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Example code of biigle/magic-sam

Informations about the package magic-sam

BIIGLE Magic SAM Module

Test status

This is a BIIGLE module that offers the Magic SAM image annotation instrument.

Installation

  1. Run composer require biigle/magic-sam.
  2. Run php artisan vendor:publish --tag=public to refresh the public assets of the modules. Do this for every update of this module.

  3. Configure a storage disk for the image embedding files. Set the MAGIC_SAM_EMBEDDING_STORAGE_DISK variable in the .env file to the name of the respective storage disk. The content of the storage disk should be publicly accessible. Example for local disks:

    This requires the link storage -> ../storage/app/public in the public directory.

Configuration

Image embeddings are generated by a Python worker process that requires a dedicated Docker Compose configuration. The Docker container can be based on ghcr.io/biigle/pyworker but also must satisfy the Python requirements of this repository. The SAM model type and checkpoint URL are configured via environment variables, as shown below. Here is a full example configuration:

While image embeddings can be generated on the CPU it is much faster on a GPU.

Image embedding files are automatically deleted after 30 days. You can configure this with the MAGIC_SAM_PRUNE_AGE_DAYS environment variable.

References

Reference publications that you should cite if you use Magic SAM for one of your studies.

Developing

Take a look at the development guide of the core repository to get started with the development setup.

Want to develop a new module? Head over to the biigle/module template repository.

Contributions and bug reports

Contributions to BIIGLE are always welcome. Check out the contribution guide to get started.

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