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code cleanup and commenting

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This commit is contained in:
Marcel Paffrath 2016-05-19 11:20:37 +02:00
parent dbaead4754
commit 3138bbfa93
1 changed files with 146 additions and 24 deletions
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170
pylot/core/active/fmtomoUtils.py
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@ -6,23 +6,15 @@ import datetime
import numpy as np
class Tomo3d(object):
def __init__(self, nproc, iterations, citer = 0, overwrite = False):
def __init__(self, citer = 0, overwrite = False):
'''
Class build from FMTOMO script tomo3d. Can be used to run several instances of FMM code in parallel.
:param: nproc, number of parallel processes
:type: integer
:param: iterations, number of iterations
:type: integer
:param: citer, current iteration (default = 0: start new model)
:type: integer
'''
self.setCWD()
self.defParas()
self.nproc = nproc
self.iter = iterations # number of iterations
self.citer = citer # current iteration
self.sources = self.readSrcFile()
self.traces = self.readTraces()
@ -34,21 +26,37 @@ class Tomo3d(object):
self.defInvParas()
def defFMMParas(self):
'''
Initiates parameters for the forward calculation.
'''
# Name of fast marching program
self.fmm = '{0}/fm3d'.format(self.cwd)
# Name of program calculating Frechet derivatives
self.frechgen = '{0}/frechgen'.format(self.cwd)
# Name of current velocity/inversion grid
self.cvg = 'vgrids.in'
# Name of current interfaces grid
self.cig = 'interfaces.in'
# Name of file containing current source locations
self.csl = 'sources.in'
# Name of file containing propagation grid
self.pg = 'propgrid.in'
# Name of file containing receiver coordinates
self.rec = 'receivers.in'
self.frech = 'frechet.in'
self.frechout = 'frechet.dat'
# Name of file containing measured data
self.ot = 'otimes.dat'
# Name of file containing output velocity information
self.ttim = 'arrivals.dat'
self.mode = 'mode_set.in'
# Name of temporary folders created for each process
self.folder = '.proc_'
def defInvParas(self):
'''
Initiates inversion parameters for FMTOMO.
'''
# Name of program for performing inversion
self.inv = '{0}/invert3d'.format(self.cwd)
# Name of file containing current model traveltimes
@ -67,19 +75,41 @@ class Tomo3d(object):
self.resout = 'residuals.dat'
def copyRef(self):
# Copies reference grids to used grids (e.g. sourcesref.in to sources.in)
'''
Copies reference grids to used grids (e.g. sourcesref.in to sources.in)
'''
os.system('cp %s %s'%(self.ivg, self.cvg))
os.system('cp %s %s'%(self.iig, self.cig))
os.system('cp %s %s'%(self.isl, self.csl))
def setCWD(self):
self.cwd = subprocess.check_output(['pwd'])[0:-1]
print('Working directory is pwd: %s'%self.cwd)
def setCWD(self, directory = None):
'''
Set working directory containing all necessary files.
Default: pwd
'''
if directory == None:
directory = subprocess.check_output(['pwd'])[0:-1]
self.cwd = directory
print('Working directory is: %s'%self.cwd)
def runFrech(self):
os.system(self.frechgen)
def runTOMO3D(self):
def runTOMO3D(self, nproc, iterations):
'''
Starts up the FMTOMO code for the set number of iterations on nproc parallel processes.
:param: nproc, number of parallel processes
:type: integer
:param: iterations, number of iterations
:type: integer
'''
self.nproc = nproc
self.iter = iterations # number of iterations
starttime = datetime.datetime.now()
print('Starting TOMO3D on %s parallel processes for %s iteration(s).'
%(self.nproc, self.iter))
@ -104,6 +134,10 @@ class Tomo3d(object):
print('runTOMO3D: Finished %s iterations after %s.'%(self.iter, tdelta))
def runFmm(self, directory, logfile, processes):
'''
Calls an instance of the FMM code in the process directory.
Requires a list of all active processes and returns an updated list.
'''
os.chdir(directory)
fout = open(logfile, 'w')
processes.append(subprocess.Popen(self.fmm, stdout = fout))
@ -112,6 +146,9 @@ class Tomo3d(object):
return processes
def startForward(self, logdir):
'''
Runs an instance of the FMM code in the process directory.
'''
self._printLine()
print('Starting forward simulation for iteration %s.'%(self.citer))
@ -128,8 +165,8 @@ class Tomo3d(object):
logfn = 'fm3dlog_' + str(procID) + '.out'
log_out = os.path.join(logdir, logfn)
self.writeSrcFile(procID, directory)
self.writeTracesFile(procID, directory)
self.writeSrcFile(procID)
self.writeTracesFile(procID)
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))
@ -149,10 +186,16 @@ class Tomo3d(object):
print('Finished Forward calculation after %s'%tdelta)
def startInversion(self):
'''
Simply calls the inversion program.
'''
print('Calling %s...'%self.inv)
os.system(self.inv)
def calcRes(self):
'''
Calls residual calculation program.
'''
resout = os.path.join(self.cwd, self.resout)
if self.citer == 0:
os.system('%s > %s'%(self.resid, resout))
@ -185,11 +228,17 @@ class Tomo3d(object):
raise RuntimeError('Could not create directory: %s'%directory)
def makeDirectories(self):
'''
Makes temporary directories for all processes.
'''
for procID in range(1, self.nproc + 1):
directory = self.getProcDir(procID)
self.makeDir(directory)
def makeInvIterDir(self):
'''
Makes directories for each iteration step for the output.
'''
invIterDir = self.cwd + '/it_%s'%(self.citer)
err = os.system('mkdir %s'%invIterDir)
if err is 256:
@ -200,12 +249,18 @@ class Tomo3d(object):
self.cInvIterDir = invIterDir
def clearDir(self, directory):
'''
Wipes a certain directory.
'''
print('Wiping directory %s...'%directory)
for filename in os.listdir(directory):
filenp = os.path.join(directory, filename)
os.remove(filenp)
def clearDirectories(self):
'''
Wipes all generated temporary directories.
'''
for directory in self.directories:
self.clearDir(directory)
@ -214,14 +269,24 @@ class Tomo3d(object):
return os.rmdir(directory)
def removeDirectories(self):
'''
Removes all generated temporary directories.
'''
for directory in self.directories:
self.rmDir(directory)
self.directories = []
def getProcDir(self, procID):
'''
Returns the temporary directory for a certain process
with procID = process number.
'''
return os.path.join(self.cwd, self.folder) + str(procID)
def getTraceIDs4Sources(self, sourceIDs):
'''
Returns corresponding trace IDs for a set of given source IDs.
'''
traceIDs = []
for traceID in self.traces.keys():
if self.traces[traceID]['source'] in sourceIDs:
@ -229,6 +294,9 @@ class Tomo3d(object):
return traceIDs
def getTraceIDs4Source(self, sourceID):
'''
Returns corresponding trace IDs for a source ID.
'''
traceIDs = []
for traceID in self.traces.keys():
if self.traces[traceID]['source'] == sourceID:
@ -236,22 +304,38 @@ class Tomo3d(object):
return traceIDs
def copyArrivals(self, target = None):
'''
Copies the FMM output file (self.ttim) to a specific target file.
Default target is self.mtrav (model travel times).
'''
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')
'''
Saves the current velocity grid for the current iteration step.
'''
vgpath = os.path.join(self.cwd, self.cvg)
os.system('cp %s %s'%(vgpath, self.cInvIterDir))
def calcSrcPerKernel(self):
'''
(Equally) distributes all sources depending on the number of processes (kernels).
Returns two integer values.
First: minimum number of sources for each process
Second: remaining sources (always less than number of processes)
'''
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):
'''
Calculates and returns all source IDs for a given process ID.
'''
proc = procID - 1
nsrc = self.readNsrc()
srcPK, remain = self.calcSrcPerKernel()
@ -274,12 +358,18 @@ class Tomo3d(object):
return nsrc
def readNtraces(self):
'''
Reads the total number of traces from self.rec header.
'''
recfile = open(self.rec, 'r')
nrec = int(recfile.readline())
recfile.close()
return nrec
def readSrcFile(self):
'''
Reads the whole sourcefile and returns structured information in a dictionary.
'''
nsrc = self.readNsrc()
srcfile = open(self.csl, 'r')
@ -309,6 +399,10 @@ class Tomo3d(object):
return sources
def readTraces(self):
'''
Reads the receiver input file and returns the information
in a structured dictionary.
'''
recfile = open(self.rec, 'r')
ntraces = self.readNtraces()
@ -330,8 +424,13 @@ class Tomo3d(object):
return traces
def readArrivals(self, procID):
'''
Reads the arrival times from a temporary process directory,
changes local to global sourceIDs and traceIDs and returns
a list of arrival times.
'''
directory = self.getProcDir(procID)
arrfile = open(directory + '/arrivals.dat', 'r')
arrfile = open(os.path.join(directory, self.ttime), 'r')
sourceIDs = self.srcIDs4Kernel(procID)
arrivals = []
@ -347,6 +446,10 @@ class Tomo3d(object):
return arrivals
def readRays(self, procID):
'''
Reads rays output from a temporary process directory and returns
the information in a structured dictionary.
'''
directory = self.getProcDir(procID)
raysfile = open(directory + '/rays.dat', 'r')
sourceIDs = self.srcIDs4Kernel(procID)
@ -385,8 +488,12 @@ class Tomo3d(object):
}
return rays
def writeSrcFile(self, procID, directory):
srcfile = open('%s/sources.in'%directory, 'w')
def writeSrcFile(self, procID):
'''
Writes a source input file for a process with ID = procID.
'''
directory = self.getProcDir(procID)
srcfile = open(os.path,join(directory, self.csl), 'w')
sourceIDs = self.srcIDs4Kernel(procID)
srcfile.write('%s\n'%len(sourceIDs))
@ -401,7 +508,11 @@ class Tomo3d(object):
srcfile.write('%s %s\n'%(int(interactions[0]), int(interactions[1])))
srcfile.write('%s\n'%source['veltype'])
def writeTracesFile(self, procID, directory):
def writeTracesFile(self, procID):
'''
Writes a receiver input file for a process with ID = procID.
'''
directory = self.getProcDir(procID)
recfile = open('%s/receivers.in'%directory, 'w')
sourceIDs = self.srcIDs4Kernel(procID)
traceIDs = self.getTraceIDs4Sources(sourceIDs)
@ -417,9 +528,12 @@ class Tomo3d(object):
recfile.write('%s\n'%trace['path'])
def mergeArrivals(self, directory):
'''
Merges the arrival times for all processes to self.cInvIterDir.
'''
arrfn = os.path.join(directory, self.ttim)
arrivalsOut = open(arrfn, 'w')
print('Merging arrivals.dat...')
print('Merging %s...'%self.ttim)
for procID in range(1, self.nproc + 1):
arrivals = self.readArrivals(procID)
for line in arrivals:
@ -428,6 +542,9 @@ class Tomo3d(object):
os.system('ln -fs %s %s'%(arrfn, os.path.join(self.cwd, self.ttim)))
def mergeRays(self, directory):
'''
Merges the ray paths for all processes to self.cInvIterDir.
'''
print('Merging rays.dat...')
with open(directory + '/rays.dat', 'w') as outfile:
for procID in range(1, self.nproc + 1):
@ -448,9 +565,11 @@ class Tomo3d(object):
outfile.writelines(raysec['raypoints'])
def mergeFrechet(self, directory):
print('Merging frechet.dat...')
'''
Merges the frechet derivatives for all processes to self.cInvIterDir.
'''
frechfnout = os.path.join(directory, self.frechout)
print('Merging %s...'%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)
@ -465,6 +584,9 @@ class Tomo3d(object):
os.system('ln -fs %s %s'%(frechfnout, os.path.join(self.cwd, self.frechout)))
def mergeOutput(self, directory):
'''
Calls self.mergeArrivals, self.mergeFrechet and self.mergeRays.
'''
self.mergeArrivals(directory)
self.mergeFrechet(directory)
self.mergeRays(directory)