import ij.gui.OvalRoi; //导入依赖的package包/类
/** Write an overlay, if supported */
private void writeOverlay(
        XMLStreamWriter xsw,
        Roi roi) 
        throws SlideSetException {
    if(roi instanceof Line)
        writeLine(xsw, (Line) roi);
    else if(roi instanceof OvalRoi)
        writeOvalRoi(xsw, (OvalRoi) roi);
    else if(roi instanceof PointRoi)
        writePointRoi(xsw, (PointRoi) roi);
    else if(roi instanceof PolygonRoi)
        writePolygonRoi(xsw, (PolygonRoi) roi);
    else if(roi instanceof ShapeRoi)
        writeShapeRoi(xsw, (ShapeRoi) roi);
    else if(roi.getType() == Roi.RECTANGLE)
        writeRectangle(xsw, roi);
    else
        throw new UnsupportedOverlayException(
                "Unsupported ROI type: " 
                + roi.getClass().getName());
}
 

import ij.gui.OvalRoi; //导入依赖的package包/类
/** Write an OvalRoi */
private void writeOvalRoi(
        final XMLStreamWriter xsw, 
        final OvalRoi roi) 
        throws SlideSetException {
    final double rx = roi.getFloatWidth()/2;
    final double ry = roi.getFloatHeight()/2;
    final double x = roi.getXBase();
    final double y = roi.getYBase();
    try {
        xsw.writeStartElement("ellipse");
        xsw.writeAttribute("class", "roi OvalRoi");
        xsw.writeAttribute("cx",
                String.valueOf(x+rx));
        xsw.writeAttribute("cy",
                String.valueOf(y+ry));
        xsw.writeAttribute("rx",
                String.valueOf(rx));
        xsw.writeAttribute("ry",
                String.valueOf(ry));
        applyDefaultStyles(xsw);
        xsw.writeEndElement();
    } catch(Exception e) {
        throw new SlideSetException(e);
    }
}
 

import ij.gui.OvalRoi; //导入依赖的package包/类
/** Generate an ROI from parsed ellipse data */
private Roi makeEllipseOverlay(
     double cx, double cy,
     double rx, double ry, Element element)
     throws SVGParseException {
    double[] c = {cx, cy};
    double[] n = {cx, cy + ry};
    double[] e = {cx + rx, cy};
    double[] s = {cx, cy - ry};
    double[] w = {cx - rx, cy};
    c = transformToDocumentSpace(c, element);
    n = transformToDocumentSpace(n, element);
    e = transformToDocumentSpace(e, element);
    s = transformToDocumentSpace(s, element);
    w = transformToDocumentSpace(w, element);
    if(n[0] != s[0] || e[1] != w[1] 
         || Math.abs((4 * c[0]) / (n[0] + e[0] + s[0] + w[0]) - 1) > 2*Math.ulp(c[0])
         || Math.abs((4 * c[1]) / (n[1] + e[1] + s[1] + w[1]) - 1) > 2*Math.ulp(c[1]))
        throw new SVGParseException("Can't create ROI from skewed or rotated ellipse");
    EllipseOverlay eo = new EllipseOverlay(ij);
    return new OvalRoi(w[0], s[1], 2*Math.abs(e[0] - c[0]), 2*Math.abs(n[1] - c[1]));
}
 

import ij.gui.OvalRoi; //导入依赖的package包/类
/** Paints an approximation of the pipe into the set of slices. */
static public void paint(final Pipe pipe, final Map<Layer,ImageProcessor> slices, final int value, final float scale) {
	final VectorString3D vs = pipe.asVectorString3D();
	vs.resample(1); // one pixel
	final double[] px = vs.getPoints(0);
	final double[] py = vs.getPoints(1);
	final double[] pz = vs.getPoints(2);
	final double[] pr = vs.getDependent(0);
	// For each point
	for (int i=0; i<px.length-1; i++) {
		final ImageProcessor ip = slices.get(pipe.getLayerSet().getNearestLayer(pz[i]));
		if (null == ip) continue;
		final OvalRoi ov = new OvalRoi((int)((px[i] - pr[i]) * scale),
				         (int)((py[i] - pr[i]) * scale),
					 (int)(pr[i]*2*scale), (int)(pr[i]*2*scale));
		ip.setRoi(ov);
		ip.setValue(value);
		ip.fill(ip.getMask());
	}
}
 

import ij.gui.OvalRoi; //导入依赖的package包/类
/**
 * Add series of circular ROIs to the ROI Manager based on the centre and
 * radius of a sphere
 *
 * @param imp Needed for decalibration of calibrated (x,y,z) r values
 * @param roiMan Instance of the ROI Manager i.e. RoiManager.getInstance().
 * @param sphereDim calibrated centroid (x, y, z) and radius
 * @param clearRois empty ROI manager before adding the ROIs.
 * @throws IllegalArgumentException if roiMan is null, rather than
 *           instantiating RoiManager.
 */
public static void addToRoiManager(final ImagePlus imp, final RoiManager roiMan, final double[] sphereDim,
		final boolean clearRois) throws IllegalArgumentException {
	if (roiMan == null)
		throw new IllegalArgumentException("ROI Manager has not been instantiated");
	if (clearRois) {
		RoiMan.deleteAll(roiMan);
	}
	final Calibration cal = imp.getCalibration();
	final double xs = sphereDim[0];
	final int xi = (int) (xs / cal.pixelWidth);
	final double ys = sphereDim[1];
	final int yi = (int) (ys / cal.pixelHeight);
	final double r = sphereDim[3];
	final int zc = (int) Math.round(sphereDim[2] / cal.pixelDepth);
	final int rz = (int) Math.round(r / cal.pixelDepth);
	final int zStart = Math.max(zc - rz, 1);
	final int zEnd = Math.min(zc + rz, imp.getImageStackSize());
	for (int z = zStart; z <= zEnd; z++) { // iterate through z slices
		final double zd = (zc - z) * cal.pixelDepth;
		final double rc = Math.sqrt(r * r - zd * zd);
		final int wi = (int) (rc / cal.pixelWidth);
		final int hi = (int) (rc / cal.pixelHeight);
		final OvalRoi ellipse = new OvalRoi(xi - wi, yi - hi, wi * 2, hi * 2);
		ellipse.setPosition(z);
		roiMan.addRoi(ellipse);
	}
}
 

import ij.gui.OvalRoi; //导入依赖的package包/类
/** Creates an oval selection. Removes any existing 
	selection if width or height are less than 1. */
public static void makeOval(int x, int y, int width, int height) {
	if (width<=0 || height<0)
		getImage().killRoi();
	else {
		ImagePlus img = getImage();
		img.setRoi(new OvalRoi(x, y, width, height));
	}
}
 

import ij.gui.OvalRoi; //导入依赖的package包/类
/** Generate an ROI from a {@code circle} element */
private OvalRoi parseCircle(Element n) throws SVGParseException {
    if(!"circle".equals(n.getTagName()))
        throw new SVGParseException("\'circle\' expected, but \'" + n.getLocalName() + "\' found.");
    double cx, cy, r;
    try {
        cx = parseLength(n.getAttribute("cx"));
        cy = parseLength(n.getAttribute("cy"));
        r = parseLength(n.getAttribute("r"));
    } catch(NumberFormatException e) {
        throw new SVGParseException("Bad number format in ellipse", e);
    }
    return new OvalRoi(cx, cy, r*2, r*2);
}
 

import ij.gui.OvalRoi; //导入依赖的package包/类
/** This method could get tones of improvement, which should be pumped upstream into ImageJ's RoiBrush class which is creating it at every while(true) {} iteration!!!
 * The returned area has its coordinates centered around 0,0
 */
static public Area makeBrush(int diameter, double mag) {
	if (diameter < 1) return null;
	if (mag >= 1) return new Area(new OvalRoi(-diameter/2, -diameter/2, diameter, diameter).getPolygon());
	// else, create a smaller brush and transform it up, i.e. less precise, less points to store -but precision matches what the eye sees, and allows for much better storage -less points.
	int screen_diameter = (int)(diameter * mag);
	if (0 == screen_diameter) return null; // can't paint at this mag with this diameter

	Area brush = new Area(new OvalRoi(-screen_diameter/2, -screen_diameter/2, screen_diameter, screen_diameter).getPolygon());
	// scale to world coordinates
	AffineTransform at = new AffineTransform();
	at.scale(1/mag, 1/mag);
	return brush.createTransformedArea(at);


	// smooth out edges
	/*
	Polygon pol = new OvalRoi(-diameter/2, -diameter/2, diameter, diameter).getPolygon();
	Polygon pol2 = new Polygon();
	// cheap and fast: skip every other point, since all will be square angles
	for (int i=0; i<pol.npoints; i+=2) {
		pol2.addPoint(pol.xpoints[i], pol.ypoints[i]);
	}
	return new Area(pol2);
	// the above works nice, but then the fill and fill-remove don't work properly (there are traces in the edges)
	// Needs a workround: before adding/substracting, enlarge the polygon to have square edges
	*/
}
 

import ij.gui.OvalRoi; //导入依赖的package包/类
public static OvalRoi convertToOvalROI(EllipseROI pathOval, double xOrigin, double yOrigin, double downsampleFactor) {
	Rectangle2D bounds = getTransformedBounds(pathOval, xOrigin, yOrigin, downsampleFactor);
	return setIJRoiProperties(new OvalRoi(bounds.getX(), bounds.getY(), bounds.getWidth(), bounds.getHeight()), pathOval);
}
 

import ij.gui.OvalRoi; //导入依赖的package包/类
@Override
public void run(String arg) {

	    // Open an image
	    String path = "/home/bene/PhD/brains/template.tif";
	    ImagePlus imp = IJ.openImage(path);
	    new StackConverter(imp).convertToGray8();

	    // Create a universe and show it
	    Image3DUniverse univ = new Image3DUniverse();
	    univ.show();
	    univ.rotateY(30 * Math.PI / 180);

	    // Add the image as a volume
	    Content c = univ.addVoltex(imp);
	    sleep(5);

	    // Retrieve the VoltexGroup
	    VoltexGroup voltex = (VoltexGroup)c.getContent();
	    
	    // Define a ROI
	    Roi roi = new OvalRoi(240, 220, 70, 50);
	    
	    // Define a fill color
	    byte fillValue = (byte)100;
	    
	    // Fill the part of the volume which results from the
	    // projection of the polygon onto the volume:
	    voltex.fillRoi(univ.getCanvas(), roi, fillValue);
	    sleep(5);
	    
	    // This can be optimally used for deleting some parts of
	    // the volume:
	    fillValue = (byte)0;
	    roi.setLocation(150, 150);
	    voltex.fillRoi(univ.getCanvas(), roi, fillValue);
	    sleep(5);
	    
	    // The internal image is changed, too:
	    imp.show();
  }