def seism_picker(picktype,args,stream):
"""
A simple cover function for th eobspy picking modules
:type picktype: String
:param picktype: Eother Baer or AR for Auto-regressive
:type args: Class
:param args: List of appropriate arguments for the chosen pick type -
defined in picker_par.py
:type Stream: obspy.Stream
:return: p_pick, s_pick
"""
import sys
if picktype == 'Baer':
from obspy.signal.trigger import pkBaer
p_pick=[]
phase_info=[]
station_info=[]
for tr in stream:
trp_pick, trphase_info = pkBaer(tr.data, tr.stats.sampling_rate,
args.tdownmax, args.tupevent, args.thr1,
args.thr2, args.preset_len, args.p_dur)
# 20, 60, 7.0, 12.0, 100, 100)
trp_pick=trp_pick/tr.stats.sampling_rate
p_pick+=[trp_pick]
phase_info+=[trphase_info]
station_info+=[tr.stats.station+'.'+tr.stats.channel]
return p_pick, phase_info, station_info
elif picktype == 'AR':
if len(stream) != 3:
print 'Stream must be three channels from the same station'
sys.exit()
from obspy.signal.trigger import arPick
tr1=stream.select(channel='*Z')[0]
try:
tr2=stream.select(channel='*N')[0]
except:
tr2=stream.select(channel='*1')[0]
try:
tr3=stream.select(channel='*E')[0]
except:
tr3=stream.select(channel='*2')[0]
df=tr1.stats.sampling_rate
p_pick, s_pick = arPick(tr1.data, tr2.data, tr3.data, df,
args.f1, args.f2, args.lta_p, args.sta_p,
args.lta_s, args.sta_s, args.m_p, args.m_s,
args.l_p, args.l_s, args.s_pick)
#1.0, 20.0, 1.0, 0.1, 4.0, 1.0, 2, 8, 0.1, 0.2)
return p_pick, s_pick
def ProcessLoopP(filepath):
'''The file processing loop associated with P wave tomography: Just deal with the BHZ files to save time'''
sacfiles = glob.glob('*.BHZ')
#Check to see if there is more than one location for a given station
stationnames = []
for sacfile in sorted(sacfiles):
sacfilenameparts = sacfile.split('.')
stationname = sacfilenameparts[2]
if stationname not in stationnames:
stationnames.append(stationname)
trace = read(sacfile)
evlat = trace[0].stats.sac.evla
evlon = trace[0].stats.sac.evlo
evdep = trace[0].stats.sac.evdp
stlat = trace[0].stats.sac.stla
stlon = trace[0].stats.sac.stlo
dist = locations2degrees(evlat,evlon,stlat,stlon) #find distance from the quake to the station
arcs = IRISclient.distaz(stalat=stlat,stalon=stlon,evtlat=evlat,evtlon=evlon)
az = arcs['backazimuth']
baz = arcs['azimuth']
#If we're running this code twice in a row, need to correct the evdep accordingly. The evdep that comes from obspy will be in km, but needs
#to be in the SAC header in meters. If the depth is already in meters in the SACfile, then it will almost certainly be >1000. This if statement check for
#this, and converts to km if necessary
if evdep > 1e3:
evdep = evdep/1000.0
traveltimes = getTravelTimes(dist,evdep, model='iasp91')
P = 0
S = 0
for element in traveltimes:
phaseinfo = element['phase_name']
if phaseinfo == 'P':
Ptime = element['time']
P = 1
if phaseinfo == 'S':
Stime = element['time']
S = 1
if (P==1 and S==1):
break
try:
P = Ptime
except:
Ptime = 0
try:
S = Stime
except:
Stime = 0
#Set the P and S times
trace[0].stats.sac.az = float(az)
trace[0].stats.sac.baz = float(baz)
trace[0].stats.sac.o = 0.0 #add origin time
if Ptime > 0:
trace[0].stats.sac.t1 = Ptime
if Stime > 0:
trace[0].stats.sac.t2 = Stime
trace[0].stats.sac.evdp = evdep*1000 #dbpick wants depth to be in meters
#other operations
trace[0].detrend('demean')
#THE CROSS CORRELATION CODE ASSUMES A SAMPLING RATE OF 0.05 (20 SAMPLES/SECOND). IT WILL NOT WORK
#OTHERWISE!!!
trace[0].resample(20)
if results.autop:
tracestreamP = trace.copy()
df = tracestreamP[0].stats.sampling_rate
filter1 = 0.02
filter2 = 0.1
tracestreamP.filter("bandpass",freqmin=filter1,freqmax=filter2,corners=2)
tracestreamP.taper(max_percentage=0.05, type='cosine')
p_pick, phase_info = pkBaer(tracestreamP[0].data,df,10,2,2,10,20,6) #output from this is in samples.
autoPtime = p_pick/df
#Append the autopicker's time to the
if abs(Ptime-autoPtime) < 20:
print 'Autopick accepted!'
trace[0].stats.sac.t3 = autoPtime
#Important - must write to the SAC file!
trace.write(sacfile,format='SAC')
print 'Appended arrivals to %s' %sacfile
else:
print 'Found multiple instruments at station %s. Removing all but 1' %(stationname)
os.system('rm %s' %sacfile)
#create antelope database for P arrivals
os.system('sac2db *.BHZ Z')
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)