added matVis and made merging and correcting files from different tri…

…als possible

CellSortLoadSingleFiles.m

@@ -1,24 +1,63 @@
-function [data_g, data_r] = CellSortLoadSingleFiles(green, red)
-fileListGreen = dir(green);
-fileListRed = dir(red);
+function [data_g, data_r] = CellSortLoadSingleFiles(green, red, data_g, data_r)
+trialFolders = dir;
+trialFolders(1:2) = [];
+dirFlags = [trialFolders.isdir];
+trialFolders = {trialFolders(dirFlags).name};
 
-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]);
 
-%read first frame to get resolution fily type etc..
-temp = readTiff(fileListGreen(1).name);
-data_g = zeros(size(temp,1), size(temp,2), numFiles, class(temp));
-temp = readTiff(fileListRed(1).name);
-data_r = zeros(size(temp,1), size(temp,2), numFiles, class(temp));
 
-for i=1:numFiles
-    temp = readTiff(fileListGreen(i).name);
-    data_g(:,:,i) = temp;
-    temp = readTiff(fileListRed(i).name);
-    data_r(:,:,i) = temp;
+%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;
+    end
+
+    %add data_g_temp and data_r_temp to outputData
+
+
+
+    %go back
+    cd ..;
 end
+close(wb);
 end

main.m

@@ -1,6 +1,6 @@
 %% load and prepare all single tiffs
 %importing
-[data_g,data_r] = CellSortLoadSingleFiles('ChanA*.tif', 'ChanB*.tif');
+[data_g, data_r] = CellSortLoadSingleFiles('ChanA_*_*.tif', 'ChanB_*_*.tif');
 %shiftCorrection
 %generates shift corrected files for the green and red channels, needs
 %DIPlib (available for free)