int[] smooth(int[] a, int n) { FloatProcessor fp = new FloatProcessor(n, 1); for (int i = 0; i < n; i++) fp.putPixelValue(i, 0, a[i]); GaussianBlur gb = new GaussianBlur(); gb.blur1Direction(fp, 2.0, 0.01, true, 0); for (int i = 0; i < n; i++) a[i] = (int) Math.round(fp.getPixelValue(i, 0)); return a; }
public static double[] getPixels(ImagePlus imp, int[] slices, int[] frames, int[] channels) { ImagePlus subImp = AccessImage.getSubHyperStack(imp, slices, frames, channels); ImageStack imageStack = subImp.getImageStack(); double[] pixels = new double[subImp.getWidth() * subImp.getHeight() * imageStack.getSize()]; for (int i = 0; i < imageStack.getSize(); i++) { switch (subImp.getType()) { case ImagePlus.GRAY8: ByteProcessor byteProcessor = (ByteProcessor) imageStack.getProcessor(i + 1); for (int iX = 0; iX < subImp.getWidth(); iX++) { for (int iY = 0; iY < subImp.getHeight(); iY++) { pixels[i * subImp.getWidth() * subImp.getHeight() + iY * subImp.getWidth() + iX] = (double) byteProcessor.getPixelValue(iX, iY); } } break; case ImagePlus.GRAY16: ShortProcessor shortProcessor = (ShortProcessor) imageStack.getProcessor(i + 1); for (int iX = 0; iX < subImp.getWidth(); iX++) { for (int iY = 0; iY < subImp.getHeight(); iY++) { pixels[i * subImp.getWidth() * subImp.getHeight() + iY * subImp.getWidth() + iX] = (double) shortProcessor.getPixelValue(iX, iY); } } break; case ImagePlus.GRAY32: FloatProcessor floatProcessor = (FloatProcessor) imageStack.getProcessor(i + 1); for (int iX = 0; iX < subImp.getWidth(); iX++) { for (int iY = 0; iY < subImp.getHeight(); iY++) { pixels[i * subImp.getWidth() * subImp.getHeight() + iY * subImp.getWidth() + iX] = (double) floatProcessor.getPixelValue(iX, iY); } } break; case ImagePlus.COLOR_RGB: ColorProcessor colorProcessor = (ColorProcessor) imageStack.getProcessor(i + 1); int nX = subImp.getWidth(); int nY = subImp.getHeight(); byte[] red = new byte[nX * nY]; byte[] green = new byte[nX * nY]; byte[] blue = new byte[nX * nY]; colorProcessor.getRGB(red, green, blue); int r, g, b; for (int j = 0; j < nX * nY; j++) { r = red[j] << 16; g = green[j] << 8; b = blue[j] << 0; pixels[i * nX * nY + j] = (double) (r + g + b); } break; } } return (pixels); }
public void runStuff( DimensionMap map, TreeMap<DimensionMap, ROIPlus> maximaMap, TreeMap<DimensionMap, String> segMap, TreeMap<DimensionMap, String> maskMap, TreeMap<DimensionMap, String> imageMap, TreeMap<DimensionMap, Double> results, Canceler canceler) { // Get the Maxima ROIPlus maxima = maximaMap.get(map); // Make the mask image impMask // ByteProcessor impMask = (ByteProcessor) (new // ImagePlus(maskMap.get(map)).getProcessor().convertToByte(false)); // ByteProcessor impSeg = (ByteProcessor) (new // ImagePlus(segMap.get(map)).getProcessor().convertToByte(false)); ByteProcessor impSeg = (ByteProcessor) (new ImagePlus(segMap.get(map))).getProcessor(); ByteProcessor impMask = (ByteProcessor) (new ImagePlus(maskMap.get(map))).getProcessor(); ByteBlitter blit = new ByteBlitter(impSeg); blit.copyBits(impMask, 0, 0, Blitter.AND); FloatProcessor impImage = (FloatProcessor) (new ImagePlus(imageMap.get(map))).getProcessor().convertToFloat(); Wand wand = new Wand(impSeg); Wand wand2 = new Wand(impMask); Vector<Double> measurements; for (IdPoint p : maxima.getPointList()) { if (canceler.isCanceled()) { return; } if (impSeg.getPixel(p.x, p.y) == 255) // if we land on a cell that made it through thresholding { wand.autoOutline(p.x, p.y); // outline it wand2.autoOutline(p.x, p.y); boolean partOfCellClump = !this.selectionsAreEqual( wand, wand2); // If the segmented and unsegmented masks do not agree on the roi, then this // cell is part of a clump. if (wand.npoints > 0) { Roi roi = new PolygonRoi( wand.xpoints, wand.ypoints, wand.npoints, Roi.POLYGON); // The roi helps for using getLength() (DON'T USE Roi.TRACED_ROI., // IT SCREWS UP THE Polygon OBJECTS!!!! Bug emailed to ImageJ // folks) Polygon poly = new Polygon( wand.xpoints, wand.ypoints, wand.npoints); // The polygon helps for using contains() Rectangle r = roi.getBounds(); measurements = new Vector<Double>(); for (int i = r.x; i < r.x + r.width; i++) { for (int j = r.y; j < r.y + r.height; j++) { // innerBoundary if (poly.contains(i, j) && impSeg.getPixelValue(i, j) == 255) { measurements.add((double) impImage.getPixelValue(i, j)); // Logs.log("In - " + innerT, this); } } } impMask.setRoi(roi); ImageStatistics stats = ImageStatistics.getStatistics( impMask, ImageStatistics.AREA & ImageStatistics.PERIMETER & ImageStatistics.CIRCULARITY & ImageStatistics.ELLIPSE, null); if (measurements.size() > 0) { DimensionMap resultsMap = map.copy(); resultsMap.put("Id", "" + p.id); resultsMap.put("Measurement", "X"); results.put(resultsMap.copy(), (double) p.x); resultsMap.put("Measurement", "Y"); results.put(resultsMap.copy(), (double) p.y); resultsMap.put("Measurement", "AREA"); results.put(resultsMap.copy(), stats.area); resultsMap.put("Measurement", "PERIMETER"); results.put(resultsMap.copy(), roi.getLength()); resultsMap.put("Measurement", "CIRCULARITY"); results.put( resultsMap.copy(), 4.0 * Math.PI * (stats.area / (Math.pow(roi.getLength(), 2)))); resultsMap.put("Measurement", "ELLIPSE MAJOR"); results.put(resultsMap.copy(), stats.major); resultsMap.put("Measurement", "ELLIPSE MINOR"); results.put(resultsMap.copy(), stats.minor); resultsMap.put("Measurement", "MEAN"); results.put(resultsMap.copy(), StatisticsUtility.mean(measurements)); resultsMap.put("Measurement", "MEDIAN"); results.put(resultsMap.copy(), StatisticsUtility.median(measurements)); resultsMap.put("Measurement", "SUM"); results.put(resultsMap.copy(), StatisticsUtility.sum(measurements)); resultsMap.put("Measurement", "MIN"); results.put(resultsMap.copy(), StatisticsUtility.min(measurements)); resultsMap.put("Measurement", "MAX"); results.put(resultsMap.copy(), StatisticsUtility.max(measurements)); resultsMap.put("Measurement", "STDDEV"); results.put(resultsMap.copy(), StatisticsUtility.stdDev(measurements)); resultsMap.put("Measurement", "VARIANCE"); results.put(resultsMap.copy(), StatisticsUtility.variance(measurements)); resultsMap.put("Measurement", "CLUMP"); results.put(resultsMap.copy(), (double) (partOfCellClump ? 1 : 0)); } } } } }