Merge branch 'develop'
Conflicts: pylot/core/io/phases.py
This commit is contained in:
commit
eb5f028a47
@ -4,11 +4,10 @@ import numpy as np
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from pylot.core.active import seismicshot
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from pylot.core.active.surveyUtils import cleanUp
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class Survey(object):
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def __init__(self, path, sourcefile, receiverfile, useDefaultParas=False):
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'''
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The Survey Class contains all shots [type: seismicshot] of a survey
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The Survey Class contains all shots [class: Seismicshot] of a survey
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as well as the aquisition geometry and the topography.
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It contains methods to pick all traces of all shots.
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@ -24,7 +23,7 @@ class Survey(object):
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self._generateSurvey()
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self._initiateFilenames()
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if useDefaultParas == True:
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self.setParametersForShots()
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self.setParametersForAllShots()
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self._removeAllEmptyTraces()
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self._updateShots()
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@ -51,32 +50,36 @@ class Survey(object):
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print ("Total number of traces: %d \n" % self.countAllTraces())
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def _removeAllEmptyTraces(self):
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filename = 'removeEmptyTraces.out'
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'''
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Removes traces of the dataset that are not found in the input receiver files.
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'''
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logfile = 'removeEmptyTraces.out'
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count = 0
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for shot in self.data.values():
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removed = shot.removeEmptyTraces()
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if removed is not None:
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if count == 0: outfile = open(filename, 'w')
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if count == 0: outfile = open(logfile, 'w')
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count += 1
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outfile.writelines('shot: %s, removed empty traces: %s\n'
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% (shot.getShotnumber(), removed))
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print ("\nremoveEmptyTraces: Finished! Removed %d traces" % count)
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if count > 0:
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print ("See %s for more information "
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"on removed traces." % (filename))
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"on removed traces." % (logfile))
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outfile.close()
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def _updateShots(self):
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'''
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Removes traces that do not exist in the dataset for any reason.
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Removes traces that do not exist in the dataset for any reason,
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but were set in the input files.
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'''
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filename = 'updateShots.out'
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logfile = 'updateShots.out'
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count = 0;
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countTraces = 0
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for shot in self.data.values():
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del_traceIDs = shot.updateTraceList()
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if len(del_traceIDs) > 0:
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if count == 0: outfile = open(filename, 'w')
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if count == 0: outfile = open(logfile, 'w')
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count += 1
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countTraces += len(del_traceIDs)
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outfile.writelines("shot: %s, removed traceID(s) %s because "
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@ -87,36 +90,37 @@ class Survey(object):
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"%d traces" % (count, countTraces))
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if count > 0:
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print ("See %s for more information "
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"on removed traces." % (filename))
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"on removed traces." % (logfile))
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outfile.close()
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def setArtificialPick(self, traceID, pick):
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'''
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Sets an artificial pick for a traceID of all shots in the survey object.
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(This can be used to create a pick with t = 0 at the source origin)
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(Commonly used to generate a travel time t = 0 at the source origin)
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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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def setParametersForShots(self, cutwindow=(0, 0.2), tmovwind=0.3, tsignal=0.03, tgap=0.0007):
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def setParametersForAllShots(self, cutwindow=(0, 0.2), tmovwind=0.3, tsignal=0.03, tgap=0.0007):
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if (cutwindow == (0, 0.2) and tmovwind == 0.3 and
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tsignal == 0.03 and tgap == 0.0007):
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print ("Warning: Standard values used for "
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"setParamters. This might not be clever.")
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# CHANGE this later. Parameters only needed for survey, not for each shot.
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for shot in self.data.values():
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shot.setCut(cutwindow)
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shot.setTmovwind(tmovwind)
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shot.setTsignal(tsignal)
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shot.setTgap(tgap)
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shot.setOrder(order=4)
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print ("setParametersForShots: Parameters set to:\n"
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print ("setParametersForAllShots: Parameters set to:\n"
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"cutwindow = %s, tMovingWindow = %f, tsignal = %f, tgap = %f"
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% (cutwindow, tmovwind, tsignal, tgap))
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def setManualPicksFromFiles(self, directory='picks'):
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'''
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Read manual picks from *.pck files in a directory.
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Can be used for comparison of automatic and manual picks.
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The * must be identical with the shotnumber.
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'''
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for shot in self.data.values():
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@ -125,6 +129,7 @@ class Survey(object):
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def getDiffsFromManual(self):
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'''
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Returns a dictionary with the differences between manual and automatic pick for all shots.
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Key: Seismicshot [object]
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'''
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diffs = {}
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for shot in self.data.values():
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@ -136,6 +141,10 @@ class Survey(object):
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return diffs
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def plotDiffs(self):
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'''
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Creates a plot of all Picks colored by the
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difference between automatic and manual pick.
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'''
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import matplotlib.pyplot as plt
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diffs = [];
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dists = [];
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@ -163,8 +172,12 @@ class Survey(object):
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ax.set_xlabel('Distance [m]')
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ax.set_ylabel('Time [s]')
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ax.text(0.5, 0.95, 'Plot of all MANUAL picks', transform=ax.transAxes, horizontalalignment='center')
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plt.legend()
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def plotHist(self, nbins=20, ax=None):
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'''
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Plot a histogram of the difference between automatic and manual picks.
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'''
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import matplotlib.pyplot as plt
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plt.interactive(True)
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diffs = []
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@ -180,9 +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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@ -207,7 +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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@ -231,6 +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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@ -238,6 +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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@ -251,7 +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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@ -266,18 +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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@ -288,6 +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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@ -313,6 +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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@ -334,11 +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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@ -354,13 +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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@ -393,6 +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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@ -400,6 +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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@ -422,20 +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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@ -516,6 +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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@ -547,6 +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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|
@ -6,15 +6,28 @@ import datetime
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import numpy as np
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class Tomo3d(object):
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def __init__(self, nproc, iterations):
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def __init__(self, nproc, iterations, citer = 0, overwrite = False):
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'''
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Class build from FMTOMO script tomo3d. Can be used to run several instances of FMM code in parallel.
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:param: nproc, number of parallel processes
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:type: integer
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:param: iterations, number of iterations
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:type: integer
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:param: citer, current iteration (default = 0: start new model)
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:type: integer
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'''
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self.setCWD()
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self.defParas()
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self.nproc = nproc
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self.iter = iterations # number of iterations
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self.citer = 0 # current iteration
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self.citer = citer # current iteration
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self.sources = self.readSrcFile()
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self.traces = self.readTraces()
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self.directories = []
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self.overwrite = overwrite
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def defParas(self):
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self.defFMMParas()
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@ -29,6 +42,7 @@ class Tomo3d(object):
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self.pg = 'propgrid.in'
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self.rec = 'receivers.in'
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self.frech = 'frechet.in'
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self.frechout = 'frechet.dat'
|
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self.ot = 'otimes.dat'
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self.ttim = 'arrivals.dat'
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self.mode = 'mode_set.in'
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@ -53,8 +67,8 @@ class Tomo3d(object):
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self.resout = 'residuals.dat'
|
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def copyRef(self):
|
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# Attention: Copies reference grids to used grids (e.g. sourcesref.in to sources.in)
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os.system('cp %s %s'%(self. ivg, self.cvg))
|
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# Copies reference grids to used grids (e.g. sourcesref.in to sources.in)
|
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os.system('cp %s %s'%(self.ivg, self.cvg))
|
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os.system('cp %s %s'%(self.iig, self.cig))
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os.system('cp %s %s'%(self.isl, self.csl))
|
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@ -65,6 +79,30 @@ class Tomo3d(object):
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def runFrech(self):
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os.system(self.frechgen)
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def runTOMO3D(self):
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starttime = datetime.datetime.now()
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print('Starting TOMO3D on %s parallel processes for %s iteration(s).'
|
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%(self.nproc, self.iter))
|
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if self.citer == 0:
|
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self.makeInvIterDir()
|
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self.startForward(self.cInvIterDir)
|
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self.raiseIter()
|
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|
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while self.citer <= self.iter:
|
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self.makeInvIterDir()
|
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self.startInversion()
|
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self.saveVgrid()
|
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self.startForward(self.cInvIterDir)
|
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self.raiseIter()
|
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|
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if self.citer > self.iter:
|
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self.removeDirectories()
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self.unlink(os.path.join(self.cwd, self.frechout))
|
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self.unlink(os.path.join(self.cwd, self.ttim))
|
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|
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tdelta = datetime.datetime.now() - starttime
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print('runTOMO3D: Finished %s iterations after %s.'%(self.iter, tdelta))
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|
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def runFmm(self, directory, logfile, processes):
|
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os.chdir(directory)
|
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fout = open(logfile, 'w')
|
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@ -73,6 +111,47 @@ class Tomo3d(object):
|
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os.chdir(self.cwd)
|
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return processes
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|
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def startForward(self, logdir):
|
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self._printLine()
|
||||
print('Starting forward simulation for iteration %s.'%(self.citer))
|
||||
|
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if self.citer == 0:
|
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self.copyRef()
|
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self.runFrech()
|
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self.makeDirectories()
|
||||
|
||||
starttime = datetime.datetime.now()
|
||||
processes = []
|
||||
|
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for procID in range(1, self.nproc + 1):
|
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directory = self.getProcDir(procID)
|
||||
logfn = 'fm3dlog_' + str(procID) + '.out'
|
||||
log_out = os.path.join(logdir, logfn)
|
||||
|
||||
self.writeSrcFile(procID, directory)
|
||||
self.writeTracesFile(procID, directory)
|
||||
os.system('cp {cvg} {cig} {mode} {pg} {frechin} {dest}'
|
||||
.format(cvg=self.cvg, cig=self.cig, frechin=self.frech,
|
||||
mode=self.mode, pg=self.pg, dest=directory))
|
||||
processes = self.runFmm(directory, log_out, processes)
|
||||
|
||||
for p in processes:
|
||||
p.wait()
|
||||
|
||||
self.mergeOutput(self.cInvIterDir)
|
||||
self.clearDirectories()
|
||||
self.copyArrivals()
|
||||
if self.citer == 0:
|
||||
self.copyArrivals(self.rtrav)
|
||||
|
||||
self.calcRes()
|
||||
tdelta = datetime.datetime.now() - starttime
|
||||
print('Finished Forward calculation after %s'%tdelta)
|
||||
|
||||
def startInversion(self):
|
||||
print('Calling %s...'%self.inv)
|
||||
os.system(self.inv)
|
||||
|
||||
def calcRes(self):
|
||||
resout = os.path.join(self.cwd, self.resout)
|
||||
if self.citer == 0:
|
||||
@ -85,111 +164,91 @@ class Tomo3d(object):
|
||||
RMS, var, chi2 = residuals[-1].split()
|
||||
print('Residuals: RMS = %s, var = %s, Chi^2 = %s.'%(RMS, var, chi2))
|
||||
|
||||
def runTOMO3D(self):
|
||||
starttime = datetime.datetime.now()
|
||||
print('Starting TOMO3D on %s parallel processes for %s iteration(s).'
|
||||
%(self.nproc, self.iter))
|
||||
if self.citer == 0:
|
||||
self.startForward()
|
||||
self.raiseIter()
|
||||
|
||||
while self.citer <= self.iter:
|
||||
self.startInversion()
|
||||
self.startForward()
|
||||
self.raiseIter()
|
||||
|
||||
tdelta = datetime.datetime.now() - starttime
|
||||
print('runTOMO3D: Finished %s iterations after %s.'%(self.iter, tdelta))
|
||||
|
||||
def _printLine(self):
|
||||
print('----------------------------------------')
|
||||
|
||||
def raiseIter(self):
|
||||
self.citer +=1
|
||||
self._printLine()
|
||||
invfile = open(self.cwd + '/inviter.in', 'w')
|
||||
invfile.write('%s'%self.citer)
|
||||
invfile.close()
|
||||
|
||||
def startInversion(self):
|
||||
print('Calling %s...'%self.inv)
|
||||
os.system(self.inv)
|
||||
|
||||
def startForward(self):
|
||||
self._printLine()
|
||||
print('Starting forward simulation for iteration %s.'%(self.citer))
|
||||
self.makeDirectories()
|
||||
starttime = datetime.datetime.now()
|
||||
processes = []
|
||||
|
||||
if self.citer == 0:
|
||||
self.copyRef()
|
||||
self.runFrech()
|
||||
|
||||
for procID in range(1, self.nproc + 1):
|
||||
directory = self.getProcDir(procID)
|
||||
log_out = self.cwd + '/fm3dlog_' + str(procID) + '.out'
|
||||
|
||||
self.writeSrcFile(procID, directory)
|
||||
self.writeTracesFile(procID, directory)
|
||||
os.system('cp {cvg} {cig} {mode} {pg} {frechout} {dest}'
|
||||
.format(cvg=self.cvg, cig=self.cig, frechout=self.frech,
|
||||
mode=self.mode, pg=self.pg, dest=directory))
|
||||
processes = self.runFmm(directory, log_out, processes)
|
||||
|
||||
for p in processes:
|
||||
p.wait()
|
||||
|
||||
self.mergeOutput()
|
||||
self.clearDirectories()
|
||||
self.copyArrivals()
|
||||
if self.citer == 0:
|
||||
self.copyArrivals(self.rtrav)
|
||||
|
||||
self.calcRes()
|
||||
tdelta = datetime.datetime.now() - starttime
|
||||
print('Finished Forward calculation after %s'%tdelta)
|
||||
|
||||
def copyArrivals(self, target = None):
|
||||
if target == None:
|
||||
target = self.mtrav
|
||||
os.system('cp %s %s'%(self.ttim, target))
|
||||
|
||||
def makeDIR(self, directory):
|
||||
def makeDir(self, directory):
|
||||
err = os.system('mkdir %s'%directory)
|
||||
if err is 0:
|
||||
self.directories.append(directory)
|
||||
return
|
||||
if err is 256:
|
||||
response = raw_input('Warning: Directory already existing. Continue (y/n)?\n')
|
||||
if response == 'y':
|
||||
if self.overwrite == True:
|
||||
print('Overwriting existing files.')
|
||||
else:
|
||||
sys.exit('Aborted')
|
||||
self.clearDir(directory)
|
||||
self.directories.append(directory)
|
||||
return
|
||||
raise RuntimeError('Could not create directory: %s'%directory)
|
||||
|
||||
self.directories.append(directory)
|
||||
|
||||
def clearDIR(self, directory):
|
||||
err = os.system('rm -r %s'%directory)
|
||||
|
||||
def makeDirectories(self):
|
||||
for procID in range(1, self.nproc + 1):
|
||||
directory = self.getProcDir(procID)
|
||||
self.makeDIR(directory)
|
||||
self.makeDir(directory)
|
||||
|
||||
def makeInvIterDir(self):
|
||||
invIterDir = self.cwd + '/it_%s'%(self.citer)
|
||||
err = os.system('mkdir %s'%invIterDir)
|
||||
if err is 256:
|
||||
if self.overwrite:
|
||||
self.clearDir(invIterDir)
|
||||
elif err is not 0:
|
||||
raise RuntimeError('Could not create directory: %s'%invIterDir)
|
||||
self.cInvIterDir = invIterDir
|
||||
|
||||
def clearDir(self, directory):
|
||||
print('Wiping directory %s...'%directory)
|
||||
for filename in os.listdir(directory):
|
||||
filenp = os.path.join(directory, filename)
|
||||
os.remove(filenp)
|
||||
|
||||
def clearDirectories(self):
|
||||
for directory in self.directories:
|
||||
self.clearDIR(directory)
|
||||
self.clearDir(directory)
|
||||
|
||||
def rmDir(self, directory):
|
||||
print('Removing directory %s...'%directory)
|
||||
return os.rmdir(directory)
|
||||
|
||||
def removeDirectories(self):
|
||||
for directory in self.directories:
|
||||
self.rmDir(directory)
|
||||
self.directories = []
|
||||
|
||||
def readNsrc(self):
|
||||
srcfile = open(self.csl, 'r')
|
||||
nsrc = int(srcfile.readline())
|
||||
srcfile.close()
|
||||
return nsrc
|
||||
def getProcDir(self, procID):
|
||||
return os.path.join(self.cwd, self.folder) + str(procID)
|
||||
|
||||
def readNtraces(self):
|
||||
recfile = open(self.rec, 'r')
|
||||
nrec = int(recfile.readline())
|
||||
recfile.close()
|
||||
return nrec
|
||||
def getTraceIDs4Sources(self, sourceIDs):
|
||||
traceIDs = []
|
||||
for traceID in self.traces.keys():
|
||||
if self.traces[traceID]['source'] in sourceIDs:
|
||||
traceIDs.append(traceID)
|
||||
return traceIDs
|
||||
|
||||
def getTraceIDs4Source(self, sourceID):
|
||||
traceIDs = []
|
||||
for traceID in self.traces.keys():
|
||||
if self.traces[traceID]['source'] == sourceID:
|
||||
traceIDs.append(traceID)
|
||||
return traceIDs
|
||||
|
||||
def copyArrivals(self, target = None):
|
||||
if target == None:
|
||||
target = os.path.join(self.cwd, self.mtrav)
|
||||
os.system('cp %s %s'%(os.path.join(
|
||||
self.cInvIterDir, self.ttim), target))
|
||||
|
||||
def saveVgrid(self):
|
||||
vgpath = os.path.join(self.cwd, 'vgrids.in')
|
||||
os.system('cp %s %s'%(vgpath, self.cInvIterDir))
|
||||
|
||||
def calcSrcPerKernel(self):
|
||||
nsrc = self.readNsrc()
|
||||
if self.nproc > nsrc:
|
||||
raise ValueError('Number of spawned processes higher than number of sources')
|
||||
return nsrc/self.nproc, nsrc%self.nproc
|
||||
|
||||
def srcIDs4Kernel(self, procID):
|
||||
@ -207,6 +266,18 @@ class Tomo3d(object):
|
||||
elif proc > remain:
|
||||
start = (srcPK + 1) * remain + srcPK * (proc - remain) + 1
|
||||
return range(start, start + srcPK)
|
||||
|
||||
def readNsrc(self):
|
||||
srcfile = open(self.csl, 'r')
|
||||
nsrc = int(srcfile.readline())
|
||||
srcfile.close()
|
||||
return nsrc
|
||||
|
||||
def readNtraces(self):
|
||||
recfile = open(self.rec, 'r')
|
||||
nrec = int(recfile.readline())
|
||||
recfile.close()
|
||||
return nrec
|
||||
|
||||
def readSrcFile(self):
|
||||
nsrc = self.readNsrc()
|
||||
@ -258,6 +329,62 @@ class Tomo3d(object):
|
||||
|
||||
return traces
|
||||
|
||||
def readArrivals(self, procID):
|
||||
directory = self.getProcDir(procID)
|
||||
arrfile = open(directory + '/arrivals.dat', 'r')
|
||||
sourceIDs = self.srcIDs4Kernel(procID)
|
||||
|
||||
arrivals = []
|
||||
for sourceID in sourceIDs:
|
||||
traceIDs = self.getTraceIDs4Source(sourceID)
|
||||
for traceID in traceIDs:
|
||||
line = arrfile.readline().split()
|
||||
if line != []:
|
||||
# recID and srcID for the individual processor will not be needed
|
||||
recID_proc, srcID_proc, ray, normal, arrtime, diff, head = line
|
||||
arrivals.append([traceID, sourceID, ray, normal, arrtime, diff, head])
|
||||
|
||||
return arrivals
|
||||
|
||||
def readRays(self, procID):
|
||||
directory = self.getProcDir(procID)
|
||||
raysfile = open(directory + '/rays.dat', 'r')
|
||||
sourceIDs = self.srcIDs4Kernel(procID)
|
||||
|
||||
rays = {}
|
||||
for sourceID in sourceIDs:
|
||||
traceIDs = self.getTraceIDs4Source(sourceID)
|
||||
for traceID in traceIDs:
|
||||
line1 = raysfile.readline().split()
|
||||
if line1 != []:
|
||||
# recID and srcID for the individual processor will not be needed
|
||||
recID_proc, srcID_proc, ray, normal, nsec = line1
|
||||
raysecs = {}
|
||||
|
||||
for sec in range(int(nsec)):
|
||||
line2 = raysfile.readline().split()
|
||||
npoints, region, diff, head = line2
|
||||
raypoints = []
|
||||
|
||||
for j in range(int(npoints)):
|
||||
raypoints.append(raysfile.readline() + '\n')
|
||||
|
||||
raysecs[sec] = {'npoints': npoints,
|
||||
'region': region,
|
||||
'diff': diff,
|
||||
'head': head,
|
||||
'raypoints': raypoints
|
||||
}
|
||||
|
||||
|
||||
rays[traceID] = {'sourceID': sourceID,
|
||||
'raypath': ray,
|
||||
'normal': normal,
|
||||
'nsec': nsec,
|
||||
'raysections': raysecs
|
||||
}
|
||||
return rays
|
||||
|
||||
def writeSrcFile(self, procID, directory):
|
||||
srcfile = open('%s/sources.in'%directory, 'w')
|
||||
sourceIDs = self.srcIDs4Kernel(procID)
|
||||
@ -289,154 +416,44 @@ class Tomo3d(object):
|
||||
recfile.write('%s\n'%source)
|
||||
recfile.write('%s\n'%trace['path'])
|
||||
|
||||
def getTraceIDs4Sources(self, sourceIDs):
|
||||
traceIDs = []
|
||||
for traceID in self.traces.keys():
|
||||
if self.traces[traceID]['source'] in sourceIDs:
|
||||
traceIDs.append(traceID)
|
||||
return traceIDs
|
||||
|
||||
def getTraceIDs4Source(self, sourceID):
|
||||
traceIDs = []
|
||||
for traceID in self.traces.keys():
|
||||
if self.traces[traceID]['source'] == sourceID:
|
||||
traceIDs.append(traceID)
|
||||
return traceIDs
|
||||
|
||||
def readArrivals(self, procID):
|
||||
directory = self.getProcDir(procID)
|
||||
arrfile = open(directory + '/arrivals.dat', 'r')
|
||||
sourceIDs = self.srcIDs4Kernel(procID)
|
||||
|
||||
arrivals = []
|
||||
for sourceID in sourceIDs:
|
||||
traceIDs = self.getTraceIDs4Source(sourceID)
|
||||
for traceID in traceIDs:
|
||||
line = arrfile.readline().split()
|
||||
if line != []:
|
||||
# recID and srcID for the individual processor will not be needed
|
||||
recID_proc, srcID_proc, ray, normal, arrtime, diff, head = line
|
||||
arrivals.append([traceID, sourceID, ray, normal, arrtime, diff, head])
|
||||
|
||||
return arrivals
|
||||
|
||||
def mergeArrivals(self):
|
||||
arrivalsOut = open(os.path.join(self.cwd, self.ttim), 'w')
|
||||
def mergeArrivals(self, directory):
|
||||
arrfn = os.path.join(directory, self.ttim)
|
||||
arrivalsOut = open(arrfn, 'w')
|
||||
print('Merging arrivals.dat...')
|
||||
for procID in range(1, self.nproc + 1):
|
||||
arrivals = self.readArrivals(procID)
|
||||
for line in arrivals:
|
||||
arrivalsOut.write('%6s %6s %6s %6s %15s %5s %5s\n'%tuple(line))
|
||||
|
||||
# def mergeFrechet(self):
|
||||
# print('Merging frechet.dat...')
|
||||
# frechetOut = open(self.cwd + '/frechet.dat', 'w')
|
||||
# for procID in range(1, self.nproc + 1):
|
||||
# frechet = self.readFrechet(procID)
|
||||
# traceIDs = frechet.keys()
|
||||
# traceIDs.sort()
|
||||
# for traceID in traceIDs:
|
||||
# frech = frechet[traceID]
|
||||
# frechetOut.write('%6s %6s %6s %6s %6s\n'%
|
||||
# (traceID,
|
||||
# frech['sourceID'],
|
||||
# frech['raypath'],
|
||||
# frech['normal'],
|
||||
# frech['NPDEV']))
|
||||
# for pdev in frech['PDEV']:
|
||||
# frechetOut.writelines(pdev)
|
||||
os.system('ln -fs %s %s'%(arrfn, os.path.join(self.cwd, self.ttim)))
|
||||
|
||||
def readRays(self, procID):
|
||||
directory = self.getProcDir(procID)
|
||||
raysfile = open(directory + '/rays.dat', 'r')
|
||||
sourceIDs = self.srcIDs4Kernel(procID)
|
||||
|
||||
rays = {}
|
||||
for sourceID in sourceIDs:
|
||||
traceIDs = self.getTraceIDs4Source(sourceID)
|
||||
for traceID in traceIDs:
|
||||
line1 = raysfile.readline().split()
|
||||
if line1 != []:
|
||||
# recID and srcID for the individual processor will not be needed
|
||||
recID_proc, srcID_proc, ray, normal, nsec = line1
|
||||
raysecs = {}
|
||||
|
||||
for sec in range(int(nsec)):
|
||||
line2 = raysfile.readline.split()
|
||||
npoints, region, diff, head = line2
|
||||
raypoints = []
|
||||
|
||||
for j in range(int(npoints)):
|
||||
raypoints.append(raysfile.readline() + '\n')
|
||||
|
||||
raysecs[sec] = {'npoints': npoints,
|
||||
'region': region,
|
||||
'diff': diff,
|
||||
'head': head,
|
||||
'raypoints': raypoints
|
||||
}
|
||||
|
||||
|
||||
rays[traceID] = {'sourceID': sourceID,
|
||||
'raypath': ray,
|
||||
'normal': normal,
|
||||
'nsec': nsec,
|
||||
'raysections': raysecs
|
||||
}
|
||||
return rays
|
||||
|
||||
def mergeRays(self):
|
||||
def mergeRays(self, directory):
|
||||
print('Merging rays.dat...')
|
||||
with open(self.cwd + 'rays.dat', 'w') as outfile:
|
||||
for procID in range(1, self.nproc + 1):
|
||||
rays = self.readRays(procID)
|
||||
for traceID in rays:
|
||||
ray = rays[traceID]
|
||||
outfile.write('%6s %6s %6s %6s %6s'%(traceID,
|
||||
ray['sourceID'],
|
||||
ray['raypath'],
|
||||
ray['normal'],
|
||||
ray['nsec']))
|
||||
for sec in range(int(ray['nsec'])):
|
||||
raysec = ray['raysections'][sec]
|
||||
outfile.write('%6s %6s %6s %6s'%(raysec['npoints'],
|
||||
raysec['region'],
|
||||
raysec['diff'],
|
||||
raysec['head']))
|
||||
outfile.writelines(raysec['raypoints'])
|
||||
|
||||
|
||||
# def readFrechet(self, procID):
|
||||
# directory = self.getProcDir(procID)
|
||||
# frechfile = open(directory + '/frechet.dat', 'r')
|
||||
# sourceIDs = self.srcIDs4Kernel(procID)
|
||||
|
||||
# frechet = {}
|
||||
# for sourceID in sourceIDs:
|
||||
# traceIDs = self.getTraceIDs4Source(sourceID)
|
||||
# for traceID in traceIDs:
|
||||
# line = frechfile.readline().split()
|
||||
# if line != []:
|
||||
# # recID and srcID for the individual processor will not be needed
|
||||
# PDEV = []
|
||||
# recID_proc, srcID_proc, ray, normal, NPDEV = line
|
||||
# for i in range(int(NPDEV)):
|
||||
# PDEV.append(frechfile.readline())
|
||||
|
||||
# frechet[traceID] = {'sourceID': sourceID,
|
||||
# 'raypath': ray,
|
||||
# 'normal': normal,
|
||||
# 'NPDEV': NPDEV,
|
||||
# 'PDEV': PDEV
|
||||
# }
|
||||
# return frechet
|
||||
|
||||
def mergeFrechet(self):
|
||||
print('Merging frechet.dat...')
|
||||
|
||||
with open(self.cwd + '/frechet.dat', 'w') as outfile:
|
||||
with open(directory + '/rays.dat', 'w') as outfile:
|
||||
for procID in range(1, self.nproc + 1):
|
||||
filename = self.getProcDir(procID) + '/frechet.dat'
|
||||
rays = self.readRays(procID)
|
||||
for traceID in rays:
|
||||
ray = rays[traceID]
|
||||
outfile.write('%6s %6s %6s %6s %6s\n'%(traceID,
|
||||
ray['sourceID'],
|
||||
ray['raypath'],
|
||||
ray['normal'],
|
||||
ray['nsec']))
|
||||
for sec in range(int(ray['nsec'])):
|
||||
raysec = ray['raysections'][sec]
|
||||
outfile.write('%6s %6s %6s %6s\n'%(raysec['npoints'],
|
||||
raysec['region'],
|
||||
raysec['diff'],
|
||||
raysec['head']))
|
||||
outfile.writelines(raysec['raypoints'])
|
||||
|
||||
def mergeFrechet(self, directory):
|
||||
print('Merging frechet.dat...')
|
||||
|
||||
frechfnout = os.path.join(directory, self.frechout)
|
||||
with open(frechfnout, 'w') as outfile:
|
||||
for procID in range(1, self.nproc + 1):
|
||||
filename = os.path.join(self.getProcDir(procID), self.frechout)
|
||||
with open(filename) as infile:
|
||||
for sourceID in self.srcIDs4Kernel(procID):
|
||||
for traceID in self.getTraceIDs4Source(sourceID):
|
||||
@ -445,15 +462,18 @@ class Tomo3d(object):
|
||||
for index in range(int(NPDEV)):
|
||||
outfile.write(infile.readline())
|
||||
|
||||
os.system('ln -fs %s %s'%(frechfnout, os.path.join(self.cwd, self.frechout)))
|
||||
|
||||
def getProcDir(self, procID):
|
||||
return os.path.join(self.cwd, self.folder) + str(procID)
|
||||
|
||||
def mergeOutput(self):
|
||||
self.mergeArrivals()
|
||||
self.mergeFrechet()
|
||||
self.mergeRays()
|
||||
def mergeOutput(self, directory):
|
||||
self.mergeArrivals(directory)
|
||||
self.mergeFrechet(directory)
|
||||
self.mergeRays(directory)
|
||||
|
||||
def unlink(self, filepath):
|
||||
return os.system('unlink %s'%filepath)
|
||||
|
||||
def _printLine(self):
|
||||
print('----------------------------------------')
|
||||
|
||||
def vgrids2VTK(inputfile='vgrids.in', outputfile='vgrids.vtk', absOrRel='abs', inputfileref='vgridsref.in'):
|
||||
'''
|
||||
|
@ -199,7 +199,7 @@ def picksdict_from_picks(evt):
|
||||
:param evt: Event object contain all available information
|
||||
:type evt: `~obspy.core.event.Event`
|
||||
:return: pick dictionary
|
||||
'''
|
||||
"""
|
||||
picks = {}
|
||||
for pick in evt.picks:
|
||||
phase = {}
|
||||
@ -345,7 +345,7 @@ def reassess_pilot_event(root_dir, event_id, out_dir=None, fn_param=None, verbos
|
||||
|
||||
|
||||
def writephases(arrivals, fformat, filename):
|
||||
'''
|
||||
"""
|
||||
Function of methods to write phases to the following standard file
|
||||
formats used for locating earthquakes:
|
||||
|
||||
@ -363,7 +363,7 @@ def writephases(arrivals, fformat, filename):
|
||||
|
||||
:param: filename, full path and name of phase file
|
||||
:type: string
|
||||
'''
|
||||
"""
|
||||
|
||||
if fformat == 'NLLoc':
|
||||
print ("Writing phases to %s for NLLoc" % filename)
|
||||
@ -425,7 +425,6 @@ def writephases(arrivals, fformat, filename):
|
||||
sweight))
|
||||
|
||||
fid.close()
|
||||
|
||||
elif fformat == 'HYPO71':
|
||||
print ("Writing phases to %s for HYPO71" % filename)
|
||||
fid = open("%s" % filename, 'w')
|
||||
|
Loading…
Reference in New Issue
Block a user