Fix the mamut file exporter

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

@@ -0,0 +1,94 @@
+package org.mastodon.mamut.io.importer.trackmate;
+
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_ATTRIBUTE;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_DIMENSION_ATTRIBUTE;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_ISINT_ATTRIBUTE;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_NAME_ATTRIBUTE;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_SHORT_NAME_ATTRIBUTE;
+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;
+
+public class CommonTrackMateFeatureDeclarations
+{
+
+	public static final List< CommonTrackMateFeatureDeclaration > spotFeatureDeclarations = Arrays.asList( new CommonTrackMateFeatureDeclaration[] {
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.VISIBILITY_FEATURE_NAME, "Visibility", "Visibility", "NONE", true ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_X_FEATURE_NAME, "X", "X", "POSITION", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_Y_FEATURE_NAME, "Y", "Y", "POSITION", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_Z_FEATURE_NAME, "Z", "Z", "POSITION", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_T_FEATURE_NAME, "T", "T", "TIME", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.FRAME_FEATURE_NAME, "Frame", "Frame", "NONE", true ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.RADIUS_FEATURE_NAME, "Radius", "R", "LENGTH", false ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.QUALITY_FEATURE_NAME, "Quality", "Quality", "QUALITY", false ),
+	} );
+
+	public static final List< CommonTrackMateFeatureDeclaration > edgeFeatureDeclarations = Arrays.asList( new CommonTrackMateFeatureDeclaration[] {
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.EDGE_SOURCE_ATTRIBUTE, "Source spot ID", "Source ID", "NONE", true ),
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.EDGE_TARGET_ATTRIBUTE, "Target spot ID", "Target ID", "NONE", true ),
+	} );
+
+	public static final List< CommonTrackMateFeatureDeclaration > trackFeatureDeclarations = Arrays.asList( new CommonTrackMateFeatureDeclaration[] {
+			new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.TRACK_ID_ATTRIBUTE, "Track ID", "ID", "NONE", true ),
+	} );
+
+	public static class CommonTrackMateFeatureDeclaration
+	{
+		public final String key;
+
+		public final String name;
+
+		public final String shortName;
+
+		public final String dimension;
+
+		public final boolean isInt;
+
+		public CommonTrackMateFeatureDeclaration( final String key, final String name, final String shortName, final String dimension, final boolean isInt )
+		{
+			this.key = key;
+			this.name = name;
+			this.shortName = shortName;
+			this.dimension = dimension;
+			this.isInt = isInt;
+		}
+
+		public Element toElement()
+		{
+			final Element fel = new Element( FEATURE_TAG );
+			fel.setAttribute( FEATURE_ATTRIBUTE, key );
+			fel.setAttribute( FEATURE_NAME_ATTRIBUTE, name );
+			fel.setAttribute( FEATURE_SHORT_NAME_ATTRIBUTE, shortName );
+			fel.setAttribute( FEATURE_DIMENSION_ATTRIBUTE, dimension );
+			fel.setAttribute( FEATURE_ISINT_ATTRIBUTE, "" + isInt );
+			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

@@ -54,6 +54,7 @@
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FOLDER_ATTRIBUTE;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FRAME_ATTRIBUTE;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FRAME_FEATURE_NAME;
+import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FRAME_INTERVAL_ATTRIBUTE;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.GUI_STATE_TAG;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.HEIGHT_ATTRIBUTE;
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.ID_FEATURE_NAME;
@@ -361,6 +362,7 @@ private Element imageDataToXml()
 		attributes.add( new Attribute( PIXEL_WIDTH_ATTRIBUTE, Double.toString( pixelWidth ) ) );
 		attributes.add( new Attribute( PIXEL_HEIGHT_ATTRIBUTE, Double.toString( pixelHeight ) ) );
 		attributes.add( new Attribute( VOXEL_DEPTH_ATTRIBUTE, Double.toString( voxelDepth ) ) );
+		attributes.add( new Attribute( FRAME_INTERVAL_ATTRIBUTE, Double.toString( 1. ) ) );
 
 		final Element timePointsElement = document
 				.getRootElement()
@@ -540,8 +542,15 @@ 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 +643,15 @@ 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
@@ -660,9 +676,18 @@ else if ( origName.startsWith( "IMPORTED_" ) )
 				attName = origName;
 			}
 
-			attributes.add( new Attribute(
-					attName,
-					Double.toString( p.projection.value( spot ) ) ) );
+
+			String val;
+			if ( p.projection instanceof IntFeatureProjection )
+			{
+				val = Integer.toString( (int) p.projection.value( spot ) );
+			}
+			else
+			{
+				// Assume double.
+				val = Double.toString( p.projection.value( spot ) );
+			}
+			attributes.add( new Attribute( attName, val ) );
 		}
 
 		final Element spotElement = new Element( SPOT_ELEMENT_TAG );
@@ -673,28 +698,61 @@ else if ( origName.startsWith( "IMPORTED_" ) )
 	private Element featuresDeclarationToXml()
 	{
 		final Element featuresElement = new Element( FEATURE_DECLARATION_TAG );
+		appendBasicFeatureDeclarations( featuresElement );
 		appendFeaturesDeclarationOfClass( Spot.class, featuresElement, SPOT_FEATURE_DECLARATION_TAG );
 		appendFeaturesDeclarationOfClass( Link.class, featuresElement, EDGE_FEATURE_DECLARATION_TAG );
 		// Create an empty declaration for track features, for now.
 		appendFeaturesDeclarationOfClass( Boolean.class, featuresElement, TRACK_FEATURE_DECLARATION_TAG );
 		return featuresElement;
 	}
 
+	private void appendBasicFeatureDeclarations( final Element featuresElement )
+	{
+		// Spots.
+		final Element spotFeaturesElement = getOrAddChild( featuresElement, SPOT_FEATURE_DECLARATION_TAG );
+		CommonTrackMateFeatureDeclarations.spotFeatureDeclarations.forEach( cf -> spotFeaturesElement.addContent( cf.toElement() ) );
+
+		// Edges.
+		final Element edgeFeaturesElement = getOrAddChild( featuresElement, EDGE_FEATURE_DECLARATION_TAG );
+		CommonTrackMateFeatureDeclarations.edgeFeatureDeclarations.forEach( cf -> edgeFeaturesElement.addContent( cf.toElement() ) );
+
+		// Tracks.
+		final Element trackFeaturesElement = getOrAddChild( featuresElement, TRACK_FEATURE_DECLARATION_TAG );
+		CommonTrackMateFeatureDeclarations.trackFeatureDeclarations.forEach( cf -> trackFeaturesElement.addContent( cf.toElement() ) );
+	}
+
 	@SuppressWarnings( { "unchecked", "rawtypes" } )
 	private < T > void appendFeaturesDeclarationOfClass( final Class< T > clazz, final Element featuresElement,
 			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 = new Element( classFeatureDeclarationTag );
+		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";
@@ -710,7 +768,17 @@ else if ( clazz.equals( Link.class ) )
 			fel.setAttribute( FEATURE_ISINT_ATTRIBUTE, isint );
 			classFeaturesElement.addContent( fel );
 		}
-		featuresElement.addContent( classFeaturesElement );
+	}
+
+	private Element getOrAddChild( final Element parent, final String childName )
+	{
+		Element child = parent.getChild( childName );
+		if ( null == child )
+		{
+			child = new Element( childName );
+			parent.addContent( child );
+		}
+		return child;
 	}
 
 	private static Document getSAXParsedDocument( final String fileName )
@@ -991,4 +1059,5 @@ public static final void export( final File target, final Model model, final Mam
 		exporter.appendGuiState();
 		exporter.write( target );
 	}
+
 }

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

@@ -125,6 +125,8 @@ public class TrackMateXMLKeys
 
 	public static final String NFRAMES_ATTRIBUTE = "nframes";
 
+	public static final String FRAME_INTERVAL_ATTRIBUTE = "timeinterval";
+
 	public static final String PIXEL_WIDTH_ATTRIBUTE = "pixelwidth";
 
 	public static final String PIXEL_HEIGHT_ATTRIBUTE = "pixelheight";