atacr_download_data.py

#!/usr/bin/env python

# Copyright 2019 Pascal Audet & Helen Janiszewski
#
# This file is part of OBStools.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.


# Import modules and functions
import numpy as np
import os.path
import pickle
import stdb
from obspy.clients.fdsn import Client
from obspy import Stream, UTCDateTime
from obstools.atacr import utils
from pathlib import Path

from argparse import ArgumentParser
from os.path import exists as exist
from numpy import nan


def get_daylong_arguments(argv=None):
    """
    Get Options from :class:`~optparse.OptionParser` objects.

    Calling options for the script `obs_download_data.py` that accompany this
    package.

    """

    parser = ArgumentParser(
        usage="%(prog)s [options] <indb>",
        description="Script used " +
        "to download and pre-process up to four-component " +
        "(H1, H2, Z and P), day-long seismograms to use in " +
        "noise corrections of vertical component of OBS data. " +
        "Data are requested from the internet using the client " +
        "services framework for a given date range. The stations " +
        "are processed one by one and the data are stored to disk.")
    parser.add_argument(
        "indb",
        help="Station Database to process from.",
        type=str)

    # General Settings
    parser.add_argument(
        "--keys",
        action="store",
        type=str,
        dest="stkeys",
        default="",
        help="Specify a comma-separated list of station keys " +
        "for which to perform the analysis. These must be " +
        "contained within the station database. Partial keys " +
        "will be used to match against those in the dictionary. " +
        "For instance, providing IU will match with all stations " +
        "in the IU network. " +
        "[Default processes all stations in the database]")
    parser.add_argument(
        "-C", "--channels",
        action="store",
        type=str,
        dest="channels",
        default="",
        help="Specify a comma-separated list of channels for " +
        "which to perform the transfer function analysis. " +
        "Possible options are '12' (for horizontal channels 1 and 2) " +
        "and/or 'P' (for pressure channel). Specifying '12' allows " +
        "for tilt correction. Specifying 'P' allows for compliance " +
        "correction. [Default '12,P' looks for both horizontal and " +
        "pressure and allows for both tilt AND compliance corrections]")
    parser.add_argument(
        "--zcomp",
        dest="zcomp",
        type=str,
        default="Z",
        help="Specify the Vertical Component Channel Identifier. " +
        "[Default Z].")
    parser.add_argument(
        "-O", "--overwrite",
        action="store_true",
        dest="ovr",
        default=False,
        help="Force the overwriting of pre-existing data. " +
        "[Default False]")

    # Server Settings
    ServerGroup = parser.add_argument_group(
        title="Server Settings",
        description="Settings associated with which "
        "datacenter to log into.")
    ServerGroup.add_argument(
        "--server",
        action="store",
        type=str,
        dest="server",
        default="IRIS",
        help="Base URL of FDSN web service compatible "
        "server (e.g. “http://service.iris.edu”) or key string for recognized "
        "server (one of 'AUSPASS', 'BGR', 'EARTHSCOPE', 'EIDA', 'EMSC', 'ETH', "
        "'GEOFON', 'GEONET', 'GFZ', 'ICGC', 'IESDMC', 'INGV', 'IPGP', 'IRIS', "
        "'IRISPH5', 'ISC', 'KNMI', 'KOERI', 'LMU', 'NCEDC', 'NIEP', 'NOA', "
        "'NRCAN', 'ODC', 'ORFEUS', 'RASPISHAKE', 'RESIF', 'RESIFPH5', 'SCEDC', "
        "'TEXNET', 'UIB-NORSAR', 'USGS', 'USP'). [Default 'IRIS']")
    ServerGroup.add_argument(
        "--user-auth",
        action="store",
        type=str,
        dest="userauth",
        default=None,
        help="Authentification Username and Password for the " +
        "waveform server (--user-auth='username:authpassword') to access " +
        "and download restricted data. [Default no user and password]")
    ServerGroup.add_argument(
        "--eida-token",
        action="store",
        type=str,
        dest="tokenfile",
        default=None,
        help="Token for EIDA authentication mechanism, see " +
        "http://geofon.gfz-potsdam.de/waveform/archive/auth/index.php. "
        "If a token is provided, argument --user-auth will be ignored. "
        "This mechanism is only available on select EIDA nodes. The token can "
        "be provided in form of the PGP message as a string, or the filename "
        "of a local file with the PGP message in it. [Default None]")

    """
    # Database Settings
    DataGroup = parser.add_argument_group(
        title="Local Data Settings",
        description="Settings associated with defining " +
        "and using a local data base of pre-downloaded day-long SAC files.")
    DataGroup.add_argument(
        "--local-data",
        action="store",
        type=str,
        dest="localdata",
        default=None,
        help="Specify a comma separated list of paths containing " +
        "day-long sac files of data already downloaded. " +
        "If data exists for a seismogram is already present on disk, " +
        "it is selected preferentially over downloading " +
        "the data using the Client interface")
    DataGroup.add_argument(
        "--no-data-zero",
        action="store_true",
        dest="ndval",
        default=False,
        help="Specify to force missing data to be set as zero, " +
        "rather than default behaviour which sets to nan.")
"""

    # Constants Settings
    FreqGroup = parser.add_argument_group(
        title='Frequency Settings',
        description="Miscellaneous frequency settings")
    FreqGroup.add_argument(
        "--sampling-rate",
        action="store",
        type=float,
        dest="new_sampling_rate",
        default=5.,
        help="Specify new sampling rate (float, in Hz). [Default 5.]")
    FreqGroup.add_argument(
        "--units",
        action="store",
        type=str,
        dest="units",
        default="DISP",
        help="Choose the output seismogram units. Options are: " +
        "'DISP', 'VEL', 'ACC'. [Default 'DISP']")
    FreqGroup.add_argument(
        "--pre-filt",
        action="store",
        type=str,
        dest="pre_filt",
        default=None,
        help="Specify four comma-separated corner frequencies " +
        "(float, in Hz) for deconvolution pre-filter. " +
        "[Default 0.001,0.005,45.,50.]")

    # Event Selection Criteria
    DaysGroup = parser.add_argument_group(
        title="Time Search Settings",
        description="Time settings associated with searching " +
        "for day-long seismograms")
    DaysGroup.add_argument(
        "--start",
        action="store",
        type=str,
        dest="startT",
        default="",
        help="Specify a UTCDateTime compatible string representing " +
        "the start day for the data search. This will override any " +
        "station start times. " +
        "[Default start date for each station in database]")
    DaysGroup.add_argument(
        "--end",
        action="store",
        type=str,
        dest="endT",
        default="",
        help="Specify a UTCDateTime compatible string representing " +
        "the start time for the event search. This will override any " +
        "station end times [Default end date for each station in database]")

    args = parser.parse_args(argv)

    # Check inputs
    if not exist(args.indb):
        parser.error("Input file " + args.indb + " does not exist")

    # create station key list
    if len(args.stkeys) > 0:
        args.stkeys = args.stkeys.split(',')

    # create channel list
    if len(args.channels) > 0:
        args.channels = args.channels.split(',')
    else:
        args.channels = ["12", "P"]
    for cha in args.channels:
        if cha not in ["12", "P"]:
            parser.error("Error: Channel not recognized " + str(cha))

    # construct start time
    if len(args.startT) > 0:
        try:
            args.startT = UTCDateTime(args.startT)
        except Exception:
            parser.error(
                "Error: Cannot construct UTCDateTime from start time: " +
                args.startT)
    else:
        args.startT = None

    # construct end time
    if len(args.endT) > 0:
        try:
            args.endT = UTCDateTime(args.endT)
        except Exception:
            parser.error(
                "Error: Cannot construct UTCDateTime from end time: " +
                args.endT)
    else:
        args.endT = None

    # Parse restricted data settings
    if args.tokenfile is not None:
        args.userauth = [None, None]
    else:
        if args.userauth is not None:
            tt = args.userauth.split(':')
            if not len(tt) == 2:
                msg = ("Error: Incorrect Username and Password Strings for " +
                       "User Authentification")
                parser.error(msg)
            else:
                args.userauth = tt
        else:
            args.userauth = [None, None]

    # # Parse Local Data directories
    # if args.localdata is not None:
    #     args.localdata = args.localdata.split(',')
    # else:
    #     args.localdata = []

    # # Check NoData Value
    # if args.ndval:
    #     args.ndval = 0.0
    # else:
    #     args.ndval = nan

    if args.units not in ['DISP', 'VEL', 'ACC']:
        msg = ("Error: invalid --units argument. Choose among " +
               "'DISP', 'VEL', or 'ACC'")
        parser.error(msg)

    if args.pre_filt is None:
        args.pre_filt = [0.001, 0.005, 45., 50.]
    else:
        args.pre_filt = [float(val) for val in args.pre_filt.split(',')]
        args.pre_filt = sorted(args.pre_filt)
        if (len(args.pre_filt)) != 4:
            msg = ("Error: --pre-filt should contain 4 " +
                   "comma-separated floats")
            parser.error(msg)

    return args


def main(args=None):

    if args is None:
        # Run Input Parser
        args = get_daylong_arguments()

    # Load Database
    # stdb>0.1.3
    try:
        db, stkeys = stdb.io.load_db(fname=args.indb, keys=args.stkeys)

    # stdb=0.1.3
    except Exception:
        db = stdb.io.load_db(fname=args.indb)

        # Construct station key loop
        allkeys = db.keys()
        sorted(allkeys)

        # Extract key subset
        if len(args.stkeys) > 0:
            stkeys = []
            for skey in args.stkeys:
                stkeys.extend([s for s in allkeys if skey in s])
        else:
            stkeys = db.keys()
            sorted(stkeys)

    # Loop over station keys
    for stkey in list(stkeys):

        # Extract station information from dictionary
        sta = db[stkey]

        # Define path to see if it exists
        datapath = Path('DATA') / Path(stkey)
        if not datapath.is_dir():
            print('\nPath to '+str(datapath)+' doesn`t exist - creating it')
            datapath.mkdir(parents=True)

        # Establish client
        client = Client(
            base_url=args.server,
            user=args.userauth[0],
            password=args.userauth[1],
            eida_token=args.tokenfile)

        # Get catalogue search start time
        if args.startT is None:
            tstart = sta.startdate
        else:
            tstart = args.startT

        # Get catalogue search end time
        if args.endT is None:
            tend = sta.enddate
        else:
            tend = args.endT

        if tstart > sta.enddate or tend < sta.startdate:
            continue

        # Temporary print locations
        tlocs = sta.location
        if len(tlocs) == 0:
            tlocs = ['']
        for il in range(0, len(tlocs)):
            if len(tlocs[il]) == 0:
                tlocs[il] = "--"
        sta.location = tlocs

        # Update Display
        print("\n|===============================================|")
        print("|===============================================|")
        print("|                   {0:>8s}                    |".format(
            sta.station))
        print("|===============================================|")
        print("|===============================================|")
        print("|  Station: {0:>2s}.{1:5s}                            |".format(
            sta.network, sta.station))
        print("|      Channel: {0:2s}; Locations: {1:15s}  |".format(
            sta.channel, ",".join(tlocs)))
        print("|      Lon: {0:7.2f}; Lat: {1:6.2f}                |".format(
            sta.longitude, sta.latitude))
        print("|      Start time: {0:19s}          |".format(
            sta.startdate.strftime("%Y-%m-%d")))
        print("|      End time:   {0:19s}          |".format(
            sta.enddate.strftime("%Y-%m-%d")))
        print("|-----------------------------------------------|")
        print("| Searching day-long files:                     |")
        print("|   Start: {0:19s}                  |".format(
            tstart.strftime("%Y-%m-%d")))
        print("|   End:   {0:19s}                  |".format(
            tend.strftime("%Y-%m-%d")))

        # Split into 24-hour long segments
        dt = 3600.*24.

        t1 = tstart
        t2 = tstart + dt

        while t2 <= tend:

            # Time stamp
            tstamp = str(t1.year).zfill(4)+'.'+str(t1.julday).zfill(3)+'.'

            print("\n"+"*"*60)
            print("* Downloading day-long data for key {0} " +
                  " and day {1}.{2:03d}".format(stkey, t1.year, t1.julday))
            print("*")
            print("* Channels selected: "+str(args.channels)+' and vertical')

            # Define file names (to check if files already exist)
            # Horizontal 1 channel
            file1 = datapath / (tstamp+'.'+sta.channel+'1.SAC')
            # Horizontal 2 channel
            file2 = datapath / (tstamp+'.'+sta.channel+'2.SAC')
            # Vertical channel
            fileZ = datapath / (tstamp+'.'+sta.channel+'Z.SAC')
            # Pressure channel
            fileP = datapath / (tstamp+'.'+sta.channel[0]+'DH.SAC')

            if "P" not in args.channels:

                # If data files exist, continue
                if fileZ.exists() and file1.exists() and file2.exists():
                    if not args.ovr:
                        print(
                            "*   "+tstamp +
                            "*SAC                                 ")
                        print(
                            "*   -> Files already exist, " +
                            "continuing            ")
                        t1 += dt
                        t2 += dt
                        continue

                channels = sta.channel.upper()+'1,'+sta.channel.upper() + \
                    '2,'+sta.channel.upper()+args.zcomp

                # Get waveforms from client
                try:
                    print("*   "+tstamp +
                          "*SAC                                 ")
                    print("*   -> Downloading Seismic data... ")
                    sth = client.get_waveforms(
                        network=sta.network,
                        station=sta.station,
                        location=sta.location[0],
                        channel=channels,
                        starttime=t1,
                        endtime=t2,
                        attach_response=True)
                    print("*      ...done")

                except Exception:
                    print(" Error: Unable to download ?H? components - " +
                          "continuing")
                    t1 += dt
                    t2 += dt
                    continue

                st = sth.merge()

            elif "12" not in args.channels:

                # If data files exist, continue
                if fileZ.exists() and fileP.exists():
                    if not args.ovr:
                        print("*   "+tstamp +
                              "*SAC                                 ")
                        print("*   -> Files already exist, " +
                              "continuing            ")
                        t1 += dt
                        t2 += dt
                        continue

                channels = sta.channel.upper() + args.zcomp

                # Get waveforms from client
                try:
                    print("*   "+tstamp +
                          "*SAC                                 ")
                    print("*   -> Downloading Seismic data... ")
                    sth = client.get_waveforms(
                        network=sta.network,
                        station=sta.station,
                        location=sta.location[0],
                        channel=channels,
                        starttime=t1,
                        endtime=t2,
                        attach_response=True)
                    print("*      ...done")

                except Exception:
                    print(" Error: Unable to download ?H? components - " +
                          "continuing")
                    t1 += dt
                    t2 += dt
                    continue
                try:
                    print("*   -> Downloading Pressure data...")
                    stp = client.get_waveforms(
                        network=sta.network,
                        station=sta.station,
                        location=sta.location[0],
                        channel='?DH',
                        starttime=t1,
                        endtime=t2,
                        attach_response=True)
                    print("*      ...done")
                    if len(stp) > 1:
                        print("WARNING: There are more than one ?DH trace")
                        print("*   -> Keeping the highest sampling rate")
                        print(
                            "*   -> Renaming channel to " +
                            sta.channel[0]+"DH")
                        if stp[0].stats.sampling_rate > \
                                stp[1].stats.sampling_rate:
                            stp = Stream(traces=stp[0])
                        else:
                            stp = Stream(traces=stp[1])

                except Exception:
                    print(" Error: Unable to download ?DH component - " +
                          "continuing")
                    t1 += dt
                    t2 += dt
                    continue

                st = sth.merge() + stp.merge()

            else:

                # If data files exist, continue
                if (fileZ.exists() and file1.exists() and
                        file2.exists() and fileP.exists()):
                    if not args.ovr:
                        print("*   "+tstamp +
                              "*SAC                                 ")
                        print("*   -> Files already exist, " +
                              "continuing            ")
                        t1 += dt
                        t2 += dt
                        continue

                channels = sta.channel.upper()+'1,'+sta.channel.upper() + \
                    '2,'+sta.channel.upper()+args.zcomp

                # Get waveforms from client
                try:
                    print("*   "+tstamp +
                          "*SAC                                 ")
                    print("*   -> Downloading Seismic data... ")
                    sth = client.get_waveforms(
                        network=sta.network,
                        station=sta.station,
                        location=sta.location[0],
                        channel=channels,
                        starttime=t1,
                        endtime=t2,
                        attach_response=True)
                    print("*      ...done")

                except Exception:
                    print(" Error: Unable to download ?H? components - " +
                          "continuing")
                    t1 += dt
                    t2 += dt
                    continue
                try:
                    print("*   -> Downloading Pressure data...")
                    stp = client.get_waveforms(
                        network=sta.network,
                        station=sta.station,
                        location=sta.location[0],
                        channel='?DH',
                        starttime=t1,
                        endtime=t2,
                        attach_response=True)
                    print("*      ...done")
                    if len(stp) > 1:
                        print("WARNING: There are more than one ?DH trace")
                        print("*   -> Keeping the highest sampling rate")
                        print(
                            "*   -> Renaming channel to " +
                            sta.channel[0]+"DH")
                        if stp[0].stats.sampling_rate > \
                                stp[1].stats.sampling_rate:
                            stp = Stream(traces=stp[0])
                        else:
                            stp = Stream(traces=stp[1])

                except Exception:
                    print(" Error: Unable to download ?DH component - " +
                          "continuing")
                    t1 += dt
                    t2 += dt
                    continue

                st = sth.merge() + stp.merge()

            # Detrend, filter
            st.detrend('demean')
            st.detrend('linear')
            st.filter(
                'lowpass', freq=0.5*args.new_sampling_rate,
                corners=2, zerophase=True)
            st.resample(args.new_sampling_rate)

            # Check streams
            is_ok, st = utils.QC_streams(t1, t2, st)
            if not is_ok:
                t1 += dt
                t2 += dt
                continue

            sth = st.select(component='1') + st.select(component='2') + \
                st.select(component=args.zcomp)

            # Remove responses
            print("*   -> Removing responses - Seismic data")
            sth.remove_response(pre_filt=args.pre_filt, output=args.units)

            # Extract traces - Z
            trZ = sth.select(component=args.zcomp)[0]
            trZ = utils.update_stats(
                trZ, sta.latitude, sta.longitude, sta.elevation,
                sta.channel+'Z')
            trZ.write(str(fileZ), format='SAC')

            # Extract traces - H
            if "12" in args.channels:
                tr1 = sth.select(component='1')[0]
                tr2 = sth.select(component='2')[0]
                tr1 = utils.update_stats(
                    tr1, sta.latitude, sta.longitude, sta.elevation,
                    sta.channel+'1')
                tr2 = utils.update_stats(
                    tr2, sta.latitude, sta.longitude, sta.elevation,
                    sta.channel+'2')
                tr1.write(str(file1), format='SAC')
                tr2.write(str(file2), format='SAC')

            # Extract traces - P
            if "P" in args.channels:
                stp = st.select(component='H')
                print("*   -> Removing responses - Pressure data")
                stp.remove_response(pre_filt=args.pre_filt)
                trP = stp[0]
                trP = utils.update_stats(
                    trP, sta.latitude, sta.longitude, sta.elevation,
                    sta.channel[0]+'DH')
                trP.write(str(fileP), format='SAC')

            t1 += dt
            t2 += dt


if __name__ == "__main__":

    # Run main program
    main()