ShortStatistics.java

package ij.process;
import ij.measure.Calibration;

public class ShortStatistics extends ImageStatistics {

    public ShortStatistics(ImageProcessor ip) {
        this(ip, AREA+MEAN+MODE+MIN_MAX, null);
    }

    public ShortStatistics(ImageProcessor ip, int mOptions, Calibration cal) {
        this.width = ip.getWidth();
        this.height = ip.getHeight();
        setup(ip, cal);
        nBins = 256;
        double minT = ip.getMinThreshold();
        int minThreshold,maxThreshold;
        if ((mOptions&LIMIT)==0 || minT==ip.NO_THRESHOLD)
            {minThreshold=0; maxThreshold=65535;}
        else
            {minThreshold=(int)minT; maxThreshold=(int)ip.getMaxThreshold();}
        int[] hist = ip.getHistogram(); // 65536 bin histogram
        float[] cTable = cal!=null?cal.getCTable():null;
        getRawMinAndMax(hist, minThreshold, maxThreshold);
        histMin = min;
        histMax = max;
        getStatistics(hist, (int)min, (int)max, cTable);
        if ((mOptions&MODE)!=0)
            getMode();
        if ((mOptions&ELLIPSE)!=0)
            fitEllipse(ip);
        else if ((mOptions&CENTROID)!=0)
            getCentroid(ip, minThreshold, maxThreshold);
        if ((mOptions&CENTER_OF_MASS)!=0)
            getCenterOfMass(ip, minThreshold, maxThreshold);
        if ((mOptions&MIN_MAX)!=0 && cTable!=null) {
            getCalibratedMinAndMax(hist, (int)min, (int)max, cTable);
        }
    }

    void getRawMinAndMax(int[] hist, int minThreshold, int maxThreshold) {
        int min = minThreshold;
        while ((hist[min]==0) && (min<65535))
            min++;
        this.min = min;
            
        int max = maxThreshold;
        while ((hist[max]==0) && (max>0))
            max--;
        this.max = max;
    }

    void getStatistics(int[] hist, int min, int max, float[] cTable) {
        int count;
        double value;
        double sum = 0.0;
        double sum2 = 0.0;
        binSize = (histMax-histMin)/nBins;
        double scale = 1.0/binSize;
        int hMin = (int)histMin;
        histogram = new int[nBins]; // 256 bin histogram
        int index;
        int maxCount = 0;
                
        for (int i=min; i<=max; i++) {
            count = hist[i];
            if (count>maxCount) {
                maxCount = count;
                dmode = i;
            }
            pixelCount += count;
            value = cTable==null?i:cTable[i];
            sum += value*count;
            sum2 += (value*value)*count;
            index = (int)(scale*(i-hMin));
            if (index>=nBins)
                index = nBins-1;
            histogram[index] += count;
        }
        area = pixelCount*pw*ph;
        mean = sum/pixelCount;
        umean = mean;
        calculateStdDev(pixelCount, sum, sum2);
        if (cTable!=null)
            dmode = cTable[(int)dmode];
    }
    
    void getMode() {
        int count;
        maxCount = 0;
        for (int i=0; i<nBins; i++) {
            count = histogram[i];
            if (count > maxCount) {
                maxCount = count;
                mode = i;
            }
        }
        //ij.IJ.write("mode2: "+mode+" "+dmode+" "+maxCount);
    }


    void getCentroid(ImageProcessor ip, int minThreshold, int maxThreshold) {
        short[] pixels = (short[])ip.getPixels();
        byte[] mask = ip.getMaskArray();
        boolean limit = minThreshold>0 || maxThreshold<65535;
        int count=0, xsum=0, ysum=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]&0xffff;
                        if (v>=minThreshold&&v<=maxThreshold) {
                            count++;
                            xsum+=x;
                            ysum+=y;
                        }
                    } else {
                        count++;
                        xsum+=x;
                        ysum+=y;
                    }
                }
                i++;
            }
        }
        xCentroid = ((double)xsum/count+0.5)*pw;
        yCentroid = ((double)ysum/count+0.5)*ph;
    }

    void getCenterOfMass(ImageProcessor ip,  int minThreshold, int maxThreshold) {
        short[] pixels = (short[])ip.getPixels();
        byte[] mask = ip.getMaskArray();
        int i, mi, v;
        double dv, count=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]&0xffff;
                    if (v>=minThreshold&&v<=maxThreshold) {
                        count += v;
                        xsum += x*v;
                        ysum += y*v;
                    }
                }
                i++;
            }
        }
        xCenterOfMass = (xsum/count+0.5)*pw;
        yCenterOfMass = (ysum/count+0.5)*ph;
    }

    void getCalibratedMinAndMax(int[] hist, int minValue, int maxValue, float[] cTable) {
        min = Double.MAX_VALUE;
        max = -Double.MAX_VALUE;
        double v = 0.0;
        for (int i=minValue; i<=maxValue; i++) {
            if (hist[i]>0) {
                v = cTable[i];
                if (v<min) min = v;
                if (v>max) max = v;
            }
        }
    }

}