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d666570
update signature type hints
ziw-liu Jul 2, 2025
08e3018
clarify the type of position keys
ziw-liu Jul 2, 2025
d1d1934
expose sharding in plate creation
ziw-liu Jul 3, 2025
37fa029
isort
ziw-liu Jul 3, 2025
12901ec
fix default version
ziw-liu Jul 3, 2025
c6cc49f
fix example code block format
ziw-liu Jul 7, 2025
1cf881a
fix type hints
ziw-liu Jul 7, 2025
9e8f87d
utility to split indices by shards
ziw-liu Jul 7, 2025
5d75a2e
separate apply and save
ziw-liu Jul 8, 2025
c560e45
simplify random number generation
ziw-liu Jul 8, 2025
fd67281
wip: batched writing in time
ziw-liu Jul 9, 2025
1fd0f43
match storage keys with values
ziw-liu Jul 9, 2025
5a06067
removed unused argument
ziw-liu Jul 9, 2025
a41b535
fix import
ziw-liu Jul 10, 2025
ed05be7
fix string formatting
ziw-liu Jul 10, 2025
cb0de21
add more version testing
ziw-liu Jul 10, 2025
0482c11
use tensorstore instead
ziw-liu Jul 10, 2025
e130144
control tensorstore concurrency
ziw-liu Jul 10, 2025
61e743a
memory management
ziw-liu Jul 10, 2025
67fd905
isort
ziw-liu Jul 11, 2025
1edcd30
format
ziw-liu Jul 11, 2025
f6d1e5e
remove platform check
ziw-liu Jul 11, 2025
8727973
warning if shards is specified for 0.4
ziw-liu Jul 29, 2025
e90065b
set shards to none for 0.4
ziw-liu Jul 29, 2025
6787d64
Update acquire-zarr OME v0.5 fixture / aqz test to reflect new config…
aliddell Jul 29, 2025
af7c344
add notes about upstream issues
ziw-liu Aug 9, 2025
80d809c
add example of sharded plate
ieivanov Aug 9, 2025
ffc8a9d
explicitly add layout in open_ome_zarr
ieivanov Aug 9, 2025
9efd351
Fix tensorstore empty array handling (#326)
ieivanov Aug 29, 2025
34ba711
bugfix and better type hints
ieivanov Sep 3, 2025
8c903b6
better messaging
ieivanov Sep 3, 2025
8fc3346
style
ieivanov Sep 3, 2025
e71c086
raise error if attempting sharding along channel dimension
ieivanov Sep 4, 2025
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16 changes: 13 additions & 3 deletions iohub/ngff/nodes.py
Original file line number Diff line number Diff line change
Expand Up @@ -383,7 +383,7 @@ def dask_array(self):
def downscale(self):
raise NotImplementedError

def tensorstore(self):
def tensorstore(self, concurrency: int | None = None):
"""Open the zarr array as a TensorStore object.
Needs the optional dependency ``tensorstore``.

Expand All @@ -396,10 +396,20 @@ def tensorstore(self):

ts_spec = {
"driver": "zarr2" if self.metadata.zarr_format == 2 else "zarr3",
"kvstore": (Path(self.store.root) / self.path.strip("/")).as_uri(),
"kvstore": {
"driver": "file",
"path": str(Path(self.store.root) / self.path.strip("/")),
},
}
zarr_dataset = ts.open(
ts_spec, read=True, write=not self.read_only
ts_spec,
read=True,
write=not self.read_only,
context=(
ts.Context({"data_copy_concurrency": {"limit": concurrency}})
if concurrency
else None
),
).result()
return zarr_dataset

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