[update] adding possibility to display other waveform data (e.g. denoised/synthetic) together with genuine data for comparison

PyLoT.py

@@ -76,7 +76,7 @@ from pylot.core.util.utils import fnConstructor, getLogin, \
     full_range, readFilterInformation, pick_color_plt, \
     pick_linestyle_plt, identifyPhaseID, excludeQualityClasses, \
     transform_colors_mpl, transform_colors_mpl_str, getAutoFilteroptions, check_all_obspy, \
-    check_all_pylot, get_bool, get_None, get_pylot_eventfile_with_extension
+    check_all_pylot, get_bool, get_None
 from pylot.core.util.gui import make_pen
 from pylot.core.util.event import Event
 from pylot.core.io.location import create_creation_info, create_event
@@ -84,7 +84,7 @@ 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
+    SourceSpecWindow, ChooseWaveFormWindow, SpectrogramTab
 from pylot.core.util.array_map import Array_map
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import Thread, Worker
@@ -181,6 +181,7 @@ class MainWindow(QMainWindow):
         self.autodata = Data(self)
 
         self.fnames = None
+        self.fnames_comp = None
         self._stime = None
 
         # track deleted picks for logging
@@ -1006,15 +1007,16 @@ class MainWindow(QMainWindow):
             return
         refresh = False
         events = self.project.eventlist
-        sld = SearchFileByExtensionDialog(label='Specify file extension: ', default_text='.xml',
+        sld = SingleTextLineDialog(label='Specify file extension: ', default_text='.xml')
-                                          events=events)
         if not sld.exec_():
             return
         fext = sld.lineEdit.text()
         # fext = '.xml'
         for event in events:
-            filename = get_pylot_eventfile_with_extension(event, fext)
+            path = event.path
-            if filename:
+            eventname = path.split('/')[-1]  # or event.pylot_id
+            filename = os.path.join(path, 'PyLoT_' + eventname + fext)
+            if os.path.isfile(filename):
                 self.load_data(filename, draw=False, event=event, overwrite=True)
                 refresh = True
         if not refresh:
@@ -1129,16 +1131,19 @@ 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')
@@ -1403,28 +1408,25 @@ 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']}
 
-            man_au_picks = {'manual': event.pylot_picks,
+            ma_props = {'manual': event.pylot_picks,
                         'auto': event.pylot_autopicks}
-            npicks = {'manual': {'P': 0, 'S': 0},
+            ma_count = {'manual': 0,
-                      'auto': {'P': 0, 'S': 0}}
+                        'auto': 0}
-            npicks_total = {'manual': {'P': 0, 'S': 0},
+            ma_count_total = {'manual': 0,
-                            'auto': {'P': 0, 'S': 0}}
+                              'auto': 0}
 
-            for ma in man_au_picks.keys():
+            for ma in ma_props.keys():
-                if man_au_picks[ma]:
+                if ma_props[ma]:
-                    for picks in man_au_picks[ma].values():
+                    for picks in ma_props[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'):
-                                npicks[ma][phase_ID] += 1
+                                ma_count[ma] += 1
-                            npicks_total[ma][phase_ID] += 1
+                            ma_count_total[ma] += 1
 
             event_ref = event.isRefEvent()
             event_test = event.isTestEvent()
@@ -1459,23 +1461,16 @@ class MainWindow(QMainWindow):
             if event.dirty:
                 event_str += '*'
             item_path = QStandardItem(event_str)
-            item_time = QStandardItem('{}'.format(time.strftime("%Y-%m-%d %H:%M:%S") if time else ''))
+            item_time = QStandardItem('{}'.format(time))
             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:
@@ -1896,7 +1891,6 @@ 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()
@@ -1931,6 +1925,7 @@ class MainWindow(QMainWindow):
             self.spectro_layout.addWidget(newSpectroWidget)
             self.spectroWidget = newSpectroWidget
 
+
     def newWF(self, event=None, plot=True):
         '''
         Load new data and plot if necessary.
@@ -1960,13 +1955,20 @@ 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):
         '''
@@ -1981,8 +1983,6 @@ 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?')
@@ -1999,7 +1999,7 @@ class MainWindow(QMainWindow):
             tstop = None
 
         self.data.setWFData(self.fnames,
-                            self.fnames_syn,
+                            self.fnames_comp,
                             checkRotated=True,
                             metadata=self.metadata,
                             tstart=tstart,
@@ -2007,7 +2007,7 @@ 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):
@@ -2015,8 +2015,8 @@ 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():
@@ -2138,7 +2138,7 @@ class MainWindow(QMainWindow):
 
     def finish_pg_plot(self):
         self.getPlotWidget().updateWidget()
-        plots = self.wfp_thread.data
+        plots, gaps = 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)
@@ -2297,7 +2297,7 @@ 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:
@@ -2312,8 +2312,8 @@ 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 = rval if rval else []
+        plots, gaps = rval if rval else ([], [])
-        return plots
+        return plots, gaps
 
     def adjustPlotHeight(self):
         if self.pg:
@@ -2609,18 +2609,21 @@ 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()
@@ -3644,7 +3647,7 @@ class MainWindow(QMainWindow):
             return True
         return False
 
-    def update_status(self, message, duration=10000):
+    def update_status(self, message, duration=5000):
         self.statusBar().showMessage(message, duration)
         if self.get_data() is not None:
             if not self.get_current_event() or not self.project.location:
@@ -3697,13 +3700,10 @@ class MainWindow(QMainWindow):
         if not self.okToContinue():
             return
         if not fnm:
-            settings = QSettings()
+            dlg = QFileDialog(parent=self)
-            dir = settings.value('current_project_path')
-            dlg = QFileDialog(parent=self, directory=dir)
             fnm = dlg.getOpenFileName(self, 'Open project file...', filter='Pylot project (*.plp)')[0]
             if not fnm:
                 return
-            settings.setValue('current_project_path', os.path.split(fnm)[0])
         if not os.path.exists(fnm):
             QMessageBox.warning(self, 'Could not open file',
                                 'Could not open project file {}. File does not exist.'.format(fnm))
@@ -3821,7 +3821,6 @@ class MainWindow(QMainWindow):
 
     def closeEvent(self, event):
         if self.okToContinue():
-            if hasattr(self, 'logwidget'):
             self.logwidget.close()
             event.accept()
         else:

autopylot.sh

@@ -9,4 +9,4 @@
 
 conda activate pylot_38
 
-python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_adriaarray.in -c 20 -dmt processed
+python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_janis_noisy.in -c $NSLOTS

pylot/core/io/data.py

@@ -19,7 +19,7 @@ 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, \
-    check_for_gaps_and_merge, trim_station_components, check_for_nan
+    check4gapsAndMerge, trim_station_components
 
 
 class Data(object):
@@ -64,7 +64,7 @@ class Data(object):
                     elif 'LOC' in evtdata:
                         raise NotImplementedError('PILOT location information '
                                                   'read support not yet '
-                                                  'implemented.')
+                                                  'implemeted.')
                     elif 'event.pkl' in evtdata:
                         evtdata = qml_from_obspyDMT(evtdata)
                     else:
@@ -451,27 +451,25 @@ 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
 
-        fnames = check_fname_exists(fnames)
+        # remove directories
-        fnames_syn = check_fname_exists(fnames_syn)
+        fnames = [fname for fname in fnames if not os.path.isdir(fname)]
+        fnames_alt = [fname for fname in fnames_alt if not os.path.isdir(fname)]
+
         # if obspy_dmt:
         #     wfdir = 'raw'
         #     self.processed = False
@@ -489,8 +487,8 @@ 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
 
@@ -498,9 +496,7 @@ class Data(object):
         # remove possible underscores in station names
         # self.wfdata = remove_underscores(self.wfdata)
         # check for gaps and merge
-        self.wfdata, _ = check_for_gaps_and_merge(self.wfdata)
+        self.wfdata = check4gapsAndMerge(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)
@@ -512,7 +508,7 @@ 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
@@ -525,19 +521,19 @@ class Data(object):
         if self.dirty:
             self.resetWFData()
 
-        real_or_syn_data = {True: self.wfsyn,
+        orig_or_alternative_data = {True: self.wf_alt,
                                     False: self.wfdata}
 
         warnmsg = ''
         for fname in set(fnames):
             try:
-                real_or_syn_data[synthetic] += read(fname, starttime=self.tstart, endtime=self.tstop)
+                orig_or_alternative_data[alternative] += read(fname, starttime=self.tstart, endtime=self.tstop)
             except TypeError:
                 try:
-                    real_or_syn_data[synthetic] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
+                    orig_or_alternative_data[alternative] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
                 except Exception as e:
                     try:
-                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart,
+                        orig_or_alternative_data[alternative] += read(fname, format='SEGY', starttime=self.tstart,
                                                                       endtime=self.tstop)
                     except Exception as e:
                         warnmsg += '{0}\n{1}\n'.format(fname, e)
@@ -553,8 +549,8 @@ 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/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, PickingFailedException, MissingTraceException
+    getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class
 from pylot.core.util.utils import getPatternLine, gen_Pool, \
     get_bool, identifyPhaseID, get_None, correct_iplot
 
@@ -232,6 +232,20 @@ 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):
@@ -646,7 +660,7 @@ class AutopickStation(object):
             ax1.set_ylim([-1.5, 1.5])
             ax1.set_ylabel('Normalized Counts')
 
-            if self.horizontal_traces_exist():# and self.s_data.Sflag == 1:
+            if self.horizontal_traces_exist() and self.s_data.Sflag == 1:
                 # plot E trace
                 ax2 = fig.add_subplot(3, 1, 2, sharex=ax1)
                 th1data = np.linspace(0, self.etrace.stats.endtime - self.etrace.stats.starttime,

pylot/core/pick/charfuns.py

@@ -20,8 +20,6 @@ import numpy as np
 from scipy import signal
 from obspy.core import Stream
 
-from pylot.core.pick.utils import PickingFailedException
-
 
 class CharacteristicFunction(object):
     """
@@ -295,7 +293,7 @@ class HOScf(CharacteristicFunction):
             if j < 4:
                 LTA[j] = 0
                 STA[j] = 0
-            elif j <= ista and self.getOrder() == 2:
+            elif j <= ista:
                 lta = (y[j] + lta * (j - 1)) / j
                 if self.getOrder() == 2:
                     sta = (y[j] + sta * (j - 1)) / j
@@ -490,9 +488,6 @@ 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

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

pylot/core/pick/utils.py

@@ -890,8 +890,6 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
                 input()
             except SyntaxError:
                 pass
-            except EOFError:
-                pass
             plt.close(fig)
 
     return returnflag
@@ -1334,6 +1332,22 @@ 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
@@ -1518,17 +1532,3 @@ 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

@@ -13,7 +13,6 @@ 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
@@ -280,12 +279,9 @@ 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
-        msg_reason = None
+        if ind == []:
-        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)
@@ -388,14 +384,7 @@ class Array_map(QtWidgets.QWidget):
                 try:
                     station_name = st_id.split('.')[-1]
                     # current_picks_dict: auto or manual
-                    station_picks = self.current_picks_dict().get(station_name)
+                    pick = self.current_picks_dict()[station_name][phase]
-                    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
@@ -474,17 +463,19 @@ 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

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

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, maxtasksperchild=1000)
+        pool = multiprocessing.Pool(ncores)
         pool.map(array_map_worker, input_list)
         pool.close()
         pool.join()

pylot/core/util/thread.py

@@ -160,7 +160,7 @@ class MultiThread(QThread):
         try:
             if not self.ncores:
                 self.ncores = multiprocessing.cpu_count()
-            pool = multiprocessing.Pool(self.ncores, maxtasksperchild=1000)
+            pool = multiprocessing.Pool(self.ncores)
             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

@@ -2,13 +2,11 @@
 # -*- coding: utf-8 -*-
 
 import hashlib
-import logging
 import os
 import platform
 import re
 import subprocess
 import warnings
-from functools import lru_cache
 
 import numpy as np
 from obspy import UTCDateTime, read
@@ -121,7 +119,7 @@ def gen_Pool(ncores=0):
 
     print('gen_Pool: Generated multiprocessing Pool with {} cores\n'.format(ncores))
 
-    pool = multiprocessing.Pool(ncores, maxtasksperchild=100)
+    pool = multiprocessing.Pool(ncores)
     return pool
 
 
@@ -820,6 +818,19 @@ 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
@@ -840,12 +851,12 @@ def check4gapsAndRemove(data):
     return data
 
 
-def check_for_gaps_and_merge(data):
+def check4gapsAndMerge(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, gaps returned from obspy get_gaps
+    :return: data stream
     :rtype: `~obspy.core.stream.Stream`
     """
     gaps = data.get_gaps()
@@ -856,7 +867,7 @@ def check_for_gaps_and_merge(data):
         for merged_station in merged:
             print(merged_station)
 
-    return data, gaps
+    return data
 
 
 def check4doubled(data):
@@ -886,33 +897,6 @@ 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 = eventpath.split('/')[-1]  # or event.pylot_id
-    filename = os.path.join(eventpath, 'PyLoT_' + eventname + fext)
-    if os.path.isfile(filename):
-        return filename
-
-
 def get_stations(data):
     """
     Get list of all station names in data stream
@@ -1122,7 +1106,6 @@ def identifyPhase(phase):
         return False
 
 
-@lru_cache
 def identifyPhaseID(phase):
     """
     Returns phase id (capital P or S)

pylot/core/util/widgets.py

@@ -36,7 +36,7 @@ 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, QTimer
+from PySide2.QtCore import QSettings, Qt, QUrl, Signal
 from PySide2.QtWebEngineWidgets import QWebEngineView as QWebView
 from obspy import Stream, Trace, UTCDateTime
 from obspy.core.util import AttribDict
@@ -51,10 +51,10 @@ from pylot.core.pick.autopick import fmpicker
 from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS
 from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
     pick_linestyle_plt, pick_color_plt, \
-    check4rotated, check4doubled, check_for_gaps_and_merge, check_for_nan, identifyPhase, \
+    check4rotated, check4doubled, merge_stream, identifyPhase, \
     loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
     identifyPhaseID, get_bool, get_None, pick_color, getAutoFilteroptions, SetChannelComponents, \
-    station_id_remove_channel, get_pylot_eventfile_with_extension
+    station_id_remove_channel
 from autoPyLoT import autoPyLoT
 from pylot.core.util.thread import Thread
 from pylot.core.util.dataprocessing import Metadata
@@ -793,7 +793,7 @@ 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 +804,13 @@ 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 +825,7 @@ 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 +834,11 @@ 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):
@@ -862,24 +864,9 @@ class WaveformWidgetPG(QtWidgets.QWidget):
 
     def plotWFData(self, wfdata, wfsyn=None, title=None, scaleddata=False, mapping=True,
                    component='*', nth_sample=1, verbosity=0, method='normal', gain=1., shift_syn=0.2):
-        def station_sort(nslc):
-            """Try to sort after station integer in case of a line array (e.g. active seismics)"""
-            try:
-                rval = sorted(nslc, key=lambda x: int(x.split('.')[1]))
-                return rval
-            except ValueError as e:
-                # this is the standard case for seismological stations
-                pass
-            except Exception as e:
-                print(f'Sorting by station integer failed with unknown exception: {e}')
-
-            # fallback to default sorting
-            return sorted(nslc)
-
         if not wfdata:
             print('Nothing to plot.')
             return
-
         self.title = title
         self.clearPlotDict()
         self.wfstart, self.wfend = full_range(wfdata)
@@ -897,14 +884,14 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         else:
             st_select = wfdata
 
-        # st_select, gaps = check_for_gaps_and_merge(st_select) #MP MP commented because probably done twice
+        st_select, gaps = merge_stream(st_select)
 
         # 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 = station_sort(nslc)
+        nslc.sort()
         nslc.reverse()
         plots = []
 
@@ -959,7 +946,7 @@ 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))
@@ -968,7 +955,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         self.ylabel = ''
         self.setXLims([0, self.wfend - self.wfstart])
         self.setYLims([0.5, nmax + 0.5])
-        return plots
+        return plots, gaps
 
     def minMax(self, trace, time_ax):
         '''
@@ -990,7 +977,7 @@ 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=float)
+            extreme_values = np.empty((npixel + 1, 2), dtype=np.float)
             extreme_values[:-1, 0] = min_
             extreme_values[:-1, 1] = max_
             extreme_values[-1, 0] = \
@@ -998,7 +985,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
             extreme_values[-1, 1] = \
                 trace.data[-remaining_samples:].max()
         else:
-            extreme_values = np.empty((npixel, 2), dtype=float)
+            extreme_values = np.empty((npixel, 2), dtype=np.float)
             extreme_values[:, 0] = min_
             extreme_values[:, 1] = max_
         data = extreme_values.flatten()
@@ -1148,12 +1135,12 @@ 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:
@@ -1371,11 +1358,15 @@ 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()
 
@@ -1386,21 +1377,33 @@ 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
@@ -1408,10 +1411,12 @@ class PylotCanvas(FigureCanvas):
         nslc.sort()
         nslc.reverse()
 
-        linecolor = (0., 0., 0., 1.) if not self.style else self.style['linecolor']['rgba_mpl']
-
         for n, seed_id in enumerate(nslc):
             network, station, location, channel = seed_id.split('.')
+            for wf_name, wf_dict in plot_streams.items():
+                st_select = wf_dict.get('data')
+                if not st_select:
+                    continue
                 st = st_select.select(id=seed_id)
                 trace = st[0].copy()
                 if mapping:
@@ -1435,15 +1440,17 @@ class PylotCanvas(FigureCanvas):
                         trace.detrend('constant')
                         trace.normalize(np.max(np.abs(trace.data)) * 2)
 
+                    offset = wf_dict.get('offset')
+
                     times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
-                data = [datum + n for index, datum in enumerate(trace.data) if not index % nth_sample]
+                    data = [datum + n + offset for index, datum in enumerate(trace.data) if not index % nth_sample]
                     ax.axhline(n, color="0.5", lw=0.5)
-                ax.plot(times, data, color=linecolor, linewidth=0.7)
+                    ax.plot(times, data, color=wf_dict.get('linecolor'), **wf_dict.get('plot_kwargs'))
                     if noiselevel is not None:
                         for level in [-noiselevel[channel], noiselevel[channel]]:
                             ax.plot([time_ax[0], time_ax[-1]],
                                     [n + level, n + level],
-                                color=linecolor,
+                                    color=wf_dict.get('linecolor'),
                                     linestyle='dashed')
                     self.setPlotDict(n, seed_id)
         if plot_additional and additional_channel:
@@ -1568,97 +1575,6 @@ 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.default_text = default_text
-        self.label = label
-        self.setButtons()
-        self.setupUi()
-        self.connectSignals()
-        self.showPaths()
-        self.refresh_timer = QTimer(self)
-        self.refresh_timer.timeout.connect(self.showPaths)
-        self.refresh_timer.start(10000)
-
-        self.resize(800, 450)
-
-
-    def setupUi(self):
-        self.main_layout = QtWidgets.QVBoxLayout()
-        self.header_layout = QtWidgets.QHBoxLayout()
-        #
-        self.setLayout(self.main_layout)
-
-        # widgets inside the dialog
-        self.textLabel = QtWidgets.QLabel(self.label)
-        self.lineEdit = QtWidgets.QLineEdit(self.default_text)
-
-        # optional search button, currently disabled. List refreshed when text changes
-        self.searchButton = QtWidgets.QPushButton('Search')
-        self.searchButton.setVisible(False)
-
-        self.tableWidget = QtWidgets.QTableWidget()
-        tableWidget = self.tableWidget
-        tableWidget.setColumnCount(3)
-        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.lineEdit)
-        self.header_layout.addWidget(self.searchButton)
-
-        self.main_layout.addLayout(self.header_layout)
-        self.main_layout.addWidget(self.tableWidget)
-        self.main_layout.addWidget(self.statusText)
-        self.main_layout.addWidget(self._buttonbox)
-
-    def showPaths(self):
-        self.filepaths = []
-        fext = self.lineEdit.text()
-        self.tableWidget.clearContents()
-        for index, event in enumerate(self.events):
-            filename = get_pylot_eventfile_with_extension(event, fext)
-            self.tableWidget.setItem(index, 0, 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'{filename}')
-                ts_item = QtWidgets.QTableWidgetItem(f'{datetime.datetime.fromtimestamp(ts)}')
-                self.tableWidget.setItem(index, 1, fname_item)
-                self.tableWidget.setItem(index, 2, ts_item)
-
-        # TODO: Idea -> only refresh if table contents changed. Use selection to load only a subset of files
-        if len(self.filepaths) > 0:
-            status_text = f'Found {len(self.filepaths)} eventfiles. Do you want to load them?'
-        else:
-            status_text = 'Did not find any files for specified file mask.'
-        self.statusText.setText(status_text)
-
-
-    def setButtons(self):
-        self._buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
-                                           QDialogButtonBox.Cancel)
-
-    def connectSignals(self):
-        self._buttonbox.accepted.connect(self.accept)
-        self._buttonbox.rejected.connect(self.reject)
-        self.lineEdit.textChanged.connect(self.showPaths)
-        self.searchButton.clicked.connect(self.showPaths)
-
-
-
 class SingleTextLineDialog(QtWidgets.QDialog):
     def __init__(self, parent=None, label='Text: ', default_text='.xml'):
         super(SingleTextLineDialog, self).__init__(parent)
@@ -1763,8 +1679,8 @@ 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
@@ -1773,6 +1689,7 @@ 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
@@ -1811,22 +1728,6 @@ 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:
@@ -1839,6 +1740,31 @@ 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())
 
@@ -1851,12 +1777,12 @@ 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
@@ -1873,7 +1799,7 @@ 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()
@@ -2049,8 +1975,11 @@ 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)
@@ -2385,7 +2314,7 @@ 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)
@@ -2417,7 +2346,7 @@ 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()
@@ -2490,6 +2419,12 @@ 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()
@@ -2611,11 +2546,16 @@ 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: {}. '
                                           'Make sure to select the correct channels for P and S '
@@ -2623,14 +2563,16 @@ class PickDlg(QDialog):
             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',
@@ -2640,8 +2582,8 @@ 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])
@@ -2652,12 +2594,14 @@ 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]:
+            if wfd:
+                for trace in wfd:
                     t = prepTimeAxis(trace.stats.starttime - stime, trace)
                     inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
                     trace = demeanTrace(trace, inoise)
-            # upscale trace data in a way that each trace is vertically zoomed to noiselevel*factor
+                    # upscale trace wfdata in a way that each trace is vertically zoomed to noiselevel*factor
                     channel = trace.stats.channel
                     noiselevel = noiselevels[channel]
                     noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.)
@@ -2668,7 +2612,7 @@ class PickDlg(QDialog):
         x_res = getResolutionWindow(mean_snr, parameter.get('extent'))
 
         xlims = [ini_pick - x_res, ini_pick + x_res]
-        ylims = list(np.array([-.5, .5]) + [0, len(data) - 1])
+        ylims = list(np.array([-.5, .5]) + [0, len(wfdata) - 1])
 
         title = self.getStation() + ' picking mode'
         title += ' | SNR: {}'.format(mean_snr)
@@ -2676,9 +2620,10 @@ 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,
@@ -3069,7 +3014,8 @@ 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
@@ -3077,19 +3023,22 @@ 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,
@@ -3162,6 +3111,9 @@ 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)
@@ -3672,9 +3624,8 @@ class TuneAutopicker(QWidget):
             # wfdat = remove_underscores(wfdat)
             # rotate misaligned stations to ZNE
             # check for gaps and doubled channels
-            wfdat, _ = check_for_gaps_and_merge(wfdat)
+            wfdat, gaps = merge_stream(wfdat)
-            # check for nans
+            # check4gaps(wfdat)
-            check_for_nan(wfdat)
             check4doubled(wfdat)
             wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
             # trim station components to same start value
@@ -3773,11 +3724,13 @@ 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),
@@ -3829,7 +3782,6 @@ 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),
@@ -3862,7 +3814,7 @@ 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