Tifffile support in WSIReader

monai/apps/pathology/transforms/spatial/array.py

@@ -28,9 +28,9 @@ class SplitOnGrid(Transform):
             If it's an integer, the value will be repeated for each dimension. Default is 2x2
         patch_size: a tuple or an integer that defines the output patch sizes.
             If it's an integer, the value will be repeated for each dimension.
-            The default is (0, 0), where the patch size will be infered from the grid shape.
+            The default is (0, 0), where the patch size will be inferred from the grid shape.
 
-    Note: the shape of the input image is infered based on the first image used.
+    Note: the shape of the input image is inferred based on the first image used.
     """
 
     def __init__(

monai/data/image_reader.py

@@ -676,10 +676,15 @@ class WSIReader(ImageReader):
     Read whole slide images and extract patches.
 
     Args:
-        backend: backend library to load the images, available options: "OpenSlide" or "cuCIM".
+        backend: backend library to load the images, available options: "cuCIM", "OpenSlide" and "Tifffile".
         level: the whole slide image level at which the image is extracted. (default=0)
-            Note that this is overridden by the level argument in `get_data`.
+            This is overridden if the level argument is provided in `get_data`.
 
+    Note:
+        While "cucim" and "OpenSlide" backends both can load patches from large whole slide images
+        without loading the entire image into memory, "Tifffile" backend needs to load the entire image into memory
+        before extracting any patch; thus, memory consideration is needed when using "Tifffile" backend for
+        patch extraction.
     """
 
     def __init__(self, backend: str = "OpenSlide", level: int = 0):
@@ -689,8 +694,10 @@ def __init__(self, backend: str = "OpenSlide", level: int = 0):
             self.wsi_reader, *_ = optional_import("openslide", name="OpenSlide")
         elif self.backend == "cucim":
             self.wsi_reader, *_ = optional_import("cucim", name="CuImage")
+        elif self.backend == "tifffile":
+            self.wsi_reader, *_ = optional_import("tifffile", name="TiffFile")
         else:
-            raise ValueError('`backend` should be either "cuCIM" or "OpenSlide"')
+            raise ValueError('`backend` should be "cuCIM", "OpenSlide", or "TiffFile')
         self.level = level
 
     def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool:
@@ -780,13 +787,22 @@ def _extract_region(
         level: int = 0,
         dtype: DtypeLike = np.uint8,
     ):
-        # reverse the order of dimensions for size and location to be compatible with image shape
-        location = location[::-1]
-        if size is None:
-            region = img_obj.read_region(location=location, level=level)
+        if self.backend == "tifffile":
+            with img_obj:
+                region = img_obj.asarray(level=level)
+            if size is None:
+                region = region[location[0] :, location[1] :]
+            else:
+                region = region[location[0] : location[0] + size[0], location[1] : location[1] + size[1]]
+
         else:
-            size = size[::-1]
-            region = img_obj.read_region(location=location, size=size, level=level)
+            # reverse the order of dimensions for size and location to be compatible with image shape
+            location = location[::-1]
+            if size is None:
+                region = img_obj.read_region(location=location, level=level)
+            else:
+                size = size[::-1]
+                region = img_obj.read_region(location=location, size=size, level=level)
 
         region = self.convert_to_rgb_array(region, dtype)
         return region
@@ -796,15 +812,12 @@ def convert_to_rgb_array(self, raw_region, dtype: DtypeLike = np.uint8):
         if self.backend == "openslide":
             # convert to RGB
             raw_region = raw_region.convert("RGB")
-            # convert to numpy
-            raw_region = np.asarray(raw_region, dtype=dtype)
-        else:
-            num_channels = len(raw_region.channel_names)
-            # convert to numpy
-            raw_region = np.asarray(raw_region, dtype=dtype)
-            # remove alpha channel if exist (RGBA)
-            if num_channels > 3:
-                raw_region = raw_region[:, :, :3]
+
+        # convert to numpy (if not already in numpy)
+        raw_region = np.asarray(raw_region, dtype=dtype)
+        # remove alpha channel if exist (RGBA)
+        if raw_region.shape[-1] > 3:
+            raw_region = raw_region[..., :3]
 
         return raw_region
 

tests/test_wsireader.py

@@ -112,6 +112,8 @@ def test_read_whole_image(self, file_path, level, expected_shape):
         def test_read_region(self, file_path, patch_info, expected_img):
             reader = WSIReader(self.backend)
             img_obj = reader.read(file_path)
+            # Read twice to check multiple calls
+            img = reader.get_data(img_obj, **patch_info)[0]
             img = reader.get_data(img_obj, **patch_info)[0]
             self.assertTupleEqual(img.shape, expected_img.shape)
             self.assertIsNone(assert_array_equal(img, expected_img))
@@ -171,5 +173,12 @@ def setUpClass(cls):
         cls.backend = "openslide"
 
 
+@skipUnless(has_tiff, "Requires TiffFile")
+class TestTiffFile(WSIReaderTests.Tests):
+    @classmethod
+    def setUpClass(cls):
+        cls.backend = "tifffile"
+
+
 if __name__ == "__main__":
     unittest.main()