void updateSliceSummary() { int slices = imp.getStackSize(); float[] areas = rt.getColumn(ResultsTable.AREA); if (areas == null) areas = new float[0]; String label = imp.getTitle(); if (slices > 1) { label = imp.getStack().getShortSliceLabel(slice); label = label != null && !label.equals("") ? label : "" + slice; } String aLine = null; double sum = 0.0; int start = areas.length - particleCount; if (start < 0) return; for (int i = start; i < areas.length; i++) sum += areas[i]; int places = Analyzer.getPrecision(); Calibration cal = imp.getCalibration(); String total = "\t" + ResultsTable.d2s(sum, places); String average = "\t" + ResultsTable.d2s(sum / particleCount, places); String fraction = "\t" + ResultsTable.d2s(sum * 100.0 / totalArea, 1); aLine = label + "\t" + particleCount + total + average + fraction; aLine = addMeans(aLine, areas.length > 0 ? start : -1); if (slices == 1) { Frame frame = WindowManager.getFrame("Summary"); if (frame != null && (frame instanceof TextWindow) && summaryHdr.equals(prevHdr)) tw = (TextWindow) frame; } if (tw == null) { String title = slices == 1 ? "Summary" : "Summary of " + imp.getTitle(); tw = new TextWindow(title, summaryHdr, aLine, 450, 300); prevHdr = summaryHdr; } else tw.append(aLine); }
void drawOutline(ImageProcessor ip, Roi roi, int count) { if (showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) { if (overlay == null) { overlay = new Overlay(); overlay.drawLabels(true); overlay.setLabelFont(new Font("SansSerif", Font.PLAIN, fontSize)); } Roi roi2 = (Roi) roi.clone(); roi2.setStrokeColor(Color.cyan); if (lineWidth != 1) roi2.setStrokeWidth(lineWidth); if (showChoice == OVERLAY_MASKS) roi2.setFillColor(Color.cyan); overlay.add(roi2); } else { Rectangle r = roi.getBounds(); int nPoints = ((PolygonRoi) roi).getNCoordinates(); int[] xp = ((PolygonRoi) roi).getXCoordinates(); int[] yp = ((PolygonRoi) roi).getYCoordinates(); int x = r.x, y = r.y; if (!inSituShow) ip.setValue(0.0); ip.moveTo(x + xp[0], y + yp[0]); for (int i = 1; i < nPoints; i++) ip.lineTo(x + xp[i], y + yp[i]); ip.lineTo(x + xp[0], y + yp[0]); if (showChoice != BARE_OUTLINES) { String s = ResultsTable.d2s(count, 0); ip.moveTo(r.x + r.width / 2 - ip.getStringWidth(s) / 2, r.y + r.height / 2 + fontSize / 2); if (!inSituShow) ip.setValue(1.0); ip.drawString(s); } } }
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; }
/** Displays a modal options dialog. */ public boolean showDialog() { Calibration cal = imp != null ? imp.getCalibration() : (new Calibration()); double unitSquared = cal.pixelWidth * cal.pixelHeight; if (pixelUnits) unitSquared = 1.0; if (Macro.getOptions() != null) { boolean oldMacro = updateMacroOptions(); if (oldMacro) unitSquared = 1.0; staticMinSize = 0.0; staticMaxSize = DEFAULT_MAX_SIZE; staticMinCircularity = 0.0; staticMaxCircularity = 1.0; staticShowChoice = NOTHING; } GenericDialog gd = new GenericDialog("Analyze Particles"); minSize = staticMinSize; maxSize = staticMaxSize; minCircularity = staticMinCircularity; maxCircularity = staticMaxCircularity; showChoice = staticShowChoice; if (maxSize == 999999) maxSize = DEFAULT_MAX_SIZE; options = staticOptions; String unit = cal.getUnit(); boolean scaled = cal.scaled(); if (unit.equals("inch")) { unit = "pixel"; unitSquared = 1.0; scaled = false; pixelUnits = true; } String units = unit + "^2"; int places = 0; double cmin = minSize * unitSquared; if ((int) cmin != cmin) places = 2; double cmax = maxSize * unitSquared; if ((int) cmax != cmax && cmax != DEFAULT_MAX_SIZE) places = 2; String minStr = ResultsTable.d2s(cmin, places); if (minStr.indexOf("-") != -1) { for (int i = places; i <= 6; i++) { minStr = ResultsTable.d2s(cmin, i); if (minStr.indexOf("-") == -1) break; } } String maxStr = ResultsTable.d2s(cmax, places); if (maxStr.indexOf("-") != -1) { for (int i = places; i <= 6; i++) { maxStr = ResultsTable.d2s(cmax, i); if (maxStr.indexOf("-") == -1) break; } } if (scaled) gd.setInsets(5, 0, 0); gd.addStringField("Size (" + units + "):", minStr + "-" + maxStr, 12); if (scaled) { gd.setInsets(0, 40, 5); gd.addCheckbox("Pixel units", pixelUnits); } gd.addStringField("Circularity:", IJ.d2s(minCircularity) + "-" + IJ.d2s(maxCircularity), 12); gd.addChoice("Show:", showStrings, showStrings[showChoice]); String[] labels = new String[8]; boolean[] states = new boolean[8]; labels[0] = "Display results"; states[0] = (options & SHOW_RESULTS) != 0; labels[1] = "Exclude on edges"; states[1] = (options & EXCLUDE_EDGE_PARTICLES) != 0; labels[2] = "Clear results"; states[2] = (options & CLEAR_WORKSHEET) != 0; labels[3] = "Include holes"; states[3] = (options & INCLUDE_HOLES) != 0; labels[4] = "Summarize"; states[4] = (options & DISPLAY_SUMMARY) != 0; labels[5] = "Record starts"; states[5] = (options & RECORD_STARTS) != 0; labels[6] = "Add to Manager"; states[6] = (options & ADD_TO_MANAGER) != 0; labels[7] = "In_situ Show"; states[7] = (options & IN_SITU_SHOW) != 0; gd.addCheckboxGroup(4, 2, labels, states); gd.addHelp(IJ.URL + "/docs/menus/analyze.html#ap"); gd.showDialog(); if (gd.wasCanceled()) return false; String size = gd.getNextString(); // min-max size if (scaled) pixelUnits = gd.getNextBoolean(); if (pixelUnits) unitSquared = 1.0; else unitSquared = cal.pixelWidth * cal.pixelHeight; String[] minAndMax = Tools.split(size, " -"); double mins = gd.parseDouble(minAndMax[0]); double maxs = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN; minSize = Double.isNaN(mins) ? DEFAULT_MIN_SIZE : mins / unitSquared; maxSize = Double.isNaN(maxs) ? DEFAULT_MAX_SIZE : maxs / unitSquared; if (minSize < DEFAULT_MIN_SIZE) minSize = DEFAULT_MIN_SIZE; if (maxSize < minSize) maxSize = DEFAULT_MAX_SIZE; staticMinSize = minSize; staticMaxSize = maxSize; minAndMax = Tools.split(gd.getNextString(), " -"); // min-max circularity double minc = gd.parseDouble(minAndMax[0]); double maxc = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN; minCircularity = Double.isNaN(minc) ? 0.0 : minc; maxCircularity = Double.isNaN(maxc) ? 1.0 : maxc; if (minCircularity < 0.0 || minCircularity > 1.0) minCircularity = 0.0; if (maxCircularity < minCircularity || maxCircularity > 1.0) maxCircularity = 1.0; if (minCircularity == 1.0 && maxCircularity == 1.0) minCircularity = 0.0; staticMinCircularity = minCircularity; staticMaxCircularity = maxCircularity; if (gd.invalidNumber()) { IJ.error("Bins invalid."); canceled = true; return false; } showChoice = gd.getNextChoiceIndex(); staticShowChoice = showChoice; if (gd.getNextBoolean()) options |= SHOW_RESULTS; else options &= ~SHOW_RESULTS; if (gd.getNextBoolean()) options |= EXCLUDE_EDGE_PARTICLES; else options &= ~EXCLUDE_EDGE_PARTICLES; if (gd.getNextBoolean()) options |= CLEAR_WORKSHEET; else options &= ~CLEAR_WORKSHEET; if (gd.getNextBoolean()) options |= INCLUDE_HOLES; else options &= ~INCLUDE_HOLES; if (gd.getNextBoolean()) options |= DISPLAY_SUMMARY; else options &= ~DISPLAY_SUMMARY; if (gd.getNextBoolean()) options |= RECORD_STARTS; else options &= ~RECORD_STARTS; if (gd.getNextBoolean()) options |= ADD_TO_MANAGER; else options &= ~ADD_TO_MANAGER; if (gd.getNextBoolean()) options |= IN_SITU_SHOW; else options &= ~IN_SITU_SHOW; staticOptions = options; options |= SHOW_PROGRESS; if ((options & DISPLAY_SUMMARY) != 0) Analyzer.setMeasurements(Analyzer.getMeasurements() | AREA); return true; }