mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
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Merge branch 'master' of https://bitbucket.org/cosmicvoids/void_identification
This commit is contained in:
P.M. Sutter
commit
e92d30301b
98 changed files with 22013 additions and 47 deletions
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@ -624,6 +624,9 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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# periodicLine += "z"
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# periodicLine += "' "
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launchDir = os.getcwd()
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os.chdir(voidDir)
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conf="""
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desc %s
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partzone %s
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@ -690,6 +693,8 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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fp.write("doExtraction\n")
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fp.close()
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jobString = " "+runSuffix+":"
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if not (continueRun and jobSuccessful(logFile, "Done!\n")):
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#cmd = "%s --configFile=%s &> %s" % \
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# (binPath, parmFile, logFile)
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@ -701,13 +706,13 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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log.close()
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if jobSuccessful(logFile, "Done!\n"):
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print "done"
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print jobString, "Stacking voids done"
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else:
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print "FAILED!"
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print jobString, "Stacking voids FAILED!"
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exit(-1)
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else:
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print "already done!"
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print jobString, "Stacking voids already done!"
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if os.access(parmFile, os.F_OK): os.unlink(parmFile)
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return
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@ -739,7 +744,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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os.unlink(voidDir+"/NOVOID")
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if (numVoids == "0"):
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print " No voids found; skipping!"
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print jobString, "No voids found; skipping!"
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fp = open(voidDir+"/NOVOID", "w")
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fp.write("no voids found\n")
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fp.close()
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@ -750,7 +755,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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if "EMPTY STACK" in line:
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emptyStack = True
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if emptyStack:
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print " Stack is empty; skipping!"
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print jobString, "Stack is empty; skipping!"
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fp = open(voidDir+"/NOVOID", "w")
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fp.write("empty stack\n")
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fp.close()
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@ -817,30 +822,32 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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fp.write(str(normalization)+"\n")
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fp.close()
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os.system("mv %s %s" % ("tree.data", treeFile))
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os.system("mv %s %s" % ("void_indexes.txt", voidDir+"/"))
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os.system("mv %s %s" % ("posx.nc", voidDir+"/"))
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os.system("mv %s %s" % ("posy.nc", voidDir+"/"))
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os.system("mv %s %s" % ("posz.nc", voidDir+"/"))
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os.system("mv %s %s" % ("z_void_indexes.txt", voidDir+"/"))
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os.system("mv %s %s" % ("z_posx.nc", voidDir+"/"))
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os.system("mv %s %s" % ("z_posy.nc", voidDir+"/"))
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os.system("mv %s %s" % ("z_posz.nc", voidDir+"/"))
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os.system("mv %s %s" % ("redshifts.nc", voidDir+"/"))
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os.system("mv %s %s" % ("indexes.nc", voidDir+"/"))
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os.system("mv %s %s" % ("kdtree_stackvoids.dat", voidDir+"/"))
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os.system("mv %s %s" % ("centers.txt", voidDir+"/"))
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os.system("mv %s %s" % ("z_centers.txt", voidDir+"/"))
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os.system("mv %s %s" % ("sky_positions.txt", voidDir+"/"))
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os.system("mv %s %s" % ("check.txt", voidDir+"/"))
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os.system("mv %s %s" % ("tracer.txt", voidDir+"/"))
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os.system("mv %s %s" % ("normalizations.txt", voidDir+"/"))
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os.system("mv %s %s" % ("boundaryDistances.txt", voidDir+"/"))
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#os.system("mv %s %s" % ("tree.data", treeFile))
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#os.system("mv %s %s" % ("void_indexes.txt", voidDir+"/"))
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#os.system("mv %s %s" % ("posx.nc", voidDir+"/"))
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#os.system("mv %s %s" % ("posy.nc", voidDir+"/"))
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#os.system("mv %s %s" % ("posz.nc", voidDir+"/"))
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#os.system("mv %s %s" % ("z_void_indexes.txt", voidDir+"/"))
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#os.system("mv %s %s" % ("z_posx.nc", voidDir+"/"))
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#os.system("mv %s %s" % ("z_posy.nc", voidDir+"/"))
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#os.system("mv %s %s" % ("z_posz.nc", voidDir+"/"))
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#os.system("mv %s %s" % ("redshifts.nc", voidDir+"/"))
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#os.system("mv %s %s" % ("indexes.nc", voidDir+"/"))
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#os.system("mv %s %s" % ("kdtree_stackvoids.dat", voidDir+"/"))
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#os.system("mv %s %s" % ("centers.txt", voidDir+"/"))
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#os.system("mv %s %s" % ("z_centers.txt", voidDir+"/"))
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#os.system("mv %s %s" % ("sky_positions.txt", voidDir+"/"))
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#os.system("mv %s %s" % ("check.txt", voidDir+"/"))
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#os.system("mv %s %s" % ("tracer.txt", voidDir+"/"))
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#os.system("mv %s %s" % ("normalizations.txt", voidDir+"/"))
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#os.system("mv %s %s" % ("boundaryDistances.txt", voidDir+"/"))
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if os.access(idListFile, os.F_OK): os.unlink(idListFile)
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if os.access(parmFile, os.F_OK): os.unlink(parmFile)
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os.chdir(launchDir)
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return
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# -----------------------------------------------------------------------------
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@ -851,6 +858,7 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
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runSuffix = getStackSuffix(stack.zMin, stack.zMax, stack.rMin,
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stack.rMax, thisDataPortion)
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jobString = " "+runSuffix+":"
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sys.stdout = open(logFile, 'w')
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sys.stderr = open(logFile, 'a')
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@ -1076,21 +1084,26 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
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sys.stderr = sys.__stderr__
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if jobSuccessful(logFile, "Done!\n"):
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print "done"
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print jobString, "Combining stacks done"
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else:
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print "FAILED!"
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print jobString, "Combining stacks FAILED!"
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exit(-1)
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#else:
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# print "already done!"
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# -----------------------------------------------------------------------------
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def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None):
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def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
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thisDataPortion=None):
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sampleName = sample.fullName
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runSuffix = getStackSuffix(stack.zMin, stack.zMax, stack.rMin,
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stack.rMax, thisDataPortion)
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jobString = " "+runSuffix+":"
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if os.access(voidDir+"/NOVOID", os.F_OK):
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print "no stack here; skipping!"
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print jobString, "Profile no stack here; skipping!"
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return
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numVoids = open(voidDir+"/num_voids.txt", "r").readline()
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@ -1129,13 +1142,13 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None):
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sys.stderr = sys.__stderr__
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if jobSuccessful(logFile, "Done!\n"):
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print "done", numVoids
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print jobString, "Profiling stacks done, (N_v=", numVoids,")"
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else:
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print "FAILED!"
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print jobString, "Profiling stacks FAILED!"
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exit(-1)
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else:
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print "already done!"
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print jobString, "Profiling stacks already done!"
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# -----------------------------------------------------------------------------
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@ -1147,14 +1160,16 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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runSuffix = getStackSuffix(stack.zMin, stack.zMax, stack.rMin,
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stack.rMax, thisDataPortion)
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jobString = " "+runSuffix+":"
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if not (continueRun and jobSuccessful(logFile, "Done!\n")):
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if os.access(voidDir+"/NOVOID", os.F_OK):
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print "no voids here; skipping!"
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print jobString, "Fitting no voids here; skipping!"
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return
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numVoids = int(open(voidDir+"/num_voids.txt", "r").readline())
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if numVoids < 10:
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print "not enough voids to fit; skipping!"
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print jobString, "Fitting not enough voids to fit; skipping!"
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fp = open(voidDir+"/NOFIT", "w")
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fp.write("not enough voids: %d \n" % numVoids)
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fp.close()
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@ -1165,18 +1180,18 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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# return
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if sample.partOfCombo or not sample.includeInHubble:
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print "sample not needed for further analysis; skipping!"
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print jobString, "Fitting sample not needed for further analysis; skipping!"
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fp = open(voidDir+"/NOFIT", "w")
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fp.write("sample not needed for hubble\n")
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fp.close()
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return
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if not stack.includeInHubble:
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print "radius not needed for further analysis; skipping!"
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print jobString, "Fitting radius not needed for further analysis; skipping!"
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return
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if not stack.includeInHubble:
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print "redshift not needed for further analysis; skipping!"
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print jobString, "Fitting redshift not needed for further analysis; skipping!"
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return
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if os.access(figDir+"/stackedVoid_"+sampleName+"_"+\
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@ -1241,9 +1256,9 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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sys.stdout = sys.__stdout__
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sys.stderr = sys.__stderr__
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if jobSuccessful(logFile, "Done!\n"):
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print "done (", ntries, " tries)"
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print jobString, "Fitting done (", ntries, " tries)"
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else:
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print "FAILED!"
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print jobString, "Fitting FAILED!"
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exit(-1)
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# record the measured stretch
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@ -1255,14 +1270,14 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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if os.access(voidDir+"/NOFIT", os.F_OK):
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os.unlink(voidDir+"/NOFIT")
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if ntries > maxtries:
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print " No reliable fit found; skipping!"
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print jobString, " No reliable fit found; skipping!"
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fp = open(voidDir+"/NOFIT", "w")
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fp.write("bad ellipticity fit\n")
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fp.close()
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return
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else:
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print "already done!"
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print jobString, "already done!"
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# -----------------------------------------------------------------------------
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