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fix rechunk task
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src/fractal_helper_tasks/rechunk_zarr.py

Lines changed: 4 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -126,25 +126,21 @@ def rechunk_zarr(
126126
axes_mapper=old_label.meta.axes_mapper,
127127
chunk_sizes=chunk_sizes,
128128
)
129-
ngio.images.label.derive_label(
129+
new_label = new_ome_zarr_container.derive_label(
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name=label,
131-
store=f"{rechunked_zarr_url}/labels/{label}",
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ref_image=old_label,
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chunks=new_chunksize,
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overwrite=overwrite,
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)
136-
new_ome_zarr_container = ngio.open_ome_zarr_container(rechunked_zarr_url)
137-
print(new_ome_zarr_container.list_labels())
138-
print(rechunked_zarr_url)
139135
if rebuild_pyramids:
140-
new_label = new_ome_zarr_container.get_label(name=label)
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new_label.set_array(old_label.get_array(mode="dask"))
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new_label.consolidate()
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else:
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label_pyramid_paths = old_label.meta.paths
145140
for path in label_pyramid_paths:
146-
new_ome_zarr_container.get_label(name=label, path=path).set_array(
147-
old_label.get_array(path=path, mode="dask")
141+
old_label = ome_zarr_container.get_label(name=label, path=path)
142+
new_label.set_array(
143+
old_label.get_array(mode="dask")
148144
)
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150146
if overwrite_input:

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