Merge branch 'develop' of ariadne.geophysik.rub.de:/data/git/pylot into develop

QtPyLoT.py

@@ -74,7 +74,7 @@ from pylot.core.util.connection import checkurl
 from pylot.core.util.dataprocessing import read_metadata, restitute_data
 from pylot.core.util.utils import fnConstructor, getLogin, \
     full_range, readFilterInformation, trim_station_components, check4gaps, make_pen, pick_color_plt, \
-    pick_linestyle_plt, identifyPhase, loopIdentifyPhase, remove_underscores
+    pick_linestyle_plt, identifyPhase, loopIdentifyPhase, remove_underscores, check4doubled
 from pylot.core.util.event import Event
 from pylot.core.io.location import create_creation_info, create_event
 from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
@@ -1377,7 +1377,9 @@ class MainWindow(QMainWindow):
         wfdat = self.data.getWFData()  # all available streams
         # remove possible underscores in station names
         wfdat = remove_underscores(wfdat)
+        # check for gaps and doubled channels
         check4gaps(wfdat)
+        check4doubled(wfdat)
         # trim station components to same start value
         trim_station_components(wfdat, trim_start=True, trim_end=False)
         self._stime = full_range(self.get_data().getWFData())[0]

autoPyLoT.py

@@ -26,7 +26,7 @@ from pylot.core.util.dataprocessing import restitute_data, read_metadata
 from pylot.core.util.defaults import SEPARATOR
 from pylot.core.util.event import Event
 from pylot.core.util.structure import DATASTRUCTURE
-from pylot.core.util.utils import real_None, remove_underscores, trim_station_components, check4gaps
+from pylot.core.util.utils import real_None, remove_underscores, trim_station_components, check4gaps, check4doubled
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -242,6 +242,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
             wfdat = remove_underscores(wfdat)
             # trim components for each station to avoid problems with different trace starttimes for one station
             wfdat = check4gaps(wfdat)
+            wfdat = check4doubled(wfdat)
             wfdat = trim_station_components(wfdat, trim_start=True, trim_end=False)
             metadata = read_metadata(parameter.get('invdir'))
             corr_dat = None

pylot/core/pick/autopick.py

@@ -19,7 +19,7 @@ from pylot.core.pick.picker import AICPicker, PragPicker
 from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
     getSNR, fmpicker, checkPonsets, wadaticheck
 from pylot.core.util.utils import getPatternLine, gen_Pool, identifyPhase, loopIdentifyPhase, \
-    full_range
+    real_Bool
 
 from obspy.taup import TauPyModel
 
@@ -140,7 +140,7 @@ def autopickstation(wfstream, pickparam, verbose=False,
     algoS = pickparam.get('algoS')
     sstart = pickparam.get('sstart')
     sstop = pickparam.get('sstop')
-    use_taup = pickparam.get('use_taup')
+    use_taup = real_Bool(pickparam.get('use_taup'))
     taup_model = pickparam.get('taup_model')
     bph1 = pickparam.get('bph1')
     bph2 = pickparam.get('bph2')
@@ -229,7 +229,7 @@ def autopickstation(wfstream, pickparam, verbose=False,
 
         # for global seismology: use tau-p method for estimating travel times (needs source and station coords.)
         # if not given: sets Lc to infinity to use full stream
-        if use_taup == True or use_taup == 'True':
+        if use_taup == True:
             Lc = np.inf
             print('autopickstation: use_taup flag active.')
             if not metadata[1]:
@@ -262,14 +262,23 @@ def autopickstation(wfstream, pickparam, verbose=False,
                     # modifiy pstart and pstop relative to estimated first P arrival (relative to station time axis)
                     pstart += (source_origin.time + estFirstP) - zdat[0].stats.starttime
                     pstop += (source_origin.time + estFirstP) - zdat[0].stats.starttime
-                    Lc = pstop - pstart
                     print('autopick: CF calculation times respectively:'
                           ' pstart: {} s, pstop: {} s'.format(pstart, pstop))
                 elif not origin:
                     print('No source origins given!')
-        else:
+
+        # make sure pstart and pstop are inside zdat[0]
+        pstart = max(pstart, 0)
+        pstop = min(pstop, len(zdat[0])*zdat[0].stats.delta)
+
+        if not use_taup == True or origin:
             Lc = pstop - pstart
+
         Lwf = zdat[0].stats.endtime - zdat[0].stats.starttime
+        if not Lwf > 0:
+            print('autopickstation: empty trace! Return!')
+            return
+
         Ldiff = Lwf - Lc
         if Ldiff < 0:
             msg = 'autopickstation: Cutting times are too large for actual ' \
@@ -517,16 +526,31 @@ def autopickstation(wfstream, pickparam, verbose=False,
         else:
             ndat = edat
 
-    if edat is not None and ndat is not None and len(edat) > 0 and len(
+    pickSonset = (edat is not None and ndat is not None and len(edat) > 0 and len(
-            ndat) > 0 and Pweight < 4:
+                  ndat) > 0 and Pweight < 4)
+
+    if pickSonset:
+        # determine time window for calculating CF after P onset
+        cuttimesh = [
+            round(max([mpickP + sstart, 0])), # MP MP relative time axis
+            round(min([
+                mpickP + sstop,
+                edat[0].stats.endtime-edat[0].stats.starttime,
+                ndat[0].stats.endtime-ndat[0].stats.starttime
+            ]))
+        ]
+
+        if not cuttimesh[1] >= cuttimesh[0]:
+            print('Cut window for horizontal phases too small! Will not pick S onsets.')
+            pickSonset = False
+
+    if pickSonset:
         msg = 'Go on picking S onset ...\n' \
               '##################################################\n' \
               'Working on S onset of station {0}\nFiltering horizontal ' \
               'traces ...'.format(edat[0].stats.station)
         if verbose: print(msg)
-        # determine time window for calculating CF after P onset
+
-        cuttimesh = [round(max([mpickP + sstart, 0])),
-                     round(min([mpickP + sstop, Lwf]))]
 
         if algoS == 'ARH':
             # re-create stream object including both horizontal components

pylot/core/pick/compare.py

@@ -8,6 +8,7 @@ import os
 import matplotlib.pyplot as plt
 import numpy as np
 from obspy import read_events
+from obspy.core import AttribDict
 from pylot.core.io.phases import picksdict_from_picks
 from pylot.core.util.pdf import ProbabilityDensityFunction
 from pylot.core.util.utils import find_in_list
@@ -31,7 +32,7 @@ class Comparison(object):
         for name, fn in kwargs.items():
             if isinstance(fn, PDFDictionary):
                 self._pdfs[name] = fn
-            elif isinstance(fn, dict):
+            elif isinstance(fn, dict) or isinstance(fn, AttribDict):
                 self._pdfs[name] = PDFDictionary(fn)
             else:
                 self._pdfs[name] = PDFDictionary.from_quakeml(fn)

pylot/core/util/pdf.py

@@ -248,7 +248,7 @@ class ProbabilityDensityFunction(object):
         self._x = np.array(x)
 
     @classmethod
-    def from_pick(self, lbound, barycentre, rbound, incr=0.001, decfact=0.01,
+    def from_pick(self, lbound, barycentre, rbound, incr=0.1, decfact=0.01,
                   type='exp'):
         '''
         Initialize a new ProbabilityDensityFunction object.

pylot/core/util/utils.py

@@ -221,6 +221,15 @@ def real_None(value):
         return value
 
 
+def real_Bool(value):
+    if value == 'True':
+        return True
+    elif value == 'False':
+        return False
+    else:
+        return value
+
+
 def four_digits(year):
     """
     takes a two digit year integer and returns the correct four digit equivalent
@@ -621,6 +630,31 @@ def check4gaps(data):
     return data
 
 
+def check4doubled(data):
+    '''
+    check for doubled stations for same channel in Stream and take only the first one
+    :param data: stream of seismic data
+    :return: data stream
+    '''
+    stations = get_stations(data)
+
+    for station in stations:
+        wf_station = data.select(station=station)
+        # create list of all possible channels
+        channels = []
+        for trace in wf_station:
+            channel = trace.stats.channel
+            if not channel in channels:
+                channels.append(channel)
+            else:
+                print('check4doubled: removed the following trace for station {}, as there is'
+                      ' already a trace with the same channel given:\n{}'.format(
+                    station, trace
+                ))
+                data.remove(trace)
+    return data
+
+
 def get_stations(data):
     stations = []
     for tr in data:

pylot/core/util/widgets.py

@@ -127,7 +127,7 @@ class ComparisonDialog(QDialog):
                              phasesComboBox=None,
                              histCheckBox=None)
         self._phases = 'PS'
-        self._plotprops = dict(station=self.stations[0], phase=self.phases[0])
+        self._plotprops = dict(station=list(self.stations)[0], phase=list(self.phases)[0])
         super(ComparisonDialog, self).__init__(parent)
         self.setupUI()
         self.plotcomparison()