Merge pull request #335 from mastodon-sc/dev

Release the beta-31 of Mastodon

.github/build.sh

@@ -1,3 +1,5 @@
 #!/bin/sh
+export DISPLAY=:99
+sudo Xvfb -ac :99 -screen 0 1280x1024x24 > /dev/null 2>&1 &
 curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-build.sh
 sh ci-build.sh

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>37.0.0</version>
+		<version>38.0.1</version>
 	</parent>
 
 	<groupId>org.mastodon</groupId>
@@ -63,7 +63,7 @@
 			<groupId>cisd</groupId>
 			<artifactId>jhdf5</artifactId>
 		</dependency>
-		
+
 		<!-- ImgLib2 dependencies -->
 		<dependency>
 			<groupId>org.scijava</groupId>
@@ -77,7 +77,33 @@
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-roi</artifactId>
 		</dependency>
-
+
+		<!-- N5 dependencies. -->
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-universe</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-google-cloud</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-aws-s3</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-viewer_fiji</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-ij</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-zarr</artifactId>
+		</dependency>
+
 		<!-- Misc dependencies. -->
 		<dependency>
 			<groupId>com.opencsv</groupId>
@@ -86,14 +112,25 @@
 		<dependency>
 			<groupId>io.humble</groupId>
 			<artifactId>humble-video-all</artifactId>
-		</dependency>		
+		</dependency>
+		<!-- export of panels to svg -->
+		<dependency>
+			<groupId>org.jfree</groupId>
+			<artifactId>jfreesvg</artifactId>
+		</dependency>
 
 		<!-- Test dependencies -->
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>uk.org.webcompere</groupId>
+			<artifactId>system-stubs-junit4</artifactId>
+			<version>2.1.3</version>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>sc.fiji</groupId>
 			<artifactId>TrackMate</artifactId>
@@ -104,7 +141,6 @@
 			<artifactId>MaMuT</artifactId>
 			<scope>test</scope>
 		</dependency>
-
 
 	</dependencies>
 
@@ -116,7 +152,7 @@
 					<artifactId>maven-surefire-plugin</artifactId>
 					<version>2.5</version>
 					<configuration>
-						<argLine>-Xms256m -Xmx1024m</argLine>
+						<argLine>-Xms256m -Xmx1536m</argLine>
 					</configuration>
 				</plugin>
 			</plugins>
@@ -202,6 +238,13 @@
 			<url>https://github.com/xulman</url>
 			<properties><id>xulman</id></properties>
 		</contributor>
+		<contributor>
+			<name>Stefan Hahmann</name>
+			<url>https://github.com/stefanhahmann</url>
+			<properties>
+				<id>stefanhahmann</id>
+			</properties>
+		</contributor>
 	</contributors>
 
 	<repositories>

src/main/java/org/mastodon/adapter/SelectionModelAdapter.java

@@ -162,4 +162,10 @@ public void pauseListeners()
 	{
 		selection.pauseListeners();
 	}
+
+	@Override
+	public boolean areListenersPaused()
+	{
+		return selection.areListenersPaused();
+	}
 }

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

@@ -203,6 +203,9 @@ public class MastodonIcons
 	public static final List< Image > BDV_VIEW_ICON = Arrays
 			.asList( new Image[] { BDV_ICON_SMALL.getImage(), BDV_ICON_MEDIUM.getImage(), BDV_ICON_LARGE.getImage() } );
 
+	public static final List< Image > BVV_VIEW_ICON = Arrays
+			.asList( new Image[] { BVV_ICON_SMALL.getImage(), BVV_ICON_MEDIUM.getImage(), BVV_ICON_LARGE.getImage() } );
+
 	public static final List< Image > TRACKSCHEME_VIEW_ICON =
 			Arrays.asList( new Image[] { TRACKSCHEME_ICON_SMALL.getImage(), TRACKSCHEME_ICON_MEDIUM.getImage(),
 					TRACKSCHEME_ICON_LARGE.getImage() } );

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

@@ -38,6 +38,7 @@
 import static org.mastodon.app.MastodonIcons.TAGS_ICON_MEDIUM;
 import static org.mastodon.app.MastodonIcons.TRACKSCHEME_ICON_MEDIUM;
 import static org.mastodon.app.ui.ViewMenuBuilder.item;
+import static org.mastodon.app.ui.ViewMenuBuilder.menu;
 import static org.mastodon.app.ui.ViewMenuBuilder.separator;
 import static org.mastodon.mamut.MamutMenuBuilder.fileMenu;
 
@@ -61,6 +62,7 @@
 import javax.swing.JPanel;
 import javax.swing.JSeparator;
 import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
 import javax.swing.WindowConstants;
 
 import org.mastodon.app.MastodonIcons;
@@ -73,8 +75,11 @@
 import org.mastodon.mamut.views.table.MamutViewTableFactory;
 import org.mastodon.mamut.views.trackscheme.MamutBranchViewTrackSchemeFactory;
 import org.mastodon.mamut.views.trackscheme.MamutViewTrackSchemeFactory;
+import org.mastodon.ui.commandfinder.CommandFinder;
 import org.mastodon.ui.keymap.KeyConfigContexts;
 import org.mastodon.util.RunnableActionPair;
+import org.scijava.ui.behaviour.util.Actions;
+import org.scijava.ui.behaviour.util.InputActionBindings;
 
 import bdv.ui.keymap.Keymap;
 import net.miginfocom.swing.MigLayout;
@@ -97,7 +102,8 @@ public MainWindow( final ProjectModel appModel )
 		setLocationByPlatform( true );
 		setLocationRelativeTo( null );
 
-		// Re-register save actions, this time using this frame as parent component.
+		// Re-register save actions, this time using this frame as parent
+		// component.
 		ProjectActions.installAppActions( appModel.getProjectActions(), appModel, this );
 
 		// Views:
@@ -113,7 +119,7 @@ public MainWindow( final ProjectModel appModel )
 		prepareButton( tableButton, "table", TABLE_ICON_MEDIUM );
 		buttonsPanel.add( tableButton, "grow" );
 
-		final JButton bdvButton = new JButton( new RunnableActionPair( MamutViewBdvFactory.NEW_BDV_VIEW, 
+		final JButton bdvButton = new JButton( new RunnableActionPair( MamutViewBdvFactory.NEW_BDV_VIEW,
 				() -> projectActionMap.get( MamutViewBdvFactory.NEW_BDV_VIEW ).actionPerformed( null ),
 				() -> projectActionMap.get( MamutBranchViewBdvFactory.NEW_BRANCH_BDV_VIEW ).actionPerformed( null ) ) );
 		prepareButton( bdvButton, "bdv", BDV_ICON_MEDIUM );
@@ -123,9 +129,9 @@ public MainWindow( final ProjectModel appModel )
 		prepareButton( selectionTableButton, "selection table", TABLE_ICON_MEDIUM );
 		buttonsPanel.add( selectionTableButton, "grow" );
 
-		final JButton trackschemeButton = new JButton( new RunnableActionPair( MamutViewTrackSchemeFactory.NEW_TRACKSCHEME_VIEW, 
-						() -> projectActionMap.get( MamutViewTrackSchemeFactory.NEW_TRACKSCHEME_VIEW ).actionPerformed( null ),
-						() -> projectActionMap.get( MamutBranchViewTrackSchemeFactory.NEW_BRANCH_TRACKSCHEME_VIEW ).actionPerformed( null ) ) );
+		final JButton trackschemeButton = new JButton( new RunnableActionPair( MamutViewTrackSchemeFactory.NEW_TRACKSCHEME_VIEW,
+				() -> projectActionMap.get( MamutViewTrackSchemeFactory.NEW_TRACKSCHEME_VIEW ).actionPerformed( null ),
+				() -> projectActionMap.get( MamutBranchViewTrackSchemeFactory.NEW_BRANCH_TRACKSCHEME_VIEW ).actionPerformed( null ) ) );
 		prepareButton( trackschemeButton, "trackscheme", TRACKSCHEME_ICON_MEDIUM );
 		buttonsPanel.add( trackschemeButton, "grow, wrap" );
 
@@ -209,6 +215,25 @@ public void windowClosing( final WindowEvent e )
 
 		// Register to when the project model is closed.
 		appModel.projectClosedListeners().add( () -> dispose() );
+
+		// Command finder.
+		final InputActionBindings keybindings = new InputActionBindings();
+		SwingUtilities.replaceUIActionMap( content, keybindings.getConcatenatedActionMap() );
+		SwingUtilities.replaceUIInputMap( content, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT,
+				keybindings.getConcatenatedInputMap() );
+		final Actions mwActions = new Actions( keymap.getConfig(), KeyConfigContexts.MASTODON );
+		mwActions.install( keybindings, "main" );
+		CommandFinder.build()
+				.context( appModel.getContext() )
+				.inputTriggerConfig( appModel.getKeymap().getConfig() )
+				.descriptionProvider( appModel.getWindowManager().getViewFactories().getCommandDescriptions() )
+				.keyConfigContext( KeyConfigContexts.MASTODON )
+				.register( appModel.getModelActions() )
+				.register( appModel.getProjectActions() )
+				.register( appModel.getPlugins().getPluginActions() )
+				.modificationListeners( appModel.getKeymap().updateListeners() )
+				.parent( this )
+				.installOn( mwActions );
 	}
 
 	/**
@@ -320,11 +345,16 @@ public static void addMenus( final ViewMenu menu, final ActionMap actionMap )
 						item( ProjectActions.SAVE_PROJECT ),
 						item( ProjectActions.SAVE_PROJECT_AS ),
 						separator(),
+						menu( "Import" ),
+						menu( "Export" ),
+						separator(),
+						item( ProjectActions.FIX_DATASET_PATH ),
+						separator(),
 						// item( ProjectActions.IMPORT_TGMM ),
 						// item( ProjectActions.IMPORT_SIMI ),
 						// item( ProjectActions.IMPORT_MAMUT ),
 						// item( ProjectActions.EXPORT_MAMUT ),
-						//						separator(),
+						// separator(),
 						item( WindowManager.PREFERENCES_DIALOG ),
 						separator(),
 						item( WindowManager.OPEN_ONLINE_DOCUMENTATION ) ) );

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

@@ -59,6 +59,7 @@ public class MamutMenuBuilder extends ViewMenuBuilder
 		menuTexts.put( ProjectActions.LOAD_PROJECT, "Load Project" );
 		menuTexts.put( ProjectActions.SAVE_PROJECT, "Save Project" );
 		menuTexts.put( ProjectActions.SAVE_PROJECT_AS, "Save Project As..." );
+		menuTexts.put( ProjectActions.FIX_DATASET_PATH, "Fix Image Path" );
 		menuTexts.put( ProjectActions.IMPORT_TGMM, "Import TGMM tracks" );
 		menuTexts.put( ProjectActions.IMPORT_SIMI, "Import Simi BioCell tracks" );
 		menuTexts.put( ProjectActions.IMPORT_MAMUT, "Import MaMuT project" );

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

@@ -102,7 +102,7 @@ public < T extends MamutViewI > MamutViewFactory< T > getFactory( final Class< T
 		return ( MamutViewFactory< T > ) factories.get( klass );
 	}
 
-	CommandDescriptionProvider getCommandDescriptions()
+	public CommandDescriptionProvider getCommandDescriptions()
 	{
 		return new CommandDescriptionProvider( KeyConfigScopes.MAMUT, KeyConfigContexts.MASTODON )
 		{