mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 23:31:12 +00:00
bug fixes to plotting. prepareCatalogs now handles gadget files; prepareGadgetCatalogs now deprecated
This commit is contained in:
P.M. Sutter
parent
afe22f71fa
commit
390fb2f4e2
4 changed files with 133 additions and 81 deletions
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@ -5,6 +5,7 @@
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from void_python_tools.backend import *
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from void_python_tools.plotting import *
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import imp
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import pickle
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# ------------------------------------------------------------------------------
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@ -60,6 +61,10 @@ for sample in dataSampleList:
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if not os.access(zobovDir, os.F_OK):
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os.makedirs(zobovDir)
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# save this sample's information
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with open(zobovDir+"/sample_info.dat", 'wb') as output:
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pickle.dump(sample, output, pickle.HIGHEST_PROTOCOL)
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# ---------------------------------------------------------------------------
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if (startCatalogStage <= 1) and (endCatalogStage >= 1) and not sample.isCombo:
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print " Extracting tracers from catalog...",
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@ -10,33 +10,67 @@ import sys
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import void_python_tools as vp
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import argparse
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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# CONFIGURATION
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# directory for the input simulation/observational particle files
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catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/multidark/"
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scriptDir = os.getenv("PWD")+"/multidark/"
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# path to HOD code
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hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
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outputDir = os.getenv("HOME")+"/workspace/Voids/multidark/"
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# where to put the final void catalog, figures, and output logs
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voidOutputDir = os.getenv("HOME")+"/workspace/Voids/multidark/"
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figDir = os.getenv("PWD")+"/../figs/multidark/"
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logDir = os.getenv("PWD")+"/../logs/multidark/"
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dataFormat = "multidark"
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dataUnit = 1
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# where to place the pipeline scripts
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scriptDir = os.getenv("PWD")+"/multidark/"
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# simulation or observation?
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dataType = "simulation"
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# available formats for simulation: gadget, multidark
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dataFormat = "multidark"
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dataUnit = 1 # as multiple of Mpc/h
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# place particles on the lightcone?
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useLightCone = True
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redshiftFileBase = "mdr1_particles_z"
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# common filename of particle files
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particleFileBase = "mdr1_particles_z"
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# list of file numbers for the particle files
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# to get particle file name, we take particleFileBase+fileNum
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fileNums = (("0.0", "0.53", "1.0"))
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# redshift of each file in the above list
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redshifts = (("0.0", "0.53", "1.0"))
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# how many independent slices along the z-axis?
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numSlices = 4
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# how many subdivisions along the x- and y- axis?
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# ( = 2 will make 4 subvolumes for each slice, = 3 will make 9, etc.)
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numSubvolumes = 1
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# prefix to give all outputs
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prefix = "md_"
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# list of desired subsamples
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subSamples = ((0.1, 0.05, 0.01, 0.002, 0.001, 0.0004, 0.0002))
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numPart = 1024*1024*1024 # number of particles in base catalog
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lbox = 1000
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# simulation information
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numPart = 1024*1024*1024
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lbox = 1000 # Mpc/h
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omegaM = 0.27
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hubble = 0.70
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# END CONFIGURATION
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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LIGHT_SPEED = 299792.458
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parser = argparse.ArgumentParser(description='options')
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@ -58,35 +92,31 @@ parser.add_argument('--all', dest='all', action='store_const',
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args = parser.parse_args()
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#------------------------------------------------------------------------------
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def getSampleName(prefix, base, redshift, useVel, iSlice=-1, iVol=-1):
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useVelString = ""
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if useVel: useVelString = "_pv"
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def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
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sampleName = prefix + base + useVelString + "_z" + redshift
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sampleName = setName
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if iSlice != -1:
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sampleName += "_s" + str(iSlice)
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#if useVel: sampleName += "_pv"
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if iVol != -1:
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sampleName += "_d" + iVol
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sampleName += "_z" + redshift
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#if iSlice != -1: sampleName += "_s" + str(iSlice)
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if iVol != -1: sampleName += "_d" + iVol
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return sampleName
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#------------------------------------------------------------------------------
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# for given dataset parameters, outputs a script for use with analyzeVoids
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def writeScript(prefix, base, scriptDir, catalogDir, redshifts, numSubvolumes,
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def writeScript(setName, dataFileNameBase,
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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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setName = prefix + base
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dataFileNameBase = setName #+ ".dat"
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if useVel: setName += "_pv"
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scriptFileName = scriptDir + "/" + "md_" + base
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if useVel: scriptFileName += "_pv"
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scriptFileName += ".py"
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scriptFileName = scriptDir + "/" + setName + ".py"
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scriptFile = open(scriptFileName, 'w')
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scriptFile.write("""#!/usr/bin/env/python
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@ -113,17 +143,17 @@ dataPortions = ["central"]
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dataSampleList = []
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""")
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dataInfo = """
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catalogName = "{sampleName}"
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workDir = "{outputDir}/{sampleName}/"
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inputDataDir = "{catalogDir}"
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figDir = "{figDir}/{sampleName}/"
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logDir = "{logDir}/{sampleName}/"
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dataInfo = """
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setName = "{setName}"
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workDir = "{voidOutputDir}/{setName}/"
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inputDataDir = "{inputDataDir}"
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figDir = "{figDir}/{setName}/"
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logDir = "{logDir}/{setName}/"
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"""
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scriptFile.write(dataInfo.format(sampleName=setName, figDir=figDir,
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logDir=logDir, outputDir=outputDir,
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catalogDir=catalogDir,
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scriptFile.write(dataInfo.format(setName=setName, figDir=figDir,
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logDir=logDir, voidOutputDir=voidOutputDir,
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inputDataDir=catalogDir))
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sampleInfo = """
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@ -156,15 +186,15 @@ newSample.addStack({zMin}, {zMax}, {minRadius}+6, {minRadius}+10, True, False)
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newSample.addStack({zMin}, {zMax}, {minRadius}+10, {minRadius}+18, True, False)
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newSample.addStack({zMin}, {zMax}, {minRadius}+18, {minRadius}+24, True, False)
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"""
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for redshift in redshifts:
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for (iFile, redshift) in enumerate(redshifts):
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fileNum = fileNums[iFile]
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zBox = float(redshift)
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Om = float(omegaM)
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zBoxMpc = LIGHT_SPEED/100.*vp.angularDiameter(zBox, Om=Om)
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boxMaxMpc = zBoxMpc + lbox
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# converter from redshift to comoving distance
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zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000)
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zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000)
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zVsDX = np.zeros(len(zVsDY))
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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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@ -178,31 +208,28 @@ newSample.addStack({zMin}, {zMax}, {minRadius}+18, {minRadius}+24, True, False)
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dzSafe = 0.0
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for iSlice in xrange(numSlices):
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# trim off the first and last 10,000 km/s
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sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-dzSafe)/numSlices
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sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-dzSafe)/numSlices
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sliceMinMpc = sliceMin*LIGHT_SPEED/100.
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sliceMaxMpc = sliceMax*LIGHT_SPEED/100.
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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 + "_z" + redshift + suffix
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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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mySubvolume = "%d%d" % (iX, iY)
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sampleName = getSampleName(prefix, base, sliceMin, useVel,
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iSlice=-1, iVol=mySubvolume)
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#sampleName = getSampleName(prefix, base, redshift, useVel,
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# iSlice=iSlice, iVol=mySubvolume)
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sampleName = getSampleName(setName, sliceMin, useVel,
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iSlice=iSlice, iVol=mySubvolume)
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scriptFile.write(sampleInfo.format(dataFile=dataFileName,
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scriptFile.write(sampleInfo.format(dataFile=dataFileName,
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dataFormat=dataFormat,
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dataUnit=dataUnit,
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sampleName=sampleName,
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@ -240,28 +267,37 @@ for thisSubSample in subSamples:
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if args.script or args.all:
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print " Doing subsample", thisSubSample, " scripts"
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setName = prefix+"ss"+str(thisSubSample)
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if dataFormat == "multidark":
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writeScript(prefix,
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"ss"+str(thisSubSample), scriptDir, catalogDir, redshifts,
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writeScript(setName, "md.ss"+str(thisSubSample)+"_z",
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scriptDir, catalogDir, fileNums,
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redshifts,
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numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
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subsample=1.0)
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writeScript(prefix, "ss"+str(thisSubSample), scriptDir, catalogDir,
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writeScript(setName, "md.ss"+str(thisSubSample)+"_z",
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scriptDir, catalogDir,
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fileNums,
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redshifts, numSubvolumes, numSlices, True, lbox, minRadius,
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omegaM, subsample=1.0)
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elif dataFormat == "gadget":
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writeScript("", redshiftFileBase, scriptDir, catalogDir, redshifts,
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writeScript(setName, particleFileBase, scriptDir, catalogDir, fileNums,
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redshifts,
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numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
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subsample=thisSubSample, suffix="")
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writeScript(setName, particleFileBase, scriptDir, catalogDir, fileNums,
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redshifts,
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numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
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subsample=thisSubSample, suffix="")
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if args.subsample or args.all:
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print " Doing subsample", thisSubSample
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for redshift in redshifts:
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for (iRedshift, redshift) in enumerate(redshifts):
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print " redshift", redshift
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dataFile = catalogDir+"/"+redshiftFileBase+redshift
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dataFile = catalogDir+"/"+particleFileBase+fileNums[iRedshift]
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inFile = open(dataFile, 'r')
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sampleName = getSampleName("ss"+str(thisSubSample), redshift, False)
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sampleName = "md.ss"+str(thisSubSample)+"_z"+redshift
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("%f\n" %(lbox))
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@ -293,7 +329,7 @@ for thisSubSample in subSamples:
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if args.script or args.all:
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print " Doing halo scripts"
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dataFile = catalogDir+"/mdr1_halos_z"+redshifts[0]
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dataFile = catalogDir+"/mdr1_halos_z"+fileNums[0]
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inFile = open(dataFile, 'r')
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numPart = 0
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for line in inFile: numPart += 1
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@ -302,25 +338,27 @@ if args.script or args.all:
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minRadius = 2*int(np.ceil(lbox/numPart**(1./3.)))
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if dataFormat == "multidark":
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writeScript(prefix, "halos", scriptDir, catalogDir, redshifts,
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setName = prefix+"halos"
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writeScript(setName, "md.halos_z", scriptDir, catalogDir, fileNums,
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redshifts,
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numSubvolumes, numSlices, False, lbox, minRadius, omegaM)
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writeScript(prefix, "halos", scriptDir, catalogDir, redshifts, numSubvolumes,
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writeScript(setName, "md.halos_z", scriptDir, catalogDir, fileNums,
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redshifts, numSubvolumes,
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numSlices, True, lbox, minRadius, omegaM)
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if args.halos or args.all:
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print " Doing halos"
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for redshift in redshifts:
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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dataFile = catalogDir+"/mdr1_halos_z"+redshift
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dataFile = catalogDir+"/mdr1_halos_z"+fileNums[iRedshift]
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inFile = open(dataFile, 'r')
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numPart = 0
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for line in inFile: numPart += 1
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inFile.close()
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sampleName = getSampleName("halos", redshift, False)
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sampleName = "md.halos_z"+redshift
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("%f\n" %(lbox))
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@ -390,21 +428,22 @@ root_filename hod
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if args.script or args.all:
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print " Doing DR7 HOD scripts"
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if dataFormat == "multidark":
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writeScript(prefix,
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"hod_dr72dim2", scriptDir, catalogDir, redshifts,
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setName = prefix+"hod_dr72dim2"
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writeScript(setName, "md.hod_dr72dim2_z",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, 5, omegaM)
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writeScript(prefix,
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"hod_dr72dim2", scriptDir, catalogDir, redshifts,
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writeScript(setName, "md.hod_dr72dim2_z",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, 5, omegaM)
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if args.hod or args.all:
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print " Doing DR7 HOD"
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for redshift in redshifts:
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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parFileName = "./hod.par"
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parFile = open(parFileName, 'w')
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haloFile = catalogDir+"/mdr1_halos_z"+redshift
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haloFile = catalogDir+"/mdr1_halos_z"+fileNums[iRedshift]
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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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@ -420,7 +459,7 @@ if args.hod or args.all:
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os.system(hodPath+" "+parFileName+">& /dev/null")
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sampleName = getSampleName("hod_dr72dim2", redshift, False)
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sampleName = getSampleName("md.hod_dr72dim2", redshift, False)
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outFileName = catalogDir+"/"+sampleName+".dat"
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os.system("mv hod.mock" + " " + outFileName)
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@ -431,21 +470,22 @@ if args.hod or args.all:
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if args.script or args.all:
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print " Doing DR9 HOD scripts"
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if dataFormat == "multidark":
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writeScript(prefix,
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"hod_dr9mid", scriptDir, catalogDir, redshifts,
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setName = prefix+"hod_dr9mid"
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writeScript(setName, "md.hod_dr9mid_z",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, 5, omegaM)
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writeScript(prefix,
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"hod_dr9mid", scriptDir, catalogDir, redshifts,
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writeScript(prefix, "md.hod_dr9mid_z",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, 5, omegaM)
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if args.hod or args.all:
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print " Doing DR9 HOD"
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for redshift in redshifts:
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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parFileName = "./hod.par"
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parFile = open(parFileName, 'w')
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haloFile = catalogDir+"/mdr1_halos_z"+redshift
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haloFile = catalogDir+"/mdr1_halos_z"+fileNums[iRedshift]
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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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@ -461,7 +501,7 @@ if args.hod or args.all:
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os.system(hodPath+" "+parFileName+">& /dev/null")
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sampleName = getSampleName("hod_dr9mid", redshift, False)
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sampleName = getSampleName("md.hod_dr9mid", redshift, False)
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outFileName = catalogDir+"/"+sampleName+".dat"
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os.system("mv hod.mock" + " " + outFileName)
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@ -8,7 +8,8 @@ import void_python_tools.apTools as vp
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import imp
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import pickle
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import os
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import pylab as plt
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import matplotlib.pyplot as plt
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import numpy as np
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import argparse
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# ------------------------------------------------------------------------------
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@ -17,7 +18,9 @@ workDir = "/home/psutter2/workspace/Voids/"
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figDir = "./figs"
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sampleDirList = [ "multidark/md_halos/sample_md_halos_z0.03_d00/",
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"multidark/md_ss0.1_pv/sample_md_ss0.1_pv_z0.03_d00/" ]
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"multidark/md_ss0.1/sample_md_ss0.1_z0.03_d00/",
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"multidark/md_hod_dr9mid/sample_md_hod_dr9mid_z0.03_d00/",
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"sdss_dr9/sample_lss.dr9cmassmid.dat/" ]
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plotNameBase = "compdist"
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@ -42,7 +45,7 @@ for sampleDir in sampleDirList:
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plt.clf()
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plt.xlabel("Void Radius (Mpc/h)")
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plt.ylabel(r"N > R [h^3 Mpc^{-3}]")
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plt.ylabel(r"N > R [$h^3$ Gpc$^{-3}$]")
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plt.yscale('log')
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plotName = plotNameBase
|
||||
|
|
@ -53,11 +56,15 @@ for (iSample,sample) in enumerate(dataSampleList):
|
|||
lineTitle = sampleName
|
||||
|
||||
if sample.dataType == "observation":
|
||||
boxVol = vp.getSurveyProps(sample.maskFile, stack.zMin, stack.zMax,
|
||||
boxVol = vp.getSurveyProps(sample.maskFile,
|
||||
sample.zBoundary[0], sample.zBoundary[1],
|
||||
sample.zRange[0], sample.zRange[1], "all",
|
||||
selectionFuncFile=sample.selFunFile)[0]
|
||||
else:
|
||||
boxVol = sample.boxLen*sample.boxLen*(sample.zBoundaryMpc[1]-sample.zBoundaryMpc[0])
|
||||
boxVol = sample.boxLen*sample.boxLen*(sample.zBoundaryMpc[1] -
|
||||
sample.zBoundaryMpc[0])
|
||||
|
||||
boxVol *= 1.e-9 # Mpc->Gpc
|
||||
|
||||
filename = workDir+"/"+sampleDirList[iSample]+"/centers_"+dataPortion+"_"+\
|
||||
sampleName+".out"
|
||||
|
|
|
|||
|
|
@ -223,7 +223,7 @@ def plotNumberDistribution(workDir=None, sampleList=None, figDir=None,
|
|||
|
||||
plt.clf()
|
||||
plt.xlabel("Void Radius (Mpc/h)")
|
||||
plt.ylabel(r"N > R [h^3 Mpc^{-3}]")
|
||||
plt.ylabel(r"N > R [$h^3$ Mpc$^{-3}$]")
|
||||
|
||||
plotTitle = setName
|
||||
|
||||
|
|
@ -237,13 +237,16 @@ def plotNumberDistribution(workDir=None, sampleList=None, figDir=None,
|
|||
lineTitle = sampleName
|
||||
|
||||
if sample.dataType == "observation":
|
||||
boxVol = vp.getSurveyProps(sample.maskFile, stack.zMin, stack.zMax,
|
||||
boxVol = vp.getSurveyProps(sample.maskFile,
|
||||
sample.zBoundary[0], sample.zBoundary[1],
|
||||
sample.zRange[0], sample.zRange[1], "all",
|
||||
selectionFuncFile=sample.selFunFile)[0]
|
||||
else:
|
||||
boxVol = sample.boxLen*sample.boxLen*(sample.zBoundaryMpc[1] -
|
||||
sample.zBoundaryMpc[0])
|
||||
|
||||
boxVol *= 1.e-9
|
||||
|
||||
filename = workDir+"/sample_"+sampleName+"/centers_"+dataPortion+"_"+\
|
||||
sampleName+".out"
|
||||
if not os.access(filename, os.F_OK):
|
||||
|
|
@ -265,9 +268,6 @@ def plotNumberDistribution(workDir=None, sampleList=None, figDir=None,
|
|||
plt.legend(title = "Samples", loc = "upper right")
|
||||
plt.title(plotTitle)
|
||||
|
||||
plt.xlim(xMin, xMax)
|
||||
#plt.xlim(xMin, xMax*1.4) # make room for legend
|
||||
|
||||
plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
|
||||
plt.savefig(figDir+"/fig_"+plotName+".eps", bbox_inches="tight")
|
||||
plt.savefig(figDir+"/fig_"+plotName+".png", bbox_inches="tight")
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue