Use GEFF as the main file format of TrackMate

pom.xml

@@ -403,6 +403,12 @@
 			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.assertj</groupId>
+			<artifactId>assertj-core</artifactId>
+			<version>3.27.7</version>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<repositories>

src/main/java/fiji/plugin/trackmate/FeatureModel.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>.
@@ -61,12 +61,12 @@ public class FeatureModel
 	 * track to its feature map. The feature map maps each feature to the double
 	 * value for the specified feature.
 	 */
-	Map< Integer, Map< String, Double > > trackFeatureValues = new ConcurrentHashMap<>();
+	transient Map< Integer, Map< String, Double > > trackFeatureValues = new ConcurrentHashMap<>();
 
 	/**
 	 * Feature storage for edges.
 	 */
-	private final ConcurrentHashMap< DefaultWeightedEdge, ConcurrentHashMap< String, Double > > edgeFeatureValues = new ConcurrentHashMap<>();
+	private final transient ConcurrentHashMap< DefaultWeightedEdge, ConcurrentHashMap< String, Double > > edgeFeatureValues = new ConcurrentHashMap<>();
 
 	private final Collection< String > edgeFeatures = new LinkedHashSet<>();
 
@@ -88,7 +88,7 @@ public class FeatureModel
 
 	private final Map< String, Boolean > spotFeatureIsInt = new HashMap<>();
 
-	private final Model model;
+	private transient final Model model;
 
 	/*
 	 * CONSTRUCTOR
@@ -165,7 +165,7 @@ public Double getEdgeFeature( final DefaultWeightedEdge edge, final String featu
 
 	/**
 	 * Remove the value of the designated feature for the specified edge.
-	 * 
+	 *
 	 * @param edge
 	 *            the edge
 	 * @param feature
@@ -284,7 +284,7 @@ public Map< String, Boolean > getEdgeFeatureIsInt()
 
 	/**
 	 * Returns the track features that are dealt with in this model.
-	 * 
+	 *
 	 * @return the collection of track features managed in this model.
 	 */
 	public Collection< String > getTrackFeatures()
@@ -341,7 +341,7 @@ public void declareTrackFeatures( final Collection< String > features, final Map
 	/**
 	 * Returns the name mapping of the track features that are dealt with in
 	 * this model.
-	 * 
+	 *
 	 * @return the feature name.
 	 */
 	public Map< String, String > getTrackFeatureNames()
@@ -363,7 +363,7 @@ public Map< String, String > getTrackFeatureShortNames()
 	/**
 	 * Returns the dimension mapping of the track features that are dealt with
 	 * in this model.
-	 * 
+	 *
 	 * @return the feature dimension.
 	 */
 	public Map< String, Dimension > getTrackFeatureDimensions()
@@ -410,7 +410,7 @@ public synchronized void putTrackFeature( final Integer trackID, final String fe
 	/**
 	 * Remove the value of the designated feature for the track with the
 	 * specified ID.
-	 * 
+	 *
 	 * @param trackID
 	 *            the track ID
 	 * @param feature
@@ -604,7 +604,7 @@ public String toString()
 
 	/**
 	 * Echoes the full content of this {@link FeatureModel}.
-	 * 
+	 *
 	 * @return a String representation of the full content of this model.
 	 */
 	public String echo()

src/main/java/fiji/plugin/trackmate/Logger.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>.
@@ -93,7 +93,7 @@ public void write( final char[] cbuf, final int off, final int len ) throws IOEx
 				? new Color( 0.4f, 0.4f, 0.9f )
 				: new Color( 0, 0, 0.7f );
 		GREEN_COLOR = bgIsDark
-				? new Color( 0.4f, 0.9f, 0.4f )
+				? new Color( 0.2f, 0.6f, 0.2f )
 				: new Color( 0, 0.6f, 0 );
 		ERROR_COLOR = bgIsDark
 				? new Color( 0.8f, 0, 0 ).brighter()

src/main/java/fiji/plugin/trackmate/Settings.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>.
@@ -56,7 +56,7 @@ public class Settings
 	 * {@link fiji.plugin.trackmate.visualization.TrackMateModelView} as a GUI
 	 * target.
 	 */
-	public final ImagePlus imp;
+	public final transient ImagePlus imp;
 
 	public double dt;
 
@@ -113,16 +113,16 @@ public class Settings
 	 */
 	public SpotDetectorFactoryBase< ? > detectorFactory;
 
-	/** The the tracker to use. */
-	public SpotTrackerFactory trackerFactory;
-
 	/**
 	 * Settings map for {@link fiji.plugin.trackmate.detection.SpotDetector}.
 	 *
 	 * @see fiji.plugin.trackmate.detection.DetectorKeys
 	 */
 	public Map< String, Object > detectorSettings = new HashMap<>();
 
+	/** The the tracker to use. */
+	public SpotTrackerFactory trackerFactory;
+
 	/**
 	 * Settings map for {@link fiji.plugin.trackmate.tracking.SpotTracker}.
 	 *
@@ -132,21 +132,21 @@ public class Settings
 
 	// Filters
 
-	/**
-	 * The feature filter list.
-	 */
-	protected List< FeatureFilter > spotFilters = new ArrayList<>();
-
 	/**
 	 * The initial quality filter value that is used to clip spots of low
 	 * quality from spots.
 	 */
 	public Double initialSpotFilterValue = Double.valueOf( 0 );
 
+	/**
+	 * The feature filter list.
+	 */
+	protected List< FeatureFilter > spotFilters = new ArrayList<>();
+
 	/** The track filter list that is used to prune track and spots. */
 	protected List< FeatureFilter > trackFilters = new ArrayList<>();
 
-	protected String errorMessage;
+	protected transient String errorMessage;
 
 	// Spot features
 

src/main/java/fiji/plugin/trackmate/features/FeatureUtils.java

@@ -419,6 +419,11 @@ public static final FeatureColorGenerator< Integer > createWholeTrackColorGenera
 	}
 
 	public static final double[] autoMinMax( final Model model, final TrackMateObject type, final String feature )
+	{
+		return autoMinMax( model, type, feature, true );
+	}
+
+	public static final double[] autoMinMax( final Model model, final TrackMateObject type, final String feature, final boolean visibileOnly )
 	{
 		switch ( type )
 		{
@@ -429,7 +434,7 @@ public static final double[] autoMinMax( final Model model, final TrackMateObjec
 		case SPOTS:
 		case TRACKS:
 		{
-			final double[] values = collectFeatureValues( feature, type, model, true );
+			final double[] values = collectFeatureValues( feature, type, model, visibileOnly );
 			double min = Double.POSITIVE_INFINITY;
 			double max = Double.NEGATIVE_INFINITY;
 			for ( final double val : values )

src/main/java/fiji/plugin/trackmate/gui/components/tracker/SimpleLAPTrackerSettingsPanel.java

@@ -25,7 +25,6 @@
 import static fiji.plugin.trackmate.gui.Fonts.FONT;
 import static fiji.plugin.trackmate.gui.Fonts.TEXTFIELD_DIMENSION;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_ALTERNATIVE_LINKING_COST_FACTOR;
-import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_BLOCKING_VALUE;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_CUTOFF_PERCENTILE;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_GAP_CLOSING_FEATURE_PENALTIES;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_LINKING_FEATURE_PENALTIES;
@@ -37,7 +36,6 @@
 import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALLOW_TRACK_MERGING;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALLOW_TRACK_SPLITTING;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALTERNATIVE_LINKING_COST_FACTOR;
-import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_BLOCKING_VALUE;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_CUTOFF_PERCENTILE;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_GAP_CLOSING_FEATURE_PENALTIES;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_GAP_CLOSING_MAX_DISTANCE;
@@ -190,7 +188,6 @@ public Map< String, Object > getSettings()
 		settings.put( KEY_MERGING_MAX_DISTANCE, DEFAULT_MERGING_MAX_DISTANCE );
 		settings.put( KEY_MERGING_FEATURE_PENALTIES, DEFAULT_MERGING_FEATURE_PENALTIES );
 		// Others
-		settings.put( KEY_BLOCKING_VALUE, DEFAULT_BLOCKING_VALUE );
 		settings.put( KEY_ALTERNATIVE_LINKING_COST_FACTOR, DEFAULT_ALTERNATIVE_LINKING_COST_FACTOR );
 		settings.put( KEY_CUTOFF_PERCENTILE, DEFAULT_CUTOFF_PERCENTILE );
 		// Panel ones

src/main/java/fiji/plugin/trackmate/gui/displaysettings/DisplaySettingsIO.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>.
@@ -31,6 +31,7 @@
 import java.lang.reflect.Type;
 import java.nio.file.Files;
 import java.nio.file.Paths;
+import java.util.Map;
 import java.util.stream.Collectors;
 
 import org.jdom2.Element;
@@ -63,18 +64,34 @@ public static String toJson( final DisplaySettings ds )
 		return getGson().toJson( ds );
 	}
 
-	public static DisplaySettings fromJson( final String str )
+	public static JsonElement toJsonTree( final DisplaySettings ds )
 	{
-		final DisplaySettings ds = ( str == null || str.isEmpty() ) ? readUserDefault() : getGson().fromJson( str, DisplaySettings.class );
+		return getGson().toJsonTree( ds );
+	}
 
+	private static void sanitize( final DisplaySettings ds )
+	{
 		// Sanitize min and max.
 		final double spotMin = ds.getSpotMin();
 		final double spotMax = ds.getSpotMax();
 		ds.setSpotMinMax( Math.min( spotMin, spotMax ), Math.max( spotMin, spotMax ) );
 		final double trackMin = ds.getTrackMin();
 		final double trackMax = ds.getTrackMax();
 		ds.setTrackMinMax( Math.min( trackMin, trackMax ), Math.max( trackMin, trackMax ) );
+	}
+
+	public static DisplaySettings fromJson( final String str )
+	{
+		final DisplaySettings ds = ( str == null || str.isEmpty() ) ? readUserDefault() : getGson().fromJson( str, DisplaySettings.class );
+		sanitize( ds );
+		return ds;
+	}
 
+	public static DisplaySettings fromJsonTree( final Map< String, Object > displaySettingsJson )
+	{
+		final Gson gson = getGson();
+		final DisplaySettings ds = gson.fromJson( gson.toJsonTree( displaySettingsJson ), DisplaySettings.class );
+		sanitize( ds );
 		return ds;
 	}
 

src/main/java/fiji/plugin/trackmate/gui/wizard/descriptors/StartDialogDescriptor.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>.
@@ -63,12 +63,25 @@ public class StartDialogDescriptor extends WizardPanelDescriptor
 
 	private static final String KEY = "Start";
 
+
+	public static final String PUB0_URL = "https://doi.org/10.1016/j.ymeth.2016.09.016";
+
+	public static final String PUB0_TXT = "Tinevez JY, Perry N. Schindelin J, et al. "
+			+ "'TrackMate: An open and extensible platform for single-particle tracking', "
+			+ "Methods (2017).";
+
 	public static final String PUB1_URL = "https://doi.org/10.1038/s41592-022-01507-1";
 
-	public static final String PUB1_TXT = "Ershov, D., Phan, MS., Pylvänäinen, J.W., Rigaud S.U., et al. "
-			+ "TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. "
-			+ "Nat Methods (2022). https://doi.org/10.1038/s41592-022-01507-1";
-
+	public static final String PUB1_TXT = "Ershov D, Phan MS, Pylvänäinen JW, Rigaud SU, et al. "
+			+ "'TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines' "
+			+ "Nature Methods (2022).";
+
+	public static final String PUB2_URL = "https://doi.org/10.1002/cpz1.70369";
+
+	public static final String PUB2_TXT = "Anselmet M, et al. "
+			+ "'Automated optimization of bacterial tracking pipelines with trackmate 8' "
+			+ "Current Protocols (2026).";
+
 	private final Settings settings;
 
 	private final Logger logger;
@@ -89,12 +102,14 @@ public void aboutToDisplayPanel()
 		logger.log( welcomeMessage, Logger.BLUE_COLOR );
 		logger.log( "Please note that TrackMate is available through Fiji, and is based on a publication. "
 				+ "If you use it successfully for your research please be so kind to cite our work:\n" );
+		logger.log( PUB2_TXT + "\n", Logger.GREEN_COLOR );
+		logger.log( PUB2_URL + "\n", Logger.BLUE_COLOR );
+		logger.log( "and / or:\n" );
 		logger.log( PUB1_TXT + "\n", Logger.GREEN_COLOR );
 		logger.log( PUB1_URL + "\n", Logger.BLUE_COLOR );
 		logger.log( "and / or:\n" );
-		logger.log( "Tinevez, JY.; Perry, N. & Schindelin, J. et al. (2017), 'TrackMate: An open and extensible platform for single-particle tracking.', "
-				+ "Methods 115: 80-90, PMID 27713081.\n", Logger.GREEN_COLOR );
-		logger.log( "https://www.sciencedirect.com/science/article/pii/S1046202316303346\n", Logger.BLUE_COLOR );
+		logger.log( PUB0_TXT + "\n", Logger.GREEN_COLOR );
+		logger.log( PUB0_URL + "\n", Logger.BLUE_COLOR );
 
 		logger.log( "\nNumerical feature analyzers:\n", Logger.BLUE_COLOR );
 		logger.log( settings.toStringFeatureAnalyzersInfo() );