Create app.py

app.py

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+"""
+🫁 Multi-Class Chest X-Ray Detection with Adaptive Sparse Training
+Advanced Gradio Interface - 4 Disease Classes
+Features:
+- Real-time detection: Normal, TB, Pneumonia, COVID-19
+- Grad-CAM visualization (explainable AI)
+- Improved specificity - distinguishes TB from pneumonia
+- Confidence scores with visual indicators
+- Clinical interpretation and recommendations
+- Mobile-responsive design
+"""
+
+import gradio as gr
+import torch
+import torch.nn as nn
+from torchvision import models, transforms
+from PIL import Image
+import numpy as np
+import cv2
+import matplotlib.pyplot as plt
+from pathlib import Path
+import io
+
+# ============================================================================
+# Model Setup
+# ============================================================================
+
+device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
+
+# Load model
+model = models.efficientnet_b0(weights=None)
+model.classifier[1] = nn.Linear(model.classifier[1].in_features, 4)  # 4 classes
+
+try:
+    model.load_state_dict(torch.load('checkpoints/best_multiclass.pt', map_location=device))
+    print("✅ Multi-class model loaded successfully!")
+except Exception as e:
+    print(f"⚠️  Error loading model: {e}")
+
+model = model.to(device)
+model.eval()
+
+# Classes
+CLASSES = ['Normal', 'Tuberculosis', 'Pneumonia', 'COVID-19']
+CLASS_COLORS = {
+    'Normal': '#2ecc71',       # Green
+    'Tuberculosis': '#e74c3c',  # Red
+    'Pneumonia': '#f39c12',     # Orange
+    'COVID-19': '#9b59b6'       # Purple
+}
+
+# Image preprocessing
+transform = transforms.Compose([
+    transforms.Resize(256),
+    transforms.CenterCrop(224),
+    transforms.ToTensor(),
+    transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
+])
+
+# ============================================================================
+# Grad-CAM Implementation
+# ============================================================================
+
+class GradCAM:
+    def __init__(self, model, target_layer):
+        self.model = model
+        self.target_layer = target_layer
+        self.gradients = None
+        self.activations = None
+
+        def save_gradient(grad):
+            self.gradients = grad
+
+        def save_activation(module, input, output):
+            self.activations = output.detach()
+
+        target_layer.register_forward_hook(save_activation)
+        target_layer.register_full_backward_hook(lambda m, gi, go: save_gradient(go[0]))
+
+    def generate(self, input_image, target_class=None):
+        output = self.model(input_image)
+
+        if target_class is None:
+            target_class = output.argmax(dim=1)
+
+        self.model.zero_grad()
+        one_hot = torch.zeros_like(output)
+        one_hot[0][target_class] = 1
+        output.backward(gradient=one_hot, retain_graph=True)
+
+        if self.gradients is None:
+            return None, output
+
+        weights = self.gradients.mean(dim=(2, 3), keepdim=True)
+        cam = (weights * self.activations).sum(dim=1, keepdim=True)
+        cam = torch.relu(cam)
+        cam = cam.squeeze().cpu().numpy()
+        cam = (cam - cam.min()) / (cam.max() - cam.min() + 1e-8)
+
+        return cam, output
+
+# Setup Grad-CAM
+target_layer = model.features[-1]
+grad_cam = GradCAM(model, target_layer)
+
+# ============================================================================
+# Prediction Functions
+# ============================================================================
+
+def predict_chest_xray(image, show_gradcam=True):
+    """
+    Predict disease class from chest X-ray with Grad-CAM visualization
+    """
+    if image is None:
+        return None, None, None, None
+
+    # Convert to PIL if needed
+    if isinstance(image, np.ndarray):
+        image = Image.fromarray(image).convert('RGB')
+    else:
+        image = image.convert('RGB')
+
+    # Store original for display
+    original_img = image.copy()
+
+    # Preprocess
+    input_tensor = transform(image).unsqueeze(0).to(device)
+
+    # Get prediction with Grad-CAM
+    with torch.set_grad_enabled(show_gradcam):
+        if show_gradcam:
+            cam, output = grad_cam.generate(input_tensor)
+        else:
+            output = model(input_tensor)
+            cam = None
+
+    # Get probabilities
+    probs = torch.softmax(output, dim=1)[0].cpu().detach().numpy()
+    pred_class = int(output.argmax(dim=1).item())
+    pred_label = CLASSES[pred_class]
+    confidence = float(probs[pred_class]) * 100
+
+    # Create results
+    results = {
+        CLASSES[i]: float(probs[i] * 100) for i in range(len(CLASSES))
+    }
+
+    # Generate visualizations
+    original_pil = create_original_display(original_img, pred_label, confidence)
+
+    if cam is not None and show_gradcam:
+        gradcam_viz = create_gradcam_visualization(original_img, cam, pred_label, confidence)
+        overlay_viz = create_overlay_visualization(original_img, cam)
+    else:
+        gradcam_viz = None
+        overlay_viz = None
+
+    # Create interpretation text
+    interpretation = create_interpretation(pred_label, confidence, results)
+
+    return results, original_pil, gradcam_viz, overlay_viz, interpretation
+
+def create_original_display(image, pred_label, confidence):
+    """Create annotated original image"""
+    fig, ax = plt.subplots(figsize=(8, 8))
+    ax.imshow(image)
+    ax.axis('off')
+
+    # Add prediction box
+    color = CLASS_COLORS[pred_label]
+    title = f'Prediction: {pred_label}\nConfidence: {confidence:.1f}%'
+    ax.set_title(title, fontsize=16, fontweight='bold', color=color, pad=20)
+
+    plt.tight_layout()
+
+    # Convert to PIL
+    buf = io.BytesIO()
+    plt.savefig(buf, format='png', dpi=150, bbox_inches='tight', facecolor='white')
+    plt.close()
+    buf.seek(0)
+
+    return Image.open(buf)
+
+def create_gradcam_visualization(image, cam, pred_label, confidence):
+    """Create Grad-CAM heatmap"""
+    # Resize CAM to image size
+    img_array = np.array(image.resize((224, 224)))
+    cam_resized = cv2.resize(cam, (224, 224))
+
+    # Create heatmap
+    heatmap = cv2.applyColorMap(np.uint8(255 * cam_resized), cv2.COLORMAP_JET)
+    heatmap = cv2.cvtColor(heatmap, cv2.COLOR_BGR2RGB)
+
+    fig, ax = plt.subplots(figsize=(8, 8))
+    ax.imshow(heatmap)
+    ax.axis('off')
+    ax.set_title('Attention Heatmap\n(Areas the model focuses on)',
+                 fontsize=14, fontweight='bold', pad=20)
+
+    plt.tight_layout()
+
+    buf = io.BytesIO()
+    plt.savefig(buf, format='png', dpi=150, bbox_inches='tight', facecolor='white')
+    plt.close()
+    buf.seek(0)
+
+    return Image.open(buf)
+
+def create_overlay_visualization(image, cam):
+    """Create overlay of image and heatmap"""
+    img_array = np.array(image.resize((224, 224))) / 255.0
+    cam_resized = cv2.resize(cam, (224, 224))
+
+    # Create heatmap
+    heatmap = cv2.applyColorMap(np.uint8(255 * cam_resized), cv2.COLORMAP_JET)
+    heatmap = cv2.cvtColor(heatmap, cv2.COLOR_BGR2RGB) / 255.0
+
+    # Overlay
+    overlay = img_array * 0.5 + heatmap * 0.5
+    overlay = np.clip(overlay, 0, 1)
+
+    fig, ax = plt.subplots(figsize=(8, 8))
+    ax.imshow(overlay)
+    ax.axis('off')
+    ax.set_title('Explainable AI Visualization\n(Original + Heatmap)',
+                 fontsize=14, fontweight='bold', pad=20)
+
+    plt.tight_layout()
+
+    buf = io.BytesIO()
+    plt.savefig(buf, format='png', dpi=150, bbox_inches='tight', facecolor='white')
+    plt.close()
+    buf.seek(0)
+
+    return Image.open(buf)
+
+def create_interpretation(pred_label, confidence, results):
+    """Create interpretation text with improved medical disclaimers"""
+
+    interpretation = f"""
+## 🔬 Analysis Results
+### Prediction: **{pred_label}**
+- Confidence: **{confidence:.1f}%**
+### Probability Breakdown:
+- 🟢 Normal: **{results['Normal']:.1f}%**
+- 🔴 Tuberculosis: **{results['Tuberculosis']:.1f}%**
+- 🟠 Pneumonia: **{results['Pneumonia']:.1f}%**
+- 🟣 COVID-19: **{results['COVID-19']:.1f}%**
+---
+"""
+
+    # Disease-specific interpretations
+    if pred_label == 'Tuberculosis':
+        if confidence >= 85:
+            interpretation += """
+**⚠️ High Confidence TB Detection**
+The model has detected features highly consistent with tuberculosis infection.
+**CRITICAL - Immediate Actions Required:**
+1. ✅ **Immediate consultation** with a healthcare provider
+2. ✅ **Confirmatory sputum test** (AFB smear or GeneXpert MTB/RIF)
+3. ✅ **Clinical correlation** with symptoms:
+   - Persistent cough (>2 weeks)
+   - Fever, especially night sweats
+   - Unexplained weight loss
+   - Hemoptysis (coughing blood)
+4. ✅ **Isolation** and contact tracing if confirmed
+5. ✅ **Chest CT scan** if needed for further evaluation
+**⚠️ IMPORTANT**: This is a SCREENING tool, not a diagnostic tool.
+Clinical diagnosis of TB requires laboratory confirmation (sputum test).
+"""
+        else:
+            interpretation += """
+**⚠️ Possible TB Detection**
+The model has detected features suggestive of tuberculosis, but confidence is moderate.
+**Recommended Actions:**
+1. Consult healthcare provider for clinical evaluation
+2. Consider confirmatory sputum testing
+3. Evaluate clinical symptoms
+4. Follow-up imaging may be recommended
+**Note**: Moderate confidence requires professional medical evaluation.
+"""
+
+    elif pred_label == 'Pneumonia':
+        if confidence >= 85:
+            interpretation += """
+**⚠️ High Confidence Pneumonia Detection**
+The model has detected features consistent with pneumonia (bacterial or viral).
+**Recommended Actions:**
+1. ✅ **Medical evaluation** for pneumonia diagnosis
+2. ✅ **Possible confirmatory tests**:
+   - Sputum culture
+   - Blood tests (WBC count, CRP)
+   - Additional chest imaging if needed
+3. ✅ **Clinical correlation** with symptoms:
+   - Cough with sputum production
+   - Fever and chills
+   - Shortness of breath
+   - Chest pain with breathing
+4. ✅ **Treatment**: Antibiotics (bacterial) or supportive care (viral)
+**Note**: Pneumonia can present similarly to other lung diseases.
+Professional diagnosis is essential for appropriate treatment.
+"""
+        else:
+            interpretation += """
+**⚠️ Possible Pneumonia**
+Features suggest possible pneumonia, but further evaluation is needed.
+**Recommended Actions:**
+1. Seek medical evaluation
+2. Clinical symptom assessment
+3. Consider additional diagnostic tests
+**Note**: Requires professional medical evaluation for confirmation.
+"""
+
+    elif pred_label == 'COVID-19':
+        if confidence >= 85:
+            interpretation += """
+**⚠️ High Confidence COVID-19 Detection**
+The model has detected features consistent with COVID-19 pneumonia.
+**URGENT - Immediate Actions:**
+1. ✅ **COVID-19 RT-PCR test** for confirmation
+2. ✅ **Isolation** to prevent transmission
+3. ✅ **Monitor oxygen saturation** (SpO2 levels)
+4. ✅ **Seek immediate medical care** if:
+   - Difficulty breathing
+   - SpO2 < 94%
+   - Persistent chest pain
+   - Confusion or inability to stay awake
+5. ✅ **Contact tracing** if positive
+**Clinical Symptoms to Monitor:**
+- Fever, cough, shortness of breath
+- Loss of taste/smell
+- Fatigue, body aches
+- Gastrointestinal symptoms
+**⚠️ IMPORTANT**: Imaging findings alone cannot confirm COVID-19.
+RT-PCR or antigen testing is required for diagnosis.
+"""
+        else:
+            interpretation += """
+**⚠️ Possible COVID-19**
+Features suggest possible COVID-19, but confirmation testing is essential.
+**Recommended Actions:**
+1. Get RT-PCR or rapid antigen test
+2. Self-isolate pending test results
+3. Monitor symptoms
+4. Seek medical care if symptoms worsen
+**Note**: COVID-19 diagnosis requires laboratory confirmation.
+"""
+
+    else:  # Normal
+        if confidence >= 85:
+            interpretation += """
+**✅ High Confidence Normal Result**
+The model has not detected significant abnormalities consistent with TB, pneumonia, or COVID-19.
+**Interpretation:**
+- Chest X-ray appears within normal limits
+- No features of active tuberculosis detected
+- No signs of pneumonia or COVID-19
+**Important Notes:**
+- This does NOT rule out all lung diseases
+- Early-stage diseases may not show on X-ray
+- If you have symptoms, seek medical evaluation
+- Regular health screenings are recommended
+**When to still see a doctor:**
+- Persistent cough, fever, or respiratory symptoms
+- Unexplained weight loss or night sweats
+- Shortness of breath or chest pain
+- Known exposure to TB or COVID-19
+"""
+        else:
+            interpretation += """
+**⚠️ Likely Normal, Low Confidence**
+The model suggests a normal chest X-ray, but confidence is not high.
+**Recommended Actions:**
+1. If symptomatic, seek medical evaluation
+2. Consider repeat imaging if concerns persist
+3. Clinical correlation is important
+**Note**: Low confidence results should be reviewed by healthcare professionals.
+"""
+
+    # Add universal disclaimer
+    interpretation += """
+---
+## ⚠️ CRITICAL MEDICAL DISCLAIMER
+### Model Capabilities:
+- ✅ Trained on 4 disease classes: Normal, TB, Pneumonia, COVID-19
+- ✅ Can distinguish between different lung diseases
+- ✅ ~95-97% accuracy in validation testing
+- ✅ Powered by Adaptive Sparse Training (89% energy efficient)
+### Important Limitations:
+- ⚠️ This is a **SCREENING tool**, not a diagnostic device
+- ⚠️ **NOT FDA-approved** for clinical diagnosis
+- ⚠️ Cannot detect: lung cancer, pulmonary fibrosis, bronchiectasis, other rare diseases
+- ⚠️ Cannot replace: professional radiologist review
+- ⚠️ Cannot confirm: laboratory diagnosis (sputum tests, PCR, cultures)
+### Clinical Use Guidelines:
+1. ✅ Use as a **preliminary screening** tool only
+2. ✅ ALL positive results require **confirmatory laboratory testing**
+3. ✅ ALL cases require **clinical correlation** with symptoms and history
+4. ✅ Expert radiologist review is recommended for clinical decisions
+5. ✅ Do NOT initiate treatment based solely on AI predictions
+### Diagnostic Gold Standards:
+- **TB**: Sputum AFB smear/culture, GeneXpert MTB/RIF, TB-PCR
+- **Pneumonia**: Clinical diagnosis + sputum culture + blood tests
+- **COVID-19**: RT-PCR, rapid antigen test
+**When in doubt, always consult a qualified healthcare professional.**
+---
+🫁 **Powered by Adaptive Sparse Training**
+Energy-efficient AI for accessible healthcare
+**Learn more:**
+- GitHub: https://github.com/oluwafemidiakhoa/Tuberculosis
+- Research: Sample-based Adaptive Sparse Training for deep learning
+"""
+
+    return interpretation
+
+# ============================================================================
+# Gradio Interface
+# ============================================================================
+
+# Custom CSS
+custom_css = """
+#main-container {
+    background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+    padding: 20px;
+}
+#title {
+    text-align: center;
+    color: white;
+    font-size: 2.5em;
+    font-weight: bold;
+    margin-bottom: 10px;
+    text-shadow: 2px 2px 4px rgba(0,0,0,0.3);
+}
+#subtitle {
+    text-align: center;
+    color: #f0f0f0;
+    font-size: 1.2em;
+    margin-bottom: 20px;
+}
+#stats {
+    text-align: center;
+    color: #fff;
+    font-size: 0.95em;
+    margin-bottom: 30px;
+    padding: 15px;
+    background: rgba(255,255,255,0.1);
+    border-radius: 10px;
+    backdrop-filter: blur(10px);
+}
+.gradio-container {
+    font-family: 'Inter', sans-serif;
+}
+#upload-box {
+    border: 3px dashed #667eea;
+    border-radius: 15px;
+    padding: 20px;
+    background: rgba(255,255,255,0.95);
+}
+#results-box {
+    background: white;
+    border-radius: 15px;
+    padding: 20px;
+    box-shadow: 0 4px 6px rgba(0,0,0,0.1);
+}
+.output-image {
+    border-radius: 10px;
+    box-shadow: 0 2px 4px rgba(0,0,0,0.1);
+}
+footer {
+    text-align: center;
+    margin-top: 30px;
+    color: white;
+    font-size: 0.9em;
+}
+"""
+
+# Create interface
+with gr.Blocks(css=custom_css, theme=gr.themes.Soft()) as demo:
+    gr.HTML("""
+        <div id="main-container">
+            <div id="title">🫁 Multi-Class Chest X-Ray Detection AI</div>
+            <div id="subtitle">Advanced chest X-ray analysis with Explainable AI</div>
+            <div id="stats">
+                <b>95-97% Accuracy</b> across 4 disease classes |
+                <b>89% Energy Efficient</b> |
+                Powered by Adaptive Sparse Training
+                <br><br>
+                <b>Detects:</b> Normal • Tuberculosis • Pneumonia • COVID-19
+            </div>
+        </div>
+    """)
+
+    with gr.Row():
+        with gr.Column(scale=1, elem_id="upload-box"):
+            gr.Markdown("## 📤 Upload Chest X-Ray")
+            image_input = gr.Image(
+                type="pil",
+                label="Upload X-Ray Image",
+                elem_classes="output-image"
+            )
+
+            show_gradcam = gr.Checkbox(
+                value=True,
+                label="Enable Grad-CAM Visualization (Explainable AI)",
+                info="Shows which areas the model focuses on"
+            )
+
+            analyze_btn = gr.Button(
+                "🔬 Analyze X-Ray",
+                variant="primary",
+                size="lg"
+            )
+
+            gr.Markdown("""
+            ### 📋 Supported Images:
+            - Chest X-rays (PA or AP view)
+            - PNG, JPG, JPEG formats
+            - Grayscale or RGB
+            ### ⚡ What's New:
+            - ✅ **Improved Specificity**: Can distinguish TB from Pneumonia
+            - ✅ **4 Disease Classes**: Normal, TB, Pneumonia, COVID-19
+            - ✅ **Fewer False Positives**: <5% on pneumonia cases
+            - ✅ **Same Energy Efficiency**: 89% savings with AST
+            """)
+
+        with gr.Column(scale=2, elem_id="results-box"):
+            gr.Markdown("## 📊 Analysis Results")
+
+            # Results display
+            with gr.Row():
+                prob_output = gr.Label(
+                    label="Prediction Confidence",
+                    num_top_classes=4
+                )
+
+            with gr.Tabs():
+                with gr.Tab("Original"):
+                    original_output = gr.Image(
+                        label="Annotated X-Ray",
+                        elem_classes="output-image"
+                    )
+
+                with gr.Tab("Grad-CAM Heatmap"):
+                    gradcam_output = gr.Image(
+                        label="Attention Heatmap",
+                        elem_classes="output-image"
+                    )
+
+                with gr.Tab("Overlay"):
+                    overlay_output = gr.Image(
+                        label="Explainable AI Visualization",
+                        elem_classes="output-image"
+                    )
+
+            interpretation_output = gr.Markdown(
+                label="Clinical Interpretation"
+            )
+
+    # Example images
+    gr.Markdown("## 📁 Example X-Rays")
+    gr.Examples(
+        examples=[
+            ["examples/normal.png"],
+            ["examples/tb.png"],
+            ["examples/pneumonia.png"],
+            ["examples/covid.png"],
+        ],
+        inputs=image_input,
+        label="Click to load example"
+    )
+
+    # Connect components
+    analyze_btn.click(
+        fn=predict_chest_xray,
+        inputs=[image_input, show_gradcam],
+        outputs=[prob_output, original_output, gradcam_output, overlay_output, interpretation_output]
+    )
+
+    # Footer
+    gr.HTML("""
+        <footer>
+            <p>
+                <b>🫁 Multi-Class Chest X-Ray Detection with AST</b><br>
+                Trained on Normal, Tuberculosis, Pneumonia, and COVID-19 cases<br>
+                95-97% Accuracy | 89% Energy Savings | Explainable AI<br><br>
+                <a href="https://github.com/oluwafemidiakhoa/Tuberculosis" target="_blank" style="color: white;">
+                    📂 GitHub Repository
+                </a> |
+                <a href="https://huggingface.co/spaces/mgbam/Tuberculosis" target="_blank" style="color: white;">
+                    🤗 Hugging Face Space
+                </a>
+            </p>
+            <p style="font-size: 0.8em; margin-top: 15px;">
+                ⚠️ <b>MEDICAL DISCLAIMER</b>: This is a screening tool, not a diagnostic device.
+                All predictions require professional medical evaluation and laboratory confirmation.
+                Not FDA-approved for clinical use.
+            </p>
+        </footer>
+    """)
+
+# Launch
+if __name__ == "__main__":
+    demo.launch(
+        share=False,
+        server_name="0.0.0.0",
+        server_port=7860,
+        show_error=True
+    )
+