Skip to content

tensorstore cli #120

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 3 commits into from
Dec 3, 2024
Merged

tensorstore cli #120

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
9b4b2ce
BUG: CLI zarr.storage imports for zarr-python 3.0.0b2
thewtex Dec 2, 2024
bb65a48
ENH: Add --use-tensorstore flag to CLI
thewtex Dec 2, 2024
fe41d63
ENH: Add --ome-zarr-version CLI flag
thewtex Dec 2, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
37 changes: 32 additions & 5 deletions ngff_zarr/cli.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,12 @@
)
from rich.spinner import Spinner
from rich_argparse import RichHelpFormatter
from zarr.storage import DirectoryStore
import zarr.storage

if hasattr(zarr.storage, "DirectoryStore"):
LocalStore = zarr.storage.DirectoryStore
else:
LocalStore = zarr.storage.LocalStore

from .cli_input_to_ngff_image import cli_input_to_ngff_image
from .config import config
Expand Down Expand Up @@ -61,7 +66,18 @@ def _multiscales_to_ngff_zarr(
)
)
return
to_ngff_zarr(output_store, multiscales, progress=rich_dask_progress)
if args.use_tensorstore:
if hasattr(output_store, "root"):
output_store = output_store.root
else:
output_store = output_store.path
to_ngff_zarr(
output_store,
multiscales,
progress=rich_dask_progress,
use_tensorstore=args.use_tensorstore,
version=args.ome_zarr_version,
)


def _ngff_image_to_multiscales(
Expand Down Expand Up @@ -191,6 +207,12 @@ def main():
type=int,
default=0,
)
metadata_group.add_argument(
"--ome-zarr-version",
help="OME-Zarr version",
default="0.4",
choices=["0.4", "0.5"],
Copy link
Collaborator

@joshmoore joshmoore Dec 3, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

❤️

)

processing_group = parser.add_argument_group("processing", "Processing options")
processing_group.add_argument(
Expand Down Expand Up @@ -226,6 +248,11 @@ def main():
processing_group.add_argument(
"--cache-dir", help="Directory to use for caching with large datasets"
)
processing_group.add_argument(
"--use-tensorstore",
action="store_true",
help="Use the TensorStore library for I/O",
)

args = parser.parse_args()

Expand All @@ -236,7 +263,7 @@ def main():
cache_dir = Path(args.cache_dir).resolve()
if not cache_dir.exists():
Path.makedirs(cache_dir, parents=True)
config.cache_store = zarr.storage.DirectoryStore(cache_dir, **zarr_kwargs)
config.cache_store = LocalStore(cache_dir, **zarr_kwargs)

console = Console()
progress = RichProgress(
Expand Down Expand Up @@ -303,7 +330,7 @@ def shutdown_client(sig_id, frame): # noqa: ARG001
)
output_store = None
if args.output and output_backend is ConversionBackend.NGFF_ZARR:
output_store = DirectoryStore(args.output, **zarr_kwargs)
output_store = LocalStore(args.output, **zarr_kwargs)

subtitle = "[red]generation"
if not args.output:
Expand Down Expand Up @@ -332,7 +359,7 @@ def shutdown_client(sig_id, frame): # noqa: ARG001
return

if input_backend is ConversionBackend.NGFF_ZARR:
store = zarr.storage.DirectoryStore(args.input[0])
store = LocalStore(args.input[0])
multiscales = from_ngff_zarr(store)
_multiscales_to_ngff_zarr(
live, args, output_store, rich_dask_progress, multiscales
Expand Down
Loading