%% open/read file and set up Environment
%clear;clc;close all
activateCEDS64

% Start Time
START_TIME = 0;
%AstSamples = floor(START_TIME * 1000);
AstSamples = 1;
% Wavelength
WAVELENGTH = 999;
% path to file
file = 'C:\Users\Ruth Empson\Documents\Spike8\data\191217\191217_VOR\segment_1.smr';
fhand1 = CEDS64Open(file);

%% Gather data from specific channels
% sineWave channel (8)
[ ~, sineWave, ~ ] = CEDS64ReadWaveF(fhand1, 1, 600000000, 0);

% ePhys channel (11)
[ ~, ePhys, ~ ] = CEDS64ReadWaveF(fhand1,32, 600000000, 0);

% light / dark channel (9)
[ ~, tickTimes] = CEDS64ReadMarkers(fhand1, 9, 200, 0);


%% CREATE TIMELINE OF 1s & 0s FOR ON/OFF LIGHT

lightonoff = zeros(length(ePhys),1);

for j = 1:length(tickTimes)
    if tickTimes(j).m_Code1 == 1
        windowStart = tickTimes(j).m_Time / 100;
        % if the file ends with the light on, then use end of file
        try
            windowEnd = tickTimes(j+1).m_Time / 100;
        catch
            windowEnd = length(lightonoff);
        end
        oneVec = ones(windowEnd - windowStart, 1);
        lightonoff(windowStart:windowEnd-1) = oneVec;
    end
end



%% PLOT EACH WAVE

% how many sine waves can we use? 
waveCount = floor((length(sineWave) - AstSamples) / WAVELENGTH);

currentLocation = AstSamples;

% Pre-allocate Vectors
offTotal = zeros(WAVELENGTH + 1, 1);
offCount = 0;
onTotal = zeros(WAVELENGTH + 1, 1);
onCount = 0;
badCount = 0;
sineTotal = zeros(WAVELENGTH + 1,1);

for i = 1:(waveCount - 20)

    hold on
    % get the proper ephys and sinewave slice
    waveform = ePhys( currentLocation : ( currentLocation + WAVELENGTH ));
    sineWaveSlice = sineWave( currentLocation : ( currentLocation + WAVELENGTH ));
    sineTotal = sineTotal + sineWaveSlice;
    
    % plot the slice
    figure(1)
    plot(sineWaveSlice, 'k')
    
    
    % light on?
    if lightonoff(currentLocation, 1) == 1
        if lightonoff(currentLocation + WAVELENGTH, 1) == 1
            onTotal = onTotal + waveform;
            onCount = onCount + 1;
            figure(2)
            plot(waveform,'k')
        else
            badCount = badCount + 1;
        end
    % light off?
    elseif lightonoff(currentLocation, 1) == 0
        if lightonoff(currentLocation + WAVELENGTH, 1) == 0
            offTotal = offTotal + waveform;
            offCount = offCount + 1;
            figure(3)
            plot(waveform,'k')
        else
            badCount = badCount + 1;
        end
    end

    currentLocation = currentLocation + WAVELENGTH + 1;
end

% Calculate means
onMean = onTotal ./ onCount;
offMean = offTotal ./ offCount;

figure(1)
title('All Sine Waves')

figure(3)
plot(offMean,'r')
title('All Light OFF Waveforms and Their Mean')

figure(2)
plot(onMean,'r')
title('All Light ON Waveforms and Their Mean')

figure(5)
plot(onMean)
title('Light ON Mean')

figure(6)
plot(offMean)
title('Light OFF Mean')

figure(7)
hold on
plot(offMean, 'r')
plot(onMean, 'b')
title('Light OFF Mean & Light ON Mean')
legend('Light OFF Mean', 'Light ON Mean')


fprintf('There were:\n%d bad waveforms\n%d good waveforms\n\n', badCount, (offCount + onCount))