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Adding MedSAM2 to the model zoo #4828

Merged
merged 3 commits into from
Sep 24, 2024
Merged

Adding MedSAM2 to the model zoo #4828

merged 3 commits into from
Sep 24, 2024

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prernadh
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@prernadh prernadh commented Sep 20, 2024

What changes are proposed in this pull request?

Adding MedSAM2 to the model ZOO by adding documentation to this PR by Evatt Harvey Salinger.

How is this patch tested? If it is not, please explain why.

Manually tested

Release Notes

Is this a user-facing change that should be mentioned in the release notes?

  • No. You can skip the rest of this section.
  • Yes. Give a description of this change to be included in the release
    notes for FiftyOne users.

This PR adds MedSAM2 to the FiftyOne Model Zoo. Detailed description in this PR.

What areas of FiftyOne does this PR affect?

  • App: FiftyOne application changes
  • Build: Build and test infrastructure changes
  • Core: Core fiftyone Python library changes
  • Documentation: FiftyOne documentation changes
  • Other: FiftyOne Zoo

Summary by CodeRabbit

  • New Features
    • Introduced support for handling the "med-sam" dataset, including specific dataset loading and processing logic.
    • Enhanced model application capabilities for the "med-sam" dataset with tailored conditions.
    • Integrated session launch for the FiftyOne app post-dataset processing.
  • Refactor
    • Reorganized import statements for improved structure in the utility scripts.

@prernadh
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I will rebase develop before merging :)

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coderabbitai bot commented Sep 20, 2024

Walkthrough

The changes enhance the make_model_zoo_docs.py script to specifically support the "med-sam" dataset. This includes conditional logic for loading the dataset from Hugging Face, processing detections from video frames, and applying models tailored to "med-sam." The script now differentiates between "med-sam" and other models, ensuring appropriate handling of segmentation masks and launching the FiftyOne app after processing.

Changes

File Change Summary
docs/scripts/make_model_zoo_docs.py Added functionality for handling the "med-sam" dataset, including dataset loading, processing, and model application logic.
fiftyone/utils/sam2.py Reorganized import statements for clarity; no functional changes were made.

Poem

In the meadow where data flows,
A rabbit hops where the "med-sam" grows.
With masks and frames, we dance and play,
Enhancing scripts in a joyful way!
Hooray for changes, let’s celebrate,
For every hop brings something great! 🐇✨


Recent review details

Configuration used: .coderabbit.yaml
Review profile: CHILL

Commits

Files that changed from the base of the PR and between cb4a884 and 8c1e86f.

Files ignored due to path filters (1)
  • fiftyone/zoo/models/manifest-torch.json is excluded by !**/*.json
Files selected for processing (2)
  • docs/scripts/make_model_zoo_docs.py (4 hunks)
  • fiftyone/utils/sam2.py (1 hunks)
Files skipped from review as they are similar to previous changes (2)
  • docs/scripts/make_model_zoo_docs.py
  • fiftyone/utils/sam2.py

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@@ -145,6 +163,17 @@
prompt_field="frames.detections", # can contain Detections or Keypoints
)

session = fo.launch_app(dataset)
{% elif 'med-sam' in name %}
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Suggestion: move this elif block above line 156 so that you can remove and 'med-SAM' not in tags from there?

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@brimoor brimoor left a comment

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LGTM from a static review standpoint, just left one suggestion.

Defer to @danielgural for a functional review (I didn't try running the model)

@prernadh prernadh merged commit 65cfa91 into develop Sep 24, 2024
13 checks passed
@prernadh prernadh deleted the feature/med-sam2 branch September 24, 2024 16:44
prernadh added a commit that referenced this pull request Sep 24, 2024
This was referenced Sep 25, 2024
@coderabbitai coderabbitai bot mentioned this pull request Oct 24, 2024
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5 participants