angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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`numba` parallelization fault with `relabel_segmentation` #1137

Open alex-l-kong opened 2 months ago

alex-l-kong commented 2 months ago

Describe the bug

When running functions that depend on relabel_segmentation (ex. the mask generation functions), the process will error out with an OMP error. This seems directly related to numba since it's the parallelization driver of this function and almost certainly relies on OpenMP to facilitate this.

@jranek confirmed that converting this function into a non-numba-based routine fixed it.

Expected behavior

There should be no error.

To Reproduce

Screenshot 2024-04-19 at 9 15 09 AM