Use a zarr, disk-backed impl for large images #15
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This commit makes it so that we use a zarr array backed by disk to do stitching in cases where the image is too large to fit into memory (based upon pstats's estimation of how much free memory there is as well as a heuristic multiplier of the expected memory usage of the output array). Since this uses disk for some operations, we expect some parts will be slower, and to mitigate this, we ensure that the output array ends up being level 0 of the zarr pyramid output, so that we don't have to make a second copy to disk. I added a parameter to the input parameters that lets you force using this disk mode (which is useful for testing / profiling / debugging, or potentially for limiting production memory usage). Tested by: - `./dev/run_tests.sh` - lots of manual benchmarking on images of different sizes using the CLI
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This commit makes it so that we use a zarr array backed by disk to do stitching in cases where the image is too large to fit into memory (based upon pstats's estimation of how much free memory there is as well as a heuristic multiplier of the expected memory usage of the output array). Since this uses disk for some operations, we expect some parts will be slower, and to mitigate this, we ensure that the output array ends up being level 0 of the zarr pyramid output, so that we don't have to make a second copy to disk.
I added a parameter to the input parameters that lets you force using this disk mode (which is useful for testing / profiling / debugging, or potentially for limiting production memory usage).
Tested by:
./dev/run_tests.sh