mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
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Merge branch 'master' of bitbucket.org:cosmicvoids/void_identification
This commit is contained in:
Guilhem Lavaux
commit
e9194f5c55
3 changed files with 151 additions and 98 deletions
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@ -62,7 +62,7 @@ def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
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def writeScript(setName, dataFileNameBase, dataFormat,
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scriptDir, catalogDir, fileNums, redshifts, numSubvolumes,
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numSlices, useVel, lbox, minRadius, omegaM, subsample=1.0,
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suffix=".dat"):
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suffix=".dat", dataFileNameList=None):
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if useVel: setName += "_pv"
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@ -134,7 +134,7 @@ newSample = Sample(dataFile = "{dataFile}",
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numSubvolumes = {numSubvolumes},
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mySubvolume = "{mySubvolume}",
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useLightCone = {useLightCone},
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subsample = {subsample})
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subsample = "{subsample}")
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dataSampleList.append(newSample)
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newSample.addStack(0.0, 5.0, 20, 25, False, False)
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newSample.addStack(0.0, 5.0, 30, 35, False, False)
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@ -165,33 +165,32 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False)
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for i in xrange(len(zVsDY)):
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zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
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if useLightCone:
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boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
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LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
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dzSafe = 0.03
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else:
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boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
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LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
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#boxWidthZ = lbox*100./LIGHT_SPEED
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dzSafe = 0.0
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boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
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LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
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for iSlice in xrange(numSlices):
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sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-2.*dzSafe)/numSlices
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sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-2.*dzSafe)/numSlices
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if useLightCone:
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dzSafe = 0.03
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sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-2.*dzSafe)/numSlices
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sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-2.*dzSafe)/numSlices
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sliceMinMpc = sliceMin*LIGHT_SPEED/100.
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sliceMaxMpc = sliceMax*LIGHT_SPEED/100.
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else:
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sliceMinMpc = LIGHT_SPEED/100.*vp.angularDiameter(sliceMin, Om=Om)
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sliceMaxMpc = LIGHT_SPEED/100.*vp.angularDiameter(sliceMax, Om=Om)
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sliceMinMpc = zBoxMpc + iSlice*lbox/numSlices
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sliceMaxMpc = zBoxMpc + (iSlice+1)*lbox/numSlices
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sliceMin = np.interp(sliceMinMpc*100./LIGHT_SPEED, zVsDX, zVsDY)
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sliceMax = np.interp(sliceMaxMpc*100./LIGHT_SPEED, zVsDX, zVsDY)
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sliceMin = "%0.2f" % sliceMin
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sliceMax = "%0.2f" % sliceMax
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sliceMinMpc = "%0.1f" % sliceMinMpc
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sliceMaxMpc = "%0.1f" % sliceMaxMpc
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dataFileName = dataFileNameBase + fileNum + suffix
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if (dataFileNameList != None):
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dataFileName = dataFileNameList[iFile]
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else:
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dataFileName = dataFileNameBase + fileNum + suffix
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for iX in xrange(numSubvolumes):
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for iY in xrange(numSubvolumes):
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@ -216,7 +215,7 @@ newSample.addStack(0.0, 5.0, 90, 95, False, False)
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numSubvolumes=numSubvolumes,
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mySubvolume=mySubvolume,
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useLightCone=useLightCone,
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subsample=subsample))
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subsample=str(subsample).strip('[]')))
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scriptFile.close()
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return
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@ -233,44 +232,60 @@ if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir)
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# ss0.000175 ~ SDSS DR9 mid
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baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
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prevSubSample = -1
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for thisSubSample in sorted(subSamples, reverse=True):
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subSamples = sorted(subSamples, reverse=True)
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for iSubSample in xrange(len(subSamples)):
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keepFraction = float(thisSubSample) / baseResolution
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maxKeep = keepFraction * numPart
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subSampleList = subSamples[0:iSubSample+1]
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keepFractionList = []
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for subSample in subSampleList:
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keepFractionList.append(float(subSample) / baseResolution)
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thisSubSample = subSamples[iSubSample]
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maxKeep = keepFractionList[-1] * numPart
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minRadius = int(np.ceil(lbox/maxKeep**(1./3)))
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partFileList = []
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for (iRedshift, redshift) in enumerate(redshifts):
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if particleFileDummy == '':
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partFileList.append(particleFileBase+fileNums[iRedshift])
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else:
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partFileList.append(particleFileBase.replace(particleFileDummy,
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fileNums[iRedshift]))
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if args.script or args.all:
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print " Doing subsample", thisSubSample, "scripts"
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sys.stdout.flush()
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setName = prefix+"ss"+str(thisSubSample)
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if dataFormat == "multidark":
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subSampleToUse = 1.0
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fileToUse = prefix+"ss"+str(thisSubSample)+"_z"
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suffix = ".dat"
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elif dataFormat == "gadget":
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subSampleToUse = keepFraction
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#subSampleToUse = thisSubSample
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fileToUse = particleFileBase
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suffix = ""
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elif dataFormat == "lanl":
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subSampleToUse = keepFraction
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#subSampleToUse = thisSubSample
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fileToUse = particleFileBase
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suffix = ""
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elif dataFormat == "random":
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if dataFormat == "random":
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subSampleToUse = 1.0
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fileToUse = "ran.ss"+str(thisSubSample)+"_z"
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suffix = ".dat"
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writeScript(setName, fileToUse, dataFormat,
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writeScript(setName, fileToUse, dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
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subsample=subSampleToUse, suffix=suffix)
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writeScript(setName, fileToUse, dataFormat,
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writeScript(setName, fileToUse, dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
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subsample=subSampleToUse, suffix=suffix)
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else:
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subSampleToUse = keepFractionList
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suffix = ""
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fileToUse = partFileList[0]
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writeScript(setName, fileToUse, dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
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subsample=subSampleToUse, suffix=suffix,
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dataFileNameList=partFileList)
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writeScript(setName, fileToUse, dataFormat,
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
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subsample=subSampleToUse, suffix=suffix,
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dataFileNameList=partFileList)
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if args.subsample or args.all:
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print " Doing subsample", thisSubSample
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sys.stdout.flush()
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@ -411,31 +426,37 @@ if (args.halos or args.all) and haloFileBase != "":
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sampleName = prefix+"halos_min"+str(minHaloMass)+"_z"+fileNums[iRedshift]
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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" %(numPart))
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inFile = open(dataFile, 'r')
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for (iHalo,line) in enumerate(inFile):
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if iHalo < haloFileNumComLines: continue
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line = line.split(haloFileColSep)
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if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
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x = float(line[haloFileXCol])
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y = float(line[haloFileYCol])
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z = float(line[haloFileZCol])
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vz = float(line[haloFileVZCol])
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vy = float(line[haloFileVYCol])
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vx = float(line[haloFileVXCol])
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if dataFormat == "sdf":
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# TODO process halo file with SDFcvt
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
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outFile.close()
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else:
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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inFile = open(dataFile, 'r')
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for (iHalo,line) in enumerate(inFile):
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if iHalo < haloFileNumComLines: continue
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line = line.split(haloFileColSep)
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if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
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x = float(line[haloFileXCol])
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y = float(line[haloFileYCol])
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z = float(line[haloFileZCol])
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vz = float(line[haloFileVZCol])
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vy = float(line[haloFileVYCol])
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vx = float(line[haloFileVXCol])
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# write to output file
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outFile.write("%d %e %e %e %e %e %e\n" %(iHalo,x,y,z,vz,vy,vx))
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# write to output file
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outFile.write("%d %e %e %e %e %e %e\n" %(iHalo,x,y,z,vz,vy,vx))
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outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
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inFile.close()
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outFile.close()
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outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
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outFile.close()
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inFile.close()
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# -----------------------------------------------------------------------------
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# now the HOD
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@ -510,6 +531,14 @@ if (args.hod or args.all) and haloFileBase != "":
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else:
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haloFile = catalogDir+haloFileBase.replace(haloFileDummy,
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fileNums[iRedshift])
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if dataFormat == "sdf":
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# TODO process halo file with SDFcvt
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inFile = haloFile
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outFile = haloFile+"_temp"
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haloFile = outFile
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parFile.write(parFileText.format(omegaM=omegaM,
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hubble=hubble,
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redshift=redshift,
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@ -535,4 +564,6 @@ if (args.hod or args.all) and haloFileBase != "":
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os.system("mv %s/hod.mock %s" % (catalogDir, outFileName))
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os.system("rm %s/hod.*" % catalogDir)
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os.system("rm %s" % haloFile)
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print " Done!"
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@ -105,37 +105,43 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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datafile = inputDataDir+"/"+sample.dataFile
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if regenerate:
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inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+sampleName+".par"
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outputFile = zobovDir+"/regenerated_zobov_slice_" + sampleName
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else:
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inputParameterFlag = ""
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outputFile = zobovDir+"/zobov_slice_" + sampleName
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prevSubSample = -1
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for thisSubSample in sample.subsample.split(', '):
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if prevSubSample == -1:
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inputParameterFlag = ""
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outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + thisSubSample
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keepFraction = float(thisSubSample)
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subSampleLine = "subsample %g" % keepFraction
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else:
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inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+\
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sampleName+"_ss"+prevSubSample+".par"
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outputFile = zobovDir+"/_zobov_slice_" + sampleName + "_ss" + thisSubSample
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keepFraction = float(thisSubSample)/float(prevSubSample)
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subSampleLine = "resubsample %g" % keepFraction
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if sample.usePecVel:
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includePecVelString = "peculiarVelocities"
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else:
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includePecVelString = ""
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if sample.usePecVel: includePecVelString = "peculiarVelocities"
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if sample.useLightCone:
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useLightConeString = "cosmo"
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else:
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useLightConeString = ""
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if sample.useLightCone: useLightConeString = "cosmo"
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if sample.dataFormat == "multidark" or sample.dataFormat == "random":
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dataFileLine = "multidark " + datafile
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elif sample.dataFormat == "gadget":
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dataFileLine = "gadget " + datafile
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if sample.dataFormat == "multidark" or sample.dataFormat == "random":
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dataFileLine = "multidark " + datafile
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elif sample.dataFormat == "gadget":
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dataFileLine = "gadget " + datafile
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elif sample.dataFormat == "sdf":
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dataFileLine = "sdf " + datafile
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iX = float(sample.mySubvolume[0])
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iY = float(sample.mySubvolume[1])
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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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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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conf="""
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conf="""
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%s
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output %s
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outputParameter %s
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@ -148,36 +154,52 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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rangeY_max %g
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rangeZ_min %g
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rangeZ_max %g
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subsample %g
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%s
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%s
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""" % (dataFileLine, outputFile,
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zobovDir+"/zobov_slice_"+sampleName+".par",
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outputFile+".par",
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includePecVelString,
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useLightConeString,
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sample.dataUnit,
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xMin, xMax, yMin, yMax,
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sample.zBoundaryMpc[0], sample.zBoundaryMpc[1],
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sample.subsample,inputParameterFlag)
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subSampleLine,inputParameterFlag)
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parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
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parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
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file(parmFile, mode="w").write(conf)
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file(parmFile, mode="w").write(conf)
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if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")):
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cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
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os.system(cmd)
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if jobSuccessful(logFile, "Done!\n"):
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print "done"
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else:
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print "FAILED!"
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exit(-1)
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doneLine = "Done! %5.2e\n" % keepFraction
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print "TEST", doneLine
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if not (continueRun and jobSuccessful(logFile, doneLine)):
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if (prevSubSample == -1):
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cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
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else:
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cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile)
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os.system(cmd)
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if not jobSuccessful(logFile, doneLine):
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print "FAILED!"
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exit(-1)
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else:
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print "already done!"
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# remove intermediate files
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if (prevSubSample != -1):
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os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample+".par")
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os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample)
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prevSubSample = thisSubSample
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if (continueRun and jobSuccessful(logFile, doneLine)): print "already done!"
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if jobSuccessful(logFile, doneLine): print "done"
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# place the final subsample
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os.system("mv %s %s" % (zobovDir+"/zobov_slice_"+sampleName+"_ss"+\
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prevSubSample, zobovDir+"/zobov_slice_"+sampleName))
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os.system("mv %s %s" % (zobovDir+"/zobov_slice_"+sampleName+"_ss"+\
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prevSubSample+".par", zobovDir+"/zobov_slice_"+sampleName+".par"))
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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", zobovDir))
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#os.system("mv %s %s" % ("sample_info.txt", zobovDir))
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if os.access(parmFile, os.F_OK):
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os.unlink(parmFile)
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