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initial clijx version independent from clij2
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‎.gitignore

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/target/
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/.idea/
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*.iml
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CLIJ*.txt

‎README.md

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# CLIJx is the incubator for CLIJ2
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This repository contains experimental / advanced filters based on [CLIJ](https://clij.github.io).
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Methods which turn out to be useful will become part of CLIJ 2.0.
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Right now, this is very preliminary.
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## Installation intructions
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Download Fiji and activate the `clij` update site as described [here](https://clij.github.io/clij-docs/installationInFiji).
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Furthermore, add another update site `clij2` with the url `https://sites.imagej.net/clij2/`;
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Update Fiji and restart it.
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## CLIJx reference
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The current API reference of CLIJx is available [here](https://clij.github.io/clij-advanced-filters/reference). Please note that both: The CLIJx gateway and the API are under heavy construction and can change at any point. See the [release notes](https://github.com/clij/clij-advanced-filters/releases) in case one of your experimental workflows breaks.
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## Code examples
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Have a look in the [macros](https://github.com/clij/clij-advanced-filters/tree/master/src/main/macro) folder.
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Read more on the [CLIJ Website](https://clij.github.io).
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‎_config.yml

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title: clij-advanced-filters
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logo: /images/clij2_logo.png
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description: CLIJ2 (experimental)
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show_downloads: false
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google_analytics:
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theme: jekyll-theme-minimal
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plugins:
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- jekyll-redirect-from

‎license.txt

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Copyright 2019 Robert Haase, Deborah Schmidt, Uwe Schmidt, Martin Weigert, Peter Haub, Fabrice P. Cordelières
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Max Planck Institute for Molecular Cell Biology
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and Genetics Dresden, University of Virginia
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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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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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3. Neither the name of the copyright holder nor the names of its contributors
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may be used to endorse or promote products derived from this software without
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specific prior written permission.
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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.

‎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"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
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http://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>net.haesleinhuepf</groupId>
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<artifactId>clij-parent-pom</artifactId>
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<version>1.4.6</version>
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<relativePath />
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</parent>
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<groupId>net.haesleinhuepf</groupId>
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<artifactId>clijx_</artifactId>
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<version>0.24.0</version>
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<name>clijx_</name>
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<description>clijx</description>
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<url>http://haesleinhuepf.net</url>
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<inceptionYear>2019</inceptionYear>
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<organization>
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<name>MPI CBG</name>
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<url>http://www.mpi-cbg.de</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>haesleinhuepf</id>
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<name>Robert Haase`</name>
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<url>http://haesleinhuepf.net</url>
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<organization>MPI CBG</organization>
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<roles>
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<role>developer</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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<contributor>
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<name>Peter Haub</name>
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<properties><id>iwbh15</id></properties>
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</contributor>
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<contributor>
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<name>Ruth Whelan-Jeans</name>
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<properties><id>ruthwj</id></properties>
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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>ImageSc Forum</name>
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<archive>http://forum.image.sc/</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/clij/clij</connection>
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<developerConnection>scm:git:[email protected]/clij/clij</developerConnection>
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<tag>HEAD</tag>
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<url>https://github.com/clij/clij</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/clij/clij/issues</url>
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</issueManagement>
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<ciManagement>
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<system>None</system>
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</ciManagement>
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<properties>
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<package-name>net.haesleinhuepf</package-name>
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<license.licenseName>bsd_3</license.licenseName>
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<license.copyrightOwners>Robert Haase, MPI CBG</license.copyrightOwners>
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<imagej.app.directory>C:/programs/fiji-win64/Fiji.app/</imagej.app.directory>
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<!--<imagej.app.directory>/home/rhaase/programs/fiji/Fiji.app/</imagej.app.directory>-->
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</properties>
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<dependencies>
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<dependency>
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<groupId>net.haesleinhuepf</groupId>
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<artifactId>clij_</artifactId>
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</dependency>
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<dependency>
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<groupId>net.clearcontrol</groupId>
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<artifactId>clij-clearcl</artifactId>
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</dependency>
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<dependency>
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<groupId>net.haesleinhuepf</groupId>
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<artifactId>clij2_</artifactId>
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</dependency>
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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>
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<repositories>
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<repository>
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<id>clij</id>
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<url>http://dl.bintray.com/haesleinhuepf/clij</url>
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</repository>
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</repositories>
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<distributionManagement>
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<repository>
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<id>bintray-haesleinhuepf-snapshots</id>
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<name>bintray-snapshots</name>
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<url>https://api.bintray.com/maven/haesleinhuepf/clij/clij-advanced-filters/;publish=1</url>
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</repository>
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</distributionManagement>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-plugin</artifactId>
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<version>2.4.1</version>
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<configuration>
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<argLine>-Xmx2G</argLine>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>

‎src/main/java/net/haesleinhuepf/clijx/CLIJx.java

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package net.haesleinhuepf.clijx;
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import net.haesleinhuepf.clij.CLIJ;
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import net.haesleinhuepf.clij2.CLIJ2;
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import net.haesleinhuepf.clijx.utilities.CLIJxOps;
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/**
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* The CLIJx gateway
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*/
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public class CLIJx extends CLIJ2 implements CLIJxOps {
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private static CLIJx instance;
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public CLIJx getCLIJx() {
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return this;
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}
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/**
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* Marking this as deprecated as it will very likely go away before release.
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* Use CLIJx.getInstance() instead.
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* @param clij
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*/
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@Deprecated
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public CLIJx(CLIJ clij) {
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super(clij);
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}
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public static CLIJx getInstance() {
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CLIJ clij = CLIJ.getInstance();
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if (instance == null || instance.clij != CLIJ.getInstance()) {
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instance = new CLIJx(clij);
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}
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return instance;
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}
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public static CLIJx getInstance(String id) {
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CLIJ clij = CLIJ.getInstance(id);
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if (instance == null || instance.clij != clij) {
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instance = new CLIJx(clij);
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}
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return instance;
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}
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public CLIJx __enter__() {
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clear();
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return this;
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}
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/Absolute.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_absolute")
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public class Absolute extends net.haesleinhuepf.clij2.plugins.Absolute {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/AddImageAndScalar.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_addImageAndScalar")
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public class AddImageAndScalar extends net.haesleinhuepf.clij2.plugins.AddImageAndScalar {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/AddImages.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_addImages")
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public class AddImages extends net.haesleinhuepf.clij2.plugins.AddImages {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/AddImagesWeighted.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_addImagesWeighted")
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public class AddImagesWeighted extends net.haesleinhuepf.clij2.plugins.AddImagesWeighted {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/AffineTransform.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_affineTransform")
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public class AffineTransform extends net.haesleinhuepf.clij2.plugins.AffineTransform {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/AffineTransform2D.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_affineTransform2D")
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public class AffineTransform2D extends net.haesleinhuepf.clij2.plugins.AffineTransform2D {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/AffineTransform3D.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_affineTransform3D")
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public class AffineTransform3D extends net.haesleinhuepf.clij2.plugins.AffineTransform3D {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/ApplyVectorField2D.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_applyVectorField2D")
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public class ApplyVectorField2D extends net.haesleinhuepf.clij2.plugins.ApplyVectorField2D {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/ApplyVectorField3D.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_applyVectorField3D")
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public class ApplyVectorField3D extends net.haesleinhuepf.clij2.plugins.ApplyVectorField3D {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/ArgMaximumZProjection.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_argMaximumZProjection")
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public class ArgMaximumZProjection extends net.haesleinhuepf.clij2.plugins.ArgMaximumZProjection {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/AutomaticThreshold.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_automaticThreshold")
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public class AutomaticThreshold extends net.haesleinhuepf.clij2.plugins.AutomaticThreshold {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/AverageDistanceOfNClosestPoints.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_averageDistanceOfNClosestPoints")
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public class AverageDistanceOfNClosestPoints extends net.haesleinhuepf.clij2.plugins.AverageDistanceOfNClosestPoints {
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}

‎src/main/java/net/haesleinhuepf/clijx/clij2wrappers/AverageDistanceOfTouchingNeighbors.java

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package net.haesleinhuepf.clijx.clij2wrappers;
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import net.haesleinhuepf.clij.macro.CLIJMacroPlugin;
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import org.scijava.plugin.Plugin;
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// this is generated code. See src/test/net.haesleinhuepf.clijx.codegenerator.CLIJ2WrapperGenerator for details.
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@Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_averageDistanceOfTouchingNeighbors")
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public class AverageDistanceOfTouchingNeighbors extends net.haesleinhuepf.clij2.plugins.AverageDistanceOfTouchingNeighbors {
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}

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