Project-MONAI / Project-MONAI/MONAILabel

[HAI] Prevention of inconsistent label specifications

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Human-AI Interaction
Dominant language
Python
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Forks
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Avg merge
15h 41m
Merged PRs (30d)
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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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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