Hi Mark and Johannes,
thanks for your replies, good to know I'm on the right track :)
The classpath variable does look correct:
hajaalin@biotek973:~/Software/mvn-IJ2$ echo $CP
/home/hajaalin/Software/mvn-IJ2/target/dependency/ij-core-2.0.0-beta-7.7.jar:/home/hajaalin/Software/mvn-IJ2/target/dependency/base64-2.3.8.jar:/home/hajaalin/S
...
I have Ubuntu 12.04 and Jython 2.5.1+, there is no -J-cp option. I was
wondering if I maybe specified a wrong property with -D, so I tried also
python.jythonc.classpath
(http://manpages.ubuntu.com/manpages/precise/man5/jython.conf.5.html),
but then the io classes were not found at all. So jython
-Dpython.path=$JARLIST seems correct. I picked it up from the same SO
post you also found.
Just to be sure, the SCIFIOService class is in a jar that's on the list:
java.lang.IllegalArgumentException: java.lang.IllegalArgumentException:
No compatible service: io.scif.SCIFIOService
hajaalin@biotek973:~/Software/mvn-IJ2$ jar tvf
target/dependency/scifio-0.9.2.jar |grep SCIFIOService
150 Fri Feb 14 16:24:24 EET 2014 io/scif/SCIFIOService.class
Which linux vm and Jython version did you use? Did you get the image to
open also there? I'll try and install Jython 2.5.3.
Harri
On 25/02/14 22:00, Mark Hiner wrote:
P.S. Harri I wanted to apologize if your original script did properly
format the classpath.. I tested it on OSX and becase of sed
differences it didn't appear to work to me. When I booted up a linux
vm and ran it there though, the output did look correct, so I am not
sure why it wasn't working for you - as the exception you saw
definitely looked like a classpath error. If the -J-cp + subshell
command I posted in my original reply doesn't work though, please let
me know.
On Tue, Feb 25, 2014 at 1:07 PM, Mark Hiner <[email protected]
<mailto:[email protected]>> wrote:
Hi Johannes,
On Tue, Feb 25, 2014 at 12:57 PM, Johannes Schindelin
<[email protected] <mailto:[email protected]>>
wrote:
Please note that calling the ImageJ launcher with a .py script
will
magically do the right thing:
~/Software/fiji-*/Fiji.app/ImageJ-linux64 my-script.py
Thanks! Do note though that this is similarly not working right
now for Harri's use case, as it is not properly interpreting
SCIFIOConfig.ImgMode.CELL. The only way I could get it to work was
running jython directly.
- Mark
--
__________________________________________________
Harri Jäälinoja
Light Microscopy Unit
Institute of Biotechnology, University of Helsinki
http://www.biocenter.helsinki.fi/bi/lmu/
+358 9 191 59370 fax +358 9 191 59366
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