Test for label renaming

Author: jluethi

tests/test_convert_2d_to_3d_segmentation.py

@@ -1,22 +1,29 @@
 """Test copy 2D to 3D segmentation."""
 
 import dask.array as da
+import pytest
 import zarr
 
 from fractal_helper_tasks.convert_2D_segmentation_to_3D import (
     convert_2D_segmentation_to_3D,
 )
 
 
-def test_2d_to_3d(tmp_zenodo_zarr: list[str]):
+@pytest.mark.parametrize("new_label_name", [None, "nuclei_new"])
+def test_2d_to_3d(tmp_zenodo_zarr: list[str], new_label_name):
     zarr_url = f"{tmp_zenodo_zarr[1]}/B/03/0"
     label_name = "nuclei"
 
     convert_2D_segmentation_to_3D(
         zarr_url=zarr_url,
         label_name=label_name,
+        new_label_name=new_label_name,
     )
-    zarr_3D_label_url = f"{tmp_zenodo_zarr[0]}/B/03/0/labels/{label_name}"
+
+    if not new_label_name:
+        new_label_name = label_name
+
+    zarr_3D_label_url = f"{tmp_zenodo_zarr[0]}/B/03/0/labels/{new_label_name}"
     # Check that the label has been copied correctly
     with zarr.open(zarr_3D_label_url, mode="rw+") as zarr_img:
         zarr_3D = da.from_zarr(zarr_img[0])
@@ -25,7 +32,9 @@ def test_2d_to_3d(tmp_zenodo_zarr: list[str]):
 
 # TODO: Add custom ROI tables to be copied to 3D
 
-# TODO: Add test with new label name, new table names
+# TODO: Add a feature table & have it copied over
+
+# TODO: Add test with new table names
 
 # TODO: Create a version of the test data where image suffixes need to be
 # changed, run tests on those