IJ_Props.txt

@@ -378,8 +378,9 @@ macros01="Install...",ij.plugin.MacroInstaller
 macros02="Run...",ij.plugin.Macro_Runner
 macros03="Edit...",ij.plugin.Compiler("edit")
 macros04="Startup Macros...",ij.plugin.Commands("startup")
-macros05="Record...",ij.plugin.frame.Recorder
-macros06=-
+macros05="Interactive Interpreter...[j]",ij.plugin.SimpleCommands("interactive")
+macros06="Record...",ij.plugin.frame.Recorder
+macros07=-
 
 # Plugins installed in the Plugins/Shortcuts submenu
 shortcuts01="Add Shortcut... ",ij.plugin.Hotkeys("install")

debian/changelog

+imagej (1.52j-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.3.0
+
+ -- Andreas Tille <tille@debian.org>  Sat, 26 Jan 2019 07:51:10 +0100
+
 imagej (1.52i-2) unstable; urgency=medium
 
   * Team upload.

debian/compat

-11
+12

debian/control

@@ -3,13 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: David Miguel Susano Pinto <carandraug+dev@gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
+Build-Depends: debhelper (>= 12~)
 Build-Depends-Indep: ant,
                      default-jdk-doc,
                      default-jdk-headless,
                      javahelper,
                      maven-repo-helper
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 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

ij/IJ.java

@@ -70,6 +70,7 @@ public class IJ {
 	private static DecimalFormatSymbols dfs;
 	private static boolean trustManagerCreated;
 	private static String smoothMacro;
+	private static Interpreter macroInterpreter;
 			
 	static {
 		osname = System.getProperty("os.name");
@@ -151,7 +152,7 @@ public class IJ {
 		The file is assumed to be in the macros folder
  		unless <code>name</code> is a full path.
 		The optional string argument (<code>arg</code>) can be retrieved in the called 
-		macro or script (v1.42k or later) using the getArgument() function. 
+		macro or script using the getArgument() function. 
 		Returns any string value returned by the macro, or null. Scripts always return null.
 		The equivalent macro function is runMacro(). */
 	public static String runMacroFile(String name, String arg) {
@@ -309,9 +310,17 @@ public class IJ {
 		macroRunning = false;
 		Macro.setOptions(null);
 		testAbort();
+		macroInterpreter = null;
 		//IJ.log("run2: "+command+" "+Thread.currentThread().hashCode());
 	}
 	
+	/** The macro interpreter uses this method to run commands. */
+	public static void run(Interpreter interpreter, String command, String options) {
+		macroInterpreter = interpreter;
+		run(command, options);
+		macroInterpreter = null;
+	}
+
 	/** Converts commands that have been renamed so 
 		macros using the old names continue to work. */
 	private static String convert(String command) {
@@ -572,7 +581,12 @@ public class IJ {
     
     /**Displays a "no images are open" dialog box.*/
 	public static void noImage() {
-		error("No Image", "There are no images open.");
+		String msg = "There are no images open.";
+		if (macroInterpreter!=null) {
+			macroInterpreter.abort(msg);
+			macroInterpreter = null;
+		} else
+			error("No Image", msg);
 	}
 
 	/** Displays an "out of memory" message to the "Log" window. */
@@ -645,6 +659,11 @@ public class IJ {
 		macro or JavaScript is running, it is aborted. Writes to the
 		Java console if the ImageJ window is not present.*/
 	public static void error(String msg) {
+		if (macroInterpreter!=null) {
+			macroInterpreter.abort(msg);
+			macroInterpreter = null;
+			return;
+		}
 		error(null, msg);
 		if (Thread.currentThread().getName().endsWith("JavaScript"))
 			throw new RuntimeException(Macro.MACRO_CANCELED);
@@ -914,7 +933,6 @@ public class IJ {
 				break;
 			case KeyEvent.VK_SHIFT:
 				shiftDown=true;
-				updateStatus();
 				if (debugMode) beep();
 				break;
 			case KeyEvent.VK_SPACE: {
@@ -936,7 +954,7 @@ public class IJ {
 			case KeyEvent.VK_CONTROL: controlDown=false; break;
 			case KeyEvent.VK_META: if (isMacintosh()) controlDown=false; break;
 			case KeyEvent.VK_ALT: altDown=false; updateStatus(); break;
-			case KeyEvent.VK_SHIFT: shiftDown=false; updateStatus();  if (debugMode) beep(); break;
+			case KeyEvent.VK_SHIFT: shiftDown=false; if (debugMode) beep(); break;
 			case KeyEvent.VK_SPACE:
 				spaceDown=false;
 				ImageWindow win = WindowManager.getCurrentWindow();
@@ -951,10 +969,9 @@ public class IJ {
 	private static void updateStatus() {
 		ImagePlus imp = WindowManager.getCurrentImage();
 		if (imp!=null) {
-			ImageCanvas ic = imp.getCanvas();
-			if (ic!=null && imp.getCalibration().scaled()) {
-				Point p = ic.getCursorLoc();
-				imp.mouseMoved(p.x, p.y);
+			Roi roi = imp.getRoi();
+			if (roi!=null && imp.getCalibration().scaled()) {
+				roi.showStatus();
 			}
 		}
 	}
@@ -2237,7 +2254,7 @@ public class IJ {
 	}
 	
 	static void abort() {
-		if (ij!=null || Interpreter.isBatchMode())
+		if ((ij!=null || Interpreter.isBatchMode()) && macroInterpreter==null)
 			throw new RuntimeException(Macro.MACRO_CANCELED);
 	}
 	

ij/ImageJ.java

@@ -78,8 +78,8 @@ 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 = "1.52i";
-	public static final String BUILD = "";  //52
+	public static final String VERSION = "1.52j";
+	public static final String BUILD = "";  //42
 	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);

ij/ImagePlus.java

@@ -172,7 +172,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 				return false;
 			} else {
 				locked = true;
-			if (IJ.debugMode) IJ.log(title + ": lock");
 				return true;
 			}
 		}
@@ -192,7 +191,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 	/** Unlocks the image. */
 	public synchronized void unlock() {
 		locked = false;
-		if (IJ.debugMode) IJ.log(title + ": unlock");
 	}
 		
 	private void waitForImage(Image image) {
@@ -556,7 +554,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		if (newProperties!=null)
 			newProperties = (Properties)(newProperties.clone());
 		if (imp.getWindow()!=null)
-			imp = imp.duplicateAll();
+			imp = imp.duplicate();
 		ImageStack stack2 = imp.getStack();
 		if (imp.isHyperStack())
 			setOpenAsHyperStack(true);
@@ -964,32 +962,33 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 	}
 	
 	/** Returns an ImageStatistics object generated using the
-		specified measurement options and histogram bin count. 
-		Note: except for float images, the number of bins
-		is currently fixed at 256.
-	*/
+		specified measurement options and histogram bin count.  */
 	public ImageStatistics getStatistics(int mOptions, int nBins) {
 		return getStatistics(mOptions, nBins, 0.0, 0.0);
 	}
 
 	/** Returns an ImageStatistics object generated using the
-		specified measurement options, histogram bin count and histogram range. 
-		Note: for 8-bit and RGB images, the number of bins
-		is fixed at 256 and the histogram range is always 0-255.
-	*/
+		specified measurement options, histogram bin count
+		and histogram range. */
 	public ImageStatistics getStatistics(int mOptions, int nBins, double histMin, double histMax) {
+		ImageProcessor ip2 = ip;
+		int bitDepth = getBitDepth();
+		if (nBins!=256 && (bitDepth==8||bitDepth==24))
+			ip2 =ip.convertToShort(false);
 		if (roi!=null && roi.isArea())
-			ip.setRoi(roi);
+			ip2.setRoi(roi);
 		else
-			ip.resetRoi();
-		ip.setHistogramSize(nBins);
+			ip2.resetRoi();
+		ip2.setHistogramSize(nBins);
 		Calibration cal = getCalibration();
-		if (getType()==GRAY16&& !(histMin==0.0&&histMax==0.0))
-			{histMin=cal.getRawValue(histMin); histMax=cal.getRawValue(histMax);}
-		ip.setHistogramRange(histMin, histMax);
-		ImageStatistics stats = ImageStatistics.getStatistics(ip, mOptions, cal);
-		ip.setHistogramSize(256);
-		ip.setHistogramRange(0.0, 0.0);
+		if (getType()==GRAY16&& !(histMin==0.0&&histMax==0.0)) {
+			histMin = cal.getRawValue(histMin);
+			histMax=cal.getRawValue(histMax);
+		}
+		ip2.setHistogramRange(histMin, histMax);
+		ImageStatistics stats = ImageStatistics.getStatistics(ip2, mOptions, cal);
+		ip2.setHistogramSize(256);
+		ip2.setHistogramRange(0.0, 0.0);
 		return stats;
 	}
 	
@@ -2142,20 +2141,11 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 	}
 	
 
-	/** Returns a copy of this image or stack, cropped if there is an ROI.
-	* @see #duplicateAll
+	/** Returns a copy of this image or stack.
 	* @see #crop
 	* @see ij.plugin.Duplicator#run
 	*/
 	public ImagePlus duplicate() {
-		return (new Duplicator()).run(this);
-	}
-
-	/** Returns a copy of this image or stack.
-	 * @see #duplicate
-	 * @see #crop
-	*/
-	public ImagePlus duplicateAll() {
 		Roi roi = getRoi();
 		deleteRoi();
 		ImagePlus imp2 =(new Duplicator()).run(this);
@@ -2165,7 +2155,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 
 	/** Returns a copy this image or stack slice, cropped if there is an ROI.
 	 * @see #duplicate
-	 * @see #duplicateAll
 	 * @see ij.plugin.Duplicator#crop
 	*/
 	public ImagePlus crop() {
@@ -2866,6 +2855,34 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		}
 	}
 	
+	/** Plots a 256 bin histogram of this image and returns the PlotWindow. */
+	public PlotWindow plotHistogram() {
+		return plotHistogram(256);
+	}
+
+	/** Plots a histogram of this image using the specified
+		number of bins and returns the PlotWindow. */
+	public PlotWindow plotHistogram(int bins) {
+		ImageStatistics stats = getStatistics(AREA+MEAN+MODE+MIN_MAX, bins);
+		Plot plot = new Plot("Hist_"+getTitle(), "Value", "Frequency");
+		plot.setColor("black", "#999999");
+		plot.setFont(new Font("SansSerif",Font.PLAIN,14));
+		double[] y = stats.histogram();
+		int n = y.length;
+		double[] x = new double[n];
+		int bits = getBitDepth();
+		boolean eightBit = bits==8 || bits==24;
+		double min = !eightBit?stats.min:0;
+		for (int i=0; i<n; i++)
+			x[i] = min+i*stats.binSize;
+		plot.add("bar", x, y);
+		if (bins!=256)
+			plot.addLegend(bins+" bins", "auto");
+		if (eightBit)
+			plot.setLimits(0,256,0,Double.NaN);
+		return plot.show();
+	}
+
     public String toString() {
     	return "img[\""+getTitle()+"\" ("+getID()+"), "+getBitDepth()+"-bit, "+width+"x"+height+"x"+getNChannels()+"x"+getNSlices()+"x"+getNFrames()+"]";
     }

ij/Menus.java

@@ -315,6 +315,7 @@ public class Menus {
 		addExample(submenu, "Dynamic Plot", "Dynamic_Plot.js");
 		addExample(submenu, "Plot Styles", "Plot_Styles.js");
 		addExample(submenu, "Plot Random Data", "Plot_Random_Data.js");
+		addExample(submenu, "Histogram Plots", "Histogram_Plots.js");
 		addExample(submenu, "Process Folder", "Batch_Process_Folder.js");
 		addExample(submenu, "Sine/Cosine Table", "Sine_Cosine_Table.js");
 		addExample(submenu, "Non-numeric Table", "Non-numeric_Table.js");

ij/Prefs.java

@@ -56,7 +56,7 @@ 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;
+		CANCEL_BUTTON_ON_RIGHT=1<<10, IGNORE_RESCALE_SLOPE=1<<11;
 	public static final String OPTIONS2 = "prefs.options2";
     
 	/** file.separator system property */
@@ -117,6 +117,8 @@ public class Prefs {
 	public static boolean multiPointMode;
 	/** Open DICOMs as 32-bit float images */
 	public static boolean openDicomsAsFloat;
+	/** Ignore Rescale Slope when opening DICOMs */
+	public static boolean ignoreRescaleSlope;
 	/** Plot rectangular selectons vertically */
 	public static boolean verticalProfile;
 	/** Rotate YZ orthogonal views 90 degrees */
@@ -496,6 +498,7 @@ public class Prefs {
 		doNotSaveWindowLocations = (options2&DO_NOT_SAVE_WINDOW_LOCS)!=0;
 		jFileChooserSettingChanged = (options2&JFILE_CHOOSER_CHANGED)!=0;
 		dialogCancelButtonOnRight = (options2&CANCEL_BUTTON_ON_RIGHT)!=0;
+		ignoreRescaleSlope = (options2&IGNORE_RESCALE_SLOPE)!=0;
 	}
 
 	static void saveOptions(Properties prefs) {
@@ -524,7 +527,8 @@ public class Prefs {
 			+ (autoRunExamples?AUTO_RUN_EXAMPLES:0) + (showAllPoints?SHOW_ALL_POINTS:0)
 			+ (doNotSaveWindowLocations?DO_NOT_SAVE_WINDOW_LOCS:0)
 			+ (jFileChooserSettingChanged?JFILE_CHOOSER_CHANGED:0)
-			+ (dialogCancelButtonOnRight?CANCEL_BUTTON_ON_RIGHT:0);
+			+ (dialogCancelButtonOnRight?CANCEL_BUTTON_ON_RIGHT:0)
+			+ (ignoreRescaleSlope?IGNORE_RESCALE_SLOPE:0);			
 		prefs.put(OPTIONS2, Integer.toString(options2));
 	}
 

ij/Undo.java

@@ -55,7 +55,7 @@ public class Undo {
 			calCopy = (Calibration)imp.getCalibration().clone();
 		} else if (what==TRANSFORM) {	
 			if ((!IJ.macroRunning()||Prefs.supportMacroUndo) && (imp.getStackSize()==1||imp.getDisplayMode()==IJ.COMPOSITE) && imp.getSizeInBytes()<209715200)
-				impCopy = imp.duplicateAll();
+				impCopy = imp.duplicate();
 			else
 				reset();
 		} else if (what==MACRO) {	

ij/gui/EllipseRoi.java

 package ij.gui;
 import java.awt.*;
 import java.awt.image.*;
+import java.awt.event.*;
 import ij.*;
 import ij.plugin.frame.Recorder;
 import ij.process.FloatPolygon;
@@ -77,6 +78,45 @@ public class EllipseRoi extends PolygonRoi {
 		}
 		makePolygonRelative();
 		cachedMask = null;
+		showStatus();
+	}
+	
+	public void showStatus() {
+		double[] p = getParams();
+		double dx = p[2] - p[0];
+		double dy = p[3] - p[1];
+		double major = Math.sqrt(dx*dx+dy*dy);
+		double minor = major*p[4];
+		double angle = getFloatAngle(p[0], p[1], p[2], p[3]);
+		if (imp!=null && !IJ.altKeyDown()) {
+			Calibration cal = imp.getCalibration();
+			if (cal.scaled()) {
+				dx *= cal.pixelWidth;
+				dy *= cal.pixelHeight;
+				major = Math.sqrt(dx*dx+dy*dy);
+				minor = major*p[4];
+			}
+		}
+		IJ.showStatus("major=" + IJ.d2s(major)+", minor=" + IJ.d2s(minor)+", angle=" + IJ.d2s(angle));
+	}
+
+	public void nudgeCorner(int key) {
+		if (ic==null) return;
+		double x1 = xpf[handle[2]]+x;
+		double y1 = ypf[handle[2]]+y;
+		double x2 = xpf[handle[0]]+x;
+		double y2 = ypf[handle[0]]+y;
+		double inc = 1.0/ic.getMagnification();
+		switch(key) {
+			case KeyEvent.VK_UP: y2-=inc; break;
+			case KeyEvent.VK_DOWN: y2+=inc; break;
+			case KeyEvent.VK_LEFT: x2-=inc; break;
+			case KeyEvent.VK_RIGHT: x2+=inc; break;
+		}
+		makeEllipse(x1, y1, x2, y2);
+		imp.draw();
+		notifyListeners(RoiListener.MOVED);
+		showStatus();
 	}
 
 	void makePolygonRelative() {

ij/gui/ImageCanvas.java

@@ -206,7 +206,7 @@ public class ImageCanvas extends Canvas implements MouseListener, MouseMotionLis
 	}
 
     public void paint(Graphics g) {
-		if (IJ.debugMode) IJ.log("ImageCanvas.paint: "+imp);
+		//if (IJ.debugMode) IJ.log("ImageCanvas.paint: "+imp);
 		painted = true;
 		Roi roi = imp.getRoi();		
 		if (roi!=null || overlay!=null || showAllOverlay!=null || Prefs.paintDoubleBuffered || (IJ.isLinux() && magnification<0.25)) {
@@ -237,7 +237,7 @@ public class ImageCanvas extends Canvas implements MouseListener, MouseMotionLis
 			if (roi!=null) drawRoi(roi, g);
 			if (srcRect.width<imageWidth || srcRect.height<imageHeight)
 				drawZoomIndicator(g);
-			if (IJ.debugMode) showFrameRate(g);
+			//if (IJ.debugMode) showFrameRate(g);
 		}
 		catch(OutOfMemoryError e) {IJ.outOfMemory("Paint");}
 		setPaintPending(false);
@@ -297,7 +297,7 @@ public class ImageCanvas extends Canvas implements MouseListener, MouseMotionLis
 		if (labelColor==null) labelColor = Color.white;
 		initGraphics(overlay, g, labelColor, Roi.getColor());
 		int n = overlay.size();
-		if (IJ.debugMode) IJ.log("drawOverlay: "+n);
+		//if (IJ.debugMode) IJ.log("drawOverlay: "+n);
 		int currentImage = imp!=null?imp.getCurrentSlice():-1;
 		int stackSize = imp.getStackSize();
 		if (stackSize==1)
@@ -368,9 +368,11 @@ public class ImageCanvas extends Canvas implements MouseListener, MouseMotionLis
 		}
 		if (textColor!=null) {
 			labelColor = textColor;
-			if (overlay!=null && overlay.getDrawBackgrounds())
-				bgColor = new Color(255-labelColor.getRed(), 255-labelColor.getGreen(), 255-labelColor.getBlue());
-			else
+			if (overlay!=null && overlay.getDrawBackgrounds()) {
+				double brightness = (labelColor.getRed()+labelColor.getGreen()+labelColor.getBlue())/3.0;
+				if (labelColor==Color.green) brightness = 255;
+				bgColor = brightness<=85?Color.white:Color.black;
+			} else
 				bgColor = null;
 		} else {
 			int red = defaultColor.getRed();
@@ -383,6 +385,9 @@ public class ImageCanvas extends Canvas implements MouseListener, MouseMotionLis
 			bgColor = defaultColor;
 		}
 		this.defaultColor = defaultColor;
+		Font font = overlay!=null?overlay.getLabelFont():null;
+		if (font!=null && font.getSize()>12)
+			((Graphics2D)g).setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
 		g.setColor(defaultColor);
     }
     
@@ -459,8 +464,11 @@ public class ImageCanvas extends Canvas implements MouseListener, MouseMotionLis
 			yoffset = h - 6 + pointSize;
 		}
 		if (bgColor!=null) {
+			int h2 = h;
+			if (font!=null && font.getSize()>14)
+				h2 = (int)(h2*0.8);
 			g.setColor(bgColor);
-			g.fillRoundRect(x-1+xoffset, y-h+2+yoffset, w+1, h-3, 5, 5);
+			g.fillRoundRect(x-1+xoffset, y-h2+2+yoffset, w+1, h2-2, 5, 5);
 		}
 		if (labelRects!=null && index<labelRects.length) {
 			if (pointRoi) {
@@ -536,7 +544,7 @@ public class ImageCanvas extends Canvas implements MouseListener, MouseMotionLis
 				drawRoi(roi, offScreenGraphics);
 			if (srcRect.width<imageWidth || srcRect.height<imageHeight)
 				drawZoomIndicator(offScreenGraphics);
-			if (IJ.debugMode) showFrameRate(offScreenGraphics);
+			//if (IJ.debugMode) showFrameRate(offScreenGraphics);
 			g.drawImage(offScreenImage, 0, 0, null);
 		}
 		catch(OutOfMemoryError e) {IJ.outOfMemory("Paint");}

ij/gui/Line.java

@@ -11,7 +11,6 @@ import java.util.NoSuchElementException;
 import java.awt.event.*;
 import java.awt.geom.*;
 
-
 /** This class represents a straight line selection. */
 public class Line extends Roi {
 
@@ -381,11 +380,15 @@ public class Line extends Roi {
 			drawHandle(g, sx3-size2, sy3-size2);
 		}
 		if (state!=NORMAL)
-			IJ.showStatus(imp.getLocationAsString(x2,y2)+", angle=" + IJ.d2s(getAngle()) + ", length=" + IJ.d2s(getLength()));
+			showStatus();
 		if (updateFullWindow)
 			{updateFullWindow = false; imp.draw();}
 	}
 	
+	public void showStatus() {
+		IJ.showStatus(imp.getLocationAsString(x2,y2)+", angle=" + IJ.d2s(getAngle()) + ", length=" + IJ.d2s(getLength()));
+	}
+	
 	public double getAngle() {
 		return getFloatAngle(x1d, y1d, x2d, y2d);
 	}
@@ -613,6 +616,7 @@ public class Line extends Roi {
 		}
 		grow(ic.screenXD(x+x2R), ic.screenYD(y+y2R));
 		notifyListeners(RoiListener.MOVED);
+		showStatus();
 	}
 	
 	public boolean getDrawOffset() {

ij/gui/Overlay.java

@@ -5,6 +5,7 @@ import java.awt.geom.Rectangle2D;
 import ij.*;
 import ij.process.ImageProcessor;
 import ij.plugin.filter.Analyzer;
+import ij.plugin.Colors;
 import ij.measure.ResultsTable;
 
 /** An Overlay is a list of ROIs that can be drawn non-destructively on an Image. */
@@ -133,6 +134,13 @@ public class Overlay {
 			rois[i].setStrokeColor(color);
 	}
 
+    /** Sets the stroke width of all the ROIs in this overlay. */
+    public void setStrokeWidth(Double width) {
+		Roi[] rois = toArray();
+		for (int i=0; i<rois.length; i++)
+			rois[i].setStrokeWidth(width);
+	}
+
     /** Sets the fill color of all the ROIs in this overlay. */
     public void setFillColor(Color color) {
 		Roi[] rois = toArray();
@@ -291,7 +299,7 @@ public class Overlay {
 		overlay2.drawNames(drawNames);
 		overlay2.drawBackgrounds(drawBackgrounds);
 		overlay2.setLabelColor(labelColor);
-		overlay2.setLabelFont(labelFont);
+		overlay2.setLabelFont(labelFont, scalableLabels);
 		overlay2.setIsCalibrationBar(isCalibrationBar);
 		overlay2.selectable(selectable);
 		return overlay2;
@@ -306,10 +314,6 @@ public class Overlay {
 		return overlay2;
 	}
 	
-	public String toString() {
-    	return "Overlay[size="+size()+"]";
-    }
-    
     public void drawLabels(boolean b) {
     	label = b;
     }
@@ -354,6 +358,23 @@ public class Overlay {
     	scalableLabels = scalable;
     }
 
+    /** Set the label font size with options. The options string can contain
+     * 'scale' (enlarge labels when image zoomed), 'bold'
+     * (display bold labels) or 'background' (display labels
+     * with contrasting background.
+    */
+    public void setLabelFontSize(int size, String options) {
+    	int style = Font.PLAIN;
+    	if (options!=null) {
+    		scalableLabels = options.contains("scale");
+    		if (options.contains("bold"))
+    			style = Font.BOLD;
+    		drawBackgrounds = options.contains("back");
+    	}
+    	labelFont = new Font("SansSerif", style, size);
+    	drawLabels(true);
+    }
+
     public Font getLabelFont() {
     	return labelFont;
     }
@@ -386,4 +407,8 @@ public class Overlay {
 		return scalableLabels;
 	}
 	
+	public String toString() {
+    	return "Overlay[size="+size()+" "+(scalableLabels?"scale":"")+" "+Colors.colorToString(getLabelColor())+"]";
+    }
+    
 }

ij/gui/PlotWindow.java

@@ -454,6 +454,7 @@ public class PlotWindow extends ImageWindow implements ActionListener, ItemListe
         }
 
         //arrows for modifying the plot range
+        if (plot==null) return;
         if (x < plot.leftMargin || y > plot.topMargin + plot.frameHeight) {
             if (!rangeArrowsVisible && !plot.isFrozen())
                 showRangeArrows();

ij/gui/Roi.java

@@ -1386,7 +1386,7 @@ public class Roi extends Object implements Cloneable, java.io.Serializable, Iter
 			previousRoi.modState = NO_MODS;
 	 }
 
-	protected void showStatus() {
+	public void showStatus() {
 		if (imp==null)
 			return;
 		String value;
@@ -1754,7 +1754,7 @@ public class Roi extends Object implements Cloneable, java.io.Serializable, Iter
 		prototypeOverlay.drawNames(overlay.getDrawNames());
 		prototypeOverlay.drawBackgrounds(overlay.getDrawBackgrounds());
 		prototypeOverlay.setLabelColor(overlay.getLabelColor());
-		prototypeOverlay.setLabelFont(overlay.getLabelFont());
+		prototypeOverlay.setLabelFont(overlay.getLabelFont(), overlay.scalableLabels());
 	} 
 
 	// Used by the FileOpener and RoiDecoder to restore overlay settings. */

ij/gui/RoiProperties.java

@@ -151,11 +151,10 @@ public class RoiProperties {
 		if (showListCoordinates) {
 			if ((roi instanceof PointRoi) && Toolbar.getMultiPointMode())
 				showPointCounts = true;
-			int n = roi.getFloatPolygon().npoints;
 			if (showPointCounts)
 				gd.addCheckbox("Show point counts (shortcut: alt+y)", listCoordinates);
 			else
-				gd.addCheckbox("List coordinates ("+n+")", listCoordinates);
+				gd.addCheckbox("List coordinates ("+roi.size()+")", listCoordinates);
 			if (nProperties>0)
 				gd.addCheckbox("List properties ("+nProperties+")", listProperties);
 			else {

ij/gui/RotatedRectRoi.java

 package ij.gui;
 import java.awt.*;
 import java.awt.image.*;
+import java.awt.event.*;
 import ij.*;
 import ij.plugin.frame.Recorder;
 import ij.process.FloatPolygon;
@@ -97,6 +98,46 @@ public class RotatedRectRoi extends PolygonRoi {
 		makePolygonRelative();
 		cachedMask = null;
 		DefaultRectWidth = rectWidth;
+		showStatus();
+	}
+	
+	public void showStatus() {
+		double[] p = getParams();
+		double dx = p[2] - p[0];
+		double dy = p[3] - p[1];
+		double length = Math.sqrt(dx*dx+dy*dy);
+		double width = p[4];
+		if (imp!=null && !IJ.altKeyDown()) {
+			Calibration cal = imp.getCalibration();
+			if (cal.scaled() && cal.pixelWidth==cal.pixelHeight) {
+				dx *= cal.pixelWidth;
+				dy *= cal.pixelHeight;
+				length = Math.sqrt(dx*dx+dy*dy);
+				width = p[4]*cal.pixelWidth;
+			}
+		}
+		double angle = getFloatAngle(p[0], p[1], p[2], p[3]);
+		IJ.showStatus("length=" + IJ.d2s(length)+", width=" + IJ.d2s(width)+", angle=" + IJ.d2s(angle));
+	}
+
+	public void nudgeCorner(int key) {
+		if (ic==null) return;
+		double[] p = getParams();
+		double x1 = p[0];
+		double y1 = p[1];
+		double x2 = p[2];
+		double y2 = p[3];
+		double inc = 1.0/ic.getMagnification();
+		switch(key) {
+			case KeyEvent.VK_UP: y2-=inc; break;
+			case KeyEvent.VK_DOWN: y2+=inc; break;
+			case KeyEvent.VK_LEFT: x2-=inc; break;
+			case KeyEvent.VK_RIGHT: x2+=inc; break;
+		}
+		makeRectangle(x1, y1, x2, y2);
+		imp.draw();
+		notifyListeners(RoiListener.MOVED);
+		showStatus();
 	}
 
 	void makePolygonRelative() {

ij/gui/ShapeRoi.java

@@ -613,29 +613,30 @@ public class ShapeRoi extends Roi {
 		double cx = r.getX() + r.getWidth()/2;
 		double cy = r.getY() + r.getHeight()/2;
 		AffineTransform at = new AffineTransform();
-		at.translate(cx, cy);
-		for (int i=0; i<181; i++) {
-			at.rotate(Math.PI/180.0);
+		if (pw != ph)
+			at.scale(1.0, ph/pw);  //correct for pixel aspect ratio
+		at.translate(-cx, -cy);    //shift to origin for better accuracy
+		double angleInc = 0.5;
+		AffineTransform rotator = AffineTransform.getRotateInstance(angleInc*Math.PI/180.0);
+		for (double rotAngle=0; rotAngle<90; rotAngle+=angleInc) {  //rotate in 0.5 deg increments
+			if (rotAngle > 0)
+				at.preConcatenate(rotator);  //'pre-'applying the rotation matrix means rotating as the last step
 			s = at.createTransformedShape(shape);
 			r = s.getBounds2D();
-			double max2 = Math.max(r.getWidth(), r.getHeight());
-			if (max2>diameter) {
-				diameter = max2*pw;
-				//angle = i;
+			if (r.getWidth() > diameter) {
+				diameter = r.getWidth();
+				angle = rotAngle;
+			}
+			if (r.getHeight() > diameter) {
+				diameter = r.getHeight();
+				angle = rotAngle + 90;
 			}
 			double min2 = Math.min(r.getWidth(), r.getHeight());
 			min = Math.min(min, min2);
 		}
-		if (pw!=ph) {
-			diameter = 0.0;
-			angle = 0.0;
-		}
-		if (pw==ph)
 		min *= pw;
-		else {
-			min = 0.0;
-			angle = 0.0;
-		}
+		diameter *= pw;
+
 		double[] a = new double[5];
 		a[0] = diameter;
 		a[1] = angle;
@@ -1021,7 +1022,7 @@ public class ShapeRoi extends Roi {
 			basex=r.x; basey=r.y;
 		}
 		aTx.setTransform(mag, 0.0, 0.0, mag, -basex*mag, -basey*mag);
-		aTx.translate(x, y);
+		aTx.translate(getXBase(), getYBase());
 		if (fillColor!=null) {
 			if (isActiveOverlayRoi) {
 				g2d.setColor(Color.cyan);

ij/io/FileOpener.java

@@ -181,7 +181,7 @@ public class FileOpener {
 				overlay.drawNames(proto.getDrawNames());
 				overlay.drawBackgrounds(proto.getDrawBackgrounds());
 				overlay.setLabelColor(proto.getLabelColor());
-				overlay.setLabelFont(proto.getLabelFont());
+				overlay.setLabelFont(proto.getLabelFont(), proto.scalableLabels());
 			}
 			overlay.add(roi);
 		}