🗑️ Update test_multi_task_segmentor.py

Author: shaneahmed

tests/models/test_arch_micronet.py

@@ -54,7 +54,7 @@ def test_value_error() -> None:
     toolbox_env.running_on_ci() or not ON_GPU,
     reason="Local test on machine with GPU.",
 )
-def test_micronet_output(remote_sample: Callable, tmp_path: Path) -> None:
+def test_micronet_output(remote_sample: Callable, track_tmp_path: Path) -> None:
     """Test the output of MicroNet."""
     svs_1_small = Path(remote_sample("svs-1-small"))
     micronet_output = Path(remote_sample("micronet-output"))
@@ -74,7 +74,7 @@ def test_micronet_output(remote_sample: Callable, tmp_path: Path) -> None:
         imgs=[
             svs_1_small,
         ],
-        save_dir=tmp_path / "output",
+        save_dir=track_tmp_path / "output",
     )
 
     output = np.load(output[0][1] + ".raw.0.npy")

tests/models/test_dataset.py

@@ -86,9 +86,9 @@ def test_kather_nonexisting_dir() -> None:
         _ = KatherPatchDataset(save_dir_path="non-existing-path")
 
 
-def test_kather_dataset(tmp_path: Path) -> None:
+def test_kather_dataset(track_tmp_path: Path) -> None:
     """Test for kather patch dataset."""
-    save_dir_path = tmp_path
+    save_dir_path = track_tmp_path
 
     # save to temporary location
     # remove previously generated data

tests/models/test_feature_extractor.py

@@ -24,9 +24,9 @@
 # -------------------------------------------------------------------------------------
 
 
-def test_engine(remote_sample: Callable, tmp_path: Path) -> None:
+def test_engine(remote_sample: Callable, track_tmp_path: Path) -> None:
     """Test feature extraction with DeepFeatureExtractor engine."""
-    save_dir = tmp_path / "output"
+    save_dir = track_tmp_path / "output"
     # # convert to pathlib Path to prevent wsireader complaint
     mini_wsi_svs = Path(remote_sample("wsi4_1k_1k_svs"))
 
@@ -55,10 +55,10 @@ def test_engine(remote_sample: Callable, tmp_path: Path) -> None:
     "model", [CNNBackbone("resnet50"), TimmBackbone("efficientnet_b0", pretrained=True)]
 )
 def test_full_inference(
-    remote_sample: Callable, tmp_path: Path, model: Callable
+    remote_sample: Callable, track_tmp_path: Path, model: Callable
 ) -> None:
     """Test full inference with CNNBackbone and TimmBackbone models."""
-    save_dir = tmp_path / "output"
+    save_dir = track_tmp_path / "output"
     # pre-emptive clean up
     shutil.rmtree(save_dir, ignore_errors=True)  # default output dir test
 
@@ -121,9 +121,11 @@ def test_full_inference(
     toolbox_env.running_on_ci() or not ON_GPU,
     reason="Local test on machine with GPU.",
 )
-def test_multi_gpu_feature_extraction(remote_sample: Callable, tmp_path: Path) -> None:
+def test_multi_gpu_feature_extraction(
+    remote_sample: Callable, track_tmp_path: Path
+) -> None:
     """Local functionality test for feature extraction using multiple GPUs."""
-    save_dir = tmp_path / "output"
+    save_dir = track_tmp_path / "output"
     mini_wsi_svs = Path(remote_sample("wsi4_1k_1k_svs"))
     shutil.rmtree(save_dir, ignore_errors=True)
 

tests/models/test_multi_task_segmentor.py

@@ -48,10 +48,10 @@ def semantic_postproc_func(raw_output: np.ndarray) -> np.ndarray:
     toolbox_env.running_on_ci() or not ON_GPU,
     reason="Local test on machine with GPU.",
 )
-def test_functionality_local(remote_sample: Callable, tmp_path: Path) -> None:
+def test_functionality_local(remote_sample: Callable, track_tmp_path: Path) -> None:
     """Local functionality test for multi task segmentor."""
     gc.collect()
-    root_save_dir = Path(tmp_path)
+    root_save_dir = Path(track_tmp_path)
     mini_wsi_svs = Path(remote_sample("svs-1-small"))
     save_dir = root_save_dir / "multitask"
     shutil.rmtree(save_dir, ignore_errors=True)
@@ -100,9 +100,11 @@ def test_functionality_local(remote_sample: Callable, tmp_path: Path) -> None:
     assert score > 0.95, "Heavy loss of precision!"
 
 
-def test_functionality_hovernetplus(remote_sample: Callable, tmp_path: Path) -> None:
+def test_functionality_hovernetplus(
+    remote_sample: Callable, track_tmp_path: Path
+) -> None:
     """Functionality test for multitask segmentor."""
-    root_save_dir = Path(tmp_path)
+    root_save_dir = Path(track_tmp_path)
     mini_wsi_svs = Path(remote_sample("wsi4_512_512_svs"))
     required_dims = (258, 258)
     # above image is 512 x 512 at 0.252 mpp resolution. This is 258 x 258 at 0.500 mpp.
@@ -133,9 +135,9 @@ def test_functionality_hovernetplus(remote_sample: Callable, tmp_path: Path) ->
     )
 
 
-def test_functionality_hovernet(remote_sample: Callable, tmp_path: Path) -> None:
+def test_functionality_hovernet(remote_sample: Callable, track_tmp_path: Path) -> None:
     """Functionality test for multitask segmentor."""
-    root_save_dir = Path(tmp_path)
+    root_save_dir = Path(track_tmp_path)
     mini_wsi_svs = Path(remote_sample("wsi4_512_512_svs"))
 
     save_dir = root_save_dir / "multi"
@@ -159,14 +161,14 @@ def test_functionality_hovernet(remote_sample: Callable, tmp_path: Path) -> None
     assert len(inst_dict) > 0, "Must have some nuclei."
 
 
-def test_masked_segmentor(remote_sample: Callable, tmp_path: Path) -> None:
+def test_masked_segmentor(remote_sample: Callable, track_tmp_path: Path) -> None:
     """Test segmentor when image is masked."""
-    root_save_dir = Path(tmp_path)
+    root_save_dir = Path(track_tmp_path)
     sample_wsi_svs = Path(remote_sample("svs-1-small"))
     sample_wsi_msk = remote_sample("small_svs_tissue_mask")
     sample_wsi_msk = np.load(sample_wsi_msk).astype(np.uint8)
-    imwrite(f"{tmp_path}/small_svs_tissue_mask.jpg", sample_wsi_msk)
-    sample_wsi_msk = tmp_path.joinpath("small_svs_tissue_mask.jpg")
+    imwrite(f"{track_tmp_path}/small_svs_tissue_mask.jpg", sample_wsi_msk)
+    sample_wsi_msk = track_tmp_path.joinpath("small_svs_tissue_mask.jpg")
 
     save_dir = root_save_dir / "instance"
 
@@ -208,10 +210,10 @@ def test_masked_segmentor(remote_sample: Callable, tmp_path: Path) -> None:
 
 def test_functionality_process_instance_predictions(
     remote_sample: Callable,
-    tmp_path: Path,
+    track_tmp_path: Path,
 ) -> None:
     """Test the functionality of instance predictions processing."""
-    root_save_dir = Path(tmp_path)
+    root_save_dir = Path(track_tmp_path)
     mini_wsi_svs = Path(remote_sample("wsi4_512_512_svs"))
 
     save_dir = root_save_dir / "semantic"
@@ -251,9 +253,9 @@ def test_functionality_process_instance_predictions(
     assert len(multi_segmentor._wsi_inst_info[0]) == 0
 
 
-def test_empty_image(tmp_path: Path) -> None:
+def test_empty_image(track_tmp_path: Path) -> None:
     """Test MultiTaskSegmentor for an empty image."""
-    root_save_dir = Path(tmp_path)
+    root_save_dir = Path(track_tmp_path)
     sample_patch = np.ones((256, 256, 3), dtype="uint8") * 255
     sample_patch_path = root_save_dir / "sample_tile.png"
     imwrite(sample_patch_path, sample_patch)
@@ -320,9 +322,9 @@ def test_empty_image(tmp_path: Path) -> None:
     )
 
 
-def test_functionality_semantic(remote_sample: Callable, tmp_path: Path) -> None:
+def test_functionality_semantic(remote_sample: Callable, track_tmp_path: Path) -> None:
     """Functionality test for multitask segmentor."""
-    root_save_dir = Path(tmp_path)
+    root_save_dir = Path(track_tmp_path)
 
     save_dir = root_save_dir / "multi"
     shutil.rmtree(save_dir, ignore_errors=True)
@@ -373,14 +375,14 @@ def test_functionality_semantic(remote_sample: Callable, tmp_path: Path) -> None
     assert layer_map is not None, "Must have some segmentations."
 
 
-def test_crash_segmentor(remote_sample: Callable, tmp_path: Path) -> None:
+def test_crash_segmentor(remote_sample: Callable, track_tmp_path: Path) -> None:
     """Test engine crash when given malformed input."""
-    root_save_dir = Path(tmp_path)
+    root_save_dir = Path(track_tmp_path)
     sample_wsi_svs = Path(remote_sample("svs-1-small"))
     sample_wsi_msk = remote_sample("small_svs_tissue_mask")
     sample_wsi_msk = np.load(sample_wsi_msk).astype(np.uint8)
-    imwrite(f"{tmp_path}/small_svs_tissue_mask.jpg", sample_wsi_msk)
-    sample_wsi_msk = tmp_path.joinpath("small_svs_tissue_mask.jpg")
+    imwrite(f"{track_tmp_path}/small_svs_tissue_mask.jpg", sample_wsi_msk)
+    sample_wsi_msk = track_tmp_path.joinpath("small_svs_tissue_mask.jpg")
 
     save_dir = f"{root_save_dir}/multi/"