Merge branch 'develop' of https://git.geophysik.ruhr-uni-bochum.de/marcel/pylot into develop

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 = []

pylot/core/io/data.py

@@ -1,18 +1,18 @@
-#!/usr/bin/env pyth n
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 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 PySide.QtGui 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
@@ -21,13 +21,14 @@ from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
 from pylot.core.util.utils import fnConstructor, full_range, check4rotated, \
     check4gapsAndMerge, trim_station_components
 
+
 class Data(object):
     """
     Data container with attributes wfdata holding ~obspy.core.stream.
 
-    :type parent: PySide.QtGui.QWidget object, optional
-    :param parent: A PySide.QtGui.QWidget object utilized when
-    called by a GUI to display a PySide.QtGui.QMessageBox instead of printing
+    :type parent: PySide2.QtWidgets.QWidget object, optional
+    :param parent: A PySide2.QtWidgets.QWidget object utilized when
+    called by a GUI to display a PySide2.QtWidgets.QMessageBox instead of printing
     to standard out.
     :type evtdata: ~obspy.core.event.Event object, optional
     :param evtdata ~obspy.core.event.Event object containing all derived or
@@ -47,10 +48,10 @@ class Data(object):
         elif isinstance(evtdata, dict):
             evt = readPILOTEvent(**evtdata)
             evtdata = evt
-        elif type(evtdata) in [str, unicode]:
+        elif isinstance(evtdata, str):
             try:
                 cat = read_events(evtdata)
-                if len(cat) is not 1:
+                if len(cat) != 1:
                     raise ValueError('ambiguous event information for file: '
                                      '{file}'.format(file=evtdata))
                 evtdata = cat[0]
@@ -99,7 +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
@@ -111,7 +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):
@@ -162,9 +163,8 @@ class Data(object):
 
     def checkEvent(self, event, fcheck, forceOverwrite=False):
         """
-        Check information in supplied event and own event and replace own
-        information with supplied information if own information not exiisting
-        or forced by forceOverwrite
+        Check information in supplied event and own event and replace with own
+        information if no other information are given or forced by forceOverwrite
         :param event: Event that supplies information for comparison
         :type event: pylot.core.util.event.Event
         :param fcheck: check and delete existing information
@@ -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
@@ -318,7 +318,7 @@ class Data(object):
                             del picks_copy[k]
                             break
             lendiff = len(picks) - len(picks_copy)
-            if lendiff is not 0:
+            if lendiff != 0:
                 print("Manual as well as automatic picks available. Prefered the {} manual ones!".format(lendiff))
 
             if upperErrors:
@@ -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:
@@ -794,8 +795,8 @@ class PilotDataStructure(GenericDataStructure):
 
     def __init__(self, **fields):
         if not fields:
-            fields = {'database': '2006.01',
-                      'root': '/data/Egelados/EVENT_DATA/LOCAL'}
+            fields = {'database': '',
+                      'root': ''}
 
         GenericDataStructure.__init__(self, **fields)
 

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 = {

pylot/core/io/getEventListFromXML.py

@@ -8,14 +8,18 @@
    Edited for use in PyLoT
    JG, igem, 01/2022
 """
+<<<<<<< HEAD
 
 import os
 import argparse
 import numpy as np
 import matplotlib.pyplot as plt
+=======
+import glob
+
+>>>>>>> 83ba63a3fdd8ad0a212333928cfcd6f45fcb5baa
 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 +28,15 @@ 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 +57,31 @@ 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()
-

pylot/core/io/getQualitiesfromxml.py

@@ -1,139 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-
-"""
-   Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
-   Uncertainties are tranformed into quality classes and visualized via histogram if desired.
-   Ludger Küperkoch, BESTEC GmbH, 07/2017
-   rev.: Ludger Küperkoch, igem, 10/2020
-   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):
-
-    # uncertainties 
-    ErrorsP = [0.02, 0.04, 0.08, 0.16]
-    ErrorsS = [0.04, 0.08, 0.16, 0.32]
-
-    Pw0 = []
-    Pw1 = []
-    Pw2 = []
-    Pw3 = []
-    Pw4 = []
-    Sw0 = []
-    Sw1 = []
-    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: 
-        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)      
-                elif Pick.time_errors.uncertainty > ErrorsP[0] and \
-                     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)      
-                elif Pick.time_errors.uncertainty > ErrorsP[2] and \
-                     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)      
-                else:
-                    pass
-            elif Pick.phase_hint[0] == 'S':
-                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)      
-                elif Pick.time_errors.uncertainty > ErrorsS[1] and \
-                     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)      
-                elif Pick.time_errors.uncertainty > ErrorsS[3]:
-                     Sw4.append(Pick.time_errors.uncertainty)      
-                else:
-                    pass
-            else:
-                print("Phase hint not defined for picking!")
-                pass
-    # get percentage of weights
-    numPweights = np.sum([len(Pw0), len(Pw1), len(Pw2), len(Pw3), len(Pw4)])
-    numSweights = np.sum([len(Sw0), len(Sw1), len(Sw2), len(Sw3), len(Sw4)])
-    try:
-        P0perc = 100.0 / numPweights * len(Pw0)
-    except:
-        P0perc = 0
-    try:
-        P1perc = 100.0 / numPweights * len(Pw1)
-    except:
-        P1perc = 0
-    try:
-        P2perc = 100.0 / numPweights * len(Pw2)
-    except:
-        P2perc = 0
-    try:
-        P3perc = 100.0 / numPweights * len(Pw3)
-    except:
-        P3perc = 0
-    try:
-        P4perc = 100.0 / numPweights * len(Pw4)
-    except:
-        P4perc = 0
-    try:
-        S0perc = 100.0 / numSweights * len(Sw0)
-    except:
-        Soperc = 0
-    try:
-        S1perc = 100.0 / numSweights * len(Sw1)
-    except:
-        S1perc = 0
-    try:
-        S2perc = 100.0 / numSweights * len(Sw2)
-    except:
-        S2perc = 0
-    try:
-        S3perc = 100.0 / numSweights * len(Sw3)
-    except:
-        S3perc = 0
-    try:
-        S4perc = 100.0 / numSweights * len(Sw4)
-    except:
-        S4perc = 0
-
-    weights = ('0', '1', '2', '3', '4')
-    y_pos = np.arange(len(weights))
-    width = 0.34
-    p1, = plt.bar(0 - width, P0perc, width, color='black')
-    p2, = plt.bar(0, S0perc, width, color='red')
-    plt.bar(y_pos - width, [P0perc, P1perc, P2perc, P3perc, P4perc], width, color='black')
-    plt.bar(y_pos, [S0perc, S1perc, S2perc, S3perc, S4perc], width, color='red')
-    plt.ylabel('%')
-    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.legend([p1, p2], ['P-Weights', 'S-Weights'])
-    plt.show()
-

pylot/core/io/phases.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-import pdb
 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
@@ -17,7 +17,7 @@ from pylot.core.io.location import create_event, \
     create_magnitude
 from pylot.core.pick.utils import select_for_phase, get_quality_class
 from pylot.core.util.utils import getOwner, full_range, four_digits, transformFilterString4Export, \
-    backtransformFilterString
+    backtransformFilterString, loopIdentifyPhase, identifyPhase
 
 
 def add_amplitudes(event, amplitudes):
@@ -232,7 +232,7 @@ def picksdict_from_picks(evt):
     for pick in evt.picks:
         phase = {}
         station = pick.waveform_id.station_code
-        if pick.waveform_id.channel_code == None:
+        if pick.waveform_id.channel_code is None:
             channel = ''
         else:
             channel = pick.waveform_id.channel_code
@@ -375,8 +375,7 @@ def picks_from_picksdict(picks, creation_info=None):
 
 
 def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0):
-    import glob
-
+    # TODO: change root to datapath
     db_root = os.path.join(root_dir, db_dir)
     evt_list = glob.glob1(db_root, 'e????.???.??')
 
@@ -391,9 +390,7 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
 
     from pylot.core.io.inputs import PylotParameter
     from pylot.core.pick.utils import earllatepicker
-
-    if fn_param is None:
-        fn_param = defaults.AUTOMATIC_DEFAULTS
+    # TODO: change root to datapath
 
     default = PylotParameter(fn_param, verbosity)
 
@@ -483,7 +480,6 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
             os.makedirs(out_dir)
         fnout_prefix = os.path.join(out_dir, 'PyLoT_{0}.'.format(event_id))
     evt.write(fnout_prefix + 'xml', format='QUAKEML')
-    # evt.write(fnout_prefix + 'cnv', format='VELEST')
 
 
 def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
@@ -511,14 +507,14 @@ 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)
+        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'):
@@ -572,20 +568,20 @@ 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':
@@ -594,7 +590,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         # write header
         fid.write('                                                                %s\n' %
                   parameter.get('eventID'))
-        arrivals = chooseArrivals(arrivals)
+        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
@@ -671,7 +667,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         fid = open("%s" % filename, 'w')
         # write header
         fid.write('%s, event %s \n' % (parameter.get('database'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals)
+        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') and arrivals[key]['P']['mpp'] is not None:
@@ -769,7 +765,7 @@ 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 = chooseArrivals(arrivals)
         for key in usedarrivals:
             # P onsets
             if usedarrivals[key].has_key('P'):
@@ -781,7 +777,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                     Ponset = usedarrivals[key]['P']['mpp']
                     Pweight = usedarrivals[key]['P']['weight']
                     Prt = Ponset - stime  # onset time relative to source time
-                    if n % 6 is not 0:
+                    if n % 6 != 0:
                         fid.write('%-4sP%d%6.2f' % (stat, Pweight, Prt))
                     else:
                         fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))
@@ -795,7 +791,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                     Sonset = usedarrivals[key]['S']['mpp']
                     Sweight = usedarrivals[key]['S']['weight']
                     Srt = Ponset - stime  # onset time relative to source time
-                    if n % 6 is not 0:
+                    if n % 6 != 0:
                         fid.write('%-4sS%d%6.2f' % (stat, Sweight, Srt))
                     else:
                         fid.write('%-4sS%d%6.2f\n' % (stat, Sweight, Srt))
@@ -815,9 +811,9 @@ 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,
@@ -830,7 +826,7 @@ 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 = chooseArrivals(arrivals)
         for key in usedarrivals:
             if usedarrivals[key].has_key('P'):
                 # P onsets
@@ -881,7 +877,7 @@ 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 = chooseArrivals(arrivals)
         for key in usedarrivals:
             if usedarrivals[key].has_key('P'):
                 if usedarrivals[key]['P']['weight'] < 4 and usedarrivals[key]['P']['fm'] is not None:
@@ -962,7 +958,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                 erh, erz, eventinfo.magnitudes[0]['mag'],
                 hashID))
         # Prefer Manual Picks over automatic ones if possible
-        arrivals = chooseArrivals(arrivals)
+        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         # write phase lines
         for key in arrivals:
             if arrivals[key].has_key('P'):
@@ -1009,7 +1005,8 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         fid1.close()
         fid2.close()
 
-def chooseArrival(arrivals):
+
+def chooseArrivals(arrivals):
     """
     takes arrivals and returns the manual picks if manual and automatic ones are there
     returns automatic picks if only automatic picks are there
@@ -1058,37 +1055,63 @@ def merge_picks(event, picks):
     return event
 
 
-def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
+def getQualitiesfromxml(path, errorsP, errorsS, plotflag=1, figure=None, verbosity=0):
     """
     Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
     Uncertainties are tranformed into quality classes and visualized via histogram if desired.
     Ludger Küperkoch, BESTEC GmbH, 07/2017
-    :param xmlnames: list of xml obspy event files containing picks
-    :type xmlnames: list
-    :param ErrorsP: time errors of P waves for the four discrete quality classes
-    :type ErrorsP:
-    :param ErrorsS: time errors of S waves for the four discrete quality classes
-    :type ErrorsS:
+    :param path: path containing xml files
+    :type path: str
+    :param errorsP: time errors of P waves for the four discrete quality classes
+    :type errorsP:
+    :param errorsS: time errors of S waves for the four discrete quality classes
+    :type errorsS:
     :param plotflag:
     :type plotflag:
     :return:
     :rtype:
     """
 
-    from pylot.core.pick.utils import get_quality_class
-    from pylot.core.util.utils import loopIdentifyPhase, identifyPhase
+    def calc_perc(uncertainties, ntotal):
+        ''' simple function that calculates percentage of number of uncertainties (list length)'''
+        if len(uncertainties) == 0:
+            return 0
+        else:
+            return 100. / ntotal * len(uncertainties)
+
+    def calc_weight_perc(psweights, weight_ids):
+        ''' calculate percentages of different weights (pick classes!?) of total number of uncertainties of a phase'''
+        # count total number of list items for this phase
+        numWeights = np.sum([len(weight) for weight in psweights.values()])
+
+        # iterate over all available weights to return a list with percentages for plotting
+        plot_list = []
+        for weight_id in weight_ids:
+            plot_list.append(calc_perc(psweights[weight_id], numWeights))
+
+        return plot_list, numWeights
+
+    # get all xmlfiles in path (maybe this should be changed to one xml file for this function, selectable via GUI?)
+    xmlnames = glob.glob(os.path.join(path, '*.xml'))
+    if len(xmlnames) == 0:
+        print(f'No files found in path {path}.')
+        return False
+
+    # first define possible phases here
+    phases = ['P', 'S']
+
+    # define possible weights (0-4)
+    weight_ids = list(range(5))
+
+    # put both error lists in a dictionary with P/S key so that amount of code can be halfed by simply using P/S as key
+    errors = dict(P=errorsP, S=errorsS)
+
+    # create dictionaries for each phase (P/S) with a dictionary of empty list for each weight defined in weights
+    # tuple above
+    weights = {}
+    for phase in phases:
+        weights[phase] = {weight_id: [] for weight_id in weight_ids}
 
-    # read all onset weights
-    Pw0 = []
-    Pw1 = []
-    Pw2 = []
-    Pw3 = []
-    Pw4 = []
-    Sw0 = []
-    Sw1 = []
-    Sw2 = []
-    Sw3 = []
-    Sw4 = []
     for names in xmlnames:
         print("Getting onset weights from {}".format(names))
         cat = read_events(names)
@@ -1096,117 +1119,60 @@ def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
         arrivals = cat.events[0].picks
         arrivals_copy = cat_copy.events[0].picks
         # Prefere manual picks if qualities are sufficient!
-        for Pick in arrivals:
-            if Pick.method_id.id.split('/')[1] == 'manual':
-                mstation = Pick.waveform_id.station_code
+        for pick in arrivals:
+            if pick.method_id.id.split('/')[1] == 'manual':
+                mstation = pick.waveform_id.station_code
                 mstation_ext = mstation + '_'
                 for mpick in arrivals_copy:
-                    phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint))
-                    if phase == 'P':
-                        if ((mpick.waveform_id.station_code == mstation) or
-                            (mpick.waveform_id.station_code == mstation_ext)) and \
-                                (mpick.method_id.split('/')[1] == 'auto') and \
-                                (mpick.time_errors['uncertainty'] <= ErrorsP[3]):
-                            del mpick
-                            break
-                    elif phase == 'S':
-                        if ((mpick.waveform_id.station_code == mstation) or
-                            (mpick.waveform_id.station_code == mstation_ext)) and \
-                                (mpick.method_id.split('/')[1] == 'auto') and \
-                                (mpick.time_errors['uncertainty'] <= ErrorsS[3]):
-                            del mpick
-                            break
+                    phase = identifyPhase(loopIdentifyPhase(pick.phase_hint)) # MP MP catch if this fails?
+                    if ((mpick.waveform_id.station_code == mstation) or
+                        (mpick.waveform_id.station_code == mstation_ext)) and \
+                            (mpick.method_id.id.split('/')[1] == 'auto') and \
+                            (mpick.time_errors['uncertainty'] <= errors[phase][3]):
+                        del mpick
+                        break
         lendiff = len(arrivals) - len(arrivals_copy)
-        if lendiff is not 0:
+        if lendiff != 0:
             print("Found manual as well as automatic picks, prefered the {} manual ones!".format(lendiff))
 
-        for Pick in arrivals_copy:
-            phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint))
-            if phase == 'P':
-                Pqual = get_quality_class(Pick.time_errors.uncertainty, ErrorsP)
-                if Pqual == 0:
-                    Pw0.append(Pick.time_errors.uncertainty)
-                elif Pqual == 1:
-                    Pw1.append(Pick.time_errors.uncertainty)
-                elif Pqual == 2:
-                    Pw2.append(Pick.time_errors.uncertainty)
-                elif Pqual == 3:
-                    Pw3.append(Pick.time_errors.uncertainty)
-                elif Pqual == 4:
-                    Pw4.append(Pick.time_errors.uncertainty)
-            elif phase == 'S':
-                Squal = get_quality_class(Pick.time_errors.uncertainty, ErrorsS)
-                if Squal == 0:
-                    Sw0.append(Pick.time_errors.uncertainty)
-                elif Squal == 1:
-                    Sw1.append(Pick.time_errors.uncertainty)
-                elif Squal == 2:
-                    Sw2.append(Pick.time_errors.uncertainty)
-                elif Squal == 3:
-                    Sw3.append(Pick.time_errors.uncertainty)
-                elif Squal == 4:
-                    Sw4.append(Pick.time_errors.uncertainty)
-            else:
+        for pick in arrivals_copy:
+            phase = identifyPhase(loopIdentifyPhase(pick.phase_hint))
+            uncertainty = pick.time_errors.uncertainty
+            if not uncertainty:
+                if verbosity > 0:
+                    print('No uncertainty, pick {} invalid!'.format(pick.method_id.id))
+                continue
+            # check P/S phase
+            if phase not in phases:
                 print("Phase hint not defined for picking!")
-                pass
+                continue
+
+            qual = get_quality_class(uncertainty, errors[phase])
+            weights[phase][qual].append(uncertainty)
 
     if plotflag == 0:
-        Punc = [Pw0, Pw1, Pw2, Pw3, Pw4]
-        Sunc = [Sw0, Sw1, Sw2, Sw3, Sw4]
-        return Punc, Sunc
+        p_unc = [weights['P'][weight_id] for weight_id in weight_ids]
+        s_unc = [weights['S'][weight_id] for weight_id in weight_ids]
+        return p_unc, s_unc
     else:
+        if not figure:
+            fig = plt.figure()
+        ax = fig.add_subplot(111)
         # get percentage of weights
-        numPweights = np.sum([len(Pw0), len(Pw1), len(Pw2), len(Pw3), len(Pw4)])
-        numSweights = np.sum([len(Sw0), len(Sw1), len(Sw2), len(Sw3), len(Sw4)])
-        if len(Pw0) > 0:
-            P0perc = 100 / numPweights * len(Pw0)
-        else:
-            P0perc = 0
-        if len(Pw1) > 0:
-            P1perc = 100 / numPweights * len(Pw1)
-        else:
-            P1perc = 0
-        if len(Pw2) > 0:
-            P2perc = 100 / numPweights * len(Pw2)
-        else:
-            P2perc = 0
-        if len(Pw3) > 0:
-            P3perc = 100 / numPweights * len(Pw3)
-        else:
-            P3perc = 0
-        if len(Pw4) > 0:
-            P4perc = 100 / numPweights * len(Pw4)
-        else:
-            P4perc = 0
-        if len(Sw0) > 0:
-            S0perc = 100 / numSweights * len(Sw0)
-        else:
-            S0perc = 0
-        if len(Sw1) > 0:
-            S1perc = 100 / numSweights * len(Sw1)
-        else:
-            S1perc = 0
-        if len(Sw2) > 0:
-            S2perc = 100 / numSweights * len(Sw2)
-        else:
-            S2perc = 0
-        if len(Sw3) > 0:
-            S3perc = 100 / numSweights * len(Sw3)
-        else:
-            S3perc = 0
-        if len(Sw4) > 0:
-            S4perc = 100 / numSweights * len(Sw4)
-        else:
-            S4perc = 0
+        listP, numPweights = calc_weight_perc(weights['P'], weight_ids)
+        listS, numSweights = calc_weight_perc(weights['S'], weight_ids)
 
-        weights = ('0', '1', '2', '3', '4')
-        y_pos = np.arange(len(weights))
+        y_pos = np.arange(len(weight_ids))
         width = 0.34
-        plt.bar(y_pos - width, [P0perc, P1perc, P2perc, P3perc, P4perc], width, color='black')
-        plt.bar(y_pos, [S0perc, S1perc, S2perc, S3perc, S4perc], width, color='red')
-        plt.ylabel('%')
-        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.show()
+        ax.bar(y_pos - width, listP, width, color='black')
+        ax.bar(y_pos, listS, width, color='red')
+        ax.set_ylabel('%')
+        ax.set_xticks(y_pos, weight_ids)
+        ax.set_xlim([-0.5, 4.5])
+        ax.set_xlabel('Qualities')
+        ax.set_title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights))
+
+        if not figure:
+            fig.show()
+
+        return listP, listS

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()

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):
@@ -474,13 +475,9 @@ class AutopickStation(object):
                 # TODO here the pickparams is modified, instead of a copy
                 self.pickparams["pstart"] = 0
 
-        if self.pickparams["use_taup"] is False or not self.origin or not self.metadata:
+        if self.pickparams["use_taup"] is False:
             # correct user mistake where a relative cuttime is selected (pstart < 0) but use of taupy is disabled/ has
             # not the required parameters
-            if not self.origin:
-                print('Requested use_taup but no origin given. Exit taupy.')
-            if not self.metadata:
-                print('Requested use_taup but no metadata given. Exit taupy.')
             exit_taupy()
             return
 
@@ -528,7 +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):
 
@@ -577,7 +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:
@@ -592,12 +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
@@ -635,23 +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')
@@ -671,15 +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')
@@ -720,7 +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
@@ -730,14 +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
@@ -823,15 +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)
@@ -845,7 +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
@@ -853,7 +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
@@ -865,25 +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)
@@ -891,7 +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,
@@ -964,7 +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
@@ -1119,7 +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
 
@@ -1130,8 +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()
@@ -1155,7 +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.
@@ -1243,11 +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" % (

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):
@@ -150,7 +150,7 @@ class CharacteristicFunction(object):
                 if self.cut[0] == 0 and self.cut[1] == 0:
                     start = 0
                     stop = len(self.orig_data[0])
-                elif self.cut[0] == 0 and self.cut[1] is not 0:
+                elif self.cut[0] == 0 and self.cut[1] != 0:
                     start = 0
                     stop = self.cut[1] / self.dt
                 else:
@@ -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
@@ -167,7 +167,7 @@ class CharacteristicFunction(object):
                 if self.cut[0] == 0 and self.cut[1] == 0:
                     start = 0
                     stop = min([len(self.orig_data[0]), len(self.orig_data[1])])
-                elif self.cut[0] == 0 and self.cut[1] is not 0:
+                elif self.cut[0] == 0 and self.cut[1] != 0:
                     start = 0
                     stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
                                 len(self.orig_data[1])])
@@ -187,7 +187,7 @@ class CharacteristicFunction(object):
                     start = 0
                     stop = min([self.cut[1] / self.dt, len(self.orig_data[0]),
                                 len(self.orig_data[1]), len(self.orig_data[2])])
-                elif self.cut[0] == 0 and self.cut[1] is not 0:
+                elif self.cut[0] == 0 and self.cut[1] != 0:
                     start = 0
                     stop = self.cut[1] / self.dt
                 else:
@@ -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):
         """

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()
@@ -401,6 +402,8 @@ class PDFstatistics(object):
     Takes a path as argument.
     """
 
+    # TODO: change root to datapath
+
     def __init__(self, directory):
         """Initiates some values needed when dealing with pdfs later"""
         self._rootdir = directory

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]:

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
@@ -1318,6 +1320,7 @@ def get_quality_class(uncertainty, weight_classes):
     :return: quality of pick (0-4)
     :rtype: int
     """
+    if not uncertainty: return len(weight_classes)
     try:
         # create generator expression containing all indices of values in weight classes that are >= than uncertainty.
         # call next on it once to receive first value
@@ -1328,6 +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
@@ -1343,6 +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
@@ -1354,6 +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
@@ -1364,6 +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
@@ -1392,6 +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
@@ -1451,9 +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)
@@ -1474,8 +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
@@ -1493,6 +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
@@ -1516,6 +1527,7 @@ def getQualityFromUncertainty(uncertainty, Errors):
 
     return quality
 
+
 if __name__ == '__main__':
     import doctest
 

pylot/core/util/array_map.py

@@ -1,38 +1,51 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import os
+import traceback
+
+import cartopy.crs as ccrs
+import cartopy.feature as cf
+import matplotlib
+import matplotlib.patheffects as PathEffects
 import matplotlib.pyplot as plt
 import numpy as np
 import obspy
-import traceback
-from PySide import QtGui
-from matplotlib.figure import Figure
+from PySide2 import QtWidgets
+from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
-from mpl_toolkits.basemap import Basemap
 from scipy.interpolate import griddata
 
-from pylot.core.util.widgets import PickDlg, PylotCanvas
 from pylot.core.pick.utils import get_quality_class
+from pylot.core.util.widgets import PickDlg
 
-plt.interactive(False)
+matplotlib.use('Qt5Agg')
 
 
-class Array_map(QtGui.QWidget):
-    def __init__(self, parent, metadata, parameter=None, figure=None, annotate=True, pointsize=25.,
+class MplCanvas(FigureCanvas):
+
+    def __init__(self, parent=None, extern_axes=None, width=5, height=4, dpi=100):
+        if extern_axes is None:
+            self.fig = plt.figure(figsize=(width, height), dpi=dpi)
+            self.axes = self.fig.add_subplot(111)
+        else:
+            self.fig = extern_axes.figure
+            self.axes = extern_axes
+
+        super(MplCanvas, self).__init__(self.fig)
+
+
+class Array_map(QtWidgets.QWidget):
+    def __init__(self, parent, metadata, parameter=None, axes=None, annotate=True, pointsize=25.,
                  linewidth=1.5, width=5e6, height=2e6):
-        '''
-        Create a map of the array.
-        :param parent: object of PyLoT Mainwindow class
-        :param parameter: object of PyLoT parameter class
-        :param figure:
-        '''
-        QtGui.QWidget.__init__(self)
-        assert (parameter != None or parent != None), 'either parent or parameter has to be set'
+        QtWidgets.QWidget.__init__(self, parent=parent)
+
+        assert (parameter is not None or parent is not None), 'either parent or parameter has to be set'
+        # set properties
         self._parent = parent
         self.metadata = metadata
         self.pointsize = pointsize
         self.linewidth = linewidth
+        self.extern_plot_axes = axes
         self.width = width
         self.height = height
         self.annotate = annotate
@@ -43,34 +56,228 @@ class Array_map(QtGui.QWidget):
         self.hybrids_dict = None
         self.eventLoc = None
         self.parameter = parameter if parameter else parent._inputs
-        self.figure = figure
+
         self.picks_rel = {}
         self.marked_stations = []
         self.highlighted_stations = []
+
+        # call functions to draw everything
         self.init_graphics()
         self.init_stations()
-        self.init_basemap(resolution='l')
+        self.init_crtpyMap()
         self.init_map()
-        self._style = None if not hasattr(parent, '_style') else parent._style
-        # self.show()
+        # set original map limits to fall back on when home button is pressed
+        self.org_xlim = self.canvas.axes.get_xlim()
+        self.org_ylim = self.canvas.axes.get_ylim()
+        # initial map without event
+        self.canvas.axes.set_xlim(self.org_xlim[0], self.org_xlim[1])
+        self.canvas.axes.set_ylim(self.org_ylim[0], self.org_ylim[1])
 
-    def update_hybrids_dict(self):
-        self.hybrids_dict = self.picks_dict.copy()
-        for station, pick in self.autopicks_dict.items():
-            if not station in self.hybrids_dict.keys():
-                self.hybrids_dict[station] = pick
-        return self.hybrids_dict
+        self._style = None if not hasattr(parent, '_style') else parent._style
+
+        self.show()
 
     def init_map(self):
         self.init_colormap()
         self.connectSignals()
         self.draw_everything()
-        self.canvas.setZoomBorders2content()
+
+    def init_graphics(self):
+        """
+        Initializes all GUI components and figure elements to be populated by other functions
+        """
+        # initialize figure elements
+
+        if self.extern_plot_axes is None:
+            self.canvas = MplCanvas(self)
+            self.plotWidget = FigureCanvas(self.canvas.fig)
+        else:
+            self.canvas = MplCanvas(self, extern_axes=self.extern_plot_axes)
+            self.plotWidget = FigureCanvas(self.canvas.fig)
+
+        # initialize GUI elements
+        self.status_label = QtWidgets.QLabel()
+        self.map_reset_button = QtWidgets.QPushButton('Reset Map View')
+        self.save_map_button = QtWidgets.QPushButton('Save Map')
+        self.go2eq_button = QtWidgets.QPushButton('Go to Event Location')
+
+        self.main_box = QtWidgets.QVBoxLayout()
+        self.setLayout(self.main_box)
+
+        self.top_row = QtWidgets.QHBoxLayout()
+        self.main_box.addLayout(self.top_row, 1)
+
+        self.comboBox_phase = QtWidgets.QComboBox()
+        self.comboBox_phase.insertItem(0, 'P')
+        self.comboBox_phase.insertItem(1, 'S')
+
+        self.comboBox_am = QtWidgets.QComboBox()
+        self.comboBox_am.insertItem(0, 'hybrid (prefer manual)')
+        self.comboBox_am.insertItem(1, 'manual')
+        self.comboBox_am.insertItem(2, 'auto')
+
+        self.annotations_box = QtWidgets.QCheckBox('Annotate')
+        self.annotations_box.setChecked(True)
+        self.auto_refresh_box = QtWidgets.QCheckBox('Automatic refresh')
+        self.auto_refresh_box.setChecked(True)
+        self.refresh_button = QtWidgets.QPushButton('Refresh')
+        self.cmaps_box = QtWidgets.QComboBox()
+        self.cmaps_box.setMaxVisibleItems(20)
+        [self.cmaps_box.addItem(map_name) for map_name in sorted(plt.colormaps())]
+        # try to set to hsv as default
+        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('hsv'))
+
+        self.top_row.addWidget(QtWidgets.QLabel('Select a phase: '))
+        self.top_row.addWidget(self.comboBox_phase)
+        self.top_row.setStretch(1, 1)  # set stretch of item 1 to 1
+        self.top_row.addWidget(QtWidgets.QLabel('Pick type: '))
+        self.top_row.addWidget(self.comboBox_am)
+        self.top_row.setStretch(3, 1)  # set stretch of item 1 to 1
+        self.top_row.addWidget(self.cmaps_box)
+        self.top_row.addWidget(self.annotations_box)
+        self.top_row.addWidget(self.auto_refresh_box)
+        self.top_row.addWidget(self.refresh_button)
+
+        self.main_box.addWidget(self.plotWidget, 1)
+
+        self.bot_row = QtWidgets.QHBoxLayout()
+        self.main_box.addLayout(self.bot_row, 0.3)
+        self.bot_row.addWidget(QtWidgets.QLabel(''), 5)
+        self.bot_row.addWidget(self.map_reset_button, 2)
+        self.bot_row.addWidget(self.go2eq_button, 2)
+        self.bot_row.addWidget(self.save_map_button, 2)
+        self.bot_row.addWidget(self.status_label, 5)
 
     def init_colormap(self):
         self.init_lat_lon_dimensions()
         self.init_lat_lon_grid()
-        self.init_x_y_dimensions()
+
+    def init_crtpyMap(self):
+        self.canvas.axes.cla()
+        self.canvas.axes = plt.axes(projection=ccrs.PlateCarree())
+        self.canvas.axes.add_feature(cf.LAND)
+        self.canvas.axes.add_feature(cf.OCEAN)
+        self.canvas.axes.add_feature(cf.COASTLINE, linewidth=1, edgecolor='gray')
+        self.canvas.axes.add_feature(cf.BORDERS, alpha=0.7)
+        self.canvas.axes.add_feature(cf.LAKES, alpha=0.7)
+        self.canvas.axes.add_feature(cf.RIVERS, linewidth=1)
+
+        # parallels and meridians
+        self.add_merid_paral()
+
+        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)
+        # 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
+        # self.gridlines.yformatter = LATITUDE_FORMATTER
+
+    def remove_merid_paral(self):
+        if len(self.gridlines.xline_artists):
+            self.gridlines.xline_artists[0].remove()
+            self.gridlines.yline_artists[0].remove()
+
+    def org_map_view(self):
+        self.canvas.axes.set_xlim(self.org_xlim[0], self.org_xlim[1])
+        self.canvas.axes.set_ylim(self.org_ylim[0], self.org_ylim[1])
+        # parallels and meridians
+        self.remove_merid_paral()
+        self.add_merid_paral()
+
+        self.canvas.axes.figure.canvas.draw_idle()
+
+    def go2eq(self):
+        if self.eventLoc:
+            lats, lons = self.eventLoc
+            self.canvas.axes.set_xlim(lons - 10, lons + 10)
+            self.canvas.axes.set_ylim(lats - 5, lats + 5)
+            # parallels and meridians
+            self.remove_merid_paral()
+            self.add_merid_paral()
+
+            self.canvas.axes.figure.canvas.draw_idle()
+
+        else:
+            self.status_label.setText('No event information available')
+
+    def connectSignals(self):
+        self.comboBox_phase.currentIndexChanged.connect(self._refresh_drawings)
+        self.comboBox_am.currentIndexChanged.connect(self._refresh_drawings)
+        self.cmaps_box.currentIndexChanged.connect(self._refresh_drawings)
+        self.annotations_box.stateChanged.connect(self.switch_annotations)
+        self.refresh_button.clicked.connect(self._refresh_drawings)
+        self.map_reset_button.clicked.connect(self.org_map_view)
+        self.go2eq_button.clicked.connect(self.go2eq)
+        self.save_map_button.clicked.connect(self.saveFigure)
+
+        self.plotWidget.mpl_connect('motion_notify_event', self.mouse_moved)
+        self.plotWidget.mpl_connect('scroll_event', self.mouse_scroll)
+        self.plotWidget.mpl_connect('button_press_event', self.mouseLeftPress)
+        self.plotWidget.mpl_connect('button_release_event', self.mouseLeftRelease)
+
+    # set mouse events -----------------------------------------------------
+    def mouse_moved(self, event):
+        if not event.inaxes == self.canvas.axes:
+            return
+        lat = event.ydata
+        lon = event.xdata
+        self.status_label.setText('Latitude: {:3.5f}, Longitude: {:3.5f}'.format(lat, lon))
+
+    def mouse_scroll(self, event):
+        if not event.inaxes == self.canvas.axes:
+            return
+
+        zoom = {'up': 1. / 2., 'down': 2.}
+
+        if event.button in zoom:
+            xlim = self.canvas.axes.get_xlim()
+            ylim = self.canvas.axes.get_ylim()
+
+            x, y = event.xdata, event.ydata
+
+            factor = zoom[event.button]
+            xdiff = (xlim[1] - xlim[0]) * factor
+            xl = x - 0.5 * xdiff
+            xr = x + 0.5 * xdiff
+            ydiff = (ylim[1] - ylim[0]) * factor
+            yb = y - 0.5 * ydiff
+            yt = y + 0.5 * ydiff
+
+            self.canvas.axes.set_xlim(xl, xr)
+            self.canvas.axes.set_ylim(yb, yt)
+            # parallels and meridians
+            self.remove_merid_paral()
+            self.add_merid_paral()
+
+            self.canvas.axes.figure.canvas.draw_idle()
+
+    def mouseLeftPress(self, event):
+        if not event.inaxes == self.canvas.axes:
+            return
+        self.map_x = event.xdata
+        self.map_y = event.ydata
+        self.map_xlim = self.canvas.axes.get_xlim()
+        self.map_ylim = self.canvas.axes.get_ylim()
+
+    def mouseLeftRelease(self, event):
+        if not event.inaxes == self.canvas.axes:
+            return
+        new_x = event.xdata
+        new_y = event.ydata
+
+        dx = new_x - self.map_x
+        dy = new_y - self.map_y
+
+        self.canvas.axes.set_xlim((self.map_xlim[0] - dx, self.map_xlim[1] - dx))
+        self.canvas.axes.set_ylim(self.map_ylim[0] - dy, self.map_ylim[1] - dy)
+        # parallels and meridians
+        self.remove_merid_paral()
+        self.add_merid_paral()
+
+        self.canvas.axes.figure.canvas.draw_idle()
 
     def onpick(self, event):
         ind = event.ind
@@ -84,6 +291,14 @@ class Array_map(QtGui.QWidget):
         elif button == 3:
             self.pickInfo(ind)
 
+    # data handling -----------------------------------------------------
+    def update_hybrids_dict(self):
+        self.hybrids_dict = self.picks_dict.copy()
+        for station, pick in self.autopicks_dict.items():
+            if not station in self.hybrids_dict.keys():
+                self.hybrids_dict[station] = pick
+        return self.hybrids_dict
+
     def deletePick(self, ind):
         self.update_hybrids_dict()
         for index in ind:
@@ -117,15 +332,6 @@ class Array_map(QtGui.QWidget):
             except Exception as e:
                 print('Could not delete pick for station {}.{}: {}'.format(network, station, e))
 
-    def highlight_station(self, network, station, color):
-        stat_dict = self.stations_dict['{}.{}'.format(network, station)]
-        lat = stat_dict['latitude']
-        lon = stat_dict['longitude']
-        self.highlighted_stations.append(self.basemap.scatter(lon, lat, s=self.pointsize, edgecolors=color,
-                                                              facecolors='none', latlon=True,
-                                                              zorder=12, label='deleted'))
-        self.canvas.draw()
-
     def pickInfo(self, ind):
         self.update_hybrids_dict()
         for index in ind:
@@ -139,57 +345,6 @@ class Array_map(QtGui.QWidget):
                 for key, info in picks.items():
                     print('{}: {}'.format(key, info))
 
-    def openPickDlg(self, ind):
-        data = self._parent.get_data().getWFData()
-        for index in ind:
-            network, station = self._station_onpick_ids[index].split('.')[:2]
-            pyl_mw = self._parent
-            try:
-                data = data.select(station=station)
-                if not data:
-                    self._warn('No data for station {}'.format(station))
-                    return
-                pickDlg = PickDlg(self._parent, parameter=self.parameter,
-                                  data=data, network=network, station=station,
-                                  picks=self._parent.get_current_event().getPick(station),
-                                  autopicks=self._parent.get_current_event().getAutopick(station),
-                                  filteroptions=self._parent.filteroptions, metadata=self.metadata,
-                                  event=pyl_mw.get_current_event())
-            except Exception as e:
-                message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)
-                self._warn(message)
-                print(message, e)
-                print(traceback.format_exc())
-                return
-            try:
-                if pickDlg.exec_():
-                    pyl_mw.setDirty(True)
-                    pyl_mw.update_status('picks accepted ({0})'.format(station))
-                    pyl_mw.addPicks(station, pickDlg.getPicks(picktype='manual'), type='manual')
-                    pyl_mw.addPicks(station, pickDlg.getPicks(picktype='auto'), type='auto')
-                    if self.auto_refresh_box.isChecked():
-                        self._refresh_drawings()
-                    else:
-                        self.highlight_station(network, station, color='yellow')
-                    pyl_mw.drawPicks(station)
-                    pyl_mw.draw()
-                else:
-                    pyl_mw.update_status('picks discarded ({0})'.format(station))
-            except Exception as e:
-                message = 'Could not save picks for station {st}.\n{er}'.format(st=station, er=e)
-                self._warn(message)
-                print(message, e)
-                print(traceback.format_exc())
-
-    def connectSignals(self):
-        self.comboBox_phase.currentIndexChanged.connect(self._refresh_drawings)
-        self.comboBox_am.currentIndexChanged.connect(self._refresh_drawings)
-        self.cmaps_box.currentIndexChanged.connect(self._refresh_drawings)
-        self.annotations_box.stateChanged.connect(self.switch_annotations)
-        self.refresh_button.clicked.connect(self._refresh_drawings)
-        self.canvas.mpl_connect('motion_notify_event', self.mouse_moved)
-        # self.zoom_id = self.basemap.ax.figure.canvas.mpl_connect('scroll_event', self.zoom)
-
     def _from_dict(self, function, key):
         return function(self.stations_dict.values(), key=lambda x: x[key])[key]
 
@@ -205,14 +360,6 @@ class Array_map(QtGui.QWidget):
     def get_max_from_picks(self):
         return max(self.picks_rel.values())
 
-    def mouse_moved(self, event):
-        if not event.inaxes == self.main_ax:
-            return
-        x = event.xdata
-        y = event.ydata
-        lat, lon = self.basemap(x, y, inverse=True)
-        self.status_label.setText('Latitude: {}, Longitude: {}'.format(lat, lon))
-
     def current_picks_dict(self):
         picktype = self.comboBox_am.currentText().split(' ')[0]
         auto_manu = {'auto': self.autopicks_dict,
@@ -220,57 +367,6 @@ class Array_map(QtGui.QWidget):
                      'hybrid': self.hybrids_dict}
         return auto_manu[picktype]
 
-    def init_graphics(self):
-        if not self.figure:
-            self.figure = Figure()
-
-        self.status_label = QtGui.QLabel()
-
-        self.main_ax = self.figure.add_subplot(111)
-        #self.main_ax.set_facecolor('0.7')
-        self.canvas = PylotCanvas(self.figure, parent=self._parent, multicursor=True,
-                                  panZoomX=False, panZoomY=False)
-
-        self.main_box = QtGui.QVBoxLayout()
-        self.setLayout(self.main_box)
-
-        self.top_row = QtGui.QHBoxLayout()
-        self.main_box.addLayout(self.top_row, 1)
-
-        self.comboBox_phase = QtGui.QComboBox()
-        self.comboBox_phase.insertItem(0, 'P')
-        self.comboBox_phase.insertItem(1, 'S')
-
-        self.comboBox_am = QtGui.QComboBox()
-        self.comboBox_am.insertItem(0, 'hybrid (prefer manual)')
-        self.comboBox_am.insertItem(1, 'manual')
-        self.comboBox_am.insertItem(2, 'auto')
-
-        self.annotations_box = QtGui.QCheckBox('Annotate')
-        self.annotations_box.setChecked(True)
-        self.auto_refresh_box = QtGui.QCheckBox('Automatic refresh')
-        self.auto_refresh_box.setChecked(True)
-        self.refresh_button = QtGui.QPushButton('Refresh')
-        self.cmaps_box = QtGui.QComboBox()
-        self.cmaps_box.setMaxVisibleItems(20)
-        [self.cmaps_box.addItem(map_name) for map_name in sorted(plt.colormaps())]
-        # try to set to hsv as default
-        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('hsv'))
-
-        self.top_row.addWidget(QtGui.QLabel('Select a phase: '))
-        self.top_row.addWidget(self.comboBox_phase)
-        self.top_row.setStretch(1, 1)  # set stretch of item 1 to 1
-        self.top_row.addWidget(QtGui.QLabel('Pick type: '))
-        self.top_row.addWidget(self.comboBox_am)
-        self.top_row.setStretch(3, 1)  # set stretch of item 1 to 1
-        self.top_row.addWidget(self.cmaps_box)
-        self.top_row.addWidget(self.annotations_box)
-        self.top_row.addWidget(self.auto_refresh_box)
-        self.top_row.addWidget(self.refresh_button)
-
-        self.main_box.addWidget(self.canvas, 1)
-        self.main_box.addWidget(self.status_label, 0)
-
     def init_stations(self):
         self.stations_dict = self.metadata.get_all_coordinates()
         self.latmin = self.get_min_from_stations('latitude')
@@ -323,41 +419,6 @@ class Array_map(QtGui.QWidget):
         self.londim = self.lonmax - self.lonmin
         self.latdim = self.latmax - self.latmin
 
-    def init_x_y_dimensions(self):
-        # transformation of lat/lon to ax coordinate system
-        for st_id, coords in self.stations_dict.items():
-            lat, lon = coords['latitude'], coords['longitude']
-            coords['x'], coords['y'] = self.basemap(lon, lat)
-
-        self.xdim = self.get_max_from_stations('x') - self.get_min_from_stations('x')
-        self.ydim = self.get_max_from_stations('y') - self.get_min_from_stations('y')
-
-    def init_basemap(self, resolution='l'):
-        # basemap = Basemap(projection=projection, resolution = resolution, ax=self.main_ax)
-        basemap = Basemap(projection='lcc', resolution=resolution, ax=self.main_ax,
-                          width=self.width, height=self.height,
-                          lat_0=(self.latmin + self.latmax) / 2.,
-                          lon_0=(self.lonmin + self.lonmax) / 2.)
-
-        # basemap.fillcontinents(color=None, lake_color='aqua',zorder=1)
-        basemap.drawmapboundary(zorder=2)  # fill_color='darkblue')
-        basemap.shadedrelief(zorder=3)
-        basemap.drawcountries(zorder=4)
-        basemap.drawstates(zorder=5)
-        basemap.drawcoastlines(zorder=6)
-        # labels = [left,right,top,bottom]
-        parallels = np.arange(-90, 90, 5.)
-        parallels_small = np.arange(-90, 90, 2.5)
-        basemap.drawparallels(parallels_small, linewidth=0.5, zorder=7)
-        basemap.drawparallels(parallels, zorder=7)#, labels=[1, 1, 0, 0])
-        meridians = np.arange(-180, 180, 5.)
-        meridians_small = np.arange(-180, 180, 2.5)
-        basemap.drawmeridians(meridians_small, linewidth=0.5, zorder=7)
-        basemap.drawmeridians(meridians, zorder=7)#, labels=[0, 0, 1, 1])
-        self.basemap = basemap
-        self.figure._tight = True
-        self.figure.tight_layout()
-
     def init_lat_lon_grid(self, nstep=250):
         # create a regular grid to display colormap
         lataxis = np.linspace(self.latmin, self.latmax, nstep)
@@ -367,8 +428,7 @@ class Array_map(QtGui.QWidget):
     def init_picksgrid(self):
         picks, uncertainties, lats, lons = self.get_picks_lat_lon()
         try:
-            self.picksgrid_active = griddata((lats, lons), picks, (self.latgrid, self.longrid),
-                                             method='linear')
+            self.picksgrid_active = griddata((lats, lons), picks, (self.latgrid, self.longrid), method='linear')
         except Exception as e:
             self._warn('Could not init picksgrid: {}'.format(e))
 
@@ -382,16 +442,6 @@ class Array_map(QtGui.QWidget):
             longitudes.append(coords['longitude'])
         return stations, latitudes, longitudes
 
-    def get_st_x_y_for_plot(self):
-        stations = []
-        xs = []
-        ys = []
-        for st_id, coords in self.stations_dict.items():
-            stations.append(st_id)
-            xs.append(coords['x'])
-            ys.append(coords['y'])
-        return stations, xs, ys
-
     def get_picks_lat_lon(self):
         picks = []
         uncertainties = []
@@ -404,65 +454,82 @@ class Array_map(QtGui.QWidget):
             longitudes.append(self.stations_dict[st_id]['longitude'])
         return picks, uncertainties, latitudes, longitudes
 
-    def draw_contour_filled(self, nlevel='100'):
-        # self.test_gradient()
+    # plotting -----------------------------------------------------
+    def highlight_station(self, network, station, color):
+        stat_dict = self.stations_dict['{}.{}'.format(network, station)]
+        lat = stat_dict['latitude']
+        lon = stat_dict['longitude']
+        self.highlighted_stations.append(self.canvas.axes.scatter(lon, lat, s=self.pointsize, edgecolors=color,
+                                                                  facecolors='none', zorder=12,
+                                                                  transform=ccrs.PlateCarree(), label='deleted'))
 
+    def openPickDlg(self, ind):
+        data = self._parent.get_data().getWFData()
+        for index in ind:
+            network, station = self._station_onpick_ids[index].split('.')[:2]
+            pyl_mw = self._parent
+            try:
+                data = data.select(station=station)
+                if not data:
+                    self._warn('No data for station {}'.format(station))
+                    return
+                pickDlg = PickDlg(self._parent, parameter=self.parameter,
+                                  data=data, network=network, station=station,
+                                  picks=self._parent.get_current_event().getPick(station),
+                                  autopicks=self._parent.get_current_event().getAutopick(station),
+                                  filteroptions=self._parent.filteroptions, metadata=self.metadata,
+                                  event=pyl_mw.get_current_event())
+            except Exception as e:
+                message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)
+                self._warn(message)
+                print(message, e)
+                print(traceback.format_exc())
+                return
+            try:
+                if pickDlg.exec_():
+                    pyl_mw.setDirty(True)
+                    pyl_mw.update_status('picks accepted ({0})'.format(station))
+                    pyl_mw.addPicks(station, pickDlg.getPicks(picktype='manual'), type='manual')
+                    pyl_mw.addPicks(station, pickDlg.getPicks(picktype='auto'), type='auto')
+                    if self.auto_refresh_box.isChecked():
+                        self._refresh_drawings()
+                    else:
+                        self.highlight_station(network, station, color='yellow')
+                    pyl_mw.drawPicks(station)
+                    pyl_mw.draw()
+                else:
+                    pyl_mw.update_status('picks discarded ({0})'.format(station))
+            except Exception as e:
+                message = 'Could not save picks for station {st}.\n{er}'.format(st=station, er=e)
+                self._warn(message)
+                print(message, e)
+                print(traceback.format_exc())
+
+    def draw_contour_filled(self, nlevel=50):
         levels = np.linspace(self.get_min_from_picks(), self.get_max_from_picks(), nlevel)
-        self.contourf = self.basemap.contour(self.longrid, self.latgrid, self.picksgrid_active, levels,
-                                             linewidths=self.linewidth, latlon=True, zorder=8, alpha=0.7,
-                                             cmap=self.get_colormap())
+
+        self.contourf = self.canvas.axes.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
+                                                  linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
+                                                  alpha=0.4, zorder=8, cmap=self.get_colormap())
 
     def get_colormap(self):
         return plt.get_cmap(self.cmaps_box.currentText())
 
-    def test_gradient(self):
-        st_ids = self.picks_rel.keys()
-        x, y = np.gradient(self.picksgrid_active)
-        gradient_modulus = np.sqrt(x ** 2 + y ** 2)
-        global_mean_gradient = np.nanmean(gradient_modulus)
-        delta_gradient = []
-        for st_id in st_ids:
-            pick_item = self.picks_rel.pop(st_id)
-            self.init_picksgrid()
-            x, y = np.gradient(self.picksgrid_active)
-            gradient_modulus = np.sqrt(x ** 2 + y ** 2)
-            mean_gradient = np.nanmean(gradient_modulus)
-            dgradient = global_mean_gradient - mean_gradient
-            # print('station: {}, mean gradient: {}'.format(st_id, dgradient))
-            delta_gradient.append(dgradient)
-            self.picks_rel[st_id] = pick_item
-        global_std_gradient = np.nanstd(delta_gradient)
-        marked_stations = []
-        for st_id, dg in zip(st_ids, delta_gradient):
-            if abs(dg) > global_std_gradient:
-                marked_stations.append(st_id)
-        self.marked_stations = marked_stations
-        self.init_picksgrid()
-
-        # fig = plt.figure()
-        # x = list(range(len(st_ids)))
-        # gradients = zip(x, delta_gradient)
-        # gradients.sort(key=lambda a: a[1])
-        # plt.plot(gradients[0], gradients[1])
-
-        # global_var_gradient = np.nanvar(delta_gradient)
-        # plt.plot(x, delta_gradient)
-        # plt.axhline(global_std_gradient, color='green')
-        # plt.axhline(2 * global_std_gradient, color='blue')
-        # plt.axhline(global_var_gradient, color='red')
-        # plt.xticks(x, st_ids)
-        # plt.show()
-
     def scatter_all_stations(self):
         stations, lats, lons = self.get_st_lat_lon_for_plot()
-        self.sc = self.basemap.scatter(lons, lats, s=self.pointsize, facecolor='none', latlon=True, marker='.',
-                                       zorder=10, picker=True, edgecolor='0.5', label='Not Picked')
-        self.cid = self.canvas.mpl_connect('pick_event', self.onpick)
+
+        self.sc = self.canvas.axes.scatter(lons, lats, s=self.pointsize * 3, facecolor='none', marker='.',
+                                           zorder=10, picker=True, edgecolor='0.5', label='Not Picked',
+                                           transform=ccrs.PlateCarree())
+
+        self.cid = self.plotWidget.mpl_connect('pick_event', self.onpick)
         self._station_onpick_ids = stations
         if self.eventLoc:
             lats, lons = self.eventLoc
-            self.sc_event = self.basemap.scatter(lons, lats, s=2*self.pointsize, facecolor='red',
-                                                 latlon=True, zorder=11, label='Event (might be outside map region)')
+            self.sc_event = self.canvas.axes.scatter(lons, lats, s=5 * self.pointsize, facecolor='red', zorder=11,
+                                                     label='Event (might be outside map region)', marker='*',
+                                                     edgecolors='black',
+                                                     transform=ccrs.PlateCarree())
 
     def scatter_picked_stations(self):
         picks, uncertainties, lats, lons = self.get_picks_lat_lon()
@@ -471,24 +538,16 @@ class Array_map(QtGui.QWidget):
 
         phase = self.comboBox_phase.currentText()
         timeerrors = self.parameter['timeerrors{}'.format(phase)]
-        sizes = np.array([self.pointsize * ((5. - get_quality_class(uncertainty, timeerrors)))
+        sizes = np.array([self.pointsize * (5. - get_quality_class(uncertainty, timeerrors))
                           for uncertainty in uncertainties])
 
         cmap = self.get_colormap()
-        # workaround because of an issue with latlon transformation of arrays with len <3
-        if len(lons) <= 2 and len(lats) <= 2:
-            self.sc_picked = self.basemap.scatter(lons[0], lats[0], s=sizes, edgecolors='white', cmap=cmap,
-                                                  c=picks[0], latlon=True, zorder=11)
-        if len(lons) == 2 and len(lats) == 2:
-            self.sc_picked = self.basemap.scatter(lons[1], lats[1], s=sizes, edgecolors='white', cmap=cmap,
-                                                  c=picks[1], latlon=True, zorder=11)
-        if len(lons) > 2 and len(lats) > 2:
-            self.sc_picked = self.basemap.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap,
-                                                  c=picks, latlon=True, zorder=11, label='Picked')
+        self.sc_picked = self.canvas.axes.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap,
+                                                  c=picks, zorder=11, label='Picked', transform=ccrs.PlateCarree())
 
     def annotate_ax(self):
         self.annotations = []
-        stations, xs, ys = self.get_st_x_y_for_plot()
+        stations, ys, xs = self.get_st_lat_lon_for_plot()
         # MP MP testing station highlighting if they have high impact on mean gradient of color map
         # if self.picks_rel:
         #    self.test_gradient()
@@ -501,16 +560,21 @@ class Array_map(QtGui.QWidget):
                 color = 'lightgrey'
             if st in self.marked_stations:
                 color = 'red'
-            self.annotations.append(self.main_ax.annotate(' %s' % st, xy=(x, y),
-                                                          fontsize=self.pointsize/4., fontweight='semibold',
-                                                          color=color, zorder=14))
-        self.legend = self.main_ax.legend(loc=1)
-        self.legend.get_frame().set_facecolor((1, 1, 1, 0.75))
+            self.annotations.append(
+                self.canvas.axes.annotate(' %s' % st, xy=(x + 0.003, y + 0.003), fontsize=self.pointsize / 4.,
+                                          fontweight='semibold', color=color, alpha=0.8,
+                                          transform=ccrs.PlateCarree(), zorder=14,
+                                          path_effects=[PathEffects.withStroke(
+                                              linewidth=self.pointsize / 15., foreground='k')]))
+
+        self.legend = self.canvas.axes.legend(loc=1, framealpha=1)
+        self.legend.set_zorder(100)
+        self.legend.get_frame().set_facecolor((1, 1, 1, 0.95))
 
     def add_cbar(self, label):
-        self.cbax_bg = inset_axes(self.main_ax, width="6%", height="75%", loc=5)
-        cbax = inset_axes(self.main_ax, width='2%', height='70%', loc=5)
-        cbar = self.main_ax.figure.colorbar(self.sc_picked, cax=cbax)
+        self.cbax_bg = inset_axes(self.canvas.axes, width="6%", height="75%", loc=5)
+        cbax = inset_axes(self.canvas.axes, width='2%', height='70%', loc=5)
+        cbar = self.canvas.axes.figure.colorbar(self.sc_picked, cax=cbax)
         cbar.set_label(label)
         cbax.yaxis.tick_left()
         cbax.yaxis.set_label_position('left')
@@ -521,6 +585,7 @@ class Array_map(QtGui.QWidget):
         self.cbax_bg.patch.set_facecolor((1, 1, 1, 0.75))
         return cbar
 
+    # handle drawings -----------------------------------------------------
     def refresh_drawings(self, picks=None, autopicks=None):
         self.picks_dict = picks
         self.autopicks_dict = autopicks
@@ -560,7 +625,7 @@ class Array_map(QtGui.QWidget):
             self.comboBox_phase.setEnabled(False)
         if self.annotate:
             self.annotate_ax()
-        self.canvas.draw()
+        self.plotWidget.draw_idle()
 
     def remove_drawings(self):
         self.remove_annotations()
@@ -584,7 +649,7 @@ class Array_map(QtGui.QWidget):
             self.remove_contourf()
             del self.contourf
         if hasattr(self, 'cid'):
-            self.canvas.mpl_disconnect(self.cid)
+            self.plotWidget.mpl_disconnect(self.cid)
             del self.cid
         try:
             self.sc.remove()
@@ -594,7 +659,7 @@ class Array_map(QtGui.QWidget):
             self.legend.remove()
         except Exception as e:
             print('Warning: could not remove legend. Reason: {}'.format(e))
-        self.canvas.draw()
+        self.plotWidget.draw_idle()
 
     def remove_contourf(self):
         for item in self.contourf.collections:
@@ -605,34 +670,16 @@ class Array_map(QtGui.QWidget):
             annotation.remove()
         self.annotations = []
 
-    def zoom(self, event):
-        map = self.basemap
-        xlim = map.ax.get_xlim()
-        ylim = map.ax.get_ylim()
-        x, y = event.xdata, event.ydata
-        zoom = {'up': 1. / 2.,
-                'down': 2.}
-
-        if not event.xdata or not event.ydata:
-            return
-
-        if event.button in zoom:
-            factor = zoom[event.button]
-            xdiff = (xlim[1] - xlim[0]) * factor
-            xl = x - 0.5 * xdiff
-            xr = x + 0.5 * xdiff
-            ydiff = (ylim[1] - ylim[0]) * factor
-            yb = y - 0.5 * ydiff
-            yt = y + 0.5 * ydiff
-
-            if xl < map.xmin or yb < map.ymin or xr > map.xmax or yt > map.ymax:
-                xl, xr = map.xmin, map.xmax
-                yb, yt = map.ymin, map.ymax
-            map.ax.set_xlim(xl, xr)
-            map.ax.set_ylim(yb, yt)
-            map.ax.figure.canvas.draw()
+    def saveFigure(self):
+        if self.canvas.fig:
+            fd = QtWidgets.QFileDialog()
+            fname, filter = fd.getSaveFileName(self.parent(), filter='Images (*.png *.svg *.jpg)')
+            if not fname:
+                return
+            if not any([fname.endswith(item) for item in ['.png', '.svg', '.jpg']]):
+                fname += '.png'
+            self.canvas.fig.savefig(fname)
 
     def _warn(self, message):
-        self.qmb = QtGui.QMessageBox(QtGui.QMessageBox.Icon.Warning,
-                                     'Warning', message)
+        self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Warning, 'Warning', message)
         self.qmb.show()

pylot/core/util/connection.py

@@ -2,12 +2,13 @@
 # -*- coding: utf-8 -*-
 
 try:
+    # noinspection PyUnresolvedReferences
     from urllib2 import urlopen
 except:
     from urllib.request import urlopen
 
 
-def checkurl(url='https://ariadne.geophysik.ruhr-uni-bochum.de/trac/PyLoT/'):
+def checkurl(url='https://git.geophysik.ruhr-uni-bochum.de/marcel/pylot/'):
     """
     check if URL is available
     :param url: url

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
@@ -83,10 +84,10 @@ class Metadata(object):
             print('Path {} not in inventories list.'.format(path_to_inventory))
             return
         self.inventories.remove(path_to_inventory)
-        for filename in self.inventory_files.keys():
+        for filename in list(self.inventory_files.keys()):
             if filename.startswith(path_to_inventory):
                 del (self.inventory_files[filename])
-        for seed_id in self.seed_ids.keys():
+        for seed_id in list(self.seed_ids.keys()):
             if self.seed_ids[seed_id].startswith(path_to_inventory):
                 del (self.seed_ids[seed_id])
         # have to clean self.stations_dict as well
@@ -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}
 
@@ -351,25 +353,25 @@ def check_time(datetime):
     :type datetime: list
     :return: returns True if Values are in supposed range, returns False otherwise
 
-    >>> check_time([1999, 01, 01, 23, 59, 59, 999000])
+    >>> check_time([1999, 1, 1, 23, 59, 59, 999000])
     True
-    >>> check_time([1999, 01, 01, 23, 59, 60, 999000])
+    >>> check_time([1999, 1, 1, 23, 59, 60, 999000])
     False
-    >>> check_time([1999, 01, 01, 23, 59, 59, 1000000])
+    >>> check_time([1999, 1, 1, 23, 59, 59, 1000000])
     False
-    >>> check_time([1999, 01, 01, 23, 60, 59, 999000])
+    >>> check_time([1999, 1, 1, 23, 60, 59, 999000])
     False
-    >>> check_time([1999, 01, 01, 23, 60, 59, 999000])
+    >>> check_time([1999, 1, 1, 23, 60, 59, 999000])
     False
-    >>> check_time([1999, 01, 01, 24, 59, 59, 999000])
+    >>> check_time([1999, 1, 1, 24, 59, 59, 999000])
     False
-    >>> check_time([1999, 01, 31, 23, 59, 59, 999000])
+    >>> check_time([1999, 1, 31, 23, 59, 59, 999000])
     True
-    >>> check_time([1999, 02, 30, 23, 59, 59, 999000])
+    >>> check_time([1999, 2, 30, 23, 59, 59, 999000])
     False
-    >>> check_time([1999, 02, 29, 23, 59, 59, 999000])
+    >>> check_time([1999, 2, 29, 23, 59, 59, 999000])
     False
-    >>> check_time([2000, 02, 29, 23, 59, 59, 999000])
+    >>> check_time([2000, 2, 29, 23, 59, 59, 999000])
     True
     >>> check_time([2000, 13, 29, 23, 59, 59, 999000])
     False
@@ -381,6 +383,7 @@ def check_time(datetime):
         return False
 
 
+# TODO: change root to datapath
 def get_file_list(root_dir):
     """
     Function uses a directorie to get all the *.gse files from it.
@@ -444,7 +447,7 @@ def evt_head_check(root_dir, out_dir=None):
     """
     if not out_dir:
         print('WARNING files are going to be overwritten!')
-        inp = str(raw_input('Continue? [y/N]'))
+        inp = str(input('Continue? [y/N]'))
         if not inp == 'y':
             sys.exit()
     filelist = get_file_list(root_dir)

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
@@ -21,12 +22,13 @@ class Event(ObsPyEvent):
         :param path: path to event directory
         :type path: str
         """
+        # TODO: remove rootpath and database
         self.pylot_id = path.split('/')[-1]
         # initialize super class
         super(Event, self).__init__(resource_id=ResourceIdentifier('smi:local/' + self.pylot_id))
         self.path = path
         self.database = path.split('/')[-2]
-        self.datapath = path.split('/')[-3]
+        self.datapath = os.path.split(path)[0]  # path.split('/')[-3]
         self.rootpath = '/' + os.path.join(*path.split('/')[:-3])
         self.pylot_autopicks = {}
         self.pylot_picks = {}
@@ -73,7 +75,7 @@ class Event(ObsPyEvent):
                 text = lines[0]
                 self.addNotes(text)
                 try:
-                    datetime = UTCDateTime(path.split('/')[-1])
+                    datetime = UTCDateTime(self.path.split('/')[-1])
                     origin = Origin(resource_id=self.resource_id, time=datetime, latitude=0, longitude=0, depth=0)
                     self.origins.append(origin)
                 except:
@@ -296,13 +298,13 @@ class Event(ObsPyEvent):
         :rtype: None
         """
         try:
-            import cPickle
+            import pickle
         except ImportError:
-            import _pickle as cPickle
+            import _pickle as pickle
 
         try:
             outfile = open(filename, 'wb')
-            cPickle.dump(self, outfile, -1)
+            pickle.dump(self, outfile, -1)
             self.dirty = False
         except Exception as e:
             print('Could not pickle PyLoT event. Reason: {}'.format(e))
@@ -317,11 +319,11 @@ class Event(ObsPyEvent):
         :rtype: Event
         """
         try:
-            import cPickle
+            import pickle
         except ImportError:
-            import _pickle as cPickle
+            import _pickle as pickle
         infile = open(filename, 'rb')
-        event = cPickle.load(infile)
+        event = pickle.load(infile)
         event.dirty = False
         print('Loaded %s' % filename)
         return event

pylot/core/util/generate_array_maps.py

@@ -3,24 +3,37 @@
 # 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
+os.environ["MKL_NUM_THREADS"] = num_thread
+os.environ["VECLIB_MAXIMUM_THREADS"] = num_thread
+os.environ["NUMEXPR_NUM_THREADS"] = num_thread
+os.environ["NUMEXPR_MAX_THREADS"] = num_thread
+
 import multiprocessing
+import sys
+import glob
+import matplotlib
+
+matplotlib.use('Qt5Agg')
+sys.path.append(os.path.join('/'.join(sys.argv[0].split('/')[:-1]), '../../..'))
 
 from PyLoT import Project
 from pylot.core.util.dataprocessing import Metadata
 from pylot.core.util.array_map import Array_map
 
 import matplotlib.pyplot as plt
+import argparse
+
 
 def main(project_file_path, manual=False, auto=True, file_format='png', f_ext='', ncores=None):
     project = Project.load(project_file_path)
     nEvents = len(project.eventlist)
     input_list = []
-
+    print('\n')
     for index, event in enumerate(project.eventlist):
-        # MP MP TESTING +++
-        #if not eventdir.endswith('20170908_044946.a'):
-        #    continue
-        # MP MP ----
         kwargs = dict(project=project, event=event, nEvents=nEvents, index=index, manual=manual, auto=auto,
                       file_format=file_format, f_ext=f_ext)
         input_list.append(kwargs)
@@ -30,14 +43,20 @@ def main(project_file_path, manual=False, auto=True, file_format='png', f_ext=''
             array_map_worker(item)
     else:
         pool = multiprocessing.Pool(ncores)
-        result = pool.map(array_map_worker, input_list)
+        pool.map(array_map_worker, input_list)
         pool.close()
         pool.join()
 
+
 def array_map_worker(input_dict):
     event = input_dict['event']
     eventdir = event.path
     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']))
+        return
     # check for picks
     manualpicks = event.getPicks()
     autopicks = event.getAutopicks()
@@ -51,11 +70,12 @@ def array_map_worker(input_dict):
             continue
         if not metadata:
             metadata = Metadata(inventory=metadata_path, verbosity=0)
+
         # create figure to plot on
-        fig = plt.figure(figsize=(16,9))
+        fig, ax = plt.subplots(figsize=(15, 9))
         # create array map object
-        map = Array_map(None, metadata, parameter=input_dict['project'].parameter, figure=fig,
-                        width=2.13e6, height=1.2e6, pointsize=15., linewidth=1.0)
+        map = Array_map(None, metadata, parameter=input_dict['project'].parameter, axes=ax,
+                        width=2.13e6, height=1.2e6, pointsize=25., linewidth=1.0)
         # set combobox to auto/manual to plot correct pick type
         map.comboBox_am.setCurrentIndex(map.comboBox_am.findText(pick_type))
         # add picks to map and save file
@@ -65,11 +85,13 @@ def array_map_worker(input_dict):
         fig.savefig(fpath_out, dpi=300.)
         print('Wrote file: {}'.format(fpath_out))
 
-if __name__ == '__main__':
-    dataroot = '/home/marcel'
-    infiles=['alparray_all_events_0.03-0.1_mantle_correlated_v3.plp']
 
-    for infile in infiles:
-        main(os.path.join(dataroot, infile), f_ext='_correlated_0.1Hz', ncores=10)
-    #main('E:\Shared\AlpArray\\test_aa.plp', f_ext='_correlated_0.5Hz', ncores=1)
-    #main('/home/marcel/alparray_m6.5-6.9_mantle_correlated_v3.plp', f_ext='_correlated_0.5Hz')
+if __name__ == '__main__':
+    cl = argparse.ArgumentParser()
+    cl.add_argument('--dataroot', help='Directory containing the PyLoT .plp file', type=str)
+    cl.add_argument('--infiles', help='.plp files to use', nargs='+')
+    cl.add_argument('--ncores', hepl='Specify number of parallel processes', type=int, default=1)
+    args = cl.parse_args()
+
+    for infile in args.infiles:
+        main(os.path.join(args.dataroot, infile), f_ext='_correlated_0.03-0.1', ncores=args.ncores)

pylot/core/util/gui.py

@@ -7,11 +7,10 @@ try:
 except Exception as e:
     print('Warning: Could not import module pyqtgraph.')
 try:
-    from PySide import QtCore
+    from PySide2 import QtCore
 except Exception as e:
     print('Warning: Could not import module QtCore.')
 
-
 from pylot.core.util.utils import pick_color
 
 
@@ -49,11 +48,11 @@ def which(program, parameter):
     :rtype: str
     """
     try:
-        from PySide.QtCore import QSettings
+        from PySide2.QtCore import QSettings
         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
-

pylot/core/util/obspyDMT_interface.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import os
+
 from obspy import UTCDateTime
 
 
@@ -34,17 +35,25 @@ def qml_from_obspyDMT(path):
 
     if not os.path.exists(path):
         return IOError('Could not find Event at {}'.format(path))
-    infile = open(path, 'rb')
-    event_dmt = pickle.load(infile)#, fix_imports=True)
+
+    with open(path, 'rb') as infile:
+        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'], time=event_dmt['datetime'], longitude=event_dmt['longitude'],
-                    latitude=event_dmt['latitude'], depth=event_dmt['depth'])
-    mag = Magnitude(mag=event_dmt['magnitude'], magnitude_type=event_dmt['magnitude_type'],
+
+    origin = Origin(resource_id=event_dmt['origin_id'],
+                    time=event_dmt['datetime'],
+                    longitude=event_dmt['longitude'],
+                    latitude=event_dmt['latitude'],
+                    depth=event_dmt['depth'])
+    mag = Magnitude(mag=event_dmt['magnitude'],
+                    magnitude_type=event_dmt['magnitude_type'],
                     origin_id=event_dmt['origin_id'])
+
     ev.magnitudes.append(mag)
     ev.origins.append(origin)
     return ev

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

pylot/core/util/thread.py

@@ -4,8 +4,8 @@ import os
 import sys
 import traceback
 
-from PySide.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
-from PySide.QtGui import QDialog, QProgressBar, QLabel, QHBoxLayout
+from PySide2.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
+from PySide2.QtWidgets import QDialog, QProgressBar, QLabel, QHBoxLayout, QPushButton
 
 
 class Thread(QThread):
@@ -22,9 +22,11 @@ class Thread(QThread):
         self.abortButton = abortButton
         self.finished.connect(self.hideProgressbar)
         self.showProgressbar()
+        self.old_stdout = None
 
     def run(self):
         if self.redirect_stdout:
+            self.old_stdout = sys.stdout
             sys.stdout = self
         try:
             if self.arg is not None:
@@ -39,7 +41,7 @@ class Thread(QThread):
             exctype, value = sys.exc_info()[:2]
             self._executedErrorInfo = '{} {} {}'. \
                 format(exctype, value, traceback.format_exc())
-        sys.stdout = sys.__stdout__
+        sys.stdout = self.old_stdout
 
     def showProgressbar(self):
         if self.progressText:
@@ -49,7 +51,23 @@ class Thread(QThread):
             #     self.pb_widget.setWindowFlags(Qt.SplashScreen)
             #     self.pb_widget.setModal(True)
 
-            self.pb_widget.label.setText(self.progressText)
+            # generate widget if not given in init
+            if not self.pb_widget:
+                self.pb_widget = QDialog(self.parent())
+                self.pb_widget.setWindowFlags(Qt.SplashScreen)
+                self.pb_widget.setModal(True)
+
+            # add button
+            delete_button = QPushButton('X')
+            delete_button.clicked.connect(self.exit)
+            hl = QHBoxLayout()
+            pb = QProgressBar()
+            pb.setRange(0, 0)
+            hl.addWidget(pb)
+            hl.addWidget(QLabel(self.progressText))
+            if self.abortButton:
+                hl.addWidget(delete_button)
+            self.pb_widget.setLayout(hl)
             self.pb_widget.show()
 
     def hideProgressbar(self):
@@ -80,10 +98,12 @@ class Worker(QRunnable):
         self.progressText = progressText
         self.pb_widget = pb_widget
         self.redirect_stdout = redirect_stdout
+        self.old_stdout = None
 
     @Slot()
     def run(self):
         if self.redirect_stdout:
+            self.old_stdout = sys.stdout
             sys.stdout = self
 
         try:
@@ -96,7 +116,7 @@ class Worker(QRunnable):
             self.signals.result.emit(result)
         finally:
             self.signals.finished.emit('Done')
-        sys.stdout = sys.__stdout__
+        sys.stdout = self.old_stdout
 
     def write(self, text):
         self.signals.message.emit(text)
@@ -128,11 +148,13 @@ class MultiThread(QThread):
         self.progressText = progressText
         self.pb_widget = pb_widget
         self.redirect_stdout = redirect_stdout
+        self.old_stdout = None
         self.finished.connect(self.hideProgressbar)
         self.showProgressbar()
 
     def run(self):
         if self.redirect_stdout:
+            self.old_stdout = sys.stdout
             sys.stdout = self
         try:
             if not self.ncores:
@@ -148,7 +170,7 @@ class MultiThread(QThread):
             exc_type, exc_obj, exc_tb = sys.exc_info()
             fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
             print('Exception: {}, file: {}, line: {}'.format(exc_type, fname, exc_tb.tb_lineno))
-        sys.stdout = sys.__stdout__
+        sys.stdout = self.old_stdout
 
     def showProgressbar(self):
         if self.progressText:

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
@@ -227,7 +228,7 @@ def findComboBoxIndex(combo_box, val):
     :type val: basestring
     :return: index value of item with name val or 0
     """
-    return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
+    return combo_box.findText(val) if combo_box.findText(val) != -1 else 0
 
 
 def find_in_list(list, str):
@@ -950,10 +951,13 @@ def check4rotated(data, metadata=None, verbosity=1):
         if any(rotation_required):
             t_start = full_range(wfstream)
             try:
-                azimuts = [metadata.get_coordinates(tr_id, t_start)['azimuth'] for tr_id in trace_ids]
-                dips = [metadata.get_coordinates(tr_id, t_start)['dip'] for tr_id in trace_ids]
+                azimuts = []
+                dips = []
+                for tr_id in trace_ids:
+                    azimuts.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
+                    dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
             except (KeyError, TypeError) as e:
-                print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(trace_id))
+                print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(tr_id))
                 return wfstream
             if len(wfstream) < 3:
                 print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
@@ -964,7 +968,7 @@ def check4rotated(data, metadata=None, verbosity=1):
                 z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
                                      wfstream[1], azimuts[1], dips[1],
                                      wfstream[2], azimuts[2], dips[2])
-                print('check4rotated: rotated trace {} to ZNE'.format(trace_id))
+                print('check4rotated: rotated trace {} to ZNE'.format(trace_ids))
                 # replace old data with rotated data, change the channel code to ZNE
                 z_index = dips.index(min(
                     dips))  # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90 being vertical)
@@ -1013,7 +1017,7 @@ def scaleWFData(data, factor=None, components='all'):
     :return:  scaled waveform data
     :rtype: `~obspy.core.stream.Stream` object
     """
-    if components is not 'all':
+    if components != 'all':
         for comp in components:
             if factor is None:
                 max_val = np.max(np.abs(data.select(component=comp)[0].data))

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)