Added the end consultation section ✅✅
Browse files- mediSync/app.py +627 -560
mediSync/app.py
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@@ -1,560 +1,627 @@
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import logging
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import os
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import sys
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import tempfile
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from pathlib import Path
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import gradio as gr
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import matplotlib.pyplot as plt
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from PIL import Image
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# Add parent directory to path
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parent_dir = os.path.dirname(os.path.abspath(__file__))
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sys.path.append(parent_dir)
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# Import our modules
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from models.multimodal_fusion import MultimodalFusion
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from utils.preprocessing import enhance_xray_image, normalize_report_text
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from utils.visualization import (
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plot_image_prediction,
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plot_multimodal_results,
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plot_report_entities,
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)
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# Set up logging
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logging.basicConfig(
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level=logging.INFO,
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format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
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handlers=[logging.StreamHandler(), logging.FileHandler("mediSync.log")],
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)
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logger = logging.getLogger(__name__)
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# Create temporary directory for sample data if it doesn't exist
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os.makedirs(os.path.join(parent_dir, "data", "sample"), exist_ok=True)
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class MediSyncApp:
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"""
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Main application class for the MediSync multi-modal medical analysis system.
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"""
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def __init__(self):
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"""Initialize the application and load models."""
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self.logger = logging.getLogger(__name__)
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self.logger.info("Initializing MediSync application")
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# Initialize models with None for lazy loading
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self.fusion_model = None
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self.image_model = None
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self.text_model = None
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def load_models(self):
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"""
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Load models if not already loaded.
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Returns:
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bool: True if models loaded successfully, False otherwise
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"""
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try:
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if self.fusion_model is None:
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self.logger.info("Loading models...")
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self.fusion_model = MultimodalFusion()
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self.image_model = self.fusion_model.image_analyzer
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self.text_model = self.fusion_model.text_analyzer
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self.logger.info("Models loaded successfully")
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return True
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except Exception as e:
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self.logger.error(f"Error loading models: {e}")
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return False
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def analyze_image(self, image):
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"""
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Analyze a medical image.
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Args:
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image: Image file uploaded through Gradio
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Returns:
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tuple: (image, image_results_html, plot_as_html)
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"""
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try:
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# Ensure models are loaded
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if not self.load_models() or self.image_model is None:
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return image, "Error: Models not loaded properly.", None
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# Save uploaded image to a temporary file
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temp_dir = tempfile.mkdtemp()
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temp_path = os.path.join(temp_dir, "upload.png")
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if isinstance(image, str):
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# Copy the file if it's a path
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from shutil import copyfile
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copyfile(image, temp_path)
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else:
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# Save if it's a Gradio UploadButton image
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image.save(temp_path)
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# Run image analysis
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self.logger.info(f"Analyzing image: {temp_path}")
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results = self.image_model.analyze(temp_path)
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# Create visualization
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fig = plot_image_prediction(
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image,
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results.get("predictions", []),
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f"Primary Finding: {results.get('primary_finding', 'Unknown')}",
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)
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# Convert to HTML for display
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plot_html = self.fig_to_html(fig)
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# Format results as HTML
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html_result = f"""
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<h2>X-ray Analysis Results</h2>
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<p><strong>Primary Finding:</strong> {results.get("primary_finding", "Unknown")}</p>
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<p><strong>Confidence:</strong> {results.get("confidence", 0):.1%}</p>
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<p><strong>Abnormality Detected:</strong> {"Yes" if results.get("has_abnormality", False) else "No"}</p>
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<h3>Top Predictions:</h3>
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<ul>
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"""
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# Add top 5 predictions
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for label, prob in results.get("predictions", [])[:5]:
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html_result += f"<li>{label}: {prob:.1%}</li>"
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html_result += "</ul>"
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# Add explanation
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explanation = self.image_model.get_explanation(results)
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html_result += f"<h3>Analysis Explanation:</h3><p>{explanation}</p>"
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return image, html_result, plot_html
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except Exception as e:
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self.logger.error(f"Error in image analysis: {e}")
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return image, f"Error analyzing image: {str(e)}", None
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def analyze_text(self, text):
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"""
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Analyze a medical report text.
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Args:
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text: Report text input through Gradio
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Returns:
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tuple: (text, text_results_html, entities_plot_html)
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"""
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try:
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# Ensure models are loaded
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if not self.load_models() or self.text_model is None:
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return text, "Error: Models not loaded properly.", None
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# Check for empty text
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if not text or len(text.strip()) < 10:
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return (
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text,
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"Error: Please enter a valid medical report text (at least 10 characters).",
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None,
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)
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# Normalize text
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normalized_text = normalize_report_text(text)
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# Run text analysis
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self.logger.info("Analyzing medical report text")
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results = self.text_model.analyze(normalized_text)
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# Get entities and create visualization
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entities = results.get("entities", {})
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fig = plot_report_entities(normalized_text, entities)
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# Convert to HTML for display
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entities_plot_html = self.fig_to_html(fig)
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# Format results as HTML
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html_result = f"""
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<h2>Medical Report Analysis Results</h2>
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<p><strong>Severity Level:</strong> {results.get("severity", {}).get("level", "Unknown")}</p>
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<p><strong>Severity Score:</strong> {results.get("severity", {}).get("score", 0)}/4</p>
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<p><strong>Confidence:</strong> {results.get("severity", {}).get("confidence", 0):.1%}</p>
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<h3>Key Findings:</h3>
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<ul>
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"""
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# Add findings
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findings = results.get("findings", [])
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if findings:
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for finding in findings:
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html_result += f"<li>{finding}</li>"
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else:
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html_result += "<li>No specific findings detailed.</li>"
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html_result += "</ul>"
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# Add entities
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html_result += "<h3>Extracted Medical Entities:</h3>"
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for category, items in entities.items():
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if items:
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html_result += f"<p><strong>{category.capitalize()}:</strong> {', '.join(items)}</p>"
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# Add follow-up recommendations
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html_result += "<h3>Follow-up Recommendations:</h3><ul>"
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followups = results.get("followup_recommendations", [])
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if followups:
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for rec in followups:
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html_result += f"<li>{rec}</li>"
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else:
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html_result += "<li>No specific follow-up recommendations.</li>"
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html_result += "</ul>"
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return text, html_result, entities_plot_html
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except Exception as e:
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self.logger.error(f"Error in text analysis: {e}")
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return text, f"Error analyzing text: {str(e)}", None
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def analyze_multimodal(self, image, text):
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"""
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Perform multimodal analysis of image and text.
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Args:
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image: Image file uploaded through Gradio
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text: Report text input through Gradio
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Returns:
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tuple: (results_html, multimodal_plot_html)
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"""
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try:
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# Ensure models are loaded
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if not self.load_models() or self.fusion_model is None:
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return "Error: Models not loaded properly.", None
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# Check for empty inputs
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if image is None:
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return "Error: Please upload an X-ray image for analysis.", None
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if not text or len(text.strip()) < 10:
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return (
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"Error: Please enter a valid medical report text (at least 10 characters).",
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None,
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)
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# Save uploaded image to a temporary file
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temp_dir = tempfile.mkdtemp()
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temp_path = os.path.join(temp_dir, "upload.png")
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if isinstance(image, str):
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# Copy the file if it's a path
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from shutil import copyfile
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copyfile(image, temp_path)
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else:
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# Save if it's a Gradio UploadButton image
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image.save(temp_path)
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# Normalize text
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normalized_text = normalize_report_text(text)
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# Run multimodal analysis
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self.logger.info("Performing multimodal analysis")
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results = self.fusion_model.analyze(temp_path, normalized_text)
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# Create visualization
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fig = plot_multimodal_results(results, image, text)
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# Convert to HTML for display
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plot_html = self.fig_to_html(fig)
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# Generate explanation
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explanation = self.fusion_model.get_explanation(results)
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# Format results as HTML
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html_result = f"""
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<h2>Multimodal Medical Analysis Results</h2>
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<h3>Overview</h3>
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<p><strong>Primary Finding:</strong> {results.get("primary_finding", "Unknown")}</p>
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<p><strong>Severity Level:</strong> {results.get("severity", {}).get("level", "Unknown")}</p>
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<p><strong>Severity Score:</strong> {results.get("severity", {}).get("score", 0)}/4</p>
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<p><strong>Agreement Score:</strong> {results.get("agreement_score", 0):.0%}</p>
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<h3>Detailed Findings</h3>
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<ul>
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"""
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# Add findings
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findings = results.get("findings", [])
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if findings:
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for finding in findings:
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html_result += f"<li>{finding}</li>"
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else:
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html_result += "<li>No specific findings detailed.</li>"
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html_result += "</ul>"
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# Add follow-up recommendations
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html_result += "<h3>Recommended Follow-up</h3><ul>"
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followups = results.get("followup_recommendations", [])
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if followups:
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for rec in followups:
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html_result += f"<li>{rec}</li>"
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else:
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html_result += (
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"<li>No specific follow-up recommendations provided.</li>"
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)
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html_result += "</ul>"
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# Add confidence note
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confidence = results.get("severity", {}).get("confidence", 0)
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html_result += f"""
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<p><em>Note: This analysis has a confidence level of {confidence:.0%}.
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Please consult with healthcare professionals for official diagnosis.</em></p>
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"""
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return html_result, plot_html
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except Exception as e:
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self.logger.error(f"Error in multimodal analysis: {e}")
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return f"Error in multimodal analysis: {str(e)}", None
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def enhance_image(self, image):
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"""
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Enhance X-ray image contrast.
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Args:
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image: Image file uploaded through Gradio
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Returns:
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PIL.Image: Enhanced image
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"""
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try:
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if image is None:
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return None
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# Save uploaded image to a temporary file
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temp_dir = tempfile.mkdtemp()
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temp_path = os.path.join(temp_dir, "upload.png")
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if isinstance(image, str):
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# Copy the file if it's a path
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from shutil import copyfile
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copyfile(image, temp_path)
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else:
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# Save if it's a Gradio UploadButton image
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image.save(temp_path)
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# Enhance image
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self.logger.info(f"Enhancing image: {temp_path}")
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output_path = os.path.join(temp_dir, "enhanced.png")
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enhance_xray_image(temp_path, output_path)
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# Load enhanced image
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enhanced = Image.open(output_path)
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return enhanced
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except Exception as e:
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self.logger.error(f"Error enhancing image: {e}")
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return image # Return original image on error
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def fig_to_html(self, fig):
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"""Convert matplotlib figure to HTML for display in Gradio."""
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try:
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import base64
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import io
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buf = io.BytesIO()
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fig.savefig(buf, format="png", bbox_inches="tight")
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buf.seek(0)
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img_str = base64.b64encode(buf.read()).decode("utf-8")
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plt.close(fig)
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return f'<img src="data:image/png;base64,{img_str}" alt="Analysis Plot">'
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except Exception as e:
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self.logger.error(f"Error converting figure to HTML: {e}")
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return "<p>Error displaying visualization.</p>"
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def create_interface():
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"""Create and launch the Gradio interface."""
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app = MediSyncApp()
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# Example medical report for demo
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example_report = """
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CHEST X-RAY EXAMINATION
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CLINICAL HISTORY: 55-year-old male with cough and fever.
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FINDINGS: The heart size is at the upper limits of normal. The lungs are clear without focal consolidation,
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effusion, or pneumothorax. There is mild prominence of the pulmonary vasculature. No pleural effusion is seen.
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There is a small nodular opacity noted in the right lower lobe measuring approximately 8mm, which is suspicious
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and warrants further investigation. The mediastinum is unremarkable. The visualized bony structures show no acute abnormalities.
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IMPRESSION:
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1. Mild cardiomegaly.
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2. 8mm nodular opacity in the right lower lobe, recommend follow-up CT for further evaluation.
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3. No acute pulmonary parenchymal abnormality.
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|
| 409 |
-
RECOMMENDATIONS: Follow-up chest CT to further characterize the nodular opacity in the right lower lobe.
|
| 410 |
-
"""
|
| 411 |
-
|
| 412 |
-
# Get sample image path if available
|
| 413 |
-
sample_images_dir = Path(parent_dir) / "data" / "sample"
|
| 414 |
-
sample_images = list(sample_images_dir.glob("*.png")) + list(
|
| 415 |
-
sample_images_dir.glob("*.jpg")
|
| 416 |
-
)
|
| 417 |
-
|
| 418 |
-
sample_image_path = None
|
| 419 |
-
if sample_images:
|
| 420 |
-
sample_image_path = str(sample_images[0])
|
| 421 |
-
|
| 422 |
-
# Define interface
|
| 423 |
-
with gr.Blocks(
|
| 424 |
-
title="MediSync: Multi-Modal Medical Analysis System",
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-
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-
#
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|
| 1 |
+
import logging
|
| 2 |
+
import os
|
| 3 |
+
import sys
|
| 4 |
+
import tempfile
|
| 5 |
+
from pathlib import Path
|
| 6 |
+
|
| 7 |
+
import gradio as gr
|
| 8 |
+
import matplotlib.pyplot as plt
|
| 9 |
+
from PIL import Image
|
| 10 |
+
|
| 11 |
+
# Add parent directory to path
|
| 12 |
+
parent_dir = os.path.dirname(os.path.abspath(__file__))
|
| 13 |
+
sys.path.append(parent_dir)
|
| 14 |
+
|
| 15 |
+
# Import our modules
|
| 16 |
+
from models.multimodal_fusion import MultimodalFusion
|
| 17 |
+
from utils.preprocessing import enhance_xray_image, normalize_report_text
|
| 18 |
+
from utils.visualization import (
|
| 19 |
+
plot_image_prediction,
|
| 20 |
+
plot_multimodal_results,
|
| 21 |
+
plot_report_entities,
|
| 22 |
+
)
|
| 23 |
+
|
| 24 |
+
# Set up logging
|
| 25 |
+
logging.basicConfig(
|
| 26 |
+
level=logging.INFO,
|
| 27 |
+
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
|
| 28 |
+
handlers=[logging.StreamHandler(), logging.FileHandler("mediSync.log")],
|
| 29 |
+
)
|
| 30 |
+
logger = logging.getLogger(__name__)
|
| 31 |
+
|
| 32 |
+
# Create temporary directory for sample data if it doesn't exist
|
| 33 |
+
os.makedirs(os.path.join(parent_dir, "data", "sample"), exist_ok=True)
|
| 34 |
+
|
| 35 |
+
|
| 36 |
+
class MediSyncApp:
|
| 37 |
+
"""
|
| 38 |
+
Main application class for the MediSync multi-modal medical analysis system.
|
| 39 |
+
"""
|
| 40 |
+
|
| 41 |
+
def __init__(self):
|
| 42 |
+
"""Initialize the application and load models."""
|
| 43 |
+
self.logger = logging.getLogger(__name__)
|
| 44 |
+
self.logger.info("Initializing MediSync application")
|
| 45 |
+
|
| 46 |
+
# Initialize models with None for lazy loading
|
| 47 |
+
self.fusion_model = None
|
| 48 |
+
self.image_model = None
|
| 49 |
+
self.text_model = None
|
| 50 |
+
|
| 51 |
+
def load_models(self):
|
| 52 |
+
"""
|
| 53 |
+
Load models if not already loaded.
|
| 54 |
+
|
| 55 |
+
Returns:
|
| 56 |
+
bool: True if models loaded successfully, False otherwise
|
| 57 |
+
"""
|
| 58 |
+
try:
|
| 59 |
+
if self.fusion_model is None:
|
| 60 |
+
self.logger.info("Loading models...")
|
| 61 |
+
self.fusion_model = MultimodalFusion()
|
| 62 |
+
self.image_model = self.fusion_model.image_analyzer
|
| 63 |
+
self.text_model = self.fusion_model.text_analyzer
|
| 64 |
+
self.logger.info("Models loaded successfully")
|
| 65 |
+
return True
|
| 66 |
+
|
| 67 |
+
except Exception as e:
|
| 68 |
+
self.logger.error(f"Error loading models: {e}")
|
| 69 |
+
return False
|
| 70 |
+
|
| 71 |
+
def analyze_image(self, image):
|
| 72 |
+
"""
|
| 73 |
+
Analyze a medical image.
|
| 74 |
+
|
| 75 |
+
Args:
|
| 76 |
+
image: Image file uploaded through Gradio
|
| 77 |
+
|
| 78 |
+
Returns:
|
| 79 |
+
tuple: (image, image_results_html, plot_as_html)
|
| 80 |
+
"""
|
| 81 |
+
try:
|
| 82 |
+
# Ensure models are loaded
|
| 83 |
+
if not self.load_models() or self.image_model is None:
|
| 84 |
+
return image, "Error: Models not loaded properly.", None
|
| 85 |
+
|
| 86 |
+
# Save uploaded image to a temporary file
|
| 87 |
+
temp_dir = tempfile.mkdtemp()
|
| 88 |
+
temp_path = os.path.join(temp_dir, "upload.png")
|
| 89 |
+
|
| 90 |
+
if isinstance(image, str):
|
| 91 |
+
# Copy the file if it's a path
|
| 92 |
+
from shutil import copyfile
|
| 93 |
+
|
| 94 |
+
copyfile(image, temp_path)
|
| 95 |
+
else:
|
| 96 |
+
# Save if it's a Gradio UploadButton image
|
| 97 |
+
image.save(temp_path)
|
| 98 |
+
|
| 99 |
+
# Run image analysis
|
| 100 |
+
self.logger.info(f"Analyzing image: {temp_path}")
|
| 101 |
+
results = self.image_model.analyze(temp_path)
|
| 102 |
+
|
| 103 |
+
# Create visualization
|
| 104 |
+
fig = plot_image_prediction(
|
| 105 |
+
image,
|
| 106 |
+
results.get("predictions", []),
|
| 107 |
+
f"Primary Finding: {results.get('primary_finding', 'Unknown')}",
|
| 108 |
+
)
|
| 109 |
+
|
| 110 |
+
# Convert to HTML for display
|
| 111 |
+
plot_html = self.fig_to_html(fig)
|
| 112 |
+
|
| 113 |
+
# Format results as HTML
|
| 114 |
+
html_result = f"""
|
| 115 |
+
<h2>X-ray Analysis Results</h2>
|
| 116 |
+
<p><strong>Primary Finding:</strong> {results.get("primary_finding", "Unknown")}</p>
|
| 117 |
+
<p><strong>Confidence:</strong> {results.get("confidence", 0):.1%}</p>
|
| 118 |
+
<p><strong>Abnormality Detected:</strong> {"Yes" if results.get("has_abnormality", False) else "No"}</p>
|
| 119 |
+
|
| 120 |
+
<h3>Top Predictions:</h3>
|
| 121 |
+
<ul>
|
| 122 |
+
"""
|
| 123 |
+
|
| 124 |
+
# Add top 5 predictions
|
| 125 |
+
for label, prob in results.get("predictions", [])[:5]:
|
| 126 |
+
html_result += f"<li>{label}: {prob:.1%}</li>"
|
| 127 |
+
|
| 128 |
+
html_result += "</ul>"
|
| 129 |
+
|
| 130 |
+
# Add explanation
|
| 131 |
+
explanation = self.image_model.get_explanation(results)
|
| 132 |
+
html_result += f"<h3>Analysis Explanation:</h3><p>{explanation}</p>"
|
| 133 |
+
|
| 134 |
+
return image, html_result, plot_html
|
| 135 |
+
|
| 136 |
+
except Exception as e:
|
| 137 |
+
self.logger.error(f"Error in image analysis: {e}")
|
| 138 |
+
return image, f"Error analyzing image: {str(e)}", None
|
| 139 |
+
|
| 140 |
+
def analyze_text(self, text):
|
| 141 |
+
"""
|
| 142 |
+
Analyze a medical report text.
|
| 143 |
+
|
| 144 |
+
Args:
|
| 145 |
+
text: Report text input through Gradio
|
| 146 |
+
|
| 147 |
+
Returns:
|
| 148 |
+
tuple: (text, text_results_html, entities_plot_html)
|
| 149 |
+
"""
|
| 150 |
+
try:
|
| 151 |
+
# Ensure models are loaded
|
| 152 |
+
if not self.load_models() or self.text_model is None:
|
| 153 |
+
return text, "Error: Models not loaded properly.", None
|
| 154 |
+
|
| 155 |
+
# Check for empty text
|
| 156 |
+
if not text or len(text.strip()) < 10:
|
| 157 |
+
return (
|
| 158 |
+
text,
|
| 159 |
+
"Error: Please enter a valid medical report text (at least 10 characters).",
|
| 160 |
+
None,
|
| 161 |
+
)
|
| 162 |
+
|
| 163 |
+
# Normalize text
|
| 164 |
+
normalized_text = normalize_report_text(text)
|
| 165 |
+
|
| 166 |
+
# Run text analysis
|
| 167 |
+
self.logger.info("Analyzing medical report text")
|
| 168 |
+
results = self.text_model.analyze(normalized_text)
|
| 169 |
+
|
| 170 |
+
# Get entities and create visualization
|
| 171 |
+
entities = results.get("entities", {})
|
| 172 |
+
fig = plot_report_entities(normalized_text, entities)
|
| 173 |
+
|
| 174 |
+
# Convert to HTML for display
|
| 175 |
+
entities_plot_html = self.fig_to_html(fig)
|
| 176 |
+
|
| 177 |
+
# Format results as HTML
|
| 178 |
+
html_result = f"""
|
| 179 |
+
<h2>Medical Report Analysis Results</h2>
|
| 180 |
+
<p><strong>Severity Level:</strong> {results.get("severity", {}).get("level", "Unknown")}</p>
|
| 181 |
+
<p><strong>Severity Score:</strong> {results.get("severity", {}).get("score", 0)}/4</p>
|
| 182 |
+
<p><strong>Confidence:</strong> {results.get("severity", {}).get("confidence", 0):.1%}</p>
|
| 183 |
+
|
| 184 |
+
<h3>Key Findings:</h3>
|
| 185 |
+
<ul>
|
| 186 |
+
"""
|
| 187 |
+
|
| 188 |
+
# Add findings
|
| 189 |
+
findings = results.get("findings", [])
|
| 190 |
+
if findings:
|
| 191 |
+
for finding in findings:
|
| 192 |
+
html_result += f"<li>{finding}</li>"
|
| 193 |
+
else:
|
| 194 |
+
html_result += "<li>No specific findings detailed.</li>"
|
| 195 |
+
|
| 196 |
+
html_result += "</ul>"
|
| 197 |
+
|
| 198 |
+
# Add entities
|
| 199 |
+
html_result += "<h3>Extracted Medical Entities:</h3>"
|
| 200 |
+
|
| 201 |
+
for category, items in entities.items():
|
| 202 |
+
if items:
|
| 203 |
+
html_result += f"<p><strong>{category.capitalize()}:</strong> {', '.join(items)}</p>"
|
| 204 |
+
|
| 205 |
+
# Add follow-up recommendations
|
| 206 |
+
html_result += "<h3>Follow-up Recommendations:</h3><ul>"
|
| 207 |
+
followups = results.get("followup_recommendations", [])
|
| 208 |
+
|
| 209 |
+
if followups:
|
| 210 |
+
for rec in followups:
|
| 211 |
+
html_result += f"<li>{rec}</li>"
|
| 212 |
+
else:
|
| 213 |
+
html_result += "<li>No specific follow-up recommendations.</li>"
|
| 214 |
+
|
| 215 |
+
html_result += "</ul>"
|
| 216 |
+
|
| 217 |
+
return text, html_result, entities_plot_html
|
| 218 |
+
|
| 219 |
+
except Exception as e:
|
| 220 |
+
self.logger.error(f"Error in text analysis: {e}")
|
| 221 |
+
return text, f"Error analyzing text: {str(e)}", None
|
| 222 |
+
|
| 223 |
+
def analyze_multimodal(self, image, text):
|
| 224 |
+
"""
|
| 225 |
+
Perform multimodal analysis of image and text.
|
| 226 |
+
|
| 227 |
+
Args:
|
| 228 |
+
image: Image file uploaded through Gradio
|
| 229 |
+
text: Report text input through Gradio
|
| 230 |
+
|
| 231 |
+
Returns:
|
| 232 |
+
tuple: (results_html, multimodal_plot_html)
|
| 233 |
+
"""
|
| 234 |
+
try:
|
| 235 |
+
# Ensure models are loaded
|
| 236 |
+
if not self.load_models() or self.fusion_model is None:
|
| 237 |
+
return "Error: Models not loaded properly.", None
|
| 238 |
+
|
| 239 |
+
# Check for empty inputs
|
| 240 |
+
if image is None:
|
| 241 |
+
return "Error: Please upload an X-ray image for analysis.", None
|
| 242 |
+
|
| 243 |
+
if not text or len(text.strip()) < 10:
|
| 244 |
+
return (
|
| 245 |
+
"Error: Please enter a valid medical report text (at least 10 characters).",
|
| 246 |
+
None,
|
| 247 |
+
)
|
| 248 |
+
|
| 249 |
+
# Save uploaded image to a temporary file
|
| 250 |
+
temp_dir = tempfile.mkdtemp()
|
| 251 |
+
temp_path = os.path.join(temp_dir, "upload.png")
|
| 252 |
+
|
| 253 |
+
if isinstance(image, str):
|
| 254 |
+
# Copy the file if it's a path
|
| 255 |
+
from shutil import copyfile
|
| 256 |
+
|
| 257 |
+
copyfile(image, temp_path)
|
| 258 |
+
else:
|
| 259 |
+
# Save if it's a Gradio UploadButton image
|
| 260 |
+
image.save(temp_path)
|
| 261 |
+
|
| 262 |
+
# Normalize text
|
| 263 |
+
normalized_text = normalize_report_text(text)
|
| 264 |
+
|
| 265 |
+
# Run multimodal analysis
|
| 266 |
+
self.logger.info("Performing multimodal analysis")
|
| 267 |
+
results = self.fusion_model.analyze(temp_path, normalized_text)
|
| 268 |
+
|
| 269 |
+
# Create visualization
|
| 270 |
+
fig = plot_multimodal_results(results, image, text)
|
| 271 |
+
|
| 272 |
+
# Convert to HTML for display
|
| 273 |
+
plot_html = self.fig_to_html(fig)
|
| 274 |
+
|
| 275 |
+
# Generate explanation
|
| 276 |
+
explanation = self.fusion_model.get_explanation(results)
|
| 277 |
+
|
| 278 |
+
# Format results as HTML
|
| 279 |
+
html_result = f"""
|
| 280 |
+
<h2>Multimodal Medical Analysis Results</h2>
|
| 281 |
+
|
| 282 |
+
<h3>Overview</h3>
|
| 283 |
+
<p><strong>Primary Finding:</strong> {results.get("primary_finding", "Unknown")}</p>
|
| 284 |
+
<p><strong>Severity Level:</strong> {results.get("severity", {}).get("level", "Unknown")}</p>
|
| 285 |
+
<p><strong>Severity Score:</strong> {results.get("severity", {}).get("score", 0)}/4</p>
|
| 286 |
+
<p><strong>Agreement Score:</strong> {results.get("agreement_score", 0):.0%}</p>
|
| 287 |
+
|
| 288 |
+
<h3>Detailed Findings</h3>
|
| 289 |
+
<ul>
|
| 290 |
+
"""
|
| 291 |
+
|
| 292 |
+
# Add findings
|
| 293 |
+
findings = results.get("findings", [])
|
| 294 |
+
if findings:
|
| 295 |
+
for finding in findings:
|
| 296 |
+
html_result += f"<li>{finding}</li>"
|
| 297 |
+
else:
|
| 298 |
+
html_result += "<li>No specific findings detailed.</li>"
|
| 299 |
+
|
| 300 |
+
html_result += "</ul>"
|
| 301 |
+
|
| 302 |
+
# Add follow-up recommendations
|
| 303 |
+
html_result += "<h3>Recommended Follow-up</h3><ul>"
|
| 304 |
+
followups = results.get("followup_recommendations", [])
|
| 305 |
+
|
| 306 |
+
if followups:
|
| 307 |
+
for rec in followups:
|
| 308 |
+
html_result += f"<li>{rec}</li>"
|
| 309 |
+
else:
|
| 310 |
+
html_result += (
|
| 311 |
+
"<li>No specific follow-up recommendations provided.</li>"
|
| 312 |
+
)
|
| 313 |
+
|
| 314 |
+
html_result += "</ul>"
|
| 315 |
+
|
| 316 |
+
# Add confidence note
|
| 317 |
+
confidence = results.get("severity", {}).get("confidence", 0)
|
| 318 |
+
html_result += f"""
|
| 319 |
+
<p><em>Note: This analysis has a confidence level of {confidence:.0%}.
|
| 320 |
+
Please consult with healthcare professionals for official diagnosis.</em></p>
|
| 321 |
+
"""
|
| 322 |
+
|
| 323 |
+
return html_result, plot_html
|
| 324 |
+
|
| 325 |
+
except Exception as e:
|
| 326 |
+
self.logger.error(f"Error in multimodal analysis: {e}")
|
| 327 |
+
return f"Error in multimodal analysis: {str(e)}", None
|
| 328 |
+
|
| 329 |
+
def enhance_image(self, image):
|
| 330 |
+
"""
|
| 331 |
+
Enhance X-ray image contrast.
|
| 332 |
+
|
| 333 |
+
Args:
|
| 334 |
+
image: Image file uploaded through Gradio
|
| 335 |
+
|
| 336 |
+
Returns:
|
| 337 |
+
PIL.Image: Enhanced image
|
| 338 |
+
"""
|
| 339 |
+
try:
|
| 340 |
+
if image is None:
|
| 341 |
+
return None
|
| 342 |
+
|
| 343 |
+
# Save uploaded image to a temporary file
|
| 344 |
+
temp_dir = tempfile.mkdtemp()
|
| 345 |
+
temp_path = os.path.join(temp_dir, "upload.png")
|
| 346 |
+
|
| 347 |
+
if isinstance(image, str):
|
| 348 |
+
# Copy the file if it's a path
|
| 349 |
+
from shutil import copyfile
|
| 350 |
+
|
| 351 |
+
copyfile(image, temp_path)
|
| 352 |
+
else:
|
| 353 |
+
# Save if it's a Gradio UploadButton image
|
| 354 |
+
image.save(temp_path)
|
| 355 |
+
|
| 356 |
+
# Enhance image
|
| 357 |
+
self.logger.info(f"Enhancing image: {temp_path}")
|
| 358 |
+
output_path = os.path.join(temp_dir, "enhanced.png")
|
| 359 |
+
enhance_xray_image(temp_path, output_path)
|
| 360 |
+
|
| 361 |
+
# Load enhanced image
|
| 362 |
+
enhanced = Image.open(output_path)
|
| 363 |
+
return enhanced
|
| 364 |
+
|
| 365 |
+
except Exception as e:
|
| 366 |
+
self.logger.error(f"Error enhancing image: {e}")
|
| 367 |
+
return image # Return original image on error
|
| 368 |
+
|
| 369 |
+
def fig_to_html(self, fig):
|
| 370 |
+
"""Convert matplotlib figure to HTML for display in Gradio."""
|
| 371 |
+
try:
|
| 372 |
+
import base64
|
| 373 |
+
import io
|
| 374 |
+
|
| 375 |
+
buf = io.BytesIO()
|
| 376 |
+
fig.savefig(buf, format="png", bbox_inches="tight")
|
| 377 |
+
buf.seek(0)
|
| 378 |
+
img_str = base64.b64encode(buf.read()).decode("utf-8")
|
| 379 |
+
plt.close(fig)
|
| 380 |
+
|
| 381 |
+
return f'<img src="data:image/png;base64,{img_str}" alt="Analysis Plot">'
|
| 382 |
+
|
| 383 |
+
except Exception as e:
|
| 384 |
+
self.logger.error(f"Error converting figure to HTML: {e}")
|
| 385 |
+
return "<p>Error displaying visualization.</p>"
|
| 386 |
+
|
| 387 |
+
|
| 388 |
+
def create_interface():
|
| 389 |
+
"""Create and launch the Gradio interface."""
|
| 390 |
+
|
| 391 |
+
app = MediSyncApp()
|
| 392 |
+
|
| 393 |
+
# Example medical report for demo
|
| 394 |
+
example_report = """
|
| 395 |
+
CHEST X-RAY EXAMINATION
|
| 396 |
+
|
| 397 |
+
CLINICAL HISTORY: 55-year-old male with cough and fever.
|
| 398 |
+
|
| 399 |
+
FINDINGS: The heart size is at the upper limits of normal. The lungs are clear without focal consolidation,
|
| 400 |
+
effusion, or pneumothorax. There is mild prominence of the pulmonary vasculature. No pleural effusion is seen.
|
| 401 |
+
There is a small nodular opacity noted in the right lower lobe measuring approximately 8mm, which is suspicious
|
| 402 |
+
and warrants further investigation. The mediastinum is unremarkable. The visualized bony structures show no acute abnormalities.
|
| 403 |
+
|
| 404 |
+
IMPRESSION:
|
| 405 |
+
1. Mild cardiomegaly.
|
| 406 |
+
2. 8mm nodular opacity in the right lower lobe, recommend follow-up CT for further evaluation.
|
| 407 |
+
3. No acute pulmonary parenchymal abnormality.
|
| 408 |
+
|
| 409 |
+
RECOMMENDATIONS: Follow-up chest CT to further characterize the nodular opacity in the right lower lobe.
|
| 410 |
+
"""
|
| 411 |
+
|
| 412 |
+
# Get sample image path if available
|
| 413 |
+
sample_images_dir = Path(parent_dir) / "data" / "sample"
|
| 414 |
+
sample_images = list(sample_images_dir.glob("*.png")) + list(
|
| 415 |
+
sample_images_dir.glob("*.jpg")
|
| 416 |
+
)
|
| 417 |
+
|
| 418 |
+
sample_image_path = None
|
| 419 |
+
if sample_images:
|
| 420 |
+
sample_image_path = str(sample_images[0])
|
| 421 |
+
|
| 422 |
+
# Define interface
|
| 423 |
+
with gr.Blocks(
|
| 424 |
+
title="MediSync: Multi-Modal Medical Analysis System",
|
| 425 |
+
theme=gr.themes.Soft()
|
| 426 |
+
) as interface:
|
| 427 |
+
# Get appointment ID from URL parameters if present
|
| 428 |
+
appointment_id = gr.Textbox(
|
| 429 |
+
visible=False,
|
| 430 |
+
value=gr.Request.query_params.get("appointment_id", "")
|
| 431 |
+
)
|
| 432 |
+
|
| 433 |
+
gr.Markdown("""
|
| 434 |
+
# MediSync: Multi-Modal Medical Analysis System
|
| 435 |
+
|
| 436 |
+
This AI-powered healthcare solution combines X-ray image analysis with patient report text processing
|
| 437 |
+
to provide comprehensive medical insights.
|
| 438 |
+
|
| 439 |
+
## How to Use
|
| 440 |
+
1. Upload a chest X-ray image
|
| 441 |
+
2. Enter the corresponding medical report text
|
| 442 |
+
3. Choose the analysis type: image-only, text-only, or multimodal (combined)
|
| 443 |
+
4. Click "End Consultation" when finished to complete your appointment
|
| 444 |
+
""")
|
| 445 |
+
|
| 446 |
+
with gr.Tab("Multimodal Analysis"):
|
| 447 |
+
with gr.Row():
|
| 448 |
+
with gr.Column():
|
| 449 |
+
multi_img_input = gr.Image(label="Upload X-ray Image", type="pil")
|
| 450 |
+
multi_img_enhance = gr.Button("Enhance Image")
|
| 451 |
+
|
| 452 |
+
multi_text_input = gr.Textbox(
|
| 453 |
+
label="Enter Medical Report Text",
|
| 454 |
+
placeholder="Enter the radiologist's report text here...",
|
| 455 |
+
lines=10,
|
| 456 |
+
value=example_report if sample_image_path is None else None,
|
| 457 |
+
)
|
| 458 |
+
|
| 459 |
+
multi_analyze_btn = gr.Button(
|
| 460 |
+
"Analyze Image & Text", variant="primary"
|
| 461 |
+
)
|
| 462 |
+
|
| 463 |
+
with gr.Column():
|
| 464 |
+
multi_results = gr.HTML(label="Analysis Results")
|
| 465 |
+
multi_plot = gr.HTML(label="Visualization")
|
| 466 |
+
|
| 467 |
+
# Set up examples if sample image exists
|
| 468 |
+
if sample_image_path:
|
| 469 |
+
gr.Examples(
|
| 470 |
+
examples=[[sample_image_path, example_report]],
|
| 471 |
+
inputs=[multi_img_input, multi_text_input],
|
| 472 |
+
label="Example X-ray and Report",
|
| 473 |
+
)
|
| 474 |
+
|
| 475 |
+
with gr.Tab("Image Analysis"):
|
| 476 |
+
with gr.Row():
|
| 477 |
+
with gr.Column():
|
| 478 |
+
img_input = gr.Image(label="Upload X-ray Image", type="pil")
|
| 479 |
+
img_enhance = gr.Button("Enhance Image")
|
| 480 |
+
img_analyze_btn = gr.Button("Analyze Image", variant="primary")
|
| 481 |
+
|
| 482 |
+
with gr.Column():
|
| 483 |
+
img_output = gr.Image(label="Processed Image")
|
| 484 |
+
img_results = gr.HTML(label="Analysis Results")
|
| 485 |
+
img_plot = gr.HTML(label="Visualization")
|
| 486 |
+
|
| 487 |
+
# Set up example if sample image exists
|
| 488 |
+
if sample_image_path:
|
| 489 |
+
gr.Examples(
|
| 490 |
+
examples=[[sample_image_path]],
|
| 491 |
+
inputs=[img_input],
|
| 492 |
+
label="Example X-ray Image",
|
| 493 |
+
)
|
| 494 |
+
|
| 495 |
+
with gr.Tab("Text Analysis"):
|
| 496 |
+
with gr.Row():
|
| 497 |
+
with gr.Column():
|
| 498 |
+
text_input = gr.Textbox(
|
| 499 |
+
label="Enter Medical Report Text",
|
| 500 |
+
placeholder="Enter the radiologist's report text here...",
|
| 501 |
+
lines=10,
|
| 502 |
+
value=example_report,
|
| 503 |
+
)
|
| 504 |
+
text_analyze_btn = gr.Button("Analyze Text", variant="primary")
|
| 505 |
+
|
| 506 |
+
with gr.Column():
|
| 507 |
+
text_output = gr.Textbox(label="Processed Text")
|
| 508 |
+
text_results = gr.HTML(label="Analysis Results")
|
| 509 |
+
text_plot = gr.HTML(label="Entity Visualization")
|
| 510 |
+
|
| 511 |
+
# Set up example
|
| 512 |
+
gr.Examples(
|
| 513 |
+
examples=[[example_report]],
|
| 514 |
+
inputs=[text_input],
|
| 515 |
+
label="Example Medical Report",
|
| 516 |
+
)
|
| 517 |
+
|
| 518 |
+
with gr.Tab("About"):
|
| 519 |
+
gr.Markdown("""
|
| 520 |
+
## About MediSync
|
| 521 |
+
|
| 522 |
+
MediSync is an AI-powered healthcare solution that uses multi-modal analysis to provide comprehensive insights from medical images and reports.
|
| 523 |
+
|
| 524 |
+
### Key Features
|
| 525 |
+
|
| 526 |
+
- **X-ray Image Analysis**: Detects abnormalities in chest X-rays using pre-trained vision models
|
| 527 |
+
- **Medical Report Processing**: Extracts key information from patient reports using NLP models
|
| 528 |
+
- **Multi-modal Integration**: Combines insights from both image and text data for more accurate analysis
|
| 529 |
+
|
| 530 |
+
### Models Used
|
| 531 |
+
|
| 532 |
+
- **X-ray Analysis**: facebook/deit-base-patch16-224-medical-cxr
|
| 533 |
+
- **Medical Text Analysis**: medicalai/ClinicalBERT
|
| 534 |
+
|
| 535 |
+
### Important Disclaimer
|
| 536 |
+
|
| 537 |
+
This tool is for educational and research purposes only. It is not intended to provide medical advice or replace professional healthcare. Always consult with qualified healthcare providers for medical decisions.
|
| 538 |
+
""")
|
| 539 |
+
|
| 540 |
+
# Consultation completion section
|
| 541 |
+
with gr.Row():
|
| 542 |
+
with gr.Column():
|
| 543 |
+
end_consultation_btn = gr.Button(
|
| 544 |
+
"End Consultation",
|
| 545 |
+
variant="stop",
|
| 546 |
+
size="lg"
|
| 547 |
+
)
|
| 548 |
+
completion_status = gr.HTML()
|
| 549 |
+
|
| 550 |
+
# Set up event handlers
|
| 551 |
+
multi_img_enhance.click(
|
| 552 |
+
app.enhance_image, inputs=multi_img_input, outputs=multi_img_input
|
| 553 |
+
)
|
| 554 |
+
multi_analyze_btn.click(
|
| 555 |
+
app.analyze_multimodal,
|
| 556 |
+
inputs=[multi_img_input, multi_text_input],
|
| 557 |
+
outputs=[multi_results, multi_plot],
|
| 558 |
+
)
|
| 559 |
+
|
| 560 |
+
img_enhance.click(app.enhance_image, inputs=img_input, outputs=img_output)
|
| 561 |
+
img_analyze_btn.click(
|
| 562 |
+
app.analyze_image,
|
| 563 |
+
inputs=img_input,
|
| 564 |
+
outputs=[img_output, img_results, img_plot],
|
| 565 |
+
)
|
| 566 |
+
|
| 567 |
+
text_analyze_btn.click(
|
| 568 |
+
app.analyze_text,
|
| 569 |
+
inputs=text_input,
|
| 570 |
+
outputs=[text_output, text_results, text_plot],
|
| 571 |
+
)
|
| 572 |
+
|
| 573 |
+
# Handle consultation completion
|
| 574 |
+
end_consultation_btn.click(
|
| 575 |
+
fn=complete_consultation,
|
| 576 |
+
inputs=[appointment_id],
|
| 577 |
+
outputs=completion_status
|
| 578 |
+
)
|
| 579 |
+
|
| 580 |
+
# Run the interface
|
| 581 |
+
interface.launch()
|
| 582 |
+
|
| 583 |
+
def complete_consultation(appointment_id):
|
| 584 |
+
"""Handle consultation completion by notifying the Flask app."""
|
| 585 |
+
if not appointment_id:
|
| 586 |
+
return "<div class='alert alert-error'>No appointment ID found. Please contact support.</div>"
|
| 587 |
+
|
| 588 |
+
try:
|
| 589 |
+
# Call your Flask app's completion endpoint
|
| 590 |
+
# Replace with your actual Flask app URL
|
| 591 |
+
flask_app_url = "http://127.0.0.1:600/complete_consultation"
|
| 592 |
+
|
| 593 |
+
response = requests.post(
|
| 594 |
+
flask_app_url,
|
| 595 |
+
json={"appointment_id": appointment_id},
|
| 596 |
+
timeout=10
|
| 597 |
+
)
|
| 598 |
+
|
| 599 |
+
if response.status_code == 200:
|
| 600 |
+
# Return JavaScript to redirect back to the doctors page
|
| 601 |
+
return """
|
| 602 |
+
<div class='alert alert-success'>
|
| 603 |
+
Consultation completed successfully. Redirecting...
|
| 604 |
+
<script>
|
| 605 |
+
setTimeout(function() {
|
| 606 |
+
window.location.href = "http://127.0.0.1:600/doctors";
|
| 607 |
+
}, 2000);
|
| 608 |
+
</script>
|
| 609 |
+
</div>
|
| 610 |
+
"""
|
| 611 |
+
else:
|
| 612 |
+
return f"""
|
| 613 |
+
<div class='alert alert-error'>
|
| 614 |
+
Error completing appointment (Status: {response.status_code}).
|
| 615 |
+
Please contact support.
|
| 616 |
+
</div>
|
| 617 |
+
"""
|
| 618 |
+
|
| 619 |
+
except Exception as e:
|
| 620 |
+
return f"""
|
| 621 |
+
<div class='alert alert-error'>
|
| 622 |
+
Error: {str(e)}
|
| 623 |
+
</div>
|
| 624 |
+
"""
|
| 625 |
+
|
| 626 |
+
if __name__ == "__main__":
|
| 627 |
+
create_interface()
|