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<div class="moz-cite-prefix">Hi Mark and Johannes,<br>
<br>
thanks for your replies, good to know I'm on the right track :)<br>
<br>
The classpath variable does look correct:<br>
hajaalin@biotek973:~/Software/mvn-IJ2$ echo $CP<br>
/home/hajaalin/Software/mvn-IJ2/target/dependency/ij-core-2.0.0-beta-7.7.jar:/home/hajaalin/Software/mvn-IJ2/target/dependency/base64-2.3.8.jar:/home/hajaalin/S
...<br>
<br>
I have Ubuntu 12.04 and Jython 2.5.1+, there is no -J-cp option. I
was wondering if I maybe specified a wrong property with -D, so I
tried also python.jythonc.classpath
(<a class="moz-txt-link-freetext" href="http://manpages.ubuntu.com/manpages/precise/man5/jython.conf.5.html">http://manpages.ubuntu.com/manpages/precise/man5/jython.conf.5.html</a>),
but then the io classes were not found at all. So jython
-Dpython.path=$JARLIST seems correct. I picked it up from the same
SO post you also found.<br>
<br>
Just to be sure, the SCIFIOService class is in a jar that's on the
list:<br>
java.lang.IllegalArgumentException:
java.lang.IllegalArgumentException: No compatible service:
io.scif.SCIFIOService<br>
hajaalin@biotek973:~/Software/mvn-IJ2$ jar tvf
target/dependency/scifio-0.9.2.jar |grep SCIFIOService<br>
150 Fri Feb 14 16:24:24 EET 2014 io/scif/SCIFIOService.class<br>
<br>
<br>
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.<br>
<br>
Harri<br>
<br>
<br>
On 25/02/14 22:00, Mark Hiner wrote:<br>
</div>
<blockquote
cite="mid:CA+B=mGrsTKrj2eyDuwguWhu2xoUcgVUdD8LBa9YqkcppAFjxbA@mail.gmail.com"
type="cite">
<div dir="ltr">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.<br>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Feb 25, 2014 at 1:07 PM, Mark
Hiner <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:hinerm@gmail.com" target="_blank">hinerm@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">Hi Johannes,<br>
<br>
</div>
<div class="">
<div class="gmail_extra">
<div class="gmail_quote">On Tue, Feb 25, 2014 at 12:57
PM, Johannes Schindelin <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Johannes.Schindelin@gmx.de"
target="_blank">Johannes.Schindelin@gmx.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div style="overflow:hidden">Please note that
calling the ImageJ launcher with a .py script
will<br>
magically do the right thing:<br>
<br>
~/Software/fiji-*/Fiji.app/ImageJ-linux64
my-script.py</div>
</blockquote>
</div>
<br>
</div>
</div>
<div class="gmail_extra">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.<span class="HOEnZb"><font
color="#888888"><br>
<br>
</font></span></div>
<span class="HOEnZb"><font color="#888888">
<div class="gmail_extra">- Mark<br>
</div>
</font></span></div>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
__________________________________________________
Harri Jäälinoja
Light Microscopy Unit
Institute of Biotechnology, University of Helsinki
<a class="moz-txt-link-freetext" href="http://www.biocenter.helsinki.fi/bi/lmu/">http://www.biocenter.helsinki.fi/bi/lmu/</a>
+358 9 191 59370 fax +358 9 191 59366
</pre>
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