Misc fixes

Author: tferr

src/main/java/sc/fiji/snt/SNTUI.java

@@ -708,7 +708,7 @@ public void runSecondaryLayerWizard() {
 	private void runSecondaryLayerWizard(final boolean autoCTwarning) {
 		if (!okToReplaceSecLayer())
 			return;
-		if (!plugin.accessToValidImageData()) {
+		if (accessToValidImagePlus()) { // wizard requires image to be open
 			noValidImageDataError();
 			return;
 		}
@@ -1524,7 +1524,7 @@ private JPanel viewsPanel() {
 			}
 
 			String msg = "";
-			if (plugin.accessToValidImageData()) {
+			if (accessToValidImagePlus()) {
 				msg = "Replace current image with a display canvas and ";
 			} else if (plugin.getPrefs().getTemp(SNTPrefs.NO_IMAGE_ASSOCIATED_DATA, false)) {
 				msg = "You have loaded paths without loading an image.";
@@ -1534,14 +1534,15 @@ private JPanel viewsPanel() {
 				resetPathSpacings(msg);
 			}
 
-			if (!plugin.accessToValidImageData()) {
+			if (accessToValidImagePlus()) {
 				// depending on what the user chose in the resetPathSpacings() prompt
 				// we need to check again if the plugin has access to a valid image
 				changeState(LOADING);
 				showStatus("Resizing Canvas...", false);
 				updateSinglePaneFlag();
 				if (plugin.isUnsavedChanges())
 					plugin.getPathAndFillManager().getBoundingBox(true);
+				plugin.closeAndResetAllPanes(); // flush cashed data as needed
 				plugin.rebuildDisplayCanvases(); // will change UI state
 				arrangeCanvases(false);
 				showStatus("Canvas rebuilt...", true);
@@ -1609,7 +1610,7 @@ private void validateImgDimensions() {
 				if (plugin.accessToValidImageData()) {
 					type = "image";
 					sb.append("<li>Use IJ's command Image&rarr;Adjust&rarr;Canvas Size... and press <i>Reload</i> in the Data Source widget of the Options pane</li>");
-					sb.append("<li>Close the current image and create a Display Canvas using the <i>Create Canvas</i> command in the Options pane</li>");
+					sb.append("<li>Close the current image and create a Display Canvas using <i>Create Canvas</i> in the Options pane</li>");
 				}
 				else {
 					sb.append("<li>Use the <i>Create/Resize Canvas</i> commands in the Options pane</li>");
@@ -2472,7 +2473,11 @@ private void initializeBvvFromPrompt() {
 		bvvSNT = new Bvv(plugin);
 		try {
 			if (choices[0].equals(choice)) {
-				bvvSNT.show(plugin.getImagePlus());
+				final ImagePlus imp = plugin.getImagePlus();
+				if (imp == null)
+					noValidImageDataError();
+				else
+					bvvSNT.show(imp);
 			} else if (choices[1].equals(choice)) {
 				bvvSNT.showLoadedData();
 			} else if (plugin.isSecondaryDataAvailable()) {

src/main/java/sc/fiji/snt/gui/GuiUtils.java

@@ -2744,18 +2744,42 @@ private static JMenuItem summarizeMenuItem(final SNTTable sntTable, final JTable
 		return mItem;
 	}
 
+	/**
+	 * Scrolls a JTable to show its last row.
+	 * <p>
+	 * This implementation avoids using {@link JTable#getCellRect} with row indices. That
+	 * can trigger "row index is bigger than sorter's row count" warnings when the table's
+	 * {@link RowSorter} hasn't fully synchronized. Instead, we manipulate the viewport.
+	 * </p>
+	 * <p>
+	 * The double {@link SwingUtilities#invokeLater} ensures that:
+	 * <ol>
+	 *   <li>1st pass: {@code revalidate()} triggers layout recalculation for any newly added rows</li>
+	 *   <li>2nd pass: scrolling occurs after layout is complete, so {@code table.getHeight()}
+	 *       reflects the actual table size including new rows</li>
+	 * </ol>
+	 * </p>
+	 *
+	 * @param table the table to scroll (must be inside a {@link JScrollPane})
+	 */
 	private static void scrollToBottom(final JTable table) {
 		SwingUtilities.invokeLater(() -> {
-			try {
-				final int lastRow = table.getRowCount() - 1;
-				final RowSorter<?> sorter = table.getRowSorter();
-				if (lastRow >= 0 && (sorter == null || lastRow < sorter.getViewRowCount())) {
-					final Rectangle rect = table.getCellRect(lastRow, 0, true);
-					table.scrollRectToVisible(rect);
+			table.revalidate();
+			SwingUtilities.invokeLater(() -> {
+				try {
+					final Container parent = table.getParent();
+					if (parent instanceof JViewport viewport) {
+						final int tableHeight = table.getHeight();
+						final int viewHeight = viewport.getHeight();
+						if (tableHeight > viewHeight) {
+							viewport.setViewPosition(new Point(0, tableHeight - viewHeight));
+						}
+					}
+					table.repaint();
+				} catch (final Exception ignored) {
+					// Fail silently
 				}
-			} catch (final Exception ignored) {
-				// Fail silently - scroll is non-critical
-			}
+			});
 		});
 	}
 

src/main/java/sc/fiji/snt/util/TreeUtils.java

@@ -872,7 +872,7 @@ public static Tree merge(final Collection<Tree> trees) {
         if (trees.size() == 1) return trees.iterator().next();
         final Tree holdingTree = new Tree();
         holdingTree.setLabel("Combined Paths");
-        trees.forEach(tree -> tree.list().addAll(tree.list()));
+        trees.forEach(tree -> holdingTree.list().addAll(tree.list()));
         return holdingTree;
     }