2023.09.02 (1.54g15; ImageProcessor.getSliceNumber)

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 = "1.54g";
-	public static final String BUILD = "12";
+	public static final String BUILD = "15";
 	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/ImagePlus.java

@@ -2015,6 +2015,8 @@ public synchronized void setSlice(int n) {
 				updateAndRepaintWindow();
 			else
 				img = null;
+			if (ip!=null)
+				ip.setSliceNumber(n);
 		}
 	}
 

ij/ImageStack.java

@@ -330,6 +330,7 @@ else if (stack[n-1] instanceof int[]) {
 			ip.setMinAndMax(min, max);
 		if (cTable!=null)
 			ip.setCalibrationTable(cTable);
+		ip.setSliceNumber(n);
 		return ip;
 	}
 

ij/VirtualStack.java

@@ -222,6 +222,7 @@ public ImageProcessor getProcessor(int n) {
 		}
 		if (cTable!=null)
 			ip.setCalibrationTable(cTable);
+		ip.setSliceNumber(n);
 		return ip;
 	 }
 

ij/gui/ImageWindow.java

@@ -47,7 +47,6 @@ public class ImageWindow extends Frame implements FocusListener, WindowListener,
 	private static Point nextLocation;
 	public static long setMenuBarTime;	
 	private int textGap = centerOnScreen?0:TEXT_GAP;
-	private Point initialLoc;
 	private int screenHeight, screenWidth;
 
 
@@ -161,7 +160,7 @@ private void setLocationAndSize(boolean updating) {
 		int width = imp.getWidth();
 		int height = imp.getHeight();
 
-		// load prefernces file location
+		// load preferences file location
 		Point loc = Prefs.getLocation(LOC_KEY);
 		Rectangle bounds = null;
 		if (loc!=null) {
@@ -243,10 +242,8 @@ private void setLocationAndSize(boolean updating) {
 			validate();
 		} else 
 			pack();
-		if (!updating) {
+		if (!updating)
 			setLocation(x, y);
-			initialLoc = new Point(x,y);
-		}
 	}
 
 	Rectangle getMaxWindow(int xloc, int yloc) {
@@ -455,7 +452,7 @@ else if (d.yesPressed()) {
 		if (ij!=null && ij.quitting())  // this may help avoid thread deadlocks
 			return true;
 		Rectangle bounds = getBounds();
-		if (initialLoc!=null && !bounds.equals(initialLoc) && !IJ.isMacro()
+		if (!IJ.isMacro()
 		&& bounds.y<screenHeight/3 && (bounds.y+bounds.height)<=screenHeight
 		&& (bounds.x+bounds.width)<=screenWidth) {
 			Prefs.saveLocation(LOC_KEY, new Point(bounds.x,bounds.y));
@@ -730,14 +727,12 @@ public static void setNextLocation(int x, int y) {
     public void setLocationAndSize(int x, int y, int width, int height) {
 		setBounds(x, y, width, height);
 		getCanvas().fitToWindow();
-		initialLoc = null;
 		pack();
 	}
 
     @Override
     public void setLocation(int x, int y) {
     	super.setLocation(x, y);
-		initialLoc = null;
 	}
 
 	public void setSliderHeight(int height) {

ij/gui/PlotVirtualStack.java

@@ -41,6 +41,7 @@ public ImageProcessor getProcessor(int n) {
 					ip = ip.convertToRGB();
 				else if (bitDepth==8)
 					ip =  ip.convertToByte(false);
+				ip.setSliceNumber(n);
 				return ip;
 			} catch (Exception e) {
 				IJ.handleException(e);

ij/gui/PointRoi.java

@@ -846,7 +846,7 @@ public Point[] getContainedPoints() {
 		FloatPolygon p = getFloatPolygon();
 		Point[] points = new Point[p.npoints];
 		for (int i=0; i<p.npoints; i++)
-			points[i] = new Point((int) Math.round(p.xpoints[i] - 0.5f), (int) Math.round(p.ypoints[i] - 0.5f));
+			points[i] = new Point((int) Math.round(p.xpoints[i]), (int) Math.round(p.ypoints[i]));
 		return points;
 	}
 

ij/io/Opener.java

@@ -1301,6 +1301,10 @@ public int getFileType(String path) {
 		int b0=buf[0]&255, b1=buf[1]&255, b2=buf[2]&255, b3=buf[3]&255;
 		//IJ.log("getFileType: "+ name+" "+b0+" "+b1+" "+b2+" "+b3);
 
+		 // ImspectorPro MSR
+		if (name.endsWith(".msr")||name.endsWith(".MSR"))
+			return UNKNOWN; // Open with Bio-formats plugin
+
 		 // Combined TIFF and DICOM created by GE Senographe scanners
 		if (buf[128]==68 && buf[129]==73 && buf[130]==67 && buf[131]==77
 		&& ((b0==73 && b1==73)||(b0==77 && b1==77)))

ij/plugin/AVI_Reader.java

@@ -451,12 +451,16 @@ public synchronized ImageProcessor getProcessor(int n) {
 			closeFile(rFile);
 		}
 		if (pixels == null) return null; //failed
+		ImageProcessor ip = null;
 		if (pixels instanceof byte[])
-			return new ByteProcessor(dwWidth, biHeight, (byte[])pixels, cm);
+			ip = new ByteProcessor(dwWidth, biHeight, (byte[])pixels, cm);
 		else if (pixels instanceof short[])
-			return new ShortProcessor(dwWidth, biHeight, (short[])pixels, cm);
+			ip = new ShortProcessor(dwWidth, biHeight, (short[])pixels, cm);
 		else
-			return new ColorProcessor(dwWidth, biHeight, (int[])pixels);
+			ip = new ColorProcessor(dwWidth, biHeight, (int[])pixels);
+		if (ip!=null)
+			ip.setSliceNumber(n);
+		return ip;
 	}
 
 	/** Returns the image width of the virtual stack */

ij/plugin/Concatenator.java

@@ -76,14 +76,14 @@ public static ImagePlus run(ImagePlus img1, ImagePlus img2, ImagePlus img3) {
 	/** Concatenates four images, stacks or hyperstacks. */
 	public static ImagePlus run(ImagePlus img1, ImagePlus img2, ImagePlus img3, ImagePlus img4) {
 		ImagePlus[] images = new ImagePlus[4];
-		images[0]=img1; images[1]=img2;  images[2]=img3; images[2]=img4;
+		images[0]=img1; images[1]=img2;  images[2]=img3; images[3]=img4;
 		return (new Concatenator()).concatenate(images, false);
 	}
 
 	/** Concatenates five images, stacks or hyperstacks. */
 	public static ImagePlus run(ImagePlus img1, ImagePlus img2, ImagePlus img3, ImagePlus img4, ImagePlus img5) {
 		ImagePlus[] images = new ImagePlus[5];
-		images[0]=img1; images[1]=img2;  images[2]=img3; images[2]=img4; images[5]=img5;
+		images[0]=img1; images[1]=img2;  images[2]=img3; images[3]=img4; images[4]=img5;
 		return (new Concatenator()).concatenate(images, false);
 	}
 

ij/plugin/FileInfoVirtualStack.java

@@ -220,6 +220,7 @@ public ImageProcessor getProcessor(int n) {
 		if (ip!=null) {
 			if (cTable!=null)
 				ip.setCalibrationTable(cTable);
+			ip.setSliceNumber(n);
 			return ip;
 		} else {
 			int w=getWidth(), h=getHeight();

ij/plugin/ListVirtualStack.java

@@ -164,6 +164,7 @@ public ImageProcessor getProcessor(int n) {
 			IJ.redirectErrorMessages(false);
 			if (imp2!=null)
 				imp2.setFileInfo(imp.getOriginalFileInfo());
+			ip.setSliceNumber(n);
 			return ip;
 		} else {
 				ImageProcessor ip = null;
@@ -174,6 +175,7 @@ public ImageProcessor getProcessor(int n) {
 					case 32: ip=new FloatProcessor(imageWidth,imageHeight); break;
 				}
 			IJ.redirectErrorMessages(false);
+			ip.setSliceNumber(n);
 			return ip;
 		}
 	 }

ij/plugin/filter/PlugInFilter.java

@@ -30,7 +30,8 @@ the image data converted to a FloatProcessor (3 times per
 		this method and unlock it when the filter is finished.
         For PlugInFilters specifying the {@link #NO_IMAGE_REQUIRED} flag
         and not the {@link #DONE} flag, run(ip) is called once with the
-        argument <code>null</code>.
+        argument <code>null</code>. Use ip.getSliceNumber()
+        to get the stack position (1-n).
      */
 	public void run(ImageProcessor ip);
 

ij/plugin/filter/PlugInFilterRunner.java

@@ -442,7 +442,7 @@ private void announceSliceNumber(int slice) {
 	public int getSliceNumber() {
 		synchronized(sliceForThread){
 			Integer number = (Integer)sliceForThread.get(Thread.currentThread());
-			return (number == null) ? -1 : number.intValue();
+			return (number==null) ? -1 : number.intValue();
 		}
 	}
 

ij/process/FloatPolygon.java

@@ -4,18 +4,20 @@
 import java.awt.geom.Rectangle2D;
 
 /** Used by the Roi classes to return float coordinate arrays and to
-	determine if a point is inside or outside of spline fitted selections. */
+	determine if a point is inside or outside of spline fitted selections.
+	Use the public 'xpoints' and 'ypoints' fields to access the coordinates
+	and the 'npoints' field to determine the number of points. */
 public class FloatPolygon {
 	private Rectangle bounds;
 	private float minX, minY, maxX, maxY;
 
-	/** The number of points. */
+	/** The number of points in the 'xpoints' and 'ypoints' arrays. */
 	public int npoints;
 
-	/* The array of x coordinates. */
+	/* An array containing 'npoints' x coordinates. */
 	public float xpoints[];
 
-	/* The array of y coordinates. */
+	/* An array containing 'npoints' y coordinates. */
 	public float ypoints[];
 
 	/** Constructs an empty FloatPolygon. */ 

ij/process/ImageProcessor.java

@@ -2877,15 +2877,16 @@ public void applyMacro(String macro) {
 		ij.plugin.filter.ImageMath.applyMacro(this, macro, false);
 	}
 
-	/* Returns the PlugInFilter slice number. */
+	/** Returns the stack position (1-n) of this image. */
 	public int getSliceNumber() {
 		if (sliceNumber<1)
 			return 1;
 		else
 			return sliceNumber;
 	}
 
-	/** PlugInFilterRunner uses this method to set the slice number. */
+	/** ImagePlus.setStack() and the PlugInFilterRunner
+	  use this method to set the stack position. */
 	public void setSliceNumber(int slice) {
 		sliceNumber = slice;
 	}

release-notes.html

@@ -5,7 +5,7 @@
 </head>
 <body>
 
-<li> <u>1.54g12  12 August 2023</u>
+<li> <u>1.54g15  02 September 2023</u>
 <ul>
 <li> Thanks to Nicolas De Francesco and Curtis Rueden,
 the macro language documentation (functions.html) is now included
@@ -14,6 +14,8 @@
 <li> Thanks to Robert Baer, the “Associate ’Show All’ ROIs with slices”
 option in the ROI Manager’s More&gt;&gt;Options dialog is now always
 enabled when ImageJ starts up.
+<li> Thanks to Fred Damen and Michael Schmid, the ImageProcessor.getSliceNumber()
+method no long requires a PlugInFilter to return the stack position.
 <li> Thanks to 'Phiir42', fixed bug with closed tables reopening after
 a macro finishes.
 <li> Thanks to 'Ender', fixed headless mode "Scale Bar" and "Show Info" bugs.
@@ -24,8 +26,12 @@
 RotatedRectRoi rounding bug and a bug where the resulting polygon consisted
 of 5 points instead of 4.
 <li> Thanks to Volker Backer, fixed a Roi group bug with Fiji on Linux.
+<li> Thanks to Yuekan Jiao and Michael Schmid, fixed a rounding error with
+PointRoi.getContainedPoints().
 <li> Thanks to Guenter Pudmich, fixed a 1.54d regression that caused 16-bit
 grayscale PNGs to be opened incorrectly.
+<li> Thanks to Saleh Altahini, fixed bug with opening ImspectorPro MSR files
+using Bio-Formats.
 </ul>
 
 <li> <u>1.54f  29 June 2023</u>