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gselzerwiedenm
gselzer
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wiedenm
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WIP: Copy Ops and other stuff
1 parent ac24014 commit 9ac2368

23 files changed

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‎src/main/java/net/imagej/ops/copy/CopyArrayImg.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.copy;
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import java.lang.reflect.Array;
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import java.util.function.Function;
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import net.imglib2.img.array.ArrayImg;
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import net.imglib2.img.basictypeaccess.array.ArrayDataAccess;
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import net.imglib2.type.NativeType;
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import net.imglib2.util.Intervals;
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import org.scijava.Priority;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.Op;
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import org.scijava.ops.core.computer.Computer;
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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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* Copying {@link ArrayImg} into another {@link ArrayImg}
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*
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* @author Christian Dietz (University of Konstanz)
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* @param <T>
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*/
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@Plugin(type = Op.class, name = "copy.img", priority = Priority.VERY_HIGH)
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@Parameter(key = "input")
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@Parameter(key = "copy", type = ItemIO.BOTH)
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public class CopyArrayImg<T extends NativeType<T>, A extends ArrayDataAccess<A>>
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implements Computer<ArrayImg<T, A>, ArrayImg<T, A>> {
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@Override
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public void compute(final ArrayImg<T, A> input, final ArrayImg<T, A> output) {
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if (!Intervals.equalDimensions(input, output))
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throw new IllegalArgumentException("The Dimensions of the input and copy images must be the same!");
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final Object inArray = input.update(null).getCurrentStorageArray();
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System.arraycopy(inArray, 0, output.update(null).getCurrentStorageArray(), 0, Array.getLength(inArray));
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}
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}
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@Plugin(type = Op.class, name = "copy.img", priority = Priority.VERY_HIGH)
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@Parameter(key = "input")
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@Parameter(key = "copy", type = ItemIO.OUTPUT)
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class CopyArrayImgFunction<T extends NativeType<T>, A extends ArrayDataAccess<A>>
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implements Function<ArrayImg<T, A>, ArrayImg<T, A>> {
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@OpDependency(name = "copy.img")
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private Computer<ArrayImg<T, A>, ArrayImg<T, A>> copyOp;
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@Override
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public ArrayImg<T, A> apply(ArrayImg<T, A> input) {
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// NB: Workaround for ArrayImgFactory not overriding create(Dimensions, T).
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final long[] dims = new long[input.numDimensions()];
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input.dimensions(dims);
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final ArrayImg<T, ?> copy = input.factory().create(dims, input.firstElement().createVariable());
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// TODO: Find a way to guarantee the type.
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@SuppressWarnings("unchecked")
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final ArrayImg<T, A> typedCopy = (ArrayImg<T, A>) copy;
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copyOp.compute(input, typedCopy);
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return typedCopy;
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}
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}

‎src/main/java/net/imagej/ops/copy/CopyII.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.copy;
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import java.util.function.BiFunction;
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import java.util.function.Function;
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import net.imglib2.Dimensions;
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import net.imglib2.IterableInterval;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.Op;
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import org.scijava.ops.core.computer.Computer;
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import org.scijava.ops.util.Maps;
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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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* Copies an {@link IterableInterval} into another {@link IterableInterval}
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*
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* @author Christian Dietz (University of Konstanz)
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* @param <T>
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*/
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@Plugin(type = Op.class, name = "copy.iterableInterval", priority = 1.0)
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@Parameter(key = "input")
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@Parameter(key = "output", type = ItemIO.BOTH)
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public class CopyII<T> implements Computer<IterableInterval<T>, IterableInterval<T>> {
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// used internally
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//TODO: make sure that the matcher autoLifts the type copying Op
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@OpDependency(name = "copy.type")
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private Computer<T, T> copyOp;
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@Override
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public void compute(final IterableInterval<T> input, final IterableInterval<T> output) {
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if (!input.iterationOrder().equals(output.iterationOrder()))
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throw new IllegalArgumentException("input and output must be of the same dimensions!");
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Computer<Iterable<T>, Iterable<T>> mapped = Maps.Computers.Iterables.liftBoth(copyOp);
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mapped.compute(input, output);
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}
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}
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@Plugin(type = Op.class, name = "copy.iterableInterval", priority = 1.0)
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@Parameter(key = "input")
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@Parameter(key = "output", type = ItemIO.OUTPUT)
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class CopyIIFunction<T> implements Function<IterableInterval<T>, IterableInterval<T>> {
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@OpDependency(name = "create.img")
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private BiFunction<Dimensions, T, IterableInterval<T>> imgCreator;
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@OpDependency(name = "copy.iterableInterval")
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private Computer<IterableInterval<T>, IterableInterval<T>> copyOp;
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@Override
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public IterableInterval<T> apply(IterableInterval<T> input) {
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IterableInterval<T> output = imgCreator.apply(input, input.firstElement());
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copyOp.compute(input, output);
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return output;
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}
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}

‎src/main/java/net/imagej/ops/copy/CopyImg.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.copy;
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import java.util.function.Function;
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import net.imglib2.img.Img;
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import net.imglib2.type.NativeType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.Op;
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import org.scijava.ops.core.computer.Computer;
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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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* Copying {@link Img} into another {@link Img}. Exists mainly for convenience
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* reasons.
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*
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* @author Christian Dietz (University of Konstanz)
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* @param <T>
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*/
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@Plugin(type = Op.class, name = "copy.img")
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@Parameter(key = "input")
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@Parameter(key = "output", type = ItemIO.BOTH)
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public class CopyImg<T extends NativeType<T>> implements Computer<Img<T>, Img<T>> {
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@OpDependency(name = "copy.iterableInterval")
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private Computer<Iterable<T>, Iterable<T>> copyComputer;
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@Override
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public void compute(final Img<T> input, final Img<T> output) {
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if (!input.iterationOrder().equals(output.iterationOrder()))
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throw new IllegalArgumentException("input and output must have the same iteration order!");
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copyComputer.compute(input, output);
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}
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}
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@Plugin(type = Op.class, name = "copy.img")
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@Parameter(key = "input")
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@Parameter(key = "output", type = ItemIO.OUTPUT)
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class CopyImgFunction<T extends NativeType<T>> implements Function<Img<T>, Img<T>> {
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@OpDependency(name = "copy.img")
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private Computer<Img<T>, Img<T>> copyComputer;
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@OpDependency(name = "create.img")
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private Function<Img<T>, Img<T>> createFunc;
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@Override
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public Img<T> apply(Img<T> input) {
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Img<T> output = createFunc.apply(input);
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copyComputer.compute(input, output);
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return output;
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}
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}

‎src/main/java/net/imagej/ops/copy/CopyImgLabeling.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.copy;
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import net.imagej.ops.Contingent;
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import net.imagej.ops.Ops;
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import net.imagej.ops.special.computer.Computers;
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import net.imagej.ops.special.computer.UnaryComputerOp;
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import net.imagej.ops.special.function.Functions;
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import net.imagej.ops.special.function.UnaryFunctionOp;
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import net.imagej.ops.special.hybrid.AbstractUnaryHybridCF;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.roi.labeling.ImgLabeling;
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import net.imglib2.roi.labeling.LabelingMapping;
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import net.imglib2.type.NativeType;
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import net.imglib2.type.numeric.IntegerType;
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import net.imglib2.util.Intervals;
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import net.imglib2.util.Util;
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import org.scijava.plugin.Plugin;
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/**
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* Copying {@link ImgLabeling} into another {@link ImgLabeling}
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*
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* @author Christian Dietz (University of Konstanz)
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* @param <T>
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*/
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@Plugin(type = Ops.Copy.ImgLabeling.class)
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public class CopyImgLabeling<T extends IntegerType<T> & NativeType<T>, L>
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extends AbstractUnaryHybridCF<ImgLabeling<L, T>, ImgLabeling<L, T>>
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implements Ops.Copy.ImgLabeling, Contingent {
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private UnaryComputerOp<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>> raiCopyOp;
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private UnaryComputerOp<LabelingMapping<L>, LabelingMapping<L>> mappingCopyOp;
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private UnaryFunctionOp<ImgLabeling<L, T>, ImgLabeling<L, T>> outputCreator;
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@SuppressWarnings({ "rawtypes", "unchecked" })
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@Override
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public void initialize() {
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raiCopyOp = Computers.unary(ops(), Ops.Copy.RAI.class, in().getIndexImg() ,in().getIndexImg());
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mappingCopyOp = Computers.unary(ops(), Ops.Copy.LabelingMapping.class, in().getMapping(), in().getMapping());
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outputCreator = (UnaryFunctionOp) Functions.unary(ops(), Ops.Create.ImgLabeling.class, ImgLabeling.class, in());
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}
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@Override
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public ImgLabeling<L, T> createOutput(final ImgLabeling<L, T> input) {
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return outputCreator.calculate(input);
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}
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@Override
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public void compute(final ImgLabeling<L, T> input,
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final ImgLabeling<L, T> output) {
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raiCopyOp.compute(input.getIndexImg(), output.getIndexImg());
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mappingCopyOp.compute(input.getMapping(), output.getMapping());
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}
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@Override
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public boolean conforms() {
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if (out() != null) {
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return Intervals.equalDimensions(in(), out())
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&& Util.getTypeFromInterval(in().getIndexImg()).getClass() == Util
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.getTypeFromInterval(out().getIndexImg())
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.getClass();
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}
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return true;
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}
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}

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