function [greenAdjusted, greenTime, firstTimesig, blueOnly, fs] = extractFPdata(data,Option)

if nargin == 1
    Option =1;
end
%create a time vector in seconds, relative to the trial start
time=NaN(length(data),1);
for i=1:length(data)
    %convert all time to seconds
    tHours=data(i,3)*60*60*1000;
    tMinutes=data(i,4)*60*1000;
    tSeconds=data(i,5)*1000;
    tMillisecs=data(i,6);
    time(i,1)=tHours+tMinutes+tSeconds+tMillisecs;
end
time=time/1000;
firstTimesig=time(1);
time=time-firstTimesig;

greenData=data(:,2);
redData=data(:,1);


if greenData(2,1)>greenData(1,1)
    %odd rows
    greenOnly=greenData(2:2:end,:);
    blueOnly=greenData(1:2:end-1,:);
    redOnly = redData(2:2:end,:);
    greenTime=time(2:2:end,:);
    blueTime=time(1:2:end-1,:);
    redTime = time(2:2:end,:);
else
    blueOnly=greenData(2:2:end,:);
    greenOnly=greenData(1:2:end-1,:);
    redOnly = redData(1:2:end-1,:);
    blueTime=time(2:2:end,:);
    greenTime=time(1:2:end-1,:);
    redTime=time(1:2:end-1,:);
    
end

l = min([length(greenTime) length(greenOnly)]);
greenTime = greenTime(1:l);
greenOnly = greenOnly(1:l);
blueOnly = blueOnly(1:l);
blueTime = blueTime(1:l);

fs = round(1/mean(diff(greenTime)));

switch Option
    case 1 % NPM code
        p=polyfit(blueOnly,greenOnly,1);
        greenPredicted=(blueOnly*p(1))+p(2);
        
        greenAdjusted=greenOnly(1:l)-greenPredicted;
    case 2 % lowpass filter
        [B,A]=ellip(6,.1,50,[0.001 0.5]);
        greenOnly = lowpass(greenOnly,3,fs);
        blueOnly = lowpass(blueOnly,2,fs);
        
        p=polyfit(blueOnly,greenOnly,1);
        greenPredicted=(blueOnly*p(1))+p(2);
        greenPredicted(1:fs) = greenPredicted(fs+1);
        greenPredicted((end-fs):end) = greenPredicted(end-(fs+1));
        
           greenOnly(1:fs) = greenOnly((fs+1));
        greenOnly((end-fs):end) = greenOnly(end-(fs+1));

        
        greenAdjusted=greenOnly-greenPredicted;
    case 3 
        Offset = 1; 
        FP.calcium_dependent = greenOnly;
        FP.calcium_independent = blueOnly;
        
        %fit blue with an exp2
        temp_fit = fit(blueTime(Offset:end),FP.calcium_independent(Offset:end,1),'exp2');
        
        
        %scale fit to calcium dependent data
        fit2 = fitlm(temp_fit(blueTime(Offset:end)),FP.calcium_dependent(Offset:end));
        fitted_BlueChannel = fit2.Fitted;
        
        ProcessedSignal(:,1) = greenTime(Offset:end);
        ProcessedSignal(:,2) = 100*(((FP.calcium_dependent(Offset:end) -(fit2.Fitted)) ./ (fit2.Fitted)) + abs(min(((FP.calcium_dependent(Offset:end) -(fit2.Fitted)) ./ (fit2.Fitted)))));
        greenAdjusted = smooth(ProcessedSignal(:,2)-mean(ProcessedSignal(:,2)), 'moving');
        greenAdjusted = medfilt1(greenAdjusted);
        greenTime = ProcessedSignal(:,1);
        blueOnly = fitted_BlueChannel;
        
    case 4 % NPM code with red channel
        p=polyfit(redOnly,greenOnly,1);
        greenPredicted=(redOnly*p(1))+p(2);
        greenAdjusted=greenOnly(1:l)-greenPredicted;
end