Draft PR that targets the work done towards TrackMate v9

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>TrackMate</artifactId>
-	<version>8.0.0-SNAPSHOT</version>
+	<version>9.0.0-SNAPSHOT</version>
 
 	<name>TrackMate</name>
 	<description>TrackMate plugin for Fiji.</description>
@@ -134,6 +134,7 @@
 	</ciManagement>
 
 	<properties>
+        <enforcer.skip>true</enforcer.skip>
 		<package-name>fiji.plugin.trackmate</package-name>
 		<license.licenseName>gpl_v3</license.licenseName>
 		<license.copyrightOwners>TrackMate developers.</license.copyrightOwners>
@@ -158,6 +159,12 @@
 		<dependency>
 			<groupId>sc.fiji</groupId>
 			<artifactId>labkit-ui</artifactId>
+			<exclusions>
+				<exclusion>
+					<groupId>net.imagej</groupId>
+					<artifactId>imagej-legacy</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 
 		<!-- ImageJ dependencies -->
@@ -169,6 +176,37 @@
 			<groupId>net.imagej</groupId>
 			<artifactId>imagej-common</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-mesh</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>imagej-ops</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>bigvolumeviewer</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.jogl</groupId>
+			<artifactId>jogl-all</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.gluegen</groupId>
+			<artifactId>gluegen-rt</artifactId>
+		</dependency>			
+		<dependency>
+			<groupId>org.jogamp.gluegen</groupId>
+			<artifactId>gluegen-rt</artifactId>
+			<classifier>${scijava.natives.classifier.gluegen}</classifier>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.jogl</groupId>
+			<artifactId>jogl-all</artifactId>
+			<classifier>${scijava.natives.classifier.jogl}</classifier>
+		</dependency>
+
 
 		<!-- ImgLib2 dependencies -->
 		<dependency>
@@ -205,8 +243,16 @@
 			<groupId>org.scijava</groupId>
 			<artifactId>scijava-listeners</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>ui-behaviour</artifactId>
+		</dependency>
 
 		<!-- Other dependencies -->
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+		</dependency>		
 		<dependency>
 			<groupId>com.github.vlsi.mxgraph</groupId>
 			<artifactId>jgraphx</artifactId>

src/main/java/fiji/plugin/trackmate/Dimension.java

@@ -31,8 +31,13 @@ public enum Dimension
 	POSITION,
 	VELOCITY,
 	LENGTH,
-	AREA, TIME, ANGLE, RATE, // count per frames
-	ANGLE_RATE, STRING; // for non-numeric features
+	AREA,
+	VOLUME,
+	TIME,
+	ANGLE,
+	RATE, // count per frames
+	ANGLE_RATE,
+	STRING; // for non-numeric features
 
 	/*
 	 * We separated length and position so that x,y,z are plotted on a different

src/main/java/fiji/plugin/trackmate/Model.java

@@ -81,13 +81,13 @@ public class Model
 	 */
 	private int updateLevel = 0;
 
-	private final HashSet< Spot > spotsAdded = new HashSet< >();
+	private final HashSet< Spot > spotsAdded = new HashSet<>();
 
-	private final HashSet< Spot > spotsRemoved = new HashSet< >();
+	private final HashSet< Spot > spotsRemoved = new HashSet<>();
 
-	private final HashSet< Spot > spotsMoved = new HashSet< >();
+	private final HashSet< Spot > spotsMoved = new HashSet<>();
 
-	private final HashSet< Spot > spotsUpdated = new HashSet< >();
+	private final HashSet< Spot > spotsUpdated = new HashSet<>();
 
 	/**
 	 * The event cache. During a transaction, some modifications might trigger
@@ -96,15 +96,15 @@ public class Model
 	 * the event ID in this cache in the meantime. The event cache contains only
 	 * the int IDs of the events listed in {@link ModelChangeEvent}, namely
 	 * <ul>
-	 * <li> {@link ModelChangeEvent#SPOTS_COMPUTED}
-	 * <li> {@link ModelChangeEvent#TRACKS_COMPUTED}
-	 * <li> {@link ModelChangeEvent#TRACKS_VISIBILITY_CHANGED}
+	 * <li>{@link ModelChangeEvent#SPOTS_COMPUTED}
+	 * <li>{@link ModelChangeEvent#TRACKS_COMPUTED}
+	 * <li>{@link ModelChangeEvent#TRACKS_VISIBILITY_CHANGED}
 	 * </ul>
 	 * The {@link ModelChangeEvent#MODEL_MODIFIED} cannot be cached this way,
 	 * for it needs to be configured with modification spot and edge targets, so
 	 * it uses a different system (see {@link #flushUpdate()}).
 	 */
-	private final HashSet< Integer > eventCache = new HashSet< >();
+	private final HashSet< Integer > eventCache = new HashSet<>();
 
 	// OTHERS
 
@@ -120,7 +120,7 @@ public class Model
 	/**
 	 * The list of listeners listening to model content change.
 	 */
-	Set< ModelChangeListener > modelChangeListeners = new LinkedHashSet< >();
+	Set< ModelChangeListener > modelChangeListeners = new LinkedHashSet<>();
 
 	/*
 	 * CONSTRUCTOR
@@ -130,6 +130,7 @@ public Model()
 	{
 		featureModel = createFeatureModel();
 		trackModel = createTrackModel();
+		addModelChangeListener( new SpotMeshSliceCacheInvalidator() );
 	}
 
 	/*
@@ -154,7 +155,7 @@ protected TrackModel createTrackModel()
 	 * <p>
 	 * Subclassers can override this method to have the model work with their
 	 * own subclass of {@link FeatureModel}.
-	 * 
+	 *
 	 * @return a new instance of {@link FeatureModel}.
 	 */
 	protected FeatureModel createFeatureModel()
@@ -321,7 +322,7 @@ public void clearTracks( final boolean doNotify )
 
 	/**
 	 * Returns the {@link TrackModel} that manages the tracks for this model.
-	 * 
+	 *
 	 * @return the track model.
 	 */
 	public TrackModel getTrackModel()
@@ -447,7 +448,7 @@ public void notifyFeaturesComputed()
 	/**
 	 * Set the logger that will receive the messages from the processes
 	 * occurring within this trackmate.
-	 * 
+	 *
 	 * @param logger
 	 *            the {@link Logger} to use.
 	 */
@@ -458,7 +459,7 @@ public void setLogger( final Logger logger )
 
 	/**
 	 * Return the logger currently set for this model.
-	 * 
+	 *
 	 * @return the {@link Logger} used.
 	 */
 	public Logger getLogger()
@@ -544,7 +545,7 @@ public synchronized Spot moveSpotFrom( final Spot spotToMove, final Integer from
 	 * 	model.endUpdate();
 	 * }
 	 * </pre>
-	 * 
+	 *
 	 * @param spotToAdd
 	 *            the spot to add.
 	 * @param toFrame
@@ -593,8 +594,9 @@ public synchronized Spot removeSpot( final Spot spotToRemove )
 			if ( DEBUG )
 				System.out.println( "[TrackMateModel] Removing spot " + spotToRemove + " from frame " + fromFrame );
 
-			trackModel.removeSpot( spotToRemove ); 
-			// changes to edges will be caught automatically by the TrackGraphModel
+			trackModel.removeSpot( spotToRemove );
+			// changes to edges will be caught automatically by the
+			// TrackGraphModel
 			return spotToRemove;
 		}
 		if ( DEBUG )
@@ -626,7 +628,7 @@ public synchronized Spot removeSpot( final Spot spotToRemove )
 	public synchronized void updateFeatures( final Spot spotToUpdate )
 	{
 		spotsUpdated.add( spotToUpdate ); // Enlist for feature update when
-											// transaction is marked as finished
+		// transaction is marked as finished
 		final Set< DefaultWeightedEdge > touchingEdges = trackModel.edgesOf( spotToUpdate );
 		if ( null != touchingEdges )
 		{
@@ -766,7 +768,7 @@ public synchronized boolean setTrackVisibility( final Integer trackID, final boo
 	 * The copy is made of the same spot objects but on a different graph, that
 	 * can be safely edited. The copy does not include the feature values for
 	 * edges and tracks, but the features are declared.
-	 * 
+	 *
 	 * @return a new model.
 	 */
 	public Model copy()
@@ -810,7 +812,7 @@ public Model copy()
 				featureModel.getTrackFeatureShortNames(),
 				featureModel.getTrackFeatureDimensions(),
 				featureModel.getTrackFeatureIsInt() );
-		
+
 		// Feature values are not copied.
 		return copy;
 	}
@@ -841,7 +843,7 @@ private void flushUpdate()
 		final int nEdgesToSignal = trackModel.edgesAdded.size() + trackModel.edgesRemoved.size() + trackModel.edgesModified.size();
 
 		// Do we have tracks to update?
-		final HashSet< Integer > tracksToUpdate = new HashSet< >( trackModel.tracksUpdated );
+		final HashSet< Integer > tracksToUpdate = new HashSet<>( trackModel.tracksUpdated );
 
 		// We also want to update the tracks that have edges that were modified
 		for ( final DefaultWeightedEdge modifiedEdge : trackModel.edgesModified )
@@ -853,7 +855,7 @@ private void flushUpdate()
 		final int nSpotsToUpdate = spotsAdded.size() + spotsMoved.size() + spotsUpdated.size();
 		if ( nSpotsToUpdate > 0 )
 		{
-			final HashSet< Spot > spotsToUpdate = new HashSet< >( nSpotsToUpdate );
+			final HashSet< Spot > spotsToUpdate = new HashSet<>( nSpotsToUpdate );
 			spotsToUpdate.addAll( spotsAdded );
 			spotsToUpdate.addAll( spotsMoved );
 			spotsToUpdate.addAll( spotsUpdated );
@@ -958,4 +960,20 @@ private void flushUpdate()
 		}
 	}
 
+	private static class SpotMeshSliceCacheInvalidator implements ModelChangeListener
+	{
+
+		@Override
+		public void modelChanged( final ModelChangeEvent event )
+		{
+			if ( event.getEventID() != ModelChangeEvent.MODEL_MODIFIED )
+				return;
+
+			event.getSpots()
+					.stream()
+					.filter( s -> event.getSpotFlag( s ) == ModelChangeEvent.FLAG_SPOT_MODIFIED )
+					.filter( s -> ( s instanceof SpotMesh ) )
+					.forEach( s -> ( ( SpotMesh ) s ).resetZSliceCache() );
+		}
+	}
 }

src/main/java/fiji/plugin/trackmate/Settings.java

@@ -35,8 +35,9 @@
 import fiji.plugin.trackmate.features.spot.SpotAnalyzerFactoryBase;
 import fiji.plugin.trackmate.features.track.TrackAnalyzer;
 import fiji.plugin.trackmate.providers.EdgeAnalyzerProvider;
+import fiji.plugin.trackmate.providers.Spot2DMorphologyAnalyzerProvider;
+import fiji.plugin.trackmate.providers.Spot3DMorphologyAnalyzerProvider;
 import fiji.plugin.trackmate.providers.SpotAnalyzerProvider;
-import fiji.plugin.trackmate.providers.SpotMorphologyAnalyzerProvider;
 import fiji.plugin.trackmate.providers.TrackAnalyzerProvider;
 import fiji.plugin.trackmate.tracking.SpotTrackerFactory;
 import ij.ImagePlus;
@@ -270,7 +271,7 @@ public int getYend()
 	 * copied, as well as filters, etc. The exception are analyzers: all the
 	 * analyzers that are found at runtime are added, regardless of the content
 	 * of the instance to copy.
-	 * 
+	 *
 	 * @param newImp
 	 *            the image to copy the settings for.
 	 * @return a new settings object.
@@ -531,24 +532,37 @@ public String getErrorMessage()
 	 */
 	public void addAllAnalyzers()
 	{
+		// Base spot analyzers.
 		final SpotAnalyzerProvider spotAnalyzerProvider = new SpotAnalyzerProvider( imp == null ? 1 : imp.getNChannels() );
 		final List< String > spotAnalyzerKeys = spotAnalyzerProvider.getKeys();
 		for ( final String key : spotAnalyzerKeys )
 			addSpotAnalyzerFactory( spotAnalyzerProvider.getFactory( key ) );
 
+		// Shall we add 2D morphology analyzers?
 		if ( imp != null && DetectionUtils.is2D( imp ) && detectorFactory != null && detectorFactory.has2Dsegmentation() )
 		{
-			final SpotMorphologyAnalyzerProvider spotMorphologyAnalyzerProvider = new SpotMorphologyAnalyzerProvider( imp.getNChannels() );
+			final Spot2DMorphologyAnalyzerProvider spotMorphologyAnalyzerProvider = new Spot2DMorphologyAnalyzerProvider( imp.getNChannels() );
+			final List< String > spotMorphologyAnaylyzerKeys = spotMorphologyAnalyzerProvider.getKeys();
+			for ( final String key : spotMorphologyAnaylyzerKeys )
+				addSpotAnalyzerFactory( spotMorphologyAnalyzerProvider.getFactory( key ) );
+		}
+
+		// Shall we add 3D morphology analyzers?
+		if ( imp != null && !DetectionUtils.is2D( imp ) && detectorFactory != null && detectorFactory.has3Dsegmentation() )
+		{
+			final Spot3DMorphologyAnalyzerProvider spotMorphologyAnalyzerProvider = new Spot3DMorphologyAnalyzerProvider( imp.getNChannels() );
 			final List< String > spotMorphologyAnaylyzerKeys = spotMorphologyAnalyzerProvider.getKeys();
 			for ( final String key : spotMorphologyAnaylyzerKeys )
 				addSpotAnalyzerFactory( spotMorphologyAnalyzerProvider.getFactory( key ) );
 		}
 
+		// Edge analyzers.
 		final EdgeAnalyzerProvider edgeAnalyzerProvider = new EdgeAnalyzerProvider();
 		final List< String > edgeAnalyzerKeys = edgeAnalyzerProvider.getKeys();
 		for ( final String key : edgeAnalyzerKeys )
 			addEdgeAnalyzer( edgeAnalyzerProvider.getFactory( key ) );
 
+		// Track analyzers.
 		final TrackAnalyzerProvider trackAnalyzerProvider = new TrackAnalyzerProvider();
 		final List< String > trackAnalyzerKeys = trackAnalyzerProvider.getKeys();
 		for ( final String key : trackAnalyzerKeys )