Merge pull request #15 from trackmate-sc/rework-serialization

Rework serialization. of parameter sweep.

Author: tinevez

src/main/java/fiji/plugin/trackmate/helper/ctc/CTCMetricsRunner.java

@@ -28,9 +28,6 @@
 import java.nio.file.Paths;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
-import java.util.Optional;
-import java.util.regex.Pattern;
-import java.util.stream.Stream;
 
 import org.scijava.Context;
 
@@ -57,7 +54,7 @@ public class CTCMetricsRunner extends MetricsRunner
 	/**
 	 * Path to ground truth folder.
 	 */
-	private String gtPath;
+	private final String gtPath;
 
 	public CTCMetricsRunner( final String gtPath, final String saveFolder, final Context context )
 	{
@@ -70,42 +67,6 @@ public CTCMetricsRunner( final String gtPath, final String saveFolder, final Con
 	@Override
 	public TrackingMetrics performMetricsMeasurements( final TrackMate trackmate ) throws MetricsComputationErrorException
 	{
-		// Do we have a folder for the ground-truth, or a TrackMate file?
-		if ( gtPath.toLowerCase().endsWith( ".xml" ) )
-		{
-			// Assume it's a TrackMate file, export it to CTC file format.
-			batchLogger.log( "Ground-truth is in the TrackMate file format.\n" );
-
-			final String regexPattern = "\\d{2}_GT";
-			final Pattern pattern = Pattern.compile( regexPattern );
-			try (Stream< Path > paths = Files.list( resultsRootPath ))
-			{
-				final Optional< Path > ctcGTfolder = paths
-						.filter( Files::isDirectory )
-						.filter( path -> pattern.matcher( path.getFileName().toString() ).matches() )
-						.findFirst();
-
-				if ( ctcGTfolder.isPresent() )
-				{
-					batchLogger.log( "Found a GT folder in CTC format: " + ctcGTfolder.get() + "\n" );
-					gtPath = ctcGTfolder.get().toString();
-				}
-				else
-				{
-					batchLogger.log( "Exporting GT file to CTC format.\n" );
-					gtPath = CTCExporter.exportAll( resultsRootPath.toString(), trackmate, ExportType.GOLD_TRUTH, batchLogger );
-					gtPath = Paths.get( gtPath ).getParent().toString();
-				}
-			}
-			catch ( final IOException e )
-			{
-				batchLogger.error( "Error reading the GT parent directory. Stopping."
-						+ "\n" + e.getMessage() );
-				e.printStackTrace();
-				throw new RuntimeException( e );
-			}
-		}
-
 		batchLogger.log( "Exporting test results to CTC format.\n" );
 		final int id = CTCExporter.getAvailableDatasetID( resultsRootPath.toString() );
 		final String resultsFolder = CTCExporter.getExportTrackingDataPath( resultsRootPath.toString(), id, ExportType.RESULTS, trackmate );

src/main/java/fiji/plugin/trackmate/helper/model/AbstractSweepModelBase.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -38,7 +38,7 @@ public interface ModelListener
 		public void modelChanged();
 	}
 
-	private transient Listeners.List< ModelListener > modelListeners;
+	private final transient Listeners.List< ModelListener > modelListeners = new Listeners.SynchronizedList<>();
 
 	protected final String name;
 
@@ -68,16 +68,6 @@ public String getName()
 
 	public final Listeners.List< ModelListener > listeners()
 	{
-		if ( modelListeners == null )
-		{
-			/*
-			 * Work around the listeners field being null after deserialization.
-			 * We also need to register again the sub-models.
-			 */
-			this.modelListeners = new Listeners.SynchronizedList<>();
-			for ( final AbstractParamSweepModel< ? > model : models.values() )
-				model.listeners().add( () -> notifyListeners() );
-		}
 		return modelListeners;
 	}
 

src/main/java/fiji/plugin/trackmate/helper/model/ParameterSweepModel.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -48,7 +48,7 @@
 public class ParameterSweepModel
 {
 
-	private final transient Listeners.List< ModelListener > modelListeners;
+	private final transient Listeners.List< ModelListener > modelListeners = new Listeners.SynchronizedList<>();
 
 	private final Map< String, DetectorSweepModel > detectorModels;
 
@@ -62,8 +62,6 @@ public class ParameterSweepModel
 
 	public ParameterSweepModel()
 	{
-		modelListeners = new Listeners.SynchronizedList<>();
-
 		// Auto-detect detectors & trackers.
 		detectorModels = autoDetect( DetectorSweepModel.class );
 		trackerModels = autoDetect( TrackerSweepModel.class );
@@ -78,18 +76,34 @@ public ParameterSweepModel()
 		this.spotFilterModels = new ArrayList<>();
 		this.trackFilterModels = new ArrayList<>();
 
-		registerListeners();
-	}
-
-	public void registerListeners()
-	{
-		// Forward component changes to listeners.
+		// Register models.
 		detectorModels().forEach( model -> model.listeners().add( () -> notifyListeners() ) );
 		trackerModels().forEach( model -> model.listeners().add( () -> notifyListeners() ) );
 		spotFilterModels().forEach( model -> model.listeners().add( () -> notifyListeners() ) );
 		trackFilterModels().forEach( model -> model.listeners().add( () -> notifyListeners() ) );
 	}
 
+	/**
+	 * This is used <b>only</b> for deserizalisation, to re-register listeners
+	 * in the model components of the main models.
+	 */
+	void reRegisterListeners()
+	{
+		final ModelListener notifier = () -> notifyListeners();
+		reRegisterListeners( detectorModels.values(), notifier );
+		reRegisterListeners( trackerModels.values(), notifier );
+		reRegisterListeners( spotFilterModels, notifier );
+		reRegisterListeners( spotFilterModels, notifier );
+	}
+
+	private void reRegisterListeners( final Collection< ? extends AbstractSweepModelBase > models, final ModelListener notifier )
+	{
+		models.forEach( m -> {
+			m.listeners().add( notifier );
+			m.models.values().forEach( sm -> sm.listeners().add( notifier ) );
+		} );
+	}
+
 	public Collection< DetectorSweepModel > detectorModels()
 	{
 		return detectorModels.values();
@@ -179,7 +193,7 @@ public List< TrackerSweepModel > getActiveTracker()
 	/**
 	 * Returns the count of the different settings that will be generated from
 	 * this model.
-	 * 
+	 *
 	 * @return the count of settings.
 	 */
 	public int count()
@@ -190,7 +204,7 @@ public int count()
 	/**
 	 * Returns the count of the different tracker settings that will be
 	 * generated from this model.
-	 * 
+	 *
 	 * @return the count of settings.
 	 */
 	public int countTrackerSettings()
@@ -213,7 +227,7 @@ public int countTrackerSettings()
 	/**
 	 * Returns the count of the different detector settings that will be
 	 * generated from this model.
-	 * 
+	 *
 	 * @return the count of settings.
 	 */
 	public int countDetectorSettings()
@@ -236,7 +250,7 @@ public int countDetectorSettings()
 	/**
 	 * Returns the count of the different spot filter settings that will be
 	 * generated from this model.
-	 * 
+	 *
 	 * @return the count of settings.
 	 */
 	public int countSpotFilterSettings()
@@ -260,7 +274,7 @@ public int countSpotFilterSettings()
 	/**
 	 * Returns the count of the different track filter settings that will be
 	 * generated from this model.
-	 * 
+	 *
 	 * @return the count of settings.
 	 */
 	public int countTrackFilterSettings()