From 31aa8420b4e50e48208cb57c4e0263dde5caddb0 Mon Sep 17 00:00:00 2001 From: William Patton Date: Tue, 10 Dec 2024 10:51:48 -0800 Subject: [PATCH] OME metadata support --- .../datasplits/datasets/arrays/zarr_array_config.py | 10 ++++++++-- pyproject.toml | 2 +- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/dacapo/experiments/datasplits/datasets/arrays/zarr_array_config.py b/dacapo/experiments/datasplits/datasets/arrays/zarr_array_config.py index 6f03a31a0..e3e21a78e 100644 --- a/dacapo/experiments/datasplits/datasets/arrays/zarr_array_config.py +++ b/dacapo/experiments/datasplits/datasets/arrays/zarr_array_config.py @@ -3,7 +3,7 @@ from .array_config import ArrayConfig from funlib.geometry import Coordinate -from funlib.persistence import open_ds +from funlib.persistence import open_ds, open_ome_ds from upath import UPath as Path @@ -56,9 +56,15 @@ class ZarrArrayConfig(ArrayConfig): mode: Optional[str] = attr.ib( default="a", metadata={"help_text": "The access mode!"} ) + ome_metadata: bool = attr.ib( + default=False, metadata={"help_text": "Whether to expect OME metadata"} + ) def array(self, mode="r"): - return open_ds(f"{self.file_name}/{self.dataset}", mode=mode) + if self.ome_metadata: + return open_ome_ds(f"{self.file_name}/{self.dataset}", mode=mode) + else: + return open_ds(f"{self.file_name}/{self.dataset}", mode=mode) def verify(self) -> Tuple[bool, str]: """ diff --git a/pyproject.toml b/pyproject.toml index 012def526..730611ad5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,7 +47,6 @@ dependencies = [ "funlib.geometry>=0.2", "mwatershed>=0.5.2", "cellmap-models", - "funlib.persistence>=0.5.3", "gunpowder>=1.4", "lsds", "xarray", @@ -59,6 +58,7 @@ dependencies = [ "upath", "boto3", "matplotlib", + "funlib.persistence @ git+https://github.com/funkelab/funlib.persistence.git@ome-ngff" ] # extras