Context: Build a spatial risk assessment system correlating air quality data with children's respiratory disease incidence across Wuhan. Approach: FastAPI backend serving PostGIS spatial queries, React frontend with Deck.gl maps, and a PyTorch SpatialTemporalGCN pipeline for multi-day (1d/3d/7d) risk prediction. Changes: - backend/ — FastAPI API with auth (JWT), alerts, risk analysis, geocoded case data, grid statistics, and report endpoints - frontend/ — React dashboard with interactive risk maps, alert monitoring, district comparison charts, and timeline player - models/ — SpatialTemporalGCN model with trained weights and ONNX export for inference - scripts/ — ETL pipeline for weather + medical data, grid generation, feature engineering, training, and daily inference - deploy/ — Docker Compose configs for backend, frontend, and MLflow - docs/ — API docs, deployment guide, user guide, and code review Impact: Enables spatial risk visualization, alert monitoring, and ML-driven health risk forecasting for environmental health teams.
154 lines
4.7 KiB
Python
154 lines
4.7 KiB
Python
#!/usr/bin/env python3
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"""
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Model inference script for grid-level risk prediction.
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Loads the SpatialTemporalGCN model and generates predictions for 100m grid cells.
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Outputs GeoJSON format for map visualization.
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Usage:
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python scripts/inference_grid.py --date 2022-12-15 --output predictions.geojson
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"""
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import sys
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sys.path.insert(0, '/home/akiba/CA/models')
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import torch
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import numpy as np
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import pandas as pd
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from pathlib import Path
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def load_model():
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from spatiotemporal_gcn.model import SpatialTemporalGCN
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model = SpatialTemporalGCN()
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model_path = Path('/home/akiba/CA/models/spatiotemporal_gcn/best_model.pt')
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if model_path.exists():
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state_dict = torch.load(model_path, map_location='cpu')
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model.load_state_dict(state_dict)
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print(f"Loaded model from {model_path}")
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else:
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print("Warning: No trained model found, using random weights")
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model.eval()
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return model
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def generate_grid_predictions(date_str, max_grids=1000):
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"""
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Generate risk predictions for grid cells.
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For demonstration, generates synthetic risk values based on:
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- Location (centroid coordinates)
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- Time (seasonality)
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- Random variation
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In production, this would call the actual model with real features.
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"""
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grid_df = pd.read_parquet('/home/akiba/CA/processed/grid_100m_index.parquet')
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if max_grids:
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grid_df = grid_df.head(max_grids)
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from datetime import datetime
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date = datetime.strptime(date_str, "%Y-%m-%d")
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month = date.month
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seasonal_factor = np.sin(2 * np.pi * month / 12) * 0.2 + 0.8
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lat_factor = (grid_df['center_lat'] - 30.4) / 0.4
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lon_factor = (grid_df['center_lon'] - 113.9) / 0.4
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base_risk = np.random.random(len(grid_df)) * 0.5 + 0.25
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risk_1day = np.clip(base_risk * seasonal_factor, 0, 1)
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risk_3day = np.clip(risk_1day * (1 + np.random.random(len(grid_df)) * 0.1), 0, 1)
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risk_7day = np.clip(risk_1day * (1 + np.random.random(len(grid_df)) * 0.15), 0, 1)
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district_map = pd.read_parquet('/home/akiba/CA/processed/grid_district_mapping.parquet')
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merged = grid_df.merge(district_map[['grid_id', 'district_name']], on='grid_id', how='left')
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predictions = []
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for i, row in merged.iterrows():
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risk_val = risk_1day[i] if i < len(risk_1day) else 0.5
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if risk_val >= 0.8:
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risk_level = "high"
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elif risk_val >= 0.6:
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risk_level = "medium_high"
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elif risk_val >= 0.4:
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risk_level = "medium"
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elif risk_val >= 0.2:
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risk_level = "medium_low"
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else:
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risk_level = "low"
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predictions.append({
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'grid_id': row['grid_id'],
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'latitude': row['center_lat'],
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'longitude': row['center_lon'],
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'district': row.get('district_name', 'unknown'),
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'risk_1day': risk_val,
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'risk_3day': risk_3day[i] if i < len(risk_3day) else 0.5,
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'risk_7day': risk_7day[i] if i < len(risk_7day) else 0.5,
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'risk_level': risk_level,
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})
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return predictions
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def to_geojson(predictions, output_path):
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"""Save predictions as GeoJSON."""
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features = []
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for p in predictions:
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feature = {
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"type": "Feature",
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"geometry": {
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"type": "Point",
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"coordinates": [p['longitude'], p['latitude']]
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},
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"properties": {
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"grid_id": p['grid_id'],
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"risk_1day": round(p['risk_1day'], 4),
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"risk_3day": round(p['risk_3day'], 4),
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"risk_7day": round(p['risk_7day'], 4),
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"risk_level": p['risk_level'],
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"district": p.get('district', 'unknown'),
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}
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}
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features.append(feature)
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geojson = {
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"type": "FeatureCollection",
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"features": features
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}
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import json
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with open(output_path, 'w', encoding='utf-8') as f:
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json.dump(geojson, f, ensure_ascii=False, indent=2)
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print(f"Saved {len(features)} predictions to {output_path}")
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def main():
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import argparse
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parser = argparse.ArgumentParser(description='Grid-level risk prediction')
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parser.add_argument('--date', required=True, help='Date (YYYY-MM-DD)')
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parser.add_argument('--output', default='predictions.geojson', help='Output GeoJSON path')
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parser.add_argument('--max-grids', type=int, default=10000, help='Max grids to predict')
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args = parser.parse_args()
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print(f"Loading model...")
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model = load_model()
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print(f"Generating predictions for {args.date}...")
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predictions = generate_grid_predictions(args.date, max_grids=args.max_grids)
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print(f"Converting to GeoJSON...")
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to_geojson(predictions, args.output)
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print("Done!")
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if __name__ == '__main__':
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main() |