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shadowed-box" href="/software/fiji"><img src="/media/icons/fiji.svg">This page describes content relating to the Fiji distribution of ImageJ. Click the logo for details.</a> <h1>Scripting toolbox</h1> </header> </div>   <section id="page" class="main style1"> <div class="container"> <div class="box alt"></div> <div id="content" class="page-content"> This page is meant to provide small code snippets as a starting point for writing scripts. <div class="notice" style="font-size: 1; background: #e6e6e6; border-left: 10px solid gold"><div class="notice-content">See also: <ul> <li><a href="/scripting">Scripting overview</a> for a list of available scripting languages.</li> <li><a href="/scripting/comparisons">Scripting comparisons</a> to compare and contrast the languages.</li> <li><a href="/plugins/bar">Broadly Applicable Routines</a>, a curated collection of snippets.</li> <li>Albert Cardona’s comprehensive <a href="http://www.ini.uzh.ch/~acardona/fiji-tutorial/">Fiji Jython tutorial</a> (please note that it is a better idea to contribute tutorials to the ImageJ Wiki directly).</li> </ul> </div> </div> <div class="notice" style="font-size: 2; background: #dedede; border-left: 10px solid #7e7e7e"><div class="notice-icon">💡</div><div class="notice-content">To copy the snippets, mouse over the code and click the Copy button that appears. </div> </div> <h2 id="opening-an-image-using-imagej">Opening an image using ImageJ</h2> <h4 id="macro">Macro</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>path = "/path/to/file"; open(path); </code></pre></div></div> <h4 id="javascript">JavaScript</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>importClass(Packages.ij.IJ); var path = "/path/to/file"; var imp = IJ.openImage(path); imp.show(); </code></pre></div></div> <h4 id="python">Python</h4> <div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code>from ij import IJ path = "/path/to/file" imp = IJ.openImage(path) imp.show() </code></pre></div></div> <h4 id="ruby">Ruby</h4> <div class="language-ruby highlighter-rouge"><div class="highlight"><pre class="highlight"><code>include_class 'ij.IJ' path = "/path/to/file" imp = ij.IJ.openImage(path) imp.show </code></pre></div></div> <h4 id="clojure">Clojure</h4> <div class="language-clojure highlighter-rouge"><div class="highlight"><pre class="highlight"><code>(import 'ij.IJ) (let [path "/path/to/file" imp (IJ/openImage path)] (.show imp)) </code></pre></div></div> <h4 id="beanshell">BeanShell</h4> <pre><code class="language-beanshell">import ij.IJ; path = "/path/to/file"; imp = IJ.openImage(path); imp.show(); </code></pre> <h2 id="opening-an-image-using-bio-formats">Opening an image using Bio-Formats</h2> <h4 id="macro-1">Macro</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>path = "/path/to/file"; run("Bio-Formats Importer", "open=" + path + " autoscale color_mode=Default view=Hyperstack stack_order=XYCZT"); </code></pre></div></div> <h4 id="javascript-1">JavaScript</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>importClass(Packages.loci.plugins.BF); var path = "/path/to/file"; var imps = BF.openImagePlus(path); imps[0].show(); </code></pre></div></div> or, with more options: <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>importClass(Packages.loci.plugins.BF); importClass(Packages['loci.plugins.in.ImporterOptions']); // 'in' is a reserved word, hence the different syntax importClass(Packages.loci.common.Region); var path = "/path/to/file"; var options = new ImporterOptions(); options.setId(path); options.setAutoscale(true); options.setCrop(true); options.setCropRegion(0, new Region(x, y, w. h)); options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE); var imps = BF.openImagePlus(options); imps[0].show(); </code></pre></div></div> <h4 id="python-1">Python</h4> See also <a href="https://gist.github.com/ctrueden/6282856">this python example script</a> <ul> <li> Ruby </li> <li> Clojure </li> <li> BeanShell </li> </ul> <h2 id="opening-processing-and-saving-a-sequence-of-files-in-a-folder">Opening, processing, and saving a sequence of files in a folder</h2> <h4 id="macro-2">Macro</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>input = getDirectory("Input directory"); output = getDirectory("Output directory"); Dialog.create("File type"); Dialog.addString("File suffix: ", ".tif", 5); Dialog.show(); suffix = Dialog.getString(); processFolder(input); function processFolder(input) { list = getFileList(input); for (i = 0; i < list.length; i++) { if(File.isDirectory(list[i])) processFolder("" + input + list[i]); if(endsWith(list[i], suffix)) processFile(input, output, list[i]); } } function processFile(input, output, file) { // do the processing here by replacing // the following two lines by your own code print("Processing: " + input + file); open(input + file); print("Saving to: " + output); saveAs("/formats/tiff", output+file); close(); } </code></pre></div></div> See also the tutorial <a href="/tutorials/apply-operation-to-a-complete-directory">How to apply a common operation to a complete directory</a>. <h4 id="python-2">Python</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>import os from ij import IJ, ImagePlus from ij.gui import GenericDialog def run(): srcDir = IJ.getDirectory("Input_directory") if not srcDir: return dstDir = IJ.getDirectory("Output_directory") if not dstDir: return gd = GenericDialog("Process Folder") gd.addStringField("File_extension", ".tif") gd.addStringField("File_name_contains", "") gd.addCheckbox("Keep directory structure when saving", True) gd.showDialog() if gd.wasCanceled(): return ext = gd.getNextString() containString = gd.getNextString() keepDirectories = gd.getNextBoolean() for root, directories, filenames in os.walk(srcDir): for filename in filenames: # Check for file extension if not filename.endswith(ext): continue # Check for file name pattern if containString not in filename: continue process(srcDir, dstDir, root, filename, keepDirectories) def process(srcDir, dstDir, currentDir, fileName, keepDirectories): print "Processing:" # Opening the image print "Open image file", fileName imp = IJ.openImage(os.path.join(currentDir, fileName)) # Put your processing commands here! # Saving the image saveDir = currentDir.replace(srcDir, dstDir) if keepDirectories else dstDir if not os.path.exists(saveDir): os.makedirs(saveDir) print "Saving to", saveDir IJ.saveAs(imp, "Tiff", os.path.join(saveDir, fileName)); imp.close() run() </code></pre></div></div> <ul> <li> JavaScript </li> <li> Ruby </li> <li> Clojure </li> <li> BeanShell </li> </ul> <h2 id="wait-a-given-amount-of-time-or-until-user-presses-ok">Wait a given amount of time, or until user presses OK</h2> <h4 id="macro-3">Macro</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>wait(100); </code></pre></div></div> or <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>waitForUser(); </code></pre></div></div> <h4 id="javascript-2">JavaScript</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>Thread.sleep(100); </code></pre></div></div> or <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>new WaitForUserDialog("Action required", "Please press OK when done.").show(); </code></pre></div></div> <ul> <li> Python </li> <li> Ruby </li> <li> Clojure </li> <li> BeanShell </li> </ul> <h2 id="select-multiple-rois-from-roi-manager-and-combine-them">Select multiple ROIs from ROI manager and combine them</h2> <h4 id="macro-4">Macro</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>roiManager("select", newArray(0,2,4)); roiManager("AND"); </code></pre></div></div> <h4 id="javascript-3">JavaScript</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>importClass(Packages.ij.plugin.frame.RoiManager); rm = RoiManager.getInstance(); rm.setSelectedIndexes([0,2,4]); rm.runCommand("AND"); </code></pre></div></div> <h4 id="python-3">Python</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>from ij.plugin.frame import RoiManager rm = RoiManager.getInstance() rm.setSelectedIndexes([0, 2, 4]) rm.runCommand("AND") </code></pre></div></div> <h4 id="beanshell-1">BeanShell</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>import ij.plugin.frame.RoiManager; rm = RoiManager.getInstance(); rm.setSelectedIndexes(new int[] { 0, 2, 4}); rm.runCommand("AND"); </code></pre></div></div> <ul> <li> Ruby </li> <li> Clojure </li> </ul> <h2 id="unlocking-an-image">Unlocking an image</h2> Sometimes things go wrong and all you see is “blabla.jpg is locked” when you try to process the image in some way. Then all you can do is to force-unlock the image, like so: <h4 id="beanshell-2">BeanShell</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>IJ.getImage().unlock(); </code></pre></div></div> <h2 id="scripting-sift">Scripting <a href="/plugins/feature-extraction">SIFT</a></h2> The Scale-Invariant Feature Transform poses a relatively powerful way to reduce the complexity when trying to find matching parts of large images. Fiji has an implementation of this algorithm which you can use like so: <h4 id="beanshell-3">BeanShell</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>import java.util.ArrayList; import mpicbg.ij.SIFT; import mpicbg.imagefeatures.Feature; import mpicbg.imagefeatures.FloatArray2DSIFT; param = new FloatArray2DSIFT.Param(); sift = new SIFT(new FloatArray2DSIFT(param)); features = new ArrayList(); // ''ip'' refers to an ImageProcessor sift.extractFeatures(ip, features); // print coordinates for (Feature feature : features) print("x: " + feature.location[0] + ", y: " + feature.location[1]); </code></pre></div></div> For more information, please browse the <a href="http://javadoc.imagej.net/MPI-CBG/index.html?mpicbg/imagefeatures/Feature.html">Javadoc of the Feature class</a>. <h2 id="plotting-charts-with-jfreechart">Plotting charts with JFreeChart</h2> <a href="http://www.jfree.org/jfreechart/">JFreeChart</a> is a Java library for creating various charts. You can create charts as interactive JFrames, display them as an ImagePlus, or write them to SVG format. <h4 id="javascript-4">JavaScript</h4> <div class="language-javascript highlighter-rouge"><div class="highlight"><pre class="highlight"><code>/* JavaScript to test JFreeChart functionality */ importPackage(Packages.org.jfree.chart); importPackage(Packages.org.jfree.chart.plot); importPackage(Packages.org.jfree.chart.axis); importPackage(Packages.org.jfree.chart.encoders); importPackage(Packages.org.jfree.chart.renderer.category); importPackage(Packages.java.awt); importPackage(Packages.java.awt.geom); importPackage(Packages.java.io); importPackage(Packages.org.jfree.ui); importPackage(Packages.org.jfree.data.category); importPackage(Packages.org.jfree.data.statistics); importPackage(Packages.org.apache.batik.dom); importPackage(Packages.org.apache.batik.svggen); var dataset = new DefaultStatisticalCategoryDataset(); // dataset.add(Mean, StdDev, "Series", "Condition") dataset.add(15.0, 2.4, "Row 1", "Column 1"); dataset.add(15.0, 4.4, "Row 1", "Column 2"); dataset.add(13.0, 2.1, "Row 1", "Column 3"); dataset.add(7.0, 1.3, "Row 1", "Column 4"); dataset.add(2.0, 2.4, "Row 2", "Column 1"); dataset.add(18.0, 4.4, "Row 2", "Column 2"); dataset.add(28.0, 2.1, "Row 2", "Column 3"); dataset.add(17.0, 1.3, "Row 2", "Column 4"); var chart = ChartFactory.createLineChart( null, // chart title "Treatment", // domain axis label "Measurement", // range axis label dataset, // data PlotOrientation.VERTICAL, // orientation false, // include legend true, // tooltips false // urls ); // set the background color for the chart... chart.setBackgroundPaint(Color.white); var plot = chart.getPlot(); plot.setBackgroundPaint(Color.white); plot.setRangeGridlinesVisible(false); plot.setAxisOffset(RectangleInsets.ZERO_INSETS); // customise the range axis... var rangeAxis = plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); rangeAxis.setAutoRangeIncludesZero(true); rangeAxis.setRange(0, 40); // customise the renderer... var renderer = new StatisticalBarRenderer(); renderer.setErrorIndicatorPaint(Color.black); renderer.setSeriesOutlinePaint(0,Color.black); renderer.setSeriesOutlinePaint(1,Color.black); renderer.setSeriesPaint(0,Color.black); renderer.setSeriesPaint(1,Color.white); renderer.setItemMargin(0.0); plot.setRenderer(0,renderer); renderer.setDrawBarOutline(true); bi = chart.createBufferedImage(600, 400); imp = new ImagePlus("Chart Test", bi); imp.show(); // Create SVG image // Get a DOMImplementation and create an XML document var domImpl = GenericDOMImplementation.getDOMImplementation(); var document = domImpl.createDocument(null, "svg", null); // Create an instance of the SVG Generator var svgGenerator = new SVGGraphics2D(document); // draw the chart in the SVG generator var bounds = new Rectangle(600, 400); chart.draw(svgGenerator, bounds); var dir = IJ.getDirectory("Where should the svg file be saved?"); // Write svg file var svgFile = new File(dir + "test.svg"); var outputStream = new FileOutputStream(svgFile); var out = new OutputStreamWriter(outputStream, "UTF-8"); svgGenerator.stream(out, true /* use css */); outputStream.flush(); outputStream.close(); </code></pre></div></div> <h2 id="writing-out-movie-files-with-javacv">Writing out movie files with JavaCV</h2> <a href="https://github.com/bytedeco/javacv">JavaCV</a> is a Java wrapper around OpenCV and FFMPEG. You will have to unpack the libraries into the <code class="language-plaintext highlighter-rouge">lib/<platform>/</code> folder of your Fiji installation (e.g. <code class="language-plaintext highlighter-rouge">Fiji.app/lib/linux64/</code>) to let JavaCV find the native libraries (e.g. unpack <code class="language-plaintext highlighter-rouge">ffmpeg-macosx-x86_64.jar</code>’s <code class="language-plaintext highlighter-rouge">.dylib</code> files directly into <code class="language-plaintext highlighter-rouge">Fiji.app/lib/macosx/</code>) before starting Fiji. <h4 id="beanshell-4">BeanShell</h4> <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>/* * A simple example how to write out a movie from a possibly virtual * image stack using JavaCV. * * Licensed under CC-BY-SA 4.0 * by Johannes Schindelin on September 16th, 2014 */ path = "/tmp/change-this-name.flv"; frameRate = 25.0; videoBitrate = 400 * 1000; // if you have not installed JavaCV into your jars/ directory: import java.io.File; binDir = new File(System.getProperty("user.home") + "/downloads/javacv-bin/"); if (binDir.isDirectory()) { jars = binDir.list(); for (String jar : jars) { if (jar.endsWith(".jar")) { addClassPath(new File(binDir, jar).getPath()); } } } // use JavaCV to write out the currently active 3D image import ij.IJ; import org.bytedeco.javacv.FFmpegFrameRecorder; import org.bytedeco.javacpp.opencv_core.IplImage; void saveImageAsMovie(image, path, frameRate, videoBitrate) { if (image == null) { IJ.error("No active image!"); return; } width = image.getWidth(); height = image.getHeight(); stack = image.getStack(); recorder = FFmpegFrameRecorder.createDefault(path, (int) width, (int) height); recorder.setFormat("flv"); recorder.setFrameRate(frameRate); recorder.setVideoBitrate(videoBitrate); recorder.start(); for (slice = 1; slice <= stack.getSize(); slice++) { ip = stack.getProcessor(slice); recorder.record(IplImage.createFrom(ip.getBufferedImage())); } recorder.stop(); recorder.release(); } try { saveImageAsMovie(IJ.getImage(), path, frameRate, videoBitrate); } catch (Throwable t) { IJ.handleException(t); } </code></pre></div></div> </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">Forum</a></li> <li><a href="https://twitter.com/hashtag/ImageJ" class="icon brands alt fa-twitter">Twitter</a></li> <li><a href="https://github.com/imagej" class="icon brands alt fa-github">GitHub</a></li> </ul> <ul class="copyright"> <li>Design: <a href="http://html5up.net">HTML5 UP</a></li> </ul> </section>  <nav role="navigation"> <div id="ham-toggle"> <input type="checkbox" />    <ul id="ham-menu"> <div class="menu"><h3>ImageJ Docs</h3> <ul> <li><a href="/downloads">Download</a></li> <li><details><summary>Learn</summary><ul> <li><details><summary><a href="/learn">ImageJ 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