Merge pull request #20 from AllenNeuralDynamics/release-v0.1.8

Release v0.1.8

Author: camilolaiton

src/aind_smartspim_data_transformation/__init__.py

@@ -1,3 +1,3 @@
 """Init package"""
 
-__version__ = "0.1.7"
+__version__ = "0.1.8"

src/aind_smartspim_data_transformation/compress/png_to_zarr.py

@@ -23,6 +23,8 @@
 from ome_zarr.io import parse_url
 from ome_zarr.writer import write_multiscales_metadata
 from skimage.io import imread as sk_imread
+from zarr.errors import ContainsGroupError
+from zarr.storage import contains_group
 
 from aind_smartspim_data_transformation.compress.zarr_writer import (
     BlockedArrayWriter,
@@ -498,6 +500,36 @@ def lazy_tiff_reader(
     return Array(dask_arr, name, chunks, dtype)
 
 
+def safe_create_zarr_group(store, path: str = "", **kwargs) -> zarr.Group:
+    """
+    Safe creation of the zarr group.
+
+    Parameters
+    ----------
+    store : MutableMapping or string
+        Zarr store (e.g., directory, zip file, etc.)
+    path : str
+        Path to the group inside the store (default: root group)
+
+    Returns
+    -------
+    zarr.Group
+        The Zarr group object
+    """
+    if contains_group(store, path=path):
+        # Group already exists; open in read/write mode
+        return zarr.open_group(store=store, path=path, mode="r+")
+    else:
+        # Attempt to create;
+        # catch race condition where another worker just created it
+        try:
+            return zarr.group(
+                store=store, path=path, overwrite=False, **kwargs
+            )
+        except ContainsGroupError:
+            return zarr.open_group(store=store, path=path, mode="r+")
+
+
 def smartspim_channel_zarr_writer(
     image_data: ArrayLike,
     output_path: PathLike,
@@ -567,7 +599,7 @@ def smartspim_channel_zarr_writer(
 
     # Creating Zarr dataset
     store = parse_url(path=output_path, mode="w").store
-    root_group = zarr.group(store=store)
+    root_group = safe_create_zarr_group(store=store)
 
     # Using 1 thread since is in single machine.
     # Avoiding the use of multithreaded due to GIL