[ImageJ-devel] [fiji-devel] Re: jython scripting, No compatible service: io.scif.SCIFIOService

[Harri Jäälinoja]

Hi Mark and Johannes,

thanks for your replies, good to know I'm on the right track :)

The classpath variable does look correct:
hajaalin at 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 at 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 <hinerm at gmail.com 
> <mailto:hinerm at gmail.com>> wrote:
>
>     Hi Johannes,
>
>     On Tue, Feb 25, 2014 at 12:57 PM, Johannes Schindelin
>     <Johannes.Schindelin at gmx.de <mailto:Johannes.Schindelin at gmx.de>>
>     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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-devel/attachments/20140226/762d1b8b/attachment.html>