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
This commit is contained in:
Marcel Paffrath 2015-10-19 13:15:28 +02:00
commit 195352a7ca
31 changed files with 454 additions and 289 deletions

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@ -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()

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

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

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@ -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 line in self.getReceiverlist():
for shot in self.getShotlist():
for rec in self.getReceiverlist():
numtraces += 1
return numtraces

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

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

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

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

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@ -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()

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

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@ -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 = value.replace(" ", "")
value = parameterConfig.get('vars', parameter).split('\t')[0]
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

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

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@ -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'

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

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

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@ -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])

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

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

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

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

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

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

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

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

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

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

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

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

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