mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
- fixed bug where omegaM was always 0.3 regardless of user input
- wrote out flagging of boundary and edge galaxies - turned off placing of boundary particles
This commit is contained in:
Paul M. Sutter
parent
aded7a7c2c
commit
f59fee9bf8
4 changed files with 164 additions and 102 deletions
|
|
@ -47,25 +47,36 @@ LIGHT_SPEED = 299792.458
|
|||
|
||||
# -----------------------------------------------------------------------------
|
||||
def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
|
||||
zobovDir=None, figDir=None, logFile=None, useComoving=False,
|
||||
outputDir=None, figDir=None, logFile=None, useComoving=False,
|
||||
continueRun=None, regenerate=False):
|
||||
|
||||
if sample.dataType == "observation":
|
||||
sampleName = sample.fullName
|
||||
|
||||
if regenerate:
|
||||
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+sampleName+".par"
|
||||
outputFile = zobovDir+"/regenerated_zobov_slice_" + sampleName
|
||||
inputParameterFlag = "inputParameter " + outputDir +
|
||||
"/zobov_slice_"+sampleName+".par"
|
||||
outputFile = outputDir + "/regenerated_zobov_slice_" + sampleName
|
||||
else:
|
||||
inputParameterFlag = ""
|
||||
outputFile = zobovDir+"/zobov_slice_" + sampleName
|
||||
outputFile = outputDir + "/zobov_slice_" + sampleName
|
||||
|
||||
if sample.dataFile == "":
|
||||
datafile = inputDataDir+"/"+sampleName
|
||||
else:
|
||||
datafile = inputDataDir+"/"+sample.dataFile
|
||||
|
||||
maskFile = sample.maskFile
|
||||
if sample.maskFile == "":
|
||||
maskFile = outputDir + "/constructed_mask.fits"
|
||||
figureOutMask(dataFile, sample.nsideForMask, maskFile)
|
||||
else:
|
||||
maskFile = sample.maskFile
|
||||
|
||||
edgeGalFile = outputDir + "/galaxy_edge_flags.txt"
|
||||
edgeMaskFile = outputDir + "/mask_edge_map.fits"
|
||||
findEdgeGalaxies(dataFile, maskFile, edgeGalFile, edgeMaskFile,
|
||||
sample.zBoundary[0], sample.zBoundary[1], sample.omegaM,
|
||||
useComoving)
|
||||
|
||||
if useComoving:
|
||||
useComovingFlag = "useComoving"
|
||||
|
|
@ -84,7 +95,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
|
|||
%s
|
||||
omegaM %g
|
||||
""" % (datafile, maskFile, outputFile,
|
||||
zobovDir+"/zobov_slice_"+sampleName+".par",
|
||||
outputDir+"/zobov_slice_"+sampleName+".par",
|
||||
sample.zBoundary[0], sample.zBoundary[1], sample.fakeDensity,
|
||||
useComovingFlag, inputParameterFlag, sample.omegaM)
|
||||
|
||||
|
|
@ -108,21 +119,21 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
|
|||
if os.access(parmFile, os.F_OK): os.unlink(parmFile)
|
||||
|
||||
if os.access("contour_map.fits", os.F_OK):
|
||||
os.system("mv %s %s" % ("contour_map.fits", zobovDir))
|
||||
os.system("mv %s %s" % ("mask_map.fits", zobovDir))
|
||||
os.system("mv %s %s" % ("contour_map.fits", outputDir))
|
||||
os.system("mv %s %s" % ("mask_map.fits", outputDir))
|
||||
|
||||
if os.access("comoving_distance.txt", os.F_OK):
|
||||
os.system("mv %s %s" % ("comoving_distance.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("comoving_distance.txt", outputDir))
|
||||
|
||||
if os.access("mask_index.txt", os.F_OK):
|
||||
os.system("mv %s %s" % ("mask_index.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("total_particles.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("mask_index.txt", outputDir))
|
||||
os.system("mv %s %s" % ("total_particles.txt", outputDir))
|
||||
|
||||
if os.access("galaxies.txt", os.F_OK):
|
||||
os.system("mv %s %s" % ("galaxies.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("mock_galaxies.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("mock_boundary.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("mock_sphere.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("galaxies.txt", outputDir))
|
||||
os.system("mv %s %s" % ("mock_galaxies.txt", outputDir))
|
||||
os.system("mv %s %s" % ("mock_boundary.txt", outputDir))
|
||||
os.system("mv %s %s" % ("mock_sphere.txt", outputDir))
|
||||
|
||||
else: # simulation
|
||||
sampleName = sample.fullName
|
||||
|
|
@ -142,16 +153,16 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
|
|||
|
||||
if prevSubSample == -1:
|
||||
inputParameterFlag = ""
|
||||
outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + \
|
||||
outputFile = outputDir+"/zobov_slice_" + sampleName + "_ss" + \
|
||||
thisSubSample
|
||||
keepFraction = float(thisSubSample)
|
||||
subSampleLine = "subsample %g" % keepFraction
|
||||
resubSampleLine = ""
|
||||
firstSubSample = keepFraction
|
||||
else:
|
||||
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+\
|
||||
inputParameterFlag = "inputParameter " + outputDir+"/zobov_slice_"+\
|
||||
sampleName+"_ss"+prevSubSample+".par"
|
||||
outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + \
|
||||
outputFile = outputDir+"/zobov_slice_" + sampleName + "_ss" + \
|
||||
thisSubSample
|
||||
keepFraction = float(thisSubSample)/float(prevSubSample)
|
||||
subSampleLine = "subsample %s" % firstSubSample
|
||||
|
|
@ -243,8 +254,8 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
|
|||
|
||||
# remove intermediate files
|
||||
if (prevSubSample != -1):
|
||||
os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample+".par")
|
||||
os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample)
|
||||
os.unlink(outputDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample+".par")
|
||||
os.unlink(outputDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample)
|
||||
|
||||
doneLine = "Done! %5.2e\n" % keepFraction
|
||||
if not jobSuccessful(logFile, doneLine):
|
||||
|
|
@ -256,27 +267,27 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
|
|||
if jobSuccessful(logFile, doneLine): print("done")
|
||||
|
||||
# place the final subsample
|
||||
os.system("mv %s %s" % (zobovDir+"/zobov_slice_"+sampleName+"_ss"+\
|
||||
prevSubSample, zobovDir+"/zobov_slice_"+sampleName))
|
||||
os.system("mv %s %s" % (zobovDir+"/zobov_slice_"+sampleName+"_ss"+\
|
||||
prevSubSample+".par", zobovDir+"/zobov_slice_"+sampleName+".par"))
|
||||
os.system("mv %s %s" % (outputDir+"/zobov_slice_"+sampleName+"_ss"+\
|
||||
prevSubSample, outputDir+"/zobov_slice_"+sampleName))
|
||||
os.system("mv %s %s" % (outputDir+"/zobov_slice_"+sampleName+"_ss"+\
|
||||
prevSubSample+".par", outputDir+"/zobov_slice_"+sampleName+".par"))
|
||||
|
||||
if os.access("comoving_distance.txt", os.F_OK):
|
||||
os.system("mv %s %s" % ("comoving_distance.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("comoving_distance.txt", outputDir))
|
||||
|
||||
if os.access(parmFile, os.F_OK):
|
||||
os.unlink(parmFile)
|
||||
|
||||
if os.access("mask_index.txt", os.F_OK):
|
||||
os.system("mv %s %s" % ("mask_index.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("total_particles.txt", zobovDir))
|
||||
#os.system("mv %s %s" % ("sample_info.txt", zobovDir))
|
||||
os.system("mv %s %s" % ("mask_index.txt", outputDir))
|
||||
os.system("mv %s %s" % ("total_particles.txt", outputDir))
|
||||
#os.system("mv %s %s" % ("sample_info.txt", outputDir))
|
||||
|
||||
# add to sample info file
|
||||
if sample.dataType == "observation":
|
||||
(boxVol, nbar) = getSurveyProps(sample.maskFile, sample.zRange[0],
|
||||
sample.zRange[1], sample.zRange[0], sample.zRange[1], "all",
|
||||
useComoving=useComoving)
|
||||
sample.omegaM, useComoving=useComoving)
|
||||
else:
|
||||
iX = float(sample.mySubvolume[0])
|
||||
iY = float(sample.mySubvolume[1])
|
||||
|
|
@ -290,16 +301,16 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
|
|||
boxVol = (xMax-xMin)*(yMax-yMin)*(zMax-zMin)
|
||||
nbar = 1.0
|
||||
|
||||
numTracers = int(open(zobovDir+"/mask_index.txt", "r").read())
|
||||
numTotal = int(open(zobovDir+"/total_particles.txt", "r").read())
|
||||
numTracers = int(open(outputDir+"/mask_index.txt", "r").read())
|
||||
numTotal = int(open(outputDir+"/total_particles.txt", "r").read())
|
||||
|
||||
meanSep = (1.*numTracers/boxVol/nbar)**(-1/3.)
|
||||
|
||||
# save this sample's information
|
||||
with open(zobovDir+"/sample_info.dat", mode='wb') as output:
|
||||
with open(outputDir+"/sample_info.dat", mode='wb') as output:
|
||||
pickle.dump(sample, output, pickle.HIGHEST_PROTOCOL)
|
||||
|
||||
fp = open(zobovDir+"/sample_info.txt", 'w')
|
||||
fp = open(outputDir+"/sample_info.txt", 'w')
|
||||
fp.write("Sample name: %s\n" % sample.fullName)
|
||||
fp.write("Sample nickname: %s\n" % sample.nickName)
|
||||
fp.write("Data type: %s\n" % sample.dataType)
|
||||
|
|
@ -323,13 +334,13 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
|
|||
fp.close()
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
|
||||
def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
|
||||
numZobovDivisions=None, numZobovThreads=None,
|
||||
mergingThreshold=0.2):
|
||||
|
||||
sampleName = sample.fullName
|
||||
|
||||
datafile = zobovDir+"zobov_slice_"+sampleName
|
||||
datafile = outputDir+"zobov_slice_"+sampleName
|
||||
|
||||
logFile = logDir+"/zobov_"+sampleName+".out"
|
||||
|
||||
|
|
@ -339,8 +350,8 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
|
|||
os.unlink(vozScript)
|
||||
|
||||
if sample.dataType == "observation":
|
||||
maskIndex = open(zobovDir+"/mask_index.txt", "r").read()
|
||||
totalPart = open(zobovDir+"/total_particles.txt", "r").read()
|
||||
maskIndex = open(outputDir+"/mask_index.txt", "r").read()
|
||||
totalPart = open(outputDir+"/total_particles.txt", "r").read()
|
||||
maxDen = mergingThreshold*float(maskIndex)/float(totalPart)
|
||||
else:
|
||||
maskIndex = -1
|
||||
|
|
@ -349,18 +360,18 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
|
|||
print(" WARNING! You are using a single ZOBOV division with a simulation. Periodic boundaries will not be respected!")
|
||||
|
||||
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
|
||||
for fileName in glob.glob(zobovDir+"/part._"+sampleName+".*"):
|
||||
for fileName in glob.glob(outputDir+"/part._"+sampleName+".*"):
|
||||
os.unlink(fileName)
|
||||
|
||||
if os.access(zobovDir+"/adj_"+sampleName+".dat", os.F_OK):
|
||||
os.unlink(zobovDir+"adj_"+sampleName+".dat")
|
||||
if os.access(outputDir+"/adj_"+sampleName+".dat", os.F_OK):
|
||||
os.unlink(outputDir+"adj_"+sampleName+".dat")
|
||||
|
||||
if os.access(zobovDir+"/voidDesc_"+sampleName+".out", os.F_OK):
|
||||
os.unlink(zobovDir+"/voidDesc_"+sampleName+".out")
|
||||
if os.access(outputDir+"/voidDesc_"+sampleName+".out", os.F_OK):
|
||||
os.unlink(outputDir+"/voidDesc_"+sampleName+".out")
|
||||
|
||||
cmd = [binPath+"/vozinit", datafile, "0.1", "1.0", str(numZobovDivisions), \
|
||||
"_"+sampleName, str(numZobovThreads), \
|
||||
binPath, zobovDir, str(maskIndex)]
|
||||
binPath, outputDir, str(maskIndex)]
|
||||
log = open(logFile, 'w')
|
||||
subprocess.call(cmd, stdout=log, stderr=log)
|
||||
log.close()
|
||||
|
|
@ -375,13 +386,13 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
|
|||
sample.selFunFile != None:
|
||||
|
||||
# load volumes
|
||||
volFile = zobovDir+"/vol_"+sampleName+".dat"
|
||||
volFile = outputDir+"/vol_"+sampleName+".dat"
|
||||
with open(volFile, mode="rb") as File:
|
||||
numPartTot = np.fromfile(File, dtype=np.int32,count=1)
|
||||
vols = np.fromfile(File, dtype=np.float32,count=numPartTot)
|
||||
|
||||
# load redshifts
|
||||
partFile = zobovDir+"/zobov_slice_"+sample.fullName
|
||||
partFile = outputDir+"/zobov_slice_"+sample.fullName
|
||||
with open(partFile, mode="rb") as File:
|
||||
chk = np.fromfile(File, dtype=np.int32,count=1)
|
||||
Np = np.fromfile(File, dtype=np.int32,count=1)
|
||||
|
|
@ -412,7 +423,7 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
|
|||
redshifts = np.fromfile(File, dtype=np.float32,count=Np)
|
||||
chk = np.fromfile(File, dtype=np.int32,count=1)
|
||||
|
||||
# z
|
||||
# redshift
|
||||
chk = np.fromfile(File, dtype=np.int32,count=1)
|
||||
redshifts = np.fromfile(File, dtype=np.float32,count=Np)
|
||||
chk = np.fromfile(File, dtype=np.int32,count=1)
|
||||
|
|
@ -428,29 +439,29 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
|
|||
for i in range(len(vols)):
|
||||
vols[i] *= selfunc(redshifts[i])
|
||||
|
||||
volFile = zobovDir+"/vol_weighted_"+sampleName+".dat"
|
||||
volFile = outputDir+"/vol_weighted_"+sampleName+".dat"
|
||||
with open(volFile, mode='wb') as File:
|
||||
numPartTot.astype(np.int32).tofile(File)
|
||||
vols.astype(np.float32).tofile(File)
|
||||
|
||||
volFileToUse = zobovDir+"/vol_weighted_"+sampleName+".dat"
|
||||
volFileToUse = outputDir+"/vol_weighted_"+sampleName+".dat"
|
||||
else:
|
||||
volFileToUse = zobovDir+"/vol_"+sampleName+".dat"
|
||||
volFileToUse = outputDir+"/vol_"+sampleName+".dat"
|
||||
|
||||
|
||||
cmd = [binPath+"/jozov2", \
|
||||
zobovDir+"/adj_"+sampleName+".dat", \
|
||||
outputDir+"/adj_"+sampleName+".dat", \
|
||||
volFileToUse, \
|
||||
zobovDir+"/voidPart_"+sampleName+".dat", \
|
||||
zobovDir+"/voidZone_"+sampleName+".dat", \
|
||||
zobovDir+"/voidDesc_"+sampleName+".out", \
|
||||
outputDir+"/voidPart_"+sampleName+".dat", \
|
||||
outputDir+"/voidZone_"+sampleName+".dat", \
|
||||
outputDir+"/voidDesc_"+sampleName+".out", \
|
||||
str(maxDen), str(maskIndex)]
|
||||
log = open(logFile, 'a')
|
||||
subprocess.call(cmd, stdout=log, stderr=log)
|
||||
log.close()
|
||||
|
||||
# don't need the subbox files
|
||||
for fileName in glob.glob(zobovDir+"/part._"+sampleName+".*"):
|
||||
for fileName in glob.glob(outputDir+"/part._"+sampleName+".*"):
|
||||
os.unlink(fileName)
|
||||
|
||||
if jobSuccessful(logFile, "Done!\n"):
|
||||
|
|
@ -467,19 +478,19 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
|
|||
|
||||
# -----------------------------------------------------------------------------
|
||||
def launchPrune(sample, binPath,
|
||||
summaryFile=None, logFile=None, zobovDir=None,
|
||||
summaryFile=None, logFile=None, outputDir=None,
|
||||
continueRun=None, useComoving=False, mergingThreshold=0.2,
|
||||
boundaryTolerance=1.0):
|
||||
|
||||
sampleName = sample.fullName
|
||||
|
||||
numVoids = sum(1 for line in \
|
||||
open(zobovDir+"/voidDesc_"+sampleName+".out"))
|
||||
open(outputDir+"/voidDesc_"+sampleName+".out"))
|
||||
numVoids -= 2
|
||||
|
||||
if sample.dataType == "observation":
|
||||
mockIndex = open(zobovDir+"/mask_index.txt", "r").read()
|
||||
totalPart = open(zobovDir+"/total_particles.txt", "r").read()
|
||||
mockIndex = open(outputDir+"/mask_index.txt", "r").read()
|
||||
totalPart = open(outputDir+"/total_particles.txt", "r").read()
|
||||
maxDen = mergingThreshold*float(mockIndex)/float(totalPart)
|
||||
observationLine = " --isObservation"
|
||||
#periodicLine = " --periodic=''"
|
||||
|
|
@ -497,7 +508,7 @@ def launchPrune(sample, binPath,
|
|||
|
||||
if sample.minVoidRadius == -1:
|
||||
minRadius = -1
|
||||
for line in open(zobovDir+"/sample_info.txt"):
|
||||
for line in open(outputDir+"/sample_info.txt"):
|
||||
if "Estimated mean tracer separation" in line:
|
||||
minRadius = float(line.split()[5])
|
||||
break
|
||||
|
|
@ -510,13 +521,13 @@ def launchPrune(sample, binPath,
|
|||
if not (continueRun and (jobSuccessful(logFile, "NetCDF: Not a valid ID\n") \
|
||||
or jobSuccessful(logFile, "Done!\n"))):
|
||||
cmd = binPath
|
||||
cmd += " --partFile=" + zobovDir+"/zobov_slice_"+str(sampleName)
|
||||
cmd += " --voidDesc=" + zobovDir+"/voidDesc_"+str(sampleName)+".out"
|
||||
cmd += " --void2Zone="+zobovDir+"/voidZone_"+str(sampleName)+".dat"
|
||||
cmd += " --zone2Part=" + zobovDir+"/voidPart_"+str(sampleName)+".dat"
|
||||
cmd += " --partVol=" + zobovDir+"/vol_"+str(sampleName)+".dat"
|
||||
cmd += " --partAdj=" + zobovDir+"/adj_"+str(sampleName)+".dat"
|
||||
cmd += " --extraInfo=" + zobovDir+"/zobov_slice_"+str(sampleName)+\
|
||||
cmd += " --partFile=" + outputDir+"/zobov_slice_"+str(sampleName)
|
||||
cmd += " --voidDesc=" + outputDir+"/voidDesc_"+str(sampleName)+".out"
|
||||
cmd += " --void2Zone="+outputDir+"/voidZone_"+str(sampleName)+".dat"
|
||||
cmd += " --zone2Part=" + outputDir+"/voidPart_"+str(sampleName)+".dat"
|
||||
cmd += " --partVol=" + outputDir+"/vol_"+str(sampleName)+".dat"
|
||||
cmd += " --partAdj=" + outputDir+"/adj_"+str(sampleName)+".dat"
|
||||
cmd += " --extraInfo=" + outputDir+"/zobov_slice_"+str(sampleName)+\
|
||||
".par"
|
||||
cmd += " --tolerance=" + str(boundaryTolerance)
|
||||
cmd += " --mockIndex=" + str(mockIndex)
|
||||
|
|
@ -529,7 +540,7 @@ def launchPrune(sample, binPath,
|
|||
cmd += periodicLine
|
||||
cmd += useComovingFlag
|
||||
cmd += " --omegaM=" + str(sample.omegaM)
|
||||
cmd += " --outputDir=" + zobovDir
|
||||
cmd += " --outputDir=" + outputDir
|
||||
cmd += " --sampleName=" + str(sampleName)
|
||||
log = open(logFile, 'w')
|
||||
#log.write(f"Command is {cmd}\n")
|
||||
|
|
@ -635,7 +646,7 @@ def launchVelocityStack(sample, stack, binPath,
|
|||
velField_file,
|
||||
thisDataPortion=None, logDir=None,
|
||||
voidDir=None, runSuffix=None,
|
||||
zobovDir=None,
|
||||
outputDir=None,
|
||||
summaryFile=None,
|
||||
continueRun=None, dataType=None, prefixRun=""):
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue