BVV: fix marker hotkey reliability and fly-to bookmark drift

Fix two bugs in the BVV viewer:

1. The 'M' hotkey for placing markers would silently stop working
   mid-session. Now we register SNT shortcuts through BDV's
   nputActionBindings instead, which seems way more reliable.

2. Double-clicking a bookmark to fly to its position caused progressive
   drift on repeated clicks, and flew to the wrong location entirely
   for non-axis-aligned source transforms. The old code multiplied
   world coordinates by diagonal matrix elements only, ignoring
   rotation. Now computes the full affine mapping and sets the
   translation to centre the bookmark on screen.

Author: tferr

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

@@ -419,7 +419,7 @@ private JPopupMenu importMenu() {
         menu.add(jmi);
         jmi.addActionListener(e -> {
             final File file = (sntui != null) ? sntui.openFile("csv")
-                    : guiUtils.getFile(null, "csv");
+                    : guiUtils.getFile(new File(SNTPrefs.lastKnownDir(), "Markers.csv"), "csv");
             if (file != null) {
                 recordCmd("load(\"" + file.getAbsolutePath() + "\")");
                 loadBookmarksFromFile(file);
@@ -521,7 +521,7 @@ private void saveToUserChosenFile(final File file) {
         if (noBookmarksError()) return;
         final File saveFile = (file != null) ? file
                 : (sntui != null) ? sntui.saveFile("Export Bookmarks to CSV...", "SNT_Bookmarks.csv", "csv")
-                : guiUtils.getSaveFile("Export Markers to CSV...", null, "csv");
+                : guiUtils.getSaveFile("Export Markers to CSV...", new File(SNTPrefs.lastKnownDir(), "Markers.csv"), "csv");
         if (saveFile != null) {
             recordCmd("save(\"" + saveFile.getAbsolutePath() + "\")");
             if (saveBookMarksToFile(saveFile)) {
@@ -704,11 +704,23 @@ private void flyTo(final int row) {
         final Bookmark b = model.getDataList().get(table.convertRowIndexToModel(row));
         final net.imglib2.realtransform.AffineTransform3D current = new net.imglib2.realtransform.AffineTransform3D();
         bvv.getViewerPanel().state().getViewerTransform(current);
-        // Build a target transform that centres on the bookmark world position
+        // The viewer transform maps world -> screen. To centre the bookmark on
+        // screen we keep the current rotation/scale but adjust the translation
+        // so that the bookmark's world position maps to the screen centre.
+        // screenPos = R * worldPos + t, so t_new = screenCentre - R * worldPos
+        final double[] worldPos = {b.getX(), b.getY(), b.getZ()};
+        final double[] mapped = new double[3];
+        current.apply(worldPos, mapped);
+        // mapped = R * worldPos + t_current, so R * worldPos = mapped - t_current
+        final double rx = mapped[0] - current.get(0, 3);
+        final double ry = mapped[1] - current.get(1, 3);
+        final double rz = mapped[2] - current.get(2, 3);
+        final double cX = bvv.getViewerPanel().getWidth()  / 2.0;
+        final double cY = bvv.getViewerPanel().getHeight() / 2.0;
         final net.imglib2.realtransform.AffineTransform3D target = current.copy();
-        target.set(target.get(0, 3) - b.getX() * current.get(0, 0),  0, 3);
-        target.set(target.get(1, 3) - b.getY() * current.get(1, 1),  1, 3);
-        target.set(target.get(2, 3) - b.getZ() * current.get(2, 2),  2, 3);
+        target.set(cX - rx, 0, 3);
+        target.set(cY - ry, 1, 3);
+        target.set(   - rz, 2, 3);
         bvv.getViewerPanel().setTransformAnimator(
                 new bdv.viewer.animate.SimilarityTransformAnimator(current, target, 0, 0, 300));
         bvv.getViewer().getViewer().showMessage(String.format("Flying to %s", b.label));

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

@@ -1129,13 +1129,19 @@ private void attachControlPanel(final BvvSource source) {
             bvvFrame.getCardPanel().addCard("Scene Controls", sceneControlsPanel, true);
             // SNT toolbar
             bvvFrame.getCardPanel().addCard("SNT Annotations", sntToolbar(actions), true);
-            // Register shortcuts: M key to place a marker at the current mouse position; shift+S for screenshot()
-            final InputMap iMap = bvvFrame.getViewerPanel().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
-            final ActionMap aMap = bvvFrame.getViewerPanel().getActionMap();
-            iMap.put(KeyStroke.getKeyStroke('m'), "snt-add-marker");
-            aMap.put("snt-add-marker", actions.addMarkerAction());
-            iMap.put(KeyStroke.getKeyStroke('S'), "snt-bvv-snapshot");
-            aMap.put("snt-bvv-snapshot", snapshotAction());
+            // Register shortcuts through BDV's keybindings system so they are
+            // handled at the same level as BVV's own shortcuts (e.g., Shift+B).
+            // Using Swing's InputMap/ActionMap directly gets shadowed by BDV's
+            // input trigger layer.
+            final InputMap sntIMap = new InputMap();
+            final ActionMap sntAMap = new ActionMap();
+            sntIMap.put(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_M, 0), "snt-add-marker");
+            sntAMap.put("snt-add-marker", actions.addMarkerAction());
+            sntIMap.put(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_S,
+                    java.awt.event.InputEvent.SHIFT_DOWN_MASK), "snt-bvv-snapshot");
+            sntAMap.put("snt-bvv-snapshot", snapshotAction());
+            bvvFrame.getKeybindings().addInputMap("snt", sntIMap);
+            bvvFrame.getKeybindings().addActionMap("snt", sntAMap);
             SwingUtilities.invokeLater(bvv::expandAndFocusCardPanel);
             // 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,
@@ -2636,7 +2642,8 @@ private JToolBar buildIconToolbar(final BvvActions bvvActions) {
                                     bvvInstance.repaint();
                                 }
                             }),
-                    "Show/hide coordinate axes at the volume origin",
+                    "Show/hide coordinate axes at the volume origin.\n" +
+                            "X: Red; Y: Green; Z: Blue",
                     IconFactory.GLYPH.CHART_LINE, IconFactory.GLYPH.CHART_LINE);
             axesToggle.setSelected(false);
             bar.add(axesToggle);