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

Conflicts:
	pylot/core/pick/utils.py

pylot/core/pick/utils.py

@@ -66,8 +66,8 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
 
     # get earliest possible pick
 
-    #determine all zero crossings in signal window
+    # determine all zero crossings in signal window (demeaned)
-    zc = crossings_nonzero_all(x[isignal])
+    zc = crossings_nonzero_all(x[isignal] - x[isignal].mean())
     # calculate mean half period T0 of signal as the average of the
     T0 = np.mean(np.diff(zc)) * X[0].stats.delta  # this is half wave length!
     # T0/4 is assumed as time difference between most likely and earliest possible pick!
@@ -85,7 +85,8 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
         p2, = plt.plot(t[inoise], x[inoise])
         p3, = plt.plot(t[isignal], x[isignal], 'r')
         p4, = plt.plot([t[0], t[int(len(t)) - 1]], [nlevel, nlevel], '--k')
-        p5, = plt.plot(t[isignal[0][zc]], np.zeros(len(zc)), '*g', markersize=14)
+        p5, = plt.plot(t[isignal[0][zc]], np.zeros(len(zc)), '*g',
+                       markersize=14)
         plt.legend([p1, p2, p3, p4, p5],
                    ['Data', 'Noise Window', 'Signal Window', 'Noise Level',
                     'Zero Crossings'], \
@@ -281,11 +282,13 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
 
     return FM
 
+
 def crossings_nonzero_all(data):
     pos = data > 0
     npos = ~pos
     return ((pos[:-1] & npos[1:]) | (npos[:-1] & pos[1:])).nonzero()[0]
 
+
 def getSNR(X, TSNR, t1):
     '''
     Function to calculate SNR of certain part of seismogram relative to
@@ -383,6 +386,7 @@ def getsignalwin(t, t1, tsignal):
 
     return isignal
 
+
 def wadaticheck(pickdic, dttolerance, iplot):
     '''
     Function to calculate Wadati-diagram from given P and S onsets in order
@@ -413,12 +417,18 @@ def wadaticheck(pickdic, dttolerance, iplot):
             # add S-P time to dictionary
             pickdic[key]['SPt'] = spt
             # add P onsets and corresponding S-P times to list
-           UTCPpick = UTCDateTime(pickdic[key]['P']['mpp'])
+            UTCPpick = UTCDateTime(pickdic[key]['P']['mpp']) - UTCDateTime(1970,
-           UTCSpick = UTCDateTime(pickdic[key]['S']['mpp'])
+                                                                           1, 1,
-           Ppicks.append(UTCPpick.timestamp)
+                                                                           0, 0,
-           Spicks.append(UTCSpick.timestamp)
+                                                                           0)
+            UTCSpick = UTCDateTime(pickdic[key]['S']['mpp']) - UTCDateTime(1970,
+                                                                           1, 1,
+                                                                           0, 0,
+                                                                           0)
+            Ppicks.append(UTCPpick)
+            Spicks.append(UTCSpick)
             SPtimes.append(spt)
-
+            vpvs.append(UTCPpick / UTCSpick)
 
     if len(SPtimes) >= 3:
         # calculate slope
@@ -447,12 +457,16 @@ def wadaticheck(pickdic, dttolerance, iplot):
                     pickdic[key]['S']['weight'] = 9
                 else:
                     marker = 'goodWadatiCheck'
-                    checkedPpick =  UTCDateTime(pickdic[key]['P']['mpp'])
+                    checkedPpick = UTCDateTime(pickdic[key]['P']['mpp']) - \
-                    checkedPpicks.append(checkedPpick.timestamp)
+                                   UTCDateTime(1970, 1, 1, 0, 0, 0)
-                    checkedSpick = UTCDateTime(pickdic[key]['S']['mpp'])
+                    checkedPpicks.append(checkedPpick)
-                    checkedSpicks.append(checkedSpick.timestamp)
+                    checkedSpick = UTCDateTime(pickdic[key]['S']['mpp']) - \
-                    checkedSPtime = pickdic[key]['S']['mpp'] - pickdic[key]['P']['mpp']
+                                   UTCDateTime(1970, 1, 1, 0, 0, 0)
+                    checkedSpicks.append(checkedSpick)
+                    checkedSPtime = pickdic[key]['S']['mpp'] - \
+                                    pickdic[key]['P']['mpp']
                     checkedSPtimes.append(checkedSPtime)
+                    checkedvpvs.append(checkedPpick / checkedSpick)
 
                 pickdic[key]['S']['marked'] = marker
 
@@ -482,9 +496,11 @@ def wadaticheck(pickdic, dttolerance, iplot):
             f4, = plt.plot(checkedPpicks, wdfit2, 'g')
         plt.ylabel('S-P Times [s]')
         plt.xlabel('P Times [s]')
-        plt.title('Wadati-Diagram, %d S-P Times, Vp/Vs(raw)=%5.2f, Vp/Vs(checked)=%5.2f' \
+        plt.title(
+            'Wadati-Diagram, %d S-P Times, Vp/Vs(old)=%5.2f, Vp/Vs(checked)=%5.2f' \
             % (len(SPtimes), vpvsr, cvpvsr))
-        plt.legend([f1, f2, f3, f4], ['Skipped S-Picks', 'Wadati 1', 'Reliable S-Picks', \
+        plt.legend([f1, f2, f3, f4],
+                   ['Skipped S-Picks', 'Wadati 1', 'Reliable S-Picks', \
                     'Wadati 2'], loc='best')
         plt.show()
         raw_input()

pylot/core/read/inputs.py

@@ -206,6 +206,19 @@ class FilterOptions(object):
                    order=self.getOrder())
         return hrs
 
+    def parseFilterOptions(self):
+        if self.getFilterType():
+            robject = {'type':self.getFilterType()}
+            robject['order'] = self.getOrder()
+            if len(self.getFreq()) > 1:
+                robject['freqmin'] = self.getFreq()[0]
+                robject['freqmax'] = self.getFreq()[1]
+            else:
+                robject['freq'] = self.getFreq() if type(self.getFreq()) is \
+                                                    float else self.getFreq()[0]
+            return robject
+        return None
+
     def getFreq(self):
         return self.__getattribute__('_freq')
 

pylot/core/util/utils.py

@@ -3,6 +3,7 @@
 # -*- coding: utf-8 -*-
 
 import os
+import subprocess
 import pwd
 import re
 import hashlib
@@ -10,6 +11,27 @@ import numpy as np
 from obspy.core import UTCDateTime
 import obspy.core.event as ope
 
+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)
+
+
 
 def fnConstructor(s):
     if type(s) is str: