mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
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some bug fixes to the a-p analysis scripts; fixed major bug in prunevoids; updated catalog release scripts
This commit is contained in:
P.M. Sutter
parent
06c8ddc26e
commit
022eec19bb
13 changed files with 437 additions and 239 deletions
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@ -1,8 +1,6 @@
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#!/usr/bin/env python
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# prepares input catalogs based on multidark simulations
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# (borrows heavily from generateMock, but doesn't hold much in memory)
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# also creates necessary analyzeVoids input files
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# applies a mask to a given dataset
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import numpy as np
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import os
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@ -32,6 +30,18 @@ parser.add_argument('--scripts', dest='script', action='store_const',
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parser.add_argument('--parmFile', dest='parmFile',
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default="",
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help='path to parameter file')
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parser.add_argument('--subsamples', dest='subsample', action='store_const',
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const=True, default=False,
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help='write subsamples')
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parser.add_argument('--halos', dest='halos', action='store_const',
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const=True, default=False,
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help='write halos')
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parser.add_argument('--hod', dest='hod', action='store_const',
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const=True, default=False,
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help='write hod')
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parser.add_argument('--all', dest='all', action='store_const',
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const=True, default=False,
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help='write everything')
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args = parser.parse_args()
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@ -57,9 +67,9 @@ def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
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#------------------------------------------------------------------------------
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# for given dataset parameters, outputs a script for use with analyzeVoids
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def writeScript(setName, dataFileNameBase,
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scriptDir, catalogDir, fileNums, redshifts, numSubvolumes,
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numSlices, useVel, lbox, minRadius, omegaM, subsample=1.0,
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def writeObservationScript(setName, dataFileNameBase, maskFileName,
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scriptDir, catalogDir, fileNums, redshifts,
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useVel, minRadius, omegaM,
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suffix=".dat"):
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@ -88,7 +98,7 @@ ranSeed = 101010
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useLCDM = False
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bias = 1.16
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dataPortions = ["central"]
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dataPortions = ["central", "all"]
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dataSampleList = []
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""")
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@ -112,25 +122,17 @@ numZobovThreads = {numZobovThreads}
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sampleInfo = """
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newSample = Sample(dataFile = "{dataFile}",
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dataFormat = "{dataFormat}",
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dataUnit = {dataUnit},
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fullName = "{sampleName}",
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nickName = "{sampleName}",
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dataType = "simulation",
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dataType = "observation",
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maskFile = "{maskFileName}",
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zBoundary = ({zMin}, {zMax}),
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zRange = ({zMin}, {zMax}),
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zBoundaryMpc = ({zMinMpc}, {zMaxMpc}),
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omegaM = {omegaM},
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minVoidRadius = {minRadius},
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includeInHubble = True,
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partOfCombo = False,
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isCombo = False,
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boxLen = {boxLen},
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usePecVel = {usePecVel},
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numSubvolumes = {numSubvolumes},
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mySubvolume = "{mySubvolume}",
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useLightCone = {useLightCone},
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subsample = {subsample})
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usePecVel = {usePecVel})
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dataSampleList.append(newSample)
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newSample.addStack({zMin}, {zMax}, {minRadius} , {minRadius}+2, True, False)
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newSample.addStack({zMin}, {zMax}, {minRadius} , {minRadius}+4, True, False)
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@ -142,180 +144,249 @@ newSample.addStack({zMin}, {zMax}, {minRadius}+18, {minRadius}+24, True, False)
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for (iFile, redshift) in enumerate(redshifts):
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fileNum = fileNums[iFile]
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zBox = float(redshift)
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Om = float(omegaM)
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zBoxMpc = LIGHT_SPEED/100.*vp.angularDiameter(zBox, Om=Om)
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boxMaxMpc = zBoxMpc + lbox
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zMin = zBox
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zMax = zBox + 0.1
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zMin, zMax = getMaskedZRange(lbox, zBox, zMin, zMax, omegaM)
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dataFileName = dataFileNameBase + fileNum + suffix
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# converter from redshift to comoving distance
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zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000)
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zVsDX = np.zeros(len(zVsDY))
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for i in xrange(len(zVsDY)):
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zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
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sampleName = getSampleName(setName, redshift, useVel,
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iSlice=-1, iVol=-1)
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if useLightCone:
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boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
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LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
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dzSafe = 0.03
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else:
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boxWidthZ = lbox*100./LIGHT_SPEED
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dzSafe = 0.0
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for iSlice in xrange(numSlices):
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sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-dzSafe)/numSlices
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sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-dzSafe)/numSlices
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sliceMinMpc = sliceMin*LIGHT_SPEED/100.
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sliceMaxMpc = sliceMax*LIGHT_SPEED/100.
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sliceMin = "%0.2f" % sliceMin
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sliceMax = "%0.2f" % sliceMax
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sliceMinMpc = "%0.1f" % sliceMinMpc
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sliceMaxMpc = "%0.1f" % sliceMaxMpc
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dataFileName = dataFileNameBase + fileNum + suffix
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for iX in xrange(numSubvolumes):
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for iY in xrange(numSubvolumes):
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mySubvolume = "%d%d" % (iX, iY)
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sampleName = getSampleName(setName, sliceMin, useVel,
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iSlice=iSlice, iVol=mySubvolume)
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scriptFile.write(sampleInfo.format(dataFile=dataFileName,
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scriptFile.write(sampleInfo.format(dataFile=dataFileName,
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dataFormat=dataFormat,
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dataUnit=dataUnit,
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sampleName=sampleName,
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zMin=sliceMin,
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zMax=sliceMax,
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zMinMpc=sliceMinMpc,
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zMaxMpc=sliceMaxMpc,
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omegaM=Om,
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boxLen=lbox,
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maskFileName=maskFileName,
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zMin=zMin,
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zMax=zMax,
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usePecVel=useVel,
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minRadius=minRadius,
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numSubvolumes=numSubvolumes,
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mySubvolume=mySubvolume,
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useLightCone=useLightCone,
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subsample=subsample))
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minRadius=minRadius))
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scriptFile.close()
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return
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#------------------------------------------------------------------------------
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#------------------------------------------------------------------------------
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if not os.access(scriptDir, os.F_OK): os.mkdir(scriptDir)
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if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir)
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# -----------------------------------------------------------------------------
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# now the SDSS HOD
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parFileText = """
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% cosmology
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OMEGA_M {omegaM}
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HUBBLE {hubble}
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OMEGA_B 0.0469
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SIGMA_8 0.82
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SPECTRAL_INDX 0.95
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ITRANS 5
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REDSHIFT {redshift}
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% halo definition
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%DELTA_HALO 200
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DELTA_HALO 740.74 % 200/Om_m
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M_max 1.00E+16
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% fit function types
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pdfs 11
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pdfc 2
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EXCLUSION 4
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% hod parameters
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M_min {Mmin}
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GALAXY_DENSITY 0.0111134 % computed automatically if M_min set, use for sanity
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M1 {M1}
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sigma_logM {sigma_logM}
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alpha {alpha}
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M_cut {Mcut}
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% simulation info
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real_space_xi 1
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HOD 1
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populate_sim 1
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HaloFile {haloFile}
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RESOLUTION {numPartPerSide}
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BOX_SIZE {boxSize}
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% output
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root_filename hod
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"""
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print " Doing DR9 HOD"
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# these parameters come from Manera et al 2012, eq. 26
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parFileName = "./hod.par"
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parFile = open(parFileName, 'w')
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haloFile = catalogDir+haloFileBase+fileNums[iRedshift]
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parFile.write(parFileText.format(omegaM=omegaM,
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hubble=hubble,
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redshift=redshift,
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Mmin=1.23e13,
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M1=1.e14,
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sigma_logM=0.596,
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alpha=1.0127,
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Mcut=1.19399e13,
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haloFile=haloFile,
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numPartPerSide=numPart**(1/3.),
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boxSize=lbox))
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parFile.close()
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os.system(hodPath+" "+parFileName+">& /dev/null")
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# now place these particles on a lightcone, restrict redshift range, apply mask
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mask = hp.read_map(maskFile)
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nside = hp.get_nside(mask)
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def applyMask(inFileName, outFileName, maskFileName, lbox, zBox, zMin, zMax, omegaM):
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mask = hp.read_map(maskFileName)
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nside = hp.get_nside(mask)
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inFile = open('hod.mock', 'r')
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outFile = open(catalogDir+"/mock.out"))
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inFile = open(inFileName, 'r')
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outFile = open(outFileName, 'w')
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zBox = float(redshiftRange[0])
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Om = float(omegaM)
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Om = float(omegaM)
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# converter from redshift to comoving distance
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zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000)
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zVsDX = np.zeros(len(zVsDY))
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for i in xrange(len(zVsDY)):
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zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
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for line in inFile:
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line = line.split(',')
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x = float(line[0]) - lbox/2.
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y = float(line[1]) - lbox/2.
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z = float(line[2]) - lbox/2.
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vz = float(line[5])
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# converter from redshift to comoving distance
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zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000)
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zVsDX = np.zeros(len(zVsDY))
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for i in xrange(len(zVsDY)):
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zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
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zBoxInMpc = vp.angularDiameter(zBox, Om=Om)
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redshift = np.sqrt(x*x + y*y + z*z)
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redshift = np.interp(zBoxInMpc+100./LIGHT_SPEED*redshift, zVsDX, zVsDY)
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for (iLine,line) in enumerate(inFile):
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if iLine < 5:
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print >> outFile, line.rstrip()
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continue
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if redshift < redshiftRange[0] or redshift > redshiftRange[1]: continue
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line = line.split(' ')
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uniqueID = int(line[0])
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x = float(line[1]) - lbox/2.
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y = float(line[2]) - lbox/2.
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z = float(line[3]) - lbox/2.
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vz = float(line[4])
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RA = np.atan((y-lbox/2.)/(x-lbox/2.)) * 100/np.pi + 180.
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Dec = np.asin((z-lboc/2.)/(redshift*LIGHT_SPEED/100.)) * 180/np.pi
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# TODO if usePecvel
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phi = np.pi/180. * RA
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theta = np.pi/2. - Dec*np.pi/180.
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pos = np.zeros((3))
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redshift = np.sqrt(x*x + y*y + z*z)
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redshift = np.interp(zBoxInMpc+100./LIGHT_SPEED*redshift, zVsDX, zVsDY)
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pix = hp.ang2pix(nside, theta, phi)
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if mask[pix] <= 0: continue
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if redshift < zMin or redshift > zMax: continue
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vec = np.array((x,y,z))
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theta, phi = hp.vec2ang(vec)
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theta = theta[0]
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phi = phi[0]
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RA = phi*180./np.pi
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Dec = 180./np.pi*(np.pi/2.-theta)
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pix = hp.vec2pix(nside, x, y, z)
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if mask[pix] <= 0.2: continue
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print >> outFile, RA, Dec, redshift*LIGHT_SPEED, 0., x, y, z
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print >> outFile, RA, Dec, redshift*LIGHT_SPEED, uniqueID, x, y, z
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inFile.close()
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outFile.close()
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inFile.close()
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outFile.close()
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os.system("rm ./hod.*")
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#------------------------------------------------------------------------------
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def getMaskedZRange(lbox, zBox, zMin, zMax, omegaM):
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if zMin < zBox: zMin = zBox
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Om = float(omegaM)
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# converter from redshift to comoving distance
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zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000)
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zVsDX = np.zeros(len(zVsDY))
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for i in xrange(len(zVsDY)):
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zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
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zBoxInMpc = vp.angularDiameter(zBox, Om=Om)
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boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
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LIGHT_SPEED*lbox/2., zVsDX, zVsDY)-zBox
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print "RANGE", zBox, zBox+boxWidthZ
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if zMax > zBox+boxWidthZ: zMax = zBox+boxWidthZ
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return zMin, zMax
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#------------------------------------------------------------------------------
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#------------------------------------------------------------------------------
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inCatalogDir = catalogDir
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prefix = "masked_" + prefix
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voidOutputDir += "masked/"
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figDir += "masked/"
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logDir += "masked/"
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scriptDir += "masked/"
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catalogDir += "masked/"
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dataType = "observation"
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if not os.access(scriptDir, os.F_OK): os.mkdir(scriptDir)
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if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir)
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#------------------------------------------------------------------------------
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# first the directly downsampled runs
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# Note: ss0.002 ~ SDSS DR7 dim2
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# ss0.0004 ~ SDSS DR9 mid
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baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
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for thisSubSample in subSamples:
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keepFraction = float(thisSubSample) / baseResolution
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maxKeep = keepFraction * numPart
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minRadius = int(np.ceil(lbox/maxKeep**(1./3)))
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if args.script or args.all:
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print " Doing subsample", thisSubSample, " scripts"
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setName = prefix+"ss"+str(thisSubSample)
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writeObservationScript(setName, "masked_md.ss"+str(thisSubSample)+"_z",
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maskFileName,
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scriptDir, catalogDir, fileNums,
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redshifts, False, minRadius, omegaM)
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writeObservationScript(setName, "masked_md.ss"+str(thisSubSample)+"_z",
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maskFileName,
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scriptDir, catalogDir, fileNums,
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redshifts, True, minRadius, omegaM)
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if args.subsample or args.all:
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print " Doing subsample", thisSubSample
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for (iRedshift, redshift) in enumerate(redshifts):
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print " redshift", redshift
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zMin = float(redshift)
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zMax = zMin + 0.1
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zMin, zMax = getMaskedZRange(lbox, float(redshift), zMin, zMax, omegaM)
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if dataFormat == "multidark" or dataFormat == "random":
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inFileName = inCatalogDir+"/md.ss"+str(thisSubSample)+"_z"+redshift+".dat"
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outFileName = catalogDir+"/masked_md.ss"+str(thisSubSample)+"_z"+redshift+".dat"
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applyMask(inFileName, outFileName, maskFileName, lbox, float(redshift),
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zMin, zMax, omegaM)
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# -----------------------------------------------------------------------------
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# now halos
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if (args.script or args.all) and dataFormat == "multidark":
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print " Doing halo scripts"
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for minHaloMass in minHaloMasses:
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if dataFormat == "multidark":
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setName = prefix+"halos_min"+str(minHaloMass)
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writeScript(setName, "md.halos_min"+str(minHaloMass)+"_z",
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scriptDir, catalogDir, fileNums,
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redshifts,
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numSubvolumes, numSlices, False, lbox, minRadius, omegaM)
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writeScript(setName, "md.halos_min"+str(minHaloMass)+"_z",
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scriptDir, catalogDir, fileNums,
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redshifts,
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numSubvolumes, numSlices, True, lbox, minRadius, omegaM)
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if args.halos or args.all:
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print " Doing halos"
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for minHaloMass in minHaloMasses:
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print " min halo mass = ", minHaloMass
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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dataFile = catalogDir+haloFileBase+fileNums[iRedshift]
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inFile = open(dataFile, 'r')
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numPart = 0
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for line in inFile:
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line = line.split(',')
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if minHaloMass == "none" or float(line[6]) > minHaloMass:
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numPart += 1
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inFile.close()
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sampleName = "md.halos_min"+str(minHaloMass)+"_z"+redshift
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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# -----------------------------------------------------------------------------
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# now the SDSS HOD
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if (args.script or args.all) and dataFormat == "multidark":
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print " Doing DR7 HOD scripts"
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if dataFormat == "multidark":
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setName = prefix+"hod_dr72dim2"
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writeScript(setName, "md.hod_dr72dim2_z",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, 5, omegaM)
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writeScript(setName, "md.hod_dr72dim2_z",
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scriptDir, catalogDir, fileNums, redshifts,
|
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numSubvolumes, numSlices, True, lbox, 5, omegaM)
|
||||
|
||||
if args.hod or args.all:
|
||||
print " Doing DR7 HOD"
|
||||
for (iRedshift, redshift) in enumerate(redshifts):
|
||||
print " z = ", redshift
|
||||
|
||||
sampleName = getSampleName("md.hod_dr72dim2", redshift, False)
|
||||
outFileName = catalogDir+"/"+sampleName+".dat"
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
# now the BOSS HOD
|
||||
if (args.script or args.all) and dataFormat == "multidark":
|
||||
print " Doing DR9 HOD scripts"
|
||||
if dataFormat == "multidark":
|
||||
setName = prefix+"hod_dr9mid"
|
||||
writeScript(setName, "md.hod_dr9mid_z",
|
||||
scriptDir, catalogDir, fileNums, redshifts,
|
||||
numSubvolumes, numSlices, False, lbox, 15, omegaM)
|
||||
writeScript(setName, "md.hod_dr9mid_z",
|
||||
scriptDir, catalogDir, fileNums, redshifts,
|
||||
numSubvolumes, numSlices, True, lbox, 15, omegaM)
|
||||
|
||||
if args.hod or args.all:
|
||||
print " Doing DR9 HOD"
|
||||
for (iRedshift, redshift) in enumerate(redshifts):
|
||||
print " z = ", redshift
|
||||
|
||||
outFileName = catalogDir+"/"+sampleName+".dat"
|
||||
|
||||
if dataFormat == "multidark" or dataFormat == "random":
|
||||
sampleName = getSampleName("md.hod_dr9mid", redshift, False)
|
||||
inFileName = inCatalogDir+"/"+sampleName+".dat"
|
||||
outFileName = catalogDir+"/masked_"+sampleName+".dat"
|
||||
|
||||
zMin = float(redshift)
|
||||
zMax = zMin + 0.1
|
||||
zMin, zMax = getMaskedZRange(lbox, float(redshift), zMin, zMax, omegaM)
|
||||
|
||||
applyMask(inFileName, outFileName, maskFileName, lbox, float(redshift),
|
||||
zMin, zMax, omegaM)
|
||||
|
|
|
|||
|
|
@ -49,7 +49,7 @@ numSubvolumes = 1
|
|||
prefix = "md_"
|
||||
|
||||
# list of desired subsamples - these are in unts of h Mpc^-3!
|
||||
#subSamples = [ 1.0 ]
|
||||
#subSamples = [0.0004]
|
||||
subSamples = ((0.1, 0.05, 0.01, 0.002, 0.001, 0.0004, 0.0002))
|
||||
|
||||
# common filename of halo files
|
||||
|
|
@ -62,7 +62,7 @@ minHaloMasses = (("none", 2e12, 1.23e13))
|
|||
# adjust these two parameters given the memory contraints on your system:
|
||||
# numZobovDivisions: how many sub-volumes per dimension will zobov process
|
||||
# numZobovThreads: how many sub-volumes to process at once?
|
||||
numZobovDivisions = 4
|
||||
numZobovDivisions = 2
|
||||
numZobovThreads = 2
|
||||
|
||||
# simulation information
|
||||
|
|
@ -71,6 +71,9 @@ lbox = 1000 # Mpc/h
|
|||
omegaM = 0.27
|
||||
hubble = 0.70
|
||||
|
||||
# the mask file which is used by applyMaskToMock
|
||||
maskFileName = os.getenv("HOME")+"/workspace/Voids/catalogs/boss/boss_mask_final.fits"
|
||||
|
||||
# END CONFIGURATION
|
||||
# -----------------------------------------------------------------------------
|
||||
# -----------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -9,13 +9,6 @@ import pickle
|
|||
|
||||
# ------------------------------------------------------------------------------
|
||||
|
||||
def my_import(name):
|
||||
mod = __import__(name)
|
||||
components = name.split('.')
|
||||
for comp in components[1:]:
|
||||
mod = getattr(mod, comp)
|
||||
return mod
|
||||
|
||||
if (len(sys.argv) == 0):
|
||||
print "Usage: ./anylyzeVoids.py parameter_file.py"
|
||||
exit(-1)
|
||||
|
|
|
|||
|
|
@ -11,15 +11,6 @@ import void_python_tools as vp
|
|||
import argparse
|
||||
import imp
|
||||
|
||||
# ------------------------------------------------------------------------------
|
||||
|
||||
def my_import(name):
|
||||
mod = __import__(name)
|
||||
components = name.split('.')
|
||||
for comp in components[1:]:
|
||||
mod = getattr(mod, comp)
|
||||
return mod
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
|
||||
LIGHT_SPEED = 299792.458
|
||||
|
|
@ -83,7 +74,7 @@ def writeScript(setName, dataFileNameBase,
|
|||
import os
|
||||
from void_python_tools.backend.classes import *
|
||||
|
||||
continueRun = True # set to True to enable restarting aborted jobs
|
||||
continueRun = False # set to True to enable restarting aborted jobs
|
||||
startCatalogStage = 1
|
||||
endCatalogStage = 4
|
||||
|
||||
|
|
@ -133,6 +124,7 @@ newSample = Sample(dataFile = "{dataFile}",
|
|||
zBoundaryMpc = ({zMinMpc}, {zMaxMpc}),
|
||||
omegaM = {omegaM},
|
||||
minVoidRadius = {minRadius},
|
||||
profileBinSize = 1.0,
|
||||
includeInHubble = True,
|
||||
partOfCombo = False,
|
||||
isCombo = False,
|
||||
|
|
@ -143,12 +135,12 @@ newSample = Sample(dataFile = "{dataFile}",
|
|||
useLightCone = {useLightCone},
|
||||
subsample = {subsample})
|
||||
dataSampleList.append(newSample)
|
||||
newSample.addStack({zMin}, {zMax}, {minRadius} , {minRadius}+2, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, {minRadius} , {minRadius}+4, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, {minRadius}+2, {minRadius}+6, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, {minRadius}+6, {minRadius}+10, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, {minRadius}+10, {minRadius}+18, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, {minRadius}+18, {minRadius}+24, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+2, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+4, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False)
|
||||
newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, False)
|
||||
"""
|
||||
for (iFile, redshift) in enumerate(redshifts):
|
||||
fileNum = fileNums[iFile]
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue