Merge branch 'develop' of ariadne.geophysik.ruhr-uni-bochum.de:/data/git/pylot into develop

This commit is contained in:
Marcel Paffrath 2015-12-07 11:21:50 +01:00
commit 5083c5a876
6 changed files with 549 additions and 397 deletions

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@ -24,6 +24,7 @@ https://www.iconfinder.com/iconsets/flavour
"""
import os, sys
from os.path import expanduser
import matplotlib
matplotlib.use('Qt4Agg')
@ -670,7 +671,8 @@ class MainWindow(QMainWindow):
self.logDockWidget.setWidget(self.listWidget)
self.addDockWidget(Qt.LeftDockWidgetArea, self.logDockWidget)
self.addListItem('loading default values for local data ...')
autopick_parameter = AutoPickParameter('autoPyLoT_local.in')
home = expanduser("~")
autopick_parameter = AutoPickParameter('%s/.pylot/autoPyLoT_local.in' % home)
self.addListItem(str(autopick_parameter))
# Create the worker thread and run it

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@ -6,6 +6,7 @@ import argparse
import glob
import subprocess
import string
import numpy as np
from obspy.core import read, UTCDateTime
from pylot.core.read.data import Data
from pylot.core.read.inputs import AutoPickParameter
@ -141,7 +142,8 @@ def autoPyLoT(inputfile):
# calculating seismic moment Mo and moment magnitude Mw
finalpicks = M0Mw(wfdat, None, None, parameter.getParam('iplot'), \
nllocfile, picks, parameter.getParam('rho'), \
parameter.getParam('vp'), parameter.getParam('invdir'))
parameter.getParam('vp'), parameter.getParam('Qp'), \
parameter.getParam('invdir'))
else:
print("autoPyLoT: No NLLoc-location file available!")
print("No source parameter estimation possible!")
@ -161,6 +163,8 @@ def autoPyLoT(inputfile):
picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
# write phases to NLLoc-phase file
picksExport(picks, 'NLLoc', phasefile)
# remove actual NLLoc-location file to keep only the last
os.remove(nllocfile)
# locate the event
locate(nlloccall, ctrfile)
print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
@ -180,14 +184,25 @@ def autoPyLoT(inputfile):
# calculating seismic moment Mo and moment magnitude Mw
finalpicks = M0Mw(wfdat, None, None, parameter.getParam('iplot'), \
nllocfile, picks, parameter.getParam('rho'), \
parameter.getParam('vp'), parameter.getParam('invdir'))
parameter.getParam('vp'), parameter.getParam('Qp'), \
parameter.getParam('invdir'))
# get network moment magntiude
netMw = []
for key in finalpicks.getpicdic():
if finalpicks.getpicdic()[key]['P']['Mw'] is not None:
netMw.append(finalpicks.getpicdic()[key]['P']['Mw'])
netMw = np.median(netMw)
print("Network moment magnitude: %4.1f" % netMw)
else:
print("autoPyLoT: No NLLoc-location file available! Stop iteration!")
##########################################################
# write phase files for various location routines
# HYPO71
hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, evID)
hypo71file = '%s/autoPyLoT_HYPO71.pha' % event
if finalpicks.getpicdic() is not None:
writephases(finalpicks.getpicdic(), 'HYPO71', hypo71file)
else:
writephases(picks, 'HYPO71', hypo71file)
endsplash = '''------------------------------------------\n'
-----Finished event %s!-----\n'
@ -240,7 +255,8 @@ def autoPyLoT(inputfile):
# calculating seismic moment Mo and moment magnitude Mw
finalpicks = M0Mw(wfdat, None, None, parameter.getParam('iplot'), \
nllocfile, picks, parameter.getParam('rho'), \
parameter.getParam('vp'), parameter.getParam('invdir'))
parameter.getParam('vp'), parameter.getParam('Qp'), \
parameter.getParam('invdir'))
else:
print("autoPyLoT: No NLLoc-location file available!")
print("No source parameter estimation possible!")
@ -260,6 +276,8 @@ def autoPyLoT(inputfile):
picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
# write phases to NLLoc-phase file
picksExport(picks, 'NLLoc', phasefile)
# remove actual NLLoc-location file to keep only the last
os.remove(nllocfile)
# locate the event
locate(nlloccall, ctrfile)
print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
@ -279,14 +297,25 @@ def autoPyLoT(inputfile):
# calculating seismic moment Mo and moment magnitude Mw
finalpicks = M0Mw(wfdat, None, None, parameter.getParam('iplot'), \
nllocfile, picks, parameter.getParam('rho'), \
parameter.getParam('vp'), parameter.getParam('invdir'))
parameter.getParam('vp'), parameter.getParam('Qp'), \
parameter.getParam('invdir'))
# get network moment magntiude
netMw = []
for key in finalpicks.getpicdic():
if finalpicks.getpicdic()[key]['P']['Mw'] is not None:
netMw.append(finalpicks.getpicdic()[key]['P']['Mw'])
netMw = np.median(netMw)
print("Network moment magnitude: %4.1f" % netMw)
else:
print("autoPyLoT: No NLLoc-location file available! Stop iteration!")
##########################################################
# write phase files for various location routines
# HYPO71
hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, parameter.getParam('eventID'))
if finalpicks.getpicdic() is not None:
writephases(finalpicks.getpicdic(), 'HYPO71', hypo71file)
else:
writephases(picks, 'HYPO71', hypo71file)
endsplash = '''------------------------------------------\n'
-----Finished event %s!-----\n'

View File

@ -25,16 +25,15 @@ AUTOLOC_nlloc #outpatter# %pattern of NLLoc-output file
%(returns 'eventID_outpatter')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#parameters for seismic moment estimation#
3000 #vp# %average P-wave velocity
2600 #rho# %rock density [kg/m^3]
300 #Qp# %quality factor for P waves
3530 #vp# %average P-wave velocity
2500 #rho# %average rock density [kg/m^3]
300f**0.8 #Qp# %quality factor for P waves (Qp*f^a)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
AUTOFOCMEC_AIC_HOS4_ARH.in #focmecin# %name of focmec input file containing polarities
6 #pmin# %minimum required P picks for location
4 #p0min# %minimum required P picks for location if at least
%3 excellent P picks are found
2 #smin# %minimum required S picks for location
/home/ludger/bin/run_HYPOSAT4autoPILOT.csh #cshellp# %path and name of c-shell script to run location routine
7.6 8.5 #blon# %longitude bounding for location map
49 49.4 #blat# %lattitude bounding for location map
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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@ -12,7 +12,7 @@ from obspy.core import Stream, UTCDateTime
from pylot.core.pick.utils import getsignalwin, crossings_nonzero_all
from pylot.core.util.utils import getPatternLine
from scipy.optimize import curve_fit
from scipy import integrate
from scipy import integrate, signal
from pylot.core.read.data import Data
class Magnitude(object):
@ -23,7 +23,7 @@ class Magnitude(object):
'''
def __init__(self, wfstream, To, pwin, iplot, NLLocfile=None, \
picks=None, rho=None, vp=None, invdir=None):
picks=None, rho=None, vp=None, Qp=None, invdir=None):
'''
:param: wfstream
:type: `~obspy.core.stream.Stream
@ -66,6 +66,7 @@ class Magnitude(object):
self.setrho(rho)
self.setpicks(picks)
self.setvp(vp)
self.setQp(Qp)
self.setinvdir(invdir)
self.calcwapp()
self.calcsourcespec()
@ -114,6 +115,12 @@ class Magnitude(object):
def getvp(self):
return self.vp
def setQp(self, Qp):
self.Qp = Qp
def getQp(self):
return self.Qp
def setpicks(self, picks):
self.picks = picks
@ -200,7 +207,7 @@ class WApp(Magnitude):
class M0Mw(Magnitude):
'''
Method to calculate seismic moment Mo and moment magnitude Mw.
Requires results of class w0fc for calculating plateau w0
Requires results of class calcsourcespec for calculating plateau w0
and corner frequency fc of source spectrum, respectively. Uses
subfunction calcMoMw.py. Returns modified dictionary of picks including
Dc-value, corner frequency fc, seismic moment Mo and
@ -212,17 +219,12 @@ class M0Mw(Magnitude):
picks = self.getpicks()
nllocfile = self.getNLLocfile()
wfdat = self.getwfstream()
# get vertical component data only
zdat = wfdat.select(component="Z")
if len(zdat) == 0: # check for other components
zdat = wfdat.select(component="3")
self.picdic = None
for key in picks:
if picks[key]['P']['weight'] < 4:
# select waveform
selwf = zdat.select(station=key)
# get hypocentral distance of station
# from NLLoc-location file
selwf = wfdat.select(station=key)
if len(key) > 4:
Ppattern = '%s ? ? ? P' % key
elif len(key) == 4:
@ -230,15 +232,23 @@ class M0Mw(Magnitude):
elif len(key) < 4:
Ppattern = '%s ? ? ? P' % key
nllocline = getPatternLine(nllocfile, Ppattern)
# get hypocentral distance, station azimuth and
# angle of incidence from NLLoc-location file
delta = float(nllocline.split(None)[21])
az = float(nllocline.split(None)[22])
inc = float(nllocline.split(None)[24])
# call subfunction to estimate source spectrum
# and to derive w0 and fc
[w0, fc] = calcsourcespec(selwf, picks[key]['P']['mpp'], \
self.getiplot(), self.getinvdir())
self.getinvdir(), az, inc, self.getQp(), \
self.getiplot())
if w0 is not None:
# call subfunction to calculate Mo and Mw
[Mo, Mw] = calcMoMw(selwf, w0, self.getrho(), self.getvp(), \
zdat = selwf.select(component="Z")
if len(zdat) == 0: # check for other components
zdat = selwf.select(component="3")
[Mo, Mw] = calcMoMw(zdat, w0, self.getrho(), self.getvp(), \
delta, self.getinvdir())
else:
Mo = None
@ -276,70 +286,119 @@ def calcMoMw(wfstream, w0, rho, vp, delta, inv):
def calcsourcespec(wfstream, onset, iplot, inventory):
def calcsourcespec(wfstream, onset, inventory, azimuth, incidence, Qp, iplot):
'''
Subfunction to calculate the source spectrum and to derive from that the plateau
(usually called omega0) and the corner frequency assuming Aki's omega-square
source model. Has to be derived from instrument corrected displacement traces,
thus restitution and integration necessary!
thus restitution and integration necessary! Integrated traces have to be rotated
into ray-coordinate system ZNE => LQT!
'''
print ("Calculating source spectrum ....")
# get Q value
qu = Qp.split('f**')
# constant Q
Q = int(qu[0])
# A, i.e. power of frequency
A = float(qu[1])
fc = None
w0 = None
data = Data()
z_copy = wfstream.copy()
[corzdat, restflag] = data.restituteWFData(inventory, z_copy)
wf_copy = wfstream.copy()
[cordat, restflag] = data.restituteWFData(inventory, wf_copy)
if restflag == 1:
# integrate to displacment
corintzdat = integrate.cumtrapz(corzdat[0], None, corzdat[0].stats.delta)
z_copy[0].data = corintzdat
tr = z_copy[0]
zdat = cordat.select(component="Z")
if len(zdat) == 0:
zdat = cordat.select(component="3")
cordat_copy = cordat.copy()
# get equal time stamps and lengths of traces
# necessary for rotation of traces
tr0start = cordat_copy[0].stats.starttime
tr0start = tr0start.timestamp
tr0end = cordat_copy[0].stats.endtime
tr0end = tr0end.timestamp
tr1start = cordat_copy[1].stats.starttime
tr1start = tr1start.timestamp
tr1end = cordat_copy[1].stats.endtime
tr1end = tr1end.timestamp
tr2start = cordat_copy[2].stats.starttime
tr2start = tr2start.timestamp
tr2end = cordat_copy[0].stats.endtime
tr2end = tr2end.timestamp
trstart = UTCDateTime(max([tr0start, tr1start, tr2start]))
trend = UTCDateTime(min([tr0end, tr1end, tr2end]))
cordat_copy.trim(trstart, trend)
minlen = min([len(cordat_copy[0]), len(cordat_copy[1]), len(cordat_copy[2])])
cordat_copy[0].data = cordat_copy[0].data[0:minlen]
cordat_copy[1].data = cordat_copy[1].data[0:minlen]
cordat_copy[2].data = cordat_copy[2].data[0:minlen]
try:
# rotate into LQT (ray-coordindate-) system using Obspy's rotate
# L: P-wave direction
# Q: SV-wave direction
# T: SH-wave direction
LQT=cordat_copy.rotate('ZNE->LQT',azimuth, incidence)
ldat = LQT.select(component="L")
if len(ldat) == 0:
# yet Obspy's rotate can not handle channels 3/2/1
ldat = LQT.select(component="Z")
# integrate to displacement
# unrotated vertical component (for copmarison)
inttrz = signal.detrend(integrate.cumtrapz(zdat[0].data, None, \
zdat[0].stats.delta))
# rotated component Z => L
Ldat = signal.detrend(integrate.cumtrapz(ldat[0].data, None, \
ldat[0].stats.delta))
# get window after P pulse for
# calculating source spectrum
if tr.stats.sampling_rate <= 100:
winzc = tr.stats.sampling_rate
elif tr.stats.sampling_rate > 100 and \
tr.stats.sampling_rate <= 200:
winzc = 0.5 * tr.stats.sampling_rate
elif tr.stats.sampling_rate > 200 and \
tr.stats.sampling_rate <= 400:
winzc = 0.2 * tr.stats.sampling_rate
elif tr.stats.sampling_rate > 400:
winzc = tr.stats.sampling_rate
tstart = UTCDateTime(tr.stats.starttime)
if zdat[0].stats.sampling_rate <= 100:
winzc = zdat[0].stats.sampling_rate
elif zdat[0].stats.sampling_rate > 100 and \
zdat[0].stats.sampling_rate <= 200:
winzc = 0.5 * zdat[0].stats.sampling_rate
elif zdat[0].stats.sampling_rate > 200 and \
zdat[0].stats.sampling_rate <= 400:
winzc = 0.2 * zdat[0].stats.sampling_rate
elif zdat[0].stats.sampling_rate > 400:
winzc = zdat[0].stats.sampling_rate
tstart = UTCDateTime(zdat[0].stats.starttime)
tonset = onset.timestamp -tstart.timestamp
impickP = tonset * tr.stats.sampling_rate
wfzc = tr.data[impickP : impickP + winzc]
impickP = tonset * zdat[0].stats.sampling_rate
wfzc = Ldat[impickP : impickP + winzc]
# get time array
t = np.arange(0, len(tr) * tr.stats.delta, tr.stats.delta)
t = np.arange(0, len(inttrz) * zdat[0].stats.delta, \
zdat[0].stats.delta)
# calculate spectrum using only first cycles of
# waveform after P onset!
zc = crossings_nonzero_all(wfzc)
if np.size(zc) == 0 or len(zc) <= 3:
print ("Something is wrong with the waveform, "
print ("calcsourcespec: Something is wrong with the waveform, "
"no zero crossings derived!")
print ("No calculation of source spectrum possible!")
plotflag = 0
else:
plotflag = 1
index = min([3, len(zc) - 1])
calcwin = (zc[index] - zc[0]) * z_copy[0].stats.delta
calcwin = (zc[index] - zc[0]) * zdat[0].stats.delta
iwin = getsignalwin(t, tonset, calcwin)
xdat = tr.data[iwin]
xdat = Ldat[iwin]
# fft
fny = tr.stats.sampling_rate / 2
l = len(xdat) / tr.stats.sampling_rate
n = tr.stats.sampling_rate * l # number of fft bins after Bath
fny = zdat[0].stats.sampling_rate / 2
l = len(xdat) / zdat[0].stats.sampling_rate
# number of fft bins after Bath
n = zdat[0].stats.sampling_rate * l
# find next power of 2 of data length
m = pow(2, np.ceil(np.log(len(xdat)) / np.log(2)))
N = int(np.power(m, 2))
y = tr.stats.delta * np.fft.fft(xdat, N)
y = zdat[0].stats.delta * np.fft.fft(xdat, N)
Y = abs(y[: N/2])
L = (N - 1) / tr.stats.sampling_rate
L = (N - 1) / zdat[0].stats.sampling_rate
f = np.arange(0, fny, 1/L)
# remove zero-frequency and frequencies above
@ -348,51 +407,65 @@ def calcsourcespec(wfstream, onset, iplot, inventory):
fi = np.where((f >= 1) & (f < 100))
F = f[fi]
YY = Y[fi]
# correction for attenuation
YYcor = YY.real*Q**A
# get plateau (DC value) and corner frequency
# initial guess of plateau
w0in = np.mean(YY[0:100])
w0in = np.mean(YYcor[0:100])
# initial guess of corner frequency
# where spectral level reached 50% of flat level
iin = np.where(YY >= 0.5 * w0in)
iin = np.where(YYcor >= 0.5 * w0in)
Fcin = F[iin[0][np.size(iin) - 1]]
# use of implicit scipy otimization function
fit = synthsourcespec(F, w0in, Fcin)
[optspecfit, pcov] = curve_fit(synthsourcespec, F, YY.real, [w0in, Fcin])
[optspecfit, pcov] = curve_fit(synthsourcespec, F, YYcor, [w0in, Fcin])
w01 = optspecfit[0]
fc1 = optspecfit[1]
print ("w0fc: Determined w0-value: %e m/Hz, \n"
print ("calcsourcespec: Determined w0-value: %e m/Hz, \n"
"Determined corner frequency: %f Hz" % (w01, fc1))
# use of conventional fitting
[w02, fc2] = fitSourceModel(F, YY.real, Fcin, iplot)
[w02, fc2] = fitSourceModel(F, YYcor, Fcin, iplot)
# get w0 and fc as median
w0 = np.median([w01, w02])
fc = np.median([fc1, fc2])
print("w0fc: Using w0-value = %e m/Hz and fc = %f Hz" % (w0, fc))
print("calcsourcespec: Using w0-value = %e m/Hz and fc = %f Hz" % (w0, fc))
except TypeError as er:
raise TypeError('''{0}'''.format(er))
if iplot > 1:
f1 = plt.figure()
tLdat = np.arange(0, len(Ldat) * zdat[0].stats.delta, \
zdat[0].stats.delta)
plt.subplot(2,1,1)
# show displacement in mm
plt.plot(t, np.multiply(tr, 1000), 'k')
p1, = plt.plot(t, np.multiply(inttrz, 1000), 'k')
p2, = plt.plot(tLdat, np.multiply(Ldat, 1000))
plt.legend([p1, p2], ['Displacement', 'Rotated Displacement'])
if plotflag == 1:
plt.plot(t[iwin], np.multiply(xdat, 1000), 'g')
plt.title('Seismogram and P Pulse, Station %s-%s' \
% (tr.stats.station, tr.stats.channel))
% (zdat[0].stats.station, zdat[0].stats.channel))
else:
plt.title('Seismogram, Station %s-%s' \
% (tr.stats.station, tr.stats.channel))
plt.xlabel('Time since %s' % tr.stats.starttime)
% (zdat[0].stats.station, zdat[0].stats.channel))
plt.xlabel('Time since %s' % zdat[0].stats.starttime)
plt.ylabel('Displacement [mm]')
if plotflag == 1:
plt.subplot(2,1,2)
plt.loglog(f, Y.real, 'k')
plt.loglog(F, YY.real)
plt.loglog(F, fit, 'g')
p1, = plt.loglog(f, Y.real, 'k')
p2, = plt.loglog(F, YY.real)
p3, = plt.loglog(F, YYcor, 'r')
p4, = plt.loglog(F, fit, 'g')
plt.loglog([fc, fc], [w0/100, w0], 'g')
plt.legend([p1, p2, p3, p4], ['Raw Spectrum', \
'Used Raw Spectrum', \
'Q-Corrected Spectrum', \
'Fit to Spectrum'])
plt.title('Source Spectrum from P Pulse, w0=%e m/Hz, fc=%6.2f Hz' \
% (w0, fc))
plt.xlabel('Frequency [Hz]')
@ -474,8 +547,13 @@ def fitSourceModel(f, S, fc0, iplot):
STD.append(stddc + stdFC)
# get best found w0 anf fc from minimum
if len(STD) > 0:
fc = fc[np.argmin(STD)]
w0 = w0[np.argmin(STD)]
elif len(STD) == 0:
fc = fc0
w0 = max(S)
print("fitSourceModel: best fc: %fHz, best w0: %e m/Hz" \
% (fc, w0))

View File

@ -204,7 +204,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
z_copy[0].data = tr_filt.data
zne = z_copy
if len(ndat) == 0 or len(edat) == 0:
msg = 'One or more horizontal components missing!\nSignal ' \
msg = 'One or more horizontal component(s) missing!\nSignal ' \
'length only checked on vertical component!\n' \
'Decreasing minsiglengh from {0} to ' \
'{1}'.format(minsiglength, minsiglength / 2)
@ -335,15 +335,15 @@ def autopickstation(wfstream, pickparam, verbose=False):
Sflag = 0
else:
print("autopickstation: No vertical component data available!, "
"Skipping station!")
print('autopickstation: No vertical component data available!, '
'Skipping station!')
if edat is not None and ndat is not None and len(edat) > 0 and len(
ndat) > 0 and Pweight < 4:
msg = "Go on picking S onset ...\n" \
"##################################################\n" \
"Working on S onset of station {0}\nFiltering horizontal " \
"traces ...".format(edat[0].stats.station)
msg = 'Go on picking S onset ...\n' \
'##################################################\n' \
'Working on S onset of station {0}\nFiltering horizontal ' \
'traces ...'.format(edat[0].stats.station)
if verbose: print(msg)
# determine time window for calculating CF after P onset
cuttimesh = [round(max([mpickP + sstart, 0])),
@ -424,6 +424,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
'SNR: {1}\nGo on with refined picking ...\n' \
'autopickstation: re-filtering horizontal traces ' \
'...'.format(aicarhpick.getSlope(), aicarhpick.getSNR())
if verbose: print(msg)
# re-calculate CF from re-filtered trace in vicinity of initial
# onset
cuttimesh2 = [round(aicarhpick.getpick() - Srecalcwin),
@ -774,7 +775,8 @@ def autopickstation(wfstream, pickparam, verbose=False):
# for P phase
phase = 'P'
phasepick = {'lpp': lpickP, 'epp': epickP, 'mpp': mpickP, 'spe': Perror,
'snr': SNRP, 'snrdb': SNRPdB, 'weight': Pweight, 'fm': FM}
'snr': SNRP, 'snrdb': SNRPdB, 'weight': Pweight, 'fm': FM,
'w0': None, 'fc': None, 'Mo': None, 'Mw': None}
picks = {phase: phasepick}
# add P marker
picks[phase]['marked'] = Pmarker

View File

@ -10,165 +10,60 @@ import numpy as np
from obspy.core import UTCDateTime
import obspy.core.event as ope
def runProgram(cmd, parameter=None):
"""
run an external program specified by cmd with parameters input returning the
stdout output
:param cmd: name of the command to run
:type cmd: str
:param parameter: filename of parameter file or parameter string
:type parameter: str
:return: stdout output
:rtype: str
"""
if parameter:
cmd.strip()
cmd += ' %s 2>&1' % parameter
output = subprocess.check_output('{} | tee /dev/stderr'.format(cmd),
shell = True)
def isSorted(iterable):
return sorted(iterable) == iterable
def fnConstructor(s):
if type(s) is str:
s = s.split(':')[-1]
else:
s = getHash(UTCDateTime())
badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
fn = badchars.sub('_', s)
if badsuffix.match(fn):
fn = '_' + fn
return fn
def getLogin():
return pwd.getpwuid(os.getuid())[0]
def getHash(time):
def createAmplitude(pickID, amp, unit, category, cinfo):
'''
:param time: time object for which a hash should be calculated
:type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
:return: str
:param pickID:
:param amp:
:param unit:
:param category:
:param cinfo:
:return:
'''
hg = hashlib.sha1()
hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
return hg.hexdigest()
amplitude = ope.Amplitude()
amplitude.creation_info = cinfo
amplitude.generic_amplitude = amp
amplitude.unit = ope.AmplitudeUnit(unit)
amplitude.type = ope.AmplitudeCategory(category)
amplitude.pick_id = pickID
return amplitude
def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None):
'''
createArrival - function to create an Obspy Arrival
def getOwner(fn):
return pwd.getpwuid(os.stat(fn).st_uid).pw_name
def getPatternLine(fn, pattern):
"""
Takes a file name and a pattern string to search for in the file and
returns the first line which contains the pattern string otherwise None.
:param fn: file name
:type fn: str
:param pattern: pattern string to search for
:type pattern: str
:return: the complete line containing pattern or None
>>> getPatternLine('utils.py', 'python')
'#!/usr/bin/env python\\n'
>>> print(getPatternLine('version.py', 'palindrome'))
None
"""
fobj = open(fn, 'r')
for line in fobj.readlines():
if pattern in line:
fobj.close()
return line
return None
def prepTimeAxis(stime, trace):
nsamp = trace.stats.npts
srate = trace.stats.sampling_rate
tincr = trace.stats.delta
etime = stime + nsamp / srate
time_ax = np.arange(stime, etime, tincr)
if len(time_ax) < nsamp:
print 'elongate time axes by one datum'
time_ax = np.arange(stime, etime + tincr, tincr)
elif len(time_ax) > nsamp:
print 'shorten time axes by one datum'
time_ax = np.arange(stime, etime - tincr, tincr)
if len(time_ax) != nsamp:
raise ValueError('{0} samples of data \n '
'{1} length of time vector \n'
'delta: {2}'.format(nsamp, len(time_ax), tincr))
return time_ax
def scaleWFData(data, factor=None, components='all'):
"""
produce scaled waveforms from given waveform data and a scaling factor,
waveform may be selected by their components name
:param data: waveform data to be scaled
:type data: `~obspy.core.stream.Stream` object
:param factor: scaling factor
:type factor: float
:param components: components labels for the traces in data to be scaled by
the scaling factor (optional, default: 'all')
:type components: tuple
:return: scaled waveform data
:rtype: `~obspy.core.stream.Stream` object
"""
if components is not 'all':
for comp in components:
if factor is None:
max_val = np.max(np.abs(data.select(component=comp)[0].data))
data.select(component=comp)[0].data /= 2 * max_val
:param pickresID: Resource identifier of the created pick
:type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object
:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
holding information on the creation of the returned object
:type cinfo: :class: `~obspy.core.event.CreationInfo` object
:param phase: name of the arrivals seismic phase
:type phase: str
:param azimuth: azimuth between source and receiver
:type azimuth: float or int, optional
:param dist: distance between source and receiver
:type dist: float or int, optional
:return: An ObsPy :class: `~obspy.core.event.Arrival` object
'''
arrival = ope.Arrival()
arrival.creation_info = cinfo
arrival.pick_id = pickresID
arrival.phase = phase
if azimuth is not None:
arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360.
else:
data.select(component=comp)[0].data /= 2 * factor
else:
for tr in data:
if factor is None:
max_val = float(np.max(np.abs(tr.data)))
tr.data /= 2 * max_val
else:
tr.data /= 2 * factor
return data
def demeanTrace(trace, window):
"""
returns the DATA where each trace is demean by the average value within
WINDOW
:param trace: waveform trace object
:type trace: `~obspy.core.stream.Trace`
:param inoise: range of indices of DATA within the WINDOW
:type window: tuple
:return: trace
:rtype: `~obspy.core.stream.Trace`
"""
trace.data -= trace.data[window].mean()
return trace
def getGlobalTimes(stream):
min_start = UTCDateTime()
max_end = None
for trace in stream:
if trace.stats.starttime < min_start:
min_start = trace.stats.starttime
if max_end is None or trace.stats.endtime > max_end:
max_end = trace.stats.endtime
return min_start, max_end
arrival.azimuth = azimuth
arrival.distance = dist
return arrival
def createCreationInfo(agency_id=None, creation_time=None, author=None):
'''
:param agency_id:
:param creation_time:
:param author:
:return:
'''
if author is None:
author = getLogin()
if creation_time is None:
@ -176,57 +71,6 @@ def createCreationInfo(agency_id=None, creation_time=None, author=None):
return ope.CreationInfo(agency_id=agency_id, author=author,
creation_time=creation_time)
def createResourceID(timetohash, restype, authority_id=None, hrstr=None):
'''
:param timetohash:
:param restype: type of the resource, e.g. 'orig', 'earthquake' ...
:type restype: str
:param authority_id: name of the institution carrying out the processing
:type authority_id: str, optional
:return:
'''
assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
"UTCDateTime object"
hid = getHash(timetohash)
if hrstr is None:
resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
else:
resID = ope.ResourceIdentifier(restype + '/' + hrstr + '_' + hid[0:6])
if authority_id is not None:
resID.convertIDToQuakeMLURI(authority_id=authority_id)
return resID
def createOrigin(origintime, cinfo, latitude, longitude, depth):
'''
createOrigin - function to create an ObsPy Origin
:param origintime: the origins time of occurence
:type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
:param latitude: latitude in decimal degree of the origins location
:type latitude: float
:param longitude: longitude in decimal degree of the origins location
:type longitude: float
:param depth: hypocentral depth of the origin
:type depth: float
:return: An ObsPy :class: `~obspy.core.event.Origin` object
'''
assert isinstance(origintime, UTCDateTime), "origintime has to be " \
"a UTCDateTime object, but " \
"actually is of type " \
"'%s'" % type(origintime)
origin = ope.Origin()
origin.time = origintime
origin.creation_info = cinfo
origin.latitude = latitude
origin.longitude = longitude
origin.depth = depth
return origin
def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None,
authority_id=None):
'''
@ -271,14 +115,60 @@ def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None,
event.origins = [o]
return event
def createMagnitude(originID, cinfo):
'''
createMagnitude - function to create an ObsPy Magnitude object
:param originID:
:type originID:
:param cinfo:
:type cinfo:
:return:
'''
magnitude = ope.Magnitude()
magnitude.creation_info = cinfo
magnitude.origin_id = originID
return magnitude
def createOrigin(origintime, cinfo, latitude, longitude, depth):
'''
createOrigin - function to create an ObsPy Origin
:param origintime: the origins time of occurence
:type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
:param cinfo:
:type cinfo:
:param latitude: latitude in decimal degree of the origins location
:type latitude: float
:param longitude: longitude in decimal degree of the origins location
:type longitude: float
:param depth: hypocentral depth of the origin
:type depth: float
:return: An ObsPy :class: `~obspy.core.event.Origin` object
'''
assert isinstance(origintime, UTCDateTime), "origintime has to be " \
"a UTCDateTime object, but " \
"actually is of type " \
"'%s'" % type(origintime)
origin = ope.Origin()
origin.time = origintime
origin.creation_info = cinfo
origin.latitude = latitude
origin.longitude = longitude
origin.depth = depth
return origin
def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
wfseedstr, authority_id):
'''
createPick - function to create an ObsPy Pick
:param origintime:
:type origintime:
:param picknum: number of the created pick
:type picknum: int
:param picktime:
:type picktime:
:param eventnum: human-readable event identifier
:type eventnum: str
:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
@ -306,64 +196,43 @@ def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
pick.waveform_id = ope.ResourceIdentifier(id=wfseedstr, prefix='file:/')
return pick
def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None):
def createResourceID(timetohash, restype, authority_id=None, hrstr=None):
'''
createArrival - function to create an Obspy Arrival
:param pickresID: Resource identifier of the created pick
:type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object
:param eventnum: human-readable event identifier
:type eventnum: str
:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
holding information on the creation of the returned object
:type cinfo: :class: `~obspy.core.event.CreationInfo` object
:param phase: name of the arrivals seismic phase
:type phase: str
:param station: name of the station at which the seismic phase has been
picked
:type station: str
:param timetohash:
:type timetohash
:param restype: type of the resource, e.g. 'orig', 'earthquake' ...
:type restype: str
:param authority_id: name of the institution carrying out the processing
:type authority_id: str
:param azimuth: azimuth between source and receiver
:type azimuth: float or int, optional
:param dist: distance between source and receiver
:type dist: float or int, optional
:return: An ObsPy :class: `~obspy.core.event.Arrival` object
'''
arrival = ope.Arrival()
arrival.creation_info = cinfo
arrival.pick_id = pickresID
arrival.phase = phase
if azimuth is not None:
arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360.
else:
arrival.azimuth = azimuth
arrival.distance = dist
return arrival
def createMagnitude(originID, cinfo):
'''
createMagnitude - function to create an ObsPy Magnitude object
:param originID:
:param cinfo:
:param authority_id:
:type authority_id: str, optional
:param hrstr:
:type hrstr:
:return:
'''
magnitude = ope.Magnitude()
magnitude.creation_info = cinfo
magnitude.origin_id = originID
return magnitude
assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
"UTCDateTime object"
hid = getHash(timetohash)
if hrstr is None:
resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
else:
resID = ope.ResourceIdentifier(restype + '/' + hrstr + '_' + hid[0:6])
if authority_id is not None:
resID.convertIDToQuakeMLURI(authority_id=authority_id)
return resID
def createAmplitude(pickID, amp, unit, category, cinfo):
amplitude = ope.Amplitude()
amplitude.creation_info = cinfo
amplitude.generic_amplitude = amp
amplitude.unit = ope.AmplitudeUnit(unit)
amplitude.type = ope.AmplitudeCategory(category)
amplitude.pick_id = pickID
return amplitude
def demeanTrace(trace, window):
"""
returns the DATA where each trace is demean by the average value within
WINDOW
:param trace: waveform trace object
:type trace: `~obspy.core.stream.Trace`
:param window:
:type window: tuple
:return: trace
:rtype: `~obspy.core.stream.Trace`
"""
trace.data -= trace.data[window].mean()
return trace
def findComboBoxIndex(combo_box, val):
"""
@ -372,11 +241,184 @@ def findComboBoxIndex(combo_box, val):
:param combo_box: Combo box object.
:type combo_box: QComboBox
:param val: Name of a combo box to search for.
:type val:
:return: index value of item with name val or 0
"""
return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
def fnConstructor(s):
'''
:param s:
:type s:
:return:
'''
if type(s) is str:
s = s.split(':')[-1]
else:
s = getHash(UTCDateTime())
badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
fn = badchars.sub('_', s)
if badsuffix.match(fn):
fn = '_' + fn
return fn
def getGlobalTimes(stream):
'''
:param stream:
:type stream
:return:
'''
min_start = UTCDateTime()
max_end = None
for trace in stream:
if trace.stats.starttime < min_start:
min_start = trace.stats.starttime
if max_end is None or trace.stats.endtime > max_end:
max_end = trace.stats.endtime
return min_start, max_end
def getHash(time):
'''
:param time: time object for which a hash should be calculated
:type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
:return: str
'''
hg = hashlib.sha1()
hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
return hg.hexdigest()
def getLogin():
'''
:return:
'''
return pwd.getpwuid(os.getuid())[0]
def getOwner(fn):
'''
:param fn:
:type fn:
:return:
'''
return pwd.getpwuid(os.stat(fn).st_uid).pw_name
def getPatternLine(fn, pattern):
"""
Takes a file name and a pattern string to search for in the file and
returns the first line which contains the pattern string otherwise None.
:param fn: file name
:type fn: str
:param pattern: pattern string to search for
:type pattern: str
:return: the complete line containing pattern or None
>>> getPatternLine('utils.py', 'python')
'#!/usr/bin/env python\\n'
>>> print(getPatternLine('version.py', 'palindrome'))
None
"""
fobj = open(fn, 'r')
for line in fobj.readlines():
if pattern in line:
fobj.close()
return line
return None
def isSorted(iterable):
'''
:param iterable:
:type iterable:
:return:
'''
return sorted(iterable) == iterable
def prepTimeAxis(stime, trace):
'''
:param stime:
:type stime:
:param trace:
:type trace:
:return:
'''
nsamp = trace.stats.npts
srate = trace.stats.sampling_rate
tincr = trace.stats.delta
etime = stime + nsamp / srate
time_ax = np.arange(stime, etime, tincr)
if len(time_ax) < nsamp:
print 'elongate time axes by one datum'
time_ax = np.arange(stime, etime + tincr, tincr)
elif len(time_ax) > nsamp:
print 'shorten time axes by one datum'
time_ax = np.arange(stime, etime - tincr, tincr)
if len(time_ax) != nsamp:
raise ValueError('{0} samples of data \n '
'{1} length of time vector \n'
'delta: {2}'.format(nsamp, len(time_ax), tincr))
return time_ax
def scaleWFData(data, factor=None, components='all'):
"""
produce scaled waveforms from given waveform data and a scaling factor,
waveform may be selected by their components name
:param data: waveform data to be scaled
:type data: `~obspy.core.stream.Stream` object
:param factor: scaling factor
:type factor: float
:param components: components labels for the traces in data to be scaled by
the scaling factor (optional, default: 'all')
:type components: tuple
:return: scaled waveform data
:rtype: `~obspy.core.stream.Stream` object
"""
if components is not 'all':
for comp in components:
if factor is None:
max_val = np.max(np.abs(data.select(component=comp)[0].data))
data.select(component=comp)[0].data /= 2 * max_val
else:
data.select(component=comp)[0].data /= 2 * factor
else:
for tr in data:
if factor is None:
max_val = float(np.max(np.abs(tr.data)))
tr.data /= 2 * max_val
else:
tr.data /= 2 * factor
return data
def runProgram(cmd, parameter=None):
"""
run an external program specified by cmd with parameters input returning the
stdout output
:param cmd: name of the command to run
:type cmd: str
:param parameter: filename of parameter file or parameter string
:type parameter: str
:return: stdout output
:rtype: str
"""
if parameter:
cmd.strip()
cmd += ' %s 2>&1' % parameter
output = subprocess.check_output('{} | tee /dev/stderr'.format(cmd),
shell = True)
if __name__ == "__main__":
import doctest
doctest.testmod()