Developing Fiji

Revision as of 04:06, 2 December 2014 by Schindelin (talk | contribs) (Contributing: remove obsolete information, refer to Ignacio's tutorial instead)


Template:Development

Fiji is a community effort. So we are happy whenever we see new people developing Fiji!

Purpose

The purpose of this tutorial is to get you started hacking on Fiji's source code (i.e., the core Fiji plugins). If you need to develop a new plugin for ImageJ, you do not actually need Fiji's source. Rather, see these resources:

See also Developing Fiji in Eclipse for a tutorial specific to the Eclipse IDE.

Getting started

First, you have to download and build Fiji. If you do not know Git yet, we have a concise introduction for you.

The ImageJ launcher

There is a program called "ImageJ-win32.exe", "ImageJ-linux64" or similar in Fiji's root directory. Its main purpose is to load a Java virtual machine with known-good options, and then launch ImageJ.

However, it is much more powerful than that. Amongst other things, you can

  • Open images: ./ImageJ-<platform> example.jpg
  • Call Jython scripts: ./ImageJ-<platform> example.py (also works for JRuby scripts when they have an .rb extension, for Beanshell scripts with .bsh extension, .clj for Clojure and .js for Javascript)
  • Call the Jython interpreter: ./ImageJ-<platform> --jython (the classpath will be the same as when calling ImageJA), and likewise --jruby, --bsh and --js for the respective language's command-line interpreters
  • Run Fiji with the system Java instead of its own one: ./ImageJ-<platform> --system. But beware: this might fail since some plugins need at least Java 1.5, and the 3D viewer needs Java3D.
  • Show the java command line instead of running Fiji: ./ImageJ-<platform> --dry-run
  • Compile a Java class: ./ImageJ-<platform> --javac example.java
  • Run a Java class' main() method: ./ImageJ-<platform> --main-class=example
  • Pass some Java options: ./ImageJ-<platform> -server -- (everything that comes before a -- is interpreted as Java option)
  • Add . to the classpath and execute the given class' main() method: ./ImageJ-<platform> Example.class
  • Link Fiji into the PATH: ln -s $(pwd)/ImageJ-<platform> $HOME/bin/fiji && fiji
  • Start Fiji and run a menu entry directly: ./ImageJ-<platform> --run System_Clipboard (the underscore was used in place of a space to avoid having to quote the argument)

The ImageJ launcher can do more, just call ./ImageJ-<platform> --help for a short description.

Building Fiji

Fiji is organized into a set of Maven projects. For convenience and speed, there is SciJava's minimal Maven-lookalike MiniMaven to build Fiji, but it is recommended to use an Integrated Development Environment, or at least real Maven.

For details, please see Downloading and Building Fiji From Source. See also the Supported Compilers page for more information.

Testing

It is strongly recommended to write regression tests (also known as unit tests). It is easy.

Furthermore, it is highly recommended to write and run unit tests in an Integrated Development Environment for efficient debugging.

You may also want to measure the code coverage of your tests - one way is described in the page Code Coverage in Fiji.

At some point, you might want to debug whatever you wrote. There's a small Debugging intro page.

Discussing code

When you want to discuss your changes to some Fiji component, the preferred way is to inline a patch and send it to the fiji-devel mailing list. You can also send a link to your repository, e.g. a fork of the Fiji repository on github.com, but then commenting is not as easy (and the discussion will involve fewer developers).

When discussing larger chunks of code (or a patch) on IRC, please do not paste them directly, but use a pastebin instead.

To point at specific code on IRC or via mail, you can also do so by posting links to our Gitweb. See also GitHub Tricks.

Contributing

Please have a look at the excellent How to contribute to an existing plugin or library tutorial.

Providing documentation

A plugin wants to be used. Therefore you want to give users some information about it, and most likely also a tutorial how to use it.

If you have an account on this Wiki, you can easily create new tutorials with the Tutorial Maker.

Further reading for developers