Fix instance detection by BigDataLoader and minor fixes to Stream mode

Author: tferr

src/main/java/sc/fiji/snt/gui/cmds/BigDataLoaderCmd.java

@@ -235,7 +235,7 @@ public void run() {
         final boolean threeD = viewerType != null && viewerType.toLowerCase().contains("bvv");
         final boolean tracer = tracingEnabled;
 
-        if (tracer && SNTUtils.getInstance() != null) {
+        if (tracer && SNTUtils.getInstance() != null && SNTUtils.getInstance().getUI() != null) {
             error("SNT seems to be already running. Please close the current instance and re-run.");
             return;
         }

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

@@ -242,11 +242,29 @@ public Dimension getMinimumSize() {
         };
     }
 
+    /** Recursively finds the widest preferred width among any JToolBar descendants of {@code c} */
+    private static int widestToolbarPreferredWidth(final Container c) {
+        int widest = 0;
+        for (final Component comp : c.getComponents()) {
+            if (comp instanceof JToolBar) {
+                widest = Math.max(widest, comp.getPreferredSize().width);
+            } else if (comp instanceof Container) {
+                widest = Math.max(widest, widestToolbarPreferredWidth((Container) comp));
+            }
+        }
+        return widest;
+    }
+
     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
+        // Toolbars built by createToolbar() report a zeroed minimum width by design (see its
+        // javadoc), so GridBagLayout's minimum-size pass never sees their real button-row width.
+        // Recover it from each toolbar's preferred width instead (glue there contributes zero)
+        // and widen cardPrefW to fit the widest one too
+        final int cardPrefW = Math.max(refPanel.getMinimumSize().width,
+                widestToolbarPreferredWidth(refPanel)) + 16; // extra padding avoids clipping at frame edge
         SwingUtilities.invokeLater(() -> {
             final javax.swing.JSplitPane split = getViewerSplitPanel();
             if (split == null) return;
@@ -1095,7 +1113,7 @@ protected JButton autoBrightnessButton(final Actions actions) {
         menu.add(new JMenuItem(actions.autoBrightnessAllAction()));
         final JButton button = GuiUtils.Buttons.OptionsButton(IconFactory.GLYPH.ADJUST, 1f, menu);
         button.setToolTipText("<html>Recompute brightness/contrast from data percentiles.<br>Useful to retry "
-                + "after loading large/remote datasets, where the automatic estimate is bounded by a timeout "
+                + "after loading large/remote datasets,<br>where the automatic estimate is bounded by a timeout<br>"
                 + "and may fall back to a default range.</html>");
         return button;
     }
@@ -1651,6 +1669,8 @@ protected JToolBar buildBaseSceneControlToolbar() {
                 "Fit view to the current (selected) source"));
         bar.add(autoBrightnessButton(actions));
         bar.addSeparator();
+        bar.add(Box.createHorizontalGlue());
+        bar.addSeparator();
         // Action names match those registered by BDV/BVV NavigationActions
         final java.util.HashMap<String, List<IconFactory.GLYPH>> planes = new java.util.LinkedHashMap<>();
         planes.put("align XY plane", List.of(IconFactory.GLYPH.X, IconFactory.GLYPH.Y));

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

@@ -3176,6 +3176,9 @@ public void actionPerformed(final java.awt.event.ActionEvent e) {
                 // Guards posSlider.setValue() calls that are programmatic (not from the user
                 // dragging the slider), so slabListener does not fire a second applySlab().
                 final boolean[] updatingSlab = {false};
+                // Slab Paths defaults to following Slab View (activated whenever Slab View is turned
+                // on) until the user manually toggles Slab Paths themselves, at which point it decouples
+                final boolean[] slabPathsUserOverride = {false};
 
                 final VolumeViewerPanel viewerPanel = bvvInstance.currentBvv.getViewer();
 
@@ -3421,8 +3424,12 @@ public void mousePressed(final java.awt.event.MouseEvent e) {
                         slabAxis.set(axis0);
                         reconfigureAndApplySlab.run();
                         slabPathsToggle.setEnabled(true);
-                        // Slab Paths' *selected* state is a persistent user preference (left alone on deactivation),
-                        // but renderingOptions.isClipPathsToSlab() is the actual  effective flag and was forced false
+                        // Slab Paths defaults to activating alongside Slab View (synced) unless the user has
+                        // manually toggled Slab Paths before (decoupled)
+                        if (!slabPathsUserOverride[0]) {
+                            slabPathsToggle.setSelected(true);
+                        }
+                        // renderingOptions.isClipPathsToSlab() is the actual effective flag and was forced false
                         // on deactivation since it's meaningless while there's no active slab. Re-sync it here to
                         // whatever the toggle currently shows, or re-activating slab would silently render all paths
                         // (front and back) despite Slab Paths still looking selected
@@ -3467,6 +3474,7 @@ public void mousePressed(final java.awt.event.MouseEvent e) {
                 thickSpinner.addChangeListener(slabListener);
 
                 slabPathsToggle.addActionListener(ev -> {
+                    slabPathsUserOverride[0] = true; // user acted on it directly: decouple from Slab View's default
                     final boolean clip = slabPathsToggle.isSelected();
                     renderingOptions.setClipPathsToSlab(clip);
                     overlayRenderer.invalidateCache();
@@ -3507,29 +3515,34 @@ private JToolBar buildSceneControlToolbar(final BvvActions bvvActions) {
                     IconFactory.GLYPH.CROSSHAIR, IconFactory.GLYPH.CROSSHAIR);
             crosshairToggle.setSelected(true);
             bar.add(crosshairToggle);
-            final JToggleButton axesToggle = GuiUtils.Buttons.toolbarToggleButton(
-                    BvvActions.overlayToggleAction("Axes", false, show -> {
-                        if (sceneOverlay != null) { sceneOverlay.showAxes = show; bvvInstance.repaint(); }
-                    }),
-                    "Show/hide coordinate axes at the volume origin.\nX: Red; Y: Green; Z: Blue",
-                    IconFactory.GLYPH.CHART_LINE, IconFactory.GLYPH.CHART_LINE);
-            axesToggle.setSelected(false);
-            bar.add(axesToggle);
-            final JToggleButton boxToggle = GuiUtils.Buttons.toolbarToggleButton(
-                    BvvActions.overlayToggleAction("Volume Box", false, show -> {
-                        if (sceneOverlay != null) { sceneOverlay.showBox = show; bvvInstance.repaint(); }
-                    }),
-                    "Show/hide bounding box around all loaded volumes",
-                    IconFactory.GLYPH.CUBE, IconFactory.GLYPH.CUBE);
-            boxToggle.setSelected(false);
-            bar.add(boxToggle);
+            bar.add(axesButton());
             bar.addSeparator();
             bar.add(Box.createHorizontalGlue());
             bar.addSeparator();
             bar.add(optionsButton(bvvActions));
             return bar;
         }
 
+        private JButton axesButton() {
+            final JPopupMenu menu = new JPopupMenu();
+            final JButton button = GuiUtils.Buttons.OptionsButton(IconFactory.GLYPH.CUBE, 1f, menu);
+            final JCheckBoxMenuItem axesItem = new JCheckBoxMenuItem(
+                    BvvActions.overlayToggleAction("Axes", false, show -> {
+                        if (sceneOverlay != null) { sceneOverlay.showAxes = show; bvvInstance.repaint(); }
+                    }));
+            axesItem.setToolTipText("Show/hide coordinate axes at the volume origin. X: Red; Y: Green; Z: Blue");
+            axesItem.setSelected(false);
+            menu.add(axesItem);
+            final JCheckBoxMenuItem boxItem = new JCheckBoxMenuItem(
+                    BvvActions.overlayToggleAction("Volume Box", false, show -> {
+                        if (sceneOverlay != null) { sceneOverlay.showBox = show; bvvInstance.repaint(); }
+                    }));
+            boxItem.setToolTipText("Show/hide bounding box around all loaded volumes");
+            boxItem.setSelected(false);
+            menu.add(boxItem);
+            return button;
+        }
+
         private JButton optionsButton(final BvvActions actions) {
             final JPopupMenu menu = new JPopupMenu();
             final JButton oButton = GuiUtils.Buttons.OptionsButton(IconFactory.GLYPH.OPTIONS, 1f, menu);
@@ -3796,7 +3809,7 @@ public void drawOverlays(final java.awt.Graphics g) {
             final double x0 = b[0], y0 = b[1], z0 = b[2], x1 = b[3], y1 = b[4], z1 = b[5];
 
             if (showAxes) {
-                g2.setStroke(new java.awt.BasicStroke(3f));
+                g2.setStroke(new java.awt.BasicStroke(4f));
                 final float axisLen = 0.20f * (float) Math.min(x1 - x0, Math.min(y1 - y0, z1 - z0));
                 drawLine3D(g2, project, new double[]{x0, y0, z0}, new double[]{x0 + axisLen, y0, z0}, new java.awt.Color(220, 60, 60));
                 drawLine3D(g2, project, new double[]{x0, y0, z0}, new double[]{x0, y0 + axisLen, z0}, new java.awt.Color(60, 200, 60));