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Add converter plugins for ImgLib2 types
1 parent f85aaac commit cca82cd

4 files changed

Lines changed: 151 additions & 7 deletions

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‎pom.xml‎

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@@ -115,22 +115,27 @@
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<version>${appose.version}</version>
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</dependency>
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<!-- Test dependencies -->
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<!-- TODO: Move the image-specific parts of this code to a dedicated imagej-appose component. -->
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<!-- ImgLib2 dependencies -->
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<scope>test</scope>
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<groupId>net.imglib2</groupId>
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<artifactId>imglib2</artifactId>
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</dependency>
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<dependency>
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<groupId>net.imglib2</groupId>
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<artifactId>imglib2-appose</artifactId>
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<version>${imglib2-appose.version}</version>
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<scope>test</scope>
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</dependency>
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<!-- ImageJ2 dependencies -->
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<dependency>
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<!-- For net.imglib2.img.Img parameter handling. -->
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<groupId>net.imagej</groupId>
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<artifactId>imagej-common</artifactId>
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</dependency>
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<!-- Test dependencies -->
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<scope>test</scope>
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</dependency>
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</dependencies>

‎src/main/java/org/scijava/plugins/scripting/appose/python/ApposePythonScriptLanguage.java‎

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package org.scijava.plugins.scripting.appose.python;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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‎src/main/java/org/scijava/plugins/scripting/appose/python/NDArrayToImgConverter.java‎

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/*
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* #%L
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* Python scripting language plugin to be used via scyjava.
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* %%
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* Copyright (C) 2021 - 2025 SciJava 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 org.scijava.plugins.scripting.appose.python;
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import org.apposed.appose.NDArray;
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import org.scijava.convert.Converter;
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import org.scijava.plugin.Plugin;
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import net.imagej.convert.ConciseConverter;
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import net.imglib2.img.Img;
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import net.imglib2.img.planar.PlanarImgFactory;
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import net.imglib2.appose.ShmImg;
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import net.imglib2.type.NativeType;
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import net.imglib2.util.ImgUtil;
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/**
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* Converts an Appose {@link NDArray} to an ImgLib2 {@link Img}.
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* <p>
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* The {@code NDArray} is first wrapped as a {@link ShmImg}, then copied into a
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* {@link net.imglib2.img.planar.PlanarImg}. The copy step is necessary because
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* {@code ShmImg} is backed by a direct NIO buffer (not a Java primitive array),
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* which is incompatible with ImageJ1's {@code ImageProcessorUtils}.
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* </p>
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*
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* @author Curtis Rueden
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*/
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@SuppressWarnings("rawtypes")
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@Plugin(type = Converter.class)
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public class NDArrayToImgConverter extends ConciseConverter<NDArray, Img> {
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public NDArrayToImgConverter() {
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super(NDArray.class, Img.class, NDArrayToImgConverter::doConvert);
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}
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private static <T extends NativeType<T>> Img<T> doConvert(
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final NDArray ndArray)
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{
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final ShmImg<T> shmImg = new ShmImg<>(ndArray);
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final PlanarImgFactory<T> factory =
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new PlanarImgFactory<>(shmImg.getType());
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final Img<T> result = factory.create(shmImg);
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ImgUtil.copy(shmImg, result);
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return result;
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}
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}

‎src/main/java/org/scijava/plugins/scripting/appose/python/RAIToNDArrayConverter.java‎

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/*
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* #%L
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* Python scripting language plugin to be used via scyjava.
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* %%
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* Copyright (C) 2021 - 2025 SciJava developers.
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* %%
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* Redistribution and use in source and binary forms, with or without
8+
* 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,
11+
* 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
23+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
24+
* 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 org.scijava.plugins.scripting.appose.python;
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import org.apposed.appose.NDArray;
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import org.scijava.convert.Converter;
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import org.scijava.plugin.Plugin;
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import net.imagej.convert.ConciseConverter;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.appose.NDArrays;
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import net.imglib2.type.NativeType;
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/**
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* Converts a {@link RandomAccessibleInterval} to an Appose {@link NDArray}.
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* <p>
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* If the input already wraps an {@code NDArray} (e.g., a {@code ShmImg}),
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* the existing {@code NDArray} is returned without copying. Otherwise the
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* image is copied into a new shared-memory {@code NDArray}.
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* </p>
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*
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* @author Curtis Rueden
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*/
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@SuppressWarnings("rawtypes")
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@Plugin(type = Converter.class)
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public class RAIToNDArrayConverter
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extends ConciseConverter<RandomAccessibleInterval, NDArray>
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{
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public RAIToNDArrayConverter() {
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//noinspection unchecked
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super(RandomAccessibleInterval.class, NDArray.class,
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RAIToNDArrayConverter::doConvert);
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}
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63+
private static <T extends NativeType<T>> NDArray doConvert(
64+
final RandomAccessibleInterval<T> rai)
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{
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return NDArrays.asNDArray(rai);
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}
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}

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