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

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This commit is contained in:
Marcel Paffrath 2015-11-12 19:09:08 +01:00
commit 165419cb88
5 changed files with 93 additions and 37 deletions
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54
autoPyLoT.py
View File

@ -6,7 +6,7 @@ import os
import argparse
import glob
import subprocess
import string
from obspy.core import read
from pylot.core.read.data import Data
from pylot.core.read.inputs import AutoPickParameter
@ -88,7 +88,9 @@ def autoPyLoT(inputfile):
nllocoutpatter = parameter.getParam('outpatter')
else:
locflag = 0
print ("!!No location routine available, autoPyLoT just picks the events without locating them!!")
print (" !!! ")
print ("!!No location routine available, autoPyLoT is running in non-location mode!!")
print (" !!! ")
# multiple event processing
@ -99,7 +101,6 @@ def autoPyLoT(inputfile):
data.setWFData(glob.glob(os.path.join(datapath, event, '*')))
print('Working on event %s' % event)
print(data)
wfdat = data.getWFData() # all available streams
##########################################################
# !automated picking starts here!
@ -114,7 +115,8 @@ def autoPyLoT(inputfile):
# For locating the event the NLLoc-control file has to be modified!
# create comment line for NLLoc-control file
# NLLoc-output file
nllocout = '%s/loc/%s_%s' % (nllocroot, event, nllocoutpatter)
evID = event[string.rfind(event, "/") + 1 : len(events) - 1]
nllocout = '%s/loc/%s_%s' % (nllocroot, evID, nllocoutpatter)
locfiles = 'LOCFILES %s NLLOC_OBS %s %s 0' % (phasefile, ttpatter, nllocout)
print ("Modifying NLLoc-control file %s ..." % locfile)
# modification of NLLoc-control file
@ -130,20 +132,28 @@ def autoPyLoT(inputfile):
# locate the event
subprocess.call([nlloccall, locfile])
# !iterative picking if traces remained unpicked or with bad picks!
# get theoretical onset times for picks with weights >= 4
# in order to reprocess them using smaller time windows
##########################################################
# write phase files for various location routines
# HYPO71
hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, eventID)
hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, evID)
writephases(picks, 'HYPO71', hypo71file)
print '------------------------------------------'
print '-----Finished event %s!-----' % event
print '------------------------------------------'
endsplash = '''------------------------------------------\n'
-----Finished event %s!-----\n'
------------------------------------------'''.format \
(version=_getVersionString()) % evID
print(endsplash)
if locflag == 0:
print("autoPyLoT was running in non-location mode!")
# single event processing
else:
data.setWFData(glob.glob(os.path.join(datapath, parameter.getParam('eventID'), '*')))
print 'Working on event ', parameter.getParam('eventID')
print("Working on event "), parameter.getParam('eventID')
print data
wfdat = data.getWFData() # all available streams
@ -175,22 +185,30 @@ def autoPyLoT(inputfile):
# locate the event
subprocess.call([nlloccall, locfile])
# !iterative picking if traces remained unpicked or with bad picks!
# get theoretical onset times for picks with weights >= 4
# in order to reprocess them using smaller time windows
##########################################################
# write phase files for various location routines
# HYPO71
hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, parameter.getParam('eventID'))
writephases(picks, 'HYPO71', hypo71file)
endsplash = '''------------------------------------------\n'
-----Finished event %s!-----\n'
------------------------------------------'''.format \
(version=_getVersionString()) % parameter.getParam('eventID')
print(endsplash)
if locflag == 0:
print("autoPyLoT was running in non-location mode!")
print '------------------------------------------'
print '-------Finished event %s!-------' % parameter.getParam('eventID')
print '------------------------------------------'
print '####################################'
print '************************************'
print '*********autoPyLoT terminates*******'
print 'The Python picking and Location Tool'
print '************************************'
endsp = '''####################################\n
************************************\n
*********autoPyLoT terminates*******\n
The Python picking and Location Tool\n
************************************'''.format(version=_getVersionString())
print(endsp)
if __name__ == "__main__":
# parse arguments

18
pylot/core/loc/nll.py
View File

@ -2,8 +2,13 @@
# -*- coding: utf-8 -*-
import subprocess
import os
from obspy.core.event import readEvents
from pylot.core.pick.utils import writephases
from pylot.core.util.utils import getPatternLine
from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
def picksExport(picks, phasefile):
'''
@ -16,7 +21,7 @@ def picksExport(picks, phasefile):
# write phases to NLLoc-phase file
writephases(picks, 'NLLoc', phasefile)
def modfiyInputFile(fn, root, outpath, phasefile, tttable):
def modfiyInputFile(fn, root, outpath, phasefn, tttn):
'''
:param fn:
@ -29,18 +34,21 @@ def modfiyInputFile(fn, root, outpath, phasefile, tttable):
# For locating the event we have to modify the NLLoc-control file!
# create comment line for NLLoc-control file NLLoc-output file
print ("Modifying NLLoc-control file %s ..." % fn)
nllocout = '%s/loc/%s_%s' % (root, outpath)
locfiles = 'LOCFILES %s NLLOC_OBS %s %s 0' % (phasefile, tttable, nllocout)
nllocout = os.path.join(root,'loc', outpath)
phasefile = os.path.join(root, 'obs', phasefn)
tttable = os.path.join(root, 'time', tttn)
locfiles = 'LOCFILES %s NLLOC_OBS %s %s 0\n' % (phasefile, tttable, nllocout)
# modification of NLLoc-control file
curlocfiles = getPatternLine(fn, 'LOCFILES')
nllfile = open(fn, 'r')
filedata = nllfile.read()
if filedata.find(locfiles) < 0:
# replace old command
filedata = filedata.replace('LOCFILES', locfiles)
filedata = filedata.replace(curlocfiles, locfiles)
nllfile = open(fn, 'w')
nllfile.write(filedata)
nllfile.close()
nllfile.close()
def locate(call, fnin):
'''

17
pylot/core/pick/autopick.py
View File

@ -28,7 +28,6 @@ def autopickevent(data, param):
wdttolerance = param.getParam('wdttolerance')
mdttolerance = param.getParam('mdttolerance')
iplot = param.getParam('iplot')
for n in range(len(data)):
station = data[n].stats.station
if station not in stations:
@ -141,6 +140,8 @@ def autopickstation(wfstream, pickparam):
# split components
zdat = wfstream.select(component="Z")
if len(zdat) == 0: # check for other components
zdat = wfstream.select(component="3")
edat = wfstream.select(component="E")
if len(edat) == 0: # check for other components
edat = wfstream.select(component="2")
@ -330,17 +331,17 @@ def autopickstation(wfstream, pickparam):
# calculate spectrum using only first cycles of
# waveform after P onset!
zc = crossings_nonzero_all(wfzc)
if np.size(zc) == 0:
if np.size(zc) == 0 or len(zc) <= 3:
print ("Something is wrong with the waveform, "
"no zero crossings derived!")
print ("Cannot calculate source spectrum!")
else:
index = min([3, len(zc) - 1])
calcwin = (zc[index] - zc[0]) * z_copy[0].stats.delta
# calculate source spectrum and get w0 and fc
specpara = DCfc(z_copy, mpickP, calcwin, iplot)
w0 = specpara.getw0()
fc = specpara.getfc()
# calculate source spectrum and get w0 and fc
specpara = DCfc(z_copy, mpickP, calcwin, iplot)
w0 = specpara.getw0()
fc = specpara.getfc()
print ("autopickstation: P-weight: %d, SNR: %f, SNR[dB]: %f, "
"Polarity: %s" % (Pweight, SNRP, SNRPdB, FM))
@ -759,12 +760,12 @@ def autopickstation(wfstream, pickparam):
plt.close()
##########################################################################
# calculate "real" onset times
if mpickP is not None:
if mpickP is not None and epickP is not None and mpickP is not None:
lpickP = zdat[0].stats.starttime + lpickP
epickP = zdat[0].stats.starttime + epickP
mpickP = zdat[0].stats.starttime + mpickP
if mpickS is not None:
if mpickS is not None and epickS is not None and mpickS is not None:
lpickS = edat[0].stats.starttime + lpickS
epickS = edat[0].stats.starttime + epickS
mpickS = edat[0].stats.starttime + mpickS

11
pylot/core/pick/utils.py
View File

@ -8,7 +8,7 @@
:author: Ludger Kueperkoch / MAGS2 EP3 working group
"""
import pdb
import numpy as np
import matplotlib.pyplot as plt
from obspy.core import Stream, UTCDateTime
@ -91,9 +91,8 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, stealthMode = False):
# determine all zero crossings in signal window (demeaned)
zc = crossings_nonzero_all(x[pis] - x[pis].mean())
# calculate mean half period T0 of signal as the average of the
T0 = np.mean(np.diff(zc)) * X[0].stats.delta # this is half wave length
# T0/4 is assumed as time difference between most likely and earliest possible pick!
EPick = Pick1 - T0 / 2
T0 = np.mean(np.diff(zc)) * X[0].stats.delta # this is half wave length!
EPick = Pick1 - T0 # half wavelength as suggested by Diehl et al.
# get symmetric pick error as mean from earliest and latest possible pick
@ -867,6 +866,8 @@ def checkZ4S(X, pick, zfac, checkwin, iplot):
# split components
zdat = X.select(component="Z")
if len(zdat) == 0: # check for other components
zdat = X.select(component="3")
edat = X.select(component="E")
if len(edat) == 0: # check for other components
edat = X.select(component="2")
@ -962,6 +963,8 @@ def writephases(arrivals, fformat, filename):
for key in arrivals:
if arrivals[key]['P']['weight'] < 4:
fm = arrivals[key]['P']['fm']
if fm == None:
fm = '?'
onset = arrivals[key]['P']['mpp']
year = onset.year
month = onset.month

30
pylot/core/util/utils.py
View File

@ -1,7 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# -*- coding: utf-8 -*-
import os
import subprocess
@ -69,6 +67,30 @@ def getHash(time):
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
@ -342,3 +364,7 @@ def createAmplitude(pickID, amp, unit, category, cinfo):
amplitude.type = ope.AmplitudeCategory(category)
amplitude.pick_id = pickID
return amplitude
if __name__ == "__main__":
import doctest
doctest.testmod()