FloatStatistics.java

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

public class FloatStatistics extends ImageStatistics {

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

    public FloatStatistics(ImageProcessor ip, int mOptions, Calibration cal) {
        this.width = ip.getWidth();
        this.height = ip.getHeight();
        setup(ip, cal);
        double minT = ip.getMinThreshold();
        double minThreshold,maxThreshold;
        if ((mOptions&LIMIT)==0 || minT==ip.NO_THRESHOLD)
            {minThreshold=-Float.MAX_VALUE; maxThreshold=Float.MAX_VALUE;}
        else
            {minThreshold=minT; maxThreshold=ip.getMaxThreshold();}
        getStatistics(ip, minThreshold, maxThreshold);
        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);
    }

    void getStatistics(ImageProcessor ip, double minThreshold, double maxThreshold) {
        double v;
        float[] pixels = (float[])ip.getPixels();
        nBins = ip.getHistogramSize();
        histMin = ip.getHistogramMin();
        histMax = ip.getHistogramMax();
        histogram = new int[nBins];
        double sum = 0;
        double sum2 = 0;
        byte[] mask = ip.getMaskArray();
        
        // Find image min and max
        double roiMin = Double.MAX_VALUE;
        double roiMax = -Double.MAX_VALUE;
        double roiMin2 = Double.MAX_VALUE;
        double roiMax2 = -Double.MAX_VALUE;
        for (int y=ry, my=0; y<(ry+rh); y++, my++) {
            int i = y * width + rx;
            int mi = my * rw;
            for (int x=rx; x<(rx+rw); x++) {
                if (mask==null || mask[mi++]!=0) {
                    v = pixels[i];
                    if (v>=minThreshold && v<=maxThreshold) {
                        if (v<roiMin) roiMin = v;
                        if (v>roiMax) roiMax = v;
                    }
                }
                i++;
            }
        }
        min = roiMin; max = roiMax;
        if (histMin==0.0 && histMax==0.0) {
            histMin = min; 
            histMax = max;
        } else {
            if (min<histMin) min = histMin;
            if (max>histMax) max = histMax;
        }
        binSize = (histMax-histMin)/nBins;

        // Generate histogram
        double scale = nBins/(histMax-histMin);
        int index;
        pixelCount = 0;
        for (int y=ry, my=0; y<(ry+rh); y++, my++) {
            int i = y * width + rx;
            int mi = my * rw;
            for (int x=rx; x<(rx+rw); x++) {
                if (mask==null || mask[mi++]!=0) {
                    v = pixels[i];
                    if (v>=minThreshold && v<=maxThreshold && v>=histMin && v<=histMax) {
                        pixelCount++;
                        sum += v;
                        sum2 += v*v;
                        index = (int)(scale*(v-histMin));
                        if (index>=nBins)
                            index = nBins-1;
                        histogram[index]++;
                    }
                }
                i++;
            }
        }
        area = pixelCount*pw*ph;
        mean = sum/pixelCount;
        calculateStdDev(pixelCount, sum, sum2);
    }

    void getMode() {
        int count;
        maxCount = 0;
        for (int i = 0; i < nBins; i++) {
            count = histogram[i];
            if (count > maxCount) {
                maxCount = count;
                mode = i;
            }
        }
        dmode = histMin+mode*binSize;
        if (binSize!=1.0)
            dmode += binSize/2.0;           
    }

    void getCenterOfMass(ImageProcessor ip, double minThreshold, double maxThreshold) {
        float[] pixels = (float[])ip.getPixels();
        byte[] mask = ip.getMaskArray();
        int i, mi;
        double v, 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]+Double.MIN_VALUE;
                    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 getCentroid(ImageProcessor ip, double minThreshold, double maxThreshold) {
        float[] pixels = (float[])ip.getPixels();
        byte[] mask = ip.getMaskArray();
        double count=0.0, xsum=0.0, ysum=0.0, v;
        int i, mi;
        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];
                    if (v>=minThreshold && v<=maxThreshold) {
                        count++;
                        xsum+=x;
                        ysum+=y;
                    }
                }
                i++;
            }
        }
        xCentroid = ((double)xsum/count+0.5)*pw;
        yCentroid = ((double)ysum/count+0.5)*ph;
    }

}