2024.09.04 (1.54k16; Multi-point ROIs)

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 = "12";
+	public static final String BUILD = "16";
 	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/gui/ImageCanvas.java

@@ -359,6 +359,11 @@ else if (t==1)
 					position = getSliceNumber(roi.getName());
 				if (position>0 && imp.getCompositeMode()==IJ.COMPOSITE)
 					position = 0;
+				if (position == PointRoi.POINTWISE_POSITION)
+					position = 0;
+				if ((roi instanceof PointRoi) && Prefs.showAllPoints)
+					position = 0;
+				//IJ.log(c+" "+z+" "+t+" p="+position+"getP="+roi.getPosition()+" "+roiManagerShowAllMode);
 				if (position==0 || position==currentImage || roiManagerShowAllMode)
 					drawRoi(g, roi, drawLabels?i+LIST_OFFSET:-1);
 			}

ij/gui/PointRoi.java

@@ -6,6 +6,7 @@
 import ij.plugin.PointToolOptions;
 import ij.plugin.filter.Analyzer;
 import ij.plugin.frame.Recorder;
+import ij.util.Tools;
 import ij.util.Java2;
 import java.awt.*;
 import java.awt.image.*;
@@ -22,6 +23,8 @@ public class PointRoi extends PolygonRoi {
 	public static final String[] sizes = {"Tiny", "Small", "Medium", "Large", "Extra Large", "XXL", "XXXL"};
 	public static final String[] types = {"Hybrid", "Cross", "Dot", "Circle"};
 	public static final int HYBRID=0, CROSS=1, CROSSHAIR=1, DOT=2, CIRCLE=3;
+	/**	Returned by getPosition if point stack positions are different */
+	public static final int POINTWISE_POSITION = -2;
 	private static final String TYPE_KEY = "point.type";
 	private static final String SIZE_KEY = "point.size";
 	private static final String CROSS_COLOR_KEY = "point.cross.color";
@@ -215,12 +218,13 @@ public void draw(Graphics g) {
 			if (fontSize>9)
 				Java2.setAntialiasedText(g, true);
 		}
-		int slice = imp!=null&&positions!=null&&imp.getStackSize()>1?imp.getCurrentSlice():0;
+		int[] positions = this.positions;	//use a copy to avoid NullPointerException on asynchronous change to null
+		int slice = imp!=null && positions!=null && imp.getStackSize()>1?imp.getCurrentSlice():0;
 		ImageCanvas ic = imp!=null?imp.getCanvas():null;
 		if (ic!=null && overlay && ic.getShowAllList()!=null && ic.getShowAllList().contains(this) && !Prefs.showAllSliceOnly)
-			slice = 0;  // draw point irrespective of currently selected slice
+			slice = 0;  // In RoiManager's "show all" mode and not "associate with slice", draw point irrespective of currently selected slice
 		if (Prefs.showAllPoints)
-			slice = 0;
+			slice = 0;  // "Show on all slices" in Point tool options 
 		//IJ.log("draw: "+positions+" "+imp.getCurrentSlice());
 		for (int i=0; i<nPoints; i++) {
 			//IJ.log(i+" "+slice+" "+(positions!=null?positions[i]:-1)+"  "+getPosition());
@@ -690,6 +694,52 @@ public void updateCounts() {
 			counts[(counters==null || counters[i]>=counts.length) ? 0 : counters[i]] ++;
 	}
 
+	/** Sets the stack position (image number) of all points in this Roi.
+	 *  The points are only displayed when the stack is at the specified position.
+	 *  Set to zero to have the points displayed on all images in the stack.
+	 *  The stack position, when set, determines the visibility of this Roi
+	 *  (i) if it is part of an overlay (normal overlay or the RoiManager's
+	 *      'Show All' overlay), or
+	 *  (ii) if it is the currently active Roi and Prefs.showAllPoints
+	 *       ('Show an all slices' in the Point Tool Options dialog) is off.
+	 *  Clears any association of this Roi to a hyperstack position.
+	 *
+	 *  Note that the behavior differs from that of the other Roi types:
+	 *  For the other Roi types, setPosition does not restrict the visibility
+	 *  to stack slice 'n' if that roi is the currently active Roi; it only
+	 *  affects the visibility if that Roi is part of an overlay.
+	 */
+	public void setPosition(int n) {
+		if (n<0 && n!=POINTWISE_POSITION)
+			n = 0;
+		if (n == 0) {
+			positions = null;
+		} else {
+			if (positions == null)
+				positions = new int[counters == null ? nPoints*2 : counters.length];
+			if (n != POINTWISE_POSITION)
+				Arrays.fill(positions, n);
+		}
+		hyperstackPosition = false;
+	}
+
+	/** Returns the stack position (image number) of the points in this Roi, if
+	 *  all points have the same position. Returns 0 if none of the points is
+	 *  associated with a particular stack image, and PointRoi.POINTWISE_POSITION = -2
+	 *  if there are different stack positions for different points.
+	 */
+	public int getPosition() {
+		if (positions == null || nPoints < 1) {
+			return 0;
+		} else {
+			int position = positions[0];
+			for (int i=1; i<nPoints; i++)
+				if (positions[i] != position)
+					return POINTWISE_POSITION;
+			return position;
+		}
+	}
+
 	/** Returns the stack slice of the point with the given index, or 0 if no slice defined for this point */
 	public int getPointPosition(int index) {
 		if (positions!=null && index<nPoints)
@@ -698,6 +748,18 @@ public int getPointPosition(int index) {
 			return 0;
 	}
 
+	/** Returns whether this Roi contains a point associated to the given stack slice.
+	 *  Returns true for (non-existant) slice 0.
+	 *  Does not care whether points would be shown irrespective of the slice number
+	 *  (as given by the Point Tool options "Show on all slices", Prefs.showAllPoints).
+	 */
+	public boolean hasPointPosition(int slice) {
+		if (slice < 0)  return false;
+		if (slice == 0) return true;
+		if (positions == null) return true;
+		return Tools.indexOf(positions, slice) >= 0;
+	}
+
 	public void displayCounts() {
 		ImagePlus imp = getImage();
 		String firstColumnHdr = "Slice";

ij/gui/Roi.java

@@ -114,7 +114,7 @@ public class Roi extends Object implements Cloneable, java.io.Serializable, Iter
 	private String name;
 	private int position;
 	private int channel, slice, frame;
-	private boolean hyperstackPosition;
+	protected boolean hyperstackPosition;
 	private Overlay prototypeOverlay;
 	private boolean subPixel;
 	private boolean activeOverlayRoi;
@@ -2186,6 +2186,7 @@ public int getRoundRectArcSize() {
 	/** Sets the stack position (image number) of this ROI. In an overlay, this
 	* ROI is only displayed when the stack is at the specified position.
 	* Set to zero to have the ROI displayed on all images in the stack.
+	* Clears the hyperStackPosition, if there was one.
 	* @see ij.gui.Overlay
 	*/
 	public void setPosition(int n) {
@@ -2195,8 +2196,10 @@ public void setPosition(int n) {
 		hyperstackPosition = false;
 	}
 
-	/** Returns the stack position (image number) of this ROI, or
-	*  zero if the ROI is not associated with a particular stack image.
+	/** Returns the stack position (image number) for displaying this ROI,
+	*   in an overlay (or the RoiManager's 'Show All'. Returns zero if the
+	*   ROI is not associated with a particular stack image.
+	*   PointRois can also return PointRoi.POINTWISE_POSITION.
 	* @see ij.gui.Overlay
 	*/
 	public int getPosition() {
@@ -2244,14 +2247,14 @@ public final int getCPosition() {
 	}
 
 	/** Returns the slice position of this ROI, or zero
-	*  if this ROI is not associated with a particular slice.
+	*   if this ROI is not associated with a particular slice.
 	*/
 	public final int getZPosition() {
-		return slice==0&&!hyperstackPosition?position:slice;
+		return slice==0&&!hyperstackPosition ? position : slice;
 	}
 
 	/** Returns the frame position of this ROI, or zero
-	*  if this ROI is not associated with a particular frame.
+	*   if this ROI is not associated with a particular frame.
 	*/
 	public final int getTPosition() {
 		return frame;

ij/gui/RoiProperties.java

@@ -31,7 +31,9 @@ public class RoiProperties implements TextListener, WindowListener {
 	private TextField groupField, colorField;
 	private Label groupName;
 
-	/** Constructs a ColorChooser using the specified title and initial color. */
+	/** 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) {
 		if (roi==null)
 			throw new IllegalArgumentException("ROI is null");
@@ -81,6 +83,8 @@ public boolean showDialog() {
 			position =  roi.getCPosition() +","+roi.getZPosition()+","+ roi.getTPosition();
 		if (position.equals("0"))
 			position = "none";
+		else if (position.equals(""+PointRoi.POINTWISE_POSITION))
+			position = "point-specific";
 		String group = ""+roi.getGroup();
 		if (group.equals("0"))
 			group = "none";
@@ -97,8 +101,8 @@ public boolean showDialog() {
 			String label = "Position:";
 			ImagePlus imp = WindowManager.getCurrentImage();
 			if (position.contains(",") || (imp!=null&&imp.isHyperStack()))
-				label = "Position (c,s,f):";
-			gd.addStringField(label, position);
+				label = "Position (c,z,t):";
+			gd.addStringField(label, position, 20);
 			gd.addStringField("Group:", group);
 			gd.addToSameRow(); gd.addMessage("wwwwwwwwwwww");
 		}
@@ -125,7 +129,6 @@ public boolean showDialog() {
 			colorField = (TextField)v.elementAt(v.size()-1);
 		}
 
-
 		if (!isLine) {
 			if (isPoint) {
 				int index = ((PointRoi)roi).getPointType();

ij/io/RoiDecoder.java

@@ -376,19 +376,20 @@ else if (type==angle)
 				roi.setProperties(props);
 		}
 
+		roi.setPosition(position);
+		if (channel>0 || slice>0 || frame>0)
+			roi.setPosition(channel, slice, frame);
+
 		if (version>=227) {
 			int[] counters = getPointCounters(n);
 			if (counters!=null && (roi instanceof PointRoi))
-				((PointRoi)roi).setCounters(counters);
+				((PointRoi)roi).setCounters(counters);	//must be after roi.setPosition()
 		}
 
 		// set group (1.52t or later)
 		if (version>=228 && group>0)
 			roi.setGroup(group);
 
-		roi.setPosition(position);
-		if (channel>0 || slice>0 || frame>0)
-			roi.setPosition(channel, slice, frame);
 		decodeOverlayOptions(roi, version, options, overlayLabelColor, overlayFontSize);
 		return roi;
 	}

ij/measure/Calibration.java

@@ -3,7 +3,6 @@
 import ij.plugin.filter.Analyzer;
 
 /** Calibration objects contain an image's spatial and density calibration data. */
-
 public class Calibration implements Cloneable {
 
 	public static final int STRAIGHT_LINE=0,POLY2=1,POLY3=2,POLY4=3,
@@ -75,20 +74,20 @@ public class Calibration implements Cloneable {
 	private boolean zeroClip;
 	private boolean invertY;
 
+
 	/** Constructs a new Calibration object using the default values. */ 
+	public Calibration() {
+	}
+
+	/* Obsolete */
 	public Calibration(ImagePlus imp) {
 		if (imp!=null) {
 			bitDepth = imp.getBitDepth();
 			if (bitDepth!=UNKNOWN)
 				invertedLut=imp.isInvertedLut();
 		}
 	}
-
-	/** Constructs a new Calibration object using the default values.
-		For density calibration, the image is assumed to be 8-bits. */ 
-	public Calibration() {
-	}
-
+
 	/** Returns 'true' if this image is spatially calibrated. */
 	public boolean scaled() {
 		return pixelWidth!=1.0 || pixelHeight!=1.0 || pixelDepth!=1.0 || !unit.equals("pixel");

ij/plugin/Resizer.java

@@ -127,6 +127,10 @@ else if (z1>1 && z1<stackSize)
 			interpolationMethod = gd.getNextChoiceIndex();
 			if (constrain && newWidth==0)
 				sizeToHeight = true;
+			String options = Macro.getOptions();
+			if (options != null && options.contains("constrain")
+					&& options.contains("height=") && !options.contains("width="))
+				sizeToHeight = true;
 			if (newWidth<=0.0 && !constrain)  newWidth = 50;
 			if (newHeight<=0.0) newHeight = 50;
 		}

ij/plugin/filter/ParticleAnalyzer.java

@@ -346,8 +346,8 @@ public boolean showDialog() {
 		}
 		gd.addStringField("Circularity:", IJ.d2s(minCircularity)+"-"+IJ.d2s(maxCircularity), 12);
 		gd.addChoice("Show:", showStrings2, showStrings[showChoice]);
-		String[] labels = new String[8];
-		boolean[] states = new boolean[8];
+		String[] labels = new String[10];
+		boolean[] states = new boolean[10];
 		labels[0]="Display results"; states[0] = (options&SHOW_RESULTS)!=0;
 		labels[1]="Exclude on edges"; states[1]=(options&EXCLUDE_EDGE_PARTICLES)!=0;
 		labels[2]="Clear results"; states[2]=(options&CLEAR_WORKSHEET)!=0;
@@ -356,7 +356,8 @@ public boolean showDialog() {
 		labels[5]="Overlay"; states[5]=(options&OVERLAY)!=0;
 		labels[6]="Add to Manager"; states[6]=(options&ADD_TO_MANAGER)!=0;
 		labels[7]="Composite ROIs"; states[7]=(options&COMPOSITE_ROIS)!=0;
-		gd.addCheckboxGroup(4, 2, labels, states);
+		labels[8]="Record starts"; states[8]=(options&RECORD_STARTS)!=0;
+		gd.addCheckboxGroup(5, 2, labels, states);
 		gd.addHelp(IJ.URL2+"/docs/menus/analyze.html#ap");
 		gd.showDialog();
 		if (gd.wasCanceled())
@@ -419,6 +420,8 @@ public boolean showDialog() {
 			options |= ADD_TO_MANAGER; else options &= ~ADD_TO_MANAGER;
 		if (gd.getNextBoolean())
 			options |= COMPOSITE_ROIS; else options &= ~COMPOSITE_ROIS;
+		if (gd.getNextBoolean())
+			options |= RECORD_STARTS; else options &= ~RECORD_STARTS;
 		staticOptions = options;
 		options |= SHOW_PROGRESS;
 		if ((options&DISPLAY_SUMMARY)!=0)

ij/plugin/frame/RoiManager.java

@@ -413,7 +413,7 @@ else if (color==null && defaultColor!=null)
 		listModel.addElement(label);
 		roi.setName(label);
 		Roi roiCopy = (Roi)roi.clone();
-		boolean hasPosition = roiCopy.getPosition()>0 || roiCopy.hasHyperStackPosition(); 		
+		boolean hasPosition = roiCopy.getPosition()>0 || roiCopy.getPosition()==PointRoi.POINTWISE_POSITION || roiCopy.hasHyperStackPosition(); 		
 		if (!hasPosition && imp!=null && imp.getStackSize()>1)
 			roiCopy.setPosition(imp); // set ROI position to current stack position
 		if (lineWidth>1)
@@ -626,7 +626,8 @@ boolean update(boolean clone) {
 			if (clone) {
 				String name = (String)listModel.getElementAt(index);
 				Roi roi2 = (Roi)roi.clone();
-				roi2.setPosition(imp);
+				if (roi2.getPosition() != PointRoi.POINTWISE_POSITION)
+					roi2.setPosition(imp);
 				roi.setName(name);
 				roi2.setName(name);
 				rois.set(index, roi2);
@@ -705,6 +706,8 @@ else if (roi.getZPosition()>0 && imp.getNSlices()==imp.getStackSize())
 				imp.setSlice(roi.getZPosition());
 			else if (position>0 && position<=imp.getStackSize())
 				imp.setSlice(position);
+			else if ((roi instanceof PointRoi) && !Prefs.showAllPoints && !((PointRoi)roi).hasPointPosition(imp.getSlice()))
+				imp.setSlice(((PointRoi)roi).getPointPosition(0));
 			else {
 				String label = (String)listModel.getElementAt(index);
 				int n = getSliceNumber(roi, label);
@@ -1559,6 +1562,7 @@ void setProperties(Color color, int lineWidth, Color fillColor) {
 			if (group>=0)
 				roi.setGroup(group);
 			if (rpRoi!=null) {
+				//IJ.log("new pos="+rpRoi.getPosition());
 				if (rpRoi.hasHyperStackPosition())
 					roi.setPosition(rpRoi.getCPosition(), rpRoi.getZPosition(), rpRoi.getTPosition());
 				else
@@ -1806,7 +1810,7 @@ void specify() {
 		runCommand("add");
 	}
 
-	private static boolean channel=false, slice=true, frame=false;
+	private static boolean channel=false, slice=true, frame=false;  //remembers checkbox states for removePositions
 
 	private void removePositions(int position) {
 		int[] indexes = getIndexes();
@@ -1832,11 +1836,11 @@ private void removePositions(int position) {
 			gd.setInsets(5,15,0);
 			gd.addMessage("Remove positions for:      ", font);
 			gd.setInsets(6,25,0);
-			gd.addCheckbox("Channels:", channel);
+			gd.addCheckbox("Channels c:", channel);
 			gd.setInsets(0,25,0);
-			gd.addCheckbox("Slices:", slice);
+			gd.addCheckbox("Slices z:", slice);
 			gd.setInsets(0,25,0);
-			gd.addCheckbox("Frames:", frame);
+			gd.addCheckbox("Frames t:", frame);
 			gd.showDialog();
 			if (gd.wasCanceled())
 				return;
@@ -1862,12 +1866,12 @@ private void removePositions(int position) {
 			int c = roi.getCPosition();
 			int z = roi.getZPosition();
 			int t = roi.getTPosition();
-			if (c>0 || t>0) {
+			if (roi.hasHyperStackPosition()) {
 				if (removeChannels) c = 0;
 				if (removeSlices) z = 0;
 				if (removeFrames) t = 0;
 				roi.setPosition(c, z, t);
-			} else
+			} else if (removeSlices)
 				roi.setPosition(0);
 		}
 		if (imp!=null)