refactor: rename writephases; add write hash to write_phases

# Conflicts:
#	pylot/core/io/data.py
#	pylot/core/util/widgets.py

PyLoT.py

@@ -25,6 +25,7 @@ https://www.iconfinder.com/iconsets/flavour
 
 import argparse
 import json
+import logging
 import os
 import platform
 import shutil
@@ -60,7 +61,7 @@ except ImportError:
     from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
 
-from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude, calcsourcespec
+from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude
 from pylot.core.io.data import Data
 from pylot.core.io.inputs import FilterOptions, PylotParameter
 from autoPyLoT import autoPyLoT
@@ -72,11 +73,11 @@ from pylot.core.util.errors import DatastructureError, \
     OverwriteError
 from pylot.core.util.connection import checkurl
 from pylot.core.util.dataprocessing import Metadata, restitute_data
-from pylot.core.util.utils import fnConstructor, getLogin, \
+from pylot.core.util.utils import fnConstructor, get_login, \
     full_range, readFilterInformation, pick_color_plt, \
     pick_linestyle_plt, identifyPhaseID, excludeQualityClasses, \
     transform_colors_mpl, transform_colors_mpl_str, getAutoFilteroptions, check_all_obspy, \
-    check_all_pylot, get_bool, get_None
+    check_all_pylot, get_bool, get_none
 from pylot.core.util.gui import make_pen
 from pylot.core.util.event import Event
 from pylot.core.io.location import create_creation_info, create_event
@@ -84,7 +85,7 @@ from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
     PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
     ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
     CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget, PickQualitiesFromXml, \
-    SourceSpecWindow, ChooseWaveFormWindow, SpectrogramTab
+    SpectrogramTab, SearchFileByExtensionDialog
 from pylot.core.util.array_map import Array_map
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import Thread, Worker
@@ -113,11 +114,7 @@ class MainWindow(QMainWindow):
     def __init__(self, parent=None, infile=None, reset_qsettings=False):
         super(MainWindow, self).__init__(parent)
 
-        # check for default pylot.in-file
-        if not infile:
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-        if os.path.isfile(infile) is False:
+        if infile and os.path.isfile(infile) is False:
             infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')[0]
 
             if not os.path.exists(infile):
@@ -197,7 +194,7 @@ class MainWindow(QMainWindow):
                 if settings.value("user/FullName", None) is None:
                     fulluser = QInputDialog.getText(self, "Enter Name:", "Full name")
                     settings.setValue("user/FullName", fulluser)
-                    settings.setValue("user/Login", getLogin())
+                    settings.setValue("user/Login", get_login())
                 if settings.value("agency_id", None) is None:
                     agency = QInputDialog.getText(self,
                                                   "Enter authority/institution name:",
@@ -254,7 +251,7 @@ class MainWindow(QMainWindow):
             self._inputs.reset_defaults()
             # check for default pylot.in-file
             infile = os.path.join(pylot_config_dir, '.pylot.in')
-            print('Using default input file {}'.format(infile))
+            logging.warning('Using default input file {}'.format(infile))
             self._inputs.export2File(infile)
         self.infile = infile
 
@@ -1007,18 +1004,17 @@ class MainWindow(QMainWindow):
             return
         refresh = False
         events = self.project.eventlist
-        sld = SingleTextLineDialog(label='Specify file extension: ', default_text='.xml')
+        sld = SearchFileByExtensionDialog(label='Specify file extension: ', default_text='.xml',
+                                          events=events)
         if not sld.exec_():
             return
-        fext = sld.lineEdit.text()
-        # fext = '.xml'
+
+        filenames = sld.getChecked()
         for event in events:
-            path = event.path
-            eventname = path.split('/')[-1]  # or event.pylot_id
-            filename = os.path.join(path, 'PyLoT_' + eventname + fext)
-            if os.path.isfile(filename):
-                self.load_data(filename, draw=False, event=event, overwrite=True)
-                refresh = True
+            for filename in filenames:
+                if os.path.isfile(filename) and event.pylot_id in filename:
+                    self.load_data(filename, draw=False, event=event, ask_user=True, merge_strategy=sld.merge_strategy)
+                    refresh = True
         if not refresh:
             return
         if self.get_current_event().pylot_picks:
@@ -1026,8 +1022,8 @@ class MainWindow(QMainWindow):
         self.fill_eventbox()
         self.setDirty(True)
 
-    def load_data(self, fname=None, loc=False, draw=True, event=None, overwrite=False):
-        if not overwrite:
+    def load_data(self, fname=None, loc=False, draw=True, event=None, ask_user=False, merge_strategy='Overwrite'):
+        if not ask_user:
             if not self.okToContinue():
                 return
         if fname is None:
@@ -1041,9 +1037,12 @@ class MainWindow(QMainWindow):
         data = Data(self, event)
         try:
             data_new = Data(self, evtdata=str(fname))
-            # MP MP commented because adding several picks might cause inconsistencies
-            data = data_new
-            # data += data_new
+            if merge_strategy == 'Overwrite':
+                data = data_new
+            elif merge_strategy == 'Merge':
+                data += data_new
+            else:
+                raise NotImplementedError(f'Unknown merge strategy: {merge_strategy}')
         except ValueError:
             qmb = QMessageBox(self, icon=QMessageBox.Question,
                               text='Warning: Missmatch in event identifiers {} and {}. Continue?'.format(
@@ -1408,25 +1407,28 @@ class MainWindow(QMainWindow):
 
         for id, event in enumerate(self.project.eventlist):
             event_path = event.path
-            phaseErrors = {'P': self._inputs['timeerrorsP'],
-                           'S': self._inputs['timeerrorsS']}
+            #phaseErrors = {'P': self._inputs['timeerrorsP'],
+            #               'S': self._inputs['timeerrorsS']}
 
-            ma_props = {'manual': event.pylot_picks,
-                        'auto': event.pylot_autopicks}
-            ma_count = {'manual': 0,
-                        'auto': 0}
-            ma_count_total = {'manual': 0,
-                              'auto': 0}
+            man_au_picks = {'manual': event.pylot_picks,
+                            'auto': event.pylot_autopicks}
+            npicks = {'manual': {'P': 0, 'S': 0},
+                      'auto': {'P': 0, 'S': 0}}
+            npicks_total = {'manual': {'P': 0, 'S': 0},
+                            'auto': {'P': 0, 'S': 0}}
 
-            for ma in ma_props.keys():
-                if ma_props[ma]:
-                    for picks in ma_props[ma].values():
+            for ma in man_au_picks.keys():
+                if man_au_picks[ma]:
+                    for picks in man_au_picks[ma].values():
                         for phasename, pick in picks.items():
                             if not type(pick) in [dict, AttribDict]:
                                 continue
+                            phase_ID = identifyPhaseID(phasename)
+                            if not phase_ID in npicks[ma].keys():
+                                continue
                             if pick.get('spe'):
-                                ma_count[ma] += 1
-                            ma_count_total[ma] += 1
+                                npicks[ma][phase_ID] += 1
+                            npicks_total[ma][phase_ID] += 1
 
             event_ref = event.isRefEvent()
             event_test = event.isTestEvent()
@@ -1461,16 +1463,23 @@ class MainWindow(QMainWindow):
             if event.dirty:
                 event_str += '*'
             item_path = QStandardItem(event_str)
-            item_time = QStandardItem('{}'.format(time))
+            item_time = QStandardItem('{}'.format(time.strftime("%Y-%m-%d %H:%M:%S") if time else ''))
             item_lat = QStandardItem('{}'.format(lat))
             item_lon = QStandardItem('{}'.format(lon))
             item_depth = QStandardItem('{}'.format(depth))
             item_localmag = QStandardItem('{}'.format(localmag))
             item_momentmag = QStandardItem('{}'.format(momentmag))
-            item_nmp = QStandardItem('{}({})'.format(ma_count['manual'], ma_count_total['manual']))
+
+            item_nmp = QStandardItem()
+            item_nap = QStandardItem()
             item_nmp.setIcon(self.manupicksicon_small)
-            item_nap = QStandardItem('{}({})'.format(ma_count['auto'], ma_count_total['auto']))
             item_nap.setIcon(self.autopicksicon_small)
+
+            for picktype, item_np in [('manual', item_nmp), ('auto', item_nap)]:
+                npicks_str = f"{npicks[picktype]['P']}|{npicks[picktype]['S']}"
+                #npicks_str += f"({npicks_total[picktype]['P']}/{npicks_total[picktype]['S']})"
+                item_np.setText(npicks_str)
+
             item_ref = QStandardItem()  # str(event_ref))
             item_test = QStandardItem()  # str(event_test))
             if event_ref:
@@ -1891,6 +1900,7 @@ class MainWindow(QMainWindow):
         # which will read in data input twice. Therefore current tab is changed to 0
         # in loadProject before calling this function.
         self.fill_eventbox()
+        #print(f'{self.get_current_event()=}')
         plotted = False
         if self.tabs.currentIndex() == 2:
             self.init_event_table()
@@ -1925,7 +1935,6 @@ class MainWindow(QMainWindow):
             self.spectro_layout.addWidget(newSpectroWidget)
             self.spectroWidget = newSpectroWidget
 
-
     def newWF(self, event=None, plot=True):
         '''
         Load new data and plot if necessary.
@@ -1983,6 +1992,8 @@ class MainWindow(QMainWindow):
         #     ans = False
 
         settings = QSettings()
+        # process application events to wait for event items to appear in event box
+        QApplication.processEvents()
         curr_event = self.get_current_event()
         if not curr_event:
             print('Could not find current event. Try reload?')
@@ -1990,8 +2001,8 @@ class MainWindow(QMainWindow):
 
         if len(curr_event.origins) > 0:
             origin_time = curr_event.origins[0].time
-            tstart = settings.value('tstart') if get_None(settings.value('tstart')) else 0
-            tstop = settings.value('tstop') if get_None(settings.value('tstop')) else 0
+            tstart = settings.value('tstart') if get_none(settings.value('tstart')) else 0
+            tstop = settings.value('tstop') if get_none(settings.value('tstop')) else 0
             tstart = origin_time + float(tstart)
             tstop = origin_time + float(tstop)
         else:
@@ -2138,7 +2149,7 @@ class MainWindow(QMainWindow):
 
     def finish_pg_plot(self):
         self.getPlotWidget().updateWidget()
-        plots, gaps = self.wfp_thread.data
+        plots = self.wfp_thread.data
         # do not show plot if no data are given
         self.wf_scroll_area.setVisible(len(plots) > 0)
         self.no_data_label.setVisible(not len(plots) > 0)
@@ -2306,14 +2317,14 @@ class MainWindow(QMainWindow):
         # wfst += self.get_data().getWFData().select(component=alter_comp)
         plotWidget = self.getPlotWidget()
         self.adjustPlotHeight()
-        if get_bool(settings.value('large_dataset')):
+        if get_bool(settings.value('large_dataset')) == True:
             self.plot_method = 'fast'
         else:
             self.plot_method = 'normal'
         rval = plotWidget.plotWFData(wfdata=wfst, wfsyn=wfsyn, title=title, mapping=False, component=comp,
                                      nth_sample=int(nth_sample), method=self.plot_method, gain=self.gain)
-        plots, gaps = rval if rval else ([], [])
-        return plots, gaps
+        plots = rval if rval else []
+        return plots
 
     def adjustPlotHeight(self):
         if self.pg:
@@ -3002,10 +3013,16 @@ class MainWindow(QMainWindow):
             event = self.get_current_event()
         event.pylot_picks = {}
         event.pylot_autopicks = {}
-        picksdict = picksdict_from_picks(evt=self.get_data().get_evt_data())
+        picksdict = picksdict_from_picks(evt=self.get_data().get_evt_data(), parameter=self.getParameter())
         event.addPicks(picksdict['manual'])
         event.addAutopicks(picksdict['auto'])
 
+    def getParameter(self):
+        if hasattr(self.project, 'parameter') and isinstance(self.project.parameter, PylotParameter):
+            return self.project.parameter
+        else:
+            return self._inputs
+
     def drawPicks(self, station=None, picktype=None, stime=None):
         # if picktype not specified, draw both
         if not stime:
@@ -3647,7 +3664,7 @@ class MainWindow(QMainWindow):
             return True
         return False
 
-    def update_status(self, message, duration=5000):
+    def update_status(self, message, duration=10000):
         self.statusBar().showMessage(message, duration)
         if self.get_data() is not None:
             if not self.get_current_event() or not self.project.location:
@@ -3700,10 +3717,13 @@ class MainWindow(QMainWindow):
         if not self.okToContinue():
             return
         if not fnm:
-            dlg = QFileDialog(parent=self)
+            settings = QSettings()
+            dir = settings.value('current_project_path')
+            dlg = QFileDialog(parent=self, directory=dir)
             fnm = dlg.getOpenFileName(self, 'Open project file...', filter='Pylot project (*.plp)')[0]
             if not fnm:
                 return
+            settings.setValue('current_project_path', os.path.split(fnm)[0])
         if not os.path.exists(fnm):
             QMessageBox.warning(self, 'Could not open file',
                                 'Could not open project file {}. File does not exist.'.format(fnm))
@@ -3821,7 +3841,8 @@ class MainWindow(QMainWindow):
 
     def closeEvent(self, event):
         if self.okToContinue():
-            self.logwidget.close()
+            if hasattr(self, 'logwidget'):
+                self.logwidget.close()
             event.accept()
         else:
             event.ignore()

autoPyLoT.py

@@ -28,7 +28,7 @@ from pylot.core.util.dataprocessing import restitute_data, Metadata
 from pylot.core.util.defaults import SEPARATOR
 from pylot.core.util.event import Event
 from pylot.core.util.structure import DATASTRUCTURE
-from pylot.core.util.utils import get_None, trim_station_components, check4gapsAndRemove, check4doubled, \
+from pylot.core.util.utils import get_none, trim_station_components, check4gapsAndRemove, check4doubled, \
     check4rotated
 from pylot.core.util.version import get_git_version as _getVersionString
 
@@ -91,9 +91,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                                                               sp=sp_info)
     print(splash)
 
-    parameter = get_None(parameter)
-    inputfile = get_None(inputfile)
-    eventid = get_None(eventid)
+    parameter = get_none(parameter)
+    inputfile = get_none(inputfile)
+    eventid = get_none(eventid)
 
     fig_dict = None
     fig_dict_wadatijack = None
@@ -119,13 +119,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
             obspyDMT_wfpath = input_dict['obspyDMT_wfpath']
 
     if not parameter:
-        if inputfile:
-            parameter = PylotParameter(inputfile)
-            # iplot = parameter['iplot']
-        else:
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-            parameter = PylotParameter(infile)
+        if not inputfile:
+            print('Using default input parameter')
+        parameter = PylotParameter(inputfile)
     else:
         if not type(parameter) == PylotParameter:
             print('Wrong input type for parameter: {}'.format(type(parameter)))
@@ -154,7 +150,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
         datastructure.setExpandFields(exf)
 
         # check if default location routine NLLoc is available and all stations are used
-        if get_None(parameter['nllocbin']) and station == 'all':
+        if get_none(parameter['nllocbin']) and station == 'all':
             locflag = 1
             # get NLLoc-root path
             nllocroot = parameter.get('nllocroot')

autopylot.sh

@@ -3,10 +3,10 @@
 #$ -l low
 #$ -cwd
 #$ -pe smp 40
-#$ -l mem=2G
-#$ -l h_vmem=2G
+##$ -l mem=3G
+#$ -l h_vmem=6G
 #$ -l os=*stretch
 
-conda activate pylot_38
+conda activate pylot_311
 
-python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_janis_noisy.in -c $NSLOTS
+python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_adriaarray.in -c 20 -dmt processed

pylot/core/io/data.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import copy
+import logging
 import os
 
 from PySide2.QtWidgets import QMessageBox
@@ -19,7 +20,7 @@ from pylot.core.util.errors import FormatError, OverwriteError
 from pylot.core.util.event import Event
 from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
 from pylot.core.util.utils import fnConstructor, full_range, check4rotated, \
-    check4gapsAndMerge, trim_station_components
+    check_for_gaps_and_merge, trim_station_components, check_for_nan
 
 
 class Data(object):
@@ -64,7 +65,7 @@ class Data(object):
                     elif 'LOC' in evtdata:
                         raise NotImplementedError('PILOT location information '
                                                   'read support not yet '
-                                                  'implemeted.')
+                                                  'implemented.')
                     elif 'event.pkl' in evtdata:
                         evtdata = qml_from_obspyDMT(evtdata)
                     else:
@@ -408,18 +409,16 @@ class Data(object):
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '_focmec.in':
                 try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
+                    parameter = PylotParameter()
+                    logging.warning('Using default input parameter')
                     focmec.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '.pha':
                 try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
+                    parameter = PylotParameter()
+                    logging.warning('Using default input parameter')
                     hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
@@ -458,6 +457,11 @@ class Data(object):
         :param fnames_alt: alternative data to show (e.g. synthetic/processed)
         :type fnames: list
         """
+        def check_fname_exists(filenames: list) -> list:
+            if filenames:
+                filenames = [fn for fn in filenames if os.path.isfile(fn)]
+            return filenames
+
         self.wfdata = Stream()
         self.wforiginal = None
         self.wf_alt = Stream()
@@ -467,8 +471,8 @@ class Data(object):
         self.tstop = tstop
 
         # remove directories
-        fnames = [fname for fname in fnames if not os.path.isdir(fname)]
-        fnames_alt = [fname for fname in fnames_alt if not os.path.isdir(fname)]
+        fnames = check_fname_exists(fnames)
+        fnames_alt = check_fname_exists(fnames_alt)
 
         # if obspy_dmt:
         #     wfdir = 'raw'
@@ -496,7 +500,9 @@ class Data(object):
         # remove possible underscores in station names
         # self.wfdata = remove_underscores(self.wfdata)
         # check for gaps and merge
-        self.wfdata = check4gapsAndMerge(self.wfdata)
+        self.wfdata, _ = check_for_gaps_and_merge(self.wfdata)
+        # check for nans
+        check_for_nan(self.wfdata)
         # check for stations with rotated components
         if checkRotated and metadata is not None:
             self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)

pylot/core/io/location.py

@@ -1,7 +1,7 @@
 from obspy import UTCDateTime
 from obspy.core import event as ope
 
-from pylot.core.util.utils import getLogin, getHash
+from pylot.core.util.utils import get_login, get_hash
 
 
 def create_amplitude(pickID, amp, unit, category, cinfo):
@@ -61,7 +61,7 @@ def create_creation_info(agency_id=None, creation_time=None, author=None):
     :return:
     '''
     if author is None:
-        author = getLogin()
+        author = get_login()
     if creation_time is None:
         creation_time = UTCDateTime()
     return ope.CreationInfo(agency_id=agency_id, author=author,
@@ -210,7 +210,7 @@ def create_resourceID(timetohash, restype, authority_id=None, hrstr=None):
     '''
     assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
                                                 "UTCDateTime object"
-    hid = getHash(timetohash)
+    hid = get_hash(timetohash)
     if hrstr is None:
         resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
     else:

pylot/core/io/phases.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import glob
+import logging
 import os
 import warnings
 
@@ -16,29 +17,10 @@ from pylot.core.io.inputs import PylotParameter
 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, \
+from pylot.core.util.utils import get_owner, full_range, four_digits, transformFilterString4Export, \
     backtransformFilterString, loopIdentifyPhase, identifyPhase
 
 
-def add_amplitudes(event, amplitudes):
-    amplitude_list = []
-    for pick in event.picks:
-        try:
-            a0 = amplitudes[pick.waveform_id.station_code]
-            amplitude = ope.Amplitude(generic_amplitude=a0 * 1e-3)
-            amplitude.unit = 'm'
-            amplitude.category = 'point'
-            amplitude.waveform_id = pick.waveform_id
-            amplitude.magnitude_hint = 'ML'
-            amplitude.pick_id = pick.resource_id
-            amplitude.type = 'AML'
-            amplitude_list.append(amplitude)
-        except KeyError:
-            continue
-    event.amplitudes = amplitude_list
-    return event
-
-
 def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     """
     readPILOTEvent - function
@@ -58,7 +40,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     if phasfn is not None and os.path.isfile(phasfn):
         phases = sio.loadmat(phasfn)
         phasctime = UTCDateTime(os.path.getmtime(phasfn))
-        phasauthor = getOwner(phasfn)
+        phasauthor = get_owner(phasfn)
     else:
         phases = None
         phasctime = None
@@ -66,7 +48,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     if locfn is not None and os.path.isfile(locfn):
         loc = sio.loadmat(locfn)
         locctime = UTCDateTime(os.path.getmtime(locfn))
-        locauthor = getOwner(locfn)
+        locauthor = get_owner(locfn)
     else:
         loc = None
         locctime = None
@@ -192,32 +174,7 @@ def convert_pilot_times(time_array):
     return UTCDateTime(*times)
 
 
-def picksdict_from_obs(fn):
-    """
-    create pick dictionary from obs file
-    :param fn: filename
-    :type fn:
-    :return:
-    :rtype:
-    """
-    picks = dict()
-    station_name = str()
-    for line in open(fn, 'r'):
-        if line.startswith('#'):
-            continue
-        else:
-            phase_line = line.split()
-            if not station_name == phase_line[0]:
-                phase = dict()
-            station_name = phase_line[0]
-            phase_name = phase_line[4].upper()
-            pick = UTCDateTime(phase_line[6] + phase_line[7] + phase_line[8])
-            phase[phase_name] = dict(mpp=pick, fm=phase_line[5])
-            picks[station_name] = phase
-    return picks
-
-
-def picksdict_from_picks(evt):
+def picksdict_from_picks(evt, parameter=None):
     """
     Takes an Event object and return the pick dictionary commonly used within
     PyLoT
@@ -230,6 +187,7 @@ def picksdict_from_picks(evt):
         'auto': {}
     }
     for pick in evt.picks:
+        errors = None
         phase = {}
         station = pick.waveform_id.station_code
         if pick.waveform_id.channel_code is None:
@@ -273,32 +231,28 @@ def picksdict_from_picks(evt):
         phase['epp'] = epp
         phase['lpp'] = lpp
         phase['spe'] = spe
-        try:
-            phase['weight'] = weight
-        except:
-            # get onset weight from uncertainty
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-            parameter = PylotParameter(infile)
+        weight = phase.get('weight')
+        if not weight:
+            if not parameter:
+                logging.warning('Using ')
+                logging.warning('Using default input parameter')
+                parameter = PylotParameter()
             pick.phase_hint = identifyPhase(pick.phase_hint)
             if pick.phase_hint == 'P':
                 errors = parameter['timeerrorsP']
             elif pick.phase_hint == 'S':
                 errors = parameter['timeerrorsS']
-            weight = get_quality_class(spe, errors)
-            phase['weight'] = weight
+            if errors:
+                weight = get_quality_class(spe, errors)
+                phase['weight'] = weight
         phase['channel'] = channel
         phase['network'] = network
         phase['picker'] = pick_method
-        try:
-            if pick.polarity == 'positive':
-                phase['fm'] = 'U'
-            elif pick.polarity == 'negative':
-                phase['fm'] = 'D'
-            else:
-                phase['fm'] = 'N'
-        except:
-            print("No FM info available!")
+        if pick.polarity == 'positive':
+            phase['fm'] = 'U'
+        elif pick.polarity == 'negative':
+            phase['fm'] = 'D'
+        else:
             phase['fm'] = 'N'
         phase['filter_id'] = filter_id if filter_id is not None else ''
 
@@ -375,636 +329,228 @@ def picks_from_picksdict(picks, creation_info=None):
     return picks_list
 
 
-def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0):
-    # TODO: change root to datapath
-    db_root = os.path.join(root_dir, db_dir)
-    evt_list = glob.glob1(db_root, 'e????.???.??')
-
-    for evt in evt_list:
-        if verbosity > 0:
-            print('Reassessing event {0}'.format(evt))
-        reassess_pilot_event(root_dir, db_dir, evt, out_dir, fn_param, verbosity)
-
-
-def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None, verbosity=0):
-    from obspy import read
-
-    from pylot.core.io.inputs import PylotParameter
-    from pylot.core.pick.utils import earllatepicker
-    # TODO: change root to datapath
-
-    default = PylotParameter(fn_param, verbosity)
-
-    search_base = os.path.join(root_dir, db_dir, event_id)
-    phases_file = glob.glob(os.path.join(search_base, 'PHASES.mat'))
-    if not phases_file:
-        return
-    if verbosity > 1:
-        print('Opening PILOT phases file: {fn}'.format(fn=phases_file[0]))
-    picks_dict = picksdict_from_pilot(phases_file[0])
-    if verbosity > 0:
-        print('Dictionary read from PHASES.mat:\n{0}'.format(picks_dict))
-    datacheck = list()
-    info = None
-    for station in picks_dict.keys():
-        fn_pattern = os.path.join(search_base, '{0}*'.format(station))
-        try:
-            st = read(fn_pattern)
-        except TypeError as e:
-            if 'Unknown format for file' in e.message:
-                try:
-                    st = read(fn_pattern, format='GSE2')
-                except ValueError as e:
-                    if e.message == 'second must be in 0..59':
-                        info = 'A known Error was raised. Please find the list of corrupted files and double-check these files.'
-                        datacheck.append(fn_pattern + ' (time info)\n')
-                        continue
-                    else:
-                        raise ValueError(e.message)
-                except Exception as e:
-                    if 'No file matching file pattern:' in e.message:
-                        if verbosity > 0:
-                            warnings.warn('no waveform data found for station {station}'.format(station=station),
-                                          RuntimeWarning)
-                        datacheck.append(fn_pattern + ' (no data)\n')
-                        continue
-                    else:
-                        raise e
-            else:
-                raise e
-        for phase in picks_dict[station].keys():
-            try:
-                mpp = picks_dict[station][phase]['mpp']
-            except KeyError as e:
-                print(e.message, station)
-                continue
-            sel_st = select_for_phase(st, phase)
-            if not sel_st:
-                msg = 'no waveform data found for station {station}'.format(station=station)
-                warnings.warn(msg, RuntimeWarning)
-                continue
-            stime, etime = full_range(sel_st)
-            rel_pick = mpp - stime
-            epp, lpp, spe = earllatepicker(sel_st,
-                                           default.get('nfac{0}'.format(phase)),
-                                           default.get('tsnrz' if phase == 'P' else 'tsnrh'),
-                                           Pick1=rel_pick,
-                                           iplot=0,
-                                           verbosity=0)
-            if epp is None or lpp is None:
-                continue
-            epp = stime + epp
-            lpp = stime + lpp
-            min_diff = 3 * st[0].stats.delta
-            if lpp - mpp < min_diff:
-                lpp = mpp + min_diff
-            if mpp - epp < min_diff:
-                epp = mpp - min_diff
-            picks_dict[station][phase] = dict(epp=epp, mpp=mpp, lpp=lpp, spe=spe)
-    if datacheck:
-        if info:
-            if verbosity > 0:
-                print(info + ': {0}'.format(search_base))
-        fncheck = open(os.path.join(search_base, 'datacheck_list'), 'w')
-        fncheck.writelines(datacheck)
-        fncheck.close()
-        del datacheck
-    # create Event object for export
-    evt = ope.Event(resource_id=event_id)
-    evt.picks = picks_from_picksdict(picks_dict)
-    # write phase information to file
-    if not out_dir:
-        fnout_prefix = os.path.join(root_dir, db_dir, event_id, 'PyLoT_{0}.'.format(event_id))
-    else:
-        out_dir = os.path.join(out_dir, db_dir)
-        if not os.path.isdir(out_dir):
-            os.makedirs(out_dir)
-        fnout_prefix = os.path.join(out_dir, 'PyLoT_{0}.'.format(event_id))
-    evt.write(fnout_prefix + 'xml', format='QUAKEML')
-
-
-def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
+def write_phases(arrivals, fformat, filename, parameter=None, eventinfo=None):
     """
-    Function of methods to write phases to the following standard file
-    formats used for locating earthquakes:
+    Writes earthquake phase data to different file formats.
 
-    HYPO71, NLLoc, VELEST, HYPOSAT, FOCMEC, and hypoDD
-
-    :param arrivals:dictionary containing all phase information including
-     station ID, phase, first motion, weight (uncertainty), ...
+    :param arrivals: Dictionary containing phase information (station ID, phase, first motion, weight, etc.)
     :type arrivals: dict
-
-    :param fformat: chosen file format (location routine),
-    choose between NLLoc, HYPO71, HYPOSAT, VELEST,
-    HYPOINVERSE, FOCMEC, and hypoDD
+    :param fformat: File format to write to (e.g., 'NLLoc', 'HYPO71', 'HYPOSAT', 'VELEST', 'HYPODD', 'FOCMEC')
     :type fformat: str
-
-    :param filename: full path and name of phase file
-    :type filename:  string
-
-    :param parameter: all input information
-    :type parameter:  object
-
-    :param eventinfo: optional, needed for VELEST-cnv file
-            and FOCMEC- and HASH-input files 
-    :type eventinfo: `obspy.core.event.Event` object
+    :param filename: Path and name of the output phase file
+    :type filename: str
+    :param parameter: Additional parameters for writing the phase data
+    :type parameter: object
+    :param eventinfo: Event information needed for specific formats like VELEST, FOCMEC, and HASH
+    :type eventinfo: obspy.core.event.Event
     """
-    if fformat == 'NLLoc':
-        print("Writing phases to %s for NLLoc" % filename)
-        fid = open("%s" % filename, 'w')
-        # write header
-        fid.write('# EQEVENT: %s Label: EQ%s  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n' %
-                  (parameter.get('database'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
-        for key in arrivals:
-            # P onsets
-            if 'P' in arrivals[key]:
-                try:
-                    fm = arrivals[key]['P']['fm']
-                except KeyError as e:
-                    print(e)
-                    fm = None
-                if fm is None:
-                    fm = '?'
-                onset = arrivals[key]['P']['mpp']
-                year = onset.year
-                month = onset.month
-                day = onset.day
-                hh = onset.hour
-                mm = onset.minute
-                ss = onset.second
-                ms = onset.microsecond
-                ss_ms = ss + ms / 1000000.0
-                pweight = 1  # use pick
-                try:
-                    if arrivals[key]['P']['weight'] >= 4:
-                        pweight = 0  # do not use pick
-                        print("Station {}: Uncertain pick, do not use it!".format(key))
-                except KeyError as e:
-                    print(e.message + '; no weight set during processing')
-                fid.write('%s ? ? ? P   %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
-                                                                                           fm,
-                                                                                           year,
-                                                                                           month,
-                                                                                           day,
-                                                                                           hh,
-                                                                                           mm,
-                                                                                           ss_ms,
-                                                                                           pweight))
-            # S onsets
-            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
-                fm = '?'
-                onset = arrivals[key]['S']['mpp']
-                year = onset.year
-                month = onset.month
-                day = onset.day
-                hh = onset.hour
-                mm = onset.minute
-                ss = onset.second
-                ms = onset.microsecond
-                ss_ms = ss + ms / 1000000.0
-                sweight = 1  # use pick
-                try:
-                    if arrivals[key]['S']['weight'] >= 4:
-                        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
-                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 %9.2f 0 0 %d \n' % (key,
-                                                                                               fm,
-                                                                                               year,
-                                                                                               month,
-                                                                                               day,
-                                                                                               hh,
-                                                                                               mm,
-                                                                                               ss_ms,
-                                                                                               Ao,
-                                                                                               sweight))
 
-        fid.close()
-    elif fformat == 'HYPO71':
-        print("Writing phases to %s for HYPO71" % filename)
-        fid = open("%s" % filename, 'w')
-        # write header
-        fid.write('                                                                %s\n' %
-                  parameter.get('eventID'))
-        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
-                if len(stat) > 4:  # HYPO71 handles only 4-string station IDs
-                    stat = stat[1:5]
-                Ponset = arrivals[key]['P']['mpp']
-                Sonset = arrivals[key]['S']['mpp']
-                pweight = arrivals[key]['P']['weight']
-                sweight = arrivals[key]['S']['weight']
-                fm = arrivals[key]['P']['fm']
-                if fm is None:
-                    fm = '-'
-                Ao = arrivals[key]['S']['Ao']
-                if Ao is None:
-                    Ao = ''
-                else:
-                    Ao = str('%7.2f' % Ao)
-                year = Ponset.year
-                if year >= 2000:
-                    year = year - 2000
-                else:
-                    year = year - 1900
-                month = Ponset.month
-                day = Ponset.day
-                hh = Ponset.hour
-                mm = Ponset.minute
-                ss = Ponset.second
-                ms = Ponset.microsecond
-                ss_ms = ss + ms / 1000000.0
-                if pweight < 2:
-                    pstr = 'I'
-                elif pweight >= 2:
-                    pstr = 'E'
-                if arrivals[key]['S']['weight'] < 4:
-                    Sss = Sonset.second
-                    Sms = Sonset.microsecond
-                    Sss_ms = Sss + Sms / 1000000.0
-                    Sss_ms = str('%5.02f' % Sss_ms)
-                    if sweight < 2:
-                        sstr = 'I'
-                    elif sweight >= 2:
-                        sstr = 'E'
-                    fid.write('%-4s%sP%s%d %02d%02d%02d%02d%02d%5.2f       %s%sS %d   %s\n' % (stat,
-                                                                                               pstr,
-                                                                                               fm,
-                                                                                               pweight,
-                                                                                               year,
-                                                                                               month,
-                                                                                               day,
-                                                                                               hh,
-                                                                                               mm,
-                                                                                               ss_ms,
-                                                                                               Sss_ms,
-                                                                                               sstr,
-                                                                                               sweight,
-                                                                                               Ao))
-                else:
-                    fid.write('%-4s%sP%s%d %02d%02d%02d%02d%02d%5.2f                  %s\n' % (stat,
-                                                                                               pstr,
-                                                                                               fm,
-                                                                                               pweight,
-                                                                                               year,
-                                                                                               month,
-                                                                                               day,
-                                                                                               hh,
-                                                                                               mm,
-                                                                                               ss_ms,
-                                                                                               Ao))
+    def write_nlloc():
+        with open(filename, 'w') as fid:
+            fid.write('# EQEVENT: {} Label: EQ{}  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n'.format(
+                parameter.get('database'), parameter.get('eventID')))
+            for key, value in arrivals.items():
+                for phase in ['P', 'S']:
+                    if phase in value:
+                        fm = value[phase].get('fm', '?')
+                        onset = value[phase]['mpp']
+                        ss_ms = onset.second + onset.microsecond / 1000000.0
+                        weight = 1 if value[phase].get('weight', 0) < 4 else 0
+                        amp = value[phase].get('Ao', 0.0) if phase == 'S' else ''
+                        fid.write('{} ? ? ? {}   {}{}{} {}{} {:7.4f} GAU 0 {} 0 0 {}\n'.format(
+                            key, phase, fm, onset.year, onset.month, onset.day, onset.hour, onset.minute, ss_ms, amp,
+                            weight))
 
-        fid.close()
+    def write_hypo71():
+        with open(filename, 'w') as fid:
+            fid.write(
+                '                                                                {}\n'.format(parameter.get('eventID')))
+            for key, value in arrivals.items():
+                if value['P'].get('weight', 0) < 4:
+                    stat = key[:4]
+                    Ponset = value['P']['mpp']
+                    Sonset = value.get('S', {}).get('mpp')
+                    pweight = value['P'].get('weight', 0)
+                    sweight = value.get('S', {}).get('weight', 0)
+                    fm = value['P'].get('fm', '-')
+                    Ao = value.get('S', {}).get('Ao', '')
+                    year = Ponset.year - 2000 if Ponset.year >= 2000 else Ponset.year - 1900
+                    ss_ms = Ponset.second + Ponset.microsecond / 1000000.0
+                    if Sonset:
+                        Sss_ms = Sonset.second + Sonset.microsecond / 1000000.0
+                        fid.write('{}P{}{}{} {}{}{}{}{} {:5.2f}       {}{}S {}   {}\n'.format(
+                            stat, 'I' if pweight < 2 else 'E', fm, pweight, year, Ponset.month, Ponset.day,
+                            Ponset.hour, Ponset.minute, ss_ms, Sss_ms, 'I' if sweight < 2 else 'E', sweight, Ao))
+                    else:
+                        fid.write('{}P{}{}{} {}{}{}{}{} {:5.2f}                  {}\n'.format(
+                            stat, 'I' if pweight < 2 else 'E', fm, pweight, year, Ponset.month, Ponset.day,
+                            Ponset.hour, Ponset.minute, ss_ms, Ao))
 
-    elif fformat == 'HYPOSAT':
-        print("Writing phases to %s for HYPOSAT" % filename)
-        fid = open("%s" % filename, 'w')
-        # write header
-        fid.write('%s, event %s \n' % (parameter.get('database'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
-        for key in arrivals:
-            # P onsets
-            if 'P' in  arrivals[key] and arrivals[key]['P']['mpp'] is not None:
-                if arrivals[key]['P']['weight'] < 4:
-                    Ponset = arrivals[key]['P']['mpp']
-                    pyear = Ponset.year
-                    pmonth = Ponset.month
-                    pday = Ponset.day
-                    phh = Ponset.hour
-                    pmm = Ponset.minute
-                    pss = Ponset.second
-                    pms = Ponset.microsecond
-                    Pss = pss + pms / 1000000.0
-                    # use symmetrized picking error as std
-                    # (read the HYPOSAT manual)
-                    pstd = arrivals[key]['P']['spe']
-                    if pstd is None:
-                        errorsP = parameter.get('timeerrorsP')
-                        if arrivals[key]['P']['weight'] == 0:
-                            pstd = errorsP[0]
-                        elif arrivals[key]['P']['weight'] == 1:
-                            pstd = errorsP[1]
-                        elif arrivals[key]['P']['weight'] == 2:
-                            pstd = errorsP[2]
-                        elif arrivals[key]['P']['weight'] == 3:
-                            psrd = errorsP[3]
-                        else:
-                            pstd = errorsP[4]
-                    fid.write('%-5s P1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n'
-                              % (key, pyear, pmonth, pday, phh, pmm, Pss, pstd))
-            # S onsets
-            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
-                if arrivals[key]['S']['weight'] < 4:
-                    Sonset = arrivals[key]['S']['mpp']
-                    syear = Sonset.year
-                    smonth = Sonset.month
-                    sday = Sonset.day
-                    shh = Sonset.hour
-                    smm = Sonset.minute
-                    sss = Sonset.second
-                    sms = Sonset.microsecond
-                    Sss = sss + sms / 1000000.0
-                    sstd = arrivals[key]['S']['spe']
-                    if pstd is None:
-                        errorsS = parameter.get('timeerrorsS')
-                        if arrivals[key]['S']['weight'] == 0:
-                            pstd = errorsS[0]
-                        elif arrivals[key]['S']['weight'] == 1:
-                            pstd = errorsS[1]
-                        elif arrivals[key]['S']['weight'] == 2:
-                            pstd = errorsS[2]
-                        elif arrivals[key]['S']['weight'] == 3:
-                            psrd = errorsS[3]
-                        else:
-                            pstd = errorsP[4]
-                    fid.write('%-5s S1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n'
-                              % (key, syear, smonth, sday, shh, smm, Sss, sstd))
-        fid.close()
+    def write_hyposat():
+        with open(filename, 'w') as fid:
+            fid.write('{}, event {} \n'.format(parameter.get('database'), parameter.get('eventID')))
+            for key, value in arrivals.items():
+                for phase in ['P', 'S']:
+                    if phase in value and value[phase].get('weight', 0) < 4:
+                        onset = value[phase]['mpp']
+                        ss_ms = onset.second + onset.microsecond / 1000000.0
+                        std = value[phase].get('spe', parameter.get('timeerrorsP')[value[phase].get('weight', 0)])
+                        fid.write(
+                            '{:<5} {}1       {:4} {:02} {:02} {:02} {:02} {:05.02f}   {:5.3f} -999.   0.00 -999.  0.00\n'.format(
+                                key, phase, onset.year, onset.month, onset.day, onset.hour, onset.minute, ss_ms, std))
 
-    elif fformat == 'VELEST':
-        print("Writing phases to %s for VELEST" % filename)
-        fid = open("%s" % filename, 'w')
-        # get informations needed in cnv-file
-        # check, whether latitude is N or S and longitude is E or W
-        try:
-            eventsource = eventinfo.origins[0]
-        except:
+    def write_velest():
+        if not eventinfo:
             print("No source origin calculated yet, thus no cnv-file creation possible!")
             return
-        if eventsource['latitude'] < 0:
-            cns = 'S'
-        else:
-            cns = 'N'
-        if eventsource['longitude'] < 0:
-            cew = 'W'
-        else:
-            cew = 'E'
-        # get last two integers of origin year
-        stime = eventsource['time']
-        if stime.year - 2000 >= 0:
-            syear = stime.year - 2000
-        else:
-            syear = stime.year - 1900
-        ifx = 0  # default value, see VELEST manual, pp. 22-23
-        # write header
-        fid.write('%s%02d%02d %02d%02d %05.2f %7.4f%c %8.4f%c %7.2f %6.2f     %02.0f  0.0 0.03  1.0  1.0\n' % (
-            syear, stime.month, stime.day, stime.hour, stime.minute, stime.second, eventsource['latitude'],
-            cns, eventsource['longitude'], cew, eventsource['depth'], eventinfo.magnitudes[0]['mag'], ifx))
-        n = 0
-        # check whether arrivals are dictionaries (autoPyLoT) or pick object (PyLoT)
-        if isinstance(arrivals, dict) == False:
-            # convert pick object (PyLoT) into dictionary
-            evt = ope.Event(resource_id=eventinfo['resource_id'])
-            evt.picks = arrivals
-            arrivals = picksdict_from_picks(evt)
-        # check for automatic and manual picks
-        # prefer manual picks
-        usedarrivals = chooseArrivals(arrivals)
-        for key in usedarrivals:
-            # P onsets
-            if 'P' in usedarrivals[key]:
-                if usedarrivals[key]['P']['weight'] < 4:
-                    n += 1
-                    stat = key
-                    if len(stat) > 4:  # VELEST handles only 4-string station IDs
-                        stat = stat[1:5]
-                    Ponset = usedarrivals[key]['P']['mpp']
-                    Pweight = usedarrivals[key]['P']['weight']
-                    Prt = Ponset - stime  # onset time relative to source time
-                    if n % 6 != 0:
-                        fid.write('%-4sP%d%6.2f' % (stat, Pweight, Prt))
-                    else:
-                        fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))
-                        # S onsets
-            if 'S' in usedarrivals[key]:
-                if usedarrivals[key]['S']['weight'] < 4:
-                    n += 1
-                    stat = key
-                    if len(stat) > 4:  # VELEST handles only 4-string station IDs
-                        stat = stat[1:5]
-                    Sonset = usedarrivals[key]['S']['mpp']
-                    Sweight = usedarrivals[key]['S']['weight']
-                    Srt = Ponset - stime  # onset time relative to source time
-                    if n % 6 != 0:
-                        fid.write('%-4sS%d%6.2f' % (stat, Sweight, Srt))
-                    else:
-                        fid.write('%-4sS%d%6.2f\n' % (stat, Sweight, Srt))
-        fid.close()
+        with open(filename, 'w') as fid:
+            origin = eventinfo.origins[0]
+            lat_dir = 'S' if origin.latitude < 0 else 'N'
+            lon_dir = 'W' if origin.longitude < 0 else 'E'
+            year = origin.time.year - 2000 if origin.time.year >= 2000 else origin.time.year - 1900
+            fid.write(
+                '{}{}{} {}{} {} {:05.2f} {:7.4f}{} {:8.4f}{} {:7.2f} {:6.2f}     {:02.0f}  0.0 0.03  1.0  1.0\n'.format(
+                    year, origin.time.month, origin.time.day, origin.time.hour, origin.time.minute, origin.time.second,
+                    origin.latitude, lat_dir, origin.longitude, lon_dir, origin.depth, eventinfo.magnitudes[0].mag, 0))
+            for key, value in arrivals.items():
+                for phase in ['P', 'S']:
+                    if phase in value and value[phase].get('weight', 0) < 4:
+                        onset = value[phase]['mpp']
+                        rt = (onset - origin.time).total_seconds()
+                        fid.write('{:<4}{}{}{:6.2f}\n'.format(key[:4], phase, value[phase].get('weight', 0), rt))
 
-    elif fformat == 'HYPODD':
-        print("Writing phases to %s for hypoDD" % filename)
-        fid = open("%s" % filename, 'w')
-        # get event information needed for hypoDD-phase file
-        try:
-            eventsource = eventinfo.origins[0]
-        except:
+    def write_hypodd():
+        if not eventinfo:
             print("No source origin calculated yet, thus no hypoDD-infile creation possible!")
             return
-        stime = eventsource['time']
-        try:
-            event = eventinfo['pylot_id']
-            hddID = event.split('.')[0][1:5]
-        except:
-            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,
-            eventinfo.magnitudes[0]['mag'], eventsource['quality']['standard_error'], hddID))
-        # check whether arrivals are dictionaries (autoPyLoT) or pick object (PyLoT)
-        if isinstance(arrivals, dict) == False:
-            # convert pick object (PyLoT) into dictionary
-            evt = ope.Event(resource_id=eventinfo['resource_id'])
-            evt.picks = arrivals
-            arrivals = picksdict_from_picks(evt)
-        # check for automatic and manual picks
-        # prefer manual picks
-        usedarrivals = chooseArrivals(arrivals)
-        for key in usedarrivals:
-            if 'P' in usedarrivals[key]:
-                # P onsets
-                if usedarrivals[key]['P']['weight'] < 4:
-                    Ponset = usedarrivals[key]['P']['mpp']
-                    Prt = Ponset - stime  # onset time relative to source time
-                    fid.write('%s    %6.3f  1  P\n' % (key, Prt))
-            if 'S' in usedarrivals[key]:
-                # S onsets
-                if usedarrivals[key]['S']['weight'] < 4:
-                    Sonset = usedarrivals[key]['S']['mpp']
-                    Srt = Sonset - stime  # onset time relative to source time
-                    fid.write('%-5s    %6.3f  1  S\n' % (key, Srt))
+        with open(filename, 'w') as fid:
+            origin = eventinfo.origins[0]
+            stime = origin.time
+            fid.write('# {}  {} {} {} {} {} {:7.4f} +{:6.4f} {:7.4f} {:4.2f} 0.1 0.5 {:4.2f}      {}\n'.format(
+                stime.year, stime.month, stime.day, stime.hour, stime.minute, stime.second,
+                origin.latitude, origin.longitude, origin.depth / 1000, eventinfo.magnitudes[0].mag,
+                origin.quality.standard_error, "00000"))
+            for key, value in arrivals.items():
+                for phase in ['P', 'S']:
+                    if phase in value and value[phase].get('weight', 0) < 4:
+                        onset = value[phase]['mpp']
+                        rt = (onset - stime).total_seconds()
+                        fid.write('{}    {:6.3f}  1  {}\n'.format(key, rt, phase))
 
-        fid.close()
-
-    elif fformat == 'FOCMEC':
-        print("Writing phases to %s for FOCMEC" % filename)
-        fid = open("%s" % filename, 'w')
-        # get event information needed for FOCMEC-input file
-        try:
-            eventsource = eventinfo.origins[0]
-        except:
+    def write_focmec():
+        if not eventinfo:
             print("No source origin calculated yet, thus no FOCMEC-infile creation possible!")
             return
-        stime = eventsource['time']
-
-        # avoid printing '*' in focmec-input file
-        if parameter.get('eventid') == '*' or parameter.get('eventid') is None:
-            evID = 'e0000'
-        else:
-            evID = parameter.get('eventid')
-
-        # write header line including event information
-        fid.write('%s %d%02d%02d%02d%02d%02.0f %7.4f %6.4f %3.1f %3.1f\n' % (evID,
-                                                                             stime.year, stime.month, stime.day,
-                                                                             stime.hour, stime.minute, stime.second,
-                                                                             eventsource['latitude'],
-                                                                             eventsource['longitude'],
-                                                                             eventsource['depth'] / 1000,
-                                                                             eventinfo.magnitudes[0]['mag']))
-        picks = eventinfo.picks
-        # check whether arrivals are dictionaries (autoPyLoT) or pick object (PyLoT)
-        if isinstance(arrivals, dict) == False:
-            # convert pick object (PyLoT) into dictionary
-            evt = ope.Event(resource_id=eventinfo['resource_id'])
-            evt.picks = arrivals
-            arrivals = picksdict_from_picks(evt)
-        # check for automatic and manual picks
-        # prefer manual picks
-        usedarrivals = chooseArrivals(arrivals)
-        for key in usedarrivals:
-            if 'P' in usedarrivals[key]:
-                if usedarrivals[key]['P']['weight'] < 4 and usedarrivals[key]['P']['fm'] is not None:
-                    stat = key
-                    for i in range(len(picks)):
-                        station = picks[i].waveform_id.station_code
-                        if station == stat:
-                            # get resource ID
-                            resid_picks = picks[i].get('resource_id')
-                            # find same ID in eventinfo
-                            # there it is the pick_id!!
-                            for j in range(len(eventinfo.origins[0].arrivals)):
-                                resid_eventinfo = eventinfo.origins[0].arrivals[j].get('pick_id')
-                                if resid_eventinfo == resid_picks and eventinfo.origins[0].arrivals[j].phase == 'P':
-                                    if len(stat) > 4:  # FOCMEC handles only 4-string station IDs
-                                        stat = stat[1:5]
-                                    az = eventinfo.origins[0].arrivals[j].get('azimuth')
-                                    inz = eventinfo.origins[0].arrivals[j].get('takeoff_angle')
-                                    fid.write('%-4s  %6.2f  %6.2f%s \n' % (stat,
-                                                                           az,
-                                                                           inz,
-                                                                           usedarrivals[key]['P']['fm']))
+        with open(filename, 'w') as fid:
+            origin = eventinfo.origins[0]
+            stime = origin.time
+            fid.write('{} {}{:02d}{:02d}{:02d}{:02d}{:02.0f} {:7.4f} {:6.4f} {:3.1f} {:3.1f}\n'.format(
+                parameter.get('eventid', 'e0000'), stime.year, stime.month, stime.day, stime.hour, stime.minute,
+                stime.second, origin.latitude, origin.longitude, origin.depth / 1000, eventinfo.magnitudes[0].mag))
+            for key, value in arrivals.items():
+                if 'P' in value and value['P'].get('weight', 0) < 4 and value['P'].get('fm'):
+                    for pick in eventinfo.picks:
+                        if pick.waveform_id.station_code == key:
+                            for arrival in origin.arrivals:
+                                if arrival.pick_id == pick.resource_id and arrival.phase == 'P':
+                                    stat = key[:4]
+                                    az = arrival.azimuth
+                                    inz = arrival.takeoff_angle
+                                    fid.write('{:<4}  {:6.2f}  {:6.2f}{}\n'.format(stat, az, inz, value['P']['fm']))
                                     break
 
-        fid.close()
+    def write_hash():
+        # Define filenames for HASH driver 1 and 2
+        filename1 = f"{filename}drv1.phase"
+        filename2 = f"{filename}drv2.phase"
 
+        print(f"Writing phases to {filename1} for HASH-driver 1")
+        print(f"Writing phases to {filename2} for HASH-driver 2")
+
+        # Open files for writing
+        with open(filename1, 'w') as fid1, open(filename2, 'w') as fid2:
+            # Get event information needed for HASH-input file
+            try:
+                eventsource = eventinfo.origins[0]
+            except IndexError:
+                print("No source origin calculated yet, thus no cnv-file creation possible!")
+                return
+
+            event = parameter.get('eventID')
+            hashID = event.split('.')[0][1:5]
+            latdeg = eventsource['latitude']
+            latmin = (eventsource['latitude'] * 60) / 10000
+            londeg = eventsource['longitude']
+            lonmin = (eventsource['longitude'] * 60) / 10000
+
+            erh = (eventsource.origin_uncertainty['min_horizontal_uncertainty'] +
+                   eventsource.origin_uncertainty['max_horizontal_uncertainty']) / 2000
+            erz = eventsource.depth_errors['uncertainty']
+
+            stime = eventsource['time']
+            syear = stime.year % 100  # Calculate two-digit year
+
+            picks = eventinfo.picks
+
+            # Write header line including event information for HASH-driver 1
+            fid1.write(f"{syear:02d}{stime.month:02d}{stime.day:02d}{stime.hour:02d}{stime.minute:02d}"
+                       f"{stime.second:05.2f}{latdeg:2d}N{latmin:05.2f}{londeg:3d}E{lonmin:05.2f}"
+                       f"{eventsource['depth']:6.2f}{eventinfo.magnitudes[0]['mag']:4.2f}{erh:5.2f}{erz:5.2f}{hashID}\n")
+
+            # Write header line including event information for HASH-driver 2
+            fid2.write(f"{syear:02d}{stime.month:02d}{stime.day:02d}{stime.hour:02d}{stime.minute:02d}"
+                       f"{stime.second:05.2f}{latdeg}N{latmin:05.2f}{londeg}E{lonmin:6.2f}{eventsource['depth']:5.2f}"
+                       f"{eventsource['quality']['used_phase_count']:3d}{erh:5.2f}{erz:5.2f}"
+                       f"{eventinfo.magnitudes[0]['mag']:4.2f}{hashID}\n")
+
+            # Write phase lines
+            for key, arrival in arrivals.items():
+                if 'P' in arrival and arrival['P']['weight'] < 4 and arrival['P']['fm'] is not None:
+                    stat = key
+                    ccode = arrival['P']['channel']
+                    ncode = arrival['P']['network']
+                    Pqual = 'I' if arrival['P']['weight'] < 2 else 'E'
+
+                    for pick in picks:
+                        if pick.waveform_id.station_code == stat:
+                            resid_picks = pick.get('resource_id')
+                            for origin_arrival in eventinfo.origins[0].arrivals:
+                                if (origin_arrival.get('pick_id') == resid_picks and
+                                        origin_arrival.phase == 'P'):
+                                    if len(stat) > 4:  # HASH handles only 4-character station IDs
+                                        stat = stat[1:5]
+
+                                    az = origin_arrival.get('azimuth')
+                                    inz = origin_arrival.get('takeoff_angle')
+                                    dist = origin_arrival.get('distance')
+
+                                    # Write phase line for HASH-driver 1
+                                    fid1.write(f"{stat:<4}{Pqual}P{arrival['P']['fm']}{arrival['P']['weight']:d}"
+                                               f"{dist:3.1f}{inz:03d}{az:03d}{ccode}\n")
+
+                                    # Write phase line for HASH-driver 2
+                                    fid2.write(f"{stat:<4} {ncode} {ccode} {Pqual} {arrival['P']['fm']}\n")
+                                    break
+
+            fid1.write(f"{'':<36}{hashID}")
+
+    # Prefer Manual Picks over automatic ones if possible
+    arrivals = chooseArrivals(arrivals)  # Function not defined, assumed to exist
+
+    if fformat == 'NLLoc':
+        write_nlloc()
+    elif fformat == 'HYPO71':
+        write_hypo71()
+    elif fformat == 'HYPOSAT':
+        write_hyposat()
+    elif fformat == 'VELEST':
+        write_velest()
+    elif fformat == 'HYPODD':
+        write_hypodd()
+    elif fformat == 'FOCMEC':
+        write_focmec()
     elif fformat == 'HASH':
-        # two different input files for 
-        # HASH-driver 1 and 2 (see HASH manual!)
-        filename1 = filename + 'drv1' + '.phase'
-        filename2 = filename + 'drv2' + '.phase'
-        print("Writing phases to %s for HASH for HASH-driver 1" % filename1)
-        fid1 = open("%s" % filename1, 'w')
-        print("Writing phases to %s for HASH for HASH-driver 2" % filename2)
-        fid2 = open("%s" % filename2, 'w')
-        # get event information needed for HASH-input file
-        try:
-            eventsource = eventinfo.origins[0]
-        except:
-            print("No source origin calculated yet, thus no cnv-file creation possible!")
-            return
-        eventsource = eventinfo.origins[0]
-        event = parameter.get('eventID')
-        hashID = event.split('.')[0][1:5]
-        latdeg = eventsource['latitude']
-        latmin = eventsource['latitude'] * 60 / 10000
-        londeg = eventsource['longitude']
-        lonmin = eventsource['longitude'] * 60 / 10000
-        erh = 1 / 2 * (eventsource.origin_uncertainty['min_horizontal_uncertainty'] +
-                       eventsource.origin_uncertainty['max_horizontal_uncertainty']) / 1000
-        erz = eventsource.depth_errors['uncertainty']
-        stime = eventsource['time']
-        if stime.year - 2000 >= 0:
-            syear = stime.year - 2000
-        else:
-            syear = stime.year - 1900
-        picks = eventinfo.picks
-        # write header line including event information
-        # for HASH-driver 1
-        fid1.write('%s%02d%02d%02d%02d%5.2f%2dN%5.2f%3dE%5.2f%6.3f%4.2f%5.2f%5.2f%s\n' % (syear,
-                                                                                          stime.month, stime.day,
-                                                                                          stime.hour, stime.minute,
-                                                                                          stime.second,
-                                                                                          latdeg, latmin, londeg,
-                                                                                          lonmin, eventsource['depth'],
-                                                                                          eventinfo.magnitudes[0][
-                                                                                              'mag'], erh, erz,
-                                                                                          hashID))
-        # write header line including event information
-        # for HASH-driver 2
-        fid2.write(
-            '%d%02d%02d%02d%02d%5.2f%dN%5.2f%3dE%6.2f%5.2f    %d                                          %5.2f %5.2f                                        %4.2f      %s \n' % (
-                syear, stime.month, stime.day,
-                stime.hour, stime.minute, stime.second,
-                latdeg, latmin, londeg, lonmin,
-                eventsource['depth'],
-                eventsource['quality']['used_phase_count'],
-                erh, erz, eventinfo.magnitudes[0]['mag'],
-                hashID))
-        # Prefer Manual Picks over automatic ones if possible
-        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
-        # write phase lines
-        for key in arrivals:
-            if 'P' in arrivals[key]:
-                if arrivals[key]['P']['weight'] < 4 and arrivals[key]['P']['fm'] is not None:
-                    stat = key
-                    ccode = arrivals[key]['P']['channel']
-                    ncode = arrivals[key]['P']['network']
-
-                    if arrivals[key]['P']['weight'] < 2:
-                        Pqual = 'I'
-                    else:
-                        Pqual = 'E'
-
-                    for i in range(len(picks)):
-                        station = picks[i].waveform_id.station_code
-                        if station == stat:
-                            # get resource ID
-                            resid_picks = picks[i].get('resource_id')
-                            # find same ID in eventinfo
-                            # there it is the pick_id!!
-                            for j in range(len(eventinfo.origins[0].arrivals)):
-                                resid_eventinfo = eventinfo.origins[0].arrivals[j].get('pick_id')
-                                if resid_eventinfo == resid_picks and eventinfo.origins[0].arrivals[j].phase == 'P':
-                                    if len(stat) > 4:  # HASH handles only 4-string station IDs
-                                        stat = stat[1:5]
-                                    az = eventinfo.origins[0].arrivals[j].get('azimuth')
-                                    inz = eventinfo.origins[0].arrivals[j].get('takeoff_angle')
-                                    dist = eventinfo.origins[0].arrivals[j].get('distance')
-                                    # write phase line for HASH-driver 1
-                                    fid1.write(
-                                        '%-4s%sP%s%d                   0                                   %3.1f          %03d %03d   2     1   %s\n' % (
-                                            stat, Pqual, arrivals[key]['P']['fm'], arrivals[key]['P']['weight'],
-                                            dist, inz, az, ccode))
-                                    # write phase line for HASH-driver 2
-                                    fid2.write('%-4s %s   %s %s %s                    \n' % (
-                                        stat,
-                                        ncode,
-                                        ccode,
-                                        Pqual,
-                                        arrivals[key]['P']['fm']))
-                                    break
-
-        fid1.write('                                    %s' % hashID)
-        fid1.close()
-        fid2.close()
+        write_hash()
 
 
 def chooseArrivals(arrivals):
@@ -1124,7 +670,7 @@ def getQualitiesfromxml(path, errorsP, errorsS, plotflag=1, figure=None, verbosi
                 mstation = pick.waveform_id.station_code
                 mstation_ext = mstation + '_'
                 for mpick in arrivals_copy:
-                    phase = identifyPhase(loopIdentifyPhase(pick.phase_hint)) # MP MP catch if this fails?
+                    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 \

pylot/core/loc/focmec.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -25,4 +25,4 @@ def export(picks, fnout, parameter, eventinfo):
     :type eventinfo:  list object
     '''
     # write phases to FOCMEC-phase file
-    writephases(picks, 'FOCMEC', fnout, parameter, eventinfo)
+    write_phases(picks, 'FOCMEC', fnout, parameter, eventinfo)

pylot/core/loc/hash.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -25,4 +25,4 @@ def export(picks, fnout, parameter, eventinfo):
     :type eventinfo:  list object
     '''
     # write phases to HASH-phase file
-    writephases(picks, 'HASH', fnout, parameter, eventinfo)
+    write_phases(picks, 'HASH', fnout, parameter, eventinfo)

pylot/core/loc/hypo71.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -22,4 +22,4 @@ def export(picks, fnout, parameter):
     :type parameter:  object
     '''
     # write phases to HYPO71-phase file
-    writephases(picks, 'HYPO71', fnout, parameter)
+    write_phases(picks, 'HYPO71', fnout, parameter)

pylot/core/loc/hypodd.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -25,4 +25,4 @@ def export(picks, fnout, parameter, eventinfo):
     :type eventinfo:  list object
     '''
     # write phases to hypoDD-phase file
-    writephases(picks, 'HYPODD', fnout, parameter, eventinfo)
+    write_phases(picks, 'HYPODD', fnout, parameter, eventinfo)

pylot/core/loc/hyposat.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -22,4 +22,4 @@ def export(picks, fnout, parameter):
     :type parameter:  object
     '''
     # write phases to HYPOSAT-phase file
-    writephases(picks, 'HYPOSAT', fnout, parameter)
+    write_phases(picks, 'HYPOSAT', fnout, parameter)

pylot/core/loc/nll.py

@@ -7,7 +7,7 @@ import subprocess
 
 from obspy import read_events
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 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
@@ -34,7 +34,7 @@ def export(picks, fnout, parameter):
     :type parameter:  object
     '''
     # write phases to NLLoc-phase file
-    writephases(picks, 'NLLoc', fnout, parameter)
+    write_phases(picks, 'NLLoc', fnout, parameter)
 
 
 def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):

pylot/core/loc/velest.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -25,4 +25,4 @@ def export(picks, fnout, eventinfo, parameter=None):
     :type parameter:  object
     '''
     # write phases to VELEST-phase file
-    writephases(picks, 'VELEST', fnout, parameter, eventinfo)
+    write_phases(picks, 'VELEST', fnout, parameter, eventinfo)

pylot/core/pick/autopick.py

@@ -20,9 +20,9 @@ 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_quality_class
+    getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class, PickingFailedException, MissingTraceException
 from pylot.core.util.utils import getPatternLine, gen_Pool, \
-    get_bool, identifyPhaseID, get_None, correct_iplot
+    get_bool, identifyPhaseID, get_none, correct_iplot
 
 
 def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
@@ -232,20 +232,6 @@ class PickingContainer:
         self.Sflag = 0
 
 
-class MissingTraceException(ValueError):
-    """
-    Used to indicate missing traces in a obspy.core.stream.Stream object
-    """
-    pass
-
-
-class PickingFailedException(Exception):
-    """
-    Raised when picking fails due to missing values etc.
-    """
-    pass
-
-
 class AutopickStation(object):
 
     def __init__(self, wfstream, pickparam, verbose, iplot=0, fig_dict=None, metadata=None, origin=None):
@@ -272,7 +258,7 @@ class AutopickStation(object):
         self.pickparams = copy.deepcopy(pickparam)
         self.verbose = verbose
         self.iplot = correct_iplot(iplot)
-        self.fig_dict = get_None(fig_dict)
+        self.fig_dict = get_none(fig_dict)
         self.metadata = metadata
         self.origin = origin
 
@@ -660,7 +646,7 @@ class AutopickStation(object):
             ax1.set_ylim([-1.5, 1.5])
             ax1.set_ylabel('Normalized Counts')
 
-            if self.horizontal_traces_exist() and self.s_data.Sflag == 1:
+            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,

pylot/core/pick/charfuns.py

@@ -20,6 +20,8 @@ import numpy as np
 from scipy import signal
 from obspy.core import Stream
 
+from pylot.core.pick.utils import PickingFailedException
+
 
 class CharacteristicFunction(object):
     """
@@ -293,7 +295,7 @@ class HOScf(CharacteristicFunction):
             if j < 4:
                 LTA[j] = 0
                 STA[j] = 0
-            elif j <= ista:
+            elif j <= ista and self.getOrder() == 2:
                 lta = (y[j] + lta * (j - 1)) / j
                 if self.getOrder() == 2:
                     sta = (y[j] + sta * (j - 1)) / j
@@ -488,6 +490,9 @@ class ARHcf(CharacteristicFunction):
         print('Calculating AR-prediction error from both horizontal traces ...')
 
         xnp = self.getDataArray(self.getCut())
+        if len(xnp[0]) == 0:
+            raise PickingFailedException('calcCF: Found empty data trace for cut times. Return')
+
         n0 = np.isnan(xnp[0].data)
         if len(n0) > 1:
             xnp[0].data[n0] = 0

pylot/core/pick/picker.py

@@ -178,7 +178,9 @@ class AICPicker(AutoPicker):
         aic = tap * self.cf + max(abs(self.cf))
         # smooth AIC-CF
         ismooth = int(round(self.Tsmooth / self.dt))
-        aicsmooth = np.zeros(len(aic))
+        # MP MP better start with original data than zeros if array shall be smoothed, created artificial value before
+        # when starting with i in range(1...) loop below and subtracting offset afterwards
+        aicsmooth = np.copy(aic)
         if len(aic) < ismooth:
             print('AICPicker: Tsmooth larger than CF!')
             return
@@ -188,7 +190,7 @@ class AICPicker(AutoPicker):
                     ii1 = i - ismooth
                     aicsmooth[i] = aicsmooth[i - 1] + (aic[i] - aic[ii1]) / ismooth
                 else:
-                    aicsmooth[i] = np.mean(aic[1: i])
+                    aicsmooth[i] = np.mean(aic[0: i]) # MP MP created np.nan for i=1
         # remove offset in AIC function
         offset = abs(min(aic) - min(aicsmooth))
         aicsmooth = aicsmooth - offset
@@ -197,7 +199,7 @@ class AICPicker(AutoPicker):
         # minimum in AIC function 
         icfmax = np.argmax(cf)
 
-        # MP MP testing threshold
+        # TODO: If this shall be kept, maybe add thresh_factor to pylot parameters
         thresh_hit = False
         thresh_factor = 0.7
         thresh = thresh_factor * cf[icfmax]
@@ -209,7 +211,6 @@ class AICPicker(AutoPicker):
                 if sample <= cf[index - 1]:
                     icfmax = index - 1
                     break
-        # MP MP ---
 
         # find minimum in AIC-CF front of maximum of HOS/AR-CF
         lpickwindow = int(round(self.PickWindow / self.dt))

pylot/core/pick/utils.py

@@ -15,7 +15,7 @@ import numpy as np
 from obspy.core import Stream, UTCDateTime
 from scipy.signal import argrelmax
 
-from pylot.core.util.utils import get_bool, get_None, SetChannelComponents
+from pylot.core.util.utils import get_bool, get_none, SetChannelComponents
 
 
 def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
@@ -136,7 +136,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
     PickError = symmetrize_error(diffti_te, diffti_tl)
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -275,7 +275,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P1 = np.polyfit(xslope1, xraw[islope1], 1)
                 datafit1 = np.polyval(P1, xslope1)
-            except Exception as e:
+            except ValueError as e:
                 print("fmpicker: Problems with data fit! {}".format(e))
                 print("Skip first motion determination!")
                 return FM
@@ -321,7 +321,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P2 = np.polyfit(xslope2, xfilt[islope2], 1)
                 datafit2 = np.polyval(P2, xslope2)
-            except Exception as e:
+            except ValueError as e:
                 emsg = 'fmpicker: polyfit failed: {}'.format(e)
                 print(emsg)
                 return FM
@@ -344,7 +344,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
         print("fmpicker: Found polarity %s" % FM)
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -868,7 +868,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
             returnflag = 0
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -890,6 +890,8 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
                 input()
             except SyntaxError:
                 pass
+            except EOFError:
+                pass
             plt.close(fig)
 
     return returnflag
@@ -1211,14 +1213,14 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
             t = np.linspace(diff_dict[key], trace.stats.endtime - trace.stats.starttime + diff_dict[key],
                             trace.stats.npts)
             if i == 0:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax1 = fig.add_subplot(3, 1, i + 1)
                 ax = ax1
                 ax.set_title('CheckZ4S, Station %s' % zdat[0].stats.station)
             else:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax = fig.add_subplot(3, 1, i + 1, sharex=ax1)
@@ -1332,22 +1334,6 @@ def get_quality_class(uncertainty, weight_classes):
     return quality
 
 
-def set_NaNs_to(data, nan_value):
-    """
-    Replace all NaNs in data with nan_value
-    :param data: array holding data
-    :type data: `~numpy.ndarray`
-    :param nan_value: value which all NaNs are set to
-    :type nan_value: float, int
-    :return: data array with all NaNs replaced with nan_value
-    :rtype: `~numpy.ndarray`
-    """
-    nn = np.isnan(data)
-    if np.any(nn):
-        data[nn] = nan_value
-    return data
-
-
 def taper_cf(cf):
     """
     Taper cf data to get rid off of side maximas
@@ -1508,7 +1494,7 @@ def getQualityFromUncertainty(uncertainty, Errors):
     # set initial quality to 4 (worst) and change only if one condition is hit
     quality = 4
 
-    if get_None(uncertainty) is None:
+    if get_none(uncertainty) is None:
         return quality
 
     if uncertainty <= Errors[0]:
@@ -1532,3 +1518,17 @@ if __name__ == '__main__':
     import doctest
 
     doctest.testmod()
+
+
+class PickingFailedException(Exception):
+    """
+    Raised when picking fails due to missing values etc.
+    """
+    pass
+
+
+class MissingTraceException(ValueError):
+    """
+    Used to indicate missing traces in a obspy.core.stream.Stream object
+    """
+    pass

pylot/core/util/array_map.py

@@ -13,6 +13,7 @@ import obspy
 from PySide2 import QtWidgets
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
+from pylot.core.util.utils import identifyPhaseID
 from scipy.interpolate import griddata
 
 from pylot.core.pick.utils import get_quality_class
@@ -123,8 +124,8 @@ class Array_map(QtWidgets.QWidget):
         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'))
+        # try to set to viridis as default
+        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('viridis'))
 
         self.top_row.addWidget(QtWidgets.QLabel('Select a phase: '))
         self.top_row.addWidget(self.comboBox_phase)
@@ -279,9 +280,12 @@ class Array_map(QtWidgets.QWidget):
         self.canvas.axes.figure.canvas.draw_idle()
 
     def onpick(self, event):
+        btn_msg = {1: ' in selection. Aborted', 2: ' to delete a pick on. Aborted', 3: ' to display info.'}
         ind = event.ind
         button = event.mouseevent.button
-        if ind == []:
+        msg_reason = None
+        if len(ind) > 1:
+            self._parent.update_status(f'Found more than one station {btn_msg.get(button)}')
             return
         if button == 1:
             self.openPickDlg(ind)
@@ -384,7 +388,14 @@ class Array_map(QtWidgets.QWidget):
                 try:
                     station_name = st_id.split('.')[-1]
                     # current_picks_dict: auto or manual
-                    pick = self.current_picks_dict()[station_name][phase]
+                    station_picks = self.current_picks_dict().get(station_name)
+                    if not station_picks:
+                        continue
+                    for phase_hint, pick in station_picks.items():
+                        if identifyPhaseID(phase_hint) == phase:
+                            break
+                    else:
+                        continue
                     if pick['picker'] == 'auto':
                         if not pick['spe']:
                             continue

pylot/core/util/dataprocessing.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import glob
+import logging
 import os
 import sys
 
@@ -189,7 +190,11 @@ class Metadata(object):
         metadata = self.get_metadata(seed_id, time)
         if not metadata:
             return
-        return metadata['data'].get_coordinates(seed_id, time)
+        try:
+            return metadata['data'].get_coordinates(seed_id, time)
+        # no specific exception defined in obspy inventory
+        except Exception as e:
+            logging.warning(f'Could not get metadata for {seed_id}')
 
     def get_all_coordinates(self):
         def stat_info_from_parser(parser):

pylot/core/util/generate_array_maps.py

@@ -42,7 +42,7 @@ def main(project_file_path, manual=False, auto=True, file_format='png', f_ext=''
         for item in input_list:
             array_map_worker(item)
     else:
-        pool = multiprocessing.Pool(ncores)
+        pool = multiprocessing.Pool(ncores, maxtasksperchild=1000)
         pool.map(array_map_worker, input_list)
         pool.close()
         pool.join()

pylot/core/util/thread.py

@@ -160,7 +160,7 @@ class MultiThread(QThread):
         try:
             if not self.ncores:
                 self.ncores = multiprocessing.cpu_count()
-            pool = multiprocessing.Pool(self.ncores)
+            pool = multiprocessing.Pool(self.ncores, maxtasksperchild=1000)
             self.data = pool.map_async(self.func, self.args, callback=self.emitDone)
             # self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned
             pool.close()

pylot/core/util/utils.py

@@ -1,12 +1,15 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-
+import glob
 import hashlib
+import logging
 import os
 import platform
 import re
 import subprocess
 import warnings
+from typing import Literal, Tuple, Type
+from functools import lru_cache
 
 import numpy as np
 from obspy import UTCDateTime, read
@@ -18,6 +21,10 @@ from pylot.core.io.inputs import PylotParameter, FilterOptions
 from pylot.core.util.obspyDMT_interface import check_obspydmt_eventfolder
 from pylot.styles import style_settings
 
+Rgba: Type[tuple] = Tuple[int, int, int, int]
+Mplrgba: Type[tuple] = Tuple[float, float, float, float]
+Mplrgbastr: Type[tuple] = Tuple[str, str, str, str]
+
 
 def _pickle_method(m):
     if m.im_self is None:
@@ -81,25 +88,6 @@ def fit_curve(x, y):
     return splev, splrep(x, y)
 
 
-def getindexbounds(f, eta):
-    """
-    Get indices of values closest below and above maximum value in an array
-    :param f: array
-    :type f: `~numpy.ndarray`
-    :param eta: look for value in array that is closes to max_value * eta
-    :type eta: float
-    :return: tuple containing index of max value, index of value closest below max value,
-     index of value closest above max value
-    :rtype: (int, int, int)
-    """
-    mi = f.argmax()  # get indices of max values
-    m = max(f)  # get maximum value
-    b = m * eta  #
-    l = find_nearest(f[:mi], b)  # find closest value below max value
-    u = find_nearest(f[mi:], b) + mi  # find closest value above max value
-    return mi, l, u
-
-
 def gen_Pool(ncores=0):
     """
     Generate mulitprocessing pool object utilizing ncores amount of cores
@@ -119,7 +107,7 @@ def gen_Pool(ncores=0):
 
     print('gen_Pool: Generated multiprocessing Pool with {} cores\n'.format(ncores))
 
-    pool = multiprocessing.Pool(ncores)
+    pool = multiprocessing.Pool(ncores, maxtasksperchild=100)
     return pool
 
 
@@ -165,11 +153,11 @@ def clims(lim1, lim2):
     """
     takes two pairs of limits and returns one pair of common limts
     :param lim1: limit 1
-    :type lim1: int
+    :type lim1: List[int]
     :param lim2: limit 2
-    :type lim2: int
+    :type lim2: List[int]
     :return: new upper and lower limit common to both given limits
-    :rtype: [int, int]
+    :rtype: List[int]
 
     >>> clims([0, 4], [1, 3])
     [0, 4]
@@ -301,7 +289,7 @@ def fnConstructor(s):
     if type(s) is str:
         s = s.split(':')[-1]
     else:
-        s = getHash(UTCDateTime())
+        s = get_hash(UTCDateTime())
 
     badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
     badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
@@ -313,15 +301,32 @@ def fnConstructor(s):
     return fn
 
 
-def get_None(value):
+def get_none(value):
     """
     Convert "None" to None
     :param value:
-    :type value: str, bool
+    :type value: str, NoneType
     :return:
-    :rtype: bool
+    :rtype: type(value) or NoneType
+
+    >>> st = read()
+    >>> print(get_none(st))
+    3 Trace(s) in Stream:
+    BW.RJOB..EHZ | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHN | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHE | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    >>> get_none('Stream')
+    'Stream'
+    >>> get_none(0)
+    0
+    >>> get_none(0.)
+    0.0
+    >>> print(get_none('None'))
+    None
+    >>> print(get_none(None))
+    None
     """
-    if value == 'None':
+    if value is None or (type(value) is str and value == 'None'):
         return None
     else:
         return value
@@ -329,11 +334,32 @@ def get_None(value):
 
 def get_bool(value):
     """
-    Convert string representations of bools to their true boolean value
+    Convert string representations of bools to their true boolean value. Return value if it cannot be identified as bool.
     :param value:
-    :type value: str, bool
+    :type value: str, bool, int, float
     :return: true boolean value
     :rtype: bool
+
+    >>> get_bool(True)
+    True
+    >>> get_bool(False)
+    False
+    >>> get_bool(0)
+    False
+    >>> get_bool(0.)
+    False
+    >>> get_bool(0.1)
+    True
+    >>> get_bool(2)
+    True
+    >>> get_bool(-1)
+    False
+    >>> get_bool(-0.3)
+    False
+    >>> get_bool(None)
+    None
+    >>> get_bool('Stream')
+    'Stream'
     """
     if type(value) is bool:
         return value
@@ -341,8 +367,14 @@ def get_bool(value):
         return True
     elif value in ['False', 'false']:
         return False
+    elif isinstance(value, float) or isinstance(value, int):
+        if value > 0. or value > 0:
+            return True
+        else:
+            return False
     else:
-        return bool(value)
+        return value
+
 
 def four_digits(year):
     """
@@ -353,8 +385,8 @@ def four_digits(year):
     :return: four digit year correspondent
     :rtype: int
 
-    >>> four_digits(20)
-    1920
+    >>> four_digits(75)
+    1975
     >>> four_digits(16)
     2016
     >>> four_digits(00)
@@ -436,36 +468,53 @@ def backtransformFilterString(st):
     return st
 
 
-def getHash(time):
+def get_hash(time):
     """
     takes a time object and returns the corresponding SHA1 hash of the formatted date string
     :param time: time object for which a hash should be calculated
     :type time: `~obspy.core.utcdatetime.UTCDateTime`
     :return: SHA1 hash
     :rtype: str
+
+    >>> time = UTCDateTime(0)
+    >>> get_hash(time)
+    '7627cce3b1b58dd21b005dac008b34d18317dd15'
+    >>> get_hash(0)
+    Traceback (most recent call last):
+    ...
+    AssertionError: 'time' is not an ObsPy UTCDateTime object
     """
+    assert isinstance(time, UTCDateTime), '\'time\' is not an ObsPy UTCDateTime object'
     hg = hashlib.sha1()
-    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
+    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f').encode('utf-8'))
     return hg.hexdigest()
 
 
-def getLogin():
+def get_login():
     """
-    returns the actual user's login ID
-    :return: login ID
+    returns the actual user's name
+    :return: login name
     :rtype: str
     """
     import getpass
     return getpass.getuser()
 
 
-def getOwner(fn):
+def get_owner(fn):
     """
     takes a filename and return the login ID of the actual owner of the file
     :param fn: filename of the file tested
     :type fn: str
     :return: login ID of the file's owner
     :rtype: str
+
+    >>> import tempfile
+    >>> with tempfile.NamedTemporaryFile() as tmpfile:
+    ...     tmpfile.write(b'') and True
+    ...     tmpfile.flush()
+    ...     get_owner(tmpfile.name) == os.path.expanduser('~').split('/')[-1]
+    0
+    True
     """
     system_name = platform.system()
     if system_name in ["Linux", "Darwin"]:
@@ -511,6 +560,11 @@ def is_executable(fn):
     :param fn: path to the file to be tested
     :return: True or False
     :rtype: bool
+
+    >>> is_executable('/bin/ls')
+    True
+    >>> is_executable('/var/log/system.log')
+    False
     """
     return os.path.isfile(fn) and os.access(fn, os.X_OK)
 
@@ -537,24 +591,36 @@ def isSorted(iterable):
     >>> isSorted([2,3,1,4])
     False
     """
-    assert isIterable(iterable), 'object is not iterable; object: {' \
-                                 '}'.format(iterable)
+    assert is_iterable(iterable), "object is not iterable; object: {}".format(iterable)
     if type(iterable) is str:
         iterable = [s for s in iterable]
     return sorted(iterable) == iterable
 
 
-def isIterable(obj):
+def is_iterable(obj):
     """
     takes a python object and returns True is the object is iterable and
     False otherwise
     :param obj: a python object
-    :type obj: object
+    :type obj: obj
     :return: True of False
     :rtype: bool
+
+    >>> is_iterable(1)
+    False
+    >>> is_iterable(True)
+    False
+    >>> is_iterable(0.)
+    False
+    >>> is_iterable((0,1,3,4))
+    True
+    >>> is_iterable([1])
+    True
+    >>> is_iterable('a')
+    True
     """
     try:
-        iterator = iter(obj)
+        iter(obj)
     except TypeError as te:
         return False
     return True
@@ -563,13 +629,19 @@ def isIterable(obj):
 def key_for_set_value(d):
     """
     takes a dictionary and returns the first key for which's value the
-    boolean is True
+    boolean representation is True
     :param d: dictionary containing values
     :type d: dict
     :return: key to the first non-False value found; None if no value's
     boolean equals True
-    :rtype:
+    :rtype: bool or NoneType
+
+    >>> key_for_set_value({'one': 0, 'two': 1})
+    'two'
+    >>> print(key_for_set_value({1: 0, 2: False}))
+    None
     """
+    assert type(d) is dict, "Function only defined for inputs of type 'dict'."
     r = None
     for k, v in d.items():
         if v:
@@ -577,32 +649,53 @@ def key_for_set_value(d):
     return r
 
 
-def prepTimeAxis(stime, trace, verbosity=0):
+def prep_time_axis(offset, trace, verbosity=0):
     """
-    takes a starttime and a trace object and returns a valid time axis for
+    takes an offset and a trace object and returns a valid time axis for
     plotting
-    :param stime: start time of the actual seismogram as UTCDateTime
-    :type stime: `~obspy.core.utcdatetime.UTCDateTime`
+    :param offset: offset of the actual seismogram on plotting axis
+    :type offset: float or int
     :param trace: seismic trace object
     :type trace: `~obspy.core.trace.Trace`
     :param verbosity: if != 0, debug output will be written to console
     :type verbosity: int
     :return: valid numpy array with time stamps for plotting
     :rtype: `~numpy.ndarray`
+
+    >>> tr = read()[0]
+    >>> prep_time_axis(0., tr)
+    array([0.00000000e+00, 1.00033344e-02, 2.00066689e-02, ...,
+           2.99799933e+01, 2.99899967e+01, 3.00000000e+01])
+    >>> prep_time_axis(22.5, tr)
+    array([22.5       , 22.51000333, 22.52000667, ..., 52.47999333,
+           52.48999667, 52.5       ])
+    >>> prep_time_axis(tr.stats.starttime, tr)
+    Traceback (most recent call last):
+    ...
+    AssertionError: 'offset' is not of type 'float' or 'int'; type: <class 'obspy.core.utcdatetime.UTCDateTime'>
+    >>> tr.stats.npts -= 1
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033356e-02, 2.00066711e-02, ...,
+           2.99699933e+01, 2.99799967e+01, 2.99900000e+01])
+    >>> tr.stats.npts += 2
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033333e-02, 2.00066667e-02, ...,
+           2.99899933e+01, 2.99999967e+01, 3.00100000e+01])
     """
+    assert isinstance(offset, (float, int)), "'offset' is not of type 'float' or 'int'; type: {}".format(type(offset))
     nsamp = trace.stats.npts
     srate = trace.stats.sampling_rate
     tincr = trace.stats.delta
-    etime = stime + nsamp / srate
-    time_ax = np.linspace(stime, etime, nsamp)
+    etime = offset + nsamp / srate
+    time_ax = np.linspace(offset, etime, nsamp)
     if len(time_ax) < nsamp:
         if verbosity:
             print('elongate time axes by one datum')
-        time_ax = np.arange(stime, etime + tincr, tincr)
+        time_ax = np.arange(offset, etime + tincr, tincr)
     elif len(time_ax) > nsamp:
         if verbosity:
             print('shorten time axes by one datum')
-        time_ax = np.arange(stime, etime - tincr, tincr)
+        time_ax = np.arange(offset, etime - tincr, tincr)
     if len(time_ax) != nsamp:
         print('Station {0}, {1} samples of data \n '
               '{2} length of time vector \n'
@@ -618,13 +711,13 @@ def find_horizontals(data):
     :param data: waveform data
     :type data: `obspy.core.stream.Stream`
     :return: components list
-    :rtype: list
+    :rtype: List(str)
 
     ..example::
 
     >>> st = read()
     >>> find_horizontals(st)
-    [u'N', u'E']
+    ['N', 'E']
     """
     rval = []
     for tr in data:
@@ -635,7 +728,7 @@ def find_horizontals(data):
     return rval
 
 
-def pick_color(picktype, phase, quality=0):
+def pick_color(picktype: Literal['manual', 'automatic'], phase: Literal['P', 'S'], quality: int = 0) -> Rgba:
     """
     Create pick color by modifying the base color by the quality.
 
@@ -648,7 +741,7 @@ def pick_color(picktype, phase, quality=0):
     :param quality: quality of pick. Decides the new intensity of the modifier color
     :type quality: int
     :return: tuple containing modified rgba color values
-    :rtype: (int, int, int, int)
+    :rtype: Rgba
     """
     min_quality = 3
     bpc = base_phase_colors(picktype, phase)  # returns dict like {'modifier': 'g', 'rgba': (0, 0, 255, 255)}
@@ -704,17 +797,17 @@ def pick_linestyle_plt(picktype, key):
     return linestyles[picktype][key]
 
 
-def modify_rgba(rgba, modifier, intensity):
+def modify_rgba(rgba: Rgba, modifier: Literal['r', 'g', 'b'], intensity: float) -> Rgba:
     """
     Modify rgba color by adding the given intensity to the modifier color
     :param rgba: tuple containing rgba values
-    :type rgba: (int, int, int, int)
-    :param modifier: which color should be modified, eg. 'r', 'g', 'b'
-    :type modifier: str
+    :type rgba: Rgba
+    :param modifier: which color should be modified; options: 'r', 'g', 'b'
+    :type modifier: Literal['r', 'g', 'b']
     :param intensity: intensity to be added to selected color
     :type intensity: float
     :return: tuple containing rgba values
-    :rtype: (int, int, int, int)
+    :rtype: Rgba
     """
     rgba = list(rgba)
     index = {'r': 0,
@@ -748,18 +841,20 @@ def transform_colors_mpl_str(colors, no_alpha=False):
     Transforms rgba color values to a matplotlib string of color values with a range of [0, 1]
     :param colors: tuple of rgba color values ranging from [0, 255]
     :type colors: (float, float, float, float)
-    :param no_alpha: Wether to return a alpha value in the matplotlib color string
+    :param no_alpha: Whether to return an alpha value in the matplotlib color string
     :type no_alpha: bool
     :return: String containing r, g, b values and alpha value if no_alpha is False (default)
     :rtype: str
+
+    >>> transform_colors_mpl_str((255., 255., 255., 255.), True)
+    '(1.0, 1.0, 1.0)'
+    >>> transform_colors_mpl_str((255., 255., 255., 255.))
+    '(1.0, 1.0, 1.0, 1.0)'
     """
-    colors = list(colors)
-    colors_mpl = tuple([color / 255. for color in colors])
     if no_alpha:
-        colors_mpl = '({}, {}, {})'.format(*colors_mpl)
+        return '({}, {}, {})'.format(*transform_colors_mpl(colors))
     else:
-        colors_mpl = '({}, {}, {}, {})'.format(*colors_mpl)
-    return colors_mpl
+        return '({}, {}, {}, {})'.format(*transform_colors_mpl(colors))
 
 
 def transform_colors_mpl(colors):
@@ -769,27 +864,16 @@ def transform_colors_mpl(colors):
     :type colors: (float, float, float, float)
     :return: tuple of rgba color values ranging from [0, 1]
     :rtype: (float, float, float, float)
+
+    >>> transform_colors_mpl((127.5, 0., 63.75, 255.))
+    (0.5, 0.0, 0.25, 1.0)
+    >>> transform_colors_mpl(())
     """
     colors = list(colors)
     colors_mpl = tuple([color / 255. for color in colors])
     return colors_mpl
 
 
-def remove_underscores(data):
-    """
-    takes a `obspy.core.stream.Stream` object and removes all underscores
-    from station names
-    :param data: stream of seismic data
-    :type data: `~obspy.core.stream.Stream`
-    :return: data stream
-    :rtype: `~obspy.core.stream.Stream`
-    """
-    # for tr in data:
-    #    # remove underscores
-    #    tr.stats.station = tr.stats.station.strip('_')
-    return data
-
-
 def trim_station_components(data, trim_start=True, trim_end=True):
     """
     cut a stream so only the part common to all three traces is kept to avoid dealing with offsets
@@ -818,19 +902,6 @@ def trim_station_components(data, trim_start=True, trim_end=True):
     return data
 
 
-def merge_stream(stream):
-    gaps = stream.get_gaps()
-    if gaps:
-        # list of merged stations (seed_ids)
-        merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
-        stream.merge(method=1)
-        print('Merged the following stations because of gaps:')
-        for merged_station in merged:
-            print(merged_station)
-
-    return stream, gaps
-
-
 def check4gapsAndRemove(data):
     """
     check for gaps in Stream and remove them
@@ -851,12 +922,12 @@ def check4gapsAndRemove(data):
     return data
 
 
-def check4gapsAndMerge(data):
+def check_for_gaps_and_merge(data):
     """
     check for gaps in Stream and merge if gaps are found
     :param data: stream of seismic data
     :type data: `~obspy.core.stream.Stream`
-    :return: data stream
+    :return: data stream, gaps returned from obspy get_gaps
     :rtype: `~obspy.core.stream.Stream`
     """
     gaps = data.get_gaps()
@@ -867,7 +938,7 @@ def check4gapsAndMerge(data):
         for merged_station in merged:
             print(merged_station)
 
-    return data
+    return data, gaps
 
 
 def check4doubled(data):
@@ -897,13 +968,53 @@ def check4doubled(data):
     return data
 
 
+def check_for_nan(data, nan_value=0.):
+    """
+    Replace all NaNs in data with nan_value (in place)
+    :param data: stream of seismic data
+    :type data: `~obspy.core.stream.Stream`
+    :param nan_value: value which all NaNs are set to
+    :type nan_value: float, int
+    :return: None
+    """
+    if not data:
+        return
+    for trace in data:
+        np.nan_to_num(trace.data, copy=False, nan=nan_value)
+
+
+def get_pylot_eventfile_with_extension(event, fext):
+    if hasattr(event, 'path'):
+        eventpath = event.path
+    else:
+        logging.warning('No attribute path found for event.')
+        return
+    eventname = event.pylot_id #path.split('/')[-1]  # or event.pylot_id
+    filename = os.path.join(eventpath, 'PyLoT_' + eventname + fext)
+    if os.path.isfile(filename):
+        return filename
+
+
+def get_possible_pylot_eventfile_extensions(event, fext):
+    if hasattr(event, 'path'):
+        eventpath = event.path
+    else:
+        logging.warning('No attribute path found for event.')
+        return []
+    eventname = event.pylot_id
+    filename = os.path.join(eventpath, 'PyLoT_' + eventname + fext)
+    filenames = glob.glob(filename)
+    extensions = [os.path.split(path)[-1].split('PyLoT_' + eventname)[-1] for path in filenames]
+    return extensions
+
+
 def get_stations(data):
     """
-    Get list of all station names in data stream
+    Get list of all station names in data-stream
     :param data: stream containing seismic traces
     :type data: `~obspy.core.stream.Stream`
     :return: list of all station names in data, no duplicates
-    :rtype: list of str
+    :rtype: List(str)
     """
     stations = []
     for tr in data:
@@ -930,66 +1041,87 @@ def check4rotated(data, metadata=None, verbosity=1):
     :rtype: `~obspy.core.stream.Stream`
     """
 
-    def rotate_components(wfstream, metadata=None):
+    def rotation_required(trace_ids):
+        """
+        Derive if any rotation is required from the orientation code of the input.
+
+        :param trace_ids: string identifier of waveform data trace
+        :type trace_ids: List(str)
+        :return: boolean representing if rotation is necessary for any of the traces
+        :rtype: bool
+        """
+        orientations = [trace_id[-1] for trace_id in trace_ids]
+        return any([orientation.isnumeric() for orientation in orientations])
+
+    def rotate_components(wfs_in, metadata=None):
         """
         Rotate components if orientation code is numeric (= non traditional orientation).
 
         Azimut and dip are fetched from metadata. To be rotated, traces of a station have to be cut to the same length.
         Returns unrotated traces of no metadata is provided
-        :param wfstream: stream containing seismic traces of a station
-        :type wfstream: `~obspy.core.stream.Stream`
+        :param wfs_in: stream containing seismic traces of a station
+        :type wfs_in: `~obspy.core.stream.Stream`
         :param metadata: tuple containing metadata type string and metadata parser object
         :type metadata: (str, `~obspy.io.xseed.parser.Parser`)
         :return: stream object with traditionally oriented traces (ZNE)
         :rtype: `~obspy.core.stream.Stream`
         """
 
-        # check if any traces in this station need to be rotated
-        trace_ids = [trace.id for trace in wfstream]
-        orientations = [trace_id[-1] for trace_id in trace_ids]
-        rotation_required = [orientation.isnumeric() for orientation in orientations]
-        if any(rotation_required):
-            t_start = full_range(wfstream)
-            try:
-                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(tr_id))
-                return wfstream
-            if len(wfstream) < 3:
-                print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
-                return wfstream
-            # to rotate all traces must have same length, so trim them
-            wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
-            try:
-                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_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)
-                wfstream[z_index].data = z
-                wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
-                del trace_ids[z_index]
-                for trace_id in trace_ids:
-                    coordinates = metadata.get_coordinates(trace_id, t_start)
-                    dip, az = coordinates['dip'], coordinates['azimuth']
-                    trace = wfstream.select(id=trace_id)[0]
-                    if az > 315 or az <= 45 or az > 135 and az <= 225:
-                        trace.data = n
-                        trace.stats.channel = trace.stats.channel[0:-1] + 'N'
-                    elif az > 45 and az <= 135 or az > 225 and az <= 315:
-                        trace.data = e
-                        trace.stats.channel = trace.stats.channel[0:-1] + 'E'
-            except (ValueError) as e:
-                print(e)
-                return wfstream
+        if len(wfs_in) < 3:
+            print(f"Stream {wfs_in=}, has not enough components to rotate.")
+            return wfs_in
 
-        return wfstream
+        # check if any traces in this station need to be rotated
+        trace_ids = [trace.id for trace in wfs_in]
+        if not rotation_required(trace_ids):
+            logging.debug(f"Stream does not need any rotation: Traces are {trace_ids=}")
+            return wfs_in
+
+        # check metadata quality
+        t_start = full_range(wfs_in)
+        try:
+            azimuths = []
+            dips = []
+            for tr_id in trace_ids:
+                azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
+                dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
+        except (KeyError, TypeError) as err:
+            logging.error(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
+                  f"available in metadata. Stream remains unchanged.")
+            return wfs_in
+        except Exception as err:
+            print(f"Unexpected {err=}, {type(err)=}")
+            raise
+
+        # to rotate all traces must have same length, so trim them
+        wfs_out = trim_station_components(wfs_in, trim_start=True, trim_end=True)
+        try:
+            z, n, e = rotate2zne(wfs_out[0], azimuths[0], dips[0],
+                                 wfs_out[1], azimuths[1], dips[1],
+                                 wfs_out[2], azimuths[2], dips[2])
+            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)
+            wfs_out[z_index].data = z
+            wfs_out[z_index].stats.channel = wfs_out[z_index].stats.channel[0:-1] + 'Z'
+            del trace_ids[z_index]
+            for trace_id in trace_ids:
+                coordinates = metadata.get_coordinates(trace_id, t_start)
+                dip, az = coordinates['dip'], coordinates['azimuth']
+                trace = wfs_out.select(id=trace_id)[0]
+                if az > 315 or az <= 45 or 135 < az <= 225:
+                    trace.data = n
+                    trace.stats.channel = trace.stats.channel[0:-1] + 'N'
+                elif 45 < az <= 135 or 225 < az <= 315:
+                    trace.data = e
+                    trace.stats.channel = trace.stats.channel[0:-1] + 'E'
+        except ValueError as err:
+            print(f"{err=} Rotation failed. Stream remains unchanged.")
+            return wfs_in
+
+        return wfs_out
 
     if metadata is None:
         if verbosity:
@@ -1003,38 +1135,6 @@ def check4rotated(data, metadata=None, verbosity=1):
     return data
 
 
-def scaleWFData(data, factor=None, components='all'):
-    """
-    produce scaled waveforms from given waveform data and a scaling factor,
-    waveform may be selected by their components name
-    :param data: waveform data to be scaled
-    :type data: `~obspy.core.stream.Stream` object
-    :param factor: scaling factor
-    :type factor: float
-    :param components: components labels for the traces in data to be scaled by
-     the scaling factor (optional, default: 'all')
-    :type components: tuple
-    :return:  scaled waveform data
-    :rtype: `~obspy.core.stream.Stream` object
-    """
-    if components != 'all':
-        for comp in components:
-            if factor is None:
-                max_val = np.max(np.abs(data.select(component=comp)[0].data))
-                data.select(component=comp)[0].data /= 2 * max_val
-            else:
-                data.select(component=comp)[0].data /= 2 * factor
-    else:
-        for tr in data:
-            if factor is None:
-                max_val = float(np.max(np.abs(tr.data)))
-                tr.data /= 2 * max_val
-            else:
-                tr.data /= 2 * factor
-
-    return data
-
-
 def runProgram(cmd, parameter=None):
     """
     run an external program specified by cmd with parameters input returning the
@@ -1106,6 +1206,7 @@ def identifyPhase(phase):
         return False
 
 
+@lru_cache
 def identifyPhaseID(phase):
     """
     Returns phase id (capital P or S)

pylot/core/util/widgets.py

@@ -7,6 +7,7 @@ Created on Wed Mar 19 11:27:35 2014
 import copy
 import datetime
 import getpass
+import glob
 import multiprocessing
 import os
 import subprocess
@@ -16,6 +17,7 @@ import traceback
 
 import matplotlib
 import numpy as np
+from pylot.core.io.phases import getQualitiesfromxml
 
 matplotlib.use('QT5Agg')
 
@@ -36,7 +38,7 @@ from PySide2.QtWidgets import QAction, QApplication, QCheckBox, QComboBox, \
     QGridLayout, QLabel, QLineEdit, QMessageBox, \
     QTabWidget, QToolBar, QVBoxLayout, QHBoxLayout, QWidget, \
     QPushButton, QFileDialog, QInputDialog
-from PySide2.QtCore import QSettings, Qt, QUrl, Signal
+from PySide2.QtCore import QSettings, Qt, QUrl, Signal, QTimer
 from PySide2.QtWebEngineWidgets import QWebEngineView as QWebView
 from obspy import Stream, Trace, UTCDateTime
 from obspy.core.util import AttribDict
@@ -49,12 +51,12 @@ from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
 from pylot.core.pick.compare import Comparison
 from pylot.core.pick.autopick import fmpicker
 from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS
-from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
+from pylot.core.util.utils import prep_time_axis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
     pick_linestyle_plt, pick_color_plt, \
-    check4rotated, check4doubled, merge_stream, identifyPhase, \
+    check4rotated, check4doubled, check_for_gaps_and_merge, check_for_nan, identifyPhase, \
     loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
-    identifyPhaseID, get_bool, get_None, pick_color, getAutoFilteroptions, SetChannelComponents, \
-    station_id_remove_channel
+    identifyPhaseID, get_bool, get_none, pick_color, getAutoFilteroptions, SetChannelComponents, \
+    station_id_remove_channel, get_pylot_eventfile_with_extension, get_possible_pylot_eventfile_extensions
 from autoPyLoT import autoPyLoT
 from pylot.core.util.thread import Thread
 from pylot.core.util.dataprocessing import Metadata
@@ -864,9 +866,24 @@ class WaveformWidgetPG(QtWidgets.QWidget):
 
     def plotWFData(self, wfdata, wfsyn=None, title=None, scaleddata=False, mapping=True,
                    component='*', nth_sample=1, verbosity=0, method='normal', gain=1., shift_syn=0.2):
+        def station_sort(nslc):
+            """Try to sort after station integer in case of a line array (e.g. active seismics)"""
+            try:
+                rval = sorted(nslc, key=lambda x: int(x.split('.')[1]))
+                return rval
+            except ValueError as e:
+                # this is the standard case for seismological stations
+                pass
+            except Exception as e:
+                print(f'Sorting by station integer failed with unknown exception: {e}')
+
+            # fallback to default sorting
+            return sorted(nslc)
+
         if not wfdata:
             print('Nothing to plot.')
             return
+
         self.title = title
         self.clearPlotDict()
         self.wfstart, self.wfend = full_range(wfdata)
@@ -884,14 +901,14 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         else:
             st_select = wfdata
 
-        st_select, gaps = merge_stream(st_select)
+        # st_select, gaps = check_for_gaps_and_merge(st_select) #MP MP commented because probably done twice
 
         # list containing tuples of network, station, channel (for sorting)
         nslc = []
         for trace in st_select:
             nslc.append(
                 trace.get_id())  # (trace.stats.network, trace.stats.station, trace.stats.location trace.stats.channel))
-        nslc.sort()
+        nslc = station_sort(nslc)
         nslc.reverse()
         plots = []
 
@@ -923,10 +940,10 @@ class WaveformWidgetPG(QtWidgets.QWidget):
                 msg = 'plotting %s channel of station %s' % (channel, station)
                 print(msg)
             stime = trace.stats.starttime - self.wfstart
-            time_ax = prepTimeAxis(stime, trace)
+            time_ax = prep_time_axis(stime, trace)
             if st_syn:
                 stime_syn = trace_syn.stats.starttime - self.wfstart
-                time_ax_syn = prepTimeAxis(stime_syn, trace_syn)
+                time_ax_syn = prep_time_axis(stime_syn, trace_syn)
 
             if method == 'fast':
                 trace.data, time_ax = self.minMax(trace, time_ax)
@@ -955,7 +972,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         self.ylabel = ''
         self.setXLims([0, self.wfend - self.wfstart])
         self.setYLims([0.5, nmax + 0.5])
-        return plots, gaps
+        return plots
 
     def minMax(self, trace, time_ax):
         '''
@@ -977,7 +994,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         min_ = data.min(axis=1)
         max_ = data.max(axis=1)
         if remaining_samples:
-            extreme_values = np.empty((npixel + 1, 2), dtype=np.float)
+            extreme_values = np.empty((npixel + 1, 2), dtype=float)
             extreme_values[:-1, 0] = min_
             extreme_values[:-1, 1] = max_
             extreme_values[-1, 0] = \
@@ -985,7 +1002,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
             extreme_values[-1, 1] = \
                 trace.data[-remaining_samples:].max()
         else:
-            extreme_values = np.empty((npixel, 2), dtype=np.float)
+            extreme_values = np.empty((npixel, 2), dtype=float)
             extreme_values[:, 0] = min_
             extreme_values[:, 1] = max_
         data = extreme_values.flatten()
@@ -1395,7 +1412,7 @@ class PylotCanvas(FigureCanvas):
             plot_streams['wfdata']['data'] = wfdata
             if wfdata_compare:
                 plot_streams['wfdata_comp']['data'] = wfdata_compare
-            
+
         st_main = plot_streams['wfdata']['data']
 
         if mapping:
@@ -1427,7 +1444,7 @@ class PylotCanvas(FigureCanvas):
                     msg = 'plotting %s channel of station %s' % (channel, station)
                     print(msg)
                 stime = trace.stats.starttime - wfstart
-                time_ax = prepTimeAxis(stime, trace)
+                time_ax = prep_time_axis(stime, trace)
                 if time_ax is not None:
                     if scaleToChannel:
                         st_scale = wfdata.select(channel=scaleToChannel)
@@ -1467,7 +1484,7 @@ class PylotCanvas(FigureCanvas):
                 if not scaleddata:
                     trace.detrend('constant')
                     trace.normalize(np.max(np.abs(trace.data)) * 2)
-                time_ax = prepTimeAxis(stime, trace)
+                time_ax = prep_time_axis(stime, trace)
                 times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
                 p_data = compare_stream[0].data
                 # #normalize
@@ -1575,6 +1592,178 @@ class PylotCanvas(FigureCanvas):
         self.draw()
 
 
+class SearchFileByExtensionDialog(QtWidgets.QDialog):
+    def __init__(self, parent=None, label='Text: ', default_text='.xml', events=None):
+        super(SearchFileByExtensionDialog, self).__init__(parent)
+        self.events = events
+        self.filepaths = []
+        self.file_extensions = []
+        self.check_all_state = True
+        self.merge_strategy = None
+        self.default_text = default_text
+        self.label = label
+        self.setButtons()
+        self.setupUi()
+        self.connectSignals()
+        self.showPaths()
+        self.refreshSelectionBox()
+        # self.refresh_timer = QTimer(self)
+        # self.refresh_timer.timeout.connect(self.showPaths)
+        # self.refresh_timer.start(10000)
+
+        self.resize(800, 450)
+
+    def setupUi(self):
+        ncol = 4
+        self.main_layout = QtWidgets.QVBoxLayout()
+        self.header_layout = QtWidgets.QHBoxLayout()
+        self.footer_layout = QtWidgets.QHBoxLayout()
+        #
+        self.setLayout(self.main_layout)
+
+        # widgets inside the dialog
+        self.textLabel = QtWidgets.QLabel(self.label)
+        self.comboBox = QtWidgets.QComboBox()
+        self.comboBox.addItem(self.default_text)
+        self.comboBox.setEditable(True)
+
+        # optional search button, currently disabled. List refreshed when text changes
+        self.searchButton = QtWidgets.QPushButton('Search')
+        self.searchButton.setVisible(False)
+
+        # check/uncheck button for table
+        self.checkAllButton = QtWidgets.QPushButton('Check/Uncheck all')
+
+        # radiobutton for merge selection
+        self.mergeRadioButtonGroup = QtWidgets.QButtonGroup()
+        self.merge_button = QtWidgets.QRadioButton('Merge')
+        self.overwrite_button = QtWidgets.QRadioButton('Overwrite')
+        self.mergeRadioButtonGroup.addButton(self.merge_button)
+        self.mergeRadioButtonGroup.addButton(self.overwrite_button)
+        self.merge_button.setChecked(True)
+        self.merge_strategy = self.merge_button.text()
+
+        # table
+        self.tableWidget = QtWidgets.QTableWidget()
+        tableWidget = self.tableWidget
+        tableWidget.setColumnCount(ncol)
+        tableWidget.setRowCount(len(self.events))
+        tableWidget.setHorizontalHeaderLabels(('', 'Event ID', 'Filename', 'Last modified'))
+        tableWidget.setEditTriggers(tableWidget.NoEditTriggers)
+        tableWidget.setSortingEnabled(True)
+        header = tableWidget.horizontalHeader()
+        header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
+        header.setStretchLastSection(True)
+
+        self.statusText = QtWidgets.QLabel()
+
+        self.header_layout.addWidget(self.textLabel)
+        self.header_layout.addWidget(self.comboBox)
+        self.header_layout.addWidget(self.searchButton)
+
+        self.footer_layout.addWidget(self.checkAllButton)
+        self.footer_layout.addWidget(self.statusText)
+        self.footer_layout.addWidget(self.merge_button)
+        self.footer_layout.addWidget(self.overwrite_button)
+
+        self.footer_layout.setStretch(0, 0)
+        self.footer_layout.setStretch(1, 1)
+
+        self.main_layout.addLayout(self.header_layout)
+        self.main_layout.addWidget(self.tableWidget)
+        self.main_layout.addLayout(self.footer_layout)
+        self.main_layout.addWidget(self._buttonbox)
+
+    def showPaths(self):
+        self.filepaths = []
+        fext = self.comboBox.currentText()
+        self.tableWidget.clearContents()
+        for index, event in enumerate(self.events):
+            filename = get_pylot_eventfile_with_extension(event, fext)
+            pf_selected_item = QtWidgets.QTableWidgetItem()
+            check_state = QtCore.Qt.Checked if filename else QtCore.Qt.Unchecked
+            pf_selected_item.setCheckState(check_state)
+            self.tableWidget.setItem(index, 0, pf_selected_item)
+            self.tableWidget.setItem(index, 1, QtWidgets.QTableWidgetItem(f'{event.pylot_id}'))
+            if filename:
+                self.filepaths.append(filename)
+                ts = int(os.path.getmtime(filename))
+
+                # create QTableWidgetItems of filepath and last modification time
+                fname_item = QtWidgets.QTableWidgetItem(f'{os.path.split(filename)[-1]}')
+                fname_item.setData(3, filename)
+                ts_item = QtWidgets.QTableWidgetItem(f'{datetime.datetime.fromtimestamp(ts)}')
+                self.tableWidget.setItem(index, 2, fname_item)
+                self.tableWidget.setItem(index, 3, ts_item)
+
+        self.update_status()
+
+    def refreshSelectionBox(self):
+        fext = self.comboBox.currentText()
+        self.file_extensions = [fext]
+
+        for event in self.events:
+            extensions = get_possible_pylot_eventfile_extensions(event, '*.xml')
+            for ext in extensions:
+                if not ext in self.file_extensions:
+                    self.file_extensions.append(ext)
+
+        self.comboBox.clear()
+        for ext in sorted(self.file_extensions):
+            self.comboBox.addItem(ext)
+
+    def setButtons(self):
+        self._buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
+                                           QDialogButtonBox.Cancel)
+
+    def toggleCheckAll(self):
+        self.check_all_state = not self.check_all_state
+        self.checkAll(self.check_all_state)
+
+    def checkAll(self, state):
+        state = QtCore.Qt.Checked if state else QtCore.Qt.Unchecked
+        for row_ind in range(self.tableWidget.rowCount()):
+            item = self.tableWidget.item(row_ind, 0)
+            item.setCheckState(state)
+
+    def getChecked(self):
+        filepaths = []
+        for row_ind in range(self.tableWidget.rowCount()):
+            item_check = self.tableWidget.item(row_ind, 0)
+            if item_check.checkState() == QtCore.Qt.Checked:
+                item_fname = self.tableWidget.item(row_ind, 2)
+                if item_fname:
+                    filepath = item_fname.data(3)
+                    filepaths.append(filepath)
+        return filepaths
+
+    def update_status(self, row=None, col=None):
+        if col is not None and col != 0:
+            return
+        filepaths = self.getChecked()
+        if len(filepaths) > 0:
+            status_text = f"Found {len(filepaths)} eventfile{'s' if len(filepaths) > 1 else ''}. Do you want to load them?"
+        else:
+            status_text = 'Did not find/select any files for specified file mask.'
+        self.statusText.setText(status_text)
+
+    def update_merge_strategy(self):
+        for button in (self.merge_button, self.overwrite_button):
+            if button.isChecked():
+                self.merge_strategy = button.text()
+
+    def connectSignals(self):
+        self._buttonbox.accepted.connect(self.accept)
+        self._buttonbox.rejected.connect(self.reject)
+        self.comboBox.editTextChanged.connect(self.showPaths)
+        self.searchButton.clicked.connect(self.showPaths)
+        self.checkAllButton.clicked.connect(self.toggleCheckAll)
+        self.checkAllButton.clicked.connect(self.update_status)
+        self.tableWidget.cellClicked.connect(self.update_status)
+        self.merge_button.clicked.connect(self.update_merge_strategy)
+        self.overwrite_button.clicked.connect(self.update_merge_strategy)
+
+
 class SingleTextLineDialog(QtWidgets.QDialog):
     def __init__(self, parent=None, label='Text: ', default_text='.xml'):
         super(SingleTextLineDialog, self).__init__(parent)
@@ -2064,10 +2253,12 @@ class PickDlg(QDialog):
         station_id = trace.get_id()
         starttime = trace.stats.starttime
         station_coords = self.metadata.get_coordinates(station_id, starttime)
+        if not station_coords:
+            print('get_arrivals: No station coordinates found. Return!')
+            return
         origins = self.pylot_event.origins
         if phases == ['None', 'None']:
-            print("get_arrivals: Creation info (manual or auto) not available!")
-            print("Return!")
+            print("get_arrivals: Creation info (manual or auto) not available! Return!")
             return
         if origins:
             source_origin = origins[0]
@@ -2179,7 +2370,7 @@ class PickDlg(QDialog):
 
                 # create action and add to menu
                 # phase name transferred using lambda function
-                slot = lambda phase=phase, phaseID=phaseID: phaseSelect[phaseID](phase)
+                slot = lambda ph=phase, phID=phaseID: phaseSelect[phID](ph)
                 picksAction = createAction(parent=self, text=phase,
                                            slot=slot,
                                            shortcut=shortcut)
@@ -2598,7 +2789,7 @@ class PickDlg(QDialog):
         for wfd in [wfdata, wfdata_comp]:
             if wfd:
                 for trace in wfd:
-                    t = prepTimeAxis(trace.stats.starttime - stime, trace)
+                    t = prep_time_axis(trace.stats.starttime - stime, trace)
                     inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
                     trace = demeanTrace(trace, inoise)
                     # upscale trace wfdata in a way that each trace is vertically zoomed to noiselevel*factor
@@ -3624,8 +3815,9 @@ class TuneAutopicker(QWidget):
             # wfdat = remove_underscores(wfdat)
             # rotate misaligned stations to ZNE
             # check for gaps and doubled channels
-            wfdat, gaps = merge_stream(wfdat)
-            # check4gaps(wfdat)
+            wfdat, _ = check_for_gaps_and_merge(wfdat)
+            # check for nans
+            check_for_nan(wfdat)
             check4doubled(wfdat)
             wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
             # trim station components to same start value
@@ -3782,6 +3974,7 @@ class TuneAutopicker(QWidget):
         st = self.data.getWFData()
         tr = st.select(station=self.get_current_station())[0]
         starttime = tr.stats.starttime
+        # create two lists with figure names and subindices (for subplots) to get the correct axes
         p_axes = [
             ('mainFig', 0),
             ('aicFig', 0),
@@ -4729,8 +4922,8 @@ class InputsTab(PropTab):
         self.tstopBox = QSpinBox()
         for spinbox in [self.tstartBox, self.tstopBox]:
             spinbox.setRange(-99999, 99999)
-        self.tstartBox.setValue(float(settings.value('tstart')) if get_None(settings.value('tstart')) else 0)
-        self.tstopBox.setValue(float(settings.value('tstop')) if get_None(settings.value('tstop')) else 1e6)
+        self.tstartBox.setValue(float(settings.value('tstart')) if get_none(settings.value('tstart')) else 0)
+        self.tstopBox.setValue(float(settings.value('tstop')) if get_none(settings.value('tstop')) else 1e6)
         self.cuttimesLayout.addWidget(self.tstartBox, 10)
         self.cuttimesLayout.addWidget(QLabel('[s] and'), 0)
         self.cuttimesLayout.addWidget(self.tstopBox, 10)
@@ -5726,7 +5919,7 @@ class ChooseWaveFormWindow(QWidget):
         #self.currentSpectro = self.traces[
         #    self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
         #self.currentSpectro.show()
-        applyFFT()
+        self.applyFFT()
 
     def applyFFT(self, trace):
         tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']