Support 3D segmentation with TrackMate-Weka.

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>34.0.0</version>
+		<version>37.0.0</version>
 		<relativePath />
 	</parent>
 
@@ -86,7 +86,7 @@
 
 		<javaGeom.version>0.11.1</javaGeom.version>
 
-		<TrackMate.version>7.10.2</TrackMate.version>
+		<TrackMate.version>8.0.0-SNAPSHOT</TrackMate.version>
 	</properties>
 
 	<dependencies>

src/main/java/fiji/plugin/trackmate/weka/WekaDetectionPreviewer.java

@@ -22,6 +22,7 @@
 package fiji.plugin.trackmate.weka;
 
 import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_TARGET_CHANNEL;
+import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SMOOTHING_SCALE;
 import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_CLASSIFIER_FILEPATH;
 import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_CLASS_INDEX;
 import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_PROBA_THRESHOLD;
@@ -108,13 +109,16 @@ protected Pair< Model, Double > runPreviewDetection(
 		 */
 
 		final Map< String, Object > dsettings = new HashMap<>( detectorSettings );
-		@SuppressWarnings( "unchecked" )
 		final ImgPlus< T > img = TMUtils.rawWraps( settings.imp );
 		final int channel = ( Integer ) dsettings.get( KEY_TARGET_CHANNEL ) - 1;
 		final ImgPlus< T > input = TMUtils.hyperSlice( img, channel, frame );
 		final int classIndex = ( Integer ) dsettings.get( KEY_CLASS_INDEX );
 		final double probaThreshold = ( Double ) dsettings.get( KEY_PROBA_THRESHOLD );
 		final boolean simplify = true;
+		final Object smoothingObj = dsettings.get( KEY_SMOOTHING_SCALE );
+		final double smoothingScale = smoothingObj == null
+				? -1.
+				: ( ( Number ) smoothingObj ).doubleValue();
 
 		final boolean is3D = input.dimensionIndex( Axes.Z ) >= 0;
 		// First test to make sure we can read the classifier file.
@@ -180,7 +184,7 @@ protected Pair< Model, Double > runPreviewDetection(
 		}
 
 		logger.log( "Creating spots from probabilities." );
-		final List< Spot > spots = wekaRunner.getSpotsFromLastProbabilities( probaThreshold, simplify );
+		final List< Spot > spots = wekaRunner.getSpotsFromLastProbabilities( probaThreshold, simplify, smoothingScale );
 		if ( spots == null )
 		{
 			logger.error( "Problem creating spots: " + wekaRunner.getErrorMessage() );

src/main/java/fiji/plugin/trackmate/weka/WekaDetector.java

@@ -59,20 +59,24 @@ public class WekaDetector< T extends RealType< T > & NativeType< T > > implement
 
 	private final boolean simplify;
 
+	private final double smoothingScale;
+
 	public WekaDetector(
 			final WekaRunner< T > runner,
 			final ImgPlus< T > img,
 			final Interval interval,
 			final int classIndex,
 			final double probaThreshold,
-			final boolean simplify )
+			final boolean simplify,
+			final double smoothingScale )
 	{
 		this.runner = runner;
 		this.img = img;
 		this.interval = DetectionUtils.squeeze( interval );
 		this.classIndex = classIndex;
 		this.probaThreshold = probaThreshold;
 		this.simplify = simplify;
+		this.smoothingScale = smoothingScale;
 		this.baseErrorMessage = BASE_ERROR_MESSAGE;
 	}
 
@@ -99,7 +103,7 @@ public boolean process()
 			return false;
 		}
 
-		spots = runner.getSpots( probabilities, TMUtils.getSpatialCalibration( img ), probaThreshold, simplify );
+		spots = runner.getSpots( probabilities, TMUtils.getSpatialCalibration( img ), probaThreshold, simplify, smoothingScale );
 		if ( spots == null )
 		{
 			System.err.println( "Problem creating spots: " + runner.getErrorMessage() );

src/main/java/fiji/plugin/trackmate/weka/WekaDetectorConfigurationPanel.java

@@ -22,6 +22,7 @@
 package fiji.plugin.trackmate.weka;
 
 import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_TARGET_CHANNEL;
+import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SMOOTHING_SCALE;
 import static fiji.plugin.trackmate.gui.Fonts.BIG_FONT;
 import static fiji.plugin.trackmate.gui.Fonts.FONT;
 import static fiji.plugin.trackmate.gui.Fonts.SMALL_FONT;
@@ -30,15 +31,12 @@
 import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_CLASS_INDEX;
 import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_PROBA_THRESHOLD;
 
-import java.awt.Dimension;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.awt.Insets;
 import java.beans.PropertyChangeListener;
 import java.io.File;
 import java.net.URL;
-import java.text.DecimalFormat;
-import java.text.NumberFormat;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -49,7 +47,6 @@
 import javax.swing.ImageIcon;
 import javax.swing.JButton;
 import javax.swing.JComboBox;
-import javax.swing.JFormattedTextField;
 import javax.swing.JLabel;
 import javax.swing.JSlider;
 import javax.swing.JTextField;
@@ -64,6 +61,8 @@
 import fiji.plugin.trackmate.Settings;
 import fiji.plugin.trackmate.gui.GuiUtils;
 import fiji.plugin.trackmate.gui.components.ConfigurationPanel;
+import fiji.plugin.trackmate.gui.components.PanelProbaThreshold;
+import fiji.plugin.trackmate.gui.components.PanelSmoothContour;
 import fiji.plugin.trackmate.util.EverythingDisablerAndReenabler;
 import fiji.plugin.trackmate.util.FileChooser;
 import fiji.plugin.trackmate.util.FileChooser.DialogType;
@@ -78,8 +77,6 @@ public class WekaDetectorConfigurationPanel extends ConfigurationPanel
 
 	private static final long serialVersionUID = 1L;
 
-	private static final NumberFormat THRESHOLD_FORMAT = new DecimalFormat( "#.##" );
-
 	protected static final ImageIcon ICON = new ImageIcon( getResource( "images/TrackMateWeka-logo-100px.png" ) );
 
 	private static final String TITLE = WekaDetectorFactory.NAME;
@@ -94,14 +91,16 @@ public class WekaDetectorConfigurationPanel extends ConfigurationPanel
 
 	private final JButton btnBrowse;
 
-	private final JFormattedTextField ftfProbaThreshold;
-
 	protected final PrefService prefService;
 
 	private final WekaDetectionPreviewer< ? > previewer;
 
 	private final boolean is3D;
 
+	private final PanelSmoothContour smoothingPanel;
+
+	private final PanelProbaThreshold probaThresholdPanel;
+
 	/**
 	 * Create the panel.
 	 */
@@ -238,25 +237,29 @@ public WekaDetectorConfigurationPanel( final Settings settings, final Model mode
 		 * Proba threshold.
 		 */
 
-		final JLabel lblScoreTreshold = new JLabel( "Threshold on probability:" );
-		lblScoreTreshold.setFont( SMALL_FONT );
-		final GridBagConstraints gbcLblScoreTreshold = new GridBagConstraints();
-		gbcLblScoreTreshold.anchor = GridBagConstraints.EAST;
-		gbcLblScoreTreshold.insets = new Insets( 5, 5, 5, 5 );
-		gbcLblScoreTreshold.gridx = 0;
-		gbcLblScoreTreshold.gridy = 6;
-		add( lblScoreTreshold, gbcLblScoreTreshold );
-
-		ftfProbaThreshold = new JFormattedTextField( THRESHOLD_FORMAT );
-		ftfProbaThreshold.setFont( SMALL_FONT );
-		ftfProbaThreshold.setMinimumSize( new Dimension( 60, 20 ) );
-		ftfProbaThreshold.setHorizontalAlignment( SwingConstants.CENTER );
+		probaThresholdPanel = new PanelProbaThreshold( 0.5 );
 		final GridBagConstraints gbcScore = new GridBagConstraints();
 		gbcScore.fill = GridBagConstraints.HORIZONTAL;
+		gbcScore.anchor = GridBagConstraints.NORTHWEST;
 		gbcScore.insets = new Insets( 5, 5, 5, 5 );
-		gbcScore.gridx = 1;
+		gbcScore.gridx = 0;
 		gbcScore.gridy = 6;
-		add( ftfProbaThreshold, gbcScore );
+		gbcScore.gridwidth = 3;
+		add( probaThresholdPanel, gbcScore );
+
+		/*
+		 * Smooth output.
+		 */
+
+		smoothingPanel = new PanelSmoothContour( -1., model.getSpaceUnits() );
+		final GridBagConstraints gbSmoothPanel = new GridBagConstraints();
+		gbSmoothPanel.anchor = GridBagConstraints.NORTHWEST;
+		gbSmoothPanel.insets = new Insets( 5, 5, 5, 5 );
+		gbSmoothPanel.gridwidth = 3;
+		gbSmoothPanel.gridx = 0;
+		gbSmoothPanel.gridy = 7;
+		gbSmoothPanel.fill = GridBagConstraints.HORIZONTAL;
+		this.add( smoothingPanel, gbSmoothPanel );
 
 		/*
 		 * Refresh class names.
@@ -269,7 +272,7 @@ public WekaDetectorConfigurationPanel( final Settings settings, final Model mode
 		gbcBtnClassNames.anchor = GridBagConstraints.SOUTHWEST;
 		gbcBtnClassNames.insets = new Insets( 5, 5, 5, 5 );
 		gbcBtnClassNames.gridx = 0;
-		gbcBtnClassNames.gridy = 7;
+		gbcBtnClassNames.gridy = 8;
 		add( btnClassNames, gbcBtnClassNames );
 
 		/*
@@ -283,7 +286,7 @@ public WekaDetectorConfigurationPanel( final Settings settings, final Model mode
 		gbcBtnLastProba.anchor = GridBagConstraints.SOUTHEAST;
 		gbcBtnLastProba.insets = new Insets( 5, 5, 5, 5 );
 		gbcBtnLastProba.gridx = 1;
-		gbcBtnLastProba.gridy = 7;
+		gbcBtnLastProba.gridy = 8;
 		add( btnLastProba, gbcBtnLastProba );
 
 		/*
@@ -295,7 +298,7 @@ public WekaDetectorConfigurationPanel( final Settings settings, final Model mode
 		gbcBtnPreview.fill = GridBagConstraints.BOTH;
 		gbcBtnPreview.insets = new Insets( 5, 5, 5, 5 );
 		gbcBtnPreview.gridx = 0;
-		gbcBtnPreview.gridy = 8;
+		gbcBtnPreview.gridy = 9;
 
 		previewer = new WekaDetectionPreviewer<>(
 				model,
@@ -355,8 +358,11 @@ public Map< String, Object > getSettings()
 		final int classID = cmbboxClassId.getSelectedIndex();
 		settings.put( KEY_CLASS_INDEX, classID );
 
-		final double probaThreshold = ( ( Number ) ftfProbaThreshold.getValue() ).doubleValue();
+		final double probaThreshold = probaThresholdPanel.getThreshold();
 		settings.put( KEY_PROBA_THRESHOLD, probaThreshold );
+
+		final double scale = smoothingPanel.getScale();
+		settings.put( KEY_SMOOTHING_SCALE, scale );
 		return settings;
 	}
 
@@ -369,7 +375,14 @@ public void setSettings( final Map< String, Object > settings )
 		modelFileTextField.setText( filePath );
 		cmbboxClassId.setSelectedIndex( ( Integer ) settings.get( KEY_CLASS_INDEX ) );
 		sliderChannel.setValue( ( Integer ) settings.get( KEY_TARGET_CHANNEL ) );
-		ftfProbaThreshold.setValue( settings.get( KEY_PROBA_THRESHOLD ) );
+
+		final Object thresholdObj = settings.get( KEY_PROBA_THRESHOLD );
+		final double threshold = thresholdObj == null ? -1. : ( ( Number ) thresholdObj ).doubleValue();
+		probaThresholdPanel.setThreshold( threshold );
+
+		final Object scaleObj = settings.get( KEY_SMOOTHING_SCALE );
+		final double scale = scaleObj == null ? -1. : ( ( Number ) scaleObj ).doubleValue();
+		smoothingPanel.setScale( scale );
 	}
 
 	@Override

src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -23,12 +23,14 @@
 
 import static fiji.plugin.trackmate.detection.DetectorKeys.DEFAULT_TARGET_CHANNEL;
 import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_TARGET_CHANNEL;
+import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SMOOTHING_SCALE;
 import static fiji.plugin.trackmate.io.IOUtils.readDoubleAttribute;
 import static fiji.plugin.trackmate.io.IOUtils.readIntegerAttribute;
 import static fiji.plugin.trackmate.io.IOUtils.readStringAttribute;
 import static fiji.plugin.trackmate.io.IOUtils.writeAttribute;
 import static fiji.plugin.trackmate.io.IOUtils.writeTargetChannel;
 import static fiji.plugin.trackmate.util.TMUtils.checkMapKeys;
+import static fiji.plugin.trackmate.util.TMUtils.checkOptionalParameter;
 import static fiji.plugin.trackmate.util.TMUtils.checkParameter;
 
 import java.util.ArrayList;
@@ -39,6 +41,7 @@
 import javax.swing.ImageIcon;
 
 import org.jdom2.Element;
+import org.scijava.Priority;
 import org.scijava.plugin.Plugin;
 
 import fiji.plugin.trackmate.Model;
@@ -54,7 +57,7 @@
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
 
-@Plugin( type = SpotDetectorFactory.class )
+@Plugin( type = SpotDetectorFactory.class, priority = Priority.LOW - 4.1 )
 public class WekaDetectorFactory< T extends RealType< T > & NativeType< T > > implements SpotDetectorFactory< T >
 {
 
@@ -92,7 +95,8 @@ public class WekaDetectorFactory< T extends RealType< T > & NativeType< T > > im
 	public static final String INFO_TEXT = "<html>"
 			+ "This detector relies on the 'Trainable Weka segmentation' plugin to detect objects."
 			+ "<p>"
-			+ "It works for 2D and 3D images, but returns contours only for 2D images."
+			+ "It works for 2D and 3D images, returns contours for 2D images and meshes"
+			+ "for 3D images."
 			+ "<p>"
 			+ "You need to provide the path to a classifier previously trained and saved using the "
 			+ "'Trainable Weka segmentation' plugin. It will classically be a '.model' file. "
@@ -132,13 +136,18 @@ public SpotDetector< T > getDetector( final Interval interval, final int frame )
 		final int classIndex = ( Integer ) settings.get( KEY_CLASS_INDEX );
 		final double probaThreshold = ( Double ) settings.get( KEY_PROBA_THRESHOLD );
 		final boolean simplify = true;
+		final Object smoothingObj = settings.get( KEY_SMOOTHING_SCALE );
+		final double smoothingScale = smoothingObj == null
+				? -1.
+				: ( ( Number ) smoothingObj ).doubleValue();
 		final WekaDetector< T > detector = new WekaDetector<>(
 				runner,
 				input,
 				interval,
 				classIndex,
 				probaThreshold,
-				simplify );
+				simplify,
+				smoothingScale );
 		return detector;
 	}
 
@@ -197,6 +206,7 @@ public boolean marshall( final Map< String, Object > settings, final Element ele
 		ok = ok && writeAttribute( settings, element, KEY_CLASSIFIER_FILEPATH, String.class, errorHolder );
 		ok = ok && writeAttribute( settings, element, KEY_CLASS_INDEX, Integer.class, errorHolder );
 		ok = ok && writeAttribute( settings, element, KEY_PROBA_THRESHOLD, Double.class, errorHolder );
+		ok = ok && writeAttribute( settings, element, KEY_SMOOTHING_SCALE, Double.class, errorHolder );
 
 		if ( !ok )
 			errorMessage = errorHolder.toString();
@@ -214,6 +224,7 @@ public boolean unmarshall( final Element element, final Map< String, Object > se
 		ok = ok && readStringAttribute( element, settings, KEY_CLASSIFIER_FILEPATH, errorHolder );
 		ok = ok && readIntegerAttribute( element, settings, KEY_CLASS_INDEX, errorHolder );
 		ok = ok && readDoubleAttribute( element, settings, KEY_PROBA_THRESHOLD, errorHolder );
+		ok = ok & readDoubleAttribute( element, settings, KEY_SMOOTHING_SCALE, errorHolder );
 
 		if ( !ok )
 		{
@@ -237,6 +248,7 @@ public Map< String, Object > getDefaultSettings()
 		settings.put( KEY_CLASS_INDEX, DEFAULT_CLASS_INDEX );
 		settings.put( KEY_PROBA_THRESHOLD, DEFAULT_PROBA_THRESHOLD );
 		settings.put( KEY_CLASSIFIER_FILEPATH, null );
+		settings.put( KEY_SMOOTHING_SCALE, -1. );
 		return settings;
 	}
 
@@ -249,12 +261,15 @@ public boolean checkSettings( final Map< String, Object > settings )
 		ok = ok & checkParameter( settings, KEY_CLASS_INDEX, Integer.class, errorHolder );
 		ok = ok & checkParameter( settings, KEY_PROBA_THRESHOLD, Double.class, errorHolder );
 		ok = ok & checkParameter( settings, KEY_CLASSIFIER_FILEPATH, String.class, errorHolder );
+		ok = ok & checkOptionalParameter( settings, KEY_SMOOTHING_SCALE, Double.class, errorHolder );
 		final List< String > mandatoryKeys = new ArrayList<>();
 		mandatoryKeys.add( KEY_TARGET_CHANNEL );
 		mandatoryKeys.add( KEY_CLASS_INDEX );
 		mandatoryKeys.add( KEY_PROBA_THRESHOLD );
 		mandatoryKeys.add( KEY_CLASSIFIER_FILEPATH );
-		ok = ok & checkMapKeys( settings, mandatoryKeys, null, errorHolder );
+		final List< String > optionalKeys = new ArrayList<>();
+		optionalKeys.add( KEY_SMOOTHING_SCALE );
+		ok = ok & checkMapKeys( settings, mandatoryKeys, optionalKeys, errorHolder );
 		if ( !ok )
 			errorMessage = errorHolder.toString();