Fix UX inconsistencies

Author: tferr

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

@@ -431,6 +431,7 @@ private JPopupMenu assembleTablePopupMenu(final BookmarkTable table) {
             pMenu.add(mi);
             pMenu.addSeparator();
         }
+
         mi = new JMenuItem("Delete...", IconFactory.menuIcon(IconFactory.GLYPH.TRASH));
         mi.addActionListener(e -> {
             if (noBookmarksError()) return;

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

@@ -122,13 +122,14 @@ label images, or neuropil annotations (e.g., cortical layers, biomarkers, or cou
                 """;
         gbc.weighty = 0.1;
         container.add(GuiUtils.longSmallMsg(msg, container), gbc);
-        gbc.weighty = 0;
+        gbc.weighty = 0.5;
         final JScrollPane sp = new JScrollPane(delineationsPanel);
         sp.setMinimumSize(delineationsPanel.getPreferredSize());
         sp.setBorder(null);
         gbc.gridy++;
         container.add(sp, gbc);
         gbc.gridy++;
+        gbc.weighty = 0.1;
         container.add(outsideColorAndAddMoreEntriesWidget(), gbc);
         gbc.insets = new Insets(5, 0, 5, 0);
         gbc.gridy++;
@@ -238,7 +239,7 @@ private JToolBar outsideColorAndAddMoreEntriesWidget() {
             delineationsPanel.repaint();
         });
 
-        final JLabel label = new JLabel(" Outside color:");
+        final JLabel label = new JLabel("Non-delineating color:");
         label.setToolTipText("Fallback color for non-delineated sections");
         toolbar.add(label);
         final JButton fColorButton = new JButton(IconFactory.accentIcon(fallbackColor, true));

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

@@ -34,7 +34,6 @@
 import ij3d.ContentConstants;
 import ij3d.Image3DUniverse;
 import ij3d.ImageWindow3D;
-import net.imglib2.RandomAccessibleInterval;
 import org.apache.commons.lang3.StringUtils;
 import org.scijava.command.Command;
 import org.scijava.command.CommandModule;
@@ -2094,7 +2093,9 @@ private JPanel legacy3DViewerPanel() throws java.lang.NoClassDefFoundError {
         final JButton applyUnivChoice = new JButton("Apply");
         final JComboBox<String> displayChoice = new JComboBox<>();
         final JButton applyDisplayChoice = new JButton("Apply");
-        final JButton refreshList = GuiUtils.Buttons.sync(null);
+        final JButton refreshList = GuiUtils.Buttons.sync(false);
+        refreshList.setToolTipText("Refresh list");
+        refreshList.setPreferredSize(new Dimension(refreshList.getPreferredSize().width, applyUnivChoice.getPreferredSize().height));
         final JComboBox<String> actionChoice = new JComboBox<>();
         final JButton applyActionChoice = new JButton("Apply");
 
@@ -4161,9 +4162,8 @@ private JPanel statusBar() {
         toolbar.addSeparator();
 
         // Quick Toggles dropdown
-        final JButton quickToggles = new JButton(IconFactory.menuIcon('\ue0b7', true, IconFactory.defaultColor()));
+        final JButton quickToggles = GuiUtils.Buttons.OptionsButton(GLYPH.BOLT, 1f,quickTogglesMenu() );
         quickToggles.setToolTipText("Quick Toggles for common actions");
-        quickToggles.addActionListener(e -> quickTogglesMenu().show(quickToggles, 0, quickToggles.getHeight()));
         toolbar.add(quickToggles);
 
         // Status text (full width, below toolbar)

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

@@ -4492,9 +4492,12 @@ public static JButton undo(final Action action) {
 			return button;
 		}
 
-		public static JButton sync(final Action action) {
-			final JButton button = (action == null) ? new JButton() : new JButton(action);
-			makeSmallBorderless(button, GLYPH.SYNC, UIManager.getColor("Spinner.buttonArrowColor"));
+		public static JButton sync(final boolean borderless) {
+			final JButton button = new JButton();
+			if (borderless)
+				makeSmallBorderless(button, GLYPH.SYNC, UIManager.getColor("Spinner.buttonArrowColor"));
+			else
+				IconFactory.assignIcon(button, GLYPH.SYNC, UIManager.getColor("Spinner.buttonArrowColor"), .8f);
 			return button;
 		}
 

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

@@ -56,6 +56,7 @@ public enum GLYPH {
         BEZIER_CURVE('\uf55b', true),//
         BINOCULARS('\uf1e5', true), //
         BOLD('\uf032', true),//
+        BOLT('\ue0b7', true),//
         BOOKMARK('\uf02e', true), //
         BOOK_READER('\uf5da', true), //
         BRAIN('\uf5dc', true), //

src/main/java/sc/fiji/snt/viewer/AbstractBigViewer.java

@@ -117,12 +117,39 @@ public Dimension getMinimumSize() {
         };
     }
 
+    void resizeCardPanelsAsNeeded(final JComponent refPanel) {
+        // Ensure the card panel is wide enough to show all controls without clipping.
+        // Use the Scene Controls panel's own preferred width since it's the widest,
+        // and its GridBagLayout has already computed the correct natural width.
+        final int cardPrefW = refPanel.getMinimumSize().width + 16; // minor padding
+        SwingUtilities.invokeLater(() -> {
+            final javax.swing.JSplitPane split = getViewerSplitPanel();
+            if (split == null) return;
+            final java.awt.Component cards = split.getRightComponent();
+            if (cards == null) return;
+            cards.setPreferredSize(new java.awt.Dimension(cardPrefW, cards.getPreferredSize().height));
+            final JFrame frame = getViewerFrame();
+            final int frameW = frame != null ? frame.getWidth() : 0;
+            if (frameW > cardPrefW)
+                split.setDividerLocation(frameW - cardPrefW - split.getDividerSize());
+            if (frame != null) frame.revalidate();
+        });
+    }
+
     /**
-     * Returns the top-level Swing window for this viewer.
-     * May be null if the viewer has not been opened yet.
+     * Returns the top-level Swing window for this viewer, or null if not yet open.
      */
     public abstract JFrame getViewerFrame();
 
+    /**
+     * Returns the JSplitPane that separates the viewer canvas from the card panel.
+     * Both BDV and BVV frames expose this via their own getSplitPanel() methods,
+     * but those classes share no common supertype above JFrame, so this method
+     * lets subclasses expose the split pane without the abstract method returning
+     * a viewer-specific frame type.
+     */
+    protected abstract javax.swing.JSplitPane getViewerSplitPanel();
+
     /**
      * Returns the width of the viewer canvas in logical pixels,
      * or 0 if the viewer is not yet initialized.
@@ -515,7 +542,6 @@ protected void showCalibrationDialog(final java.awt.Component parent) {
     /**
      * Builds the shared scene-control toolbar: fit-source button, align-plane
      * buttons (XY, XZ, YZ), minimap toggle, text-overlay toggle, scale-bar toggle.
-     *
      * Subclasses call this and may prepend or append viewer-specific buttons.
      *
      * @return a partially populated JToolBar ready for additional buttons

src/main/java/sc/fiji/snt/viewer/Bdv.java

@@ -23,6 +23,7 @@
 package sc.fiji.snt.viewer;
 
 import bdv.tools.InitializeViewerState;
+import bdv.viewer.ViewerFrame;
 import mpicbg.spim.data.generic.AbstractSpimData;
 import net.imglib2.type.numeric.NumericType;
 import sc.fiji.snt.*;
@@ -147,11 +148,8 @@ public BdvStackSource<?> show(final ImagePlus imp) {
                 final BdvOptions chOpts = (firstSrc == null)
                         ? baseOpts()
                         : BdvOptions.options().addTo(bdvHandle);
-                // BDV requires 3D sources; add singleton Z for 2D images
-                RandomAccessibleInterval<?> chRai = ImpUtils.toImgPlus(ch);
-                if (chRai.numDimensions() < 3) chRai = Views.addDimension(chRai, 0, 0);
                 final BdvStackSource<?> cs = showCalibratedBdvSource(
-                        chRai, imp.getTitle() + " [C" + c + "]", chOpts);
+                        ImpUtils.toImgPlus(ch), imp.getTitle() + " [C" + c + "]", chOpts);
                 if (firstSrc == null) {
                     firstSrc = cs;
                     if (bdvHandle == null) {
@@ -214,9 +212,7 @@ public <T extends RealType<T> & NativeType<T>> BdvStackSource<?> show(final ImgP
             BdvStackSource<?> firstSrc = null;
             final int nC = (int) img.dimension(chDim);
             for (int c = 0; c < nC; c++) {
-                // BDV requires 3D sources; add singleton Z for 2D images
-                RandomAccessibleInterval<T> ch = Views.hyperSlice(img, chDim, c);
-                if (ch.numDimensions() < 3) ch = Views.addDimension(ch, 0, 0);
+                final RandomAccessibleInterval<T> ch = Views.hyperSlice(img, chDim, c);
                 final BdvOptions chOpts = (firstSrc == null)
                         ? baseOpts().sourceTransform(calToTransform())
                         : BdvOptions.options().addTo(bdvHandle).sourceTransform(calToTransform());
@@ -324,9 +320,15 @@ public List<BdvStackSource<?>> show(final AbstractSpimData<?> spimData, final St
     }
 
     @Override
-    public JFrame getViewerFrame() {
-        return (bdvHandle == null) ? null
-                : bdvHandle.getSplitPanel().getTopLevelAncestor() instanceof JFrame f ? f : null;
+    public ViewerFrame getViewerFrame() {
+        if (bdvHandle == null) return null;
+        final java.awt.Container top = bdvHandle.getSplitPanel().getTopLevelAncestor();
+        return (top instanceof ViewerFrame f) ? f : null;
+    }
+
+    @Override
+    protected JSplitPane getViewerSplitPanel() {
+        return (bdvHandle == null) ? null : bdvHandle.getSplitPanel();
     }
 
     @Override
@@ -561,9 +563,12 @@ private BdvStackSource<?> showCalibratedBdvSource(
             final RandomAccessibleInterval<?> rai,
             final String name,
             final BdvOptions opts) {
+        // BDV's renderer always calls realMax(2); add a singleton Z for 2D inputs
+        final RandomAccessibleInterval<?> rai3d = (rai.numDimensions() < 3)
+                ? Views.addDimension(rai, 0, 0) : rai;
         final SpimDataUtils.CalibratedSource src =
                 new SpimDataUtils.CalibratedSource(
-                        rai, (NumericType) rai.getType(), calToTransform(), name,
+                        rai3d, (NumericType) rai3d.getType(), calToTransform(), name,
                         cal != null ? cal : new double[]{1, 1, 1},
                         calUnit != null ? calUnit : "pixel");
         return BdvFunctions.show(src, 1, opts);
@@ -601,11 +606,12 @@ private void initializeCardPanel() {
         if (cp != null) {
             cp.addCard("Scene Controls", buildSceneControlToolbar(), true);
             cp.addCard("SNT Annotations", sntAnnotationsCard(actions), true);
-            cp.setCardExpanded("Groups", false);
             SwingUtilities.invokeLater(() -> {
+                cp.setCardExpanded("Groups", false);
                 cp.setCardExpanded("Scene Controls", true);
                 cp.setCardExpanded("SNT Annotations", true);
             });
+            resizeCardPanelsAsNeeded(cp.getComponent());
         }
 
         // M and H keys via BDV's keybindings system so the trigger layer sees them
@@ -874,7 +880,7 @@ public void actionPerformed(final java.awt.event.ActionEvent e) {
         }
 
         Action syncPathManagerAction() {
-            return new AbstractAction("Sync Path Manager Changes", IconFactory.menuIcon(IconFactory.GLYPH.REDO)) {
+            return new AbstractAction("Sync Path Manager Changes", IconFactory.menuIcon(IconFactory.GLYPH.SYNC)) {
                 @Override
                 public void actionPerformed(final java.awt.event.ActionEvent e) {
                     if (syncPathManagerList()) {

src/main/java/sc/fiji/snt/viewer/Bvv.java

@@ -1194,20 +1194,7 @@ public void actionPerformed(final java.awt.event.ActionEvent e) {
             bvvFrame.getKeybindings().addInputMap("snt", sntIMap);
             bvvFrame.getKeybindings().addActionMap("snt", sntAMap);
             SwingUtilities.invokeLater(bvv::expandAndFocusCardPanel);
-            // Ensure the card panel is wide enough to show all controls without clipping.
-            // Use the Scene Controls panel's own preferred width since it's the widest,
-            // and its GridBagLayout has already computed the correct natural width.
-            final int cardPrefW = sceneControlsCard.getMinimumSize().width + 16; // minor padding
-            SwingUtilities.invokeLater(() -> {
-                final javax.swing.JSplitPane split = bvv.getViewerFrame().getSplitPanel();
-                final java.awt.Component cards = split.getRightComponent();
-                if (cards == null) return;
-                cards.setPreferredSize(new java.awt.Dimension(cardPrefW, cards.getPreferredSize().height));
-                final int frameW = bvv.getViewerFrame().getWidth();
-                if (frameW > cardPrefW)
-                    split.setDividerLocation(frameW - cardPrefW - split.getDividerSize());
-                bvv.getViewerFrame().revalidate();
-            });
+            resizeCardPanelsAsNeeded(sceneControlsCard);
         }
         // Initialize brightness from data percentiles (BVV doesn't do this automatically)
         SwingUtilities.invokeLater(() ->
@@ -1838,6 +1825,11 @@ public VolumeViewerFrame getViewerFrame() {
         return (currentBvv == null) ? null : currentBvv.getViewerFrame();
     }
 
+    @Override
+    protected JSplitPane getViewerSplitPanel() {
+        return (currentBvv==null) ? null : currentBvv.getViewerFrame().getSplitPanel();
+    }
+
     /**
      * @return a reference to the viewer's options.
      */
@@ -4750,7 +4742,7 @@ public void actionPerformed(final java.awt.event.ActionEvent e) {
         }
 
         Action syncPathManagerAction() {
-            return new AbstractAction("Sync Path Manager Changes", IconFactory.menuIcon(IconFactory.GLYPH.REDO)) {
+            return new AbstractAction("Sync Path Manager Changes", IconFactory.menuIcon(IconFactory.GLYPH.SYNC)) {
                 @Override
                 public void actionPerformed(final java.awt.event.ActionEvent e) {
                     if (pathOverlay != null && syncPathManagerList()) {