Merge remote-tracking branch 'origin/develop' into develop

pylot/core/pick/charfuns.py

@@ -222,9 +222,9 @@ class AICcf(CharacteristicFunction):
 
         x = self.getDataArray()
         xnp = x[0].data
-        nn = np.isnan(xnp)
+        ind = np.where(~np.isnan(xnp))[0]
-        if len(nn) > 1:
+        if ind.size:
-            xnp[nn] = 0
+            xnp[:ind[0]] = xnp[ind[0]]
         datlen = len(xnp)
         k = np.arange(1, datlen)
         cf = np.zeros(datlen)
@@ -335,6 +335,7 @@ class ARZcf(CharacteristicFunction):
         cf = tap * cf
         io = np.where(cf == 0)
         ino = np.where(cf > 0)
+        if np.size(ino):
             cf[io] = cf[ino[0][0]]
 
         self.cf = cf
@@ -467,6 +468,7 @@ class ARHcf(CharacteristicFunction):
         cf = tap * cf
         io = np.where(cf == 0)
         ino = np.where(cf > 0)
+        if np.size(ino):
             cf[io] = cf[ino[0][0]]
 
         self.cf = cf
@@ -609,6 +611,7 @@ class AR3Ccf(CharacteristicFunction):
         cf = tap * cf
         io = np.where(cf == 0)
         ino = np.where(cf > 0)
+        if np.size(ino):
             cf[io] = cf[ino[0][0]]
 
         self.cf = cf

pylot/core/pick/utils.py

@@ -591,6 +591,7 @@ def wadaticheck(pickdic, dttolerance, iplot=0, fig_dict=None):
     Ppicks = []
     Spicks = []
     SPtimes = []
+    stations = []
     for key in list(pickdic.keys()):
         if pickdic[key]['P']['weight'] < 4 and pickdic[key]['S']['weight'] < 4:
             # calculate S-P time
@@ -624,6 +625,7 @@ def wadaticheck(pickdic, dttolerance, iplot=0, fig_dict=None):
         ibad = 0
         for key in list(pickdic.keys()):
             if 'SPt' in pickdic[key]:
+                stations.append(key)
                 wddiff = abs(pickdic[key]['SPt'] - wdfit[ii])
                 ii += 1
                 # check, if deviation is larger than adjusted
@@ -684,15 +686,21 @@ def wadaticheck(pickdic, dttolerance, iplot=0, fig_dict=None):
             linecolor = 'k'
             plt_flag = 1
         ax = fig.add_subplot(111)
+        if ibad > 0:
             ax.plot(Ppicks, SPtimes, 'ro', label='Skipped S-Picks')
         if wfitflag == 0:
             ax.plot(Ppicks, wdfit, color=linecolor, linewidth=0.7, label='Wadati 1')
+            ax.plot(Ppicks, wdfit+dttolerance, color='0.9', linewidth=0.5, label='Wadati 1 Tolerance')
+            ax.plot(Ppicks, wdfit-dttolerance, color='0.9', linewidth=0.5)
+            ax.plot(checkedPpicks, wdfit2, 'g', label='Wadati 2')
             ax.plot(checkedPpicks, checkedSPtimes, color=linecolor,
                     linewidth=0, marker='o', label='Reliable S-Picks')
-            ax.plot(checkedPpicks, wdfit2, 'g', label='Wadati 2')
+            for Ppick, SPtime, station in zip(Ppicks, SPtimes, stations):
+                ax.text(Ppick, SPtime + 0.01, '{0}'.format(station))
+
             ax.set_title('Wadati-Diagram, %d S-P Times, Vp/Vs(raw)=%5.2f,' \
                       'Vp/Vs(checked)=%5.2f' % (len(SPtimes), vpvsr, cvpvsr))
-            ax.legend(loc=1)
+            ax.legend(loc=1, numpoints=1)
         else:
             ax.set_title('Wadati-Diagram, %d S-P Times' % len(SPtimes))
 
@@ -911,19 +919,22 @@ def checkPonsets(pickdic, dttolerance, jackfactor=5, iplot=0, fig_dict=None):
             plt_flag = 1
         ax = fig.add_subplot(111)
 
-        ax.plot(np.arange(0, len(Ppicks)), Ppicks, 'ro', markersize=14)
+        if len(badstations) > 0:
-        if len(badstations) < 1 and len(badjkstations) < 1:
+            ax.plot(ibad, np.array(Ppicks)[ibad], marker ='o', markerfacecolor='orange', markersize=14,
-            ax.plot(np.arange(0, len(Ppicks)), Ppicks, 'go', markersize=14, label='Skipped P Picks')
+                    linestyle='None', label='Median Skipped P Picks')
-        else:
+        if len(badjkstations) > 0:
+            ax.plot(badjk[0], np.array(Ppicks)[badjk], 'ro', markersize=14, label='Jackknife Skipped P Picks')
         ax.plot(igood, np.array(Ppicks)[igood], 'go', markersize=14, label='Good P Picks')
-            ax.plot([0, len(Ppicks) - 1], [pmedian, pmedian], 'g',
+        ax.plot([0, len(Ppicks) - 1], [pmedian, pmedian], 'g', linewidth=2, label='Median')
-                       linewidth=2, label='Median')
+        ax.plot([0, len(Ppicks) - 1], [pmedian + dttolerance, pmedian + dttolerance], 'g--', linewidth=1.2,
-        for i in range(0, len(Ppicks)):
+                dashes=[25, 25], label='Median Tolerance')
-            ax.text(i, Ppicks[i] + 0.01, '{0}'.format(stations[i]))
+        ax.plot([0, len(Ppicks) - 1], [pmedian - dttolerance, pmedian - dttolerance], 'g--', linewidth=1.2,
-
+                dashes=[25, 25])
+        for index, pick in enumerate(Ppicks):
+            ax.text(index, pick + 0.01, '{0}'.format(stations[i]))
         ax.set_xlabel('Number of P Picks')
         ax.set_ylabel('Onset Time [s] from 1.1.1970')
-        ax.legend(loc=1)
+        ax.legend(loc=1, numpoints=1)
         ax.set_title('Jackknifing and Median Tests on P Onsets')
         if plt_flag:
             fig.show()

pylot/core/util/widgets.py

@@ -48,7 +48,8 @@ from pylot.core.pick.compare import Comparison
 from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS, \
     SetChannelComponents
 from pylot.core.util.utils import prepTimeAxis, full_range, scaleWFData, \
-    demeanTrace, isSorted, findComboBoxIndex, clims, pick_linestyle_plt, pick_color_plt
+    demeanTrace, isSorted, findComboBoxIndex, clims, pick_linestyle_plt, pick_color_plt, \
+    check4rotated, check4doubled, check4gaps, remove_underscores
 from autoPyLoT import autoPyLoT
 from pylot.core.util.thread import Thread
 
@@ -1601,6 +1602,7 @@ class PickDlg(QDialog):
         return self.station
 
     def getChannelID(self, key):
+        if key < 0: key = 0
         return self.multicompfig.getPlotDict()[int(key)][1]
 
     def getTraceID(self, channels):
@@ -2493,6 +2495,7 @@ class TuneAutopicker(QWidget):
 
     def init_stationlist(self):
         self.stationBox = QtGui.QComboBox()
+        self.stationBox.setMaxVisibleItems(42)
         self.trace_layout.addWidget(self.stationBox)
         self.fill_stationbox()
         self.figure_tabs.setCurrentIndex(0)
@@ -2507,10 +2510,15 @@ class TuneAutopicker(QWidget):
         fnames = self.parent().getWFFnames_from_eventbox(eventbox=self.eventBox)
         self.data.setWFData(fnames)
         wfdat = self.data.getWFData()  # all available streams
+        # remove possible underscores in station names
+        wfdat = remove_underscores(wfdat)
+        # rotate misaligned stations to ZNE
+        # check for gaps and doubled channels
+        check4gaps(wfdat)
+        check4doubled(wfdat)
+        wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
         # trim station components to same start value
         trim_station_components(wfdat, trim_start=True, trim_end=False)
-        # rotate misaligned stations to ZNE
-        wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
         self.stationBox.clear()
         stations = []
         for trace in self.data.getWFData():