mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
significant improvements and streamlining of a-p analysis
This commit is contained in:
P.M. Sutter
parent
b8ad7f8752
commit
3f5a767b48
4 changed files with 159 additions and 116 deletions
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@ -438,6 +438,18 @@ def launchPrune(sample, binPath,
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else:
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useComovingFlag = ""
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if sample.minVoidRadius == -1:
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minRadius = -1
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for line in open(zobovDir+"/sample_info.txt"):
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if "Estimated mean tracer separation" in line:
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minRadius = float(line.split()[5])
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break
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if minRadius == -1:
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print "Could not grab mean tracer separation!?"
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exit(-1)
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else:
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minRadius = sample.minVoidRadius
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if not (continueRun and (jobSuccessful(logFile, "NetCDF: Not a valid ID\n") \
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or jobSuccessful(logFile, "Done!\n"))):
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cmd = binPath
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@ -454,7 +466,7 @@ def launchPrune(sample, binPath,
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cmd += " --maxCentralDen=" + str(maxDen)
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cmd += " --zMin=" + str(sample.zRange[0])
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cmd += " --zMax=" + str(sample.zRange[1])
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cmd += " --rMin=" + str(sample.minVoidRadius)
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cmd += " --rMin=" + str(minRadius)
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cmd += " --numVoids=" + str(numVoids)
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cmd += observationLine
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cmd += periodicLine
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@ -595,8 +607,6 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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if useComoving or not useLightCone:
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zMin = LIGHT_SPEED/100.*vp.angularDiameter(zMin, Om=omegaM)
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zMax = LIGHT_SPEED/100.*vp.angularDiameter(zMax, Om=omegaM)
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print min(sample.zRange[1],stack.zMax)*LIGHT_SPEED/100., zMax, sample.zBoundaryMpc[1]
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print max(sample.zRange[0],stack.zMin)*LIGHT_SPEED/100., zMin, sample.zBoundaryMpc[0]
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else:
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zMin *= LIGHT_SPEED/100.
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zMax *= LIGHT_SPEED/100.
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@ -608,6 +618,8 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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Rextracut = stack.rMin*3 + 1
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Rcircular = stack.rMin*3 + 2
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#Rextracut = stack.rMax*3 + 1
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#Rcircular = stack.rMax*3 + 2
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if dataType == "observation":
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maskIndex = open(zobovDir+"/mask_index.txt", "r").read()
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@ -765,7 +777,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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line = line.split()
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numVoids = line[1]
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if "Number of particles =" in line:
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if "Final zobov stack size" in line:
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line = line.split()
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numParticles = line[4]
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@ -793,51 +805,6 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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fp.close()
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return
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# figure out box volume and average density
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if sample.dataType == "observation":
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maskFile = sample.maskFile
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sulFunFile = sample.selFunFile
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if not os.access(sample.selFunFile, os.F_OK) and not sample.volumeLimited:
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print " Cannot find", selFunFile, "!"
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exit(-1)
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sys.stdout = open(logFile, 'a')
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#sys.stderr = open(logFile, 'a')
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zMin = sample.zRange[0]
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zMax = sample.zRange[1]
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if not sample.volumeLimited:
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props = vp.getSurveyProps(maskFile, stack.zMin,
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stack.zMax, zMin, zMax, "all",
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selectionFuncFile=sample.selFunFile)
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else:
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zMinForVol = sample.zBoundary[0]
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zMaxForVol = sample.zBoundary[1]
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props = vp.getSurveyProps(maskFile, zMinForVol,
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zMaxForVol, zMin, zMax, "all")
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props = ((1.0,1.0))
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sys.stdout = sys.__stdout__
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#sys.stderr = sys.__stderr__
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boxVol = props[0]
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nbar = props[1]
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if sample.volumeLimited:
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nbar = 1.0
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else:
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nbar = 1.0
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iX = float(sample.mySubvolume[0])
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iY = float(sample.mySubvolume[1])
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xMin = iX/sample.numSubvolumes * sample.boxLen
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yMin = iY/sample.numSubvolumes * sample.boxLen
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xMax = (iX+1)/sample.numSubvolumes * sample.boxLen
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yMax = (iY+1)/sample.numSubvolumes * sample.boxLen
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zMin = sample.zBoundaryMpc[0]
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zMax = sample.zBoundaryMpc[1]
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boxVol = (xMax-xMin)*(yMax-yMin)*(zMax-zMin)
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summaryLine = runSuffix + " " + \
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thisDataPortion + " " + \
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str(stack.zMin) + " " + \
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@ -847,8 +814,14 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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if summaryFile != None:
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open(summaryFile, "a").write(summaryLine+"\n")
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# move local outputs to storage directory
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# write out individual normalizations for each void
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if os.access("tree.data", os.F_OK):
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for line in open(zobovDir+"/sample_info.txt"):
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if "Number of real" in line:
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numParticles = line.split()[-1]
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if "Estimated volume" in line:
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boxVol = line.split()[-1]
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nbar = 1.0
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normalization = float(numParticles)/float(boxVol)/nbar
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dataTemp = file("centers.txt", "r").readlines()
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fp = file("normalizations.txt", "w")
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@ -1144,7 +1117,9 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
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numParticles = open(voidDir+"/num_particles.txt", "r").readline()
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Rextracut = stack.rMin*3 + 1
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Rcircular = stack.rMin*3 + 2
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Rcircular = stack.rMin*2 + 2
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#Rextracut = stack.rMax*3 + 1
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#Rcircular = stack.rMax*3 + 2
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if not (continueRun and jobSuccessful(logFile, "Done!\n")):
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profileParmFile = voidDir+"/params.txt"
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@ -1163,7 +1138,9 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
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# return
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if sample.profileBinSize == "auto":
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density = 0.5 * 50 / Rcircular / 2
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#density = 0.5 * 50 / Rcircular / 2
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density = stack.rMax / 5.
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#density = stack.rMax / 10.
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else:
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density = sample.profileBinSize
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@ -1176,7 +1153,8 @@ def launchProfile(sample, stack, voidDir=None, logFile=None, continueRun=None,
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#sys.stderr = sys.__stderr__
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if jobSuccessful(logFile, "Done!\n"):
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print jobString, "Profiling stacks done, (N_v=", numVoids,")"
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print jobString, "Profiling stacks done (N_v=%s, N_p=%s)" % \
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(numVoids,numParticles)
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else:
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print jobString, "Profiling stacks FAILED!"
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exit(-1)
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@ -1203,13 +1181,21 @@ def launchFit(sample, stack, useComoving=None,
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return
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numVoids = int(open(voidDir+"/num_voids.txt", "r").readline())
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if numVoids < 10:
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if numVoids < 1:
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print jobString, "Fitting not enough voids to fit; skipping!"
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fp = open(voidDir+"/NOFIT", "w")
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fp.write("not enough voids: %d \n" % numVoids)
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fp.close()
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return
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numPart = int(open(voidDir+"/num_particles.txt", "r").readline())
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if numPart < 1:
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print jobString, "Fitting not enough particles to fit; skipping!"
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fp = open(voidDir+"/NOFIT", "w")
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fp.write("not enough particles: %d \n" % numPart)
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fp.close()
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return
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#if stack.zMin < sample.zRange[0] or stack.zMax > sample.zRange[1]:
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# print "outside sample redshift range; skipping!"
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# return
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@ -1243,23 +1229,28 @@ def launchFit(sample, stack, useComoving=None,
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while badChain:
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ntries += 1
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#Rexpect = (stack.rMin+stack.rMax)/2
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#Rtruncate = stack.rMin*3. + 1 # TEST
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#if sample.dataType == "observation":
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# ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
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# Niter=300000,
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# Nburn=100000,
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# Rextracut=Rtruncate)
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#else:
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# ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
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# Niter=300000,
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# Nburn=100000,
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# Rextracut=Rtruncate)
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#badChain = (args[0][0] > 0.5 or args[0][1] > 2.*stack.rMax or \
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# args[0][2] > 2.*stack.rMax) and \
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# (ntries < maxtries)
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ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="2d", nBootstraps=500, rMaxInertia=0.7)
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badChain = False
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Rexpect = (stack.rMin+stack.rMax)/2
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#Rtruncate = stack.rMax*2. # TEST
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#Rtruncate = stack.rMax*3. # TEST
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Rtruncate = stack.rMin*3. + 1 # TEST
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if sample.dataType == "observation":
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ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
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nbar_init=1.0,
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Niter=300000,
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Nburn=100000,
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Rextracut=Rtruncate)
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else:
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ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect,
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nbar_init=1.0,
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Niter=300000,
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Nburn=100000,
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Rextracut=Rtruncate)
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print "TEST", stack.rMax, args[0][0], args[0][1], args[0][2]
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badChain = (args[0][0] > 0.5 or args[0][1] > 2.*stack.rMax or \
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args[0][2] > 2.*stack.rMax) and \
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(ntries < maxtries)
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#ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="2d", nBootstraps=100, rMaxInertia=0.7)
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#badChain = False
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## rescale to expected stretch if using comoving coords
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#if useComoving or not sample.useLightCone:
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@ -1282,7 +1273,7 @@ def launchFit(sample, stack, useComoving=None,
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else:
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rescaleFactor = 1.0
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vp.draw_fit(*args, delta_tick=0.2, vmax=1.0, delta_v=0.01,
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vp.draw_fit(*args, delta_tick=0.2, vmax=1.4, delta_v=0.01,
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nocontour=True, model_max=1.0, delta_model=0.1,
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plotTitle=plotTitle, show_ratio=showRatio,
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showContours=showContours,
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@ -1293,30 +1284,31 @@ def launchFit(sample, stack, useComoving=None,
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"_"+runSuffix+".pdf")
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figure(1).savefig(figDir+"/stackedVoid_"+sampleName+\
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"_"+runSuffix+".png")
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print "Done!"
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sys.stdout = sys.__stdout__
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#sys.stderr = sys.__stderr__
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if jobSuccessful(logFile, "Done!\n"):
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print jobString, "Fitting done (", ntries, " tries)"
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else:
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print jobString, "Fitting FAILED!"
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exit(-1)
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# record the measured stretch
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exp = args[1]
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expError = args[2]
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outline = str(exp) + " " + str(expError)
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open(voidDir+"/expansion.out", "w").write(outline)
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print "Done!"
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sys.stdout = sys.__stdout__
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#sys.stderr = sys.__stderr__
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if os.access(voidDir+"/NOFIT", os.F_OK):
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os.unlink(voidDir+"/NOFIT")
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if ntries > maxtries:
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print jobString, " No reliable fit found; skipping!"
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if ntries >= maxtries:
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print jobString, "No reliable fit found; skipping!"
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fp = open(voidDir+"/NOFIT", "w")
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fp.write("bad ellipticity fit\n")
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fp.close()
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return
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#return
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else:
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if jobSuccessful(logFile, "Done!\n"):
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print jobString, "Fitting done (%d tries)" % ntries
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else:
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print jobString, "Fitting FAILED!"
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exit(-1)
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else:
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print jobString, "already done!"
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@ -1360,7 +1352,7 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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if not alreadyHere:
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allZBins.append(stack)
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allExpList = np.zeros((numSamplesForHubble,len(allRBins),len(allZBins),3))
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allExpList = np.zeros((numSamplesForHubble,len(allRBins),len(allZBins),5))
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allExpList[:] = -1
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aveDistList = np.zeros((len(allZBins),3))
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@ -1436,6 +1428,10 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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expList[0, iR, iZBin, 2] = aveDist
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voidDir = zobovDir+"/stacks_" + runSuffix
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numVoids = open(voidDir+"/num_voids.txt", "r").readline()
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numParticles = open(voidDir+"/num_particles.txt", "r").readline()
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for (iZCheck,zBinCheck) in enumerate(allZBins):
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for (iRCheck,rBinCheck) in enumerate(allRBins):
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if zBin.zMin == zBinCheck.zMin and zBin.zMax == zBinCheck.zMax:
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@ -1445,6 +1441,8 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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allExpList[iSample, iRCheck, iZCheck, 0] = exp
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allExpList[iSample, iRCheck, iZCheck, 1] = expError
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allExpList[iSample, iRCheck, iZCheck, 3] = numVoids
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allExpList[iSample, iRCheck, iZCheck, 4] = numParticles
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fp.write(str(exp) + " " + str(expError) + " "+ " "+ \
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str(aveDist) + " -1 " + runSuffix+"\n")
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@ -1467,22 +1465,22 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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sys.stdout = open(logFile, 'w')
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#sys.stderr = open(logFile, 'a')
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plotTitle = "Sample: "+sample.nickName+", "+thisDataPortion+" voids"
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if doPlot:
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#if doPlot:
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#vp.do_all_obs(sample, zbase, expList, workDir+"/avedistortion_",
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vp.do_all_obs(sample, zbase, expList, aveDistList,
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rlist, plotTitle=plotTitle, plotAve=True)
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figure(1).savefig(figDir+"/hubble_"+setName+"_"+sampleName+"_"+\
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thisDataPortion+\
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".eps",bbox_inches='tight')
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figure(1).savefig(figDir+"/hubble_"+setName+"_"+sampleName+"_"+\
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thisDataPortion+\
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".pdf",bbox_inches='tight')
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figure(1).savefig(figDir+"/hubble_"+setName+"_"+sampleName+"_"+\
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thisDataPortion+\
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".png",bbox_inches='tight')
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else:
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print "Skipping plot"
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print "Done!"
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#vp.do_all_obs(sample, zbase, expList, aveDistList,
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# rlist, plotTitle=plotTitle, plotAve=True)
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#figure(1).savefig(figDir+"/hubble_"+setName+"_"+sampleName+"_"+\
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# thisDataPortion+\
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# ".eps",bbox_inches='tight')
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#figure(1).savefig(figDir+"/hubble_"+setName+"_"+sampleName+"_"+\
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# thisDataPortion+\
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# ".pdf",bbox_inches='tight')
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#figure(1).savefig(figDir+"/hubble_"+setName+"_"+sampleName+"_"+\
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# thisDataPortion+\
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# ".png",bbox_inches='tight')
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#else:
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print "Skipping plot"
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print "Done!"
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sys.stdout = sys.__stdout__
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#sys.stderr = sys.__stderr__
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@ -1520,6 +1518,8 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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line = fp.readline().split()
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allExpList[iSample,iR,iZ,2] = allExpList[iSample,iR,iZ,1]
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allExpList[iSample,iR,iZ,1] = float(line[1])
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allExpList[iSample,iR,iZ,3] = float(line[2])
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allExpList[iSample,iR,iZ,4] = float(line[3])
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fp.close()
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@ -1617,9 +1617,25 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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for iR in xrange(len(allExpList[0,:,0,0])):
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fp.write(str(allExpList[iSample,iR,iZ,0]) + " " +\
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str(allExpList[iSample,iR,iZ,1]) + " " +\
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str(allExpList[iSample,iR,iZ,2]) + "\n")
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str(allExpList[iSample,iR,iZ,2]) + " " +\
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str(allExpList[iSample,iR,iZ,3]) + " " +\
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str(allExpList[iSample,iR,iZ,4]) + "\n")
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fp.close()
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fp = file(workDir+'/calculatedExpansions_reduced_'+thisDataPortion+'.txt',
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mode="w")
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for iZ in xrange(len(allExpList[0,0,:,0])):
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for iSample in xrange(len(allExpList[:,0,0,0])):
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for iR in xrange(len(allExpList[0,:,0,0])):
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if (allExpList[iSample,iR,iZ,0] == -1): continue
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fp.write(str(allExpList[iSample,iR,iZ,0]) + " " +\
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str(allExpList[iSample,iR,iZ,1]) + " " +\
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str(allExpList[iSample,iR,iZ,2]) + " " +\
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str(allExpList[iSample,iR,iZ,3]) + " " +\
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str(allExpList[iSample,iR,iZ,4]) + "\n")
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fp.close()
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# save all void distribution data to a single file
|
||||
fp = file(workDir+'/voidDistributions_'+thisDataPortion+'.txt',
|
||||
mode="w")
|
||||
|
|
@ -1823,8 +1839,8 @@ def launchVelocityStack(sample, stack, binPath,
|
|||
# Rmax =
|
||||
|
||||
centralRadius = stack.rMin * 0.25
|
||||
Rextracut = stack.rMin*3 + 1
|
||||
Rcircular = stack.rMin*3 + 2
|
||||
Rextracut = stack.rMax*3 + 1
|
||||
Rcircular = stack.rMax*3 + 2
|
||||
|
||||
parameters="--velocityField=%s --voidCenters=%s --Rmax=%e --L0=%e --numBins=%d" % (velField_file, voidCenters, Rmax, Boxsize, numBins)
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue