pylot/autoPyLoT.py

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#!/usr/bin/python
# -*- coding: utf-8 -*-
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from __future__ import print_function
import argparse
import glob
import os
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import datetime
from obspy import read_events
from obspy.core.event import ResourceIdentifier
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import pylot.core.loc.hyposat as hyposat
import pylot.core.loc.hypo71 as hypo71
import pylot.core.loc.velest as velest
import pylot.core.loc.hypodd as hypodd
import pylot.core.loc.focmec as focmec
import pylot.core.loc.hash as hash
import pylot.core.loc.nll as nll
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#from PySide.QtGui import QWidget, QInputDialog
from pylot.core.analysis.magnitude import MomentMagnitude, LocalMagnitude
from pylot.core.io.data import Data
from pylot.core.io.inputs import PylotParameter
from pylot.core.pick.autopick import autopickevent, iteratepicker
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from pylot.core.util.dataprocessing import restitute_data, read_metadata, \
remove_underscores
from pylot.core.util.structure import DATASTRUCTURE
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from pylot.core.util.version import get_git_version as _getVersionString
from pylot.core.util.event import Event
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__version__ = _getVersionString()
def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, eventid=None, savepath=None, station='all', iplot=0):
"""
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.io.inputs.PylotParameter`
:type inputfile: str
:return:
.. rubric:: Example
"""
splash = '''************************************\n
*********autoPyLoT starting*********\n
The Python picking and Location Tool\n
Version {version} 2015\n
\n
Authors:\n
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S. Wehling-Benatelli (Ruhr-Universitaet Bochum)\n
L. Kueperkoch (BESTEC GmbH, Landau i. d. Pfalz)\n
K. Olbert (Christian-Albrechts Universitaet zu Kiel)\n
***********************************'''.format(version=_getVersionString())
print(splash)
locflag = 1
if input_dict and isinstance(input_dict, dict):
if input_dict.has_key('parameter'):
parameter = input_dict['parameter']
if input_dict.has_key('fig_dict'):
fig_dict = input_dict['fig_dict']
if input_dict.has_key('station'):
station = input_dict['station']
if input_dict.has_key('fnames'):
fnames = input_dict['fnames']
if input_dict.has_key('iplot'):
iplot = input_dict['iplot']
if input_dict.has_key('locflag'):
locflag = input_dict['locflag']
if not parameter:
if inputfile:
parameter = PylotParameter(inputfile)
iplot = parameter['iplot']
else:
print('No parameters set and no input file given. Choose either of both.')
return
else:
if not type(parameter) == PylotParameter:
print('Wrong input type for parameter: {}'.format(type(parameter)))
return
if inputfile:
print('Parameters set and input file given. Choose either of both.')
return
data = Data()
evt = None
# reading parameter file
if parameter.hasParam('datastructure'):
# getting information on data structure
datastructure = DATASTRUCTURE[parameter.get('datastructure')]()
dsfields = {'root': parameter.get('rootpath'),
'dpath': parameter.get('datapath'),
'dbase': parameter.get('database')}
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exf = ['root', 'dpath', 'dbase']
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if parameter['eventID'] is not '*' and fnames == 'None':
dsfields['eventID'] = parameter['eventID']
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exf.append('eventID')
datastructure.modifyFields(**dsfields)
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datastructure.setExpandFields(exf)
# check if default location routine NLLoc is available
if parameter['nllocbin'] and locflag:
# get NLLoc-root path
nllocroot = parameter.get('nllocroot')
# get path to NLLoc executable
nllocbin = parameter.get('nllocbin')
nlloccall = '%s/NLLoc' % nllocbin
# get name of phase file
phasef = parameter.get('phasefile')
phasefile = '%s/obs/%s' % (nllocroot, phasef)
# get name of NLLoc-control file
ctrf = parameter.get('ctrfile')
ctrfile = '%s/run/%s' % (nllocroot, ctrf)
# pattern of NLLoc ttimes from location grid
ttpat = parameter.get('ttpatter')
# pattern of NLLoc-output file
nllocoutpatter = parameter.get('outpatter')
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maxnumit = 3 # maximum number of iterations for re-picking
else:
locflag = 0
print(" !!! ")
print("!!No location routine available, autoPyLoT is running in non-location mode!!")
print("!!No source parameter estimation possible!!")
print(" !!! ")
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if not input_dict:
# started in production mode
datapath = datastructure.expandDataPath()
if fnames == 'None' and parameter['eventID'] is '*':
# multiple event processing
# read each event in database
events = [events for events in glob.glob(os.path.join(datapath, '*')) if os.path.isdir(events)]
elif fnames == 'None' and parameter['eventID'] is not '*':
# single event processing
events = glob.glob(os.path.join(datapath, parameter['eventID']))
else:
# autoPyLoT was initialized from GUI
events = []
events.append(eventid)
evID = os.path.split(eventid)[-1]
locflag = 2
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else:
# started in tune mode
datapath = os.path.join(parameter['rootpath'],
parameter['datapath'])
events = []
events.append(os.path.join(datapath,
parameter['database'],
parameter['eventID']))
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if not events:
print('autoPyLoT: No events given. Return!')
return
for event in events:
pylot_event = Event(event) #event should be path to event directory
data.setEvtData(pylot_event)
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if fnames == 'None':
data.setWFData(glob.glob(os.path.join(datapath, event, '*')))
evID = os.path.split(event)[-1]
# the following is necessary because within
# multiple event processing no event ID is provided
# in autopylot.in
try:
parameter.get('eventID')
except:
now = datetime.datetime.now()
eventID = '%d%02d%02d%02d%02d' % (now.year,
now.month,
now.day,
now.hour,
now.minute)
parameter.setParam(eventID=eventID)
else:
data.setWFData(fnames)
event = events[0]
#now = datetime.datetime.now()
#evID = '%d%02d%02d%02d%02d' % (now.year,
# now.month,
# now.day,
# now.hour,
# now.minute)
parameter.setParam(eventID=eventid)
wfdat = data.getWFData() # all available streams
if not station == 'all':
wfdat = wfdat.select(station=station)
if not wfdat:
print('Could not find station {}. STOP!'.format(station))
return
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wfdat = remove_underscores(wfdat)
metadata = read_metadata(parameter.get('invdir'))
print("Restitute data ...")
corr_dat = restitute_data(wfdat.copy(), *metadata)
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print('Working on event %s. Stations: %s' % (event, station))
print(wfdat)
##########################################################
# !automated picking starts here!
if input_dict:
if input_dict.has_key('fig_dict'):
fig_dict = input_dict['fig_dict']
picks = autopickevent(wfdat, parameter, iplot=iplot, fig_dict=fig_dict)
else:
picks = autopickevent(wfdat, parameter, iplot=iplot)
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##########################################################
# locating
if locflag > 0:
# write phases to NLLoc-phase file
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nll.export(picks, phasefile, parameter)
# For locating the event the NLLoc-control file has to be modified!
nllocout = '%s_%s' % (evID, nllocoutpatter)
# create comment line for NLLoc-control file
nll.modify_inputs(ctrf, nllocroot, nllocout, phasef,
ttpat)
# locate the event
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nll.locate(ctrfile, inputfile)
# !iterative picking if traces remained unpicked or occupied with bad picks!
# get theoretical onset times for picks with weights >= 4
# in order to reprocess them using smaller time windows around theoretical onset
# get stations with bad onsets
badpicks = []
for key in picks:
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if picks[key]['P']['weight'] >= 4 or picks[key]['S']['weight'] >= 4:
badpicks.append([key, picks[key]['P']['mpp']])
# TODO keep code DRY (Don't Repeat Yourself) the following part is written twice
# suggestion: delete block and modify the later similar block to work properly
if len(badpicks) == 0:
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print("autoPyLoT: No bad onsets found, thus no iterative picking necessary!")
# get NLLoc-location file
locsearch = '%s/loc/%s.????????.??????.grid?.loc.hyp' % (nllocroot, nllocout)
if len(glob.glob(locsearch)) > 0:
# get latest NLLoc-location file if several are available
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nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
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evt = read_events(nllocfile)[0]
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# calculate seismic moment Mo and moment magnitude Mw
moment_mag = MomentMagnitude(corr_dat, evt, parameter.get('vp'),
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parameter.get('Qp'),
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parameter.get('rho'), True, \
iplot)
# update pick with moment property values (w0, fc, Mo)
for station, props in moment_mag.moment_props.items():
picks[station]['P'].update(props)
evt = moment_mag.updated_event()
net_mw = moment_mag.net_magnitude()
print("Network moment magnitude: %4.1f" % net_mw.mag)
# calculate local (Richter) magntiude
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WAscaling = parameter.get('WAscaling')
magscaling = parameter.get('magscaling')
local_mag = LocalMagnitude(corr_dat, evt,
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parameter.get('sstop'),
WAscaling, True, iplot)
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for station, amplitude in local_mag.amplitudes.items():
picks[station]['S']['Ao'] = amplitude.generic_amplitude
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print("Local station magnitudes scaled with:")
print("log(Ao) + %f * log(r) + %f * r + %f" % (WAscaling[0],
WAscaling[1],
WAscaling[2]))
evt = local_mag.updated_event(magscaling)
net_ml = local_mag.net_magnitude(magscaling)
print("Network local magnitude: %4.1f" % net_ml.mag)
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print("Network local magnitude scaled with:")
print("%f * Ml + %f" % (magscaling[0], magscaling[1]))
else:
print("autoPyLoT: No NLLoc-location file available!")
print("No source parameter estimation possible!")
locflag = 9
else:
# get theoretical P-onset times from NLLoc-location file
locsearch = '%s/loc/%s.????????.??????.grid?.loc.hyp' % (nllocroot, nllocout)
if len(glob.glob(locsearch)) > 0:
# get latest file if several are available
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nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
nlloccounter = 0
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while len(badpicks) > 0 and nlloccounter <= maxnumit:
nlloccounter += 1
if nlloccounter > maxnumit:
print("autoPyLoT: Number of maximum iterations reached, stop iterative picking!")
break
print("autoPyLoT: Starting with iteration No. %d ..." % nlloccounter)
if input_dict:
if input_dict.has_key('fig_dict'):
fig_dict = input_dict['fig_dict']
picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter, fig_dict=fig_dict)
else:
picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
# write phases to NLLoc-phase file
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nll.export(picks, phasefile, parameter)
# remove actual NLLoc-location file to keep only the last
os.remove(nllocfile)
# locate the event
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nll.locate(ctrfile, inputfile)
print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
# get updated NLLoc-location file
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nllocfile = max(glob.glob(locsearch), key=os.path.getctime)
# check for bad picks
badpicks = []
for key in picks:
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if picks[key]['P']['weight'] >= 4 or picks[key]['S']['weight'] >= 4:
badpicks.append([key, picks[key]['P']['mpp']])
print("autoPyLoT: After iteration No. %d: %d bad onsets found ..." % (nlloccounter, \
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len(badpicks)))
if len(badpicks) == 0:
print("autoPyLoT: No more bad onsets found, stop iterative picking!")
nlloccounter = maxnumit
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evt = read_events(nllocfile)[0]
if locflag < 2:
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# calculate seismic moment Mo and moment magnitude Mw
moment_mag = MomentMagnitude(corr_dat, evt, parameter.get('vp'),
parameter.get('Qp'),
parameter.get('rho'), True, \
iplot)
# update pick with moment property values (w0, fc, Mo)
for station, props in moment_mag.moment_props.items():
picks[station]['P'].update(props)
evt = moment_mag.updated_event()
net_mw = moment_mag.net_magnitude()
print("Network moment magnitude: %4.1f" % net_mw.mag)
# calculate local (Richter) magntiude
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WAscaling = parameter.get('WAscaling')
magscaling = parameter.get('magscaling')
local_mag = LocalMagnitude(corr_dat, evt,
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parameter.get('sstop'),
WAscaling, True, iplot)
for station, amplitude in local_mag.amplitudes.items():
picks[station]['S']['Ao'] = amplitude.generic_amplitude
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print("Local station magnitudes scaled with:")
print("log(Ao) + %f * log(r) + %f * r + %f" % (WAscaling[0],
WAscaling[1],
WAscaling[2]))
evt = local_mag.updated_event(magscaling)
net_ml = local_mag.net_magnitude(magscaling)
print("Network local magnitude: %4.1f" % net_ml.mag)
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print("Network local magnitude scaled with:")
print("%f * Ml + %f" % (magscaling[0], magscaling[1]))
else:
print("autoPyLoT: No NLLoc-location file available! Stop iteration!")
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locflag = 9
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##########################################################
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# write phase files for various location
# and fault mechanism calculation routines
# ObsPy event object
data.applyEVTData(picks)
if evt is not None:
event_id = event.split('/')[-1]
evt.resource_id = ResourceIdentifier('smi:local/' + event_id)
data.applyEVTData(evt, 'event')
fnqml = '%s/PyLoT_%s' % (event, evID)
data.exportEvent(fnqml, fnext='.xml', fcheck='manual')
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if locflag == 1:
# HYPO71
hypo71file = '%s/PyLoT_%s_HYPO71_phases' % (event, evID)
hypo71.export(picks, hypo71file, parameter)
# HYPOSAT
hyposatfile = '%s/PyLoT_%s_HYPOSAT_phases' % (event, evID)
hyposat.export(picks, hyposatfile, parameter)
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# VELEST
velestfile = '%s/PyLoT_%s_VELEST_phases.cnv' % (event, evID)
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velest.export(picks, velestfile, parameter, evt)
# hypoDD
hypoddfile = '%s/PyLoT_%s_hypoDD_phases.pha' % (event, evID)
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hypodd.export(picks, hypoddfile, parameter, evt)
# FOCMEC
focmecfile = '%s/PyLoT_%s_FOCMEC.in' % (event, evID)
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focmec.export(picks, focmecfile, parameter, evt)
# HASH
hashfile = '%s/PyLoT_%s_HASH' % (event, evID)
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hash.export(picks, hashfile, parameter, evt)
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endsplash = '''------------------------------------------\n'
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-----Finished event %s!-----\n'
------------------------------------------'''.format \
(version=_getVersionString()) % evID
print(endsplash)
if locflag == 0:
print("autoPyLoT was running in non-location mode!")
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endsp = '''####################################\n
************************************\n
*********autoPyLoT terminates*******\n
The Python picking and Location Tool\n
************************************'''.format(version=_getVersionString())
print(endsp)
return picks
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if __name__ == "__main__":
# parse arguments
parser = argparse.ArgumentParser(
description='''autoPyLoT automatically picks phase onset times using higher order statistics,
autoregressive prediction and AIC followed by locating the seismic events using
NLLoc''')
#parser.add_argument('-d', '-D', '--input_dict', type=str,
# action='store',
# help='''optional, dictionary containing processing parameters''')
#parser.add_argument('-p', '-P', '--parameter', type=str,
# action='store',
# help='''parameter file, default=None''')
parser.add_argument('-i', '-I', '--inputfile', type=str,
action='store',
help='''full path to the file containing the input
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parameters for autoPyLoT''')
parser.add_argument('-f', '-F', '--fnames', type=str,
action='store',
help='''optional, list of data file names''')
parser.add_argument('-e', '-E', '--eventid', type=str,
action='store',
help='''optional, event path incl. event ID''')
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parser.add_argument('-s', '-S', '--spath', type=str,
action='store',
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help='''optional, save path for autoPyLoT output''')
#parser.add_argument('-v', '-V', '--version', action='version',
# version='autoPyLoT ' + __version__,
# help='show version information and exit')
cla = parser.parse_args()
picks = autoPyLoT(inputfile=str(cla.inputfile), fnames=str(cla.fnames),
eventid=str(cla.eventid), savepath=str(cla.spath))