gistfile1.txt

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