Add CentroidTuple3d op

pom.xml

@@ -266,6 +266,14 @@
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-math3</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.joml</groupId>
+			<artifactId>joml</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>gov.nist.math</groupId>
+			<artifactId>jama</artifactId>
+		</dependency>
 
 		<!-- Test scope dependencies -->
 		<dependency>
@@ -294,10 +302,5 @@
 			<artifactId>ij</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>net.imglib2</groupId>
-			<artifactId>imglib2-ij</artifactId>
-			<scope>test</scope>
-		</dependency>
 	</dependencies>
 </project>

src/main/java/net/imagej/ops/geom/CentroidVector3d.java

@@ -0,0 +1,37 @@
+
+package net.imagej.ops.geom;
+
+import java.util.Iterator;
+
+import net.imagej.ops.Ops;
+import net.imagej.ops.special.function.AbstractUnaryFunctionOp;
+
+import org.joml.Vector3d;
+import org.joml.Vector3dc;
+import org.scijava.plugin.Plugin;
+
+/**
+ * Calculates the centroid (geometrical centre) of the vectors
+ *
+ * @author Richard Domander (Royal Veterinary College, London)
+ */
+@Plugin(type = Ops.Geometric.Centroid.class)
+public class CentroidVector3d extends
+	AbstractUnaryFunctionOp<Iterable<Vector3dc>, Vector3d> implements
+	Ops.Geometric.Centroid
+{
+
+	@Override
+	public Vector3d calculate(final Iterable<Vector3dc> input) {
+		final Iterator<Vector3dc> iterator = input.iterator();
+		final Vector3d sum = new Vector3d();
+		long count = 0;
+		while (iterator.hasNext()) {
+			final Vector3dc v = iterator.next();
+			sum.add(v);
+			count++;
+		}
+		sum.div(count);
+		return sum;
+	}
+}

src/main/java/net/imagej/ops/geom/GeomNamespace.java

@@ -50,6 +50,8 @@
 import net.imglib2.util.Pair;
 
 import org.apache.commons.math3.linear.RealMatrix;
+import org.joml.Vector3d;
+import org.joml.Vector3dc;
 import org.scijava.plugin.Plugin;
 
 /**
@@ -228,6 +230,11 @@ public RealLocalizable centroid(final Mesh in) {
 		return result;
 	}
 
+	@OpMethod(op = net.imagej.ops.geom.CentroidVector3d.class)
+	public Vector3d centroid(final Iterable<Vector3dc> in) {
+		return (Vector3d) ops().run(net.imagej.ops.Ops.Geometric.Centroid.class, in);
+	}
+
 	@OpMethod(op = net.imagej.ops.geom.geom2d.DefaultCircularity.class)
 	public DoubleType circularity(final Polygon2D in) {
 		final DoubleType result =

src/test/java/net/imagej/ops/geom/CentroidVector3dTest.java

@@ -0,0 +1,66 @@
+
+package net.imagej.ops.geom;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.stream.DoubleStream;
+
+import net.imagej.ops.AbstractOpTest;
+
+import org.joml.Vector3d;
+import org.junit.Test;
+
+/**
+ * Unit tests for {@link CentroidVector3d}
+ *
+ * @author Richard Domander (Royal Veterinary College, London)
+ */
+public class CentroidVector3dTest extends AbstractOpTest {
+
+	@Test
+	public void testCalculate() {
+		final Vector3d expected = new Vector3d(0.5, 0.5, 0.5);
+		//@formatter:off
+        final List<Vector3d> cubeVectors = Arrays.asList(
+                new Vector3d(0.0, 0.0, 0.0),
+                new Vector3d(1.0, 0.0, 0.0),
+                new Vector3d(1.0, 1.0, 0.0),
+                new Vector3d(0.0, 1.0, 0.0),
+                new Vector3d(0.0, 0.0, 1.0),
+                new Vector3d(1.0, 0.0, 1.0),
+                new Vector3d(1.0, 1.0, 1.0),
+                new Vector3d(0.0, 1.0, 1.0)
+        );
+        //@formatter:on
+
+		final Vector3d result = (Vector3d) ops.run(CentroidVector3d.class,
+			cubeVectors);
+
+		assertEquals("Incorrect centroid vector", expected, result);
+	}
+
+	@Test
+	public void testCalculateEmptyCollection() {
+		final List<Vector3d> emptyList = Collections.emptyList();
+
+		final Vector3d result = (Vector3d) ops.run(CentroidVector3d.class,
+			emptyList);
+
+		assertTrue("Coordinates should all be NaN", DoubleStream.of(result.x,
+			result.y, result.z).allMatch(Double::isNaN));
+	}
+
+	@Test
+	public void testCalculateSingleVector() {
+		final Vector3d vector = new Vector3d(1.0, 2.0, 3.0);
+		final List<Vector3d> vectors = Collections.singletonList(vector);
+
+		final Vector3d result = (Vector3d) ops.run(CentroidVector3d.class, vectors);
+
+		assertEquals("Incorrect centroid vector", vector, result);
+	}
+}