% 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

clear; close all 

% ~~~~ Important settings to change ~~~~
cd('C:\Users\Phil\Documents\flora\Code for paper\Latest')

makePCAImages = 1; % Use images generated from PCA filtering
frameOn = 1; % Analyse from the first frame
useVesselTraceData = 1; % 0 to not utilise the blood vessel masks
% ~~~~ End important settings ~~~~

[theTifName,p] = uigetfile('*_reg.tif');
theTifInfo = imfinfo(theTifName);
numFrames = length(theTifInfo);

load([theTifName(1:end-8) '.mat'],'binFactor');
load([theTifName(1:end-8) '.mat'],'stackLength');
frameRate = numFrames/stackLength; 
ySize = theTifInfo(1).Height / binFactor;
xSize = theTifInfo(1).Width / binFactor;
 
% Time points
all_x = linspace(0,stackLength,numFrames - frameOn + 1);

% Loop each pixel in the intensity matrix and do the curve fit
plotIndividual = 0;

if useVesselTraceData    
    numRuns = 4;    
else    
    numRuns = 1;  
end

colorVec = 'rbmg'; % Plot color for arteries, veins, all large vessels, all small vessels

load([theTifName(1:end-8) '.mat'],'pixOfInterest')
origPixOfInterest = pixOfInterest; % The ROI (intersection of a circle and a square that we selected earlier)

for nn = 1:numRuns
        
    if makePCAImages
        load([theTifName(1:end-8) '_PCA.mat'],'intensityTraceMatrix');
    else
        load([theTifName(1:end-8) '.mat'],'intensityTraceMatrix');
    end        
    
    if useVesselTraceData
        
        temp = zeros(ySize,xSize);        
        temp(origPixOfInterest) = 1;
        
        switch nn
            case 1
                load([theTifName(1:end-8) ' traced_artMask.mat'])
                pixOfInterest = find(arteryMask & temp);
            case 2
                load([theTifName(1:end-8) ' traced_venMask.mat'])
                pixOfInterest = find(veinMask & temp);
            case 3
                load([theTifName(1:end-8) ' traced_lrgMask.mat'])
                pixOfInterest = find(largeVesselMask & temp);
            case 4
                load([theTifName(1:end-8) ' traced_capMask.mat'])
                smallVesselMask(end,:) = 0;
                pixOfInterest = find(smallVesselMask & temp);                
            otherwise
        end
        
        pixOfInterest = intersect(pixOfInterest,origPixOfInterest);
        
        currentMask = false(ySize,xSize);
        currentMask(pixOfInterest) = 1;
        
        origPix_i = zeros(length(pixOfInterest),1);
        
        for pp = 1:length(pixOfInterest)            
            origPix_i(pp) = find(pixOfInterest(pp) == origPixOfInterest);
        end
        
    else        
        origPix_i = 1:length(origPixOfInterest);
    end
    
   coefficientStore = zeros(length(origPixOfInterest),3); % initialize an array to store measured parameters: time to half peak, slope at half peak, time to fall half way from peak, peak intensity and offset

    for pCount = 1:length(pixOfInterest)

        pp = origPix_i(pCount);
        fitThisPixel

    end

    riseTimeImage = NaN * ones(ySize,xSize);
    fallTimeImage = NaN * ones(ySize,xSize);
    offsetImage = NaN * ones(ySize,xSize);

    % Reshape the stored data into images
    riseTimeImage(pixOfInterest) = coefficientStore(origPix_i,1);
    fallTimeImage(pixOfInterest) = coefficientStore(origPix_i,2);
    offsetImage(pixOfInterest) = coefficientStore(origPix_i,3); 

    plotIndividual = 1;
    plotPCA = 0;

    load([theTifName(1:end-8) '.mat'],'refImageNumber');
    refImage = single(imread(theTifName,'tif',refImageNumber));
    
    % Show the figures, adjusting the colormap label to factor in the scaling above        
        
        figMaps = figure; hold on;
        subplot(3,1,1); imagesc(riseTimeImage); axis image; title('Half rise time (s)'); set(gca,'XTick',[]); set(gca,'YTick',[]); colorbar
        subplot(3,1,2); imagesc(fallTimeImage); axis image; title('Half fall time (s)');set(gca,'XTick',[]); set(gca,'YTick',[]); colorbar
        subplot(3,1,3); imagesc(offsetImage); axis image; title('Offset relative to peak');set(gca,'XTick',[]); set(gca,'YTick',[]); colorbar
   
    if numRuns > 1        
        plotIndividual = 0;
    end

     save([theTifName(1:end-8) '_fitted.mat'],'riseTimeImage')
     save([theTifName(1:end-8) '_fitted.mat'],'fallTimeImage','-append')
     save([theTifName(1:end-8) '_fitted.mat'],'offsetImage','-append')    

end