<div dir="ltr"><div>Hi Harri,<br><br></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">[ERROR] Cannot create plugin: class='<a href="http://io.scif.bf" target="_blank">io.scif.bf</a>.<br>
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<br></blockquote><div bgcolor="#FFFFFF"><br></div><div bgcolor="#FFFFFF">This ugly stack trace comes up from the jar containing BioFormatsFormat, part of the <a href="https://github.com/scifio/scifio-bf-compat" target="_blank">SCIFIO-BF-Compat</a> layer, being out of date.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.<br>
<br><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">at
io.scif.ome.xml.meta.OMEXMLFormat$Checker.<init>(OMEXMLFormat.java:244)<br><div bgcolor="#FFFFFF">...<br></div>java.lang.NoSuchFieldError: java.lang.NoSuchFieldError:
suffixNecessary<br></blockquote><br></div><div bgcolor="#FFFFFF">Similarly, the <a href="https://github.com/scifio/ome-formats" target="_blank">OME-Formats</a> component was out of date and did not adhere to the latest SCIFIO API. Ideally it would be great to get this working properly as it adds better support for ome.tiffs.<br>
</div><div bgcolor="#FFFFFF"><br></div><div bgcolor="#FFFFFF"><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">export CLASSPATH=`find /home/hajaalin/Software/mvn-IJ2/target/dependency -name '*.jar' |sed ':a;N;$!ba;s/\n/:/g'`<br>
</blockquote><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">jython /home/hajaalin/Software/fiji-20140219/Fiji.app/macros/imglib1.py /home/hajaalin/Data/Misha/composite1.ome.tif<br>
</blockquote><div id=":c1d" class=""><br></div><div id=":c1d" class="">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).<br>
<br></div><div id=":c1d" class="">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.<br>
<br><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">Now there are no errors and I get directly the Java elf, but still no image.<br></blockquote><br>
</div><div id=":c1d" class="">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 <a href="https://github.com/imagej/imagej/issues/21">this ticket</a> 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:<br></div><div id=":c1d" class=""><br></div><div id=":c1d" class="">* Fiji (legacy mode)<br></div><div id=":c1d" class="">* IJ2 (Fiji -> Switch to modern mode)<br></div><div id=":c1d" class="">* your script via Fiji<br>
</div><div id=":c1d" class="">* your script via jython<br></div><div id=":c1d" class=""><br></div><div id=":c1d" class="">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.<br>
<br></div><div id=":c1d" class="">Anyway, I hope the latest Fiji works for you. Give it a try and let me know if you run into any more problems.<br><br></div><div id=":c1d" class="">Thank you for your persistence!<br><br>
</div><div id=":c1d" class="">- Mark<br></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Feb 27, 2014 at 5:04 AM, Harri Jäälinoja <span dir="ltr"><<a href="mailto:harri.jaalinoja@helsinki.fi" target="_blank">harri.jaalinoja@helsinki.fi</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi again,<br>
<br>
I tried also with the set of jars I got with the maven and the pom.xml I sent earlier:<br>
<br>
export CLASSPATH=`find /home/hajaalin/Software/mvn-<u></u>IJ2/target/dependency -name '*.jar' |sed ':a;N;$!ba;s/\n/:/g'`<br>
jython /home/hajaalin/Software/fiji-<u></u>20140219/Fiji.app/macros/<u></u>imglib1.py /home/hajaalin/Data/Misha/<u></u>composite1.ome.tif<br>
<br>
Now there are no errors and I get directly the Java elf, but still no image.<span class="HOEnZb"><font color="#888888"><br>
<br>
Harri</font></span><div class="im HOEnZb"><br>
<br>
-- <br>
______________________________<u></u>____________________<br>
Harri Jäälinoja<br>
Light Microscopy Unit<br>
Institute of Biotechnology, University of Helsinki<br>
<a href="http://www.biocenter.helsinki.fi/bi/lmu/" target="_blank">http://www.biocenter.helsinki.<u></u>fi/bi/lmu/</a><br>
<a href="tel:%2B358%209%20191%2059370" value="+358919159370" target="_blank">+358 9 191 59370</a> fax <a href="tel:%2B358%209%20191%2059366" value="+358919159366" target="_blank">+358 9 191 59366</a><br>
<br>
<br></div><div class="HOEnZb"><div class="h5">
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