[add] for global seismology CF pick windows will now be calculated
relative to estimated tt from TauPy, metadata and source location (in XML file) needed [TO DO]: automatic export of XML (esp. source loc) before autopicking
This commit is contained in:
parent
60ebaa6528
commit
17a93cf62f
@ -67,14 +67,13 @@ from pylot.core.pick.compare import Comparison
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from pylot.core.pick.utils import symmetrize_error
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from pylot.core.io.phases import picksdict_from_picks
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import pylot.core.loc.nll as nll
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from pylot.core.util.defaults import FILTERDEFAULTS, SetChannelComponents, \
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readFilterInformation
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from pylot.core.util.defaults import FILTERDEFAULTS, SetChannelComponents
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from pylot.core.util.errors import FormatError, DatastructureError, \
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OverwriteError
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from pylot.core.util.connection import checkurl
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from pylot.core.util.dataprocessing import read_metadata, restitute_data
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from pylot.core.util.utils import fnConstructor, getLogin, \
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full_range
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full_range, readFilterInformation
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from pylot.core.util.event import Event
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from pylot.core.io.location import create_creation_info, create_event
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from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
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@ -722,7 +721,7 @@ class MainWindow(QMainWindow):
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fext = '.xml'
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for event in events:
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path = event.path
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eventname = path.split('/')[-1]
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eventname = path.split('/')[-1] #or event.pylot_id
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filename = os.path.join(path, 'PyLoT_' + eventname + fext)
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if os.path.isfile(filename):
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self.load_data(filename, draw=False, event=event, overwrite=True)
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52
autoPyLoT.py
52
autoPyLoT.py
@ -111,8 +111,6 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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print('Parameters set and input file given. Choose either of both.')
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return
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data = Data()
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evt = None
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# reading parameter file
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@ -192,16 +190,24 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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return
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# transform system path separator to '/'
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for index, event in enumerate(events):
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event = event.replace(SEPARATOR, '/')
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events[index] = event
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for index, eventpath in enumerate(events):
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eventpath = eventpath.replace(SEPARATOR, '/')
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events[index] = eventpath
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for event in events:
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pylot_event = Event(event) # event should be path to event directory
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data.setEvtData(pylot_event)
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for eventpath in events:
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evID = os.path.split(eventpath)[-1]
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fext = '.xml'
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filename = os.path.join(eventpath, 'PyLoT_' + evID + fext)
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try:
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data = Data(evtdata=filename)
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print('Reading event data from filename {}...'.format(filename))
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except Exception as e:
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print('Could not read event from file {}: {}'.format(filename, e))
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data = Data()
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pylot_event = Event(eventpath) # event should be path to event directory
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data.setEvtData(pylot_event)
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if fnames == 'None':
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data.setWFData(glob.glob(os.path.join(datapath, event, '*')))
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evID = os.path.split(event)[-1]
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data.setWFData(glob.glob(os.path.join(datapath, eventpath, '*')))
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# the following is necessary because within
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# multiple event processing no event ID is provided
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# in autopylot.in
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@ -218,7 +224,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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else:
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data.setWFData(fnames)
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event = events[0]
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eventpath = events[0]
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# now = datetime.datetime.now()
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# evID = '%d%02d%02d%02d%02d' % (now.year,
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# now.month,
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@ -238,16 +244,18 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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corr_dat = restitute_data(wfdat.copy(), *metadata, ncores=ncores)
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if not corr_dat and locflag:
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locflag = 2
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print('Working on event %s. Stations: %s' % (event, station))
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print('Working on event %s. Stations: %s' % (eventpath, station))
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print(wfdat)
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##########################################################
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# !automated picking starts here!
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if input_dict:
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if 'fig_dict' in input_dict:
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fig_dict = input_dict['fig_dict']
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picks = autopickevent(wfdat, parameter, iplot=iplot, fig_dict=fig_dict, ncores=ncores)
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picks = autopickevent(wfdat, parameter, iplot=iplot, fig_dict=fig_dict,
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ncores=ncores, metadata=metadata, origin=data.get_evt_data().origins)
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else:
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picks = autopickevent(wfdat, parameter, iplot=iplot, ncores=ncores)
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picks = autopickevent(wfdat, parameter, iplot=iplot,
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ncores=ncores, metadata=metadata, origin=data.get_evt_data().origins)
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##########################################################
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# locating
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if locflag > 0:
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@ -393,29 +401,29 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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# ObsPy event object
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data.applyEVTData(picks)
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if evt is not None:
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event_id = event.split('/')[-1]
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event_id = eventpath.split('/')[-1]
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evt.resource_id = ResourceIdentifier('smi:local/' + event_id)
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data.applyEVTData(evt, 'event')
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fnqml = '%s/PyLoT_%s' % (event, evID)
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fnqml = '%s/PyLoT_%s' % (eventpath, evID)
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data.exportEvent(fnqml, fnext='.xml', fcheck=['auto', 'magnitude', 'origin'])
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if locflag == 1:
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# HYPO71
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hypo71file = '%s/PyLoT_%s_HYPO71_phases' % (event, evID)
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hypo71file = '%s/PyLoT_%s_HYPO71_phases' % (eventpath, evID)
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hypo71.export(picks, hypo71file, parameter)
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# HYPOSAT
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hyposatfile = '%s/PyLoT_%s_HYPOSAT_phases' % (event, evID)
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hyposatfile = '%s/PyLoT_%s_HYPOSAT_phases' % (eventpath, evID)
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hyposat.export(picks, hyposatfile, parameter)
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# VELEST
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velestfile = '%s/PyLoT_%s_VELEST_phases.cnv' % (event, evID)
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velestfile = '%s/PyLoT_%s_VELEST_phases.cnv' % (eventpath, evID)
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velest.export(picks, velestfile, parameter, evt)
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# hypoDD
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hypoddfile = '%s/PyLoT_%s_hypoDD_phases.pha' % (event, evID)
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hypoddfile = '%s/PyLoT_%s_hypoDD_phases.pha' % (eventpath, evID)
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hypodd.export(picks, hypoddfile, parameter, evt)
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# FOCMEC
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focmecfile = '%s/PyLoT_%s_FOCMEC.in' % (event, evID)
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focmecfile = '%s/PyLoT_%s_FOCMEC.in' % (eventpath, evID)
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focmec.export(picks, focmecfile, parameter, evt)
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# HASH
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hashfile = '%s/PyLoT_%s_HASH' % (event, evID)
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hashfile = '%s/PyLoT_%s_HASH' % (eventpath, evID)
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hash.export(picks, hashfile, parameter, evt)
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endsplash = '''------------------------------------------\n'
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@ -87,12 +87,14 @@ defaults = {'rootpath': {'type': str,
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'namestring': ('Quality factor', 'Qp1', 'Qp2')},
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'pstart': {'type': float,
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'tooltip': 'start time [s] for calculating CF for P-picking',
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'tooltip': 'start time [s] for calculating CF for P-picking (if TauPy:'
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' seconds relative to estimated onset)',
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'value': 15.0,
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'namestring': 'P start'},
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'pstop': {'type': float,
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'tooltip': 'end time [s] for calculating CF for P-picking',
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'tooltip': 'end time [s] for calculating CF for P-picking (if TauPy:'
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' seconds relative to estimated onset)',
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'value': 60.0,
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'namestring': 'P stop'},
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@ -381,12 +383,12 @@ defaults = {'rootpath': {'type': str,
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'use_taup': {'type': bool,
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'tooltip': 'use estimated traveltimes from TauPy for calculating windows for CF',
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'value': True,
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'namestring': 'Use Taupy'},
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'namestring': 'Use TauPy'},
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'taup_model': {'type': str,
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'tooltip': 'define TauPy model for traveltime estimation',
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'value': 'iasp91',
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'namestring': 'Taupy model'}
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'namestring': 'TauPy model'}
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}
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settings_main = {
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@ -18,10 +18,13 @@ from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
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from pylot.core.pick.picker import AICPicker, PragPicker
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from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
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getSNR, fmpicker, checkPonsets, wadaticheck
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from pylot.core.util.utils import getPatternLine, gen_Pool
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from pylot.core.util.utils import getPatternLine, gen_Pool, identifyPhase, loopIdentifyPhase, \
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full_range
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from obspy.taup import TauPyModel
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def autopickevent(data, param, iplot=0, fig_dict=None, ncores=0):
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def autopickevent(data, param, iplot=0, fig_dict=None, ncores=0, metadata=None, origin=None):
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stations = []
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all_onsets = {}
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input_tuples = []
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@ -42,9 +45,11 @@ def autopickevent(data, param, iplot=0, fig_dict=None, ncores=0):
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topick = data.select(station=station)
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if not iplot:
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input_tuples.append((topick, param, apverbose))
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input_tuples.append((topick, param, apverbose, metadata, origin))
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if iplot > 0:
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all_onsets[station] = autopickstation(topick, param, verbose=apverbose, iplot=iplot, fig_dict=fig_dict)
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all_onsets[station] = autopickstation(topick, param, verbose=apverbose,
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iplot=iplot, fig_dict=fig_dict,
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metadata=metadata, origin=origin)
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if iplot > 0:
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print('iPlot Flag active: NO MULTIPROCESSING possible.')
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@ -69,12 +74,13 @@ def autopickevent(data, param, iplot=0, fig_dict=None, ncores=0):
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def call_autopickstation(input_tuple):
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wfstream, pickparam, verbose = input_tuple
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wfstream, pickparam, verbose, metadata, origin = input_tuple
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# multiprocessing not possible with interactive plotting
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return autopickstation(wfstream, pickparam, verbose, iplot=0)
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return autopickstation(wfstream, pickparam, verbose, iplot=0, metadata=metadata, origin=origin)
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def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
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def autopickstation(wfstream, pickparam, verbose=False,
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iplot=0, fig_dict=None, metadata=None, origin=None):
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"""
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:param wfstream: `~obspy.core.stream.Stream` containing waveform
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:type wfstream: obspy.core.stream.Stream
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@ -117,6 +123,8 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
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algoS = pickparam.get('algoS')
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sstart = pickparam.get('sstart')
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sstop = pickparam.get('sstop')
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use_taup = pickparam.get('use_taup')
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taup_model = pickparam.get('taup_model')
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bph1 = pickparam.get('bph1')
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bph2 = pickparam.get('bph2')
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tsnrh = pickparam.get('tsnrh')
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@ -182,6 +190,8 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
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if len(ndat) == 0: # check for other components
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ndat = wfstream.select(component="1")
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wfstart, wfend = full_range(wfstream)
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if algoP == 'HOS' or algoP == 'ARZ' and zdat is not None:
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msg = '##################################################\nautopickstation:' \
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' Working on P onset of station {station}\nFiltering vertical ' \
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@ -197,7 +207,47 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
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z_copy[0].data = tr_filt.data
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##############################################################
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# check length of waveform and compare with cut times
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Lc = pstop - pstart
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# for global seismology: use tau-p method for estimating travel times (needs source and station coords.)
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# if not given: sets Lc to infinity to use full stream
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if use_taup:
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Lc = np.inf
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print('autopickstation: use_taup flag active.')
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if not metadata[1]:
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print('Warning: Could not use TauPy to estimate onsets as there are no metadata given.')
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else:
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if origin:
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source_origin = origin[0]
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station_id = wfstream[0].get_id()
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parser = metadata[1]
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station_coords = parser.get_coordinates(station_id)
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model = TauPyModel(taup_model)
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arrivals = model.get_travel_times_geo(
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source_origin.depth,
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source_origin.latitude,
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source_origin.longitude,
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station_coords['latitude'],
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station_coords['longitude']
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)
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phases = {'P': [],
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'S': []}
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for arr in arrivals:
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phases[identifyPhase(loopIdentifyPhase(arr.phase.name))].append(arr)
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# get first P and S onsets from arrivals list
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arrP, estFirstP = min([(arr, arr.time) for arr in phases['P']], key = lambda t: t[1])
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arrS, estFirstS = min([(arr, arr.time) for arr in phases['S']], key = lambda t: t[1])
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print('autopick: estimated first arrivals for P: {}, S:{} using TauPy'.format(estFirstP, estFirstS))
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# modifiy pstart and pstop relative to estimated first P arrival (relative to station time axis)
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pstart += (source_origin.time + estFirstP) - wfstart
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pstop += (source_origin.time + estFirstP) - wfstart
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Lc = pstop - pstart
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else:
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print('No source origins given!')
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else:
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Lc = pstop - pstart
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Lwf = zdat[0].stats.endtime - zdat[0].stats.starttime
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Ldiff = Lwf - Lc
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if Ldiff < 0:
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@ -238,6 +288,12 @@ def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None):
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else:
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fig = None
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aicpick = AICPicker(aiccf, tsnrz, pickwinP, iplot, None, tsmoothP, fig=fig)
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# add pstart and pstop to aic plot
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if fig.axes:
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for ax in fig.axes:
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ax.vlines(pstart, ax.get_ylim()[0], ax.get_ylim()[1], color='c', linestyles='dashed', label='P start')
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ax.vlines(pstop, ax.get_ylim()[0], ax.get_ylim()[1], color='c', linestyles='dashed', label='P stop')
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ax.legend()
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##############################################################
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if aicpick.getpick() is not None:
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# check signal length to detect spuriously picked noise peaks
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@ -9,7 +9,7 @@ Created on Wed Feb 26 12:31:25 2014
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import os
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import platform
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from pylot.core.io.inputs import PylotParameter
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from pylot.core.util.utils import readDefaultFilterInformation
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from pylot.core.loc import hypo71
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from pylot.core.loc import hypodd
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from pylot.core.loc import hyposat
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@ -17,23 +17,6 @@ from pylot.core.loc import nll
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from pylot.core.loc import velest
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def readDefaultFilterInformation(fname):
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pparam = PylotParameter(fname)
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return readFilterInformation(pparam)
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def readFilterInformation(pylot_parameter):
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p_filter = {'filtertype': pylot_parameter['filter_type'][0],
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'freq': [pylot_parameter['minfreq'][0], pylot_parameter['maxfreq'][0]],
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'order': int(pylot_parameter['filter_order'][0])}
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s_filter = {'filtertype': pylot_parameter['filter_type'][1],
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'freq': [pylot_parameter['minfreq'][1], pylot_parameter['maxfreq'][1]],
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'order': int(pylot_parameter['filter_order'][1])}
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filter_information = {'P': p_filter,
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'S': s_filter}
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return filter_information
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# determine system dependent path separator
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system_name = platform.system()
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if system_name in ["Linux", "Darwin"]:
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@ -10,8 +10,8 @@ import subprocess
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import numpy as np
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from obspy import UTCDateTime, read
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from pylot.core.io.inputs import PylotParameter
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from scipy.interpolate import splrep, splev
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from scipy.interpolate import splrep, splev
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def _pickle_method(m):
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if m.im_self is None:
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@ -20,6 +20,23 @@ def _pickle_method(m):
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return getattr, (m.im_self, m.im_func.func_name)
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def readDefaultFilterInformation(fname):
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pparam = PylotParameter(fname)
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return readFilterInformation(pparam)
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def readFilterInformation(pylot_parameter):
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p_filter = {'filtertype': pylot_parameter['filter_type'][0],
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'freq': [pylot_parameter['minfreq'][0], pylot_parameter['maxfreq'][0]],
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'order': int(pylot_parameter['filter_order'][0])}
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s_filter = {'filtertype': pylot_parameter['filter_type'][1],
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'freq': [pylot_parameter['minfreq'][1], pylot_parameter['maxfreq'][1]],
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'order': int(pylot_parameter['filter_order'][1])}
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filter_information = {'P': p_filter,
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'S': s_filter}
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return filter_information
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def fit_curve(x, y):
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return splev, splrep(x, y)
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@ -551,6 +568,51 @@ def which(program, infile=None):
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return None
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def loopIdentifyPhase(phase):
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'''
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Loop through phase string and try to recognize its type (P or S wave).
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Global variable ALTSUFFIX gives alternative suffix for phases if they do not end with P, p or S, s.
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If ALTSUFFIX is not given, the function will cut the last letter of the phase string until string ends
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with P or S.
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:param phase: phase name (str)
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:return:
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'''
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from pylot.core.util.defaults import ALTSUFFIX
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phase_copy = phase
|
||||
while not identifyPhase(phase_copy):
|
||||
identified = False
|
||||
for alt_suf in ALTSUFFIX:
|
||||
if phase_copy.endswith(alt_suf):
|
||||
phase_copy = phase_copy.split(alt_suf)[0]
|
||||
identified = True
|
||||
if not identified:
|
||||
phase_copy = phase_copy[:-1]
|
||||
if len(phase_copy) < 1:
|
||||
print('Warning: Could not identify phase {}!'.format(phase))
|
||||
return
|
||||
return phase_copy
|
||||
|
||||
|
||||
def identifyPhase(phase):
|
||||
'''
|
||||
Returns capital P or S if phase string is identified by last letter. Else returns False.
|
||||
:param phase: phase name (str)
|
||||
:return: 'P', 'S' or False
|
||||
'''
|
||||
# common phase suffix for P and S
|
||||
common_P = ['P', 'p']
|
||||
common_S = ['S', 's']
|
||||
if phase[-1] in common_P:
|
||||
return 'P'
|
||||
if phase[-1] in common_S:
|
||||
return 'S'
|
||||
else:
|
||||
return False
|
||||
|
||||
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
import doctest
|
||||
|
||||
|
||||
@ -21,7 +21,7 @@ except:
|
||||
pg = None
|
||||
|
||||
from matplotlib.figure import Figure
|
||||
from pylot.core.util.utils import find_horizontals
|
||||
from pylot.core.util.utils import find_horizontals, identifyPhase, loopIdentifyPhase
|
||||
|
||||
try:
|
||||
from matplotlib.backends.backend_qt4agg import FigureCanvas
|
||||
@ -46,7 +46,7 @@ from pylot.core.io.inputs import FilterOptions, PylotParameter
|
||||
from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
|
||||
getResolutionWindow
|
||||
from pylot.core.pick.compare import Comparison
|
||||
from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS, ALTSUFFIX, \
|
||||
from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS, \
|
||||
SetChannelComponents
|
||||
from pylot.core.util.utils import prepTimeAxis, full_range, scaleWFData, \
|
||||
demeanTrace, isSorted, findComboBoxIndex, clims
|
||||
@ -118,34 +118,6 @@ def createAction(parent, text, slot=None, shortcut=None, icon=None,
|
||||
return action
|
||||
|
||||
|
||||
def loopIdentifyPhase(phase):
|
||||
phase_copy = phase
|
||||
while not identifyPhase(phase_copy):
|
||||
identified = False
|
||||
for alt_suf in ALTSUFFIX:
|
||||
if phase_copy.endswith(alt_suf):
|
||||
phase_copy = phase_copy.split(alt_suf)[0]
|
||||
identified = True
|
||||
if not identified:
|
||||
phase_copy = phase_copy[:-1]
|
||||
if len(phase_copy) < 1:
|
||||
print('Warning: Could not identify phase {}!'.format(phase))
|
||||
return
|
||||
return phase_copy
|
||||
|
||||
|
||||
def identifyPhase(phase):
|
||||
# common phase suffix for P and S
|
||||
common_P = ['P', 'p']
|
||||
common_S = ['S', 's']
|
||||
if phase[-1] in common_P:
|
||||
return 'P'
|
||||
if phase[-1] in common_S:
|
||||
return 'S'
|
||||
else:
|
||||
return False
|
||||
|
||||
|
||||
class ComparisonDialog(QDialog):
|
||||
def __init__(self, c, parent=None):
|
||||
self._data = c
|
||||
|
||||
Loading…
Reference in New Issue
Block a user