Bug fix and improvement in WSI (#4216)

bhashemian · web-flow · commit 209db9e08129 · 2022-05-06T19:28:08.000Z
* Make all transforms optional

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Update wsireader tests

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Remove optional from PersistentDataset and its derivatives

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Add unittests for cache without transform

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Add default replace_rate

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Add default value

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Set default replace_rate to 0.1

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Update metadata to include path

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Adds SmartCachePatchWSIDataset

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Add unittests for SmartCachePatchWSIDataset

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Update references

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Update docs

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Remove smart cache

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Remove unused imports

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Add path metadata for OpenSlide

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Update metadata to be unified across different backends

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Update wsi metadata for multi wsi objects

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;

* Add unittests for wsi metadata

Signed-off-by: Behrooz &lt;3968947+drbeh@users.noreply.github.com&gt;
diff --git a/monai/data/wsi_datasets.py b/monai/data/wsi_datasets.py
@@ -10,7 +10,7 @@
 # limitations under the License.
 
 import inspect
-from typing import Callable, Dict, List, Optional, Tuple, Union
+from typing import Callable, Dict, Optional, Sequence, Tuple, Union
 
 import numpy as np
 
@@ -32,10 +32,12 @@ 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: 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.
+        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.
+            - a class (inherited from `BaseWSIReader`), it is initialized and set as wsi_reader.
+            - 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:
@@ -45,14 +47,14 @@ class PatchWSIDataset(Dataset):
 
             [
                 {"image": "path/to/image1.tiff", "location": [200, 500], "label": 0},
-                {"image": "path/to/image2.tiff", "location": [100, 700], "label": 1}
+                {"image": "path/to/image2.tiff", "location": [100, 700], "size": [20, 20], "level": 2, "label": 1}
             ]
 
     """
 
     def __init__(
         self,
-        data: List,
+        data: Sequence,
         size: Optional[Union[int, Tuple[int, int]]] = None,
         level: Optional[int] = None,
         transform: Optional[Callable] = None,
diff --git a/monai/data/wsi_reader.py b/monai/data/wsi_reader.py
@@ -10,6 +10,7 @@
 # limitations under the License.
 
 from abc import abstractmethod
+from os.path import abspath
 from typing import Any, Dict, List, Optional, Sequence, Tuple, Union
 
 import numpy as np
@@ -53,6 +54,7 @@ class BaseWSIReader(ImageReader):
     """
 
     supported_suffixes: List[str] = []
+    backend = ""
 
     def __init__(self, level: int, **kwargs):
         super().__init__()
@@ -63,7 +65,7 @@ def __init__(self, level: int, **kwargs):
     @abstractmethod
     def get_size(self, wsi, level: int) -> Tuple[int, int]:
         """
-        Returns the size of the whole slide image at a given level.
+        Returns the size (height, width) of the whole slide image at a given level.
 
         Args:
             wsi: a whole slide image object loaded from a file
@@ -83,6 +85,11 @@ def get_level_count(self, wsi) -> int:
         """
         raise NotImplementedError(f"Subclass {self.__class__.__name__} must implement this method.")
 
+    @abstractmethod
+    def get_file_path(self, wsi) -> str:
+        """Return the file path for the WSI object"""
+        raise NotImplementedError(f"Subclass {self.__class__.__name__} must implement this method.")
+
     @abstractmethod
     def get_patch(
         self, wsi, location: Tuple[int, int], size: Tuple[int, int], level: int, dtype: DtypeLike, mode: str
@@ -102,20 +109,29 @@ def get_patch(
         """
         raise NotImplementedError(f"Subclass {self.__class__.__name__} must implement this method.")
 
-    @abstractmethod
-    def get_metadata(self, patch: np.ndarray, location: Tuple[int, int], size: Tuple[int, int], level: int) -> Dict:
+    def get_metadata(
+        self, wsi, patch: np.ndarray, location: Tuple[int, int], size: Tuple[int, int], level: int
+    ) -> Dict:
         """
         Returns metadata of the extracted patch from the whole slide image.
 
         Args:
+            wsi: the whole slide image object, from which the patch is loaded
             patch: extracted patch from whole slide image
             location: (top, left) tuple giving the top left pixel in the level 0 reference frame. Defaults to (0, 0).
             size: (height, width) tuple giving the patch size at the given level (`level`).
                 If None, it is set to the full image size at the given level.
             level: the level number. Defaults to 0
 
         """
-        raise NotImplementedError(f"Subclass {self.__class__.__name__} must implement this method.")
+        metadata: Dict = {
+            "backend": self.backend,
+            "original_channel_dim": 0,
+            "spatial_shape": np.asarray(patch.shape[1:]),
+            "wsi": {"path": self.get_file_path(wsi)},
+            "patch": {"location": location, "size": size, "level": level},
+        }
+        return metadata
 
     def get_data(
         self,
@@ -194,8 +210,26 @@ def get_data(
             patch_list.append(patch)
 
             # Set patch-related metadata
-            each_meta = self.get_metadata(patch=patch, location=location, size=size, level=level)
-            metadata.update(each_meta)
+            each_meta = self.get_metadata(wsi=each_wsi, patch=patch, location=location, size=size, level=level)
+
+            if len(wsi) == 1:
+                metadata = each_meta
+            else:
+                if not metadata:
+                    metadata = {
+                        "backend": each_meta["backend"],
+                        "original_channel_dim": each_meta["original_channel_dim"],
+                        "spatial_shape": each_meta["spatial_shape"],
+                        "wsi": [each_meta["wsi"]],
+                        "patch": [each_meta["patch"]],
+                    }
+                else:
+                    if metadata["original_channel_dim"] != each_meta["original_channel_dim"]:
+                        raise ValueError("original_channel_dim is not consistent across wsi objects.")
+                    if any(metadata["spatial_shape"] != each_meta["spatial_shape"]):
+                        raise ValueError("spatial_shape is not consistent across wsi objects.")
+                    metadata["wsi"].append(each_meta["wsi"])
+                    metadata["patch"].append(each_meta["patch"])
 
         return _stack_images(patch_list, metadata), metadata
 
@@ -247,7 +281,7 @@ def get_level_count(self, wsi) -> int:
 
     def get_size(self, wsi, level: int) -> Tuple[int, int]:
         """
-        Returns the size of the whole slide image at a given level.
+        Returns the size (height, width) of the whole slide image at a given level.
 
         Args:
             wsi: a whole slide image object loaded from a file
@@ -256,19 +290,9 @@ def get_size(self, wsi, level: int) -> Tuple[int, int]:
         """
         return self.reader.get_size(wsi, level)
 
-    def get_metadata(self, patch: np.ndarray, location: Tuple[int, int], size: Tuple[int, int], level: int) -> Dict:
-        """
-        Returns metadata of the extracted patch from the whole slide image.
-
-        Args:
-            patch: extracted patch from whole slide image
-            location: (top, left) tuple giving the top left pixel in the level 0 reference frame. Defaults to (0, 0).
-            size: (height, width) tuple giving the patch size at the given level (`level`).
-                If None, it is set to the full image size at the given level.
-            level: the level number. Defaults to 0
-
-        """
-        return self.reader.get_metadata(patch=patch, size=size, location=location, level=level)
+    def get_file_path(self, wsi) -> str:
+        """Return the file path for the WSI object"""
+        return self.reader.get_file_path(wsi)
 
     def get_patch(
         self, wsi, location: Tuple[int, int], size: Tuple[int, int], level: int, dtype: DtypeLike, mode: str
@@ -317,6 +341,7 @@ class CuCIMWSIReader(BaseWSIReader):
     """
 
     supported_suffixes = ["tif", "tiff", "svs"]
+    backend = "cucim"
 
     def __init__(self, level: int = 0, **kwargs):
         super().__init__(level, **kwargs)
@@ -335,7 +360,7 @@ def get_level_count(wsi) -> int:
     @staticmethod
     def get_size(wsi, level: int) -> Tuple[int, int]:
         """
-        Returns the size of the whole slide image at a given level.
+        Returns the size (height, width) of the whole slide image at a given level.
 
         Args:
             wsi: a whole slide image object loaded from a file
@@ -344,27 +369,9 @@ def get_size(wsi, level: int) -> Tuple[int, int]:
         """
         return (wsi.resolutions["level_dimensions"][level][1], wsi.resolutions["level_dimensions"][level][0])
 
-    def get_metadata(self, patch: np.ndarray, location: Tuple[int, int], size: Tuple[int, int], level: int) -> Dict:
-        """
-        Returns metadata of the extracted patch from the whole slide image.
-
-        Args:
-            patch: extracted patch from whole slide image
-            location: (top, left) tuple giving the top left pixel in the level 0 reference frame. Defaults to (0, 0).
-            size: (height, width) tuple giving the patch size at the given level (`level`).
-                If None, it is set to the full image size at the given level.
-            level: the level number. Defaults to 0
-
-        """
-        metadata: Dict = {
-            "backend": "cucim",
-            "spatial_shape": np.asarray(patch.shape[1:]),
-            "original_channel_dim": 0,
-            "location": location,
-            "size": size,
-            "level": level,
-        }
-        return metadata
+    def get_file_path(self, wsi) -> str:
+        """Return the file path for the WSI object"""
+        return str(abspath(wsi.path))
 
     def read(self, data: Union[Sequence[PathLike], PathLike, np.ndarray], **kwargs):
         """
@@ -440,6 +447,7 @@ class OpenSlideWSIReader(BaseWSIReader):
     """
 
     supported_suffixes = ["tif", "tiff", "svs"]
+    backend = "openslide"
 
     def __init__(self, level: int = 0, **kwargs):
         super().__init__(level, **kwargs)
@@ -458,7 +466,7 @@ def get_level_count(wsi) -> int:
     @staticmethod
     def get_size(wsi, level: int) -> Tuple[int, int]:
         """
-        Returns the size of the whole slide image at a given level.
+        Returns the size (height, width) of the whole slide image at a given level.
 
         Args:
             wsi: a whole slide image object loaded from a file
@@ -467,27 +475,9 @@ def get_size(wsi, level: int) -> Tuple[int, int]:
         """
         return (wsi.level_dimensions[level][1], wsi.level_dimensions[level][0])
 
-    def get_metadata(self, patch: np.ndarray, location: Tuple[int, int], size: Tuple[int, int], level: int) -> Dict:
-        """
-        Returns metadata of the extracted patch from the whole slide image.
-
-        Args:
-            patch: extracted patch from whole slide image
-            location: (top, left) tuple giving the top left pixel in the level 0 reference frame. Defaults to (0, 0).
-            size: (height, width) tuple giving the patch size at the given level (`level`).
-                If None, it is set to the full image size at the given level.
-            level: the level number. Defaults to 0
-
-        """
-        metadata: Dict = {
-            "backend": "openslide",
-            "spatial_shape": np.asarray(patch.shape[1:]),
-            "original_channel_dim": 0,
-            "location": location,
-            "size": size,
-            "level": level,
-        }
-        return metadata
+    def get_file_path(self, wsi) -> str:
+        """Return the file path for the WSI object"""
+        return str(abspath(wsi._filename))
 
     def read(self, data: Union[Sequence[PathLike], PathLike, np.ndarray], **kwargs):
         """
diff --git a/tests/test_wsireader_new.py b/tests/test_wsireader_new.py
@@ -125,8 +125,13 @@ class Tests(unittest.TestCase):
         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 = reader.get_data(img_obj)[0]
+                img, meta = reader.get_data(img_obj)
             self.assertTupleEqual(img.shape, expected_shape)
+            self.assertEqual(meta["backend"], self.backend)
+            self.assertEqual(meta["wsi"]["path"], str(os.path.abspath(file_path)))
+            self.assertEqual(meta["patch"]["level"], level)
+            self.assertTupleEqual(meta["patch"]["size"], expected_shape[1:])
+            self.assertTupleEqual(meta["patch"]["location"], (0, 0))
 
         @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
         def test_read_region(self, file_path, patch_info, expected_img):
@@ -138,29 +143,39 @@ def test_read_region(self, file_path, patch_info, expected_img):
                         reader.get_data(img_obj, **patch_info)[0]
                 else:
                     # Read twice to check multiple calls
-                    img = reader.get_data(img_obj, **patch_info)[0]
+                    img, meta = reader.get_data(img_obj, **patch_info)
                     img2 = reader.get_data(img_obj, **patch_info)[0]
                     self.assertTupleEqual(img.shape, img2.shape)
                     self.assertIsNone(assert_array_equal(img, img2))
                     self.assertTupleEqual(img.shape, expected_img.shape)
                     self.assertIsNone(assert_array_equal(img, expected_img))
+                    self.assertEqual(meta["backend"], self.backend)
+                    self.assertEqual(meta["wsi"]["path"], str(os.path.abspath(file_path)))
+                    self.assertEqual(meta["patch"]["level"], patch_info["level"])
+                    self.assertTupleEqual(meta["patch"]["size"], expected_img.shape[1:])
+                    self.assertTupleEqual(meta["patch"]["location"], patch_info["location"])
 
         @parameterized.expand([TEST_CASE_3])
-        def test_read_region_multi_wsi(self, file_path, patch_info, expected_img):
+        def test_read_region_multi_wsi(self, file_path_list, patch_info, expected_img):
             kwargs = {"name": None, "offset": None} if self.backend == "tifffile" else {}
             reader = WSIReader(self.backend, **kwargs)
-            img_obj = reader.read(file_path, **kwargs)
+            img_obj_list = reader.read(file_path_list, **kwargs)
             if self.backend == "tifffile":
                 with self.assertRaises(ValueError):
-                    reader.get_data(img_obj, **patch_info)[0]
+                    reader.get_data(img_obj_list, **patch_info)[0]
             else:
                 # Read twice to check multiple calls
-                img = reader.get_data(img_obj, **patch_info)[0]
-                img2 = reader.get_data(img_obj, **patch_info)[0]
+                img, meta = reader.get_data(img_obj_list, **patch_info)
+                img2 = reader.get_data(img_obj_list, **patch_info)[0]
                 self.assertTupleEqual(img.shape, img2.shape)
                 self.assertIsNone(assert_array_equal(img, img2))
                 self.assertTupleEqual(img.shape, expected_img.shape)
                 self.assertIsNone(assert_array_equal(img, expected_img))
+                self.assertEqual(meta["backend"], self.backend)
+                self.assertEqual(meta["wsi"][0]["path"], str(os.path.abspath(file_path_list[0])))
+                self.assertEqual(meta["patch"][0]["level"], patch_info["level"])
+                self.assertTupleEqual(meta["patch"][0]["size"], expected_img.shape[1:])
+                self.assertTupleEqual(meta["patch"][0]["location"], patch_info["location"])
 
         @parameterized.expand([TEST_CASE_RGB_0, TEST_CASE_RGB_1])
         @skipUnless(has_tiff, "Requires tifffile.")
