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Create module imagej2-legacy
This module will house components integrating SciJava3 with ImageJ2
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‎imagej/imagej2-legacy/LICENSE.txt‎

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Copyright (c) 2016 - 2022, ImageJ2 developers.
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All rights reserved.
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Redistribution and use in source and binary forms, with or without modification,
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are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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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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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 HOLDER 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.

‎imagej/imagej2-legacy/README.md‎

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# ImageJ2 Legacy: An interface between SciJava 3 and ImageJ2
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This library provides a bridge between SciJava 3 and ImageJ2.
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For Maven projects, this library can be used by adding to your `pom.xml`:
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```java
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<dependency>
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<groupId>net.imagej</groupId>
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<artifactId>imagej2-legacy</artifactId>
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<version>0-SNAPSHOT</version>
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</dependency>
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```

‎imagej/imagej2-legacy/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-incubator</artifactId>
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<version>0-SNAPSHOT</version>
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<relativePath>../..</relativePath>
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</parent>
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<groupId>net.imagej</groupId>
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<artifactId>imagej2-legacy</artifactId>
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<name>ImageJ2 Legacy</name>
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<description>An interface between SciJava 3 and ImageJ2.</description>
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<url>https://github.com/scijava/scijava</url>
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<inceptionYear>2023</inceptionYear>
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<organization>
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<name>ImageJ</name>
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<url>https://imagej.net/</url>
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</organization>
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<licenses>
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<license>
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<name>Simplified BSD License</name>
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<distribution>repo</distribution>
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</license>
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</licenses>
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<developers>
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<developer>
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<id>ctrueden</id>
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<name>Curtis Rueden</name>
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<url>https://imagej.net/people/ctrueden</url>
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<roles>
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<role>founder</role>
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<role>debugger</role>
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<role>reviewer</role>
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<role>maintainer</role>
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</roles>
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</developer>
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<developer>
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<id>gselzer</id>
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<name>Gabriel Selzer</name>
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<url>https://imagej.net/people/gselzer</url>
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<roles>
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<role>founder</role>
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<role>debugger</role>
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<role>reviewer</role>
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<role>maintainer</role>
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</roles>
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</developer>
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</developers>
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<contributors>
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<!--
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NB: Need at least one element to override the parent.
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See: https://issues.apache.org/jira/browse/MNG-5220
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-->
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<contributor>
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<name>None</name>
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</contributor>
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</contributors>
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<mailingLists>
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<mailingList>
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<name>Image.sc Forum</name>
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<archive>https://forum.image.sc/tag/imagej2</archive>
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</mailingList>
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</mailingLists>
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<scm>
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<connection>scm:git:git://github.com/scijava/incubator</connection>
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<developerConnection>scm:git:git@github.com:scijava/incubator</developerConnection>
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<tag>HEAD</tag>
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<url>https://github.com/scijava/incubator</url>
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</scm>
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<issueManagement>
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<system>GitHub Issues</system>
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<url>https://github.com/imagej/imagej-ops2/issues</url>
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</issueManagement>
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<ciManagement>
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<system>GitHub Actions</system>
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<url>https://github.com/scijava/incubator/actions</url>
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</ciManagement>
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<properties>
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<package-name>net.imagej.legacy2</package-name>
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<license.licenseName>bsd_2</license.licenseName>
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<license.copyrightOwners>ImageJ2 developers.</license.copyrightOwners>
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<license.projectName>ImageJ2 software for multidimensional image processing and analysis.</license.projectName>
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<!-- NB: Deploy releases to the SciJava Maven repository. -->
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<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
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</properties>
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<repositories>
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<repository>
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<id>scijava.public</id>
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<url>https://maven.scijava.org/content/groups/public</url>
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</repository>
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<repository>
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<id>imagej.snapshots</id>
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<url>https://maven.scijava.org/content/groups/snapshots</url>
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</repository>
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</repositories>
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<dependencies>
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<!-- ImageJ2 dependencies -->
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<dependency>
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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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<!-- SciJava dependencies -->
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-collections</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-priority</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-types</artifactId>
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<version>${project.version}</version>
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</dependency>
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<!-- ImgLib2 dependencies -->
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<dependency>
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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>org.apache.commons</groupId>
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<artifactId>commons-math3</artifactId>
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</dependency>
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<!-- Test scope dependencies -->
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-api</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-engine</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>net.imglib2</groupId>
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<artifactId>imglib2-roi</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-testutil</artifactId>
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<version>${project.version}</version>
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<scope>test</scope>
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</dependency>
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</dependencies>
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</project>

‎imagej/imagej2-legacy/src/main/java/module-info.java‎

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import net.imagej2.legacy.types.DatasetTypeExtractor;
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/*-
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* #%L
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* ImageJ2 software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2022 ImageJ2 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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module net.imagej2.legacy {
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requires net.imagej;
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requires org.scijava.types;
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requires org.scijava.priority;
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provides org.scijava.types.TypeExtractor with net.imagej2.legacy.types.DatasetTypeExtractor;
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}

‎imagej/imagej2-legacy/src/main/java/net/imagej2/legacy/types/DatasetTypeExtractor.java‎

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package net.imagej2.legacy.types;
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import java.lang.reflect.Type;
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import org.scijava.priority.Priority;
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import org.scijava.types.TypeExtractor;
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import org.scijava.types.TypeReifier;
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import net.imagej.Dataset;
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public class DatasetTypeExtractor implements TypeExtractor {
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@Override
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public double getPriority() {
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return Priority.HIGH;
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}
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@Override
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public boolean canReify(TypeReifier r, Class<?> object) {
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return Dataset.class.isAssignableFrom(object);
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}
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@Override public Type reify(TypeReifier r, Object object) {
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if (!(object instanceof Dataset)) throw new IllegalArgumentException(object + " cannot be reified because it is not a Dataset!");
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return r.reify(((Dataset) object).getImgPlus());
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}
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}

‎imagej/imagej2-legacy/src/test/java/net/imagej2/legacy/types/DatasetTypeExtractorTest.java‎

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package net.imagej2.legacy.types;
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import java.lang.reflect.Type;
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import java.util.ServiceLoader;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.Test;
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import org.scijava.Context;
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import org.scijava.discovery.Discoverer;
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import org.scijava.log2.StderrLoggerFactory;
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import org.scijava.types.Any;
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import org.scijava.types.DefaultTypeReifier;
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import org.scijava.types.Types;
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import net.imagej.DefaultDataset;
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import net.imagej.ImgPlus;
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import net.imglib2.img.array.ArrayImgs;
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/**
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* Tests {@link DatasetTypeExtractor}
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*
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* @author Gabriel Selzer
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*/
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public class DatasetTypeExtractorTest {
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@Test
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public void testDatasetTypeExtractor() {
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// Create a TypeReifier
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var log = new StderrLoggerFactory().create();
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var reifier = new DefaultTypeReifier(log, Discoverer.all(
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ServiceLoader::load));
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// Create a Dataset
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var ctx = new Context();
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var img = ArrayImgs.unsignedBytes(10, 10);
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var imgPlus = new ImgPlus<>(img);
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var ds = new DefaultDataset(ctx, imgPlus);
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// Assert correct reification
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// NB without a dependency on imagej-ops2 we cannot reify
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// the ImgPlus, but asserting an ImgPlus is the reified type
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// is enough to unit test the TypeExtractor
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var actual = new DatasetTypeExtractor().reify(reifier, ds);
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var expected = Types.parameterize(ImgPlus.class, new Type[] { new Any() });
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Assertions.assertEquals(expected, actual);
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}
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}

‎pom.xml‎

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<module>imagej/imagej-mesh2</module>
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<module>imagej/imagej-ops2</module>
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<module>imagej/imagej-testutil</module>
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<module>imagej/imagej2-legacy</module>
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<module>scijava/scijava-collections</module>
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<module>scijava/scijava-common3</module>
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<module>scijava/scijava-discovery</module>

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