doc: javadoc corrections and updates

src/main/java/bdv/gui/BigWarpInitDialog.java

@@ -788,10 +788,7 @@ protected void updateImagePlusDropdown()
 	}
 
 	/**
-	 * Adds first two image plus images to the sourc list automatically.
-	 *
-	 * Make sure to call {@link updateImagePlusDropdown} before calling this
-	 * method.
+	 * Adds first two image plus images to the source list automatically.
 	 */
 	public void initializeImagePlusSources()
 	{

src/main/java/bdv/gui/BigWarpViewerFrame.java

@@ -246,7 +246,7 @@ public void setTransformEnabled( final boolean enabled )
 
 	/**
 	 * Get {@code Behaviours} hook where TransformEventHandler behaviours are installed.
-	 * This is installed in {@link #getTriggerbindings} with the id "transform".
+	 * This is installed in {@link #getTriggerBindings} with the id "transform".
 	 * The hook can be used to update the keymap and install additional behaviours.
 	 */
 	public Behaviours getTransformBehaviours()

src/main/java/bdv/ij/BigWarpToDeformationFieldPlugIn.java

@@ -474,7 +474,7 @@ else if ( nd == 3 )
 	 *
 	 * @param data the bigwarp data storing the fixed transformations
 	 * @param transform the current transformation
-	 * @param concat concatenate the current with fixed transformation
+	 * @param concatPreTransforms concatenate the current with fixed transformation
 	 * @param ignoreAffine whether the output should include the affine part of the transformation
 	 * @return the transformation
 	 */
@@ -857,9 +857,11 @@ private static RealTransform getTpsAffineToggle( final BigWarpTransform bwXfm, f
 	}
 
 	/**
-	 * @param tps
+	 * Get the affine part of a thin-plate spline transform. The affine will  be 2D (3D)
+	 * if the transformation is 2D (3D).
 	 *
-	 * @return
+	 * @param tps the {@link ThinPlateR2LogRSplineKernelTransform} instance
+	 * @return the {@link AffineGet} instance.
 	 *
 	 * @deprecated Use {@link BigWarpTransform} method instead
 	 */

src/main/java/bdv/viewer/BigWarpViewerPanel.java

@@ -29,6 +29,7 @@
 import bdv.viewer.animate.RotationAnimator;
 import bdv.viewer.animate.SimilarityTransformAnimator3D;
 import bdv.viewer.overlay.BigWarpMaskSphereOverlay;
+import bigwarp.BigWarp;
 import bigwarp.BigWarpData;
 import bigwarp.source.SourceInfo;
 import bigwarp.util.Rotation2DHelpers;
@@ -156,7 +157,7 @@ public void setHoveredIndex( int index )
 	 * Makes the first group contain all the moving images and the second group
 	 * contain all the fixed images
 	 * <p>
-	 * Deprecated. use {@link BigWarp#createMovingTargetGroup()}
+	 * @deprecated use {@link BigWarp#createMovingTargetGroups}
 	 *
 	 * @return the number sources in the moving group
 	 */

src/main/java/bigwarp/BigWarp.java

@@ -3734,8 +3734,9 @@ public BoundingBoxEstimation getBoxEstimation()
 	}
 
 	/**
-	 * Use getTps, getTpsBase, or getTransformation instead
-	 * @return
+	 * @deprecated Use getTps, getTpsBase, or getTransformation instead
+	 *
+	 * @return the {@link ThinPlateR2LogRSplineKernelTransform} iinnstance
 	 */
 	@Deprecated
 	public ThinPlateR2LogRSplineKernelTransform getTransform()
@@ -3980,7 +3981,7 @@ public File getBigwarpSettingsFolder()
 	/**
 	 * Returns the {@link BigWarpAutoSaver}.
 	 *
-	 * @return
+	 * @return the {@link BigWarpAutoSaver} instance.
 	 */
 	public BigWarpAutoSaver getAutoSaver()
 	{

src/main/java/bigwarp/BigWarpData.java

@@ -225,7 +225,7 @@ public boolean isMoving( SourceAndConverter<?> sac ) {
 	}
 
 	/**
-	 * @Deprecated only handled maintaing the moving lists, now a no-op
+	 * @deprecated only handled maintaing the moving lists, now a no-op
 	 */
 	@Deprecated
 	public void wrapUp()

src/main/java/bigwarp/BigWarpInit.java

@@ -257,12 +257,12 @@ public static < T extends RealType< T > > void initSourceReal( final Source< T >
 	}
 
 	/**
-	 * @return
+	 * Initialize BigWarp.
 	 *
-	 * @Deprecated Use
-	 *             {@link #createSources(BigWarpData, ImagePlus, int, int, boolean)}
-	 *             instaed, and pass output to
-	 *             {@link #add(BigWarpData, LinkedHashMap, RealTransform)}
+	 * @return the number of sources
+	 *
+	 * @deprecated Use {@code createSources(BigWarpData,ImagePlus,int,int,boolean)} instead, and pass output to
+	 *             {@code add(BigWarpData,LinkedHashMap)}
 	 */
 	@Deprecated
 	public static < T > int add( BigWarpData< T > bwdata, ImagePlus ip, int setupId, int numTimepoints, boolean isMoving )
@@ -315,9 +315,11 @@ public static < T > LinkedHashMap< Source< T >, SourceInfo > createSources( BigW
 	}
 
 	/**
-	 * @return
+	 * Initialize BigWarp.
+	 *
+	 * @return a {@link BigWarpData} instance
 	 *
-	 * @Deprecated Use the output from one of the
+	 * @deprecated Use the output from one of the
 	 *             {{@link #createSources(BigWarpData, String, int, boolean)}}
 	 *             to call {{@link #add(BigWarpData, LinkedHashMap)}} instead
 	 */
@@ -346,12 +348,13 @@ public static < T > BigWarpData< T > add( BigWarpData< T > bwdata, LinkedHashMap
 	}
 
 	/**
-	 * @return
+	 * Initialize BigWarp.
 	 *
-	 * @Deprecated Use the output from one of the
-	 *             {{@link #createSources(BigWarpData, String, int, boolean)}}
-	 *             to call
-	 *             {{@link #add(BigWarpData, LinkedHashMap, RealTransform)}}
+	 * @return a {@link BigWarpData} instance
+	 *
+	 * @deprecated Use the output from one of the
+	 *             {{@code createSources(BigWarpData, String, int, boolean)}}
+	 *             to call {{@code add(BigWarpData, LinkedHashMap, RealTransform)}}
 	 *             instead
 	 */
 	@SuppressWarnings( { "unchecked", "rawtypes" } )
@@ -582,13 +585,13 @@ else if ( new File( uri ).isDirectory() )
 	}
 
 	/**
-	 * @return
+	 * Initialize BigWarp.
+	 *
+	 * @return a {@link SpimData} instance
 	 *
-	 * @Deprecated Use output from
-	 *             {@link #createSources(BigWarpData, boolean, int, String, String)}
-	 *             and add with
-	 *             {@link #add(BigWarpData, LinkedHashMap, RealTransform)}
-	 *             instead.
+	 * @deprecated Use output from
+	 *             {@code createSources(BigWarpData, boolean, int, String, String)} and add with
+	 *             {@code add(BigWarpData, LinkedHashMap, RealTransform)} instead.
 	 */
 	@Deprecated
 	public static < T > SpimData addToData( final BigWarpData< T > bwdata, final boolean isMoving, final int setupId, final String rootPath, final String dataset )

src/main/java/bigwarp/landmarks/LandmarkTableModel.java

@@ -1267,9 +1267,10 @@ public void loadCsv( File f, boolean invert ) throws IOException
 	}
 
 	/**
-	 * Loads this table from a file
-	 * @param f the file
-	 * @param invert invert the moving and target point sets
+	 * Loads this table from a file.
+	 *
+	 * @param invert if true, the moving and target point sets are inverted
+	 * @param rows a list of strings containing rows of a csv file
 	 * @throws IOException an exception
 	 */
 	protected void loadCsvHelper( boolean invert, final List<String[]> rows ) throws IOException

src/main/java/bigwarp/source/PlateauSphericalMaskRealRandomAccessible.java

@@ -101,14 +101,14 @@ public void setOverlays( final List< BigWarpMaskSphereOverlay > overlays ) {
 
 	public static void main( String[] args )
 	{
-		long S = 50;
-		double[] center = new double[] { S, S, S };
-		RealPoint pt = RealPoint.wrap( center );
+		final long S = 50;
+		final double[] center = new double[] { S, S, S };
+		final RealPoint pt = RealPoint.wrap( center );
 
-		PlateauSphericalMaskRealRandomAccessible img = new PlateauSphericalMaskRealRandomAccessible( pt );
+		final PlateauSphericalMaskRealRandomAccessible img = new PlateauSphericalMaskRealRandomAccessible( pt );
 		img.setRadius( 10 );
 		img.setSigma( 10 );
-		Interval interval = Intervals.createMinSize( 0, 0, 0, 2 * S, 2 * S, 2 * S );
+		final Interval interval = Intervals.createMinSize( 0, 0, 0, 2 * S, 2 * S, 2 * S );
 //
 ////		BdvOptions options = BdvOptions.options().screenScales( new double[] { 1 } );
 //		BdvOptions options = BdvOptions.options();
@@ -127,7 +127,7 @@ public static void main( String[] args )
 ////		bdv.getBdvHandle().getViewerPanel().getDisplay().addMouseListener( ml );
 //
 		double x = 50;
-		RealRandomAccess< DoubleType > access = img.realRandomAccess();
+		final RealRandomAccess< DoubleType > access = img.realRandomAccess();
 		access.setPosition( center );
 		while ( x < 100 )
 		{
@@ -337,12 +337,12 @@ public void fromJson( JsonObject json )
 	}
 
 	/**
-	 * Re.turns the sigma that makes a Gaussian shape most like a cosine with period T.
+	 * Returns the sigma that makes a Gaussian shape most like a cosine with period T.
 	 * <p>
 	 * see https://gist.github.com/bogovicj/d212b236868c76798edfd11150b2c9a0
 	 *
 	 * @param T the cosine period
-	 * @return
+	 * @return the appropriate sigma
 	 */
 	public static double gaussSigma( double T )
 	{
@@ -363,7 +363,7 @@ public GaussianFalloff( PlateauSphericalMaskRealRandomAccessible mask )
 		public void accept( RealLocalizable x, DoubleType v )
 		{
 			v.setZero();
-			double r2 = squaredDistance( x, mask.center );
+			final double r2 = squaredDistance( x, mask.center );
 			if ( r2 <= mask.plateauR2 )
 				v.setOne();
 			else
@@ -403,7 +403,7 @@ else if ( r >= mask.plateauR + mask.sigma )
 //				final double t = (r2 - plateauR2);
 //				final double r = Math.sqrt( r2 );
 				final double t = ( r - mask.plateauR );
-				double val = 0.5 + 0.5 * Math.cos( t * PI / mask.sigma );
+				final double val = 0.5 + 0.5 * Math.cos( t * PI / mask.sigma );
 				v.set( val );
 			}
 		}
@@ -463,7 +463,7 @@ public void write( final JsonWriter out, final RealPoint value ) throws IOExcept
 		public RealPoint read( final JsonReader in ) throws IOException
 		{
 			in.beginArray();
-			ArrayList< Double > pos = new ArrayList<>();
+			final ArrayList< Double > pos = new ArrayList<>();
 			while ( in.hasNext() )
 			{
 				pos.add( in.nextDouble() );

src/main/java/org/janelia/utility/geom/BoundingSphereRitter.java

@@ -3,20 +3,20 @@
 import java.util.List;
 
 /**
- * Estimates the smallest sphere that bounds given points. 
+ * Estimates the smallest sphere that bounds given points.
  * <p>
- * Ritter, Jack (1990), "An efficient bounding sphere", in Glassner, Andrew S. (ed.), Graphics Gems, San Diego, CA, US: Academic Press Professional, Inc., pp. 301–303, 
- * 
+ * Ritter, Jack (1990), "An efficient bounding sphere", in Glassner, Andrew S. (ed.), Graphics Gems, San Diego, CA, US: Academic Press Professional, Inc., pp. 301–303,
+ *
  * @author John Bogovic
  *
  */
 public class BoundingSphereRitter
 {
 
 	/**
-	 * Returns an estimate of the smallest {@link ImmutableSphere} that contains the input points.
-	 * 
-	 * @param points a collection of points 
+	 * Returns an estimate of the smallest {@link Sphere} that contains the input points.
+	 *
+	 * @param points a collection of points
 	 * @return the bounding sphere
 	 */
 	public static Sphere boundingSphere( final List<double[]> points )
@@ -45,24 +45,24 @@ public static Sphere boundingSphere( final List<double[]> points )
 		for ( int d = 0; d < nd; d++ )
 			center[d] = 0.5 * ( x[d] + y[d] );
 
-		Sphere sph = new Sphere( center, Math.sqrt( maxSqrDist ) / 2 );
+		final Sphere sph = new Sphere( center, Math.sqrt( maxSqrDist ) / 2 );
 		boolean allCovered = false;
 		int k = 0;
 		while( !allCovered && k < 5)
 		{
 			allCovered = false;
-			for( double[] p : points )
+			for( final double[] p : points )
 			{
 				allCovered |= updateSphere( sph, p );
 			}
 			k++;
 		}
 		return sph;
 	}
-	
+
 	/**
 	 * return the point in point farthest from p
-	 * 
+	 *
 	 * @param points a list of points
 	 * @param p a base point
 	 * @return the point farthest from p
@@ -82,19 +82,19 @@ public static double[] furthestFrom( final List<double[]> points, double[] p )
 		}
 		return points.get( maxIndex );
 	}
-	
+
 	/**
 	 * Changes the value of the input sphere such that it contains the given point p.
 	 * Returns true if the sphere was modified.
-	 * 
+	 *
 	 * @param sphere
 	 * @param p
 	 * @return true if the sphere was changed
 	 */
 	public static boolean updateSphere( final Sphere sphere, final double[] p )
 	{
-		double sqrDist = GeomUtils.squaredDistance( sphere.getCenterArray(), p );
-		double r = sphere.getRadius();
+		final double sqrDist = GeomUtils.squaredDistance( sphere.getCenterArray(), p );
+		final double r = sphere.getRadius();
 		if ( sqrDist <= r*r )
 		{
 			return false;