Posted by
Dr. Michael DOUBE on
Dec 17, 2018; 5:19am
URL: http://imagej.273.s1.nabble.com/bonej-tp5021576p5021579.html
Hi Larry,
Quick update:
I have replicated your bug. I don't think it's a BoneJ-specific thing,
looks more like a core ImageJ / SciJava thing. Yes it is because the
data is too big. Try again on a cropped subset of the data. Under other
circumstances I'd suggest downsampling your data (e.g. scaling by 0.5 in
x, y, z), but that would destroy some of the fractal nature of your image.
Let me take care of notifying the IJ devs. Thanks for the report.
Best regards,
Michael
On 15/12/2018 06:59, Anovitz, Lawrence {Larry} M. wrote:
> HI all,
> I am trying to get Bonej to run 3D fractal dimension analysis
>
> Didn’t have any luck with FIJI/BoneJ2 due to some sort of Java exception (posted last Monday, analyzing an approx. 2300 slice stack)
> So I went to Bonej1. The problem now is that 3D viewer won’t correctly install Java3D.
> I get the following error when I attempt to auto-install it from 3D viewer.
> Can anyone please tell me how to fix this (or get BoneJ2 running? Thank you
> --Larry
>
>
> downloading
http://132.187.25.13/java3d/j3d-1_5_2-macosx.zip> to /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/j3d-1_5_2-macosx.zip
> create folder /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T//java3d
> Extracting j3d-jre.zip to /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d
> create folder /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d/j3d-1_5_2-macosx/
> Extracting j3d-1_5_2-macosx/j3d-jre.zip to /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d
> Extracting all to /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d
> create folder /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d/lib/
> create folder /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d/lib/ext/
> Extracting lib/ext/j3dcore.jar to /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d
> Extracting lib/ext/j3dutils.jar to /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d
> Extracting lib/ext/vecmath.jar to /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d
> Found java extension folder: /Applications/Fiji-Java6.app/java/macosx-java3d/Home/lib/ext
> moving /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d/lib/ext/j3dcore.jar to /Applications/Fiji-Java6.app/java/macosx-java3d/Home/lib/ext/j3dcore.jar
> moving /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d/lib/ext/j3dutils.jar to /Applications/Fiji-Java6.app/java/macosx-java3d/Home/lib/ext/j3dutils.jar
> moving /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/java3d/lib/ext/vecmath.jar to /Applications/Fiji-Java6.app/java/macosx-java3d/Home/lib/ext/vecmath.jar
> Detecting Mac OS X operating system, installing Jogl
> downloading
http://download.java.net/media/jogl/builds/archive/jsr-231-1.1.1/jogl-1.1.1-macosx-universal.zip> to /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/jogl-1.1.1-macosx-universal.zip
> create folder /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T//jogl
> /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/jogl not created; exists already
> Extracting all to /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/jogl
> /var/folders/sc/wm52xk5528b2m95ztnh15clj5lkhmb/T/jogl-1.1.1-macosx-universal.zip is not a valid zip file.
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
Dr. Michael DOUBE
Associate Professor
Jockey Club College of Veterinary Medicine and Life Sciences
City University of Hong Kong
Tat Chee Avenue, Kowloon
Hong Kong
Tel: +852 3442 6782
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