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Merge branch 'master' of bitbucket.org:cosmicvoids/void_identification

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Guilhem Lavaux 2013-03-06 00:59:38 +01:00
commit aa3410bc78
1 changed files with 58 additions and 44 deletions
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102
python_tools/pipeline_source/prepareCatalogs.in.py
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@ -391,21 +391,22 @@ if (args.script or args.all) and haloFileBase != "":
sys.stdout.flush() sys.stdout.flush()
# estimate number of halos to get density # estimate number of halos to get density
if haloFileDummy == '': #if haloFileDummy == '':
dataFile = catalogDir+haloFileBase+fileNums[0] # dataFile = catalogDir+haloFileBase+fileNums[0]
else: #else:
dataFile = catalogDir+haloFileBase.replace(haloFileDummy, fileNums[0]) # dataFile = catalogDir+haloFileBase.replace(haloFileDummy, fileNums[0])
#
#inFile = open(dataFile, 'r')
#numPart = 0
#for (iLine, line) in enumerate(inFile):
# if iLine < haloFileNumComLines: continue
# line = line.split(haloFileColSep)
# if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
# numPart += 1
#inFile.close()
inFile = open(dataFile, 'r') #minRadius = 2*int(np.ceil(lbox/numPart**(1./3.)))
numPart = 0 minRadies = 10
for (iLine, line) in enumerate(inFile):
if iLine < haloFileNumComLines: continue
line = line.split(haloFileColSep)
if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
numPart += 1
inFile.close()
minRadius = 2*int(np.ceil(lbox/numPart**(1./3.)))
setName = prefix+"halos_min"+str(minHaloMass) setName = prefix+"halos_min"+str(minHaloMass)
writeScript(setName, prefix+"halos_min"+str(minHaloMass)+"_z", "multidark", writeScript(setName, prefix+"halos_min"+str(minHaloMass)+"_z", "multidark",
@ -436,29 +437,40 @@ if (args.halos or args.all) and haloFileBase != "":
fileNums[iRedshift]) fileNums[iRedshift])
inFile = open(dataFile, 'r') inFile = open(dataFile, 'r')
numPart = 0 numPart = 0
for (iLine, line) in enumerate(inFile): if dataFormat == "sdf":
if iLine < haloFileNumComLines: continue for line in inFile:
line = line.split(haloFileColSep) if "nhalos" in line:
if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass: numPart = int(line.split()[3].strip(';'))
numPart += 1 break
inFile.close() inFile.close()
else:
for (iLine, line) in enumerate(inFile):
if iLine < haloFileNumComLines: continue
line = line.split(haloFileColSep)
if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
numPart += 1
inFile.close()
sampleName = prefix+"halos_min"+str(minHaloMass)+"_z"+fileNums[iRedshift] sampleName = prefix+"halos_min"+str(minHaloMass)+"_z"+fileNums[iRedshift]
outFile = open(catalogDir+"/"+sampleName+".dat", 'w') outFileName = catalogDir+"/"+sampleName+".dat"
outFile = open(outFileName, 'w')
outFile.write("%f\n" %(lbox)) outFile.write("%f\n" %(lbox))
outFile.write("%s\n" %(omegaM)) outFile.write("%s\n" %(omegaM))
outFile.write("%s\n" %(hubble)) outFile.write("%s\n" %(hubble))
outFile.write("%s\n" %(redshift)) outFile.write("%s\n" %(redshift))
outFile.write("%d\n" %(numPart)) outFile.write("%d\n" %(numPart))
outFile.close()
if dataFormat == "sdf": if dataFormat == "sdf":
# TODO process halo file with SDFcvt SDFcvt_PATH = "@CMAKE_BINARY_DIR@/external/libsdf/apps/SDFcvt/SDFcvt.x86_64"
SDFcvt_PATH = "@CMAKE_BINARY_DIR@/ep_build/sdf/bin/SDFcvt/" if minHaloMass == "none": minHaloMass = 0.0
outFile = open(catalogDir+"/"+sampleName+".dat", 'w') command = "%s %s mass id x y z vz vy vx | awk '{if ($1>%g) print $2, $3, $4, $5, $6, $7, $8}'>>%s" % (SDFcvt_PATH, dataFile, minHaloMass, outFileName )
os.system(command)
outFile = open(outFileName, 'a')
outFile.write("-99 -99 -99 -99 -99 -99 -99\n") outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
outFile.close() outFile.close()
else: else:
outFile = open(catalogDir+"/"+sampleName+".dat", 'w') outFile = open(outFileName, 'a')
inFile = open(dataFile, 'r') inFile = open(dataFile, 'r')
for (iHalo,line) in enumerate(inFile): for (iHalo,line) in enumerate(inFile):
if iHalo < haloFileNumComLines: continue if iHalo < haloFileNumComLines: continue
@ -525,7 +537,7 @@ if (args.script or args.all) and haloFileBase != "":
print " Doing HOD scripts" print " Doing HOD scripts"
sys.stdout.flush() sys.stdout.flush()
for thisHod in hodParmList: for thisHod in hodParmList:
print " ", thisHod['name'] print " ", thisHod['name']
setName = prefix+"hod_"+thisHod['name'] setName = prefix+"hod_"+thisHod['name']
writeScript(setName, prefix+"hod_"+thisHod['name']+"_z", "multidark", writeScript(setName, prefix+"hod_"+thisHod['name']+"_z", "multidark",
scriptDir, catalogDir, fileNums, redshifts, scriptDir, catalogDir, fileNums, redshifts,
@ -537,28 +549,30 @@ if (args.script or args.all) and haloFileBase != "":
if (args.hod or args.all) and haloFileBase != "": if (args.hod or args.all) and haloFileBase != "":
print " Doing HOD" print " Doing HOD"
sys.stdout.flush() sys.stdout.flush()
for thisHod in hodParmList: for (iRedshift, redshift) in enumerate(redshifts):
print " ", thisHod['name'] print " z = ", redshift
sys.stdout.flush() sys.stdout.flush()
for (iRedshift, redshift) in enumerate(redshifts):
print " z = ", redshift if haloFileDummy == '':
haloFile = catalogDir+haloFileBase+fileNums[iRedshift]
else:
haloFile = catalogDir+haloFileBase.replace(haloFileDummy,
fileNums[iRedshift])
if dataFormat == "sdf":
inFile = haloFile
outFile = haloFile+"_temp"
SDFcvt_PATH = "@CMAKE_BINARY_DIR@/external/libsdf/apps/SDFcvt/SDFcvt.x86_64"
command = "%s %s mass x y z vx vy vz>>%s" % (SDFcvt_PATH, inFile, outFile)
os.system(command)
haloFile = outFile
for thisHod in hodParmList:
print " ", thisHod['name']
sys.stdout.flush() sys.stdout.flush()
parFileName = "./hod.par" parFileName = "./hod.par"
parFile = open(parFileName, 'w') parFile = open(parFileName, 'w')
if haloFileDummy == '':
haloFile = catalogDir+haloFileBase+fileNums[iRedshift]
else:
haloFile = catalogDir+haloFileBase.replace(haloFileDummy,
fileNums[iRedshift])
if dataFormat == "sdf":
# TODO process halo file with SDFcvt
inFile = haloFile
outFile = haloFile+"_temp"
haloFile = outFile
parFile.write(parFileText.format(omegaM=omegaM, parFile.write(parFileText.format(omegaM=omegaM,
hubble=hubble, hubble=hubble,
redshift=redshift, redshift=redshift,
@ -584,6 +598,6 @@ if (args.hod or args.all) and haloFileBase != "":
os.system("mv %s/hod.mock %s" % (catalogDir, outFileName)) os.system("mv %s/hod.mock %s" % (catalogDir, outFileName))
os.system("rm %s/hod.*" % catalogDir) os.system("rm %s/hod.*" % catalogDir)
os.system("rm %s" % haloFile) if dataFormat == "sdf": os.system("rm %s" % haloFile)
print " Done!" print " Done!"