Fix coverage: add /api/coverage route, remove stray gather code from loadCoverage
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Floppyrj45
325
h5_api_server.py
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325
h5_api_server.py
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#!/usr/bin/env python3
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"""
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Flask API server for SeaKESP H5 data and node metadata
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Provides both H5 data access and node/date endpoints
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"""
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from flask import Flask, jsonify, request, send_file
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from flask_cors import CORS
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import h5py
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import numpy as np
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import os
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import json
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from pathlib import Path
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from datetime import datetime
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app = Flask(__name__)
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CORS(app)
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# Paths
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DATA_DIR = Path("/data")
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H5_DIR = DATA_DIR / "h5"
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DOCS_DIR = DATA_DIR / "docs"
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INDEX_FILE = DATA_DIR / "index.json"
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# Load node index
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nodes_data = {}
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dates_list = []
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def load_index():
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"""Load node data from index.json"""
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global nodes_data, dates_list
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if not INDEX_FILE.exists():
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print(f"Warning: {INDEX_FILE} not found")
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return
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try:
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with open(INDEX_FILE, 'r') as f:
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data = json.load(f)
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nodes_data = data.get('nodes', {})
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dates_list = data.get('dates', [])
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print(f"Loaded {len(nodes_data)} nodes and {len(dates_list)} dates from index.json")
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except Exception as e:
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print(f"Error loading index.json: {e}")
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# Load index on startup
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load_index()
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# ============================================================================
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# Node & Date Endpoints (replacing Node.js backend)
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# ============================================================================
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@app.route('/api/nodes', methods=['GET'])
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def get_nodes():
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"""Return list of all nodes with metadata"""
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nodes_list = []
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for node_id, node_info in nodes_data.items():
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nodes_list.append({
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'id': node_id,
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'position': node_info.get('position', {}),
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'file_count': len(node_info.get('files', []))
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})
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return jsonify(nodes_list)
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@app.route('/api/dates', methods=['GET'])
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def get_dates():
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"""Return list of available dates"""
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return jsonify(dates_list)
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@app.route('/api/migration-status', methods=['GET'])
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def migration_status():
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"""Return H5 migration status summary"""
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h5_count = len(list(H5_DIR.glob("*.h5"))) if H5_DIR.exists() else 0
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return jsonify({
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'total_h5_files': h5_count,
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'nodes_count': len(nodes_data),
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'dates_count': len(dates_list),
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'last_updated': datetime.now().isoformat()
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})
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@app.route('/api/rms-timeline', methods=['GET'])
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def rms_timeline():
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"""Placeholder for RMS timeline (requires processing)"""
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return jsonify([])
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@app.route('/api/global-history', methods=['GET'])
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def global_history():
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"""Placeholder for global history (requires processing)"""
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return jsonify([])
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# ============================================================================
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# H5 Data Endpoints
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# ============================================================================
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@app.route('/api/h5/files', methods=['GET'])
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def list_h5_files():
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"""List all H5 files with metadata"""
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if not H5_DIR.exists():
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return jsonify([])
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files = []
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for h5_file in sorted(H5_DIR.glob("*.h5")):
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try:
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with h5py.File(h5_file, 'r') as f:
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metadata = dict(f['metadata'].attrs)
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# Extract node ID and date from filename
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# Format: node_NODEID_YYYYMMDD.h5
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parts = h5_file.stem.split('_')
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node_id = parts[1] if len(parts) > 1 else "unknown"
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date_str = parts[2] if len(parts) > 2 else "unknown"
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files.append({
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'filename': h5_file.name,
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'path': str(h5_file),
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'nodeId': node_id,
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'date': date_str,
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'duration_sec': float(metadata.get('duration_sec', 0)),
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'sample_rate_hz': int(metadata.get('sample_rate_hz', 500)),
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'n_channels': int(metadata.get('n_channels', 4)),
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'n_samples': int(metadata.get('n_samples', 0))
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})
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except Exception as e:
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print(f"Error reading {h5_file}: {e}")
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return jsonify(files)
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@app.route('/api/h5/data', methods=['GET'])
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def get_h5_data():
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"""Get waveform data from H5 file"""
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filename = request.args.get('file')
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channel = request.args.get('channel', 'channel_1')
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start = float(request.args.get('start', 0))
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duration = float(request.args.get('duration', 10))
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if not filename:
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return jsonify({'error': 'Missing file parameter'}), 400
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h5_path = DATA_DIR / filename
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if not h5_path.exists():
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return jsonify({'error': 'File not found'}), 404
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try:
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with h5py.File(h5_path, 'r') as f:
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# Get metadata
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sample_rate = int(f['metadata'].attrs['sample_rate_hz'])
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# Calculate sample range
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start_sample = int(start * sample_rate)
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n_samples = int(duration * sample_rate)
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end_sample = start_sample + n_samples
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# Read calibrated data
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data = f['calibrated_data'][channel][start_sample:end_sample]
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# Calculate statistics
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stats = {
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'mean': float(np.mean(data)),
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'std': float(np.std(data)),
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'min': float(np.min(data)),
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'max': float(np.max(data)),
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'rms': float(np.sqrt(np.mean(data**2)))
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}
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# Create time array
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time = np.arange(len(data)) / sample_rate + start
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return jsonify({
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'time': time.tolist(),
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'data': data.tolist(),
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'stats': stats,
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'sample_rate': sample_rate,
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'channel': channel,
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'start': start,
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'duration': duration,
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'n_samples': len(data)
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})
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except Exception as e:
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return jsonify({'error': str(e)}), 500
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@app.route('/api/h5/coverage', methods=['GET'])
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def h5_coverage():
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"""Get H5 coverage summary by node and date"""
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if not H5_DIR.exists():
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return jsonify([])
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coverage = {}
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for h5_file in H5_DIR.glob("*.h5"):
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try:
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parts = h5_file.stem.split('_')
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node_id = parts[1] if len(parts) > 1 else "unknown"
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date_str = parts[2] if len(parts) > 2 else "unknown"
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key = f"{node_id}_{date_str}"
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with h5py.File(h5_file, 'r') as f:
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duration = float(f['metadata'].attrs.get('duration_sec', 0))
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if key not in coverage:
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coverage[key] = {
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'nodeId': node_id,
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'date': date_str,
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'total_duration_hours': 0,
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'file_count': 0
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}
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coverage[key]['total_duration_hours'] += duration / 3600
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coverage[key]['file_count'] += 1
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except Exception as e:
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print(f"Error processing {h5_file}: {e}")
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return jsonify(list(coverage.values()))
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@app.route('/api/h5/gaps', methods=['GET'])
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def h5_gaps():
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"""Identify gaps in H5 data coverage"""
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# TODO: Implement gap detection logic
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return jsonify([])
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# ============================================================================
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# Campaign Documentation Endpoints
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# ============================================================================
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@app.route('/api/docs/manifest', methods=['GET'])
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def get_docs_manifest():
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"""Get campaign documentation manifest"""
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manifest_path = DOCS_DIR / "campaign_manifest.json"
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if not manifest_path.exists():
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return jsonify({'error': 'Manifest not found'}), 404
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try:
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with open(manifest_path, 'r') as f:
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manifest = json.load(f)
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return jsonify(manifest)
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except Exception as e:
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return jsonify({'error': str(e)}), 500
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@app.route('/api/docs/<filename>', methods=['GET'])
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def download_doc(filename):
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"""Download a campaign document"""
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doc_path = DOCS_DIR / filename
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if not doc_path.exists():
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return jsonify({'error': 'Document not found'}), 404
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return send_file(doc_path, as_attachment=True)
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# ============================================================================
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# Health Check
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# ============================================================================
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@app.route('/health', methods=['GET'])
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def health():
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"""Health check endpoint"""
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return jsonify({
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'status': 'ok',
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'h5_files': len(list(H5_DIR.glob("*.h5"))) if H5_DIR.exists() else 0,
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'nodes_loaded': len(nodes_data),
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'dates_loaded': len(dates_list)
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})
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if __name__ == '__main__':
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app.run(host='0.0.0.0', port=3004, debug=False, threaded=True)
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# === Additional routes for frontend compatibility ===
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@app.route('/api/files', methods=['GET'])
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def list_files_alias():
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"""Alias for /api/h5/files — used by the SeiSee frontend"""
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return list_h5_files()
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@app.route('/api/file/<path:filename>', methods=['GET'])
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def get_file_info(filename):
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"""Get detailed file info including datasets — needed for channel selector"""
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h5_path = DATA_DIR / filename
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if not h5_path.exists():
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return jsonify({'error': 'File not found'}), 404
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try:
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with h5py.File(h5_path, 'r') as f:
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metadata = dict(f['metadata'].attrs) if 'metadata' in f else {}
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calibration = dict(f['calibration'].attrs) if 'calibration' in f else {}
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datasets = []
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def collect_datasets(name, obj):
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if isinstance(obj, h5py.Dataset):
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datasets.append({
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'path': name,
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'shape': list(obj.shape),
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'dtype': str(obj.dtype),
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'chunks': list(obj.chunks) if obj.chunks else None,
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'compression': obj.compression
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})
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f.visititems(collect_datasets)
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duration_sec = float(metadata.get('duration_sec', 0))
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sample_rate = int(metadata.get('sample_rate_hz', 500))
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n_channels = int(metadata.get('n_channels', 4))
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n_samples = int(metadata.get('n_samples', 0))
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# Human readable duration
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hours = int(duration_sec // 3600)
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mins = int((duration_sec % 3600) // 60)
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duration_human = f'{hours}h{mins:02d}' if hours else f'{mins}min'
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return jsonify({
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'filename': filename,
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'type': 'h5',
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'duration_sec': duration_sec,
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'duration_human': duration_human,
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'sample_rate_hz': sample_rate,
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'num_channels': n_channels,
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'samples_per_channel': n_samples,
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'datasets': datasets,
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'calibration': {k: float(v) if hasattr(v, '__float__') else str(v) for k, v in calibration.items()},
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'metadata': {k: float(v) if hasattr(v, '__float__') else str(v) for k, v in metadata.items()}
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})
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except Exception as e:
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return jsonify({'error': str(e)}), 500
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