void calRefPixels() {
int[] nRange = new int[2];
CommonMethods.getDataRange(m_pnPixels, nRange);
MeanSem0 ms = CommonStatisticsMethods.buildMeanSem(m_pnPixels);
int nMin;
switch (m_nRefType) {
case export_AutoCorrelation.originalRef:
m_pnPixelsLR = new int[h][w];
CommonStatisticsMethods.copyArray(m_pnPixels, m_pnPixelsLR);
break;
case export_AutoCorrelation.globalMeanRef:
m_pnPixelsLR = new int[h][w];
CommonStatisticsMethods.copyArray(m_pnPixels, m_pnPixelsLR);
CommonStatisticsMethods.shiftArray(m_pnPixelsLR, -(int) (ms.mean + 0.5));
break;
case export_AutoCorrelation.globalMedianRef:
m_pnPixelsLR = new int[h][w];
CommonStatisticsMethods.copyArray(m_pnPixels, m_pnPixelsLR);
CommonStatisticsMethods.shiftArray(
m_pnPixelsLR, -CommonStatisticsMethods.getQuantile(m_pnPixels, 0.5));
break;
case export_AutoCorrelation.localMeanRef:
m_pnPixelsLR = CommonMethods.getPixelValus_LocalReference(impl, m_cRefRing, m_nRefType);
break;
case export_AutoCorrelation.localMedianRef:
m_pnPixelsLR = CommonMethods.getPixelValus_LocalReference(impl, m_cRefRing, m_nRefType);
break;
default:
m_pnPixelsLR = new int[h][w];
CommonStatisticsMethods.copyArray(m_pnPixels, m_pnPixelsLR);
break;
}
updateHistograms();
}
int calCompensatedPixels() {
int numRings = m_cvRings.size();
CommonStatisticsMethods.copyArray(m_pnPixels, m_pnPixelsCompensated);
CommonMethods.displayPixels(m_pnPixelsCompensated, "before compensation", impl.getType());
m_cIMSC.reset();
Point pt;
int index, step = 0, pixel, i, r0;
double dm, dsur;
ImageShape shape;
while (true) {
pt = m_cIMSC.getPosition();
index = getPercentileIndex(step);
dsur = m_pcRingMeanSems_Mean[index][m_nRMax].mean;
r0 = m_pnAveRadius[index];
//
// m_pnPixelsCompensated[pt.y][pt.x]-=(int)(m_cPixelMeanSems_trail[index].mean-dsur);
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(pt);
ImageShapeHandler.addValue(m_pnPixelsCompensated, shape, -pixel);
}
if (m_cIMSC.done()) break;
m_cIMSC.move();
step++;
}
CommonMethods.displayPixels(m_pnPixelsCompensated, "after compensation", impl.getType());
return 1;
}
public void buildIPOGContourShapes(int[][] pixelsCompensated, int[][] pnScratch, int cutoff) {
int h = pixelsCompensated.length, w = pixelsCompensated[0].length;
intRange xRange3 = new intRange(), yRange3 = new intRange();
IPOGaussianNodeHandler.getRanges3(IPOGNode.IPOGs, xRange, yRange);
xRange.setCommonRange(new intRange(0, w - 1));
yRange.setCommonRange(new intRange(0, h - 1));
CommonStatisticsMethods.copyArray(
pixelsCompensated,
pnScratch,
yRange.getMin(),
yRange.getMax(),
xRange.getMin(),
xRange.getMax());
IPOGaussianNodeHandler.getSuperImposition(pnScratch, IPOGNode.IPOGs);
if (pnScratch[cy][cx] < cutoff) {
cContourShape = new CircleImage(3);
cContourShape.setCenter(new Point(cx, cy));
cContourShape.setFrameRanges(new intRange(0, w - 1), new intRange(0, h - 1));
} else {
ArrayList<Point> contour =
ContourFollower.getContour_Out(
pnScratch, w, h, new Point(cx, cy), cutoff, Integer.MAX_VALUE, true);
cContourShape = ImageShapeHandler.buildImageShape(contour);
}
}