Bugfixes, general improvements.

Data-Analyzer/+Helper/batchAnalyze.m

@@ -38,14 +38,9 @@ function results_all = batchAnalyze(dataSources, options)
             end
 
             % Build folder path
-            folderPath = fullfile(baseFolder, runID);
+            folderPath         = fullfile(baseFolder, runID);
-            if ~endsWith(folderPath, filesep)
-                folderPath = [char(folderPath) filesep];
-            else
-                folderPath = char(folderPath);
-            end
             options.folderPath = folderPath;
-
+            
             try
                 % Convert struct -> name-value args
                 args = [fieldnames(options), struct2cell(options)]';

Data-Analyzer/+Helper/collectODImages.m

@@ -32,11 +32,17 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
         critical_fields = {'folderPath','cam','angle','ImagingMode','PulseDuration','center','span','fraction','removeFringes','skipUnshuffling','scan_reference_values'};
 
         if ~haveOptionsChanged(options, prior_options, critical_fields)
-            fprintf('\nReusing processed OD images, scan parameters, and file list from memory (options unchanged).\n');
+            fprintf('\nReusing processed OD images, scan parameters, and file list from memory.\n');
             od_imgs               = evalin('base','od_imgs');
             scan_parameter_values = evalin('base','scan_parameter_values');
             file_list             = evalin('base','file_list');
-            return; % ✅ skip rest of the function
+
+            % --- Ensure figures exist if requested now ---
+            if ~options.skipSaveFigures
+                saveODFigures(od_imgs, options.saveDirectory);
+            end
+
+            return; % ✅ safe to exit now
         else
             fprintf('\nProcessed-data-related options changed. Reprocessing full OD image dataset...\n');
         end
@@ -46,7 +52,8 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
     fullDataExists = evalin('base', 'exist(''full_od_imgs'', ''var'')') && ...
                      evalin('base', 'exist(''full_bkg_imgs'', ''var'')') && ...
                      evalin('base', 'exist(''raw_scan_parameter_values'', ''var'')') && ...
-                     evalin('base', 'exist(''raw_file_list'', ''var'')');
+                     evalin('base', 'exist(''raw_file_list'', ''var'')') && ...
+                     evalin('base', 'exist(''prior_options'',''var'')');
 
     if fullDataExists
         % Both required datasets exist, check if raw-data options changed
@@ -174,25 +181,17 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
     assignin('base', 'file_list', file_list);
     assignin('base', 'prior_options', options);
     
-    % --- Optionally save OD images as figures ---
+    % --- Save OD images as figures if requested ---
     if ~options.skipSaveFigures
-        odFolder = fullfile(options.saveDirectory, "Results", "ODImages");
+        saveODFigures(od_imgs, options.saveDirectory);
-        if ~exist(odFolder, 'dir')
-            mkdir(odFolder);
-        end
-    
-        for k = 1:length(od_imgs)
-            img = od_imgs{k};
-            fileName = fullfile(odFolder, sprintf('OD_img_%03d.png', k));
-            imwrite(mat2gray(img), fileName);
-        end
     end
 
     fprintf('\nOD image dataset ready for further analysis.\n');
 
 end
 
-% --- Local helper function to compare options ---
+%% --- Local helper functions ---
+
 function changed = haveOptionsChanged(options, prior_options, critical_fields)
     changed = false;
     for f = critical_fields
@@ -205,4 +204,35 @@ function changed = haveOptionsChanged(options, prior_options, critical_fields)
             changed = true; return
         end
     end
-end
+end
+
+function saveODFigures(od_imgs, saveDirectory)
+    odFolder = fullfile(saveDirectory, "Results", "ODImages");
+    if ~exist(odFolder, 'dir')
+        mkdir(odFolder);
+    end
+
+    nImgs = length(od_imgs);
+    filesExist = all(arrayfun(@(k) isfile(fullfile(odFolder, sprintf('OD_img_%03d.fig', k))), 1:nImgs));
+
+    if filesExist
+        fprintf('\nOD figures already exist in %s. Skipping save.\n', odFolder);
+        return;
+    end
+
+    fprintf('\nSaving OD figures to %s ...\n', odFolder);
+    for k = 1:nImgs
+        img = od_imgs{k};
+
+        % Create invisible figure for saving
+        hFig = figure('Visible','off');
+        imagesc(img);
+        axis image off; colormap gray;
+        fileName = fullfile(odFolder, sprintf('OD_img_%03d.fig', k));
+
+        % Save as .fig
+        savefig(hFig, fileName);
+        close(hFig);
+    end
+    fprintf('OD figures saved successfully.\n');
+end

Data-Analyzer/+Scripts/BECToDropletsToStripes/plotImages.m

@@ -103,7 +103,7 @@ set(0,'DefaultUicontrolFontSize',10);  % increase default font size
                               'ListString', allPaths, ...
                               'ListSize',[400, 300]); % width x height in pixels
 if tf
-    options.folderPath = allPaths{selectedIndex}; % ✅ store in options
+    options.folderPath = fullfile(allPaths{selectedIndex}); % ✅ store in options
     fprintf('Path set to selection: %s\n', options.folderPath);
 else
     error('No path selected. Aborting.');

Data-Analyzer/+Scripts/BECToDropletsToStripes/runFullAnalysis.m

@@ -67,7 +67,7 @@ options.skipPreprocessing         = true;
 options.skipMasking               = true;
 options.skipIntensityThresholding = true;
 options.skipBinarization          = true;
-options.skipSaveFigures           = false;
+options.skipSaveFigures           = true;
 options.skipLivePlot              = false;
 options.showProgressBar           = true;