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https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
improved handling of SDF files
This commit is contained in:
P.M. Sutter
parent
eb7446e4f5
commit
b19fbca2ad
3 changed files with 91 additions and 135 deletions
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@ -69,6 +69,39 @@ if not os.access(filename, os.F_OK):
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parms = imp.load_source("name", filename)
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globals().update(vars(parms))
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#------------------------------------------------------------------------------
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def getSDFTags(dataFile):
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idTag = "id"
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for line in open(dataFile):
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if "int64_t id" in line:
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idTag = "id"
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break
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if "int64_t ident" in line:
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idTag = "ident"
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break
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massTag = "mass"
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for line in open(dataFile):
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if "float m200b" in line:
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massTag = "m200b"
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break
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if "float mass" in line:
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massTag = "mass"
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break
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pidTag = ""
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iLine = 0
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for line in open(dataFile):
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iLine += 1
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if iLine > 100: break
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if "parent_id" in line:
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pidTag = "parent_id"
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break
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if "pid" in line:
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pidTag = "pid"
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break
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return idTag, massTag, pidTag
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#------------------------------------------------------------------------------
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def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
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@ -566,26 +599,7 @@ if (args.script or args.all) and haloFileBase != "":
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numPart = 0
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if dataFormat == "sdf":
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SDFcvt_PATH = "@CMAKE_BINARY_DIR@/external/libsdf/apps/SDFcvt/SDFcvt.x86_64"
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massTag = "mass"
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for line in open(dataFile):
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if "float m200b" in line:
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massTag = "m200b"
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break
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if "float mass" in line:
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massTag = "mass"
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break
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pidTag = ""
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iLine = 0
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for line in open(dataFile):
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iLine += 1
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if iLine > 100: break
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if "parent_id" in line:
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pidTag = "parent_id"
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break
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if "pid" in line:
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pidTag = "pid"
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break
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idTag, massTag, pidTag = getSDFTags(dataFile)
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if minHaloMass == "none":
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command = "%s -a 200000 %s %s %s | awk '{if ($2==-1) print $1}' | wc" % (SDFcvt_PATH, dataFile, massTag, pidTag)
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@ -686,35 +700,7 @@ if (args.halos or args.all) and haloFileBase != "" and len(minHaloMasses) > 0:
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outFile.close()
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if dataFormat == "sdf":
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idTag = "id"
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for line in open(dataFile):
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if "int64_t id" in line:
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idTag = "id"
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break
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if "int64_t ident" in line:
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idTag = "ident"
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break
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massTag = "mass"
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for line in open(dataFile):
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if "float m200b" in line:
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massTag = "m200b"
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break
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if "float mass" in line:
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massTag = "mass"
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break
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pidTag = ""
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iLine = 0
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for line in open(dataFile):
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iLine += 1
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if iLine > 100: break
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if "parent_id" in line:
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pidTag = "parent_id"
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break
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if "pid" in line:
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pidTag = "pid"
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break
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idTag, massTag, pidTag = getSDFTags(dataFile)
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SDFcvt_PATH = "@CMAKE_BINARY_DIR@/external/libsdf/apps/SDFcvt/SDFcvt.x86_64"
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if minHaloMass == "none":
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@ -832,6 +818,7 @@ if (args.halos or args.all) and haloFileBase != "":
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print " ERROR: not enough halos to support that density! Maximum is %g" % (1.*numPart / lbox**3)
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exit(-1)
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sampleName = prefix+"halos_den"+str(haloDen)+"_z"+redshifts[iRedshift]
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outFileName = catalogDir+"/"+sampleName+".dat"
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outFile = open(outFileName, 'w')
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@ -843,48 +830,42 @@ if (args.halos or args.all) and haloFileBase != "":
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outFile.close()
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if dataFormat == "sdf":
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idTag = "id"
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for line in open(dataFile):
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if "int64_t id" in line:
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idTag = "id"
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break
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if "int64_t ident" in line:
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idTag = "ident"
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break
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massTag = "mass"
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for line in open(dataFile):
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if "float m200b" in line:
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massTag = "m200b"
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break
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if "float mass" in line:
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massTag = "mass"
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break
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pidTag = ""
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iLine = 0
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for line in open(dataFile):
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iLine += 1
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if iLine > 100: break
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if "parent_id" in line:
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pidTag = "parent_id"
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break
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if "pid" in line:
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pidTag = "pid"
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break
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print "TEST", massTag, pidTag
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idTag, massTag, pidTag = getSDFTags(dataFile)
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tempFile = catalogDir+"/temp_"+sampleName+".dat"
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SDFcvt_PATH = "@CMAKE_BINARY_DIR@/external/libsdf/apps/SDFcvt/SDFcvt.x86_64"
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command = "%s -a 200000 %s %s %s x y z vz vy vx %s | sort -rg -k 1 | awk '{if ($9==-1 && NR < %d) print $2, $3, $4, $5, $6, $7, $8, $1}'>>%s" % (SDFcvt_PATH, dataFile, massTag, idTag, pidTag, numPartExpect, outFileName )
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command = "%s -a 200000 %s %s %s x y z vz vy vx %s | awk '{if ($9==-1) print $2, $3, $4, $5, $6, $7, $8, $1}'>>%s" % (SDFcvt_PATH, dataFile, massTag, idTag, pidTag, tempFile )
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#os.system(command)
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subprocess.call(command, shell=True)
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outFile = open(outFileName, 'a')
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# do the check again since now we've filtered out subhalos
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numPart = 0
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for line in enumerate(tempFile):
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numPart += 1
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actualDen = 1.*numPart / lbox**3
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keepFraction = haloDen / actualDen
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if numPart < numPartExpect:
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print " ERROR: not enough galaxies to support that density! Maximum is %g" % (1.*numPart / lbox**3)
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exit(-1)
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numKept = 0
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for (iLine,line) in enumerate(inFile):
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if np.random.uniform() > keepFraction: continue
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outFile.write(line)
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numKept += 1
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outFile.write("-99 -99 -99 -99 -99 -99 -99 -99\n")
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outFile.close()
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else:
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actualDen = 1.*numPart / lbox**3
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keepFraction = haloDen / actualDen
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inFile = open(dataFile, 'r')
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haloList = []
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outFile = open(outFileName, 'a')
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for (iHalo,line) in enumerate(inFile):
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if iHalo < haloFileNumComLines: continue
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if np.random.uniform() > keepFraction: continue
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line = line.split(haloFileColSep)
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x = float(line[haloFileXCol]) * haloFilePosRescale
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y = float(line[haloFileYCol]) * haloFilePosRescale
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@ -893,31 +874,13 @@ if (args.halos or args.all) and haloFileBase != "":
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vy = float(line[haloFileVYCol])
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vx = float(line[haloFileVXCol])
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mass = float(line[haloFileMCol])
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haloList.append((x,y,z,vz,vy,vx,mass))
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inFile.close()
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haloList = np.array(haloList)
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haloMasses = haloList[:,6]
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haloList = haloList[np.argsort(haloMasses)[::-1]]
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outFile = open(outFileName, 'a')
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for iHalo in xrange(numPartExpect):
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x = haloList[iHalo,0]
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y = haloList[iHalo,1]
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z = haloList[iHalo,2]
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vz = haloList[iHalo,3]
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vy = haloList[iHalo,4]
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vx = haloList[iHalo,5]
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mass = haloList[iHalo,6]
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# write to output file
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outFile.write("%d %e %e %e %e %e %e %e\n" %(iHalo,x,y,z,
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vz,vy,vx,mass))
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outFile.write("%d %e %e %e %e %e %e %e\n" %(iHalo,x,y,z,
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vz,vy,vx,mass))
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outFile.write("-99 -99 -99 -99 -99 -99 -99 -99\n")
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inFile.close()
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outFile.close()
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# -----------------------------------------------------------------------------
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# now the HOD
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parFileText = """
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@ -1010,26 +973,7 @@ if (args.hod or args.all) and haloFileBase != "":
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inFile = haloFile
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outFile = haloFile+"_temp"
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massTag = "mass"
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for line in open(inFile):
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if "float m200b" in line:
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massTag = "m200b"
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break
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if "float mass" in line:
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massTag = "mass"
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break
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pidTag = ""
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iLine = 0
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for line in open(inFile):
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iLine += 1
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if iLine > 100: break
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if "parent_id" in line:
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pidTag = "parent_id"
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break
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if "pid" in line:
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pidTag = "pid"
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break
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idTag, massTag, pidTag = getSDFTags(inFile)
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SDFcvt_PATH = "@CMAKE_BINARY_DIR@/external/libsdf/apps/SDFcvt/SDFcvt.x86_64"
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command = "%s -a 200000 %s %s x y z vx vy vz %s | awk '{if ($8 ==-1) print $1, $2, $3, $4, $5, $6, $7}'>>%s" % (SDFcvt_PATH, inFile, massTag, pidTag, outFile)
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@ -1106,14 +1050,17 @@ if (args.hod or args.all) and haloFileBase != "":
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inFile = open(catalogDir+"/hod_"+sampleName+".mock")
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("%f\n" %(lbox))
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outFile.write("%s\n" %(omegaM))
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outFile.write("%s\n" %(hubble))
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outFile.write("%s\n" %(redshift))
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outFile.write("%d\n" %(numPartExpect))
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#outFile.write("%f\n" %(lbox))
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#outFile.write("%s\n" %(omegaM))
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#outFile.write("%s\n" %(hubble))
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#outFile.write("%s\n" %(redshift))
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#outFile.write("%d\n" %(numPartExpect))
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numKept = 0
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for (iLine,line) in enumerate(inFile):
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if iLine < 5:
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outFile.write(line)
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continue
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if np.random.uniform() > keepFraction: continue
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outFile.write(line)
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numKept += 1
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@ -21,6 +21,8 @@
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import os
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from numpy import abs
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import matplotlib
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matplotlib.use('Agg')
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LIGHT_SPEED = 299792.458
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@ -325,6 +325,9 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
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else:
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maskIndex = -1
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maxDen = 0.2
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# TEST
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#maxDen = 1.e99
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# END TEST
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if not (continueRun and jobSuccessful(logFile, "Done!\n")):
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for fileName in glob.glob(zobovDir+"/part._"+sampleName+".*"):
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@ -413,6 +416,9 @@ def launchPrune(sample, binPath,
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mockIndex = -1
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maxDen = 0.2
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observationLine = ""
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# TEST
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#maxDen = 1.e99
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# END TEST
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#periodicLine = " --periodic='"
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#if sample.numSubvolumes == 1: periodicLine += "xy"
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@ -577,7 +583,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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centralRadius = stack.rMin * 0.25
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# restrict to relavent ranges of sample
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# restrict to relevant ranges of sample
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zMin = max(sample.zRange[0],stack.zMin) * 3000
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zMax = min(sample.zRange[1],stack.zMax) * 3000
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@ -596,6 +602,9 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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else:
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maskIndex = 999999999
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maxDen = 0.2
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# TEST
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#maxDen = 1.e99
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# END TEST
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if INCOHERENT:
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nullTestFlag = "INCOHERENT"
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@ -1219,8 +1228,8 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=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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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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@ -1231,11 +1240,9 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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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] > stack.rMax or \
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# args[0][2] > stack.rMax) and \
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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_radial_inertia(voidDir, stack.rMax, mode="symmetric", nBootstraps=5)
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#ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, nBootstraps=100, rMaxInertia=1.0)
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ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="2d", nBootstraps=500, rMaxInertia=0.7)
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#ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="symmetric", nBootstraps=500, rMaxInertia=100)
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badChain = False
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