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Update app.py
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app.py
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# -*- coding: utf-8
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# π₯ Gemma 3N SOAP Note Generator
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#-*- coding: utf-8
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# π₯ Gemma 3N SOAP Note Generator
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# Enable widgets
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# Enable widgets
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import torch
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from transformers import AutoProcessor, AutoModelForImageTextToText
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import gradio as gr
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import ipywidgets as widgets
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from IPython.display import display, clear_output
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import io
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import base64
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from datetime import datetime
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from huggingface_hub import login
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import getpass
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# Authenticate with HuggingFace
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# Replace the authentication section (lines around the getpass part) with this:
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# Import libraries and authenticate
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import torch
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from transformers import AutoProcessor, AutoModelForImageTextToText
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import gradio as gr
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import ipywidgets as widgets
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from IPython.display import display, clear_output
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import io
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import base64
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from datetime import datetime
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from huggingface_hub import login
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import os
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import easyocr
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from PIL import Image
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# Authenticate with HuggingFace
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print("π HuggingFace Authentication Required")
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# Try to get token from environment variable first (for production/HF Spaces)
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hf_token = os.environ.get('HF_TOKEN') or os.environ.get('HUGGINGFACE_TOKEN')
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print("β
Found HF token in environment variables")
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try:
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print("β
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print("
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device = "cuda" if torch.cuda.is_available() else "cpu"
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device
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if torch.cuda.is_available():
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else:
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print("
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# SOAP Note Generation
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def
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"""
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"""
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if not doctor_notes.strip():
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return "β Please enter some medical notes to process."
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{doctor_notes}
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Please
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- SUBJECTIVE: Patient's reported symptoms and history
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- OBJECTIVE: Physical examination findings, vital signs, and
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- ASSESSMENT: Clinical diagnosis and reasoning
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- PLAN: Treatment
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# Process input
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inputs = processor(text=prompt, return_tensors="pt").to(device)
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with torch.no_grad():
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outputs = model.generate(
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**inputs,
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max_new_tokens=
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temperature=0.
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do_sample=True,
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)
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# Decode response
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generated_text =
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# Extract only the
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if include_timestamp:
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timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
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header = f"""π SOAP NOTE - Generated by Gemma
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π Timestamp: {timestamp}
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π€ Model:
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π Processed locally on device
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{'='*60}
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"""
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return header + soap_response
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return soap_response
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except Exception as e:
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"""
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}
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def on_generate_click(b):
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with output_area:
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output_area.value = '<p style="color: #007bff;">π Processing with Gemma 3N... Please wait...</p>'
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# Get text from input or uploaded file
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text_to_process = notes_input.value
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# Check if file was uploaded
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if file_upload.value and len(file_upload.value) > 0:
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try:
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uploaded_file = list(file_upload.value.values())[0]
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file_content = uploaded_file['content'].decode('utf-8')
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text_to_process = file_content
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notes_input.value = file_content # Show in text area
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except Exception as e:
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output_area.value = f'<p style="color: #dc3545;">β Error reading file: {str(e)}</p>'
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return
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if not text_to_process.strip():
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output_area.value = '<p style="color: #dc3545;">β Please enter medical notes or upload a file!</p>'
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return
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# Generate SOAP note
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soap_note = generate_soap_note(text_to_process)
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# Format output as HTML
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formatted_output = f'<pre style="font-family: monospace; font-size: 12px; line-height: 1.4; white-space: pre-wrap;">{soap_note}</pre>'
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output_area.value = formatted_output
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def on_example1_click(b):
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notes_input.value = examples['chest_pain']
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output_area.value = '<p style="color: #28a745;">β
Chest pain example loaded! Click "Generate SOAP Note" to process.</p>'
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def on_example2_click(b):
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notes_input.value = examples['diabetes']
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output_area.value = '<p style="color: #28a745;">β
Diabetes follow-up example loaded! Click "Generate SOAP Note" to process.</p>'
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def on_example3_click(b):
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notes_input.value = examples['pediatric']
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output_area.value = '<p style="color: #28a745;">β
Pediatric example loaded! Click "Generate SOAP Note" to process.</p>'
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def on_clear_click(b):
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notes_input.value = ''
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file_upload.value = ()
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output_area.value = '<p style="color: #666;">π Ready to generate SOAP notes! Enter medical notes above or upload a file.</p>'
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# Bind event handlers
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generate_btn.on_click(on_generate_click)
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example1_btn.on_click(on_example1_click)
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example2_btn.on_click(on_example2_click)
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example3_btn.on_click(on_example3_click)
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clear_btn.on_click(on_clear_click)
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print("β
Event handlers configured!")
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# Define example medical notes first
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example_notes_1 = """
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Patient: John Smith, 45-year-old male
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Chief Complaint: Chest pain for 2 hours
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History: Patient reports sudden onset of sharp chest pain while at work. Pain is 7/10 intensity, located substernal, radiating to left arm. Associated with shortness of breath and diaphoresis. No previous cardiac history. Denies nausea or vomiting.
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Physical Exam: VS: BP 150/90, HR 110, RR 22, O2 Sat 96% on RA. Patient appears anxious and diaphoretic. Heart: Regular rhythm, no murmurs. Lungs: Clear bilaterally. Extremities: No edema.
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Assessment: Acute chest pain, rule out myocardial infarction
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Plan: EKG, cardiac enzymes, chest X-ray, aspirin 325mg, continuous cardiac monitoring
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"""
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example_notes_2 = """
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Patient: Sarah Johnson, 28-year-old female
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Chief Complaint: Severe headache and fever
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History: 3-day history of progressive headache, fever up to 101.5Β°F, photophobia, and neck stiffness. Patient reports this is the worst headache of her life. No recent travel or sick contacts. No rash noted.
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Physical Exam: VS: T 101.2Β°F, BP 130/80, HR 95, RR 18. Patient appears ill and photophobic. HEENT: Pupils equal and reactive. Neck: Stiff with positive Kernig's sign. Neurologic: Alert and oriented x3, no focal deficits.
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Assessment: Suspected meningitis
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Plan: Lumbar puncture, blood cultures, empiric antibiotics, supportive care
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"""
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Patient: Robert Davis, 62-year-old male
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Chief Complaint: Shortness of breath and leg swelling
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History: 2-week history of progressive dyspnea on exertion, orthopnea, and bilateral lower extremity edema. Patient has history of hypertension and diabetes. Reports sleeping on 3 pillows due to breathing difficulty.
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Physical Exam: VS: BP 140/85, HR 88, RR 24, O2 Sat 92% on RA. Heart: S3 gallop present, JVD elevated. Lungs: Bilateral rales in lower fields. Extremities: 2+ pitting edema bilaterally.
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Assessment: Congestive heart failure exacerbation
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Plan: Chest X-ray, BNP, echocardiogram, furosemide, ACE inhibitor, daily weights
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"""
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#
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def
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# Update the HTML widget directly
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output_area.value = '<p style="color: #007bff;">π Processing with Gemma 3N... Please wait...</p>'
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# Get input text
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input_text = notes_input.value.strip()
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# Check if file was uploaded
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if file_upload.value:
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try:
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# Process uploaded file
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uploaded_file = list(file_upload.value.values())[0]
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file_content = uploaded_file['content'].decode('utf-8')
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input_text = file_content
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except Exception as upload_error:
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output_area.value = f'<p style="color: #ff6b6b;">β File upload error: {str(upload_error)}</p>'
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return
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if not input_text:
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output_area.value = '<p style="color: #ff6b6b;">β οΈ Please enter medical notes or upload a file first!</p>'
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return
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# Check if generate_soap_note function exists
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if 'generate_soap_note' not in globals():
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output_area.value = '<p style="color: #ff6b6b;">β Error: generate_soap_note function not found. Please define it first.</p>'
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return
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# Generate SOAP note using Gemma
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soap_note = generate_soap_note(input_text)
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# Escape HTML in soap_note to prevent rendering issues
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import html
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escaped_soap_note = html.escape(soap_note)
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# Display result
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output_area.value = f'''
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<div style="background: #f8f9fa; padding: 15px; border-radius: 8px; border-left: 4px solid #28a745;">
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<h4 style="color: #28a745; margin-top: 0;">β
Generated SOAP Note:</h4>
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<pre style="white-space: pre-wrap; font-family: 'Courier New', monospace; background: white; padding: 15px; border-radius: 5px; border: 1px solid #ddd;">{escaped_soap_note}</pre>
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</div>
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'''
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except Exception as e:
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import traceback
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error_details = traceback.format_exc()
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output_area.value = f'''
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<div style="color: #ff6b6b; background: #ffe6e6; padding: 15px; border-radius: 5px;">
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<h4>β Error Details:</h4>
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<p><strong>Error:</strong> {str(e)}</p>
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<details>
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<summary>Click for full traceback</summary>
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<pre style="font-size: 12px; background: #fff; padding: 10px; border-radius: 3px; margin-top: 10px;">{error_details}</pre>
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</details>
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</div>
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'''
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def on_clear_click(b):
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try:
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except Exception as e:
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def on_example_click(example_text):
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def handler(b):
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try:
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notes_input.value = example_text
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output_area.value = '<p style="color: #28a745;">π Example loaded! Click "Generate SOAP Note" to process.</p>'
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except Exception as e:
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output_area.value = f'<p style="color: #ff6b6b;">β Example load error: {str(e)}</p>'
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return handler
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# Connect event handlers to buttons
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try:
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generate_btn.on_click(on_generate_click)
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clear_btn.on_click(on_clear_click)
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example1_btn.on_click(on_example_click(example_notes_1))
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example2_btn.on_click(on_example_click(example_notes_2))
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example3_btn.on_click(on_example_click(example_notes_3))
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print("β
Event handlers connected successfully!")
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print("π Example notes loaded:")
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print(" - Example 1: Chest pain case")
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print(" - Example 2: Suspected meningitis")
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print(" - Example 3: Heart failure")
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except Exception as e:
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print(f"β Error connecting event handlers: {str(e)}")
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| 382 |
-
import traceback
|
| 383 |
-
traceback.print_exc()
|
| 384 |
-
|
| 385 |
-
"""## π Alternative: Gradio Web Interface
|
| 386 |
-
### Run this cell for a shareable web interface
|
| 387 |
-
"""
|
| 388 |
-
|
| 389 |
-
# Install required packages for image processing and OCR
|
| 390 |
-
|
| 391 |
-
import gradio as gr
|
| 392 |
-
import torch
|
| 393 |
-
from PIL import Image
|
| 394 |
-
import pytesseract
|
| 395 |
-
import cv2
|
| 396 |
-
import numpy as np
|
| 397 |
-
import easyocr
|
| 398 |
-
import io
|
| 399 |
-
|
| 400 |
-
# First, make sure you have the examples dictionary defined
|
| 401 |
-
examples = {
|
| 402 |
-
'chest_pain': """Patient: John Smith, 45-year-old male
|
| 403 |
-
Chief Complaint: Chest pain for 2 hours
|
| 404 |
-
History: Patient reports sudden onset of sharp chest pain while at work. Pain is 7/10 intensity, located substernal, radiating to left arm. Associated with shortness of breath and diaphoresis. No previous cardiac history. Denies nausea or vomiting.
|
| 405 |
-
Physical Exam: VS: BP 150/90, HR 110, RR 22, O2 Sat 96% on RA. Patient appears anxious and diaphoretic. Heart: Regular rhythm, no murmurs. Lungs: Clear bilaterally. Extremities: No edema.
|
| 406 |
-
Assessment: Acute chest pain, rule out myocardial infarction
|
| 407 |
-
Plan: EKG, cardiac enzymes, chest X-ray, aspirin 325mg, continuous cardiac monitoring""",
|
| 408 |
-
|
| 409 |
-
'diabetes': """Patient: Maria Garcia, 52-year-old female
|
| 410 |
-
Chief Complaint: Increased thirst and frequent urination for 3 weeks
|
| 411 |
-
History: Patient reports polyuria, polydipsia, and unintentional weight loss of 10 lbs over past month. Family history of diabetes. Denies fever, abdominal pain, or vision changes.
|
| 412 |
-
Physical Exam: VS: BP 140/85, HR 88, RR 16, BMI 28. Patient appears well but slightly dehydrated. HEENT: Dry mucous membranes. Cardiovascular: Regular rate and rhythm. Extremities: No diabetic foot changes noted.
|
| 413 |
-
Assessment: New onset diabetes mellitus, likely Type 2
|
| 414 |
-
Plan: HbA1c, fasting glucose, comprehensive metabolic panel, diabetic education, metformin initiation""",
|
| 415 |
-
|
| 416 |
-
'pediatric': """Patient: Emma Thompson, 8-year-old female
|
| 417 |
-
Chief Complaint: Fever and sore throat for 2 days
|
| 418 |
-
History: Mother reports fever up to 102Β°F, sore throat, difficulty swallowing, and decreased appetite. No cough or runny nose. Several classmates have been sick with similar symptoms.
|
| 419 |
-
Physical Exam: VS: T 101.8Β°F, HR 110, RR 20, O2 Sat 99%. Patient appears mildly ill but alert. HEENT: Throat erythematous with tonsillar exudate, anterior cervical lymphadenopathy. Heart and lungs: Normal.
|
| 420 |
-
Assessment: Streptococcal pharyngitis (probable)
|
| 421 |
-
Plan: Rapid strep test, throat culture, amoxicillin if positive, supportive care, return if worsening"""
|
| 422 |
-
}
|
| 423 |
-
|
| 424 |
-
# Initialize EasyOCR reader (better for handwritten text)
|
| 425 |
-
try:
|
| 426 |
-
ocr_reader = easyocr.Reader(['en'])
|
| 427 |
-
print("β
EasyOCR initialized successfully")
|
| 428 |
-
except:
|
| 429 |
-
ocr_reader = None
|
| 430 |
-
print("β οΈ EasyOCR not available, using Tesseract only")
|
| 431 |
-
|
| 432 |
-
def preprocess_image_for_ocr(image):
|
| 433 |
-
"""
|
| 434 |
-
Preprocess image to improve OCR accuracy
|
| 435 |
-
"""
|
| 436 |
-
# Convert PIL Image to numpy array
|
| 437 |
-
img_array = np.array(image)
|
| 438 |
-
|
| 439 |
-
# Convert to grayscale if needed
|
| 440 |
-
if len(img_array.shape) == 3:
|
| 441 |
-
gray = cv2.cvtColor(img_array, cv2.COLOR_RGB2GRAY)
|
| 442 |
-
else:
|
| 443 |
-
gray = img_array
|
| 444 |
-
|
| 445 |
-
# Apply image preprocessing for better OCR
|
| 446 |
-
# 1. Resize image if too small
|
| 447 |
-
height, width = gray.shape
|
| 448 |
-
if height < 300 or width < 300:
|
| 449 |
-
scale_factor = max(300/height, 300/width)
|
| 450 |
-
new_width = int(width * scale_factor)
|
| 451 |
-
new_height = int(height * scale_factor)
|
| 452 |
-
gray = cv2.resize(gray, (new_width, new_height), interpolation=cv2.INTER_CUBIC)
|
| 453 |
-
|
| 454 |
-
# 2. Noise removal
|
| 455 |
-
denoised = cv2.medianBlur(gray, 3)
|
| 456 |
|
| 457 |
-
|
| 458 |
-
|
| 459 |
-
enhanced = clahe.apply(denoised)
|
| 460 |
-
|
| 461 |
-
# 4. Thresholding
|
| 462 |
-
_, thresh = cv2.threshold(enhanced, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)
|
| 463 |
-
|
| 464 |
-
return thresh
|
| 465 |
-
|
| 466 |
-
def extract_text_from_image(image):
|
| 467 |
-
"""
|
| 468 |
-
Extract text from image using multiple OCR methods
|
| 469 |
-
"""
|
| 470 |
if image is None:
|
| 471 |
return "β No image provided"
|
| 472 |
-
|
| 473 |
try:
|
| 474 |
-
# Preprocess
|
| 475 |
-
processed_img =
|
| 476 |
-
|
| 477 |
-
|
|
|
|
|
|
|
| 478 |
if ocr_reader is not None:
|
| 479 |
try:
|
| 480 |
-
|
| 481 |
-
|
| 482 |
-
|
| 483 |
-
|
| 484 |
-
|
| 485 |
-
easyocr_text = ' '.join([result[1] for result in results])
|
| 486 |
-
|
| 487 |
-
if len(easyocr_text.strip()) > 20: # If we got good results
|
| 488 |
-
return clean_extracted_text(easyocr_text)
|
| 489 |
-
|
| 490 |
except Exception as e:
|
| 491 |
print(f"EasyOCR failed: {e}")
|
| 492 |
-
|
| 493 |
-
#
|
| 494 |
try:
|
| 495 |
-
|
| 496 |
-
|
|
|
|
|
|
|
|
|
|
| 497 |
tesseract_text = pytesseract.image_to_string(processed_img, config=custom_config)
|
| 498 |
-
|
| 499 |
-
if len(tesseract_text.strip()) >
|
| 500 |
-
return
|
| 501 |
-
|
| 502 |
except Exception as e:
|
| 503 |
print(f"Tesseract failed: {e}")
|
| 504 |
-
|
| 505 |
-
return "β Could not extract text from image. Please
|
| 506 |
-
|
| 507 |
except Exception as e:
|
| 508 |
return f"β Error processing image: {str(e)}"
|
| 509 |
|
| 510 |
-
def
|
| 511 |
-
"""
|
| 512 |
-
|
| 513 |
-
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|
| 514 |
# Remove excessive whitespace and empty lines
|
| 515 |
lines = [line.strip() for line in text.split('\n') if line.strip()]
|
| 516 |
-
|
| 517 |
-
|
| 518 |
-
|
| 519 |
-
|
| 520 |
-
|
| 521 |
-
|
| 522 |
-
|
| 523 |
-
|
| 524 |
-
|
| 525 |
-
|
| 526 |
-
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|
|
|
|
| 527 |
text_to_process = medical_notes.strip() if medical_notes else ""
|
| 528 |
-
|
| 529 |
-
#
|
| 530 |
if uploaded_image is not None:
|
| 531 |
try:
|
| 532 |
-
print("π Extracting text from
|
| 533 |
-
extracted_text = extract_text_from_image(uploaded_image)
|
| 534 |
-
|
| 535 |
-
|
| 536 |
-
|
| 537 |
-
|
| 538 |
-
|
| 539 |
-
|
| 540 |
-
if not text_to_process:
|
| 541 |
-
text_to_process = extracted_text
|
| 542 |
else:
|
| 543 |
-
|
| 544 |
-
|
| 545 |
except Exception as e:
|
| 546 |
return f"β Error processing image: {str(e)}"
|
| 547 |
-
|
| 548 |
if not text_to_process:
|
| 549 |
-
return "β Please enter medical notes manually or upload
|
| 550 |
-
|
| 551 |
-
#
|
| 552 |
-
if 'generate_soap_note' not in globals():
|
| 553 |
-
return "β Error: generate_soap_note function not found. Please define it first."
|
| 554 |
-
|
| 555 |
try:
|
| 556 |
-
return
|
| 557 |
except Exception as e:
|
| 558 |
return f"β Error generating SOAP note: {str(e)}"
|
| 559 |
|
| 560 |
-
#
|
| 561 |
-
|
| 562 |
-
"""
|
| 563 |
-
|
| 564 |
-
|
| 565 |
-
|
| 566 |
-
|
| 567 |
-
|
| 568 |
-
|
| 569 |
-
|
| 570 |
-
|
| 571 |
-
|
| 572 |
-
|
| 573 |
-
|
| 574 |
-
|
| 575 |
-
|
| 576 |
-
|
| 577 |
-
|
| 578 |
-
|
| 579 |
-
|
| 580 |
-
|
| 581 |
-
|
| 582 |
-
|
| 583 |
-
|
| 584 |
-
|
| 585 |
-
|
| 586 |
-
|
| 587 |
-
|
| 588 |
-
fn=gradio_generate_soap,
|
| 589 |
-
inputs=[
|
| 590 |
-
gr.Textbox(
|
| 591 |
-
lines=6,
|
| 592 |
-
placeholder="Enter medical notes manually (optional)...\n\nOr upload an image below and text will be extracted automatically.",
|
| 593 |
-
label="π Medical Notes (Manual Entry)"
|
| 594 |
-
),
|
| 595 |
-
gr.Image(
|
| 596 |
-
type="pil",
|
| 597 |
-
label="π· Upload Medical Image (PNG/JPG only)",
|
| 598 |
-
sources=["upload", "webcam"], # FIXED: Changed "camera" to "webcam"
|
| 599 |
-
image_mode="RGB"
|
| 600 |
-
)
|
| 601 |
-
],
|
| 602 |
-
outputs=[
|
| 603 |
-
gr.Textbox(
|
| 604 |
-
lines=15,
|
| 605 |
-
label="π Generated SOAP Note",
|
| 606 |
-
show_copy_button=True
|
| 607 |
-
)
|
| 608 |
-
],
|
| 609 |
-
title="π₯ Medical Image SOAP Note Generator",
|
| 610 |
-
description="""
|
| 611 |
-
Transform medical images (PNG/JPG) into professional SOAP documentation using OCR + Gemma 3N model.
|
| 612 |
-
|
| 613 |
-
πΈ **How to use:**
|
| 614 |
-
1. Upload a PNG or JPG image of medical notes (typed or handwritten)
|
| 615 |
-
2. Or enter text manually in the text box above
|
| 616 |
-
3. The system will extract text from images using OCR
|
| 617 |
-
4. Generate structured SOAP notes automatically
|
| 618 |
-
|
| 619 |
-
π‘ **Tips for better OCR results:**
|
| 620 |
-
- Use clear, high-resolution images
|
| 621 |
-
- Ensure good lighting and contrast
|
| 622 |
-
- Keep text horizontal (not tilted)
|
| 623 |
-
- Handwritten text works best when clearly written
|
| 624 |
-
""",
|
| 625 |
-
examples=[
|
| 626 |
-
[examples['chest_pain'], None],
|
| 627 |
-
[examples['diabetes'], None],
|
| 628 |
-
[examples['pediatric'], None]
|
| 629 |
-
],
|
| 630 |
-
theme=gr.themes.Soft(),
|
| 631 |
-
flagging_mode="never"
|
| 632 |
-
)
|
| 633 |
-
|
| 634 |
-
# Launch Gradio interface with flexible port selection
|
| 635 |
-
print("π Launching Medical Image SOAP Generator...")
|
| 636 |
|
| 637 |
-
|
| 638 |
-
|
| 639 |
-
|
| 640 |
-
|
| 641 |
-
|
| 642 |
-
|
| 643 |
-
|
| 644 |
-
|
| 645 |
-
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
| 646 |
)
|
| 647 |
-
|
| 648 |
-
|
| 649 |
-
|
| 650 |
-
|
| 651 |
-
|
| 652 |
-
|
| 653 |
-
|
| 654 |
-
|
| 655 |
-
|
| 656 |
-
|
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|
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|
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|
|
|
|
|
|
| 657 |
show_error=True,
|
| 658 |
quiet=False
|
| 659 |
)
|
| 660 |
-
|
| 661 |
-
except Exception as e:
|
| 662 |
-
|
| 663 |
-
|
| 664 |
-
print("gradio_interface.launch(show_error=True)")
|
| 665 |
-
|
| 666 |
-
print("π― Medical Image SOAP Generator ready!")
|
| 667 |
-
print("πΈ Upload PNG/JPG images of medical notes for automatic text extraction and SOAP generation")
|
| 668 |
-
|
| 669 |
-
"""## π Usage Statistics & Model Info"""
|
| 670 |
-
|
| 671 |
-
# Display model and system information
|
| 672 |
-
import psutil
|
| 673 |
-
import GPUtil
|
| 674 |
-
|
| 675 |
-
def show_system_info():
|
| 676 |
-
print("π§ SYSTEM INFORMATION")
|
| 677 |
-
print("="*50)
|
| 678 |
-
print(f"π₯οΈ Device: {device.upper()}")
|
| 679 |
-
print(f"π§ CPU Usage: {psutil.cpu_percent(interval=1):.1f}%")
|
| 680 |
-
print(f"πΎ RAM Usage: {psutil.virtual_memory().percent:.1f}%")
|
| 681 |
-
|
| 682 |
-
if torch.cuda.is_available():
|
| 683 |
-
try:
|
| 684 |
-
gpus = GPUtil.getGPUs()
|
| 685 |
-
if gpus:
|
| 686 |
-
gpu = gpus[0]
|
| 687 |
-
print(f"π GPU: {gpu.name}")
|
| 688 |
-
print(f"π GPU Usage: {gpu.load*100:.1f}%")
|
| 689 |
-
print(f"π₯ GPU Memory: {gpu.memoryUsed}/{gpu.memoryTotal} MB ({gpu.memoryPercent:.1f}%)")
|
| 690 |
-
print(f"π‘οΈ GPU Temp: {gpu.temperature}Β°C")
|
| 691 |
-
except:
|
| 692 |
-
print(f"π GPU Memory: {torch.cuda.memory_allocated()/1e9:.1f}GB / {torch.cuda.memory_reserved()/1e9:.1f}GB")
|
| 693 |
-
|
| 694 |
-
print("\nπ€ MODEL INFORMATION")
|
| 695 |
-
print("="*50)
|
| 696 |
-
print(f"π‘ Model ID: {model_id}")
|
| 697 |
-
print(f"π― Model Type: Multimodal (Text, Image, Audio)")
|
| 698 |
-
print(f"π Model Size: ~2.9GB")
|
| 699 |
-
print(f"π’ Parameters: ~2.9B")
|
| 700 |
-
print(f"π Languages: 140 text + 35 multimodal")
|
| 701 |
-
print(f"π½ Precision: {model.dtype}")
|
| 702 |
-
|
| 703 |
-
print("\nβ
Ready for SOAP note generation!")
|
| 704 |
-
|
| 705 |
-
show_system_info()
|
| 706 |
-
|
| 707 |
-
"""---
|
| 708 |
-
## π SOAP Note Format Reference
|
| 709 |
-
|
| 710 |
-
**S - SUBJECTIVE**: Patient's reported symptoms and history
|
| 711 |
-
**O - OBJECTIVE**: Observable clinical findings
|
| 712 |
-
**A - ASSESSMENT**: Clinical diagnosis/impression
|
| 713 |
-
**P - PLAN**: Treatment and follow-up plan
|
| 714 |
-
|
| 715 |
-
---
|
| 716 |
-
*π€ Powered by Google's Gemma 3N Model | π All processing performed locally*
|
| 717 |
-
"""
|
| 718 |
-
|
|
|
|
| 1 |
+
# -*- coding: utf-8 -*-
|
| 2 |
+
# π₯ Gemma 3N SOAP Note Generator with Unsloth
|
| 3 |
+
# Optimized for offline medical documentation
|
| 4 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
| 5 |
import torch
|
|
|
|
| 6 |
import gradio as gr
|
|
|
|
|
|
|
| 7 |
import io
|
| 8 |
import base64
|
| 9 |
from datetime import datetime
|
|
|
|
| 10 |
import os
|
| 11 |
import easyocr
|
| 12 |
+
from PIL import Image, ImageDraw, ImageFont
|
| 13 |
+
import cv2
|
| 14 |
+
import numpy as np
|
| 15 |
+
import psutil
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 16 |
|
| 17 |
+
# Import Unsloth for optimized Gemma 3n
|
|
|
|
| 18 |
try:
|
| 19 |
+
from unsloth import FastModel
|
| 20 |
+
print("β
Unsloth imported successfully")
|
| 21 |
+
UNSLOTH_AVAILABLE = True
|
| 22 |
+
except ImportError:
|
| 23 |
+
print("β Unsloth not available. Install with: pip install unsloth")
|
| 24 |
+
UNSLOTH_AVAILABLE = False
|
| 25 |
+
|
| 26 |
+
# Device setup
|
| 27 |
+
def setup_device():
|
| 28 |
+
device = "cuda" if torch.cuda.is_available() else "cpu"
|
| 29 |
+
print(f"π₯οΈ Using device: {device}")
|
| 30 |
+
|
| 31 |
+
if torch.cuda.is_available():
|
| 32 |
+
print(f"π GPU: {torch.cuda.get_device_name(0)}")
|
| 33 |
+
print(f"πΎ GPU Memory: {torch.cuda.get_device_properties(0).total_memory / 1e9:.1f} GB")
|
| 34 |
+
else:
|
| 35 |
+
print("β οΈ Running on CPU - will be slower but works offline")
|
| 36 |
+
|
| 37 |
+
return device
|
| 38 |
+
|
| 39 |
+
# Load Unsloth Gemma 3n model
|
| 40 |
+
def load_unsloth_gemma_model(device):
|
| 41 |
+
"""Load optimized Gemma 3n model using Unsloth"""
|
| 42 |
+
|
| 43 |
+
if not UNSLOTH_AVAILABLE:
|
| 44 |
+
print("β Unsloth not available. Using fallback method.")
|
| 45 |
+
return load_fallback_model()
|
| 46 |
+
|
| 47 |
+
try:
|
| 48 |
+
print("π‘ Loading Unsloth-optimized Gemma 3n model...")
|
| 49 |
+
|
| 50 |
+
# Use the 4-bit quantized model for efficiency
|
| 51 |
+
model_name = "unsloth/gemma-3n-E4B-it-unsloth-bnb-4bit"
|
| 52 |
+
|
| 53 |
+
print(f"π§ Loading model: {model_name}")
|
| 54 |
+
|
| 55 |
+
# Load with Unsloth optimizations
|
| 56 |
+
model, tokenizer = FastModel.from_pretrained(
|
| 57 |
+
model_name=model_name,
|
| 58 |
+
dtype=None, # Auto-detect
|
| 59 |
+
max_seq_length=1024, # Good for medical notes
|
| 60 |
+
load_in_4bit=True, # 4-bit quantization for efficiency
|
| 61 |
+
full_finetuning=False,
|
| 62 |
+
)
|
| 63 |
+
|
| 64 |
+
print("β
Unsloth Gemma 3n model loaded successfully!")
|
| 65 |
+
print(f"π Model: {model_name}")
|
| 66 |
+
print(f"πΎ Memory optimized with 4-bit quantization")
|
| 67 |
+
print(f"π― Ready for medical SOAP note generation!")
|
| 68 |
+
|
| 69 |
+
return model, tokenizer
|
| 70 |
+
|
| 71 |
+
except Exception as e:
|
| 72 |
+
print(f"β Error loading Unsloth model: {e}")
|
| 73 |
+
print("π‘ Trying fallback model...")
|
| 74 |
+
return load_fallback_model()
|
| 75 |
|
| 76 |
+
def load_fallback_model():
|
| 77 |
+
"""Fallback model if Unsloth fails"""
|
| 78 |
+
try:
|
| 79 |
+
from transformers import AutoTokenizer, AutoModelForCausalLM
|
| 80 |
+
|
| 81 |
+
print("π Loading fallback model...")
|
| 82 |
+
model_name = "microsoft/DialoGPT-medium"
|
| 83 |
+
|
| 84 |
+
tokenizer = AutoTokenizer.from_pretrained(model_name)
|
| 85 |
+
if tokenizer.pad_token is None:
|
| 86 |
+
tokenizer.pad_token = tokenizer.eos_token
|
| 87 |
+
|
| 88 |
+
model = AutoModelForCausalLM.from_pretrained(
|
| 89 |
+
model_name,
|
| 90 |
+
torch_dtype=torch.float16 if torch.cuda.is_available() else torch.float32,
|
| 91 |
+
low_cpu_mem_usage=True
|
| 92 |
+
)
|
| 93 |
+
|
| 94 |
+
print("β
Fallback model loaded!")
|
| 95 |
+
return model, tokenizer
|
| 96 |
+
|
| 97 |
+
except Exception as e:
|
| 98 |
+
print(f"β Fallback model also failed: {e}")
|
| 99 |
+
return None, None
|
| 100 |
|
| 101 |
+
# Enhanced SOAP Note Generation with Gemma 3n
|
| 102 |
+
def generate_soap_note_gemma(doctor_notes, model=None, tokenizer=None, include_timestamp=True):
|
| 103 |
+
"""Generate SOAP note using Gemma 3n model"""
|
| 104 |
+
|
|
|
|
| 105 |
if not doctor_notes.strip():
|
| 106 |
return "β Please enter some medical notes to process."
|
| 107 |
+
|
| 108 |
+
if model is None or tokenizer is None:
|
| 109 |
+
return generate_template_soap(doctor_notes, include_timestamp)
|
| 110 |
+
|
| 111 |
+
# Medical-specific prompt for Gemma 3n
|
| 112 |
+
prompt = f"""<bos><start_of_turn>user
|
| 113 |
+
You are a medical AI assistant specialized in creating SOAP notes. Convert the following unstructured medical notes into a professional SOAP note format.
|
| 114 |
+
|
| 115 |
+
Medical Notes:
|
| 116 |
{doctor_notes}
|
| 117 |
|
| 118 |
+
Please create a structured SOAP note with these sections:
|
| 119 |
+
- SUBJECTIVE: Patient's reported symptoms, complaints, and relevant history
|
| 120 |
+
- OBJECTIVE: Physical examination findings, vital signs, and observable data
|
| 121 |
+
- ASSESSMENT: Clinical diagnosis, differential diagnosis, and medical reasoning
|
| 122 |
+
- PLAN: Treatment recommendations, medications, tests, and follow-up care
|
| 123 |
|
| 124 |
+
<end_of_turn>
|
| 125 |
+
<start_of_turn>model
|
| 126 |
+
SOAP NOTE:
|
| 127 |
|
| 128 |
+
SUBJECTIVE:"""
|
|
|
|
|
|
|
| 129 |
|
| 130 |
+
try:
|
| 131 |
+
# Tokenize input
|
| 132 |
+
inputs = tokenizer(
|
| 133 |
+
prompt,
|
| 134 |
+
return_tensors="pt",
|
| 135 |
+
truncation=True,
|
| 136 |
+
max_length=512,
|
| 137 |
+
padding=True
|
| 138 |
+
)
|
| 139 |
+
|
| 140 |
+
# Generate with optimized settings for medical text
|
| 141 |
with torch.no_grad():
|
| 142 |
outputs = model.generate(
|
| 143 |
**inputs,
|
| 144 |
+
max_new_tokens=400,
|
| 145 |
+
temperature=0.2, # Lower temperature for medical precision
|
| 146 |
+
top_p=0.9,
|
| 147 |
do_sample=True,
|
| 148 |
+
repetition_penalty=1.1,
|
| 149 |
+
pad_token_id=tokenizer.eos_token_id,
|
| 150 |
+
eos_token_id=tokenizer.eos_token_id
|
| 151 |
)
|
| 152 |
+
|
| 153 |
# Decode response
|
| 154 |
+
generated_text = tokenizer.decode(outputs[0], skip_special_tokens=True)
|
| 155 |
+
|
| 156 |
+
# Extract only the SOAP note part
|
| 157 |
+
if "SOAP NOTE:" in generated_text:
|
| 158 |
+
soap_response = generated_text.split("SOAP NOTE:")[1].strip()
|
| 159 |
+
else:
|
| 160 |
+
soap_response = generated_text[len(prompt):].strip()
|
| 161 |
+
|
| 162 |
+
# Clean up response
|
| 163 |
+
soap_response = clean_soap_response(soap_response)
|
| 164 |
+
|
| 165 |
+
# Add professional header
|
| 166 |
if include_timestamp:
|
| 167 |
timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
|
| 168 |
+
header = f"""π SOAP NOTE - Generated by Gemma 3n
|
| 169 |
π Timestamp: {timestamp}
|
| 170 |
+
π€ Model: Unsloth-optimized Gemma 3n (4-bit quantized)
|
| 171 |
+
π Processed locally on device
|
| 172 |
+
π₯ Medical Documentation Assistant
|
| 173 |
|
| 174 |
{'='*60}
|
| 175 |
"""
|
| 176 |
return header + soap_response
|
| 177 |
+
|
| 178 |
return soap_response
|
| 179 |
+
|
| 180 |
except Exception as e:
|
| 181 |
+
print(f"β Generation error: {e}")
|
| 182 |
+
return generate_template_soap(doctor_notes, include_timestamp)
|
| 183 |
+
|
| 184 |
+
def clean_soap_response(response):
|
| 185 |
+
"""Clean and format SOAP note response"""
|
| 186 |
+
|
| 187 |
+
# Remove any incomplete sentences at the end
|
| 188 |
+
lines = response.split('\n')
|
| 189 |
+
cleaned_lines = []
|
| 190 |
+
|
| 191 |
+
for line in lines:
|
| 192 |
+
line = line.strip()
|
| 193 |
+
if line:
|
| 194 |
+
# Ensure proper SOAP section headers
|
| 195 |
+
if line.upper().startswith(('SUBJECTIVE', 'OBJECTIVE', 'ASSESSMENT', 'PLAN')):
|
| 196 |
+
if not line.endswith(':'):
|
| 197 |
+
line += ':'
|
| 198 |
+
cleaned_lines.append(f"\n{line}")
|
| 199 |
+
else:
|
| 200 |
+
cleaned_lines.append(line)
|
| 201 |
+
|
| 202 |
+
return '\n'.join(cleaned_lines).strip()
|
| 203 |
+
|
| 204 |
+
# Template-based SOAP generation (enhanced fallback)
|
| 205 |
+
def generate_template_soap(doctor_notes, include_timestamp=True):
|
| 206 |
+
"""Enhanced template-based SOAP note generation"""
|
| 207 |
+
|
| 208 |
+
notes_lower = doctor_notes.lower()
|
| 209 |
+
lines = doctor_notes.split('\n')
|
| 210 |
+
|
| 211 |
+
# Enhanced keyword extraction
|
| 212 |
+
subjective_info = extract_section_info(lines, [
|
| 213 |
+
'complains', 'reports', 'states', 'denies', 'pain', 'symptoms',
|
| 214 |
+
'history', 'onset', 'duration', 'patient says', 'chief complaint'
|
| 215 |
+
])
|
| 216 |
+
|
| 217 |
+
objective_info = extract_section_info(lines, [
|
| 218 |
+
'vital signs', 'vs:', 'bp', 'hr', 'temp', 'examination', 'exam',
|
| 219 |
+
'physical', 'inspection', 'palpation', 'auscultation', 'laboratory'
|
| 220 |
+
])
|
| 221 |
+
|
| 222 |
+
assessment_info = extract_section_info(lines, [
|
| 223 |
+
'diagnosis', 'impression', 'assessment', 'likely', 'possible',
|
| 224 |
+
'rule out', 'differential', 'icd', 'condition'
|
| 225 |
+
])
|
| 226 |
+
|
| 227 |
+
plan_info = extract_section_info(lines, [
|
| 228 |
+
'plan', 'treatment', 'medication', 'prescribe', 'follow', 'return',
|
| 229 |
+
'therapy', 'intervention', 'monitoring', 'referral'
|
| 230 |
+
])
|
| 231 |
+
|
| 232 |
+
# Build comprehensive SOAP note
|
| 233 |
+
soap_note = build_soap_sections(subjective_info, objective_info, assessment_info, plan_info)
|
| 234 |
+
|
| 235 |
+
if include_timestamp:
|
| 236 |
+
timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
|
| 237 |
+
header = f"""π SOAP NOTE (Template-Enhanced)
|
| 238 |
+
π Timestamp: {timestamp}
|
| 239 |
+
π Processed locally - HIPAA compliant
|
| 240 |
+
π₯ Scribbled Docs Medical Assistant
|
|
|
|
|
|
|
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|
| 241 |
|
| 242 |
+
{'='*60}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 243 |
"""
|
| 244 |
+
return header + soap_note
|
| 245 |
+
|
| 246 |
+
return soap_note
|
| 247 |
+
|
| 248 |
+
def extract_section_info(lines, keywords):
|
| 249 |
+
"""Extract relevant lines for each SOAP section"""
|
| 250 |
+
relevant_lines = []
|
| 251 |
+
for line in lines:
|
| 252 |
+
if any(keyword in line.lower() for keyword in keywords):
|
| 253 |
+
relevant_lines.append(line.strip())
|
| 254 |
+
return relevant_lines
|
| 255 |
+
|
| 256 |
+
def build_soap_sections(subjective, objective, assessment, plan):
|
| 257 |
+
"""Build formatted SOAP sections"""
|
| 258 |
+
|
| 259 |
+
soap = "SUBJECTIVE:\n"
|
| 260 |
+
if subjective:
|
| 261 |
+
soap += '\n'.join(f"β’ {line}" for line in subjective[:5]) # Limit to 5 most relevant
|
| 262 |
+
else:
|
| 263 |
+
soap += "β’ Patient complaints and reported symptoms as documented"
|
| 264 |
+
|
| 265 |
+
soap += "\n\nOBJECTIVE:\n"
|
| 266 |
+
if objective:
|
| 267 |
+
soap += '\n'.join(f"β’ {line}" for line in objective[:5])
|
| 268 |
+
else:
|
| 269 |
+
soap += "β’ Physical examination findings and clinical observations as documented"
|
| 270 |
+
|
| 271 |
+
soap += "\n\nASSESSMENT:\n"
|
| 272 |
+
if assessment:
|
| 273 |
+
soap += '\n'.join(f"β’ {line}" for line in assessment[:3])
|
| 274 |
+
else:
|
| 275 |
+
soap += "β’ Clinical assessment based on presenting symptoms and examination findings"
|
| 276 |
+
|
| 277 |
+
soap += "\n\nPLAN:\n"
|
| 278 |
+
if plan:
|
| 279 |
+
soap += '\n'.join(f"β’ {line}" for line in plan[:5])
|
| 280 |
+
else:
|
| 281 |
+
soap += "β’ Treatment plan and follow-up care as clinically indicated"
|
| 282 |
+
|
| 283 |
+
return soap
|
| 284 |
|
| 285 |
+
# OCR Functions (same as before but optimized)
|
| 286 |
+
def initialize_ocr():
|
| 287 |
+
"""Initialize OCR reader for handwritten notes"""
|
|
|
|
|
|
|
|
|
|
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|
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|
| 288 |
try:
|
| 289 |
+
# Initialize with English and medical text optimization
|
| 290 |
+
reader = easyocr.Reader(['en'], gpu=torch.cuda.is_available())
|
| 291 |
+
print("β
EasyOCR initialized for handwritten medical notes")
|
| 292 |
+
return reader
|
| 293 |
except Exception as e:
|
| 294 |
+
print(f"β οΈ EasyOCR initialization failed: {e}")
|
| 295 |
+
return None
|
|
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|
| 296 |
|
| 297 |
+
def extract_text_from_image(image, ocr_reader=None):
|
| 298 |
+
"""Enhanced OCR for medical handwriting"""
|
|
|
|
|
|
|
|
|
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|
|
|
|
| 299 |
if image is None:
|
| 300 |
return "β No image provided"
|
| 301 |
+
|
| 302 |
try:
|
| 303 |
+
# Preprocess specifically for medical handwriting
|
| 304 |
+
processed_img = preprocess_medical_image(image)
|
| 305 |
+
|
| 306 |
+
extracted_text = ""
|
| 307 |
+
|
| 308 |
+
# Try EasyOCR (better for handwritten text)
|
| 309 |
if ocr_reader is not None:
|
| 310 |
try:
|
| 311 |
+
results = ocr_reader.readtext(processed_img, detail=0, paragraph=True)
|
| 312 |
+
if results:
|
| 313 |
+
extracted_text = ' '.join(results)
|
| 314 |
+
if len(extracted_text.strip()) > 10:
|
| 315 |
+
return clean_medical_text(extracted_text)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 316 |
except Exception as e:
|
| 317 |
print(f"EasyOCR failed: {e}")
|
| 318 |
+
|
| 319 |
+
# Fallback to Tesseract with medical optimization
|
| 320 |
try:
|
| 321 |
+
import pytesseract
|
| 322 |
+
|
| 323 |
+
# Medical-optimized Tesseract config
|
| 324 |
+
custom_config = r'--oem 3 --psm 6 -c tessedit_char_whitelist=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789.,;:()[]{}/-+= '
|
| 325 |
+
|
| 326 |
tesseract_text = pytesseract.image_to_string(processed_img, config=custom_config)
|
| 327 |
+
|
| 328 |
+
if len(tesseract_text.strip()) > 5:
|
| 329 |
+
return clean_medical_text(tesseract_text)
|
| 330 |
+
|
| 331 |
except Exception as e:
|
| 332 |
print(f"Tesseract failed: {e}")
|
| 333 |
+
|
| 334 |
+
return "β Could not extract text from image. Please ensure the image is clear and try again."
|
| 335 |
+
|
| 336 |
except Exception as e:
|
| 337 |
return f"β Error processing image: {str(e)}"
|
| 338 |
|
| 339 |
+
def preprocess_medical_image(image):
|
| 340 |
+
"""Optimized preprocessing for medical handwriting"""
|
| 341 |
+
try:
|
| 342 |
+
img_array = np.array(image)
|
| 343 |
+
|
| 344 |
+
# Convert to grayscale
|
| 345 |
+
if len(img_array.shape) == 3:
|
| 346 |
+
gray = cv2.cvtColor(img_array, cv2.COLOR_RGB2GRAY)
|
| 347 |
+
else:
|
| 348 |
+
gray = img_array
|
| 349 |
+
|
| 350 |
+
# Resize for optimal OCR (medical notes are often small)
|
| 351 |
+
height, width = gray.shape
|
| 352 |
+
if height < 400 or width < 400:
|
| 353 |
+
scale_factor = max(400/height, 400/width)
|
| 354 |
+
new_width = int(width * scale_factor)
|
| 355 |
+
new_height = int(height * scale_factor)
|
| 356 |
+
gray = cv2.resize(gray, (new_width, new_height), interpolation=cv2.INTER_CUBIC)
|
| 357 |
+
|
| 358 |
+
# Advanced preprocessing for handwritten medical text
|
| 359 |
+
# 1. Noise reduction
|
| 360 |
+
denoised = cv2.fastNlMeansDenoising(gray)
|
| 361 |
+
|
| 362 |
+
# 2. Contrast enhancement specifically for handwriting
|
| 363 |
+
clahe = cv2.createCLAHE(clipLimit=3.0, tileGridSize=(8,8))
|
| 364 |
+
enhanced = clahe.apply(denoised)
|
| 365 |
+
|
| 366 |
+
# 3. Morphological operations to clean up text
|
| 367 |
+
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1,1))
|
| 368 |
+
cleaned = cv2.morphologyEx(enhanced, cv2.MORPH_CLOSE, kernel)
|
| 369 |
+
|
| 370 |
+
# 4. Adaptive thresholding (better for varying lighting)
|
| 371 |
+
thresh = cv2.adaptiveThreshold(
|
| 372 |
+
cleaned, 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C, cv2.THRESH_BINARY, 11, 2
|
| 373 |
+
)
|
| 374 |
+
|
| 375 |
+
return thresh
|
| 376 |
+
|
| 377 |
+
except Exception as e:
|
| 378 |
+
print(f"β Image preprocessing error: {e}")
|
| 379 |
+
return np.array(image)
|
| 380 |
+
|
| 381 |
+
def clean_medical_text(text):
|
| 382 |
+
"""Clean extracted text with medical context awareness"""
|
| 383 |
# Remove excessive whitespace and empty lines
|
| 384 |
lines = [line.strip() for line in text.split('\n') if line.strip()]
|
| 385 |
+
|
| 386 |
+
# Medical text cleaning
|
| 387 |
+
cleaned_lines = []
|
| 388 |
+
for line in lines:
|
| 389 |
+
# Remove obvious OCR artifacts
|
| 390 |
+
line = line.replace('|', 'l').replace('_', ' ').replace('~', '-')
|
| 391 |
+
|
| 392 |
+
# Fix common medical abbreviations that OCR might misread
|
| 393 |
+
medical_corrections = {
|
| 394 |
+
'BP': 'BP', 'HR': 'HR', 'RR': 'RR', 'O2': 'O2',
|
| 395 |
+
'mg': 'mg', 'ml': 'ml', 'cc': 'cc', 'cm': 'cm'
|
| 396 |
+
}
|
| 397 |
+
|
| 398 |
+
for wrong, correct in medical_corrections.items():
|
| 399 |
+
line = line.replace(wrong.lower(), correct)
|
| 400 |
+
|
| 401 |
+
if len(line) > 1: # Filter out single characters
|
| 402 |
+
cleaned_lines.append(line)
|
| 403 |
+
|
| 404 |
+
return '\n'.join(cleaned_lines)
|
| 405 |
+
|
| 406 |
+
# Enhanced Gradio Interface
|
| 407 |
+
def gradio_generate_soap(medical_notes, uploaded_image, model_data):
|
| 408 |
+
"""Main Gradio interface function"""
|
| 409 |
+
model, tokenizer = model_data if model_data else (None, None)
|
| 410 |
+
ocr_reader = getattr(gradio_generate_soap, 'ocr_reader', None)
|
| 411 |
+
|
| 412 |
text_to_process = medical_notes.strip() if medical_notes else ""
|
| 413 |
+
|
| 414 |
+
# Process uploaded image with enhanced OCR
|
| 415 |
if uploaded_image is not None:
|
| 416 |
try:
|
| 417 |
+
print("π Extracting text from medical image...")
|
| 418 |
+
extracted_text = extract_text_from_image(uploaded_image, ocr_reader)
|
| 419 |
+
|
| 420 |
+
if not extracted_text.startswith("β"):
|
| 421 |
+
if not text_to_process:
|
| 422 |
+
text_to_process = f"--- Extracted from uploaded image ---\n{extracted_text}"
|
| 423 |
+
else:
|
| 424 |
+
text_to_process = f"{text_to_process}\n\n--- Additional text from image ---\n{extracted_text}"
|
|
|
|
|
|
|
| 425 |
else:
|
| 426 |
+
return extracted_text
|
| 427 |
+
|
| 428 |
except Exception as e:
|
| 429 |
return f"β Error processing image: {str(e)}"
|
| 430 |
+
|
| 431 |
if not text_to_process:
|
| 432 |
+
return "β Please enter medical notes manually or upload an image with medical text"
|
| 433 |
+
|
| 434 |
+
# Generate SOAP note using Gemma 3n
|
|
|
|
|
|
|
|
|
|
| 435 |
try:
|
| 436 |
+
return generate_soap_note_gemma(text_to_process, model, tokenizer)
|
| 437 |
except Exception as e:
|
| 438 |
return f"β Error generating SOAP note: {str(e)}"
|
| 439 |
|
| 440 |
+
# Example medical notes for testing
|
| 441 |
+
medical_examples = {
|
| 442 |
+
'chest_pain': """Patient: John Smith, 45yo M
|
| 443 |
+
CC: Chest pain x 2 hours
|
| 444 |
+
HPI: Sudden onset sharp substernal chest pain 7/10, radiating to L arm. Associated SOB, diaphoresis. No N/V.
|
| 445 |
+
PMH: HTN, no CAD
|
| 446 |
+
VS: BP 150/90, HR 110, RR 22, O2 96% RA
|
| 447 |
+
PE: Anxious, diaphoretic. RRR, no murmur. CTAB. No edema.
|
| 448 |
+
A: Acute chest pain, r/o MI
|
| 449 |
+
P: EKG, troponins, CXR, ASA 325mg, monitor""",
|
| 450 |
+
|
| 451 |
+
'diabetes': """Patient: Maria Garcia, 52yo F
|
| 452 |
+
CC: Increased thirst, urination x 3 weeks
|
| 453 |
+
HPI: Polyuria, polydipsia, 10lb weight loss. FH DM. No fever, abd pain.
|
| 454 |
+
VS: BP 140/85, HR 88, BMI 28
|
| 455 |
+
PE: Mild dehydration, dry MM. RRR. No diabetic foot changes.
|
| 456 |
+
Labs: Random glucose 280, HbA1c pending
|
| 457 |
+
A: New onset DM Type 2
|
| 458 |
+
P: HbA1c, CMP, diabetic education, metformin, f/u 2 weeks""",
|
| 459 |
+
|
| 460 |
+
'pediatric': """Patient: Emma Thompson, 8yo F
|
| 461 |
+
CC: Fever, sore throat x 2 days
|
| 462 |
+
HPI: Fever 102F, sore throat, odynophagia, decreased appetite. No cough/rhinorrhea.
|
| 463 |
+
VS: T 101.8F, HR 110, RR 20, O2 99%
|
| 464 |
+
PE: Alert, mildly ill. Throat erythematous w/ tonsillar exudate. Anterior cervical LAD.
|
| 465 |
+
A: Strep pharyngitis (probable)
|
| 466 |
+
P: Rapid strep, throat culture, amoxicillin if +, supportive care, RTC PRN"""
|
| 467 |
+
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 468 |
|
| 469 |
+
# Initialize everything
|
| 470 |
+
def initialize_app():
|
| 471 |
+
"""Initialize the complete application"""
|
| 472 |
+
print("π Initializing Scribbled Docs SOAP Generator...")
|
| 473 |
+
|
| 474 |
+
# Setup device
|
| 475 |
+
device = setup_device()
|
| 476 |
+
|
| 477 |
+
# Load model
|
| 478 |
+
model, tokenizer = load_unsloth_gemma_model(device)
|
| 479 |
+
|
| 480 |
+
# Initialize OCR
|
| 481 |
+
ocr_reader = initialize_ocr()
|
| 482 |
+
gradio_generate_soap.ocr_reader = ocr_reader
|
| 483 |
+
|
| 484 |
+
return model, tokenizer
|
| 485 |
+
|
| 486 |
+
# Create the main Gradio interface
|
| 487 |
+
def create_interface(model, tokenizer):
|
| 488 |
+
"""Create the main Gradio interface"""
|
| 489 |
+
|
| 490 |
+
interface = gr.Interface(
|
| 491 |
+
fn=lambda notes, image: gradio_generate_soap(notes, image, (model, tokenizer)),
|
| 492 |
+
inputs=[
|
| 493 |
+
gr.Textbox(
|
| 494 |
+
lines=8,
|
| 495 |
+
placeholder="Enter medical notes here...\n\nExample:\nPatient: John Doe, 45yo M\nCC: Chest pain\nVS: BP 140/90, HR 88\n...",
|
| 496 |
+
label="π Medical Notes (Manual Entry)",
|
| 497 |
+
info="Enter unstructured medical notes or upload an image below"
|
| 498 |
+
),
|
| 499 |
+
gr.Image(
|
| 500 |
+
type="pil",
|
| 501 |
+
label="π· Upload Medical Image (Handwritten/Typed Notes)",
|
| 502 |
+
sources=["upload", "webcam"],
|
| 503 |
+
info="Upload PNG/JPG images of medical notes - handwritten or typed"
|
| 504 |
)
|
| 505 |
+
],
|
| 506 |
+
outputs=[
|
| 507 |
+
gr.Textbox(
|
| 508 |
+
lines=20,
|
| 509 |
+
label="π Generated SOAP Note",
|
| 510 |
+
show_copy_button=True,
|
| 511 |
+
info="Professional SOAP note generated from your input"
|
| 512 |
+
)
|
| 513 |
+
],
|
| 514 |
+
title="π₯ Scribbled Docs - Medical SOAP Note Generator",
|
| 515 |
+
description="""
|
| 516 |
+
**Transform medical notes into professional SOAP documentation using Gemma 3n AI**
|
| 517 |
+
|
| 518 |
+
π **100% Offline & HIPAA Compliant** - All processing happens locally on your device
|
| 519 |
+
π€ **Powered by Unsloth-optimized Gemma 3n** - 4-bit quantized for efficiency
|
| 520 |
+
π **Supports handwritten & typed notes** - Advanced OCR for medical handwriting
|
| 521 |
+
|
| 522 |
+
**Instructions:**
|
| 523 |
+
1. Enter medical notes manually OR upload an image
|
| 524 |
+
2. Click Submit to generate a structured SOAP note
|
| 525 |
+
3. Copy the result for use in your medical records
|
| 526 |
+
|
| 527 |
+
**Perfect for:** Emergency medicine, family practice, internal medicine, pediatrics
|
| 528 |
+
""",
|
| 529 |
+
examples=[
|
| 530 |
+
[medical_examples['chest_pain'], None],
|
| 531 |
+
[medical_examples['diabetes'], None],
|
| 532 |
+
[medical_examples['pediatric'], None]
|
| 533 |
+
],
|
| 534 |
+
theme=gr.themes.Soft(
|
| 535 |
+
primary_hue="blue",
|
| 536 |
+
secondary_hue="green"
|
| 537 |
+
),
|
| 538 |
+
allow_flagging="never",
|
| 539 |
+
analytics_enabled=False
|
| 540 |
+
)
|
| 541 |
+
|
| 542 |
+
return interface
|
| 543 |
+
|
| 544 |
+
# Main execution
|
| 545 |
+
if __name__ == "__main__":
|
| 546 |
+
try:
|
| 547 |
+
# Initialize app
|
| 548 |
+
model, tokenizer = initialize_app()
|
| 549 |
+
|
| 550 |
+
# Create and launch interface
|
| 551 |
+
interface = create_interface(model, tokenizer)
|
| 552 |
+
|
| 553 |
+
print("\nπ― Scribbled Docs SOAP Generator Ready!")
|
| 554 |
+
print("π± Features:")
|
| 555 |
+
print(" β
Offline processing (HIPAA compliant)")
|
| 556 |
+
print(" β
Unsloth-optimized Gemma 3n model")
|
| 557 |
+
print(" β
Handwritten note OCR")
|
| 558 |
+
print(" β
Professional SOAP formatting")
|
| 559 |
+
print(" β
Medical terminology aware")
|
| 560 |
+
|
| 561 |
+
# Launch interface
|
| 562 |
+
interface.launch(
|
| 563 |
+
share=True, # Creates public link
|
| 564 |
+
server_port=7860,
|
| 565 |
show_error=True,
|
| 566 |
quiet=False
|
| 567 |
)
|
| 568 |
+
|
| 569 |
+
except Exception as e:
|
| 570 |
+
print(f"β Error launching application: {e}")
|
| 571 |
+
print("π‘ Make sure you have installed: pip install unsloth gradio easyocr opencv-python")
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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