Using an interpreter
All scripting languages use the same basic interpreter, with the following common features.
General key bindings
- up arrow: bring the previously typed command.
- down arrow: bring the next typed command.
- enter or return: execute the contents of the prompt.
Multiline editing and keybidings
You can enlarge the prompt by dragging the middle bar.
- shift + enter: create a new line within the prompt.
- shift + up arrow: move to the line above within the prompt.
- shift + down arrow: id, down.
Selecting and executing text from the screen
On selecting text, a popup offers to:
- save to a new file
Using the script editor
You can create, edit and run scripts using Fiji's script editor. For details, please see the Script Editor documentation.
Creating scripts and using "refresh scripts"
On startup, ImageJ will run all "refresh scripts" plugins, one for each supported language. This will result in all scripts present within the plugins folders to be added to the menus.
To run a script, just select it from the plugins menus.
If you edit a script that is already placed in the menus, you don't need to do anything else: just save the text file and run it again by selecting it from the menus.
If you add a new script and ImageJ is running, just go to Plugins - Scripting and run the appropriate Refresh * Scripts for the language.
Running Scripts in Headless Mode
If you want to run scripts in headless mode (i.e. without the GUI, by invoking fiji with the --headless option) then you have to make sure you run the appropriate "Refresh ... Scripts" plugin first. Also, you need to append -batch to the command. For example, if you have a script called test_ruby.rb, which appears in the Plugins menu somewhere as "test ruby", then you can run that with:
fiji --headless -eval 'run("Refresh JRuby Scripts",""); run("test ruby","");' -batch
(If this gives you a NullPointerException in RefreshScripts, then you need a newer version of Fiji - a bug with this was fixed quite recently.)