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
19 changed files with 673 additions and 327 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
@ -84,7 +85,7 @@ from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
    PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
    ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
    CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget, PickQualitiesFromXml, \
-    SourceSpecWindow, ChooseWaveFormWindow, SpectrogramTab
+    SpectrogramTab, SearchFileByExtensionDialog
 from pylot.core.util.array_map import Array_map
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import Thread, Worker
@ -113,11 +114,7 @@ class MainWindow(QMainWindow):
    def __init__(self, parent=None, infile=None, reset_qsettings=False):
        super(MainWindow, self).__init__(parent)

-        # check for default pylot.in-file
-        if not infile:
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-        if os.path.isfile(infile) is False:
+        if infile and os.path.isfile(infile) is False:
            infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')[0]

            if not os.path.exists(infile):
@ -181,6 +178,7 @@ class MainWindow(QMainWindow):
        self.autodata = Data(self)

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

        # track deleted picks for logging
@ -253,7 +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

@ -508,6 +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)
@ -1004,17 +1004,16 @@ 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)
+            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
@ -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
+            if merge_strategy == 'Overwrite':
                data = data_new
-            # 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')
@ -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,
+            man_au_picks = {'manual': event.pylot_picks,
                            'auto': event.pylot_autopicks}
-            ma_count = {'manual': 0,
-                        'auto': 0}
-            ma_count_total = {'manual': 0,
-                              'auto': 0}
+            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:
@ -1885,6 +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()
@ -1919,7 +1935,6 @@ class MainWindow(QMainWindow):
            self.spectro_layout.addWidget(newSpectroWidget)
            self.spectroWidget = newSpectroWidget

-
    def newWF(self, event=None, plot=True):
        '''
        Load new data and plot if necessary.
@ -1949,13 +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):
        '''
@ -1970,6 +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?')
@ -1986,7 +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,
@ -1994,7 +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):
@ -2002,8 +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():
@ -2125,7 +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)
@ -2284,7 +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:
@ -2299,8 +2323,8 @@ class MainWindow(QMainWindow):
            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:
@ -2596,18 +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()
@ -2986,10 +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:
@ -3457,7 +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)
@ -3631,7 +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:
@ -3684,10 +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))
@ -3805,6 +3841,7 @@ class MainWindow(QMainWindow):

    def closeEvent(self, event):
        if self.okToContinue():
+            if hasattr(self, 'logwidget'):
                self.logwidget.close()
            event.accept()
        else:
--- 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
@ -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:
+        if not inputfile:
+            print('Using default input parameter')
        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)
    else:
        if not type(parameter) == PylotParameter:
            print('Wrong input type for parameter: {}'.format(type(parameter)))
--- 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:
@ -408,18 +409,16 @@ class Data(object):
                                     not implemented: {1}'''.format(evtformat, e))
            if fnext == '_focmec.in':
                try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
+                    parameter = PylotParameter()
+                    logging.warning('Using default input parameter')
                    focmec.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                except KeyError as e:
                    raise KeyError('''{0} export format
                                     not implemented: {1}'''.format(evtformat, e))
            if fnext == '.pha':
                try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
+                    parameter = PylotParameter()
+                    logging.warning('Using default input parameter')
                    hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                except KeyError as e:
                    raise KeyError('''{0} export format
@ -451,20 +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
@ -482,8 +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

@ -491,7 +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)
@ -503,7 +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
@ -516,19 +527,19 @@ class Data(object):
        if self.dirty:
            self.resetWFData()

-        real_or_syn_data = {True: self.wfsyn,
+        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,
+                        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)
@ -544,8 +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/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

@ -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:
@ -273,32 +275,29 @@ 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']
+            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!")
-            phase['fm'] = 'N'
        phase['filter_id'] = filter_id if filter_id is not None else ''

        onsets[pick.phase_hint] = phase.copy()
--- 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
@ -20,7 +20,7 @@ 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

@ -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):
@ -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)
--- 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
@ -62,7 +62,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
    plt_flag = 0
    try:
        iplot = int(iplot)
-    except:
+    except ValueError:
        if get_bool(iplot):
            iplot = 2
        else:
@ -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
@ -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
@ -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
+        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/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
@ -160,7 +160,7 @@ class MultiThread(QThread):
        try:
            if not self.ncores:
                self.ncores = multiprocessing.cpu_count()
-            pool = multiprocessing.Pool(self.ncores)
+            pool = multiprocessing.Pool(self.ncores, maxtasksperchild=1000)
            self.data = pool.map_async(self.func, self.args, callback=self.emitDone)
            # self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned
            pool.close()
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@ -1,13 +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
@ -105,7 +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


@ -332,7 +334,7 @@ def get_none(value):

 def get_bool(value):
    """
-    Convert string representations of bools to their true boolean value
+    Convert string representations of bools to their true boolean value. Return value if it cannot be identified as bool.
    :param value:
    :type value: str, bool, int, float
    :return: true boolean value
@ -354,17 +356,22 @@ def get_bool(value):
    False
    >>> get_bool(-0.3)
    False
+    >>> get_bool(None)
+    None
    """
-    if type(value) == bool:
+    if type(value) is bool:
        return value
    elif value in ['True', 'true']:
        return True
    elif value in ['False', 'false']:
        return False
-    elif value > 0. or value > 0:
+    elif isinstance(value, float) or isinstance(value, int):
+        if value > 0. or value > 0:
            return True
        else:
            return False
+    else:
+        return value


 def four_digits(year):
@ -893,19 +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
@ -926,12 +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()
@ -942,7 +936,7 @@ def check4gapsAndMerge(data):
        for merged_station in merged:
            print(merged_station)

-    return data
+    return data, gaps


 def check4doubled(data):
@ -972,6 +966,46 @@ 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
@ -1038,7 +1072,7 @@ def check4rotated(data, metadata=None, verbosity=1):
        # 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):
-            print(f"Stream does not need any rotation: Traces are {trace_ids=}")
+            logging.debug(f"Stream does not need any rotation: Traces are {trace_ids=}")
            return wfs_in

        # check metadata quality
@ -1050,7 +1084,7 @@ def check4rotated(data, metadata=None, verbosity=1):
                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:
-            print(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
+            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:
@ -1170,6 +1204,7 @@ def identifyPhase(phase):
        return False


+@lru_cache
 def identifyPhaseID(phase):
    """
    Returns phase id (capital P or S)
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@ -7,6 +7,7 @@ Created on Wed Mar 19 11:27:35 2014
 import copy
 import datetime
 import getpass
+import glob
 import multiprocessing
 import os
 import subprocess
@ -16,6 +17,7 @@ import traceback

 import matplotlib
 import numpy as np
+from pylot.core.io.phases import getQualitiesfromxml

 matplotlib.use('QT5Agg')

@ -36,7 +38,7 @@ from PySide2.QtWidgets import QAction, QApplication, QCheckBox, QComboBox, \
    QGridLayout, QLabel, QLineEdit, QMessageBox, \
    QTabWidget, QToolBar, QVBoxLayout, QHBoxLayout, QWidget, \
    QPushButton, QFileDialog, QInputDialog
-from PySide2.QtCore import QSettings, Qt, QUrl, Signal
+from PySide2.QtCore import QSettings, Qt, QUrl, Signal, QTimer
 from PySide2.QtWebEngineWidgets import QWebEngineView as QWebView
 from obspy import Stream, Trace, UTCDateTime
 from obspy.core.util import AttribDict
@ -51,10 +53,10 @@ from pylot.core.pick.autopick import fmpicker
 from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS
 from pylot.core.util.utils import prep_time_axis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
    pick_linestyle_plt, pick_color_plt, \
-    check4rotated, check4doubled, merge_stream, identifyPhase, \
+    check4rotated, check4doubled, check_for_gaps_and_merge, check_for_nan, identifyPhase, \
    loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
    identifyPhaseID, get_bool, get_none, pick_color, getAutoFilteroptions, SetChannelComponents, \
-    station_id_remove_channel
+    station_id_remove_channel, get_pylot_eventfile_with_extension, get_possible_pylot_eventfile_extensions
 from autoPyLoT import autoPyLoT
 from pylot.core.util.thread import Thread
 from pylot.core.util.dataprocessing import Metadata
@ -793,7 +795,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):

    def connect_signals(self):
        self.qcombo_processed.activated.connect(self.parent().newWF)
-        self.syn_checkbox.clicked.connect(self.parent().newWF)
+        self.comp_checkbox.clicked.connect(self.parent().newWF)

    def init_labels(self):
        self.label_layout.addWidget(self.status_label)
@ -804,13 +806,13 @@ class WaveformWidgetPG(QtWidgets.QWidget):
        # use widgets as placeholder, so that child widgets keep position when others are hidden
        mid_layout = QHBoxLayout()
        right_layout = QHBoxLayout()
-        mid_layout.addWidget(self.syn_checkbox)
+        mid_layout.addWidget(self.comp_checkbox)
        right_layout.addWidget(self.qcombo_processed)
        mid_widget.setLayout(mid_layout)
        right_widget.setLayout(right_layout)
        self.label_layout.addWidget(mid_widget)
        self.label_layout.addWidget(right_widget)
-        self.syn_checkbox.setLayoutDirection(Qt.RightToLeft)
+        self.comp_checkbox.setLayoutDirection(Qt.RightToLeft)
        self.label_layout.setStretch(0, 4)
        self.label_layout.setStretch(1, 0)
        self.label_layout.setStretch(2, 0)
@ -825,7 +827,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
            label = QtWidgets.QLabel()
            self.perm_labels.append(label)
        self.qcombo_processed = QtWidgets.QComboBox()
-        self.syn_checkbox = QtWidgets.QCheckBox('synthetics')
+        self.comp_checkbox = QtWidgets.QCheckBox('Load comparison data')
        self.addQCboxItem('processed', 'green')
        self.addQCboxItem('raw', 'black')
        # self.perm_qcbox_right.setAlignment(2)
@ -834,9 +836,11 @@ class WaveformWidgetPG(QtWidgets.QWidget):
    def getPlotDict(self):
        return self.plotdict

-    def activateObspyDMToptions(self, activate):
-        self.syn_checkbox.setVisible(activate)
-        self.qcombo_processed.setVisible(activate)
+    def activateObspyDMToptions(self, activate: bool) -> None:
+        self.qcombo_processed.setEnabled(activate)
+
+    def activateCompareOptions(self, activate: bool) -> None:
+        self.comp_checkbox.setEnabled(activate)

    def setPermText(self, number, text=None, color='black'):
        if not 0 <= number < len(self.perm_labels):
@ -860,13 +864,26 @@ class WaveformWidgetPG(QtWidgets.QWidget):
    def clearPlotDict(self):
        self.plotdict = dict()

-    def plotWFData(self, wfdata, wfsyn=None, title=None, zoomx=None, zoomy=None,
-                   noiselevel=None, scaleddata=False, mapping=True,
-                   component='*', nth_sample=1, iniPick=None, verbosity=0,
-                   method='normal', gain=1.):
+    def plotWFData(self, wfdata, wfsyn=None, title=None, scaleddata=False, mapping=True,
+                   component='*', nth_sample=1, verbosity=0, method='normal', gain=1., shift_syn=0.2):
+        def station_sort(nslc):
+            """Try to sort after station integer in case of a line array (e.g. active seismics)"""
+            try:
+                rval = sorted(nslc, key=lambda x: int(x.split('.')[1]))
+                return rval
+            except ValueError as e:
+                # this is the standard case for seismological stations
+                pass
+            except Exception as e:
+                print(f'Sorting by station integer failed with unknown exception: {e}')
+
+            # fallback to default sorting
+            return sorted(nslc)
+
        if not wfdata:
            print('Nothing to plot.')
            return
+
        self.title = title
        self.clearPlotDict()
        self.wfstart, self.wfend = full_range(wfdata)
@ -884,14 +901,14 @@ class WaveformWidgetPG(QtWidgets.QWidget):
        else:
            st_select = wfdata

-        st_select, gaps = merge_stream(st_select)
+        # st_select, gaps = check_for_gaps_and_merge(st_select) #MP MP commented because probably done twice

        # list containing tuples of network, station, channel (for sorting)
        nslc = []
        for trace in st_select:
            nslc.append(
                trace.get_id())  # (trace.stats.network, trace.stats.station, trace.stats.location trace.stats.channel))
-        nslc.sort()
+        nslc = station_sort(nslc)
        nslc.reverse()
        plots = []

@ -946,7 +963,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
                    [time for index, time in enumerate(time_ax_syn) if not index % nth_sample] if st_syn else [])
                trace.data = np.array(
                    [datum * gain + n for index, datum in enumerate(trace.data) if not index % nth_sample])
-                trace_syn.data = np.array([datum + n for index, datum in enumerate(trace_syn.data)
+                trace_syn.data = np.array([datum + n + shift_syn for index, datum in enumerate(trace_syn.data)
                                           if not index % nth_sample] if st_syn else [])
                plots.append((times, trace.data,
                              times_syn, trace_syn.data))
@ -955,7 +972,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
        self.ylabel = ''
        self.setXLims([0, self.wfend - self.wfstart])
        self.setYLims([0.5, nmax + 0.5])
-        return plots, gaps
+        return plots

    def minMax(self, trace, time_ax):
        '''
@ -977,7 +994,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
        min_ = data.min(axis=1)
        max_ = data.max(axis=1)
        if remaining_samples:
-            extreme_values = np.empty((npixel + 1, 2), dtype=np.float)
+            extreme_values = np.empty((npixel + 1, 2), dtype=float)
            extreme_values[:-1, 0] = min_
            extreme_values[:-1, 1] = max_
            extreme_values[-1, 0] = \
@ -985,7 +1002,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
            extreme_values[-1, 1] = \
                trace.data[-remaining_samples:].max()
        else:
-            extreme_values = np.empty((npixel, 2), dtype=np.float)
+            extreme_values = np.empty((npixel, 2), dtype=float)
            extreme_values[:, 0] = min_
            extreme_values[:, 1] = max_
        data = extreme_values.flatten()
@ -1135,12 +1152,12 @@ class PylotCanvas(FigureCanvas):
        ax.set_xlim(self.cur_xlim)
        ax.set_ylim(self.cur_ylim)
        self.refreshPickDlgText()
-        ax.figure.canvas.draw()
+        ax.figure.canvas.draw_idle()

    def panRelease(self, gui_event):
        self.press = None
        self.press_rel = None
-        self.figure.canvas.draw()
+        self.figure.canvas.draw_idle()

    def panZoom(self, gui_event, threshold=2., factor=1.1):
        if not gui_event.x and not gui_event.y:
@ -1358,11 +1375,15 @@ class PylotCanvas(FigureCanvas):
            plot_positions[channel] = plot_pos
        return plot_positions

-    def plotWFData(self, wfdata, title=None, zoomx=None, zoomy=None,
+    def plotWFData(self, wfdata, wfdata_compare=None, title=None, zoomx=None, zoomy=None,
                   noiselevel=None, scaleddata=False, mapping=True,
                   component='*', nth_sample=1, iniPick=None, verbosity=0,
                   plot_additional=False, additional_channel=None, scaleToChannel=None,
                   snr=None):
+        def get_wf_dict(data: Stream = Stream(), linecolor = 'k', offset: float = 0., **plot_kwargs):
+            return dict(data=data, linecolor=linecolor, offset=offset, plot_kwargs=plot_kwargs)
+
+
        ax = self.axes[0]
        ax.cla()

@ -1373,21 +1394,33 @@ class PylotCanvas(FigureCanvas):
        settings = QSettings()
        compclass = SetChannelComponents.from_qsettings(settings)

+        linecolor = (0., 0., 0., 1.) if not self.style else self.style['linecolor']['rgba_mpl']
+
+        plot_streams = dict(wfdata=get_wf_dict(linecolor=linecolor, linewidth=0.7),
+                            wfdata_comp=get_wf_dict(offset=0.1, linecolor='b', alpha=0.7, linewidth=0.5))
+
        if not component == '*':
            alter_comp = compclass.getCompPosition(component)
            # alter_comp = str(alter_comp[0])

-            st_select = wfdata.select(component=component)
-            st_select += wfdata.select(component=alter_comp)
+            plot_streams['wfdata']['data'] = wfdata.select(component=component)
+            plot_streams['wfdata']['data'] += wfdata.select(component=alter_comp)
+            if wfdata_compare:
+                plot_streams['wfdata_comp']['data'] = wfdata_compare.select(component=component)
+                plot_streams['wfdata_comp']['data'] += wfdata_compare.select(component=alter_comp)
        else:
-            st_select = wfdata
+            plot_streams['wfdata']['data'] = wfdata
+            if wfdata_compare:
+                plot_streams['wfdata_comp']['data'] = wfdata_compare
+
+        st_main = plot_streams['wfdata']['data']

        if mapping:
-            plot_positions = self.calcPlotPositions(st_select, compclass)
+            plot_positions = self.calcPlotPositions(st_main, compclass)

        # list containing tuples of network, station, channel and plot position (for sorting)
        nslc = []
-        for plot_pos, trace in enumerate(st_select):
+        for plot_pos, trace in enumerate(st_main):
            if not trace.stats.channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
                print('Warning: Unrecognized channel {}'.format(trace.stats.channel))
                continue
@ -1395,10 +1428,12 @@ class PylotCanvas(FigureCanvas):
        nslc.sort()
        nslc.reverse()

-        linecolor = (0., 0., 0., 1.) if not self.style else self.style['linecolor']['rgba_mpl']
-
        for n, seed_id in enumerate(nslc):
            network, station, location, channel = seed_id.split('.')
+            for wf_name, wf_dict in plot_streams.items():
+                st_select = wf_dict.get('data')
+                if not st_select:
+                    continue
                st = st_select.select(id=seed_id)
                trace = st[0].copy()
                if mapping:
@ -1422,15 +1457,17 @@ class PylotCanvas(FigureCanvas):
                        trace.detrend('constant')
                        trace.normalize(np.max(np.abs(trace.data)) * 2)

+                    offset = wf_dict.get('offset')
+
                    times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
-                data = [datum + n for index, datum in enumerate(trace.data) if not index % nth_sample]
+                    data = [datum + n + offset for index, datum in enumerate(trace.data) if not index % nth_sample]
                    ax.axhline(n, color="0.5", lw=0.5)
-                ax.plot(times, data, color=linecolor, linewidth=0.7)
+                    ax.plot(times, data, color=wf_dict.get('linecolor'), **wf_dict.get('plot_kwargs'))
                    if noiselevel is not None:
                        for level in [-noiselevel[channel], noiselevel[channel]]:
                            ax.plot([time_ax[0], time_ax[-1]],
                                    [n + level, n + level],
-                                color=linecolor,
+                                    color=wf_dict.get('linecolor'),
                                    linestyle='dashed')
                    self.setPlotDict(n, seed_id)
        if plot_additional and additional_channel:
@ -1555,6 +1592,178 @@ class PylotCanvas(FigureCanvas):
        self.draw()


+class SearchFileByExtensionDialog(QtWidgets.QDialog):
+    def __init__(self, parent=None, label='Text: ', default_text='.xml', events=None):
+        super(SearchFileByExtensionDialog, self).__init__(parent)
+        self.events = events
+        self.filepaths = []
+        self.file_extensions = []
+        self.check_all_state = True
+        self.merge_strategy = None
+        self.default_text = default_text
+        self.label = label
+        self.setButtons()
+        self.setupUi()
+        self.connectSignals()
+        self.showPaths()
+        self.refreshSelectionBox()
+        # self.refresh_timer = QTimer(self)
+        # self.refresh_timer.timeout.connect(self.showPaths)
+        # self.refresh_timer.start(10000)
+
+        self.resize(800, 450)
+
+    def setupUi(self):
+        ncol = 4
+        self.main_layout = QtWidgets.QVBoxLayout()
+        self.header_layout = QtWidgets.QHBoxLayout()
+        self.footer_layout = QtWidgets.QHBoxLayout()
+        #
+        self.setLayout(self.main_layout)
+
+        # widgets inside the dialog
+        self.textLabel = QtWidgets.QLabel(self.label)
+        self.comboBox = QtWidgets.QComboBox()
+        self.comboBox.addItem(self.default_text)
+        self.comboBox.setEditable(True)
+
+        # optional search button, currently disabled. List refreshed when text changes
+        self.searchButton = QtWidgets.QPushButton('Search')
+        self.searchButton.setVisible(False)
+
+        # check/uncheck button for table
+        self.checkAllButton = QtWidgets.QPushButton('Check/Uncheck all')
+
+        # radiobutton for merge selection
+        self.mergeRadioButtonGroup = QtWidgets.QButtonGroup()
+        self.merge_button = QtWidgets.QRadioButton('Merge')
+        self.overwrite_button = QtWidgets.QRadioButton('Overwrite')
+        self.mergeRadioButtonGroup.addButton(self.merge_button)
+        self.mergeRadioButtonGroup.addButton(self.overwrite_button)
+        self.merge_button.setChecked(True)
+        self.merge_strategy = self.merge_button.text()
+
+        # table
+        self.tableWidget = QtWidgets.QTableWidget()
+        tableWidget = self.tableWidget
+        tableWidget.setColumnCount(ncol)
+        tableWidget.setRowCount(len(self.events))
+        tableWidget.setHorizontalHeaderLabels(('', 'Event ID', 'Filename', 'Last modified'))
+        tableWidget.setEditTriggers(tableWidget.NoEditTriggers)
+        tableWidget.setSortingEnabled(True)
+        header = tableWidget.horizontalHeader()
+        header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
+        header.setStretchLastSection(True)
+
+        self.statusText = QtWidgets.QLabel()
+
+        self.header_layout.addWidget(self.textLabel)
+        self.header_layout.addWidget(self.comboBox)
+        self.header_layout.addWidget(self.searchButton)
+
+        self.footer_layout.addWidget(self.checkAllButton)
+        self.footer_layout.addWidget(self.statusText)
+        self.footer_layout.addWidget(self.merge_button)
+        self.footer_layout.addWidget(self.overwrite_button)
+
+        self.footer_layout.setStretch(0, 0)
+        self.footer_layout.setStretch(1, 1)
+
+        self.main_layout.addLayout(self.header_layout)
+        self.main_layout.addWidget(self.tableWidget)
+        self.main_layout.addLayout(self.footer_layout)
+        self.main_layout.addWidget(self._buttonbox)
+
+    def showPaths(self):
+        self.filepaths = []
+        fext = self.comboBox.currentText()
+        self.tableWidget.clearContents()
+        for index, event in enumerate(self.events):
+            filename = get_pylot_eventfile_with_extension(event, fext)
+            pf_selected_item = QtWidgets.QTableWidgetItem()
+            check_state = QtCore.Qt.Checked if filename else QtCore.Qt.Unchecked
+            pf_selected_item.setCheckState(check_state)
+            self.tableWidget.setItem(index, 0, pf_selected_item)
+            self.tableWidget.setItem(index, 1, QtWidgets.QTableWidgetItem(f'{event.pylot_id}'))
+            if filename:
+                self.filepaths.append(filename)
+                ts = int(os.path.getmtime(filename))
+
+                # create QTableWidgetItems of filepath and last modification time
+                fname_item = QtWidgets.QTableWidgetItem(f'{os.path.split(filename)[-1]}')
+                fname_item.setData(3, filename)
+                ts_item = QtWidgets.QTableWidgetItem(f'{datetime.datetime.fromtimestamp(ts)}')
+                self.tableWidget.setItem(index, 2, fname_item)
+                self.tableWidget.setItem(index, 3, ts_item)
+
+        self.update_status()
+
+    def refreshSelectionBox(self):
+        fext = self.comboBox.currentText()
+        self.file_extensions = [fext]
+
+        for event in self.events:
+            extensions = get_possible_pylot_eventfile_extensions(event, '*.xml')
+            for ext in extensions:
+                if not ext in self.file_extensions:
+                    self.file_extensions.append(ext)
+
+        self.comboBox.clear()
+        for ext in sorted(self.file_extensions):
+            self.comboBox.addItem(ext)
+
+    def setButtons(self):
+        self._buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
+                                           QDialogButtonBox.Cancel)
+
+    def toggleCheckAll(self):
+        self.check_all_state = not self.check_all_state
+        self.checkAll(self.check_all_state)
+
+    def checkAll(self, state):
+        state = QtCore.Qt.Checked if state else QtCore.Qt.Unchecked
+        for row_ind in range(self.tableWidget.rowCount()):
+            item = self.tableWidget.item(row_ind, 0)
+            item.setCheckState(state)
+
+    def getChecked(self):
+        filepaths = []
+        for row_ind in range(self.tableWidget.rowCount()):
+            item_check = self.tableWidget.item(row_ind, 0)
+            if item_check.checkState() == QtCore.Qt.Checked:
+                item_fname = self.tableWidget.item(row_ind, 2)
+                if item_fname:
+                    filepath = item_fname.data(3)
+                    filepaths.append(filepath)
+        return filepaths
+
+    def update_status(self, row=None, col=None):
+        if col is not None and col != 0:
+            return
+        filepaths = self.getChecked()
+        if len(filepaths) > 0:
+            status_text = f"Found {len(filepaths)} eventfile{'s' if len(filepaths) > 1 else ''}. Do you want to load them?"
+        else:
+            status_text = 'Did not find/select any files for specified file mask.'
+        self.statusText.setText(status_text)
+
+    def update_merge_strategy(self):
+        for button in (self.merge_button, self.overwrite_button):
+            if button.isChecked():
+                self.merge_strategy = button.text()
+
+    def connectSignals(self):
+        self._buttonbox.accepted.connect(self.accept)
+        self._buttonbox.rejected.connect(self.reject)
+        self.comboBox.editTextChanged.connect(self.showPaths)
+        self.searchButton.clicked.connect(self.showPaths)
+        self.checkAllButton.clicked.connect(self.toggleCheckAll)
+        self.checkAllButton.clicked.connect(self.update_status)
+        self.tableWidget.cellClicked.connect(self.update_status)
+        self.merge_button.clicked.connect(self.update_merge_strategy)
+        self.overwrite_button.clicked.connect(self.update_merge_strategy)
+
+
 class SingleTextLineDialog(QtWidgets.QDialog):
    def __init__(self, parent=None, label='Text: ', default_text='.xml'):
        super(SingleTextLineDialog, self).__init__(parent)
@ -1659,8 +1868,8 @@ class PhaseDefaults(QtWidgets.QDialog):
 class PickDlg(QDialog):
    update_picks = QtCore.Signal(dict)

-    def __init__(self, parent=None, data=None, station=None, network=None, location=None, picks=None,
-                 autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None,
+    def __init__(self, parent=None, data=None, data_compare=None, station=None, network=None, location=None, picks=None,
+                 autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, show_comp_data=False,
                 event=None, filteroptions=None, model=None, wftype=None):
        super(PickDlg, self).__init__(parent, Qt.Window)
        self.orig_parent = parent
@ -1669,6 +1878,7 @@ class PickDlg(QDialog):
        # initialize attributes
        self.parameter = parameter
        self._embedded = embedded
+        self.showCompData = show_comp_data
        self.station = station
        self.network = network
        self.location = location
@ -1707,22 +1917,6 @@ class PickDlg(QDialog):
        else:
            self.filteroptions = FILTERDEFAULTS
        self.pick_block = False
-        self.nextStation = QtWidgets.QCheckBox('Continue with next station ')
-
-        # comparison channel
-        self.compareChannel = QtWidgets.QComboBox()
-        self.compareChannel.activated.connect(self.resetPlot)
-
-        # scale channel
-        self.scaleChannel = QtWidgets.QComboBox()
-        self.scaleChannel.activated.connect(self.resetPlot)
-
-        # initialize panning attributes
-        self.press = None
-        self.xpress = None
-        self.ypress = None
-        self.cur_xlim = None
-        self.cur_ylim = None

        # set attribute holding data
        if data is None or not data:
@ -1735,6 +1929,31 @@ class PickDlg(QDialog):
                raise Exception(errmsg)
        else:
            self.data = data
+        self.data_compare = data_compare
+
+        self.nextStation = QtWidgets.QCheckBox('Continue with next station ')
+
+        # comparison channel
+        self.referenceChannel = QtWidgets.QComboBox()
+        self.referenceChannel.activated.connect(self.resetPlot)
+
+        # comparison channel
+        self.compareCB = QtWidgets.QCheckBox()
+        self.compareCB.setChecked(self.showCompData)
+        self.compareCB.clicked.connect(self.switchCompData)
+        self.compareCB.clicked.connect(self.resetPlot)
+        self.compareCB.setVisible(bool(self.data_compare))
+
+        # scale channel
+        self.scaleChannel = QtWidgets.QComboBox()
+        self.scaleChannel.activated.connect(self.resetPlot)
+
+        # initialize panning attributes
+        self.press = None
+        self.xpress = None
+        self.ypress = None
+        self.cur_xlim = None
+        self.cur_ylim = None

        self.stime, self.etime = full_range(self.getWFData())

@ -1747,12 +1966,12 @@ class PickDlg(QDialog):
        self.setupUi()

        # fill compare and scale channels
-        self.compareChannel.addItem('-', None)
+        self.referenceChannel.addItem('-', None)
        self.scaleChannel.addItem('individual', None)

        for trace in self.getWFData():
            channel = trace.stats.channel
-            self.compareChannel.addItem(channel, trace)
+            self.referenceChannel.addItem(channel, trace)
            if not channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
                print('Skipping unknown channel for scaling: {}'.format(channel))
                continue
@ -1769,7 +1988,7 @@ class PickDlg(QDialog):
        if self.wftype is not None:
            title += ' | ({})'.format(self.wftype)

-        self.multicompfig.plotWFData(wfdata=self.getWFData(),
+        self.multicompfig.plotWFData(wfdata=self.getWFData(), wfdata_compare=self.getWFDataComp(),
                                     title=title)

        self.multicompfig.setZoomBorders2content()
@ -1786,7 +2005,7 @@ class PickDlg(QDialog):

        # init expected picks using obspy Taup
        try:
-            if self.metadata and model is not None:
+            if self.metadata and model != "None":
                self.model = TauPyModel(model)
                self.get_arrivals()
                self.drawArrivals()
@ -1945,8 +2164,11 @@ class PickDlg(QDialog):
        _dialtoolbar.addWidget(est_label)
        _dialtoolbar.addWidget(self.plot_arrivals_button)
        _dialtoolbar.addSeparator()
-        _dialtoolbar.addWidget(QtWidgets.QLabel('Compare to channel: '))
-        _dialtoolbar.addWidget(self.compareChannel)
+        _dialtoolbar.addWidget(QtWidgets.QLabel('Plot reference channel: '))
+        _dialtoolbar.addWidget(self.referenceChannel)
+        _dialtoolbar.addSeparator()
+        _dialtoolbar.addWidget(QtWidgets.QLabel('Compare: '))
+        _dialtoolbar.addWidget(self.compareCB)
        _dialtoolbar.addSeparator()
        _dialtoolbar.addWidget(QtWidgets.QLabel('Scaling: '))
        _dialtoolbar.addWidget(self.scaleChannel)
@ -2031,10 +2253,12 @@ class PickDlg(QDialog):
        station_id = trace.get_id()
        starttime = trace.stats.starttime
        station_coords = self.metadata.get_coordinates(station_id, starttime)
+        if not station_coords:
+            print('get_arrivals: No station coordinates found. Return!')
+            return
        origins = self.pylot_event.origins
        if phases == ['None', 'None']:
-            print("get_arrivals: Creation info (manual or auto) not available!")
-            print("Return!")
+            print("get_arrivals: Creation info (manual or auto) not available! Return!")
            return
        if origins:
            source_origin = origins[0]
@ -2146,7 +2370,7 @@ class PickDlg(QDialog):

                # create action and add to menu
                # phase name transferred using lambda function
-                slot = lambda phase=phase, phaseID=phaseID: phaseSelect[phaseID](phase)
+                slot = lambda ph=phase, phID=phaseID: phaseSelect[phID](ph)
                picksAction = createAction(parent=self, text=phase,
                                           slot=slot,
                                           shortcut=shortcut)
@ -2281,7 +2505,7 @@ class PickDlg(QDialog):
    def activatePicking(self):
        self.leave_rename_phase()
        self.renamePhaseAction.setEnabled(False)
-        self.compareChannel.setEnabled(False)
+        self.referenceChannel.setEnabled(False)
        self.scaleChannel.setEnabled(False)
        phase = self.currentPhase
        phaseID = self.getPhaseID(phase)
@ -2313,7 +2537,7 @@ class PickDlg(QDialog):
        self.disconnectPressEvent()
        self.multicompfig.connectEvents()
        self.renamePhaseAction.setEnabled(True)
-        self.compareChannel.setEnabled(True)
+        self.referenceChannel.setEnabled(True)
        self.scaleChannel.setEnabled(True)
        self.connect_pick_delete()
        self.draw()
@ -2386,6 +2610,12 @@ class PickDlg(QDialog):
    def getWFData(self):
        return self.data

+    def getWFDataComp(self):
+        if self.showCompData:
+            return self.data_compare
+        else:
+            return Stream()
+
    def selectWFData(self, channel):
        component = channel[-1].upper()
        wfdata = Stream()
@ -2507,24 +2737,33 @@ class PickDlg(QDialog):

        stime = self.getStartTime()

-        # copy data for plotting
-        data = self.getWFData().copy()
-        data = self.getPickPhases(data, phase)
-        data.normalize()
-        if not data:
+        # copy wfdata for plotting
+        wfdata = self.getWFData().copy()
+        wfdata_comp = self.getWFDataComp().copy()
+        wfdata = self.getPickPhases(wfdata, phase)
+        wfdata_comp = self.getPickPhases(wfdata_comp, phase)
+        for wfd in [wfdata, wfdata_comp]:
+            if wfd:
+                wfd.normalize()
+
+        if not wfdata:
            QtWidgets.QMessageBox.warning(self, 'No channel to plot',
-                                          'No channel to plot for phase: {}.'.format(phase))
+                                          'No channel to plot for phase: {}. '
+                                          'Make sure to select the correct channels for P and S '
+                                          'in the menu in the top panel.'.format(phase))
            self.leave_picking_mode()
            return

-        # filter data and trace on which is picked prior to determination of SNR
+        # filter wfdata and trace on which is picked prior to determination of SNR
        filterphase = self.currentFilterPhase()
        if filterphase:
            filteroptions = self.getFilterOptions(filterphase).parseFilterOptions()
            try:
-                data.detrend('linear')
-                data.filter(**filteroptions)
-                # wfdata.filter(**filteroptions)# MP MP removed filtering of original data
+                for wfd in [wfdata, wfdata_comp]:
+                    if wfd:
+                        wfd.detrend('linear')
+                        wfd.filter(**filteroptions)
+                # wfdata.filter(**filteroptions)# MP MP removed filtering of original wfdata
            except ValueError as e:
                self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information,
                                                 'Denied',
@ -2534,8 +2773,8 @@ class PickDlg(QDialog):
        snr = []
        noiselevels = {}
        # determine SNR and noiselevel
-        for trace in data.traces:
-            st = data.select(channel=trace.stats.channel)
+        for trace in wfdata.traces:
+            st = wfdata.select(channel=trace.stats.channel)
            stime_diff = trace.stats.starttime - stime
            result = getSNR(st, (noise_win, gap_win, signal_win), ini_pick - stime_diff)
            snr.append(result[0])
@ -2546,12 +2785,14 @@ class PickDlg(QDialog):
                noiselevel = nfac
            noiselevels[trace.stats.channel] = noiselevel

-        # prepare plotting of data
-        for trace in data:
+        # prepare plotting of wfdata
+        for wfd in [wfdata, wfdata_comp]:
+            if wfd:
+                for trace in wfd:
                    t = prep_time_axis(trace.stats.starttime - stime, trace)
                    inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
                    trace = demeanTrace(trace, inoise)
-            # upscale trace data in a way that each trace is vertically zoomed to noiselevel*factor
+                    # upscale trace wfdata in a way that each trace is vertically zoomed to noiselevel*factor
                    channel = trace.stats.channel
                    noiselevel = noiselevels[channel]
                    noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.)
@ -2562,7 +2803,7 @@ class PickDlg(QDialog):
        x_res = getResolutionWindow(mean_snr, parameter.get('extent'))

        xlims = [ini_pick - x_res, ini_pick + x_res]
-        ylims = list(np.array([-.5, .5]) + [0, len(data) - 1])
+        ylims = list(np.array([-.5, .5]) + [0, len(wfdata) - 1])

        title = self.getStation() + ' picking mode'
        title += ' | SNR: {}'.format(mean_snr)
@ -2570,9 +2811,10 @@ class PickDlg(QDialog):
            filtops_str = transformFilteroptions2String(filteroptions)
            title += ' | Filteroptions: {}'.format(filtops_str)

-        plot_additional = bool(self.compareChannel.currentText())
-        additional_channel = self.compareChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=data,
+        plot_additional = bool(self.referenceChannel.currentText())
+        additional_channel = self.referenceChannel.currentText()
+        self.multicompfig.plotWFData(wfdata=wfdata,
+                                     wfdata_compare=wfdata_comp,
                                     title=title,
                                     zoomx=xlims,
                                     zoomy=ylims,
@ -2653,7 +2895,7 @@ class PickDlg(QDialog):
            minFMSNR = parameter.get('minFMSNR')
            quality = get_quality_class(spe, parameter.get('timeerrorsP'))
            if quality <= minFMweight and snr >= minFMSNR:
-                FM = fmpicker(self.getWFData().select(channel=channel), wfdata, parameter.get('fmpickwin'),
+                FM = fmpicker(self.getWFData().select(channel=channel).copy(), wfdata.copy(), parameter.get('fmpickwin'),
                              pick - stime_diff)

        # save pick times for actual phase
@ -2963,7 +3205,8 @@ class PickDlg(QDialog):
        self.cur_xlim = self.multicompfig.axes[0].get_xlim()
        self.cur_ylim = self.multicompfig.axes[0].get_ylim()
        # self.multicompfig.updateCurrentLimits()
-        data = self.getWFData().copy()
+        wfdata = self.getWFData().copy()
+        wfdata_comp = self.getWFDataComp().copy()
        title = self.getStation()
        if filter:
            filtoptions = None
@ -2971,19 +3214,22 @@ class PickDlg(QDialog):
                filtoptions = self.getFilterOptions(self.getPhaseID(phase), gui_filter=True).parseFilterOptions()

            if filtoptions is not None:
-                data.detrend('linear')
-                data.taper(0.02, type='cosine')
-                data.filter(**filtoptions)
+                for wfd in [wfdata, wfdata_comp]:
+                    if wfd:
+                        wfd.detrend('linear')
+                        wfd.taper(0.02, type='cosine')
+                        wfd.filter(**filtoptions)
                filtops_str = transformFilteroptions2String(filtoptions)
                title += ' | Filteroptions: {}'.format(filtops_str)

        if self.wftype is not None:
            title += ' | ({})'.format(self.wftype)

-        plot_additional = bool(self.compareChannel.currentText())
-        additional_channel = self.compareChannel.currentText()
+        plot_additional = bool(self.referenceChannel.currentText())
+        additional_channel = self.referenceChannel.currentText()
        scale_channel = self.scaleChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=data, title=title,
+        self.multicompfig.plotWFData(wfdata=wfdata, wfdata_compare=wfdata_comp,
+                                     title=title,
                                     zoomx=self.getXLims(),
                                     zoomy=self.getYLims(),
                                     plot_additional=plot_additional,
@ -3056,6 +3302,9 @@ class PickDlg(QDialog):
        self.resetZoom()
        self.refreshPlot()

+    def switchCompData(self):
+        self.showCompData = self.compareCB.isChecked()
+
    def refreshPlot(self):
        if self.autoFilterAction.isChecked():
            self.filterActionP.setChecked(False)
@ -3566,8 +3815,9 @@ class TuneAutopicker(QWidget):
            # wfdat = remove_underscores(wfdat)
            # rotate misaligned stations to ZNE
            # check for gaps and doubled channels
-            wfdat, gaps = merge_stream(wfdat)
-            # check4gaps(wfdat)
+            wfdat, _ = check_for_gaps_and_merge(wfdat)
+            # check for nans
+            check_for_nan(wfdat)
            check4doubled(wfdat)
            wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
            # trim station components to same start value
@ -3611,14 +3861,14 @@ class TuneAutopicker(QWidget):
        self.listWidget.scrollToBottom()

    def get_current_event(self):
-        path = self.eventBox.currentText()
+        path = self.get_current_event_fp()
        return self.parent().project.getEventFromPath(path)

    def get_current_event_name(self):
-        return self.eventBox.currentText().split('/')[-1].split('*')[0]
+        return self.eventBox.currentText().split('/')[-1].rstrip('*')

    def get_current_event_fp(self):
-        return self.eventBox.currentText().split('*')[0]
+        return self.eventBox.currentText().rstrip('*')

    def get_current_event_picks(self, station):
        event = self.get_current_event()
@ -3666,11 +3916,13 @@ class TuneAutopicker(QWidget):
            location = None

        wfdata = self.data.getWFData()
+        wfdata_comp = self.data.getWFDataComp()
        metadata = self.parent().metadata
        event = self.get_current_event()
        filteroptions = self.parent().filteroptions
        wftype = self.wftype if self.obspy_dmt else ''
        self.pickDlg = PickDlg(self.parent(), data=wfdata.select(station=station).copy(),
+                               data_comp=wfdata_comp.select(station=station).copy(),
                               station=station, network=network,
                               location=location, parameter=self.parameter,
                               picks=self.get_current_event_picks(station),
@ -3722,6 +3974,7 @@ class TuneAutopicker(QWidget):
        st = self.data.getWFData()
        tr = st.select(station=self.get_current_station())[0]
        starttime = tr.stats.starttime
+        # create two lists with figure names and subindices (for subplots) to get the correct axes
        p_axes = [
            ('mainFig', 0),
            ('aicFig', 0),
@ -3754,7 +4007,7 @@ class TuneAutopicker(QWidget):
            self.plot_manual_pick_to_ax(ax=ax, picks=picks, phase='S',
                                        starttime=starttime, quality=qualitySpick)
        for canvas in self.parent().canvas_dict.values():
-            canvas.draw()
+            canvas.draw_idle()

    def plot_manual_pick_to_ax(self, ax, picks, phase, starttime, quality):
        mpp = picks[phase]['mpp'] - starttime
@ -5666,7 +5919,7 @@ class ChooseWaveFormWindow(QWidget):
        #self.currentSpectro = self.traces[
        #    self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
        #self.currentSpectro.show()
-        applyFFT()
+        self.applyFFT()

    def applyFFT(self, trace):
        tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']
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	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