ALCF Reconstruction and Segmentation for bl832#114

Draft

davramov wants to merge 32 commits intoals-computing:mainfrom

davramov:alcf_recon_segmentation

Commits on Jan 28, 2026

Updating ALCF endpoints to include the synaps-i allocation (to be set up)
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Updating bl832 config.py to distinguish IRI and SYNAPS-I ALCF endpoints
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Adding the config.yaml file for setting up the globus compute endpoint for reconstruction on ALCF
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Adding the config.yaml file for setting up the globus compute endpoint for segmentation on ALCF. Still needs to be configured for GPU and the environment with dependencies
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Adding segmentation Prefect task, and segmentation globus compute code for the TomographyController. Turning off TIFF to ZARR on ALCF for the demo
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ensuring self.config for scicat and ghcr images
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linting
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Making separate ALCF SYNAPS-I endpoint configs for raw, reconstructed, and segmented data
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Refactoring ALCF reconstruction flow to use the prune_controller class
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Removing old commented out prune code
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linting and docstrings
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Docstrings, linting, and type hints
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Updating globus compute config for segmentation
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turning ALCF recon+segmentation into a separate flow from recon+zarr conversion
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updating pytest for alcf reconstruction
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Adjusting endpoint names for synaps
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adding the alcf_forge_recon_segment flow to prefect.yaml as a separate deployment
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updating bl832 dispatcher to include alcf_forge_recon_segment as a separate option
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Commits on Feb 2, 2026

Commits on Feb 3, 2026

Adding a separate wrapper for segmentation v2. At some point we may want to collapse these into the final version, but for testing purposes I'm leaving both codes
davramov
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