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https://bitbucket.org/cosmicvoids/vide_public.git
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3dce2593d9
Some general housekeeping, making sure some new parameters are passed around correctly, and removing the storage of some unused files. This update is considered HIGHLY UNSTABLE. It will almost certainly break somewhere for simulations. Still under active development.
234 lines
7.6 KiB
Python
234 lines
7.6 KiB
Python
#+
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# VIDE -- Void IDentification and Examination -- ./python_tools/vide/backend/classes.py
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# Copyright (C) 2010-2014 Guilhem Lavaux
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# Copyright (C) 2011-2014 P. M. Sutter
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; version 2 of the License.
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#
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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#+
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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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import matplotlib as mpl
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mpl.use('Agg')
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LIGHT_SPEED = 299792.458
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class Stack:
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zMin = 0.0
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zMax = 0.1
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rMin = 5
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rMax = 15
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zMinPlot = 0.0
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zMaxPlot = 0.1
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includeInHubble = True
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partOfCombo = False
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needProfile = True
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rescaleMode = "rmax" # options: "rmax" to scale to largest void in stack
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# "rv" normalize each void
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maxVoids = -1 # maximum number of voids to allow in the stack
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def __init__(self, zMin, zMax, rMin, rMax, includeInHubble, partOfCombo,
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zMinPlot=None, needProfile=True, rescaleMode="rmax",
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maxVoids=-1, fittingMode="mcmc"):
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self.zMin = zMin
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self.zMax = zMax
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self.rMin = rMin
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self.rMax = rMax
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self.zMaxPlot = zMax
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self.includeInHubble = includeInHubble
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self.partOfCombo = partOfCombo
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self.needProfile = needProfile
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self.rescaleMode = rescaleMode
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self.maxVoids = maxVoids
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self.fittingMode = fittingMode
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if zMinPlot == None:
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self.zMinPlot = self.zMin
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else:
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self.zMinPlot = zMinPlot
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class Sample:
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dataType = "observation"
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dataFormat = "sdss"
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dataFile = "lss.dr72dim.dat"
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dataUnit = 1
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fullName = "lss.dr72dim.dat"
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nickName = "dim"
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outputDir = ""
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maskFile = "rast_window_512.fits"
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nsideForContour = 128
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selFunFile = "czselfunc.all.dr72dim.dat"
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zBoundary = (0.0, 0.1)
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zBoundaryMpc = (0., 300)
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boundaryWidth = 0.02
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shiftSimZ = False
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zRange = (0.0, 0.1)
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omegaM = 0.27
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minVoidRadius = -1
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meanPartSep = 1 # calculated mean particle separation
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fakeDensity = 0.01 # TODO - remove
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hasWeightedVolumes = False
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profileBinSize = 2 # Mpc
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autoNumInStack = -1 # set to >0 to automatically generate stacks of size N
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autoPartInStack = -1 # set to >0 to automatically generate stacks with N particles
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numAPSlices = 1
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volumeLimited = True
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includeInHubble = True
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partOfCombo = False
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isCombo = False
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comboList = []
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# applies to simulations only
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boxLen = 1024 # Mpc/h
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usePecVel = False
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subsample = 1.0
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numSubvolumes = 1
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mySubvolume = 1
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stacks = []
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def __init__(self, dataFile="", fullName="", dataUnit=1,
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nickName="", maskFile="", nsideForContour=128, selFunFile="",
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zBoundary=(), zRange=(), zBoundaryMpc=(), boundaryWidth=0.1,
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shiftSimZ=False, meanPartSep = 1,
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minVoidRadius=-1, fakeDensity=0.01, volumeLimited=True,
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numAPSlices=1, hasWeightedVolumes=False,
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includeInHubble=True, partOfCombo=False, isCombo=False,
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comboList=(), profileBinSize=2.0,
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boxLen=1024, usePecVel=False, omegaM=0.27,
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numSubvolumes=1, mySubvolume=1, dataFormat="sdss",
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useComoving=True,
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dataType="observation",
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subsample=1.0, useLightCone=False, autoNumInStack=-1,
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autoPartInStack=-1):
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self.dataFile = dataFile
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self.fullName = fullName
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self.nickName = nickName
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self.maskFile = maskFile
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self.nsideForContour = nsideForContour
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self.selFunFile = selFunFile
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self.zBoundary = zBoundary
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self.zBoundaryMpc = zBoundaryMpc
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self.boundaryWidth = boundaryWidth
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self.shiftSimZ = shiftSimZ
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self.zRange = zRange
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self.minVoidRadius = minVoidRadius
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self.meanPartSep = meanPartSep
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self.fakeDensity = fakeDensity
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self.hasWeightedVolumes = hasWeightedVolumes
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self.volumeLimited = volumeLimited
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self.includeInHubble = includeInHubble
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self.partOfCombo = partOfCombo
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self.isCombo = isCombo
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self.comboList = comboList
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self.numAPSlices = numAPSlices
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self.outputDir = None
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self.profileBinSize = profileBinSize
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self.dataType = dataType
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self.boxLen = boxLen
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self.usePecVel = usePecVel
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self.omegaM = omegaM
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self.numSubvolumes = numSubvolumes
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self.mySubvolume = mySubvolume
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self.dataFormat = dataFormat
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self.subsample = subsample
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self.useLightCone = useLightCone
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self.dataUnit = dataUnit
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self.useComoving = useComoving
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self.autoNumInStack = autoNumInStack
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self.autoPartInStack = autoPartInStack
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self.stacks = []
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def addStack(self, zMin, zMax, rMin, rMax,
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includeInHubble, partOfCombo,zMinPlot=None,
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needProfile=True, rescaleMode="rmax",
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maxVoids=-1, fittingMode="mcmc"):
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self.stacks.append(Stack(zMin, zMax, rMin, rMax,
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includeInHubble, partOfCombo,
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zMinPlot=zMinPlot, needProfile=needProfile,
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rescaleMode=rescaleMode,
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maxVoids=maxVoids,
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fittingMode=fittingMode))
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def getHubbleStacks(self):
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stacksForHubble = []
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for stack in self.stacks:
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if stack.includeInHubble:
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stacksForHubble.append(stack)
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return stacksForHubble
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def getUniqueRBins(self):
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uniqueRStacks = []
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for stack in self.stacks:
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if not stack.includeInHubble:
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continue
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alreadyHere = False
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for stackCheck in uniqueRStacks:
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if stack.rMin == stackCheck.rMin and stack.rMax == stackCheck.rMax:
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alreadyHere = True
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break
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if not alreadyHere:
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uniqueRStacks.append(stack)
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return uniqueRStacks
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def getUniqueZBins(self):
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uniqueZStacks = []
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for stack in self.stacks:
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if not stack.includeInHubble:
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continue
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alreadyHere = False
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for stackCheck in uniqueZStacks:
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if stack.zMin == stackCheck.zMin and stack.zMax == stackCheck.zMax:
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alreadyHere = True
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break
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if not alreadyHere:
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uniqueZStacks.append(stack)
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return uniqueZStacks
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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def jobSuccessful(logFile, doneString):
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jobDone = False
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checkLine = ""
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if os.access(logFile, os.F_OK):
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#filelines = file(logFile, "r").readlines()
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#if len(filelines) >= 1:
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# checkLine = filelines[-1]
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for line in open(logFile, 'r'):
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if doneString in line: jobDone = True
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return jobDone
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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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for comp in components[1:]:
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mod = getattr(mod, comp)
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return mod
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