Initial commit

skills/clinical-reports/scripts/extract_clinical_data.py

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+#!/usr/bin/env python3
+"""
+Extract structured clinical data from reports.
+
+Usage:
+    python extract_clinical_data.py <report_file>
+"""
+
+import argparse
+import json
+import re
+
+
+def extract_vital_signs(content: str) -> dict:
+    """Extract vital signs."""
+    vitals = {}
+    patterns = {
+        "temperature": r"(?i)temp(?:erature)?[:]\s*([\d.]+)\s*°?F",
+        "bp": r"(?i)BP[:]\s*(\d+/\d+)",
+        "hr": r"(?i)HR[:]\s*(\d+)",
+        "rr": r"(?i)RR[:]\s*(\d+)",
+        "spo2": r"(?i)SpO2[:]\s*([\d.]+)%",
+    }
+    
+    for vital, pattern in patterns.items():
+        match = re.search(pattern, content)
+        if match:
+            vitals[vital] = match.group(1)
+    
+    return vitals
+
+
+def extract_demographics(content: str) -> dict:
+    """Extract patient demographics."""
+    demographics = {}
+    patterns = {
+        "age": r"(?i)(\d+)[\s-]year[\s-]old",
+        "sex": r"(?i)(male|female|M|F)",
+    }
+    
+    for demo, pattern in patterns.items():
+        match = re.search(pattern, content)
+        if match:
+            demographics[demo] = match.group(1)
+    
+    return demographics
+
+
+def extract_medications(content: str) -> list:
+    """Extract medication list."""
+    meds = []
+    # Simple pattern for common medication format
+    pattern = r"(?i)(\w+)\s+(\d+\s*mg)\s+(PO|IV|SC)\s+(daily|BID|TID|QID)"
+    matches = re.findall(pattern, content)
+    
+    for match in matches:
+        meds.append({
+            "drug": match[0],
+            "dose": match[1],
+            "route": match[2],
+            "frequency": match[3]
+        })
+    
+    return meds
+
+
+def main():
+    """Main entry point."""
+    parser = argparse.ArgumentParser(description="Extract clinical data")
+    parser.add_argument("input_file", help="Path to clinical report")
+    parser.add_argument("--output", "-o", help="Output JSON file")
+    
+    args = parser.parse_args()
+    
+    try:
+        with open(args.input_file, 'r', encoding='utf-8') as f:
+            content = f.read()
+        
+        extracted_data = {
+            "demographics": extract_demographics(content),
+            "vital_signs": extract_vital_signs(content),
+            "medications": extract_medications(content),
+        }
+        
+        if args.output:
+            with open(args.output, 'w') as f:
+                json.dump(extracted_data, f, indent=2)
+            print(f"✓ Data extracted to: {args.output}")
+        else:
+            print(json.dumps(extracted_data, indent=2))
+        
+        return 0
+        
+    except Exception as e:
+        print(f"Error: {e}")
+        return 1
+
+
+if __name__ == "__main__":
+    import sys
+    sys.exit(main())
+