CellSortLoadTrialsShiftCorrOnTrials.m

function [data_g_array, data_r_array, numFrameList, fn_green, fn_red, greenFiles, redFiles] = CellSortLoadTrialsShiftCorrOnTrials(folder_corr)
%%
cd(folder_corr);
greenFiles = dir('*green*.tif*');
redFiles = dir('red*.tif*');
fn_green = greenFiles(1).name;
fn_red = redFiles(1).name;
%load files
numberGreen = size(greenFiles,1);
numberRed = size(redFiles,1);
if numberGreen ~= numberRed
    error('Unequal number of red and green channel files!!!');
end

%load trials
disp('Loading Trial Files..');
parfor i = 1:numberGreen
    data_r{i} = readTiff(redFiles(i).name);
    data_g{i} = readTiff(greenFiles(i).name);
end

%do shift correction
disp('Performing Shift Correction On All Trials..');
reference = median(data_r{1},3);
for i = 1:numberGreen
    disp(['Working on Trial ' num2str(i)]);
    medianProj = median(data_r{i},3);
    shiftVector = findshift(reference, medianProj, 'iter');
    %shift frames
    for f = 1:size(data_r{i},3)
        data_r{i}(:,:,f)  = imtranslate(data_r{i}(:,:,f),shiftVector', 'linear');
        data_g{i}(:,:,f)  = imtranslate(data_g{i}(:,:,f),shiftVector', 'linear');
    end
end
%put them in single arrays
numFrames = 0;
numFrameList = zeros(1,numberGreen);
for i = 1:numberGreen
    numFrames = numFrames + size(data_g{i},3);
    numFrameList(i+1) = numFrames;
end

%preallocate data
data_r_array = zeros(size(data_g{i},1),size(data_g{i},2),numFrames, class(data_r{1}));
data_g_array = zeros(size(data_g{i},1),size(data_g{i},2),numFrames, class(data_g{1}));
disp('Creating Big Data Set..');
for i = 1:numberGreen
    data_r_array(:,:,(numFrameList(i)+1):numFrameList(i+1)) = data_r{i};
    data_r{i} = [];
    data_g_array(:,:,(numFrameList(i)+1):numFrameList(i+1)) = data_g{i};
    data_g{i} = [];
end

%calculate quality plot
reference = mean(data_r_array, 3);
qualityPlot = zeros(1,size(data_r_array, 3));
parfor i = 1:size(data_r_array,3)
    qualityPlot(i) = sqrt(squeeze(mean(mean((cast(data_r_array(:,:,i),'like', reference) - reference).^2,1),2)));
end
figure('Name','Quality Plot');
plot(qualityPlot);
for i=1:numberGreen
    vline(numFrameList(i), 'black', greenFiles(i).name);
end
title('Quality Of Shift Correction');
xlabel('frame');
ylabel('std of frame');

disp('Finished Loading Trial Files!');
end