Developing ImageJ2 in IntelliJ IDEA

<!DOCTYPE html> <html> <head> <title>Developing ImageJ2 in IntelliJ IDEA</title> <meta charset="utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=3" /> <meta content="ImageJ Wiki" property="og:site_name"> <meta content="Developing ImageJ2 in IntelliJ IDEA" property="og:title"> <meta content="article" property="og:type"> <meta content="The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants, including ImageJ2, Fiji, and others." property="og:description"> <meta content="https://imagej.github.io/develop/intellij" property="og:url"> <meta content="https://imagej.github.io/media/icons/imagej2.png" property="og:image"> <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png"> <link rel="icon" type="image/png" sizes="32x32" href="/favicon-32x32.png"> <link rel="icon" type="image/png" 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class="sidebar dock">   <div id="toc" class="toc menu dockable"> <div class="drag-handle"></div> <h3>Page contents</h3> <ul data-toc="#content" data-toc-headings="h1,h2,h3,h4,h5,h6"></ul> </div> </section>  <div class="container"> <header class="major special"> <a class="project-icon shadowed-box" href="/software/imagej2"><span class="tooltip"><img src="/media/icons/imagej2.png"><span class="tooltiptext" style="top: 80%; left: 25%; width: 20em">This page describes content relating to the ImageJ2 platform. Click the logo for details.</span></span></a> <h1>Developing ImageJ2 in IntelliJ IDEA</h1> <span class="project-counterweight"> </span> </header> </div>   <section id="page" class="main style1"> <div class="container"> <div class="box alt"></div> <div id="content" class="page-content"> <div class="notice" style="font-size: 2; background: #ebf2f8; border-left: 10px solid #67a1fe"><div class="notice-icon"><img src="/media/icons/info.svg" width="32"></div><div class="notice-content"><p>The content of this page has not been vetted since shifting away from MediaWiki. If you’d like to help, check out the <a href="/events/wiki-grand-opening/how-to-help">how to help guide</a>!</p> </div> </div> <p>This article explains how to install and configure IntelliJ IDEA for use with <a href="/software/imagej2">ImageJ2</a> development. Directions correspond to IntelliJ IDEA 11.1, and may need adjustment for other versions.</p> <h2 id="install-and-configure-idea">Install and configure IDEA</h2> <ul> <li> <p><strong>Install OpenJDK.</strong> Download and install <a href="https://www.azul.com/downloads/?package=jdk">OpenJDK</a>. Or install it via a package manager, if possible.</p> </li> <li> <p><strong>Install IDEA.</strong> Download and install IDEA from the <a href="http://www.jetbrains.com/idea/download/">IDEA website</a>.</p> </li> </ul> <h2 id="import-the-imagej2-source">Import the ImageJ2 source</h2> <ol> <li>From the IDEA menu, choose <span class="bc"><span>Version Control</span> › <span>Checkout from Version Control</span> › <span>Git</span></span></li> <li>For the Git Repository URL, enter: <a href="git://github.com/imagej/imagej2"><code class="language-plaintext highlighter-rouge">git://github.com/imagej/imagej</code></a></li> <li>Specify a Parent Directory, click Clone, and wait</li> <li>When prompted, click Yes to create an IntelliJ IDEA project from the sources</li> </ol> <p>On some platforms, the first time you perform this procedure, you may be prompted to select the project JDK:</p> <ol> <li>Click the plus sign and choose “JSDK”</li> <li>Navigate to the directory containing your JDK installation</li> </ol> <h2 id="launch-the-program">Launch the program</h2> <ol> <li>Choose <span class="bc"><span>Run</span> › <span>Edit Configurations</span></span> from the menu</li> <li>Click the Plus icon and choose Application</li> <li>In the Name field, type ImageJ2</li> <li>Type “net.imagej.Main” for the Main class</li> <li>For “Use classpath and JDK of module” select “imagej2” from the list</li> <li>Click OK</li> <li>Choose <span class="bc"><span>Run</span> › <span>Run ImageJ2</span></span> from the menu</li> </ol> <p>The project automatically builds before launching, so it may take a little while the first time.</p> <h2 id="code-style-profiles">Code style profiles</h2> <p>This section is a short guide on how to start using the Eclipse code style profile of ImageJ2.</p> <h3 id="installing-eclipse-code-formatter-plugin">Installing Eclipse code formatter plugin</h3> <p>The first step is to install the Eclipse code formatter (ECF) plugin to your IntelliJ:</p> <ol> <li>Open <span class="bc"><span>File</span> › <span>Settings</span></span></li> <li>Select <em>Plugins</em> from the left-hand pane</li> <li>Click <em>Browse repositories…</em></li> <li>Type <em>Eclipse code formatter</em> to the search field</li> <li>Select the plugin from the list and click <em>install</em> on the right-hand pane</li> <li>Click <em>Restart IntelliJ</em></li> </ol> <p>A tutorial on IntelliJ plugins can be found <a href="https://www.jetbrains.com/help/idea/2016.2/installing-updating-and-uninstalling-repository-plugins.html">here</a>.</p> <h3 id="plugin-setup">Plugin setup</h3> <p>After installing the ECF plugin you need to set it to use the Eclipse code styles file of the ImageJ project:</p> <ol> <li>Download <a href="https://github.com/scijava/scijava-coding-style/blob/-/preferences.epf">eclipse-preferences.epf</a></li> <li>Open Eclipse and follow <a href="http://help.eclipse.org/luna/index.jsp?topic=%2Forg.eclipse.platform.doc.user%2Ftasks%2Ftimpandexp.htm">these</a> steps to import an <code class="language-plaintext highlighter-rouge">.epf</code> file</li> <li>Open <span class="bc"><span>Window</span> › <span>Preferences</span> › <span>Java</span> › <span>Code Style</span> › <span>Formatter</span></span></li> <li>Set <em>Active Profile</em> to <em>ImageJ</em></li> <li>Click <em>Export All…</em> and save the XML file</li> <li>Open IntelliJ</li> <li>Open your project</li> <li>Open <span class="bc"><span>File</span> › <span>Settings</span> › <span>Eclipse Code Formatter</span></span></li> <li>Check the <em>Use the Eclipse code formatter</em> radio button</li> <li>Set <em>Eclipse Java Formatter config file</em> to the XML file you just created</li> <li>Set <em>Java formatter profile</em> to <em>ImageJ</em></li> <li>Check <em>Optimize Imports</em></li> <li>Set <em>Import order</em> to <em>Manual configuration</em> and write <code class="language-plaintext highlighter-rouge">com;io;java;javax;net;org;</code></li> </ol> <p><strong>NB</strong> You can skip the first five steps if you use <a href="https://github.com/imagej/imagej2/blob/bcb4eddf41e90ffba6d520b83e691d3a02d65739/config/eclipse-code-clean-up-profile.xml">this XML file</a>. But note that it is old and possibly out of date.</p> <p>More information on setting up the ECF plugin can be found <a href="https://github.com/krasa/EclipseCodeFormatter#instructions">here</a>.</p> <h2 id="troubleshooting">Troubleshooting</h2> <h3 id="renaming-scijava-plugin-annotated-classes">Renaming SciJava <code class="language-plaintext highlighter-rouge">@Plugin</code> annotated classes</h3> <p>When renaming a classname which was annotated with SciJava’s <code class="language-plaintext highlighter-rouge">@Plugin</code> annotation, an error may occur during launch of the application looking like:</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>[ERROR] Exception during event handling: [Event] org.scijava.module.event.ModulesUpdatedEvent context = org.scijava.Context@1a05aced consumed = false items[0] = label='About ImageJ...', iconPath='/icons/commands/information.png', priority=0.0, enabled=true, pluginType=Command items[1] = label='Preferences', priority=0.0, enabled=true, pluginType=Command items[2] = label='Quit', iconPath='/icons/commands/door_in.png', priority=0.0, enabled=true, pluginType=Command [Subscriber] org.scijava.menu.DefaultMenuService [priority = 0.0] [Method] protected void org.scijava.menu.DefaultMenuService.onEvent(org.scijava.module.event.ModulesUpdatedEvent) java.lang.IllegalStateException: Can't overwrite cause with org.scijava.InstantiableException: Class not found: the.plugin.you.just.Renamed </code></pre></div></div> <p>The error may be related to some caching mechanism in the IDE. 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