2025.09.05 (1.54r2; Point selections)

Author: rasband

ij/ImageJ.java

@@ -78,8 +78,8 @@ 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 = "1.54q";
-	public static final String BUILD = ""; //21
+	public static final String VERSION = "1.54r";
+	public static final String BUILD = "2";
 	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/ImageCanvas.java

@@ -345,7 +345,8 @@ private void drawOverlay(Overlay overlay, Graphics g) {
 					else if (t==0)
 						t = position;
 				}
-				if (((c==0||c==channel) && (z==0||z==slice) && (t==0||t==frame)) || roiManagerShowAllMode)
+				//IJ.log("drawOverlay: i="+i+", pos="+roi.getPosition());
+				if (((c==0||c==channel) && (z==0||z==slice) && (t==0||t==frame)) || roiManagerShowAllMode || position == PointRoi.POINTWISE_POSITION)
 					drawRoi(g, roi, drawLabels?i+LIST_OFFSET:-1);
 			} else {
 				int position = stackSize>1?roi.getPosition():0;
@@ -363,7 +364,7 @@ else if (t==1)
 					position = 0;
 				if ((roi instanceof PointRoi) && Prefs.showAllPoints)
 					position = 0;
-				//IJ.log(c+" "+z+" "+t+" p="+position+"getP="+roi.getPosition()+" "+roiManagerShowAllMode);
+				//IJ.log("drawOverlay: i="+i+", pos="+roi.getPosition()+", pos2="+position);
 				if (position==0 || position==currentImage || roiManagerShowAllMode)
 					drawRoi(g, roi, drawLabels?i+LIST_OFFSET:-1);
 			}

ij/gui/PointRoi.java

@@ -57,7 +57,6 @@ public class PointRoi extends PolygonRoi {
 	private int nMarkers;
 	private boolean addToOverlay;
 	public static PointRoi savedPoints;
-	private boolean positionSet;
 
 	static {
 		setDefaultType((int)Prefs.get(TYPE_KEY, HYBRID));
@@ -423,8 +422,6 @@ private synchronized void incrementCounter(ImagePlus imp) {
 			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();
@@ -728,8 +725,7 @@ public void setPosition(int n) {
 			if (n != POINTWISE_POSITION)
 				Arrays.fill(positions, n);
 		}
-		hyperstackPosition = false;
-		positionSet = true;
+		super.setPosition(0);
 	}
 
 	/** Returns the stack position (image number) of the points in this Roi, if
@@ -738,16 +734,19 @@ public void setPosition(int n) {
 	 *  if there are different stack positions for different points.
 	 */
 	public int getPosition() {
-		//if (positions==null || nPoints<1 || !positionSet)
+		int position = 0;
 		if (positions==null || nPoints<1)
-			return 0;
+			position = 0;
+		else if (nPoints==1)
+			position = super.getPosition();
 		else {
-			int position = positions[0];
-			for (int i=1; i<nPoints; i++)
+			position = positions[0];
+			for (int i=1; i<nPoints; i++) {
 				if (positions[i] != position)
-					return POINTWISE_POSITION;
-			return position;
+					position = POINTWISE_POSITION;
+			}
 		}
+		return position;
 	}
 
 	/** Returns the stack slice of the point with the given index, or 0 if no slice defined for this point */

ij/gui/Roi.java

@@ -115,7 +115,6 @@ public class Roi extends Object implements Cloneable, java.io.Serializable, Iter
 	private String name;
 	private int position;
 	private int channel, slice, frame;
-	protected boolean hyperstackPosition;
 	private Overlay prototypeOverlay;
 	private boolean subPixel;
 	private boolean activeOverlayRoi;
@@ -1848,7 +1847,6 @@ public static synchronized void setGroupName(int groupNumber, String name) {
 				temp[i] = groupNames[i];
 			groupNames = temp;
 		}
-		//IJ.log("setGroupName: "+groupNumber+"  "+name+"  "+groupNames.length);
 		groupNames[groupNumber-1] = name;
 		groupNamesChanged = true;
 	}
@@ -2201,7 +2199,6 @@ public void setPosition(int n) {
 		if (n<0) n=0;
 		position = n;
 		channel = slice = frame = 0;
-		hyperstackPosition = false;
 	}
 
 	/** Returns the stack position (image number) for displaying this ROI,
@@ -2237,12 +2234,14 @@ public void setPosition(int channel, int slice, int frame) {
 		if (frame<0) frame=0;
 		this.frame = frame;
 		position = 0;
-		hyperstackPosition = true;
 	}
 
 	/** Returns 'true' if setPosition(C,Z,T) has been called. */
 	public boolean hasHyperStackPosition() {
-		return hyperstackPosition;
+		if (getPosition()==PointRoi.POINTWISE_POSITION)
+			return false;
+		else
+			return channel>0 || slice>0 || frame>0;
 	}
 
 	/** Sets the position of this ROI based on the stack position of the specified image.  */
@@ -2269,7 +2268,7 @@ public final int getCPosition() {
 	*   if this ROI is not associated with a particular slice.
 	*/
 	public final int getZPosition() {
-		return slice==0&&!hyperstackPosition ? getPosition() : slice;
+		return slice==0&&!hasHyperStackPosition() ? getPosition() : slice;
 	}
 
 	/** Returns the frame position of this ROI, or zero

ij/plugin/OverlayCommands.java

@@ -251,6 +251,9 @@ void addImage(boolean createImageRoi) {
 	}
 
 	private void setPosition(ImagePlus imp, Roi roi) {
+		//IJ.log("Overlay.setPosition: "+roi.size());
+		if (roi instanceof PointRoi && roi.size()>1)
+			return;
 		int stackSize = imp.getStackSize();
 		if (roi.hasHyperStackPosition() && imp.isHyperStack())
 			return;

ij/plugin/frame/RoiManager.java

@@ -703,7 +703,6 @@ boolean restore(ImagePlus imp, int index, boolean setSlice) {
 		Roi roi = (Roi)rois.get(index);
 		if (imp==null || roi==null)
 			return false;
-			//IJ.log("restore: "+roi.getPosition()+"  "+roi.getZPosition()+"  "+imp.getNSlices()+"  "+imp.getStackSize());
 		if (setSlice) {
 			boolean hyperstack = imp.isHyperStack();
 			int position = roi.getPosition();
@@ -1575,7 +1574,6 @@ void setProperties(Color color, int lineWidth, Color fillColor) {
 			if (group>=0)
 				roi.setGroup(group);
 			if (rpRoi!=null) {
-				//IJ.log("new pos="+rpRoi.getPosition());
 				if (rpRoi.hasHyperStackPosition())
 					roi.setPosition(rpRoi.getCPosition(), rpRoi.getZPosition(), rpRoi.getTPosition());
 				else
@@ -2717,7 +2715,6 @@ public void mouseWheelMoved(MouseWheelEvent event) {
 			index += rot;
 			if (index<0) index = 0;
 			if (index>=getCount()) index = getCount();
-			//IJ.log(index+"  "+rot);
 			select(index);
 			if (IJ.isWindows())
 				list.requestFocusInWindow();

release-notes.html

@@ -5,6 +5,11 @@
 </head>
 <body>
 
+<li> <u>1.54r2 5 September 2025</u>
+<ul> Fixed several bugs with displaying and positioning
+point selections in the ROI Manager and in overlays.
+</ul>
+
 <li> <u>1.54q 2 September 2025</u>
 <ul>
 <li> Thanks to 'AFMiJ', updated <i>Image&gt;Adjust&gt;Brightness/Contrast</i>