Updates to MoNuSeg

[anwai98]

• Added processing for the monuseg inputs (including xml to numpy array conversion) (kept the expected directory formats consistent)
• (WIP) Add the test split
• (TODO) Check the organ splits from the challenge's metadata and make those splits (mentioned in TODOs)

[constantinpape]

Hi @anwai98 ,
not sure if this is ready to review yet, but I had a quick look. In addition to the comments in the code, I tried the download, but it fails with

Access denied with the following error:

        Cannot retrieve the public link of the file. You may need to change
        the permission to 'Anyone with the link', or have had many accesses. 

You may still be able to access the file from the browser:

         https://drive.google.com/uc?export=download&id=1ZgqFJomqQGNnsx7w7QBzQQMVA16lbVCA 

[anwai98]

Hi @anwai98 , not sure if this is ready to review yet, but I had a quick look. In addition to the comments in the code, I tried the download, but it fails with

Access denied with the following error:

        Cannot retrieve the public link of the file. You may need to change
        the permission to 'Anyone with the link', or have had many accesses. 

You may still be able to access the file from the browser:

         https://drive.google.com/uc?export=download&id=1ZgqFJomqQGNnsx7w7QBzQQMVA16lbVCA 

Hmm, pretty interesting. I just tried it again and the download works for me. Is it related to the gdown version?
It works with the following version for me:

gdown                     4.7.1              pyhd8ed1ab_0    conda-forge

[constantinpape]

This looks good in principle, but do you still want to implement the organ selection before we merge it?

[anwai98]

This looks good in principle, but do you still want to implement the organ selection before we merge it?

Yes, I wanted to complete the setup, hence took it back as a draft. Would take care of it and put it back to review later. Thanks.