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; }
/** Ask for parameters and then execute. */ public void run(String arg) { // 1 - Obtain the currently active image: ImagePlus imp = IJ.getImage(); if (null == imp) { IJ.showMessage("There must be at least one image open"); return; } if (imp.getBitDepth() != 8) { IJ.showMessage("Error", "Only 8-bit images are supported"); return; } // 2 - Ask for parameters: GenericDialog gd = new GenericDialog("Auto Local Threshold"); String[] methods = { "Try all", "Bernsen", "Contrast", "Mean", "Median", "MidGrey", "Niblack", "Otsu", "Phansalkar", "Sauvola" }; gd.addMessage("Auto Local Threshold v1.5"); gd.addChoice("Method", methods, methods[0]); gd.addNumericField("Radius", 15, 0); gd.addMessage("Special paramters (if different from default)"); gd.addNumericField("Parameter_1", 0, 0); gd.addNumericField("Parameter_2", 0, 0); gd.addCheckbox("White objects on black background", true); if (imp.getStackSize() > 1) { gd.addCheckbox("Stack", false); } gd.addMessage("Thresholded result is always shown in white [255]."); gd.showDialog(); if (gd.wasCanceled()) return; // 3 - Retrieve parameters from the dialog String myMethod = gd.getNextChoice(); int radius = (int) gd.getNextNumber(); double par1 = (double) gd.getNextNumber(); double par2 = (double) gd.getNextNumber(); boolean doIwhite = gd.getNextBoolean(); boolean doIstack = false; int stackSize = imp.getStackSize(); if (stackSize > 1) doIstack = gd.getNextBoolean(); // 4 - Execute! // long start = System.currentTimeMillis(); if (myMethod.equals("Try all")) { ImageProcessor ip = imp.getProcessor(); int xe = ip.getWidth(); int ye = ip.getHeight(); int ml = methods.length; ImagePlus imp2, imp3; ImageStack tstack = null, stackNew; if (stackSize > 1 && doIstack) { boolean doItAnyway = true; if (stackSize > 25) { YesNoCancelDialog d = new YesNoCancelDialog( IJ.getInstance(), "Auto Local Threshold", "You might run out of memory.\n \nDisplay " + stackSize + " slices?\n \n \'No\' will process without display and\noutput results to the log window."); if (!d.yesPressed()) { // doIlog=true; //will show in the log window doItAnyway = false; } if (d.cancelPressed()) return; } for (int j = 1; j <= stackSize; j++) { imp.setSlice(j); ip = imp.getProcessor(); tstack = new ImageStack(xe, ye); for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate()); imp2 = new ImagePlus("Auto Threshold", tstack); imp2.updateAndDraw(); for (int k = 1; k < ml; k++) { imp2.setSlice(k); Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite); } // if (doItAnyway){ CanvasResizer cr = new CanvasResizer(); stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1); imp3 = new ImagePlus("Auto Threshold", stackNew); imp3.updateAndDraw(); MontageMaker mm = new MontageMaker(); mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true); // 3 columns and 3 rows } imp.setSlice(1); // if (doItAnyway) IJ.run("Images to Stack", "method=[Copy (center)] title=Montage"); return; } else { // single image try all tstack = new ImageStack(xe, ye); for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate()); imp2 = new ImagePlus("Auto Threshold", tstack); imp2.updateAndDraw(); for (int k = 1; k < ml; k++) { imp2.setSlice(k); // IJ.log("analyzing slice with "+methods[k]); Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite); } // imp2.setSlice(1); CanvasResizer cr = new CanvasResizer(); stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1); imp3 = new ImagePlus("Auto Threshold", stackNew); imp3.updateAndDraw(); MontageMaker mm = new MontageMaker(); mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true); return; } } else { // selected a method if (stackSize > 1 && doIstack) { // whole stack // if (doIstackHistogram) {// one global histogram // Object[] result = exec(imp, myMethod, noWhite, noBlack, doIwhite, doIset, doIlog, // doIstackHistogram ); // } // else{ // slice by slice for (int k = 1; k <= stackSize; k++) { imp.setSlice(k); Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite); } // } imp.setSlice(1); } else { // just one slice Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite); } // 5 - If all went well, show the image: // not needed here as the source image is binarised } }
/** * 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; }
/*------------------------------------------------------------------*/ void doIt(ImageProcessor ip) { int width = ip.getWidth(); int height = ip.getHeight(); double hLine[] = new double[width]; double vLine[] = new double[height]; if (!(ip.getPixels() instanceof float[])) { throw new IllegalArgumentException("Float image required"); } switch (operation) { case GRADIENT_MAGNITUDE: { ImageProcessor h = ip.duplicate(); ImageProcessor v = ip.duplicate(); float[] floatPixels = (float[]) ip.getPixels(); float[] floatPixelsH = (float[]) h.getPixels(); float[] floatPixelsV = (float[]) v.getPixels(); getHorizontalGradient(h, FLT_EPSILON); getVerticalGradient(v, FLT_EPSILON); for (int y = 0, k = 0; (y < height); y++) { for (int x = 0; (x < width); x++, k++) { floatPixels[k] = (float) Math.sqrt( floatPixelsH[k] * floatPixelsH[k] + floatPixelsV[k] * floatPixelsV[k]); } stepProgressBar(); } } break; case GRADIENT_DIRECTION: { ImageProcessor h = ip.duplicate(); ImageProcessor v = ip.duplicate(); float[] floatPixels = (float[]) ip.getPixels(); float[] floatPixelsH = (float[]) h.getPixels(); float[] floatPixelsV = (float[]) v.getPixels(); getHorizontalGradient(h, FLT_EPSILON); getVerticalGradient(v, FLT_EPSILON); for (int y = 0, k = 0; (y < height); y++) { for (int x = 0; (x < width); x++, k++) { floatPixels[k] = (float) Math.atan2(floatPixelsH[k], floatPixelsV[k]); } stepProgressBar(); } } break; case LAPLACIAN: { ImageProcessor hh = ip.duplicate(); ImageProcessor vv = ip.duplicate(); float[] floatPixels = (float[]) ip.getPixels(); float[] floatPixelsHH = (float[]) hh.getPixels(); float[] floatPixelsVV = (float[]) vv.getPixels(); getHorizontalHessian(hh, FLT_EPSILON); getVerticalHessian(vv, FLT_EPSILON); for (int y = 0, k = 0; (y < height); y++) { for (int x = 0; (x < width); x++, k++) { floatPixels[k] = (float) (floatPixelsHH[k] + floatPixelsVV[k]); } stepProgressBar(); } } break; case LARGEST_HESSIAN: { ImageProcessor hh = ip.duplicate(); ImageProcessor vv = ip.duplicate(); ImageProcessor hv = ip.duplicate(); float[] floatPixels = (float[]) ip.getPixels(); float[] floatPixelsHH = (float[]) hh.getPixels(); float[] floatPixelsVV = (float[]) vv.getPixels(); float[] floatPixelsHV = (float[]) hv.getPixels(); getHorizontalHessian(hh, FLT_EPSILON); getVerticalHessian(vv, FLT_EPSILON); getCrossHessian(hv, FLT_EPSILON); for (int y = 0, k = 0; (y < height); y++) { for (int x = 0; (x < width); x++, k++) { floatPixels[k] = (float) (0.5 * (floatPixelsHH[k] + floatPixelsVV[k] + Math.sqrt( 4.0 * floatPixelsHV[k] * floatPixelsHV[k] + (floatPixelsHH[k] - floatPixelsVV[k]) * (floatPixelsHH[k] - floatPixelsVV[k])))); } stepProgressBar(); } } break; case SMALLEST_HESSIAN: { ImageProcessor hh = ip.duplicate(); ImageProcessor vv = ip.duplicate(); ImageProcessor hv = ip.duplicate(); float[] floatPixels = (float[]) ip.getPixels(); float[] floatPixelsHH = (float[]) hh.getPixels(); float[] floatPixelsVV = (float[]) vv.getPixels(); float[] floatPixelsHV = (float[]) hv.getPixels(); getHorizontalHessian(hh, FLT_EPSILON); getVerticalHessian(vv, FLT_EPSILON); getCrossHessian(hv, FLT_EPSILON); for (int y = 0, k = 0; (y < height); y++) { for (int x = 0; (x < width); x++, k++) { floatPixels[k] = (float) (0.5 * (floatPixelsHH[k] + floatPixelsVV[k] - Math.sqrt( 4.0 * floatPixelsHV[k] * floatPixelsHV[k] + (floatPixelsHH[k] - floatPixelsVV[k]) * (floatPixelsHH[k] - floatPixelsVV[k])))); } stepProgressBar(); } } break; case HESSIAN_ORIENTATION: { ImageProcessor hh = ip.duplicate(); ImageProcessor vv = ip.duplicate(); ImageProcessor hv = ip.duplicate(); float[] floatPixels = (float[]) ip.getPixels(); float[] floatPixelsHH = (float[]) hh.getPixels(); float[] floatPixelsVV = (float[]) vv.getPixels(); float[] floatPixelsHV = (float[]) hv.getPixels(); getHorizontalHessian(hh, FLT_EPSILON); getVerticalHessian(vv, FLT_EPSILON); getCrossHessian(hv, FLT_EPSILON); for (int y = 0, k = 0; (y < height); y++) { for (int x = 0; (x < width); x++, k++) { if (floatPixelsHV[k] < 0.0) { floatPixels[k] = (float) (-0.5 * Math.acos( (floatPixelsHH[k] - floatPixelsVV[k]) / Math.sqrt( 4.0 * floatPixelsHV[k] * floatPixelsHV[k] + (floatPixelsHH[k] - floatPixelsVV[k]) * (floatPixelsHH[k] - floatPixelsVV[k])))); } else { floatPixels[k] = (float) (0.5 * Math.acos( (floatPixelsHH[k] - floatPixelsVV[k]) / Math.sqrt( 4.0 * floatPixelsHV[k] * floatPixelsHV[k] + (floatPixelsHH[k] - floatPixelsVV[k]) * (floatPixelsHH[k] - floatPixelsVV[k])))); } } stepProgressBar(); } } break; default: throw new IllegalArgumentException("Invalid operation"); } ip.resetMinAndMax(); imp.updateAndDraw(); } /* end doIt */