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[reformat] code reformatting with PyCharm

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This commit is contained in:
Marcel Paffrath 2017-08-03 09:41:54 +02:00
parent 4107f0249d
commit 20b31a1c5c
49 changed files with 3255 additions and 3194 deletions
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13
QtPyLoT.py
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@ -23,10 +23,11 @@ https://www.iconfinder.com/iconsets/flavour
(http://www.gnu.org/copyleft/lesser.html)
"""
import os
import sys
import platform
import argparse
import os
import platform
import sys
import matplotlib
matplotlib.use('Qt4Agg')
@ -66,10 +67,10 @@ from pylot.core.pick.compare import Comparison
from pylot.core.pick.utils import symmetrize_error
from pylot.core.io.phases import picksdict_from_picks
import pylot.core.loc.nll as nll
from pylot.core.util.defaults import FILTERDEFAULTS, OUTPUTFORMATS, SetChannelComponents, \
from pylot.core.util.defaults import FILTERDEFAULTS, SetChannelComponents, \
readFilterInformation
from pylot.core.util.errors import FormatError, DatastructureError, \
OverwriteError, ProcessingError
OverwriteError
from pylot.core.util.connection import checkurl
from pylot.core.util.dataprocessing import read_metadata, restitute_data
from pylot.core.util.utils import fnConstructor, getLogin, \
@ -81,7 +82,7 @@ from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
getDataType, ComparisonDialog, TuneAutopicker, PylotParaBox
from pylot.core.util.map_projection import map_projection
from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.util.thread import AutoPickThread, Thread, Worker
from pylot.core.util.thread import Thread, Worker
from pylot.core.util.version import get_git_version as _getVersionString
if sys.version_info.major == 3:

29
autoPyLoT.py
View File

@ -4,18 +4,19 @@
from __future__ import print_function
import argparse
import datetime
import glob
import os
import datetime
from obspy import read_events
from obspy.core.event import ResourceIdentifier
import pylot.core.loc.hyposat as hyposat
import pylot.core.loc.hypo71 as hypo71
import pylot.core.loc.velest as velest
import pylot.core.loc.hypodd as hypodd
import pylot.core.loc.focmec as focmec
import pylot.core.loc.hash as hash
import pylot.core.loc.hypo71 as hypo71
import pylot.core.loc.hypodd as hypodd
import pylot.core.loc.hyposat as hyposat
import pylot.core.loc.nll as nll
import pylot.core.loc.velest as velest
from obspy import read_events
from obspy.core.event import ResourceIdentifier
# from PySide.QtGui import QWidget, QInputDialog
from pylot.core.analysis.magnitude import MomentMagnitude, LocalMagnitude
from pylot.core.io.data import Data
@ -23,16 +24,17 @@ from pylot.core.io.inputs import PylotParameter
from pylot.core.pick.autopick import autopickevent, iteratepicker
from pylot.core.util.dataprocessing import restitute_data, read_metadata, \
remove_underscores
from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.util.version import get_git_version as _getVersionString
from pylot.core.util.event import Event
from pylot.core.util.utils import real_None
from pylot.core.util.defaults import SEPARATOR
from pylot.core.util.event import Event
from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.util.utils import real_None
from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, eventid=None, savepath=None, station='all', iplot=0):
def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, eventid=None, savepath=None, station='all',
iplot=0):
"""
Determine phase onsets automatically utilizing the automatic picking
algorithms by Kueperkoch et al. 2010/2012.
@ -310,7 +312,8 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
if input_dict:
if 'fig_dict' in input_dict:
fig_dict = input_dict['fig_dict']
picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter, fig_dict=fig_dict)
picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter,
fig_dict=fig_dict)
else:
picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
# write phases to NLLoc-phase file

6
help/index.html
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@ -1,4 +1,5 @@
<html><head><title>PyLoT - the Python picking and Localisation Tool</title></head>
<html>
<head><title>PyLoT - the Python picking and Localisation Tool</title></head>
<body>
<p><b>PyLoT</b> is a program which is capable of picking seismic phases,
exporting these as numerous standard phase format and localize the corresponding
@ -14,4 +15,5 @@ seismic event with external software as, e.g.:</p>
<p>Bug reports are very much appreciated and can also be delivered on our
<a href="https://ariadne.geophysik.rub.de/trac/PyLoT">PyLoT TracPage</a> after
successful registration.</p>
</body></html>
</body>
</html>

2
makePyLoT.py
View File

@ -190,8 +190,6 @@ def installPyLoT(verbosity=None):
os.symlink(destination, link_dest)
def cleanUp(verbosity=None):
if verbosity >= 1:
print('cleaning up build files...')

9
pylot/core/analysis/magnitude.py
View File

@ -6,16 +6,16 @@ Revised/extended summer 2017.
:author: Ludger Küperkoch / MAGS2 EP3 working group
"""
import os
import matplotlib.pyplot as plt
import numpy as np
import obspy.core.event as ope
from obspy.geodetics import degrees2kilometers
from scipy import integrate, signal
from scipy.optimize import curve_fit
from pylot.core.pick.utils import getsignalwin, crossings_nonzero_all, \
select_for_phase
from pylot.core.util.utils import common_range, fit_curve
from scipy import integrate, signal
from scipy.optimize import curve_fit
def richter_magnitude_scaling(delta):
distance = np.array([0, 10, 20, 25, 30, 35, 40, 45, 50, 60, 70, 75, 85, 90, 100, 110,
@ -276,7 +276,8 @@ class LocalMagnitude(Magnitude):
a0 = a0 * 1e03 # mm to nm (see Havskov & Ottemöller, 2010)
magnitude = ope.StationMagnitude(mag=np.log10(a0) \
+ self.wascaling[0] * np.log10(delta) + self.wascaling[1]
* delta + self.wascaling[2])
* delta + self.wascaling[
2])
magnitude.origin_id = self.origin_id
magnitude.waveform_id = pick.waveform_id
magnitude.amplitude_id = amplitude.resource_id

6
pylot/core/analysis/magnitude.py.orig
View File

@ -12,6 +12,7 @@ from obspy.core import Stream
from pylot.core.pick.utils import getsignalwin
from scipy.optimize import curve_fit
class Magnitude(object):
'''
Superclass for calculating Wood-Anderson peak-to-peak
@ -45,7 +46,6 @@ class Magnitude(object):
self.calcwapp()
self.calcsourcespec()
def getwfstream(self):
return self.wfstream
@ -85,6 +85,7 @@ class Magnitude(object):
def calcsourcespec(self):
self.sourcespek = None
class WApp(Magnitude):
'''
Method to derive peak-to-peak amplitude as seen on a Wood-Anderson-
@ -188,14 +189,12 @@ class DCfc(Magnitude):
print("DCfc: Determined DC-value: %e m/Hz, \n" \
"Determined corner frequency: %f Hz" % (self.w0, self.fc))
# if self.getiplot() > 1:
iplot = 2
if iplot > 1:
print("DCfc: Determined DC-value: %e m/Hz, \n"
"Determined corner frequency: %f Hz" % (self.w0, self.fc))
if self.getiplot() > 1:
f1 = plt.figure()
plt.subplot(2, 1, 1)
@ -239,4 +238,3 @@ def synthsourcespec(f, omega0, fcorner):
ssp = omega0 / (1 + pow(2, (f / fcorner)))
return ssp

10
pylot/core/io/data.py
View File

@ -3,15 +3,17 @@
import copy
import os
from obspy import read_events
from obspy.core import read, Stream, UTCDateTime
from obspy.io.sac import SacIOError
from obspy.core.event import Event as ObsPyEvent
from obspy.io.sac import SacIOError
from pylot.core.io.phases import readPILOTEvent, picks_from_picksdict, \
picksdict_from_pilot, merge_picks
from pylot.core.util.errors import FormatError, OverwriteError
from pylot.core.util.utils import fnConstructor, full_range
from pylot.core.util.event import Event
from pylot.core.util.utils import fnConstructor, full_range
class Data(object):
"""
@ -273,7 +275,6 @@ class Data(object):
del evtdata_copy.picks[i]
break
if fnext == '.obs':
try:
evtdata_copy.write(fnout + fnext, format=evtformat)
@ -297,7 +298,6 @@ class Data(object):
raise KeyError('''{0} export format
not implemented: {1}'''.format(evtformat, e))
def getComp(self):
"""
@ -449,7 +449,6 @@ class Data(object):
# ID.convertIDToQuakeMLURI(authority_id=authority_id)
# self.get_evt_data().resource_id = ID
def applyEvent(event):
"""
takes an `obspy.core.event.Event` object and applies all new
@ -478,7 +477,6 @@ class Data(object):
self._new = False
class GenericDataStructure(object):
"""
GenericDataBase type holds all information about the current data-

3
pylot/core/io/inputs.py
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@ -1,8 +1,9 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from pylot.core.util.errors import ParameterError
from pylot.core.io import default_parameters
from pylot.core.util.errors import ParameterError
class PylotParameter(object):
'''

49
pylot/core/io/phases.py
View File

@ -2,22 +2,23 @@
# -*- coding: utf-8 -*-
import glob
import obspy.core.event as ope
from obspy.core.event import read_events
import os
import scipy.io as sio
import warnings
import matplotlib.pyplot as plt
import numpy as np
import warnings
import obspy.core.event as ope
import scipy.io as sio
from obspy.core import UTCDateTime
from obspy.core.event import read_events
from obspy.core.util import AttribDict
from pylot.core.io.inputs import PylotParameter
from pylot.core.io.location import create_arrival, create_event, \
create_magnitude, create_origin, create_pick
from pylot.core.io.location import create_event, \
create_magnitude
from pylot.core.pick.utils import select_for_phase
from pylot.core.util.utils import getOwner, full_range, four_digits
def add_amplitudes(event, amplitudes):
amplitude_list = []
for pick in event.picks:
@ -36,6 +37,7 @@ def add_amplitudes(event, amplitudes):
event.amplitudes = amplitude_list
return event
def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
"""
readPILOTEvent - function
@ -233,6 +235,7 @@ def picksdict_from_picks(evt):
picks[station] = onsets.copy()
return picks
def picks_from_picksdict(picks, creation_info=None):
picks_list = list()
for station, onsets in picks.items():
@ -297,7 +300,6 @@ def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0
reassess_pilot_event(root_dir, db_dir, evt, out_dir, fn_param, verbosity)
def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None, verbosity=0):
from obspy import read
@ -305,7 +307,6 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
from pylot.core.pick.utils import earllatepicker
if fn_param is None:
import pylot.core.util.defaults as defaults
fn_param = defaults.AUTOMATIC_DEFAULTS
default = PylotParameter(fn_param, verbosity)
@ -339,7 +340,8 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
except Exception as e:
if 'No file matching file pattern:' in e.message:
if verbosity > 0:
warnings.warn('no waveform data found for station {station}'.format(station=station), RuntimeWarning)
warnings.warn('no waveform data found for station {station}'.format(station=station),
RuntimeWarning)
datacheck.append(fn_pattern + ' (no data)\n')
continue
else:
@ -707,8 +709,11 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
stime = eventsource['time']
# write header line including event information
fid.write('%s %d%02d%02d%02d%02d%02.0f %7.4f %6.4f %3.1f %3.1f\n' % (parameter.get('eventID'),
stime.year, stime.month, stime.day, stime.hour, stime.minute, stime.second,
eventsource['latitude'], eventsource['longitude'], eventsource['depth'] / 1000,
stime.year, stime.month, stime.day,
stime.hour, stime.minute, stime.second,
eventsource['latitude'],
eventsource['longitude'],
eventsource['depth'] / 1000,
eventinfo.magnitudes[0]['mag']))
picks = eventinfo.picks
for key in arrivals:
@ -766,13 +771,19 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
# write header line including event information
# for HASH-driver 1
fid1.write('%s%02d%02d%02d%02d%5.2f%2dN%5.2f%3dE%5.2f%6.3f%4.2f%5.2f%5.2f%s\n' % (syear,
stime.month, stime.day, stime.hour, stime.minute, stime.second,
latdeg, latmin, londeg, lonmin, eventsource['depth'],
eventinfo.magnitudes[0]['mag'], erh, erz,
stime.month, stime.day,
stime.hour, stime.minute,
stime.second,
latdeg, latmin, londeg,
lonmin, eventsource['depth'],
eventinfo.magnitudes[0][
'mag'], erh, erz,
hashID))
# write header line including event information
# for HASH-driver 2
fid2.write('%d%02d%02d%02d%02d%5.2f%dN%5.2f%3dE%6.2f%5.2f %d %5.2f %5.2f %4.2f %s \n' % (syear, stime.month, stime.day,
fid2.write(
'%d%02d%02d%02d%02d%5.2f%dN%5.2f%3dE%6.2f%5.2f %d %5.2f %5.2f %4.2f %s \n' % (
syear, stime.month, stime.day,
stime.hour, stime.minute, stime.second,
latdeg, latmin, londeg, lonmin,
eventsource['depth'],
@ -809,7 +820,9 @@ def writephases(arrivals, fformat, filename, parameter, eventinfo=None):
inz = eventinfo.origins[0].arrivals[j].get('takeoff_angle')
dist = eventinfo.origins[0].arrivals[j].get('distance')
# write phase line for HASH-driver 1
fid1.write('%-4s%sP%s%d 0 %3.1f %03d %03d 2 1 %s\n' % (stat, Pqual, arrivals[key]['P']['fm'], arrivals[key]['P']['weight'],
fid1.write(
'%-4s%sP%s%d 0 %3.1f %03d %03d 2 1 %s\n' % (
stat, Pqual, arrivals[key]['P']['fm'], arrivals[key]['P']['weight'],
dist, inz, az, ccode))
# write phase line for HASH-driver 2
fid2.write('%-4s %s %s %s %s \n' % (
@ -849,6 +862,7 @@ def merge_picks(event, picks):
del time, err, phase, station, network, method
return event
def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
"""
Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
@ -994,4 +1008,3 @@ def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
plt.xlabel('Qualities')
plt.title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights))
plt.show()

1
pylot/core/loc/focmec.py
View File

@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
def export(picks, fnout, parameter, eventinfo):
'''
Take <picks> dictionary and exports picking data to a focmec

1
pylot/core/loc/hash.py
View File

@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
def export(picks, fnout, parameter, eventinfo):
'''
Take <picks> dictionary and exports picking data to a HASH

1
pylot/core/loc/hypo71.py
View File

@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
def export(picks, fnout, parameter):
'''
Take <picks> dictionary and exports picking data to a HYPO71

1
pylot/core/loc/hypodd.py
View File

@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
def export(picks, fnout, parameter, eventinfo):
'''
Take <picks> dictionary and exports picking data to a hypoDD

1
pylot/core/loc/hyposat.py
View File

@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
def export(picks, fnout, parameter):
'''
Take <picks> dictionary and exports picking data to a HYPOSAT

7
pylot/core/loc/nll.py
View File

@ -1,9 +1,10 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import subprocess
import os
import glob
import os
import subprocess
from obspy import read_events
from pylot.core.io.phases import writephases
from pylot.core.util.utils import getPatternLine, runProgram, which
@ -11,9 +12,11 @@ from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
class NLLocError(EnvironmentError):
pass
def export(picks, fnout, parameter):
'''
Take <picks> dictionary and exports picking data to a NLLOC-obs

1
pylot/core/loc/velest.py
View File

@ -6,6 +6,7 @@ from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
def export(picks, fnout, parameter, eventinfo):
'''
Take <picks> dictionary and exports picking data to a VELEST-cnv

4
pylot/core/pick/autopick.py
View File

@ -11,14 +11,14 @@ function conglomerate utils.
import matplotlib.pyplot as plt
import numpy as np
from pylot.core.io.data import Data
from pylot.core.io.inputs import PylotParameter
from pylot.core.pick.picker import AICPicker, PragPicker
from pylot.core.pick.charfuns import CharacteristicFunction
from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
from pylot.core.pick.picker import AICPicker, PragPicker
from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
getSNR, fmpicker, checkPonsets, wadaticheck
from pylot.core.util.utils import getPatternLine, gen_Pool
from pylot.core.io.data import Data
def autopickevent(data, param, iplot=0, fig_dict=None):

1
pylot/core/pick/charfuns.py
View File

@ -17,7 +17,6 @@ autoregressive prediction: application ot local and regional distances, Geophys.
:author: MAGS2 EP3 working group
"""
import matplotlib.pyplot as plt
import numpy as np
from obspy.core import Stream

8
pylot/core/pick/compare.py
View File

@ -4,11 +4,10 @@
import copy
import operator
import os
import numpy as np
import glob
import matplotlib.pyplot as plt
from obspy import read_events
import matplotlib.pyplot as plt
import numpy as np
from obspy import read_events
from pylot.core.io.phases import picksdict_from_picks
from pylot.core.util.pdf import ProbabilityDensityFunction
from pylot.core.util.utils import find_in_list
@ -352,7 +351,6 @@ class PDFstatistics(object):
Takes a path as argument.
"""
def __init__(self, directory):
"""Initiates some values needed when dealing with pdfs later"""
self._rootdir = directory

21
pylot/core/pick/picker.py
View File

@ -19,12 +19,13 @@ calculated after Diehl & Kissling (2009).
:author: MAGS2 EP3 working group / Ludger Kueperkoch
"""
import numpy as np
import matplotlib.pyplot as plt
from pylot.core.pick.utils import getnoisewin, getsignalwin
from pylot.core.pick.charfuns import CharacteristicFunction
import warnings
import matplotlib.pyplot as plt
import numpy as np
from pylot.core.pick.charfuns import CharacteristicFunction
from pylot.core.pick.utils import getnoisewin, getsignalwin
class AutoPicker(object):
'''
@ -288,12 +289,16 @@ class AICPicker(AutoPicker):
ax2 = fig.add_subplot(2, 1, 2, sharex=ax1)
ax2.plot(self.Tcf, x, 'k', label='Data')
ax1.axvspan(self.Tcf[inoise[0]], self.Tcf[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
ax1.axvspan(self.Tcf[isignal[0]],self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
ax1.axvspan(self.Tcf[iislope[0]],self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0, label='Slope Window')
ax1.axvspan(self.Tcf[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0,
label='Signal Window')
ax1.axvspan(self.Tcf[iislope[0]], self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0,
label='Slope Window')
ax2.axvspan(self.Tcf[inoise[0]], self.Tcf[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
ax2.axvspan(self.Tcf[isignal[0]],self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
ax2.axvspan(self.Tcf[iislope[0]],self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0, label='Slope Window')
ax2.axvspan(self.Tcf[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0,
label='Signal Window')
ax2.axvspan(self.Tcf[iislope[0]], self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0,
label='Slope Window')
ax2.plot(self.Tcf[iislope], datafit, 'g', linewidth=2, label='Slope')
ax1.set_title('Station %s, SNR=%7.2f, Slope= %12.2f counts/s' % (self.Data[0].stats.station,

3
pylot/core/pick/utils.py
View File

@ -9,6 +9,7 @@
"""
import warnings
import matplotlib.pyplot as plt
import numpy as np
from obspy.core import Stream, UTCDateTime
@ -645,12 +646,14 @@ def wadaticheck(pickdic, dttolerance, iplot):
return checkedonsets
def RMS(X):
'''
Function returns root mean square of a given array X
'''
return np.sqrt(np.sum(np.power(X, 2)) / len(X))
def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fig=None):
'''
Function to detect spuriously picked noise peaks.

22
pylot/core/pick/utils.py.orig
View File

@ -8,12 +8,12 @@
:author: Ludger Kueperkoch / MAGS2 EP3 working group
"""
import pdb
import numpy as np
import matplotlib.pyplot as plt
from obspy.core import Stream, UTCDateTime
import warnings
import matplotlib.pyplot as plt
import numpy as np
from obspy.core import Stream, UTCDateTime
def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, stealthMode=False):
'''
@ -45,7 +45,8 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, stealthMode = False):
EPick = None
PickError = None
if stealthMode is False:
print 'earllatepicker: Get earliest and latest possible pick relative to most likely pick ...'
print
'earllatepicker: Get earliest and latest possible pick relative to most likely pick ...'
x = X[0].data
t = np.arange(0, X[0].stats.npts / X[0].stats.sampling_rate,
@ -70,7 +71,8 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, stealthMode = False):
# get earliest possible pick
EPick = np.nan; count = 0
EPick = np.nan;
count = 0
pis = isignal
# if EPick stays NaN the signal window size will be doubled
@ -97,7 +99,6 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, stealthMode = False):
# T0/4 is assumed as time difference between most likely and earliest possible pick!
EPick = Pick1 - T0 / 2
# get symmetric pick error as mean from earliest and latest possible pick
# by weighting latest possible pick two times earliest possible pick
diffti_tl = LPick - Pick1
@ -496,7 +497,6 @@ def wadaticheck(pickdic, dttolerance, iplot):
Spicks.append(UTCSpick.timestamp)
SPtimes.append(spt)
if len(SPtimes) >= 3:
# calculate slope
p1 = np.polyfit(Ppicks, SPtimes, 1)
@ -876,7 +876,6 @@ def checkZ4S(X, pick, zfac, checkwin, iplot):
if len(ndat) == 0: # check for other components
ndat = X.select(component="1")
z = zdat[0].data
tz = np.arange(0, zdat[0].stats.npts / zdat[0].stats.sampling_rate,
zdat[0].stats.delta)
@ -955,7 +954,6 @@ def writephases(arrivals, fformat, filename):
:type: string
'''
if fformat == 'NLLoc':
print("Writing phases to %s for NLLoc" % filename)
fid = open("%s" % filename, 'w')
@ -994,9 +992,7 @@ def writephases(arrivals, fformat, filename):
fid.close()
if __name__ == '__main__':
import doctest
doctest.testmod()

3
pylot/core/util/dataprocessing.py
View File

@ -1,12 +1,11 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import glob
import os
import sys
import numpy as np
from obspy import UTCDateTime, read_inventory, read
from obspy.io.xseed import Parser
from pylot.core.util.utils import key_for_set_value, find_in_list, \

10
pylot/core/util/defaults.py
View File

@ -9,17 +9,19 @@ Created on Wed Feb 26 12:31:25 2014
import os
import platform
from pylot.core.loc import nll
from pylot.core.loc import hyposat
from pylot.core.io.inputs import PylotParameter
from pylot.core.loc import hypo71
from pylot.core.loc import hypodd
from pylot.core.loc import hyposat
from pylot.core.loc import nll
from pylot.core.loc import velest
from pylot.core.io.inputs import PylotParameter
def readDefaultFilterInformation(fname):
pparam = PylotParameter(fname)
return readFilterInformation(pparam)
def readFilterInformation(pylot_parameter):
p_filter = {'filtertype': pylot_parameter['filter_type'][0],
'freq': [pylot_parameter['minfreq'][0], pylot_parameter['maxfreq'][0]],
@ -31,6 +33,7 @@ def readFilterInformation(pylot_parameter):
'S': s_filter}
return filter_information
# determine system dependent path separator
system_name = platform.system()
if system_name in ["Linux", "Darwin"]:
@ -107,4 +110,3 @@ class SetChannelComponents(object):
else:
errMsg = 'getCompPosition: Unrecognized component {}. Expecting one of {} or {}.'
raise ValueError(errMsg.format(component, self.compPosition_Map.keys(), self.compName_Map.keys()))

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

@ -25,5 +25,6 @@ class OverwriteError(IOError):
class ParameterError(Exception):
pass
class ProcessingError(RuntimeError):
pass

2
pylot/core/util/event.py
View File

@ -6,7 +6,6 @@ import os
from obspy import UTCDateTime
from obspy.core.event import Event as ObsPyEvent
from obspy.core.event import Origin, ResourceIdentifier
from pylot.core.io.phases import picks_from_picksdict
@ -14,6 +13,7 @@ class Event(ObsPyEvent):
'''
Pickable class derived from ~obspy.core.event.Event containing information on a single event.
'''
def __init__(self, path):
self.pylot_id = path.split('/')[-1]
# initialize super class

15
pylot/core/util/map_projection.py
View File

@ -1,16 +1,15 @@
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import numpy as np
import obspy
from matplotlib import cm
from scipy.interpolate import griddata
from PySide import QtGui
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
from PySide import QtCore, QtGui
from mpl_toolkits.basemap import Basemap
from pylot.core.util.widgets import PickDlg
from scipy.interpolate import griddata
plt.interactive(False)
class map_projection(QtGui.QWidget):
def __init__(self, parent, figure=None):
'''
@ -136,6 +135,7 @@ class map_projection(QtGui.QWidget):
def init_picks(self):
phase = self.comboBox_phase.currentText()
def get_picks(station_names):
picks = []
for station in station_names:
@ -235,7 +235,8 @@ class map_projection(QtGui.QWidget):
def init_picksgrid(self):
self.picksgrid_no_nan = griddata((self.lat_no_nan, self.lon_no_nan),
self.picks_no_nan, (self.latgrid, self.longrid), method='linear') ##################
self.picks_no_nan, (self.latgrid, self.longrid),
method='linear') ##################
def draw_contour_filled(self, nlevel='50'):
levels = np.linspace(min(self.picks_no_nan), max(self.picks_no_nan), nlevel)
@ -369,5 +370,3 @@ class map_projection(QtGui.QWidget):
self.qmb = QtGui.QMessageBox(QtGui.QMessageBox.Icon.Warning,
'Warning', message)
self.qmb.show()

8
pylot/core/util/pdf.py
View File

@ -2,20 +2,23 @@
# -*- coding: utf-8 -*-
import warnings
import numpy as np
from obspy import UTCDateTime
from pylot.core.util.utils import fit_curve, find_nearest, clims
from pylot.core.util.utils import fit_curve, clims
from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
__author__ = 'sebastianw'
def create_axis(x0, incr, npts):
ax = np.zeros(npts)
for i in range(npts):
ax[i] = x0 + incr * i
return ax
def gauss_parameter(te, tm, tl, eta):
'''
takes three onset times and returns the parameters sig1, sig2, a1 and a2
@ -394,7 +397,6 @@ class ProbabilityDensityFunction(object):
qu = self.quantile(1 - prob_value)
return qu - ql
def quantile_dist_frac(self, x):
"""
takes a probability value and returns the fraction of two
@ -413,7 +415,6 @@ class ProbabilityDensityFunction(object):
raise ValueError('Value out of range.')
return self.quantile_distance(0.5 - x) / self.quantile_distance(x)
def plot(self, label=None):
import matplotlib.pyplot as plt
@ -486,4 +487,3 @@ class ProbabilityDensityFunction(object):
x0, npts = self.commonlimits(incr, other)
return x0, incr, npts

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

@ -3,6 +3,7 @@
import matplotlib.pyplot as plt
def create_bin_list(l_boundary, u_boundary, nbins=100):
"""
takes two boundaries and a number of bins and creates a list of bins for

6
pylot/core/util/thread.py
View File

@ -1,6 +1,9 @@
# -*- coding: utf-8 -*-
import sys, os, traceback
import multiprocessing
import os
import sys
import traceback
from PySide.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
from PySide.QtGui import QDialog, QProgressBar, QLabel, QHBoxLayout, QPushButton
@ -109,6 +112,7 @@ class Worker(QRunnable):
'''
'''
def __init__(self, fun, args,
progressText=None,
pb_widget=None,

15
pylot/core/util/utils.py
View File

@ -2,15 +2,15 @@
# -*- coding: utf-8 -*-
import hashlib
import numpy as np
from scipy.interpolate import splrep, splev
import os
import platform
import re
import warnings
import subprocess
import numpy as np
from obspy import UTCDateTime, read
from pylot.core.io.inputs import PylotParameter
from scipy.interpolate import splrep, splev
def _pickle_method(m):
@ -19,9 +19,11 @@ def _pickle_method(m):
else:
return getattr, (m.im_self, m.im_func.func_name)
def fit_curve(x, y):
return splev, splrep(x, y)
def getindexbounds(f, eta):
mi = f.argmax()
m = max(f)
@ -106,6 +108,7 @@ def findComboBoxIndex(combo_box, val):
"""
return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
def find_in_list(list, str):
"""
takes a list of strings and a string and returns the first list item
@ -135,6 +138,7 @@ def find_in_list(list, str):
return rlist[0]
return None
def find_nearest(array, value):
'''
function find_nearest takes an array and a value and returns the
@ -181,12 +185,14 @@ def fnConstructor(s):
fn = '_' + fn
return fn
def real_None(value):
if value == 'None':
return None
else:
return value
def four_digits(year):
"""
takes a two digit year integer and returns the correct four digit equivalent
@ -307,6 +313,7 @@ def getPatternLine(fn, pattern):
return None
def is_executable(fn):
"""
takes a filename and returns True if the file is executable on the system
@ -492,6 +499,7 @@ def runProgram(cmd, parameter=None):
subprocess.check_output('{} | tee /dev/stderr'.format(cmd), shell=True)
def which(program, infile=None):
"""
takes a program name and returns the full path to the executable or None
@ -538,6 +546,7 @@ def which(program, infile=None):
return None
if __name__ == "__main__":
import doctest

23
pylot/core/util/widgets.py
View File

@ -5,16 +5,15 @@ Created on Wed Mar 19 11:27:35 2014
@author: sebastianw
"""
import os
import sys
import multiprocessing
import subprocess
import getpass
import warnings
import copy
import datetime
import getpass
import multiprocessing
import os
import subprocess
import sys
import numpy as np
import matplotlib.pyplot as plt
try:
import pyqtgraph as pg
@ -33,7 +32,7 @@ from matplotlib.widgets import MultiCursor
from PySide import QtCore, QtGui
from PySide.QtGui import QAction, QApplication, QCheckBox, QComboBox, \
QDateTimeEdit, QDialog, QDialogButtonBox, QDoubleSpinBox, QGroupBox, \
QGridLayout, QIcon, QKeySequence, QLabel, QLineEdit, QMessageBox, \
QGridLayout, QIcon, QLabel, QLineEdit, QMessageBox, \
QPixmap, QSpinBox, QTabWidget, QToolBar, QVBoxLayout, QHBoxLayout, QWidget, \
QPushButton, QFileDialog, QInputDialog, QKeySequence
from PySide.QtCore import QSettings, Qt, QUrl, Signal, Slot
@ -48,16 +47,16 @@ from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
getResolutionWindow
from pylot.core.pick.compare import Comparison
from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS, ALTSUFFIX, \
LOCTOOLS, SetChannelComponents
SetChannelComponents
from pylot.core.util.utils import prepTimeAxis, full_range, scaleWFData, \
demeanTrace, isSorted, findComboBoxIndex, clims
from autoPyLoT import autoPyLoT
from pylot.core.util.thread import Thread
if sys.version_info.major == 3:
import icons_rc_3 as icons_rc
pass
elif sys.version_info.major == 2:
import icons_rc_2 as icons_rc
pass
else:
raise ImportError('Could not determine python version.')
@ -118,6 +117,7 @@ def createAction(parent, text, slot=None, shortcut=None, icon=None,
action.setCheckable(True)
return action
def loopIdentifyPhase(phase):
phase_copy = phase
while not identifyPhase(phase_copy):
@ -133,6 +133,7 @@ def loopIdentifyPhase(phase):
return
return phase_copy
def identifyPhase(phase):
# common phase suffix for P and S
common_P = ['P', 'p']

3
pylot/testing/testHelpForm.py
View File

@ -1,7 +1,8 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys, time
import sys
from PySide.QtGui import QApplication
from pylot.core.util.widgets import HelpForm

2
pylot/testing/testPickDlg.py
View File

@ -2,6 +2,7 @@
# -*- coding: utf-8 -*-
import sys
import matplotlib
matplotlib.use('Qt4Agg')
@ -10,7 +11,6 @@ matplotlib.rcParams['backend.qt4'] = 'PySide'
from PySide.QtGui import QApplication
from obspy.core import read
from pylot.core.util.widgets import PickDlg
import icons_rc
app = QApplication(sys.argv)

3
pylot/testing/testPropDlg.py
View File

@ -1,7 +1,8 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys, time
import sys
from PySide.QtGui import QApplication
from pylot.core.util.widgets import PropertiesDlg

4
pylot/testing/testUIcomponents.py
View File

@ -2,7 +2,9 @@
# -*- coding: utf-8 -*-
import sys, time
import sys
import time
from PySide.QtGui import QApplication
from pylot.core.util.widgets import FilterOptionsDialog, PropertiesDlg, HelpForm

4
pylot/testing/testUtils.py
View File

@ -8,16 +8,12 @@ import unittest
class Test(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def testName(self):
pass

2
pylot/testing/testWidgets.py
View File

@ -8,8 +8,6 @@ import unittest
class Test(unittest.TestCase):
def testName(self):
pass

30
pylot/testing/test_autopick.py
View File

@ -6,13 +6,13 @@
Only for test purposes!
"""
import argparse
import glob
from obspy.core import read
import matplotlib.pyplot as plt
import numpy as np
from pylot.core.pick.charfuns import *
from pylot.core.pick.picker import *
import glob
import argparse
def run_makeCF(project, database, event, iplot, station=None):
# parameters for CF calculation
@ -52,8 +52,10 @@ def run_makeCF(project, database, event, iplot, station=None):
wfnfiles = glob.glob(dpn)
if wfzfiles:
for i in range(len(wfzfiles)):
print 'Vertical component data found ...'
print wfzfiles[i]
print
'Vertical component data found ...'
print
wfzfiles[i]
st = read('%s' % wfzfiles[i])
st_copy = st.copy()
# filter and taper data
@ -100,13 +102,17 @@ def run_makeCF(project, database, event, iplot, station=None):
# get earliest and latest possible picks
arzELpick = EarlLatePicker(arzcf, 1.5, TSNRarz, None, 10, None, None, arzpick.getpick())
elif not wfzfiles:
print 'No vertical component data found!'
print
'No vertical component data found!'
if wfefiles and wfnfiles:
for i in range(len(wfefiles)):
print 'Horizontal component data found ...'
print wfefiles[i]
print wfnfiles[i]
print
'Horizontal component data found ...'
print
wfefiles[i]
print
wfnfiles[i]
# merge streams
H = read('%s' % wfefiles[i])
H += read('%s' % wfnfiles[i])
@ -195,7 +201,8 @@ def run_makeCF(project, database, event, iplot, station=None):
plt.xlabel('Time [s]')
plt.ylabel('Normalized Counts')
plt.title('%s, %s, CF-SNR=%7.2f, CF-Slope=%12.2f' % (tr.stats.station, \
tr.stats.channel, aicpick.getSNR(), aicpick.getSlope()))
tr.stats.channel, aicpick.getSNR(),
aicpick.getSlope()))
plt.suptitle(tr.stats.starttime)
plt.legend([p1, p2, p3, p4, p5], ['Data', 'HOS-CF', 'HOSAIC-CF', 'ARZ-CF', 'ARZAIC-CF'])
# plot horizontal traces
@ -291,6 +298,7 @@ def run_makeCF(project, database, event, iplot, station=None):
raw_input()
plt.close()
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--project', type=str, help='project name (e.g. Insheim)')

1
pylot/testing/test_pdf.py
View File

@ -2,6 +2,7 @@
# -*- coding: utf-8 -*-
from pylot.core.util.pdf import ProbabilityDensityFunction
pdf = ProbabilityDensityFunction.from_pick(0.34, 0.5, 0.54, type='exp')
pdf2 = ProbabilityDensityFunction.from_pick(0.34, 0.5, 0.54, type='exp')
diff = pdf - pdf2

1
scripts/pylot-noisewindow.py
View File

@ -2,6 +2,7 @@
# -*- coding: utf-8 -*-
import argparse
import numpy
from pylot.core.pick.utils import getnoisewin

1
scripts/pylot-pick-earliest-latest.py
View File

@ -11,6 +11,7 @@
"""
import argparse
import obspy
from pylot.core.pick.utils import earllatepicker

1
scripts/pylot-pick-firstmotion.py
View File

@ -8,6 +8,7 @@
"""
import argparse
import obspy
from pylot.core.pick.utils import fmpicker

2
scripts/pylot-reasses-pilot-db.py
View File

@ -3,8 +3,8 @@
import argparse
from pylot.core.util.version import get_git_version as _getVersionString
from pylot.core.io.phases import reassess_pilot_db
from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
__author__ = 'S. Wehling-Benatelli'

2
scripts/pylot-reasses-pilot-event.py
View File

@ -3,8 +3,8 @@
import argparse
from pylot.core.util.version import get_git_version as _getVersionString
from pylot.core.io.phases import reassess_pilot_event
from pylot.core.util.version import get_git_version as _getVersionString
__version__ = _getVersionString()
__author__ = 'S. Wehling-Benatelli'

1
scripts/pylot-signalwindow.py
View File

@ -2,6 +2,7 @@
# -*- coding: utf-8 -*-
import argparse
import numpy
from pylot.core.pick.utils import getsignalwin

4
scripts/pylot-snr.py
View File

@ -9,6 +9,7 @@
"""
import argparse
import obspy
from pylot.core.pick.utils import getSNR
@ -27,4 +28,5 @@ if __name__ == "__main__":
'are calculated',
dest='time')
args = parser.parse_args()
print getSNR(args.data, args.tsnr, args.time)
print
getSNR(args.data, args.tsnr, args.time)

37
scripts/run_makeCF.py
View File

@ -6,14 +6,12 @@
Only for test purposes!
"""
from obspy.core import read
import matplotlib.pyplot as plt
import numpy as np
from pylot.core.pick.charfuns import CharacteristicFunction
from pylot.core.pick.picker import AutoPicker
from pylot.core.pick.utils import *
import glob
import argparse
import glob
from obspy.core import read
from pylot.core.pick.utils import *
def run_makeCF(project, database, event, iplot, station=None):
# parameters for CF calculation
@ -50,8 +48,10 @@ def run_makeCF(project, database, event, iplot, station=None):
wfnfiles = glob.glob(dpn)
if wfzfiles:
for i in range(len(wfzfiles)):
print 'Vertical component data found ...'
print wfzfiles[i]
print
'Vertical component data found ...'
print
wfzfiles[i]
st = read('%s' % wfzfiles[i])
st_copy = st.copy()
# filter and taper data
@ -82,7 +82,8 @@ def run_makeCF(project, database, event, iplot, station=None):
#############################################################
# get SNR
[SNR, SNRdB] = getSNR(st_copy, TSNRhos, hospick.getpick())
print 'SNR:', SNR, 'SNR[dB]:', SNRdB
print
'SNR:', SNR, 'SNR[dB]:', SNRdB
##########################################################
# get first motion of onset
hosfm = fmpicker(st, st_copy, 0.2, hospick.getpick(), 11)
@ -106,13 +107,17 @@ def run_makeCF(project, database, event, iplot, station=None):
st_copy[0].data = tr_filt.data
[lpickarz, epickarz, pickerrarz] = earllatepicker(st_copy, 1.5, TSNRarz, arzpick.getpick(), 10)
elif not wfzfiles:
print 'No vertical component data found!'
print
'No vertical component data found!'
if wfefiles and wfnfiles:
for i in range(len(wfefiles)):
print 'Horizontal component data found ...'
print wfefiles[i]
print wfnfiles[i]
print
'Horizontal component data found ...'
print
wfefiles[i]
print
wfnfiles[i]
# merge streams
H = read('%s' % wfefiles[i])
H += read('%s' % wfnfiles[i])
@ -210,7 +215,8 @@ def run_makeCF(project, database, event, iplot, station=None):
plt.xlabel('Time [s]')
plt.ylabel('Normalized Counts')
plt.title('%s, %s, CF-SNR=%7.2f, CF-Slope=%12.2f' % (tr.stats.station,
tr.stats.channel, aicpick.getSNR(), aicpick.getSlope()))
tr.stats.channel, aicpick.getSNR(),
aicpick.getSlope()))
plt.suptitle(tr.stats.starttime)
plt.legend([p1, p2, p3, p4, p5], ['Data', 'HOS-CF', 'HOSAIC-CF', 'ARZ-CF', 'ARZAIC-CF'])
# plot horizontal traces
@ -296,6 +302,7 @@ def run_makeCF(project, database, event, iplot, station=None):
raw_input()
plt.close()
parser = argparse.ArgumentParser()
parser.add_argument('--project', type=str, help='project name (e.g. Insheim)')
parser.add_argument('--database', type=str, help='event data base (e.g. 2014.09_Insheim)')