Java PolygonRoi类代码示例

import ij.gui.PolygonRoi; //导入依赖的package包/类
/**
 * Convert a labelled image into a list of PolygonRois by tracing.
 * Note that labels are assumed not to contain any holes or nested ROIs; ROIs produced by this command will not contain holes.
 * Some entries in the resulting array may be null if this is not the case, or if not all labels are found.
 * Otherwise, pixels with the integer label L will belong to the Roi in the output array at entry L-1
 * 
 * @param ipLabels
 * @param n - maximum number of labels
 * @return
 */
public static PolygonRoi[] labelsToFilledROIs(ImageProcessor ipLabels, int n) {
	PolygonRoi[] rois = new PolygonRoi[n];
	int w = ipLabels.getWidth();
	int h = ipLabels.getHeight();
	ByteProcessor bpCompleted = new ByteProcessor(w, h);
	bpCompleted.setValue(255);
	for (int y = 0; y < h; y++) {
		for (int x = 0; x < w; x++) {
			if (bpCompleted.get(x, y) != 0)
				continue;
			float val = ipLabels.getf(x, y);
			if (val > 0 && val <= n) {
				Wand wand = new Wand(ipLabels);
				wand.autoOutline(x, y, val, val, Wand.EIGHT_CONNECTED);
				PolygonRoi roi = wandToRoi(wand);
				rois[(int)val-1] = roi;
				bpCompleted.fill(roi);
			}
		}
	}
	return rois;
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
/**
 * Convert a labelled image into a list of PolygonRois by tracing.
 * 
 * Unlike labelsToFilledROIs, the order in which ROIs are returned is arbitrary.
 * 
 * Also, the multiple Rois may be created for the same label, if unconnected regions are used.
 * 
 * @param ipLabels
 * @param n - maximum number of labels
 * @return
 */
public static List<PolygonRoi> labelsToFilledRoiList(final ImageProcessor ipLabels, final boolean conn8) {
	List<PolygonRoi> rois = new ArrayList<>();
	int w = ipLabels.getWidth();
	int h = ipLabels.getHeight();
	ByteProcessor bpCompleted = new ByteProcessor(w, h);
	bpCompleted.setValue(255);
	for (int y = 0; y < h; y++) {
		for (int x = 0; x < w; x++) {
			if (bpCompleted.get(x, y) != 0)
				continue;
			float val = ipLabels.getf(x, y);
			if (val > 0) {
				Wand wand = new Wand(ipLabels);
				wand.autoOutline(x, y, val, val, conn8 ? Wand.EIGHT_CONNECTED : Wand.FOUR_CONNECTED);
				PolygonRoi roi = wandToRoi(wand);
				rois.add(roi);
				bpCompleted.fill(roi);
			}
		}
	}
	return rois;
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
/**
	 * Create a ROI from an ImageJ Roi.
	 * 
	 * @param pathROI
	 * @param pathImage
	 * @return
	 */
	public static ROI convertToPathROI(Roi roi, Calibration cal, double downsampleFactor, final int c, final int z, final int t) {
//		if (roi.getType() == Roi.POLYGON || roi.getType() == Roi.TRACED_ROI)
//			return convertToPolygonROI((PolygonRoi)roi, cal, downsampleFactor);
		if (roi.getType() == Roi.RECTANGLE && roi.getCornerDiameter() == 0)
			return getRectangleROI(roi, cal, downsampleFactor, c, z, t);
		if (roi.getType() == Roi.OVAL)
			return convertToEllipseROI(roi, cal, downsampleFactor, c, z, t);
		if (roi instanceof Line)
			return convertToLineROI((Line)roi, cal, downsampleFactor, c, z, t);
		if (roi instanceof PointRoi)
			return convertToPointROI((PolygonRoi)roi, cal, downsampleFactor, c, z, t);
//		if (roi instanceof ShapeRoi)
//			return convertToAreaROI((ShapeRoi)roi, cal, downsampleFactor);
//		// Shape ROIs should be able to handle most eventualities
		if (roi instanceof ShapeRoi)
			return convertToAreaROI((ShapeRoi)roi, cal, downsampleFactor, c, z, t);
		if (roi.isArea())
			return convertToPolygonOrAreaROI(roi, cal, downsampleFactor, c, z, t);
		// TODO: Integrate ROI not supported exception...?
		return null;	
	}
 

import ij.gui.PolygonRoi; //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.PolygonRoi; //导入依赖的package包/类
/** Write a PolygonRoi */
private void writePolygonRoi(
        final XMLStreamWriter xsw, 
        final PolygonRoi roi) 
        throws SlideSetException {
    final FloatPolygon fp = roi.getFloatPolygon();
    try {
        if(roi.getType() == Roi.POLYGON)
            xsw.writeStartElement("polygon");
        else
            xsw.writeStartElement("polyline");
        xsw.writeAttribute("class", "roi PolygonRoi");
        String coords = "";
        for(int i=0; i < fp.npoints; i++) {
            coords += String.valueOf(
                    fp.xpoints[i]) +
                    "," + String.valueOf(
                    fp.ypoints[i]) + " ";
        }
        xsw.writeAttribute("points", coords);
        applyDefaultStyles(xsw);
        xsw.writeEndElement();
    } catch(Exception e) {
        throw new SlideSetException(e);
    }
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
/** Generate an ROI from a {@code polyline} element */
private PolygonRoi parsePolyline(Element n) throws SVGParseException {
    if(!"polyline".equals(n.getTagName()))
        throw new SVGParseException("\'polyline\' expected, but \'" + n.getLocalName() + "\' found.");
    String points = n.getAttribute("points");
    ArrayList<double[]> pts;
    try {
        pts = parseListOfPoints(points);
    } catch(NumberFormatException e) {
        throw new SVGParseException("Bad list of points in polyline: " + points, e);
    }
    if(pts.isEmpty())
        return null;
    final float[] xs = new float[pts.size()];
    final float[] ys = new float[pts.size()];
    double[] pt = transformToDocumentSpace(pts.get(0), n);
    xs[0] = (float) pt[0];
    ys[0] = (float) pt[1];
    for(int i = 1; i < pts.size(); i++) {
        pt = transformToDocumentSpace(pts.get(i), n);
        xs[i] = (float) pt[0];
        ys[i] = (float) pt[1];
    }
    return new PolygonRoi(xs, ys, PolygonRoi.POLYLINE);
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
/** Generate an ROI from a {@code polygon} element */
private PolygonRoi parsePolygon(Element n) throws SVGParseException {
    if(!"polygon".equals(n.getTagName()))
        throw new SVGParseException("\'polygon\' expected, but \'" + n.getLocalName() + "\' found.");
    String points = n.getAttribute("points");
    ArrayList<double[]> pts;
    try {
        pts = parseListOfPoints(points);
    } catch(NumberFormatException e) {
        throw new SVGParseException("Bad points list: " + points, e);
    }
    if(pts.isEmpty())
        return null;
    final float[] xs = new float[pts.size()];
    final float[] ys = new float[pts.size()];
    double[] pt = transformToDocumentSpace(pts.get(0), n);
    xs[0] = (float) pt[0];
    ys[0] = (float) pt[1];
    for(int i = 1; i < pts.size(); i++) {
        pt = transformToDocumentSpace(pts.get(i), n);
        xs[i] = (float) pt[0];
        ys[i] = (float) pt[1];
    }
    return new PolygonRoi(xs, ys, PolygonRoi.POLYGON);
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
private Roi createRoi(ConvexHull hull, boolean forcePolygon)
{
	// Convert the Hull to the correct image scale.
	float[] x2 = hull.x.clone();
	float[] y2 = hull.y.clone();
	for (int i = 0; i < x2.length; i++)
	{
		x2[i] = image.mapX(x2[i]);
		y2[i] = image.mapY(y2[i]);
	}
	// Note: The hull can be a single point or a line
	if (!forcePolygon)
	{
		if (x2.length == 1)
			return new PointRoi(x2[0], y2[0]);
		if (x2.length == 2)
			return new Line(x2[0], y2[0], x2[1], y2[1]);
	}
	return new PolygonRoi(x2, y2, Roi.POLYGON);
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
public int setup(String arg, ImagePlus imp)
{
	UsageTracker.recordPlugin(this.getClass(), arg);

	if (imp == null)
	{
		return DONE;
	}
	if (imp.getRoi() == null || imp.getRoi().getType() != ij.gui.PolygonRoi.POINT)
	{
		IJ.error("Please select a centre point using the ROI tool");
		return DONE;
	}
	this.imp = imp;
	kernels = null;
	roi = (PointRoi) imp.getRoi();
	xpoints = roi.getPolygon().xpoints;
	ypoints = roi.getPolygon().ypoints;

	return flags;
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
/**
 * @param roi
 *            The polygon to fit
 * @param weightMap
 */
public DifferentiableEllipticalFitFunction(PolygonRoi roi, FloatProcessor weightMap)
{
	// These methods try to minimise the difference between a target value and your model value.
	// The target value is the polygon outline. The model is currently an elliptical path.
	this.weightMap = weightMap;
	nPoints = roi.getNCoordinates();
	xPoints = Arrays.copyOf(roi.getXCoordinates(), nPoints);
	yPoints = Arrays.copyOf(roi.getYCoordinates(), nPoints);
	Rectangle bounds = roi.getBounds();
	for (int i = 0; i < nPoints; i++)
	{
		xPoints[i] += bounds.x;
		yPoints[i] += bounds.y;
	}
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
private int findRoiPointIndex(PointRoi roi, int ox, int oy)
{
	Polygon p = ((PolygonRoi) roi).getNonSplineCoordinates();
	int n = p.npoints;
	Rectangle bounds = roi.getBounds();

	for (int i = 0; i < n; i++)
	{
		int x = bounds.x + p.xpoints[i];
		int y = bounds.y + p.ypoints[i];
		if (x == ox && y == oy)
			return i;
	}

	return -1;
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
public static ArrayList<Roi> generateVisualizationRoisFromTrack(Subtrajectory t, Color c, boolean showID, double pixelsize){
	ArrayList<Roi> proi = new ArrayList<Roi>();
	FloatPolygon p = new FloatPolygon();
	double sumx = 0;
	double sumy = 0;
	TextRoi.setFont("TimesRoman", 5, Font.PLAIN);
	for(int i = 0; i < t.getParent().size(); i++){
		int to = t.size();
		if(i< t.size()){
			
			sumx += t.get(i).x/pixelsize;
			sumy += t.get(i).y/pixelsize;
			p.addPoint(t.get(i).x/pixelsize, t.get(i).y/pixelsize);
			
			to = i+1;
		}
		
		PolygonRoi pr = new PolygonRoi(new FloatPolygon(p.xpoints, p.ypoints,to), PolygonRoi.POLYLINE);
		pr.setStrokeColor(c);
		pr.setPosition(t.getRelativeStartTimepoint()+i+1);
		proi.add(pr);
		
		if(showID){
			long parentID = t.getParent().getID();
			TextRoi troi = new TextRoi(sumx/to, sumy/to," "+parentID+":"+t.getID()+" ");
			troi.setPosition(t.getRelativeStartTimepoint()+i+1);
			troi.setFillColor(Color.BLACK);
			troi.setStrokeColor(c);
			troi.setAntialiased(true);
			proi.add(troi);
		}
	}
	return proi;
}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
private static PolygonRoi smoothPolygonRoi(PolygonRoi r) {
			FloatPolygon poly = r.getFloatPolygon();
			FloatPolygon poly2 = new FloatPolygon();
			int nPoints = poly.npoints;
			for (int i = 0; i < nPoints; i += 2) {
				int iMinus = (i + nPoints - 1) % nPoints;
				int iPlus = (i + 1) % nPoints;
				poly2.addPoint((poly.xpoints[iMinus] + poly.xpoints[iPlus] + poly.xpoints[i])/3, 
						(poly.ypoints[iMinus] + poly.ypoints[iPlus] + poly.ypoints[i])/3);
			}
//			return new PolygonRoi(poly2, r.getType());
			return new PolygonRoi(poly2, Roi.POLYGON);
		}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
/**
	 * Get filled Polygon ROIs using distinct labels, creating a map between labels and ROIs.
	 * <p>
	 * Note that discontinuous ROIs are not supported; if labelled regions are discontinuous,
	 * then ROIs detected earlier will be discarded from the map.
	 * 
	 * @param ip
	 * @param wandMode
	 * @return
	 */
	public static Map<Float, PolygonRoi> getFilledPolygonROIsFromLabels(ImageProcessor ip, int wandMode) {
//		Wand wand = new Wand(ip);
		double threshLower = ip.getMinThreshold();
		if (threshLower == ImageProcessor.NO_THRESHOLD)
			threshLower = Double.NEGATIVE_INFINITY;
		double threshHigher = ip.getMaxThreshold();
		if (threshHigher == ImageProcessor.NO_THRESHOLD)
			threshHigher = Double.POSITIVE_INFINITY;
		int w = ip.getWidth();
		int h = ip.getHeight();
//		List<PolygonRoi> rois = new ArrayList<>();
		ByteProcessor bpCompleted = new ByteProcessor(w, h);
		bpCompleted.setValue(255);
		TreeMap<Float, PolygonRoi> map = new TreeMap<>();
		for (int y = 0; y < h; y++) {
			for (int x = 0; x < w; x++) {
				if (bpCompleted.get(x, y) != 0)
					continue;
				float val = ip.getf(x, y);
				if (val >= threshLower && val <= threshHigher) {
					Wand wand = new Wand(ip);
					wand.autoOutline(x, y, threshLower, threshHigher, wandMode);
					PolygonRoi roi = wandToRoi(wand);
//					rois.add(roi);
					Float key = val;
					if (map.containsKey(key))
						logger.warn("Polygon ROI is being inserted twice into map for the same key {}", key);
					map.put(val, roi);
					bpCompleted.fill(roi);
				}
			}
		}
		return map;
	}
 

import ij.gui.PolygonRoi; //导入依赖的package包/类
public static List<PolygonRoi> getFilledPolygonROIs(ImageProcessor ip, int wandMode) {
//		Wand wand = new Wand(ip);
		double threshLower = ip.getMinThreshold();
		if (threshLower == ImageProcessor.NO_THRESHOLD)
			threshLower = Double.NEGATIVE_INFINITY;
		double threshHigher = ip.getMaxThreshold();
		if (threshHigher == ImageProcessor.NO_THRESHOLD)
			threshHigher = Double.POSITIVE_INFINITY;
		int w = ip.getWidth();
		int h = ip.getHeight();
		List<PolygonRoi> rois = new ArrayList<>();
		ByteProcessor bpCompleted = new ByteProcessor(w, h);
		bpCompleted.setValue(255);
		for (int y = 0; y < h; y++) {
			for (int x = 0; x < w; x++) {
				if (bpCompleted.get(x, y) != 0)
					continue;
				float val = ip.getf(x, y);
				if (val >= threshLower && val <= threshHigher) {
					Wand wand = new Wand(ip);
					wand.autoOutline(x, y, threshLower, threshHigher, wandMode);
					PolygonRoi roi = wandToRoi(wand);
					rois.add(roi);
					bpCompleted.fill(roi);
				}
			}
		}
		return rois;
	}