2025.03.19 (1.54q6; Record starts)

Author: rasband

ij/ImageJ.java

@@ -79,7 +79,7 @@ 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 = "1.54q";
-	public static final String BUILD = "2";
+	public static final String BUILD = "6";
 	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);

ij/gui/GenericDialog.java

@@ -1259,6 +1259,8 @@ private void recordOption(Object component, String value) {
 	}
 
 	private void recordCheckboxOption(Checkbox cb) {
+		if (labels==null)
+			return;
 		String label = (String)labels.get((Object)cb);
 		if (label!=null) {
 			if (cb.getState()) // checked

ij/macro/Functions.java

@@ -4546,11 +4546,11 @@ else if (str.startsWith("Error: "))
 	}
 
 	String openAsRawString() {
-		int max = 5000;
+		long max = 5000;
 		String path = getFirstString();
 		boolean specifiedMax = false;
 		if (interp.nextToken()==',') {
-			max = (int)getNextArg();
+			max = (long)getNextArg();
 			specifiedMax = true;
 		}
 		interp.getRightParen();
@@ -4567,12 +4567,12 @@ String openAsRawString() {
 			interp.error("File not found");
 		try {
 			StringBuffer sb = new StringBuffer(5000);
-			int len = (int)file.length();
+			long len = file.length();
 			if (max>len || (path.endsWith(".txt")&&!specifiedMax))
 				max = len;
 			InputStream in = new BufferedInputStream(new FileInputStream(path));
 			DataInputStream dis = new DataInputStream(in);
-			byte[] buffer = new byte[max];
+			byte[] buffer = new byte[(int)max];
 			dis.readFully(buffer);
 			dis.close();
 			char[] buffer2 = new char[buffer.length];

ij/plugin/Duplicator.java

@@ -41,10 +41,6 @@ public void run(String arg) {
 		Roi roiA = imp.getRoi();
 		ImagePlus impA = imp;
 		boolean isRotatedRect = (roiA!=null &&  roiA instanceof RotatedRectRoi);
-		if (isRotatedRect) {
-			Rectangle bounds = imp.getRoi().getBounds();
-			imp.setRoi(bounds);
-		}
 		boolean roiOutside = false;
 		if (roiA!=null) {
 			Rectangle r = roiA.getBounds();
@@ -63,13 +59,17 @@ public void run(String arg) {
 			if (imp.isHyperStack() || imp.isComposite()) {
 				if (roiOutside)
 					imp.deleteRoi();
-				duplicateHyperstack(imp, newTitle);			
-				if (isRotatedRect)
+				boolean ok = duplicateHyperstack(imp, newTitle);			
+				if (ok && isRotatedRect)
 					straightenRotatedRect(impA, roiA, IJ.getImage());								
 				return;
 			} else
 				newTitle = showDialog(imp, "Duplicate...", "Title: ");
 		}
+		if (isRotatedRect) {
+			Rectangle bounds = imp.getRoi().getBounds();
+			imp.setRoi(bounds);
+		}
 		if (newTitle==null) {
 			if (isRotatedRect)
 				imp.setRoi(roiA);
@@ -551,10 +551,10 @@ private String getNewTitle() {
 		return title;
 	}
 
-	void duplicateHyperstack(ImagePlus imp, String newTitle) {
+	boolean duplicateHyperstack(ImagePlus imp, String newTitle) {
 		newTitle = showHSDialog(imp, newTitle);
 		if (newTitle==null)
-			return;
+			return false;
 		ImagePlus imp2 = null;
 		Roi roi = imp.getRoi();
 		if (!duplicateStack) {
@@ -569,11 +569,11 @@ void duplicateHyperstack(ImagePlus imp, String newTitle) {
 			firstT = lastT = imp.getFrame();
 		}
 		imp2 = run(imp, firstC, lastC, firstZ, lastZ, firstT, lastT);
-		if (imp2==null) return;
+		if (imp2==null) return false;
 		imp2.setTitle(newTitle);
 		if (imp2.getWidth()==0 || imp2.getHeight()==0) {
 			IJ.error("Duplicator", "Selection is outside the image");
-			return;
+			return false;
 		}
 		if (roi!=null && roi.isArea() && roi.getType()!=Roi.RECTANGLE) {
 			Roi roi2 = (Roi)cropRoi(imp, roi).clone();
@@ -584,6 +584,7 @@ void duplicateHyperstack(ImagePlus imp, String newTitle) {
 		imp2.setPosition(imp.getC(), imp.getZ(), imp.getT());
 		if (IJ.isMacro()&&imp2.getWindow()!=null)
 			IJ.wait(50);
+		return true;
 	}
 
 	String showHSDialog(ImagePlus imp, String newTitle) {

ij/plugin/Straightener.java

@@ -36,7 +36,7 @@ public void run(String arg) {
 			gd.addStringField("Title:", newTitle, 15);
 			gd.addNumericField("Line Width:", width, 0, 3, "pixels");
 			if (stackSize>1)
-				gd.addCheckbox("Process Entire Stack", processStack);
+				gd.addCheckbox("Process entire stack", processStack);
 			gd.showDialog();
 			if (gd.wasCanceled()) {imp.unlock(); return;}
 			newTitle = gd.getNextString();

ij/plugin/filter/ParticleAnalyzer.java

@@ -346,8 +346,8 @@ public boolean showDialog() {
 		}
 		gd.addStringField("Circularity:", IJ.d2s(minCircularity)+"-"+IJ.d2s(maxCircularity), 12);
 		gd.addChoice("Show:", showStrings2, showStrings[showChoice]);
-		String[] labels = new String[10];
-		boolean[] states = new boolean[10];
+		String[] labels = new String[8];
+		boolean[] states = new boolean[8];
 		labels[0]="Display results"; states[0] = (options&SHOW_RESULTS)!=0;
 		labels[1]="Exclude on edges"; states[1]=(options&EXCLUDE_EDGE_PARTICLES)!=0;
 		labels[2]="Clear results"; states[2]=(options&CLEAR_WORKSHEET)!=0;
@@ -356,8 +356,7 @@ public boolean showDialog() {
 		labels[5]="Overlay"; states[5]=(options&OVERLAY)!=0;
 		labels[6]="Add to Manager"; states[6]=(options&ADD_TO_MANAGER)!=0;
 		labels[7]="Composite ROIs"; states[7]=(options&COMPOSITE_ROIS)!=0;
-		labels[8]="Record starts"; states[8]=(options&RECORD_STARTS)!=0;
-		gd.addCheckboxGroup(5, 2, labels, states);
+		gd.addCheckboxGroup(4, 2, labels, states);
 		gd.addHelp(IJ.URL2+"/docs/menus/analyze.html#ap");
 		gd.showDialog();
 		if (gd.wasCanceled())
@@ -420,8 +419,6 @@ public boolean showDialog() {
 			options |= ADD_TO_MANAGER; else options &= ~ADD_TO_MANAGER;
 		if (gd.getNextBoolean())
 			options |= COMPOSITE_ROIS; else options &= ~COMPOSITE_ROIS;
-		if (gd.getNextBoolean())
-			options |= RECORD_STARTS; else options &= ~RECORD_STARTS;
 		staticOptions = options;
 		options |= SHOW_PROGRESS;
 		if ((options&DISPLAY_SUMMARY)!=0)

release-notes.html

@@ -6,11 +6,19 @@
 <body>
 
 
-<li> <u>1.54q2  14 March 2025</u>
+<li> <u>1.54q6  19 March 2025</u>
 <ul>
+<li> Removed the particle analyzers's "Record starts" option because
+it caused a NullPointerException when running in Fiji headless
+mode.
 <li> Thanks to Michael Schmid, fixed bug where <i>Image&gt;Stacks&gt;Label</i>
 produces a NullPointerException in "overlay" mode when previewing
 and the current stack slice is not the first one.
+<li> Thanks to Christophe Leterrier, Jurgen Gluch and Guenter Pudmich,
+fixed bug with the File.openAsRawString() macro function not working with
+files larger than 2GB.
+<li> Thanks to 'scouser27', fixed bug with cancelling the duplication of
+a rotated rectangle on a hyperstack.
 <li> Thanks to Michael Schmid, fixed 1.54m9 <i>Analyze&gt;Plot Profile</i>
 regression where ImageProcessor.getLine() did not sample the
 correct points.