#!/usr/bin/env python # prepares input catalogs based on multidark simulations # (borrows heavily from generateMock, but doesn't hold much in memory) # also creates necessary analyzeVoids input files import numpy as np import os import sys 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 parser = argparse.ArgumentParser(description='options') parser.add_argument('--scripts', dest='script', action='store_const', const=True, default=False, help='write scripts') parser.add_argument('--subsamples', dest='subsample', action='store_const', const=True, default=False, help='write subsamples') parser.add_argument('--halos', dest='halos', action='store_const', const=True, default=False, help='write halos') parser.add_argument('--hod', dest='hod', action='store_const', const=True, default=False, help='write hod') parser.add_argument('--all', dest='all', action='store_const', const=True, default=False, help='write everything') parser.add_argument('--parmFile', dest='parmFile', default="", help='path to parameter file') args = parser.parse_args() filename = args.parmFile print " Loading parameters from", filename if not os.access(filename, os.F_OK): print " Cannot find parameter file %s!" % filename exit(-1) parms = imp.load_source("name", filename) globals().update(vars(parms)) #------------------------------------------------------------------------------ def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1): sampleName = setName sampleName += "_z" + redshift if iVol != -1: sampleName += "_d" + iVol return sampleName #------------------------------------------------------------------------------ # for given dataset parameters, outputs a script for use with analyzeVoids def writeScript(setName, dataFileNameBase, scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, useVel, lbox, minRadius, omegaM, subsample=1.0, suffix=".dat"): if useVel: setName += "_pv" scriptFileName = scriptDir + "/" + setName + ".py" scriptFile = open(scriptFileName, 'w') scriptFile.write("""#!/usr/bin/env/python import os from void_python_tools.backend.classes import * continueRun = True # set to True to enable restarting aborted jobs startCatalogStage = 1 endCatalogStage = 4 startAPStage = 1 endAPStage = 7 ZOBOV_PATH = os.getenv("PWD")+"/../zobov/" CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/" freshStack = True errorBars = "CALCULATED" numIncoherentRuns = 100 ranSeed = 101010 useLCDM = False bias = 1.16 dataPortions = ["central"] dataSampleList = [] """) dataInfo = """ setName = "{setName}" workDir = "{voidOutputDir}/{setName}/" inputDataDir = "{inputDataDir}" figDir = "{figDir}/{setName}/" logDir = "{logDir}/{setName}/" numZobovDivisions = {numZobovDivisions} numZobovThreads = {numZobovThreads} """ scriptFile.write(dataInfo.format(setName=setName, figDir=figDir, logDir=logDir, voidOutputDir=voidOutputDir, inputDataDir=catalogDir, numZobovDivisions=numZobovDivisions, numZobovThreads=numZobovThreads)) sampleInfo = """ newSample = Sample(dataFile = "{dataFile}", dataFormat = "{dataFormat}", dataUnit = {dataUnit}, fullName = "{sampleName}", nickName = "{sampleName}", dataType = "simulation", zBoundary = ({zMin}, {zMax}), zRange = ({zMin}, {zMax}), zBoundaryMpc = ({zMinMpc}, {zMaxMpc}), omegaM = {omegaM}, minVoidRadius = {minRadius}, includeInHubble = True, partOfCombo = False, isCombo = False, boxLen = {boxLen}, usePecVel = {usePecVel}, numSubvolumes = {numSubvolumes}, mySubvolume = "{mySubvolume}", 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) """ for (iFile, redshift) in enumerate(redshifts): fileNum = fileNums[iFile] zBox = float(redshift) Om = float(omegaM) zBoxMpc = LIGHT_SPEED/100.*vp.angularDiameter(zBox, Om=Om) boxMaxMpc = zBoxMpc + lbox # converter from redshift to comoving distance zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000) zVsDX = np.zeros(len(zVsDY)) for i in xrange(len(zVsDY)): zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om) if useLightCone: boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \ LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox dzSafe = 0.03 else: boxWidthZ = lbox*100./LIGHT_SPEED dzSafe = 0.0 for iSlice in xrange(numSlices): sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-dzSafe)/numSlices sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-dzSafe)/numSlices sliceMinMpc = sliceMin*LIGHT_SPEED/100. sliceMaxMpc = sliceMax*LIGHT_SPEED/100. sliceMin = "%0.2f" % sliceMin sliceMax = "%0.2f" % sliceMax sliceMinMpc = "%0.1f" % sliceMinMpc sliceMaxMpc = "%0.1f" % sliceMaxMpc dataFileName = dataFileNameBase + fileNum + suffix for iX in xrange(numSubvolumes): for iY in xrange(numSubvolumes): mySubvolume = "%d%d" % (iX, iY) sampleName = getSampleName(setName, sliceMin, useVel, iSlice=iSlice, iVol=mySubvolume) scriptFile.write(sampleInfo.format(dataFile=dataFileName, dataFormat=dataFormat, dataUnit=dataUnit, sampleName=sampleName, zMin=sliceMin, zMax=sliceMax, zMinMpc=sliceMinMpc, zMaxMpc=sliceMaxMpc, omegaM=Om, boxLen=lbox, usePecVel=useVel, minRadius=minRadius, numSubvolumes=numSubvolumes, mySubvolume=mySubvolume, useLightCone=useLightCone, subsample=subsample)) scriptFile.close() return #------------------------------------------------------------------------------ #------------------------------------------------------------------------------ if not os.access(scriptDir, os.F_OK): os.mkdir(scriptDir) if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir) #------------------------------------------------------------------------------ # first the directly downsampled runs # Note: ss0.002 ~ SDSS DR7 dim2 # ss0.0004 ~ SDSS DR9 mid baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3 for thisSubSample in subSamples: keepFraction = float(thisSubSample) / baseResolution maxKeep = keepFraction * numPart minRadius = int(np.ceil(lbox/maxKeep**(1./3))) if args.script or args.all: print " Doing subsample", thisSubSample, " scripts" setName = prefix+"ss"+str(thisSubSample) if dataFormat == "multidark": writeScript(setName, "md.ss"+str(thisSubSample)+"_z", scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, False, lbox, minRadius, omegaM, subsample=1.0) writeScript(setName, "md.ss"+str(thisSubSample)+"_z", scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, True, lbox, minRadius, omegaM, subsample=1.0) elif dataFormat == "gadget": writeScript(setName, particleFileBase, scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, False, lbox, minRadius, omegaM, subsample=thisSubSample, suffix="") writeScript(setName, particleFileBase, scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, True, lbox, minRadius, omegaM, subsample=thisSubSample, suffix="") elif dataFormat == "random": writeScript(setName, "ran.ss"+str(thisSubSample)+"_z", scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, False, lbox, minRadius, omegaM, subsample=1.0) if args.subsample or args.all: print " Doing subsample", thisSubSample for (iRedshift, redshift) in enumerate(redshifts): print " redshift", redshift if dataFormat == "multidark": dataFile = catalogDir+"/"+particleFileBase+fileNums[iRedshift] inFile = open(dataFile, 'r') sampleName = "md.ss"+str(thisSubSample)+"_z"+redshift outFile = open(catalogDir+"/"+sampleName+".dat", 'w') outFile.write("%f\n" %(lbox)) outFile.write("%s\n" %(omegaM)) outFile.write("%s\n" %(hubble)) outFile.write("%s\n" %(redshift)) outFile.write("%d\n" %(maxKeep)) numKept = 0 for (i,line) in enumerate(inFile): if np.random.uniform() > keepFraction: continue numKept += 1 if numKept > maxKeep: break line = line.split(',') x = float(line[0]) y = float(line[1]) z = float(line[2]) vz = float(line[3]) outFile.write("%d %e %e %e %e\n" %(i,x,y,z,vz)) outFile.write("-99 -99 -99 -99 -99\n") inFile.close() outFile.close() elif dataFormat == "random": sampleName = "ran.ss"+str(thisSubSample)+"_z"+redshift outFile = open(catalogDir+"/"+sampleName+".dat", 'w') outFile.write("%f\n" %(lbox)) outFile.write("%s\n" %(omegaM)) outFile.write("%s\n" %(hubble)) outFile.write("%s\n" %(redshift)) outFile.write("%d\n" %(maxKeep)) for i in xrange(int(maxKeep)): x = np.random.uniform()*lbox y = np.random.uniform()*lbox z = np.random.uniform()*lbox outFile.write("%d %e %e %e %e\n" % (i, x,y,z, 0.)) outFile.write("-99 -99 -99 -99 -99\n") outFile.close() # ----------------------------------------------------------------------------- # now halos if (args.script or args.all) and dataFormat == "multidark": print " Doing halo scripts" for minHaloMass in minHaloMasses: # estimate number of halos to get density dataFile = catalogDir+haloFileBase+fileNums[0] inFile = open(dataFile, 'r') numPart = 0 for line in inFile: line = line.split(',') if minHaloMass == "none" or float(line[6]) > minHaloMass: numPart += 1 inFile.close() minRadius = 2*int(np.ceil(lbox/numPart**(1./3.))) if dataFormat == "multidark": setName = prefix+"halos_min"+str(minHaloMass) writeScript(setName, "md.halos_min"+str(minHaloMass)+"_z", scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, False, lbox, minRadius, omegaM) writeScript(setName, "md.halos_min"+str(minHaloMass)+"_z", scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, 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+haloFileBase+fileNums[iRedshift] inFile = open(dataFile, 'r') numPart = 0 for line in inFile: line = line.split(',') if minHaloMass == "none" or float(line[6]) > minHaloMass: numPart += 1 inFile.close() sampleName = "md.halos_z"+redshift outFile = open(catalogDir+"/"+sampleName+".dat", 'w') outFile.write("%f\n" %(lbox)) outFile.write("%s\n" %(omegaM)) outFile.write("%s\n" %(hubble)) outFile.write("%s\n" %(redshift)) outFile.write("%d\n" %(numPart)) inFile = open(dataFile, 'r') for (iHalo,line) in enumerate(inFile): line = line.split(',') if minHaloMass == "none" or float(line[6]) > minHaloMass: x = float(line[0]) y = float(line[1]) z = float(line[2]) vz = float(line[5]) # write to output file outFile.write("%d %e %e %e %e\n" %(iHalo,x,y,z,vz)) inFile.close() outFile.close() # ----------------------------------------------------------------------------- # now the SDSS HOD parFileText = """ % cosmology OMEGA_M {omegaM} HUBBLE {hubble} OMEGA_B 0.0469 SIGMA_8 0.82 SPECTRAL_INDX 0.95 ITRANS 5 REDSHIFT {redshift} % halo definition %DELTA_HALO 200 DELTA_HALO 740.74 % 200/Om_m M_max 1.00E+16 % fit function types pdfs 11 pdfc 2 EXCLUSION 4 % hod parameters M_min {Mmin} GALAXY_DENSITY 0.0111134 % computed automatically if M_min set, use for sanity M1 {M1} sigma_logM {sigma_logM} alpha {alpha} M_cut {Mcut} % simulation info real_space_xi 1 HOD 1 populate_sim 1 HaloFile {haloFile} RESOLUTION {numPartPerSide} BOX_SIZE {boxSize} % output root_filename hod """ if (args.script or args.all) and dataFormat == "multidark": print " Doing DR7 HOD scripts" if dataFormat == "multidark": setName = prefix+"hod_dr72dim2" writeScript(setName, "md.hod_dr72dim2_z", scriptDir, catalogDir, fileNums, redshifts, numSubvolumes, numSlices, False, lbox, 5, omegaM) writeScript(setName, "md.hod_dr72dim2_z", scriptDir, catalogDir, fileNums, redshifts, 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 parFileName = "./hod.par" parFile = open(parFileName, 'w') haloFile = catalogDir+"/mdr1_halos_z"+fileNums[iRedshift] parFile.write(parFileText.format(omegaM=omegaM, hubble=hubble, redshift=redshift, Mmin=1.99526e12, M1=3.80189e13, sigma_logM=0.21, alpha=1.12, Mcut=6.91831e11, haloFile=haloFile, numPartPerSide=numPart**(1/3.), boxSize=lbox)) parFile.close() os.system(hodPath+" "+parFileName+">& /dev/null") sampleName = getSampleName("md.hod_dr72dim2", redshift, False) outFileName = catalogDir+"/"+sampleName+".dat" os.system("mv hod.mock" + " " + outFileName) os.system("rm ./hod.*") # ----------------------------------------------------------------------------- # 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 # these parameters come from Manera et al 2012, eq. 26 parFileName = "./hod.par" parFile = open(parFileName, 'w') haloFile = catalogDir+"/mdr1_halos_z"+fileNums[iRedshift] parFile.write(parFileText.format(omegaM=omegaM, hubble=hubble, redshift=redshift, Mmin=1.23e13, M1=1.e14, sigma_logM=0.596, alpha=1.0127, Mcut=1.19399e13, haloFile=haloFile, numPartPerSide=numPart**(1/3.), boxSize=lbox)) parFile.close() os.system(hodPath+" "+parFileName+">& /dev/null") sampleName = getSampleName("md.hod_dr9mid", redshift, False) outFileName = catalogDir+"/"+sampleName+".dat" os.system("mv hod.mock" + " " + outFileName) os.system("rm ./hod.*")