Fix javadoc errors and warnings.

Author: tinevez

src/main/java/fiji/plugin/trackmate/Spot.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>.
@@ -257,7 +257,7 @@ public String getName()
 
 	/**
 	 * Set the name of this Spot.
-	 * 
+	 *
 	 * @param name
 	 *            the name to use.
 	 */
@@ -284,7 +284,7 @@ public String toString()
 
 	/**
 	 * Return a string representation of this spot, with calculated features.
-	 * 
+	 *
 	 * @return a string representation of the spot.
 	 */
 	public String echo()
@@ -369,10 +369,14 @@ public void putFeature( final String feature, final Double value )
 	}
 
 	/**
-	 * Copy the listed features of the spot src to the current spot
-	 * 
+	 * Copy the listed features of the source spot to this spot.
+	 *
+	 * @param src
+	 *            the source spot.
+	 * @param features
+	 *            the features to copy.
 	 */
-	public void copyFeatures( Spot src, final Map< String, Double > features )
+	public void copyFeatures( final Spot src, final Map< String, Double > features )
 	{
 		if ( null == features || features.isEmpty() )
 			return;

src/main/java/fiji/plugin/trackmate/SpotRoi.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>.
@@ -61,12 +61,14 @@ public SpotRoi copy()
 	/**
 	 * Returns a new <code>int</code> array containing the X pixel coordinates
 	 * to which to paint this polygon.
-	 * 
+	 *
 	 * @param calibration
 	 *            the pixel size in X, to convert physical coordinates to pixel
 	 *            coordinates.
 	 * @param xcorner
 	 *            the top-left X corner of the view in the image to paint.
+	 * @param spotXCenter
+	 *            the X coordinate of the spot center.
 	 * @param magnification
 	 *            the magnification of the view.
 	 * @return a new <code>int</code> array.
@@ -85,12 +87,14 @@ public double[] toPolygonX( final double calibration, final double xcorner, fina
 	/**
 	 * Returns a new <code>int</code> array containing the Y pixel coordinates
 	 * to which to paint this polygon.
-	 * 
+	 *
 	 * @param calibration
 	 *            the pixel size in Y, to convert physical coordinates to pixel
 	 *            coordinates.
 	 * @param ycorner
 	 *            the top-left Y corner of the view in the image to paint.
+	 * @param spotYCenter
+	 *            the spot Y center in physical units.
 	 * @param magnification
 	 *            the magnification of the view.
 	 * @return a new <code>int</code> array.

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

@@ -52,6 +52,10 @@ public interface TrackMateFactoryBase< F extends TrackMateFactoryBase< F > > ext
 	 * {@value DetectorKeys#XML_ATTRIBUTE_DETECTOR_NAME} that saves the target
 	 * {@link SpotDetectorFactory} key.
 	 *
+	 * @param settings
+	 *            the map to marshal.
+	 * @param element
+	 *            the JDom element to update.
 	 * @return an error message if marshaling was unsuccessful. If successful,
 	 *         returns <code>null</code>.
 	 */

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

@@ -128,8 +128,11 @@ else if ( imp.getType() == ImagePlus.COLOR_RGB )
 	 * launched by this plugin.
 	 *
 	 * @param trackmate
+	 *            the {@link TrackMate} instance to use.
 	 * @param selectionModel
+	 *            the {@link SelectionModel} to use.
 	 * @param displaySettings
+	 *            the {@link DisplaySettings} to use.
 	 * @return a new sequence.
 	 */
 	protected WizardSequence createSequence( final TrackMate trackmate, final SelectionModel selectionModel, final DisplaySettings displaySettings )
@@ -143,7 +146,7 @@ protected WizardSequence createSequence( final TrackMate trackmate, final Select
 	 * {@link TrackMate} instance.
 	 *
 	 * @param imp
-	 *
+	 *            the {@link ImagePlus} to operate on.
 	 * @return a new {@link Model} instance.
 	 */
 	protected Model createModel( final ImagePlus imp )
@@ -178,6 +181,10 @@ 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 use.
+	 * @param settings
+	 *            the settings to use.
 	 * @return a new {@link TrackMate} instance.
 	 */
 	protected TrackMate createTrackMate( final Model model, final Settings settings )

src/main/java/fiji/plugin/trackmate/action/CTCExporter.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>.
@@ -77,7 +77,7 @@
  * Cell-Tracking-Challenge convention.
  * <p>
  * See http://celltrackingchallenge.net/
- * 
+ *
  * @author Jean-Yves Tinevez
  *
  */
@@ -173,7 +173,7 @@ public static String exportAll( final String exportRootFolder, final TrackMate t
 
 	/**
 	 * Saves the settings part as XML for reference.
-	 * 
+	 *
 	 * @param exportRootFolder
 	 *            the root folder for exporting.
 	 * @param saveId
@@ -183,6 +183,8 @@ public static String exportAll( final String exportRootFolder, final TrackMate t
 	 *            the trackmate to export.
 	 * @param logger
 	 *            a logger to report progress.
+	 * @throws IOException
+	 *             if a problem happens during writing.
 	 */
 	public static void exportSettingsFile( final String exportRootFolder, final int saveId, final TrackMate trackmate, final Logger logger ) throws IOException
 	{
@@ -202,7 +204,7 @@ public static void exportSettingsFile( final String exportRootFolder, final int
 	 * For instance the first id return will be '1', which means that the
 	 * original image data will be saved under the folder '01'. If '01' already
 	 * exists, then this method will return 2, etc.
-	 * 
+	 *
 	 * @param exportRootFolder
 	 *            the root folder in which to export the data.
 	 * @return an integer id that can be passed in the other method of this
@@ -269,7 +271,7 @@ public static void exportOriginalImageData( final String exportRootFolder, final
 	 * <p>
 	 * Only exports the spots that have a ROI, and write only the frames that
 	 * have at least one spot with a ROI.
-	 * 
+	 *
 	 * @param exportRootFolder
 	 *            the root of the export folder.
 	 * @param saveId
@@ -338,7 +340,7 @@ public static void exportSegmentationData( final String exportRootFolder, final
 		final Function< Long, String > tifNameGen = nFrames > 999
 				? i -> String.format( "man_seg%04d.tif", i )
 				: i -> String.format( "man_seg%03d.tif", i );
-				
+
 		// Only save frames with spots in.
 		for ( final int frame : framesToWrite )
 		{
@@ -508,7 +510,7 @@ public static String exportTrackingData( final String exportRootFolder, final in
 
 	/**
 	 * Returns the folder in which the tracking data will be exported.
-	 * 
+	 *
 	 * @param exportRootFolder
 	 *            the root folder to export in.
 	 * @param saveId
@@ -559,7 +561,7 @@ private static final Model sanitizeAndCopy( final Model model )
 					final Spot s2 = spots.get( j );
 					final double r2 = s2.getFeature( Spot.RADIUS ).doubleValue();
 					final double d = Math.sqrt( s1.squareDistanceTo( s2 ) );
-					
+
 					if ( fudgeFactor * r1 > ( d + r2 ) || fudgeFactor * r2 > ( d + r1 ) )
 					{
 						// They overlap too much. We must fix this.
@@ -609,7 +611,7 @@ private static final Model sanitizeAndCopy( final Model model )
 							else
 								sources.add( trackModel.getEdgeSource( edge ) );
 						}
-						
+
 						model.beginUpdate();
 						try
 						{

src/main/java/fiji/plugin/trackmate/action/CaptureOverlayAction.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>.
@@ -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 {@link Logger} to report 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

@@ -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>.
@@ -212,7 +212,7 @@ public static final ImagePlus createLabelImagePlus(
 	 *            different from the track IDs and different for each spot.
 	 * @param labelIdPainting
 	 *            specifies how to paint the label ID of spots.
-	 * 
+	 *
 	 * @return a new {@link ImagePlus}.
 	 */
 	public static final ImagePlus createLabelImagePlus(
@@ -285,6 +285,10 @@ public static final ImagePlus createLabelImagePlus(
 	 *            the desired dimensions of the output image (width, height,
 	 *            nZSlices, nFrames) as a 4 element long array. Spots outside
 	 *            these dimensions are ignored.
+	 * @param calibration
+	 *            the desired calibration of the output image (pixel width,
+	 *            pixel height, pixel depth, frame interval) as a 4 element
+	 *            double array.
 	 * @param exportSpotsAsDots
 	 *            if <code>true</code>, spots will be painted as single dots
 	 *            instead their shape.
@@ -295,7 +299,7 @@ public static final ImagePlus createLabelImagePlus(
 	 *            different from the track IDs and different for each spot.
 	 * @param labelIdPainting
 	 *            specifies how to paint the label ID of spots.
-	 * 
+	 *
 	 * @return a new {@link ImagePlus}.
 	 */
 	public static final ImagePlus createLabelImagePlus(
@@ -319,6 +323,10 @@ 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 desired calibration of the output image (pixel width,
+	 *            pixel height, pixel depth, frame interval) as a 4 element
+	 *            double array.
 	 * @param exportSpotsAsDots
 	 *            if <code>true</code>, spots will be painted as single dots
 	 *            instead their shape.
@@ -367,6 +375,10 @@ public static final ImagePlus createLabelImagePlus(
 	 *            the desired dimensions of the output image (width, height,
 	 *            nZSlices, nFrames) as a 4 element long array. Spots outside
 	 *            these dimensions are ignored.
+	 * @param calibration
+	 *            the desired calibration of the output image (pixel width,
+	 *            pixel height, pixel depth, frame interval) as a 4 element
+	 *            double array.
 	 * @param exportSpotsAsDots
 	 *            if <code>true</code>, spots will be painted as single dots
 	 *            instead their shape.
@@ -377,7 +389,7 @@ public static final ImagePlus createLabelImagePlus(
 	 *            different from the track IDs and different for each spot.
 	 * @param labelIdPainting
 	 *            specifies how to paint the label ID of spots.
-	 * 
+	 *
 	 * @return a new {@link Img}.
 	 */
 	public static final Img< FloatType > createLabelImg(
@@ -401,6 +413,10 @@ public static final Img< FloatType > createLabelImg(
 	 *            the desired dimensions of the output image (width, height,
 	 *            nZSlices, nFrames) as a 4 element long array. Spots outside
 	 *            these dimensions are ignored.
+	 * @param calibration
+	 *            the desired calibration of the output image (pixel width,
+	 *            pixel height, pixel depth, frame interval) as a 4 element
+	 *            double.
 	 * @param exportSpotsAsDots
 	 *            if <code>true</code>, spots will be painted as single dots
 	 *            instead their shape.
@@ -471,27 +487,34 @@ public static final Img< FloatType > createLabelImg(
 
 
 	/**
-	 * Creates a new label {@link ImgPlus} of {@link FloatType} where the spots
-	 * are painted with an ID. All visible spots are painted, whether they are
-	 * in a track or not.
-	 * 
+	 * Creates a new label {@link ImgPlus} of specified pixel type where the
+	 * spots are painted with an ID. All visible spots are painted, whether they
+	 * are in a track or not.
+	 *
 	 * @param spots
 	 *            the spots to paint.
 	 * @param dimensions
 	 *            the desired dimensions of the output image (width, height,
 	 *            nZSlices, nFrames) as a 4 element long array. Spots outside
 	 *            these dimensions are ignored.
+	 * @param calibration
+	 *            the desired calibration of the output image (pixel width,
+	 *            pixel height, pixel depth, frame interval) as a 4 element
+	 *            double array.
 	 * @param exportSpotsAsDots
 	 *            if <code>true</code>, spots will be painted as single dots
 	 *            instead of their shape.
 	 * @param labelIdPainting
 	 *            specifies how to paint the label ID of spots. The
 	 *            {@link LabelIdPainting#LABEL_IS_TRACK_ID} is not supported and
 	 *            defaults to {@link LabelIdPainting#LABEL_IS_SPOT_ID}.
+	 * @param outputType
+	 *            the output pixel type.
 	 * @param logger
 	 *            a {@link Logger} instance, to report progress of the export
 	 *            process.
-	 *
+	 * @param <T>
+	 *            the pixel type of the output image.
 	 * @return a new {@link ImgPlus}.
 	 */
 	public static < T extends RealType< T > & NativeType< T > > ImgPlus< T > createLabelImg(