Add tuple3d centroid op

Author: rimadoma

pom.xml

@@ -260,6 +260,10 @@
 			<groupId>org.scijava</groupId>
 			<artifactId>scripting-javascript</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>vecmath</artifactId>
+		</dependency>
 
 		<!-- Third party dependencies -->
 		<dependency>

src/main/java/net/imagej/ops/geom/CentroidTuple3D.java

@@ -0,0 +1,32 @@
+package net.imagej.ops.geom;
+
+import net.imagej.ops.Ops;
+import net.imagej.ops.special.function.AbstractUnaryFunctionOp;
+import org.scijava.plugin.Plugin;
+import org.scijava.vecmath.Tuple3d;
+import org.scijava.vecmath.Vector3d;
+
+import java.util.Collection;
+
+/**
+ * Calculates the centroid (geometrical centre) of the given tuples
+ *
+ * @author Richard Domander (Royal Veterinary College, London)
+ */
+@Plugin(type = Ops.Geometric.Centroid.class)
+public class CentroidTuple3D extends AbstractUnaryFunctionOp<Collection<? extends Tuple3d>, Vector3d>
+        implements Ops.Geometric.Centroid {
+    @Override
+    public Vector3d compute1(final Collection<? extends Tuple3d> input) {
+        final int vectors = input.size();
+        if (vectors == 0) {
+            return new Vector3d(Double.NaN, Double.NaN, Double.NaN);
+        }
+
+        final Vector3d sum = new Vector3d(0.0, 0.0, 0.0);
+        input.stream().forEach(sum::add);
+        sum.scale(1.0 / vectors);
+
+        return sum;
+    }
+}

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

@@ -51,6 +51,10 @@
 
 import org.apache.commons.math3.linear.RealMatrix;
 import org.scijava.plugin.Plugin;
+import org.scijava.vecmath.Tuple3d;
+import org.scijava.vecmath.Vector3d;
+
+import java.util.Collection;
 
 /**
  * Namespace for Geom.
@@ -228,6 +232,11 @@ public RealLocalizable centroid(final Mesh in) {
 		return result;
 	}
 
+	@OpMethod(op = net.imagej.ops.geom.CentroidTuple3D.class)
+	public Vector3d centroid(final Collection<? extends Tuple3d> 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/CentroidTuple3DTest.java

@@ -0,0 +1,59 @@
+package net.imagej.ops.geom;
+
+import net.imagej.ops.AbstractOpTest;
+import org.junit.Test;
+import org.scijava.vecmath.Vector3d;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.stream.DoubleStream;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+/**
+ * Unit tests for {@link CentroidTuple3D}
+ *
+ * @author Richard Domander (Royal Veterinary College, London)
+ */
+public class CentroidTuple3DTest extends AbstractOpTest {
+    @Test
+    public void testCompute1EmptyCollection() throws Exception {
+        final List<Vector3d> emptyList = Collections.emptyList();
+
+        final Vector3d result = (Vector3d) ops.run(CentroidTuple3D.class, emptyList);
+
+        assertTrue("Coordinates should all be NaN",
+                DoubleStream.of(result.x, result.y, result.z).allMatch(Double::isNaN));
+    }
+
+    @Test
+    public void testCompute1SingleVector() throws Exception {
+        final Vector3d vector = new Vector3d(1.0, 2.0, 3.0);
+        final List<Vector3d> vectors = Collections.singletonList(vector);
+
+        final Vector3d result = (Vector3d) ops.run(CentroidTuple3D.class, vectors);
+
+        assertEquals("Incorrect centroid vector", vector, result);
+    }
+
+    @Test
+    public void testCompute1() throws Exception {
+        final Vector3d expected = new Vector3d(0.5, 0.5, 0.5);
+        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)
+        );
+
+        final Vector3d result = (Vector3d) ops.run(CentroidTuple3D.class, cubeVectors);
+
+        assertEquals("Incorrect centroid vector", expected, result);
+    }
+}