Merge branch 'develop' into dev-define-engines-abc

Author: shaneahmed

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.5.1 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.5.2 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.5.1
+    rev: v0.5.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

requirements/requirements_dev.txt

@@ -11,7 +11,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.5.1  # This will be updated by pre-commit bot to latest version
+ruff==0.5.2  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tiatoolbox/tools/registration/wsi_registration.py

@@ -332,7 +332,7 @@ class DFBRFeatureExtractor(torch.nn.Module):
 
     """
 
-    def __init__(self: torch.nn.Module) -> None:
+    def __init__(self: DFBRFeatureExtractor) -> None:
         """Initialize :class:`DFBRFeatureExtractor`."""
         super().__init__()
         output_layers_id: list[str] = ["16", "23", "30"]
@@ -434,8 +434,8 @@ class DFBRegister:
     def __init__(self: DFBRegister, patch_size: tuple[int, int] = (224, 224)) -> None:
         """Initialize :class:`DFBRegister`."""
         self.patch_size = patch_size
-        self.x_scale: list[float] = []
-        self.y_scale: list[float] = []
+        self.x_scale: np.ndarray
+        self.y_scale: np.ndarray
         self.feature_extractor = DFBRFeatureExtractor()
 
     # Make this function private when full pipeline is implemented.
@@ -796,7 +796,7 @@ def find_points_inside_boundary(mask: np.ndarray, points: np.ndarray) -> np.ndar
         return PatchExtractor.filter_coordinates(
             mask_reader,
             bbox_coord,
-            mask.shape[::-1],
+            (mask.shape[1], mask.shape[0]),
         )
 
     def filtering_matching_points(
@@ -1521,21 +1521,21 @@ def get_patch_dimensions(
         """
         width, height = size[0], size[1]
 
-        x = [
+        x_info = [
             np.linspace(1, width, width, endpoint=True),
             np.ones(height) * width,
             np.linspace(1, width, width, endpoint=True),
             np.ones(height),
         ]
-        x = np.array(list(itertools.chain.from_iterable(x)))
+        x = np.array(list(itertools.chain.from_iterable(x_info)))
 
-        y = [
+        y_info = [
             np.ones(width),
             np.linspace(1, height, height, endpoint=True),
             np.ones(width) * height,
             np.linspace(1, height, height, endpoint=True),
         ]
-        y = np.array(list(itertools.chain.from_iterable(y)))
+        y = np.array(list(itertools.chain.from_iterable(y_info)))
 
         points = np.array([x, y]).transpose()
         transform = transform * [[1, 1, 0], [1, 1, 0], [1, 1, 1]]  # remove translation

tiatoolbox/utils/metrics.py

@@ -103,5 +103,5 @@ def dice(gt_mask: np.ndarray, pred_mask: np.ndarray) -> float:
     pred_mask = pred_mask.astype(np.bool_)
     sum_masks = gt_mask.sum() + pred_mask.sum()
     if sum_masks == 0:
-        return np.NAN
+        return np.nan
     return 2 * np.logical_and(gt_mask, pred_mask).sum() / sum_masks