IJ_Props.txt

@@ -435,31 +435,29 @@ open02="Bat Cochlea Volume (19K)",ij.plugin.URLOpener("bat-cochlea-volume.zip")
 open03="Bat Cochlea Renderings (449K)",ij.plugin.URLOpener("bat-cochlea-renderings.zip")
 open04="Blobs (25K)[B]",ij.plugin.URLOpener("blobs.gif")
 open05="Boats (356K)",ij.plugin.URLOpener("boats.gif")
-open06="Bridge (174K)",ij.plugin.URLOpener("bridge.gif")
-open07="Cardio (768K, RGB DICOM)",ij.plugin.URLOpener("cardio.dcm.zip")
-open08="Cell Colony (31K)",ij.plugin.URLOpener("Cell_Colony.jpg")
-open09="Clown (14K)",ij.plugin.URLOpener("clown.jpg")
-open10="Confocal Series (2.2MB)",ij.plugin.URLOpener("confocal-series.zip")
-open11="CT (420K, 16-bit DICOM)",ij.plugin.URLOpener("ct.dcm.zip")
-open12="Dot Blot (7K)",ij.plugin.URLOpener("Dot_Blot.jpg")
-open13="Embryos (42K)",ij.plugin.URLOpener("embryos.jpg")
-open14="Fluorescent Cells (400K)",ij.plugin.URLOpener("FluorescentCells.zip")
-open15="Fly Brain (1MB)",ij.plugin.URLOpener("flybrain.zip")
-open16="Gel (105K)",ij.plugin.URLOpener("gel.gif")
-open17="HeLa Cells (1.3M, 48-bit RGB)",ij.plugin.URLOpener("hela-cells.zip")
-open18="Image with Overlay",ij.plugin.URLOpener("ImageWithOverlay.zip")
-open19="Leaf (36K)",ij.plugin.URLOpener("leaf.jpg")
-open20="Lena (68K)",ij.plugin.URLOpener("lena-std.tif")
-open21="Line Graph (21K)",ij.plugin.URLOpener("LineGraph.jpg")
-open22="Mitosis (26MB, 5D stack)",ij.plugin.URLOpener("Spindly-GFP.zip")
-open23="MRI Stack (528K)",ij.plugin.URLOpener("mri-stack.zip")
-open24="M51 Galaxy (177K, 16-bits)",ij.plugin.URLOpener("m51.zip")
-open25="Neuron (1.6M, 5 channels)",ij.plugin.URLOpener("Rat_Hippocampal_Neuron.zip")
-open26="Nile Bend (1.9M)",ij.plugin.URLOpener("NileBend.jpg")
-open27="Organ of Corti (2.8M, 4D stack)",ij.plugin.URLOpener("organ-of-corti.zip")
-open28="Particles (75K)",ij.plugin.URLOpener("particles.gif")
-open29="T1 Head (2.4M, 16-bits)",ij.plugin.URLOpener("t1-head.zip")
-open30="T1 Head Renderings (736K)",ij.plugin.URLOpener("t1-rendering.zip")
-open31="TEM Filter (112K)",ij.plugin.URLOpener("TEM_filter_sample.jpg")
-open32="Tree Rings (48K)",ij.plugin.URLOpener("Tree_Rings.jpg")
+open06="Cardio (768K, RGB DICOM)",ij.plugin.URLOpener("cardio.dcm.zip")
+open07="Cell Colony (31K)",ij.plugin.URLOpener("Cell_Colony.jpg")
+open08="Clown (14K)",ij.plugin.URLOpener("clown.jpg")
+open09="Confocal Series (2.2MB)",ij.plugin.URLOpener("confocal-series.zip")
+open10="CT (420K, 16-bit DICOM)",ij.plugin.URLOpener("ct.dcm.zip")
+open11="Dot Blot (7K)",ij.plugin.URLOpener("Dot_Blot.jpg")
+open12="Embryos (42K)",ij.plugin.URLOpener("embryos.jpg")
+open13="Fluorescent Cells (400K)",ij.plugin.URLOpener("FluorescentCells.zip")
+open14="Fly Brain (1MB)",ij.plugin.URLOpener("flybrain.zip")
+open15="Gel (105K)",ij.plugin.URLOpener("gel.gif")
+open16="HeLa Cells (1.3M, 48-bit RGB)",ij.plugin.URLOpener("hela-cells.zip")
+open17="Image with Overlay",ij.plugin.URLOpener("ImageWithOverlay.zip")
+open18="Leaf (36K)",ij.plugin.URLOpener("leaf.jpg")
+open19="Line Graph (21K)",ij.plugin.URLOpener("LineGraph.jpg")
+open20="Mitosis (26MB, 5D stack)",ij.plugin.URLOpener("Spindly-GFP.zip")
+open21="MRI Stack (528K)",ij.plugin.URLOpener("mri-stack.zip")
+open22="M51 Galaxy (177K, 16-bits)",ij.plugin.URLOpener("m51.zip")
+open23="Neuron (1.6M, 5 channels)",ij.plugin.URLOpener("Rat_Hippocampal_Neuron.zip")
+open24="Nile Bend (1.9M)",ij.plugin.URLOpener("NileBend.jpg")
+open25="Organ of Corti (2.8M, 4D stack)",ij.plugin.URLOpener("organ-of-corti.zip")
+open26="Particles (75K)",ij.plugin.URLOpener("particles.gif")
+open27="T1 Head (2.4M, 16-bits)",ij.plugin.URLOpener("t1-head.zip")
+open28="T1 Head Renderings (736K)",ij.plugin.URLOpener("t1-rendering.zip")
+open29="TEM Filter (112K)",ij.plugin.URLOpener("TEM_filter_sample.jpg")
+open30="Tree Rings (48K)",ij.plugin.URLOpener("Tree_Rings.jpg")
 

debian/changelog

+imagej (1.52p-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Re-add some docs to main package
+  * Provide extremely simple autopkgtest (just output help screen)
+
+ -- Andreas Tille <tille@debian.org>  Thu, 08 Aug 2019 14:11:51 +0200
+
 imagej (1.52j-1) unstable; urgency=medium
 
   * Team upload.

debian/compat

-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 (>= 12~)
+Build-Depends: debhelper-compat (= 12)
 Build-Depends-Indep: ant,
                      default-jdk-doc,
                      default-jdk-headless,
                      javahelper,
                      maven-repo-helper
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 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

debian/imagej.docs

+IJ_Props.txt
+release-notes.html

debian/tests/control

+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr

debian/tests/run-unit-test

+#!/bin/bash
+set -e
+
+pkg=imagej
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  # Double quote below to expand the temporary directory variable now versus
+  # later is on purpose.
+  # shellcheck disable=SC2064
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+imagej -h

ij/IJ.java

@@ -199,10 +199,11 @@ public class IJ {
 				((PlugIn)thePlugIn).run(arg);
  			else
 				new PlugInFilterRunner(thePlugIn, commandName, arg);
-		}
-		catch (ClassNotFoundException e) {
-			if (IJ.getApplet()==null)
+		} catch (ClassNotFoundException e) {
 			log("Plugin or class not found: \"" + className + "\"\n(" + e+")");
+			String path = Prefs.getCustomPropsPath();
+			if (path!=null);
+				log("Error may be due to custom properties at " + path);
 		}
 		catch (InstantiationException e) {log("Unable to load plugin (ins)");}
 		catch (IllegalAccessException e) {log("Unable to load plugin, possibly \nbecause it is not public.");}
@@ -231,7 +232,9 @@ public class IJ {
 				new PlugInFilterRunner(thePlugIn, commandName, arg);
 		}
 		catch (ClassNotFoundException e) {
-			if (className.contains("_")  && !suppressPluginNotFoundError)
+			if (className.startsWith("macro:"))
+				runMacro(className.substring(6));
+			else if (className.contains("_")  && !suppressPluginNotFoundError)
 				error("Plugin or class not found: \"" + className + "\"\n(" + e+")");
 		}
 		catch (NoClassDefFoundError e) {
@@ -581,7 +584,7 @@ public class IJ {
     
     /**Displays a "no images are open" dialog box.*/
 	public static void noImage() {
-		String msg = "There are no images open.";
+		String msg = "There are no images open";
 		if (macroInterpreter!=null) {
 			macroInterpreter.abort(msg);
 			macroInterpreter = null;
@@ -659,11 +662,6 @@ 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);
@@ -675,6 +673,11 @@ 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 title, String msg) {
+		if (macroInterpreter!=null) {
+			macroInterpreter.abort(msg);
+			macroInterpreter = null;
+			return;
+		}
 		if (msg!=null && msg.endsWith(Macro.MACRO_CANCELED))
 			return;
 		String title2 = title!=null?title:"ImageJ";
@@ -1550,7 +1553,7 @@ public class IJ {
 					if (EventQueue.isDispatchThread())
 						new MacroRunner(smoothMacro); // run on separate thread
 					else
-						IJ.runMacro(smoothMacro);
+						Macro.eval(smoothMacro);
 				}
 			}
 		}
@@ -1605,6 +1608,14 @@ public class IJ {
 		return img;
 	}
 	
+	/**The macro interpreter uses this method to call getImage().*/
+	public static ImagePlus getImage(Interpreter interpreter) {
+		macroInterpreter = interpreter;
+		ImagePlus imp =  getImage();
+		macroInterpreter = null;
+		return imp;
+	}
+	
 	/** Returns the active image or stack slice as an ImageProcessor, or displays
 		an error message and aborts the plugin or macro if no images are open. */
 	public static ImageProcessor getProcessor() {
@@ -1930,9 +1941,9 @@ public class IJ {
 		} else if (format.indexOf("lut")!=-1) {
 			path = updateExtension(path, ".lut");
 			format = "LUT...";
-		} else if (format.indexOf("results")!=-1 || format.indexOf("measurements")!=-1) {
+		} else if (format.contains("results") || format.contains("measurements") || format.contains("table")) {
 			format = "Results...";
-		} else if (format.indexOf("selection")!=-1 || format.indexOf("roi")!=-1) {
+		} else if (format.contains("selection") || format.contains("roi")) {
 			path = updateExtension(path, ".roi");
 			format = "Selection...";
 		} else if (format.indexOf("xy")!=-1 || format.indexOf("coordinates")!=-1) {
@@ -2213,23 +2224,8 @@ public class IJ {
 	
 	/** Returns the size, in pixels, of the primary display. */
 	public static Dimension getScreenSize() {
-		Rectangle bounds = GUI.getZeroBasedMaxBounds();
-		if (bounds!=null)
+		Rectangle bounds = GUI.getScreenBounds();
 		return new Dimension(bounds.width, bounds.height);
-		if (isWindows())  // GraphicsEnvironment.getConfigurations is *very* slow on Windows
-			return Toolkit.getDefaultToolkit().getScreenSize();
-		if (GraphicsEnvironment.isHeadless())
-			return new Dimension(0, 0);
-		// Can't use Toolkit.getScreenSize() on Linux because it returns 
-		// size of all displays rather than just the primary display.
-		GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
-		GraphicsDevice[] gd = ge.getScreenDevices();
-		GraphicsConfiguration[] gc = gd[0].getConfigurations();
-		bounds = gc[0].getBounds();
-		if ((bounds.x==0&&bounds.y==0) || (IJ.isLinux()&&gc.length>1))
-			return new Dimension(bounds.width, bounds.height);
-		else
-			return Toolkit.getDefaultToolkit().getScreenSize();
 	}
 	
 	/** Returns, as an array of strings, a list of the LUTs in the Image/Lookup Tables menu. */

ij/ImageJ.java

@@ -18,7 +18,6 @@ import java.awt.image.*;
 import javax.swing.ImageIcon;
 import javax.swing.JLabel;
 
-
 /**
 This frame is the main ImageJ class.
 <p>
@@ -47,7 +46,7 @@ The following command line options are recognized by ImageJ:
 
   -batch path [arg]
     Runs a macro or script (JavaScript, BeanShell or Python) in
-    batch (no GUI) mode, passing it an optional argument.
+    batch (no GUI) mode, passing an optional argument.
     ImageJ exits when the macro finishes.
 
   -eval "macro code"
@@ -78,8 +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 = "1.52j";
-	public static final String BUILD = "";  //42
+	public static final String VERSION = "1.52p";
+	public static final String BUILD = "";  //61
 	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);
@@ -165,11 +164,12 @@ public class ImageJ extends Frame implements ActionListener,
 		statusBar.setForeground(Color.black);
 		statusBar.setBackground(backgroundColor);
 		statusLine = new JLabel();
-		statusLine.setFont(new Font("SansSerif", Font.PLAIN, 13));
+		double scale = Prefs.getGuiScale();
+		statusLine.setFont(new Font("SansSerif", Font.PLAIN, (int)(13*scale)));
 		statusLine.addKeyListener(this);
 		statusLine.addMouseListener(this);
 		statusBar.add("Center", statusLine);
-		progressBar = new ProgressBar(ProgressBar.WIDTH, ProgressBar.HEIGHT);
+		progressBar = new ProgressBar((int)(ProgressBar.WIDTH*scale), (int)(ProgressBar.HEIGHT*scale));
 		progressBar.addKeyListener(this);
 		progressBar.addMouseListener(this);
 		statusBar.add("East", progressBar);
@@ -186,10 +186,10 @@ public class ImageJ extends Frame implements ActionListener,
 		setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug
 		if (mode!=NO_SHOW) {
 			if (IJ.isWindows()) try {setIcon();} catch(Exception e) {}
-			setLocation(loc.x, loc.y);
 			setResizable(false);
 			setAlwaysOnTop(Prefs.alwaysOnTop);
 			pack();
+			setLocation(loc.x, loc.y);
 			setVisible(true);
 			Dimension size = getSize();
 			if (size!=null) {
@@ -202,7 +202,7 @@ public class ImageJ extends Frame implements ActionListener,
 					if (!Prefs.jFileChooserSettingChanged)
 						Prefs.useJFileChooser = true;
 				} else if (IJ.isMacOSX()) {
-					Rectangle maxBounds = GUI.getMaxWindowBounds();
+					Rectangle maxBounds = GUI.getMaxWindowBounds(this);
 					if (loc.x+size.width>maxBounds.x+maxBounds.width)
 						setLocation(loc.x, loc.y);
 				}
@@ -277,9 +277,9 @@ public class ImageJ extends Frame implements ActionListener,
 	}
 	
 	public Point getPreferredLocation() {
-		Rectangle maxBounds = GUI.getMaxWindowBounds();
 		int ijX = Prefs.getInt(IJ_X,-99);
 		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))
 			return new Point(ijX, ijY);
@@ -464,7 +464,7 @@ public class ImageJ extends Frame implements ActionListener,
 			|| (keyCode>=KeyEvent.VK_NUMPAD0 && keyCode<=KeyEvent.VK_NUMPAD9);			
 		if ((!Prefs.requireControlKey||control||meta||functionKey||numPad) && keyChar!='+') {
 			Hashtable shortcuts = Menus.getShortcuts();
-			if (shift)
+			if (shift && !functionKey)
 				cmd = (String)shortcuts.get(new Integer(keyCode+200));
 			else
 				cmd = (String)shortcuts.get(new Integer(keyCode));
@@ -609,17 +609,25 @@ public class ImageJ extends Frame implements ActionListener,
 		IJ.setKeyUp(e.getKeyCode());
 	}
 			
+	/** called when escape pressed */
 	void abortPluginOrMacro(ImagePlus imp) {
 		if (imp!=null) {
 			ImageWindow win = imp.getWindow();
 			if (win!=null) {
+				Roi roi = imp.getRoi();
+				if (roi!=null && roi.getState()!=Roi.NORMAL) {
+					roi.abortModification(imp);
+					return;
+				} else {
 					win.running = false;
 					win.running2 = false;
 				}
 			}
+		}
 		Macro.abort();
 		Interpreter.abort();
-		if (Interpreter.getInstance()!=null) IJ.beep();
+		if (Interpreter.getInstance()!=null)
+			IJ.beep();
 	}
 
 	public void windowClosing(WindowEvent e) {
@@ -678,10 +686,6 @@ public class ImageJ extends Frame implements ActionListener,
 	/** Called once when ImageJ quits. */
 	public void savePreferences(Properties prefs) {
 		Point loc = getLocation();
-		if (IJ.isLinux()) {
-			Rectangle bounds = GUI.getMaxWindowBounds();
-			loc.y = bounds.y;
-		}
 		prefs.put(IJ_X, Integer.toString(loc.x));
 		prefs.put(IJ_Y, Integer.toString(loc.y));
 	}
@@ -865,4 +869,12 @@ public class ImageJ extends Frame implements ActionListener,
 		commandName = name;
 	}
 	
+	public void resize() {
+		double scale = Prefs.getGuiScale();
+		toolbar.init();
+		statusLine.setFont(new Font("SansSerif", Font.PLAIN, (int)(13*scale)));
+		progressBar.init((int)(ProgressBar.WIDTH*scale), (int)(ProgressBar.HEIGHT*scale));
+		pack();
+	}
+
 }

ij/ImagePlus.java

@@ -97,6 +97,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 	private boolean ignoreGlobalCalibration;
 	private boolean oneSliceStack;
 	public boolean setIJMenuBar = Prefs.setIJMenuBar;
+	private Plot plot;
 			
 
     /** Constructs an uninitialized ImagePlus. */
@@ -269,6 +270,17 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		draw();
 	}
 	
+	/** Use to update the image when the underlying virtual stack changes. */
+	public void updateVirtualSlice() {
+		ImageStack vstack = getStack();
+		if (vstack.isVirtual()) {
+			double min=getDisplayRangeMin(), max=getDisplayRangeMax();
+			setProcessor(vstack.getProcessor(getCurrentSlice()));
+			setDisplayRange(min,max);
+		} else
+			throw new IllegalArgumentException("Virtual stack required");
+	}
+	
 	/** Sets the display mode of composite color images, where 'mode' 
 		 should be IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE. */
 	public void setDisplayMode(int mode) {
@@ -429,7 +441,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			if (roi!=null) roi.setImage(this);
 			if (overlay!=null && getCanvas()!=null)
 				getCanvas().setOverlay(overlay);
-			draw();
 			IJ.showStatus(statusMessage);
 			if (IJ.isMacro()) { // wait for window to be activated
 				long start = System.currentTimeMillis();
@@ -872,9 +883,10 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		return mask;
 	}
 	
-	/** Returns an 8-bit binary (0 and 255) ROI or overlay mask
-	 *  that has the same dimensions as this image. Creates an
-	 * ROI mask If the image has both an ROI and an overlay.
+	/** Returns an 8-bit binary (foreground=255, background=0)
+	 * ROI or overlay mask that has the same dimensions 
+	 * as this image. Creates an ROI mask If the image has both
+	 * both an ROI and an overlay. Set the threshold of the mask to 255.
 	 * @see #createThresholdMask
 	 * @see ij.gui.Roi#getMask
 	*/
@@ -902,16 +914,21 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 					mask.fill(overlay2.get(i));	
 			}		
 		} 
+		mask.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
 		return mask;
 	}
 
-	/** Returns an 8-bit binary (0 and 255) threshold mask
+	/** Returns an 8-bit binary threshold mask
+	 * (foreground=255, background=0)
 	 * that has the same dimensions as this image.
+	 * The threshold of the mask is set to 255.
 	 * @see ij.plugin.Thresholder#createMask
 	 * @see ij.process.ImageProcessor#createMask
 	*/
 	public ByteProcessor createThresholdMask() {
-		return Thresholder.createMask(this);
+		ByteProcessor mask = Thresholder.createMask(this);
+		mask.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
+		return mask;
 	}
 
 	/** Get calibrated statistics for this image or ROI, including 
@@ -926,18 +943,22 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
          IJ.log("Mean: "+stats.mean);
          IJ.log("Max: "+stats.max);
 		</pre>
+		@return an {@link ij.process.ImageStatistics} object
 		@see #getAllStatistics
 		@see #getRawStatistics
 		@see ij.process.ImageProcessor#getStats
-		@see ij.process.ImageStatistics
-		@see ij.process.ImageStatistics#getStatistics
 		*/
 	public ImageStatistics getStatistics() {
 		return getStatistics(AREA+MEAN+STD_DEV+MODE+MIN_MAX+RECT);
 	}
 	
-	/** This method returns complete calibrated statistics for this image or ROI
-		(with "Limit to threshold"), but it is up to 70 times slower than getStatistics().*/
+	/** This method returns complete calibrated statistics for this
+	 * image or ROI (with "Limit to threshold"), but it is up to 70 times
+	 * slower than getStatistics().
+	 * @return an {@link ij.process.ImageStatistics} object
+	 * @see #getStatistics
+	 * @see ij.process.ImageProcessor#getStatistics
+	*/
 	public ImageStatistics getAllStatistics() {
 		return getStatistics(ALL_STATS+LIMIT);
 	}
@@ -954,7 +975,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 
 	/** Returns an ImageStatistics object generated using the
 		specified measurement options.
-		@see ij.process.ImageStatistics
 		@see ij.measure.Measurements
 	*/
 	public ImageStatistics getStatistics(int mOptions) {
@@ -975,10 +995,16 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		int bitDepth = getBitDepth();
 		if (nBins!=256 && (bitDepth==8||bitDepth==24))
 			ip2 =ip.convertToShort(false);
-		if (roi!=null && roi.isArea())
-			ip2.setRoi(roi);
-		else
+		Roi roi2 = roi;
+		if (roi2==null)
 			ip2.resetRoi();
+		else if (roi2.isArea())
+			ip2.setRoi(roi2);			
+		else if ((roi2 instanceof PointRoi) && roi2.size()==1) {
+				// needed to be consistent with ImageProcessor.getStatistics()
+				FloatPolygon p = roi2.getFloatPolygon();
+				ip2.setRoi((int)p.xpoints[0], (int)p.ypoints[0], 1, 1);
+		}
 		ip2.setHistogramSize(nBins);
 		Calibration cal = getCalibration();
 		if (getType()==GRAY16&& !(histMin==0.0&&histMax==0.0)) {
@@ -1474,9 +1500,10 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			}
 			s.addSlice(label, ip2);
 			s.update(ip2);
-			setStack(s);
+			this.stack = s;
 			ip = ip2;
 			oneSliceStack = true;
+			setCurrentSlice(1);
 		} else {
 			s = stack;
 			if (ip!=null) {
@@ -1662,8 +1689,10 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			Roi roi = getRoi();
 			if (roi!=null)
 				roi.endPaste();
-			if (isProcessor())
+			if (isProcessor()) {
+				if (currentSlice==0) currentSlice=1;
 				stack.setPixels(ip.getPixels(),currentSlice);
+			}
 			setCurrentSlice(n);
 			Object pixels = null;
 			Overlay overlay2 = null;
@@ -1752,8 +1781,10 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			if (newRoi==null)
 				{deleteRoi(); return;}
 		}
-		if (bounds.width==0 && bounds.height==0 && !(newRoi.getType()==Roi.POINT||newRoi.getType()==Roi.LINE))
-			{deleteRoi(); return;}
+		if (bounds.width==0 && bounds.height==0 && !(newRoi.getType()==Roi.POINT||newRoi.getType()==Roi.LINE)) {
+			deleteRoi();
+			return;
+		}
 		roi = newRoi;
 		if (ip!=null) {
 			ip.setMask(null);
@@ -1789,7 +1820,10 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		the tool bar is active. The user interactively sets the selection size and shape. */
 	public void createNewRoi(int sx, int sy) {
 		Roi previousRoi = roi;
-		deleteRoi();
+		deleteRoi();   //also saves the roi as <code>Roi.previousRoi</code> if non-null
+		if (Roi.previousRoi != null)
+			Roi.previousRoi.setImage(previousRoi== null ? null : this); //with 'this' it will be recalled in case of ESC
+
 		switch (Toolbar.getToolId()) {
 			case Toolbar.RECTANGLE:
 				if (Toolbar.getRectToolType()==Toolbar.ROTATED_RECT_ROI)
@@ -1880,6 +1914,23 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		}
 	}
 	
+	public boolean okToDeleteRoi() {
+		if (roi!=null && (roi instanceof PointRoi) && getWindow()!=null && ((PointRoi)roi).promptBeforeDeleting()) {
+			int npoints = ((PolygonRoi)roi).getNCoordinates();
+			int counters = ((PointRoi)roi).getNCounters();
+			String msg = "Delete this multi-point selection ("+npoints+" points, "+counters+" counter"+(counters>1?"s":"")+")?";
+			GenericDialog gd=new GenericDialog("Delete Points?");
+			gd.addMessage(msg+"\nRestore using Edit>Selection>Restore Selection.");
+			gd.addHelp(PointToolOptions.help);
+			gd.setOKLabel("Keep");
+			gd.setCancelLabel("Delete");
+			gd.showDialog();
+			if (gd.wasOKed())
+				return false;
+		}
+		return true;
+	}
+	
 	/** Deletes the current region of interest. */
 	public void killRoi() {
 		deleteRoi();
@@ -1894,10 +1945,20 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 				Roi.previousRoi = (Roi)roi2.clone();
 				if (IJ.debugMode) IJ.log("saveRoi: "+roi2);
 			}
+			if ((roi2 instanceof PointRoi) && ((PointRoi)roi2).promptBeforeDeleting()) {
+				PointRoi.savedPoints = (PointRoi)roi2.clone();
+				if (IJ.debugMode) IJ.log("saveRoi: saving multi-point selection");
+			}
 		}
 	}
     
 	public void restoreRoi() {
+		if (Toolbar.getToolId()==Toolbar.POINT && PointRoi.savedPoints!=null) {
+			roi = (Roi)PointRoi.savedPoints.clone();
+			draw();
+			roi.notifyListeners(RoiListener.MODIFIED);
+			return;
+		}
 		if (Roi.previousRoi!=null) {
 			Roi pRoi = Roi.previousRoi;
 			Rectangle r = pRoi.getBounds();
@@ -1909,7 +1970,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 				else if (r.width==width && r.height==height) // is it the same size as the image
 					roi.setLocation(0, 0);
 				draw();
-				roi.notifyListeners(RoiListener.CREATED);
+				roi.notifyListeners(RoiListener.MODIFIED);
 			}
 		}
 	}
@@ -1924,8 +1985,12 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 	
 	/** Implements the File/Revert command. */
 	public void revert() {
-		if (getStackSize()>1 && getStack().isVirtual())
+		if (getStackSize()>1 && getStack().isVirtual()) {
+			int thisSlice = currentSlice;
+			currentSlice = 0;
+			setSlice(thisSlice);
 			return;
+		}
 		FileInfo fi = getOriginalFileInfo();
 		boolean isFileInfo = fi!=null && fi.fileFormat!=FileInfo.UNKNOWN;
 		if (!isFileInfo && url==null)
@@ -2037,7 +2102,8 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
     	switch (imageType) {
 			case GRAY8: case COLOR_256:
 				LookUpTable lut = createLut();
-    			if (imageType==COLOR_256 || !lut.isGrayscale())
+				boolean customLut = !lut.isGrayscale() || (ip!=null&&!ip.isDefaultLut());
+				if (imageType==COLOR_256 || customLut)
 					fi.fileType = FileInfo.COLOR8;
 				else
 					fi.fileType = FileInfo.GRAY8;
@@ -2053,7 +2119,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 					fi.fileType = fi.GRAY16_UNSIGNED;
 				if (!compositeImage) {
     				lut = createLut();
-    				if (!lut.isGrayscale())
+    				if (!lut.isGrayscale() || (ip!=null&&!ip.isDefaultLut()))
     					addLut(lut, fi);
 				}
 				break;
@@ -2061,7 +2127,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 				fi.fileType = fi.GRAY32_FLOAT;
 				if (!compositeImage) {
     				lut = createLut();
-    				if (!lut.isGrayscale())
+    				if (!lut.isGrayscale() || (ip!=null&&!ip.isDefaultLut()))
     					addLut(lut, fi);
 				}
 				break;
@@ -2161,6 +2227,34 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		return (new Duplicator()).crop(this);
 	}
 
+	/** Returns a cropped copy this image or stack, where 'options'
+	 * can be "stack", "slice" or a range (e.g., "20-30").
+	 * @see #duplicate
+	 * @see #crop
+	 * @see ij.plugin.Duplicator#crop
+	*/
+	public ImagePlus crop(String options) {
+		String msg = "crop: \"stack\", \"slice\" or a range (e.g., \"20-30\") expected";
+		int stackSize = getStackSize();
+		if (options==null || options.equals("stack"))
+			return (new Duplicator()).run(this);
+		else if (options.equals("slice") || stackSize==1)
+			return crop();
+		else {
+			String[] range = Tools.split(options, " -");
+			if (range.length!=2)
+				throw new IllegalArgumentException(msg);
+			double s1 = Tools.parseDouble(range[0]);
+			double s2 = Tools.parseDouble(range[1]);
+			if (Double.isNaN(s1) || Double.isNaN(s2))
+				throw new IllegalArgumentException(msg);
+			if (s1<1) s1 = 1;
+			if (s2>stackSize) s2 = stackSize;
+			if (s1>s2) {s1=1; s2=stackSize;}
+			return new Duplicator().run(this, (int)s1, (int)s2);
+		}
+	}
+
 	/** Returns a new ImagePlus with this image's attributes
 		(e.g. spatial scale), but no image. */
 	public ImagePlus createImagePlus() {
@@ -2899,4 +2993,12 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
     	return stack!=null;
     }
     
+    public void setPlot(Plot plot) {
+    	this.plot = plot;
+    }
+    
+    public Plot getPlot() {
+    	return plot;
+    }
+
 }

ij/ImageStack.java

@@ -102,8 +102,15 @@ public class ImageStack {
 	/** Adds the image in 'ip' to the end of the stack, setting
 		the string 'sliceLabel' as the slice metadata. */
 	public void addSlice(String sliceLabel, ImageProcessor ip) {
-		if (ip.getWidth()!=width || ip.getHeight()!=height)
+		if (ip.getWidth()!=width || ip.getHeight()!=height) {
+			if (width==0 && height==0) {
+				width = ip.getWidth();
+				height = ip.getHeight();
+				stack = new Object[INITIAL_SIZE];
+				label = new String[INITIAL_SIZE];
+			} else
 				throw new IllegalArgumentException("ImageStack.addSlice(): dimensions do not match");
+		}
 		if (nSlices==0) {
 			cm = ip.getColorModel();
 			min = ip.getMin();
@@ -346,10 +353,11 @@ public class ImageStack {
 		return ("stack["+getWidth()+"x"+getHeight()+"x"+getSize()+v+"]");
 	}
 	
-	/** Returns, as a double, the specified voxel. Returns
-	 * NaN if x, y or z are beyond the stack limits. Use the
-	 * ImagePlus.getStackIndex() method to convert a C,Z,T
-	 * hyperstack position (one-based) into a z index (zero-based).
+	/** Returns, as a double, the value of the specified voxel.
+	 * Throws an IndexOutOfBoundsException if x, y or z are
+	 * beyond the stack limits. Use the ImagePlus.getStackIndex()
+	 * method to convert a C,Z,T hyperstack position (one-based)
+	 * into a z index (zero-based).
 	 * @see ij.ImagePlus#getStackIndex
 	*/
 	public final double getVoxel(int x, int y, int z) {

ij/Macro.java

@@ -167,5 +167,12 @@ public class Macro {
 		return key;
 	}
 	
+	/** Evaluates 'code' and returns the output, or any error, 
+	 * as a String (e.g., Macro.eval("2+2") returns "4").	
+	*/
+	public static String eval(String code) {
+		return new Interpreter().eval(code);
+	}
+
 }
 

ij/Menus.java

@@ -80,6 +80,7 @@ public class Menus {
 	private static int defaultFontSize = IJ.isWindows()?15:0;
 	private static int fontSize = Prefs.getInt(Prefs.MENU_SIZE, defaultFontSize);
 	private static Font menuFont;
+	private static double scale = 1.0;
 
 	static boolean jnlp; // true when using Java WebStart
 	public static int setMenuBarCount;
@@ -92,6 +93,9 @@ public class Menus {
 	}
 
 	String addMenuBar() {
+		scale = Prefs.getGuiScale();
+		if ((scale>=1.5&&scale<2.0) || (scale>=2.5&&scale<3.0))
+			scale = (int)Math.round(scale);
 		nPlugins = nMacros = userPluginsIndex = 0;
 		addSorted = installingJars = duplicateCommand = false;
 		error = null;
@@ -111,6 +115,15 @@ public class Menus {
 		addPlugInItem(openSamples, "Cache Sample Images ", "ij.plugin.URLOpener(\"cache\")", 0, false);
 		addOpenRecentSubMenu(file);
 		Menu importMenu = getMenu("File>Import", true);		
+		Menu showFolderMenu = new Menu("Show Folder");
+		file.add(showFolderMenu);
+		addPlugInItem(showFolderMenu, "Image", "ij.plugin.SimpleCommands(\"showdirImage\")", 0, false);
+		addPlugInItem(showFolderMenu, "Plugins", "ij.plugin.SimpleCommands(\"showdirPlugins\")", 0, false);
+		addPlugInItem(showFolderMenu, "Macros", "ij.plugin.SimpleCommands(\"showdirMacros\")", 0, false);
+		addPlugInItem(showFolderMenu, "LUTs", "ij.plugin.SimpleCommands(\"showdirLuts\")", 0, false);
+		addPlugInItem(showFolderMenu, "ImageJ", "ij.plugin.SimpleCommands(\"showdirImageJ\")", 0, false);
+		addPlugInItem(showFolderMenu, "temp", "ij.plugin.SimpleCommands(\"showdirTemp\")", 0, false);
+		addPlugInItem(showFolderMenu, "Home", "ij.plugin.SimpleCommands(\"showdirHome\")", 0, false);
 		file.addSeparator();
 		addPlugInItem(file, "Close", "ij.plugin.Commands(\"close\")", KeyEvent.VK_W, false);
 		addPlugInItem(file, "Close All", "ij.plugin.Commands(\"close-all\")", KeyEvent.VK_W, true);
@@ -249,13 +262,18 @@ public class Menus {
 		file.addSeparator();
 		addPlugInItem(file, "Quit", "ij.plugin.Commands(\"quit\")", 0, false);
 
-		if (fontSize!=0)
+		//System.out.println("MenuBar.setFont: "+fontSize+" "+scale+"  "+getFont());
+		if (fontSize!=0 || scale>1.0)
 			mbar.setFont(getFont());
 		if (ij!=null) {
 			ij.setMenuBar(mbar);
 			Menus.setMenuBarCount++;
 		}
 		
+		// Add deleted sample images to commands table
+		pluginsTable.put("Lena (68K)", "ij.plugin.URLOpener(\"lena-std.tif\")");
+		pluginsTable.put("Bridge (174K)", "ij.plugin.URLOpener(\"bridge.gif\")");
+		
 		if (pluginError!=null)
 			error = error!=null?error+="\n"+pluginError:pluginError;
 		if (jarError!=null)
@@ -296,6 +314,7 @@ public class Menus {
 		addExample(submenu, "Custom Measurement", "Custom_Measurement.ijm");
 		addExample(submenu, "Synthetic Images", "Synthetic_Images.ijm");
 		addExample(submenu, "Spiral Rotation", "Spiral_Rotation.ijm");
+		addExample(submenu, "Curve Fitting", "Curve_Fitting.ijm");
 		submenu.addSeparator();
 		addExample(submenu, "Circle Tool", "Circle_Tool.ijm");
 		addExample(submenu, "Star Tool", "Star_Tool.ijm");
@@ -327,6 +346,7 @@ public class Menus {
 		addExample(submenu, "Terabyte VirtualStack", "Terabyte_VirtualStack.js");
 		addExample(submenu, "Event Listener", "Event_Listener.js");
 		addExample(submenu, "FFT Filter", "FFT_Filter.js");
+		addExample(submenu, "Curve Fitting", "Curve_Fitting.js");
 		submenu.addActionListener(listener);
 		menu.add(submenu);
 		submenu = new Menu("BeanShell");
@@ -1148,9 +1168,8 @@ public class Menus {
 		int count = 0;
 		MenuItem mi;
 		popup = new PopupMenu("");
-		if (fontSize!=0)
+		if (fontSize!=0 || scale>1.0)
 			popup.setFont(getFont());
-
 		while (true) {
 			count++;
 			s = Prefs.getString("popup" + (count/10)%10 + count%10);
@@ -1609,12 +1628,17 @@ public class Menus {
 	/** Returns the size (in points) used for the fonts in ImageJ menus. Returns
 		0 if the default font size is being used or if this is a Macintosh. */
 	public static int getFontSize() {
-		return IJ.isMacintosh()?0:fontSize;
+		return fontSize;
+		//return IJ.isMacintosh()?0:fontSize;
 	}
 	
 	public static Font getFont() {
-		if (menuFont==null)
-			menuFont =  new Font("SanSerif", Font.PLAIN, fontSize==0?12:fontSize);
+		if (menuFont==null) {
+			int size = fontSize==0?12:fontSize;
+			size = (int)Math.round(size*scale);
+			menuFont =  new Font("SanSerif", Font.PLAIN, size);
+		}
+		//System.out.println("Menus.getFont: "+scale+" "+fontSize+" "+menuFont);
 		return menuFont;
 	}
 
@@ -1648,4 +1672,26 @@ public class Menus {
 		IJ.showStatus("Menus updated: "+m.nPlugins + " commands, " + m.nMacros + " macros");
 	}
 	
+	public static void updateFont() {
+		scale = (int)Math.round(Prefs.getGuiScale());
+		Font font = getFont();
+		mbar.setFont(font);
+		if (ij!=null)
+			ij.setMenuBar(mbar);
+		popup.setFont(font);
+	}
+	
+	/** Adds a command to the ImageJ menu bar. */
+	public static void add(String menuPath, String plugin) {
+		if (pluginsTable==null)
+			return;
+		int index = menuPath.lastIndexOf(">");
+		if (index==-1 || index==menuPath.length()-1)
+			return;
+		String label = menuPath.substring(index+1, menuPath.length());
+		menuPath = menuPath.substring(0, index);
+		pluginsTable.put(label, plugin);
+		addItem(getMenu(menuPath), label, 0, false);
+	}
+	
 }

ij/Prefs.java

@@ -36,6 +36,7 @@ public class Prefs {
     public static final String DIV_BY_ZERO_VALUE = "div-by-zero";
     public static final String NOISE_SD = "noise.sd";
     public static final String MENU_SIZE = "menu.size";
+    public static final String GUI_SCALE = "gui.scale";
     public static final String THREADS = "threads";
 	public static final String KEY_PREFIX = ".";
  
@@ -169,7 +170,7 @@ public class Prefs {
 	public static boolean splineFitLines;
 	/** Enable this option to workaround a bug with some Linux window
 		managers that causes windows to wander down the screen. */
-	public static boolean doNotSaveWindowLocations = true;
+	public static boolean doNotSaveWindowLocations;
 	/** Use JFileChooser setting changed/ */
 	public static boolean jFileChooserSettingChanged;
 	/** Convert tiff units to microns if pixel width is less than 0.0001 cm. */
@@ -188,43 +189,58 @@ public class Prefs {
 	static Properties props = new Properties(ijPrefs);
 	static String prefsDir;
 	static String imagesURL;
-	static String homeDir; // ImageJ folder
+	static String ImageJDir;
 	static int threads;
 	static int transparentIndex = -1;
 	private static boolean resetPreferences;
-
-	/** Finds and loads the ImageJ configuration file, "IJ_Props.txt".
-		@return	an error message if "IJ_Props.txt" not found.
+	private static double guiScale = 1.0;
+	private static Properties locKeys = new Properties();
+	private static String propertiesPath; // location of custom IJ_Props.txt
+	private static String preferencesPath; // location of custom IJ_Prefs.txt
+
+	/** Finds and loads the configuration file ("IJ_Props.txt")
+	 * and the preferences file ("IJ_Prefs.txt").
+	 * @return	an error message if "IJ_Props.txt" not found.
 	*/
 	public static String load(Object ij, Applet applet) {
-		InputStream f = ij.getClass().getResourceAsStream("/"+PROPS_NAME);
-		if (applet!=null)
-			return loadAppletProps(f, applet);
-		if (homeDir==null)
-			homeDir = System.getProperty("user.dir");
+		if (ImageJDir==null)
+			ImageJDir = System.getProperty("user.dir");
+		InputStream f = null;
+		try { // Look for IJ_Props.txt in ImageJ folder
+			f = new FileInputStream(ImageJDir+"/"+PROPS_NAME);
+			propertiesPath = ImageJDir+"/"+PROPS_NAME;
+		} catch (FileNotFoundException e) {
+			f = null;
+		}
 		if (f==null) {
-			try {f = new FileInputStream(homeDir+"/"+PROPS_NAME);}
-			catch (FileNotFoundException e) {f=null;}
+			// Look in ij.jar if not found in ImageJ folder
+			f = ij.getClass().getResourceAsStream("/"+PROPS_NAME);
 		}			
+		if (applet!=null)
+			return loadAppletProps(f, applet);
 		if (f==null)
-			return PROPS_NAME+" not found in ij.jar or in "+homeDir;
+			return PROPS_NAME+" not found in ij.jar or in "+ImageJDir;
 		f = new BufferedInputStream(f);
-		try {props.load(f); f.close();}
-		catch (IOException e) {return("Error loading "+PROPS_NAME);}
+		try {
+			props.load(f);
+			f.close();
+		} catch (IOException e) {
+			return("Error loading "+PROPS_NAME);
+		}
 		imagesURL = props.getProperty("images.location");
 		loadPreferences();
 		loadOptions();
+		guiScale = get(GUI_SCALE, 1.0);
 		return null;
 	}
 
 	/*
-	static void dumpPrefs(String title) {
-		IJ.log("");
-		IJ.log(title);
+	static void dumpPrefs() {
+		System.out.println("");
 		Enumeration e = ijPrefs.keys();
 		while (e.hasMoreElements()) {
 			String key = (String) e.nextElement();
-			IJ.log(key+": "+ijPrefs.getProperty(key));
+			System.out.println(key+": "+ijPrefs.getProperty(key));
 		}
 	}
 	*/
@@ -258,14 +274,14 @@ public class Prefs {
 	/** Obsolete, replaced by getImageJDir(), which, unlike this method, 
 		returns a path that ends with File.separator. */
 	public static String getHomeDir() {
-		return homeDir;
+		return ImageJDir;
 	}
 
 	/** Returns the path, ending in File.separator, to the ImageJ directory. */
 	public static String getImageJDir() {
 		String path = Menus.getImageJPath();
 		if (path==null)
-			return homeDir + File.separator;
+			return ImageJDir + File.separator;
 		else
 			return path;
 	}
@@ -273,6 +289,15 @@ public class Prefs {
 	/** Returns the path to the directory where the 
 		preferences file (IJPrefs.txt) is saved. */
 	public static String getPrefsDir() {
+		if (prefsDir==null) {
+			if (ImageJDir==null)
+				ImageJDir = System.getProperty("user.dir");
+			File f = new File(ImageJDir+File.separator+PREFS_NAME);
+			if (f.exists()) {
+				prefsDir = ImageJDir;
+				preferencesPath = ImageJDir+"/"+PREFS_NAME;
+			}
+			//System.out.println("getPrefsDir: "+f+"  "+prefsDir);
 			if (prefsDir==null) {
 				String dir = System.getProperty("user.home");
 				if (IJ.isMacOSX())
@@ -281,6 +306,7 @@ public class Prefs {
 					dir += File.separator+".imagej";
 				prefsDir = dir;
 			}
+		}
 		return prefsDir;
 	}
 
@@ -288,7 +314,7 @@ public class Prefs {
 	static void setHomeDir(String path) {
 		if (path.endsWith(File.separator))
 			path = path.substring(0, path.length()-1);
-		homeDir = path;
+		ImageJDir = path;
 	}
 
 	/** Returns the default directory, if any, or null. */
@@ -299,7 +325,7 @@ public class Prefs {
 			return getString(DIR_IMAGE);
 	}
 
-	/** Finds an string in IJ_Props or IJ_Prefs.txt. */
+	/** Finds a string in IJ_Props or IJ_Prefs.txt. */
 	public static String getString(String key) {
 		return props.getProperty(key);
 	}
@@ -366,13 +392,13 @@ public class Prefs {
 		return separator;
 	}
 
-	/** Opens the IJ_Prefs.txt file. */
+	/** Opens the ImageJ preferences file ("IJ_Prefs.txt") file. */
 	static void loadPreferences() {
 		String path = getPrefsDir()+separator+PREFS_NAME;
 		boolean ok =  loadPrefs(path);
 		if (!ok) { // not found
 			if (IJ.isWindows())
-				path = homeDir +separator+PREFS_NAME; // ImageJ folder
+				path = ImageJDir +separator+PREFS_NAME;
 			else
 				path = System.getProperty("user.home")+separator+PREFS_NAME; //User's home dir
 			ok = loadPrefs(path);
@@ -499,6 +525,7 @@ public class Prefs {
 		jFileChooserSettingChanged = (options2&JFILE_CHOOSER_CHANGED)!=0;
 		dialogCancelButtonOnRight = (options2&CANCEL_BUTTON_ON_RIGHT)!=0;
 		ignoreRescaleSlope = (options2&IGNORE_RESCALE_SLOPE)!=0;
+		;
 	}
 
 	static void saveOptions(Properties prefs) {
@@ -622,15 +649,20 @@ public class Prefs {
 		double yloc = Tools.parseDouble(value.substring(index+1));
 		if (Double.isNaN(yloc)) return null;
 		Point p = new Point((int)xloc, (int)yloc);
-		Dimension screen = null;
-		if (IJ.debugMode)
-			screen = Toolkit.getDefaultToolkit().getScreenSize();
-		else
-			screen = IJ.getScreenSize();
-		if (p.x>screen.width-100 || p.y>screen.height-40)
-			return null;
-		else
+		Rectangle bounds = GUI.getScreenBounds(p); // get bounds of screen that contains p
+		if (bounds!=null && p.x+100<=bounds.x+bounds.width && p.y+ 40<=bounds.y+bounds.height) {
+			if (locKeys.get(key)==null) { // first time for this key? 
+				locKeys.setProperty(key, "");
+				Rectangle primaryScreen = GUI.getMaxWindowBounds();
+				ImageJ ij = IJ.getInstance();
+				Point ijLoc = ij!=null?ij.getLocation():null;
+				//System.out.println("getLoc: "+key+" "+(ijLoc!=null&&primaryScreen.contains(ijLoc)) + "  "+!primaryScreen.contains(p));
+				if ((ijLoc!=null&&primaryScreen.contains(ijLoc)) && !primaryScreen.contains(p))
+					return null; // return null if "ImageJ" window on primary screen and this location is not
+			}
 			return p;
+		} else
+			return null;
 	}
 
 	/** Save plugin preferences. */
@@ -686,5 +718,28 @@ public class Prefs {
 		return get("options.ext", ".csv");
 	}
 		
+	/** Sets the GenericDialog and Command Finder text scale (0.5 to 3.0). */
+	public static void setGuiScale(double scale) {
+		if (scale>=0.5 && scale<=3.0) {
+			guiScale = scale;
+			set(GUI_SCALE, guiScale);
+		}
+	}
+
+	/** Returns the GenericDialog and Command Finder text scale. */
+	public static double getGuiScale() {
+		return guiScale;
+	}
+
+	/** Returns the custom properties (IJ_Props.txt) file path. */
+	public static String getCustomPropsPath() {
+		return propertiesPath;
+	}
+
+	/** Returns the custom preferences (IJ_Prefs.txt) file path. */
+	public static String getCustomPrefsPath() {
+		return preferencesPath;
+	}
+
 }
 

ij/Undo.java

@@ -59,8 +59,9 @@ public class Undo {
 			else
 				reset();
 		} else if (what==MACRO) {	
-			impCopy = new ImagePlus(imp.getTitle(), imp.getProcessor().duplicate());
-			whatToUndo = TRANSFORM;
+			ipCopy = imp.getProcessor().duplicate();
+			calCopy = (Calibration)imp.getCalibration().clone();
+			impCopy = null;
 		} else if (what==COMPOUND_FILTER) {
 			ImageProcessor ip = imp.getProcessor();
 			if (ip!=null)
@@ -99,7 +100,6 @@ public class Undo {
 		lutCopy = null;
 	}	
 
-
 	public static void undo() {
 		ImagePlus imp = WindowManager.getCurrentImage();
 		if (IJ.debugMode) IJ.log("Undo.undo: "+ whatToUndo+" "+imp+"  "+impCopy);
@@ -153,6 +153,12 @@ public class Undo {
 				setup(ROI, imp); // setup redo
 				imp.setRoi(roiCopy2);
 				return; //don't reset
+			case MACRO:
+				if (ipCopy!=null) {
+					imp.setProcessor(ipCopy);
+					if (calCopy!=null) imp.setCalibration(calCopy);
+				}
+				break;
 			case OVERLAY_ADDITION:
 				Overlay overlay = imp.getOverlay();
 				if (overlay==null) 

ij/VirtualStack.java

@@ -3,6 +3,7 @@ import ij.process.*;
 import ij.io.*;
 import ij.gui.ImageCanvas;
 import ij.util.Tools;
+import ij.plugin.FolderOpener;
 import java.io.*;
 import java.awt.*;
 import java.awt.image.ColorModel;
@@ -132,8 +133,14 @@ public class VirtualStack extends ImageStack {
 			int type = imp.getType();
 			ColorModel cm = imp.getProcessor().getColorModel();
 			String info = (String)imp.getProperty("Info");
-			if (info!=null && !(info.startsWith("Software")||info.startsWith("ImageDescription")))
+			if (info!=null) {
+				if (FolderOpener.useInfo(info))
 					labels[n-1] = info;
+			} else {
+				String sliceLabel = imp.getStack().getSliceLabel(1);
+				if (FolderOpener.useInfo(sliceLabel))
+					labels[n-1] = "Label: "+sliceLabel;
+			}
 			depthThisImage = imp.getBitDepth();
 			ip = imp.getProcessor();
 			ip.setOverlay(imp.getOverlay());
@@ -189,10 +196,12 @@ public class VirtualStack extends ImageStack {
 		String label = labels[n-1];
 		if (label==null)
 			return names[n-1];
-		else if (label.length()>100 && label.indexOf('\n')>0)
-			return names[n-1]+"\n"+label;
+		else {
+			if (label.startsWith("Label: "))  // slice label
+				return label.substring(7,label.length());
 			else
-			return label;
+				return names[n-1]+"\n"+label;
+		}
 	}
 	
 	/** Returns null. */
@@ -215,7 +224,10 @@ public class VirtualStack extends ImageStack {
 	
 	/** Returns the path to the directory containing the images. */
 	public String getDirectory() {
-		return path;
+		String path2 = path;
+		if (!(path2.endsWith("/") || path2.endsWith(File.separator)))
+			path2 = path2 + "/";
+		return path2;
 	}
 		
 	/** Returns the file name of the specified slice, were 1<=n<=nslices. */

ij/WindowManager.java

@@ -375,7 +375,8 @@ public class WindowManager {
 		int index = imageList.indexOf(win);
 		if (index==-1)
 			return;  // not on the window list
-		imageList.removeElementAt(index);
+		try {
+			imageList.remove(win);
 			activations.remove(win);
 			if (imageList.size()>1 && !Prefs.closingAll) {
 				ImageWindow win2 = activations.size()>0?(ImageWindow)activations.get(activations.size()-1):null;
@@ -389,11 +390,12 @@ public class WindowManager {
 			Menus.removeWindowMenuItem(nonImageCount+index);
 			Menus.updateMenus();
 			Undo.reset();
+		}  catch (Exception e) { }
 	}
 
 	/** The specified Window becomes the front window. */
 	public static void setWindow(Window win) {
-		//System.out.println("setWindow: "+win);
+		//System.out.println("setWindow(W): "+win);
 		frontWindow = win;
 		if (win instanceof Frame)
 			frontFrame = (Frame)win;
@@ -403,7 +405,7 @@ public class WindowManager {
 	public static void setWindow(Frame win) {
 		frontWindow = win;
 		frontFrame = win;
-		//System.out.println("Set window: "+(win!=null?win.getTitle():"null"));
+		//System.out.println("Set window(F): "+(win!=null?win.getTitle():"null"));
     }
 
 	/** Closes all windows. Stops and returns false if an image or Editor "save changes" dialog is canceled. */

ij/gui/Arrow.java

@@ -61,8 +61,7 @@ public class Arrow extends Line {
 		if (fillColor!=null) color = fillColor;
 		g.setColor(color);
 		Graphics2D g2 = (Graphics2D)g;
-		if (!overlay)
-			g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+		setRenderingHint(g2);
 		AffineTransform at = g2.getDeviceConfiguration().getDefaultTransform();
 		double mag = getMagnification();
 		int xbase=0, ybase=0;

ij/gui/ColorChooser.java

@@ -17,6 +17,7 @@ public class ColorChooser implements TextListener, AdjustmentListener {
 	boolean useHSB;
 	String title;
 	Frame frame;
+	double scale = Prefs.getGuiScale();
 
 	/** Constructs a ColorChooser using the specified title and initial color. */
 	public ColorChooser(String title, Color initialColor, boolean useHSB) {
@@ -40,7 +41,7 @@ public class ColorChooser implements TextListener, AdjustmentListener {
 		gd.addSlider("Red:", 0, 255, red);
 		gd.addSlider("Green:", 0, 255, green);
 		gd.addSlider("Blue:", 0, 255, blue);
-		panel = new ColorPanel(initialColor);
+		panel = new ColorPanel(initialColor, scale);
 		gd.addPanel(panel, GridBagConstraints.CENTER, new Insets(10, 0, 0, 0));
 		colors = gd.getNumericFields();
 		for (int i=0; i<colors.size(); i++)
@@ -80,16 +81,19 @@ public class ColorChooser implements TextListener, AdjustmentListener {
 }
 
 class ColorPanel extends Panel {
-	static final int WIDTH=150, HEIGHT=50;
-	static Font font = new Font("Monospaced", Font.PLAIN, 18);
-	Color c;
+	private int width=150, height=50;
+	private Font font;
+	private Color c;
 	 
-	ColorPanel(Color c) {
+	ColorPanel(Color c, double scale) {
 		this.c = c;
+		width = (int)(width*scale);
+		height = (int)(height*scale);
+		font = new Font("Monospaced", Font.PLAIN, (int)(18*scale));
 	}
 
 	public Dimension getPreferredSize() {
-		return new Dimension(WIDTH, HEIGHT);
+		return new Dimension(width, height);
 	}
 
 	void setColor(Color c) {
@@ -97,21 +101,21 @@ class ColorPanel extends Panel {
 	}
 
 	public Dimension getMinimumSize() {
-		return new Dimension(WIDTH, HEIGHT);
+		return new Dimension(width, height);
 	}
 
 	public void paint(Graphics g) {
 		g.setColor(c);
-		g.fillRect(0, 0, WIDTH, HEIGHT);
+		g.fillRect(0, 0, width, height);
 		int intensity = (c.getRed()+c.getGreen()+c.getBlue())/3;
 		Color c2 = intensity<128?Color.white:Color.black;
 		g.setColor(c2);
 		g.setFont(font);
 		Java2.setAntialiasedText(g, true);
 		String s = Colors.colorToString(c);
-		g.drawString(s, 5, HEIGHT-5);
+		g.drawString(s, 5, height-5);
 		g.setColor(Color.black);
-		g.drawRect(0, 0, WIDTH-1, HEIGHT-1);
+		g.drawRect(0, 0, width-1, height-1);
 	}
 
 }

ij/gui/EllipseRoi.java

@@ -243,13 +243,22 @@ public class EllipseRoi extends PolygonRoi {
 			pw = cal.pixelWidth;
 			ph = cal.pixelHeight;
 		}
+		if (pw != ph)    //the following calculation holds only for pixel aspect ratio == 1 (otherwise different axes in distorted ellipse)
+			return a;
 		double[] p = getParams();
-		double dx = (p[2] - p[0])*pw;
-		double dy = (p[3] - p[1])*ph;
+		double dx = p[2] - p[0];  //this is always major axis; aspect ratio p[4] is limited to <= 1
+		double dy = p[3] - p[1];
 		double major = Math.sqrt(dx*dx + dy*dy);
 		double minor = major*p[4];
-		a[0] = major;
-		a[2] = (pw==ph)?minor:a[2];
+		a[0] = major*pw; //Feret from convex hull should be accurate anyhow
+		a[2] = minor*pw; //here our own calculation is better
+		System.arraycopy(p, 0, a, 8, 4);  //MaxFeret endpoints
+		double xCenter = 0.5*(p[2] + p[0]);
+		double yCenter = 0.5*(p[3] + p[1]);
+		double semiMinorX = dy * 0.5 * p[4];
+		double semiMinorY = dx * (-0.5) * p[4];
+		a[12] = xCenter + semiMinorX; a[14] = xCenter - semiMinorX;
+		a[13] = yCenter + semiMinorY; a[15] = yCenter - semiMinorY;
 		return a;
 	}