public void run(String arg) { imp = IJ.getImage(); Roi roi = imp.getRoi(); if (roi != null && !roi.isArea()) imp.killRoi(); // ignore any line selection ImageProcessor ip = imp.getProcessor(); if (!showDialog(ip)) return; if (ip.getWidth() > 1 && ip.getHeight() > 1) ip.setInterpolate(interpolate); else ip.setInterpolate(false); ip.setBackgroundValue(bgValue); imp.startTiming(); try { if (newWindow && imp.getStackSize() > 1 && processStack) createNewStack(imp, ip); else scale(ip); } catch (OutOfMemoryError o) { IJ.outOfMemory("Scale"); } IJ.showProgress(1.0); }
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 String addMean(int column, String line, int start) { if (start == -1) { line += "\tNaN"; summaryHdr += "\t" + ResultsTable.getDefaultHeading(column); } else { float[] c = column >= 0 ? rt.getColumn(column) : null; if (c != null) { ImageProcessor ip = new FloatProcessor(c.length, 1, c, null); if (ip == null) return line; ip.setRoi(start, 0, ip.getWidth() - start, 1); ip = ip.crop(); ImageStatistics stats = new FloatStatistics(ip); if (stats == null) return line; line += n(stats.mean); } else line += "\tNaN"; summaryHdr += "\t" + rt.getColumnHeading(column); } return line; }
/** * 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; }
private boolean isThresholdedRGB(ImagePlus imp) { Object obj = imp.getProperty("Mask"); if (obj == null || !(obj instanceof ImageProcessor)) return false; ImageProcessor mask = (ImageProcessor) obj; return mask.getWidth() == imp.getWidth() && mask.getHeight() == imp.getHeight(); }