running fiji from Eclipse

[Aryeh Weiss]

I finally decided to take the plunge and learn how to develop my python
scripts in a real IDE.
So I muddled through a number of on-line resources and tutorials, and
managed to install eclipse with pydev, and somehow I got it to work. I
more or less used the following:

http://wiki.cmci.info/documents/100825imagej_jython_eclipse
https://www.rose-hulman.edu/class/csse/resources/Eclipse/eclipse-python-configuration.htm

I have some questions about this.

1. When I first set it up, and added all of the jars and plugins to the
Pydev-PYTHONPATH, I still could not run commands like IJ.run("3D OC
Options", "long argument list....
The error was that 3D OC Options was not found.

However, after I added :

from java.lang import System
from ij import ImageJ
pluginsDir2 = "/Applications/local/fiji/Fiji.app/plugins"
System.setProperty("plugins.dir", pluginsDir2);
ImageJ(); #this will launch ImageJ GUI

which launches the GUI, then all was well with these commands.

S0 my question is -- is this the best way to do this, or is there a way
to run these commands  without launching the GUI. My instinct tells me
that this may be related to running "headless", but I do not know enough
about it.

Aside -- is there a "direct" API way to use 3D OC Option, or the
extended particle analyzer, or CLAHE, etc. Sometimes I find how to do it
in the documentation, but other times I cannot find an API for some plugin.

2. Is there a better way to launch the GUI if I am using the Fiji
distribution? My GUI is labeled ImageJ, not Fiji, but it seems to
contain the entire FIji distribution.

3. I have cases where my script beaks in the middle. In this case I had
image windows left open that I could not close, until i figured out to
kill multiple  instances of Jython that were running. Is there something
that I should be doing to prevent Jython  processes from hanging around?

4. Is there a better way to add the required jars to the PYTHONPATH 
than to manually add them in the Properties as external libraries?

I apologize for the elementary nature of these questions -- there is lot
of material on-line that no doubt covers this, but I am still a confused
beginner with this. (For example, finding that I needed xerces was
dauntng, until I found that the fiji jars directory has it...)

Thanks in advance
--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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