mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
Merge branch 'master' of https://bitbucket.org/cosmicvoids/void_identification
This commit is contained in:
Guilhem Lavaux
commit
ecb4479178
98 changed files with 20520 additions and 493 deletions
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@ -235,17 +235,20 @@ for thisSubSample in sorted(subSamples, reverse=True):
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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 == "multidark":
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subSampleToUse = 1.0
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fileToUse = prefix+"ss"+str(thisSubSample)+"_z"
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suffix = ".dat"
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elif dataFormat == "gadget":
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subSampleToUse = thisSubSample
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subSampleToUse = keepFraction
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#subSampleToUse = thisSubSample
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fileToUse = particleFileBase
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suffix = ""
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elif dataFormat == "lanl":
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subSampleToUse = thisSubSample
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subSampleToUse = keepFraction
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#subSampleToUse = thisSubSample
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fileToUse = particleFileBase
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suffix = ""
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elif dataFormat == "random":
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@ -264,9 +267,11 @@ for thisSubSample in sorted(subSamples, reverse=True):
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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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@ -296,7 +301,7 @@ for thisSubSample in sorted(subSamples, reverse=True):
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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 numKept > maxKeep: break
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if (prevSubSample == -1):
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line = line.split(',')
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@ -304,8 +309,10 @@ for thisSubSample in sorted(subSamples, reverse=True):
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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\n" %(uniqueID,x,y,z,vz))
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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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@ -328,7 +335,7 @@ for thisSubSample in sorted(subSamples, reverse=True):
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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 %e\n" % (i, x,y,z, 0.))
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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\n")
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outFile.close()
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@ -341,9 +348,14 @@ 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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dataFile = catalogDir+haloFileBase+fileNums[0]
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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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@ -367,14 +379,21 @@ if (args.script or args.all) and haloFileBase != "":
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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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dataFile = catalogDir+haloFileBase+fileNums[iRedshift]
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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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@ -402,16 +421,18 @@ if (args.halos or args.all) and haloFileBase != "":
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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\n" %(iHalo,x,y,z,vz))
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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\n")
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inFile.close()
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outFile.close()
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# -----------------------------------------------------------------------------
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# now the SDSS HOD
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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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@ -454,91 +475,56 @@ 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 DR7 HOD scripts"
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setName = prefix+"hod_dr72dim2"
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writeScript(setName, prefix+"hod_dr72dim2_z", dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, 5, omegaM)
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writeScript(setName, prefix+"hod_dr72dim2_z", dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, 5, omegaM)
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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 DR7 HOD"
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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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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haloFile = catalogDir+haloFileBase+fileNums[iRedshift]
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parFile.write(parFileText.format(omegaM=omegaM,
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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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parFile.write(parFileText.format(omegaM=omegaM,
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hubble=hubble,
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redshift=redshift,
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Mmin=1.99526e12,
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M1=3.80189e13,
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sigma_logM=0.21,
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alpha=1.12,
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Mcut=6.91831e11,
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galden=0.02,
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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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sampleName = getSampleName(prefix+"hod_dr72dim2", 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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# -----------------------------------------------------------------------------
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# now the BOSS HOD
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if (args.script or args.all) and haloFileBase != "":
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print " Doing DR9 HOD scripts"
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setName = prefix+"hod_dr9mid"
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writeScript(setName, prefix+"hod_dr9mid_z", dataFormat,
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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_dr9mid_z", dataFormat,
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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 DR9 HOD"
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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# these parameters come from Manera et al 2012, eq. 26
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# modified to match the observed galaxy density
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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=0.0,
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Mmin=thisHod['Mmin'],
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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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galden=galDens,
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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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parFile.close()
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os.system(hodPath+" "+parFileName+">& /dev/null")
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os.system(hodPath+" "+parFileName+">& /dev/null")
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sampleName = getSampleName(prefix+"hod_dr9mid", 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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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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|
|
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@ -276,7 +276,8 @@ def launchPrune(sample, binPath, thisDataPortion=None,
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periodicLine += "' "
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periodicLine = ""
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if not (continueRun and jobSuccessful(logFile, "NetCDF: Not a valid ID\n")):
|
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if not (continueRun and (jobSuccessful(logFile, "NetCDF: Not a valid ID\n") \
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or jobSuccessful(logFile, "Done!\n"))):
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cmd = binPath
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cmd += " --partFile=" + zobovDir+"/zobov_slice_"+str(sampleName)
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cmd += " --voidDesc=" + zobovDir+"/voidDesc_"+str(sampleName)+".out"
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@ -310,6 +311,9 @@ def launchPrune(sample, binPath, thisDataPortion=None,
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cmd += " --outSkyPositions=" + zobovDir+"/sky_positions_"+\
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str(thisDataPortion)+"_"+\
|
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str(sampleName)+".out"
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cmd += " --outShapes=" + zobovDir+"/shapes_"+\
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str(thisDataPortion)+"_"+\
|
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str(sampleName)+".out"
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cmd += " --outDistances=" + zobovDir+"/boundaryDistances_"+\
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str(thisDataPortion)+"_"+\
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str(sampleName)+".out"
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@ -682,10 +686,15 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
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shutil.copy(sourceStackDir+"/posx.nc", voidDir)
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shutil.copy(sourceStackDir+"/posy.nc", voidDir)
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shutil.copy(sourceStackDir+"/posz.nc", voidDir)
|
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shutil.copy(sourceStackDir+"/z_posx.nc", voidDir)
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||||
shutil.copy(sourceStackDir+"/z_posy.nc", voidDir)
|
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shutil.copy(sourceStackDir+"/z_posz.nc", voidDir)
|
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shutil.copy(sourceStackDir+"/indexes.nc", voidDir)
|
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shutil.copy(sourceStackDir+"/redshifts.nc", voidDir)
|
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shutil.copy(sourceStackDir+"/centers.txt", voidDir)
|
||||
shutil.copy(sourceStackDir+"/void_indexes.txt", voidDir)
|
||||
shutil.copy(sourceStackDir+"/z_centers.txt", voidDir)
|
||||
shutil.copy(sourceStackDir+"/z_void_indexes.txt", voidDir)
|
||||
shutil.copy(sourceStackDir+"/sky_positions.txt", voidDir)
|
||||
shutil.copy(sourceStackDir+"/normalizations.txt", voidDir)
|
||||
shutil.copy(sourceStackDir+"/boundaryDistances.txt", voidDir)
|
||||
|
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@ -710,20 +719,73 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
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dataTemp = str(dataTemp[0])
|
||||
file(voidDir+"/num_particles.txt", "w").write(str(dataTemp))
|
||||
|
||||
dataTemp = file(sourceStackDir+"/z_centers.txt", "r").read()
|
||||
file(voidDir+"/z_centers.txt", "a").write(dataTemp)
|
||||
|
||||
dataTemp = file(sourceStackDir+"/centers.txt", "r").read()
|
||||
file(voidDir+"/centers.txt", "a").write(dataTemp)
|
||||
dataTemp = file(sourceStackDir+"/normalizations.txt", "r").\
|
||||
read()
|
||||
|
||||
dataTemp = file(sourceStackDir+"/normalizations.txt", "r").read()
|
||||
file(voidDir+"/normalizations.txt", "a").write(dataTemp)
|
||||
|
||||
dataTemp = file(sourceStackDir+"/boundaryDistances.txt","r").\
|
||||
read()
|
||||
dataTemp = file(sourceStackDir+"/boundaryDistances.txt","r").read()
|
||||
file(voidDir+"/boundaryDistances.txt", "a").write(dataTemp)
|
||||
|
||||
dataTemp = file(sourceStackDir+"/sky_positions.txt", "r").\
|
||||
read()
|
||||
file(voidDir+"/sky_positions.txt", "a").write(dataTemp)
|
||||
|
||||
idxTemp = file(sourceStackDir+"/z_void_indexes.txt", "r").\
|
||||
readlines()
|
||||
idxTemp = np.array(idxTemp, dtype='i')
|
||||
dataTemp = (NetCDFFile(voidDir+"/z_posx.nc").\
|
||||
variables['array'])[0:]
|
||||
idxTemp[:] += len(dataTemp)
|
||||
fp = open(voidDir+"/z_void_indexes.txt", "a")
|
||||
for idx in idxTemp:
|
||||
fp.write(str(idx)+"\n")
|
||||
fp.close()
|
||||
dataTemp = ()
|
||||
|
||||
fp = NetCDFFile(voidDir+"/z_posx.nc")
|
||||
dataTemp = fp.variables['array'][0:]
|
||||
fp.close()
|
||||
fp = NetCDFFile(sourceStackDir+"/z_posx.nc")
|
||||
dataTemp2 = fp.variables['array'][0:]
|
||||
fp.close()
|
||||
dataTemp = np.append(dataTemp, dataTemp2)
|
||||
outFile = NetCDFFile(voidDir+"/z_posx.nc", mode='w')
|
||||
outFile.createDimension("dim", len(dataTemp))
|
||||
v = outFile.createVariable("array", ncFloat, ("dim",))
|
||||
v[:] = dataTemp
|
||||
outFile.close()
|
||||
|
||||
fp = NetCDFFile(voidDir+"/z_posy.nc")
|
||||
dataTemp = fp.variables['array'][0:]
|
||||
fp.close()
|
||||
fp = NetCDFFile(sourceStackDir+"/z_posy.nc")
|
||||
dataTemp2 = fp.variables['array'][0:]
|
||||
fp.close()
|
||||
dataTemp = np.append(dataTemp, dataTemp2)
|
||||
outFile = NetCDFFile(voidDir+"/z_posy.nc", mode='w')
|
||||
outFile.createDimension("dim", len(dataTemp))
|
||||
v = outFile.createVariable("array", ncFloat, ("dim",))
|
||||
v[:] = dataTemp
|
||||
outFile.close()
|
||||
|
||||
fp = NetCDFFile(voidDir+"/z_posz.nc")
|
||||
dataTemp = fp.variables['array'][0:]
|
||||
fp.close()
|
||||
fp = NetCDFFile(sourceStackDir+"/z_posz.nc")
|
||||
dataTemp2 = fp.variables['array'][0:]
|
||||
fp.close()
|
||||
dataTemp = np.append(dataTemp, dataTemp2)
|
||||
outFile = NetCDFFile(voidDir+"/z_posz.nc", mode='w')
|
||||
outFile.createDimension("dim", len(dataTemp))
|
||||
v = outFile.createVariable("array", ncFloat, ("dim",))
|
||||
v[:] = dataTemp
|
||||
outFile.close()
|
||||
|
||||
idxTemp = file(sourceStackDir+"/void_indexes.txt", "r").\
|
||||
readlines()
|
||||
idxTemp = np.array(idxTemp, dtype='i')
|
||||
|
|
@ -775,6 +837,7 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
|
|||
v[:] = dataTemp
|
||||
outFile.close()
|
||||
|
||||
|
||||
fp = NetCDFFile(voidDir+"/redshifts.nc")
|
||||
dataTemp = fp.variables['array'][0:]
|
||||
fp.close()
|
||||
|
|
@ -892,6 +955,14 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
|
|||
print "no voids here; skipping!"
|
||||
return
|
||||
|
||||
numVoids = int(open(voidDir+"/num_voids.txt", "r").readline())
|
||||
if numVoids < 15:
|
||||
print "not enough voids to fit; skipping!"
|
||||
fp = open(voidDir+"/NOFIT", "w")
|
||||
fp.write("not enough voids: %d \n" % numVoids)
|
||||
fp.close()
|
||||
return
|
||||
|
||||
if stack.zMin < sample.zRange[0] or stack.zMax > sample.zRange[1]:
|
||||
print "outside sample redshift range; skipping!"
|
||||
return
|
||||
|
|
@ -938,7 +1009,7 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
|
|||
#badChain = (args[0][0] > 0.5 or args[0][1] > stack.rMax or \
|
||||
# args[0][2] > stack.rMax) and \
|
||||
# (ntries < maxtries)
|
||||
ret,fits,args = vp.compute_inertia(voidDir, stack.rMax)
|
||||
ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="symmetric")
|
||||
badChain = False
|
||||
ntries += 1
|
||||
|
||||
|
|
@ -1003,7 +1074,7 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
|
|||
def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
||||
INCOHERENT=None, workDir=None, figDir=None, errorBars=None,
|
||||
ZOBOV_PATH=None, continueRun=None, voidDir=None,
|
||||
doPlot = True):
|
||||
doPlot = True, setName=None):
|
||||
|
||||
for thisDataPortion in dataPortions:
|
||||
print " For data portion", thisDataPortion
|
||||
|
|
@ -1239,13 +1310,15 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
sys.stdout = open(logFile, 'w')
|
||||
sys.stderr = open(logFile, 'a')
|
||||
if doPlot:
|
||||
print "DOING PLOT"
|
||||
if INCOHERENT:
|
||||
#plotTitle = "all samples, incoherent "+\
|
||||
# thisDataPortion+" voids"
|
||||
plotTitle = ''
|
||||
else:
|
||||
#plotTitle = "all samples, "+thisDataPortion+" voids"
|
||||
plotTitle = ''
|
||||
plotTitle = setName
|
||||
#plotTitle = ''
|
||||
vp.do_all_obs(zbase, allExpList, aveDistList,
|
||||
rlist, plotTitle=plotTitle, sampleNames=shortSampleNames,
|
||||
plotAve=True, mulfac = 1.0, biasLine = 1.16,
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue