Project-MONAI / Project-MONAI/MONAILabel
[HAI] Prevention of inconsistent label specifications
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- Dominant language
- Python
- Stars
- 891
- Forks
- 269
- Avg merge
- 15h 41m
- Merged PRs (30d)
- 1
Description
Currently some models have inconsistent label ids if you compare their REST specification and the results.
E.g.:
Inconsistent label ids for deepedit:
"labels":{"spleen": 1, "right kidney": 2, "left kidney": 3, "liver": 6, "stomach": 7, "aorta": 8, "inferior vena cava": 9, "background": 0}- However, the nifty file response has the label ids contiguous ie. 0 – 7
- ‘Secret’ request parameter restore_label_idx introduced but remains undocumented.
Incorrect labels specification for localization_spine: Model returns binary mask even though there is a whole lot of labels exposed in the API.
May be we could establish a basic smoke/consistency testing protocol, to catch such problems. E.g. linter/schema checker for the profile JSONs; generate a test result and checking if it is matching to specification. May be with easy tooling and good documentation it would be also easier to motivate devs that contribute a algorithm to provide this simple unit test for a model.
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 comparing the REST label specifications with the nifty file response for deepedit, and inspect the undocumented restore_label_idx parameter. Check localization_spine's exposed labels against its binary mask result. Done means a defined smoke or schema-checking protocol detects these inconsistencies, with the resulting test and model-contributor guidance documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- api, machine-learning, testing-qa
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100