2023.04.19 (1.54e21; Scaled 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 = "1.54e";
-	public static final String BUILD = "11";
+	public static final String BUILD = "22";
 	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/Prefs.java

@@ -58,7 +58,8 @@ public class Prefs {
 		REVERSE_NEXT_PREVIOUS_ORDER=1<<5, AUTO_RUN_EXAMPLES=1<<6, SHOW_ALL_POINTS=1<<7,
 		DO_NOT_SAVE_WINDOW_LOCS=1<<8, JFILE_CHOOSER_CHANGED=1<<9,
 		CANCEL_BUTTON_ON_RIGHT=1<<10, IGNORE_RESCALE_SLOPE=1<<11,
-		NON_BLOCKING_DIALOGS=1<<12, FIXED_DICOM_SCALINGg=1<<13;
+		NON_BLOCKING_DIALOGS=1<<12, FIXED_DICOM_SCALING=1<<13,
+		CALIBRATE_CONVERSIONS=1<<14;
 	public static final String OPTIONS2 = "prefs.options2";
 
 	/** file.separator system property */
@@ -192,6 +193,8 @@ public class Prefs {
 	public static boolean autoLivePlots;
 	/** Use full range for 16-bit inversions */
 	public static boolean fullRange16bitInversions;
+	/** Calibrate image type conversions */
+	public static boolean calibrateConversions;
 
 	//Save location of moved image windows */	
 	//public static boolean saveImageLocation = true;
@@ -589,7 +592,8 @@ static void loadOptions() {
 		dialogCancelButtonOnRight = (options2&CANCEL_BUTTON_ON_RIGHT)!=0;
 		ignoreRescaleSlope = (options2&IGNORE_RESCALE_SLOPE)!=0;
 		nonBlockingFilterDialogs = (options2&NON_BLOCKING_DIALOGS)!=0;
-		fixedDicomScaling = (options2&FIXED_DICOM_SCALINGg)!=0;
+		fixedDicomScaling = (options2&FIXED_DICOM_SCALING)!=0;
+		//calibrateConversions = (options2&CALIBRATE_CONVERSIONS)!=0;
 	}
 
 	static void saveOptions(Properties prefs) {
@@ -621,7 +625,8 @@ static void saveOptions(Properties prefs) {
 			+ (dialogCancelButtonOnRight?CANCEL_BUTTON_ON_RIGHT:0)
 			+ (ignoreRescaleSlope?IGNORE_RESCALE_SLOPE:0)
 			+ (nonBlockingFilterDialogs?NON_BLOCKING_DIALOGS:0)
-			+ (fixedDicomScaling?FIXED_DICOM_SCALINGg:0);
+			+ (fixedDicomScaling?FIXED_DICOM_SCALING:0);
+			//+ (calibrateConversions?CALIBRATE_CONVERSIONS:0);
 		prefs.put(OPTIONS2, Integer.toString(options2));
 	}
 

ij/gui/ImageCanvas.java

@@ -404,7 +404,7 @@ void drawRoi(Graphics g, Roi roi, int index) {
 		ImagePlus imp2 = roi.getImage();
 		roi.setImage(imp);
 		Color saveColor = roi.getStrokeColor();
-		if (saveColor==null)
+		if (saveColor==null && roi.getFillColor()==null)
 			roi.setStrokeColor(defaultColor);
 		if (roi.getStroke()==null)
 			((Graphics2D)g).setStroke(Roi.onePixelWide);

ij/gui/PolygonRoi.java

@@ -271,11 +271,11 @@ private void drawSpline(Graphics g, float[] xpoints, float[] ypoints, int npoint
 		if (xpoints==null || xpoints.length==0)
 			return;
 		boolean doScaling = ic!=null; //quicker drawing if we don't need to convert to screen coordinates
-		if (ic!=null) {
+		if (ic!=null) try {
 			Rectangle srcRect = ic.getSrcRect();
-			if (srcRect!=null && srcRect.x == 0 && srcRect.y == 0 && ic!=null && ic.getMagnification()==1.0)
+			if (srcRect!=null && srcRect.x==0 && srcRect.y==0 && ic.getMagnification()==1.0)
 				doScaling = false;
-		}
+		} catch(Exception e) {}
 		double xd = getXBase();
 		double yd = getYBase();
 		Graphics2D g2d = (Graphics2D)g;

ij/gui/Roi.java

@@ -1936,14 +1936,19 @@ public static Color getColor() {
 		return ROIColor;
 	}
 
-	/** Sets the color used by this ROI to draw its outline. This color, if not null,
-	 * overrides the global color set by the static setColor() method.
+	/** Sets the color used by this ROI to draw its outline.
+	 * This color, if not null, overrides the global color set
+	 * by the static setColor() method. Set the stroke color
+	 * after setting the fill color to both fill and outline
+	 * the ROI.
 	 * @see #getStrokeColor
 	 * @see #setStrokeWidth
 	 * @see ij.ImagePlus#setOverlay(ij.gui.Overlay)
 	 */
 	public void setStrokeColor(Color c) {
-		 strokeColor = c;
+		strokeColor = c;
+		//if (getType()==TRACED_ROI && c!=null && fillColor!=null)
+		//	throw new IllegalArgumentException();
 	}
 
 	/** Returns the the color used to draw the ROI outline or null if the default color is being used.
@@ -1964,7 +1969,8 @@ public static void setDefaultColor(Color color) {
 	 */
 	public void setFillColor(Color color) {
 		fillColor = color;
-		if (isArea()) strokeColor=null;
+		if (fillColor!=null && isArea())
+			strokeColor=null;
 	}
 
 	/** Returns the fill color used to display this ROI, or null if it is displayed transparently.

ij/macro/Functions.java

@@ -4734,9 +4734,10 @@ else if (arg1.startsWith("supportmacroundo"))
 			Prefs.supportMacroUndo = state;
 		else if (arg1.equals("inverty"))
 			getImage().getCalibration().setInvertY(state);
-		else if (arg1.equals("scaleconversions"))
+		else if (arg1.equals("scaleconversions")) {
 			ImageConverter.setDoScaling(state);
-		else if (arg1.startsWith("copyhead"))
+			Prefs.calibrateConversions = false;
+		} else if (arg1.startsWith("copyhead"))
 			Prefs.copyColumnHeaders = state;
 		else if (arg1.equals("waitforcompletion"))
 			waitForCompletion = state;
@@ -4748,10 +4749,10 @@ else if (arg1.startsWith("monospaced"))
 			TextWindow.setMonospaced(state);
 		else if (arg1.startsWith("fullrange"))
 			Prefs.fullRange16bitInversions = state;
-		//else if (arg1.startsWith("saveimageloc")) {
-		//	Prefs.saveImageLocation = state;
-		//	if (!state) Prefs.set(ImageWindow.LOC_KEY,null);
-		else
+		else if (arg1.startsWith("calibrate")) {
+			Prefs.calibrateConversions = state;
+			ImageConverter.setDoScaling(true);
+		} else
 			interp.error("Invalid option");
 	}
 

ij/plugin/ImageInfo.java

@@ -193,8 +193,11 @@ private String getInfo(ImagePlus imp, ImageProcessor ip) {
 				s += "(" + lut + ")\n";
 				if (imp.getNChannels()>1)
 					s += displayRanges(imp);
-				else
+				else {
 					s += "Display range: "+(int)ip.getMin()+"-"+(int)ip.getMax()+"\n";
+					ImageStatistics stats = ip.getStats();
+					s += "Pixel value range: "+(int)stats.min+"-"+(int)stats.max+"\n";
+				}
 				break;
 	    	case ImagePlus.GRAY16: case ImagePlus.GRAY32:
 	    		if (type==ImagePlus.GRAY16) {
@@ -205,15 +208,31 @@ private String getInfo(ImagePlus imp, ImageProcessor ip) {
 				if (imp.getNChannels()>1)
 					s += displayRanges(imp);
 				else {
+					String pvrLabel = "Pixel value range: ";
 					s += "Display range: ";
 					double min = ip.getMin();
 					double max = ip.getMax();
-					if (cal.calibrated()) {
+					if (type==ImagePlus.GRAY32)
+						s += d2s(min) + " - " + 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";
+					} else
+						s += (int)min+"-"+(int)max+"\n";
+					ImageStatistics stats = ip.getStats();
+					String dash = "-";
+					if (ip.isSigned16Bit()) {
+						stats.min -= 32768;
+						stats.max -= 32768;
+						dash = " - ";
 					}
-					s += d2s(min) + " - " + d2s(max) + "\n";
-				}
+					if (type==ImagePlus.GRAY32)
+						s += pvrLabel+d2s(stats.min)+dash+d2s(stats.max)+"\n";
+					else
+						s += pvrLabel+(int)stats.min+dash+(int)stats.max+"\n";
+			}
 				break;
 	    	case ImagePlus.COLOR_256:
 	    		s += "Bits per pixel: 8 (color LUT)\n";

ij/plugin/Options.java

@@ -167,6 +167,8 @@ void conversions() {
 		//boolean weighted = !(Math.abs(weights[0]-1d/3d)<0.0001 && Math.abs(weights[1]-1d/3d)<0.0001 && Math.abs(weights[2]-1d/3d)<0.0001);
 		GenericDialog gd = new GenericDialog("Conversion Options");
 		gd.addCheckbox("Scale when converting", ImageConverter.getDoScaling());
+		gd.setInsets(0,40,0);
+		gd.addCheckbox("Calibrate", Prefs.calibrateConversions);
 		String prompt = "Weighted RGB conversions";
 		if (weighted)
 			prompt += " (" + IJ.d2s(weights[0]) + "," + IJ.d2s(weights[1]) + ","+ IJ.d2s(weights[2]) + ")";
@@ -177,8 +179,11 @@ void conversions() {
 		if (gd.wasCanceled())
 			return;
 		ImageConverter.setDoScaling(gd.getNextBoolean());
+		Prefs.calibrateConversions = gd.getNextBoolean();
 		Prefs.weightedColor = gd.getNextBoolean();
 		Prefs.fullRange16bitInversions = gd.getNextBoolean();
+		if (Prefs.calibrateConversions)
+			ImageConverter.setDoScaling(true);
 		if (!Prefs.weightedColor)
 			ColorProcessor.setWeightingFactors(1d/3d, 1d/3d, 1d/3d);
 		else if (Prefs.weightedColor && !weighted)

ij/plugin/OverlayCommands.java

@@ -139,7 +139,7 @@ void addSelection() {
 		String name = roi.getName();
 		boolean newOverlay = name!=null && name.equals("new-overlay");
 		Roi roiClone = (Roi)roi.clone();
-		if (roi.getStrokeColor()==null)
+		if (roi.getStrokeColor()==null && roi.getFillColor()==null)
 			roi.setStrokeColor(Roi.getColor());
 		if (overlay==null || newOverlay)
 			overlay = OverlayLabels.createOverlay();

ij/plugin/frame/RoiManager.java

@@ -1528,7 +1528,7 @@ void setProperties(Color color, int lineWidth, Color fillColor) {
 				fillColor =	 rpRoi.getFillColor();
 				rpName = rpRoi.getName();
 			}
-			if (rpRoi.getStrokeColor()==null)
+			if (rpRoi.getStrokeColor()==null && rpRoi.getFillColor()==null)
 				rpRoi.setStrokeColor(Roi.getColor());
 			rpRoi = (Roi) rpRoi.clone();
 			if (n>1)

ij/process/ImageConverter.java

@@ -28,8 +28,13 @@ public synchronized void convertToGray8() {
 		}
 		ImageProcessor ip = imp.getProcessor();
 		if (type==ImagePlus.GRAY16 || type==ImagePlus.GRAY32) {
-			imp.setProcessor(null, ip.convertToByte(doScaling));
-			imp.setCalibration(imp.getCalibration()); //update calibration
+			if (Prefs.calibrateConversions) {
+				doScaling = true;
+				convertAndCalibrate(imp,"8-bit");
+			} else {
+				imp.setProcessor(null, ip.convertToByte(doScaling));
+				imp.setCalibration(imp.getCalibration()); //update calibration
+			}
 			record();
 		} else if (type==ImagePlus.COLOR_RGB)
 	    	imp.setProcessor(null, ip.convertToByte(doScaling));
@@ -62,17 +67,63 @@ public void convertToGray16() {
 		if (type==ImagePlus.GRAY32)
 			record();
 		imp.trimProcessor();
-		imp.setProcessor(null, ip.convertToShort(doScaling));
-		imp.setCalibration(imp.getCalibration()); //update calibration
+		if (Prefs.calibrateConversions && imp.getBitDepth()==32) {
+			doScaling = true;
+			convertAndCalibrate(imp,"16-bit");
+		} else {
+			imp.setProcessor(null, ip.convertToShort(doScaling));
+			imp.setCalibration(imp.getCalibration()); //update calibration
+		}
+	}
+
+	public static void convertAndCalibrate(ImagePlus imp, String type) {
+		ImageProcessor ip = imp.getProcessor();
+		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();
+		int maxRange = eightBitConversion?255:65535;
+		double[] x = {0,maxRange};		
+		double[] y = {min2,max2};
+		CurveFitter cf = new CurveFitter(x,y);
+		cf.doFit(CurveFitter.STRAIGHT_LINE, false);
+		int np = cf.getNumParams();
+		double[] p = cf.getParams();
+		double[] parameters = new double[np];
+		for (int i=0; i<np; i++)
+			parameters[i] = p[i];
+		cal.setFunction(Calibration.STRAIGHT_LINE, parameters, type+" converted");
+		min = cal.getRawValue(min);
+		max = cal.getRawValue(max);
+		if (IJ.debugMode) IJ.log("convertAndCalibrate: "+min+" "+max);
+		imp.setDisplayRange(min,max);
+		imp.updateAndDraw();
 	}
 
 	public static void record() {
 		if (Recorder.record) {
-			Boolean state = ImageConverter.getDoScaling();
-			if (Recorder.scriptMode())
-				Recorder.recordCall("ImageConverter.setDoScaling("+state+");", true);
-			else
-				Recorder.recordString("setOption(\"ScaleConversions\", "+state+");\n");
+			if (Prefs.calibrateConversions) {
+				boolean state = true;
+				if (Recorder.scriptMode())
+					Recorder.recordCall("Prefs.calibrateConversions = true;", true);
+				else
+					Recorder.recordString("setOption(\"CalibrateConversions\", "+state+");\n");
+			} else {
+				Boolean state = ImageConverter.getDoScaling();
+				if (Recorder.scriptMode())
+					Recorder.recordCall("ImageConverter.setDoScaling("+state+");", true);
+				else
+					Recorder.recordString("setOption(\"ScaleConversions\", "+state+");\n");
+			}
 		}
 	}
 

ij/process/IntProcessor.java

@@ -1,5 +1,4 @@
 package ij.process;
-
 import java.util.*;
 import java.awt.*;
 import java.awt.image.*;
@@ -9,12 +8,12 @@
 public class IntProcessor extends ColorProcessor {
 	private byte[] pixels8;
 
-	/**Creates a blank IntProcessor with the specified dimensions. */
+	/** Creates a blank IntProcessor with the specified dimensions. */
 	public IntProcessor(int width, int height) {
 		this(width, height, new int[width*height]);
 	}
 
-	/**Creates an IntProcessor from a pixel array. */
+	/** Creates an IntProcessor from a pixel array. */
 	public IntProcessor(int width, int height, int[] pixels) {
 		super(width, height, pixels);
 		makeDefaultColorModel();

ij/process/ShortProcessor.java

@@ -9,12 +9,12 @@
 	and methods that operate on that image. */
 public class ShortProcessor extends ImageProcessor {
 
-	private int min, max, snapshotMin, snapshotMax;
-	private short[] pixels;
-	private byte[] pixels8;
+	protected int min, max, snapshotMin, snapshotMax; //wsr
+	protected short[] pixels;
+	protected byte[] pixels8;
 	private short[] snapshotPixels;
 	private byte[] LUT;
-	private boolean fixedScale;
+	protected boolean fixedScale;
 	private int bgValue;
 
 
@@ -292,7 +292,7 @@ public int getPixel(int x, int y) {
 			return 0;
 	}
 
-	public final int get(int x, int y) {
+	public int get(int x, int y) { //wsr final
 		return pixels[y*width+x]&0xffff;
 	}
 

release-notes.html

@@ -5,12 +5,19 @@
 </head>
 <body>
 
-<li> <u>1.54e11  11 April 2023</u>
+<li> <u>1.54e21  19 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
+function
+(<a href="http://wsr.imagej.net/macros/CalibrateConversions.ijm">example</a>).
+<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>
 command works with composite selections with holes.
 <li> Thanks to Philippe Carl and Michael Schmid, added the