Merge branch 'develop' into update_waveformwidget

pylot/core/util/utils.py

@@ -9,6 +9,9 @@ import subprocess
 
 import numpy as np
 from obspy import UTCDateTime, read
+from obspy.signal.rotate import rotate2zne
+from obspy.io.xseed.utils import SEEDParserException
+
 from pylot.core.io.inputs import PylotParameter
 
 from scipy.interpolate import splrep, splev
@@ -696,6 +699,94 @@ def get_stations(data):
     return stations
 
 
+def check4rotated(data, metadata=None):
+
+    def rotate_components(wfstream, metadata=None):
+        """rotates components if orientation code is numeric.
+        azimut and dip are fetched from metadata"""
+        try:
+            # indexing fails if metadata is None
+            metadata[0]
+        except:
+            msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
+            print(msg)
+            return wfstream
+        if metadata[0] is None:
+            # sometimes metadata is (None, (None,))
+            msg = 'Warning: could not rotate traces since no metadata was given\nCheck inventory directory!'
+            print(msg)
+            return wfstream
+        else:
+            parser = metadata[1]
+
+        def get_dip_azimut(parser, trace_id):
+            """gets azimut and dip for a trace out of the metadata parser"""
+            dip = None
+            azimut = None
+            try:
+                blockettes = parser._select(trace_id)
+            except SEEDParserException as e:
+                print(e)
+                raise ValueError
+            for blockette_ in blockettes:
+                if blockette_.id != 52:
+                    continue
+                dip = blockette_.dip
+                azimut = blockette_.azimuth
+                break
+            if dip is None or azimut is None:
+                error_msg = 'Dip and azimuth not available for trace_id {}'.format(trace_id)
+                raise ValueError(error_msg)
+            return dip, azimut
+
+        trace_ids = [trace.id for trace in wfstream]
+        for trace_id in trace_ids:
+            orientation = trace_id[-1]
+            if orientation.isnumeric():
+                # misaligned channels have a number as orientation
+                azimuts = []
+                dips = []
+                for trace_id in trace_ids:
+                    try:
+                        dip, azimut = get_dip_azimut(parser, trace_id)
+                    except ValueError as e:
+                        print(e)
+                        print('Failed to rotate station {}, no azimuth or dip available in metadata'.format(trace_id))
+                        return wfstream
+                    azimuts.append(azimut)
+                    dips.append(dip)
+                # to rotate all traces must have same length
+                wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
+                z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
+                                          wfstream[1], azimuts[1], dips[1],
+                                          wfstream[2], azimuts[2], dips[2])
+                print('check4rotated: rotated station {} to ZNE'.format(trace_id))
+                z_index = dips.index(min(dips)) # get z-trace index (dip is measured from 0 to -90
+                wfstream[z_index].data = z
+                wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
+                del trace_ids[z_index]
+                for trace_id in trace_ids:
+                    dip, az = get_dip_azimut(parser, trace_id)
+                    trace = wfstream.select(id=trace_id)[0]
+                    if az > 315 and az <= 45 or az > 135 and az <= 225:
+                        trace.data = n
+                        trace.stats.channel = trace.stats.channel[0:-1] + 'N'
+                    elif az > 45 and az <= 135 or az > 225 and az <= 315:
+                        trace.data = e
+                        trace.stats.channel = trace.stats.channel[0:-1] + 'E'
+                break
+            else:
+                continue
+        return wfstream
+
+    stations = get_stations(data)
+
+    for station in stations:
+        wf_station = data.select(station=station)
+        wf_station = rotate_components(wf_station, metadata)
+    return data
+
+
 def scaleWFData(data, factor=None, components='all'):
     """
     produce scaled waveforms from given waveform data and a scaling factor,

pylot/core/util/widgets.py

@@ -23,7 +23,7 @@ except:
 
 from matplotlib.figure import Figure
 from pylot.core.util.utils import find_horizontals, identifyPhase, loopIdentifyPhase, trim_station_components, \
-    identifyPhaseID
+    identifyPhaseID, check4rotated
 
 try:
     from matplotlib.backends.backend_qt4agg import FigureCanvas
@@ -440,6 +440,7 @@ class WaveformWidgetPG(QtGui.QWidget):
         self.plotWidget.showGrid(x=False, y=True, alpha=0.2)
         self.plotWidget.hideAxis('bottom')
         self.plotWidget.hideAxis('left')
+        self.wfstart, self.wfend = 0, 0
         self.reinitMoveProxy()
         self._proxy = pg.SignalProxy(self.plotWidget.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved)
 
@@ -457,8 +458,9 @@ class WaveformWidgetPG(QtGui.QWidget):
             # if x > 0:# and index < len(data1):
             wfID = self._parent.getWFID(y)
             station = self._parent.getStationName(wfID)
+            abstime = self.wfstart + x
             if self._parent.get_current_event():
-                self.label.setText("station = {}, t = {} [s]".format(station, x))
+                self.label.setText("station = {}, T = {}, t = {} [s]".format(station, abstime, x))
             self.vLine.setPos(mousePoint.x())
             self.hLine.setPos(mousePoint.y())
 
@@ -482,7 +484,7 @@ class WaveformWidgetPG(QtGui.QWidget):
                    component='*', nth_sample=1, iniPick=None, verbosity=0):
         self.title = title
         self.clearPlotDict()
-        wfstart, wfend = full_range(wfdata)
+        self.wfstart, self.wfend = full_range(wfdata)
         nmax = 0
 
         settings = QSettings()
@@ -510,7 +512,7 @@ class WaveformWidgetPG(QtGui.QWidget):
 
         try:
             self.plotWidget.getPlotItem().vb.setLimits(xMin=float(0),
-                                                       xMax=float(wfend - wfstart),
+                                                       xMax=float(self.wfend - self.wfstart),
                                                        yMin=-0.5,
                                                        yMax=len(nsc) + 0.5)
         except:
@@ -528,7 +530,7 @@ class WaveformWidgetPG(QtGui.QWidget):
             if verbosity:
                 msg = 'plotting %s channel of station %s' % (channel, station)
                 print(msg)
-            stime = trace.stats.starttime - wfstart
+            stime = trace.stats.starttime - self.wfstart
             time_ax = prepTimeAxis(stime, trace)
             if time_ax is not None:
                 if not scaleddata:
@@ -538,9 +540,9 @@ class WaveformWidgetPG(QtGui.QWidget):
                 data = [datum + n for index, datum in enumerate(trace.data) if not index % nth_sample]
                 plots.append((times, data))
                 self.setPlotDict(n, (station, channel, network))
-        self.xlabel = 'seconds since {0}'.format(wfstart)
+        self.xlabel = 'seconds since {0}'.format(self.wfstart)
         self.ylabel = ''
-        self.setXLims([0, wfend - wfstart])
+        self.setXLims([0, self.wfend - self.wfstart])
         self.setYLims([-0.5, nmax + 0.5])
         return plots
 
@@ -2291,6 +2293,8 @@ class TuneAutopicker(QWidget):
         wfdat = self.data.getWFData()  # all available streams
         # 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)
         self.stationBox.clear()
         stations = []
         for trace in self.data.getWFData():