code cleanup and commenting
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@ -193,9 +193,21 @@ class Survey(object):
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plt.xlabel('Difference in time (auto - manual) [s]')
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return diffs
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def pickAllShots(self, windowsize, HosAic='hos', vmin=333, vmax=5500, folm=0.6):
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def pickAllShots(self, vmin=333, vmax=5500, folm=0.6, HosAic='hos', aicwindow=(10, 0)):
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'''
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Automatically pick all traces of all shots of the survey.
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:param: vmin, vmax, minimum (maximum) permitted apparent velocity on direct path between src and rec
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:type: real
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:param: folm, fraction of local maximum for HOS pick (0.6 = 60% of the highest maximum)
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:type: real
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:param: HosAic, pick with hos only ('hos') or use AIC ('aic')
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:type: string
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:param: aicwindow, window around the initial pick to search for local AIC min (samples)
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:type: tuple
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'''
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from datetime import datetime
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starttime = datetime.now()
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@ -220,7 +232,7 @@ class Survey(object):
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pickwin_used = (pwleft, pwright)
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shot.setPickwindow(traceID, pickwin_used)
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shot.pickTraces(traceID, windowsize, folm, HosAic) # picker
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shot.pickTraces(traceID, folm, HosAic, aicwindow) # picker
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shot.setSNR(traceID)
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# if shot.getSNR(traceID)[0] < snrthreshold:
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@ -244,6 +256,9 @@ class Survey(object):
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% (pickedtraces, ntraces, float(pickedtraces) / float(ntraces) * 100.))
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def cleanBySPE(self, maxSPE):
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'''
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Sets all picks as invalid if they exceed a certain value of the symmetric pick error.
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'''
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for shot in self.data.values():
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for traceID in shot.getTraceIDlist():
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if shot.getPickFlag(traceID) == 1:
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@ -251,6 +266,9 @@ class Survey(object):
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shot.setPickFlag(traceID, 0)
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def plotSPE(self):
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'''
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Plots the symmetric pick error sorted by magnitude.
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'''
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import matplotlib.pyplot as plt
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spe = []
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for shot in self.data.values():
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@ -264,7 +282,7 @@ class Survey(object):
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def recover(self):
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'''
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Recovers all (accidently) removed picks. Still regards SNR threshold.
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Recovers all manually removed picks. Still regards SNR threshold.
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'''
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print('Recovering survey...')
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numpicks = 0
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@ -279,18 +297,28 @@ class Survey(object):
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print('Recovered %d picks' % numpicks)
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def setArtificialPick(self, traceID, pick):
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'''
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Sets an artificial pick for a certain receiver (traceID) for all shots.
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'''
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for shot in self.data.values():
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shot.setPick(traceID, pick)
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shot.setPickwindow(traceID, shot.getCut())
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def countAllTraces(self):
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'''
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Returns the number of traces in total.
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'''
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numtraces = 0
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for shot in self.getShotlist():
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for rec in self.getReceiverlist(): ### shot.getReceiverlist etc.
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for rec in self.getReceiverlist():
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numtraces += 1
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return numtraces
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def getShotlist(self):
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'''
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Returns a list of all shotnumbers contained in the set Sourcefile.
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'''
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filename = self.getPath() + self.getSourcefile()
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srcfile = open(filename, 'r')
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shotlist = []
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@ -301,6 +329,9 @@ class Survey(object):
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return shotlist
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def getReceiverlist(self):
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'''
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Returns a list of all trace IDs contained in the set Receiverfile.
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'''
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filename = self.getPath() + self.getReceiverfile()
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recfile = open(filename, 'r')
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reclist = []
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@ -326,6 +357,12 @@ class Survey(object):
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return self._obsdir
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def getStats(self):
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'''
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Generates and returns a dictionary containing statistical information
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of the survey.
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Key: shotnumber
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'''
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info_dict = {}
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for shot in self.data.values():
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pickedTraces = 0
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@ -347,11 +384,17 @@ class Survey(object):
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return info_dict
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def getShotForShotnumber(self, shotnumber):
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'''
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Returns Seismicshot [object] of a certain shotnumber if possible.
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'''
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for shot in self.data.values():
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if shot.getShotnumber() == shotnumber:
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return shot
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def exportFMTOMO(self, directory='FMTOMO_export', sourcefile='input_sf.in', ttFileExtension='.tt'):
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'''
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Exports all picks into a directory as travel time files readable by FMTOMO obsdata.
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'''
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def getAngle(distance):
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PI = np.pi
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R = 6371.
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@ -367,13 +410,13 @@ class Survey(object):
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srcfile.writelines('%10s\n' % len(self.data)) # number of sources
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for shotnumber in self.getShotlist():
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shot = self.getShotForShotnumber(shotnumber)
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ttfilename = str(shotnumber) + ttFileExtension
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ttfilename = str(shotnumber) + ttFileExtension # filename of travel time file for this shot
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(x, y, z) = shot.getSrcLoc() # getSrcLoc returns (x, y, z)
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srcfile.writelines('%10s %10s %10s\n' % (getAngle(y), getAngle(x), (-1) * z)) # lat, lon, depth
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srcfile.writelines('%10s %10s %10s\n' % (getAngle(y), getAngle(x), (-1) * z)) # transform to lat, lon, depth
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LatAll.append(getAngle(y));
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LonAll.append(getAngle(x));
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DepthAll.append((-1) * z)
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srcfile.writelines('%10s\n' % 1) #
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srcfile.writelines('%10s\n' % 1)
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srcfile.writelines('%10s %10s %10s\n' % (1, 1, ttfilename))
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ttfile = open(directory + '/' + ttfilename, 'w')
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traceIDlist = shot.getTraceIDlist()
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@ -406,6 +449,9 @@ class Survey(object):
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print(msg)
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def countPickedTraces(self, shot):
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'''
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Counts all picked traces of a shot (type Seismicshot).
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'''
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count = 0
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for traceID in shot.getTraceIDlist():
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if shot.getPickFlag(traceID) is not 0:
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@ -413,6 +459,9 @@ class Survey(object):
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return count
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def countAllPickedTraces(self):
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'''
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Counts all picked traces of the survey.
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'''
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count = 0
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for shot in self.data.values():
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for traceID in shot.getTraceIDlist():
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@ -435,20 +484,9 @@ class Survey(object):
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figPerSubplot = columns * rows
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index = 1
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# shotnames = []
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# shotnumbers = []
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# for shot in self.data.values():
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# shotnames.append(shot.getShotname())
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# shotnumbers.append(shot.getShotnumber())
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# shotnumbers = [shotnumbers for (shotnumbers, shotnames) in sorted(zip(shotnumbers, shotnames))]
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for shotnumber in self.getShotlist():
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if index <= figPerSubplot:
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# ax = fig.add_subplot(3,3,i, projection = '3d', title = 'shot:'
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# +str(shot_dict[shotnumber].getShotnumber()), xlabel = 'X', ylabel = 'Y', zlabel = 'traveltime')
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# shot_dict[shotnumber].plot3dttc(ax = ax, plotpicks = True)
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ax = fig.add_subplot(rows, columns, index)
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if mode == '3d':
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self.getShot(shotnumber).matshow(ax=ax, colorbar=False, annotations=True, legend=False)
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@ -529,6 +567,9 @@ class Survey(object):
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return ax
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def createPlot(self, dist, pick, inkByVal, label, ax=None, cbar=None):
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'''
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Used by plotAllPicks.
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'''
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import matplotlib.pyplot as plt
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plt.interactive(True)
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cm = plt.cm.jet
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@ -560,6 +601,10 @@ class Survey(object):
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sys.stdout.flush()
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def saveSurvey(self, filename='survey.pickle'):
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'''
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Save Survey object to a file.
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Can be loaded by using Survey.from_pickle(filename).
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'''
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import cPickle
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cleanUp(self)
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outfile = open(filename, 'wb')
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