void stampIPOs() {
calAveRadius();
int i, j;
for (i = 0; i < h; i++) {
for (j = 0; j < w; j++) {
m_pnStamp[i][j] = 0;
}
}
int numRings = m_cvRings.size();
m_cIMSC.reset();
Point pt;
int index, step = 0, r0;
ImageShape shape;
while (true) {
pt = m_cIMSC.getPosition();
index = getPercentileIndex(step);
r0 = m_pnAveRadius[index];
for (i = 0; i <= r0; i++) {
shape = m_cvRings.get(i);
shape.setCenter(pt);
ImageShapeHandler.setValue(m_pnStamp, shape, m_nExcludingType);
}
if (m_cIMSC.done()) break;
m_cIMSC.move();
step++;
}
}
void constructRings() {
m_dvRs = new ArrayList();
m_cvRings = new ArrayList();
m_cvRings.add(new CircleImage(0));
m_dvRs.add(0.);
double r = 1., dr = 0.001;
double ri = r - dr, ro = r + dr;
m_cvRings.add(new Ring(ri, ro));
m_dvRs.add(r);
r = Math.sqrt(2);
ri = r - dr;
ro = r + dr;
m_cvRings.add(new Ring(ri, ro));
m_dvRs.add(r);
int nr;
for (nr = 2; nr <= m_nRMax; nr++) {
m_cvRings.add(new Ring(nr - 1, nr));
m_dvRs.add((double) nr);
}
m_cRefRing = new Ring(m_nRRefI, m_nRRefO);
m_cvRings.add(m_cRefRing);
m_dvRs.add((double) m_nRMax + 1);
ImageShapeHandler.setFrameRanges(m_cvRings, new intRange(0, w - 1), new intRange(0, h - 1));
}
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);
}
}
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;
}