Add instance_id to .obs before required in ShapesModel

scverse · Aug 4, 2023 · 7a8ab20 · 7a8ab20
1 parent c341044
commit 7a8ab20
Showing 1 changed file with 11 additions and 11 deletions.
diff --git a/src/spatialdata_io/readers/seqfish.py b/src/spatialdata_io/readers/seqfish.py
@@ -112,17 +112,6 @@ def seqfish(
         for x in range(1, n + 1)
     }
 
-    radii = np.sqrt(adata.obs[SeqfishKeys.AREA].to_numpy() / np.pi)
-    shapes = {
-        f"{SeqfishKeys.REGION.value}_{section}": ShapesModel.parse(
-            adata.obsm[SeqfishKeys.SPATIAL_KEY],
-            geometry=0,
-            radius=radii,
-            index=adata.obs[SeqfishKeys.INSTANCE_KEY_TABLE],
-        )
-        for section, adata in adatas.items()
-    }
-
     adata = ad.concat(adatas)
     adata.obs[SeqfishKeys.REGION_KEY] = SeqfishKeys.REGION
     adata.obs[SeqfishKeys.REGION_KEY] = adata.obs[SeqfishKeys.REGION_KEY].astype("category")
@@ -135,6 +124,17 @@ def seqfish(
         instance_key=SeqfishKeys.INSTANCE_KEY_TABLE.value,
     )
 
+    radii = np.sqrt(adata.obs[SeqfishKeys.AREA].to_numpy() / np.pi)
+    shapes = {
+        f"{SeqfishKeys.REGION.value}_{section}": ShapesModel.parse(
+            adata.obsm[SeqfishKeys.SPATIAL_KEY],
+            geometry=0,
+            radius=radii,
+            index=adata.obs[SeqfishKeys.INSTANCE_KEY_TABLE],
+        )
+        for section, adata in adatas.items()
+    }
+
     sdata = SpatialData(images=images, labels=labels, points=points, table=table, shapes=shapes)
 
     return sdata