/*------------------------------------------------------------------*/
  void putRow(ImageProcessor ip, int y, double[] row) {
    int rowLength = ip.getWidth();

    if (rowLength != row.length) {
      throw new IndexOutOfBoundsException("Incoherent array sizes");
    }
    y *= rowLength;
    if (ip.getPixels() instanceof float[]) {
      float[] floatPixels = (float[]) ip.getPixels();
      for (int i = 0; (i < rowLength); i++) {
        floatPixels[y++] = (float) row[i];
      }
    } else {
      throw new IllegalArgumentException("Float image required");
    }
  } /* end putRow */
  /*------------------------------------------------------------------*/
  void putColumn(ImageProcessor ip, int x, double[] column) {
    int width = ip.getWidth();

    if (ip.getHeight() != column.length) {
      throw new IndexOutOfBoundsException("Incoherent array sizes");
    }
    if (ip.getPixels() instanceof float[]) {
      float[] floatPixels = (float[]) ip.getPixels();
      for (int i = 0; (i < column.length); i++) {
        floatPixels[x] = (float) column[i];
        x += width;
      }
    } else {
      throw new IllegalArgumentException("Float image required");
    }
  } /* end putColumn */
Exemple #3
0
 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);
 }
  /*------------------------------------------------------------------*/
  public void getHorizontalGradient(ImageProcessor ip, double tolerance) {
    if (!(ip.getPixels() instanceof float[])) {
      throw new IllegalArgumentException("Float image required");
    }

    float[] floatPixels = (float[]) ip.getPixels();
    int width = ip.getWidth();
    int height = ip.getHeight();
    double line[] = new double[width];

    for (int y = 0; (y < height); y++) {
      getRow(ip, y, line);
      getSplineInterpolationCoefficients(line, tolerance);
      getGradient(line);
      putRow(ip, y, line);
      stepProgressBar();
    }
  } /* end getHorizontalGradient */
  /*------------------------------------------------------------------*/
  public void getVerticalHessian(ImageProcessor ip, double tolerance) {
    if (!(ip.getPixels() instanceof float[])) {
      throw new IllegalArgumentException("Float image required");
    }

    float[] floatPixels = (float[]) ip.getPixels();
    int width = ip.getWidth();
    int height = ip.getHeight();
    double line[] = new double[height];

    for (int x = 0; (x < width); x++) {
      getColumn(ip, x, line);
      getSplineInterpolationCoefficients(line, tolerance);
      getHessian(line);
      putColumn(ip, x, line);
      stepProgressBar();
    }
  } /* end getVerticalHessian */
Exemple #6
0
 ImagePlus doMedianProjection() {
   IJ.showStatus("Calculating median...");
   ImageStack stack = imp.getStack();
   ImageProcessor[] slices = new ImageProcessor[sliceCount];
   int index = 0;
   for (int slice = startSlice; slice <= stopSlice; slice += increment)
     slices[index++] = stack.getProcessor(slice);
   ImageProcessor ip2 = slices[0].duplicate();
   ip2 = ip2.convertToFloat();
   float[] values = new float[sliceCount];
   int width = ip2.getWidth();
   int height = ip2.getHeight();
   int inc = Math.max(height / 30, 1);
   for (int y = 0; y < height; y++) {
     if (y % inc == 0) IJ.showProgress(y, height - 1);
     for (int x = 0; x < width; x++) {
       for (int i = 0; i < sliceCount; i++) values[i] = slices[i].getPixelValue(x, y);
       ip2.putPixelValue(x, y, median(values));
     }
   }
   if (imp.getBitDepth() == 8) ip2 = ip2.convertToByte(false);
   IJ.showProgress(1, 1);
   return new ImagePlus(makeTitle(), ip2);
 }
  /*------------------------------------------------------------------*/
  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 */