[ImageJ-devel] Analyze Skeleton in jython

[Johannes Schindelin]

Hi Harri,

On Mon, 15 Sep 2014, Harri Jäälinoja wrote:

> I would like to use the Analyze Skeleton plugin in a silent mode
> (http://fiji.sc/AnalyzeSkeleton) in Jython, but I don't know how to import the
> module.
> 
> Based on the jar-file contents...
> dev at 192e0e6fb8a5:~/lmu-users/jaakko$ jar tvf
> /Fiji.app/plugins/AnalyzeSkeleton_-2.0.0-SNAPSHOT.jar
>      0 Tue Apr 15 17:25:22 UTC 2014 META-INF/
>    519 Tue Apr 15 17:25:20 UTC 2014 META-INF/MANIFEST.MF
>      0 Tue Apr 15 17:25:20 UTC 2014 skeleton_analysis/
>   1936 Tue Apr 15 17:25:20 UTC 2014 skeleton_analysis/Edge.class
>   1111 Tue Apr 15 17:25:20 UTC 2014 skeleton_analysis/Point.class

A better way is to inspect the Javadoc:

	http://jenkins.imagej.net/job/Fiji-javadoc/javadoc/skeleton_analysis/package-summary.html

or the source code directly:

	https://github.com/fiji/AnalyzeSkeleton

> ... I have tried
> import skeleton_analysis
> 
> ... but I get the error
> ImportError: No module named skeleton_analysis

For performance reasons, we had to disable the wildcard imports (Jython's
startup was just really unbearably slow otherwise). Therefore, you have to
import the classes explicitly:

	from skeleton_analysis import Edge, Graph, AnalyzeSkeleton_

Please feel free to become an active part of the community by enhancing
the documentation on the ImageJ/Fiji wiki. As a rule of thumb: if the
documentation could have done a better job helping you do your job, please
just edit it accordingly, to help the community.

Ciao,
Johannes