JOML rotate ops

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>net.imagej</groupId>
 	<artifactId>imagej-ops</artifactId>
-	<version>0.41.2-SNAPSHOT</version>
+	<version>0.42.0-SNAPSHOT</version>
 
 	<name>ImageJ Ops</name>
 	<description>ImageJ Operations: a framework for reusable algorithms.</description>
@@ -266,6 +266,10 @@
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-math3</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.joml</groupId>
+			<artifactId>joml</artifactId>
+		</dependency>
 
 		<!-- Test scope dependencies -->
 		<dependency>

src/main/java/net/imagej/ops/OpEnvironment.java

@@ -51,6 +51,7 @@
 import net.imagej.ops.image.ImageNamespace;
 import net.imagej.ops.imagemoments.ImageMomentsNamespace;
 import net.imagej.ops.labeling.LabelingNamespace;
+import net.imagej.ops.linalg.LinAlgNamespace;
 import net.imagej.ops.logic.LogicNamespace;
 import net.imagej.ops.map.neighborhood.CenterAwareComputerOp;
 import net.imagej.ops.math.MathNamespace;
@@ -890,6 +891,11 @@ default LBPNamespace lbp() {
 		return namespace(LBPNamespace.class);
 	}
 
+	/** Gateway into ops of the "linalg" namespace */
+	default LinAlgNamespace linalg() {
+		return namespace(LinAlgNamespace.class);
+	}
+
 	/** Gateway into ops of the "logic" namespace. */
 	default LogicNamespace logic() {
 		return namespace(LogicNamespace.class);

src/main/java/net/imagej/ops/linalg/LinAlgNamespace.java

@@ -0,0 +1,134 @@
+/*-
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 - 2018 ImageJ developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package net.imagej.ops.linalg;
+
+import net.imagej.ops.AbstractNamespace;
+import net.imagej.ops.Namespace;
+import net.imagej.ops.OpMethod;
+import net.imagej.ops.linalg.rotate.Rotate3d;
+import net.imagej.ops.linalg.rotate.Rotate3f;
+
+import org.joml.AxisAngle4d;
+import org.joml.AxisAngle4f;
+import org.joml.Quaterniond;
+import org.joml.Quaterniondc;
+import org.joml.Quaternionf;
+import org.joml.Quaternionfc;
+import org.joml.Vector3d;
+import org.joml.Vector3f;
+import org.scijava.plugin.Plugin;
+
+/**
+ * The linear algebra namespace has ops for vectors and matrices.
+ *
+ * @author Richard Domander (Royal Veterinary College, London)
+ */
+@Plugin(type = Namespace.class)
+public class LinAlgNamespace extends AbstractNamespace {
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
+	public Vector3f rotate(final Vector3f v, final Quaternionfc q) {
+		return (Vector3f) ops().run(Rotate3f.class, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
+	public Vector3f rotate(final Vector3f out, final Vector3f v,
+		final Quaternionfc q)
+	{
+		return (Vector3f) ops().run(Rotate3f.class, out, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
+	public Vector3d rotate(final Vector3d v, final Quaterniondc q) {
+		return (Vector3d) ops().run(Rotate3d.class, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
+	public Vector3d rotate(final Vector3d out, final Vector3d v,
+		final Quaterniondc q)
+	{
+		return (Vector3d) ops().run(Rotate3d.class, out, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
+	public Vector3d rotate(final Vector3d v, final AxisAngle4d axisAngle) {
+		final Quaterniondc q = new Quaterniond(axisAngle);
+		return (Vector3d) ops().run(Rotate3d.class, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
+	public Vector3f rotate(final Vector3f v, final AxisAngle4f axisAngle) {
+		final Quaternionfc q = new Quaternionf(axisAngle);
+		return (Vector3f) ops().run(Rotate3f.class, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
+	public Vector3d rotate(final Vector3d out, final Vector3d v,
+		final AxisAngle4d axisAngle)
+	{
+		final Quaterniondc q = new Quaterniond(axisAngle);
+		return (Vector3d) ops().run(Rotate3d.class, out, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
+	public Vector3f rotate(final Vector3f out, final Vector3f v,
+		final AxisAngle4f axisAngle)
+	{
+		final Quaternionfc q = new Quaternionf(axisAngle);
+		return (Vector3f) ops().run(Rotate3f.class, out, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
+	public Vector3d rotate1(final Vector3d v, final Quaterniondc q) {
+		return (Vector3d) ops().run(Rotate3d.class, v, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
+	public Vector3f rotate1(final Vector3f v, final Quaternionfc q) {
+		return (Vector3f) ops().run(Rotate3f.class, v, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
+	public Vector3d rotate1(final Vector3d v, final AxisAngle4d axisAngle) {
+		final Quaterniondc q = new Quaterniond(axisAngle);
+		return (Vector3d) ops().run(Rotate3d.class, v, v, q);
+	}
+
+	@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
+	public Vector3f rotate1(final Vector3f v, final AxisAngle4f axisAngle) {
+		final Quaternionfc q = new Quaternionf(axisAngle);
+		return (Vector3f) ops().run(Rotate3f.class, v, v, q);
+	}
+
+	@Override
+	public String getName() {
+		return "linalg";
+	}
+}

src/main/java/net/imagej/ops/linalg/rotate/Rotate3d.java

@@ -0,0 +1,69 @@
+/*-
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 - 2018 ImageJ developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package net.imagej.ops.linalg.rotate;
+
+import net.imagej.ops.Ops;
+import net.imagej.ops.special.hybrid.AbstractBinaryHybridCFI1;
+
+import org.joml.Quaterniondc;
+import org.joml.Vector3d;
+import org.scijava.plugin.Plugin;
+
+/**
+ * Rotates the vector by the quaternion.
+ *
+ * @author Richard Domander (Royal Veterinary College, London)
+ */
+@Plugin(type = Ops.LinAlg.Rotate.class)
+public class Rotate3d extends
+	AbstractBinaryHybridCFI1<Vector3d, Quaterniondc, Vector3d> implements
+	Ops.LinAlg.Rotate
+{
+
+	@Override
+	public void compute(final Vector3d v, final Quaterniondc q,
+		final Vector3d vDot)
+	{
+		vDot.set(v);
+		vDot.rotate(q);
+	}
+
+	@Override
+	public Vector3d createOutput(final Vector3d input1,
+		final Quaterniondc input2)
+	{
+		return new Vector3d();
+	}
+
+	@Override
+	public void mutate1(final Vector3d v, final Quaterniondc q) {
+		v.rotate(q);
+	}
+}

src/main/java/net/imagej/ops/linalg/rotate/Rotate3f.java

@@ -0,0 +1,67 @@
+/*-
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 - 2018 ImageJ developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package net.imagej.ops.linalg.rotate;
+
+import net.imagej.ops.Ops;
+import net.imagej.ops.special.hybrid.AbstractBinaryHybridCFI1;
+
+import org.joml.Quaternionfc;
+import org.joml.Vector3f;
+import org.scijava.plugin.Plugin;
+
+/**
+ * Rotates the vector by the quaternion.
+ *
+ * @author Richard Domander (Royal Veterinary College, London)
+ */
+@Plugin(type = Ops.LinAlg.Rotate.class)
+public class Rotate3f extends
+	AbstractBinaryHybridCFI1<Vector3f, Quaternionfc, Vector3f> implements
+	Ops.LinAlg.Rotate
+{
+
+	@Override
+	public void compute(final Vector3f v, final Quaternionfc q,
+		final Vector3f vDot)
+	{
+		vDot.set(v);
+		vDot.rotate(q);
+	}
+
+	@Override
+	public Vector3f createOutput(final Vector3f v, final Quaternionfc q) {
+		return new Vector3f();
+	}
+
+	@Override
+	public void mutate1(final Vector3f v, final Quaternionfc q) {
+		v.rotate(q);
+	}
+}

src/main/templates/net/imagej/ops/Ops.list

@@ -240,6 +240,9 @@ namespaces = ```
 	[name: "lbp", iface: "LBP", ops: [
 		[name: "lbp2D", 				iface: "LBP2D"]
 	]],
+	[name: "linalg", iface: "LinAlg", ops: [
+	    [name: "rotate", 				         iface: "Rotate"]
+	]],
 	[name: "logic", iface: "Logic", ops: [
 		[name: "and",                            iface: "And"],
 		[name: "bool",                           iface: "Bool"],