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Commit 1022d073 authored by Andrey Aristov's avatar Andrey Aristov
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combine zarrs

parent ff252a88
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import dask.array as da
import os
from zarr_tools.convert import to_zarr
import fire
def combine(BF_zarr_2D_path:str, TRITC_zarr_3D_path:str, out_zarr_path:str):
bd2d = da.from_zarr(os.path.join(BF_zarr_2D_path,'0/'))
print('Opened BF:', bd2d)
fd3d = da.from_zarr(os.path.join(TRITC_zarr_3D_path,'0/'))
print('Opened TRITC:', fd3d)
fd2d = fd3d.max(axis=1)
bd2d = da.stack([bd2d, fd2d], axis=1)
print('Resulting stack:', bd2d)
to_zarr(
bd2d,
path=out_zarr_path,
steps=4,
name=['BF','TRITC'],
colormap=['gray','orange'],
lut=((1000,30000),(440, 600)),
)
# combine(snakemake.input[0], snakemake.input[1], snakemake.output[0])
if __name__ == "__main__":
fire.Fire(combine)
\ No newline at end of file
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