added an alignment script, added a load function in main for alignmen…

…t script data

alignmentScript.m

@@ -0,0 +1,137 @@
+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(data_r_save, [outFolder filesep folders(i).name  '_r.tif']);
+    saveastiff(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!');

functions/CellSortLoadFilesFromAlignmentScript.m

@@ -0,0 +1,59 @@
+function [data_g_array, data_r_array, numFrameList, fn_green, fn_red, greenFiles, redFiles] = CellSortLoadFilesFromAlignmentScript(outFolder)
+greenFiles = dir('*_g*.tif*');
+redFiles = dir('*_r*.tif*');
+%delete complete file from file list
+greenFiles(end)=[];
+redFiles(end)=[];
+
+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
+
+%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