User Tools

Site Tools



This shows you the differences between two versions of the page.

Link to this comparison view

faq:technical:how_do_i_run_imagej_without_a_graphics_environment_headless [2019/04/12 11:13] (current)
Line 1: Line 1:
 +====== FAQ: How do I run ImageJ without a graphics environment (headless)? ======
 +**I want to run ImageJ on a cluster, by executing batch macros. To do that, I use ssh to log on, but ImageJ throws an exception that it cannot create a Menu in headless mode. What to do?**
 +There are at least two methods:
 +  - Install a virtual framebuffer (Xvfb) if you are on Unix. On a Mac, this will not necessarily help.
 +  - Use Fiji's [[http://​​Headless|headless mode]] (available via the command-line option ''​--headless''​.
 +**Technical explanation:​**
 +ImageJ1 conflates the macro argument handling with the GUI that asks the user for the values when not run in macro mode.
 +The problem is that font metrics require a graphical desktop. And even when using GUI elements such as text fields that are never shown, the font metrics are still required to calculate the layout.
 +Unfortunately,​ there seems to be no good way to solve that problem, since even when the class Menus actually does not instantiate a java.awt.Menu,​ most plugins still instantiate an ij.gui.GenericDialog,​ which inherits from java.awt.Dialog. And because a couple of plugins use the fact that the GenericDialog is derived from java.awt.Dialog to show lists or previews, this design cannot be changed.
 +The workaround is to use replacements for ij.Menus and ij.gui.GenericDialog,​ which were stripped of all GUI references. Of course, this works for most, but not all, plugins, and only in headless mode.
faq/technical/how_do_i_run_imagej_without_a_graphics_environment_headless.txt ยท Last modified: 2019/04/12 11:13 (external edit)