MonaiLabel

Download Models

Initialize MedSAM Bundle's model from huggingface:

docker compose exec -it monailabel bash
python # start a python interpreter in monailabel container

from transformers import SamModel, SamProcessor
import torch

MonaiLabel requires model.pt and model_best.pt in the bundle:

model = SamModel.from_pretrained("flaviagiammarino/medsam-vit-base", local_files_only=False)
torch.save(model.state_dict(), '/monailabel/apps/monaibundle/model/MedSamBundle/models/model.pt')
torch.save(model.state_dict(), '/monailabel/apps/monaibundle/model/MedSamBundle/models/model_best.pt')

Loading weights if needed for custom models:

# loaded_weights = torch.load('/monailabel/apps/monaibundle/model/MedSamBundle/models/model.pt', weights_only=True)
# model.load_state_dict(loaded_weights)

Restart MonaiLabel

docker compose restart monailabel

Changes to MonaiLabel and GIT

If you make some edits to monailabel you need to check it into git first.

cd monailabel
git branch add-changes
git add <file>
git commit -m "Your commit message for submodule changes"

git checkout main
git merge add-changes
git push origin main
git branch -d add-changes

cd ..
git add monailabel
git commit -m "commit message"
git push