2021.04.27 (1.53j26; Bug fixes)

ij/IJ.java

@@ -2462,10 +2462,8 @@ public static String[] getLuts() {
 			return new String[0];
 		for (int i=0; i<lutsMenu.getItemCount(); i++) {
 			MenuItem menuItem = lutsMenu.getItem(i);
-			if (menuItem.getActionListeners().length == 0) // separator?
-				continue;
 			String label = menuItem.getLabel();
-			if (label.equals("Invert LUT") || label.equals("Apply LUT"))
+			if (label.equals("-") || label.equals("Invert LUT") || label.equals("Apply LUT"))
 				continue;
 			String command = (String)commands.get(label);
 			if (command==null || command.startsWith("ij.plugin.LutLoader"))

ij/ImageJ.java

@@ -78,7 +78,7 @@ public class ImageJ extends Frame implements ActionListener,
 
 	/** Plugins should call IJ.getVersion() or IJ.getFullVersion() to get the version string. */
 	public static final String VERSION = "1.53j";
-	public static final String BUILD = "18";
+	public static final String BUILD = "26";
 	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);
@@ -734,7 +734,8 @@ else if (delta>0 && DEFAULT_PORT+delta<65536)
 		if (!noGUI && (ij==null || (ij!=null && !ij.isShowing()))) {
 			ij = new ImageJ(null, mode);
 			ij.exitWhenQuitting = true;
-		}
+		} else if (batchMode && noGUI)
+			Prefs.load(null, null);
 		int macros = 0;
 		for (int i=0; i<nArgs; i++) {
 			String arg = args[i];

ij/Menus.java

@@ -825,6 +825,8 @@ void addJarErrorHeading(String jar) {
 
 	/** Returns the specified ImageJ menu (e.g., "File>New") or null if it is not found. */
 	public static Menu getImageJMenu(String menuPath) {
+		if (menus==null)
+			IJ.init();
 		if (menus==null)
 			return null;
 		if (menus.get(menuPath)!=null)
@@ -1333,6 +1335,8 @@ public static String getMacrosPath() {
 
 	/** Returns the hashtable that associates commands with plugins. */
 	public static Hashtable getCommands() {
+		if (pluginsTable==null)
+			IJ.init();
 		return pluginsTable;
 	}
 

ij/Prefs.java

@@ -288,29 +288,31 @@ public static boolean get(String key, boolean defaultValue) {
 	public static String load(Object ij, Applet applet) {
 		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) {
-			// 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 "+ImageJDir;
-		f = new BufferedInputStream(f);
-		try {
-			props.load(f);
-			f.close();
-		} catch (IOException e) {
-			return("Error loading "+PROPS_NAME);
+		if (ij!=null) {
+			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) {
+				// 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 "+ImageJDir;
+			f = new BufferedInputStream(f);
+			try {
+				props.load(f);
+				f.close();
+			} catch (IOException e) {
+				return("Error loading "+PROPS_NAME);
+			}
+			imagesURL = props.getProperty(IJ.isJava18()?"images.location":"images.location2");
 		}
-		imagesURL = props.getProperty(IJ.isJava18()?"images.location":"images.location2");
 		loadPreferences();
 		loadOptions();
 		guiScale = get(GUI_SCALE, 1.0);

ij/gui/GenericDialog.java

@@ -730,14 +730,23 @@ public void addMessage(String text, Font font, Color color) {
     public void addTextAreas(String text1, String text2, int rows, int columns) {
 		if (textArea1!=null) return;
 		Panel panel = new Panel();
+		int scrollbars = TextArea.SCROLLBARS_NONE;
+		if (text1.endsWith("SCROLLBARS_BOTH")) {
+			scrollbars = TextArea.SCROLLBARS_BOTH;
+			text1 = text1.substring(0, text1.length()-15);
+		}
+		if (text1.endsWith("SCROLLBARS_VERTICAL_ONLY")) {
+			scrollbars = TextArea.SCROLLBARS_VERTICAL_ONLY;
+			text1 = text1.substring(0, text1.length()-24);
+		}
 		Font font = new Font("SansSerif", Font.PLAIN, (int)(14*Prefs.getGuiScale()));
-		textArea1 = new TextArea(text1,rows,columns,TextArea.SCROLLBARS_NONE);
+		textArea1 = new TextArea(text1,rows,columns,scrollbars);
 		if (IJ.isLinux()) textArea1.setBackground(Color.white);
 		textArea1.setFont(font);
 		textArea1.addTextListener(this);
 		panel.add(textArea1);
 		if (text2!=null) {
-			textArea2 = new TextArea(text2,rows,columns,TextArea.SCROLLBARS_NONE);
+			textArea2 = new TextArea(text2,rows,columns,scrollbars);
 			if (IJ.isLinux()) textArea2.setBackground(Color.white);
 			textArea2.setFont(font);
 			panel.add(textArea2);

ij/plugin/FolderOpener.java

@@ -18,7 +18,7 @@ public class FolderOpener implements PlugIn {
 	private static final int MAX_SEPARATE = 40;
 	private static final String DIR_KEY = "import.sequence.dir";
 	private static final String[] types = {"default", "16-bit", "32-bit", "RGB"};
-	private static String[] excludedTypes = {".txt", ".lut", ".roi", ".pty", ".hdr", ".java", ".ijm", ".py", ".js", ".bsh", ".xml"};
+	private static String[] excludedTypes = {".txt", ".lut", ".roi", ".pty", ".hdr", ".java", ".ijm", ".py", ".js", ".bsh", ".xml", ".rar"};
 	private static boolean staticSortFileNames = true;
 	private static boolean staticOpenAsVirtualStack;
 	private boolean convertToRGB;
@@ -422,7 +422,10 @@ else if (label2!=null && !label2.equals(""))
 				}
 			}
 			if (imp2.getStackSize()==1) {
-				imp2.setProperty("Label", list[0]);
+				int idx = this.start-1;
+				if (idx<0 || idx>=list.length)
+					idx = 0;
+				imp2.setProperty("Label", list[idx]);
 				if (info1!=null)
 					imp2.setProperty("Info", info1);
 			}

ij/plugin/ImagesToStack.java

@@ -92,11 +92,11 @@ public void convertImagesToStack() {
 				gd.addChoice("Method:", methods, methods[staticMethod]);
 			}
 			gd.addStringField("Name:", name, 12);
-			gd.addStringField("Title Contains:", "", 12);
+			gd.addStringField("Title contains:", "", 12);
 			if (sizesDiffer)
-				gd.addCheckbox("Bicubic Interpolation", staticBicubic);
-			gd.addCheckbox("Use Titles as Labels", staticTitlesAsLabels);
-			gd.addCheckbox("Keep Source Images", staticKeep);
+				gd.addCheckbox("Bicubic interpolation", staticBicubic);
+			gd.addCheckbox("Use titles as labels", staticTitlesAsLabels);
+			gd.addCheckbox("Keep source images", staticKeep);
 			gd.showDialog();
 			if (gd.wasCanceled()) return;
 			if (sizesDiffer)
@@ -150,6 +150,8 @@ private ImagePlus convert(ImagePlus[] images, int count) {
 			if (ip.getMin()<min) min = ip.getMin();
 			if (ip.getMax()>max) max = ip.getMax();
 			String label = titlesAsLabels?images[i].getTitle():null;
+			if (label==null)
+				label = (String)images[i].getProperty("Label");
 			if (label!=null) {
 				String info = (String)images[i].getProperty("Info");
 				if (info!=null) label += "\n" + info;

ij/plugin/RoiEnlarger.java

@@ -5,11 +5,18 @@
 import ij.measure.Calibration;
 import ij.plugin.filter.EDM;
 import ij.plugin.filter.ThresholdToSelection;
+import ij.plugin.frame.Recorder;
 import java.awt.*;
+import java.util.Vector;
 
 /** This plugin, which enlarges or shrinks selections, implements the Edit/Selection/Enlarge command. */
-public class RoiEnlarger implements PlugIn {
-	private static double defaultDistance = 15; // pixels
+public class RoiEnlarger implements PlugIn, DialogListener {
+	private static final String DISTANCE_KEY = "enlarger.distance";
+	private static final String USE_PIXELS_KEY = "enlarger.pixels";
+	private double defaultDistance = Prefs.get(DISTANCE_KEY, 15); // pixels
+	private boolean defaultUsePixels = Prefs.get(USE_PIXELS_KEY, false);
+	private Calibration cal;
+	private Label unitsLabel;
 
 	public void run(String arg) {
 		ImagePlus imp = IJ.getImage();
@@ -21,42 +28,111 @@ public void run(String arg) {
 		if (!imp.okToDeleteRoi())
 			return;
 		double n = showDialog(imp, defaultDistance);
-		if (n==Double.NaN)
+		if (Double.isNaN(n))
 			return;
+		Prefs.set(DISTANCE_KEY, defaultDistance);
+		Prefs.set(USE_PIXELS_KEY, defaultUsePixels);
 		Roi roi2 = Math.abs(n)<256?enlarge255(roi,n):enlarge(roi,n);
 		if (roi2!=null) {
 			imp.setRoi(roi2);
 			Roi.setPreviousRoi(roi);
 			defaultDistance = n;
 		}
+		int pixels = (int)Math.round(n);
+		Recorder.recordCall("RoiEnlarger.enlarge(imp, "+pixels+");");
 	}
-
+
+	public static void enlarge(ImagePlus imp, int pixels) {
+		Roi roi = imp.getRoi();
+		if (roi==null || roi.isLine() || (roi instanceof PointRoi))
+			return;
+		Roi roi2 = Math.abs(pixels)<256?enlarge255(roi,pixels):enlarge(roi,pixels);
+		if (roi2!=null)
+			imp.setRoi(roi2);
+	}
+
 	public double showDialog(ImagePlus imp, double pixels) {
-		Calibration cal = imp.getCalibration();
+		cal = imp.getCalibration();
 		boolean scaled = cal.scaled();
-		boolean usePixels = false;
-		double n = pixels*cal.pixelWidth;
+		double pixelWidth = cal.pixelWidth;
+		boolean xyScaleDifferent = scaled && cal.pixelWidth != cal.pixelHeight;
+		boolean usePixels = defaultUsePixels;
+		double n = pixels;
 		int decimalPlaces = 0;
-		if (Math.floor(n)!=n)
-			decimalPlaces = 2;
+		if (scaled && !usePixels) {
+			n *= pixelWidth;
+			decimalPlaces = getDecimalPlaces(pixelWidth, n);
+		}
 		GenericDialog gd = new GenericDialog("Enlarge Selection");
-		gd.addNumericField("Enlarge by", n, decimalPlaces, 4, cal.getUnits());
+		gd.addNumericField("Enlarge by", n, decimalPlaces);
+		String units = scaled && !usePixels ? cal.getUnits()+"       " : "pixels ";
+		gd.addToSameRow();
+		gd.addMessage(units.replace('\n', ' ')); //just in case of a newline character, which would make it a MultiLineLabel
+		unitsLabel = (Label)gd.getMessage();
 		if (scaled) {
-			gd.setInsets(0, 20, 0);
+			gd.setInsets(0, 20, 0);     //top left bottom
 			gd.addCheckbox("Pixel units", usePixels);
 		}
 		gd.setInsets(10, 0, 0);
 		gd.addMessage("Enter negative number to shrink", null, Color.darkGray);
+		if (xyScaleDifferent) {
+			gd.setInsets(5, 0, 0);
+			gd.addMessage(" \n ", null, Color.RED);
+		}
+		gd.addDialogListener(this);
+		if (xyScaleDifferent && Macro.getOptions()==null)
+			updateWarning(gd); //in interactive mode only
 		gd.showDialog();
 		if (gd.wasCanceled())
 			return Double.NaN;
 		n = gd.getNextNumber();
 		if (scaled)
 			usePixels = gd.getNextBoolean();
-		pixels = usePixels?n:n/cal.pixelWidth;
+		pixels = usePixels ? n : n/pixelWidth;
+		defaultDistance = pixels;
+		defaultUsePixels = usePixels;
 		return pixels;
 	}
-
+
+	public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
+		Vector checkboxes = gd.getCheckboxes();
+		Checkbox usePixelsCbx = checkboxes == null ? null : (Checkbox)checkboxes.get(0);
+		double n = gd.getNextNumber();
+		boolean usePixels = cal.scaled() ? gd.getNextBoolean() : true; //getNextBoolean also needed for macro recorded
+		if (e != null && e.getSource() == usePixelsCbx) {
+			double pixelWidth = cal.pixelWidth;
+			int decimalPlaces = 0;
+			if (usePixels) {
+				n /= pixelWidth;    //scaled to pixels
+			} else {
+				n *= pixelWidth;    //pixels to scaled
+				decimalPlaces = getDecimalPlaces(pixelWidth, n);
+			}
+			TextField numberField = (TextField)gd.getNumericFields().get(0);
+			numberField.setText(IJ.d2s(n, decimalPlaces));
+			if (unitsLabel != null) unitsLabel.setText(usePixels ? "pixels" : cal.getUnits());
+			boolean xyScaleDifferent = cal.scaled() && cal.pixelWidth != cal.pixelHeight;
+			if (xyScaleDifferent && usePixelsCbx != null) updateWarning(gd);
+		}
+		return !gd.invalidNumber();
+	}
+
+	private void updateWarning(GenericDialog gd) {
+		Checkbox usePixelsCbx = (Checkbox)gd.getCheckboxes().get(0);
+		MultiLineLabel warningLabel = (MultiLineLabel)gd.getMessage();
+		boolean showWarning = !usePixelsCbx.getState(); //warn if not pixels units
+		warningLabel.setText(showWarning ? "WARNING: x & y scales differ\nConversion to pixels uses x scale" : " \n ");
+	}
+
+	//decimal places for displaying the scaled enlarge/shrink value
+	private static int getDecimalPlaces(double pixelWidth, double number) {
+		if (number == (int)number || pixelWidth == 1) return 0;
+		int decimalPlaces = (int)(-Math.log10(pixelWidth)+1.9);
+		if (decimalPlaces < 0) decimalPlaces = 0;
+		if (decimalPlaces >9) decimalPlaces = 9;
+		return decimalPlaces;
+	}
+
 	public static Roi enlarge(Roi roi, double pixels) {
 		if (pixels==0)
 			return roi;
@@ -86,14 +162,14 @@ public static Roi enlarge(Roi roi, double pixels) {
 		edm.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE);
 		roi2 = (new ThresholdToSelection()).convert(edm);
 		if (roi2==null)
-			return roi;	
+			return roi;
 		roi2.copyAttributes(roi);
 		roi2.setLocation(bounds.x-n+xoffset, bounds.y-n+yoffset);
 		if (roi.getStroke()!=null)
 			roi2.setStroke(roi.getStroke());
 		return roi2;
 	}
-	
+
 	private static Roi enlargeRectOrOval(Roi roi, int n) {
 		Rectangle bounds = roi.getBounds();
 		bounds.x -= n;
@@ -110,7 +186,7 @@ private static Roi enlargeRectOrOval(Roi roi, int n) {
 		roi2.copyAttributes(roi);
 		return roi2;
 	}
-   
+
 	private static Roi shrink(Roi roi, int n) {
 		Rectangle bounds = roi.getBounds();
 		int width = bounds.width + 2;
@@ -120,7 +196,7 @@ private static Roi shrink(Roi roi, int n) {
 		ip.setColor(255);
 		ip.fill(roi);
 		roi.setLocation(bounds.x, bounds.y);
-		FloatProcessor edm = new EDM().makeFloatEDM (ip, 0, false);		
+		FloatProcessor edm = new EDM().makeFloatEDM (ip, 0, false);
 		edm.setThreshold(n+1, Float.MAX_VALUE, ImageProcessor.NO_LUT_UPDATE);
 		Roi roi2 = (new ThresholdToSelection()).convert(edm);
 		if (roi2==null)
@@ -132,7 +208,7 @@ private static Roi shrink(Roi roi, int n) {
 		roi2.setLocation(bounds.x+bounds2.x-1, bounds.y+bounds2.y-1);
 		return roi2;
 	}
-	
+
 	public static Roi enlarge255(Roi roi, double pixels) {
 		if (pixels==0)
 			return roi;
@@ -165,14 +241,14 @@ public static Roi enlarge255(Roi roi, double pixels) {
 		ip.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE);
 		roi2 = (new ThresholdToSelection()).convert(ip);
 		if (roi2==null)
-			return roi;	
+			return roi;
 		roi2.copyAttributes(roi);
 		roi2.setLocation(bounds.x-n+xoffset, bounds.y-n+yoffset);
 		if (roi.getStroke()!=null)
 			roi2.setStroke(roi.getStroke());
 		return roi2;
 	}
-	
+
 	private static Roi shrink255(Roi roi, int n) {
 		Rectangle bounds = roi.getBounds();
 		int width = bounds.width + 2;