Update cellemetry/services/sam.py

cellemetry/services/sam.py

@@ -93,7 +93,35 @@ def execute_segmentation(deps: AnalysisDeps, request: ComponentRequest) -> str:
     print(f"[Engine] Inference took {time.time() - t_inf:.2f}s")
 
     # 5. REMOVED: Morphological Filtering (Solidity/Circularity)
-    # We now trust the SAM model and the Agent's bounding box completely.
+
+    # Morphology filtering
+    keep_indices_morph = []
+    for i, mask_tensor in enumerate(results["masks"]):
+        mask_np = mask_tensor.cpu().numpy()
+        mask_np = np.squeeze(mask_np).astype(int)
+
+        if mask_np.ndim != 2:
+            keep_indices_morph.append(False)
+            continue
+
+        props = regionprops(mask_np)
+        if not props:
+            keep_indices_morph.append(False)
+            continue
+
+        prop = props[0]
+        perimeter = prop.perimeter
+        circularity = (4 * np.pi * prop.area) / (perimeter ** 2) if perimeter > 0 else 0
+
+        is_solid = prop.solidity > MIN_SOLIDITY
+        is_round_enough = circularity > MIN_CIRCULARITY
+        keep_indices_morph.append(is_solid and is_round_enough)
+
+    if any(keep_indices_morph):
+        keep_indices_tensor = torch.tensor(keep_indices_morph, device=results["masks"].device)
+        before_count = len(results["masks"])
+        results = _filter_results(results, keep_indices_tensor)
+        print(f"[Filter] Morphology: Dropped {before_count - len(results['masks'])} debris-like objects.")
 
     # 6. NMS (Keep this to remove duplicate detections on the same object)
     pred_boxes = results["boxes"]