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general code clean-up

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This commit is contained in:
Sebastian Wehling-Benatelli 2015-10-19 05:32:10 +02:00
parent b49206407a
commit 0fa701a878
30 changed files with 270 additions and 249 deletions
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2
autoPyLoT.py
View File

@ -8,11 +8,11 @@ import glob
import matplotlib.pyplot as plt
from obspy.core import read
from pylot.core.util import _getVersionString
from pylot.core.read.data import Data
from pylot.core.read.inputs import AutoPickParameter
from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.pick.autopick import autopickevent
from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()

8
icons.qrc
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@ -1,10 +1,10 @@
<RCC>
<qresource>
<file>icons/pylot.ico</file>
<file>icons/pylot.png</file>
<file>icons/pylot.ico</file>
<file>icons/pylot.png</file>
<file>icons/printer.png</file>
<file>icons/delete.png</file>
<file>icons/key_E.png</file>
<file>icons/key_E.png</file>
<file>icons/key_N.png</file>
<file>icons/key_P.png</file>
<file>icons/key_Q.png</file>
@ -14,7 +14,7 @@
<file>icons/key_U.png</file>
<file>icons/key_V.png</file>
<file>icons/key_W.png</file>
<file>icons/key_Z.png</file>
<file>icons/key_Z.png</file>
<file>icons/filter.png</file>
<file>icons/sync.png</file>
<file>icons/zoom_0.png</file>

1
pylot/core/__init__.py
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@ -0,0 +1 @@
# -*- coding: utf-8 -*-

1
pylot/core/active/__init__.py
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@ -1 +1,2 @@
# -*- coding: utf-8 -*-
__author__ = 'sebastianw'

5
pylot/core/active/activeSeismoPick.py
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@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
import sys
import numpy as np
from pylot.core.active import seismicshot
@ -144,8 +145,8 @@ class Survey(object):
def countAllTraces(self):
numtraces = 0
for line in self.getShotlist():
for line in self.getReceiverlist():
for shot in self.getShotlist():
for rec in self.getReceiverlist():
numtraces += 1
return numtraces

1
pylot/core/active/fmtomo2vtk.py
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@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
import numpy as np
def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk'):

1
pylot/core/active/picking_script.py
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@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
import sys
from obspy import read
from obspy import Stream

1
pylot/core/active/seismicArrayPreparation.py
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@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
import sys
import numpy as np
from scipy.interpolate import griddata

1
pylot/core/active/seismicArrayPreperation.py
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@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
import sys
import numpy as np
from scipy.interpolate import griddata

3
pylot/core/active/seismicshot.py
View File

@ -35,8 +35,7 @@ class SeismicShot(object):
self.snr = {}
self.snrthreshold = {}
self.timeArray = {}
self.paras = {}
self.paras['shotname'] = obsfile
self.paras = {'shotname': obsfile}
def removeEmptyTraces(self):
traceIDs = []

1
pylot/core/active/surveyPlotTools.py
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@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
plt.interactive(True)

1
pylot/core/analysis/__init__.py
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@ -0,0 +1 @@
# -*- coding: utf-8 -*-

2
pylot/core/analysis/coinctimes.py
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@ -6,7 +6,7 @@ from obspy.signal.trigger import coincidenceTrigger
class CoincidenceTimes():
class CoincidenceTimes(object):
def __init__(self, st, comp='Z', coinum=4, sta=1., lta=10., on=5., off=1.):
_type = 'recstalta'

3
pylot/core/analysis/magnitude.py
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@ -1,3 +1,4 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created August/September 2015.
@ -142,7 +143,7 @@ class DCfc(Magnitude):
'''
def calcsourcespec(self):
print ("Calculating source spectrum ....")
print ("Calculating source spectrum ....")
self.w0 = None # DC-value
self.fc = None # corner frequency

5
pylot/core/pick/CharFuns.py
View File

@ -1,3 +1,4 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created Oct/Nov 2014
@ -315,7 +316,7 @@ class ARZcf(CharacteristicFunction):
cf = np.zeros(len(xnp))
loopstep = self.getARdetStep()
arcalci = ldet + self.getOrder() #AR-calculation index
for i in range(ldet + self.getOrder(), tend - lpred - 1):
for i in range(ldet + self.getOrder(), tend - lpred - 1):
if i == arcalci:
#determination of AR coefficients
#to speed up calculation, AR-coefficients are calculated only every i+loopstep[1]!
@ -362,7 +363,7 @@ class ARZcf(CharacteristicFunction):
rhs = np.zeros(self.getOrder())
for k in range(0, self.getOrder()):
for i in range(rind, ldet+1):
ki = k + 1
ki = k + 1
rhs[k] = rhs[k] + data[i] * data[i - ki]
#recursive calculation of data array (second sum at left part of eq. 6.5 in Kueperkoch et al. 2012)

2
pylot/core/pick/Picker.py
View File

@ -312,7 +312,7 @@ class PragPicker(AutoPicking):
else:
for i in range(1, len(self.cf)):
if i > ismooth:
ii1 = i - ismooth;
ii1 = i - ismooth
cfsmooth[i] = cfsmooth[i - 1] + (self.cf[i] - self.cf[ii1]) / ismooth
else:
cfsmooth[i] = np.mean(self.cf[1 : i])

1
pylot/core/pick/__init__.py
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@ -1 +1,2 @@
# -*- coding: utf-8 -*-
#

46
pylot/core/pick/autopick.py
View File

@ -317,29 +317,29 @@ def autopickstation(wfstream, pickparam):
data = Data()
[corzdat, restflag] = data.restituteWFData(invdir, zdat)
if restflag == 1:
# integrate to displacement
corintzdat = integrate.cumtrapz(corzdat[0], None, corzdat[0].stats.delta)
# class needs stream object => build it
z_copy = zdat.copy()
z_copy[0].data = corintzdat
# largest detectable period == window length
# after P pulse for calculating source spectrum
winzc = (1 / bpz2[0]) * z_copy[0].stats.sampling_rate
impickP = mpickP * z_copy[0].stats.sampling_rate
wfzc = z_copy[0].data[impickP : impickP + winzc]
# calculate spectrum using only first cycles of
# waveform after P onset!
zc = crossings_nonzero_all(wfzc)
if np.size(zc) == 0:
print ("Something is wrong with the waveform, " \
"no zero crossings derived!")
print ("Cannot calculate source spectrum!")
else:
calcwin = (zc[3] - 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()
# integrate to displacement
corintzdat = integrate.cumtrapz(corzdat[0], None, corzdat[0].stats.delta)
# class needs stream object => build it
z_copy = zdat.copy()
z_copy[0].data = corintzdat
# largest detectable period == window length
# after P pulse for calculating source spectrum
winzc = (1 / bpz2[0]) * z_copy[0].stats.sampling_rate
impickP = mpickP * z_copy[0].stats.sampling_rate
wfzc = z_copy[0].data[impickP : impickP + winzc]
# calculate spectrum using only first cycles of
# waveform after P onset!
zc = crossings_nonzero_all(wfzc)
if np.size(zc) == 0:
print ("Something is wrong with the waveform, " \
"no zero crossings derived!")
print ("Cannot calculate source spectrum!")
else:
calcwin = (zc[3] - 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()
print ("autopickstation: P-weight: %d, SNR: %f, SNR[dB]: %f, " \
"Polarity: %s" % (Pweight, SNRP, SNRPdB, FM))

127
pylot/core/pick/utils.py
View File

@ -1,4 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# -*- coding: utf-8 -*-
"""
@ -493,9 +494,9 @@ def wadaticheck(pickdic, dttolerance, iplot):
if len(SPtimes) >= 3:
# calculate slope
p1 = np.polyfit(Ppicks, SPtimes, 1)
wdfit = np.polyval(p1, Ppicks)
# calculate slope
p1 = np.polyfit(Ppicks, SPtimes, 1)
wdfit = np.polyval(p1, Ppicks)
wfitflag = 0
# calculate vp/vs ratio before check
@ -532,40 +533,40 @@ def wadaticheck(pickdic, dttolerance, iplot):
pickdic[key]['S']['marked'] = marker
if len(checkedPpicks) >= 3:
# calculate new slope
p2 = np.polyfit(checkedPpicks, checkedSPtimes, 1)
wdfit2 = np.polyval(p2, checkedPpicks)
# calculate new slope
p2 = np.polyfit(checkedPpicks, checkedSPtimes, 1)
wdfit2 = np.polyval(p2, checkedPpicks)
# calculate vp/vs ratio after check
cvpvsr = p2[0] + 1
print ("wadaticheck: Average Vp/Vs ratio after check: %f" % cvpvsr)
print ("wadatacheck: Skipped %d S pick(s)" % ibad)
# calculate vp/vs ratio after check
cvpvsr = p2[0] + 1
print ("wadaticheck: Average Vp/Vs ratio after check: %f" % cvpvsr)
print ("wadatacheck: Skipped %d S pick(s)" % ibad)
else:
print ("###############################################")
print ("wadatacheck: Not enough checked S-P times available!")
print ("Skip Wadati check!")
print ("###############################################")
print ("wadatacheck: Not enough checked S-P times available!")
print ("Skip Wadati check!")
checkedonsets = pickdic
else:
print ("wadaticheck: Not enough S-P times available for reliable regression!")
print ("wadaticheck: Not enough S-P times available for reliable regression!")
print ("Skip wadati check!")
wfitflag = 1
# plot results
if iplot > 1:
plt.figure(iplot)
f1, = plt.plot(Ppicks, SPtimes, 'ro')
plt.figure(iplot)
f1, = plt.plot(Ppicks, SPtimes, 'ro')
if wfitflag == 0:
f2, = plt.plot(Ppicks, wdfit, 'k')
f3, = plt.plot(checkedPpicks, checkedSPtimes, 'ko')
f4, = plt.plot(checkedPpicks, wdfit2, 'g')
plt.title('Wadati-Diagram, %d S-P Times, Vp/Vs(raw)=%5.2f,' \
'Vp/Vs(checked)=%5.2f' % (len(SPtimes), vpvsr, cvpvsr))
plt.legend([f1, f2, f3, f4], ['Skipped S-Picks', 'Wadati 1', \
'Reliable S-Picks', 'Wadati 2'], loc='best')
f2, = plt.plot(Ppicks, wdfit, 'k')
f3, = plt.plot(checkedPpicks, checkedSPtimes, 'ko')
f4, = plt.plot(checkedPpicks, wdfit2, 'g')
plt.title('Wadati-Diagram, %d S-P Times, Vp/Vs(raw)=%5.2f,' \
'Vp/Vs(checked)=%5.2f' % (len(SPtimes), vpvsr, cvpvsr))
plt.legend([f1, f2, f3, f4], ['Skipped S-Picks', 'Wadati 1', \
'Reliable S-Picks', 'Wadati 2'], loc='best')
else:
plt.title('Wadati-Diagram, %d S-P Times' % len(SPtimes))
plt.title('Wadati-Diagram, %d S-P Times' % len(SPtimes))
plt.ylabel('S-P Times [s]')
plt.xlabel('P Times [s]')
@ -612,7 +613,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot):
print ("Checking signal length ...")
if len(X) > 1:
# all three components available
# all three components available
# make sure, all components have equal lengths
ilen = min([len(X[0].data), len(X[1].data), len(X[2].data)])
x1 = X[0][0:ilen]
@ -639,7 +640,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot):
numoverthr = len(np.where(rms[isignal] >= minsiglevel)[0])
if numoverthr >= minnum:
print ("checksignallength: Signal reached required length.")
print ("checksignallength: Signal reached required length.")
returnflag = 1
else:
print ("checksignallength: Signal shorter than required minimum signal length!")
@ -649,7 +650,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot):
if iplot == 2:
plt.figure(iplot)
p1, = plt.plot(t,rms, 'k')
p1, = plt.plot(t,rms, 'k')
p2, = plt.plot(t[inoise], rms[inoise], 'c')
p3, = plt.plot(t[isignal],rms[isignal], 'r')
p4, = plt.plot([t[isignal[0]], t[isignal[len(isignal)-1]]], \
@ -729,27 +730,27 @@ def checkPonsets(pickdic, dttolerance, iplot):
badjkmarker = 'badjkcheck'
for i in range(0, len(goodstations)):
# mark P onset as checked and keep P weight
pickdic[goodstations[i]]['P']['marked'] = goodmarker
pickdic[goodstations[i]]['P']['marked'] = goodmarker
for i in range(0, len(badstations)):
# mark P onset and downgrade P weight to 9
# (not used anymore)
pickdic[badstations[i]]['P']['marked'] = badmarker
pickdic[badstations[i]]['P']['weight'] = 9
# mark P onset and downgrade P weight to 9
# (not used anymore)
pickdic[badstations[i]]['P']['marked'] = badmarker
pickdic[badstations[i]]['P']['weight'] = 9
for i in range(0, len(badjkstations)):
# mark P onset and downgrade P weight to 9
# (not used anymore)
pickdic[badjkstations[i]]['P']['marked'] = badjkmarker
pickdic[badjkstations[i]]['P']['weight'] = 9
# mark P onset and downgrade P weight to 9
# (not used anymore)
pickdic[badjkstations[i]]['P']['marked'] = badjkmarker
pickdic[badjkstations[i]]['P']['weight'] = 9
checkedonsets = pickdic
if iplot > 1:
p1, = plt.plot(np.arange(0, len(Ppicks)), Ppicks, 'r+', markersize=14)
p1, = plt.plot(np.arange(0, len(Ppicks)), Ppicks, 'r+', markersize=14)
p2, = plt.plot(igood, np.array(Ppicks)[igood], 'g*', markersize=14)
p3, = plt.plot([0, len(Ppicks) - 1], [pmedian, pmedian], 'g', \
linewidth=2)
for i in range(0, len(Ppicks)):
plt.text(i, Ppicks[i] + 0.2, stations[i])
plt.text(i, Ppicks[i] + 0.2, stations[i])
plt.xlabel('Number of P Picks')
plt.ylabel('Onset Time [s] from 1.1.1970')
@ -789,37 +790,37 @@ def jackknife(X, phi, h):
g = len(X) / h
if type(g) is not int:
print ("jackknife: Cannot divide quantity X in equal sized subgroups!")
print ("jackknife: Cannot divide quantity X in equal sized subgroups!")
print ("Choose another size for subgroups!")
return PHI_jack, PHI_pseudo, PHI_sub
else:
# estimator of undisturbed spot check
if phi == 'MEA':
phi_sc = np.mean(X)
# estimator of undisturbed spot check
if phi == 'MEA':
phi_sc = np.mean(X)
elif phi == 'VAR':
phi_sc = np.var(X)
phi_sc = np.var(X)
elif phi == 'MED':
phi_sc = np.median(X)
phi_sc = np.median(X)
# estimators of subgroups
# estimators of subgroups
PHI_pseudo = []
PHI_sub = []
for i in range(0, g - 1):
# subgroup i, remove i-th sample
xx = X[:]
del xx[i]
# calculate estimators of disturbed spot check
if phi == 'MEA':
phi_sub = np.mean(xx)
elif phi == 'VAR':
phi_sub = np.var(xx)
elif phi == 'MED':
phi_sub = np.median(xx)
# subgroup i, remove i-th sample
xx = X[:]
del xx[i]
# calculate estimators of disturbed spot check
if phi == 'MEA':
phi_sub = np.mean(xx)
elif phi == 'VAR':
phi_sub = np.var(xx)
elif phi == 'MED':
phi_sub = np.median(xx)
PHI_sub.append(phi_sub)
# pseudo values
phi_pseudo = g * phi_sc - ((g - 1) * phi_sub)
PHI_pseudo.append(phi_pseudo)
PHI_sub.append(phi_sub)
# pseudo values
phi_pseudo = g * phi_sc - ((g - 1) * phi_sub)
PHI_pseudo.append(phi_pseudo)
# jackknife estimator
PHI_jack = np.mean(PHI_pseudo)
@ -899,17 +900,17 @@ def checkZ4S(X, pick, zfac, checkwin, iplot):
# vertical P-coda level must exceed horizontal P-coda level
# zfac times encodalevel
if zcodalevel < minsiglevel:
print ("checkZ4S: Maybe S onset? Skip this P pick!")
print ("checkZ4S: Maybe S onset? Skip this P pick!")
else:
print ("checkZ4S: P onset passes checkZ4S test!")
returnflag = 1
if iplot > 1:
te = np.arange(0, edat[0].stats.npts / edat[0].stats.sampling_rate,
te = np.arange(0, edat[0].stats.npts / edat[0].stats.sampling_rate,
edat[0].stats.delta)
tn = np.arange(0, ndat[0].stats.npts / ndat[0].stats.sampling_rate,
tn = np.arange(0, ndat[0].stats.npts / ndat[0].stats.sampling_rate,
ndat[0].stats.delta)
plt.plot(tz, z / max(z), 'k')
plt.plot(tz, z / max(z), 'k')
plt.plot(tz[isignal], z[isignal] / max(z), 'r')
plt.plot(te, edat[0].data / max(edat[0].data) + 1, 'k')
plt.plot(te[isignal], edat[0].data[isignal] / max(edat[0].data) + 1, 'r')

2
pylot/core/read/__init__.py
View File

@ -1 +1 @@
# -*- coding: utf-8 -*-

3
pylot/core/read/inputs.py
View File

@ -208,8 +208,7 @@ class FilterOptions(object):
def parseFilterOptions(self):
if self.getFilterType():
robject = {'type':self.getFilterType()}
robject['corners'] = self.getOrder()
robject = {'type': self.getFilterType(), 'corners': self.getOrder()}
if len(self.getFreq()) > 1:
robject['freqmin'] = self.getFreq()[0]
robject['freqmax'] = self.getFreq()[1]

1
pylot/core/util/__init__.py
View File

@ -1 +1,2 @@
# -*- coding: utf-8 -*-
from pylot.core.util.version import get_git_version as _getVersionString

1
pylot/core/util/testUtils.py
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@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
'''
Created on 10.11.2014

1
pylot/core/util/testWidgets.py
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@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
'''
Created on 10.11.2014

1
pylot/core/util/thread.py
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@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
import sys
from PySide.QtCore import QThread, Signal

1
pylot/core/util/utils.py
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@ -1,4 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# -*- coding: utf-8 -*-

1
testHelpForm.py
View File

@ -1,4 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys, time
from PySide.QtGui import QApplication

1
testPickDlg.py
View File

@ -1,4 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import matplotlib

1
testPropDlg.py
View File

@ -1,4 +1,5 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys, time
from PySide.QtGui import QApplication

10
testUIcomponents.py
View File

@ -1,4 +1,6 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys, time
from PySide.QtGui import QApplication
@ -9,7 +11,7 @@ dialogs = [FilterOptionsDialog, PropertiesDlg, HelpForm]
app = QApplication(sys.argv)
for dlg in dialogs:
win = dlg()
win.show()
time.sleep(1)
win.destroy()
win = dlg()
win.show()
time.sleep(1)
win.destroy()