Exemple #1
0
 void skeletonize(ImageProcessor ip) {
   if (Prefs.blackBackground) ip.invert();
   boolean edgePixels = hasEdgePixels(ip);
   ImageProcessor ip2 = expand(ip, edgePixels);
   ((ByteProcessor) ip2).skeletonize();
   ip = shrink(ip, ip2, edgePixels);
   if (Prefs.blackBackground) ip.invert();
 }
  public static void run() {

    ImagePlus imgPlus = new ImagePlus("data/in/sample1.tiff");

    ImageProcessor imgProcessor = imgPlus.getProcessor();
    imgProcessor.invert();
    FileSaver fs = new FileSaver(imgPlus);

    fs.saveAsJpeg("data/out/sample1-inverted.jpg");
  }
 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;
 }
Exemple #4
0
 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;
 }
Exemple #5
0
 void outline(ImageProcessor ip) {
   if (Prefs.blackBackground) ip.invert();
   ((ByteProcessor) ip).outline();
   if (Prefs.blackBackground) ip.invert();
 }
    void apply(ImagePlus imp, ImageProcessor ip) {
      // this.setCursor(wait);
      // IJ.showStatus("Bandpassing slice "+previousSlice);
      java.awt.Color col;

      if (invert.getState()) col = Toolbar.getForegroundColor();
      else col = Toolbar.getBackgroundColor();

      ip.setColor(col);

      int fill = ip.BLACK;
      int keep = 0;

      if (bandPassH.getState() && bandPassS.getState() && bandPassB.getState()) { // PPP All pass
        for (int j = 0; j < numPixels; j++) {
          int hue = hSource[j] & 0xff;
          int sat = sSource[j] & 0xff;
          int bri = bSource[j] & 0xff;
          if (((hue < minHue) || (hue > maxHue))
              || ((sat < minSat) || (sat > maxSat))
              || ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
          else fillMask[j] = keep;
        }
      } else if (!bandPassH.getState()
          && !bandPassS.getState()
          && !bandPassB.getState()) { // SSS All stop
        for (int j = 0; j < numPixels; j++) {
          int hue = hSource[j] & 0xff;
          int sat = sSource[j] & 0xff;
          int bri = bSource[j] & 0xff;
          if (((hue >= minHue) && (hue <= maxHue))
              || ((sat >= minSat) && (sat <= maxSat))
              || ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
          else fillMask[j] = keep;
        }
      } else if (bandPassH.getState() && bandPassS.getState() && !bandPassB.getState()) { // PPS
        for (int j = 0; j < numPixels; j++) {
          int hue = hSource[j] & 0xff;
          int sat = sSource[j] & 0xff;
          int bri = bSource[j] & 0xff;
          if (((hue < minHue) || (hue > maxHue))
              || ((sat < minSat) || (sat > maxSat))
              || ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
          else fillMask[j] = keep;
        }
      } else if (!bandPassH.getState() && !bandPassS.getState() && bandPassB.getState()) { // SSP
        for (int j = 0; j < numPixels; j++) {
          int hue = hSource[j] & 0xff;
          int sat = sSource[j] & 0xff;
          int bri = bSource[j] & 0xff;
          if (((hue >= minHue) && (hue <= maxHue))
              || ((sat >= minSat) && (sat <= maxSat))
              || ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
          else fillMask[j] = keep;
        }
      } else if (bandPassH.getState() && !bandPassS.getState() && !bandPassB.getState()) { // PSS
        for (int j = 0; j < numPixels; j++) {
          int hue = hSource[j] & 0xff;
          int sat = sSource[j] & 0xff;
          int bri = bSource[j] & 0xff;
          if (((hue < minHue) || (hue > maxHue))
              || ((sat >= minSat) && (sat <= maxSat))
              || ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
          else fillMask[j] = keep;
        }
      } else if (!bandPassH.getState() && bandPassS.getState() && bandPassB.getState()) { // SPP
        for (int j = 0; j < numPixels; j++) {
          int hue = hSource[j] & 0xff;
          int sat = sSource[j] & 0xff;
          int bri = bSource[j] & 0xff;
          if (((hue >= minHue) && (hue <= maxHue))
              || ((sat < minSat) || (sat > maxSat))
              || ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
          else fillMask[j] = keep;
        }
      } else if (!bandPassH.getState() && bandPassS.getState() && !bandPassB.getState()) { // SPS
        for (int j = 0; j < numPixels; j++) {
          int hue = hSource[j] & 0xff;
          int sat = sSource[j] & 0xff;
          int bri = bSource[j] & 0xff;
          if (((hue >= minHue) && (hue <= maxHue))
              || ((sat < minSat) || (sat > maxSat))
              || ((bri >= minBri) && (bri <= maxBri))) fillMask[j] = fill;
          else fillMask[j] = keep;
        }
      } else if (bandPassH.getState() && !bandPassS.getState() && bandPassB.getState()) { // PSP
        for (int j = 0; j < numPixels; j++) {
          int hue = hSource[j] & 0xff;
          int sat = sSource[j] & 0xff;
          int bri = bSource[j] & 0xff;
          if (((hue < minHue) || (hue > maxHue))
              || ((sat >= minSat) && (sat <= maxSat))
              || ((bri < minBri) || (bri > maxBri))) fillMask[j] = fill;
          else fillMask[j] = keep;
        }
      }

      ip.fill(fillMask);

      if (threshold.getState()) {
        ip.invert();
        for (int j = 0; j < numPixels; j++) {
          if (fillMask[j] == fill) fillMask[j] = keep;
          else fillMask[j] = fill;
        }
        ip.fill(fillMask);
        ip.invert();
      }
    }