Rename new illumination_correction argument to `illumination_profil…

…es_folder` (ref #414)
fractal-analytics-platform · Jun 15, 2023 · cddea5a · cddea5a
1 parent 9a1da58
commit cddea5a
Show file tree

Hide file tree

Showing 3 changed files with 11 additions and 8 deletions.
diff --git a/fractal_tasks_core/tasks/illumination_correction.py b/fractal_tasks_core/tasks/illumination_correction.py
@@ -103,7 +103,7 @@ def illumination_correction(
     component: str,
     metadata: Dict[str, Any],
     # Task-specific arguments
-    root_path_corr: str,
+    illumination_profiles_folder: str,
     dict_corr: dict[str, str],
     background: int = 110,
     new_component: Optional[str] = None,
@@ -143,7 +143,8 @@ def illumination_correction(
                      downsampling when building the pyramid.
                      (standard argument for Fractal tasks,
                      managed by Fractal server)
-    :param root_path_corr: FIXME -- see issue 414 on fractal-tasks-core
+    :param illumination_profiles_folder: FIXME -- see issue 414 on
+                                         fractal-tasks-core
     :param dict_corr: FIXME -- see issue 414 on fractal-tasks-core
     :param background: Background value that is subtracted from the image
                        before the illumination correction is applied. Set it
@@ -241,7 +242,9 @@ def illumination_correction(
     for channel in channels:
         wavelength_id = channel.wavelength_id
         corrections[wavelength_id] = imread(
-            (Path(root_path_corr) / dict_corr[wavelength_id]).as_posix()
+            (
+                Path(illumination_profiles_folder) / dict_corr[wavelength_id]
+            ).as_posix()
         )
         if corrections[wavelength_id].shape != (img_size_y, img_size_x):
             raise Exception(

diff --git a/tests/tasks/test_unit_illumination_correction.py b/tests/tasks/test_unit_illumination_correction.py
@@ -51,6 +51,7 @@ def test_illumination_correction(
         "A01_C01": "illum_corr_matrix.png",
         "A01_C02": "illum_corr_matrix.png",
     }
+    illumination_profiles_folder = f"{testdata_str}/illumination_correction/"
     with open(zarrurl + ".zattrs") as fin:
         zattrs = json.load(fin)
         num_levels = len(zattrs["multiscales"][0]["datasets"])
@@ -95,7 +96,7 @@ def patched_correct(*args, **kwargs):
             metadata=metadata,
             component=component,
             overwrite=overwrite,
-            root_path_corr=f"{testdata_str}/illumination_correction/",
+            illumination_profiles_folder=illumination_profiles_folder,
             dict_corr=illum_params,
             background=0,
         )

diff --git a/tests/tasks/test_workflows.py b/tests/tasks/test_workflows.py
@@ -313,9 +313,8 @@ def test_illumination_correction(
     metadata = {}
 
     testdata_str = testdata_path.as_posix()
-    illum_params = {
-        "A01_C01": "illum_corr_matrix.png",
-    }
+    illum_params = {"A01_C01": "illum_corr_matrix.png"}
+    illumination_profiles_folder = f"{testdata_str}/illumination_correction/"
 
     # Create zarr structure
     metadata_update = create_ome_zarr(
@@ -351,7 +350,7 @@ def test_illumination_correction(
             metadata=metadata,
             component=component,
             overwrite=True,
-            root_path_corr=f"{testdata_str}/illumination_correction/",
+            illumination_profiles_folder=illumination_profiles_folder,
             dict_corr=illum_params,
         )
     print(caplog.text)