[reformat] code reformatting with PyCharm

QtPyLoT.py

@@ -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:

autoPyLoT.py

@@ -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

help/index.html

@@ -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>

makePyLoT.py

@@ -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...')

pylot/core/analysis/magnitude.py

@@ -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

pylot/core/analysis/magnitude.py.orig

@@ -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
-

pylot/core/io/data.py

@@ -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-

pylot/core/io/inputs.py

@@ -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):
     '''

pylot/core/io/phases.py

@@ -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, \
+from pylot.core.io.location import create_event, \
-    create_magnitude, create_origin, create_pick
+    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,
+                                                                             stime.year, stime.month, stime.day,
-                   eventsource['latitude'], eventsource['longitude'], eventsource['depth'] / 1000,
+                                                                             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, 
+                                                                                          stime.month, stime.day,
-                                       latdeg, latmin, londeg, lonmin, eventsource['depth'], 
+                                                                                          stime.hour, stime.minute,
-                                                   eventinfo.magnitudes[0]['mag'], erh, erz, 
+                                                                                          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()
-

pylot/core/loc/focmec.py

@@ -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

pylot/core/loc/hash.py

@@ -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

pylot/core/loc/hypo71.py

@@ -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

pylot/core/loc/hypodd.py

@@ -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

pylot/core/loc/hyposat.py

@@ -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

pylot/core/loc/nll.py

@@ -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

pylot/core/loc/velest.py

@@ -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

pylot/core/pick/autopick.py

@@ -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):

pylot/core/pick/charfuns.py

@@ -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
 

pylot/core/pick/compare.py

@@ -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

pylot/core/pick/picker.py

@@ -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[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0,
-                ax1.axvspan(self.Tcf[iislope[0]],self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0, label='Slope Window')
+                            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[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0,
-                ax2.axvspan(self.Tcf[iislope[0]],self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0, label='Slope Window')                
+                            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,

pylot/core/pick/utils.py

@@ -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.

pylot/core/pick/utils.py.orig

@@ -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()

pylot/core/util/dataprocessing.py

@@ -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, \

pylot/core/util/defaults.py

@@ -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.io.inputs import PylotParameter
-from pylot.core.loc import hyposat
 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()))
-   

pylot/core/util/errors.py

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

pylot/core/util/event.py

@@ -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

pylot/core/util/map_projection.py

@@ -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 PySide import QtGui
-from scipy.interpolate import griddata
 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()
-            
-    

pylot/core/util/pdf.py

@@ -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
-

pylot/core/util/plotting.py

@@ -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

pylot/core/util/thread.py

@@ -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,

pylot/core/util/utils.py

@@ -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
 

pylot/core/util/widgets.py

@@ -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']

pylot/testing/testHelpForm.py

@@ -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
 

pylot/testing/testPickDlg.py

@@ -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)
 

pylot/testing/testPropDlg.py

@@ -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
 

pylot/testing/testUIcomponents.py

@@ -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
 

pylot/testing/testUtils.py

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

pylot/testing/testWidgets.py

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

pylot/testing/test_autopick.py

@@ -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
-          print wfzfiles[i]
+            '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
-          print wfefiles[i]
+            'Horizontal component data found ...'
-          print wfnfiles[i]
+            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)')

pylot/testing/test_pdf.py

@@ -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

scripts/pylot-noisewindow.py

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

scripts/pylot-pick-earliest-latest.py

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

scripts/pylot-pick-firstmotion.py

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

scripts/pylot-reasses-pilot-db.py

@@ -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'

scripts/pylot-reasses-pilot-event.py

@@ -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'

scripts/pylot-signalwindow.py

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

scripts/pylot-snr.py

@@ -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)

scripts/run_makeCF.py

@@ -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
-          print wfzfiles[i]
+            '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
-          print wfefiles[i]
+            'Horizontal component data found ...'
-          print wfnfiles[i]
+            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)')