Fix javadocs and images being displayed on some headless scripts

Author: tferr

src/main/java/sc/fiji/snt/SNT.java

@@ -335,13 +335,19 @@ public String toString() {
 	 * Script-friendly constructor for Instantiating and initializing SNT in
 	 * 'Tracing Mode' (typically headless operations). The channel/frame to
 	 * be traced is assumed to be the image's active CT position.
+	 * <p>
+	 *     Note that the image is not displayed. For interactive display of the image call
+	 *     {@link #initialize(ImagePlus)}/{@link #startUI()} directly.
+	 * </p>
 	 *
 	 * @param sourceImage the source image
 	 * @throws IllegalArgumentException If sourceImage is of type 'RGB'
 	 */
 	public SNT(final ImagePlus sourceImage) throws IllegalArgumentException {
 		this(SNTUtils.getContext(), sourceImage);
-		initialize(true, sourceImage.getChannel(), sourceImage.getFrame());
+		// NB: Previous versions called: initialize(true, sourceImage.getChannel(), sourceImage.getFrame());
+		// which caused the image to be displayed even in non-interactive scripts. This call was removed
+		// for consistency: callers wanting full UI should use startUI() or initialize(imp) explicitly
 	}
 
 	/**

src/main/java/sc/fiji/snt/SNTPrefs.java

@@ -649,7 +649,7 @@ public static void setLastKnownDir(final File file) {
 
 	/**
 	 * Returns the list of filename suffixes used to identify images when navigating
-	 * to the next/previous image in a folder (see {@link SNTUI). Matching is
+	 * to the next/previous image in a folder (see {@link SNTUI}). Matching is
 	 * case-insensitive and applied to the end of the filename (i.e., {@code endsWith}).
 	 * Suffixes may include a leading dot (e.g., {@code ".tif"}) or a partial filename
 	 * suffix (e.g., {@code "_max.tif"}).

src/main/java/sc/fiji/snt/util/ImgUtils.java

@@ -1272,14 +1272,12 @@ public static void save(final RandomAccessibleInterval<? extends RealType<?>> im
      * values to the target type's range automatically (e.g. 16-bit unsigned
      * values are clamped to [0, 65535]).
      * </p>
-     * <p>
      * Typical usage:
      * <pre>
      *   ImgUtils.save(rai, "/path/to/out.tif", new UnsignedShortType());
      *   ImgUtils.save(rai, "/path/to/out.tif", new UnsignedByteType());
      *   ImgUtils.save(rai, "/path/to/out.tif", new FloatType());
      * </pre>
-     * </p>
      *
      * @param <T>      the output pixel type; must be a {@link NativeType} so
      *                 that an {@link ArrayImgFactory} can allocate it
@@ -1440,13 +1438,13 @@ public static String axisReport(final ImgPlus<?> img) {
      * Returns a new {@link ImgPlus} with two axes swapped. The underlying data
      * is a lazy permuted view (no pixel data is copied). Axis metadata (type,
      * scale, unit) is reordered to match the new dimension order.
-     * <p>
      * Example: swap Z and Channel in an XYZCT image:
      * <pre>
+     *   {@code
      *   ImgPlus<?> xyzct = ImgUtils.open("image.tif");
      *   ImgPlus<?> xyczT = ImgUtils.swapAxes(xyzct, Axes.Z, Axes.CHANNEL);
+     *   }
      * </pre>
-     * </p>
      *
      * @param <T>   the pixel type
      * @param img   the source image

src/main/java/sc/fiji/snt/viewer/Bvv.java

@@ -347,13 +347,11 @@ public void setChannelColors(final String... colorNames) {
      * Sets per-channel colors for a specific source group. Each color is applied
      * to the corresponding channel in order; extra colors are ignored, and channels
      * without a supplied color are left unchanged.
-     * <p>
-     * Typical Groovy/PySNT usage:
+     * Typical script usage:
      * <pre>
      *   def bvv = Bvv.open([reference, moving])
      *   bvv.setChannelColors(bvv.getMultiSources().get(0), Color.RED, Color.GREEN, Color.BLUE)
      * </pre>
-     * </p>
      *
      * @param group  the target source group, obtained from {@link #getMultiSources()}
      * @param colors one color per channel, in channel order
@@ -383,13 +381,11 @@ private void applyChannelColors(final BvvMultiSource group, final Color... color
      * To apply the same color pattern to every group independently, call
      * {@link #setChannelColors(BvvMultiSource, Color...)} per group.
      * </p>
-     * <p>
-     * Typical Groovy/PySNT usage:
+     * Typical script usage:
      * <pre>
      *   def bvv = Bvv.open(img)
      *   bvv.setChannelColors(Color.RED, Color.GREEN, Color.BLUE)
      * </pre>
-     * </p>
      *
      * @param colors colors assigned sequentially across all channels in all groups
      */
@@ -594,14 +590,14 @@ public static Bvv open(final SNT snt) {
      * <p>
      * The caller is responsible for constructing the {@link AbstractSpimData}
      * object, typically via an XML/HDF5 loader:
+     * </p>
      * <pre>
      *   import bdv.spimdata.XmlIoSpimDataMinimal
      *   spimData = new XmlIoSpimDataMinimal().load("/path/to/dataset.xml")
      *   def bvv = Bvv.open(spimData)
      * </pre>
      * or via Bio-Formats/IMS loaders that produce a {@link AbstractSpimData} with
      * a multiresolution pyramid.
-     * </p>
      *
      * @param spimData the dataset to display
      * @return the fully initialised {@link Bvv} instance