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:
Paul Matthew Sutter
commit
adb35245de
99 changed files with 22172 additions and 128 deletions
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@ -476,9 +476,8 @@ for iSubSample in xrange(len(subSamples)):
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rescale_velocity,
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rescale_velocity,
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convertedFile )
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os.system(command)
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os.system(command)
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#os.system(command)
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subprocess.call(command, shell=True)
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dataFile = convertedFile
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inFile = open(dataFile, 'r')
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@ -670,7 +669,8 @@ if (args.halos or args.all) and haloFileBase != "":
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command = "%s -a 200000 %s mass ident x y z vz vy vx parent_id | awk '{if ($9==-1) print $2, $3, $4, $5, $6, $7, $8, $1}'>>%s" % (SDFcvt_PATH, dataFile, outFileName )
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else:
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command = "%s -a 200000 %s mass ident x y z vz vy vx parent_id | awk '{if ($1>%g && $9==-1) print $2, $3, $4, $5, $6, $7, $8, $1}'>>%s" % (SDFcvt_PATH, dataFile, minHaloMass, outFileName )
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os.system(command)
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#os.system(command)
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subprocess.call(command, shell=True)
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outFile = open(outFileName, 'a')
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outFile.write("-99 -99 -99 -99 -99 -99 -99 -99\n")
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outFile.close()
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@ -737,7 +737,7 @@ 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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root_filename {workDir}/hod_{sampleName}
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"""
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if (args.script or args.all) and haloFileBase != "":
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@ -804,7 +804,8 @@ if (args.hod or args.all) and haloFileBase != "":
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outFile = haloFile+"_temp"
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SDFcvt_PATH = "@CMAKE_BINARY_DIR@/external/libsdf/apps/SDFcvt/SDFcvt.x86_64"
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command = "%s -a 200000 %s mass x y z vx vy vz parent_id | awk '{if ($8 ==-1) print $1, $2, $3, $4, $5, $6, $7}'>>%s" % (SDFcvt_PATH, inFile, outFile)
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os.system(command)
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#os.system(command)
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subprocess.call(command, shell=True)
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haloFile = outFile
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for thisHod in hodParmList:
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@ -826,12 +827,18 @@ if (args.hod or args.all) and haloFileBase != "":
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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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workDir=catalogDir,
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sampleName=sampleName))
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parFile.close()
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sampleName = getSampleName(prefix+"hod_"+thisHod['name'], redshift, False)
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tempFile = "./hod.out_"+sampleName
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os.system(hodPath+" "+parFileName+">& " + tempFile)
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output = open(tempFile, 'w')
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HOD_PATH = "/home/psutter2/projects/Voids/vide/c_tools/hod/hod"
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#os.system(HOD_PATH+" "+parFileName+">& " + tempFile)
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subprocess.call(HOD_PATH+" "+parFileName, stdout=output, stderr=output, shell=True)
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output.close()
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for line in open(tempFile):
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if "MLO" in line:
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print " (minimum halo mass = ", line.split()[1], ")"
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@ -839,7 +846,7 @@ if (args.hod or args.all) and haloFileBase != "":
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os.unlink(tempFile)
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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("mv %s/hod_%s.mock %s" % (catalogDir, sampleName, outFileName))
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os.system("rm %s/hod.*" % catalogDir)
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os.system("rm ./hod.par")
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os.system("rm ./hod-usedvalues")
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@ -89,8 +89,12 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")):
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file(parmFile, mode="w").write(conf)
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cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
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os.system(cmd)
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arg1 = "-configFile=%s" % parmFile
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log = open(logFile, 'w')
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subprocess.call([binPath, arg1], stdout=log, stderr=log)
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log.close()
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#cmd = "%s --configFile=%s >& %s" % (binPath,parmFile,logFile)
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#os.system(cmd)
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if jobSuccessful(logFile, "Done!\n"):
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print "done"
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else:
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@ -206,10 +210,16 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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file(parmFile, mode="w").write(conf)
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if (prevSubSample == -1):
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cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
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#cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
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log = open(logFile, 'w')
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else:
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cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile)
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os.system(cmd)
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#cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile)
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log = open(logFile, 'a')
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arg1 = "--configFile=%s" % parmFile
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subprocess.call([binPath, arg1], stdout=log, stderr=log)
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#subprocess.call([binPath, arg1], stdout=log, stderr=log)
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log.close()
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#os.system(cmd)
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# remove intermediate files
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if (prevSubSample != -1):
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@ -324,24 +334,49 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
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if os.access(zobovDir+"/voidDesc_"+sampleName+".out", os.F_OK):
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os.unlink(zobovDir+"/voidDesc_"+sampleName+".out")
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cmd = "%s/vozinit %s 0.1 1.0 %g %s %g %s %s %s &> %s" % \
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(binPath, datafile, numZobovDivisions, \
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"_"+sampleName, numZobovThreads, \
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binPath, zobovDir, maskIndex, logFile)
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os.system(cmd)
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#cmd = "%s/vozinit %s 0.1 1.0 %g %s %g %s %s %s &> %s" % \
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# (binPath, datafile, numZobovDivisions, \
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# "_"+sampleName, numZobovThreads, \
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# binPath, zobovDir, maskIndex, logFile)
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#os.system(cmd)
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cmd = [binPath+"/vozinit", datafile, "0.1", "1.0", str(numZobovDivisions), \
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"_"+sampleName, str(numZobovThreads), \
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binPath, zobovDir, str(maskIndex)]
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log = open(logFile, 'w')
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subprocess.call(cmd, stdout=log, stderr=log)
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log.close()
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#cmd = "./%s >> %s 2>&1" % (vozScript, logFile)
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#os.system(cmd)
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cmd = ["./%s" % vozScript]
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log = open(logFile, 'a')
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subprocess.call(cmd, stdout=log, stderr=log)
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log.close()
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cmd = "./%s >> %s 2>&1" % (vozScript, logFile)
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os.system(cmd)
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# cmd = "%s/jozov %s %s %s %s %s %g %s >> %s 2>&1" % \
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cmd = "%s/../c_tools/zobov2/jozov2/jozov2 %s %s %s %s %s %g %s >> %s 2>&1" % \
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(binPath, \
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#cmd = "%s/../c_tools/zobov2/jozov2/jozov2 %s %s %s %s %s %g %s >> %s 2>&1" % \
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# (binPath, \
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# zobovDir+"/adj_"+sampleName+".dat", \
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# zobovDir+"/vol_"+sampleName+".dat", \
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# zobovDir+"/voidPart_"+sampleName+".dat", \
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# zobovDir+"/voidZone_"+sampleName+".dat", \
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# zobovDir+"/voidDesc_"+sampleName+".out", \
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# maxDen, maskIndex, logFile)
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#os.system(cmd)
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cmd = [binPath+"../c_tools/zobov2/jozov2/jozov2", \
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zobovDir+"/adj_"+sampleName+".dat", \
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zobovDir+"/vol_"+sampleName+".dat", \
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zobovDir+"/voidPart_"+sampleName+".dat", \
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zobovDir+"/voidZone_"+sampleName+".dat", \
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zobovDir+"/voidDesc_"+sampleName+".out", \
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maxDen, maskIndex, logFile)
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os.system(cmd)
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str(maxDen), str(maskIndex)]
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log = open(logFile, 'a')
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subprocess.call(cmd, stdout=log, stderr=log)
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log.close()
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# don't need the subbox files
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for fileName in glob.glob(zobovDir+"/part._"+sampleName+".*"):
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os.unlink(fileName)
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if jobSuccessful(logFile, "Done!\n"):
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print "done"
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@ -414,11 +449,14 @@ def launchPrune(sample, binPath,
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cmd += useComovingFlag
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cmd += " --outputDir=" + zobovDir
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cmd += " --sampleName=" + str(sampleName)
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cmd += " &> " + logFile
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f=file("run_prune.sh",mode="w")
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f.write(cmd)
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f.close()
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os.system(cmd)
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#cmd += " &> " + logFile
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#f=file("run_prune.sh",mode="w")
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#f.write(cmd)
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#f.close()
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#os.system(cmd)
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log = open(logFile, 'w')
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subprocess.call(cmd, stdout=log, stderr=log, shell=True)
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log.close()
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if jobSuccessful(logFile, "NetCDF: Not a valid ID\n") or \
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jobSuccessful(logFile, "Done!\n"):
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@ -436,7 +474,7 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
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binPath, thisDataPortion=None,
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logFile=None, workDir=None,
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continueRun=None, outputFile=None,
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matchMethod=None):
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matchMethod=None, strictMatch=False):
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sampleName1 = sample1.fullName
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sampleName2 = sample2.fullName
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@ -448,6 +486,11 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
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# periodicLine += "z"
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#periodicLine += "' "
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if strictMatch:
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matchPrefix = ""
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else:
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matchPrefix = "trimmed_nodencut_"
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if not (continueRun and jobSuccessful(logFile, "Done!\n")):
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cmd = binPath
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cmd += " --partFile1=" + sample1Dir+"/zobov_slice_" + \
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@ -471,14 +514,14 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
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str(sampleName2)
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cmd += " --volFile2=" + sample2Dir+"/vol_" + \
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str(sampleName2)+".dat"
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cmd += " --voidFile2=" + sample2Dir+"/trimmed_nodencut_voidDesc_" + \
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cmd += " --voidFile2=" + sample2Dir+"/"+matchPrefix+"voidDesc_" + \
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thisDataPortion+"_"+str(sampleName2)+".out"
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cmd += " --infoFile2=" + sample2Dir+"/zobov_slice_" + \
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str(sampleName2)+".par"
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cmd += " --centerFile2=" + sample2Dir + \
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"/trimmed_nodencut_barycenters_"+thisDataPortion+"_"+str(sampleName2)+".out"
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"/"+matchPrefix+"barycenters_"+thisDataPortion+"_"+str(sampleName2)+".out"
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cmd += " --shapeFile2=" + sample2Dir + \
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"/trimmed_nodencut_shapes_"+thisDataPortion+"_"+str(sampleName2)+".out"
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"/"+matchPrefix+"shapes_"+thisDataPortion+"_"+str(sampleName2)+".out"
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cmd += " --zoneFile2=" + sample2Dir+"/voidZone_" + \
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str(sampleName2)+".dat"
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cmd += " --zonePartFile2=" + sample2Dir+"/voidPart_" + \
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|
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@ -487,9 +530,12 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
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if matchMethod == "useID": cmd += " --useID"
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cmd += periodicLine
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cmd += " --outfile=" + outputFile
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cmd += " &> " + logFile
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open("temp.par",'w').write(cmd)
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os.system(cmd)
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#cmd += " &> " + logFile
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#open("temp.par",'w').write(cmd)
|
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#os.system(cmd)
|
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log = open(logFile, 'w')
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subprocess.call(cmd, stdout=log, stderr=log, shell=True)
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log.close()
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|
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if jobSuccessful(logFile, "Done!\n"):
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print "done"
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|
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@ -585,6 +631,9 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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# periodicLine += "z"
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# periodicLine += "' "
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|
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launchDir = os.getcwd()
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os.chdir(voidDir)
|
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|
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conf="""
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desc %s
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partzone %s
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|
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@ -651,19 +700,26 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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fp.write("doExtraction\n")
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fp.close()
|
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|
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jobString = " "+runSuffix+":"
|
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|
||||
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
|
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cmd = "%s --configFile=%s &> %s" % \
|
||||
(binPath, parmFile, logFile)
|
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os.system(cmd)
|
||||
#cmd = "%s --configFile=%s &> %s" % \
|
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# (binPath, parmFile, logFile)
|
||||
#os.system(cmd)
|
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cmd = "%s --configFile=%s" % \
|
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(binPath, parmFile)
|
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log = open(logFile, 'w')
|
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subprocess.call(cmd, stdout=log, stderr=log, shell=True)
|
||||
log.close()
|
||||
|
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if jobSuccessful(logFile, "Done!\n"):
|
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print "done"
|
||||
print jobString, "Stacking voids done"
|
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else:
|
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print "FAILED!"
|
||||
print jobString, "Stacking voids FAILED!"
|
||||
exit(-1)
|
||||
|
||||
else:
|
||||
print "already done!"
|
||||
print jobString, "Stacking voids already done!"
|
||||
if os.access(parmFile, os.F_OK): os.unlink(parmFile)
|
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return
|
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|
||||
|
|
@ -695,7 +751,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
|
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os.unlink(voidDir+"/NOVOID")
|
||||
|
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if (numVoids == "0"):
|
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print " No voids found; skipping!"
|
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print jobString, "No voids found; skipping!"
|
||||
fp = open(voidDir+"/NOVOID", "w")
|
||||
fp.write("no voids found\n")
|
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fp.close()
|
||||
|
|
@ -706,7 +762,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
|
|||
if "EMPTY STACK" in line:
|
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emptyStack = True
|
||||
if emptyStack:
|
||||
print " Stack is empty; skipping!"
|
||||
print jobString, "Stack is empty; skipping!"
|
||||
fp = open(voidDir+"/NOVOID", "w")
|
||||
fp.write("empty stack\n")
|
||||
fp.close()
|
||||
|
|
@ -722,7 +778,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
|
|||
exit(-1)
|
||||
|
||||
sys.stdout = open(logFile, 'a')
|
||||
sys.stderr = open(logFile, 'a')
|
||||
#sys.stderr = open(logFile, 'a')
|
||||
zMin = sample.zRange[0]
|
||||
zMax = sample.zRange[1]
|
||||
if not sample.volumeLimited:
|
||||
|
|
@ -734,8 +790,10 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
|
|||
zMaxForVol = sample.zBoundary[1]
|
||||
props = vp.getSurveyProps(maskFile, zMinForVol,
|
||||
zMaxForVol, zMin, zMax, "all")
|
||||
props = ((1.0,1.0))
|
||||
|
||||
sys.stdout = sys.__stdout__
|
||||
sys.stderr = sys.__stderr__
|
||||
#sys.stderr = sys.__stderr__
|
||||
|
||||
boxVol = props[0]
|
||||
nbar = props[1]
|
||||
|
|
@ -773,30 +831,32 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
|
|||
fp.write(str(normalization)+"\n")
|
||||
fp.close()
|
||||
|
||||
os.system("mv %s %s" % ("tree.data", treeFile))
|
||||
os.system("mv %s %s" % ("void_indexes.txt", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("posx.nc", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("posy.nc", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("posz.nc", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("z_void_indexes.txt", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("z_posx.nc", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("z_posy.nc", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("z_posz.nc", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("redshifts.nc", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("indexes.nc", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("kdtree_stackvoids.dat", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("centers.txt", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("z_centers.txt", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("sky_positions.txt", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("check.txt", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("tracer.txt", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("normalizations.txt", voidDir+"/"))
|
||||
os.system("mv %s %s" % ("boundaryDistances.txt", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("tree.data", treeFile))
|
||||
#os.system("mv %s %s" % ("void_indexes.txt", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("posx.nc", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("posy.nc", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("posz.nc", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("z_void_indexes.txt", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("z_posx.nc", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("z_posy.nc", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("z_posz.nc", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("redshifts.nc", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("indexes.nc", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("kdtree_stackvoids.dat", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("centers.txt", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("z_centers.txt", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("sky_positions.txt", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("check.txt", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("tracer.txt", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("normalizations.txt", voidDir+"/"))
|
||||
#os.system("mv %s %s" % ("boundaryDistances.txt", voidDir+"/"))
|
||||
|
||||
if os.access(idListFile, os.F_OK): os.unlink(idListFile)
|
||||
|
||||
if os.access(parmFile, os.F_OK): os.unlink(parmFile)
|
||||
|
||||
os.chdir(launchDir)
|
||||
|
||||
return
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
|
|
@ -807,9 +867,10 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
|
|||
|
||||
runSuffix = getStackSuffix(stack.zMin, stack.zMax, stack.rMin,
|
||||
stack.rMax, thisDataPortion)
|
||||
jobString = " "+runSuffix+":"
|
||||
|
||||
sys.stdout = open(logFile, 'w')
|
||||
sys.stderr = open(logFile, 'a')
|
||||
#sys.stderr = open(logFile, 'a')
|
||||
|
||||
if os.access(voidDir+"/num_voids.txt", os.F_OK):
|
||||
os.unlink(voidDir+"/num_voids.txt")
|
||||
|
|
@ -1029,24 +1090,29 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
|
|||
print "Done!"
|
||||
|
||||
sys.stdout = sys.__stdout__
|
||||
sys.stderr = sys.__stderr__
|
||||
#sys.stderr = sys.__stderr__
|
||||
|
||||
if jobSuccessful(logFile, "Done!\n"):
|
||||
print "done"
|
||||
print jobString, "Combining stacks done"
|
||||
else:
|
||||
print "FAILED!"
|
||||
print jobString, "Combining stacks FAILED!"
|
||||
exit(-1)
|
||||
|
||||
#else:
|
||||
# print "already done!"
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None):
|
||||
def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
|
||||
thisDataPortion=None):
|
||||
|
||||
sampleName = sample.fullName
|
||||
|
||||
runSuffix = getStackSuffix(stack.zMin, stack.zMax, stack.rMin,
|
||||
stack.rMax, thisDataPortion)
|
||||
jobString = " "+runSuffix+":"
|
||||
|
||||
if os.access(voidDir+"/NOVOID", os.F_OK):
|
||||
print "no stack here; skipping!"
|
||||
print jobString, "Profile no stack here; skipping!"
|
||||
return
|
||||
|
||||
numVoids = open(voidDir+"/num_voids.txt", "r").readline()
|
||||
|
|
@ -1077,21 +1143,21 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None):
|
|||
density = sample.profileBinSize
|
||||
|
||||
sys.stdout = open(logFile, 'w')
|
||||
sys.stderr = open(logFile, 'a')
|
||||
#sys.stderr = open(logFile, 'a')
|
||||
vp.build_1d_profile(base_dir=voidDir, density=density,
|
||||
rescaleMode=stack.rescaleMode)
|
||||
vp.build_2d_profile(base_dir=voidDir, density=density)
|
||||
sys.stdout = sys.__stdout__
|
||||
sys.stderr = sys.__stderr__
|
||||
#sys.stderr = sys.__stderr__
|
||||
|
||||
if jobSuccessful(logFile, "Done!\n"):
|
||||
print "done", numVoids
|
||||
print jobString, "Profiling stacks done, (N_v=", numVoids,")"
|
||||
else:
|
||||
print "FAILED!"
|
||||
print jobString, "Profiling stacks FAILED!"
|
||||
exit(-1)
|
||||
|
||||
else:
|
||||
print "already done!"
|
||||
print jobString, "Profiling stacks already done!"
|
||||
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
|
|
@ -1103,14 +1169,16 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
|
|||
runSuffix = getStackSuffix(stack.zMin, stack.zMax, stack.rMin,
|
||||
stack.rMax, thisDataPortion)
|
||||
|
||||
jobString = " "+runSuffix+":"
|
||||
|
||||
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
|
||||
if os.access(voidDir+"/NOVOID", os.F_OK):
|
||||
print "no voids here; skipping!"
|
||||
print jobString, "Fitting no voids here; skipping!"
|
||||
return
|
||||
|
||||
numVoids = int(open(voidDir+"/num_voids.txt", "r").readline())
|
||||
if numVoids < 10:
|
||||
print "not enough voids to fit; skipping!"
|
||||
print jobString, "Fitting not enough voids to fit; skipping!"
|
||||
fp = open(voidDir+"/NOFIT", "w")
|
||||
fp.write("not enough voids: %d \n" % numVoids)
|
||||
fp.close()
|
||||
|
|
@ -1121,18 +1189,18 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
|
|||
# return
|
||||
|
||||
if sample.partOfCombo or not sample.includeInHubble:
|
||||
print "sample not needed for further analysis; skipping!"
|
||||
print jobString, "Fitting sample not needed for further analysis; skipping!"
|
||||
fp = open(voidDir+"/NOFIT", "w")
|
||||
fp.write("sample not needed for hubble\n")
|
||||
fp.close()
|
||||
return
|
||||
|
||||
if not stack.includeInHubble:
|
||||
print "radius not needed for further analysis; skipping!"
|
||||
print jobString, "Fitting radius not needed for further analysis; skipping!"
|
||||
return
|
||||
|
||||
if not stack.includeInHubble:
|
||||
print "redshift not needed for further analysis; skipping!"
|
||||
print jobString, "Fitting redshift not needed for further analysis; skipping!"
|
||||
return
|
||||
|
||||
if os.access(figDir+"/stackedVoid_"+sampleName+"_"+\
|
||||
|
|
@ -1141,14 +1209,16 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
|
|||
runSuffix+".eps")
|
||||
|
||||
sys.stdout = open(logFile, 'w')
|
||||
sys.stderr = open(logFile, 'a')
|
||||
#sys.stderr = open(logFile, 'a')
|
||||
|
||||
badChain = True
|
||||
ntries = 0
|
||||
maxtries = 5
|
||||
while badChain:
|
||||
Rexpect = (stack.rMin+stack.rMax)/2
|
||||
Rtruncate = stack.rMin*3. + 1 # TEST
|
||||
ntries += 1
|
||||
|
||||
#Rexpect = (stack.rMin+stack.rMax)/2
|
||||
#Rtruncate = stack.rMin*3. + 1 # TEST
|
||||
#if sample.dataType == "observation":
|
||||
# ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
|
||||
# Niter=300000,
|
||||
|
|
@ -1156,15 +1226,16 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
|
|||
# Rextracut=Rtruncate)
|
||||
#else:
|
||||
# ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
|
||||
# Niter=300000,
|
||||
# Niter=500000,
|
||||
# Nburn=100000,
|
||||
# Rextracut=Rtruncate)
|
||||
# Rextracut=Rtruncate)
|
||||
#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, mode="symmetric", nBootstraps=500)
|
||||
#ret,fits,args = vp.compute_radial_inertia(voidDir, stack.rMax, mode="symmetric", nBootstraps=5)
|
||||
ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, nBootstraps=100, rMaxInertia=1.0)
|
||||
#ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="symmetric", nBootstraps=500, rMaxInertia=1.5)
|
||||
badChain = False
|
||||
ntries += 1
|
||||
|
||||
#np.save(voidDir+"/chain.npy", ret)
|
||||
np.savetxt(voidDir+"/fits.out", fits)
|
||||
|
|
@ -1196,11 +1267,11 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
|
|||
|
||||
print "Done!"
|
||||
sys.stdout = sys.__stdout__
|
||||
sys.stderr = sys.__stderr__
|
||||
#sys.stderr = sys.__stderr__
|
||||
if jobSuccessful(logFile, "Done!\n"):
|
||||
print "done (", ntries, " tries)"
|
||||
print jobString, "Fitting done (", ntries, " tries)"
|
||||
else:
|
||||
print "FAILED!"
|
||||
print jobString, "Fitting FAILED!"
|
||||
exit(-1)
|
||||
|
||||
# record the measured stretch
|
||||
|
|
@ -1212,14 +1283,14 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
|
|||
if os.access(voidDir+"/NOFIT", os.F_OK):
|
||||
os.unlink(voidDir+"/NOFIT")
|
||||
if ntries > maxtries:
|
||||
print " No reliable fit found; skipping!"
|
||||
print jobString, " No reliable fit found; skipping!"
|
||||
fp = open(voidDir+"/NOFIT", "w")
|
||||
fp.write("bad ellipticity fit\n")
|
||||
fp.close()
|
||||
return
|
||||
|
||||
else:
|
||||
print "already done!"
|
||||
print jobString, "already done!"
|
||||
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
|
|
@ -1289,7 +1360,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
aveDist = vp.aveStretchCone(stack.zMin, stack.zMax,
|
||||
skyFrac = sample.skyFraction)
|
||||
else:
|
||||
aveDist = vp.aveStretch(stack.zMin, stack.zMax)
|
||||
aveDist = vp.aveStretch(stack.zMin, stack.zMax, Om=sample.omegaM)
|
||||
|
||||
aveDistList[iZBin, 0] = stack.zMin
|
||||
aveDistList[iZBin, 1] = aveDist
|
||||
|
|
@ -1338,7 +1409,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
aveDist = vp.aveStretchCone(zBin.zMin, zBin.zMax,
|
||||
skyFrac = sample.skyFraction)
|
||||
else:
|
||||
aveDist = vp.aveStretch(zBin.zMin, zBin.zMax)
|
||||
aveDist = vp.aveStretch(zBin.zMin, zBin.zMax, Om=sample.omegaOm)
|
||||
|
||||
expList[0, iR, iZBin, 2] = aveDist
|
||||
|
||||
|
|
@ -1374,7 +1445,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
|
||||
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
|
||||
sys.stdout = open(logFile, 'w')
|
||||
sys.stderr = open(logFile, 'a')
|
||||
#sys.stderr = open(logFile, 'a')
|
||||
plotTitle = "Sample: "+sample.nickName+", "+thisDataPortion+" voids"
|
||||
if doPlot:
|
||||
#vp.do_all_obs(zbase, expList, workDir+"/avedistortion_",
|
||||
|
|
@ -1390,7 +1461,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
print "Skipping plot"
|
||||
print "Done!"
|
||||
sys.stdout = sys.__stdout__
|
||||
sys.stderr = sys.__stderr__
|
||||
#sys.stderr = sys.__stderr__
|
||||
|
||||
if jobSuccessful(logFile, "Done!\n"):
|
||||
print "done"
|
||||
|
|
@ -1405,7 +1476,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
print " For data set combined...",
|
||||
sys.stdout.flush()
|
||||
|
||||
logFile = logDir+"/hubble_combined_"+thisDataPortion+".out"
|
||||
logFile = logDir+"/hubble_combined_"+sampleName+"_"+thisDataPortion+".out"
|
||||
|
||||
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
|
||||
|
||||
|
|
@ -1453,6 +1524,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
aveDistList[iZ, 0] = zBin.zMin
|
||||
aveDistList[iZ, 1] = aveDist
|
||||
aveDistList[iZ, 2] = 0.00125
|
||||
if plotZmax > 1.5: plotZmax = 1.5
|
||||
|
||||
|
||||
shortSampleNames = list()
|
||||
|
|
@ -1460,7 +1532,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
if sample.includeInHubble:
|
||||
shortSampleNames.append(sample.nickName)
|
||||
sys.stdout = open(logFile, 'w')
|
||||
sys.stderr = open(logFile, 'a')
|
||||
#sys.stderr = open(logFile, 'a')
|
||||
if doPlot:
|
||||
if INCOHERENT:
|
||||
#plotTitle = "all samples, incoherent "+\
|
||||
|
|
@ -1473,12 +1545,15 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
vp.do_all_obs(zbase, allExpList, aveDistList,
|
||||
rlist, plotTitle=plotTitle, sampleNames=shortSampleNames,
|
||||
plotAve=True, mulfac = 1.0, biasLine = 1.16,
|
||||
plotZmin=plotZmin, plotZmax=plotZmax+0.2)
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+thisDataPortion+\
|
||||
plotZmin=plotZmin, plotZmax=plotZmax)
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+setName+"_"+ \
|
||||
thisDataPortion+\
|
||||
".eps",bbox_inches='tight')
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+thisDataPortion+\
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+setName+"_"+ \
|
||||
thisDataPortion+\
|
||||
".pdf",bbox_inches='tight')
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+thisDataPortion+\
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+setName+"_"+ \
|
||||
thisDataPortion+\
|
||||
".png",bbox_inches='tight')
|
||||
|
||||
if INCOHERENT:
|
||||
|
|
@ -1491,18 +1566,21 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
vp.do_all_obs(zbase, allExpList, aveDistList,
|
||||
rlist, plotTitle=plotTitle, sampleNames=shortSampleNames,
|
||||
plotAve=True, mulfac = 1.16,
|
||||
plotZmin=plotZmin, plotZmax=plotZmax+0.2)
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+thisDataPortion+\
|
||||
plotZmin=plotZmin, plotZmax=plotZmax)
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+setName+"_"+\
|
||||
thisDataPortion+\
|
||||
"_debiased.eps",bbox_inches='tight')
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+thisDataPortion+\
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+setName+"_"+\
|
||||
thisDataPortion+\
|
||||
"_debiased.pdf",bbox_inches='tight')
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+thisDataPortion+\
|
||||
figure(1).savefig(figDir+"/hubble_combined_"+setName+"_"+\
|
||||
thisDataPortion+\
|
||||
"_debiased.png",bbox_inches='tight')
|
||||
else:
|
||||
print "Skipping plot"
|
||||
print "Done!"
|
||||
sys.stdout = sys.__stdout__
|
||||
sys.stderr = sys.__stderr__
|
||||
#sys.stderr = sys.__stderr__
|
||||
|
||||
# save all expansion data to a single file
|
||||
fp = file(workDir+'/calculatedExpansions_'+thisDataPortion+'.txt',
|
||||
|
|
@ -1540,8 +1618,13 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
|
|||
voidRedshifts = np.loadtxt(centersFile)
|
||||
if voidRedshifts.ndim > 1:
|
||||
voidRedshifts = voidRedshifts[:,5]
|
||||
np.savetxt(fp, voidRedshifts[None])
|
||||
else:
|
||||
voidRedshifts = voidRedshifts[5]
|
||||
if (len(voidRedshifts) > 0):
|
||||
voidRedshifts = voidRedshifts[5]
|
||||
np.savetxt(fp, voidRedshifts[None])
|
||||
else:
|
||||
fp.write("-1\n")
|
||||
#fp.write(str(len(voidRedshifts))+" ")
|
||||
np.savetxt(fp, voidRedshifts[None])
|
||||
else:
|
||||
|
|
@ -1571,7 +1654,7 @@ def launchLikelihood(dataPortions=None, logDir=None, workDir=None,
|
|||
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
|
||||
|
||||
sys.stdout = open(logFile, 'w')
|
||||
sys.stderr = open(logFile, 'a')
|
||||
#sys.stderr = open(logFile, 'a')
|
||||
|
||||
vp.build1dLikelihood(workDir+"/calculatedExpansions_"+\
|
||||
thisDataPortion+".txt",
|
||||
|
|
@ -1588,7 +1671,7 @@ def launchLikelihood(dataPortions=None, logDir=None, workDir=None,
|
|||
useBinAve = False)
|
||||
|
||||
sys.stdout = sys.__stdout__
|
||||
sys.stderr = sys.__stderr__
|
||||
#sys.stderr = sys.__stderr__
|
||||
|
||||
if jobSuccessful(logFile, "Done!\n"):
|
||||
print "done"
|
||||
|
|
@ -1724,8 +1807,12 @@ def launchVelocityStack(sample, stack, binPath,
|
|||
parameters="--velocityField=%s --voidCenters=%s --Rmax=%e --L0=%e --numBins=%d" % (velField_file, voidCenters, Rmax, Boxsize, numBins)
|
||||
|
||||
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
|
||||
cmd = "%s %s &> %s" % (binPath,parameters,logFile)
|
||||
os.system(cmd)
|
||||
#cmd = "%s %s &> %s" % (binPath,parameters,logFile)
|
||||
#os.system(cmd)
|
||||
cmd = "%s %s" % (binPath,parameters)
|
||||
log = open(logFile, 'w')
|
||||
subprocess.call(cmd, stdout=log, stderr=log, shell=True)
|
||||
log.close()
|
||||
if jobSuccessful(logFile, "Done!\n"):
|
||||
print "done"
|
||||
else:
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue