Tips for developers

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<h1>Tips for developers</h1> </header> </div>   <section id="page" class="main style1"> <div class="container"> <div class="box alt"></div> <div id="content" class="page-content"> An unsorted list of hints that you might find useful. <h1 id="compile--execute-a-class">Compile & Execute a Class</h1> You do not need to call <code class="language-plaintext highlighter-rouge">javac</code> yourself with a long classpath: <div class="language-shell highlighter-rouge"><div class="highlight"><pre class="highlight"><code>$ ./fiji --javac YourClass.java </code></pre></div></div> and you can call its <code class="language-plaintext highlighter-rouge">main()</code> method just as easy: <div class="language-shell highlighter-rouge"><div class="highlight"><pre class="highlight"><code>$ ./fiji YourClass.class argument1 argument2 </code></pre></div></div> <h1 id="rapidly-prototype-a-plugin">Rapidly Prototype a Plugin</h1> It is often easier to start out with a Jython, JRuby or BeanShell script, as you do not have to care about strict typing, exceptions or recompiling. Just place your script (with the correct extension – .py, .rb or .bsh) into the plugins/ folder and execute the script. Fiji will always execute the current version of the script, so you can edit and run the script without restarting Fiji. Of course, it is even more convenient to use the <a href="/scripting/script-editor">Script Editor</a>… Once you have working code, you can turn it into a proper plugin (this is easiest with BeanShell, as its syntax is closest to Java already), adding strict typing and exception handling as needed. <h1 id="find-the-jar-file-containing-a-certain-class">Find the .jar File Containing a Certain Class</h1> Sometimes, the compiler complains about a class not having a certain method or interface, but you know it must contain it. More often than not, that class exists in different versions in your classpath. Find out with <div class="language-shell highlighter-rouge"><div class="highlight"><pre class="highlight"><code>$ ./fiji bin/find-jar-for-class.py the.class.youre.looking.For </code></pre></div></div> If you want to do that with an installed Fiji (i.e. when bin/ is missing), you can start the <a href="/scripting/script-editor">Script Editor</a> and execute a BeanShell like this: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code> import ij.IJ; print(IJ.getClassLoader() .loadClass("the.class.youre.looking.For") .getResource("For.class").toString()); </code></pre></div></div> This will output the URL to the .class file, including the path to the enclosing .jar file. <h1 id="using-imagej-effectively">Using ImageJ Effectively</h1> ImageJ has a simple API, but it is also big, so here are a few pointers to some useful parts. <h2 id="how-to-read-a-file-into-an-imageplus">How to read a file into an ImagePlus</h2> <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code> ImagePlus image = IJ.openImage(path); </code></pre></div></div> <h2 id="how-to-get-the-current-image">How to get the current image</h2> <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ImagePlus img = WindowManager.getCurrentImage(); // current image ImageProcessor ip = img.getProcessor(); // current slice </code></pre></div></div> <h2 id="making-a-new-image-stack--quickly">Making a new image stack – quickly!</h2> <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ImagePlus image = IJ.createImage("my image", "RGB", 640, 480, 20); </code></pre></div></div> <h2 id="how-to-display-an-exception-in-a-window">How to display an exception in a window</h2> This is especially useful on Windows, where you usually do not see the console: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>IJ.handleException(exception); </code></pre></div></div> This is available since ImageJ 1.43g, as well as the option to set a different exception handler using <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code> IJ.setExceptionHandler(new IJ.ExceptionHandler() { public void handle(Throwable exception) { // do something } }); </code></pre></div></div> <h2 id="how-to-show-a-plot">How to show a plot</h2> ImageJ offers the <code class="language-plaintext highlighter-rouge">ij.gui.Plot</code> class to make a window showing a plot. Use it like this: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>Plot plot = new Plot("The window title", "labels on the x-axis", "labels on the y-axis", float_array_of_x_values, float_array_of_y_values); plot.show(); </code></pre></div></div> Instead of float arrays, you can also use double arrays. If you need to update the plot at some stage, you need to save the return value of show(): <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>Plot plot = new Plot("The window title", "labels on the x-axis", "labels on the y-axis", float_array_of_x_values, float_array_of_y_values); PlotWindow window = plot.show(); // ... Plot update = new Plot("Dummy", "x labels", "y labels", x_values, y_values); window.drawPlot(update); </code></pre></div></div> To add another plot to the same window, use the <code class="language-plaintext highlighter-rouge">addPoints()</code> method: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>plot.addPoints(float_array_of_x_values, float_array_of_y_values, Plot.LINE); </code></pre></div></div> The plots can be drawn in different colors like this: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>Plot plot = new Plot("The window title", "labels on the x-axis", "labels on the y-axis", float_array_of_x_values, float_array_of_y_values); plot.setColor(Color.RED); plot.draw(); plot.addPoints(float_array_of_x_values, another_float_array_of_y_values, Plot.LINE); plot.setColor(Color.BLUE); plot.draw(); </code></pre></div></div> You might need to adjust the bounding box if the second plot does not match the bounding box of the first one by using the <code class="language-plaintext highlighter-rouge">setLimits()</code> method before the call to <code class="language-plaintext highlighter-rouge">plot.draw();</code> <h2 id="duplicate-or-convert-between-imageprocessor-types">Duplicate, or convert between, <code class="language-plaintext highlighter-rouge">ImageProcessor</code> types</h2> The <code class="language-plaintext highlighter-rouge">ImageProcessor</code> class has several useful methods: <a href="https://javadoc.scijava.org/ImageJ1/ij/process/ImageProcessor.html#duplicate>()"><code class="language-plaintext highlighter-rouge">duplicate()</code></a>, <a href="https://javadoc.scijava.org/ImageJ1/ij/process/ImageProcessor.html#convertToByte(boolean)"><code class="language-plaintext highlighter-rouge">convertToByte()</code></a>, <a href="https://javadoc.scijava.org/ImageJ1/ij/process/ImageProcessor.html#convertToFloat"><code class="language-plaintext highlighter-rouge">convertToFloat()</code></a>, <a href="https://javadoc.scijava.org/ImageJ1/ij/process/ImageProcessor.html#convertToRGB()"><code class="language-plaintext highlighter-rouge">convertToRGB()</code></a>, and <a href="https://javadoc.scijava.org/ImageJ1/ij/process/ImageProcessor.html#convertToShort(boolean)"><code class="language-plaintext highlighter-rouge">convertToShort()</code></a>. This <a href="https://javadoc.scijava.org/ImageJ1/ij/process/ImageProcessor.html">class</a> also has some other goodies, such as methods for convolution. <h2 id="how-to-store-settings-persistently">How to store settings persistently</h2> ImageJ (and therefore Fiji, too) has a way to store key/value pairs persistently, i.e. they are available even after a restart. The settings are stored in a file called IJ_Prefs.txt in the subdirectory called .imagej/ in your home directory (on Windows, directly in your home directory; on Mac, in ~/Library/Preferences). <div class="notice" style="font-size: 2; background: #e6e6e6; border-left: 10px solid #901913"><div class="notice-icon"><img src="/media/icons/note.svg" width="32" /></div><div class="notice-content">The settings are only saved upon regular exit of Fiji; If you kill the process, or if the Java Runtime crashes, they are not saved. You can ask for the settings to be saved explicitly, though. </div> </div> Example: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>import ij.Prefs; ... // save key/value pairs Prefs.set("my.persistent.name", "Grizzly Adams"); Prefs.set("my.persistent.number", 10); .... // retrieve the values (with default values) int myNumber = Prefs.get("my.persistent.number", 0); // explicitly save the preferences _now_ Prefs.savePreferences(); <div class="notice" style="font-size: 2; background: #e6e6e6; border-left: 10px solid #901913"><div class="notice-icon"><img src="/media/icons/note.svg" width="32"></div><div class="notice-content">Do not use the <code class="language-plaintext highlighter-rouge">getString()</code> or <code class="language-plaintext highlighter-rouge">getInt()</code>; These methods do not have any setter methods, and they do not access the same values as the <code class="language-plaintext highlighter-rouge">get()</code> method (<code class="language-plaintext highlighter-rouge">get()</code> actually prefixes the keys with a dot)!</p> </div> </div> </code></pre></div></div> <h2 id="how-to-turn-a-number-into-a-string-using-a-given-number-of-decimal-places">How to turn a number into a string, using a given number of decimal places</h2> Use the <code class="language-plaintext highlighter-rouge">d2s()</code> method of the <code class="language-plaintext highlighter-rouge">ij.IJ</code> class: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>String message = "The current temperature is " + IJ.d2s(degrees, 1) + "° Celsius"; </code></pre></div></div> <h2 id="how-to-abort-a-plugin-completely">How to abort a plugin completely</h2> Sometimes, you want to abort a plugin without catching an exception at the highest level(s), without having ImageJ show an exception window. You can do that: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>throw new RuntimeException(Macro.MACRO_CANCELED); </code></pre></div></div> The special message Macro.MACRO_CANCELED will tell ImageJ not to show the exception message and stack trace in a text window. <h2 id="interact-with-the-roi-manager">Interact with the ROI manager</h2> To add ROIs to the ROI manager, do something like this: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>RoiManager manager = RoiManager.getInstance(); if (manager == null) manager = new RoiManager(); manager.addRoi(roi); </code></pre></div></div> If you want to add the ROI with a slice label, you have to jump through a hoop: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>int currentSlice = image.getCurrentSlice(); RoiManager manager = RoiManager.getInstance(); if (manager == null) manager = new RoiManager(); // the first slice is 1 (not 0) image.setSliceWithoutUpdate(slice); manager.add(image, rois[i], slice); image.setSlice(currentSlice); </code></pre></div></div> To retrieve all ROIs from the ROI manager, do this: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>RoiManager manager = RoiManager.getInstance(); if (manager != null) { Hashtable<String, Roi> table = (Hashtable<String, Roi>)manager.getROIs(); for (String label : table.keySet()) { int slice = manager.getSliceNumber(label); Roi roi = table.get(label); ... <do something with the ROI and the slice> ... } } </code></pre></div></div> If you need to preserve the order of the ROIs in the ROI manager, unfortunately you’ll have to access the AWT listbox: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>import java.awt.List; ... RoiManager manager = RoiManager.getInstance(); if (manager != null) { List labels = manager.getList(); Hashtable<String, Roi> table = (Hashtable<String, Roi>)manager.getROIs(); for (int i = 0; i < labels.getItemCount(); i++) { String label = labels.getItem(i); int slice = manager.getSliceNumber(label); Roi roi = table.get(label); ... <do something with the ROI and the slice> ... } } </code></pre></div></div> To get just the selected ROIs, use code similar to this: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>import java.awt.List; ... RoiManager manager = RoiManager.getInstance(); if (manager != null) { String[] labels = manager.getList().getSelectedItems(); Hashtable<String, Roi> table = (Hashtable<String, Roi>)manager.getROIs(); for (String label : labels) { int slice = manager.getSliceNumber(label); Roi roi = table.get(label); ... <do something with the ROI and the slice> ... } } </code></pre></div></div> <h2 id="show-a-results-table">Show a results table</h2> First you need to get the results table instance (or create one): <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ResultsTable rt = Analyzer.getResultsTable(); if (rt == null) { rt = new ResultsTable(); Analyzer.setResultsTable(rt); } </code></pre></div></div> Then you can add a new row: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>rt.incrementCounter(); </code></pre></div></div> … and add entries by column label: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>rt.addValue("slice", slice); rt.addValue("bratwurst", -1); </code></pre></div></div> Finally make sure that the result table is displayed/updated: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>rt.show("Results"); </code></pre></div></div> <h2 id="how-to-find-equivalent-api-commands-between-imagej-1x-and-imagej2">How to find equivalent API commands between ImageJ 1.x and ImageJ2?</h2> <a href="/develop/ij1-ij2-cheat-sheet">ImageJ1-ImageJ2 cheat sheet</a> is available. <h1 id="tips-for-graphical-user-interface-gui-programming">Tips for Graphical User Interface (GUI) programming</h1> <h2 id="programming-with-swing-components">Programming with Swing components</h2> When programming with Swing, beware that Swing is not thread safe. Swing’s golden rule states that: Once a Swing component has been realized, all code that might affect or depend on the state of that component should be executed in the event-dispatching thread. When has a Swing component been realized? When it is visible inside Window or JFrame that got a call to <code class="language-plaintext highlighter-rouge">setVisible(true)</code>. This implies that its <code class="language-plaintext highlighter-rouge">paint(Graphics)</code> method has been called or will be called soon. These are the methods that can realize a component, or rather, methods called on a Window or Frame or JFrame that will realize all its children components: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>setVisible(true) show() pack() // this might surprise you </code></pre></div></div> There is a class which helps you with all this: <a href="http://download.oracle.com/javase/6/docs/api/javax/swing/SwingUtilities.html">SwingUtilities</a>. Example: to call <code class="language-plaintext highlighter-rouge">pack()</code> from within the constructor (which might or might not be called from the Event Dispatch Thread): <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>if (SwingUtilities.isEventDispatchThread()) pack(); else try { SwingUtilities.invokeAndWait(new Runnable() { public void run() { pack(); }}); } catch (Exception e) { /* ignore */ } </code></pre></div></div> Information extracted from the <a href="http://web.archive.org/web/20120801194837/http://java.sun.com/products/jfc/tsc/articles/threads/threads1.html">Swing guide</a> (now only available from via web.archive.org as Oracle removed the original docs), additional information can be found in the <a href="http://docs.oracle.com/javase/tutorial/uiswing/concurrency/index.html">Concurrency in Swing</a> lesson of The Java Tutorials. <h1 id="arcane-quirks">Arcane Quirks</h1> <h2 id="softreference-and-outofmemoryerror">SoftReference and OutOfMemoryError</h2> We have recently learned an interesting fact about Java’s <a href="http://docs.oracle.com/javase/6/docs/api/java/lang/ref/SoftReference.html">SoftReference</a> and the potential occurence of an <a href="http://docs.oracle.com/javase/6/docs/api/java/lang/OutOfMemoryError.html">OutOfMemoryError</a>. The result first: An <a href="http://docs.oracle.com/javase/6/docs/api/java/lang/OutOfMemoryError.html">OutOfMemoryError</a> may be thrown in a situation where <a href="http://docs.oracle.com/javase/6/docs/api/java/lang/ref/SoftReference.html">SoftReferences</a> can be released after which enough memory would be available. The reason is that normal garbage collection happens in an independent thread and does not halt other threads when they allocate memory. Only an explicit <a href="http://docs.oracle.com/javase/6/docs/api/java/lang/System.html#gc%28%29">System.gc()</a> waits until the memory is freed . The consequence is that whenever you allocate memory then you should do that with the following clause: <div class="language-java highlighter-rouge"><div class="highlight"><pre class="highlight"><code>final MyObject o; try { o = new MyObject(); } catch (OutOfMemoryError e) { System.gc(); o = new MyObject(); } </code></pre></div></div> We found this by implementing a simple cache using a <a href="http://docs.oracle.com/javase/6/docs/api/java/util/HashMap.html">HashMap</a> of <a href="http://docs.oracle.com/javase/6/docs/api/java/lang/ref/SoftReference.html">SoftReferences</a> to an object that on finalize removes the corresponding key in the <a href="http://docs.oracle.com/javase/6/docs/api/java/util/HashMap.html">HashMap</a>. That cache is used to store image tiles for an <a href="/libs/imglib2">ImgLib2</a> backend that uses a <a href="http://fly.mpi-cbg.de/~saalfeld/catmaid/">CATMAID</a> stack (<a href="https://github.com/imglib/imglib/blob/9f38afca3f0a4aa7b3ddc77160430a710a20501a/imglib2/tests/src/test/java/catmaid/CATMAIDRandomAccessibleInterval.java">GitHub</a>). It turned out that the painter thread in an interactive viewer was fetching new tiles quicker than the garbage collector would finalize <a href="http://docs.oracle.com/javase/6/docs/api/java/lang/ref/SoftReference.html">SoftReferences</a> and stopped with an <a href="http://docs.oracle.com/javase/6/docs/api/java/lang/OutOfMemoryError.html">OutOfMemoryError</a>. We could solve that with the the above construct. </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 Basics</a></summary><ul> <li><a href="/tutorials">Tutorials</a></li> <li><a href="/learn/user-guides">User Guides</a></li> <li><a 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