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Changed hard-wired chunk size to 128,256,256 #60

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May 1, 2024
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Changed hard-wired chunk size to 128,256,256 #60

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6 changes: 3 additions & 3 deletions src/aind_exaspim_pipeline_utils/n5tozarr/n5tozarr_da.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@ def run_n5tozarr(
arr = dask.array.from_array(zg["s0"], chunks=zg["s0"].chunks)
arr = chunk_utils.ensure_array_5d(arr)
LOGGER.debug("Re-chunk dask array to desired output chunk size.")
arr = arr.rechunk((1, 1, 256, 256, 256))
arr = arr.rechunk((1, 1, 128, 256, 256))

LOGGER.info(f"Input array: {arr}")
LOGGER.info(f"Input array size: {arr.nbytes / 2 ** 20} MiB")
Expand Down Expand Up @@ -196,7 +196,7 @@ def run_zarr_multiscale(
zg["0"], chunks=zg["0"].chunks
) # For metadata writing we need the full resolution shape
arrZero = chunk_utils.ensure_array_5d(arrZero)
arrZero = arrZero.rechunk((1, 1, 256, 256, 256))
arrZero = arrZero.rechunk((1, 1, 128, 256, 256))

LOGGER.info(f"Full resolution array: {arrZero}")
LOGGER.info(f"Full resolution input array size: {arrZero.nbytes / 2 ** 20} MiB")
Expand Down Expand Up @@ -226,7 +226,7 @@ def run_zarr_multiscale(
LOGGER.info("Initialize dask source array from Zarr source level %s", prevLevel)
arr = dask.array.from_array(zg[prevLevel], chunks=zg[prevLevel].chunks)
arr = chunk_utils.ensure_array_5d(arr)
arr = arr.rechunk((1, 1, 256, 256, 256))
arr = arr.rechunk((1, 1, 128, 256, 256))
else:
arr = arrZero

Expand Down
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