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did a lot of memory optimizations, calculations are now mostly done i…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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(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!'); |