Merge pull request #11 from trackmate-sc/compute-metrics-plugin

Tool to compute tracking metrics

src/main/java/fiji/plugin/trackmate/helper/HelperRunner.java

@@ -303,7 +303,7 @@ public void run()
 						final double trackingTiming = runner.execTracking( trackmate );
 
 						// Perform and save metrics measurements.
-						runner.performMetricsMeasurements( trackmate, detectionTiming, trackingTiming );
+						runner.performAndSaveMetricsMeasurements( trackmate, detectionTiming, trackingTiming );
 
 						// Save TrackMate file if required.
 						if ( saveTrackMateFiles )
@@ -625,7 +625,7 @@ else if ( typeStr.equals( "SPT" ) )
 							str.append( "Max pairing distance for SPT metrics has not been set.\n" );
 							ok = false;
 						}
-						this.type = new SPTTrackingMetricsType( maxDist );
+						this.type = new SPTTrackingMetricsType( maxDist, "image units" );
 					}
 					else
 					{

src/main/java/fiji/plugin/trackmate/helper/MetricsRunner.java

@@ -75,7 +75,47 @@ public MetricsRunner( final Path resultsRootPath, final TrackingMetricsType type
 		this.nameGenWithID = ( imName, i ) -> String.format( "%s_" + type.csvSuffix() + "_%02d.csv", imName, i );
 	}
 
-	public abstract void performMetricsMeasurements( TrackMate trackmate, double detectionTiming, double trackingTiming );
+	/**
+	 * Performs the tracking metrics measurements for the tracks in the model in
+	 * the specified TrackMate instance, against the ground truth given at
+	 * construction. Metric values are returned as a {@link TrackingMetrics}.
+	 * 
+	 * @param trackmate
+	 *            the tracks on which to measure tracking metrics.
+	 * @return the metric values.
+	 */
+	public abstract TrackingMetrics performMetricsMeasurements( final TrackMate trackmate ) throws MetricsComputationErrorException;
+
+	/**
+	 * Performs the tracking metrics measurements for the tracks in the model in
+	 * the specified TrackMate instance, against the ground truth given at
+	 * construction, and save the results in an adequate CSV file.
+	 * 
+	 * @param trackmate
+	 *            the tracks on which to measure tracking metrics.
+	 * @param detectionTiming
+	 *            the metric measuring the detection time.
+	 * @param trackingTiming
+	 *            the metric measuring the tracking time.
+	 */
+	public void performAndSaveMetricsMeasurements( final TrackMate trackmate, final double detectionTiming, final double trackingTiming )
+	{
+		final Settings settings = trackmate.getSettings();
+		final File csvFile = findSuitableCSVFile( settings );
+		final String[] csvHeader1 = toCSVHeader( settings );
+
+		try
+		{
+			final TrackingMetrics metrics = performMetricsMeasurements( trackmate );
+			batchLogger.log( "SPT metrics:\n" );
+			batchLogger.log( metrics.toString() + '\n' );
+			writeResults( csvFile, metrics, detectionTiming, trackingTiming, settings, csvHeader1 );
+		}
+		catch ( final MetricsComputationErrorException e )
+		{
+			writeFailedResults( csvFile, settings, csvHeader1 );
+		}
+	}
 
 	public ValuePair< TrackMate, Double > execDetection( final Settings settings )
 	{
@@ -154,9 +194,14 @@ public double execTracking( final TrackMate trackmate )
 		return trackingTiming;
 	}
 
-	protected File findSuitableCSVFile( final Settings settings )
+	private File findSuitableCSVFile( final Settings settings )
 	{
-		final String imFileName = settings.imp.getShortTitle();
+		final String imFileName;
+		if ( settings.imp == null )
+			imFileName = "";
+		else
+			imFileName = settings.imp.getShortTitle();
+
 		// Prepare CSV headers.
 		final String[] csvHeader1 = toCSVHeader( settings );
 		final String[] csvHeader = type.concatWithHeader( csvHeader1 );
@@ -220,7 +265,7 @@ protected File findSuitableCSVFile( final Settings settings )
 	 * @param csvHeader
 	 *            the header name for each setting value.
 	 */
-	protected void writeResults(
+	private void writeResults(
 			final File csvFile,
 			final TrackingMetrics metrics,
 			final double detectionTiming, 
@@ -232,8 +277,6 @@ protected void writeResults(
 		metrics.set( TrackingMetricsType.TIM, detectionTiming + trackingTiming );
 		metrics.set( TrackingMetricsType.DETECTION_TIME, detectionTiming );
 		metrics.set( TrackingMetricsType.TRACKING_TIME, trackingTiming );
-		batchLogger.log( "SPT metrics:\n" );
-		batchLogger.log( metrics.toString() + '\n' );
 
 		// Write to CSV.
 		final String[] line1 = toCSVLine( settings, csvHeader );
@@ -267,7 +310,7 @@ protected void writeResults(
 	 * @param csvHeader
 	 *            the header name for each setting value.
 	 */
-	protected void writeFailedResults( final File csvFile, final Settings settings, final String[] csvHeader )
+	private void writeFailedResults( final File csvFile, final Settings settings, final String[] csvHeader )
 	{
 		// Write default values to CSV.
 		final String[] settingsValueColumns = toCSVLine( settings, csvHeader );
@@ -324,7 +367,7 @@ private final File getCSVFile( final String resultsRootPath, final String imageN
 		return csvFilePath.toFile();
 	}
 
-	protected static final String[] toCSVHeader( final Settings settings )
+	private static final String[] toCSVHeader( final Settings settings )
 	{
 		final int nDetectorParams = settings.detectorSettings.size();
 		final int nTrackerParams = settings.trackerSettings.size();
@@ -341,7 +384,7 @@ protected static final String[] toCSVHeader( final Settings settings )
 		return out;
 	}
 
-	protected static final String[] toCSVLine( final Settings settings, final String[] csvHeader )
+	private static final String[] toCSVLine( final Settings settings, final String[] csvHeader )
 	{
 		final int nDetectorParams = settings.detectorSettings.size();
 		final int nTrackerParams = settings.trackerSettings.size();
@@ -363,4 +406,11 @@ protected static final String[] toCSVLine( final Settings settings, final String
 		}
 		return out;
 	}
+
+	public static class MetricsComputationErrorException extends Exception
+	{
+
+		private static final long serialVersionUID = 1L;
+
+	}
 }

src/main/java/fiji/plugin/trackmate/helper/TrackMateComputeMetricsPlugin.java

@@ -0,0 +1,45 @@
+/*-
+ * #%L
+ * TrackMate: your buddy for everyday tracking.
+ * %%
+ * Copyright (C) 2021 - 2024 TrackMate developers.
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * 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>.
+ * #L%
+ */
+package fiji.plugin.trackmate.helper;
+
+import javax.swing.SwingUtilities;
+
+import fiji.plugin.trackmate.helper.ui.MetricsLauncherController;
+import ij.plugin.PlugIn;
+import net.imagej.ImageJ;
+
+public class TrackMateComputeMetricsPlugin implements PlugIn
+{
+
+	@Override
+	public void run( final String arg )
+	{
+		SwingUtilities.invokeLater( () -> new MetricsLauncherController() );
+	}
+
+	public static void main( final String[] args )
+	{
+		final ImageJ ij = new ImageJ();
+		ij.launch( args );
+		new TrackMateComputeMetricsPlugin().run( null );
+	}
+}

src/main/java/fiji/plugin/trackmate/helper/TrackMateParameterSweepPlugin.java

@@ -21,6 +21,8 @@
  */
 package fiji.plugin.trackmate.helper;
 
+import javax.swing.SwingUtilities;
+
 import fiji.plugin.trackmate.helper.ui.HelperLauncherController;
 import ij.plugin.PlugIn;
 
@@ -30,6 +32,6 @@ public class TrackMateParameterSweepPlugin implements PlugIn
 	@Override
 	public void run( final String arg )
 	{
-		new HelperLauncherController();
+		SwingUtilities.invokeLater( () -> new HelperLauncherController() );
 	}
 }

src/main/java/fiji/plugin/trackmate/helper/TrackMateParameterSweepResultsPlugin.java

@@ -89,7 +89,7 @@ public void run( final String arg )
 		else if ( typeStr.equals( "SPT" ) )
 		{
 			// SPT max distance does not matter for inspection.
-			type = new SPTTrackingMetricsType( 1. );
+			type = new SPTTrackingMetricsType( 1., "image units" );
 		}
 		else
 		{

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

@@ -21,7 +21,6 @@
  */
 package fiji.plugin.trackmate.helper.ctc;
 
-import java.io.File;
 import java.io.IOException;
 import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
@@ -32,7 +31,6 @@
 
 import org.scijava.Context;
 
-import fiji.plugin.trackmate.Settings;
 import fiji.plugin.trackmate.TrackMate;
 import fiji.plugin.trackmate.action.CTCExporter;
 import fiji.plugin.trackmate.action.CTCExporter.ExportType;
@@ -67,12 +65,9 @@ public CTCMetricsRunner( final String gtPath, final String saveFolder, final Con
 	}
 
 	@Override
-	public void performMetricsMeasurements( final TrackMate trackmate, final double detectionTiming, final double trackingTiming )
+	public TrackingMetrics performMetricsMeasurements( final TrackMate trackmate ) throws MetricsComputationErrorException
 	{
 		batchLogger.log( "Exporting as CTC results.\n" );
-		final Settings settings = trackmate.getSettings();
-		final File csvFile = findSuitableCSVFile( settings );
-		final String[] csvHeader1 = toCSVHeader( settings );
 
 		final int id = CTCExporter.getAvailableDatasetID( resultsRootPath.toString() );
 		final String resultsFolder = CTCExporter.getExportTrackingDataPath( resultsRootPath.toString(), id, ExportType.RESULTS, trackmate );
@@ -84,13 +79,12 @@ public void performMetricsMeasurements( final TrackMate trackmate, final double
 			// Perform CTC measurements.
 			batchLogger.log( "Performing CTC metrics measurements.\n" );
 			final TrackingMetrics metrics = ctc.process( gtPath, resultsFolder );
-
-			writeResults( csvFile, metrics, detectionTiming, trackingTiming, settings, csvHeader1 );
+			return metrics;
 		}
 		catch ( final IOException | IllegalArgumentException e )
 		{
 			batchLogger.error( "Could not export tracking data to CTC files:\n" + e.getMessage() + '\n' );
-			writeFailedResults( csvFile, settings, csvHeader1 );
+			throw new MetricsComputationErrorException();
 		}
 		finally
 		{

src/main/java/fiji/plugin/trackmate/helper/spt/SPTMetricsRunner.java

@@ -23,16 +23,21 @@
 
 import java.io.File;
 import java.nio.file.Paths;
+import java.util.ArrayList;
 import java.util.List;
 
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
 import fiji.plugin.trackmate.Model;
-import fiji.plugin.trackmate.Settings;
 import fiji.plugin.trackmate.TrackMate;
 import fiji.plugin.trackmate.helper.MetricsRunner;
 import fiji.plugin.trackmate.helper.TrackingMetrics;
 import fiji.plugin.trackmate.helper.spt.importer.SPTFormatImporter;
+import fiji.plugin.trackmate.helper.spt.importer.XMLUtil;
 import fiji.plugin.trackmate.helper.spt.measure.DistanceTypes;
 import fiji.plugin.trackmate.helper.spt.measure.TrackSegment;
+import fiji.plugin.trackmate.io.TmXmlReader;
 
 public class SPTMetricsRunner extends MetricsRunner
 {
@@ -41,32 +46,60 @@ public class SPTMetricsRunner extends MetricsRunner
 
 	private final double maxDist;
 
-	public SPTMetricsRunner( final String gtPath, final String saveFolder, final double maxDist )
+	private final String units;
+
+	public SPTMetricsRunner( final String gtPath, final String saveFolder, final double maxDist, final String units )
 	{
-		super( Paths.get( saveFolder ), new SPTTrackingMetricsType( maxDist ) );
+		super( Paths.get( saveFolder ), new SPTTrackingMetricsType( maxDist, units ) );
 		this.maxDist = maxDist;
-		this.referenceTracks = SPTFormatImporter.fromXML( new File( gtPath ) );
+		this.units = units;
+
+		// Is the GT a TrackMate or a ISBI challenge file?
+		final File gtFile = new File( gtPath );
+		final Document document = XMLUtil.loadDocument( gtFile );
+		final Element root = XMLUtil.getRootElement( document );
+		if ( root == null )
+			throw new IllegalArgumentException( "can't find: <root> tag." );
+
+		final ArrayList< Element > rootEls = XMLUtil.getElements( root, "TrackContestISBI2012" );
+		if ( rootEls.size() == 0 )
+		{
+			// Not an ISBI challenge file.
+			final TmXmlReader reader = new TmXmlReader( gtFile );
+			if ( !reader.isReadingOk() )
+				throw new IllegalArgumentException( "Ground-truth file is neither a TrackMate file nor a ISBI SPT challenge file." );
+
+			final Model model = reader.getModel();
+			try
+			{
+				this.referenceTracks = SPTFormatImporter.fromTrackMate( model );
+			}
+			catch ( final Exception iae )
+			{
+				throw new IllegalArgumentException( "TrackMate ground-truth file cannot be used with SPT metrics:\n" + iae.getMessage() );
+			}
+		}
+		else
+		{
+			// ISBI challenge file.
+			this.referenceTracks = SPTFormatImporter.fromXML( gtFile );
+		}
 	}
 
 	@Override
-	public void performMetricsMeasurements( final TrackMate trackmate, final double detectionTiming, final double trackingTiming )
+	public TrackingMetrics performMetricsMeasurements( final TrackMate trackmate )
 	{
-		final Settings settings = trackmate.getSettings();
 		final Model model = trackmate.getModel();
-		final File csvFile = findSuitableCSVFile( settings );
-		final String[] csvHeader1 = toCSVHeader( settings );
-
 		final List< TrackSegment > candidateTracks = SPTFormatImporter.fromTrackMate( model );
-
 		// Perform SPT measurements.
 		batchLogger.log( String.format( "Performing SPT metrics measurements with max pairing dist = %.2f %s\n",
-				maxDist, settings.imp.getCalibration().getUnits() ) );
+				maxDist, units ) );
 		final double[] score = ISBIScoring.score( referenceTracks, candidateTracks, maxDist, DistanceTypes.DISTANCE_EUCLIDIAN );
 
 		final TrackingMetrics metrics = new TrackingMetrics( type );
 		for ( int i = 0; i < score.length; i++ )
 			metrics.set( i, score[ i ] );
 
-		writeResults( csvFile, metrics, detectionTiming, trackingTiming, settings, csvHeader1 );
+		return metrics;
 	}
 }

src/main/java/fiji/plugin/trackmate/helper/spt/SPTTrackingMetricsType.java

@@ -60,6 +60,8 @@ public class SPTTrackingMetricsType extends TrackingMetricsType
 
 	private final double maxDist;
 
+	private final String units;
+
 	/**
 	 * Builds a new metrics type based on the SPT challenge, with the specified
 	 * max pairing distance <b>given in physical units</b>.
@@ -72,17 +74,20 @@ public class SPTTrackingMetricsType extends TrackingMetricsType
 	 * 
 	 * @param maxDist
 	 *            the max pairing distance.
+	 * @param units
+	 *            the physical units in which <code>maxDist</code> is specified.
 	 */
-	public SPTTrackingMetricsType( final double maxDist )
+	public SPTTrackingMetricsType( final double maxDist, final String units )
 	{
 		super( KEYS );
 		this.maxDist = maxDist;
+		this.units = units;
 	}
 
 	@Override
 	public MetricsRunner runner( final String gtPath, final String saveFolder )
 	{
-		return new SPTMetricsRunner( gtPath, saveFolder, maxDist );
+		return new SPTMetricsRunner( gtPath, saveFolder, maxDist, units );
 	}
 
 	@Override