Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add executor widget #110

Open
wants to merge 3 commits into
base: main
Choose a base branch
from

Conversation

jo-mueller
Copy link

#108

This adds a new action to the dropdown of the downloaded models in the ModelList of the bioimage.io widget. In essence, it retrieves the doi from the downloaded rdf spec, spawns the predictor function as shown in this notebook, and wraps it with magicgui in a separate predictor widget.

I started working on this at the ome-ngff-Hackathon at the biovisioncenter last week and would be happy for some feedback on it.

Minor thoughts:

  • The predict_image functions checks under the hood whether the image dimensions line up with what the model expects - including some singleton dimensions. I don't think a prediction should fail if a model expects, say, [1x1xZxYxX] and receives [ZxYxX]. Maybe missing singleton dimensions could be added under the hood?
  • Threaded execution: Currently, the created function returns normally, but maybe it should use the yield statement to allow for threaded execution.
  • Zarr-compatibility: For large image data, it may be worthwhile to chunk the data under the hood and run chunkwise to not have to deal with overflowing memory.

@lorenzocerrone @jdeschamps could be interesting for you? Would be interested in your thoughts - I will leave this as draft PR for now.

@jo-mueller jo-mueller marked this pull request as ready for review November 29, 2023 10:33
@jo-mueller
Copy link
Author

@oeway is this plugin still maintained? I would love to hear your thoughts on this or what changes I'd have to make to see it through.

Thanks :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant