Integrate LabKit in TrackMate to edit segmentation results

pom.xml

@@ -156,6 +156,11 @@
 			<groupId>sc.fiji</groupId>
 			<artifactId>fiji-lib</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>labkit-ui</artifactId>
+			<version>0.3.12-SNAPSHOT</version>
+		</dependency>
 
 		<!-- ImageJ dependencies -->
 		<dependency>
@@ -208,10 +213,10 @@
 			<groupId>com.github.vlsi.mxgraph</groupId>
 			<artifactId>jgraphx</artifactId>
 		</dependency>
-		<dependency>
+		<!--<dependency>
 			<groupId>com.google.code.gson</groupId>
 			<artifactId>gson</artifactId>
-		</dependency>
+		</dependency> -->
 		<dependency>
 			<groupId>com.itextpdf</groupId>
 			<artifactId>itextpdf</artifactId>

src/main/java/fiji/plugin/trackmate/LoadTrackMatePlugIn.java

@@ -24,6 +24,7 @@
 import static fiji.plugin.trackmate.gui.Icons.TRACKMATE_ICON;
 
 import java.awt.Color;
+import java.awt.Dimension;
 import java.io.File;
 
 import javax.swing.JFrame;
@@ -65,8 +66,6 @@ public class LoadTrackMatePlugIn extends TrackMatePlugIn
 	@Override
 	public void run( final String filePath )
 	{
-//		GuiUtils.setSystemLookAndFeel();
-
 		final Logger logger = Logger.IJ_LOGGER;
 		File file;
 		if ( null == filePath || filePath.length() == 0 )
@@ -215,6 +214,8 @@ public void run( final String filePath )
 		frame.setIconImage( TRACKMATE_ICON.getImage() );
 		GuiUtils.positionWindow( frame, settings.imp.getWindow() );
 		frame.setVisible( true );
+		final Dimension size = frame.getSize();
+		frame.setSize( size.width, size.height + 1 );
 
 		// Text
 		final LogPanelDescriptor2 logDescriptor = ( LogPanelDescriptor2 ) sequence.logDescriptor();
@@ -230,7 +231,7 @@ public void run( final String filePath )
 		final String warning = reader.getErrorMessage();
 		if ( !warning.isEmpty() )
 		{
-			logger2.log( "Warnings occured during reading the file:\n"
+			logger2.log( "Warnings occurred during reading the file:\n"
 					+ "--------------------\n"
 					+ warning
 					+ "--------------------\n",
@@ -292,11 +293,12 @@ protected TmXmlReader createReader( final File lFile )
 
 	public static void main( final String[] args )
 	{
+		GuiUtils.setSystemLookAndFeel();
 		ImageJ.main( args );
 		final LoadTrackMatePlugIn plugIn = new LoadTrackMatePlugIn();
-		plugIn.run( null );
+//		plugIn.run( null );
 //		plugIn.run( "samples/FakeTracks.xml" );
-//		plugIn.run( "samples/MAX_Merged.xml" );
+		plugIn.run( "samples/MAX_Merged.xml" );
 //		plugIn.run( "c:/Users/tinevez/Development/TrackMateWS/TrackMate-Cellpose/samples/R2_multiC.xml" );
 //		plugIn.run( "/Users/tinevez/Desktop/230901_DeltaRcsB-ZipA-mCh_timestep5min_Stage9_reg/230901_DeltaRcsB-ZipA-mCh_timestep5min_Stage9_reg_merge65.xml" );
 	}

src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java

@@ -23,17 +23,23 @@
 
 import java.awt.Polygon;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.concurrent.ExecutorService;
+
 import fiji.plugin.trackmate.Spot;
 import fiji.plugin.trackmate.SpotRoi;
+import fiji.plugin.trackmate.util.SpotUtil;
 import fiji.plugin.trackmate.util.Threads;
-import ij.ImagePlus;
 import ij.gui.PolygonRoi;
-import ij.measure.Measurements;
 import ij.process.FloatPolygon;
+import net.imagej.ImgPlus;
+import net.imagej.axis.Axes;
+import net.imagej.axis.AxisType;
 import net.imglib2.Interval;
+import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
@@ -45,15 +51,13 @@
 import net.imglib2.histogram.Real1dBinMapper;
 import net.imglib2.img.Img;
 import net.imglib2.img.ImgFactory;
-import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.roi.labeling.ImgLabeling;
 import net.imglib2.roi.labeling.LabelRegion;
 import net.imglib2.roi.labeling.LabelRegionCursor;
 import net.imglib2.roi.labeling.LabelRegions;
 import net.imglib2.type.BooleanType;
 import net.imglib2.type.logic.BitType;
 import net.imglib2.type.numeric.IntegerType;
-import net.imglib2.type.numeric.NumericType;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.integer.IntType;
 import net.imglib2.util.Util;
@@ -428,7 +432,7 @@ public static < T extends RealType< T >, R extends RealType< R > > List< Spot >
 	 *            the image in which to read the quality value.
 	 * @return a list of spots, with ROI.
 	 */
-	public static final < T extends RealType< T >, S extends NumericType< S > > List< Spot > fromThresholdWithROI(
+	public static final < T extends RealType< T >, S extends RealType< S > > List< Spot > fromThresholdWithROI(
 			final RandomAccessible< T > input,
 			final Interval interval,
 			final double[] calibration,
@@ -439,15 +443,15 @@ public static final < T extends RealType< T >, S extends NumericType< S > > List
 	{
 		if ( input.numDimensions() != 2 )
 			throw new IllegalArgumentException( "Can only process 2D images with this method, but got " + input.numDimensions() + "D." );
-		
+
 		// Get labeling.
 		final ImgLabeling< Integer, IntType > labeling = toLabeling( input, interval, threshold, numThreads );
 		return fromLabelingWithROI( labeling, interval, calibration, simplify, qualityImage );
 	}
 
 	/**
 	 * Creates spots <b>with ROIs</b> from a <b>2D</b> label image. The quality
-	 * value is read from a secondary image, byt taking the max value in each
+	 * value is read from a secondary image, by taking the max value in each
 	 * ROI.
 	 * 
 	 * @param <R>
@@ -468,7 +472,51 @@ public static final < T extends RealType< T >, S extends NumericType< S > > List
 	 *            the image in which to read the quality value.
 	 * @return a list of spots, with ROI.
 	 */
-	public static < R extends IntegerType< R >, S extends NumericType< S > > List< Spot > fromLabelingWithROI(
+	public static < R extends IntegerType< R >, S extends RealType< S > > List< Spot > fromLabelingWithROI(
+			final ImgLabeling< Integer, R > labeling,
+			final Interval interval,
+			final double[] calibration,
+			final boolean simplify,
+			final RandomAccessibleInterval< S > qualityImage )
+	{
+		final Map< Integer, List< Spot > > map = fromLabelingWithROIMap( labeling, interval, calibration, simplify, qualityImage );
+		final List<Spot> spots = new ArrayList<>();
+		for ( final List< Spot > s : map.values() )
+			spots.addAll( s );
+
+		return spots;
+	}
+
+	/**
+	 * Creates spots <b>with ROIs</b> from a <b>2D</b> label image. The quality
+	 * value is read from a secondary image, by taking the max value in each
+	 * ROI.
+	 * <p>
+	 * The spots are returned in a map, where the key is the integer value of
+	 * the label they correspond to in the label image. Because one spot
+	 * corresponds to one connected component in the label image, there might be
+	 * several spots for a label, hence the values of the map are list of spots.
+	 * 
+	 * @param <R>
+	 *            the type that backs-up the labeling.
+	 * @param <S>
+	 *            the type of the quality image. Must be real, scalar.
+	 * @param labeling
+	 *            the labeling, must be zero-min and 2D..
+	 * @param interval
+	 *            the interval, used to reposition the spots from the zero-min
+	 *            labeling to the proper coordinates.
+	 * @param calibration
+	 *            the physical calibration.
+	 * @param simplify
+	 *            if <code>true</code> the polygon will be post-processed to be
+	 *            smoother and contain less points.
+	 * @param qualityImage
+	 *            the image in which to read the quality value.
+	 * @return a map linking the label integer value to the list of spots, with
+	 *         ROI, it corresponds to.
+	 */
+	public static < R extends IntegerType< R >, S extends RealType< S > > Map< Integer, List< Spot > > fromLabelingWithROIMap(
 			final ImgLabeling< Integer, R > labeling,
 			final Interval interval,
 			final double[] calibration,
@@ -480,9 +528,14 @@ public static < R extends IntegerType< R >, S extends NumericType< S > > List< S
 
 		final LabelRegions< Integer > regions = new LabelRegions< Integer >( labeling );
 
-		// Parse regions to create polygons on boundaries.
-		final List< Polygon > polygons = new ArrayList<>( regions.getExistingLabels().size() );
+		/*
+		 * Map of label in the label image to a collection of polygons around
+		 * this label. Because 1 polygon correspond to 1 connected component,
+		 * there might be several polygons for a label.
+		 */
+		final Map< Integer, List< Polygon > > polygonsMap = new HashMap<>( regions.getExistingLabels().size() );
 		final Iterator< LabelRegion< Integer > > iterator = regions.iterator();
+		// Parse regions to create polygons on boundaries.
 		while ( iterator.hasNext() )
 		{
 			final LabelRegion< Integer > region = iterator.next();
@@ -492,55 +545,75 @@ public static < R extends IntegerType< R >, S extends NumericType< S > > List< S
 			for ( final Polygon polygon : pp )
 				polygon.translate( ( int ) region.min( 0 ), ( int ) region.min( 1 ) );
 
-			polygons.addAll( pp );
+			final Integer label = region.getLabel();
+			polygonsMap.put( label, pp );
 		}
 
-		// Quality image.
-		final List< Spot > spots = new ArrayList<>( polygons.size() );
-		final ImagePlus qualityImp = ( null == qualityImage )
-				? null
-				: ImageJFunctions.wrap( qualityImage, "QualityImage" );
+
+		// Storage for results.
+		final Map< Integer, List< Spot > > output = new HashMap<>( polygonsMap.size() );
 
 		// Simplify them and compute a quality.
-		for ( final Polygon polygon : polygons )
+		for ( final Integer label : polygonsMap.keySet() )
 		{
-			final PolygonRoi roi = new PolygonRoi( polygon, PolygonRoi.POLYGON );
+			final List< Spot > spots = new ArrayList<>( polygonsMap.size() );
+			output.put( label, spots );
+
+			final List< Polygon > polygons = polygonsMap.get( label );
+			for ( final Polygon polygon : polygons )
+			{
+				final PolygonRoi roi = new PolygonRoi( polygon, PolygonRoi.POLYGON );
 
-			// Create Spot ROI.
-			final PolygonRoi fRoi;
-			if ( simplify )
-				fRoi = simplify( roi, SMOOTH_INTERVAL, DOUGLAS_PEUCKER_MAX_DISTANCE );
-			else
-				fRoi = roi;
+				// Create Spot ROI.
+				final PolygonRoi fRoi;
+				if ( simplify )
+					fRoi = simplify( roi, SMOOTH_INTERVAL, DOUGLAS_PEUCKER_MAX_DISTANCE );
+				else
+					fRoi = roi;
 
-			// Don't include ROIs that have been shrunk to < 1 pixel.
-			if ( fRoi.getNCoordinates() < 3 || fRoi.getStatistics().area <= 0. )
-				continue;
+				// Don't include ROIs that have been shrunk to < 1 pixel.
+				if ( fRoi.getNCoordinates() < 3 || fRoi.getStatistics().area <= 0. )
+					continue;
 
-			// Measure quality.
-			final double quality;
-			if ( null == qualityImp )
-			{
-				quality = fRoi.getStatistics().area;
-			}
-			else
-			{
-				qualityImp.setRoi( fRoi );
-				quality = qualityImp.getStatistics( Measurements.MIN_MAX ).max;
-			}
+				final Polygon fPolygon = fRoi.getPolygon();
+				final double[] xpoly = new double[ fPolygon.npoints ];
+				final double[] ypoly = new double[ fPolygon.npoints ];
+				for ( int i = 0; i < fPolygon.npoints; i++ )
+				{
+					xpoly[ i ] = calibration[ 0 ] * ( interval.min( 0 ) + fPolygon.xpoints[ i ] - 0.5 );
+					ypoly[ i ] = calibration[ 1 ] * ( interval.min( 1 ) + fPolygon.ypoints[ i ] - 0.5 );
+				}
 
-			final Polygon fPolygon = fRoi.getPolygon();
-			final double[] xpoly = new double[ fPolygon.npoints ];
-			final double[] ypoly = new double[ fPolygon.npoints ];
-			for ( int i = 0; i < fPolygon.npoints; i++ )
-			{
-				xpoly[ i ] = calibration[ 0 ] * ( interval.min( 0 ) + fPolygon.xpoints[ i ] - 0.5 );
-				ypoly[ i ] = calibration[ 1 ] * ( interval.min( 1 ) + fPolygon.ypoints[ i ] - 0.5 );
-			}
+				final Spot spot = SpotRoi.createSpot( xpoly, ypoly, -1. );
 
-			spots.add( SpotRoi.createSpot( xpoly, ypoly, quality ) );
+				// Measure quality.
+				final double quality;
+				if ( null == qualityImage )
+				{
+					quality = fRoi.getStatistics().area;
+				}
+				else
+				{
+					final String name = "QualityImage";
+					final AxisType[] axes = new AxisType[] { Axes.X, Axes.Y };
+					final double[] cal = new double[] { calibration[ 0 ], calibration[ 1 ] };
+					final String[] units = new String[] { "unitX", "unitY" };
+					final ImgPlus< S > qualityImgPlus = new ImgPlus<>( ImgPlus.wrapToImg( qualityImage ), name, axes, cal, units );
+					final IterableInterval< S > iterable = SpotUtil.iterable( spot, qualityImgPlus );
+					double max = Double.NEGATIVE_INFINITY;
+					for ( final S s : iterable )
+					{
+						final double val = s.getRealDouble();
+						if ( val > max )
+							max = val;
+					}
+					quality = max;
+				}
+				spot.putFeature( Spot.QUALITY, quality );
+				spots.add( spot );
+			}
 		}
-		return spots;
+		return output;
 	}
 
 	private static final double distanceSquaredBetweenPoints( final double vx, final double vy, final double wx, final double wy )
@@ -636,7 +709,7 @@ private static final void douglasPeucker( final List< double[] > list, final int
 	 */
 	public static final List< double[] > douglasPeucker( final List< double[] > list, final double epsilon )
 	{
-		final List< double[] > resultList = new ArrayList< >();
+		final List< double[] > resultList = new ArrayList<>();
 		douglasPeucker( list, 0, list.size(), epsilon, resultList );
 		return resultList;
 	}

src/main/java/fiji/plugin/trackmate/gui/GuiUtils.java

@@ -87,6 +87,12 @@ public static final void selectAllOnFocus( final JTextField tf )
 		tf.addFocusListener( selectAllFocusListener );
 	}
 
+	public static final void setFont( final JComponent panel, final Font font )
+	{
+		for ( final Component c : panel.getComponents() )
+			c.setFont( font );
+	}
+
 	/**
 	 * Returns the black color or white color depending on the specified
 	 * background color, to ensure proper readability of the text on said
@@ -394,7 +400,7 @@ public static final ImageIcon scaleImage( final ImageIcon icon, final int w, fin
 			nw = ( icon.getIconWidth() * nh ) / icon.getIconHeight();
 		}
 
-		return new ImageIcon( icon.getImage().getScaledInstance( nw, nh, Image.SCALE_DEFAULT ) );
+		return new ImageIcon( icon.getImage().getScaledInstance( nw, nh, Image.SCALE_SMOOTH ) );
 	}
 
 	public static URL getResource( final String name, final Class< ? > clazz )