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bonej

Anovitz, Lawrence {Larry} M.
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.

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Re: bonej

Dr. Michael DOUBE
Hi Larry,

We're now providing support for BoneJ via the forum:
https://forum.image.sc/tags/bonej

Since many of the same people are here and there, I'll reply to this
issue on the mailing list. Thanks for raising it.

> Didn’t have any luck with FIJI/BoneJ2 due to some sort of Java exception (posted last Monday, analyzing an approx. 2300 slice stack)

Where did you post this exception? I may have missed it. Would you mind
posting a bug report on GitHub?
https://github.com/bonej-org/BoneJ2/issues

> So I went to Bonej1. The problem now is that 3D viewer won’t correctly install Java3D.

Better to stick with BoneJ2. Please bear with us while we iron out the bugs.

> I get the following error when I attempt to auto-install it from 3D viewer.

Not sure about this one. Mac has been problematic for us in general.
this is one of the things that has forced us to move to ImageJ2 / Java8.

> Can anyone please tell me how to fix this (or get BoneJ2 running? Thank you

Please post your exception in a bug report on the BoneJ2 issue tracker.

Thanks,

Michael

--
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


Disclaimer: This email (including any attachments) is for the use of the intended recipient only and may contain confidential information and/or copyright material. If you are not the intended recipient, please notify the sender immediately and delete this email and all copies from your system. Any unauthorized use, disclosure, reproduction, copying, distribution, or other form of unauthorized dissemination of the contents is expressly prohibited.

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Re: bonej

Dr. Michael DOUBE
In reply to this post by Anovitz, Lawrence {Larry} M.
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


Disclaimer: This email (including any attachments) is for the use of the intended recipient only and may contain confidential information and/or copyright material. If you are not the intended recipient, please notify the sender immediately and delete this email and all copies from your system. Any unauthorized use, disclosure, reproduction, copying, distribution, or other form of unauthorized dissemination of the contents is expressly prohibited.

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Re: bonej

Anovitz, Lawrence {Larry} M.
In reply to this post by Dr. Michael DOUBE
Hi Michael
     I went to the bonej2/issues on Github and it looks to me like you have already found my initial posting and reposted it there,
so I didn't repost. Is this right?  I also see that you commented, but assume that comment is not a solution for me, but a suggestion for
those who might fix the problem

I'm happy to stick with bonej2.  If you need the original image that was causing the problems just let me know and I will send it to you at
Whatever address you wish. I can also run other test on my machine if that would help.  Just let me know.

Many thanks for all your help.

--Larry


On 12/16/18, 11:05 PM, "ImageJ Interest Group on behalf of Dr. Michael DOUBE" <[hidden email] on behalf of [hidden email]> wrote:

    Hi Larry,
   
    We're now providing support for BoneJ via the forum:
    https://forum.image.sc/tags/bonej
   
    Since many of the same people are here and there, I'll reply to this
    issue on the mailing list. Thanks for raising it.
   
    > Didn’t have any luck with FIJI/BoneJ2 due to some sort of Java exception (posted last Monday, analyzing an approx. 2300 slice stack)
   
    Where did you post this exception? I may have missed it. Would you mind
    posting a bug report on GitHub?
    https://github.com/bonej-org/BoneJ2/issues
   
    > So I went to Bonej1. The problem now is that 3D viewer won’t correctly install Java3D.
   
    Better to stick with BoneJ2. Please bear with us while we iron out the bugs.
   
    > I get the following error when I attempt to auto-install it from 3D viewer.
   
    Not sure about this one. Mac has been problematic for us in general.
    this is one of the things that has forced us to move to ImageJ2 / Java8.
   
    > Can anyone please tell me how to fix this (or get BoneJ2 running? Thank you
   
    Please post your exception in a bug report on the BoneJ2 issue tracker.
   
    Thanks,
   
    Michael
   
    --
    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
   
   
    Disclaimer: This email (including any attachments) is for the use of the intended recipient only and may contain confidential information and/or copyright material. If you are not the intended recipient, please notify the sender immediately and delete this email and all copies from your system. Any unauthorized use, disclosure, reproduction, copying, distribution, or other form of unauthorized dissemination of the contents is expressly prohibited.
   
    --
    ImageJ mailing list: http://imagej.nih.gov/ij/list.html
   


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Re: bonej

Dr. Michael DOUBE
Hi Larry,

>       I went to the bonej2/issues on Github and it looks to me like you have already found my initial posting and reposted it there,
> so I didn't repost. Is this right?

Yes that's correct. I've also chatted with some of the core Ops
developers on Gitter and tried a couple of things but so far we haven't
got a proper solution for larger data implemented.

>  I also see that you commented, but assume that comment is not a solution for me, but a suggestion for
> those who might fix the problem

That's correct, I've just flagged where the problem is coming from. In
short it seems like the way we are transforming ImageJ1-style ImagePlus
into ImageJ2-style Img is leading to a hard limit of data size. I'm
testing at the moment and can run fractal dimension on data
1024x1024x2048 successfully (but not 1024x1024x4096, which causes the
same exception), so hopefully you don't have to crop too much. Could you
try cropping and report back?

> I'm happy to stick with bonej2.

Great, thanks!

> If you need the original image that was causing the problems just let me know and I will send it to you

Thanks for the offer - not needed at the moment becuase I can replicate
just by using File>Image>New... and inputting your stack dimensions on a
black 8-bit image.

Michael

>
>
> On 12/16/18, 11:05 PM, "ImageJ Interest Group on behalf of Dr. Michael DOUBE" <[hidden email] on behalf of [hidden email]> wrote:
>
>      Hi Larry,
>      
>      We're now providing support for BoneJ via the forum:
>      https://forum.image.sc/tags/bonej
>      
>      Since many of the same people are here and there, I'll reply to this
>      issue on the mailing list. Thanks for raising it.
>      
>      > Didn’t have any luck with FIJI/BoneJ2 due to some sort of Java exception (posted last Monday, analyzing an approx. 2300 slice stack)
>      
>      Where did you post this exception? I may have missed it. Would you mind
>      posting a bug report on GitHub?
>      https://github.com/bonej-org/BoneJ2/issues
>      
>      > So I went to Bonej1. The problem now is that 3D viewer won’t correctly install Java3D.
>      
>      Better to stick with BoneJ2. Please bear with us while we iron out the bugs.
>      
>      > I get the following error when I attempt to auto-install it from 3D viewer.
>      
>      Not sure about this one. Mac has been problematic for us in general.
>      this is one of the things that has forced us to move to ImageJ2 / Java8.
>      
>      > Can anyone please tell me how to fix this (or get BoneJ2 running? Thank you
>      
>      Please post your exception in a bug report on the BoneJ2 issue tracker.
>      
>      Thanks,
>      
>      Michael
>      
>      --
>      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
>      
>      
>      Disclaimer: This email (including any attachments) is for the use of the intended recipient only and may contain confidential information and/or copyright material. If you are not the intended recipient, please notify the sender immediately and delete this email and all copies from your system. Any unauthorized use, disclosure, reproduction, copying, distribution, or other form of unauthorized dissemination of the contents is expressly prohibited.
>      
>      --
>      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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: bonej

Anovitz, Lawrence {Larry} M.
Hi Michael
    I tried cropping to 1206 x 1206 x 2293  (the real squared edges of our sample, which is actually a cylinder) and to 1024 x 1024 x 2293 and both
Failed.  I put this info on Github
--Larry

On 12/18/18, 1:25 AM, "Dr. Michael DOUBE" <[hidden email]> wrote:

    Hi Larry,
   
    >       I went to the bonej2/issues on Github and it looks to me like you have already found my initial posting and reposted it there,
    > so I didn't repost. Is this right?
   
    Yes that's correct. I've also chatted with some of the core Ops
    developers on Gitter and tried a couple of things but so far we haven't
    got a proper solution for larger data implemented.
   
    >  I also see that you commented, but assume that comment is not a solution for me, but a suggestion for
    > those who might fix the problem
   
    That's correct, I've just flagged where the problem is coming from. In
    short it seems like the way we are transforming ImageJ1-style ImagePlus
    into ImageJ2-style Img is leading to a hard limit of data size. I'm
    testing at the moment and can run fractal dimension on data
    1024x1024x2048 successfully (but not 1024x1024x4096, which causes the
    same exception), so hopefully you don't have to crop too much. Could you
    try cropping and report back?
   
    > I'm happy to stick with bonej2.
   
    Great, thanks!
   
    > If you need the original image that was causing the problems just let me know and I will send it to you
   
    Thanks for the offer - not needed at the moment becuase I can replicate
    just by using File>Image>New... and inputting your stack dimensions on a
    black 8-bit image.
   
    Michael
   
    >
    >
    > On 12/16/18, 11:05 PM, "ImageJ Interest Group on behalf of Dr. Michael DOUBE" <[hidden email] on behalf of [hidden email]> wrote:
    >
    >      Hi Larry,
    >      
    >      We're now providing support for BoneJ via the forum:
    >      https://forum.image.sc/tags/bonej
    >      
    >      Since many of the same people are here and there, I'll reply to this
    >      issue on the mailing list. Thanks for raising it.
    >      
    >      > Didn’t have any luck with FIJI/BoneJ2 due to some sort of Java exception (posted last Monday, analyzing an approx. 2300 slice stack)
    >      
    >      Where did you post this exception? I may have missed it. Would you mind
    >      posting a bug report on GitHub?
    >      https://github.com/bonej-org/BoneJ2/issues
    >      
    >      > So I went to Bonej1. The problem now is that 3D viewer won’t correctly install Java3D.
    >      
    >      Better to stick with BoneJ2. Please bear with us while we iron out the bugs.
    >      
    >      > I get the following error when I attempt to auto-install it from 3D viewer.
    >      
    >      Not sure about this one. Mac has been problematic for us in general.
    >      this is one of the things that has forced us to move to ImageJ2 / Java8.
    >      
    >      > Can anyone please tell me how to fix this (or get BoneJ2 running? Thank you
    >      
    >      Please post your exception in a bug report on the BoneJ2 issue tracker.
    >      
    >      Thanks,
    >      
    >      Michael
    >      
    >      --
    >      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
    >      
    >      
    >      Disclaimer: This email (including any attachments) is for the use of the intended recipient only and may contain confidential information and/or copyright material. If you are not the intended recipient, please notify the sender immediately and delete this email and all copies from your system. Any unauthorized use, disclosure, reproduction, copying, distribution, or other form of unauthorized dissemination of the contents is expressly prohibited.
    >      
    >      --
    >      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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