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https://bitbucket.org/cosmicvoids/vide_public.git
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checking for periodicity now pushed to function
This commit is contained in:
P.M. Sutter
parent
c088a87809
commit
0cc5529b08
2 changed files with 72 additions and 30 deletions
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@ -20,6 +20,7 @@
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# classes and routines used to support scripts
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import os
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from numpy import abs
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LIGHT_SPEED = 299792.458
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@ -188,6 +189,15 @@ def getStackSuffix(zMin, zMax, rMin, rMax, dataPortion, customLine=""):
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return "z"+str(zMin)+"-"+str(zMax)+"_"+str(rMin)+"-"+str(rMax)+\
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"Mpc"+customLine+"_"+dataPortion
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def getPeriodic(sample):
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periodicLine = ""
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if sample.dataType != "observation":
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if sample.numSubvolumes == 1: periodicLine += "xy"
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if abs(sample.zBoundaryMpc[1] - sample.zBoundaryMpc[0] - \
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sample.boxLen) <= 1.e-1:
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periodicLine += "z"
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return periodicLine
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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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@ -84,9 +84,8 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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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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if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")):
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file(parmFile, mode="w").write(conf)
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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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@ -98,8 +97,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
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else:
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print "already done!"
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if os.access(parmFile, os.F_OK):
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os.unlink(parmFile)
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if os.access(parmFile, os.F_OK): os.unlink(parmFile)
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if os.access("contour_map.fits", os.F_OK):
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os.system("mv %s %s" % ("contour_map.fits", zobovDir))
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@ -316,18 +314,20 @@ def launchPrune(sample, binPath,
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totalPart = open(zobovDir+"/total_particles.txt", "r").read()
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maxDen = 0.2*float(mockIndex)/float(totalPart)
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observationLine = " --isObservation"
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periodicLine = " --periodic=''"
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#periodicLine = " --periodic=''"
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else:
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mockIndex = -1
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maxDen = 0.2
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observationLine = ""
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periodicLine = " --periodic='"
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if sample.numSubvolumes == 1: periodicLine += "xy"
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if np.abs(sample.zBoundaryMpc[1] - sample.zBoundaryMpc[0] - \
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sample.boxLen) <= 1.e-1:
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periodicLine += "z"
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periodicLine += "' "
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#periodicLine = " --periodic='"
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#if sample.numSubvolumes == 1: periodicLine += "xy"
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#if np.abs(sample.zBoundaryMpc[1] - sample.zBoundaryMpc[0] - \
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# sample.boxLen) <= 1.e-1:
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# periodicLine += "z"
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#periodicLine += "' "
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periodicLine = " --periodic='" + getPeriodic + "'"
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if not (continueRun and (jobSuccessful(logFile, "NetCDF: Not a valid ID\n") \
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or jobSuccessful(logFile, "Done!\n"))):
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@ -377,12 +377,12 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
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sampleName1 = sample1.fullName
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sampleName2 = sample2.fullName
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periodicLine = " --periodic='"
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if sample1.dataType != "observation":
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if sample1.numSubvolumes == 1: periodicLine += "xy"
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if np.abs(sample1.zBoundaryMpc[1] - sample1.zBoundaryMpc[0] - sample1.boxLen) <= 1.e-1:
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periodicLine += "z"
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periodicLine += "' "
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periodicLine = " --periodic='" + getPeriodic(sample1) + "' "
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#if sample1.dataType != "observation":
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# if sample1.numSubvolumes == 1: periodicLine += "xy"
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# if np.abs(sample1.zBoundaryMpc[1] - sample1.zBoundaryMpc[0] - sample1.boxLen) <= 1.e-1:
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# periodicLine += "z"
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#periodicLine += "' "
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if not (continueRun and jobSuccessful(logFile, "Done!\n")):
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cmd = binPath
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@ -390,7 +390,7 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
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str(sampleName1)
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cmd += " --volFile1=" + sample1Dir+"/vol_" + \
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str(sampleName1)+".dat"
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cmd += " --voidFile1=" + sample1Dir+"/untrimmed_voidDesc_" + \
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cmd += " --voidFile1=" + sample1Dir+"/voidDesc_" + \
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thisDataPortion+"_"+str(sampleName1)+".out"
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cmd += " --infoFile1=" + sample1Dir+"/zobov_slice_" + \
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str(sampleName1)+".par"
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@ -506,6 +506,17 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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rMinToUse = stack.rMin
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rMaxToUse = stack.rMax
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periodicLine = "periodic='" + getPeriodic(sample) + "'"
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#if sample.dataType == "observation":
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# periodicLine = "periodic=''"
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#else:
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# periodicLine = "periodic='"
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# if sample.numSubvolumes == 1: periodicLine += "xy"
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# if np.abs(sample.zBoundaryMpc[1] - sample.zBoundaryMpc[0] - \
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# sample.boxLen) <= 1.e-1:
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# periodicLine += "z"
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# periodicLine += "' "
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conf="""
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desc %s
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partzone %s
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@ -529,6 +540,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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boundaryDistances %s
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%s
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%s
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%s
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""" % \
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(zobovDir+"/voidDesc_"+thisDataPortion+"_"+sampleName+".out",
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zobovDir+"/voidPart_"+sampleName+".dat",
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@ -551,11 +563,11 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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zobovDir+"/barycenters_"+thisDataPortion+"_"+sampleName+".out",
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zobovDir+"/boundaryDistances_"+thisDataPortion+"_"+sampleName+".out",
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rescaleFlag,
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idListFlag
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idListFlag,
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periodicLine
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)
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parmFile = os.getcwd()+("/%sstack_"%prefixRun)+sample.fullName+".par"
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fp = file(parmFile, mode="w")
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fp.write(conf)
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@ -584,6 +596,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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else:
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print "already done!"
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if os.access(parmFile, os.F_OK): os.unlink(parmFile)
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return
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minDist = None
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@ -662,7 +675,17 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
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nbar = 1.0
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else:
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nbar = 1.0
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boxVol = sample.boxLen**3
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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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zMin = sample.zBoundaryMpc[0]
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zMax = sample.zBoundaryMpc[1]
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boxVol = (xMax-xMin)*(yMax-yMin)*(zMax-zMin)
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summaryLine = runSuffix + " " + \
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thisDataPortion + " " + \
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@ -1091,10 +1114,8 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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else:
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rescaleFactor = 1.0
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vp.draw_fit(*args, delta_tick=0.2, vmax=10.0, delta_v=0.1,
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nocontour=True, model_max=10.0, delta_model=1.0,
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#vp.draw_fit(*args, delta_tick=0.2, vmax=1.0, delta_v=0.01,
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# nocontour=True, model_max=1.0, delta_model=0.1,
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vp.draw_fit(*args, delta_tick=0.2, vmax=1.0, delta_v=0.01,
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nocontour=True, model_max=1.0, delta_model=0.1,
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plotTitle=plotTitle, show_ratio=showRatio,
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showContours=showContours,
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rescaleFactor=rescaleFactor)
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@ -1513,14 +1534,20 @@ def launchLikelihood(dataPortions=None, logDir=None, workDir=None,
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# -----------------------------------------------------------------------------
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def launchEstimateErrorBars(workDir=None, nullDir=None, numNulls=None,
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dataPortion=None):
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dataPortion=None, nullDirList=None):
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IVALUE = 0
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IERROR = 1
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# open first null file to get sizes
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nullFile = nullDir + "/" + str(1) + "/calculatedExpansions_" + \
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str(dataPortion) + ".txt"
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if nullDirList == None:
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nullFile = nullDir + "/" + str(1) + "/calculatedExpansions_" + \
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str(dataPortion) + ".txt"
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else:
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nullFile = nullDirList[0] + "/calculatedExpansions_" + str(dataPortion) + \
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".txt"
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numNulls = len(nullDirList)
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fp = open(nullFile, "r")
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binLine = fp.readline()
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numSamples = int(binLine.split(" ")[0])
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@ -1534,8 +1561,13 @@ def launchEstimateErrorBars(workDir=None, nullDir=None, numNulls=None,
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nullData = np.zeros([numNulls, numBins, 2])
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for iNull in xrange(numNulls):
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nullFile = nullDir + "/" + str(iNull) + "/calculatedExpansions_" + \
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str(dataPortion) + ".txt"
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if nullDirList == None:
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nullFile = nullDir + "/" + str(iNull) + "/calculatedExpansions_" + \
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str(dataPortion) + ".txt"
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else:
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nullFile = nullDirList[iNull] + "/calculatedExpansions_" + \
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str(dataPortion) + ".txt"
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fp = open(nullFile, "r")
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binLine = fp.readline()
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