Merge branch 'feature/dae' into develop

# Conflicts: # pylot/core/io/data.py # pylot/core/util/widgets.py
[minor] inform if station coordinates were not found in metadata
2024-06-12 16:19:21 +02:00 · 2024-06-12 16:11:53 +02:00 · 2024-06-12 13:44:02 +02:00 · 2024-06-07 15:56:05 +02:00 · 2024-06-07 15:04:16 +02:00 · 2024-06-07 14:34:27 +02:00
21 changed files with 1159 additions and 613 deletions
--- a/PyLoT.py
+++ b/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, 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
@@ -113,21 +114,19 @@ 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) == False:
-            infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')
+        if infile and os.path.isfile(infile) is False:
+            infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')[0]

-            if not os.path.exists(infile[0]):
+            if not os.path.exists(infile):
                QMessageBox.warning(self, "PyLoT Warning",
-                                    "No PyLoT-input file declared!")
-                sys.exit(0)
-            self.infile = infile[0]
-        else:
-            self.infile = infile
+                                    "No PyLoT-input file declared! Using default parameters!")
+                infile = None
+
        self._inputs = PylotParameter(infile)
+        if not infile:
+            self._inputs.reset_defaults()
+
+        self.infile = infile
        self._props = None

        self.gain = 1.
@@ -179,6 +178,7 @@ class MainWindow(QMainWindow):
        self.autodata = Data(self)

        self.fnames = None
+        self.fnames_comp = None
        self._stime = None

        # track deleted picks for logging
@@ -194,7 +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:",
@@ -251,7 +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

@@ -481,7 +481,7 @@ class MainWindow(QMainWindow):
                                                              "automatic pick "
                                                              "data.", False)
        self.compare_action.setEnabled(False)
-        self.qualities_action = self.createAction(parent=self, text='Show pick qualitites...',
+        self.qualities_action = self.createAction(parent=self, text='Show pick qualities...',
                                                  slot=self.pickQualities, shortcut='Alt+Q',
                                                  icon=qualities_icon, tip='Histogram of pick qualities')
        self.qualities_action.setEnabled(False)
@@ -494,7 +494,6 @@ class MainWindow(QMainWindow):
                                                      icon=eventlist_xml_icon,
                                                      tip='Create an Eventlist from a XML File')
        self.eventlist_xml_action.setEnabled(False)
-
        printAction = self.createAction(self, "&Print event ...",
                                        self.show_event_information, QKeySequence.Print,
                                        print_icon,
@@ -507,6 +506,8 @@ class MainWindow(QMainWindow):
        logAction = self.createAction(self, "&Show Log", self.showLogWidget,
                                      tip="""Display Log""")

+        logAction.setEnabled(use_logwidget)
+
        # create button group for component selection

        componentGroup = QActionGroup(self)
@@ -696,14 +697,17 @@ class MainWindow(QMainWindow):
        wf_tab = QtWidgets.QWidget(self)
        array_tab = QtWidgets.QWidget(self)
        events_tab = QtWidgets.QWidget(self)
+        spectro_tab = QtWidgets.QWidget(self)

        # init main widgets layouts
        self.wf_layout = QtWidgets.QVBoxLayout()
        self.array_layout = QtWidgets.QVBoxLayout()
        self.events_layout = QtWidgets.QVBoxLayout()
+        self.spectro_layout = QtWidgets.QVBoxLayout()
        wf_tab.setLayout(self.wf_layout)
        array_tab.setLayout(self.array_layout)
        events_tab.setLayout(self.events_layout)
+        spectro_tab.setLayout(self.spectro_layout)

        # tighten up layouts inside tabs
        for layout in [self.wf_layout, self.array_layout, self.events_layout]:
@@ -714,12 +718,14 @@ class MainWindow(QMainWindow):
        self.tabs.addTab(wf_tab, 'Waveform Plot')
        self.tabs.addTab(array_tab, 'Array Map')
        self.tabs.addTab(events_tab, 'Eventlist')
+        self.tabs.addTab(spectro_tab, 'Spectro')

        self.wf_layout.addWidget(self.no_data_label)
        self.wf_layout.addWidget(self.wf_scroll_area)
        self.wf_scroll_area.setWidgetResizable(True)
        self.init_array_tab()
        self.init_event_table()
+        self.init_spectro_tab()
        self.tabs.setCurrentIndex(0)

        self.eventLabel = QLabel()
@@ -732,19 +738,13 @@ class MainWindow(QMainWindow):
        _widget.setLayout(self._main_layout)
        _widget.showFullScreen()

+
        if use_logwidget:
            self.logwidget = LogWidget(parent=None)
            self.logwidget.show()
            self.stdout = self.logwidget.stdout
            self.stderr = self.logwidget.stderr

-            sys.stdout = self.stdout
-            sys.stderr = self.stderr
-
-            # Not sure why but the lines above kept messing with the Ouput even with use_logwidget disabled
-            sys.stdout = self.stdout
-            sys.stderr = self.stderr
-
        self.setCentralWidget(_widget)

        # Need to store PickQualities Window somewhere so it doesnt disappear
@@ -1004,18 +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:
@@ -1023,8 +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:
@@ -1038,9 +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(
@@ -1128,16 +1130,19 @@ class MainWindow(QMainWindow):
            else:
                return

-    def getWFFnames_from_eventbox(self, eventbox=None):
+    def getWFFnames_from_eventbox(self, eventbox: str = None, subpath: str = None) -> list:
        '''
        Return waveform filenames from event in eventbox.
        '''
        # TODO: add dataStructure class for obspyDMT here, this is just a workaround!
        eventpath = self.get_current_event_path(eventbox)
-        basepath = eventpath.split(os.path.basename(eventpath))[0]
+        if subpath:
+            eventpath = os.path.join(eventpath, subpath)
+        if not os.path.isdir(eventpath):
+            return []
        if self.dataStructure:
            if not eventpath:
-                return
+                return []
            fnames = [os.path.join(eventpath, f) for f in os.listdir(eventpath)]
        else:
            raise DatastructureError('not specified')
@@ -1181,7 +1186,7 @@ class MainWindow(QMainWindow):
        '''
        if not self.project:
            self.createNewProject()
-        ed = getExistingDirectories(self, 'Select event directories...')
+        ed = GetExistingDirectories(self, 'Select event directories...')
        if ed.exec_():
            eventlist = [event for event in ed.selectedFiles() if not event.endswith('EVENTS-INFO')]
            basepath = eventlist[0].split(os.path.basename(eventlist[0]))[0]
@@ -1382,7 +1387,7 @@ class MainWindow(QMainWindow):
        index = eventBox.currentIndex()
        tv = QtWidgets.QTableView()
        header = tv.horizontalHeader()
-        header.setResizeMode(QtWidgets.QHeaderView.ResizeToContents)
+        header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
        header.setStretchLastSection(True)
        header.hide()
        tv.verticalHeader().hide()
@@ -1402,25 +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()
@@ -1455,16 +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:
@@ -1679,20 +1694,20 @@ class MainWindow(QMainWindow):

    def pickQualities(self):
        path = self.get_current_event_path()
-        (_, _, plot) = getQualitiesfromxml(path, self._inputs.get('timeerrorsP'), self._inputs.get('timeerrorsS'),plotflag=1)
+        (_, plot) = getQualitiesfromxml(path, self._inputs.get('timeerrorsP'), self._inputs.get('timeerrorsS'),plotflag=1)
        self.pickQualitiesWindow = PickQualitiesFromXml(figure=plot, path=self.get_current_event_path(),inputVar=self._inputs)
        self.pickQualitiesWindow.showUI()
        return 

    # WIP JG
-    def eventlistXml2(self):
+    def eventlistXml(self):
        path = self._inputs['rootpath'] + '/' + self._inputs['datapath'] + '/' + self._inputs['database']
        outpath = self.project.location[:self.project.location.rfind('/')]
        geteventlistfromxml(path, outpath)
        return

-    # WIP JG
-    def eventlistXml(self):
+        # WIP JG
+    def spectogramView(self):
        global test
        stations = []
        names = []
@@ -1707,12 +1722,25 @@ class MainWindow(QMainWindow):
            for tr in self.get_data().wfdata.select(component=ch).traces:
                traces[tr.stats.station][ch] = tr

-
        names.sort()
        a = self.get_current_event()
-        test = ChooseWaveFormWindow(WaveForms=names, traces=traces, stream=self.get_data())
-        #self.get_data().wfdata.spectrogram()
-        test.show()
+
+        print (self.get_data().wfdata.traces[0])
+
+        test = SpectrogramTab(traces, self.get_data().wfdata)
+        height = self.tabs.widget(0).height()
+        width = self.tabs.widget(0).width()
+        self.tabs.setCurrentIndex(3)
+        figCanvas = test.makeSpecFig(direction=self.dispComponent, height = height, width = width, parent = self.tabs.widget)
+        return figCanvas
+        #self.spectro_layout.addWidget()
+        # self.get_data().wfdata.spectrogram()
+        # self.tabs.addTab(figCanvas, 'Spectrogram')
+        # self.tabs[3] = figCanvas
+        # self.refreshTabs()
+        # test.show()
+
+

    def compareMulti(self):
        if not self.compareoptions:
@@ -1872,6 +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()
@@ -1899,6 +1928,12 @@ class MainWindow(QMainWindow):
                    self.newWF(plot=False)
                self.update_obspy_dmt()
                self.refresh_array_map()
+        if self.tabs.currentIndex() == 3:
+            if self.spectroWidget != None:
+                self.spectro_layout.removeWidget(self.spectroWidget)
+            newSpectroWidget = self.spectogramView()
+            self.spectro_layout.addWidget(newSpectroWidget)
+            self.spectroWidget = newSpectroWidget

    def newWF(self, event=None, plot=True):
        '''
@@ -1929,13 +1964,20 @@ class MainWindow(QMainWindow):

    def prepareLoadWaveformData(self):
        self.fnames = self.getWFFnames_from_eventbox()
-        self.fnames_syn = []
+        self.fnames_comp = []
+        fnames_comp = self.getWFFnames_from_eventbox(subpath='compare')
+        self.dataPlot.activateCompareOptions(bool(fnames_comp))
+        if fnames_comp:
+            if self.dataPlot.comp_checkbox.isChecked():
+                self.fnames_comp = fnames_comp
+
        eventpath = self.get_current_event_path()
        basepath = eventpath.split(os.path.basename(eventpath))[0]
        self.obspy_dmt = check_obspydmt_structure(basepath)
        self.dataPlot.activateObspyDMToptions(self.obspy_dmt)
        if self.obspy_dmt:
            self.prepareObspyDMT_data(eventpath)
+            self.dataPlot.activateCompareOptions(True)

    def loadWaveformData(self):
        '''
@@ -1950,6 +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?')
@@ -1957,8 +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:
@@ -1966,7 +2010,7 @@ class MainWindow(QMainWindow):
            tstop = None

        self.data.setWFData(self.fnames,
-                            self.fnames_syn,
+                            self.fnames_comp,
                            checkRotated=True,
                            metadata=self.metadata,
                            tstart=tstart,
@@ -1974,7 +2018,7 @@ class MainWindow(QMainWindow):

    def prepareObspyDMT_data(self, eventpath):
        qcbox_processed = self.dataPlot.qcombo_processed
-        qcheckb_syn = self.dataPlot.syn_checkbox
+        qcheckb_syn = self.dataPlot.comp_checkbox
        qcbox_processed.setEnabled(False)
        qcheckb_syn.setEnabled(False)
        for fpath in os.listdir(eventpath):
@@ -1982,8 +2026,8 @@ class MainWindow(QMainWindow):
            if 'syngine' in fpath:
                eventpath_syn = os.path.join(eventpath, fpath)
                qcheckb_syn.setEnabled(True)
-                if self.dataPlot.syn_checkbox.isChecked():
-                    self.fnames_syn = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
+                if self.dataPlot.comp_checkbox.isChecked():
+                    self.fnames_comp = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
            if 'processed' in fpath:
                qcbox_processed.setEnabled(True)
        if qcbox_processed.isEnabled():
@@ -2105,7 +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)
@@ -2156,6 +2200,7 @@ class MainWindow(QMainWindow):
            self.locateEventAction.setEnabled(True)
            self.qualities_action.setEnabled(True)
            self.eventlist_xml_action.setEnabled(True)
+
        if True in self.comparable.values():
            self.compare_action.setEnabled(True)
        self.draw()
@@ -2263,7 +2308,7 @@ class MainWindow(QMainWindow):
        comp = self.getComponent()
        title = 'section: {0} components'.format(zne_text[comp])
        wfst = self.get_data().getWFData()
-        wfsyn = self.get_data().getSynWFData()
+        wfsyn = self.get_data().getAltWFdata()
        if self.filterActionP.isChecked() and filter:
            self.filterWaveformData(plot=False, phase='P')
        elif self.filterActionS.isChecked() and filter:
@@ -2272,14 +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')) == True:
+        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:
@@ -2575,18 +2620,21 @@ class MainWindow(QMainWindow):
            print("Warning! No network, station, and location info available!")
            return
        self.update_status('picking on station {0}'.format(station))
-        data = self.get_data().getOriginalWFData().copy()
+        wfdata = self.get_data().getOriginalWFData().copy()
+        wfdata_comp = self.get_data().getAltWFdata().copy()
        event = self.get_current_event()
        wftype = self.dataPlot.qcombo_processed.currentText() if self.obspy_dmt else None
        pickDlg = PickDlg(self, parameter=self._inputs,
-                          data=data.select(station=station),
+                          data=wfdata.select(station=station),
+                          data_compare=wfdata_comp.select(station=station),
                          station=station, network=network,
                          location=location,
                          picks=self.getPicksOnStation(station, 'manual'),
                          autopicks=self.getPicksOnStation(station, 'auto'),
                          metadata=self.metadata, event=event,
                          model=self.inputs.get('taup_model'),
-                          filteroptions=self.filteroptions, wftype=wftype)
+                          filteroptions=self.filteroptions, wftype=wftype,
+                          show_comp_data=self.dataPlot.comp_checkbox.isChecked())
        if self.filterActionP.isChecked():
            pickDlg.currentPhase = "P"
            pickDlg.filterWFData()
@@ -2898,7 +2946,9 @@ class MainWindow(QMainWindow):
        self.log_deleted_picks([deleted_pick])

    def log_deleted_picks(self, deleted_picks, event_path=None):
-        ''' Log deleted picks to list self.deleted_picks '''
+        '''
+        Log deleted picks to list self.deleted_picks
+        '''
        if not event_path:
            event_path = self.get_current_event_path()
        for deleted_pick in deleted_picks:
@@ -2912,7 +2962,9 @@ class MainWindow(QMainWindow):
            self.deleted_picks[event_path].append(deleted_pick)

    def dump_deleted_picks(self, event_path):
-        ''' Save deleted picks to json file for event in event_path. Load old file before and merge'''
+        '''
+        Save deleted picks to json file for event in event_path. Load old file before and merge
+        '''
        try:
            deleted_picks_from_file = self.load_deleted_picks(event_path)
        except Exception as e:
@@ -2961,10 +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:
@@ -3125,7 +3183,7 @@ class MainWindow(QMainWindow):
        phasefile = os.path.join(obsdir, filename + '.obs')
        lt.modify_inputs(ctrfile, locroot, filename, phasefile, ttt)
        try:
-            lt.locate(ctrfile, self.obspy_dmt)
+            lt.locate(ctrfile, self._inputs)
        except RuntimeError as e:
            print(e.message)
        # finally:
@@ -3179,7 +3237,7 @@ class MainWindow(QMainWindow):
        '''
        if checked: pass  # dummy argument for QAction trigger signal
        self.tabs.setCurrentIndex(1)
-        # if there is no metadata (invetories is an empty list), just initialize the default empty tab
+        # if there is no metadata (inventories is an empty list), just initialize the default empty tab
        if not self.metadata.inventories:
            self.init_array_tab()
            return
@@ -3201,6 +3259,15 @@ class MainWindow(QMainWindow):
        self.tabs.setCurrentIndex(index)
        self.refresh_array_map()

+    def init_spectro_tab(self):
+        '''
+        Init spectrogram tab with currently selected event.
+        '''
+        self.spectroWidget = None
+        #self.spectro_layout.addWidget( self.spectogramView() )
+        pass
+
+
    def array_map_thread(self):
        '''
        Start modal thread to init the array_map object.
@@ -3423,7 +3490,7 @@ class MainWindow(QMainWindow):
                    self.event_table.setCellWidget(r_index, c_index, item)

        header = self.event_table.horizontalHeader()
-        header.setResizeMode(QtWidgets.QHeaderView.ResizeToContents)
+        header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
        header.setStretchLastSection(True)
        self.event_table.cellChanged[int, int].connect(cell_changed)
        self.event_table.cellClicked[int, int].connect(cell_clicked)
@@ -3597,7 +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:
@@ -3650,10 +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))
@@ -3709,7 +3779,7 @@ class MainWindow(QMainWindow):
            filename = fnm[0] + '.plp'
        self.project.parameter = self._inputs
        settings = QSettings()
-        autosaveXML = get_Bool(settings.value('autosaveXML', True))
+        autosaveXML = get_bool(settings.value('autosaveXML', True))
        if autosaveXML:
            self.exportEvents()
        if not self.project.save(filename): return False
@@ -3733,7 +3803,7 @@ class MainWindow(QMainWindow):
                self.metadata.clear_inventory()
                self.project.parameter = self._inputs
                settings = QSettings()
-                autosaveXML = get_Bool(settings.value('autosaveXML', True))
+                autosaveXML = get_bool(settings.value('autosaveXML', True))
                if autosaveXML:
                    self.exportEvents()
                if not self.project.save(): return False
@@ -3771,7 +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()
@@ -3822,7 +3893,7 @@ class MainWindow(QMainWindow):
    def helpHelp(self):
        if checkurl():
            form = HelpForm(self,
-                            'https://ariadne.geophysik.ruhr-uni-bochum.de/trac/PyLoT/wiki')
+                            'https://github.com/seismology-RUB/PyLoT')
        else:
            form = HelpForm(self, ':/help.html')
        form.show()
@@ -4002,13 +4073,13 @@ class Project(object):
        return project


-class getExistingDirectories(QFileDialog):
+class GetExistingDirectories(QFileDialog):
    '''
    File dialog with possibility to select multiple folders.
    '''

    def __init__(self, *args):
-        super(getExistingDirectories, self).__init__(*args)
+        super(GetExistingDirectories, self).__init__(*args)
        self.setOption(self.DontUseNativeDialog, True)
        self.setOption(self.ReadOnly, True)
        self.setFileMode(self.Directory)
@@ -4034,16 +4105,7 @@ def create_window():
    return app, app_created


-def main(args=None):
-    project_filename = None
-    # args.project_filename = 'C:/Shared/AlpArray/alparray_data/project_alparray_test.plp'
-    pylot_infile = None
-    if args:
-        if args.project_filename:
-            project_filename = args.project_filename
-        if args.input_filename:
-            pylot_infile = args.input_filename
-        reset_qsettings = args.reset_qsettings
+def main(project_filename=None, pylot_infile=None, reset_qsettings=False):

    # create the Qt application
    pylot_app, app_created = create_window()
@@ -4092,4 +4154,5 @@ if __name__ == "__main__":
    parser.add_argument('--reset_qsettings', default=False, action='store_true',
                        help='reset qsettings (debug option)')
    args = parser.parse_args()
-    sys.exit(main(args))
+    sys.exit(main(project_filename=args.project_filename, pylot_infile=args.input_filename,
+                  reset_qsettings=args.reset_qsettings))
--- a/README.md
+++ b/README.md
@@ -99,7 +99,7 @@ We hope to solve these with the next release.

 ## Staff

-Original author(s): L. Kueperkoch, S. Wehling-Benatelli, M. Bischoff (PILOT)
+Original author(s): M. Rische, S. Wehling-Benatelli, L. Kueperkoch, M. Bischoff (PILOT)

 Developer(s): S. Wehling-Benatelli, M. Paffrath, L. Kueperkoch, K. Olbert, M. Bischoff, C. Wollin, M. Rische, D. Arnold, K. Cökerim, S. Zimmermann

--- a/autoPyLoT.py
+++ b/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')
--- a/autopylot.sh
+++ b/autopylot.sh
@@ -3,8 +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

-python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in -dmt processed -c $NSLOTS
+conda activate pylot_311
+
+python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_adriaarray.in -c 20 -dmt processed
--- a/pylot.yml
+++ b/pylot.yml
@@ -8,7 +8,7 @@ dependencies:
  - numpy=1.22.3
  - obspy=1.3.0
  - pyqtgraph=0.12.4
-  - pyside2=5.13.2
+  - pyside2>=5.13.2
  - python=3.8.12
-  - qt=5.12.9
+  - qt>=5.12.9
  - scipy=1.8.0
--- a/pylot/core/analysis/magnitude.py
+++ b/pylot/core/analysis/magnitude.py
@@ -418,6 +418,10 @@ class MomentMagnitude(Magnitude):
            distance = degrees2kilometers(a.distance)
            azimuth = a.azimuth
            incidence = a.takeoff_angle
+            if not 0. <= incidence <= 360.:
+                if self.verbose:
+                    print(f'WARNING: Incidence angle outside bounds - {incidence}')
+                return
            w0, fc = calcsourcespec(scopy, onset, self.p_velocity, distance,
                                    azimuth, incidence, self.p_attenuation,
                                    self.plot_flag, self.verbose)
--- a/pylot/core/io/data.py
+++ b/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:
@@ -260,7 +261,6 @@ class Data(object):
        can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
        """
        from pylot.core.util.defaults import OUTPUTFORMATS
-
        if not type(fcheck) == list:
            fcheck = [fcheck]

@@ -321,35 +321,61 @@ class Data(object):
            if lendiff != 0:
                print("Manual as well as automatic picks available. Prefered the {} manual ones!".format(lendiff))

+
+            no_uncertainties_p = []
+            no_uncertainties_s = []
            if upperErrors:
                # check for pick uncertainties exceeding adjusted upper errors
                # Picks with larger uncertainties will not be saved in output file!
                for j in range(len(picks)):
                    for i in range(len(picks_copy)):
                        if picks_copy[i].phase_hint[0] == 'P':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]) or \
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
+                            # Skipping pick if no upper_uncertainty is found and warning user
+                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
+                                #print("{1} P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
+                                 #   picks_copy[i].waveform_id.station_code,
+                                  #  picks_copy[i].method_id))
+                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_p:
+                                    no_uncertainties_p.append(picks_copy[i].waveform_id.station_code)
+                                continue
+
+                            #print ("checking for upper_uncertainty")
+                            if  (picks_copy[i].time_errors['uncertainty'] is None) or \
+                                    (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]):
                                print("Uncertainty exceeds or equal adjusted upper time error!")
                                print("Adjusted uncertainty: {}".format(upperErrors[0]))
                                print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
                                print("{1} P-Pick of station {0} will not be saved in outputfile".format(
                                    picks_copy[i].waveform_id.station_code,
                                    picks_copy[i].method_id))
-                                print("#")
                                del picks_copy[i]
                                break
                        if picks_copy[i].phase_hint[0] == 'S':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]) or \
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
+
+                            # Skipping pick if no upper_uncertainty is found and warning user
+                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
+                                #print("{1} S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
+                                    #picks_copy[i].waveform_id.station_code,
+                                    #picks_copy[i].method_id))
+                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_s:
+                                    no_uncertainties_s.append(picks_copy[i].waveform_id.station_code)
+                                continue
+
+
+                            if (picks_copy[i].time_errors['uncertainty'] is None) or \
+                                (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]):
                                print("Uncertainty exceeds or equal adjusted upper time error!")
                                print("Adjusted uncertainty: {}".format(upperErrors[1]))
                                print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
                                print("{1} S-Pick of station {0} will not be saved in outputfile".format(
                                    picks_copy[i].waveform_id.station_code,
                                    picks_copy[i].method_id))
-                                print("#")
                                del picks_copy[i]
                                break
+            for s in no_uncertainties_p:
+                print("P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
+            for s in no_uncertainties_s:
+                print("S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))

            if fnext == '.obs':
                try:
@@ -383,18 +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
@@ -426,20 +450,30 @@ class Data(object):
        data.filter(**kwargs)
        self.dirty = True

-    def setWFData(self, fnames, fnames_syn=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
+    def setWFData(self, fnames, fnames_alt=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
        """
        Clear current waveform data and set given waveform data
        :param fnames: waveform data names to append
+        :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.wfsyn = Stream()
+        self.wf_alt = Stream()
        if tstart == tstop:
            tstart = tstop = None
        self.tstart = tstart
        self.tstop = tstop

+        # remove directories
+        fnames = check_fname_exists(fnames)
+        fnames_alt = check_fname_exists(fnames_alt)
+
        # if obspy_dmt:
        #     wfdir = 'raw'
        #     self.processed = False
@@ -457,8 +491,8 @@ class Data(object):
        #     wffnames = fnames
        if fnames is not None:
            self.appendWFData(fnames)
-            if fnames_syn is not None:
-                self.appendWFData(fnames_syn, synthetic=True)
+            if fnames_alt is not None:
+                self.appendWFData(fnames_alt, alternative=True)
        else:
            return False

@@ -466,7 +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)
@@ -478,7 +514,7 @@ class Data(object):
        self.dirty = False
        return True

-    def appendWFData(self, fnames, synthetic=False):
+    def appendWFData(self, fnames, alternative=False):
        """
        Read waveform data from fnames and append it to current wf data
        :param fnames: waveform data to append
@@ -491,20 +527,20 @@ class Data(object):
        if self.dirty:
            self.resetWFData()

-        real_or_syn_data = {True: self.wfsyn,
-                            False: self.wfdata}
+        orig_or_alternative_data = {True: self.wf_alt,
+                                    False: self.wfdata}

        warnmsg = ''
        for fname in set(fnames):
            try:
-                real_or_syn_data[synthetic] += read(fname, starttime=self.tstart, endtime=self.tstop)
+                orig_or_alternative_data[alternative] += read(fname, starttime=self.tstart, endtime=self.tstop)
            except TypeError:
                try:
-                    real_or_syn_data[synthetic] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
+                    orig_or_alternative_data[alternative] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
                except Exception as e:
                    try:
-                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart,
-                                                            endtime=self.tstop)
+                        orig_or_alternative_data[alternative] += read(fname, format='SEGY', starttime=self.tstart,
+                                                                      endtime=self.tstop)
                    except Exception as e:
                        warnmsg += '{0}\n{1}\n'.format(fname, e)
            except SacIOError as se:
@@ -519,8 +555,8 @@ class Data(object):
    def getOriginalWFData(self):
        return self.wforiginal

-    def getSynWFData(self):
-        return self.wfsyn
+    def getAltWFdata(self):
+        return self.wf_alt

    def resetWFData(self):
        """
--- a/pylot/core/io/location.py
+++ b/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:
--- a/pylot/core/io/phases.py
+++ b/pylot/core/io/phases.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import glob
+import logging
 import os
 import warnings

@@ -16,7 +17,7 @@ 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


@@ -58,7 +59,7 @@ 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 +67,7 @@ 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
@@ -217,7 +218,7 @@ def picksdict_from_obs(fn):
    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 +231,7 @@ 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:
@@ -273,31 +275,28 @@ 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 ''

@@ -517,7 +516,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
        for key in arrivals:
            # P onsets
-            if arrivals[key].has_key('P'):
+            if 'P' in arrivals[key]:
                try:
                    fm = arrivals[key]['P']['fm']
                except KeyError as e:
@@ -551,7 +550,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                                                                                           ss_ms,
                                                                                           pweight))
            # S onsets
-            if arrivals[key].has_key('S') and arrivals[key]['S']['mpp'] is not None:
+            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
                fm = '?'
                onset = arrivals[key]['S']['mpp']
                year = onset.year
@@ -670,7 +669,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
        for key in arrivals:
            # P onsets
-            if arrivals[key].has_key('P') and arrivals[key]['P']['mpp'] is not None:
+            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
@@ -699,7 +698,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                    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 arrivals[key].has_key('S') and arrivals[key]['S']['mpp'] is not None:
+            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
@@ -768,7 +767,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
        usedarrivals = chooseArrivals(arrivals)
        for key in usedarrivals:
            # P onsets
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                if usedarrivals[key]['P']['weight'] < 4:
                    n += 1
                    stat = key
@@ -782,7 +781,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                    else:
                        fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))
                        # S onsets
-            if usedarrivals[key].has_key('S'):
+            if 'S' in usedarrivals[key]:
                if usedarrivals[key]['S']['weight'] < 4:
                    n += 1
                    stat = key
@@ -828,13 +827,13 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
        # prefer manual picks
        usedarrivals = chooseArrivals(arrivals)
        for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
+            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 usedarrivals[key].has_key('S'):
+            if 'S' in usedarrivals[key]:
                # S onsets
                if usedarrivals[key]['S']['weight'] < 4:
                    Sonset = usedarrivals[key]['S']['mpp']
@@ -879,7 +878,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
        # prefer manual picks
        usedarrivals = chooseArrivals(arrivals)
        for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
+            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)):
@@ -961,7 +960,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
        # write phase lines
        for key in arrivals:
-            if arrivals[key].has_key('P'):
+            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']
@@ -1014,7 +1013,6 @@ def chooseArrivals(arrivals):
    :return: arrivals but with the manual picks prefered if possible
    """
    # If len of arrivals is greater than 2 it comes from autopicking so only autopicks are available
-    print("=== CHOOSE ===")
    if len(arrivals) > 2:
        return arrivals
    if arrivals['auto'] and arrivals['manual']:
--- a/pylot/core/loc/nll.py
+++ b/pylot/core/loc/nll.py
@@ -82,8 +82,8 @@ def locate(fnin, parameter=None):
    :param fnin: external program name
    :return: None
    """
-    exe_path = parameter['nllocbin'] + '/bin/NLLoc'    
-    if exe_path is None:
+    exe_path = os.path.join(parameter['nllocbin'], 'NLLoc')
+    if not os.path.isfile(exe_path):
        raise NLLocError('NonLinLoc executable not found; check your '
                         'environment variables')

--- a/pylot/core/pick/autopick.py
+++ b/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

@@ -477,7 +463,7 @@ class AutopickStation(object):
            if self.pickparams["sstart"] < 0:
                self.pickparams["sstart"] = 0

-        if get_Bool(self.pickparams["use_taup"]) is False:
+        if get_bool(self.pickparams["use_taup"]) is False:
            # correct user mistake where a relative cuttime is selected (pstart < 0) but use of taupy is disabled/ has
            # not the required parameters
            exit_taupy()
@@ -525,7 +511,7 @@ class AutopickStation(object):
        :rtype: dict
        """

-        if get_Bool(self.pickparams['use_taup']) is True and self.origin is not None:
+        if get_bool(self.pickparams['use_taup']) is True and self.origin is not None:
            try:
                # modify pstart, pstop, sstart, sstop to be around theoretical onset if taupy should be used,
                # else do nothing
@@ -544,7 +530,7 @@ class AutopickStation(object):

        if self.horizontal_traces_exist():
            if (self.p_results.weight is not None and self.p_results.weight < 4) or \
-                    get_Bool(self.pickparams.get('use_taup')):
+                    get_bool(self.pickparams.get('use_taup')):
                try:
                    self.pick_s_phase()
                except MissingTraceException as mte:
@@ -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,
@@ -936,7 +922,7 @@ class AutopickStation(object):
            "minFMSNR"]:
            # if SNR is high enough, try to determine first motion of onset
            self.set_current_figure('fm_picker')
-            self.p_results.fm = fmpicker(self.zstream, z_copy, self.pickparams["fmpickwin"], self.p_results.mpp,
+            self.p_results.fm = fmpicker(self.zstream.copy(), z_copy, self.pickparams["fmpickwin"], self.p_results.mpp,
                                         self.iplot, self.current_figure, self.current_linecolor)
        msg = "autopickstation: P-weight: {}, SNR: {}, SNR[dB]: {}, Polarity: {}"
        msg = msg.format(self.p_results.weight, self.p_results.snr, self.p_results.snrdb, self.p_results.fm)
@@ -1148,7 +1134,7 @@ class AutopickStation(object):
                  ''.format(self.s_results.weight, self.s_results.snr, self.s_results.snrdb))

    def pick_s_phase(self):
-        if get_Bool(self.pickparams.get('use_taup')) is True:
+        if get_bool(self.pickparams.get('use_taup')) is True:
            cuttimesh = (self.pickparams.get('sstart'), self.pickparams.get('sstop'))
        else:
            # determine time window for calculating CF after P onset
--- a/pylot/core/pick/charfuns.py
+++ b/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
--- a/pylot/core/pick/picker.py
+++ b/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))
@@ -336,7 +337,7 @@ class AICPicker(AutoPicker):
                    self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
                    # normalize slope to maximum of cf to make it unit independent
                    self.slope /= aicsmooth[iaicmax]
-            except ValueError as e:
+            except Exception as e:
                print("AICPicker: Problems with data fitting! {}".format(e))

        else:
--- a/pylot/core/pick/utils.py
+++ b/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'):
@@ -62,8 +62,8 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
    plt_flag = 0
    try:
        iplot = int(iplot)
-    except:
-        if get_Bool(iplot):
+    except ValueError:
+        if get_bool(iplot):
            iplot = 2
        else:
            iplot = 0
@@ -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
@@ -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
@@ -816,7 +816,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
    try:
        iplot = int(iplot)
    except:
-        if get_Bool(iplot):
+        if get_bool(iplot):
            iplot = 2
        else:
            iplot = 0
@@ -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
@@ -1130,7 +1132,7 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
    try:
        iplot = int(iplot)
    except:
-        if get_Bool(iplot):
+        if get_bool(iplot):
            iplot = 2
        else:
            iplot = 0
@@ -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
@@ -1499,7 +1485,7 @@ def get_pickparams(pickparam):
    first_motion_params = dict(zip(first_motion_names, fm_parameter_values))
    signal_length_params = dict(zip(signal_length_names, sl_parameter_values))

-    p_params['use_taup'] = get_Bool(p_params['use_taup'])
+    p_params['use_taup'] = get_bool(p_params['use_taup'])

    return p_params, s_params, first_motion_params, signal_length_params

@@ -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
--- a/pylot/core/util/array_map.py
+++ b/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
@@ -75,7 +76,6 @@ class Array_map(QtWidgets.QWidget):

        self._style = None if not hasattr(parent, '_style') else parent._style

-        self.show()

    def init_map(self):
        self.init_colormap()
@@ -124,8 +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)
@@ -280,9 +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)
@@ -385,7 +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
@@ -464,17 +474,19 @@ class Array_map(QtWidgets.QWidget):
                                                                  transform=ccrs.PlateCarree(), label='deleted'))

    def openPickDlg(self, ind):
-        data = self._parent.get_data().getWFData()
+        wfdata = self._parent.get_data().getWFData()
+        wfdata_comp = self._parent.get_data().getWFDataComp()
        for index in ind:
            network, station = self._station_onpick_ids[index].split('.')[:2]
            pyl_mw = self._parent
            try:
-                data = data.select(station=station)
-                if not data:
+                wfdata = wfdata.select(station=station)
+                wfdata_comp = wfdata_comp.select(station=station)
+                if not wfdata:
                    self._warn('No data for station {}'.format(station))
                    return
                pickDlg = PickDlg(self._parent, parameter=self.parameter,
-                                  data=data, network=network, station=station,
+                                  data=wfdata.copy(), data_compare=wfdata_comp.copy(), network=network, station=station,
                                  picks=self._parent.get_current_event().getPick(station),
                                  autopicks=self._parent.get_current_event().getAutopick(station),
                                  filteroptions=self._parent.filteroptions, metadata=self.metadata,
--- a/pylot/core/util/dataprocessing.py
+++ b/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):
@@ -271,7 +276,7 @@ class Metadata(object):
                    continue
            invtype, robj = self._read_metadata_file(os.path.join(path_to_inventory, fname))
            try:
-                robj.get_coordinates(station_seed_id)
+                # robj.get_coordinates(station_seed_id)  # TODO: Commented out, failed with Parser, is this needed?
                self.inventory_files[fname] = {'invtype': invtype,
                                               'data': robj}
                if station_seed_id in self.seed_ids.keys():
--- a/pylot/core/util/defaults.py
+++ b/pylot/core/util/defaults.py
@@ -26,9 +26,7 @@ elif system_name == "Windows":
 # suffix for phase name if not phase identified by last letter (P, p, etc.)
 ALTSUFFIX = ['diff', 'n', 'g', '1', '2', '3']

-FILTERDEFAULTS = readDefaultFilterInformation(os.path.join(os.path.expanduser('~'),
-                                                           '.pylot',
-                                                           'pylot.in'))
+FILTERDEFAULTS = readDefaultFilterInformation()

 TIMEERROR_DEFAULTS = os.path.join(os.path.expanduser('~'),
                                  '.pylot',
--- a/pylot/core/util/generate_array_maps.py
+++ b/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()
--- a/pylot/core/util/thread.py
+++ b/pylot/core/util/thread.py
@@ -41,7 +41,8 @@ class Thread(QThread):
            exctype, value = sys.exc_info()[:2]
            self._executedErrorInfo = '{} {} {}'. \
                format(exctype, value, traceback.format_exc())
-        sys.stdout = self.old_stdout
+        if self.redirect_stdout:
+            sys.stdout = self.old_stdout

    def showProgressbar(self):
        if self.progressText:
@@ -159,7 +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()
--- a/pylot/core/util/utils.py
+++ b/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:
@@ -37,15 +44,14 @@ def getAutoFilteroptions(phase, parameter):
    return filteroptions


-def readDefaultFilterInformation(fname):
+def readDefaultFilterInformation():
    """
    Read default filter information from pylot.in file
-    :param fname: path to pylot.in file
-    :type fname: str
    :return: dictionary containing the defailt filter information
    :rtype: dict
    """
-    pparam = PylotParameter(fname)
+    pparam = PylotParameter()
+    pparam.reset_defaults()
    return readFilterInformation(pparam)


@@ -82,25 +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
@@ -120,7 +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


@@ -166,11 +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]
@@ -302,7 +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)(\.|$)')
@@ -314,32 +301,75 @@ 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


-def get_Bool(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
    """
-    if value in ['True', 'true']:
+    if type(value) is bool:
+        return value
+    elif value in ['True', 'true']:
        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 value

@@ -353,8 +383,8 @@ 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 +466,53 @@ 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 +558,11 @@ 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 +589,36 @@ 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 +627,19 @@ 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 +647,53 @@ 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 +709,13 @@ 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 +726,7 @@ 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 +739,7 @@ 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 +795,17 @@ 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 +839,20 @@ 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 +862,16 @@ 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 +900,6 @@ 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 +920,12 @@ 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 +936,7 @@ def check4gapsAndMerge(data):
        for merged_station in merged:
            print(merged_station)

-    return data
+    return data, gaps


 def check4doubled(data):
@@ -897,13 +966,53 @@ 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 +1039,87 @@ 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 +1133,6 @@ 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 +1204,7 @@ def identifyPhase(phase):
        return False


+@lru_cache
 def identifyPhaseID(phase):
    """
    Returns phase id (capital P or S)
@@ -1169,7 +1268,7 @@ def correct_iplot(iplot):
    try:
        iplot = int(iplot)
    except ValueError:
-        if get_Bool(iplot):
+        if get_bool(iplot):
            iplot = 2
        else:
            iplot = 0
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
Author	SHA1	Message	Date
Marcel	6cce05b035	Merge branch 'feature/dae' into develop # Conflicts: # pylot/core/io/data.py # pylot/core/util/widgets.py	2024-06-12 16:19:21 +02:00
Marcel	7326f061e5	[minor] inform if station coordinates were not found in metadata	2024-06-12 16:11:53 +02:00
Marcel	1a18401fe3	[bugfix] added missing Parameter object in call for picksdict_from_picks	2024-06-12 13:44:02 +02:00
Marcel	ec930dbc12	[minor] removed unneeded imports	2024-06-07 15:56:05 +02:00
Marcel	b991f771af	[bugfix] removing redundancy and wrong bullsh.. try-except code	2024-06-07 15:04:16 +02:00
Marcel	2c3b1876ab	[minor] switch default cmap for array_map to 'viridis'	2024-06-07 14:34:27 +02:00
Marcel	0acd23d4d0	[update] further improved Pickfile selection dialog, now providing methods "overwrite" or "merge"	2024-06-07 14:32:57 +02:00
Marcel	f349c8bc7e	[update] improve pickfile selection, give the ability to select only specific files	2024-06-07 13:09:34 +02:00
Marcel	6688ef845d	[bugfix] re-implement ability of get_bool to return unidentifiable input	2024-06-07 13:08:51 +02:00
Marcel	5b18e9ab71	[merge] merge branch 'improve-util-utils' of pull request #35 into develop	2024-06-07 10:29:39 +02:00
Marcel	c79e886d77	[minor] update default shell script for SGE	2024-06-06 15:55:47 +02:00
Marcel	76f2d5d972	[update] improve SearchForFileExtensionDialog now proposing available file endings	2024-06-06 15:54:36 +02:00
Marcel	2d08fd029d	[hotfix] datetime formatting caused error when time not set	2024-06-06 13:55:11 +02:00
Marcel	8f22d438d3	[update] changed eventbox overview to show P and S onsets separately	2024-06-05 16:18:25 +02:00
Marcel	93b7de3baa	[update] raising PickingFailedException when CF cannot be calculated due to missing signal (too short waveform) [update] raising PickingFailedException when CF cannot be calculated due to missing signal (too short waveform)	2024-06-05 14:31:09 +02:00
Marcel	05642e775b	[minor] some tweaks (convenience) [update] raising PickingFailedException when CF cannot be calculated due to missing signal (too short waveform)	2024-06-05 14:31:07 +02:00
Marcel	47205ca493	[update] improved calculation of smoothed AIC. Old code always created an artificial value and a np.nan at the array start	2024-06-05 14:31:07 +02:00
Marcel	5c7f0b56eb	[update] improved SearchFileByExtensionDialog widget	2024-06-05 14:19:17 +02:00
Marcel	c574031931	[bugfix] the implementation approach of STA/LTA inside characteristic function calculation (skewness/kurtosis) corrupted the old, working code due to a mistake in the logic	2024-06-05 14:17:57 +02:00
Marcel	e1a0fde619	[update] improved array map to identify and display other phase names than P / S	2024-05-29 11:43:31 +02:00
Marcel	48d196df11	[update] improved SearchFileByExtensionDialog widget (table, auto refresh)	2024-05-29 11:42:10 +02:00
Marcel	6cc9cb4a96	[minor] reduced maxtasksperchild for multiprocessing	2024-05-29 11:40:34 +02:00
Marcel	5eab686445	[bugfix] accidentally removed return value	2024-05-24 16:10:32 +02:00
Marcel	b12e7937ac	[update] added a widget for loading pick files that lists available files depending on chosen filemask	2024-05-22 10:58:07 +02:00
Marcel	78f2dbcab2	[update] added check for nan values in waveforms which crashed obspy filter routines [minor] some tweaks and optimisations	2024-04-30 15:48:54 +02:00
Marcel	8b95c7a0fe	[update] changed sorting of traces overview if all station names are numeric (e.g. active experiments)	2024-04-09 16:02:31 +02:00
Marcel	65dbaad446	[update] adding possibility to display other waveform data (e.g. denoised/synthetic) together with genuine data for comparison	2024-03-22 17:12:04 +01:00
Marcel	5b97d51517	[minor] mpl.figure.canvas.draw -> draw_idle	2024-03-22 17:12:04 +01:00
Marcel	f03ace75e7	[bugfix] QWidget.show() killed figure axis dimensions creating unexpected error of fig.aspect=0 when creating colorbar inset_axes in Python 3.11	2024-03-22 17:10:04 +01:00
Marcel	9c78471d20	[bugfix] header resize method renamed in QT5	2024-03-22 15:34:05 +01:00
Marcel	09d2fb1022	[bugfix] pt2 of fmpicker fix, make sure to also copy stream in autoPyLoT closes #24	2023-08-24 12:55:30 +02:00
Marcel	3cae6d3a78	[bugfix] use copies of wfdata when calling fmpicker to prevent modification of actual data used inside GUI	2023-08-24 11:28:30 +02:00
Marcel	2e85d083a3	[bugfix] do not call calcsourcespec if incidence angle is outside bounds (for whatever reason)	2023-08-24 11:27:30 +02:00
Marcel	ba4e6cfe50	[bugfix] bin directory + /bin creates "/bin/bin". Also it is not taken care of os compatibility and also compatibility with existing code (line 86ff was useless after recent change in line 85)	2023-08-23 14:48:21 +02:00
Marcel	1f16d01648	[minor] give more precise user warning if no pick channel was selected	2023-08-23 09:38:16 +02:00
Marcel	3069e7d526	[minor] commented - possibly unnecessary - line of code that created an error when using old metadata Parser	2023-08-22 15:53:49 +02:00
Marcel	a9aeb7aaa3	[bugfix] set simple phase hint (P or S)	2023-08-22 15:53:49 +02:00
Marcel	b9adb182ad	[bugfix] could not handle asterisk-marked events when opening tune-autopicker	2023-08-22 15:53:49 +02:00
Marcel	a823eb2440	[workaround] using explicit Exception definition without a special handling does not make sense. Function broke on other errors in polyfit. Still might need fixes in the two lines above the "except" block(s).	2023-08-22 15:53:49 +02:00
Marcel Paffrath	486e3dc9c3	Merge pull request 'Disabled button in case flag is false' (#31 ) from disable-show-log-widget into develop Reviewed-on: #31	2023-08-22 12:05:33 +02:00
Marcel	8d356050d7	[update] corrected original authors of PILOT	2023-08-22 12:01:51 +02:00
Jeldrik Gaal	43cab3767f	[Bugfix] fixxed wrong check for taupymodel	2023-06-27 08:04:00 +02:00
Sebastian Wehling-Benatelli	b3fdbc811e	Merge branch 'develop' into improve-util-utils	2023-06-23 09:37:54 +02:00
Jeldrik Gaal	a1f6c5ffca	Bugfixxes, spectogram tab wip	2023-06-14 13:11:54 +02:00
Jeldrik Gaal	e4e7afa996	Minor changes to adjust to python 3. Temporary Fix for file exporting not working properly. WIP spectrogram view.	2023-04-27 10:24:55 +02:00
Sebastian Wehling-Benatelli	9fce4998d3	bugfix: remove unused functions; correct for wrong formatting (PEP)	2023-04-23 22:05:11 +02:00
Sebastian Wehling-Benatelli	c468bfbe84	feat: add type hints and tests for plot utils	2023-04-23 21:37:20 +02:00
Sebastian Wehling-Benatelli	4861d33e9a	bugfix: add tests to key_for_set_value	2023-04-16 09:58:51 +02:00
Sebastian Wehling-Benatelli	f5f4635c3d	bugfix: rename is_iterable and add doc tests	2023-04-16 09:50:42 +02:00
Sebastian Wehling-Benatelli	b12d92eebb	bugfix: refactor get_owner and get_hash; add tests	2023-04-12 21:22:58 +02:00
Sebastian Wehling-Benatelli	e9da81376e	bugfix: add new tests and refactor get_none	2023-04-12 20:32:44 +02:00
Sebastian Wehling-Benatelli	e68fc849f0	bugfix: correct erroneous and add new doctests	2023-04-10 19:14:23 +02:00
Sebastian Wehling-Benatelli	efb117177c	bugfix: update check4rotate	2023-04-10 18:35:58 +02:00
Sebastian Wehling-Benatelli	0634d24814	fix: disabled button in case flag is false The button was not disabled in case the flag variable was false. The get_Bool function was renamed and improved to also work in case in the input variable is of type int or float. Additionally, the environment file was corrected to also work for macOS installations with ARM architecture.	2023-04-06 16:40:20 +02:00
Jeldrik Gaal	43c2b97b3d	Small changes	2023-01-24 11:45:12 +01:00
ann-christin	8d94440e77	[bugfix] logwidget always initiated	2022-11-14 14:14:59 +01:00
ann-christin	66b7dea706	[update] pylot.in no longer mandatory	2022-11-14 14:14:12 +01:00
ann-christin	ebf6d4806a	[minor] reformating	2022-11-14 11:52:25 +01:00
ann-christin	207d0b3a6f	[update] directly pass args from arg parser	2022-11-14 11:18:15 +01:00
ann-christin	3b3bbc29d1	Merge remote-tracking branch 'origin/develop' into develop	2022-11-14 10:30:38 +01:00
ann-christin	a8c6f4c972	[reformat] spell checking	2022-08-25 15:31:08 +02:00
ann-christin	0d91f9e3fe	update github link	2022-08-25 14:03:05 +02:00
ann-christin	494d281d61	update github link	2022-08-25 14:00:37 +02:00