h5 model file unavailable?

[nicoa47]

In CLI, after a quick attempt at running ut init --name <...> --model usleep followed by ut predict I get an error saying RuntimeError: Did not find any model parameter files in model subfolder <...>. Model files should have extension '.h5' to be recognized.

Is it normal that no h5 file is located in the model subfolder after init?

[perslev]

Hi nicoa47,

The ut init script simply prepares a new (empty) project folder. I.e., a folder that stores templates for the hyperparameter files needed to fit a specific type of model. You will need to fit the model yourself in order to use it for prediction.

If you are only looking to use the U-Sleep model as presented in this paper, you can do so for free at https://sleep.ai.ku.dk for research purposes. There is also an API with a CLI here, e.g. to score an EDF file:

pip install usleep-api
usleep-api ./my_psg.edf ./hypnogram.tsv --anonymize

This will upload an anonymized version of the file ./my_psg.edf to the U-Sleep webservice, then download the scored hypnogram and save it to ./hypnogram.tsv.

If you are not able to upload (anonymized) data to the webservice, please let me know.

Cheers
Mathias

[nicoa47]

Thanks for the very quick and helpful response! I will try the web api. Another short question: Do the results obtained from using this API include confidence scores? I am wondering since I couldn't find any when I directly uploaded data to the https://sleep.ai.ku.dk/ interface.

[perslev]

No problem! The API does not currently support getting confidence scores, but this is something I could implement as it may be generally useful. I will take a look to see how much work would be required and get back to you.

[perslev]

This turned out to be relative straight forward, so you can now download .npy array files with confidence scores from both the web interface and using the API/CLI:

>> usleep-api ./my_psg.edf ./hypnogram.npy --anonymize --with-confidence-scores

Good luck with your project!

Edit: you should update the usleep-api package to version 0.1.3 before running the above.

[nicoa47]

thanks so much!

[perslev]

No problem!