🐛 Fix saving annotation properties

Author: shaneahmed

tests/engines/test_semantic_segmentor.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import sqlite3
 from pathlib import Path
 
 import numpy as np
@@ -89,7 +90,8 @@ def test_semantic_segmentor_patches(
 
 def test_save_annotation_store(
     sample_patch1: Path, sample_patch2: Path, tmp_path: Path
-):
+) -> None:
+    """Test for saving output as annotation store."""
     segmentor = SemanticSegmentor(
         model="fcn-tissue_mask", batch_size=32, verbose=False, device=device
     )
@@ -106,17 +108,19 @@ def test_save_annotation_store(
         output_type="annotationstore",
     )
 
-    assert output == tmp_path / "output1" / "output.zarr"
+    assert output == tmp_path / "output1" / "output.db"
+    con = sqlite3.connect(output)
+    cur = con.cursor()
+    annotations_properties = list(cur.execute("SELECT properties FROM annotations"))
 
-    output = zarr.open(output, mode="r")
-    assert 0.24 < np.mean(output["predictions"][:]) < 0.25
-    assert "probabilities" not in output.keys()  # noqa: SIM118
+    assert annotations_properties is not None
 
 
 def test_hovernet_dat() -> None:
+    """Test for comparing annotation store saving."""
     from pathlib import Path
 
     from tiatoolbox.utils.misc import store_from_dat
 
     path_to_file = Path.cwd().parent.parent / "output" / "0.dat"
-    out = store_from_dat(path_to_file, scale_factor=(1.0, 1.0))
+    _ = store_from_dat(path_to_file, scale_factor=(1.0, 1.0))

tiatoolbox/utils/misc.py

@@ -1265,6 +1265,8 @@ def dict_to_store_semantic_segmentor(
     count = 1
     store = SQLiteStore()
 
+    _ = class_dict  # use it once overlay is working
+
     annotations = []
 
     for type_class in layer_list:
@@ -1290,14 +1292,16 @@ def dict_to_store_semantic_segmentor(
                     "coordinates": scaled_coords,
                 },
             )
-            annotations.append(
-                Annotation(
-                    geometry=make_valid_poly(
-                        feature_geom,
-                        origin=origin,
-                    ),
-                    properties={"type": "mask"},
-                )
+            annotations.extend(
+                [
+                    Annotation(
+                        geometry=make_valid_poly(
+                            feature_geom,
+                            origin=origin,
+                        ),
+                        properties={"type": "mask"},
+                    )
+                ]
             )
 
     _ = store.append_many(annotations, [str(i) for i in range(len(annotations))])