ClearVolume minimal example

clearvolume
Tags: #<Tag:0x00007fd69c1237f0>

#1

Hi everyone

(especially @fjug)

A collaborator of mine is running a hackathon this week. The students are interested in trying to get ClearVolume working within their plugin. They mentioned to me they were having trouble getting the maven dependencies to work… I gave it a shot and was defeated as well.

My attempt is here

The pom is here

Something is wrong with the coremem link

“C:\Users\bnorthan.m2\repository\net\coremem\CoreMem\0.4.3-1-gf91e850\CoreMem-0.4.3-1-gf91e850.jar; error in opening zip file”

Does anybody have a link to a working pom that includes all the clearvolume dependencies?? I found one on the maven repository, but when using that reference, it still looks for and complains about coremem.

It would be awesome if anyone has any advice. I think the hackathon ends tomorrow. Thanks


#2

I tried to run the net.clearvolume:clearvolume artifact using the jrun tool by @ctrueden:

jrun -v net.clearvolume:clearvolume

but it fails with:

No versions available for net.coremem.CoreMem:jar:[0.1.6,1.0.0]

As far as I can see, CoreMem is not available from maven.imagej.net. In addition, the latest version of clearvolume there is 1.2.1, whereas the latest version should be 1.3.26 (and Loic Royer updated the CoreMem dependencies recently).

https://github.com/ClearVolume/ClearVolume/commit/8c2b97adb536ce94c811bfae4fb168c2e68038af


Edit: FWIW, I invited Loic to this forum discussion. However, I think he’s currently attending the ELMI meeting, so it might take a while for him to respond.


#3

Hi @/all,

we have the CSBD inauguration next week. Since there will be a bunch of live demos all our code base in pretty much in ‘movement’, let’s say… I’m sorry that this causes this inconvenient problems for you.

On the good side: since there will be the Learnathon in Dresden next month you can be ensured that it will work like charm very soon again. Plus: there will be online-material in the form of exercises and minimal examples. Yay! :slight_smile:

Best,
Florian


#4

Looks like imglib2-clearvolume has a working pom, courtesy of @ctrueden.

I was able to get an example project compiling, though the examples don’t seem to show anything. Perhaps it is a driver issue (testing on Windows 10, nvidia drivers and cuda have been installed and updated)

I fully understand things are in flux, and will be smoother soon. Hopefully the hacking group I was talking to, gains an interest in ImageJ and ClearVolume, and checks back to see updates and progress. If anyone has any suggestions for the following issues let me know…

a) Running testOpenClearVolumeOnToyVolume gives

ClearGLWindow: GLProfile[GL4bc/GL4bc.hw]

but then lClearVolumeRenderer.isShowing() is false, and the program ends.

b) Running testImageJClearVolumePlugin gives

com.jogamp.opengl.util.AnimatorBase$UncaughtAnimatorException: com.jogamp.opengl.GLException: Caught UnsupportedWrappingException: Cannot wrap a non-native NIO Buffer on thread SciJava-14bae047-Thread-0-FPSAWTAnimator#00-Timer0

#5

Hi @bnorthan,

I just got rid of the error in b) by updating dependencies to more current versions:

https://github.com/ClearVolume/imglib2-clearvolume/compare/master...haesleinhuepf:master

Cheers,
Robert