dada

functions/CellSortLoadTrialsShiftCorrOnTrials.m

@@ -18,18 +18,17 @@
     data_r{i} = readTiff(redFiles(i).name);
     data_g{i} = readTiff(greenFiles(i).name);
 end
-disp('Finished Loading Trial Files..');
 
 %do shift correction
-disp('Finished Performing Shift Correction On All Trials..');
+disp('Performing Shift Correction On All Trials..');
 reference = median(data_r{1},3);
 for i = 1:numberGreen
     medianProj = median(data_r{i},3);
     shiftVector = findshift(reference, medianProj, 'iter');
     %shift frames
     for f = 1:size(data_r{i},3)
-        data_r{i}(:,:,r)  = shift(data_r{i}(:,:,r),shiftVector);
-        data_g{i}(:,:,r)  = shift(data_g{i}(:,:,r),shiftVector);
+        data_r{i}(:,:,i)  = shift(data_r{i}(:,:,i),shiftVector);
+        data_g{i}(:,:,i)  = shift(data_g{i}(:,:,i),shiftVector);
     end
 end
 %put them in single arrays
@@ -50,7 +49,6 @@
     data_g_array(:,:,(numFrameList(i)+1):numFrameList(i+1)) = data_g{i};
     data_g{i} = [];
 end
-disp('Finished Creating Big Data Set');
 
 disp('Finished Loading Trial Files!');
 end

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 = 'D:\data\rawDataICAPCA';
-outFolder = 'D:\data\corr';
+inFolder = 'F:\Arbeit\testData\PCAICA';
+outFolder = 'F:\Arbeit\testData\PCAICA\corr';
 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 = 'F:\Arbeit\testData\PCAICA';
 %[data_g, data_r, frames, fn_green, fn_red, fileNamesGreen, fileNamesRed] = CellSortLoadTrials(outFolder);
 [data_g, data_r, frames, fn_green, fn_red, fileNamesGreen, fileNamesRed] = CellSortLoadTrialsShiftCorrOnTrials(outFolder);
 %If you want to load single files, use the functions below.