pylot/autoPyLoT.py

#!/usr/bin/python
# -*- coding: utf-8 -*-


import os
import argparse
import glob

import matplotlib.pyplot as plt
from obspy.core import read
from pylot.core.util import _getVersionString
from pylot.core.read import Data, AutoPickParameter
from pylot.core.pick.run_autopicking import run_autopicking
from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.pick.utils import wadaticheck
__version__ = _getVersionString()


def autoPyLoT(inputfile):
    '''
    Determine phase onsets automatically utilizing the automatic picking
    algorithms by Kueperkoch et al. 2010/2012.

    :param inputfile: path to the input file containing all parameter
    information for automatic picking (for formatting details, see.
    `~pylot.core.read.input.AutoPickParameter`
    :type inputfile: str
    :return:

    .. rubric:: Example

    '''

    # reading parameter file

    parameter = AutoPickParameter(inputfile)

    # get some parameters for quality control from 
    # parameter input file (usually autoPyLoT.in).
    wdttolerance = parameter.getParam('wdttolerance')
    iplot = parameter.getParam('iplot')

    data = Data()

    # getting information on data structure

    if parameter.hasParam('datastructure'):
        datastructure = DATASTRUCTURE[parameter.getParam('datastructure')]()
        dsfields = {'root':parameter.getParam('rootpath'),
                    'dpath':parameter.getParam('datapath'),
                    'dbase':parameter.getParam('database')}

        exf = ['root', 'dpath', 'dbase']

        if parameter.hasParam('eventID'):
            dsfields['eventID'] = parameter.getParam('eventID')
            exf.append('eventID')

        datastructure.modifyFields(**dsfields)
        datastructure.setExpandFields(exf)

        # multiple event processing 
        # read each event in database
        datapath = datastructure.expandDataPath()
        if not parameter.hasParam('eventID'):
            for event in [events for events in glob.glob(os.path.join(datapath, '*')) if os.path.isdir(events)]:
                data.setWFData(glob.glob(os.path.join(datapath, event, '*')))
                print 'Working on event %s' %event 
                print data

                wfdat = data.getWFData() # all available streams
                ##########################################################
                # !automated picking starts here!   
                procstats = []
                # initialize dictionary for onsets
                picks = None
                station = wfdat[0].stats.station
                allonsets = {station: picks}
                for i in range(len(wfdat)):
                    stationID = wfdat[i].stats.station
                    # check if station has already been processed
                    if stationID not in procstats:
                        procstats.append(stationID)
                        # find corresponding streams
                        statdat = wfdat.select(station=stationID)
                        ######################################################
                        # get onset times and corresponding picking errors
                        picks = run_autopicking(statdat, parameter)
                        ######################################################
                        # add station and corresponding onsets to dictionary
                        station = stationID
                        allonsets[station] = picks

                # quality control
                # jackknife on P onset times
                # check S-P times (Wadati) 
                checkedonsets = wadaticheck(allonsets, wdttolerance, iplot)
                # jackknife on S onset times
                print '------------------------------------------'
                print '-----Finished event %s!-----' % event
                print '------------------------------------------'

        # single event processing
        else:
            data.setWFData(glob.glob(os.path.join(datapath, parameter.getParam('eventID'), '*')))
            print 'Working on event ', parameter.getParam('eventID')
            print data
       
            wfdat = data.getWFData() # all available streams
            ##########################################################
            # !automated picking starts here!   
            procstats = []
            # initialize dictionary for onsets
            picks = None
            station = wfdat[0].stats.station
            allonsets = {station: picks}
            for i in range(len(wfdat)):
            #for i in range(0,5):
                stationID = wfdat[i].stats.station
                #check if station has already been processed
                if stationID not in procstats:
                    procstats.append(stationID)
                    #find corresponding streams
                    statdat = wfdat.select(station=stationID)
                    ######################################################
                    # get onset times and corresponding picking parameters
                    picks = run_autopicking(statdat, parameter)
                    ######################################################
                    # add station and corresponding onsets to dictionary
                    station = stationID
                    allonsets[station] = picks

            #quality control
            #jackknife on P onset times
            #check S-P times (Wadati) 
            checkedonsets = wadaticheck(allonsets, wdttolerance, iplot)
            #jackknife on S onset times
            print '------------------------------------------'
            print '-------Finished event %s!-------' % parameter.getParam('eventID')
            print '------------------------------------------'
            

if __name__ == "__main__":
    # parse arguments
    parser = argparse.ArgumentParser(
        description='''autoPyLoT automatically picks phase onset times using higher order statistics, 
                       autoregressive prediction and AIC''')

    parser.add_argument('-i', '-I', '--inputfile', type=str,
                        action='store',
                        help='''full path to the file containing the input
                        parameters for autoPyLoT''',
                        default=os.path.join(os.path.expanduser('~'), '.pylot',
                                             'autoPyLoT.in')
                        )
    parser.add_argument('-v', '-V', '--version', action='version',
                        version='autoPyLoT ' + __version__,
                        help='show version information and exit')

    cla = parser.parse_args()

    autoPyLoT(str(cla.inputfile))