Пример #1
0
  public void calAutoCorrelation_RingMean(
      int
          nRefType) { // crosscorrelation coefficients between pixel valuse and the means and
                      // medians of the pixels located on the cocentric rings with radius up to
                      // m_nRMax
    m_nRefType = nRefType;
    int numRings = m_cvRings.size();
    calRefPixels();
    int r, c;
    int len = m_cIMSC.m_nTotalSteps + 1;
    double[] pixels0 = new double[len];
    double[] meanr = new double[len];
    double[] medianr = new double[len];

    int index = 0;

    Point p;
    index = 0;
    while (true) {
      p = m_cIMSC.getPosition();
      pixels0[index] = m_pnPixelsLR[p.y][p.x];
      index++;
      if (m_cIMSC.done()) break;
      m_cIMSC.move();
    }

    ImageShape shape;
    Histogram hist = CommonMethods.getDefaultHistogram(m_pnPixelsLR);

    int y, y0 = 0;
    int nRef;
    for (c = 0; c < numRings - 1; c++) {
      index = 0;
      m_cIMSC.reset();
      y0 = m_cIMSC.getPosition().y;
      shape = m_cvRings.get(c);
      while (true) {
        p = m_cIMSC.getPosition();
        nRef = getRefPixel(p);
        y = p.y;
        if (y > y0) {
          IJ.showStatus(
              "calAutoCorrelation_RingMean: r="
                  + PrintAssist.ToString(c + 1)
                  + "   y="
                  + PrintAssist.ToString(y));
          y0 = y;
        }
        CommonMethods.fillHistogram(m_pnPixels, nRef, shape, p, hist);
        meanr[index] = hist.getMean();
        medianr[index] = hist.getPercentileValue();
        index++;
        if (m_cIMSC.done()) break;
        m_cIMSC.move();
      }
      m_pdAutoCorr_mean[c] = CommonStatisticsMethods.crossCorrelationCoefficient(pixels0, meanr, 0);
      m_pdAutoCorr_median[c] =
          CommonStatisticsMethods.crossCorrelationCoefficient(pixels0, medianr, 0);
    }
  }
Пример #2
0
  int refinePixelStatitics() {
    stampIPOs();
    int[][] pixelsTemp = m_pnPixels;
    m_pnPixels = m_pnPixelsCompensated;

    m_cIMSC.reset();
    int len = m_cIMSC.m_nTotalSteps + 1;
    int i, c, step = 0;
    Point p = m_cIMSC.getPosition();
    int index = 0;
    ImageShape shape;
    Histogram hist;
    double mean, median;
    int y, y0 = 0;
    int pixel, nRef;
    double dsur;
    int numRings = m_cvRings.size();
    while (true) {
      p = m_cIMSC.getPosition();
      y = p.y;
      if (y > y0)
        IJ.showStatus(
            "refinePixelStatistics "
                + PrintAssist.ToString(y)
                + "-th line of "
                + PrintAssist.ToString(h)
                + " lines!");
      index = getPercentileIndex(step);
      dsur = m_pcRingMeanSems_Mean[index][m_nRMax].mean;
      ImageShapeHandler.copyElements(m_pnPixelsCompensated, m_pnPixelsTemp, m_cvRings, p);
      for (i = 0; i < numRings; i++) {
        pixel = (int) (m_pcRingMeanSems_Mean[index][i].mean - dsur);
        if (pixel < 1) break;
        shape = m_cvRings.get(i);
        shape.setCenter(p);
        ImageShapeHandler.addValue(m_pnPixelsTemp, shape, pixel);
      }
      nRef =
          (int) ImageShapeHandler.getMean(m_pnPixelsTemp, m_cRefRing, m_pnStamp, m_nExcludingType);
      CommonMethods.fillHistogram(
          m_pnPixelsTemp,
          nRef,
          m_cvRings.get(numRings - 1),
          p,
          m_cvHists.get(numRings - 1),
          m_pnStamp,
          m_nExcludingType);
      CommonMethods.fillHistograms(m_pnPixelsTemp, nRef, m_cvRings, p, m_cvHists);
      for (i = 0; i < numRings; i++) {
        hist = m_cvHists.get(i);
        mean = hist.getMeanSem().mean;
        median = hist.getPercentileValue();
        m_pdRingMean[step][i] = mean;
        m_pdRingMedian[step][i] = median;
      }
      //            m_pnPixels_trail[step]=m_pnPixelsTemp[p.y][p.x]-nRef;
      if (m_cIMSC.done()) break;
      m_cIMSC.move();
      step++;
    }
    for (c = 0; c < numRings; c++) {
      m_pcMeanSems_Median[c] = CommonStatisticsMethods.buildMeanSem(m_pdRingMedian, c);
      m_pcMeanSems_Mean[c] = CommonStatisticsMethods.buildMeanSem(m_pdRingMean, c);
    }
    if (m_bPresetPoints) {
      len = pixelsOfPresetPoints.size();
      int num = len / m_nPercentileDivision;
      int rI, rF;
      for (i = 0; i < m_nPercentileDivision; i++) {
        rI = Math.max(0, (int) ((i - .5) * num));
        rF = Math.min(len - 1, (int) ((i + .5) * num));
        for (c = 0; c < numRings; c++) {
          m_pcRingMeanSems_Median[i][c] =
              CommonStatisticsMethods.buildMeanSem(m_pdRingMedian, rI, rF, 1, c);
          m_pcRingMeanSems_Mean[i][c] =
              CommonStatisticsMethods.buildMeanSem(m_pdRingMean, rI, rF, 1, c);
        }
      }
    }
    m_pnPixels = pixelsTemp;
    return 1;
  }
Пример #3
0
  public void calAutoCorrelation(
      int
          nRefType) { // computing the cross correlation coefficient between pixel values of points
                      // separated by the radius of rings
    m_nRefType = nRefType;
    int numRings = m_cvRings.size();
    calRefPixels();
    m_cPixelMeanSems = CommonStatisticsMethods.buildMeanSem(m_pnPixelsLR);
    int len;

    double mean = m_cPixelMeanSems.mean, sem2 = m_cPixelMeanSems.sem2;
    double medianMean[] = new double[numRings - 1];
    double medianSem2[] = new double[numRings - 1];

    double crossProduct[] = new double[numRings - 1];
    double numCrossPairs[] = new double[numRings - 1];
    double crossProduct_median[] = new double[numRings - 1];
    double numCrossPairs_median[] = new double[numRings - 1];

    ArrayList<Double> medians[] = new ArrayList[numRings - 1];
    int i, j, pixel0;

    for (i = 0; i < numRings - 1; i++) {
      crossProduct[i] = 0;
      numCrossPairs[i] = 0;
      crossProduct_median[i] = 0;
      numCrossPairs_median[i] = 0;
      medianMean[i] = 0;
      medianSem2[i] = 0;
      medians[i] = new ArrayList();
    }

    int[][] pixels_LMC = new int[h][w];

    ImageShape shape;
    ArrayList<Point> points = new ArrayList();
    ArrayList<Point> scanningTrace = new ArrayList();

    double dp, median;
    Point p0, p;
    int index = 0, y0 = 0, y;
    Histogram hist;
    int nRef, mean1;
    while (true) {
      p0 = new Point(m_cIMSC.getPosition());
      y = p0.y;
      scanningTrace.add(p0);
      pixel0 = m_pnPixelsLR[p0.y][p0.x];
      nRef = getRefPixel(p0);
      dp = pixel0 - mean;
      CommonMethods.fillHistograms(m_pnPixels, nRef, m_cvRings, p0, m_cvHists);
      for (i = 0; i < numRings - 1; i++) {
        shape = m_cvRings.get(i);
        shape.setCenter(p0);
        shape.setFrameRanges(
            new intRange(p0.x, w - 1),
            new intRange(
                p0.y,
                h - 1)); // this is to avoid double counting the pair of points with given distance
        shape.getInnerPoints(points);
        shape.setFrameRanges(new intRange(0, w - 1), new intRange(0, h - 1));
        len = points.size();
        for (j = 0; j < len; j++) {
          p = points.get(j);
          crossProduct[i] += dp * (m_pnPixels[p.y][p.x] - nRef - mean);
        }
        numCrossPairs[i] += len;

        numCrossPairs_median[i] += 1;

        hist = m_cvHists.get(i);
        median = hist.getPercentileValue();
        medianMean[i] += median;
        medianSem2[i] += median * median;
        medians[i].add(median);
        if (y > y0) {
          IJ.showStatus("computing autocorrelation: " + PrintAssist.ToString(y) + "-th line");
          IJ.showProgress(y / h);
          y0 = y;
        }
      }
      if (m_cIMSC.done()) break;
      m_cIMSC.move();
      index++;
    }
    double dAutoCorr_mean, meanMedian, cp;
    MeanSem0 ms = new MeanSem0();
    int num;
    for (i = 0; i < numRings - 1; i++) {
      m_pdAutoCorr_mean[i] = crossProduct[i] / (Math.sqrt(sem2 * sem2) * (numCrossPairs[i]));
      num = medians[i].size();
      medianMean[i] /= num;
      medianSem2[i] /= num;
      ms.updateMeanSquareSum(num, medianMean[i], medianSem2[i]);
      meanMedian = ms.mean;
      cp = 0;
      for (j = 0; j < num; j++) {
        p = scanningTrace.get(j);
        cp += (m_pnPixelsLR[p.y][p.x] - mean) * (medians[i].get(j) - meanMedian);
      }
      m_pdAutoCorr_median[i] = cp / (Math.sqrt(sem2 * ms.sem2) * (num));
    }
  }
Пример #4
0
  void calPixelStatistics() {
    calRefPixels();
    int len = m_cIMSC.m_nTotalSteps + 1;
    int numRings = m_cvRings.size();

    m_pdRingMean = new double[len][numRings];
    m_pdRingMedian = new double[len][numRings];

    int i, c;
    Point p = m_cIMSC.getPosition();
    int index = 0;
    //        ImageShape shape;
    Histogram hist;
    double mean, median;
    int y, y0 = 0;
    int nRef;
    while (true) {
      p = m_cIMSC.getPosition();
      y = p.y;
      if (y > y0)
        IJ.showStatus(
            "calPixelStatistics "
                + PrintAssist.ToString(y)
                + "-th line of "
                + PrintAssist.ToString(h)
                + " lines!");
      //            m_cRefRing.setCenter(p);
      nRef = getRefPixel(p);
      CommonMethods.fillHistograms(m_pnPixels, nRef, m_cvRings, p, m_cvHists);
      for (i = 0; i <= m_nRMax; i++) {
        hist = m_cvHists.get(i);
        mean = hist.getMeanSem().mean;
        median = hist.getPercentileValue();
        m_pdRingMean[index][i] = mean;
        m_pdRingMedian[index][i] = median;
      }
      if (m_cIMSC.done()) break;
      m_cIMSC.move();
      index++;
    }
    m_cPixelMeanSems = CommonStatisticsMethods.buildMeanSem(m_pnPixelsLR);
    //        m_cPixelMeanSem_trail=CommonStatisticsMethods.buildMeanSem(m_pnPixels_trail);
    for (c = 0; c <= m_nRMax; c++) {
      m_pcMeanSems_Median[c] = CommonStatisticsMethods.buildMeanSem(m_pdRingMedian, c);
      m_pcMeanSems_Mean[c] = CommonStatisticsMethods.buildMeanSem(m_pdRingMean, c);
    }
    if (m_bPresetPoints) {
      len = pixelsOfPresetPoints.size();
      int num = len / m_nPercentileDivision;
      int rI, rF;
      for (i = 0; i < m_nPercentileDivision; i++) {
        rI = Math.max(0, (int) ((i - .5) * num));
        rF = Math.min(len - 1, (int) ((i + .5) * num));
        //
        // m_cPixelMeanSems_trail[i]=CommonStatisticsMethods.buildMeanSem(m_pnPixels_trail,rI,rF,1);
        for (c = 0; c < numRings; c++) {
          m_pcRingMeanSems_Median[i][c] =
              CommonStatisticsMethods.buildMeanSem(m_pdRingMedian, rI, rF, 1, c);
          m_pcRingMeanSems_Mean[i][c] =
              CommonStatisticsMethods.buildMeanSem(m_pdRingMean, rI, rF, 1, c);
        }
      }
    }
  }