added basic bookmarking capabilities. Still missing:

- animate "go to bookmark"
- rotation-only bookmarks
- different (permanent) overlay for bookmark messages

core/src/main/java/bdv/BigDataViewer.java

@@ -44,6 +44,7 @@ import bdv.tools.HelpDialog;
 import bdv.tools.InitializeViewerState;
 import bdv.tools.RecordMovieDialog;
 import bdv.tools.VisibilityAndGroupingDialog;
+import bdv.tools.bookmarks.BookmarkEditor;
 import bdv.tools.brightness.BrightnessDialog;
 import bdv.tools.brightness.ConverterSetup;
 import bdv.tools.brightness.MinMaxGroup;
@@ -81,6 +82,8 @@ public class BigDataViewer
 
 	protected final ManualTransformationEditor manualTransformationEditor;
 
+	protected final BookmarkEditor bookmarkEditor;
+
 	protected final JFileChooser fileChooser;
 
 	protected File proposedSettingsFile;
@@ -90,6 +93,16 @@ public class BigDataViewer
 		manualTransformationEditor.toggle();
 	}
 
+	public void initSetBookmark()
+	{
+		bookmarkEditor.initSetBookmark();
+	}
+
+	public void initGoToBookmark()
+	{
+		bookmarkEditor.initGoToBookmark();
+	}
+
 	private static String createSetupName( final BasicViewSetup setup )
 	{
 		if ( setup.hasName() )
@@ -252,6 +265,8 @@ public class BigDataViewer
 		manualTransformation = new ManualTransformation( viewer );
 		manualTransformationEditor = new ManualTransformationEditor( viewer, viewerFrame.getKeybindings() );
 
+		bookmarkEditor = new BookmarkEditor( viewer, viewerFrame.getKeybindings() );
+
 		setupAssignments = new SetupAssignments( converterSetups, 0, 65535 );
 		if ( setupAssignments.getMinMaxGroups().size() > 0 )
 		{
@@ -449,8 +464,9 @@ public class BigDataViewer
 
 	public static void main( final String[] args )
 	{
-		final String fn = "/Users/Pietzsch/Desktop/spimrec2/dataset.xml";
+//		final String fn = "/Users/Pietzsch/Desktop/spimrec2/dataset.xml";
 //		final String fn = "/Users/Pietzsch/Desktop/bdv example/drosophila 2.xml";
+		final String fn = "/Users/pietzsch/Desktop/data/clusterValia/140219-1/valia-140219-1.xml";
 //		final String fn = "/Users/Pietzsch/Desktop/data/catmaid.xml";
 //		final String fn = "/Users/Pietzsch/Desktop/data/openconnectome-bock11-neariso.xml";
 //		final String fn = "/Users/Pietzsch/Desktop/data/catmaid-confocal.xml";
@@ -462,7 +478,7 @@ public class BigDataViewer
 //		final String fn = "/Users/pietzsch/Desktop/data/fibsem.xml";
 //		final String fn = "/Users/pietzsch/Desktop/data/fibsem-remote.xml";
 //		final String fn = "/Users/pietzsch/Desktop/url-valia.xml";
-//		final String fn = "/Users/pietzsch/Desktop/data/Valia/valia.xml";
+//		final String fn = "/Users/pietzsch/Desktop/data/clusterValia/140219-1/valia-140219-1.xml";
 //		final String fn = "/Users/pietzsch/workspace/data/111010_weber_full.xml";
 //		final String fn = "/Volumes/projects/tomancak_lightsheet/Mette/ZeissZ1SPIM/Maritigrella/021013_McH2BsGFP_CAAX-mCherry/11-use/hdf5/021013_McH2BsGFP_CAAX-mCherry-11-use.xml";
 		try

core/src/main/java/bdv/BigDataViewerActions.java

@@ -7,8 +7,8 @@ import javax.swing.InputMap;
 
 import bdv.tools.ToggleDialogAction;
 import bdv.util.AbstractNamedAction;
-import bdv.util.KeyProperties;
 import bdv.util.AbstractNamedAction.NamedActionAdder;
+import bdv.util.KeyProperties;
 import bdv.util.KeyProperties.KeyStrokeAdder;
 import bdv.viewer.InputActionBindings;
 
@@ -22,6 +22,8 @@ public class BigDataViewerActions
 	public static final String SAVE_SETTINGS = "save settings";
 	public static final String LOAD_SETTINGS = "load settings";
 	public static final String RECORD_MOVIE = "record movie";
+	public static final String SET_BOOKMARK = "set bookmark";
+	public static final String GO_TO_BOOKMARK = "go to bookmark";
 
 	/**
 	 * Create BigDataViewer actions and install them in the specified
@@ -56,6 +58,8 @@ public class BigDataViewerActions
 		map.put( RECORD_MOVIE, "F10" );
 		map.put( SAVE_SETTINGS, "F11" );
 		map.put( LOAD_SETTINGS, "F12" );
+		map.put( GO_TO_BOOKMARK, "B" );
+		map.put( SET_BOOKMARK, "shift B" );
 
 		return inputMap;
 	}
@@ -71,6 +75,8 @@ public class BigDataViewerActions
 		map.put( new ToggleDialogAction( RECORD_MOVIE, bdv.movieDialog ) );
 		map.put( new ToggleDialogAction( SHOW_HELP, bdv.helpDialog ) );
 		map.put( new ManualTransformAction( bdv ) );
+		map.put( new SetBookmarkAction( bdv ) );
+		map.put( new GoToBookmarkAction( bdv ) );
 		map.put( new SaveSettingsAction( bdv ) );
 		map.put( new LoadSettingsAction( bdv ) );
 
@@ -106,6 +112,38 @@ public class BigDataViewerActions
 		private static final long serialVersionUID = 1L;
 	}
 
+	public static class SetBookmarkAction extends ViewerAction
+	{
+		public SetBookmarkAction( final BigDataViewer bdv )
+		{
+			super( SET_BOOKMARK, bdv );
+		}
+
+		@Override
+		public void actionPerformed( final ActionEvent e )
+		{
+			bdv.initSetBookmark();
+		}
+
+		private static final long serialVersionUID = 1L;
+	}
+
+	public static class GoToBookmarkAction extends ViewerAction
+	{
+		public GoToBookmarkAction( final BigDataViewer bdv )
+		{
+			super( GO_TO_BOOKMARK, bdv );
+		}
+
+		@Override
+		public void actionPerformed( final ActionEvent e )
+		{
+			bdv.initGoToBookmark();
+		}
+
+		private static final long serialVersionUID = 1L;
+	}
+
 	public static class SaveSettingsAction extends ViewerAction
 	{
 		public SaveSettingsAction( final BigDataViewer bdv )

core/src/main/java/bdv/tools/bookmarks/BookmarkEditor.java

+package bdv.tools.bookmarks;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.util.HashMap;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.ActionMap;
+import javax.swing.InputMap;
+import javax.swing.KeyStroke;
+
+import net.imglib2.realtransform.AffineTransform3D;
+import bdv.viewer.InputActionBindings;
+import bdv.viewer.ViewerPanel;
+
+public class BookmarkEditor
+{
+	private boolean active = false;
+
+	private boolean setBookmark = false;
+
+	private final ViewerPanel viewer;
+
+	private final InputActionBindings bindings;
+
+	private final ActionMap actionMap;
+
+	private final InputMap inputMap;
+
+	private final HashMap< String, AffineTransform3D > bookmarks;
+
+	public BookmarkEditor( final ViewerPanel viewer, final InputActionBindings inputActionBindings )
+	{
+		this.viewer = viewer;
+		bindings = inputActionBindings;
+		bookmarks = new HashMap< String, AffineTransform3D >();
+
+		final KeyStroke abortKey = KeyStroke.getKeyStroke( KeyEvent.VK_ESCAPE, 0 );
+		final Action abortAction = new AbstractAction( "abort bookmark" )
+		{
+			@Override
+			public void actionPerformed( final ActionEvent e )
+			{
+				abort();
+			}
+
+			private static final long serialVersionUID = 1L;
+		};
+		actionMap = new ActionMap();
+		inputMap = new InputMap();
+		actionMap.put( "abort bookmark", abortAction );
+		inputMap.put( abortKey, "abort bookmark" );
+		bindings.addActionMap( "bookmarks", actionMap );
+
+		viewer.getDisplay().addKeyListener( new KeyAdapter()
+		{
+			@Override
+			public void keyTyped( final KeyEvent e )
+			{
+				if ( active && e.getKeyChar() != 'b' && e.getKeyChar() != 'B' )
+				{
+					final String key = String.valueOf( e.getKeyChar() );
+					if ( setBookmark )
+					{
+						final AffineTransform3D t = new AffineTransform3D();
+						viewer.getState().getViewerTransform( t );
+						bookmarks.put( key, t );
+						viewer.showMessage( "set bookmark " + key );
+					}
+					else
+					{
+						final AffineTransform3D t = bookmarks.get( key );
+						if ( t != null )
+							viewer.setCurrentViewerTransform( t );
+						viewer.showMessage( "go to bookmark " + key );
+					}
+					done();
+				}
+			}
+		} );
+	}
+
+	public synchronized void abort()
+	{
+		if ( active )
+		{
+			viewer.showMessage( "aborted" );
+			done();
+		}
+	}
+
+	public synchronized void initSetBookmark()
+	{
+		active = true;
+		setBookmark = true;
+		bindings.addInputMap( "bookmarks", inputMap, "bdv", "navigation" );
+		viewer.showMessage( " bookmark" );
+	}
+
+	public synchronized void initGoToBookmark()
+	{
+		active = true;
+		setBookmark = false;
+		bindings.addInputMap( "bookmarks", inputMap, "bdv", "navigation" );
+		viewer.showMessage( "go to bookmark" );
+	}
+
+	public synchronized void done()
+	{
+		active = false;
+		bindings.removeInputMap( "bookmarks" );
+	}
+}