https://github.com/imagej/example-bio-formats-legacy-plugin
Simple example of calling Bio-Formats with ImageJ 1.x + Java 6
https://github.com/imagej/example-bio-formats-legacy-plugin
Last synced: 16 days ago
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Simple example of calling Bio-Formats with ImageJ 1.x + Java 6
- Host: GitHub
- URL: https://github.com/imagej/example-bio-formats-legacy-plugin
- Owner: imagej
- Created: 2017-10-17T14:50:02.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2017-10-17T15:58:13.000Z (over 8 years ago)
- Last Synced: 2025-02-22T07:51:28.850Z (over 1 year ago)
- Language: Java
- Homepage:
- Size: 4.88 KB
- Stars: 2
- Watchers: 6
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
This is an example Maven project implementing an ImageJ 1.x plugin
that calls the [Bio-Formats](https://imagej.net/Bio-Formats) library.
It was adapted from the
[example-legacy-plugin project](https://github.com/imagej/example-legacy-plugin).
It is intended as a starting point to develop new ImageJ 1.x plugins
in an IDE of your choice. You can even collaborate with developers using a
different IDE than you.
* In [Eclipse](http://eclipse.org), for example, it is as simple as
_File>Import...>Existing Maven Project_.
* In [NetBeans](http://netbeans.org), it is even simpler:
_File>Open Project_.
* The same works in [IntelliJ](http://jetbrains.net).
* If [jEdit](http://jedit.org) is your preferred IDE, you will need the
[Maven Plugin](http://plugins.jedit.org/plugins/?MavenPlugin).
Die-hard command-line developers can use Maven directly by calling `mvn`
in the project root.
However you build the project, in the end you will have the `.jar` file
(called *artifact* in Maven speak) in the `target/` subdirectory.
To copy the artifact into the correct place, you can call
`mvn -Dimagej.app.directory=/path/to/ImageJ.app/`.
This will not only copy your artifact, but also all the dependencies. Restart
your ImageJ or call *Help>Refresh Menus* to see your plugin in the menus.
Developing plugins in an IDE is convenient, especially for debugging. To that
end, the plugin contains a `main` method which starts ImageJ and runs the
plugin. See also
[this page](https://imagej.net/Debugging#Debugging_plugins_in_an_IDE_.28Netbeans.2C_IntelliJ.2C_Eclipse.2C_etc.29)
for information how ImageJ makes it easier to debug in IDEs.
How to use this project as a starting point
===========================================
Either
* `git clone git://github.com/imagej/example-bio-formats-legacy-plugin`, or
* unpack https://github.com/imagej/example-bio-formats-legacy-plugin/archive/master.zip
Then:
1. Edit the `pom.xml` file. Every entry should be pretty self-explanatory.
In particular, change
1. the *artifactId* (**NOTE**: should contain a '_' character)
2. the *groupId*, ideally to a reverse domain name your organization owns
3. the *version* (note that you typically want to use a version number
ending in *-SNAPSHOT* to mark it as a work in progress rather than a
final version)
4. the *dependencies* (read how to specify the correct
*groupId/artifactId/version* triplet
[here](https://imagej.net/Maven#How_to_find_a_dependency.27s_groupId.2FartifactId.2Fversion_.28GAV.29.3F))
5. the *developer* information
6. the *scm* information
2. Remove the `Simple_Read.java` file and add your own `.java` files
to `src/main/java//` (if you need supporting files -- like icons
-- in the resulting `.jar` file, put them into `src/main/resources/`)
3. Edit `src/main/resources/plugins.config`
4. Replace the contents of `README.md` with information about your project.
If you cloned the `example-bio-formats-legacy-plugin` repository, you probably
want to publish the result in your own repository:
1. Call `git status` to verify .gitignore lists all the files (or file
patterns) that should be ignored
2. Call `git add .` and `git add -u` to stage the current files for
commit
3. Call `git commit` or `git gui` to commit the changes
4. [Create a new GitHub repository](https://github.com/new)
5. `git remote set-url origin git@github.com:/`
6. `git push origin HEAD`
### Eclipse: To ensure that Maven copies the plugin to your ImageJ folder
1. Go to _Run Configurations..._
2. Choose _Maven Build_
3. Add the following parameter:
- name: `imagej.app.directory`
- value: `/path/to/ImageJ.app/`
This ensures that the final `.jar` file will also be copied to your ImageJ
plugins folder everytime you run the Maven Build