Fix level choice in 2d to 3d task

Author: jluethi

src/fractal_helper_tasks/convert_2D_segmentation_to_3D.py

@@ -50,7 +50,9 @@ def convert_2D_segmentation_to_3D(
             the 3D OME-Zarr
         new_table_names: Optionally overwriting the names of the tables
             in the 3D OME-Zarr
-        level: Level of the 2D OME-Zarr label to copy from
+        level: Level of the 2D OME-Zarr label to copy from. Valid choices are
+            "0", "1", etc. (depending on which levels are available in the
+            OME-Zarr label).
         plate_suffix: Suffix of the 2D OME-Zarr that needs to be removed to
             generate the path to the 3D OME-Zarr. If the 2D OME-Zarr is
             "/path/to/my_plate_mip.zarr/B/03/0" and the 3D OME-Zarr is located
@@ -75,8 +77,6 @@ def convert_2D_segmentation_to_3D(
     # Normalize zarr_url
     zarr_url = zarr_url.rstrip("/")
     # 0) Preparation
-    if level != 0:
-        raise NotImplementedError("Only level 0 is supported at the moment")
     if new_table_names:
         if not tables_to_copy:
             raise ValueError(
@@ -116,7 +116,7 @@ def convert_2D_segmentation_to_3D(
 
     # 1) Load a 2D label image
     ome_zarr_container_2d = ngio.open_ome_zarr_container(zarr_url)
-    label_img = ome_zarr_container_2d.get_label(label_name, path=str(level))
+    label_img = ome_zarr_container_2d.get_label(label_name, path=level)
 
     if not label_img.is_2d:
         raise ValueError(

tests/test_convert_2d_to_3d_segmentation.py

@@ -77,6 +77,26 @@ def test_2d_to_3d_label_renaming(tmp_path: Path, new_label_name):
         assert ome_zarr_3d.list_labels() == [new_label_name]
 
 
+@pytest.mark.parametrize("level", ["0", "1", "2"])
+def test_2d_to_3d_varying_levels(tmp_path: Path, level):
+    """Test that the z-spacing is copied correctly."""
+    zarr_url = str(tmp_path / "plate_mip.zarr" / "B" / "03" / "0")
+    zarr_url_3d = str(tmp_path / "plate.zarr" / "B" / "03" / "0")
+    label_name = "nuclei"
+
+    create_synthetic_data(zarr_url, zarr_url_3d, label_name, z_spacing=1.0)
+
+    convert_2D_segmentation_to_3D(
+        zarr_url=zarr_url,
+        level=level,
+        label_name=label_name,
+        tables_to_copy=["masking_ROI_table"],
+    )
+    ome_zarr_3d = ngio.open_ome_zarr_container(zarr_url_3d)
+    label_img = ome_zarr_3d.get_label(name="nuclei")
+    assert label_img.pixel_size.x == 0.5 * (2 ** int(level))
+
+
 @pytest.mark.parametrize("new_table_names", [None, ["new_table_names"]])
 def test_2d_to_3d_table_renaming(tmp_path: Path, new_table_names):
     """Test that the z-spacing is copied correctly."""