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much more flexible for handling different stacking and AP approaches

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This commit is contained in:
P.M. Sutter 2014-03-11 12:49:02 -05:00
parent a9100b2604
commit 73c6aedfc2
4 changed files with 132 additions and 87 deletions
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5
python_tools/pipeline_source/defaults.py
View file

@ -36,6 +36,11 @@ dataPortions = ["central"]
# auto for AP analysis, "fixed" for catalog comparison
stackMode = "fixed"
maxVoidsInStack = -1
stackRescaleMode = "rv"
fittingMode = "mcmc"
minVoidsToFit = 20
minPartToFit = 2
# directory for the input simulation/observational particle files
catalogDir = os.getenv("HOME")+"/workspace/Voids/catalog/"

87
python_tools/pipeline_source/prepareCatalogs.in.py
View file

@ -188,6 +188,11 @@ bias = 1.16
dataPortions = {dataPortions}
dataSampleList = []
# for the A-P test
minVoidsToFit = {minVoidsToFit}
minPartToFit = {minPartToFit}
fittingMode = '{fittingMode}'
"""
scriptFile.write(header.format(startCatalogStage=startCatalogStage,
@ -195,7 +200,11 @@ dataSampleList = []
startAPStage=startAPStage,
endAPStage=endAPStage,
continueRun=continueRun,
dataPortions=dataPortions))
dataPortions=dataPortions,
minVoidsToFit=minVoidsToFit,
minPartToFit=minPartToFit,
fittingMode=fittingMode,
))
dataInfo = """
setName = "{setName}"
@ -245,38 +254,38 @@ dataSampleList.append(newSample)
if stackMode == "fixed":
stackInfo = """
# {zMin}, {zMax}, {minRadius}
newSample.addStack(0.0, 5.0, 5 , 10, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 10, 15, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 15, 20, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 20, 25, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 25, 30, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 30, 35, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 35, 40, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 40, 45, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 45, 50, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 50, 55, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 55, 60, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 60, 65, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 65, 70, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 70, 75, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 75, 80, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 80, 85, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 85, 90, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 90, 95, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 95, 100, False, False, rescaleMode="rv")
newSample.addStack(0.0, 5.0, 5 , 10, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 10, 15, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 15, 20, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 20, 25, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 25, 30, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 30, 35, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 35, 40, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 40, 45, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 45, 50, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 50, 55, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 55, 60, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 60, 65, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 65, 70, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 70, 75, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 75, 80, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 80, 85, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 85, 90, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 90, 95, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack(0.0, 5.0, 95, 100, False, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
"""
elif stackMode == "sample_thick":
stackInfo = """
# {zMin}, {zMax}, {minRadius}
newSample.addStack({zMin}, {zMax}, 10, 20, True, False, rescaleMode="rmax")
newSample.addStack({zMin}, {zMax}, 20, 30, True, False, rescaleMode="rmax")
newSample.addStack({zMin}, {zMax}, 30, 40, True, False, rescaleMode="rmax")
newSample.addStack({zMin}, {zMax}, 40, 50, True, False, rescaleMode="rmax")
newSample.addStack({zMin}, {zMax}, 50, 60, True, False, rescaleMode="rmax")
newSample.addStack({zMin}, {zMax}, 60, 70, True, False, rescaleMode="rmax")
newSample.addStack({zMin}, {zMax}, 70, 80, True, False, rescaleMode="rmax")
newSample.addStack({zMin}, {zMax}, 80, 90, True, False, rescaleMode="rmax")
newSample.addStack({zMin}, {zMax}, 90, 100, True, False, rescaleMode="rmax")
newSample.addStack({zMin}, {zMax}, 10, 20, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 20, 30, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 30, 40, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 40, 50, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 50, 60, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 60, 70, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 70, 80, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 80, 90, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 90, 100, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
"""
elif stackMode == "log":
@ -289,18 +298,18 @@ newSample.addStack({zMin}, {zMax}, 90, 100, True, False, rescaleMode="rmax")
while rEnd < rMax:
rEnd = (1+0.5*dlogR)*rStart/(1-0.5*dlogR)
stackInfo += """newSample.addStack({zMin}, {zMax}"""+ ", %g, %g, True, False, rescaleMode='rv')" % (rStart, rEnd)
stackInfo += """newSample.addStack({zMin}, {zMax}"""+ ", %g, %g, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})" % (rStart, rEnd)
rStart = rEnd
elif stackMode == "auto":
stackInfo = """
newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+2, True, False, rescaleMode="rv")
newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+4, True, False, rescaleMode="rv")
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False, rescaleMode="rv")
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False, rescaleMode="rv")
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False, rescaleMode="rv")
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, False, rescaleMode="rv")
newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+2, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+4, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, False, rescaleMode='{rescaleMode}', maxVoids={maxVoids})
"""
else:
stackInfo = """
@ -389,7 +398,11 @@ newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, Fal
sliceAPMax = "%0.2f" % sliceAPMax
scriptFile.write(stackInfo.format(zMin=sliceAPMin,
zMax=sliceAPMax,
minRadius=minRadius))
minRadius=minRadius,
rescaleMode=stackRescaleMode,
maxVoids=maxVoidsInStack,
fittingMode=fittingMode
))
scriptFile.close()

13
python_tools/void_python_tools/backend/classes.py
View file

@ -38,9 +38,11 @@ class Stack:
needProfile = True
rescaleMode = "rmax" # options: "rmax" to scale to largest void in stack
# "rv" normalize each void
maxVoids = -1 # maximum number of voids to allow in the stack
def __init__(self, zMin, zMax, rMin, rMax, includeInHubble, partOfCombo,
zMinPlot=None, needProfile=True, rescaleMode="rmax"):
zMinPlot=None, needProfile=True, rescaleMode="rmax",
maxVoids=-1, fittingMode="mcmc"):
self.zMin = zMin
self.zMax = zMax
self.rMin = rMin
@ -50,6 +52,8 @@ class Stack:
self.partOfCombo = partOfCombo
self.needProfile = needProfile
self.rescaleMode = rescaleMode
self.maxVoids = maxVoids
self.fittingMode = fittingMode
if zMinPlot == None:
self.zMinPlot = self.zMin
@ -143,11 +147,14 @@ class Sample:
def addStack(self, zMin, zMax, rMin, rMax,
includeInHubble, partOfCombo,zMinPlot=None,
needProfile=True, rescaleMode="rmax"):
needProfile=True, rescaleMode="rmax",
maxVoids=-1, fittingMode="mcmc"):
self.stacks.append(Stack(zMin, zMax, rMin, rMax,
includeInHubble, partOfCombo,
zMinPlot=zMinPlot, needProfile=needProfile,
rescaleMode=rescaleMode))
rescaleMode=rescaleMode,
maxVoids=maxVoids,
fittingMode=fittingMode))
def getHubbleStacks(self):
stacksForHubble = []

114
python_tools/void_python_tools/backend/launchers.py
View file

@ -616,10 +616,10 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
else:
obsFlag = ""
Rextracut = stack.rMin*3 + 1
Rcircular = stack.rMin*3 + 2
#Rextracut = stack.rMax*3 + 1
#Rcircular = stack.rMax*3 + 2
#Rextracut = stack.rMin*3 + 1
#Rcircular = stack.rMin*3 + 2
Rextracut = stack.rMax*3 + 1
Rcircular = stack.rMax*3 + 2
if dataType == "observation":
maskIndex = open(zobovDir+"/mask_index.txt", "r").read()
@ -643,6 +643,11 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
else:
rescaleFlag = ""
if stack.maxVoids != -1:
maxVoidsFlag = "maxVoids="+str(stack.maxVoids)
else:
maxVoidsFlag = ""
idListFile = "idlist.temp"
if idList != None:
idListFlag = "idList " + idListFile
@ -695,6 +700,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
%s
%s
%s
%s
""" % \
(zobovDir+"/voidDesc_"+thisDataPortion+"_"+sampleName+".out",
zobovDir+"/voidPart_"+sampleName+".dat",
@ -717,6 +723,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
zobovDir+"/barycenters_"+thisDataPortion+"_"+sampleName+".out",
zobovDir+"/boundaryDistances_"+thisDataPortion+"_"+sampleName+".out",
rescaleFlag,
maxVoidsFlag,
idListFlag,
periodicLine
)
@ -1116,10 +1123,10 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
numVoids = open(voidDir+"/num_voids.txt", "r").readline()
numParticles = open(voidDir+"/num_particles.txt", "r").readline()
Rextracut = stack.rMin*3 + 1
Rcircular = stack.rMin*2 + 2
#Rextracut = stack.rMax*3 + 1
#Rcircular = stack.rMax*3 + 2
#Rextracut = stack.rMin*3 + 1
#Rcircular = stack.rMin*2 + 2
Rextracut = stack.rMax*3 + 1
Rcircular = stack.rMax*3 + 2
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
profileParmFile = voidDir+"/params.txt"
@ -1139,8 +1146,8 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
if sample.profileBinSize == "auto":
#density = 0.5 * 50 / Rcircular / 2
density = stack.rMax / 5.
#density = stack.rMax / 10.
density = stack.rMin / 5.
#density = stack.rMax / 5.
else:
density = sample.profileBinSize
@ -1166,7 +1173,9 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
# -----------------------------------------------------------------------------
def launchFit(sample, stack, useComoving=None,
logFile=None, voidDir=None, figDir=None,
continueRun=None, thisDataPortion=None):
continueRun=None, thisDataPortion=None,
fittingMode=None, minVoidsToFit=None,
minPartToFit=None):
sampleName = sample.fullName
@ -1181,7 +1190,7 @@ def launchFit(sample, stack, useComoving=None,
return
numVoids = int(open(voidDir+"/num_voids.txt", "r").readline())
if numVoids < 1:
if numVoids < minVoidsToFit:
print jobString, "Fitting not enough voids to fit; skipping!"
fp = open(voidDir+"/NOFIT", "w")
fp.write("not enough voids: %d \n" % numVoids)
@ -1189,7 +1198,7 @@ def launchFit(sample, stack, useComoving=None,
return
numPart = int(open(voidDir+"/num_particles.txt", "r").readline())
if numPart < 1:
if numPart < minPartToFit:
print jobString, "Fitting not enough particles to fit; skipping!"
fp = open(voidDir+"/NOFIT", "w")
fp.write("not enough particles: %d \n" % numPart)
@ -1229,28 +1238,31 @@ def launchFit(sample, stack, useComoving=None,
while badChain:
ntries += 1
Rexpect = (stack.rMin+stack.rMax)/2
#Rtruncate = stack.rMax*2. # TEST
#Rtruncate = stack.rMax*3. # TEST
Rtruncate = stack.rMin*3. + 1 # TEST
if sample.dataType == "observation":
ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
nbar_init=1.0,
Niter=300000,
Nburn=100000,
Rextracut=Rtruncate)
else:
ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
nbar_init=1.0,
Niter=300000,
Nburn=100000,
Rextracut=Rtruncate)
print "TEST", stack.rMax, args[0][0], args[0][1], args[0][2]
badChain = (args[0][0] > 0.5 or args[0][1] > 2.*stack.rMax or \
args[0][2] > 2.*stack.rMax) and \
(ntries < maxtries)
#ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="2d", nBootstraps=100, rMaxInertia=0.7)
#badChain = False
if fittingMode == "mcmc":
Rexpect = (stack.rMin+stack.rMax)/2
#Rtruncate = stack.rMax*2. # TEST
Rtruncate = stack.rMax*3. # TEST
#Rtruncate = stack.rMin*3. + 1 # TEST
if sample.dataType == "observation":
ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
nbar_init=1.0,
Niter=300000,
Nburn=100000,
Rextracut=Rtruncate)
else:
ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
nbar_init=1.0,
Niter=300000,
Nburn=100000,
Rextracut=Rtruncate)
#print "TEST", stack.rMax, args[0][0], args[0][1], args[0][2]
badChain = (args[0][0] > 0.5 or args[0][1] > 2.*stack.rMax or \
args[1] > 2.0 or \
args[0][2] > 2.*stack.rMax) and \
(ntries < maxtries)
elif fittingMode == "inertia":
ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="2d", nBootstraps=100, rMaxInertia=0.7)
badChain = False
## rescale to expected stretch if using comoving coords
#if useComoving or not sample.useLightCone:
@ -1296,7 +1308,7 @@ def launchFit(sample, stack, useComoving=None,
if os.access(voidDir+"/NOFIT", os.F_OK):
os.unlink(voidDir+"/NOFIT")
if ntries >= maxtries:
if ntries > maxtries:
print jobString, "No reliable fit found; skipping!"
fp = open(voidDir+"/NOFIT", "w")
fp.write("bad ellipticity fit\n")
@ -1664,7 +1676,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
else:
fp.write("-1\n")
#fp.write(str(len(voidRedshifts))+" ")
np.savetxt(fp, voidRedshifts[None])
#np.savetxt(fp, voidRedshifts[None])
else:
fp.write("-1\n")
fp.close()
@ -1680,8 +1692,13 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
print "already done!"
# -----------------------------------------------------------------------------
def launchLikelihood(dataPortions=None, logDir=None, workDir=None,
continueRun=False):
def launchLikelihood(dataSampleList=None,
dataPortions=None, logDir=None, workDir=None,
continueRun=False):
# check for comoving from first sample
useComoving = not dataSampleList[0].useLightCone or \
dataSampleList[0].useComoving
for thisDataPortion in dataPortions:
print " For data portion", thisDataPortion, "...",
@ -1691,24 +1708,27 @@ def launchLikelihood(dataPortions=None, logDir=None, workDir=None,
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
sys.stdout = open(logFile, 'w')
#sys.stdout = open(logFile, 'w')
#sys.stderr = open(logFile, 'a')
vp.build1dLikelihood(workDir+"/calculatedExpansions_"+\
vp.build1dLikelihood(dataSampleList[0],
workDir+"/calculatedExpansions_"+\
thisDataPortion+".txt",
workDir+"/voidDistributions_" + \
thisDataPortion+".txt",
nbins = 20,
OmStart = 0.0,
OmEnd = 1.0,
biasStart = 1.0,
biasEnd = 1.32,
#biasStart = 1.15,
#biasEnd = 1.17,
#biasStart = 1.0,
#biasEnd = 1.32,
biasStart = 1.16,
biasEnd = 1.16,
outputBase = workDir+"/1dlikelihoods_"+thisDataPortion+"_",
useBinAve = False)
useBinAve = False,
useComoving = useComoving,
OmFid=dataSampleList[0].omegaM)
sys.stdout = sys.__stdout__
#sys.stdout = sys.__stdout__
#sys.stderr = sys.__stderr__
if jobSuccessful(logFile, "Done!\n"):