2022.12.14 (1.54a16; Multi-point tool)

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 = "1.54a";
-	public static final String BUILD = "14";
+	public static final String BUILD = "16";
 	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/PointRoi.java

@@ -369,8 +369,10 @@ public PointRoi addPoint(double x, double y) {
 	/** Adds a point at the specified stack position. */
 	public void addPoint(double x, double y, int position) {
 		if (counters==null) {
-			counters = new short[100];
-			positions = new int[100];
+			int size = nPoints*2;
+			if (size<100) size=100;
+			counters = new short[size];
+			positions = new int[size];
 		}
 		addPoint(null, x, y);
 		positions[nPoints-1] = position;	
@@ -395,22 +397,24 @@ private synchronized void incrementCounter(ImagePlus imp) {
 		boolean isStack = imp!=null && imp.getStackSize()>1;
 		if (counter!=0 || isStack || counters!=null) {
 			if (counters==null) {
-				counters = new short[nPoints*2];
-				positions = new int[nPoints*2];
+				int size = nPoints*2;
+				if (size<100) size=100;
+				counters = new short[size];
+				positions = new int[size];
 			}
-			counters[nPoints-1] = (short)counter;
-			if (imp!=null)
-					positions[nPoints-1] = imp.getStackSize()>1 ? imp.getCurrentSlice() : 0;
-			//if (positions[nPoints-1]==0 || positions[nPoints-1]==1 || counters[nPoints-1]==0)
-			//	IJ.log("incrementCounter: "+nPoints+" "+" "+positions[nPoints-1]+" "+counters[nPoints-1]+" "+imp);
-			if (nPoints+1==counters.length) {
+			if (nPoints>=counters.length) {
 				short[] temp = new short[counters.length*2];
 				System.arraycopy(counters, 0, temp, 0, counters.length);
 				counters = temp;
 				int[] temp1 = new int[counters.length*2];
 				System.arraycopy(positions, 0, temp1, 0, positions.length);
 				positions = temp1;
 			}
+			counters[nPoints-1] = (short)counter;
+			if (imp!=null)
+					positions[nPoints-1] = imp.getStackSize()>1 ? imp.getCurrentSlice() : 0;
+			//if (positions[nPoints-1]==0 || positions[nPoints-1]==1 || counters[nPoints-1]==0)
+			//IJ.log("incrementCounter: "+nPoints+" "+counters.length+" "+counters[nPoints-1]+"   "+positions[nPoints-1]+" "+imp);
 		}
 		if (rt!=null && WindowManager.getFrame(getCountsTitle())!=null)
 			displayCounts();

ij/plugin/AboutBox.java

@@ -21,7 +21,7 @@ public void run(String arg) {
 		text[0] = "ImageJ "+ImageJ.VERSION+ImageJ.BUILD;
 		text[1] = "Wayne Rasband and contributors";
 		text[2] = "National Institutes of Health, USA";
-		text[3] = IJ.URL;
+		text[3] = "http://imagej.org";
 		text[4] = "Java "+System.getProperty("java.version")+(IJ.is64Bit()?" (64-bit)":" (32-bit)");
 		text[5] = IJ.freeMemory();
 		text[6] = "ImageJ is in the public domain";

ij/plugin/BrowserLauncher.java

@@ -60,7 +60,7 @@ public class BrowserLauncher implements PlugIn {
 	public void run(String theURL) {
 		if (error) return;
 		if (theURL==null || theURL.equals(""))
-			theURL = IJ.URL;
+			theURL = "http://imagej.org";
 		try {openURL(theURL);}
 		catch (IOException e) {}
 	}

ij/plugin/filter/Binary.java

@@ -169,8 +169,7 @@ void outline(ImageProcessor ip) {
     void median(ImageProcessor ip) {
     	ip.resetThreshold();
 		new RankFilters().rank(ip, medianRadius, RankFilters.MEAN);
-		//ip.threshold(128,255);
-		ip.threshold(127);
+		ip.threshold(128,255);
 	}
 
 	void skeletonize(ImageProcessor ip) {

ij/process/ImageProcessor.java

@@ -1940,31 +1940,7 @@ public int[] getPixel(int x, int y, int[] iArray) {
 	public void putPixel(int x, int y, int[] iArray) {
 		putPixel(x, y, iArray[0]);
 	}
-
-	/*
-	public int[] getRGBValue(int index, int[] rgb) {
-		if (rgb==null) rgb = new int[3];
-		if (this instanceof ColorProcessor)
-			return rgb;
-		if (rLUT1==null) {
-			if (cm==null)
-				makeDefaultColorModel();
-			baseCM = cm;
-			IndexColorModel m = (IndexColorModel)cm;
-			rLUT1 = new byte[256]; gLUT1 = new byte[256]; bLUT1 = new byte[256];
-			m.getReds(rLUT1); m.getGreens(gLUT1); m.getBlues(bLUT1);
-		}
-		int min2=(int)getMin(), max2=(int)getMax();
-		double scale = 256.0/(max2-min2+1);
-		double value = getf(index)-min2;
-		if (value<0.0) value = 0.0;
-		int v = (int)(value*scale+0.5);
-		if (v>255) v = 255;
-		rgb[0]=rLUT1[v]; rgb[1]=gLUT1[v]; rgb[2]=bLUT1[v];		
-		return rgb;
-	}
-	*/
-
+
 	/** Uses the current interpolation method (bilinear or bicubic)
 		to find the pixel value at real coordinates (x,y). */
 	public abstract double getInterpolatedPixel(double x, double y);

release-notes.html

@@ -5,11 +5,12 @@
 </head>
 <body>
 
-<li> <u>1.54a14  10 December 2022</u>
+<li> <u>1.54a16  14 December 2022</u>
 <ul>
 <li> Thanks to Herbie Gluender, added the 
 <i>Process&gt;Binary&gt;Median</i>
-command.
+command and the ImageProcessor.threshold(level1,level2)
+method.
 <li> Thanks to Christian Tischer, added the
 AVI_Reader.open(path,options) method.
 <li> Thanks to Wilhelm Burger, added a GenericDialog.addEnumChoice()
@@ -24,6 +25,8 @@
 (<a href="http://wsr.imagej.net/macros/PlotsWithVaryingSizeSymbols.ijm">example</a>).
 <li> Thanks to 'rlazevedo1', fixed a bug that caused the range arrow overlay to
 be included when saving a plot in tiff format.
+<li> Thanks to Eg Laf, fixed a bug that caused the multi-point tool
+to throw an exception when used for counting.
 </ul>
 
 <li> <u>1.53v  21 November 2022</u>