Created
April 30, 2024 11:06
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from pathlib import Path | |
import shutil | |
import sys | |
import dask.array as da | |
import glymur | |
from numcodecs import Blosc | |
from loguru import logger | |
import stack_to_chunk | |
logger.enable("stack_to_chunk") | |
logger.add(sys.stdout, level="INFO") | |
input_dir = Path( | |
"/Volumes/Media/Data/2.45um_LADAF-2020-27_lung-left_VOI-06-lower-lobe-basal_pag-0.02_0.04_jp2_" | |
) | |
output_dir = Path("/Volumes/Media/Data/2.45um_LADAF-2020-27_lung-left_VOI-06-lower-lobe-basal.ome.zarr") | |
if __name__ == "__main__": | |
"""print("Constructing Jp2ks...") | |
slices = sorted(input_dir.glob("*.jp2")) | |
slices = slices[:256] | |
j2ks = [glymur.Jp2k(f) for f in slices] | |
volume = da.stack([da.from_array(j2k) for j2k in j2ks], axis=-1) | |
print("Finished stacking data") | |
group = stack_to_chunk.MultiScaleGroup( | |
output_dir, | |
name="my_zarr_group", | |
spatial_unit="micrometer", | |
voxel_size=(2.45, 2.45, 2.45), | |
) | |
group.add_full_res_data( | |
volume, | |
chunk_size=128, | |
compressor=Blosc(cname="zstd", clevel=8, shuffle=1), | |
n_processes=1, | |
)""" | |
group = stack_to_chunk.open_multiscale_group(output_dir) | |
group.add_downsample_level(1) | |
# https://github.com/HiPCTProject/stack-to-chunk/pull/26 | |
# time: | |
# memory: | |
# | |
# https://github.com/HiPCTProject/stack-to-chunk/tree/downsample | |
# time: 2 mins | |
# memory: not much |
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