Example #1
0
  private void fitDataUpdate(FitPeak fit, double[] deltas) {
    // update sign and clamp solution if appears to be oscillating
    for (int i = 0; i < deltas.length; i++) {
      if (fit.sign[i] != 0) {
        if ((fit.sign[i] == 1) && (deltas[i] < 0.0)) {
          fit.clamp[i] *= 0.5;
        } else if ((fit.sign[i] == -1) && (deltas[i] > 0.0)) {
          fit.clamp[i] *= 0.5;
        }
      }
      if (deltas[i] > 0.0) {
        fit.sign[i] = (byte) +1;
      } else {
        fit.sign[i] = (byte) -1;
      }
      // update values based on delta and clamp
      if (deltas[i] != 0.0) {
        final double update = deltas[i] / (1.0 + Math.abs(deltas[i]) / fit.clamp[i]);
        fit.peak.addToParameter(i, -update);
      }
    }
    // update peak center with HYSTERESIS
    if (Math.abs(fit.peak.getXCenter() - ((double) fit.xc) - 0.5) > this.HYSTERESIS) {
      fit.xc = (int) fit.peak.getXCenter();
    }
    if (Math.abs(fit.peak.getYCenter() - ((double) fit.yc) - 0.5) > this.HYSTERESIS) {
      fit.yc = (int) fit.peak.getYCenter();
    }
    // check that the peak has not moved too close of the
    // edge of the image, flag peak as bad if it has
    int xc = fit.xc;
    int yc = fit.yc;

    if ((xc < this.MARGIN)
        || (xc >= (imgSizeX - this.MARGIN))
        || (yc < this.MARGIN)
        || (yc >= (imgSizeY - this.MARGIN))) {
      fit.peak.setStatus(PeakStatus.BADPEAK);
    }
    // check for negative background or height
    if ((fit.peak.getBackground() < 0.0) || (fit.peak.getHeight() < 0.0)) {
      fit.peak.setStatus(PeakStatus.ERROR);
    }
    // check for negative widths
    if ((fit.peak.getXWidth() < 0.0) || (fit.peak.getYWidth() < 0.0)) {
      fit.peak.setStatus(PeakStatus.ERROR);
    }
    // Opt 1 : peak errors if z is out of range
    /*
     if ((cur.peak.zCenter < this.minZ) ||
         (cur.peak.zCenter > this.maxZ)) {
         cur.status = PeakStatus.Error;
     }
    */
    // Opt 2: Clamp Z value Range
    if (fit.peak.getZCenter() < this.minZ) fit.peak.setZCenter(this.minZ);
    if (fit.peak.getZCenter() > this.maxZ) fit.peak.setZCenter(this.maxZ);
  }
Example #2
0
  // -------------------------------------------
  // Constructor
  // -------------------------------------------
  public MultiFit(
      double[] image,
      ArrayList<Peak> params,
      double tolerance,
      int imageSizeX,
      int imageSizeY,
      boolean zFitting) {
    assert (tolerance < 1.0e-1);
    assert (image != null && image.length == (imageSizeX * imageSizeY));

    this.tolerance = tolerance;

    this.imgData = image;
    this.imgSizeX = imageSizeX;
    this.imgSizeY = imageSizeY;

    this.fgData = new double[image.length];
    this.bgData = new double[image.length];
    this.bgCounts = new int[image.length];

    this.fits = new ArrayList<FitPeak>(params.size());
    for (Peak p : params) {
      FitPeak newFit = new FitPeak(p, 10);
      if (newFit.peak.hasStatus(PeakStatus.RUNNING)) {
        newFit.error = 0.0;
        newFit.errorOld = 0.0;
      } else {
        newFit.error = newFit.peak.getIError();
        newFit.errorOld = newFit.error;
      }

      if (zFitting) {
        calcWidthsFromZ(newFit);
      } else {
        newFit.peak.setXWidth(1.0 / (2.0 * Math.pow(newFit.peak.getXWidth(), 2)));
        newFit.peak.setYWidth(1.0 / (2.0 * Math.pow(newFit.peak.getYWidth(), 2)));
      }
      newFit.xc = (int) newFit.peak.getXCenter();
      newFit.yc = (int) newFit.peak.getYCenter();

      // possible bug casting fromm double to int in original version
      newFit.wx = calcWidth(newFit.peak.getXWidth(), -10);
      newFit.wy = calcWidth(newFit.peak.getYWidth(), -10);
      // todo these are annoying constants
      newFit.setClampHeight(1000.0);
      newFit.setClampBackground(100.0);
      newFit.setClampXCenter(1.0);
      newFit.setClampYCenter(1.0);
      newFit.setClampXWidth(0.3);
      newFit.setClampYWidth(0.3);
      newFit.setClampZCenter(0.1);

      this.fits.add(newFit);
    }
    calcFit();
    calcError();
  }