Merge pull request #32 from fractal-analytics-platform/29-deprecate-support-for-213-fractal-server

Enable >=0.2.3 ngio

Author: jluethi

pyproject.toml

@@ -27,7 +27,7 @@ authors = [
 # Required Python version and dependencies
 requires-python = ">=3.11"
 dependencies = [
-    "ngio==0.2.2",
+    "ngio>=0.2.3, <0.3.0",
     "fractal-task-tools==0.0.12",
 ]
 

src/fractal_helper_tasks/rechunk_zarr.py

@@ -10,6 +10,8 @@
 from typing import Any, Optional
 
 import ngio
+import ngio.images
+import ngio.images.label
 from ngio.ome_zarr_meta import AxesMapper
 from pydantic import validate_call
 
@@ -124,22 +126,21 @@ def rechunk_zarr(
                 axes_mapper=old_label.meta.axes_mapper,
                 chunk_sizes=chunk_sizes,
             )
-            ngio.images.label._derive_label(
+            new_label = new_ome_zarr_container.derive_label(
                 name=label,
-                store=f"{rechunked_zarr_url}/labels/{label}",
                 ref_image=old_label,
                 chunks=new_chunksize,
                 overwrite=overwrite,
             )
             if rebuild_pyramids:
-                new_label = new_ome_zarr_container.get_label(name=label)
                 new_label.set_array(old_label.get_array(mode="dask"))
                 new_label.consolidate()
             else:
                 label_pyramid_paths = old_label.meta.paths
                 for path in label_pyramid_paths:
-                    new_ome_zarr_container.get_label(name=label, path=path).set_array(
-                        old_label.get_array(path=path, mode="dask")
+                    old_label = ome_zarr_container.get_label(name=label, path=path)
+                    new_label.set_array(
+                        old_label.get_array(mode="dask")
                     )
 
     if overwrite_input: