[bugfix] pickDlg takes into account timeshift of trace.starttime for different components

[add] initial pick displayed in pickDlg

QtPyLoT.py

@@ -1616,18 +1616,24 @@ class MainWindow(QMainWindow):
             colors = phase_col[phase[0].upper()]
 
             mpp = picks['mpp'] - stime
+            if picks['epp'] and picks['lpp']:
                 epp = picks['epp'] - stime
                 lpp = picks['lpp'] - stime
             spe = picks['spe']
-            if not spe:
+            
+            if not spe and epp and lpp:
                 spe = symmetrize_error(mpp - epp, lpp - mpp)
 
             if picktype == 'manual':
+                if picks['epp'] and picks['lpp']:
                     ax.fill_between([epp, lpp], ylims[0], ylims[1],
-                                alpha=.25, color=colors[0])
+                                    alpha=.25, color=colors[0], label='EPP, LPP')
-                ax.plot([mpp - spe, mpp - spe], ylims, colors[1],
+                if spe:
-                        [mpp, mpp], ylims, colors[2],
+                    ax.plot([mpp - spe, mpp - spe], ylims, colors[1], label='{}-SPE'.format(phase))
-                        [mpp + spe, mpp + spe], ylims, colors[1])
+                    ax.plot([mpp + spe, mpp + spe], ylims, colors[1])
+                    ax.plot([mpp, mpp], ylims, colors[2], label='{}-Pick'.format(phase))
+                else:
+                    ax.plot([mpp, mpp], ylims, colors[6], label='{}-Pick (NO PICKERROR)'.format(phase))
             elif picktype == 'auto':
                 ax.plot(mpp, ylims[1], colors[3],
                         mpp, ylims[0], colors[4])

pylot/RELEASE-VERSION

@@ -1 +1 @@
-eaa4-dirty
+0430-dirty

pylot/core/io/phases.py

@@ -358,7 +358,7 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
                                            default.get('tsnrz' if phase == 'P' else 'tsnrh'),
                                            Pick1=rel_pick,
                                            iplot=None,
-                                           stealth_mode=True)
+                                           verbosity=0)
             if epp is None or lpp is None:
                 continue
             epp = stime + epp

pylot/core/pick/utils.py

@@ -14,7 +14,7 @@ import numpy as np
 from obspy.core import Stream, UTCDateTime
 
 
-def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, stealth_mode=False, fig=None):
+def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, verbosity=1, fig=None):
     '''
     Function to derive earliest and latest possible pick after Diehl & Kissling (2009)
     as reasonable uncertainties. Latest possible pick is based on noise level,
@@ -40,10 +40,16 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, stealth_mode=False, fig=Non
 
     assert isinstance(X, Stream), "%s is not a stream object" % str(X)
 
+    if verbosity == 2:
+        print('earllatepicker:')        
+        print('nfac:', nfac)
+        print('Init pick:', Pick1)
+        print('TSNR (T_noise, T_gap, T_signal):', TSNR)
+        
     LPick = None
     EPick = None
     PickError = None
-    if stealth_mode is False:
+    if verbosity:
         print('earllatepicker: Get earliest and latest possible pick'
               ' relative to most likely pick ...')
 
@@ -57,11 +63,18 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, stealth_mode=False, fig=Non
     x = x - np.mean(x[inoise])
     # calculate noise level
     nlevel = np.sqrt(np.mean(np.square(x[inoise]))) * nfac
+    if verbosity == 2:
+        print('x:', x)
+        print('t:', t)
+        print('x_inoise:', x[inoise])
+        print('x_isignal:', x[isignal])
+        print('nlevel:', nlevel)
+    
     # get time where signal exceeds nlevel
     ilup, = np.where(x[isignal] > nlevel)
     ildown, = np.where(x[isignal] < -nlevel)
     if not ilup.size and not ildown.size:
-        if stealth_mode is False:
+        if verbosity:
             print ("earllatepicker: Signal lower than noise level!\n"
                    "Skip this trace!")
         return LPick, EPick, PickError
@@ -78,7 +91,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, stealth_mode=False, fig=Non
     # if EPick stays NaN the signal window size will be doubled
     while np.isnan(EPick):
         if count > 0:
-            if stealth_mode is False:
+            if verbosity:
                 print("\nearllatepicker: Doubled signal window size %s time(s) "
                       "because of NaN for earliest pick." % count)
             isigDoubleWinStart = pis[-1] + 1
@@ -87,7 +100,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, stealth_mode=False, fig=Non
             if (isigDoubleWinStart + len(pis)) < X[0].data.size:
                 pis = np.concatenate((pis, isignalDoubleWin))
             else:
-                if stealth_mode is False:
+                if verbosity:
                     print("Could not double signal window. Index out of bounds.")
                 break
         count += 1

pylot/core/util/dataprocessing.py

@@ -169,7 +169,8 @@ def read_metadata(path_to_inventory):
     dlfile = list()
     invfile = list()
     respfile = list()
-    inv = dict(dless=dlfile, xml=invfile, resp=respfile)
+    # possible file extensions specified here:
+    inv = dict(dless=dlfile, xml=invfile, resp=respfile, dseed=dlfile)
     if os.path.isfile(path_to_inventory):
         ext = os.path.splitext(path_to_inventory)[1].split('.')[1]
         inv[ext] += [path_to_inventory]

pylot/core/util/widgets.py

@@ -431,7 +431,7 @@ class WaveformWidget(FigureCanvas):
 
     def plotWFData(self, wfdata, title=None, zoomx=None, zoomy=None,
                    noiselevel=None, scaleddata=False, mapping=True,
-                   component='*', nth_sample=1):
+                   component='*', nth_sample=1, iniPick=None):
         self.getAxes().cla()
         self.clearPlotDict()
         wfstart, wfend = full_range(wfdata)
@@ -477,6 +477,11 @@ class WaveformWidget(FigureCanvas):
                    for level in noiselevel:
                        self.getAxes().plot([time_ax[0], time_ax[-1]],
                                            [level, level], '--k')
+                if iniPick:
+                    ax = self.getAxes()
+                    ax.vlines(iniPick, ax.get_ylim()[0], ax.get_ylim()[1],
+                              colors='green', linestyles='dashed',
+                              linewidth=2)
                 self.setPlotDict(n, (station, channel, network))
         xlabel = 'seconds since {0}'.format(wfstart)
         ylabel = ''
@@ -965,6 +970,9 @@ class PickDlg(QDialog):
         while itrace > len(wfdata) - 1:
             itrace -= 1
 
+        stime = self.getStartTime()
+        stime_diff = wfdata[itrace].stats.starttime-stime
+            
         # copy data for plotting
         data = self.getWFData().copy()
 
@@ -975,7 +983,7 @@ class PickDlg(QDialog):
             data.filter(**filteroptions)
             wfdata.filter(**filteroptions)
 
-        result = getSNR(wfdata, (noise_win, gap_win, signal_win), ini_pick, itrace)
+        result = getSNR(wfdata, (noise_win, gap_win, signal_win), ini_pick-stime_diff, itrace)
 
         snr = result[0]
         noiselevel = result[2]
@@ -988,8 +996,8 @@ class PickDlg(QDialog):
 
         # remove mean noise level from waveforms
         for trace in data:
-            t = prepTimeAxis(trace.stats.starttime - self.getStartTime(), trace)
+            t = prepTimeAxis(trace.stats.starttime - stime, trace)
-            inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
+            inoise = getnoisewin(t, ini_pick-stime_diff, noise_win, gap_win)
             trace = demeanTrace(trace=trace, window=inoise)
 
         self.setXLims([ini_pick - x_res, ini_pick + x_res])
@@ -1001,7 +1009,8 @@ class PickDlg(QDialog):
                                         zoomx=self.getXLims(),
                                         zoomy=self.getYLims(),
                                         noiselevel=(trace_number + noiselevel,
-                                                    trace_number - noiselevel))
+                                                    trace_number - noiselevel),
+                                        iniPick=ini_pick)
 
     def setIniPickS(self, gui_event, wfdata):
 
@@ -1014,6 +1023,9 @@ class PickDlg(QDialog):
         gap_win = twins[1]
         signal_win = twins[2]
 
+        stime = self.getStartTime()
+        stime_diff = wfdata[0].stats.starttime-stime
+        
         # copy data for plotting
         data = self.getWFData().copy()
 
@@ -1025,7 +1037,7 @@ class PickDlg(QDialog):
             wfdata.filter(**filteroptions)
 
         # determine SNR and noiselevel
-        result = getSNR(wfdata, (noise_win, gap_win, signal_win), ini_pick)
+        result = getSNR(wfdata, (noise_win, gap_win, signal_win), ini_pick-stime_diff)
         snr = result[0]
         noiselevel = result[2]
 
@@ -1036,8 +1048,8 @@ class PickDlg(QDialog):
 
         # prepare plotting of data
         for trace in data:
-            t = prepTimeAxis(trace.stats.starttime - self.getStartTime(), trace)
+            t = prepTimeAxis(trace.stats.starttime - stime, trace)
-            inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
+            inoise = getnoisewin(t, ini_pick-stime_diff, noise_win, gap_win)
             trace = demeanTrace(trace, inoise)
 
         # scale waveform for plotting
@@ -1060,7 +1072,8 @@ class PickDlg(QDialog):
                                         zoomx=self.getXLims(),
                                         zoomy=self.getYLims(),
                                         noiselevel=noiselevels,
-                                        scaleddata=True)
+                                        scaleddata=True,
+                                        iniPick=ini_pick)
 
     def setPick(self, gui_event):
 
@@ -1092,13 +1105,17 @@ class PickDlg(QDialog):
             nfac = parameter.get('nfacS')
             TSNR = parameter.get('tsnrh')
             
-        [epp, lpp, spe] = earllatepicker(wfdata, nfac, (TSNR[0], TSNR[1], TSNR[2]), pick)
-
         # return absolute time values for phases
         stime = self.getStartTime()
-        epp = stime + epp
+        stime_diff = wfdata[0].stats.starttime-stime
+           
+        [epp, lpp, spe] = earllatepicker(wfdata, nfac, (TSNR[0], TSNR[1], TSNR[2]), pick-stime_diff, verbosity=2)
+        
         mpp = stime + pick
-        lpp = stime + lpp
+        if epp:
+            epp = stime + epp + stime_diff
+        if lpp:
+            lpp = stime + lpp + stime_diff
 
         # save pick times for actual phase
         phasepicks = dict(epp=epp, lpp=lpp, mpp=mpp, spe=spe,
@@ -1147,8 +1164,8 @@ class PickDlg(QDialog):
         ax = self.getPlotWidget().axes
         ylims = self.getGlobalLimits('y')
         phase_col = {
-            'P': ('c', 'c--', 'b-', 'bv', 'b^', 'b'),
+            'P': ('c', 'c--', 'b-', 'bv', 'b^', 'b', 'c:'),
-            'S': ('m', 'm--', 'r-', 'rv', 'r^', 'r')
+            'S': ('m', 'm--', 'r-', 'rv', 'r^', 'r', 'm:')
         }
         if self.getPicks(picktype):
             if phase is not None and type(self.getPicks(picktype)[phase]) is dict:
@@ -1164,23 +1181,29 @@ class PickDlg(QDialog):
             return
 
         mpp = picks['mpp'] - self.getStartTime()
+        if picks['epp'] and picks['lpp']:
             epp = picks['epp'] - self.getStartTime()
             lpp = picks['lpp'] - self.getStartTime()
         spe = picks['spe']
 
         if picktype == 'manual':
+            if picks['epp'] and picks['lpp']:            
                 ax.fill_between([epp, lpp], ylims[0], ylims[1],
-                            alpha=.25, color=colors[0])
+                                alpha=.25, color=colors[0], label='EPP, LPP')
             if spe:
-                ax.plot([mpp - spe, mpp - spe], ylims, colors[1],
+                ax.plot([mpp - spe, mpp - spe], ylims, colors[1], label='{}-SPE'.format(phase))
-                        [mpp, mpp], ylims, colors[2],
+                ax.plot([mpp + spe, mpp + spe], ylims, colors[1])
-                        [mpp + spe, mpp + spe], ylims, colors[1])
+                ax.plot([mpp, mpp], ylims, colors[2], label='{}-Pick'.format(phase))
+            else:
+                ax.plot([mpp, mpp], ylims, colors[6], label='{}-Pick (NO PICKERROR)'.format(phase)) 
+                
         elif picktype == 'auto':
             ax.plot(mpp, ylims[1], colors[3],
                     mpp, ylims[0], colors[4])
             ax.vlines(mpp, ylims[0], ylims[1], colors[5], linestyles='dotted')
         else:
             raise TypeError('Unknown picktype {0}'.format(picktype))
+        ax.legend()
             
 
     def panPress(self, gui_event):