Expose z chunking options & improve defaults. Closes #21

Author: jluethi

src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json

@@ -116,6 +116,11 @@
             "type": "string",
             "description": "If the image name between 2D & 3D don't match, this is the suffix that should be added to the 3D image. If the 2D image is in \"/path/to/my_plate_mip.zarr/B/03/0\" and the 3D image is in \"/path/to/my_plate.zarr/B/03/0_illum_corr\", the value should be \"_illum_corr\"."
           },
+          "z_chunks": {
+            "title": "Z Chunks",
+            "type": "integer",
+            "description": "Chunking for the Z dimension"
+          },
           "overwrite": {
             "default": false,
             "title": "Overwrite",

src/fractal_helper_tasks/convert_2D_segmentation_to_3D.py

@@ -99,6 +99,7 @@ def convert_2D_segmentation_to_3D(
     plate_suffix: str = "_mip",
     image_suffix_2D_to_remove: Optional[str] = None,
     image_suffix_3D_to_add: Optional[str] = None,
+    z_chunks: Optional[int] = None,
     overwrite: bool = False,
 ) -> None:
     """Convert 2D segmentation to 3D segmentation.
@@ -141,6 +142,7 @@ def convert_2D_segmentation_to_3D(
             If the 2D image is in "/path/to/my_plate_mip.zarr/B/03/0" and the
             3D image is in "/path/to/my_plate.zarr/B/03/0_illum_corr", the
             value should be "_illum_corr".
+        z_chunks: Chunking for the Z dimension
         overwrite: If `True`, overwrite existing label and ROI tables in the
             3D OME-Zarr
     """
@@ -179,6 +181,13 @@ def convert_2D_segmentation_to_3D(
     with zarr.open(zarr_3D_url, mode="rw+") as zarr_img:
         zarr_3D = da.from_zarr(zarr_img[0])
         new_z_planes = zarr_3D.shape[-3]
+        z_chunk_3d = zarr_3D.chunksize[-3]
+
+    # TODO: Improve axis detection in ngio refactor?
+    if z_chunks:
+        chunks[-3] = z_chunks
+    else:
+        chunks[-3] = z_chunk_3d
 
     image_meta = load_NgffImageMeta(zarr_3D_url)
     z_pixel_size = image_meta.get_pixel_sizes_zyx(level=0)[0]