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https://bitbucket.org/cosmicvoids/vide_public.git
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removed mock particle tracking, since that is no longer used
This commit is contained in:
Paul M. Sutter
parent
fc2d7157f4
commit
d9efa15474
8 changed files with 71 additions and 173 deletions
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@ -32,7 +32,6 @@ import shutil
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import glob
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import subprocess
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import sys
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from pylab import figure
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from netCDF4 import Dataset
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from backend.classes import *
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from backend.cosmologyTools import *
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@ -120,7 +119,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
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sample.zRange[1], sample.zRange[0], sample.zRange[1], "all",
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sample.omegaM, useComoving=useComoving)
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numTracers = int(open(outputDir+"/mask_index.txt", "r").read())
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numTracers = int(open("total_particles.txt", "r").read())
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sample.meanPartSep = (1.*numTracers/boxVol/nbar)**(-1/3.)
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# flag edge galaxies with python routine for now
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@ -158,7 +157,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
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sample.zRange[1], sample.zRange[0], sample.zRange[1], "all",
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sample.omegaM, useComoving=useComoving)
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numTracers = int(open(outputDir+"/mask_index.txt", "r").read())
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numTracers = int(open("total_particles.txt", "r").read())
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sample.meanPartSep = (1.*numTracers/boxVol/nbar)**(-1/3.)
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if os.access(parmFile, os.F_OK): os.unlink(parmFile)
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@ -169,8 +168,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
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if os.access("comoving_distance.txt", os.F_OK):
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os.system("mv %s %s" % ("comoving_distance.txt", outputDir))
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if os.access("mask_index.txt", os.F_OK):
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os.system("mv %s %s" % ("mask_index.txt", outputDir))
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if os.access("total_particles.txt", os.F_OK):
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os.system("mv %s %s" % ("total_particles.txt", outputDir))
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if os.access("galaxies.txt", os.F_OK):
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@ -333,10 +331,8 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
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if os.access(parmFile, os.F_OK):
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os.unlink(parmFile)
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if os.access("mask_index.txt", os.F_OK):
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os.system("mv %s %s" % ("mask_index.txt", outputDir))
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if os.access("total_particles.txt", os.F_OK):
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os.system("mv %s %s" % ("total_particles.txt", outputDir))
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#os.system("mv %s %s" % ("sample_info.txt", outputDir))
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# save this sample's information
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with open(outputDir+"/sample_info.dat", mode='wb') as output:
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@ -382,15 +378,9 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
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if os.access(vozScript, os.F_OK):
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os.unlink(vozScript)
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if sample.dataType == "observation":
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maskIndex = open(outputDir+"/mask_index.txt", "r").read()
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totalPart = open(outputDir+"/total_particles.txt", "r").read()
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maxDen = mergingThreshold*float(maskIndex)/float(totalPart)
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else:
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maskIndex = -1
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maxDen = mergingThreshold
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if numZobovDivisions == 1:
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print(" WARNING! You are using a single ZOBOV division with a simulation. Periodic boundaries will not be respected!")
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maxDen = mergingThreshold
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if sample.dataType == "simulation" and numZobovDivisions == 1:
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print(" WARNING! You are using a single ZOBOV division with a simulation. Periodic boundaries will not be respected!")
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if not (continueRun and jobSuccessful(logFile, "Done!\n")):
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for fileName in glob.glob(outputDir+"/part._"+sampleName+".*"):
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@ -404,7 +394,7 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
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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, outputDir, str(maskIndex)]
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binPath, outputDir]
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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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@ -483,21 +473,24 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
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else:
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volFileToUse = outputDir+"/vol_"+sampleName+".dat"
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# double-check to make sure galaxies were flagged correctly.
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# if any non-edge galaxies have bad tesselations, flag them
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# also, re-weight the volumes of any edge galaxies to prevent watershed
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# from spilling outside of survey region
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# Zobov places guard particles at the domain walls; adjacenies to these
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# guard particles are not tracked in the final tesselation.
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# Therefore, if a galaxy marked as "interior" is missing an adjancency, that
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# means it erroneously connected to a guard particle.
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#
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# Re-weight the volumes of any edge galaxies to prevent watershed
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# from spilling outside of survey region.
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if sample.dataType == "observation":
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log = open(logFile, 'a')
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log.write("\nDouble-checking all edge flags.\n\n")
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log.write("\nDouble-checking all edge flags.\n")
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# read in the edge flag information
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edgeFile = outputDir+"/galaxy_edge_flags.txt"
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edgeFlags = np.loadtxt(edgeFile, dtype=np.int32)
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# load in and count adjacenies
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log.write("Loading adjancies...\n")
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log.write(" Loading adjancies...\n")
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part = []
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adjFile = outputDir+"adj_"+sampleName+".dat"
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with open(adjFile, mode="rb") as File:
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@ -516,21 +509,18 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
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part[p].adjs.append(pAdj)
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part[pAdj].adjs.append(p)
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# if the number of expected adjancies != actual adjacenies, this galaxy
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# connected to a guard point on the boundary. This is fine for edge
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# galaxies, but occasionally interior galaxies slip through the
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# boundary handling, so we'll mark those as an edge
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for p in range(numPart):
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nHave = len(part[p].adjs)
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nExpected = nadjPerPart[p]
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#print("Working on %d: %d vs %d" % (p, nHave, nExpected))
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if nHave != nExpected and edgeFlags[p] == 0:
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log.write("Found an unflagged galaxy: %d. Correcting.\n" % (p))
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# an interior galaxy slipped through the boundary
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if edgeFlags[p] == 0 and nHave != nExpected:
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log.write(" Found an unflagged galaxy: %d. Correcting.\n" % (p))
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edgeFlags[p] = 4
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# re-write the new edge flag information
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np.savetxt(edgeFile, edgeFlags, fmt="%d")
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log.write("\nDone double-checking. New flags saved.\n")
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log.write(" Done double-checking. New flags saved.\n")
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# read in the appropriate volume file
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log.write("Re-weighting edge galaxy volumes...\n")
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@ -599,15 +589,11 @@ def launchPrune(sample, binPath,
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open(outputDir+"/voidDesc_"+sampleName+".out"))
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numVoids -= 2
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maxDen = mergingThreshold
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if sample.dataType == "observation":
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mockIndex = open(outputDir+"/mask_index.txt", "r").read()
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totalPart = open(outputDir+"/total_particles.txt", "r").read()
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maxDen = mergingThreshold*float(mockIndex)/float(totalPart)
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observationLine = " --isObservation"
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#periodicLine = " --periodic=''"
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else:
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mockIndex = -1
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maxDen = mergingThreshold
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observationLine = ""
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periodicLine = " --periodic='" + getPeriodic(sample) + "'"
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@ -646,7 +632,6 @@ def launchPrune(sample, binPath,
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cmd += " --partEdge=" + outputDir+"galaxy_edge_flags.txt"
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cmd += " --extraInfo=" + outputDir+"/zobov_slice_"+str(sampleName)+".par"
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cmd += " --tolerance=" + str(boundaryTolerance)
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cmd += " --mockIndex=" + str(mockIndex)
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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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