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An action to export tracking results to a label image.
This action creates a label image from the tracking results. " A new 16-bit image is generated, of same dimension and size that of the input image. The label image has one channel, with black baground (0 value) everywhere, except where there are spots. Each spot is painted with a uniform integer value equal to the trackID it belongs to. Spots that do not belong to tracks are painted with a unique integer larger than the last trackID in the dataset. Only visible spots are painted.
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‎src/main/java/fiji/plugin/trackmate/action/LabelImgExporter.java‎

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package fiji.plugin.trackmate.action;
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import java.util.Set;
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import java.util.concurrent.atomic.AtomicInteger;
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import javax.swing.ImageIcon;
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import org.scijava.plugin.Plugin;
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import fiji.plugin.trackmate.Model;
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import fiji.plugin.trackmate.Spot;
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import fiji.plugin.trackmate.TrackMate;
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import fiji.plugin.trackmate.gui.TrackMateGUIController;
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import fiji.plugin.trackmate.gui.TrackMateWizard;
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import fiji.plugin.trackmate.util.SpotNeighborhood;
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import ij.ImagePlus;
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import net.imagej.ImgPlus;
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import net.imagej.axis.Axes;
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import net.imagej.axis.AxisType;
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import net.imglib2.Dimensions;
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import net.imglib2.FinalDimensions;
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import net.imglib2.img.Img;
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import net.imglib2.img.display.imagej.ImageJFunctions;
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import net.imglib2.meta.view.HyperSliceImgPlus;
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import net.imglib2.type.numeric.integer.UnsignedShortType;
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import net.imglib2.util.Util;
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@SuppressWarnings( "deprecation" )
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public class LabelImgExporter extends AbstractTMAction
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{
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public static final String INFO_TEXT = "<html>"
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+ "This action creates a label image from the tracking results. "
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+ "<p> "
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+ "A new 16-bit image is generated, of same dimension and size that "
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+ "of the input image. The label image has one channel, with black baground (0 value) "
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+ "everywhere, except where there are spots. Each spot is painted with "
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+ "a uniform integer value equal to the trackID it belongs to. "
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+ "Spots that do not belong to tracks are painted with a unique integer "
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+ "larger than the last trackID in the dataset. "
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+ "<p> "
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+ "Only visible spots are painted. "
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+ "</html>";
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public static final String KEY = "EXPORT_LABEL_IMG";
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public static final ImageIcon ICON = new ImageIcon( TrackMateWizard.class.getResource( "images/picture_key.png" ) );
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public static final String NAME = "Export label image";
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@Override
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public void execute( final TrackMate trackmate )
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{
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createLabelImagePlus( trackmate ).show();
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}
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public static final ImagePlus createLabelImagePlus( final TrackMate trackmate )
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{
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return createLabelImagePlus( trackmate.getModel(), trackmate.getSettings().imp );
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}
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public static final ImagePlus createLabelImagePlus( final Model model, final ImagePlus imp )
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{
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final int[] dimensions = imp.getDimensions();
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final int[] dims = new int[] { dimensions[ 0 ], dimensions[ 1 ], dimensions[ 3 ], dimensions[ 4 ] };
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final ImagePlus lblImp = createLabelImagePlus( model, dims );
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lblImp.setCalibration( imp.getCalibration().copy() );
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lblImp.setTitle( "LblImg_" + imp.getTitle() );
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return lblImp;
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}
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/**
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* @param model
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* @param dimensions
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* the dimensions of the output image (width, height, nZSlices,
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* nFrames) as a 4 element int array.
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* @return a new {@link ImagePlus}
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*/
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public static final ImagePlus createLabelImagePlus( final Model model, final int[] dimensions )
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{
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final long[] dims = new long[ 4 ];
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for ( int d = 0; d < dims.length; d++ )
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dims[ d ] = dimensions[ d ];
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final ImagePlus lblImp = ImageJFunctions.wrap( createLabelImg( model, dims ), "LblImage" );
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lblImp.setDimensions( 1, dimensions[ 2 ], dimensions[ 3 ] );
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lblImp.setOpenAsHyperStack( true );
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return lblImp;
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}
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/**
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* @param model
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* @param dimensions
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* the dimensions of the output image (width, height, nZSlices,
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* nFrames) as a 4 element int array.
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* @return a new {@link ImagePlus}
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*/
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public static final Img< UnsignedShortType > createLabelImg( final Model model, final long[] dimensions )
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{
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/*
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* Create target image.
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*/
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final Dimensions targetSize = FinalDimensions.wrap( dimensions );
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final Img< UnsignedShortType > lblImg = Util.getArrayOrCellImgFactory( targetSize, new UnsignedShortType() ).create( targetSize );
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final AxisType[] axes = new AxisType[] {
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Axes.X,
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Axes.Y,
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Axes.Z,
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Axes.TIME };
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final ImgPlus< UnsignedShortType > imgPlus = new ImgPlus<>( lblImg, "LblImg", axes );
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/*
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* Determine the starting id for spots not in tracks.
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*/
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int maxTrackID = -1;
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final Set< Integer > trackIDs = model.getTrackModel().trackIDs( false );
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if ( null != trackIDs )
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for ( final Integer trackID : trackIDs )
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if ( trackID > maxTrackID )
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maxTrackID = trackID.intValue();
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final AtomicInteger lonelySpotID = new AtomicInteger( maxTrackID + 2 );
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/*
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* Frame by frame iteration.
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*/
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for ( int frame = 0; frame < dimensions[ 3 ]; frame++ )
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{
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final ImgPlus< UnsignedShortType > imgC = HyperSliceImgPlus.fixChannelAxis( imgPlus, 0 );
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final ImgPlus< UnsignedShortType > imgCT = HyperSliceImgPlus.fixTimeAxis( imgC, frame );
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for ( final Spot spot : model.getSpots().iterable( frame, true ) )
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{
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final int id;
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final Integer trackID = model.getTrackModel().trackIDOf( spot );
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if ( null == trackID || !model.getTrackModel().isVisible( trackID ) )
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id = lonelySpotID.getAndIncrement();
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else
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id = 1 + trackID.intValue();
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final SpotNeighborhood< UnsignedShortType > neighborhood = new SpotNeighborhood< UnsignedShortType >( spot, imgCT );
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for ( final UnsignedShortType pixel : neighborhood )
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pixel.set( id );
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}
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}
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return lblImg;
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}
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@Plugin( type = TrackMateActionFactory.class )
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public static class Factory implements TrackMateActionFactory
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{
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@Override
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public String getInfoText()
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{
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return INFO_TEXT;
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}
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@Override
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public String getKey()
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{
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return KEY;
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}
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@Override
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public TrackMateAction create( final TrackMateGUIController controller )
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{
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return new LabelImgExporter();
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}
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@Override
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public ImageIcon getIcon()
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{
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return ICON;
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}
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@Override
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public String getName()
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{
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return NAME;
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}
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}
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}

‎src/main/resources/fiji/plugin/trackmate/gui/images/picture_key.png‎

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