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Merge branch 'develop' of ariadne.geophysik.rub.de:/data/git/pylot into develop

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Conflicts:
	pylot/core/pick/utils.py
This commit is contained in:
Ludger Küperkoch 2015-06-22 11:27:01 +02:00
commit 635ac1686b
3 changed files with 115 additions and 64 deletions
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100
pylot/core/pick/utils.py
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@ -49,13 +49,13 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
t = np.arange(0, X[0].stats.npts / X[0].stats.sampling_rate, t = np.arange(0, X[0].stats.npts / X[0].stats.sampling_rate,
X[0].stats.delta) X[0].stats.delta)
# get latest possible pick # get latest possible pick
#get noise window # get noise window
inoise = getnoisewin(t, Pick1, TSNR[0], TSNR[1]) inoise = getnoisewin(t, Pick1, TSNR[0], TSNR[1])
#get signal window # get signal window
isignal = getsignalwin(t, Pick1, TSNR[2]) isignal = getsignalwin(t, Pick1, TSNR[2])
#calculate noise level # calculate noise level
nlevel = np.sqrt(np.mean(np.square(x[inoise]))) * nfac nlevel = np.sqrt(np.mean(np.square(x[inoise]))) * nfac
#get time where signal exceeds nlevel # get time where signal exceeds nlevel
ilup, = np.where(x[isignal] > nlevel) ilup, = np.where(x[isignal] > nlevel)
ildown, = np.where(x[isignal] < -nlevel) ildown, = np.where(x[isignal] < -nlevel)
if not ilup.size and not ildown.size: if not ilup.size and not ildown.size:
@ -64,17 +64,17 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
np.min(ildown) if ildown.size else float('inf')) np.min(ildown) if ildown.size else float('inf'))
LPick = t[isignal][il] LPick = t[isignal][il]
#get earliest possible pick # get earliest possible pick
#determine all zero crossings in signal window # determine all zero crossings in signal window (demeaned)
zc = crossings_nonzero_all(x[isignal]) zc = crossings_nonzero_all(x[isignal] - x[isignal].mean())
#calculate mean half period T0 of signal as the average of the # 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 = 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! # T0/4 is assumed as time difference between most likely and earliest possible pick!
EPick = Pick1 - T0 / 2 EPick = Pick1 - T0 / 2
#get symmetric pick error as mean from earliest and latest possible pick # get symmetric pick error as mean from earliest and latest possible pick
#by weighting latest possible pick two times earliest possible pick # by weighting latest possible pick two times earliest possible pick
diffti_tl = LPick - Pick1 diffti_tl = LPick - Pick1
diffti_te = Pick1 - EPick diffti_te = Pick1 - EPick
PickError = (diffti_te + 2 * diffti_tl) / 3 PickError = (diffti_te + 2 * diffti_tl) / 3
@ -85,7 +85,8 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
p2, = plt.plot(t[inoise], x[inoise]) p2, = plt.plot(t[inoise], x[inoise])
p3, = plt.plot(t[isignal], x[isignal], 'r') p3, = plt.plot(t[isignal], x[isignal], 'r')
p4, = plt.plot([t[0], t[int(len(t)) - 1]], [nlevel, nlevel], '--k') p4, = plt.plot([t[0], t[int(len(t)) - 1]], [nlevel, nlevel], '--k')
p5, = plt.plot(t[isignal[0][zc]], np.zeros(len(zc)), '*g', markersize=14) p5, = plt.plot(t[isignal[0][zc]], np.zeros(len(zc)), '*g',
markersize=14)
plt.legend([p1, p2, p3, p4, p5], plt.legend([p1, p2, p3, p4, p5],
['Data', 'Noise Window', 'Signal Window', 'Noise Level', ['Data', 'Noise Window', 'Signal Window', 'Noise Level',
'Zero Crossings'], \ 'Zero Crossings'], \
@ -150,13 +151,13 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
# get pick window # get pick window
ipick = np.where( ipick = np.where(
(t <= min([Pick + pickwin, len(Xraw[0])])) & (t >= Pick)) (t <= min([Pick + pickwin, len(Xraw[0])])) & (t >= Pick))
#remove mean # remove mean
xraw[ipick] = xraw[ipick] - np.mean(xraw[ipick]) xraw[ipick] = xraw[ipick] - np.mean(xraw[ipick])
xfilt[ipick] = xfilt[ipick] - np.mean(xfilt[ipick]) xfilt[ipick] = xfilt[ipick] - np.mean(xfilt[ipick])
#get next zero crossing after most likely pick # get next zero crossing after most likely pick
#initial onset is assumed to be the first zero crossing # initial onset is assumed to be the first zero crossing
#first from unfiltered trace # first from unfiltered trace
zc1 = [] zc1 = []
zc1.append(Pick) zc1.append(Pick)
index1 = [] index1 = []
@ -172,9 +173,9 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
if len(zc1) == 3: if len(zc1) == 3:
break break
#if time difference betweeen 1st and 2cnd zero crossing # if time difference betweeen 1st and 2cnd zero crossing
#is too short, get time difference between 1st and 3rd # is too short, get time difference between 1st and 3rd
#to derive maximum # to derive maximum
if zc1[1] - zc1[0] <= Xraw[0].stats.delta: if zc1[1] - zc1[0] <= Xraw[0].stats.delta:
li1 = index1[1] li1 = index1[1]
else: else:
@ -185,13 +186,13 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
else: else:
imax1 = np.argmax(abs(xraw[ipick[0][1]:ipick[0][li1]])) imax1 = np.argmax(abs(xraw[ipick[0][1]:ipick[0][li1]]))
islope1 = np.where((t >= Pick) & (t <= Pick + t[imax1])) islope1 = np.where((t >= Pick) & (t <= Pick + t[imax1]))
#calculate slope as polynomal fit of order 1 # calculate slope as polynomal fit of order 1
xslope1 = np.arange(0, len(xraw[islope1]), 1) xslope1 = np.arange(0, len(xraw[islope1]), 1)
P1 = np.polyfit(xslope1, xraw[islope1], 1) P1 = np.polyfit(xslope1, xraw[islope1], 1)
datafit1 = np.polyval(P1, xslope1) datafit1 = np.polyval(P1, xslope1)
#now using filterd trace # now using filterd trace
#next zero crossing after most likely pick # next zero crossing after most likely pick
zc2 = [] zc2 = []
zc2.append(Pick) zc2.append(Pick)
index2 = [] index2 = []
@ -207,9 +208,9 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
if len(zc2) == 3: if len(zc2) == 3:
break break
#if time difference betweeen 1st and 2cnd zero crossing # if time difference betweeen 1st and 2cnd zero crossing
#is too short, get time difference between 1st and 3rd # is too short, get time difference between 1st and 3rd
#to derive maximum # to derive maximum
if zc2[1] - zc2[0] <= Xfilt[0].stats.delta: if zc2[1] - zc2[0] <= Xfilt[0].stats.delta:
li2 = index2[1] li2 = index2[1]
else: else:
@ -220,12 +221,12 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
else: else:
imax2 = np.argmax(abs(xfilt[ipick[0][1]:ipick[0][li2]])) imax2 = np.argmax(abs(xfilt[ipick[0][1]:ipick[0][li2]]))
islope2 = np.where((t >= Pick) & (t <= Pick + t[imax2])) islope2 = np.where((t >= Pick) & (t <= Pick + t[imax2]))
#calculate slope as polynomal fit of order 1 # calculate slope as polynomal fit of order 1
xslope2 = np.arange(0, len(xfilt[islope2]), 1) xslope2 = np.arange(0, len(xfilt[islope2]), 1)
P2 = np.polyfit(xslope2, xfilt[islope2], 1) P2 = np.polyfit(xslope2, xfilt[islope2], 1)
datafit2 = np.polyval(P2, xslope2) datafit2 = np.polyval(P2, xslope2)
#compare results # compare results
if P1 is not None and P2 is not None: if P1 is not None and P2 is not None:
if P1[0] < 0 and P2[0] < 0: if P1[0] < 0 and P2[0] < 0:
FM = 'D' FM = 'D'
@ -281,11 +282,13 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
return FM return FM
def crossings_nonzero_all(data): def crossings_nonzero_all(data):
pos = data > 0 pos = data > 0
npos = ~pos npos = ~pos
return ((pos[:-1] & npos[1:]) | (npos[:-1] & pos[1:])).nonzero()[0] return ((pos[:-1] & npos[1:]) | (npos[:-1] & pos[1:])).nonzero()[0]
def getSNR(X, TSNR, t1): def getSNR(X, TSNR, t1):
''' '''
Function to calculate SNR of certain part of seismogram relative to Function to calculate SNR of certain part of seismogram relative to
@ -312,7 +315,7 @@ def getSNR(X, TSNR, t1):
# get noise window # get noise window
inoise = getnoisewin(t, t1, TSNR[0], TSNR[1]) inoise = getnoisewin(t, t1, TSNR[0], TSNR[1])
#get signal window # get signal window
isignal = getsignalwin(t, t1, TSNR[2]) isignal = getsignalwin(t, t1, TSNR[2])
if np.size(inoise) < 1: if np.size(inoise) < 1:
print 'getSNR: Empty array inoise, check noise window!' print 'getSNR: Empty array inoise, check noise window!'
@ -321,7 +324,7 @@ def getSNR(X, TSNR, t1):
print 'getSNR: Empty array isignal, check signal window!' print 'getSNR: Empty array isignal, check signal window!'
return return
#calculate ratios # calculate ratios
noiselevel = np.sqrt(np.mean(np.square(x[inoise]))) noiselevel = np.sqrt(np.mean(np.square(x[inoise])))
signallevel = np.sqrt(np.mean(np.square(x[isignal]))) signallevel = np.sqrt(np.mean(np.square(x[isignal])))
SNR = signallevel / noiselevel SNR = signallevel / noiselevel
@ -383,6 +386,7 @@ def getsignalwin(t, t1, tsignal):
return isignal return isignal
def wadaticheck(pickdic, dttolerance, iplot): def wadaticheck(pickdic, dttolerance, iplot):
''' '''
Function to calculate Wadati-diagram from given P and S onsets in order Function to calculate Wadati-diagram from given P and S onsets in order
@ -413,12 +417,18 @@ def wadaticheck(pickdic, dttolerance, iplot):
# add S-P time to dictionary # add S-P time to dictionary
pickdic[key]['SPt'] = spt pickdic[key]['SPt'] = spt
# add P onsets and corresponding S-P times to list # add P onsets and corresponding S-P times to list
UTCPpick = UTCDateTime(pickdic[key]['P']['mpp']) UTCPpick = UTCDateTime(pickdic[key]['P']['mpp']) - UTCDateTime(1970,
UTCSpick = UTCDateTime(pickdic[key]['S']['mpp']) 1, 1,
Ppicks.append(UTCPpick.timestamp) 0, 0,
Spicks.append(UTCSpick.timestamp) 0)
UTCSpick = UTCDateTime(pickdic[key]['S']['mpp']) - UTCDateTime(1970,
1, 1,
0, 0,
0)
Ppicks.append(UTCPpick)
Spicks.append(UTCSpick)
SPtimes.append(spt) SPtimes.append(spt)
vpvs.append(UTCPpick / UTCSpick)
if len(SPtimes) >= 3: if len(SPtimes) >= 3:
# calculate slope # calculate slope
@ -447,12 +457,16 @@ def wadaticheck(pickdic, dttolerance, iplot):
pickdic[key]['S']['weight'] = 9 pickdic[key]['S']['weight'] = 9
else: else:
marker = 'goodWadatiCheck' marker = 'goodWadatiCheck'
checkedPpick = UTCDateTime(pickdic[key]['P']['mpp']) checkedPpick = UTCDateTime(pickdic[key]['P']['mpp']) - \
checkedPpicks.append(checkedPpick.timestamp) UTCDateTime(1970, 1, 1, 0, 0, 0)
checkedSpick = UTCDateTime(pickdic[key]['S']['mpp']) checkedPpicks.append(checkedPpick)
checkedSpicks.append(checkedSpick.timestamp) checkedSpick = UTCDateTime(pickdic[key]['S']['mpp']) - \
checkedSPtime = pickdic[key]['S']['mpp'] - pickdic[key]['P']['mpp'] UTCDateTime(1970, 1, 1, 0, 0, 0)
checkedSpicks.append(checkedSpick)
checkedSPtime = pickdic[key]['S']['mpp'] - \
pickdic[key]['P']['mpp']
checkedSPtimes.append(checkedSPtime) checkedSPtimes.append(checkedSPtime)
checkedvpvs.append(checkedPpick / checkedSpick)
pickdic[key]['S']['marked'] = marker pickdic[key]['S']['marked'] = marker
@ -482,9 +496,11 @@ def wadaticheck(pickdic, dttolerance, iplot):
f4, = plt.plot(checkedPpicks, wdfit2, 'g') f4, = plt.plot(checkedPpicks, wdfit2, 'g')
plt.ylabel('S-P Times [s]') plt.ylabel('S-P Times [s]')
plt.xlabel('P Times [s]') plt.xlabel('P Times [s]')
plt.title('Wadati-Diagram, %d S-P Times, Vp/Vs(raw)=%5.2f, Vp/Vs(checked)=%5.2f' \ plt.title(
'Wadati-Diagram, %d S-P Times, Vp/Vs(old)=%5.2f, Vp/Vs(checked)=%5.2f' \
% (len(SPtimes), vpvsr, cvpvsr)) % (len(SPtimes), vpvsr, cvpvsr))
plt.legend([f1, f2, f3, f4], ['Skipped S-Picks', 'Wadati 1', 'Reliable S-Picks', \ plt.legend([f1, f2, f3, f4],
['Skipped S-Picks', 'Wadati 1', 'Reliable S-Picks', \
'Wadati 2'], loc='best') 'Wadati 2'], loc='best')
plt.show() plt.show()
raw_input() raw_input()

13
pylot/core/read/inputs.py
View File

@ -206,6 +206,19 @@ class FilterOptions(object):
order=self.getOrder()) order=self.getOrder())
return hrs return hrs
def parseFilterOptions(self):
if self.getFilterType():
robject = {'type':self.getFilterType()}
robject['order'] = self.getOrder()
if len(self.getFreq()) > 1:
robject['freqmin'] = self.getFreq()[0]
robject['freqmax'] = self.getFreq()[1]
else:
robject['freq'] = self.getFreq() if type(self.getFreq()) is \
float else self.getFreq()[0]
return robject
return None
def getFreq(self): def getFreq(self):
return self.__getattribute__('_freq') return self.__getattribute__('_freq')

22
pylot/core/util/utils.py
View File

@ -3,6 +3,7 @@
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import os import os
import subprocess
import pwd import pwd
import re import re
import hashlib import hashlib
@ -10,6 +11,27 @@ import numpy as np
from obspy.core import UTCDateTime from obspy.core import UTCDateTime
import obspy.core.event as ope 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 fnConstructor(s): def fnConstructor(s):
if type(s) is str: if type(s) is str: