mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 23:31:12 +00:00
Merge
This commit is contained in:
Guilhem Lavaux
commit
9e79c784f3
29 changed files with 1679 additions and 2007 deletions
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@ -1,2 +1,3 @@
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from classes import *
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from launchers import *
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from catalogPrep import *
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File diff suppressed because it is too large
Load diff
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@ -38,6 +38,7 @@ class Sample:
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dataType = "observation"
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dataFormat = "sdss"
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dataFile = "lss.dr72dim.dat"
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dataUNit = 1
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fullName = "lss.dr72dim.dat"
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nickName = "dim"
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zobovDir = ""
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@ -62,22 +63,21 @@ class Sample:
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usePecVel = False
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subsample = 1.0
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useLightCone = True
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numSubDivisions = 1
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numSubvolumes = 1
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mySubvolume = 1
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stacks = []
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def __init__(self, dataFile="", fullName="",
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def __init__(self, dataFile="", fullName="", dataUnit=1,
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nickName="", maskFile="", selFunFile="",
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zBoundary=(), zRange=(), zBoundaryMpc=(),
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minVoidRadius=0, fakeDensity=0.01, volumeLimited=True,
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includeInHubble=True, partOfCombo=False, isCombo=False,
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comboList=(), profileBinSize=2.0, skyFraction=0.19,
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dataType="observation", numSubDivisions=2,
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boxLen=1024, usePecVel=False, omegaM=0.27,
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numSubvolumes=1, mySubvolume=1, dataFormat="sdss",
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subsample="1.0", useLightCone=True):
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dataType="observation",
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subsample=1.0, useLightCone=True):
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self.dataFile = dataFile
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self.fullName = fullName
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self.nickName = nickName
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@ -97,7 +97,6 @@ class Sample:
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self.profileBinSize = profileBinSize
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self.skyFraction = skyFraction
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self.dataType = dataType
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self.numSubDivisions = numSubDivisions
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self.boxLen = boxLen
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self.usePecVel = usePecVel
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self.omegaM = omegaM
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@ -106,6 +105,7 @@ class Sample:
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self.dataFormat = dataFormat
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self.subsample = subsample
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self.useLightCone = useLightCone
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self.dataUnit = dataUnit
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self.stacks = []
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@ -84,7 +84,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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if os.access("mask_index.txt", os.F_OK):
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os.system("mv %s %s" % ("mask_index.txt", zobovDir))
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os.system("mv %s %s" % ("total_particles.txt", zobovDir))
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os.system("mv %s %s" % ("sample_info.txt", zobovDir))
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#os.system("mv %s %s" % ("sample_info.txt", zobovDir))
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if os.access("galaxies.txt", os.F_OK):
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os.system("mv %s %s" % ("galaxies.txt", zobovDir))
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@ -102,11 +102,16 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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else:
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includePecVelString = ""
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if sample.dataFormat == "multidark":
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if sample.useLightCone:
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useLightConeString = "cosmo"
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else:
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useLightConeString = ""
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if sample.dataFormat == "multidark" or sample.dataFormat == "random":
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dataFileLine = "multidark " + datafile
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elif sample.dataFormat == "gadget":
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dataFileLine = "gadget " + datafile
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iX = float(sample.mySubvolume[0])
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iY = float(sample.mySubvolume[1])
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@ -120,16 +125,20 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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output %s
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outputParameter %s
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%s
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%s
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gadgetUnit %g
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rangeX_min %g
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rangeX_max %g
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rangeY_min %g
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rangeY_max %g
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rangeZ_min %g
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rangeZ_max %g
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subsample %g
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subsample %s
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""" % (dataFileLine, zobovDir+"/zobov_slice_"+sampleName,
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zobovDir+"/zobov_slice_"+sampleName+".par",
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includePecVelString,
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useLightConeString,
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sample.dataUnit,
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xMin, xMax, yMin, yMax,
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sample.zBoundaryMpc[0], sample.zBoundaryMpc[1],
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sample.subsample)
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@ -150,11 +159,16 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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else:
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print "already done!"
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if os.access("comoving_distance.txt", os.F_OK):
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os.system("mv %s %s" % ("comoving_distance.txt", zobovDir))
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#os.system("mv %s %s" % ("sample_info.txt", zobovDir))
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if os.access(parmFile, os.F_OK):
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os.unlink(parmFile)
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# -----------------------------------------------------------------------------
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def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None):
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def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
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numZobovDivisions=None, numZobovThreads=None):
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sampleName = sample.fullName
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@ -185,9 +199,9 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None):
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if os.access(zobovDir+"/voidDesc_"+sampleName+".out", os.F_OK):
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os.unlink(zobovDir+"/voidDesc_"+sampleName+".out")
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cmd = "%s/vozinit %s 0.1 1.0 2 %s %g %s %s %s >& %s" % \
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(binPath, datafile, \
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"_"+sampleName, sample.numSubDivisions, \
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cmd = "%s/vozinit %s 0.1 1.0 %g %s %g %s %s %s >& %s" % \
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(binPath, datafile, numZobovDivisions, \
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"_"+sampleName, numZobovThreads, \
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binPath, zobovDir, maskIndex, logFile)
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os.system(cmd)
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@ -232,11 +246,18 @@ def launchPrune(sample, binPath, thisDataPortion=None,
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totalPart = open(zobovDir+"/total_particles.txt", "r").read()
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maxDen = 0.2*float(mockIndex)/float(totalPart)
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observationLine = " --isObservation"
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periodicLine = " --periodic=''"
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else:
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mockIndex = -1
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maxDen = 0.2
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observationLine = ""
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periodicLine = " --periodic='"
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if sample.numSubvolumes == 1: periodicLine += "xy"
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if sample.zBoundaryMpc[0] == 0 and \
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sample.zBoundaryMpc[1] == sample.boxLen : periodicLine += "z"
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periodicLine += "' "
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if not (continueRun and jobSuccessful(logFile, "NetCDF: Not a valid ID\n")):
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cmd = binPath
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cmd += " --partFile=" + zobovDir+"/zobov_slice_"+str(sampleName)
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@ -255,6 +276,7 @@ def launchPrune(sample, binPath, thisDataPortion=None,
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cmd += " --rMin=" + str(sample.minVoidRadius)
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cmd += " --numVoids=" + str(numVoids)
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cmd += observationLine
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cmd += periodicLine
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cmd += " --output=" + zobovDir+"/voidDesc_"+\
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str(thisDataPortion)+"_"+\
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str(sampleName)+".out"
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@ -276,7 +298,8 @@ def launchPrune(sample, binPath, thisDataPortion=None,
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cmd += " >& " + logFile
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os.system(cmd)
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if jobSuccessful(logFile, "NetCDF: Not a valid ID\n"):
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if jobSuccessful(logFile, "NetCDF: Not a valid ID\n") or \
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jobSuccessful(logFile, "Done!\n"):
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print "done"
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else:
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print "FAILED!"
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@ -356,8 +379,8 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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%s
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ranSeed %d
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dataPortion %s
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barycenters %s
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boundaryDistances %s
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#barycenters %s
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#boundaryDistances %s
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%s
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""" % \
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(zobovDir+"/voidDesc_"+thisDataPortion+"_"+sampleName+".out",
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@ -460,34 +483,37 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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return
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# figure out box volume and average density
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maskFile = sample.maskFile
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sulFunFile = sample.selFunFile
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if sample.dataType == "observation":
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maskFile = sample.maskFile
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sulFunFile = sample.selFunFile
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if not os.access(sample.selFunFile, os.F_OK) and not volumeLimited:
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print " Cannot find", selFunFile, "!"
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exit(-1)
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if not os.access(sample.selFunFile, os.F_OK) and not sample.volumeLimited:
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print " Cannot find", selFunFile, "!"
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exit(-1)
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sys.stdout = open(logFile, 'a')
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sys.stderr = open(logFile, 'a')
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zMin = sample.zRange[0]
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zMax = sample.zRange[1]
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if not sample.volumeLimited:
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props = vp.getSurveyProps(maskFile, stack.zMin,
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stack.zMax, zMin, zMax, "all",
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selectionFuncFile=sample.selFunFile)
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sys.stdout = open(logFile, 'a')
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sys.stderr = open(logFile, 'a')
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zMin = sample.zRange[0]
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zMax = sample.zRange[1]
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if not sample.volumeLimited:
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props = vp.getSurveyProps(maskFile, stack.zMin,
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stack.zMax, zMin, zMax, "all",
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selectionFuncFile=sample.selFunFile)
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else:
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zMinForVol = sample.zBoundary[0]
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zMaxForVol = sample.zBoundary[1]
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props = vp.getSurveyProps(maskFile, zMinForVol,
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zMaxForVol, zMin, zMax, "all")
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sys.stdout = sys.__stdout__
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sys.stderr = sys.__stderr__
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boxVol = props[0]
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nbar = props[1]
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if sample.volumeLimited:
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nbar = 1.0
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else:
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zMinForVol = sample.zBoundary[0]
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zMaxForVol = sample.zBoundary[1]
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props = vp.getSurveyProps(maskFile, zMinForVol,
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zMaxForVol, zMin, zMax, "all")
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sys.stdout = sys.__stdout__
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sys.stderr = sys.__stderr__
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boxVol = props[0]
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nbar = props[1]
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if sample.volumeLimited:
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nbar = 1.0
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boxVol = sample.boxLen**3
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summaryLine = runSuffix + " " + \
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thisDataPortion + " " + \
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@ -809,7 +835,7 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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maxtries = 5
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while badChain:
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Rexpect = (stack.rMin+stack.rMax)/2
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Rtruncate = stack.rMax*3. + 1 # TEST
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Rtruncate = stack.rMin*3. + 1 # TEST
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ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
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Niter=300000,
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Nburn=100000,
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@ -1173,7 +1199,11 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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voidDir = sample.zobovDir+"/stacks_" + runSuffix
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centersFile = voidDir+"/centers.txt"
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if os.access(centersFile, os.F_OK):
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voidRedshifts = np.loadtxt(centersFile)[:,5]
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voidRedshifts = np.loadtxt(centersFile)
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if voidRedshifts.ndim > 1:
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voidRedshifts = voidRedshifts[:,5]
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else:
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voidRedshifts = voidRedshifts[5]
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#fp.write(str(len(voidRedshifts))+" ")
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np.savetxt(fp, voidRedshifts[None])
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else:
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|
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@ -1,3 +1,5 @@
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LIGHT_SPEED = 299792.458
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colorList = ['r', 'b', 'g', 'y', 'c', 'm', 'y',
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'brown', 'grey',
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'darkred', 'orange', 'pink', 'darkblue',
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@ -1,17 +1,20 @@
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__all__=['plotNumberCounts']
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__all__=['plotRedshiftDistribution', 'plotSizeDistribution', 'plot1dProfiles',
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'plotMarg1d', 'plotNumberDistribution']
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from void_python_tools.backend.classes import *
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from plotDefs import *
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import numpy as np
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import os
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import pylab as plt
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import void_python_tools.apTools as vp
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# -----------------------------------------------------------------------------
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def plotNumberCounts(workDir=None, sampleList=None, figDir=None, plotNameBase="numbercount",
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def plotRedshiftDistribution(workDir=None, sampleList=None, figDir=None,
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plotNameBase="zdist",
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showPlot=False, dataPortion=None, setName=None):
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plt.clf()
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plt.xlabel("Comoving Distance (Mpc/h)")
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plt.xlabel("Redshift")
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plt.ylabel("Number of Voids")
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plotTitle = setName
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@ -41,7 +44,7 @@ def plotNumberCounts(workDir=None, sampleList=None, figDir=None, plotNameBase="n
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zMax = sample.zRange[1]
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range = (zMin, zMax)
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nbins = np.ceil((zMax-zMin)/0.1)
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nbins = np.ceil((zMax-zMin)/0.02)
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thisMax = np.max(data[:,5])
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thisMin = np.min(data[:,5])
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@ -67,3 +70,210 @@ def plotNumberCounts(workDir=None, sampleList=None, figDir=None, plotNameBase="n
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os.system("display %s" % figDir+"/fig_"+plotName+".png")
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# -----------------------------------------------------------------------------
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def plotSizeDistribution(workDir=None, sampleList=None, figDir=None,
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plotNameBase="sizedist",
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showPlot=False, dataPortion=None, setName=None):
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plt.clf()
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plt.xlabel("Void Radius (Mpc/h)")
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plt.ylabel("Number of Voids")
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plotTitle = setName
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plotName = plotNameBase
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xMin = 1.e00
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xMax = 0
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for (iSample,sample) in enumerate(sampleList):
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sampleName = sample.fullName
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lineTitle = sampleName
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filename = workDir+"/sample_"+sampleName+"/centers_"+dataPortion+"_"+\
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sampleName+".out"
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if not os.access(filename, os.F_OK):
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print "File not found: ", filename
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continue
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data = np.loadtxt(filename, comments="#")
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if data.ndim == 1:
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print " Too few!"
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continue
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xMin = 5
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xMax = 140
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range = (xMin, xMax)
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nbins = np.ceil((xMax-xMin)/5)
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#thisMax = np.max(data[:,5])
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#thisMin = np.min(data[:,5])
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#if thisMax > xMax: xMax = thisMax
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#if thisMin < xMin: xMin = thisMin
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plt.hist(data[:,4], bins=nbins,
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label=lineTitle, color=colorList[iSample],
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histtype = "step", range=range,
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linewidth=linewidth)
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|
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plt.legend(title = "Samples", loc = "upper right")
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plt.title(plotTitle)
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plt.xlim(xMin, xMax)
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#plt.xlim(xMin, xMax*1.4) # make room for legend
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plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
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plt.savefig(figDir+"/fig_"+plotName+".eps", bbox_inches="tight")
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plt.savefig(figDir+"/fig_"+plotName+".png", bbox_inches="tight")
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||||
|
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if showPlot:
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os.system("display %s" % figDir+"/fig_"+plotName+".png")
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|
||||
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# -----------------------------------------------------------------------------
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def plot1dProfiles(workDir=None, sampleList=None, figDir=None,
|
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plotNameBase="1dprofile",
|
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showPlot=False, dataPortion=None, setName=None):
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|
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plt.clf()
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plt.xlabel(r"$R/R_{v,\mathrm{max}}$")
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plt.ylabel(r"$n / \bar n$")
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for (iSample,sample) in enumerate(sampleList):
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sampleName = sample.fullName
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for (iStack,stack) in enumerate(sample.stacks):
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|
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plotTitle = setName
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plotName = plotNameBase
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|
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runSuffix = getStackSuffix(stack.zMin, stack.zMax, stack.rMin,
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stack.rMax, dataPortion)
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|
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plotTitle = sampleName + ", z = "+str(stack.zMin)+"-"+str(stack.zMax)+", R = "+str(stack.rMin)+"-"+str(stack.rMax)+ r" $h^{-1}$ Mpc"
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|
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filename = workDir+"/sample_"+sampleName+"/stacks_"+runSuffix+\
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"profile_1d.txt"
|
||||
|
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if not os.access(filename, os.F_OK):
|
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print "File not found: ", filename
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continue
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|
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data = np.loadtxt(filename, comments="#")
|
||||
if data.ndim == 1:
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print " Too few!"
|
||||
continue
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|
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data[:,1] /= stack.rMax
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plt.ylim(ymin=0.0, ymax=np.amax(data[:,2])+0.1)
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plt.xlim(xmin=0.0, xmax=2.1)
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plt.plot(data[:,1], data[:,2], label=lineTitle, color=colorList[0],
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linewidth=linewidth)
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plt.title(plotTitle)
|
||||
|
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plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
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plt.savefig(figDir+"/fig_"+plotName+".eps", bbox_inches="tight")
|
||||
plt.savefig(figDir+"/fig_"+plotName+".png", bbox_inches="tight")
|
||||
|
||||
if showPlot:
|
||||
os.system("display %s" % figDir+"/fig_"+plotName+".png")
|
||||
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
def plotMarg1d(workDir=None, sampleList=None, figDir=None,
|
||||
plotNameBase="marg1d",
|
||||
showPlot=False, dataPortion=None, setName=None):
|
||||
|
||||
plotNames = ("Om", "w0", "wa")
|
||||
plotTitles = ("$\Omega_M$", "$w_0$", "$w_a$")
|
||||
files = ("Om", "w0", "wa")
|
||||
|
||||
for iPlot in range(len(plotNames)):
|
||||
|
||||
plt.clf()
|
||||
|
||||
plotName = plotNameBase+"_"+plotNames[iPlot]+"_"+dataPortion
|
||||
plotTitle = plotTitles[iPlot]
|
||||
dataFile = workDir + "/likelihoods_"+dataPortion+"_"+files[iPlot]+".dat"
|
||||
|
||||
plt.xlabel(plotTitle, fontsize="20")
|
||||
plt.ylabel("Likelihood", fontsize="20")
|
||||
plt.ylim(0.0, 1.0)
|
||||
|
||||
data = np.loadtxt(dataFile, comments="#")
|
||||
plt.plot(data[:,0], data[:,1], color='k', linewidth=linewidth)
|
||||
|
||||
plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
|
||||
plt.savefig(figDir+"/fig_"+plotName+".eps", bbox_inches="tight")
|
||||
plt.savefig(figDir+"/fig_"+plotName+".png", bbox_inches="tight")
|
||||
|
||||
if showPlot:
|
||||
os.system("display %s" % figDir+"/fig_"+plotName+".png")
|
||||
|
||||
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
def plotNumberDistribution(workDir=None, sampleList=None, figDir=None,
|
||||
plotNameBase="numberdist",
|
||||
showPlot=False, dataPortion=None, setName=None):
|
||||
|
||||
plt.clf()
|
||||
plt.xlabel("Void Radius (Mpc/h)")
|
||||
plt.ylabel(r"N > R [$h^3$ Mpc$^{-3}$]")
|
||||
|
||||
plotTitle = setName
|
||||
|
||||
plotName = plotNameBase
|
||||
|
||||
plt.yscale('log')
|
||||
|
||||
for (iSample,sample) in enumerate(sampleList):
|
||||
|
||||
sampleName = sample.fullName
|
||||
lineTitle = sampleName
|
||||
|
||||
if sample.dataType == "observation":
|
||||
boxVol = vp.getSurveyProps(sample.maskFile,
|
||||
sample.zBoundary[0], sample.zBoundary[1],
|
||||
sample.zRange[0], sample.zRange[1], "all",
|
||||
selectionFuncFile=sample.selFunFile)[0]
|
||||
else:
|
||||
boxVol = sample.boxLen*sample.boxLen*(sample.zBoundaryMpc[1] -
|
||||
sample.zBoundaryMpc[0])
|
||||
|
||||
boxVol *= 1.e-9
|
||||
|
||||
filename = workDir+"/sample_"+sampleName+"/centers_"+dataPortion+"_"+\
|
||||
sampleName+".out"
|
||||
if not os.access(filename, os.F_OK):
|
||||
print "File not found: ", filename
|
||||
continue
|
||||
|
||||
data = np.loadtxt(filename, comments="#")
|
||||
if data.ndim == 1:
|
||||
print " Too few!"
|
||||
continue
|
||||
data = data[:,4]
|
||||
indices = np.arange(0, len(data), 1)
|
||||
sorted = np.sort(data)
|
||||
|
||||
plt.plot(sorted, indices[::-1]/boxVol, '-',
|
||||
label=lineTitle, color=colorList[iSample],
|
||||
linewidth=linewidth)
|
||||
|
||||
plt.legend(title = "Samples", loc = "upper right")
|
||||
plt.title(plotTitle)
|
||||
|
||||
plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
|
||||
plt.savefig(figDir+"/fig_"+plotName+".eps", bbox_inches="tight")
|
||||
plt.savefig(figDir+"/fig_"+plotName+".png", bbox_inches="tight")
|
||||
|
||||
if showPlot:
|
||||
os.system("display %s" % figDir+"/fig_"+plotName+".png")
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue