Merge pull request #944 from fractal-analytics-platform/rename-variable

Rename variable in projection task

Author: jluethi

CHANGELOG.md

@@ -3,7 +3,7 @@
 # 1.5.0
 
 * Tasks:
-    * Refactor `projection` task to use the new `ngio` API (\#937, \#943).
+    * Refactor `projection` task to use the new `ngio` API (\#937, \#943, \#944).
     * Refactor `copy_ome_zarr_plate` init task to support the upcoming flexibility.
     * Rely on `fractal-task-tools` for `run_fractal_task` wrapper (\#923).
     * Mark some existing tasks as _converter_ tasks(\#923).

fractal_tasks_core/__FRACTAL_MANIFEST__.json

@@ -676,9 +676,9 @@
             "title": "Method",
             "description": "Choose which method to use for intensity projection along the Z axis. mip is the default and performs a maximum intensity projection. minip performs a minimum intensity projection, meanip a mean intensity projection and sumip a sum intensity projection."
           },
-          "overwrite_images": {
+          "overwrite": {
             "default": false,
-            "title": "Overwrite Images",
+            "title": "Overwrite",
             "type": "boolean",
             "description": "If `True`, overwrite the MIP images if they are already present in the new OME-Zarr Plate."
           },

fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py

@@ -93,7 +93,7 @@ def copy_ome_zarr_hcs_plate(
     zarr_dir: str,
     method: DaskProjectionMethod = DaskProjectionMethod.MIP,
     # Advanced parameters
-    overwrite_images: bool = False,
+    overwrite: bool = False,
     re_initialize_plate: bool = False,
 ) -> dict[str, Any]:
     """
@@ -122,7 +122,7 @@ def copy_ome_zarr_hcs_plate(
             Z axis. mip is the default and performs a maximum intensity
             projection. minip performs a minimum intensity projection, meanip
             a mean intensity projection and sumip a sum intensity projection.
-        overwrite_images: If `True`, overwrite the MIP images if they are
+        overwrite: If `True`, overwrite the MIP images if they are
             already present in the new OME-Zarr Plate.
         re_initialize_plate: If `True`, re-initialize the plate, deleting all
             existing wells and images. If `False`, the task will only
@@ -184,10 +184,10 @@ def copy_ome_zarr_hcs_plate(
         proj_image_path = f"{row}/{column}/{image_path}"
 
         if proj_image_path in proj_plate_images_paths:
-            if not overwrite_images:
+            if not overwrite:
                 raise NgioFileExistsError(
                     f"Image {proj_image_path} already exists in "
-                    f"{proj_plate_url}. Set `overwrite_images=True` "
+                    f"{proj_plate_url}. Set `overwrite=True` "
                     "to overwrite it."
                 )
             logger.info(

tests/tasks/test_import_ome_zarr.py

@@ -65,7 +65,7 @@ def test_import_ome_zarr_plate(tmp_path, zenodo_zarr):
     parallelization_list = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir="tmp_out",
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
     debug(parallelization_list)
@@ -248,7 +248,7 @@ def test_import_ome_zarr_plate_no_ROI_tables(tmp_path, zenodo_zarr):
     parallelization_list = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir="tmp_out",
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
     debug(parallelization_list)

tests/tasks/test_registration.py

@@ -290,7 +290,7 @@ def test_multiplexing_registration(
     parallelization_list = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls_3D,
         zarr_dir=zarr_dir,
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
     debug(parallelization_list)

tests/tasks/test_unit_copy_hcs.py

@@ -56,7 +56,7 @@ def test_MIP(
     parallelization_list = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir="tmp_out",
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
     debug(parallelization_list)
@@ -65,7 +65,7 @@ def test_MIP(
     parallelization_list_2 = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir="tmp_out",
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
     assert parallelization_list_2 == parallelization_list
@@ -75,7 +75,7 @@ def test_MIP(
         _ = copy_ome_zarr_hcs_plate(
             zarr_urls=zarr_urls,
             zarr_dir="tmp_out",
-            overwrite_images=False,
+            overwrite=False,
             re_initialize_plate=False,
         )
 

tests/tasks/test_workflows.py

@@ -321,7 +321,7 @@ def test_MIP(
     parallelization_list = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir=str(zarr_path),
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
     debug(parallelization_list)
@@ -330,7 +330,7 @@ def test_MIP(
     parallelization_list_2 = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir=str(zarr_path),
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
     assert parallelization_list_2 == parallelization_list
@@ -416,7 +416,7 @@ def test_projection_methods(
         zarr_urls=zarr_urls,
         zarr_dir=str(zarr_path),
         method=method,
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
 
@@ -499,7 +499,7 @@ def test_MIP_subset_of_images(
     parallelization_list = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir=str(zarr_dir),
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
     debug(parallelization_list)

tests/tasks/test_workflows_multiplexing.py

@@ -393,7 +393,7 @@ def test_multiplexing_MIP(
     parallelization_list = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir=str(zarr_dir),
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )["parallelization_list"]
     debug(parallelization_list)

tests/tasks_v2/test_projection_task.py

@@ -13,7 +13,7 @@ def test_mip_task(cardiomyocyte_tiny_path: Path, tmp_path: Path) -> None:
     parallel_list = copy_ome_zarr_hcs_plate(
         zarr_urls=[image_url],
         zarr_dir=str(tmp_path / "tmp_out"),
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )
 

tests/tasks_v2/test_unit_copy_ome_hcs_plate.py

@@ -63,14 +63,14 @@ def test_flexibility_copy_hcs(tmp_path: Path):
     parallel_list_1 = copy_ome_zarr_hcs_plate(
         zarr_urls=[zarr_urls[0]],
         zarr_dir=subset_dir,
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )
     # Subset 2
     _ = copy_ome_zarr_hcs_plate(
         zarr_urls=[zarr_urls[1]],
         zarr_dir=subset_dir,
-        overwrite_images=False,
+        overwrite=False,
         re_initialize_plate=False,
     )
 
@@ -82,7 +82,7 @@ def test_flexibility_copy_hcs(tmp_path: Path):
     parallel_list_all = copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir=all_dir,
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )
     zarr_url = parallel_list_all["parallelization_list"][0]["zarr_url"]
@@ -100,7 +100,7 @@ def test_fail_overwrite(tmp_path: Path):
     copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir=str(tmp_path),
-        overwrite_images=False,
+        overwrite=False,
         re_initialize_plate=False,
     )
 
@@ -109,15 +109,15 @@ def test_fail_overwrite(tmp_path: Path):
     copy_ome_zarr_hcs_plate(
         zarr_urls=zarr_urls,
         zarr_dir=str(tmp_path),
-        overwrite_images=False,
+        overwrite=False,
         re_initialize_plate=True,
     )
 
     with pytest.raises(FileExistsError):
         copy_ome_zarr_hcs_plate(
             zarr_urls=zarr_urls,
             zarr_dir=str(tmp_path),
-            overwrite_images=False,
+            overwrite=False,
             re_initialize_plate=False,
         )
 
@@ -130,7 +130,7 @@ def test_new_plate_name(tmp_path: Path):
             zarr_urls=[zarr_urls[0]],
             zarr_dir=str(tmp_path),
             method=method,
-            overwrite_images=False,
+            overwrite=False,
             re_initialize_plate=False,
         )
 
@@ -148,7 +148,7 @@ def test_fail_not_plate_url():
         copy_ome_zarr_hcs_plate(
             zarr_urls=["/tmp/plate.zarr"],
             zarr_dir="/tmp",
-            overwrite_images=False,
+            overwrite=False,
             re_initialize_plate=False,
         )
 
@@ -161,7 +161,7 @@ def test_reinit_true(tmp_path: Path):
     parallel_list_1 = copy_ome_zarr_hcs_plate(
         zarr_urls=[zarr_urls[0]],
         zarr_dir=str(tmp_path),
-        overwrite_images=True,
+        overwrite=True,
         re_initialize_plate=True,
     )
 
@@ -173,7 +173,7 @@ def test_reinit_true(tmp_path: Path):
     parallel_list_2 = copy_ome_zarr_hcs_plate(
         zarr_urls=[zarr_urls[1]],
         zarr_dir=str(tmp_path),
-        overwrite_images=False,
+        overwrite=False,
         re_initialize_plate=True,
     )