void createEllipse(ImagePlus imp) { IJ.showStatus("Fitting ellipse"); Roi roi = imp.getRoi(); if (roi == null) { noRoi("Fit Ellipse"); return; } if (roi.isLine()) { IJ.error("Fit Ellipse", "\"Fit Ellipse\" does not work with line selections"); return; } ImageProcessor ip = imp.getProcessor(); ip.setRoi(roi); int options = Measurements.CENTROID + Measurements.ELLIPSE; ImageStatistics stats = ImageStatistics.getStatistics(ip, options, null); double dx = stats.major * Math.cos(stats.angle / 180.0 * Math.PI) / 2.0; double dy = -stats.major * Math.sin(stats.angle / 180.0 * Math.PI) / 2.0; double x1 = stats.xCentroid - dx; double x2 = stats.xCentroid + dx; double y1 = stats.yCentroid - dy; double y2 = stats.yCentroid + dy; double aspectRatio = stats.minor / stats.major; imp.killRoi(); imp.setRoi(new EllipseRoi(x1, y1, x2, y2, aspectRatio)); }
void setHistogram(ImagePlus imp, int j) { ImageProcessor ip = imp.getProcessor(); ImageStatistics stats = ImageStatistics.getStatistics(ip, AREA + MODE, null); int maxCount2 = 0; histogram = stats.histogram; for (int i = 0; i < stats.nBins; i++) if ((histogram[i] > maxCount2) && (i != stats.mode)) maxCount2 = histogram[i]; hmax = stats.maxCount; if ((hmax > (maxCount2 * 1.5)) && (maxCount2 != 0)) { // GL 1.5 was 2 hmax = (int) (maxCount2 * 1.1); // GL 1.1 was 1.5 histogram[stats.mode] = hmax; } os = null; ColorModel cm = ip.getColorModel(); if (!(cm instanceof IndexColorModel)) return; IndexColorModel icm = (IndexColorModel) cm; int mapSize = icm.getMapSize(); if (mapSize != 256) return; byte[] r = new byte[256]; byte[] g = new byte[256]; byte[] b = new byte[256]; icm.getReds(r); icm.getGreens(g); icm.getBlues(b); hColors = new Color[256]; if (isRGB) { if (j == 0) { for (int i = 0; i < 256; i++) hColors[i] = new Color(i & 255, 0 & 255, 0 & 255); } else if (j == 1) { for (int i = 0; i < 256; i++) hColors[i] = new Color(0 & 255, i & 255, 0 & 255); } else if (j == 2) { for (int i = 0; i < 256; i++) hColors[i] = new Color(0 & 255, 0 & 255, i & 255); } } else { if (j == 0) { for (int i = 0; i < 256; i++) hColors[i] = new Color(r[i] & 255, g[i] & 255, b[i] & 255); } else if (j == 1) { for (int i = 0; i < 256; i++) // hColors[i] = new Color(127-i/2&255, 127+i/2&255, 127-i/2&255); hColors[i] = new Color(192 - i / 4 & 255, 192 + i / 4 & 255, 192 - i / 4 & 255); } else if (j == 2) { for (int i = 0; i < 256; i++) hColors[i] = new Color(i & 255, i & 255, 0 & 255); } } }
boolean eraseOutsideRoi(ImageProcessor ip, Rectangle r, ImageProcessor mask) { int width = ip.getWidth(); int height = ip.getHeight(); ip.setRoi(r); if (excludeEdgeParticles && polygon != null) { ImageStatistics stats = ImageStatistics.getStatistics(ip, MIN_MAX, null); if (fillColor >= stats.min && fillColor <= stats.max) { double replaceColor = level1 - 1.0; if (replaceColor < 0.0 || replaceColor == fillColor) { replaceColor = level2 + 1.0; int maxColor = imageType == BYTE ? 255 : 65535; if (replaceColor > maxColor || replaceColor == fillColor) { IJ.error("Particle Analyzer", "Unable to remove edge particles"); return false; } } for (int y = minY; y < maxY; y++) { for (int x = minX; x < maxX; x++) { int v = ip.getPixel(x, y); if (v == fillColor) ip.putPixel(x, y, (int) replaceColor); } } } } ip.setValue(fillColor); if (mask != null) { mask = mask.duplicate(); mask.invert(); ip.fill(mask); } ip.setRoi(0, 0, r.x, height); ip.fill(); ip.setRoi(r.x, 0, r.width, r.y); ip.fill(); ip.setRoi(r.x, r.y + r.height, r.width, height - (r.y + r.height)); ip.fill(); ip.setRoi(r.x + r.width, 0, width - (r.x + r.width), height); ip.fill(); ip.resetRoi(); // IJ.log("erase: "+fillColor+" "+level1+" "+level2+" "+excludeEdgeParticles); // (new ImagePlus("ip2", ip.duplicate())).show(); return true; }
/* if selection is closed shape, create a circle with the same area and centroid, otherwise use<br> the Pratt method to fit a circle to the points that define the line or multi-point selection.<br> Reference: Pratt V., Direct least-squares fitting of algebraic surfaces", Computer Graphics, Vol. 21, pages 145-152 (1987).<br> Original code: Nikolai Chernov's MATLAB script for Newton-based Pratt fit.<br> (http://www.math.uab.edu/~chernov/cl/MATLABcircle.html)<br> Java version: https://github.com/mdoube/BoneJ/blob/master/src/org/doube/geometry/FitCircle.java<br> @authors Nikolai Chernov, Michael Doube, Ved Sharma */ void fitCircle(ImagePlus imp) { Roi roi = imp.getRoi(); if (roi == null) { noRoi("Fit Circle"); return; } if (roi.isArea()) { // create circle with the same area and centroid ImageProcessor ip = imp.getProcessor(); ip.setRoi(roi); ImageStatistics stats = ImageStatistics.getStatistics(ip, Measurements.AREA + Measurements.CENTROID, null); double r = Math.sqrt(stats.pixelCount / Math.PI); imp.killRoi(); int d = (int) Math.round(2.0 * r); IJ.makeOval( (int) Math.round(stats.xCentroid - r), (int) Math.round(stats.yCentroid - r), d, d); return; } Polygon poly = roi.getPolygon(); int n = poly.npoints; int[] x = poly.xpoints; int[] y = poly.ypoints; if (n < 3) { IJ.error("Fit Circle", "At least 3 points are required to fit a circle."); return; } // calculate point centroid double sumx = 0, sumy = 0; for (int i = 0; i < n; i++) { sumx = sumx + poly.xpoints[i]; sumy = sumy + poly.ypoints[i]; } double meanx = sumx / n; double meany = sumy / n; // calculate moments double[] X = new double[n], Y = new double[n]; double Mxx = 0, Myy = 0, Mxy = 0, Mxz = 0, Myz = 0, Mzz = 0; for (int i = 0; i < n; i++) { X[i] = x[i] - meanx; Y[i] = y[i] - meany; double Zi = X[i] * X[i] + Y[i] * Y[i]; Mxy = Mxy + X[i] * Y[i]; Mxx = Mxx + X[i] * X[i]; Myy = Myy + Y[i] * Y[i]; Mxz = Mxz + X[i] * Zi; Myz = Myz + Y[i] * Zi; Mzz = Mzz + Zi * Zi; } Mxx = Mxx / n; Myy = Myy / n; Mxy = Mxy / n; Mxz = Mxz / n; Myz = Myz / n; Mzz = Mzz / n; // calculate the coefficients of the characteristic polynomial double Mz = Mxx + Myy; double Cov_xy = Mxx * Myy - Mxy * Mxy; double Mxz2 = Mxz * Mxz; double Myz2 = Myz * Myz; double A2 = 4 * Cov_xy - 3 * Mz * Mz - Mzz; double A1 = Mzz * Mz + 4 * Cov_xy * Mz - Mxz2 - Myz2 - Mz * Mz * Mz; double A0 = Mxz2 * Myy + Myz2 * Mxx - Mzz * Cov_xy - 2 * Mxz * Myz * Mxy + Mz * Mz * Cov_xy; double A22 = A2 + A2; double epsilon = 1e-12; double ynew = 1e+20; int IterMax = 20; double xnew = 0; int iterations = 0; // Newton's method starting at x=0 for (int iter = 1; iter <= IterMax; iter++) { iterations = iter; double yold = ynew; ynew = A0 + xnew * (A1 + xnew * (A2 + 4. * xnew * xnew)); if (Math.abs(ynew) > Math.abs(yold)) { if (IJ.debugMode) IJ.log("Fit Circle: wrong direction: |ynew| > |yold|"); xnew = 0; break; } double Dy = A1 + xnew * (A22 + 16 * xnew * xnew); double xold = xnew; xnew = xold - ynew / Dy; if (Math.abs((xnew - xold) / xnew) < epsilon) break; if (iter >= IterMax) { if (IJ.debugMode) IJ.log("Fit Circle: will not converge"); xnew = 0; } if (xnew < 0) { if (IJ.debugMode) IJ.log("Fit Circle: negative root: x = " + xnew); xnew = 0; } } if (IJ.debugMode) IJ.log("Fit Circle: n=" + n + ", xnew=" + IJ.d2s(xnew, 2) + ", iterations=" + iterations); // calculate the circle parameters double DET = xnew * xnew - xnew * Mz + Cov_xy; double CenterX = (Mxz * (Myy - xnew) - Myz * Mxy) / (2 * DET); double CenterY = (Myz * (Mxx - xnew) - Mxz * Mxy) / (2 * DET); double radius = Math.sqrt(CenterX * CenterX + CenterY * CenterY + Mz + 2 * xnew); if (Double.isNaN(radius)) { IJ.error("Fit Circle", "Points are collinear."); return; } CenterX = CenterX + meanx; CenterY = CenterY + meany; imp.killRoi(); IJ.makeOval( (int) Math.round(CenterX - radius), (int) Math.round(CenterY - radius), (int) Math.round(2 * radius), (int) Math.round(2 * radius)); }
void drawEllipse(ImageProcessor ip, ImageStatistics stats, int count) { stats.drawEllipse(ip); }
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); }
/** * Performs particle analysis on the specified ImagePlus and ImageProcessor. Returns false if * there is an error. */ public boolean analyze(ImagePlus imp, ImageProcessor ip) { if (this.imp == null) this.imp = imp; showResults = (options & SHOW_RESULTS) != 0; excludeEdgeParticles = (options & EXCLUDE_EDGE_PARTICLES) != 0; resetCounter = (options & CLEAR_WORKSHEET) != 0; showProgress = (options & SHOW_PROGRESS) != 0; floodFill = (options & INCLUDE_HOLES) == 0; recordStarts = (options & RECORD_STARTS) != 0; addToManager = (options & ADD_TO_MANAGER) != 0; displaySummary = (options & DISPLAY_SUMMARY) != 0; inSituShow = (options & IN_SITU_SHOW) != 0; outputImage = null; ip.snapshot(); ip.setProgressBar(null); if (Analyzer.isRedirectImage()) { redirectImp = Analyzer.getRedirectImage(imp); if (redirectImp == null) return false; int depth = redirectImp.getStackSize(); if (depth > 1 && depth == imp.getStackSize()) { ImageStack redirectStack = redirectImp.getStack(); redirectIP = redirectStack.getProcessor(imp.getCurrentSlice()); } else redirectIP = redirectImp.getProcessor(); } else if (imp.getType() == ImagePlus.COLOR_RGB) { ImagePlus original = (ImagePlus) imp.getProperty("OriginalImage"); if (original != null && original.getWidth() == imp.getWidth() && original.getHeight() == imp.getHeight()) { redirectImp = original; redirectIP = original.getProcessor(); } } if (!setThresholdLevels(imp, ip)) return false; width = ip.getWidth(); height = ip.getHeight(); if (!(showChoice == NOTHING || showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS)) { blackBackground = Prefs.blackBackground && inSituShow; if (slice == 1) outlines = new ImageStack(width, height); if (showChoice == ROI_MASKS) drawIP = new ShortProcessor(width, height); else drawIP = new ByteProcessor(width, height); drawIP.setLineWidth(lineWidth); if (showChoice == ROI_MASKS) { } // Place holder for now... else if (showChoice == MASKS && !blackBackground) drawIP.invertLut(); else if (showChoice == OUTLINES) { if (!inSituShow) { if (customLut == null) makeCustomLut(); drawIP.setColorModel(customLut); } drawIP.setFont(new Font("SansSerif", Font.PLAIN, fontSize)); if (fontSize > 12 && inSituShow) drawIP.setAntialiasedText(true); } outlines.addSlice(null, drawIP); if (showChoice == ROI_MASKS || blackBackground) { drawIP.setColor(Color.black); drawIP.fill(); drawIP.setColor(Color.white); } else { drawIP.setColor(Color.white); drawIP.fill(); drawIP.setColor(Color.black); } } calibration = redirectImp != null ? redirectImp.getCalibration() : imp.getCalibration(); if (rt == null) { rt = Analyzer.getResultsTable(); analyzer = new Analyzer(imp); } else analyzer = new Analyzer(imp, measurements, rt); if (resetCounter && slice == 1) { if (!Analyzer.resetCounter()) return false; } beginningCount = Analyzer.getCounter(); byte[] pixels = null; if (ip instanceof ByteProcessor) pixels = (byte[]) ip.getPixels(); if (r == null) { r = ip.getRoi(); mask = ip.getMask(); if (displaySummary) { if (mask != null) totalArea = ImageStatistics.getStatistics(ip, AREA, calibration).area; else totalArea = r.width * calibration.pixelWidth * r.height * calibration.pixelHeight; } } minX = r.x; maxX = r.x + r.width; minY = r.y; maxY = r.y + r.height; if (r.width < width || r.height < height || mask != null) { if (!eraseOutsideRoi(ip, r, mask)) return false; } int offset; double value; int inc = Math.max(r.height / 25, 1); int mi = 0; ImageWindow win = imp.getWindow(); if (win != null) win.running = true; if (measurements == 0) measurements = Analyzer.getMeasurements(); if (showChoice == ELLIPSES) measurements |= ELLIPSE; measurements &= ~LIMIT; // ignore "Limit to Threshold" roiNeedsImage = (measurements & PERIMETER) != 0 || (measurements & SHAPE_DESCRIPTORS) != 0 || (measurements & FERET) != 0; particleCount = 0; wand = new Wand(ip); pf = new PolygonFiller(); if (floodFill) { ImageProcessor ipf = ip.duplicate(); ipf.setValue(fillColor); ff = new FloodFiller(ipf); } roiType = Wand.allPoints() ? Roi.FREEROI : Roi.TRACED_ROI; for (int y = r.y; y < (r.y + r.height); y++) { offset = y * width; for (int x = r.x; x < (r.x + r.width); x++) { if (pixels != null) value = pixels[offset + x] & 255; else if (imageType == SHORT) value = ip.getPixel(x, y); else value = ip.getPixelValue(x, y); if (value >= level1 && value <= level2) analyzeParticle(x, y, imp, ip); } if (showProgress && ((y % inc) == 0)) IJ.showProgress((double) (y - r.y) / r.height); if (win != null) canceled = !win.running; if (canceled) { Macro.abort(); break; } } if (showProgress) IJ.showProgress(1.0); if (showResults) rt.updateResults(); imp.killRoi(); ip.resetRoi(); ip.reset(); if (displaySummary && IJ.getInstance() != null) updateSliceSummary(); if (addToManager && roiManager != null) roiManager.setEditMode(imp, true); maxParticleCount = (particleCount > maxParticleCount) ? particleCount : maxParticleCount; totalCount += particleCount; if (!canceled) showResults(); return true; }