2023.04.26 (1.54e25; Scaled stack 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 = "1.54e";
-	public static final String BUILD = "22";
+	public static final String BUILD = "25";
 	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

@@ -2778,8 +2778,10 @@ public void setIgnoreGlobalCalibration(boolean ignoreGlobalCalibration) {
     */
 	public void mouseMoved(int x, int y) {
 		Roi roi2 = getRoi();
-		if (ij!=null && !IJ.statusBarProtected() && (roi2==null || roi2.getState()==Roi.NORMAL))
-			ij.showStatus(getLocationAsString(x,y) + getValueAsString(x,y));
+		if (ij!=null && !IJ.statusBarProtected() && (roi2==null || roi2.getState()==Roi.NORMAL)) {
+			String title = IJ.altKeyDown()?" ("+getTitle()+")":"";
+			ij.showStatus(getLocationAsString(x,y) + getValueAsString(x,y)+title);
+		}
 	}
 
     /** Redisplays the (x,y) coordinates and pixel value (which may

ij/plugin/ImageInfo.java

@@ -195,6 +195,7 @@ private String getInfo(ImagePlus imp, ImageProcessor ip) {
 					s += displayRanges(imp);
 				else {
 					s += "Display range: "+(int)ip.getMin()+"-"+(int)ip.getMax()+"\n";
+					ip.resetRoi();
 					ImageStatistics stats = ip.getStats();
 					s += "Pixel value range: "+(int)stats.min+"-"+(int)stats.max+"\n";
 				}
@@ -212,21 +213,23 @@ private String getInfo(ImagePlus imp, ImageProcessor ip) {
 					s += "Display range: ";
 					double min = ip.getMin();
 					double max = ip.getMax();
+					String dash = "-";
+					if (type==ImagePlus.GRAY32||cal.calibrated())
+						dash = " - ";
 					if (type==ImagePlus.GRAY32)
-						s += d2s(min) + " - " + d2s(max) + "\n";
+						s += d2s(min) + dash + d2s(max) + "\n";
 					else if (cal.calibrated()) {
 						pvrLabel = "Raw pixel value range: ";
 						min = cal.getCValue((int)min);
 						max = cal.getCValue((int)max);
-						s += d2s(min) + " - " + d2s(max) + "\n";
+						s += d2s(min) + dash + d2s(max) + "\n";
 					} else
-						s += (int)min+"-"+(int)max+"\n";
+						s += (int)min+dash+(int)max+"\n";
+					ip.resetRoi();
 					ImageStatistics stats = ip.getStats();
-					String dash = "-";
 					if (ip.isSigned16Bit()) {
 						stats.min -= 32768;
 						stats.max -= 32768;
-						dash = " - ";
 					}
 					if (type==ImagePlus.GRAY32)
 						s += pvrLabel+d2s(stats.min)+dash+d2s(stats.max)+"\n";
@@ -408,7 +411,7 @@ else if (curveFit==Calibration.CUSTOM)
 			s += "Macro is running"+(Interpreter.isBatchMode()?" in batch mode":"")+"\n";
 
 	    Roi roi = imp.getRoi();
-	    if (roi == null) {
+	    if (roi==null) {
 			if (cal.calibrated())
 	    		s += " \n";
 	    	s += "No selection\n";

ij/plugin/Startup.java

@@ -21,7 +21,8 @@ public class Startup implements PlugIn, ItemListener {
 			"Splash Screen",
 			"Bolder selections",
 			"Add to overlay",
-			"Flip FITS images"
+			"Flip FITS images",
+			"Calibrate conversions"
 		};
 	private String macro = "";
 	private int originalLength;
@@ -100,6 +101,8 @@ else if (item.equals(code[8]))
 			statement = "setOption(\"Add to overlay\", true);\n";
 		else if (item.equals(code[9]))
 			statement = "setOption(\"FlipFitsImages\", false);\n";
+		else if (item.equals(code[10]))
+			statement = "setOption(\"CalibrateConversions\", true);\n";
 		if (statement!=null) {
 			TextArea ta = gd.getTextArea1();
 			ta.insert(statement, ta.getCaretPosition());

ij/process/ImageConverter.java

@@ -29,7 +29,8 @@ public synchronized void convertToGray8() {
 		ImageProcessor ip = imp.getProcessor();
 		if (type==ImagePlus.GRAY16 || type==ImagePlus.GRAY32) {
 			if (Prefs.calibrateConversions) {
-				doScaling = true;
+				if (type==ImagePlus.GRAY16 && imp.getCalibration().calibrated())
+					convertToGray32();
 				convertAndCalibrate(imp,"8-bit");
 			} else {
 				imp.setProcessor(null, ip.convertToByte(doScaling));
@@ -67,30 +68,39 @@ public void convertToGray16() {
 		if (type==ImagePlus.GRAY32)
 			record();
 		imp.trimProcessor();
-		if (Prefs.calibrateConversions && imp.getBitDepth()==32) {
-			doScaling = true;
+		if (Prefs.calibrateConversions && type==ImagePlus.GRAY32)
 			convertAndCalibrate(imp,"16-bit");
-		} else {
+		else {
 			imp.setProcessor(null, ip.convertToShort(doScaling));
 			imp.setCalibration(imp.getCalibration()); //update calibration
 		}
 	}
 
 	public static void convertAndCalibrate(ImagePlus imp, String type) {
+		setDoScaling(true);
+		Calibration cal = imp.getCalibration();
 		ImageProcessor ip = imp.getProcessor();
+		int stackSize = imp.getStackSize();
 		double min = ip.getMin();
 		double max = ip.getMax();
 		ip.resetMinAndMax();
 		double min2 = ip.getMin();
 		double max2 = ip.getMax();
 		boolean eightBitConversion = type.equals("8-bit");
-		ImageProcessor ip2 = null;
-		if (eightBitConversion)
-			ip2 = ip.convertToByte(true);
-		else
-			ip2 = ip.convertToShort(true);
-		imp.setProcessor(null,ip2);
-		Calibration cal = imp.getCalibration();
+		if (stackSize>1) {
+			cal.disableDensityCalibration();
+			ImageStatistics stats = new StackStatistics(imp);
+			min2 = stats.min;
+			max2 = stats.max;
+			convertStack(imp, eightBitConversion, min2, max2);
+		} else {
+			ImageProcessor ip2 = null;
+			if (eightBitConversion)
+				ip2 = ip.convertToByte(true);
+			else
+				ip2 = ip.convertToShort(true);
+			imp.setProcessor(null,ip2);
+		}
 		int maxRange = eightBitConversion?255:65535;
 		double[] x = {0,maxRange};		
 		double[] y = {min2,max2};
@@ -109,6 +119,36 @@ public static void convertAndCalibrate(ImagePlus imp, String type) {
 		imp.updateAndDraw();
 	}
 
+	private static void convertStack(ImagePlus imp, boolean eightBitConversion, double min, double max) {
+		int nSlices = imp.getStackSize();
+		int width = imp.getWidth();
+		int height = imp.getHeight();
+		ImageStack stack1 = imp.getStack();
+		ImageStack stack2 = new ImageStack(width, height);
+		String label;
+	    int inc = nSlices/20;
+	    if (inc<1) inc = 1;
+	    ImageProcessor ip1, ip2;
+		for(int i=1; i<=nSlices; i++) {
+			label = stack1.getSliceLabel(1);
+			ip1 = stack1.getProcessor(1);
+			ip1.setMinAndMax(min, max);
+			if (eightBitConversion)
+				ip2 = ip1.convertToByte(true);
+			else
+				ip2 = ip1.convertToShort(true);
+			stack1.deleteSlice(1);
+			stack2.addSlice(label, ip2);
+			if ((i%inc)==0) {
+				IJ.showProgress((double)i/nSlices);
+				IJ.showStatus("Converting to 16-bits: "+i+"/"+nSlices);
+			}
+		}
+		IJ.showProgress(1.0);
+		imp.setStack(null, stack2);
+		ImageConverter.record();
+	}
+
 	public static void record() {
 		if (Recorder.record) {
 			if (Prefs.calibrateConversions) {

ij/process/ShortProcessor.java

@@ -476,7 +476,7 @@ public void applyTable(int[] lut) {
 		findMinAndMax();
 	}
 
-	private void process(int op, double value) {
+	protected void process(int op, double value) { //wsr
 		int v1, v2;
 		double range = getMax()-getMin();
 		//boolean resetMinMax = roiWidth==width && roiHeight==height && !(op==FILL);

ij/process/StackConverter.java

@@ -42,6 +42,12 @@ public void convertToGray8() {
 			imp.setSlice(currentSlice);
 			return;
 		}
+		if (Prefs.calibrateConversions && !composite && (type==ImagePlus.GRAY16||type==ImagePlus.GRAY32)) {
+			if (type==ImagePlus.GRAY16 && imp.getCalibration().calibrated())
+				convertToGray32();
+			ImageConverter.convertAndCalibrate(imp,"8-bit");
+			return;
+		}
 
 		ImageStack stack2 = new ImageStack(width, height);
 		Image img;
@@ -116,6 +122,10 @@ public void convertToGray16() {
 			return;
 		if (!(type==ImagePlus.GRAY8 || type==ImagePlus.GRAY32))
 			throw new IllegalArgumentException("Unsupported conversion");
+		if (Prefs.calibrateConversions && imp.getNChannels()==1 && type==ImagePlus.GRAY32) {
+			ImageConverter.convertAndCalibrate(imp,"16-bit");
+			return;
+		}
 		ImageStack stack1 = imp.getStack();
 		ImageStack stack2 = new ImageStack(width, height);
 		int channels = imp.getNChannels();

ij/text/TextCanvas.java

@@ -129,7 +129,7 @@ synchronized char[] getChars(int column, int row) {
 			return null;
 		if (row>=tp.vData.size())
 			return null;
-		char[] chars = row<tp.vData.size()?(char[])(tp.vData.elementAt(row)):null;
+		char[] chars = row>=0&&row<tp.vData.size()?(char[])(tp.vData.elementAt(row)):null;
 		if (chars==null || chars.length==0)
 			return null;
 

release-notes.html

@@ -5,17 +5,20 @@
 </head>
 <body>
 
-<li> <u>1.54e21  19 April 2023</u>
+<li> <u>1.54e25  29 April 2023</u>
 <ul>
 <li> Thanks to Jerome Mutterer, selections can now be both
 filled and outlined.  For an example, use the new
 <i>Help&gt;Examples&gt;Macro&gt;Easter Eggs</i>
 command.
 <li> Thanks to Eric Kischell, added a "Calibrate" checkbox to the
 <i>Edit&gt;Options&gt;Conversions</i> dialog and a
-setOption("CalibrateConversions",boolean) macro DOCUMENT
+setOption("CalibrateConversions",boolean) macro
 function
 (<a href="http://wsr.imagej.net/macros/CalibrateConversions.ijm">example</a>).
+<li> Thanks to Chris Ambrose, the title is displayed in the
+status bar when the cursor is moved over an image with the
+alt key down.
 <li> Thanks to 'Nottsuni', the <i>Image&gt;Show Info</i> command
 displays both the pixel value range and the display range.
 <li> Thanks to Michael Ellis, the <i>Edit&gt;Selection&gt;Interpolate</i>
@@ -37,7 +40,7 @@
 use the <i>Help&gt;Examples&gt;Macro&gt;Turtle Graphics</i>
 command.
 <li> Thanks to Stein Rorvik and Dennis Chang, added the
-"Full range 16-bit inversons" option to the
+"Full range 16-bit inversions" option to the
 <i>Edit&gt;Options&gt;Conversions</i> dialog
 and the setOption("fullRangeInversions")
 macro function.
@@ -102,11 +105,11 @@
 TextWindow.setAntialiased(boolean) method.
 <li> Fixed a bug that caused the selectImage(n) macro function,
 where n&gt;0, to sometimes fail in batch mode macros.
-<li> Thanks go 'Sethur', fixed a bug that caused the current
+<li> Thanks to 'Sethur', fixed a bug that caused the current
 working directory to not be transferred to plugins executed
 from command line macros.
 <li> Thanks to 'Sethur', fixed a bug the caused the
-ImagePlus.setPositionWithoutupdate(c,z,t) method to not
+ImagePlus.setPositionWithoutUpdate(c,z,t) method to not
 work as expected.
 <li> Thanks to Eugene Katrukha, fixed a bug that caused the
 <i>Edit&gt;Selection&gt;Fit Spline</i> command to