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

[Mark Hiner]

Hi Harri,

[ERROR] Cannot create plugin: class='io.scif.bf.
> BioFormatsFormat', priority=10000.0, enabled=true, pluginType=Format
> java.lang.IllegalAccessError: tried to access field
> io.scif.AbstractFormat.suffixes from class io.scif.bf.BioFormatsFormat
>

This ugly stack trace comes up from the jar containing BioFormatsFormat,
part of the SCIFIO-BF-Compat
<https://github.com/scifio/scifio-bf-compat>layer, being out of date.
In and of itself, that is not a critical problem
as long as there are other formats that can open your dataset. But
something that should still be fixed, certainly.

at io.scif.ome.xml.meta.OMEXMLFormat$Checker.<init>(OMEXMLFormat.java:244)
> ...
> java.lang.NoSuchFieldError: java.lang.NoSuchFieldError: suffixNecessary
>

Similarly, the OME-Formats
<https://github.com/scifio/ome-formats>component was out of date and
did not adhere to the latest SCIFIO API.
Ideally it would be great to get this working properly as it adds better
support for ome.tiffs.

export CLASSPATH=`find /home/hajaalin/Software/mvn-IJ2/target/dependency
> -name '*.jar' |sed ':a;N;$!ba;s/\n/:/g'`
>
jython /home/hajaalin/Software/fiji-20140219/Fiji.app/macros/imglib1.py
> /home/hajaalin/Data/Misha/composite1.ome.tif
>

This is tangential, but I feel like I am doing a disservice by using the
command line invocations as examples in my e-mails. You were doing the
exact correct thing by using Fiji.app/ImageJ-linux64 to execute your
script, and that is something I would like to encourage (additionally
because if there are problems using fiji to run your script, I want to
ensure they are fixed).

I will still test with both Fiji and jython directly on my end to ensure
they behave equivalently, but I would encourage you to just stick with
using Fiji for general use, as it takes care of bookkeeping for you and
really should be both simpler and superior.

Now there are no errors and I get directly the Java elf, but still no image.
>

OK, so I uploaded several new components to Fiji this morning to at least
fix the jar skew errors you were seeing (although we won't have perfect
ome.tif support until this
ticket<https://github.com/imagej/imagej/issues/21>is complete -
hopefully soon). I tested on my Linux VM by downloading a
fresh Fiji, and got your datasets (thank you for that!). On my end, I was
able to open both composite1.ome.tif and joo.jpg from all of:

* Fiji (legacy mode)
* IJ2 (Fiji -> Switch to modern mode)
* your script via Fiji
* your script via jython

These datasets definitely look worse from the script than Fiji/IJ2, which
is reasonable since they aren't composited or autoscaled or anything... but
they do look correct to me and opened without error.

Anyway, I hope the latest Fiji works for you. Give it a try and let me know
if you run into any more problems.

Thank you for your persistence!

- Mark


On Thu, Feb 27, 2014 at 5:04 AM, Harri Jäälinoja <
harri.jaalinoja at helsinki.fi> wrote:

> Hi again,
>
> I tried also with the set of jars I got with the maven and the pom.xml I
> sent earlier:
>
> export CLASSPATH=`find /home/hajaalin/Software/mvn-IJ2/target/dependency
> -name '*.jar' |sed ':a;N;$!ba;s/\n/:/g'`
> jython /home/hajaalin/Software/fiji-20140219/Fiji.app/macros/imglib1.py
> /home/hajaalin/Data/Misha/composite1.ome.tif
>
> Now there are no errors and I get directly the Java elf, but still no
> image.
>
> Harri
>
>
> --
> __________________________________________________
> 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
>
>
> _______________________________________________
> ImageJ-devel mailing list
> ImageJ-devel at imagej.net
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>
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