void interpolate() { Roi roi = imp.getRoi(); if (roi == null) { noRoi("Interpolate"); return; } if (roi.getType() == Roi.POINT) return; if (IJ.isMacro() && Macro.getOptions() == null) Macro.setOptions("interval=1"); GenericDialog gd = new GenericDialog("Interpolate"); gd.addNumericField("Interval:", 1.0, 1, 4, "pixel"); gd.addCheckbox("Smooth", IJ.isMacro() ? false : smooth); gd.showDialog(); if (gd.wasCanceled()) return; double interval = gd.getNextNumber(); smooth = gd.getNextBoolean(); Undo.setup(Undo.ROI, imp); FloatPolygon poly = roi.getInterpolatedPolygon(interval, smooth); int t = roi.getType(); int type = roi.isLine() ? Roi.FREELINE : Roi.FREEROI; if (t == Roi.POLYGON && interval > 1.0) type = Roi.POLYGON; if ((t == Roi.RECTANGLE || t == Roi.OVAL || t == Roi.FREEROI) && interval >= 5.0) type = Roi.POLYGON; if ((t == Roi.LINE || t == Roi.FREELINE) && interval >= 5.0) type = Roi.POLYLINE; if (t == Roi.POLYLINE && interval >= 1.0) type = Roi.POLYLINE; ImageCanvas ic = imp.getCanvas(); if (poly.npoints <= 150 && ic != null && ic.getMagnification() >= 12.0) type = roi.isLine() ? Roi.POLYLINE : Roi.POLYGON; Roi p = new PolygonRoi(poly, type); if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth()); p.setStrokeColor(roi.getStrokeColor()); p.setName(roi.getName()); transferProperties(roi, p); imp.setRoi(p); }
boolean updateMacroOptions() { String options = Macro.getOptions(); int index = options.indexOf("maximum="); if (index == -1) return false; index += 8; int len = options.length(); while (index < len - 1 && options.charAt(index) != ' ') index++; if (index == len - 1) return false; int min = (int) Tools.parseDouble(Macro.getValue(options, "minimum", "1")); int max = (int) Tools.parseDouble(Macro.getValue(options, "maximum", "999999")); options = "size=" + min + "-" + max + options.substring(index, len); Macro.setOptions(options); return true; }
void runMacro(String arg) { Roi roi = imp.getRoi(); if (IJ.macroRunning()) { String options = Macro.getOptions(); if (options != null && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) { IJ.run("Rotate... ", options); // run Image>Transform>Rotate return; } } if (roi == null) { noRoi("Rotate>Selection"); return; } roi = (Roi) roi.clone(); if (arg.equals("rotate")) { double d = Tools.parseDouble(angle); if (Double.isNaN(d)) angle = "15"; String value = IJ.runMacroFile("ij.jar:RotateSelection", angle); if (value != null) angle = value; } else if (arg.equals("enlarge")) { String value = IJ.runMacroFile("ij.jar:EnlargeSelection", enlarge); if (value != null) enlarge = value; Roi.previousRoi = roi; } }
void fitSpline() { Roi roi = imp.getRoi(); if (roi == null) { noRoi("Spline"); 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) { if (p.subPixelResolution()) p = trimFloatPolygon(p, p.getUncalibratedLength()); else 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(); }
/** * Saves statistics for one particle in a results table. This is a method subclasses may want to * override. */ protected void saveResults(ImageStatistics stats, Roi roi) { analyzer.saveResults(stats, roi); if (recordStarts) { rt.addValue("XStart", stats.xstart); rt.addValue("YStart", stats.ystart); } if (addToManager) { if (roiManager == null) { if (Macro.getOptions() != null && Interpreter.isBatchMode()) roiManager = Interpreter.getBatchModeRoiManager(); if (roiManager == null) { Frame frame = WindowManager.getFrame("ROI Manager"); if (frame == null) IJ.run("ROI Manager..."); frame = WindowManager.getFrame("ROI Manager"); if (frame == null || !(frame instanceof RoiManager)) { addToManager = false; return; } roiManager = (RoiManager) frame; } if (resetCounter) roiManager.runCommand("reset"); } if (imp.getStackSize() > 1) roi.setPosition(imp.getCurrentSlice()); if (lineWidth != 1) roi.setStrokeWidth(lineWidth); roiManager.add(imp, roi, rt.getCounter()); } if (showResults) rt.addResults(); }
private void rotate(ImagePlus imp) { Roi roi = imp.getRoi(); if (IJ.macroRunning()) { String options = Macro.getOptions(); if (options != null && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) { IJ.run("Rotate... ", options); // run Image>Transform>Rotate return; } } (new RoiRotator()).run(""); }
void runMacro(String arg, ImagePlus imp) { boolean rotate = arg.equals("rotate"); Roi roi = imp.getRoi(); if (rotate && IJ.macroRunning()) { String options = Macro.getOptions(); if (options != null && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) { IJ.run("Rotate... ", options); // run Image>Transform>Rotate return; } } if (roi == null) { noRoi(rotate ? "Rotate" : "Enlarge"); return; } double dangle = Tools.parseDouble(angle); if (Double.isNaN(dangle)) { dangle = 15; angle = "" + dangle; } if (rotate && (roi instanceof ImageRoi)) { dangle = IJ.getNumber("Angle (degrees):", dangle); ((ImageRoi) roi).rotate(dangle); imp.draw(); angle = "" + dangle; return; } Undo.setup(Undo.ROI, imp); roi = (Roi) roi.clone(); if (rotate) { String value = IJ.runMacroFile("ij.jar:RotateSelection", angle); Roi roi2 = imp.getRoi(); transferProperties(roi, roi2); imp.setRoi(roi2); if (value != null) angle = value; } else if (arg.equals("enlarge")) (new RoiEnlarger()).run(""); }
/** * 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; }
/** 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; }
boolean showDialog(ImageProcessor ip) { String macroOptions = Macro.getOptions(); if (macroOptions != null) { if (macroOptions.indexOf(" interpolate") != -1) macroOptions.replaceAll(" interpolate", " interpolation=Bilinear"); else if (macroOptions.indexOf(" interpolation=") == -1) macroOptions = macroOptions + " interpolation=None"; Macro.setOptions(macroOptions); } int bitDepth = imp.getBitDepth(); int stackSize = imp.getStackSize(); boolean isStack = stackSize > 1; oldDepth = stackSize; if (isStack) { xstr = "1.0"; ystr = "1.0"; zstr = "1.0"; } r = ip.getRoi(); int width = newWidth; if (width == 0) width = r.width; int height = (int) ((double) width * r.height / r.width); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); zscale = 1.0; if (xscale != 0.0 && yscale != 0.0) { width = (int) (r.width * xscale); height = (int) (r.height * yscale); } else { xstr = "-"; ystr = "-"; } GenericDialog gd = new GenericDialog("Scale"); gd.addStringField("X Scale:", xstr); gd.addStringField("Y Scale:", ystr); if (isStack) gd.addStringField("Z Scale:", zstr); gd.setInsets(5, 0, 5); gd.addStringField("Width (pixels):", "" + width); gd.addStringField("Height (pixels):", "" + height); if (isStack) { String label = "Depth (images):"; if (imp.isHyperStack()) { int slices = imp.getNSlices(); int frames = imp.getNFrames(); if (slices == 1 && frames > 1) { label = "Depth (frames):"; oldDepth = frames; } else { label = "Depth (slices):"; oldDepth = slices; } } gd.addStringField(label, "" + oldDepth); } fields = gd.getStringFields(); for (int i = 0; i < fields.size(); i++) { ((TextField) fields.elementAt(i)).addTextListener(this); ((TextField) fields.elementAt(i)).addFocusListener(this); } xField = (TextField) fields.elementAt(0); yField = (TextField) fields.elementAt(1); if (isStack) { zField = (TextField) fields.elementAt(2); widthField = (TextField) fields.elementAt(3); heightField = (TextField) fields.elementAt(4); depthField = (TextField) fields.elementAt(5); } else { widthField = (TextField) fields.elementAt(2); heightField = (TextField) fields.elementAt(3); } fieldWithFocus = xField; gd.addChoice("Interpolation:", methods, methods[interpolationMethod]); if (bitDepth == 8 || bitDepth == 24) gd.addCheckbox("Fill with background color", fillWithBackground); gd.addCheckbox("Average when downsizing", averageWhenDownsizing); boolean hyperstack = imp.isHyperStack() || imp.isComposite(); if (isStack && !hyperstack) gd.addCheckbox("Process entire stack", processStack); gd.addCheckbox("Create new window", newWindow); title = WindowManager.getUniqueName(imp.getTitle()); gd.setInsets(10, 0, 0); gd.addStringField("Title:", title, 12); gd.showDialog(); if (gd.wasCanceled()) return false; xstr = gd.getNextString(); ystr = gd.getNextString(); xscale = Tools.parseDouble(xstr, 0.0); yscale = Tools.parseDouble(ystr, 0.0); if (isStack) { zstr = gd.getNextString(); zscale = Tools.parseDouble(ystr, 0.0); } String wstr = gd.getNextString(); newWidth = (int) Tools.parseDouble(wstr, 0); newHeight = (int) Tools.parseDouble(gd.getNextString(), 0); if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0"))) newWidth = (int) (newHeight * (double) r.width / r.height); if (newWidth == 0 || newHeight == 0) { IJ.error("Scaler", "Width or height is 0"); return false; } if (xscale > 0.0 && yscale > 0.0) { newWidth = (int) (r.width * xscale); newHeight = (int) (r.height * yscale); } if (isStack) newDepth = (int) Tools.parseDouble(gd.getNextString(), 0); interpolationMethod = gd.getNextChoiceIndex(); if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean(); averageWhenDownsizing = gd.getNextBoolean(); if (isStack && !hyperstack) processStack = gd.getNextBoolean(); if (hyperstack) processStack = true; newWindow = gd.getNextBoolean(); if (xscale == 0.0) { xscale = (double) newWidth / r.width; yscale = (double) newHeight / r.height; } title = gd.getNextString(); if (fillWithBackground) { Color bgc = Toolbar.getBackgroundColor(); if (bitDepth == 8) bgValue = ip.getBestIndex(bgc); else if (bitDepth == 24) bgValue = bgc.getRGB(); } else bgValue = 0.0; return true; }