fixed wrong indexing in kloading of files, which prevented the second…

… run of shift correction

functions/CellSortLoadTrialsShiftCorrOnTrials.m

@@ -22,13 +22,14 @@
 %do shift correction
 disp('Performing Shift Correction On All Trials..');
 reference = median(data_r{1},3);
-parfor i = 1:numberGreen
+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}(:,:,i)  = shift(data_r{i}(:,:,i),shiftVector);
-        data_g{i}(:,:,i)  = shift(data_g{i}(:,:,i),shiftVector);
+        data_r{i}(:,:,f)  = shift(data_r{i}(:,:,f),shiftVector);
+        data_g{i}(:,:,f)  = shift(data_g{i}(:,:,f),shiftVector);
     end
 end
 %put them in single arrays

functions/trialAlignmentScript_Leona.m

@@ -0,0 +1,147 @@
+clear all
+close all
+clc
+%% Load Trial Files
+inFolder = 'D:\data\session_1';
+outFolder = 'D:\data\out';
+binningFactor = [1, 1, 2];
+nSubIm = 10;
+
+
+
+%% load single tif files of trials to ram
+%operations
+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]);
+    %do the shift correction
+    [rs, cs] = medAlign(data_r, nSubIm, 50, -inf);
+
+    %shift red and green channel
+    disp(['Shift Data Arrays Of Files In Folder ', folders(f).name]);
+    parfor i = 1:numFiles
+        data_r(:,:,i) = circshift(data_r(:,:,i),[rs(i),cs(i)]);
+        data_g(:,:,i) = circshift(data_g(:,:,i),[rs(i),cs(i)]);
+    end
+
+    %binning
+    data_r = uint16(binning(data_r, binningFactor, 'mean'));
+    data_g = uint16(binning(data_g, binningFactor, 'mean'));
+
+    %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
+
+disp('Finished Shift Correction And Fusing Of Data!');
+%go back to old current folder
+cd(currentFolder);
+
+%% shift correct trials to each other
+%do shift correction
+clear data_r data_g
+data_r = data_r_complete;
+data_g = data_g_complete;
+clear data_r_complete data_g_complete
+disp('Performing Shift Correction On All Trials..');
+reference = median(data_r{1},3);
+numberGreen = size(data_g,2);
+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)  = shift(data_r{i}(:,:,f),shiftVector);
+        data_g{i}(:,:,f)  = shift(data_g{i}(:,:,f),shiftVector);
+    end
+end
+
+%save tiff files
+for i=1:numberGreen
+    saveastiff(data_r{i}, [outFolder filesep folders(i).name  '_r.tif']);
+    saveastiff(data_g{i}, [outFolder filesep folders(i).name  '_g.tif']);
+end
+
+%% generate quality plot
+%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');
+%% Finished
+disp('Finished Complete Script!!!');

main.m

@@ -4,14 +4,14 @@
 %also choose a binning factor [x, y, t]. nSubIm ist the number of
 %iterations the shift correction will do. The more the better, but of
 %course it is more time consuming. The standard value here is 10.
-inFolder = 'F:\Arbeit\testData\PCAICA';
-outFolder = 'F:\Arbeit\testData\PCAICA\corr';
+inFolder = 'D:\data\session_1';
+outFolder = 'D:\data\out';
 binningFactor = [1, 1, 2];
 nSubIm = 10;
 CellSortXCorr(inFolder, outFolder, nSubIm, binningFactor);
 %% load files
 %go to corr folder
-outFolder = 'X:\Projects\ICA_PCA\data_dendrites\51EA\day_1';
+outFolder = 'D:\data\out';
 %shifft correction on all frames
 %[data_g, data_r, frames, fn_green, fn_red, fileNamesGreen, fileNamesRed] = CellSortLoadTrials(outFolder);
 %shift correction only on trials