fix: standardize TiffFile output to uint8 and correct CuCIM typing

Signed-off-by: Nikolas Schmitz <nikolas.schmitz@rwth-aachen.de>

Author: NikolasSchmitz

monai/data/wsi_reader.py

@@ -127,7 +127,7 @@ def set_dtype(self, dtype):
             self.dtype = np.dtype(dtype)
 
     def set_device(self, device):
-        if device is None or isinstance(device, (torch.device, str)):
+        if device is None or isinstance(device, torch.device | str):
             self.device = device
         else:
             raise ValueError(f"`device` must be `torch.device`, `str` or `None` but {type(device)} is given.")
@@ -358,7 +358,7 @@ def get_data(
         metadata_list: list = []
 
         # CuImage object is iterable, so ensure_tuple won't work on single object
-        if not isinstance(wsi, (list, tuple)):
+        if not isinstance(wsi, list | tuple):
             wsi = (wsi,)
         for each_wsi in ensure_tuple(wsi):
             # get the valid level based on resolution info
@@ -835,7 +835,9 @@ def get_mpp(self, wsi, level: int) -> tuple[float, float]:
 
         raise ValueError("`mpp` cannot be obtained for this file. Please use `level` instead.")
 
-    def get_wsi_at_mpp(self, wsi, mpp: float | tuple[float, float], atol: float = 0.00, rtol: float = 0.05) -> Any:
+    def get_wsi_at_mpp(
+        self, wsi, mpp: float | tuple[float, float], atol: float = 0.00, rtol: float = 0.05
+    ) -> np.ndarray:
         """
         Returns the representation of the whole slide image at a given micro-per-pixel (mpp) resolution.
         The optional tolerance parameters are considered at the level whose mpp value is closest to the one provided by the user.
@@ -852,7 +854,7 @@ def get_wsi_at_mpp(self, wsi, mpp: float | tuple[float, float], atol: float = 0.
             rtol: the acceptable relative tolerance for resolution in micro per pixel.
 
         Returns:
-            Cupy array containing the whole slide image at the requested MPP resolution.
+            Numpy array containing the whole slide image at the requested MPP resolution.
 
         """
         cp, _ = optional_import("cupy")
@@ -1423,7 +1425,8 @@ def get_wsi_at_mpp(
         if within_tolerance:
             # If the image at the desired mpp resolution is within tolerances, return the image at closest_level.
             # TiffFile does not expose `read_region`; read the whole page instead (consistent with `_get_patch`).
-            closest_lvl_wsi = wsi.pages[closest_lvl].asarray()
+            pil_image, _ = optional_import("PIL", name="Image")
+            closest_lvl_wsi = pil_image.fromarray(wsi.pages[closest_lvl].asarray())
 
         elif closest_level_is_bigger:
             # Otherwise, select the level closest to the desired mpp with a higher resolution and downsample it.
@@ -1437,6 +1440,9 @@ def get_wsi_at_mpp(
                 closest_lvl = closest_lvl - 1
                 closest_lvl_wsi = self._resize_to_mpp_res(wsi, closest_lvl, mpp_list, mpp)
 
+        # Convert to specified mode to normalize dtype
+        closest_lvl_wsi = closest_lvl_wsi.convert(self.mode)
+
         wsi_arr = np.array(closest_lvl_wsi)
 
         # Ensure channel dimension exists for grayscale
@@ -1561,4 +1567,4 @@ def _resize_to_mpp_res(self, wsi, closest_lvl, mpp_list, user_mpp: tuple):
         # PIL `resize` takes (W, H); use the same row/col order as OpenSlide.
         closest_lvl_wsi = closest_lvl_wsi.resize((target_res_y, target_res_x), pil_image.BILINEAR)
 
-        return closest_lvl_wsi
+        return closest_lvl_wsi

tests/utils/enums/test_wsireader.py

@@ -41,7 +41,9 @@
 WSI_GENERIC_TIFF_PATH = os.path.join(TESTS_PATH, "testing_data", f"temp_{WSI_GENERIC_TIFF_KEY}.tiff")
 
 WSI_GENERIC_TIFF_CORRECT_MPP_KEY = "wsi_generic_tiff_correct_mpp"
-WSI_GENERIC_TIFF_CORRECT_MPP_PATH = os.path.join(TESTS_PATH, "testing_data", f"temp_{WSI_GENERIC_TIFF_CORRECT_MPP_KEY}.tiff")
+WSI_GENERIC_TIFF_CORRECT_MPP_PATH = os.path.join(
+    TESTS_PATH, "testing_data", f"temp_{WSI_GENERIC_TIFF_CORRECT_MPP_KEY}.tiff"
+)
 
 WSI_APERIO_SVS_KEY = "wsi_aperio_svs"
 WSI_APERIO_SVS_PATH = os.path.join(TESTS_PATH, "testing_data", f"temp_{WSI_APERIO_SVS_KEY}.svs")
@@ -307,11 +309,7 @@
     {"openslide": (3, 10949, 15303), "cucim": (3, 10949, 15303), "tifffile": (3, 10949, 15303)},
 ]
 
-TEST_CASE_SVS_MPP_SCALAR = [
-    WSI_APERIO_SVS_PATH,
-    {"mpp": 8.0},
-    {"openslide": (3, 2057, 2875), "cucim": (3, 2057, 2875)},
-]
+TEST_CASE_SVS_MPP_SCALAR = [WSI_APERIO_SVS_PATH, {"mpp": 8.0}, {"openslide": (3, 2057, 2875), "cucim": (3, 2057, 2875)}]
 
 TEST_CASE_DEVICE_2 = [
     WSI_GENERIC_TIFF_PATH,
@@ -470,17 +468,17 @@ class WSIReaderTests:
     class Tests(unittest.TestCase):
         backend = None
 
-        # @parameterized.expand([TEST_CASE_WHOLE_0])
-        # def test_read_whole_image(self, file_path, level, expected_shape):
-        #     reader = WSIReader(self.backend, level=level)
-        #     with reader.read(file_path) as img_obj:
-        #         img, meta = reader.get_data(img_obj)
-        #     self.assertTupleEqual(img.shape, expected_shape)
-        #     self.assertEqual(meta["backend"], self.backend)
-        #     self.assertEqual(meta[WSIPatchKeys.PATH].lower(), str(os.path.abspath(file_path)).lower())
-        #     self.assertEqual(meta[WSIPatchKeys.LEVEL], level)
-        #     assert_allclose(meta[WSIPatchKeys.SIZE], expected_shape[1:], type_test=False)
-        #     assert_allclose(meta[WSIPatchKeys.LOCATION], (0, 0), type_test=False)
+        @parameterized.expand([TEST_CASE_WHOLE_0])
+        def test_read_whole_image(self, file_path, level, expected_shape):
+            reader = WSIReader(self.backend, level=level)
+            with reader.read(file_path) as img_obj:
+                img, meta = reader.get_data(img_obj)
+            self.assertTupleEqual(img.shape, expected_shape)
+            self.assertEqual(meta["backend"], self.backend)
+            self.assertEqual(meta[WSIPatchKeys.PATH].lower(), str(os.path.abspath(file_path)).lower())
+            self.assertEqual(meta[WSIPatchKeys.LEVEL], level)
+            assert_allclose(meta[WSIPatchKeys.SIZE], expected_shape[1:], type_test=False)
+            assert_allclose(meta[WSIPatchKeys.LOCATION], (0, 0), type_test=False)
 
         @parameterized.expand(
             [