948 lines
33 KiB
Python
948 lines
33 KiB
Python
# -*- coding: utf-8 -*-
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import os
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import sys
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import subprocess
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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, 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 = 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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self.defInvParas()
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def defFMMParas(self):
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self.fmm = '{0}/fm3d'.format(self.cwd)
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self.frechgen = '{0}/frechgen'.format(self.cwd)
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self.cvg = 'vgrids.in'
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self.cig = 'interfaces.in'
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self.csl = 'sources.in'
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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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self.folder = '.proc_'
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def defInvParas(self):
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# Name of program for performing inversion
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self.inv = '{0}/invert3d'.format(self.cwd)
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# Name of file containing current model traveltimes
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self.mtrav = 'mtimes.dat'
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# Name of file containing reference model traveltimes
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self.rtrav = 'rtimes.dat'
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# Name of file containing initial velocity grid
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self.ivg = 'vgridsref.in'
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# Name of file containing initial interface grid
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self.iig = 'interfacesref.in'
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# Name of file containing initial source locations
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self.isl = 'sourcesref.in'
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# Name of program for calculating traveltime residuals
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self.resid = '{0}/residuals'.format(self.cwd)
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# Name of output file for calculating traveltime residuals
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self.resout = 'residuals.dat'
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def copyRef(self):
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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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def setCWD(self):
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self.cwd = subprocess.check_output(['pwd'])[0:-1]
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print('Working directory is pwd: %s'%self.cwd)
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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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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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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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tdelta = datetime.datetime.now() - starttime
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print('runTOMO3D: Finished %s iterations after %s.'%(self.iter, tdelta))
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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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processes.append(subprocess.Popen(self.fmm, stdout = fout))
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fout.close()
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os.chdir(self.cwd)
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return processes
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def startForward(self, logdir):
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self._printLine()
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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()
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starttime = datetime.datetime.now()
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processes = []
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for procID in range(1, self.nproc + 1):
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directory = self.getProcDir(procID)
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logfn = 'fm3dlog_' + str(procID) + '.out'
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log_out = os.path.join(logdir, logfn)
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self.writeSrcFile(procID, directory)
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self.writeTracesFile(procID, directory)
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os.system('cp {cvg} {cig} {mode} {pg} {frechin} {dest}'
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.format(cvg=self.cvg, cig=self.cig, frechin=self.frech,
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mode=self.mode, pg=self.pg, dest=directory))
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processes = self.runFmm(directory, log_out, processes)
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for p in processes:
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p.wait()
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self.mergeOutput(self.cInvIterDir)
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self.clearDirectories()
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self.copyArrivals()
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if self.citer == 0:
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self.copyArrivals(self.rtrav)
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self.calcRes()
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tdelta = datetime.datetime.now() - starttime
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print('Finished Forward calculation after %s'%tdelta)
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def startInversion(self):
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print('Calling %s...'%self.inv)
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os.system(self.inv)
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def calcRes(self):
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resout = os.path.join(self.cwd, self.resout)
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if self.citer == 0:
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os.system('%s > %s'%(self.resid, resout))
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else:
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os.system('%s >> %s'%(self.resid, resout))
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with open(resout, 'r') as infile:
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residuals = infile.readlines()
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RMS, var, chi2 = residuals[-1].split()
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print('Residuals: RMS = %s, var = %s, Chi^2 = %s.'%(RMS, var, chi2))
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def raiseIter(self):
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self.citer +=1
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self._printLine()
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invfile = open(self.cwd + '/inviter.in', 'w')
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invfile.write('%s'%self.citer)
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invfile.close()
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def makeDir(self, directory):
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err = os.system('mkdir %s'%directory)
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if err is 0:
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self.directories.append(directory)
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return
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if err is 256:
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if self.overwrite == True:
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print('Overwriting existing files.')
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self.clearDir(directory)
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self.directories.append(directory)
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return
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raise RuntimeError('Could not create directory: %s'%directory)
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def makeDirectories(self):
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for procID in range(1, self.nproc + 1):
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directory = self.getProcDir(procID)
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self.makeDir(directory)
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def makeInvIterDir(self):
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invIterDir = self.cwd + '/it_%s'%(self.citer)
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err = os.system('mkdir %s'%invIterDir)
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if err is 256:
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if self.overwrite:
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self.clearDir(invIterDir)
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elif err is not 0:
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raise RuntimeError('Could not create directory: %s'%invIterDir)
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self.cInvIterDir = invIterDir
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def clearDir(self, directory):
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print('Wiping directory %s...'%directory)
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for filename in os.listdir(directory):
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filenp = os.path.join(directory, filename)
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os.remove(filenp)
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def clearDirectories(self):
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for directory in self.directories:
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self.clearDir(directory)
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def rmDir(self, directory):
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print('Removing directory %s...'%directory)
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return os.rmdir(directory)
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def removeDirectories(self):
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for directory in self.directories:
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self.rmDir(directory)
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self.directories = []
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def getProcDir(self, procID):
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return os.path.join(self.cwd, self.folder) + str(procID)
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def getTraceIDs4Sources(self, sourceIDs):
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traceIDs = []
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for traceID in self.traces.keys():
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if self.traces[traceID]['source'] in sourceIDs:
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traceIDs.append(traceID)
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return traceIDs
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def getTraceIDs4Source(self, sourceID):
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traceIDs = []
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for traceID in self.traces.keys():
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if self.traces[traceID]['source'] == sourceID:
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traceIDs.append(traceID)
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return traceIDs
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def copyArrivals(self, target = None):
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if target == None:
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target = os.path.join(self.cwd, self.mtrav)
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os.system('cp %s %s'%(os.path.join(
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self.cInvIterDir, self.ttim), target))
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def saveVgrid(self):
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vgpath = os.path.join(self.cwd, 'vgrids.in')
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os.system('cp %s %s'%(vgpath, self.cInvIterDir))
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def calcSrcPerKernel(self):
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nsrc = self.readNsrc()
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if self.nproc > nsrc:
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raise ValueError('Number of spawned processes higher than number of sources')
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return nsrc/self.nproc, nsrc%self.nproc
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def srcIDs4Kernel(self, procID):
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proc = procID - 1
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nsrc = self.readNsrc()
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srcPK, remain = self.calcSrcPerKernel()
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if procID > self.nproc:
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sys.exit('STOP: Kernel ID exceeds available number.')
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if proc < remain:
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start = (srcPK + 1) * (proc) + 1
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return range(start, start + srcPK + 1)
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elif proc == remain:
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start = (srcPK + 1) * (proc) + 1
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return range(start, start + srcPK)
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elif proc > remain:
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start = (srcPK + 1) * remain + srcPK * (proc - remain) + 1
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return range(start, start + srcPK)
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def readNsrc(self):
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srcfile = open(self.csl, 'r')
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nsrc = int(srcfile.readline())
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srcfile.close()
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return nsrc
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def readNtraces(self):
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recfile = open(self.rec, 'r')
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nrec = int(recfile.readline())
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recfile.close()
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return nrec
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def readSrcFile(self):
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nsrc = self.readNsrc()
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srcfile = open(self.csl, 'r')
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sources = {}
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temp = srcfile.readline()
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for index in range(nsrc):
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teleflag = int(srcfile.readline())
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coords = srcfile.readline().split()
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numpaths = int(srcfile.readline())
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steps = int(srcfile.readline())
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interactions = srcfile.readline().split()
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veltype = int(srcfile.readline())
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if teleflag is not 0:
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sys.exit('Script not yet usable for teleseismic.')
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if numpaths is not 1:
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sys.exit('Script not yet usable for more than one path per source.')
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sources[index + 1] = {'teleflag': teleflag,
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'coords': coords,
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'numpaths': numpaths,
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'steps': steps,
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'interactions': interactions,
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'veltype': veltype
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}
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return sources
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def readTraces(self):
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recfile = open(self.rec, 'r')
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ntraces = self.readNtraces()
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traces = {}
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temp = recfile.readline()
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for index in range(ntraces):
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coords = recfile.readline().split()
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paths = int(recfile.readline())
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source = int(recfile.readline())
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path = int(recfile.readline())
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traces[index + 1] = { 'coords': coords,
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'paths': paths,
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'source': source,
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'path': path
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}
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return traces
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def readArrivals(self, procID):
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directory = self.getProcDir(procID)
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arrfile = open(directory + '/arrivals.dat', 'r')
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sourceIDs = self.srcIDs4Kernel(procID)
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arrivals = []
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for sourceID in sourceIDs:
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traceIDs = self.getTraceIDs4Source(sourceID)
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for traceID in traceIDs:
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line = arrfile.readline().split()
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if line != []:
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# recID and srcID for the individual processor will not be needed
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recID_proc, srcID_proc, ray, normal, arrtime, diff, head = line
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arrivals.append([traceID, sourceID, ray, normal, arrtime, diff, head])
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return arrivals
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def readRays(self, procID):
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directory = self.getProcDir(procID)
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raysfile = open(directory + '/rays.dat', 'r')
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sourceIDs = self.srcIDs4Kernel(procID)
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rays = {}
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for sourceID in sourceIDs:
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traceIDs = self.getTraceIDs4Source(sourceID)
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for traceID in traceIDs:
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line1 = raysfile.readline().split()
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if line1 != []:
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# recID and srcID for the individual processor will not be needed
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recID_proc, srcID_proc, ray, normal, nsec = line1
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raysecs = {}
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for sec in range(int(nsec)):
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line2 = raysfile.readline().split()
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npoints, region, diff, head = line2
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raypoints = []
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for j in range(int(npoints)):
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raypoints.append(raysfile.readline() + '\n')
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raysecs[sec] = {'npoints': npoints,
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'region': region,
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'diff': diff,
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'head': head,
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'raypoints': raypoints
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}
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rays[traceID] = {'sourceID': sourceID,
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'raypath': ray,
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'normal': normal,
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'nsec': nsec,
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'raysections': raysecs
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}
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return rays
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def writeSrcFile(self, procID, directory):
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srcfile = open('%s/sources.in'%directory, 'w')
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sourceIDs = self.srcIDs4Kernel(procID)
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srcfile.write('%s\n'%len(sourceIDs))
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for sourceID in sourceIDs:
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source = self.sources[sourceID]
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coords = source['coords']
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interactions = source['interactions']
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srcfile.write('%s\n'%source['teleflag'])
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srcfile.write('%s %s %s\n'%(float(coords[0]), float(coords[1]), float(coords[2])))
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srcfile.write('%s\n'%source['numpaths'])
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srcfile.write('%s\n'%source['steps'])
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srcfile.write('%s %s\n'%(int(interactions[0]), int(interactions[1])))
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srcfile.write('%s\n'%source['veltype'])
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def writeTracesFile(self, procID, directory):
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recfile = open('%s/receivers.in'%directory, 'w')
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sourceIDs = self.srcIDs4Kernel(procID)
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traceIDs = self.getTraceIDs4Sources(sourceIDs)
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recfile.write('%s\n'%len(traceIDs))
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for traceID in traceIDs:
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trace = self.traces[traceID]
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coords = trace['coords']
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source = int(trace['source']) - sourceIDs[0] + 1
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recfile.write('%s %s %s\n'%(float(coords[0]), float(coords[1]), float(coords[2])))
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recfile.write('%s\n'%trace['paths'])
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recfile.write('%s\n'%source)
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recfile.write('%s\n'%trace['path'])
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def mergeArrivals(self, directory):
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arrfn = os.path.join(directory, self.ttim)
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arrivalsOut = open(arrfn, 'w')
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print('Merging arrivals.dat...')
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for procID in range(1, self.nproc + 1):
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arrivals = self.readArrivals(procID)
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for line in arrivals:
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arrivalsOut.write('%6s %6s %6s %6s %15s %5s %5s\n'%tuple(line))
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os.system('ln -fs %s %s'%(arrfn, os.path.join(self.cwd, self.ttim)))
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def mergeRays(self, directory):
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print('Merging rays.dat...')
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with open(directory + '/rays.dat', 'w') as outfile:
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for procID in range(1, self.nproc + 1):
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rays = self.readRays(procID)
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for traceID in rays:
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ray = rays[traceID]
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outfile.write('%6s %6s %6s %6s %6s\n'%(traceID,
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ray['sourceID'],
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ray['raypath'],
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ray['normal'],
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ray['nsec']))
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for sec in range(int(ray['nsec'])):
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raysec = ray['raysections'][sec]
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outfile.write('%6s %6s %6s %6s\n'%(raysec['npoints'],
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raysec['region'],
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raysec['diff'],
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raysec['head']))
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outfile.writelines(raysec['raypoints'])
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def mergeFrechet(self, directory):
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print('Merging frechet.dat...')
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frechfnout = os.path.join(directory, self.frechout)
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with open(frechfnout, 'w') as outfile:
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for procID in range(1, self.nproc + 1):
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filename = os.path.join(self.getProcDir(procID), self.frechout)
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with open(filename) as infile:
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for sourceID in self.srcIDs4Kernel(procID):
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for traceID in self.getTraceIDs4Source(sourceID):
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recID_proc, srcID_proc, ray, normal, NPDEV = infile.readline().split()
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outfile.write('%6s %6s %6s %6s %6s\n'%(traceID, sourceID, ray, normal, NPDEV))
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for index in range(int(NPDEV)):
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outfile.write(infile.readline())
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os.system('ln -fs %s %s'%(frechfnout, os.path.join(self.cwd, self.frechout)))
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def mergeOutput(self, directory):
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self.mergeArrivals(directory)
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self.mergeFrechet(directory)
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self.mergeRays(directory)
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def unlink(self, filepath):
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return os.system('unlink %s'%filepath)
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def _printLine(self):
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print('----------------------------------------')
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def vgrids2VTK(inputfile='vgrids.in', outputfile='vgrids.vtk', absOrRel='abs', inputfileref='vgridsref.in'):
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'''
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Generate a vtk-file readable by e.g. paraview from FMTOMO output vgrids.in
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'''
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R = 6371. # earth radius
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outfile = open(outputfile, 'w')
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number, delta, start, vel = _readVgrid(inputfile)
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nR, nTheta, nPhi = number
|
|
dR, dTheta, dPhi = delta
|
|
sR, sTheta, sPhi = start
|
|
|
|
thetaGrid, phiGrid, rGrid = _generateGrids(number, delta, start)
|
|
|
|
nPoints = nR * nTheta * nPhi
|
|
|
|
nX = nPhi;
|
|
nY = nTheta;
|
|
nZ = nR
|
|
|
|
sZ = sR - R
|
|
sX = _getDistance(sPhi)
|
|
sY = _getDistance(sTheta)
|
|
|
|
dX = _getDistance(dPhi)
|
|
dY = _getDistance(dTheta)
|
|
dZ = dR
|
|
|
|
# write header
|
|
print("Writing header for VTK file...")
|
|
outfile.write('# vtk DataFile Version 3.1\n')
|
|
outfile.write('Velocity on FMTOMO vgrids.in points\n')
|
|
outfile.write('ASCII\n')
|
|
outfile.write('DATASET STRUCTURED_POINTS\n')
|
|
|
|
outfile.write('DIMENSIONS %d %d %d\n' % (nX, nY, nZ))
|
|
outfile.write('ORIGIN %f %f %f\n' % (sX, sY, sZ))
|
|
outfile.write('SPACING %f %f %f\n' % (dX, dY, dZ))
|
|
|
|
outfile.write('POINT_DATA %15d\n' % (nPoints))
|
|
if absOrRel == 'abs':
|
|
outfile.write('SCALARS velocity float %d\n' %(1))
|
|
if absOrRel == 'relDepth':
|
|
outfile.write('SCALARS velocity2depthMean float %d\n' %(1))
|
|
elif absOrRel == 'rel':
|
|
outfile.write('SCALARS velChangePercent float %d\n' % (1))
|
|
outfile.write('LOOKUP_TABLE default\n')
|
|
|
|
pointsPerR = nTheta * nPhi
|
|
|
|
# write velocity
|
|
if absOrRel == 'abs':
|
|
print("Writing velocity values to VTK file...")
|
|
for velocity in vel:
|
|
outfile.write('%10f\n' %velocity)
|
|
elif absOrRel == 'relDepth':
|
|
print("Writing velocity values to VTK file relative to mean of each depth...")
|
|
index = 0; count = 0
|
|
veldepth = []
|
|
for velocity in vel:
|
|
count += 1
|
|
veldepth.append(velocity)
|
|
if count%pointsPerR == 0:
|
|
velmean = np.mean(veldepth)
|
|
#print velmean, count, count/pointsPerR
|
|
for vel in veldepth:
|
|
outfile.write('%10f\n' %(vel - velmean))
|
|
veldepth = []
|
|
elif absOrRel == 'rel':
|
|
nref, dref, sref, velref = _readVgrid(inputfileref)
|
|
nR_ref, nTheta_ref, nPhi_ref = nref
|
|
if not len(velref) == len(vel):
|
|
print('ERROR: Number of gridpoints mismatch for %s and %s' % (inputfile, inputfileref))
|
|
return
|
|
# velrel = [((vel - velref) / velref * 100) for vel, velref in zip(vel, velref)]
|
|
velrel = []
|
|
for velocities in zip(vel, velref):
|
|
v, vref = velocities
|
|
if not vref == 0:
|
|
velrel.append((v - vref) / vref * 100)
|
|
else:
|
|
velrel.append(0)
|
|
|
|
if not nR_ref == nR and nTheta_ref == nTheta and nPhi_ref == nPhi:
|
|
print('ERROR: Dimension mismatch of grids %s and %s' % (inputfile, inputfileref))
|
|
return
|
|
print("Writing velocity values to VTK file...")
|
|
for velocity in velrel:
|
|
outfile.write('%10f\n' % velocity)
|
|
print('Pertubations: min: %s %%, max: %s %%' % (min(velrel), max(velrel)))
|
|
|
|
outfile.close()
|
|
print("Wrote velocity grid for %d points to file: %s" % (nPoints, outputfile))
|
|
return
|
|
|
|
|
|
def rays2VTK(fnin, fdirout='./vtk_files/', nthPoint=50):
|
|
'''
|
|
Writes VTK file(s) for FMTOMO rays from rays.dat
|
|
|
|
:param: nthPoint, plot every nth point of the ray
|
|
:type: integer
|
|
'''
|
|
infile = open(fnin, 'r')
|
|
R = 6371
|
|
rays = {}
|
|
raynumber = 0
|
|
nPoints = 0
|
|
|
|
### NOTE: rays.dat seems to be in km and radians
|
|
while True:
|
|
raynumber += 1
|
|
firstline = infile.readline()
|
|
if firstline == '': break # break at EOF
|
|
raynumber = int(firstline.split()[0])
|
|
shotnumber = int(firstline.split()[1])
|
|
rayValid = int(firstline.split()[4]) # is zero if the ray is invalid
|
|
if rayValid == 0:
|
|
print('Invalid ray number %d for shot number %d' % (raynumber, shotnumber))
|
|
continue
|
|
nRayPoints = int(infile.readline().split()[0])
|
|
if not shotnumber in rays.keys():
|
|
rays[shotnumber] = {}
|
|
rays[shotnumber][raynumber] = []
|
|
for index in range(nRayPoints):
|
|
if index % nthPoint is 0 or index == (nRayPoints - 1):
|
|
rad, lat, lon = infile.readline().split()
|
|
rays[shotnumber][raynumber].append(
|
|
[_getDistance(np.rad2deg(float(lon))), _getDistance(np.rad2deg(float(lat))), float(rad) - R])
|
|
else:
|
|
dummy = infile.readline()
|
|
|
|
infile.close()
|
|
|
|
for shotnumber in rays.keys():
|
|
fnameout = fdirout + 'rays%03d.vtk' % (shotnumber)
|
|
outfile = open(fnameout, 'w')
|
|
|
|
nPoints = 0
|
|
for raynumber in rays[shotnumber]:
|
|
for ray in rays[shotnumber][raynumber]:
|
|
nPoints += 1
|
|
|
|
# write header
|
|
# print("Writing header for VTK file...")
|
|
print("Writing shot %d to file %s" % (shotnumber, fnameout))
|
|
outfile.write('# vtk DataFile Version 3.1\n')
|
|
outfile.write('FMTOMO rays\n')
|
|
outfile.write('ASCII\n')
|
|
outfile.write('DATASET POLYDATA\n')
|
|
outfile.write('POINTS %15d float\n' % (nPoints))
|
|
|
|
# write coordinates
|
|
# print("Writing coordinates to VTK file...")
|
|
for raynumber in rays[shotnumber].keys():
|
|
for raypoint in rays[shotnumber][raynumber]:
|
|
outfile.write('%10f %10f %10f \n' % (raypoint[0], raypoint[1], raypoint[2]))
|
|
|
|
outfile.write('LINES %15d %15d\n' % (len(rays[shotnumber]), len(rays[shotnumber]) + nPoints))
|
|
|
|
# write indices
|
|
# print("Writing indices to VTK file...")
|
|
count = 0
|
|
for raynumber in rays[shotnumber].keys():
|
|
outfile.write('%d ' % (len(rays[shotnumber][raynumber])))
|
|
for index in range(len(rays[shotnumber][raynumber])):
|
|
outfile.write('%d ' % (count))
|
|
count += 1
|
|
outfile.write('\n')
|
|
|
|
|
|
def _readVgrid(filename):
|
|
def readNumberOfPoints(filename):
|
|
fin = open(filename, 'r')
|
|
vglines = fin.readlines()
|
|
|
|
nR = int(vglines[1].split()[0])
|
|
nTheta = int(vglines[1].split()[1])
|
|
nPhi = int(vglines[1].split()[2])
|
|
|
|
print('readNumberOf Points: Awaiting %d grid points in %s'
|
|
% (nR * nTheta * nPhi, filename))
|
|
fin.close()
|
|
return nR, nTheta, nPhi
|
|
|
|
def readDelta(filename):
|
|
fin = open(filename, 'r')
|
|
vglines = fin.readlines()
|
|
|
|
dR = float(vglines[2].split()[0])
|
|
dTheta = float(vglines[2].split()[1])
|
|
dPhi = float(vglines[2].split()[2])
|
|
|
|
fin.close()
|
|
return dR, dTheta, dPhi
|
|
|
|
def readStartpoints(filename):
|
|
fin = open(filename, 'r')
|
|
vglines = fin.readlines()
|
|
|
|
sR = float(vglines[3].split()[0])
|
|
sTheta = float(vglines[3].split()[1])
|
|
sPhi = float(vglines[3].split()[2])
|
|
|
|
fin.close()
|
|
return sR, sTheta, sPhi
|
|
|
|
def readVelocity(filename):
|
|
'''
|
|
Reads in velocity from vgrids file and returns a list containing all values in the same order
|
|
'''
|
|
vel = [];
|
|
count = 0
|
|
fin = open(filename, 'r')
|
|
vglines = fin.readlines()
|
|
|
|
for line in vglines:
|
|
count += 1
|
|
if count > 4:
|
|
vel.append(float(line.split()[0]))
|
|
|
|
print("Read %d points out of file: %s" % (count - 4, filename))
|
|
return vel
|
|
|
|
# Theta, Phi in radians, R in km
|
|
nR, nTheta, nPhi = readNumberOfPoints(filename)
|
|
dR, dThetaRad, dPhiRad = readDelta(filename)
|
|
sR, sThetaRad, sPhiRad = readStartpoints(filename)
|
|
vel = readVelocity(filename)
|
|
|
|
dTheta, dPhi = np.rad2deg((dThetaRad, dPhiRad))
|
|
sTheta, sPhi = np.rad2deg((sThetaRad, sPhiRad))
|
|
|
|
number = (nR, nTheta, nPhi)
|
|
delta = (dR, dTheta, dPhi)
|
|
start = (sR, sTheta, sPhi)
|
|
return number, delta, start, vel
|
|
|
|
|
|
def _generateGrids(number, delta, start):
|
|
nR, nTheta, nPhi = number
|
|
dR, dTheta, dPhi = delta
|
|
sR, sTheta, sPhi = start
|
|
|
|
eR = sR + (nR - 1) * dR
|
|
ePhi = sPhi + (nPhi - 1) * dPhi
|
|
eTheta = sTheta + (nTheta - 1) * dTheta
|
|
|
|
thetaGrid = np.linspace(sTheta, eTheta, num=nTheta)
|
|
phiGrid = np.linspace(sPhi, ePhi, num=nPhi)
|
|
rGrid = np.linspace(sR, eR, num=nR)
|
|
|
|
return (thetaGrid, phiGrid, rGrid)
|
|
|
|
|
|
def addCheckerboard(spacing=10., pertubation=0.1, inputfile='vgrids.in',
|
|
outputfile='vgrids_cb.in', ampmethod='linear', rect=(None, None)):
|
|
'''
|
|
Add a checkerboard to an existing vgrids.in velocity model.
|
|
|
|
:param: spacing, size of the tiles
|
|
type: float
|
|
|
|
:param: pertubation, pertubation (default: 0.1 = 10%)
|
|
type: float
|
|
'''
|
|
|
|
def correctSpacing(spacing, delta, disttype=None):
|
|
if spacing > delta:
|
|
spacing_corr = round(spacing / delta) * delta
|
|
elif spacing < delta:
|
|
spacing_corr = delta
|
|
print('The spacing of the checkerboard of %s (%s) was corrected to '
|
|
'a value of %s to fit the grid spacing of %s.' % (spacing, disttype, spacing_corr, delta))
|
|
return spacing_corr
|
|
|
|
def linearAmp(InCell):
|
|
decimal = InCell - np.floor(InCell)
|
|
return (-abs(decimal - 0.5) + 0.5) * 2
|
|
|
|
def rectAmp(InCell, rect):
|
|
decimal = InCell - np.floor(InCell)
|
|
r1, r2 = rect
|
|
if r1 <= decimal <= r2:
|
|
return 1
|
|
else:
|
|
return 0
|
|
|
|
def ampFunc(InCell, method='linear', rect=None):
|
|
if method == 'linear':
|
|
return linearAmp(InCell)
|
|
if method == 'rect' and rect is not None:
|
|
return rectAmp(InCell, rect)
|
|
else:
|
|
print('ampFunc: Could not amplify cb pattern')
|
|
|
|
decm = 0.3 # diagonal elements of the covariance matrix (grid3dg's default value is 0.3)
|
|
outfile = open(outputfile, 'w')
|
|
|
|
number, delta, start, vel = _readVgrid(inputfile)
|
|
|
|
nR, nTheta, nPhi = number
|
|
dR, dTheta, dPhi = delta
|
|
sR, sTheta, sPhi = start
|
|
|
|
thetaGrid, phiGrid, rGrid = _generateGrids(number, delta, start)
|
|
|
|
nPoints = nR * nTheta * nPhi
|
|
|
|
# write header for velocity grid file (in RADIANS)
|
|
outfile.write('%10s %10s \n' % (1, 1))
|
|
outfile.write('%10s %10s %10s\n' % (nR, nTheta, nPhi))
|
|
outfile.write('%10s %10s %10s\n' % (dR, np.deg2rad(dTheta), np.deg2rad(dPhi)))
|
|
outfile.write('%10s %10s %10s\n' % (sR, np.deg2rad(sTheta), np.deg2rad(sPhi)))
|
|
|
|
spacR = correctSpacing(spacing, dR, '[meter], R')
|
|
spacTheta = correctSpacing(_getAngle(spacing), dTheta, '[degree], Theta')
|
|
spacPhi = correctSpacing(_getAngle(spacing), dPhi, '[degree], Phi')
|
|
|
|
count = 0
|
|
evenOdd = 1
|
|
even = 0;
|
|
odd = 0
|
|
|
|
# In the following loop it is checked whether the positive distance from the border of the model
|
|
# for a point on the grid divided by the spacing is even or odd and then pertubated.
|
|
# The position is also shifted by half of the delta so that the position is directly on the point and
|
|
# not on the border between two points.
|
|
# "InCell" points e.g. rInCell are floats with their integer number corresponding to the cell number and
|
|
# their decimal place (0 - 1) corresponding to the position inside the cell.
|
|
# The amplification factor ampFactor comes from a linear relationship and ranges between 0 (cell border)
|
|
# and 1 (cell middle)
|
|
for radius in rGrid:
|
|
rInCell = (radius - sR - dR / 2) / spacR
|
|
ampR = ampFunc(rInCell, ampmethod, rect)
|
|
if np.floor(rInCell) % 2:
|
|
evenOddR = 1
|
|
else:
|
|
evenOddR = -1
|
|
for theta in thetaGrid:
|
|
thetaInCell = (theta - sTheta - dTheta / 2) / spacTheta
|
|
ampTheta = ampFunc(thetaInCell, ampmethod, rect)
|
|
if np.floor(thetaInCell) % 2:
|
|
evenOddT = 1
|
|
else:
|
|
evenOddT = -1
|
|
for phi in phiGrid:
|
|
phiInCell = (phi - sPhi - dPhi / 2) / spacPhi
|
|
ampPhi = ampFunc(phiInCell, ampmethod, rect)
|
|
if np.floor(phiInCell) % 2:
|
|
evenOddP = 1
|
|
else:
|
|
evenOddP = -1
|
|
velocity = vel[count]
|
|
ampFactor = (ampR + ampTheta + ampPhi) / 3
|
|
evenOdd = evenOddR * evenOddT * evenOddP * ampFactor
|
|
velocity += evenOdd * pertubation * velocity
|
|
|
|
outfile.write('%10s %10s\n' % (velocity, decm))
|
|
count += 1
|
|
|
|
progress = float(count) / float(nPoints) * 100
|
|
_update_progress(progress)
|
|
|
|
print('Added checkerboard to the grid in file %s with a spacing of %s and a pertubation of %s %%. '
|
|
'Outputfile: %s.' % (inputfile, spacing, pertubation * 100, outputfile))
|
|
outfile.close()
|
|
|
|
|
|
def addBox(x=(None, None), y=(None, None), z=(None, None),
|
|
boxvelocity=1.0, inputfile='vgrids.in',
|
|
outputfile='vgrids_box.in'):
|
|
'''
|
|
Add a box with constant velocity to an existing vgrids.in velocity model.
|
|
|
|
:param: x, borders of the box (xleft, xright)
|
|
type: tuple
|
|
|
|
:param: y, borders of the box (yleft, yright)
|
|
type: tuple
|
|
|
|
:param: z, borders of the box (bot, top)
|
|
type: tuple
|
|
|
|
:param: boxvelocity, default: 1.0 km/s
|
|
type: float
|
|
'''
|
|
R = 6371.
|
|
decm = 0.3 # diagonal elements of the covariance matrix (grid3dg's default value is 0.3)
|
|
outfile = open(outputfile, 'w')
|
|
|
|
theta1 = _getAngle(y[0])
|
|
theta2 = _getAngle(y[1])
|
|
phi1 = _getAngle(x[0])
|
|
phi2 = _getAngle(x[1])
|
|
r1 = R + z[0]
|
|
r2 = R + z[1]
|
|
|
|
print('Adding box to grid with theta = (%s, %s), phi = (%s, %s), '
|
|
'r = (%s, %s), velocity = %s [km/s]'
|
|
% (theta1, theta2, phi1, phi2, r1, r2, boxvelocity))
|
|
|
|
number, delta, start, vel = _readVgrid(inputfile)
|
|
|
|
nR, nTheta, nPhi = number
|
|
dR, dTheta, dPhi = delta
|
|
sR, sTheta, sPhi = start
|
|
|
|
thetaGrid, phiGrid, rGrid = _generateGrids(number, delta, start)
|
|
|
|
nPoints = nR * nTheta * nPhi
|
|
|
|
# write header for velocity grid file (in RADIANS)
|
|
outfile.write('%10s %10s \n' % (1, 1))
|
|
outfile.write('%10s %10s %10s\n' % (nR, nTheta, nPhi))
|
|
outfile.write('%10s %10s %10s\n' % (dR, np.deg2rad(dTheta), np.deg2rad(dPhi)))
|
|
outfile.write('%10s %10s %10s\n' % (sR, np.deg2rad(sTheta), np.deg2rad(sPhi)))
|
|
|
|
count = 0
|
|
for radius in rGrid:
|
|
if r1 <= radius <= r2:
|
|
rFlag = 1
|
|
else:
|
|
rFlag = 0
|
|
for theta in thetaGrid:
|
|
if theta1 <= theta <= theta2:
|
|
thetaFlag = 1
|
|
else:
|
|
thetaFlag = 0
|
|
for phi in phiGrid:
|
|
if phi1 <= phi <= phi2:
|
|
phiFlag = 1
|
|
else:
|
|
phiFlag = 0
|
|
velocity = vel[count]
|
|
if rFlag * thetaFlag * phiFlag is not 0:
|
|
velocity = boxvelocity
|
|
|
|
outfile.write('%10s %10s\n' % (velocity, decm))
|
|
count += 1
|
|
|
|
progress = float(count) / float(nPoints) * 100
|
|
_update_progress(progress)
|
|
|
|
print('Added box to the grid in file %s. '
|
|
'Outputfile: %s.' % (inputfile, outputfile))
|
|
outfile.close()
|
|
|
|
|
|
def _update_progress(progress):
|
|
sys.stdout.write("%d%% done \r" % (progress))
|
|
sys.stdout.flush()
|
|
|
|
|
|
def _getAngle(distance):
|
|
'''
|
|
Function returns the angle on a Sphere of the radius R = 6371 [km] for a distance [km].
|
|
'''
|
|
PI = np.pi
|
|
R = 6371.
|
|
angle = distance * 180. / (PI * R)
|
|
return angle
|
|
|
|
|
|
def _getDistance(angle):
|
|
PI = np.pi
|
|
R = 6371.
|
|
distance = angle / 180 * (PI * R)
|
|
return distance
|