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570 lines
20 KiB
Python
Executable file
570 lines
20 KiB
Python
Executable file
#!/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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# -----------------------------------------------------------------------------
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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('--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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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, dataFormat,
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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", dataFileNameList=None):
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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 = False # set to True to enable restarting aborted jobs
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startCatalogStage = 1
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endCatalogStage = 3
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startAPStage = 1
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endAPStage = 1
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regenerateFlag = False
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ZOBOV_PATH = "@CMAKE_BINARY_DIR@/zobov/"
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CTOOLS_PATH = "@CMAKE_BINARY_DIR@/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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profileBinSize = "auto",
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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(0.0, 5.0, 20, 25, False, False)
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newSample.addStack(0.0, 5.0, 30, 35, False, False)
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newSample.addStack(0.0, 5.0, 40, 45, False, False)
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newSample.addStack(0.0, 5.0, 50, 55, False, False)
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newSample.addStack(0.0, 5.0, 60, 65, False, False)
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newSample.addStack(0.0, 5.0, 70, 75, False, False)
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newSample.addStack(0.0, 5.0, 80, 85, False, False)
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newSample.addStack(0.0, 5.0, 90, 95, False, False)
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#newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+2, True, False)
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#newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+4, True, False)
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#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False)
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#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False)
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#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False)
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#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{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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boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
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LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
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for iSlice in xrange(numSlices):
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if useLightCone:
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dzSafe = 0.03
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sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-2.*dzSafe)/numSlices
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sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-2.*dzSafe)/numSlices
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sliceMinMpc = sliceMin*LIGHT_SPEED/100.
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sliceMaxMpc = sliceMax*LIGHT_SPEED/100.
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else:
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sliceMinMpc = zBoxMpc + iSlice*lbox/numSlices
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sliceMaxMpc = zBoxMpc + (iSlice+1)*lbox/numSlices
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sliceMin = np.interp(sliceMinMpc*100./LIGHT_SPEED, zVsDX, zVsDY)
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sliceMax = np.interp(sliceMaxMpc*100./LIGHT_SPEED, zVsDX, zVsDY)
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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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if (dataFileNameList != None):
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dataFileName = dataFileNameList[iFile]
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else:
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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=str(subsample).strip('[]')))
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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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# first the directly downsampled runs
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# Note: ss0.002 ~ SDSS DR7 dim2
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# ss0.000175 ~ SDSS DR9 mid
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baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
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prevSubSample = -1
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subSamples = sorted(subSamples, reverse=True)
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for iSubSample in xrange(len(subSamples)):
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subSampleList = subSamples[0:iSubSample+1]
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keepFractionList = []
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for subSample in subSampleList:
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keepFractionList.append(float(subSample) / baseResolution)
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thisSubSample = subSamples[iSubSample]
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maxKeep = keepFractionList[-1] * numPart
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minRadius = int(np.ceil(lbox/maxKeep**(1./3)))
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partFileList = []
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for (iRedshift, redshift) in enumerate(redshifts):
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if particleFileDummy == '':
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partFileList.append(particleFileBase+fileNums[iRedshift])
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else:
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partFileList.append(particleFileBase.replace(particleFileDummy,
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fileNums[iRedshift]))
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if args.script or args.all:
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print " Doing subsample", thisSubSample, "scripts"
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sys.stdout.flush()
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setName = prefix+"ss"+str(thisSubSample)
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if dataFormat == "random":
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subSampleToUse = 1.0
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fileToUse = "ran.ss"+str(thisSubSample)+"_z"
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suffix = ".dat"
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writeScript(setName, fileToUse, dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
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subsample=subSampleToUse, suffix=suffix)
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writeScript(setName, fileToUse, dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
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subsample=subSampleToUse, suffix=suffix)
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else:
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subSampleToUse = keepFractionList
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suffix = ""
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fileToUse = partFileList[0]
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writeScript(setName, fileToUse, dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
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subsample=subSampleToUse, suffix=suffix,
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dataFileNameList=partFileList)
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writeScript(setName, fileToUse, dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
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subsample=subSampleToUse, suffix=suffix,
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dataFileNameList=partFileList)
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if args.subsample or args.all:
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print " Doing subsample", thisSubSample
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sys.stdout.flush()
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for (iRedshift, redshift) in enumerate(redshifts):
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print " redshift", redshift
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sys.stdout.flush()
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if dataFormat == "multidark":
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# reuse previous subamples in order to:
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# - preserve unique IDs across multiple subsamples
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# - reuse smaller files for faster processing
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if prevSubSample == -1:
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dataFile = catalogDir+"/"+particleFileBase+fileNums[iRedshift]
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else:
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sampleName = prefix+"ss"+str(prevSubSample)+"_z"+redshift
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dataFile = catalogDir+"/"+sampleName+".dat"
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keepFraction = float(thisSubSample) / float(prevSubSample)
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inFile = open(dataFile, 'r')
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sampleName = prefix+"ss"+str(thisSubSample)+"_z"+redshift
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("%f\n" %(lbox))
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outFile.write("%s\n" %(omegaM))
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outFile.write("%s\n" %(hubble))
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outFile.write("%s\n" %(redshift))
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outFile.write("%d\n" %(maxKeep))
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numKept = 0
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for (i,line) in enumerate(inFile):
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if (prevSubSample != -1 and i < 5): continue # skip header
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if np.random.uniform() > keepFraction: continue
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numKept += 1
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#if numKept > maxKeep: break
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if (prevSubSample == -1):
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line = line.split(',')
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x = float(line[0])
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y = float(line[1])
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z = float(line[2])
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vz = float(line[3])
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vy = float(line[4])
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vx = float(line[5])
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uniqueID = i
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outFile.write("%d %e %e %e %e %e %e\n" %(uniqueID,x,y,z,vz,vy,vx))
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else:
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outFile.write(line)
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outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
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inFile.close()
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outFile.close()
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elif dataFormat == "random":
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sampleName = "ran.ss"+str(thisSubSample)+"_z"+redshift
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("%f\n" %(lbox))
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outFile.write("%s\n" %(omegaM))
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outFile.write("%s\n" %(hubble))
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outFile.write("%s\n" %(redshift))
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outFile.write("%d\n" %(maxKeep))
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for i in xrange(int(maxKeep)):
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x = np.random.uniform()*lbox
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y = np.random.uniform()*lbox
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z = np.random.uniform()*lbox
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outFile.write("%d %e %e %e 0. 0. 0.\n" % (i, x,y,z))
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outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
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outFile.close()
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prevSubSample = thisSubSample
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# -----------------------------------------------------------------------------
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# now halos
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if (args.script or args.all) and haloFileBase != "":
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for minHaloMass in minHaloMasses:
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print " Doing halo script", minHaloMass
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sys.stdout.flush()
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# estimate number of halos to get density
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if haloFileDummy == '':
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dataFile = catalogDir+haloFileBase+fileNums[0]
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else:
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dataFile = catalogDir+haloFileBase.replace(haloFileDummy, fileNums[0])
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inFile = open(dataFile, 'r')
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numPart = 0
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for (iLine, line) in enumerate(inFile):
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if iLine < haloFileNumComLines: continue
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line = line.split(haloFileColSep)
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if minHaloMass == "none" or float(line[haloFileMCol]) > 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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setName = prefix+"halos_min"+str(minHaloMass)
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writeScript(setName, prefix+"halos_min"+str(minHaloMass)+"_z", "multidark",
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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, prefix+"halos_min"+str(minHaloMass)+"_z", "multidark",
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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) and haloFileBase != "":
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print " Doing halos"
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sys.stdout.flush()
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for minHaloMass in minHaloMasses:
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print " min halo mass = ", minHaloMass
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sys.stdout.flush()
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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sys.stdout.flush()
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if haloFileDummy == '':
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dataFile = catalogDir+haloFileBase+fileNums[iRedshift]
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else:
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dataFile = catalogDir+haloFileBase.replace(haloFileDummy,
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fileNums[iRedshift])
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inFile = open(dataFile, 'r')
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numPart = 0
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for (iLine, line) in enumerate(inFile):
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if iLine < haloFileNumComLines: continue
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line = line.split(haloFileColSep)
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if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
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numPart += 1
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inFile.close()
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sampleName = prefix+"halos_min"+str(minHaloMass)+"_z"+fileNums[iRedshift]
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("%f\n" %(lbox))
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outFile.write("%s\n" %(omegaM))
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outFile.write("%s\n" %(hubble))
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outFile.write("%s\n" %(redshift))
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outFile.write("%d\n" %(numPart))
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if dataFormat == "sdf":
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# TODO process halo file with SDFcvt
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SDFcvt_PATH = "@CMAKE_BINARY_DIR@/ep_build/sdf/bin/SDFcvt/"
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
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outFile.close()
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else:
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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inFile = open(dataFile, 'r')
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for (iHalo,line) in enumerate(inFile):
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if iHalo < haloFileNumComLines: continue
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line = line.split(haloFileColSep)
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if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
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x = float(line[haloFileXCol])
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y = float(line[haloFileYCol])
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z = float(line[haloFileZCol])
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vz = float(line[haloFileVZCol])
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vy = float(line[haloFileVYCol])
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vx = float(line[haloFileVXCol])
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# write to output file
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outFile.write("%d %e %e %e %e %e %e\n" %(iHalo,x,y,z,vz,vy,vx))
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outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
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outFile.close()
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inFile.close()
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# -----------------------------------------------------------------------------
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# now the 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 {galden} % 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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HaloFileFormat {haloFileFormat}
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RESOLUTION {numPartPerSide}
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BOX_SIZE {boxSize}
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% output
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root_filename {workDir}/hod
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"""
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if (args.script or args.all) and haloFileBase != "":
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print " Doing HOD scripts"
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sys.stdout.flush()
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for thisHod in hodParmList:
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print " ", thisHod['name']
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setName = prefix+"hod_"+thisHod['name']
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writeScript(setName, prefix+"hod_"+thisHod['name']+"_z", "multidark",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, 15, omegaM)
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writeScript(setName, prefix+"hod_"+thisHod['name']+"_z", "multidark",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, 15, omegaM)
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if (args.hod or args.all) and haloFileBase != "":
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print " Doing HOD"
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sys.stdout.flush()
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for thisHod in hodParmList:
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print " ", thisHod['name']
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sys.stdout.flush()
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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sys.stdout.flush()
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parFileName = "./hod.par"
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parFile = open(parFileName, 'w')
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if haloFileDummy == '':
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haloFile = catalogDir+haloFileBase+fileNums[iRedshift]
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else:
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haloFile = catalogDir+haloFileBase.replace(haloFileDummy,
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fileNums[iRedshift])
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if dataFormat == "sdf":
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# TODO process halo file with SDFcvt
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inFile = haloFile
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outFile = haloFile+"_temp"
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haloFile = outFile
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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=thisHod['Mmin'],
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#Mmin=1.23e13,
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M1=thisHod['M1'],
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sigma_logM=thisHod['sigma_logM'],
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alpha=thisHod['alpha'],
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Mcut=thisHod['Mcut'],
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galden=thisHod['galDens'],
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#galden=0.000225,
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haloFile=haloFile,
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haloFileFormat=dataFormat,
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numPartPerSide=numPart**(1/3.),
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boxSize=lbox,
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workDir=catalogDir))
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parFile.close()
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os.system(hodPath+" "+parFileName+">& /dev/null")
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|
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sampleName = getSampleName(prefix+"hod_"+thisHod['name'], redshift, False)
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outFileName = catalogDir+"/"+sampleName+".dat"
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os.system("mv %s/hod.mock %s" % (catalogDir, outFileName))
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os.system("rm %s/hod.*" % catalogDir)
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os.system("rm %s" % haloFile)
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print " Done!"
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