Fix all javadoc warnings.

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

@@ -49,8 +49,11 @@ public SpotMesh(
 	 * calculated from the mesh.
 	 * 
 	 * @param quality
+	 *            the spot quality.
 	 * @param name
+	 *            the spot name.
 	 * @param m
+	 *            the mesh to create the spot from.
 	 */
 	public SpotMesh(
 			final Mesh m,
@@ -93,7 +96,9 @@ public SpotMesh(
 	 * otherwise.
 	 * 
 	 * @param ID
+	 *            the ID to create the spot with.
 	 * @param mesh
+	 *            the mesh used to create the spot.
 	 */
 	public SpotMesh( final int ID, final BufferMesh mesh )
 	{
@@ -190,7 +195,9 @@ public void resetZSliceCache()
 	/**
 	 * Returns the radius of the equivalent sphere with the same volume that of
 	 * the specified mesh.
-	 *
+	 * 
+	 * @param mesh
+	 *            the mesh.
 	 * @return the radius in physical units.
 	 */
 	public static final double radius( final Mesh mesh )

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

@@ -67,8 +67,11 @@ public SpotRoi(
 	 * otherwise.
 	 * 
 	 * @param ID
+	 *            the ID to use when creating the spot.
 	 * @param x
+	 *            the spot contour X coordinates.
 	 * @param y
+	 *            the spot contour Y coordinates.
 	 */
 	public SpotRoi(
 			final int ID,

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

@@ -111,8 +111,11 @@ else if ( imp.getType() == ImagePlus.COLOR_RGB )
 	 * launched by this plugin.
 	 * 
 	 * @param trackmate
+	 *            the TrackMate instance.
 	 * @param selectionModel
+	 *            the selection model.
 	 * @param displaySettings
+	 *            the display settings.
 	 * @return a new sequence.
 	 */
 	protected WizardSequence createSequence( final TrackMate trackmate, final SelectionModel selectionModel, final DisplaySettings displaySettings )
@@ -126,7 +129,7 @@ protected WizardSequence createSequence( final TrackMate trackmate, final Select
 	 * {@link TrackMate} instance.
 	 * 
 	 * @param imp
-	 *
+	 *            the image the tracking data will be created on.
 	 * @return a new {@link Model} instance.
 	 */
 	protected Model createModel( final ImagePlus imp )
@@ -161,7 +164,11 @@ protected Settings createSettings( final ImagePlus imp )
 	/**
 	 * Hook for subclassers: <br>
 	 * Creates the TrackMate instance that will be controlled in the GUI.
-	 *
+	 * 
+	 * @param model
+	 *            the model to create the TrackMate instance with.
+	 * @param settings
+	 *            the settings to create the TrackMate instance with.
 	 * @return a new {@link TrackMate} instance.
 	 */
 	protected TrackMate createTrackMate( final Model model, final Settings settings )
@@ -175,7 +182,9 @@ protected TrackMate createTrackMate( final Model model, final Settings settings
 		model.setPhysicalUnits( spaceUnits, timeUnits );
 
 		final TrackMate trackmate = new TrackMate( model, settings );
-		ObjectService objectService = TMUtils.getContext().service( ObjectService.class );
+
+		// Register it to the object service.
+		final ObjectService objectService = TMUtils.getContext().service( ObjectService.class );
 		if ( objectService != null )
 			objectService.addObject( trackmate );
 

src/main/java/fiji/plugin/trackmate/action/CTCExporter.java

@@ -184,6 +184,8 @@ public static String exportAll( final String exportRootFolder, final TrackMate t
 	 *            the trackmate to export.
 	 * @param logger
 	 *            a logger to report progress.
+	 * @throws IOException
+	 *             if there's any problem writing.
 	 */
 	public static void exportSettingsFile( final String exportRootFolder, final int saveId, final TrackMate trackmate, final Logger logger ) throws IOException
 	{

src/main/java/fiji/plugin/trackmate/action/CaptureOverlayAction.java

@@ -120,7 +120,7 @@ public void execute( final TrackMate trackmate, final SelectionModel selectionMo
 					TMUtils.getSpatialCalibration( imp ) );
 			if ( whiteBackground )
 			{
-				ImageProcessor ip = imp2.getProcessor();
+				final ImageProcessor ip = imp2.getProcessor();
 				ip.invertLut();
 				if ( imp2.getStackSize() > 1 )
 					imp2.getStack().setColorModel( ip.getColorModel() );
@@ -153,6 +153,8 @@ public void execute( final TrackMate trackmate, final SelectionModel selectionMo
 	 *            the first frame, inclusive, to capture.
 	 * @param last
 	 *            the last frame, inclusive, to capture.
+	 * @param logger
+	 *            a logger instance to echo capture progress.
 	 * @return a new ImagePlus.
 	 */
 	public static ImagePlus capture( final TrackMate trackmate, final int first, final int last, final Logger logger )

src/main/java/fiji/plugin/trackmate/action/LabelImgExporter.java

@@ -294,6 +294,9 @@ public static final ImagePlus createLabelImagePlus(
 	 *            the desired dimensions of the output image (width, height,
 	 *            nZSlices, nFrames) as a 4 element int array. Spots outside
 	 *            these dimensions are ignored.
+	 * @param calibration
+	 *            the pixel size to map physical spot coordinates to pixel
+	 *            coordinates.
 	 * @param exportSpotsAsDots
 	 *            if <code>true</code>, spots will be painted as single dots
 	 *            instead of ellipsoids.
@@ -303,10 +306,10 @@ public static final ImagePlus createLabelImagePlus(
 	 *            belonging to a track will be painted with a unique ID,
 	 *            different from the track IDs and different for each spot.
 	 * @param useSpotIDsAsLabels
-	 * 	          if <code>true</code>, the label mask images will contain 
-	 * 	          the spot ID. If <code>false</code>, the label mask images 
-	 * 	          will contain the track ID.
-	 * 	          
+	 *            if <code>true</code>, the label mask images will contain the
+	 *            spot ID. If <code>false</code>, the label mask images will
+	 *            contain the track ID.
+	 * 
 	 * @return a new {@link ImagePlus}.
 	 */
 	public static final ImagePlus createLabelImagePlus(
@@ -331,6 +334,9 @@ public static final ImagePlus createLabelImagePlus(
 	 *            the desired dimensions of the output image (width, height,
 	 *            nZSlices, nFrames) as a 4 element int array. Spots outside
 	 *            these dimensions are ignored.
+	 * @param calibration
+	 *            the pixel size to map physical spot coordinates to pixel
+	 *            coordinates.
 	 * @param exportSpotsAsDots
 	 *            if <code>true</code>, spots will be painted as single dots
 	 *            instead of ellipsoids.
@@ -340,9 +346,9 @@ public static final ImagePlus createLabelImagePlus(
 	 *            belonging to a track will be painted with a unique ID,
 	 *            different from the track IDs and different for each spot.
 	 * @param useSpotIDsAsLabels
-	 * 	          if <code>true</code>, the label mask images will contain 
-	 * 	          the spot ID. If <code>false</code>, the label mask images 
-	 * 	          will contain the track ID.
+	 *            if <code>true</code>, the label mask images will contain the
+	 *            spot ID. If <code>false</code>, the label mask images will
+	 *            contain the track ID.
 	 * @param logger
 	 *            a {@link Logger} instance, to report progress of the export
 	 *            process.
@@ -381,6 +387,9 @@ public static final ImagePlus createLabelImagePlus(
 	 *            the desired dimensions of the output image (width, height,
 	 *            nZSlices, nFrames) as a 4 element int array. Spots outside
 	 *            these dimensions are ignored.
+	 * @param calibration
+	 *            the pixel size to map physical spot coordinates to pixel
+	 *            coordinates.
 	 * @param exportSpotsAsDots
 	 *            if <code>true</code>, spots will be painted as single dots
 	 *            instead of ellipsoids.
@@ -390,10 +399,10 @@ public static final ImagePlus createLabelImagePlus(
 	 *            belonging to a track will be painted with a unique ID,
 	 *            different from the track IDs and different for each spot.
 	 * @param useSpotIDsAsLabels
-	 * 	          if <code>true</code>, the label mask images will contain 
-	 * 	          the spot ID. If <code>false</code>, the label mask images 
-	 * 	          will contain the track ID.
-	 * 	          
+	 *            if <code>true</code>, the label mask images will contain the
+	 *            spot ID. If <code>false</code>, the label mask images will
+	 *            contain the track ID.
+	 * 
 	 * @return a new {@link Img}.
 	 */
 	public static final Img< UnsignedShortType > createLabelImg(
@@ -418,6 +427,9 @@ public static final Img< UnsignedShortType > createLabelImg(
 	 *            the desired dimensions of the output image (width, height,
 	 *            nZSlices, nFrames) as a 4 element int array. Spots outside
 	 *            these dimensions are ignored.
+	 * @param calibration
+	 *            the pixel size to map physical spot coordinates to pixel
+	 *            coordinates.
 	 * @param exportSpotsAsDots
 	 *            if <code>true</code>, spots will be painted as single dots
 	 *            instead of ellipsoids.
@@ -427,9 +439,9 @@ public static final Img< UnsignedShortType > createLabelImg(
 	 *            belonging to a track will be painted with a unique ID,
 	 *            different from the track IDs and different for each spot.
 	 * @param useSpotIDsAsLabels
-	 * 	          if <code>true</code>, the label mask images will contain 
-	 * 	          the spot ID. If <code>false</code>, the label mask images 
-	 * 	          will contain the track ID.
+	 *            if <code>true</code>, the label mask images will contain the
+	 *            spot ID. If <code>false</code>, the label mask images will
+	 *            contain the track ID.
 	 * @param logger
 	 *            a {@link Logger} instance, to report progress of the export
 	 *            process.

src/main/java/fiji/plugin/trackmate/action/TrackMateAction.java

@@ -54,6 +54,9 @@ public interface TrackMateAction
 
 	/**
 	 * Sets the logger that will receive logs when this action is executed.
+	 * 
+	 * @param logger
+	 *            the logger.
 	 */
 	public void setLogger( Logger logger );
 }

src/main/java/fiji/plugin/trackmate/action/closegaps/GapClosingMethod.java

@@ -88,7 +88,9 @@ public default List< GapClosingParameter > getParameters()
 	 * Performs the gap closing.
 	 * 
 	 * @param trackmate
+	 *            the trackmate instance to operate on.
 	 * @param logger
+	 *            a logger instance to echoes the gap-closing process.
 	 */
 	public void execute( TrackMate trackmate, Logger logger );
 

src/main/java/fiji/plugin/trackmate/action/fit/SpotFitterPanel.java

@@ -200,9 +200,9 @@ public SpotFitterPanel( final List< String > fits, final List< String > docs, fi
 	}
 
 	/**
-	 * 1-based.
+	 * Returns the selected channel. 1-based.
 	 * 
-	 * @return
+	 * @return the selected channel.
 	 */
 	public int getSelectedChannel()
 	{

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

@@ -40,8 +40,8 @@
 import fiji.plugin.trackmate.SpotCollection;
 import fiji.plugin.trackmate.TrackMate;
 import fiji.plugin.trackmate.detection.util.MedianFilter2D;
-import fiji.plugin.trackmate.util.Threads;
 import fiji.plugin.trackmate.util.TMUtils;
+import fiji.plugin.trackmate.util.Threads;
 import ij.ImagePlus;
 import net.imagej.ImgPlus;
 import net.imagej.axis.Axes;
@@ -271,6 +271,8 @@ public static final Img< FloatType > createLoGKernel( final double radius, final
 	 * @return a new float Img. Careful: even if the specified interval does not
 	 *         start at (0, 0), the new image will have its first pixel at
 	 *         coordinates (0, 0).
+	 * @param <T>
+	 *            the pixel type of the input image.
 	 */
 	public static final < T extends RealType< T > > Img< FloatType > copyToFloatImg( final RandomAccessible< T > img, final Interval interval, final ImgFactory< FloatType > factory )
 	{
@@ -323,7 +325,14 @@ public static final Interval squeeze( final Interval interval )
 	}
 
 	/**
-	 * Apply a simple 3x3 median filter to the target image.
+	 * Applies a simple 3x3 median filter to the target image.
+	 * 
+	 * @param <R>
+	 *            the pixel type in the image.
+	 * @param image
+	 *            the image to filter.
+	 * @return the filtered image, as a new image, or <code>null</code> if there
+	 *         was a problem during processing.
 	 */
 	public static final < R extends RealType< R > & NativeType< R > > Img< R > applyMedianFilter( final RandomAccessibleInterval< R > image )
 	{

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

@@ -298,12 +298,14 @@ public static < R extends IntegerType< R > > List< Spot > fromLabeling(
 
 	/**
 	 * Creates spots by thresholding a grayscale image. A spot is created for
-	 * each connected-component object in the thresholded input, with a size that
-	 * matches the mask size. The quality of the spots is read from another
+	 * each connected-component object in the thresholded input, with a size
+	 * that matches the mask size. The quality of the spots is read from another
 	 * image, by taking the max pixel value of this image with the ROI.
 	 *
 	 * @param <T>
-	 *            the type of the input image. Must be real, scalar.
+	 *            the pixel type of the input image. Must be real, scalar.
+	 * @param <R>
+	 *            the pixel type of the quality image. Must be real, scalar.
 	 * @param input
 	 *            the input image.
 	 * @param interval

src/main/java/fiji/plugin/trackmate/detection/Process2DZ.java

@@ -40,6 +40,7 @@
  * @author Jean-Yves Tinevez, 2023
  *
  * @param <T>
+ *            the pixel type in the image processed.
  */
 public class Process2DZ< T extends RealType< T > & NativeType< T > >
 		extends MultiThreadedBenchmarkAlgorithm

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

@@ -35,6 +35,7 @@
  * @author Jean-Yves Tinevez
  *
  * @param <T>
+ *            the pixel type in the image processed by the detector.
  */
 public interface SpotDetectorFactory< T extends RealType< T > & NativeType< T > > extends SpotDetectorFactoryBase< T >
 {
@@ -53,6 +54,7 @@ public interface SpotDetectorFactory< T extends RealType< T > & NativeType< T >
 	 *            then the interval must be 3D).
 	 * @param frame
 	 *            the frame index in the source image to operate on
+	 * @return a new detector.
 	 */
 	public SpotDetector< T > getDetector( final Interval interval, int frame );
 }

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

@@ -65,25 +65,31 @@ public interface SpotDetectorFactoryBase< T extends RealType< T > & NativeType<
 	 * @see #setTarget(ImgPlus, Map)
 	 * @see #marshall(Map, Element)
 	 * @see #unmarshall(Element, Map)
+	 * @return an error message.
 	 */
 	public String getErrorMessage();
 
 	/**
-	 * Marshalls a settings map to a JDom element, ready for saving to XML. The
+	 * Marshals a settings map to a JDom element, ready for saving to XML. The
 	 * element is <b>updated</b> with new attributes.
 	 * <p>
 	 * Only parameters specific to the specific detector factory are marshalled.
 	 * The element also always receive an attribute named
 	 * {@value DetectorKeys#XML_ATTRIBUTE_DETECTOR_NAME} that saves the target
 	 * {@link SpotDetectorFactory} key.
 	 *
+	 * @param settings
+	 *            the settings map to marshal.
+	 * @param element
+	 *            the element to marshal to.
 	 * @return <code>true</code> if marshalling was successful. If not, check
 	 *         {@link #getErrorMessage()}
+	 * 
 	 */
 	public boolean marshall( final Map< String, Object > settings, final Element element );
 
 	/**
-	 * Un-marshalls a JDom element to update a settings map.
+	 * Un-marshals a JDom element to update a settings map.
 	 *
 	 * @param element
 	 *            the JDom element to read from.
@@ -106,6 +112,7 @@ public interface SpotDetectorFactoryBase< T extends RealType< T > & NativeType<
 	 * @param model
 	 *            the current model, used to get info to display on the GUI
 	 *            panel.
+	 * @return a new configuration panel.
 	 */
 	public ConfigurationPanel getDetectorConfigurationPanel( final Settings settings, final Model model );
 
@@ -118,7 +125,7 @@ public interface SpotDetectorFactoryBase< T extends RealType< T > & NativeType<
 	public Map< String, Object > getDefaultSettings();
 
 	/**
-	 * Check that the given settings map is suitable for target detector.
+	 * Checks that the given settings map is suitable for target detector.
 	 *
 	 * @param settings
 	 *            the map to test.
@@ -127,8 +134,8 @@ public interface SpotDetectorFactoryBase< T extends RealType< T > & NativeType<
 	public boolean checkSettings( final Map< String, Object > settings );
 
 	/**
-	 * Return <code>true</code> for the detectors that can provide a spot with a
-	 * 2D <code>SpotRoi</code> when they operate on 2D images.
+	 * Returns <code>true</code> for the detectors that can provide a spot with
+	 * a 2D <code>SpotRoi</code> when they operate on 2D images.
 	 * <p>
 	 * This flag may be used by clients to exploit the fact that the spots
 	 * created with this detector will have a contour that can be used
@@ -145,8 +152,8 @@ public default boolean has2Dsegmentation()
 	}
 
 	/**
-	 * Return <code>true</code> for the detectors that can provide a spot with a
-	 * 3D <code>SpotMesh</code> when they operate on 3D images.
+	 * Returns <code>true</code> for the detectors that can provide a spot with
+	 * a 3D <code>SpotMesh</code> when they operate on 3D images.
 	 * <p>
 	 * This flag may be used by clients to exploit the fact that the spots
 	 * created with this detector will have a 3D mesh that can be used