Class RankFilters

ij/src/main/java/ij/plugin/filter/RankFilters.java:24–953

 //                                 Uses AtomicIntegers. Top-hat filter added

public class RankFilters implements ExtendedPlugInFilter, DialogListener {
	public static final int	 MEAN=0, MIN=1, MAX=2, VARIANCE=3, MEDIAN=4, OUTLIERS=5, DESPECKLE=6, REMOVE_NAN=7,
			OPEN=8, CLOSE=9, TOP_HAT=10; //when adding a new filter, set HIGHEST_FILTER below.
	public static final int BRIGHT_OUTLIERS = 0, DARK_OUTLIERS = 1;
	private static final String[] outlierStrings = {"Bright","Dark"};
	private static int HIGHEST_FILTER = TOP_HAT;
	// Filter parameters
	private int filterType;
	private double radius;
	private double threshold;        //this and the next for 'remove outliers' only
	private int whichOutliers;
	private boolean lightBackground = Prefs.get("bs.background", true); //this and the next for top hat only
	private boolean dontSubtract;
	// Remember filter parameters for the next time
	private static double[] lastRadius = new double[HIGHEST_FILTER+1]; //separate for each filter type
	private static double lastThreshold = 50.;
	private static int lastWhichOutliers = BRIGHT_OUTLIERS;
	private static boolean lastLightBackground = false;
	private static boolean lastDontSubtract = false;
	//
	// F u r t h e r   c l a s s   v a r i a b l e s
	int flags = DOES_ALL|SUPPORTS_MASKING|KEEP_PREVIEW;
	private ImagePlus imp;
	private int nPasses = 1;			// The number of passes (color channels * stack slices)
	private PlugInFilterRunner pfr;
	private int pass;
	private boolean previewing = false;
	// M u l t i t h r e a d i n g - r e l a t e d
	private int numThreads = Prefs.getThreads();
	// The current state of multithreaded processing is in class variables.
	// Thus, stack parallelization must be done ONLY with one thread for the image
	// (not using these class variables).
	// Atomic objects are used to avoid caching (i.e., to ensure that always the current state of the variable is read).
	private AtomicInteger highestYinCache = new AtomicInteger(Integer.MIN_VALUE);	// the highest line read into the cache so far
	private AtomicInteger nThreadsWaiting = new AtomicInteger(0);			// number of threads waiting until they may read data
	private AtomicBoolean copyingToCache  = new AtomicBoolean(false);		// whether a thread is currently copying data to the cache

	/** OPEN, CLOSE, TOPHAT need more than one run of the underlying filter */
	private boolean isMultiStepFilter(int filterType) {
		return filterType>=OPEN && filterType<=TOP_HAT;
	}

	/** Setup of the PlugInFilter. Returns the flags specifying the capabilities and needs
	 * of the filter.
	 *
	 * @param arg	Defines type of filter operation
	 * @param imp	The ImagePlus to be processed
	 * @return		Flags specifying further action of the PlugInFilterRunner
	 */
	public int setup(String arg, ImagePlus imp) {
		this.imp = imp;
		if (arg.equals("mean"))
			filterType = MEAN;
		else if (arg.equals("min"))
			filterType = MIN;
		else if (arg.equals("max"))
			filterType = MAX;
		else if (arg.equals("variance")) {