Installing a python script in ImageJ

Question

I’m trying to install a Python script in ImageJ. My preference is to use the script with ImageJ 1.x but can use Fiji if required.

I am trying to use the script with ImageJ 1.x by placing it in the plugins folder. The script appears in the plugins menu but when I try to run it I get an error that it can't find __future__

Traceback (most recent call last): 
File "<string>", line 1, in <module> 
ImportError: No module named __future__

This makes no sense to me as the __future__ module is being used to import the with_statement module and python version is listed as :

2.5.4rc1 (2.5:723492dbab02, Feb 8 2013, 10:13:55) 
[Java HotSpot(TM) 64-Bit Server VM (Oracle Corporation)]

from __future__ import with_statement is specifically designed for use with Python versions 2.5.x

https://docs.python.org/3/library/future.html

So ... moving on ...

I tired to use Fiji instead since it is based on ImageJ2.

I'm able to paste the code into the Script Editor using File > New > Script ...

The code runs when executed from there. However, when saved I can't get it to show up in the plugins menu. I've tried saving it to :

Fiji/plugins

Fiji/plugins/Scripts

Fiji/plugins/Scripts/Plugins

The file name has an _ in it.

The version of Fiji I'm running is ImageJ 2.0.0 rc-68/1.52e / Java1.8.0_172 (64-bit)

The version of ImageJ 1.x I'm running is ImageJ 1.52e / Java1.8.0_172 (64-bit)

Any help would be greatly appreciated.

Thanks

ctrueden · Accepted Answer · 2018-08-05 04:19:37Z

2

The canonical place to put scripts for ImageJ2 is scripts/Foo/Bar/My_Script.py, if you want it located in the menu at Foo > Bar > My Script.

It also works for backwards compatibility to use plugins or plugins/Scripts. However, there was recently a critical bug preventing scripts from appearing in the plugins-based locations; see this thread. The bug is fixed in the latest release.

edited Aug 5, 2018 at 4:19

answered Jul 30, 2018 at 20:13

ctrueden

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2 Comments

Zythyr Over a year ago

This worked! However, where exactly is this documented?

ctrueden Over a year ago

@Zythyr It is explained here: imagej.net/Scripting#Adding_scripts_to_the_Plugins_menu

felix the cat · Accepted Answer · 2018-07-30 07:04:44Z

0

you might want to have a look here on the ij-wiki. Also, there ij2 has its own, very active forum where this topic is also activeley discussed.

Best,

Felix

answered Jul 30, 2018 at 7:04

felix the cat

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2 Comments

agf1997 Over a year ago

Posted to the imagej email listserv. No response.

ctrueden Over a year ago

@agf1997 When posting the same question to multiple places, please disclose and cross-link, so that people can keep track of the discussion and avoid duplication of effort.

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