<div dir="ltr"><div>Hi Harri,<br><br><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">thanks a lot, setting CLASSPATH did the trick, after I removed the
unnecessary lines. I didn't understand them anyway, I was just
parroting <a href="http://fiji.sc/ImgLib2_Examples" target="_blank">http://fiji.sc/ImgLib2_Examples</a>.<br></blockquote><br></div><div>The <a href="https://github.com/scifio/scifio/blob/master/scifio/src/main/java/io/scif/config/SCIFIOConfig.java">SCIFIOConfig</a> class allows control over various aspects of the I/O behavior. In the example you were copying, it was encouraging images to be opened using the SCIFIOCell class, which allows for dynamic caching of planes, which is useful if your dataset won't fit in memory. It's basically a writeable virtual image. SCIFIO uses a heuristic to check image size vs. available memory though, and will automatically select CELL mode if the image won't reasonably be expected to fit.<br>
<br></div><div>Anyway, I did a little more experimentation and realized two things:<br></div><div>1) apparently you need to import the fully qualified nested enum path<br></div><div>2) jython seems to not support Java varargs, and always converts them to array arguments<br>
</div><div><br></div>This is the script that is working for me right now:<br><div><br><div style="margin-left:40px">import sys<br><br>from io.scif.config import SCIFIOConfig<br>import io.scif.config.SCIFIOConfig.ImgMode<br>
from io.scif.img import ImgIOException,ImgOpener<br><br>from <a href="http://java.io">java.io</a> import File<br><br>from net.imglib2.img import Img<br>from net.imglib2.img.display.imagej import ImageJFunctions<br>from net.imglib2.type import NativeType<br>
from net.imglib2.type.numeric import RealType<br><br>filename = sys.argv[1]<br><br>mode = [io.scif.config.SCIFIOConfig.ImgMode.CELL]<br>opener = ImgOpener()<br>config = SCIFIOConfig()<br>config.imgOpenerSetImgModes( mode )<br>
img = opener.openImg( filename, config )<br><br>ImageJFunctions.show( img )<br></div><br></div><div>But if you don't want to use the config, like I said, it is not required unless you find the default behavior to be insufficient. Just wanted to share my discoveries :)<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 it sort of works, but I still don't see the image. I get an
icon with the Java guy on the launcher bar, with the image name
and "(V) (3.1%)". If I click that, all other windows disappear and
there a small stick-like artefact on the top of the screen, but
nothing more.<br></blockquote><br></div><div>A good litmus test here would be to open your Fiji installation that you're harvesting your dependencies from, run Help > Switch to Modern Mode, and try using File > Open on your dataset. That should go through the same/very similar SCIFIO API you're testing in your jython script.<br>
<br>I mentioned that proprietary formats aren't currently supported by SCIFIO because of outdated jars in Fiji, but additionally the OME-TIFF support is probably similarly outdated (since it's not core SCIFIO). The TIFF reader should still be capable of rendering an ome.tiff correctly, but it's entirely possible you're running into a bug here.<br>
<br>If the dataset looks OK in Fiji's modern mode, then we at least know there's something else going on at the jython level. If it looks the same as when running your script, we know it's just an outdated dependency issue.<br>
<br></div><div>Also, feel free to <a href="http://fiji.sc/Upload_Sample_Image">upload your dataset</a>. I can then take a closer look at what's going on, and see if I can reproduce the display error you saw.<br><br></div>
<div>- Mark<br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Feb 26, 2014 at 9:19 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">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Mark, <br>
<br>
thanks a lot, setting CLASSPATH did the trick, after I removed the
unnecessary lines. I didn't understand them anyway, I was just
parroting <a href="http://fiji.sc/ImgLib2_Examples" target="_blank">http://fiji.sc/ImgLib2_Examples</a>.<br>
<br>
Now it sort of works, but I still don't see the image. I get an
icon with the Java guy on the launcher bar, with the image name
and "(V) (3.1%)". If I click that, all other windows disappear and
there a small stick-like artefact on the top of the screen, but
nothing more.<br>
<br>
Good progress anyway, more tomorrow.<span class="HOEnZb"><font color="#888888"><br>
<br>
Harri</font></span><div><div class="h5"><br>
<br>
On 26/02/14 16:41, Mark Hiner wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">Hi Harri,<br>
<br>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">java.lang.
<div>IllegalArgumentException:
java.lang.IllegalArgumentException: No compatible service:
io.scif.SCIFIOService<br>
</div>
hajaalin@biotek973:~/Software/
<div>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</div>
</blockquote>
<br>
</div>
<div class="gmail_extra">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).<br>
<br>
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.<br>
<br>
</div>
<div class="gmail_extra"> 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.<br>
<br>
</div>
<div class="gmail_extra"> 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 $CLASSPATH environment variable)
and run the equivalent of:<br>
<br>
</div>
<div class="gmail_extra">jython macros/imglib0.py
/home/hajaalin/Data/Misha/composite1.ome.tif<br>
<br>
</div>
<div class="gmail_extra">it works! Thus I believe that
python.path has a bug and although jython supports discovery
of classes on python.path, it does not preserve their
annotations (or some similar metadata is being lost).<br>
<br>
</div>
<div class="gmail_extra">So instead of setting CP and passing it
via -Dpython.path, just use:<br>
<br>
</div>
<div class="gmail_extra">export CLASSPATH=`find
/home/hajaalin/Software/fiji-20140219/Fiji.app/jars -name
'*.jar' |sed ':a;N;$!ba;s/\n/:/g'`<br>
<br>
</div>
<div class="gmail_extra">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.<br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Moving on...<br>
</div>
<div class="gmail_extra"><br>
jython macros/imglib0.py
/home/hajaalin/Data/Misha/composite1.ome.tif<br>
<br>
</div>
<div class="gmail_extra">
^ 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).<br>
<br>
</div>
<div class="gmail_extra">
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..<br>
<br>
</div>
<div class="gmail_extra">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.<br>
<br>
</div>
<div class="gmail_extra">I hope this helps. Let me know if you
can't get this working on your end.<br>
<br>
</div>
<div class="gmail_extra">- Mark<br>
</div>
</div>
</blockquote>
<br>
<br>
</div></div><div class=""><pre cols="72">--
__________________________________________________
Harri Jäälinoja
Light Microscopy Unit
Institute of Biotechnology, University of Helsinki
<a href="http://www.biocenter.helsinki.fi/bi/lmu/" target="_blank">http://www.biocenter.helsinki.fi/bi/lmu/</a>
<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>
</pre>
</div></div>
</blockquote></div><br></div>