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andwang1 / BrainSurfaceTK

BrainSurfaceTK provides a suite of tools to apply Deep Learning techniques to brain surfaces and visualise the results in an easy to use Web Application.
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Question on Python version #1

Open yangheeim opened 5 months ago

yangheeim commented 5 months ago

Hi! Thank you for sharing your code, I would like to implement your code, but I've failed.

I've tried python3.7, 3.8, 3.9, 3.10 but every version results in errors..

I would really appreciate if you can give advice for this, Thanks!

cemlyn007 commented 5 months ago

Hi @yangheeim, I'll have a look tonight and see if I can update the branch. I suspect the problem is that dependencies have changed!

yangheeim commented 5 months ago

Hi! Thank you for your response! For your information, this is my trial log and environments!

Commands

conda create -n venv python=3.7 <3.8,3.9,3.10> source activate venv /anaconda_path/envs/venv/bin/pip install -r requirements1.txt -f https://download.pytorch.org/whl/torch_stable.html /anaconda_path/envs/venv/bin/pip install -r requirements2.txt -f https://pytorch-geometric.com/whl/torch-1.5.0.html /anaconda_path/envs/venv/bin/python3 -m scripts.segmentation.PointNet.run_pointnet_segmentation

Error

error mainly occured while importing torch_geometric saying 'No module something'

OS

cat /etc/os-release NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"

Anaconda

conda -V conda 23.5.2

cemlyn007 commented 5 months ago

I think I managed to have some luck after modifying the CPU requirements to pip install something! Would CPU requirements be enough for your exploration? I think I need some more time to get GPU requirements for CUDA 12!

cemlyn007 commented 5 months ago

@yangheeim please try the requirements in this fork. I was able to pip install them with Python 3.7 and was able to get past your torch_geometric missing import error however because I don't have any data to test on I can't properly test any further :(

yangheeim commented 5 months ago

@cemlyn007 Hi! I will try implementing with CPU requirements then. thank you for your help! Also, are you or anyone in your group still working on the project related to this by any chances?

cemlyn007 commented 5 months ago

Maybe @amiralansary? Otherwise I don't think anyone else is working on applying deep learning (DL) to brains but most if not all of us are still working on DL applications

yangheeim commented 5 months ago

I see thanks! :)

yangheeim commented 5 months ago

@cemlyn007 Hi again! Sorry for bothering you again. I tried the requirements in this fork as you said above with Python 3.7. However, I got the following error. Do you think it's negligible? Thanks so much!

error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [1 lines of output] error in jsmin setup command: use_2to3 is invalid. [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details.

cemlyn007 commented 5 months ago

Without more logging I can't see why jsmin had a problem on your machine, but since it's probably a dependency for the Django webserver, you could try removing it as a requirement?