An action to smooth meshes with Tuabin smoothing.

src/main/java/fiji/plugin/trackmate/action/meshtools/MeshSmoother.java

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+package fiji.plugin.trackmate.action.meshtools;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+import fiji.plugin.trackmate.Logger;
+import fiji.plugin.trackmate.Spot;
+import fiji.plugin.trackmate.SpotMesh;
+import net.imglib2.mesh.Mesh;
+import net.imglib2.mesh.Meshes;
+import net.imglib2.mesh.alg.TaubinSmoothing;
+import net.imglib2.mesh.alg.TaubinSmoothing.TaubinWeightType;
+import net.imglib2.mesh.impl.nio.BufferMesh;
+
+public class MeshSmoother
+{
+
+	private final Map< SpotMesh, BufferMesh > undoMap;
+
+	private final Logger logger;
+
+	public MeshSmoother( final Iterable< Spot > spots, final Logger logger )
+	{
+		this.logger = logger;
+		// Store undo.
+		this.undoMap = new HashMap<>();
+		final double[] center = new double[ 3 ];
+		for ( final Spot spot : spots )
+		{
+			if ( SpotMesh.class.isInstance( spot ) )
+			{
+				final SpotMesh sm = ( SpotMesh ) spot;
+				final Mesh mesh = sm.getMesh();
+				final BufferMesh meshCopy = new BufferMesh( mesh.vertices().size(), mesh.triangles().size() );
+				Meshes.copy( mesh, meshCopy );
+				sm.localize( center );
+				Meshes.translate( meshCopy, center );
+				undoMap.put( sm, meshCopy );
+			}
+		}
+	}
+
+	public void undo()
+	{
+		logger.setStatus( "Undoing mesh smoothing" );
+		final Set< SpotMesh > keys = undoMap.keySet();
+		final int nSpots = keys.size();
+		int i = 0;
+		for ( final SpotMesh sm : keys )
+		{
+			final BufferMesh old = undoMap.get( sm );
+			sm.setMesh( old );
+			logger.setProgress( ( double ) ( ++i ) / nSpots );
+		}
+		logger.setStatus( "" );
+	}
+
+	public void smooth( final int nIters, final double mu, final double lambda, final TaubinWeightType weightType )
+	{
+		logger.setStatus( "Taubin smoothing" );
+		final Set< SpotMesh > keys = undoMap.keySet();
+		final int nSpots = keys.size();
+		int i = 0;
+		final double[] center = new double[ 3 ];
+		for ( final SpotMesh sm : keys )
+		{
+			final Mesh mesh = sm.getMesh();
+			sm.localize( center );
+			Meshes.translate( mesh, center );
+			final BufferMesh smoothedMesh = TaubinSmoothing.smooth( mesh, nIters, lambda, mu, weightType );
+			sm.setMesh( smoothedMesh );
+			logger.setProgress( ( double ) ( ++i ) / nSpots );
+		}
+		logger.setStatus( "" );
+	}
+}

src/main/java/fiji/plugin/trackmate/action/meshtools/MeshSmootherAction.java

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+package fiji.plugin.trackmate.action.meshtools;
+
+import java.awt.Frame;
+
+import javax.swing.ImageIcon;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+
+import org.scijava.plugin.Plugin;
+
+import fiji.plugin.trackmate.ModelChangeEvent;
+import fiji.plugin.trackmate.SelectionModel;
+import fiji.plugin.trackmate.TrackMate;
+import fiji.plugin.trackmate.action.AbstractTMAction;
+import fiji.plugin.trackmate.action.TrackMateAction;
+import fiji.plugin.trackmate.action.TrackMateActionFactory;
+import fiji.plugin.trackmate.gui.GuiUtils;
+import fiji.plugin.trackmate.gui.Icons;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
+import fiji.plugin.trackmate.util.EverythingDisablerAndReenabler;
+
+public class MeshSmootherAction extends AbstractTMAction
+{
+
+	@Override
+	public void execute( final TrackMate trackmate, final SelectionModel selectionModel, final DisplaySettings displaySettings, final Frame parent )
+	{
+		final MeshSmoother smoother = new MeshSmoother( trackmate.getModel().getSpots().iterable( true ), logger );
+
+		final MeshSmootherModel model = new MeshSmootherModel();
+		final MeshSmootherPanel panel = new MeshSmootherPanel( model );
+
+		panel.btnRun.addActionListener( e -> {
+			new Thread( () -> {
+				final EverythingDisablerAndReenabler enabler = new EverythingDisablerAndReenabler( panel, new Class[] { JLabel.class } );
+				try
+				{
+					enabler.disable();
+					smoother.smooth( model.getNIters(), model.getMu(), model.getLambda(), model.getWeightType() );
+					// Trigger refresh.
+					trackmate.getModel().getModelChangeListener().forEach( l -> l.modelChanged( new ModelChangeEvent( this, ModelChangeEvent.SPOTS_COMPUTED ) ) );
+				}
+				finally
+				{
+					enabler.reenable();
+				}
+			}, "TrackMate mesh smoother" ).start();
+		} );
+
+		panel.btnUndo.addActionListener( e -> {
+			new Thread( () -> {
+				final EverythingDisablerAndReenabler enabler = new EverythingDisablerAndReenabler( panel, new Class[] { JLabel.class } );
+				try
+				{
+					enabler.disable();
+					smoother.undo();
+					// Trigger refresh.
+					trackmate.getModel().getModelChangeListener().forEach( l -> l.modelChanged( new ModelChangeEvent( this, ModelChangeEvent.SPOTS_COMPUTED ) ) );
+				}
+				finally
+				{
+					enabler.reenable();
+				}
+			}, "TrackMate mesh smoother" ).start();
+		} );
+
+		final JFrame frame = new JFrame( "Smoothing params" );
+		frame.getContentPane().add( panel );
+		frame.setSize( 400, 300 );
+		GuiUtils.positionWindow( frame, parent );
+		frame.setVisible( true );
+	}
+
+	@Plugin( type = TrackMateActionFactory.class )
+	public static class Factory implements TrackMateActionFactory
+	{
+
+		public static final String NAME = "Smooth 3D meshes";
+
+		public static final String KEY = "MESH_SMOOTHER";
+
+		public static final String INFO_TEXT = "<html>"
+				+ "Displays a tool to smooth the 3D mesh present in "
+				+ "the data, using the Taubin smoothing algorithm.</html>";
+
+		@Override
+		public String getInfoText()
+		{
+			return INFO_TEXT;
+		}
+
+		@Override
+		public String getKey()
+		{
+			return KEY;
+		}
+
+		@Override
+		public TrackMateAction create()
+		{
+			return new MeshSmootherAction();
+		}
+
+		@Override
+		public ImageIcon getIcon()
+		{
+			return Icons.VECTOR_ICON;
+		}
+
+		@Override
+		public String getName()
+		{
+			return NAME;
+		}
+	}
+
+}

src/main/java/fiji/plugin/trackmate/action/meshtools/MeshSmootherModel.java

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+package fiji.plugin.trackmate.action.meshtools;
+
+import net.imglib2.mesh.alg.TaubinSmoothing.TaubinWeightType;
+
+public class MeshSmootherModel
+{
+
+	private int nIters = 10;
+
+	private double mu = 0.5;
+
+	private double lambda = -0.53;
+
+	private TaubinWeightType weightType = TaubinWeightType.NAIVE;
+
+	public void setWeightType( final TaubinWeightType weightType )
+	{
+		this.weightType = weightType;
+	}
+
+	public void setMu( final double mu )
+	{
+		this.mu = Math.min( 1., Math.max( 0, mu ) );
+	}
+
+	public void setLambda( final double lambda )
+	{
+		this.lambda = Math.min( 0., Math.max( -1., lambda ) );
+	}
+
+	public void setNIters( final int nIters )
+	{
+		this.nIters = Math.max( 0, nIters );
+	}
+
+	public double getMu()
+	{
+		return mu;
+	}
+
+	public double getLambda()
+	{
+		return lambda;
+	}
+
+	public int getNIters()
+	{
+		return nIters;
+	}
+
+	public TaubinWeightType getWeightType()
+	{
+		return weightType;
+	}
+
+	/**
+	 * Ad-hoc method setting parameters for little smoothing (close to 0) or a
+	 * lot of smoothing (close to 1).
+	 * 
+	 * @param smoothing
+	 *            the smoothing parameter.
+	 */
+	public void setSmoothing( final double smoothing )
+	{
+		setMu( Math.max( 0, Math.min( 0.97, smoothing ) ) );
+		setLambda( -mu - 0.03 );
+	}
+}