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README.md
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---
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title: Scribbled Docs Notes
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emoji: π¨
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colorFrom: pink
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colorTo: yellow
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sdk: gradio
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sdk_version: 5.36.2
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app_file: app.py
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pinned: false
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license: mit
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short_description: An app to convert doc notes to SOAP
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---
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Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
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app.py
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# -*- coding: utf-8 -*-
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"""gemma_3n_colab.ipynb
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Automatically generated by Colab.
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Original file is located at
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https://colab.research.google.com/drive/1U5pbaYG8qD7HFANwU7PI1jbLGOPvArnP
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# π₯ Gemma 3N SOAP Note Generator
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## Interactive Medical Documentation Assistant
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This notebook provides a complete interface for generating SOAP notes from medical text using the Gemma 3N model.
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"""
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# Install required packages
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!pip install -q transformers torch torchvision torchaudio timm accelerate
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!pip install -q ipywidgets gradio
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!pip install -q --upgrade huggingface_hub
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!pip install GPUtil
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# Enable widgets
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from IPython.display import display, HTML
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display(HTML("<script src='https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js'></script>"))
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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 getpass
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# Authenticate with HuggingFace
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print("π HuggingFace Authentication Required")
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print("Please enter your HuggingFace token (it will be hidden):")
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hf_token = getpass.getpass("HF Token: ")
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try:
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login(token=hf_token)
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print("β
Successfully authenticated with HuggingFace!")
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except Exception as e:
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print(f"β Authentication failed: {e}")
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print("Please check your token and try again.")
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# Check GPU availability
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device = "cuda" if torch.cuda.is_available() else "cpu"
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print(f"π₯οΈ Using device: {device}")
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if torch.cuda.is_available():
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print(f"π GPU: {torch.cuda.get_device_name(0)}")
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print(f"πΎ GPU Memory: {torch.cuda.get_device_properties(0).total_memory / 1e9:.1f} GB")
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else:
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print("β οΈ Running on CPU - this will be slower")
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# Load Gemma 3N model
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print("π‘ Loading Gemma 3N model...")
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model_id = "google/gemma-3n-e2b-it"
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print("π§ Loading processor...")
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processor = AutoProcessor.from_pretrained(model_id)
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print("π€ Loading Gemma 3N model (this may take a few minutes)...")
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model = AutoModelForImageTextToText.from_pretrained(
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model_id,
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torch_dtype=torch.float16 if device == "cuda" else torch.float32,
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low_cpu_mem_usage=True,
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).to(device)
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print("β
Gemma 3N model loaded successfully!")
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print(f"π Model size: ~2.9GB")
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print(f"π― Ready for SOAP note generation!")
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# SOAP Note Generation Function
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def generate_soap_note(doctor_notes, include_timestamp=True):
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"""
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Generate a SOAP note from unstructured doctor's notes
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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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prompt = f"""You are a medical AI assistant. Convert the following unstructured doctor's notes into a professional SOAP note format.
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Doctor's Notes:
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{doctor_notes}
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Please generate a structured SOAP note with the following sections:
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- SUBJECTIVE: Patient's reported symptoms and history
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- OBJECTIVE: Physical examination findings, vital signs, and test results
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- ASSESSMENT: Clinical diagnosis and reasoning
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- PLAN: Treatment plan, medications, and follow-up
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Format your response as a proper medical SOAP note with specific details extracted from the notes."""
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try:
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# Process input
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inputs = processor(text=prompt, return_tensors="pt").to(device)
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# Generate response
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print("π Generating SOAP note with Gemma 3N...")
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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=512,
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temperature=0.3, # Lower temperature for medical precision
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do_sample=True,
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pad_token_id=processor.tokenizer.eos_token_id
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)
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# Decode response
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generated_text = processor.decode(outputs[0], skip_special_tokens=True)
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# Extract only the generated part (remove the prompt)
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soap_response = generated_text[len(prompt):].strip()
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# Add header if requested
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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 3N
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π Timestamp: {timestamp}
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π€ Model: google/gemma-3n-e2b-it
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π Processed locally on device: {device.upper()}
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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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return f"β Error generating SOAP note: {str(e)}"
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print("β
SOAP generation function ready!")
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"""## π Interactive SOAP Note Generator
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### Enter medical notes below and generate professional SOAP documentation
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"""
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# Create interactive widgets
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print("π¨ Creating interactive interface...")
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# Text input area
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notes_input = widgets.Textarea(
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value='',
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placeholder='Enter unstructured doctor notes here...\n\nExample:\nPatient John Smith, 45yo male, came in complaining of chest pain for 2 days. Pain is sharp, 7/10 intensity, worse with movement. Vital signs: BP 140/90, HR 88, Temp 98.6F...',
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description='Medical Notes:',
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layout=widgets.Layout(width='100%', height='200px')
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)
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# File upload widget
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153 |
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file_upload = widgets.FileUpload(
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accept='.txt,.doc,.docx,.pdf',
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multiple=False,
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description='Or upload file:',
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layout=widgets.Layout(width='300px')
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)
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# Generate button
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161 |
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generate_btn = widgets.Button(
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description='π€ Generate SOAP Note',
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button_style='primary',
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layout=widgets.Layout(width='200px', height='40px')
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)
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+
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# Output area
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168 |
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output_area = widgets.HTML(
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value='<p style="color: #666;">π Ready to generate SOAP notes! Enter medical notes above or upload a file.</p>',
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layout=widgets.Layout(width='100%', height='400px', overflow='auto', border='1px solid #ddd', padding='10px')
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)
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+
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# Example buttons
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174 |
+
example1_btn = widgets.Button(description='π Chest Pain Example', button_style='info', layout=widgets.Layout(width='180px'))
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175 |
+
example2_btn = widgets.Button(description='π©Ί Diabetes Follow-up', button_style='info', layout=widgets.Layout(width='180px'))
|
176 |
+
example3_btn = widgets.Button(description='πΆ Pediatric Visit', button_style='info', layout=widgets.Layout(width='180px'))
|
177 |
+
|
178 |
+
# Clear button
|
179 |
+
clear_btn = widgets.Button(description='ποΈ Clear', button_style='warning', layout=widgets.Layout(width='100px'))
|
180 |
+
|
181 |
+
print("β
Interface widgets created!")
|
182 |
+
|
183 |
+
# Example medical notes
|
184 |
+
examples = {
|
185 |
+
'chest_pain': """Patient John Smith, 45yo male, came in complaining of chest pain for 2 days. Pain is sharp, 7/10 intensity, worse with movement. No radiation to arms. Vital signs: BP 140/90, HR 88, Temp 98.6F, RR 16, O2 sat 98%. Physical exam shows tenderness over left chest wall, no murmurs. EKG normal sinus rhythm. Chest X-ray clear. Diagnosed with costochondritis. Prescribed ibuprofen 600mg TID and advised rest. Follow up in 1 week if symptoms persist.""",
|
186 |
+
|
187 |
+
'diabetes': """Sarah Johnson, 62yo female with Type 2 diabetes, here for routine follow-up. Says blood sugars have been running high lately, 180-220 mg/dL. Taking metformin 1000mg BID. Diet has been poor due to holiday stress. Weight increased 5 lbs since last visit. BP 150/85, BMI 32. HbA1c 8.2% (was 7.1% 3 months ago). Feet exam normal, no neuropathy. Plan to increase metformin to 1000mg TID, refer to nutritionist, recheck labs in 3 months.""",
|
188 |
+
|
189 |
+
'pediatric': """Tommy Rodriguez, 8yo male, brought by mother for fever and cough x3 days. Fever up to 102F, productive cough with yellow sputum. Decreased appetite, no vomiting or diarrhea. Vital signs: Temp 101.2F, HR 110, RR 24, BP 95/60. Exam shows bilateral crackles in lower lobes, no wheeze. Throat clear. Diagnosed with bacterial pneumonia. Prescribed amoxicillin 500mg BID x10 days. Return if fever persists >48 hours on antibiotics."""
|
190 |
+
}
|
191 |
+
|
192 |
+
# Event handlers
|
193 |
+
def on_generate_click(b):
|
194 |
+
with output_area:
|
195 |
+
output_area.value = '<p style="color: #007bff;">π Processing with Gemma 3N... Please wait...</p>'
|
196 |
+
|
197 |
+
# Get text from input or uploaded file
|
198 |
+
text_to_process = notes_input.value
|
199 |
+
|
200 |
+
# Check if file was uploaded
|
201 |
+
if file_upload.value and len(file_upload.value) > 0:
|
202 |
+
try:
|
203 |
+
uploaded_file = list(file_upload.value.values())[0]
|
204 |
+
file_content = uploaded_file['content'].decode('utf-8')
|
205 |
+
text_to_process = file_content
|
206 |
+
notes_input.value = file_content # Show in text area
|
207 |
+
except Exception as e:
|
208 |
+
output_area.value = f'<p style="color: #dc3545;">β Error reading file: {str(e)}</p>'
|
209 |
+
return
|
210 |
+
|
211 |
+
if not text_to_process.strip():
|
212 |
+
output_area.value = '<p style="color: #dc3545;">β Please enter medical notes or upload a file!</p>'
|
213 |
+
return
|
214 |
+
|
215 |
+
# Generate SOAP note
|
216 |
+
soap_note = generate_soap_note(text_to_process)
|
217 |
+
|
218 |
+
# Format output as HTML
|
219 |
+
formatted_output = f'<pre style="font-family: monospace; font-size: 12px; line-height: 1.4; white-space: pre-wrap;">{soap_note}</pre>'
|
220 |
+
output_area.value = formatted_output
|
221 |
+
|
222 |
+
def on_example1_click(b):
|
223 |
+
notes_input.value = examples['chest_pain']
|
224 |
+
output_area.value = '<p style="color: #28a745;">β
Chest pain example loaded! Click "Generate SOAP Note" to process.</p>'
|
225 |
+
|
226 |
+
def on_example2_click(b):
|
227 |
+
notes_input.value = examples['diabetes']
|
228 |
+
output_area.value = '<p style="color: #28a745;">β
Diabetes follow-up example loaded! Click "Generate SOAP Note" to process.</p>'
|
229 |
+
|
230 |
+
def on_example3_click(b):
|
231 |
+
notes_input.value = examples['pediatric']
|
232 |
+
output_area.value = '<p style="color: #28a745;">β
Pediatric example loaded! Click "Generate SOAP Note" to process.</p>'
|
233 |
+
|
234 |
+
def on_clear_click(b):
|
235 |
+
notes_input.value = ''
|
236 |
+
file_upload.value = ()
|
237 |
+
output_area.value = '<p style="color: #666;">π Ready to generate SOAP notes! Enter medical notes above or upload a file.</p>'
|
238 |
+
|
239 |
+
# Bind event handlers
|
240 |
+
generate_btn.on_click(on_generate_click)
|
241 |
+
example1_btn.on_click(on_example1_click)
|
242 |
+
example2_btn.on_click(on_example2_click)
|
243 |
+
example3_btn.on_click(on_example3_click)
|
244 |
+
clear_btn.on_click(on_clear_click)
|
245 |
+
|
246 |
+
print("β
Event handlers configured!")
|
247 |
+
|
248 |
+
# Define example medical notes first
|
249 |
+
example_notes_1 = """
|
250 |
+
Patient: John Smith, 45-year-old male
|
251 |
+
Chief Complaint: Chest pain for 2 hours
|
252 |
+
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.
|
253 |
+
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.
|
254 |
+
Assessment: Acute chest pain, rule out myocardial infarction
|
255 |
+
Plan: EKG, cardiac enzymes, chest X-ray, aspirin 325mg, continuous cardiac monitoring
|
256 |
+
"""
|
257 |
+
|
258 |
+
example_notes_2 = """
|
259 |
+
Patient: Sarah Johnson, 28-year-old female
|
260 |
+
Chief Complaint: Severe headache and fever
|
261 |
+
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.
|
262 |
+
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.
|
263 |
+
Assessment: Suspected meningitis
|
264 |
+
Plan: Lumbar puncture, blood cultures, empiric antibiotics, supportive care
|
265 |
+
"""
|
266 |
+
|
267 |
+
example_notes_3 = """
|
268 |
+
Patient: Robert Davis, 62-year-old male
|
269 |
+
Chief Complaint: Shortness of breath and leg swelling
|
270 |
+
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.
|
271 |
+
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.
|
272 |
+
Assessment: Congestive heart failure exacerbation
|
273 |
+
Plan: Chest X-ray, BNP, echocardiogram, furosemide, ACE inhibitor, daily weights
|
274 |
+
"""
|
275 |
+
|
276 |
+
# Event handlers
|
277 |
+
def on_generate_click(b):
|
278 |
+
try:
|
279 |
+
# Update the HTML widget directly
|
280 |
+
output_area.value = '<p style="color: #007bff;">π Processing with Gemma 3N... Please wait...</p>'
|
281 |
+
|
282 |
+
# Get input text
|
283 |
+
input_text = notes_input.value.strip()
|
284 |
+
|
285 |
+
# Check if file was uploaded
|
286 |
+
if file_upload.value:
|
287 |
+
try:
|
288 |
+
# Process uploaded file
|
289 |
+
uploaded_file = list(file_upload.value.values())[0]
|
290 |
+
file_content = uploaded_file['content'].decode('utf-8')
|
291 |
+
input_text = file_content
|
292 |
+
except Exception as upload_error:
|
293 |
+
output_area.value = f'<p style="color: #ff6b6b;">β File upload error: {str(upload_error)}</p>'
|
294 |
+
return
|
295 |
+
|
296 |
+
if not input_text:
|
297 |
+
output_area.value = '<p style="color: #ff6b6b;">β οΈ Please enter medical notes or upload a file first!</p>'
|
298 |
+
return
|
299 |
+
|
300 |
+
# Check if generate_soap_note function exists
|
301 |
+
if 'generate_soap_note' not in globals():
|
302 |
+
output_area.value = '<p style="color: #ff6b6b;">β Error: generate_soap_note function not found. Please define it first.</p>'
|
303 |
+
return
|
304 |
+
|
305 |
+
# Generate SOAP note using Gemma
|
306 |
+
soap_note = generate_soap_note(input_text)
|
307 |
+
|
308 |
+
# Escape HTML in soap_note to prevent rendering issues
|
309 |
+
import html
|
310 |
+
escaped_soap_note = html.escape(soap_note)
|
311 |
+
|
312 |
+
# Display result
|
313 |
+
output_area.value = f'''
|
314 |
+
<div style="background: #f8f9fa; padding: 15px; border-radius: 8px; border-left: 4px solid #28a745;">
|
315 |
+
<h4 style="color: #28a745; margin-top: 0;">β
Generated SOAP Note:</h4>
|
316 |
+
<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>
|
317 |
+
</div>
|
318 |
+
'''
|
319 |
+
|
320 |
+
except Exception as e:
|
321 |
+
import traceback
|
322 |
+
error_details = traceback.format_exc()
|
323 |
+
output_area.value = f'''
|
324 |
+
<div style="color: #ff6b6b; background: #ffe6e6; padding: 15px; border-radius: 5px;">
|
325 |
+
<h4>β Error Details:</h4>
|
326 |
+
<p><strong>Error:</strong> {str(e)}</p>
|
327 |
+
<details>
|
328 |
+
<summary>Click for full traceback</summary>
|
329 |
+
<pre style="font-size: 12px; background: #fff; padding: 10px; border-radius: 3px; margin-top: 10px;">{error_details}</pre>
|
330 |
+
</details>
|
331 |
+
</div>
|
332 |
+
'''
|
333 |
+
|
334 |
+
def on_clear_click(b):
|
335 |
+
try:
|
336 |
+
notes_input.value = ""
|
337 |
+
file_upload.value = ()
|
338 |
+
output_area.value = '<p>π Ready to generate SOAP notes! Enter medical notes above or upload a file.</p>'
|
339 |
+
except Exception as e:
|
340 |
+
output_area.value = f'<p style="color: #ff6b6b;">β Clear error: {str(e)}</p>'
|
341 |
+
|
342 |
+
def on_example_click(example_text):
|
343 |
+
def handler(b):
|
344 |
+
try:
|
345 |
+
notes_input.value = example_text
|
346 |
+
output_area.value = '<p style="color: #28a745;">π Example loaded! Click "Generate SOAP Note" to process.</p>'
|
347 |
+
except Exception as e:
|
348 |
+
output_area.value = f'<p style="color: #ff6b6b;">β Example load error: {str(e)}</p>'
|
349 |
+
return handler
|
350 |
+
|
351 |
+
# Connect event handlers to buttons
|
352 |
+
try:
|
353 |
+
generate_btn.on_click(on_generate_click)
|
354 |
+
clear_btn.on_click(on_clear_click)
|
355 |
+
example1_btn.on_click(on_example_click(example_notes_1))
|
356 |
+
example2_btn.on_click(on_example_click(example_notes_2))
|
357 |
+
example3_btn.on_click(on_example_click(example_notes_3))
|
358 |
+
|
359 |
+
print("β
Event handlers connected successfully!")
|
360 |
+
print("π Example notes loaded:")
|
361 |
+
print(" - Example 1: Chest pain case")
|
362 |
+
print(" - Example 2: Suspected meningitis")
|
363 |
+
print(" - Example 3: Heart failure")
|
364 |
+
|
365 |
+
except Exception as e:
|
366 |
+
print(f"β Error connecting event handlers: {str(e)}")
|
367 |
+
import traceback
|
368 |
+
traceback.print_exc()
|
369 |
+
|
370 |
+
"""## π Alternative: Gradio Web Interface
|
371 |
+
### Run this cell for a shareable web interface
|
372 |
+
"""
|
373 |
+
|
374 |
+
# Install required packages for image processing and OCR
|
375 |
+
!pip install -q pytesseract opencv-python pillow easyocr
|
376 |
+
!apt-get install -q tesseract-ocr
|
377 |
+
|
378 |
+
import gradio as gr
|
379 |
+
import torch
|
380 |
+
from PIL import Image
|
381 |
+
import pytesseract
|
382 |
+
import cv2
|
383 |
+
import numpy as np
|
384 |
+
import easyocr
|
385 |
+
import io
|
386 |
+
|
387 |
+
# First, make sure you have the examples dictionary defined
|
388 |
+
examples = {
|
389 |
+
'chest_pain': """Patient: John Smith, 45-year-old male
|
390 |
+
Chief Complaint: Chest pain for 2 hours
|
391 |
+
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.
|
392 |
+
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.
|
393 |
+
Assessment: Acute chest pain, rule out myocardial infarction
|
394 |
+
Plan: EKG, cardiac enzymes, chest X-ray, aspirin 325mg, continuous cardiac monitoring""",
|
395 |
+
|
396 |
+
'diabetes': """Patient: Maria Garcia, 52-year-old female
|
397 |
+
Chief Complaint: Increased thirst and frequent urination for 3 weeks
|
398 |
+
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.
|
399 |
+
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.
|
400 |
+
Assessment: New onset diabetes mellitus, likely Type 2
|
401 |
+
Plan: HbA1c, fasting glucose, comprehensive metabolic panel, diabetic education, metformin initiation""",
|
402 |
+
|
403 |
+
'pediatric': """Patient: Emma Thompson, 8-year-old female
|
404 |
+
Chief Complaint: Fever and sore throat for 2 days
|
405 |
+
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.
|
406 |
+
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.
|
407 |
+
Assessment: Streptococcal pharyngitis (probable)
|
408 |
+
Plan: Rapid strep test, throat culture, amoxicillin if positive, supportive care, return if worsening"""
|
409 |
+
}
|
410 |
+
|
411 |
+
# Initialize EasyOCR reader (better for handwritten text)
|
412 |
+
try:
|
413 |
+
ocr_reader = easyocr.Reader(['en'])
|
414 |
+
print("β
EasyOCR initialized successfully")
|
415 |
+
except:
|
416 |
+
ocr_reader = None
|
417 |
+
print("β οΈ EasyOCR not available, using Tesseract only")
|
418 |
+
|
419 |
+
def preprocess_image_for_ocr(image):
|
420 |
+
"""
|
421 |
+
Preprocess image to improve OCR accuracy
|
422 |
+
"""
|
423 |
+
# Convert PIL Image to numpy array
|
424 |
+
img_array = np.array(image)
|
425 |
+
|
426 |
+
# Convert to grayscale if needed
|
427 |
+
if len(img_array.shape) == 3:
|
428 |
+
gray = cv2.cvtColor(img_array, cv2.COLOR_RGB2GRAY)
|
429 |
+
else:
|
430 |
+
gray = img_array
|
431 |
+
|
432 |
+
# Apply image preprocessing for better OCR
|
433 |
+
# 1. Resize image if too small
|
434 |
+
height, width = gray.shape
|
435 |
+
if height < 300 or width < 300:
|
436 |
+
scale_factor = max(300/height, 300/width)
|
437 |
+
new_width = int(width * scale_factor)
|
438 |
+
new_height = int(height * scale_factor)
|
439 |
+
gray = cv2.resize(gray, (new_width, new_height), interpolation=cv2.INTER_CUBIC)
|
440 |
+
|
441 |
+
# 2. Noise removal
|
442 |
+
denoised = cv2.medianBlur(gray, 3)
|
443 |
+
|
444 |
+
# 3. Contrast enhancement
|
445 |
+
clahe = cv2.createCLAHE(clipLimit=2.0, tileGridSize=(8,8))
|
446 |
+
enhanced = clahe.apply(denoised)
|
447 |
+
|
448 |
+
# 4. Thresholding
|
449 |
+
_, thresh = cv2.threshold(enhanced, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)
|
450 |
+
|
451 |
+
return thresh
|
452 |
+
|
453 |
+
def extract_text_from_image(image):
|
454 |
+
"""
|
455 |
+
Extract text from image using multiple OCR methods
|
456 |
+
"""
|
457 |
+
if image is None:
|
458 |
+
return "β No image provided"
|
459 |
+
|
460 |
+
try:
|
461 |
+
# Preprocess image
|
462 |
+
processed_img = preprocess_image_for_ocr(image)
|
463 |
+
|
464 |
+
# Method 1: Try EasyOCR (better for handwritten text)
|
465 |
+
if ocr_reader is not None:
|
466 |
+
try:
|
467 |
+
# Convert back to PIL Image for EasyOCR
|
468 |
+
pil_img = Image.fromarray(processed_img)
|
469 |
+
results = ocr_reader.readtext(np.array(pil_img))
|
470 |
+
|
471 |
+
# Extract text from EasyOCR results
|
472 |
+
easyocr_text = ' '.join([result[1] for result in results])
|
473 |
+
|
474 |
+
if len(easyocr_text.strip()) > 20: # If we got good results
|
475 |
+
return clean_extracted_text(easyocr_text)
|
476 |
+
|
477 |
+
except Exception as e:
|
478 |
+
print(f"EasyOCR failed: {e}")
|
479 |
+
|
480 |
+
# Method 2: Tesseract OCR (fallback)
|
481 |
+
try:
|
482 |
+
# Configure Tesseract for medical text
|
483 |
+
custom_config = r'--oem 3 --psm 6'
|
484 |
+
tesseract_text = pytesseract.image_to_string(processed_img, config=custom_config)
|
485 |
+
|
486 |
+
if len(tesseract_text.strip()) > 10:
|
487 |
+
return clean_extracted_text(tesseract_text)
|
488 |
+
|
489 |
+
except Exception as e:
|
490 |
+
print(f"Tesseract failed: {e}")
|
491 |
+
|
492 |
+
return "β Could not extract text from image. Please try a clearer image or enter text manually."
|
493 |
+
|
494 |
+
except Exception as e:
|
495 |
+
return f"β Error processing image: {str(e)}"
|
496 |
+
|
497 |
+
def clean_extracted_text(text):
|
498 |
+
"""
|
499 |
+
Clean up extracted text
|
500 |
+
"""
|
501 |
+
# Remove excessive whitespace and empty lines
|
502 |
+
lines = [line.strip() for line in text.split('\n') if line.strip()]
|
503 |
+
cleaned_text = '\n'.join(lines)
|
504 |
+
|
505 |
+
# Remove special characters that might interfere
|
506 |
+
cleaned_text = cleaned_text.replace('|', '').replace('_', ' ')
|
507 |
+
|
508 |
+
return cleaned_text.strip()
|
509 |
+
|
510 |
+
def gradio_generate_soap(medical_notes, uploaded_image):
|
511 |
+
"""
|
512 |
+
Modified Gradio interface function for SOAP generation from images
|
513 |
+
"""
|
514 |
+
text_to_process = medical_notes.strip() if medical_notes else ""
|
515 |
+
|
516 |
+
# If image is uploaded, extract text using OCR
|
517 |
+
if uploaded_image is not None:
|
518 |
+
try:
|
519 |
+
print("π Extracting text from uploaded image...")
|
520 |
+
extracted_text = extract_text_from_image(uploaded_image)
|
521 |
+
|
522 |
+
# Check if OCR was successful
|
523 |
+
if extracted_text.startswith("β"):
|
524 |
+
return extracted_text
|
525 |
+
|
526 |
+
# Use extracted text if manual text is empty or append to manual text
|
527 |
+
if not text_to_process:
|
528 |
+
text_to_process = extracted_text
|
529 |
+
else:
|
530 |
+
text_to_process = f"{text_to_process}\n\n--- Extracted from image ---\n{extracted_text}"
|
531 |
+
|
532 |
+
except Exception as e:
|
533 |
+
return f"β Error processing image: {str(e)}"
|
534 |
+
|
535 |
+
if not text_to_process:
|
536 |
+
return "β Please enter medical notes manually or upload a PNG/JPG image with medical text"
|
537 |
+
|
538 |
+
# Check if generate_soap_note function exists
|
539 |
+
if 'generate_soap_note' not in globals():
|
540 |
+
return "β Error: generate_soap_note function not found. Please define it first."
|
541 |
+
|
542 |
+
try:
|
543 |
+
return generate_soap_note(text_to_process)
|
544 |
+
except Exception as e:
|
545 |
+
return f"β Error generating SOAP note: {str(e)}"
|
546 |
+
|
547 |
+
# Create example images (you can replace these with actual medical note images)
|
548 |
+
def create_example_image(text, filename):
|
549 |
+
"""
|
550 |
+
Create example images from text (for demonstration)
|
551 |
+
"""
|
552 |
+
from PIL import Image, ImageDraw, ImageFont
|
553 |
+
|
554 |
+
# Create a white image
|
555 |
+
img = Image.new('RGB', (800, 600), color='white')
|
556 |
+
draw = ImageDraw.Draw(img)
|
557 |
+
|
558 |
+
try:
|
559 |
+
# Try to use a default font
|
560 |
+
font = ImageFont.load_default()
|
561 |
+
except:
|
562 |
+
font = None
|
563 |
+
|
564 |
+
# Add text to image
|
565 |
+
lines = text.split('\n')
|
566 |
+
y_offset = 20
|
567 |
+
for line in lines[:15]: # Limit to first 15 lines
|
568 |
+
draw.text((20, y_offset), line, fill='black', font=font)
|
569 |
+
y_offset += 25
|
570 |
+
|
571 |
+
return img
|
572 |
+
|
573 |
+
# Create Gradio interface
|
574 |
+
gradio_interface = gr.Interface(
|
575 |
+
fn=gradio_generate_soap,
|
576 |
+
inputs=[
|
577 |
+
gr.Textbox(
|
578 |
+
lines=6,
|
579 |
+
placeholder="Enter medical notes manually (optional)...\n\nOr upload an image below and text will be extracted automatically.",
|
580 |
+
label="π Medical Notes (Manual Entry)"
|
581 |
+
),
|
582 |
+
gr.Image(
|
583 |
+
type="pil",
|
584 |
+
label="π· Upload Medical Image (PNG/JPG only)",
|
585 |
+
sources=["upload", "webcam"], # FIXED: Changed "camera" to "webcam"
|
586 |
+
image_mode="RGB"
|
587 |
+
)
|
588 |
+
],
|
589 |
+
outputs=[
|
590 |
+
gr.Textbox(
|
591 |
+
lines=15,
|
592 |
+
label="π Generated SOAP Note",
|
593 |
+
show_copy_button=True
|
594 |
+
)
|
595 |
+
],
|
596 |
+
title="π₯ Medical Image SOAP Note Generator",
|
597 |
+
description="""
|
598 |
+
Transform medical images (PNG/JPG) into professional SOAP documentation using OCR + Gemma 3N model.
|
599 |
+
|
600 |
+
πΈ **How to use:**
|
601 |
+
1. Upload a PNG or JPG image of medical notes (typed or handwritten)
|
602 |
+
2. Or enter text manually in the text box above
|
603 |
+
3. The system will extract text from images using OCR
|
604 |
+
4. Generate structured SOAP notes automatically
|
605 |
+
|
606 |
+
π‘ **Tips for better OCR results:**
|
607 |
+
- Use clear, high-resolution images
|
608 |
+
- Ensure good lighting and contrast
|
609 |
+
- Keep text horizontal (not tilted)
|
610 |
+
- Handwritten text works best when clearly written
|
611 |
+
""",
|
612 |
+
examples=[
|
613 |
+
[examples['chest_pain'], None],
|
614 |
+
[examples['diabetes'], None],
|
615 |
+
[examples['pediatric'], None]
|
616 |
+
],
|
617 |
+
theme=gr.themes.Soft(),
|
618 |
+
flagging_mode="never"
|
619 |
+
)
|
620 |
+
|
621 |
+
# Launch Gradio interface with flexible port selection
|
622 |
+
print("π Launching Medical Image SOAP Generator...")
|
623 |
+
|
624 |
+
try:
|
625 |
+
# Try different ports if 7860 is busy
|
626 |
+
for port in [7860, 7861, 7862, 7863, 7864]:
|
627 |
+
try:
|
628 |
+
gradio_interface.launch(
|
629 |
+
share=True, # Creates a public shareable link
|
630 |
+
server_port=port,
|
631 |
+
show_error=True,
|
632 |
+
quiet=False
|
633 |
+
)
|
634 |
+
print(f"β
Interface launched successfully on port {port}")
|
635 |
+
break
|
636 |
+
except OSError as port_error:
|
637 |
+
print(f"β οΈ Port {port} is busy, trying next port...")
|
638 |
+
continue
|
639 |
+
else:
|
640 |
+
# If all ports are busy, let Gradio choose automatically
|
641 |
+
print("π All preferred ports busy, letting Gradio choose automatically...")
|
642 |
+
gradio_interface.launch(
|
643 |
+
share=True,
|
644 |
+
show_error=True,
|
645 |
+
quiet=False
|
646 |
+
)
|
647 |
+
|
648 |
+
except Exception as e:
|
649 |
+
print(f"β Error launching Gradio interface: {str(e)}")
|
650 |
+
print("π‘ Alternative: Try running without share=True:")
|
651 |
+
print("gradio_interface.launch(show_error=True)")
|
652 |
+
|
653 |
+
print("π― Medical Image SOAP Generator ready!")
|
654 |
+
print("πΈ Upload PNG/JPG images of medical notes for automatic text extraction and SOAP generation")
|
655 |
+
|
656 |
+
"""## π Usage Statistics & Model Info"""
|
657 |
+
|
658 |
+
# Display model and system information
|
659 |
+
import psutil
|
660 |
+
import GPUtil
|
661 |
+
|
662 |
+
def show_system_info():
|
663 |
+
print("π§ SYSTEM INFORMATION")
|
664 |
+
print("="*50)
|
665 |
+
print(f"π₯οΈ Device: {device.upper()}")
|
666 |
+
print(f"π§ CPU Usage: {psutil.cpu_percent(interval=1):.1f}%")
|
667 |
+
print(f"πΎ RAM Usage: {psutil.virtual_memory().percent:.1f}%")
|
668 |
+
|
669 |
+
if torch.cuda.is_available():
|
670 |
+
try:
|
671 |
+
gpus = GPUtil.getGPUs()
|
672 |
+
if gpus:
|
673 |
+
gpu = gpus[0]
|
674 |
+
print(f"π GPU: {gpu.name}")
|
675 |
+
print(f"π GPU Usage: {gpu.load*100:.1f}%")
|
676 |
+
print(f"π₯ GPU Memory: {gpu.memoryUsed}/{gpu.memoryTotal} MB ({gpu.memoryPercent:.1f}%)")
|
677 |
+
print(f"π‘οΈ GPU Temp: {gpu.temperature}Β°C")
|
678 |
+
except:
|
679 |
+
print(f"π GPU Memory: {torch.cuda.memory_allocated()/1e9:.1f}GB / {torch.cuda.memory_reserved()/1e9:.1f}GB")
|
680 |
+
|
681 |
+
print("\nπ€ MODEL INFORMATION")
|
682 |
+
print("="*50)
|
683 |
+
print(f"π‘ Model ID: {model_id}")
|
684 |
+
print(f"π― Model Type: Multimodal (Text, Image, Audio)")
|
685 |
+
print(f"π Model Size: ~2.9GB")
|
686 |
+
print(f"π’ Parameters: ~2.9B")
|
687 |
+
print(f"π Languages: 140 text + 35 multimodal")
|
688 |
+
print(f"π½ Precision: {model.dtype}")
|
689 |
+
|
690 |
+
print("\nβ
Ready for SOAP note generation!")
|
691 |
+
|
692 |
+
show_system_info()
|
693 |
+
|
694 |
+
"""---
|
695 |
+
## π SOAP Note Format Reference
|
696 |
+
|
697 |
+
**S - SUBJECTIVE**: Patient's reported symptoms and history
|
698 |
+
**O - OBJECTIVE**: Observable clinical findings
|
699 |
+
**A - ASSESSMENT**: Clinical diagnosis/impression
|
700 |
+
**P - PLAN**: Treatment and follow-up plan
|
701 |
+
|
702 |
+
---
|
703 |
+
*π€ Powered by Google's Gemma 3N Model | π All processing performed locally*
|
704 |
+
"""
|
705 |
+
|
706 |
+
!gradio deploy
|