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Zarr L0 #148

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Merged
davramov merged 2 commits into from
Aug 25, 2026
+2 −2
Merged

Zarr L0 #148

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4383ae5
Patching ngff-zarr==0.39.0 to fix L0 clipping bug
davramov Aug 25, 2026
17a1fb5
pinning Zarr version in tiff_to_zarr.py
davramov Aug 25, 2026
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2 changes: 1 addition & 1 deletion orchestration/flows/bl832/nersc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -877,7 +877,7 @@ def build_multi_resolution(
--volume {pscratch_path}/8.3.2:/alsdata \
--volume {pscratch_path}/8.3.2:/alsuser/ \
{multires_image} \
bash -c "python tiff_to_zarr.py {recon_path} --raw_file {raw_path}"
bash -c "python -m pip install --user --no-deps 'ngff-zarr==0.39.0' && python tiff_to_zarr.py {recon_path} --raw_file {raw_path}"

date
"""
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2 changes: 1 addition & 1 deletion scripts/perlmutter/tiff_to_zarr.py
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Expand Up @@ -89,7 +89,7 @@ def main():
image.scale = read_pixelsize_from_hdf5(args.raw_file)
image.axes_units = {'x': 'micrometer', 'y': 'micrometer', 'z': 'micrometer'}
multiscales = to_multiscales(image, method=Methods.DASK_IMAGE_GAUSSIAN, cache=False)
to_ngff_zarr(zarr_dir, multiscales)
to_ngff_zarr(zarr_dir, multiscales, version="0.4")
print('NGFF Zarr created')

# Set permissions for the output directory and its contents
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