Upload scripts/makeh5.py

scripts/makeh5.py

@@ -0,0 +1,753 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import csv
+import argparse
+from pathlib import Path
+from collections import defaultdict
+from concurrent.futures import ThreadPoolExecutor, wait, FIRST_COMPLETED
+
+import h5py
+import numpy as np
+from obspy import read, UTCDateTime
+
+
+DEFAULT_LOCATION = "--"
+
+
+def normalize_location(location, default=DEFAULT_LOCATION):
+    if location is None:
+        return default
+    location = str(location).strip()
+    return location if location else default
+
+
+def make_station_id(network, station, location, default_location=DEFAULT_LOCATION):
+    network = str(network or "").strip()
+    station = str(station or "").strip()
+    location = normalize_location(location, default_location)
+    return f"{network}.{station}.{location}"
+
+
+def make_station_key(network, station):
+    network = str(network or "").strip()
+    station = str(station or "").strip()
+    return f"{network}.{station}"
+
+
+def split_station_id(station_id, default_location=DEFAULT_LOCATION):
+    parts = str(station_id).split(".")
+    network = parts[0] if len(parts) > 0 else ""
+    station = parts[1] if len(parts) > 1 else ""
+    location = parts[2] if len(parts) > 2 else default_location
+    return network, station, normalize_location(location, default_location)
+
+
+def parse_utc_or_none(value):
+    value = str(value or "").strip()
+    if not value:
+        return None
+    return UTCDateTime(value)
+
+
+def utc_to_group_id(t: UTCDateTime, level: str) -> str:
+    if level == "year":
+        return f"{t.year:04d}-01-01T00:00:00.000000Z"
+    if level == "day":
+        return f"{t.year:04d}-{t.month:02d}-{t.day:02d}T00:00:00.000000Z"
+    raise ValueError(f"Unsupported level: {level}")
+
+
+def day_file_id(t: UTCDateTime) -> str:
+    return f"{t.year:04d}{t.month:02d}{t.day:02d}"
+
+
+def set_common_attrs(obj, level, node_type, parent_type):
+    obj.attrs["level"] = level
+    obj.attrs["type"] = node_type
+    obj.attrs["parent_type"] = parent_type
+
+
+def load_station_locations_csv(loc_file, default_location=DEFAULT_LOCATION):
+    """
+    支持两种格式：
+
+    1. 有表头：
+       net,sta,lat,lon,elev_m,start,end
+
+    2. 无表头：
+       CI,WBM,35.60839,-117.89049,892.0,1979-09-26T00:00:00.000000Z,3000-01-01T00:00:00.000000Z
+
+    注意：
+    位置匹配只使用 network.station，不使用 location。
+    """
+    locations = defaultdict(list)
+
+    if not loc_file or not os.path.exists(loc_file):
+        print(f"[WARN] Location CSV file not found: {loc_file}")
+        return dict(locations)
+
+    with open(loc_file, "r", encoding="utf-8-sig", newline="") as f:
+        sample = f.readline()
+        f.seek(0)
+
+        first_cols = [x.strip().lower() for x in sample.strip().split(",")]
+        has_header = {"net", "sta", "lat", "lon"}.issubset(set(first_cols))
+
+        if has_header:
+            reader = csv.DictReader(f)
+
+            for line_no, row in enumerate(reader, start=2):
+                try:
+                    net = row["net"].strip()
+                    sta = row["sta"].strip()
+                    loc = normalize_location(row.get("location", default_location), default_location)
+
+                    start = parse_utc_or_none(row["start"])
+                    end = parse_utc_or_none(row["end"])
+
+                    key = make_station_key(net, sta)
+
+                    locations[key].append(
+                        {
+                            "network": net,
+                            "station": sta,
+                            "location": loc,
+                            "latitude": float(row["lat"]),
+                            "longitude": float(row["lon"]),
+                            "elevation": float(row["elev_m"]),
+                            "start": start,
+                            "end": end,
+                            "starttime": str(start) if start is not None else "",
+                            "endtime": str(end) if end is not None else "",
+                        }
+                    )
+                except Exception as e:
+                    print(f"[WARN] Failed to parse location CSV line {line_no}: {row}, error={e}")
+
+        else:
+            reader = csv.reader(f)
+
+            for line_no, row in enumerate(reader, start=1):
+                if not row or len(row) < 7:
+                    continue
+
+                try:
+                    net = row[0].strip()
+                    sta = row[1].strip()
+                    lat = float(row[2])
+                    lon = float(row[3])
+                    elev = float(row[4])
+                    start = parse_utc_or_none(row[5])
+                    end = parse_utc_or_none(row[6])
+
+                    key = make_station_key(net, sta)
+
+                    locations[key].append(
+                        {
+                            "network": net,
+                            "station": sta,
+                            "location": default_location,
+                            "latitude": lat,
+                            "longitude": lon,
+                            "elevation": elev,
+                            "start": start,
+                            "end": end,
+                            "starttime": str(start) if start is not None else "",
+                            "endtime": str(end) if end is not None else "",
+                        }
+                    )
+                except Exception as e:
+                    print(f"[WARN] Failed to parse location CSV line {line_no}: {row}, error={e}")
+
+    for key in locations:
+        locations[key].sort(
+            key=lambda x: x["start"] if x["start"] is not None else UTCDateTime(0)
+        )
+
+    return dict(locations)
+
+
+def match_station_location(
+    station_locations,
+    station_id,
+    trace_start=None,
+    trace_end=None,
+    allow_fallback=True,
+):
+    """
+    只按 network.station 匹配台站位置。
+    不使用 location code。
+
+    例如：
+        waveform station_id = BK.BDM.00
+        location key        = BK.BDM
+    """
+    net, sta, _ = split_station_id(station_id)
+    station_key = make_station_key(net, sta)
+
+    records = station_locations.get(station_key, [])
+
+    if not records:
+        return None, "default_nan_no_station_record"
+
+    if trace_start is None and trace_end is None:
+        if allow_fallback:
+            return records[-1], "fallback_nearest_time_network_station_only"
+        return None, "default_nan_no_time_matched_position"
+
+    matched = []
+
+    for rec in records:
+        rec_start = rec.get("start")
+        rec_end = rec.get("end")
+
+        left_ok = True if rec_end is None or trace_start is None else trace_start < rec_end
+        right_ok = True if rec_start is None or trace_end is None else trace_end >= rec_start
+
+        if left_ok and right_ok:
+            matched.append(rec)
+
+    if matched:
+        def strict_score(rec):
+            rec_start = rec.get("start")
+            if rec_start is None or trace_start is None:
+                return 0
+            if rec_start <= trace_start:
+                return abs(trace_start - rec_start)
+            return abs(trace_start - rec_start) + 1e12
+
+        return sorted(matched, key=strict_score)[0], "strict_time_matched_network_station_only"
+
+    if not allow_fallback:
+        return None, "default_nan_no_time_matched_position"
+
+    def fallback_score(rec):
+        if trace_start is None:
+            return 0
+
+        candidates = []
+        if rec.get("start") is not None:
+            candidates.append(abs(trace_start - rec["start"]))
+        if rec.get("end") is not None:
+            candidates.append(abs(trace_start - rec["end"]))
+
+        return min(candidates) if candidates else 0
+
+    return sorted(records, key=fallback_score)[0], "fallback_nearest_time_network_station_only"
+
+
+def find_mseed_files(input_dir):
+    input_dir = Path(input_dir)
+
+    suffixes = {
+        ".mseed", ".msd", ".miniseed", ".seed",
+        ".MSEED", ".MSD", ".MINISEED", ".SEED",
+    }
+
+    return sorted(
+        p for p in input_dir.rglob("*")
+        if p.is_file() and p.suffix in suffixes
+    )
+
+
+def read_one_mseed(mseed_file, default_location=DEFAULT_LOCATION):
+    records = []
+
+    try:
+        st = read(str(mseed_file))
+    except Exception as e:
+        return records, f"[WARN] Failed to read {mseed_file}: {e}"
+
+    for tr in st:
+        net = tr.stats.network or ""
+        sta = tr.stats.station or ""
+        loc = normalize_location(tr.stats.location, default_location)
+        cha = tr.stats.channel or ""
+
+        start = tr.stats.starttime
+        end = tr.stats.endtime
+
+        station_id = make_station_id(net, sta, loc, default_location)
+
+        records.append(
+            {
+                "year_id": utc_to_group_id(start, "year"),
+                "day_id": utc_to_group_id(start, "day"),
+                "day_file_id": day_file_id(start),
+                "station_id": station_id,
+                "channel": cha,
+                "starttime_obj": start,
+                "endtime_obj": end,
+                "starttime": str(start),
+                "endtime": str(end),
+                "sampling_rate": float(tr.stats.sampling_rate),
+                "delta": float(tr.stats.delta),
+                "npts": int(tr.stats.npts),
+                "network": net,
+                "station": sta,
+                "location": loc,
+                "data": np.asarray(tr.data),
+                "dtype": str(tr.data.dtype),
+                "source_file": str(mseed_file),
+            }
+        )
+
+    return records, None
+
+
+def write_position_attrs(obj, matched, match_mode):
+    obj.attrs["position_match_mode"] = match_mode
+    obj.attrs["position_is_fallback"] = "fallback" in str(match_mode)
+
+    if matched is not None:
+        obj.attrs["longitude"] = matched.get("longitude", np.nan)
+        obj.attrs["latitude"] = matched.get("latitude", np.nan)
+        obj.attrs["elevation"] = matched.get("elevation", np.nan)
+        obj.attrs["location_available"] = True
+        obj.attrs["location_source"] = match_mode
+        obj.attrs["station_position_starttime"] = matched.get("starttime", "")
+        obj.attrs["station_position_endtime"] = matched.get("endtime", "")
+    else:
+        obj.attrs["longitude"] = np.nan
+        obj.attrs["latitude"] = np.nan
+        obj.attrs["elevation"] = np.nan
+        obj.attrs["location_available"] = False
+        obj.attrs["location_source"] = match_mode
+        obj.attrs["station_position_starttime"] = ""
+        obj.attrs["station_position_endtime"] = ""
+
+
+def write_station_position_history(station_grp, station_id, station_locations, default_location):
+    if "position_history" in station_grp:
+        return
+
+    net, sta, _ = split_station_id(station_id, default_location)
+    station_key = make_station_key(net, sta)
+
+    pos_grp = station_grp.create_group("position_history")
+    set_common_attrs(pos_grp, "position_history", "position_history_group", "station_group")
+
+    records = station_locations.get(station_key, [])
+    pos_grp.attrs["record_count"] = len(records)
+    pos_grp.attrs["match_key"] = station_key
+    pos_grp.attrs["match_rule"] = "network.station only; location ignored"
+
+    for i, rec in enumerate(records):
+        item_grp = pos_grp.create_group(str(i))
+        set_common_attrs(item_grp, "position_record", "position_record_group", "position_history_group")
+
+        item_grp.attrs["network"] = rec.get("network", "")
+        item_grp.attrs["station"] = rec.get("station", "")
+        item_grp.attrs["location"] = rec.get("location", default_location)
+        item_grp.attrs["longitude"] = rec.get("longitude", np.nan)
+        item_grp.attrs["latitude"] = rec.get("latitude", np.nan)
+        item_grp.attrs["elevation"] = rec.get("elevation", np.nan)
+        item_grp.attrs["starttime"] = rec.get("starttime", "")
+        item_grp.attrs["endtime"] = rec.get("endtime", "")
+
+
+def init_hdf5_root(h5, default_location, split_by_day=False):
+    set_common_attrs(h5, "root", "hdf5_file", "none")
+    h5.attrs["description"] = "Continuous waveform dataset converted from MiniSEED"
+    h5.attrs["station_id_format"] = "network.station.location"
+    h5.attrs["station_location_match_rule"] = "network.station only; location ignored"
+    h5.attrs["empty_location_value"] = default_location
+    h5.attrs["missing_coordinate_value"] = "NaN"
+    h5.attrs["station_location_format"] = (
+        "CSV with header: net,sta,lat,lon,elev_m,start,end "
+        "or no-header: net,sta,lat,lon,elev_m,start,end"
+    )
+    h5.attrs["split_by_day"] = bool(split_by_day)
+
+
+def get_or_create_station_group(
+    h5,
+    year_id,
+    day_id,
+    station_id,
+    station_locations,
+    trace_start,
+    trace_end,
+    default_location,
+):
+    year_grp = h5.require_group(year_id)
+    set_common_attrs(year_grp, "year", "year_group", "root")
+    year_grp.attrs["utc_time"] = year_id
+
+    day_grp = year_grp.require_group(day_id)
+    set_common_attrs(day_grp, "day", "day_group", "year_group")
+    day_grp.attrs["utc_time"] = day_id
+
+    stations_grp = day_grp.require_group("stations")
+    set_common_attrs(stations_grp, "stations", "stations_group", "day_group")
+    stations_grp.attrs["description"] = "Container group for all stations under this day"
+
+    station_grp = stations_grp.require_group(station_id)
+    set_common_attrs(station_grp, "station", "station_group", "stations_group")
+
+    network, station, location = split_station_id(station_id, default_location)
+    station_grp.attrs["station_id"] = station_id
+    station_grp.attrs["station_key"] = make_station_key(network, station)
+    station_grp.attrs["network"] = network
+    station_grp.attrs["station"] = station
+    station_grp.attrs["location"] = location
+    station_grp.attrs["location_default_value"] = default_location
+    station_grp.attrs["location_is_default"] = location == default_location
+    station_grp.attrs["instrument_time_range_start"] = str(trace_start)
+    station_grp.attrs["instrument_time_range_end"] = str(trace_end)
+
+    matched, match_mode = match_station_location(
+        station_locations=station_locations,
+        station_id=station_id,
+        trace_start=trace_start,
+        trace_end=trace_end,
+        allow_fallback=True,
+    )
+    write_position_attrs(station_grp, matched, match_mode)
+
+    write_station_position_history(
+        station_grp=station_grp,
+        station_id=station_id,
+        station_locations=station_locations,
+        default_location=default_location,
+    )
+
+    waveform_grp = station_grp.require_group("waveform")
+    set_common_attrs(waveform_grp, "waveform", "waveform_group", "station_group")
+
+    return station_grp, waveform_grp
+
+
+def next_dataset_index(channel_grp):
+    max_idx = -1
+    for key in channel_grp.keys():
+        if str(key).isdigit():
+            max_idx = max(max_idx, int(key))
+    return max_idx + 1
+
+
+def update_channel_summary_attrs(channel_grp, rec):
+    channel_grp.attrs["channel"] = rec["channel"]
+
+    old_count = int(channel_grp.attrs.get("segment_count", 0))
+    channel_grp.attrs["segment_count"] = old_count + 1
+
+    rec_start = rec["starttime_obj"]
+    rec_end = rec["endtime_obj"]
+
+    old_start = channel_grp.attrs.get("starttime", "")
+    old_end = channel_grp.attrs.get("endtime", "")
+
+    if not old_start:
+        channel_grp.attrs["starttime"] = str(rec_start)
+    else:
+        old_start_t = UTCDateTime(str(old_start))
+        channel_grp.attrs["starttime"] = str(min(old_start_t, rec_start))
+
+    if not old_end:
+        channel_grp.attrs["endtime"] = str(rec_end)
+    else:
+        old_end_t = UTCDateTime(str(old_end))
+        channel_grp.attrs["endtime"] = str(max(old_end_t, rec_end))
+
+
+def write_one_record(
+    h5,
+    rec,
+    station_locations,
+    default_location,
+    compression,
+    compression_opts,
+    shuffle,
+):
+    station_grp, waveform_grp = get_or_create_station_group(
+        h5=h5,
+        year_id=rec["year_id"],
+        day_id=rec["day_id"],
+        station_id=rec["station_id"],
+        station_locations=station_locations,
+        trace_start=rec["starttime_obj"],
+        trace_end=rec["endtime_obj"],
+        default_location=default_location,
+    )
+
+    channel_grp = waveform_grp.require_group(rec["channel"])
+    set_common_attrs(channel_grp, "channel", "channel_group", "waveform_group")
+
+    update_channel_summary_attrs(channel_grp, rec)
+
+    matched, match_mode = match_station_location(
+        station_locations=station_locations,
+        station_id=rec["station_id"],
+        trace_start=rec["starttime_obj"],
+        trace_end=rec["endtime_obj"],
+        allow_fallback=True,
+    )
+    write_position_attrs(channel_grp, matched, match_mode)
+
+    ds_name = str(next_dataset_index(channel_grp))
+
+    create_kwargs = {}
+    if compression and compression.lower() != "none":
+        create_kwargs["compression"] = compression
+        if compression.lower() == "gzip":
+            create_kwargs["compression_opts"] = compression_opts
+        create_kwargs["shuffle"] = shuffle
+
+    ds = channel_grp.create_dataset(
+        ds_name,
+        data=rec["data"],
+        **create_kwargs,
+    )
+
+    set_common_attrs(ds, "segment", "waveform_dataset", "channel_group")
+
+    write_position_attrs(ds, matched, match_mode)
+
+    ds.attrs["segment_index"] = int(ds_name)
+    ds.attrs["network"] = rec["network"]
+    ds.attrs["station"] = rec["station"]
+    ds.attrs["station_key"] = make_station_key(rec["network"], rec["station"])
+    ds.attrs["location"] = rec["location"]
+    ds.attrs["location_is_default"] = rec["location"] == default_location
+    ds.attrs["channel"] = rec["channel"]
+    ds.attrs["sampling_rate"] = rec["sampling_rate"]
+    ds.attrs["delta"] = rec["delta"]
+    ds.attrs["npts"] = rec["npts"]
+    ds.attrs["starttime"] = rec["starttime"]
+    ds.attrs["endtime"] = rec["endtime"]
+    ds.attrs["mseed_source_file"] = rec["source_file"]
+    ds.attrs["dtype"] = rec["dtype"]
+
+
+def output_path_for_day(output, day_id):
+    output = Path(output)
+
+    if output.suffix.lower() in [".h5", ".hdf5"]:
+        out_dir = output.parent
+        stem = output.stem
+    else:
+        out_dir = output
+        stem = "continuous_waveform"
+
+    out_dir.mkdir(parents=True, exist_ok=True)
+    return out_dir / f"{stem}_{day_id}.h5"
+
+
+def convert_mseed_to_hdf5_streaming(
+    mseed_files,
+    station_locations,
+    output_file,
+    num_workers=4,
+    max_pending=16,
+    default_location=DEFAULT_LOCATION,
+    compression="gzip",
+    compression_opts=4,
+    shuffle=True,
+    split_by_day=False,
+):
+    total = len(mseed_files)
+    submitted = 0
+    finished = 0
+    written_records = 0
+
+    h5_files = {}
+
+    def get_h5_for_record(rec):
+        if not split_by_day:
+            key = "__single__"
+            if key not in h5_files:
+                output_path = Path(output_file)
+                output_path.parent.mkdir(parents=True, exist_ok=True)
+                h5 = h5py.File(output_path, "w")
+                init_hdf5_root(h5, default_location, split_by_day=False)
+                h5_files[key] = h5
+            return h5_files[key]
+
+        key = rec["day_file_id"]
+        if key not in h5_files:
+            output_path = output_path_for_day(output_file, key)
+            h5 = h5py.File(output_path, "w")
+            init_hdf5_root(h5, default_location, split_by_day=True)
+            h5.attrs["day_file_id"] = key
+            h5_files[key] = h5
+        return h5_files[key]
+
+    try:
+        with ThreadPoolExecutor(max_workers=num_workers) as executor:
+            pending = set()
+
+            def submit_more():
+                nonlocal submitted
+                while submitted < total and len(pending) < max_pending:
+                    future = executor.submit(
+                        read_one_mseed,
+                        mseed_files[submitted],
+                        default_location,
+                    )
+                    pending.add(future)
+                    submitted += 1
+
+            submit_more()
+
+            while pending:
+                done, pending_remaining = wait(pending, return_when=FIRST_COMPLETED)
+                pending = pending_remaining
+
+                for future in done:
+                    finished += 1
+                    records, warning = future.result()
+
+                    if warning:
+                        print(warning)
+
+                    records.sort(
+                        key=lambda r: (
+                            r["day_file_id"],
+                            r["year_id"],
+                            r["day_id"],
+                            r["station_id"],
+                            r["channel"],
+                            r["starttime_obj"],
+                        )
+                    )
+
+                    for rec in records:
+                        h5 = get_h5_for_record(rec)
+
+                        write_one_record(
+                            h5=h5,
+                            rec=rec,
+                            station_locations=station_locations,
+                            default_location=default_location,
+                            compression=compression,
+                            compression_opts=compression_opts,
+                            shuffle=shuffle,
+                        )
+                        written_records += 1
+
+                    if finished % 100 == 0 or finished == total:
+                        print(
+                            f"[INFO] Progress: files {finished}/{total}, "
+                            f"written waveform segments {written_records}, "
+                            f"open hdf5 files {len(h5_files)}"
+                        )
+
+                    del records
+
+                submit_more()
+
+    finally:
+        for h5 in h5_files.values():
+            h5.close()
+
+    print(f"[OK] Written waveform segments: {written_records}")
+
+    if split_by_day:
+        print(f"[OK] HDF5 files written by day under: {Path(output_file).parent if Path(output_file).suffix else output_file}")
+    else:
+        print(f"[OK] HDF5 written to: {output_file}")
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Convert MiniSEED files to hierarchical HDF5."
+    )
+
+    parser.add_argument(
+        "--input_dir",
+        default="data/continous_usa/data",
+        help="Directory containing MiniSEED files.",
+    )
+
+    parser.add_argument(
+        "--loc_file",
+        default="data/continous_usa/stations.csv",
+        help="Station CSV file.",
+    )
+
+    parser.add_argument(
+        "--output",
+        default="data/hdf5/continuous_waveform_usa.h5",
+        help=(
+            "Output HDF5 file. If --split_by_day is enabled, this is used as "
+            "a filename prefix, e.g. continuous_waveform_usa_20190701.h5."
+        ),
+    )
+
+    parser.add_argument(
+        "--split_by_day",
+        action="store_true",
+        default=True, 
+        help="Write one HDF5 file per day.",
+    )
+
+    parser.add_argument(
+        "--num_workers",
+        type=int,
+        default=2,
+        help="Number of threads for reading MiniSEED files.",
+    )
+
+    parser.add_argument(
+        "--max_pending",
+        type=int,
+        default=4,
+        help="Maximum number of pending read tasks.",
+    )
+
+    parser.add_argument(
+        "--default_location",
+        default=DEFAULT_LOCATION,
+        help='Default location code when MiniSEED location is empty. Default: "--".',
+    )
+
+    parser.add_argument(
+        "--compression",
+        default="gzip",
+        choices=["gzip", "lzf", "none"],
+        help="Dataset compression method.",
+    )
+
+    parser.add_argument(
+        "--compression_opts",
+        type=int,
+        default=4,
+        help="Compression level for gzip.",
+    )
+
+    parser.add_argument(
+        "--no_shuffle",
+        action="store_true",
+        help="Disable HDF5 shuffle filter.",
+    )
+
+    args = parser.parse_args()
+
+    station_locations = load_station_locations_csv(
+        args.loc_file,
+        default_location=args.default_location,
+    )
+    print(f"[INFO] Loaded station location histories for {len(station_locations)} station keys.")
+
+    mseed_files = find_mseed_files(args.input_dir)
+    print(f"[INFO] Found {len(mseed_files)} MiniSEED files.")
+
+    convert_mseed_to_hdf5_streaming(
+        mseed_files=mseed_files,
+        station_locations=station_locations,
+        output_file=args.output,
+        num_workers=args.num_workers,
+        max_pending=args.max_pending,
+        default_location=args.default_location,
+        compression=args.compression,
+        compression_opts=args.compression_opts,
+        shuffle=not args.no_shuffle,
+        split_by_day=args.split_by_day,
+    )
+
+
+if __name__ == "__main__":
+    main()