Merge branch 'develop' of git.geophysik.ruhr-uni-bochum.de:marcel/pylot into develop

PyLoT.py

@@ -254,7 +254,7 @@ class MainWindow(QMainWindow):
             self._inputs.export2File(infile)
         self.infile = infile
 
-    def setupUi(self, use_logwidget=True):
+    def setupUi(self, use_logwidget=False):
         try:
             self.startTime = min(
                 [tr.stats.starttime for tr in self.data.wfdata])
@@ -734,11 +734,9 @@ class MainWindow(QMainWindow):
         if use_logwidget:
             self.logwidget = LogWidget(parent=None)
             self.logwidget.show()
-            self.stdout = self.logwidget.stdout
-            self.stderr = self.logwidget.stderr
 
-            sys.stdout = self.stdout
+            sys.stdout = self.logwidget.stdout
-            sys.stderr = self.stderr
+            sys.stderr = self.logwidget.stderr
 
         self.setCentralWidget(_widget)
 
@@ -2550,6 +2548,7 @@ class MainWindow(QMainWindow):
                           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)
         if self.filterActionP.isChecked():
             pickDlg.currentPhase = "P"
@@ -2663,7 +2662,7 @@ class MainWindow(QMainWindow):
         self.init_fig_dict()
         # if not self.tap:
         # init TuneAutopicker object
-        self.tap = TuneAutopicker(self)
+        self.tap = TuneAutopicker(self, self.obspy_dmt)
         # first call of update to init tabs with empty canvas
         self.update_autopicker()
         # connect update signal of TuneAutopicker with update function

README.md

@@ -24,10 +24,10 @@ It is highly recommended to use Anaconda for a simple creation of a Python insta
 
 Afterwards run (from the PyLoT main directory where the files *requirements.txt* and *pylot.yml* are located)
 
-    conda create --name pylot_38 --file requirements.txt
+    conda env create -f pylot.yml
 or
     
-    conda env create -f pylot.yml
+    conda create --name pylot_38 --file requirements.txt
 
 to create a new Anaconda environment called "pylot_38".
 
@@ -101,11 +101,11 @@ We hope to solve these with the next release.
 
 Original author(s): L. Kueperkoch, S. Wehling-Benatelli, M. Bischoff (PILOT)
 
-Developer(s): S. Wehling-Benatelli, L. Kueperkoch, K. Olbert, M. Bischoff, C. Wollin, M. Rische, M. Paffrath
+Developer(s): S. Wehling-Benatelli, M. Paffrath, L. Kueperkoch, K. Olbert, M. Bischoff, C. Wollin, M. Rische, D. Arnold, K. Cökerim, S. Zimmermann
 
 Others: A. Bruestle, T. Meier, W. Friederich
 
 
 [ObsPy]: http://github.com/obspy/obspy/wiki
 
-September 2017
+April 2022

pylot/core/pick/autopick.py

@@ -429,7 +429,7 @@ class AutopickStation(object):
             if station_coords is None:
                 exit_taupy()
                 raise AttributeError('Warning: Could not find station in metadata')
-            # TODO raise when metadata.get_coordinates returns None
+            # TODO: raise when metadata.get_coordinates returns None
             source_origin = origin[0]
             model = TauPyModel(taup_model)
             taup_phases = self.pickparams['taup_phases']
@@ -471,11 +471,13 @@ class AutopickStation(object):
             """If taupy failed to calculate theoretical starttimes, picking continues.
             For this a clean exit is required, since the P starttime is no longer relative to the theoretic onset but
             to the vertical trace starttime, eg. it can't be < 0."""
-            if self.pickparams["pstart"] < 0:
             # TODO here the pickparams is modified, instead of a copy
+            if self.pickparams["pstart"] < 0:
                 self.pickparams["pstart"] = 0
+            if self.pickparams["sstart"] < 0:
+                self.pickparams["sstart"] = 0
 
-        if self.pickparams["use_taup"] is False:
+        if get_Bool(self.pickparams["use_taup"]) is False:
             # correct user mistake where a relative cuttime is selected (pstart < 0) but use of taupy is disabled/ has
             # not the required parameters
             exit_taupy()
@@ -499,6 +501,20 @@ class AutopickStation(object):
         self.pickparams["pstart"] = max(self.pickparams["pstart"], 0)
         self.pickparams["pstop"] = min(self.pickparams["pstop"], len(self.ztrace) * self.ztrace.stats.delta)
 
+        if self.horizontal_traces_exist():
+            # for the two horizontal components take earliest and latest time to make sure that the s onset is not clipped
+            # if start and endtime of horizontal traces differ, the s windowsize will automatically increase
+            trace_s_start = min([self.etrace.stats.starttime, self.ntrace.stats.starttime])
+            # modifiy sstart and sstop relative to estimated first S arrival (relative to station time axis)
+            self.pickparams["sstart"] += (self.origin[0].time + estFirstS) - trace_s_start
+            self.pickparams["sstop"] += (self.origin[0].time + estFirstS) - trace_s_start
+            print('autopick: CF calculation times respectively:'
+                  ' sstart: {} s, sstop: {} s'.format(self.pickparams["sstart"], self.pickparams["sstop"]))
+            # make sure pstart and pstop are inside the starttime/endtime of horizontal traces
+            self.pickparams["sstart"] = max(self.pickparams["sstart"], 0)
+            self.pickparams["sstop"] = min(self.pickparams["sstop"], len(self.ntrace) * self.ntrace.stats.delta,
+                                           len(self.etrace) * self.etrace.stats.delta)
+
     def autopickstation(self):
         """
         Main function of autopickstation, which calculates P and S picks and returns them in a dictionary.
@@ -508,6 +524,17 @@ class AutopickStation(object):
         station's value is the station name on which the picks were calculated.
         :rtype: dict
         """
+
+        if get_Bool(self.pickparams['use_taup']) is True and self.origin is not None:
+            try:
+                # modify pstart, pstop, sstart, sstop to be around theoretical onset if taupy should be used,
+                # else do nothing
+                self.modify_starttimes_taupy()
+            except AttributeError as ae:
+                print(ae)
+            except MissingTraceException as mte:
+                print(mte)
+
         try:
             self.pick_p_phase()
         except MissingTraceException as mte:
@@ -515,7 +542,9 @@ class AutopickStation(object):
         except PickingFailedException as pfe:
             print(pfe)
 
-        if self.horizontal_traces_exist() and self.p_results.weight is not None and self.p_results.weight < 4:
+        if self.horizontal_traces_exist():
+            if (self.p_results.weight is not None and self.p_results.weight < 4) or \
+                    get_Bool(self.pickparams.get('use_taup')):
                 try:
                     self.pick_s_phase()
                 except MissingTraceException as mte:
@@ -661,13 +690,14 @@ class AutopickStation(object):
                         ax2.plot([self.s_results.lpp, self.s_results.lpp], [-1.1, 1.1], 'g--', label='lpp')
                         ax2.plot([self.s_results.epp, self.s_results.epp], [-1.1, 1.1], 'g--', label='epp')
                         title = '{channel}, S weight={sweight}, SNR={snr:7.2}, SNR[dB]={snrdb:7.2}'
-                        ax2.set_title(title.format(channel=self.etrace.stats.channel,
+                        ax2.set_title(title.format(channel=str(self.etrace.stats.channel),
-                                                   sweight=self.s_results.weight,
+                                                   sweight=str(self.s_results.weight),
-                                                   snr=self.s_results.snr,
+                                                   snr=str(self.s_results.snr),
-                                                   snrdb=self.s_results.snrdb))
+                                                   snrdb=str(self.s_results.snrdb)))
                     else:
                         title = '{channel}, S weight={sweight}, SNR=None, SNR[dB]=None'
-                        ax2.set_title(title.format(channel=self.etrace.stats.channel, sweight=self.s_results.weight))
+                        ax2.set_title(title.format(channel=str(self.etrace.stats.channel),
+                                                   sweight=str(self.s_results.weight)))
                 ax2.legend(loc=1)
                 ax2.set_yticks([])
                 ax2.set_ylim([-1.5, 1.5])
@@ -795,15 +825,6 @@ class AutopickStation(object):
         # save filtered trace in instance for later plotting
         self.tr_filt_z_bpz2 = tr_filt
 
-        if get_Bool(self.pickparams['use_taup']) is True and self.origin is not None:
-            try:
-                # modify pstart, pstop to be around theoretical onset if taupy should be used, else does nothing
-                self.modify_starttimes_taupy()
-            except AttributeError as ae:
-                print(ae)
-            except MissingTraceException as mte:
-                print(mte)
-
         Lc = self.pickparams['pstop'] - self.pickparams['pstart']
 
         Lwf = self.ztrace.stats.endtime - self.ztrace.stats.starttime
@@ -1127,7 +1148,9 @@ class AutopickStation(object):
                   ''.format(self.s_results.weight, self.s_results.snr, self.s_results.snrdb))
 
     def pick_s_phase(self):
-
+        if get_Bool(self.pickparams.get('use_taup')) is True:
+            cuttimesh = (self.pickparams.get('sstart'), self.pickparams.get('sstop'))
+        else:
             # determine time window for calculating CF after P onset
             cuttimesh = self._calculate_cuttimes(type='S', iteration=1)
 

pylot/core/util/array_map.py

@@ -478,6 +478,7 @@ class Array_map(QtWidgets.QWidget):
                                   picks=self._parent.get_current_event().getPick(station),
                                   autopicks=self._parent.get_current_event().getAutopick(station),
                                   filteroptions=self._parent.filteroptions, metadata=self.metadata,
+                                  model=self.parameter.get('taup_model'),
                                   event=pyl_mw.get_current_event())
             except Exception as e:
                 message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)

pylot/core/util/widgets.py

@@ -123,7 +123,7 @@ class LogWidget(QtWidgets.QWidget):
         self.layout.addWidget(self.tabs)
 
     def active_error(self):
-        if self.current_active_error == False:
+        if not self.current_active_error:
             self.current_active_error = True
             self.show()
             self.activateWindow()
@@ -3679,6 +3679,7 @@ class TuneAutopicker(QWidget):
                                picks=self.get_current_event_picks(station),
                                autopicks=self.get_current_event_autopicks(station),
                                metadata=metadata, event=event, filteroptions=filteroptions,
+                               model=self.parameter.get('taup_model'),
                                embedded=True, wftype=wftype)
         self.pickDlg.update_picks.connect(self.picks_from_pickdlg)
         self.pickDlg.update_picks.connect(self.fill_eventbox)