These are chat archives for fiji/fiji

20th
Mar 2018
Varun Kapoor
@kapoorlab
Mar 20 2018 10:26
@ctrueden Thanks Curtis, I got it working. About the 3D displayer, is it out already? When I try to use it I get: java.lang.NoClassDefFoundError: org/scijava/java3d/utils/universe/SimpleUniverse, Is hyperstack viewer the only other option left?
odinsbane
@odinsbane
Mar 20 2018 10:36
Is there a way for providing an incremental update without updating an update site?
Jan Eglinger
@imagejan
Mar 20 2018 10:39
@kapoorlab the class org.scijava.java3d.utils.universe.SimpleUniverse is in the org.scijava.j3dutils artifact: http://maven.imagej.net/#nexus-search;classname~org.scijava.java3d.utils.universe.SimpleUniverse
AFAICT, this is related to the 'old' 3D Viewer, and not SciView (if this is what you meant with "3D displayer"). SciView can be used via separate update site.
Jan Eglinger
@imagejan
Mar 20 2018 10:45
@odinsbane what do you mean by incremental update? There's currently no possibility to define "inter-dependencies" between update sites. You can also point people to jar files built automatically by Travis and uploaded to the maven repository.
(If it's just for testing etc)
Why not uploading to the existing update site?
odinsbane
@odinsbane
Mar 20 2018 10:48
I am doing some work with the plugin, so I might have more updates in the near future. Ill probably just upload to the existing site though.
I don't really have a good reason not to. It is just a pretty small change.
Varun Kapoor
@kapoorlab
Mar 20 2018 10:56
@imagejan Thanks, I did that and now I get a new error: java.util.concurrent.ExecutionException: java.lang.UnsatisfiedLinkError: Can't load library: /Users/aimachine/PreProcessingSuite/natives/macosx-universal//gluegen-rt
There is no directory called natives in my PreProcessingSuite folder
Varun Kapoor
@kapoorlab
Mar 20 2018 11:10
Maybe I will just try SciView
Varun Kapoor
@kapoorlab
Mar 20 2018 11:20
@tinevez Same error in Trackmate when I try to run it from Eclipse as a cloned repo (execture TrackMatePLugin_.java): Exception in thread "TrackMate view rendering thread" java.lang.UnsatisfiedLinkError: Can't load library: /Users/aimachine/TrackMate/natives/macosx-universal//gluegen-rt
odinsbane
@odinsbane
Mar 20 2018 12:07
@kapoorlab they should be in a jar file something along the line of gluegen-natives-rt or some such thing.
I don't know why, but for working with Intellij I had to unpack the jarfiles and then add the libraries to the java.library.path when I run programs with java3d.
Varun Kapoor
@kapoorlab
Mar 20 2018 12:12
@odinsbane where did you get those jar files from?
The all platforms will have everything, including other platforms. I just use the natives-macosx-universal.jar (s) Four of them.
On linux the native jar files load fine, but on osx, for some reason I had to unpack them. Although I think fiji/3d viewer works out of the box for me.
Varun Kapoor
@kapoorlab
Mar 20 2018 12:18
The file has an extension of 7z, how do you unpack such a file?
odinsbane
@odinsbane
Mar 20 2018 12:20
There is a program 7zip.
@kapoorlab Do you have a version of fiji working with the 3D viewer? If so it will have the jar files you need.
Varun Kapoor
@kapoorlab
Mar 20 2018 12:22
Ah let me check
odinsbane
@odinsbane
Mar 20 2018 12:24
When I go into the Fiji.app folder, they're under jars/macosx/ Then there are four of them.
Varun Kapoor
@kapoorlab
Mar 20 2018 12:24
Oh yeah the 3D viewer works in Fiji, just not on eclipse
odinsbane
@odinsbane
Mar 20 2018 12:24
I spent a little time trying to get Intellij to work with the native jar files and not unpack them, but I just ended up unpacking them and it worked.
Varun Kapoor
@kapoorlab
Mar 20 2018 12:26
I c, so I have to point these jars on the java build path for the repo I want to use the 3D viewer in, right?
odinsbane
@odinsbane
Mar 20 2018 12:33
The only way I could get it to work was to unpack the jarfiles and then when I run the program include an argument to the jvm. -Djava.library.path=/path/to/folder/with/jnilibs
Hopefully somebody chimes in with the correct way to do this. I would much prefer to just include the jarfiles.
Varun Kapoor
@kapoorlab
Mar 20 2018 12:41
No it works that way, I just did this to trackmate in eclipse: Right click on repo, -> Build Path -> Add external Archives -> Then add all the four jars in the Fiji macos folder that you mentioned and then it works
Curtis Rueden
@ctrueden
Mar 20 2018 17:31
@odinsbane It should not be necessary to manually unpack natives from JARs in IntelliJ. The Java code is supposed to provide magic to take care of that for you. Maybe @skalarproduktraum has some insight?