IJ_Props.txt

@@ -153,8 +153,8 @@ stacks10="Reslice [/]...",ij.plugin.Slicer
 stacks11="Orthogonal Views[H]",ij.plugin.Orthogonal_Views
 stacks12="Z Project...",ij.plugin.ZProjector
 stacks13="3D Project...",ij.plugin.Projector
-stacks14="Plot XY Profile",ij.plugin.StackPlotter
-stacks15="Plot Z-axis Profile",ij.plugin.ZAxisProfiler
+stacks14="Plot Z-axis Profile",ij.plugin.ZAxisProfiler
+stacks15="Measure Stack...",ij.plugin.SimpleCommands("measure")
 stacks16="Label...",ij.plugin.filter.StackLabeler
 stacks17="Statistics",ij.plugin.Stack_Statistics
 
@@ -166,14 +166,16 @@ animation_03="Animation Options...",ij.plugin.Animator("options")
 # Plugins installed in the Image/Stacks/Tools submenu
 tools_01="Combine...",ij.plugin.StackCombiner
 tools_02="Concatenate...",ij.plugin.Concatenator
-tools_03="Reduce...",ij.plugin.StackReducer
-tools_04="Reverse",ij.plugin.StackReverser
-tools_05="Insert...",ij.plugin.StackInserter
-tools_06="Montage to Stack...",ij.plugin.StackMaker
-tools_07="Make Substack...",ij.plugin.SubstackMaker
-tools_08="Grouped Z Project...",ij.plugin.GroupedZProjector
-tools_09="Set Label...",ij.plugin.SimpleCommands("set")
+tools_03="Grouped Z Project...",ij.plugin.GroupedZProjector
+tools_04="Insert...",ij.plugin.StackInserter
+tools_05="Magic Montage Tools",ij.plugin.SimpleCommands("magic")
+tools_06="Make Substack...",ij.plugin.SubstackMaker
+tools_07="Montage to Stack...",ij.plugin.StackMaker
+tools_08="Plot XY Profile",ij.plugin.StackPlotter
+tools_09="Reduce...",ij.plugin.StackReducer
 tools_10="Remove Slice Labels",ij.plugin.SimpleCommands("remove")
+tools_11="Reverse",ij.plugin.StackReverser
+tools_12="Set Label...",ij.plugin.SimpleCommands("set")
 
 # Plugins installed in the Image/Hyperstacks submenu
 hyperstacks01="New Hyperstack...",ij.plugin.HyperStackMaker

debian/changelog

+imagej (1.52i-1) UNRELEASED; urgency=medium
+
+  * New upstream version 1.52i
+
+ -- David Miguel Susano Pinto <carandraug+dev@gmail.com>  Wed, 12 Dec 2018 17:57:38 +0000
+
 imagej (1.52g-1) unstable; urgency=medium
 
   * Team upload.
@@ -465,4 +471,3 @@ imagej (1.37m-1) unstable; urgency=low
   * Initial release (Closes: #4526773, #6353442).
 
  -- Paolo Ariano <paolo.ariano@unito.it>  Fri, 28 Apr 2006 11:41:53 +0200
-

debian/pom.xml

@@ -8,13 +8,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>16.2.0</version>
+		<version>23.2.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>net.imagej</groupId>
 	<artifactId>ij</artifactId>
-	<version>1.51p</version>
+	<version>1.52i</version>
 
 	<name>ImageJ</name>
 	<description>ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.</description>
@@ -61,11 +61,8 @@
 			<archive>https://list.nih.gov/archives/imagej.html</archive>
 		</mailingList>
 		<mailingList>
-			<name>ImageJ-devel</name>
-			<subscribe>https://imagej.net/mailman/listinfo/imagej-devel</subscribe>
-			<unsubscribe>https://imagej.net/mailman/listinfo/imagej-devel</unsubscribe>
-			<post>imagej-devel@imagej.net</post>
-			<archive>https://imagej.net/pipermail/imagej-devel/</archive>
+			<name>Image.sc Forum</name>
+			<archive>https://forum.image.sc/</archive>
 		</mailingList>
 	</mailingLists>
 
@@ -90,6 +87,7 @@
 		<license.copyrightOwners>N/A</license.copyrightOwners>
 
 		<scijava.jvm.version>1.6</scijava.jvm.version>
+		<scijava.jvm.build.version>1.6</scijava.jvm.build.version>
 		<javac.path>${java.home}/../lib/tools.jar</javac.path>
 	</properties>
 

debian/upstream/metadata

@@ -17,5 +17,3 @@ Registry:
    Entry: imagej
  - Name: SciCrunch
    Entry: SCR_003070
- - Name: OMICtools
-   Entry: OMICS_13947

ij/CompositeImage.java

@@ -315,7 +315,6 @@ public class CompositeImage extends ImagePlus {
 			imageSource.newPixels();	
 	}
 
-	/** Uses less memory but only works correctly with Java 1.6 and later. */
 	void createBufferedImage() {
 		if (rgbSampleModel==null)
 			rgbSampleModel = getRGBSampleModel();
@@ -510,6 +509,11 @@ public class CompositeImage extends ImagePlus {
 		setup(nChannels, getImageStack());
 	}
 	
+	public void completeReset() {
+		cip = null;
+		lut = null;
+	}
+	
 	/* Sets the LUT of the current channel. */
 	public void setChannelLut(LUT table) {
 		int c = getChannelIndex();

ij/IJ.java

@@ -642,8 +642,8 @@ public class IJ {
 	}
 
 	/** Displays a message in a dialog box titled "ImageJ". If a 
-		macro is running, it is aborted. Writes to the Java console
-		if the ImageJ window is not present.*/
+		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) {
 		error(null, msg);
 		if (Thread.currentThread().getName().endsWith("JavaScript"))
@@ -652,9 +652,9 @@ public class IJ {
 			Macro.abort();
 	}
 	
-	/**Displays a message in a dialog box with the specified title.
-		If a macro is running, it is aborted. Writes to the Java  
-		console if ImageJ is not present. */
+	/** Displays a message in a dialog box with the specified title. If a 
+		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 (msg!=null && msg.endsWith(Macro.MACRO_CANCELED))
 			return;
@@ -672,6 +672,13 @@ public class IJ {
 			Macro.abort();
 	}
 
+	/** Aborts any currently running JavaScript, or use IJ.error(string)
+		to abort a JavaScript with a message. */
+	public static void exit() {
+		if (Thread.currentThread().getName().endsWith("JavaScript"))
+			throw new RuntimeException(Macro.MACRO_CANCELED);
+	}
+
 	/** 
 	 * Returns the last error message written by IJ.error() or null if there
 	 * was no error since the last time this method was called.

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 = "1.52g";
-	public static final String BUILD = "";  //5
+	public static final String VERSION = "1.52i";
+	public static final String BUILD = "";  //52
 	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);
@@ -418,7 +418,7 @@ public class ImageJ extends Frame implements ActionListener,
 		ImagePlus imp = WindowManager.getCurrentImage();
 		boolean isStack = (imp!=null) && (imp.getStackSize()>1);
 		
-		if (imp!=null && ((keyChar>=32 && keyChar<=255) || keyChar=='\b' || keyChar=='\n')) {
+		if (imp!=null && !meta && ((keyChar>=32 && keyChar<=255) || keyChar=='\b' || keyChar=='\n')) {
 			Roi roi = imp.getRoi();
 			if (roi!=null && roi instanceof TextRoi) {
 				if (imp.getOverlay()!=null && (control || alt || meta)

ij/ImagePlus.java

@@ -90,6 +90,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 	private boolean noUpdateMode;
 	private ImageCanvas flatteningCanvas;
 	private Overlay overlay;
+	private boolean compositeChanges;
 	private boolean hideOverlay;
 	private static int default16bitDisplayRange;
 	private boolean antialiasRendering = true;
@@ -156,7 +157,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
     
     private void setID() {
     	ID = --currentID;
-    	//IJ.log("New "+this);
 	}
 	   
 	/** Locks the image so other threads can test to see if it
@@ -556,28 +556,38 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		if (newProperties!=null)
 			newProperties = (Properties)(newProperties.clone());
 		if (imp.getWindow()!=null)
-			imp = imp.duplicate();
+			imp = imp.duplicateAll();
 		ImageStack stack2 = imp.getStack();
 		if (imp.isHyperStack())
 			setOpenAsHyperStack(true);
 		LUT[] luts = null;
-		if (imp.isComposite() && this.isComposite()) {
+		if (imp.isComposite() && (this instanceof CompositeImage)) {
 			if (((CompositeImage)imp).getMode()!=((CompositeImage)this).getMode())
 				((CompositeImage)this).setMode(((CompositeImage)imp).getMode());
 			luts = ((CompositeImage)imp).getLuts();
 		}
+		LUT lut = !imp.isComposite()?imp.getProcessor().getLut():null;
 		setStack(stack2, imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
+		compositeImage = imp.isComposite();
 		if (luts!=null) {
 			((CompositeImage)this).setLuts(luts);
-			updateAndDraw();
+			((CompositeImage)this).setMode(((CompositeImage)imp).getMode());
+			updateAndRepaintWindow();
+		} else if (lut!=null) {
+			getProcessor().setLut(lut);
+			updateAndRepaintWindow();
 		}
+		setTitle(imp.getTitle());
 		setCalibration(imp.getCalibration());
+		setOverlay(imp.getOverlay());
 		properties = newProperties;		
 		if (getProperty(Plot.PROPERTY_KEY)!=null && win instanceof PlotWindow) {
 			Plot plot = (Plot)(getProperty(Plot.PROPERTY_KEY));
 			((PlotWindow)win).setPlot(plot);
 			plot.setImagePlus(this);
 		}
+		setFileInfo(imp.getOriginalFileInfo());
+		setProperty ("Info", imp.getProperty ("Info"));
 	}
 	
 	/** Replaces the ImageProcessor with the one specified and updates the
@@ -659,9 +669,10 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 	/** Replaces the image with the specified stack and updates 
 		the display. Set 'title' to null to leave the title unchanged. */
     public void setStack(String title, ImageStack newStack) {
+		//IJ.log("setStack1: "+nChannels+" "+nSlices+" "+nFrames);
+		int bitDepth1 = getBitDepth();
 		int previousStackSize = getStackSize();
 		int newStackSize = newStack.getSize();
-		//IJ.log("setStack: "+newStackSize+" "+this);
 		if (newStackSize==0)
 			throw new IllegalArgumentException("Stack is empty");
 		if (!newStack.isVirtual()) {
@@ -687,16 +698,25 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
     	this.stack = newStack;
     	oneSliceStack = false;
     	setProcessor2(title, ip, newStack);
+		if (bitDepth1!=0 && bitDepth1!=getBitDepth())
+			compositeChanges = true;
+		if (compositeChanges && (this instanceof CompositeImage)) {
+			this.compositeImage = getStackSize()!=getNSlices();
+			((CompositeImage)this).completeReset();
+			if (bitDepth1!=0 && bitDepth1!=getBitDepth())
+				((CompositeImage)this).resetDisplayRanges();
+		}
+		compositeChanges = false;
 		if (win==null) {
 			if (resetCurrentSlice) setSlice(currentSlice);
 			return;
 		}
-		boolean invalidDimensions = (isDisplayedHyperStack()||isComposite()) && (win instanceof StackWindow) && !((StackWindow)win).validDimensions();
+		boolean invalidDimensions = (isDisplayedHyperStack()||(this instanceof CompositeImage)) && (win instanceof StackWindow) && !((StackWindow)win).validDimensions();
 		if (newStackSize>1 && !(win instanceof StackWindow)) {
 			if (isDisplayedHyperStack())
 				setOpenAsHyperStack(true);
 			activated = false;
-			win = new StackWindow(this, getCanvas());   // replaces this window
+			win = new StackWindow(this, dimensionsChanged?null:getCanvas());   // replaces this window
 			if (IJ.isMacro()) { // wait for stack window to be activated
 				long start = System.currentTimeMillis();
 				while (!activated) {
@@ -724,24 +744,16 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		}
 		if (resetCurrentSlice)
 			setSlice(currentSlice);
-		if (isComposite() && previousStackSize!=newStackSize)
-			compositeImage = false;
     }
     
 	public void setStack(ImageStack newStack, int channels, int slices, int frames) {
 		if (newStack==null || channels*slices*frames!=newStack.getSize())
 			throw new IllegalArgumentException("channels*slices*frames!=stackSize");
-		int channelsBefore = this.nChannels;
-		if (IJ.debugMode) IJ.log("setStack: "+newStack.getSize()+" "+channels+" ("+channelsBefore+") "+slices+" "+frames+" "+isComposite());
+		if (IJ.debugMode) IJ.log("setStack: "+newStack.getSize()+" "+channels+" "+slices+" "+frames+" "+isComposite());
+		compositeChanges = channels!=this.nChannels;
 		this.nChannels = channels;
 		this.nSlices = slices;
 		this.nFrames = frames;
-		if (channelsBefore!=channels && isComposite()) {
-			ImageStack stack2 = this.stack;
-			this.stack = newStack;
-			((CompositeImage)this).reset();
-			this.stack = stack2;
-		}
 		setStack(null, newStack);
 	}
 
@@ -863,7 +875,9 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 	}
 	
 	/** Returns an 8-bit binary (0 and 255) ROI or overlay mask
-	 *  that has the same dimensions as this image.
+	 *  that has the same dimensions as this image. Creates an
+	 * ROI mask If the image has both an ROI and an overlay.
+	 * @see #createThresholdMask
 	 * @see ij.gui.Roi#getMask
 	*/
 	public ByteProcessor createRoiMask() {
@@ -873,11 +887,23 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			throw new IllegalArgumentException("ROI or overlay required");
 		ByteProcessor mask = new ByteProcessor(getWidth(),getHeight());
 		mask.setColor(255);
-		if (overlay2!=null) {
+		if (roi2!=null)
+			mask.fill(roi2);
+		else if (overlay2!=null) {
+			if (overlay2.size()==1 && (overlay2.get(0) instanceof ImageRoi)) {
+				ImageRoi iRoi = (ImageRoi)overlay2.get(0);
+				ImageProcessor ip = iRoi.getProcessor();
+				if (ip.getWidth()!=mask.getWidth() || ip.getHeight()!=mask.getHeight())
+					return mask;
+				for (int i=0; i<ip.getPixelCount(); i++) {
+					if (ip.get(i)!=0)
+						mask.set(i, 255);
+				}
+			} else {
 				for (int i=0; i<overlay2.size(); i++)
 					mask.fill(overlay2.get(i));	
-		} else if (roi2!=null)
-			mask.fill(roi2);
+			}		
+		} 
 		return mask;
 	}
 
@@ -1012,14 +1038,28 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			notifyListeners(UPDATED);
     }
 
+    /** Returns the width of this image in pixels. */
     public int getWidth() {
     	return width;
     }
 
+    /** Returns the height of this image in pixels. */
     public int getHeight() {
     	return height;
     }
     
+    /** Returns the size of this image in bytes. */
+    public double getSizeInBytes() {
+    	double size = ((double)getWidth()*getHeight()*getStackSize());
+		int type = getType();
+    	switch (type) {
+	    	case ImagePlus.GRAY16: size *= 2.0; break;
+	    	case ImagePlus.GRAY32: size *= 4.0; break;
+	    	case ImagePlus.COLOR_RGB: size *= 4.0; break;
+    	}
+    	return size;
+	}
+    
 	/** If this is a stack, returns the number of slices, else returns 1. */
 	public int getStackSize() {
 		if (stack==null || oneSliceStack)
@@ -1074,7 +1114,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			new StackWindow(this);
 		}
 		dimensionsSet = true;
-		//IJ.log("setDimensions: "+ nChannels+"  "+nSlices+"  "+nFrames);
 	}
 	
 	/** Returns 'true' if this image is a hyperstack. */
@@ -1105,7 +1144,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 
 	/** Returns the image depth (number of z-slices). */
 	public int getNSlices() {
-		//IJ.log("getNSlices: "+ nChannels+"  "+nSlices+"  "+nFrames);
 		verifyDimensions();
 		return nSlices;
 	}
@@ -1268,6 +1306,8 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		index1 = findKey(info, key+": "); // standard 'key: value' pair?
 		if (index1<0) // Bio-Formats metadata?
 			index1 = findKey(info, key+" = ");
+		if (index1<0) // '=' with no spaces
+			index1 = findKey(info, key+"=");
 		if (index1<0) // otherwise not found
 			return null;
 		if (index1==info.length())
@@ -1519,7 +1559,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			boolean channelChanged = channel!=getChannel();
 			setSlice((frame-1)*nChannels*nSlices + (slice-1)*nChannels + channel);
 			updatePosition(channel, slice, frame);
-			if (channelChanged && isComposite())
+			if (channelChanged && isComposite() && !noUpdateMode)
 				updateImage();
 		}
 	}
@@ -1724,8 +1764,14 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 				ip.resetRoi();
 		}
 		roi.setImage(this);
+		if ((roi instanceof PointRoi) && ((PointRoi)roi).addToOverlay()) {
+			IJ.run(this, "Add Selection...", "");
+			roi = null;
+			return;
+		}
 		if (updateDisplay)
 			draw();
+		if (roi!=null)
 			roi.notifyListeners(RoiListener.CREATED);
 	}
 	
@@ -1743,6 +1789,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		starting screen coordinates. The selection type is determined by which tool in
 		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();
 		switch (Toolbar.getToolId()) {
 			case Toolbar.RECTANGLE:
@@ -1774,6 +1821,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 				break;
 			case Toolbar.TEXT:
 				roi = new TextRoi(sx, sy, this);
+				((TextRoi)roi).setPreviousRoi(previousRoi);
 				break;
 			case Toolbar.POINT:
 				roi = new PointRoi(sx, sy, this);
@@ -1924,7 +1972,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			url2 = fi.url;
 		} else
 			return;
-		//IJ.log("revert: "+path+"  "+fi);
 		IJ.showStatus("Loading: " + path);
 		ImagePlus imp = IJ.openImage(path);
 		if (imp!=null) {
@@ -2096,6 +2143,7 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 	
 
 	/** Returns a copy of this image or stack, cropped if there is an ROI.
+	* @see #duplicateAll
 	* @see #crop
 	* @see ij.plugin.Duplicator#run
 	*/
@@ -2103,8 +2151,21 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		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);
+		setRoi(roi);
+		return imp2;
+	}
+
 	/** 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() {
@@ -2381,8 +2442,6 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 			case ImagePlus.GRAY16: bytesPerPixel = 2; break;
 			case ImagePlus.GRAY32: case ImagePlus.COLOR_RGB: bytesPerPixel = 4;
 		}
-		//Roi roi3 = clipboard.getRoi();
-		//IJ.log("copy: "+clipboard +" "+ "roi3="+(roi3!=null?""+roi3:""));
 		if (!batchMode) {
 			msg = (cut)?"Cut":"Copy";
 			IJ.showStatus(msg + ": " + (clipboard.getWidth()*clipboard.getHeight()*bytesPerPixel)/1024 + "k");
@@ -2411,13 +2470,11 @@ public class ImagePlus implements ImageObserver, Measurements, Cloneable {
 		if (cr==null)
 			cr = new Rectangle(0, 0, w, h);
 		if (r==null || (cr.width!=r.width || cr.height!=r.height)) {		
-			// create a new roi centered on visible part of image
-			ImageCanvas ic = null;
-			if (win!=null)
-				ic = win.getCanvas();
+			// Create a new roi centered on visible part of image, or centered on image if clipboard is >= image
+			ImageCanvas ic = win!=null?ic = win.getCanvas():null;
 			Rectangle srcRect = ic!=null?ic.getSrcRect():new Rectangle(0,0,width,height);
-			int xCenter = srcRect.x + srcRect.width/2;
-			int yCenter = srcRect.y + srcRect.height/2;
+			int xCenter = w>=width ? width/2 : srcRect.x + srcRect.width/2;
+			int yCenter = h>=height ? height/2 : srcRect.y + srcRect.height/2;
 			if (cRoi!=null && cRoi.getType()!=Roi.RECTANGLE) {
 				cRoi.setImage(this);
 				cRoi.setLocation(xCenter-w/2, yCenter-h/2);

ij/Menus.java

@@ -276,6 +276,8 @@ public class Menus {
 		addExample(submenu, "Histograms", "Histograms_.ijm");
 		addExample(submenu, "Bar Charts", "Bar_Charts_.ijm");
 		addExample(submenu, "Shapes", "Plot_Shapes_.ijm");
+		addExample(submenu, "Plot Styles", "Plot_Styles_.ijm");
+		addExample(submenu, "Random Data", "Random_Data_.ijm");
 		submenu.addActionListener(listener);
 		menu.add(submenu);
 		
@@ -311,6 +313,8 @@ public class Menus {
 		addExample(submenu, "Semi-log Plot", "Semi-log_Plot.js");
 		addExample(submenu, "Arrow Plot", "Arrow_Plot.js");
 		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, "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

@@ -178,6 +178,8 @@ public class Prefs {
 	public static boolean closingAll;
 	/** Dialog "Cancel" button is on right on Linux */
 	public static boolean dialogCancelButtonOnRight;
+	/** Support TRANSFORM Undo in macros */
+	public static boolean supportMacroUndo;
 
 	static boolean commandLineMacro;
 	static Properties ijPrefs = new Properties();

ij/Undo.java

@@ -12,11 +12,14 @@ import java.awt.image.*;
 public class Undo {
 
 	public static final int NOTHING = 0;
+	/** Undo using ImageProcessor.snapshot. */
 	public static final int FILTER = 1;
+	/** Undo using an ImageProcessor copy. */
 	public static final int TYPE_CONVERSION = 2;
 	public static final int PASTE = 3;
 	public static final int COMPOUND_FILTER = 4;
 	public static final int COMPOUND_FILTER_DONE = 5;
+	/** Undo using a single image, or composite color stack, copy (limited to 200MB). */
 	public static final int TRANSFORM = 6;
 	public static final int OVERLAY_ADDITION = 7;
 	public static final int ROI = 8;
@@ -51,8 +54,10 @@ public class Undo {
 			ipCopy = imp.getProcessor();
 			calCopy = (Calibration)imp.getCalibration().clone();
 		} else if (what==TRANSFORM) {	
-			if (!IJ.macroRunning())
-				impCopy = new ImagePlus(imp.getTitle(), imp.getProcessor().duplicate());
+			if ((!IJ.macroRunning()||Prefs.supportMacroUndo) && (imp.getStackSize()==1||imp.getDisplayMode()==IJ.COMPOSITE) && imp.getSizeInBytes()<209715200)
+				impCopy = imp.duplicateAll();
+			else
+				reset();
 		} else if (what==MACRO) {	
 			impCopy = new ImagePlus(imp.getTitle(), imp.getProcessor().duplicate());
 			whatToUndo = TRANSFORM;
@@ -82,6 +87,7 @@ public class Undo {
 	}
 		
 	public static void reset() {
+		if (IJ.debugMode) IJ.log("Undo.reset: "+ whatToUndo+" "+impCopy);
 		if (whatToUndo==COMPOUND_FILTER || whatToUndo==OVERLAY_ADDITION)
 			return;
 		whatToUndo = NOTHING;
@@ -91,13 +97,12 @@ public class Undo {
 		calCopy = null;
 		roiCopy = null;
 		lutCopy = null;
-		//if (IJ.debugMode) IJ.log("Undo.reset");
 	}
 	
 
 	public static void undo() {
 		ImagePlus imp = WindowManager.getCurrentImage();
-		if (IJ.debugMode) IJ.log("Undo.undo: "+ whatToUndo+" "+imp+" "+imageID);
+		if (IJ.debugMode) IJ.log("Undo.undo: "+ whatToUndo+" "+imp+"  "+impCopy);
 		if (imp==null || imageID!=imp.getID()) {
 			if (imp!=null && !IJ.macroRunning()) { // does image still have an undo buffer?
 				ImageProcessor ip2 = imp.getProcessor();
@@ -113,8 +118,6 @@ public class Undo {
 				if (ip!=null) {
 					if (!IJ.macroRunning()) {
 						ip.swapPixelArrays();
-						//IJ.log("undo-filter: "+displayRangeMin+" "+displayRangeMax);
-						//ip.setMinAndMax(displayRangeMin,displayRangeMax);
 						imp.updateAndDraw();
 						return; // don't reset
 					} else {
@@ -138,7 +141,7 @@ public class Undo {
 				break;
 			case TRANSFORM:
 				if (impCopy!=null)
-					imp.setProcessor(impCopy.getTitle(), impCopy.getProcessor());
+					imp.setStack(impCopy.getStack());
 				break;
 			case PASTE:
 				Roi roi = imp.getRoi();

ij/gui/GUI.java

@@ -54,7 +54,7 @@ public class GUI {
 	public static Rectangle getZeroBasedMaxBounds() {
 		if (maxBounds==null)
 			getMaxWindowBounds();
-		if (IJ.debugMode) IJ.log("GUI.getZeroBasedMaxBounds: "+zeroBasedMaxBounds);
+		//if (IJ.debugMode) IJ.log("GUI.getZeroBasedMaxBounds: "+zeroBasedMaxBounds);
 		return zeroBasedMaxBounds;
 	}
 	
@@ -110,7 +110,7 @@ public class GUI {
 					break;
 			}
 		}
-		if (IJ.debugMode) IJ.log("GUI.getZeroBasedMonitor: "+bounds2);
+		//if (IJ.debugMode) IJ.log("GUI.getZeroBasedMonitor: "+bounds2);
 		if (bounds2!=null) {
 			bounds = bounds2;
 			zeroBasedMaxBounds = bounds2;

ij/gui/GenericDialog.java

@@ -1508,13 +1508,17 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
 
 	public void paint(Graphics g) {
 		super.paint(g);		
-		if (firstPaint && IJ.isMacOSX() && IJ.isJava18()) {
-			IJ.wait(25);
+		if (firstPaint && IJ.isMacOSX() && IJ.isJava18()) { // fix for incompletely drawn dialogs on Macs
+			EventQueue.invokeLater(new Runnable() {
+				public void run() {
+					IJ.wait(50);
 					Dimension size = getSize();
 					if (size!=null)
 						setSize(size.width+2,size.height+2);
 					firstPaint = false;
 				}
+			});
+		}
 	}
 
     public void windowClosing(WindowEvent e) {
@@ -1532,9 +1536,12 @@ FocusListener, ItemListener, KeyListener, AdjustmentListener, WindowListener {
     }
 
 	void showHelp() {
-		if (helpURL.startsWith("<html>"))
-			new HTMLDialog(this, "", helpURL);
-		else {
+		if (helpURL.startsWith("<html>")) {	
+			if (this instanceof NonBlockingGenericDialog)
+				new HTMLDialog("", helpURL, false); // non blocking
+			else
+				new HTMLDialog(this, "", helpURL); //modal
+		} else {
 			String macro = "run('URL...', 'url="+helpURL+"');";
 			new MacroRunner(macro);
 		}

ij/gui/HistogramWindow.java

@@ -506,24 +506,6 @@ public class HistogramWindow extends ImageWindow implements Measurements, Action
 		this.imp.updateAndDraw();
 	}
 		
-	/*
-	void rescale() {
-		Graphics g = img.getGraphics();
-		plotScale *= 2;
-		if ((newMaxCount/plotScale)<50) {
-			plotScale = 1;
-			frame = new Rectangle(XMARGIN, YMARGIN, HIST_WIDTH, HIST_HEIGHT);
-			g.setColor(Color.white);
-			g.fillRect(frame.x, frame.y, frame.width, frame.height);
-			g.setColor(Color.black);
-		}
-		drawPlot(newMaxCount/plotScale, g);
-		//ImageProcessor ip = new ColorProcessor(img);
-		//this.imp.setProcessor(null, ip);
-		this.imp.setImage(img);
-	}
-	*/
-	
 	public void actionPerformed(ActionEvent e) {
 		Object b = e.getSource();
 		if (b==live)

ij/gui/ImageRoi.java

@@ -126,6 +126,7 @@ public class ImageRoi extends Roi {
 		ImagePlus imp = new ImagePlus("", img);
 		roi2.setProcessor(imp.getProcessor());
 		roi2.setOpacity(getOpacity());
+		roi2.zeroTransparent = !zeroTransparent;
 		roi2.setZeroTransparent(zeroTransparent);
 		return roi2;
 	}

ij/gui/ImageWindow.java

@@ -353,13 +353,7 @@ public class ImageWindow extends Frame implements FocusListener, WindowListener,
     public static String getImageSize(ImagePlus imp) {
     	if (imp==null)
     		return null;
-		double size = ((double)imp.getWidth()*imp.getHeight()*imp.getStackSize())/1024.0;
-		int type = imp.getType();
-    	switch (type) {
-	    	case ImagePlus.GRAY16: size *= 2.0; break;
-	    	case ImagePlus.GRAY32: size *= 4.0; break;
-	    	case ImagePlus.COLOR_RGB: size *= 4.0; break;
-    	}
+    	double size = imp.getSizeInBytes()/1024.0;
    		String s2=null, s3=null;
     	if (size<1024.0)
     		{s2=IJ.d2s(size,0); s3="K";}

ij/gui/Line.java

@@ -612,6 +612,7 @@ public class Line extends Roi {
 			case KeyEvent.VK_RIGHT: x2R+=inc; break;
 		}
 		grow(ic.screenXD(x+x2R), ic.screenYD(y+y2R));
+		notifyListeners(RoiListener.MOVED);
 	}
 	
 	public boolean getDrawOffset() {

ij/gui/Overlay.java

@@ -90,6 +90,15 @@ public class Overlay {
     	}
     }
     
+    /** Returns the ROI with the specified name or null if not found. */
+    public Roi get(String name) {
+    	int index = getIndex(name);
+    	if (index==-1)
+    		return null;
+    	else
+    		return get(index);   		
+    }
+
     /** Returns the index of the ROI with the specified name, or -1 if not found. */
     public int getIndex(String name) {
     	if (name==null) return -1;