2019.09.10 (1.52q47; Lines to ShapeRois)

ij/IJ.java

@@ -937,6 +937,14 @@ public static String pad(int n, int digits) {
 		return str;
 	}
 
+	/** Pad 's' with leading zeros to the specified number of digits. */
+	public static String pad(String s, int digits) {
+		String str = ""+s;
+		while (str.length()<digits)
+			str = "0"+str;
+		return str;
+	}
+
 	/** Adds the specified class to a Vector to keep it from being garbage
 	collected, which would cause the classes static fields to be reset. 
 	Probably not needed with Java 1.2 or later. */

ij/ImageJ.java

@@ -78,7 +78,7 @@ 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 = "1.52q";
-	public static final String BUILD = "44";
+	public static final String BUILD = ""; //47
 	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/Roi.java

@@ -6,7 +6,6 @@
 import ij.plugin.filter.Analyzer;
 import ij.plugin.filter.ThresholdToSelection;
 import ij.plugin.RectToolOptions;
-import ij.plugin.Selection;
 import ij.macro.Interpreter;
 import ij.io.RoiDecoder;
 import java.awt.*;
@@ -610,15 +609,11 @@ protected FloatPolygon getInterpolatedPolygon(FloatPolygon p, double interval, b
 	 * @see #iterator()
 	 */
 	public Point[] getContainedPoints() {
-		if (isLine()) {
-			FloatPolygon p = getInterpolatedPolygon();
-			Point[] points = new Point[p.npoints];
-			for (int i=0; i<p.npoints; i++)
-				points[i] = new Point((int)Math.round(p.xpoints[i]),(int)Math.round(p.ypoints[i]));
-			return points;
-		}
-		ImageProcessor mask = getMask();
-		Rectangle bounds = getBounds();
+		Roi roi = this;
+		if (isLine())
+			roi = toArea();
+		ImageProcessor mask = roi.getMask();
+		Rectangle bounds = roi.getBounds();
 		ArrayList points = new ArrayList();
 		for (int y=0; y<bounds.height; y++) {
 			for (int x=0; x<bounds.width; x++) {
@@ -639,7 +634,7 @@ public FloatPolygon getContainedFloatPoints() {
 			if (getStrokeWidth()<=1)
 				return roi2.getInterpolatedPolygon();
 			else
-				roi2 = Selection.lineToArea(this);
+				roi2 = toArea();
 		}
 		ImageProcessor mask = roi2.getMask();
 		Rectangle bounds = roi2.getBounds();
@@ -2254,7 +2249,59 @@ public double[] getContourCentroid() {
 		yC /= lSum;
 		return new double[]{xC, yC};
 	}
-
+
+	/** Converts this selection into an area selection. */
+	public Roi toArea() {
+		if (!isLine())
+			return this;
+		Roi roi = (Roi)this.clone();
+		Roi roi2 = null;
+		if (roi.getType()==Roi.LINE) {
+			double width = roi.getStrokeWidth();
+			if (width<=1.0)
+				roi.setStrokeWidth(1.0000001);
+			FloatPolygon p = roi.getFloatPolygon();
+			roi.setStrokeWidth(width);
+			roi2 = new PolygonRoi(p, Roi.POLYGON);
+			roi2.setDrawOffset(roi.getDrawOffset());
+		} else {
+			int lwidth = (int)roi.getStrokeWidth();
+			if (lwidth<1)
+				lwidth = 1;
+			Rectangle bounds = roi.getBounds();
+			int width = bounds.width + lwidth*2;
+			int height = bounds.height + lwidth*2;
+			ImageProcessor ip2 = new ByteProcessor(width, height);
+			roi.setLocation(lwidth, lwidth);
+			ip2.setColor(255);
+			roi.drawPixels(ip2);
+			ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
+			ThresholdToSelection tts = new ThresholdToSelection();
+			roi2 = tts.convert(ip2);
+			if (roi2==null)
+				return roi;
+			if (bounds.x==0&&bounds.y==0)
+				roi2.setLocation(0, 0);
+			else
+				roi2.setLocation(bounds.x-lwidth/2, bounds.y-lwidth/2);
+		}
+		transferProperties(roi, roi2);
+		roi2.setStrokeWidth(0);
+		Color c = roi2.getStrokeColor();
+		if (c!=null)  // remove any transparency
+			roi2.setStrokeColor(new Color(c.getRed(),c.getGreen(),c.getBlue()));
+		return roi2;
+	}
+
+	private static void transferProperties(Roi roi1, Roi roi2) {
+		if (roi1==null || roi2==null)
+			return;
+		roi2.setStrokeColor(roi1.getStrokeColor());
+		if (roi1.getStroke()!=null)
+			roi2.setStroke(roi1.getStroke());
+		roi2.setDrawOffset(roi1.getDrawOffset());
+	}
+
 	/** Returns a hashcode for this Roi that typically changes 
 		if it is moved, even though it is still the same object. */
 	public int getHashCode() {
@@ -2320,7 +2367,7 @@ private class RoiPointsIteratorMask implements Iterator<Point> {
 
 		RoiPointsIteratorMask() {
 			if (isLine()) {
-				Roi roi2 = Selection.lineToArea(Roi.this);
+				Roi roi2 = Roi.this.toArea();
 				mask = roi2.getMask();
 				xbase = roi2.x;
 				ybase = roi2.y;

ij/gui/ShapeRoi.java

@@ -139,11 +139,9 @@ public ShapeRoi(float[] shapeArray) {
 		x = r.x;
 		y = r.y;
 		width = r.width;
-		height = r.height;
-
+		height = r.height;		
 		state = NORMAL;
-		oldX=x; oldY=y; oldWidth=width; oldHeight=height;
-
+		oldX=x; oldY=y; oldWidth=width; oldHeight=height;				
 		AffineTransform at = new AffineTransform();
 		at.translate(-x, -y);
 		shape = new GeneralPath(at.createTransformedShape(shape));
@@ -267,6 +265,8 @@ ShapeRoi unaryOp(ShapeRoi sr, int op) {
 	 *
 	 */
 	private Shape roiToShape(Roi roi) {
+		if (roi.isLine())
+			roi = roi.toArea();
 		Shape shape = null;
 		Rectangle r = roi.getBounds();
 		boolean closeShape = true;

ij/macro/Functions.java

@@ -6189,7 +6189,7 @@ private String ijCall() {
 			interp.error("Function name expected: ");
 		String name = interp.tokenString;
 		if (name.equals("pad"))
-			return IJ.pad((int)getFirstArg(), (int)getLastArg());
+			return pad();
 		else if (name.equals("deleteRows"))
 			IJ.deleteRows((int)getFirstArg(), (int)getLastArg());
 		else if (name.equals("log"))
@@ -6212,6 +6212,21 @@ else if (name.equals("getFullVersion"))
 			interp.error("Unrecognized IJ function name");
 		return null;
 	}
+
+	private String pad() {
+		int intArg = 0;
+		String stringArg = null;
+		interp.getLeftParen();
+		if (isStringArg())
+			stringArg = getString();
+		else
+			intArg = (int)interp.getExpression();
+		int digits = (int)getLastArg();
+		if (stringArg!=null)
+			return IJ.pad(stringArg, digits);
+		else
+			return IJ.pad(intArg, digits);
+	}
 
 	private void renameResults() {
 		String arg1 = getFirstString();

ij/plugin/Selection.java

@@ -637,43 +637,7 @@ private void lineToArea(ImagePlus imp) {
 
 	/** Converts a line selection into an area selection. */
 	public static Roi lineToArea(Roi roi) {
-		Roi roi2 = null;
-		if (roi.getType()==Roi.LINE) {
-			double width = roi.getStrokeWidth();
-			if (width<=1.0)
-				roi.setStrokeWidth(1.0000001);
-			FloatPolygon p = roi.getFloatPolygon();
-			roi.setStrokeWidth(width);
-			roi2 = new PolygonRoi(p, Roi.POLYGON);
-			roi2.setDrawOffset(roi.getDrawOffset());
-		} else {
-			roi = (Roi)roi.clone();
-			int lwidth = (int)roi.getStrokeWidth();
-			if (lwidth<1)
-				lwidth = 1;
-			Rectangle bounds = roi.getBounds();
-			int width = bounds.width + lwidth*2;
-			int height = bounds.height + lwidth*2;
-			ImageProcessor ip2 = new ByteProcessor(width, height);
-			roi.setLocation(lwidth, lwidth);
-			ip2.setColor(255);
-			roi.drawPixels(ip2);
-			ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
-			ThresholdToSelection tts = new ThresholdToSelection();
-			roi2 = tts.convert(ip2);
-			if (roi2==null)
-				return roi;
-			if (bounds.x==0&&bounds.y==0)
-				roi2.setLocation(0, 0);
-			else
-				roi2.setLocation(bounds.x-lwidth/2, bounds.y-lwidth/2);
-		}
-		transferProperties(roi, roi2);
-		roi2.setStrokeWidth(0);
-		Color c = roi2.getStrokeColor();
-		if (c!=null)  // remove any transparency
-			roi2.setStrokeColor(new Color(c.getRed(),c.getGreen(),c.getBlue()));
-		return roi2;
+		return roi.toArea();
 	}
 
 	void areaToLine(ImagePlus imp) {

ij/plugin/frame/RoiManager.java

@@ -1473,20 +1473,15 @@ private int countPointRois(Roi[] rois) {
 	private void combineRois(ImagePlus imp, Roi[] rois) {
 		IJ.resetEscape();
 		ShapeRoi s1=null, s2=null;
-		ImageProcessor ip = null;
 		for (int i=0; i<rois.length; i++) {
 			IJ.showProgress(i, rois.length-1);
 			if (IJ.escapePressed()) {
 				IJ.showProgress(1.0);
 				return;
 			}
 			Roi roi = rois[i];
-			if (!roi.isArea() && roi.getType() != Roi.POINT) {
-				if (ip==null)
-					ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
-				roi = convertLineToPolygon(roi, ip);
-				if (roi==null) continue;
-			}
+			if (!roi.isArea() && roi.getType() != Roi.POINT) 
+			 roi = roi.toArea();
 			if (s1==null) {
 				if (roi instanceof ShapeRoi)
 					s1 = (ShapeRoi)roi;
@@ -1506,22 +1501,6 @@ private void combineRois(ImagePlus imp, Roi[] rois) {
 			imp.setRoi(s1.trySimplify());
 	}
 
-	Roi convertLineToPolygon(Roi roi, ImageProcessor ip) {
-		if (roi==null) return null;
-		ip.resetRoi();
-		ip.setColor(0);
-		ip.fill();
-		ip.setColor(255);
-		if (roi.getType()==Roi.LINE && roi.getStrokeWidth()>1)
-			ip.fillPolygon(roi.getPolygon());
-		else
-			roi.drawPixels(ip);
-		//new ImagePlus("ip", ip.duplicate()).show();
-		ip.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
-		ThresholdToSelection tts = new ThresholdToSelection();
-		return tts.convert(ip);
-	}
-
 	void combinePoints(ImagePlus imp, Roi[] rois) {
 		int n = rois.length;
 		FloatPolygon fp = new FloatPolygon();
@@ -1533,7 +1512,7 @@ void combinePoints(ImagePlus imp, Roi[] rois) {
 		imp.setRoi(new PointRoi(fp));
 	}
 
-	/** Intersection of area rois or PointRois.
+	/** calculates the intersection of area, line and point selections.
 	 *  If there is one PointRoi in the list of selected Rois, the points inside all selected area rois are kept.
 	 *  If more than one PointRoi is selected, the PointRois get converted to area rois with each pixel containing
 	 *  at least one point selected. */
@@ -1549,10 +1528,10 @@ void and() {
 		ShapeRoi s1=null;
 		PointRoi pointRoi = null;
 		for (Roi roi : rois) {
-			if (roi==null || !(roi.isArea() || roi.getType() == Roi.POINT))
+			if (roi==null)
 				continue;
 			if (s1==null) {
-				if (nPointRois == 1 && roi.getType() == Roi.POINT) {
+				if (nPointRois==1 && roi.getType() == Roi.POINT) {
 					pointRoi = (PointRoi)roi;
 					continue;  //PointRoi will be handled at the end
 				}
@@ -1562,7 +1541,7 @@ void and() {
 					s1 = new ShapeRoi(roi);
 				if (s1==null) continue;
 			} else {
-				if (nPointRois == 1 && roi.getType() == Roi.POINT) {
+				if (nPointRois==1 && roi.getType()==Roi.POINT) {
 					pointRoi = (PointRoi)roi;
 					continue;  //PointRoi will be handled at the end
 				}
@@ -1576,9 +1555,12 @@ void and() {
 			}
 		}
 		if (s1==null) return;
-		if (pointRoi != null) imp.setRoi(pointRoi.containedPoints(s1));
-		else imp.setRoi(s1.trySimplify());
-		if (record()) Recorder.record("roiManager", "AND");
+		if (pointRoi!=null)
+			imp.setRoi(pointRoi.containedPoints(s1));
+		else
+			imp.setRoi(s1.trySimplify());
+		if (record())
+			Recorder.record("roiManager", "AND");
 	}
 
 	void xor() {
@@ -1594,7 +1576,7 @@ void xor() {
 		ShapeRoi s1=null, s2=null;
 		for (int i=0; i<indexes.length; i++) {
 			Roi roi = (Roi)rois.get(indexes[i]);
-			if (roi==null || !(roi.isArea() || roi.getType() == Roi.POINT))
+			if (roi==null)
 				continue;
 			if (s1==null) {
 				if (roi instanceof ShapeRoi)

ij/plugin/frame/SyncWindows.java

@@ -561,8 +561,7 @@ public void actionPerformed(ActionEvent e) {
 					v.addElement(I);
 				}
 				addWindows(v);
-			}
-			else if(bpressed==bUnsyncAll) {
+			} else if(bpressed==bUnsyncAll) {
 				removeAllWindows();
 			}
 		} else if (wList != null && source == wList) {

release-notes.html

@@ -5,7 +5,7 @@
 </head>
 <body>
 
-<li> <u>1.52q44 26 August 2019</u>
+<li> <u>1.52q47 10 September 2019</u>
 <ul>
 <li> Thanks to Michael Schmid, added the "Non-blocking filter dialogs"
 option to <i>Edit&gt;Options&gt;Misc</i>. The Convolve,
@@ -29,6 +29,8 @@
 plot window commands also now use labels.
 <li> Thanks to Jerome Mutterer, added the getValue("Length")
 macro function.
+<li> Thanks to Jerome Mutterer, added the IJ.pad(string,digits)
+macro function and method.
 <li> Thanks to Michael Schmid, the ImagePlus lock() and unlock()
 methods now support multiple lock/unlock operations by the
 same thread.
@@ -68,17 +70,21 @@
 <li> Thanks to Norbert Vischer, fixed a bug that caused
 the getPixel(x,y) macro function to not return raw pixel values
 when x or y were real numbers.
-<li> Thanks to Hyung-song Nam and Curtis Rueden, fixed a bug
-that caused the Channels tool on macOS to become unresponsive.
-<li> Thanks to Florian Jug, fixed a bug that caused the "Auto"
-button in the "B&C" tool to not have focus on macOS.
+<li> Thanks to 'mountain_man', fixed a bug that caused
+line selections to not be correctly converted to ShapeRois.
 <li> Thanks to Jeremy Adler, fixed a regression that caused the
 the makeSelection(10, xpoints, ypoints) macro function to
 throw an exception.
 <li> Thanks to Dan McDonald, fixed a regression that caused the
 Raw File Opener to throw an exception.
 <li> Fixed a 1.52a regression that caused tables created by
 the gel analyzer to not have row numbers.
+<li> Thanks to Hyung-song Nam and Curtis Rueden, fixed a
+1.52o regression that caused the Channels tool on macOS
+to become unresponsive.
+<li> Thanks to Florian Jug, fixed a 1.52o regression that
+caused the "Auto" button in the "B&C" tool to not have
+focus on macOS.
 </ul>
 
 <li> <u>1.52p 22 June 2019</u>