Modified to save analysis data that once done does not need to be redone if it needs to be plotted again or differently.

Data-Analyzer/+Analyzer/performAnalysis.m

@@ -32,6 +32,8 @@ function results = performAnalysis(options)
         options.skipNormalization (1,1) logical
         options.skipLivePlot (1,1) logical
         options.skipSaveFigures (1,1) logical
+        options.skipSaveData (1,1) logical
+        options.skipSaveOD (1,1) logical
         options.showProgressBar (1,1) logical
         options.measurementName (1,:) char
         options.folderPath (1,:) char

Data-Analyzer/+Helper/batchAnalyze.m

@@ -57,6 +57,11 @@ function results_all = batchAnalyze(dataSources, options)
                 result.path     = folderPath;
                 result.results  = analysisResults;
                 
+                % Save each dataset as its own MAT file
+                if ~isfield(options, 'skipSaveData') || ~options.skipSaveData
+                    saveResultStruct(result, options.saveDirectory);
+                end
+                
                 % Append to output
                 results_all{end+1,1} = result;
 
@@ -67,3 +72,35 @@ function results_all = batchAnalyze(dataSources, options)
         end
     end
 end
+
+%% ---- Local function for saving results ----
+function saveResultStruct(result, saveDirectory)
+    % Define results folder
+    resultsFolder = fullfile(saveDirectory, "Results", "AnalysisSavedData");
+    if ~exist(resultsFolder, 'dir')
+        mkdir(resultsFolder);
+    end
+
+    % Path to index file
+    indexFile = fullfile(resultsFolder, "datasetsIndex.mat");
+
+    % Load or initialize index
+    if isfile(indexFile)
+        S = load(indexFile, "nextIdx");
+        nextIdx = S.nextIdx;
+    else
+        nextIdx = 1;
+    end
+
+    % Variable name and file path
+    varName = sprintf('Dataset_%d', nextIdx);
+    savePath = fullfile(resultsFolder, varName + ".mat");
+
+    % Save dataset as struct inside MAT file
+    S.(varName) = result;
+    save(savePath, '-struct', 'S');
+
+    % Update index
+    nextIdx = nextIdx + 1;
+    save(indexFile, "nextIdx");
+end

Data-Analyzer/+Helper/collectODImages.m

@@ -38,7 +38,7 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
             file_list             = evalin('base','file_list');
 
             % --- Ensure figures exist if requested now ---
-            if ~options.skipSaveFigures
+            if ~options.skipSaveOD
                 saveODFigures(od_imgs, options.saveDirectory);
             end
 
@@ -200,7 +200,7 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
     assignin('base', 'prior_options', options);
     
     % --- Save OD images as figures if requested ---
-    if ~options.skipSaveFigures
+    if ~options.skipSaveOD
         saveODFigures(od_imgs, options.saveDirectory);
     end
 

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

@@ -68,6 +68,8 @@ options.skipMasking               = true;
 options.skipIntensityThresholding = true;
 options.skipBinarization          = true;
 options.skipSaveFigures           = true;
+options.skipSaveData              = false;
+options.skipSaveOD                = true;
 options.skipLivePlot              = false;
 options.showProgressBar           = true;
 

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

@@ -67,8 +67,8 @@ options.skipPreprocessing         = true;
 options.skipMasking               = true;
 options.skipIntensityThresholding = true;
 options.skipBinarization          = true;
-options.skipMovieRender           = true;
 options.skipSaveFigures           = true;
+options.skipSaveData              = false;
 options.skipSaveOD                = true;
 options.skipLivePlot              = false;
 options.showProgressBar           = true;