Sync with ImageJ 1.43e

IJ_Props.txt

@@ -6,7 +6,7 @@
 
 # Note that commands must be unique.
 
-# Version 1.42
+# Version 1.43
 
 # Popup Menu
 popup01=Undo
@@ -265,6 +265,11 @@ filters08="Variance...",ij.plugin.filter.RankFilters("variance")
 filters09=-
 filters10="Show Circular Masks...",ij.plugin.filter.RankFilters("masks")
 
+# Plugins installed in the File/Batch submenu
+batch01="Measure...",ij.plugin.BatchMeasure
+batch02="Convert...",ij.plugin.BatchConverter
+batch03="Process...",ij.plugin.BatchProcesser
+
 # Plugins installed in the Analyze/Gels submenu
 gels01="Select First Lane[1]",ij.plugin.GelAnalyzer("first")
 gels02="Select Next Lane[2]",ij.plugin.GelAnalyzer("next")

ij/CommandListener.java

@@ -1,9 +1,16 @@
 package ij;
 
-	/** Plugins that implement this interface are notified
-		when ImageJ is about to run a menu command. */
+	/** Plugins that implement this interface are notified when ImageJ
+		is about to run a menu command. There is an example plugin at
+		http://rsb.info.nih.gov/ij/plugins/download/misc/Command_Listener.java
+	*/
 	public interface CommandListener {
 
+	/*	The method is called when ImageJ is about to run a menu command, 
+		where 'command' is the name of the command. Return this string 
+		and ImageJ will run the command, return a different command name
+		and ImageJ will run that command, or return null to not run a command.
+	*/
 	public String commandExecuting(String command);
 
 }

ij/Executer.java

@@ -62,7 +62,7 @@ public void run() {
 				IJ.setKeyUp(IJ.ALL_KEYS);  // set keys up except for "<", ">", "+" and "-" shortcuts
 		} catch(Throwable e) {
 			IJ.showStatus("");
-			IJ.showProgress(1.0);
+			IJ.showProgress(1, 1);
 			ImagePlus imp = WindowManager.getCurrentImage();
 			if (imp!=null) imp.unlock();
 			String msg = e.getMessage();

ij/IJ.java

@@ -82,16 +82,19 @@ public static ImageJ getInstance() {
 	}
 
 	/** Runs the macro contained in the string <code>macro</code>.
-		Returns any string value returned by the macro, or null. 
-		The equivalent macro function is eval(). */
+		Returns any string value returned by the macro, null if the macro
+		does not return a value, or "[aborted]" if the macro was aborted
+		due to an error. The equivalent macro function is eval(). */
 	public static String runMacro(String macro) {
 		return runMacro(macro, "");
 	}
 
 	/** Runs the macro contained in the string <code>macro</code>.
 		The optional string argument can be retrieved in the
 		called macro using the getArgument() macro function. 
-		Returns any string value returned by the macro, or null. */
+		Returns any string value returned by the macro, null if the macro
+		does not return a value, or "[aborted]" if the macro was aborted
+		due to an error.  */
 	public static String runMacro(String macro, String arg) {
 		Macro_Runner mr = new Macro_Runner();
 		return mr.runMacro(macro, arg);
@@ -467,7 +470,11 @@ public static void showProgress(double progress) {
     The bar is updated only if more than 90 ms have passed since the last call.
     Does nothing if the ImageJ window is not present. */
     public static void showProgress(int currentIndex, int finalIndex) {
-		if (progressBar!=null) progressBar.show(currentIndex, finalIndex);
+		if (progressBar!=null) {
+			progressBar.show(currentIndex, finalIndex);
+			if (currentIndex==finalIndex)
+				progressBar.setBatchMode(false);
+		}
 	}
 
 	/** Displays a message in a dialog box titled "Message".
@@ -1018,6 +1025,8 @@ public static void selectWindow(int id) {
 
 	/** Activates the window with the specified title. */
 	public static void selectWindow(String title) {
+		if (title.equals("ImageJ")&&ij!=null)
+			{ij.toFront(); return;}
 		long start = System.currentTimeMillis();
 		while (System.currentTimeMillis()-start<3000) { // 3 sec timeout
 			Frame frame = WindowManager.getFrame(title);
@@ -1411,8 +1420,9 @@ static String updateExtension(String path, String extension) {
 		return path;
 	}
 
-	/** Saves a string as a file. Returns an error message 
-		if there is  an exception, otherwise returns null. */
+	/** Saves a string as a file. Displays a file save dialog if
+		'path' is null or blank. Returns an error message 
+		if there is an exception, otherwise returns null. */
 	public static String saveString(String string, String path) {
 		return write(string, path, false);
 	}
@@ -1425,6 +1435,13 @@ public static String append(String string, String path) {
 	}
 
 	private static String write(String string, String path, boolean append) {
+		if (path==null || path.equals("")) {
+			String msg = append?"Append String...":"Save String...";
+			SaveDialog sd = new SaveDialog(msg, "Untitled", ".txt");
+			String name = sd.getFileName();
+			if (name==null) return null;
+			path = sd.getDirectory() + name;
+		}
 		try {
 			BufferedWriter out = new BufferedWriter(new FileWriter(path, append));
 			out.write(string);
@@ -1435,6 +1452,41 @@ private static String write(String string, String path, boolean append) {
 		return null;
 	}
 
+	/** Opens a text file as a string. Displays a file open dialog
+		if path is null or blank. Returns null if the user cancels
+		the file open dialog. If there is an error, returns a 
+		 message in the form "Error: message". */
+	public static String openAsString(String path) {
+		if (path==null || path.equals("")) {
+			OpenDialog od = new OpenDialog("Open As String", "");
+			String directory = od.getDirectory();
+			String name = od.getFileName();
+			if (name==null) return null;
+			path = directory + name;
+		}
+		String str = "";
+		File file = new File(path);
+		if (!file.exists())
+			return "Error: file not found";
+		try {
+			StringBuffer sb = new StringBuffer(5000);
+			BufferedReader r = new BufferedReader(new FileReader(file));
+			while (true) {
+				String s=r.readLine();
+				if (s==null)
+					break;
+				else
+					sb.append(s+"\n");
+			}
+			r.close();
+			str = new String(sb);
+		}
+		catch (Exception e) {
+			str = "Error: "+e.getMessage();
+		}
+		return str;
+	}
+
 	 /** Creates a new imagePlus. <code>Type</code> should contain "8-bit", "16-bit", "32-bit" or "RGB". 
 		 In addition, it can contain "white", "black" or "ramp" (the default is "white"). <code>Width</code> 
 	 	and <code>height</code> specify the width and height of the image in pixels.  

ij/ImageJ.java

@@ -69,7 +69,7 @@ public class ImageJ extends Frame implements ActionListener,
 	MouseListener, KeyListener, WindowListener, ItemListener, Runnable {
 
 	/** Plugins should call IJ.getVersion() to get the version string. */
-	public static final String VERSION = "1.43d";
+	public static final String VERSION = "1.43e";
 	public static Color backgroundColor = new Color(220,220,220); //224,226,235
 	/** SansSerif, 12-point, plain font. */
 	public static final Font SansSerif12 = new Font("SansSerif", Font.PLAIN, 12);
@@ -329,6 +329,7 @@ public void mouseClicked(MouseEvent e) {}
 	public void mouseEntered(MouseEvent e) {}
 
  	public void keyPressed(KeyEvent e) {
+ 		//if (e.isConsumed()) return;
 		int keyCode = e.getKeyCode();
 		IJ.setKeyDown(keyCode);
 		hotkey = false;

ij/Menus.java

@@ -171,6 +171,7 @@ String addMenuBar() {
 		getMenu("Process>FFT", true);
 		Menu filtersMenu = getMenu("Process>Filters", true);
 		process.addSeparator();
+		getMenu("Process>Batch", true);
 		addPlugInItem(process, "Image Calculator...", "ij.plugin.ImageCalculator", 0, false);
 		addPlugInItem(process, "Subtract Background...", "ij.plugin.filter.BackgroundSubtracter", 0, false);
 		addItem(process, "Repeat Command", KeyEvent.VK_R, true);

ij/gui/GenericDialog.java

@@ -452,7 +452,7 @@ public void addTextAreas(String text1, String text2, int rows, int columns) {
 		c.gridx = 0; c.gridy = y;
 		c.gridwidth = 2;
 		c.anchor = GridBagConstraints.WEST;
-		c.insets = new Insets(15, 20, 0, 0);
+		c.insets = getInsets(15, 20, 0, 0);
 		grid.setConstraints(panel, c);
 		add(panel);
 		y++;

ij/gui/ImageCanvas.java

@@ -465,30 +465,6 @@ void setMagnification2(double magnification) {
 		imp.setTitle(imp.getTitle());
 	}
 
-	/*
-	public void setMagnification(double mag, int x, int y) {
-		if (mag>32.0) magnification = 32.0;
-		if (mag<0.03125) mag = 0.03125;
-		int newWidth = (int)(imageWidth*mag);
-		int newHeight = (int)(imageHeight*mag);
-		Dimension newSize = canEnlarge(newWidth, newHeight);
-		if (newSize!=null) {
-			setDrawingSize(newSize.width, newSize.height);
-			if (newSize.width!=newWidth || newSize.height!=newHeight)
-				adjustSourceRect(mag, x, y);
-			else
-				setMagnification(mag);
-			imp.getWindow().pack();
-		} else
-			adjustSourceRect(mag, x, y);
-		repaint();
-		if (srcRect.width<imageWidth || srcRect.height<imageHeight)
-			resetMaxBounds();
-		this.magnification = magnification;
-		imp.setTitle(imp.getTitle());
-	}
-	*/
-
 	public Rectangle getSrcRect() {
 		return srcRect;
 	}
@@ -634,7 +610,6 @@ protected Dimension canEnlarge(int newWidth, int newHeight) {
 		ImageWindow win = imp.getWindow();
 		if (win==null) return null;
 		Rectangle r1 = win.getBounds();
-
 		Insets insets = win.getInsets();
 		Point loc = getLocation();
 		if (loc.x>insets.left+5 || loc.y>insets.top+5) {
@@ -645,7 +620,7 @@ protected Dimension canEnlarge(int newWidth, int newHeight) {
 			r1.width = r1.width - dstWidth + newWidth+10;
 			r1.height = r1.height - dstHeight + newHeight+10;
 		}
-		Rectangle max = win.getMaxWindow();
+		Rectangle max = win.getMaxWindow(r1.x, r1.y);
 		boolean fitsHorizontally = r1.x+r1.width<max.x+max.width;
 		boolean fitsVertically = r1.y+r1.height<max.y+max.height;
 		if (fitsHorizontally && fitsVertically)

ij/gui/ImageWindow.java

@@ -163,7 +163,7 @@ public void show() {
 	private void setLocationAndSize(boolean updating) {
 		int width = imp.getWidth();
 		int height = imp.getHeight();
-		Rectangle maxWindow = getMaxWindow();
+		Rectangle maxWindow = getMaxWindow(0,0);
 		if (maxWindow.x==maxWindow.width)  // work around for Linux bug
 			maxWindow = new Rectangle(0, maxWindow.y, maxWindow.width, maxWindow.height);
 		if (WindowManager.getWindowCount()<=1)
@@ -215,17 +215,37 @@ private void setLocationAndSize(boolean updating) {
 			pack();
 	}
 
-	Rectangle getMaxWindow() {
+	Rectangle getMaxWindow(int xloc, int yloc) {
 		GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
-		Rectangle maxWindow = ge.getMaximumWindowBounds();
+		Rectangle bounds = ge.getMaximumWindowBounds();
+		if (xloc>bounds.x+bounds.width || yloc>bounds.y+bounds.height) {
+			Rectangle bounds2 = getSecondaryMonitorBounds(ge, xloc, yloc);
+			if (bounds2!=null) return bounds2;
+		}
 		Dimension ijSize = ij!=null?ij.getSize():new Dimension(0,0);
-		if (maxWindow.height>600) {
-			maxWindow.y += ijSize.height;
-			maxWindow.height -= ijSize.height;
+		if (bounds.height>600) {
+			bounds.y += ijSize.height;
+			bounds.height -= ijSize.height;
 		}
-		return maxWindow;
+		return bounds;
 	}
-
+
+	private Rectangle getSecondaryMonitorBounds(GraphicsEnvironment ge, int xloc, int yloc) {
+		//IJ.log("getSecondaryMonitorBounds "+wb);
+		GraphicsDevice[] gs = ge.getScreenDevices();
+		for (int j=0; j<gs.length; j++) {
+			GraphicsDevice gd = gs[j];
+			GraphicsConfiguration[] gc = gd.getConfigurations();
+			for (int i=0; i<gc.length; i++) {
+				Rectangle bounds = gc[i].getBounds();
+				//IJ.log(j+" "+i+" "+bounds+"  "+bounds.contains(wb.x, wb.y));
+				if (bounds!=null && bounds.contains(xloc, yloc))
+					return bounds;
+			}
+		}		
+		return null;
+	}
+
 	public double getInitialMagnification() {
 		return initialMagnification;
 	}

ij/gui/ProgressBar.java

@@ -13,6 +13,7 @@ public class ProgressBar extends Canvas {
 	private double percent;
     private long lastTime = 0;
 	private boolean showBar;
+	private boolean batchMode;
 
 	private Color barColor = Color.gray;
 	private Color fillColor = new Color(204,204,255);
@@ -55,7 +56,7 @@ public void show(double percent) {
      * batch mode.
      */
     public void show(double percent, boolean showInBatchMode) {
-        if (!showInBatchMode && Interpreter.isBatchMode()) return;
+        if (!showInBatchMode && (batchMode||Interpreter.isBatchMode())) return;
         if (percent>=1.0) {     //clear the progress bar
 			percent = 0.0;
 			showBar = false;
@@ -109,4 +110,8 @@ public Dimension getPreferredSize() {
         return new Dimension(canvasWidth, canvasHeight);
     }
 
+    public void setBatchMode(boolean batchMode) {
+        this.batchMode = batchMode;
+    }
+
 }

ij/gui/Roi.java

@@ -320,6 +320,8 @@ protected void grow(int sx, int sy) {
 		}
 		if (constrain) {
 			// constrain selection to be square
+			if (!center)
+				{growConstrained(xNew, yNew); return;}
 			int dx, dy, d;
 			dx = xNew - x;
 			dy = yNew - y;
@@ -330,7 +332,6 @@ protected void grow(int sx, int sy) {
 			xNew = x + d;
 			yNew = y + d;
 		}
-
 		if (center) {
 			width = Math.abs(xNew - startX)*2;
 			height = Math.abs(yNew - startY)*2;
@@ -354,6 +355,29 @@ protected void grow(int sx, int sy) {
 		oldHeight = height;
 	}
 
+	private void growConstrained(int xNew, int yNew) {
+		int dx = xNew - startX;
+		int dy = yNew - startY;
+		width = height = (int)Math.round(Math.sqrt(dx*dx + dy*dy));
+		if (type==RECTANGLE) {
+			x = (xNew>=startX)?startX:startX - width;
+			y = (yNew>=startY)?startY:startY - height;
+			if (x<0) x = 0;
+			if (y<0) y = 0;
+			if ((x+width) > xMax) width = xMax-x;
+			if ((y+height) > yMax) height = yMax-y;
+		} else {
+			x = startX + dx/2 - width/2;
+			y = startY + dy/2 - height/2;
+		}
+		updateClipRect();
+		imp.draw(clipX, clipY, clipWidth, clipHeight);
+		oldX = x;
+		oldY = y;
+		oldWidth = width;
+		oldHeight = height;
+	}
+
 	protected void moveHandle(int sx, int sy) {
 		double asp;
 		if (clipboard!=null) return;
@@ -454,10 +478,10 @@ protected void moveHandle(int sx, int sy) {
 		}
 
 		if(constrain) {
-
-			if(activeHandle==1 || activeHandle==5) width=height;
-			else height=width;
-
+			if (activeHandle==1 || activeHandle==5)
+				width=height;
+			else
+				height=width;
 			if(center){
 				x=xc-width/2;
 				y=yc-height/2;