merged 3 files

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

Conflicts:
	pylot/core/active/activeSeismoPick.py
	pylot/core/active/seismicshot.py
	pylot/core/active/surveyPlotTools.py

autoPyLoT.py

@@ -8,11 +8,11 @@ import glob
 
 import matplotlib.pyplot as plt
 from obspy.core import read
-from pylot.core.util import _getVersionString
 from pylot.core.read.data import Data
 from pylot.core.read.inputs import AutoPickParameter
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.pick.autopick import autopickevent
+from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
 

pylot/core/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

pylot/core/active/__init__.py

@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 __author__ = 'sebastianw'

pylot/core/active/activeSeismoPick.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 import numpy as np
 from pylot.core.active import seismicshot
@@ -166,8 +167,8 @@ class Survey(object):
 
     def countAllTraces(self):
         numtraces = 0
-        for line in self.getShotlist():
+        for shot in self.getShotlist():
-            for line in self.getReceiverlist():
+            for rec in self.getReceiverlist():
                 numtraces += 1
         return numtraces
 

pylot/core/active/fmtomo2vtk.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 
 def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk'):

pylot/core/active/picking_script.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 from obspy import read
 from obspy import Stream

pylot/core/active/seismicArrayPreparation.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 import numpy as np
 from scipy.interpolate import griddata

pylot/core/active/seismicArrayPreperation.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 import numpy as np
 from scipy.interpolate import griddata

pylot/core/active/seismicshot.py

@@ -1,3 +1,6 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
 import os
 import numpy as np
 from obspy.core import read
@@ -31,8 +34,7 @@ class SeismicShot(object):
         self.snr = {}
         self.snrthreshold = {}
         self.timeArray = {}
-        self.paras = {}
+        self.paras = {'shotname': obsfile}
-        self.paras['shotname'] = obsfile
 
     def removeEmptyTraces(self):
         traceIDs = []
@@ -154,7 +156,7 @@ class SeismicShot(object):
     def getPickError(self, traceID):
         pickerror = abs(self.getEarliest(traceID) - self.getLatest(traceID))
         if np.isnan(pickerror) == True:
-            print "SPE is NaN for shot %s, traceID %s"%(self.getShotnumber(), traceID)
+            print("SPE is NaN for shot %s, traceID %s"%(self.getShotnumber(), traceID))
         return pickerror
 
     def getStreamTraceIDs(self):
@@ -179,7 +181,7 @@ class SeismicShot(object):
     def getPickwindow(self, traceID):
         try:
             self.pickwindow[traceID]
-        except KeyError, e:
+        except KeyError as e:
             print('no pickwindow for trace %s, set to %s' % (traceID, self.getCut()))
             self.setPickwindow(traceID, self.getCut())
         return self.pickwindow[traceID]
@@ -262,17 +264,21 @@ class SeismicShot(object):
             return Stream(traces)
         else:
             self.setPick(traceID, None)
-            print 'Warning: ambigious or empty traceID: %s' % traceID
+            print('Warning: ambigious or empty traceID: %s' % traceID)
 
         #raise ValueError('ambigious or empty traceID: %s' % traceID)
 
-    def pickTraces(self, traceID, windowsize, folm = 0.6, HosAic = 'hos'): ########## input variables ##########
+    def pickTraces(self, traceID, pickmethod, windowsize, folm = 0.6, HosAic = 'hos'): ########## input variables ##########
+        # LOCALMAX NOT IMPLEMENTED!
         '''
         Intitiate picking for a trace.
 
         :param: traceID
         :type: int
 
+        :param: pickmethod, use either 'threshold' or 'localmax' method. (localmax not yet implemented 04_08_15)
+        :type: string
+
         :param: cutwindow (equals HOScf 'cut' variable)
         :type: tuple
 
@@ -296,8 +302,14 @@ class SeismicShot(object):
 
         self.timeArray[traceID] = hoscf.getTimeArray()
 
+        if pickmethod == 'threshold':
             aiccftime, hoscftime = self.threshold(hoscf, aiccf, windowsize, self.getPickwindow(traceID), folm)
 
+        #setpick = {'threshold':self.threshold,
+         #          'localmax':self.localmax}
+
+        #aiccftime, hoscftime = setpick[pickmethod](hoscf, aiccf, windowsize, pickwindow)
+
         setHosAic = {'hos': hoscftime,
                      'aic': aiccftime}
 
@@ -497,6 +509,7 @@ class SeismicShot(object):
 
         :param: (tnoise, tgap, tsignal), as used in pylot SNR
         '''
+
         from pylot.core.pick.utils import getSNR
 
         tgap = self.getTgap()

pylot/core/active/surveyPlotTools.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import matplotlib.pyplot as plt
 import math
 import numpy as np

pylot/core/active/surveyUtils.py

@@ -1,16 +1,69 @@
-import numpy as np
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from pylab import *
+startpos = []
+endpos = []
+
+def generateSurvey(obsdir, shotlist):
+    from obspy.core import read
+    from pylot.core.active import seismicshot
+
+    shot_dict = {}
+    for shotnumber in shotlist:       # loop over data files
+        # generate filenames and read manual picks to a list
+        obsfile = obsdir + str(shotnumber) + '_pickle.dat'
+        #obsfile = obsdir + str(shotnumber) + '.dat'
+
+        if not obsfile in shot_dict.keys():
+            shot_dict[shotnumber] = []
+        shot_dict[shotnumber] = seismicshot.SeismicShot(obsfile)
+        shot_dict[shotnumber].setParameters('shotnumber', shotnumber)
+
+    return shot_dict
+
+def setParametersForShots(cutwindow, tmovwind, tsignal, tgap, receiverfile, sourcefile, shot_dict):
+    for shot in shot_dict.values():
+        shot.setCut(cutwindow)
+        shot.setTmovwind(tmovwind)
+        shot.setTsignal(tsignal)
+        shot.setTgap(tgap)
+        shot.setRecfile(receiverfile)
+        shot.setSourcefile(sourcefile)
+        shot.setOrder(order = 4)
+
+def removeEmptyTraces(shot_dict):
+    filename = 'removeEmptyTraces.out'
+    filename2 = 'updateTraces.out'
+    outfile = open(filename, 'w')
+    outfile2 = open(filename2, 'w')
+    for shot in shot_dict.values():
+        del_traceIDs = shot.updateTraceList()
+        removed = shot.removeEmptyTraces()
+        if removed is not None:
+            outfile.writelines('shot: %s, removed empty traces: %s\n' %(shot.getShotnumber(), removed))
+            outfile2.writelines('shot: %s, removed traceID(s) %s because they were not found in the corresponding stream\n' %(shot.getShotnumber(), del_traceIDs))
+    print '\nremoveEmptyTraces, updateTraces: Finished! See %s and %s for more information of removed traces.\n' %(filename, filename2)
+    outfile.close()
+    outfile2.close()
+
 
 def readParameters(parfile, parameter):
     from ConfigParser import ConfigParser
     parameterConfig = ConfigParser()
     parameterConfig.read('parfile')
 
-    value = parameterConfig.get('vars', parameter).split('#')[0]
+    value = parameterConfig.get('vars', parameter).split('\t')[0]
-    value = value.replace(" ", "")
 
     return value
 
+def setArtificialPick(shot_dict, traceID, pick):
+    for shot in shot_dict.values():
+        shot.setPick(traceID, pick)
+        shot.setPickwindow(traceID, shot.getCut())
+
 def fitSNR4dist(shot_dict, shiftdist = 5):
+    import numpy as np
     dists = []
     picks = []
     snrs = []
@@ -31,6 +84,7 @@ def fitSNR4dist(shot_dict, shiftdist = 5):
     plotFittedSNR(dists, snrthresholds, snrs)
     return fit_fn #### ZU VERBESSERN, sollte fertige funktion wiedergeben
 
+
 def plotFittedSNR(dists, snrthresholds, snrs):
     import matplotlib.pyplot as plt
     plt.interactive(True)
@@ -42,12 +96,84 @@ def plotFittedSNR(dists, snrthresholds, snrs):
     plt.legend()
 
 def setFittedSNR(shot_dict, shiftdist = 5, p1 = 0.004, p2 = -0.004):
+    import numpy as np
     #fit_fn = fitSNR4dist(shot_dict)
     fit_fn = np.poly1d([p1, p2])
     for shot in shot_dict.values():
         for traceID in shot.getTraceIDlist(): ### IMPROVE
             shot.setSNRthreshold(traceID, 1/(fit_fn(shot.getDistance(traceID) + shiftdist)**2)) ### s.o.
-    print "\nsetFittedSNR: Finished setting of fitted SNR-threshold"
+    print "setFittedSNR: Finished setting of fitted SNR-threshold"
+
+#def linearInterp(dist_med, dist_start
+
+def exportFMTOMO(shot_dict, directory = 'FMTOMO_export', sourcefile = 'input_sf.in', ttFileExtension = '.tt'):
+    count = 0
+    fmtomo_factor = 1000 # transforming [m/s] -> [km/s]
+    LatAll = []; LonAll = []; DepthAll = []
+    srcfile = open(directory + '/' + sourcefile, 'w')
+    srcfile.writelines('%10s\n' %len(shot_dict)) # number of sources
+    for shotnumber in getShotlist(shot_dict):
+        shot = getShotForShotnumber(shot_dict, shotnumber)
+        ttfilename = str(shotnumber) + ttFileExtension
+        (x, y, z) = shot.getSrcLoc() # getSrcLoc returns (x, y, z)
+        srcfile.writelines('%10s %10s %10s\n' %(getAngle(y), getAngle(x), (-1)*z)) # lat, lon, depth
+        LatAll.append(getAngle(y)); LonAll.append(getAngle(x)); DepthAll.append((-1)*z)
+        srcfile.writelines('%10s\n' %1) #
+        srcfile.writelines('%10s %10s %10s\n' %(1, 1, ttfilename))
+        ttfile = open(directory + '/' + ttfilename, 'w')
+        traceIDlist = shot.getTraceIDlist()
+        traceIDlist.sort()
+        ttfile.writelines(str(countPickedTraces(shot)) + '\n')
+        for traceID in traceIDlist:
+            if shot.getPick(traceID) is not None:
+                pick = shot.getPick(traceID) * fmtomo_factor
+                delta = shot.getPickError(traceID) * fmtomo_factor
+                (x, y, z) = shot.getRecLoc(traceID)
+                ttfile.writelines('%20s %20s %20s %10s %10s\n' %(getAngle(y), getAngle(x), (-1)*z, pick, delta))
+                LatAll.append(getAngle(y)); LonAll.append(getAngle(x)); DepthAll.append((-1)*z)
+                count += 1
+        ttfile.close()
+    srcfile.close()
+    print 'Wrote output for %s traces' %count
+    print 'WARNING: output generated for FMTOMO-obsdata. Obsdata seems to take Lat, Lon, Depth and creates output for FMTOMO as Depth, Lat, Lon'
+    print 'Dimensions of the seismic Array, transformed for FMTOMO, are Depth(%s, %s), Lat(%s, %s), Lon(%s, %s)'%(
+        min(DepthAll), max(DepthAll), min(LatAll), max(LatAll), min(LonAll), max(LonAll))
+
+def getShotlist(shot_dict):
+    shotlist = []
+    for shot in shot_dict.values():
+        shotlist.append(shot.getShotnumber())
+    shotlist.sort()
+    return shotlist
+
+def getShotForShotnumber(shot_dict, shotnumber):
+    for shot in shot_dict.values():
+        if shot.getShotnumber() == shotnumber:
+            return shot
+
+def getAngle(distance):
+    '''
+    Function returns the angle on a Sphere of the radius R = 6371 [km] for a distance [km].
+    '''
+    import numpy as np
+    PI = np.pi
+    R = 6371.
+    angle = distance * 180 / (PI * R)
+    return angle
+
+def countPickedTraces(shot):
+    numtraces = 0
+    for traceID in shot.getTraceIDlist():
+        if shot.getPick(traceID) is not None:
+            numtraces += 1
+    print "countPickedTraces: Found %s picked traces in shot number %s"  %(numtraces, shot.getShotnumber())
+    return numtraces
+
+def countAllPickedTraces(shot_dict):
+    traces = 0
+    for shot in shot_dict.values():
+        traces += countPickedTraces(shot)
+    return traces
 
 def findTracesInRanges(shot_dict, distancebin, pickbin):
     '''
@@ -61,6 +187,7 @@ def findTracesInRanges(shot_dict, distancebin, pickbin):
 
     :param: pickbin
     :type: tuple, (t1[s], t2[s])
+
     '''
     shots_found = {}
     for shot in shot_dict.values():
@@ -72,3 +199,6 @@ def findTracesInRanges(shot_dict, distancebin, pickbin):
                     shots_found[shot.getShotnumber()].append(traceID)
 
     return shots_found
+
+
+

pylot/core/analysis/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

pylot/core/analysis/coinctimes.py

@@ -6,7 +6,7 @@ from obspy.signal.trigger import coincidenceTrigger
 
 
 
-class CoincidenceTimes():
+class CoincidenceTimes(object):
 
     def __init__(self, st, comp='Z', coinum=4, sta=1., lta=10., on=5., off=1.):
         _type = 'recstalta'

pylot/core/analysis/magnitude.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
 Created August/September 2015.

pylot/core/pick/CharFuns.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """
 Created Oct/Nov 2014

pylot/core/pick/Picker.py

@@ -312,7 +312,7 @@ class PragPicker(AutoPicking):
             else:
                 for i in range(1, len(self.cf)):
                     if i > ismooth:
-                        ii1 = i - ismooth;
+                        ii1 = i - ismooth
                         cfsmooth[i] = cfsmooth[i - 1] + (self.cf[i] - self.cf[ii1]) / ismooth
                     else:
                         cfsmooth[i] = np.mean(self.cf[1 : i])

pylot/core/pick/__init__.py

@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 #

pylot/core/pick/utils.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 #
 # -*- coding: utf-8 -*-
 """

pylot/core/read/__init__.py

@@ -1 +1 @@
-
+# -*- coding: utf-8 -*-

pylot/core/read/inputs.py

@@ -208,8 +208,7 @@ class FilterOptions(object):
 
     def parseFilterOptions(self):
         if self.getFilterType():
-            robject = {'type':self.getFilterType()}
+            robject = {'type': self.getFilterType(), 'corners': self.getOrder()}
-            robject['corners'] = self.getOrder()
             if len(self.getFreq()) > 1:
                 robject['freqmin'] = self.getFreq()[0]
                 robject['freqmax'] = self.getFreq()[1]

pylot/core/util/__init__.py

@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 from pylot.core.util.version import get_git_version as _getVersionString

pylot/core/util/testUtils.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Created on 10.11.2014
 

pylot/core/util/testWidgets.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Created on 10.11.2014
 

pylot/core/util/thread.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import sys
 from PySide.QtCore import QThread, Signal
 

pylot/core/util/utils.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 #
 # -*- coding: utf-8 -*-
 

testHelpForm.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 
 import sys, time
 from PySide.QtGui import QApplication

testPickDlg.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 
 import sys
 import matplotlib

testPropDlg.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 
 import sys, time
 from PySide.QtGui import QApplication

testUIcomponents.py

@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
 
 import sys, time
 from PySide.QtGui import QApplication