Deprecate Old Pathology Components (#4415)

* Deprecate pathology datasets

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update min test exclusion

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Update test file names for deprecated component and update prob map deprecation

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Author: bhashemian

monai/apps/pathology/data/datasets.py

@@ -17,11 +17,12 @@
 
 from monai.data import Dataset, SmartCacheDataset
 from monai.data.image_reader import WSIReader
-from monai.utils import ensure_tuple_rep
+from monai.utils import deprecated, ensure_tuple_rep
 
 __all__ = ["PatchWSIDataset", "SmartCachePatchWSIDataset", "MaskedInferenceWSIDataset"]
 
 
+@deprecated(since="0.8", msg_suffix="use `monai.data.PatchWSIDataset` instead.")
 class PatchWSIDataset(Dataset):
     """
     This dataset reads whole slide images, extracts regions, and creates patches.
@@ -103,6 +104,7 @@ def __getitem__(self, index):
         return patches
 
 
+@deprecated(since="0.8", msg_suffix="use `monai.data.SmartCacheDataset` with `monai.data.PatchWSIDataset` instead.")
 class SmartCachePatchWSIDataset(SmartCacheDataset):
     """Add SmartCache functionality to `PatchWSIDataset`.
 
@@ -177,6 +179,7 @@ def __init__(
         )
 
 
+@deprecated(since="0.8", msg_suffix="use `monai.data.MaskedPatchWSIDataset` instead.")
 class MaskedInferenceWSIDataset(Dataset):
     """
     This dataset load the provided foreground masks at an arbitrary resolution level,

monai/apps/pathology/handlers/prob_map_producer.py

@@ -27,7 +27,10 @@
 
 @deprecated(
     since="0.8",
-    msg_suffix="use `monai.handler.ProbMapProducer` (with `monai.data.wsi_dataset.SlidingPatchWSIDataset`) instead.",
+    msg_suffix=(
+        "use `monai.handler.ProbMapProducer` (with `monai.data.wsi_dataset.MaskedPatchWSIDataset` or "
+        "`monai.data.wsi_dataset.SlidingPatchWSIDataset`) instead."
+    ),
 )
 class ProbMapProducer:
     """

monai/data/image_reader.py

@@ -28,7 +28,7 @@
     orientation_ras_lps,
 )
 from monai.transforms.utility.array import EnsureChannelFirst
-from monai.utils import MetaKeys, SpaceKeys, ensure_tuple, ensure_tuple_rep, optional_import, require_pkg
+from monai.utils import MetaKeys, SpaceKeys, deprecated, ensure_tuple, ensure_tuple_rep, optional_import, require_pkg
 
 if TYPE_CHECKING:
     import itk
@@ -1218,6 +1218,7 @@ def _get_spatial_shape(self, img):
         return np.asarray((img.width, img.height))
 
 
+@deprecated(since="0.8", msg_suffix="use `monai.wsi_reader.WSIReader` instead.")
 class WSIReader(ImageReader):
     """
     Read whole slide images and extract patches.

tests/min_tests.py

@@ -162,7 +162,6 @@ def run_testsuit():
         "test_vitautoenc",
         "test_write_metrics_reports",
         "test_wsireader",
-        "test_wsireader_new",
         "test_zoom",
         "test_zoom_affine",
         "test_zoomd",