/** Returns a copy of this PolygonRoi. */ public synchronized Object clone() { PolygonRoi r = (PolygonRoi) super.clone(); if (xpf != null) { r.xpf = new float[maxPoints]; r.ypf = new float[maxPoints]; } else { r.xp = new int[maxPoints]; r.yp = new int[maxPoints]; } r.xp2 = new int[maxPoints]; r.yp2 = new int[maxPoints]; for (int i = 0; i < nPoints; i++) { if (xpf != null) { r.xpf[i] = xpf[i]; r.ypf[i] = ypf[i]; } else { r.xp[i] = xp[i]; r.yp[i] = yp[i]; } r.xp2[i] = xp2[i]; r.yp2[i] = yp2[i]; } if (xSpline != null) { r.xSpline = new float[splinePoints]; r.ySpline = new float[splinePoints]; r.splinePoints = splinePoints; for (int i = 0; i < splinePoints; i++) { r.xSpline[i] = xSpline[i]; r.ySpline[i] = ySpline[i]; } } return r; }
public void mouseMoved(MouseEvent e) { // if (ij==null) return; int sx = e.getX(); int sy = e.getY(); int ox = offScreenX(sx); int oy = offScreenY(sy); flags = e.getModifiers(); setCursor(sx, sy, ox, oy); IJ.setInputEvent(e); Roi roi = imp.getRoi(); if (roi != null && (roi.getType() == Roi.POLYGON || roi.getType() == Roi.POLYLINE || roi.getType() == Roi.ANGLE) && roi.getState() == roi.CONSTRUCTING) { PolygonRoi pRoi = (PolygonRoi) roi; pRoi.handleMouseMove(ox, oy); } else { if (ox < imageWidth && oy < imageHeight) { ImageWindow win = imp.getWindow(); // Cursor must move at least 12 pixels before text // displayed using IJ.showStatus() is overwritten. if ((sx - sx2) * (sx - sx2) + (sy - sy2) * (sy - sy2) > 144) showCursorStatus = true; if (win != null && showCursorStatus) win.mouseMoved(ox, oy); } else IJ.showStatus(""); } }
void fitSpline() { Roi roi = imp.getRoi(); if (roi == null) { IJ.error("Spline", "Selection required"); return; } int type = roi.getType(); boolean segmentedSelection = type == Roi.POLYGON || type == Roi.POLYLINE; if (!(segmentedSelection || type == Roi.FREEROI || type == Roi.TRACED_ROI || type == Roi.FREELINE)) { IJ.error("Spline", "Polygon or polyline selection required"); return; } if (roi instanceof EllipseRoi) return; PolygonRoi p = (PolygonRoi) roi; if (!segmentedSelection) p = trimPolygon(p, p.getUncalibratedLength()); String options = Macro.getOptions(); if (options != null && options.indexOf("straighten") != -1) p.fitSplineForStraightening(); else if (options != null && options.indexOf("remove") != -1) p.removeSplineFit(); else p.fitSpline(); imp.draw(); LineWidthAdjuster.update(); }
PolygonRoi trimFloatPolygon(PolygonRoi roi, double length) { FloatPolygon poly = roi.getFloatPolygon(); float[] x = poly.xpoints; float[] y = poly.ypoints; int n = poly.npoints; x = smooth(x, n); y = smooth(y, n); float[] curvature = getCurvature(x, y, n); double threshold = rodbard(length); // IJ.log("trim: "+length+" "+threshold); double distance = Math.sqrt((x[1] - x[0]) * (x[1] - x[0]) + (y[1] - y[0]) * (y[1] - y[0])); int i2 = 1; double x1, y1, x2 = 0, y2 = 0; for (int i = 1; i < n - 1; i++) { x1 = x[i]; y1 = y[i]; x2 = x[i + 1]; y2 = y[i + 1]; distance += Math.sqrt((x2 - x1) * (x2 - x1) + (y2 - y1) * (y2 - y1)) + 1; distance += curvature[i] * 2; if (distance >= threshold) { x[i2] = (float) x2; y[i2] = (float) y2; i2++; distance = 0.0; } } int type = roi.getType() == Roi.FREELINE ? Roi.POLYLINE : Roi.POLYGON; if (type == Roi.POLYLINE && distance > 0.0) { x[i2] = (float) x2; y[i2] = (float) y2; i2++; } PolygonRoi p = new PolygonRoi(x, y, i2, type); if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth()); p.setStrokeColor(roi.getStrokeColor()); p.setName(roi.getName()); imp.setRoi(p); return p; }
PolygonRoi trimPolygon(PolygonRoi roi, double length) { int[] x = roi.getXCoordinates(); int[] y = roi.getYCoordinates(); int n = roi.getNCoordinates(); x = smooth(x, n); y = smooth(y, n); float[] curvature = getCurvature(x, y, n); Rectangle r = roi.getBounds(); double threshold = rodbard(length); // IJ.log("trim: "+length+" "+threshold); double distance = Math.sqrt((x[1] - x[0]) * (x[1] - x[0]) + (y[1] - y[0]) * (y[1] - y[0])); x[0] += r.x; y[0] += r.y; int i2 = 1; int x1, y1, x2 = 0, y2 = 0; for (int i = 1; i < n - 1; i++) { x1 = x[i]; y1 = y[i]; x2 = x[i + 1]; y2 = y[i + 1]; distance += Math.sqrt((x2 - x1) * (x2 - x1) + (y2 - y1) * (y2 - y1)) + 1; distance += curvature[i] * 2; if (distance >= threshold) { x[i2] = x2 + r.x; y[i2] = y2 + r.y; i2++; distance = 0.0; } } int type = roi.getType() == Roi.FREELINE ? Roi.POLYLINE : Roi.POLYGON; if (type == Roi.POLYLINE && distance > 0.0) { x[i2] = x2 + r.x; y[i2] = y2 + r.y; i2++; } PolygonRoi p = new PolygonRoi(x, y, i2, type); imp.setRoi(p); return p; }
void analyzeParticle(int x, int y, ImagePlus imp, ImageProcessor ip) { // Wand wand = new Wand(ip); ImageProcessor ip2 = redirectIP != null ? redirectIP : ip; wand.autoOutline(x, y, level1, level2, wandMode); if (wand.npoints == 0) { IJ.log("wand error: " + x + " " + y); return; } Roi roi = new PolygonRoi(wand.xpoints, wand.ypoints, wand.npoints, roiType); Rectangle r = roi.getBounds(); if (r.width > 1 && r.height > 1) { PolygonRoi proi = (PolygonRoi) roi; pf.setPolygon(proi.getXCoordinates(), proi.getYCoordinates(), proi.getNCoordinates()); ip2.setMask(pf.getMask(r.width, r.height)); if (floodFill) ff.particleAnalyzerFill(x, y, level1, level2, ip2.getMask(), r); } ip2.setRoi(r); ip.setValue(fillColor); ImageStatistics stats = getStatistics(ip2, measurements, calibration); boolean include = true; if (excludeEdgeParticles) { if (r.x == minX || r.y == minY || r.x + r.width == maxX || r.y + r.height == maxY) include = false; if (polygon != null) { Rectangle bounds = roi.getBounds(); int x1 = bounds.x + wand.xpoints[wand.npoints - 1]; int y1 = bounds.y + wand.ypoints[wand.npoints - 1]; int x2, y2; for (int i = 0; i < wand.npoints; i++) { x2 = bounds.x + wand.xpoints[i]; y2 = bounds.y + wand.ypoints[i]; if (!polygon.contains(x2, y2)) { include = false; break; } if ((x1 == x2 && ip.getPixel(x1, y1 - 1) == fillColor) || (y1 == y2 && ip.getPixel(x1 - 1, y1) == fillColor)) { include = false; break; } x1 = x2; y1 = y2; } } } ImageProcessor mask = ip2.getMask(); if (minCircularity > 0.0 || maxCircularity < 1.0) { double perimeter = roi.getLength(); double circularity = perimeter == 0.0 ? 0.0 : 4.0 * Math.PI * (stats.pixelCount / (perimeter * perimeter)); if (circularity > 1.0) circularity = 1.0; // IJ.log(circularity+" "+perimeter+" "+stats.area); if (circularity < minCircularity || circularity > maxCircularity) include = false; } if (stats.pixelCount >= minSize && stats.pixelCount <= maxSize && include) { particleCount++; if (roiNeedsImage) roi.setImage(imp); stats.xstart = x; stats.ystart = y; saveResults(stats, roi); if (showChoice != NOTHING) drawParticle(drawIP, roi, stats, mask); } if (redirectIP != null) ip.setRoi(r); ip.fill(mask); }