t-test between two ImageJ1 images

Two_Images_T-test.bsh

/*
 * IJ BAR: https://github.com/tferr/Scripts#scripts
 *
 * Performs a t-test between two open images (http://thread.gmane.org/gmane.comp.java.imagej/35266) using
 * commons-math:
 * http://commons.apache.org/proper/commons-math/userguide/stat.html
 * http://commons.apache.org/proper/commons-math/apidocs/org/apache/commons/math3/stat/inference/TTest.html
 *
 */

import ij.IJ;
import ij.WindowManager;

import org.apache.commons.math3.stat.inference.TTest;
import org.apache.commons.math3.stat.StatUtils;

/*
 * Casts any array type (byte[], short[], float[], int[]) into double[].
 * This is required as we do not know which image types we'll be dealing with
 */
double[] toDoubleArray(array) {
	double[] dArray = new double[array.length];
	for (i=0; i<array.length; i++) {
		dArray[i] = (double) array[i];
	}
	return dArray;
}


int[] ids = WindowManager.getIDList();
if (ids==null || ids.length<2) {
	IJ.error("At least 2 images required");
	return;
}

img1 = WindowManager.getImage(ids[0]);
img2 = WindowManager.getImage(ids[1]);
sample1 = toDoubleArray(img1.getProcessor().getPixels());
sample2 = toDoubleArray(img2.getProcessor().getPixels());

pValue = new TTest().tTest(sample1, sample2);
s1variance = StatUtils.variance(sample1);
s2variance = StatUtils.variance(sample2);

IJ.log("\n*** Two-sample, two-tailed t-test ***");
IJ.log(""+ img1.getTitle() +" vs "+ img2.getTitle());
IJ.log("p-value: "+ pValue);
IJ.log("Image 1 variance: "+ s1variance);
IJ.log("Image 2 variance: "+ s2variance);