misc fixes/improvements

- Fix Bvv axes not visible when scene bounding box is also displayed
- Fix Bvv overlay annotations not respecting rendering options at startup
- Improve SNT controls tollbar in Bvv

Author: tferr

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

@@ -26,8 +26,10 @@
 import org.scijava.module.MutableModuleItem;
 import org.scijava.plugin.Parameter;
 import org.scijava.util.ColorRGB;
+import org.scijava.widget.Button;
 import org.scijava.widget.ChoiceWidget;
 import org.scijava.widget.NumberWidget;
+import sc.fiji.snt.SNTPrefs;
 import sc.fiji.snt.viewer.AbstractBigViewer;
 
 /**
@@ -44,42 +46,45 @@ public abstract class BigViewerRenderingOptionsCmd extends DynamicCommand {
     protected static final String STYLE_RADII = "Frusta (uses path radii)";
 
     @Parameter(label = "Path rendering style", choices = {STYLE_LINE, STYLE_RADII},
-            style = ChoiceWidget.RADIO_BUTTON_VERTICAL_STYLE,
+            style = ChoiceWidget.RADIO_BUTTON_VERTICAL_STYLE, persist = false,
             description = "<html>Centerline rendering is recommended for large datasets.<br>"
                     + "Frusta (tapered tubes) use per-node radii for a more accurate 3D appearance")
     private String renderingStyle;
 
-    @Parameter(label = "Use path radii",
-            description = "Sets whether to use path radius for thickness calculation. "
+    @Parameter(label = "Use path radii", persist = false,
+            description = "Sets whether to use path radius for thickness calculation.\n"
                     + "Disable for paths with uniform thickness.")
     private boolean usePathRadius;
 
     @Parameter(label = "Thickness multiplier", min = "0.1", max = "10.0", stepSize = "0.1",
-            style = "slider,format:0.00",
-            description = "Scale factor applied to all path radii. "
+            style = "slider,format:0.00", persist = false,
+            description = "Scale factor applied to all path radii.\n"
                     + "1.0x = natural size; increase if paths appear too thin.")
     private double thicknessMultiplier;
 
     @Parameter(label = "Min. thickness", min = "0.1", max = "20.0", stepSize = "0.1",
-            style = "slider,format:0.0",
-            description = "Minimum rendered thickness in physical units. "
+            style = "slider,format:0.0", persist = false,
+            description = "Minimum rendered thickness in physical units.\n"
                     + "Controls line width in centerline mode and the floor radius in tube mode.")
     private double minThickness;
 
     @Parameter(label = "Max. thickness", min = "1", max = "100.0", stepSize = "0.5",
-            style = "slider,format:0.0",
-            description = "Maximum rendered thickness in physical units. "
+            style = "slider,format:0.0", persist = false,
+            description = "Maximum rendered thickness in physical units.\n"
                     + "Controls line width in centerline mode and the ceiling radius in tube mode.")
     private double maxThickness;
 
     @Parameter(label = "Transparency (%)", min = "0", max = "100", stepSize = "1",
-            style = NumberWidget.SLIDER_STYLE,
-            description = "Opacity of all path overlays. 0% = fully opaque; 100% = fully transparent.")
+            style = NumberWidget.SLIDER_STYLE, persist = false,
+            description = "Opacity of all path overlays.\n0% = fully opaque; 100% = fully transparent.")
     private double transparency;
 
     @Parameter(required = false, label = "Default color", persist = false)
     private ColorRGB defaultColor;
 
+    @Parameter(required = false, label = "Reset to Defaults", persist = false, callback = "reset")
+    private Button reset;
+
     /**
      * Returns the viewer instance to configure. Implementations return their
      * specific viewer (Bvv or Bdv) injected via a @Parameter field.
@@ -95,9 +100,22 @@ protected void init() {
         usePathRadius = opts.isUsePathRadius();
         transparency = (1.0 - opts.getTransparency()) * 100; // invert and scale: 0% = opaque, 100% = transparent
         defaultColor = new ColorRGB(opts.fallbackColor.getRed(), opts.fallbackColor.getGreen(), opts.fallbackColor.getBlue());
-        // update widget
-        final MutableModuleItem<ColorRGB> mi = getInfo().getMutableInput("defaultColor", ColorRGB.class);
-        mi.setValue(this, defaultColor);
+        updateColorWidget(defaultColor);
+    }
+
+    private void reset() {
+        renderingStyle = STYLE_RADII;
+        thicknessMultiplier = 1.0f;
+        minThickness = 1.0f;
+        maxThickness = 100.0f;
+        usePathRadius = true;
+        transparency = 0; // inverted: 0% = opaque
+        defaultColor = new ColorRGB(
+                SNTPrefs.DEFAULT_DESELECTED_COLOR.getRed(),
+                SNTPrefs.DEFAULT_DESELECTED_COLOR.getGreen(),
+                SNTPrefs.DEFAULT_DESELECTED_COLOR.getBlue());
+        updateColorWidget(defaultColor);
+        updateOverlay(getViewer());
     }
 
     @Override
@@ -111,7 +129,19 @@ public void run() {
         opts.setUsePathRadius(usePathRadius);
         opts.fallbackColor = new java.awt.Color(defaultColor.getRed(), defaultColor.getGreen(), defaultColor.getBlue());
         opts.setTransparency((float) (100 - transparency) / 100);
-        viewer.setDisplayRadii(STYLE_RADII.equals(renderingStyle)); // invalidates the overlay cache before syncing
-        viewer.syncOverlays();
+        updateOverlay(viewer);
+    }
+
+    private void updateColorWidget(final ColorRGB newColor) {
+        final MutableModuleItem<ColorRGB> mi = getInfo().getMutableInput("defaultColor", ColorRGB.class);
+        mi.setValue(this, newColor);
     }
+
+    private void updateOverlay(final AbstractBigViewer viewer) {
+        if (viewer != null) {
+            viewer.setDisplayRadii(STYLE_RADII.equals(renderingStyle)); // invalidates the overlay cache before syncing
+            viewer.syncOverlays();
+        }
+    }
+
 }

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

@@ -29,8 +29,7 @@
 import sc.fiji.snt.viewer.Bvv;
 
 /**
- * Command providing a GUI for configuring {@link AbstractBigViewer.PathRenderingOptions} in
- * a {@link Bvv} viewer.
+ * Command providing a GUI for configuring {@link AbstractBigViewer.PathRenderingOptions} in a {@link Bvv} viewer.
  *
  * @author Tiago Ferreira
  * @see BdvRenderingOptionsCmd

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

@@ -202,7 +202,7 @@ private double[] getClickedPosition(final MouseEvent e) {
      *
      * @param worldPos calibrated (x,y,z) position to search from
      * @return the nearest rendered path, or {@code null} if nothing is currently rendered
-     * @see  {@code Tracer#handleClick}. Mirrors {@code InteractiveTracerCanvas#selectNearestPathToMousePointer},
+     * @see Tracer#handleClick(MouseEvent) Mirrors {@code InteractiveTracerCanvas#selectNearestPathToMousePointer},
      */
     private Path findNearestRenderedPath(final double[] worldPos) {
         Path nearest = null;
@@ -1836,6 +1836,11 @@ private JComponent sntToolbar(final BvvActions actions) {
         toolbar.addSeparator();
         toolbar.add(offsetActivate);
         toolbar.addSeparator();
+        if (tracer != null) {
+            toolbar.add(GuiUtils.Buttons.toolbarButton(actions.syncPathManagerAction(),
+                    "Sync Path Manager changes"));
+            toolbar.addSeparator();
+        }
         toolbar.add(Box.createHorizontalGlue());
         toolbar.addSeparator();
 
@@ -1867,8 +1872,6 @@ public void componentHidden(java.awt.event.ComponentEvent e) {
                 "Set rendering options of annotations"));
 
         if (tracer != null) {
-            toolbar.add(GuiUtils.Buttons.toolbarButton(actions.syncPathManagerAction(),
-                    "Sync Path Manager changes"));
             final JPanel panel = new JPanel(new BorderLayout());
             panel.add(toolbar, BorderLayout.NORTH);
             panel.add(tracingStatusRow(), BorderLayout.SOUTH);
@@ -2505,7 +2508,10 @@ private double[] searchPeakAcrossSources(final java.util.Collection<bdv.viewer.S
 
     @Override
     public float getDefaultMarkerSize() {
-        return renderingOptions.getMinThickness();
+        // Clamped to getMaxThickness() as a safety net against extreme multiplier values
+        // see OverlayRenderer#recolor/computeScreenData)
+        return Math.min(renderingOptions.getMinThickness() * renderingOptions.getThicknessMultiplier(),
+                renderingOptions.getMaxThickness());
     }
 
     @Override
@@ -3844,9 +3850,7 @@ public void drawOverlays(final java.awt.Graphics g) {
             final double cy = canvasH / 2.0;
 
             final java.awt.Graphics2D g2 = (java.awt.Graphics2D) g.create();
-            g2.setRenderingHint(java.awt.RenderingHints.KEY_ANTIALIASING,
-                    java.awt.RenderingHints.VALUE_ANTIALIAS_ON);
-            g2.setStroke(new java.awt.BasicStroke(1.5f));
+            g2.setRenderingHint(java.awt.RenderingHints.KEY_ANTIALIASING, java.awt.RenderingHints.VALUE_ANTIALIAS_ON);
 
             // World → screen projection (same formula as AnnotationOverlay)
             final java.util.function.Function<double[], double[]> project = world -> {
@@ -3865,12 +3869,14 @@ 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));
                 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));
                 drawLine3D(g2, project, new double[]{x0, y0, z0}, new double[]{x0, y0, z0 + axisLen}, new java.awt.Color(80, 120, 255));
             }
 
+            g2.setStroke(new java.awt.BasicStroke(1.5f));
             if (showBox) {
                 g2.setColor(new java.awt.Color(255, 255, 255, 180));
                 // 12 edges of the bounding box
@@ -3942,7 +3948,7 @@ public void drawOverlays(final java.awt.Graphics g) {
 
                     final java.awt.Color slabColor = new java.awt.Color(40, 90, 160);
                     final java.awt.Stroke savedStroke = g2.getStroke();
-                    g2.setStroke(new java.awt.BasicStroke(1.2f, java.awt.BasicStroke.CAP_BUTT,
+                    g2.setStroke(new java.awt.BasicStroke(1.5f, java.awt.BasicStroke.CAP_BUTT,
                             java.awt.BasicStroke.JOIN_MITER, 4f, new float[]{6f, 4f}, 0f));
                     g2.setColor(slabColor);
                     final int[][] edges = {
@@ -5859,7 +5865,7 @@ public void actionPerformed(final java.awt.event.ActionEvent e) {
                     // Choose the moving source (the one carrying the manual transform)
                     final Map<String, BvvMultiSource> choiceMap = multiSourceToChoiceMap(multiSources);
                     if (choiceMap.size()==1) {
-                        getGuiUtils().error("Only one source available.");
+                        getGuiUtils().error("There is only one source available.");
                         return;
                     }
                     final String[] choiceKeys = choiceMap.keySet().toArray(new String[0]);