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layer, being out of date.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component was out of date and did not adhere to the latest SCIFIO API.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.jaalin...@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@imagej.net > http://imagej.net/mailman/listinfo/imagej-devel >
_______________________________________________ ImageJ-devel mailing list ImageJ-devel@imagej.net http://imagej.net/mailman/listinfo/imagej-devel
