[update] added check for nan values in waveforms which crashed obspy filter routines

[minor] some tweaks and optimisations

PyLoT.py

@@ -181,7 +181,6 @@ class MainWindow(QMainWindow):
         self.autodata = Data(self)
 
         self.fnames = None
-        self.fnames_comp = None
         self._stime = None
 
         # track deleted picks for logging
@@ -1131,19 +1130,16 @@ class MainWindow(QMainWindow):
             else:
                 return
 
-    def getWFFnames_from_eventbox(self, eventbox: str = None, subpath: str = None) -> list:
+    def getWFFnames_from_eventbox(self, eventbox=None):
         '''
         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)
-        if subpath:
-            eventpath = os.path.join(eventpath, subpath)
-        if not os.path.isdir(eventpath):
-            return []
+        basepath = eventpath.split(os.path.basename(eventpath))[0]
         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')
@@ -1955,20 +1951,13 @@ class MainWindow(QMainWindow):
 
     def prepareLoadWaveformData(self):
         self.fnames = self.getWFFnames_from_eventbox()
-        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
-
+        self.fnames_syn = []
         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):
         '''
@@ -1999,7 +1988,7 @@ class MainWindow(QMainWindow):
             tstop = None
 
         self.data.setWFData(self.fnames,
-                            self.fnames_comp,
+                            self.fnames_syn,
                             checkRotated=True,
                             metadata=self.metadata,
                             tstart=tstart,
@@ -2007,7 +1996,7 @@ class MainWindow(QMainWindow):
 
     def prepareObspyDMT_data(self, eventpath):
         qcbox_processed = self.dataPlot.qcombo_processed
-        qcheckb_syn = self.dataPlot.comp_checkbox
+        qcheckb_syn = self.dataPlot.syn_checkbox
         qcbox_processed.setEnabled(False)
         qcheckb_syn.setEnabled(False)
         for fpath in os.listdir(eventpath):
@@ -2015,8 +2004,8 @@ class MainWindow(QMainWindow):
             if 'syngine' in fpath:
                 eventpath_syn = os.path.join(eventpath, fpath)
                 qcheckb_syn.setEnabled(True)
-                if self.dataPlot.comp_checkbox.isChecked():
-                    self.fnames_comp = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
+                if self.dataPlot.syn_checkbox.isChecked():
+                    self.fnames_syn = [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 +2127,7 @@ 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)
@@ -2297,7 +2286,7 @@ class MainWindow(QMainWindow):
         comp = self.getComponent()
         title = 'section: {0} components'.format(zne_text[comp])
         wfst = self.get_data().getWFData()
-        wfsyn = self.get_data().getAltWFdata()
+        wfsyn = self.get_data().getSynWFData()
         if self.filterActionP.isChecked() and filter:
             self.filterWaveformData(plot=False, phase='P')
         elif self.filterActionS.isChecked() and filter:
@@ -2312,8 +2301,8 @@ class MainWindow(QMainWindow):
             self.plot_method = 'normal'
         rval = plotWidget.plotWFData(wfdata=wfst, wfsyn=wfsyn, title=title, mapping=False, component=comp,
                                      nth_sample=int(nth_sample), method=self.plot_method, gain=self.gain)
-        plots, gaps = rval if rval else ([], [])
-        return plots, gaps
+        plots = rval if rval else []
+        return plots
 
     def adjustPlotHeight(self):
         if self.pg:
@@ -2609,21 +2598,18 @@ class MainWindow(QMainWindow):
             print("Warning! No network, station, and location info available!")
             return
         self.update_status('picking on station {0}'.format(station))
-        wfdata = self.get_data().getOriginalWFData().copy()
-        wfdata_comp = self.get_data().getAltWFdata().copy()
+        data = self.get_data().getOriginalWFData().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=wfdata.select(station=station),
-                          data_compare=wfdata_comp.select(station=station),
+                          data=data.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,
-                          show_comp_data=self.dataPlot.comp_checkbox.isChecked())
+                          filteroptions=self.filteroptions, wftype=wftype)
         if self.filterActionP.isChecked():
             pickDlg.currentPhase = "P"
             pickDlg.filterWFData()
@@ -3821,7 +3807,8 @@ class MainWindow(QMainWindow):
 
     def closeEvent(self, event):
         if self.okToContinue():
-            self.logwidget.close()
+            if hasattr(self, 'logwidget'):
+                self.logwidget.close()
             event.accept()
         else:
             event.ignore()

autopylot.sh

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

pylot/core/io/data.py

@@ -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, \
-    check4gapsAndMerge, trim_station_components
+    check_for_gaps_and_merge, trim_station_components, check_for_nan
 
 
 class Data(object):
@@ -64,7 +64,7 @@ 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:
@@ -451,25 +451,27 @@ class Data(object):
         data.filter(**kwargs)
         self.dirty = True
 
-    def setWFData(self, fnames, fnames_alt=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
+    def setWFData(self, fnames, fnames_syn=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.wf_alt = Stream()
+        self.wfsyn = Stream()
         if tstart == tstop:
             tstart = tstop = None
         self.tstart = tstart
         self.tstop = tstop
 
-        # remove directories
-        fnames = [fname for fname in fnames if not os.path.isdir(fname)]
-        fnames_alt = [fname for fname in fnames_alt if not os.path.isdir(fname)]
-
+        fnames = check_fname_exists(fnames)
+        fnames_syn = check_fname_exists(fnames_syn)
         # if obspy_dmt:
         #     wfdir = 'raw'
         #     self.processed = False
@@ -487,8 +489,8 @@ class Data(object):
         #     wffnames = fnames
         if fnames is not None:
             self.appendWFData(fnames)
-            if fnames_alt is not None:
-                self.appendWFData(fnames_alt, alternative=True)
+            if fnames_syn is not None:
+                self.appendWFData(fnames_syn, synthetic=True)
         else:
             return False
 
@@ -496,7 +498,9 @@ 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)
@@ -508,7 +512,7 @@ class Data(object):
         self.dirty = False
         return True
 
-    def appendWFData(self, fnames, alternative=False):
+    def appendWFData(self, fnames, synthetic=False):
         """
         Read waveform data from fnames and append it to current wf data
         :param fnames: waveform data to append
@@ -521,20 +525,20 @@ class Data(object):
         if self.dirty:
             self.resetWFData()
 
-        orig_or_alternative_data = {True: self.wf_alt,
-                                    False: self.wfdata}
+        real_or_syn_data = {True: self.wfsyn,
+                            False: self.wfdata}
 
         warnmsg = ''
         for fname in set(fnames):
             try:
-                orig_or_alternative_data[alternative] += read(fname, starttime=self.tstart, endtime=self.tstop)
+                real_or_syn_data[synthetic] += read(fname, starttime=self.tstart, endtime=self.tstop)
             except TypeError:
                 try:
-                    orig_or_alternative_data[alternative] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
+                    real_or_syn_data[synthetic] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
                 except Exception as e:
                     try:
-                        orig_or_alternative_data[alternative] += read(fname, format='SEGY', starttime=self.tstart,
-                                                                      endtime=self.tstop)
+                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart,
+                                                            endtime=self.tstop)
                     except Exception as e:
                         warnmsg += '{0}\n{1}\n'.format(fname, e)
             except SacIOError as se:
@@ -549,8 +553,8 @@ class Data(object):
     def getOriginalWFData(self):
         return self.wforiginal
 
-    def getAltWFdata(self):
-        return self.wf_alt
+    def getSynWFData(self):
+        return self.wfsyn
 
     def resetWFData(self):
         """

pylot/core/pick/autopick.py

@@ -660,7 +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/utils.py

@@ -1332,22 +1332,6 @@ 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

pylot/core/util/array_map.py

@@ -463,19 +463,17 @@ class Array_map(QtWidgets.QWidget):
                                                                   transform=ccrs.PlateCarree(), label='deleted'))
 
     def openPickDlg(self, ind):
-        wfdata = self._parent.get_data().getWFData()
-        wfdata_comp = self._parent.get_data().getWFDataComp()
+        data = self._parent.get_data().getWFData()
         for index in ind:
             network, station = self._station_onpick_ids[index].split('.')[:2]
             pyl_mw = self._parent
             try:
-                wfdata = wfdata.select(station=station)
-                wfdata_comp = wfdata_comp.select(station=station)
-                if not wfdata:
+                data = data.select(station=station)
+                if not data:
                     self._warn('No data for station {}'.format(station))
                     return
                 pickDlg = PickDlg(self._parent, parameter=self.parameter,
-                                  data=wfdata.copy(), data_compare=wfdata_comp.copy(), network=network, station=station,
+                                  data=data, 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/utils.py

@@ -818,19 +818,6 @@ def trim_station_components(data, trim_start=True, trim_end=True):
     return data
 
 
-def merge_stream(stream):
-    gaps = stream.get_gaps()
-    if gaps:
-        # list of merged stations (seed_ids)
-        merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
-        stream.merge(method=1)
-        print('Merged the following stations because of gaps:')
-        for merged_station in merged:
-            print(merged_station)
-
-    return stream, gaps
-
-
 def check4gapsAndRemove(data):
     """
     check for gaps in Stream and remove them
@@ -851,12 +838,12 @@ def check4gapsAndRemove(data):
     return data
 
 
-def check4gapsAndMerge(data):
+def check_for_gaps_and_merge(data):
     """
     check for gaps in Stream and merge if gaps are found
     :param data: stream of seismic data
     :type data: `~obspy.core.stream.Stream`
-    :return: data stream
+    :return: data stream, gaps returned from obspy get_gaps
     :rtype: `~obspy.core.stream.Stream`
     """
     gaps = data.get_gaps()
@@ -867,7 +854,7 @@ def check4gapsAndMerge(data):
         for merged_station in merged:
             print(merged_station)
 
-    return data
+    return data, gaps
 
 
 def check4doubled(data):
@@ -897,6 +884,21 @@ 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_stations(data):
     """
     Get list of all station names in data stream

pylot/core/util/widgets.py

@@ -51,7 +51,7 @@ 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, 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
@@ -793,7 +793,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
 
     def connect_signals(self):
         self.qcombo_processed.activated.connect(self.parent().newWF)
-        self.comp_checkbox.clicked.connect(self.parent().newWF)
+        self.syn_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.comp_checkbox)
+        mid_layout.addWidget(self.syn_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.comp_checkbox.setLayoutDirection(Qt.RightToLeft)
+        self.syn_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.comp_checkbox = QtWidgets.QCheckBox('Load comparison data')
+        self.syn_checkbox = QtWidgets.QCheckBox('synthetics')
         self.addQCboxItem('processed', 'green')
         self.addQCboxItem('raw', 'black')
         # self.perm_qcbox_right.setAlignment(2)
@@ -834,11 +834,9 @@ class WaveformWidgetPG(QtWidgets.QWidget):
     def getPlotDict(self):
         return self.plotdict
 
-    def activateObspyDMToptions(self, activate: bool) -> None:
-        self.qcombo_processed.setEnabled(activate)
-
-    def activateCompareOptions(self, activate: bool) -> None:
-        self.comp_checkbox.setEnabled(activate)
+    def activateObspyDMToptions(self, activate):
+        self.syn_checkbox.setVisible(activate)
+        self.qcombo_processed.setVisible(activate)
 
     def setPermText(self, number, text=None, color='black'):
         if not 0 <= number < len(self.perm_labels):
@@ -864,9 +862,24 @@ class WaveformWidgetPG(QtWidgets.QWidget):
 
     def plotWFData(self, wfdata, wfsyn=None, title=None, scaleddata=False, mapping=True,
                    component='*', nth_sample=1, verbosity=0, method='normal', gain=1., shift_syn=0.2):
+        def station_sort(nslc):
+            """Try to sort after station integer in case of a line array (e.g. active seismics)"""
+            try:
+                rval = sorted(nslc, key=lambda x: int(x.split('.')[1]))
+                return rval
+            except ValueError as e:
+                # this is the standard case for seismological stations
+                pass
+            except Exception as e:
+                print(f'Sorting by station integer failed with unknown exception: {e}')
+
+            # fallback to default sorting
+            return sorted(nslc)
+
         if not wfdata:
             print('Nothing to plot.')
             return
+
         self.title = title
         self.clearPlotDict()
         self.wfstart, self.wfend = full_range(wfdata)
@@ -884,14 +897,14 @@ 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 +959,7 @@ 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 + shift_syn for index, datum in enumerate(trace_syn.data)
+                trace_syn.data = np.array([datum + n 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 +968,7 @@ 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 +990,7 @@ 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 +998,7 @@ 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 +1148,12 @@ class PylotCanvas(FigureCanvas):
         ax.set_xlim(self.cur_xlim)
         ax.set_ylim(self.cur_ylim)
         self.refreshPickDlgText()
-        ax.figure.canvas.draw_idle()
+        ax.figure.canvas.draw()
 
     def panRelease(self, gui_event):
         self.press = None
         self.press_rel = None
-        self.figure.canvas.draw_idle()
+        self.figure.canvas.draw()
 
     def panZoom(self, gui_event, threshold=2., factor=1.1):
         if not gui_event.x and not gui_event.y:
@@ -1358,15 +1371,11 @@ class PylotCanvas(FigureCanvas):
             plot_positions[channel] = plot_pos
         return plot_positions
 
-    def plotWFData(self, wfdata, wfdata_compare=None, title=None, zoomx=None, zoomy=None,
+    def plotWFData(self, wfdata, 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()
 
@@ -1377,33 +1386,21 @@ 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])
 
-            plot_streams['wfdata']['data'] = wfdata.select(component=component)
-            plot_streams['wfdata']['data'] += wfdata.select(component=alter_comp)
-            if wfdata_compare:
-                plot_streams['wfdata_comp']['data'] = wfdata_compare.select(component=component)
-                plot_streams['wfdata_comp']['data'] += wfdata_compare.select(component=alter_comp)
+            st_select = wfdata.select(component=component)
+            st_select += wfdata.select(component=alter_comp)
         else:
-            plot_streams['wfdata']['data'] = wfdata
-            if wfdata_compare:
-                plot_streams['wfdata_comp']['data'] = wfdata_compare
-            
-        st_main = plot_streams['wfdata']['data']
+            st_select = wfdata
 
         if mapping:
-            plot_positions = self.calcPlotPositions(st_main, compclass)
+            plot_positions = self.calcPlotPositions(st_select, compclass)
 
         # list containing tuples of network, station, channel and plot position (for sorting)
         nslc = []
-        for plot_pos, trace in enumerate(st_main):
+        for plot_pos, trace in enumerate(st_select):
             if not trace.stats.channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
                 print('Warning: Unrecognized channel {}'.format(trace.stats.channel))
                 continue
@@ -1411,48 +1408,44 @@ 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:
-                    n = plot_positions[trace.stats.channel]
-                if n > nmax:
-                    nmax = n
-                if verbosity:
-                    msg = 'plotting %s channel of station %s' % (channel, station)
-                    print(msg)
-                stime = trace.stats.starttime - wfstart
-                time_ax = prepTimeAxis(stime, trace)
-                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:
+            st = st_select.select(id=seed_id)
+            trace = st[0].copy()
+            if mapping:
+                n = plot_positions[trace.stats.channel]
+            if n > nmax:
+                nmax = n
+            if verbosity:
+                msg = 'plotting %s channel of station %s' % (channel, station)
+                print(msg)
+            stime = trace.stats.starttime - wfstart
+            time_ax = prepTimeAxis(stime, trace)
+            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(trace.data)) * 2)
+                        trace.normalize(np.max(np.abs(tr.data)) * 2)
+                        scaleddata = True
+                if not scaleddata:
+                    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 + 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=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=wf_dict.get('linecolor'),
-                                    linestyle='dashed')
-                    self.setPlotDict(n, seed_id)
+                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]
+                ax.axhline(n, color="0.5", lw=0.5)
+                ax.plot(times, data, color=linecolor, linewidth=0.7)
+                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,
+                                linestyle='dashed')
+                self.setPlotDict(n, seed_id)
         if plot_additional and additional_channel:
             compare_stream = wfdata.select(channel=additional_channel)
             if compare_stream:
@@ -1679,8 +1672,8 @@ class PhaseDefaults(QtWidgets.QDialog):
 class PickDlg(QDialog):
     update_picks = QtCore.Signal(dict)
 
-    def __init__(self, parent=None, data=None, data_compare=None, station=None, network=None, location=None, picks=None,
-                 autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, show_comp_data=False,
+    def __init__(self, parent=None, data=None, station=None, network=None, location=None, picks=None,
+                 autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None,
                  event=None, filteroptions=None, model=None, wftype=None):
         super(PickDlg, self).__init__(parent, Qt.Window)
         self.orig_parent = parent
@@ -1689,7 +1682,6 @@ 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
@@ -1728,32 +1720,11 @@ class PickDlg(QDialog):
         else:
             self.filteroptions = FILTERDEFAULTS
         self.pick_block = False
-
-        # set attribute holding data
-        if data is None or not data:
-            try:
-                data = parent.get_data().getWFData().copy()
-                self.data = data.select(station=station)
-            except AttributeError as e:
-                errmsg = 'You either have to put in a data or an appropriate ' \
-                         'parent (PyLoT MainWindow) object: {0}'.format(e)
-                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))
+        self.compareChannel = QtWidgets.QComboBox()
+        self.compareChannel.activated.connect(self.resetPlot)
 
         # scale channel
         self.scaleChannel = QtWidgets.QComboBox()
@@ -1766,6 +1737,18 @@ class PickDlg(QDialog):
         self.cur_xlim = None
         self.cur_ylim = None
 
+        # set attribute holding data
+        if data is None or not data:
+            try:
+                data = parent.get_data().getWFData().copy()
+                self.data = data.select(station=station)
+            except AttributeError as e:
+                errmsg = 'You either have to put in a data or an appropriate ' \
+                         'parent (PyLoT MainWindow) object: {0}'.format(e)
+                raise Exception(errmsg)
+        else:
+            self.data = data
+
         self.stime, self.etime = full_range(self.getWFData())
 
         # initialize plotting widget
@@ -1777,12 +1760,12 @@ class PickDlg(QDialog):
         self.setupUi()
 
         # fill compare and scale channels
-        self.referenceChannel.addItem('-', None)
+        self.compareChannel.addItem('-', None)
         self.scaleChannel.addItem('individual', None)
 
         for trace in self.getWFData():
             channel = trace.stats.channel
-            self.referenceChannel.addItem(channel, trace)
+            self.compareChannel.addItem(channel, trace)
             if not channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
                 print('Skipping unknown channel for scaling: {}'.format(channel))
                 continue
@@ -1799,7 +1782,7 @@ class PickDlg(QDialog):
         if self.wftype is not None:
             title += ' | ({})'.format(self.wftype)
 
-        self.multicompfig.plotWFData(wfdata=self.getWFData(), wfdata_compare=self.getWFDataComp(),
+        self.multicompfig.plotWFData(wfdata=self.getWFData(),
                                      title=title)
 
         self.multicompfig.setZoomBorders2content()
@@ -1975,11 +1958,8 @@ class PickDlg(QDialog):
         _dialtoolbar.addWidget(est_label)
         _dialtoolbar.addWidget(self.plot_arrivals_button)
         _dialtoolbar.addSeparator()
-        _dialtoolbar.addWidget(QtWidgets.QLabel('Plot reference channel: '))
-        _dialtoolbar.addWidget(self.referenceChannel)
-        _dialtoolbar.addSeparator()
-        _dialtoolbar.addWidget(QtWidgets.QLabel('Compare: '))
-        _dialtoolbar.addWidget(self.compareCB)
+        _dialtoolbar.addWidget(QtWidgets.QLabel('Compare to channel: '))
+        _dialtoolbar.addWidget(self.compareChannel)
         _dialtoolbar.addSeparator()
         _dialtoolbar.addWidget(QtWidgets.QLabel('Scaling: '))
         _dialtoolbar.addWidget(self.scaleChannel)
@@ -2314,7 +2294,7 @@ class PickDlg(QDialog):
     def activatePicking(self):
         self.leave_rename_phase()
         self.renamePhaseAction.setEnabled(False)
-        self.referenceChannel.setEnabled(False)
+        self.compareChannel.setEnabled(False)
         self.scaleChannel.setEnabled(False)
         phase = self.currentPhase
         phaseID = self.getPhaseID(phase)
@@ -2346,7 +2326,7 @@ class PickDlg(QDialog):
         self.disconnectPressEvent()
         self.multicompfig.connectEvents()
         self.renamePhaseAction.setEnabled(True)
-        self.referenceChannel.setEnabled(True)
+        self.compareChannel.setEnabled(True)
         self.scaleChannel.setEnabled(True)
         self.connect_pick_delete()
         self.draw()
@@ -2419,12 +2399,6 @@ 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()
@@ -2546,16 +2520,11 @@ class PickDlg(QDialog):
 
         stime = self.getStartTime()
 
-        # copy wfdata for plotting
-        wfdata = self.getWFData().copy()
-        wfdata_comp = self.getWFDataComp().copy()
-        wfdata = self.getPickPhases(wfdata, phase)
-        wfdata_comp = self.getPickPhases(wfdata_comp, phase)
-        for wfd in [wfdata, wfdata_comp]:
-            if wfd:
-                wfd.normalize()
-
-        if not wfdata:
+        # copy data for plotting
+        data = self.getWFData().copy()
+        data = self.getPickPhases(data, phase)
+        data.normalize()
+        if not data:
             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 '
@@ -2563,16 +2532,14 @@ class PickDlg(QDialog):
             self.leave_picking_mode()
             return
 
-        # filter wfdata and trace on which is picked prior to determination of SNR
+        # filter data and trace on which is picked prior to determination of SNR
         filterphase = self.currentFilterPhase()
         if filterphase:
             filteroptions = self.getFilterOptions(filterphase).parseFilterOptions()
             try:
-                for wfd in [wfdata, wfdata_comp]:
-                    if wfd:
-                        wfd.detrend('linear')
-                        wfd.filter(**filteroptions)
-                # wfdata.filter(**filteroptions)# MP MP removed filtering of original wfdata
+                data.detrend('linear')
+                data.filter(**filteroptions)
+                # wfdata.filter(**filteroptions)# MP MP removed filtering of original data
             except ValueError as e:
                 self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information,
                                                  'Denied',
@@ -2582,8 +2549,8 @@ class PickDlg(QDialog):
         snr = []
         noiselevels = {}
         # determine SNR and noiselevel
-        for trace in wfdata.traces:
-            st = wfdata.select(channel=trace.stats.channel)
+        for trace in data.traces:
+            st = data.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])
@@ -2594,25 +2561,23 @@ class PickDlg(QDialog):
                 noiselevel = nfac
             noiselevels[trace.stats.channel] = noiselevel
 
-        # prepare plotting of wfdata
-        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 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.)
-                    trace.data *= noiseScaleFactor
-                    noiselevels[channel] *= noiseScaleFactor
+        # prepare plotting of data
+        for trace in data:
+            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
+            channel = trace.stats.channel
+            noiselevel = noiselevels[channel]
+            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(wfdata) - 1])
+        ylims = list(np.array([-.5, .5]) + [0, len(data) - 1])
 
         title = self.getStation() + ' picking mode'
         title += ' | SNR: {}'.format(mean_snr)
@@ -2620,10 +2585,9 @@ class PickDlg(QDialog):
             filtops_str = transformFilteroptions2String(filteroptions)
             title += ' | Filteroptions: {}'.format(filtops_str)
 
-        plot_additional = bool(self.referenceChannel.currentText())
-        additional_channel = self.referenceChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=wfdata,
-                                     wfdata_compare=wfdata_comp,
+        plot_additional = bool(self.compareChannel.currentText())
+        additional_channel = self.compareChannel.currentText()
+        self.multicompfig.plotWFData(wfdata=data,
                                      title=title,
                                      zoomx=xlims,
                                      zoomy=ylims,
@@ -3014,8 +2978,7 @@ class PickDlg(QDialog):
         self.cur_xlim = self.multicompfig.axes[0].get_xlim()
         self.cur_ylim = self.multicompfig.axes[0].get_ylim()
         # self.multicompfig.updateCurrentLimits()
-        wfdata = self.getWFData().copy()
-        wfdata_comp = self.getWFDataComp().copy()
+        data = self.getWFData().copy()
         title = self.getStation()
         if filter:
             filtoptions = None
@@ -3023,22 +2986,19 @@ class PickDlg(QDialog):
                 filtoptions = self.getFilterOptions(self.getPhaseID(phase), gui_filter=True).parseFilterOptions()
 
             if filtoptions is not None:
-                for wfd in [wfdata, wfdata_comp]:
-                    if wfd:
-                        wfd.detrend('linear')
-                        wfd.taper(0.02, type='cosine')
-                        wfd.filter(**filtoptions)
+                data.detrend('linear')
+                data.taper(0.02, type='cosine')
+                data.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.referenceChannel.currentText())
-        additional_channel = self.referenceChannel.currentText()
+        plot_additional = bool(self.compareChannel.currentText())
+        additional_channel = self.compareChannel.currentText()
         scale_channel = self.scaleChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=wfdata, wfdata_compare=wfdata_comp,
-                                     title=title,
+        self.multicompfig.plotWFData(wfdata=data, title=title,
                                      zoomx=self.getXLims(),
                                      zoomy=self.getYLims(),
                                      plot_additional=plot_additional,
@@ -3111,9 +3071,6 @@ 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)
@@ -3624,8 +3581,9 @@ class TuneAutopicker(QWidget):
             # wfdat = remove_underscores(wfdat)
             # rotate misaligned stations to ZNE
             # check for gaps and doubled channels
-            wfdat, gaps = merge_stream(wfdat)
-            # check4gaps(wfdat)
+            wfdat, _ = check_for_gaps_and_merge(wfdat)
+            # check for nans
+            check_for_nan(wfdat)
             check4doubled(wfdat)
             wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
             # trim station components to same start value
@@ -3724,13 +3682,11 @@ 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),
@@ -3782,6 +3738,7 @@ 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),
@@ -3814,7 +3771,7 @@ 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_idle()
+            canvas.draw()
 
     def plot_manual_pick_to_ax(self, ax, picks, phase, starttime, quality):
         mpp = picks[phase]['mpp'] - starttime