[edit] reformatted code
Code indentation and PEP 8 violations automatically reduced with IDE tool
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@ -11,15 +11,17 @@ function conglomerate utils.
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import matplotlib.pyplot as plt
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import numpy as np
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from pylot.core.read.inputs import AutoPickParameter
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from pylot.core.pick.picker import AICPicker, PragPicker
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from pylot.core.pick.charfuns import CharacteristicFunction
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from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
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from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker,\
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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
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from pylot.core.read.data import Data
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from pylot.core.analysis.magnitude import WApp
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def autopickevent(data, param):
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stations = []
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all_onsets = {}
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@ -46,14 +48,18 @@ def autopickevent(data, param):
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# check S-P times (Wadati)
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return wadaticheck(jk_checked_onsets, wdttolerance, iplot)
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def autopickstation(wfstream, pickparam, verbose=False):
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"""
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:param: wfstream
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:type: `~obspy.core.stream.Stream`
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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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:param: pickparam
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:type: container of picking parameters from input file,
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:param pickparam: container of picking parameters from input file,
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usually autoPyLoT.in
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:type pickparam: AutoPickParameter
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:param verbose:
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:type verbose: bool
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"""
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# declaring pickparam variables (only for convenience)
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@ -137,7 +143,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
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Pflag = 0
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Sflag = 0
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Pmarker = []
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Ao = None # Wood-Anderson peak-to-peak amplitude
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Ao = None # Wood-Anderson peak-to-peak amplitude
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# split components
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zdat = wfstream.select(component="Z")
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@ -152,9 +158,9 @@ def autopickstation(wfstream, pickparam, verbose=False):
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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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'trace ...\n{data}'.format(station=zdat[0].stats.station,
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data=str(zdat))
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' Working on P onset of station {station}\nFiltering vertical ' \
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'trace ...\n{data}'.format(station=zdat[0].stats.station,
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data=str(zdat))
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if verbose: print(msg)
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z_copy = zdat.copy()
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# filter and taper data
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@ -169,8 +175,8 @@ def autopickstation(wfstream, pickparam, verbose=False):
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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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msg = 'autopickstation: Cutting times are too large for actual ' \
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'waveform!\nUsing entire waveform instead!'
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msg = 'autopickstation: Cutting times are too large for actual ' \
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'waveform!\nUsing entire waveform instead!'
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if verbose: print(msg)
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pstart = 0
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pstop = len(zdat[0].data) * zdat[0].stats.delta
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@ -190,8 +196,9 @@ def autopickstation(wfstream, pickparam, verbose=False):
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# CharacteristicFunction
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# class needs stream object => build it
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assert isinstance(cf1, CharacteristicFunction), 'cf2 is not set ' \
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'correctly: maybe the algorithm name ({algoP}) is ' \
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'corrupted'.format(algoP=algoP)
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'correctly: maybe the algorithm name ({algoP}) is ' \
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'corrupted'.format(
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algoP=algoP)
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tr_aic = tr_filt.copy()
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tr_aic.data = cf1.getCF()
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z_copy[0].data = tr_aic.data
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@ -221,10 +228,10 @@ def autopickstation(wfstream, pickparam, verbose=False):
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trH1_filt = edat.copy()
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trH2_filt = ndat.copy()
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trH1_filt.filter('bandpass', freqmin=bph1[0],
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freqmax=bph1[1],
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freqmax=bph1[1],
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zerophase=False)
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trH2_filt.filter('bandpass', freqmin=bph1[0],
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freqmax=bph1[1],
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freqmax=bph1[1],
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zerophase=False)
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trH1_filt.taper(max_percentage=0.05, type='hann')
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trH2_filt.taper(max_percentage=0.05, type='hann')
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@ -253,8 +260,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
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##############################################################
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# go on with processing if AIC onset passes quality control
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if (aicpick.getSlope() >= minAICPslope and
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aicpick.getSNR() >= minAICPSNR and
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Pflag == 1):
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aicpick.getSNR() >= minAICPSNR and Pflag == 1):
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aicPflag = 1
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msg = 'AIC P-pick passes quality control: Slope: {0} counts/s, ' \
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'SNR: {1}\nGo on with refined picking ...\n' \
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@ -288,15 +294,16 @@ def autopickstation(wfstream, pickparam, verbose=False):
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##############################################################
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# get refined onset time from CF2 using class Picker
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assert isinstance(cf2, CharacteristicFunction), 'cf2 is not set ' \
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'correctly: maybe the algorithm name ({algoP}) is ' \
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'corrupted'.format(algoP=algoP)
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'correctly: maybe the algorithm name ({algoP}) is ' \
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'corrupted'.format(
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algoP=algoP)
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refPpick = PragPicker(cf2, tsnrz, pickwinP, iplot, ausP, tsmoothP,
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aicpick.getpick())
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mpickP = refPpick.getpick()
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#############################################################
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if mpickP is not None:
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# quality assessment
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# get earliest and latest possible pick and symmetrized uncertainty
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# get earliest/latest possible pick and symmetrized uncertainty
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[lpickP, epickP, Perror] = earllatepicker(z_copy, nfacP, tsnrz,
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mpickP, iplot)
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@ -481,7 +488,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
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#############################################################
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if mpickS is not None:
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# quality assessment
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# get earliest and latest possible pick and symmetrized uncertainty
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# get earliest/latest possible pick and symmetrized uncertainty
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h_copy[0].data = trH1_filt.data
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[lpickS1, epickS1, Serror1] = earllatepicker(h_copy, nfacS,
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tsnrh,
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@ -496,28 +503,30 @@ def autopickstation(wfstream, pickparam, verbose=False):
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epick = [epickS1, epickS2]
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lpick = [lpickS1, lpickS2]
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pickerr = [Serror1, Serror2]
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if epickS1 == None and epickS2 is not None:
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if epickS1 is None and epickS2 is not None:
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ipick = 1
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elif epickS1 is not None and epickS2 == None:
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elif epickS1 is not None and epickS2 is None:
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ipick = 0
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elif epickS1 is not None and epickS2 is not None:
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ipick = np.argmin([epickS1, epickS2])
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elif algoS == 'AR3':
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[lpickS3, epickS3, Serror3] = earllatepicker(h_copy, nfacS,
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[lpickS3, epickS3, Serror3] = earllatepicker(h_copy,
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nfacS,
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tsnrh,
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mpickS, iplot)
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mpickS,
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iplot)
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# get earliest pick of all three picks
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epick = [epickS1, epickS2, epickS3]
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lpick = [lpickS1, lpickS2, lpickS3]
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pickerr = [Serror1, Serror2, Serror3]
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if epickS1 == None and epickS2 is not None \
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if epickS1 is None and epickS2 is not None \
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and epickS3 is not None:
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ipick = np.argmin([epickS2, epickS3])
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elif epickS1 is not None and epickS2 == None \
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elif epickS1 is not None and epickS2 is None \
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and epickS3 is not None:
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ipick = np.argmin([epickS2, epickS3])
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elif epickS1 is not None and epickS2 is not None \
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and epickS3 == None:
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and epickS3 is None:
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ipick = np.argmin([epickS1, epickS2])
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elif epickS1 is not None and epickS2 is not None \
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and epickS3 is not None:
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@ -546,7 +555,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
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'SNR[dB]: {2}\n'
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'################################################'
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''.format(Sweight, SNRS, SNRSdB))
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##################################################################
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################################################################
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# get Wood-Anderson peak-to-peak amplitude
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# initialize Data object
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data = Data()
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@ -563,8 +572,8 @@ def autopickstation(wfstream, pickparam, verbose=False):
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else:
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# use larger window for getting peak-to-peak amplitude
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# as the S pick is quite unsure
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wapp = WApp(cordat, mpickP, mpickP + sstop + \
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(0.5 * (mpickP + sstop)), iplot)
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wapp = WApp(cordat, mpickP, mpickP + sstop +
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(0.5 * (mpickP + sstop)), iplot)
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Ao = wapp.getwapp()
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@ -593,7 +602,8 @@ def autopickstation(wfstream, pickparam, verbose=False):
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# calculate WA-peak-to-peak amplitude
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# using subclass WApp of superclass Magnitude
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wapp = WApp(cordat, mpickP, mpickP + sstop + (0.5 * (mpickP
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+ sstop)), iplot)
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+ sstop)),
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iplot)
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Ao = wapp.getwapp()
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else:
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@ -650,7 +660,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
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plt.title('%s, %s, P Weight=%d' % (tr_filt.stats.station,
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tr_filt.stats.channel,
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Pweight))
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plt.yticks([])
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plt.ylim([-1.5, 1.5])
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plt.ylabel('Normalized Counts')
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@ -789,7 +799,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
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phase = 'P'
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phasepick = {'lpp': lpickP, 'epp': epickP, 'mpp': mpickP, 'spe': Perror,
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'snr': SNRP, 'snrdb': SNRPdB, 'weight': Pweight, 'fm': FM,
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'w0': None, 'fc': None, 'Mo': None, 'Mw': None}
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'w0': None, 'fc': None, 'Mo': None, 'Mw': None}
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picks = {phase: phasepick}
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# add P marker
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picks[phase]['marked'] = Pmarker
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@ -801,7 +811,6 @@ def autopickstation(wfstream, pickparam, verbose=False):
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# add Wood-Anderson amplitude
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picks[phase]['Ao'] = Ao
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return picks
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@ -827,70 +836,72 @@ def iteratepicker(wf, NLLocfile, picks, badpicks, pickparameter):
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newpicks = {}
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for i in range(0, len(badpicks)):
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if len(badpicks[i][0]) > 4:
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Ppattern = '%s ? ? ? P' % badpicks[i][0]
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elif len(badpicks[i][0]) == 4:
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Ppattern = '%s ? ? ? P' % badpicks[i][0]
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elif len(badpicks[i][0]) < 4:
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Ppattern = '%s ? ? ? P' % badpicks[i][0]
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nllocline = getPatternLine(NLLocfile, Ppattern)
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res = nllocline.split(None)[16]
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# get theoretical P-onset time from residuum
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badpicks[i][1] = picks[badpicks[i][0]]['P']['mpp'] - float(res)
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if len(badpicks[i][0]) > 4:
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Ppattern = '%s ? ? ? P' % badpicks[i][0]
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elif len(badpicks[i][0]) == 4:
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Ppattern = '%s ? ? ? P' % badpicks[i][0]
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elif len(badpicks[i][0]) < 4:
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Ppattern = '%s ? ? ? P' % badpicks[i][0]
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nllocline = getPatternLine(NLLocfile, Ppattern)
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res = nllocline.split(None)[16]
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# get theoretical P-onset time from residuum
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badpicks[i][1] = picks[badpicks[i][0]]['P']['mpp'] - float(res)
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# get corresponding waveform stream
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msg = '#######################################################\n' \
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'iteratepicker: Re-picking station {0}'.format(badpicks[i][0])
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print(msg)
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wf2pick = wf.select(station=badpicks[i][0])
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# get corresponding waveform stream
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msg = '#######################################################\n' \
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'iteratepicker: Re-picking station {0}'.format(badpicks[i][0])
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print(msg)
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wf2pick = wf.select(station=badpicks[i][0])
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# modify some picking parameters
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pstart_old = pickparameter.getParam('pstart')
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pstop_old = pickparameter.getParam('pstop')
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sstop_old = pickparameter.getParam('sstop')
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pickwinP_old = pickparameter.getParam('pickwinP')
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Precalcwin_old = pickparameter.getParam('Precalcwin')
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noisefactor_old = pickparameter.getParam('noisefactor')
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zfac_old = pickparameter.getParam('zfac')
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pickparameter.setParam(pstart=max([0, badpicks[i][1] - wf2pick[0].stats.starttime \
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- pickparameter.getParam('tlta')]))
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pickparameter.setParam(pstop=pickparameter.getParam('pstart') + \
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(3 * pickparameter.getParam('tlta')))
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pickparameter.setParam(sstop=pickparameter.getParam('sstop') / 2)
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pickparameter.setParam(pickwinP=pickparameter.getParam('pickwinP') / 2)
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pickparameter.setParam(Precalcwin=pickparameter.getParam('Precalcwin') / 2)
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pickparameter.setParam(noisefactor=1.0)
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pickparameter.setParam(zfac=1.0)
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print("iteratepicker: The following picking parameters have been modified for iterative picking:")
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print("pstart: %fs => %fs" % (pstart_old, pickparameter.getParam('pstart')))
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print("pstop: %fs => %fs" % (pstop_old, pickparameter.getParam('pstop')))
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print("sstop: %fs => %fs" % (sstop_old, pickparameter.getParam('sstop')))
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print("pickwinP: %fs => %fs" % (pickwinP_old, pickparameter.getParam('pickwinP')))
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print("Precalcwin: %fs => %fs" % (Precalcwin_old, pickparameter.getParam('Precalcwin')))
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print("noisefactor: %f => %f" % (noisefactor_old, pickparameter.getParam('noisefactor')))
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print("zfac: %f => %f" % (zfac_old, pickparameter.getParam('zfac')))
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# modify some picking parameters
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pstart_old = pickparameter.getParam('pstart')
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pstop_old = pickparameter.getParam('pstop')
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sstop_old = pickparameter.getParam('sstop')
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pickwinP_old = pickparameter.getParam('pickwinP')
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Precalcwin_old = pickparameter.getParam('Precalcwin')
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noisefactor_old = pickparameter.getParam('noisefactor')
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zfac_old = pickparameter.getParam('zfac')
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pickparameter.setParam(
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pstart=max([0, badpicks[i][1] - wf2pick[0].stats.starttime \
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- pickparameter.getParam('tlta')]))
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pickparameter.setParam(pstop=pickparameter.getParam('pstart') + \
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(3 * pickparameter.getParam('tlta')))
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pickparameter.setParam(sstop=pickparameter.getParam('sstop') / 2)
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pickparameter.setParam(pickwinP=pickparameter.getParam('pickwinP') / 2)
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pickparameter.setParam(
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Precalcwin=pickparameter.getParam('Precalcwin') / 2)
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pickparameter.setParam(noisefactor=1.0)
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pickparameter.setParam(zfac=1.0)
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print(
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"iteratepicker: The following picking parameters have been modified for iterative picking:")
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print(
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"pstart: %fs => %fs" % (pstart_old, pickparameter.getParam('pstart')))
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print(
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"pstop: %fs => %fs" % (pstop_old, pickparameter.getParam('pstop')))
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print(
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"sstop: %fs => %fs" % (sstop_old, pickparameter.getParam('sstop')))
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print("pickwinP: %fs => %fs" % (
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pickwinP_old, pickparameter.getParam('pickwinP')))
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print("Precalcwin: %fs => %fs" % (
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Precalcwin_old, pickparameter.getParam('Precalcwin')))
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print("noisefactor: %f => %f" % (
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noisefactor_old, pickparameter.getParam('noisefactor')))
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print("zfac: %f => %f" % (zfac_old, pickparameter.getParam('zfac')))
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# repick station
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newpicks = autopickstation(wf2pick, pickparameter)
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# repick station
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newpicks = autopickstation(wf2pick, pickparameter)
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# replace old dictionary with new one
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picks[badpicks[i][0]] = newpicks
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# replace old dictionary with new one
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picks[badpicks[i][0]] = newpicks
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# reset temporary change of picking parameters
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print("iteratepicker: Resetting picking parameters ...")
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pickparameter.setParam(pstart=pstart_old)
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pickparameter.setParam(pstop=pstop_old)
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pickparameter.setParam(sstop=sstop_old)
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pickparameter.setParam(pickwinP=pickwinP_old)
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pickparameter.setParam(Precalcwin=Precalcwin_old)
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pickparameter.setParam(noisefactor=noisefactor_old)
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pickparameter.setParam(zfac=zfac_old)
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# reset temporary change of picking parameters
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print("iteratepicker: Resetting picking parameters ...")
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pickparameter.setParam(pstart=pstart_old)
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pickparameter.setParam(pstop=pstop_old)
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pickparameter.setParam(sstop=sstop_old)
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pickparameter.setParam(pickwinP=pickwinP_old)
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pickparameter.setParam(Precalcwin=Precalcwin_old)
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pickparameter.setParam(noisefactor=noisefactor_old)
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pickparameter.setParam(zfac=zfac_old)
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return picks
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