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tineveztinevez
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Add basic feature declarations expected by TrackMate
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Lines changed: 98 additions & 2 deletions

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

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package org.mastodon.mamut.io.importer.trackmate;
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import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_ATTRIBUTE;
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import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_DIMENSION_ATTRIBUTE;
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import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_ISINT_ATTRIBUTE;
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import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_NAME_ATTRIBUTE;
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import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_SHORT_NAME_ATTRIBUTE;
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import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_TAG;
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import java.util.Arrays;
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import java.util.List;
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import org.jdom2.Element;
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public class CommonTrackMateFeatureDeclarations
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{
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public static final List< CommonTrackMateFeatureDeclaration > spotFeatureDeclarations = Arrays.asList( new CommonTrackMateFeatureDeclaration[] {
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.VISIBILITY_FEATURE_NAME, "Visibility", "Visibility", "NONE", true ),
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_X_FEATURE_NAME, "X", "X", "POSITION", false ),
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_Y_FEATURE_NAME, "Y", "Y", "POSITION", false ),
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_Z_FEATURE_NAME, "Z", "Z", "POSITION", false ),
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.POSITION_T_FEATURE_NAME, "T", "T", "TIME", false ),
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.FRAME_FEATURE_NAME, "Frame", "Frame", "NONE", true ),
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.RADIUS_FEATURE_NAME, "Radius", "R", "LENGTH", false ),
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.QUALITY_FEATURE_NAME, "Quality", "Quality", "QUALITY", false ),
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} );
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public static final List< CommonTrackMateFeatureDeclaration > edgeFeatureDeclarations = Arrays.asList( new CommonTrackMateFeatureDeclaration[] {
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.EDGE_SOURCE_ATTRIBUTE, "Source spot ID", "Source ID", "NONE", true ),
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.EDGE_TARGET_ATTRIBUTE, "Target spot ID", "Target ID", "NONE", true ),
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} );
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public static final List< CommonTrackMateFeatureDeclaration > trackFeatureDeclarations = Arrays.asList( new CommonTrackMateFeatureDeclaration[] {
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new CommonTrackMateFeatureDeclaration( TrackMateXMLKeys.TRACK_ID_ATTRIBUTE, "Track ID", "ID", "NONE", true ),
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} );
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public static class CommonTrackMateFeatureDeclaration
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{
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public final String key;
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public final String name;
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public final String shortName;
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public final String dimension;
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public final boolean isInt;
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public CommonTrackMateFeatureDeclaration( final String key, final String name, final String shortName, final String dimension, final boolean isInt )
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{
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this.key = key;
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this.name = name;
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this.shortName = shortName;
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this.dimension = dimension;
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this.isInt = isInt;
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}
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public Element toElement()
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{
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final Element fel = new Element( FEATURE_TAG );
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fel.setAttribute( FEATURE_ATTRIBUTE, key );
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fel.setAttribute( FEATURE_NAME_ATTRIBUTE, name );
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fel.setAttribute( FEATURE_SHORT_NAME_ATTRIBUTE, shortName );
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fel.setAttribute( FEATURE_DIMENSION_ATTRIBUTE, dimension );
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fel.setAttribute( FEATURE_ISINT_ATTRIBUTE, "" + isInt );
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return fel;
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}
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}
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}

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

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Original file line numberDiff line numberDiff line change
@@ -682,13 +682,29 @@ else if ( origName.startsWith( "IMPORTED_" ) )
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private Element featuresDeclarationToXml()
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{
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final Element featuresElement = new Element( FEATURE_DECLARATION_TAG );
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appendBasicFeatureDeclarations( featuresElement );
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appendFeaturesDeclarationOfClass( Spot.class, featuresElement, SPOT_FEATURE_DECLARATION_TAG );
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appendFeaturesDeclarationOfClass( Link.class, featuresElement, EDGE_FEATURE_DECLARATION_TAG );
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// Create an empty declaration for track features, for now.
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appendFeaturesDeclarationOfClass( Boolean.class, featuresElement, TRACK_FEATURE_DECLARATION_TAG );
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return featuresElement;
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}
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private void appendBasicFeatureDeclarations( final Element featuresElement )
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{
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// Spots.
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final Element spotFeaturesElement = getOrAddChild( featuresElement, SPOT_FEATURE_DECLARATION_TAG );
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CommonTrackMateFeatureDeclarations.spotFeatureDeclarations.forEach( cf -> spotFeaturesElement.addContent( cf.toElement() ) );
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// Edges.
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final Element edgeFeaturesElement = getOrAddChild( featuresElement, EDGE_FEATURE_DECLARATION_TAG );
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CommonTrackMateFeatureDeclarations.edgeFeatureDeclarations.forEach( cf -> edgeFeaturesElement.addContent( cf.toElement() ) );
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// Tracks.
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final Element trackFeaturesElement = getOrAddChild( featuresElement, TRACK_FEATURE_DECLARATION_TAG );
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CommonTrackMateFeatureDeclarations.trackFeatureDeclarations.forEach( cf -> trackFeaturesElement.addContent( cf.toElement() ) );
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}
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@SuppressWarnings( { "unchecked", "rawtypes" } )
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private < T > void appendFeaturesDeclarationOfClass( final Class< T > clazz, final Element featuresElement,
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final String classFeatureDeclarationTag )
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else
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projections = Collections.emptyList();
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final Element classFeaturesElement = new Element( classFeatureDeclarationTag );
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final Element classFeaturesElement = getOrAddChild( featuresElement, classFeatureDeclarationTag );
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for ( final ExportFeatureProjection< T > p : projections )
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{
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final String isint = ( p.projection instanceof IntFeatureProjection )
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fel.setAttribute( FEATURE_ISINT_ATTRIBUTE, isint );
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classFeaturesElement.addContent( fel );
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}
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featuresElement.addContent( classFeaturesElement );
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}
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private Element getOrAddChild( final Element parent, final String childName )
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{
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Element child = parent.getChild( childName );
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if ( null == child )
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{
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child = new Element( childName );
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parent.addContent( child );
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}
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return child;
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}
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private static Document getSAXParsedDocument( final String fileName )

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