Viewer3D: Complete Ux restructuring...

- Fix ping-pong animation speed
- Add customizeAxes command
- Add anatomical labels to animation prompt
- Fix centering dialog prompts when parent is not a frame
- Improve split pane
- Improve snapshot retrieval

Author: tferr

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

@@ -1382,7 +1382,10 @@ public static void centerOnParent(final Component parent, final Window dialog) {
 			dialog.setLocationRelativeTo(null);
 			return;
 		}
-		centerOnParent(parent.getBounds(), parent.getGraphicsConfiguration(), dialog);
+		final java.awt.Point screenLoc = parent.getLocationOnScreen();
+		final Rectangle screenBounds = new Rectangle(screenLoc.x, screenLoc.y,
+				parent.getWidth(), parent.getHeight());
+		centerOnParent(screenBounds, parent.getGraphicsConfiguration(), dialog);
 	}
 
 	public static void centerOnParent(final Rectangle parentBounds, final Window dialog) {
@@ -3495,6 +3498,30 @@ public static void expandAllNodes(final javax.swing.JTree tree) {
 			for (int i = 0; i < tree.getRowCount(); i++) tree.expandRow(i);
 		}
 
+		public static void scrollToLastRow(final javax.swing.JTree tree) {
+			int lastRow = tree.getRowCount() - 1;
+			if (lastRow >= 0) {
+				tree.scrollRowToVisible(lastRow);
+			}
+		}
+
+		public static void expandToLevel(final javax.swing.JTree tree, final int level) {
+			final DefaultMutableTreeNode root = (DefaultMutableTreeNode) tree.getModel().getRoot();
+			expandToLevel(tree, new TreePath(root), level);
+		}
+
+		private static void expandToLevel(final javax.swing.JTree tree, final TreePath parentPath, final int level) {
+			final DefaultMutableTreeNode node = (DefaultMutableTreeNode) parentPath.getLastPathComponent();
+			if (node.getLevel() < level) {
+				tree.expandPath(parentPath);
+				final Enumeration<? extends TreeNode> children = node.children();
+				while (children.hasMoreElements()) {
+					final DefaultMutableTreeNode child = (DefaultMutableTreeNode) children.nextElement();
+					expandToLevel(tree, parentPath.pathByAddingChild(child), level);
+				}
+			}
+		}
+
 		public static void collapseNodesOfSameLevel(final javax.swing.JTree tree, final TreePath path) {
 			final DefaultMutableTreeNode root = (DefaultMutableTreeNode)tree.getModel().getRoot();
 			final DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
@@ -3673,4 +3700,102 @@ else if (current instanceof Container) {
 			return null;
 		}
 	}
+
+	public static class SplitPanes {
+
+		public static JSplitPane nonDraggableRightSplitPane() {
+			final JSplitPane splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
+			splitPane.setOneTouchExpandable(true);
+			splitPane.putClientProperty("JSplitPane.expandableSide", "left");
+			splitPane.putClientProperty(FlatClientProperties.STYLE,
+					"style: plain;" +
+					"arrowType: triangle;" + //oneTouchArrowColor; oneTouchHoverArrowColor
+					"oneTouchHoverArrowColor: " + SNTColor.colorToString(getSelectionColor()) + ";" +
+					"oneTouchArrowColor: " + SNTColor.colorToString(IconFactory.defaultColor()) + ";");
+			splitPane.setResizeWeight(1.0); // give all extra space to the left side
+			splitPane.setBorder(null);
+			// Non: resizable: reset cursor and vertically center the one-touch buttons along the divider's length
+			final javax.swing.plaf.basic.BasicSplitPaneDivider divider =
+					((javax.swing.plaf.basic.BasicSplitPaneUI) splitPane.getUI()).getDivider();
+			SplitPanes.applyDefaultCursor(divider);
+			SplitPanes.centerOneTouchButtons(splitPane, divider);
+			return splitPane;
+		}
+
+		public static void applyDefaultCursor(final javax.swing.plaf.basic.BasicSplitPaneDivider divider) {
+			divider.setCursor(java.awt.Cursor.getDefaultCursor());
+		}
+
+		public static void centerOneTouchButtons(final javax.swing.JSplitPane splitPane,
+												 final javax.swing.plaf.basic.BasicSplitPaneDivider divider) {
+			divider.setLayout(new java.awt.LayoutManager() {
+				@Override
+				public void addLayoutComponent(final String name, final Component comp) {
+				}
+
+				@Override
+				public void removeLayoutComponent(final Component comp) {
+				}
+
+				@Override
+				public java.awt.Dimension preferredLayoutSize(final Container parent) {
+					return null;
+				}
+
+				@Override
+				public java.awt.Dimension minimumLayoutSize(final Container parent) {
+					return null;
+				}
+
+				@Override
+				public void layoutContainer(final Container parent) {
+					// Replicate FlatDividerLayout's visibility logic: when a side
+					// is collapsed, show only the button that can restore it.
+					// Otherwise, respect the expandableSide client property.
+					final Component[] comps = parent.getComponents();
+					final java.awt.Insets insets = splitPane.getInsets();
+					final int loc = splitPane.getDividerLocation();
+					final boolean horiz = splitPane.getOrientation() == javax.swing.JSplitPane.HORIZONTAL_SPLIT;
+					final boolean leftCollapsed = horiz
+							? loc <= insets.left
+							: loc <= insets.top;
+					final boolean rightCollapsed = horiz
+							? loc >= splitPane.getWidth() - divider.getWidth() - insets.right
+							: loc >= splitPane.getHeight() - divider.getHeight() - insets.bottom;
+					for (int i = 0; i < comps.length; i++) {
+						if (!(comps[i] instanceof javax.swing.JButton)) continue;
+						if (leftCollapsed || rightCollapsed) {
+							// Collapsed: show only the button that restores the collapsed side
+							comps[i].setVisible(i == 0 ? !leftCollapsed : !rightCollapsed);
+						} else {
+							final Object expandSide = splitPane.getClientProperty(
+									FlatClientProperties.SPLIT_PANE_EXPANDABLE_SIDE);
+							if (FlatClientProperties.SPLIT_PANE_EXPANDABLE_SIDE_LEFT.equals(expandSide))
+								comps[i].setVisible(i > 0);
+							else if (FlatClientProperties.SPLIT_PANE_EXPANDABLE_SIDE_RIGHT.equals(expandSide))
+								comps[i].setVisible(i == 0);
+						}
+					}
+					// Collect visible buttons and center them vertically
+					final java.util.List<Component> buttons = new java.util.ArrayList<>();
+					for (final Component c : comps) {
+						if (c instanceof javax.swing.JButton && c.isVisible())
+							buttons.add(c);
+					}
+					if (buttons.isEmpty()) return;
+					final int divW = parent.getWidth();
+					final int divH = parent.getHeight();
+					final int btnW = Math.min(divW, buttons.getFirst().getPreferredSize().width);
+					final int btnH = buttons.getFirst().getPreferredSize().height;
+					final int totalH = buttons.size() * btnH;
+					int y = (divH - totalH) / 2;
+					final int x = (divW - btnW) / 2;
+					for (final Component btn : buttons) {
+						btn.setBounds(x, y, btnW, btnH);
+						y += btnH;
+					}
+				}
+			});
+		}
+	}
 }

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

@@ -0,0 +1,111 @@
+/*-
+ * #%L
+ * Fiji distribution of ImageJ for the life sciences.
+ * %%
+ * Copyright (C) 2010 - 2026 Fiji developers.
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * 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>.
+ * #L%
+ */
+
+package sc.fiji.snt.gui.cmds;
+
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.command.ContextCommand;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+import java.util.HashMap;
+
+/**
+ * Command for customizing axis-to-anatomy mappings in Reconstruction Viewer.
+ * Allows the user to specify which anatomical dimension (Anterior-Posterior,
+ * Dorsal-Ventral, Left-Right) corresponds to each world axis (X, Y, Z), and
+ * the direction of the dorsal axis. The mapping determines the camera up
+ * vector and the axis-swap behavior for constrained 2D views.
+ *
+ * @author Tiago Ferreira
+ */
+@Plugin(type = Command.class, visible = false, label = "Axes Mapping...")
+public class CustomizeAxesCmd extends ContextCommand {
+
+    /** Anatomical axis choices. */
+    private static final String AP = "Anterior-Posterior";
+    private static final String DV = "Dorsal-Ventral";
+    private static final String LR = "Left-Right (ML)";
+    private static final String NONE = "None";
+
+    private static final String DIR_POS = "Positive (+)";
+    private static final String DIR_NEG = "Negative (-)";
+
+    @Parameter(label = "X axis:", choices = {AP, DV, LR, NONE})
+    private String xAxisMapping;
+
+    @Parameter(label = "Y axis:", choices = {AP, DV, LR, NONE})
+    private String yAxisMapping;
+
+    @Parameter(label = "Z axis:", choices = {AP, DV, LR, NONE})
+    private String zAxisMapping;
+
+    @Parameter(label = "Dorsal direction:", choices = {DIR_POS, DIR_NEG},
+            description = "The direction along the Dorsal-Ventral axis in which dorsal values increase.\n"
+                    + "Set to 'Negative' if dorsal is at the origin (e.g. Allen CCF).")
+    private String dorsalDirection;
+
+    @Parameter(type = ItemIO.OUTPUT, required = false, persist = false)
+    private HashMap<String, String> outMap;
+
+    /**
+     * Returns the axis identifier ("X", "Y", or "Z") assigned to the
+     * Dorsal-Ventral role, or {@code null} if none is assigned.
+     */
+    public static String getDVAxis(final HashMap<String, String> map) {
+        if (DV.equals(map.get("xAxis"))) return "X";
+        if (DV.equals(map.get("yAxis"))) return "Y";
+        if (DV.equals(map.get("zAxis"))) return "Z";
+        return null;
+    }
+
+    /**
+     * Returns the sign of the dorsal direction: {@code -1} for negative,
+     * {@code +1} for positive.
+     */
+    public static int getDorsalSign(final HashMap<String, String> map) {
+        return DIR_NEG.equals(map.get("dorsalDir")) ? -1 : 1;
+    }
+
+    /**
+     * Returns the axis labels derived from the mapping, suitable for
+     * {@code Viewer3D.setAxesLabels()}.
+     */
+    public static String[] getLabels(final HashMap<String, String> map) {
+        return new String[]{
+                NONE.equals(map.get("xAxis")) ? "X" : map.get("xAxis"),
+                NONE.equals(map.get("yAxis")) ? "Y" : map.get("yAxis"),
+                NONE.equals(map.get("zAxis")) ? "Z" : map.get("zAxis")
+        };
+    }
+
+    @Override
+    public void run() {
+        outMap = new HashMap<>();
+        outMap.put("xAxis", xAxisMapping);
+        outMap.put("yAxis", yAxisMapping);
+        outMap.put("zAxis", zAxisMapping);
+        outMap.put("dorsalDir", dorsalDirection);
+    }
+
+}

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

@@ -58,6 +58,8 @@ public class RecViewerPrefsCmd extends ContextCommand {
 	public static String DEF_ANIMATION_MODE = "Full Rotation";
 	/** Default sensitivity setting for 3D viewer controls */
 	public static String DEF_CONTROLS_SENSITIVITY = "High";
+	/** Default WYSIWYG snapshot mode (off: use GL readback) */
+	public static boolean DEF_SNAPSHOT_WYSIWYG = false;
 	/** Default file extension for scripts */
 	public static String DEF_SCRIPT_EXTENSION = ".groovy";
 
@@ -71,17 +73,22 @@ public class RecViewerPrefsCmd extends ContextCommand {
 		description = "Directory where static snapshots and animated sequences will be saved")
 	private File snapshotDir;
 
+	@Parameter(label = "WYSIWYG snapshots", required = false, persist = true,
+		description = "Use screen capture for pixel-perfect snapshots matching \n" +
+				"the on-screen rendering (bypasses GL framebuffer readback)")
+	private boolean snapshotWYSIWYG;
+
 	@Parameter(label = "Animated Rotations:", required = false,
 		visibility = ItemVisibility.MESSAGE)
 	private String SUB_HEADER1;
 
 	@Parameter(label = "Animation mode", required = false, persist = true,
-		description = "Full Rotation: continuous 360° sweep. Ping-pong: oscillates back and forth over the specified arc",
+		description = "Full Rotation: continuous 360° sweep.\nPing-pong: oscillates back and forth over the specified arc",
 		choices = { "Full Rotation", "Ping-pong" })
 	private String animationMode;
 
 	@Parameter(required = false, persist = true, label = "Rotation degrees",
-		description = "Full Rotation: total sweep angle. Ping-pong: oscillation arc (camera rocks ±half this angle)",
+		description = "Full Rotation: total sweep angle.\nPing-pong: oscillation arc (camera rocks ±half this angle)",
 		style = NumberWidget.SCROLL_BAR_STYLE, stepSize = "10", min = "30",
 		max = "360d")
 	private double rotationAngle;
@@ -157,6 +164,7 @@ private void init() {
 
 	private void defaults() {
 		snapshotDir = null;
+		snapshotWYSIWYG = DEF_SNAPSHOT_WYSIWYG;
 		animationMode = null;
 		rotationAngle = 0;
 		rotationDuration = 0;

src/main/java/sc/fiji/snt/util/ImpUtils.java

@@ -437,6 +437,10 @@ public static ImagePlus getSystemClipboard(final boolean asMultiChannel) {
         return null;
     }
 
+    public static ImagePlus fromBufferedImage(final String title, final BufferedImage image) {
+        return new ImagePlus(title, new ij.process.ColorProcessor(image));
+    }
+
     private static boolean isGrayscale(final BufferedImage image, final int width, final int height) {
         for (int i = 0; i < width; i++) { // https://stackoverflow.com/a/36173328
             for (int j = 0; j < height; j++) {