Fix UIScaling issues on Linux

Author: tferr

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

@@ -1815,7 +1815,7 @@ void populateFromFile(final File file) throws IOException {
         final int cIdx = bvvMode ? -1 : table.findColumnIndex(HEADER[5]);
         final int tIdx = bvvMode ? -1 : table.findColumnIndex(HEADER[6]);
 
-        if (lIdx == -1 || xIdx == -1 || yIdx == -1 || zIdx == -1)
+        if (xIdx == -1 || yIdx == -1 || zIdx == -1)
             throw new IOException("Unexpected column header(s) in CSV file.");
         final List<Bookmark> dataList = new ArrayList<>();
         for (int i = 0; i < table.getRowCount(); i++) {
@@ -1829,7 +1829,8 @@ void populateFromFile(final File file) throws IOException {
                     } catch (final IllegalArgumentException ignored) {}
                 }
             }
-            final Bookmark b = new Bookmark((String) table.get(lIdx, i),
+            final String label = (tagIdx != -1) ? ((String) table.get(lIdx, i)) : "Loc";
+            final Bookmark b = new Bookmark(label,
                     (double) table.get(xIdx, i), (double) table.get(yIdx, i), (double) table.get(zIdx, i),
                     (cIdx == -1) ? 1 : (int) ((double) table.get(cIdx, i)),
                     (tIdx == -1) ? 1 : (int) ((double) table.get(tIdx, i)),

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

@@ -396,8 +396,8 @@ public void windowClosing(final WindowEvent e) {
         c3.gridy++;
         InternalUtils.addSeparatorWithURL(tab3, "sciview:", false, c3);
         ++c3.gridy;
-        final String msg3 = "3D visualization framework supporting large image volumes, reconstructions, " +
-                "meshes, virtual reality, and Cx3D simulations. Discrete graphics card recommended.";
+        final String msg3 = "3D visualization framework supporting image volumes, meshes, virtual " +
+                "reality, and Cx3D neurodevelopmental simulations. Discrete graphics card recommended.";
         tab3.add(GuiUtils.longSmallMsg(msg3, "sciview-logo-icon.svg", tab3), c3);
         c3.gridy++;
         tab3.add(sciViewerPanel(viewerPanelBuilder), c3);

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

@@ -1682,6 +1682,7 @@ private static class SvgBackgroundJTextArea extends JTextArea {
 		private final FlatSVGIcon svgIcon;
 		private FlatSVGIcon derivedIcon = null;
 		private int derivedIconWidth = 0;
+		private float osScale = 1f;
 
 		SvgBackgroundJTextArea(final String svgFileName) {
 			this.svgIcon = new FlatSVGIcon("gui/" + svgFileName);
@@ -1696,19 +1697,26 @@ public void addNotify() {
 			// Compute the derived icon here (not in paintComponent) to avoid feedback
 			// loops between icon size, insets, wrapping, and component height
 			super.addNotify();
-			// Size the icon to 3 text rows: getRowHeight() is font-based and should be stable
-			final int iconHeight = getRowHeight() * 3;
+			// osScale = FlatLaF uiScale / AWT device scale
+			// It seems that on  macOS and Windows, Java handles HiDPI natively: AWT deviceScale == uiScale,
+			// so osScale == 1 and all sizes are already in FlatLaF logical units. On Linux with GDK_SCALE, the OS
+			// scales everything _before_(!?) Java sees it: AWT deviceScale stays at 1 while uiScale absorbs
+			// the  GDK factor, so sizes become in device pixels and must be divided by osScale to get FlatLaF logical
+			// units. FlatSVGIcon.derive() and getInsets() both expect  FlatLaF logical units on the icon side
+			osScale = osScale(this);
+			final int iconHeight = (int) (getRowHeight() * 3 / osScale);
 			final float scale = (float) iconHeight / svgIcon.getIconHeight();
 			derivedIconWidth = Math.round(svgIcon.getIconWidth() * scale);
 			derivedIcon = svgIcon.derive(derivedIconWidth, iconHeight);
 		}
 
 		@Override
 		public Insets getInsets() {
-			// Reserve left space equal to icon width + one 'M' gap for readability
+			// derivedIconWidth is in FlatLaF logical units; multiply by osScale to convert to Swing layout coordinates.
+			// charWidth is also in FlatLaF logical units (it seems GDK_SCALE is already applied on Linux)
 			final Insets base = super.getInsets();
-			final int gap = getFontMetrics(getFont()).stringWidth("M");
-			return new Insets(base.top, base.left + derivedIconWidth + gap, base.bottom, base.right);
+			final int gap = (int) (getFontMetrics(getFont()).charWidth('m') * osScale);
+			return new Insets(base.top, base.left + (int)(derivedIconWidth * osScale) + gap, base.bottom, base.right);
 		}
 
 		@Override
@@ -1912,6 +1920,47 @@ public static double uiScale() {
 		return Math.max(1.0, ij.Prefs.getGuiScale());
 	}
 
+	/**
+	 * Returns the OS-level scale factor that is NOT already accounted for by Java's HiDPI awareness.
+	 * <p>
+	 * On macOS and Windows, Java intercepts HiDPI natively: so this returns 1.0. On Linux with GDK_SCALE, the OS seems
+	 * to scale everything before Java sees it: AWT/Swing stay at 1.0 scaling while {@link #uiScale()} absorbs the GDK
+	 * factor, so font sizes, etc.  are in device pixels and must be divided by the returned value to reach FlatLaF
+	 * logical units.
+	 * </p>
+	 * Uses the default screen device; prefer {@link #osScale(Component)} when a
+	 * component is available so multi-monitor setups are handled correctly.
+	 */
+	public static float osScale() {
+		try {
+			final double deviceScale = GraphicsEnvironment.getLocalGraphicsEnvironment()
+					.getDefaultScreenDevice()
+					.getDefaultConfiguration()
+					.getDefaultTransform()
+					.getScaleX();
+			return (float) (uiScale() / Math.max(1.0, deviceScale));
+		} catch (final Exception ignored) {
+			return 1f;
+		}
+	}
+
+	/**
+	 * Component-aware variant of {@link #osScale()}: uses the component's own
+	 * {@link java.awt.GraphicsConfiguration} so the correct scale is returned on
+	 * multi-monitor setups where screens may have different DPI.
+	 */
+	public static float osScale(final Component c) {
+		if (c == null) return osScale();
+		try {
+			final java.awt.GraphicsConfiguration gc = c.getGraphicsConfiguration();
+			if (gc == null) return osScale();
+			final double deviceScale = gc.getDefaultTransform().getScaleX();
+			return (float) (uiScale() / Math.max(1.0, deviceScale));
+		} catch (final Exception ignored) {
+			return 1f;
+		}
+	}
+
 	public static void initSplashScreen() {
 		splashScreen = new SplashScreen();
 		splashScreen.addMouseListener(new MouseAdapter() {

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

@@ -24,7 +24,6 @@
 
 import com.formdev.flatlaf.FlatLaf;
 import com.formdev.flatlaf.icons.FlatAbstractIcon;
-import org.scijava.util.PlatformUtils;
 
 import javax.swing.*;
 import javax.swing.border.TitledBorder;
@@ -440,8 +439,10 @@ else if (isExpanded)
     }
 
     public static Icon accentIcon(final Color color, final boolean squarify) {
-        final int size = (int) (FADerivedIcon.defSize() * (PlatformUtils.isLinux() ? .6f : .9f));
-        return new AccentIcon(color, (squarify) ? size : size *2, size);
+        // defSize() is based on uiFontSize(), which on Linux HiDPI (GDK_SCALE) is inflated
+        // by the OS scale factor. Divide by osScale() to get FlatLaF logical units
+        final int size = (int) (FADerivedIcon.defSize() / GuiUtils.osScale());
+        return new AccentIcon(color, (squarify) ? size : size * 2, size);
     }
 
     /* Creation of colorful JTree node icons */

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

@@ -22,6 +22,7 @@
 
 package sc.fiji.snt.gui;
 
+import com.formdev.flatlaf.ui.FlatRoundBorder;
 import com.jidesoft.swing.Searchable;
 import com.jidesoft.swing.SearchableBar;
 import com.jidesoft.swing.SearchableBarIconsFactory;
@@ -306,6 +307,7 @@ private SearchField getModifiedTextField(final String placeholder) {
 			updateHistoryMenu();
 			optionsMenu.show(sf.optionsButton(), 0, sf.optionsButton().getHeight());
 		});
+		sf.setBorder(new FlatRoundBorder());
 		return sf;
 	}