Unable to use the assistant on 3d images #52
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Hi @DirkRemmers , I can run the outlined procedure on my computer (with an NVidia RTX 3050 Ti mobile, 4 GB RAM) with no issues. I presume it is a hardware issue on your side. Would you mind executing this code, e.g. from a Jupyter notebook and posting its output here? Best, |
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Hi Robert, Thank you for the quick reply. The output is the following: Thank you, |
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Hi Robert, You are probably very busy, but I wanted to ask you if you have any clue how I can fix this? Thanks, |
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Hi @DirkRemmers , I would love to help, but unfortunately I cannot reproduce the issue. I can only recommend updating drivers and setting up a fresh conda environment with recent napari and clesperanto versions. It might also be interesting to see what happens when processing a 10x10x10 large image. I hope that helps! Let me know if there are any updates or insights. Best, |
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Hi Robert and Dirk, I am experiencing the similar problems as Dirk if I want to process 3D images in the napari viewer. I created a new environment and installed the recent napari and clesperanto versions. I tried it on a 10x10x10 large image and get the same error as with any other 3D image, and no operation is performed: The output after executing Executing pyclesperanto_prototype functions via jupyter notebook works, however. I appreciate any further ideas how to solve the issue. Thanks for your help! Best, Carla |
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Hi @carladan and @DirkRemmers , if you call cle-operations from a Jupyter notebook and afterwards open napari from the notebook e.g. using the following code, does it work then? And one more question: what operating system (versions) are you using? Best, |
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And one more idea: Can you go to the menu Also, if you install cupy, and select it in that pulldown, does it work then? |
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Hi @haesleinhuepf and @carladan, I just made a fresh environment and tested Roberts suggestions. My operating system is Ubuntu 20.04.4 LTS Before installing cupy: When using a 10x10x10 image, I still get the same error as before, just as @carladan pointed out. However, when I try and use the assistant within napari to do the same operation, I get the previously mentioned error. When I try to get to the I want to let you know that I can see multiple options to open the assistant in napari as well. I see the options 'clEsperanto: Assistant', 'napari-assistant: Assistant' and 'clEsperanto' within the 'Plugins' menu, while I see 'Tools > Utilities > Assistant (na)' as well. I tried all of these options, and I do get some error messages with some of them:
After installing cupy: Hopefully this testing contains some value 😄 Dirk |
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Hi @haesleinhuepf and @DirkRemmers, I followed your instructions and opened napari from the notebook after calling cle-operations in the code. The operations work in the Jupyter notebook, but not in the napari viewer. If I go to the menu My operating system is Ubuntu 20.04.4 LTS as well. I hope this helps! Thanks very much for your input. Carla |
This sounds exactly like what I got here #59 |
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Hi @psobolewskiPhD , My versions are: When I update the Interestingly, I now do get the possibility to select the
Unfortunately updating to 0.18.2 did not solve the issue, good suggestion though! Thanks for all the help everyone! |
@DirkRemmers @carladan you are obviously both running Linux. I guess that's no random coincidence. Which Nvidia driver version do you have installed? |
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My nvidia driver version is 510.73.05 |
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Hi, |
Hello,
I recently started working with this amazing tool, and I have to say I like it a lot! It is really powerful to have all the pyclesperanto_prototype functionality in the napari viewer. All the 2d functions are working perfectly fine. However, the one thing that I can't get to work is 3d image processing (which is working fine for me with pyclesperanto_prototype).
Everytime I want to do any sort of operation on a 3d image, I get a big error that looks like this:
Just to be sure I don't have anything wrong in my environment, I made a new environment based on the installation instructions in the readme.
The version of napari, the assistant and numpy in this environment are:
napari (version = 0.4.14, source = pypi)
napari-pyclesperanto-assistant (version = 0.15.4, source = pypi)
numpy (version = 1.22.2, source = conda-forge)
This is a MRE to mimic what is wrong:
Hopefully I'm not doing anything wrong here. If you need more information about this issue, please let me know.
Thank you in advance for the help, and also thank you for creating such a nice tool!
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