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Merge pull request #562 from bonej-org/rotate
JOML rotate ops
2 parents 2def69b + 25b3852 commit c486a51

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8 files changed

+489
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lines changed

‎pom.xml‎

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

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

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

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

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/*-
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2018 ImageJ developers.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package net.imagej.ops.linalg;
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import net.imagej.ops.AbstractNamespace;
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import net.imagej.ops.Namespace;
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import net.imagej.ops.OpMethod;
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import net.imagej.ops.linalg.rotate.Rotate3d;
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import net.imagej.ops.linalg.rotate.Rotate3f;
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import org.joml.AxisAngle4d;
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import org.joml.AxisAngle4f;
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import org.joml.Quaterniond;
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import org.joml.Quaterniondc;
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import org.joml.Quaternionf;
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import org.joml.Quaternionfc;
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import org.joml.Vector3d;
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import org.joml.Vector3f;
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import org.scijava.plugin.Plugin;
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/**
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* The linear algebra namespace has ops for vectors and matrices.
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*
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* @author Richard Domander (Royal Veterinary College, London)
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*/
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@Plugin(type = Namespace.class)
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public class LinAlgNamespace extends AbstractNamespace {
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
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public Vector3f rotate(final Vector3f v, final Quaternionfc q) {
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return (Vector3f) ops().run(Rotate3f.class, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
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public Vector3f rotate(final Vector3f out, final Vector3f v,
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final Quaternionfc q)
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{
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return (Vector3f) ops().run(Rotate3f.class, out, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
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public Vector3d rotate(final Vector3d v, final Quaterniondc q) {
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return (Vector3d) ops().run(Rotate3d.class, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
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public Vector3d rotate(final Vector3d out, final Vector3d v,
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final Quaterniondc q)
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{
77+
return (Vector3d) ops().run(Rotate3d.class, out, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
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public Vector3d rotate(final Vector3d v, final AxisAngle4d axisAngle) {
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final Quaterniondc q = new Quaterniond(axisAngle);
83+
return (Vector3d) ops().run(Rotate3d.class, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
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public Vector3f rotate(final Vector3f v, final AxisAngle4f axisAngle) {
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final Quaternionfc q = new Quaternionf(axisAngle);
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return (Vector3f) ops().run(Rotate3f.class, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
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public Vector3d rotate(final Vector3d out, final Vector3d v,
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final AxisAngle4d axisAngle)
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{
96+
final Quaterniondc q = new Quaterniond(axisAngle);
97+
return (Vector3d) ops().run(Rotate3d.class, out, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
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public Vector3f rotate(final Vector3f out, final Vector3f v,
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final AxisAngle4f axisAngle)
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{
104+
final Quaternionfc q = new Quaternionf(axisAngle);
105+
return (Vector3f) ops().run(Rotate3f.class, out, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
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public Vector3d rotate1(final Vector3d v, final Quaterniondc q) {
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return (Vector3d) ops().run(Rotate3d.class, v, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
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public Vector3f rotate1(final Vector3f v, final Quaternionfc q) {
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return (Vector3f) ops().run(Rotate3f.class, v, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3d.class)
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public Vector3d rotate1(final Vector3d v, final AxisAngle4d axisAngle) {
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final Quaterniondc q = new Quaterniond(axisAngle);
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return (Vector3d) ops().run(Rotate3d.class, v, v, q);
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}
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@OpMethod(op = net.imagej.ops.linalg.rotate.Rotate3f.class)
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public Vector3f rotate1(final Vector3f v, final AxisAngle4f axisAngle) {
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final Quaternionfc q = new Quaternionf(axisAngle);
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return (Vector3f) ops().run(Rotate3f.class, v, v, q);
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}
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@Override
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public String getName() {
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return "linalg";
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}
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}

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

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/*-
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2018 ImageJ developers.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
21+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
22+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
23+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
24+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
25+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package net.imagej.ops.linalg.rotate;
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import net.imagej.ops.Ops;
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import net.imagej.ops.special.hybrid.AbstractBinaryHybridCFI1;
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import org.joml.Quaterniondc;
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import org.joml.Vector3d;
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import org.scijava.plugin.Plugin;
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/**
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* Rotates the vector by the quaternion.
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*
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* @author Richard Domander (Royal Veterinary College, London)
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*/
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@Plugin(type = Ops.LinAlg.Rotate.class)
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public class Rotate3d extends
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AbstractBinaryHybridCFI1<Vector3d, Quaterniondc, Vector3d> implements
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Ops.LinAlg.Rotate
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{
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@Override
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public void compute(final Vector3d v, final Quaterniondc q,
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final Vector3d vDot)
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{
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vDot.set(v);
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vDot.rotate(q);
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}
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@Override
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public Vector3d createOutput(final Vector3d input1,
60+
final Quaterniondc input2)
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{
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return new Vector3d();
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}
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@Override
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public void mutate1(final Vector3d v, final Quaterniondc q) {
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v.rotate(q);
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}
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}

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

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/*-
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
4+
* %%
5+
* Copyright (C) 2014 - 2018 ImageJ developers.
6+
* %%
7+
* Redistribution and use in source and binary forms, with or without
8+
* modification, are permitted provided that the following conditions are met:
9+
*
10+
* 1. Redistributions of source code must retain the above copyright notice,
11+
* this list of conditions and the following disclaimer.
12+
* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
14+
* and/or other materials provided with the distribution.
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*
16+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
18+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
19+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
20+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
21+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
22+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
23+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
24+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
25+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
26+
* POSSIBILITY OF SUCH DAMAGE.
27+
* #L%
28+
*/
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package net.imagej.ops.linalg.rotate;
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import net.imagej.ops.Ops;
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import net.imagej.ops.special.hybrid.AbstractBinaryHybridCFI1;
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import org.joml.Quaternionfc;
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import org.joml.Vector3f;
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import org.scijava.plugin.Plugin;
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/**
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* Rotates the vector by the quaternion.
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*
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* @author Richard Domander (Royal Veterinary College, London)
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*/
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@Plugin(type = Ops.LinAlg.Rotate.class)
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public class Rotate3f extends
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AbstractBinaryHybridCFI1<Vector3f, Quaternionfc, Vector3f> implements
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Ops.LinAlg.Rotate
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{
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@Override
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public void compute(final Vector3f v, final Quaternionfc q,
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final Vector3f vDot)
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{
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vDot.set(v);
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vDot.rotate(q);
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}
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@Override
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public Vector3f createOutput(final Vector3f v, final Quaternionfc q) {
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return new Vector3f();
61+
}
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@Override
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public void mutate1(final Vector3f v, final Quaternionfc q) {
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v.rotate(q);
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}
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}

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

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[name: "lbp", iface: "LBP", ops: [
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[name: "lbp2D", iface: "LBP2D"]
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]],
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[name: "linalg", iface: "LinAlg", ops: [
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[name: "rotate", iface: "Rotate"]
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]],
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[name: "logic", iface: "Logic", ops: [
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[name: "and", iface: "And"],
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[name: "bool", iface: "Bool"],

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