atacr_transfer_functions.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
from obspy import UTCDateTime
import pickle
import stdb
from obstools.atacr import StaNoise, Power, Cross, Rotation, TFNoise
from obstools.atacr import utils, plotting
from pathlib import Path

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


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

    Calling options for the script `obs_transfer_functions.py` that accompanies
    this package.

    """

    parser = ArgumentParser(
        usage="%(prog)s [options] <indb>",
        description="Script used "
        "to calculate transfer functions between various " +
        "components, to be used in cleaning vertical " +
        "component of OBS data. The noise data can be " +
        "those obtained from the daily spectra (i.e., " +
        "from `obs_daily_spectra.py`) or those obtained " +
        "from the averaged noise spectra (i.e., from " +
        "`obs_clean_spectra.py`). Flags are available " +
        "to specify the source of data to use as well as " +
        "the time range over which to calculate the " +
        "transfer functions. 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(
        "-O", "--overwrite",
        action="store_true",
        dest="ovr",
        default=False,
        help="Force the overwriting of pre-existing data. " +
        "[Default False]")

    # 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 of 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 data search. "
        "This will override any station end times. " +
        "[Default end date of each station in database]")

    # Constants Settings
    ConstGroup = parser.add_argument_group(
        title='Parameter Settings',
        description="Miscellaneous default values " +
        "and settings")
    ConstGroup.add_argument(
        "--skip-daily",
        action="store_true",
        dest="skip_daily",
        default=False,
        help="Skip daily spectral averages in construction " +
        "of transfer functions. [Default False]")
    ConstGroup.add_argument(
        "--skip-clean",
        action="store_true",
        dest="skip_clean",
        default=False,
        help="Skip cleaned spectral averages in " +
        "construction of transfer functions. Defaults " +
        "to True if data cannot be found in default " +
        "directory. [Default False]")

    # Constants Settings
    FigureGroup = parser.add_argument_group(
        title='Figure Settings',
        description="Flags for plotting figures")
    FigureGroup.add_argument(
        "--figTF",
        action="store_true",
        dest="fig_TF",
        default=False,
        help="Plot transfer function figure. " +
        "[Default does not plot figure]")
    FigureGroup.add_argument(
        "--save-fig",
        action="store_true",
        dest="saveplot",
        default=False,
        help="Set this option if you wish to save the figure(s). [Default " +
        "does not save figure]")
    FigureGroup.add_argument(
        "--format",
        action="store",
        type=str,
        dest="form",
        default="png",
        help="Specify format of figure. Can be any one of the valid" +
        "matplotlib formats: 'png', 'jpg', 'eps', 'pdf'. [Default 'png']")

    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(',')

    # 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

    if args.skip_clean and args.skip_daily:
        parser.error(
            "Error: cannot skip both daily and clean averages")

    return args


def main(args=None):

    if args is None:
        # Run Input Parser
        args = get_transfer_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]

        if not args.skip_daily:
            # Path where spectra are located
            specpath = Path('SPECTRA') / stkey
            if not specpath.is_dir():
                raise(Exception(
                    "Path to "+str(specpath)+" doesn't exist - aborting"))

        if not args.skip_clean:
            # Path where average spectra will be saved
            avstpath = Path('AVG_STA') / stkey
            if not avstpath.is_dir():
                print("Path to "+str(avstpath) +
                      " doesn't exist - skipping cleaned station spectra")
                args.skip_clean = True

        if args.skip_daily and args.skip_clean:
            print("skipping both daily and clean spectra")
            continue

        # Path where transfer functions will be located
        tfpath = Path('TF_STA') / stkey
        if not tfpath.is_dir():
            print("Path to "+str(tfpath)+" doesn't exist - creating it")
            tfpath.mkdir(parents=True)

        # Path where plots will be saved
        if args.saveplot:
            plotpath = tfpath / 'PLOTS'
            if not plotpath.is_dir():
                plotpath.mkdir(parents=True)
        else:
            plotpath = False

        # 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(" ")
        print(" ")
        print("|===============================================|")
        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 %H:%M:%S")))
        print("|      End time:   {0:19s}          |".format(
            sta.enddate.strftime("%Y-%m-%d %H:%M:%S")))
        print("|-----------------------------------------------|")

        # Filename for output transfer functions
        dstart = str(tstart.year).zfill(4)+'.'+str(tstart.julday).zfill(3)+'-'
        dend = str(tend.year).zfill(4)+'.'+str(tend.julday).zfill(3)+'.'
        fileavst = avstpath / (dstart+dend+'avg_sta.pkl')

        # Find all files in directories
        p = specpath.glob('*spectra.pkl')
        spectra_files = [x for x in p if x.is_file()]
        if not args.skip_clean:
            p = avstpath.glob('*avg_sta.pkl')
            average_files = [x for x in p if x.is_file()]

        if not args.skip_daily:

            day_transfer_functions = []

            # Cycle through available files
            for filespec in spectra_files:

                year = filespec.name.split('.')[0]
                jday = filespec.name.split('.')[1]

                print("\n"+"*"*60)
                print("* Calculating transfer functions for key " +
                      stkey+" and day "+year+"."+jday)
                tstamp = year+'.'+jday+'.'
                filename = tfpath / (tstamp + 'transfunc.pkl')

                # Load file
                file = open(filespec, 'rb')
                daynoise = pickle.load(file)
                file.close()

                # Load spectra into TFNoise object
                daytransfer = TFNoise(daynoise)

                # Calculate the transfer functions
                daytransfer.transfer_func()

                # Store the frequency axis
                f = daytransfer.f

                # Append to list of transfer functions
                day_transfer_functions.append(daytransfer.transfunc)

                # Save daily transfer functions to file
                daytransfer.save(filename)

        # Create empty daynoise if not loaded
        # else:
        #     XXX

        if not args.skip_clean:

            # Cycle through available files
            for fileavst in average_files:

                name = fileavst.name.split('avg_sta')

                print("\n"+"*"*60)
                print("* Calculating transfer functions for key " +
                      stkey+" and range "+name[0])
                filename = tfpath / (name[0] + 'transfunc.pkl')

                # Load file
                file = open(fileavst, 'rb')
                stanoise = pickle.load(file)
                file.close()

                # Load spectra into TFNoise object - no Rotation object
                # for station averages
                rotation = Rotation(None, None, None)
                statransfer = TFNoise(stanoise)

                # Calculate the transfer functions
                statransfer.transfer_func()

                # Store the frequency axis
                f = statransfer.f

                # Extract the transfer functions
                sta_transfer_functions = statransfer.transfunc

                # Save average transfer functions to file
                statransfer.save(filename)

        # Create empty stanoise if not loaded
        # else:
            # XXX

        if args.fig_TF:
            fname = stkey + '.' + 'transfer_functions'
            plot = plotting.fig_TF(
                f, day_transfer_functions, daynoise.tf_list,
                sta_transfer_functions, stanoise.tf_list, skey=stkey)

            if plotpath:
                plot.savefig(
                    plotpath / (fname + '.' + args.form),
                    dpi=300, bbox_inches='tight', format=args.form)
            else:
                plot.show()


if __name__ == "__main__":

    # Run main program
    main()