

currTraceMax = 0;
for i=1:length(files)
    fn = files(i).name;
    load(fn)
    dashes = strfind(fn, '_');
    fileTimeStamp = fn(dashes(2)+(-2:5));
    audioDataFile = dir(['*Audio*' fileTimeStamp '*.csv']);
    signalDataFile = dir(['*signal*' fileTimeStamp '*.csv']);
    audioFile = dir([fn(1:end-12) '.wav']);
    [song,fs ] =audioread(audioFile.name);
    
    if isempty(signalDataFile)
        fileTimeStamp(end-1:end) = num2str(str2double(fileTimeStamp(end-1:end))-1,'%02.f');
        signalDataFile = dir(['*signal*' fileTimeStamp '*.csv']);
        audioDataFile = dir(['*Audio*' fileTimeStamp '*.csv']);
    end
    
    %Choose inner == 1 or outer == 2
    
    data = importFPfile(signalDataFile(1).name);
    
    
    audiodata = importFPfile(audioDataFile.name, [1, Inf]);
    [greenAdjusted, greenTime, firstTimeSig, blueOnly, fs] = extractFPdata(data,3);
    [audioTime,firstTimeAudio]= extractFPAudioTime(audiodata);
    
    alignLetter = 'i';
    introNote = strfind(labels,alignLetter);
    sigFS = round(1/mean(diff(greenTime)));
    beforeTime = 10;
    afterTime = 10;
    timeSpan = -beforeTime:1/sigFS:afterTime;
    frameSpan = timeSpan*sigFS;
    ts = onsets(introNote);
    timeLag = firstTimeAudio - firstTimeSig;
    
    
    if ~isempty(ts)
        inds_i = [1; find(diff(ts)/1000>2)+1];
        ts = ts(inds_i);
        if strcmp(alignLetter,'i')
            motifLetter = 'a';
            refineFlag = 1;
        elseif strcmp(alignLetter,'j')
            motifLetter = 'b';
            refineFlag = 1;
        end
        
        
        for j = 1:length(ts)
            onset = ts(j)/1000;
            sigOnset = find(abs(onset-(greenTime+timeLag))==min(abs(onset-(greenTime+timeLag))));
            baseline = mean(greenAdjusted(round(sigOnset+(-2.5:1/sigFS:-2)*sigFS)));
            currTrace = greenAdjusted(round(sigOnset+frameSpan));
            currTime = greenTime(round(sigOnset+frameSpan))-greenTime(sigOnset);
            currTraceNorm = greenAdjusted(round(sigOnset+frameSpan))-baseline;
            currTraceNorm = currTraceNorm/max(currTraceNorm(140:end));
            
            resampledTrace(k,:) = interp1(currTime,currTrace,-beforeTime:0.01:afterTime,'PCHIP');
            resampledTraceNorm(k,:) = interp1(currTime,currTraceNorm,-beforeTime:0.01:afterTime,'PCHIP');
            inds = [onset-beforeTime onset+afterTime]*fs;
            
            
            k = k+1;
        end
    end
    
end