diff --git a/src/main/java/bdv/gui/BigWarpInitDialog.java b/src/main/java/bdv/gui/BigWarpInitDialog.java index a8fa4222..72e7829c 100644 --- a/src/main/java/bdv/gui/BigWarpInitDialog.java +++ b/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() { diff --git a/src/main/java/bdv/gui/BigWarpViewerFrame.java b/src/main/java/bdv/gui/BigWarpViewerFrame.java index 32c52598..e892e9cc 100644 --- a/src/main/java/bdv/gui/BigWarpViewerFrame.java +++ b/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() diff --git a/src/main/java/bdv/ij/BigWarpToDeformationFieldPlugIn.java b/src/main/java/bdv/ij/BigWarpToDeformationFieldPlugIn.java index e67240b0..1bceb401 100644 --- a/src/main/java/bdv/ij/BigWarpToDeformationFieldPlugIn.java +++ b/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 */ diff --git a/src/main/java/bdv/viewer/BigWarpViewerPanel.java b/src/main/java/bdv/viewer/BigWarpViewerPanel.java index ceb898d6..de353058 100644 --- a/src/main/java/bdv/viewer/BigWarpViewerPanel.java +++ b/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 *
- * Deprecated. use {@link BigWarp#createMovingTargetGroup()}
+ * @deprecated use {@link BigWarp#createMovingTargetGroups}
*
* @return the number sources in the moving group
*/
diff --git a/src/main/java/bigwarp/BigWarp.java b/src/main/java/bigwarp/BigWarp.java
index eb393e81..e80ed662 100755
--- a/src/main/java/bigwarp/BigWarp.java
+++ b/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()
{
diff --git a/src/main/java/bigwarp/BigWarpData.java b/src/main/java/bigwarp/BigWarpData.java
index c55aac5a..1d5a3465 100644
--- a/src/main/java/bigwarp/BigWarpData.java
+++ b/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()
diff --git a/src/main/java/bigwarp/BigWarpInit.java b/src/main/java/bigwarp/BigWarpInit.java
index e60fe6a9..13144358 100644
--- a/src/main/java/bigwarp/BigWarpInit.java
+++ b/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 )
diff --git a/src/main/java/bigwarp/landmarks/LandmarkTableModel.java b/src/main/java/bigwarp/landmarks/LandmarkTableModel.java
index 76f82674..37540aa1 100644
--- a/src/main/java/bigwarp/landmarks/LandmarkTableModel.java
+++ b/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
* 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() );
diff --git a/src/main/java/org/janelia/utility/geom/BoundingSphereRitter.java b/src/main/java/org/janelia/utility/geom/BoundingSphereRitter.java
index 17a21bfa..95ced48a 100644
--- a/src/main/java/org/janelia/utility/geom/BoundingSphereRitter.java
+++ b/src/main/java/org/janelia/utility/geom/BoundingSphereRitter.java
@@ -3,10 +3,10 @@
import java.util.List;
/**
- * Estimates the smallest sphere that bounds given points.
+ * Estimates the smallest sphere that bounds given points.
*
- * 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
*
*/
@@ -14,9 +14,9 @@ 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