ImageProcessor shrink(ImageProcessor ip, ImageProcessor ip2, boolean hasEdgePixels) { if (hasEdgePixels) { int width = ip.getWidth(); int height = ip.getHeight(); for (int y = 0; y < height; y++) for (int x = 0; x < width; x++) ip.putPixel(x, y, ip2.getPixel(x + 1, y + 1)); } return ip; }
boolean hasEdgePixels(ImageProcessor ip) { int width = ip.getWidth(); int height = ip.getHeight(); boolean edgePixels = false; for (int x = 0; x < width; x++) { // top edge if (ip.getPixel(x, 0) == foreground) edgePixels = true; } for (int x = 0; x < width; x++) { // bottom edge if (ip.getPixel(x, height - 1) == foreground) edgePixels = true; } for (int y = 0; y < height; y++) { // left edge if (ip.getPixel(0, y) == foreground) edgePixels = true; } for (int y = 0; y < height; y++) { // right edge if (ip.getPixel(width - 1, y) == foreground) edgePixels = true; } return edgePixels; }
// Binary fill by Gabriel Landini, G.Landini at bham.ac.uk // 21/May/2008 void fill(ImageProcessor ip, int foreground, int background) { int width = ip.getWidth(); int height = ip.getHeight(); FloodFiller ff = new FloodFiller(ip); ip.setColor(127); for (int y = 0; y < height; y++) { if (ip.getPixel(0, y) == background) ff.fill(0, y); if (ip.getPixel(width - 1, y) == background) ff.fill(width - 1, y); } for (int x = 0; x < width; x++) { if (ip.getPixel(x, 0) == background) ff.fill(x, 0); if (ip.getPixel(x, height - 1) == background) ff.fill(x, height - 1); } byte[] pixels = (byte[]) ip.getPixels(); int n = width * height; for (int i = 0; i < n; i++) { if (pixels[i] == 127) pixels[i] = (byte) background; else pixels[i] = (byte) foreground; } }
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; }
private void makeBand(ImagePlus imp) { Roi roi = imp.getRoi(); if (roi == null) { noRoi("Make Band"); return; } if (!roi.isArea()) { IJ.error("Make Band", "Area selection required"); return; } Calibration cal = imp.getCalibration(); double pixels = bandSize; double size = pixels * cal.pixelWidth; int decimalPlaces = 0; if ((int) size != size) decimalPlaces = 2; GenericDialog gd = new GenericDialog("Make Band"); gd.addNumericField("Band Size:", size, decimalPlaces, 4, cal.getUnits()); gd.showDialog(); if (gd.wasCanceled()) return; size = gd.getNextNumber(); if (Double.isNaN(size)) { IJ.error("Make Band", "invalid number"); return; } int n = (int) Math.round(size / cal.pixelWidth); if (n > 255) { IJ.error("Make Band", "Cannot make bands wider that 255 pixels"); return; } int width = imp.getWidth(); int height = imp.getHeight(); Rectangle r = roi.getBounds(); ImageProcessor ip = roi.getMask(); if (ip == null) { ip = new ByteProcessor(r.width, r.height); ip.invert(); } ImageProcessor mask = new ByteProcessor(width, height); mask.insert(ip, r.x, r.y); ImagePlus edm = new ImagePlus("mask", mask); boolean saveBlackBackground = Prefs.blackBackground; Prefs.blackBackground = false; IJ.run(edm, "Distance Map", ""); Prefs.blackBackground = saveBlackBackground; ip = edm.getProcessor(); ip.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE); int xx = -1, yy = -1; for (int x = r.x; x < r.x + r.width; x++) { for (int y = r.y; y < r.y + r.height; y++) { if (ip.getPixel(x, y) < n) { xx = x; yy = y; break; } } if (xx >= 0 || yy >= 0) break; } int count = IJ.doWand(edm, xx, yy, 0, null); if (count <= 0) { IJ.error("Make Band", "Unable to make band"); return; } ShapeRoi roi2 = new ShapeRoi(edm.getRoi()); if (!(roi instanceof ShapeRoi)) roi = new ShapeRoi(roi); ShapeRoi roi1 = (ShapeRoi) roi; roi2 = roi2.not(roi1); imp.setRoi(roi2); bandSize = n; }
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; }
void sample() { byte[] hsSource, ssSource, bsSource; // ImageProcessor ip2; // ip2 = imp.getProcessor(); Rectangle myroi = ip.getRoi(); int swidth = myroi.width; int sheight = myroi.height; int sy = myroi.y; int sx = myroi.x; if (swidth == width && sheight == height) { IJ.showMessage("Select a rectangular ROI"); IJ.beep(); return; } IJ.run("Select None"); int snumPixels = swidth * sheight; hsSource = new byte[snumPixels]; ssSource = new byte[snumPixels]; bsSource = new byte[snumPixels]; int[] pixs = new int[snumPixels]; int[] bin = new int[256]; int counter = 0, pi = 0, rangePassH = 0, rangeStopH = 0, rangePassL = 0, rangeStopL = 0, i, j; for (i = sy; i < sy + sheight; i++) { for (j = sx; j < sx + swidth; j++) { pixs[counter++] = ip.getPixel(j, i); } } // Get hsb or rgb from roi. ColorProcessor cp2 = new ColorProcessor(swidth, sheight, pixs); int iminhue = 256, imaxhue = -1, iminsat = 256, imaxsat = -1, iminbri = 256, imaxbri = -1; int iminred = 256, imaxred = -1, imingre = 256, imaxgre = -1, iminblu = 256, imaxblu = -1; if (isRGB) cp2.getRGB(hsSource, ssSource, bsSource); else cp2.getHSB(hsSource, ssSource, bsSource); for (i = 0; i < snumPixels; i++) { bin[hsSource[i] & 255] = 1; if ((hsSource[i] & 255) > imaxhue) imaxhue = (hsSource[i] & 255); if ((hsSource[i] & 255) < iminhue) iminhue = (hsSource[i] & 255); if ((ssSource[i] & 255) > imaxsat) imaxsat = (ssSource[i] & 255); if ((ssSource[i] & 255) < iminsat) iminsat = (ssSource[i] & 255); if ((bsSource[i] & 255) > imaxbri) imaxbri = (bsSource[i] & 255); if ((bsSource[i] & 255) < iminbri) iminbri = (bsSource[i] & 255); // IJ.showMessage("h:"+minhue+"H:"+maxhue+"s:"+minsat+"S:"+maxsat+"b:"+minbri+"B:"+maxbri); } if (!isRGB) { // get pass or stop filter whichever has a narrower range for (i = 0; i < 256; i++) { if (bin[i] > 0) { rangePassL = i; break; } } for (i = 255; i >= 0; i--) { if (bin[i] > 0) { rangePassH = i; break; } } for (i = 0; i < 256; i++) { if (bin[i] == 0) { rangeStopL = i; break; } } for (i = 255; i >= 0; i--) { if (bin[i] == 0) { rangeStopH = i; break; } } if ((rangePassH - rangePassL) < (rangeStopH - rangeStopL)) { bandPassH.setState(true); bandStopH.setState(false); iminhue = rangePassL; imaxhue = rangePassH; } else { bandPassH.setState(false); bandStopH.setState(true); iminhue = rangeStopL; imaxhue = rangeStopH; } } else { bandPassH.setState(true); bandStopH.setState(false); } adjustMinHue(iminhue); minSlider.setValue(iminhue); adjustMaxHue(imaxhue); maxSlider.setValue(imaxhue); adjustMinSat(iminsat); minSlider2.setValue(iminsat); adjustMaxSat(imaxsat); maxSlider2.setValue(imaxsat); adjustMinBri(iminbri); minSlider3.setValue(iminbri); adjustMaxBri(imaxbri); maxSlider3.setValue(imaxbri); originalB.setEnabled(true); // IJ.showStatus("done"); }