🐛 Add comprehensive logging and remove CMPO mapping

- Add detailed logging throughout analysis pipeline for debugging
- Remove CMPO phenotype mapping to simplify app and focus on 4-stage VLM
- Add error traceback display for better debugging
- Add status messages during analysis process

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

app.py

@@ -10,6 +10,15 @@ from pathlib import Path
 import numpy as np
 from PIL import Image
 import random
+import logging
+import traceback
+
+# Setup logging
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(levelname)s - %(message)s'
+)
+logger = logging.getLogger(__name__)
 
 # Setup page
 st.set_page_config(
@@ -112,8 +121,7 @@ sys.path.append(str(Path(__file__).parent))
 try:
     from anton.core.pipeline import AnalysisPipeline
     from anton.utils.image_io import ImageLoader
-    from anton.cmpo.mapping import map_to_cmpo
-    from anton.cmpo.ontology import CMPOOntology
+    # CMPO mapping removed for simplicity
     anton_available = True
 except ImportError as e:
     anton_available = False
@@ -214,12 +222,19 @@ if current_image is not None:
     
     # Run analysis
     if analyze_btn:
+        logger.info("Analysis button pressed")
+        st.info("Starting analysis...")
+        
         # Check API keys
         vlm_provider = "mock"
         if os.getenv('GOOGLE_API_KEY'):
             vlm_provider = "gemini"
+            logger.info("Using Gemini VLM provider")
         elif os.getenv('ANTHROPIC_API_KEY'):
             vlm_provider = "claude"
+            logger.info("Using Claude VLM provider")
+        else:
+            logger.info("Using mock VLM provider (no API keys found)")
         
         # Configure pipeline
         if use_sample and sample_images:
@@ -229,22 +244,28 @@ if current_image is not None:
                 "protein": "FKHR-GFP",
                 "readout": "nuclear_vs_cytoplasmic_localization"
             }
+            logger.info("Using sample image context: protein translocation")
         else:
             biological_context = {
                 "experiment_type": "general_microscopy",
                 "readout": "cellular_morphology_and_phenotypes"
             }
+            logger.info("Using general microscopy context")
         
         config = {
             "vlm_provider": vlm_provider,
             "biological_context": biological_context
         }
+        logger.info(f"Pipeline config: {config}")
         
         # Run analysis
         with st.spinner("Analyzing..."):
             try:
+                logger.info(f"Creating pipeline with image: {image_to_analyze}")
                 pipeline = AnalysisPipeline(config)
+                logger.info("Pipeline created, starting analysis...")
                 results = pipeline.run_pipeline_sync(image_to_analyze)
+                logger.info(f"Analysis completed. Results keys: {list(results.keys()) if results else 'None'}")
                 
                 # Display results
                 st.markdown('<div class="results-container">', unsafe_allow_html=True)
@@ -272,33 +293,8 @@ if current_image is not None:
                             
                             st.write(content[:1000] + "..." if len(content) > 1000 else content)
                 
-                # CMPO Phenotypes
-                try:
-                    cmpo_mapper = CMPOOntology()
-                    all_cmpo_results = []
-                    
-                    for stage_name, stage_key in stages:
-                        if stage_key in results and results[stage_key]:
-                            stage_data = results[stage_key]
-                            stage_text = stage_data.get('description', 
-                                        stage_data.get('segmentation_guidance', 
-                                        stage_data.get('population_summary', '')))
-                            
-                            if stage_text and len(stage_text) > 50:
-                                cmpo_context = 'protein_localization' if use_sample else 'general_microscopy'
-                                cmpo_results = map_to_cmpo(stage_text, cmpo_mapper, context=cmpo_context)
-                                if cmpo_results:
-                                    all_cmpo_results.extend(cmpo_results[:2])
-                    
-                    if all_cmpo_results:
-                        st.markdown("### 🧬 Detected Phenotypes")
-                        for mapping in all_cmpo_results[:5]:
-                            confidence = mapping.get('confidence', 0)
-                            icon = "🟢" if confidence >= 4.5 else "🟡" if confidence >= 3.5 else "🟠"
-                            st.markdown(f"{icon} **{mapping.get('term_name', 'Unknown')}** ({confidence:.1f}/5)")
-                
-                except Exception as e:
-                    st.warning("Phenotype classification unavailable")
+                # Skip CMPO mapping for now
+                logger.info("Analysis results displayed successfully")
                 
                 st.markdown('</div>', unsafe_allow_html=True)
                 
@@ -310,7 +306,11 @@ if current_image is not None:
                         pass
                         
             except Exception as e:
-                st.error(f"Analysis failed: {str(e)}")
+                error_msg = f"Analysis failed: {str(e)}"
+                logger.error(error_msg)
+                logger.error(f"Full traceback: {traceback.format_exc()}")
+                st.error(error_msg)
+                st.code(traceback.format_exc())
 else:
     st.markdown('<div class="upload-section">', unsafe_allow_html=True)
     st.markdown("**Upload an image or select a sample to begin analysis**")