use llm for structuring

Author: tony.liu

transcription/qwen.py

@@ -17,15 +17,24 @@ def map_to_logbook_template(json_output):
     with open("templates/modified_templates.json", 'r') as f:
         modified_templates = json.load(f)
 
-    # Get the field names in order
-    modified_fields = list(modified_templates["adult_cardiac_log_2"].keys())
-    logbook_fields = list(logbook_templates["Adult_cardiac_log_2"].keys())
+    # Initialize result dictionary with all fields from both templates set to None
+    result = {}
+    result.update({key: None for key in logbook_templates["Adult_cardiac_log"].keys()})
+    result.update({key: None for key in logbook_templates["Adult_cardiac_log_2"].keys()})
 
-    # Create result dictionary with all fields initialized to None
-    result = {key: None for key in logbook_fields}
+    # Map fields for adult_cardiac_log
+    modified_fields_1 = list(modified_templates["Adult_cardiac_log"].keys())
+    logbook_fields_1 = list(logbook_templates["Adult_cardiac_log"].keys())
 
-    # Map fields by position
-    for modified_field, logbook_field in zip(modified_fields, logbook_fields):
+    for modified_field, logbook_field in zip(modified_fields_1, logbook_fields_1):
+        if modified_field in json_output:
+            result[logbook_field] = json_output[modified_field].replace("###SECTION###", "")
+    
+    # Map fields for adult_cardiac_log_2
+    modified_fields_2 = list(modified_templates["adult_cardiac_log_2"].keys())
+    logbook_fields_2 = list(logbook_templates["Adult_cardiac_log_2"].keys())
+    
+    for modified_field, logbook_field in zip(modified_fields_2, logbook_fields_2):
         if modified_field in json_output:
             result[logbook_field] = json_output[modified_field].replace("###SECTION###", "")
 
@@ -42,6 +51,21 @@ def process_image(image_path):
 
 def qwen(image_paths=["../assets/kkl3.jpg", "../assets/kkl2.jpg"]):
     try:
+        # Load templates first
+        with open("templates/modified_templates.json", 'r') as f:
+            modified_templates = json.load(f)
+        
+        # Get all field names from both templates
+        field_names = []
+        field_names.extend(list(modified_templates["Adult_cardiac_log"].keys()))
+        field_names.extend(list(modified_templates["adult_cardiac_log_2"].keys()))
+        
+        if not field_names:
+            raise ValueError("No field names found in templates")
+            
+        # Ensure field names are unique
+        field_names = list(dict.fromkeys(field_names))
+        
         # Load the model and processor with explicit trust_remote_code
         model_name = "Qwen/Qwen2.5-VL-3B-Instruct"
 
@@ -188,9 +212,9 @@ def qwen(image_paths=["../assets/kkl3.jpg", "../assets/kkl2.jpg"]):
         section_order = ["basics", "case_details", "hpi", "social", "PMHx", "medications", "allergies", "exam", "veins", "allen_test", "INVx", "CXR/CT", "surgical_plan", "flags", "operative_notes", "post_op_notes", "learning_points"]
         combined_text = SECTION_SEPARATOR.join(all_transcribed_sections.get(section, "") for section in section_order)
 
-        # Convert to JSON using the existing parser
-        json_output = process_text_file(combined_text)
-        
+        # Convert to JSON using the text processor with field names
+        json_output = process_text_file(combined_text, field_names)
+        json_output['type'] = 'adult_cardiac_logs'
         # Map to logbook template format
         final_output = map_to_logbook_template(json_output)
 

transcription/templates/modified_templates.json

@@ -1,4 +1,58 @@
 {
+    "Adult_cardiac_log": {
+        "Case No": null,
+        "Type": null,
+        "Patient ID": null,
+        "Age": null,
+        "Surgeon": null,
+        "OR Date": null,
+        "Indication for Surgery/Reason for Referral": null,
+        "HPI": null,
+        "PMHx HTM": null,
+        "PMHx DM2": null,
+        "PMHx DLP": null,
+        "PMHx CVA": null,
+        "Gender": null,
+        "Social EtOH": null,
+        "Smoking": null,
+        "Drugs": null,
+        "Allergies": null,
+        "Meds [last dose]": null,
+        "exam_weight": null,
+        "exam_height": null,
+        "exam_bmi": null,
+        "Veins": null,
+        "Allen Test": null,
+        "Echo EF": null,
+        "RVFx": null,
+        "WMA": null,
+        "Aorta": null,
+        "Valves": null,
+        "CXR": null,
+        "exam_pulses_top_left": null,
+        "exam_pulses_top_right": null,
+        "exam_pulses_bottom_left": null,
+        "exam_pulses_bottom_right": null,
+        "invx_echo": null,
+        "invx_hb": null,
+        "invx_w": null,
+        "invx_pl": null,
+        "labs_w": null,
+        "labs_hb": null,
+        "labs_plt": null,
+        "labs_hct": null,
+        "labs_na": null,
+        "labs_cl": null,
+        "labs_bun": null,
+        "labs_glu": null,
+        "labs_creat": null,
+        "labs_co2": null,
+        "labs_k": null,
+        "cath_image": null,
+        "cath_text": null,
+        "ct_image": null,
+        "CT": null
+    },
 "adult_cardiac_log_2": {
     "Surgical Plan": "",
     "1 Operator": "",