recent changes we made together at processing computer

CellSortLoadSingleFiles.m

@@ -9,55 +9,57 @@
 %go into trial folders and import files
 wb = waitbar(0, 'Loading Files..');
 for i=1:size(trialFolders,2)
-    waitbar(i/size(trialFolders,2));
-    %go into trialFodlers and import data
-    cd(num2str(i));
-    %import data
-    fileListGreen = dir(green);
-    fileListRed = dir(red);
-    numFilesGreen = size(fileListGreen,1);
-    numFilesRed = size(fileListRed,1);
-
-
-
-    if numFilesGreen ~= numFilesRed
-        disp('Green and Red Channel have different number of Images, take the smaller value..');
-    end
-    numFiles = min([numFilesRed, numFilesGreen]);
-    temp = readTiff(fileListGreen(1).name);
-    data_g_temp = zeros(size(temp,1), size(temp,2), numFiles, class(temp));
-    temp = readTiff(fileListRed(1).name);
-    data_r_temp = zeros(size(temp,1), size(temp,2), numFiles, class(temp));
-
-    for j=1:numFiles
-        temp = readTiff(fileListGreen(j).name);
-        data_g_temp(:,:,j) = temp;
-        temp = readTiff(fileListRed(j).name);
-        data_r_temp(:,:,j) = temp;
-    end
-
-    %if data is no existent, preallocate it one time when i == 1
-    if i==1 && ~exist('data_g', 'var') && ~exist('data_r','var')
-        data_g = data_g_temp;
-        data_r = data_r_temp;
-    else
-        temp_data = zeros(size(temp,1), size(temp,2), size(data_g,3)+numFiles, class(temp));
-        temp_data(:,:,1:size(data_g,3)) = data_g;
-        temp_data(:,:,(size(data_g,3)+1):end) = data_g_temp;
-        data_g = temp_data;
-
-        temp_data = zeros(size(temp,1), size(temp,2), size(data_r,3)+numFiles, class(temp));
-        temp_data(:,:,1:size(data_r,3)) = data_r;
-        temp_data(:,:,(size(data_r,3)+1):end) = data_r_temp;
-        data_r = temp_data;
+    if exist(num2str(i), 'dir')
+        waitbar(i/size(trialFolders,2));
+        %go into trialFodlers and import data
+        cd(num2str(i));
+        %import data
+        fileListGreen = dir(green);
+        fileListRed = dir(red);
+        numFilesGreen = size(fileListGreen,1);
+        numFilesRed = size(fileListRed,1);
+
+
+
+        if numFilesGreen ~= numFilesRed
+            disp('Green and Red Channel have different number of Images, take the smaller value..');
+        end
+        numFiles = min([numFilesRed, numFilesGreen]);
+        temp = readTiff(fileListGreen(1).name);
+        data_g_temp = zeros(size(temp,1), size(temp,2), numFiles, class(temp));
+        temp = readTiff(fileListRed(1).name);
+        data_r_temp = zeros(size(temp,1), size(temp,2), numFiles, class(temp));
+
+        parfor j=1:numFiles
+            temp = readTiff(fileListGreen(j).name);
+            data_g_temp(:,:,j) = temp;
+            temp = readTiff(fileListRed(j).name);
+            data_r_temp(:,:,j) = temp;
+        end
+
+        %if data is no existent, preallocate it one time when i == 1
+        if i==1 && ~exist('data_g', 'var') && ~exist('data_r','var')
+            data_g = data_g_temp;
+            data_r = data_r_temp;
+        else
+            temp_data = zeros(size(temp,1), size(temp,2), size(data_g,3)+numFiles, class(temp));
+            temp_data(:,:,1:size(data_g,3)) = data_g;
+            temp_data(:,:,(size(data_g,3)+1):end) = data_g_temp;
+            data_g = temp_data;
+
+            temp_data = zeros(size(temp,1), size(temp,2), size(data_r,3)+numFiles, class(temp));
+            temp_data(:,:,1:size(data_r,3)) = data_r;
+            temp_data(:,:,(size(data_r,3)+1):end) = data_r_temp;
+            data_r = temp_data;
+        end
+
+        %add data_g_temp and data_r_temp to outputData
+
+
+
+        %go back
+        cd ..;
     end
-
-    %add data_g_temp and data_r_temp to outputData
-
-
-
-    %go back
-    cd ..;
 end
 close(wb);
 end

CellSortShiftCorrection.m

@@ -1,13 +1,16 @@
-function [data_g, data_r] = CellSortShiftCorrection(data_g, data_r)
+function [data_g, data_r] = CellSortShiftCorrection(data_g, data_r, firstRedFrame)
 %% shiftcorrection
 %import green channel
 disp('Performing Shift Correction..');
 %shift correction
-firstRedFrame = data_r(:,:,1);
-parfor r = 2:size(data_g, 3)
+% wb = waitbar(0, 'Performing Shift Correction..');
+parfor r = 1:size(data_g, 3)
+%     waitbar(r/size(data_g, 3), wb,[num2str(r) ' of ' num2str(size(data_g, 3))]);
     shiftVector = findshift(firstRedFrame, data_r(:,:,r), 'iter');
     data_r(:,:,r)  = shift(data_r(:,:,r),shiftVector);
     data_g(:,:,r)  = shift(data_g(:,:,r),shiftVector);
+
 end
 disp('finished');
+% close(wb);
 end

CellSortTemporalBinning.m

@@ -3,5 +3,8 @@
 class_r = class(data_r);
 
 data_g = cast(binning(data_g, binningFactor, 'mean'), class_g);
+
 data_r = cast(binning(data_r, binningFactor, 'mean'), class_r);
+
+
 end

main.m

@@ -1,22 +1,29 @@
 %% load and prepare all single tiffs
 %importing
 [data_g, data_r] = CellSortLoadSingleFiles('ChanA_*_*.tif', 'ChanB_*_*.tif');
-%shiftCorrection
+% [data_g, data_r] = CellSortLoadSingleFiles('ChanA_*_*.tif', 'ChanB_*_*.tif', data_g, data_r);
+%% 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);
+[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);
-%% export
-fn_green = 'green.tif';
-fn_red = 'red.tif';
+
+fn_green = 'green.tiff';
+fn_red = 'red.tiff';
 CellSortExportTifStack(data_g, fn_green);
 CellSortExportTifStack(data_r, fn_red);
 %% load files
 %if you haven't used the shiftCorrection you have to load the already processed files
-fn_green = 'green.tif';
-fn_red = 'red.tif';
+fn_green = 'green.tiff';
+fn_red = 'red.tiff';
 data_g = readTiff(fn_green);
 data_r = readTiff(fn_red);
 %% 1. PCA
@@ -88,23 +95,6 @@
 %optionally, plot signals
 figure(2)
 CellsortICAplot('series', ica_filters, ica_sig, movm, tlims, dt, 1, 2, [1:20], spt, spc);
-%% prepare georgis data for visualization
-%optionally, if you want to use the alternative evaluation georgi was using, import the
-%mask and run this section
-fn='green_13.tiff';
-info = imfinfo(fn);
-num_images = numel(info);
-data_g = readTiff(fn);
-%make mask logical
-mask1 = logical(mask.*(mask > 0));
-ica_segments = permute(mask, [3 1 2]);
-mask1 = repmat(mask, [1 1 1 size(data_g,3)]);
-%generate cell_sig for every feature
-cellsig = zeros(size(mask1,3), size(data_g,3));
-for i=1:size(mask1,3)
-    cell_sig(i,:) = squeeze(mean(mean(squeeze(mask1(:,:,i,:)).*data_g(:,:,:),1),2));
-end
-clear mask
 %% show signal of cells (cell_sig)
 %caluclate correlation matrix for cell_sig
 [ica_segments, cluster, subPlotCols, subPlotWidth, sortedIdx] = calcCorrEff(cell_sig, ica_segments);