Fix gremlin characters, hidden icons, and title case inconsistencies

Author: tferr

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

@@ -3833,7 +3833,7 @@ public PathAndFillManager transformPaths(final PathTransformer transformation,
     }
 
     /**
-     * Downsamples alls path using Ramer–Douglas–Peucker simplification.
+     * Downsamples alls path using Ramer-Douglas-Peucker simplification.
      * Downsampling occurs only between branch points and terminal points.
      *
      * @param maximumPermittedDistance the maximum permitted distance between

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

@@ -527,7 +527,7 @@ private <T extends RealType<T>> void fitCircles() {
 
             if (Math.abs(scale_a - scale_b) / scale_iso > 0.1) {
                 SNTUtils.log(String.format(
-                        "  Node %d: Anisotropic tangent plane (%.3f vs %.3f µm). Using %.3f µm.",
+                        "  Node %d: Anisotropic tangent plane (%.3f vs %.3f µm). Using %.3f µm.",
                         i, scale_a, scale_b, scale_iso
                 ));
             }

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

@@ -217,7 +217,7 @@ public PathManagerUI(final SNT plugin) {
 
         jmi = new JMenuItem(MultiPathActionListener.SPECIFY_CT_POSITION_CMD);
         jmi.setToolTipText("Changes CT position of selected path(s)");
-        jmi.setIcon(IconFactory.menuIcon(IconFactory.GLYPH.LAYERS));
+        IconFactory.assignDoubleLetterIcon(jmi, 'C', 'T', true);
         jmi.addActionListener(multiPathListener);
         editMenu.add(jmi);
         jmi = new JMenuItem(MultiPathActionListener.SPECIFY_RADIUS_CMD);

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

@@ -79,14 +79,20 @@ private static Font loadFont(final String fontName) {
     }
 
     @Override
-    public void paintIcon(final Component ignored, final Graphics g, final int x, final int y) {
+    public void paintIcon(final Component c, final Graphics g, final int x, final int y) {
         final Graphics2D graphics = (Graphics2D) g;
         GuiUtils.setRenderingHints(graphics);
         final Font previousFont = graphics.getFont();
+        final Paint previousPaint = graphics.getPaint();
         graphics.setFont(font);
-        graphics.setPaint(color);
+        // Graphics2D#setPaint(null) is a documented no-op: it would otherwise silently keep whatever Paint the caller
+        // last set, e.g. a selection/hover background fill painted immediately before this icon
+        // (see BasicMenuItemUI/FlatLaf), making a null-colored glyph disappear into it. Fall back to the component's
+        // own foreground, which is the conventional meaning of a null icon color
+        graphics.setPaint((color != null) ? color : (c != null) ? c.getForeground() : IconFactory.defaultColor());
         graphics.drawString(symbol, x, y + ascent);
         graphics.setFont(previousFont);
+        graphics.setPaint(previousPaint);
     }
 
     protected ImageIcon asImage() {

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

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -377,9 +377,56 @@ public static Icon doubleIcon(final GLYPH entry1, final GLYPH entry2, final floa
         return dropdownIcon(entry1, scalingFactor, color, rightIcon);
     }
 
+    /**
+     * Creates a two-letter icon (e.g., "CT"), analogous to {@link #doubleIcon(GLYPH, GLYPH, float, Color)} but
+     * built from two plain characters rather than {@link GLYPH} entries. Useful for {@link JMenuItem} icons that
+     * combine single-letter tags, such as the "C"(hannel)/"T"(frame) Path Manager tags.
+     *
+     * @param letter1 the first (left) letter, e.g., 'C'
+     * @param letter2 the second (right) letter, e.g., 'T'
+     * @param solid whether the letters are rendered using the solid (vs. regular) weight font
+     * @param scalingFactor the icon's scaling factor relative to the default size
+     * @param color the icon's color
+     * @return the icon
+     */
+    public static Icon doubleLetterIcon(final char letter1, final char letter2, final boolean solid,
+                                        final float scalingFactor, final Color color) {
+        final float size = scalingFactor * FADerivedIcon.defSize();
+        final Icon leftIcon = cachedIcon(letter1, size, color, solid);
+        final Icon rightIcon = cachedIcon(letter2, size, color, solid);
+        return new DropdownIcon(leftIcon, rightIcon);
+    }
+
+    /**
+     * Convenience method for {@link #doubleLetterIcon(char, char, boolean, float, Color)} using a scaling
+     * factor of 1f and solid font weight.
+     *
+     * @param letter1 the first (left) letter, e.g., 'C'
+     * @param letter2 the second (right) letter, e.g., 'T'
+     * @param color the icon's color
+     * @return the icon
+     */
+    public static Icon doubleLetterIcon(final char letter1, final char letter2, final Color color) {
+        return doubleLetterIcon(letter1, letter2, true, 1f, color);
+    }
+
+    /**
+     * Assigns a two-letter icon (see {@link #doubleLetterIcon(char, char, Color)}) to a menu item, including
+     * its disabled state.
+     *
+     * @param item the menu item to be assigned an icon
+     * @param letter1 the first (left) letter, e.g., 'C'
+     * @param letter2 the second (right) letter, e.g., 'T'
+     * @param solid whether the letters are rendered using the solid (vs. regular) weight font
+     */
+    public static void assignDoubleLetterIcon(final JMenuItem item, final char letter1, final char letter2, final boolean solid) {
+        item.setIcon(doubleLetterIcon(letter1, letter2, solid, .75f, defaultColor()));
+        item.setDisabledIcon(doubleLetterIcon(letter1, letter2, solid, .75f, disabledColor()));
+    }
+
     /**
      * Overlays a small notification dot on an icon's upper right corner within the icon's own  bounds
-     * (the icon's reported size is unchanged). 
+     * (the icon's reported size is unchanged).
      *
      * @param icon the source icon
      * @param dotColor the dot's fill color
@@ -425,39 +472,37 @@ public static Icon dropdownMenuIcon(final GLYPH entry, final float scalingFactor
     }
 
     private static Icon dropdownIcon(final GLYPH entry, final float scalingFactor, final Color color, final Icon rightIcon) {
-        class DropdownIcon implements Icon {
+        return new DropdownIcon(entry, scalingFactor, rightIcon, color);
+    }
 
-            static final int ICON_GAP = 2;
-            final Icon leftIcon;
-            final Icon rightIcon;
+    private record DropdownIcon(Icon leftIcon, Icon rightIcon) implements Icon {
 
-            DropdownIcon(final GLYPH entry, final float scalingFactor, final Icon rightIcon) {
-                leftIcon = cachedIcon(entry.id, scalingFactor * FADerivedIcon.defSize(), color, entry.solid);
-                this.rightIcon = rightIcon;
-            }
+        static final int ICON_GAP = 2;
 
-            @Override
-            public void paintIcon(final Component c, final Graphics g, int x, int y) {
-                final Graphics2D g2 = (Graphics2D) g;
-                GuiUtils.setRenderingHints(g2);
-                final int mid = getIconHeight() / 2;
-                final int y1 = y + mid - leftIcon.getIconHeight() / 2;
-                final int y2 = y + mid - rightIcon.getIconHeight() / 2;
-                leftIcon.paintIcon(c, g2, x, y1);
-                rightIcon.paintIcon(c, g2, x + leftIcon.getIconWidth() + ICON_GAP, y2);
-            }
+        DropdownIcon(final GLYPH entry, final float scalingFactor, final Icon rightIcon, final Color color) {
+            this(cachedIcon(entry.id, scalingFactor * FADerivedIcon.defSize(), color, entry.solid), rightIcon);
+        }
 
-            @Override
-            public int getIconWidth() {
-                return leftIcon.getIconWidth() + rightIcon.getIconWidth() + ICON_GAP;
-            }
+        @Override
+        public void paintIcon(final Component c, final Graphics g, int x, int y) {
+            final Graphics2D g2 = (Graphics2D) g;
+            GuiUtils.setRenderingHints(g2);
+            final int mid = getIconHeight() / 2;
+            final int y1 = y + mid - leftIcon.getIconHeight() / 2;
+            final int y2 = y + mid - rightIcon.getIconHeight() / 2;
+            leftIcon.paintIcon(c, g2, x, y1);
+            rightIcon.paintIcon(c, g2, x + leftIcon.getIconWidth() + ICON_GAP, y2);
+        }
 
-            @Override
-            public int getIconHeight() {
-                return Math.max(leftIcon.getIconHeight(), rightIcon.getIconHeight());
-            }
+        @Override
+        public int getIconWidth() {
+            return leftIcon.getIconWidth() + rightIcon.getIconWidth() + ICON_GAP;
+        }
+
+        @Override
+        public int getIconHeight() {
+            return Math.max(leftIcon.getIconHeight(), rightIcon.getIconHeight());
         }
-        return new DropdownIcon(entry, scalingFactor, rightIcon);
     }
 
     // Returns an icon whose pixels are the average of src's pixels and tint, achieved by overlaying tint at 50%
@@ -551,9 +596,13 @@ public static void assignDoubleIcon(final JMenuItem menuItem, final GLYPH defaul
             menuItem.setDisabledIcon(disabledIcon);
             return;
         }
-        final Icon rawSelectedIcon = doubleIcon(selectedIcon, secondaryIcon, .9f, selectedColor());
-        final Icon rawDisabledSelectedIcon = doubleIcon(selectedIcon, secondaryIcon, .9f,
-                SNTColor.average(List.of(disabledColor(), selectedColor())));
+        // NB: FlatLaf swaps to getSelectedIcon() whenever the item is armed (highlighted by the cursor), not only when
+        // a JCheckBoxMenuItem is actually checked, and paints it right after filling the hover highlight.
+        // selectedColor() is a background swatch (List.selectionBackground); using it here would color the glyph the
+        // same as that highlight, making it disappear on hover. Keep the same foreground colors as the  default/disabled
+        // icons so the swapped glyph stays legible while armed
+        final Icon rawSelectedIcon = doubleIcon(selectedIcon, secondaryIcon, .9f, defaultColor());
+        final Icon rawDisabledSelectedIcon = doubleIcon(selectedIcon, secondaryIcon, .9f, disabledColor());
         // defaultIcon/selectedIcon glyphs (e.g., EYE vs EYE_SLASH) rarely share the same font-metrics
         final int refWidth = Math.max(icon.getIconWidth(), rawSelectedIcon.getIconWidth());
         final Icon fixedIcon = fixedWidthIcon(icon, refWidth);
@@ -577,7 +626,7 @@ public static void assignDoubleIcon(final JMenuItem menuItem, final GLYPH defaul
      *
      * @param button the button to decorate
      * @param dotColor the dot's fill color (e.g., Color.RED)
-     * @see #notificationIcon(Icon, Color, Color) 
+     * @see #notificationIcon(Icon, Color, Color)
      */
     public static void assignNotification(final AbstractButton button, final Color dotColor) {
         final Color bkgColor = button.getBackground();

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

@@ -22,6 +22,7 @@
 
 package sc.fiji.snt.gui;
 
+import org.apache.commons.lang.WordUtils;
 import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
 import org.scijava.command.CommandModule;
 import org.scijava.command.CommandService;
@@ -97,20 +98,20 @@ private JMenu getImageFilterMenu() {
 		final JMenu imgFilteringMenu = new JMenu("Select by Image Property");
 		imgFilteringMenu.setIcon(IconFactory.menuIcon(
 			IconFactory.GLYPH.IMAGE));
-		JMenuItem mi1 = new JMenuItem("Traced channel...");
-		mi1.addActionListener(e -> doImageFiltering("Traced channel"));
+		JMenuItem mi1 = new JMenuItem("Traced Channel...");
+		mi1.addActionListener(e -> doImageFiltering("traced channel"));
 		mi1.setIcon(IconFactory.menuIcon('C', false));
 		imgFilteringMenu.add(mi1);
-		mi1 = new JMenuItem("Traced frame...");
-		mi1.addActionListener(e -> doImageFiltering("Traced frame"));
+		mi1 = new JMenuItem("Traced Frame...");
+		mi1.addActionListener(e -> doImageFiltering("traced frame"));
 		mi1.setIcon(IconFactory.menuIcon('T', false));
 		imgFilteringMenu.add(mi1);
-		mi1 = new JMenuItem("Z-slice of first node...");
-		mi1.addActionListener(e -> doImageFiltering("Z-slice of first node"));
+		mi1 = new JMenuItem("Z-slice Of First Node...");
+		mi1.addActionListener(e -> doImageFiltering("z-slice of first node"));
 		mi1.setIcon(IconFactory.menuIcon('Z', false));
 		imgFilteringMenu.add(mi1);
-		mi1 = new JMenuItem("Z-slice of last node...");
-		mi1.addActionListener(e -> doImageFiltering("Z-slice of last node"));
+		mi1 = new JMenuItem("Z-slice Of Last Node...");
+		mi1.addActionListener(e -> doImageFiltering("z-slice of last node"));
 		mi1.setIcon(IconFactory.menuIcon('Z', true));
 		imgFilteringMenu.add(mi1);
 		return imgFilteringMenu;
@@ -182,7 +183,7 @@ private JMenuItem angleFilterMenuItem() {
 	}
 
 	private JMenuItem morphoFilterMenuItem(final String pathAnalyzerMetric, final String unit) {
-		final JMenuItem mi = new JMenuItem(pathAnalyzerMetric + "...");
+		final JMenuItem mi = new JMenuItem(WordUtils.capitalizeFully(pathAnalyzerMetric, new char[]{'/', ' '}) + "...");
 		mi.addActionListener(e -> doMorphoFiltering(pathAnalyzerMetric, unit));
 		switch (pathAnalyzerMetric) {
 			case PathStatistics.N_CHILDREN:

src/main/java/sc/fiji/snt/plugin/StrahlerCmd.java

@@ -206,11 +206,11 @@ private CategoryChart getSingleTreeChart(final StrahlerData sd) throws IllegalAr
 		series.setValues(sd.analyzer.getAvgFragmentations());
 		series.setStyle(plotService.newSeriesStyle(colors[4], LineStyle.SOLID, MarkerStyle.CIRCLE));
 		series = chart.addLineSeries();
-		series.setLabel("Avg. ext. angle (°)");
+		series.setLabel("Avg. ext. angle (°)");
 		series.setValues(sd.analyzer.getAvgExtensionAngles(false));
 		series.setStyle(plotService.newSeriesStyle(colors[5], LineStyle.SOLID, MarkerStyle.CIRCLE));
 		series = chart.addLineSeries();
-		series.setLabel("Avg. ext.angle (Rel.) (°)");
+		series.setLabel("Avg. ext.angle (Rel.) (°)");
 		series.setValues(sd.analyzer.getAvgExtensionAngles(true));
 		series.setStyle(plotService.newSeriesStyle(colors[6], LineStyle.SOLID, MarkerStyle.CIRCLE));
 		return chart;
@@ -493,7 +493,7 @@ else if (metric.contains("frag"))
 		else if (metric.contains("contract"))
 			return "Avg. contraction";
 		else if (metric.contains("extension") || metric.contains("angle"))
-			return "Avg. relative extension angle (°)";
+			return "Avg. relative extension angle (°)";
 		else
 			throw new IllegalArgumentException("Unrecognized metric");
 	}