Add StatusService to provide progress updates in LinkPrediction, RegionPropsComputation, and TrackastraLinker.

Author: Stefan Hahmann

src/main/java/org/mastodon/mamut/linking/trackastra/TrackastraLinker.java

@@ -46,12 +46,15 @@ public class TrackastraLinker< V extends Vertex< E > & HasTimepoint & RealLocali
 	public void mutate1( final ReadOnlyGraph< V, E > graph, final SpatioTemporalIndex< V > index )
 	{
 		long start = System.currentTimeMillis();
+		statusService.clearStatus();
+		statusService.showStatus( "Trackastra linking." );
 		try
 		{
 			List< SingleTimepointRegionProps > regionProps = computeRegionProps( index );
 			if ( !isCanceled() )
 				runLinkPrediction( index, regionProps );
 			ok = true;
+			statusService.clearStatus();
 		}
 		catch ( TrackastraLinkingException e )
 		{
@@ -87,7 +90,7 @@ private List< SingleTimepointRegionProps > computeRegionProps( final SpatioTempo
 			throw new IllegalArgumentException(
 					String.format( "Window size (%d) exceeds time range (%d). Adjust window size or time range.", windowSize, timeRange ) );
 
-		try (RegionPropsComputation computation = new RegionPropsComputation( logger, model, this ))
+		try (RegionPropsComputation computation = new RegionPropsComputation( logger, model, this, this.statusService ))
 		{
 			return computation.computeRegionPropsForSource( source, level, Cast.unchecked( index ), minTimepoint, maxTimepoint );
 		}
@@ -103,7 +106,8 @@ private void runLinkPrediction( final SpatioTemporalIndex< V > index, final List
 		log.info( "Performing Trackastra link prediction" );
 		try (RegionProps props = new RegionProps( regionProps );
 				LinkPrediction prediction =
-						new LinkPrediction( settings, Cast.unchecked( index ), Cast.unchecked( edgeCreator ), props, logger, this ))
+						new LinkPrediction( settings, Cast.unchecked( index ), Cast.unchecked( edgeCreator ), props, logger, this,
+								statusService ))
 		{
 			prediction.predictAndCreateLinks();
 		}

src/main/java/org/mastodon/mamut/linking/trackastra/appose/computation/LinkPrediction.java

@@ -34,6 +34,7 @@
 import org.mastodon.spatial.SpatioTemporalIndex;
 import org.mastodon.tracking.linking.EdgeCreator;
 import org.scijava.Cancelable;
+import org.scijava.app.StatusService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -52,9 +53,11 @@ public class LinkPrediction extends ApposeProcess
 
 	private final Cancelable cancelable;
 
+	private final StatusService statusService;
+
 	public LinkPrediction( final Map< String, Object > settings, final SpatioTemporalIndex< Spot > index,
 			final EdgeCreator< Spot > edgeCreator, final RegionProps regionProps, final org.scijava.log.Logger uiLogger,
-			final Cancelable cancelable
+			final Cancelable cancelable, final StatusService statusService
 	) throws IOException
 	{
 		super();
@@ -64,6 +67,7 @@ public LinkPrediction( final Map< String, Object > settings, final SpatioTempora
 		this.regionProps = regionProps;
 		this.uiLogger = uiLogger;
 		this.cancelable = cancelable;
+		this.statusService = statusService;
 	}
 
 	public void predictAndCreateLinks() throws IOException
@@ -90,7 +94,10 @@ public void predictAndCreateLinks() throws IOException
 				uiLogger.info( "Link prediction canceled by user.\n" );
 				return;
 			}
+			uiLogger.info( "Link prediction finished. Now writing edges.\n" );
+			statusService.showProgress( 9, 10 ); // 90% after prediction
 			writeEdges( result );
+			statusService.showProgress( 1, 1 ); // 100% after writing edges
 		}
 		finally
 		{

src/main/java/org/mastodon/mamut/linking/trackastra/appose/computation/RegionPropsComputation.java

@@ -38,6 +38,7 @@
 import org.mastodon.mamut.util.ResourceUtils;
 import org.mastodon.spatial.SpatioTemporalIndex;
 import org.scijava.Cancelable;
+import org.scijava.app.StatusService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -53,13 +54,17 @@ public class RegionPropsComputation extends ApposeProcess
 
 	private final Cancelable cancelable;
 
-	public RegionPropsComputation( final org.scijava.log.Logger uiLogger, final String model, final Cancelable cancelable )
+	private final StatusService statusService;
+
+	public RegionPropsComputation( final org.scijava.log.Logger uiLogger, final String model, final Cancelable cancelable,
+			final StatusService statusService )
 			throws IOException
 	{
 		super();
 		this.uiLogger = uiLogger;
 		this.model = model;
 		this.cancelable = cancelable;
+		this.statusService = statusService;
 	}
 
 	public List< SingleTimepointRegionProps > computeRegionPropsForSource( final Source< ? > source, final int level,
@@ -146,6 +151,7 @@ private SingleTimepointRegionProps computeSingleTimepointProps( final Source< ?
 	private void formatProgress( final int done, final int todo )
 	{
 		double progress = ( double ) done / todo;
+		statusService.showProgress( ( int ) ( 0.75d * done ), todo ); // reserve 25% for link prediction
 		NumberFormat percentFormatter = NumberFormat.getPercentInstance();
 		percentFormatter.setMinimumFractionDigits( 0 );
 		percentFormatter.setMaximumFractionDigits( 0 );