Developing Fiji

Revision as of 03:57, 2 December 2014 by Schindelin (talk | contribs) (Remove thoroughly obsolete sections)


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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

When you are testing Fiji, you may 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. There is even a little shell script in fiji.git that helps you finding the link:

bin/open-in-gitweb.sh fiji.cxx

This script will open the appropriate link with xdg-open. It can deal with files, even in submodules, and commits (for commits, your current directory must be inside the appropriate Git checkout). For files, you can append ":<linenumber>" to the file name to get a link to a specific line.

Contributing

Please make sure that you are a little familiar with Git, or you can learn basic git knowledge interactively with GitHub. Once you are, you can easily make a local contrib branch and push it.

Forking on GitHub

Alternatively, you can make an account for yourself on GitHub and fork fiji.git:

  1. create an account on GitHub
  2. Fork Fiji:
GitHub-fork.png
  1. clone it

If you already worked in an existing checkout of fiji.git, no problem, you can connect that to the new remote:

  1. git remote add github github.com:<user>/fiji (where <user> is your account on GitHub)
  2. git config branch.<branch>.remote github (where "<branch>" is the branch you want to connect to GitHub, typically master)
  3. git config branch.<branch>.merge refs/heads/<branch>
  4. git push github <branch> to push the current state

Contributing to Fiji's existing plugins

Sometimes you may want to contribute to Fiji's existing plugins, for example, a bug is found in one plugin and you want to fix it, or you would like to improve one plugin by adding more functions.

Every plugin has its own git repository in Fiji. For example, the GraphCut plugin's repository is GraphCut. This structure allows for easy, independent development of the individual parts of which the base version of Fiji consists.

To contribute to Fiji's GraphCut plugin:

  1. Fork that repository by clicking the "Fork" button
  2. Clone it - git clone https://github.com/username/Graph_Cut.git
  3. Configure remotes
    1. cd Graph_Cut
    2. git remote add upstream https://github.com/fiji/Graph_Cut.git
    3. git fetch upstream
  4. Create a topic branch
    1. git branch mybranch
    2. git checkout mybranch
  5. Make changes and commit them to your topic branch
  6. Push the commits to your github repository
  7. Send the pull request

You can learn more about Git fork and branch model from Fork A Repo, including how to send a pull request from Pull Request.

Letting us know

After you published your contributions, you probably also want to let us know what you did, so just send a mail to the Fiji devel mailing list.

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