com.actelion.research.orbit.utils.StdStats Maven / Gradle / Ivy
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2016 Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see
* Library of statistical functions.
*
* The test client reads an array of real numbers from standard
* input, and computes the minimum, mean, maximum, and
* standard deviation.
*
* The functions all throw a NullPointerException if the array
* passed in is null.
*
* The floating-point functions all return NaN if any input is NaN.
*
* Unlike Math.min() and Math.max(), the min() and max() functions
* do not differentiate between -0.0 and 0.0.
*
* % more tiny.txt
* 5
* 3.0 1.0 2.0 5.0 4.0
*
* % java StdStats < tiny.txt
* min 1.000
* mean 3.000
* max 5.000
* std dev 1.581
*
* Should these funtions use varargs instead of array arguments?
*************************************************************************/
/**
* Standard statistics. This class provides methods for computing
* statistics such as min, max, mean, sample standard deviation, and
* sample variance.
*
* For additional documentation, see
* Section 2.2 of
* Introduction to Programming in Java: An Interdisciplinary Approach
* by Robert Sedgewick and Kevin Wayne.
*
* @author Robert Sedgewick
* @author Kevin Wayne
*
* GPL License
*/
public final class StdStats {
private StdStats() {
}
/**
* Returns the maximum value in the array a[], -infinity if no such value.
*/
public static double max(double[] a) {
double max = Double.NEGATIVE_INFINITY;
for (int i = 0; i < a.length; i++) {
if (Double.isNaN(a[i])) return Double.NaN;
if (a[i] > max) max = a[i];
}
return max;
}
/**
* Returns the maximum value in the subarray a[lo..hi], -infinity if no such value.
*/
public static double max(double[] a, int lo, int hi) {
if (lo < 0 || hi >= a.length || lo > hi)
throw new RuntimeException("Subarray indices out of bounds");
double max = Double.NEGATIVE_INFINITY;
for (int i = lo; i <= hi; i++) {
if (Double.isNaN(a[i])) return Double.NaN;
if (a[i] > max) max = a[i];
}
return max;
}
/**
* Returns the maximum value in the array a[], Integer.MIN_VALUE if no such value.
*/
public static int max(int[] a) {
int max = Integer.MIN_VALUE;
for (int i = 0; i < a.length; i++) {
if (a[i] > max) max = a[i];
}
return max;
}
/**
* Returns the minimum value in the array a[], +infinity if no such value.
*/
public static double min(double[] a) {
double min = Double.POSITIVE_INFINITY;
for (int i = 0; i < a.length; i++) {
if (Double.isNaN(a[i])) return Double.NaN;
if (a[i] < min) min = a[i];
}
return min;
}
/**
* Returns the minimum value in the subarray a[lo..hi], +infinity if no such value.
*/
public static double min(double[] a, int lo, int hi) {
if (lo < 0 || hi >= a.length || lo > hi)
throw new RuntimeException("Subarray indices out of bounds");
double min = Double.POSITIVE_INFINITY;
for (int i = lo; i <= hi; i++) {
if (Double.isNaN(a[i])) return Double.NaN;
if (a[i] < min) min = a[i];
}
return min;
}
/**
* Returns the minimum value in the array a[], Integer.MAX_VALUE if no such value.
*/
public static int min(int[] a) {
int min = Integer.MAX_VALUE;
for (int i = 0; i < a.length; i++) {
if (a[i] < min) min = a[i];
}
return min;
}
/**
* Returns the average value in the array a[], NaN if no such value.
*/
public static double mean(double[] a) {
if (a.length == 0) return Double.NaN;
double sum = sum(a);
return sum / a.length;
}
/**
* Returns the average value in the subarray a[lo..hi], NaN if no such value.
*/
public static double mean(double[] a, int lo, int hi) {
int length = hi - lo + 1;
if (lo < 0 || hi >= a.length || lo > hi)
throw new RuntimeException("Subarray indices out of bounds");
if (length == 0) return Double.NaN;
double sum = sum(a, lo, hi);
return sum / length;
}
/**
* Returns the average value in the array a[], NaN if no such value.
*/
public static double mean(int[] a) {
if (a.length == 0) return Double.NaN;
double sum = 0.0;
for (int i = 0; i < a.length; i++) {
sum = sum + a[i];
}
return sum / a.length;
}
/**
* Returns the sample variance in the array a[], NaN if no such value.
*/
public static double var(double[] a) {
if (a.length == 0) return Double.NaN;
double avg = mean(a);
double sum = 0.0;
for (int i = 0; i < a.length; i++) {
sum += (a[i] - avg) * (a[i] - avg);
}
return sum / (a.length - 1);
}
/**
* Returns the sample variance in the array a[], NaN if no such value.
*/
public static double var(double[] a, double avg) {
if (a.length == 0) return Double.NaN;
double sum = 0.0;
for (int i = 0; i < a.length; i++) {
sum += (a[i] - avg) * (a[i] - avg);
}
return sum / (a.length - 1);
}
/**
* Returns the sample variance in the subarray a[lo..hi], NaN if no such value.
*/
public static double var(double[] a, int lo, int hi) {
int length = hi - lo + 1;
if (lo < 0 || hi >= a.length || lo > hi)
throw new RuntimeException("Subarray indices out of bounds");
if (length == 0) return Double.NaN;
double avg = mean(a, lo, hi);
double sum = 0.0;
for (int i = lo; i <= hi; i++) {
sum += (a[i] - avg) * (a[i] - avg);
}
return sum / (length - 1);
}
/**
* Returns the sample variance in the array a[], NaN if no such value.
*/
public static double var(int[] a) {
if (a.length == 0) return Double.NaN;
double avg = mean(a);
double sum = 0.0;
for (int i = 0; i < a.length; i++) {
sum += (a[i] - avg) * (a[i] - avg);
}
return sum / (a.length - 1);
}
/**
* Returns the population variance in the array a[], NaN if no such value.
*/
public static double varp(double[] a) {
if (a.length == 0) return Double.NaN;
double avg = mean(a);
double sum = 0.0;
for (int i = 0; i < a.length; i++) {
sum += (a[i] - avg) * (a[i] - avg);
}
return sum / a.length;
}
/**
* Returns the population variance in the subarray a[lo..hi], NaN if no such value.
*/
public static double varp(double[] a, int lo, int hi) {
int length = hi - lo + 1;
if (lo < 0 || hi >= a.length || lo > hi)
throw new RuntimeException("Subarray indices out of bounds");
if (length == 0) return Double.NaN;
double avg = mean(a, lo, hi);
double sum = 0.0;
for (int i = lo; i <= hi; i++) {
sum += (a[i] - avg) * (a[i] - avg);
}
return sum / length;
}
/**
* Returns the sample standard deviation in the array a[], NaN if no such value.
*/
public static double stddev(double[] a) {
return Math.sqrt(var(a));
}
/**
* Returns the sample standard deviation in the array a[], NaN if no such value.
*/
public static double stddev(double[] a, double avg) {
return Math.sqrt(var(a, avg));
}
/**
* Returns the sample standard deviation in the subarray a[lo..hi], NaN if no such value.
*/
public static double stddev(double[] a, int lo, int hi) {
return Math.sqrt(var(a, lo, hi));
}
/**
* Returns the sample standard deviation in the array a[], NaN if no such value.
*/
public static double stddev(int[] a) {
return Math.sqrt(var(a));
}
/**
* Returns the population standard deviation in the array a[], NaN if no such value.
*/
public static double stddevp(double[] a) {
return Math.sqrt(varp(a));
}
/**
* Returns the population standard deviation in the subarray a[lo..hi], NaN if no such value.
*/
public static double stddevp(double[] a, int lo, int hi) {
return Math.sqrt(varp(a, lo, hi));
}
/**
* Returns the sum of all values in the array a[].
*/
public static double sum(double[] a) {
double sum = 0.0;
for (int i = 0; i < a.length; i++) {
sum += a[i];
}
return sum;
}
/**
* Returns the sum of all values in the subarray a[lo..hi].
*/
public static double sum(double[] a, int lo, int hi) {
if (lo < 0 || hi >= a.length || lo > hi)
throw new RuntimeException("Subarray indices out of bounds");
double sum = 0.0;
for (int i = lo; i <= hi; i++) {
sum += a[i];
}
return sum;
}
/**
* Returns the sum of all values in the array a[].
*/
public static int sum(int[] a) {
int sum = 0;
for (int i = 0; i < a.length; i++) {
sum += a[i];
}
return sum;
}
}