String n(double n) { String s; if (Math.round(n) == n) s = ResultsTable.d2s(n, 0); else s = ResultsTable.d2s(n, Analyzer.getPrecision()); return "\t" + s; }
public boolean get_errors(double[] params, int[] fixes) { GenericDialog gd = new GenericDialog("Error Options"); String[] methods = {"Support Plane", "Monte Carlo"}; gd.addChoice("Method", methods, methods[0]); float conf = 0.67f; gd.addNumericField("SP_Confidence Limit (%)", (int) (conf * 100.0f), 5, 10, null); String[] labels = {"P1", "P2", "P3", "P4", "P5", "P6", "P7", "P8", "P9", "P10"}; gd.addChoice("SP_Parameter", labels, labels[0]); double spacing = 0.01; gd.addNumericField("SP_Chi^2_plot_spacing (% of value)?", spacing * 100.0, 2, 10, null); int ntrials = 100; gd.addNumericField("MC_#_Trials", ntrials, 0); gd.showDialog(); if (gd.wasCanceled()) { return false; } int methodindex = gd.getNextChoiceIndex(); conf = 0.01f * (float) gd.getNextNumber(); int paramindex = gd.getNextChoiceIndex(); spacing = 0.01 * gd.getNextNumber(); ntrials = (int) gd.getNextNumber(); if (methodindex == 0) { support_plane_errors_v2 erclass = new support_plane_errors_v2(this, 0.0001, 50, false, 0.1); int errindex = paramindex; int nfit = 0; for (int i = 0; i < labels.length; i++) { if (fixes[i] == 0) { nfit++; } } int npts = tempdata.length; int dofnum = npts - (nfit - 1) - 1; int dofden = npts - nfit - 1; double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf); IJ.log("FLimit = " + (float) flim); if (flim == Double.NaN && flim < 1.0) { IJ.showMessage("Invalid Limiting F Value"); return false; } double truespacing = Math.abs(params[errindex] * spacing); double[][] c2plot = erclass.geterrors( params, fixes, constraints, tempdata, weights, flim, truespacing, errindex); IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]); IJ.log( "upper error = " + (c2plot[1][0] - params[errindex]) + " lower error = " + (params[errindex] - c2plot[0][0])); int templength = c2plot[0].length; float[][] c2plotf = new float[2][templength - 1]; for (int i = 0; i < (templength - 1); i++) { c2plotf[0][i] = (float) c2plot[0][i + 1]; c2plotf[1][i] = (float) c2plot[1][i + 1]; } new PlotWindow4("c2 plot", labels[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw(); } else { StringBuffer sb = new StringBuffer(); sb.append("Trial\t"); for (int i = 0; i < labels.length; i++) { if (fixes[i] == 0) sb.append(labels[i] + "\t"); } sb.append("chi^2"); tw = new TextWindow("Monte Carlo Results", sb.toString(), "", 400, 400); redirect = true; monte_carlo_errors_v2 erclass = new monte_carlo_errors_v2(this, 0.0001, 50, false, 0.1); double[][] errors = erclass.geterrors(params, fixes, constraints, tempdata, weights, ntrials); sb = new StringBuffer(); sb.append("StDev\t"); for (int i = 0; i < errors.length; i++) { float[] ferr = new float[errors[0].length]; for (int j = 0; j < ferr.length; j++) ferr[j] = (float) errors[i][j]; float stdev = jstatistics.getstatistic("StDev", ferr, null); sb.append("" + stdev); if (i < (errors.length - 1)) sb.append("\t"); } tw.append(sb.toString()); redirect = false; } return true; }
/** * 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; }