2024.11.06 (1.54m18; Hyperstack type conversions)

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 = "1.54m";
-	public static final String BUILD = "16";
+	public static final String BUILD = "18";
 	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/plugin/ImageInfo.java

@@ -192,7 +192,7 @@ private String getInfo(ImagePlus imp, ImageProcessor ip) {
 	    		String lut = getLutInfo(imp);
 				s += "(" + lut + ")\n";
 				if (imp.getNChannels()>1)
-					s += displayRanges(imp);
+					s += getDisplayRanges(imp);
 				else {
 					s += "Display range: "+(int)ip.getMin()+"-"+(int)ip.getMax()+"\n";
 					ip.resetRoi();
@@ -207,7 +207,7 @@ private String getInfo(ImagePlus imp, ImageProcessor ip) {
 	    		} else
 	    			s += "Bits per pixel: 32 (float, "+getLutInfo(imp)+")\n";
 				if (imp.getNChannels()>1)
-					s += displayRanges(imp);
+					s += getDisplayRanges(imp);
 				else {
 					String pvrLabel = "Pixel value range: ";
 					s += "Display range: ";
@@ -494,7 +494,7 @@ private String getLutInfo(ImagePlus imp) {
 		return lut;
 	}
 
-	private String displayRanges(ImagePlus imp) {
+	public static String getDisplayRanges(ImagePlus imp) {
 		LUT[] luts = imp.getLuts();
 		if (luts==null)
 			return "";
@@ -529,7 +529,7 @@ private void showInfo(ImagePlus imp, String info, int width, int height) {
 		//ed.create("Info for "+imp.getTitle(), info);
 	}
 
-    private String d2s(double n) {
+    private static String d2s(double n) {
 		return IJ.d2s(n,Tools.getDecimalPlaces(n));
     }
 

ij/plugin/Orthogonal_Views.java

@@ -53,6 +53,7 @@ public class Orthogonal_Views implements PlugIn, MouseListener, MouseMotionListe
 	private boolean initialized;
 	private boolean sliceSet;
 	private Thread thread;
+	final static String CROSS = "|OV|";
 
 
 	public void run(String arg) {
@@ -563,7 +564,7 @@ void updateZYView(Point p, ImageStack is) {
 
 	}
 
-	/** draws the crosses in the images */
+	/** draws the crosses on the images */
 	void drawCross(ImagePlus imp, Point p, GeneralPath path) {
 		int width=imp.getWidth();
 		int height=imp.getHeight();
@@ -580,7 +581,17 @@ void dispose() {
 			done = true;
 			notify();
 		}
-		imp.setOverlay(null);
+		Overlay overlay = imp.getOverlay();
+		if (overlay!=null) {
+			overlay.remove(CROSS);
+			ImageCanvas ic = imp.getCanvas();
+			if (ic!=null)
+				ic.setCustomRoi(true);
+			if (overlay.size()==0)
+				imp.setOverlay(null);
+			else
+				imp.draw();
+		}
 		if (canvas!=null) {
 			canvas.removeMouseListener(this);
 			canvas.removeMouseMotionListener(this);
@@ -747,15 +758,30 @@ private void exec() {
 		updateViews(p, is);
 		GeneralPath path = new GeneralPath();
 		drawCross(imp, p, path);
-		if (!done)
-			imp.setOverlay(path, color, new BasicStroke(1));
+		if (!done) {
+			if (imp.getOverlay()==null)
+				imp.setOverlay(new Overlay());
+			setOverlay(imp, path);
+		}
 		canvas.setCustomRoi(true);
 		updateCrosses(p.x, p.y, arat, brat);
 		if (syncZoom) updateMagnification(p.x, p.y);
 		arrangeWindows(sticky);
 		initialized = true;
 	}
 
+	private void setOverlay(ImagePlus imp, GeneralPath path) {
+		Overlay overlay = imp.getOverlay();
+		if (overlay==null)
+			overlay = new Overlay();
+		Roi roi = new ShapeRoi(path);
+		roi.setStrokeColor(color);
+		roi.setStroke(new BasicStroke(1));
+		overlay.remove(CROSS);
+		overlay.add(roi, CROSS);
+		imp.setOverlay(overlay);
+	}
+
 	private void updateCrosses(int x, int y, double arat, double brat) {
 		Point p;
 		int z=imp.getNSlices();
@@ -768,7 +794,7 @@ private void updateCrosses(int x, int y, double arat, double brat) {
 		GeneralPath path = new GeneralPath();
 		drawCross(xz_image, p, path);
 		if (!done)
-			xz_image.setOverlay(path, color, new BasicStroke(1));
+			setOverlay(xz_image, path);
 		if (rotateYZ) {
 			if (flipXZ)
 				zcoord=(int)Math.round(brat*(z-zlice));
@@ -782,7 +808,7 @@ private void updateCrosses(int x, int y, double arat, double brat) {
 		path = new GeneralPath();
 		drawCross(yz_image, p, path);
 		if (!done)
-			yz_image.setOverlay(path, color, new BasicStroke(1));
+			setOverlay(yz_image, path);
 		IJ.showStatus(imp.getLocationAsString(crossLoc.x, crossLoc.y));
 	}
 

ij/process/StackConverter.java

@@ -5,7 +5,7 @@
 import ij.*;
 import ij.gui.*;
 import ij.measure.*;
-import ij.plugin.RGBStackConverter;
+import ij.plugin.*;
 
 /** This class does stack type conversions. */
 public class StackConverter {
@@ -57,6 +57,7 @@ public void convertToGray8() {
 	    int inc = nSlices/20;
 	    if (inc<1) inc = 1;
 	    LUT[] luts = composite?((CompositeImage)imp).getLuts():null;
+		boolean scale = ImageConverter.getDoScaling();
 		for(int i=1; i<=nSlices; i++) {
 			label = stack1.getSliceLabel(1);
 			ip = stack1.getProcessor(1);
@@ -67,7 +68,6 @@ public void convertToGray8() {
 				max = luts[index].max;
 			}
 			ip.setMinAndMax(min, max);
-			boolean scale = ImageConverter.getDoScaling();
 			stack2.addSlice(label, ip.convertToByte(scale));
 			if ((i%inc)==0) {
 				IJ.showProgress((double)i/nSlices);
@@ -76,9 +76,14 @@ public void convertToGray8() {
 		}
 		imp.setStack(null, stack2);
 		imp.setCalibration(imp.getCalibration()); //update calibration
-		if (imp.isComposite()) {
-			((CompositeImage)imp).resetDisplayRanges();
-			((CompositeImage)imp).updateAllChannelsAndDraw();
+		if (composite && luts!=null) {
+			if (scale) {
+				for (int i=0; i<luts.length; i++) {
+					luts[i].min = 0;
+					luts[i].max = 255;
+				}
+			}
+			((CompositeImage)imp).setLuts(luts);
 		}
 		ImageConverter.record();
 		imp.setSlice(currentSlice);
@@ -99,7 +104,7 @@ void convertRGBToGray8() {
 		String label;
 	    int inc = nSlices/20;
 	    if (inc<1) inc = 1;
-		for(int i=1; i<=nSlices; i++) {
+		for (int i=1; i<=nSlices; i++) {
 			label = stack1.getSliceLabel(1);
 			ip = stack1.getProcessor(1);
 			stack1.deleteSlice(1);
@@ -116,7 +121,7 @@ void convertRGBToGray8() {
 		IJ.showProgress(1.0);
 	}
 
-	/** Converts this Stack to 16-bit grayscale. */
+	/** Converts this Stack to 16-bit grayscale. */	
 	public void convertToGray16() {
 		if (type==ImagePlus.GRAY16)
 			return;
@@ -126,6 +131,9 @@ public void convertToGray16() {
 			ImageConverter.convertAndCalibrate(imp,"16-bit");
 			return;
 		}
+		ImageProcessor ip = imp.getProcessor();
+		double min = ip.getMin();
+		double max = ip.getMax();
 		ImageStack stack1 = imp.getStack();
 		ImageStack stack2 = new ImageStack(width, height);
 		int channels = imp.getNChannels();
@@ -137,13 +145,15 @@ public void convertToGray16() {
 	    if (inc<1) inc = 1;
 	    boolean scale = type==ImagePlus.GRAY32 && ImageConverter.getDoScaling();
 	    ImageProcessor ip1, ip2;
-		for(int i=1; i<=nSlices; i++) {
+		for (int i=1; i<=nSlices; i++) {
 			label = stack1.getSliceLabel(1);
 			ip1 = stack1.getProcessor(1);
 			if (luts!=null) {
-				int index = ((i-1)%channels);
-				ip1.setMinAndMax(luts[index].min,luts[index].max);
+				int index = (i-1)%luts.length;
+				min = luts[index].min;
+				max = luts[index].max;
 			}
+			ip1.setMinAndMax(min, max);
 			ip2 = ip1.convertToShort(scale);
 			stack1.deleteSlice(1);
 			stack2.addSlice(label, ip2);
@@ -154,13 +164,16 @@ public void convertToGray16() {
 		}
 		IJ.showProgress(1.0);
 		imp.setStack(null, stack2);
-		if (scale) {
-			for (int c=channels; c>=1; c--) {
-				imp.setPosition(c,imp.getSlice(),imp.getFrame());
-				imp.setDisplayRange(0,65535);
+		if (imp.isComposite() && luts!=null) {
+			if (scale) {
+				for (int i=0; i<luts.length; i++) {
+					luts[i].min = 0;
+					luts[i].max = 65535;
+				}
 			}
+			((CompositeImage)imp).setLuts(luts);
+			imp.updateAndDraw();
 		}
-		ImageConverter.record();
 	}
 
 	/** Converts this Stack to 32-bit (float) grayscale. */
@@ -176,6 +189,12 @@ public void convertToGray32() {
 	    if (inc<1) inc = 1;
 	    ImageProcessor ip1, ip2;
 	    Calibration cal = imp.getCalibration();
+	    double min = imp.getDisplayRangeMin();
+		double max = imp.getDisplayRangeMax();
+	    int channels = imp.getNChannels();
+	    LUT[] luts = imp.getLuts();
+	    if ((luts!=null && luts.length!=channels) || cal.calibrated())
+	    	luts = null;
 		for(int i=1; i<=nSlices; i++) {
 			label = stack1.getSliceLabel(1);
 			ip1 = stack1.getProcessor(1);
@@ -195,6 +214,11 @@ public void convertToGray32() {
 			imp.resetDisplayRange();
 			imp.updateAndDraw();
 		}
+		if (imp.isHyperStack() && luts!=null)
+			((CompositeImage)imp).setLuts(luts);
+		else if (!cal.calibrated())
+			imp.setDisplayRange(min, max);
+
 	}
 
 	/** Converts the Stack to RGB. */

ij/process/TypeConverter.java

@@ -235,11 +235,13 @@ FloatProcessor convertShortToFloat(float[] cTable) {
 		if (cTable!=null && cTable.length==65536)
 			for (int i=0; i<width*height; i++)
 				pixels32[i] = cTable[pixels16[i]&0xffff];
-		else
+		else {
 			for (int i=0; i<width*height; i++)
 				pixels32[i] = pixels16[i]&0xffff;
+		}
 	    ColorModel cm = ip.getColorModel();
-	    return new FloatProcessor(width, height, pixels32, cm);
+	    FloatProcessor fp = new FloatProcessor(width, height, pixels32, cm);
+	    return fp;
 	}
 
 	/** Converts processor to a ColorProcessor. */

release-notes.html

@@ -8,6 +8,8 @@
 
 <li> <u>1.54m16  28 October 2024</u>
 <ul>
+<li> Thanks to Michael Cammer, the <i>Orthogonal Views</i> command
+no longer removes overlays.
 <li> Thanks to 'Patricia' and Herbie Gluender, the
 <i>Image&gt;Transform&gt;Image to Results</i> command
 now shows NaNs when values are outside non-rectangular