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

[minor] some tweaks and optimisations

PyLoT.py

@@ -2127,7 +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)
@@ -2301,8 +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 ([], [])
+        plots = rval if rval else []
-        return plots, gaps
+        return plots
 
     def adjustPlotHeight(self):
         if self.pg:
@@ -3807,7 +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:
@@ -457,6 +457,11 @@ class Data(object):
         :param fnames: waveform data names to append
         :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()
@@ -465,6 +470,8 @@ class Data(object):
         self.tstart = tstart
         self.tstop = tstop
 
+        fnames = check_fname_exists(fnames)
+        fnames_syn = check_fname_exists(fnames_syn)
         # if obspy_dmt:
         #     wfdir = 'raw'
         #     self.processed = False
@@ -491,7 +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)

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/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
@@ -897,7 +897,7 @@ 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 = []
@@ -968,7 +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):
         '''
@@ -990,7 +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] = \
@@ -998,7 +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()
@@ -3581,8 +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)
+            wfdat, _ = check_for_gaps_and_merge(wfdat)
-            # check4gaps(wfdat)
+            # check for nans
+            check_for_nan(wfdat)
             check4doubled(wfdat)
             wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
             # trim station components to same start value
@@ -3737,6 +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),