These are chat archives for fiji/fiji

8th
Apr 2016
George Marselis
@georgemarselis
Apr 08 2016 10:46
Hey guys, I am trying to run fiji to do some cell image processing
i am getting the following error: .ImageJ_3D_Viewer.props (No such file or directory)
i am running java 1.8 and the latest fiji version
any clues please?
Stefan Helfrich
@stelfrich
Apr 08 2016 11:17
hey @georgemarselis. which operating system are you running?
George Marselis
@georgemarselis
Apr 08 2016 11:27
hhey @stelfrich . MacOSX Le (sic) capitan
Stefan Helfrich
@stelfrich
Apr 08 2016 11:35
This seems to be a known issue, that should actually be fixed (imagej/imagej#120)..
I am still on Yosemite, so I can’t reproduce the problem now
George Marselis
@georgemarselis
Apr 08 2016 11:35
@stelfrich yeah, i saw that bug report, so, i was wondering what was going on
hokay. hm can i provide you with a macosx vm?
i'll roll one with vagrant
Stefan Helfrich
@stelfrich
Apr 08 2016 11:36
You could to that. Although @ctrueden is running El Capitan, afaik, to investigate such issues.
George Marselis
@georgemarselis
Apr 08 2016 11:37
alright. I'll wait for @ctrueden to respond
thanks!
odinsbane
@odinsbane
Apr 08 2016 11:37
I don't see how #120 is relevant?
sorry, I meant the link above. imagej/imagej#120
Stefan Helfrich
@stelfrich
Apr 08 2016 11:38
You could open a thread on the forum.. that makes things easier accessible for future reference
George Marselis
@georgemarselis
Apr 08 2016 11:39
will do. thank you!
Stefan Helfrich
@stelfrich
Apr 08 2016 11:39
@odinsbane I actually just searched for the filename.. http://fiji.sc/bugzilla/show_bug.cgi?id=1122 @hinerm mentioned the issue in there..
And imagej/imagej#120 is closed, so I thought the issue should be gone by now..
George Marselis
@georgemarselis
Apr 08 2016 11:40
just to clarify i'm trying to see a stack in 3D
Stefan Helfrich
@stelfrich
Apr 08 2016 11:41
Yep, via the Plugins>3D Viewer I assume?
odinsbane
@odinsbane
Apr 08 2016 11:41
@georgemarselis does the console pop up?
George Marselis
@georgemarselis
Apr 08 2016 11:41
@odinsbane negative
@odinsbane well, it does, but only to give me an error
^mentioned above
@stelfrich affermative
odinsbane
@odinsbane
Apr 08 2016 11:42
@stelfrich When I click I see more information, when it popped up here I didn't see how it was relevant.
@georgemarselis does it say which 3D version your are using? eg. 3D [dev] 1.x.x ...
George Marselis
@georgemarselis
Apr 08 2016 11:45
@odinsbane looking
negative
odinsbane
@odinsbane
Apr 08 2016 11:49
It does down there at the bottom of the console. That is the current java3d though. I am not sure if this is the same issue.
George Marselis
@georgemarselis
Apr 08 2016 11:49
@odinsbane ooh, yeah, sorry missed it. ENOCOFFEE
odinsbane
@odinsbane
Apr 08 2016 12:03
Did you try starting fiji, and starting the 3D viewer w/out running another plugin?
George Marselis
@georgemarselis
Apr 08 2016 12:04
@odinsbane yup, that's exactly what i'm doing no other plugin. want me to record a video?
odinsbane
@odinsbane
Apr 08 2016 12:07
@georgemarselis No, that is fine. Did you start a forum post? I just thought you might have been starting the 3d viewer from another plugin since the stacktrace has trackem2 classes in it.
George Marselis
@georgemarselis
Apr 08 2016 12:08
need to write these last 10 lines of code for this bash script and will start the forum post asap
Curtis Rueden
@ctrueden
Apr 08 2016 13:54
@georgemarselis You have the Java-8 update site enabled right?
George Marselis
@georgemarselis
Apr 08 2016 14:17
@ctrueden ya
Curtis Rueden
@ctrueden
Apr 08 2016 14:21
@georgemarselis Did you try just creating that missing file?
The TrakEM2 stack trace is a known issue. TrakEM2 does not work with the Java-8 update site enabled yet. The code is fixed, but not yet released by @axtimwalde.
George Marselis
@georgemarselis
Apr 08 2016 14:21
@ctrueden hmmm. touch -a .ImageJ_3D_Viewer.props ?
just empty?
Curtis Rueden
@ctrueden
Apr 08 2016 14:22
Yeah, give it a try.
Obviously, that's just a workaround—we should fix this bug—but it might get you going.
I'm booting up my Windows VM now to see whether I have that file, and if so, what's in there.
no dice
Curtis Rueden
@ctrueden
Apr 08 2016 14:24
Like I said: TrakEM2 definitely will not work, regardless.
But the 3D Viewer should.
If you need TrakEM2 support, like, now, download a Life-Line version of Fiji and then update it fully. It will be the latest Java-6-compatible version, which will work with TrakEM2.
George Marselis
@georgemarselis
Apr 08 2016 14:29
nah, i just need the 3d viewer to work
Curtis Rueden
@ctrueden
Apr 08 2016 14:29
The latest Fiji downloads are bundled with Java 8 now, with the Java-8 update site enabled, and TrakEM2 will not (at the moment) work. But we are in the process of fixing that.
OK. I'm curious why you have TrakEM2 in your stack trace, then.
George Marselis
@georgemarselis
Apr 08 2016 14:30
@ctrueden dunno either. to be honest this is my first week with this software. i'm learning as i crash/go along.
Curtis Rueden
@ctrueden
Apr 08 2016 14:31
Sorry for all the speed bumps. This is a messy time, because we are transitioning to Java 8, but we want to do it without breakages for legacy workflows.
And Java 3D is one of the most major culprits for problems with this transition.
George Marselis
@georgemarselis
Apr 08 2016 14:31
@ctrueden hey man, don't apologise. you are providing scientific software for free
i be buying beer
or $beverageofchoice
Curtis Rueden
@ctrueden
Apr 08 2016 14:32
Sure. I'm glad you appreciate that. But it still costs many people lots of time when there are major bugs like this. I hope things will be better within the next months after we are fully on Java 8. (A few users will whine about that, but too bad—Java 6 is majorly EOL at this point, and causes lots of other problems.)
George Marselis
@georgemarselis
Apr 08 2016 14:33
ok, how can i turn off TrakEM2? it's not in the modules
Curtis Rueden
@ctrueden
Apr 08 2016 14:33
Huh. So... that stack trace appears for you when you try to run Plugins > 3D Viewer? That is so odd.
What is your exact workflow here?
Mine is:
1) File > Open Samples > T1 Head
2) Image > Type > 8-bit
3) Plugins > 3D Viewer
Are you doing something different?
(BTW, you can press L for the Command Finder, to launch these plugins much faster.)
George Marselis
@georgemarselis
Apr 08 2016 14:34
  1. double click on "stack_test" directory
  1. drag drop test.xml on fiji bar
3) wait for files to load
4) hit 3
Curtis Rueden
@ctrueden
Apr 08 2016 14:35
What is test.xml? Because TrakEM2 is interpreting that as its project file here.
George Marselis
@georgemarselis
Apr 08 2016 14:36
it's a test project file full of info about rat brain cancer cells
Curtis Rueden
@ctrueden
Apr 08 2016 14:36
"test project file" from what kind of system? A microscope acquisition system? What flavor? Or do you mean a TrakEM2 project?
Because .xml, as you know, is a very general format and could be many different things.
Anyway, it is unlikely that opening a .xml file directly will work as you desire here?
George Marselis
@georgemarselis
Apr 08 2016 14:37
i'm sorry i didn't get the last thing you said
Curtis Rueden
@ctrueden
Apr 08 2016 14:39
I don't understand. Are you using the Gitter web client? Gitter is a server-centric protocol—I verified that all the things I've said (the last one started with "Anyway, it is unlikely...") were submitted properly. So... just reload the page?
George Marselis
@georgemarselis
Apr 08 2016 14:39
cross-talk sorry :D
@ctrueden hm. hold up let me ask, cuz you lost me at "what kind of system? A microscope acquisition system? What flavor? Or do you mean a TrakEM2 project?"
<-- newly minted grad student.
Curtis Rueden
@ctrueden
Apr 08 2016 14:41
Where did this data come from? What are the directory contents? The test.xml and a bunch of TIFF files? Or file extensions?
Are you able to load the data into Fiji using File > Open? Or File > Import > Bio-Formats?
George Marselis
@georgemarselis
Apr 08 2016 14:41
File > open
Curtis Rueden
@ctrueden
Apr 08 2016 14:42
So, it is a TrakEM2 project!
George Marselis
@georgemarselis
Apr 08 2016 14:42
^-- whole contents
ooh. ok
sorry!
Curtis Rueden
@ctrueden
Apr 08 2016 14:43
So, you cannot use Java 8 for that data right now.
George Marselis
@georgemarselis
Apr 08 2016 14:43
ah!
go back to java 6
@ctrueden where do i send the beer?
Curtis Rueden
@ctrueden
Apr 08 2016 14:43
Yeah. Easiest way: download latest Life-Line version of Fiji. Then fully update it.
It comes bundled with Java 1.6.0_24
George Marselis
@georgemarselis
Apr 08 2016 14:43
excellent
Curtis Rueden
@ctrueden
Apr 08 2016 14:43
Again: it sucks that TrakEM2 does not work with Java 8 right now. And we are in the process of fixing that. So... keep an eye on the news posts and it should work "soon" :-)
George Marselis
@georgemarselis
Apr 08 2016 14:44
thank you man!
appreciate it!
Curtis Rueden
@ctrueden
Apr 08 2016 14:44
Glad to help!
Stephan Saalfeld
@axtimwalde
Apr 08 2016 14:56
Good morning everybody
Richard Domander
@rimadoma
Apr 08 2016 14:57
Afternoon
Stephan Saalfeld
@axtimwalde
Apr 08 2016 14:57
@ctrueden could you make
<dependency>
  <groupId>ch.systems.cisd</groupId>
  <artifactId>jhdf5</artifactId>
  <version>14.12.5</version>
</dependency>
available?
this version contains a fix for losing file handles by garbage collection which is very useful for BDV code that we're currently writing
Curtis Rueden
@ctrueden
Apr 08 2016 14:59
@axtimwalde On it...
Stephan Saalfeld
@axtimwalde
Apr 08 2016 14:59
their svn is currently not responding but they do have a zip download on the wiki https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page
Stephan Saalfeld
@axtimwalde
Apr 08 2016 15:06
@ctrueden thanks!
Curtis Rueden
@ctrueden
Apr 08 2016 15:07
@axtimwalde Note that the ch.systems.cisd groupId is from the OME Maven repository, not the ImageJ one. The ImageJ repository—and corresponding pom-scijava version management—uses groupId cisd.
Curtis Rueden
@ctrueden
Apr 08 2016 15:15
I uploaded 14.12.1 through 14.12.5 and updated pom-scijava to the latest as well (scijava/pom-scijava@7dfefb9).
So just to be clear: it should work now, if you change the groupId to cisd.
Pretty sure @axtimwalde was talking in UGT above.
Richard Domander
@rimadoma
Apr 08 2016 15:21
@ctrueden Heh, ok
Stephan Saalfeld
@axtimwalde
Apr 08 2016 17:25
@ctrueden Thanks!
Curtis Rueden
@ctrueden
Apr 08 2016 19:04
@tpietzsch @bogovicj I just ran into a snag updating Fiji to the latest component versions:
  Found in:
    sc.fiji:bigdataviewer-core:jar:2.2.1:runtime
    sc.fiji:bigwarp_fiji:jar:2.1.1:runtime
  Duplicate classes:
    net/imglib2/display/ARGBARGBColorConverter.class
    net/imglib2/display/ARGBARGBColorConverter$VolatileToGray.class
    net/imglib2/display/ARGBARGBColorConverter$ToGray.class
@tpietzsch Where is this class ultimately intended to live? Can we migrate it to its final destination, then have these two components both depend on that one?
Curtis Rueden
@ctrueden
Apr 08 2016 19:36
@tpietzsch @bogovicj For the moment, I worked around it by pinning Fiji to the older 2.1.0 version of bigdataviewer-core. Once it is resolved on the bigwarp_fiji side, we can upgrade both components in Fiji again.
I tried to make a PR for bigwarp_fiji to facilitate this, but bigwarp_fiji also has other build errors when updating to pom-fiji 22.0.0, so I gave up.
Curtis Rueden
@ctrueden
Apr 08 2016 20:04
I see that bigdataviewer-core 2.2.1 was already uploaded to Fiji. I just left it that way, even though it has duplicate classes with bigwarp_fiji. In practice this will be OK as long as the classes are congruent.
But the fiji/fiji repository master branch is currently pinned to bigdataviewer-core 2.1.0 as a workaround, so the build succeeds.
Curtis Rueden
@ctrueden
Apr 08 2016 21:34
@/all New version of ImageJ released: 2.0.0-rc-47. Lots of new stuff, including a revamped (but still buggy/alpha-level!) Script Interpreter. Also fixes the long-standing inability to use "choices" in a parameterized script, as well as a recent BeanShell bug. And tons of other things I don't have time to to mention at this moment.
@kephale Sorry to say that Clojure isn't working in the Script Interpreter yet for some reason...
@skalarproduktraum This version of the Script Interpreter UI is built on that new ScriptREPL I showed you back at the hackathon. It now has a variables sidebar so you can see the names and values of stuff. And you can switch language on the fly. But only some languages work currently, for various reasons.