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

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Guilhem Lavaux 2013-02-26 17:46:11 -05:00
commit c6dd08bd7d
5 changed files with 318 additions and 257 deletions
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26
python_tools/pipeline_source/prepareCatalogs.in.py
View file

@ -76,7 +76,7 @@ from void_python_tools.backend.classes import *
continueRun = False # set to True to enable restarting aborted jobs
startCatalogStage = 1
endCatalogStage = 4
endCatalogStage = 3
startAPStage = 1
endAPStage = 1
@ -170,15 +170,21 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False)
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
dzSafe = 0.03
else:
boxWidthZ = lbox*100./LIGHT_SPEED
boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
#boxWidthZ = lbox*100./LIGHT_SPEED
dzSafe = 0.0
for iSlice in xrange(numSlices):
sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-dzSafe)/numSlices
sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-dzSafe)/numSlices
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.
if useLightCone:
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)
sliceMin = "%0.2f" % sliceMin
sliceMax = "%0.2f" % sliceMax
@ -316,7 +322,7 @@ for thisSubSample in sorted(subSamples, reverse=True):
else:
outFile.write(line)
outFile.write("-99 -99 -99 -99 -99\n")
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
inFile.close()
outFile.close()
@ -337,7 +343,7 @@ for thisSubSample in sorted(subSamples, reverse=True):
outFile.write("%d %e %e %e 0. 0. 0.\n" % (i, x,y,z))
outFile.write("-99 -99 -99 -99 -99\n")
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
outFile.close()
prevSubSample = thisSubSample
@ -427,7 +433,7 @@ if (args.halos or args.all) and haloFileBase != "":
# 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\n")
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
inFile.close()
outFile.close()
@ -528,3 +534,5 @@ if (args.hod or args.all) and haloFileBase != "":
outFileName = catalogDir+"/"+sampleName+".dat"
os.system("mv %s/hod.mock %s" % (catalogDir, outFileName))
os.system("rm %s/hod.*" % catalogDir)
print " Done!"

38
python_tools/void_python_tools/backend/launchers.py
View file

@ -247,7 +247,7 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
os.unlink(vozScript)
# -----------------------------------------------------------------------------
def launchPrune(sample, binPath, thisDataPortion=None,
def launchPrune(sample, binPath,
summaryFile=None, logFile=None, zobovDir=None,
continueRun=None):
@ -274,7 +274,6 @@ def launchPrune(sample, binPath, thisDataPortion=None,
sample.boxLen <= 1.e-1:
periodicLine += "z"
periodicLine += "' "
periodicLine = ""
if not (continueRun and (jobSuccessful(logFile, "NetCDF: Not a valid ID\n") \
or jobSuccessful(logFile, "Done!\n"))):
@ -287,7 +286,6 @@ def launchPrune(sample, binPath, thisDataPortion=None,
cmd += " --extraInfo=" + zobovDir+"/zobov_slice_"+str(sampleName)+\
".par"
cmd += " --tolerance=1.0"
cmd += " --dataPortion=" + thisDataPortion
cmd += " --mockIndex=" + str(mockIndex)
cmd += " --maxCentralDen=" + str(maxDen)
cmd += " --zMin=" + str(sample.zRange[0])
@ -296,27 +294,8 @@ def launchPrune(sample, binPath, thisDataPortion=None,
cmd += " --numVoids=" + str(numVoids)
cmd += observationLine
cmd += periodicLine
cmd += " --output=" + zobovDir+"/voidDesc_"+\
str(thisDataPortion)+"_"+\
str(sampleName)+".out"
cmd += " --outCenters=" + zobovDir+"/barycenters_"+\
str(thisDataPortion)+"_"+\
str(sampleName)+".out"
cmd += " --outInfo=" + zobovDir+"/centers_"+\
str(thisDataPortion)+"_"+\
str(sampleName)+".out"
cmd += " --outNoCutInfo=" + zobovDir+"/centers_nocut_"+\
str(thisDataPortion)+"_"+\
str(sampleName)+".out"
cmd += " --outSkyPositions=" + zobovDir+"/sky_positions_"+\
str(thisDataPortion)+"_"+\
str(sampleName)+".out"
cmd += " --outShapes=" + zobovDir+"/shapes_"+\
str(thisDataPortion)+"_"+\
str(sampleName)+".out"
cmd += " --outDistances=" + zobovDir+"/boundaryDistances_"+\
str(thisDataPortion)+"_"+\
str(sampleName)+".out"
cmd += " --outputDir=" + zobovDir
cmd += " --sampleName=" + str(sampleName)
cmd += " &> " + logFile
f=file("run_prune.sh",mode="w")
f.write(cmd)
@ -956,7 +935,7 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
return
numVoids = int(open(voidDir+"/num_voids.txt", "r").readline())
if numVoids < 15:
if numVoids < 10:
print "not enough voids to fit; skipping!"
fp = open(voidDir+"/NOFIT", "w")
fp.write("not enough voids: %d \n" % numVoids)
@ -1334,8 +1313,9 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
plotTitle = "all samples, incoherent "+\
thisDataPortion+" voids (systematics corrected)"
else:
plotTitle = "all samples, "+thisDataPortion+\
" voids (systematics corrected)"
#plotTitle = "all samples, "+thisDataPortion+\
# " voids (systematics corrected)"
plotTitle = setName + "(sysematics corrected)"
vp.do_all_obs(zbase, allExpList, aveDistList,
rlist, plotTitle=plotTitle, sampleNames=shortSampleNames,
plotAve=True, mulfac = 1.16,
@ -1429,7 +1409,9 @@ def launchLikelihood(dataPortions=None, logDir=None, workDir=None,
OmStart = 0.0,
OmEnd = 1.0,
biasStart = 1.0,
biasEnd = 1.2,
biasEnd = 1.32,
#biasStart = 1.15,
#biasEnd = 1.17,
outputBase = workDir+"/1dlikelihoods_"+thisDataPortion+"_",
useBinAve = False)