Release beta-34

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>38.0.1</version>
+		<version>40.0.0</version>
 	</parent>
 
 	<groupId>org.mastodon</groupId>
@@ -31,11 +31,6 @@
 	<dependencies>
 
 		<!-- Mastodon dependencies -->
-		<dependency>
-			<groupId>org.mastodon</groupId>
-			<artifactId>mastodon-collection</artifactId>
-			<version>${mastodon-collection.version}</version>
-		</dependency>
 		<dependency>
 			<groupId>org.mastodon</groupId>
 			<artifactId>mastodon-graph</artifactId>
@@ -189,8 +184,7 @@
 		<license.organizationName>Mastodon authors</license.organizationName>
 		<license.copyrightOwners>Tobias Pietzsch, Jean-Yves Tinevez</license.copyrightOwners>
 
-		<mastodon-collection.version>1.0.0-beta-29</mastodon-collection.version>
-		<mastodon-graph.version>1.0.0-beta-29</mastodon-graph.version>
+		<mastodon-graph.version>1.0.0-beta-30</mastodon-graph.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

src/main/java/org/mastodon/app/MastodonIcons.java

@@ -227,7 +227,7 @@ public class MastodonIcons
 	 */
 
 	public static final Image MAINWINDOW_BG =
-			new ImageIcon( MastodonIcons.class.getResource( "MastodonMainWindowBG.png" ) ).getImage();
+			new ImageIcon( MastodonIcons.class.getResource( "MastodonMainWindowBG-flipped.png" ) ).getImage();
 
 	/*
 	 * General use icons.
@@ -248,4 +248,8 @@ public class MastodonIcons
 
 	public static final ImageIcon REMOVE_ICON = new ImageIcon( AbstractTagTable.class.getResource( "delete.png" ) );
 
+	public static final ImageIcon BIN_EMPTY_ICON = new ImageIcon( FeatureComputationPanel.class.getResource( "bin.png" ) );
+
+	public static final ImageIcon BIN_ICON = new ImageIcon( FeatureComputationPanel.class.getResource( "bin_closed.png" ) );
+
 }

src/main/java/org/mastodon/mamut/MainWindow.java

@@ -52,6 +52,8 @@
 import javax.swing.AbstractAction;
 import javax.swing.Action;
 import javax.swing.ActionMap;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
 import javax.swing.ImageIcon;
 import javax.swing.JButton;
 import javax.swing.JComponent;
@@ -105,12 +107,27 @@ public MainWindow( final ProjectModel appModel )
 		// Re-register save actions, this time using this frame as parent
 		// component.
 		ProjectActions.installAppActions( appModel.getProjectActions(), appModel, this );
+		final ActionMap projectActionMap = appModel.getProjectActions().getActionMap();
 
-		// Views:
+		// Main Panel
 		final JPanel buttonsPanel = new JPanel();
-		buttonsPanel.setLayout( new MigLayout() );
-		final ActionMap projectActionMap = appModel.getProjectActions().getActionMap();
+		buttonsPanel.setLayout( new MigLayout( "wrap 2", "[150px!]10[150px!]" ) );
+
+		// Project:
+		final JPanel titlePanel = new JPanel();
+		final BoxLayout boxLayout = new BoxLayout( titlePanel, BoxLayout.LINE_AXIS );
+		titlePanel.setLayout( boxLayout );
+		titlePanel.setOpaque( false );
+		final JLabel projectLabel = new JLabel( "Project: " );
+		projectLabel.setFont( buttonsPanel.getFont().deriveFont( Font.BOLD ) );
+		final JLabel projectNameLabel = new JLabel( appModel.getProjectName() );
+		titlePanel.add( projectLabel );
+		titlePanel.add( Box.createHorizontalGlue() );
+		titlePanel.add( projectNameLabel );
+		buttonsPanel.add( titlePanel, "span 2, grow, wrap, align left" );
+		buttonsPanel.add( new JSeparator(), "span, grow, wrap" );
 
+		// Views:
 		final JLabel viewsLabel = new JLabel( "Views:" );
 		viewsLabel.setFont( buttonsPanel.getFont().deriveFont( Font.BOLD ) );
 		buttonsPanel.add( viewsLabel, "span, wrap" );
@@ -182,7 +199,9 @@ public MainWindow( final ProjectModel appModel )
 			public void paintComponent( final Graphics g )
 			{
 				super.paintComponent( g );
-				g.drawImage( MAINWINDOW_BG, 0, 0, this );
+				final int x = getWidth() - MAINWINDOW_BG.getWidth( null );
+                final int y = 0;
+				g.drawImage( MAINWINDOW_BG, x, y, this );
 			}
 		};
 		setContentPane( content );

src/main/java/org/mastodon/mamut/launcher/LauncherGUI.java

@@ -275,7 +275,7 @@ public void insertString( final FilterBypass fb, final int offset, final String
 			final StringBuilder modifiedText = new StringBuilder();
 			for ( final char c : string.toCharArray() )
 			{
-				if ( c == '/' )
+				if ( c == '/' || c == '\\' )
 				{
 					modifiedText.append( c ).append( ' ' );
 				}
@@ -385,7 +385,8 @@ public void mouseClicked( final java.awt.event.MouseEvent e )
 		public void paintComponent( final Graphics g )
 		{
 			super.paintComponent( g );
-			g.drawImage( MAINWINDOW_BG, 0, 0, this );
+			final int x = getWidth() - MAINWINDOW_BG.getWidth( null );
+			g.drawImage( MAINWINDOW_BG, x, 0, this );
 		}
 	}
 

src/main/java/org/mastodon/mamut/launcher/RecentProjectsPanel.java

@@ -28,8 +28,10 @@
  */
 package org.mastodon.mamut.launcher;
 
-import java.awt.Font;
 import java.awt.Desktop;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.io.IOException;
@@ -41,11 +43,11 @@
 import javax.swing.JButton;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
+import javax.swing.JScrollPane;
 import javax.swing.JSeparator;
 import javax.swing.JTextArea;
 import javax.swing.ScrollPaneConstants;
 import javax.swing.SwingConstants;
-import javax.swing.JScrollPane;
 
 import org.mastodon.app.MastodonIcons;
 import org.mastodon.ui.util.RecentProjects;
@@ -61,7 +63,7 @@ public class RecentProjectsPanel extends JPanel
 
 	public RecentProjectsPanel( final Consumer< String > projectOpener )
 	{
-		setLayout( new MigLayout( "fill, wrap 3", "[grow, fill][shrink 0][shrink 0]", "[][grow, fill][]" ) );
+		setLayout( new MigLayout( "fill", "[grow]", "[]10[grow]10[]10[]" ) );
 		remakeGUI( projectOpener );
 	}
 
@@ -71,63 +73,84 @@ private void remakeGUI( final Consumer< String > projectOpener )
 
 		final JLabel lblTitle = new JLabel( "Recent projects" );
 		lblTitle.setFont( lblTitle.getFont().deriveFont( lblTitle.getFont().getStyle() | Font.BOLD ) );
-		lblTitle.setHorizontalAlignment( SwingConstants.CENTER );
-		add( lblTitle, "span, wrap" );
-
-		final JPanel listPanel = new JPanel( new MigLayout( "fillx, wrap 3", "[fill][shrink 0][shrink 0]", "" ) );
-		final JScrollPane scrollPane = new JScrollPane( listPanel );
-		scrollPane.setVerticalScrollBarPolicy( ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED );
-		scrollPane.setHorizontalScrollBarPolicy( ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER );
-		add( scrollPane, "span, wrap" );
+		add( lblTitle, "align center, wrap" );
 
+		final JPanel listPanel;
 		if ( !recentProjects.isempty() )
 		{
+			listPanel = new JPanel( new MigLayout( "fillx", "[grow]", "[]10[]" ) );
 			final JLabel lblTitleHint = new JLabel( "Double-click to open the containing folder." );
 			lblTitleHint.setFont( lblTitleHint.getFont().deriveFont( lblTitleHint.getFont().getStyle() | Font.ITALIC ) );
-			lblTitleHint.setHorizontalAlignment( SwingConstants.CENTER );
-			listPanel.add( lblTitleHint, "span, wrap" );
+			listPanel.add( lblTitleHint, "align center, wrap" );
 
+			// list of recent projects
 			for ( final String projectPath : recentProjects )
 			{
-				final JTextArea ta = new JTextArea( projectPath );
-				ta.setEditable( true );
-				ta.setLineWrap( true );
-				ta.addMouseListener( new MouseDblClickOpenPath( ta.getText() ) );
-				listPanel.add( ta );
-
-				final JButton btnOpen = new JButton( MastodonIcons.LOAD_ICON_SMALL );
-				btnOpen.addActionListener( l -> projectOpener.accept( ta.getText() ) ); // Recent projects will be updated in the launcher method.
-				listPanel.add( btnOpen );
-
-				final JButton btnClear = new JButton( MastodonIcons.REMOVE_ICON );
-				btnClear.addActionListener( l -> {
-					recentProjects.remove( projectPath );
-					remakeGUI( projectOpener );
-				} );
-				listPanel.add( btnClear, "wrap" );
+				final ListItem listItem = new ListItem( projectPath, projectOpener );
+				listPanel.add( listItem, "grow, wrap" );
 			}
 		}
 		else
 		{
+			// No recent projects.
+			listPanel = new JPanel( new GridBagLayout() );
 			final JLabel lblNo = new JLabel( "No recent projects." );
 			lblNo.setFont( getFont().deriveFont( getFont().getStyle() | Font.ITALIC ) );
-			lblNo.setHorizontalAlignment( SwingConstants.CENTER );
-			listPanel.add( lblNo, "span, wrap" );
+			listPanel.add( lblNo, new GridBagConstraints() );
 		}
 
-		add( new JSeparator(), "span, wrap" );
+		final JScrollPane scrollPane = new JScrollPane( listPanel );
+		scrollPane.setVerticalScrollBarPolicy( ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED );
+		scrollPane.setHorizontalScrollBarPolicy( ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER );
+		add( scrollPane, "grow, wrap" );
+
+		add( new JSeparator(), "span" );
+		add( getBottomPanel( projectOpener ), "right" );
+
+		revalidate();
+		repaint();
+	}
+
+	private class ListItem extends JPanel
+	{
+		private static final long serialVersionUID = 1L;
+
+		private ListItem( final String path, final Consumer< String > projectOpener )
+		{
+			super( new MigLayout( "fill, ins 0, gapy 0", "[fill][][]", "" ) );
+
+			final JTextArea ta = new JTextArea( path );
+			ta.setEditable( true );
+			ta.setLineWrap( true );
+			ta.addMouseListener( new MouseDblClickOpenPath( ta.getText() ) );
+			add( ta, "pushx, w 0:5" );
+
+			final JButton btnOpen = new JButton( MastodonIcons.LOAD_ICON_SMALL );
+			btnOpen.addActionListener( l -> projectOpener.accept( ta.getText() ) ); // Recent projects will be updated in the launcher method.
+			add( btnOpen, "" );
+
+			final JButton btnClear = new JButton( MastodonIcons.BIN_ICON );
+			btnClear.addActionListener( l -> {
+				recentProjects.remove( path );
+				remakeGUI( projectOpener );
+			} );
+			add( btnClear, "wrap" );
+		}
+	}
+
+	private static JPanel getBottomPanel( final Consumer< String > projectOpener )
+	{
+		final JPanel bottomPanel = new JPanel( new MigLayout( "", "[][]", "" ) );
 
 		final JLabel lblTitle2 = new JLabel( "Open another project" );
 		lblTitle2.setHorizontalAlignment( SwingConstants.CENTER );
 		lblTitle2.setFont( lblTitle2.getFont().deriveFont( lblTitle2.getFont().getStyle() | Font.BOLD ) );
-		add( lblTitle2 );
+		bottomPanel.add( lblTitle2, "" );
 
 		final JButton btnBrowse = new JButton( MastodonIcons.LOAD_ICON_SMALL );
 		btnBrowse.addActionListener( l -> projectOpener.accept( null ) );
-		add( btnBrowse );
-
-		revalidate();
-		repaint();
+		bottomPanel.add( btnBrowse, "" );
+		return bottomPanel;
 	}
 
 	public static final class MouseDblClickOpenPath implements MouseListener
@@ -140,26 +163,26 @@ public MouseDblClickOpenPath( final String pathOnDblClick )
 		}
 
 		@Override
-		public void mouseClicked( MouseEvent mouseEvent )
+		public void mouseClicked( final MouseEvent mouseEvent )
 		{
 			if ( mouseEvent.getClickCount() == 2 )
 				openUrl( Uri );
 		}
 
 		@Override
-		public void mousePressed( MouseEvent mouseEvent )
+		public void mousePressed( final MouseEvent mouseEvent )
 		{ /* empty */ }
 
 		@Override
-		public void mouseReleased( MouseEvent mouseEvent )
+		public void mouseReleased( final MouseEvent mouseEvent )
 		{ /* empty */ }
 
 		@Override
-		public void mouseEntered( MouseEvent mouseEvent )
+		public void mouseEntered( final MouseEvent mouseEvent )
 		{ /* empty */ }
 
 		@Override
-		public void mouseExited( MouseEvent mouseEvent )
+		public void mouseExited( final MouseEvent mouseEvent )
 		{ /* empty */ }
 	}
 

src/main/java/org/mastodon/mamut/views/MamutBranchView.java

@@ -157,12 +157,6 @@ public MamutBranchView( final ProjectModel appModel, final VG viewGraph, final S
 		final ModelBranchGraph branchGraph = appModel.getModel().getBranchGraph();
 		final ModelGraph graph = appModel.getModel().getGraph();
 
-		// Highlight.
-		final HighlightModel< Spot, Link > graphHighlightModel = appModel.getHighlightModel();
-		final HighlightModel< BranchSpot, BranchLink > branchHighlightModel =
-				new BranchGraphHighlightAdapter<>( branchGraph, graph, graph.getGraphIdBimap(), graphHighlightModel );
-		this.highlightModel = new HighlightModelAdapter<>( branchHighlightModel, vertexMap, edgeMap );
-
 		// Focus
 		final FocusModel< Spot > graphFocusModel = appModel.getFocusModel();
 		final FocusModel< BranchSpot > branchFocusfocusModel =
@@ -185,6 +179,12 @@ public MamutBranchView( final ProjectModel appModel, final VG viewGraph, final S
 		// Time-point.
 		this.timepointModel = new TimepointModelAdapter( groupHandle.getModel( appModel.TIMEPOINT ) );
 
+		// Highlight.
+		final HighlightModel< Spot, Link > graphHighlightModel = appModel.getHighlightModel();
+		final HighlightModel< BranchSpot, BranchLink > branchHighlightModel =
+				new BranchGraphHighlightAdapter<>( branchGraph, graph, graph.getGraphIdBimap(), graphHighlightModel, timepointModel );
+		this.highlightModel = new HighlightModelAdapter<>( branchHighlightModel, vertexMap, edgeMap );
+
 		// Tag-set.
 		this.tagSetModel = branchTagSetModel( appModel );
 

src/main/java/org/mastodon/mamut/views/grapher/GrapherInitializer.java

@@ -129,7 +129,7 @@ public class GrapherInitializer< V extends Vertex< E > & HasTimepoint & HasLabel
 	GrapherInitializer( final DataGraph< V, E > graph, final ProjectModel appModel,
 			final SelectionModel< DataVertex, DataEdge > selectionModel, final NavigationHandler< DataVertex, DataEdge > navigationHandler,
 			final FocusModel< DataVertex > focusModel, final HighlightModel< DataVertex, DataEdge > highlightModel,
-			final GroupHandle groupHandle
+			final GroupHandle groupHandle, final DataContextListener< V > contextListener
 	)
 	{
 		this.viewGraph = graph;
@@ -143,8 +143,7 @@ public class GrapherInitializer< V extends Vertex< E > & HasTimepoint & HasLabel
 		layout = new DataGraphLayout<>( viewGraph, selectionModel );
 
 		// ContextChooser
-		final DataContextListener< V > contextListener = new DataContextListener<>( viewGraph );
-		contextChooser = new ContextChooser<>( contextListener );
+		this.contextChooser = contextListener == null ? null : new ContextChooser<>( contextListener );
 
 		// Style
 		final DataDisplayStyleManager dataDisplayStyleManager = appModel.getWindowManager().getManager( DataDisplayStyleManager.class );
@@ -178,7 +177,8 @@ public class GrapherInitializer< V extends Vertex< E > & HasTimepoint & HasLabel
 
 		// Panel
 		this.panel = frame.getDataDisplayPanel();
-		contextListener.setContextListener( panel );
+		if ( contextListener != null )
+			contextListener.setContextListener( panel );
 
 		// Style listener
 		styleUpdateListener = panel::repaint;

src/main/java/org/mastodon/mamut/views/grapher/MamutBranchViewGrapher.java

@@ -43,8 +43,6 @@
 import org.mastodon.ui.coloring.HasColorBarOverlay;
 import org.mastodon.ui.coloring.HasColoringModel;
 import org.mastodon.ui.keymap.KeyConfigContexts;
-import org.mastodon.views.context.ContextChooser;
-import org.mastodon.views.context.HasContextChooser;
 import org.mastodon.views.grapher.datagraph.DataEdge;
 import org.mastodon.views.grapher.datagraph.DataGraph;
 import org.mastodon.views.grapher.datagraph.DataVertex;
@@ -59,7 +57,7 @@
 import java.util.function.BiConsumer;
 
 public class MamutBranchViewGrapher extends MamutBranchView< DataGraph< BranchSpot, BranchLink >, DataVertex, DataEdge >
-		implements HasContextChooser< BranchSpot >, HasColoringModel, HasColorBarOverlay, DataDisplayFrameSupplier< BranchSpot, BranchLink >
+		implements HasColoringModel, HasColorBarOverlay, DataDisplayFrameSupplier< BranchSpot, BranchLink >
 {
 
 	private final GrapherInitializer< BranchSpot, BranchLink > grapherInitializer;
@@ -74,7 +72,7 @@ public class MamutBranchViewGrapher extends MamutBranchView< DataGraph< BranchSp
 				new String[] { KeyConfigContexts.GRAPHER } );
 
 		grapherInitializer = new GrapherInitializer<>( viewGraph, appModel, selectionModel, navigationHandler, focusModel, highlightModel,
-				getGroupHandle() );
+				getGroupHandle(), null );
 		grapherInitializer.getFrame().setTitle( "Grapher Branch" );
 		InertialScreenTransformEventHandler handler = grapherInitializer.getFrame().getDataDisplayPanel().getTransformEventHandler();
 		handler.setMinScaleX( 0.1d );
@@ -119,12 +117,6 @@ public DataDisplayFrame< BranchSpot, BranchLink > getFrame()
 		return ( DataDisplayFrame< BranchSpot, BranchLink > ) super.getFrame();
 	}
 
-	@Override
-	public ContextChooser< BranchSpot > getContextChooser()
-	{
-		return grapherInitializer.getContextChooser();
-	}
-
 	@Override
 	public ColoringModel getColoringModel()
 	{