mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
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Supports minimum halo mass cuts. Start of scripts to generate masked mock sets, some files added to later support more general preparation scripts
This commit is contained in:
Paul Matt Sutter
parent
a53e3bf290
commit
10dfe29a26
9 changed files with 557 additions and 58 deletions
321
pipeline/applyMaskToMock.py
Executable file
321
pipeline/applyMaskToMock.py
Executable file
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@ -0,0 +1,321 @@
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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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import numpy as np
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import os
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import sys
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import void_python_tools as vp
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import argparse
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import imp
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import healpy as hp
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# ------------------------------------------------------------------------------
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def my_import(name):
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mod = __import__(name)
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components = name.split('.')
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for comp in components[1:]:
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mod = getattr(mod, comp)
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return mod
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# -----------------------------------------------------------------------------
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LIGHT_SPEED = 299792.458
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parser = argparse.ArgumentParser(description='options')
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parser.add_argument('--scripts', dest='script', action='store_const',
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const=True, default=False,
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help='write scripts')
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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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args = parser.parse_args()
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filename = args.parmFile
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print " Loading parameters from", filename
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if not os.access(filename, os.F_OK):
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print " Cannot find parameter file %s!" % filename
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exit(-1)
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parms = imp.load_source("name", filename)
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globals().update(vars(parms))
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#------------------------------------------------------------------------------
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def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
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sampleName = setName
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sampleName += "_z" + redshift
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if iVol != -1: sampleName += "_d" + iVol
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return sampleName
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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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suffix=".dat"):
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if useVel: setName += "_pv"
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scriptFileName = scriptDir + "/" + setName + ".py"
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scriptFile = open(scriptFileName, 'w')
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scriptFile.write("""#!/usr/bin/env/python
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import os
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from void_python_tools.backend.classes import *
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continueRun = True # set to True to enable restarting aborted jobs
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startCatalogStage = 1
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endCatalogStage = 4
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startAPStage = 1
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endAPStage = 7
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ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
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CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/"
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freshStack = True
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errorBars = "CALCULATED"
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numIncoherentRuns = 100
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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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dataSampleList = []
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""")
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dataInfo = """
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setName = "{setName}"
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workDir = "{voidOutputDir}/{setName}/"
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inputDataDir = "{inputDataDir}"
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figDir = "{figDir}/{setName}/"
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logDir = "{logDir}/{setName}/"
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numZobovDivisions = {numZobovDivisions}
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numZobovThreads = {numZobovThreads}
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"""
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scriptFile.write(dataInfo.format(setName=setName, figDir=figDir,
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logDir=logDir, voidOutputDir=voidOutputDir,
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inputDataDir=catalogDir,
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numZobovDivisions=numZobovDivisions,
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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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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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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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newSample.addStack({zMin}, {zMax}, {minRadius}+2, {minRadius}+6, True, False)
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newSample.addStack({zMin}, {zMax}, {minRadius}+6, {minRadius}+10, True, False)
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newSample.addStack({zMin}, {zMax}, {minRadius}+10, {minRadius}+18, True, False)
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newSample.addStack({zMin}, {zMax}, {minRadius}+18, {minRadius}+24, True, False)
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"""
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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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# 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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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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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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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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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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inFile = open('hod.mock', 'r')
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outFile = open(catalogDir+"/mock.out"))
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zBox = float(redshiftRange[0])
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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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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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if redshift < redshiftRange[0] or redshift > redshiftRange[1]: continue
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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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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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pix = hp.ang2pix(nside, theta, phi)
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if mask[pix] <= 0: continue
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print >> outFile, RA, Dec, redshift*LIGHT_SPEED, 0., x, y, z
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inFile.close()
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outFile.close()
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os.system("rm ./hod.*")
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62
pipeline/datasets/mock_dr9mid.py
Normal file
62
pipeline/datasets/mock_dr9mid.py
Normal file
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@ -0,0 +1,62 @@
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import os
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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# CONFIGURATION
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# directory for the input simulation/observational particle files
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catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/mock_dr9mid/"
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# path to HOD code
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hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
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# path to mask
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maskFile = os.getenv("HOME")+"/workspace/Voids/catalogs/boss/final_boss_mask.fits")
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# where to put the final void catalog, figures, and output logs
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voidOutputDir = os.getenv("HOME")+"/workspace/Voids/mock_dr9mid/"
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figDir = os.getenv("PWD")+"/../figs/mock_dr9mid/"
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logDir = os.getenv("PWD")+"/../logs/mock_dr9mid/"
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# where to place the pipeline scripts
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scriptDir = os.getenv("PWD")+"/mock_dr9mid/"
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# simulation or observation?
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dataType = "observation"
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# available formats for simulation: gadget, multidark
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dataFormat = "multidark"
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dataUnit = 1 # as multiple of Mpc/h
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# place particles on the lightcone?
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useLightCone = True
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# list of file numbers for the particle files
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# to get particle file name, we take particleFileBase+fileNum
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fileNums = (("0.53"))
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# redshift range of the mock
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redshiftRange = (0.53, 0.6)
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# prefix to give all outputs
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prefix = "mock_"
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# common filename of halo files
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haloFileBase = "mdr1_halos_z"
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# adjust these two parameters given the memory contraints on your system:
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# numZobovDivisions: how many sub-volumes per dimension will zobov process
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# numZobovThreads: how many sub-volumes to process at once?
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numZobovDivisions = 2
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numZobovThreads = 2
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# simulation information
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numPart = 1024*1024*1024
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lbox = 1000 # Mpc/h
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omegaM = 0.27
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hubble = 0.70
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# END CONFIGURATION
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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@ -52,6 +52,13 @@ prefix = "md_"
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#subSamples = [ 1.0 ]
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subSamples = ((0.1, 0.05, 0.01, 0.002, 0.001, 0.0004, 0.0002))
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# common filename of halo files
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haloFileBase = "mdr1_halos_z"
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# minimum halo mass cuts to apply for the halo catalog
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# use "none" to get all halos
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minHaloMasses = (("none", 2e12, 1.23e13))
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# adjust these two parameters given the memory contraints on your system:
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# numZobovDivisions: how many sub-volumes per dimension will zobov process
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# numZobovThreads: how many sub-volumes to process at once?
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@ -64,6 +64,9 @@ for sample in dataSampleList:
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# save this sample's information
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with open(zobovDir+"/sample_info.dat", 'wb') as output:
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pickle.dump(sample, output, pickle.HIGHEST_PROTOCOL)
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fp = open(zobovDir+"/sample_info.txt", 'w')
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fp.write("Redshift range: %f - %f" %(sample.zBoundary[0], sample.zBoundary[1])
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fp.close()
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# ---------------------------------------------------------------------------
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if (startCatalogStage <= 1) and (endCatalogStage >= 1) and not sample.isCombo:
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@ -60,12 +60,8 @@ def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
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sampleName = setName
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#if useVel: sampleName += "_pv"
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sampleName += "_z" + redshift
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#if iSlice != -1: sampleName += "_s" + str(iSlice)
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if iVol != -1: sampleName += "_d" + iVol
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return sampleName
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@ -87,7 +83,7 @@ def writeScript(setName, dataFileNameBase,
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import os
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from void_python_tools.backend.classes import *
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continueRun = False
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continueRun = True # set to True to enable restarting aborted jobs
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startCatalogStage = 1
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endCatalogStage = 4
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@ -326,33 +322,42 @@ for thisSubSample in subSamples:
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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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dataFile = catalogDir+"/mdr1_halos_z"+fileNums[0]
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for minHaloMass in minHaloMasses:
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dataFile = catalogDir+haloFileBase+fileNums[0]
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inFile = open(dataFile, 'r')
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numPart = 0
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for line in inFile: numPart += 1
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for line in inFile:
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line = line.split(',')
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if numHaloMass == "none" or float(line[6]) > minHaloMass:
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numPart += 1
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inFile.close()
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minRadius = 2*int(np.ceil(lbox/numPart**(1./3.)))
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if dataFormat == "multidark":
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setName = prefix+"halos"
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writeScript(setName, "md.halos_z", scriptDir, catalogDir, fileNums,
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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_z", scriptDir, catalogDir, fileNums,
|
||||
redshifts, numSubvolumes,
|
||||
writeScript(setName, "md.halos_min"+str(minHaloMass)+"_z",
|
||||
scriptDir, catalogDir, fileNums,
|
||||
numSlices, True, lbox, minRadius, omegaM)
|
||||
|
||||
if args.halos or args.all:
|
||||
print " Doing halos"
|
||||
|
||||
for minHaloMass in minHaloMasses:
|
||||
print " min halo mass = ", minHaloMass
|
||||
|
||||
for (iRedshift, redshift) in enumerate(redshifts):
|
||||
print " z = ", redshift
|
||||
|
||||
dataFile = catalogDir+"/mdr1_halos_z"+fileNums[iRedshift]
|
||||
dataFile = catalogDir+haloFileBase+fileNums[iRedshift]
|
||||
inFile = open(dataFile, 'r')
|
||||
numPart = 0
|
||||
for line in inFile: numPart += 1
|
||||
for line in inFile:
|
||||
line = line.split(',')
|
||||
if numHaloMass == "none" or float(line[6]) > minHaloMass:
|
||||
inFile.close()
|
||||
|
||||
sampleName = "md.halos_z"+redshift
|
||||
|
|
@ -367,6 +372,7 @@ if args.halos or args.all:
|
|||
inFile = open(dataFile, 'r')
|
||||
numKept = 0
|
||||
for line in inFile:
|
||||
if numHaloMass == "none" or float(line[6]) > minHaloMass:
|
||||
numKept += 1
|
||||
line = line.split(',')
|
||||
x = float(line[0])
|
||||
|
|
|
|||
17
plotting/datasetsToPlot.py
Executable file
17
plotting/datasetsToPlot.py
Executable file
|
|
@ -0,0 +1,17 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
|
||||
workDir = "/home/psutter2/workspace/Voids/"
|
||||
figDir = "./figs"
|
||||
|
||||
sampleDirList = [ "multidark/md_ss0.1_pv/sample_md_ss0.1_pv_z0.56_d00/",
|
||||
"multidark/md_ss01.0_pv/sample_md_ss1.0_pv_z0.56_d00/",
|
||||
"multidark/md_halos_min1.23e13_pv/sample_md_halos_min1.23e13_pv_z0.56_d00/",
|
||||
"random/ran_ss0.0004/sample_ran_ss0.0004_z0.56_d00/",
|
||||
"random/ran_ss0.1/sample_ran_ss0.1_z0.56_d00/",
|
||||
"multidark/md_hod_dr9mid_pv/sample_md_hod_dr9mid_pv_z0.56_d00/",
|
||||
"multidark/md_ss0.0004_pv/sample_md_ss0.0004_pv_z0.56_d00/",
|
||||
"sdss_dr9/sample_lss.dr9cmassmid.dat/" ]
|
||||
|
||||
dataPortion = "central"
|
||||
|
||||
93
plotting/plotCompareDensCon.py
Executable file
93
plotting/plotCompareDensCon.py
Executable file
|
|
@ -0,0 +1,93 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# plots cumulative distributions of number counts versus density contrast
|
||||
|
||||
from void_python_tools.backend import *
|
||||
from void_python_tools.plotting import *
|
||||
import void_python_tools.apTools as vp
|
||||
import imp
|
||||
import pickle
|
||||
import os
|
||||
import matplotlib.pyplot as plt
|
||||
import numpy as np
|
||||
import argparse
|
||||
|
||||
# ------------------------------------------------------------------------------
|
||||
|
||||
from datasetsToPlot import *
|
||||
|
||||
plotNameBase = "compdenscon"
|
||||
|
||||
obsFudgeFactor = .66 # what fraction of the volume are we *reall* capturing?
|
||||
|
||||
parser = argparse.ArgumentParser(description='Plot.')
|
||||
parser.add_argument('--show', dest='showPlot', action='store_const',
|
||||
const=True, default=False,
|
||||
help='display the plot (default: just write eps)')
|
||||
args = parser.parse_args()
|
||||
|
||||
# ------------------------------------------------------------------------------
|
||||
|
||||
if not os.access(figDir, os.F_OK):
|
||||
os.makedirs(figDir)
|
||||
|
||||
dataSampleList = []
|
||||
|
||||
for sampleDir in sampleDirList:
|
||||
with open(workDir+sampleDir+"/sample_info.dat", 'rb') as input:
|
||||
dataSampleList.append(pickle.load(input))
|
||||
|
||||
plt.clf()
|
||||
plt.xlabel("Void Radius (Mpc/h)")
|
||||
plt.ylabel(r"N > R [$h^3$ Gpc$^{-3}$]")
|
||||
plt.yscale('log')
|
||||
plt.xlim(xmax=80.)
|
||||
|
||||
plotName = plotNameBase
|
||||
|
||||
for (iSample,sample) in enumerate(dataSampleList):
|
||||
|
||||
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]
|
||||
boxVol *= obsFudgeFactor
|
||||
else:
|
||||
boxVol = sample.boxLen*sample.boxLen*(sample.zBoundaryMpc[1] -
|
||||
sample.zBoundaryMpc[0])
|
||||
|
||||
boxVol *= 1.e-9 # Mpc->Gpc
|
||||
|
||||
filename = workDir+"/"+sampleDirList[iSample]+"/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[:,8]
|
||||
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", prop={'size':8})
|
||||
#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 args.showPlot:
|
||||
os.system("display %s" % figDir+"/fig_"+plotName+".png")
|
||||
|
||||
|
||||
|
|
@ -14,21 +14,10 @@ import argparse
|
|||
|
||||
# ------------------------------------------------------------------------------
|
||||
|
||||
workDir = "/home/psutter2/workspace/Voids/"
|
||||
figDir = "./figs"
|
||||
|
||||
sampleDirList = [ "multidark/md_ss0.1_pv/sample_md_ss0.1_pv_z0.56_d00/",
|
||||
"multidark/md_halos_pv/sample_md_halos_pv_z0.56_d00/",
|
||||
"random/ran_ss0.0004/sample_ran_ss0.0004_z0.56_d00/",
|
||||
"random/ran_ss0.1/sample_ran_ss0.1_z0.56_d00/",
|
||||
"multidark/md_hod_dr9mid_pv/sample_md_hod_dr9mid_pv_z0.56_d00/",
|
||||
"multidark/md_ss0.0004_pv/sample_md_ss0.0004_pv_z0.56_d00/",
|
||||
"sdss_dr9/sample_lss.dr9cmassmid.dat/" ]
|
||||
from datasetsToPlot import *
|
||||
|
||||
plotNameBase = "compdist"
|
||||
|
||||
dataPortion = "central"
|
||||
|
||||
obsFudgeFactor = .66 # what fraction of the volume are we *reall* capturing?
|
||||
|
||||
parser = argparse.ArgumentParser(description='Plot.')
|
||||
|
|
|
|||
|
|
@ -1,2 +1,3 @@
|
|||
from classes import *
|
||||
from launchers import *
|
||||
from catalogPrep import *
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue