def tunePickers(DF,picker='pkBaer',filt=[1,10,2,True]):
DF['AutoPick']=dict
DF['Resids']=float
minresids=999999999999999999999.0
for p1 in np.linspace(2,160,num=50):
for p2 in np.linspace(p1+1,800,num=50):
for a in DF.iterrows():
if picker=='pkBaer':
TR=obspy.core.read(a[1].FileName)
TR.filter('bandpass',freqmin=filt[0],freqmax=filt[1],corners=filt[2],zerophase=filt[3])
TR=TR.select(channel="*Z")
outdict={}
for b in TR:
cft=recSTALTA(b[0].data, int(p1), int(p2))
p_pick=cft.argmax()
Pstamp=p_pick/(float(b.stats.sampling_rate))+b.stats.starttime.timestamp
idd=b.stats.station
outdict[idd]=Pstamp
DF.AutoPick[a[0]]=outdict
sq=np.square(pd.Series(outdict)-pd.Series(DF.UTCPtime[a[0]]))
DF.Resids[a[0]]=np.sqrt(np.average(sq[~np.isnan(sq)]))
Resids=np.sum(DF.Resids.values)
if Resids<minresids:
bestparams=[p1,p2]
print Resids
return bestparams
"""
def normalize(self, method='trace_max', **kwargs):
"""
Normalizes all trace in the stream.
"""
logging.info("Normalizing {:} traces with method '{:}'...",
len(self.traces), method)
if method == 'trace_max':
ObspyStream.normalize(self, global_max=False)
elif method == 'global_max':
ObspyStream.normalize(self, global_max=True)
elif method == 'onebit':
for tr in self.traces:
tr.data = np.sign(tr.data)
elif method == 'stalta':
_apply = kwargs.get('apply', True)
sta = kwargs.get('sta', 3.)
lta = kwargs.get('lta', 10.)
trigger_on = kwargs.get('trigger_on', 1.1)
trigger_off = kwargs.get('trigger_off', 1.0)
for tr in self.traces:
df = tr.stats['sampling_rate']
_sta = int(sta * df)
_lta = int(lta * df)
cft = trigger.recSTALTA(tr.data, _sta, _lta)
tr.trg = trigger.triggerOnset(cft, trigger_on, trigger_off)
if _apply:
for on, off in tr.trg:
tr.data[on:off] = 0
else:
raise ValueError("Unknown method '{:}'".format(method))
from obspy.core import UTCDateTime
from obspy.arclink import Client
from obspy.signal.trigger import recSTALTA, triggerOnset
import matplotlib.pyplot as plt
import numpy as np
# Retrieve waveforms via ArcLink
client = Client(host="erde.geophysik.uni-muenchen.de", port=18001)
t = UTCDateTime("2009-08-24 00:19:45")
st = client.getWaveform('BW', 'RTSH', '', 'EHZ', t, t + 50)
# For convenience
tr = st[0] # only one trace in mseed volume
df = tr.stats.sampling_rate
# Characteristic function and trigger onsets
cft = recSTALTA(tr.data, int(2.5 * df), int(10. * df))
on_of = triggerOnset(cft, 3.5, 0.5)
# Plotting the results
ax = plt.subplot(211)
plt.plot(tr.data, 'k')
ymin, ymax = ax.get_ylim()
plt.vlines(on_of[:, 0], ymin, ymax, color='r', linewidth=2)
plt.vlines(on_of[:, 1], ymin, ymax, color='b', linewidth=2)
plt.subplot(212, sharex=ax)
plt.plot(cft, 'k')
plt.hlines([3.5, 0.5], 0, len(cft), color=['r', 'b'], linestyle='--')
plt.axis('tight')
plt.show()
from obspy.core import UTCDateTime
from obspy.arclink import Client
from obspy.signal.trigger import recSTALTA, triggerOnset
import matplotlib.pyplot as plt
# Retrieve waveforms via ArcLink
client = Client(host="erde.geophysik.uni-muenchen.de", port=18001)
t = UTCDateTime("2009-08-24 00:19:45")
st = client.getWaveform('BW', 'RTSH', '', 'EHZ', t, t + 50)
# For convenience
tr = st[0] # only one trace in mseed volume
df = tr.stats.sampling_rate
# Characteristic function and trigger onsets
cft = recSTALTA(tr.data, int(2.5 * df), int(10. * df))
on_of = triggerOnset(cft, 3.5, 0.5)
# Plotting the results
ax = plt.subplot(211)
plt.plot(tr.data, 'k')
ymin, ymax = ax.get_ylim()
plt.vlines(on_of[:, 0], ymin, ymax, color='r', linewidth=2)
plt.vlines(on_of[:, 1], ymin, ymax, color='b', linewidth=2)
plt.subplot(212, sharex=ax)
plt.plot(cft, 'k')
plt.hlines([3.5, 0.5], 0, len(cft), color=['r', 'b'], linestyle='--')
plt.axis('tight')
plt.show()
def refTrigger(self, RefWaveform):
Config = self.Config
cfg = ConfigObj(dict=Config)
name = ('%s.%s.%s.%s') % (
RefWaveform[0].stats.network, RefWaveform[0].stats.station,
RefWaveform[0].stats.location, RefWaveform[0].stats.channel)
i = self.searchMeta(name, self.StationMeta)
de = loc2degrees(self.Origin, i)
ptime = 0
Phase = cake.PhaseDef('P')
model = cake.load_model()
if cfg.colesseo_input() == True:
arrivals = model.arrivals([de, de],
phases=Phase,
zstart=self.Origin.depth,
zstop=0.)
else:
arrivals = model.arrivals([de, de],
phases=Phase,
zstart=self.Origin.depth * km,
zstop=0.)
try:
ptime = arrivals[0].t
except:
arrivals = model.arrivals([de, de],
phases=Phase,
zstart=o_depth * km - 0.1)
ptime = arrivals[0].t
phasename = ('%sphase') % (os.path.basename(self.AF))
if ptime == 0:
print '\033[31mAvailable phases for reference station %s in range %f deegree\033[0m' % (
i, de)
print '\033[31m' + '|'.join(
[str(item['phase_name']) for item in tt]) + '\033[0m'
print '\033[31myou tried phase %s\033[0m' % (
self.Config[phasename])
raise Exception("\033[31mILLEGAL: phase definition\033[0m")
tw = self.calculateTimeWindows(ptime)
if cfg.pyrocko_download() == True:
stP = self.readWaveformsPicker_pyrocko(i, tw, self.Origin, ptime)
elif cfg.colesseo_input() == True:
stP = self.readWaveformsPicker_colos(i, tw, self.Origin, ptime)
else:
stP = self.readWaveformsPicker(i, tw, self.Origin, ptime)
refuntouchname = os.path.basename(self.AF) + '-refstation-raw.mseed'
stP.write(os.path.join(self.EventPath, refuntouchname),
format='MSEED',
byteorder='>')
stP.filter("bandpass",
freqmin=float(self.Config['refstationfreqmin']),
freqmax=float(self.Config['refstationfreqmax']))
stP.trim(tw['xcorrstart'], tw['xcorrend'])
trP = stP[0]
trP.stats.starttime = UTCDateTime(3600)
refname = os.path.basename(self.AF) + '-refstation-filtered.mseed'
trP.write(os.path.join(self.EventPath, refname),
format='MSEED',
byteorder='>')
sta = float(self.Config['refsta'])
lta = float(self.Config['reflta'])
cft = recSTALTA(trP.data, int(sta * trP.stats.sampling_rate),
int(lta * trP.stats.sampling_rate))
t = triggerOnset(cft, lta, sta)
try:
onset = t[0][0] / trP.stats.sampling_rate
print 'ONSET ', onset
except:
onset = self.mintforerun
trigger = trP.stats.starttime + onset
print 'TRIGGER ', trigger
print 'THEORETICAL: ', UTCDateTime(3600) + self.mintforerun
tdiff = (trP.stats.starttime + onset) - (UTCDateTime(3600) +
self.mintforerun)
print 'TDIFF: ', tdiff
refp = UTCDateTime(self.Origin.time) + ptime
reftriggeronset = refp + onset - self.mintforerun
if int(self.Config['autoxcorrcorrectur']) == 1:
try:
refmarkername = os.path.join(self.EventPath, ('%s-marker') %
(os.path.basename(self.AF)))
fobjrefmarkername = open(refmarkername, 'w')
fobjrefmarkername.write(
'# Snuffler Markers File Version 0.2\n')
fobjrefmarkername.write((
'phase: %s 0 %s None None None XWStart None False\n'
) % (tw['xcorrstart'].strftime('%Y-%m-%d %H:%M:%S.%f'), name))
fobjrefmarkername.write((
'phase: %s 0 %s None None None XWEnd None False\n'
) % (tw['xcorrend'].strftime('%Y-%m-%d %H:%M:%S.%f'), name))
fobjrefmarkername.write((
'phase: %s 1 %s None None None TheoP None False\n'
) % (refp.strftime('%Y-%m-%d %H:%M:%S.%f'), name))
fobjrefmarkername.write((
'phase: %s 3 %s None None None XTrig None False'
) % (reftriggeronset.strftime('%Y-%m-%d %H:%M:%S.%f'), name))
fobjrefmarkername.close()
cmd = 'snuffler %s --markers=%s&' % (os.path.join(
self.EventPath, refuntouchname), refmarkername)
os.system(cmd)
thrOn = float(self.Config['reflta']) # 4
thrOff = float(self.Config['refsta']) # 0.7
plotTrigger(trP, cft, thrOn, thrOff)
selection = float(
raw_input('Enter self picked phase in seconds: '))
tdiff = selection - self.mintforerun
refname = os.path.basename(self.AF) + '-shift.mseed'
trP.stats.starttime = trP.stats.starttime - selection
trP.write(os.path.join(self.EventPath, refname),
format='MSEED')
except:
selection = 0.
refname = os.path.basename(self.AF) + '-shift.mseed'
trP.stats.starttime = trP.stats.starttime - selection - self.mintforerun
trP.write(os.path.join(self.EventPath, refname),
format='MSEED')
'''
tdiff = 0
trigger = trP.stats.starttime
'''
To = Trigger(name, trigger, os.path.basename(self.AF), tdiff)
return tdiff, To
def AutoPick(pickdir='Trigs',outputFormat='HYP',outdir='PickTimes',picker='pkBaer',goodPick='goodpicking',
startnum='StartHere.txt',filelist=None):
StaKey=pd.read_csv('StationKey.csv')
if not os.path.isdir(outdir):
os.makedirs(outdir)
if not os.path.isdir(goodPick):
os.makedirs(goodPick)
latmin,latmax,lonmin,lonmax=_getLimits(StaKey)
dA,A=_getdA(6371) #calculates symbolically the partial derivatives of the operator for location inversion
count=0
if isinstance(filelist,list):
files=filelist
else:
files=glob.glob(os.path.join(pickdir,'*'))
try: #Look for startnum txt to see where to begin
start=int(np.loadtxt(startnum).tolist()+int(np.random.rand()*10))
except:
print 'No progress file, begining at 0'
for fil in range(start,len(files)):
ST=obspy.core.read(files[fil])
filename=os.path.basename(files[fil]).replace('msd','pha')
with open(os.path.join(outdir,filename),'wb') as pik:
Stations=StaKey.STATION
STR=[0]*len(Stations)
pks=[1]*len(Stations)
cou=0
Key=StaKey.copy()
Key['Ppick']=0.000000000
Key['Spick']=0.000000000
Key['Trace']=object
for sta in Key.iterrows():
st=ST.copy()
st=st.select(station=sta[1].STATION)
if len(st)==0: #If station not found skip iteration
continue
sr=st[0].stats.sampling_rate
STR[cou]=st.copy()
cou+=1
for tr in range(len(STR)):
if picker=='arPick':
Z,N,E=STR[tr].select(channel='*Z').copy(), STR[tr].select(channel='*N').copy(),STR[tr].select(channel='*E').copy()
p_pick, s_pick = arPick(Z[0].data, N[0].data,E[0].data, Z[0].stats.sampling_rate,1.0, 15.0, 1.0, 0.1, 4.0, 1.0, 2, 8, 0.1, 0.2)
elif picker=='pkBaer':
zst=STR[tr].select(channel='*Z')
p_pick, phase_info = pkBaer(zst[0].data, sr,20, 60, 1.2, 10.0, 100, 100)
if p_pick==1 or p_pick<0: #if baer/arPicker pick failes resort to basic recursive STA/LTA picks
cft=recSTALTA(STR[tr].select(channel='*Z')[0].data, int(1 * sr), int(10 * sr))
p_pick=cft.argmax()
pks[tr]=p_pick
Key['Ppick'][int(tr)]=STR[tr][0].stats.starttime.timestamp+p_pick/float(sr)
Key['Trace'][int(tr)]=STR[tr][0]
#print (p_pick)
for sta in Key.drop_duplicates(cols='Ppick').iterrows():
if outputFormat=='NNL':
if picker=='arPick':
line1,line2=_makeArPickNLLLine(sta[1].Ppick,s_pick,STR[tr])
pik.write(line1)
pik.write(line2)
if picker=='pkBaer':
line1=_makePkBaerNLLLine(sta[1].Ppick,sta[1].Trace.stats.sampling_rate,sta[1].Trace)
pik.write(line1)
if outputFormat=='HYP':
if picker=='pkBaer':
try:
line=_makePkBaerHYPLine(sta[1].Ppick,sta[1].Trace.stats.sampling_rate,sta[1].Trace)
except:
break
pik.write(line)
m=invertForLocation(Key,dA,A)
if outputFormat=='NNL':
pass #write this in later
if outputFormat=='HYP' and m[0]>-90 and m[0]<90 and m[1]>-180 and m[1]<180:
endline=writeEndLine(m,Key)
#print np.min(np.min(Key.Ppick.values))
pik.write(endline)
pik.write('\n')
#Key=_genSynthetics(Key,A)
if m[0] < latmin or m[0] > latmax or m[1] < lonmin or m[1] > lonmax: #If rough location is in station peremeter make picks and copy file
os.remove(os.path.join(outdir,filename))
else:
shutil.copy(files[fil],os.path.join(goodPick,os.path.basename(files[fil])))
print filename
count+=1
if count%10==0:
_writeProgressFile(count)
from obspy.core import read
from obspy.signal.trigger import recSTALTA, plotTrigger
trace = read("http://examples.obspy.org/ev0_6.a01.gse2")[0]
df = trace.stats.sampling_rate
cft = recSTALTA(trace.data, int(5 * df), int(10 * df))
plotTrigger(trace, cft, 1.2, 0.5)
