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https://bitbucket.org/cosmicvoids/vide_public.git
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much more flexible for handling different stacking and AP approaches
This commit is contained in:
P.M. Sutter
parent
a9100b2604
commit
73c6aedfc2
4 changed files with 132 additions and 87 deletions
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@ -616,10 +616,10 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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else:
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obsFlag = ""
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Rextracut = stack.rMin*3 + 1
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Rcircular = stack.rMin*3 + 2
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#Rextracut = stack.rMax*3 + 1
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#Rcircular = stack.rMax*3 + 2
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#Rextracut = stack.rMin*3 + 1
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#Rcircular = stack.rMin*3 + 2
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Rextracut = stack.rMax*3 + 1
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Rcircular = stack.rMax*3 + 2
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if dataType == "observation":
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maskIndex = open(zobovDir+"/mask_index.txt", "r").read()
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@ -643,6 +643,11 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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else:
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rescaleFlag = ""
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if stack.maxVoids != -1:
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maxVoidsFlag = "maxVoids="+str(stack.maxVoids)
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else:
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maxVoidsFlag = ""
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idListFile = "idlist.temp"
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if idList != None:
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idListFlag = "idList " + idListFile
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@ -695,6 +700,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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%s
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%s
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%s
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%s
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""" % \
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(zobovDir+"/voidDesc_"+thisDataPortion+"_"+sampleName+".out",
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zobovDir+"/voidPart_"+sampleName+".dat",
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@ -717,6 +723,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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zobovDir+"/barycenters_"+thisDataPortion+"_"+sampleName+".out",
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zobovDir+"/boundaryDistances_"+thisDataPortion+"_"+sampleName+".out",
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rescaleFlag,
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maxVoidsFlag,
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idListFlag,
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periodicLine
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)
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@ -1116,10 +1123,10 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
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numVoids = open(voidDir+"/num_voids.txt", "r").readline()
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numParticles = open(voidDir+"/num_particles.txt", "r").readline()
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Rextracut = stack.rMin*3 + 1
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Rcircular = stack.rMin*2 + 2
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#Rextracut = stack.rMax*3 + 1
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#Rcircular = stack.rMax*3 + 2
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#Rextracut = stack.rMin*3 + 1
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#Rcircular = stack.rMin*2 + 2
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Rextracut = stack.rMax*3 + 1
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Rcircular = stack.rMax*3 + 2
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if not (continueRun and jobSuccessful(logFile, "Done!\n")):
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profileParmFile = voidDir+"/params.txt"
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@ -1139,8 +1146,8 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
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if sample.profileBinSize == "auto":
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#density = 0.5 * 50 / Rcircular / 2
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density = stack.rMax / 5.
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#density = stack.rMax / 10.
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density = stack.rMin / 5.
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#density = stack.rMax / 5.
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else:
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density = sample.profileBinSize
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@ -1166,7 +1173,9 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
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# -----------------------------------------------------------------------------
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def launchFit(sample, stack, useComoving=None,
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logFile=None, voidDir=None, figDir=None,
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continueRun=None, thisDataPortion=None):
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continueRun=None, thisDataPortion=None,
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fittingMode=None, minVoidsToFit=None,
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minPartToFit=None):
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sampleName = sample.fullName
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@ -1181,7 +1190,7 @@ def launchFit(sample, stack, useComoving=None,
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return
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numVoids = int(open(voidDir+"/num_voids.txt", "r").readline())
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if numVoids < 1:
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if numVoids < minVoidsToFit:
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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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@ -1189,7 +1198,7 @@ def launchFit(sample, stack, useComoving=None,
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return
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numPart = int(open(voidDir+"/num_particles.txt", "r").readline())
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if numPart < 1:
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if numPart < minPartToFit:
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print jobString, "Fitting not enough particles to fit; skipping!"
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fp = open(voidDir+"/NOFIT", "w")
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fp.write("not enough particles: %d \n" % numPart)
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@ -1229,28 +1238,31 @@ def launchFit(sample, stack, useComoving=None,
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while badChain:
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ntries += 1
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Rexpect = (stack.rMin+stack.rMax)/2
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#Rtruncate = stack.rMax*2. # TEST
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#Rtruncate = stack.rMax*3. # TEST
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Rtruncate = stack.rMin*3. + 1 # TEST
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if sample.dataType == "observation":
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ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
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nbar_init=1.0,
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Niter=300000,
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Nburn=100000,
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Rextracut=Rtruncate)
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else:
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ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
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nbar_init=1.0,
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Niter=300000,
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Nburn=100000,
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Rextracut=Rtruncate)
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print "TEST", stack.rMax, args[0][0], args[0][1], args[0][2]
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badChain = (args[0][0] > 0.5 or args[0][1] > 2.*stack.rMax or \
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args[0][2] > 2.*stack.rMax) and \
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(ntries < maxtries)
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#ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="2d", nBootstraps=100, rMaxInertia=0.7)
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#badChain = False
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if fittingMode == "mcmc":
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Rexpect = (stack.rMin+stack.rMax)/2
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#Rtruncate = stack.rMax*2. # TEST
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Rtruncate = stack.rMax*3. # TEST
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#Rtruncate = stack.rMin*3. + 1 # TEST
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if sample.dataType == "observation":
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ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
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nbar_init=1.0,
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Niter=300000,
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Nburn=100000,
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Rextracut=Rtruncate)
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else:
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ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
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nbar_init=1.0,
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Niter=300000,
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Nburn=100000,
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Rextracut=Rtruncate)
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#print "TEST", stack.rMax, args[0][0], args[0][1], args[0][2]
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badChain = (args[0][0] > 0.5 or args[0][1] > 2.*stack.rMax or \
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args[1] > 2.0 or \
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args[0][2] > 2.*stack.rMax) and \
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(ntries < maxtries)
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elif fittingMode == "inertia":
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ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="2d", nBootstraps=100, rMaxInertia=0.7)
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badChain = False
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## rescale to expected stretch if using comoving coords
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#if useComoving or not sample.useLightCone:
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@ -1296,7 +1308,7 @@ def launchFit(sample, stack, useComoving=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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if ntries > maxtries:
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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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@ -1664,7 +1676,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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else:
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fp.write("-1\n")
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#fp.write(str(len(voidRedshifts))+" ")
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np.savetxt(fp, voidRedshifts[None])
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#np.savetxt(fp, voidRedshifts[None])
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else:
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fp.write("-1\n")
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fp.close()
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@ -1680,8 +1692,13 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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print "already done!"
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# -----------------------------------------------------------------------------
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def launchLikelihood(dataPortions=None, logDir=None, workDir=None,
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continueRun=False):
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def launchLikelihood(dataSampleList=None,
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dataPortions=None, logDir=None, workDir=None,
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continueRun=False):
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# check for comoving from first sample
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useComoving = not dataSampleList[0].useLightCone or \
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dataSampleList[0].useComoving
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for thisDataPortion in dataPortions:
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print " For data portion", thisDataPortion, "...",
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@ -1691,24 +1708,27 @@ def launchLikelihood(dataPortions=None, logDir=None, workDir=None,
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if not (continueRun and jobSuccessful(logFile, "Done!\n")):
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sys.stdout = open(logFile, 'w')
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#sys.stdout = open(logFile, 'w')
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#sys.stderr = open(logFile, 'a')
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vp.build1dLikelihood(workDir+"/calculatedExpansions_"+\
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vp.build1dLikelihood(dataSampleList[0],
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workDir+"/calculatedExpansions_"+\
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thisDataPortion+".txt",
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workDir+"/voidDistributions_" + \
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thisDataPortion+".txt",
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nbins = 20,
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OmStart = 0.0,
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OmEnd = 1.0,
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biasStart = 1.0,
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biasEnd = 1.32,
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#biasStart = 1.15,
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#biasEnd = 1.17,
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#biasStart = 1.0,
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#biasEnd = 1.32,
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biasStart = 1.16,
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biasEnd = 1.16,
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outputBase = workDir+"/1dlikelihoods_"+thisDataPortion+"_",
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useBinAve = False)
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useBinAve = False,
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useComoving = useComoving,
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OmFid=dataSampleList[0].omegaM)
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sys.stdout = sys.__stdout__
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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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