...#1481
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np.load without mmap_mode copies the full relabeling vector into each Dask worker for every tile. mmap_mode='r' reads only the pages needed per block, avoiding multi-GB RAM spikes on large whole-slide runs. Co-authored-by: Cursor <cursoragent@cursor.com>
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Summary
Avoid loading the full
new_labeling.npyarray into memory on every Dask tile during the distributed relabeling step.Problem
After stitching,
distributed_evalsaves a largenew_labelingvector to disk and relabels the unstitched segmentation with:np.loadwithoutmmap_modecopies the entire.npyfile into each worker process for every block. On whole-slide runs this array can be multi-GB, so relabeling multiplies RAM use by the number of concurrent workers and can cause OOM or severe swapping.Using
mmap_mode='r'memory-maps the file so each block only reads the pages it needs.