Improve WSIReader (#3241)

* Add level argument to __init__ for WSIReader

Signed-off-by: Behrooz <[email protected]>

* Change reader_lib to backend

Signed-off-by: Behrooz <[email protected]>

* Update some comments

Signed-off-by: Behrooz <[email protected]>

* Update docstring

Signed-off-by: Behrooz <[email protected]>

Author: bhashemian

monai/data/image_reader.py

@@ -667,22 +667,25 @@ def _get_spatial_shape(self, img):
 
 class WSIReader(ImageReader):
     """
-    Read whole slide imaging and extract patches.
+    Read whole slide images and extract patches.
 
     Args:
-        reader_lib: backend library to load the images, available options: "OpenSlide" or "cuCIM".
+        backend: backend library to load the images, available options: "OpenSlide" or "cuCIM".
+        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`.
 
     """
 
-    def __init__(self, reader_lib: str = "OpenSlide"):
+    def __init__(self, backend: str = "OpenSlide", level: int = 0):
         super().__init__()
-        self.reader_lib = reader_lib.lower()
-        if self.reader_lib == "openslide":
+        self.backend = backend.lower()
+        if self.backend == "openslide":
             self.wsi_reader, *_ = optional_import("openslide", name="OpenSlide")
-        elif self.reader_lib == "cucim":
+        elif self.backend == "cucim":
             self.wsi_reader, *_ = optional_import("cucim", name="CuImage")
         else:
-            raise ValueError('`reader_lib` should be either "cuCIM" or "OpenSlide"')
+            raise ValueError('`backend` should be either "cuCIM" or "OpenSlide"')
+        self.level = level
 
     def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool:
         """
@@ -696,19 +699,21 @@ def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool:
 
     def read(self, data: Union[Sequence[str], str, np.ndarray], **kwargs):
         """
-        Read image data from specified file or files.
-        Note that the returned object is CuImage or list of CuImage objects.
+        Read image data from given file or list of files.
 
         Args:
             data: file name or a list of file names to read.
 
+        Returns:
+            image object or list of image objects
+
         """
         img_: List = []
 
         filenames: Sequence[str] = ensure_tuple(data)
         for name in filenames:
             img = self.wsi_reader(name)
-            if self.reader_lib == "openslide":
+            if self.backend == "openslide":
                 img.shape = (img.dimensions[1], img.dimensions[0], 3)
             img_.append(img)
 
@@ -719,7 +724,7 @@ def get_data(
         img,
         location: Tuple[int, int] = (0, 0),
         size: Optional[Tuple[int, int]] = None,
-        level: int = 0,
+        level: Optional[int] = None,
         dtype: DtypeLike = np.uint8,
         grid_shape: Tuple[int, int] = (1, 1),
         patch_size: Optional[Union[int, Tuple[int, int]]] = None,
@@ -738,9 +743,11 @@ def get_data(
             grid_shape: (row, columns) tuple define a grid to extract patches on that
             patch_size: (height, width) the size of extracted patches at the given level
         """
+        if level is None:
+            level = self.level
 
-        if self.reader_lib == "openslide" and size is None:
-            # the maximum size is set to WxH
+        if self.backend == "openslide" and size is None:
+            # the maximum size is set to WxH at the specified level
             size = (img.shape[0] // (2 ** level) - location[0], img.shape[1] // (2 ** level) - location[1])
 
         region = self._extract_region(img, location=location, size=size, level=level, dtype=dtype)
@@ -780,7 +787,7 @@ def _extract_region(
 
     def convert_to_rgb_array(self, raw_region, dtype: DtypeLike = np.uint8):
         """Convert to RGB mode and numpy array"""
-        if self.reader_lib == "openslide":
+        if self.backend == "openslide":
             # convert to RGB
             raw_region = raw_region.convert("RGB")
             # convert to numpy