New upstream version 1.52d (a91eca7c) · Commits · Debian Med / imagej

IJ_Props.txt

+0 −1

Original line number	Diff line number	Diff line
		@@ -414,7 +414,6 @@ new_07="Plugin Frame",ij.plugin.NewPlugin("frame")
		new_08="Plugin Tool",ij.plugin.NewPlugin("plugin-tool")
		new_09=-
		new_10="Text Window...",ij.plugin.NewPlugin("text+dialog")
		new_11="Table...",ij.plugin.NewPlugin("table")

		# Plugins installed in the Help/About submenu
		about01="About This Submenu...",ij.plugin.SimpleCommands("about")

build.xml

+1 −1

Original line number	Diff line number	Diff line
		@@ -6,7 +6,7 @@
		<!-- First, ensure the build directory exists. -->
		<mkdir dir="build" />
		<!-- Build everything; add debug="on" to debug -->
		<javac srcdir="./ij" destdir="build" optimize="on" source="1.5" target="1.5" debug="on" includeantruntime="false" encoding="utf-8">
		<javac srcdir="./ij" destdir="build" optimize="on" source="1.6" target="1.6" debug="on" includeantruntime="false" encoding="utf-8">
		</javac>
		</target>

ij/Executer.java

+8 −47

Original line number	Diff line number	Diff line
		@@ -146,58 +146,19 @@ public class Executer implements Runnable {
		if (openRecent(cmd))
		return;
		// is it an example in Help>Examples menu?
		if (openExample(cmd))
		if (Editor.openExample(cmd))
		return;
		if ("Auto Threshold".equals(cmd)&&(String)table.get("Auto Threshold...")!=null)
		runCommand("Auto Threshold...");
		else if ("Enhance Local Contrast (CLAHE)".equals(cmd)&&(String)table.get("CLAHE ")!=null)
		runCommand("CLAHE ");
		else {
		if ("Table...".equals(cmd))
		IJ.runPlugIn("ij.plugin.NewPlugin", "table");
		else
		IJ.error("Unrecognized command: \"" + cmd+"\"");
		}
		}

		private boolean openExample(String name) {
		boolean isMacro = name.endsWith(".ijm");
		boolean isJava = name.endsWith(".java");
		boolean isJavaScript = name.endsWith(".js");
		boolean isBeanShell = name.endsWith(".bsh");
		boolean isPython = name.endsWith(".py");
		if (!(isMacro\|\|isJava\|\|isJavaScript\|\|isBeanShell\|\|isPython))
		return false;
		boolean run = !isJava && (Prefs.autoRunExamples\|\|IJ.shiftKeyDown()\|\|IJ.controlKeyDown()\|\|IJ.altKeyDown());
		int rows = 24;
		int columns = 70;
		int options = Editor.MENU_BAR;
		String text = null;
		Editor ed = new Editor(rows, columns, 0, options);
		String dir = "Macro/";
		if (isJava)
		dir = "Java/";
		else if (isJavaScript)
		dir = "JavaScript/";
		else if (isBeanShell)
		dir = "BeanShell/";
		else if (isPython)
		dir = "Python/";
		String url = "http://wsr.imagej.net/download/Examples/"+dir+name;
		text = IJ.openUrlAsString(url);
		if (text.startsWith("<Error: ")) {
		IJ.error("Open Example", text);
		return true;
		}
		ed.create(name, text);
		if (run) {
		if (isJavaScript)
		ed.evaluateScript(".js");
		else if (isBeanShell)
		ed.evaluateScript(".bsh");
		else if (isPython)
		ed.evaluateScript(".py");
		else if (!name.contains("_Tool"))
		IJ.runMacro(text);
		}
		return true;
		}

		/** Opens a .lut file from the ImageJ/luts directory and returns 'true' if successful. */

ij/IJ.java

+56 −29

Original line number	Diff line number	Diff line
		@@ -49,7 +49,8 @@ public class IJ {
		private static ProgressBar progressBar;
		private static TextPanel textPanel;
		private static String osname, osarch;
		private static boolean isMac, isWin, isJava16, isJava17, isJava18, isJava19, isLinux, is64Bit;
		private static boolean isMac, isWin, isLinux, is64Bit;
		private static int javaVersion;
		private static boolean controlDown, altDown, spaceDown, shiftDown;
		private static boolean macroRunning;
		private static Thread previousThread;
		@@ -75,13 +76,23 @@ public class IJ {
		isWin = osname.startsWith("Windows");
		isMac = !isWin && osname.startsWith("Mac");
		isLinux = osname.startsWith("Linux");
		String version = System.getProperty("java.version").substring(0,3);
		if (version.compareTo("2.9")<=0) { // JVM on Sharp Zaurus PDA claims to be "3.1"!
		isJava16 = version.compareTo("1.5")>0;
		isJava17 = version.compareTo("1.6")>0;
		isJava18 = version.compareTo("1.7")>0;
		isJava19 = version.compareTo("1.8")>0;
		}
		String version = System.getProperty("java.version");
		if (version.startsWith("1.8"))
		javaVersion = 8;
		else if (version.startsWith("1.6"))
		javaVersion = 6;
		else if (version.startsWith("1.9")\|\|version.startsWith("9"))
		javaVersion = 9;
		else if (version.startsWith("10"))
		javaVersion = 10;
		else if (version.startsWith("11"))
		javaVersion = 11;
		else if (version.startsWith("12"))
		javaVersion = 12;
		else if (version.startsWith("1.7"))
		javaVersion = 7;
		else
		javaVersion = 6;
		dfs = new DecimalFormatSymbols(Locale.US);
		df = new DecimalFormat[10];
		df[0] = new DecimalFormat("0", dfs);
		@@ -144,8 +155,6 @@ public class IJ {
		Returns any string value returned by the macro, or null. Scripts always return null.
		The equivalent macro function is runMacro(). */
		public static String runMacroFile(String name, String arg) {
		if (ij==null && Menus.getCommands()==null)
		init();
		Macro_Runner mr = new Macro_Runner();
		return mr.runMacroFile(name, arg);
		}
		@@ -501,7 +510,7 @@ public class IJ {
		Frame frame = WindowManager.getFrontWindow();
		if (frame!=null && (frame instanceof TextWindow)) {
		TextWindow tw = (TextWindow)frame;
		if (tw.getTextPanel().getResultsTable()==null) {
		if (tw.getResultsTable()==null) {
		IJ.error("Rename", "\""+tw.getTitle()+"\" is not a results table");
		return;
		}
		@@ -513,7 +522,7 @@ public class IJ {
		}
		}

		/** Changes the name of a results window from 'oldTitle' to 'newTitle'. */
		/** Changes the name of a table window from 'oldTitle' to 'newTitle'. */
		public static void renameResults(String oldTitle, String newTitle) {
		Frame frame = WindowManager.getFrame(oldTitle);
		if (frame==null) {
		@@ -521,22 +530,20 @@ public class IJ {
		return;
		} else if (frame instanceof TextWindow) {
		TextWindow tw = (TextWindow)frame;
		if (tw.getTextPanel().getResultsTable()==null) {
		error("Rename", "\""+oldTitle+"\" is not a results table");
		if (tw.getResultsTable()==null) {
		error("Rename", "\""+oldTitle+"\" is not a table");
		return;
		}
		tw.rename(newTitle);
		} else
		error("Rename", "\""+oldTitle+"\" is not a results table");
		error("Rename", "\""+oldTitle+"\" is not a table");
		}

		/** Deletes 'row1' through 'row2' of the "Results" window. Arguments
		must be in the range 0-Analyzer.getCounter()-1. */
		/** Deletes 'row1' through 'row2' of the "Results" window, where
		'row1' and 'row2' must be in the range 0-Analyzer.getCounter()-1. */
		public static void deleteRows(int row1, int row2) {
		int n = row2 - row1 + 1;
		ResultsTable rt = Analyzer.getResultsTable();
		for (int i=row1; i<row1+n; i++)
		rt.deleteRow(row1);
		rt.deleteRows(row1, row2);
		rt.show("Results");
		}

		@@ -956,6 +963,11 @@ public class IJ {
		return isWin;
		}

		/** Returns the Java version (6, 7, 8, 9, 10, etc.). */
		public static int javaVersion() {
		return javaVersion;
		}

		/** Always returns true. */
		public static boolean isJava2() {
		return true;
		@@ -973,22 +985,22 @@ public class IJ {

		/** Returns true if ImageJ is running on a Java 1.6 or greater JVM. */
		public static boolean isJava16() {
		return isJava16;
		return javaVersion >= 6;
		}

		/** Returns true if ImageJ is running on a Java 1.7 or greater JVM. */
		public static boolean isJava17() {
		return isJava17;
		return javaVersion >= 7;
		}

		/** Returns true if ImageJ is running on a Java 1.8 or greater JVM. */
		public static boolean isJava18() {
		return isJava18;
		return javaVersion >= 8;
		}

		/** Returns true if ImageJ is running on a Java 1.9 or greater JVM. */
		public static boolean isJava19() {
		return isJava19;
		return javaVersion >= 9;
		}

		/** Returns true if ImageJ is running on Linux. */
		@@ -1151,6 +1163,16 @@ public class IJ {
		img.setRoi(new PointRoi(x, y));
		}

		/** Creates an Roi. */
		public static Roi Roi(double x, double y, double width, double height) {
		return new Roi(x, y, width, height);
		}

		/** Creates an OvalRoi. */
		public static OvalRoi OvalRoi(double x, double y, double width, double height) {
		return new OvalRoi(x, y, width, height);
		}

		/** Sets the display range (minimum and maximum displayed pixel values) of the current image. */
		public static void setMinAndMax(double min, double max) {
		setMinAndMax(getImage(), min, max, 7);
		@@ -1327,8 +1349,11 @@ public class IJ {
		if (impC!=null && impC!=imp && impT!=null)
		impC.saveRoi();
		WindowManager.setTempCurrentImage(imp);
		Interpreter.activateImage(imp);
		WindowManager.setWindow(null);
		} else {
		if (imp==null)
		return;
		ImageWindow win = imp.getWindow();
		if (win!=null) {
		win.toFront();
		@@ -1821,10 +1846,12 @@ public class IJ {
		return;
		} else if (format.indexOf("jpeg")!=-1 \|\| format.indexOf("jpg")!=-1) {
		path = updateExtension(path, ".jpg");
		format = "Jpeg...";
		JpegWriter.save(imp, path, FileSaver.getJpegQuality());
		return;
		} else if (format.indexOf("gif")!=-1) {
		path = updateExtension(path, ".gif");
		format = "Gif...";
		GifWriter.save(imp, path);
		return;
		} else if (format.indexOf("text image")!=-1) {
		path = updateExtension(path, ".txt");
		format = "Text Image...";
		@@ -2010,8 +2037,8 @@ public class IJ {
		options = NewImage.FILL_BLACK;
		else if (type.contains("ramp"))
		options = NewImage.FILL_RAMP;
		else if (type.contains("random"))
		options = NewImage.FILL_RANDOM;
		else if (type.contains("noise") \|\| type.contains("random"))
		options = NewImage.FILL_NOISE;
		options += NewImage.CHECK_AVAILABLE_MEMORY;
		return NewImage.createImage(title, width, height, depth, bitDepth, options);
		}

ij/ImageJ.java

+47 −47

Original line number	Diff line number	Diff line
		@@ -9,7 +9,6 @@ import ij.text.*;
		import ij.macro.Interpreter;
		import ij.io.Opener;
		import ij.util.*;
		import ij.macro.MacroRunner;
		import java.awt.*;
		import java.util.*;
		import java.awt.event.*;
		@@ -79,7 +78,7 @@ 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 = "1.51q";
		public static final String VERSION = "1.52d";
		public static final String BUILD = "";
		public static Color backgroundColor = new Color(237,237,237);
		/** SansSerif, 12-point, plain font. */
		@@ -118,6 +117,7 @@ public class ImageJ extends Frame implements ActionListener,
		private boolean embedded;
		private boolean windowClosed;
		private static String commandName;
		private static boolean batchMode;

		boolean hotkey;

		@@ -180,7 +180,6 @@ public class ImageJ extends Frame implements ActionListener,
		addWindowListener(this);
		setFocusTraversalKeysEnabled(false);
		m.installStartupMacroSet(); //add custom tools
		runStartupMacro();

		Point loc = getPreferredLocation();
		Dimension tbSize = toolbar.getPreferredSize();
		@@ -195,7 +194,7 @@ public class ImageJ extends Frame implements ActionListener,
		Dimension size = getSize();
		if (size!=null) {
		if (IJ.debugMode) IJ.log("size: "+size);
		if (IJ.isWindows() && size.height>108) {
		if (IJ.isWindows() && (size.height>108\|\|IJ.javaVersion()>=10)) {
		// workaround for IJ window layout and FileDialog freeze problems with Windows 10 Creators Update
		IJ.wait(10);
		pack();
		@@ -217,23 +216,20 @@ public class ImageJ extends Frame implements ActionListener,
		}
		if (IJ.isMacintosh()&&applet==null) {
		Object qh = null;
		try {
		qh = IJ.runPlugIn("MacAdapter", "");
		} catch(Throwable e) {}
		if (qh==null)
		IJ.runPlugIn("QuitHandler", "");
		}
		if (applet==null)
		IJ.runPlugIn("ij.plugin.DragAndDrop", "");
		String str = m.getMacroCount()==1?" macro":" macros";
		IJ.showStatus(version()+ m.getPluginCount() + " commands; " + m.getMacroCount() + str);
		configureProxy();
		if (applet==null)
		loadCursors();
		}

		private void runStartupMacro() {
		String macro = (new Startup()).getStartupMacro();
		if (macro!=null && macro.length()>4)
		new MacroRunner(macro);
		(new ij.macro.StartupRunner()).run(batchMode); // run RunAtStartup and AutoRun macros
		IJ.showStatus(version()+ m.getPluginCount() + " commands; " + m.getMacroCount() + str);
		}

		private void loadCursors() {
		@@ -373,7 +369,7 @@ public class ImageJ extends Frame implements ActionListener,
		MenuItem item = (MenuItem)e.getSource();
		MenuComponent parent = (MenuComponent)item.getParent();
		String cmd = e.getItem().toString();
		if ("Autorun".equals(cmd)) // Examples>Autorun
		if ("Autorun Examples".equals(cmd)) // Examples>Autorun Examples
		Prefs.autoRunExamples = e.getStateChange()==1;
		else if ((Menu)parent==Menus.window)
		WindowManager.activateWindow(cmd, item);
		@@ -455,7 +451,13 @@ public class ImageJ extends Frame implements ActionListener,
		}
		}

		if ((!Prefs.requireControlKey \|\| control \|\| meta) && keyChar!='+') {
		if (keyCode==KeyEvent.VK_SEPARATOR)
		keyCode = KeyEvent.VK_DECIMAL;
		boolean functionKey = keyCode>=KeyEvent.VK_F1 && keyCode<=KeyEvent.VK_F12;
		boolean numPad = keyCode==KeyEvent.VK_DIVIDE \|\| keyCode==KeyEvent.VK_MULTIPLY
		\|\| keyCode==KeyEvent.VK_DECIMAL
		\|\| (keyCode>=KeyEvent.VK_NUMPAD0 && keyCode<=KeyEvent.VK_NUMPAD9);
		if ((!Prefs.requireControlKey\|\|control\|\|meta\|\|functionKey\|\|numPad) && keyChar!='+') {
		Hashtable shortcuts = Menus.getShortcuts();
		if (shift)
		cmd = (String)shortcuts.get(new Integer(keyCode+200));
		@@ -477,13 +479,15 @@ public class ImageJ extends Frame implements ActionListener,
		if (cmd==null) {
		switch (keyCode) {
		case KeyEvent.VK_TAB: WindowManager.putBehind(); return;
		case KeyEvent.VK_BACK_SPACE: // delete
		case KeyEvent.VK_BACK_SPACE: case KeyEvent.VK_DELETE:
		if (!(shift\|\|control\|\|alt\|\|meta)) {
		if (deleteOverlayRoi(imp))
		return;
		if (imp!=null&&imp.getOverlay()!=null&&imp==GelAnalyzer.getGelImage())
		return;
		cmd="Clear";
		hotkey=true;
		}
		break;
		//case KeyEvent.VK_BACK_SLASH: cmd=IJ.altKeyDown()?"Animation Options...":"Start Animation"; break;
		case KeyEvent.VK_EQUALS: cmd="In [+]"; break;
		@@ -678,31 +682,28 @@ public class ImageJ extends Frame implements ActionListener,
		}

		public static void main(String args[]) {
		if (System.getProperty("java.version").substring(0,3).compareTo("1.5")<0) {
		javax.swing.JOptionPane.showMessageDialog(null,"ImageJ "+VERSION+" requires Java 1.5 or later.");
		System.exit(0);
		}
		boolean noGUI = false;
		int mode = STANDALONE;
		arguments = args;
		//System.setProperty("file.encoding", "UTF-8");
		int nArgs = args!=null?args.length:0;
		boolean commandLine = false;
		for (int i=0; i<nArgs; i++) {
		String arg = args[i];
		if (arg==null) continue;
		if (args[i].startsWith("-")) {
		if (args[i].startsWith("-batch"))
		if (arg.startsWith("-batch")) {
		noGUI = true;
		else if (args[i].startsWith("-debug"))
		batchMode = true;
		} else if (arg.startsWith("-macro") \|\| arg.endsWith(".ijm") \|\| arg.endsWith(".txt"))
		batchMode = true;
		else if (arg.startsWith("-debug"))
		IJ.setDebugMode(true);
		else if (args[i].startsWith("-ijpath") && i+1<nArgs) {
		else if (arg.startsWith("-ijpath") && i+1<nArgs) {
		if (IJ.debugMode) IJ.log("-ijpath: "+args[i+1]);
		Prefs.setHomeDir(args[i+1]);
		commandLine = true;
		args[i+1] = null;
		} else if (args[i].startsWith("-port")) {
		int delta = (int)Tools.parseDouble(args[i].substring(5, args[i].length()), 0.0);
		} else if (arg.startsWith("-port")) {
		int delta = (int)Tools.parseDouble(arg.substring(5, arg.length()), 0.0);
		commandLine = true;
		if (delta==0)
		mode = EMBEDDED;
		@@ -710,7 +711,6 @@ public class ImageJ extends Frame implements ActionListener,
		port = DEFAULT_PORT+delta;
		}
		}
		}
		// If existing ImageJ instance, pass arguments to it and quit.
		boolean passArgs = mode==STANDALONE && !noGUI;
		if (IJ.isMacOSX() && !commandLine)