New upstream version 1.52i (7ff3890b) · Commits · Debian Med / imagej

IJ_Props.txt

+11 −9

Original line number	Diff line number	Diff line
		@@ -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

ij/CompositeImage.java

+5 −1

Original line number	Diff line number	Diff line
		@@ -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

+12 −5

Original line number	Diff line number	Diff line
		@@ -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

+3 −3

Original line number	Diff line number	Diff line
		@@ -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

+98 −41

Original line number	Diff line number	Diff line
		@@ -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 \|\| channelsslicesframes!=newStack.getSize())
		throw new IllegalArgumentException("channelsslicesframes!=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)nChannelsnSlices + (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);