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https://bitbucket.org/cosmicvoids/vide_public.git
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applyMaskToMock now accepts build path
This commit is contained in:
P.M. Sutter
parent
082bfde711
commit
c781c5ee50
2 changed files with 47 additions and 422 deletions
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@ -1,392 +0,0 @@
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#!/usr/bin/env python
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# applies a mask to a given dataset
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import numpy as np
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import os
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import sys
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import void_python_tools as vp
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import argparse
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import imp
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import healpy as hp
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# ------------------------------------------------------------------------------
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def my_import(name):
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mod = __import__(name)
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components = name.split('.')
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for comp in components[1:]:
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mod = getattr(mod, comp)
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return mod
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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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parser.add_argument('--scripts', dest='script', action='store_const',
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const=True, default=False,
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help='write scripts')
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parser.add_argument('--parmFile', dest='parmFile',
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default="",
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help='path to parameter file')
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parser.add_argument('--subsamples', dest='subsample', action='store_const',
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const=True, default=False,
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help='write subsamples')
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parser.add_argument('--halos', dest='halos', action='store_const',
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const=True, default=False,
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help='write halos')
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parser.add_argument('--hod', dest='hod', action='store_const',
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const=True, default=False,
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help='write hod')
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parser.add_argument('--all', dest='all', action='store_const',
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const=True, default=False,
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help='write everything')
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args = parser.parse_args()
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filename = args.parmFile
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print " Loading parameters from", filename
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if not os.access(filename, os.F_OK):
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print " Cannot find parameter file %s!" % filename
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exit(-1)
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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 getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
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sampleName = setName
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sampleName += "_z" + redshift
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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 writeObservationScript(setName, dataFileNameBase, maskFileName,
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scriptDir, catalogDir, fileNums, redshifts,
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useVel, minRadius, omegaM,
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suffix=".dat"):
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if useVel: setName += "_pv"
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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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import os
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from void_python_tools.backend.classes import *
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continueRun = True # set to True to enable restarting aborted jobs
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startCatalogStage = 1
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endCatalogStage = 4
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startAPStage = 1
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endAPStage = 7
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ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
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CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/"
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freshStack = True
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errorBars = "CALCULATED"
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numIncoherentRuns = 100
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ranSeed = 101010
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useLCDM = False
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bias = 1.16
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dataPortions = ["central", "all"]
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dataSampleList = []
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""")
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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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numZobovDivisions = {numZobovDivisions}
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numZobovThreads = {numZobovThreads}
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"""
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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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numZobovDivisions=numZobovDivisions,
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numZobovThreads=numZobovThreads))
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sampleInfo = """
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newSample = Sample(dataFile = "{dataFile}",
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fullName = "{sampleName}",
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nickName = "{sampleName}",
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dataType = "observation",
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maskFile = "{maskFileName}",
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zBoundary = ({zMin}, {zMax}),
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zRange = ({zMin}, {zMax}),
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minVoidRadius = {minRadius},
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includeInHubble = True,
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partOfCombo = False,
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isCombo = False,
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usePecVel = {usePecVel})
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dataSampleList.append(newSample)
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newSample.addStack({zMin}, {zMax}, {minRadius} , {minRadius}+2, True, False)
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newSample.addStack({zMin}, {zMax}, {minRadius} , {minRadius}+4, True, False)
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newSample.addStack({zMin}, {zMax}, {minRadius}+2, {minRadius}+6, True, False)
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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 (iFile, redshift) in enumerate(redshifts):
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fileNum = fileNums[iFile]
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zBox = float(redshift)
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zMin = zBox
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zMax = zBox + 0.1
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zMin, zMax = getMaskedZRange(lbox, zBox, zMin, zMax, omegaM)
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dataFileName = dataFileNameBase + fileNum + suffix
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sampleName = getSampleName(setName, redshift, useVel,
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iSlice=-1, iVol=-1)
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scriptFile.write(sampleInfo.format(dataFile=dataFileName,
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dataFormat=dataFormat,
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sampleName=sampleName,
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maskFileName=maskFileName,
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zMin=zMin,
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zMax=zMax,
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usePecVel=useVel,
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minRadius=minRadius))
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scriptFile.close()
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return
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#------------------------------------------------------------------------------
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# now place these particles on a lightcone, restrict redshift range, apply mask
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def applyMask(inFileName, outFileName, maskFileName, lbox, zBox, zMin, zMax, omegaM):
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mask = hp.read_map(maskFileName)
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nside = hp.get_nside(mask)
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inFile = open(inFileName, 'r')
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outFile = open(outFileName, 'w')
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Om = float(omegaM)
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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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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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zBoxInMpc = vp.angularDiameter(zBox, Om=Om)
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for (iLine,line) in enumerate(inFile):
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if iLine < 5:
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print >> outFile, line.rstrip()
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continue
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line = line.split(' ')
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uniqueID = int(line[0])
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x = float(line[1]) - lbox/2.
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y = float(line[2]) - lbox/2.
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z = float(line[3]) - lbox/2.
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vz = float(line[4])
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# TODO if usePecvel
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redshift = np.sqrt(x*x + y*y + z*z)
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redshift = np.interp(zBoxInMpc+100./LIGHT_SPEED*redshift, zVsDX, zVsDY)
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if redshift < zMin or redshift > zMax: continue
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vec = np.array((x,y,z))
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theta, phi = hp.vec2ang(vec)
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theta = theta[0]
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phi = phi[0]
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RA = phi*180./np.pi
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Dec = 180./np.pi*(np.pi/2.-theta)
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pix = hp.vec2pix(nside, x, y, z)
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if mask[pix] <= 0.2: continue
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print >> outFile, RA, Dec, redshift*LIGHT_SPEED, uniqueID, x, y, z
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inFile.close()
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outFile.close()
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#------------------------------------------------------------------------------
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def getMaskedZRange(lbox, zBox, zMin, zMax, omegaM):
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if zMin < zBox: zMin = zBox
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Om = float(omegaM)
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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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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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zBoxInMpc = vp.angularDiameter(zBox, Om=Om)
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boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
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LIGHT_SPEED*lbox/2., zVsDX, zVsDY)-zBox
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print "RANGE", zBox, zBox+boxWidthZ
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if zMax > zBox+boxWidthZ: zMax = zBox+boxWidthZ
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return zMin, zMax
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#------------------------------------------------------------------------------
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#------------------------------------------------------------------------------
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inCatalogDir = catalogDir
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prefix = "masked_" + prefix
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voidOutputDir += "masked/"
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figDir += "masked/"
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logDir += "masked/"
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scriptDir += "masked/"
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catalogDir += "masked/"
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dataType = "observation"
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if not os.access(scriptDir, os.F_OK): os.mkdir(scriptDir)
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if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir)
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#------------------------------------------------------------------------------
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# first the directly downsampled runs
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# Note: ss0.002 ~ SDSS DR7 dim2
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# ss0.0004 ~ SDSS DR9 mid
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baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
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for thisSubSample in subSamples:
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keepFraction = float(thisSubSample) / baseResolution
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maxKeep = keepFraction * numPart
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minRadius = int(np.ceil(lbox/maxKeep**(1./3)))
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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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writeObservationScript(setName, "masked_md.ss"+str(thisSubSample)+"_z",
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maskFileName,
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scriptDir, catalogDir, fileNums,
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redshifts, False, minRadius, omegaM)
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writeObservationScript(setName, "masked_md.ss"+str(thisSubSample)+"_z",
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maskFileName,
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scriptDir, catalogDir, fileNums,
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redshifts, True, minRadius, omegaM)
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if args.subsample or args.all:
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print " Doing subsample", thisSubSample
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for (iRedshift, redshift) in enumerate(redshifts):
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print " redshift", redshift
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zMin = float(redshift)
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zMax = zMin + 0.1
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zMin, zMax = getMaskedZRange(lbox, float(redshift), zMin, zMax, omegaM)
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if dataFormat == "multidark" or dataFormat == "random":
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inFileName = inCatalogDir+"/md.ss"+str(thisSubSample)+"_z"+redshift+".dat"
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outFileName = catalogDir+"/masked_md.ss"+str(thisSubSample)+"_z"+redshift+".dat"
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applyMask(inFileName, outFileName, maskFileName, lbox, float(redshift),
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zMin, zMax, omegaM)
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# -----------------------------------------------------------------------------
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# now halos
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if (args.script or args.all) and dataFormat == "multidark":
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print " Doing halo scripts"
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for minHaloMass in minHaloMasses:
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if dataFormat == "multidark":
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setName = prefix+"halos_min"+str(minHaloMass)
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writeScript(setName, "md.halos_min"+str(minHaloMass)+"_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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writeScript(setName, "md.halos_min"+str(minHaloMass)+"_z",
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scriptDir, catalogDir, fileNums,
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redshifts,
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numSubvolumes, 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 minHaloMass in minHaloMasses:
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print " min halo mass = ", minHaloMass
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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dataFile = catalogDir+haloFileBase+fileNums[iRedshift]
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inFile = open(dataFile, 'r')
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numPart = 0
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for line in inFile:
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line = line.split(',')
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if minHaloMass == "none" or float(line[6]) > minHaloMass:
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numPart += 1
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inFile.close()
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sampleName = "md.halos_min"+str(minHaloMass)+"_z"+redshift
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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# -----------------------------------------------------------------------------
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# now the SDSS HOD
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if (args.script or args.all) and dataFormat == "multidark":
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print " Doing DR7 HOD scripts"
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if dataFormat == "multidark":
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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(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 (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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sampleName = getSampleName("md.hod_dr72dim2", redshift, False)
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outFileName = catalogDir+"/"+sampleName+".dat"
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# -----------------------------------------------------------------------------
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# now the BOSS HOD
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if (args.script or args.all) and dataFormat == "multidark":
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print " Doing DR9 HOD scripts"
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if dataFormat == "multidark":
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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, 15, omegaM)
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writeScript(setName, "md.hod_dr9mid_z",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, 15, omegaM)
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if args.hod or args.all:
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print " Doing DR9 HOD"
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for (iRedshift, redshift) in enumerate(redshifts):
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print " z = ", redshift
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outFileName = catalogDir+"/"+sampleName+".dat"
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if dataFormat == "multidark" or dataFormat == "random":
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sampleName = getSampleName("md.hod_dr9mid", redshift, False)
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inFileName = inCatalogDir+"/"+sampleName+".dat"
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outFileName = catalogDir+"/masked_"+sampleName+".dat"
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zMin = float(redshift)
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zMax = zMin + 0.1
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zMin, zMax = getMaskedZRange(lbox, float(redshift), zMin, zMax, omegaM)
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applyMask(inFileName, outFileName, maskFileName, lbox, float(redshift),
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zMin, zMax, omegaM)
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