Slight re-organization of C/C++ tools. Significant modifications to support observational data. Python and pipeline scripts added

python_tools/void_python_tools/backend/__init__.py

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+from classes import *
+from launchers import *

python_tools/void_python_tools/backend/classes.py

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+# classes and routines used to support scripts
+
+import os
+
+LIGHT_SPEED = 299792.458
+
+class Stack:
+  zMin = 0.0
+  zMax = 0.1
+  rMin = 5
+  rMax = 15
+  zMinPlot = 0.0
+  zMaxPlot = 0.1
+  includeInHubble = True
+  partOfCombo = False
+  needProfile = True
+  rescaleMode = "rmax" # options: "rmax" to scale to largest void in stack
+                       #          "rv"   normalize each void
+
+  def __init__(self, zMin, zMax, rMin, rMax, includeInHubble, partOfCombo, 
+               zMinPlot=None, needProfile=True, rescaleMode="rmax"):
+    self.zMin = zMin
+    self.zMax = zMax
+    self.rMin = rMin
+    self.rMax = rMax
+    self.zMaxPlot = zMax
+    self.includeInHubble = includeInHubble
+    self.partOfCombo = partOfCombo
+    self.needProfile = needProfile
+    self.rescaleMode = rescaleMode
+   
+    if zMinPlot == None:
+      self.zMinPlot = self.zMin
+    else:
+      self.zMinPlot = zMinPlot
+
+class Sample:
+  dataType = "observation"
+  dataFormat = "sdss"
+  dataFile = "lss.dr72dim.dat"
+  fullName = "lss.dr72dim.dat"
+  nickName = "dim"
+  zobovDir = ""
+  maskFile = "rast_window_512.fits"
+  selFunFile = "czselfunc.all.dr72dim.dat"
+  skyFraction = 0.19
+  zBoundary = (0.0, 0.1)
+  zBoundaryMpc = (0., 300)
+  zRange    = (0.0, 0.1)
+  omegaM    = 0.27
+  minVoidRadius = 5
+  fakeDensity = 0.01
+  profileBinSize = 2 # Mpc
+  volumeLimited = True
+  includeInHubble = True
+  partOfCombo  = False
+  isCombo = False
+  comboList = []
+
+  # applies to simulations only
+  boxLen = 1024 # Mpc/h
+  usePecVel = False
+  subsample = 1.0
+  useLightCone = True
+  numSubDivisions = 1
+  numSubvolumes = 1
+  mySubvolume = 1
+
+  stacks = []
+
+  def __init__(self, dataFile="", fullName="", 
+               nickName="", maskFile="", selFunFile="",
+               zBoundary=(), zRange=(), zBoundaryMpc=(),
+               minVoidRadius=0, fakeDensity=0.01, volumeLimited=True,
+               includeInHubble=True, partOfCombo=False, isCombo=False, 
+               comboList=(), profileBinSize=2.0, skyFraction=0.19,
+               dataType="observation", numSubDivisions=2, 
+               boxLen=1024, usePecVel=False, omegaM=0.27, 
+               numSubvolumes=1, mySubvolume=1, dataFormat="sdss",
+               subsample="1.0", useLightCone=True):
+    self.dataFile = dataFile
+    self.fullName = fullName
+    self.nickName = nickName
+    self.maskFile = maskFile
+    self.selFunFile = selFunFile
+    self.zBoundary = zBoundary 
+    self.zBoundaryMpc = zBoundaryMpc
+    self.zRange = zRange
+    self.minVoidRadius = minVoidRadius
+    self.fakeDensity = fakeDensity
+    self.volumeLimited = volumeLimited
+    self.includeInHubble = includeInHubble 
+    self.partOfCombo = partOfCombo 
+    self.isCombo = isCombo
+    self.comboList = comboList
+    self.zobovDir = None
+    self.profileBinSize = profileBinSize
+    self.skyFraction = skyFraction
+    self.dataType = dataType
+    self.numSubDivisions = numSubDivisions
+    self.boxLen = boxLen
+    self.usePecVel = usePecVel
+    self.omegaM = omegaM
+    self.numSubvolumes = numSubvolumes
+    self.mySubvolume = mySubvolume
+    self.dataFormat = dataFormat
+    self.subsample = subsample
+    self.useLightCone = useLightCone
+
+    self.stacks = []
+
+  def addStack(self, zMin, zMax, rMin, rMax, 
+                includeInHubble, partOfCombo,zMinPlot=None, 
+                needProfile=True, rescaleMode="rmax"):
+    self.stacks.append(Stack(zMin, zMax, rMin, rMax,
+                            includeInHubble, partOfCombo, 
+                            zMinPlot=zMinPlot, needProfile=needProfile,
+                            rescaleMode=rescaleMode))
+
+  def getHubbleStacks(self):
+    stacksForHubble = []
+    for stack in self.stacks:
+      if stack.includeInHubble:
+        stacksForHubble.append(stack)
+    return stacksForHubble
+
+  def getUniqueRBins(self):
+    uniqueRStacks = []
+    for stack in self.stacks:
+      if not stack.includeInHubble:
+        continue
+      alreadyHere = False
+      for stackCheck in uniqueRStacks:
+        if stack.rMin == stackCheck.rMin and stack.rMax == stackCheck.rMax:
+          alreadyHere = True
+          break
+      if not alreadyHere:
+        uniqueRStacks.append(stack)
+    return uniqueRStacks
+
+  def getUniqueZBins(self):
+    uniqueZStacks = []
+    for stack in self.stacks:
+      if not stack.includeInHubble:
+        continue
+      alreadyHere = False
+      for stackCheck in uniqueZStacks:
+        if stack.zMin == stackCheck.zMin and stack.zMax == stackCheck.zMax:
+          alreadyHere = True
+          break
+      if not alreadyHere:
+        uniqueZStacks.append(stack)
+    return uniqueZStacks
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+def jobSuccessful(logFile, doneString):
+  jobDone = False
+  checkLine = ""
+  if os.access(logFile, os.F_OK):
+    filelines = file(logFile, "r").readlines()
+    if len(filelines) >= 1:
+      checkLine = filelines[-1]
+    jobDone = (checkLine == doneString)
+  return jobDone
+
+def getStackSuffix(zMin, zMax, rMin, rMax, dataPortion):
+  return "z"+str(zMin)+"-"+str(zMax)+"_"+str(rMin)+"-"+str(rMax)+\
+         "Mpc"+"_"+dataPortion