Improve automatic tracker

src/main/java/org/mastodon/tracking/detection/DetectionUtil.java

@@ -38,6 +38,7 @@
 import static org.mastodon.tracking.detection.DetectorKeys.DEFAULT_THRESHOLD;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_ADD_BEHAVIOR;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_DETECTION_TYPE;
+import static org.mastodon.tracking.detection.DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_MAX_TIMEPOINT;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_MIN_TIMEPOINT;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_RADIUS;
@@ -502,6 +503,7 @@ public static final boolean checkSettingsValidity( final Map< String, Object > s
 		ok = ok & checkParameter( settings, KEY_MAX_TIMEPOINT, Integer.class, errorHolder );
 		ok = ok & checkParameter( settings, KEY_RADIUS, Double.class, errorHolder );
 		ok = ok & checkParameter( settings, KEY_THRESHOLD, Double.class, errorHolder );
+		ok = ok & checkParameter( settings, KEY_DO_SUBPIXEL_LOCALIZATION, Boolean.class, errorHolder );
 //		ok = ok & checkParameter( settings, KEY_ADD_BEHAVIOR, String.class, errorHolder );
 
 		// Check key presence.
@@ -511,6 +513,7 @@ public static final boolean checkSettingsValidity( final Map< String, Object > s
 		mandatoryKeys.add( KEY_MAX_TIMEPOINT );
 		mandatoryKeys.add( KEY_RADIUS );
 		mandatoryKeys.add( KEY_THRESHOLD );
+		mandatoryKeys.add( KEY_DO_SUBPIXEL_LOCALIZATION );
 		final List< String > optionalKeys = new ArrayList<>();
 		optionalKeys.add( KEY_ADD_BEHAVIOR );
 		optionalKeys.add( KEY_ROI );

src/main/java/org/mastodon/tracking/detection/DetectorKeys.java

@@ -131,6 +131,23 @@ public class DetectorKeys
 	 */
 	public static final String DEFAULT_ADD_BEHAVIOR = null;
 
+	/**
+	 * The key identifying the parameter setting whether we use sub-pixel
+	 * localization for spot position. Accepted values are {@link Boolean}s.
+	 * <p>
+	 * Currently used by:
+	 * <ul>
+	 * <li>{@link LogDetectorOp}
+	 * <li>{@link DogDetectorOp}
+	 * </ul>
+	 */
+	public static final String KEY_DO_SUBPIXEL_LOCALIZATION = "DO_SUBPIXEL_LOCALIZATION";
+
+	/**
+	 * Default value for the {@link #KEY_DO_SUBPIXEL_LOCALIZATION} parameter.
+	 */
+	public static final Boolean DEFAULT_DO_SUBPIXEL_LOCALIZATION = true;
+
 	private DetectorKeys()
 	{}
 }

src/main/java/org/mastodon/tracking/detection/DoGDetectorOp.java

@@ -29,6 +29,7 @@
 package org.mastodon.tracking.detection;
 
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_DETECTION_TYPE;
+import static org.mastodon.tracking.detection.DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_MAX_TIMEPOINT;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_MIN_TIMEPOINT;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_RADIUS;
@@ -104,6 +105,7 @@ public void mutate1( final DetectionCreatorFactory detectionCreatorFactory, fina
 		final double threshold = ( double ) settings.get( KEY_THRESHOLD );
 		final Interval roi = ( Interval ) settings.get( KEY_ROI );
 		final DetectionType detectionType = DetectionType.getOrDefault( ( String ) settings.get( KEY_DETECTION_TYPE ), DetectionType.MINIMA );
+		final boolean doSubpixelLocalization = ( boolean ) settings.get( KEY_DO_SUBPIXEL_LOCALIZATION );
 
 		statusService.showStatus( "DoG detection." );
 		for ( int tp = minTimepoint; tp <= maxTimepoint; tp++ )
@@ -209,7 +211,9 @@ public void mutate1( final DetectionCreatorFactory detectionCreatorFactory, fina
 					threshold,
 					true );
 			dog.setExecutorService( threadService.getExecutorService() );
-			final ArrayList< RefinedPeak< Point > > refinedPeaks = dog.getSubpixelPeaks();
+			final ArrayList< RefinedPeak< Point > > refinedPeaks = doSubpixelLocalization ? 
+				dog.getSubpixelPeaks() :
+				dog.getPeaks().stream().map( p -> new RefinedPeak< Point >( p, p, 0, false ) ).collect( ArrayList::new, ArrayList::add, ArrayList::addAll );
 
 			final double[] pos = new double[ 3 ];
 			final RealPoint sp = RealPoint.wrap( pos );

src/main/java/org/mastodon/tracking/mamut/trackmate/semiauto/SemiAutomaticTracker.java

@@ -34,6 +34,7 @@
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_ROI;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_SETUP_ID;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_THRESHOLD;
+import static org.mastodon.tracking.detection.DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION;
 import static org.mastodon.tracking.mamut.trackmate.semiauto.SemiAutomaticTrackerKeys.KEY_ALLOW_LINKING_IF_HAS_INCOMING;
 import static org.mastodon.tracking.mamut.trackmate.semiauto.SemiAutomaticTrackerKeys.KEY_ALLOW_LINKING_IF_HAS_OUTGOING;
 import static org.mastodon.tracking.mamut.trackmate.semiauto.SemiAutomaticTrackerKeys.KEY_ALLOW_LINKING_TO_EXISTING;
@@ -190,6 +191,7 @@ public void compute( final Collection< Spot > input, final Map< String, Object >
 		final boolean continueIfLinkExists = ( boolean ) settings.get( KEY_CONTINUE_IF_LINK_EXISTS );
 		final double neighborhoodFactor = Math.max( NEIGHBORHOOD_FACTOR, distanceFactor + 1. );
 		final boolean detectSpots = ( boolean ) settings.get( KEY_DETECT_SPOT );
+		final boolean doSubpixelLocalization = ( boolean ) settings.get( KEY_DO_SUBPIXEL_LOCALIZATION );
 
 		/*
 		 * Units.
@@ -441,6 +443,7 @@ else if ( detectSpots )
 					detectorSettings.put( KEY_MIN_TIMEPOINT, Integer.valueOf( tp ) );
 					detectorSettings.put( KEY_MAX_TIMEPOINT, Integer.valueOf( tp ) );
 					detectorSettings.put( KEY_ROI, roi );
+					detectorSettings.put( KEY_DO_SUBPIXEL_LOCALIZATION, Boolean.valueOf( doSubpixelLocalization ) );
 
 					final DetectorOp detector = ( DetectorOp ) Inplaces.binary1( ops(), DoGDetectorOp.class,
 							detectionCreator, sources, detectorSettings );

src/main/java/org/mastodon/tracking/mamut/trackmate/semiauto/SemiAutomaticTrackerKeys.java

@@ -60,6 +60,7 @@ public static final Map< String, Object > getDefaultDetectorSettingsMap()
 		settings.put( KEY_ALLOW_LINKING_IF_HAS_OUTGOING, DEFAULT_ALLOW_LINKING_IF_HAS_OUTGOING );
 		settings.put( KEY_CONTINUE_IF_LINK_EXISTS, DEFAULT_CONTINUE_IF_LINK_EXISTS );
 		settings.put( KEY_DETECT_SPOT, DEFAULT_DETECT_SPOT );
+		settings.put( KEY_DO_SUBPIXEL_LOCALIZATION, DEFAULT_DO_SUBPIXEL_LOCALIZATION ); 
 		return settings;
 	}
 
@@ -95,6 +96,7 @@ public static final boolean checkSettingsValidity( final Map< String, Object > s
 		ok = ok & checkParameter( settings, KEY_ALLOW_LINKING_IF_HAS_OUTGOING, Boolean.class, errorHolder );
 		ok = ok & checkParameter( settings, KEY_CONTINUE_IF_LINK_EXISTS, Boolean.class, errorHolder );
 		ok = ok & checkParameter( settings, KEY_DETECT_SPOT, Boolean.class, errorHolder );
+		ok = ok & checkParameter( settings, KEY_DO_SUBPIXEL_LOCALIZATION, Boolean.class, errorHolder );
 
 		// Check key presence.
 		final List< String > mandatoryKeys = new ArrayList< String >();
@@ -108,6 +110,7 @@ public static final boolean checkSettingsValidity( final Map< String, Object > s
 		mandatoryKeys.add( KEY_ALLOW_LINKING_IF_HAS_OUTGOING );
 		mandatoryKeys.add( KEY_CONTINUE_IF_LINK_EXISTS );
 		mandatoryKeys.add( KEY_DETECT_SPOT );
+		mandatoryKeys.add( KEY_DO_SUBPIXEL_LOCALIZATION );
 		final List< String > optionalKeys = new ArrayList< String >();
 		optionalKeys.add( KEY_RESOLUTION_LEVEL );
 		ok = ok & checkMapKeys( settings, mandatoryKeys, optionalKeys, errorHolder );
@@ -299,6 +302,23 @@ public static final boolean checkSettingsValidity( final Map< String, Object > s
 	 */
 	public static final boolean DEFAULT_DETECT_SPOT = true;
 
+	/**
+	 * The key identifying the parameter setting whether we use sub-pixel
+	 * localization for spot position. Accepted values are {@link Boolean}s.
+	 * <p>
+	 * Currently used by:
+	 * <ul>
+	 * <li>{@link LogDetectorOp}
+	 * <li>{@link DogDetectorOp}
+	 * </ul>
+	 */
+	public static final String KEY_DO_SUBPIXEL_LOCALIZATION = "DO_SUBPIXEL_LOCALIZATION";
+
+	/**
+	 * Default value for the {@link #KEY_DO_SUBPIXEL_LOCALIZATION} parameter.
+	 */
+	public static final Boolean DEFAULT_DO_SUBPIXEL_LOCALIZATION = true;
+
 	/** Minimal size of neighborhoods, in spot diameter units. */
 	public static final double NEIGHBORHOOD_FACTOR = 2.;
 

src/main/java/org/mastodon/tracking/mamut/trackmate/semiauto/ui/SemiAutomaticTrackerConfigPanel.java

@@ -119,6 +119,11 @@ public class SemiAutomaticTrackerConfigPanel extends JPanel
 			+ "to create spots to link to from the image data. "
 			+ "</p></html>";
 
+	private static final String DO_SUBPIXEL_LOCALIZATION_TOOLTIP = "<html><p width=\"500\"> "
+			+ "Parameter that specifies whether we use sub-pixel "
+			+ "localization for spot detection. "
+			+ "</p></html>";
+
 	/**
 	 * The cancel button.
 	 */
@@ -140,9 +145,9 @@ public SemiAutomaticTrackerConfigPanel(
 
 		final GridBagLayout gbl = new GridBagLayout();
 		gbl.columnWidths = new int[] { 0, 0, 0 };
-		gbl.rowHeights = new int[] { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
+		gbl.rowHeights = new int[] { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
 		gbl.columnWeights = new double[] { 0.0, 1.0, Double.MIN_VALUE };
-		gbl.rowWeights = new double[] { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, Double.MIN_VALUE };
+		gbl.rowWeights = new double[] { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, Double.MIN_VALUE };
 		setLayout( gbl );
 
 		final JLabel lblDetection = new JLabel( "Detection." );
@@ -355,6 +360,17 @@ public SemiAutomaticTrackerConfigPanel(
 		gbcChckbxDetectSpot.gridy = 14;
 		add( chckbxDetectSpot, gbcChckbxDetectSpot );
 
+		final JCheckBox chckbxDoSubpixelLocalization = new JCheckBox("Do sub-pixel localization?");
+		chckbxDoSubpixelLocalization.setToolTipText( DO_SUBPIXEL_LOCALIZATION_TOOLTIP );
+		chckbxDoSubpixelLocalization.addItemListener( ( e ) -> editedSettings.setDoSubpixelLocalization( chckbxDoSubpixelLocalization.isSelected() ) );
+		final GridBagConstraints gbcChckbxDoSubpixelLocalization = new GridBagConstraints();
+		gbcChckbxDoSubpixelLocalization.anchor = GridBagConstraints.WEST;
+		gbcChckbxDoSubpixelLocalization.gridwidth = 2;
+		gbcChckbxDoSubpixelLocalization.insets = new Insets( 5, 5, 5, 0 );
+		gbcChckbxDoSubpixelLocalization.gridx = 0;
+		gbcChckbxDoSubpixelLocalization.gridy = 15;
+		add( chckbxDoSubpixelLocalization, gbcChckbxDoSubpixelLocalization );
+
 		final JSeparator sep3 = new JSeparator();
 		sep3.setMinimumSize( new Dimension( 5, 10 ) );
 		final GridBagConstraints gbcSeparator3 = new GridBagConstraints();
@@ -363,7 +379,7 @@ public SemiAutomaticTrackerConfigPanel(
 		gbcSeparator3.gridwidth = 2;
 		gbcSeparator3.insets = new Insets( 0, 0, 5, 0 );
 		gbcSeparator3.gridx = 0;
-		gbcSeparator3.gridy = 15;
+		gbcSeparator3.gridy = 16;
 		add( sep3, gbcSeparator3 );
 
 		final JLabel lblNavigation = new JLabel( "Navigation." );
@@ -373,7 +389,7 @@ public SemiAutomaticTrackerConfigPanel(
 		gbcLblNavigation.gridwidth = 2;
 		gbcLblNavigation.insets = new Insets( 5, 5, 5, 0 );
 		gbcLblNavigation.gridx = 0;
-		gbcLblNavigation.gridy = 16;
+		gbcLblNavigation.gridy = 17;
 		add( lblNavigation, gbcLblNavigation );
 
 		if ( null != groupHandle )
@@ -384,7 +400,7 @@ public SemiAutomaticTrackerConfigPanel(
 			gbcGroupLocksPanel.insets = new Insets( 0, 0, 5, 0 );
 			gbcGroupLocksPanel.fill = GridBagConstraints.BOTH;
 			gbcGroupLocksPanel.gridx = 0;
-			gbcGroupLocksPanel.gridy = 17;
+			gbcGroupLocksPanel.gridy = 18;
 			add( groupLocksPanel, gbcGroupLocksPanel );
 		}
 
@@ -395,7 +411,7 @@ public SemiAutomaticTrackerConfigPanel(
 		gbcPanelButtons.insets = new Insets( 5, 5, 0, 0 );
 		gbcPanelButtons.fill = GridBagConstraints.HORIZONTAL;
 		gbcPanelButtons.gridx = 0;
-		gbcPanelButtons.gridy = 19;
+		gbcPanelButtons.gridy = 20;
 		add( panelButtons, gbcPanelButtons );
 		panelButtons.setLayout( new BoxLayout( panelButtons, BoxLayout.X_AXIS ) );
 
@@ -417,6 +433,7 @@ public SemiAutomaticTrackerConfigPanel(
 			chckbxLinkOutgoing.setSelected( editedSettings.allowIfOutgoingLinks() );
 			chckbxContinueTracking.setSelected( editedSettings.continueIfLinked() );
 			chckbxDetectSpot.setSelected( editedSettings.detectSpot() );
+			chckbxDoSubpixelLocalization.setSelected( editedSettings.doSubpixelLocalization() );
 			repaint();
 		};
 		final ItemListener disabler = ( e ) -> {

src/main/java/org/mastodon/tracking/mamut/trackmate/semiauto/ui/SemiAutomaticTrackerSettings.java

@@ -28,7 +28,9 @@
  */
 package org.mastodon.tracking.mamut.trackmate.semiauto.ui;
 
+import static org.mastodon.tracking.detection.DetectorKeys.DEFAULT_DO_SUBPIXEL_LOCALIZATION;
 import static org.mastodon.tracking.detection.DetectorKeys.DEFAULT_SETUP_ID;
+import static org.mastodon.tracking.detection.DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION;
 import static org.mastodon.tracking.detection.DetectorKeys.KEY_SETUP_ID;
 import static org.mastodon.tracking.mamut.trackmate.semiauto.SemiAutomaticTrackerKeys.DEFAULT_ALLOW_LINKING_IF_HAS_INCOMING;
 import static org.mastodon.tracking.mamut.trackmate.semiauto.SemiAutomaticTrackerKeys.DEFAULT_ALLOW_LINKING_IF_HAS_OUTGOING;
@@ -92,6 +94,8 @@ public interface UpdateListener
 
 	private boolean detectSpot;
 
+	private boolean doSubpixelLocalization;
+
 	private static final SemiAutomaticTrackerSettings defSats;
 	static
 	{
@@ -106,6 +110,7 @@ public interface UpdateListener
 		defSats.allowIfOutgoingLinks = DEFAULT_ALLOW_LINKING_IF_HAS_OUTGOING;
 		defSats.continueIfLinked = DEFAULT_CONTINUE_IF_LINK_EXISTS;
 		defSats.detectSpot = DEFAULT_DETECT_SPOT;
+		defSats.doSubpixelLocalization = DEFAULT_DO_SUBPIXEL_LOCALIZATION;
 		defSats.name = "Forward";
 	}
 
@@ -123,6 +128,7 @@ public interface UpdateListener
 		backSats.allowIfOutgoingLinks = Boolean.valueOf( true );
 		backSats.continueIfLinked = Boolean.valueOf( false );
 		backSats.detectSpot = DEFAULT_DETECT_SPOT;
+		backSats.doSubpixelLocalization = DEFAULT_DO_SUBPIXEL_LOCALIZATION;
 		backSats.name = "Backtracking";
 	}
 
@@ -169,6 +175,7 @@ public void set( final SemiAutomaticTrackerSettings stas )
 		this.allowIfOutgoingLinks = stas.allowIfOutgoingLinks;
 		this.continueIfLinked = stas.continueIfLinked;
 		this.detectSpot = stas.detectSpot;
+		this.doSubpixelLocalization = stas.doSubpixelLocalization;
 		notifyListeners();
 	}
 
@@ -185,6 +192,7 @@ public Map< String, Object > getAsSettingsMap()
 		map.put( KEY_ALLOW_LINKING_IF_HAS_OUTGOING, Boolean.valueOf( allowIfOutgoingLinks ) );
 		map.put( KEY_CONTINUE_IF_LINK_EXISTS, Boolean.valueOf( continueIfLinked ) );
 		map.put( KEY_DETECT_SPOT, Boolean.valueOf( detectSpot ) );
+		map.put( KEY_DO_SUBPIXEL_LOCALIZATION, Boolean.valueOf( doSubpixelLocalization ) );
 		return map;
 	}
 
@@ -328,6 +336,20 @@ public void setDetectSpot( final boolean detectSpot )
 		}
 	}
 
+	public boolean doSubpixelLocalization()
+	{
+		return doSubpixelLocalization;
+	}
+
+	public void setDoSubpixelLocalization( final boolean doSubpixelLocalization )
+	{
+		if ( this.doSubpixelLocalization != doSubpixelLocalization )
+		{
+			this.doSubpixelLocalization = doSubpixelLocalization;
+			notifyListeners();
+		}
+	}
+
 	@Override
 	public SemiAutomaticTrackerSettings copy()
 	{

src/main/java/org/mastodon/tracking/mamut/trackmate/semiauto/ui/SemiAutomaticTrackerSettingsIO.java

@@ -28,6 +28,7 @@
  */
 package org.mastodon.tracking.mamut.trackmate.semiauto.ui;
 
+import static org.mastodon.tracking.detection.DetectorKeys.DEFAULT_DO_SUBPIXEL_LOCALIZATION;
 import static org.mastodon.tracking.mamut.trackmate.semiauto.SemiAutomaticTrackerKeys.DEFAULT_ALLOW_LINKING_IF_HAS_INCOMING;
 import static org.mastodon.tracking.mamut.trackmate.semiauto.SemiAutomaticTrackerKeys.DEFAULT_ALLOW_LINKING_IF_HAS_OUTGOING;
 import static org.mastodon.tracking.mamut.trackmate.semiauto.SemiAutomaticTrackerKeys.DEFAULT_ALLOW_LINKING_TO_EXISTING;
@@ -121,6 +122,7 @@ public Node representData( final Object data )
 			mapping.put( "allowIfOutgoingLinks", s.allowIfOutgoingLinks() );
 			mapping.put( "continueIfLinked", s.continueIfLinked() );
 			mapping.put( "detectSpot", s.detectSpot() );
+			mapping.put( "doSubpixelLocalization", s.doSubpixelLocalization() );
 
 			final Node node = representMapping( getTag(), mapping, getDefaultFlowStyle() );
 			return node;
@@ -152,6 +154,7 @@ public Object construct( final Node node ) throws YAMLException
 			s.setAllowIfOutgoingLinks( getBooleanOrDefault( mapping, "allowIfOutgoingLinks", DEFAULT_ALLOW_LINKING_IF_HAS_OUTGOING ) );
 			s.setContinueIfLinked( getBooleanOrDefault( mapping, "continueIfLinked", DEFAULT_CONTINUE_IF_LINK_EXISTS ) );
 			s.setDetectSpot( getBooleanOrDefault( mapping, "detectSpot", DEFAULT_DETECT_SPOT ) );
+			s.setDoSubpixelLocalization( getBooleanOrDefault( mapping, "doSubpixelLocalization", DEFAULT_DO_SUBPIXEL_LOCALIZATION ) );
 
 			return s;
 		}

src/main/java/org/mastodon/tracking/mamut/trackmate/wizard/descriptors/AdvancedDoGDetectorDescriptor.java

@@ -155,8 +155,9 @@ public void aboutToHidePanel()
 		final double minSizePixel = DoGDetectorOp.MIN_SPOT_PIXEL_SIZE / 2.;
 		final int timepoint = ( int ) settings.values.getDetectorSettings().get( KEY_MIN_TIMEPOINT );
 		final double threshold = ( double ) settings.values.getDetectorSettings().get( KEY_THRESHOLD );
+		final boolean doSubpixelLocalization = ( boolean ) settings.values.getDetectorSettings().get( DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION );
 		final List< SourceAndConverter< ? > > sources = settings.values.getSources();
-		logger.info( WizardUtils.echoDetectorConfigInfo( sources, minSizePixel, timepoint, setupID, radius, threshold ) );
+		logger.info( WizardUtils.echoDetectorConfigInfo( sources, minSizePixel, timepoint, setupID, radius, threshold, doSubpixelLocalization ) );
 		final String addBehavior = ( String ) settings.values.getDetectorSettings().get( KEY_ADD_BEHAVIOR );
 		logger.info( String.format( "  - dealing with existing spot: %s.\n", addBehavior ) );
 	}