[refactor] automatic code reformatting (Pycharm)

2022-03-09 14:41:34 +01:00
parent 79f3d40714
commit e35d5d6df9
34 changed files with 818 additions and 501 deletions
--- a/pylot/core/analysis/magnitude.py
+++ b/pylot/core/analysis/magnitude.py
@@ -223,14 +223,14 @@ class LocalMagnitude(Magnitude):
                 in 'Z3']
        # checking horizontal count and calculating power_sum accordingly
        if len(power) == 1:
-                print ('WARNING: Only one horizontal found for station {0}.'.format(st[0].stats.station))
-                power_sum = power[0]
+            print('WARNING: Only one horizontal found for station {0}.'.format(st[0].stats.station))
+            power_sum = power[0]
        elif len(power) == 2:
-                power_sum = power[0] + power[1]
-        else: 
-                raise ValueError('Wood-Anderson aomplitude defintion only valid for'
-                        ' up to two horizontals: {0} given'.format(len(power)))
- 
+            power_sum = power[0] + power[1]
+        else:
+            raise ValueError('Wood-Anderson aomplitude defintion only valid for'
+                             ' up to two horizontals: {0} given'.format(len(power)))
+
        sqH = np.sqrt(power_sum)

        # get time array
@@ -325,7 +325,7 @@ class LocalMagnitude(Magnitude):
            if self.verbose:
                print(
                    "Local Magnitude for station {0}: ML = {1:3.1f}".format(
-                       station, magnitude.mag))
+                        station, magnitude.mag))
            magnitude.origin_id = self.origin_id
            magnitude.waveform_id = pick.waveform_id
            magnitude.amplitude_id = amplitude.resource_id
@@ -404,7 +404,7 @@ class MomentMagnitude(Magnitude):
            if not wf:
                continue
            try:
-               scopy = wf.copy()
+                scopy = wf.copy()
            except AssertionError:
                print("WARNING: Something's wrong with the data,"
                      "station {},"
@@ -464,7 +464,7 @@ def calcMoMw(wfstream, w0, rho, vp, delta, verbosity=False):

    # additional common parameters for calculating Mo
    # average radiation pattern of P waves (Aki & Richards, 1980)
-    rP = 2 / np.sqrt(15)  
+    rP = 2 / np.sqrt(15)
    freesurf = 2.0  # free surface correction, assuming vertical incidence

    Mo = w0 * 4 * np.pi * rho * np.power(vp, 3) * delta / (rP * freesurf)
@@ -524,7 +524,7 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
            iplot = 2
        else:
            iplot = 0
-    
+
    # get Q value
    Q, A = qp

@@ -594,13 +594,13 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,

        # fft
        fny = freq / 2
-        #l = len(xdat) / freq
+        # l = len(xdat) / freq
        # number of fft bins after Bath
-        #n = freq * l
+        # n = freq * l
        # find next power of 2 of data length
        m = pow(2, np.ceil(np.log(len(xdat)) / np.log(2)))
        N = min(int(np.power(m, 2)), 16384)
-        #N = int(np.power(m, 2))
+        # N = int(np.power(m, 2))
        y = dt * np.fft.fft(xdat, N)
        Y = abs(y[: N / 2])
        L = (N - 1) / freq
@@ -643,8 +643,8 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
        w0 = np.median([w01, w02])
        Fc = np.median([fc1, fc2])
        if verbosity:
-           print("calcsourcespec: Using w0-value = %e m/Hz and fc = %f Hz" % (
-              w0, Fc))
+            print("calcsourcespec: Using w0-value = %e m/Hz and fc = %f Hz" % (
+                w0, Fc))
    if iplot >= 1:
        f1 = plt.figure()
        tLdat = np.arange(0, len(Ldat) * dt, dt)
@@ -733,7 +733,7 @@ def fitSourceModel(f, S, fc0, iplot, verbosity=False):
            iplot = 2
        else:
            iplot = 0
-    
+
    w0 = []
    stdw0 = []
    fc = []
--- a/pylot/core/io/data.py
+++ b/pylot/core/io/data.py
@@ -3,16 +3,16 @@

 import copy
 import os
+
+from PySide2.QtWidgets import QMessageBox
 from obspy import read_events
 from obspy.core import read, Stream, UTCDateTime
 from obspy.core.event import Event as ObsPyEvent
 from obspy.io.sac import SacIOError

-from PySide2.QtWidgets import QMessageBox
-
-import pylot.core.loc.velest as velest
 import pylot.core.loc.focmec as focmec
 import pylot.core.loc.hypodd as hypodd
+import pylot.core.loc.velest as velest
 from pylot.core.io.phases import readPILOTEvent, picks_from_picksdict, \
    picksdict_from_pilot, merge_picks, PylotParameter
 from pylot.core.util.errors import FormatError, OverwriteError
@@ -100,7 +100,7 @@ class Data(object):
                                      old_pick.phase_hint == new_pick.phase_hint,
                                      old_pick.method_id == new_pick.method_id]
                        if all(comparison):
-                            del(old_pick)
+                            del (old_pick)
                old_picks.append(new_pick)
        elif not other.isNew() and self.isNew():
            new = other + self
@@ -112,7 +112,7 @@ class Data(object):
            return self + other
        else:
            raise ValueError("both Data objects have differing "
-              "unique Event identifiers")
+                             "unique Event identifiers")
        return self

    def getPicksStr(self):
@@ -250,7 +250,7 @@ class Data(object):
            for pick in self.get_evt_data().picks:
                if picktype in str(pick.method_id.id):
                    picks.append(pick)
-                
+
    def exportEvent(self, fnout, fnext='.xml', fcheck='auto', upperErrors=None):
        """
        Export event to file
@@ -260,7 +260,7 @@ class Data(object):
        can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
        """
        from pylot.core.util.defaults import OUTPUTFORMATS
-        
+
        if not type(fcheck) == list:
            fcheck = [fcheck]

@@ -293,7 +293,7 @@ class Data(object):
                    return
                self.checkEvent(event, fcheck)
                self.setEvtData(event)
-                
+
            self.get_evt_data().write(fnout + fnext, format=evtformat)

        # try exporting event
@@ -360,13 +360,13 @@ class Data(object):
                    nllocfile = open(fnout + fnext)
                    l = nllocfile.readlines()
                    # Adding A0/Generic Amplitude to .obs file
-                    #l2 = []
-                    #for li in l:
+                    # l2 = []
+                    # for li in l:
                    #    for amp in evtdata_org.amplitudes:
                    #        if amp.waveform_id.station_code == li[0:5].strip():
                    #            li = li[0:64] + '{:0.2e}'.format(amp.generic_amplitude) + li[73:-1] + '\n'
                    #            l2.append(li)
-                    #l = l2
+                    # l = l2
                    nllocfile.close()
                    l.insert(0, header)
                    nllocfile = open(fnout + fnext, 'w')
@@ -503,7 +503,8 @@ class Data(object):
                    real_or_syn_data[synthetic] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
                except Exception as e:
                    try:
-                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart, endtime=self.tstop)
+                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart,
+                                                            endtime=self.tstop)
                    except Exception as e:
                        warnmsg += '{0}\n{1}\n'.format(fname, e)
            except SacIOError as se:
--- a/pylot/core/io/default_parameters.py
+++ b/pylot/core/io/default_parameters.py
@@ -515,9 +515,9 @@ defaults = {'rootpath': {'type': str,
                           'namestring': 'TauPy model'},

            'taup_phases': {'type': str,
-                           'tooltip': 'Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.',
-                           'value': 'ttall',
-                           'namestring': 'TauPy phases'},
+                            'tooltip': 'Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.',
+                            'value': 'ttall',
+                            'namestring': 'TauPy phases'},
            }

 settings_main = {
--- a/pylot/core/io/getEventListFromXML.py
+++ b/pylot/core/io/getEventListFromXML.py
@@ -8,14 +8,10 @@
   Edited for use in PyLoT
   JG, igem, 01/2022
 """
-import pdb
-import os
-import argparse
-import numpy as np
-import matplotlib.pyplot as plt
+import glob
+
 from obspy.core.event import read_events
 from pyproj import Proj
-import glob

 """
 Creates an eventlist file summarizing all events found in a certain folder. Only called by pressing UI Button eventlis_xml_action
@@ -24,14 +20,15 @@ Creates an eventlist file summarizing all events found in a certain folder. Only
 :param path: Path to root folder where single Event folder are to found
 """

+
 def geteventlistfromxml(path, outpath):
    p = Proj(proj='utm', zone=32, ellps='WGS84')

-
    # open eventlist file and write header
    evlist = outpath + '/eventlist'
    evlistobj = open(evlist, 'w')
-    evlistobj.write('EventID      Date      To    Lat    Lon     EAST    NORTH  Dep  Ml  NoP  NoS RMS  errH  errZ  Gap \n')
+    evlistobj.write(
+        'EventID      Date      To    Lat    Lon     EAST    NORTH  Dep  Ml  NoP  NoS RMS  errH  errZ  Gap \n')

    # data path
    dp = path + "/e*/*.xml"
@@ -52,28 +49,31 @@ def geteventlistfromxml(path, outpath):
            NoP = []
            NoS = []
        except IndexError:
-            print ('Insufficient data found for event (not localised): ' + names.split('/')[-1].split('_')[-1][:-4] + ' Skipping event for eventlist.' )
+            print('Insufficient data found for event (not localised): ' + names.split('/')[-1].split('_')[-1][
+                                                                          :-4] + ' Skipping event for eventlist.')
            continue
- 
+
        for i in range(len(cat.events[0].origins[0].arrivals)):
            if cat.events[0].origins[0].arrivals[i].phase == 'P':
                NoP.append(cat.events[0].origins[0].arrivals[i].phase)
            elif cat.events[0].origins[0].arrivals[i].phase == 'S':
                NoS.append(cat.events[0].origins[0].arrivals[i].phase)
-        #NoP = cat.events[0].origins[0].quality.used_station_count
+        # NoP = cat.events[0].origins[0].quality.used_station_count
        errH = cat.events[0].origins[0].origin_uncertainty.max_horizontal_uncertainty
        errZ = cat.events[0].origins[0].depth_errors.uncertainty
        Gap = cat.events[0].origins[0].quality.azimuthal_gap
-        #evID = names.split('/')[6]
+        # evID = names.split('/')[6]
        evID = names.split('/')[-1].split('_')[-1][:-4]
        Date = str(st.year) + str('%02d' % st.month) + str('%02d' % st.day)
        To = str('%02d' % st.hour) + str('%02d' % st.minute) + str('%02d' % st.second) + \
-                  '.' + str('%06d' % st.microsecond)
+             '.' + str('%06d' % st.microsecond)

        # write into eventlist
-        evlistobj.write('%s %s %s %9.6f %9.6f %13.6f %13.6f %8.6f %3.1f %d %d NaN %d %d %d\n' %(evID, \
-                         Date, To, Lat, Lon, EAST, NORTH, Dep, Ml, len(NoP), len(NoS), errH, errZ, Gap))
-        print ('Adding Event ' + names.split('/')[-1].split('_')[-1][:-4]  + ' to eventlist')
+        evlistobj.write('%s %s %s %9.6f %9.6f %13.6f %13.6f %8.6f %3.1f %d %d NaN %d %d %d\n' % (evID, \
+                                                                                                 Date, To, Lat, Lon,
+                                                                                                 EAST, NORTH, Dep, Ml,
+                                                                                                 len(NoP), len(NoS),
+                                                                                                 errH, errZ, Gap))
+        print('Adding Event ' + names.split('/')[-1].split('_')[-1][:-4] + ' to eventlist')
    print('Eventlist created and saved in: ' + outpath)
    evlistobj.close()
-
--- a/pylot/core/io/getQualitiesfromxml.py
+++ b/pylot/core/io/getQualitiesfromxml.py
@@ -9,15 +9,15 @@
   Edited for usage in PyLoT: Jeldrik Gaal, igem, 01/2022
 """

-import argparse
-import numpy as np
-import matplotlib.pyplot as plt
-from obspy.core.event import read_events
 import glob

-def getQualitiesfromxml(path):
+import matplotlib.pyplot as plt
+import numpy as np
+from obspy.core.event import read_events

-    # uncertainties 
+
+def getQualitiesfromxml(path):
+    # uncertainties
    ErrorsP = [0.02, 0.04, 0.08, 0.16]
    ErrorsS = [0.04, 0.08, 0.16, 0.32]

@@ -31,48 +31,48 @@ def getQualitiesfromxml(path):
    Sw2 = []
    Sw3 = []
    Sw4 = []
-    
+
    # data path
    dp = path + '/e*/*.xml'
    # list of all available xml-files
    xmlnames = glob.glob(dp)

    # read all onset weights
-    for names in xmlnames: 
+    for names in xmlnames:
        print("Getting onset weights from {}".format(names))
        cat = read_events(names)
        arrivals = cat.events[0].picks
        for Pick in arrivals:
            if Pick.phase_hint[0] == 'P':
-                if Pick.time_errors.uncertainty <= ErrorsP[0]:     
-                    Pw0.append(Pick.time_errors.uncertainty)      
+                if Pick.time_errors.uncertainty <= ErrorsP[0]:
+                    Pw0.append(Pick.time_errors.uncertainty)
                elif Pick.time_errors.uncertainty > ErrorsP[0] and \
-                     Pick.time_errors.uncertainty <= ErrorsP[1]:
-                     Pw1.append(Pick.time_errors.uncertainty)      
+                        Pick.time_errors.uncertainty <= ErrorsP[1]:
+                    Pw1.append(Pick.time_errors.uncertainty)
                elif Pick.time_errors.uncertainty > ErrorsP[1] and \
-                     Pick.time_errors.uncertainty <= ErrorsP[2]:
-                     Pw2.append(Pick.time_errors.uncertainty)      
+                        Pick.time_errors.uncertainty <= ErrorsP[2]:
+                    Pw2.append(Pick.time_errors.uncertainty)
                elif Pick.time_errors.uncertainty > ErrorsP[2] and \
-                     Pick.time_errors.uncertainty <= ErrorsP[3]:
-                     Pw3.append(Pick.time_errors.uncertainty)      
+                        Pick.time_errors.uncertainty <= ErrorsP[3]:
+                    Pw3.append(Pick.time_errors.uncertainty)
                elif Pick.time_errors.uncertainty > ErrorsP[3]:
-                     Pw4.append(Pick.time_errors.uncertainty)      
+                    Pw4.append(Pick.time_errors.uncertainty)
                else:
                    pass
            elif Pick.phase_hint[0] == 'S':
-                if Pick.time_errors.uncertainty <= ErrorsS[0]:     
-                     Sw0.append(Pick.time_errors.uncertainty)      
+                if Pick.time_errors.uncertainty <= ErrorsS[0]:
+                    Sw0.append(Pick.time_errors.uncertainty)
                elif Pick.time_errors.uncertainty > ErrorsS[0] and \
-                     Pick.time_errors.uncertainty <= ErrorsS[1]:
-                     Sw1.append(Pick.time_errors.uncertainty)      
+                        Pick.time_errors.uncertainty <= ErrorsS[1]:
+                    Sw1.append(Pick.time_errors.uncertainty)
                elif Pick.time_errors.uncertainty > ErrorsS[1] and \
-                     Pick.time_errors.uncertainty <= ErrorsS[2]:
-                     Sw2.append(Pick.time_errors.uncertainty)      
+                        Pick.time_errors.uncertainty <= ErrorsS[2]:
+                    Sw2.append(Pick.time_errors.uncertainty)
                elif Pick.time_errors.uncertainty > ErrorsS[2] and \
-                     Pick.time_errors.uncertainty <= ErrorsS[3]:
-                     Sw3.append(Pick.time_errors.uncertainty)      
+                        Pick.time_errors.uncertainty <= ErrorsS[3]:
+                    Sw3.append(Pick.time_errors.uncertainty)
                elif Pick.time_errors.uncertainty > ErrorsS[3]:
-                     Sw4.append(Pick.time_errors.uncertainty)      
+                    Sw4.append(Pick.time_errors.uncertainty)
                else:
                    pass
            else:
@@ -133,7 +133,6 @@ def getQualitiesfromxml(path):
    plt.xticks(y_pos, weights)
    plt.xlim([-0.5, 4.5])
    plt.xlabel('Qualities')
-    plt.title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights)) 
+    plt.title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights))
    plt.legend([p1, p2], ['P-Weights', 'S-Weights'])
    plt.show()
-
--- a/pylot/core/io/phases.py
+++ b/pylot/core/io/phases.py
@@ -1,12 +1,13 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import glob
+import os
+import warnings
+
 import matplotlib.pyplot as plt
 import numpy as np
 import obspy.core.event as ope
-import os
 import scipy.io as sio
-import warnings
 from obspy.core import UTCDateTime
 from obspy.core.event import read_events
 from obspy.core.util import AttribDict
@@ -507,14 +508,14 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
    :param eventinfo: optional, needed for VELEST-cnv file
            and FOCMEC- and HASH-input files 
    :type eventinfo: `obspy.core.event.Event` object
-    """    
+    """
    if fformat == 'NLLoc':
        print("Writing phases to %s for NLLoc" % filename)
        fid = open("%s" % filename, 'w')
        # write header
        fid.write('# EQEVENT: %s Label: EQ%s  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n' %
                  (parameter.get('database'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals) # MP MP what is chooseArrivals? It is not defined anywhere
+        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
        for key in arrivals:
            # P onsets
            if arrivals[key].has_key('P'):
@@ -568,20 +569,20 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                        sweight = 0  # do not use pick
                except KeyError as e:
                    print(str(e) + '; no weight set during processing')
-                Ao = arrivals[key]['S']['Ao'] # peak-to-peak amplitude
+                Ao = arrivals[key]['S']['Ao']  # peak-to-peak amplitude
                if Ao == None:
                    Ao = 0.0
-                #fid.write('%s ? ? ? S   %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
+                # fid.write('%s ? ? ? S   %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
                fid.write('%s ? ? ? S   %s %d%02d%02d %02d%02d %7.4f GAU 0 %9.2f 0 0 %d \n' % (key,
-                                                                                           fm,
-                                                                                           year,
-                                                                                           month,
-                                                                                           day,
-                                                                                           hh,
-                                                                                           mm,
-                                                                                           ss_ms,
-                                                                                           Ao,
-                                                                                           sweight))
+                                                                                               fm,
+                                                                                               year,
+                                                                                               month,
+                                                                                               day,
+                                                                                               hh,
+                                                                                               mm,
+                                                                                               ss_ms,
+                                                                                               Ao,
+                                                                                               sweight))

        fid.close()
    elif fformat == 'HYPO71':
@@ -590,7 +591,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
        # write header
        fid.write('                                                                %s\n' %
                  parameter.get('eventID'))
-        arrivals = chooseArrivals(arrivals) # MP MP what is chooseArrivals? It is not defined anywhere
+        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
        for key in arrivals:
            if arrivals[key]['P']['weight'] < 4:
                stat = key
@@ -765,7 +766,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
            arrivals = picksdict_from_picks(evt)
        # check for automatic and manual picks
        # prefer manual picks
-        usedarrivals = chooseArrival(arrivals) 
+        usedarrivals = chooseArrival(arrivals)
        for key in usedarrivals:
            # P onsets
            if usedarrivals[key].has_key('P'):
@@ -811,9 +812,9 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
            event = eventinfo['pylot_id']
            hddID = event.split('.')[0][1:5]
        except:
-            print ("Error 1111111!")
-            hddID = "00000"       
-        # write header
+            print("Error 1111111!")
+            hddID = "00000"
+            # write header
        fid.write('# %d  %d %d %d %d %5.2f %7.4f +%6.4f %7.4f %4.2f 0.1 0.5 %4.2f      %s\n' % (
            stime.year, stime.month, stime.day, stime.hour, stime.minute, stime.second,
            eventsource['latitude'], eventsource['longitude'], eventsource['depth'] / 1000,
@@ -1005,6 +1006,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
        fid1.close()
        fid2.close()

+
 def chooseArrival(arrivals):
    """
    takes arrivals and returns the manual picks if manual and automatic ones are there
--- a/pylot/core/loc/nll.py
+++ b/pylot/core/loc/nll.py
@@ -4,11 +4,12 @@
 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
 from pylot.core.util.gui import which
+from pylot.core.util.utils import getPatternLine, runProgram
 from pylot.core.util.version import get_git_version as _getVersionString

 __version__ = _getVersionString()
--- a/pylot/core/pick/autopick.py
+++ b/pylot/core/pick/autopick.py
@@ -9,21 +9,21 @@ function conglomerate utils.
 :author: MAGS2 EP3 working group / Ludger Kueperkoch
 """
 import copy
+import traceback
+
 import matplotlib.pyplot as plt
 import numpy as np
-import traceback
+from obspy import Trace
 from obspy.taup import TauPyModel

 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, get_pickparams, get_quality_class
-from pylot.core.util.utils import getPatternLine, gen_Pool,\
+    getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class
+from pylot.core.util.utils import getPatternLine, gen_Pool, \
    get_Bool, identifyPhaseID, get_None, correct_iplot

-from obspy.taup import TauPyModel
-from obspy import Trace

 def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
    """
@@ -182,25 +182,25 @@ class PickingResults(dict):
        # TODO What are those?
        self.w0 = None
        self.fc = None
-        self.Ao = None          # Wood-Anderson peak-to-peak amplitude
+        self.Ao = None  # Wood-Anderson peak-to-peak amplitude

        # Station information
        self.network = None
        self.channel = None

        # pick information
-        self.picker = 'auto'    # type of pick
+        self.picker = 'auto'  # type of pick
        self.marked = []

        # pick results
-        self.epp = None         # earliest possible pick
-        self.mpp = None         # most likely onset
-        self.lpp = None         # latest possible pick
-        self.fm = 'N'           # first motion polarity, can be set to 'U' (Up) or 'D' (Down)
-        self.snr = None         # signal-to-noise ratio of onset
-        self.snrdb = None       # signal-to-noise ratio of onset [dB]
-        self.spe = None         # symmetrized picking error
-        self.weight = 4         # weight of onset
+        self.epp = None  # earliest possible pick
+        self.mpp = None  # most likely onset
+        self.lpp = None  # latest possible pick
+        self.fm = 'N'  # first motion polarity, can be set to 'U' (Up) or 'D' (Down)
+        self.snr = None  # signal-to-noise ratio of onset
+        self.snrdb = None  # signal-to-noise ratio of onset [dB]
+        self.spe = None  # symmetrized picking error
+        self.weight = 4  # weight of onset

    # to correctly provide dot access to dictionary attributes, all attribute access of the class is forwarded to the
    # dictionary
@@ -335,9 +335,10 @@ class AutopickStation(object):
        """
        waveform_data = {}
        for key in self.channelorder:
-            waveform_data[key] = self.wfstream.select(component=key) # try ZNE first
+            waveform_data[key] = self.wfstream.select(component=key)  # try ZNE first
            if len(waveform_data[key]) == 0:
-                waveform_data[key] = self.wfstream.select(component=str(self.channelorder[key])) # use 123 as second option
+                waveform_data[key] = self.wfstream.select(
+                    component=str(self.channelorder[key]))  # use 123 as second option
        return waveform_data['Z'], waveform_data['N'], waveform_data['E']

    def get_traces_from_streams(self):
@@ -524,7 +525,7 @@ class AutopickStation(object):

        self.plot_pick_results()
        self.finish_picking()
-        return [{'P': self.p_results, 'S':self.s_results}, self.ztrace.stats.station]
+        return [{'P': self.p_results, 'S': self.s_results}, self.ztrace.stats.station]

    def finish_picking(self):

@@ -573,7 +574,7 @@ class AutopickStation(object):

        self.s_results.channel = self.etrace.stats.channel
        self.s_results.network = self.etrace.stats.network
-        self.s_results.fm = None    # override default value 'N'
+        self.s_results.fm = None  # override default value 'N'

    def plot_pick_results(self):
        if self.iplot > 0:
@@ -588,12 +589,14 @@ class AutopickStation(object):
                plt_flag = 0
            fig._tight = True
            ax1 = fig.add_subplot(311)
-            tdata = np.linspace(start=0, stop=self.ztrace.stats.endtime-self.ztrace.stats.starttime, num=self.ztrace.stats.npts)
+            tdata = np.linspace(start=0, stop=self.ztrace.stats.endtime - self.ztrace.stats.starttime,
+                                num=self.ztrace.stats.npts)
            # plot tapered trace filtered with bpz2 filter settings
-            ax1.plot(tdata, self.tr_filt_z_bpz2.data/max(self.tr_filt_z_bpz2.data), color=linecolor, linewidth=0.7, label='Data')
+            ax1.plot(tdata, self.tr_filt_z_bpz2.data / max(self.tr_filt_z_bpz2.data), color=linecolor, linewidth=0.7,
+                     label='Data')
            if self.p_results.weight < 4:
                # plot CF of initial onset (HOScf or ARZcf)
-                ax1.plot(self.cf1.getTimeArray(), self.cf1.getCF()/max(self.cf1.getCF()), 'b', label='CF1')
+                ax1.plot(self.cf1.getTimeArray(), self.cf1.getCF() / max(self.cf1.getCF()), 'b', label='CF1')
            if self.p_data.p_aic_plot_flag == 1:
                aicpick = self.p_data.aicpick
                refPpick = self.p_data.refPpick
@@ -631,23 +634,28 @@ class AutopickStation(object):
            if self.horizontal_traces_exist() and self.s_data.Sflag == 1:
                # plot E trace
                ax2 = fig.add_subplot(3, 1, 2, sharex=ax1)
-                th1data = np.linspace(0, self.etrace.stats.endtime-self.etrace.stats.starttime, self.etrace.stats.npts)
+                th1data = np.linspace(0, self.etrace.stats.endtime - self.etrace.stats.starttime,
+                                      self.etrace.stats.npts)
                # plot filtered and tapered waveform
-                ax2.plot(th1data, self.etrace.data / max(self.etrace.data), color=linecolor, linewidth=0.7, label='Data')
+                ax2.plot(th1data, self.etrace.data / max(self.etrace.data), color=linecolor, linewidth=0.7,
+                         label='Data')
                if self.p_results.weight < 4:
                    # plot initial CF (ARHcf or AR3Ccf)
-                    ax2.plot(self.arhcf1.getTimeArray(), self.arhcf1.getCF() / max(self.arhcf1.getCF()), 'b', label='CF1')
+                    ax2.plot(self.arhcf1.getTimeArray(), self.arhcf1.getCF() / max(self.arhcf1.getCF()), 'b',
+                             label='CF1')
                    if self.s_data.aicSflag == 1 and self.s_results.weight <= 4:
                        aicarhpick = self.aicarhpick
                        refSpick = self.refSpick
                        # plot second cf, used for determing precise onset (ARHcf or AR3Ccf)
-                        ax2.plot(self.arhcf2.getTimeArray(), self.arhcf2.getCF() / max(self.arhcf2.getCF()), 'm', label='CF2')
+                        ax2.plot(self.arhcf2.getTimeArray(), self.arhcf2.getCF() / max(self.arhcf2.getCF()), 'm',
+                                 label='CF2')
                        # plot preliminary onset time, calculated from CF1
                        ax2.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'g', label='Initial S Onset')
                        ax2.plot([aicarhpick.getpick() - 0.5, aicarhpick.getpick() + 0.5], [1, 1], 'g')
                        ax2.plot([aicarhpick.getpick() - 0.5, aicarhpick.getpick() + 0.5], [-1, -1], 'g')
                        # plot precise onset time, calculated from CF2
-                        ax2.plot([refSpick.getpick(), refSpick.getpick()], [-1.3, 1.3], 'g', linewidth=2, label='Final S Pick')
+                        ax2.plot([refSpick.getpick(), refSpick.getpick()], [-1.3, 1.3], 'g', linewidth=2,
+                                 label='Final S Pick')
                        ax2.plot([refSpick.getpick() - 0.5, refSpick.getpick() + 0.5], [1.3, 1.3], 'g', linewidth=2)
                        ax2.plot([refSpick.getpick() - 0.5, refSpick.getpick() + 0.5], [-1.3, -1.3], 'g', linewidth=2)
                        ax2.plot([self.s_results.lpp, self.s_results.lpp], [-1.1, 1.1], 'g--', label='lpp')
@@ -667,15 +675,19 @@ class AutopickStation(object):

                # plot N trace
                ax3 = fig.add_subplot(3, 1, 3, sharex=ax1)
-                th2data= np.linspace(0, self.ntrace.stats.endtime-self.ntrace.stats.starttime, self.ntrace.stats.npts)
+                th2data = np.linspace(0, self.ntrace.stats.endtime - self.ntrace.stats.starttime,
+                                      self.ntrace.stats.npts)
                # plot trace
-                ax3.plot(th2data, self.ntrace.data / max(self.ntrace.data), color=linecolor, linewidth=0.7, label='Data')
+                ax3.plot(th2data, self.ntrace.data / max(self.ntrace.data), color=linecolor, linewidth=0.7,
+                         label='Data')
                if self.p_results.weight < 4:
-                    p22, = ax3.plot(self.arhcf1.getTimeArray(), self.arhcf1.getCF() / max(self.arhcf1.getCF()), 'b', label='CF1')
+                    p22, = ax3.plot(self.arhcf1.getTimeArray(), self.arhcf1.getCF() / max(self.arhcf1.getCF()), 'b',
+                                    label='CF1')
                    if self.s_data.aicSflag == 1:
                        aicarhpick = self.aicarhpick
                        refSpick = self.refSpick
-                        ax3.plot(self.arhcf2.getTimeArray(), self.arhcf2.getCF() / max(self.arhcf2.getCF()), 'm', label='CF2')
+                        ax3.plot(self.arhcf2.getTimeArray(), self.arhcf2.getCF() / max(self.arhcf2.getCF()), 'm',
+                                 label='CF2')
                        ax3.plot([aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'g', label='Initial S Onset')
                        ax3.plot([aicarhpick.getpick() - 0.5, aicarhpick.getpick() + 0.5], [1, 1], 'g')
                        ax3.plot([aicarhpick.getpick() - 0.5, aicarhpick.getpick() + 0.5], [-1, -1], 'g')
@@ -716,7 +728,8 @@ class AutopickStation(object):
        if aicpick.getpick() is None:
            msg = "Bad initial (AIC) P-pick, skipping this onset!\nAIC-SNR={0}, AIC-Slope={1}counts/s\n " \
                  "(min. AIC-SNR={2}, min. AIC-Slope={3}counts/s)"
-            msg = msg.format(aicpick.getSNR(), aicpick.getSlope(), self.pickparams["minAICPSNR"], self.pickparams["minAICPslope"])
+            msg = msg.format(aicpick.getSNR(), aicpick.getSlope(), self.pickparams["minAICPSNR"],
+                             self.pickparams["minAICPslope"])
            self.vprint(msg)
            return 0
        # Quality check initial pick with minimum signal length
@@ -726,14 +739,16 @@ class AutopickStation(object):
        if len(self.nstream) == 0 or len(self.estream) == 0:
            msg = 'One or more horizontal component(s) missing!\n' \
                  'Signal length only checked on vertical component!\n' \
-                  'Decreasing minsiglengh from {0} to {1}'\
-                  .format(minsiglength, minsiglength / 2)
+                  'Decreasing minsiglengh from {0} to {1}' \
+                .format(minsiglength, minsiglength / 2)
            self.vprint(msg)
            minsiglength = minsiglength / 2
        else:
            # filter, taper other traces as well since signal length is compared on all traces
-            trH1_filt, _ = self.prepare_wfstream(self.estream, freqmin=self.pickparams["bph1"][0], freqmax=self.pickparams["bph1"][1])
-            trH2_filt, _ = self.prepare_wfstream(self.nstream, freqmin=self.pickparams["bph1"][0], freqmax=self.pickparams["bph1"][1])
+            trH1_filt, _ = self.prepare_wfstream(self.estream, freqmin=self.pickparams["bph1"][0],
+                                                 freqmax=self.pickparams["bph1"][1])
+            trH2_filt, _ = self.prepare_wfstream(self.nstream, freqmin=self.pickparams["bph1"][0],
+                                                 freqmax=self.pickparams["bph1"][1])
            zne += trH1_filt
            zne += trH2_filt
            minsiglength = minsiglength
@@ -819,15 +834,18 @@ class AutopickStation(object):
        # get preliminary onset time from AIC-CF
        self.set_current_figure('aicFig')
        aicpick = AICPicker(aiccf, self.pickparams["tsnrz"], self.pickparams["pickwinP"], self.iplot,
-                            Tsmooth=self.pickparams["aictsmooth"], fig=self.current_figure, linecolor=self.current_linecolor)
+                            Tsmooth=self.pickparams["aictsmooth"], fig=self.current_figure,
+                            linecolor=self.current_linecolor)
        # save aicpick for plotting later
        self.p_data.aicpick = aicpick
        # add pstart and pstop to aic plot
        if self.current_figure:
            # TODO remove plotting from picking, make own plot function
            for ax in self.current_figure.axes:
-                ax.vlines(self.pickparams["pstart"], ax.get_ylim()[0], ax.get_ylim()[1], color='c', linestyles='dashed', label='P start')
-                ax.vlines(self.pickparams["pstop"], ax.get_ylim()[0], ax.get_ylim()[1], color='c', linestyles='dashed', label='P stop')
+                ax.vlines(self.pickparams["pstart"], ax.get_ylim()[0], ax.get_ylim()[1], color='c', linestyles='dashed',
+                          label='P start')
+                ax.vlines(self.pickparams["pstop"], ax.get_ylim()[0], ax.get_ylim()[1], color='c', linestyles='dashed',
+                          label='P stop')
                ax.legend(loc=1)

        Pflag = self._pick_p_quality_control(aicpick, z_copy, tr_filt)
@@ -841,7 +859,8 @@ class AutopickStation(object):
            error_msg = 'AIC P onset slope to small: got {}, min {}'.format(slope, self.pickparams["minAICPslope"])
            raise PickingFailedException(error_msg)
        if aicpick.getSNR() < self.pickparams["minAICPSNR"]:
-            error_msg = 'AIC P onset SNR to small: got {}, min {}'.format(aicpick.getSNR(), self.pickparams["minAICPSNR"])
+            error_msg = 'AIC P onset SNR to small: got {}, min {}'.format(aicpick.getSNR(),
+                                                                          self.pickparams["minAICPSNR"])
            raise PickingFailedException(error_msg)

        self.p_data.p_aic_plot_flag = 1
@@ -849,7 +868,8 @@ class AutopickStation(object):
              'autopickstation: re-filtering vertical trace...'.format(aicpick.getSlope(), aicpick.getSNR())
        self.vprint(msg)
        # refilter waveform with larger bandpass
-        tr_filt, z_copy = self.prepare_wfstream(self.zstream, freqmin=self.pickparams["bpz2"][0], freqmax=self.pickparams["bpz2"][1])
+        tr_filt, z_copy = self.prepare_wfstream(self.zstream, freqmin=self.pickparams["bpz2"][0],
+                                                freqmax=self.pickparams["bpz2"][1])
        # save filtered trace in instance for later plotting
        self.tr_filt_z_bpz2 = tr_filt
        # determine new times around initial onset
@@ -861,25 +881,29 @@ class AutopickStation(object):
        else:
            self.cf2 = None
        assert isinstance(self.cf2, CharacteristicFunction), 'cf2 is not set correctly: maybe the algorithm name () is ' \
-                                                        'corrupted'.format(self.pickparams["algoP"])
+                                                             'corrupted'.format(self.pickparams["algoP"])
        self.set_current_figure('refPpick')
        # get refined onset time from CF2
-        refPpick = PragPicker(self.cf2, self.pickparams["tsnrz"], self.pickparams["pickwinP"], self.iplot, self.pickparams["ausP"],
-                              self.pickparams["tsmoothP"], aicpick.getpick(), self.current_figure, self.current_linecolor)
+        refPpick = PragPicker(self.cf2, self.pickparams["tsnrz"], self.pickparams["pickwinP"], self.iplot,
+                              self.pickparams["ausP"],
+                              self.pickparams["tsmoothP"], aicpick.getpick(), self.current_figure,
+                              self.current_linecolor)
        # save PragPicker result for plotting
        self.p_data.refPpick = refPpick
        self.p_results.mpp = refPpick.getpick()
        if self.p_results.mpp is None:
            msg = 'Bad initial (AIC) P-pick, skipping this onset!\n AIC-SNR={}, AIC-Slope={}counts/s\n' \
                  '(min. AIC-SNR={}, min. AIC-Slope={}counts/s)'
-            msg.format(aicpick.getSNR(), aicpick.getSlope(), self.pickparams["minAICPSNR"], self.pickparams["minAICPslope"])
+            msg.format(aicpick.getSNR(), aicpick.getSlope(), self.pickparams["minAICPSNR"],
+                       self.pickparams["minAICPslope"])
            self.vprint(msg)
            self.s_data.Sflag = 0
            raise PickingFailedException(msg)
        # quality assessment, get earliest/latest pick and symmetrized uncertainty
-        #todo quality assessment in own function
+        # todo quality assessment in own function
        self.set_current_figure('el_Ppick')
-        elpicker_results = earllatepicker(z_copy, self.pickparams["nfacP"], self.pickparams["tsnrz"], self.p_results.mpp,
+        elpicker_results = earllatepicker(z_copy, self.pickparams["nfacP"], self.pickparams["tsnrz"],
+                                          self.p_results.mpp,
                                          self.iplot, fig=self.current_figure, linecolor=self.current_linecolor)
        self.p_results.epp, self.p_results.lpp, self.p_results.spe = elpicker_results
        snr_results = getSNR(z_copy, self.pickparams["tsnrz"], self.p_results.mpp)
@@ -887,7 +911,8 @@ class AutopickStation(object):

        # weight P-onset using symmetric error
        self.p_results.weight = get_quality_class(self.p_results.spe, self.pickparams["timeerrorsP"])
-        if self.p_results.weight <= self.pickparams["minfmweight"] and self.p_results.snr >= self.pickparams["minFMSNR"]:
+        if self.p_results.weight <= self.pickparams["minfmweight"] and self.p_results.snr >= self.pickparams[
+            "minFMSNR"]:
            # if SNR is high enough, try to determine first motion of onset
            self.set_current_figure('fm_picker')
            self.p_results.fm = fmpicker(self.zstream, z_copy, self.pickparams["fmpickwin"], self.p_results.mpp,
@@ -960,7 +985,7 @@ class AutopickStation(object):
            trH1_filt, _ = self.prepare_wfstream(self.zstream, filter_freq_min, filter_freq_max)
            trH2_filt, _ = self.prepare_wfstream(self.estream, filter_freq_min, filter_freq_max)
            trH3_filt, _ = self.prepare_wfstream(self.nstream, filter_freq_min, filter_freq_max)
-            h_copy =self. hdat.copy()
+            h_copy = self.hdat.copy()
            h_copy[0].data = trH1_filt.data
            h_copy[1].data = trH2_filt.data
            h_copy[2].data = trH3_filt.data
@@ -1115,7 +1140,8 @@ class AutopickStation(object):
        # get preliminary onset time from AIC cf
        self.set_current_figure('aicARHfig')
        aicarhpick = AICPicker(haiccf, self.pickparams["tsnrh"], self.pickparams["pickwinS"], self.iplot,
-                               Tsmooth=self.pickparams["aictsmoothS"], fig=self.current_figure, linecolor=self.current_linecolor)
+                               Tsmooth=self.pickparams["aictsmoothS"], fig=self.current_figure,
+                               linecolor=self.current_linecolor)
        # save pick for later plotting
        self.aicarhpick = aicarhpick

@@ -1126,8 +1152,10 @@ class AutopickStation(object):

        # get refined onset time from CF2
        self.set_current_figure('refSpick')
-        refSpick = PragPicker(arhcf2, self.pickparams["tsnrh"], self.pickparams["pickwinS"], self.iplot, self.pickparams["ausS"],
-                              self.pickparams["tsmoothS"], aicarhpick.getpick(), self.current_figure, self.current_linecolor)
+        refSpick = PragPicker(arhcf2, self.pickparams["tsnrh"], self.pickparams["pickwinS"], self.iplot,
+                              self.pickparams["ausS"],
+                              self.pickparams["tsmoothS"], aicarhpick.getpick(), self.current_figure,
+                              self.current_linecolor)
        # save refSpick for later plotitng
        self.refSpick = refSpick
        self.s_results.mpp = refSpick.getpick()
@@ -1151,7 +1179,6 @@ class AutopickStation(object):
        self.current_linecolor = plot_style['linecolor']['rgba_mpl']


-
 def autopickstation(wfstream, pickparam, verbose=False, iplot=0, fig_dict=None, metadata=None, origin=None):
    """
    Main function to calculate picks for the station.
@@ -1239,11 +1266,11 @@ def iteratepicker(wf, NLLocfile, picks, badpicks, pickparameter, fig_dict=None):
        print(
            "iteratepicker: The following picking parameters have been modified for iterative picking:")
        print(
-                "pstart: %fs => %fs" % (pstart_old, pickparameter.get('pstart')))
+            "pstart: %fs => %fs" % (pstart_old, pickparameter.get('pstart')))
        print(
-                "pstop: %fs => %fs" % (pstop_old, pickparameter.get('pstop')))
+            "pstop: %fs => %fs" % (pstop_old, pickparameter.get('pstop')))
        print(
-                "sstop: %fs => %fs" % (sstop_old, pickparameter.get('sstop')))
+            "sstop: %fs => %fs" % (sstop_old, pickparameter.get('sstop')))
        print("pickwinP: %fs => %fs" % (
            pickwinP_old, pickparameter.get('pickwinP')))
        print("Precalcwin: %fs => %fs" % (
--- a/pylot/core/pick/charfuns.py
+++ b/pylot/core/pick/charfuns.py
@@ -18,8 +18,8 @@ autoregressive prediction: application ot local and regional distances, Geophys.
 """

 import numpy as np
-from scipy import signal
 from obspy.core import Stream
+from scipy import signal


 class CharacteristicFunction(object):
@@ -159,7 +159,7 @@ class CharacteristicFunction(object):
                zz = self.orig_data.copy()
                z1 = zz[0].copy()
                zz[0].data = z1.data[int(start):int(stop)]
-                if zz[0].stats.npts == 0: # cut times do not fit data length!
+                if zz[0].stats.npts == 0:  # cut times do not fit data length!
                    zz[0].data = z1.data  # take entire data
                data = zz
                return data
@@ -241,7 +241,7 @@ class AICcf(CharacteristicFunction):
        ff = np.where(inf is True)
        if len(ff) >= 1:
            cf[ff] = 0
-      
+
        self.cf = cf - np.mean(cf)
        self.xcf = x

@@ -305,7 +305,7 @@ class HOScf(CharacteristicFunction):
        if ind.size:
            first = ind[0]
            LTA[:first] = LTA[first]
-        
+
        self.cf = LTA
        self.xcf = x

@@ -313,7 +313,8 @@ class HOScf(CharacteristicFunction):
 class ARZcf(CharacteristicFunction):

    def __init__(self, data, cut, t1, t2, pickparams):
-        super(ARZcf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Parorder"], fnoise=pickparams["addnoise"])
+        super(ARZcf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Parorder"],
+                                    fnoise=pickparams["addnoise"])

    def calcCF(self, data):
        """
@@ -448,7 +449,8 @@ class ARZcf(CharacteristicFunction):
 class ARHcf(CharacteristicFunction):

    def __init__(self, data, cut, t1, t2, pickparams):
-        super(ARHcf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Sarorder"], fnoise=pickparams["addnoise"])
+        super(ARHcf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Sarorder"],
+                                    fnoise=pickparams["addnoise"])

    def calcCF(self, data):
        """
@@ -600,7 +602,8 @@ class ARHcf(CharacteristicFunction):
 class AR3Ccf(CharacteristicFunction):

    def __init__(self, data, cut, t1, t2, pickparams):
-        super(AR3Ccf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Sarorder"], fnoise=pickparams["addnoise"])
+        super(AR3Ccf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Sarorder"],
+                                     fnoise=pickparams["addnoise"])

    def calcCF(self, data):
        """
--- a/pylot/core/pick/compare.py
+++ b/pylot/core/pick/compare.py
@@ -2,10 +2,11 @@
 # -*- coding: utf-8 -*-

 import copy
-import matplotlib.pyplot as plt
-import numpy as np
 import operator
 import os
+
+import matplotlib.pyplot as plt
+import numpy as np
 from obspy.core import AttribDict

 from pylot.core.util.pdf import ProbabilityDensityFunction
@@ -117,7 +118,7 @@ class Comparison(object):

        pdf_a = self.get('auto').generate_pdf_data(type)
        pdf_b = self.get('manu').generate_pdf_data(type)
-        
+
        for station, phases in pdf_a.items():
            if station in pdf_b.keys():
                compare_pdf = dict()
@@ -400,6 +401,7 @@ class PDFstatistics(object):
    This object can be used to get various statistic values from probability density functions.
    Takes a path as argument.
    """
+
    # TODO: change root to datapath

    def __init__(self, directory):
--- a/pylot/core/pick/picker.py
+++ b/pylot/core/pick/picker.py
@@ -19,9 +19,10 @@ calculated after Diehl & Kissling (2009).
 :author: MAGS2 EP3 working group / Ludger Kueperkoch
 """

+import warnings
+
 import matplotlib.pyplot as plt
 import numpy as np
-import warnings
 from scipy.signal import argrelmax, argrelmin

 from pylot.core.pick.charfuns import CharacteristicFunction
@@ -476,7 +477,7 @@ class PragPicker(AutoPicker):
            cfpick_r = 0
            cfpick_l = 0
            lpickwindow = int(round(self.PickWindow / self.dt))
-            #for i in range(max(np.insert(ipick, 0, 2)), min([ipick1 + lpickwindow + 1, len(self.cf) - 1])):
+            # for i in range(max(np.insert(ipick, 0, 2)), min([ipick1 + lpickwindow + 1, len(self.cf) - 1])):
            #    # local minimum
            #    if self.cf[i + 1] > self.cf[i] <= self.cf[i - 1]:
            #        if cfsmooth[i - 1] * (1 + aus1) >= cfsmooth[i]:
@@ -509,7 +510,7 @@ class PragPicker(AutoPicker):
                self.Pick = pick_l
                pickflag = 1
            elif flagpick_l > 0 and flagpick_r > 0 and cfpick_l >= cfpick_r:
-                self.Pick = pick_r # MP MP there is no pick_r defined, commented out after commit of LK on 29.07.2020 (see above)
+                self.Pick = pick_r  # MP MP there is no pick_r defined, commented out after commit of LK on 29.07.2020 (see above)
                pickflag = 1
            elif flagpick_l == 0 and flagpick_r > 0 and cfpick_l >= cfpick_r:
                self.Pick = pick_l
--- a/pylot/core/pick/utils.py
+++ b/pylot/core/pick/utils.py
@@ -9,10 +9,11 @@
 """

 import warnings
+
 import matplotlib.pyplot as plt
 import numpy as np
-from scipy.signal import argrelmax
 from obspy.core import Stream, UTCDateTime
+from scipy.signal import argrelmax

 from pylot.core.util.utils import get_Bool, get_None, SetChannelComponents

@@ -73,7 +74,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol

    x = X[0].data
    t = np.linspace(0, X[0].stats.endtime - X[0].stats.starttime,
-                  X[0].stats.npts)
+                    X[0].stats.npts)
    inoise = getnoisewin(t, Pick1, TSNR[0], TSNR[1])
    # get signal window
    isignal = getsignalwin(t, Pick1, TSNR[2])
@@ -218,7 +219,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
        xraw = Xraw[0].data
        xfilt = Xfilt[0].data
        t = np.linspace(0, Xraw[0].stats.endtime - Xraw[0].stats.starttime,
-                      Xraw[0].stats.npts)
+                        Xraw[0].stats.npts)
        # get pick window
        ipick = np.where((t <= min([Pick + pickwin, len(Xraw[0])])) & (t >= Pick))
        if len(ipick[0]) <= 1:
@@ -536,9 +537,10 @@ def getslopewin(Tcf, Pick, tslope):
    :rtype: `numpy.ndarray`
    """
    # TODO: fill out docstring
-    slope = np.where( (Tcf <= min(Pick + tslope, Tcf[-1])) & (Tcf >= Pick) )
+    slope = np.where((Tcf <= min(Pick + tslope, Tcf[-1])) & (Tcf >= Pick))
    return slope[0]

+
 def getResolutionWindow(snr, extent):
    """
    Produce the half of the time resolution window width from given SNR value
@@ -848,7 +850,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
        print("Presumably picked noise peak, pick is rejected!")
        print("(min. signal length required: %s s)" % minsiglength)
        returnflag = 0
-    else:    
+    else:
        # calculate minimum adjusted signal level
        minsiglevel = np.mean(rms[inoise]) * nfac
        # minimum adjusted number of samples over minimum signal level
@@ -1207,7 +1209,7 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
            rms = rms_dict[key]
            trace = traces_dict[key]
            t = np.linspace(diff_dict[key], trace.stats.endtime - trace.stats.starttime + diff_dict[key],
-                          trace.stats.npts)
+                            trace.stats.npts)
            if i == 0:
                if get_None(fig) is None:
                    fig = plt.figure()  # self.iplot) ### WHY? MP MP
@@ -1329,6 +1331,7 @@ def get_quality_class(uncertainty, weight_classes):
        quality = len(weight_classes)
    return quality

+
 def set_NaNs_to(data, nan_value):
    """
    Replace all NaNs in data with nan_value
@@ -1344,6 +1347,7 @@ def set_NaNs_to(data, nan_value):
        data[nn] = nan_value
    return data

+
 def taper_cf(cf):
    """
    Taper cf data to get rid off of side maximas
@@ -1355,6 +1359,7 @@ def taper_cf(cf):
    tap = np.hanning(len(cf))
    return tap * cf

+
 def cf_positive(cf):
    """
    Shifts cf so that all values are positive
@@ -1365,6 +1370,7 @@ def cf_positive(cf):
    """
    return cf + max(abs(cf))

+
 def smooth_cf(cf, t_smooth, delta):
    """
    Smooth cf by taking samples over t_smooth length
@@ -1393,6 +1399,7 @@ def smooth_cf(cf, t_smooth, delta):
    cf_smooth -= offset  # remove offset from smoothed function
    return cf_smooth

+
 def check_counts_ms(data):
    """
    check if data is in counts or m/s
@@ -1452,9 +1459,9 @@ def calcSlope(Data, datasmooth, Tcf, Pick, TSNR):
        if imax == 0:
            print("AICPicker: Maximum for slope determination right at the beginning of the window!")
            print("Choose longer slope determination window!")
-            raise  IndexError
+            raise IndexError
        iislope = islope[0][0:imax + 1]  # cut index so it contains only the first maximum
-    dataslope = Data[0].data[iislope] # slope will only be calculated to the first maximum
+    dataslope = Data[0].data[iislope]  # slope will only be calculated to the first maximum
    # calculate slope as polynomal fit of order 1
    xslope = np.arange(0, len(dataslope))
    P = np.polyfit(xslope, dataslope, 1)
@@ -1475,8 +1482,10 @@ def get_pickparams(pickparam):
    :rtype: (dict, dict, dict, dict)
    """
    # Define names of all parameters in different groups
-    p_parameter_names = 'algoP pstart pstop use_taup taup_model tlta tsnrz hosorder bpz1 bpz2 pickwinP aictsmooth tsmoothP ausP nfacP tpred1z tdet1z Parorder addnoise Precalcwin minAICPslope minAICPSNR timeerrorsP checkwindowP minfactorP'.split(' ')
-    s_parameter_names = 'algoS sstart sstop bph1 bph2 tsnrh pickwinS tpred1h tdet1h tpred2h tdet2h Sarorder aictsmoothS tsmoothS ausS minAICSslope minAICSSNR Srecalcwin nfacS timeerrorsS zfac checkwindowS minfactorS'.split(' ')
+    p_parameter_names = 'algoP pstart pstop use_taup taup_model tlta tsnrz hosorder bpz1 bpz2 pickwinP aictsmooth tsmoothP ausP nfacP tpred1z tdet1z Parorder addnoise Precalcwin minAICPslope minAICPSNR timeerrorsP checkwindowP minfactorP'.split(
+        ' ')
+    s_parameter_names = 'algoS sstart sstop bph1 bph2 tsnrh pickwinS tpred1h tdet1h tpred2h tdet2h Sarorder aictsmoothS tsmoothS ausS minAICSslope minAICSSNR Srecalcwin nfacS timeerrorsS zfac checkwindowS minfactorS'.split(
+        ' ')
    first_motion_names = 'minFMSNR fmpickwin minfmweight'.split(' ')
    signal_length_names = 'minsiglength minpercent noisefactor'.split(' ')
    # Get list of values from pickparam by name
@@ -1494,6 +1503,7 @@ def get_pickparams(pickparam):

    return p_params, s_params, first_motion_params, signal_length_params

+
 def getQualityFromUncertainty(uncertainty, Errors):
    # set initial quality to 4 (worst) and change only if one condition is hit
    quality = 4
@@ -1517,6 +1527,7 @@ def getQualityFromUncertainty(uncertainty, Errors):

    return quality

+
 if __name__ == '__main__':
    import doctest

--- a/pylot/core/util/array_map.py
+++ b/pylot/core/util/array_map.py
@@ -1,27 +1,22 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-

-import sys
-import os
-import matplotlib
-
-from PySide2 import QtCore, QtGui, QtWidgets
-from PySide2.QtCore import Qt
-from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
-import matplotlib.patheffects as PathEffects
+import traceback

 import cartopy.crs as ccrs
-import matplotlib.pyplot as plt
 import cartopy.feature as cf
-from cartopy.mpl.gridliner import LongitudeFormatter, LatitudeFormatter
-
-import traceback
-import obspy
+import matplotlib
+import matplotlib.patheffects as PathEffects
+import matplotlib.pyplot as plt
 import numpy as np
+import obspy
+from PySide2 import QtWidgets
+from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 from scipy.interpolate import griddata
-from pylot.core.util.widgets import PickDlg
+
 from pylot.core.pick.utils import get_quality_class
+from pylot.core.util.widgets import PickDlg

 matplotlib.use('Qt5Agg')

@@ -173,7 +168,8 @@ class Array_map(QtWidgets.QWidget):
        self.canvas.fig.tight_layout()

    def add_merid_paral(self):
-        self.gridlines = self.canvas.axes.gridlines(draw_labels=False, alpha=0.6, color='gray', linewidth=self.linewidth/2, zorder=7)
+        self.gridlines = self.canvas.axes.gridlines(draw_labels=False, alpha=0.6, color='gray',
+                                                    linewidth=self.linewidth / 2, zorder=7)
        # TODO: current cartopy version does not support label removal. Devs are working on it.
        #  Should be fixed in coming cartopy versions
        # self.gridlines.xformatter = LONGITUDE_FORMATTER
@@ -513,7 +509,7 @@ class Array_map(QtWidgets.QWidget):
        levels = np.linspace(self.get_min_from_picks(), self.get_max_from_picks(), nlevel)

        self.contourf = self.canvas.axes.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
-                                                  linewidths=self.linewidth*5, transform=ccrs.PlateCarree(),
+                                                  linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
                                                  alpha=0.4, zorder=8, cmap=self.get_colormap())

    def get_colormap(self):
--- a/pylot/core/util/dataprocessing.py
+++ b/pylot/core/util/dataprocessing.py
@@ -2,9 +2,10 @@
 # -*- coding: utf-8 -*-

 import glob
-import numpy as np
 import os
 import sys
+
+import numpy as np
 from obspy import UTCDateTime, read_inventory, read
 from obspy.io.xseed import Parser

@@ -46,7 +47,7 @@ class Metadata(object):
    def __repr__(self):
        return self.__str__()

-    def add_inventory(self, path_to_inventory, obspy_dmt_inv = False):
+    def add_inventory(self, path_to_inventory, obspy_dmt_inv=False):
        """
        Add path to list of inventories.
        :param path_to_inventory: Path to a folder
@@ -211,6 +212,7 @@ class Metadata(object):
                        self.stations_dict[st_id] = {'latitude': station[0].latitude,
                                                     'longitude': station[0].longitude,
                                                     'elevation': station[0].elevation}
+
        read_stat = {'xml': stat_info_from_inventory,
                     'dless': stat_info_from_parser}

@@ -380,6 +382,7 @@ def check_time(datetime):
    except ValueError:
        return False

+
 # TODO: change root to datapath
 def get_file_list(root_dir):
    """
--- a/pylot/core/util/event.py
+++ b/pylot/core/util/event.py
@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-

 import os
+
 from obspy import UTCDateTime
 from obspy.core.event import Event as ObsPyEvent
 from obspy.core.event import Origin, ResourceIdentifier
--- a/pylot/core/util/generate_array_maps.py
+++ b/pylot/core/util/generate_array_maps.py
@@ -3,6 +3,7 @@
 # small script that creates array maps for each event within a previously generated PyLoT project

 import os
+
 num_thread = "16"
 os.environ["OMP_NUM_THREADS"] = num_thread
 os.environ["OPENBLAS_NUM_THREADS"] = num_thread
@@ -15,6 +16,7 @@ import multiprocessing
 import sys
 import glob
 import matplotlib
+
 matplotlib.use('Qt5Agg')
 sys.path.append(os.path.join('/'.join(sys.argv[0].split('/')[:-1]), '../../..'))

@@ -52,7 +54,8 @@ def array_map_worker(input_dict):
    print('Working on event: {} ({}/{})'.format(eventdir, input_dict['index'] + 1, input_dict['nEvents']))
    xml_picks = glob.glob(os.path.join(eventdir, f'*{input_dict["f_ext"]}.xml'))
    if not len(xml_picks):
-        print('Event {} does not have any picks associated with event file extension {}'. format(eventdir, input_dict['f_ext']))
+        print('Event {} does not have any picks associated with event file extension {}'.format(eventdir,
+                                                                                                input_dict['f_ext']))
        return
    # check for picks
    manualpicks = event.getPicks()
@@ -92,4 +95,3 @@ if __name__ == '__main__':

    for infile in args.infiles:
        main(os.path.join(args.dataroot, infile), f_ext='_correlated_0.03-0.1', ncores=args.ncores)
-
--- a/pylot/core/util/gui.py
+++ b/pylot/core/util/gui.py
@@ -11,7 +11,6 @@ try:
 except Exception as e:
    print('Warning: Could not import module QtCore.')

-
 from pylot.core.util.utils import pick_color


@@ -53,7 +52,7 @@ def which(program, parameter):
        settings = QSettings()
        for key in settings.allKeys():
            if 'binPath' in key:
-                os.environ['PATH'] += ':{0}'.format(settings.value(key))	
+                os.environ['PATH'] += ':{0}'.format(settings.value(key))
        nllocpath = ":" + parameter.get('nllocbin')
        os.environ['PATH'] += nllocpath
    except Exception as e:
@@ -73,7 +72,7 @@ def which(program, parameter):
            return program
    else:
        for path in os.environ["PATH"].split(os.pathsep):
-            exe_file = os.path.join(path, program) 
+            exe_file = os.path.join(path, program)
            for candidate in ext_candidates(exe_file):
                if is_exe(candidate):
                    return candidate
@@ -101,4 +100,3 @@ def make_pen(picktype, phase, key, quality):
        linestyle, width = pick_linestyle_pg(picktype, key)
        pen = pg.mkPen(rgba, width=width, style=linestyle)
        return pen
-
--- a/pylot/core/util/obspyDMT_interface.py
+++ b/pylot/core/util/obspyDMT_interface.py
@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-

 import os
+
 from obspy import UTCDateTime


@@ -36,12 +37,12 @@ def qml_from_obspyDMT(path):
        return IOError('Could not find Event at {}'.format(path))

    with open(path, 'rb') as infile:
-        event_dmt = pickle.load(infile)#, fix_imports=True)
+        event_dmt = pickle.load(infile)  # , fix_imports=True)

    event_dmt['origin_id'].id = str(event_dmt['origin_id'].id)

    ev = Event(resource_id=event_dmt['event_id'])
-    #small bugfix "unhashable type: 'newstr' "
+    # small bugfix "unhashable type: 'newstr' "
    event_dmt['origin_id'].id = str(event_dmt['origin_id'].id)

    origin = Origin(resource_id=event_dmt['origin_id'],
--- a/pylot/core/util/pdf.py
+++ b/pylot/core/util/pdf.py
@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-

-import numpy as np
 import warnings
+
+import numpy as np
 from obspy import UTCDateTime

 from pylot.core.util.utils import fit_curve, clims
--- a/pylot/core/util/thread.py
+++ b/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 PySide2.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
 from PySide2.QtWidgets import QDialog, QProgressBar, QLabel, QHBoxLayout, QPushButton

@@ -102,9 +105,9 @@ class Worker(QRunnable):
        try:
            result = self.fun(self.args)
        except:
-            exctype, value = sys.exc_info ()[:2]
+            exctype, value = sys.exc_info()[:2]
            print(exctype, value, traceback.format_exc())
-            self.signals.error.emit ((exctype, value, traceback.format_exc ()))
+            self.signals.error.emit((exctype, value, traceback.format_exc()))
        else:
            self.signals.result.emit(result)
        finally:
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -2,12 +2,13 @@
 # -*- coding: utf-8 -*-

 import hashlib
-import numpy as np
 import os
 import platform
 import re
 import subprocess
 import warnings
+
+import numpy as np
 from obspy import UTCDateTime, read
 from obspy.core import AttribDict
 from obspy.signal.rotate import rotate2zne
--- a/pylot/core/util/version.py
+++ b/pylot/core/util/version.py
@@ -35,9 +35,9 @@ from __future__ import print_function

 __all__ = "get_git_version"

+import inspect
 # NO IMPORTS FROM PYLOT IN THIS FILE! (file gets used at installation time)
 import os
-import inspect
 from subprocess import Popen, PIPE

 # NO IMPORTS FROM PYLOT IN THIS FILE! (file gets used at installation time)
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@@ -8,15 +8,16 @@ Created on Wed Mar 19 11:27:35 2014
 import copy
 import datetime
 import getpass
-import matplotlib
 import multiprocessing
-import numpy as np
 import os
 import subprocess
 import sys
 import time
 import traceback

+import matplotlib
+import numpy as np
+
 matplotlib.use('QT5Agg')

 from matplotlib.figure import Figure
@@ -36,7 +37,7 @@ from PySide2.QtWidgets import QAction, QApplication, QCheckBox, QComboBox, \
    QGridLayout, QLabel, QLineEdit, QMessageBox, \
    QTabWidget, QToolBar, QVBoxLayout, QHBoxLayout, QWidget, \
    QPushButton, QFileDialog, QInputDialog
-from PySide2.QtCore import QSettings, Qt, QUrl, Signal, Slot
+from PySide2.QtCore import QSettings, Qt, QUrl, Signal
 from PySide2.QtWebEngineWidgets import QWebEngineView as QWebView
 from obspy import Stream, Trace, UTCDateTime
 from obspy.core.util import AttribDict
@@ -65,19 +66,20 @@ else:
    raise ImportError(f'Python version {sys.version_info.major} of current interpreter not supported.'
                      f'\nPlease use Python 3+.')

-
 # workaround to prevent PyCharm from deleting icons_rc import when optimizing imports
-# icons_rc = icons_rc
+icons_rc = icons_rc


 class QSpinBox(QtWidgets.QSpinBox):
    ''' Custom SpinBox, insensitive to Mousewheel (prevents accidental changes when scrolling through parameters) '''
+
    def wheelEvent(self, event):
        event.ignore()


 class QDoubleSpinBox(QtWidgets.QDoubleSpinBox):
    ''' Custom DoubleSpinBox, insensitive to Mousewheel (prevents accidental changes when scrolling through parameters) '''
+
    def wheelEvent(self, event):
        event.ignore()

@@ -131,7 +133,7 @@ class LogWidget(QtWidgets.QWidget):
    def reset_error(self):
        # used to make sure that write errors is finished before raising new Message box etc.
        self.current_active_error = False
-        self.stderr.append(60*'#' + '\n\n')
+        self.stderr.append(60 * '#' + '\n\n')


 def getDataType(parent):