ThresholdAdjuster.java

package ij.plugin.frame;
import java.awt.*;
import java.awt.event.*;
import java.awt.image.*;
import ij.*;
import ij.plugin.*;
import ij.process.*;
import ij.gui.*;
import ij.measure.*;
import ij.plugin.frame.Recorder;
import ij.plugin.filter.*;
import ij.plugin.ChannelSplitter;
import ij.plugin.Thresholder;

/** Adjusts the lower and upper threshold levels of the active image. This
	class is multi-threaded to provide a more responsive user interface. */
public class ThresholdAdjuster extends PlugInDialog implements PlugIn, Measurements,
	Runnable, ActionListener, AdjustmentListener, ItemListener, ImageListener {

	public static final String LOC_KEY = "threshold.loc";
	public static final String MODE_KEY = "threshold.mode";
	public static final String DARK_BACKGROUND = "threshold.dark";
	static final int RED=0, BLACK_AND_WHITE=1, OVER_UNDER=2;
	static final String[] modes = {"Red","B&W", "Over/Under"};
	static final double defaultMinThreshold = 85; 
	static final double defaultMaxThreshold = 170;
	static final int DEFAULT = 0;
	static boolean fill1 = true;
	static boolean fill2 = true;
	static boolean useBW = true;
	static boolean backgroundToNaN = true;
	static ThresholdAdjuster instance;
	static int mode = RED;	
	static String[] methodNames = AutoThresholder.getMethods();
	static String method = methodNames[DEFAULT];
	static AutoThresholder thresholder = new AutoThresholder();
	ThresholdPlot plot = new ThresholdPlot();
	Thread thread;
	
	int minValue = -1;
	int maxValue = -1;
	int sliderRange = 256;
	boolean doAutoAdjust,doReset,doApplyLut,doStateChange,doSet;
	
	Panel panel;
	Button autoB, resetB, applyB, setB;
	int previousImageID;
	int previousImageType;
	int previousRoiHashCode;
	double previousMin, previousMax;
	int previousSlice;
	boolean imageWasUpdated;
	ImageJ ij;
	double minThreshold, maxThreshold;  // 0-255
	Scrollbar minSlider, maxSlider;
	Label label1, label2;               // for current threshold
	Label percentiles;
	boolean done;
	int lutColor;
	Choice methodChoice, modeChoice;
	Checkbox darkBackground, stackHistogram;
	boolean firstActivation = true;


	public ThresholdAdjuster() {
		super("Threshold");
		ImagePlus cimp = WindowManager.getCurrentImage();
		if (cimp!=null && cimp.getBitDepth()==24) {
			IJ.run(cimp, "Color Threshold...", "");
			return;
		}
		if (instance!=null) {
			instance.firstActivation = true;
			instance.toFront();
			instance.setup(cimp, true);
			return;
		}
		
		WindowManager.addWindow(this);
		instance = this;
		mode = (int)Prefs.get(MODE_KEY, RED);
		if (mode<RED || mode>OVER_UNDER) mode = RED;
		setLutColor(mode);
		IJ.register(PasteController.class);

		ij = IJ.getInstance();
		Font font = new Font("SansSerif", Font.PLAIN, 10);
		GridBagLayout gridbag = new GridBagLayout();
		GridBagConstraints c = new GridBagConstraints();
		setLayout(gridbag);
		
		// plot
		int y = 0;
		c.gridx = 0;
		c.gridy = y++;
		c.gridwidth = 2;
		c.fill = GridBagConstraints.BOTH;
		c.anchor = GridBagConstraints.CENTER;
		c.insets = new Insets(10, 10, 0, 10); //top left bottom right
		add(plot, c);
		plot.addKeyListener(ij);

		// percentiles
		c.gridx = 0;
		c.gridy = y++;
		c.insets = new Insets(1, 10, 0, 10);
		percentiles = new Label("");
		percentiles.setFont(font);
		add(percentiles, c);

		// minThreshold slider
		minSlider = new Scrollbar(Scrollbar.HORIZONTAL, sliderRange/3, 1, 0, sliderRange);
		GUI.fix(minSlider);
		c.gridx = 0;
		c.gridy = y++;
		c.gridwidth = 1;
		c.weightx = IJ.isMacintosh()?90:100;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.insets = new Insets(1, 10, 0, 0);
		add(minSlider, c);
		minSlider.addAdjustmentListener(this);
		minSlider.addKeyListener(ij);
		minSlider.setUnitIncrement(1);
		minSlider.setFocusable(false);
		
		// minThreshold slider label
		c.gridx = 1;
		c.gridwidth = 1;
		c.weightx = IJ.isMacintosh()?10:0;
		c.insets = new Insets(5, 0, 0, 10);
		String text = IJ.isMacOSX()?"000000":"00000000";
		label1 = new Label(text, Label.RIGHT);
    	label1.setFont(font);
		add(label1, c);
		
		// maxThreshold slider
		maxSlider = new Scrollbar(Scrollbar.HORIZONTAL, sliderRange*2/3, 1, 0, sliderRange);
		GUI.fix(maxSlider);
		c.gridx = 0;
		c.gridy = y++;
		c.gridwidth = 1;
		c.weightx = 100;
		c.insets = new Insets(2, 10, 0, 0);
		add(maxSlider, c);
		maxSlider.addAdjustmentListener(this);
		maxSlider.addKeyListener(ij);
		maxSlider.setUnitIncrement(1);
		maxSlider.setFocusable(false);
		
		// maxThreshold slider label
		c.gridx = 1;
		c.gridwidth = 1;
		c.weightx = 0;
		c.insets = new Insets(2, 0, 0, 10);
		label2 = new Label(text, Label.RIGHT);
    	label2.setFont(font);
		add(label2, c);
				
		// choices
		panel = new Panel();
		methodChoice = new Choice();
		for (int i=0; i<methodNames.length; i++)
			methodChoice.addItem(methodNames[i]);
		methodChoice.select(method);
		methodChoice.addItemListener(this);
		//methodChoice.addKeyListener(ij);
		panel.add(methodChoice);
		modeChoice = new Choice();
		for (int i=0; i<modes.length; i++)
			modeChoice.addItem(modes[i]);
		modeChoice.select(mode);
		modeChoice.addItemListener(this);
		//modeChoice.addKeyListener(ij);
		panel.add(modeChoice);
		c.gridx = 0;
		c.gridy = y++;
		c.gridwidth = 2;
		c.insets = new Insets(8, 5, 0, 5);
		c.anchor = GridBagConstraints.CENTER;
		c.fill = GridBagConstraints.NONE;
		add(panel, c);

		// checkboxes
		panel = new Panel();
		boolean db = Prefs.get(DARK_BACKGROUND, Prefs.blackBackground?true:false);
        darkBackground = new Checkbox("Dark background");
        darkBackground.setState(db);
        darkBackground.addItemListener(this);
        panel.add(darkBackground);
        stackHistogram = new Checkbox("Stack histogram");
        stackHistogram.setState(false);
        stackHistogram.addItemListener(this);
        panel.add(stackHistogram);
        c.gridx = 0;
        c.gridy = y++;
        c.gridwidth = 2;
		c.insets = new Insets(5, 5, 0, 5);
        add(panel, c);

		// buttons
		int trim = IJ.isMacOSX()?11:0;
		panel = new Panel();
		autoB = new TrimmedButton("Auto",trim);
		autoB.addActionListener(this);
		autoB.addKeyListener(ij);
		panel.add(autoB);
		applyB = new TrimmedButton("Apply",trim);
		applyB.addActionListener(this);
		applyB.addKeyListener(ij);
		panel.add(applyB);
		resetB = new TrimmedButton("Reset",trim);
		resetB.addActionListener(this);
		resetB.addKeyListener(ij);
		panel.add(resetB);
		setB = new TrimmedButton("Set",trim);
		setB.addActionListener(this);
		setB.addKeyListener(ij);
		panel.add(setB);
		c.gridx = 0;
		c.gridy = y++;
		c.gridwidth = 2;
		c.insets = new Insets(0, 5, 10, 5);
		add(panel, c);
		
 		addKeyListener(ij);  // ImageJ handles keyboard shortcuts
		pack();
		Point loc = Prefs.getLocation(LOC_KEY);
		if (loc!=null)
			setLocation(loc);
		else
			GUI.center(this);
		if (IJ.isMacOSX()) setResizable(false);
		show();

		thread = new Thread(this, "ThresholdAdjuster");
		//thread.setPriority(thread.getPriority()-1);
		thread.start();
		ImagePlus imp = WindowManager.getCurrentImage();
		ImagePlus.addImageListener(this);
		if (imp!=null)
			setup(imp, true);
	}
	
	public synchronized void adjustmentValueChanged(AdjustmentEvent e) {
		if (e.getSource()==minSlider)
			minValue = minSlider.getValue();
		else
			maxValue = maxSlider.getValue();
		notify();
	}

	public synchronized  void actionPerformed(ActionEvent e) {
		Button b = (Button)e.getSource();
		if (b==null) return;
		if (b==resetB)
			doReset = true;
		else if (b==autoB)
			doAutoAdjust = true;
		else if (b==applyB)
			doApplyLut = true;
		else if (b==setB)
			doSet = true;
		notify();
	}

	public void imageUpdated(ImagePlus imp) {
		if (imp.getID() == previousImageID && Thread.currentThread() != thread)
			imageWasUpdated = true;
	}

	public void imageOpened(ImagePlus imp) {}
	public void imageClosed(ImagePlus imp) {}

	void setLutColor(int mode) {
		switch (mode) {
			case RED:
				lutColor = ImageProcessor.RED_LUT;
				break;
			case BLACK_AND_WHITE:
				lutColor = ImageProcessor.BLACK_AND_WHITE_LUT;
				break;
			case OVER_UNDER:
				lutColor = ImageProcessor.OVER_UNDER_LUT; 
				break;
		}
	}
	
	public synchronized void itemStateChanged(ItemEvent e) {
		Object source = e.getSource();
		if (source==methodChoice) {
			method = methodChoice.getSelectedItem();
			doAutoAdjust = true;
		} else if (source==modeChoice) {
			mode = modeChoice.getSelectedIndex();
			setLutColor(mode);
			doStateChange = true;
		} else
			doAutoAdjust = true;
		notify();
	}

	ImageProcessor setup(ImagePlus imp, boolean enableAutoThreshold) {
		ImageProcessor ip;
		int type = imp.getType();
		if (type==ImagePlus.COLOR_RGB || (imp.isComposite()&&((CompositeImage)imp).getMode()==IJ.COMPOSITE))
			return null;
		ip = imp.getProcessor();
		boolean minMaxChange = false;		
        boolean not8Bits = type==ImagePlus.GRAY16 || type==ImagePlus.GRAY32;
		int slice = imp.getCurrentSlice();
		if (not8Bits) {
			if (ip.getMin()==plot.stackMin && ip.getMax()==plot.stackMax && !imageWasUpdated)
				minMaxChange = false;
			else if (ip.getMin()!=previousMin || ip.getMax()!=previousMax || imageWasUpdated) {
				minMaxChange = true;
	 			previousMin = ip.getMin();
	 			previousMax = ip.getMax();
	 		} else if (slice!=previousSlice)
	 			minMaxChange = true;
		}
		int id = imp.getID();
		int roiHashCode = roiHashCode(imp.getRoi());
		if (minMaxChange || id!=previousImageID || type!=previousImageType ||
				imageWasUpdated || roiHashCode!=previousRoiHashCode) {
			minThreshold = ip.getMinThreshold();
			maxThreshold = ip.getMaxThreshold();
			boolean isThresholded = minThreshold != ImageProcessor.NO_THRESHOLD
					&& ip.getCurrentColorModel() != ip.getColorModel(); //does not work???
			//IJ.log("Changed: min/max:"+minMaxChange +" id:"+ (id!=previousImageID)+" type:"+(type!=previousImageType)+" updated:"+imageWasUpdated+". isThresh="+isThresholded);
			//IJ.log(minThreshold+"..."+maxThreshold);
            //Undo.reset(); removed 2014-02-06 M. Schmid - why was it there?
            if (not8Bits && minMaxChange && !isThresholded)
                ip.resetMinAndMax();        //imp.updateAndDraw() is below
			ImageStatistics stats = plot.setHistogram(imp, entireStack(imp));
			if (stats == null)
				return null;
			if (isThresholded) {
				minThreshold = scaleDown(ip, minThreshold);
				maxThreshold = scaleDown(ip, maxThreshold);
			} else {
				if (enableAutoThreshold && !isThresholded)
					autoSetLevels(ip, stats);
				else
					minThreshold = ImageProcessor.NO_THRESHOLD;  //may be an invisible threshold after 'apply'
			}
			scaleUpAndSet(ip, minThreshold, maxThreshold);
			updateLabels(imp, ip);
			updatePercentiles(imp, ip);
			updatePlot(ip);
			updateScrollBars();
			imp.updateAndDraw();
			imageWasUpdated = false;
		}
	 	previousImageID = id;
	 	previousImageType = type;
	 	previousRoiHashCode = roiHashCode;
	 	previousSlice = slice;
	 	firstActivation = false;
	 	return ip;
	}
	
    boolean entireStack(ImagePlus imp) {
        return stackHistogram!=null && stackHistogram.getState() && imp.getStackSize()>1;
    }

	void autoSetLevels(ImageProcessor ip, ImageStatistics stats) {
		if (stats==null || stats.histogram==null) {
			minThreshold = defaultMinThreshold;
			maxThreshold = defaultMaxThreshold;
			return;
		}
		//int threshold = ip.getAutoThreshold(stats.histogram);
		boolean darkb = darkBackground!=null && darkBackground.getState();
		boolean invertedLut = ip.isInvertedLut();
		int modifiedModeCount = stats.histogram[stats.mode];
		if (!method.equals(methodNames[DEFAULT]))
			stats.histogram[stats.mode] = plot.originalModeCount;
		int threshold = thresholder.getThreshold(method, stats.histogram);
		stats.histogram[stats.mode] = modifiedModeCount;
		if (darkb) {
			if (invertedLut)
				{minThreshold=0; maxThreshold=threshold;}
			else
				{minThreshold=threshold+1; maxThreshold=255;}
		} else {
			if (invertedLut)
				{minThreshold=threshold+1; maxThreshold=255;}
			else
				{minThreshold=0; maxThreshold=threshold;}
		}
		if (minThreshold>255) minThreshold = 255;
		if (Recorder.record) {
			boolean stack = stackHistogram!=null && stackHistogram.getState();
			String options = method+(darkb?" dark":"")+(stack?" stack":"");
			if (Recorder.scriptMode())
				Recorder.recordCall("IJ.setAutoThreshold(imp, \""+options+"\");");
			else
				Recorder.record("setAutoThreshold", options);
		}
	}
	
	/** Scales threshold levels in the range 0-255 to the actual levels. */
	void scaleUpAndSet(ImageProcessor ip, double minThreshold, double maxThreshold) {
		if (!(ip instanceof ByteProcessor) && minThreshold!=ImageProcessor.NO_THRESHOLD) {
			double min = ip.getMin();
			double max = ip.getMax();
			if (max>min) {
				minThreshold = min + (minThreshold/255.0)*(max-min);
				maxThreshold = min + (maxThreshold/255.0)*(max-min);
			} else
				minThreshold = maxThreshold = min;
		}
		ip.setThreshold(minThreshold, maxThreshold, lutColor);
		//ip.setSnapshotPixels(null); // disable undo removed 20140206 M. Schmid
	}

	/** Scales a threshold level to the range 0-255. */
	double scaleDown(ImageProcessor ip, double threshold) {
		if (ip instanceof ByteProcessor)
			return threshold;
		double min = ip.getMin();
		double max = ip.getMax();
		if (max>min)
			return ((threshold-min)/(max-min))*255.0;
		else
			return ImageProcessor.NO_THRESHOLD;
	}
	
	/** Scales a threshold level in the range 0-255 to the actual level. */
	double scaleUp(ImageProcessor ip, double threshold) {
		double min = ip.getMin();
		double max = ip.getMax();
		if (max>min)
			return min + (threshold/255.0)*(max-min);
		else
			return ImageProcessor.NO_THRESHOLD;
	}

	void updatePlot(ImageProcessor ip) {
		plot.minThreshold = ip.getMinThreshold()==ImageProcessor.NO_THRESHOLD ?
				-1 : (int)Math.round(minThreshold);
		plot.maxThreshold = (int)Math.round(maxThreshold);
		plot.mode = mode;
		plot.repaint();
	}

	void updatePercentiles(ImagePlus imp, ImageProcessor ip) {
		if (percentiles==null)
			return;
		ImageStatistics stats = plot.stats;
		int minThresholdInt = (int)Math.round(minThreshold);
		int maxThresholdInt = (int)Math.round(maxThreshold);
		if (stats != null && stats.histogram != null && stats.histogram.length==256 &&
		ip.getMinThreshold()!=ImageProcessor.NO_THRESHOLD &&
		minThresholdInt>=0 && minThresholdInt<256 && maxThresholdInt>=0 && maxThresholdInt<256) {
			int[] histogram = stats.histogram;
			int below = 0, inside = 0, above = 0;
			int minValue=0, maxValue=255;
			if (imp.getBitDepth()==16 && !entireStack(imp)) {
				ip.setRoi(imp.getRoi());
				histogram = ip.getHistogram();
				minThresholdInt = (int)Math.round(ip.getMinThreshold());
				maxThresholdInt = (int)Math.round(ip.getMaxThreshold());
				minValue=(int)ip.getMin(); maxValue=(int)ip.getMax();
			}
			for (int i=minValue; i<minThresholdInt; i++)
				below += histogram[i];
			for (int i=minThresholdInt; i<=maxThresholdInt; i++)
				inside += histogram[i];
			for (int i=maxThresholdInt+1; i<maxValue; i++)
				above += histogram[i];
			int total = below + inside + above;
			//IJ.log("<"+minThresholdInt+":"+below+" in:"+inside+"; >"+maxThresholdInt+":"+above+" sum="+total);
			int digits = imp.getCalibration()!=null || (ip instanceof FloatProcessor) ?
			Math.max(Analyzer.getPrecision(), 2) : 0;
			if (mode==OVER_UNDER)
				percentiles.setText("below: "+IJ.d2s(100.*below/total)+" %,  above: "+IJ.d2s(100.*above/total)+" %");
			else
				percentiles.setText(IJ.d2s(100.*inside/total)+" %");
		} else
			percentiles.setText("");
	}

	void updateLabels(ImagePlus imp, ImageProcessor ip) {
		if (label1==null || label2==null)
			return;
		double min = ip.getMinThreshold();
		double max = ip.getMaxThreshold();
		if (min==ImageProcessor.NO_THRESHOLD) {
			label1.setText("");
			label2.setText("");
		} else {
			Calibration cal = imp.getCalibration();
			if (cal.calibrated()) {
				min = cal.getCValue((int)min);
				max = cal.getCValue((int)max);
			}
			if (((int)min==min && (int)max==max) || (ip instanceof ShortProcessor) || max>99999.0) {
				label1.setText(""+(int)min);
				label2.setText(""+(int)max);
			} else {
				label1.setText(""+IJ.d2s(min,2));
				label2.setText(""+IJ.d2s(max,2));
			}
		}
	}

	void updateScrollBars() {
		minSlider.setValue((int)minThreshold);
		maxSlider.setValue((int)maxThreshold);
	}
	
	/** Restore image outside non-rectangular roi. */
  	void doMasking(ImagePlus imp, ImageProcessor ip) {
		ImageProcessor mask = imp.getMask();
		if (mask!=null)
			ip.reset(mask);
	}

	void adjustMinThreshold(ImagePlus imp, ImageProcessor ip, double value) {
		if (IJ.altKeyDown() || IJ.shiftKeyDown() ) {
			double width = maxThreshold-minThreshold;
			if (width<1.0) width = 1.0;
			minThreshold = value;
			maxThreshold = minThreshold+width;
			if ((minThreshold+width)>255) {
				minThreshold = 255-width;
				maxThreshold = minThreshold+width;
				minSlider.setValue((int)minThreshold);
			}
			maxSlider.setValue((int)maxThreshold);
			scaleUpAndSet(ip, minThreshold, maxThreshold);
			return;
		}
		minThreshold = value;
		if (maxThreshold<minThreshold) {
			maxThreshold = minThreshold;
			maxSlider.setValue((int)maxThreshold);
		}
		scaleUpAndSet(ip, minThreshold, maxThreshold);
	}

	void adjustMaxThreshold(ImagePlus imp, ImageProcessor ip, int cvalue) {
		maxThreshold = cvalue;
		if (minThreshold>maxThreshold) {
			minThreshold = maxThreshold;
			minSlider.setValue((int)minThreshold);
		}
		if (minThreshold < 0) {     //remove NO_THRESHOLD
			minThreshold = 0;
			minSlider.setValue((int)minThreshold);
		}
		scaleUpAndSet(ip, minThreshold, maxThreshold);
		IJ.setKeyUp(KeyEvent.VK_ALT);
		IJ.setKeyUp(KeyEvent.VK_SHIFT);
	}

	void reset(ImagePlus imp, ImageProcessor ip) {
		ip.resetThreshold();
		ImageStatistics stats = plot.setHistogram(imp, entireStack(imp));
		if (!(ip instanceof ByteProcessor)) {
			if (entireStack(imp))
				ip.setMinAndMax(stats.min, stats.max);
			else
				ip.resetMinAndMax();
		}
		updateScrollBars();
		if (Recorder.record) {
			if (Recorder.scriptMode())
				Recorder.recordCall("IJ.resetThreshold(imp);");
			else
				Recorder.record("resetThreshold");
		}
	}

	void doSet(ImagePlus imp, ImageProcessor ip) {
		double level1 = ip.getMinThreshold();
		double level2 = ip.getMaxThreshold();
		if (level1==ImageProcessor.NO_THRESHOLD) {
			level1 = scaleUp(ip, defaultMinThreshold);
			level2 = scaleUp(ip, defaultMaxThreshold);
		}
		Calibration cal = imp.getCalibration();
		int digits = (ip instanceof FloatProcessor)||cal.calibrated()?2:0;
		level1 = cal.getCValue(level1);
		level2 = cal.getCValue(level2);
		GenericDialog gd = new GenericDialog("Set Threshold Levels");
		gd.addNumericField("Lower Threshold Level: ", level1, digits);
		gd.addNumericField("Upper Threshold Level: ", level2, digits);
		gd.showDialog();
		if (gd.wasCanceled())
			return;
		level1 = gd.getNextNumber();
		level2 = gd.getNextNumber();
		level1 = cal.getRawValue(level1);
		level2 = cal.getRawValue(level2);
		if (level2<level1)
			level2 = level1;
		double minDisplay = ip.getMin();
		double maxDisplay = ip.getMax();
		ip.resetMinAndMax();
		double minValue = ip.getMin();
		double maxValue = ip.getMax();
		if (level1<minValue) level1 = minValue;
		if (level2>maxValue) level2 = maxValue;
		IJ.wait(500);
		ip.setThreshold(level1, level2, lutColor);
		ip.setSnapshotPixels(null); // disable undo
		setup(imp, false);
		if (Recorder.record) {
			if (imp.getBitDepth()==32) {
				if (Recorder.scriptMode())
					Recorder.recordCall("IJ.setThreshold("+ip.getMinThreshold()+", "+ip.getMaxThreshold()+");");
				else
					Recorder.record("setThreshold", ip.getMinThreshold(), ip.getMaxThreshold());
			} else {
				int min = (int)ip.getMinThreshold();
				int max = (int)ip.getMaxThreshold();
				if (cal.isSigned16Bit()) {
					min = (int)cal.getCValue(level1);
					max = (int)cal.getCValue(level2);
				}
				if (Recorder.scriptMode())
					Recorder.recordCall("IJ.setThreshold(imp, "+min+", "+max+");");
				else
					Recorder.record("setThreshold", min, max);
			}
		}
	}

	void changeState(ImagePlus imp, ImageProcessor ip) {
		scaleUpAndSet(ip, minThreshold, maxThreshold);
		updateScrollBars();
	}

	void autoThreshold(ImagePlus imp, ImageProcessor ip) {
		ip.resetThreshold();
		previousImageID = 0;
		setup(imp, true);
 	}
 	
 	void apply(ImagePlus imp) {
 		try {
 			if (imp.getBitDepth()==32) {
				GenericDialog gd = new GenericDialog("NaN Backround");
				gd.addCheckbox("Set Background Pixels to NaN", backgroundToNaN);
				gd.showDialog();
				if (gd.wasCanceled()) {
 					runThresholdCommand();
					return;
				}
				backgroundToNaN = gd.getNextBoolean();
				if (backgroundToNaN) {
					Recorder.recordInMacros = true;
 					IJ.run("NaN Background");
					Recorder.recordInMacros = false;
 				} else
 					runThresholdCommand();
 			} else
 				runThresholdCommand();
 		} catch (Exception e)
 			{/* do nothing */}
 		//close();
 	}
 	
 	void runThresholdCommand() {
		Thresholder.setMethod(method);
		Thresholder.setBackground(darkBackground.getState()?"Dark":"Light");
		if (Recorder.record) {
			Recorder.setCommand("Convert to Mask");
			(new Thresholder()).run("mask");
			Recorder.saveCommand();
		} else
			(new Thresholder()).run("mask");
	}
	
	static final int RESET=0, AUTO=1, HIST=2, APPLY=3, STATE_CHANGE=4, MIN_THRESHOLD=5, MAX_THRESHOLD=6, SET=7;

	// Separate thread that does the potentially time-consuming processing 
	public void run() {
		while (!done) {
			synchronized(this) {
				try {wait();}
				catch(InterruptedException e) {}
			}
			doUpdate();
		}
	}

	void doUpdate() {
		ImagePlus imp;
		ImageProcessor ip;
		int action;
		int min = minValue;
		int max = maxValue;
		if (doReset) action = RESET;
		else if (doAutoAdjust) action = AUTO;
		else if (doApplyLut) action = APPLY;
		else if (doStateChange) action = STATE_CHANGE;
		else if (doSet) action = SET;
		else if (minValue>=0) action = MIN_THRESHOLD;
		else if (maxValue>=0) action = MAX_THRESHOLD;
		else return;
		minValue = -1;
		maxValue = -1;
		doReset = false;
		doAutoAdjust = false;
		doApplyLut = false;
		doStateChange = false;
		doSet = false;
		imp = WindowManager.getCurrentImage();
		if (imp==null) {
			IJ.beep();
			IJ.showStatus("No image");
			return;
		}
		ip = setup(imp, false);
		if (ip==null) {
			imp.unlock();
			IJ.beep();
			if (imp.isComposite())
				IJ.showStatus("\"Composite\" mode images cannot be thresholded");
			else
				IJ.showStatus("RGB images cannot be thresholded");
			return;
		}
		//IJ.write("setup: "+(imp==null?"null":imp.getTitle()));
		switch (action) {
			case RESET: reset(imp, ip); break;
			case AUTO: autoThreshold(imp, ip); break;
			case APPLY: apply(imp); break;
			case STATE_CHANGE: changeState(imp, ip); break;
			case SET: doSet(imp, ip); break;
			case MIN_THRESHOLD: adjustMinThreshold(imp, ip, min); break;
			case MAX_THRESHOLD: adjustMaxThreshold(imp, ip, max); break;
		}
		updatePlot(ip);
		updateLabels(imp, ip);
		updatePercentiles(imp, ip);
		ip.setLutAnimation(true);
		imp.updateAndDraw();
	}

    /** Overrides close() in PlugInFrame. */
    public void close() {
    	super.close();
		instance = null;
		done = true;
		Prefs.saveLocation(LOC_KEY, getLocation());
		Prefs.set(MODE_KEY, mode);
		Prefs.set(DARK_BACKGROUND, darkBackground.getState());
		synchronized(this) {
			notify();
		}
	}

    public void windowActivated(WindowEvent e) {
    	super.windowActivated(e);
    	plot.requestFocus();
		ImagePlus imp = WindowManager.getCurrentImage();
		if (!firstActivation && imp!=null)
			setup(imp, false);
	}

	// Returns a hashcode for the specified ROI that typically changes 
	// if it is moved,  even though is still the same object.
	int roiHashCode(Roi roi) {
		return roi!=null?roi.getHashCode():0;
	}

    /** Notifies the ThresholdAdjuster that the image has changed.
     *  If the image has no threshold, it does not autothreshold the image. */
    public static void update() {
		if (instance!=null) {
			ThresholdAdjuster ta = ((ThresholdAdjuster)instance);
			ImagePlus imp = WindowManager.getCurrentImage();
			if (imp!=null && ta.previousImageID==imp.getID()) {
				ta.previousImageID = 0;
				ta.setup(imp, false);
			}
		}
    }

	/** Returns the current method ("Default", "Huang", etc). */
	public static String getMethod() {
		return method;
	}
	
	/** Returns the current mode ("Red","B&W" or"Over/Under"). */
	public static String getMode() {
		return modes[mode];
	}

} // ThresholdAdjuster class


class ThresholdPlot extends Canvas implements Measurements, MouseListener {
	static final int WIDTH = 256, HEIGHT=48;
	int minThreshold = -1;
	int maxThreshold = 170;
	ImageStatistics stats;
	int[] histogram;
	Color[] hColors;
	int hmax;
	Image os;
	Graphics osg;
	int mode;
	int originalModeCount;
	double stackMin, stackMax;
	int imageID2;
	boolean entireStack2;
	double mean2;
	
	public ThresholdPlot() {
		addMouseListener(this);
		setSize(WIDTH+2, HEIGHT+2);
	}
	
    /** Overrides Component getPreferredSize(). Added to work 
    	around a bug in Java 1.4.1 on Mac OS X.*/
    public Dimension getPreferredSize() {
        return new Dimension(WIDTH+2, HEIGHT+2);
    }

	ImageStatistics setHistogram(ImagePlus imp, boolean entireStack) {
		double mean = entireStack?imp.getProcessor().getStatistics().mean:0.0;
		if (entireStack && stats!=null && imp.getID()==imageID2 
		&& entireStack==entireStack2 && mean==mean2)
			return stats;
		mean2 = mean;
		ImageProcessor ip = imp.getProcessor();
   		ColorModel cm = ip.getColorModel();
		stats = null;
		if (entireStack) {
			if (imp.isHyperStack()) {
				ImageStack stack = ChannelSplitter.getChannel(imp, imp.getChannel());
				stats = new StackStatistics(new ImagePlus("", stack));
			} else
				stats = new StackStatistics(imp);
		}
		if (!(ip instanceof ByteProcessor)) {
			if (entireStack) {
				if (imp.getLocalCalibration().isSigned16Bit()) 
					{stats.min += 32768; stats.max += 32768;}
				stackMin = stats.min;
				stackMax = stats.max;
				ip.setMinAndMax(stackMin, stackMax);
				imp.updateAndDraw();
			} else {
				stackMin = stackMax = 0.0;
				if (entireStack2) {
					ip.resetMinAndMax();
					imp.updateAndDraw();
				}
			}
			Calibration cal = imp.getCalibration();
			if (ip instanceof FloatProcessor) {
				int digits = Math.max(Analyzer.getPrecision(), 2);
				IJ.showStatus("min="+IJ.d2s(ip.getMin(),digits)+", max="+IJ.d2s(ip.getMax(),digits));
			} else
				IJ.showStatus("min="+(int)cal.getCValue(ip.getMin())+", max="+(int)cal.getCValue(ip.getMax()));
			ip = ip.convertToByte(true);
			ip.setColorModel(ip.getDefaultColorModel());
		}
		Roi roi = imp.getRoi();
		if (roi!=null && !roi.isArea()) roi = null;
		ip.setRoi(roi);
		if (stats==null)
			stats = ImageStatistics.getStatistics(ip, AREA+MIN_MAX+MODE, null);
		int maxCount2 = 0;
		histogram = stats.histogram;
		originalModeCount = histogram[stats.mode];
		for (int i = 0; i < stats.nBins; i++)
			if ((histogram[i] > maxCount2) && (i != stats.mode))
				maxCount2 = histogram[i];
		hmax = stats.maxCount;
		if ((hmax>(maxCount2 * 2)) && (maxCount2 != 0))
			hmax = (int)(maxCount2 * 1.5);
		os = null;

		if (!(cm instanceof IndexColorModel))
			return null;
		IndexColorModel icm = (IndexColorModel)cm;
		int mapSize = icm.getMapSize();
		if (mapSize!=256)
			return null;
		byte[] r = new byte[256];
		byte[] g = new byte[256];
		byte[] b = new byte[256];
		icm.getReds(r); 
		icm.getGreens(g); 
		icm.getBlues(b);
		hColors = new Color[256];
		final int brightnessLimit = 1800; // 0 ... 2550 scale; brightness is reduced above
		for (int i=0; i<256; i++) {     //avoid colors that are too bright (invisible)
			int sum = 4*(r[i]&255) + 5*(g[i]&255) + (b[i]&255);
			if (sum > brightnessLimit) {
				r[i] = (byte)(((r[i]&255)*brightnessLimit*2)/(sum+brightnessLimit));
				g[i] = (byte)(((g[i]&255)*brightnessLimit*2)/(sum+brightnessLimit));
				b[i] = (byte)(((b[i]&255)*brightnessLimit*2)/(sum+brightnessLimit));
			}
			hColors[i] = new Color(r[i]&255, g[i]&255, b[i]&255);
		}
		imageID2 = imp.getID();
		entireStack2 = entireStack;
		return stats;
	}
	
	public void update(Graphics g) {
		paint(g);
	}

	public void paint(Graphics g) {
		if (g==null) return;
		if (histogram!=null) {
			if (os==null && hmax>0) {
				os = createImage(WIDTH,HEIGHT);
				osg = os.getGraphics();
				osg.setColor(Color.white);
				osg.fillRect(0, 0, WIDTH, HEIGHT);
				osg.setColor(Color.gray);
				for (int i = 0; i < WIDTH; i++) {
					if (hColors!=null) osg.setColor(hColors[i]);
					int histValue = histogram[i]<hmax ? histogram[i] : hmax;
					osg.drawLine(i, HEIGHT, i, HEIGHT - (HEIGHT*histogram[i]+hmax-1)/hmax);
				}
				osg.dispose();
			}
			if (os==null) return;
			g.drawImage(os, 1, 1, this);
		} else {
			g.setColor(Color.white);
			g.fillRect(1, 1, WIDTH, HEIGHT);
		}
		g.setColor(Color.black);
 		g.drawRect(0, 0, WIDTH+1, HEIGHT+1);
 		if (minThreshold>=0 && minThreshold<=255 && maxThreshold>=0 && maxThreshold<=255) {
			if (mode==ThresholdAdjuster.OVER_UNDER) {
				g.setColor(Color.blue);
	 			g.drawRect(0, 0, minThreshold, HEIGHT+1);
	 			g.drawRect(0, 1, minThreshold, 1);
	 			g.setColor(Color.green);
	 			g.drawRect(maxThreshold+2, 0, WIDTH-maxThreshold-1, HEIGHT+1);
	 			g.drawLine(maxThreshold+2, 1, WIDTH+1,1);
				return;
			}
			if (mode==ThresholdAdjuster.RED)
				g.setColor(Color.red);
 			g.drawRect(minThreshold+1, 0, maxThreshold-minThreshold, HEIGHT+1);
	 		g.drawLine(minThreshold+1, 1, maxThreshold+1, 1);
 		}
     }

	public void mousePressed(MouseEvent e) {}
	public void mouseReleased(MouseEvent e) {}
	public void mouseExited(MouseEvent e) {}
	public void mouseClicked(MouseEvent e) {}
	public void mouseEntered(MouseEvent e) {}

} // ThresholdPlot class