2024.09.07 (1.54k19; Overlay positions)

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 = "1.54k";
-	public static final String BUILD = "16";
+	public static final String BUILD = "19";
 	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/Undo.java

@@ -24,6 +24,8 @@ public class Undo {
 	public static final int OVERLAY_ADDITION = 7;
 	public static final int ROI = 8;
 	public static final int MACRO = 9;
+	/** Undo of overlay modification */
+	public static final int OVERLAY = 10;
 
 	private static int whatToUndo = NOTHING;
 	private static int imageID;
@@ -34,6 +36,7 @@ public class Undo {
 	private static double displayRangeMin, displayRangeMax;
 	private static LUT lutCopy;
 	private static Overlay overlayCopy;
+	private static int overlayImageID;
 
 	public static void setup(int what, ImagePlus imp) {
 		if (imp==null) {
@@ -81,18 +84,23 @@ public static void setup(int what, ImagePlus imp) {
 				roiCopy.setImage(null);
 			} else
 				whatToUndo = NOTHING;
+		} else if (what==OVERLAY) {
+			saveOverlay(imp);
 		} else {
 			ipCopy = null;
-			ImageProcessor ip = imp.getProcessor();
+			//ImageProcessor ip = imp.getProcessor();
 			//lutCopy = (LUT)ip.getLut().clone();
 		}
 	}
-
+
+	/** This function should be called from PlugInFilters that modify the overlay prior to the operation.
+	 *  For the type 'FILTER', undo of overlays requires that the modified image also has an overlay. */
 	public static void saveOverlay(ImagePlus imp) {
 		Overlay overlay = imp!=null?imp.getOverlay():null;
-		if (overlay!=null)
+		if (overlay!=null) {
 			overlayCopy = overlay.duplicate();
-		else
+			overlayImageID = imp.getID();
+		} else
 			overlayCopy = null;
 	}
 
@@ -114,7 +122,7 @@ public static void undo() {
 		ImagePlus imp = WindowManager.getCurrentImage();
 		if (IJ.debugMode) IJ.log("Undo.undo: "+ whatToUndo+" "+imp+"  "+impCopy);
 		if (imp==null || imageID!=imp.getID()) {
-			if (imp!=null && !IJ.macroRunning()) { // does image still have an undo buffer?
+			if (imp!=null && !IJ.macroRunning()) { // does foreground image still have an undo buffer?
 				ImageProcessor ip2 = imp.getProcessor();
 				ip2.swapPixelArrays();
 				imp.updateAndDraw();
@@ -124,7 +132,7 @@ public static void undo() {
 		}
 		switch (whatToUndo) {
 			case FILTER:
-				undoOverlay(imp);
+				undoOverlay(imp, true);
 				ImageProcessor ip = imp.getProcessor();
 				if (ip!=null) {
 					if (!IJ.macroRunning()) {
@@ -148,8 +156,8 @@ public static void undo() {
 						return;
 					} else
 						imp.setProcessor(null, ipCopy);
-					if (whatToUndo==COMPOUND_FILTER_DONE)
-						undoOverlay(imp);
+					if (whatToUndo==COMPOUND_FILTER_DONE || whatToUndo==TYPE_CONVERSION)
+						undoOverlay(imp, true);
 				}
 				break;
 			case TRANSFORM:
@@ -184,18 +192,22 @@ public static void undo() {
 					IJ.beep();
 					return;
 				}
-	    		return; //don't reset
+	    		return; //don't reset; successive undo removes further rois
+			case OVERLAY:
+				undoOverlay(imp, false);
+				imp.draw();
+				break;
     	}
     	reset();
 	}
-
-	private static void undoOverlay(ImagePlus imp) {
-		if (overlayCopy!=null) {
+
+	/** Reverts the overlay to the saved version. */
+	private static void undoOverlay(ImagePlus imp, boolean onlyModifyOvly) {
+		if (overlayCopy!=null && imp.getID()==overlayImageID) {
 			Overlay overlay = imp.getOverlay();
-			if (overlay!=null) {
-				imp.setOverlay(overlayCopy);
-				overlayCopy = overlay.duplicate();
-			}
+			imp.setOverlay(overlayCopy);
+			if (overlay != null)
+				overlayCopy = overlay.duplicate();	//swap
 		}
 	}
 

ij/gui/RoiProperties.java

@@ -31,13 +31,15 @@ public class RoiProperties implements TextListener, WindowListener {
 	private TextField groupField, colorField;
 	private Label groupName;
 
-	/** Constructs a RoiProperties using the specified title for a given roi;
+	/** Constructs a RoiProperties using the specified title for a given image and roi;
 	 *  call showDialog for the actual dialog.
 	 *  Note that the title determines which fields will be shown in the dialog. */
-	public RoiProperties(String title, Roi roi) {
+	public RoiProperties(String title, ImagePlus imp, Roi roi) {
 		if (roi==null)
 			throw new IllegalArgumentException("ROI is null");
 		this.title = title;
+		this.imp = imp;
+		this.roi = roi;
 		showName = title.startsWith("Prop");
 		showListCoordinates = showName && title.endsWith(" ");
 		nProperties = showListCoordinates?roi.getPropertyCount():0;
@@ -48,12 +50,19 @@ public RoiProperties(String title, Roi roi) {
 			overlay = imp!=null?imp.getOverlay():null;
 			setPositions = roi.getPosition()!=0;
 		}
-		this.roi = roi;
+	}
+
+	/** Constructs a RoiProperties using the specified title for a given roi;
+	 *  call showDialog for the actual dialog.
+	 *  Note that the title determines which fields will be shown in the dialog. */
+
+	public RoiProperties(String title, Roi roi) {
+		this(title, WindowManager.getCurrentImage(), roi);
 	}
 
 	/** Displays the dialog box and returns 'false' if the user cancels it. */
 	public boolean showDialog() {
-		String name= roi.getName();
+		String name = roi.getName();
 		boolean isRange = name!=null && name.startsWith("range:");
 		String nameLabel = isRange?"Range:":"Name:";
 		if (isRange) name = name.substring(7);
@@ -99,7 +108,6 @@ else if (position.equals(""+PointRoi.POINTWISE_POSITION))
 		if (showName) {
 			gd.addStringField(nameLabel, name, 20);
 			String label = "Position:";
-			ImagePlus imp = WindowManager.getCurrentImage();
 			if (position.contains(",") || (imp!=null&&imp.isHyperStack()))
 				label = "Position (c,z,t):";
 			gd.addStringField(label, position, 20);
@@ -140,6 +148,9 @@ else if (position.equals(""+PointRoi.POINTWISE_POSITION))
 				gd.addStringField("Fill color:", fillc);
 			}
 		}
+		boolean askShowOnAllSlices = addToOverlay && imp!=null && imp.getNSlices()>1;
+		if (askShowOnAllSlices)
+			gd.addCheckbox("Show on all Slices", roi.getPosition()==0&&!roi.hasHyperStackPosition());
 		if (addToOverlay)
 			gd.addCheckbox("New overlay", false);
 		if (overlayOptions) {
@@ -211,8 +222,15 @@ else if (position.equals(""+PointRoi.POINTWISE_POSITION))
 			} else
 				fillc = gd.getNextString();
 		}
+		if (askShowOnAllSlices) {
+			boolean overlayOnAllSlices = gd.getNextBoolean();
+			if (overlayOnAllSlices)
+				roi.setPosition(0);
+			else if (roi.getPosition() == 0)
+				roi.setPosition(imp);
+		}
 		boolean applyToOverlay = false;
-		boolean newOverlay = addToOverlay?gd.getNextBoolean():false;
+		boolean newOverlay = addToOverlay ? gd.getNextBoolean() : false;
 		if (overlayOptions) {
 			setPositions = gd.getNextBoolean();
 			if (overlay!=null) {
@@ -267,12 +285,19 @@ else if (position.equals(""+PointRoi.POINTWISE_POSITION))
 		if (applyToOverlay) {
 			if (imp==null || overlay==null)
 				return true;
+			Undo.setup(Undo.OVERLAY, imp);
 			Roi[] rois = overlay.toArray();
 			for (int i=0; i<rois.length; i++) {
-				rois[i].setStrokeColor(strokeColor);
+				if (strokeColor != null)
+					rois[i].setStrokeColor(strokeColor);
 				if (strokeWidth2!=strokeWidth)
 					rois[i].setStrokeWidth((float)strokeWidth2);
 				rois[i].setFillColor(fillColor);
+				if (setPositions) {
+					if (rois[i].getPosition()==0 && !rois[i].hasHyperStackPosition())
+						rois[i].setPosition(imp);
+				} else
+					rois[i].setPosition(0);
 			}
 			imp.draw();
 			imp.getProcessor(); // needed for correct recordering

ij/plugin/OverlayCommands.java

@@ -111,8 +111,10 @@ void addSelection() {
 			gd.addCheckbox("Remove existing overlay", false);
 			gd.showDialog();
 			if (gd.wasCanceled()) return;
-			if (gd.getNextBoolean())
+			if (gd.getNextBoolean()) {
+				Undo.setup(Undo.OVERLAY, imp);
 				imp.setOverlay(null);
+			}
 			return;
  		}
 		if (roi==null) {
@@ -130,13 +132,17 @@ void addSelection() {
 				roi.setFillColor(defaultRoi.getFillColor());
 		}
 		setPosition(imp, roi);
+		boolean hasPosition = roi.getPosition()!=0 || roi.hasHyperStackPosition();
 		boolean points = roi instanceof PointRoi && ((PolygonRoi)roi).getNCoordinates()>1;
 		if (IJ.altKeyDown() || (IJ.macroRunning() && Macro.getOptions()!=null)) {
 			RoiProperties rp = new RoiProperties("Add to Overlay", roi);
 			if (!rp.showDialog()) return;
+			boolean hasPosition2 = roi.getPosition()!=0 || roi.hasHyperStackPosition();
 			defaultRoi.setStrokeColor(roi.getStrokeColor());
 			defaultRoi.setStrokeWidth(roi.getStrokeWidth());
 			defaultRoi.setFillColor(roi.getFillColor());
+			if (hasPosition2 != hasPosition)
+				defaultRoi.setPosition(hasPosition2 ? 1 : 0);
 		}
 		String name = roi.getName();
 		boolean newOverlay = name!=null && name.equals("new-overlay");
@@ -289,6 +295,7 @@ void remove() {
 			ImageCanvas ic = imp.getCanvas();
 			if (ic!=null)
 				ic.setShowAllList(null);
+			Undo.setup(Undo.OVERLAY, imp);
 			imp.setOverlay(null);
 		}
 	}
@@ -403,7 +410,7 @@ void options() {
 		boolean points = roi instanceof PointRoi && ((PolygonRoi)roi).getNCoordinates()>1;
 		if (points) roi.setStrokeColor(Color.red);
 		roi.setPosition(defaultRoi.getPosition());
-		RoiProperties rp = new RoiProperties("Overlay Options", roi);
+		RoiProperties rp = new RoiProperties("Overlay Options", imp, roi);
 		if (!rp.showDialog()) return;
 		defaultRoi = roi;
 	}

ij/plugin/Resizer.java

@@ -142,7 +142,10 @@ else if (z1>1 && z1<stackSize)
 				newHeight = (int)Math.round(newWidth*(origHeight/origWidth));
 		}
 		ip.setInterpolationMethod(interpolationMethod);
-		Undo.setup(crop?Undo.TRANSFORM:Undo.TYPE_CONVERSION, imp);
+		if (stackSize==1)
+			Undo.setup(crop?Undo.TRANSFORM:Undo.TYPE_CONVERSION, imp);
+		if (imp.getOverlay() != null)
+			Undo.saveOverlay(imp);
 
 		if (roi!=null || newWidth!=origWidth || newHeight!=origHeight) {
 			try {

ij/plugin/Selection.java

@@ -68,7 +68,7 @@ else if (arg.equals("toarea"))
 		else if (arg.equals("toline"))
 			areaToLine(imp); 
 		else if (arg.equals("properties"))
-			{setProperties("Properties ", imp.getRoi()); imp.draw();}
+			{setProperties("Properties ", imp); imp.draw();}
 		else if (arg.equals("band"))
 			makeBand(imp);
 		else if (arg.equals("tobox"))
@@ -800,8 +800,12 @@ void addToRoiManager(ImagePlus imp) {
 		rm.allowRecording(false);
 		IJ.setKeyUp(IJ.ALL_KEYS);
 	}
-
-	boolean setProperties(String title, Roi roi) {
+
+	/** Implements the Edit>Selection>Properties command.
+	 *  With the alt key down and a multipoint selection, shows the point counts instead. */
+	boolean setProperties(String title, ImagePlus imp) {
+		if (imp == null) return false;	//should never happen (called only from 'run', where imp!=null)
+		Roi roi = imp.getRoi();
 		if ((roi instanceof PointRoi) && Toolbar.getMultiPointMode() && IJ.altKeyDown()) {
 			((PointRoi)roi).displayCounts();
 			return true;
@@ -820,7 +824,7 @@ boolean setProperties(String title, Roi roi) {
 		Color color = roi.getStrokeColor();
 		Color fillColor = roi.getFillColor();
 		int width = (int)roi.getStrokeWidth();
-		RoiProperties rp = new RoiProperties(title, roi);
+		RoiProperties rp = new RoiProperties(title, imp, roi);
 		boolean ok = rp.showDialog();
 		if (Recorder.record) {
 			boolean groupChanged = false;

ij/plugin/frame/ContrastAdjuster.java

@@ -435,25 +435,24 @@ void updateLabels(ImagePlus imp) {
 			max = cal.getCValue((int)max);
 			realValue = true;
 		}
+		digits = realValue?4:0;
+		if (realValue) {
+			double s = min<0||max<0?0.1:1.0;
+			double amin = Math.abs(min);
+			double amax = Math.abs(max);
+			if (amin>99.0*s||amax>99.0*s) digits = 3;
+			if (amin>999.0*s||amax>999.0*s) digits = 2;
+			if (amin>9999.0*s||amax>9999.0*s) digits = 1;
+			if (amin>99999.0*s||amax>99999.0*s) digits = 0;
+			if (amin>9999999.0*s||amax>9999999.0*s) digits = -2;
+			if ((amin>0&&amin<0.001)||(amax>0&&amax<0.001)) digits = -2;
+		}
 		if (windowLevel) {
-			digits = realValue?3:0;
 			double window = max-min;
 			double level = min+(window)/2.0;
 			windowLabel.setText(ResultsTable.d2s(window, digits));
 			levelLabel.setText(ResultsTable.d2s(level, digits));
 		} else {
-			digits = realValue?4:0;
-			if (realValue) {
-				double s = min<0||max<0?0.1:1.0;
-				double amin = Math.abs(min);
-				double amax = Math.abs(max);
-				if (amin>99.0*s||amax>99.0*s) digits = 3;
-				if (amin>999.0*s||amax>999.0*s) digits = 2;
-				if (amin>9999.0*s||amax>9999.0*s) digits = 1;
-				if (amin>99999.0*s||amax>99999.0*s) digits = 0;
-				if (amin>9999999.0*s||amax>9999999.0*s) digits = -2;
-				if ((amin>0&&amin<0.001)||(amax>0&&amax<0.001)) digits = -2;
-			}
 			String minString = IJ.d2s(min, min==0.0?0:digits) + blankLabel8;
 			minLabel.setText(minString.substring(0,blankLabel8.length()));
 			String maxString = blankLabel8 + IJ.d2s(max, digits);
@@ -868,7 +867,6 @@ void setMinAndMax(ImagePlus imp, ImageProcessor ip) {
 		min = imp.getDisplayRangeMin();
 		max = imp.getDisplayRangeMax();
 		Calibration cal = imp.getCalibration();
-		//int digits = (ip instanceof FloatProcessor)||cal.calibrated()?2:0;
 		double minValue = cal.getCValue(min);
 		double maxValue = cal.getCValue(max);
 		int channels = imp.getNChannels();
@@ -1024,15 +1022,14 @@ void setWindowLevel(ImagePlus imp, ImageProcessor ip) {
 		min = imp.getDisplayRangeMin();
 		max = imp.getDisplayRangeMax();
 		Calibration cal = imp.getCalibration();
-		int digits = (ip instanceof FloatProcessor)||cal.calibrated()?2:0;
 		double minValue = cal.getCValue(min);
 		double maxValue = cal.getCValue(max);
 		//IJ.log("setWindowLevel: "+min+" "+max);
 		double windowValue = maxValue - minValue;
 		double levelValue = minValue + windowValue/2.0;
 		GenericDialog gd = new GenericDialog("Set W&L");
-		gd.addNumericField("Window Center (Level): ", levelValue, digits);
-		gd.addNumericField("Window Width: ", windowValue, digits);
+		gd.addNumericField("Window Center (Level): ", levelValue, digits, 9, "");
+		gd.addNumericField("Window Width: ", windowValue, digits, 9, "");
 		gd.addCheckbox("Propagate to all open images", false);
 		gd.showDialog();
 		if (gd.wasCanceled())