alignmentScript.m

clear all
close all
clc
%% Set Paramters
inFolder = 'D:\data\Leona';
outFolder = 'D:\data\out';
binningFactor = [1, 1, 2];
nSubIm = 1000;%number of subImages for med align
referenceChannel = 0; %0: green, 1: red; reference channel for shift corrections
numShiftCorrections = 1; %number of shift corrections
%% Load Files
currentFolder = pwd;
cd(inFolder);
folders = dir;

for k = length(folders):-1:1
    % remove non-folders
    if ~folders(k).isdir
        folders(k) = [ ];
        continue
    end
    % remove folders starting with .
    fname = folders(k).name;
    if fname(1) == '.'
        folders(k) = [ ];
    end
end

numFolders = length(folders);

%iterate through all folders
for f = 1:numFolders
    %go into folder
    cd(inFolder);
    cd(folders(f).name);
    greenFiles = dir('ChanA_*_*.tif');
    redFiles = dir('ChanB_*_*.tif');
    %check if fileNumber is the same
    if size(greenFiles, 1) ~= size(redFiles, 1)
        error(['Unequal number of files in trial folder "', folders(f).name, '"!!']);
    end
    numFiles = size(greenFiles, 1);
    
    %load first red frame to get resolution and being able to preallocate
    temp = readTiffNoStack(redFiles(1).name);
    res = size(temp);
    
    %preallocate data_r
    data_r = zeros(res(1), res(2), numFiles);
    data_g = zeros(res(1), res(2), numFiles);
    %load data
    disp(['Loading Files In Folder ', folders(f).name]);
    parfor i=1:numFiles
        data_r(:,:,i) = readTiffNoStack(redFiles(i).name);
        data_g(:,:,i) = readTiffNoStack(greenFiles(i).name);
    end
    disp(['Shift Correction Of Files In Folder ', folders(f).name]);
    
    %save stacks in memory
    cd(outFolder);
    disp(['Write Files Of Folder ', folders(f).name ' in ' outFolder ' to RAM']);
    data_r_complete{f} = data_r;
    data_g_complete{f} = data_g;
end

%go back to old current folder
cd(currentFolder);
clear data_r data_g
data_r = data_r_complete;
data_g = data_g_complete;
%create big array
numFrames = 0;
numFrameList = zeros(1,numFolders);
for i = 1:numFolders
    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}));
for i = 1:numFolders
    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
clear data_r_complete data_g_complete data_r data_g
data_r = data_r_array;
data_g = data_g_array;
clear data_g_array data_r_array
%% Do Shift Correction
wb = waitbar(0, 'Performing Shift Correction');

for j = 1:numShiftCorrections
    if referenceChannel
        referenceChannelData = data_r;
    else
        referenceChannelData = data_g;
    end
    %Med Align
    parfor f=1:size(referenceChannelData,3)
        referenceChannelData(:,:,f) = imgaussfilt(referenceChannelData(:,:,f),2);
    end
    [rs, cs] = medAlign(referenceChannelData, nSubIm, 50, -inf);
    %shift red and green channel
    waitbar(j/numShiftCorrections, wb, 'Performing Med Align..');
    parfor i = 1:size(data_g,3)
        data_r(:,:,i) = circshift(data_r(:,:,i),[rs(i),cs(i)]);
        data_g(:,:,i) = circshift(data_g(:,:,i),[rs(i),cs(i)]);
    end
end
%matVis(data_r,data_g);
%% Export Files
%save trial files
for i=1:numFolders
    waitbar(i/numFolders, wb, 'Saving Trial Tiff Files..');
    %binning
    data_r_save = uint16(binning(data_r(:,:,numFrameList(i)+1:numFrameList(i+1)), binningFactor, 'mean'));
    data_g_save = uint16(binning(data_g(:,:,numFrameList(i)+1:numFrameList(i+1)), binningFactor, 'mean'));
    
    saveastiff(uint16(data_r_save), [outFolder filesep folders(i).name  '_r.tif']);
    saveastiff(uint16(data_g_save), [outFolder filesep folders(i).name  '_g.tif']);
end

%save big tiff file
data_r = uint16(binning(data_r, binningFactor, 'mean'));
data_g = uint16(binning(data_g, binningFactor, 'mean'));
disp('Saving Big Data Set..');
waitbar(0, wb, 'Saving Big Tiff Files..');
options.big = true;
saveastiff(data_r, [outFolder filesep 'complete_r.tif'], options);
waitbar(0.5, wb, 'Saving Big Tiff Files..');
saveastiff(data_g, [outFolder filesep 'complete_g.tif'], options);
%%
close(wb);
disp('Finished Script!');