# -*- coding: utf-8 -*-
"""
obspy.clients.filesystem.sds - read support for SeisComP Data Structure
=======================================================================
This module provides read support for data stored locally in a SeisComP Data
Structure (SDS) directory structure.
The directory and file layout of SDS is defined as::
<SDSdir>/YEAR/NET/STA/CHAN.TYPE/NET.STA.LOC.CHAN.TYPE.YEAR.DAY
These fields are defined by SDS as follows::
SDSdir : arbitrary base directory
YEAR : 4 digit year
NET : Network code/identifier, up to 8 characters, no spaces
STA : Station code/identifier, up to 8 characters, no spaces
CHAN : Channel code/identifier, up to 8 characters, no spaces
TYPE : 1 characters indicating the data type, recommended types are:
'D' - Waveform data
'E' - Detection data
'L' - Log data
'T' - Timing data
'C' - Calibration data
'R' - Response data
'O' - Opaque data
LOC : Location identifier, up to 8 characters, no spaces
DAY : 3 digit day of year, padded with zeros
See https://www.seiscomp3.org/wiki/doc/applications/slarchive/SDS.
:copyright:
The ObsPy Development Team (devs@obspy.org)
:license:
GNU Lesser General Public License, Version 3
(https://www.gnu.org/copyleft/lesser.html)
"""
import glob
import os
import re
import warnings
from datetime import timedelta
import numpy as np
from obspy import Stream, read, UTCDateTime
from obspy.core.stream import _headonly_warning_msg
from obspy.core.util.misc import BAND_CODE
from obspy.io.mseed import ObsPyMSEEDFilesizeTooSmallError
SDS_FMTSTR = os.path.join(
"{year}", "{network}", "{station}", "{channel}.{sds_type}",
"{network}.{station}.{location}.{channel}.{sds_type}.{year}.{doy:03d}")
FORMAT_STR_PLACEHOLDER_REGEX = r"{(\w+?)?([!:].*?)?}"
[docs]
class Client(object):
"""
Request client for SeisComP Data Structure archive on local filesystem.
For details see the :meth:`~obspy.clients.filesystem.sds.Client.__init__()`
method.
"""
FMTSTR = SDS_FMTSTR
[docs]
def __init__(self, sds_root, sds_type="D", format="MSEED",
fileborder_seconds=30, fileborder_samples=5000):
"""
Initialize a SDS local filesystem client.
>>> from obspy.clients.filesystem.sds import Client
>>> client = Client("/my/SDS/archive/root") # doctest: +SKIP
:type sds_root: str
:param sds_root: Root directory of SDS archive.
:type sds_type: str
:param sds_type: SDS data type identifier, one single character. Types
recommended by the SDS definition are: 'D' - Waveform data,
'E' - Detection data, 'L' - Log data, 'T' - Timing data,
'C' - Calibration data, 'R' - Response data, 'O' - Opaque data. Can
also be wildcarded by setting to ``?`` or ``*``.
:type format: str
:param format: File format the data is stored in, see
:func:`~obspy.core.stream.read()` for a list of file formats
supported by ObsPy. Usually, SDS archives are stored in "MSEED"
format. Can be set to ``None`` for file format autodetection
(slowing down the reading).
:type fileborder_seconds: float
:param fileborder_seconds: Defines in which cases the client checks the
previous/next daily file for the requested data (data in SDS
archives usually spill over on the day break, at least for a few
seconds). For example setting ``fileborder_seconds=30`` means that
for a request with ``starttime`` at ``00:00:29`` UTC (or an
``endtime`` at ``23:59:31``), the previous daily file is also
checked, if it contains matching data. The maximum of both
``fileborder_seconds`` and ``fileborder_samples`` is used when
determining if previous/next day should be checked for data.
:type fileborder_samples: int
:param fileborder_samples: Similar to ``fileborder_seconds``. The given
number of samples is converted to seconds by mapping the band
code of the requested channel to sampling frequency. The maximum of
both ``fileborder_seconds`` and ``fileborder_samples`` is used when
determining if previous/next day should be checked for data.
"""
if not os.path.isdir(sds_root):
msg = ("SDS root is not a local directory: " + sds_root)
raise IOError(msg)
self.sds_root = sds_root
self.sds_type = sds_type
self.format = format and format.upper()
self.fileborder_seconds = fileborder_seconds
self.fileborder_samples = fileborder_samples
[docs]
def _get_filenames(self, network, station, location, channel, starttime,
endtime, sds_type=None):
"""
Get list of filenames for certain waveform and time span.
:type network: str
:param network: Network code of requested data (e.g. "IU").
:type station: str
:param station: Station code of requested data (e.g. "ANMO").
:type location: str
:param location: Location code of requested data (e.g. "").
:type channel: str
:param channel: Channel code of requested data (e.g. "HHZ").
:type starttime: :class:`~obspy.core.utcdatetime.UTCDateTime`
:param starttime: Start of time span.
:type endtime: :class:`~obspy.core.utcdatetime.UTCDateTime`
:param endtime: End of time span.
:type sds_type: str
:param sds_type: Override SDS data type identifier that was specified
during client initialization.
:rtype: list[str]
"""
sds_type = sds_type or self.sds_type
# SDS has data sometimes in adjacent days, so also try to read the
# requested data from those files. Usually this is only a few seconds
# of data after midnight, but for now we play safe here to catch all
# requested data (and with MiniSEED - the usual SDS file format - we
# can use starttime/endtime kwargs anyway to read only desired parts).
year_doy = set()
# determine how far before starttime/after endtime we should check
# other dayfiles for the data
t_buffer = self.fileborder_samples / BAND_CODE.get(channel[:1], 20.0)
t_buffer = max(t_buffer, self.fileborder_seconds)
t = starttime - t_buffer
t_max = endtime + t_buffer
# make a list of year/doy combinations that covers the whole requested
# time window (plus day before and day after)
while t < t_max:
year_doy.add((t.year, t.julday))
t += timedelta(days=1)
year_doy.add((t_max.year, t_max.julday))
full_paths = set()
for year, doy in year_doy:
filename = self.FMTSTR.format(
network=network, station=station, location=location,
channel=channel, year=year, doy=doy, sds_type=sds_type)
full_path = os.path.join(self.sds_root, filename)
full_paths = full_paths.union(glob.glob(full_path))
return full_paths
[docs]
def _get_filename(self, network, station, location, channel, time,
sds_type=None):
"""
Get filename for certain waveform.
:type network: str
:param network: Network code of requested data (e.g. "IU").
:type station: str
:param station: Station code of requested data (e.g. "ANMO").
:type location: str
:param location: Location code of requested data (e.g. "").
:type channel: str
:param channel: Channel code of requested data (e.g. "HHZ").
:type time: :class:`~obspy.core.utcdatetime.UTCDateTime`
:param time: Time of interest.
:type sds_type: str
:param sds_type: Override SDS data type identifier that was specified
during client initialization.
:rtype: str
"""
sds_type = sds_type or self.sds_type
filename = self.FMTSTR.format(
network=network, station=station, location=location,
channel=channel, year=time.year, doy=time.julday,
sds_type=sds_type)
return os.path.join(self.sds_root, filename)
[docs]
def get_availability_percentage(self, network, station, location, channel,
starttime, endtime, sds_type=None):
"""
Get percentage of available data.
:type network: str
:param network: Network code of requested data (e.g. "IU").
:type station: str
:param station: Station code of requested data (e.g. "ANMO").
:type location: str
:param location: Location code of requested data (e.g. "").
:type channel: str
:param channel: Channel code of requested data (e.g. "HHZ").
:type starttime: :class:`~obspy.core.utcdatetime.UTCDateTime`
:param starttime: Start of requested time window.
:type endtime: :class:`~obspy.core.utcdatetime.UTCDateTime`
:param endtime: End of requested time window.
:type sds_type: str
:param sds_type: Override SDS data type identifier that was specified
during client initialization.
:rtype: tuple(float, int)
:returns: 2-tuple of percentage of available data (``0.0`` to ``1.0``)
and number of gaps/overlaps.
"""
if starttime >= endtime:
msg = ("'endtime' must be after 'starttime'.")
raise ValueError(msg)
sds_type = sds_type or self.sds_type
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore", _headonly_warning_msg, UserWarning,
"obspy.core.stream")
st = self.get_waveforms(network, station, location, channel,
starttime, endtime, sds_type=sds_type,
headonly=True, _no_trim_or_merge=True)
# even if the warning was silently caught and not shown it gets
# registered in the __warningregistry__ and will not be shown
# subsequently in a place were it's not caught
# see https://bugs.python.org/issue4180
# see e.g. http://blog.ionelmc.ro/2013/06/26/testing-python-warnings/
try:
from obspy.core.stream import __warningregistry__ as \
stream_warningregistry
except ImportError:
# import error means no warning has been issued from
# obspy.core.stream before, so nothing to do.
pass
else:
for key in list(stream_warningregistry.keys()):
if key[0] == _headonly_warning_msg:
stream_warningregistry.pop(key)
st.sort(keys=['starttime', 'endtime'])
st.traces = [tr for tr in st
if not (tr.stats.endtime < starttime or
tr.stats.starttime > endtime)]
if not st:
return (0, 1)
total_duration = endtime - starttime
# sum up gaps in the middle
gaps = [gap[6] for gap in st.get_gaps()]
gap_sum = np.sum(gaps)
gap_count = len(gaps)
# check if we have a gap at start or end
earliest = min([tr.stats.starttime for tr in st])
latest = max([tr.stats.endtime for tr in st])
if earliest > starttime:
gap_sum += earliest - starttime
gap_count += 1
if latest < endtime:
gap_sum += endtime - latest
gap_count += 1
return (1 - (gap_sum / total_duration), gap_count)
[docs]
def _get_current_endtime(self, network, station, location, channel,
sds_type=None, stop_time=None,
check_has_no_data=True):
"""
Get time of last sample for given stream.
``None`` is returned if no data at all is encountered when going
backwards until `stop_time` (defaults to Jan 1st 1950).
:type network: str
:param network: Network code of requested data (e.g. "IU").
:type station: str
:param station: Station code of requested data (e.g. "ANMO").
:type location: str
:param location: Location code of requested data (e.g. "").
:type channel: str
:param channel: Channel code of requested data (e.g. "HHZ").
:type sds_type: str
:param sds_type: Override SDS data type identifier that was specified
during client initialization.
:type stop_time: :class:`~obspy.core.utcdatetime.UTCDateTime`
:param stop_time: Time at which the search for data is stopped and
``None`` is returned. If not specified, stops at ``1950-01-01T00``.
:type check_has_no_data: bool
:param check_has_no_data: Whether to perform a check with
:meth:`has_data` if any data is available at all for the given SEED
ID. Turns out that this check can take a long time on slow
filesystems (e.g. NFS), so it might actually make the latency check
take longer than necessary, so deactivating it might be worth a try
if speed issues occur.
:rtype: :class:`~obspy.core.utcdatetime.UTCDateTime` or ``None``
"""
sds_type = sds_type or self.sds_type
seed_pattern = ".".join((network, station, location, channel))
if check_has_no_data and not self.has_data(
network=network, station=station, location=location,
channel=channel, sds_type=sds_type):
return None
stop_time = stop_time or UTCDateTime(1950, 1, 1)
st = None
time = UTCDateTime()
while not st:
if time < stop_time:
return None
filename = self._get_filename(
network=network, station=station, location=location,
channel=channel, time=time, sds_type=sds_type)
if os.path.isfile(filename):
try:
st = read(filename, format=self.format, headonly=True,
sourcename=seed_pattern)
except ObsPyMSEEDFilesizeTooSmallError:
# just ignore small MSEED files, in use cases working with
# near-realtime data these are usually just being created
# right at request time, e.g. when fetching current data
# right after midnight
st = None
else:
st = st.select(network=network, station=station,
location=location, channel=channel)
if st:
break
time -= 24 * 3600
return max([tr.stats.endtime for tr in st])
[docs]
def get_latency(self, network, station, location, channel,
sds_type=None, stop_time=None, check_has_no_data=True):
"""
Get latency for given stream, i.e. difference of current time and
latest available data for stream in SDS archive. ``None`` is returned
if no data at all is encountered when going backwards until
`stop_time` (defaults to Jan 1st 1950).
:type network: str
:param network: Network code of requested data (e.g. "IU").
:type station: str
:param station: Station code of requested data (e.g. "ANMO").
:type location: str
:param location: Location code of requested data (e.g. "").
:type channel: str
:param channel: Channel code of requested data (e.g. "HHZ").
:type sds_type: str
:param sds_type: Override SDS data type identifier that was specified
during client initialization.
:type stop_time: :class:`~obspy.core.utcdatetime.UTCDateTime`
:param stop_time: Time at which the search for data is stopped and
``None`` is returned. If not specified, stops at ``1950-01-01T00``.
:type check_has_no_data: bool
:param check_has_no_data: Whether to perform a check with
:meth:`has_data` if any data is available at all for the given SEED
ID. Turns out that this check can take a long time on slow
filesystems (e.g. NFS), so it might actually make the latency check
take longer than necessary, so deactivating it might be worth a try
if speed issues occur.
:rtype: float or ``None``
:returns: Latency in seconds or ``None`` if no data was encountered
from current time backwards until ``stop_time``.
"""
endtime = self._get_current_endtime(
network=network, station=station, location=location,
channel=channel, sds_type=sds_type, stop_time=stop_time,
check_has_no_data=check_has_no_data)
if endtime is None:
return endtime
return UTCDateTime() - endtime
[docs]
def has_data(self, network, station, location, channel, sds_type=None):
"""
Check if specified stream has any data.
Actually just checks whether a file is encountered in a folder that is
expected to contain data.
:type network: str
:param network: Network code of requested data (e.g. "IU").
:type station: str
:param station: Station code of requested data (e.g. "ANMO").
:type location: str
:param location: Location code of requested data (e.g. "").
:type channel: str
:param channel: Channel code of requested data (e.g. "HHZ").
:type sds_type: str
:param sds_type: Override SDS data type identifier that was specified
during client initialization.
:rtype: bool
"""
sds_type = sds_type or self.sds_type
pattern = re.sub(
FORMAT_STR_PLACEHOLDER_REGEX,
_wildcarded_except(["network", "station", "location", "channel",
"sds_type"]),
self.FMTSTR)
pattern = pattern.format(
network=network, station=station, location=location,
channel=channel, sds_type=sds_type)
pattern = os.path.join(self.sds_root, pattern)
if glob.glob(pattern):
return True
else:
return False
[docs]
def get_all_nslc(self, sds_type=None, datetime=None):
"""
Return information on what streams are included in archive.
Note that this can be very slow on network file systems because every
single file has to be touched (because available location codes can not
be discovered from folder structure alone).
:type sds_type: str
:param sds_type: Override SDS data type identifier that was specified
during client initialization.
:type datetime: :class:`~obspy.core.utcdatetime.UTCDateTime`
:param datetime: Only return all streams that have data at specified
time (checks if file exists that should have the data, i.e. streams
might be returned that have data on the same day but not at exactly
this point in time).
:rtype: list
:returns: List of (network, station, location, channel) 4-tuples of all
available streams in archive.
"""
sds_type = sds_type or self.sds_type
result = set()
# wildcarded pattern to match all files of interest
if datetime is None:
pattern = re.sub(
FORMAT_STR_PLACEHOLDER_REGEX,
_wildcarded_except(["sds_type"]),
self.FMTSTR).format(sds_type=sds_type)
pattern = os.path.join(self.sds_root, pattern)
else:
pattern = self._get_filename("*", "*", "*", "*", datetime)
all_files = glob.glob(pattern)
# set up inverse regex to extract kwargs/values from full paths
pattern_ = os.path.join(self.sds_root, self.FMTSTR)
group_map = {i: groups[0] for i, groups in
enumerate(re.findall(FORMAT_STR_PLACEHOLDER_REGEX,
pattern_))}
for file_ in all_files:
dict_ = _parse_path_to_dict(file_, pattern_, group_map)
try:
network = dict_["network"]
station = dict_["station"]
location = dict_["location"]
channel = dict_["channel"]
except KeyError as e:
msg = (
"Failed to extract key from pattern '{}' in path "
"'{}': {}").format(pattern, file_, e)
warnings.warn(msg)
continue
result.add((network, station, location, channel))
return sorted(result)
[docs]
def get_all_stations(self, sds_type=None):
"""
Return information on what stations are included in archive.
This method assumes that network/station combinations can be discovered
from the folder structure alone (as opposed to the filenames).
:type sds_type: str
:param sds_type: Override SDS data type identifier that was specified
during client initialization.
:rtype: list
:returns: List of (network, station) 2-tuples of all available stations
in archive.
"""
sds_type = sds_type or self.sds_type
result = set()
# wildcarded pattern to match all files of interest
fmtstr = os.path.dirname(self.FMTSTR)
pattern = re.sub(
FORMAT_STR_PLACEHOLDER_REGEX,
_wildcarded_except(["sds_type"]),
fmtstr).format(sds_type=sds_type)
pattern = os.path.join(self.sds_root, pattern)
all_files = glob.glob(pattern)
# set up inverse regex to extract kwargs/values from full paths
pattern_ = os.path.join(self.sds_root, fmtstr)
group_map = {i: groups[0] for i, groups in
enumerate(re.findall(FORMAT_STR_PLACEHOLDER_REGEX,
pattern_))}
for file_ in all_files:
dict_ = _parse_path_to_dict(file_, pattern_, group_map)
try:
network = dict_["network"]
station = dict_["station"]
except (TypeError, KeyError) as e:
if isinstance(e, TypeError) and dict_ is not None:
raise
msg = (
"Failed to extract key from pattern '{}' in path "
"'{}': {}").format(pattern_, file_, e)
warnings.warn(msg)
continue
result.add((network, station))
return sorted(result)
[docs]
def _wildcarded_except(exclude=[]):
"""
Function factory for :mod:`re` ``repl`` functions used in :func:`re.sub`,
replacing all format string place holders with ``*`` wildcards, except
named fields as specified in ``exclude``.
"""
def _wildcarded(match):
if match.group(1) in exclude:
return match.group(0)
return "*"
return _wildcarded
[docs]
def _parse_path_to_dict(path, pattern, group_map):
# escape special regex characters "." and "\"
# in principle we should escape all special characters in Python regex:
# . ^ $ * + ? { } [ ] \ | ( )
# and also only replace them if outside of format string placeholders..
regex = re.sub(r'([\.\\])', r'\\\1', pattern)
# replace each format string placeholder with a regex group, matching
# alphanumerics. append end-of-line otherwise the last non-greedy match
# doesn't catch anything if it's at the end of the regex
regex = re.sub(FORMAT_STR_PLACEHOLDER_REGEX, r'(\\w*?)', regex) + "$"
match = re.match(regex, path)
if match is None:
return None
result = {}
for i, value in enumerate(match.groups()):
key = group_map[i]
if key in result:
if result[key] != value:
msg = (
"Failed to parse path '{}': Mismatching information "
"for key '{}' from pattern '{}'.").format(
path, key, pattern)
warnings.warn(msg)
return None
result[key] = value
return result
if __name__ == '__main__':
import doctest
doctest.testmod(exclude_empty=True)