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

QtPyLoT.py

@@ -24,6 +24,7 @@ https://www.iconfinder.com/iconsets/flavour
 """
 
 import os, sys
+from os.path import expanduser
 import matplotlib
 
 matplotlib.use('Qt4Agg')
@@ -670,7 +671,8 @@ class MainWindow(QMainWindow):
         self.logDockWidget.setWidget(self.listWidget)
         self.addDockWidget(Qt.LeftDockWidgetArea, self.logDockWidget)
         self.addListItem('loading default values for local data ...')
-        autopick_parameter = AutoPickParameter('autoPyLoT_local.in')
+        home = expanduser("~")
+        autopick_parameter = AutoPickParameter('%s/.pylot/autoPyLoT_local.in' % home)
         self.addListItem(str(autopick_parameter))
 
         # Create the worker thread and run it

autoPyLoT.py

@@ -6,6 +6,7 @@ import argparse
 import glob
 import subprocess
 import string
+import numpy as np
 from obspy.core import read, UTCDateTime
 from pylot.core.read.data import Data
 from pylot.core.read.inputs import AutoPickParameter
@@ -141,7 +142,8 @@ def autoPyLoT(inputfile):
                             # calculating seismic moment Mo and moment magnitude Mw
                             finalpicks = M0Mw(wfdat, None, None,  parameter.getParam('iplot'), \
                                           nllocfile, picks, parameter.getParam('rho'), \
-                                          parameter.getParam('vp'), parameter.getParam('invdir'))
+                                          parameter.getParam('vp'), parameter.getParam('Qp'), \
+                                          parameter.getParam('invdir'))
                         else:
                             print("autoPyLoT: No NLLoc-location file available!")
                             print("No source parameter estimation possible!")
@@ -161,6 +163,8 @@ def autoPyLoT(inputfile):
                                 picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
                                 # write phases to NLLoc-phase file
                                 picksExport(picks, 'NLLoc', phasefile)
+                                # remove actual NLLoc-location file to keep only the last
+                                os.remove(nllocfile)
                                 # locate the event
                                 locate(nlloccall, ctrfile)
                                 print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
@@ -180,14 +184,25 @@ def autoPyLoT(inputfile):
                             # calculating seismic moment Mo and moment magnitude Mw
                             finalpicks = M0Mw(wfdat, None, None,  parameter.getParam('iplot'), \
                                           nllocfile, picks, parameter.getParam('rho'), \
-                                          parameter.getParam('vp'), parameter.getParam('invdir'))
+                                          parameter.getParam('vp'), parameter.getParam('Qp'), \
+                                          parameter.getParam('invdir'))
+                            # get network moment magntiude
+                            netMw = []
+                            for key in finalpicks.getpicdic(): 
+                                 if finalpicks.getpicdic()[key]['P']['Mw'] is not None:
+                                     netMw.append(finalpicks.getpicdic()[key]['P']['Mw'])
+                            netMw = np.median(netMw)
+                            print("Network moment magnitude: %4.1f" % netMw)
                         else:
                             print("autoPyLoT: No NLLoc-location file available! Stop iteration!")
                 ##########################################################
                 # write phase files for various location routines
                 # HYPO71
-                hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, evID)
+                hypo71file = '%s/autoPyLoT_HYPO71.pha' % event
+                if finalpicks.getpicdic() is not None:
                     writephases(finalpicks.getpicdic(), 'HYPO71', hypo71file)
+                else:
+                    writephases(picks, 'HYPO71', hypo71file)
 
                 endsplash = '''------------------------------------------\n'
                                -----Finished event %s!-----\n' 
@@ -240,7 +255,8 @@ def autoPyLoT(inputfile):
                         # calculating seismic moment Mo and moment magnitude Mw
                         finalpicks = M0Mw(wfdat, None, None,  parameter.getParam('iplot'), \
                                       nllocfile, picks, parameter.getParam('rho'), \
-                                      parameter.getParam('vp'), parameter.getParam('invdir'))
+                                      parameter.getParam('vp'), parameter.getParam('Qp'), \
+                                      parameter.getParam('invdir'))
                     else:
                         print("autoPyLoT: No NLLoc-location file available!")
                         print("No source parameter estimation possible!")
@@ -260,6 +276,8 @@ def autoPyLoT(inputfile):
                             picks = iteratepicker(wfdat, nllocfile, picks, badpicks, parameter)
                             # write phases to NLLoc-phase file
                             picksExport(picks, 'NLLoc', phasefile)
+                            # remove actual NLLoc-location file to keep only the last
+                            os.remove(nllocfile)
                             # locate the event
                             locate(nlloccall, ctrfile)
                             print("autoPyLoT: Iteration No. %d finished." % nlloccounter)
@@ -279,14 +297,25 @@ def autoPyLoT(inputfile):
                         # calculating seismic moment Mo and moment magnitude Mw
                         finalpicks = M0Mw(wfdat, None, None,  parameter.getParam('iplot'), \
                                       nllocfile, picks, parameter.getParam('rho'), \
-                                      parameter.getParam('vp'), parameter.getParam('invdir'))
+                                      parameter.getParam('vp'), parameter.getParam('Qp'), \
+                                      parameter.getParam('invdir'))
+                        # get network moment magntiude
+                        netMw = []
+                        for key in finalpicks.getpicdic(): 
+                             if finalpicks.getpicdic()[key]['P']['Mw'] is not None:
+                                 netMw.append(finalpicks.getpicdic()[key]['P']['Mw'])
+                        netMw = np.median(netMw)
+                        print("Network moment magnitude: %4.1f" % netMw)
                     else:
                         print("autoPyLoT: No NLLoc-location file available! Stop iteration!")
             ##########################################################
             # write phase files for various location routines
             # HYPO71
             hypo71file = '%s/%s/autoPyLoT_HYPO71.pha' % (datapath, parameter.getParam('eventID'))
+            if finalpicks.getpicdic() is not None:
                 writephases(finalpicks.getpicdic(), 'HYPO71', hypo71file)
+            else:
+                writephases(picks, 'HYPO71', hypo71file)
            
             endsplash = '''------------------------------------------\n'
                            -----Finished event %s!-----\n' 

autoPyLoT_local.in

@@ -25,16 +25,15 @@ AUTOLOC_nlloc                       #outpatter#    %pattern of NLLoc-output file
                                                    %(returns 'eventID_outpatter')
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #parameters for seismic moment estimation#
-3000                                #vp#           %average P-wave velocity
+3530                                #vp#           %average P-wave velocity
-2600                                #rho#          %rock density [kg/m^3]
+2500                                #rho#          %average rock density [kg/m^3]
-300                                 #Qp#           %quality factor for P waves
+300f**0.8                           #Qp#           %quality factor for P waves (Qp*f^a)
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 AUTOFOCMEC_AIC_HOS4_ARH.in          #focmecin#     %name of focmec input file containing polarities
 6                                   #pmin#         %minimum required P picks for location
 4                                   #p0min#        %minimum required P picks for location if at least
                                                    %3 excellent P picks are found
 2                                   #smin#         %minimum required S picks for location
-/home/ludger/bin/run_HYPOSAT4autoPILOT.csh #cshellp# %path and name of c-shell script to run location routine
 7.6 8.5                             #blon#         %longitude bounding for location map
 49 49.4                             #blat#         %lattitude bounding for location map
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

pylot/core/analysis/magnitude.py

@@ -12,7 +12,7 @@ from obspy.core import Stream, UTCDateTime
 from pylot.core.pick.utils import getsignalwin, crossings_nonzero_all
 from pylot.core.util.utils import getPatternLine
 from scipy.optimize import curve_fit
-from scipy import integrate
+from scipy import integrate, signal
 from pylot.core.read.data import Data
 
 class Magnitude(object):
@@ -23,7 +23,7 @@ class Magnitude(object):
     '''
 
     def __init__(self, wfstream, To, pwin, iplot, NLLocfile=None, \
-                 picks=None, rho=None, vp=None, invdir=None):
+                 picks=None, rho=None, vp=None, Qp=None, invdir=None):
         '''
         :param: wfstream
         :type: `~obspy.core.stream.Stream
@@ -66,6 +66,7 @@ class Magnitude(object):
         self.setrho(rho)
         self.setpicks(picks)
         self.setvp(vp)
+        self.setQp(Qp)
         self.setinvdir(invdir)
         self.calcwapp()
         self.calcsourcespec()
@@ -114,6 +115,12 @@ class Magnitude(object):
     def getvp(self):
         return self.vp
 
+    def setQp(self, Qp):
+        self.Qp = Qp
+  
+    def getQp(self):
+        return self.Qp
+
     def setpicks(self, picks):
         self.picks = picks
 
@@ -200,7 +207,7 @@ class WApp(Magnitude):
 class M0Mw(Magnitude):
     '''
     Method to calculate seismic moment Mo and moment magnitude Mw.
-    Requires results of class w0fc for calculating plateau w0 
+    Requires results of class calcsourcespec for calculating plateau w0 
     and corner frequency fc of source spectrum, respectively. Uses 
     subfunction calcMoMw.py. Returns modified dictionary of picks including 
     Dc-value, corner frequency fc, seismic moment Mo and 
@@ -212,17 +219,12 @@ class M0Mw(Magnitude):
         picks = self.getpicks()
         nllocfile = self.getNLLocfile()
         wfdat = self.getwfstream()
-        # get vertical component data only
+        self.picdic = None
-        zdat = wfdat.select(component="Z")
-        if len(zdat) == 0:  # check for other components
-            zdat = wfdat.select(component="3")
 
         for key in picks:
              if picks[key]['P']['weight'] < 4:
                  # select waveform
-                 selwf = zdat.select(station=key)
+                 selwf = wfdat.select(station=key)
-                 # get hypocentral distance of station
-                 # from NLLoc-location file
                  if len(key) > 4:
                      Ppattern = '%s  ?    ?    ? P' % key
                  elif len(key) == 4:
@@ -230,15 +232,23 @@ class M0Mw(Magnitude):
                  elif len(key) < 4:
                      Ppattern = '%s    ?    ?    ? P' % key
                  nllocline = getPatternLine(nllocfile, Ppattern)
+                 # get hypocentral distance, station azimuth and
+                 # angle of incidence from NLLoc-location file
                  delta = float(nllocline.split(None)[21])
+                 az = float(nllocline.split(None)[22])
+                 inc = float(nllocline.split(None)[24])
                  # call subfunction to estimate source spectrum
                  # and to derive w0 and fc 
                  [w0, fc] = calcsourcespec(selwf, picks[key]['P']['mpp'], \
-                             self.getiplot(), self.getinvdir())
+                             self.getinvdir(), az, inc, self.getQp(), \
+                             self.getiplot())
 
                  if w0 is not None:
                      # call subfunction to calculate Mo and Mw
-                     [Mo, Mw] = calcMoMw(selwf, w0, self.getrho(), self.getvp(), \
+                     zdat = selwf.select(component="Z")
+                     if len(zdat) == 0:  # check for other components
+                         zdat = selwf.select(component="3")
+                     [Mo, Mw] = calcMoMw(zdat, w0, self.getrho(), self.getvp(), \
                                  delta, self.getinvdir())
                  else:
                      Mo = None
@@ -276,70 +286,119 @@ def calcMoMw(wfstream, w0, rho, vp, delta, inv):
 
         
 
-def calcsourcespec(wfstream, onset, iplot, inventory):
+def calcsourcespec(wfstream, onset, inventory, azimuth, incidence, Qp, iplot):
     '''
     Subfunction to calculate the source spectrum and to derive from that the plateau
     (usually called omega0) and the corner frequency assuming Aki's omega-square
     source model. Has to be derived from instrument corrected displacement traces,
-    thus restitution and integration necessary!
+    thus restitution and integration necessary! Integrated traces have to be rotated
+    into ray-coordinate system ZNE => LQT!
     '''
     print ("Calculating source spectrum ....")
 
+    # get Q value
+    qu = Qp.split('f**')
+    # constant Q
+    Q = int(qu[0])
+    # A, i.e. power of frequency
+    A = float(qu[1])
+
     fc = None
     w0 = None
     data = Data()
-    z_copy = wfstream.copy()
+    wf_copy = wfstream.copy()
-
-    [corzdat, restflag] = data.restituteWFData(inventory, z_copy)
 
+    [cordat, restflag] = data.restituteWFData(inventory, wf_copy)
     if restflag == 1:
-        # integrate to displacment
+        zdat = cordat.select(component="Z")
-        corintzdat = integrate.cumtrapz(corzdat[0], None, corzdat[0].stats.delta)
+        if len(zdat) == 0:
-        z_copy[0].data = corintzdat
+            zdat = cordat.select(component="3")
-        tr = z_copy[0]
+        cordat_copy = cordat.copy()
+        # get equal time stamps and lengths of traces
+        # necessary for rotation of traces
+        tr0start = cordat_copy[0].stats.starttime
+        tr0start = tr0start.timestamp
+        tr0end = cordat_copy[0].stats.endtime
+        tr0end = tr0end.timestamp
+        tr1start = cordat_copy[1].stats.starttime
+        tr1start = tr1start.timestamp
+        tr1end = cordat_copy[1].stats.endtime
+        tr1end = tr1end.timestamp
+        tr2start = cordat_copy[2].stats.starttime
+        tr2start = tr2start.timestamp
+        tr2end = cordat_copy[0].stats.endtime
+        tr2end = tr2end.timestamp
+        trstart = UTCDateTime(max([tr0start, tr1start, tr2start]))
+        trend = UTCDateTime(min([tr0end, tr1end, tr2end]))
+        cordat_copy.trim(trstart, trend)
+        minlen = min([len(cordat_copy[0]), len(cordat_copy[1]), len(cordat_copy[2])])
+        cordat_copy[0].data = cordat_copy[0].data[0:minlen]
+        cordat_copy[1].data = cordat_copy[1].data[0:minlen]
+        cordat_copy[2].data = cordat_copy[2].data[0:minlen]
+        try:
+            # rotate into LQT (ray-coordindate-) system using Obspy's rotate
+            # L: P-wave direction
+            # Q: SV-wave direction
+            # T: SH-wave direction
+            LQT=cordat_copy.rotate('ZNE->LQT',azimuth, incidence)
+            ldat = LQT.select(component="L")
+            if len(ldat) == 0:
+                # yet Obspy's rotate can not handle channels 3/2/1
+                ldat = LQT.select(component="Z")
+
+            # integrate to displacement
+            # unrotated vertical component (for copmarison)
+            inttrz = signal.detrend(integrate.cumtrapz(zdat[0].data, None, \
+                      zdat[0].stats.delta))
+            # rotated component Z => L
+            Ldat = signal.detrend(integrate.cumtrapz(ldat[0].data, None, \
+                    ldat[0].stats.delta))
+
             # get window after P pulse for 
             # calculating source spectrum
-        if tr.stats.sampling_rate <= 100:
+            if zdat[0].stats.sampling_rate <= 100:
-            winzc = tr.stats.sampling_rate
+                winzc = zdat[0].stats.sampling_rate
-        elif tr.stats.sampling_rate > 100 and \
+            elif zdat[0].stats.sampling_rate > 100 and \
-              tr.stats.sampling_rate <= 200:
+                  zdat[0].stats.sampling_rate <= 200:
-             winzc = 0.5 * tr.stats.sampling_rate
+                 winzc = 0.5 * zdat[0].stats.sampling_rate
-        elif tr.stats.sampling_rate > 200 and \
+            elif zdat[0].stats.sampling_rate > 200 and \
-              tr.stats.sampling_rate <= 400:
+                  zdat[0].stats.sampling_rate <= 400:
-             winzc = 0.2 * tr.stats.sampling_rate
+                 winzc = 0.2 * zdat[0].stats.sampling_rate
-        elif tr.stats.sampling_rate > 400:
+            elif zdat[0].stats.sampling_rate > 400:
-             winzc = tr.stats.sampling_rate
+                 winzc = zdat[0].stats.sampling_rate
-        tstart = UTCDateTime(tr.stats.starttime)
+            tstart = UTCDateTime(zdat[0].stats.starttime)
             tonset = onset.timestamp -tstart.timestamp
-        impickP = tonset * tr.stats.sampling_rate
+            impickP = tonset * zdat[0].stats.sampling_rate
-        wfzc = tr.data[impickP : impickP + winzc]
+            wfzc = Ldat[impickP : impickP + winzc]
             # get time array
-        t = np.arange(0, len(tr) * tr.stats.delta, tr.stats.delta)
+            t = np.arange(0, len(inttrz) * zdat[0].stats.delta, \
+                 zdat[0].stats.delta)
             # calculate spectrum using only first cycles of
             # waveform after P onset!
             zc = crossings_nonzero_all(wfzc)
             if np.size(zc) == 0 or len(zc) <= 3:
-            print ("Something is wrong with the waveform, "
+                print ("calcsourcespec: Something is wrong with the waveform, "
                        "no zero crossings derived!")
                 print ("No calculation of source spectrum possible!")
                 plotflag = 0
             else:
                 plotflag = 1
                 index = min([3, len(zc) - 1])
-            calcwin = (zc[index] - zc[0]) * z_copy[0].stats.delta
+                calcwin = (zc[index] - zc[0]) * zdat[0].stats.delta
                 iwin = getsignalwin(t, tonset, calcwin)
-            xdat = tr.data[iwin]
+                xdat = Ldat[iwin]
 
                 # fft
-            fny = tr.stats.sampling_rate / 2
+                fny = zdat[0].stats.sampling_rate / 2
-            l = len(xdat) / tr.stats.sampling_rate
+                l = len(xdat) / zdat[0].stats.sampling_rate
-            n = tr.stats.sampling_rate * l # number of fft bins after Bath
+                # number of fft bins after Bath
+                n = zdat[0].stats.sampling_rate * l 
                 # find next power of 2 of data length
                 m = pow(2, np.ceil(np.log(len(xdat)) / np.log(2)))
                 N = int(np.power(m, 2))
-            y = tr.stats.delta * np.fft.fft(xdat, N)
+                y = zdat[0].stats.delta * np.fft.fft(xdat, N)
                 Y = abs(y[: N/2])
-            L = (N - 1) / tr.stats.sampling_rate
+                L = (N - 1) / zdat[0].stats.sampling_rate
                 f = np.arange(0, fny, 1/L)
 
                 # remove zero-frequency and frequencies above
@@ -348,51 +407,65 @@ def calcsourcespec(wfstream, onset, iplot, inventory):
                 fi = np.where((f >= 1) & (f < 100))
                 F = f[fi]
                 YY = Y[fi]
+                # correction for attenuation 
+                YYcor = YY.real*Q**A
                 # get plateau (DC value) and corner frequency
                 # initial guess of plateau
-            w0in = np.mean(YY[0:100])
+                w0in = np.mean(YYcor[0:100])
                 # initial guess of corner frequency
                 # where spectral level reached 50% of flat level
-            iin = np.where(YY >= 0.5 * w0in)
+                iin = np.where(YYcor >= 0.5 * w0in)
                 Fcin = F[iin[0][np.size(iin) - 1]]
 
                 # use of implicit scipy otimization function
                 fit = synthsourcespec(F, w0in, Fcin)
-            [optspecfit, pcov] = curve_fit(synthsourcespec, F, YY.real, [w0in, Fcin])
+                [optspecfit, pcov] = curve_fit(synthsourcespec, F, YYcor, [w0in, Fcin])
                 w01 = optspecfit[0]
                 fc1 = optspecfit[1]
-            print ("w0fc: Determined w0-value: %e m/Hz, \n"
+                print ("calcsourcespec: Determined w0-value: %e m/Hz, \n"
                        "Determined corner frequency: %f Hz" % (w01, fc1))
         
                 # use of conventional fitting 
-            [w02, fc2] = fitSourceModel(F, YY.real, Fcin, iplot)
+                [w02, fc2] = fitSourceModel(F, YYcor, Fcin, iplot)
  
                 # get w0 and fc as median 
                 w0 = np.median([w01, w02])
                 fc = np.median([fc1, fc2])
-            print("w0fc: Using w0-value = %e m/Hz and fc = %f Hz" % (w0, fc))
+                print("calcsourcespec: Using w0-value = %e m/Hz and fc = %f Hz" % (w0, fc))
+   
+        except TypeError as er:
+            raise TypeError('''{0}'''.format(er))
 
         if iplot > 1:
             f1 = plt.figure()
+            tLdat = np.arange(0, len(Ldat) * zdat[0].stats.delta, \
+                 zdat[0].stats.delta)
             plt.subplot(2,1,1)
             # show displacement in mm
-        plt.plot(t, np.multiply(tr, 1000), 'k')
+            p1, = plt.plot(t, np.multiply(inttrz, 1000), 'k')
+            p2, = plt.plot(tLdat, np.multiply(Ldat, 1000))
+            plt.legend([p1, p2], ['Displacement', 'Rotated Displacement'])
             if plotflag == 1:
                 plt.plot(t[iwin], np.multiply(xdat, 1000), 'g')
                 plt.title('Seismogram and P Pulse, Station %s-%s' \
-                        % (tr.stats.station, tr.stats.channel))
+                            % (zdat[0].stats.station, zdat[0].stats.channel))
             else:
                 plt.title('Seismogram, Station %s-%s' \
-                        % (tr.stats.station, tr.stats.channel))
+                            % (zdat[0].stats.station, zdat[0].stats.channel))
-        plt.xlabel('Time since %s' % tr.stats.starttime)
+            plt.xlabel('Time since %s' % zdat[0].stats.starttime)
             plt.ylabel('Displacement [mm]')
 
             if plotflag == 1:
                 plt.subplot(2,1,2)
-            plt.loglog(f, Y.real, 'k')
+                p1, = plt.loglog(f, Y.real, 'k')
-            plt.loglog(F, YY.real)
+                p2, = plt.loglog(F, YY.real)
-            plt.loglog(F, fit, 'g')
+                p3, = plt.loglog(F, YYcor, 'r')
+                p4, = plt.loglog(F, fit, 'g')
                 plt.loglog([fc, fc], [w0/100, w0], 'g') 
+                plt.legend([p1, p2, p3, p4], ['Raw Spectrum', \
+                                              'Used Raw Spectrum', \
+                                              'Q-Corrected Spectrum', \
+                                              'Fit to Spectrum'])
                 plt.title('Source Spectrum from P Pulse, w0=%e m/Hz, fc=%6.2f Hz' \
                            % (w0, fc))
                 plt.xlabel('Frequency [Hz]')
@@ -474,8 +547,13 @@ def fitSourceModel(f, S, fc0, iplot):
         STD.append(stddc + stdFC)
 
     # get best found w0 anf fc from minimum
+    if len(STD) > 0:
         fc = fc[np.argmin(STD)]
         w0 = w0[np.argmin(STD)]
+    elif len(STD) == 0:
+        fc = fc0
+        w0 = max(S)
+ 
     print("fitSourceModel: best fc: %fHz, best w0: %e m/Hz" \
            % (fc, w0))
 

pylot/core/pick/autopick.py

@@ -204,7 +204,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
             z_copy[0].data = tr_filt.data
             zne = z_copy
             if len(ndat) == 0 or len(edat) == 0:
-                msg = 'One or more horizontal components missing!\nSignal ' \
+                msg = 'One or more horizontal component(s) missing!\nSignal ' \
                       'length only checked on vertical component!\n' \
                       'Decreasing minsiglengh from {0} to ' \
                       '{1}'.format(minsiglength, minsiglength / 2)
@@ -335,15 +335,15 @@ def autopickstation(wfstream, pickparam, verbose=False):
             Sflag = 0
 
     else:
-        print("autopickstation: No vertical component data available!, "
+        print('autopickstation: No vertical component data available!, '
-              "Skipping station!")
+              'Skipping station!')
 
     if edat is not None and ndat is not None and len(edat) > 0 and len(
             ndat) > 0 and Pweight < 4:
-        msg = "Go on picking S onset ...\n" \
+        msg = 'Go on picking S onset ...\n' \
-              "##################################################\n" \
+              '##################################################\n' \
-              "Working on S onset of station {0}\nFiltering horizontal " \
+              'Working on S onset of station {0}\nFiltering horizontal ' \
-              "traces ...".format(edat[0].stats.station)
+              '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])),
@@ -424,6 +424,7 @@ def autopickstation(wfstream, pickparam, verbose=False):
                   'SNR: {1}\nGo on with refined picking ...\n' \
                   'autopickstation: re-filtering horizontal traces ' \
                   '...'.format(aicarhpick.getSlope(), aicarhpick.getSNR())
+            if verbose: print(msg)
             # re-calculate CF from re-filtered trace in vicinity of initial
             # onset
             cuttimesh2 = [round(aicarhpick.getpick() - Srecalcwin),
@@ -774,7 +775,8 @@ def autopickstation(wfstream, pickparam, verbose=False):
     # for P phase
     phase = 'P'
     phasepick = {'lpp': lpickP, 'epp': epickP, 'mpp': mpickP, 'spe': Perror,
-                 'snr': SNRP, 'snrdb': SNRPdB, 'weight': Pweight, 'fm': FM}
+                 'snr': SNRP, 'snrdb': SNRPdB, 'weight': Pweight, 'fm': FM,
+                   'w0': None, 'fc': None, 'Mo': None, 'Mw': None}
     picks = {phase: phasepick}
     # add P marker
     picks[phase]['marked'] = Pmarker

pylot/core/util/utils.py

@@ -10,165 +10,60 @@ import numpy as np
 from obspy.core import UTCDateTime
 import obspy.core.event as ope
 
-def runProgram(cmd, parameter=None):
+def createAmplitude(pickID, amp, unit, category, cinfo):
-    """
-    run an external program specified by cmd with parameters input returning the
-    stdout output
-
-    :param cmd: name of the command to run
-    :type cmd: str
-    :param parameter: filename of parameter file  or parameter string
-    :type parameter: str
-    :return: stdout output
-    :rtype: str
-    """
-
-    if parameter:
-        cmd.strip()
-        cmd += ' %s 2>&1' % parameter
-
-    output = subprocess.check_output('{} | tee /dev/stderr'.format(cmd),
-                                     shell = True)
-
-def isSorted(iterable):
-    return sorted(iterable) == iterable
-
-def fnConstructor(s):
-    if type(s) is str:
-        s = s.split(':')[-1]
-    else:
-        s = getHash(UTCDateTime())
-
-    badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
-    badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
-
-    fn = badchars.sub('_', s)
-
-    if badsuffix.match(fn):
-        fn = '_' + fn
-    return fn
-
-
-def getLogin():
-    return pwd.getpwuid(os.getuid())[0]
-
-
-def getHash(time):
     '''
-    :param time: time object for which a hash should be calculated
+
-    :type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
+    :param pickID:
-    :return: str
+    :param amp:
+    :param unit:
+    :param category:
+    :param cinfo:
+    :return:
     '''
-    hg = hashlib.sha1()
+    amplitude = ope.Amplitude()
-    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
+    amplitude.creation_info = cinfo
-    return hg.hexdigest()
+    amplitude.generic_amplitude = amp
+    amplitude.unit = ope.AmplitudeUnit(unit)
+    amplitude.type = ope.AmplitudeCategory(category)
+    amplitude.pick_id = pickID
+    return amplitude
 
+def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None):
+    '''
+    createArrival - function to create an Obspy Arrival
 
-def getOwner(fn):
+    :param pickresID: Resource identifier of the created pick
-    return pwd.getpwuid(os.stat(fn).st_uid).pw_name
+    :type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object
-
+    :param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
-def getPatternLine(fn, pattern):
+    holding information on the creation of the returned object
-    """
+    :type cinfo: :class: `~obspy.core.event.CreationInfo` object
-    Takes a file name and a pattern string to search for in the file and
+    :param phase: name of the arrivals seismic phase
-    returns the first line which contains the pattern string otherwise None.
+    :type phase: str
-
+    :param azimuth: azimuth between source and receiver
-    :param fn: file name
+    :type azimuth: float or int, optional
-    :type fn: str
+    :param dist: distance between source and receiver
-    :param pattern: pattern string to search for
+    :type dist: float or int, optional
-    :type pattern: str
+    :return: An ObsPy :class: `~obspy.core.event.Arrival` object
-    :return: the complete line containing pattern or None
+    '''
-
+    arrival = ope.Arrival()
-    >>> getPatternLine('utils.py', 'python')
+    arrival.creation_info = cinfo
-    '#!/usr/bin/env python\\n'
+    arrival.pick_id = pickresID
-    >>> print(getPatternLine('version.py', 'palindrome'))
+    arrival.phase = phase
-    None
+    if azimuth is not None:
-    """
+        arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360.
-    fobj = open(fn, 'r')
-    for line in fobj.readlines():
-        if pattern in line:
-            fobj.close()
-            return line
-
-    return None
-
-
-def prepTimeAxis(stime, trace):
-    nsamp = trace.stats.npts
-    srate = trace.stats.sampling_rate
-    tincr = trace.stats.delta
-    etime = stime + nsamp / srate
-    time_ax = np.arange(stime, etime, tincr)
-    if len(time_ax) < nsamp:
-        print 'elongate time axes by one datum'
-        time_ax = np.arange(stime, etime + tincr, tincr)
-    elif len(time_ax) > nsamp:
-        print 'shorten time axes by one datum'
-        time_ax = np.arange(stime, etime - tincr, tincr)
-    if len(time_ax) != nsamp:
-        raise ValueError('{0} samples of data \n '
-                         '{1} length of time vector \n'
-                         'delta: {2}'.format(nsamp, len(time_ax), tincr))
-    return time_ax
-
-
-def scaleWFData(data, factor=None, components='all'):
-    """
-    produce scaled waveforms from given waveform data and a scaling factor,
-    waveform may be selected by their components name
-    :param data: waveform data to be scaled
-    :type data: `~obspy.core.stream.Stream` object
-    :param factor: scaling factor
-    :type factor: float
-    :param components: components labels for the traces in data to be scaled by
-     the scaling factor (optional, default: 'all')
-    :type components: tuple
-    :return:  scaled waveform data
-    :rtype: `~obspy.core.stream.Stream` object
-    """
-    if components is not 'all':
-        for comp in components:
-            if factor is None:
-                max_val = np.max(np.abs(data.select(component=comp)[0].data))
-                data.select(component=comp)[0].data /= 2 * max_val
     else:
-                data.select(component=comp)[0].data /= 2 * factor
+        arrival.azimuth = azimuth
-    else:
+    arrival.distance = dist
-        for tr in data:
+    return arrival
-            if factor is None:
-                max_val = float(np.max(np.abs(tr.data)))
-                tr.data /= 2 * max_val
-            else:
-                tr.data /= 2 * factor
-
-    return data
-
-def demeanTrace(trace, window):
-    """
-    returns the DATA where each trace is demean by the average value within
-    WINDOW
-    :param trace: waveform trace object
-    :type trace: `~obspy.core.stream.Trace`
-    :param inoise: range of indices of DATA within the WINDOW
-    :type window: tuple
-    :return: trace
-    :rtype: `~obspy.core.stream.Trace`
-    """
-    trace.data -= trace.data[window].mean()
-    return trace
-
-
-def getGlobalTimes(stream):
-    min_start = UTCDateTime()
-    max_end = None
-    for trace in stream:
-        if trace.stats.starttime < min_start:
-            min_start = trace.stats.starttime
-        if max_end is None or trace.stats.endtime > max_end:
-            max_end = trace.stats.endtime
-    return min_start, max_end
-
 
 def createCreationInfo(agency_id=None, creation_time=None, author=None):
+    '''
+
+    :param agency_id:
+    :param creation_time:
+    :param author:
+    :return:
+    '''
     if author is None:
         author = getLogin()
     if creation_time is None:
@@ -176,57 +71,6 @@ def createCreationInfo(agency_id=None, creation_time=None, author=None):
     return ope.CreationInfo(agency_id=agency_id, author=author,
                             creation_time=creation_time)
 
-
-def createResourceID(timetohash, restype, authority_id=None, hrstr=None):
-    '''
-
-    :param timetohash:
-    :param restype: type of the resource, e.g. 'orig', 'earthquake' ...
-    :type restype: str
-    :param authority_id: name of the institution carrying out the processing
-    :type authority_id: str, optional
-    :return:
-    '''
-    assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
-                                                "UTCDateTime object"
-    hid = getHash(timetohash)
-    if hrstr is None:
-        resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
-    else:
-        resID = ope.ResourceIdentifier(restype + '/' + hrstr + '_' + hid[0:6])
-    if authority_id is not None:
-        resID.convertIDToQuakeMLURI(authority_id=authority_id)
-    return resID
-
-
-def createOrigin(origintime, cinfo, latitude, longitude, depth):
-    '''
-    createOrigin - function to create an ObsPy Origin
-    :param origintime: the origins time of occurence
-    :type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
-    :param latitude: latitude in decimal degree of the origins location
-    :type latitude: float
-    :param longitude: longitude in decimal degree of the origins location
-    :type longitude: float
-    :param depth: hypocentral depth of the origin
-    :type depth: float
-    :return: An ObsPy :class: `~obspy.core.event.Origin` object
-    '''
-
-    assert isinstance(origintime, UTCDateTime), "origintime has to be " \
-                                                "a UTCDateTime object, but " \
-                                                "actually is of type " \
-                                                "'%s'" % type(origintime)
-
-    origin = ope.Origin()
-    origin.time = origintime
-    origin.creation_info = cinfo
-    origin.latitude = latitude
-    origin.longitude = longitude
-    origin.depth = depth
-    return origin
-
-
 def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None,
                 authority_id=None):
     '''
@@ -271,14 +115,60 @@ def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None,
         event.origins = [o]
     return event
 
+def createMagnitude(originID, cinfo):
+    '''
+    createMagnitude - function to create an ObsPy Magnitude object
+    :param originID:
+    :type originID:
+    :param cinfo:
+    :type cinfo:
+    :return:
+    '''
+    magnitude = ope.Magnitude()
+    magnitude.creation_info = cinfo
+    magnitude.origin_id = originID
+    return magnitude
+
+def createOrigin(origintime, cinfo, latitude, longitude, depth):
+    '''
+    createOrigin - function to create an ObsPy Origin
+    :param origintime: the origins time of occurence
+    :type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
+    :param cinfo:
+    :type cinfo:
+    :param latitude: latitude in decimal degree of the origins location
+    :type latitude: float
+    :param longitude: longitude in decimal degree of the origins location
+    :type longitude: float
+    :param depth: hypocentral depth of the origin
+    :type depth: float
+    :return: An ObsPy :class: `~obspy.core.event.Origin` object
+    '''
+
+    assert isinstance(origintime, UTCDateTime), "origintime has to be " \
+                                                "a UTCDateTime object, but " \
+                                                "actually is of type " \
+                                                "'%s'" % type(origintime)
+
+    origin = ope.Origin()
+    origin.time = origintime
+    origin.creation_info = cinfo
+    origin.latitude = latitude
+    origin.longitude = longitude
+    origin.depth = depth
+    return origin
 
 def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
                wfseedstr, authority_id):
     '''
     createPick - function to create an ObsPy Pick
 
+    :param origintime:
+    :type origintime:
     :param picknum: number of the created pick
     :type picknum: int
+    :param picktime:
+    :type picktime:
     :param eventnum: human-readable event identifier
     :type eventnum: str
     :param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
@@ -306,64 +196,43 @@ def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
     pick.waveform_id = ope.ResourceIdentifier(id=wfseedstr, prefix='file:/')
     return pick
 
-
+def createResourceID(timetohash, restype, authority_id=None, hrstr=None):
-def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None):
     '''
-    createArrival - function to create an Obspy Arrival
+
-    :param pickresID: Resource identifier of the created pick
+    :param timetohash:
-    :type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object
+    :type timetohash
-    :param eventnum: human-readable event identifier
+    :param restype: type of the resource, e.g. 'orig', 'earthquake' ...
-    :type eventnum: str
+    :type restype: str
-    :param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
-    holding information on the creation of the returned object
-    :type cinfo: :class: `~obspy.core.event.CreationInfo` object
-    :param phase: name of the arrivals seismic phase
-    :type phase: str
-    :param station: name of the station at which the seismic phase has been
-    picked
-    :type station: str
     :param authority_id: name of the institution carrying out the processing
-    :type authority_id: str
+    :type authority_id: str, optional
-    :param azimuth: azimuth between source and receiver
+    :param hrstr:
-    :type azimuth: float or int, optional
+    :type hrstr:
-    :param dist: distance between source and receiver
-    :type dist: float or int, optional
-    :return: An ObsPy :class: `~obspy.core.event.Arrival` object
-    '''
-    arrival = ope.Arrival()
-    arrival.creation_info = cinfo
-    arrival.pick_id = pickresID
-    arrival.phase = phase
-    if azimuth is not None:
-        arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360.
-    else:
-        arrival.azimuth = azimuth
-    arrival.distance = dist
-    return arrival
-
-
-def createMagnitude(originID, cinfo):
-    '''
-    createMagnitude - function to create an ObsPy Magnitude object
-    :param originID:
-    :param cinfo:
-    :param authority_id:
     :return:
     '''
-    magnitude = ope.Magnitude()
+    assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
-    magnitude.creation_info = cinfo
+                                                "UTCDateTime object"
-    magnitude.origin_id = originID
+    hid = getHash(timetohash)
-    return magnitude
+    if hrstr is None:
+        resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
+    else:
+        resID = ope.ResourceIdentifier(restype + '/' + hrstr + '_' + hid[0:6])
+    if authority_id is not None:
+        resID.convertIDToQuakeMLURI(authority_id=authority_id)
+    return resID
 
-
+def demeanTrace(trace, window):
-def createAmplitude(pickID, amp, unit, category, cinfo):
+    """
-    amplitude = ope.Amplitude()
+    returns the DATA where each trace is demean by the average value within
-    amplitude.creation_info = cinfo
+    WINDOW
-    amplitude.generic_amplitude = amp
+    :param trace: waveform trace object
-    amplitude.unit = ope.AmplitudeUnit(unit)
+    :type trace: `~obspy.core.stream.Trace`
-    amplitude.type = ope.AmplitudeCategory(category)
+    :param window:
-    amplitude.pick_id = pickID
+    :type window: tuple
-    return amplitude
+    :return: trace
+    :rtype: `~obspy.core.stream.Trace`
+    """
+    trace.data -= trace.data[window].mean()
+    return trace
 
 def findComboBoxIndex(combo_box, val):
     """
@@ -372,11 +241,184 @@ def findComboBoxIndex(combo_box, val):
     :param combo_box: Combo box object.
     :type combo_box: QComboBox
     :param val: Name of a combo box to search for.
+    :type val:
     :return: index value of item with name val or 0
     """
-
     return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
 
+def fnConstructor(s):
+    '''
+
+    :param s:
+    :type s:
+    :return:
+    '''
+    if type(s) is str:
+        s = s.split(':')[-1]
+    else:
+        s = getHash(UTCDateTime())
+
+    badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
+    badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
+
+    fn = badchars.sub('_', s)
+
+    if badsuffix.match(fn):
+        fn = '_' + fn
+    return fn
+
+def getGlobalTimes(stream):
+    '''
+
+    :param stream:
+    :type stream
+    :return:
+    '''
+    min_start = UTCDateTime()
+    max_end = None
+    for trace in stream:
+        if trace.stats.starttime < min_start:
+            min_start = trace.stats.starttime
+        if max_end is None or trace.stats.endtime > max_end:
+            max_end = trace.stats.endtime
+    return min_start, max_end
+
+def getHash(time):
+    '''
+    :param time: time object for which a hash should be calculated
+    :type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
+    :return: str
+    '''
+    hg = hashlib.sha1()
+    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
+    return hg.hexdigest()
+
+def getLogin():
+    '''
+
+    :return:
+    '''
+    return pwd.getpwuid(os.getuid())[0]
+
+def getOwner(fn):
+    '''
+
+    :param fn:
+    :type fn:
+    :return:
+    '''
+    return pwd.getpwuid(os.stat(fn).st_uid).pw_name
+
+def getPatternLine(fn, pattern):
+    """
+    Takes a file name and a pattern string to search for in the file and
+    returns the first line which contains the pattern string otherwise None.
+
+    :param fn: file name
+    :type fn: str
+    :param pattern: pattern string to search for
+    :type pattern: str
+    :return: the complete line containing pattern or None
+
+    >>> getPatternLine('utils.py', 'python')
+    '#!/usr/bin/env python\\n'
+    >>> print(getPatternLine('version.py', 'palindrome'))
+    None
+    """
+    fobj = open(fn, 'r')
+    for line in fobj.readlines():
+        if pattern in line:
+            fobj.close()
+            return line
+
+    return None
+
+def isSorted(iterable):
+    '''
+
+    :param iterable:
+    :type iterable:
+    :return:
+    '''
+    return sorted(iterable) == iterable
+
+def prepTimeAxis(stime, trace):
+    '''
+
+    :param stime:
+    :type stime:
+    :param trace:
+     :type trace:
+    :return:
+    '''
+    nsamp = trace.stats.npts
+    srate = trace.stats.sampling_rate
+    tincr = trace.stats.delta
+    etime = stime + nsamp / srate
+    time_ax = np.arange(stime, etime, tincr)
+    if len(time_ax) < nsamp:
+        print 'elongate time axes by one datum'
+        time_ax = np.arange(stime, etime + tincr, tincr)
+    elif len(time_ax) > nsamp:
+        print 'shorten time axes by one datum'
+        time_ax = np.arange(stime, etime - tincr, tincr)
+    if len(time_ax) != nsamp:
+        raise ValueError('{0} samples of data \n '
+                         '{1} length of time vector \n'
+                         'delta: {2}'.format(nsamp, len(time_ax), tincr))
+    return time_ax
+
+def scaleWFData(data, factor=None, components='all'):
+    """
+    produce scaled waveforms from given waveform data and a scaling factor,
+    waveform may be selected by their components name
+    :param data: waveform data to be scaled
+    :type data: `~obspy.core.stream.Stream` object
+    :param factor: scaling factor
+    :type factor: float
+    :param components: components labels for the traces in data to be scaled by
+     the scaling factor (optional, default: 'all')
+    :type components: tuple
+    :return:  scaled waveform data
+    :rtype: `~obspy.core.stream.Stream` object
+    """
+    if components is not 'all':
+        for comp in components:
+            if factor is None:
+                max_val = np.max(np.abs(data.select(component=comp)[0].data))
+                data.select(component=comp)[0].data /= 2 * max_val
+            else:
+                data.select(component=comp)[0].data /= 2 * factor
+    else:
+        for tr in data:
+            if factor is None:
+                max_val = float(np.max(np.abs(tr.data)))
+                tr.data /= 2 * max_val
+            else:
+                tr.data /= 2 * factor
+
+    return data
+
+def runProgram(cmd, parameter=None):
+    """
+    run an external program specified by cmd with parameters input returning the
+    stdout output
+
+    :param cmd: name of the command to run
+    :type cmd: str
+    :param parameter: filename of parameter file  or parameter string
+    :type parameter: str
+    :return: stdout output
+    :rtype: str
+    """
+
+    if parameter:
+        cmd.strip()
+        cmd += ' %s 2>&1' % parameter
+
+    output = subprocess.check_output('{} | tee /dev/stderr'.format(cmd),
+                                     shell = True)
+
 if __name__ == "__main__":
     import doctest
     doctest.testmod()