Do not re-export common TrackMate features values and declaration.

Without this commit, they are exported twice with different names.

Author: tinevez

src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java

@@ -8,6 +8,7 @@
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_TAG;
 
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 import org.jdom2.Element;
@@ -67,4 +68,27 @@ public Element toElement()
 			return fel;
 		}
 	}
+
+	/**
+	 * List of Mastodon spot projection keys, translated to the TrackMate export
+	 * name, that are not needed in the exported XML file, as they are already
+	 * exported via TrackMate builtin features.
+	 */
+	public static final List< String > redundantSpotProjectionKeys = Arrays.asList(
+			"Spot_position_X", "Spot_position_Y", "Spot_position_Z", "Spot_radius", "Spot_frame" );
+
+	/**
+	 * List of Mastodon link projection keys, translated to the TrackMate export
+	 * name, that are not needed in the exported XML file, as they are already
+	 * exported via TrackMate builtin features.
+	 */
+	public static final List< String > redundantLinkProjectionKeys = Arrays.asList(
+			"Link_target_IDs_Source_spot_id", "Link_target_IDs_Target_spot_id" );
+
+	/**
+	 * List of Mastodon track projection keys, translated to the TrackMate
+	 * export name, that are not needed in the exported XML file, as they are
+	 * already exported via TrackMate builtin features.
+	 */
+	public static final List< String > redundantTrackProjectionKeys = Collections.emptyList();
 }

src/main/java/org/mastodon/mamut/io/importer/trackmate/MamutExporter.java

@@ -540,8 +540,15 @@ private Element edgeToXml( final Link edge, final int sourceSpotID, final int ta
 		// Link features.
 		for ( final ExportFeatureProjection< Link > p : linkFeatureProjections )
 		{
-			final String attName;
 			final String origName = p.attributeName;
+			/*
+			 * Do not export link features that are common TrackMate features
+			 * and that we already exported above.
+			 */
+			if ( CommonTrackMateFeatureDeclarations.redundantLinkProjectionKeys.contains( origName ) )
+				continue;
+
+			final String attName;
 			/*
 			 * If the model to export was imported from a TrackMate or a MaMuT
 			 * file, it will already contain features with the same name that
@@ -634,8 +641,15 @@ private Element spotToXml( final Spot spot )
 
 		for (final ExportFeatureProjection< Spot > p : spotFeatureProjections )
 		{
-			final String attName;
 			final String origName = p.attributeName;
+			/*
+			 * Do not export spot features that are common TrackMate features
+			 * and that we already exported above.
+			 */
+			if ( CommonTrackMateFeatureDeclarations.redundantSpotProjectionKeys.contains( origName ) )
+				continue;
+
+			final String attName;
 			/*
 			 * If the model to export was imported from a TrackMate or a MaMuT
 			 * file, it will already contain features with the same name that
@@ -710,16 +724,33 @@ private < T > void appendFeaturesDeclarationOfClass( final Class< T > clazz, fin
 			final String classFeatureDeclarationTag )
 	{
 		final List< ExportFeatureProjection< T > > projections;
+		List< String > redundantFeatures;
 		if ( clazz.equals( Spot.class ) )
+		{
 			projections = ( List ) spotFeatureProjections;
+			redundantFeatures = CommonTrackMateFeatureDeclarations.redundantSpotProjectionKeys;
+		}
 		else if ( clazz.equals( Link.class ) )
+		{
 			projections = ( List ) linkFeatureProjections;
+			redundantFeatures = CommonTrackMateFeatureDeclarations.redundantLinkProjectionKeys;
+		}
 		else
+		{
 			projections = Collections.emptyList();
+			redundantFeatures = CommonTrackMateFeatureDeclarations.redundantTrackProjectionKeys;
+		}
 
 		final Element classFeaturesElement = getOrAddChild( featuresElement, classFeatureDeclarationTag );
 		for ( final ExportFeatureProjection< T > p : projections )
 		{
+			/*
+			 * Do not export features that are common TrackMate features and
+			 * that we already declared.
+			 */
+			if ( redundantFeatures.contains( p.attributeName ) )
+				continue;
+
 			final String isint = ( p.projection instanceof IntFeatureProjection )
 					? "true"
 					: "false";