Example #1
0
  /** Generate output image whose type is same as input image. */
  private ImagePlus makeOutputImage(ImagePlus imp, FloatProcessor fp, int ptype) {
    int width = imp.getWidth();
    int height = imp.getHeight();
    float[] pixels = (float[]) fp.getPixels();
    ImageProcessor oip = null;

    // Create output image consistent w/ type of input image.
    int size = pixels.length;
    switch (ptype) {
      case BYTE_TYPE:
        oip = imp.getProcessor().createProcessor(width, height);
        byte[] pixels8 = (byte[]) oip.getPixels();
        for (int i = 0; i < size; i++) pixels8[i] = (byte) pixels[i];
        break;
      case SHORT_TYPE:
        oip = imp.getProcessor().createProcessor(width, height);
        short[] pixels16 = (short[]) oip.getPixels();
        for (int i = 0; i < size; i++) pixels16[i] = (short) pixels[i];
        break;
      case FLOAT_TYPE:
        oip = new FloatProcessor(width, height, pixels, null);
        break;
    }

    // Adjust for display.
    // Calling this on non-ByteProcessors ensures image
    // processor is set up to correctly display image.
    oip.resetMinAndMax();

    // Create new image plus object. Don't use
    // ImagePlus.createImagePlus here because there may be
    // attributes of input image that are not appropriate for
    // projection.
    return new ImagePlus(makeTitle(), oip);
  }
Example #2
0
 void setStackDisplayRange(ImagePlus imp) {
   ImageStack stack = imp.getStack();
   double min = Double.MAX_VALUE;
   double max = -Double.MAX_VALUE;
   int n = stack.getSize();
   for (int i = 1; i <= n; i++) {
     if (!silentMode) IJ.showStatus("Calculating stack min and max: " + i + "/" + n);
     ImageProcessor ip = stack.getProcessor(i);
     ip.resetMinAndMax();
     if (ip.getMin() < min) min = ip.getMin();
     if (ip.getMax() > max) max = ip.getMax();
   }
   imp.getProcessor().setMinAndMax(min, max);
   imp.updateAndDraw();
 }
Example #3
0
  /*------------------------------------------------------------------*/
  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 */