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package ij.process;
import ij.measure.Calibration;
/** 8-bit image statistics, including histogram. */
public class ByteStatistics extends ImageStatistics {
/** Construct an ImageStatistics object from a ByteProcessor
using the standard measurement options (area, mean,
mode, min and max) and no calibration. */
public ByteStatistics(ImageProcessor ip) {
this(ip, AREA+MEAN+MODE+MIN_MAX, null);
}
/** Constructs a ByteStatistics object from a ByteProcessor using
the specified measurement and calibration. */
public ByteStatistics(ImageProcessor ip, int mOptions, Calibration cal) {
ByteProcessor bp = (ByteProcessor)ip;
histogram = bp.getHistogram();
setup(ip, cal);
double minT = ip.getMinThreshold();
int minThreshold,maxThreshold;
if ((mOptions&LIMIT)==0 || minT==ImageProcessor.NO_THRESHOLD)
{minThreshold=0; maxThreshold=255;}
else
{minThreshold=(int)minT; maxThreshold=(int)ip.getMaxThreshold();}
float[] cTable = cal!=null?cal.getCTable():null;
if (cTable!=null)
getCalibratedStatistics(minThreshold,maxThreshold,cTable);
else
getRawStatistics(minThreshold,maxThreshold);
if ((mOptions&MIN_MAX)!=0) {
if (cTable!=null)
getCalibratedMinAndMax(minThreshold, maxThreshold, cTable);
else
getRawMinAndMax(minThreshold, maxThreshold);
}
if ((mOptions&ELLIPSE)!=0 || (mOptions&SHAPE_DESCRIPTORS)!=0)
fitEllipse(ip, mOptions);
else if ((mOptions&CENTROID)!=0)
getCentroid(ip, minThreshold, maxThreshold);
if ((mOptions&(CENTER_OF_MASS|SKEWNESS|KURTOSIS))!=0)
calculateMoments(ip, minThreshold, maxThreshold, cTable);
if ((mOptions&MEDIAN)!=0)
calculateMedian(histogram, minThreshold, maxThreshold, cal);
if ((mOptions&AREA_FRACTION)!=0)
calculateAreaFraction(ip, histogram);
}
void getCalibratedStatistics(int minThreshold, int maxThreshold, float[] cTable) {
int count;
double value;
double sum = 0;
double sum2 = 0.0;
double isum = 0.0;
for (int i=minThreshold; i<=maxThreshold; i++) {
count = histogram[i];
value = cTable[i];
if (count>0 && !Double.isNaN(value)) {
pixelCount += count;
sum += value*count;
isum += i*count;
sum2 += (value*value)*count;
if (count>maxCount) {
maxCount = count;
mode = i;
}
}
}
area = pixelCount*pw*ph;
mean = sum/pixelCount;
umean = isum/pixelCount;
dmode = cTable[mode];
calculateStdDev(pixelCount,sum,sum2);
histMin = 0.0;
histMax = 255.0;
}
void getCentroid(ImageProcessor ip, int minThreshold, int maxThreshold) {
byte[] pixels = (byte[])ip.getPixels();
byte[] mask = ip.getMaskArray();
boolean limit = minThreshold>0 || maxThreshold<255;
double xsum=0, ysum=0;
int count=0,i,mi,v;
for (int y=ry,my=0; y<(ry+rh); y++,my++) {
i = y*width + rx;
mi = my*rw;
for (int x=rx; x<(rx+rw); x++) {
if (mask==null||mask[mi++]!=0) {
if (limit) {
v = pixels[i]&255;
if (v>=minThreshold&&v<=maxThreshold) {
count++;
xsum+=x;
ysum+=y;
}
} else {
count++;
xsum+=x;
ysum+=y;
}
}
i++;
}
}
xCentroid = xsum/count+0.5;
yCentroid = ysum/count+0.5;
if (cal!=null) {
xCentroid = cal.getX(xCentroid);
yCentroid = cal.getY(yCentroid, height);
}
}
void calculateMoments(ImageProcessor ip, int minThreshold, int maxThreshold, float[] cTable) {
byte[] pixels = (byte[])ip.getPixels();
byte[] mask = ip.getMaskArray();
int v, i, mi;
double dv, dv2, sum1=0.0, sum2=0.0, sum3=0.0, sum4=0.0, xsum=0.0, ysum=0.0;
for (int y=ry,my=0; y<(ry+rh); y++,my++) {
i = y*width + rx;
mi = my*rw;
for (int x=rx; x<(rx+rw); x++) {
if (mask==null || mask[mi++]!=0) {
v = pixels[i]&255;
if (v>=minThreshold&&v<=maxThreshold) {
dv = ((cTable!=null)?cTable[v]:v)+Double.MIN_VALUE;
dv2 = dv*dv;
sum1 += dv;
sum2 += dv2;
sum3 += dv*dv2;
sum4 += dv2*dv2;
xsum += x*dv;
ysum += y*dv;
}
}
i++;
}
}
double mean2 = mean*mean;
double variance = sum2/pixelCount - mean2;
double sDeviation = Math.sqrt(variance);
skewness = ((sum3 - 3.0*mean*sum2)/pixelCount + 2.0*mean*mean2)/(variance*sDeviation);
kurtosis = (((sum4 - 4.0*mean*sum3 + 6.0*mean2*sum2)/pixelCount - 3.0*mean2*mean2)/(variance*variance)-3.0);
xCenterOfMass = xsum/sum1+0.5;
yCenterOfMass = ysum/sum1+0.5;
if (cal!=null) {
xCenterOfMass = cal.getX(xCenterOfMass);
yCenterOfMass = cal.getY(yCenterOfMass, height);
}
}
void getCalibratedMinAndMax(int minThreshold, int maxThreshold, float[] cTable) {
if (pixelCount==0)
{min=0.0; max=0.0; return;}
min = Double.MAX_VALUE;
max = -Double.MAX_VALUE;
double v = 0.0;
for (int i=minThreshold; i<=maxThreshold; i++) {
if (histogram[i]>0) {
v = cTable[i];
if (v<min) min = v;
if (v>max) max = v;
}
}
}
}
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