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