[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

tests/engines/test_semantic_segmentor.py

@@ -87,7 +87,9 @@ def test_semantic_segmentor_patches(
     assert "probabilities" not in output.keys()  # noqa: SIM118
 
 
-def test_save_annotation_store(sample_patch1: Path, sample_patch2: Path, tmp_path: Path):
+def test_save_annotation_store(
+    sample_patch1: Path, sample_patch2: Path, tmp_path: Path
+):
     segmentor = SemanticSegmentor(
         model="fcn-tissue_mask", batch_size=32, verbose=False, device=device
     )
@@ -112,7 +114,9 @@ def test_save_annotation_store(sample_patch1: Path, sample_patch2: Path, tmp_pat
 
 
 def test_hovernet_dat() -> None:
-    from tiatoolbox.utils.misc import store_from_dat
     from pathlib import Path
+
+    from tiatoolbox.utils.misc import store_from_dat
+
     path_to_file = Path.cwd().parent.parent / "output" / "0.dat"
     out = store_from_dat(path_to_file, scale_factor=(1.0, 1.0))

tests/test_utils.py

@@ -1692,7 +1692,9 @@ def test_patch_pred_store_cdict() -> None:
         "other": "other",
     }
     class_dict = {0: "class0", 1: "class1"}
-    store = misc.dict_to_store_patch_predictions(patch_output, (1.0, 1.0), class_dict=class_dict)
+    store = misc.dict_to_store_patch_predictions(
+        patch_output, (1.0, 1.0), class_dict=class_dict
+    )
 
     # Check that it is an SQLiteStore containing the expected annotations
     assert isinstance(store, SQLiteStore)
@@ -1770,7 +1772,9 @@ def test_patch_pred_store_persist(tmp_path: pytest.TempPathFactory) -> None:
     }
     save_path = tmp_path / "patch_output" / "output.db"
 
-    store_path = misc.dict_to_store_patch_predictions(patch_output, (1.0, 1.0), save_path=save_path)
+    store_path = misc.dict_to_store_patch_predictions(
+        patch_output, (1.0, 1.0), save_path=save_path
+    )
 
     print("Annotation store path: ", store_path)
     assert Path.exists(store_path), "Annotation Store output file does not exist"
@@ -1804,7 +1808,9 @@ def test_patch_pred_store_persist_ext(tmp_path: pytest.TempPathFactory) -> None:
     # sends the path of a jpeg source image, expects .db file in the same directory
     save_path = tmp_path / "patch_output" / "output.jpeg"
 
-    store_path = misc.dict_to_store_patch_predictions(patch_output, (1.0, 1.0), save_path=save_path)
+    store_path = misc.dict_to_store_patch_predictions(
+        patch_output, (1.0, 1.0), save_path=save_path
+    )
 
     print("Annotation store path: ", store_path)
     assert Path.exists(store_path), "Annotation Store output file does not exist"

tiatoolbox/models/engine/semantic_segmentor_new.py

@@ -3,14 +3,14 @@
 from __future__ import annotations
 
 import shutil
+from pathlib import Path
 from typing import TYPE_CHECKING
 
 import zarr
 from typing_extensions import Unpack
-from pathlib import Path
 
+from ...utils.misc import dict_to_store_semantic_segmentor, dict_to_zarr
 from .patch_predictor import PatchPredictor, PredictorRunParams
-from ...utils.misc import dict_to_zarr, dict_to_store_semantic_segmentor
 
 if TYPE_CHECKING:  # pragma: no cover
     import os

tiatoolbox/utils/misc.py

@@ -1285,11 +1285,11 @@ def dict_to_store_semantic_segmentor(
             origin = (0, 0)
             scaled_coords = np.array([scale_factor * coords])
             feature_geom = feature2geometry(
-                            {
-                                "type": "Polygon",
-                                "coordinates": scaled_coords,
-                            },
-                        )
+                {
+                    "type": "Polygon",
+                    "coordinates": scaled_coords,
+                },
+            )
             annotations.append(
                 Annotation(
                     geometry=make_valid_poly(