% Code by Phil Bedggood and Flora Hui
% Questions to pabedg@unimelb.edu.au or huif@unimelb.edu.au
% Citation: Hui F, et al (2014). "Quantitative spatial and temporal analysis of 
% fluorescein angiography dynamics in the eye". PLoS ONE xxx.
%
% Main input: A grayscale fluorescein angiogram TIFF stack (example "Sample.tif" included)
% Main output: A registered version of this TIFF stack
% Workflow: registerTiffStack -> PCAsmooth -> readTraceMask -> fitRegisteredTif

if plotIndividual
    if plotPCA
        load([theTifName(1:end-8) '_PCA.mat'],'intensityTraceMatrix');  
    else
        load([theTifName(1:end-8) '.mat'],'intensityTraceMatrix'); 
    end
end    

thisTrace = intensityTraceMatrix(pp,:);

 % Apply a median filter to thisTrace when not using PCA
    if ~makePCAImages
        thisTrace = medfilt1(thisTrace);
    end

thisMax = max(thisTrace);

    %% Find the first time at which there was a peak, and the last time at which there was a peak
    peakLocation_1st = find(thisTrace == thisMax,1);
    peakLocation_2nd = find(thisTrace(end:-1:1) == thisMax,1);
    peakLocation_2nd = numFrames - peakLocation_2nd + 1;
    
    peakLocation_1st_orig = peakLocation_1st;
                
    if thisMax == 255

        % To mitigate saturation issues, average the two peak locations
         peakLocation_1st = round(mean([peakLocation_1st peakLocation_2nd]));
         peakLocation_2nd = peakLocation_1st;

    end

    % Determine the half rise time, half fall time and offset:
    firstFrameToConsider = 1;
    firstIndices = firstFrameToConsider : peakLocation_1st;
    theXData_1st = all_x(firstIndices); 

    secondIndices = peakLocation_2nd : numFrames;
    theXData_2nd = all_x(secondIndices); 
    
    halfMax_1st = (thisMax - thisTrace(1))/2 + thisTrace(1);
    halfMax_2nd = (thisMax - thisTrace(end))/2 + thisTrace(end);

    firstTrace = thisTrace(firstIndices); 
    secondTrace = thisTrace(secondIndices);

    risingHalfPeakLocation = find(abs(firstTrace - halfMax_1st) == min(abs(firstTrace - halfMax_1st)) ,1);
    risingHalfPeakTime = theXData_1st(risingHalfPeakLocation);

    fallingHalfPeakLocation = find(abs(secondTrace - halfMax_2nd) == min(abs(secondTrace - halfMax_2nd)) ,1);
    fallingHalfPeakTime = theXData_2nd(fallingHalfPeakLocation);   

    % Use an average of the last 2 seconds of data to work out the offset
    lastSecondFrames = round(numFrames/all_x(1,end));
    baseline = sum(thisTrace(1,(1:(2*lastSecondFrames))))/(2*(lastSecondFrames)); % Baseline correction by first two seconds
    correctedTrace = thisTrace - baseline;
    lastSecond = sum(correctedTrace(1,(end-(2*(lastSecondFrames)-1):end)))/(2*(lastSecondFrames));
    offset = (lastSecond/max(correctedTrace)); % Calculate the offset relative to peak
    if offset < 0 % gets rid of negative values
       offset = 0;
    end

    coefficientStore(pp,:) = [risingHalfPeakTime fallingHalfPeakTime offset]; % Store the coefficients for this pixel