Scripting

<!DOCTYPE html> <html> <head> <title>Scripting</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="Scripting" 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/scripting/index" 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" sizes="16x16" href="/favicon-16x16.png"> <link 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</ul></details></li>  <li><details open><summary><a class="current-page">Scripting</a></summary><ul> <li><a href="/scripting/basics">Scripting Basics</a></li> <li><a href="/scripting/script-editor">Script Editor</a></li> <li><a href="/scripting/parameters">Parameters</a></li> <li><a href="/scripting/user-input">User Input</a></li> <li><a href="/scripting/auto-imports">Auto Import</a></li> <li><a href="/scripting/templates">Templates</a></li> <li><a href="/scripting/batch">Batch Processing</a></li> <li><a href="/scripting/headless">Running Headlessly</a></li> <li><a href="/scripting/comparisons">Scripting Comparisons</a></li> <li><a href="/scripting/toolbox">Toolbox</a></li> <li><details><summary>Languages</summary><ul> <li><a href="/scripting/beanshell">BeanShell Scripting</a></li> <li><a href="/scripting/groovy">Groovy Scripting</a></li> <li><a href="/scripting/macro">ImageJ Macro</a></li> <li><a href="/scripting/javascript">JavaScript</a></li> <li><a href="/scripting/clojure">Lisp 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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>Scripting</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鈥檇 like to help, check out the <a href="/events/wiki-grand-opening/how-to-help">how to help guide</a>!</p> </div> </div> <p>ImageJ2 allows you to write scripts in several different languages.</p> <h1 id="getting-started">Getting started</h1> <ul> <li>Read the <a href="/tutorials/notebooks">ImageJ2 tutorial notebooks</a> to learn how to write scripts.</li> <li>Press the <kbd class="key">[</kbd> key to open the <a href="/scripting/script-editor">Script Editor</a> (or <kbd class="key">⇧ Shift</kbd>-<kbd class="key">[</kbd> to open the <a href="/scripting/interpreter">Script Interpreter</a>).</li> <li>Optionally, choose a template from the <span class="bc"><span>Templates</span></span> menu to get you started.</li> <li>Otherwise, choose your language from the <span class="bc"><span>Language</span></span> menu.</li> <li>Grab code snippets for common tasks from the <a href="/scripting/toolbox">Scripting toolbox</a>.</li> <li>See <a href="/scripting/comparisons">Scripting comparisons</a> for a side-by-side comparison of scripting languages.</li> </ul> <h1 id="supported-languages">Supported languages</h1> <p>ImageJ2鈥檚 <a href="/scripting/script-editor">Script Editor</a> supports many different languages. The following table summarizes the possibilities.</p> <table> <tbody> <tr> <td colspan=2>Recommended options</td> </tr> <tr> <td><a href="/scripting/groovy">Groovy</a></td> <td> <a href="https://en.wikipedia.org/wiki/Groovy_(programming_language)">Groovy</a> is a flexible and powerful scripting language, Java-like but less verbose and dynamically typed. Learn this, and using Java later (if needed) will become easier. </td> </tr> <tr> <td style="white-space: nowrap"><a href="/scripting/macro">ImageJ Macro</a></td> <td> The <a href="/software/imagej">ImageJ</a> macro language is less powerful than the other scripting languages, but is designed to be easy to learn and use. </td> </tr> <tr> <td><a href="/scripting/python">Python</a></td> <td> <a href="https://en.wikipedia.org/wiki/Python_(programming_language)">Python</a> is a popular choice among scientists. You can write [Jython scripts](/scripting/jython) (a Java-based Python 2 dialect) from inside ImageJ using its [script editor](/scripting/script-editor), or use [PyImageJ](/scripting/pyimagej) to invoke ImageJ functions from Python scripts. </td> </tr> <tr> <td><a href="/scripting/javascript">JavaScript</a></td> <td> <a href="https://en.wikipedia.org/wiki/JavaScript">JavaScript</a> is a popular choice among web developers. </td> </tr> <tr> <td style="white-space: nowrap"><a href="/scripting/jruby">Ruby (JRuby)</a></td> <td> <a href="https://en.wikipedia.org/wiki/Ruby_(programming_language)">Ruby</a> is another popular choice among web developers. </td> </tr> <tr> <td style="white-space: nowrap"><a href="/scripting/clojure">Lisp (Clojure)</a></td> <td> <a href="https://en.wikipedia.org/wiki/Lisp_(programming_language)">Lisp</a> is a popular choice among computer scientists. </td> </tr> <tr> <td style="white-space: nowrap"><a href="/scripting/renjin">R (Renjin)</a></td> <td> <a href="https://en.wikipedia.org/wiki/R_(programming_language)">R</a> is a popular choice among scientists and statisticians. </td> </tr> <tr> <td colspan=2>Other options</td> </tr> <tr> <td><a href="/develop/plugins">Java</a></td> <td> You can code Java plugins in the Script Editor. This is the most difficult path, but also the most powerful. </td> </tr> <tr> <td><a href="/scripting/matlab">MATLAB</a></td> <td> ImageJ2 can interface bidirectionally with MATLAB. See the <a href="/scripting/matlab">MATLAB Scripting</a> page for details. </td> </tr> <tr> <td><a href="/scripting/beanshell">BeanShell</a></td> <td> <a href="https://en.wikipedia.org/wiki/BeanShell">BeanShell</a> is an old script language, maintained mostly for backwards compatibility. It is nearly 100% compatible with Java syntax, but so is <a href="/scripting/groovy">Groovy</a>. </td> </tr> <tr> <td><a href="/scripting/scala">Scala</a></td> <td> <a href="https://en.wikipedia.org/wiki/Scala_(programming_language)">Scala</a> support is currently experimental, and has bugs. </td> </tr> </tbody> </table> <h1 id="script-parameters">Script parameters</h1> <p>There is a universal script parameter notation available across all scripts for declaring inputs and outputs. This approach is preferred to using <code class="language-plaintext highlighter-rouge">GenericDialog</code> because it is totally agnostic to the user interface, allowing such scripts to run in a variety of contexts.</p> <p>See the <a href="/scripting/parameters">script parameters</a> page for details.</p> <h1 id="using-an-interpreter">Using an interpreter</h1> <p>All scripting languages use the same basic interpreter, with the following common features.</p> <h2 id="general-key-bindings">General key bindings</h2> <ul> <li><kbd class="key">↑ Up</kbd>: bring the previously typed command.</li> <li><kbd class="key">↓ Down</kbd>: bring the next typed command.</li> <li><kbd class="key">&crarr; Enter</kbd>: execute the contents of the prompt.</li> </ul> <h2 id="multiline-editing-and-keybindings">Multiline editing and keybindings</h2> <p>You can enlarge the prompt by dragging the middle bar.</p> <ul> <li><kbd class="key">⇧ Shift</kbd>聽+聽<kbd class="key">&crarr; Enter</kbd>: create a new line within the prompt.</li> <li><kbd class="key">⇧ Shift</kbd>聽+聽<kbd class="key">↑ Up</kbd>: move to the line above within the prompt.</li> <li><kbd class="key">⇧ Shift</kbd>聽+聽<kbd class="key">↓ Down</kbd>: move to the line below within the prompt.</li> </ul> <h2 id="selecting-and-executing-text-from-the-screen">Selecting and executing text from the screen</h2> <p>On selecting text, a popup offers to:</p> <ul> <li>copy</li> <li>execute</li> <li>save to a new file</li> </ul> <h1 id="using-the-script-editor">Using the script editor</h1> <p>You can create, edit and run scripts using the built-in <a href="/scripting/script-editor">Script Editor</a>. For details, please see <a href="/scripting/script-editor">the Script Editor documentation</a>.</p> <h1 id="adding-scripts-to-the-plugins-menu">Adding scripts to the Plugins menu</h1> <p>For the script to appear in the menus, the following must apply:</p> <div class="notice" style="font-size: 2; background: #ffcccb; border-left: 10px solid #f57900"><div class="notice-icon"><img src="/media/icons/warning.png" /></div><div class="notice-content"><p><code class="language-plaintext highlighter-rouge">.txt</code> is not a supported script extension</p> </div> </div> <ol> <li>The script file is saved in the <code class="language-plaintext highlighter-rouge">ImageJ2.app/scripts</code> or the <code class="language-plaintext highlighter-rouge">ImageJ2.app/plugins/Scripts</code> directory (or a subdirectory thereof).</li> <li>The script name ends in a supported script extension. For example: <ul> <li><code class="language-plaintext highlighter-rouge">.groovy</code> for groovy,</li> <li><code class="language-plaintext highlighter-rouge">.js</code> for javascript,</li> <li><code class="language-plaintext highlighter-rouge">.py</code> for jython,</li> <li><code class="language-plaintext highlighter-rouge">.rb</code> for jruby,</li> <li><code class="language-plaintext highlighter-rouge">.clj</code> for clojure,</li> <li><code class="language-plaintext highlighter-rouge">.bsh</code> for beanshell, and</li> <li><code class="language-plaintext highlighter-rouge">.ijm</code> for ImageJ 1.x macros.</li> </ul> </li> <li>The script name contains a <code class="language-plaintext highlighter-rouge">_</code> (underscore) character, e.g. <code class="language-plaintext highlighter-rouge">MyScript_.ijm</code>.</li> </ol> <div class="notice" style="font-size: 2; background: #e6e6e6; border-left: 10px solid #65a4e3"><div class="notice-icon"><img src="/media/icons/fiji.svg" width="32" /></div><div class="notice-content"><p>Fiji users: replace <code class="language-plaintext highlighter-rouge">ImageJ2.app</code> with <code class="language-plaintext highlighter-rouge">Fiji.app</code></p> </div> </div> <p>The extension will be stripped and any underscores will be turned into spaces before the script is added to the menus.</p> <p>Scripts in the top-level <code class="language-plaintext highlighter-rouge">ImageJ2.app/plugins</code> directory will appear at the bottom of the <em>Plugins</em> menu. Scripts can be placed in other menus by nesting subdirectories, for example placing a script in the <code class="language-plaintext highlighter-rouge">ImageJ2.app/scripts/File</code> directory will add it to the <span class="bc"><span>File</span></span> menu.</p> <p>If you aren鈥檛 able to find your script, you can always use the <a href="/learn#the-search-bar">search bar</a> to verify its location (or absence).</p> <p>Commands added to the menu in the described way can be called from other scripts. Use the <a href="/scripting/macro#the-recorder">macro recorder</a> to get the required code for doing so.</p> <h2 id="adding-jar-packaged-scripts-to-the-menu">Adding JAR-packaged scripts to the menu</h2> <p>Scripts can be packaged in a JAR file for easier distribution to your colleagues and via <a href="/update-sites">Update Sites</a>. For this purpose, <a href="https://github.com/imagej/example-script-collection">example-script-collection</a> can be used as the template Maven project.</p> <p>Inside the example-script-collection jar, the scripts are in <code class="language-plaintext highlighter-rouge">./resources/scripts.</code> and therefore get added to the menu when the JAR is on the classpath (i.e. in <code class="language-plaintext highlighter-rouge">./plugins/</code> or <code class="language-plaintext highlighter-rouge">./jars/</code>).</p> <p>ImageJ2 (and therefore Fiji) looks for scripts in subfolders of <code class="language-plaintext highlighter-rouge">./scripts/</code> as it is already described in the previous section, and for jars in <code class="language-plaintext highlighter-rouge">./jars/</code>. The original <a href="/software/imagej">ImageJ</a> recognizes plugins and scripts in <code class="language-plaintext highlighter-rouge">./plugins/</code>.</p> <h1 id="running-scripts-in-headless-mode">Running scripts in headless mode</h1> <p>See the <a href="/scripting/headless">Scripting Headless</a> page for instructions on executing scripts headlessly.</p> </div> </div> </section>  <section id="footer"> <ul class="icons"> <li><a href="https://forum.image.sc/tag/imagej" class="icon alt"><img src="/media/icons/image-sc.png" width="24" style="vertical-align: middle; margin-top: -10px"><span class="label">Forum</span></a></li> <li><a href="https://twitter.com/hashtag/ImageJ" class="icon brands alt fa-twitter"><span class="label">Twitter</span></a></li> <li><a href="https://github.com/imagej" class="icon brands alt fa-github"><span class="label">GitHub</span></a></li> </ul> <ul class="copyright"> <li>Design: <a href="http://html5up.net">HTML5 UP</a></li> </ul> </section>  <nav 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