Project-MONAI / Project-MONAI/tutorials
Auto3DSeg BundleGen clobbers existing bundles
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Description
Problem
I just discovered the hard way that BundleGen completely clobbers existing bundles, not only overwriting files, but deleting files it does not write (like training output).
Desired solution
It would be nice to have a clobber=True kind of option, where the default would be to give a warning that the bundle directory already exists.
Example code
Here are the relevant parts of what I ran:
from monai.apps.auto3dseg import BundleGen
bundle_generator = BundleGen(
algo_path=work_dir,
data_stats_filename=datastats_file,
data_src_cfg_name=input_yaml,
)
bundle_generator.generate(work_dir, num_fold=5)
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the Auto3DSeg BundleGen implementation and its generate(work_dir, num_fold=5) entry point. Reproduce the issue with an existing bundle directory containing unrelated training output, then verify that default handling warns instead of deleting it and that explicit clobber behavior is distinguishable.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100