Merge branch 'feature/dae' into develop

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

PyLoT.py

@@ -25,6 +25,7 @@ https://www.iconfinder.com/iconsets/flavour
 
 import argparse
 import json
+import logging
 import os
 import platform
 import shutil
@@ -60,7 +61,7 @@ except ImportError:
     from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
 
-from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude, calcsourcespec
+from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude
 from pylot.core.io.data import Data
 from pylot.core.io.inputs import FilterOptions, PylotParameter
 from autoPyLoT import autoPyLoT
@@ -84,7 +85,7 @@ from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
     PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
     ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
     CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget, PickQualitiesFromXml, \
-    SourceSpecWindow, ChooseWaveFormWindow
+    SpectrogramTab, SearchFileByExtensionDialog
 from pylot.core.util.array_map import Array_map
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import Thread, Worker
@@ -113,11 +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 infile and os.path.isfile(infile) is False:
-        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:
             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
 
@@ -496,7 +494,6 @@ class MainWindow(QMainWindow):
                                                       icon=eventlist_xml_icon,
                                                       tip='Create an Eventlist from a XML File')
         self.eventlist_xml_action.setEnabled(False)
-
         printAction = self.createAction(self, "&Print event ...",
                                         self.show_event_information, QKeySequence.Print,
                                         print_icon,
@@ -509,6 +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)
@@ -698,14 +697,17 @@ class MainWindow(QMainWindow):
         wf_tab = QtWidgets.QWidget(self)
         array_tab = QtWidgets.QWidget(self)
         events_tab = QtWidgets.QWidget(self)
+        spectro_tab = QtWidgets.QWidget(self)
 
         # init main widgets layouts
         self.wf_layout = QtWidgets.QVBoxLayout()
         self.array_layout = QtWidgets.QVBoxLayout()
         self.events_layout = QtWidgets.QVBoxLayout()
+        self.spectro_layout = QtWidgets.QVBoxLayout()
         wf_tab.setLayout(self.wf_layout)
         array_tab.setLayout(self.array_layout)
         events_tab.setLayout(self.events_layout)
+        spectro_tab.setLayout(self.spectro_layout)
 
         # tighten up layouts inside tabs
         for layout in [self.wf_layout, self.array_layout, self.events_layout]:
@@ -716,12 +718,14 @@ class MainWindow(QMainWindow):
         self.tabs.addTab(wf_tab, 'Waveform Plot')
         self.tabs.addTab(array_tab, 'Array Map')
         self.tabs.addTab(events_tab, 'Eventlist')
+        self.tabs.addTab(spectro_tab, 'Spectro')
 
         self.wf_layout.addWidget(self.no_data_label)
         self.wf_layout.addWidget(self.wf_scroll_area)
         self.wf_scroll_area.setWidgetResizable(True)
         self.init_array_tab()
         self.init_event_table()
+        self.init_spectro_tab()
         self.tabs.setCurrentIndex(0)
 
         self.eventLabel = QLabel()
@@ -734,16 +738,13 @@ class MainWindow(QMainWindow):
         _widget.setLayout(self._main_layout)
         _widget.showFullScreen()
 
-        self.logwidget = LogWidget(parent=None)
+
         if use_logwidget:
+            self.logwidget = LogWidget(parent=None)
             self.logwidget.show()
             self.stdout = self.logwidget.stdout
             self.stderr = self.logwidget.stderr
 
-            # Not sure why but the lines above kept messing with the Ouput even with use_logwidget disabled
-            sys.stdout = self.stdout
-            sys.stderr = self.stderr
-
         self.setCentralWidget(_widget)
 
         # Need to store PickQualities Window somewhere so it doesnt disappear
@@ -1003,18 +1004,17 @@ class MainWindow(QMainWindow):
             return
         refresh = False
         events = self.project.eventlist
-        sld = SingleTextLineDialog(label='Specify file extension: ', default_text='.xml')
+        sld = SearchFileByExtensionDialog(label='Specify file extension: ', default_text='.xml',
+                                          events=events)
         if not sld.exec_():
             return
-        fext = sld.lineEdit.text()
+
-        # fext = '.xml'
+        filenames = sld.getChecked()
         for event in events:
-            path = event.path
+            for filename in filenames:
-            eventname = path.split('/')[-1]  # or event.pylot_id
+                if os.path.isfile(filename) and event.pylot_id in filename:
-            filename = os.path.join(path, 'PyLoT_' + eventname + fext)
+                    self.load_data(filename, draw=False, event=event, ask_user=True, merge_strategy=sld.merge_strategy)
-            if os.path.isfile(filename):
+                    refresh = True
-                self.load_data(filename, draw=False, event=event, overwrite=True)
-                refresh = True
         if not refresh:
             return
         if self.get_current_event().pylot_picks:
@@ -1022,8 +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):
+    def load_data(self, fname=None, loc=False, draw=True, event=None, ask_user=False, merge_strategy='Overwrite'):
-        if not overwrite:
+        if not ask_user:
             if not self.okToContinue():
                 return
         if fname is None:
@@ -1037,9 +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
-            # 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(
@@ -1127,16 +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')
@@ -1381,7 +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()
@@ -1401,25 +1407,28 @@ class MainWindow(QMainWindow):
 
         for id, event in enumerate(self.project.eventlist):
             event_path = event.path
-            phaseErrors = {'P': self._inputs['timeerrorsP'],
+            #phaseErrors = {'P': self._inputs['timeerrorsP'],
-                           'S': self._inputs['timeerrorsS']}
+            #               'S': self._inputs['timeerrorsS']}
 
-            ma_props = {'manual': event.pylot_picks,
+            man_au_picks = {'manual': event.pylot_picks,
-                        'auto': event.pylot_autopicks}
+                            'auto': event.pylot_autopicks}
-            ma_count = {'manual': 0,
+            npicks = {'manual': {'P': 0, 'S': 0},
-                        'auto': 0}
+                      'auto': {'P': 0, 'S': 0}}
-            ma_count_total = {'manual': 0,
+            npicks_total = {'manual': {'P': 0, 'S': 0},
-                              'auto': 0}
+                            'auto': {'P': 0, 'S': 0}}
 
-            for ma in ma_props.keys():
+            for ma in man_au_picks.keys():
-                if ma_props[ma]:
+                if man_au_picks[ma]:
-                    for picks in ma_props[ma].values():
+                    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
+                                npicks[ma][phase_ID] += 1
-                            ma_count_total[ma] += 1
+                            npicks_total[ma][phase_ID] += 1
 
             event_ref = event.isRefEvent()
             event_test = event.isTestEvent()
@@ -1454,16 +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:
@@ -1678,20 +1694,20 @@ class MainWindow(QMainWindow):
 
     def pickQualities(self):
         path = self.get_current_event_path()
-        (_, _, plot) = getQualitiesfromxml(path, self._inputs.get('timeerrorsP'), self._inputs.get('timeerrorsS'),plotflag=1)
+        (_, plot) = getQualitiesfromxml(path, self._inputs.get('timeerrorsP'), self._inputs.get('timeerrorsS'),plotflag=1)
         self.pickQualitiesWindow = PickQualitiesFromXml(figure=plot, path=self.get_current_event_path(),inputVar=self._inputs)
         self.pickQualitiesWindow.showUI()
         return 
 
     # WIP JG
-    def eventlistXml2(self):
+    def eventlistXml(self):
         path = self._inputs['rootpath'] + '/' + self._inputs['datapath'] + '/' + self._inputs['database']
         outpath = self.project.location[:self.project.location.rfind('/')]
         geteventlistfromxml(path, outpath)
         return
 
-    # WIP JG
+        # WIP JG
-    def eventlistXml(self):
+    def spectogramView(self):
         global test
         stations = []
         names = []
@@ -1706,12 +1722,25 @@ class MainWindow(QMainWindow):
             for tr in self.get_data().wfdata.select(component=ch).traces:
                 traces[tr.stats.station][ch] = tr
 
-
         names.sort()
         a = self.get_current_event()
-        test = ChooseWaveFormWindow(WaveForms=names, traces=traces, stream=self.get_data())
+
-        #self.get_data().wfdata.spectrogram()
+        print (self.get_data().wfdata.traces[0])
-        test.show()
+
+        test = SpectrogramTab(traces, self.get_data().wfdata)
+        height = self.tabs.widget(0).height()
+        width = self.tabs.widget(0).width()
+        self.tabs.setCurrentIndex(3)
+        figCanvas = test.makeSpecFig(direction=self.dispComponent, height = height, width = width, parent = self.tabs.widget)
+        return figCanvas
+        #self.spectro_layout.addWidget()
+        # self.get_data().wfdata.spectrogram()
+        # self.tabs.addTab(figCanvas, 'Spectrogram')
+        # self.tabs[3] = figCanvas
+        # self.refreshTabs()
+        # test.show()
+
+
 
     def compareMulti(self):
         if not self.compareoptions:
@@ -1871,6 +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()
@@ -1898,6 +1928,12 @@ class MainWindow(QMainWindow):
                     self.newWF(plot=False)
                 self.update_obspy_dmt()
                 self.refresh_array_map()
+        if self.tabs.currentIndex() == 3:
+            if self.spectroWidget != None:
+                self.spectro_layout.removeWidget(self.spectroWidget)
+            newSpectroWidget = self.spectogramView()
+            self.spectro_layout.addWidget(newSpectroWidget)
+            self.spectroWidget = newSpectroWidget
 
     def newWF(self, event=None, plot=True):
         '''
@@ -1928,13 +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):
         '''
@@ -1949,6 +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?')
@@ -1965,7 +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,
@@ -1973,7 +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):
@@ -1981,8 +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():
+                if self.dataPlot.comp_checkbox.isChecked():
-                    self.fnames_syn = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
+                    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():
@@ -2104,7 +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)
@@ -2155,6 +2200,7 @@ class MainWindow(QMainWindow):
             self.locateEventAction.setEnabled(True)
             self.qualities_action.setEnabled(True)
             self.eventlist_xml_action.setEnabled(True)
+
         if True in self.comparable.values():
             self.compare_action.setEnabled(True)
         self.draw()
@@ -2262,7 +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:
@@ -2277,8 +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 ([], [])
+        plots = rval if rval else []
-        return plots, gaps
+        return plots
 
     def adjustPlotHeight(self):
         if self.pg:
@@ -2574,18 +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()
@@ -2964,10 +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:
@@ -3128,7 +3183,7 @@ class MainWindow(QMainWindow):
         phasefile = os.path.join(obsdir, filename + '.obs')
         lt.modify_inputs(ctrfile, locroot, filename, phasefile, ttt)
         try:
-            lt.locate(ctrfile, self.obspy_dmt)
+            lt.locate(ctrfile, self._inputs)
         except RuntimeError as e:
             print(e.message)
         # finally:
@@ -3182,7 +3237,7 @@ class MainWindow(QMainWindow):
         '''
         if checked: pass  # dummy argument for QAction trigger signal
         self.tabs.setCurrentIndex(1)
-        # if there is no metadata (invetories is an empty list), just initialize the default empty tab
+        # if there is no metadata (inventories is an empty list), just initialize the default empty tab
         if not self.metadata.inventories:
             self.init_array_tab()
             return
@@ -3204,6 +3259,15 @@ class MainWindow(QMainWindow):
         self.tabs.setCurrentIndex(index)
         self.refresh_array_map()
 
+    def init_spectro_tab(self):
+        '''
+        Init spectrogram tab with currently selected event.
+        '''
+        self.spectroWidget = None
+        #self.spectro_layout.addWidget( self.spectogramView() )
+        pass
+
+
     def array_map_thread(self):
         '''
         Start modal thread to init the array_map object.
@@ -3426,7 +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)
@@ -3600,7 +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:
@@ -3653,10 +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))
@@ -3774,7 +3841,8 @@ class MainWindow(QMainWindow):
 
     def closeEvent(self, event):
         if self.okToContinue():
-            self.logwidget.close()
+            if hasattr(self, 'logwidget'):
+                self.logwidget.close()
             event.accept()
         else:
             event.ignore()

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
 

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:
-            parameter = PylotParameter(inputfile)
+            print('Using default input parameter')
-            # iplot = parameter['iplot']
+        parameter = PylotParameter(inputfile)
-        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)))

autopylot.sh

@@ -3,8 +3,10 @@
 #$ -l low
 #$ -cwd
 #$ -pe smp 40
-#$ -l mem=2G
+##$ -l mem=3G
-#$ -l h_vmem=2G
+#$ -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

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

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)

pylot/core/io/data.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import copy
+import logging
 import os
 
 from PySide2.QtWidgets import QMessageBox
@@ -19,7 +20,7 @@ from pylot.core.util.errors import FormatError, OverwriteError
 from pylot.core.util.event import Event
 from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
 from pylot.core.util.utils import fnConstructor, full_range, check4rotated, \
-    check4gapsAndMerge, trim_station_components
+    check_for_gaps_and_merge, trim_station_components, check_for_nan
 
 
 class Data(object):
@@ -64,7 +65,7 @@ class Data(object):
                     elif 'LOC' in evtdata:
                         raise NotImplementedError('PILOT location information '
                                                   'read support not yet '
-                                                  'implemeted.')
+                                                  'implemented.')
                     elif 'event.pkl' in evtdata:
                         evtdata = qml_from_obspyDMT(evtdata)
                     else:
@@ -260,7 +261,6 @@ class Data(object):
         can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
         """
         from pylot.core.util.defaults import OUTPUTFORMATS
-
         if not type(fcheck) == list:
             fcheck = [fcheck]
 
@@ -321,35 +321,61 @@ class Data(object):
             if lendiff != 0:
                 print("Manual as well as automatic picks available. Prefered the {} manual ones!".format(lendiff))
 
+
+            no_uncertainties_p = []
+            no_uncertainties_s = []
             if upperErrors:
                 # check for pick uncertainties exceeding adjusted upper errors
                 # Picks with larger uncertainties will not be saved in output file!
                 for j in range(len(picks)):
                     for i in range(len(picks_copy)):
                         if picks_copy[i].phase_hint[0] == 'P':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]) or \
+                            # Skipping pick if no upper_uncertainty is found and warning user
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
+                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
+                                #print("{1} P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
+                                 #   picks_copy[i].waveform_id.station_code,
+                                  #  picks_copy[i].method_id))
+                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_p:
+                                    no_uncertainties_p.append(picks_copy[i].waveform_id.station_code)
+                                continue
+
+                            #print ("checking for upper_uncertainty")
+                            if  (picks_copy[i].time_errors['uncertainty'] is None) or \
+                                    (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]):
                                 print("Uncertainty exceeds or equal adjusted upper time error!")
                                 print("Adjusted uncertainty: {}".format(upperErrors[0]))
                                 print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
                                 print("{1} P-Pick of station {0} will not be saved in outputfile".format(
                                     picks_copy[i].waveform_id.station_code,
                                     picks_copy[i].method_id))
-                                print("#")
                                 del picks_copy[i]
                                 break
                         if picks_copy[i].phase_hint[0] == 'S':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]) or \
+
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
+                            # Skipping pick if no upper_uncertainty is found and warning user
+                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
+                                #print("{1} S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
+                                    #picks_copy[i].waveform_id.station_code,
+                                    #picks_copy[i].method_id))
+                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_s:
+                                    no_uncertainties_s.append(picks_copy[i].waveform_id.station_code)
+                                continue
+
+
+                            if (picks_copy[i].time_errors['uncertainty'] is None) or \
+                                (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]):
                                 print("Uncertainty exceeds or equal adjusted upper time error!")
                                 print("Adjusted uncertainty: {}".format(upperErrors[1]))
                                 print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
                                 print("{1} S-Pick of station {0} will not be saved in outputfile".format(
                                     picks_copy[i].waveform_id.station_code,
                                     picks_copy[i].method_id))
-                                print("#")
                                 del picks_copy[i]
                                 break
+            for s in no_uncertainties_p:
+                print("P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
+            for s in no_uncertainties_s:
+                print("S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
 
             if fnext == '.obs':
                 try:
@@ -383,18 +409,16 @@ class Data(object):
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '_focmec.in':
                 try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
+                    parameter = PylotParameter()
-                    print('Using default input file {}'.format(infile))
+                    logging.warning('Using default input parameter')
-                    parameter = PylotParameter(infile)
                     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')
+                    parameter = PylotParameter()
-                    print('Using default input file {}'.format(infile))
+                    logging.warning('Using default input parameter')
-                    parameter = PylotParameter(infile)
                     hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
@@ -426,20 +450,30 @@ class Data(object):
         data.filter(**kwargs)
         self.dirty = True
 
-    def setWFData(self, fnames, fnames_syn=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
+    def setWFData(self, fnames, fnames_alt=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
         """
         Clear current waveform data and set given waveform data
         :param fnames: waveform data names to append
+        :param fnames_alt: alternative data to show (e.g. synthetic/processed)
         :type fnames: list
         """
+        def check_fname_exists(filenames: list) -> list:
+            if filenames:
+                filenames = [fn for fn in filenames if os.path.isfile(fn)]
+            return filenames
+
         self.wfdata = Stream()
         self.wforiginal = None
-        self.wfsyn = Stream()
+        self.wf_alt = Stream()
         if tstart == tstop:
             tstart = tstop = None
         self.tstart = tstart
         self.tstop = tstop
 
+        # remove directories
+        fnames = check_fname_exists(fnames)
+        fnames_alt = check_fname_exists(fnames_alt)
+
         # if obspy_dmt:
         #     wfdir = 'raw'
         #     self.processed = False
@@ -457,8 +491,8 @@ class Data(object):
         #     wffnames = fnames
         if fnames is not None:
             self.appendWFData(fnames)
-            if fnames_syn is not None:
+            if fnames_alt is not None:
-                self.appendWFData(fnames_syn, synthetic=True)
+                self.appendWFData(fnames_alt, alternative=True)
         else:
             return False
 
@@ -466,7 +500,9 @@ class Data(object):
         # remove possible underscores in station names
         # self.wfdata = remove_underscores(self.wfdata)
         # check for gaps and merge
-        self.wfdata = check4gapsAndMerge(self.wfdata)
+        self.wfdata, _ = check_for_gaps_and_merge(self.wfdata)
+        # check for nans
+        check_for_nan(self.wfdata)
         # check for stations with rotated components
         if checkRotated and metadata is not None:
             self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)
@@ -478,7 +514,7 @@ class Data(object):
         self.dirty = False
         return True
 
-    def appendWFData(self, fnames, synthetic=False):
+    def appendWFData(self, fnames, alternative=False):
         """
         Read waveform data from fnames and append it to current wf data
         :param fnames: waveform data to append
@@ -491,20 +527,20 @@ class Data(object):
         if self.dirty:
             self.resetWFData()
 
-        real_or_syn_data = {True: self.wfsyn,
+        orig_or_alternative_data = {True: self.wf_alt,
-                            False: self.wfdata}
+                                    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)
+                                                                      endtime=self.tstop)
                     except Exception as e:
                         warnmsg += '{0}\n{1}\n'.format(fname, e)
             except SacIOError as se:
@@ -519,8 +555,8 @@ class Data(object):
     def getOriginalWFData(self):
         return self.wforiginal
 
-    def getSynWFData(self):
+    def getAltWFdata(self):
-        return self.wfsyn
+        return self.wf_alt
 
     def resetWFData(self):
         """

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:
@@ -273,31 +275,28 @@ def picksdict_from_picks(evt):
         phase['epp'] = epp
         phase['lpp'] = lpp
         phase['spe'] = spe
-        try:
+        weight = phase.get('weight')
-            phase['weight'] = weight
+        if not weight:
-        except:
+            if not parameter:
-            # get onset weight from uncertainty
+                logging.warning('Using ')
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
+                logging.warning('Using default input parameter')
-            print('Using default input file {}'.format(infile))
+                parameter = PylotParameter()
-            parameter = PylotParameter(infile)
+            pick.phase_hint = identifyPhase(pick.phase_hint)
             if pick.phase_hint == 'P':
                 errors = parameter['timeerrorsP']
             elif pick.phase_hint == 'S':
                 errors = parameter['timeerrorsS']
-            weight = get_quality_class(spe, errors)
+            if errors:
-            phase['weight'] = weight
+                weight = get_quality_class(spe, errors)
+                phase['weight'] = weight
         phase['channel'] = channel
         phase['network'] = network
         phase['picker'] = pick_method
-        try:
+        if pick.polarity == 'positive':
-            if pick.polarity == 'positive':
+            phase['fm'] = 'U'
-                phase['fm'] = 'U'
+        elif pick.polarity == 'negative':
-            elif pick.polarity == 'negative':
+            phase['fm'] = 'D'
-                phase['fm'] = 'D'
+        else:
-            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 ''
 
@@ -517,7 +516,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets
-            if arrivals[key].has_key('P'):
+            if 'P' in arrivals[key]:
                 try:
                     fm = arrivals[key]['P']['fm']
                 except KeyError as e:
@@ -551,7 +550,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                                                                                            ss_ms,
                                                                                            pweight))
             # S onsets
-            if arrivals[key].has_key('S') and arrivals[key]['S']['mpp'] is not None:
+            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
                 fm = '?'
                 onset = arrivals[key]['S']['mpp']
                 year = onset.year
@@ -670,7 +669,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets
-            if arrivals[key].has_key('P') and arrivals[key]['P']['mpp'] is not None:
+            if 'P' in  arrivals[key] and arrivals[key]['P']['mpp'] is not None:
                 if arrivals[key]['P']['weight'] < 4:
                     Ponset = arrivals[key]['P']['mpp']
                     pyear = Ponset.year
@@ -699,7 +698,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                     fid.write('%-5s P1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n'
                               % (key, pyear, pmonth, pday, phh, pmm, Pss, pstd))
             # S onsets
-            if arrivals[key].has_key('S') and arrivals[key]['S']['mpp'] is not None:
+            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
                 if arrivals[key]['S']['weight'] < 4:
                     Sonset = arrivals[key]['S']['mpp']
                     syear = Sonset.year
@@ -768,7 +767,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         usedarrivals = chooseArrivals(arrivals)
         for key in usedarrivals:
             # P onsets
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                 if usedarrivals[key]['P']['weight'] < 4:
                     n += 1
                     stat = key
@@ -782,7 +781,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                     else:
                         fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))
                         # S onsets
-            if usedarrivals[key].has_key('S'):
+            if 'S' in usedarrivals[key]:
                 if usedarrivals[key]['S']['weight'] < 4:
                     n += 1
                     stat = key
@@ -828,13 +827,13 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         # prefer manual picks
         usedarrivals = chooseArrivals(arrivals)
         for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                 # P onsets
                 if usedarrivals[key]['P']['weight'] < 4:
                     Ponset = usedarrivals[key]['P']['mpp']
                     Prt = Ponset - stime  # onset time relative to source time
                     fid.write('%s    %6.3f  1  P\n' % (key, Prt))
-            if usedarrivals[key].has_key('S'):
+            if 'S' in usedarrivals[key]:
                 # S onsets
                 if usedarrivals[key]['S']['weight'] < 4:
                     Sonset = usedarrivals[key]['S']['mpp']
@@ -879,7 +878,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         # prefer manual picks
         usedarrivals = chooseArrivals(arrivals)
         for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                 if usedarrivals[key]['P']['weight'] < 4 and usedarrivals[key]['P']['fm'] is not None:
                     stat = key
                     for i in range(len(picks)):
@@ -961,7 +960,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         # write phase lines
         for key in arrivals:
-            if arrivals[key].has_key('P'):
+            if 'P' in arrivals[key]:
                 if arrivals[key]['P']['weight'] < 4 and arrivals[key]['P']['fm'] is not None:
                     stat = key
                     ccode = arrivals[key]['P']['channel']
@@ -1014,7 +1013,6 @@ def chooseArrivals(arrivals):
     :return: arrivals but with the manual picks prefered if possible
     """
     # If len of arrivals is greater than 2 it comes from autopicking so only autopicks are available
-    print("=== CHOOSE ===")
     if len(arrivals) > 2:
         return arrivals
     if arrivals['auto'] and arrivals['manual']:

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'    
+    exe_path = os.path.join(parameter['nllocbin'], 'NLLoc')
-    if exe_path is None:
+    if not os.path.isfile(exe_path):
         raise NLLocError('NonLinLoc executable not found; check your '
                          'environment variables')
 

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)

pylot/core/pick/charfuns.py

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

pylot/core/pick/picker.py

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

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

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
+        # try to set to viridis as default
-        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('hsv'))
+        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)
+                wfdata = wfdata.select(station=station)
-                if not data:
+                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,

pylot/core/util/dataprocessing.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import glob
+import logging
 import os
 import sys
 
@@ -189,7 +190,11 @@ class Metadata(object):
         metadata = self.get_metadata(seed_id, time)
         if not metadata:
             return
-        return metadata['data'].get_coordinates(seed_id, time)
+        try:
+            return metadata['data'].get_coordinates(seed_id, time)
+        # no specific exception defined in obspy inventory
+        except Exception as e:
+            logging.warning(f'Could not get metadata for {seed_id}')
 
     def get_all_coordinates(self):
         def stat_info_from_parser(parser):
@@ -271,7 +276,7 @@ class Metadata(object):
                     continue
             invtype, robj = self._read_metadata_file(os.path.join(path_to_inventory, fname))
             try:
-                robj.get_coordinates(station_seed_id)
+                # robj.get_coordinates(station_seed_id)  # TODO: Commented out, failed with Parser, is this needed?
                 self.inventory_files[fname] = {'invtype': invtype,
                                                'data': robj}
                 if station_seed_id in self.seed_ids.keys():

pylot/core/util/generate_array_maps.py

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

pylot/core/util/thread.py

@@ -41,7 +41,8 @@ class Thread(QThread):
             exctype, value = sys.exc_info()[:2]
             self._executedErrorInfo = '{} {} {}'. \
                 format(exctype, value, traceback.format_exc())
-        sys.stdout = self.old_stdout
+        if self.redirect_stdout:
+            sys.stdout = self.old_stdout
 
     def showProgressbar(self):
         if self.progressText:
@@ -159,7 +160,7 @@ class MultiThread(QThread):
         try:
             if not self.ncores:
                 self.ncores = multiprocessing.cpu_count()
-            pool = multiprocessing.Pool(self.ncores)
+            pool = multiprocessing.Pool(self.ncores, maxtasksperchild=1000)
             self.data = pool.map_async(self.func, self.args, callback=self.emitDone)
             # self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned
             pool.close()

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):
-        return True
+        if value > 0. or value > 0:
+            return True
+        else:
+            return False
     else:
-        return False
+        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)

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):
+    def activateObspyDMToptions(self, activate: bool) -> None:
-        self.syn_checkbox.setVisible(activate)
+        self.qcombo_processed.setEnabled(activate)
-        self.qcombo_processed.setVisible(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,
+    def plotWFData(self, wfdata, wfsyn=None, title=None, scaleddata=False, mapping=True,
-                   noiselevel=None, scaleddata=False, mapping=True,
+                   component='*', nth_sample=1, verbosity=0, method='normal', gain=1., shift_syn=0.2):
-                   component='*', nth_sample=1, iniPick=None, verbosity=0,
+        def station_sort(nslc):
-                   method='normal', gain=1.):
+            """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)
+            plot_streams['wfdata']['data'] = wfdata.select(component=component)
-            st_select += wfdata.select(component=alter_comp)
+            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
@@ -1395,44 +1428,48 @@ 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('.')
-            st = st_select.select(id=seed_id)
+            for wf_name, wf_dict in plot_streams.items():
-            trace = st[0].copy()
+                st_select = wf_dict.get('data')
-            if mapping:
+                if not st_select:
-                n = plot_positions[trace.stats.channel]
+                    continue
-            if n > nmax:
+                st = st_select.select(id=seed_id)
-                nmax = n
+                trace = st[0].copy()
-            if verbosity:
+                if mapping:
-                msg = 'plotting %s channel of station %s' % (channel, station)
+                    n = plot_positions[trace.stats.channel]
-                print(msg)
+                if n > nmax:
-            stime = trace.stats.starttime - wfstart
+                    nmax = n
-            time_ax = prep_time_axis(stime, trace)
+                if verbosity:
-            if time_ax is not None:
+                    msg = 'plotting %s channel of station %s' % (channel, station)
-                if scaleToChannel:
+                    print(msg)
-                    st_scale = wfdata.select(channel=scaleToChannel)
+                stime = trace.stats.starttime - wfstart
-                    if st_scale:
+                time_ax = prep_time_axis(stime, trace)
-                        tr = st_scale[0]
+                if time_ax is not None:
+                    if scaleToChannel:
+                        st_scale = wfdata.select(channel=scaleToChannel)
+                        if st_scale:
+                            tr = st_scale[0]
+                            trace.detrend('constant')
+                            trace.normalize(np.max(np.abs(tr.data)) * 2)
+                            scaleddata = True
+                    if not scaleddata:
                         trace.detrend('constant')
-                        trace.normalize(np.max(np.abs(tr.data)) * 2)
+                        trace.normalize(np.max(np.abs(trace.data)) * 2)
-                        scaleddata = True
-                if not scaleddata:
-                    trace.detrend('constant')
-                    trace.normalize(np.max(np.abs(trace.data)) * 2)
 
-                times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
+                    offset = wf_dict.get('offset')
-                data = [datum + n for index, datum in enumerate(trace.data) if not index % nth_sample]
+
-                ax.axhline(n, color="0.5", lw=0.5)
+                    times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
-                ax.plot(times, data, color=linecolor, linewidth=0.7)
+                    data = [datum + n + offset for index, datum in enumerate(trace.data) if not index % nth_sample]
-                if noiselevel is not None:
+                    ax.axhline(n, color="0.5", lw=0.5)
-                    for level in [-noiselevel[channel], noiselevel[channel]]:
+                    ax.plot(times, data, color=wf_dict.get('linecolor'), **wf_dict.get('plot_kwargs'))
-                        ax.plot([time_ax[0], time_ax[-1]],
+                    if noiselevel is not None:
-                                [n + level, n + level],
+                        for level in [-noiselevel[channel], noiselevel[channel]]:
-                                color=linecolor,
+                            ax.plot([time_ax[0], time_ax[-1]],
-                                linestyle='dashed')
+                                    [n + level, n + level],
-                self.setPlotDict(n, seed_id)
+                                    color=wf_dict.get('linecolor'),
+                                    linestyle='dashed')
+                    self.setPlotDict(n, seed_id)
         if plot_additional and additional_channel:
             compare_stream = wfdata.select(channel=additional_channel)
             if compare_stream:
@@ -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,
+    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,
+                 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(QtWidgets.QLabel('Plot reference channel: '))
-        _dialtoolbar.addWidget(self.compareChannel)
+        _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("get_arrivals: Creation info (manual or auto) not available! Return!")
-            print("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
+        # copy wfdata for plotting
-        data = self.getWFData().copy()
+        wfdata = self.getWFData().copy()
-        data = self.getPickPhases(data, phase)
+        wfdata_comp = self.getWFDataComp().copy()
-        data.normalize()
+        wfdata = self.getPickPhases(wfdata, phase)
-        if not data:
+        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')
+                for wfd in [wfdata, wfdata_comp]:
-                data.filter(**filteroptions)
+                    if wfd:
-                # wfdata.filter(**filteroptions)# MP MP removed filtering of original data
+                        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:
+        for trace in wfdata.traces:
-            st = data.select(channel=trace.stats.channel)
+            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])
@@ -2546,23 +2785,25 @@ class PickDlg(QDialog):
                 noiselevel = nfac
             noiselevels[trace.stats.channel] = noiselevel
 
-        # prepare plotting of data
+        # prepare plotting of wfdata
-        for trace in data:
+        for wfd in [wfdata, wfdata_comp]:
-            t = prep_time_axis(trace.stats.starttime - stime, trace)
+            if wfd:
-            inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
+                for trace in wfd:
-            trace = demeanTrace(trace, inoise)
+                    t = prep_time_axis(trace.stats.starttime - stime, trace)
-            # upscale trace data in a way that each trace is vertically zoomed to noiselevel*factor
+                    inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
-            channel = trace.stats.channel
+                    trace = demeanTrace(trace, inoise)
-            noiselevel = noiselevels[channel]
+                    # upscale trace wfdata in a way that each trace is vertically zoomed to noiselevel*factor
-            noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.)
+                    channel = trace.stats.channel
-            trace.data *= noiseScaleFactor
+                    noiselevel = noiselevels[channel]
-            noiselevels[channel] *= noiseScaleFactor
+                    noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.)
+                    trace.data *= noiseScaleFactor
+                    noiselevels[channel] *= noiseScaleFactor
 
         mean_snr = np.mean(snr)
         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())
+        plot_additional = bool(self.referenceChannel.currentText())
-        additional_channel = self.compareChannel.currentText()
+        additional_channel = self.referenceChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=data,
+        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')
+                for wfd in [wfdata, wfdata_comp]:
-                data.taper(0.02, type='cosine')
+                    if wfd:
-                data.filter(**filtoptions)
+                        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())
+        plot_additional = bool(self.referenceChannel.currentText())
-        additional_channel = self.compareChannel.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)
+            wfdat, _ = check_for_gaps_and_merge(wfdat)
-            # check4gaps(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
@@ -5663,9 +5916,23 @@ class ChooseWaveFormWindow(QWidget):
     def submit(self):
         matplotlib.pyplot.close(self.currentSpectro)
         t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
-        self.currentSpectro = self.traces[
+        #self.currentSpectro = self.traces[
-            self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
+        #    self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
-        self.currentSpectro.show()
+        #self.currentSpectro.show()
+        self.applyFFT()
+
+    def applyFFT(self, trace):
+        tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']
+        transformed = abs(np.fft.rfft(tra.data))
+        print ( transformed )
+        matplotlib.pyplot.plot ( transformed )
+        matplotlib.pyplot.show()
+
+    def applyFFTs(self, tra):
+        transformed = abs(np.fft.rfft(tra.data))
+        print ( transformed )
+        matplotlib.pyplot.plot ( transformed )
+        matplotlib.pyplot.show()
 
     def submitN(self):
         matplotlib.pyplot.close(self.currentSpectro)
@@ -5681,13 +5948,6 @@ class ChooseWaveFormWindow(QWidget):
             self.chooseBoxTraces.currentText()[3:]]['E'].spectrogram(show=False, title=t)
         self.currentSpectro.show()
 
-    def submitZ(self):
-        matplotlib.pyplot.close(self.currentSpectro)
-        t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
-        self.currentSpectro = self.traces[
-            self.chooseBoxTraces.currentText()[3:]]['Z'].spectrogram(show=False, title=t)
-        self.currentSpectro.show()
-
     # Creates a QComboBox and adds all traces provided
     def createComboBoxTraces(self):
         if len(self.wFs) <= 0:
@@ -5714,7 +5974,87 @@ class ChooseWaveFormWindow(QWidget):
         pass
 
 
+class SpectrogramTab(QWidget):
+    def __init__(self, traces, wfdata, parent=None):
+        super(SpectrogramTab, self).__init__(parent)
+        self.setupUi()
+        self.traces = traces
+        self.wfdata = wfdata
+
+    def setupUi(self):
+        pass
+    def makeSpecFig(self, direction = 'Z', height = 0, width = 0, parent = None):
+
+        i = 0
+        grams = []
+        figure, axis = matplotlib.pyplot.subplots(len(self.traces), sharex=True)
+
+        start, end = full_range(self.wfdata)
+
+        if height != 0 and width != 0:
+            figure.figsize = (width, height)
+            figure.set_figwidth = width
+            figure.set_figheight = height
+
+        #figure.tight_layout()
+
+        for t in self.traces:
+            tra = self.traces[t][direction]
+            #print(start, end)
+
+            # Set Title
+            if i == 0:
+                if direction == 'Z':
+                    figure.suptitle("section: vertical components")
+                elif direction == 'E':
+                    figure.suptitle("section: east-west components")
+                elif direction == 'N':
+                    figure.suptitle("section: north-south components")
+                axis[i].vlines(0, axis[i].get_ylim()[0], axis[i].get_ylim()[1],
+                          colors='m', linestyles='dashed',
+                          linewidth=2)
+
+            # Different axis settings for visual improvements
+            # axis[i].set_xlim(left=0, right=end - start)
+            # axis[i].spines['top'].set_visible(False)
+            # axis[i].spines['right'].set_visible(False)
+            # # axis[i].spines['left'].set_visible(False)
+
+            # axis[i].tick_params(axis='x', which='both', bottom=False, top=False, labelbottom=False)
+            # if not (len(self.traces) == i - 1):
+                # axis[i].spines['bottom'].set_visible(False)
+            # axis[i].set_yticks([])
+            # axis[i].set_ylabel(t, loc='center', rotation='horizontal')
+
+            #ax.axhline(n, color="0.5", lw=0.5)
+
+
+            grams.append(tra.spectrogram(show=False, axes=axis[i]))
+            i+=1
+
+        #figure.setXLims([0, end - start])
+        figure.set_tight_layout(True)
+        fC = FigureCanvas(figure)
+        return fC
+
+    #for t in self.traces:
+       # tra = self.traces[t]['Z']
+       # transformed = abs(np.fft.rfft(tra.data))
+       # axis[i].plot(transformed, label=t)
+       # # axis[i].tick_params(labelbottom=False)
+       # axis[i].spines['top'].set_visible(False)
+       # axis[i].spines['right'].set_visible(False)
+       # axis[i].spines['left'].set_visible(False)
+       # if not (len(self.traces) == i - 1):
+       #     axis[i].spines['bottom'].set_visible(False)
+       # axis[i].set_yticks([])
+       # axis[i].set_ylabel(t, loc='center', rotation='horizontal')
+       # # axis[i].axis('off')
+       # i += 1
+       # # self.applyFFTs(t)
+
+
 if __name__ == '__main__':
     import doctest
 
-    doctest.testmod()
+    doctest.testmod()