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gselzer
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WIP: port geom namespace
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‎src/main/java/net/imagej/ops/geom/AbstractBoundarySizeConvexHull.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.geom;
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import java.util.function.Function;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.computer.Computer;
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/**
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* Generic implementation of
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* {@link net.imagej.ops.Ops.Geometric.BoundarySizeConvexHull}.
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*
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* @author Tim-Oliver Buchholz (University of Konstanz)
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*/
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public abstract class AbstractBoundarySizeConvexHull<I> implements Computer<I, DoubleType> {
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@OpDependency(name = "geom.convexHull")
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private Function<I, I> convexHullFunc;
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@OpDependency(name = "geom.boundarySize")
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private Function<I, DoubleType> perimeterFunc;
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@Override
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public void compute(I input, DoubleType output) {
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output.set(perimeterFunc.apply(convexHullFunc.apply(input)));
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}
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}

‎src/main/java/net/imagej/ops/geom/AbstractBoxivity.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.geom;
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import java.util.function.Function;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.computer.Computer;
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/**
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* Generic implementation of {@link net.imagej.ops.Ops.Geometric.Boxivity}.
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*
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* Based on http://www.math.uci.edu/icamp/summer/research_11/park/
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* shape_descriptors_survey.pdf, where boxivity is called rectangularity.
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*
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* @author Tim-Oliver Buchholz (University of Konstanz)
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*/
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public abstract class AbstractBoxivity<I> implements Computer<I, DoubleType> {
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@OpDependency(name = "geom.size")
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private Function<I, DoubleType> areaFunc;
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@OpDependency(name = "geom.smallestEnclosingBoundingBox")
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private Function<I, I> smallestEnclosingRectangleFunc;
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@Override
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public void compute(I input, DoubleType output) {
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output.set(areaFunc.apply(input).getRealDouble()
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/ areaFunc.apply(smallestEnclosingRectangleFunc.apply(input)).getRealDouble());
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}
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}

‎src/main/java/net/imagej/ops/geom/AbstractConvexity.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.geom;
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import java.util.function.Function;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.computer.Computer;
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/**
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* Generic implementation of {@link net.imagej.ops.Ops.Geometric.Convexity}.
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*
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* Based on
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* http://www.math.uci.edu/icamp/summer/research_11/park/shape_descriptors_survey.pdf.
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*
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* @author Tim-Oliver Buchholz (University of Konstanz)
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*/
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public abstract class AbstractConvexity<I> implements Computer<I, DoubleType> {
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@OpDependency(name = "geom.boundarySize")
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private Function<I, DoubleType> boundarySize;
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@OpDependency(name = "geom.boundarySizeConvexHull")
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private Function<I, DoubleType> boundarySizeConvexHull;
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@Override
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public void compute(final I input, final DoubleType output) {
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output.set(boundarySizeConvexHull.apply(input).get() / boundarySize.apply(input).get());
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}
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}

‎src/main/java/net/imagej/ops/geom/AbstractSizeConvexHull.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.geom;
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import java.util.function.Function;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.computer.Computer;
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/**
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* Generic implementation of {@link net.imagej.ops.Ops.Geometric.SizeConvexHull}
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* .
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*
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* @author Tim-Oliver Buchholz (University of Konstanz)
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*/
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public abstract class AbstractSizeConvexHull<I> implements Computer<I, DoubleType> {
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@OpDependency(name = "geom.convexHull")
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private Function<I, I> convexHullFunc;
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@OpDependency(name = "geom.size")
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private Function<I, DoubleType> sizeFunc;
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@Override
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public void compute(final I input, final DoubleType output) {
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output.set(sizeFunc.apply(convexHullFunc.apply(input)));
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}
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}

‎src/main/java/net/imagej/ops/geom/AbstractSolidity.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.geom;
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import java.util.function.Function;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.computer.Computer;
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/**
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* Generic implementation of {@link net.imagej.ops.Ops.Geometric.Solidity}.
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*
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* Based on https://de.mathworks.com/help/images/ref/regionprops.html.
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*
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* @author Tim-Oliver Buchholz (University of Konstanz)
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*/
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public abstract class AbstractSolidity<I> implements Computer<I, DoubleType> {
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@OpDependency(name = "geom.size")
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private Function<I, DoubleType> volume;
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@OpDependency(name = "geom.sizeConvexHull")
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private Function<I, DoubleType> convexHullVolume;
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@Override
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public void compute(final I input, final DoubleType output) {
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output.set(volume.apply(input).get() / convexHullVolume.apply(input).get());
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}
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}

‎src/main/java/net/imagej/ops/geom/CentroidII.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
14+
* 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
18+
* 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
22+
* 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.geom;
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import java.util.function.Function;
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import net.imglib2.Cursor;
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import net.imglib2.IterableInterval;
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import net.imglib2.RealLocalizable;
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import net.imglib2.RealPoint;
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import net.imglib2.roi.IterableRegion;
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import org.scijava.ops.core.Op;
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import org.scijava.param.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.struct.ItemIO;
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/**
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* This {@link Op} computes the centroid of a {@link IterableRegion} (Label).
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*
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* @author Tim-Oliver Buchholz (University of Konstanz)
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*/
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@Plugin(type = Op.class, name = "geom.centroid", priority = 1)
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@Parameter(key = "input")
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@Parameter(key = "centroid", type = ItemIO.OUTPUT)
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public class CentroidII implements Function<IterableInterval<?>, RealLocalizable> {
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@Override
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public RealLocalizable apply(final IterableInterval<?> input) {
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int numDimensions = input.numDimensions();
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double[] output = new double[numDimensions];
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Cursor<?> c = input.localizingCursor();
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double[] pos = new double[numDimensions];
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while (c.hasNext()) {
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c.fwd();
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c.localize(pos);
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for (int i = 0; i < output.length; i++) {
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output[i] += pos[i];
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}
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}
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for (int i = 0; i < output.length; i++) {
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output[i] = output[i] / input.size();
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}
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return new RealPoint(output);
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}
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}

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