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

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This commit is contained in:
Guilhem Lavaux 2013-03-02 10:45:10 -06:00
commit e9194f5c55
3 changed files with 151 additions and 98 deletions
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8
c_tools/stacking/pruneVoids.cpp
View file

@ -548,7 +548,7 @@ int main(int argc, char **argv) {
}
}
voids.resize(iGood);
printf(" 1st filter: reiGoodected %d obviously bad\n", numWrong);
printf(" 1st filter: rejected %d obviously bad\n", numWrong);
iGood = 0;
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
@ -559,7 +559,7 @@ int main(int argc, char **argv) {
}
}
voids.resize(iGood);
printf(" 2nd filter: reiGoodected %d too small\n", numTooSmall);
printf(" 2nd filter: rejected %d too small\n", numTooSmall);
iGood = 0;
@ -572,7 +572,7 @@ int main(int argc, char **argv) {
}
}
voids.resize(iGood);
printf(" 3rd filter: reiGoodected %d too close to high redshift boundaries\n", numNearZ);
printf(" 3rd filter: rejected %d too close to high redshift boundaries\n", numNearZ);
numNearZ = 0;
iGood = 0;
@ -586,7 +586,7 @@ int main(int argc, char **argv) {
}
}
voids.resize(iGood);
printf(" 4th filter: reiGoodected %d too close to low redshift boundaries\n", numNearZ);
printf(" 4th filter: rejected %d too close to low redshift boundaries\n", numNearZ);
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
if (voids[iVoid].centralDen > args.maxCentralDen_arg) {

141
python_tools/pipeline_source/prepareCatalogs.in.py
View file

@ -62,7 +62,7 @@ def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
def writeScript(setName, dataFileNameBase, dataFormat,
scriptDir, catalogDir, fileNums, redshifts, numSubvolumes,
numSlices, useVel, lbox, minRadius, omegaM, subsample=1.0,
suffix=".dat"):
suffix=".dat", dataFileNameList=None):
if useVel: setName += "_pv"
@ -134,7 +134,7 @@ newSample = Sample(dataFile = "{dataFile}",
numSubvolumes = {numSubvolumes},
mySubvolume = "{mySubvolume}",
useLightCone = {useLightCone},
subsample = {subsample})
subsample = "{subsample}")
dataSampleList.append(newSample)
newSample.addStack(0.0, 5.0, 20, 25, False, False)
newSample.addStack(0.0, 5.0, 30, 35, False, False)
@ -165,33 +165,32 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False)
for i in xrange(len(zVsDY)):
zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
if useLightCone:
boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
dzSafe = 0.03
else:
boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
#boxWidthZ = lbox*100./LIGHT_SPEED
dzSafe = 0.0
boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
for iSlice in xrange(numSlices):
sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-2.*dzSafe)/numSlices
sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-2.*dzSafe)/numSlices
if useLightCone:
dzSafe = 0.03
sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-2.*dzSafe)/numSlices
sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-2.*dzSafe)/numSlices
sliceMinMpc = sliceMin*LIGHT_SPEED/100.
sliceMaxMpc = sliceMax*LIGHT_SPEED/100.
else:
sliceMinMpc = LIGHT_SPEED/100.*vp.angularDiameter(sliceMin, Om=Om)
sliceMaxMpc = LIGHT_SPEED/100.*vp.angularDiameter(sliceMax, Om=Om)
sliceMinMpc = zBoxMpc + iSlice*lbox/numSlices
sliceMaxMpc = zBoxMpc + (iSlice+1)*lbox/numSlices
sliceMin = np.interp(sliceMinMpc*100./LIGHT_SPEED, zVsDX, zVsDY)
sliceMax = np.interp(sliceMaxMpc*100./LIGHT_SPEED, zVsDX, zVsDY)
sliceMin = "%0.2f" % sliceMin
sliceMax = "%0.2f" % sliceMax
sliceMinMpc = "%0.1f" % sliceMinMpc
sliceMaxMpc = "%0.1f" % sliceMaxMpc
dataFileName = dataFileNameBase + fileNum + suffix
if (dataFileNameList != None):
dataFileName = dataFileNameList[iFile]
else:
dataFileName = dataFileNameBase + fileNum + suffix
for iX in xrange(numSubvolumes):
for iY in xrange(numSubvolumes):
@ -216,7 +215,7 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False)
numSubvolumes=numSubvolumes,
mySubvolume=mySubvolume,
useLightCone=useLightCone,
subsample=subsample))
subsample=str(subsample).strip('[]')))
scriptFile.close()
return
@ -233,44 +232,60 @@ if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir)
# ss0.000175 ~ SDSS DR9 mid
baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
prevSubSample = -1
for thisSubSample in sorted(subSamples, reverse=True):
subSamples = sorted(subSamples, reverse=True)
for iSubSample in xrange(len(subSamples)):
keepFraction = float(thisSubSample) / baseResolution
maxKeep = keepFraction * numPart
subSampleList = subSamples[0:iSubSample+1]
keepFractionList = []
for subSample in subSampleList:
keepFractionList.append(float(subSample) / baseResolution)
thisSubSample = subSamples[iSubSample]
maxKeep = keepFractionList[-1] * numPart
minRadius = int(np.ceil(lbox/maxKeep**(1./3)))
partFileList = []
for (iRedshift, redshift) in enumerate(redshifts):
if particleFileDummy == '':
partFileList.append(particleFileBase+fileNums[iRedshift])
else:
partFileList.append(particleFileBase.replace(particleFileDummy,
fileNums[iRedshift]))
if args.script or args.all:
print " Doing subsample", thisSubSample, "scripts"
sys.stdout.flush()
setName = prefix+"ss"+str(thisSubSample)
if dataFormat == "multidark":
subSampleToUse = 1.0
fileToUse = prefix+"ss"+str(thisSubSample)+"_z"
suffix = ".dat"
elif dataFormat == "gadget":
subSampleToUse = keepFraction
#subSampleToUse = thisSubSample
fileToUse = particleFileBase
suffix = ""
elif dataFormat == "lanl":
subSampleToUse = keepFraction
#subSampleToUse = thisSubSample
fileToUse = particleFileBase
suffix = ""
elif dataFormat == "random":
if dataFormat == "random":
subSampleToUse = 1.0
fileToUse = "ran.ss"+str(thisSubSample)+"_z"
suffix = ".dat"
writeScript(setName, fileToUse, dataFormat,
writeScript(setName, fileToUse, dataFormat,
scriptDir, catalogDir, fileNums, redshifts,
numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
subsample=subSampleToUse, suffix=suffix)
writeScript(setName, fileToUse, dataFormat,
writeScript(setName, fileToUse, dataFormat,
scriptDir, catalogDir, fileNums, redshifts,
numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
subsample=subSampleToUse, suffix=suffix)
else:
subSampleToUse = keepFractionList
suffix = ""
fileToUse = partFileList[0]
writeScript(setName, fileToUse, dataFormat,
scriptDir, catalogDir, fileNums, redshifts,
numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
subsample=subSampleToUse, suffix=suffix,
dataFileNameList=partFileList)
writeScript(setName, fileToUse, dataFormat,
scriptDir, catalogDir, fileNums, redshifts,
numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
subsample=subSampleToUse, suffix=suffix,
dataFileNameList=partFileList)
if args.subsample or args.all:
print " Doing subsample", thisSubSample
sys.stdout.flush()
@ -411,31 +426,37 @@ if (args.halos or args.all) and haloFileBase != "":
sampleName = prefix+"halos_min"+str(minHaloMass)+"_z"+fileNums[iRedshift]
outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
outFile.write("%f\n" %(lbox))
outFile.write("%s\n" %(omegaM))
outFile.write("%s\n" %(hubble))
outFile.write("%s\n" %(redshift))
outFile.write("%d\n" %(numPart))
inFile = open(dataFile, 'r')
for (iHalo,line) in enumerate(inFile):
if iHalo < haloFileNumComLines: continue
line = line.split(haloFileColSep)
if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
x = float(line[haloFileXCol])
y = float(line[haloFileYCol])
z = float(line[haloFileZCol])
vz = float(line[haloFileVZCol])
vy = float(line[haloFileVYCol])
vx = float(line[haloFileVXCol])
if dataFormat == "sdf":
# TODO process halo file with SDFcvt
outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
outFile.close()
else:
outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
inFile = open(dataFile, 'r')
for (iHalo,line) in enumerate(inFile):
if iHalo < haloFileNumComLines: continue
line = line.split(haloFileColSep)
if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
x = float(line[haloFileXCol])
y = float(line[haloFileYCol])
z = float(line[haloFileZCol])
vz = float(line[haloFileVZCol])
vy = float(line[haloFileVYCol])
vx = float(line[haloFileVXCol])
# write to output file
outFile.write("%d %e %e %e %e %e %e\n" %(iHalo,x,y,z,vz,vy,vx))
# write to output file
outFile.write("%d %e %e %e %e %e %e\n" %(iHalo,x,y,z,vz,vy,vx))
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
inFile.close()
outFile.close()
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
outFile.close()
inFile.close()
# -----------------------------------------------------------------------------
# now the HOD
@ -510,6 +531,14 @@ if (args.hod or args.all) and haloFileBase != "":
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,
hubble=hubble,
redshift=redshift,
@ -535,4 +564,6 @@ if (args.hod or args.all) and haloFileBase != "":
os.system("mv %s/hod.mock %s" % (catalogDir, outFileName))
os.system("rm %s/hod.*" % catalogDir)
os.system("rm %s" % haloFile)
print " Done!"

100
python_tools/void_python_tools/backend/launchers.py
View file

@ -105,37 +105,43 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
datafile = inputDataDir+"/"+sample.dataFile
if regenerate:
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+sampleName+".par"
outputFile = zobovDir+"/regenerated_zobov_slice_" + sampleName
else:
inputParameterFlag = ""
outputFile = zobovDir+"/zobov_slice_" + sampleName
prevSubSample = -1
for thisSubSample in sample.subsample.split(', '):
if prevSubSample == -1:
inputParameterFlag = ""
outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + thisSubSample
keepFraction = float(thisSubSample)
subSampleLine = "subsample %g" % keepFraction
else:
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+\
sampleName+"_ss"+prevSubSample+".par"
outputFile = zobovDir+"/_zobov_slice_" + sampleName + "_ss" + thisSubSample
keepFraction = float(thisSubSample)/float(prevSubSample)
subSampleLine = "resubsample %g" % keepFraction
if sample.usePecVel:
includePecVelString = "peculiarVelocities"
else:
includePecVelString = ""
if sample.usePecVel: includePecVelString = "peculiarVelocities"
if sample.useLightCone:
useLightConeString = "cosmo"
else:
useLightConeString = ""
if sample.useLightCone: useLightConeString = "cosmo"
if sample.dataFormat == "multidark" or sample.dataFormat == "random":
dataFileLine = "multidark " + datafile
elif sample.dataFormat == "gadget":
dataFileLine = "gadget " + datafile
if sample.dataFormat == "multidark" or sample.dataFormat == "random":
dataFileLine = "multidark " + datafile
elif sample.dataFormat == "gadget":
dataFileLine = "gadget " + datafile
elif sample.dataFormat == "sdf":
dataFileLine = "sdf " + datafile
iX = float(sample.mySubvolume[0])
iY = float(sample.mySubvolume[1])
iX = float(sample.mySubvolume[0])
iY = float(sample.mySubvolume[1])
xMin = iX/sample.numSubvolumes * sample.boxLen
yMin = iY/sample.numSubvolumes * sample.boxLen
xMax = (iX+1)/sample.numSubvolumes * sample.boxLen
yMax = (iY+1)/sample.numSubvolumes * sample.boxLen
xMin = iX/sample.numSubvolumes * sample.boxLen
yMin = iY/sample.numSubvolumes * sample.boxLen
xMax = (iX+1)/sample.numSubvolumes * sample.boxLen
yMax = (iY+1)/sample.numSubvolumes * sample.boxLen
conf="""
conf="""
%s
output %s
outputParameter %s
@ -148,36 +154,52 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
rangeY_max %g
rangeZ_min %g
rangeZ_max %g
subsample %g
%s
%s
""" % (dataFileLine, outputFile,
zobovDir+"/zobov_slice_"+sampleName+".par",
outputFile+".par",
includePecVelString,
useLightConeString,
sample.dataUnit,
xMin, xMax, yMin, yMax,
sample.zBoundaryMpc[0], sample.zBoundaryMpc[1],
sample.subsample,inputParameterFlag)
subSampleLine,inputParameterFlag)
parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
file(parmFile, mode="w").write(conf)
file(parmFile, mode="w").write(conf)
if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")):
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
os.system(cmd)
if jobSuccessful(logFile, "Done!\n"):
print "done"
else:
print "FAILED!"
exit(-1)
doneLine = "Done! %5.2e\n" % keepFraction
print "TEST", doneLine
if not (continueRun and jobSuccessful(logFile, doneLine)):
if (prevSubSample == -1):
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
else:
cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile)
os.system(cmd)
if not jobSuccessful(logFile, doneLine):
print "FAILED!"
exit(-1)
else:
print "already done!"
# remove intermediate files
if (prevSubSample != -1):
os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample+".par")
os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample)
prevSubSample = thisSubSample
if (continueRun and jobSuccessful(logFile, doneLine)): print "already done!"
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"))
if os.access("comoving_distance.txt", os.F_OK):
os.system("mv %s %s" % ("comoving_distance.txt", zobovDir))
#os.system("mv %s %s" % ("sample_info.txt", zobovDir))
if os.access(parmFile, os.F_OK):
os.unlink(parmFile)