From 6ac65455222137d28d53c699e241227d8423b5bc Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Wed, 20 Apr 2022 17:41:08 +0000
Subject: [PATCH 01/16] Implement PatchWSIDataset

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 monai/data/__init__.py     |   1 +
 monai/data/wsi_datasets.py | 116 +++++++++++++++++++++++++++++++++++++
 2 files changed, 117 insertions(+)
 create mode 100644 monai/data/wsi_datasets.py

diff --git a/monai/data/__init__.py b/monai/data/__init__.py
index ca4be87ef6..8dea59ba4f 100644
--- a/monai/data/__init__.py
+++ b/monai/data/__init__.py
@@ -88,3 +88,4 @@
     zoom_affine,
 )
 from .wsi_reader import BaseWSIReader, CuCIMWSIReader, WSIReader
+from .wsi_datasets import PatchWSIDataset
diff --git a/monai/data/wsi_datasets.py b/monai/data/wsi_datasets.py
new file mode 100644
index 0000000000..1a03cc4ca8
--- /dev/null
+++ b/monai/data/wsi_datasets.py
@@ -0,0 +1,116 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from typing import Callable, Dict, List, Optional, Tuple, Union
+
+import numpy as np
+
+from monai.data import Dataset
+from monai.data.wsi_reader import WSIReader
+from monai.utils import ensure_tuple_rep
+
+__all__ = ["PatchWSIDataset"]
+
+
+class PatchWSIDataset(Dataset):
+    """
+    This dataset extracts patches from whole slide images (without loading the whole image)
+    It also reads labels for each patch and provides each patch with its associated class labels.
+
+    Args:
+        data: the list of input samples including image, location, and label (see the note below for more details).
+        size: the size of patch to be extracted from the whole slide image.
+        level: the level at which the patches to be extracted (default to 0).
+        transform: transforms to be executed on input data.
+        reader_name: the name of library to be used for loading whole slide imaging, as the backend of `monai.data.WSIReader`
+            Defaults to CuCIM.
+
+    Note:
+        The input data has the following form as an example:
+
+        .. code-block:: python
+
+            [
+                {"image": "path/to/image1.tiff", "location": [200, 500], "label": 0},
+                {"image": "path/to/image2.tiff", "location": [100, 700], "label": 1}
+            ]
+
+    """
+
+    def __init__(
+        self,
+        data: List,
+        size: Optional[Union[int, Tuple[int, int]]] = None,
+        level: Optional[int] = None,
+        transform: Optional[Callable] = None,
+        reader_name: str = "cuCIM",
+    ):
+        super().__init__(data, transform)
+
+        # Ensure patch size is a two dimensional tuple
+        if size is None:
+            self.size = None
+        else:
+            self.size = ensure_tuple_rep(size, 2)
+
+        # Create a default level
+        self.level = level
+
+        # Setup the WSI reader backend
+        self.reader_name = reader_name.lower()
+        self.image_reader = WSIReader(backend=self.reader_name)
+
+        # Initialized an empty whole slide image object dict
+        self.wsi_object_dict: Dict = {}
+
+    def _get_wsi_object(self, sample):
+        image_path = sample["image"]
+        if image_path not in self.wsi_object_dict:
+            self.wsi_object_dict[image_path] = self.image_reader.read(image_path)
+        return self.wsi_object_dict[image_path]
+
+    def _empty_wsi_object_dict(self):
+        self.wsi_object_dict = {}
+
+    def _get_label(self, sample):
+        return np.array(sample["label"], dtype=np.float32)
+
+    def _get_location(self, sample):
+        size = self._get_size(sample)
+        return [sample["location"][i] - size[i] // 2 for i in range(len(size))]
+
+    def _get_level(self, sample):
+        if self.level is None:
+            return sample.get("level")
+        return self.level
+
+    def _get_size(self, sample):
+        if self.size is None:
+            return ensure_tuple_rep(sample.get("size"), 2)
+        return self.size
+
+    def _get_data(self, sample):
+        if self.reader_name == "openslide":
+            self._empty_wsi_object_dict()
+        wsi_obj = self._get_wsi_object(sample)
+        location = self._get_location(sample)
+        level = self._get_level(sample)
+        size = self._get_size(sample)
+        return self.image_reader.get_data(wsi=wsi_obj, location=location, size=size, level=level)
+
+    def __getitem__(self, index):
+        sample = self.data[index]
+        image, metadata = self._get_data(sample)
+        label = self._get_label(sample)
+        patch = {"image": image, "label": label, "metadata": metadata}
+        if self.transform:
+            patch = self.transform(patch)
+        return patch

From d227b551153719e394c3d8802dc027053e634886 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Wed, 20 Apr 2022 17:41:29 +0000
Subject: [PATCH 02/16] Add unittests

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 tests/test_patch_wsi_dataset_new.py | 130 ++++++++++++++++++++++++++++
 1 file changed, 130 insertions(+)
 create mode 100644 tests/test_patch_wsi_dataset_new.py

diff --git a/tests/test_patch_wsi_dataset_new.py b/tests/test_patch_wsi_dataset_new.py
new file mode 100644
index 0000000000..4f5f4be1f7
--- /dev/null
+++ b/tests/test_patch_wsi_dataset_new.py
@@ -0,0 +1,130 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os
+import unittest
+from unittest import skipUnless
+
+import numpy as np
+from numpy.testing import assert_array_equal
+from parameterized import parameterized
+
+from monai.data import PatchWSIDataset
+from monai.utils import optional_import
+from tests.utils import download_url_or_skip_test, testing_data_config
+
+cucim, has_cucim = optional_import("cucim")
+has_cucim = has_cucim and hasattr(cucim, "CuImage")
+openslide, has_osl = optional_import("openslide")
+imwrite, has_tiff = optional_import("tifffile", name="imwrite")
+_, has_codec = optional_import("imagecodecs")
+has_tiff = has_tiff and has_codec
+
+FILE_KEY = "wsi_img"
+FILE_URL = testing_data_config("images", FILE_KEY, "url")
+base_name, extension = os.path.basename(f"{FILE_URL}"), ".tiff"
+FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + base_name + extension)
+
+TEST_CASE_0 = [
+    {
+        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}],
+        "size": (1, 1),
+        "reader_name": "cuCIM",
+    },
+    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
+]
+
+TEST_CASE_0_L1 = [
+    {
+        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}],
+        "size": (1, 1),
+        "level": 1,
+        "reader_name": "cuCIM",
+    },
+    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
+]
+
+TEST_CASE_0_L2 = [
+    {
+        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}],
+        "size": (1, 1),
+        "level": 1,
+        "reader_name": "cuCIM",
+    },
+    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
+]
+
+
+TEST_CASE_1 = [
+    {
+        "data": [{"image": FILE_PATH, "location": [0, 0], "size": 1, "label": [1]}],
+    },
+    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
+]
+
+TEST_CASE_2 = [
+    {
+        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}],
+        "size": 1,
+        "reader_name": "cuCIM",
+    },
+    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
+]
+
+TEST_CASE_3 = [
+    {
+        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}],
+        "size": 1,
+        "reader_name": "cuCIM",
+    },
+    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
+]
+
+
+@skipUnless(has_cucim or has_osl or has_tiff, "Requires cucim, openslide, or tifffile!")
+def setUpModule():  # noqa: N802
+    hash_type = testing_data_config("images", FILE_KEY, "hash_type")
+    hash_val = testing_data_config("images", FILE_KEY, "hash_val")
+    download_url_or_skip_test(FILE_URL, FILE_PATH, hash_type=hash_type, hash_val=hash_val)
+
+
+class PatchWSIDatasetTests:
+    class Tests(unittest.TestCase):
+        backend = None
+
+        @parameterized.expand(
+            [
+                TEST_CASE_0,
+                TEST_CASE_0_L1,
+                TEST_CASE_0_L2,
+                TEST_CASE_1,
+                TEST_CASE_2,
+                TEST_CASE_3,
+            ]
+        )
+        def test_read_patches_cucim(self, input_parameters, expected):
+            dataset = PatchWSIDataset(**input_parameters)
+            sample = dataset[0]
+            self.assertTupleEqual(sample["label"].shape, expected["label"].shape)
+            self.assertTupleEqual(sample["image"].shape, expected["image"].shape)
+            self.assertIsNone(assert_array_equal(sample["label"], expected["label"]))
+            self.assertIsNone(assert_array_equal(sample["image"], expected["image"]))
+
+
+@skipUnless(has_cucim, "Requires cucim")
+class TestCuCIM(PatchWSIDatasetTests.Tests):
+    @classmethod
+    def setUpClass(cls):
+        cls.backend = "cucim"
+
+
+if __name__ == "__main__":
+    unittest.main()

From a2d9a111aa33d0e6a0982ed220dbcd7e78917594 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Wed, 20 Apr 2022 17:43:06 +0000
Subject: [PATCH 03/16] Add docs

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 docs/source/data.rst | 46 ++++++++++++++++++++++++++++----------------
 1 file changed, 29 insertions(+), 17 deletions(-)

diff --git a/docs/source/data.rst b/docs/source/data.rst
index c968d72945..4f58e52c1a 100644
--- a/docs/source/data.rst
+++ b/docs/source/data.rst
@@ -152,23 +152,6 @@ PILReader
 .. autoclass:: PILReader
   :members:
 
-Whole slide image reader
-------------------------
-
-BaseWSIReader
-~~~~~~~~~~~~~
-.. autoclass:: BaseWSIReader
-  :members:
-
-WSIReader
-~~~~~~~~~
-.. autoclass:: WSIReader
-  :members:
-
-CuCIMWSIReader
-~~~~~~~~~~~~~~
-.. autoclass:: CuCIMWSIReader
-  :members:
 
 Image writer
 ------------
@@ -295,3 +278,32 @@ MetaTensor
 ----------
 .. autoclass:: monai.data.MetaTensor
    :members:
+
+
+
+Whole slide image reader
+------------------------
+
+BaseWSIReader
+~~~~~~~~~~~~~
+.. autoclass:: monai.data.BaseWSIReader
+  :members:
+
+WSIReader
+~~~~~~~~~
+.. autoclass:: monai.data.WSIReader
+  :members:
+
+CuCIMWSIReader
+~~~~~~~~~~~~~~
+.. autoclass:: monai.data.CuCIMWSIReader
+  :members:
+
+
+Whole slide image datasets
+--------------------------
+
+PatchWSIDataset
+~~~~~~~~~~~~~~~
+.. autoclass:: monai.data.PatchWSIDataset
+  :members:

From f1324d1b024f721e17afba2ab81b0733f97b679a Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Wed, 20 Apr 2022 17:49:36 +0000
Subject: [PATCH 04/16] Reorder imports

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 monai/data/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/monai/data/__init__.py b/monai/data/__init__.py
index 8dea59ba4f..09225b19a0 100644
--- a/monai/data/__init__.py
+++ b/monai/data/__init__.py
@@ -87,5 +87,5 @@
     worker_init_fn,
     zoom_affine,
 )
-from .wsi_reader import BaseWSIReader, CuCIMWSIReader, WSIReader
 from .wsi_datasets import PatchWSIDataset
+from .wsi_reader import BaseWSIReader, CuCIMWSIReader, WSIReader

From 39a679a788c7eb69553a697f265f3c61cd8208a7 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Wed, 20 Apr 2022 18:07:40 +0000
Subject: [PATCH 05/16] formatting:

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 tests/test_patch_wsi_dataset_new.py | 27 ++++-----------------------
 1 file changed, 4 insertions(+), 23 deletions(-)

diff --git a/tests/test_patch_wsi_dataset_new.py b/tests/test_patch_wsi_dataset_new.py
index 4f5f4be1f7..a388aa589e 100644
--- a/tests/test_patch_wsi_dataset_new.py
+++ b/tests/test_patch_wsi_dataset_new.py
@@ -34,11 +34,7 @@
 FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + base_name + extension)
 
 TEST_CASE_0 = [
-    {
-        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}],
-        "size": (1, 1),
-        "reader_name": "cuCIM",
-    },
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": (1, 1), "reader_name": "cuCIM"},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
@@ -64,18 +60,12 @@
 
 
 TEST_CASE_1 = [
-    {
-        "data": [{"image": FILE_PATH, "location": [0, 0], "size": 1, "label": [1]}],
-    },
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "size": 1, "label": [1]}]},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
 TEST_CASE_2 = [
-    {
-        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}],
-        "size": 1,
-        "reader_name": "cuCIM",
-    },
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": 1, "reader_name": "cuCIM"},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
@@ -100,16 +90,7 @@ class PatchWSIDatasetTests:
     class Tests(unittest.TestCase):
         backend = None
 
-        @parameterized.expand(
-            [
-                TEST_CASE_0,
-                TEST_CASE_0_L1,
-                TEST_CASE_0_L2,
-                TEST_CASE_1,
-                TEST_CASE_2,
-                TEST_CASE_3,
-            ]
-        )
+        @parameterized.expand([TEST_CASE_0, TEST_CASE_0_L1, TEST_CASE_0_L2, TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
         def test_read_patches_cucim(self, input_parameters, expected):
             dataset = PatchWSIDataset(**input_parameters)
             sample = dataset[0]

From 688ff044bd7987528d575e081335e7b5d1275c77 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Thu, 21 Apr 2022 21:45:42 +0000
Subject: [PATCH 06/16] Address comments

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 monai/data/wsi_datasets.py | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/monai/data/wsi_datasets.py b/monai/data/wsi_datasets.py
index 1a03cc4ca8..1da4f378b0 100644
--- a/monai/data/wsi_datasets.py
+++ b/monai/data/wsi_datasets.py
@@ -71,43 +71,40 @@ def __init__(
         # Initialized an empty whole slide image object dict
         self.wsi_object_dict: Dict = {}
 
-    def _get_wsi_object(self, sample):
+    def _get_wsi_object(self, sample: Dict):
         image_path = sample["image"]
         if image_path not in self.wsi_object_dict:
             self.wsi_object_dict[image_path] = self.image_reader.read(image_path)
         return self.wsi_object_dict[image_path]
 
-    def _empty_wsi_object_dict(self):
-        self.wsi_object_dict = {}
-
-    def _get_label(self, sample):
+    def _get_label(self, sample: Dict):
         return np.array(sample["label"], dtype=np.float32)
 
-    def _get_location(self, sample):
+    def _get_location(self, sample: Dict):
         size = self._get_size(sample)
         return [sample["location"][i] - size[i] // 2 for i in range(len(size))]
 
-    def _get_level(self, sample):
+    def _get_level(self, sample: Dict):
         if self.level is None:
             return sample.get("level")
         return self.level
 
-    def _get_size(self, sample):
+    def _get_size(self, sample: Dict):
         if self.size is None:
             return ensure_tuple_rep(sample.get("size"), 2)
         return self.size
 
-    def _get_data(self, sample):
+    def _get_data(self, sample: Dict):
         if self.reader_name == "openslide":
-            self._empty_wsi_object_dict()
+            self.wsi_object_dict = {}
         wsi_obj = self._get_wsi_object(sample)
         location = self._get_location(sample)
         level = self._get_level(sample)
         size = self._get_size(sample)
         return self.image_reader.get_data(wsi=wsi_obj, location=location, size=size, level=level)
 
-    def __getitem__(self, index):
-        sample = self.data[index]
+    def __getitem__(self, index: int):
+        sample: Dict = self.data[index]
         image, metadata = self._get_data(sample)
         label = self._get_label(sample)
         patch = {"image": image, "label": label, "metadata": metadata}

From 4092159e83a104dd958bc894dc74d3eeb9292362 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 02:59:10 +0000
Subject: [PATCH 07/16] Update to be compatible with Dataset

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 monai/data/wsi_datasets.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/monai/data/wsi_datasets.py b/monai/data/wsi_datasets.py
index 1da4f378b0..ef9dd9b9d0 100644
--- a/monai/data/wsi_datasets.py
+++ b/monai/data/wsi_datasets.py
@@ -15,6 +15,7 @@
 
 from monai.data import Dataset
 from monai.data.wsi_reader import WSIReader
+from monai.transforms import apply_transform
 from monai.utils import ensure_tuple_rep
 
 __all__ = ["PatchWSIDataset"]
@@ -103,11 +104,14 @@ def _get_data(self, sample: Dict):
         size = self._get_size(sample)
         return self.image_reader.get_data(wsi=wsi_obj, location=location, size=size, level=level)
 
-    def __getitem__(self, index: int):
+    def _transform(self, index: int):
+        # Get a single entry of data
         sample: Dict = self.data[index]
+        # Extract patch image and associated metadata
         image, metadata = self._get_data(sample)
+        # Get the label
         label = self._get_label(sample)
+
+        # Create put all patch information together and apply transforms
         patch = {"image": image, "label": label, "metadata": metadata}
-        if self.transform:
-            patch = self.transform(patch)
-        return patch
+        return apply_transform(self.transform, patch) if self.transform else patch

From d9d7b82f10b6d24c865cd5f617eaef0ded254fa3 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 03:56:58 +0000
Subject: [PATCH 08/16] Update reader to accept str, class, object

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 monai/data/wsi_datasets.py | 40 ++++++++++++++++++++++++++------------
 1 file changed, 28 insertions(+), 12 deletions(-)

diff --git a/monai/data/wsi_datasets.py b/monai/data/wsi_datasets.py
index ef9dd9b9d0..1d90f4d8d5 100644
--- a/monai/data/wsi_datasets.py
+++ b/monai/data/wsi_datasets.py
@@ -9,12 +9,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import inspect
 from typing import Callable, Dict, List, Optional, Tuple, Union
 
 import numpy as np
 
 from monai.data import Dataset
-from monai.data.wsi_reader import WSIReader
+from monai.data.wsi_reader import BaseWSIReader, WSIReader
 from monai.transforms import apply_transform
 from monai.utils import ensure_tuple_rep
 
@@ -31,8 +32,10 @@ class PatchWSIDataset(Dataset):
         size: the size of patch to be extracted from the whole slide image.
         level: the level at which the patches to be extracted (default to 0).
         transform: transforms to be executed on input data.
-        reader_name: the name of library to be used for loading whole slide imaging, as the backend of `monai.data.WSIReader`
-            Defaults to CuCIM.
+        reader: the module to be used for loading whole slide imaging,
+            - if `reader` is a string, it defines the backend of `monai.data.WSIReader`. Defaults to cuCIM.
+            - if `reader` is a class (inherited from `BaseWSIReader`), it is initialized and set as wsi_reader.
+            - if `reader` is an instance of a a class inherited from `BaseWSIReader`, it is set as the wsi_reader.
 
     Note:
         The input data has the following form as an example:
@@ -52,7 +55,8 @@ def __init__(
         size: Optional[Union[int, Tuple[int, int]]] = None,
         level: Optional[int] = None,
         transform: Optional[Callable] = None,
-        reader_name: str = "cuCIM",
+        reader="cuCIM",
+        **kwargs,
     ):
         super().__init__(data, transform)
 
@@ -62,12 +66,23 @@ def __init__(
         else:
             self.size = ensure_tuple_rep(size, 2)
 
-        # Create a default level
+        # Create a default level that override all levels if it is not None
         self.level = level
-
-        # Setup the WSI reader backend
-        self.reader_name = reader_name.lower()
-        self.image_reader = WSIReader(backend=self.reader_name)
+        # Set the default WSIReader's level to 0 if level is not provided
+        if level is None:
+            level = 0
+
+        # Setup the WSI reader
+        self.wsi_reader: Union[WSIReader, BaseWSIReader]
+        if isinstance(reader, str):
+            self.reader_name = reader.lower()
+            self.wsi_reader = WSIReader(backend=self.reader_name, level=level, **kwargs)
+        elif inspect.isclass(reader) and issubclass(reader, BaseWSIReader):
+            self.wsi_reader = reader(level=level, **kwargs)
+        elif isinstance(reader, BaseWSIReader):
+            self.wsi_reader = reader
+        else:
+            raise ValueError(f"unsupported reader type: {reader}.")
 
         # Initialized an empty whole slide image object dict
         self.wsi_object_dict: Dict = {}
@@ -75,7 +90,7 @@ def __init__(
     def _get_wsi_object(self, sample: Dict):
         image_path = sample["image"]
         if image_path not in self.wsi_object_dict:
-            self.wsi_object_dict[image_path] = self.image_reader.read(image_path)
+            self.wsi_object_dict[image_path] = self.wsi_reader.read(image_path)
         return self.wsi_object_dict[image_path]
 
     def _get_label(self, sample: Dict):
@@ -87,7 +102,7 @@ def _get_location(self, sample: Dict):
 
     def _get_level(self, sample: Dict):
         if self.level is None:
-            return sample.get("level")
+            return sample.get("level", 0)
         return self.level
 
     def _get_size(self, sample: Dict):
@@ -97,12 +112,13 @@ def _get_size(self, sample: Dict):
 
     def _get_data(self, sample: Dict):
         if self.reader_name == "openslide":
+            # to avoid OpenSlide internal cache
             self.wsi_object_dict = {}
         wsi_obj = self._get_wsi_object(sample)
         location = self._get_location(sample)
         level = self._get_level(sample)
         size = self._get_size(sample)
-        return self.image_reader.get_data(wsi=wsi_obj, location=location, size=size, level=level)
+        return self.wsi_reader.get_data(wsi=wsi_obj, location=location, size=size, level=level)
 
     def _transform(self, index: int):
         # Get a single entry of data

From 31d722ca13ddb8782dcd2cbd373d4a79c0e285d0 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 03:57:24 +0000
Subject: [PATCH 09/16] Add test cases for various reader and level arguments

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 tests/test_patch_wsi_dataset_new.py | 48 +++++++++++++++++++----------
 1 file changed, 32 insertions(+), 16 deletions(-)

diff --git a/tests/test_patch_wsi_dataset_new.py b/tests/test_patch_wsi_dataset_new.py
index a388aa589e..1f8adb9f5b 100644
--- a/tests/test_patch_wsi_dataset_new.py
+++ b/tests/test_patch_wsi_dataset_new.py
@@ -18,6 +18,7 @@
 from parameterized import parameterized
 
 from monai.data import PatchWSIDataset
+from monai.data.wsi_reader import CuCIMWSIReader
 from monai.utils import optional_import
 from tests.utils import download_url_or_skip_test, testing_data_config
 
@@ -34,27 +35,17 @@
 FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + base_name + extension)
 
 TEST_CASE_0 = [
-    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": (1, 1), "reader_name": "cuCIM"},
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1], "level": 0}], "size": (1, 1), "reader": "cuCIM"},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
 TEST_CASE_0_L1 = [
-    {
-        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}],
-        "size": (1, 1),
-        "level": 1,
-        "reader_name": "cuCIM",
-    },
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": (1, 1), "level": 1, "reader": "cuCIM"},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
 TEST_CASE_0_L2 = [
-    {
-        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}],
-        "size": (1, 1),
-        "level": 1,
-        "reader_name": "cuCIM",
-    },
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": (1, 1), "level": 1, "reader": "cuCIM"},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
@@ -65,15 +56,29 @@
 ]
 
 TEST_CASE_2 = [
-    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": 1, "reader_name": "cuCIM"},
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": 1, "level": 0, "reader": "cuCIM"},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
 TEST_CASE_3 = [
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}], "size": 1, "reader": "cuCIM"},
+    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
+]
+
+TEST_CASE_4 = [
+    {
+        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}],
+        "size": 1,
+        "reader": CuCIMWSIReader,
+    },
+    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
+]
+
+TEST_CASE_5 = [
     {
         "data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}],
         "size": 1,
-        "reader_name": "cuCIM",
+        "reader": CuCIMWSIReader(level=0),
     },
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
 ]
@@ -90,7 +95,18 @@ class PatchWSIDatasetTests:
     class Tests(unittest.TestCase):
         backend = None
 
-        @parameterized.expand([TEST_CASE_0, TEST_CASE_0_L1, TEST_CASE_0_L2, TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
+        @parameterized.expand(
+            [
+                TEST_CASE_0,
+                TEST_CASE_0_L1,
+                TEST_CASE_0_L2,
+                TEST_CASE_1,
+                TEST_CASE_2,
+                TEST_CASE_3,
+                TEST_CASE_4,
+                TEST_CASE_5,
+            ]
+        )
         def test_read_patches_cucim(self, input_parameters, expected):
             dataset = PatchWSIDataset(**input_parameters)
             sample = dataset[0]

From 15a9b28564f06221848903885c2bba14f07281ec Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 03:59:21 +0000
Subject: [PATCH 10/16] Update comment about OpenSlide cache

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 monai/data/wsi_datasets.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/monai/data/wsi_datasets.py b/monai/data/wsi_datasets.py
index 1d90f4d8d5..68672a1c3b 100644
--- a/monai/data/wsi_datasets.py
+++ b/monai/data/wsi_datasets.py
@@ -111,8 +111,8 @@ def _get_size(self, sample: Dict):
         return self.size
 
     def _get_data(self, sample: Dict):
+        # Don't store OpenSlide objects to avoid issues with OpenSlide internal cache
         if self.reader_name == "openslide":
-            # to avoid OpenSlide internal cache
             self.wsi_object_dict = {}
         wsi_obj = self._get_wsi_object(sample)
         location = self._get_location(sample)

From 48dc0a3866a6f9e6ea59c94b52d6a4d18ecd09ee Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 04:05:53 +0000
Subject: [PATCH 11/16] Rename reader_name to backend

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 monai/data/wsi_datasets.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/monai/data/wsi_datasets.py b/monai/data/wsi_datasets.py
index 68672a1c3b..e723286b24 100644
--- a/monai/data/wsi_datasets.py
+++ b/monai/data/wsi_datasets.py
@@ -74,15 +74,16 @@ def __init__(
 
         # Setup the WSI reader
         self.wsi_reader: Union[WSIReader, BaseWSIReader]
+        self.backend = ""
         if isinstance(reader, str):
-            self.reader_name = reader.lower()
-            self.wsi_reader = WSIReader(backend=self.reader_name, level=level, **kwargs)
+            self.backend = reader.lower()
+            self.wsi_reader = WSIReader(backend=self.backend, level=level, **kwargs)
         elif inspect.isclass(reader) and issubclass(reader, BaseWSIReader):
             self.wsi_reader = reader(level=level, **kwargs)
         elif isinstance(reader, BaseWSIReader):
             self.wsi_reader = reader
         else:
-            raise ValueError(f"unsupported reader type: {reader}.")
+            raise ValueError(f"Unsupported reader type: {reader}.")
 
         # Initialized an empty whole slide image object dict
         self.wsi_object_dict: Dict = {}
@@ -112,7 +113,7 @@ def _get_size(self, sample: Dict):
 
     def _get_data(self, sample: Dict):
         # Don't store OpenSlide objects to avoid issues with OpenSlide internal cache
-        if self.reader_name == "openslide":
+        if self.backend == "openslide":
             self.wsi_object_dict = {}
         wsi_obj = self._get_wsi_object(sample)
         location = self._get_location(sample)

From ab3472c1bc7642f6bd9a5183277bf68478226578 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 12:31:38 +0000
Subject: [PATCH 12/16] Add new test cases

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 tests/test_patch_wsi_dataset_new.py | 86 +++++++++++++++++++----------
 1 file changed, 56 insertions(+), 30 deletions(-)

diff --git a/tests/test_patch_wsi_dataset_new.py b/tests/test_patch_wsi_dataset_new.py
index 1f8adb9f5b..d994c9f93e 100644
--- a/tests/test_patch_wsi_dataset_new.py
+++ b/tests/test_patch_wsi_dataset_new.py
@@ -18,7 +18,7 @@
 from parameterized import parameterized
 
 from monai.data import PatchWSIDataset
-from monai.data.wsi_reader import CuCIMWSIReader
+from monai.data.wsi_reader import CuCIMWSIReader, OpenSlideWSIReader
 from monai.utils import optional_import
 from tests.utils import download_url_or_skip_test, testing_data_config
 
@@ -35,51 +35,31 @@
 FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + base_name + extension)
 
 TEST_CASE_0 = [
-    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1], "level": 0}], "size": (1, 1), "reader": "cuCIM"},
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1], "level": 0}], "size": (1, 1)},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
 TEST_CASE_0_L1 = [
-    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": (1, 1), "level": 1, "reader": "cuCIM"},
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": (1, 1), "level": 1},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
 TEST_CASE_0_L2 = [
-    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": (1, 1), "level": 1, "reader": "cuCIM"},
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": (1, 1), "level": 1},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
-
-
 TEST_CASE_1 = [
     {"data": [{"image": FILE_PATH, "location": [0, 0], "size": 1, "label": [1]}]},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
 TEST_CASE_2 = [
-    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": 1, "level": 0, "reader": "cuCIM"},
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [1]}], "size": 1, "level": 0},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([1])},
 ]
 
 TEST_CASE_3 = [
-    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}], "size": 1, "reader": "cuCIM"},
-    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
-]
-
-TEST_CASE_4 = [
-    {
-        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}],
-        "size": 1,
-        "reader": CuCIMWSIReader,
-    },
-    {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
-]
-
-TEST_CASE_5 = [
-    {
-        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}],
-        "size": 1,
-        "reader": CuCIMWSIReader(level=0),
-    },
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}], "size": 1},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
 ]
 
@@ -103,12 +83,58 @@ class Tests(unittest.TestCase):
                 TEST_CASE_1,
                 TEST_CASE_2,
                 TEST_CASE_3,
-                TEST_CASE_4,
-                TEST_CASE_5,
             ]
         )
-        def test_read_patches_cucim(self, input_parameters, expected):
-            dataset = PatchWSIDataset(**input_parameters)
+        def test_read_patches_str(self, input_parameters, expected):
+            dataset = PatchWSIDataset(reader=self.backend, **input_parameters)
+            sample = dataset[0]
+            self.assertTupleEqual(sample["label"].shape, expected["label"].shape)
+            self.assertTupleEqual(sample["image"].shape, expected["image"].shape)
+            self.assertIsNone(assert_array_equal(sample["label"], expected["label"]))
+            self.assertIsNone(assert_array_equal(sample["image"], expected["image"]))
+
+        @parameterized.expand(
+            [
+                TEST_CASE_0,
+                TEST_CASE_0_L1,
+                TEST_CASE_0_L2,
+                TEST_CASE_1,
+                TEST_CASE_2,
+                TEST_CASE_3,
+            ]
+        )
+        def test_read_patches_class(self, input_parameters, expected):
+            if self.backend == "openslide":
+                reader = OpenSlideWSIReader
+            elif self.backend == "cucim":
+                reader = CuCIMWSIReader
+            else:
+                raise ValueError("Unsupported backend: {self.backend}")
+            dataset = PatchWSIDataset(reader=reader, **input_parameters)
+            sample = dataset[0]
+            self.assertTupleEqual(sample["label"].shape, expected["label"].shape)
+            self.assertTupleEqual(sample["image"].shape, expected["image"].shape)
+            self.assertIsNone(assert_array_equal(sample["label"], expected["label"]))
+            self.assertIsNone(assert_array_equal(sample["image"], expected["image"]))
+
+        @parameterized.expand(
+            [
+                TEST_CASE_0,
+                TEST_CASE_0_L1,
+                TEST_CASE_0_L2,
+                TEST_CASE_1,
+                TEST_CASE_2,
+                TEST_CASE_3,
+            ]
+        )
+        def test_read_patches_object(self, input_parameters, expected):
+            if self.backend == "openslide":
+                reader = OpenSlideWSIReader(level=input_parameters.get("level", 0))
+            elif self.backend == "cucim":
+                reader = CuCIMWSIReader(level=input_parameters.get("level", 0))
+            else:
+                raise ValueError("Unsupported backend: {self.backend}")
+            dataset = PatchWSIDataset(reader=reader, **input_parameters)
             sample = dataset[0]
             self.assertTupleEqual(sample["label"].shape, expected["label"].shape)
             self.assertTupleEqual(sample["image"].shape, expected["image"].shape)

From 10ee84f83ebe1e562c0c765e600d27c0a95bc340 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 12:35:32 +0000
Subject: [PATCH 13/16] Add unittests for openslide

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 tests/test_patch_wsi_dataset_new.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tests/test_patch_wsi_dataset_new.py b/tests/test_patch_wsi_dataset_new.py
index d994c9f93e..5107a24b18 100644
--- a/tests/test_patch_wsi_dataset_new.py
+++ b/tests/test_patch_wsi_dataset_new.py
@@ -143,11 +143,18 @@ def test_read_patches_object(self, input_parameters, expected):
 
 
 @skipUnless(has_cucim, "Requires cucim")
-class TestCuCIM(PatchWSIDatasetTests.Tests):
+class TestPatchWSIDatasetCuCIM(PatchWSIDatasetTests.Tests):
     @classmethod
     def setUpClass(cls):
         cls.backend = "cucim"
 
 
+@skipUnless(has_osl, "Requires cucim")
+class TestPatchWSIDatasetOpenSlide(PatchWSIDatasetTests.Tests):
+    @classmethod
+    def setUpClass(cls):
+        cls.backend = "openslide"
+
+
 if __name__ == "__main__":
     unittest.main()

From bab87beae061137fb689cfcc34234d1cbb07d3e2 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 13:04:36 +0000
Subject: [PATCH 14/16] Add new test cases

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 tests/test_patch_wsi_dataset_new.py | 74 +++++++++++++++++------------
 1 file changed, 43 insertions(+), 31 deletions(-)

diff --git a/tests/test_patch_wsi_dataset_new.py b/tests/test_patch_wsi_dataset_new.py
index 5107a24b18..81ad0ba1e9 100644
--- a/tests/test_patch_wsi_dataset_new.py
+++ b/tests/test_patch_wsi_dataset_new.py
@@ -59,10 +59,40 @@
 ]
 
 TEST_CASE_3 = [
-    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}], "size": 1},
+    {
+        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}],
+        "size": 1,
+    },
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
 ]
 
+TEST_CASE_4 = [
+    {
+        "data": [
+            {"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]},
+            {"image": FILE_PATH, "location": [0, 0], "label": [[[1, 0], [0, 0]]]},
+        ],
+        "size": 1,
+    },
+    [
+        {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
+        {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[1, 0], [0, 0]]])},
+    ],
+]
+
+TEST_CASE_5 = [
+    {
+        "data": [
+            {"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]], "size": 1, "level": 1},
+            {"image": FILE_PATH, "location": [100, 100], "label": [[[1, 0], [0, 0]]], "size": 1, "level": 1},
+        ],
+    },
+    [
+        {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
+        {"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8), "label": np.array([[[1, 0], [0, 0]]])},
+    ],
+]
+
 
 @skipUnless(has_cucim or has_osl or has_tiff, "Requires cucim, openslide, or tifffile!")
 def setUpModule():  # noqa: N802
@@ -75,16 +105,7 @@ class PatchWSIDatasetTests:
     class Tests(unittest.TestCase):
         backend = None
 
-        @parameterized.expand(
-            [
-                TEST_CASE_0,
-                TEST_CASE_0_L1,
-                TEST_CASE_0_L2,
-                TEST_CASE_1,
-                TEST_CASE_2,
-                TEST_CASE_3,
-            ]
-        )
+        @parameterized.expand([TEST_CASE_0, TEST_CASE_0_L1, TEST_CASE_0_L2, TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
         def test_read_patches_str(self, input_parameters, expected):
             dataset = PatchWSIDataset(reader=self.backend, **input_parameters)
             sample = dataset[0]
@@ -93,16 +114,7 @@ def test_read_patches_str(self, input_parameters, expected):
             self.assertIsNone(assert_array_equal(sample["label"], expected["label"]))
             self.assertIsNone(assert_array_equal(sample["image"], expected["image"]))
 
-        @parameterized.expand(
-            [
-                TEST_CASE_0,
-                TEST_CASE_0_L1,
-                TEST_CASE_0_L2,
-                TEST_CASE_1,
-                TEST_CASE_2,
-                TEST_CASE_3,
-            ]
-        )
+        @parameterized.expand([TEST_CASE_0, TEST_CASE_0_L1, TEST_CASE_0_L2, TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
         def test_read_patches_class(self, input_parameters, expected):
             if self.backend == "openslide":
                 reader = OpenSlideWSIReader
@@ -117,16 +129,7 @@ def test_read_patches_class(self, input_parameters, expected):
             self.assertIsNone(assert_array_equal(sample["label"], expected["label"]))
             self.assertIsNone(assert_array_equal(sample["image"], expected["image"]))
 
-        @parameterized.expand(
-            [
-                TEST_CASE_0,
-                TEST_CASE_0_L1,
-                TEST_CASE_0_L2,
-                TEST_CASE_1,
-                TEST_CASE_2,
-                TEST_CASE_3,
-            ]
-        )
+        @parameterized.expand([TEST_CASE_0, TEST_CASE_0_L1, TEST_CASE_0_L2, TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
         def test_read_patches_object(self, input_parameters, expected):
             if self.backend == "openslide":
                 reader = OpenSlideWSIReader(level=input_parameters.get("level", 0))
@@ -141,6 +144,15 @@ def test_read_patches_object(self, input_parameters, expected):
             self.assertIsNone(assert_array_equal(sample["label"], expected["label"]))
             self.assertIsNone(assert_array_equal(sample["image"], expected["image"]))
 
+        @parameterized.expand([TEST_CASE_4, TEST_CASE_5])
+        def test_read_patches_str_multi(self, input_parameters, expected):
+            dataset = PatchWSIDataset(reader=self.backend, **input_parameters)
+            for i in range(len(dataset)):
+                self.assertTupleEqual(dataset[i]["label"].shape, expected[i]["label"].shape)
+                self.assertTupleEqual(dataset[i]["image"].shape, expected[i]["image"].shape)
+                self.assertIsNone(assert_array_equal(dataset[i]["label"], expected[i]["label"]))
+                self.assertIsNone(assert_array_equal(dataset[i]["image"], expected[i]["image"]))
+
 
 @skipUnless(has_cucim, "Requires cucim")
 class TestPatchWSIDatasetCuCIM(PatchWSIDatasetTests.Tests):

From c725103c22475f7341249ed3e1af4ce300674e95 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 13:17:35 +0000
Subject: [PATCH 15/16] sorts

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 tests/test_patch_wsi_dataset_new.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/tests/test_patch_wsi_dataset_new.py b/tests/test_patch_wsi_dataset_new.py
index 81ad0ba1e9..0be30536de 100644
--- a/tests/test_patch_wsi_dataset_new.py
+++ b/tests/test_patch_wsi_dataset_new.py
@@ -59,10 +59,7 @@
 ]
 
 TEST_CASE_3 = [
-    {
-        "data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}],
-        "size": 1,
-    },
+    {"data": [{"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]]}], "size": 1},
     {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
 ]
 
@@ -85,7 +82,7 @@
         "data": [
             {"image": FILE_PATH, "location": [0, 0], "label": [[[0, 1], [1, 0]]], "size": 1, "level": 1},
             {"image": FILE_PATH, "location": [100, 100], "label": [[[1, 0], [0, 0]]], "size": 1, "level": 1},
-        ],
+        ]
     },
     [
         {"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},

From 4838ec1c17c6e6c496f494abdb5e3fe0759a2f06 Mon Sep 17 00:00:00 2001
From: Behrooz <3968947+drbeh@users.noreply.github.com>
Date: Fri, 22 Apr 2022 13:48:22 +0000
Subject: [PATCH 16/16] Add docstring for kwargs

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
---
 monai/data/wsi_datasets.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/monai/data/wsi_datasets.py b/monai/data/wsi_datasets.py
index e723286b24..a895e8aa45 100644
--- a/monai/data/wsi_datasets.py
+++ b/monai/data/wsi_datasets.py
@@ -36,6 +36,7 @@ class PatchWSIDataset(Dataset):
             - if `reader` is a string, it defines the backend of `monai.data.WSIReader`. Defaults to cuCIM.
             - if `reader` is a class (inherited from `BaseWSIReader`), it is initialized and set as wsi_reader.
             - if `reader` is an instance of a a class inherited from `BaseWSIReader`, it is set as the wsi_reader.
+        kwargs: additional arguments to pass to `WSIReader` or provided whole slide reader class
 
     Note:
         The input data has the following form as an example: