Reflect modifications in OMEROBatchPlugin

README.md

@@ -8,8 +8,8 @@ An ImageJ plugin to run a script on a batch of images from/to OMERO.
 
 1. Install the [OMERO.insight plugin](https://omero-guides.readthedocs.io/en/latest/fiji/docs/installation.html) (if you
    haven't already).
-2. Download the JAR file for this [library](https://github.com/GReD-Clermont/simple-omero-client/releases/tag/5.12.1/).
-3. Download the JAR file ([for this plugin](https://github.com/GReD-Clermont/omero_batch-plugin/releases/tag/1.0.5/)).
+2. Download the JAR file for this [library](https://github.com/GReD-Clermont/simple-omero-client/releases/tag/5.16.0/).
+3. Download the JAR file ([for this plugin](https://github.com/GReD-Clermont/omero_batch-plugin/releases/tag/2.0.0/)).
 4. Place these JAR files in your "plugins" folder.
 
 ## How to use

src/main/java/fr/igred/ij/gui/OMEROConnectDialog.java

@@ -1,5 +1,5 @@
 /*
- *  Copyright (C) 2021-2022 MICA & GReD
+ *  Copyright (C) 2021-2023 MICA & GReD
  *
  * This program is free software; you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software

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

@@ -87,7 +87,9 @@ public ImagePlus getImagePlus(ROIMode mode) {
 			imp = imageWrapper.toImagePlus(client);
 			// Store image "annotate" permissions as a property in the ImagePlus object
 			imp.setProp("Annotatable", String.valueOf(imageWrapper.canAnnotate()));
-			loadROIs(imp, mode);
+			if (imp != null) {
+				loadROIs(imp, mode);
+			}
 		} catch (ExecutionException | ServiceException | AccessException e) {
 			LOGGER.severe("Could not load image: " + e.getMessage());
 		}

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

@@ -1,5 +1,5 @@
 /*
- *  Copyright (C) 2021-2022 MICA & GReD
+ *  Copyright (C) 2021-2023 MICA & GReD
  *
  * This program is free software; you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software
@@ -97,6 +97,7 @@ public class OMEROBatchRunner extends Thread {
 
 	private BatchListener listener;
 
+
 	public OMEROBatchRunner(ScriptRunner script, List<BatchImage> images, Client client) {
 		this(script, images, client, new ProgressLog(LOGGER));
 	}
@@ -139,7 +140,7 @@ private static String removeExtension(String title) {
 			} else {
 				String afterExt = TITLE_AFTER_EXT.matcher(title.substring(index + 1)).replaceAll("$1");
 				String beforeExt = title.substring(0, index);
-				if(beforeExt.toLowerCase().endsWith(".ome") && beforeExt.lastIndexOf('.') > 0) {
+				if (beforeExt.toLowerCase().endsWith(".ome") && beforeExt.lastIndexOf('.') > 0) {
 					beforeExt = beforeExt.substring(0, beforeExt.lastIndexOf('.'));
 				}
 				return afterExt.isEmpty() ? beforeExt : beforeExt + "_" + afterExt;

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

@@ -1,5 +1,5 @@
 /*
- *  Copyright (C) 2021-2022 MICA & GReD
+ *  Copyright (C) 2021-2023 MICA & GReD
  *
  * This program is free software; you can redistribute it and/or modify it under
  * the terms of the GNU General Public License as published by the Free Software
@@ -18,6 +18,7 @@
 
 import fr.igred.ij.gui.OMEROConnectDialog;
 import fr.igred.ij.gui.ProgressDialog;
+import fr.igred.ij.io.BatchImage;
 import fr.igred.ij.macro.BatchListener;
 import fr.igred.ij.macro.OMEROBatchRunner;
 import fr.igred.ij.macro.ScriptRunner;
@@ -58,6 +59,8 @@
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
 
+import static fr.igred.ij.io.LocalBatchImage.listImages;
+import static fr.igred.ij.io.OMEROBatchImage.listImages;
 import static javax.swing.JOptionPane.showMessageDialog;
 
 /**
@@ -920,43 +923,48 @@ private void previewDataset() {
 	 */
 	public void start(ActionEvent e) {
 		ProgressDialog progress = new ProgressDialog();
-		OMEROBatchRunner runner = new OMEROBatchRunner(script, client, progress);
-		runner.setListener(this);
+		OMEROBatchRunner runner;
 
-		// initiation of success variables
+		// initialization of success variables
 		boolean checkInput;
 		boolean checkMacro = getMacro();
 		boolean checkOutput = getOutput();
 
 		// input data
-		if (omero.isSelected()) {
-			runner.setInputOnOMERO(true);
-			int index = datasetListIn.getSelectedIndex();
-			DatasetWrapper dataset = datasets.get(index);
-			long inputDatasetId = dataset.getId();
-			runner.setInputDatasetId(inputDatasetId);
+		List<BatchImage> images;
+		long inputDatasetId = -1L;
+		try {
+			if (omero.isSelected()) {
+				int index = datasetListIn.getSelectedIndex();
+				DatasetWrapper dataset = datasets.get(index);
+				inputDatasetId = dataset.getId();
+				List<ImageWrapper> imageWrappers = dataset.getImages(client);
+				images = listImages(client, imageWrappers);
+				checkInput = true;
+			} else { // local.isSelected()
+				checkInput = getLocalInput();
+				images = listImages(directoryIn, recursive.isSelected());
+			}
+			runner = new OMEROBatchRunner(script, images, client, progress);
 			runner.setOutputDatasetId(inputDatasetId);
-			checkInput = true;
-		} else { // local.isSelected()
-			runner.setInputOnOMERO(false);
-			checkInput = getLocalInput();
-			runner.setDirectoryIn(directoryIn);
-			runner.setRecursive(recursive.isSelected());
+			runner.setListener(this);
+
+			runner.setSuffix(suffix.getText());
+			runner.setLoadROIS(checkLoadROIs.isSelected());
+			runner.setClearROIS(checkDelROIs.isSelected());
+			runner.setSaveImage(checkImage.isSelected());
+			runner.setSaveResults(checkResults.isSelected());
+			runner.setSaveROIs(checkROIs.isSelected());
+			runner.setSaveLog(checkLog.isSelected());
+		} catch (ServiceException | AccessException | ExecutionException | IOException exception) {
+			IJ.error(exception.getMessage());
+			return;
 		}
 
 		if (!checkInput || !checkMacro || !checkOutput) {
 			return;
 		}
 
-		// suffix
-		runner.setSuffix(suffix.getText());
-
-		runner.setLoadROIS(checkLoadROIs.isSelected());
-		runner.setClearROIS(checkDelROIs.isSelected());
-		runner.setSaveImage(checkImage.isSelected());
-		runner.setSaveResults(checkResults.isSelected());
-		runner.setSaveROIs(checkROIs.isSelected());
-		runner.setSaveLog(checkLog.isSelected());
 		if (onlineOutput.isSelected()) {
 			runner.setOutputOnOMERO(true);
 			if (checkResults.isSelected()) {