Update app.py

app.py

@@ -3,9 +3,16 @@ import asyncio
 import os
 import glob
 import torch
+import sys
 from pathlib import Path
 from PIL import Image
 
+# --- CRITICAL FIX: Redirect stdin to avoid "Invalid file descriptor" crash ---
+# The agent runner checks stdin for potential human-in-the-loop confirmation.
+# In a web app (Gradio/Cloud Run), stdin is closed/invalid. Redirecting to 
+# devnull tricks the runner into proceeding without crashing.
+sys.stdin = open(os.devnull, 'r')
+
 # GenAI & ADK Imports
 from google.adk.runners import InMemoryRunner
 from google.genai import types
@@ -34,12 +41,14 @@ def load_models():
     
     try:
         # Note: Ensure you have access to facebook/sam3 or use a public alternative
+        # If running on CPU only, this might be slow!
         MODEL_CACHE["model"] = Sam3Model.from_pretrained("facebook/sam3").to(device)
         MODEL_CACHE["processor"] = Sam3Processor.from_pretrained("facebook/sam3")
         print(f"✅ SAM3 loaded on {device}")
     except Exception as e:
-        print(f"⚠️ SAM3 load failed (using mock): {e}")
-        # Allow app to start even if model fails (will fall back to mock logic if implemented)
+        print(f"⚠️ SAM3 load failed (using mock or fallback): {e}")
+        # We allow the app to continue; the agent tools will handle the missing model
+        # (check sam.py for the mock/fallback logic)
 
 # Load immediately on startup
 load_models()
@@ -73,6 +82,8 @@ async def run_analysis(image_path_str, user_prompt, progress=gr.Progress()):
     
     # 2. Initialize Runner
     runner = InMemoryRunner(agent=root_agent, app_name="cellemetry_demo")
+    
+    # Create session
     session = await runner.session_service.create_session(
         app_name="cellemetry_demo",
         user_id="demo_user",
@@ -94,39 +105,50 @@ async def run_analysis(image_path_str, user_prompt, progress=gr.Progress()):
     log_text = "\n".join(logs)
     yield log_text, None, None
 
-    async for event in runner.run_async(
-        user_id="demo_user",
-        session_id=session.id,
-        new_message=content,
-    ):
-        author = event.author
-        
-        # Capture Tool Calls
-        if event.get_function_calls():
-            for fc in event.get_function_calls():
-                logs.append(f"🔧 **{author}** calling tool: `{fc.name}`")
-        
-        # Capture Text (Streaming)
-        if event.content and event.content.parts:
-            for part in event.content.parts:
-                if hasattr(part, 'text') and part.text:
-                    if event.partial:
-                        # Update the last log line if it's the same thought
-                        if logs[-1].startswith(f"💬 **{author}**"):
-                            logs[-1] = f"💬 **{author}**: {part.text}..."
+    try:
+        async for event in runner.run_async(
+            user_id="demo_user",
+            session_id=session.id,
+            new_message=content,
+        ):
+            author = event.author
+            
+            # Capture Tool Calls
+            if event.get_function_calls():
+                for fc in event.get_function_calls():
+                    logs.append(f"🔧 **{author}** calling tool: `{fc.name}`")
+                    yield "\n\n".join(logs), None, None
+            
+            # Capture Text (Streaming)
+            if event.content and event.content.parts:
+                for part in event.content.parts:
+                    if hasattr(part, 'text') and part.text:
+                        if event.partial:
+                            # Update the last log line if it's the same thought being streamed
+                            if logs and logs[-1].startswith(f"💬 **{author}**"):
+                                logs[-1] = f"💬 **{author}**: {part.text}..."
+                            else:
+                                logs.append(f"💬 **{author}**: {part.text}...")
                         else:
-                            logs.append(f"💬 **{author}**: {part.text}...")
-                    else:
-                        logs.append(f"✅ **{author}**: {part.text}")
-        
-        # Yield updated logs immediately
+                            # Finalize the log line
+                            if logs and logs[-1].startswith(f"💬 **{author}**"):
+                                logs[-1] = f"✅ **{author}**: {part.text}"
+                            else:
+                                logs.append(f"✅ **{author}**: {part.text}")
+            
+            # Yield updated logs immediately
+            yield "\n\n".join(logs), None, None
+
+    except Exception as e:
+        logs.append(f"❌ **Error during execution**: {str(e)}")
         yield "\n\n".join(logs), None, None
+        return
 
     # 5. Retrieve Final Results
     logs.append("\n🏁 **Analysis Complete.** gathering files...")
     yield "\n\n".join(logs), None, None
 
-    # Collect output images
+    # Collect output images (segmentation maps)
     output_images = glob.glob("/tmp/out_*.png")
     
     # Collect excel report