Add choice to load ROIs to ROI Manager or Overlay

src/main/java/fr/igred/ij/io/LocalBatchImage.java

@@ -173,7 +173,7 @@ public ImageWrapper getImageWrapper() {
 	@Override
 	public ImagePlus getImagePlus(ROIMode mode) {
 		ImagePlus imp = null;
-		boolean loadROIs = !mode.toString().isEmpty();
+		boolean loadROIs = mode != ROIMode.DO_NOT_LOAD;
 		try {
 			ImporterOptions options = initImporterOptions();
 			options.setShowROIs(loadROIs);

src/main/java/fr/igred/ij/io/ROIMode.java

@@ -25,9 +25,9 @@
  */
 public enum ROIMode {
 	/**
-	 * Do not load ROIs (empty String for ImporterOptions).
+	 * Do not load ROIs.
 	 */
-	DO_NOT_LOAD(""),
+	DO_NOT_LOAD("No"),
 	/**
 	 * Load ROIs in the ROI Manager.
 	 */
@@ -38,7 +38,7 @@ public enum ROIMode {
 	OVERLAY(ImporterOptions.ROIS_MODE_OVERLAY);
 
 	/**
-	 * ROI mode String value for ImporterOptions.
+	 * ROI mode String value for ImporterOptions and user selection.
 	 */
 	private final String value;
 

src/main/java/fr/igred/ij/macro/BatchParameters.java

@@ -17,12 +17,15 @@
 package fr.igred.ij.macro;
 
 
+import fr.igred.ij.io.ROIMode;
+
+
 /**
  * Holds the parameters to batch run scripts.
  */
 public class BatchParameters {
 
-	private boolean loadROIs;
+	private ROIMode roiMode;
 	private boolean saveImages;
 	private boolean saveROIs;
 	private boolean saveResults;
@@ -40,7 +43,7 @@ public class BatchParameters {
 	 * Default constructor.
 	 */
 	public BatchParameters() {
-		this.loadROIs = false;
+		this.roiMode = ROIMode.DO_NOT_LOAD;
 		this.saveImages = false;
 		this.saveROIs = false;
 		this.saveResults = false;
@@ -61,7 +64,7 @@ public BatchParameters() {
 	 * @param parameters The parameters to copy.
 	 */
 	public BatchParameters(BatchParameters parameters) {
-		this.loadROIs = parameters.loadROIs;
+		this.roiMode = parameters.roiMode;
 		this.saveImages = parameters.saveImages;
 		this.saveROIs = parameters.saveROIs;
 		this.saveResults = parameters.saveResults;
@@ -185,18 +188,18 @@ public void setSaveImages(boolean saveImages) {
 	 *
 	 * @return See above.
 	 */
-	public boolean shouldLoadROIs() {
-		return loadROIs;
+	public ROIMode getROIMode() {
+		return roiMode;
 	}
 
 
 	/**
 	 * Sets whether the ROIs should be loaded or not.
 	 *
-	 * @param loadROIs See above.
+	 * @param roiMode See above.
 	 */
-	public void setLoadROIS(boolean loadROIs) {
-		this.loadROIs = loadROIs;
+	public void setROIMode(ROIMode roiMode) {
+		this.roiMode = roiMode;
 	}
 
 

src/main/java/fr/igred/ij/macro/OMEROBatchRunner.java

@@ -494,23 +494,19 @@ private List<ROIWrapper> getROIsFromManager(ImagePlus imp, String property) {
 	/**
 	 * Runs a macro on images and saves the results.
 	 */
-	void runMacro() {
+	private void runMacro() {
 		String property = ROIWrapper.IJ_PROPERTY;
 		WindowManager.closeAllWindows();
 
 		// Initialize ROI Manager
 		initRoiManager();
-		ROIMode roiMode = ROIMode.DO_NOT_LOAD;
-		if (params.shouldLoadROIs()) {
-			roiMode = ROIMode.MANAGER;
-		}
 
 		int index = 0;
 		for (BatchImage image : images) {
 			//noinspection HardcodedFileSeparator
 			setProgress("Image " + (index + 1) + "/" + images.size());
 			setState("Opening image...");
-			ImagePlus imp = image.getImagePlus(roiMode);
+			ImagePlus imp = image.getImagePlus(params.getROIMode());
 			// If image could not be loaded, continue to next image.
 			if (imp != null) {
 				ImageWrapper imageWrapper = image.getImageWrapper();

src/main/java/fr/igred/ij/plugin/frame/OMEROBatchPlugin.java

@@ -20,6 +20,7 @@
 import fr.igred.ij.gui.OMEROConnectDialog;
 import fr.igred.ij.gui.ProgressDialog;
 import fr.igred.ij.io.BatchImage;
+import fr.igred.ij.io.ROIMode;
 import fr.igred.ij.macro.BatchListener;
 import fr.igred.ij.macro.BatchParameters;
 import fr.igred.ij.macro.OMEROBatchRunner;
@@ -97,7 +98,7 @@ public class OMEROBatchPlugin extends PlugInFrame implements BatchListener {
 	// choices of input images
 	private final JPanel input1a = new JPanel();
 	private final JPanel input1b = new JPanel();
-	private final JPanel input1c = new JPanel();
+	private final JPanel input3 = new JPanel();
 	private final JPanel input2 = new JPanel();
 
 	// group and user selection
@@ -113,8 +114,8 @@ public class OMEROBatchPlugin extends PlugInFrame implements BatchListener {
 	private final JComboBox<String> datasetListIn = new JComboBox<>();
 	/** The checkbox to delete ROIs. */
 	private final JCheckBox checkDelROIs = new JCheckBox("Clear ROIs each time");
-	/** The checkbox to load ROIs. */
-	private final JCheckBox checkLoadROIs = new JCheckBox("Load ROIs");
+	/** The list of possible output projects. */
+	private final JComboBox<ROIMode> roiMode = new JComboBox<>(ROIMode.values());
 
 	// choice of the record
 	/** The input folder. */
@@ -286,9 +287,6 @@ public OMEROBatchPlugin() {
 		projectListIn.setFont(listFont);
 		datasetListIn.setFont(listFont);
 
-		input1c.add(checkLoadROIs);
-		input1c.add(checkDelROIs);
-
 		JLabel inputFolderLabel = new JLabel("Images folder: ");
 		JButton inputFolderBtn = new JButton(browse);
 		inputFolderLabel.setLabelFor(inputFolder);
@@ -300,11 +298,16 @@ public OMEROBatchPlugin() {
 		input2.add(recursive);
 		inputFolderBtn.addActionListener(e -> chooseDirectory(inputFolder));
 
+		JLabel labelROIMode = new JLabel("Load ROIs: ");
+		input3.add(labelROIMode);
+		input3.add(roiMode);
+		input3.add(checkDelROIs);
+
 		JPanel panelInput = new JPanel();
 		panelInput.add(input1a);
 		panelInput.add(input1b);
-		panelInput.add(input1c);
 		panelInput.add(input2);
+		panelInput.add(input3);
 		panelInput.setLayout(new BoxLayout(panelInput, BoxLayout.PAGE_AXIS));
 		panelInput.setBorder(BorderFactory.createTitledBorder("Input"));
 		super.add(panelInput);
@@ -422,12 +425,12 @@ public OMEROBatchPlugin() {
 		input2.setVisible(false);
 		input1a.setVisible(true);
 		input1b.setVisible(true);
-		input1c.setVisible(true);
+		input3.setVisible(true);
 		super.pack();
 
 		input1a.setMaximumSize(new Dimension(input1a.getMaximumSize().width, input1a.getHeight()));
 		input1b.setMaximumSize(new Dimension(input1b.getMaximumSize().width, input1b.getHeight()));
-		input1c.setMaximumSize(new Dimension(input1c.getMaximumSize().width, input1c.getHeight()));
+		input3.setMaximumSize(new Dimension(input3.getMaximumSize().width, input3.getHeight()));
 
 		local.setSelected(true);
 
@@ -799,17 +802,15 @@ private void updateInput(ItemEvent e) {
 			if (connected) {
 				input1a.setVisible(true);
 				input1b.setVisible(true);
-				input1c.setVisible(true);
-				input1c.add(checkLoadROIs);
 				input2.setVisible(false);
+				checkDelROIs.setVisible(true);
 			} else {
 				local.setSelected(true);
 			}
 		} else { //local.isSelected()
 			input2.setVisible(true);
-			input2.add(checkLoadROIs);
 			checkDelROIs.setSelected(false);
-			input1c.setVisible(false);
+			checkDelROIs.setVisible(false);
 			input1b.setVisible(false);
 			input1a.setVisible(false);
 		}
@@ -999,7 +1000,7 @@ public void start(ActionEvent e) {
 
 		// input data
 		params.setSuffix(suffix.getText());
-		params.setLoadROIS(checkLoadROIs.isSelected());
+		params.setROIMode(roiMode.getItemAt(roiMode.getSelectedIndex()));
 		params.setClearROIS(checkDelROIs.isSelected());
 		params.setSaveImages(checkImage.isSelected());
 		params.setSaveResults(checkResults.isSelected());