2025.09.18 (1.54r6; Fit Spline)

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 = "1.54r";
-	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/ImageCanvas.java

@@ -210,7 +210,6 @@ public void update(Graphics g) {
 	}
 
     public void paint(Graphics g) {
-		// if (IJ.debugMode) IJ.log("paint: "+imp);
 		painted = true;
 		Roi roi = imp.getRoi();
 		Overlay overlay = imp.getOverlay();
@@ -301,7 +300,6 @@ private void drawOverlay(Overlay overlay, Graphics g) {
 		if (labelColor==null) labelColor = Color.white;
 		initGraphics(overlay, g, labelColor, Roi.getColor());
 		int n = overlay.size();
-		//if (IJ.debugMode) IJ.log("drawOverlay: "+n);
 		int currentImage = imp!=null?imp.getCurrentSlice():-1;
 		int stackSize = imp.getStackSize();
 		if (stackSize==1)
@@ -338,14 +336,13 @@ private void drawOverlay(Overlay overlay, Graphics g) {
 			int t = roi.getTPosition();
 			if (hyperstack) {
 				int position = roi.getPosition();
-				//IJ.log(c+" "+z+" "+t+"  "+channel+" "+position+" "+roiManagerShowAllMode);
 				if (position>0) {
 					if (z==0 && imp.getNSlices()>1)
 						z = position;
 					else if (t==0)
 						t = position;
 				}
-				//IJ.log("drawOverlay: i="+i+", pos="+roi.getPosition());
+				//IJ.log("drawOverlay: i="+i+", pos="+roi.getPosition()+" "+c+" "+z+" "+t);
 				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 {
@@ -364,7 +361,6 @@ else if (t==1)
 					position = 0;
 				if ((roi instanceof PointRoi) && Prefs.showAllPoints)
 					position = 0;
-				//IJ.log("drawOverlay: i="+i+", pos="+roi.getPosition()+", pos2="+position);
 				if (position==0 || position==currentImage || roiManagerShowAllMode)
 					drawRoi(g, roi, drawLabels?i+LIST_OFFSET:-1);
 			}
@@ -496,7 +492,6 @@ void drawRoiLabel(Graphics g, int index, Roi roi) {
 			} else
 				labelRects[index] = new Rectangle(x-3, y-h+1, w+4, h);
 		}		
-		//IJ.log("drawRoiLabel: "+" "+label+" "+x+" "+y+" "+flattening);
 		g.setColor(labelColor);
 		g.drawString(label, x+xoffset, y-2+yoffset);
 		g.setColor(defaultColor);
@@ -743,7 +738,6 @@ void setMagnification2(double magnification) {
 	/** Resizes the canvas when the user resizes the window. */
 	void resizeCanvas(int width, int height) {
 		ImageWindow win = imp.getWindow();
-		//IJ.log("resizeCanvas: "+srcRect+" "+imageWidth+"  "+imageHeight+" "+width+"  "+height+" "+dstWidth+"  "+dstHeight+" "+win.maxBounds);
 		if (!maxBoundsReset&& (width>dstWidth||height>dstHeight)&&win!=null&&win.maxBounds!=null&&width!=win.maxBounds.width-10) {
 			if (resetMaxBoundsCount!=0)
 				resetMaxBounds(); // Works around problem that prevented window from being larger than maximized size
@@ -768,7 +762,6 @@ void resizeCanvas(int width, int height) {
 				srcRect.y = imageHeight-srcRect.height;
 			repaint();
 		}
-		//IJ.log("resizeCanvas2: "+srcRect+" "+dstWidth+"  "+dstHeight+" "+width+"  "+height);
 	}
 
 	public void fitToWindow() {
@@ -870,7 +863,6 @@ public void zoomIn(int sx, int sy) {
 
 	/** Centers the viewable area on offscreen (image) coordinates x, y */
 	void adjustSourceRect(double newMag, int x, int y) {
-		//IJ.log("adjustSourceRect1: "+newMag+" "+dstWidth+"  "+dstHeight);
 		int w = (int)Math.round(dstWidth/newMag);
 		if (w*newMag<dstWidth) w++;
 		int h = (int)Math.round(dstHeight/newMag);
@@ -882,7 +874,6 @@ void adjustSourceRect(double newMag, int x, int y) {
 		if (r.y+h>imageHeight) r.y = imageHeight-h;
 		srcRect = r;
 		setMagnification(newMag);
-		//IJ.log("adjustSourceRect2: "+srcRect+" "+dstWidth+"  "+dstHeight);
 	}
 
     /** Returns the size to which the window can be enlarged, or null if it can't be enlarged.
@@ -949,12 +940,10 @@ public void zoomOut(int sx, int sy) {
 			if (newSrcX<0) newSrcX = 0;
 			if (newSrcY<0) newSrcY = 0;
 			srcRect = new Rectangle(newSrcX, newSrcY, newSrcWidth, newSrcHeight);
-            //IJ.log(newMag+" "+srcRect+" "+dstWidth+" "+dstHeight);
-			int newDstWidth = (int)(srcRect.width*newMag);
+ 			int newDstWidth = (int)(srcRect.width*newMag);
 			int newDstHeight = (int)(srcRect.height*newMag);
 			setMagnification(newMag);
 			setMaxBounds();
-            //IJ.log(newDstWidth+" "+dstWidth+" "+newDstHeight+" "+dstHeight);
 			if (newDstWidth<dstWidth || newDstHeight<dstHeight) {
 				setSize(newDstWidth, newDstHeight);
 				imp.getWindow().pack();
@@ -1034,7 +1023,6 @@ public void zoom100Percent() {
 	protected void scroll(int sx, int sy) {
 		int ox = xSrcStart + (int)(sx/magnification);  //convert to offscreen coordinates
 		int oy = ySrcStart + (int)(sy/magnification);
-		//IJ.log("scroll: "+ox+" "+oy+" "+xMouseStart+" "+yMouseStart);
 		int newx = xSrcStart + (xMouseStart-ox);
 		int newy = ySrcStart + (yMouseStart-oy);
 		if (newx<0) newx = 0;
@@ -1043,7 +1031,6 @@ protected void scroll(int sx, int sy) {
 		if ((newy+srcRect.height)>imageHeight) newy = imageHeight-srcRect.height;
 		srcRect.x = newx;
 		srcRect.y = newy;
-		//IJ.log(sx+"  "+sy+"  "+newx+"  "+newy+"  "+srcRect);
 		imp.draw();
 		Thread.yield();
 	}	
@@ -1056,7 +1043,6 @@ Color getColor(int index){
 	/** Sets the foreground drawing color (or background color if 
 		'setBackground' is true) to the color of the pixel at (ox,oy). */
 	public void setDrawingColor(int ox, int oy, boolean setBackground) {
-		//IJ.log("setDrawingColor: "+setBackground+this);
 		int type = imp.getType();
 		int[] v = imp.getPixel(ox, oy);
 		switch (type) {
@@ -1260,7 +1246,6 @@ public void run() {
 						&& r2.y==r1.y  && r2.width==r1.width && r2.height==r1.height && size2==size1
 						&& !(size2>1&&state==Roi.CONSTRUCTING);
 					boolean cursorMoved = !getCursorLoc().equals(cursorLoc);
-					//IJ.log(size2+" "+empty+" "+unchanged+" "+state+" "+roi1+"  "+roi2);			
 					if ((roi1==null && (size2<=1||empty)) || unchanged) {
 						if (roi1==null) imp.deleteRoi();
 						if (!cursorMoved && Toolbar.getToolId()!=Toolbar.HAND)
@@ -1355,7 +1340,6 @@ public void mouseDragged(MouseEvent e) {
 		yMouse = offScreenY(y);
 		flags = e.getModifiers();
 		mousePressedX = mousePressedY = -1;
-		//IJ.log("mouseDragged: "+flags);
 		if (flags==0)  // workaround for Mac OS 9 bug
 			flags = InputEvent.BUTTON1_MASK;
 		if (Toolbar.getToolId()==Toolbar.HAND || IJ.spaceBarDown())
@@ -1465,7 +1449,6 @@ else if (e.isAltDown())
 			roi.modState = Roi.SUBTRACT_FROM_ROI;
 		else
 			roi.modState = Roi.NO_MODS;
-		//IJ.log("setRoiModState: "+roi.modState+" "+ roi.state);
 	}
 
 	/** Disable/enable popup menu. */
@@ -1670,7 +1653,6 @@ private boolean activateOverlayRoi(int ox, int oy) {
 			Roi roi = o.get(i);
 			if (roi==null)
 				continue;
-			//IJ.log(".isAltDown: "+roi.contains(ox, oy));
 			boolean containsMousePoint = false;
 			if (roi instanceof Line) {	//grab line roi near its center
 				double grabLineWidth = 1.1 + 5./magnification;

ij/gui/PointRoi.java

@@ -421,7 +421,7 @@ private synchronized void incrementCounter(ImagePlus imp) {
 			}
 			counters[nPoints-1] = (short)counter;
 			if (imp!=null)
-					positions[nPoints-1] = imp.getStackSize()>1 ? imp.getCurrentSlice() : 0;
+				positions[nPoints-1] = imp.getStackSize()>1 ? imp.getCurrentSlice() : 0;
 		}
 		if (rt!=null && WindowManager.getFrame(getCountsTitle())!=null)
 			displayCounts();
@@ -725,9 +725,9 @@ public void setPosition(int n) {
 			if (n != POINTWISE_POSITION)
 				Arrays.fill(positions, n);
 		}
-		super.setPosition(0);
+		super.setPosition(nPoints>1?0:n);
 	}
-
+	
 	/** Returns the stack position (image number) of the points in this Roi, if
 	 *  all points have the same position. Returns 0 if none of the points is
 	 *  associated with a particular stack image, and PointRoi.POINTWISE_POSITION = -2
@@ -738,7 +738,7 @@ public int getPosition() {
 		if (positions==null || nPoints<1)
 			position = 0;
 		else if (nPoints==1)
-			position = super.getPosition();
+			return super.getPosition();
 		else {
 			position = positions[0];
 			for (int i=1; i<nPoints; i++) {

ij/gui/PolygonRoi.java

@@ -690,7 +690,6 @@ void updateClipRectAndDraw() {
 	}
 
 	protected void resetBoundingRect() {
-		//IJ.log("resetBoundingRect");
 		if (xpf!=null) {
 			resetSubPixelBoundingRect();
 			xp = toInt(xpf, xp, nPoints);
@@ -715,7 +714,6 @@ protected void resetBoundingRect() {
 			for (int i=0; i<nPoints; i++)
 				yp[i] -= ymin;
 		}
-		//IJ.log("reset: "+ymin+" "+before+" "+yp[0]);
 		x+=xmin; y+=ymin;
 		width=xmax-xmin; height=ymax-ymin;
 		if (useLineSubpixelConvention()) {
@@ -725,7 +723,6 @@ protected void resetBoundingRect() {
 	}
 
 	private void resetSubPixelBoundingRect() {
-		//IJ.log("resetSubPixelBoundingRect: "+state+" "+bounds);
 		if (xSpline!=null) {
 			resetSplineFitBoundingRect();
 			return;
@@ -946,11 +943,8 @@ void setSpline(float[] xSpline, float[] ySpline) {
 	 *  points remains unchanged.
 	 *  @return Arrays of x coordinates and y coordinates */
 	float[][] getSpline(int evaluationPoints, float[] xSpline, float[] ySpline) {
-		if (xpf==null) {
-			xpf = toFloat(xp);
-			ypf = toFloat(yp);
+		if (xpf==null)
 			enableSubPixelResolution();
-		}
 		if (xSpline==null || xSpline.length!=evaluationPoints)
 			xSpline = new float[evaluationPoints];
 		if (ySpline==null || ySpline.length!=evaluationPoints)
@@ -1065,7 +1059,6 @@ static float[][] getEquidistantPoints(float[] xpoints, float[] ypoints, int npoi
 			while ((distanceOverNextWrite >= 0.0 || i==npoints-1) && pointsWritten < npOut) {  // we have to write a new point
 				double fractionOverNextWrite = distanceOverNextWrite/distance;
 				if (distance==0) fractionOverNextWrite = 0;
-				//IJ.log("i="+i+" n="+pointsWritten+"/"+npOut+" leng="+IJ.d2s(lengthRead)+"/"+IJ.d2s(length)+" done="+IJ.d2s(pointsWritten*step)+" over="+IJ.d2s(fractionOverNextWrite)+" x,y="+IJ.d2s(x2 - fractionOverNextWrite*dx)+","+IJ.d2s(y2 - fractionOverNextWrite*dy));
 				xpOut[pointsWritten] = (float)(x2 - fractionOverNextWrite*dx);
 				ypOut[pointsWritten] = (float)(y2 - fractionOverNextWrite*dy);
 				distanceOverNextWrite -= step;

ij/plugin/OverlayCommands.java

@@ -251,7 +251,7 @@ void addImage(boolean createImageRoi) {
 	}
 
 	private void setPosition(ImagePlus imp, Roi roi) {
-		//IJ.log("Overlay.setPosition: "+roi.size());
+		//IJ.log("Overlay.setPosition: "+roi+" "+roi.getPositionAsString()+" "+roi.hasHyperStackPosition());
 		if (roi instanceof PointRoi && roi.size()>1)
 			return;
 		int stackSize = imp.getStackSize();

ij/plugin/Selection.java

@@ -245,6 +245,7 @@ void fitSpline() {
 		if (roi instanceof EllipseRoi)
 			return;
 		PolygonRoi p = (PolygonRoi)roi;
+		p = (PolygonRoi)p.clone();
 		Undo.setup(Undo.ROI, imp);
 		if (!segmentedSelection && p.getNCoordinates()>3) {
 			if (p.subPixelResolution())
@@ -259,6 +260,7 @@ else if (options!=null && options.indexOf("remove")!=-1)
 			p.removeSplineFit();
 		else
 			p.fitSpline();
+		imp.setRoi(p);
 		imp.draw();
 		LineWidthAdjuster.update(); 
 	}
@@ -344,7 +346,6 @@ PolygonRoi trimPolygon(PolygonRoi roi, double length) {
 		float[] curvature = getCurvature(x, y, n);
 		Rectangle r = roi.getBounds();
 		double threshold = rodbard(length);
-		//IJ.log("trim: "+length+" "+threshold);
 		double distance = Math.sqrt((x[1]-x[0])*(x[1]-x[0])+(y[1]-y[0])*(y[1]-y[0]));
 		x[0] += r.x; y[0]+=r.y;
 		int i2 = 1;
@@ -465,7 +466,6 @@ PolygonRoi trimFloatPolygon(PolygonRoi roi, double length) {
 		y = smooth(y, n);
 		float[] curvature = getCurvature(x, y, n);
 		double threshold = rodbard(length);
-		//IJ.log("trim: "+length+" "+threshold);
 		double distance = Math.sqrt((x[1]-x[0])*(x[1]-x[0])+(y[1]-y[0])*(y[1]-y[0]));
 		int i2 = 1;
 		double x1,y1,x2=0,y2=0;

release-notes.html

@@ -5,9 +5,13 @@
 </head>
 <body>
 
-<li> <u>1.54r2 5 September 2025</u>
-<ul> Fixed several bugs with displaying and positioning
+<li> <u>1.54r6 18 September 2025</u>
+<ul>
+<li>Fixed several bugs with displaying and positioning
 point selections in the ROI Manager and in overlays.
+<li> Thanks to Matthieu Vermeren, fixed bug where Fit Spline
+fails with ROIs in ROI Manager or overlays
+(<a href="http://wsr.imagej.net/macros/bugs/FitSpline.ijm">example</a>).
 </ul>
 
 <li> <u>1.54q 2 September 2025</u>