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IsoNet-cryoET / IsoNet

Self-supervised learning for isotropic cryoET reconstruction
https://www.nature.com/articles/s41467-022-33957-8
MIT License
67 stars 12 forks source link

Error Reading some .mrc files #41

Closed fonsecareyna82 closed 1 year ago

fonsecareyna82 commented 1 year ago

Reading some .mrc files I get the following error: RuntimeWarning: Unrecognised machine stamp: 0x00 0x00 0x00 0x00. I have solved it by adding to the IsoNet code in the instructions "with mrcfile.open(.........)" permissive=True e.g. with mrcfile.open(subtomo_name, mode='r', permissive=True) as s: ....

procyontao commented 1 year ago

I have not encountered the problem before. But added "permissive=True" in line 78 of bin/isonet.py in new commit. could you let me know whether it is appropriate?

fonsecareyna82 commented 1 year ago

Hi @procyontao. I am a Scipion developer(https://scipion-em.github.io/docs/release-3.0.0/index.html). We are currently developing and integrating tomography modules(as plugins) into our project. I am integrating IsoNet into Scipion. I will report every problem that I find. On the other hand, I have seen that the last tag is from August of last year. Do you plan to make other tags? Do you think about turning it into a pypi module?

procyontao commented 1 year ago

It's great to hear that you're integrating IsoNet into Scipion. Thank you for reporting problems.

When you confirm it works well as plugin in Scipion, I can create a new tag so that you can refer to.

Turning it into a PyPI module is something that we have considered, but we have not got a change to look into. We will make that happen when we figure out how to do that.

fonsecareyna82 commented 1 year ago

Sure!! As soon as I finish integrating it, I'll let you know. Right now I have it almost complete. I am installing the v0.2.1 tag (do you recommend that I install the master branch?). I have fixed the bugs that I have been mentioning but I think I have made others that I have not reported. I am going to do a new installation for where it fails to tell you. I can also make a branch that starts from master and then upload all my changes and make a pull request. Regarding converting it into a pypi package I can help you if that's okay with you.

fonsecareyna82 commented 1 year ago

Captura desde 2023-02-05 20-12-27

fonsecareyna82 commented 1 year ago

Hi @procyontao. In these files I have found the same problem that I have mentioned in the issues:

On the other hand, I already have the plugin functional. I am going to improve the installation process to install the correct versions of tensorflow and cudnn depending on the cuda. Now I am installing the code that is in master until there is a new tag.

We use Discord channels to communicate with developers of other software. If you wish, we can communicate there.

procyontao commented 1 year ago

Thank you for looking for problems in the code. I fixed what you listed except for "IsoNet/bin/predict.py L40: permissive=True", which I can not find. The master branch is what you should install.

It would be great if you can help converting it to PyPi module. We can talk on discord, my account is Yuntao#4385