feat: miniSEED store for local file (#44)

* Add miniSEED store for io

Signed-off-by: Yiyu Ni <[email protected]>

* Fix pre-commit

Signed-off-by: Yiyu Ni <[email protected]>

* Add tests for mSEED store

Signed-off-by: Yiyu Ni <[email protected]>

* Correct pre-commit

---------

Signed-off-by: Yiyu Ni <[email protected]>

src/noisepy/seis/io/mseedstore.py

@@ -0,0 +1,118 @@
+import glob
+import logging
+import os
+from datetime import datetime, timedelta, timezone
+from typing import Callable, List
+
+import obspy
+from datetimerange import DateTimeRange
+from tqdm.autonotebook import tqdm
+
+from .channelcatalog import ChannelCatalog
+from .datatypes import Channel, ChannelData, ChannelType, Station
+from .stores import RawDataStore
+from .utils import fs_join, get_filesystem
+
+logger = logging.getLogger(__name__)
+
+
+class MiniSeedDataStore(RawDataStore):
+    """
+    A data store implementation to read from a directory of miniSEED data files
+    We use SCEDC convention to organize and name miniSEED files. See **Continuous Waveforms** on
+    https://scedc.caltech.edu/data/cloud.html for full details of this naming strategy.
+    """
+
+    def __init__(
+        self,
+        path: str,
+        chan_catalog: ChannelCatalog,
+        chan_filter: Callable[[Channel], bool] = None,
+        date_range: DateTimeRange = None,
+    ):
+        """
+        Parameters:
+            path: path to look for ms files. Should be a local file directory
+            chan_catalog: ChannelCatalog to retrieve inventory information for the channels
+            chan_filter: Optional function to decide whether a channel should be used or not,
+                            if None, all channels are used
+            date_range: Optional date range to filter the data
+        """
+        super().__init__()
+        self.fs = get_filesystem(path)
+        self.chan_catalog = chan_catalog
+        self.path = os.path.abspath(path)
+        self.paths = {}
+        # to store a dict of {timerange: list of channels}
+        self.channels = {}
+        if chan_filter is None:
+            chan_filter = lambda s: True  # noqa: E731
+
+        dt = date_range.end_datetime - date_range.start_datetime
+        for d in tqdm(range(0, dt.days), desc="Loading channel data"):
+            date = date_range.start_datetime + timedelta(days=d)
+            self._load_channels(self.get_path(date), chan_filter)
+
+    def _load_channels(self, full_path: str, chan_filter: Callable[[Channel], bool]):
+        # The data path follows SCEDC convention: $DATA/YYYY/YYYY_DOY
+        year, doy = full_path.split(os.path.sep)[-2:]
+        doy = doy[-3:]
+
+        for i in glob.glob(fs_join(full_path, "*")):
+            timespan = MiniSeedDataStore._parse_timespan(int(year), int(doy))
+            key = str(timespan)
+            self.paths[timespan.start_datetime] = full_path
+            stream = obspy.read(i, headonly=True)
+            ids = set([t.id for t in stream])
+            for id in ids:
+                channel = MiniSeedDataStore._parse_channel(id)
+                if not chan_filter(channel):
+                    continue
+                if key not in self.channels:
+                    self.channels[key] = [channel]
+                else:
+                    self.channels[key].append(channel)
+
+    def get_path(self, date: datetime) -> str:
+        # The data path follows SCEDC convention: $DATA/YYYY/YYYY_DOY
+        return fs_join(self.path, fs_join(str(date.year), f"{str(date.year)}_{date.strftime('%j').zfill(3)}"))
+
+    def get_filename(self, timespan: DateTimeRange, chan: Channel) -> str:
+        # By default, file names follow the SCEDC convention, e.g., NP5058_HNE10_2024001.ms
+        year = timespan.start_datetime.year
+        doy = str(timespan.start_datetime.timetuple().tm_yday).zfill(3)
+        net = chan.station.network
+        sta = chan.station.name
+        loc = chan.type.location
+        cha = chan.type.name
+
+        return f"{net.ljust(2, '_')}{sta.ljust(5, '_')}{cha}{loc.ljust(3, '_')}{year}{doy}.ms"
+
+    def get_channels(self, timespan: DateTimeRange) -> List[Channel]:
+        tmp_channels = self.channels.get(str(timespan), [])
+        return list(map(lambda c: self.chan_catalog.get_full_channel(timespan, c), tmp_channels))
+
+    def get_timespans(self) -> List[DateTimeRange]:
+        return list([DateTimeRange.from_range_text(d) for d in sorted(self.channels.keys())])
+
+    def read_data(self, timespan: DateTimeRange, chan: Channel) -> ChannelData:
+        filename = fs_join(self.paths[timespan.start_datetime], self.get_filename(timespan, chan))
+        stream = obspy.read(filename)
+        return ChannelData(stream)
+
+    def get_inventory(self, timespan: DateTimeRange, station: Station) -> obspy.Inventory:
+        return self.chan_catalog.get_inventory(timespan, station)
+
+    def _parse_timespan(year: int, doy: int) -> DateTimeRange:
+        jan1 = datetime(year, 1, 1, tzinfo=timezone.utc)
+        return DateTimeRange(jan1 + timedelta(days=doy - 1), jan1 + timedelta(days=doy))
+
+    def _parse_channel(record: str) -> Channel:
+        net, sta, loc, cha = record.split(".")
+
+        c = Channel(
+            ChannelType(cha, loc),
+            # lat/lon/elev will be populated later
+            Station(net, sta, location=loc),
+        )
+        return c