These are chat archives for fiji/fiji

5th
Feb 2016
Brian Northan
@bnorthan
Feb 05 2016 20:51

@ctrueden I wrapped particle analyzer and an overlay step in a command... and it seems to work, even headless.

The one thing I can't get working in a headless IJ2 is Auto Local Threshold. I guess because it is a fiji plugin...

Curtis Rueden
@ctrueden
Feb 05 2016 20:51
How does it fail?
Brian Northan
@bnorthan
Feb 05 2016 20:52
Dialog box "Unrecognized command: Auto Local Threshold"
Curtis Rueden
@ctrueden
Feb 05 2016 20:53
Oh, so it's probably not in your runtime class-path then?
I.e. sc.fiji:Auto_Threshold
Brian Northan
@bnorthan
Feb 05 2016 20:54

yes...I tried adding the maven reference....

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>Auto_Threshold</artifactId>
<version>1.16.1</version>
<scope>runtime</scope>
</dependency>

It works if I copy my commands to fiji... ofcourse
Curtis Rueden
@ctrueden
Feb 05 2016 20:54
Ah, you are in Eclipse.
That issue seems to be cropping up a lot for people lately.
I haven't had time to investigate what causes it yet.
I guess it is slightly different: maybe you aren't even setting plugins.dir?
Huh, I guess I am still surprised that ImageJ1 cannot find the plugin, when it is actually on the system class-path.
Can you load the class? Like, if you write Class.forName("fiji.threshold.Auto_Local_Threshold") does it find it?
Brian Northan
@bnorthan
Feb 05 2016 20:58
yes that seems to work
Anyway not a big deal for me right now. I run my own plugins within Fiji.
I was just curious based on the question from the listserv if it would run as an independent app... no Fiji, just the Fiji plugins I use.