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

[Mark Hiner]

Hi Harri,

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
>

So this exception may be slightly misleading. SCIFIOService is a marker
interface for all the services that are part of SCIFIO. When an
org.scijava.Context is initialized as it is here, it's typically given a
set of base service interfaces and then loads all implementations of that
service. So it seems like the Context knows about the SCIFIOService
interface, but didn't discover any implementations (things like
DefaultFormatService, DefaultImgUtilityService).

 So this brings me to my next point: I think there is either a) a bug in
jython where annotations are not preserved or b) a bug with the class
loading logic used by Fiji/IJ2. I am leaning towards a) right now.

 I am using an Ubuntu 12.04 64-bit VM. I installed Jython 2.5.3, but I
suspect you can get this working with 2.5.1.

 Anyway, I went back to OSX and tested jython with the -Dpython.path
option, and got the same missing service exception. But! If I set
$CLASSPATH (java automatically picks up the $CLASSPATH environment
variable) and run the equivalent of:

jython macros/imglib0.py /home/hajaalin/Data/Misha/composite1.ome.tif

it works! Thus I believe that python.path has a bug and although jython
supports discovery of classes on python.path, it does not preserve their
annotations (or some similar metadata is being lost).

So instead of setting CP and passing it via -Dpython.path, just use:

export CLASSPATH=`find /home/hajaalin/Software/fiji-20140219/Fiji.app/jars
-name '*.jar' |sed ':a;N;$!ba;s/\n/:/g'`

A simple rule of thumb is, try running a random SCIFIO class like "java
io.scif.SCIFIOService" from the command line. If you get a NoClassDef
error, your CLASSPATH is not configured correctly. If you get a
"NoSuchMethodError: main", your CLASSPATH is correct and your jython will
pick up all the desired classes.

Moving on...

jython macros/imglib0.py /home/hajaalin/Data/Misha/composite1.ome.tif

^ That then works a bit better with my CLASSPATH set, except I get a
different runtime error about how ImgMode.CELL can't be coerced to ImgMode.
(same error I get when running using Fiji).

I notice that you aren't actually using the SCIFIOConfig you construct, so
if you delete those lines and I'm finally able to open an image. The
SCIFIOConfig isn't strictly necessary either - SCIFIO will open it as a
CellImg automatically if it needs to. I will try to investigate further as
to how to get the types working for a nested enum in jython..

You may see yet another error message about io.scif.bf.BioFormatsFormat
failing. This is because some jars in Fiji are out of date, but that
shouldn't cause catastrophic failure (it just means that some proprietary
formats won't be supported right now). These jars should be updated this
week.

I hope this helps. Let me know if you can't get this working on your end.

- Mark
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