fix post_proc behaviour in AnnotationStoreReader

Author: measty

tests/test_wsireader.py

@@ -2977,11 +2977,10 @@ def test_post_proc_logic_across_readers(wsi: WSIReader) -> None:
     called: dict[str, bool] = {"flag": False}
     mock_post_proc = _make_mock_post_proc(called)
 
-    skip_check = isinstance(wsi, AnnotationStoreReader)  # and wsi.base_wsi is None
+    skip_check = isinstance(wsi, AnnotationStoreReader)
 
-    if skip_check is False:
-        # Recursively inject post_proc into the actual reader
-        _inject_post_proc_recursive(wsi, mock_post_proc)
+    # Recursively inject post_proc into the actual reader
+    _inject_post_proc_recursive(wsi, mock_post_proc)
 
     patch_utils = _should_patch_background_composite(wsi)
 
@@ -2999,7 +2998,7 @@ def test_post_proc_logic_across_readers(wsi: WSIReader) -> None:
     if skip_check:
         assert isinstance(rect, np.ndarray)
         assert isinstance(region, np.ndarray)
-        assert not called["flag"]
+        assert called["flag"]
         return
 
     if isinstance(wsi, NGFFWSIReader):
@@ -3107,6 +3106,10 @@ def test_explicit_none_postproc(sample_svs: Path) -> None:
     assert isinstance(region, np.ndarray)
     assert region.shape == (50, 50, 3)
 
+    region = reader.read_rect((0, 0), (50, 50), coord_space="resolution")
+    assert isinstance(region, np.ndarray)
+    assert region.shape == (50, 50, 3)
+
 
 def test_fsspec_json_wsi_reader_instantiation() -> None:
     """Test if FsspecJsonWSIReader is instantiated.

tiatoolbox/wsicore/wsireader.py

@@ -6486,8 +6486,6 @@ def read_rect(
                 coord_space=coord_space,
                 **kwargs,
             )
-            if self.post_proc is not None:
-                base_region = self.post_proc(base_region)
             base_region = Image.fromarray(
                 utils.transforms.background_composite(base_region, alpha=True),
             )
@@ -6498,7 +6496,12 @@ def read_rect(
                 )
             base_region = Image.alpha_composite(base_region, im_region)
             base_region = base_region.convert("RGB")
-            return np.array(base_region)
+            base_region = np.array(base_region)
+            if self.post_proc is not None:
+                base_region = self.post_proc(base_region)
+            return base_region
+        if self.post_proc is not None:
+            im_region = self.post_proc(im_region)
         return utils.transforms.background_composite(im_region, alpha=False)
 
     def read_bounds(
@@ -6681,8 +6684,6 @@ class docstrings for more information.
                 coord_space=coord_space,
                 **kwargs,
             )
-            if self.post_proc is not None:
-                base_region = self.post_proc(base_region)
             base_region = Image.fromarray(
                 utils.transforms.background_composite(base_region, alpha=True),
             )
@@ -6693,7 +6694,12 @@ class docstrings for more information.
                 )
             base_region = Image.alpha_composite(base_region, im_region)
             base_region = base_region.convert("RGB")
-            return np.array(base_region)
+            base_region = np.array(base_region)
+            if self.post_proc is not None:
+                base_region = self.post_proc(base_region)
+            return base_region
+        if self.post_proc is not None:
+            im_region = self.post_proc(im_region)
         return utils.transforms.background_composite(im_region, alpha=False)