debian/changelog

+imagej (1.52r-1) unstable; urgency=medium
+
+  * Team upload
+  * Correct sorting of Java alternatives in Wrapper script
+  * Avoid dpkg-architecture in wrapper script which is not necessarily
+    installed on users machine and use dpkg --print-architecture instead
+    Closes: #931268
+  * Standards-Version: 4.4.1
+  * Fix day-of-week for changelog entries 1.39q-2.
+
+ -- Andreas Tille <tille@debian.org>  Wed, 04 Dec 2019 14:35:53 +0100
+
 imagej (1.52p-1) unstable; urgency=medium
 
   * Team upload.
@@ -432,7 +444,7 @@ imagej (1.39q-2) unstable; urgency=high
 
   * New man page.
 
- -- Paolo Ariano <paolo.ariano@unito.it>  Fri, 06 Mar 2008 15:29:56 +0100
+ -- Paolo Ariano <paolo.ariano@unito.it>  Thu, 06 Mar 2008 15:29:56 +0100
 
 imagej (1.39q-1) unstable; urgency=low
 

debian/control

@@ -9,7 +9,7 @@ Build-Depends-Indep: ant,
                      default-jdk-headless,
                      javahelper,
                      maven-repo-helper
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/imagej
 Vcs-Git: https://salsa.debian.org/med-team/imagej.git
 Homepage: https://imagej.nih.gov/ij

debian/extra/imagej

@@ -29,7 +29,7 @@ shopt -s extglob # allow extended pattern matching
 
 if [ -z "$JAVA_HOME" ] ; then
     # This does not work see #505315
-    JAVA_HOME=`/usr/sbin/update-java-alternatives -l | grep openjdk | grep $(dpkg-architecture -q DEB_TARGET_ARCH) | sort | tail -1 | tr -s ' ' | cut -d' ' -f 3`
+    JAVA_HOME=`/usr/sbin/update-java-alternatives -l | grep openjdk | grep $(dpkg --print-architecture) | sort -u -k2 | tail -1 | tr -s ' ' | cut -d' ' -f 3`
     # Reverted to old version - see #558222 (Andreas Tille)
     # JAVA_HOME=$(dirname $(dirname $(dirname $(readlink /etc/alternatives/java))))
     # Also suggested by From: JR Coding <jr.coding@googlemail.com>; To: 740439@bugs.debian.org

ij/Executer.java

@@ -17,23 +17,23 @@ public class Executer implements Runnable {
 	private static String previousCommand;
 	private static CommandListener listener;
 	private static Vector listeners = new Vector();
-	
+
 	private String command;
 	private Thread thread;
-	
+
 	/** Create an Executer to run the specified menu command
 		in this thread using the active image. */
 	public Executer(String cmd) {
 		command = cmd;
 	}
 
-	/** Create an Executer that runs the specified menu 
+	/** Create an Executer that runs the specified menu
 		command in a separate thread using the specified image,
 		or using the active image if 'imp' is null. */
 	public Executer(String cmd, ImagePlus imp) {
 		if (cmd.startsWith("Repeat")) {
 			command = previousCommand;
-			IJ.setKeyUp(KeyEvent.VK_SHIFT);		
+			IJ.setKeyUp(KeyEvent.VK_SHIFT);
 		} else {
 			command = cmd;
 			if (!(cmd.equals("Undo")||cmd.equals("Close")))
@@ -117,7 +117,7 @@ public class Executer implements Runnable {
 				WindowManager.setTempCurrentImage(null);
 		}
 	}
-	    
+
 	void runCommand(String cmd) {
 		Hashtable table = Menus.getCommands();
 		String className = (String)table.get(cmd);
@@ -131,6 +131,17 @@ public class Executer implements Runnable {
 					className = className.substring(0, argStart);
 				}
 			}
+			if (Prefs.nonBlockingFilterDialogs) {
+				// we have the plugin class name, let us see whether it is allowed to run it
+				ImagePlus imp = WindowManager.getCurrentImage();
+				boolean imageLocked = imp!=null && imp.isLockedByAnotherThread();
+				if (imageLocked && !allowedWithLockedImage(className)) {
+					IJ.beep();
+					IJ.showStatus("\""+cmd + "\" blocked because \"" + imp.getTitle() + "\" is locked");
+					return;
+				}
+			}
+			// run the plugin
 			if (IJ.shiftKeyDown() && className.startsWith("ij.plugin.Macro_Runner") && !Menus.getShortcuts().contains("*"+cmd))
     			IJ.open(IJ.getDirectory("plugins")+arg);
     		else
@@ -159,7 +170,17 @@ public class Executer implements Runnable {
 					IJ.error("Unrecognized command: \"" + cmd+"\"");
 			}
 	 	}
-    }   
+    }
+
+	/** If the foreground image is locked during a filter operation with NonBlockingGenericDialog,
+	 *  the following plugins are allowed */
+	boolean allowedWithLockedImage(String className) {
+		return className.equals("ij.plugin.Zoom") ||
+				className.equals("ij.plugin.frame.ContrastAdjuster") ||
+				className.equals("ij.plugin.SimpleCommands") ||  //includes Plugins>Utiltites>Reset (needed to reset a locked image)
+				className.equals("ij.plugin.WindowOrganizer") ||
+				className.equals("ij.plugin.URLOpener");
+	}
 
     /** Opens a .lut file from the ImageJ/luts directory and returns 'true' if successful. */
     public static boolean loadLut(String name) {
@@ -182,7 +203,7 @@ public class Executer implements Runnable {
 		return false;
     }
 
-    /** Opens a file from the File/Open Recent menu 
+    /** Opens a file from the File/Open Recent menu
  	      and returns 'true' if successful. */
     boolean openRecent(String cmd) {
 		Menu menu = Menus.getOpenRecentMenu();
@@ -201,17 +222,17 @@ public class Executer implements Runnable {
 	public static String getCommand() {
 		return previousCommand;
 	}
-	
+
 	/** Adds the specified command listener. */
 	public static void addCommandListener(CommandListener listener) {
 		listeners.addElement(listener);
 	}
-	
+
 	/** Removes the specified command listener. */
 	public static void removeCommandListener(CommandListener listener) {
 		listeners.removeElement(listener);
 	}
-	
+
 	public static int getListenerCount() {
 		return listeners.size();
 	}

ij/IJ.java

@@ -24,6 +24,7 @@ import java.net.*;
 import javax.net.ssl.*;
 import java.security.cert.*;
 import java.security.KeyStore;
+import java.nio.ByteBuffer;
 
 
 /** This class consists of static utility methods. */
@@ -564,9 +565,52 @@ public class IJ {
 		'row1' and 'row2' must be in the range 0-Analyzer.getCounter()-1. */
 	public static void deleteRows(int row1, int row2) {
 		ResultsTable rt = Analyzer.getResultsTable();
+		int tableSize = rt.size();
 		rt.deleteRows(row1, row2);
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp!=null)
+			Overlay.updateTableOverlay(imp, row1, row2, tableSize);
 		rt.show("Results");
 	}
+	
+	/** Returns a measurement result, where 'measurement' is "Area", 
+	 * "Mean", "StdDev", "Mode", "Min", "Max", "X", "Y", "XM", "YM",
+	 * "Perim.", "BX", "BY", "Width", "Height", "Major", "Minor", "Angle",
+	 * "Circ.", "Feret", "IntDen", "Median", "Skew", "Kurt", "%Area",
+	 * "RawIntDen", "Ch", "Slice", "Frame", "FeretX", "FeretY",
+	 * "FeretAngle", "MinFeret", "AR", "Round", "Solidity", "MinThr"
+	 * or "MaxThr". Add " raw" to the argument to disable calibration,
+	 * for example IJ.getValue("Mean raw"). Add " limit" to enable
+	 * the "limit to threshold" option.
+	*/
+	public static double getValue(ImagePlus imp, String measurement) {
+		String options = "";
+		int index = measurement.indexOf(" ");
+		if (index>0) {
+			if (index<measurement.length()-1)
+				options = measurement.substring(index+1, measurement.length());
+			measurement = measurement.substring(0, index);
+		}
+		int measurements = Measurements.ALL_STATS + Measurements.SLICE;
+		if (options.contains("limit"))
+			measurements += Measurements.LIMIT;
+		Calibration cal = null;
+		if (options.contains("raw")) {
+			cal = imp.getCalibration();
+			imp.setCalibration(null);
+		}
+		ImageStatistics stats = imp.getStatistics(measurements);
+		ResultsTable rt = new ResultsTable();
+		Analyzer analyzer = new Analyzer(imp, measurements, rt);
+		analyzer.saveResults(stats, imp.getRoi());
+		double value = Double.NaN;
+		try {
+			value = rt.getValue(measurement, 0);
+		} catch (Exception e) {};
+		if (cal!=null)
+			imp.setCalibration(cal);
+		return value;
+	}
 
 	/** Returns a reference to the "Results" window TextPanel.
 		Opens the "Results" window if it is currently not open.
@@ -894,6 +938,14 @@ public class IJ {
 		return str;
 	}
 
+	/** Pad 's' with leading zeros to the specified number of digits. */
+	public static String pad(String s, int digits) {
+		String str = ""+s;
+		while (str.length()<digits)
+			str = "0"+str;
+		return str;
+	}
+
 	/** Adds the specified class to a Vector to keep it from being garbage
 	collected, which would cause the classes static fields to be reset. 
 	Probably not needed with Java 1.2 or later. */
@@ -1644,8 +1696,8 @@ public class IJ {
 		return ImageJ.VERSION+build;
 	}
 
-	/** Returns the path to the home ("user.home"), startup, ImageJ, plugins, macros, 
-		luts, temp, current or image directory if <code>title</code> is "home", "startup", 
+	/** Returns the path to the home ("user.home"), downloads, startup, ImageJ, plugins, macros, 
+		luts, temp, current or image directory if <code>title</code> is "home", "downloads", "startup", 
 		"imagej", "plugins", "macros", "luts", "temp", "current", "default", "image", otherwise, 
 		displays a dialog and returns the path to the directory selected by the user. 
 		Returns null if the specified directory is not found or the user
@@ -1665,6 +1717,8 @@ public class IJ {
 				return null;
 		} else if (title2.equals("home"))
 			return System.getProperty("user.home") + File.separator;
+		else if (title2.equals("downloads"))
+			return System.getProperty("user.home")+File.separator+"Downloads"+File.separator;
 		else if (title2.equals("startup"))
 			return Prefs.getImageJDir();
 		else if (title2.equals("imagej"))
@@ -2062,6 +2116,34 @@ public class IJ {
 		}
 		return str;
 	}
+	
+	public static ByteBuffer openAsByteBuffer(String path) {
+		if (path==null || path.equals("")) {
+			OpenDialog od = new OpenDialog("Open as ByteBuffer", "");
+			String directory = od.getDirectory();
+			String name = od.getFileName();
+			if (name==null) return null;
+			path = directory + name;
+		}
+		File file = new File(path);
+		if (!file.exists()) {
+			error("OpenAsByteBuffer", "File not found");
+			return null;
+		}
+		int len = (int)file.length();
+		byte[] buffer = new byte[len];
+		try {
+			InputStream in = new BufferedInputStream(new FileInputStream(path));
+			DataInputStream dis = new DataInputStream(in);
+			dis.readFully(buffer);
+			dis.close();
+		}
+		catch (Exception e) {
+			error("OpenAsByteBuffer", e.getMessage());
+			return null;
+		}
+		return ByteBuffer.wrap(buffer);
+	}
 
 	/** Creates a new image.
 	*  @param title   image name

ij/ImageJ.java

@@ -77,8 +77,8 @@ public class ImageJ extends Frame implements ActionListener,
 	MouseListener, KeyListener, WindowListener, ItemListener, Runnable {
 
 	/** Plugins should call IJ.getVersion() or IJ.getFullVersion() to get the version string. */
-	public static final String VERSION = "1.52p";
-	public static final String BUILD = "";  //61
+	public static final String VERSION = "1.52r";
+	public static final String BUILD = ""; //57
 	public static Color backgroundColor = new Color(237,237,237);
 	/** SansSerif, 12-point, plain font. */
 	public static final Font SansSerif12 = new Font("SansSerif", Font.PLAIN, 12);
@@ -265,6 +265,8 @@ public class ImageJ extends Frame implements ActionListener,
 			props.put("proxySet", "true");
 			props.put("http.proxyHost", server);
 			props.put("http.proxyPort", ""+port);
+			props.put("https.proxyHost", server);
+			props.put("https.proxyPort", ""+port);
 		}
 		//new ProxySettings().logProperties();
 	}
@@ -281,7 +283,8 @@ public class ImageJ extends Frame implements ActionListener,
 		int ijY = Prefs.getInt(IJ_Y,-99);
 		Rectangle maxBounds = GUI.getMaxWindowBounds();
 		//System.out.println("getPreferredLoc1: "+ijX+" "+ijY+" "+maxBounds);
-		if (ijX>=maxBounds.x && ijY>=maxBounds.y && ijX<(maxBounds.x+maxBounds.width-75))
+		if (ijX>=maxBounds.x && ijY>=maxBounds.y && ijX<(maxBounds.x+maxBounds.width-75)
+		&& ijY<(maxBounds.y+maxBounds.height-75))
 			return new Point(ijX, ijY);
 		Dimension tbsize = toolbar.getPreferredSize();
 		int ijWidth = tbsize.width+10;

ij/Menus.java

@@ -1231,13 +1231,6 @@ public class Menus {
     		else if (stack.isLab())
     			type = LAB_STACK;
     	}
-		if (type==ImagePlus.GRAY8) {
-			ImageProcessor ip = imp.getProcessor();
-			if (ip!=null && ip.getMinThreshold()==ImageProcessor.NO_THRESHOLD && ip.isColorLut() && !ip.isPseudoColorLut()) {
-				type = ImagePlus.COLOR_256;
-				imp.setType(ImagePlus.COLOR_256);
-			}
-		}
     	switch (type) {
     		case ImagePlus.GRAY8:
 				gray8Item.setState(true);

ij/Prefs.java

@@ -57,7 +57,8 @@ public class Prefs {
 		SUBPIXEL_RESOLUTION=1<<2, ENHANCED_LINE_TOOL=1<<3, SKIP_RAW_DIALOG=1<<4,
 		REVERSE_NEXT_PREVIOUS_ORDER=1<<5, AUTO_RUN_EXAMPLES=1<<6, SHOW_ALL_POINTS=1<<7,
 		DO_NOT_SAVE_WINDOW_LOCS=1<<8, JFILE_CHOOSER_CHANGED=1<<9,
-		CANCEL_BUTTON_ON_RIGHT=1<<10, IGNORE_RESCALE_SLOPE=1<<11;
+		CANCEL_BUTTON_ON_RIGHT=1<<10, IGNORE_RESCALE_SLOPE=1<<11,
+		NON_BLOCKING_DIALOGS=1<<12;
 	public static final String OPTIONS2 = "prefs.options2";
     
 	/** file.separator system property */
@@ -183,6 +184,8 @@ public class Prefs {
 	public static boolean dialogCancelButtonOnRight;
 	/** Support TRANSFORM Undo in macros */
 	public static boolean supportMacroUndo;
+	/** Use NonBlockingGenericDialogs in filters */	
+	public static boolean nonBlockingFilterDialogs;
 
 	static boolean commandLineMacro;
 	static Properties ijPrefs = new Properties();
@@ -525,7 +528,7 @@ public class Prefs {
 		jFileChooserSettingChanged = (options2&JFILE_CHOOSER_CHANGED)!=0;
 		dialogCancelButtonOnRight = (options2&CANCEL_BUTTON_ON_RIGHT)!=0;
 		ignoreRescaleSlope = (options2&IGNORE_RESCALE_SLOPE)!=0;
-		;
+		nonBlockingFilterDialogs = (options2&NON_BLOCKING_DIALOGS)!=0;
 	}
 
 	static void saveOptions(Properties prefs) {
@@ -555,7 +558,8 @@ public class Prefs {
 			+ (doNotSaveWindowLocations?DO_NOT_SAVE_WINDOW_LOCS:0)
 			+ (jFileChooserSettingChanged?JFILE_CHOOSER_CHANGED:0)
 			+ (dialogCancelButtonOnRight?CANCEL_BUTTON_ON_RIGHT:0)
-			+ (ignoreRescaleSlope?IGNORE_RESCALE_SLOPE:0);
+			+ (ignoreRescaleSlope?IGNORE_RESCALE_SLOPE:0)
+			+ (nonBlockingFilterDialogs?NON_BLOCKING_DIALOGS:0);
 		prefs.put(OPTIONS2, Integer.toString(options2));
 	}
 

ij/VirtualStack.java

@@ -27,9 +27,18 @@ public class VirtualStack extends ImageStack {
 		super(width, height);
 	}
 
-	/** Creates an empty virtual stack. */
+	/** Creates an empty virtual stack.
+	 * @param width		image width
+	 * @param height	image height
+	 * @param cm	ColorModel or null
+	 * @param path	file path of directory containing the images
+	 * @see #addSlice(String)
+	 * @see <a href="http://wsr.imagej.net/macros/js/OpenAsVirtualStack.js">OpenAsVirtualStack.js</a>
+	*/
 	public VirtualStack(int width, int height, ColorModel cm, String path) {
 		super(width, height, cm);
+		if (path.length()>0 && !(path.endsWith(File.separator)||path.endsWith("/")))
+			path = path + "/";
 		this.path = path;
 		names = new String[INITIAL_SIZE];
 		labels = new String[INITIAL_SIZE];
@@ -50,12 +59,18 @@ public class VirtualStack extends ImageStack {
 		bitDepth = 8;
 	}
 
-	 /** Adds an image to the end of the stack. */
-	public void addSlice(String name) {
-		if (name==null) 
-			throw new IllegalArgumentException("'name' is null!");
+	/** Adds an image to the end of the stack. The argument 
+	 * can be a full file path (e.g., "C:/Users/wayne/dir1/image.tif")
+	 * if the 'path' argument in the constructor is "". File names
+	 * that start with '.' are ignored.
+	*/
+	public void addSlice(String fileName) {
+		if (fileName==null) 
+			throw new IllegalArgumentException("'fileName' is null!");
+		if (fileName.startsWith("."))
+			return;
 		nSlices++;
-	   //IJ.log("addSlice: "+nSlices+"	"+name);
+	   //IJ.log("addSlice: "+nSlices+"	"+fileName);
 	   if (nSlices==names.length) {
 			String[] tmp = new String[nSlices*2];
 			System.arraycopy(names, 0, tmp, 0, nSlices);
@@ -64,7 +79,7 @@ public class VirtualStack extends ImageStack {
 			System.arraycopy(labels, 0, tmp, 0, nSlices);
 			labels = tmp;
 		}
-		names[nSlices-1] = name;
+		names[nSlices-1] = fileName;
 	}
 
    /** Does nothing. */
@@ -123,7 +138,7 @@ public class VirtualStack extends ImageStack {
 		Opener opener = new Opener();
 		opener.setSilentMode(true);
 		IJ.redirectErrorMessages(true);
-		ImagePlus imp = opener.openImage(path, names[n-1]);
+		ImagePlus imp = opener.openImage(path+names[n-1]);
 		IJ.redirectErrorMessages(false);
 		ImageProcessor ip = null;
 		int depthThisImage = 0;

ij/gui/GenericDialog.java

@@ -80,6 +80,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 	private static GenericDialog instance;
 	private boolean firstPaint = true;
 	private boolean fontSizeSet;
+	private boolean showDialogCalled;
 
 
     /** Creates a new GenericDialog with the specified title. Uses the current image
@@ -120,6 +121,17 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 		addWindowListener(this);
     }
 
+	/** Adds a numeric field. The first word of the label must be
+		unique or command recording will not work.
+	* @param label			the label
+	* @param defaultValue	value to be initially displayed
+	*/
+	public void addNumericField(String label, double defaultValue) {
+		int decimalPlaces = (int)defaultValue==defaultValue?0:3;
+		int columnWidth = decimalPlaces==3?8:6;
+		addNumericField(label, defaultValue, decimalPlaces, columnWidth, null);
+	}
+
 	/** Adds a numeric field. The first word of the label must be
 		unique or command recording will not work.
 	* @param label			the label
@@ -210,7 +222,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
     		labels = new Hashtable();
     	if (label.length()>0)
     		label = Macro.trimKey(label.trim());
-    	if (hasLabel(label)) {                      // not a unique label?
+    	if (label.length()>0 && hasLabel(label)) {                      // not a unique label?
     		label += "_0";
     		for (int n=1; hasLabel(label); n++) {   // while still not a unique label
     			label = label.substring(0, label.lastIndexOf('_')); //remove counter
@@ -241,6 +253,8 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 	* @param columns			width of the text field. If columns is 8 or more, additional items may be added to this line with addToSameRow()
 	*/
 	public void addStringField(String label, String defaultText, int columns) {
+		if (addToSameRow && label.equals("_"))
+			label = "";
    		String label2 = label;
    		if (label2.indexOf('_')!=-1)
    			label2 = label2.replace('_', ' ');
@@ -628,13 +642,15 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 		}
 		addSlider( label, minValue, maxValue, defaultValue, scale, digits);
 	}
-	
+
 	/** This vesion of addSlider() adds a 'stepSize' argument.<br>
 	 * Example: http://wsr.imagej.net/macros/SliderDemo.txt
 	*/
 	public void addSlider(String label, double minValue, double maxValue, double defaultValue, double stepSize) {
 		if ( stepSize <= 0 ) stepSize  = 1;
-		int digits = digits(stepSize);		
+		int digits = digits(stepSize);
+		if (digits==1 && "Angle:".equals(label))
+			digits = 2;
 		double scale = 1.0 / Math.abs( stepSize );
 		if ( scale <= 0 ) scale = 1;
 		if ( defaultValue < minValue ) defaultValue = minValue;
@@ -644,7 +660,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 		defaultValue *= scale;
 		addSlider(label, minValue, maxValue, defaultValue, scale, digits);
 	}
-	
+
 	private int digits( double d ) {
 		if ( d == (int) d ) return 0;
 		String s = Double.toString(d);
@@ -656,6 +672,9 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 		int columns = 4 + digits - 2;
 		if ( columns < 4 ) columns = 4;
 		if (minValue<0.0) columns++;
+		String mv = IJ.d2s(maxValue,0);
+		if (mv.length()>4 && digits==0)
+			columns += mv.length()-4;
    		String label2 = label;
    		if (label2.indexOf('_')!=-1)
    			label2 = label2.replace('_', ' ');
@@ -676,12 +695,14 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 			slider = new Vector(5);
 			sliderIndexes = new Vector(5);
 			sliderScales = new Vector(5);
-			sliderDigits = new Vector(5);	
+			sliderDigits = new Vector(5);
 		}
 		Scrollbar s = new Scrollbar(Scrollbar.HORIZONTAL, (int)defaultValue, 1, (int)minValue, (int)maxValue+1);
 		slider.addElement(s);
 		s.addAdjustmentListener(this);
 		s.setUnitIncrement(1);
+		if (IJ.isMacOSX())
+			s.addKeyListener(this);
 
 		if (numberField==null) {
 			numberField = new Vector(5);
@@ -789,7 +810,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
      *  addMessage, addPanel, and before the showDialog() method
      *  (in the latter case, the buttons appear to the right of the previous item).
      *  Note that addMessage (and addStringField, if its column width is more than 8) use
-     *  the remaining width, so it must be the last item of a row. 
+     *  the remaining width, so it must be the last item of a row.
      */
     public void addToSameRow() {
         addToSameRow = true;
@@ -884,12 +905,12 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 
 	/** Returns the contents of the next numeric field,
 		or NaN if the field does not contain a number. */
-   public double getNextNumber() {
+    public double getNextNumber() {
 		if (numberField==null)
 			return -1.0;
 		TextField tf = (TextField)numberField.elementAt(nfIndex);
 		String theText = tf.getText();
-        String label=null;
+		String label=null;
 		if (macro) {
 			label = (String)labels.get((Object)tf);
 			theText = Macro.getValue(macroOptions, label, theText);
@@ -920,7 +941,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 							+"   Key: \""+label.toLowerCase(Locale.US)+"\"\n"
 							+"   Value or variable name: \""+theText+"\"");
 					}
-                }
+				}
 			}
 		}
 		if (recorderOn && !skipRecording) {
@@ -995,8 +1016,8 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 			return "";
 		TextField tf = (TextField)(stringField.elementAt(sfIndex));
 		theText = tf.getText();
+		String label = labels!=null?(String)labels.get((Object)tf):"";
 		if (macro) {
-			String label = (String)labels.get((Object)tf);
 			theText = Macro.getValue(macroOptions, label, theText);
 			if (theText!=null && (theText.startsWith("&")||label.toLowerCase(Locale.US).startsWith(theText))) {
 				// Is the value a macro variable?
@@ -1006,7 +1027,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 				if (s!=null) theText = s;
 			}
 		}
-		if (recorderOn) {
+		if (recorderOn && !label.equals("")) {
 			String s = theText;
 			if (s!=null&&s.length()>=3&&Character.isLetter(s.charAt(0))&&s.charAt(1)==':'&&s.charAt(2)=='\\')
 				s = s.replaceAll("\\\\", "/");  // replace "\" with "/" in Windows file paths
@@ -1184,6 +1205,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 
 	/** Displays this dialog box. */
 	public void showDialog() {
+		showDialogCalled = true;
 		if (macro) {
 			dispose();
 			recorderOn = Recorder.record && Recorder.recordInMacros;
@@ -1232,7 +1254,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 			c.insets = new Insets(15, 0, 0, 0);
 			add(buttons, c);
 			if (IJ.isMacOSX()&&IJ.isJava18())
-				instance = this;				
+				instance = this;
 			Font font = getFont();
 			if (IJ.debugMode) IJ.log("GenericDialog font: "+fontSizeSet+" "+font);
 			if (!fontSizeSet && font!=null && Prefs.getGuiScale()!=1.0) {
@@ -1242,13 +1264,25 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 			pack();
 			setup();
 			if (centerDialog)
-				GUI.centerOnImageJScreen(this); 
+				GUI.centerOnImageJScreen(this);
 			setVisible(true);
 			recorderOn = Recorder.record;
 			IJ.wait(25);
 		}
-
-		/* For plugins that read their input only via dialogItemChanged, call it at least once */
+		if (!(this instanceof NonBlockingGenericDialog))
+		    finalizeRecording();
+		resetCounters();
+	}
+	
+	@Override
+	public void show() {
+		super.show();
+		if (!showDialogCalled)
+			IJ.error("GenericDialog Error", "show() called instead of showDialog()");
+	}
+		
+	/** For plugins that read their input only via dialogItemChanged, call it at least once, then stop recording */
+	void finalizeRecording() {
 		if (!wasCanceled && dialogListeners!=null && dialogListeners.size()>0) {
 			resetCounters();
 			((DialogListener)dialogListeners.elementAt(0)).dialogItemChanged(this,null);
@@ -1256,7 +1290,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 		}
 		resetCounters();
 	}
-	
+
 	@Override
 	public void setFont(Font font) {
 		super.setFont(!fontSizeSet&&Prefs.getGuiScale()!=1.0?font.deriveFont((float)(font.getSize()*Prefs.getGuiScale())):font);
@@ -1426,8 +1460,28 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 	}
 
 	public void keyPressed(KeyEvent e) {
+		Component component = e.getComponent();
 		int keyCode = e.getKeyCode();
 		IJ.setKeyDown(keyCode);
+		if ((component instanceof Scrollbar) && (keyCode==KeyEvent.VK_LEFT||keyCode==KeyEvent.VK_RIGHT)) {
+			Scrollbar sb = (Scrollbar)component;
+			int value = sb.getValue();
+			if (keyCode==KeyEvent.VK_RIGHT)
+				sb.setValue(value+1);
+			else
+				sb.setValue(value-1);				
+			for (int i=0; i<slider.size(); i++) {
+				if (sb==slider.elementAt(i)) {
+					int index = ((Integer)sliderIndexes.get(i)).intValue();
+					TextField tf = (TextField)numberField.elementAt(index);
+					double scale = ((Double)sliderScales.get(i)).doubleValue();
+					int digits = ((Integer)sliderDigits.get(i)).intValue();
+					tf.setText(""+IJ.d2s(sb.getValue()/scale,digits));
+				}
+			}
+			notifyListeners(e);
+			return;
+		}
 		if (keyCode==KeyEvent.VK_ENTER && textArea1==null && okay!=null && okay.isEnabled()) {
 			wasOKed = true;
 			if (IJ.isMacOSX())
@@ -1526,7 +1580,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 	}
 
 	public void paint(Graphics g) {
-		super.paint(g);		
+		super.paint(g);
 		if (firstPaint && IJ.isMacOSX() && IJ.isJava18()) { // fix for incompletely drawn dialogs on Macs
 			EventQueue.invokeLater(new Runnable() {
 				public void run() {
@@ -1555,7 +1609,7 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
     }
 
 	void showHelp() {
-		if (helpURL.startsWith("<html>")) {	
+		if (helpURL.startsWith("<html>")) {
 			if (this instanceof NonBlockingGenericDialog)
 				new HTMLDialog("", helpURL, false); // non blocking
 			else
@@ -1585,5 +1639,5 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
     public void windowIconified(WindowEvent e) {}
     public void windowDeiconified(WindowEvent e) {}
     public void windowDeactivated(WindowEvent e) {}
-    
+
 }

ij/gui/ImageWindow.java

@@ -394,6 +394,8 @@ public class ImageWindow extends Frame implements FocusListener, WindowListener,
 				msg = "Save changes to\n" + "\"" + name + "\"?";
 			else
 				msg = "Save changes to \"" + name + "\"?";
+			if (imp.isLocked())
+				msg += "\nWARNING: This image is locked.\nProbably, processing is unfinished (slow or still previewing).";
 			toFront();
 			YesNoCancelDialog d = new YesNoCancelDialog(this, "ImageJ", msg);
 			if (d.cancelPressed())

ij/gui/NonBlockingGenericDialog.java

@@ -6,7 +6,9 @@ import java.awt.EventQueue;
 /** This is an extension of GenericDialog that is non-modal.
  *	@author Johannes Schindelin
  */
-public class NonBlockingGenericDialog extends GenericDialog {
+public class NonBlockingGenericDialog extends GenericDialog implements ImageListener {
+
+	ImagePlus imp;	//when non-null, this dialog gets closed when the image is closed
 
 	public NonBlockingGenericDialog(String title) {
 		super(title, null);
@@ -52,5 +54,38 @@ public class NonBlockingGenericDialog extends GenericDialog {
 		super.dispose();
 		WindowManager.removeWindow(this);
 	}
+	
+	/** Returns a new NonBlockingGenericDialog with given title, unless
+	 *  java is running in headless mode; then a GenericDialog will be
+	 *  returned (headless mode does not support the NonBlockingGenericDialog).
+	 *  @param title Dialog title
+	 *  @param imp   The image associated with this dialog
+	*/
+	public static GenericDialog newDialog(String title, ImagePlus imp) {
+		if (Prefs.nonBlockingFilterDialogs && imp!=null && imp.getWindow()!=null) {
+			NonBlockingGenericDialog gd = new NonBlockingGenericDialog(title);
+			gd.imp = imp;
+			imp.addImageListener(gd);
+			ImageWindow win = imp.getWindow();
+			//if (win!=null) win.addWindowListener(gd);
+			return gd;
+		} else
+			return new GenericDialog(title);
+	}
+		
+	public void imageClosed(ImagePlus imp) {
+		if (imp == this.imp)
+			super.windowClosing(null);	// sets wasCanceled=true and does dispose()
+	}
+
+	public void imageOpened(ImagePlus imp) {}
+	public void imageUpdated(ImagePlus imp) {}
+
+	/** Put the dialog into the foreground when the image we work on gets into the foreground */
+    public void windowActivated(WindowEvent e) {
+		if ((e.getWindow() instanceof ImageWindow) && e.getOppositeWindow()!=this)
+			toFront();
+	}
 
 }
+

ij/gui/OvalRoi.java

@@ -387,9 +387,10 @@ public class OvalRoi extends Roi {
 	}
 
 	public ImageProcessor getMask() {
-		if (cachedMask!=null && cachedMask.getPixels()!=null)
-			return cachedMask;
-		ImageProcessor mask = new ByteProcessor(width, height);
+		ImageProcessor mask = cachedMask;
+		if (mask!=null && mask.getPixels()!=null && mask.getWidth()==width && mask.getHeight()==height)
+			return mask;
+		mask = new ByteProcessor(width, height);
 		double a=width/2.0, b=height/2.0;
 		double a2=a*a, b2=b*b;
         a -= 0.5; b -= 0.5;

ij/gui/Overlay.java

@@ -411,4 +411,37 @@ public class Overlay {
     	return "Overlay[size="+size()+" "+(scalableLabels?"scale":"")+" "+Colors.colorToString(getLabelColor())+"]";
     }
     
+    /** Updates overlays created by the particle analyzer
+    	after rows are deleted from the Results table. */
+    public static void updateTableOverlay(ImagePlus imp, int first, int last, int tableSize) {
+		if (imp==null)
+			return;
+		Overlay overlay = imp.getOverlay();
+		if (overlay==null)
+			return;
+		if (overlay.size()!=tableSize)
+			return;
+		if (first<0)
+			first = 0;
+		if (last>tableSize-1)
+			last = tableSize-1;
+		if (first>last)
+			return;
+		String name1 = overlay.get(0).getName();
+		String name2 = overlay.get(overlay.size()-1).getName();
+		if (!"1".equals(name1) || !(""+tableSize).equals(name2))
+			return;
+		int count = last-first+1;
+		if (overlay.size()==count && !IJ.isMacro()) {
+			if (count==1 || IJ.showMessageWithCancel("ImageJ", "Delete "+overlay.size()+" element overlay?  "))
+				imp.setOverlay(null);
+			return;
+		}
+		for (int i=0; i<count; i++)
+			overlay.remove(first);
+		for (int i=first; i<overlay.size(); i++)
+			overlay.get(i).setName(""+(i+1));
+		imp.draw();
+	}
+    
 }

ij/gui/PlotWindow.java

@@ -76,7 +76,7 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 
 	private Button list, data, more, live;
 	private PopupMenu dataPopupMenu, morePopupMenu;
-	private static final int NUM_MENU_ITEMS = 18; //how many menu items we have in total
+	private static final int NUM_MENU_ITEMS = 20; //how many menu items we have in total
 	private MenuItem[] menuItems = new MenuItem[NUM_MENU_ITEMS];
 	private Label coordinates;
 	private static String defaultDirectory = null;
@@ -92,9 +92,13 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 	private Thread bgThread;		// thread for plotting (in the background)
 	private boolean doUpdate;		// tells the background thread to update
 
-	private Roi[] rangeArrowRois;	// these constitute the arrow overlays for changing the range
+	private Roi[] rangeArrowRois;	// the overlays (arrows etc) for changing the range. Note: #10-15 must correspond to PlotDialog.dialogType!
 	private boolean rangeArrowsVisible;
 	private int activeRangeArrow = -1;
+	private static Color inactiveRangeArrowColor = Color.GRAY;
+	private static Color inactiveRangeRectColor = new Color(0x20404040, true); //transparent gray
+	private static Color activeRangeArrowColor = Color.RED;
+	private static Color activeRangeRectColor = new Color(0x18ff0000, true); //transparent red
 
 	// static initializer
 	static {
@@ -257,7 +261,7 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		else
 			imp.updateAndDraw();
 		if (listValues)
-			showList();
+			showList(/*useLabels=*/false);
 		else
 			ic.requestFocus();	//have focus on the canvas, not the button, so that pressing the space bar allows panning
 	}
@@ -304,10 +308,10 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 	}
 
 	/** Names for popupMenu items. Update NUM_MENU_ITEMS at the top when adding new ones! */
-	private static int SAVE=0, COPY=1, COPY_ALL=2, ADD_FROM_TABLE=3, ADD_FROM_PLOT=4, ADD_FIT=5, //data menu
-			SET_RANGE=6, PREV_RANGE=7, RESET_RANGE=8, FIT_RANGE=9,  //the rest is in the more menu
-			ZOOM_SELECTION=10, AXIS_OPTIONS=11, LEGEND=12, STYLE=13, RESET_PLOT=14,
-			FREEZE=15, HI_RESOLUTION=16, PROFILE_PLOT_OPTIONS=17;
+	private static int SAVE=0, COPY=1, COPY_ALL=2, LIST_SIMPLE=3, ADD_FROM_TABLE=4, ADD_FROM_PLOT=5, ADD_FIT=6, //data menu
+			SET_RANGE=7, PREV_RANGE=8, RESET_RANGE=9, FIT_RANGE=10,  //the rest is in the more menu
+			ZOOM_SELECTION=11, AXIS_OPTIONS=12, LEGEND=13, STYLE=14, TEMPLATE=15, RESET_PLOT=16,
+			FREEZE=17, HI_RESOLUTION=18, PROFILE_PLOT_OPTIONS=19;
 	//the following commands are disabled when the plot is frozen
 	private static int[] DISABLED_WHEN_FROZEN = new int[]{ADD_FROM_TABLE, ADD_FROM_PLOT, ADD_FIT,
 			SET_RANGE, PREV_RANGE, RESET_RANGE, FIT_RANGE, ZOOM_SELECTION, AXIS_OPTIONS, LEGEND, STYLE, RESET_PLOT};
@@ -319,6 +323,7 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		menuItems[SAVE] = addPopupItem(dataPopupMenu, "Save Data...");
 		menuItems[COPY] = addPopupItem(dataPopupMenu, "Copy 1st Data Set");
 		menuItems[COPY_ALL] = addPopupItem(dataPopupMenu, "Copy All Data");
+		menuItems[LIST_SIMPLE] = addPopupItem(dataPopupMenu, "List (Simple Headings)");
 		dataPopupMenu.addSeparator();
 		menuItems[ADD_FROM_TABLE] = addPopupItem(dataPopupMenu, "Add from Table...");
 		menuItems[ADD_FROM_PLOT] = addPopupItem(dataPopupMenu, "Add from Plot...");
@@ -339,6 +344,7 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		menuItems[AXIS_OPTIONS] = addPopupItem(morePopupMenu, "Axis Options...");
 		menuItems[LEGEND] = addPopupItem(morePopupMenu, "Legend...");
 		menuItems[STYLE] = addPopupItem(morePopupMenu, "Contents Style...");
+		menuItems[TEMPLATE] = addPopupItem(morePopupMenu, "Use Template...");
 		menuItems[RESET_PLOT] = addPopupItem(morePopupMenu, "Reset Format");
 		menuItems[FREEZE] = addPopupItem(morePopupMenu, "Freeze Plot", true);
 		menuItems[HI_RESOLUTION] = addPopupItem(morePopupMenu, "High-Resolution Plot...");
@@ -371,7 +377,7 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		if (b==live)
 			toggleLiveProfiling();
 		else if (b==list)
-			showList();
+			showList(/*useLabels=*/true);
 		else if (b==data) {
 			enableDisableMenuItems();
 			dataPopupMenu.show((Component)b, 1, 1);
@@ -384,6 +390,8 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 			copyToClipboard(false);
 		else if (b==menuItems[COPY_ALL])
 			copyToClipboard(true);
+		else if (b==menuItems[LIST_SIMPLE])
+			showList(/*useLabels=*/false);
 		else if (b==menuItems[ADD_FROM_TABLE])
 			new PlotContentsDialog(plot, PlotContentsDialog.ADD_FROM_TABLE).showDialog(this);
 		else if (b==menuItems[ADD_FROM_PLOT])
@@ -407,6 +415,8 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 			new PlotDialog(plot, PlotDialog.LEGEND).showDialog(this);
 		else if (b==menuItems[STYLE])
 			new PlotContentsDialog(plot, PlotContentsDialog.STYLE).showDialog(this);
+		else if (b==menuItems[TEMPLATE])
+			new PlotDialog(plot, PlotDialog.TEMPLATE).showDialog(this);
 		else if (b==menuItems[RESET_PLOT]) {
 			plot.setFont(Font.PLAIN, Prefs.getInt(PREFS_FONT_SIZE, FONT_SIZE));
 			plot.setAxisLabelFont(Font.PLAIN, Prefs.getInt(PREFS_FONT_SIZE, FONT_SIZE));
@@ -443,50 +453,57 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 	/**
 	 * Updates the X and Y values when the mouse is moved and, if appropriate,
 	 * shows/hides the overlay with the triangular buttons for changing the axis
-	 * range limits Overrides mouseMoved() in ImageWindow.
+	 * range limits.
+	 * Overrides mouseMoved() in ImageWindow.
 	 *
 	 * @see ij.gui.ImageWindow#mouseMoved
 	 */
-    public void mouseMoved(int x, int y) {
-        super.mouseMoved(x, y);
-        if (plot == null)
-            return;
-        if (coordinates != null) {	//coordinate readout
-            String coords = plot.getCoordinates(x, y) + blankLabel;
-            coordinates.setText(coords.substring(0, blankLabel.length()));
-        }
+	public void mouseMoved(int x, int y) {
+		super.mouseMoved(x, y);
+		if (plot == null)
+			return;
+		if (coordinates != null) {	//coordinate readout
+			String coords = plot.getCoordinates(x, y) + blankLabel;
+			coordinates.setText(coords.substring(0, blankLabel.length()));
+		}
 
-        //arrows for modifying the plot range
-        if (plot==null) return;
-        if (x < plot.leftMargin || y > plot.topMargin + plot.frameHeight) {
-            if (!rangeArrowsVisible && !plot.isFrozen())
-                showRangeArrows();
-            if (activeRangeArrow == 8)      //it's the 'R' icon
-                coordinates.setText("Reset Range");
-            else if (activeRangeArrow == 9) //it's the 'F' icon
-                coordinates.setText("Full Range (Fit All)");
-            else if (activeRangeArrow >= 10) //space between arrow-pairs
-                coordinates.setText("Set limit...");
-            if (activeRangeArrow >= 0 && !rangeArrowRois[activeRangeArrow].contains(x, y)) {
-				if(activeRangeArrow>=10) //numerical box
-					rangeArrowRois[activeRangeArrow].setFillColor(new Color(235, 235, 235));
-				else //arrow
-					rangeArrowRois[activeRangeArrow].setFillColor(Color.GRAY);
-                ic.repaint();			//de-highlight arrow where cursor has moved out
-                activeRangeArrow = -1;
-            }
-            if (activeRangeArrow < 0) { //highlight arrow below cursor (if any)
-                int i = getRangeArrowIndex(x, y);
-                if (i >= 0) {			//we have an arrow at cursor position
-
-                    rangeArrowRois[i].setFillColor(Color.RED);
-                    activeRangeArrow = i;
-                    ic.repaint();
-                }
-            }
-        } else if (rangeArrowsVisible)
-            hideRangeArrows();
-    }
+		//arrows and other symbols for modifying the plot range
+		if (x < plot.leftMargin || y > plot.topMargin + plot.frameHeight) {
+			if (!rangeArrowsVisible && !plot.isFrozen())
+				showRangeArrows();
+			if (activeRangeArrow < 0)       //mouse is not on one of the symbols, ignore (nothing to display)
+				{}
+			else if (activeRangeArrow < 8)  //mouse over an arrow: 0,3,4,7 for increase, 1,2,5,6 for decrease
+				coordinates.setText(((activeRangeArrow+1)&0x02) != 0 ? "Decrease Range" : "Increase Range");
+			else if (activeRangeArrow == 8) //it's the 'R' icon
+				coordinates.setText("Reset Range");
+			else if (activeRangeArrow == 9) //it's the 'F' icon
+				coordinates.setText("Full Range (Fit All)");
+			else if (activeRangeArrow >= 10 &&
+					activeRangeArrow < 14)  //space between arrow-pairs for single number
+				coordinates.setText("Set limit...");
+			else if (activeRangeArrow >= 14)
+				coordinates.setText("Axis Range & Options...");
+			boolean repaint = false;
+			if (activeRangeArrow >= 0 && !rangeArrowRois[activeRangeArrow].contains(x, y)) {
+				rangeArrowRois[activeRangeArrow].setFillColor(
+						activeRangeArrow < 10 ? inactiveRangeArrowColor : inactiveRangeRectColor);
+				repaint = true;             //de-highlight arrow where cursor has moved out
+				activeRangeArrow = -1;
+			}
+			if (activeRangeArrow < 0) {     //no currently highlighted arrow, do we have a new one?
+				int i = getRangeArrowIndex(x, y);
+				if (i >= 0) {               //we have an arrow or symbol at cursor position
+					rangeArrowRois[i].setFillColor(
+							i < 14 ? activeRangeArrowColor : activeRangeRectColor);
+					activeRangeArrow = i;
+					repaint = true;
+				}
+			}
+			if (repaint) ic.repaint();
+		} else if (rangeArrowsVisible)
+			hideRangeArrows();
+	}
 
 	/** Called by PlotCanvas */
 	void mouseExited(MouseEvent e) {
@@ -504,7 +521,7 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		int amount = e.getScrollAmount();
 		if (e.getX() < plot.leftMargin || e.getX() > plot.leftMargin + plot.frameWidth)//n__
 			return;
-		if (e.getY() < plot.topMargin || e.getY() > plot.topMargin + plot.frameHeight) 
+		if (e.getY() < plot.topMargin || e.getY() > plot.topMargin + plot.frameHeight)
 			return;
 		boolean ctrl = (e.getModifiers()&Event.CTRL_MASK)!=0;
 		if (amount<1) amount=1;
@@ -523,14 +540,14 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 	}
 
     /**
-     * Creates an overlay with triangular buttons for changing the axis range
+     * Creates an overlay with triangular buttons and othr symbols for changing the axis range
      * limits and shows it
      */
     void showRangeArrows() {
         if (imp == null)
             return;
         hideRangeArrows(); //in case we have old arrows from a different plot size or so
-        rangeArrowRois = new Roi[4 * 2 + 2 + 4]; //4 arrows per axis, plus 'Reset' and 'Fit All' icons, plus 4 numerical input boxes
+        rangeArrowRois = new Roi[4 * 2 + 2 + 4 + 2]; //4 arrows per axis, + 'Reset' and 'Fit All' icons, + 4 numerical input boxes + 2 axes
         int i = 0;
         int height = imp.getHeight();
         int arrowH = plot.topMargin < 14 ? 6 : 8; //height of arrows and distance between them; base is twice that value
@@ -560,18 +577,27 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		rangeArrowRois[11] = new Roi(plot.leftMargin + plot.frameWidth - arrowH/2 + 1, height - 5 * arrowH / 2, arrowH - 2, arrowH * 2);//numerical box right
         rangeArrowRois[12] = new Roi(arrowH / 2, plot.topMargin + plot.frameHeight - arrowH/2 + 1, arrowH * 2, arrowH -2);//numerical box bottom
         rangeArrowRois[13] = new Roi(arrowH / 2, plot.topMargin - arrowH/2 + 1,  arrowH * 2, arrowH - 2   );//numerical box top
- 
+
+        int topMargin = plot.topMargin;
+        int bottomMargin = topMargin + plot.frameHeight;
+        int leftMargin = plot.leftMargin;
+        int rightMargin = plot.leftMargin + plot.frameWidth;
+        rangeArrowRois[14] = new Roi(leftMargin, bottomMargin+2,        // area to click for x axis options
+				rightMargin - leftMargin + 1, 2*arrowH);
+        rangeArrowRois[15] = new Roi(leftMargin-2*arrowH-2, topMargin,  // area to click for y axis options
+				2*arrowH, bottomMargin - topMargin + 1);
+
         Overlay ovly = imp.getOverlay();
         if (ovly == null)
             ovly = new Overlay();
         for (Roi roi : rangeArrowRois) {
-            if (roi instanceof PolygonRoi) 
-                   roi.setFillColor(Color.GRAY);
+            if (roi instanceof PolygonRoi)
+                   roi.setFillColor(inactiveRangeArrowColor);
 			else if (roi instanceof TextRoi) {
                 roi.setStrokeColor(Color.WHITE);
-                roi.setFillColor(Color.GRAY);
+                roi.setFillColor(inactiveRangeArrowColor);
             } else
-                roi.setFillColor(new Color(235, 235, 235));
+                roi.setFillColor(inactiveRangeRectColor); //transparent gray for single number boxes and axis range
             ovly.add(roi);
         }
         imp.setOverlay(ovly);
@@ -590,9 +616,13 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		activeRangeArrow = -1;
 	}
 
-	/** Returns the index of the range arrow at cursor position x,y, or -1 of none.
-	 *	Index numbers start with 0 at the 'down' arrow of the lower side of the x axis
-	 *	and end with the up arrow at the upper side of the y axis. */
+	/** Returns the index of the range-modifying symbol or axis at the
+	 *  cursor position x,y, or -1 of none.
+	 *  Index numbers for arrows start with 0 at the 'down' arrow of the
+	 *  lower side of the x axis and end with 7 the up arrow at the upper
+	 *  side of the y axis. Numbers 8 & 9 are for "Reset Range" and "Fit All";
+	 *  numbers 10-13 for a dialog to set a single limit, and 14-15 for the axis options. */
+
 	int getRangeArrowIndex(int x, int y) {
 		if (!rangeArrowsVisible) return -1;
 		for (int i=0; i<rangeArrowRois.length; i++)
@@ -603,8 +633,8 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 
 
 	/** Shows the data of the backing plot in a Textwindow with columns */
-	void showList(){
-		ResultsTable rt = plot.getResultsTable(saveXValues);
+	void showList(boolean useLabels){
+		ResultsTable rt = plot.getResultsTable(saveXValues, useLabels);
 		if (rt==null) return;
 		rt.show("Plot Values");
 		if (autoClose) {
@@ -613,7 +643,8 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		}
 	}
 
-	/** Returns the plot values as a ResultsTable. */
+	/** Returns the plot values with simple headings (X, Y, Y1 etc, not the labels) as a ResultsTable.
+	 *  Use plot.getResultsTableWithLabels for a table with data set labels as column headings */
 	public ResultsTable getResultsTable() {
 		return plot.getResultsTable(saveXValues);
 	}
@@ -641,7 +672,7 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		String directory = sd.getDirectory();
 		IJ.wait(250);  // give system time to redraw ImageJ window
 		IJ.showStatus("Saving plot values...");
-		ResultsTable rt = getResultsTable();
+		ResultsTable rt = plot.getResultsTable(/*writeFirstXColumn=*/saveXValues, /*useLabels=*/true);
 		try {
 			rt.saveAs(directory+name);
 		} catch (IOException e) {
@@ -667,7 +698,7 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 		PrintWriter pw = new PrintWriter(aw); //uses platform's line termination characters
 
 		if (writeAllColumns) {
-			ResultsTable rt = plot.getResultsTable(true);
+			ResultsTable rt = plot.getResultsTableWithLabels();
 			if (!Prefs.dontSaveHeaders) {
 				String headings = rt.getColumnHeadings();
 				pw.println(headings);
@@ -818,7 +849,8 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
 			IJ.wait(50);	//delay to make sure the roi has been updated
 			Plot plot = plotMaker!=null?plotMaker.getPlot():null;
 			if (doUpdate && plot!=null && plot.getNumPlotObjects()>0) {
-				plot.useTemplate(this.plot, this.plot.templateFlags);
+				plot.useTemplate(this.plot, this.plot.templateFlags | Plot.COPY_SIZE | Plot.COPY_LABELS | Plot.COPY_AXIS_STYLE |
+						Plot.COPY_CONTENTS_STYLE | Plot.COPY_LEGEND | Plot.COPY_EXTRA_OBJECTS);
 				plot.setPlotMaker(plotMaker);
 				this.plot = plot;
 				((PlotCanvas)ic).setPlot(plot);

ij/gui/PointRoi.java

@@ -17,15 +17,16 @@ import java.awt.geom.*;
  * @see <a href="http://wsr.imagej.net/macros/js/PointProperties.js">PointProperties.js</a>
 */
 public class PointRoi extends PolygonRoi {
-	public static final String[] sizes = {"Tiny", "Small", "Medium", "Large", "Extra Large"};
+	public static final String[] sizes = {"Tiny", "Small", "Medium", "Large", "Extra Large", "XXL", "XXXL"};
 	public static final String[] types = {"Hybrid", "Cross", "Dot", "Circle"};
 	private static final String TYPE_KEY = "point.type";
 	private static final String SIZE_KEY = "point.size";
 	private static final String CROSS_COLOR_KEY = "point.cross.color";
-	private static final int TINY=1, SMALL=3, MEDIUM=5, LARGE=7, EXTRA_LARGE=11;
+	private static final int TINY=1, SMALL=3, MEDIUM=5, LARGE=7, EXTRA_LARGE=11, XXL=17, XXXL=25;
 	private static final int HYBRID=0, CROSS=1, CROSSHAIR=1, DOT=2, CIRCLE=3;
 	private static final BasicStroke twoPixelsWide = new BasicStroke(2);
 	private static final BasicStroke threePixelsWide = new BasicStroke(3);
+	private static final BasicStroke fivePixelsWide = new BasicStroke(5);
 	private static int defaultType = HYBRID;
 	private static int defaultSize = SMALL;
 	private static Font font;
@@ -129,7 +130,7 @@ public class PointRoi extends PolygonRoi {
 		size = defaultSize;
 		showLabels = !Prefs.noPointLabels;
 		if (imp!=null) {
-			int r = 10;
+			int r = 10 + size;
 			double mag = ic!=null?ic.getMagnification():1;
 			if (mag<1)
 				r = (int)(r/mag);
@@ -156,6 +157,8 @@ public class PointRoi extends PolygonRoi {
 		else if (options.contains("medium")) size=MEDIUM;
 		else if (options.contains("extra")) size=EXTRA_LARGE;
 		else if (options.contains("large")) size=LARGE;
+		else if (options.contains("xxxl")) size=XXXL;
+		else if (options.contains("xxl")) size=XXL;
 		if (options.contains("cross")) type=CROSS;
 		else if (options.contains("dot")) type=DOT;
 		else if (options.contains("circle")) type=CIRCLE;
@@ -198,10 +201,10 @@ public class PointRoi extends PolygonRoi {
 		updatePolygon();
 		if (showLabels && nPoints>1) {
 			fontSize = 8;
-			fontSize += convertSizeToIndex(size);
-			if (fontSize>18)
-				fontSize = 18;
+			double scale = size>=XXL?2:1.5;
+			fontSize += scale*convertSizeToIndex(size);
 			fontSize = (int)Math.round(fontSize);
+			//IJ.log("fontSize: "+fontSize+" "+scale);
 			font = new Font("SansSerif", Font.PLAIN, fontSize);
 			g.setFont(font);
 			if (fontSize>9)
@@ -254,7 +257,9 @@ public class PointRoi extends PolygonRoi {
 				g.setColor(color);
 				colorSet = true;
 			}
-			if (size>LARGE)
+			if (size>XXL)
+				g2d.setStroke(fivePixelsWide);
+			else if (size>LARGE)
 				g2d.setStroke(threePixelsWide);
 			g.drawLine(x-(size+2), y, x+size+2, y);
 			g.drawLine(x, y-(size+2), x, y+size+2);
@@ -278,16 +283,20 @@ public class PointRoi extends PolygonRoi {
 				g.fillRect(x-size2, y-size2, size, size);
 		}
 		if (showLabels && nPoints>1) {
-			int offset = (int)Math.round(0.4);
-			if (offset<1) offset=1;
-			offset++;
+			int xoffset = 2;
+			if (size==LARGE) xoffset=3;
+			if (size==EXTRA_LARGE) xoffset=4;
+			if (size==XXL) xoffset=5;
+			if (size==XXXL) xoffset=7;
+			int yoffset = xoffset;
+			if (size>=LARGE) yoffset=yoffset-1;
 			if (nCounters==1) {
 				if (!colorSet)
 					g.setColor(color);
-				g.drawString(""+n, x+offset, y+offset+fontSize);
+				g.drawString(""+n, x+xoffset, y+yoffset+fontSize);
 			} else if (counters!=null) {
 				g.setColor(getColor(counters[n-1]));
-				g.drawString(""+counters[n-1], x+offset, y+offset+fontSize);
+				g.drawString(""+counters[n-1], x+xoffset, y+yoffset+fontSize);
 			}
 		}
 		if ((size>TINY||type==DOT) && (type==HYBRID||type==DOT)) {
@@ -551,6 +560,8 @@ public class PointRoi extends PolygonRoi {
 			case MEDIUM: return 2;
 			case LARGE: return 3;
 			case EXTRA_LARGE: return 4;
+			case XXL: return 5;
+			case XXXL: return 6;
 		}
 		return 1;
 	}
@@ -562,6 +573,8 @@ public class PointRoi extends PolygonRoi {
 			case 2: return MEDIUM;
 			case 3: return LARGE;
 			case 4: return EXTRA_LARGE;
+			case 5: return XXL;
+			case 6: return XXXL;
 		}
 		return SMALL;
 	}

ij/gui/PolygonRoi.java

@@ -672,7 +672,7 @@ public class PolygonRoi extends Roi {
 		if (yClipMax>ymax2) ymax2 = yClipMax;
 		xClipMin=xmin; yClipMin=ymin; xClipMax=xmax; yClipMax=ymax;
 		double mag = ic.getMagnification();
-		int handleSize = type==POINT?HANDLE_SIZE+12:HANDLE_SIZE;
+		int handleSize = type==POINT?HANDLE_SIZE+25:HANDLE_SIZE;
 		double strokeWidth = getStrokeWidth();
 		if (strokeWidth<1.0) strokeWidth=1.0;
 		if (handleSize<strokeWidth && isLine())
@@ -1070,14 +1070,21 @@ public class PolygonRoi extends Roi {
 			samePoint = (xpf[nPoints-2]==xpf[nPoints-1] && ypf[nPoints-2]==ypf[nPoints-1]);
 		else
 			samePoint = (xp[nPoints-2]==xp[nPoints-1] && yp[nPoints-2]==yp[nPoints-1]);
+		boolean doubleClick = (System.currentTimeMillis()-mouseUpTime)<=250;
 		Rectangle biggerStartBox = new Rectangle(ic.screenXD(startXD)-5, ic.screenYD(startYD)-5, 10, 10);
 		if (nPoints>2 && (biggerStartBox.contains(sx, sy)
 		|| (ic.offScreenXD(sx)==startXD && ic.offScreenYD(sy)==startYD)
-		|| (samePoint && (System.currentTimeMillis()-mouseUpTime)<=500))) {
-			nPoints--;
-			addOffset();
-			finishPolygon();
-			return;
+		|| (samePoint && doubleClick))) {
+			boolean okayToFinish = true;
+			if (type==POLYGON && samePoint && doubleClick && nPoints>25) {
+				okayToFinish = IJ.showMessageWithCancel("Polygon Tool", "Complete the selection?");
+			}
+			if (okayToFinish) {
+				nPoints--;
+				addOffset();
+				finishPolygon();
+				return;
+			}
 		} else if (!samePoint) {
 			mouseUpTime = System.currentTimeMillis();
 			if (type==ANGLE && nPoints==3) {