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Added checking for legacy attributes in zarr metadata #3

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Mar 19, 2024
Merged

Added checking for legacy attributes in zarr metadata #3

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45 changes: 23 additions & 22 deletions funlib/persistence/arrays/datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -251,28 +251,29 @@ def _read_attrs(ds, order="C"):
# check recursively for multiscales attribute in the zarr store tree
multiscales, multiscale_group = check_for_multiscale(group = access_parent(ds))

# check N5 store
if isinstance(ds.store, (zarr.n5.N5Store, zarr.n5.N5FSStore)):
if multiscales:
voxel_size, offset, units = check_for_attrs_multiscale(ds, multiscale_group, multiscales)
# if multiscale attribute is missing
if voxel_size == None or offset == None:
voxel_size = check_for_voxel_size(ds, order)
offset = check_for_offset(ds, order)
units = check_for_units(ds, order)
else:
return voxel_size, offset, units
# check zarr store
else:
#check for attributes in zarr group multiscale
if multiscales:
voxel_size, offset, units = check_for_attrs_multiscale(ds, multiscale_group, multiscales)
if voxel_size != None and offset != None:
return voxel_size, offset, units
else:
raise ValueError(f"Although multiscale exists within n5 container, no attributes were found.")
else:
raise ValueError(f"No multiscales attribute was found")

#check for attributes in zarr group multiscale
if multiscales:
voxel_size, offset, units = check_for_attrs_multiscale(ds, multiscale_group, multiscales)

# if multiscale attribute is missing
if voxel_size == None:
voxel_size = check_for_voxel_size(ds, order)
if offset == None:
offset = check_for_offset(ds, order)
if units == None:
units = check_for_units(ds, order)

if voxel_size != None and offset != None and units != None:
return voxel_size, offset, units
elif voxel_size == None:
raise ValueError(f"No voxel_size attribute was found")
elif offset == None:
raise ValueError(f"No offset attribute was found")
elif units == None:
raise ValueError(f"No units attribute was found")


return voxel_size, offset, units

def regularize_offset(voxel_size_float, offset_float):
Expand Down