deleted iterative shift correction and implemented cross correlation

CellSortXCorr.m

@@ -0,0 +1,73 @@
+function CellSortXCorr(nSubIm, nImages, m, n)
+% nSubIm = 10;
+% nImages = 1344;
+% m=14;
+% n=24;
+
+for k = m:n;
+    % Compose image stack from filenames
+    folder = sprintf('/storage/letz/Data/Data/Elisabeth_Abs/75EA/habituation/%u', k)
+    if exist(folder) == 0
+        continue
+    end
+    folder_corr = '/storage/letz/Data/Data/Elisabeth_Abs/75EA/habituation/corrected';
+
+    file_image_red = [folder, 'ChanB_0001_0001_0001_0001.tif'];
+    filePrefix_red = 'ChanB_0001_0001_0001_';
+
+    file_image_green = [folder, 'ChanA_0001_0001_0001_0001.tif'];
+    filePrefix_green = 'ChanA_0001_0001_0001_';
+
+    filename_red = sprintf([folder,filesep,filePrefix_red,'%04u.tif'],1);
+    im_red = imread(filename_red);
+
+    filename_green = sprintf([folder,filesep,filePrefix_green,'%04u.tif'],1);
+    im_green = imread(filename_green);
+
+    %preallocate data variable
+    allIm_red = zeros(size(im_red,1),size(im_red,2),nImages);
+    %read tiffs
+    for i = 1:nImages
+        filename_red = sprintf([folder,filesep,filePrefix_red,'%04u.tif'],i);
+        allIm_red(:,:,i) = readTiffNoStack(filename_red);
+    end
+
+    %preallocate data variable
+    allIm_green = zeros(size(im_green,1),size(im_green,2),nImages);
+    %read tiffs
+    for i = 1:nImages
+        filename_green = sprintf([folder,filesep,filePrefix_green,'%04u.tif'],i);
+        allIm_green(:,:,i) = readTiffNoStack(filename_green);
+    end
+
+
+    [rs, cs] = medAlign(allIm_red, nSubIm, 50, -inf);
+
+    registered = zeros(size(allIm_red,1),size(allIm_red,2),size(allIm_red,3), class(allIm_red));
+    parfor i = 1:nImages
+        registered(:,:,i) = circshift(allIm_red(:,:,i),[rs(i),cs(i)]);
+    end
+
+    data = binning(registered,[1,1,2],'mean');
+
+    filename = sprintf([folder_corr,filesep,'red_%u.tiff'],k);
+    for j=1:(nImages/2)
+        imwrite(uint16(data(:,:,j)),filename, 'tiff','WriteMode','append');
+    end
+
+
+
+    %align green channel with parameters from red alignment
+    parfor i = 1:nImages
+        registered(:,:,i) = circshift(allIm_green(:,:,i),[rs(i),cs(i)]);
+    end
+
+    data = binning(registered,[1,1,2],'mean');
+
+    filename = sprintf([folder_corr,filesep,'green_%u.tiff'],k);
+    for j=1:(nImages/2)
+        imwrite(uint16(data(:,:,j)),filename, 'tiff','WriteMode','append');
+    end
+
+
+end

main.m

@@ -1,29 +1,16 @@
-%% load and prepare all single tiffs
-%importing
-[data_g, data_r] = CellSortLoadSingleFiles('ChanA_*_*.tif', 'ChanB_*_*.tif');
-%% matVis
-matVis(data_r);
-%% get ref frame for shift correction
-interval = 1:20;
-refFrame = cast(mean(data_r(:,:,interval), 3), class(data_r));
-matVis(refFrame);
-%% shiftCorrection
-%generates shift corrected files for the green and red channels, needs
-%DIPlib (available for free)
-[data_g, data_r] = CellSortShiftCorrection(data_g, data_r, refFrame);
-%temporal binning
-binningFactor = [1 1 2]; %x, y, t
-[data_g, data_r] = CellSortTemporalBinning(data_g, data_r, binningFactor);
-
-fn = 'processedData.mat';
-save(fn, 'data_g', 'data_r', '-v7.3');
+%% load files and do cross correlation alignment
+nSubIm = 10;
+nImages = 1344;
+m=14;
+n=24;
+CellSortXCorr(nSubIm, nImages, m, n);
 %% load files
-%if you haven't used the shiftCorrection you have to load the already processed files
-fn= 'processedData.mat';
-load(fn);
+fn_green = 'data_g.tif';
+fn_red = 'data_r.tif';
+data_g = readTiff(fn_green);
+data_r = readTiff(fn_red);
 %% 1. PCA
 %calculate PCAs
-fn_green = 'processedData.mat';
 nPCs = 100;
 flims = [];
 dSamp = [1 1]; %temporal, spatial downsampling

readTiffNoStack.m

@@ -0,0 +1,4 @@
+function data = readTiffNoStack(filename)
+t_g = Tiff(filename, 'r');
+data = t_g.read();
+end

testOfDifferentTifImports.m

@@ -0,0 +1,32 @@
+fn = 'test.tif';
+
+tic;
+
+for i=1:5000
+data = readTiff(fn);
+end
+
+timeReadTiff = toc;
+
+tic;
+for i=1:5000
+data = imread(fn);
+end
+
+timeImread = toc;
+
+
+tic;
+for i=1:5000
+data = readTiffNoStack(fn);
+end
+
+timeNoStack = toc;
+
+tic;
+for i=1:5000
+t_g = Tiff(fn, 'r');
+data = t_g.read();
+end
+
+timeNoStackNoFunction = toc;