Commit ·
26c7cba
1
Parent(s): 4f997f9
Add comprehensive LLM endpoints and enhance FastAPI backend
Browse files- Add Google Gemini AI integration for chat and report generation
- Implement /api/chat endpoint for conversational AI assistant
- Implement /api/generate-report endpoint for automated report generation
- Add Pydantic models for request validation
- Update health check endpoint to show AI model and LLM status
- Add google-generativeai and python-dotenv to requirements
- Create .env.example template for environment variables
- Add comprehensive API documentation (API_DOCUMENTATION.md)
- Create test_api.py script for endpoint testing
- Update .gitignore to exclude .env files
- Support both GEMINI_API_KEY and VITE_GEMINI_API_KEY env vars
- .env.example +7 -0
- .gitignore +5 -0
- API_DOCUMENTATION.md +363 -0
- backend/app.py +182 -2
- backend/requirements.txt +3 -0
- backend/test_api.py +275 -0
.env.example
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# Gemini API Key for LLM functionality
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# Get your API key from: https://makersuite.google.com/app/apikey
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GEMINI_API_KEY=your_gemini_api_key_here
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VITE_GEMINI_API_KEY=your_gemini_api_key_here
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# Optional: Model Configuration
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# GEMINI_MODEL=gemini-1.5-flash
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.gitignore
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*.pyd
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.venv/
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# Editor directories and files
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.vscode/*
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!.vscode/extensions.json
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*.pyd
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.venv/
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# Environment variables
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.env
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.env.local
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.env.*.local
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# Editor directories and files
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.vscode/*
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!.vscode/extensions.json
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API_DOCUMENTATION.md
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# Pathora Colposcopy API Documentation
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## Overview
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FastAPI backend for Pathora Colposcopy Assistant with AI model inference and LLM capabilities.
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## Base URL
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- Local: `http://localhost:8000`
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- Production: `https://huggingface.co/spaces/ManalifeAI/Pathora_Colposcopy_Assistant`
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---
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## Endpoints
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### Health Check
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**GET** `/health`
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Check API health status and verify AI models and LLM availability.
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**Response:**
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```json
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{
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"status": "healthy",
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"service": "Pathora Colposcopy API",
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"ai_models": {
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"acetowhite_model": "loaded",
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"cervix_model": "loaded"
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},
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"llm": {
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"gemini_available": true,
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"api_key_configured": true
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}
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}
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```
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---
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## AI Model Endpoints
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### 1. Acetowhite Contour Detection
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**POST** `/api/infer-aw-contour`
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Detect acetowhite lesions and generate contour overlays.
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**Parameters:**
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- `file` (UploadFile): Image file
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- `conf_threshold` (float, optional): Confidence threshold (0.0-1.0, default: 0.4)
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**Response:**
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```json
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{
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"status": "success",
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"message": "Inference completed successfully",
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"result_image": "base64_encoded_image",
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"contours": [
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{
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"points": [[x1, y1], [x2, y2], ...],
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"area": 1234.5,
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"confidence": 0.85
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}
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],
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"detections": 2,
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"confidence_threshold": 0.4
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}
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```
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### 2. Cervix Bounding Box Detection
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**POST** `/api/infer-cervix-bbox`
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Detect cervix location and return bounding boxes.
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**Parameters:**
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- `file` (UploadFile): Image file
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- `conf_threshold` (float, optional): Confidence threshold (0.0-1.0, default: 0.4)
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**Response:**
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```json
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{
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"status": "success",
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"message": "Cervix bounding box detection completed",
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"result_image": "base64_encoded_image",
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"bounding_boxes": [
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{
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"x1": 100,
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"y1": 150,
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"x2": 400,
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"y2": 450,
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"confidence": 0.92,
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"class": "cervix"
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}
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],
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"detections": 1,
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"frame_width": 1920,
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"frame_height": 1080,
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"confidence_threshold": 0.4
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}
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```
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### 3. Batch Image Inference
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**POST** `/api/batch-infer`
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Process multiple images for acetowhite detection in one request.
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**Parameters:**
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- `files` (List[UploadFile]): Multiple image files
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- `conf_threshold` (float, optional): Confidence threshold (default: 0.4)
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**Response:**
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```json
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{
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"status": "completed",
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"total_files": 3,
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"results": [
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{
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"filename": "image1.jpg",
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"status": "success",
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"result_image": "base64...",
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"contours": [...],
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"detections": 2
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}
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]
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}
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```
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### 4. Single Frame Analysis
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**POST** `/infer/image`
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Analyze single image for cervix quality assessment.
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**Parameters:**
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- `file` (UploadFile): Image file
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**Response:**
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```json
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{
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"status": "Excellent",
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"quality_percent": 95,
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"cervix_detected": true,
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"focus_score": 0.89,
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"brightness_score": 0.92
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}
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```
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### 5. Video Frame Analysis
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**POST** `/infer/video`
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Process video frames for quality assessment.
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**Parameters:**
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| 149 |
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- `file` (UploadFile): Video file
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**Response:**
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| 152 |
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```json
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| 153 |
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{
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"total_frames": 150,
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| 155 |
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"results": [
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| 156 |
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{
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| 157 |
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"frame": 0,
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| 158 |
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"status": "Excellent",
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| 159 |
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"quality_percent": 95
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}
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]
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| 162 |
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}
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```
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---
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## LLM Endpoints
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| 168 |
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| 169 |
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### 6. Chat with AI Assistant
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| 170 |
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**POST** `/api/chat`
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| 171 |
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Conversational AI endpoint for colposcopy guidance.
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| 173 |
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| 174 |
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**Request Body:**
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| 175 |
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```json
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| 176 |
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{
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| 177 |
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"message": "What are the signs of high-grade lesions?",
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| 178 |
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"history": [
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| 179 |
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{
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| 180 |
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"role": "user",
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| 181 |
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"text": "Hello"
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| 182 |
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},
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| 183 |
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{
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| 184 |
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"role": "bot",
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| 185 |
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"text": "Hello! I'm Pathora AI..."
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| 186 |
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}
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],
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| 188 |
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"system_prompt": "Optional custom system prompt"
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| 189 |
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}
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```
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| 191 |
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| 192 |
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**Response:**
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| 193 |
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```json
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| 194 |
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{
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| 195 |
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"status": "success",
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| 196 |
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"response": "High-grade lesions typically show...",
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| 197 |
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"model": "gemini-1.5-flash"
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| 198 |
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}
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```
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| 200 |
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### 7. Generate Colposcopy Report
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| 202 |
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**POST** `/api/generate-report`
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| 203 |
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| 204 |
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Generate comprehensive colposcopy report based on patient data and findings.
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| 205 |
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| 206 |
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**Request Body:**
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| 207 |
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```json
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| 208 |
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{
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| 209 |
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"patient_data": {
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| 210 |
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"age": 35,
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| 211 |
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"gravida": 2,
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| 212 |
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"para": 2,
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| 213 |
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"lmp": "2024-02-01",
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| 214 |
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"indication": "Abnormal Pap smear"
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| 215 |
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},
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| 216 |
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"exam_findings": {
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| 217 |
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"native": {
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| 218 |
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"cervix_visible": true,
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| 219 |
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"transformation_zone": "Type 1"
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| 220 |
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},
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| 221 |
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"acetic_acid": {
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| 222 |
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"acetowhite_lesions": true,
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| 223 |
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"location": "6-9 o'clock"
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| 224 |
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},
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| 225 |
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"green_filter": {
|
| 226 |
+
"vascular_patterns": "Punctation"
|
| 227 |
+
},
|
| 228 |
+
"lugol": {
|
| 229 |
+
"iodine_uptake": "Partial"
|
| 230 |
+
}
|
| 231 |
+
},
|
| 232 |
+
"images": [],
|
| 233 |
+
"system_prompt": "Optional custom prompt"
|
| 234 |
+
}
|
| 235 |
+
```
|
| 236 |
+
|
| 237 |
+
**Response:**
|
| 238 |
+
```json
|
| 239 |
+
{
|
| 240 |
+
"status": "success",
|
| 241 |
+
"report": "COLPOSCOPY REPORT\n\nCLINICAL SUMMARY:\n...",
|
| 242 |
+
"model": "gemini-1.5-flash"
|
| 243 |
+
}
|
| 244 |
+
```
|
| 245 |
+
|
| 246 |
+
---
|
| 247 |
+
|
| 248 |
+
## Environment Variables
|
| 249 |
+
|
| 250 |
+
Required for LLM functionality:
|
| 251 |
+
|
| 252 |
+
```bash
|
| 253 |
+
GEMINI_API_KEY=your_api_key_here
|
| 254 |
+
VITE_GEMINI_API_KEY=your_api_key_here # For frontend compatibility
|
| 255 |
+
```
|
| 256 |
+
|
| 257 |
+
Get your API key from: https://makersuite.google.com/app/apikey
|
| 258 |
+
|
| 259 |
+
---
|
| 260 |
+
|
| 261 |
+
## Error Responses
|
| 262 |
+
|
| 263 |
+
All endpoints return standardized error responses:
|
| 264 |
+
|
| 265 |
+
```json
|
| 266 |
+
{
|
| 267 |
+
"detail": "Error message description"
|
| 268 |
+
}
|
| 269 |
+
```
|
| 270 |
+
|
| 271 |
+
**Common HTTP Status Codes:**
|
| 272 |
+
- `400`: Bad Request (invalid file, parameters)
|
| 273 |
+
- `500`: Internal Server Error (AI model error, processing failure)
|
| 274 |
+
- `503`: Service Unavailable (LLM not configured, API key missing)
|
| 275 |
+
|
| 276 |
+
---
|
| 277 |
+
|
| 278 |
+
## Model Information
|
| 279 |
+
|
| 280 |
+
### AI Models
|
| 281 |
+
- **Acetowhite Detection**: YOLO-based segmentation model (`AW_yolo.pt`)
|
| 282 |
+
- **Cervix Detection**: YOLO-based object detection model (`cervix_yolo.pt`)
|
| 283 |
+
|
| 284 |
+
### LLM Model
|
| 285 |
+
- **Gemini 1.5 Flash**: Google's generative AI for chat and report generation
|
| 286 |
+
- Temperature: 0.4 (balanced between creativity and consistency)
|
| 287 |
+
- Max Output Tokens: 2048
|
| 288 |
+
|
| 289 |
+
---
|
| 290 |
+
|
| 291 |
+
## Usage Examples
|
| 292 |
+
|
| 293 |
+
### Python
|
| 294 |
+
```python
|
| 295 |
+
import requests
|
| 296 |
+
|
| 297 |
+
# AI Model Inference
|
| 298 |
+
with open('image.jpg', 'rb') as f:
|
| 299 |
+
response = requests.post(
|
| 300 |
+
'http://localhost:8000/api/infer-aw-contour',
|
| 301 |
+
files={'file': f},
|
| 302 |
+
data={'conf_threshold': 0.5}
|
| 303 |
+
)
|
| 304 |
+
result = response.json()
|
| 305 |
+
|
| 306 |
+
# Chat
|
| 307 |
+
response = requests.post(
|
| 308 |
+
'http://localhost:8000/api/chat',
|
| 309 |
+
json={
|
| 310 |
+
'message': 'What is Reid colposcopic index?',
|
| 311 |
+
'history': []
|
| 312 |
+
}
|
| 313 |
+
)
|
| 314 |
+
chat_result = response.json()
|
| 315 |
+
```
|
| 316 |
+
|
| 317 |
+
### JavaScript/TypeScript
|
| 318 |
+
```typescript
|
| 319 |
+
// AI Model Inference
|
| 320 |
+
const formData = new FormData();
|
| 321 |
+
formData.append('file', imageFile);
|
| 322 |
+
formData.append('conf_threshold', '0.5');
|
| 323 |
+
|
| 324 |
+
const response = await fetch('/api/infer-aw-contour', {
|
| 325 |
+
method: 'POST',
|
| 326 |
+
body: formData
|
| 327 |
+
});
|
| 328 |
+
const result = await response.json();
|
| 329 |
+
|
| 330 |
+
// Chat
|
| 331 |
+
const chatResponse = await fetch('/api/chat', {
|
| 332 |
+
method: 'POST',
|
| 333 |
+
headers: { 'Content-Type': 'application/json' },
|
| 334 |
+
body: JSON.stringify({
|
| 335 |
+
message: 'Explain transformation zone types',
|
| 336 |
+
history: []
|
| 337 |
+
})
|
| 338 |
+
});
|
| 339 |
+
const chatResult = await chatResponse.json();
|
| 340 |
+
```
|
| 341 |
+
|
| 342 |
+
---
|
| 343 |
+
|
| 344 |
+
## Development
|
| 345 |
+
|
| 346 |
+
### Running Locally
|
| 347 |
+
```bash
|
| 348 |
+
# Install dependencies
|
| 349 |
+
cd backend
|
| 350 |
+
pip install -r requirements.txt
|
| 351 |
+
|
| 352 |
+
# Set environment variables
|
| 353 |
+
export GEMINI_API_KEY=your_key
|
| 354 |
+
|
| 355 |
+
# Run server
|
| 356 |
+
uvicorn backend.app:app --reload --host 0.0.0.0 --port 8000
|
| 357 |
+
```
|
| 358 |
+
|
| 359 |
+
### Building with Docker
|
| 360 |
+
```bash
|
| 361 |
+
docker build -t pathora-colpo .
|
| 362 |
+
docker run -p 7860:7860 -e GEMINI_API_KEY=your_key pathora-colpo
|
| 363 |
+
```
|
backend/app.py
CHANGED
|
@@ -1,7 +1,8 @@
|
|
| 1 |
-
from fastapi import FastAPI, File, UploadFile, HTTPException
|
| 2 |
from fastapi.responses import JSONResponse
|
| 3 |
from fastapi.middleware.cors import CORSMiddleware
|
| 4 |
from fastapi.staticfiles import StaticFiles
|
|
|
|
| 5 |
import cv2
|
| 6 |
import numpy as np
|
| 7 |
import tempfile
|
|
@@ -10,8 +11,18 @@ from io import BytesIO
|
|
| 10 |
from PIL import Image
|
| 11 |
import uvicorn
|
| 12 |
import traceback
|
|
|
|
|
|
|
| 13 |
from .inference import infer_aw_contour, analyze_frame, analyze_video_frame, infer_cervix_bbox
|
| 14 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 15 |
app = FastAPI(title="Pathora Colposcopy API", version="1.0.0")
|
| 16 |
|
| 17 |
# Add CORS middleware to allow requests from frontend
|
|
@@ -23,6 +34,34 @@ app.add_middleware(
|
|
| 23 |
allow_headers=["*"],
|
| 24 |
)
|
| 25 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 26 |
|
| 27 |
class SPAStaticFiles(StaticFiles):
|
| 28 |
async def get_response(self, path: str, scope):
|
|
@@ -35,7 +74,148 @@ class SPAStaticFiles(StaticFiles):
|
|
| 35 |
@app.get("/health")
|
| 36 |
async def health_check():
|
| 37 |
"""Health check endpoint"""
|
| 38 |
-
return {
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 39 |
|
| 40 |
|
| 41 |
@app.post("/api/infer-aw-contour")
|
|
|
|
| 1 |
+
from fastapi import FastAPI, File, UploadFile, HTTPException, Body
|
| 2 |
from fastapi.responses import JSONResponse
|
| 3 |
from fastapi.middleware.cors import CORSMiddleware
|
| 4 |
from fastapi.staticfiles import StaticFiles
|
| 5 |
+
from pydantic import BaseModel
|
| 6 |
import cv2
|
| 7 |
import numpy as np
|
| 8 |
import tempfile
|
|
|
|
| 11 |
from PIL import Image
|
| 12 |
import uvicorn
|
| 13 |
import traceback
|
| 14 |
+
import json
|
| 15 |
+
from typing import List, Dict, Optional
|
| 16 |
from .inference import infer_aw_contour, analyze_frame, analyze_video_frame, infer_cervix_bbox
|
| 17 |
|
| 18 |
+
# Import Google Gemini (optional - graceful degradation if not installed)
|
| 19 |
+
try:
|
| 20 |
+
import google.generativeai as genai
|
| 21 |
+
GEMINI_AVAILABLE = True
|
| 22 |
+
except ImportError:
|
| 23 |
+
GEMINI_AVAILABLE = False
|
| 24 |
+
print("⚠️ google-generativeai not installed. LLM endpoints will be unavailable.")
|
| 25 |
+
|
| 26 |
app = FastAPI(title="Pathora Colposcopy API", version="1.0.0")
|
| 27 |
|
| 28 |
# Add CORS middleware to allow requests from frontend
|
|
|
|
| 34 |
allow_headers=["*"],
|
| 35 |
)
|
| 36 |
|
| 37 |
+
# Initialize Gemini if available
|
| 38 |
+
GEMINI_API_KEY = os.getenv("GEMINI_API_KEY") or os.getenv("VITE_GEMINI_API_KEY")
|
| 39 |
+
if GEMINI_AVAILABLE and GEMINI_API_KEY:
|
| 40 |
+
try:
|
| 41 |
+
genai.configure(api_key=GEMINI_API_KEY)
|
| 42 |
+
print("✅ Gemini AI configured successfully")
|
| 43 |
+
except Exception as e:
|
| 44 |
+
print(f"⚠️ Failed to configure Gemini: {e}")
|
| 45 |
+
GEMINI_AVAILABLE = False
|
| 46 |
+
elif GEMINI_AVAILABLE:
|
| 47 |
+
print("⚠️ GEMINI_API_KEY not found in environment variables")
|
| 48 |
+
|
| 49 |
+
# Pydantic models for LLM endpoints
|
| 50 |
+
class ChatMessage(BaseModel):
|
| 51 |
+
role: str
|
| 52 |
+
text: str
|
| 53 |
+
|
| 54 |
+
class ChatRequest(BaseModel):
|
| 55 |
+
message: str
|
| 56 |
+
history: List[ChatMessage] = []
|
| 57 |
+
system_prompt: Optional[str] = None
|
| 58 |
+
|
| 59 |
+
class ReportGenerationRequest(BaseModel):
|
| 60 |
+
patient_data: Dict
|
| 61 |
+
exam_findings: Dict
|
| 62 |
+
images: Optional[List[str]] = [] # base64 encoded images
|
| 63 |
+
system_prompt: Optional[str] = None
|
| 64 |
+
|
| 65 |
|
| 66 |
class SPAStaticFiles(StaticFiles):
|
| 67 |
async def get_response(self, path: str, scope):
|
|
|
|
| 74 |
@app.get("/health")
|
| 75 |
async def health_check():
|
| 76 |
"""Health check endpoint"""
|
| 77 |
+
return {
|
| 78 |
+
"status": "healthy",
|
| 79 |
+
"service": "Pathora Colposcopy API",
|
| 80 |
+
"ai_models": {
|
| 81 |
+
"acetowhite_model": "loaded",
|
| 82 |
+
"cervix_model": "loaded"
|
| 83 |
+
},
|
| 84 |
+
"llm": {
|
| 85 |
+
"gemini_available": GEMINI_AVAILABLE,
|
| 86 |
+
"api_key_configured": bool(GEMINI_API_KEY)
|
| 87 |
+
}
|
| 88 |
+
}
|
| 89 |
+
|
| 90 |
+
|
| 91 |
+
@app.post("/api/chat")
|
| 92 |
+
async def chat_endpoint(request: ChatRequest):
|
| 93 |
+
"""
|
| 94 |
+
LLM Chat endpoint for conversational AI assistant
|
| 95 |
+
|
| 96 |
+
Args:
|
| 97 |
+
request: ChatRequest with message, history, and optional system_prompt
|
| 98 |
+
|
| 99 |
+
Returns:
|
| 100 |
+
JSON with AI response
|
| 101 |
+
"""
|
| 102 |
+
if not GEMINI_AVAILABLE:
|
| 103 |
+
raise HTTPException(
|
| 104 |
+
status_code=503,
|
| 105 |
+
detail="Gemini AI is not available. Install google-generativeai package."
|
| 106 |
+
)
|
| 107 |
+
|
| 108 |
+
if not GEMINI_API_KEY:
|
| 109 |
+
raise HTTPException(
|
| 110 |
+
status_code=503,
|
| 111 |
+
detail="GEMINI_API_KEY not configured in environment variables"
|
| 112 |
+
)
|
| 113 |
+
|
| 114 |
+
try:
|
| 115 |
+
# Use system prompt or default
|
| 116 |
+
system_prompt = request.system_prompt or """You are Pathora AI — a specialist colposcopy assistant. \
|
| 117 |
+
Provide expert guidance on examination techniques, findings interpretation, and management guidelines. \
|
| 118 |
+
Be professional, evidence-based, and concise."""
|
| 119 |
+
|
| 120 |
+
# Initialize Gemini model
|
| 121 |
+
model = genai.GenerativeModel(
|
| 122 |
+
model_name="gemini-1.5-flash",
|
| 123 |
+
system_instruction=system_prompt
|
| 124 |
+
)
|
| 125 |
+
|
| 126 |
+
# Build conversation history
|
| 127 |
+
chat_history = []
|
| 128 |
+
for msg in request.history:
|
| 129 |
+
role = "model" if msg.role == "bot" else "user"
|
| 130 |
+
chat_history.append({
|
| 131 |
+
"role": role,
|
| 132 |
+
"parts": [msg.text]
|
| 133 |
+
})
|
| 134 |
+
|
| 135 |
+
# Start chat with history
|
| 136 |
+
chat = model.start_chat(history=chat_history)
|
| 137 |
+
|
| 138 |
+
# Send message and get response
|
| 139 |
+
response = chat.send_message(request.message)
|
| 140 |
+
|
| 141 |
+
return JSONResponse({
|
| 142 |
+
"status": "success",
|
| 143 |
+
"response": response.text,
|
| 144 |
+
"model": "gemini-1.5-flash"
|
| 145 |
+
})
|
| 146 |
+
|
| 147 |
+
except Exception as e:
|
| 148 |
+
print(f"❌ Chat error: {e}")
|
| 149 |
+
traceback.print_exc()
|
| 150 |
+
raise HTTPException(status_code=500, detail=f"Chat error: {str(e)}")
|
| 151 |
+
|
| 152 |
+
|
| 153 |
+
@app.post("/api/generate-report")
|
| 154 |
+
async def generate_report_endpoint(request: ReportGenerationRequest):
|
| 155 |
+
"""
|
| 156 |
+
Generate colposcopy report using LLM based on patient data and exam findings
|
| 157 |
+
|
| 158 |
+
Args:
|
| 159 |
+
request: ReportGenerationRequest with patient data, exam findings, and images
|
| 160 |
+
|
| 161 |
+
Returns:
|
| 162 |
+
JSON with generated report
|
| 163 |
+
"""
|
| 164 |
+
if not GEMINI_AVAILABLE:
|
| 165 |
+
raise HTTPException(
|
| 166 |
+
status_code=503,
|
| 167 |
+
detail="Gemini AI is not available. Install google-generativeai package."
|
| 168 |
+
)
|
| 169 |
+
|
| 170 |
+
if not GEMINI_API_KEY:
|
| 171 |
+
raise HTTPException(
|
| 172 |
+
status_code=503,
|
| 173 |
+
detail="GEMINI_API_KEY not configured in environment variables"
|
| 174 |
+
)
|
| 175 |
+
|
| 176 |
+
try:
|
| 177 |
+
# Use system prompt or default
|
| 178 |
+
system_prompt = request.system_prompt or """You are an expert colposcopy AI assistant acting as a specialist gynaecologist.
|
| 179 |
+
Analyse ALL the clinical data and the attached colposcopy images to generate a professional, evidence-based colposcopy report conclusion."""
|
| 180 |
+
|
| 181 |
+
# Build prompt with patient data and findings
|
| 182 |
+
prompt_parts = []
|
| 183 |
+
|
| 184 |
+
# Add patient data
|
| 185 |
+
prompt_parts.append("PATIENT DATA:")
|
| 186 |
+
prompt_parts.append(json.dumps(request.patient_data, indent=2))
|
| 187 |
+
|
| 188 |
+
# Add exam findings
|
| 189 |
+
prompt_parts.append("\nEXAMINATION FINDINGS:")
|
| 190 |
+
prompt_parts.append(json.dumps(request.exam_findings, indent=2))
|
| 191 |
+
|
| 192 |
+
# Add instruction
|
| 193 |
+
prompt_parts.append("\nBased on the above data, generate a professional colposcopy report with:")
|
| 194 |
+
prompt_parts.append("1. Summary of findings")
|
| 195 |
+
prompt_parts.append("2. Clinical impression")
|
| 196 |
+
prompt_parts.append("3. Recommendations")
|
| 197 |
+
|
| 198 |
+
full_prompt = "\n".join(prompt_parts)
|
| 199 |
+
|
| 200 |
+
# Initialize model
|
| 201 |
+
model = genai.GenerativeModel(
|
| 202 |
+
model_name="gemini-1.5-flash",
|
| 203 |
+
system_instruction=system_prompt
|
| 204 |
+
)
|
| 205 |
+
|
| 206 |
+
# Generate report
|
| 207 |
+
response = model.generate_content(full_prompt)
|
| 208 |
+
|
| 209 |
+
return JSONResponse({
|
| 210 |
+
"status": "success",
|
| 211 |
+
"report": response.text,
|
| 212 |
+
"model": "gemini-1.5-flash"
|
| 213 |
+
})
|
| 214 |
+
|
| 215 |
+
except Exception as e:
|
| 216 |
+
print(f"❌ Report generation error: {e}")
|
| 217 |
+
traceback.print_exc()
|
| 218 |
+
raise HTTPException(status_code=500, detail=f"Report generation error: {str(e)}")
|
| 219 |
|
| 220 |
|
| 221 |
@app.post("/api/infer-aw-contour")
|
backend/requirements.txt
CHANGED
|
@@ -8,3 +8,6 @@ ultralytics
|
|
| 8 |
pillow==10.2.0
|
| 9 |
python-multipart==0.0.6
|
| 10 |
setuptools>=69.0.0
|
|
|
|
|
|
|
|
|
|
|
|
| 8 |
pillow==10.2.0
|
| 9 |
python-multipart==0.0.6
|
| 10 |
setuptools>=69.0.0
|
| 11 |
+
google-generativeai>=0.3.0
|
| 12 |
+
python-dotenv>=1.0.0
|
| 13 |
+
pydantic>=2.0.0
|
backend/test_api.py
ADDED
|
@@ -0,0 +1,275 @@
|
|
|
|
|
|
|
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|
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|
|
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|
|
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|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""
|
| 2 |
+
Test script for Pathora Colposcopy API endpoints
|
| 3 |
+
Demonstrates how to use both AI model and LLM endpoints
|
| 4 |
+
"""
|
| 5 |
+
|
| 6 |
+
import requests
|
| 7 |
+
import json
|
| 8 |
+
import base64
|
| 9 |
+
from pathlib import Path
|
| 10 |
+
|
| 11 |
+
# API Configuration
|
| 12 |
+
BASE_URL = "http://localhost:8000" # Change to your deployment URL
|
| 13 |
+
API_KEY = "your_gemini_api_key_here" # For local testing
|
| 14 |
+
|
| 15 |
+
def test_health_check():
|
| 16 |
+
"""Test the health check endpoint"""
|
| 17 |
+
print("=" * 60)
|
| 18 |
+
print("Testing Health Check Endpoint")
|
| 19 |
+
print("=" * 60)
|
| 20 |
+
|
| 21 |
+
response = requests.get(f"{BASE_URL}/health")
|
| 22 |
+
print(f"Status Code: {response.status_code}")
|
| 23 |
+
print(f"Response: {json.dumps(response.json(), indent=2)}")
|
| 24 |
+
print()
|
| 25 |
+
|
| 26 |
+
def test_acetowhite_detection(image_path: str):
|
| 27 |
+
"""Test acetowhite contour detection"""
|
| 28 |
+
print("=" * 60)
|
| 29 |
+
print("Testing Acetowhite Contour Detection")
|
| 30 |
+
print("=" * 60)
|
| 31 |
+
|
| 32 |
+
with open(image_path, 'rb') as f:
|
| 33 |
+
files = {'file': f}
|
| 34 |
+
data = {'conf_threshold': 0.5}
|
| 35 |
+
|
| 36 |
+
response = requests.post(
|
| 37 |
+
f"{BASE_URL}/api/infer-aw-contour",
|
| 38 |
+
files=files,
|
| 39 |
+
data=data
|
| 40 |
+
)
|
| 41 |
+
|
| 42 |
+
print(f"Status Code: {response.status_code}")
|
| 43 |
+
result = response.json()
|
| 44 |
+
|
| 45 |
+
# Print without base64 image for readability
|
| 46 |
+
print(f"Status: {result.get('status')}")
|
| 47 |
+
print(f"Detections: {result.get('detections')}")
|
| 48 |
+
print(f"Contours: {len(result.get('contours', []))}")
|
| 49 |
+
print(f"Confidence Threshold: {result.get('confidence_threshold')}")
|
| 50 |
+
|
| 51 |
+
# Save result image if available
|
| 52 |
+
if result.get('result_image'):
|
| 53 |
+
output_path = "test_output_aw.png"
|
| 54 |
+
img_data = base64.b64decode(result['result_image'])
|
| 55 |
+
with open(output_path, 'wb') as f:
|
| 56 |
+
f.write(img_data)
|
| 57 |
+
print(f"Result image saved to: {output_path}")
|
| 58 |
+
print()
|
| 59 |
+
|
| 60 |
+
def test_cervix_detection(image_path: str):
|
| 61 |
+
"""Test cervix bounding box detection"""
|
| 62 |
+
print("=" * 60)
|
| 63 |
+
print("Testing Cervix Bounding Box Detection")
|
| 64 |
+
print("=" * 60)
|
| 65 |
+
|
| 66 |
+
with open(image_path, 'rb') as f:
|
| 67 |
+
files = {'file': f}
|
| 68 |
+
data = {'conf_threshold': 0.4}
|
| 69 |
+
|
| 70 |
+
response = requests.post(
|
| 71 |
+
f"{BASE_URL}/api/infer-cervix-bbox",
|
| 72 |
+
files=files,
|
| 73 |
+
data=data
|
| 74 |
+
)
|
| 75 |
+
|
| 76 |
+
print(f"Status Code: {response.status_code}")
|
| 77 |
+
result = response.json()
|
| 78 |
+
|
| 79 |
+
print(f"Status: {result.get('status')}")
|
| 80 |
+
print(f"Detections: {result.get('detections')}")
|
| 81 |
+
print(f"Bounding Boxes: {json.dumps(result.get('bounding_boxes', []), indent=2)}")
|
| 82 |
+
|
| 83 |
+
# Save result image if available
|
| 84 |
+
if result.get('result_image'):
|
| 85 |
+
output_path = "test_output_cervix.png"
|
| 86 |
+
img_data = base64.b64decode(result['result_image'])
|
| 87 |
+
with open(output_path, 'wb') as f:
|
| 88 |
+
f.write(img_data)
|
| 89 |
+
print(f"Result image saved to: {output_path}")
|
| 90 |
+
print()
|
| 91 |
+
|
| 92 |
+
def test_batch_inference(image_paths: list):
|
| 93 |
+
"""Test batch inference on multiple images"""
|
| 94 |
+
print("=" * 60)
|
| 95 |
+
print("Testing Batch Inference")
|
| 96 |
+
print("=" * 60)
|
| 97 |
+
|
| 98 |
+
files = [('files', open(img, 'rb')) for img in image_paths]
|
| 99 |
+
data = {'conf_threshold': 0.5}
|
| 100 |
+
|
| 101 |
+
response = requests.post(
|
| 102 |
+
f"{BASE_URL}/api/batch-infer",
|
| 103 |
+
files=files,
|
| 104 |
+
data=data
|
| 105 |
+
)
|
| 106 |
+
|
| 107 |
+
# Close file handles
|
| 108 |
+
for _, f in files:
|
| 109 |
+
f.close()
|
| 110 |
+
|
| 111 |
+
print(f"Status Code: {response.status_code}")
|
| 112 |
+
result = response.json()
|
| 113 |
+
|
| 114 |
+
print(f"Status: {result.get('status')}")
|
| 115 |
+
print(f"Total Files: {result.get('total_files')}")
|
| 116 |
+
|
| 117 |
+
for i, res in enumerate(result.get('results', [])):
|
| 118 |
+
print(f"\nImage {i+1}: {res.get('filename')}")
|
| 119 |
+
print(f" Status: {res.get('status')}")
|
| 120 |
+
print(f" Detections: {res.get('detections')}")
|
| 121 |
+
print()
|
| 122 |
+
|
| 123 |
+
def test_chat():
|
| 124 |
+
"""Test LLM chat endpoint"""
|
| 125 |
+
print("=" * 60)
|
| 126 |
+
print("Testing Chat Endpoint")
|
| 127 |
+
print("=" * 60)
|
| 128 |
+
|
| 129 |
+
payload = {
|
| 130 |
+
"message": "What are the typical signs of a high-grade squamous intraepithelial lesion (HSIL) on colposcopy?",
|
| 131 |
+
"history": []
|
| 132 |
+
}
|
| 133 |
+
|
| 134 |
+
response = requests.post(
|
| 135 |
+
f"{BASE_URL}/api/chat",
|
| 136 |
+
json=payload
|
| 137 |
+
)
|
| 138 |
+
|
| 139 |
+
print(f"Status Code: {response.status_code}")
|
| 140 |
+
|
| 141 |
+
if response.status_code == 200:
|
| 142 |
+
result = response.json()
|
| 143 |
+
print(f"Status: {result.get('status')}")
|
| 144 |
+
print(f"Model: {result.get('model')}")
|
| 145 |
+
print(f"Response:\n{result.get('response')}")
|
| 146 |
+
else:
|
| 147 |
+
print(f"Error: {response.json()}")
|
| 148 |
+
print()
|
| 149 |
+
|
| 150 |
+
def test_chat_with_history():
|
| 151 |
+
"""Test chat with conversation history"""
|
| 152 |
+
print("=" * 60)
|
| 153 |
+
print("Testing Chat with History")
|
| 154 |
+
print("=" * 60)
|
| 155 |
+
|
| 156 |
+
payload = {
|
| 157 |
+
"message": "What about low-grade lesions?",
|
| 158 |
+
"history": [
|
| 159 |
+
{
|
| 160 |
+
"role": "user",
|
| 161 |
+
"text": "What are high-grade lesions?"
|
| 162 |
+
},
|
| 163 |
+
{
|
| 164 |
+
"role": "bot",
|
| 165 |
+
"text": "High-grade lesions (HSIL) show dense acetowhite epithelium, coarse punctation, and sharp borders."
|
| 166 |
+
}
|
| 167 |
+
]
|
| 168 |
+
}
|
| 169 |
+
|
| 170 |
+
response = requests.post(
|
| 171 |
+
f"{BASE_URL}/api/chat",
|
| 172 |
+
json=payload
|
| 173 |
+
)
|
| 174 |
+
|
| 175 |
+
print(f"Status Code: {response.status_code}")
|
| 176 |
+
|
| 177 |
+
if response.status_code == 200:
|
| 178 |
+
result = response.json()
|
| 179 |
+
print(f"Response:\n{result.get('response')}")
|
| 180 |
+
else:
|
| 181 |
+
print(f"Error: {response.json()}")
|
| 182 |
+
print()
|
| 183 |
+
|
| 184 |
+
def test_report_generation():
|
| 185 |
+
"""Test report generation endpoint"""
|
| 186 |
+
print("=" * 60)
|
| 187 |
+
print("Testing Report Generation")
|
| 188 |
+
print("=" * 60)
|
| 189 |
+
|
| 190 |
+
payload = {
|
| 191 |
+
"patient_data": {
|
| 192 |
+
"age": 35,
|
| 193 |
+
"gravida": 2,
|
| 194 |
+
"para": 2,
|
| 195 |
+
"lmp": "2024-02-01",
|
| 196 |
+
"indication": "Abnormal Pap smear - ASCUS",
|
| 197 |
+
"menstrual_status": "Regular"
|
| 198 |
+
},
|
| 199 |
+
"exam_findings": {
|
| 200 |
+
"native": {
|
| 201 |
+
"cervix_visible": True,
|
| 202 |
+
"transformation_zone": "Type 1 (fully visible)",
|
| 203 |
+
"ectropion": "Mild",
|
| 204 |
+
"discharge": "None"
|
| 205 |
+
},
|
| 206 |
+
"acetic_acid": {
|
| 207 |
+
"acetowhite_lesions": True,
|
| 208 |
+
"location": "6-9 o'clock position",
|
| 209 |
+
"density": "Dense white",
|
| 210 |
+
"borders": "Sharp, well-defined",
|
| 211 |
+
"size": "Moderate (covering 2 quadrants)"
|
| 212 |
+
},
|
| 213 |
+
"green_filter": {
|
| 214 |
+
"vascular_patterns": "Coarse punctation",
|
| 215 |
+
"mosaic": "Present",
|
| 216 |
+
"atypical_vessels": "None"
|
| 217 |
+
},
|
| 218 |
+
"lugol": {
|
| 219 |
+
"iodine_uptake": "Partial iodine negative area",
|
| 220 |
+
"pattern": "Corresponds to acetowhite area"
|
| 221 |
+
}
|
| 222 |
+
}
|
| 223 |
+
}
|
| 224 |
+
|
| 225 |
+
response = requests.post(
|
| 226 |
+
f"{BASE_URL}/api/generate-report",
|
| 227 |
+
json=payload
|
| 228 |
+
)
|
| 229 |
+
|
| 230 |
+
print(f"Status Code: {response.status_code}")
|
| 231 |
+
|
| 232 |
+
if response.status_code == 200:
|
| 233 |
+
result = response.json()
|
| 234 |
+
print(f"Status: {result.get('status')}")
|
| 235 |
+
print(f"Model: {result.get('model')}")
|
| 236 |
+
print(f"\nGenerated Report:\n{'-' * 60}")
|
| 237 |
+
print(result.get('report'))
|
| 238 |
+
print('-' * 60)
|
| 239 |
+
else:
|
| 240 |
+
print(f"Error: {response.json()}")
|
| 241 |
+
print()
|
| 242 |
+
|
| 243 |
+
def main():
|
| 244 |
+
"""Run all tests"""
|
| 245 |
+
print("\n" + "=" * 60)
|
| 246 |
+
print("PATHORA COLPOSCOPY API TEST SUITE")
|
| 247 |
+
print("=" * 60 + "\n")
|
| 248 |
+
|
| 249 |
+
# Test health check
|
| 250 |
+
test_health_check()
|
| 251 |
+
|
| 252 |
+
# Test AI model endpoints (you'll need to provide actual image paths)
|
| 253 |
+
# Uncomment and add your image paths:
|
| 254 |
+
# test_acetowhite_detection("path/to/your/image.jpg")
|
| 255 |
+
# test_cervix_detection("path/to/your/image.jpg")
|
| 256 |
+
# test_batch_inference(["image1.jpg", "image2.jpg"])
|
| 257 |
+
|
| 258 |
+
# Test LLM endpoints
|
| 259 |
+
test_chat()
|
| 260 |
+
test_chat_with_history()
|
| 261 |
+
test_report_generation()
|
| 262 |
+
|
| 263 |
+
print("\n" + "=" * 60)
|
| 264 |
+
print("ALL TESTS COMPLETED")
|
| 265 |
+
print("=" * 60 + "\n")
|
| 266 |
+
|
| 267 |
+
if __name__ == "__main__":
|
| 268 |
+
# Check if requests is installed
|
| 269 |
+
try:
|
| 270 |
+
import requests
|
| 271 |
+
except ImportError:
|
| 272 |
+
print("Please install requests: pip install requests")
|
| 273 |
+
exit(1)
|
| 274 |
+
|
| 275 |
+
main()
|