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Interface with Scipion framework #9
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Hi! Count with our assistance... I think now is the right timing for this. We are preparing a release of the scipion-tomo set of plugins with Eman, imod, some xmipp methods....dynamo is on board too. |
Better this page, we very soon will update it https://scipion-em.github.io/docs/docs/developer/developers.html |
@pconesa great! If you could help us with the interfacing, that would be wonderful! |
What would be the simplest method to integrate...my idea is to: 1.- We create a basic plugin for you with one of the methods integrated. How does it sound? |
Sounds good! The simplest method we have is particle picking. Perhaps we could start from here. |
Great, I've got an skeleton ready. Soon will need your input to call the
picker.
El jue., 21 nov. 2019 2:53, xulabs <notifications@github.com> escribió:
… Sounds good!
The simplest method we have is particle picking.
https://github.com/xulabs/aitom_doc/tree/master/tutorials/008_particle_picking
Perhaps we could start from here.
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Great. Thanks. |
HI @xulabs , I've pushed the scipion plugin for Aitom (a VERY basic one) to scipion-em organization. It is perfectly ok if you want to have it here under xulabs. You can find in the readme what do you need....there are though a few items I'd like to comment: 1.- Installation: The plugin is able to install aitom in a conda VE, but for that I needed a release (thus I forked aitom repo and just made a release to have the tar.gz files). There are better ways to do this, this is just a quick hack. The usual way to do it is to use pypi and just do pip install xxxxx. 2.- To invoke the picking I also created an entry point, so in a terminal you can run
The picking script is a slight adaptation os your picking tutorial script. 3.- Picking itself....It is parsing the coordinates in the json, but ....there is no boxsize, I've hardcoded it to 100 but I'm sure this is incorrect. My doubt is if there any information about the boxsize per coordinate. How does it work? |
Thanks a lot @pconesa |
Great! We can add whoever you want to our slack channel. |
HI @pconesa , I successfully install 'scipion-em' in devel mode but meet some problems while testing (after running 'scipion test aitom.tests.tests_picking.TestAitomPicking'). It seems 'picking' command not found.
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We have seen many issues when we run conda apps. Note that you need to adapt at least the path or even the shell type (in case you don't use bash)) |
@zhuzhenxi when you say scipion-em .....what actually do you mean? Which one have you installed. The plugin I initiated targets Scipion 2.0, so python 2.7 |
Thanks a lot @pconesa , I will try again. |
Conda seems to work, but 'picking' is still 'command not found'(non-zero exit status 127). @pconesa |
Hi @zhuzhenxi , that might be because I changed slightly your code to have an entry point for the picking. Please do not take it literally it was just an approach that worked for me: I find it very easy to have those entry points, so the user/scipion does not need to know where the scripts are, they are available as commands. |
Hi @pconesa , the plugin works pretty well, thanks a lot. |
Nice! It should work, I actually did it getting the release from my fork, but now that you have your own it should be a matter of pointing to your release. |
Actually, I manually install AITom in conda VE 'aitom-0.1'. So how can I depend on the release and maybe install AITom automatically like other Scipion plugins(more friendly to users)? |
Yep, I've added you as admin of the plugin repository. This line is the one grabbing the aitom release from my fork, just need to be adapted to take your url. https://github.com/scipion-em/scipion-em-aitom/blob/devel/aitom/__init__.py#L133 |
Your release url should be this one: https://github.com/xulabs/aitom/archive/0.1.tar.gz Optionally you can deploy aitom to pipy and then the installation will become a "pip install aitom" |
Ok, I will discuss with Xu for further development. |
@zhuzhenxi yes we may deploy it to pipy. Please check how to do it and let me know. Thanks. |
You are almost there, your code is ready to be deploy, you just need an account and push it. We have some instructions for our plugins but there is nothing specific to Scipion there, all is standard pypi.org commands: https://scipion-em.github.io/docs/docs/developer/creating-a-plugin#create-and-upload-distribution Except fo the -c "scipion-2.0" (you don't need that for uploading aitom.) |
@pconesa got it. Will do. Thank you. |
@pconesa @zhuzhenxi the code is now available at @zhuzhenxi I have modified the version from 0.1 to 0.01 because it is a very alpha release. Please change the related code and tutorial accordingly if needed. |
Great, now we just need to do the pip install using it, not sure how to use a pip package from test.pipy but should be documented somewhere...I can make a PR with that change. |
Hi, this completely went out of my radar. We even organized a tomo course and didn't mention this integration effort. Maybe is a good time to catch up? How are things going? Do you need any assistance? |
We will gradually interface AITom with the Scipion framework as a mid-term effort.
https://github.com/I2PC/scipion/wiki
https://github.com/scipion-em
https://journals.iucr.org/d/issues/2019/10/00/ic5108/index.html
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