Use new NgffImage model in yokogawa_to_ome_zarr task (ref #351, ref

#150)

fractal_tasks_core/tasks/yokogawa_to_ome_zarr.py

@@ -27,6 +27,7 @@
 from fractal_tasks_core.lib_channels import get_omero_channel_list
 from fractal_tasks_core.lib_channels import OmeroChannel
 from fractal_tasks_core.lib_glob import glob_with_multiple_patterns
+from fractal_tasks_core.lib_image import NgffImage
 from fractal_tasks_core.lib_parse_filename_metadata import parse_filename
 from fractal_tasks_core.lib_pyramid_creation import build_pyramid
 from fractal_tasks_core.lib_read_fractal_metadata import (
@@ -36,7 +37,6 @@
     convert_ROI_table_to_indices,
 )
 from fractal_tasks_core.lib_write import OverwriteNotAllowedError
-from fractal_tasks_core.lib_zattrs_utils import extract_zyx_pixel_sizes
 
 
 logger = logging.getLogger(__name__)
@@ -110,11 +110,13 @@ def yokogawa_to_ome_zarr(
         raise NotImplementedError
     zarrurl = Path(input_paths[0]).as_posix() + f"/{component}"
 
+    ngff_image = NgffImage(**zarr.open_group(zarrurl).attrs.asdict())
+    num_levels = ngff_image.num_levels
+    coarsening_xy = ngff_image.coarsening_xy
+
     parameters = get_parameters_from_metadata(
         keys=[
             "original_paths",
-            "num_levels",
-            "coarsening_xy",
             "image_extension",
             "image_glob_patterns",
         ],
@@ -125,8 +127,6 @@ def yokogawa_to_ome_zarr(
         image_zarr_path=(Path(output_path) / component),
     )
     original_path_list = parameters["original_paths"]
-    num_levels = parameters["num_levels"]
-    coarsening_xy = parameters["coarsening_xy"]
     image_extension = parameters["image_extension"]
     image_glob_patterns = parameters["image_glob_patterns"]
 
@@ -145,7 +145,7 @@ def yokogawa_to_ome_zarr(
 
     # Read useful information from ROI table and .zattrs
     adata = read_zarr(f"{zarrurl}/tables/FOV_ROI_table")
-    pxl_size = extract_zyx_pixel_sizes(f"{zarrurl}/.zattrs")
+    pxl_size = ngff_image.get_pixel_sizes_zyx(level=0)
     fov_indices = convert_ROI_table_to_indices(
         adata, full_res_pxl_sizes_zyx=pxl_size
     )