remove unused code

Author: Jiaqi-Lv

tests/engines/test_nucleus_detection_engine.py

@@ -90,7 +90,7 @@ def test_write_detection_records_to_store_no_class_dict() -> None:
 
 
 def test_nucleus_detector_patch_annotation_store_output(
-    remote_sample: Callable, tmp_path: Path
+    remote_sample: Callable, track_tmp_path: Path
 ) -> None:
     """Test for nucleus detection engine in patch mode."""
     mini_wsi_svs = Path(remote_sample("wsi1_2k_2k_svs"))
@@ -106,7 +106,7 @@ def test_nucleus_detector_patch_annotation_store_output(
 
     pretrained_model = "sccnn-conic"
 
-    save_dir = tmp_path
+    save_dir = track_tmp_path
 
     nucleus_detector = NucleusDetector(model=pretrained_model)
     _ = nucleus_detector.run(
@@ -195,7 +195,7 @@ def test_nucleus_detector_patches_dict_output(
 
 
 def test_nucleus_detector_patches_zarr_output(
-    remote_sample: Callable, tmp_path: Path
+    remote_sample: Callable, track_tmp_path: Path
 ) -> None:
     """Test for nucleus detection engine in patch mode."""
     mini_wsi_svs = Path(remote_sample("wsi1_2k_2k_svs"))
@@ -212,7 +212,7 @@ def test_nucleus_detector_patches_zarr_output(
 
     nucleus_detector = NucleusDetector(model=pretrained_model)
 
-    save_dir = tmp_path
+    save_dir = track_tmp_path
 
     output_path = nucleus_detector.run(
         patch_mode=True,
@@ -240,13 +240,13 @@ def test_nucleus_detector_patches_zarr_output(
     _rm_dir(save_dir)
 
 
-def test_nucleus_detector_wsi(remote_sample: Callable, tmp_path: Path) -> None:
+def test_nucleus_detector_wsi(remote_sample: Callable, track_tmp_path: Path) -> None:
     """Test for nucleus detection engine."""
     mini_wsi_svs = Path(remote_sample("wsi4_512_512_svs"))
 
     pretrained_model = "sccnn-conic"
 
-    save_dir = tmp_path
+    save_dir = track_tmp_path
 
     nucleus_detector = NucleusDetector(model=pretrained_model)
     nucleus_detector.drop_keys = []

tiatoolbox/cli/nucleus_detector.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import shutil
 from typing import TYPE_CHECKING
 
 from tiatoolbox.cli.common import (
@@ -173,3 +174,5 @@ def nucleus_detector(
         overwrite=overwrite,
         verbose=verbose,
     )
+
+    shutil.rmtree(cache_path)

tiatoolbox/models/engine/nucleus_detector.py

@@ -713,52 +713,6 @@ def _save_predictions_annotation_store(
             class_dict=class_dict,
         )
 
-    @staticmethod
-    def _extract_nonzero(
-        block: np.ndarray, block_info: dict | None = None
-    ) -> np.ndarray:
-        """Extract non-zero detections from a block with global coordinates.
-
-        Args:
-            block: Input block array of shape (H, W, C).
-            block_info: Dask block information containing array location.
-
-        Returns:
-            2D array of shape (N, 4) where each row is [y, x, class, prob].
-            If no detections, returns array of shape (0, 4).
-
-        """
-        # Local indices within this chunk
-        ys, xs, classes = np.nonzero(block)
-        probs = block[ys, xs, classes]
-
-        # Get chunk offset from block_info
-        if block_info is not None:
-            info = block_info[0]
-            locs = info["array-location"]
-            y_offset = locs[0][0]
-            x_offset = locs[1][0]
-
-            # Adjust to global coordinates
-            ys = ys + y_offset
-            xs = xs + x_offset
-
-        # Stack into (N, 4) array: [y, x, class, prob]
-        if len(ys) > 0:
-            result = np.column_stack(
-                [
-                    ys.astype(np.uint32),
-                    xs.astype(np.uint32),
-                    classes.astype(np.uint32),
-                    probs.astype(np.float32),
-                ]
-            )
-        else:
-            # Return empty array with correct shape
-            result = np.empty((0, 4), dtype=np.float32)
-
-        return result
-
     @staticmethod
     def _centroid_maps_to_detection_arrays(
         detection_maps: da.Array,